Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011017.1 Kokia drynarioides strain JFW-HI SEQ_125988, 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: 81664
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:654 original size:9 final size:9
Alignment explanation
Indices: 637--693 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
627 CATCTTTACC
*
637 TCTCATTTT
1 TCTCTTTTT
646 TCTCTTTTT
1 TCTCTTTTT
*
655 TTTCTTTCTT
1 TCTCTTT-TT
*
665 TCTTTTTCTT
1 TCTCTTT-TT
*
675 TCTTTTTTT
1 TCTCTTTTT
*
684 TGTCTTTTT
1 TCTCTTTTT
693 T
1 T
694 TAGAGGAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
9 24 0.59
10 17 0.41
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (9 bp):
TCTCTTTTT
Found at i:693 original size:10 final size:9
Alignment explanation
Indices: 642--694 Score: 54
Period size: 10 Copynumber: 5.7 Consensus size: 9
632 TTACCTCTCA
*
642 TTTTTCTCT
1 TTTTTTTCT
651 TTTTTTTC-
1 TTTTTTTCT
*
659 TTTCTTTCT
1 TTTTTTTCT
668 TTTTCTTTCTT
1 TTTT-TTTC-T
679 TTTTTTGTCT
1 TTTTTT-TCT
689 TTTTTT
1 TTTTTT
695 AGAGGAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.19
9 10 0.27
10 13 0.35
11 7 0.19
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:694 original size:14 final size:14
Alignment explanation
Indices: 644--694 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
634 ACCTCTCATT
644 TTTCTCTTTTTTTTC
1 TTTCT-TTTTTTTTC
*
659 TTTCTTTCTTTTTC
1 TTTCTTTTTTTTTC
673 TTTCTTTTTTTTGTC
1 TTTCTTTTTTTT-TC
688 TTT-TTTT
1 TTTCTTTT
695 AGAGGAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 23 0.70
15 10 0.30
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTTTTTC
Found at i:10739 original size:20 final size:22
Alignment explanation
Indices: 10703--10744 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
10693 TTTTAGATGA
10703 AAGAATCTTACAAACAA-ATAC
1 AAGAATCTTACAAACAATATAC
*
10724 AAGAATCTT-GAAACAATATAC
1 AAGAATCTTACAAACAATATAC
10745 TCTAATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (22 bp):
AAGAATCTTACAAACAATATAC
Found at i:11682 original size:31 final size:30
Alignment explanation
Indices: 11623--11696 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
11613 AAAAAAAAAT
**
11623 TCAACTTTTAAGGGGCCCAAAATTTTTTTA
1 TCAACTTTTAAGGGGCCCAAAAAGTTTTTA
* * *
11653 TCAATTTTTAAGGGGGCCTAAAAAGTTTTTTC
1 TCAACTTTTAA-GGGGCCCAAAAAG-TTTTTA
11685 TCCAACTTTTAA
1 T-CAACTTTTAA
11697 TGGATAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
30 10 0.29
31 10 0.29
32 6 0.17
33 9 0.26
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (30 bp):
TCAACTTTTAAGGGGCCCAAAAAGTTTTTA
Found at i:11695 original size:33 final size:30
Alignment explanation
Indices: 11623--11696 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 30
11613 AAAAAAAAAT
* *
11623 TCAACTTTTAAGGGGCCCAAAATTTTTTTA
1 TCAACTTTTAAGGGGCCAAAAAGTTTTTTA
* *
11653 TCAATTTTTAAGGGGGCCTAAAAAGTTTTTTC
1 TCAACTTTTAA-GGGGCC-AAAAAGTTTTTTA
11685 TCCAACTTTTAA
1 T-CAACTTTTAA
11697 TGGATAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 10 0.28
31 6 0.17
32 11 0.31
33 9 0.25
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (30 bp):
TCAACTTTTAAGGGGCCAAAAAGTTTTTTA
Found at i:15027 original size:45 final size:45
Alignment explanation
Indices: 14963--15052 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
14953 CTATGGTTGC
14963 TCCTTTATACCAACATTTCTTCATTCTGTGTCCCAATCCCAATCT
1 TCCTTTATACCAACATTTCTTCATTCTGTGTCCCAATCCCAATCT
15008 TCCTTTATACCAACATTTCTTCATTCTGTGTCCCAATCCCAATCT
1 TCCTTTATACCAACATTTCTTCATTCTGTGTCCCAATCCCAATCT
15053 GCTGTATAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.33, G:0.04, T:0.40
Consensus pattern (45 bp):
TCCTTTATACCAACATTTCTTCATTCTGTGTCCCAATCCCAATCT
Found at i:16047 original size:14 final size:16
Alignment explanation
Indices: 16012--16048 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16002 AAACTAAGAA
*
16012 GAGGTGAATTCTGTTT
1 GAGGTGAATTCTGTTG
16028 GAGGTGAATT-T-TTG
