Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011024.1 Corchorus olitorius cultivar O-4 contig11057, 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, 797
Length: 1329
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Found at i:500 original size:154 final size:153
Alignment explanation
Indices: 15--1329 Score: 1842
Period size: 154 Copynumber: 8.6 Consensus size: 153
5 TTGAGATTTC
* * * *
15 CCAAATCGAAGACGATTCAGAACGACAATAATGGGTCCGGATAGGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGG-CCTGATAGGCCCAAAATAACAAGTGTTCC
* *
80 AAATAAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
65 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* *
145 TGGAAAGAAAAGCATTGAGGTTTG
130 TGGAAAGAAAAGCATCGAGGGTTG
** * *
169 CCAAATCGAAGACGATTCAAAACGGAACTAATCGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAAT-GGGCCTGATAGGCCCAAAATAACAAGTGTTCC
*
234 AAATGAGCTAAAAACTTCAACAGTGGACTAATCTCACAAAAATGATTATAGTTAGGCCATAAACA
65 AAATGAGCTAAAAACTTC-ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
** * * *
299 ATGGAAAGAAAAATATTGAGGTTTA
129 ATGGAAAGAAAAGCATCGAGGGTTG
* * *
324 CCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC-TGATAGGCCCAAAATAACAAGTGTTCC
* *
389 AAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAAAGATTATAGTTAGGCCATAAACAA
65 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
454 TGGAAAGAAAAGCATCGAGGGTTG
130 TGGAAAGAAAAGCATCGAGGGTTG
** *
478 CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTTGATAGACCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC-TGATAGGCCCAAAATAACAAGTGTTCC
* ** *
543 AAATGAGCTAAAAACTTCACAATGTTCTAATCTCACCGAAATGATTATAGTTAGGCCATAAACAA
65 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
608 TGGAAAGAAAAGCATCGAGGGTTG
130 TGGAAAGAAAAGCATCGAGGGTTG
** *
632 CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGG-CCTGATAGGCCCAAAATAACAAGTGTTCC
* ** *
697 AAATGAGCCAAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTATAGTTAGGCCATAAACA
65 AAATGAG-CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* *
762 ATGGAAAGAAAAGCATCAAAGGTTG
129 ATGGAAAGAAAAGCATCGAGGGTTG
** * *
787 CCAAATCGATTACGATTCCAAACGTCACTAAAGGGCCATGATAGGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC-TGATAGGCCCAAAATAACAAGTGTTCC
852 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
65 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* ** *
917 TGGAAAGAAAAGCATTGAGATTTC
130 TGGAAAGAAAAGCATCGAGGGTTG
* * *
941 CCAAATCGAAGACGATTCAGAAA-GACACTAATGGGTCCCGATAGGCCCAAAATAACAAGTGTTT
1 CCAAATCGAAGACGATTCA-AAACGTCACTAATGGG-CCTGATAGGCCCAAAATAACAAGTGTTC
** * *
1005 CAAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTACAGTTAGGCCATAAACA
64 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
*
1070 ATGGAAAGAAAAGCATCAAGGGTTG
129 ATGGAAAGAAAAGCATCGAGGGTTG
** *
1095 CCAAATCGATTACGATTCAAAACGTCACTAATGGGCCTTGATAGGCCTAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC-TGATAGGCCCAAAATAACAAGTGTTCC
* *
1160 AAATGAGCTAAAAACTTCACAGGTGGACTAATCTCACGAAAATGATTATAGTTTGGCCATAAACA
65 AAATGAGCTAAAAACTTCACA-GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
** * *
1225 ATGGAAAGAAAAATATTGAGGTTTTG
129 ATGGAAAGAAAAGCATCGAGG-GTTG
* *
1251 -CAAATCGAAGACGATTTAAAACGTCACTGATGGG-C----A----CAAAATAACAAGTGTTCCA
1 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTGATAGGCCCAAAATAACAAGTGTTCCA
1306 AATGAGCTAAAAACTTCACAGTGG
66 AATGAGCTAAAAACTTCACAGTGG
Statistics
Matches: 1049, Mismatches: 100, Indels: 34
0.89 0.08 0.03
Matches are distributed among these distances:
144 4 0.00
145 38 0.04
149 1 0.00
153 5 0.00
154 628 0.60
155 370 0.35
156 3 0.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (153 bp):
CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTGATAGGCCCAAAATAACAAGTGTTCCA
AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
GGAAAGAAAAGCATCGAGGGTTG
Found at i:713 original size:309 final size:309
Alignment explanation
Indices: 3--1329 Score: 1896
Period size: 309 Copynumber: 4.3 Consensus size: 309
