Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001293.1 Kokia drynarioides strain JFW-HI SEQ_112692, 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: 89893
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1071 original size:19 final size:18
Alignment explanation
Indices: 1034--1072 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1024 ATTTTTTCTA
1034 ATTTATAATAATTTTTAT
1 ATTTATAATAATTTTTAT
* *
1052 ATTTTTAATTATTATTTAT
1 ATTTATAATAATT-TTTAT
1071 AT
1 AT
1073 AATTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTATAATAATTTTTAT
Found at i:1082 original size:19 final size:19
Alignment explanation
Indices: 1005--1089 Score: 55
Period size: 19 Copynumber: 4.8 Consensus size: 19
995 TTATTAGTGT
1005 TTTTTTAATTATTT-TATGAA
1 TTTTTT-ATTATTTATAT-AA
* *
1025 TTTTTTCTAATTTATAATAA
1 TTTTTTATTATTTAT-ATAA
1045 -TTTTTA-TATTT-T-TAA
1 TTTTTTATTATTTATATAA
1060 ----TTATTATTTATATAA
1 TTTTTTATTATTTATATAA
1075 TTTTTTATT-TTTATA
1 TTTTTTATTATTTATA
1090 CAATAATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 20
0.68 0.05 0.26
Matches are distributed among these distances:
12 3 0.06
13 5 0.10
14 1 0.02
15 6 0.12
17 1 0.02
18 10 0.19
19 15 0.29
20 9 0.17
21 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTTTATTATTTATATAA
Found at i:10566 original size:18 final size:18
Alignment explanation
Indices: 10543--10580 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10533 ATGATTTGTT
*
10543 ATTTAAAATATTATAATA
1 ATTTAAAATAATATAATA
*
10561 ATTTAACATAATATAATA
1 ATTTAAAATAATATAATA
10579 AT
1 AT
10581 AATTAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAAATAATATAATA
Found at i:14167 original size:3 final size:3
Alignment explanation
Indices: 14161--14193 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
14151 TATATATAAC
14161 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14194 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:26803 original size:19 final size:20
Alignment explanation
Indices: 26774--26811 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
26764 GTGTCATGTA
26774 ATATATTATAAAAAAATAAC
1 ATATATTATAAAAAAATAAC
26794 ATAT-TTATAAAAAAATAA
1 ATATATTATAAAAAAATAA
26812 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATATTATAAAAAAATAAC
Found at i:32675 original size:2 final size:2
Alignment explanation
Indices: 32668--32719 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
32658 TTTCTTTTAC
*
32668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32710 AT AT AT AT AT
1 AT AT AT AT AT
32720 GTTGACAGGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35883 original size:5 final size:5
Alignment explanation
Indices: 35873--35899 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
35863 GGAATTCCCC
35873 AGGGG AGGGG AGGGG AGGGG AGGGG AG
1 AGGGG AGGGG AGGGG AGGGG AGGGG AG
35900 CCAAGCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (5 bp):
AGGGG
Found at i:38300 original size:32 final size:32
Alignment explanation
Indices: 38264--38328 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
38254 GCCAATAAAG
38264 TGCCATCCTAAATCCCCGAGGAAACAGAACTT
1 TGCCATCCTAAATCCCCGAGGAAACAGAACTT
38296 TGCCATCCTAAATCCCCGAGGAAACAGAACTT
1 TGCCATCCTAAATCCCCGAGGAAACAGAACTT
38328 T
1 T
