Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014987.1 Kokia drynarioides strain JFW-HI SEQ_130031, 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: 45883
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:20747 original size:36 final size:37
Alignment explanation
Indices: 20701--20774 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
20691 ATCAAATAAA
*
20701 AATTTTATATTTCAAAAAAATAA-TAATAATTTTAAT
1 AATTTAATATTTCAAAAAAATAATTAATAATTTTAAT
20737 AATTTAATATTTCAAAAAAATAATTTTAATAATTTTAA
1 AATTTAATATTTCAAAAAAATAA--TTAATAATTTTAA
20775 AATCATTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 22 0.65
39 12 0.35
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (37 bp):
AATTTAATATTTCAAAAAAATAATTAATAATTTTAAT
Found at i:20759 original size:21 final size:23
Alignment explanation
Indices: 20734--20776 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20724 TAATAATTTT
20734 AATAA-TTTAAT-ATTTCAAAAA
1 AATAATTTTAATAATTTCAAAAA
*
20755 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTCAAAA
20777 TCATTTACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAATTTTAATAATTTCAAAAA
Found at i:21462 original size:21 final size:21
Alignment explanation
Indices: 21438--21477 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21428 TACCCTGTAC
* * *
21438 TTCTATCGATACATGTAAGAA
1 TTCTACCGAAACAAGTAAGAA
21459 TTCTACCGAAACAAGTAAG
1 TTCTACCGAAACAAGTAAG
21478 CAGAATTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCTACCGAAACAAGTAAGAA
Found at i:23565 original size:2 final size:2
Alignment explanation
Indices: 23560--23623 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
23550 TCAATATACA
*
23560 AT AT AT AT AT AT AT AT AT AT AT TT 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 AT AT AT AT
23602 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
23624 CTTGATAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:25750 original size:39 final size:39
Alignment explanation
Indices: 25696--25775 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
25686 TTGAATAGTT
25696 CAATTTCGAATCATTACCCTTTGCTCTTAGATACTTTAG
1 CAATTTCGAATCATTACCCTTTGCTCTTAGATACTTTAG
*
25735 CAATTTCGGATCATTACCCTTTGCTCTTAGATACTTTAG
1 CAATTTCGAATCATTACCCTTTGCTCTTAGATACTTTAG
25774 CA
1 CA
25776 CTAGAACGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.40
Consensus pattern (39 bp):
CAATTTCGAATCATTACCCTTTGCTCTTAGATACTTTAG
Found at i:26118 original size:13 final size:13
Alignment explanation
Indices: 26100--26134 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
26090 GAGCTTCGAT
26100 GAGAGCAACGGTC
1 GAGAGCAACGGTC
26113 GAGAGCAACGGTC
1 GAGAGCAACGGTC
26126 GAGAGCAAC
1 GAGAGCAAC
26135 ATGGCTAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.23, G:0.37, T:0.06
Consensus pattern (13 bp):
GAGAGCAACGGTC
Found at i:35902 original size:90 final size:88
Alignment explanation
Indices: 35807--35978 Score: 231
Period size: 92 Copynumber: 1.9 Consensus size: 88
35797 TTTTTTTCTT
* * *
35807 TTTTTTTG-CACTCAATT-AGATACTTGAATTTTTAAAATGCATTAAAAAAAACCCCTCAAACTT
1 TTTTTTTGCCACTCAATTGAG-TACTTGAACTTTCAAAATGCA-TAAAAAAAA-CCCTCAAAATT
35870 CTTCAAAAAAAGCAATTAAGCCCATTC
63 -TTCAAAAAAAGCAATTAAGCCCATTC
35897 TTTTTTTGCCCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAAACCCTCAAAATTTT
1 TTTTTTTG-CCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAAACCCTCAAAATTTT
** *
35962 TGAATAAAGCAATTAAG
