Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014110.1 Corchorus olitorius cultivar O-4 contig14143, 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: 3776
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:1631 original size:334 final size:334
Alignment explanation
Indices: 63--3775 Score: 4194
Period size: 334 Copynumber: 11.2 Consensus size: 334
53 TTCCGCATTT
* * * * * ** **
63 ATTTTTAATTAAATCGAAATAAAATTCAGATGCTCGTAAAAGA-AACCCT-TAAATCCAATTTGG
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAA-ACAAATCTGTAAATCCAACGTGG
* * * * * * *
126 ATAAGATTTGGTTATATGAAAATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATT
65 CTGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACT
* * * * *
191 GAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTGCACGA--T---C---
130 GAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
* * * * ** * * * * *
248 --TCTTGCTAAAAATTGACCCAAAAACTTTTTTCTC-ATTTTTGGCCACACA-ATTCTGAAAAAA
195 AATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACA-ATACTCAG-AAAAA
** * ** * * * *
309 T-ATATAATTCAAAGCCAAAAAGAATTGAAGGGCTTTTGACGCTTCAAATATCGTTTTTCCATTT
258 TCATATAATTCAATTCCAAAAA-TATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTT
* * ** **
373 TTTCCCTGAATTT
322 TCTGCCACAATAC
* * * * * * * ** ** *
386 ATTTCTAATTAAATCGAAACAAAATTTAGATGCTTGTTAAAAGAAATCCCTAAATCCAAATTTGC
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* * * * * * *
451 TGAGATTTGGTTATATGAATATAGATAATTCAAGGTGTCTTTCTGTCAAAAATCATGCAAAACAG
66 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
* * * * * * * * * *
516 AGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAACCCGTGA-----CGTACACG--GT-AGATGAT
131 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * ** * ** * *
573 A-TGTGCTAAAAGTTGA-CCG-AAA-ACTTTCTTCACATTTTTTGCCACACTACTCTGAAAAAAT
196 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCA-ATTTTTTGCCACAATACTCAG-AAAAAT
** ** * * * *
634 -ATATAATTCAAAGCCAAAAAATATTGAAGGGTTTTTCACCCTTCCAATATCGTTTTTCGATTTT
259 CATATAATTCAATTCC-AAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTT
* * **
698 -TTCC-GAATTT
323 CTGCCACAATAC
* * * * * * * * ** *
708 ATTTTTAATTAAATCGAAACAAAATTCAAATGCTCGTAAAAAGAAACCTTTTAATCTAAATTGGA
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* * * * *
773 TGAGATTTGTTGTTATAAGAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAAC
66 TGAGATTTG--GTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAAC
* * * * *
838 TGAG-CCGGTGCCGCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATATCGGCT
129 TGAGTCAGG-GCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT
902 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
193 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
* * * *
967 TCATATAATTCAATTCCAAAAATATTTTAGGGGTTTTCACGCTTCTAATATCATTTTTTCATTTT
258 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTT
*
1032 CTGCCAAAATAC
323 CTGCCACAATAC
* * * **
1044 ATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAATCCATTGTGGC
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* * * * *
1109 TGAAAGATTTGATTAGATGAATATAGATATTTGGAGAAGTCTTTGTGCCAAAAATCATGCAAAAC
66 TG--AGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAAC
* * *
1174 TTAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGATA
129 TGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
* *
1239 AAATTTTGCAAAAAACTGAGCCGAAAAGATTTTCCCCAATTTTATGCCACAATACTCAGAAAAAT
194 AAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAAT
* *
1304 CATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGTTTATAATATCGTTCTTCCATTTTC
259 CATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTTC
1369 TGCCACAATAC
324 TGCCACAATAC
*
1380 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAACTCTGTAAATCCAACGTGGC
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* *
1445 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTATGCCGAAAATCATGCAAAACTG
66 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
*
1510 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAGA
131 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
*
1575 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAGTTTTTTGCCA-AATTACTCAGAAAAATC
196 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAA-TACTCAGAAAAATC
*
1639 ATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCA-TCTTCTAATATCGTTCTTCCATTTTCT
260 ATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTTCT
* *
1703 ACCATAATAC
325 GCCACAATAC
* *
1713 ATTTCTAGTTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCTGTAAATCCAACGTGGC
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* * *
1778 -AAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTTTTTCTGCCGAAAATCATGCAAAACTG
66 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
** * * *
1842 AGTCAGAACCTCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGATAAA
131 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
*
1907 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCA-AATTACGCAGAAAAATC
196 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAA-TACTCAGAAAAATC
*
