Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019402.1 Corchorus olitorius cultivar O-4 contig19435, 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: 12748
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:11717 original size:331 final size:326
Alignment explanation
Indices: 10866--11869 Score: 1139
Period size: 331 Copynumber: 3.0 Consensus size: 326
10856 TGTTACCAAA
* * * *
10866 AACGCGTTTTTAATCAAAAACTGTGATGGTTAAGTACACGATTTTGGCTAAAAATTTGCAAAAAT
1 AACGCGTTTTTAGTCAAAAACCGTGA-GGTT-AGTACACGATTTCGGCTAAAATTTTGCAAAAAT
* *
10931 TGACACGAAACA-TTTCTCCTCAATTTTCGGCCACAATACTCATAAAAAATATATAACTCAACGC
64 TGAC-CCAAAAATTTTCT-CTCAATTTT-GGCCACAATACTCATAAAAAATATATAACTCAACG-
* * *
10995 CAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATTGTTTTTTC-TATTTTTTCCGAGTTAATTT
125 CAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATTGATTTTCCAT-TTTTTTCCGAATTAATTT
* * * *
11059 CTAATTAAATTGAAACTGGATTGAAATGCTCGTAAAAAAAAATCCTTAAATCCAATCTGGCTGAC
189 CTAATTAAATCGAAACT-GATTCAAATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAG
* * *
11124 ATTTCGTTAGATAAAT-TAGATATTTCAATGAGTCTTGATGCCAAAAATCATGCAAAACTTAGCC
253 ATTTCGTTAGATAGATATAGATATTTCAATGAGTCTTGGTGCCAAAAATCATGCAAAAC-AAGCC
11188 AGGGCCCCGG
317 AGGGCCCCGG
* * * * * *
11198 AACGCGTTTTTAGCCAAAAACCGTGA--TAAATACACGATTTCGGCAAAAATTTTGCAAAAAATA
1 AACGCGTTTTTAGTCAAAAACCGTGAGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
* * * * *
11261 ACCCGAAAGAGTTTTC-CTCAATTTTTGACAAAGATACTCATAAAAAATATAT-ACTTCAACACC
66 ACCC-AAA-AATTTTCTCTCAATTTTGGCCACA-ATACTCATAAAAAATATATAAC-TCAAC-GC
* * *
11324 AAAAAGATTGAAAGGCTAT-TCACGCTTCTAATATTGGTTTTCC-TATTTTTCCGAATTAATTTC
126 AAAAAGATTGAAGGGCT-TCTCACGCTTCTAATATTGATTTTCCATTTTTTTCCGAATTAATTTC
* * * * * * *
11387 TAATTAAATCGAAACATGACTCAAATGCTTGTAAAAATAAATCCTTCAATCCTATGTGGGTAAGA
190 TAATTAAATCGAAAC-TGATTCAAATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGA
* * * * * * **
11452 TTTGGTTAAATAGATATAGATATTTCAATAAGACTTGGCGCCAAAAATCGTGCAAAACAGAGCTG
254 TTTCGTTAGATAGATATAGATATTTCAATGAGTCTTGGTGCCAAAAATCATGCAAAACA-AGCCA
*
11517 GGGCTCCGG
318 GGGCCCCGG
**
11526 AACGCGTTTTTAGTCAAAAACCGTGACGGTTAGTACACGATTTCCACTAAAATTTTGCAAAAATT
1 AACGCGTTTTTAGTCAAAAACCGTGA-GGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT
*
11591 GACCCAAAAATTTTCTTCTCAATTTTGGGCCACAATACTAATAAAAAATATATAACTCAACGCAA
65 GACCCAAAAATTTTC-TCTCAATTTT-GGCCACAATACTCATAAAAAATATATAACTCAACGCAA
* * * * *
11656 AAAAATTGAAGGGCTTCTCACGCTTCTTATA-TCAATTTCCAATTTTTTTCAGAATTAATTTCTA