65 CAAAAAAAGCAATTAAG
35979 TCCTTGCTCT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
89 16 0.22
90 18 0.25
91 9 0.12
92 28 0.38
93 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (88 bp):
TTTTTTTGCCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAAACCCTCAAAATTTTC
AAAAAAAGCAATTAAGCCCATTC
Found at i:36427 original size:29 final size:27
Alignment explanation
Indices: 36391--36493 Score: 102
Period size: 29 Copynumber: 3.7 Consensus size: 27
36381 TTATATTTTA
*
36391 TATAATTTTCTTACGACTTTATAAAATTT
1 TATAATTTT-TTACTA-TTTATAAAATTT
* *
36420 TATAATTTTTTTA-TATTTTTATATATTT
1 TATAA-TTTTTTACTATTTATA-AAATTT
36448 TATAATTTTTTACTATTTTTATAAAATTT
1 TATAATTTTTTACTA--TTTATAAAATTT
*
36477 TACAATTTTTTA-TATTT
1 TATAATTTTTTACTATTT
36494 TTTACTATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
26 3 0.05
27 12 0.19
28 15 0.24
29 24 0.38
30 9 0.14
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (27 bp):
TATAATTTTTTACTATTTATAAAATTT
Found at i:36456 original size:28 final size:27
Alignment explanation
Indices: 36416--36533 Score: 123
Period size: 28 Copynumber: 4.2 Consensus size: 27
36406 ACTTTATAAA
36416 ATTTTATAATTTTTTTATATTTTTATAT
1 ATTTTATAA-TTTTTTATATTTTTATAT
*
36444 ATTTTATAATTTTTTACTATTTTTATAAA
1 ATTTTATAATTTTTTA-TATTTTTAT-AT
*
36473 ATTTTACAATTTTTTATATTTTT-TACT
1 ATTTTATAATTTTTTATATTTTTATA-T
* *
36500 ATTTTTATATTTTTTTCTAATTTTTA-AT
1 A-TTTTATAATTTTTTAT-ATTTTTATAT
36528 AATTTT
1 -ATTTT
36534 TATTAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
26 1 0.01
27 9 0.12
28 43 0.56
29 24 0.31
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (27 bp):
ATTTTATAATTTTTTATATTTTTATAT
Found at i:36459 original size:38 final size:37
Alignment explanation
Indices: 36424--36534 Score: 123
Period size: 38 Copynumber: 2.9 Consensus size: 37
36414 AAATTTTATA
*
36424 ATTTTTTTATATTTTTATATATTTTATAATTTTTTACT
1 ATTTTTATATATTTTTATA-ATTTTATAATTTTTTACT
* * * *
36462 ATTTTTATAAAATTTTACAATTTTTTATATTTTTTACT
1 ATTTTTATATATTTTTATAATTTTATA-ATTTTTTACT
* *
36500 ATTTTTATATTTTTTTCTAATTTTTAATAATTTTT
1 ATTTTTATATATTTTTATAA-TTTT-ATAATTTTT
36535 ATTAAAATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
37 7 0.12
38 40 0.68
39 10 0.17
40 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (37 bp):
ATTTTTATATATTTTTATAATTTTATAATTTTTTACT
Found at i:36469 original size:57 final size:55
Alignment explanation
Indices: 36369--36533 Score: 183
Period size: 56 Copynumber: 2.9 Consensus size: 55
36359 TTGTTACGAA
* * *
36369 TTTTATATTTCTTTATATTTTATATAATTTTCTTACGA-CTTTATAAAATTTTATAATTT
1 TTTTATATTT-TTTATA-TTT-TATAATTTT-TTACTATTTTTATAAAATTTTACAA-TT
36428 TTTTATATTTTTATATATTTTATAATTTTTTACTATTTTTATAAAATTTTACAATT
1 TTTTATATTTTT-TATATTTTATAATTTTTTACTATTTTTATAAAATTTTACAATT
* *
36484 TTTTATATTTTTTACTATTTT-TATATTTTTTTCTAATTTTTA-ATAATTTT
1 TTTTATATTTTTTA-TATTTTATA-ATTTTTTACT-ATTTTTATAAAATTTT
36534 TATTAAAATT
Statistics
Matches: 96, Mismatches: 5, Indels: 13
0.84 0.04 0.11
Matches are distributed among these distances:
55 4 0.04
56 41 0.43
57 32 0.33
58 5 0.05
59 14 0.15
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (55 bp):
TTTTATATTTTTTATATTTTATAATTTTTTACTATTTTTATAAAATTTTACAATT
Found at i:36515 original size:10 final size:9
Alignment explanation
Indices: 36417--36514 Score: 76
Period size: 9 Copynumber: 10.4 Consensus size: 9
36407 CTTTATAAAA
36417 TTTTATAATT
1 TTTTAT-ATT
36427 TTTT-TATAT
1 TTTTATAT-T
