Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011665.1 Corchorus olitorius cultivar O-4 contig11698, 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: 2729
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1302 Score: 1973
Period size: 154 Copynumber: 8.5 Consensus size: 154
*
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATATGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
* *
66 AAAATAACAAGTGTTCCAAATGAGCTAAAAACCTCACAGTGGACTAATCTCACCAATATGATTAT
66 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
*
131 AGTTAGTCCATAAACAATGAAAAG
131 AGTTAGTCCATAAACAATGGAAAG
* * * * * * * *
155 AAAAGC-TTTAGGGTTTGACGAATTGAAGACAATTAAAAACGTCACTAAAGGGCCTCGATAGGCC
1 AAAAGCATTGA-GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCC
* *
219 CAAATTAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
65 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
284 TAGTTAGTCCATAAACAATGGAAAG
130 TAGTTAGTCCATAAACAATGGAAAG
* * *
309 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATATGTCACAAATGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
* * *
374 AAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAGTCTCACCAAAATGATAAT
66 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
439 AGTTAGGCCATAAACATTGGAAAG
131 AGTTAGTCCATAAACAATGGAAAG
* ** *
463 AAAAGCATTGAGGTTTGCCAAATCGATGACGATTCAAAACGGAAATAATGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
*
528 AAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
66 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
*
593 AGTTAGGCCATAAACAATGGAAAG
131 AGTTAGTCCATAAACAATGGAAAG
* ** *
617 AAAAACATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCTC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
* ** *
682 AAAATAACAAGTGGTCCAAATGAGCTAATGACTTCACAGTGGACTAATCTCACCAATATGATTAT
66 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
*
747 AGTTAGTCCATAAACAATGAAAAG
131 AGTTAGTCCATAAACAATGGAAAG
* * ** *
771 AAAAGCA-TAAGGGTTTGCCGAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCT
1 AAAAGCATTGA-GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCC
* ** *
835 CAAAATAACAAGTGGTCCAAATGAGCTAATGACTTCACAGTGGACTAATCTCACCAATAT-ATTA
65 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
*
899 TAGTTAGTCCATAAACAATGAAAAG
130 TAGTTAGTCCATAAACAATGGAAAG
* * * *
924 AAAAGC-TTTAGAGATTGCCGAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCC
1 AAAAGCATTGAG-GTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGG-C
* * *
988 CCAAATTAATAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
64 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
*
1053 ATAGTTAGTCGATAAACAATGGAAAG
129 ATAGTTAGTCCATAAACAATGGAAAG
* * *
1079 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATATGTCACAAATGGGCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
*
1144 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTAT
66 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
*
1209 AGTTAGGCCATAAACAATGGAAAG
131 AGTTAGTCCATAAACAATGGAAAG
** *
1233 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGATAGGCCC
1 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
1298 AAAAT
66 AAAAT
1303 CCAAAATGAT
Statistics
Matches: 1049, Mismatches: 91, Indels: 16
0.91 0.08 0.01
Matches are distributed among these distances:
152 1 0.00
153 88 0.08
154 876 0.84
155 80 0.08
156 4 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCC
AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
AGTTAGTCCATAAACAATGGAAAG
Found at i:1506 original size:260 final size:261
Alignment explanation
Indices: 1042--1562 Score: 832
Period size: 260 Copynumber: 2.0 Consensus size: 261
1032 ACTAATCTCA
* *
1042 CCAAAATGATTATAGTTAGTCGATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * *
1107 ACGATTCAATATGTCACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
66 ACGATTCAAAACGTCACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAA
1172 AAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
131 AAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
*
1237 GCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGATAGGCCCAAAA
196 GCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
1302 T
261 T
* *
1303 CCAAAATGATTATTGTTAGTCCATAAACAATGAAAAGAAAAGCATT-AGGGTTT-CCGAATCGAA
1 CCAAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATTGA-GGTTTGCCAAATCGAA
* * *
1366 GACGATTTAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTA
65 GACGATTCAAAACGTCACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTA
* * * *
1431 AGAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAGACAACT-TAAAGAA
130 AAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAA
* * * *
1495 TAGCTTTGAGGTTTGCCAAATTGAAGACGATTCAAAACGGAACTAATGGGCCCCGATATGCCCAA
194 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
1560 AAT
259 AAT
1563 AACAAGTGTT
Statistics
Matches: 239, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
260 190 0.79
261 49 0.21
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (261 bp):
CCAAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
ACGATTCAAAACGTCACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAA
AAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
GCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
T
Found at i:1591 original size:154 final size:153
Alignment explanation