1 AG
* * * * * *
3 CATTGAGATTTCCCAAATCGAAGACGATTCAGAAC-GACAATAATGGGTCCGGATAGGCCCAAAA
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGACACTAATGGGCCCCGATAGGCCCAAAA
* *
67 TAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
** *
132 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAAC
131 AGGCCATAAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGAAGACGATTCAAAACGGAAC
* **
197 TAATCGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAACAGTGGAC
196 TAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC-ACAGTGGAC
*
262 TAATCTCACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
260 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
* * * * ** * *
312 TATTGAGGTTTACCAAATCGAAGACGATTTAAAAC-GTCACTAATGGGCCTTGATGGGCACAAAA
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGACACTAATGGGCCCCGATAGGCCCAAAA
* *
376 TAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAAAGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
441 AGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAAC
131 AGGCCATAAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGAAGACGATTCAAAACGGAAC
* * **
506 TAATGGGCCTTGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGTTCT
196 TAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* *
571 AATCTCACCGAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
261 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
* *
620 CATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCCCAAAA
1 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGACACTAATGGGCCCCGATAGGCCCAAAA
* ** *
684 TAACAAGTGTTCCAAATGAGCCAAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTATAGT
66 TAACAAGTGTTCCAAATGAG-CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
* ** * **
749 TAGGCCATAAACAATGGAAAGAAAAGCATCAAAGGTTGCCAAATCGATTACGATTCCAAACGTCA
130 TAGGCCATAAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA
* *
814 CTAAAGGGCCATGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
195 CTAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
879 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
260 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
* * *
929 CATTGAGATTTCCCAAATCGAAGACGATTCAGAAA--GACACTAATGGGTCCCGATAGGCCCAAA
1 CATTGAGGTTTGCCAAATCGAAGACGATTCA-AAACGGACACTAATGGGCCCCGATAGGCCCAAA
* ** * *
992 ATAACAAGTGTTTCAAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTACAGT
65 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
** **
1057 TAGGCCATAAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGATTACGATTCAAAACGTCA
130 TAGGCCATAAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA
*
1122 CTAATGGGCCTTGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGGTGGA
195 CTAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA-GTGGA
* *
1187 CTAATCTCACGAAAATGATTATAGTTTGGCCATAAACAATGGAAAGAAAAA
259 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
* * * *
1238 TATTGAGGTTTTG-CAAATCGAAGACGATTTAAAAC-GTCACTGATGGG---C---A----CAAA
1 CATTGAGG-TTTGCCAAATCGAAGACGATTCAAAACGGACACTAATGGGCCCCGATAGGCCCAAA
1291 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
65 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
Statistics
Matches: 929, Mismatches: 82, Indels: 24
0.90 0.08 0.02
Matches are distributed among these distances:
299 41 0.04
303 1 0.00
306 1 0.00
308 291 0.31
309 589 0.63
310 6 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (309 bp):
CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGACACTAATGGGCCCCGATAGGCCCAAAA
TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
AGGCCATAAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGAAGACGATTCAAAACGGAAC
TAATGGGCCTTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
Found at i:880 original size:463 final size:460
Alignment explanation
Indices: 1--1329 Score: 2004
Period size: 463 Copynumber: 2.9 Consensus size: 460
* * * * *
1 AGCATTGAGATTTCCCAAATCGAAGACGATTCAGAACGACAATAATGGGTCCGGATAGGCCCAAA
