Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013751.1 Kokia drynarioides strain JFW-HI SEQ_128779, 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: 109874
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 196 characters in sequence are not A, C, G, or T
Found at i:19006 original size:27 final size:26
Alignment explanation
Indices: 18963--19020 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
18953 AAATACGATT
*
18963 AAAA-ATAATAGAAAATACAAATTTTA
1 AAAATATAATAGAAAATA-AAATTATA
18989 AAAATATAATA-AATAATAAAATTATA
1 AAAATATAATAGAA-AATAAAATTATA
*
19015 TAAATA
1 AAAATA
19021 ATTTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AAAATATAATAGAAAATAAAATTATA
Found at i:19008 original size:18 final size:17
Alignment explanation
Indices: 18965--19022 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
18955 ATACGATTAA
* *
18965 AAATAATAGAAA-ATAC
1 AAATAATAAAAATATAT
**
18981 AAATTTTAAAAATATAAT
1 AAATAATAAAAATAT-AT
*
18999 AAATAATAAAATTATAT
1 AAATAATAAAAATATAT
19016 AAATAAT
1 AAATAAT
19023 TTAATATTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 9 0.27
17 11 0.33
18 13 0.39
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
AAATAATAAAAATATAT
Found at i:19017 original size:17 final size:18
Alignment explanation
Indices: 18987--19022 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
18977 ATACAAATTT
18987 TAAAAATATAATAAATAA
1 TAAAAATATAATAAATAA
*
19005 TAAAATTAT-ATAAATAA
1 TAAAAATATAATAAATAA
19022 T
1 T
19023 TTAATATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATATAATAAATAA
Found at i:23260 original size:2 final size:2
Alignment explanation
Indices: 23253--23277 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23243 GATCACTATT
23253 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
23278 TTTTTTTTAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25102 original size:5 final size:5
Alignment explanation
Indices: 25092--25119 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
25082 ATGGAAGGAT
25092 GCAAA GCAAA GCAAA GCAAA GCAAA GCA
1 GCAAA GCAAA GCAAA GCAAA GCAAA GCA
25120 TTTTTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.21, G:0.21, T:0.00
Consensus pattern (5 bp):
GCAAA
Found at i:25191 original size:6 final size:6
Alignment explanation
Indices: 25180--25205 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25170 GAAATAGGTG
25180 TCTTCC TCTTCC TCTTCC TCTTCC TC
1 TCTTCC TCTTCC TCTTCC TCTTCC TC
25206 GCATGGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCC
Found at i:32963 original size:61 final size:60
Alignment explanation
Indices: 32853--32966 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 60
32843 ATTGAGGAAT
* *
32853 AAATTTATTGAATTTTTAGAATTTGAATTAAAATGATAAATTTAGTAAATATTGAAAGTA
1 AAATTTATTGAATTTTTAGAATTTGAATTAAAATAATAAATGTAGTAAATATTGAAAGTA
* * *
32913 AAATTTATTGAATTTTTTA-TATTTATAATTAAATTAATAAAATGTA-TAAATATT
1 AAATTTATTGAA-TTTTTAGAATTT-GAATTAAAATAAT-AAATGTAGTAAATATT
32967 AGAGGACTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
60 16 0.35
61 24 0.52
62 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (60 bp):
AAATTTATTGAATTTTTAGAATTTGAATTAAAATAATAAATGTAGTAAATATTGAAAGTA
Found at i:38120 original size:18 final size:17
Alignment explanation
Indices: 38099--38135 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
38089 ATATTCTAAC
38099 TTTTTTTTA-TCTTCCAT
1 TTTTTTTTACTCTTCC-T
38116 TTTTTTTTACTCTTCCT
1 TTTTTTTTACTCTTCCT
38133 TTT
1 TTT
38136 GCTTTCCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTTTACTCTTCCT
Found at i:42649 original size:31 final size:31
Alignment explanation
Indices: 42611--42687 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
42601 CACCATCACA
** * *
42611 ATTAATTTAATACTTATGTTAAT-AGTATTTT
1 ATTAATTTAATA-TTACCTTAATAAATATTAT
*
42642 ATTAATTTAATATTACCTTGATAAATATTAT
1 ATTAATTTAATATTACCTTAATAAATATTAT
42673 ATTAATTTAATATTA
1 ATTAATTTAATATTA
42688 AAGTAATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 7 0.17
31 33 0.82
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (31 bp):
ATTAATTTAATATTACCTTAATAAATATTAT
Found at i:42825 original size:108 final size:110
Alignment explanation
