Data Set 1:

Homework 5 – Footprinter Analysis

Data Set 1

Organisms:

Organism: Mycoplasma Pneumoniae

Description: phenylalanyl-tRNA synthetase alpha-subunit

PID: 13507844

Length of upstream non-coding sequence: 831

Label: MPN105

135731..136756 + 342 13507844 pheS COG0016 MPN105 phenylalanyl-tRNA synthetase alpha-subunit

Organism:Mycoplasma genitalium

Description: phenylalanyl-tRNA synthetase, subunit alpha (pheS)

PID: 12045046

Length of upstream non-coding sequence: 2942

Label: sll0454

232007..233032 + 342 12045046 pheS COG0016 MG194 phenylalanyl-tRNA synthetase, subunit alpha (pheS)

Organism: Lactococcus lactis

Description: phenylalanil-tRNA synthetase alpha chain (EC 6.1.1.20)

PID: 15673911

Length of upstream non-coding sequence: 454

Label: L0354

2009087..2010127 - 347 15673911 pheS COG0016 L0354 phenylalanil-tRNA synthetase alpha chain (EC 6.1.1.20)

Organism: Pseudomonas aeruginosa PA01

Description: phenylalanyl-tRNA synthetase, alpha-subunit

PID: 15597936

Length of upstream non-coding sequence: 98

Label: PA2740

3102528..3103544 - 339 15597936 pheS COG0016 PA2740 phenylalanyl-tRNA synthetase,

alpha-subunit

Organism: Synechocystis sp. PCC6803

Description: phenylalanyl-tRNA synthetase alpha chain

PID: 16331530

Length of upstream non-coding sequence: 203

Label: MG194

2629271..2630266 - 332 16331530 pheS COG0016 sll0454 phenylalanyl-tRNA synthetase alpha chain

Footprinter URL:

http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/__webquery__.fasta0.7564001785477390.882894665453918.main.html

Footprinter motifs found:

PA2740
AGCCCTACGACAATCACCGGACTTCGGTCCGGACGTAACGTCACCGATAGGGGAAGAGCCTTACCGCTCTTCCCCT A T T T T GTATCTGGAGTCCATAC
SLL0454
GTTTTTAACCTTTCAATAACCTAAAACACAATCTTTAAAACAAGGTTGTGTTTTTTTGTTTTTTGTCACTTTTCACTAAACTTGCAATTTAGAGAGTGGATATGAAAAGAACAGTTAAAAAAATAAAACCTGACCACTTGTTTAATAAAA
AGCAGTGGCACTTACTGAGTGAAGAGATCAGTGATAACCCAATGATTAAGCGTTATTGACTCAAACAACAAAAGCGTCAGCTTGCCAAACTAAAAAAACGCCGTT A T T T T AAAAATTAACTATGTATTCTACTTTAAGACAA
L0354
TTAAATTTCTTCTTTCTAAACAT A T T T T ATAAACATGTTTTAAATATATATTTATTATAAAATACGTTTTTTGTTTTGTCAAGATAAAAATATACACTTTCTTAAAGTTGACAAATCTTATGAAAGTGATAAAATTAAGCATAGATGTAA
GAAGAGTAGATTGTCTATGAAATTTGAGGGAATTGTGGTCACCGACTGAAAGCCACAATATGGAATTGCAATTGAAGTTCACCTTACTAAAGAAAGCTATTTTTAATCTATCATTTAGAGTGATAGTCTAAAAGGTAGGTTT
MPN105
CCATTCCAAAATAAAAATACCAACAGTCAATCCTTAAAAAGTTCACTGTTGGTATTTTTATTCACTCAAAAAATTCTTAAAATTTTTTTGTAATTTGTCGTCACTTCGAAATAACTGAATCAATTTATTTAGTGGAGGAGTAATTATGAG
TAACTTTGAATTTTGATTAATCCTTCAGAAAGGAGGATTTGATTATGAAAGATGAAACAAATATTTGTTCTCAATCTTTAAAAAGACCTTTAAGCGAAGACCAATTGATAGAGT A T T T G AGTACTTATGAAATAACTTTATT
MG194
ATAACAAAGGATTTGCGCTCTCTGCTGGGGTAGAATCGGTAACGGGCGATTTTTCCTAGGTTTAGCCGATGTTGGCCTTGACCATGGCCGAGGAAAGACCAATTATCCCCTGTTGATCAACCTGACCAGCGCTAATCAGT A T T T G ATCCA
TCCCCATAAACAAGGCCTTTGCTAGGGCGGAATTACGAGAGACCCATTTTTCC

