Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014013.1 Corchorus olitorius cultivar O-4 contig14046, 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, 861
Length: 1435
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Found at i:478 original size:154 final size:154
Alignment explanation
Indices: 1--1429 Score: 2006
Period size: 154 Copynumber: 9.3 Consensus size: 154
* * *
1 GGGTTGCCAAATC-AATGACGATTCAAAACGTCACTAATCGGCCTTGATAGGCCCAAAATAACAA
1 GGGTTACCAAATCGAA-GACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAA
** *
65 GTGTTCCAAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAATAGATTATAGTTAGGCC
65 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT-GATTATAGTTAGGCC
**
130 ATAAACAAATGGAAAGAAAAGCATCAA
129 ATAAAC-AATGGAAAGAAAAGCATTGA
* * *
157 GGGTTGCCAAATC-AATGACGATTCAAAACGTCACTAATGGGCCTTGATAGACCCAAAATAACAA
1 GGGTTACCAAATCGAA-GACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAA
* ** * * *
221 GTGTTCCAAATGTAGCCAAAAACTTCACAGTGTTCTAATCTCACGAAAATGATAAGAGTTAGGCC
65 GTGTTCCAAATG-AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
286 ATAAACAATGGAAAGAAAAGCATTGA
129 ATAAACAATGGAAAGAAAAGCATTGA
* * * * * *
312 -GATTTCTCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGACAGGCCCAAAATAACAA
1 GGGTTAC-CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAA
*** *
376 GTGTTCCAAATGAGCTAAAAACTTCACAAAAGACTAATCTCACCAAATTGATTATAGTTAGGCCA
65 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* *
441 TAAACAATGGAAACAAAAGCATCGA
130 TAAACAATGGAAAGAAAAGCATTGA
* * ** * * *
466 GGGTTGCCAAATCGAATACGATTCAAAACGGAACTAAT-GGCCACGAAAGGCCTAAAATAACAAG
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAG
*
530 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGTTTATAGTTAGGCCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* *
595 AAACAATGGAAAGAAAATCATCGA
131 AAACAATGGAAAGAAAAGCATTGA
* ** * * *
619 GGGTTAACAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAG
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAG
* *
684 TGTTCTAAATGAGCCAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
*
749 AAACAATGGAAAGAAAAACATTGA
131 AAACAATGGAAAGAAAAGCATTGA
* * * * * *
773 GGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAACAACAAG
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAG
838 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
*
903 AAACAATGGCAAGAAAA-CATTGA
131 AAACAATGGAAAGAAAAGCATTGA
* * * * * *
926 GGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAACAACAAG
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAG
991 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
1056 AAACAATGGAAAGAAAAGCATTGA
131 AAACAATGGAAAGAAAAGCATTGA
* * * * * *
1080 GGTTTCCCAAATCGAATACGATTCAAAACGACACTAATGGGCCCCGTTAGGCCCAAAATAACAAG
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAG
* * * * * *
1145 TGTTCCAAATAAGCTAAAAACTTCACTGTGGACTAATCTCACGACAATGATAATAGTTAGGCTAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
**
1210 AAACAATGGAAAGAAAAGCATCAA
131 AAACAATGGAAAGAAAAGCATTGA
* * * * *
1234 GGGTTGCCAAATCGATGACGATTCAAAACGTCACTAATGGGTCTTGATACGCCCAAAATAACAAG
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAG
*
1299 TGTTCCAAATGAG-TAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
1363 AAACAATGGAAAGAAAAGCATTGA
131 AAACAATGGAAAGAAAAGCATTGA
* * *
1387 GGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATCGGCC
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
1430 CCATTA
Statistics
Matches: 1155, Mismatches: 112, Indels: 15
0.90 0.09 0.01
Matches are distributed among these distances:
153 396 0.34
154 547 0.47
155 83 0.07
156 95 0.08
157 34 0.03
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAG
TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
AAACAATGGAAAGAAAAGCATTGA
Found at i:1103 original size:461 final size:460
Alignment explanation
Indices: 7--1429 Score: 2084
Period size: 461 Copynumber: 3.1 Consensus size: 460
1 GGGTTG
7 CCAAATC-AATGACGATTCAAAACGTCACTAATCGGCCTTGATAGGCCCAAAATAACAAGTGTTC
1 CCAAATCGAA-GACGATTCAAAACGTCACTAATCGGCCTTGATAGG-CCAAAATAACAAGTGTTC
