Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010565.1 Kokia drynarioides strain JFW-HI SEQ_125487, 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: 48847
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:1139 original size:20 final size:20
Alignment explanation
Indices: 1090--1162 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
1080 TGTTTTAGTA
*
1090 AATAATTAATAAATAATAAA-
1 AATAA-TAATAAATACTAAAT
*
1110 ATATAGTAATAAATACCT-AAT
1 A-ATAATAATAAATA-CTAAAT
* * *
1131 AATACTAATTAATATTAAAT
1 AATAATAATAAATACTAAAT
1151 AATAATAATAAA
1 AATAATAATAAA
1163 GAAGTTTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.02
20 36 0.86
21 5 0.12
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (20 bp):
AATAATAATAAATACTAAAT
Found at i:1540 original size:14 final size:15
Alignment explanation
Indices: 1508--1550 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
1498 TTCTTTCTTC
1508 ATTTTT-GTAT-TTT
1 ATTTTTCGTATATTT
*
1521 ATTTTTCTTATATTT
1 ATTTTTCGTATATTT
1536 A-TTTTCGTATATTT
1 ATTTTTCGTATATTT
1550 A
1 A
1551 CTCATTCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 6 0.23
14 16 0.62
15 4 0.15
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (15 bp):
ATTTTTCGTATATTT
Found at i:2568 original size:19 final size:19
Alignment explanation
Indices: 2544--2581 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2534 TGAGATGATT
2544 GTGCTCACAAAAGGGTGTA
1 GTGCTCACAAAAGGGTGTA
*
2563 GTGCTCACAGAAGGGTGTA
1 GTGCTCACAAAAGGGTGTA
2582 ACGCTGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.34, T:0.21
Consensus pattern (19 bp):
GTGCTCACAAAAGGGTGTA
Found at i:14440 original size:17 final size:17
Alignment explanation
Indices: 14415--14458 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
14405 CATGCATTTC
14415 TTTTAATTGTCATTGCA
1 TTTTAATTGTCATTGCA
* *
14432 TTTTTATTGTCTTTGCA
1 TTTTAATTGTCATTGCA
*
14449 TTTTATTTGT
1 TTTTAATTGT
14459 TTTAGCATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (17 bp):
TTTTAATTGTCATTGCA
Found at i:14466 original size:17 final size:16
Alignment explanation
Indices: 14415--14468 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
14405 CATGCATTTC
*
14415 TTTTAATTGTCATTGCA
1 TTTT-ATTGTCTTTGCA
14432 TTTTTATTGTCTTTGCA
1 -TTTTATTGTCTTTGCA
14449 TTTTATTTGT-TTTAGCA
1 TTTTA-TTGTCTTT-GCA
14466 TTT
1 TTT
14469 GCATTGTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 8 0.24
17 21 0.64
18 4 0.12
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (16 bp):
TTTTATTGTCTTTGCA
Found at i:18335 original size:20 final size:19
Alignment explanation
Indices: 18310--18349 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
18300 TTAAATTTAT
* *
18310 ATATATATAAATTCTAAAAA
1 ATATATAAAAAAT-TAAAAA
18330 ATATATAAAAAATTAAAAA
1 ATATATAAAAAATTAAAAA
18349 A
1 A
18350 ATTTCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
ATATATAAAAAATTAAAAA
Found at i:21594 original size:17 final size:16
Alignment explanation
Indices: 21572--21605 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
21562 TTTGTATGGA
21572 AATTAAAATTAAAGTCT
1 AATTAAAATTAAA-TCT
21589 AATTAAAATTAAATCT
1 AATTAAAATTAAATCT
21605 A
1 A