This was the best motif I could find in this data set. Notice that we have a maximum of 2 mutations and a motif size of 7. Neither Dialign nor CLUSTALW was able to find this motif.

Command line:

-details

-triplet_filtering -post_filtering

-size 7

-max_mutations 2

-max_mutations_per_branch 2

-losses /homes/gws/blanchem/FootPrinterWeb/universal7.config

-compute_branch_lengths

-loss_cost 0.5

-sequence_type upstream

-subregion_size 100

-position_change_cost 0

Dialign Motifs found:

MPN105 1 ccattccaaa a--------- ---------- ---------- --------TA

sll0454 1 ---------- ---------- ---------- ------GTTT TTAACCTTTC

L0354 1 ttaaatttct tctttctaaa catattttat aaacatGTTT TAAATATATA

PA2740 1 agccctacg- ---------- ---------- ---------- ----------

MG194 1 ataacaa--- ---------- ---------- ---------- ----------

MPN105 14 AAAATACCAA CAGTCAATCC TTAAAAagtt cactgttggt atttttattc

sll0454 15 AATAACCTAA AACACAATCT TTAAAAcaag gttgtg---- ----------

L0354 51 TTTATTATAA AATACg---- ---------- ---------- ----------

PA2740 10 ---------- ---ACAATCa ccgg------ ---------- ----------

MG194 8 ---------- ---------- ---------- ---------- ----------

This “motif” was not found by footprinter. Upon further examination, there is a mutation in every sequence. Even though Dialign did a good of aligning the sequences, these are not likely regulatory elements.

MPN105 114 actgaatCAA TTTATTTAGT GGAGGAGTAA TTATGAGTAA c---------

sll0454 82 ttg----CAA TTTAGAGAGT GGATATGAAA AGAACAGTTA AAAAAATAa-

L0354 82 ---------- ---------- ---------- -----AGATA AAAATATAca

PA2740 32 gac------- ---------- ---------- ---------- ----------

MG194 8 ---------- ---------- ---------- ---------- ----------

Here we have a motif that Dialign found but Footprinter did not. The last 2 groupings have too many mutations and my definition of “well conserved” was again to liberal. If we look at the first group, though, it is an alignment with 10 pairs and only 3 mutations; Footprinter could not find it even when I set the maximum parsimony score to be high.

MPN105 247 ---------- ---------- ---------- --AAGACCAA TTGATAG---

sll0454 127 ---------- ---------- ---------- ---------- ----------

L0354 137 ---------- ---------- ---------- --AAGCATAG ATGTAAG---

PA2740 40 ---------- ---------- ---------- ---------- ----------

MG194 63 tagccgatgt tggccttgac catggccgag gaAAGACCAA TTatcccctg

Here we have 8 nucleotides aligned with 3 mutations. Footprinter did not determine that this was a good match.

MPN105 293 ---------- ---------- ---------- ---------- ----------

sll0454 190 CAATGATTAA GCGTTATTGA CTCAAAcaac aaaagcgtca gcttgccaaa

L0354 258 CTATCATTTA GAGTGATAGT CTAAAAggta ggttt----- ----------

PA2740 86 CTggagtcca tac------- ---------- ---------- ----------

MG194 204 ---------- ---------- ---------- ---------- ----------

Again, here we have an alignment that I called well-conserved in homework 4, but was in fact, not good enough for footprinter.

