Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006045.1 Kokia drynarioides strain JFW-HI SEQ_120511, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 154353
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:13356 original size:108 final size:107
Alignment explanation
Indices: 13239--13515 Score: 401
Period size: 108 Copynumber: 2.6 Consensus size: 107
13229 TAAGTGTAAT
* * * *
13239 CCCAACTCTAGTTGGACAAACTAACGATATTGCACCCAACGCTAGTCAGATAAACCGAAAAAAGT
1 CCCAACTCTAGTTGGATAAACCAACAATATTGCGCCCAACGCTAGTC-GATAAACCGAAAAAAGT
* *
13304 GTGCCCATCACTAGTCAGATAAACTGACGATATTATTAATGAG
65 GTGCCCAGCACTAGTCAGACAAACTGACGATATTATTAATGAG
* * * **
13347 CCCAGCTCTAATTGGATAAGCCAACAATATTGCGCCCAACGCTAGTCGGATAAACCGACGAAAGT
1 CCCAACTCTAGTTGGATAAACCAACAATATTGCGCCCAACGCTAGTC-GATAAACCGAAAAAAGT
* *
13412 GTGCCTAGCACTAGTCAGACAAACTGGCGATATTATTAATGAG
65 GTGCCCAGCACTAGTCAGACAAACTGACGATATTATTAATGAG
* *
13455 CCCAACTCTAGTTGGATAAACCAACAATATTGCGCCCAACGCTAGTCGATTAACTGAAAAA
1 CCCAACTCTAGTTGGATAAACCAACAATATTGCGCCCAACGCTAGTCGATAAACCGAAAAA
13516 TTGTACATGT
Statistics
Matches: 148, Mismatches: 21, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
107 10 0.07
108 138 0.93
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (107 bp):
CCCAACTCTAGTTGGATAAACCAACAATATTGCGCCCAACGCTAGTCGATAAACCGAAAAAAGTG
TGCCCAGCACTAGTCAGACAAACTGACGATATTATTAATGAG
Found at i:14802 original size:25 final size:25
Alignment explanation
Indices: 14772--14822 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
14762 AAATCAATTT
14772 AAACATTGCTCTAATAATTAAGTAG
1 AAACATTGCTCTAATAATTAAGTAG
14797 AAACATTGCTCTAATAATTAAGTAG
1 AAACATTGCTCTAATAATTAAGTAG
14822 A
1 A
14823 CATAGCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (25 bp):
AAACATTGCTCTAATAATTAAGTAG
Found at i:20610 original size:13 final size:13
Alignment explanation
Indices: 20594--20634 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
20584 TAAATATAAA
20594 ATAGTGTATATGT
1 ATAGTGTATATGT
20607 ATAGTGTATATGT
1 ATAGTGTATATGT
* *
20620 GTA-TGTATATAT
1 ATAGTGTATATGT
20632 ATA
1 ATA
20635 TATAAATGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (13 bp):
ATAGTGTATATGT
Found at i:21311 original size:2 final size:2
Alignment explanation
Indices: 21304--21352 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
21294 AAGAATGACA
21304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21346 AT AT AT A
1 AT AT AT A
21353 AGAAGCATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38138 original size:52 final size:52
Alignment explanation
Indices: 38058--38354 Score: 432
Period size: 52 Copynumber: 5.7 Consensus size: 52
38048 AAATGAAAAA
* * *
38058 AGGTCCGATGACTAAGTGTCATCGTGAGTGTATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
38110 AGGTCCGATGATTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
38162 AGGTCCGGTGATTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
38214 AGGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
38266 AGGTCCGATGGCTATGTGTCATCATGAGTATACGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
38318 AGGTCTGGTGGCTATGTGTCATTGTGAGTATATGAAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
38355 GAAATGATAT
Statistics
