Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005098.1 Kokia drynarioides strain JFW-HI SEQ_118919, 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: 92394
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 122 characters in sequence are not A, C, G, or T
Found at i:4245 original size:16 final size:17
Alignment explanation
Indices: 4222--4263 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
4212 CGCCAGCAAA
4222 AAAAATATTTATTTTTT
1 AAAAATATTTATTTTTT
* *
4239 -TAAATA-TAATTTTTT
1 AAAAATATTTATTTTTT
4254 AAAAATATTT
1 AAAAATATTT
4264 TAAAATTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 4
0.70 0.15 0.15
Matches are distributed among these distances:
15 8 0.42
16 10 0.53
17 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAAAATATTTATTTTTT
Found at i:4266 original size:11 final size:11
Alignment explanation
Indices: 4246--4286 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
4236 TTTTAAATAT
4246 AATT-TTTTAA
1 AATTATTTTAA
*
4256 AAATATTTTAA
1 AATTATTTTAA
*
4267 AATTAATTTAA
1 AATTATTTTAA
4278 AATTATTTT
1 AATTATTTT
4287 TTAAATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 3 0.12
11 23 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:5312 original size:18 final size:17
Alignment explanation
Indices: 5275--5311 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5265 TTTTAAAATA
5275 TTTAAAAAAAATTATAT
1 TTTAAAAAAAATTATAT
5292 TTTAAAAAATAATTA-AT
1 TTTAAAAAA-AATTATAT
5309 TTT
1 TTT
5312 TTTGCTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAAAAAATTATAT
Found at i:7453 original size:30 final size:29
Alignment explanation
Indices: 7419--7475 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
7409 AATTTACAAG
*
7419 AATTGAATC-AAATCAAAATTTTATATATAT
1 AATTGAA-CAAAATC-AAAGTTTATATATAT
*
7449 AATTGCACAAAATCAAAGTTTATATAT
1 AATTGAACAAAATCAAAGTTTATATAT
7476 GCAATTACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (29 bp):
AATTGAACAAAATCAAAGTTTATATATAT
Found at i:7481 original size:29 final size:30
Alignment explanation
Indices: 7428--7486 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
7418 GAATTGAATC
* * *
7428 AAATCAAAATTTTATATATATAATTGCACA
1 AAATCAAAAGTTTATATATACAATTACACA
*
7458 AAATC-AAAGTTTATATATGCAATTACACA
1 AAATCAAAAGTTTATATATACAATTACACA
7487 TTAAATCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (30 bp):
AAATCAAAAGTTTATATATACAATTACACA
Found at i:8421 original size:18 final size:19
Alignment explanation
Indices: 8387--8422 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8377 GTGTGGACAT
*
8387 TATGTGTTTAGAATACAAA
1 TATGCGTTTAGAATACAAA
8406 TATGCGTTTA-AATACAA
1 TATGCGTTTAGAATACAA
8423 CATACAAGAG
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:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (19 bp):
TATGCGTTTAGAATACAAA
Found at i:10848 original size:3 final size:3
Alignment explanation
Indices: 10833--10863 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
10823 AGACAACGCC
*
10833 CAG CAG CAA CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
10864 CACAAGAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.35, G:0.29, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:10850 original size:12 final size:12