1 GAGGTGAATTCTGTTG
16042 GAGGTGA
1 GAGGTGA
16049 TGCACGACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 10 0.50
ACGTcount: A:0.22, C:0.03, G:0.38, T:0.38
Consensus pattern (16 bp):
GAGGTGAATTCTGTTG
Found at i:27632 original size:17 final size:17
Alignment explanation
Indices: 27606--27640 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
27596 TTATCTAAGA
27606 AAGTAGTCAATAATAGG
1 AAGTAGTCAATAATAGG
*
27623 AAGTATTCAATAATAGG
1 AAGTAGTCAATAATAGG
27640 A
1 A
27641 TTATTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (17 bp):
AAGTAGTCAATAATAGG
Found at i:31018 original size:22 final size:23
Alignment explanation
Indices: 30993--31040 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
30983 AATATGTAGA
**
30993 TATTTCATAAT-ATTTTATTATT
1 TATTTCATAATAAAATTATTATT
*
31015 TA-TTCATATTAAAATTATTATT
1 TATTTCATAATAAAATTATTATT
31037 TATT
1 TATT
31041 AGTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.33
22 13 0.62
23 1 0.05
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTCATAATAAAATTATTATT
Found at i:31387 original size:52 final size:52
Alignment explanation
Indices: 31327--31446 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
31317 TCCAAAAAAA
*
31327 TTACTTCTCCCTAAACCCCCA-ATTTTTTTCCTTTTACTTTATCTCAAAACTT
1 TTACTTCTCCC-AAACCCCCATATTTTTTTCCTTTTACTTTATCTAAAAACTT
* * * * ** *
31379 TTATTTCTCTCAAACCTCCATTTTTTTTTCCTTTTGGTTTCTCTAAAAACTT
1 TTACTTCTCCCAAACCCCCATATTTTTTTCCTTTTACTTTATCTAAAAACTT
*
31431 TTACTTCTTCCAAACC
1 TTACTTCTCCCAAACC
31447 TCAATCTTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 8 0.14
52 48 0.86
ACGTcount: A:0.22, C:0.28, G:0.02, T:0.48
Consensus pattern (52 bp):
TTACTTCTCCCAAACCCCCATATTTTTTTCCTTTTACTTTATCTAAAAACTT
Found at i:31391 original size:18 final size:19
Alignment explanation
Indices: 31357--31392 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31347 AATTTTTTTC
31357 CTTTTACTTTATCTCAAAA
1 CTTTTACTTTATCTCAAAA
*
31376 CTTTTA-TTTCTCTCAAA
1 CTTTTACTTTATCTCAAA
31393 CCTCCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (19 bp):
CTTTTACTTTATCTCAAAA
Found at i:32426 original size:39 final size:40
Alignment explanation
Indices: 32373--32452 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
32363 AAGAGGTATG
*
32373 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTCTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTCTCCA
* * *
32413 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTCTCCA
32452 T
1 T
32453 TGAGTGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTCTCCA
Found at i:58320 original size:18 final size:18
Alignment explanation
Indices: 58299--58345 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
58289 GATATTCAAT
*
58299 TTATTTGAATTATTCGTG
1 TTATTTGAATTATTCGAG
*
58317 TTATTCGAATTATTCGAG
1 TTATTTGAATTATTCGAG
58335 TTATTTGAATT
1 TTATTTGAATT
58346 CGAAAATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (18 bp):
TTATTTGAATTATTCGAG
Found at i:59403 original size:2 final size:2
Alignment explanation
Indices: 59396--59423 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59386 AATTGTATCG
59396 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
59424 AAAACTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:63580 original size:15 final size:15
Alignment explanation
Indices: 63541--63581 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
63531 TAACTACCTT
63541 TTTATAG-TTTTAGA
1 TTTATAGATTTTAGA
*
63555 TTTATATATTTTAGAA
1 TTTATAGATTTTAG-A
63571 TTT-TAGATTTT
1 TTTATAGATTTT
63582 TTTTTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 6 0.26
15 13 0.57
16 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (15 bp):
TTTATAGATTTTAGA
Found at i:64300 original size:18 final size:19
Alignment explanation
Indices: 64279--64314 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
64269 TGTTTGGATT
64279 TGTTTTT-AATTTTGTTTG
1 TGTTTTTCAATTTTGTTTG
*
64297 TGTTTTTCTATTTTGTTT
1 TGTTTTTCAATTTTGTTT
