Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000535.1 Kokia drynarioides strain JFW-HI SEQ_111430, 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: 57197
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:495 original size:21 final size:22
Alignment explanation
Indices: 471--512 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
461 ATAAGAGAAT
471 GGAAAATAAAA-AAAATAAAAC
1 GGAAAATAAAATAAAATAAAAC
* *
492 GGAAATTAAAATAACATAAAA
1 GGAAAATAAAATAAAATAAAA
513 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.14
Consensus pattern (22 bp):
GGAAAATAAAATAAAATAAAAC
Found at i:1497 original size:2 final size:2
Alignment explanation
Indices: 1492--1525 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1482 TATCACACAC
1492 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
1526 GAATAACGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14790 original size:20 final size:22
Alignment explanation
Indices: 14765--14806 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
14755 TTATAATTTT
14765 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
14785 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
14807 TCATTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:14807 original size:20 final size:19
Alignment explanation
Indices: 14755--14812 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
14745 GGGATGATGA
14755 TTATAATTTT--AATAATT
1 TTATAATTTTAAAATAATT
14772 TTAT-ATTTTAAAAAATAATT
1 TTATAATTTT--AAAATAATT
*
14792 TTAATAATTTTAAAATCATT
1 TT-ATAATTTTAAAATAATT
14812 T
1 T
14813 ATTGATGTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
16 5 0.15
17 4 0.12
20 18 0.53
21 2 0.06
22 5 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATAATTTTAAAATAATT
Found at i:17754 original size:8 final size:8
Alignment explanation
Indices: 17741--17767 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17731 TATTTAAACA
17741 AAAAAAAG
1 AAAAAAAG
17749 AAAAAAAG
1 AAAAAAAG
17757 AAAAAAAG
1 AAAAAAAG
17765 AAA
1 AAA
17768 TATAATGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:20773 original size:19 final size:19
Alignment explanation
Indices: 20749--20787 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
20739 CCATTGTAAC
20749 ACTCCTATACCCGATTCAT
1 ACTCCTATACCCGATTCAT
*
20768 ACTCCTATACCCGGTTCAT
1 ACTCCTATACCCGATTCAT
20787 A
1 A
20788 TGTATAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.36, G:0.08, T:0.31
Consensus pattern (19 bp):
ACTCCTATACCCGATTCAT
Found at i:21312 original size:25 final size:25
Alignment explanation
Indices: 21278--21349 Score: 110
Period size: 25 Copynumber: 2.8 Consensus size: 25
21268 CGAAGTACTT
21278 AACAGAAGCACATAAGTGCTGGGGA
1 AACAGAAGCACATAAGTGCTGGGGA
21303 AACAGAAGCACATAAGTGCT-GGGA
1 AACAGAAGCACATAAGTGCTGGGGA
*
21327 AACAGTAGGCACATACAGTGCTG
1 AACAG-AAGCACATA-AGTGCTG
21350 AATGAAAGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
24 9 0.21
25 28 0.65
26 6 0.14
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.14
Consensus pattern (25 bp):
AACAGAAGCACATAAGTGCTGGGGA
Found at i:21366 original size:22 final size:22
Alignment explanation
Indices: 21303--21403 Score: 98
Period size: 22 Copynumber: 4.4 Consensus size: 22
21293 GTGCTGGGGA
*
21303 AACAGAAGCACATA-AGTGCTGGG
1 AACAGAAGCACACACAGTGCT--G
* *
21326 AAACAGTAGGCACATACAGTGCTG
1 -AACAG-AAGCACACACAGTGCTG
*
21350 AA-TGAAAGCACACACAGTGCTG
1 AACAG-AAGCACACACAGTGCTG
21372 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
21394 AACAGTAAGC
1 AACAG-AAGC
21404 GCGCTAGCGT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
22 40 0.60
23 7 0.10
24 6 0.09
25 8 0.12
26 6 0.09
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.13
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:22032 original size:9 final size:10
Alignment explanation
Indices: 22008--22034 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21998 GTCTCTAATA
22008 ATTTTTCTAT
1 ATTTTTCTAT
22018 ATTTTTCTAT
1 ATTTTTCTAT
22028 ATTTTTC
1 ATTTTTC
22035 AAAGTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTTTCTAT
Found at i:23674 original size:15 final size:15
Alignment explanation
Indices: 23618--23676 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
23608 ACCCGATCCT
23618 TAAATATTT-AATAA
1 TAAATATTTGAATAA
23632 -AAATATTTATGAA-AA
1 TAAATA-TT-TGAATAA
* *