1971 ATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAAAATCGTTCTTCCATTTTCT
260 ATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTTCT
2036 GCCACAATAC
325 GCCACAATAC
* * *
2046 ATTTCTAATTAAATCGAAAAAAGATTCAAATACTCGTAAAAACAAATCTGTGAATCGAACGTGGC
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* *
2111 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTTTTTCTG---AAAATCATACAAAACTG
66 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
* *
2173 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGA-AGTTAGTACACGATTTCGGATAAA
131 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
*
2237 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTATGCCACAATACTCAGAAAAATCA
196 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCA
* *
2302 TATAATTCAATTTCC-AAAATATTTTAGGGTTTTTAACGCATCTAATATCGTTCTTCCATTTTCT
261 TATAATTCAA-TTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTTCT
*
2366 GCCTCAATAC
325 GCCACAATAC
* * * *
2376 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAATAAATCCGTAAGTTCAACGTGGC
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* * *
2441 TGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCAAAAATCATGCAAAACTT
66 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
* * * * * ** *
2506 AGTCAGGGCACTGAAACGCATTTTCAGGCAAAAATCGT-AACG-T--T-CACGATTTCGGATAAA
131 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * *
2566 ATTTTGCAAAAAACAGACCCGAAAAGATTTT-CCCAAATTTTTGCCACAATACACAGAAAACTCA
196 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCA
*
2630 TATAATTCAATTCCAAAAATA-TTTAGGGTTTTTCACGCATCTAATATCGTTCTTCCATTTTCTG
261 TATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTTCTG
2694 CCACAATAC
326 CCACAATAC
* *
2703 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTCTAAATCCAACGTGGA
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* * *
2768 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTTTTTCTGCCGAAAATCATGCTAAACTG
66 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
* * * *
2833 AGTCAGGGTCACGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACAAGATTTCGGCTAGA
131 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* *
2898 ATTTTGCAAAAAATTGACCCGAAAAGATTGTCCCCAATTTTTTGCCA-AATTACTCAGAAAAATC
196 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAA-TACTCAGAAAAATC
* *
2962 ATATAATTCAATTCCAAAAATATTTTAGGATTTTTCACGTTTCTAATATCGTTCTTCCATTTTCT
260 ATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTTCT
*
3027 GTCACAATAC
325 GCCACAATAC
* * * * *
3037 ATTTCTAATTAAATCGAAAGAAGATTCAAATACACGTAAAAATAAATCCGTAAATTCAACGTGGC
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* * * * *
3102 TAAGATTTGATTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCAAAAATCATGCAAAACTT
66 TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
*
3167 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCTGCTAAA
131 AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
** * * *
3232 ATTTTGCAAAAAACAAAACCGAAAAGTTTTTCCCCAATTTTTTGCCACAATACTCAGTAAAATCA
196 ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCA
** * * * * *
3297 TATAATTCAACGCCGAAAGTATTATAGAGTTTTTAACGCTTCTAATATCGTT-TCTCCAAATTTT
261 TATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCT-TCC--ATTTT
* * **
3361 -TTCC-GAATTT
323 CTGCCACAATAC
* * * * * **
3371 ATTTCTAATTTAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGC
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
* * * *
3436 TGAGATTTTGGTTAGATGAATACTCAGAAAAATCATATAATTCAACGCCAAGTAC--TCTGTCTA
66 TGAGA-TTTGGTTAGATGAATA--CAG-------ATAT--TTCGA-G--GAGT-CTTTCTGCCAA
* * * * * * *
3499 AAGTCATGCAAAACTGAGGT-AGGACCTCGAAACGCGTTTTTAGCTACAAATCGTGATGGTTAGT
115 AAATCATGCAAAACTGA-GTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGT
** * * * *
3563 ACACGATTTTTGCAAAAAGTTTCCAAAAAAACTGACCCGAAAAGTTTTTCCCCAATTTTTTGCCA
179 ACACGATTTCGGCTAAAATTTTGC-AAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCA
* * ** ** *
3628 CAATACTAAAAAAAATCATATAATTCAACGCCAAAAGA-A-TGAAGGGGTTTTCACGCTTCTAAT
243 CAATACTCAGAAAAATCATATAATTCAATTCCAAAA-ATATTTTAGGGTTTTTCACGCTTCTAAT
* * ** ** **
3691 ATCGTTTTTCTATTTT-TTTCTGAATTT
307 ATCGTTCTTCCATTTTCTGCCACAATAC
* * * *
3718 ATTTCTAATTAAATCGATACAAGATTCAGATACTGGTAAAAATAAATCCT-TAAATCCA
1 ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAAT-CTGTAAATCCA
3776 T
Statistics
Matches: 2968, Mismatches: 343, Indels: 134
0.86 0.10 0.04
Matches are distributed among these distances:
319 7 0.00
322 74 0.02
323 48 0.02
324 268 0.09
325 17 0.01
327 203 0.07
328 47 0.02
329 54 0.02
330 248 0.08
331 61 0.02
332 268 0.09
333 298 0.10
334 691 0.23
335 57 0.02
336 360 0.12
337 6 0.00
338 7 0.00
344 4 0.00
346 12 0.00
347 55 0.02
348 106 0.04
349 76 0.03
350 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (334 bp):
ATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCTGTAAATCCAACGTGGC
TGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
AGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
ATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCA
TATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTTCTG
CCACAATAC
Done.