Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006282.1 Corchorus capsularis cultivar CVL-1 contig06301, 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, 629
Length: 1049
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Found at i:284 original size:154 final size:154
Alignment explanation
Indices: 1--1047 Score: 1568
Period size: 154 Copynumber: 6.8 Consensus size: 154
*
1 CAGTGGACTAATCTCACCAAAATGATTATCGTTAGGCCGTAAACAATTGAAAGAAAAGACTTTGT
1 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAG-CTTTGT
* *
66 GGTTTGCCAAATC-AATGACAATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCTAAATAACAA
65 GGTTTGCCAAATCGAA-GACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAA
*
130 GTGTTCTGAATGAGCTAAAATCTTCA
129 GTGTTCTGAATGAGCTAAAAACTTCA
* *
156 CAGTGGAGTAATCTCA-CAACAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTCTGT
1 CAGTGGACTAATCTCACCAA-AATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGT
* * *
220 GGTTTGCCAAATCGAAGACGATTCTAAACAGCACAAATGGGCCTCGAAAGGCCCGAAATAACAAG
65 GGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAG
*
285 TGTTTTGAATGAGCTAAAAACTTCA
130 TGTTCTGAATGAGCTAAAAACTTCA
* * * * *
310 CAATGGACTAATCTCAACAAAATAATTATAGTTAGGTCGTAAACTATTGAAAGAAAAGCTTTGTG
1 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGTG
* * * * *
375 GTTTGCCAAATTGAAGCCGATACAAAACAGCAGTAATGGGCCCCGAAAGGCCCTAAATAACAAGT
66 GTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGT
* * *
440 GTTCTGATTGAGCTAAAATCATCA
131 GTTCTGAATGAGCTAAAAACTTCA
*
464 CAGTGGACTAATCTCACCAAAATGATTATCGTTAGGCCGTAAACAATTTG-AAGAAAAGCTTTGT
1 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAA-TTGAAAGAAAAGCTTTGT
* *
528 GGTTTGCGAAATCGAAGACGAATTCAAAACAGTCACTAATGGGCCCCGAAAGGTCCTGAAATAAC
65 GGTTTGCCAAATCGAAGACG-ATTCAAAACAG-CACTAATGGGCCCCGAAAGG-CCCGAAATAAC
593 AAGTAGTTCTGAATGAGCTAAAAACTTCA
127 AAGT-GTTCTGAATGAGCTAAAAACTTCA
*
622 CAGTGTACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGTG
1 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGTG
* * * * *
687 GTTTGCTAAATCGAAGCCGATTCAATACAGCACTAAAGGGCCCCGAAAGGCCTGAAATAACAAGT
66 GTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGT
*
752 GTCCTGAATGAGCTAAAAACTTCA
131 GTTCTGAATGAGCTAAAAACTTCA
* *
776 CAGTGTACTAATCTCACCAAAATGATTATA-TAACGGCCGTAAACAATTGAAAGAAAAGCTTTGT
1 CAGTGGACTAATCTCACCAAAATGATTATAGTTA-GGCCGTAAACAATTGAAAGAAAAGCTTTGT
* *
840 GGTTTGCGAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAG
65 GGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAG
905 TGTTCTGAATGAAGCTAAAAAACTTCA
130 TGTTCTGAATG-AGCT-AAAAACTTCA
* *
932 CAGTGTACTAATCTCACCAAAATGATTATA--TAGGCCGTAAACAATTGAAAGAAAAGCTTTTTT
1 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGC-TTTGT
*
995 GGTTTGCAAAATCGAAGACGATTTCAAAACAGCACTAATGGGCCCCG-AAGGCC
65 GGTTTGCCAAATCGAAGACGA-TTCAAAACAGCACTAATGGGCCCCGAAAGGCC
1048 TG
Statistics
Matches: 818, Mismatches: 60, Indels: 28
0.90 0.07 0.03
Matches are distributed among these distances:
153 2 0.00
154 470 0.57
155 120 0.15
156 103 0.13
157 26 0.03
158 97 0.12
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (154 bp):
CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGTG
GTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGT
GTTCTGAATGAGCTAAAAACTTCA
Found at i:869 original size:466 final size:465
Alignment explanation
Indices: 1--1047 Score: 1607
Period size: 466 Copynumber: 2.3 Consensus size: 465
1 CAGTGGACTAATCTCACCAAAATGATTATCGTTAGGCCGTAAACAATTGAAAGAAAAGACTTTGT