Alignment explanation
Indices: 10833--10899 Score: 75
Period size: 12 Copynumber: 5.6 Consensus size: 12
10823 AGACAACGCC
*
10833 CAGCAGCAACAG
1 CAGCAGCCACAG
10845 CAGCAG-CAGCAG
1 CAGCAGCCA-CAG
10857 CAGCAGCCACAAG
1 CAGCAGCCAC-AG
*
10870 -AGCAGCCACAA
1 CAGCAGCCACAG
*
10881 CAGCAGCCACAA
1 CAGCAGCCACAG
10893 CAGCAGC
1 CAGCAGC
10900 TGCCTCGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
11 2 0.04
12 43 0.88
13 4 0.08
ACGTcount: A:0.39, C:0.37, G:0.24, T:0.00
Consensus pattern (12 bp):
CAGCAGCCACAG
Found at i:20375 original size:28 final size:29
Alignment explanation
Indices: 20344--20400 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
20334 TTCGAAGAAA
* *
20344 AAAAAGAAAAT-ATTTTCGTATTGCCTGT
1 AAAAAGAAAATGATTATCGTATTACCTGT
* *
20372 AAAAATAAAATGATTATGGTATTACCTGT
1 AAAAAGAAAATGATTATCGTATTACCTGT
20401 TGTTGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (29 bp):
AAAAAGAAAATGATTATCGTATTACCTGT
Found at i:26941 original size:19 final size:19
Alignment explanation
Indices: 26919--26988 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
26909 AAAATATAAG
26919 ATTTTGAATTTTTATAAA-T
1 ATTTTGAATTTTTA-AAATT
* *
26938 ATTTTGAAATTTAAAAATT
1 ATTTTGAATTTTTAAAATT
*
26957 ATTTTAAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
26977 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
26989 TTTTTTTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 3 0.07
19 29 0.67
20 11 0.26
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:32272 original size:20 final size:20
Alignment explanation
Indices: 32226--32263 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
32216 ATTGTATAGG
*
32226 TAAAAGTGGAGTTCTACCGA
1 TAAAAGTGGAGTTCTACAGA
32246 TAAAAGTGGAGTTCTACA
1 TAAAAGTGGAGTTCTACA
32264 AGTAGAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (20 bp):
TAAAAGTGGAGTTCTACAGA
Found at i:32682 original size:21 final size:21
Alignment explanation
Indices: 32657--32700 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
32647 TTGATAGATA
* *
32657 ATTTTT-TTAAATAAGCTTTT
1 ATTTTTATGAAATAAGATTTT
*
32677 ATTTTTATGAAATAATATTTT
1 ATTTTTATGAAATAAGATTTT
32698 ATT
1 ATT
32701 ATATTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTTATGAAATAAGATTTT
Found at i:33498 original size:13 final size:12
Alignment explanation
Indices: 33466--33491 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33456 AGTAAAAACG
33466 CATAAAAAATAA
1 CATAAAAAATAA
33478 CATAAAAAATAA
1 CATAAAAAATAA
33490 CA
1 CA
33492 ATCAAAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (12 bp):
CATAAAAAATAA
Found at i:33532 original size:23 final size:23
Alignment explanation
Indices: 33471--33543 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
33461 AAACGCATAA
*
33471 AAAATAACATAAAAAATAACAATC
1 AAAACAACATAAAAAATAACAA-C
**
33495 AAAACAGA-AGCAAAAATAACAAC
1 AAAACA-ACATAAAAAATAACAAC
* *
33518 AAAACAACATTAAAAACAACAA-
1 AAAACAACATAAAAAATAACAAC
33540 AAAA
1 AAAA
33544 TAGCAAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
22 5 0.12
23 18 0.44
24 17 0.41
25 1 0.02
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.10
Consensus pattern (23 bp):
AAAACAACATAAAAAATAACAAC
