Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014736.1 Kokia drynarioides strain JFW-HI SEQ_129775, 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: 32491
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:589 original size:61 final size:61
Alignment explanation
Indices: 523--639 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
513 AATTTATTGA
* * ** *
523 ATTTTTTAAAATT-AGAACTAAATTGAAAAAAATTGTAAATTTTGAGGGCTAAATTTAATTT
1 ATTTTTTAAAATTCA-AACGAAAATGAAAAAAATTGTAAACATTAAGGGCTAAATTTAATTT
* **
584 ATTTTTTAGAATTCAAACGAAAATGAAAAATTTTGTAAACATTAAGGGCTAAATTT
1 ATTTTTTAAAATTCAAACGAAAATGAAAAAAATTGTAAACATTAAGGGCTAAATTT
640 GTTGAATGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
61 46 0.98
62 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.38
Consensus pattern (61 bp):
ATTTTTTAAAATTCAAACGAAAATGAAAAAAATTGTAAACATTAAGGGCTAAATTTAATTT
Found at i:20334 original size:40 final size:40
Alignment explanation
Indices: 20297--20533 Score: 269
Period size: 40 Copynumber: 5.9 Consensus size: 40
20287 AGAGATATAA
* * *
20297 TTCAAGCTACGACTTAGCAGGCTTTAAGCTGGTGATATGT
1 TTCAAGCTACGGCTTAACAGGCTTTGAGCTGGTGATATGT
* * * *
20337 CTCAAGCTACGTCTTAACAGGCTTTGAGCCGATGATATGT
1 TTCAAGCTACGGCTTAACAGGCTTTGAGCTGGTGATATGT
* *
20377 TTCAAGCTACGGCTTAATAGGCTTTGAGCTGCTGATATGT
1 TTCAAGCTACGGCTTAACAGGCTTTGAGCTGGTGATATGT
* * * *
20417 TTCAAGCTATGGCTTAGCAGACTTTGAGTTGGTGATATGT
1 TTCAAGCTACGGCTTAACAGGCTTTGAGCTGGTGATATGT
* * * * * *
20457 TTCAAGCTATGGGTTAATAGGCCTTAAGCTAGTGATATGT
1 TTCAAGCTACGGCTTAACAGGCTTTGAGCTGGTGATATGT
* *
20497 TTCAAGCTACGGCTTAGA-ATGCTTTGAGCCGGTGATA
1 TTCAAGCTACGGCTTA-ACAGGCTTTGAGCTGGTGATA
20534 AATTTTGGGC
Statistics
Matches: 164, Mismatches: 32, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
40 163 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TTCAAGCTACGGCTTAACAGGCTTTGAGCTGGTGATATGT
Found at i:20503 original size:120 final size:120
Alignment explanation
Indices: 20297--20525 Score: 300
Period size: 120 Copynumber: 1.9 Consensus size: 120
20287 AGAGATATAA
* * *
20297 TTCAAGCTACGACTTAGCAGGCTTTAAGCTGGTGATATGTCTCAAGCTACGTCTTAACAGGCTTT
1 TTCAAGCTACGACTTAGCAGACTTTAAGCTGGTGATATGTCTCAAGCTACGGCTTAACAGGCCTT
* *
20362 GAGCCGATGATATGTTTCAAGCTACGGCTTA-ATAGGCTTTGAGCTGCTGATATGT
66 AAGCAGATGATATGTTTCAAGCTACGGCTTAGA-AGGCTTTGAGCTGCTGATATGT
* * * * * * * *
20417 TTCAAGCTATGGCTTAGCAGACTTTGAGTTGGTGATATGTTTCAAGCTATGGGTTAATAGGCCTT
1 TTCAAGCTACGACTTAGCAGACTTTAAGCTGGTGATATGTCTCAAGCTACGGCTTAACAGGCCTT
*
20482 AAGCTAG-TGATATGTTTCAAGCTACGGCTTAGAATGCTTTGAGC
66 AAGC-AGATGATATGTTTCAAGCTACGGCTTAGAAGGCTTTGAGC
20526 CGGTGATAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
120 91 0.98
121 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (120 bp):
TTCAAGCTACGACTTAGCAGACTTTAAGCTGGTGATATGTCTCAAGCTACGGCTTAACAGGCCTT
AAGCAGATGATATGTTTCAAGCTACGGCTTAGAAGGCTTTGAGCTGCTGATATGT
Found at i:23567 original size:30 final size:30
Alignment explanation
Indices: 23533--23590 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
23523 CTGGCGATTG
*
23533 ATATG-TGTAATATAGGGTATGAAAATGATA
1 ATATGATG-AATACAGGGTATGAAAATGATA
