Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011785.1 Corchorus olitorius cultivar O-4 contig11818, 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, 612
Length: 1021
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1016 Score: 1591
Period size: 154 Copynumber: 6.6 Consensus size: 154
**
1 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
1 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
* *
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAGAACTTCACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* *
131 CACACCAAATTGATTATAGTTAGG
131 CTCACCAAATTGATTATAGTTAGT
**
155 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
1 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
* * * *
220 TGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACATCATAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
*
285 CTCACCAAATTGATTACAGTTAGT
131 CTCACCAAATTGATTATAGTTAGT
* * **
309 CCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
1 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
*
374 TGGGCCCCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* *
439 CTCACCAAAATGATTATAGTGAGT
131 CTCACCAAATTGATTATAGTTAGT
* * * * *
463 CTATAAAAAATAGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAA
1 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
528 TGGGCCCCGATAAGGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
66 TGGGCCCCGAT-AGG-CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
*
593 ATATCACCAAAATTGATTATAGTTAGT
129 ATCTCACC-AAATTGATTATAGTTAGT
* *
620 CCATAAAAAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAA
1 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
* * *
685 TGGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATTAGCTAAGAACTTCACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
*
750 CTCACCAAATTGATTATAGTTAGG
131 CTCACCAAATTGATTATAGTTAGT
* *
774 CCATAAACAATGGAAAGAAAAGCATTGAGTTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
1 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
*
839 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAAT
66 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* *
904 CTCATCAAAATGATTATAGTTAGT
131 CTCACCAAATTGATTATAGTTAGT
*** * * *
928 CCATAAACAACATAAAGAAAAACTTTGAGGTTTACCAAATCGAAGACGATCCAAAAACGTCACTA
1 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTC-AAAACGTCACTA
* *
993 ATGGGCACCGATAGGCCAAAAATA
65 ATGGGCCCCGATAGGCCCAAAATA
1017 CAAAT
Statistics
Matches: 800, Mismatches: 58, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
154 563 0.70
155 90 0.11
156 58 0.07
157 89 0.11
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
CTCACCAAATTGATTATAGTTAGT
Found at i:881 original size:465 final size:463
Alignment explanation
Indices: 1--1016 Score: 1635
Period size: 465 Copynumber: 2.2 Consensus size: 463
* **
1 CCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
1 CCATAAACAATAGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
*
66 TGGGCCCCGAT-AGGCCCAAAATAACAAGTGATCCAAATGAGCTAAGAACTTCACAGTGGACTAA
66 TGGGCCCCGATAAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
130 TCACACCAAATTGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
131 TCACACCAAATTGATTATAGTTAGGCCATAAAAAATGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
*
195 CGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAATTGA
196 CGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGATCCAATTGA
* * *
260 GCTAAAAACATCATAGTGGACTAATCTCACCAAATTGATTACAGTTAGTCCATAAATAATGGAAA
261 GCTAAAAACATCACAGTGGACTAATCTCACCAAATTGATTACAGTTAGGCCATAAACAATGGAAA
*
325 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGTC
326 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
*
390 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
391 CAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
455 TAGTGAGT
456 TAGTGAGT
* * * *
463 CTATAAAAAATAGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAA
1 CCATAAACAATAGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
*
528 TGGGCCCCGATAAGGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
66 TGGGCCCCGATAAGG-CCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTA
*
593 AT-ATCACCAAAATTGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGCTTTGAGGTTTGCCA
130 ATCA-CACC-AAATTGATTATAGTTAGGCCATAAAAAATGGAAAGAAAAGCTTTGAGGTTTGCCA
* ** *
657 AATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAA
193 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGATCC-AA
* * *
722 TT-AGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAATG
257 TTGAGCTAAAAACATCACAGTGGACTAATCTCACCAAATTGATTACAGTTAGGCCATAAACAATG
* **
786 GAAAGAAAAGCATTGAGTTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATA
322 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA
*
851 GGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCAAAATG
387 GGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
*
916 ATTATAGTTAGT
452 ATTATAGTGAGT
* * * * *
928 CCATAAACAACATAAAGAAAAACTTTGAGGTTTACCAAATCGAAGACGATCCAAAAACGTCACTA
1 CCATAAACAATAGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTC-AAAACGTCACTA
* *
993 ATGGGCACCGAT-AGGCCAAAAATA
65 ATGGGCCCCGATAAGGCCCAAAATA
1017 CAAAT
Statistics
Matches: 508, Mismatches: 40, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
462 69 0.14
463 4 0.01
464 61 0.12
465 348 0.69
466 26 0.05
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (463 bp):
CCATAAACAATAGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
TGGGCCCCGATAAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTAA
TCACACCAAATTGATTATAGTTAGGCCATAAAAAATGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
CGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGATCCAATTGA
GCTAAAAACATCACAGTGGACTAATCTCACCAAATTGATTACAGTTAGGCCATAAACAATGGAAA
GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
CAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
TAGTGAGT
Done.