38329 CTAGGAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.31, G:0.15, T:0.20
Consensus pattern (32 bp):
TGCCATCCTAAATCCCCGAGGAAACAGAACTT
Found at i:42166 original size:16 final size:16
Alignment explanation
Indices: 42147--42177 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42137 ATTTATAATA
*
42147 TTTTATATTATATTAT
1 TTTTATATTACATTAT
42163 TTTTATATTACATTA
1 TTTTATATTACATTA
42178 CACATTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATATTACATTAT
Found at i:57449 original size:68 final size:68
Alignment explanation
Indices: 57371--57509 Score: 278
Period size: 68 Copynumber: 2.0 Consensus size: 68
57361 AATAATTTTA
57371 TTGTAAAGTTGGAGGACCAAATAAATCATTATACTTATATTTTATTCAATTTATTAAGATAATAT
1 TTGTAAAGTTGGAGGACCAAATAAATCATTATACTTATATTTTATTCAATTTATTAAGATAATAT
57436 GAT
66 GAT
57439 TTGTAAAGTTGGAGGACCAAATAAATCATTATACTTATATTTTATTCAATTTATTAAGATAATAT
1 TTGTAAAGTTGGAGGACCAAATAAATCATTATACTTATATTTTATTCAATTTATTAAGATAATAT
57504 GAT
66 GAT
57507 TTG
1 TTG
57510 AATAAAATTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (68 bp):
TTGTAAAGTTGGAGGACCAAATAAATCATTATACTTATATTTTATTCAATTTATTAAGATAATAT
GAT
Found at i:58876 original size:23 final size:23
Alignment explanation
Indices: 58845--58888 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
58835 TGATAGTCTA
*
58845 AATACTAAAATAAAATAAATTTT
1 AATACTAAAATAAAAGAAATTTT
* *
58868 AATATTAAAGTAAAAGAAATT
1 AATACTAAAATAAAAGAAATT
58889 ATAAAGTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (23 bp):
AATACTAAAATAAAAGAAATTTT
Found at i:63258 original size:12 final size:12
Alignment explanation
Indices: 63241--63300 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
63231 CGTTTGTTTA
63241 ATGTTCACGAAC
1 ATGTTCACGAAC
63253 ATGTTCA--AAC
1 ATGTTCACGAAC
63263 ATGTTCACGAAC
1 ATGTTCACGAAC
* * *
63275 AT-ATAATTGAAC
1 ATGTTCA-CGAAC
63287 ATGTTCACGAAC
1 ATGTTCACGAAC
63299 AT
1 AT
63301 ATAATTGAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
10 10 0.26
11 2 0.05
12 24 0.63
13 2 0.05
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.28
Consensus pattern (12 bp):
ATGTTCACGAAC
Found at i:63292 original size:24 final size:24
Alignment explanation
Indices: 63260--63318 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
63250 AACATGTTCA
63260 AACATGTTCACGAACATATAATTG
1 AACATGTTCACGAACATATAATTG
63284 AACATGTTCACGAACATATAATTG
1 AACATGTTCACGAACATATAATTG
63308 AACATGTTCAC
1 AACATGTTCAC
63319 CATGAACACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (24 bp):
AACATGTTCACGAACATATAATTG
Found at i:66707 original size:30 final size:30
Alignment explanation
Indices: 66653--66714 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 30
66643 CCGTCCAATC
*
66653 ACTTAAATAAAAGGTTTTGAATAGTTTAGTG
1 ACTTAAATAAAA-GTTTGGAATAGTTTAGTG
66684 ACTTAAATGAAAA-TTTGGAATAGTTTAGTG
1 ACTTAAAT-AAAAGTTTGGAATAGTTTAGTG
66714 A
1 A
66715 TATTTTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 17 0.59
31 8 0.28
32 4 0.14
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (30 bp):
ACTTAAATAAAAGTTTGGAATAGTTTAGTG
Found at i:72847 original size:48 final size:48
Alignment explanation
Indices: 72776--72880 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
72766 GATCTTTACC
* ** * * * *
