Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014043.1 Kokia drynarioides strain JFW-HI SEQ_129074, 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: 92634
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:51 original size:4 final size:4
Alignment explanation
Indices: 44--82 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
34 TTCTTCCTTC
*
44 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TT
83 TTCCTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:94 original size:21 final size:21
Alignment explanation
Indices: 51--96 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41 TTCTTCTTTC
* *
51 TTTCTTTCTTTCTTTCTCTTT
1 TTTCTTTCTTTCTTCCTCATT
72 TTTCTTTCTTT-TTCCTTCATT
1 TTTCTTTCTTTCTTCC-TCATT
93 TTTC
1 TTTC
97 GTTGGTCCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTCTTTCTTTCTTCCTCATT
Found at i:3762 original size:19 final size:18
Alignment explanation
Indices: 3717--3762 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
3707 TGCAATAGGA
*
3717 ATAATATTTTAATTTTAGT
1 ATAAT-TTTTAATTTTAAT
3736 ATAGATTTTTAATTTTAAAT
1 ATA-ATTTTTAATTTT-AAT
3756 ATAATTT
1 ATAATTT
3763 ATATGTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
ATAATTTTTAATTTTAAT
Found at i:6756 original size:18 final size:19
Alignment explanation
Indices: 6719--6758 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
6709 CCAACCCACA
6719 ATTTGCTTGATAAAAAAACTC
1 ATTTGCTTGAT--AAAAACTC
6740 ATTTGCTTGAT-AAAACTC
1 ATTTGCTTGATAAAAACTC
6758 A
1 A
6759 AACTGGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
21 11 0.58
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (19 bp):
ATTTGCTTGATAAAAACTC
Found at i:6922 original size:21 final size:19
Alignment explanation
Indices: 6860--6915 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 19
6850 TGGTGATTAG
6860 AATTTTAAAATAATTTTAT
1 AATTTTAAAATAATTTTAT
6879 -ATTTTAAAAAATAATTTTAAT
1 AATTTT--AAAATAATTTT-AT
6900 AATTTTAAAATAATTT
1 AATTTTAAAATAATTT
6916 ACTATAAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 5 0.15
20 21 0.64
21 2 0.06
22 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTTAAAATAATTTTAT
Found at i:8008 original size:15 final size:15
Alignment explanation
Indices: 7988--8023 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
7978 TATGGACAGA
7988 ATTTTTTATA-AATAT
1 ATTTTTTATATAA-AT
8003 ATTTTTTATATAAAT
1 ATTTTTTATATAAAT
8018 ATTTTT
1 ATTTTT
8024 ACCTAGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTTTATATAAAT
Found at i:8014 original size:17 final size:15
Alignment explanation
Indices: 7989--8023 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
7979 ATGGACAGAA
7989 TTTTTTATAAATATAT
1 TTTTTTATAAATAT-T
8005 TTTTTATATAAATATT
1 TTTTT-TATAAATATT
8021 TTT
1 TTT
8024 ACCTAGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTTATAAATATT
Found at i:10784 original size:6 final size:6
Alignment explanation
Indices: 10773--10799 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10763 TTTTAACTCG
10773 ATTGAT ATTGAT ATTGAT ATTGAT ATT
1 ATTGAT ATTGAT ATTGAT ATTGAT ATT
