Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014541.1 Corchorus olitorius cultivar O-4 contig14574, 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: 71917
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:584 original size:2 final size:2
Alignment explanation
Indices: 577--606 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
567 CCAAGCTTAC
577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
607 GACTATCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7223 original size:23 final size:23
Alignment explanation
Indices: 7202--7274 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
7192 TATACTTAAC
*
7202 TTAAAATTACAACTTAAATTAAG
1 TTAAAATTACAACTTAAATAAAG
*
7225 TTAAAA--ACAACTTAAAGAAAG
1 TTAAAATTACAACTTAAATAAAG
*
7246 TTAAAATTACAACTTAAATAAAT
1 TTAAAATTACAACTTAAATAAAG
7269 TTAAAA
1 TTAAAA
7275 AACAAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.43
23 25 0.57
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (23 bp):
TTAAAATTACAACTTAAATAAAG
Found at i:7236 original size:21 final size:21
Alignment explanation
Indices: 7210--7275 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 21
7200 ACTTAAAATT
*
7210 ACAACTTAAATTAAGTTAAAA
1 ACAACTTAAATAAAGTTAAAA
*
7231 ACAACTTAAAGAAAGTTAAAA
1 ACAACTTAAATAAAGTTAAAA
*
7252 TTACAACTTAAATAAATTTAAAA
1 --ACAACTTAAATAAAGTTAAAA
7275 A
1 A
7276 ACAAAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 20 0.51
23 19 0.49
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (21 bp):
ACAACTTAAATAAAGTTAAAA
Found at i:7784 original size:15 final size:16
Alignment explanation
Indices: 7756--7785 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7746 GTTCATTTCG
7756 TCATTTTCTTTCTTTT
1 TCATTTTCTTTCTTTT
7772 TCATTTT-TTTCTTT
1 TCATTTTCTTTCTTT
7786 CTTCCTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TCATTTTCTTTCTTTT
Found at i:8984 original size:136 final size:133
Alignment explanation
Indices: 8621--9522 Score: 1261
Period size: 136 Copynumber: 6.6 Consensus size: 133
8611 CACAATTTGA
* * * * *
8621 GGAACAGATAAGGATTCAAA-CAACGGTCACATTTCAATCTCACTTTGAATCCAATGGTTGGATT
1 GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTT-AATCCAACGGTT-GATT
* * * * * * *
8685 GAGATAATGTTAAATTATCATCAATTTATTGACTGTTGTGTTATATTTTCTGACATATCTTGGAT
64 GAGATAA-GTTAGATTCTC-TGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGAT
8750 ATTGTGT
127 ATTGTGT
* *** * *
8757 GGAAGAGATAA-GTTTTTCATCAACGGTCACATTTGAATC-CAACTTTTATCCAACGGTTGGATT
1 GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTC-ACTTTAATCCAACGGTT-GATT
* * *
8820 AAGATAATGTTAGATTCTCTGAAATTATTGGCTATTGTATTAGATTTTCTGACATAACTTGGATA
64 GAGATAA-GTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATA
8885 TTGTGT
128 TTGTGT
8891 GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTCTTAATCCAACGGTTGATTT
1 GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACT-TTAATCCAACGGTTGA-TT
8956 GAGATAAGATTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATA
64 GAGATAAG-TTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATA
9021 TTGTGT
128 TTGTGT
* *
9027 GGAAGAGATAACGATTCAAATTAGCGGTCACATTTGAATCTCACTTTTAATCCAATGGTTGAATT
1 GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCAC-TTTAATCCAACGGTTG-ATT
* * *
9092 GAAATAAGGTTAGATTCTCTGAAATTATTGGCTACTGTGTTAGATTTTCTGACATATCTTGGACA
64 GAGATAA-GTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATA
9157 TTGTGT
128 TTGTGT
*
9163 GGAAGAGATAACGATTCAAATTAACAGTCACATTTGAATCTCACTTTTAATCCAACGGTTGAATT
1 GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCAC-TTTAATCCAACGGTTG-ATT
*
9228 GAGATAAGCTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGGCATATCTTGGATA
64 GAGATAAG-TTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATA
9293 TTGTGT
128 TTGTGT
* **
9299 GGAAGAGATGACGATTCAAATTAACGGTCACATTTGAATCTCACTTTCAATCCAACAATTGAATT
1 GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTT-AATCCAACGGTTG-ATT
* * *
9364 GAGATAAGGTTAGATTCTCTGAAATTATTTGCTATTGTGTTAGATTTTCTGACATATTTTAGATA
64 GAGATAA-GTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATA
9429 TTGTGT
128 TTGTGT
