Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015623.1 Corchorus capsularis cultivar CVL-1 contig15644, 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: 51091
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:12305 original size:77 final size:77
Alignment explanation
Indices: 12203--12401 Score: 267
Period size: 77 Copynumber: 2.6 Consensus size: 77
12193 ATATCAACAC
* * * * **
12203 ATGTGGTATTGAGT-AAAATTCACTCAAAATTCCTTAAATAAGATTTCAGATTCAAATCATGTGA
1 ATGTCGTATTGAGTAAAAATT-ACTCAATATTCCTTAAATAAGATTTCAAATTCAAATAATGCAA
*
12267 ACAAAGAAAATAG
65 ACAAAGAAAATAA
*
12280 ATGAT-GTATTGAGTAAAAATTACTCAATATTCCTTAAATAAGATCTCAAATTCAAATAATGCAA
1 ATG-TCGTATTGAGTAAAAATTACTCAATATTCCTTAAATAAGATTTCAAATTCAAATAATGCAA
*
12344 ACAAATAAAATAA
65 ACAAAGAAAATAA
* *
12357 ATGTCGTATTGAGTAAAAGTTTCTCAATATTCCTTAAATAAGATT
1 ATGTCGTATTGAGTAAAAATTACTCAATATTCCTTAAATAAGATT
12402 CGAGTCATGA
Statistics
Matches: 108, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
76 1 0.01
77 100 0.93
78 7 0.06
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (77 bp):
ATGTCGTATTGAGTAAAAATTACTCAATATTCCTTAAATAAGATTTCAAATTCAAATAATGCAAA
CAAAGAAAATAA
Found at i:14586 original size:318 final size:312
Alignment explanation
Indices: 13891--14715 Score: 1023
Period size: 318 Copynumber: 2.6 Consensus size: 312
13881 CTGGTTGGCT
*
13891 GAGGTTTCACCTCATTCTCCACAGGTTGCTTCATACTCCCTTCCTTGAACTGCACTCCTCCCTTC
1 GAGGTTTCACCTCATTCTCTACAGGTTGCTTCATAC-CCCTTCCTTGAACTGCACTCCTCCCTTC
* * * * * *
13956 CTTTCCAAAGGCTTTGCTCCTTTACAATGCTTCTTACCCTTTGATTTACCCAGATCATCTTTAAA
65 CCTTCCAAAGG-TTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTAAA
* * * * * * * * **
14021 CGGCCTCTTCTCTGTTTGACTACTTTCATGATGACCAAGCTGAGTTGTAGTTTGATGTACTATTC
129 AGGCCTCTTCTTTGTTTGACTACTTTCATAATGAACAAGCTGACTT-TACTTTGATTTTCTGGTC
* * *
14086 CTAGATTTTCTGTTAACTCTGTCTTTATTTCATTAGAATTATTCAGAACAGAAACCTTAGATGTA
193 CTAGATGTTCTGTTAACTCTGTCTTTATTTCATCAGAATTATTCAGAACAGAAACATTAGATGTA
** *
14151 ATTTTAACATGATTGGTAGCAACACTATCCCCAATAGTATCCCTACTAATTGGCA
258 ATTTTAACATGATTGGTAGCAACACTATCCCCAATAGTATCCCTACTAATCAGAA
*
14206 GAGGTTTTACCTCATTCTCTACAGGTTGCTT-ATCACCCCCTTCCTTGAACTGCACTCCTCCCTT
1 GAGGTTTCACCTCATTCTCTACAGGTTGCTTCAT-A-CCCCTTCCTTGAACTGCACTCCTCCCTT
14270 CCCTTCCAAATGGTTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTAA
64 CCCTTCCAAA-GGTTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTAA
* * *
14335 AAGGCCTCTTCTTTGTTTGACTACTTCCACAATGAACAAGCTGACCTTTACTTTGTTTTTCTGGT
128 AAGGCCTCTTCTTTGTTTGACTACTTTCATAATGAACAAGCTGA-CTTTACTTTGATTTTCTGGT
* * **
14400 CCTAGATGTTCTGTTAACTTTGTCTTATTTTTTTCATCAGAATTATTGGGAACAG-AACTATTAG
192 CCTAGATGTTCTGTTAACTCTGTC---TTTATTTCATCAGAATTATTCAGAACAGAAAC-ATTAG
* *** * *
14464 -TGGTAGTTTTAACCA-GATCT-GTAGCAATGTTATCCCCTATAGTGTCCCTACTAATCAGAA
253 AT-GTAATTTTAA-CATGAT-TGGTAGCAACACTATCCCCAATAGTATCCCTACTAATCAGAA
*
14524 GAGGTTTCACCTCATTCTCTACAGGTTGCTTCCTACCCACTTCCTTGAACTGCACTCCTCCCTTC
1 GAGGTTTCACCTCATTCTCTACAGGTTGCTTCATACCC-CTTCCTTGAACTGCACTCCTCCCTTC
** * *
14589 CCTTCCAAAAGCG-TCACTCCTTTACATTGCTTTTTACCCTTTGATTTATCAAGATCTTCTGCAA
65 CCTTCC-AAAG-GTTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTAA
** * * *
14653 AAACCCTCTTCTTTGTTTGACTACTTTCATTATGAACAAGCTCAGTTTTACTTTGATTTTCTG
128 AAGGCCTCTTCTTTGTTTGACTACTTTCATAATGAACAAGCTGA-CTTTACTTTGATTTTCTG
14716 TTAACTTTAT
Statistics
Matches: 443, Mismatches: 52, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
314 2 0.00
315 184 0.42
316 5 0.01
317 7 0.02
318 237 0.53
319 8 0.02
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (312 bp):
GAGGTTTCACCTCATTCTCTACAGGTTGCTTCATACCCCTTCCTTGAACTGCACTCCTCCCTTCC
CTTCCAAAGGTTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTAAAAG
GCCTCTTCTTTGTTTGACTACTTTCATAATGAACAAGCTGACTTTACTTTGATTTTCTGGTCCTA
GATGTTCTGTTAACTCTGTCTTTATTTCATCAGAATTATTCAGAACAGAAACATTAGATGTAATT
TTAACATGATTGGTAGCAACACTATCCCCAATAGTATCCCTACTAATCAGAA
Found at i:38976 original size:14 final size:14
Alignment explanation
Indices: 38958--38994 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
38948 ATCGTTTCCG
38958 TTTTTTTGTTTT-T
1 TTTTTTTGTTTTGT
*
38971 TGTTTTTGTTTTGT
1 TTTTTTTGTTTTGT
38985 TTTTTTTGTT
1 TTTTTTTGTT
38995 GTGAAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTTTTGTTTTGT
Done.