Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011608.1 Corchorus olitorius cultivar O-4 contig11641, 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, 703
Length: 1173
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Found at i:536 original size:154 final size:154
Alignment explanation
Indices: 2--1173 Score: 1623
Period size: 154 Copynumber: 7.6 Consensus size: 154
1 A
* * * * *
2 AAAGAAAAGCATTTAGGTTT-CTAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAA
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
*
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGA
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
131 TTATAGTTAGGCCATAAACAATGG
131 TTATAGTTAGGCCATAAACAATGG
* * * * * *
155 AAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATTG
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
* *** *
220 GCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAAAGACTAATCTCACCAAAGTAG
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT-G
285 ATTATAGTTAGGCCATAAACAATGG
130 ATTATAGTTAGGCCATAAACAATGG
* * * ** * * * * * *
310 AAACAAAAGCATCGAGGATTGACAAATCTAATACGATTTAAAACGTCACTAATGGGCCTTGATTG
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
* * * *
375 ACACAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTGACCAAAATGA
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
*
440 TTATAGGTAGGCCATAAACAATGG
131 TTATAGTTAGGCCATAAACAATGG
* * *
464 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACAACACTAATGGGCCCCGATAG
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
* * *
529 GCCCAAAATAACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAATATGA
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
*
594 TAATAGTTAGGCCATAAACAATGG
131 TTATAGTTAGGCCATAAACAATGG
* * *
618 AAAGAAAAGCATTGAGGTTTCTCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCAGATAG
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
*** *
683 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAAAGACTAATCTCACCAATATGA
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
*
748 TAATAGTTAGGCCATAAACAATGG
131 TTATAGTTAGGCCATAAACAATGG
* ** * * * * *
772 AAAGAAAAACGCTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATTG
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
* *
837 GCACAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* *
902 TTATAGGTAGGACATAAACAATGG
131 TTATAGTTAGGCCATAAACAATGG
* *
926 AAAGAAAAGCATTGAGGTTTCTCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
***
991 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAAAGACTAATCTCACCAAAATGA
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1056 TTATAGTTAGGCCATAAACAATGG
131 TTATAGTTAGGCCATAAACAATGG
* * * * * * * * *
1080 AAACAAAAGCATCGAGGGTTGCCAAATCGAATACGA-TAAAAACGGA-ACTAAT-TGCCCCGAGA
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAAC-GACACTAATGGGCCCTGATA
*
1142 GGCCTAAAATAACAAGTGTTCCAAATGAGCTA
65 GGCCCAAAATAACAAGTGTTCCAAATGAGCTA
Statistics
Matches: 902, Mismatches: 114, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
152 38 0.04
153 30 0.03
154 695 0.77
155 139 0.15
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
TTATAGTTAGGCCATAAACAATGG
Found at i:922 original size:462 final size:462
Alignment explanation
Indices: 2--1173 Score: 1849
Period size: 462 Copynumber: 2.5 Consensus size: 462
1 A
* * *
2 AAAGAAAAGCATTTAGGTTT-CTAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAA
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAG
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGA
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGA
* *
131 TTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATTTAA
131 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT-CCAAATCGAAGACGATTAAA
* ** * *
196 AACGTCACTAATGGGCCTTGATTGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
195 AACGACACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* *
261 AAAAGACTAATCTCACCAAAGTAGATTATAGTTAGGCCATAAACAATGGAAACAAAAGCATCGAG
260 AAAAGACTAATCTCACCAAAGTAGATAATAGTTAGGCCATAAACAATGGAAAAAAAAGCATCGAG
* *
326 GATTGACAAATCTAATACGATTTAAAACGTCACTAATGGGCCTTGATTGACACAAAATAACAAGT
325 GATTGACAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATTGACACAAAATAACAAGT
* *
391 GTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTGACCAAAATGATTATAGGTAGGCCATA
390 GTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGACATA
456 AACAATGG
455 AACAATGG
*
464 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACAACACTAATGGGCCCCGATAG
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAG
* *
529 GCCCAAAATAACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAATATGA
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGA
* * *
594 TAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCTCAAATCAAAGACGATTCAA
131 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTC-CAAATCGAAGACGATTAAA
659 AACGACACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
195 AACGACACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
724 AAAAGACTAATCTCACC-AA-TATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAACGC-T-
260 AAAAGACTAATCTCACCAAAGTA-GATAATAGTTAGGCCATAAACAATGGAAA-AAAAA-GCATC
* *
785 GAGG-TTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATTGGCACAAAATAAC
322 GAGGATTGA-CAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATTGACACAAAATAAC
849 AAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGA
386 AAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGA
914 CATAAACAATGG
451 CATAAACAATGG
* * * *
926 AAAGAAAAGCATTGAGGTTTCTCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCTGATAG
1 AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAG
*** *
991 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAAAGACTAATCTCACCAAAATGA
66 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGA
* * * *
1056 TTATAGTTAGGCCATAAACAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGA-TAAA
131 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTCCAAATCGAAGACGATTAAA
* * * *
1120 AACGGA-ACTAAT-TGCCCCGAGAGGCCTAAAATAACAAGTGTTCCAAATGAGCTA
195 AAC-GACACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
Statistics
Matches: 657, Mismatches: 45, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
460 38 0.06
461 17 0.03
462 350 0.53
463 250 0.38
464 2 0.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (462 bp):
AAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAG
GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGA
TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCAAATCGAAGACGATTAAAA
ACGACACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
AAAGACTAATCTCACCAAAGTAGATAATAGTTAGGCCATAAACAATGGAAAAAAAAGCATCGAGG
ATTGACAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATTGACACAAAATAACAAGTG
TTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGACATAA
ACAATGG
Done.