Found at i:33543 original size:11 final size:11
Alignment explanation
Indices: 33506--33585 Score: 52
Period size: 12 Copynumber: 6.6 Consensus size: 11
33496 AAACAGAAGC
*
33506 AAAAATAACAA
1 AAAAACAACAA
* *
33517 CAAAACAACATT
1 AAAAACAACA-A
33529 AAAAACAACAA
1 AAAAACAACAA
*
33540 AAAATAGCAAAAA
1 AAAA-A-CAACAA
33553 GAAAACAGCAACAA
1 -AAAA-A-CAACAA
*
33567 AAATAACAGCAA
1 AAA-AACAACAA
33579 AAAAACA
1 AAAAACA
33586 CGACAACAGC
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 16 0.29
12 18 0.33
13 9 0.16
14 12 0.22
ACGTcount: A:0.72, C:0.16, G:0.05, T:0.06
Consensus pattern (11 bp):
AAAAACAACAA
Found at i:33562 original size:14 final size:13
Alignment explanation
Indices: 33538--33583 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
33528 TAAAAACAAC
*
33538 AAAAAATAGCAAA
1 AAAAAACAGCAAA
33551 AAGAAAACAGCAACA
1 AA-AAAACAGCAA-A
33566 AAAATAACAGCAAA
1 AAAA-AACAGCAAA
33580 AAAA
1 AAAA
33584 CACGACAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.07
14 16 0.55
15 11 0.38
ACGTcount: A:0.74, C:0.13, G:0.09, T:0.04
Consensus pattern (13 bp):
AAAAAACAGCAAA
Found at i:47500 original size:17 final size:18
Alignment explanation
Indices: 47467--47505 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
47457 AAAACGTCCT
*
47467 ATAA-AATATTATACAAC
1 ATAATAATAATATACAAC
47484 ATAATAATAATAT-CAAC
1 ATAATAATAATATACAAC
47501 ATAAT
1 ATAAT
47506 GAGAAGACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATAATAATATACAAC
Found at i:54772 original size:14 final size:15
Alignment explanation
Indices: 54755--54783 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54745 ATATAATTTT
54755 TAAAAT-TTTAAAAA
1 TAAAATATTTAAAAA
54769 TAAAATATTTAAAAA
1 TAAAATATTTAAAAA
54784 ATGTTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATATTTAAAAA
Found at i:59361 original size:29 final size:30
Alignment explanation
Indices: 59319--59376 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
59309 TTGAATTTAT
*
59319 TTGATTCTTTTTAATAATATAGAGATTAAA
1 TTGATTCTATTTAATAATATAGAGATTAAA
59349 TTGA-TCTATTTAATAATATAGAGATTAA
1 TTGATTCTATTTAATAATATAGAGATTAA
59377 TTTAATCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (30 bp):
TTGATTCTATTTAATAATATAGAGATTAAA
Found at i:60986 original size:120 final size:121
Alignment explanation
Indices: 60761--61104 Score: 453
Period size: 123 Copynumber: 2.9 Consensus size: 121
60751 AGTTTGAGAT
* *
60761 TGAGGATCCGCCGTCGTCATTGGTGGTTTAGGCTCAGTTACAGCC-TT--TGGAGGTGACGGTAC
1 TGAGGAACCGCCGTCGCCATTGGTGGTTTAGGCTCAGTTACAGCCTTTGGTGGAGGTGACGGTAC
* * * *
60823 TTTCTGGTCTCTTTGTTTTTCGATACCGGAGGCTGAAGCTACAGTAATTTGAGCC-
66 TTTCTGGTCTCTTTGTTTTTCAACACCGGAAGCTGAAGCTACAGCAATTTGAGCCG
* *
60878 TGAGGAACTGCCGTCGCCATTTGTGGTTTAGGCTCAGTTACAGCCTTTGGTGGAGGTGACGGTAC
1 TGAGGAACCGCCGTCGCCATTGGTGGTTTAGGCTCAGTTACAGCCTTTGGTGGAGGTGACGGTAC
* * * *
60943 TTTCTGGTCTCTTTGTTTTTCAACGCCGGAAGTTGAAGGTACAGCAGTTTGAGCCTG
66 TTTCTGGTCTCTTTGTTTTTCAACACCGGAAGCTGAAGCTACAGCAATTTGAGCC-G
* * * * *
61000 TGGAGGAGCCGTCGTCGCCATTGGTGGTTTAGGCTCAGATACAGACTTCGGTGGAGGTGACGGTA
1 T-GAGGAACCGCCGTCGCCATTGGTGGTTTAGGCTCAGTTACAGCCTTTGGTGGAGGTGACGGTA
* * * *
61065 CTTTTTGGCCTCTTTGTTTTTCAACAGCGGAGGCTGAAGC
65 CTTTCTGGTCTCTTTGTTTTTCAACACCGGAAGCTGAAGC
