Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024667.1 Corchorus olitorius cultivar O-4 contig24700, 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: 6666
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Found at i:3512 original size:22 final size:22
Alignment explanation
Indices: 3486--3533 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
3476 TCAAAGCATC
*
3486 AATTACTAATCTAATAGAATTA
1 AATTACTAATCTAATAGAACTA
3508 AATTACTAATCTAATAGAACTA
1 AATTACTAATCTAATAGAACTA
3530 AATT
1 AATT
3534 GAAGCAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.35
Consensus pattern (22 bp):
AATTACTAATCTAATAGAACTA
Found at i:4431 original size:329 final size:331
Alignment explanation
Indices: 3695--4728 Score: 998
Period size: 329 Copynumber: 3.1 Consensus size: 331
3685 AAAAATTGTG
* * * * * *
3695 ATGGTTAATACACGATTTCGGTTAAAATTTTGCAAAAATTTACCCAAAAGAATTTTCCTAAATTT
1 ATGGTTAGTACACGATTTCTGCTAAAATTTTGC-AAAATTGACCCGAAAGAATTTT-CTTAATTT
* * * *
3760 TTTGCCACGATACTCATAAAAAAATATATAATTCAACACCAAAAAGATTGAAA-GGCTTTTCACA
64 TTTGCCACAATACTCAT-AAAAAATATATAATTCAATACCAAAAATATT-AAAGGGCTTTTCACG
* * *
3824 CTTCTAATATCGGTTTTCCTATTTTTTCCAAATTAATTTCTAATTAATTCGAAACATGATATTTC
127 CTTCTAATATCGTTTTTCCTATTTTTT-CAAATTAA-TTCTAATTAAATCGAAACA--AGA-TTC
* * * * *
3889 AGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGGATATAGCTA
187 TGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATGAATATAGATA
* * * ** * * * *
3954 TATCAATGAGACTTGGCGCCAAAAATCATGCAAAGCAGAGTCGGGGACCCCGAAACGCGTTTTTA
252 TTTCAAGGAGTCCCGACGCAAAAAATCATGCAAAACAGAGCCGGGGACCCCGAAACGCGTTTTTA
** *
4019 GTTAAAAGCTATGAT
317 GCAAAAAACTATGAT
* * * * * *
4034 ATGGTTAGTACACGATTTCTGCAAAAATTTTGCAAAATTGACTCGAAAAAGATTTCCTTTAGTTT
1 ATGGTTAGTACACGATTTCTGCTAAAATTTTGCAAAATTGACCCGAAAGA-ATTTTCTTAATTTT
** * * *
4099 TTGCCACAATACTTGTAAAAGATATATAATTCAATTCCAAAAATATTAAAGGGCATTTCACGCTT
65 TTGCCACAATACTCATAAAAAATATATAATTCAATACCAAAAATATTAAAGGGCTTTTCACGCTT
* * * * *
4164 CGAATATCGTTTTTGCTATTTTTTCTAATCAATTCATAATAAAATCGAAACAAGATTCTGATGCT
130 CTAATATCGTTTTTCCTATTTTTTCAAATTAATTC-TAATTAAATCGAAACAAGATTCTGATGCT
*
4229 CGTAAAAAAAAATCCTT-AATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAG
194 CGTAAAAAAAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATGAATATAGATATTTCAAG
* * * * *
4293 GAGTCCCGACGCAAAAAATCATGTAAAACTGAGCCGGGG-TCCCGGAATGCGTTTTTAGCAAAAA
