Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017964.1 Corchorus olitorius cultivar O-4 contig17997, 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: 1895
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:1009 original size:337 final size:337
Alignment explanation
Indices: 495--1712 Score: 1238
Period size: 337 Copynumber: 3.6 Consensus size: 337
485 TTTTTTCTGA
* * * *
495 AATATTCAGAAAAAATATATAATTTAATGTTAAAAAGATTGACAGGCTTTTCACGCTTCTAATAT
1 AATATTCAGAAAAAATATATAATTCAATGCTAAAAAAATTGACAGGCTTTTCACACTTCTAATAT
* * ** * * *
560 CGTTTTTCCATTTTTTTACCGAA-AGACTTTCTAATTAAATCAAAACTAGATTGAGATGCTCGTA
66 CATTTTTCCATTTTTTT-CTGAATTTA-TTTCTAATAAAATCAAAACAAGATTGAGATGCTCATA
* *
624 AAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGT
129 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGT
**
689 CTTTATGCCAAAAATCATGTAAAATTGAGCCGTGACTTTGGAACCCATTTTTAGCCAAAAACAGT
194 CTTTATGCCAAAAATCATGTAAAATTGAGCCGTGACTCCGGAACCCATTTTTAGCCAAAAACAGT
*
754 GATGATTAGTACACGATTTCGGCTAAAATTTTGCAATAAAAAAACTGACCTGAAAAGTTTTTCCT
259 GATGATTAGTACACGATTTCGGCTAAAA-TTTGCAATAAAAAAACTGACCCGAAAAGTTTTTCCT
819 CAAATTTTTTTCCAC
323 CAAATTTTTTTCCAC
* * * *
834 AATACTCAGAAAAAATATATAATTCAATAG-AAAAAAAATTGA-AGGGTTTTTCACGCTTCTAAT
1 AATATTCAGAAAAAATATATAATTCAAT-GCTAAAAAAATTGACA-GGCTTTTCACACTTCTAAT
* *
897 ATCATTTTTCC-CTTTTTTCTGAATTTATTTCTAATAAAATCAAAACAAGATTTAGATGCTCATA
64 ATCATTTTTCCATTTTTTTCTGAATTTATTTCTAATAAAATCAAAACAAGATTGAGATGCTCATA
* * * *
961 AAAACAAATCCTTAAATCCATTTTGGCTAAGATTTGGTTAC-TTGAATATAGATATTTCAAGGAG
129 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT-CGATGAATATAGATATTTCAAGGAG
* * * * * * * * ** ** *
1025 TCTTTCTGCCATAAATCATGCAAAACTAAGCCG-GGCCCCGAAACGCGTTTTTTAGCCGTAAACT
193 TCTTTATGCCAAAAATCATGTAAAATTGAGCCGTGACTCCGGAAC-CCATTTTTAGCCAAAAACA
* * *
1089 GTGATGGTTAGTACACGATTTCGGCT--AA-----AAT-------CTGACCCGAAAATTTTTTTC
257 GTGATGATTAGTACACGATTTCGGCTAAAATTTGCAATAAAAAAACTGACCCGAAAAGTTTTTCC
* * *
1140 ACAATATTTTCTGT-GA-
322 TCAA-ATTTT-TTTCCAC
* * *
1156 AGTATTCGGAAAAAATATATAATTCAATGCTAAAAAGATTGACAGGCTTTTCACACTTCTAATAT
1 AATATTCAGAAAAAATATATAATTCAATGCTAAAAAAATTGACAGGCTTTTCACACTTCTAATAT
* *** * * *
1221 CGTTTTTCCATTTTTTTCTGAACGAATTTCTAATTAAATCAAAACAAGATTGAGATGTTCGTAAA
66 CATTTTTCCATTTTTTTCTGAATTTATTTCTAATAAAATCAAAACAAGATTGAGATGCTCATAAA
* * *
1286 AACAAATCCTTATATCCAATGTGGCTGAGATTTGATTCGATTAATATAGATATTTCAAGGAGTCT
131 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCT
* * *
1351 TTACGCCAAAGATCATGTAAAATTGAGCCGTGACTCCGGAACGCATTTTTAGCCAAAAACAGTGA
196 TTATGCCAAAAATCATGTAAAATTGAGCCGTGACTCCGGAACCCATTTTTAGCCAAAAACA--G-
* * *
1416 TATTGGCTAAAATTTTGATTAGTACACGATTT-TGCAAAAAATTTGC-A-AAAAAAACTGACCCA
258 ---T-G-----A---TGATTAGTACACGATTTCGGC-TAAAATTTGCAATAAAAAAACTGACCCG
*
1478 AAAAGTTTTTCCTC--ATTTTTTGCCAC
310 AAAAGTTTTTCCTCAAATTTTTTTCCAC
* * ** * *
1504 AATAGTCAGAAAAAATGTATAATTCAACACCAAAAAAATTGA-AGGGTTTTTCACACTTCTAATA
1 AATATTCAGAAAAAATATATAATTCAATGCTAAAAAAATTGACA-GGCTTTTCACACTTCTAATA
* * *
1568 -CATTTTT-CTTTTTTTTCTGAATTTATTTATAATAAAATCAAAACAAGATTTAGATGCTCATAA
65 TCATTTTTCCATTTTTTTCTGAATTTATTTCTAATAAAATCAAAACAAGATTGAGATGCTCATAA
