Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015841.1 Corchorus olitorius cultivar O-4 contig15874, 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: 31172
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:394 original size:31 final size:30
Alignment explanation
Indices: 306--394 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
296 CTTAGTTAAC
306 TCCACTTCA-GGACTCAATTGCT-CATTTT-T
1 TCCACTTCAGGGAC-CAATTGCTAC-TTTTAT
* *
335 T-CACTTGAGGGACCAATTTGCTAGTTTTAT
1 TCCACTTCAGGGACCAA-TTGCTACTTTTAT
365 TCCACTTCAGGGACCAATTGCGTACTTTTA
1 TCCACTTCAGGGACCAATTGC-TACTTTTA
395 CTGTAGTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
28 9 0.18
29 14 0.28
30 6 0.12
31 21 0.42
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (30 bp):
TCCACTTCAGGGACCAATTGCTACTTTTAT
Found at i:1361 original size:490 final size:490
Alignment explanation
Indices: 441--1381 Score: 1819
Period size: 490 Copynumber: 1.9 Consensus size: 490
431 TAGATCTGAT
441 CTAGAATTATGACCCTTACTTTATTTCGGGTTAGGAATTCGTATTACATTATTTATGATGAAATT
1 CTAGAATTATGACCCTTACTTTATTTCGGGTTAGGAATTCGTATTACATTATTTATGATGAAATT
506 TTATTTTTTAGAGCAATGCTAGTTGCTCCGCCTAATTTTACCATATGAACGTCCCAATCGATGAA
66 TTATTTTTTAGAGCAATGCTAGTTGCTCCGCCTAATTTTACCATATGAACGTCCCAATCGATGAA
* *
571 AAAATTATTATATTGGATTGTCCCACCACGTCATGTATGGGACTAACCAATAGAATTGTGTCATG
131 AAAATTATTAGATTGGATTGTCCCACCACGTCATGTATGAGACTAACCAATAGAATTGTGTCATG
636 TCAAATGAACTTCTAAATTTAGACTCAATTTTAGCTCAGGGTTTAACCCCCTTTTAAAATAATCA
196 TCAAATGAACTTCTAAATTTAGACTCAATTTTAGCTCAGGGTTTAACCCCCTTTTAAAATAATCA
701 TGCTTAGGGTAAGTCCCCAAATTTGAGATATTATTAGGATAGGGTTTTAAAAAATTGATGAGTTG
261 TGCTTAGGGTAAGTCCCCAAATTTGAGATATTATTAGGATAGGGTTTTAAAAAATTGATGAGTTG
*
766 TCATCATATTATTGATTAGTCCCATGGATGACGTGGTGGGTTAGTTCCACCTAATAATTTCTCCG
326 TCATCATATTATTGATTAGTCCCATGGATGACGTGGTGGGCTAGTTCCACCTAATAATTTCTCCG
831 TCAGACGGGATATTTTTGCGAGTCAAATAGACGGGTTGTGTAGCATTACTCGATTTAAAATATGT
391 TCAGACGGGATATTTTTGCGAGTCAAATAGACGGGTTGTGTAGCATTACTCGATTTAAAATATGT
896 GTAGCCTCTCCCTTCAATAGATCTGATCGGTAACC
456 GTAGCCTCTCCCTTCAATAGATCTGATCGGTAACC
*
931 CTAGAATTATGACCTTTACTTTATTTCGGGTTAGGAATTCGTATTACATTATTTATGATGAAATT
1 CTAGAATTATGACCCTTACTTTATTTCGGGTTAGGAATTCGTATTACATTATTTATGATGAAATT
996 TTATTTTTTAGAGCAATGCTAGTTGCTCCGCCTAATTTTACCATATGAACGTCCCAATCGATGAA
66 TTATTTTTTAGAGCAATGCTAGTTGCTCCGCCTAATTTTACCATATGAACGTCCCAATCGATGAA
1061 AAAATTATTAGATTGGATTGTCCCACCACGTCATGTATGAGACTAACCAATAGAATTGTGTCATG
131 AAAATTATTAGATTGGATTGTCCCACCACGTCATGTATGAGACTAACCAATAGAATTGTGTCATG
* *
1126 TCAAATGAACTTCTAAATTTAGGCTCAATTTTAGCTTAGGGTTTAACCCCCTTTTAAAATAATCA