259 GAGTCCCGACGCAAAAAATCATGCAAAACAGAGCCGGGGACCCCGAAACGCGTTTTTAGCAAAAA
4357 ACTAT-A-
324 ACTATGAT
** * *
4363 ATGGTTAGTATGCGATTTCTGCTAAAATTTTGCAAAACTGACCCGAATGAATTTGTCTTAATTTT
1 ATGGTTAGTACACGATTTCTGCTAAAATTTTGCAAAATTGACCCGAAAGAATTT-TCTTAATTTT
* * * * *
4428 TTGCCACAATACGCATAAAAAATATATAATTC-ATCGCCAAAAATATTGAAGAGCTTTTTACGCT
65 TTGCCACAATACTCATAAAAAATATATAATTCAAT-ACCAAAAATATTAAAGGGCTTTTCACGCT
* * * ** *
4492 TCTAATATCGTTTTTCCTATTATTCTCCGAATTATTTTCTAATTAAATCGAAACTGGTTTTCTGA
129 TCTAATATCGTTTTTCCTATT-TT-TTCAAATTA-ATTCTAATTAAATCGAAACAAG-ATTCTGA
* * * * * * * *
4557 TACTCGTAAAAAAGAATCTTTCAATCCAATATGGATCG-GATTTCGTTAGATGAAAATAGATACT
190 TGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGAT-GAGATTTGGTTAGATGAATATAGATATT
* * * *** * *
4621 TCAAGGAGTCCAAGAAC-C-AAAAATCATTCAAAACAGAGTCATCG-TCCCGGAACGCGTTTTTA
254 TCAAGGAGTCC-CG-ACGCAAAAAATCATGCAAAACAGAGCCGGGGACCCCGAAACGCGTTTTTA
*
4683 GCCAAAACGAAC-GTG--
317 G-CAAAA--AACTATGAT
4698 ATGGTTAGTACACGATTTC-GCCTAAAATTTT
1 ATGGTTAGTACACGATTTCTG-CTAAAATTTT
4729 CAGAACTGGC
Statistics
Matches: 577, Mismatches: 100, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
328 6 0.01
329 121 0.21
330 3 0.01
331 45 0.08
332 99 0.17
333 108 0.19
334 11 0.02
335 33 0.06
336 26 0.05
337 60 0.10
338 32 0.06
339 33 0.06
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (331 bp):
ATGGTTAGTACACGATTTCTGCTAAAATTTTGCAAAATTGACCCGAAAGAATTTTCTTAATTTTT
TGCCACAATACTCATAAAAAATATATAATTCAATACCAAAAATATTAAAGGGCTTTTCACGCTTC
TAATATCGTTTTTCCTATTTTTTCAAATTAATTCTAATTAAATCGAAACAAGATTCTGATGCTCG
TAAAAAAAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATGAATATAGATATTTCAAGGA
GTCCCGACGCAAAAAATCATGCAAAACAGAGCCGGGGACCCCGAAACGCGTTTTTAGCAAAAAAC
TATGAT
Found at i:5556 original size:316 final size:319
Alignment explanation
Indices: 4997--5663 Score: 736
Period size: 316 Copynumber: 2.1 Consensus size: 319
4987 ATTGGAGGGT
* ** * * * *
4997 TTTCATGCTTCGAATATCGAATTTCATTATTTTTATCCAGAATAAATTTCTAATTAAATCGAATC
1 TTTCACGCTTCGAATATCGTTTTTCACTATTTTTATCCAGAATAAATTTATAATAAAATCGAAAC
* * * *
5062 CAGTTTCAGATGCTCGTGAAAAAAAAAATCTTTAAATCCAATGTGGCTCAGATTTGGTTAGAAGA
66 AAGATTCAGATACTCGT-AAAAAAAAAATCCTTAAATCCAATGTGGCTCAGATTTGGTTAGAAGA
*
5127 AAATAGATATTTCAAGGAGTTTAAAAATCAGACAAAACTGAGTCATGGCCCCGGAACGCGTTTTT
130 AAATAGATATTTCAAGGAGTTTAAAAATCAGACAAAACTGAGTCATGGCCCCGAAACGCGTTTTT