72776 TATCTTGATTTTAATTCATTCGATTTTATTAATGAGTTGATAATAATT
1 TATCTTGATTCTAACACATTCGATCTCATTAATGAGCTGATAACAATT
*
72824 TATCTTGATTCTAACACGTTCGATCTCATTAATGAGCTGATAACAATT
1 TATCTTGATTCTAACACATTCGATCTCATTAATGAGCTGATAACAATT
*
72872 T-TCATGATT
1 TATCTTGATT
72881 TATCAAATTA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
47 7 0.15
48 41 0.85
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (48 bp):
TATCTTGATTCTAACACATTCGATCTCATTAATGAGCTGATAACAATT
Found at i:73014 original size:18 final size:19
Alignment explanation
Indices: 72987--73037 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
72977 TTTATGATTC
*
72987 AATTAATAAAAATAAAT-A
1 AATTATTAAAAATAAATAA
*
73005 AATTATTAAAAATTAATTAA
1 AATTATTAAAAA-TAAATAA
*
73025 AAATATTAAAAAT
1 AATTATTAAAAAT
73038 TAAAAAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.39
19 5 0.18
20 12 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTATTAAAAATAAATAA
Found at i:73017 original size:10 final size:10
Alignment explanation
Indices: 73004--73039 Score: 56
Period size: 9 Copynumber: 3.6 Consensus size: 10
72994 AAAAATAAAT
73004 AAATTATTAA
1 AAATTATTAA
73014 AAATTAATTAA
1 AAATT-ATTAA
73025 AAA-TATTAA
1 AAATTATTAA
73034 AAATTA
1 AAATTA
73040 AAAAACTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.33
10 8 0.33
11 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATTATTAA
Found at i:73034 original size:28 final size:27
Alignment explanation
Indices: 72987--73043 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
72977 TTTATGATTC
*
72987 AATTAATAAAAATAAATAAATTATTAAA
1 AATTAATAAAAATAAATAAA-AATTAAA
*
73015 AATTAATTAAAAAT-ATTAAAAATTAAA
1 AATTAA-TAAAAATAAATAAAAATTAAA
73042 AA
1 AA
73044 ACTCTATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 8 0.31
28 11 0.42
29 7 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AATTAATAAAAATAAATAAAAATTAAA
Found at i:86239 original size:54 final size:55
Alignment explanation
Indices: 86169--86317 Score: 178
Period size: 54 Copynumber: 2.7 Consensus size: 55
86159 GTCAATTTTT
* *
86169 AAAGACGAAATTATATTATCATATTTGAAAAATAAATTGATC-GGTCGATCTTTA
1 AAAGACAAAATGATATTATCATATTTGAAAAATAAATTGATCAGGTCGATCTTTA
* *
86223 AAAGACAAAATGATATTATCATATTT-ATAAAGTAAATTGATCATATGTCGATCTTTA
1 AAAGACAAAATGATATTATCATATTTGA-AAAATAAATTGATC--AGGTCGATCTTTA
* * * *
86280 AAAGTCTAAATGATATTATCGTA-TTGCAAAATAAATTG
1 AAAGACAAAATGATATTATCATATTTGAAAAATAAATTG
86318 GCCGGTCTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
53 1 0.01
54 37 0.46
56 12 0.15
57 31 0.38
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.36
Consensus pattern (55 bp):
AAAGACAAAATGATATTATCATATTTGAAAAATAAATTGATCAGGTCGATCTTTA
Found at i:86249 original size:27 final size:26
Alignment explanation
Indices: 86219--86304 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 26
86209 TCGGTCGATC
86219 TTTAAAAGACAAAATGATATTATCATA
1 TTTAAAAG-CAAAATGATATTATCATA
* * * *
86246 TTTATAAAGTAAATTGATCATATGTCGATC
1 TTTA-AAAGCAAAATGAT-AT-TATC-ATA
* *
86276 TTTAAAAGTCTAAATGATATTATCGTA
1 TTTAAAAG-CAAAATGATATTATCATA
86303 TT
1 TT
86305 GCAAAATAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
27 14 0.32
28 9 0.20
29 9 0.20
30 12 0.27
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (26 bp):
TTTAAAAGCAAAATGATATTATCATA
Done.