128 AAAGATTGAAGGGCTTCTCACGCTTCTAATATTGATTTTCC-ATTTTTTTCCGAATTAATTTCTA
* * * * * *
11720 TTTAAATCGATACCGGATTCATATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
192 ATTAAATCGA-AACTGATTCAAATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGATT
* * * *
11785 TCGTTAGA-CGAATATAGATATTTCAATGAGTCTTTGTGCCAAAATTCACGCAAAACTAAGCCAG
256 TCGTTAGATAG-ATATAGATATTTCAATGAGTCTTGGTGCCAAAAATCATGCAAAAC-AAGCCAG
11849 GGCCCCGG
319 GGCCCCGG
11857 AACGCGTTTTTAG
1 AACGCGTTTTTAG
11870 CCGAAACAAG
Statistics
Matches: 557, Mismatches: 92, Indels: 47
0.80 0.13 0.07
Matches are distributed among these distances:
327 88 0.16
328 181 0.32
329 15 0.03
330 37 0.07
331 204 0.37
332 32 0.06
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (326 bp):
AACGCGTTTTTAGTCAAAAACCGTGAGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
ACCCAAAAATTTTCTCTCAATTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCAAAAA
GATTGAAGGGCTTCTCACGCTTCTAATATTGATTTTCCATTTTTTTCCGAATTAATTTCTAATTA
AATCGAAACTGATTCAAATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTCGTT
AGATAGATATAGATATTTCAATGAGTCTTGGTGCCAAAAATCATGCAAAACAAGCCAGGGCCCCG
G
Found at i:12010 original size:144 final size:144
Alignment explanation
Indices: 11749--12015 Score: 383
Period size: 144 Copynumber: 1.9 Consensus size: 144
11739 CATATGATCG
* *
11749 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGACGAATATAGATATTTCAATGA
1 TAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTCGTTAGACGAATATAGATATTTCAAGGA
* *
11814 GTCTTTGTGCCAAAATTCACGCAAAACTAAGCCAGGGCCCCGGAACGCGTTTTTAGCCGAAACAA
66 GTCTTTGTGCCAAAAATCACGCAAAACTAAGCCAGGGCCCCAGAACGCGTTTTTAGCCGAAACAA
11879 GATTTAGATACTCA
131 GATTTAGATACTCA
* * * **
11893 TAAAAACAAATCCTTAAATCCAATGTGGATGATATTTGGTTAGATGTTTATAGATATTTCAAGGA
1 TAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTCGTTAGACGAATATAGATATTTCAAGGA
* * * * * *
11958 GTC-TTGATGCCAAAAATCATGCAAAACTGAGTCTGGGCCTCAGAACGTGTTTTTAGCC
66 GTCTTTG-TGCCAAAAATCACGCAAAACTAAGCCAGGGCCCCAGAACGCGTTTTTAGCC
12016 AAAAACCTTG
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
143 3 0.03
144 104 0.97
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (144 bp):
TAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTCGTTAGACGAATATAGATATTTCAAGGA
GTCTTTGTGCCAAAAATCACGCAAAACTAAGCCAGGGCCCCAGAACGCGTTTTTAGCCGAAACAA
GATTTAGATACTCA
Found at i:12286 original size:475 final size:474
Alignment explanation
Indices: 11418--12342 Score: 1189
Period size: 475 Copynumber: 1.9 Consensus size: 474
11408 CAAATGCTTG
* * * * *