1 CAGTGGACTAATCTCACCAAAATGATTATCGTTAGGCCGTAAACAATTGAAAGAAAAG-CTTTGT
*
66 GGTTTGCCAAATC-AATGAC-AATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCTAAATAACA
65 GGTTTGCAAAATCGAA-GACGAATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCTAAATAACA
* *
129 AGTGTTCTGAATGAGCTAAAATCTTCACAGTGGAGTAATCTCACAACAATGATTATAGTTAGGCC
129 AGTGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAACAATGATTATAGTTAGGCC
194 GTAAACAATTGAAAGAAAAGCTCTGTGGTTTGCCAAATCGAAGACGATTCTAAACAGCACAAATG
194 GTAAACAATTGAAAGAAAAGCTCTGTGGTTTGCCAAATCGAAGACGATTCTAAACAGCACAAATG
* **
259 GGCCTCGAAAGGCCCGAAATAACAAGTGTTTTGAATGAGCTAAAAACTTCACAATGGACTAATCT
259 GGCCCCGAAAGGCCCGAAATAACAAGTGTCCTGAATGAGCTAAAAACTTCACAATGGACTAATCT
* * * *
324 CAACAAAATAATTATAGTTAGGTCGTAAACTATTGAAAGAAAAGCTTTGTGGTTTGCCAAATTGA
324 CAACAAAATAATTATAGTAAGGCCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGA
* * *
389 AGCCGATACAAAACAGCAGTAATGGGCCCCGAAAGGCCCT-AAATAACAAGTGTTCTGATTG-AG
389 AGACGATACAAAACAGCACTAATGGGCCCCGAAAGG-CCTGAAATAACAAGTGTTCTGAATGAAG
*
452 CT-AAAATCATCA
453 CTAAAAAACATCA
464 CAGTGGACTAATCTCACCAAAATGATTATCGTTAGGCCGTAAACAATTTG-AAGAAAAGCTTTGT
1 CAGTGGACTAATCTCACCAAAATGATTATCGTTAGGCCGTAAACAA-TTGAAAGAAAAGCTTTGT
* *
528 GGTTTGCGAAATCGAAGACGAATTCAAAACAGTCACTAATGGGCCCCGAAAGGTCCTGAAATAAC
65 GGTTTGCAAAATCGAAGACGAATTCAAAACAG-CACTAATGGGCCCCGAAAGGCCCT-AAATAAC
*
593 AAGTAGTTCTGAATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAA-AATGATTATAGTTAG
128 AAGT-GTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CAACAATGATTATAGTTAG
* * *
657 GCCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCTAAATCGAAGCCGATTC-AATACAGCACT
191 GCCGTAAACAATTGAAAGAAAAGCTCTGTGGTTTGCCAAATCGAAGACGATTCTAA-ACAGCAC-
* * *
721 AAA-GGGCCCCGAAAGGCCTGAAATAACAAGTGTCCTGAATGAGCTAAAAACTTCACAGTGTACT
254 AAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTCCTGAATGAGCTAAAAACTTCACAATGGACT
* * *
785 AATCTCACCAAAATGATTATA-TAACGGCCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCGA
319 AATCTCAACAAAATAATTATAGTAA-GGCCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCA
*
849 AATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGAA
383 AATCGAAGACGATACAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGAA
*
914 TGAAGCTAAAAAACTTCA
448 TGAAGCTAAAAAACATCA
* * *
932 CAGTGTACTAATCTCACCAAAATGATTAT--ATAGGCCGTAAACAATTGAAAGAAAAGCTTTTTT
1 CAGTGGACTAATCTCACCAAAATGATTATCGTTAGGCCGTAAACAATTGAAAGAAAAGC-TTTGT
*
995 GGTTTGCAAAATCGAAGACGATTTCAAAACAGCACTAATGGGCCCCG-AAGGCC
65 GGTTTGCAAAATCGAAGACGAATTCAAAACAGCACTAATGGGCCCCGAAAGGCC
1048 TG
Statistics
Matches: 536, Mismatches: 33, Indels: 28
0.90 0.06 0.05
Matches are distributed among these distances:
462 21 0.04
463 68 0.13
464 26 0.05
465 26 0.05
466 315 0.59
467 44 0.08
468 36 0.07
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (465 bp):
CAGTGGACTAATCTCACCAAAATGATTATCGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGTG
GTTTGCAAAATCGAAGACGAATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCTAAATAACAAG
TGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAACAATGATTATAGTTAGGCCGT
AAACAATTGAAAGAAAAGCTCTGTGGTTTGCCAAATCGAAGACGATTCTAAACAGCACAAATGGG
CCCCGAAAGGCCCGAAATAACAAGTGTCCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCA
ACAAAATAATTATAGTAAGGCCGTAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAG
ACGATACAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGAATGAAGCTA
AAAAACATCA
Done.