** *
71 CAAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAATAGATTATAGTTAGGCCATAAAC
64 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT-GATTATAGTTAGGCCATAAAC
* * **
136 AAATGGAAAGAAAAGCATCAAGGGTTGCCAAATC-AATGACGATTCAAAACGTCACTAATGGGCC
128 -AATGGAAAGAAAAGCATCGAGGGTTACCAAATCGAAT-ACGATTCAAAACGGAACTAATGGGCC
** * **
200 TTGATAGACCCAAAATAACAAGTGTTCCAAATGTAGCCAAAAACTTCACAGTGTTCTAATCTCAC
191 CCGATAGGCCCAAAATAACAAGTGTTCCAAATG-AGCCAAAAACTTCACAGTGGACTAATCTCAC
* * *
265 GAAAATGATAAGAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTTCTCAAATCAAAGA
255 GAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTC-CAAATCGAAGA
* ** *
330 CGATTCAAAACGACACTAATGGGCCCCGACAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
319 CGATTCAAAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
** * *
395 AACTTCACAAAAGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAATGGAAACAAAAG
384 AACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
460 CATCGAGGGTTG
449 CATTGAGGTTTA
* ** ** *
472 CCAAATCGAATACGATTCAAAACGGAACTAAT-GGCCACGAAAGGCCTAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATCGGCCTTGATAGGCC-AAAATAACAAGTGTTCC
*
536 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGTTTATAGTTAGGCCATAAACAA
65 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * *
601 TGGAAAGAAAATCATCGAGGGTTAACAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
130 TGGAAAGAAAAGCATCGAGGGTTACCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGA
* * * *
666 AAGGCCTAAAATAACAAGTGTTCTAAATGAGCCAAAAACTTCACAGTGGACTAATCTCACCAAAA
195 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCCAAAAACTTCACAGTGGACTAATCTCACGAAAA
* *
731 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATT
260 TGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT-CCAAATCGAAGACGATT
* * * *
796 TAAAACGTCACTAATGGGCCTTGATGGGCACAAAACAACAAGTGTTCCAAATGAGCTAAAAACTT
324 CAAAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* *
861 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGCAAGAAAA-CATTG
389 CACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
925 AGGTTTA
454 AGGTTTA
* * * *
932 CCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAACAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATCGGCCTTGATAGGC-CAAAATAACAAGTGTTCC
997 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
65 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * *
1062 TGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAATACGATTCAAAAC-GACACTAATGGGCCCCG
130 TGGAAAGAAAAGCATCGAGGGTTACCAAATCGAATACGATTCAAAACGGA-ACTAATGGGCCCCG
* * * * *
1126 TTAGGCCCAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACTGTGGACTAATCTCACGACA
194 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCCAAAAACTTCACAGTGGACTAATCTCACGAAA
* ** * *
1191 ATGATAATAGTTAGGCTATAAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGATGACGAT
259 ATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTCCAAATCGAAGACGAT
* *
1256 TCAAAACGTCACTAATGGGTCTTGATACGCCCAAAATAACAAGTGTTCCAAATGAG-TAAAAACT
323 TCAAAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
1320 TCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
388 TCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
1385 GAGGTTTA
453 GAGGTTTA
*
1393 CCAAATCGAAGACGATTTAAAACGTCACTAATCGGCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATCGGCC
1430 CCATTA
Statistics
Matches: 860, Mismatches: 89, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
460 105 0.12
461 552 0.64
462 86 0.10
463 24 0.03
464 65 0.08
465 26 0.03
466 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (460 bp):
CCAAATCGAAGACGATTCAAAACGTCACTAATCGGCCTTGATAGGCCAAAATAACAAGTGTTCCA
AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
GGAAAGAAAAGCATCGAGGGTTACCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGAT
AGGCCCAAAATAACAAGTGTTCCAAATGAGCCAAAAACTTCACAGTGGACTAATCTCACGAAAAT
GATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCAAATCGAAGACGATTCA
AAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
CAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
GTTTA
Found at i:1424 original size:307 final size:308
Alignment explanation
Indices: 1--1431 Score: 2019
Period size: 307 Copynumber: 4.6 Consensus size: 308
* *
1 GGGTTGCCAAATC-AATGACGATTCAAAACGTCACTAATCGGCCTTGATAGGCCCAAAATAACAA
1 GGGTTACCAAATCGAA-GACGATTCAAAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAA
** *
65 GTGTTCCAAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAATAGATTATAGTTAGGCC
65 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT-GATTATAGTTAGGCC
** * *
130 ATAAACAAATGGAAAGAAAAGCATCAAGGGTTGCCAAATC-AATGACGATTCAAAACGTCACTAA
129 ATAAAC-AATGGAAAGAAAAGCATTGAGGTTTACCAAATCGAA-GACGATTCAAAACGTCACTAA
** * * **
194 TGGGCCTTGATAGACCCAAAATAACAAGTGTTCCAAATGTAGCCAAAAACTTCACAGTGTTCTAA
192 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG-AGCTAAAAACTTCACAGTGGACTAA
* * *
259 TCTCACGAAAATGATAAGAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
256 TCTCACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA
* * * * ** *
312 -GATTTCTCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGACAGGCCCAAAATAACAA
1 GGGTTAC-CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAA
*** *
376 GTGTTCCAAATGAGCTAAAAACTTCACAAAAGACTAATCTCACCAAATTGATTATAGTTAGGCCA
65 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* * * * * **
441 TAAACAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCAAAACGGAACTAAT-G
130 TAAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGTCACTAATGG
* * *
505 GCCACGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
195 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
* * *
570 ACCAAAATGTTTATAGTTAGGCCATAAACAATGGAAAGAAAATCATCGA
260 ACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA
* ** ** * *
619 GGGTTAACAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAG
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAAG
* *
684 TGTTCTAAATGAGCCAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* *
749 AAACAATGGAAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGG
131 AAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGG
** * * *
814 CCTTGATGGGCACAAAACAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
196 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
* * *
879 CCAAAATGATTATAGTTAGGCCATAAACAATGGCAAGAAAA-CATTGA
261 CCAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA
* * * * *
926 GGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAACAACAAG
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAAG
991 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * *
1056 AAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAATACGATTCAAAACGACACTAATGGG
131 AAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGG
* * *
1121 CCCCGTTAGGCCCAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACTGTGGACTAATCTCA
196 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
* * * *
1186 CGACAATGATAATAGTTAGGCTATAAACAATGGAAAGAAAAGCATCAA
261 CCAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA
* * * *
1234 GGGTTGCCAAATCGATGACGATTCAAAACGTCACTAATGGGTCTTGATACGCCCAAAATAACAAG
1 GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAAG
*
1299 TGTTCCAAATGAG-TAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
66 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* *
1363 AAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATCGG
131 AAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGG
1428 CCCC
196 CCCC
1432 ATTA
Statistics
Matches: 999, Mismatches: 115, Indels: 16
0.88 0.10 0.01
Matches are distributed among these distances:
307 622 0.62
308 207 0.21
309 50 0.05
310 27 0.03
311 91 0.09
312 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (308 bp):
GGGTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTTGATAGGCCCAAAATAACAAG
TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
AAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGG
CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
CCAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA
Done.