*
36436 TTTTATATA
1 TTTTATATT
36445 TTTTATAATT
1 TTTTAT-ATT
36455 TTTTACTA-T
1 TTTTA-TATT
**
36464 TTTTATAAAA
1 TTTTAT-ATT
*
36474 TTTTACAATT
1 TTTTA-TATT
36484 TTTTATATT
1 TTTTATATT
36493 TTTTACTA-T
1 TTTTA-TATT
36502 TTTTATATT
1 TTTTATATT
36511 TTTT
1 TTTT
36515 TCTAATTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 19
0.73 0.07 0.19
Matches are distributed among these distances:
8 5 0.07
9 38 0.53
10 28 0.39
11 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTATATT
Found at i:36523 original size:10 final size:10
Alignment explanation
Indices: 36417--36534 Score: 90
Period size: 10 Copynumber: 12.3 Consensus size: 10
36407 CTTTATAAAA
36417 TTTTATAATT
1 TTTTATAATT
36427 TTTT-T-ATAT
1 TTTTATAAT-T
*
36436 TTTTAT-ATA
1 TTTTATAATT
36445 TTTTATAATT
1 TTTTATAATT
36455 TTTTACT-A-T
1 TTTTA-TAATT
**
36464 TTTTATAAAA
1 TTTTATAATT
*
36474 TTTTACAATT
1 TTTTATAATT
36484 TTTTAT-ATT
1 TTTTATAATT
36493 TTTTACT-A-T
1 TTTTA-TAATT
*
36502 TTTTATATTT
1 TTTTATAATT
*
36512 TTTTCTAATT
1 TTTTATAATT
*
36522 TTTAATAATT
1 TTTTATAATT
36532 TTT
1 TTT
36535 ATTAAAATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 18
0.74 0.10 0.15
Matches are distributed among these distances:
8 4 0.05
9 33 0.38
10 49 0.56
11 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:36533 original size:19 final size:18
Alignment explanation
Indices: 36417--36534 Score: 64
Period size: 19 Copynumber: 6.2 Consensus size: 18
36407 CTTTATAAAA
* *
36417 TTTTATAATTTTTTTATAT
1 TTTTCTAATTTTTATA-AT
*
36436 TTTTAT-ATATTTTATAAT
1 TTTTCTAAT-TTTTATAAT
36454 TTTT-TACTATTTTTATAAAAT
1 TTTTCTA--ATTTTTAT--AAT
* *
36475 TTTAC-AATTTTTTATATT
1 TTTTCTAA-TTTTTATAAT
*
36493 TTTTACT-ATTTTTATATTT
1 TTTT-CTAATTTTTATA-AT
36512 TTTTCTAATTTTTAATAAT
1 TTTTCTAATTTTT-ATAAT
36531 TTTT
1 TTTT
36535 ATTAAAATTT
Statistics
Matches: 81, Mismatches: 5, Indels: 26
0.72 0.04 0.23
Matches are distributed among these distances:
17 1 0.01
18 23 0.28
19 38 0.47
20 12 0.15
21 7 0.09
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTCTAATTTTTATAAT
Found at i:36535 original size:10 final size:10
Alignment explanation
Indices: 36480--36564 Score: 50
Period size: 10 Copynumber: 8.8 Consensus size: 10
36470 AAAATTTTAC
*
36480 AATTTTTTAT
1 AATTTTTAAT
* *
36490 ATTTTTTACT
1 AATTTTTAAT
36500 -ATTTTT-AT
1 AATTTTTAAT
* **
36508 ATTTTTTTCT
1 AATTTTTAAT
36518 AATTTTTAAT
1 AATTTTTAAT
*
36528 AATTTTTATT
1 AATTTTTAAT
**
36538 AAAATTTAAT
1 AATTTTTAAT
*
36548 AATATTT-AT
1 AATTTTTAAT
*
36557 AACTTTTA
1 AATTTTTA
36565 TTGATTTTAA
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
8 1 0.02
9 17 0.31
10 37 0.67
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:36535 original size:57 final size:56
Alignment explanation
Indices: 36369--36533 Score: 185
Period size: 57 Copynumber: 2.9 Consensus size: 56
36359 TTGTTACGAA
* * * *
36369 TTTTATATTTCTTTATATTTTATATAATTTTCTTACGACTTTATAA-AATTTTATAATT
1 TTTTATATTT-TTTATATTTT-TATAATTTT-TTACTAATTTTTAATAATTTTACAATT
*
36427 TTTT-TATATTTTTATATATTTTATAATTTTTTACT-ATTTTTATAAAATTTTACAATT
1 TTTTATAT-TTTTTATAT-TTTTATAATTTTTTACTAATTTTTA-ATAATTTTACAATT
*
36484 TTTTATATTTTTTACTATTTTTAT-ATTTTTTTCTAATTTTTAATAATTTT
1 TTTTATATTTTTTA-TATTTTTATAATTTTTTACTAATTTTTAATAATTTT
36534 TATTAAAATT
Statistics
Matches: 94, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
55 5 0.05
56 21 0.22
57 53 0.56
58 15 0.16
