Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006628.1 Corchorus capsularis cultivar CVL-1 contig06649, 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:0.40, C:0.18, G:0.19, T:0.23
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1082 Score: 1569
Period size: 154 Copynumber: 6.9 Consensus size: 154
*
1 ATTCAAAACAGCACTAATGGGACCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGA-CATAAAA
1 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGC-TAAAA
65 ACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGC
65 ACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGC
130 TTTGTGGTTTGCCAAATCGAAGACG
130 TTTGTGGTTTGCCAAATCGAAGACG
* *
155 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTAAATGTGCTAAAAA
1 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA
*
220 CTTCACATTGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGCT
66 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGCT
*
285 TTGTGGTTTGGTCAAATACGAAGACG
131 TTGTGGTTT-GCCAAAT-CGAAGACG
*
311 ATTCAAAACAAGCACTAATGGGCCCCGGAAACGGACCCGGAAACTAAACAATTGTTCTGAATGAG
1 ATTCAAAAC-AGCACTAATGGGCCCC-GAAA-GG-CCC-GAAA-T-AACAAGTGTTCTGAATGAG
* * * * * * **
376 CTAAAAACTTCACAATGGACTAATTTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAAG
59 CTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAG
* * * *
441 AAAAGCTTTGTTGG-TTG-CAAATTGATGCCG
124 ATAAGCTTTG-TGGTTTGCCAAATCGAAGACG
* * * *
471 ATTTAACACAGCACTAATGGGCCTCGAAAGGCCCGAAATAACAACTGTTCTGAATGAGCTAAAAA
1 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA
*
536 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGCA
66 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGCT
*
601 TTGTGGTTTGGCAAATCGAAGACG
131 TTGTGGTTTGCCAAATCGAAGACG
625 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA
1 ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA
*
690 CTTCACAATGGACTAATTTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGCT
66 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGCT
755 TTGTGGTTTGTCCAAATACGAAGACG
131 TTGTGGTTTG-CCAAAT-CGAAGACG
*
781 ATTCAAAACAGCACTAATGGGCCCCGAAACGGCCCGAAACTAAACAAGTGTTCTGAATGTGCTAA
1 ATTCAAAACAGCACTAATGGGCCCCGAAA-GGCCCGAAA-T-AACAAGTGTTCTGAATGAGCTAA
* *
846 AAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGG-AAGAAA
63 AAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAA-AGGAAAGATA
* *
910 AGCTTTGTGGTTTGGCAAATCGAAAACG
127 AGCTTTGTGGTTTGCCAAATCGAAGACG
938 ATTCAAAACAGCACTAAGTCGGGACCCCGAAAGGCCCGAAATAACAACGTAGTTCTGAATGGAGC
1 ATTCAAAACAGCACTAA-T-GGG-CCCCGAAAGGCCCGAAATAACAA-GT-GTTCTGAAT-GAGC
* * * * * * **
1003 TAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGCTAGGTCGTATACAATTGAAAGA
60 TAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGA
*
1068 AAAGCTTTGTTGGTT
125 TAAGCTTTG-TGGTT
1083 AGCAAAA
Statistics
Matches: 840, Mismatches: 61, Indels: 47
0.89 0.06 0.05
Matches are distributed among these distances:
152 3 0.00
153 86 0.10
154 278 0.33
155 16 0.02
156 57 0.07
157 56 0.07
158 18 0.02
159 132 0.16
160 92 0.11
161 14 0.02
162 2 0.00
163 83 0.10
164 3 0.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (154 bp):
ATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA
CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGCT
TTGTGGTTTGCCAAATCGAAGACG
Found at i:971 original size:470 final size:471