Indices: 42659--42869 Score: 354
Period size: 108 Copynumber: 1.9 Consensus size: 110
42649 TAATATTACC
* *
42659 TTGATAAATATTATATTAATTTAATATTAAAGTAATTAAGATTAATCATAATTGAACTCTCTAAA
1 TTGATAAATATTATATTAATTTAATATTAAAGTAATTAAGATTAATCATAATTAAACTCTCAAAA
* *
42724 CTCTCCTTATATGAAAACATTATTTCA-GAAA-ATTTAAAAGTTG
66 CCCTCCTTATATAAAAACATTATTTCAGGAAATATTTAAAAGTTG
* *
42767 TTGATAAATATTATATTAATTTAATATTAAAGTGATTAAGATTAATCATAGTTAAACTCTCAAAA
1 TTGATAAATATTATATTAATTTAATATTAAAGTAATTAAGATTAATCATAATTAAACTCTCAAAA
42832 CCCTCCTTATATAAAAACATTATTTCAGGAAATATTTA
66 CCCTCCTTATATAAAAACATTATTTCAGGAAATATTTA
42870 GAGGTATTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 86 0.91
109 4 0.04
110 5 0.05
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (110 bp):
TTGATAAATATTATATTAATTTAATATTAAAGTAATTAAGATTAATCATAATTAAACTCTCAAAA
CCCTCCTTATATAAAAACATTATTTCAGGAAATATTTAAAAGTTG
Found at i:43611 original size:17 final size:17
Alignment explanation
Indices: 43591--43629 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
43581 TTCTGGGCAC
43591 TGAA-AATTGGTTTCAGT
1 TGAATAATTGGTTTCA-T
*
43608 TGAATTATTGGTTTCAT
1 TGAATAATTGGTTTCAT
43625 TGAAT
1 TGAAT
43630 GTGAATGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (17 bp):
TGAATAATTGGTTTCAT
Found at i:43619 original size:18 final size:17
Alignment explanation
Indices: 43596--43629 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
43586 GGCACTGAAA
43596 ATTGGTTTCAGTTGAATT
1 ATTGGTTTCA-TTGAATT
43614 ATTGGTTTCATTGAAT
1 ATTGGTTTCATTGAAT
43630 GTGAATGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.50
Consensus pattern (17 bp):
ATTGGTTTCATTGAATT
Found at i:56132 original size:24 final size:24
Alignment explanation
Indices: 56100--56154 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
56090 GCAACCTTGG
*
56100 CAGCCGCAGCTGCAGCCT-TTGCAA
1 CAGCAGCAGCTGCAG-CTATTGCAA
* *
56124 CAGCAGCAGCTGCTGCTATTGCCA
1 CAGCAGCAGCTGCAGCTATTGCAA
56148 CAGCAGC
1 CAGCAGC
56155 GGAAGTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.22, C:0.36, G:0.25, T:0.16
Consensus pattern (24 bp):
CAGCAGCAGCTGCAGCTATTGCAA
Found at i:58027 original size:27 final size:27
Alignment explanation
Indices: 57992--58043 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
57982 TCGCCTTGCT
*
57992 CTACGCTCAGAGGTCCCTTTGGAGCCA
1 CTACGCTCAGACGTCCCTTTGGAGCCA
*
58019 CTACTCTCAGACGTCCCTTTGGAGC
1 CTACGCTCAGACGTCCCTTTGGAGC
58044 ATCCACGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.23, T:0.25
Consensus pattern (27 bp):
CTACGCTCAGACGTCCCTTTGGAGCCA
Found at i:67963 original size:33 final size:33
Alignment explanation
Indices: 67916--67978 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
67906 AAAAAGATTA
*
67916 CAGTAACAGTAGCAGCCACTGAAGAATCAAGGG
1 CAGTAACAGTAGCAGCAACTGAAGAATCAAGGG
*
67949 CAGTGACAGTAGCAGCAACTGAAGAATCAA
1 CAGTAACAGTAGCAGCAACTGAAGAATCAA
67979 TAAGAGCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.13
Consensus pattern (33 bp):
CAGTAACAGTAGCAGCAACTGAAGAATCAAGGG
Found at i:79893 original size:17 final size:17
Alignment explanation
Indices: 79871--79909 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
79861 AGGTGGAGAA
* * *
79871 CTTGTTCGTTGAGAGTT
1 CTTGTTCATAGAGAATT
79888 CTTGTTCATAGAGAATT
1 CTTGTTCATAGAGAATT
79905 CTTGT
1 CTTGT
79910 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:84434 original size:83 final size:83
Alignment explanation
Indices: 84290--84452 Score: 317
Period size: 83 Copynumber: 2.0 Consensus size: 83
84280 GACAAGCCAG
*
84290 AGAGGGAGGCCAAGTACGGGTAACAGATGTTGATGAATTTTGACTCATTGGTACCTGATATTGCT
1 AGAGGGAGGCCAAGTACGGGTAACAGATGTTGATGAATTTTGACTCATTGGTACCTAATATTGCT
84355 CTAAGTGATAGGGTCCAA
66 CTAAGTGATAGGGTCCAA
84373 AGAGGGAGGCCAAGTACGGGTAACAGATGTTGATGAATTTTGACTCATTGGTACCTAATATTGCT
1 AGAGGGAGGCCAAGTACGGGTAACAGATGTTGATGAATTTTGACTCATTGGTACCTAATATTGCT
84438 CTAAGTGATAGGGTC
66 CTAAGTGATAGGGTC
84453 ACCGACTTCA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (83 bp):
AGAGGGAGGCCAAGTACGGGTAACAGATGTTGATGAATTTTGACTCATTGGTACCTAATATTGCT
CTAAGTGATAGGGTCCAA
Found at i:101765 original size:6 final size:6
Alignment explanation
