Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012388.1 Kokia drynarioides strain JFW-HI SEQ_127392, 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: 57957
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Found at i:1583 original size:2 final size:2
Alignment explanation
Indices: 1576--1616 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1566 TTAAATGTGA
1576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1617 CTTGGTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4703 original size:30 final size:30
Alignment explanation
Indices: 4669--4726 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
4659 GAGTATTTTT
4669 TTTTATTTC-AATATGTCACACTAACAAATA
1 TTTTATTTCGAA-ATGTCACACTAACAAATA
4699 TTTTATTTCGAAATGTCACACTAACAAA
1 TTTTATTTCGAAATGTCACACTAACAAA
4727 CTTCCATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTTATTTCGAAATGTCACACTAACAAATA
Found at i:9562 original size:22 final size:22
Alignment explanation
Indices: 9537--9584 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
9527 TTTTTTTGAA
9537 ATATAAATTTATTAAAATTATT
1 ATATAAATTTATTAAAATTATT
* * * *
9559 ATATTATTTTTTTGAAATTATT
1 ATATAAATTTATTAAAATTATT
9581 ATAT
1 ATAT
9585 GATTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATAAATTTATTAAAATTATT
Found at i:10678 original size:37 final size:39
Alignment explanation
Indices: 10623--10714 Score: 127
Period size: 37 Copynumber: 2.4 Consensus size: 39
10613 GAAAATTGGA
* * *
10623 AATTATAATCA-TATAATAATTTTATA-TTCAAAAAAAT
1 AATTATAATAATTTTAATAATTCTATATTTCAAAAAAAT
10660 AA-TATAATAATTTTAATAATTCTATATTTCAAAAAAAT
1 AATTATAATAATTTTAATAATTCTATATTTCAAAAAAAT
*
10698 AATTTTAATAATTTTAA
1 AATTATAATAATTTTAA
10715 AATCATTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 7 0.15
37 15 0.31
38 13 0.27
39 13 0.27
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (39 bp):
AATTATAATAATTTTAATAATTCTATATTTCAAAAAAAT
Found at i:12652 original size:22 final size:22
Alignment explanation
Indices: 12624--12686 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
12614 ATTTAAAATC
*
12624 TATATTTATCAAACAATTTAAT
1 TATATTTATCAAACAATTTAAA
**
12646 TATATTTCAT-AATTAATTTTAAA
1 TATATTT-ATCAAACAA-TTTAAA
*
12669 TGT-TTTATCAAACAATTT
1 TATATTTATCAAACAATTT
12687 TATAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
21 5 0.16
22 18 0.56
23 9 0.28
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (22 bp):
TATATTTATCAAACAATTTAAA
Found at i:17115 original size:21 final size:21
Alignment explanation
Indices: 17085--17128 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17075 AAAATTTTAA
*
17085 TATATATTT-ATGTAAAATAAT
1 TATATATTTAATATAAAA-AAT
*
17106 TATATCTTTAATATAAAAAAT
1 TATATATTTAATATAAAAAAT
17127 TA
1 TA
17129 ATACTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TATATATTTAATATAAAAAAT
Found at i:21465 original size:20 final size:20
Alignment explanation
Indices: 21436--21485 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 20
21426 AACAAAAAGT
21436 TATAAATATATTTATTATTA
1 TATAAATATATTTATTATTA
*
21456 TATAATTATA-TT-TT-TTA
1 TATAAATATATTTATTATTA
*
21473 TAAAAATATATTT
1 TATAAATATATTT
21486 GTATTGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 11 0.42
18 4 0.15
19 2 0.08
20 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATAAATATATTTATTATTA
Found at i:23811 original size:31 final size:32
Alignment explanation
Indices: 23776--23835 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
23766 ATAGCATTAA
23776 ATAAGTTTAGG-TATCAAATT-AATAAAAAGTG
1 ATAAG-TTAGGATATCAAATTGAATAAAAAGTG
*
23807 ATAAGTTCGGATATCAAATTGAATAAAAA
1 ATAAGTTAGGATATCAAATTGAATAAAAA
23836 AATTTAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 4 0.15
31 14 0.54
32 8 0.31
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (32 bp):
ATAAGTTAGGATATCAAATTGAATAAAAAGTG
Found at i:23874 original size:25 final size:26
Alignment explanation
Indices: 23817--23876 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
23807 ATAAGTTCGG