*** * *
5192 AGCCTTTAACCGTGATAATTAGTACACGATTTTGGCTAAAACTTTGCAAAACTGAGCCGAAAAA-
195 AGCCAAAAACCGTGATAATTAGTACACAATTTTGGCTAAAACTTTGCAAAACTGACCCGAAAAAT
*
5256 ATTC-TA-TT-GCCACAATACTTGT-TTATATAATTCAATGCCAAAAATATTAAAGGGCA
260 ATTCTTATTTCGCCACAATACTTGTATTATAAAATTCAATGCCAAAAATATTAAAGGGCA
* * *
5312 TTTCACGCTTCGAATATCGTTTTTC-CTATTTTT-TTCTGAATGAATTTATAATAAAATCGAAAC
1 TTTCACGCTTCGAATATCGTTTTTCACTATTTTTATCCAGAATAAATTTATAATAAAATCGAAAC
* *
5375 AAGATTCTGATACTCGT-AAAAACAAATCCTTAAATCCAATGTGGCTGC-G-TTTGGATTAGAAG
66 AAGATTCAGATACTCGTAAAAAAAAAATCCTTAAATCCAATGTGGCT-CAGATTTGG-TTAGAAG
* * * *
5437 AATATAGATATTTCACGGAGTCCTGGTGCAAAAAAT-ATG-CAAAATTGAG-C-TGGGGTCCCGA
129 AAAATAGATATTTCAAGGAGT--T--T---AAAAATCA-GACAAAACTGAGTCAT--GGCCCCGA
** *
5498 AACGCG-TTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCT-GCTAAAATTTTGCAAAACT
184 AACGCGTTTTTAGCCAAAAACCGTGATAATTAGTACACAATTT-TGGCTAAAACTTTGCAAAACT
* *
5561 GACCCGAAAAATTTTCTTTTATTTTTCGCCACAATAGTTGTAAAAATTATAAAATTCAATGCCAA
248 GACCCGAAAAATATTC--TTA--TTTCGCCACAATACTTGT----ATTATAAAATTCAATGCCAA
5626 AAATATTAAAGGGCA
305 AAATATTAAAGGGCA
5641 TTTCACGCTTCGAATATCGTTTT
1 TTTCACGCTTCGAATATCGTTTT
5664 GAAACAAGAA
Statistics
Matches: 294, Mismatches: 32, Indels: 38
0.81 0.09 0.10
Matches are distributed among these distances:
310 5 0.02
311 54 0.18
312 1 0.00
313 38 0.13
314 7 0.02
315 24 0.08
316 59 0.20
317 26 0.09
318 7 0.02
320 2 0.01
323 2 0.01
324 13 0.04
329 56 0.19
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (319 bp):
TTTCACGCTTCGAATATCGTTTTTCACTATTTTTATCCAGAATAAATTTATAATAAAATCGAAAC
AAGATTCAGATACTCGTAAAAAAAAAATCCTTAAATCCAATGTGGCTCAGATTTGGTTAGAAGAA
AATAGATATTTCAAGGAGTTTAAAAATCAGACAAAACTGAGTCATGGCCCCGAAACGCGTTTTTA
GCCAAAAACCGTGATAATTAGTACACAATTTTGGCTAAAACTTTGCAAAACTGACCCGAAAAATA
TTCTTATTTCGCCACAATACTTGTATTATAAAATTCAATGCCAAAAATATTAAAGGGCA
Found at i:5899 original size:294 final size:293
Alignment explanation
Indices: 5370--5957 Score: 824
Period size: 294 Copynumber: 2.0 Consensus size: 293
5360 TAATAAAATC
* * * *
5370 GAAACAAGATTCTGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGCGTTTGGATTAGA
1 GAAACAAGAATCTCATACTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGTTTGGATTAGA
** * * *
5435 AGAATATAGATATTTCACGGAGTCCTGGTGCAAAAAATATGCAAAATTGAGCTGGGGTCCCGAAA
66 AGAATATAGATATTTCAAAGAGTCCTGGCGCAAAAAATATGCAAAACTGAGCCGGGGTCCCGAAA
* *
