Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019710.1 Corchorus olitorius cultivar O-4 contig19743, 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: 12921
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:849 original size:332 final size:331
Alignment explanation
Indices: 214--1156 Score: 1212
Period size: 332 Copynumber: 2.8 Consensus size: 331
204 CAGAACGCGT
* *
214 TTTTAGGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTCCCTCAA-TTTTTCCCAAAATACT
1 TTTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTT-CCTCAATTTTTTCCCAAAATACT
* *
278 CATAAAAAATATATGATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCATCTAATATTGTTTT
65 CATAAAAAATATAT-ATTCAACGCCAAAAACATTGGAGGGCTTTTCACGCATCTAATATCGTTTT
* * * *
343 TCTTTTTTTT-CTAAATTAATTTCTACATTAAATTGAAACAAGATTCAGATGCTCATAAAAACAA
129 TCTTTTTTTTCCTGAATTAATTTCTAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * *
407 ATCCTTAAATCC-ATCATTGCTGAGATTTGGCTAGATGAA-AGTAGATATTTCAAGGAGTCTTGG
194 ATCCTTAAATCCAAT-ATTGCTGAGATTTTGTTAGATGAATA-TGGATATTTCAAGGAGTCTTGG
* * * * *
470 TGTCAAAAATCATGCAAAACTTAGTCGGGCCGTCGGAACGCGTTTTTAGGCTAAAACCGTGATGG
257 CGTCAAAAATCATGCAAAACTGAGTCGGGCCG-CGGAACGCGTTTTTAGCCAAAAACCGTCATGG
*
535 TTAGTATACGA
321 TTAGTACACGA
* *
546 -TTTCGGCTAAAATTTTGCAAAGATTGACCCGAAAGATTCTTCCTCAATTTTTTCCCAGAATACT
1 TTTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATT-TTCCTCAATTTTTTCCCAAAATACT
610 CAT-AAAAATATATCATTCAACGCCAAAAACATTGGAGGGCTTTTCACGCATCTAATATCGTTTT
65 CATAAAAAATATAT-ATTCAACGCCAAAAACATTGGAGGGCTTTTCACGCATCTAATATCGTTTT
674 TCTTTTTTTTCCTGAATTAATTTCTAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
129 TCTTTTTTTTCCTGAATTAATTTCTAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * *
739 ATCCTTAAATCCAATGTTGCCGAGCTTTTGTTAGATGAATATGGATATTTCAATGAGTCTTGGCG
194 ATCCTTAAATCCAATATTGCTGAGATTTTGTTAGATGAATATGGATATTTCAAGGAGTCTTGGCG
* * *
804 TCAAATAA-CATGCAAAACTGAGTCATGGCC-CAGGAACGTGTTTTTAGCCAAAAATCGTCATGG
259 TCAAA-AATCATGCAAAACTGAGTC-GGGCCGC-GGAACGCGTTTTTAGCCAAAAACCGTCATGG
867 TTAGTACACGA
321 TTAGTACACGA
* ** * *
878 TTTTC-GCTAAAATTGTGCAAAAATTGACCCGAAAGATTTGTCCTCAATTTTTAGCTACAATACT
1 TTTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTT-TCCTCAATTTTTTCCCAAAATACT
* * *
942 CATAAAAAATATATATAGT-AATGCC-AAAACGATTGGAGGGCTTTTCACGCTTCTAGTATCGTT
65 CATAAAAAATATATAT--TCAACGCCAAAAAC-ATTGGAGGGCTTTTCACGCATCTAATATCGTT
** * * *
1005 TTTCGAATTTTTTTTCC-GAATTAATTT-TTGATAAAATCGAAACAATATTCAGATTCTCGTAAA
127 TTTC---TTTTTTTTCCTGAATTAATTTCTAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * *
1068 AACAAATACTTAAATCAAATTTTGTTGAGATTTTGTTAGATGATTATAGG-TATTTCAAGGAGTC
189 AACAAATCCTTAAATCCAATATTGCTGAGATTTTGTTAGATGAATAT-GGATATTTCAAGGAGTC
* *
1132 TTAGCGCCAAAAATCATGCAAAACT
253 TTGGCGTCAAAAATCATGCAAAACT
1157 CTTAAACTTA
Statistics
Matches: 541, Mismatches: 51, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
331 111 0.21
332 239 0.44
333 64 0.12
334 105 0.19
335 12 0.02
336 10 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (331 bp):
TTTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTCCTCAATTTTTTCCCAAAATACTC
ATAAAAAATATATATTCAACGCCAAAAACATTGGAGGGCTTTTCACGCATCTAATATCGTTTTTC
TTTTTTTTCCTGAATTAATTTCTAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
CCTTAAATCCAATATTGCTGAGATTTTGTTAGATGAATATGGATATTTCAAGGAGTCTTGGCGTC
AAAAATCATGCAAAACTGAGTCGGGCCGCGGAACGCGTTTTTAGCCAAAAACCGTCATGGTTAGT
ACACGA
Found at i:2678 original size:333 final size:332
Alignment explanation
Indices: 1831--3072 Score: 1515
Period size: 332 Copynumber: 3.7 Consensus size: 332
1821 TAAATTGGAT
1831 AAGATTTTTCCTCAATTTTTTCCCAGAATACTCAT-AAAAATATATAATTCAACGCCAAAAAGAT