196 TCAAATGAACTTCTAAATTTAGACTCAATTTTAGCTCAGGGTTTAACCCCCTTTTAAAATAATCA
1191 TGCTTAGGGTAAGTCCCCAAATTTGAGATATTATTAGGATAGGGTTTTAAAAAATTGATGAGTTG
261 TGCTTAGGGTAAGTCCCCAAATTTGAGATATTATTAGGATAGGGTTTTAAAAAATTGATGAGTTG
*
1256 TCATCATATTATTGATTAGTCCCATGGATGACGTGGTGGGCTAGTTCCACCTCATAATTTCTCCG
326 TCATCATATTATTGATTAGTCCCATGGATGACGTGGTGGGCTAGTTCCACCTAATAATTTCTCCG
1321 TCAGACGGGATATTTTTGCGAGTCAAATAGACGGGTTGTGTAGCATTACTCGATTTAAAAT
391 TCAGACGGGATATTTTTGCGAGTCAAATAGACGGGTTGTGTAGCATTACTCGATTTAAAAT
1382 TTATTTTTGT
Statistics
Matches: 444, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
490 444 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (490 bp):
CTAGAATTATGACCCTTACTTTATTTCGGGTTAGGAATTCGTATTACATTATTTATGATGAAATT
TTATTTTTTAGAGCAATGCTAGTTGCTCCGCCTAATTTTACCATATGAACGTCCCAATCGATGAA
AAAATTATTAGATTGGATTGTCCCACCACGTCATGTATGAGACTAACCAATAGAATTGTGTCATG
TCAAATGAACTTCTAAATTTAGACTCAATTTTAGCTCAGGGTTTAACCCCCTTTTAAAATAATCA
TGCTTAGGGTAAGTCCCCAAATTTGAGATATTATTAGGATAGGGTTTTAAAAAATTGATGAGTTG
TCATCATATTATTGATTAGTCCCATGGATGACGTGGTGGGCTAGTTCCACCTAATAATTTCTCCG
TCAGACGGGATATTTTTGCGAGTCAAATAGACGGGTTGTGTAGCATTACTCGATTTAAAATATGT
GTAGCCTCTCCCTTCAATAGATCTGATCGGTAACC
Found at i:1594 original size:15 final size:15
Alignment explanation
Indices: 1574--1602 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1564 TCTTTAAAGT
1574 TAAATCTTACAACGA
1 TAAATCTTACAACGA
1589 TAAATCTTACAACG
1 TAAATCTTACAACG
1603 GGTAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (15 bp):
TAAATCTTACAACGA
Found at i:2010 original size:17 final size:18
Alignment explanation
Indices: 1985--2020 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1975 GCCACGTGTC
*
1985 TTCTCTTTTT-TTCTTTT
1 TTCTATTTTTATTCTTTT
2002 TTCTATTTTTATTCTTTT
1 TTCTATTTTTATTCTTTT
2020 T
1 T
2021 AGTAAGTTTA
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:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (18 bp):
TTCTATTTTTATTCTTTT
Found at i:4145 original size:20 final size:20
Alignment explanation
Indices: 4105--4144 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4095 ATATTTCTAC
4105 TCATTCTTTTTAAGTTATTT
1 TCATTCTTTTTAAGTTATTT
4125 TCATTCTTTTTAAGTT-TTT
1 TCATTCTTTTTAAGTTATTT
4144 T
1 T
4145 TTTTTCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (20 bp):
TCATTCTTTTTAAGTTATTT
Found at i:6145 original size:224 final size:226
Alignment explanation
Indices: 5754--6203 Score: 859
Period size: 224 Copynumber: 2.0 Consensus size: 226
5744 AATATCGTAC