23647 TAAATAGTAGAATAA
1 TAAATATTTGAATAA
*
23662 TAAATTTTTGAATAA
1 TAAATATTTGAATAA
23677 ATAATTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
13 5 0.14
14 5 0.14
15 18 0.51
16 7 0.20
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
TAAATATTTGAATAA
Found at i:26168 original size:18 final size:18
Alignment explanation
Indices: 26145--26183 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
26135 AAAAATCAAA
*
26145 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
26163 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
26181 TTT
1 TTT
26184 TTTTTCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:27242 original size:18 final size:19
Alignment explanation
Indices: 27189--27243 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 19
27179 TCTTATATTT
*
27189 TATATTATTA-ATAATA-A
1 TATATTATTAGTTAATATA
*
27206 TATATTATT-GTTTAT-TA
1 TATATTATTAGTTAATATA
27223 TAATATTATTAGTTAATATA
1 T-ATATTATTAGTTAATATA
27243 T
1 T
27244 CTTTTGATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 14 0.47
18 8 0.27
19 5 0.17
20 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
TATATTATTAGTTAATATA
Found at i:27659 original size:2 final size:2
Alignment explanation
Indices: 27654--27687 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27644 TGTGTGTGTG
27654 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27688 ATCATGTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28540 original size:3 final size:3
Alignment explanation
Indices: 28505--28529 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28495 ATGTTTTAGC
28505 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
28530 GTTGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:28780 original size:18 final size:18
Alignment explanation
Indices: 28757--28795 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
28747 TATAGGGGAT
28757 AATAACAAATATAACCCC
1 AATAACAAATATAACCCC
28775 AATAACAAATATAACCCC
1 AATAACAAATATAACCCC
28793 AAT
1 AAT
28796 CTTTACACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (18 bp):
AATAACAAATATAACCCC
Found at i:36254 original size:29 final size:28
Alignment explanation
Indices: 36222--36289 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 28
36212 GTAAATTTTA
*
36222 AGTTATTTTCGTATTTAA-TAAAAAAAATG
1 AGTTATTTT-GTAATTAATTAAAAAAAA-G
*
36251 AGTTATATATGTAATTAATTAAAAAAAAG
1 AGTTAT-TTTGTAATTAATTAAAAAAAAG
36280 AGATTATTTT
1 AG-TTATTTT
36290 TATAAAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (28 bp):
AGTTATTTTGTAATTAATTAAAAAAAAG
Found at i:37498 original size:57 final size:57
Alignment explanation
Indices: 37372--37673 Score: 252
Period size: 57 Copynumber: 5.2 Consensus size: 57
37362 TGAAAAAAAA
* * * * *
37372 TTTGGAGTGTTGGTCATGC-AATGGCCGACACCCCTTTTTTGTCAGATAAAAAATAT-AATT
1 TTTGG-GTGTTGGCCAT-CAAATGGCCGACA-CCCTCTTTTCTC-GAAAAAAAAT-TGCATT
** * * *
37432 TTTTTGTGTTAGCCATCAAATGGCCGACACTCTCTTTTCTCGAAAAAAAATTGTATT
1 TTTGGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
* *** ** * *
37489 TTTGGGTGTTGGTCATTGCATGATCGACACCCT-TTTTTTGAGAAAAAAAAATT-CAAAATT
1 TTTGGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCT-CG-AAAAAAAATTGC---ATT
**
37549 TTTTTGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
1 TTTGGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
** * * * *
37606 TTTGAATATTGGCCATCAAATGGCCAACACCTTTTTTTCTCGAAAAAAAATTGCATT
1 TTTGGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
37663 TTTGGGTGTTG
1 TTTGGGTGTTG
37674 ATCATTTTCA
Statistics
Matches: 191, Mismatches: 42, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
56 6 0.03
57 97 0.51
58 20 0.10
59 30 0.16
60 33 0.17
61 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (57 bp):
TTTGGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
Found at i:37572 original size:117 final size:117
Alignment explanation
Indices: 37372--37609 Score: 340
Period size: 117 Copynumber: 2.0 Consensus size: 117
37362 TGAAAAAAAA
* * *
37372 TTTGGAGTGTTGGTCATGCAATGGCCGACACCCCTTTTTTGTCAGATAAAAAATATAATTTTTTT
1 TTTGGAGTGTTGGTCATGCAATGACCGACACCCCTTTTTTGTCAGAAAAAAAATAAAATTTTTTT
* *
37437 GTGTTAGCCATCAAATGGCCGACACTCTCTTTTCTCGAAAAAAAATTGTATT
66 GTGTTAGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
* *
37489 TTTGG-GTGTTGGTCATTGC-ATGATCGACA-CCCTTTTTT-TGAGAAAAAAAAATTCAAAATTT