9435 GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTATTAATCCAACGGTTAGATT
1 GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACT-TTAATCCAACGGTT-GATT
* *
9500 GAGATAGGATTAGATTCTGTGAA
64 GAGATAAG-TTAGATTCTCTGAA
9523 GATAAAATTA
Statistics
Matches: 698, Mismatches: 52, Indels: 32
0.89 0.07 0.04
Matches are distributed among these distances:
134 56 0.08
135 70 0.10
136 565 0.81
137 7 0.01
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (133 bp):
GGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTAATCCAACGGTTGATTGA
GATAAGTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATATTG
TGT
Found at i:9001 original size:30 final size:31
Alignment explanation
Indices: 8965--9026 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
8955 TGAGATAAGA
*
8965 TTAGATTCTCTGAAAT-TATTGGCTATTGTG
1 TTAGATTCTCTGAAATATATTGGATATTGTG
* * *
8995 TTAGATTTTCTGACATATCTTGGATATTGTG
1 TTAGATTCTCTGAAATATATTGGATATTGTG
9026 T
1 T
9027 GGAAGAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (31 bp):
TTAGATTCTCTGAAATATATTGGATATTGTG
Found at i:19160 original size:107 final size:108
Alignment explanation
Indices: 19025--19243 Score: 350
Period size: 107 Copynumber: 2.0 Consensus size: 108
19015 TAACAAGTTG
* *
19025 ATCGGCTCACGCTGGCGCGTCGAGCATTCTTGATTTGTGGCTAGCAAATCATTTTAGTTTTAGAG
1 ATCGGCTCACGCTGGCGCGTCGAGCATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAG
*
19090 -TTTTTTTCTCTCGGTTTTTATCATATATGTGAGTAGGTGGTT
66 TTTTTTTTCTCTCGGTTCTTATCATATATGTGAGTAGGTGGTT
*
19132 ATCGGCTCGCGCTGGCGCGTCGAGCATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAG
1 ATCGGCTCACGCTGGCGCGTCGAGCATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAG
* *
19197 TTTTTTTTTTTCTCTCGGTTCTTATCATATATGTGGGTATGTGGTT
66 ---TTTTTTTTCTCTCGGTTCTTATCATATATGTGAGTAGGTGGTT
19243 A
1 A
19244 GGGAATTCGA
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
107 62 0.61
111 40 0.39
ACGTcount: A:0.17, C:0.16, G:0.25, T:0.42
Consensus pattern (108 bp):
ATCGGCTCACGCTGGCGCGTCGAGCATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAG
TTTTTTTTCTCTCGGTTCTTATCATATATGTGAGTAGGTGGTT
Found at i:40858 original size:19 final size:18
Alignment explanation
Indices: 40820--40858 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40810 GGTTCTTGTT
* *
40820 TTTGTGCAATTGATCTAA
1 TTTGTGCAATTAACCTAA
40838 TTTGTGCAATTAACCCTAA
1 TTTGTGCAATTAA-CCTAA
40857 TT
1 TT
40859 GGAGATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (18 bp):
TTTGTGCAATTAACCTAA
Found at i:51464 original size:32 final size:31
Alignment explanation
Indices: 51443--51502 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
51433 TTGCAATAGA
*
51443 AATTTCAAAACTTGTAGATTAAGACTCAAGAT
1 AATTTCAAAACTTGTAGATTAAGAAT-AAGAT
*
51475 AATTTCAAAACTTGTAGATTAAGGATAA
1 AATTTCAAAACTTGTAGATTAAGAATAA
51503 AAACTTGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (31 bp):
AATTTCAAAACTTGTAGATTAAGAATAAGAT
Found at i:52882 original size:16 final size:16
Alignment explanation
Indices: 52861--52892 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52851 TTTATAATTT
52861 TTATTAATAATATATA
1 TTATTAATAATATATA
*
52877 TTATTATTAATATATA
1 TTATTAATAATATATA
52893 AATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:52907 original size:19 final size:18
Alignment explanation
Indices: 52861--52907 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
52851 TTTATAATTT
* *
52861 TTATTAATAATATATATTA
1 TTATTAAT-ATATAAATAA
52880 TTATTAATATATAAATAA
1 TTATTAATATATAAATAA
52898 TTATATAATA
1 TTAT-TAATA
52908 AATGAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATTAATATATAAATAA
Found at i:52978 original size:35 final size:35
Alignment explanation
Indices: 52933--53009 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
52923 GATTATTATA
*
52933 TAAACGAACAATAAACGAGTCTGTTCGTGAACACT
1 TAAACGAACAATAAACGAGTATGTTCGTGAACACT
*
52968 TAAATGAACAATAAACGAGTATGTTCGTGAACA--
1 TAAACGAACAATAAACGAGTATGTTCGTGAACACT
53001 TAAACGAAC
1 TAAACGAAC
53010 TGAACATATC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
33 8 0.21
35 31 0.79