5754 AAGTTGATCGGCTCGCGCTGGCGCGTCGAGTATTCTTGATTTGTGGCTAACAAATATTCTAGTTA
1 AAGTTGATCGGCTCGCGCTGGCGCGTCGAGTATTCTTGATTTGTGGCTAACAAATATTCTAGTTA
5819 TAGAGATTTTTTTTTTCTCAGTTCTTATGATATATGTGAGTAGGTGGTTAGCAAATTCGATATTT
66 TAGAGATTTTTTTTTTCTCAGTTCTTATGATATATGTGAGTAGGTGGTTAGCAAATTCGATATTT
*
5884 TGAGCAGGTCTTATAATTGAAGAATTAATCTAGCAAAGTAAAATAATAGTGCCTTAAAACATGCT
131 TGAGCAGGTCTTAAAATTGAAGAATTAATCTAGCAAAGTAAAATAATAGTGCCTTAAAACATGCT
*
5949 GTTGTAG-AAAATAAAAGTTTTTATAGTTGG
196 GTTGTAGAAAAATAAAAATTTTTATAGTTGG
*
5979 AAGTTGATCGGCTCGCGCTGGCGCGTCGAGTATTTTTGATTTGTGGCTAACAAATATTCTAGTTA
1 AAGTTGATCGGCTCGCGCTGGCGCGTCGAGTATTCTTGATTTGTGGCTAACAAATATTCTAGTTA
6044 TAGAG-TTTTTTTTTTCTCAGTTCTTATGATATATGTGAGTAGGTGGTTAGCAAATTCGATATTT
66 TAGAGATTTTTTTTTTCTCAGTTCTTATGATATATGTGAGTAGGTGGTTAGCAAATTCGATATTT
6108 TGAGCAGGTCTTAAAATTGAAGAATTAATCTAGCAAAGTAAAATAATAGTGCCTTAAAACATGCT
131 TGAGCAGGTCTTAAAATTGAAGAATTAATCTAGCAAAGTAAAATAATAGTGCCTTAAAACATGCT
6173 GTTGTAGAAAAATAAAAATTTTTATAGTTGG
196 GTTGTAGAAAAATAAAAATTTTTATAGTTGG
6204 TGTTGCTATC
Statistics
Matches: 221, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
224 130 0.59
225 91 0.41
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (226 bp):
AAGTTGATCGGCTCGCGCTGGCGCGTCGAGTATTCTTGATTTGTGGCTAACAAATATTCTAGTTA
TAGAGATTTTTTTTTTCTCAGTTCTTATGATATATGTGAGTAGGTGGTTAGCAAATTCGATATTT
TGAGCAGGTCTTAAAATTGAAGAATTAATCTAGCAAAGTAAAATAATAGTGCCTTAAAACATGCT
GTTGTAGAAAAATAAAAATTTTTATAGTTGG
Found at i:8423 original size:20 final size:20
Alignment explanation
Indices: 8398--8436 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
8388 GAATTGTTAC
8398 ATATATATACT-TAATTATAT
1 ATATATATA-TATAATTATAT
8418 ATATATATATATAATTATA
1 ATATATATATATAATTATA
8437 ACAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATATATATAATTATAT
Found at i:9186 original size:33 final size:33
Alignment explanation
Indices: 9148--9215 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
9138 TTTAATTAAA
*
9148 TAGAACTTTGCATTAAGAAGTGAAATTAATAGT
1 TAGAACTTTGCATAAAGAAGTGAAATTAATAGT
9181 TAGAACTTTGCATAAAGAAGTGAAATTAATAGT
1 TAGAACTTTGCATAAAGAAGTGAAATTAATAGT
9214 TA
1 TA
9216 CTTAGTTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (33 bp):
TAGAACTTTGCATAAAGAAGTGAAATTAATAGT
Found at i:24854 original size:6 final size:6
Alignment explanation
Indices: 24843--24876 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
24833 TAATTAGAAC
*
24843 AACATT AACATT AACGTT AACATT AACATT AACA
1 AACATT AACATT AACATT AACATT AACATT AACA
24877 AAAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (6 bp):
AACATT
Done.