1 TTTGGAGTGTTGGTCA-TGCAATGACCGACACCCCTTTTTTGTCAG-AAAAAAAA-T-AAAATTT
*
37550 TTTTGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
62 TTTTGTGTTAGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
37606 TTTG
1 TTTG
37610 AATATTGGCC
Statistics
Matches: 109, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
114 3 0.03
115 16 0.15
116 19 0.17
117 71 0.65
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (117 bp):
TTTGGAGTGTTGGTCATGCAATGACCGACACCCCTTTTTTGTCAGAAAAAAAATAAAATTTTTTT
GTGTTAGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
Found at i:37655 original size:117 final size:117
Alignment explanation
Indices: 37428--37643 Score: 308
Period size: 117 Copynumber: 1.9 Consensus size: 117
37418 TAAAAAATAT
* *
37428 AATTTTTTTGTGTTAGCCATCAAATGGCCGACACTCTCTTTTCTCGAAAAAAAATTGTATTTTTG
1 AATTTTTTTGTGTTAGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATTTTTG
** * * *** * *
37493 GGTGTTGGTCATTGCATGATCGACACCCTTTTTTTGAGAAAAAAAAATTCAA
66 AATATTGGCCATCAAATGACCAACACCCTTTTTTTGAGAAAAAAAAATTCAA
*
37545 AATTTTTTTGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATTTTTG
1 AATTTTTTTGTGTTAGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATTTTTG
*
37610 AATATTGGCCATCAAATGGCCAACA-CCTTTTTTT
66 AATATTGGCCATCAAATGACCAACACCCTTTTTTT
37644 CTCGAAAAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
116 9 0.10
117 77 0.90
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (117 bp):
AATTTTTTTGTGTTAGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATTTTTG
AATATTGGCCATCAAATGACCAACACCCTTTTTTTGAGAAAAAAAAATTCAA
Found at i:37780 original size:62 final size:63
Alignment explanation
Indices: 37682--37843 Score: 186
Period size: 63 Copynumber: 2.6 Consensus size: 63
37672 TGATCATTTT
* * * * * *
37682 CAAAATTTTTTGGTGTTGGCCAT-CAAATGG-TCGACACTCTCTTTTCTCGGA-CAAAAAAATTA
1 CAAATTTTTTTTGTGTTGGCCATGC-AATGGCT-GACACCCCCTTTTCTCGAATAAAAAAAATTA
* *
37744 CAAATTTTTTTTGTGTTGGTCATGCAATGGCTGACACCCCCTTTTCTTGAATAAAAAAAATTA
1 CAAATTTTTTTTGTGTTGGCCATGCAATGGCTGACACCCCCTTTTCTCGAATAAAAAAAATTA
* * *
37807 CAAATTCTTTTTGTGTTGGCCATGTAATGGCCGACAC
1 CAAATTTTTTTTGTGTTGGCCATGCAATGGCTGACAC
37844 AAACTTCCTC
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
62 40 0.47
63 45 0.53
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (63 bp):
CAAATTTTTTTTGTGTTGGCCATGCAATGGCTGACACCCCCTTTTCTCGAATAAAAAAAATTA
Found at i:40982 original size:41 final size:42
Alignment explanation
Indices: 40898--40979 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
40888 GCCATTGCAT
*
40898 GGCCAACACCAAAAAAATTTACAATTTTTTTATTCGAGAAAA
1 GGCCAACACCAAAAAAATTTACAATTTTTTTACTCGAGAAAA
*
40940 GGCCAACACCAAAAAATTTTGA-AA-TTTTTT-CTCGAGAAAA
1 GGCCAACACCAAAAAAATTT-ACAATTTTTTTACTCGAGAAAA
40980 AGGAGTGTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 9 0.24
41 6 0.16
42 21 0.57
43 1 0.03
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (42 bp):
GGCCAACACCAAAAAAATTTACAATTTTTTTACTCGAGAAAA
Found at i:41482 original size:58 final size:58
Alignment explanation
Indices: 41413--41529 Score: 182
Period size: 58 Copynumber: 2.0 Consensus size: 58
41403 AAAAAGAGTT
* *
41413 GTTTATGAGTGTTATTT-AGGAATAAAATTATATCTGGGTTTAAAAATATTTAGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATCTGGGTTTAAAAATAATTAGGTTTA
* *
41471 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAAAAATAATTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATCTGGGTTTAAAAATAATTAGGTTTA
41529 G
1 G
41530 CTTGTTGATG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 3 0.06
58 51 0.94
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.44
Consensus pattern (58 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATCTGGGTTTAAAAATAATTAGGTTTA
Found at i:46350 original size:12 final size:12
Alignment explanation
Indices: 46333--46357 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46323 ATCAACTTAA
46333 AGGTGTTTATTG
1 AGGTGTTTATTG
46345 AGGTGTTTATTG
1 AGGTGTTTATTG
46357 A
1 A
46358 TTAAGTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (12 bp):
AGGTGTTTATTG
Found at i:46627 original size:2 final size:2
Alignment explanation
Indices: 46620--46649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46610 ATAACACAAC
46620 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
46650 TTGTGGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.