Data Set 2

Organism: Caulobacter crescentus CB15

Description: translation initiation factor IF-2

PID: 16124298

Length of upstream non-coding sequence: 195

Label: CC0042

42585..45698 - 1038 16124298 COG0532 CC0042 translation initiation factor IF-2

Organism: Rickettsia prowazekii

Description: TRANSLATION INITIATION FACTOR IF-2 (infB)

PID: 15604407

Length of upstream non-coding sequence: 214

Label: RP552

681937..684432 - 832 15604407 COG0532 RP552 TRANSLATION INITIATION FACTOR IF-2 (infB)

Organism: Synechocystis sp. PCC 6803

Description: initiation factor IF-2

PID: 16329288

Length of upstream non-coding sequence: 578

Label: slr0744

134437..137442 + 1002 16329288 infB COG0532 slr0744 initiation factor IF-2

Organism: Mycobacterium leprae

Description: initiation factor IF-2

PID: 15827818

Length of upstream non-coding sequence: 65

Label: ML1556

1880177..1882951 - 925 15827818 infB COG0532 ML1556 initiation factor IF-2

Organism: Mycobacterium tuberculosis H37Rv

DEFINITION infB

PID: 15609976

Length of upstream non-coding sequence: 86

Label: Rv2839c

3145168..3147870 - 901 15609976 infB COG0532 Rv2839c infB

Footprinter URL:

http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/__webquery__.fasta0.3100899678075460.892888448885046.main.html

Footprinter motifs found:

CC0042
GGGATTTTCGCCTTTGGCGGTTCCTGGGCACAGACGGCGGGCCTGTCCGCCCGGTCGGTTCGCCGGCCTTGGCAGGCGCTAGAGCTTTTCCCTCTCACCGGACCGTCCGGTGGGATGGGAAAGCTCTAGAATCTTTGAGTGAGCCCAGGT
GTTCGGCCGGGCTCGTGAGCGAAGGGTCGGGGAAACGGCTTCCTT
RP552
AATTAATAATATTTGTGTAAAAGACAT A T T T A TATTAATTTCTTATGCTTATATTTCGGAGTAAAAATATTTTCACCATTAGTACTTAACATATATTCAT G A T A A TCT T G A T A A TTTCCTTCAAACCATGTAGCATTATTTTCTTGATCA
TATGATATAATATGAGTTGCTATTCTATCTAAAAACCATCTGTC A T G A C TAATCACTAATACAC
SLR0744
GGAAAGGT T G A T A A TGCCAGCTTTGTGCTAATTTGTCCTGACCACTCCTTGCCCACCGTTGACCATGGCCCCTGGATACCGTCGTTGCCTCAGC T G T C G CAAAGTAGGCGATCGCCGACAATTTTGGCGAATTGTCCGAGTCTATCCATC
TCGAACTGTACAATTAGATCACGGTGCGGGGCGATCGGCTT A T T T A TGTCCGACCC A T G A C TGTCTGCGTAAAGCTCGCCACAAAAATCTGTTGGGGCGGGCCCTCCGAGCCCCAGTTCCCAGCCATCTCTTTGAGCAACTA
ML1556
ACAATGCGTCATAGCTAAACCCGGAGGCGCGGCCCACCAC T G T C G CCTCATAGACAGGAGATGTA
RV2839C
AGCACACCGTGAAGTCCCGATGACAATGCGTCATAGCTAAACCCGAGGCGCGGCCCACGAC T G T C G CCTCATGGACAGGAGATGTA

This data set did not yield any motifs when the spanned tree significance was set to “significant” (even of size 6, with 3 mutations), so I am doubtful whether the results here actually represent a real motif in the microbes. The motif here is, in fact, well-conserved, though it turns out that these microbes are also most related with respect to the CLUSTALW phylogenic tree.

This motif was not found by Dialign.