5500 CGCGTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCTGCTAAAATTTTGCAAAACTGACC
131 CGCGTTTTAGCCAAAAACCGTGATGG-TAGTAAACAATTTCTGCTAAAATTTTGCAAAACTAACC
* *
5565 CGAAAAATTTTCTTTTATTTTTCGCCACAATAGTTGTAAAAATTATAAAATTCAATGCCAAAAAT
195 CGAAAAATTTTCTTTTATTTTTCGCCACAATACTTGTAAAAATTATAAAATTCAATGCCAAAAAA
5630 ATTAAAGGGCATTTCACGCTTCGAATATCGTTTT
260 ATTAAAGGGCATTTCACGCTTCGAATATCGTTTT
* *
5664 GAAACAAGAATCTCATGCTCGTAAAAACAAATCCTT-AATTCAATCGTGGATGAGATTTGG-TTA
1 GAAACAAGAATCTCATACTCGTAAAAACAAATCCTTAAATCCAAT-GTGGATGAG-TTTGGATTA
* * *
5727 GATGAATATAGATATTTCAAAGAGTCTTGGCGTAAAAAATGATGCAAAACTGAGCCGGGGTCCCG
64 GAAGAATATAGATATTTCAAAGAGTCCTGGCGCAAAAAAT-ATGCAAAACTGAGCCGGGGTCCCG
* * * ** * * *
5792 GAATGCATTTTTCTCCAAAAACTGTGAT-G-AGTAAACGATTTCTGCTAATATTTTGCAAAACTA
128 AAACGC-GTTTTAGCCAAAAACCGTGATGGTAGTAAACAATTTCTGCTAAAATTTTGCAAAACTA
* * *
5855 ACCCGAAAAAATTTTCTTTTATTTTTGGCCACAATACTTGTAAAACTTATATAATTCAATGCCAA
192 ACCCG-AAAAATTTTCTTTTATTTTTCGCCACAATACTTGTAAAAATTATAAAATTCAATGCCAA
*
5920 AAAAATTAAAGGGCATTTGACGCTTCGAATATCGTTTT
256 AAAAATTAAAGGGCATTTCACGCTTCGAATATCGTTTT
5958 TCCTATTTTT
Statistics
Matches: 259, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
293 42 0.16
294 168 0.65
295 32 0.12
296 17 0.07
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (293 bp):
GAAACAAGAATCTCATACTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGTTTGGATTAGA
AGAATATAGATATTTCAAAGAGTCCTGGCGCAAAAAATATGCAAAACTGAGCCGGGGTCCCGAAA
CGCGTTTTAGCCAAAAACCGTGATGGTAGTAAACAATTTCTGCTAAAATTTTGCAAAACTAACCC
GAAAAATTTTCTTTTATTTTTCGCCACAATACTTGTAAAAATTATAAAATTCAATGCCAAAAAAA
TTAAAGGGCATTTCACGCTTCGAATATCGTTTT
Found at i:6268 original size:332 final size:331
Alignment explanation
Indices: 5662--6655 Score: 1428
Period size: 332 Copynumber: 3.0 Consensus size: 331
5652 GAATATCGTT
*
5662 TTGAAACAAGAATCTCATGCTCGTAAAAACAAATCCTTAATT-CAATCGTGGATGAGATTTGGTT
1 TTGAAACAAGATTCTCATGCTCGTAAAAACAAATCCTTAATTCCAAT-GTGGATGAGATTTGGTT
* *
5726 AGATGAATATAGATATTTCAAAGAGTCTTGGCGTAAAAAATGATGCAAAACTGAGCCGGGGTCCC
65 AGATGAATATAGATATTTCAAGGAGTCTTGGCGTAAAAAATCATGCAAAACTGAGCCGGGGTCCC
* * * *
5791 GGAATGCATTTTTCTCCAAAAACTGTGATG--AGTAAACGATTTCTGCTAATATTTTGCAAAACT
130 GGAATGCGTTTTTCGCCAAAAACTGTGATGTTAGTACACGATTTCTGCTAAAATTTTGCAAAACT
* *
5854 AACCCGAAAAAATTTTCTTTTATTTTTGGCCACAATACTTGTAAAACTTATATAATTCAATGCCA
195 GACCCGAAAAAATTTTCTTTTATTTTTGGCCACAATACTTGTAAAAATTATATAATTCAATGCCA
* *