10800 ATTATTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
ATTGAT
Found at i:16675 original size:58 final size:60
Alignment explanation
Indices: 16607--16721 Score: 164
Period size: 59 Copynumber: 1.9 Consensus size: 60
16597 GAGTTCAGTT
* * *
16607 CCCAATGTAGG-ATAATTGCCAAGTTCAGAGAT-TAACTTGGA-CAAAAAAAAGTTCAAGC
1 CCCAATGTAGGAACAATTACCAAGTTCA-AGATCTAAATTGGACCAAAAAAAAGTTCAAGC
*
16665 CCCAATGTAGGAACAATTACCAAGTTCAAGGTCTAAATTGGACCAAAAAAAAGTTCA
1 CCCAATGTAGGAACAATTACCAAGTTCAAGATCTAAATTGGACCAAAAAAAAGTTCA
16722 GATCCCAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 14 0.28
59 22 0.44
60 14 0.28
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (60 bp):
CCCAATGTAGGAACAATTACCAAGTTCAAGATCTAAATTGGACCAAAAAAAAGTTCAAGC
Found at i:32688 original size:18 final size:17
Alignment explanation
Indices: 32658--32699 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
32648 AGCTAAGGAT
*
32658 AATAT-TTATATTATTA
1 AATATATTATATTATCA
32674 AATATATTATAATTATCA
1 AATATATTAT-ATTATCA
32692 AA-ATATTA
1 AATATATTA
32700 AGAATTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 10 0.43
18 8 0.35
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATATTATATTATCA
Found at i:32697 original size:17 final size:18
Alignment explanation
Indices: 32658--32699 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
32648 AGCTAAGGAT
*
32658 AATATT-TATATTATTAA
1 AATATTATATATTATCAA
32675 ATATATTATA-ATTATCAA
1 A-ATATTATATATTATCAA
32693 AATATTA
1 AATATTA
32700 AGAATTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AATATTATATATTATCAA
Found at i:35556 original size:23 final size:22
Alignment explanation
Indices: 35530--35651 Score: 113
Period size: 23 Copynumber: 5.4 Consensus size: 22
35520 ACGCAAGCGC
35530 GCTTACTGATTCGCACT-TCGTGT
1 GCTTACTGATT-GCACTAT-GTGT
*
35553 GCTTACTGTTTCGCACCT-TGTGT
1 GCTTACTGATT-GCA-CTATGTGT
* * *
35576 GCCTACTGATTTGCGCTATGTGC
1 GCTTACTGA-TTGCACTATGTGT
* * *
35599 GCCTACTGATTGAACTGTGTGT
1 GCTTACTGATTGCACTATGTGT
35621 GCTTACTAGATTGCACTATGTGT
1 GCTTACT-GATTGCACTATGTGT
35644 GCTTACTG
1 GCTTACTG
35652 TTTCCCAGCA
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
22 18 0.22
23 60 0.72
24 5 0.06
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.39
Consensus pattern (22 bp):
GCTTACTGATTGCACTATGTGT
Found at i:37180 original size:18 final size:18
Alignment explanation
Indices: 37133--37182 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
37123 TAACTGACTG
* *
37133 AATCAATCTAATTCGGTT
1 AATCGATCTAGTTCGGTT
*
37151 AATCGATTTAGTTCGGTT
1 AATCGATCTAGTTCGGTT
37169 AA-CTGATCTAGTTC
1 AATC-GATCTAGTTC
37183 AATCGGAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (18 bp):
AATCGATCTAGTTCGGTT
Found at i:49447 original size:2 final size:2
Alignment explanation
Indices: 49440--49466 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49430 TTAAGTAGTA
49440 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 A
49467 GTAGAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53714 original size:28 final size:30
Alignment explanation
Indices: 53655--53733 Score: 126