21606 CTAACTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (16 bp):
AATTAAAATTAAATCT
Found at i:22181 original size:57 final size:59
Alignment explanation
Indices: 22108--22219 Score: 147
Period size: 57 Copynumber: 1.9 Consensus size: 59
22098 TTTTGAGTGA
*
22108 AATATAGGATTCAAAATTAAAATTTAACCATTCTTATATAATCTAAAAAAAAAAAAAAG
1 AATATAGGATTCAAAATTAAAATTTAACCATTATTATATAATCTAAAAAAAAAAAAAAG
* * * * * *
22167 AATAT-GGATT-AAAATTGAAATTTAATCATTATTTTCTCATGTAAAAAAAAAAA
1 AATATAGGATTCAAAATTAAAATTTAACCATTATTATATAATCTAAAAAAAAAAA
22220 GAAAAAAGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
57 36 0.78
58 5 0.11
59 5 0.11
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.32
Consensus pattern (59 bp):
AATATAGGATTCAAAATTAAAATTTAACCATTATTATATAATCTAAAAAAAAAAAAAAG
Found at i:22706 original size:72 final size:70
Alignment explanation
Indices: 22578--22732 Score: 197
Period size: 72 Copynumber: 2.2 Consensus size: 70
22568 TGAGGTTTGA
* * * * *
22578 TGGAAGTAAAAGTTTTGAGGGAAAGTAAAAGGAAAAAATTTTGGGGGTTTGGGGGAAGTATACTT
1 TGGAAGTAAAAGTTTTAAGGGAAAGTAAAAGAAAAAAATTTTGGAGGTTT-GGGGAAGTAAAATT
22643 TTTGAGG
65 TTTG-GG
*
22650 -GTGAAGTAAAAGTTTTAAAGGGAAAGTAGAAGAAAAAAAGTTTTGGAGGTTT-GGGAAGTAAAA
1 TG-GAAGTAAAAGTTTT-AAGGGAAAGTAAAAGAAAAAAA-TTTTGGAGGTTTGGGGAAGTAAAA
22713 TTTTTGGG
63 TTTTTGGG
22721 TGGAAGTAAAAG
1 TGGAAGTAAAAG
22733 GGTCAGGAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
71 13 0.18
72 30 0.41
73 19 0.26
74 11 0.15
ACGTcount: A:0.39, C:0.01, G:0.33, T:0.28
Consensus pattern (70 bp):
TGGAAGTAAAAGTTTTAAGGGAAAGTAAAAGAAAAAAATTTTGGAGGTTTGGGGAAGTAAAATTT
TTGGG
Found at i:36931 original size:26 final size:26
Alignment explanation
Indices: 36902--36955 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
36892 TTTAGAGATG
*
36902 CATTAGATGTGGTGTCTTTAAACAAT
1 CATTACATGTGGTGTCTTTAAACAAT
36928 CATTACATGTGGTGTCTTTAAACAAT
1 CATTACATGTGGTGTCTTTAAACAAT
36954 CA
1 CA
36956 CAAATAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (26 bp):
CATTACATGTGGTGTCTTTAAACAAT
Found at i:37035 original size:18 final size:19
Alignment explanation
Indices: 37014--37054 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
37004 TGTTAATATG
37014 GTTAAAAG-AGTTAGTGTT-
1 GTTAAAAGCAGTTA-TGTTA
37032 GTT-AAAGCAGTTATGTTA
1 GTTAAAAGCAGTTATGTTA
37050 GTTAA
1 GTTAA
37055 CAGTCTACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 8 0.40
18 11 0.55
19 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.39
Consensus pattern (19 bp):
GTTAAAAGCAGTTATGTTA
Found at i:39560 original size:30 final size:30
Alignment explanation
Indices: 39516--39583 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
39506 AAAATTTAAA
* *
39516 TTAATAAA-AATAAAATTATATTTTAATTTT
1 TTAA-AAATAATAAAATTATAATTTAATTAT
* *
39546 TTTAAAATAATAAAATTTTAATTTAATTAT
1 TTAAAAATAATAAAATTATAATTTAATTAT
39576 TTAAAAAT
1 TTAAAAAT
39584 TACATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAATTAT
Found at i:39623 original size:23 final size:24
Alignment explanation
Indices: 39557--39623 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
39547 TTAAAATAAT
* *
39557 AAAATTTTAATTTAATTAT--TTA
1 AAAATTATAATTTAATTATCGTAA
* * *
39579 AAAATTACATTTTTATTATCGTAA
1 AAAATTATAATTTAATTATCGTAA