5919 AAAAAATTAAAGGGCATTTGACGCTTCGAATATCGTTTTTCCTATTTTTTTCTAAATTAATTTAT
260 AAAAAATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTAT
5984 AATAAAA
325 AATAAAA
* *
5991 TTGAAACAAGATTCTCATGCTCGTAAAAACAAATCCTTAATTCCAATGTAGATGAGATCTGGTTA
1 TTGAAACAAGATTCTCATGCTCGTAAAAACAAATCCTTAATTCCAATGTGGATGAGATTTGGTTA
*
6056 GATGAATATAGATATTTCAAGGAGTCTTGGCGTAAAAAAT-ATGCAAAACCGAGCCGGGGTCCCG
66 GATGAATATAGATATTTCAAGGAGTCTTGGCGTAAAAAATCATGCAAAACTGAGCCGGGGTCCCG
*
6120 GAATGCGTTTTTCGCCAAAAACTGTGGATGGTTAGTACACGATTTCTGCAAAAATTTTGCAAAAC
131 GAATGCGTTTTTCGCCAAAAACTGT-GAT-GTTAGTACACGATTTCTGCTAAAATTTTGCAAAAC
6185 TGACCCGAAAAAATTTTCTTTTATTTTTGGCCACAATACTTGTAAAAATTATATAATTCAATGCC
194 TGACCCGAAAAAATTTTCTTTTATTTTTGGCCACAATACTTGTAAAAATTATATAATTCAATGCC
* *
6250 AAAAATATTAATGGGCATTTCACGCTTCGAATATCGTTTTTCCTA-TTTTTTCTGAATTAATTTA
259 AAAAAAATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTA
6314 TAATAAAA
324 TAATAAAA
* * * * * * *
6322 TAGAAACAAGATTCTGATACTTGTTAAAACAAATCCTTAAGTCCAATGTGGCTGAG-TTTGGGTT
1 TTGAAACAAGATTCTCATGCTCGTAAAAACAAATCCTTAATTCCAATGTGGATGAGATTT-GGTT
* ** * ** * * * * *
6386 ACAAAAAAATAGATATTTCCTGTAGTCCTGGCGCAAAAAATCATGCAAAACTGAGTCGGGGTCCT
65 AGATGAATATAGATATTTCAAGGAGTCTTGGCGTAAAAAATCATGCAAAACTGAGCCGGGGTCCC
* * * *
6451 GAAACGCGTTTTTAGCCAAAAACCGTGAT-TTAACGTACACGATTTCTGCTAAAATTTTGCAAAA
130 GGAATGCGTTTTTCGCCAAAAACTGTGATGTT-A-GTACACGATTTCTGCTAAAATTTTGCAAAA
* * * * *
6515 CTGACCCGAAAAAAATTTTTCATTTGTTTTTTGCCACAACACTTGTAAAAAATATATAATTCAAT
193 CTGACCCG-AAAAAA-TTTTCTTTTATTTTTGGCCACAATACTTGTAAAAATTATATAATTCAAT
* * **
6580 GCCAAAAAGATTAAAGGTCATTTCACGCAACGAATATCGTTTTTCCTATTTTTTTC-GAATTAAT
256 GCCAAAAAAATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTCTGAATTAAT
6644 TTATAATAAAA
321 TTATAATAAAA
6655 T
1 T
6656 CATAATGAAA
Statistics
Matches: 601, Mismatches: 52, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
328 46 0.08
329 101 0.17
330 8 0.01
331 150 0.25
332 182 0.30
333 107 0.18
334 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (331 bp):
TTGAAACAAGATTCTCATGCTCGTAAAAACAAATCCTTAATTCCAATGTGGATGAGATTTGGTTA
GATGAATATAGATATTTCAAGGAGTCTTGGCGTAAAAAATCATGCAAAACTGAGCCGGGGTCCCG
GAATGCGTTTTTCGCCAAAAACTGTGATGTTAGTACACGATTTCTGCTAAAATTTTGCAAAACTG
ACCCGAAAAAATTTTCTTTTATTTTTGGCCACAATACTTGTAAAAATTATATAATTCAATGCCAA
AAAAATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTATA
ATAAAA
Done.