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (35 bp):
TAAACGAACAATAAACGAGTATGTTCGTGAACACT
Found at i:56360 original size:58 final size:58
Alignment explanation
Indices: 56262--56373 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
56252 ATTAATCAAA
*
56262 TATCAAGTGACATGGTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCGAGGCT
1 TATCAAGTGACATGGTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCT
* * *
56320 TATCGAGTGACATGTTTTTTTATTAGATGTC-T-AAAAAAGACGTTTTAGGACCGA
1 TATCAAGTGACATG-GTCTTTATTAGATG-CATAAAAAAAGACGTTTTAGGACCGA
56374 TGCATGATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 34 0.71
59 13 0.27
60 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACATGGTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCT
Found at i:57686 original size:36 final size:36
Alignment explanation
Indices: 57639--57708 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
57629 TTCAATAACC
* *
57639 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
57675 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
57709 CCAAAATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:58614 original size:205 final size:199
Alignment explanation
Indices: 58226--58634 Score: 665
Period size: 205 Copynumber: 2.0 Consensus size: 199
58216 GCTTAATAAC
* *
58226 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
58291 GATACAATACATTATTATTATATATAAAACTATACCAAAAAAAAGTTGAACATTAGTGCTTGATT
66 GATACAATACACTATTATTATATATAAAACTATACCAAAAAAAAGTTGAACATTAGTGCTTGATT
58356 TATTAAATTAAACTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGA
131 TATTAAATTAAACTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGA
58421 TTTA
196 TTTA
* *
58425 TTTATCAATGATGAACGTTGTTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGTATAA
1 TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* * * *
58490 GATACAACATATTACTATTATATATATATAGAACTATACCAAAAAAATTAGTTGAATATTAGTGG
66 GATAC-A-ATA-CACTATTAT-TATATATAAAACTATACCAAAAAAA--AGTTGAACATTAGTGC
* *
58555 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTGAAAATTATAAAAGATATTAAAG
125 TTGATTTATTAAATTAAACTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
58620 ATCCGATTTA
190 ATCCGATTTA
58630 TTTAT
1 TTTAT
58635 TATTAAGGAA
Statistics
Matches: 193, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
199 66 0.34
200 1 0.01
201 3 0.02
202 7 0.04
203 24 0.12
205 92 0.48
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (199 bp):
TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAATACACTATTATTATATATAAAACTATACCAAAAAAAAGTTGAACATTAGTGCTTGATT
TATTAAATTAAACTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGA
TTTA
Found at i:58740 original size:24 final size:23
Alignment explanation
Indices: 58707--58752 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
58697 ACGTTTGCAC
58707 AAATAGCTAAGAATTTGAATTAAA
1 AAATAGCTAAGAATTT-AATTAAA
*
58731 AAATATCTAAGAATTTAATTAA
1 AAATAGCTAAGAATTTAATTAA
58753 TATAAGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (23 bp):
AAATAGCTAAGAATTTAATTAAA
Found at i:58808 original size:39 final size:40
Alignment explanation
Indices: 58743--58823 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
58733 ATATCTAAGA
*
58743 ATTTAATTAATATAAGGATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAGGATTTCAGTTATTATATATATTAC
* * *
58782 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAGGATTTCAGTTATTATATATATTAC
58822 AT
1 AT
58824 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATATAAGGATTTCAGTTATTATATATATTAC
Found at i:60234 original size:42 final size:40
Alignment explanation
Indices: 60155--60235 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 40
60145 AAACATTCAA
* * *
60155 TTTTCCTTTTGAATTTTTATGATTTTGTTTTGCTGCACTG
1 TTTTCCTTTTGAATTTTTATGATTCTGGTTTACTGCACTG
*
60195 TTTTCCCTTTTGAATTTTGTATGATTCTGGTTTATTGCACT
1 TTTT-CCTTTTGAATTTT-TATGATTCTGGTTTACTGCACT
60236 ATATATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 4 0.11
41 13 0.37
42 18 0.51
ACGTcount: A:0.14, C:0.14, G:0.15, T:0.58
Consensus pattern (40 bp):
TTTTCCTTTTGAATTTTTATGATTCTGGTTTACTGCACTG
Done.