64315 TTGGTGTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.08, C:0.03, G:0.14, T:0.75
Consensus pattern (19 bp):
TGTTTTTCAATTTTGTTTG
Found at i:67098 original size:28 final size:28
Alignment explanation
Indices: 67067--67126 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
67057 CCATATAATT
*
67067 AAACAAAACCCAATAATCTTAAAGTAAG
1 AAACAAAACCCAATAATCTTAAAGCAAG
67095 AAACAAAACCCAATAATCTTAAAGCAAG
1 AAACAAAACCCAATAATCTTAAAGCAAG
67123 AAAC
1 AAAC
67127 TATCTTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.58, C:0.20, G:0.07, T:0.15
Consensus pattern (28 bp):
AAACAAAACCCAATAATCTTAAAGCAAG
Found at i:68139 original size:20 final size:21
Alignment explanation
Indices: 68091--68141 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
68081 CCAAAATTTT
*
68091 GGTATCGATATTTTTAAGGAA
1 GGTATCGATACTTTTAAGGAA
** *
68112 ATTATCGATACTTTTAA-GAG
1 GGTATCGATACTTTTAAGGAA
68132 GGTATCGATA
1 GGTATCGATA
68142 ATCCTTCAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (21 bp):
GGTATCGATACTTTTAAGGAA
Found at i:68721 original size:27 final size:26
Alignment explanation
Indices: 68691--68742 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
68681 AAACTTTGCA
* *
68691 ATAAATATCAAAACATTTTATACCTTC
1 ATAAAGATC-AAACACTTTATACCTTC
*
68718 ATAAAGATCAATCACTTTATACCTT
1 ATAAAGATCAAACACTTTATACCTT
68743 TTTATACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (26 bp):
ATAAAGATCAAACACTTTATACCTTC
Found at i:70641 original size:20 final size:20
Alignment explanation
Indices: 70617--70689 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
70607 TTTTCCCAAG
70617 TATCGATAATTTTTGAAAAA
1 TATCGATAATTTTTGAAAAA
* * *
70637 AATCGAT-ACTTTT-AAACAGG
1 TATCGATAATTTTTGAAA-A-A
* *
70657 TATCAATAATTTTTGAAAAT
1 TATCGATAATTTTTGAAAAA
70677 TATCGATAATTTT
1 TATCGATAATTTT
70690 AAAACGGTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
18 3 0.07
19 6 0.15
20 23 0.56
21 6 0.15
22 3 0.07
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATAATTTTTGAAAAA
Found at i:70699 original size:40 final size:40
Alignment explanation
Indices: 70616--70692 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
70606 TTTTTCCCAA
* *
70616 GTATCGATAATTTTTGAAAAAAATCGATACTTTTAAACAG
1 GTATCAATAATTTTTGAAAAAAATCGATAATTTTAAACAG
**
70656 GTATCAATAATTTTTGAAAATTATCGATAATTTTAAA
1 GTATCAATAATTTTTGAAAAAAATCGATAATTTTAAA
70693 ACGGTATTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (40 bp):
GTATCAATAATTTTTGAAAAAAATCGATAATTTTAAACAG
Found at i:72979 original size:23 final size:22
Alignment explanation
Indices: 72933--72976 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
72923 GGAATATCCA
72933 AGAAAAATATCTTCATCACTTT
1 AGAAAAATATCTTCATCACTTT
72955 AGAAAAATATCTTCATCACTTT
1 AGAAAAATATCTTCATCACTTT
72977 TAGCATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (22 bp):
AGAAAAATATCTTCATCACTTT
Found at i:80597 original size:41 final size:42
Alignment explanation
Indices: 80552--80650 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 42
80542 AAAAAACACT
* * *
80552 GCTAAAGGTCAGAGCATTATCGGCGCTTGAGGG-AAAGTGCA
1 GCTAAAGGTCAGAGCATTAGCGACGCTTGAGGGAAAAGCGCA
* *
80593 GCTAAAGGTCAAAGCATTAGCGACGCTTGAGGGAAAAGCGCC
1 GCTAAAGGTCAGAGCATTAGCGACGCTTGAGGGAAAAGCGCA
80635 GCTAAAGGTCAGAGCA
1 GCTAAAGGTCAGAGCA
80651 CAAGCGCCGC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 30 0.59
42 21 0.41
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16
Consensus pattern (42 bp):
GCTAAAGGTCAGAGCATTAGCGACGCTTGAGGGAAAAGCGCA
Found at i:80685 original size:24 final size:24
Alignment explanation
Indices: 80628--80674 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
80618 CTTGAGGGAA
80628 AAGCGCCGCTAAAGGTCAGAGCAC
1 AAGCGCCGCTAAAGGTCAGAGCAC
80652 AAGCGCCGCTAAAGGTCAGAGCA
1 AAGCGCCGCTAAAGGTCAGAGCA
80675 TTAGCGGCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.28, G:0.30, T:0.09
Consensus pattern (24 bp):
AAGCGCCGCTAAAGGTCAGAGCAC
Done.