Matches: 223, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 223 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:38345 original size:156 final size:156
Alignment explanation
Indices: 38057--38354 Score: 488
Period size: 156 Copynumber: 1.9 Consensus size: 156
38047 TAAATGAAAA
* *
38057 AAGGTCCGATGACTAAGTGTCATCGTGAGTGTATGAATCCTTTACGAATTATGAGGTCCGATGAT
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGAC
* *
38122 TATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGGTGATTATGTGTCATCGT
66 TATGTGTCATCATGAGTATACGAATCCTTTACGGATTATGAGGTCCGGTGACTATGTGTCATCGT
38187 GAGTATATGAATCCTTTATGGATTAT
131 GAGTATATGAATCCTTTATGGATTAT
* * * *
38213 AAGGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGGC
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGAC
* * * *
38278 TATGTGTCATCATGAGTATACGAATCCTTTATGGATTATGAGGTCTGGTGGCTATGTGTCATTGT
66 TATGTGTCATCATGAGTATACGAATCCTTTACGGATTATGAGGTCCGGTGACTATGTGTCATCGT
38343 GAGTATATGAAT
131 GAGTATATGAAT
38355 GAAATGATAT
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
156 130 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (156 bp):
AAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGAC
TATGTGTCATCATGAGTATACGAATCCTTTACGGATTATGAGGTCCGGTGACTATGTGTCATCGT
GAGTATATGAATCCTTTATGGATTAT
Found at i:48312 original size:35 final size:36
Alignment explanation
Indices: 48249--48396 Score: 149
Period size: 35 Copynumber: 4.2 Consensus size: 36
48239 GACTGGGCTT
* *
48249 GTATGAGCTAAAATTACTGGGAGACTTGAAGAGCTC
1 GTATGAGCTAAATTTACTGGGAAACTTGAAGAGCTC
*
48285 GTATGAGCT-AATTTATTGGGAAACTTGAAGAGCTC
1 GTATGAGCTAAATTTACTGGGAAACTTGAAGAGCTC
* * * * * *
48320 ATATGAGCT-AATTTTCTAGGAAAGTAGAAGAGCTT
1 GTATGAGCTAAATTTACTGGGAAACTTGAAGAGCTC
** * *
48355 GTAAAAGCTGAA-TTACTGGGAAACTTGAAGAGATC
1 GTATGAGCTAAATTTACTGGGAAACTTGAAGAGCTC
*
48390 GTTTGAG
1 GTATGAG
48397 TATCTTCATT
Statistics
Matches: 89, Mismatches: 22, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
35 78 0.88
36 11 0.12
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (36 bp):
GTATGAGCTAAATTTACTGGGAAACTTGAAGAGCTC
Found at i:73571 original size:21 final size:22
Alignment explanation
Indices: 73540--73583 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
73530 GCTCCGGTTG
* *
73540 GTGTAAAGGACAAGAAGAGGAA
1 GTGTAAAGGACAAAAAGAAGAA
73562 GTGT-AAGGACAAAAAGAAGAA
1 GTGTAAAGGACAAAAAGAAGAA
73583 G
1 G
73584 CACAAGGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.52, C:0.05, G:0.34, T:0.09
Consensus pattern (22 bp):
GTGTAAAGGACAAAAAGAAGAA
Found at i:81834 original size:10 final size:10
Alignment explanation
Indices: 81819--81875 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
81809 TTATTGTATA
81819 TTCTTTCTTT
1 TTCTTTCTTT
81829 TTCTTTCTTT
1 TTCTTTCTTT
* *
81839 TTATTAAC-TT
1 TTCTT-TCTTT
81849 TTCTTTCTTT
1 TTCTTTCTTT
81859 TTC--TCTTT
1 TTCTTTCTTT
*
81867 TTTTTTCTT
1 TTCTTTCTT
81876 ATGCGACTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
8 7 0.18
9 1 0.03
10 29 0.76
11 1 0.03
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:88290 original size:28 final size:28
Alignment explanation
Indices: 88245--88299 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
88235 CTAGGTCACA
* *
88245 AAGAGCTTTATCTAAGTACTATTTTCCG
1 AAGAGCTTTACCTAAGTAATATTTTCCG
*
88273 AAGAGCTTTACCTTAGTAATATTTTCC
1 AAGAGCTTTACCTAAGTAATATTTTCC