*
23563 ATATGAATGATTACAGGGTATGAAAATG
1 ATATG-ATGAATACAGGGTATGAAAATG
23591 CAAATGTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.21
31 17 0.71
32 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (30 bp):
ATATGATGAATACAGGGTATGAAAATGATA
Found at i:23606 original size:31 final size:30
Alignment explanation
Indices: 23546--23646 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 30
23536 TGTGTAATAT
*
23546 AGGGTATGAAAATG-ATAATATGAATGATTAC
1 AGGGTATGAAAATGCA-AATGTG-ATGATTAC
23577 AGGGTATGAAAATGCAAATGTGATCGATTAC
1 AGGGTATGAAAATGCAAATGTGAT-GATTAC
* ** ** *
23608 AAGGTAT-ATTATGCAAATGTGAAAAGTAC
1 AGGGTATGAAAATGCAAATGTGATGATTAC
23637 AGGGTATGAA
1 AGGGTATGAA
23647 TATGTTAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
29 10 0.17
30 16 0.28
31 31 0.53
32 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.27
Consensus pattern (30 bp):
AGGGTATGAAAATGCAAATGTGATGATTAC
Found at i:24919 original size:6 final size:6
Alignment explanation
Indices: 24910--24988 Score: 58
Period size: 6 Copynumber: 13.5 Consensus size: 6
24900 ATTTGTTTAA
* **
24910 AAATTT AAATTT -ATTTT AAATTT AAATTT -GTTTAT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT AAATTT
* * *
24957 -AATTT AAGTTT AAAATT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
24989 ATTTTCATAA
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
5 14 0.25
6 35 0.64
7 6 0.11
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:24969 original size:35 final size:35
Alignment explanation
Indices: 24878--25005 Score: 152
Period size: 35 Copynumber: 3.7 Consensus size: 35
24868 CCAAACTCCC
* *
24878 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAATTTAAATTTGTTTATAAA
24913 TTTAAATTTATTTTAAATTTAAATTTGTTTATAAA
1 TTTAAATTTATTTTAAATTTAAATTTGTTTATAAA
* * * *
24948 TTTAAATTTAATTTAAGTTTAAAATTATTT-TCAAA
1 TTTAAATTTATTTTAAATTTAAATTTGTTTAT-AAA
**
24983 TTTAAAATTT-TCATAAATTTAAA
1 TTT-AAATTTATTTTAAATTTAAA
25006 ATAAATAAAG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
34 1 0.01
35 74 0.91
36 6 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTGTTTATAAA
Found at i:24991 original size:18 final size:17
Alignment explanation
Indices: 24878--24988 Score: 132
Period size: 17 Copynumber: 6.4 Consensus size: 17
24868 CCAAACTCCC
24878 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
24895 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
24913 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
24930 TTTAAATTTGTTTATAAA
1 TTTAAATTTATTT-TAAA
* *
24948 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
24965 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTT-AAA
24983 TTTAAA
1 TTTAAA
24989 ATTTTCATAA
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
17 41 0.53
18 37 0.47
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:26183 original size:13 final size:13
Alignment explanation
Indices: 26165--26213 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
26155 CCAGGCGGTG
26165 ACGCGCGATGACC
1 ACGCGCGATGACC
*
26178 ACGCGCCGAGATCGACG
1 ACGCG-C--GAT-GACC
26195 ACGCGCGATGACC
1 ACGCGCGATGACC