23817 ATATCAAATTGAATAAAAAAATTTAA
1 ATATCAAATTGAATAAAAAAATTTAA
*
23843 GTATCAAATT-AA-AAAAAAATTATAA
1 ATATCAAATTGAATAAAAAAATT-TAA
23868 A-ATTCAAAT
1 ATA-TCAAAT
23877 ACGATATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 10 0.33
25 11 0.37
26 9 0.30
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (26 bp):
ATATCAAATTGAATAAAAAAATTTAA
Found at i:26346 original size:22 final size:19
Alignment explanation
Indices: 26316--26355 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
26306 TTTTATATGG
26316 AATTTTGAATTGAAAGATTTT
1 AATTTTGAATT-AAA-ATTTT
26337 AATTATTGAATTAAAATTT
1 AATT-TTGAATTAAAATTT
26356 AATATAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (19 bp):
AATTTTGAATTAAAATTTT
Found at i:27521 original size:24 final size:24
Alignment explanation
Indices: 27493--27549 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
27483 AAACTTTGTC
* *
27493 TGGGCTCGTAAGAGTTAACCATTT
1 TGGGCTCATAAGAGCTAACCATTT
**
27517 TGGGCTCATGTGAGCTAACCATTT
1 TGGGCTCATAAGAGCTAACCATTT
27541 TGGGCTCAT
1 TGGGCTCAT
27550 GTGGGCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (24 bp):
TGGGCTCATAAGAGCTAACCATTT
Found at i:27550 original size:24 final size:24
Alignment explanation
Indices: 27508--27558 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
27498 TCGTAAGAGT
27508 TAACCATTTTGGGCTCATGTGAGC
1 TAACCATTTTGGGCTCATGTGAGC
*
27532 TAACCATTTTGGGCTCATGTGGGC
1 TAACCATTTTGGGCTCATGTGAGC
27556 TAA
1 TAA
27559 ATGTATCTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (24 bp):
TAACCATTTTGGGCTCATGTGAGC
Found at i:28146 original size:21 final size:24
Alignment explanation
Indices: 28120--28177 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 24
28110 TGACTTGAGT
28120 TGTATCGGTAGTTGA-AT-TGT-GA
1 TGTATCGGTAGTT-ATATGTGTAGA
*
28142 -GTATCTGTAGTTATATGTGTAGA
1 TGTATCGGTAGTTATATGTGTAGA
28165 TGTATCGGTAGTT
1 TGTATCGGTAGTT
28178 TACATACTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 13 0.43
22 3 0.10
23 2 0.07
24 11 0.37
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.43
Consensus pattern (24 bp):
TGTATCGGTAGTTATATGTGTAGA
Found at i:32267 original size:2 final size:2
Alignment explanation
Indices: 32226--32250 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32216 TTAAAATTAA
32226 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
32251 AATGAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35971 original size:29 final size:27
Alignment explanation
Indices: 35938--35994 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
35928 CAAAAACATT
35938 TTTATTTAATTATAATATATATTT-TAAAA
1 TTTATTTAATTA-AA-AT-TATTTATAAAA
*
35967 TTTATTTTATTAAAATTATTTATAAAA
1 TTTATTTAATTAAAATTATTTATAAAA
35994 T
1 T
35995 ATAACAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 5 0.19
27 8 0.31
28 2 0.08
29 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATTTAATTAAAATTATTTATAAAA
Found at i:44864 original size:3 final size:3
Alignment explanation
Indices: 44856--44882 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44846 TGTAATCCAT
44856 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
44883 CCTTCAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:45061 original size:17 final size:17
Alignment explanation
Indices: 45034--45067 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
45024 TAAACGGACA
45034 AATACAAATATAAATATT
1 AATACAAATAT-AATATT
45052 AATA-AAATATAATATT
1 AATACAAATATAATATT
45068 TTACTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AATACAAATATAATATT
Found at i:48666 original size:26 final size:25
Alignment explanation
Indices: 48632--48686 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
48622 CAACAAAACT
* *
48632 AAAATCTAACCTAAAAAAGAAAAGA
1 AAAACCTAAACTAAAAAAGAAAAGA
*
48657 GAAAACCTAAACTAAAAATGAAAAGA
1 -AAAACCTAAACTAAAAAAGAAAAGA
48683 AAAA
1 AAAA
48687 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.69, C:0.11, G:0.09, T:0.11
Consensus pattern (25 bp):
AAAACCTAAACTAAAAAAGAAAAGA
Done.