Indices: 101754--101792 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
101744 TGGAGCTCTA
* * *
101754 GGGTTT GGGTTT GGGTTT GGGATT GAGATT GGGTTT GGG
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGG
101793 GAGGGTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.08, C:0.00, G:0.51, T:0.41
Consensus pattern (6 bp):
GGGTTT
Found at i:102788 original size:27 final size:29
Alignment explanation
Indices: 102758--102825 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 29
102748 GATTTATATC
102758 AAAATTTTATATA-ATTT-TTTTGATT-AA
1 AAAATTTTATATATATTTATTTT-ATTCAA
*
102785 AAAATATTCGATATATATTTATTTTATTCAA
1 AAAAT-TT-TATATATATTTATTTTATTCAA
*
102816 TAAATTTTAT
1 AAAATTTTAT
102826 CACAAACGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
27 5 0.15
28 2 0.06
29 7 0.21
30 9 0.27
31 10 0.30
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (29 bp):
AAAATTTTATATATATTTATTTTATTCAA
Found at i:103024 original size:23 final size:24
Alignment explanation
Indices: 102993--103039 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
102983 TAAAAATTTT
*
102993 AAATAAGTAAATGT-ATCTGATTA
1 AAATAAGTAAATATAATCTGATTA
*
103016 AAATTAGTAAATATAATCTGATTA
1 AAATAAGTAAATATAATCTGATTA
103040 TTTTCGAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (24 bp):
AAATAAGTAAATATAATCTGATTA
Found at i:103845 original size:18 final size:17
Alignment explanation
Indices: 103814--103848 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
103804 AGTTTAGGGT
103814 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
103831 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
103849 AGATTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:107225 original size:17 final size:15
Alignment explanation
Indices: 107203--107251 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 15
107193 TTTGTGTAGA
107203 AATTTAAATTTATTT
1 AATTTAAATTTATTT
107218 CGAATTTAAATTTAATTT
1 --AATTTAAATTT-ATTT
107236 AAGTTTAAATTTATTT
1 AA-TTTAAATTTATTT
107252 TCCAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.20
17 20 0.67
18 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (15 bp):
AATTTAAATTTATTT
Found at i:109293 original size:59 final size:58
Alignment explanation
Indices: 109199--109428 Score: 293
Period size: 59 Copynumber: 3.9 Consensus size: 58
109189 CCCTAAATTG
* * *
109199 TCCAAAAATTCCATTTTTACCACCAAACTTCCAAAAATCTCATTTTTAGCCCCAAAACT
1 TCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTT-GCCCCAAAACT
* * *
109258 TCCAAAACTTCCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTG-CCCCAAAACT
* * * *
109317 TCCAAAAAACCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCGAAACT
1 TCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGCCCCAAAACT
* * * *
109374 TTCAAAAATCCCA-TTTTACCCTCAAACTTTCAAAAATCCCATTTTTTACCCCAAA
1 TCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCA-TTTTTGCCCCAAA
109429 TTTTCCCATA
Statistics
Matches: 149, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
56 5 0.03
57 38 0.26
58 37 0.25
59 69 0.46
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (58 bp):
TCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGCCCCAAAACT
Found at i:109433 original size:29 final size:28
Alignment explanation
Indices: 109199--109428 Score: 282
Period size: 29 Copynumber: 7.9 Consensus size: 28
109189 CCCTAAATTG
*
109199 TCCAAAAATTCCATTTTTACCACCAAACT
1 TCCAAAAATCCCATTTTTACC-CCAAACT
*
109228 TCCAAAAATCTCATTTTTAGCCCCAAAACT
1 TCCAAAAATCCCATTTTTA-CCCC-AAACT
* *
109258 TCCAAAACTTCCATTTTTACCCCCAAACT
1 TCCAAAAATCCCATTTTTA-CCCCAAACT
*
109287 TTCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATCCCATTTTT-ACCCC-AAACT
* *
109317 TCCAAAAAACCCATTTTTACCCCGAACT
1 TCCAAAAATCCCATTTTTACCCCAAACT
*
109345 TCCAAAAATCCCATTTTTGACCCGAAACT
1 TCCAAAAATCCCATTTTT-ACCCCAAACT
*
109374 TTCAAAAATCCCA-TTTTACCCTCAAACT
1 TCCAAAAATCCCATTTTTACCC-CAAACT
*
109402 TTCAAAAATCCCATTTTTTACCCCAAA
1 TCCAAAAATCCCA-TTTTTACCCCAAA
109429 TTTTCCCATA
Statistics
Matches: 176, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
27 4 0.02
28 43 0.24
29 72 0.41
30 57 0.32
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (28 bp):
TCCAAAAATCCCATTTTTACCCCAAACT
Done.