* * * * * *
1631 AAACAAATACTTAAATCCATTTTGGCTGAGATTCGCTTAC-ATGAATATAGATATTTCAAGGATT
130 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT-CGATGAATATAGATATTTCAAGGAGT
* *
1695 CGTTCTGCCAAAAATCAT
194 CTTTATGCCAAAAATCAT
1713 ACAAAACTGA
Statistics
Matches: 711, Mismatches: 122, Indels: 85
0.77 0.13 0.09
Matches are distributed among these distances:
321 1 0.00
322 83 0.12
323 146 0.21
324 10 0.01
325 1 0.00
329 4 0.01
330 1 0.00
335 3 0.00
336 6 0.01
337 162 0.23
338 25 0.04
339 64 0.09
340 3 0.00
344 1 0.00
346 116 0.16
347 14 0.02
348 53 0.07
350 18 0.03
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (337 bp):
AATATTCAGAAAAAATATATAATTCAATGCTAAAAAAATTGACAGGCTTTTCACACTTCTAATAT
CATTTTTCCATTTTTTTCTGAATTTATTTCTAATAAAATCAAAACAAGATTGAGATGCTCATAAA
AACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCT
TTATGCCAAAAATCATGTAAAATTGAGCCGTGACTCCGGAACCCATTTTTAGCCAAAAACAGTGA
TGATTAGTACACGATTTCGGCTAAAATTTGCAATAAAAAAACTGACCCGAAAAGTTTTTCCTCAA
ATTTTTTTCCAC
Found at i:1377 original size:660 final size:657
Alignment explanation
Indices: 263--1895 Score: 2366
Period size: 669 Copynumber: 2.5 Consensus size: 657
253 AGAAAAAATA
* * * *
263 TATAATTAAATCAAAACAAGATTTAGATGCTCATAAAAACAAATCCTTATATCCATTTTAGATGA
1 TATAATAAAATCAAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCATTTTGGCTGA
* *
328 GATTCGGTTACATGAATATAGATATTTCAATGAGTCTTTTTGCCGAAAATCATGCAAAACTGAGC
66 GATTCGGTTACATGAATATAGATATTTCAAGGAGTCTTTCTGCC-AAAATCATGCAAAACTGAGC
*
393 CGGGGCCCCGAAACGTC-TTTTTTAGCCGAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAA
130 C-GGGCCCCGAAACG-CGTTTTTTAGCCGAAACT-GTGATGGTTAGTACACGATTTCGGCTAAAA
*
457 TCTGACCCG-AAATTTTTTTCACAAATTTTTTTTTCTGAAATATTCAGAAAAAATATATAATTTA
192 TCTGACCCGAAAATTTTTTTCAC-AA--TTTTTTTGTGAAATATTCAGAAAAAATATATAATTTA
*
521 ATGTTAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTACCGAAAGA
254 ATGCTAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTACCGAAAGA
* *
586 CTTTCTAATTAAATCAAAACTAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGC
319 ATTTCTAATTAAATCAAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGC
* *
651 TGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTATGCCAAAAATCATGTAAAATTG
384 TGAGATTTGATTCGATGAATATAGATATTTCAAAGAGTCTTTACGCCAAAAATCATGTAAAATTG
**
716 AGCCGTGACTTTGGAACCCATTTTTAGCCAAAAACA-G-T-G-A-TGATTAGTACACGATTTCGG
449 AGCCGTGACTCCGGAACCCATTTTTAGCCAAAAACAGGATGGAATTGATTAGTACACGATTT-GG
* * ** *
776 CTAAAATTTTGCAATAAAAAAACTGACCTGAAAAGTTTTTCCTCAAATTTTTTTCCACAATACTC
513 CAAAAAATTTGC-A-AAAAAAACTGACCCAAAAAGTTTTTCCTC--ATTTTTTGCCACAATACTC
* * *
841 AGAAAAAATATATAATTCAATAGAAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCATTTTT
574 AGAAAAAATATATAATTCAACACAAAAAAAATTGAAGGGTTTTTCACACTTCTAATA-CATTTTT
906 CCCTTTTTTCTGAATTTATT
638 CCCTTTTTTCTGAATTTATT
* *
926 TCTAATAAAATCAAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCATTTTGGCTAA
1 TATAATAAAATCAAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCATTTTGGCTGA
* * *
991 GATTTGGTTACTTGAATATAGATATTTCAAGGAGTCTTTCTGCCATAAATCATGCAAAACTAAGC
66 GATTCGGTTACATGAATATAGATATTTCAAGGAGTCTTTCTGCCA-AAATCATGCAAAACTGAGC
