Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004656.1 Corchorus capsularis cultivar CVL-1 contig04669, 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, 653
Length: 1089
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Found at i:286 original size:154 final size:154
Alignment explanation
Indices: 1--1086 Score: 1730
Period size: 154 Copynumber: 7.0 Consensus size: 154
* * *
1 AAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTATTGGG
1 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGG
* * *
66 CCCCGAAAGGCCCGAAATAACAAGTATTCTGAATGAGCTAAAAACTTCACAATGGACTAATATCA
66 CCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCA
*
131 CCAAAATGATAATAGTTAGGTCGT
131 CCAAAATGATTATAGTTAGGTCGT
*
155 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCATTAATGGG
1 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGG
*
220 CCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
66 CCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCA
*
285 CCAAAATGATTATAGTTAGGCCGT
131 CCAAAATGATTATAGTTAGGTCGT
* * *
309 AAA-AATTGAAAGAAAAGCTTTGTGCTTTCCCAACTCGAAGCCGATTCGAAAACAGCACTAATGG
1 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTC-AAAACAGCACTAATGG
* *
373 GCCCCGAAAGGCCCGAAATAACAAGTATTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTC
65 GCCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTC
438 ACCAAAATGATTATAGTTAGGTCGT
130 ACCAAAATGATTATAGTTAGGTCGT
* * * * *
463 AAAACAATTAAAAGAAACGCTTAGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGA
1 -AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGG
* *
528 GCCCCGAAA-GACCCGAAATAACAAGTGTTCTGAATGAGCGAAAAACTTCACAGTGGACTAATCT
65 GCCCCGAAAGGA-CCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCT
592 CACCAAAATGATTATAGTTAGGTCGT
129 CACCAAAATGATTATAGTTAGGTCGT
* * *
618 AAACAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATGGAAGCCGATTCAAAACAGCACTAACGGG
1 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGG
* * *
683 CCCCGAAA-GACACGAAATAACAAGTGTTCTGATTGAGCGAAAAACTTCACAGTGGACTAATCTC
66 CCCCGAAAGGAC-CGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTC
*
747 ACCAAAATGATTATAGTTAGGCCGT
130 ACCAAAATGATTATAGTTAGGTCGT
* * *
772 AAACAATTGAAAGAAAAGCTTTATGGTTTCCCAAATCGAAGTCGATTCAAAACAGCACTAATGGG
1 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGG
* * *
837 CCCCGAAAGGCCCGAAATAACAAGGGTTCTGAATGAGTTAAAAACTTCACAATGGACTAATCTCA
66 CCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCA
*
902 CTAAAATGATTATAGTTAGGTCGT
131 CCAAAATGATTATAGTTAGGTCGT
*
926 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTAAAAACAGCACTAATGGG
1 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGG
*
991 CCCCGAAAGGACCGAAATAACAAGTGTTCTG-ATGAGCTAAAAAACTTCACAATGGACTAATGTC
66 CCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCT-AAAAACTTCACAATGGACTAATCTC
* * *
1055 ACCAAAATGATTTTAGTTAGGCCAT
130 ACCAAAATGATTATAGTTAGGTCGT
1080 AAACAAT
1 AAACAAT
1087 GGA
Statistics
Matches: 863, Mismatches: 62, Indels: 14
0.92 0.07 0.01
Matches are distributed among these distances:
153 48 0.06
154 674 0.78
155 103 0.12
156 38 0.04
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGG
CCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCA
CCAAAATGATTATAGTTAGGTCGT
Found at i:869 original size:463 final size:462
Alignment explanation
Indices: 1--1086 Score: 1793
Period size: 463 Copynumber: 2.3 Consensus size: 462
* * *
1 AAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTATTGGG
1 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGG
* * *
66 CCCCGAAAGGCCCGAAATAACAAGTATTCTGAATGAGCTAAAAACTTCACAATGGACTAATATCA
66 CCCCGAAAGACCCGAAATAACAAGTGTTCTGAATGAGCAAAAAACTTCACAATGGACTAATATCA
* *
131 CCAAAATGATAATAGTTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAG
131 CCAAAATGATTATAGTTAGGTCGTAAACAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAG
* * *
196 CCGATTCAAAACAGCATTAATGGGCCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCTAA
196 CCGATTCAAAACAGCACTAACGGGCCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCGAA
261 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAAATTGAAAGAAAAG
261 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAAATTGAAAGAAAAG
* *
326 CTTTGTGCTTTCCCAACTCGAAGCCGATTCGAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAA
326 CTTTATGCTTTCCCAAATCGAAGCCGATTCGAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAA
*
391 TAACAAGTATTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTT
391 TAACAAGGATTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTT
456 AGGTCGT
456 AGGTCGT
* * * * *
463 AAAACAATTAAAAGAAACGCTTAGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGA
1 -AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGG
* * *
528 GCCCCGAAAGACCCGAAATAACAAGTGTTCTGAATGAGCGAAAAACTTCACAGTGGACTAATCTC
65 GCCCCGAAAGACCCGAAATAACAAGTGTTCTGAATGAGCAAAAAACTTCACAATGGACTAATATC
*
593 ACCAAAATGATTATAGTTAGGTCGTAAACAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATGGAA
130 ACCAAAATGATTATAGTTAGGTCGTAAACAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAA
*
658 GCCGATTCAAAACAGCACTAACGGGCCCCGAAA-GACACGAAATAACAAGTGTTCTGATTGAGCG
195 GCCGATTCAAAACAGCACTAACGGGCCCCGAAAGGAC-CGAAATAACAAGTGTTCTGAATGAGCG
722 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAA
259 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAA-AATTGAAAGAA
* *
787 AAGCTTTATGGTTTCCCAAATCGAAGTCGATTC-AAAACAGCACTAATGGGCCCCGAAAGGCCCG
323 AAGCTTTATGCTTTCCCAAATCGAAGCCGATTCGAAAACAGCACTAATGGGCCCCGAAAGGCCCG
* * *
851 AAATAACAAGGGTTCTGAATGAGTTAAAAACTTCACAATGGACTAATCTCACTAAAATGATTATA
388 AAATAACAAGGATTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATA
916 GTTAGGTCGT
453 GTTAGGTCGT
*
926 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTAAAAACAGCACTAATGGG
1 AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGG
*
991 CCCCGAAAGGA-CCGAAATAACAAGTGTTCTG-ATGAGCTAAAAAACTTCACAATGGACTAATGT
66 CCCCGAAA-GACCCGAAATAACAAGTGTTCTGAATGAGC-AAAAAACTTCACAATGGACTAATAT
* * *
1054 CACCAAAATGATTTTAGTTAGGCCATAAACAAT
129 CACCAAAATGATTATAGTTAGGTCGTAAACAAT
1087 GGA
Statistics
Matches: 579, Mismatches: 40, Indels: 9
0.92 0.06 0.01
Matches are distributed among these distances:
461 6 0.01
462 142 0.25
463 391 0.68
464 40 0.07
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (462 bp):
AAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGG
CCCCGAAAGACCCGAAATAACAAGTGTTCTGAATGAGCAAAAAACTTCACAATGGACTAATATCA
CCAAAATGATTATAGTTAGGTCGTAAACAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAG
CCGATTCAAAACAGCACTAACGGGCCCCGAAAGGACCGAAATAACAAGTGTTCTGAATGAGCGAA
AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAAATTGAAAGAAAAG
CTTTATGCTTTCCCAAATCGAAGCCGATTCGAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAA
TAACAAGGATTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTT
AGGTCGT
Done.