1 AAGATTTTTCCTCAATTTTTTCCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGAT
* * * * *
1895 TGGACGGCTTTTCACGCTTCTAATATTGTTTTT-ATTTTTTTTCTTAATTATTTTCTAAATTAAA
66 TGGACGGCTTTTCACACTTCTAATATCGTTTTTCTTTTTTTTTCTGAATTAATTTCTAAATTAAA
* * * *
1959 TCGAAACAAGATTCAGATCCTCGTAAAAACAAATCCTTAAGTCCATCATTGCTGAGATTTGGCTA
131 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACATTGCTGAGATTTGGTTA
* ** * *
2024 GATGAAAATAGATAATTCAAGGAGTCTTGGCGTAAAAAATCATGCAAATCTCAGTCGGGCCGCCA
196 GATGAAAATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTCAGTTGGGCCGCCA
* * *
2089 GAACACGTTTTTTGCCTAAAACCATGATGGTTAGTACACGATTTCGGCTAAAATTTTGA-AAAAT
261 GAACGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTT-ACAAAAT
2153 TGACCCGA
325 TGACCCGA
* *
2161 AAGATTTTTCCTCAATTTTTTCCCAGAATACCCATAAAAAATATATAATTCAAAGCCAAAAAGAT
1 AAGATTTTTCCTCAATTTTTTCCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGAT
* * *
2226 TGGACGGCTTTTCACACTTCTAATATCGGTTTTCTTTTTTTTTCTTAATTATTTTCTAAATTAAA
66 TGGACGGCTTTTCACACTTCTAATATCGTTTTTCTTTTTTTTTCTGAATTAATTTCTAAATTAAA
* * * *
2291 TCGAAACAAGATTCAGATGCTCGTAACAACAAATCCTTAAGTCCATCATTGCTGAGATTTGGTTT
131 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACATTGCTGAGATTTGGTTA
* * * *
2356 GATCAAAATAGATATTCCAAGGAGTCTTGGCGCCAAAAATAATGCAAAACTTAGTTGGGCCGCCA
196 GATGAAAATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTCAGTTGGGCCGCCA
*
2421 GAACGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGATAAAATTTTACAAAGAT
261 GAACGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAA-AT
2486 TGACCCGA
325 TGACCCGA
** * *
2494 AAGATTTTTCCTCAACTTTTTTTTCTGAATTCTCAT-AAAAATATATAATTCAACGCCAAAAAGA
1 AAGATTTTTCCTCAA-TTTTTTCCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGA
* * *
2558 TTGTA-GGGTTCTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCTGAATTAATTTCTAAATTA
65 TTGGACGGCTT-TTCACACTTCTAATATCGTTTTTCTTTTTTTTTCTGAATTAATTTCTAAATTA
* * * *
2622 AATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCCTAAATCCAACGTTGCTGA-ACTTTTG
129 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACATTGCTGAGA-TTTGG
* * * * * * * *
2686 TTAAATGAATATGGATATTTTAATGAGTCTTGGCGTCAAATAA-CATGCAAAACTGA-TTCATGG
193 TTAGATGAAAATAGATATTTCAAGGAGTCTTGGCGCCAAA-AATCATGCAAAACTCAGTT--GGG
* * * * *
2749 -C-CCAGGAACGTGTTTTTAGCCAAAAATCGTGAGGGTTAGTACACGATTTTC-GCTAAAATTGT
255 CCGCCA-GAACGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGA-TTTCGGCTAAAATTTT
*
2811 GCAAAAATTGACCCGA
318 AC-AAAATTGACCCGA
* ** * *
2827 AAGA-TTTTCCACAATTTTTAGCCACAATACTCATAAAAAATATATATATT-AACGCCAAAACGA
1 AAGATTTTTCCTCAATTTTTTCCCAGAATACTCATAAAAAATATATA-ATTCAACGCCAAAAAGA
* * ** * * * *
2890 TTGGA-GGCCTTTTCACACTTCTAGTATCATTTTTCGATTTTTTTCCGAATTAATTTAT-GATAA
65 TTGGACGG-CTTTTCACACTTCTAATATCGTTTTTCTTTTTTTTTCTGAATTAATTTCTAAATTA
* * * * * ** * *
2953 AATCGAAACAATATTCAGATTCTCGTAAAAGCAAATACTTAAATCAAATTTTGTTGAGATTTTGT
129 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACATTGCTGAGATTTGGT
** * **
3018 TAGATGATTATAGGTATTTCAAGGAGTCTTAACGCCAAAAATCATGCAAAACTCA
194 TAGATGAAAATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTCA
3073 TAAATTTAGT
Statistics
Matches: 794, Mismatches: 100, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
330 36 0.05
331 171 0.22
332 292 0.37
333 269 0.34
334 26 0.03
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (332 bp):
AAGATTTTTCCTCAATTTTTTCCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGAT
TGGACGGCTTTTCACACTTCTAATATCGTTTTTCTTTTTTTTTCTGAATTAATTTCTAAATTAAA
TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACATTGCTGAGATTTGGTTA
GATGAAAATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTCAGTTGGGCCGCCA
GAACGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAATT
GACCCGA
Found at i:5287 original size:63 final size:62
Alignment explanation
Indices: 5204--5424 Score: 399
Period size: 63 Copynumber: 3.5 Consensus size: 62
5194 TGAAGACACG
*
5204 ACAGACACGAAGGTACACGAGAAGACAAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGAC-AGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
5267 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCT-CGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
5328 ACAGGCACGAAGGTACACGAGAAGACAAGAGAAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGAC-AGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
5391 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAG
1 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAG
5425 ACAGACACGA
Statistics
Matches: 153, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
61 43 0.28
62 42 0.27
63 68 0.44
ACGTcount: A:0.38, C:0.21, G:0.37, T:0.03
Consensus pattern (62 bp):
ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
Found at i:5442 original size:34 final size:34
Alignment explanation
Indices: 5391--5485 Score: 172
Period size: 34 Copynumber: 2.8 Consensus size: 34
5381 GGCGAGGCCA
*
5391 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAG
1 ACAGACACGAAGGTACACGAGAAGACAGAGGAAG
*
5425 ACAGACACGAAGATACACGAGAAGACAGAGGAAG
1 ACAGACACGAAGGTACACGAGAAGACAGAGGAAG
5459 ACAGACACGAAGGTACACGAGAAGACA
1 ACAGACACGAAGGTACACGAGAAGACA
5486 CAGTGGTGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.47, C:0.19, G:0.31, T:0.03
Consensus pattern (34 bp):
ACAGACACGAAGGTACACGAGAAGACAGAGGAAG
Found at i:5583 original size:2 final size:2
Alignment explanation
Indices: 5576--5600 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5566 TGGGGAAACA
5576 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
5601 GAGAGAGAGA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6384 original size:44 final size:45
Alignment explanation
Indices: 6334--6441 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
6324 GAAAACGTCC
* *
6334 AGGAGATCAAGGAAAG-TTAGAATCCATGACTGCCAAATGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
* * ** *
6378 AGGAGATCAAAGAGAGCTTTGGCCCCATGATTGCCAAATGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
*
6423 AGGAGATCAAAGAGAGCTT
1 AGGAGATCAAAGAAAGCTT
6442 TGGCTCCATG
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
44 14 0.25
45 42 0.75
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (45 bp):
AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
Found at i:6413 original size:45 final size:45
Alignment explanation
Indices: 6357--6457 Score: 184
Period size: 45 Copynumber: 2.2 Consensus size: 45
6347 AAGTTAGAAT
*
6357 CCATGACTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
*
6402 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCT
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
6447 CCATGATTGCC
1 CCATGATTGCC
6458 GAGTGCACAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (45 bp):
CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
Found at i:10619 original size:24 final size:25
Alignment explanation
Indices: 10575--10621 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
10565 AGAGAGAAAA
*
10575 AGGAAGAGAGAGAAAGTGAAAAAGG
1 AGGAAGAGAGAGAAAGAGAAAAAGG
10600 AGGAATGAGA-AGAAA-AGAAAAA
1 AGGAA-GAGAGAGAAAGAGAAAAA
10622 AGCCACAGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 10 0.50
26 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.04
Consensus pattern (25 bp):
AGGAAGAGAGAGAAAGAGAAAAAGG
Done.