1056 CGGGCCCCGAAACGCGTTTTTTAGCCGTAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATC
130 CGGGCCCCGAAACGCGTTTTTTAGCCG-AAACTGTGATGGTTAGTACACGATTTCGGCTAAAATC
* * * *
1121 TGACCCGAAAATTTTTTTCACAATATTTTCTGTGAAGTATTCGGAAAAAATATATAATTCAATGC
194 TGACCCGAAAATTTTTTTCACAAT-TTTTTTGTGAAATATTCAGAAAAAATATATAATTTAATGC
* * *
1186 TAAAAAGATTGACAGGCTTTTCACACTTCTAATATCGTTTTTCCATTTTTTT-CTGAACGAATTT
258 TAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTACCGAAAGAATTT
*
1250 CTAATTAAATCAAAACAAGATTGAGATGTTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAG
323 CTAATTAAATCAAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAG
* * *
1315 ATTTGATTCGATTAATATAGATATTTCAAGGAGTCTTTACGCCAAAGATCATGTAAAATTGAGCC
388 ATTTGATTCGATGAATATAGATATTTCAAAGAGTCTTTACGCCAAAAATCATGTAAAATTGAGCC
*
1380 GTGACTCCGGAACGCATTTTTAGCCAAAAACAGTGATATTGGCTAAAATTTTGATTAGTACACGA
453 GTGACTCCGGAACCCATTTTTAGCCAAAAACAG-G--A-TGG----AA--TTGATTAGTACACGA
* *
1445 TTTTGCAAAAAATTTGCAAAAAAAACTGACCCAAAAAGTTTTTCCTCATTTTTTGCCACAATAGT
508 TTTGGCAAAAAATTTGCAAAAAAAACTGACCCAAAAAGTTTTTCCTCATTTTTTGCCACAATACT
* *
1510 CAGAAAAAATGTATAATTCAACACCAAAAAAATTGAAGGGTTTTTCACACTTCTAATACATTTTT
573 CAGAAAAAATATATAATTCAACACAAAAAAAATTGAAGGGTTTTTCACACTTCTAATACATTTTT
**
1575 CTTTTTTTTCTGAATTTATT
638 CCCTTTTTTCTGAATTTATT
*
1595 TATAATAAAATCAAAACAAGATTTAGATGCTCATAAAAACAAATACTTAAATCCATTTTGGCTGA
1 TATAATAAAATCAAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCATTTTGGCTGA
* * * * *
1660 GATTCGCTTACATGAATATAGATATTTCAAGGATTCGTTCTGCCAAAAATCATACAAAACTGAGG
66 GATTCGGTTACATGAATATAGATATTTCAAGGAGTCTTTCTGCC-AAAATCATGCAAAACTGAGC
* ** * *
1725 CGGGCCCCGAAACGCGTTTTTTAGCAGAAACCATGATGGTTAATACACTATTTCGGCTAAAATCT
130 CGGGCCCCGAAACGCGTTTTTTAGCCGAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATCT
* * * * * *
1790 GACCCGAAAAGTTTCTTCACAATTTTTTTGTGAAATATTCTGAAAATATATATAGTTTAATGCAA
195 GACCCGAAAATTTTTTTCACAATTTTTTTGTGAAATATTCAGAAAAAATATATAATTTAATGCTA
* *
1855 AAAAGATTGGCGGGCTTTTCACGCTTC-ACATATCGTTTTTC
260 AAAAGATTGACAGGCTTTTCACGCTTCTA-ATATCGTTTTTC
Statistics
Matches: 874, Mismatches: 74, Indels: 40
0.88 0.07 0.04
Matches are distributed among these distances:
660 162 0.19
661 86 0.10
662 67 0.08
663 135 0.15
666 2 0.00
667 72 0.08
668 55 0.06
669 168 0.19
670 70 0.08
672 28 0.03
673 1 0.00
674 11 0.01
675 17 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (657 bp):
TATAATAAAATCAAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCATTTTGGCTGA
GATTCGGTTACATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAATCATGCAAAACTGAGCC
GGGCCCCGAAACGCGTTTTTTAGCCGAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATCTG
ACCCGAAAATTTTTTTCACAATTTTTTTGTGAAATATTCAGAAAAAATATATAATTTAATGCTAA
AAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTACCGAAAGAATTTCTA
ATTAAATCAAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
TGATTCGATGAATATAGATATTTCAAAGAGTCTTTACGCCAAAAATCATGTAAAATTGAGCCGTG
ACTCCGGAACCCATTTTTAGCCAAAAACAGGATGGAATTGATTAGTACACGATTTGGCAAAAAAT
TTGCAAAAAAAACTGACCCAAAAAGTTTTTCCTCATTTTTTGCCACAATACTCAGAAAAAATATA
TAATTCAACACAAAAAAAATTGAAGGGTTTTTCACACTTCTAATACATTTTTCCCTTTTTTCTGA
ATTTATT
Done.