Command line:

-details

-triplet_filtering -post_filtering

-size 7

-max_mutations 3

-max_mutations_per_branch 2

-losses /homes/gws/blanchem/FootPrinterWeb/universal7loose.config

-compute_branch_lengths

-loss_cost 0.5

-sequence_type upstream

-subregion_size 100

-position_change_cost 0

Dialign Motifs found:

None of these “motifs” were found by Footprinter.

CC0042 22 ---------- ---------- ---------- ---------- --TCCTGGGC

RP552 151 tatgatataa tatgagttgc tattctatct aaaaACCATC TGTCATGACT

slr0744 28 ---------- ---------- ---------- ----CTAATT TGTCCTGACC

ML1556 1 ---------- ---------- ---------- ----ACAATG CGTCATAGCT

Rv2839c 23 ---------- ---------- ---------- ----ACAATG CGTCATAGCT

CC0042 30 ACAGACGG-- ---------- ---------- ---------- ----------

RP552 201 AATCACT--- ---------- ---------- ---------- ----------

slr0744 44 ACTCCttgcc caccgttgac catggcccct ggataccgtc gttgcctcag

ML1556 17 AAACCCGG-- ---------- ---------- ---------- ----------

Rv2839c 39 AAACCCG--- ---------- ---------- ---------- ----------

CC0042 43 -------CTG TCCGCCcggt cggttcgccg gccttggcag gcgctagagc

RP552 209 ---------- ---------- ---------- ---------- ----------

slr0744 194 ttatgtcCGA CCCATGA--- ---------- ---------- ----------

ML1556 30 -------CGG CCCACCA--- ---------- ---------- ----------

Rv2839c 51 -------CGG CCCACGA--- ---------- ---------- ----------

CC0042 86 ttttccCTCT CACCGGACCG TCCGGTGgga tgggAAAGCT Ctagaatctt

RP552 209 ---------- ------ATAC AC-------- ---------- ----------

slr0744 211 ------CTGT Ctgcgt---- ---------- ----AAAGCT Cgccacaaaa

ML1556 40 ------CTGT CGCCTCATAG ACAGGAGATG Ta-------- ----------

Rv2839c 61 ------CTGT CGCCTCATGG ACAGGAGATG Ta-------- ----------

Data Set 3

Organism: Mesorhizobium loti

DEFINITION endopeptidase Clp ATP-binding chain B, clpB

PID: 13472967

Upstream non-coding DNA sequence: 221

Label: mll3429

2766191..2768797 - 869 13472967 COG0542 mll3429 endopeptidase Clp ATP-binding chain B,

clpB

Organism: [Caulobacter crescentus CB15].

Description: ATP-dependent Clp protease, ATP-binding subunit ClpB

PID: 16125131

Upstream non-coding DNA sequence: 99

Label: CC0878

972567..975146 + 860 16125131 COG0542 CC0878 ATP-dependent Clp protease, ATP-binding subunit ClpB

Organism: Deinococcus radiodurans

DEFINITION ATP-dependent Clp protease, ATP-binding subunit ClpB

PID: 15806066

Upstream non-coding DNA sequence: 420

Label: DR1046

1057871..1060498 + 876 15806066 DR1046 COG0542 DR1046 ATP-dependent Clp protease, ATP-binding subunit ClpB

Organism: Mycobacterium tuberculosis H37Rv

Description: clpB

PID: 15607525

Upstream non-coding DNA sequence: 133

Label: Rv0384c

459454..462000 - 849 15607525 clpB COG0542 Rv0384c clpB

Organism: Mycobacterium leprae

Description: heat shock protein

PID: 15828345

Upstream non-coding DNA sequence: 931

Label: ML2490

2963220..2965766 - 849 15828345 clpB COG0542 ML2490 heat shock protein

Organism: Haemophilus influenzae Rd

Description: ATP-dependent Clp protease, ATPase subunit (clpB)