Period size: 28 Copynumber: 2.7 Consensus size: 30
53645 CAAATGATTT
53655 TAAAATTATAAAATTATTATTTTTTAAATA
1 TAAAATTATAAAATTATTATTTTTTAAATA
53685 TAAAATTATAAAATTA-T-TTTTTTAAATA
1 TAAAATTATAAAATTATTATTTTTTAAATA
*
53713 TAAAATTATTAAAATCATTAT
1 TAAAATTA-TAAAATTATTAT
53734 CATCTTAAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 19 0.42
29 8 0.18
30 17 0.38
31 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAATTATAAAATTATTATTTTTTAAATA
Found at i:61662 original size:356 final size:356
Alignment explanation
Indices: 61009--61724 Score: 1360
Period size: 356 Copynumber: 2.0 Consensus size: 356
60999 AGGCCAAGAG
61009 TTGATCTTCCATAAGACACGCCTTCTCTTGCATCTCGATGACCTAATAATAGGGGATAGAGGCTT
1 TTGATCTTCCATAAGACACGCCTTCTCTTGCATCTCGATGACCTAATAATAGGGGATAGAGGCTT
* *
61074 GTTGCTGCTGAGAAGCTTAATCTACAAGAATGGAGGTGGCAGTAGGTTGGGATGGATGAGTTATG
66 ATTGCTGCTGAGAAGCTTAATCTACAAGAATGGAGGTGACAGTAGGTTGGGATGGATGAGTTATG
* * *
61139 AAGCAAGCAAAGACTTGTTGTAAATGGTGAGCAAACTATTCTTTAGGCTCTAGAGAGGAGTTGCT
131 AAGAAAGCAAAGACTTGTTGTAAATGGTGAGCAAACTATTCGTTAGGCTCTAGAGAGGAGTTGCC
*
61204 AGAGGGTGGTTGAGTGCTTGGGGCAGTTAGTGGAACGATGAGGGCAAGATTGATTAGAAAAGCAA
196 AGAGGGTGGTTGAGTGCTTGGGGCAGTTAGTGGAACGATGAGGGCAAGATTGATCAGAAAAGCAA
*
61269 GGAGAGGGATATTGAGAGTGGTCATAAGTTGGGTGAAAACCTCAAGAGGGCTGATAGTTGGTCTT
261 GAAGAGGGATATTGAGAGTGGTCATAAGTTGGGTGAAAACCTCAAGAGGGCTGATAGTTGGTCTT
*
61334 GTTGATTGGGTGGCAGAAGGATTAGTTTGTT
326 GTTGATTGGGTGGCAGAAGGATGAGTTTGTT
61365 TTGATCTTCCATAAGACACGCCTTCTCTTGCATCTCGATGACCTAATAATAGGGGATAGAGGCTT
1 TTGATCTTCCATAAGACACGCCTTCTCTTGCATCTCGATGACCTAATAATAGGGGATAGAGGCTT
61430 ATTGCTGCTGAGAAGCTTAATCTACAAGAATGGAGGTGACAGTAGGTTGGGATGGATGAGTTATG
66 ATTGCTGCTGAGAAGCTTAATCTACAAGAATGGAGGTGACAGTAGGTTGGGATGGATGAGTTATG
61495 AAGAAAGCAAAGACTTGTTGTAAATGGTGAGCAAACTATTCGTTAGGCTCTAGAGAGGAGTTGCC
131 AAGAAAGCAAAGACTTGTTGTAAATGGTGAGCAAACTATTCGTTAGGCTCTAGAGAGGAGTTGCC
61560 AGAGGGTGGTTGAGTGCTTGGGGCAGTTAGTGGAACGATGAGGGCAAGATTGATCAGAAAAGCAA
196 AGAGGGTGGTTGAGTGCTTGGGGCAGTTAGTGGAACGATGAGGGCAAGATTGATCAGAAAAGCAA
61625 GAAGAGGGATATTGAGAGTGGTCATAAGTTGGGTGAAAACCTCAAGAGGGCTGATAGTTGGTCTT
261 GAAGAGGGATATTGAGAGTGGTCATAAGTTGGGTGAAAACCTCAAGAGGGCTGATAGTTGGTCTT
61690 GTTGATTGGGTGGCAGAAGGATGAGTTTGTT
326 GTTGATTGGGTGGCAGAAGGATGAGTTTGTT
61721 TTGA
1 TTGA
61725 AGGGAGCTCG
Statistics
Matches: 352, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
356 352 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.27
Consensus pattern (356 bp):
TTGATCTTCCATAAGACACGCCTTCTCTTGCATCTCGATGACCTAATAATAGGGGATAGAGGCTT
ATTGCTGCTGAGAAGCTTAATCTACAAGAATGGAGGTGACAGTAGGTTGGGATGGATGAGTTATG
AAGAAAGCAAAGACTTGTTGTAAATGGTGAGCAAACTATTCGTTAGGCTCTAGAGAGGAGTTGCC
AGAGGGTGGTTGAGTGCTTGGGGCAGTTAGTGGAACGATGAGGGCAAGATTGATCAGAAAAGCAA
GAAGAGGGATATTGAGAGTGGTCATAAGTTGGGTGAAAACCTCAAGAGGGCTGATAGTTGGTCTT
GTTGATTGGGTGGCAGAAGGATGAGTTTGTT
Found at i:64355 original size:80 final size:80
Alignment explanation
Indices: 64216--64404 Score: 263
Period size: 80 Copynumber: 2.4 Consensus size: 80
64206 GACGATTCTG
* * * * *
