Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010238.1 Corchorus capsularis cultivar CVL-1 contig10259, 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: 58045
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10167 original size:2 final size:2
Alignment explanation
Indices: 10162--10187 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10152 ATATGTTGAG
10162 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
10188 GTAATCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24988 original size:15 final size:15
Alignment explanation
Indices: 24961--25030 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
24951 TATGGAAAGT
24961 ACTCT-CTTCGGAATC
1 ACTCTCCTT-GGAATC
*
24976 ACTCTCCTTGGAATG
1 ACTCTCCTTGGAATC
* * * * *
24991 ATTCTTCATGGGGAGC
1 ACTC-TCCTTGGAATC
*
25007 ACTCTCCTGGGAATC
1 ACTCTCCTTGGAATC
25022 ACTCTCCTT
1 ACTCTCCTT
25031 AGAAAACACT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
15 29 0.71
16 12 0.29
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (15 bp):
ACTCTCCTTGGAATC
Found at i:25042 original size:16 final size:16
Alignment explanation
Indices: 25021--25051 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25011 TCCTGGGAAT
25021 CACTCTCCTTAGAAAA
1 CACTCTCCTTAGAAAA
*
25037 CACTCTCGTTAGAAA
1 CACTCTCCTTAGAAA
25052 GTAACAAACG
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:0.35, C:0.29, G:0.10, T:0.26
Consensus pattern (16 bp):
CACTCTCCTTAGAAAA
Found at i:39894 original size:54 final size:54
Alignment explanation
Indices: 39836--39944 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
39826 TAACTGAACG
39836 TGATCGTCAATCACTGAAACTAAGAATTCAGTACCCTAACAAATAACAGTGAGA
1 TGATCGTCAATCACTGAAACTAAGAATTCAGTACCCTAACAAATAACAGTGAGA
* *
39890 TGATCGTCGATCACTGAAACTAAGAATTTAGTACCCTAACAAATAACAGTGAGA
1 TGATCGTCAATCACTGAAACTAAGAATTCAGTACCCTAACAAATAACAGTGAGA
39944 T
1 T
39945 TTTTCGTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (54 bp):
TGATCGTCAATCACTGAAACTAAGAATTCAGTACCCTAACAAATAACAGTGAGA
Found at i:51337 original size:60 final size:58
Alignment explanation
Indices: 51260--51429 Score: 198
Period size: 60 Copynumber: 2.9 Consensus size: 58
51250 GACTTTTCGG
* * * *
51260 TTAA-TTGCTCAAATAAGGGTTTAATATTTGTGAAAATGCTCAAATGAGGGCCCGATCTC
1 TTAATTTGCCCAAATAAGGGTCTAAT-TTT-CGAAAATGCTCAAATAAGGGCCCGATCTC
* * * * *
51319 TTAATTTGGCTAAATAAGGGCCTAATGTTATCGAAAATTCTCAAATAAGGGCCCGATCTT
1 TTAATTTGCCCAAATAAGGGTCTAAT-TT-TCGAAAATGCTCAAATAAGGGCCCGATCTC
*
51379 TTAATTTGCCCAAATAAGGGTCTAAGTTATCGAAAATGCTCAAATAAGGGC
1 TTAATTTGCCCAAATAAGGGTCTAA-TTTTCGAAAATGCTCAAATAAGGGC
51430 ATGGTGTCAA
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 25 0.27
60 66 0.71
61 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (58 bp):
TTAATTTGCCCAAATAAGGGTCTAATTTTCGAAAATGCTCAAATAAGGGCCCGATCTC
Found at i:51570 original size:60 final size:60
Alignment explanation
Indices: 51471--51623 Score: 189
Period size: 60 Copynumber: 2.5 Consensus size: 60
51461 TTCGACGCCA
* ** *
51471 AACCCTTATCTGAGCATTTTCGATAACGTTAGCCCCTTATTTGGATAAATTAAAAGATCG
1 AACCCTTATTTGAGCATTTTTAATAACGTTAGGCCCTTATTTGGATAAATTAAAAGATCG
* * ** * *
51531 AGCCCTTATTTGAGCATTTTTAATAACATTAGGGTCTTATTTGGTTAAATTAAAAGATTG
1 AACCCTTATTTGAGCATTTTTAATAACGTTAGGCCCTTATTTGGATAAATTAAAAGATCG
* * *
51591 AACTCTTATTTGAACATTTTTAAAAACGTTAGG
1 AACCCTTATTTGAGCATTTTTAATAACGTTAGG
51624 TCATCATTTG
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 78 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (60 bp):
AACCCTTATTTGAGCATTTTTAATAACGTTAGGCCCTTATTTGGATAAATTAAAAGATCG
Found at i:53197 original size:135 final size:140
Alignment explanation
Indices: 53041--53711 Score: 972
Period size: 135 Copynumber: 4.7 Consensus size: 140
53031 AAAAATATTG
53041 AATT-TAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATAT
1 AATTATAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATAT
*
53105 ATCCAAGTTTTTAATG-AAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAAC
66 ATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAAA
53169 T-A-AA-AT-
131 TAATAATATA
*
53175 AATTATAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATT-TAAAATTTTAATAT
1 AATTATAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATAT
*
53239 ATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAA
66 ATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAAA
53304 TAAAATAATTATAAA
131 T--AATAA-TAT--A
*
53319 AATATGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATACTAAAAAATTTT
1 AAT-T--A--TAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTT
*
53384 AATATATCCAATTTTTTAATG-AAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGT
61 AATATATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGT
*
53448 AAAACT-A-AA-AT-
126 AAAAATAATAATATA
*
53459 AATTATAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATT-TAAAATTTTAATAT
1 AATTATAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATAT
*
53523 ATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAA
66 ATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAAA
53588 TAAAATAATTATAAA
131 T--AATAA-TAT--A
***
53603 AATATGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAATTTTTTT
1 AAT-T--A--TAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTT
53668 AATATATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAAT
61 AATATATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAAT
53712 GAAGTAATTA
Statistics
Matches: 487, Mismatches: 17, Indels: 50
0.88 0.03 0.09
Matches are distributed among these distances:
134 61 0.13
135 183 0.38
137 1 0.00
138 2 0.00
139 5 0.01
140 3 0.01
141 4 0.01
143 2 0.00
144 6 0.01
145 4 0.01
146 1 0.00
147 2 0.00
149 136 0.28
150 77 0.16
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.35
Consensus pattern (140 bp):
AATTATAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATAT
ATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAAA
TAATAATATA
Found at i:53307 original size:14 final size:14
Alignment explanation
Indices: 53263--53309 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
53253 TGAAAAATAG
53263 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
* * * *
53277 TAAACT-TTTAAAT
1 TAAAATGGTAAAAA
53290 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
53304 TAAAAT
1 TAAAAT
53310 AATTATAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (14 bp):
TAAAATGGTAAAAA
Found at i:53339 original size:149 final size:149
Alignment explanation
Indices: 53175--53711 Score: 872
Period size: 149 Copynumber: 3.7 Consensus size: 149
53165 AAACTAAAAT
53175 AATTATAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATA
1 AATT-TAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATA
53240 TCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAAT
65 TCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAAT
53305 AAAATAATTATAAAAATATG
130 AAAATAATTATAAAAATATG
**
53325 AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATACTAAAAAATTTTAATATA
1 AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATA-TTTAAAATTTTAATATA
* * *
53390 TCCAATTTTTTAATG-AAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAACT
65 TCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAAT
53454 ---A-AA--AT---AAT-T-
130 AAAATAATTATAAAAATATG
53463 -A--TAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATAT
1 AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATAT
53525 CCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAATA
66 CCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAATA
53590 AAATAATTATAAAAATATG
131 AAATAATTATAAAAATATG
*
53609 AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATA-TTAAATTTTTTTAATAT
1 AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAA--ATTTTAATAT
53673 ATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAAT
64 ATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAAT
53712 GAAGTAATTA
Statistics
Matches: 358, Mismatches: 11, Indels: 36
0.88 0.03 0.09
Matches are distributed among these distances:
134 29 0.08
135 90 0.25
137 1 0.00
138 1 0.00
139 3 0.01
140 3 0.01
141 2 0.01
143 2 0.01
144 3 0.01
145 3 0.01
146 1 0.00
147 1 0.00
148 5 0.01
149 133 0.37
150 81 0.23
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (149 bp):
AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATAT
CCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAATA
AAATAATTATAAAAATATG
Found at i:53512 original size:284 final size:284
Alignment explanation
Indices: 52990--53711 Score: 1363
Period size: 284 Copynumber: 2.5 Consensus size: 284
52980 AGTCAATTAC
* *
52990 AATAACCTTTAAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATA-TGAATTTAATTAAATG
53055 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
65 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
53120 GAAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAACTAAAATAATTATAATT
130 GAAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAACTAAAATAATTATAATT
53185 AAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATATCCAAGTTTT
195 AAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATATCCAAGTTTT
53250 TAATGAAAAATAGTAAAATGGTAAA
260 TAATGAAAAATAGTAAAATGGTAAA
53275 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATGAATTTAATTAAATGA
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATGAATTTAATTAAATGA
* *
53340 AAATAGAGTTTTTAGTAGAATCAAACTATATACTAAAAAATTTTAATATATCCAATTTTTTAATG
66 AAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATG
53405 AAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAACTAAAATAATTATAATTA
131 AAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAACTAAAATAATTATAATTA
53470 AATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATATCCAAGTTTTT
196 AATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATATCCAAGTTTTT
53535 AATGAAAAATAGTAAAATGGTAAA
261 AATGAAAAATAGTAAAATGGTAAA
53559 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATGAATTTAATTAAATGA
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATGAATTTAATTAAATGA
***
53624 AAATAGAGTTTTTAGTAGAATCAAACTATATATTAAATTTTTTTAATATATCCAAGTTTTTAATG
66 AAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATG
53689 AAAAATAGTAAAATGGTAAAAAT
131 -AAAATAGTAAAATGGTAAAAAT
53712 GAAGTAATTA
Statistics
Matches: 427, Mismatches: 9, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
284 359 0.84
285 68 0.16
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (284 bp):
AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATGAATTTAATTAAATGA
AAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATG
AAAATAGTAAAATGGTAAAAATAAACTTTCAAATTAAAATGGTAAAACTAAAATAATTATAATTA
AATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTTAAAATTTTAATATATCCAAGTTTTT
AATGAAAAATAGTAAAATGGTAAA
Found at i:53591 original size:14 final size:14
Alignment explanation
Indices: 53547--53593 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
53537 TGAAAAATAG
53547 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
* * * *
53561 TAAACT-TTTAAAT
1 TAAAATGGTAAAAA
53574 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
53588 TAAAAT
1 TAAAAT
53594 AATTATAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (14 bp):
TAAAATGGTAAAAA
Found at i:54235 original size:27 final size:27
Alignment explanation
Indices: 54199--54250 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
54189 ACGCTCCAAT
*
54199 AATATTTAATGTAGAGCAAAAAGTTCC
1 AATAATTAATGTAGAGCAAAAAGTTCC
54226 AATAATTAATGTAGAGCAAAAAGTT
1 AATAATTAATGTAGAGCAAAAAGTT
54251 GTGGATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (27 bp):
AATAATTAATGTAGAGCAAAAAGTTCC
Found at i:55263 original size:30 final size:31
Alignment explanation
Indices: 55192--55266 Score: 82
Period size: 34 Copynumber: 2.4 Consensus size: 31
55182 GATAAATAAA
* *
55192 AATTA-ATTAAACACCATATTTACCCTTGCC
1 AATTATATGAAACACCATATTTACCCTTGAC
*
55222 AATTTACATATGAAACACCATATTTA-CCTTTAC
1 AA-TT--ATATGAAACACCATATTTACCCTTGAC
55255 AATTATATGAAA
1 AATTATATGAAA
55267 TTACATCCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 10 0.26
31 2 0.05
32 2 0.05
33 8 0.21
34 16 0.42
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (31 bp):
AATTATATGAAACACCATATTTACCCTTGAC
Found at i:56518 original size:150 final size:147
Alignment explanation
Indices: 56308--56605 Score: 510
Period size: 150 Copynumber: 2.0 Consensus size: 147
56298 AAGGATATGG
*
56308 GCTAATAGTAATATATAGTACAATCAAAAAATAAAAAGATCCGAATAATCGATAAGTGATTGGTT
1 GCTAATAGTAATATATAGCACAATCAAAAAATAAAAAGATCCGAATAATCGATAAGTGATTGGTT
*
56373 GAAATTGCAAGCGACCTTATAAGGTTGGGGGGTATGTAAGTAGTTACAAGGTCTTCAGATTTTAC
66 GAAATTGCAAGCGACCTTATAA-G--GGGGGGTATGTAAGTAGTTACAAGGTCTTCA-ACTTTAC
56438 TATAGAAACTTGTTTGGTTTA
127 TATAGAAACTTGTTTGGTTTA
*
56459 GCTAATAGTAATATATAGCACAATC-AAAAATAAAAAGA-CCTGATTAATCGATAAGTGATTGGT
1 GCTAATAGTAATATATAGCACAATCAAAAAATAAAAAGATCC-GAATAATCGATAAGTGATTGGT
56522 TGAAATTGCAAGCGACCTTATAAGGGGGGGTATGTAAGTAGTTACAAGGTCTTCAACTTTACTAT
65 TGAAATTGCAAGCGACCTTATAAGGGGGGGTATGTAAGTAGTTACAAGGTCTTCAACTTTACTAT
56587 AGAAACTTGTTTGGTTTA
130 AGAAACTTGTTTGGTTTA
56605 G
1 G
56606 TTTGTTATAT
Statistics
Matches: 143, Mismatches: 3, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
146 28 0.20
147 31 0.22
149 3 0.02
150 57 0.40
151 24 0.17
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (147 bp):
GCTAATAGTAATATATAGCACAATCAAAAAATAAAAAGATCCGAATAATCGATAAGTGATTGGTT
GAAATTGCAAGCGACCTTATAAGGGGGGGTATGTAAGTAGTTACAAGGTCTTCAACTTTACTATA
GAAACTTGTTTGGTTTA
Done.