39603 AAAATTATAATTTAATT-TCGT
1 AAAATTATAATTTAATTATCGT
39624 TTCTTAAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 15 0.43
23 4 0.11
24 16 0.46
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (24 bp):
AAAATTATAATTTAATTATCGTAA
Found at i:42040 original size:18 final size:19
Alignment explanation
Indices: 42004--42041 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
41994 TATTTTTTAC
*
42004 AAAATAAATCAACTTAAAT
1 AAAATAAATCAACTCAAAT
*
42023 AAAAT-AATGAACTCAAAT
1 AAAATAAATCAACTCAAAT
42041 A
1 A
42042 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAATAAATCAACTCAAAT
Found at i:48135 original size:30 final size:30
Alignment explanation
Indices: 48090--48300 Score: 159
Period size: 30 Copynumber: 7.2 Consensus size: 30
48080 AGTTTAGGAG
*
48090 AATTT-AGGGTCAAAATGTAATTTTGGAAA
1 AATTTAAGGGTTAAAATGTAATTTTGGAAA
48119 AATTTAAGGGTTAAAATGTAATTTT--AAGA
1 AATTTAAGGGTTAAAATGTAATTTTGGAA-A
*
48148 AGTTTAA-GGTTAAAATGTAATTTTGGAAA
1 AATTTAAGGGTTAAAATGTAATTTTGGAAA
* ** * *
48177 TATTTGGGGGGTTAAAATGTGATTTTGGGAA
1 AATTT-AAGGGTTAAAATGTAATTTTGGAAA
* ** * * * * *
48208 AGTTCGAGGATCAAAAAGTGATTTTGG-GA
1 AATTTAAGGGTTAAAATGTAATTTTGGAAA
* *
48237 AATTTAGGGGTTAAAATGCAATTTT-GAAA
1 AATTTAAGGGTTAAAATGTAATTTTGGAAA
* *
48266 AAGTTTAA-GGTTCAAAAAGTAATTTT-TAAA
1 AA-TTTAAGGGTT-AAAATGTAATTTTGGAAA
48296 AATTT
1 AATTT
48301 TGGGTGTCAA
Statistics
Matches: 143, Mismatches: 30, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
28 20 0.14
29 43 0.30
30 58 0.41
31 22 0.15
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (30 bp):
AATTTAAGGGTTAAAATGTAATTTTGGAAA
Found at i:48167 original size:28 final size:28
Alignment explanation
Indices: 48088--48172 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
48078 GAAGTTTAGG
* *
48088 AGAATTTAGGGTCAAAATGTAATTTTGGA
1 AGAATTTAAGGTTAAAATGTAATTTT-GA
*
48117 AAAATTTAAGGGTTAAAATGTAATTTT-A
1 AGAATTTAA-GGTTAAAATGTAATTTTGA
48145 AGAAGTTTAAGGTTAAAATGTAATTTTG
1 AGAA-TTTAAGGTTAAAATGTAATTTTG
48173 GAAATATTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 21 0.43
29 12 0.24
30 16 0.33
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.38
Consensus pattern (28 bp):
AGAATTTAAGGTTAAAATGTAATTTTGA
Found at i:48247 original size:59 final size:58
Alignment explanation
Indices: 48092--48300 Score: 213
Period size: 59 Copynumber: 3.5 Consensus size: 58
48082 TTTAGGAGAA
* * * *
48092 TTTAGGGTCAAAATGTAATTTTGGAAAAATTTAAGGGTTAAAATGTAATTTTAAG-AAG
1 TTTAAGGTCAAAAAGTAATTTTGG-AAAATTTAGGGGTTAAAATGTAATTTTGAGAAAG
* * * * *
48150 TTTAAGGTTAAAATGTAATTTTGGAAATATTTGGGGGGTTAAAATGTGATTTTGGGAAAG
1 TTTAAGGTCAAAAAGTAATTTTGGAAA-ATTT-AGGGGTTAAAATGTAATTTTGAGAAAG
** * * * *
48210 TTCGAGGATCAAAAAGTGATTTTGGGAAATTTAGGGGTTAAAATGCAATTTTGAAAAAG
1 TTTAAGG-TCAAAAAGTAATTTTGGAAAATTTAGGGGTTAAAATGTAATTTTGAGAAAG
**
48269 TTTAAGGTTCAAAAAGTAATTTTTAAAAATTT
1 TTTAAGG-TCAAAAAGTAATTTTGGAAAATTT
48301 TGGGTGTCAA
Statistics
Matches: 122, Mismatches: 25, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
57 3 0.02
58 26 0.21
59 65 0.53
60 12 0.10
61 16 0.13
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (58 bp):
TTTAAGGTCAAAAAGTAATTTTGGAAAATTTAGGGGTTAAAATGTAATTTTGAGAAAG
Done.