PID: 16272799

Upstream non-coding DNA sequence: 128

Label: HI0859

906976..909546 + 857 16272799 HI0859 COG0542 HI0859 ATP-dependent Clp protease, ATPase subunit (clpB)

Organism: Pasteurella multocida

Description: ClpB

PID: 15603569

Upstream non-coding DNA sequence: 279

Label: PM1704

1910791..1913358 + 856 15603569 clpB COG0542 PM1704 ClpB

Organism: Escherichia coli O157:H7 EDL933

Description: heat shock protein

PID: 15803116

Upstream non-coding DNA sequence: 118

Label: ZclpB

3521568..3524153 - 862 15803116 clpB COG0542 Z3886 heat shock protein

Organism: Pseudomonas aeruginosa PA01

DEFINITION ClpB protein

PID: 15599738

Upstream non-coding DNA sequence: 156

Label: PA4542

5087407..5089971 - 855 15599738 clpB COG0542 PA4542 ClpB protein

Organism: Synechocystis sp. PCC 6803

Description: ClpB protein

PID: 16331048

Upstream non-coding DNA sequence: 284

Label: slr1641

2062905..2065523 + 873 16331048 clpB COG0542 slr1641 ClpB protein

Organism: Synechocystis sp. PCC 6803

Description: ClpB protein

PID: 16331154

Upstream non-coding DNA sequence: 593

Label: slr0156

2194405..2197101 + 899 16331154 clpB COG0542 slr0156 ClpB protein

Organism: Lactococcus lactis subsp. lactis

Description: ClpB protein

PID: 15673507

Upstream non-coding DNA sequence: 234

Label: L166407

1566658..1569261 - 868 15673507 clpB COG0542 L166407 ClpB protein

Organism: Chlamydophila pneumoniae CWL029

Description: Clp Protease ATPase

PID: 15618068

Upstream non-coding DNA sequence: 198

Label: CPn0144

177963..180563 + 867 15618068 clpB COG0542 CPn0144 Clp Protease ATPase

Organism: Mycoplasma genitalium

Description: ATP-dependent Clp protease, ATPase subunit (clpB)

PID: 12045215

Upstream non-coding DNA sequence: 154

Label: MG355

451613..453757 - 715 12045215 clpB COG0542 MG355 ATP-dependent Clp protease, ATPase subunit (clpB)

Footprinter URL:

http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/__webquery__.fasta0.9971665280291580.503710689707063.main.html

Footprinter motifs found:

MLL3429
ATCGAACGGCATTTCAAGGCGTTGAACGGCGGAGAGAAATCTCCGCCGTTTTCGTTTCGGCTGAGGTGGAATATTATGCATTGACCGATA T C A A G G CGTCTTGAGACGGCATGGTCCATGCACCATATCTCGGCTGAACAGGACCCGGCT
CGAATGGGCGGGTCCGTCACCGCAATCTGATCCGGTGCCGCAAAGCGGGCCGGTGATGGAAGGAGACAGAT
CC0878
AGACCTTGTGTGGCGTATCGGCCACACATACATCCCCCCTGCGGACGCGTTGTGCTTGA T C A A G G CAGCGCGCTCCGATCCGCCTAGCAAGGGGACATC
HI0859
AAACCTATCATCAAATTTTTATTGATAGATAAAATCAAAATATTTCATTTTTTCTCTTGAAATTTATTCAACCGAGCTTACTTAGTTTATGCAAATGGCGAAAGCCGAAATCAAATTGAGGAAAGTGT
PM1704
TTTTCCTGTCCTTTAATTGAAACGCTGAATGACTGGCATTATAACAGGCAAGAAAAATCAGTAAATCATTACAGCGTGATGACTCTCACAAAAACTCATAAAAAATGACCGCTCTTTCTTTGCTGTAACCTATTGAAAATATGACATTTA
ATAGGTTTGAATTAAATATATCGCTTAAATACTCTTGAAAATGGTAAAAAGGGGCTTATTTATTCCTTGTAAATCGAAGGGATATTTGAACATTCCCTAACCCGATTTAATTTTTACAGGAGAGCAAAT
ZCLPB
ACCTAAAGAATCAAGACGATCCGGTACGCGTGATTTTCTTTTCACATTAATCTGGTCAATAACCTTGAATAATTGAGGGATGACCTCATTTAATCTCCAGTAGCAACTTTGATCCGTT
PA4542
GGCCCGCGCAGGTTATCCGGCGGCAACTGACCGATGTCACGGTCCGGTCGCTTGAACCGCGGAAAATCGCCCTTATCTACTGAGTCATCTCGGCGGGCTTTTCTTCATCAGGGACACCCATCGTTCCGGCCCGCTCTATAGAAGGAAGGA
CGACCC
RV0384C
GCGGCGAAACGGCGGCGGATGCACAAGTGGGTAAAATTGAGCGGAACAGACTCAACATTGACGGCGT T G A A C A ACCCGACAAGCATTTCGAACGGACCCCGAATGGAGGTGTC
ML2490
CCCACTCGACGAGCGAGGTCGGTGCGCCCGCAATGGAGGCAGTGGGCGGTGGACCCGGCTCCAGCCGGGGTGCCGTCGGCGGGACTGGGAGTGCATTCGGAACACGCCGTACCGTGTTCGGGGGCTGTCCGGGGACAGCGGGGTTGGGTC
CGGGCGGTACTAGCTCCGCTTGAAGTTGTAGTGGCGTGGAATAGTGATTATTAGGCGCAGGAGGTT T G A A C A AAGAAGCGATCAGCGGCCCCAGCTTGGGCATCGGAGCATGGTCATTCGCGTTGGAAGGCCGGCGCCCAGT
DR1046
AAAGCCCTGTCCGGCCCGCTGGGGTATGCCGTCACCTGGCTCCCCGACGCGCGCCGCGCGGATGTGGAACGGGTGCGGAAAATTCCGGGTGGACTGTCACAGACACAGGGCGAACTGGCGGGCCTTAAGCTAAAGCCGACGCGCCTGAAT
GCCTCCGCAGAAGTACGGTTTCAACCTCTGAAGAACGAACCAGCATTTGAGGAGCTGTTTCTCTCGTCACCAGCGCGAGAATTGGTGCGTATCTGGCCGTTTTTTCCACGCGGCCGTATGAGTGCAGCGTCTTGCGAGAGCA
L166407
TTTTTCTCCTATCTTTTCTATTTTGACATCTAAATCCATTATAAGGCAAAGTGTATTAAAAAGACAGCTTCACTATGATTAGTACATAAATAATTCATTTAAAAAGAGTAAATAATTTTTTATAAATAACGAATCAAAAAGTTTGACCAT
TACTGACCAAAGTATTATAATTAGAATGTAGTGAGAAAAAGATAATAATCACTACTAACTATGAAATCGAAATGAGGTGTTTTT
SLR1641
TGGCGTCTGATTCTGCGTAGGGGTCAAGATTAGCCCTTAGCTTACAAGAAAGGGGCTTTGGGGCCTAGTTGAATGGCACAAATTTTCCTTCCCTGACTGTTTTTGCGCCATTGT C T A G C T CAAAGTCAGCCTCCGGCATCCTCTAGAAAG
ACTTCCATCCCCTGGTTGAGCAAGGGTAAACCCCACCACTGCATTGGGAAAACCCTCCTTCC T A G C T C CGGATTCCACCCCCTAAAATTGATTTGGTAGTCCTTACACACCCAATAGCCAATATAGAAAATTTT
SLR0156
TCTATTTTTTCTCGATAATTTCAAGGATTCGGCGAATATAGATTGACTTGACTTTCTTGTTGTGGACGGGAATAACCAGAATAATATCATTTTTTTTGAAAATGTGATGACTACCTGTGATTCTTTCAAGATAGAAGCCTT C T A G C T C CA
GTAACTTACAGACATCACTGAATCTAATGTTGTTAGGACTATTTTTCAGGAGCGCAATGAGTTTTTTTCTTTTAGGCACAGTTTCATAACTTATCAATTGTATTCCCCA A A A T T T TACCAGAGTCTGAAATGTTTGTTGAAG
CPN0144
CAGTTCAAGAGATCACTTCCTAATGTATTTTTAGAAAGGGGAAAGAGATCCTCTTAGGTTAGACGTTTAGGTTTGGTAGTATTTCGATAGGGTTTGATAAAGTTGCCTCTTCTACATTCTCAGAGGAAAGTTTATAGATTTTTTATTATT
CCTATGTAATAAGAAAAACCTTTTTAAAAAGTGCTTGGGGTGAATTTT
MG355
ATAGTTATTTTAGGTTTCTAATTATTTTGACAAAAATATCAACTCTGATTAGATAAATTAGAGATAAACAAAAAACCTAGTTTTTAATTAGCACTCGAATGCCTTGAGTGCTAATTTTATATAATTTTTGCATTAAAAGGAGTGAGCAAT
TAAA