64216 ACACCCAGTGCCTAGCGGATAAACCACAAAAGTGAGCTCAGCTCTAGTTGTATTAACCAACAAAT
1 ACACCTAGTGCCTAGCGGATAAACCGCAAAAGTGAACTCAACTCTAGTTGGATTAACCAACAAAT
*
64281 ATCCGTCAAATCCTG
66 ATCCGTCAAATCCTA
* *
64296 TCACCTAGTGCCTAGCGGATAAACCGCAAAAGTGAAACT-AACTCTAGTTGGATTAACCAATAAA
1 ACACCTAGTGCCTAGCGGATAAACCGCAAAAGTG-AACTCAACTCTAGTTGGATTAACCAACAAA
* *
64360 TATTCGTCAAATCTTA
65 TATCCGTCAAATCCTA
*
64376 ACACCTAGTGCCTAGTGGATAAACCGCAA
1 ACACCTAGTGCCTAGCGGATAAACCGCAA
64405 TTCTGTGTCA
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 93 0.97
81 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (80 bp):
ACACCTAGTGCCTAGCGGATAAACCGCAAAAGTGAACTCAACTCTAGTTGGATTAACCAACAAAT
ATCCGTCAAATCCTA
Found at i:66786 original size:29 final size:31
Alignment explanation
Indices: 66752--66820 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 31
66742 ATTGATAATT
*
66752 CAAGTACCAGATTGAACATTTT-T-AAAATA
1 CAAGTACCAGATTAAACATTTTGTAAAAATA
* *
66781 CAAGTACCATATTAAATATTTTGTAAAAATA
1 CAAGTACCAGATTAAACATTTTGTAAAAATA
66812 CAAGTACCA
1 CAAGTACCA
66821 AATGATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 19 0.54
30 1 0.03
31 15 0.43
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.30
Consensus pattern (31 bp):
CAAGTACCAGATTAAACATTTTGTAAAAATA
Found at i:73163 original size:23 final size:23
Alignment explanation
Indices: 73119--73199 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
73109 TTAATGTTCA
*
73119 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-TGAACATTAAT
* *
73142 CGAACATGTTCAAGAACATTAAA
1 CGAACATGTTCATGAACATTAAT
* *
73165 CGAATATGTTTATGAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
*
73189 TGAACATGTTC
1 CGAACATGTTC
73200 CCGAACAATG
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
22 3 0.07
23 32 0.70
24 11 0.24
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (23 bp):
CGAACATGTTCATGAACATTAAT
Found at i:80240 original size:32 final size:33
Alignment explanation
Indices: 80197--80276 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
80187 TTGTCTTGAT
80197 GGAACTGTTGCTTACTGT-TGAGT-ATCTTCCAG
1 GGAACTGTTGCTTACTGTCTGA-TCATCTTCCAG
* * *
80229 GTAACTGTTGCTTA-TTTCTTATCATCTTCCAG
1 GGAACTGTTGCTTACTGTCTGATCATCTTCCAG
80261 GGAACTGTTGCTTACT
1 GGAACTGTTGCTTACT
80277 ACTTACTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.07
32 37 0.90
33 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (33 bp):
GGAACTGTTGCTTACTGTCTGATCATCTTCCAG
Found at i:81992 original size:2 final size:2
Alignment explanation
Indices: 81985--82024 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
81975 TCATGTTCGA
81985 AT AT AT AT AT AT AT AT AT AT AT 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
82025 CAAACACGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86448 original size:14 final size:14
Alignment explanation
Indices: 86404--86436 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
86394 GGTCTTAATA
86404 ATATACATACATAT
1 ATATACATACATAT
86418 ATATACATACATAT
1 ATATACATACATAT
86432 ATATA
1 ATATA
86437 TATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATACATACATAT
Done.