11418 TAAAAATAAATCCTTCAATCCTATGTGGGTAAGATTTGGTTAAATAGATATAGATATTTCAATAA
1 TAAAAACAAATCCTTAAATCCAATGTGGATAAGATTTGGTTAAATAGATATAGATATTTCAAGAA
* * * * *
11483 GACTTGGCGCCAAAAATCGTGCAAAACAGAGCTGGGGCTCCGGAACGCGTTTTTAGTCAAAAACC
66 GACTTGACGCCAAAAATCATGCAAAACAGAGCTGGGCCTCCAGAACGCGTTTTTAGCCAAAAACC
* * *
11548 GTGACGGTTAGTACACGATTTCCACTAAAATTTTGCAAAAATTGACCCAAAAATTTTCTTCTCAA
131 GTGACGCTTAGTACACAATTTCCACTAAAATTTTGCAAAAATTGACCCAAAAATTTTC-TCTAAA
* * *
11613 TTTTGGGCCACAATACTAATAAAAAATATATAACTCAACGCAAAAAAATTGAAGGGCTTCTCACG
195 TTTTGGGCCACAATACTAACAAAAAATATATAACTCAACGCAAAAAAATTAAAAGGCTTCTCACG
* * * * *
11678 CTTCTTATATCAATTTCCAATTTTTTTCAGAATTAATTTCTATTTAAATCGATACCGGATTCATA
260 CTTCTAATATCAATTTCCAATTTTTTTCAGAATTAATTTCTAATTAAATCGAAACAGGATTCAGA
*
11743 TGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGACGAATATAGATATTT
325 TGATCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTCGTTAGACGAATATAGATATTT
* * * * *
11808 CAATGAGTCTTTGTGCCAAAATTCACGCAAAACTAAGCCAGGGCCCCGGAACGCGTTTTTAGCCG
390 CAATGAGACTTGGCGCCAAAAATCACGCAAAACAAAGCCAGGGCCCCGGAACGCGTTTTTAGCCG
11873 AAACAAGATTTAGATACTCA
455 AAACAAGATTTAGATACTCA
* * * * *
11893 TAAAAACAAATCCTTAAATCCAATGTGGATGATATTTGGTTAGAT-GTTTATAGATATTTCAAGG
1 TAAAAACAAATCCTTAAATCCAATGTGGATAAGATTTGGTTAAATAG-ATATAGATATTTCAAGA
* * * *
11957 AGTCTTGATGCCAAAAATCATGCAAAACTGAGTCTGGGCCT-CAGAACGTGTTTTTAGCCAAAAA
65 AGACTTGACGCCAAAAATCATGCAAAACAGAG-CTGGGCCTCCAGAACGCGTTTTTAGCCAAAAA
* * ** *
12021 CCTTGATGCTTAGTACACAATTTCGGCTAAAATTTTGCAAAAATTTACCCTAAAGAATTTTC-CT
129 CCGTGACGCTTAGTACACAATTTCCACTAAAATTTTGCAAAAATTGACCC-AAA-AATTTTCTCT
* * * * * * *
12085 AAACTTTT-GGCCACGATACTCACAAAAAGTATATAATTCACCGGCAAAAAGATTAAAAGGCTTT
192 AAA-TTTTGGGCCACAATACTAACAAAAAATATATAACTCAAC-GCAAAAAAATTAAAAGGCTTC
** * *
12149 TCACGCTTCTAATATCGGTTTTCCTA-TTTTTTCA-AATTAATTTCTAATTAAATCGAAACATGA
255 TCACGCTTCTAATATC-AATTTCCAATTTTTTTCAGAATTAATTTCTAATTAAATCGAAACAGGA
* * *
12212 TTCAGAT-ACTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATGGATATA
319 TTCAGATGA-TCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTCGTTAGACGAATATA
* * * *
12276 GATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAAAGTCGGGGCCCCGGAATGCGTTT
383 GATATTTCAATGAGACTTGGCGCCAAAAATCACGCAAAACAAAGCCAGGGCCCCGGAACGCGTTT
12341 TT
448 TT
12343 CGTCTAGAAC
Statistics
Matches: 383, Mismatches: 59, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
474 2 0.01
475 314 0.82
476 54 0.14
477 13 0.03
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (474 bp):
TAAAAACAAATCCTTAAATCCAATGTGGATAAGATTTGGTTAAATAGATATAGATATTTCAAGAA