61105 AGCAGCAGCA
Statistics
Matches: 195, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
117 41 0.21
118 2 0.01
120 62 0.32
122 1 0.01
123 89 0.46
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.32
Consensus pattern (121 bp):
TGAGGAACCGCCGTCGCCATTGGTGGTTTAGGCTCAGTTACAGCCTTTGGTGGAGGTGACGGTAC
TTTCTGGTCTCTTTGTTTTTCAACACCGGAAGCTGAAGCTACAGCAATTTGAGCCG
Found at i:75667 original size:12 final size:12
Alignment explanation
Indices: 75650--75674 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75640 AGTTATCCAC
75650 TGGCTAAAGTTT
1 TGGCTAAAGTTT
75662 TGGCTAAAGTTT
1 TGGCTAAAGTTT
75674 T
1 T
75675 CGATTCATGT
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:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (12 bp):
TGGCTAAAGTTT
Found at i:78504 original size:22 final size:22
Alignment explanation
Indices: 78479--78521 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
78469 AAATTTATGT
78479 TAAAAATATTTTGATT-TGACTA
1 TAAAAATATTTTG-TTGTGACTA
**
78501 TAAATGTATTTTGTTGTGACT
1 TAAAAATATTTTGTTGTGACT
78522 GGACAGGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (22 bp):
TAAAAATATTTTGTTGTGACTA
Found at i:83247 original size:12 final size:12
Alignment explanation
Indices: 83230--83260 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
83220 TTTTGAACTT
83230 TTTTATTTTATA
1 TTTTATTTTATA
*
83242 TTTTATTTTATT
1 TTTTATTTTATA
83254 TTTTATT
1 TTTTATT
83261 CTAGTCTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:86216 original size:76 final size:76
Alignment explanation
Indices: 86123--86278 Score: 242
Period size: 76 Copynumber: 2.1 Consensus size: 76
86113 AACCACTTAA
* * * *
86123 TTAAGAATTTTCAAGTTAAATCAATTTAAGGAAAAATAAGTTTTT-TTAGTTGCATTTATCTCAC
1 TTAAGAATTCTCAAGTTAAATCAATTTAAGGAAAAATAAGTTTTTGTT-GTTACATTAATCTCAA
86187 ATATTTTCCTTT
65 ATATTTTCCTTT
* *
86199 TTAAGAATTCTCAAGTTAAATCAATTTAAGGAAAGATATGTTTTTGTTGTTACATTAATCTCAAA
1 TTAAGAATTCTCAAGTTAAATCAATTTAAGGAAAAATAAGTTTTTGTTGTTACATTAATCTCAAA
86264 TATTTTCCTTT
66 TATTTTCCTTT
86275 TTAA
1 TTAA
86279 ATTTTACCAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
76 71 0.97
77 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (76 bp):
TTAAGAATTCTCAAGTTAAATCAATTTAAGGAAAAATAAGTTTTTGTTGTTACATTAATCTCAAA
TATTTTCCTTT
Found at i:91632 original size:34 final size:34
Alignment explanation
Indices: 91561--91633 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 34
91551 AAAATTTGAT
91561 TAAAAAATTTCTTGAAAAATTAATTTGGATAATC
1 TAAAAAATTTCTTGAAAAATTAATTTGGATAATC
* *
91595 TAAATAATTT-TTGAAAAAATTAATTTTGATCAA-C
1 TAAAAAATTTCTTG-AAAAATTAATTTGGAT-AATC
91629 TAAAA
1 TAAAA
91634 TTAAATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 3 0.09
34 29 0.85
35 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.38
Consensus pattern (34 bp):
TAAAAAATTTCTTGAAAAATTAATTTGGATAATC
Found at i:91659 original size:18 final size:17
Alignment explanation
Indices: 91632--91670 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
91622 GATCAACTAA
91632 AATTAAATTAATAAAAT
1 AATTAAATTAATAAAAT
*
91649 AATTAAAATTAATATAAT
1 AATT-AAATTAATAAAAT
91667 AATT
1 AATT
91671 TTGAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATTAATAAAAT
Done.