26208 ACGCGC
1 ACGCGC
26214 AGGGATCGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 14 0.47
14 4 0.13
16 4 0.13
17 8 0.27
ACGTcount: A:0.22, C:0.39, G:0.33, T:0.06
Consensus pattern (13 bp):
ACGCGCGATGACC
Found at i:26221 original size:30 final size:30
Alignment explanation
Indices: 26164--26221 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
26154 CCCAGGCGGT
*
26164 GACGCGCGATGACCACGCGCCGAGATCGAC
1 GACGCGCGATGACCACGCGCAGAGATCGAC
*
26194 GACGCGCGATGACCACGCGCAGGGATCG
1 GACGCGCGATGACCACGCGCAGAGATCG
26222 GCGATGCACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.34, G:0.36, T:0.07
Consensus pattern (30 bp):
GACGCGCGATGACCACGCGCAGAGATCGAC
Found at i:26946 original size:59 final size:59
Alignment explanation
Indices: 26853--27171 Score: 363
Period size: 59 Copynumber: 5.4 Consensus size: 59
26843 CCCTAGACTG
*
26853 TCCAAAAATTCCATTTTGTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAACT
1 TCCAAAAATTCCATTTT-TACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * * *
26913 CCCAAAAATTCCATTTTTACCCCCGAAGTTCCAAAAAT-CCATTTTTGACCTCTAAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
*** * * * *
26971 TCCAAAAATTCCATTTTTAACCCTAAAACTTCTAACAATTCCATTTTTAACCCTAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
** ** *
27031 TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATATCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * * * **
27090 TCCGAAAATTCTATTTTTACCTCCGAACTTCCAAAAATCCCATTTTTAACCTCGAATTT
1 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
*
27149 TCCTAAAATTACCA-TTTTACCCC
1 TCCAAAAATT-CCATTTTTACCCC
27172 GGGTATCCGA
Statistics
Matches: 217, Mismatches: 39, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
58 34 0.16
59 131 0.60
60 52 0.24
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
Found at i:27157 original size:30 final size:30
Alignment explanation
Indices: 26853--27166 Score: 327
Period size: 30 Copynumber: 10.6 Consensus size: 30
26843 CCCTAGACTG
*
26853 TCCAAAAATTCCATTTTGTACCCCCG-AACT
1 TCCAAAAATTCCATTTT-TAACCCCGAAACT
*
26883 TCCAAAAATCCCATTTTTAACCCCGAAACT
1 TCCAAAAATTCCATTTTTAACCCCGAAACT
* * *
26913 CCCAAAAATTCCATTTTTACCCCCG-AAGT
1 TCCAAAAATTCCATTTTTAACCCCGAAACT
* * *
26942 TCCAAAAA-TCCATTTTTGACCTCTAAACT
1 TCCAAAAATTCCATTTTTAACCCCGAAACT
**
26971 TCCAAAAATTCCATTTTTAACCCTAAAACT
1 TCCAAAAATTCCATTTTTAACCCCGAAACT
* * **
27001 TCTAACAATTCCATTTTTAACCCTAAAACT
1 TCCAAAAATTCCATTTTTAACCCCGAAACT
*
27031 TCCAAAAATTCCATTTTT-ACCCCTAAACT
1 TCCAAAAATTCCATTTTTAACCCCGAAACT
* *
27060 TCCAAAAATAT-CATTTTTGACCCCAAAACT
1 TCCAAAAAT-TCCATTTTTAACCCCGAAACT
* *
27090 TCCGAAAATTCTATTTTT-ACCTCCG-AACT
1 TCCAAAAATTCCATTTTTAACC-CCGAAACT
* * **
27119 TCCAAAAATCCCATTTTTAACCTCGAATTT
1 TCCAAAAATTCCATTTTTAACCCCGAAACT
*
27149 TCCTAAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
27167 ACCCCGGGTA
Statistics
Matches: 240, Mismatches: 34, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.05
29 78 0.32
30 143 0.60
31 7 0.03
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.33
Consensus pattern (30 bp):
TCCAAAAATTCCATTTTTAACCCCGAAACT
Done.