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (56 bp):
TTTTATATTTTTTATATTTTTATAATTTTTTACTAATTTTTAATAATTTTACAATT
Found at i:36769 original size:94 final size:95
Alignment explanation
Indices: 36637--36825 Score: 226
Period size: 94 Copynumber: 2.0 Consensus size: 95
36627 TTTGAGAGTA
** * * *
36637 TTTTTTATGTATTCTAAAAGTTCAAGTATCCAATTGAGTGCAAAAAAAAAATAAAGA-CTTAA-T
1 TTTTTTATACATTCTAAAAATTCAAGTACCCAAATGAGT--AAAAAAAAAA-AAAGAGCTTAATT
*
36700 -TT-CTTTTTTTGAAA-AGGTTTGAAGGTTTTTT
63 ATTACTTTTTTTGAAATA-GTTTAAAGGTTTTTT
* *
36731 TTTTTTATACATTTTAAAAATTCAAGTACCCAAATGAGTAAAAAAAAAAAATGAGCTTAATTATT
1 TTTTTTATACATTCTAAAAATTCAAGTACCCAAATGAGTAAAAAAAAAAAAAGAGCTTAATTATT
*
36796 ATTTTTTTTGAAATAGTTTAAAGGTTTTTT
66 ACTTTTTTTGAAATAGTTTAAAGGTTTTTT
36826 ACACTTTTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
91 4 0.05
92 15 0.19
93 1 0.01
94 35 0.43
95 25 0.31
96 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.43
Consensus pattern (95 bp):
TTTTTTATACATTCTAAAAATTCAAGTACCCAAATGAGTAAAAAAAAAAAAAGAGCTTAATTATT
ACTTTTTTTGAAATAGTTTAAAGGTTTTTT
Found at i:37291 original size:21 final size:19
Alignment explanation
Indices: 37253--37296 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
37243 TTATTCGTGT
37253 TAATGATTAAATTTAATTA
1 TAATGATTAAATTTAATTA
*
37272 TAATTATTAAAATATTAATTA
1 TAATGATT-AAAT-TTAATTA
37293 TAAT
1 TAAT
37297 CATACGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATGATTAAATTTAATTA
Found at i:38102 original size:57 final size:57
Alignment explanation
Indices: 38034--38152 Score: 213
Period size: 57 Copynumber: 2.1 Consensus size: 57
38024 CAATCTCGTT
38034 TATATTCACTTAAATAT-AGTTTAATAAATCATTTAAAATTTGTTTATTGTTCCATTA
1 TATATTCACTTAAATATCA-TTTAATAAATCATTTAAAATTTGTTTATTGTTCCATTA
*
38091 TATATTTACTTAAATATCATTTAATAAATCATTTAAAATTTGTTTATTGTTCCATTA
1 TATATTCACTTAAATATCATTTAATAAATCATTTAAAATTTGTTTATTGTTCCATTA
38148 TATAT
1 TATAT
38153 ATAAATATAT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 59 0.98
58 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.50
Consensus pattern (57 bp):
TATATTCACTTAAATATCATTTAATAAATCATTTAAAATTTGTTTATTGTTCCATTA
Found at i:39430 original size:9 final size:9
Alignment explanation
Indices: 39413--39447 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
39403 TTTAAAATTG
*
39413 AAAATTTTT
1 AAAAATTTT
39422 AAAAATTTT
1 AAAAATTTT
39431 AAAAATTTT
1 AAAAATTTT
39440 AAAAATTT
1 AAAAATTT
39448 AAATTCGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AAAAATTTT
Found at i:43626 original size:16 final size:16
Alignment explanation
Indices: 43605--43637 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43595 GAAACCCAAT
43605 TTTATTT-TTCATTTTA
1 TTTATTTATT-ATTTTA
43621 TTTATTTATTATTTTA
1 TTTATTTATTATTTTA
43637 T
1 T
43638 GAATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTATTATTTTA
Found at i:44694 original size:30 final size:30
Alignment explanation
Indices: 44660--44751 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
44650 TCATGTTTTT
44660 ACCCTCAAATTTTCCAAAAATT-ATAATTTG
1 ACCCTCAAATTTTCCAAAAATTCA-AATTTG
** * *
44690 ACCCTTGAACTTTCTAAAAATTCAAATTTG
1 ACCCTCAAATTTTCCAAAAATTCAAATTTG
* *
44720 ACCCTTGAACTTTT-CAAAAATTCAAATTTG
1 ACCC-TCAAATTTTCCAAAAATTCAAATTTG
44750 AC
1 AC
44752 TTGGTTTTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 45 0.88
31 6 0.12
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (30 bp):
ACCCTCAAATTTTCCAAAAATTCAAATTTG
Done.