GACTTGACGCCAAAAATCATGCAAAACAGAGCTGGGCCTCCAGAACGCGTTTTTAGCCAAAAACC
GTGACGCTTAGTACACAATTTCCACTAAAATTTTGCAAAAATTGACCCAAAAATTTTCTCTAAAT
TTTGGGCCACAATACTAACAAAAAATATATAACTCAACGCAAAAAAATTAAAAGGCTTCTCACGC
TTCTAATATCAATTTCCAATTTTTTTCAGAATTAATTTCTAATTAAATCGAAACAGGATTCAGAT
GATCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTCGTTAGACGAATATAGATATTTC
AATGAGACTTGGCGCCAAAAATCACGCAAAACAAAGCCAGGGCCCCGGAACGCGTTTTTAGCCGA
AACAAGATTTAGATACTCA
Found at i:12623 original size:295 final size:294
Alignment explanation
Indices: 12089--12637 Score: 816
Period size: 295 Copynumber: 1.9 Consensus size: 294
12079 TTTCCTAAAC
* * * * *
12089 TTTTGGCCACGATACTCACAAAAAGTATATAATTCACCGGCAAAAAGATTAAAAGGCTTTTCACG
1 TTTTGGCCACAATACTCACAAAAAATATATAACTCAACGGCAAAAAGATTAAAAGGCTTCTCACG
* *
12154 CTTCTAATATCGGTTTTCCTATTTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAGAT
66 CTTCTAATATCAGTTTTCCTATTTTTTCAAATTAATTTCTAATTAAATCGAAACAGGATTCAGAT
** *
12219 ACTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATGGATATAGATATTTC
131 ACTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTCCGTTAGATGAATATAGATATTTC
* *
12284 AATGAGACTTGGCGCCAAAAATCATGCAAAACAAAGTCGGGGCCCCGGAATGCGTTTTTCGTCTA
196 AATGAGACTTGGCACCAAAAATCATGCAAAACAAAGTCGGGGCCCCAGAATGCGTTTTTCGTCTA
12349 GAACGCGTTTTGGCACGAAACATTTCTCCTCAAT
261 GAACGCGTTTTGGCACGAAACATTTCTCCTCAAT
* * *
12383 TTTTGGCCACAATACTCATAAAAAATATATAACTCAAC-GCAAAAAAGATTGAAGGGCTTCTCAC
1 TTTTGGCCACAATACTCACAAAAAATATATAACTCAACGGC-AAAAAGATTAAAAGGCTTCTCAC
* * * *
12447 GCTTCTAATATTATTTTTCCTATTTTTTCTTAATTAATTTCTAATTAAATCGAAACCGGA-TC-G
65 GCTTCTAATATCAGTTTTCCTATTTTTTC-AAATTAATTTCTAATTAAATCGAAACAGGATTCAG
* *
12510 ATATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTCCGTTAGATGAATATAGATA
129 ATA--CTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTCCGTTAGATGAATATAGATA
* ** *
12575 TTTCAATGAGTCTTGGCACCAAAAATCATGCAAAACTGAGTTGGGGCCCCAGAATGCGTTTTT
192 TTTCAATGAGACTTGGCACCAAAAATCATGCAAAACAAAGTCGGGGCCCCAGAATGCGTTTTT
12638 ACCAAAAAAC
Statistics
Matches: 226, Mismatches: 25, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
293 6 0.03
294 81 0.36
295 139 0.62
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (294 bp):
TTTTGGCCACAATACTCACAAAAAATATATAACTCAACGGCAAAAAGATTAAAAGGCTTCTCACG
CTTCTAATATCAGTTTTCCTATTTTTTCAAATTAATTTCTAATTAAATCGAAACAGGATTCAGAT
ACTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTCCGTTAGATGAATATAGATATTTC
AATGAGACTTGGCACCAAAAATCATGCAAAACAAAGTCGGGGCCCCAGAATGCGTTTTTCGTCTA
GAACGCGTTTTGGCACGAAACATTTCTCCTCAAT
Done.