Alignment explanation
Indices: 1--1049 Score: 1704
Period size: 470 Copynumber: 2.2 Consensus size: 471
*
1 ATTCAAAACAGCACTAATGGGA-CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGA-CATAAA
1 ATTCAAAACAGCACTAATGGGACCCCGAAAGGCCCGAAATAACAACTGTTCTGAATGAGC-TAAA
64 AACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAG
65 AACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAG
*
129 CTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAAT
130 CATTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAAT
* *
194 AACAAGTGTTCTAAATGTGCTAAAAACTTCACATTGGACTAATCTCATCAAAATAATTATAGTTA
195 AACAAGTGTTCTAAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTA
259 GGCCATAAACAAAGGAAAGATAAGCTTTGTGGTTTGGTCAAATACGAAGACGATTCAAAACAAGC
260 GGCCATAAACAAAGGAAAGATAAGCTTTGTGGTTTGGTCAAATACGAAGACGATTCAAAACAAGC
*
324 ACTAATGGGCCCCGGAAACGGACCCGGAAACTAAACAATTGTTCTGAATGAGCTAAAAACTTCAC
325 ACTAATGGGCCCCGGAAACGGACCCGGAAACTAAACAAGTGTTCTGAATGAGCTAAAAACTTCAC
* * * *
389 AATGGACTAATTTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTG
390 AATGGACTAATCTCACCAAAATAATTATAGCTAGGCCGTAAACAATAGAAAGAAAAGCTTTGTTG
* ***
454 GTTGCAAATTGATGCCG
455 GTTGCAAATCGAAAACG
* * *
471 ATTTAACACAGCACTAATGGG-CCTCGAAAGGCCCGAAATAACAACTGTTCTGAATGAGCTAAAA
1 ATTCAAAACAGCACTAATGGGACCCCGAAAGGCCCGAAATAACAACTGTTCTGAATGAGCTAAAA
535 ACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGC
66 ACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGC
*
600 ATTGTGGTTTGGCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATA
131 ATTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATA
* *
665 ACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATTTCATCAAAATAATTATAGTTAG
196 ACAAGTGTTCTAAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAG
730 GCCATAAACAAAGGAAAGATAAGCTTTGTGGTTT-GTCCAAATACGAAGACGATTCAAAAC-AGC
261 GCCATAAACAAAGGAAAGATAAGCTTTGTGGTTTGGT-CAAATACGAAGACGATTCAAAACAAGC
*
793 ACTAATGGGCCCC-GAAACGG-CCC-GAAACTAAACAAGTGTTCTGAATGTGCTAAAAACTTCAC
325 ACTAATGGGCCCCGGAAACGGACCCGGAAACTAAACAAGTGTTCTGAATGAGCTAAAAACTTCAC
* * *
855 AATGGACTAATCTCATCAAAATAATTATAGTTAGGCCAG-AAACAATAGGAAGAAAAGCTTTG-T
390 AATGGACTAATCTCACCAAAATAATTATAGCTAGGCC-GTAAACAATAGAAAGAAAAGCTTTGTT
918 GGTTTGGCAAATCGAAAACG
454 GG-TT-GCAAATCGAAAACG
938 ATTCAAAACAGCACTAAGTCGGGACCCCGAAAGGCCCGAAATAACAACGTAGTTCTGAATGGAGC
1 ATTCAAAACAGCACTAA-T-GGGACCCCGAAAGGCCCGAAATAACAAC-T-GTTCTGAAT-GAGC
* * *
1003 TAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGCTAGG
61 TAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGG
1050 TCGTATACAA
Statistics
Matches: 538, Mismatches: 29, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
465 3 0.01
466 92 0.17
467 29 0.05
468 8 0.01
469 21 0.04
470 326 0.61
471 2 0.00
472 9 0.02
473 48 0.09
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (471 bp):
ATTCAAAACAGCACTAATGGGACCCCGAAAGGCCCGAAATAACAACTGTTCTGAATGAGCTAAAA
ACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGC
ATTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATA
ACAAGTGTTCTAAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAG
GCCATAAACAAAGGAAAGATAAGCTTTGTGGTTTGGTCAAATACGAAGACGATTCAAAACAAGCA
CTAATGGGCCCCGGAAACGGACCCGGAAACTAAACAAGTGTTCTGAATGAGCTAAAAACTTCACA
ATGGACTAATCTCACCAAAATAATTATAGCTAGGCCGTAAACAATAGAAAGAAAAGCTTTGTTGG
TTGCAAATCGAAAACG
Done.