1 AGCATCGAGAGTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGTCCCGATAGGCCCAAA
* * *
66 ATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTAG-ACTAATCTCACCAAAATGATTATAG
66 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT-GTTCTAATCTCACCGAAATGATTATAG
* *
130 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
130 TTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
*
195 ACTAATCGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAACAGTGG
195 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC-ACAGTGG
** *
260 ACTAATCTCACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAATATTGAGGTTTAC
259 ACTAATCTCACCGAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAATATTGAGGTTTGC
*
325 CAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAATAACAAGTGTTCCA
324 CAAATCGAAGACGATTTAAAACGTCACTAA-GGGCCATGAT-GGCACAAAATAACAAGTGTTCCA
*
390 AATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAAAGATTATAGTTAGGCCATAAACAAT
387 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAAGATTATAGTTAGGCCATAAACAAT
455 GGAAAGAAA
452 GGAAAGAAA
* * * *
464 AGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGG-CCTTGATAGACCCA
1 AGCATCGAGAGTTCCCAAATCGAAGACGATTCAAAAC-GACACTAATGGGTCC-CGATAGGCCCA
*
527 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGTTCTAATCTCACCGAAATGATTATA
64 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTATA
592 GTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
129 GTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGG
*
657 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCCAAAAAACTTCACAGTG
194 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG-CTAAAAACTTCACAGTG
** ** **
722 TTCTAATCTCACCGAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCAAAGG-TT
258 GACTAATCTCACCGAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAATAT-TGAGGTTT
** ** *
786 GCCAAATCGATTACGATTCCAAACGTCACTAAAGGGCCATGATAGGCCCAAAATAACAAGTGTTC
322 GCCAAATCGAAGACGATTTAAAACGTCACT-AAGGGCCATGAT-GGCACAAAATAACAAGTGTTC
*
851 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
385 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAAGATTATAGTTAGGCCATAAACA
916 ATGGAAAGAAA
450 ATGGAAAGAAA
* *
927 AGCATTGAGATTTCCCAAATCGAAGACGATTCAGAAA-GACACTAATGGGTCCCGATAGGCCCAA
1 AGCATCGAGAGTTCCCAAATCGAAGACGATTCA-AAACGACACTAATGGGTCCCGATAGGCCCAA
* *
991 AATAACAAGTGTTTCAAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTACAG
65 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTATAG
* ** **
1056 TTAGGCCATAAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATCGATTACGATTCAAAACGTC
130 TTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA
** *
1121 ACTAATGGGCCTTGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGGTGG
195 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA-GTGG
*
1186 ACTAATCTCA-CGAAAATGATTATAGTTTGGCCATAAACAATGGAAAGAAAAATATTGAGGTTTT
259 ACTAATCTCACCG-AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAATATTGAGG-TTT
1250 G-CAAATCGAAGACGATTTAAAACGTCACT----G--ATG--GGCACAAAATAACAAGTGTTCCA
322 GCCAAATCGAAGACGATTTAAAACGTCACTAAGGGCCATGATGGCACAAAATAACAAGTGTTCCA
1306 AATGAGCTAAAAACTTCACAGTGG
387 AATGAGCTAAAAACTTCACAGTGG
Statistics
Matches: 789, Mismatches: 64, Indels: 36
0.89 0.07 0.04
Matches are distributed among these distances:
453 46 0.06
456 3 0.00
458 1 0.00
462 23 0.03
463 691 0.88
464 25 0.03
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (460 bp):
AGCATCGAGAGTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGTCCCGATAGGCCCAAA
ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTATAGT
TAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA
CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
TAATCTCACCGAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAATATTGAGGTTTGCCA
AATCGAAGACGATTTAAAACGTCACTAAGGGCCATGATGGCACAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAAGATTATAGTTAGGCCATAAACAATGGAA
AGAAA
Done.