88300 AATAGAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (28 bp):
AAGAGCTTTACCTAAGTAATATTTTCCG
Found at i:108441 original size:36 final size:35
Alignment explanation
Indices: 108394--108569 Score: 235
Period size: 36 Copynumber: 4.9 Consensus size: 35
108384 GACTGGGCTT
108394 GTATGAGCTAAAATTACTAGGAAACTTGAAGAGCTC
1 GTATGAGCT-AAATTACTAGGAAACTTGAAGAGCTC
108430 GTATGAGCTAAAATTACTAGGAAAACTTGAAGAGCTC
1 GTATGAGCT-AAATTACTAGG-AAACTTGAAGAGCTC
* * * *
108467 ATATGAGCTAATTTACTGGGAAACTTGAAGAGCTT
1 GTATGAGCTAAATTACTAGGAAACTTGAAGAGCTC
* *
108502 GTAAGAGCTAAATCTACTAGGAAACTTGAAGAGTTC
1 GTATGAGCTAAAT-TACTAGGAAACTTGAAGAGCTC
* * *
108538 GTAAGAGCTGAATTACTGGGAAACTTGAAGAG
1 GTATGAGCTAAATTACTAGGAAACTTGAAGAG
108570 ACCGTTTGAG
Statistics
Matches: 126, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
35 42 0.33
36 61 0.48
37 23 0.18
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (35 bp):
GTATGAGCTAAATTACTAGGAAACTTGAAGAGCTC
Found at i:108566 original size:71 final size:71
Alignment explanation
Indices: 108405--108569 Score: 235
Period size: 71 Copynumber: 2.3 Consensus size: 71
108395 TATGAGCTAA
* *
108405 AATTACTAGGAAACTTGAAGAGCTCGTATGAGCTAAAATTACTAGGAAAACTTGAAGAGCTCATA
1 AATTACTGGGAAACTTGAAGAGCTCGTAAGAGCTAAAATTACTAGGAAAACTTGAAGAGCTCATA
*
108470 TGAGCT
66 AGAGCT
* * *
108476 AATTTACTGGGAAACTTGAAGAGCTTGTAAGAGCT-AAATCTACTAGG-AAACTTGAAGAGTTCG
1 AA-TTACTGGGAAACTTGAAGAGCTCGTAAGAGCTAAAAT-TACTAGGAAAACTTGAAGAGCTCA
108539 TAAGAGCT
64 TAAGAGCT
108547 GAATTACTGGGAAACTTGAAGAG
1 -AATTACTGGGAAACTTGAAGAG
108570 ACCGTTTGAG
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
71 47 0.55
72 38 0.45
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (71 bp):
AATTACTGGGAAACTTGAAGAGCTCGTAAGAGCTAAAATTACTAGGAAAACTTGAAGAGCTCATA
AGAGCT
Found at i:109956 original size:21 final size:21
Alignment explanation
Indices: 109932--109975 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
109922 TAAAGAAATG
*
109932 ATAGATTTCATAATAGCATTC
1 ATAGATTTCATAACAGCATTC
*
109953 ATAGATTTCATAACATCATTC
1 ATAGATTTCATAACAGCATTC
109974 AT
1 AT
109976 CATGATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (21 bp):
ATAGATTTCATAACAGCATTC
Found at i:116018 original size:17 final size:17
Alignment explanation
Indices: 115988--116021 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
115978 TGTGTTAGCA
* *
115988 AAGAATTTTTTTAGAGG
1 AAGAAATTTCTTAGAGG
116005 AAGAAATTTCTTAGAGG
1 AAGAAATTTCTTAGAGG
116022 GAGAGAATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (17 bp):
AAGAAATTTCTTAGAGG
Found at i:117508 original size:21 final size:21
Alignment explanation
Indices: 117465--117508 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
117455 ATGCATTGCA
* *
117465 AATTGTGAACTGTATATTACG
1 AATTGTGAACTATATAATACG
* *
117486 AATTGTGAACTATGTAATGCG
1 AATTGTGAACTATATAATACG
117507 AA
1 AA
117509 CTGCGAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (21 bp):
AATTGTGAACTATATAATACG
Found at i:117987 original size:29 final size:27
Alignment explanation
Indices: 117954--118039 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 27
117944 ATGAAAAACG
*
117954 ATTGTATGCAAATTGATTATACGTGAACT
1 ATTGTATG--AATTGATTATATGTGAACT
** * *
117983 ATTGTATTGAGCTGATCATATGTGAACA
1 ATTGTA-TGAATTGATTATATGTGAACT