Indices: 1303--1849 Score: 794
Period size: 154 Copynumber: 3.6 Consensus size: 153
1293 GGCCCAAAAT
* * * *
1303 CCAAAATGATTATTGTTAGTCCATAAACAATGAAAAGAAAAGCATT-AGGGTTT-CCGAATCGAA
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTGCCAAATCGAA
* * * *
1366 GACGATTTAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTA
65 GACGATTCAAAACGTCACTAATGGGCCCCGATA-GCCCAAAATAACAAGTGTTCCAAATGAGCAA
* *
1431 AGAACTTCACAGTGGACTAATCTCA
129 AAAACTTTACAGTGGACTAATCTCA
* * * * *
1456 CCAAAATGATTATAGTTAGGCCATAGACAACT-TAAAGAATAGCTTTGAGGTTTGCCAAATTGAA
1 CCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA
**
1520 GACGATTCAAAACGGAACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCAA
65 GACGATTCAAAACGTCACTAATGGGCCCCGATA-GCCCAAAATAACAAGTGTTCCAAATGAGCAA
1585 AAAACTTTACAGTGGACTAATCTCA
129 AAAACTTTACAGTGGACTAATCTCA
*
1610 CCAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
*
1675 ACGATTCAAAACGTCACTAATGGGGCCCGATAGTCCCAAAATAACAAGTGTTCCAAATGAGCAAA
66 ACGATTCAAAACGTCACTAATGGGCCCCGATAG-CCCAAAATAACAAGTGTTCCAAATGAGCAAA
1740 AAACTTTACAGTGGACTAATCTCA
130 AAACTTTACAGTGGACTAATCTCA
* * * *
1764 CCAAAATGATTACAGATAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * *
1829 ACCATTCAAAATGTCAGTAAT
66 ACGATTCAAAACGTCACTAAT
1850 CTCGGCGTGG
Statistics
Matches: 357, Mismatches: 32, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
153 45 0.13
154 312 0.87
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (153 bp):
CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
ACGATTCAAAACGTCACTAATGGGCCCCGATAGCCCAAAATAACAAGTGTTCCAAATGAGCAAAA
AACTTTACAGTGGACTAATCTCA
Found at i:1816 original size:568 final size:569
Alignment explanation
Indices: 734--1839 Score: 1754
Period size: 568 Copynumber: 1.9 Consensus size: 569
724 ACTAATCTCA
*
734 CCAATATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATAAGGGTTTGCCGAATCGAAG
1 CCAAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATAAGGGTTTGCCGAATCGAAG
* *
799 ACGATTCAAAACGAAACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGGTCCAAATGAGCTAA
66 ACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGGTCCAAACGAGCTAA
* *
864 TGACTTCACAGTGGACTAATCTCACCAATATATTATAGTTAGTCCATAAACAATGAAAAGAAAAG
131 TGACTTCACAGTGGACTAATCTCACCAAAATATTATAGTTAGGCCATAAACAATGAAAAGAAAAG
* ** * *
929 CTTTAGAGATTGCCGAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCCAAAT
196 CTTTAGAGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCCAAAA
* **
994 TAATAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
261 TAACAAGTGTTCCAAATGAGCAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * *
1059 AGTCGATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATATGTCAC
326 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
*
1124 AAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACT
391 AAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCAAAAAACTTCACAATGGACT
* *
1189 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
456 AATCTCACCAAAATGATTACAGATAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
*
1254 ATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGATAGGCCCAAAAT
521 ATCGAAGACCATTCAAAACGGAACTAATGGTCCCCGATAGGCCCAAAAT
* *
1303 CCAAAATGATTATTGTTAGTCCATAAACAATGAAAAGAAAAGCATTAGGGTTT-CCGAATCGAAG
1 CCAAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATAAGGGTTTGCCGAATCGAAG
* ** * *
1367 ACGATTTAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAA
66 ACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGGTCCAAACGAGCTAA
* *
1432 -GAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAGACAACT-TAAAGAA
131 TG-ACTTCACAGTGGACTAATCTCACCAAAAT-ATTATAGTTAGGCCATAAACAA-TGAAAAGAA
* * * *
1495 TAGCTTT-GAGGTTTGCCAAATTGAAGACGATTCAAAACGGAACTAATGGGCCCCGATATG-CCC
193 AAGCTTTAGA-GATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCC
*
1558 AAAATAACAAGTGTTCCAAATGAGCAAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTAT
257 AAAATAACAAGTGTTCCAAATGAGCAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
*
1623 AGTTAGGCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
322 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
* * * * *
1688 TCACTAATGGGGCCCGATAGTCCCAAAATAACAAGTGTTCCAAATGAGCAAAAAACTTTACAGTG
387 TCACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCAAAAAACTTCACAATG
* *
1753 GACTAATCTCACCAAAATGATTACAGATAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTG
452 GACTAATCTCACCAAAATGATTACAGATAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
1818 CCAAATCGAAGACCATTCAAAA
517 CCAAATCGAAGACCATTCAAAA
1840 TGTCAGTAAT
Statistics
Matches: 490, Mismatches: 43, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
567 1 0.00
568 363 0.74
569 125 0.26
570 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (569 bp):
CCAAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATAAGGGTTTGCCGAATCGAAG
ACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGGTCCAAACGAGCTAA
TGACTTCACAGTGGACTAATCTCACCAAAATATTATAGTTAGGCCATAAACAATGAAAAGAAAAG
CTTTAGAGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCCAAAA
TAACAAGTGTTCCAAATGAGCAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
AAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCAAAAAACTTCACAATGGACT
AATCTCACCAAAATGATTACAGATAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
ATCGAAGACCATTCAAAACGGAACTAATGGTCCCCGATAGGCCCAAAAT
Done.