Several motifs were found in this search, that neither DiAlign nor CLUSTALW were able to find.

Command line:

-details

-triplet_filtering

-post_filtering

-size 8

-max_mutations 2

-max_mutations_per_branch 2

-losses /homes/gws/blanchem/FootPrinterWeb/universal8.config

-compute_branch_lengths

-loss_cost 1

-sequence_type upstream

-subregion_size 50

-position_change_cost 1

Dialign Motifs found:

None of these “motifs” were found by Footprinter.

mll3429 187 ---------- ---------- ---------- ---------- ----------

CC0878 100 ---------- ---------- ---------- ---------- ----------

DR1046 4 ---------- ---------- ---------- ---------- ----------

Rv0384c 114 ---------- ---------- ---------- ---------- ----------

ML2490 76 ---------- ---------- ---------- ---------- ----------

HI0859 37 ---------A AAATATTTCA TTTT------ ---------- ----------

PM1704 127 aacctattgA AAATATGACA TTTAATAGGt ttgaattaaa tatatcgctt

ZclpB 34 ---------- ---------- --TT------ ---------- ----------

PA4542 48 ---------- ---------- ---------- ---------- ----------

slr1641 49 ---------- ---------- ---------- ---------- ----------

slr0156 39 ---------- ---------- ---------- ---------- ----------

L166407 83 tacat----- AAATAATTCA TTTAAAAAGa ---------- ----------

CPn0144 135 ---------- ---------- ---------- ---------- ----------

MG355 70 ---------A AAAAACCTAG TTTT------ ---------- ----------

mll3429 187 ---------- ---------- ---------- ---------- ----------

CC0878 100 ---------- ---------- ---------- ---------- ----------

DR1046 4 ---------- ---------- ---------- ---------G CCCTg-----

Rv0384c 114 ---------- ---------- ---------- ---------- ----------

ML2490 76 ---------- ---------- ---------- ---------- ----------

HI0859 52 ---TTCT--- ---------- -CTTGAAATT TATTCAACCG AGCTTACTTA

PM1704 177 aaaTACT--- ---------- -CTTGAAAAT GGTAAAAAGG GGCTTATTTA

ZclpB 36 ---TTCT--- ---------- -TTTCACATT AAT------- ----------

PA4542 48 ----TCG--- ---------- -CTTGAACCG CGGAAAATCG CCCTTATCTA

slr1641 49 ---------- ---------- ---------- -----AAAGG GGCTTtgggg

slr0156 39 ---------- ---TAGATTG ACTTGACTTT c--------- ----------

L166407 108 ---------- ---------- ---------- ---------- ----------

CPn0144 135 ---------- ---TAGATT- ---------- ---------- ----------

MG355 85 ---Taattag cacTCGAATG CCTTGAGTgc ---------- ----------