118011 ATTGTATGGGAATTGATTATATGTGAACT
1 ATTGTAT--GAATTGATTATATGTGAACT
118040 GAATGCGAGC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.02
28 20 0.44
29 22 0.49
30 2 0.04
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (27 bp):
ATTGTATGAATTGATTATATGTGAACT
Found at i:123227 original size:52 final size:52
Alignment explanation
Indices: 123140--123378 Score: 261
Period size: 52 Copynumber: 4.6 Consensus size: 52
123130 ATTTCACTTC
** * ** *
123140 ATTCATATACTTGCGATGACACATA-CCTACCGGACCTTATAATCCGTAAGGG
1 ATTCATATACTCACGATGACACATAGTC-ATTGGACCTTATAATCCGTAAAGG
* *
123192 ATTCATATACTCACGATGACACAGAGTCATTGGACCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATTGGACCTTATAATCCGTAAAGG
* * * * *
123244 ATTCATATACACACGATGACACTTAGTCATCGAACCTCT-TAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGTCATTGGACCT-TATAATCCGTAAAGG
* * *
123296 ATTCATATACTCACGAAGACACATAG-C-TGTCGGACCTTATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACATAGTCAT-T-GGACCTTATAATCCGTAAAGG
*
123348 ATTCATATACTCATGATGACACATAGTCATT
1 ATTCATATACTCACGATGACACATAGTCATT
123379 AGTCCTCTTT
Statistics
Matches: 156, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
50 1 0.01
51 2 0.01
52 148 0.95
53 4 0.03
54 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATTGGACCTTATAATCCGTAAAGG
Found at i:137308 original size:34 final size:34
Alignment explanation
Indices: 137268--137336 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
137258 AATTTTTATG
137268 TTCAATTTCTCAATTTTTTGCTATTTTTACTTGT
1 TTCAATTTCTCAATTTTTTGCTATTTTTACTTGT
137302 TTCAATTTCTCAATTTTTTGCTATTTTTACTTGT
1 TTCAATTTCTCAATTTTTTGCTATTTTTACTTGT
137336 T
1 T
137337 CGTTACTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.62
Consensus pattern (34 bp):
TTCAATTTCTCAATTTTTTGCTATTTTTACTTGT
Found at i:142145 original size:72 final size:76
Alignment explanation
Indices: 142023--142220 Score: 269
Period size: 78 Copynumber: 2.6 Consensus size: 76
142013 TAGAAATTAA
* ** ** *
142023 AATTGAATAATTCTGTTTCAGGATTTATTAATATCATTCGACAGAATTTATTC-A-TTT-TTTT-
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCATTCAACAGAATTTATTCTATTTTATTTTC
142084 AAACAAGAATT
66 AAACAAGAATT
* * *
142095 AATTAAATAATTCTGTTTTAGGATTTATTCCTGCCGTTCAACAAAATTTATTCTATTTTTTATTT
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCATTCAACAGAATTTATTCTA--TTTTATTT
142160 TCAAACAAGAATT
64 TCAAACAAGAATT
142173 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCATTCAACAGAATT
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCATTCAACAGAATT
142221 CATTTTGATT
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
72 44 0.41
73 1 0.01
76 3 0.03
77 4 0.04
78 56 0.52
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (76 bp):
AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCATTCAACAGAATTTATTCTATTTTATTTTC
AAACAAGAATT
Found at i:150406 original size:26 final size:26
Alignment explanation
Indices: 150359--150410 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
150349 AACTTGGGAC
* *
150359 ATAAGATATTAACATCATAATATAAA
1 ATAAGAAATTAACATCAGAATATAAA
* *
150385 ATAAGAAATTAACCTTAGAATATAAA
1 ATAAGAAATTAACATCAGAATATAAA
150411 GTTTAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.29
Consensus pattern (26 bp):
ATAAGAAATTAACATCAGAATATAAA
Done.