Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006244.1 Corchorus capsularis cultivar CVL-1 contig06263, 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, 618
Length: 1030
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Found at i:607 original size:154 final size:153
Alignment explanation
Indices: 1--1030 Score: 1562
Period size: 154 Copynumber: 6.6 Consensus size: 153
*
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGACAGAAAAGCTTTGTGGTT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTGA-AGAAAAGCTTTGTGGTT
*
66 TGCCCAAATCGAAGCCGATTCAAAACAGCACGTAACTAGGGCCCCGAAAAGGACCCAAAATAACA
65 TG-CCAAATCGAAGCCGATTCAAAACAGCAC-TAA-T-GGGCCCCG-AAA-GACCCGAAATAACA
131 AGTGTTCTGAATAGAGCTAAAAACTTCACAA
124 AGTGTTCTGAAT-GAGCTAAAAACTTCACAA
* *
162 CGGACTAATACTACACCAAAATGATTATAGTTAGGTCGTAAACAATTAAAAGAAAAGCTTTGTGG
1 TGGACTAAT-CT-CACCAAAATGATTATAGTTAGGTCGTAAACAATT-GAAGAAAAGCTTTGTGG
*
227 TTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCCCGAAACGACCCGAAATAACAAGT
63 TTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCGAAA-GACCCGAAATAACAAGT
* * *
292 GTTCTGAATGACCGAAAAACTTCACAG
127 GTTCTGAATGAGCTAAAAACTTCACAA
* * * *
319 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAAAATTGAAAGAAAAGCATTGTGCTT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTG-AAGAAAAGCTTTGTGGTT
* * * *
384 TCCCAACTCGAAGCCCGATTCAAAACAGCACTAATGGGACCCCGAAAGGCCCGAAATAACAAGTT
65 TGCCAAATCGAAG-CCGATTCAAAACAGCACTAATGGG-CCCCGAAAGACCCGAAATAACAAGTG
449 TTCTGAATGAGCTAAAAACTTCACAA
128 TTCTGAATGAGCTAAAAACTTCACAA
*
475 TGGACTAATCTCACC-AAAT-ATTATAGTTAGGTCGT-AACAATTAGAAGAAAAGCTATGTGGTT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT-GAAGAAAAGCTTTGTGGTT
* *
537 TGCCAAATCGAAGCTGATTAGAAAACGAGCACTAATGGGACCCCGAAAGACCCGAAATAACAAGT
65 TGCCAAATCGAAGCCGATT-CAAAAC-AGCACTAATGGG-CCCCGAAAGACCCGAAATAACAAGT
602 GTTCTGAATGAGCTAAAAACTTCACAA
127 GTTCTGAATGAGCTAAAAACTTCACAA
629 TGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTGAAAGAAAAGTCTTTGTGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTG-AAGAAAAG-CTTTGTGGT
* * *
694 TTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCTGAAAGGCCCAAAATAACAAGTGT
64 TTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCGAAAGACCCGAAATAACAAGTGT
759 TCTGAATGAGCTAAAAACTTCACAA
129 TCTGAATGAGCTAAAAACTTCACAA
* *
784 CGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTAAAAGAAAAGCTTTGTGGTT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT-GAAGAAAAGCTTTGTGGTT
*
849 TGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCCCGAAAGACCCGAAATAACAAGTGTT
65 TGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCGAAAGACCCGAAATAACAAGTGTT
*
914 CTGAATGAGCGAAAAACTTCACAA
130 CTGAATGAGCTAAAAACTTCACAA
* * *
938 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGTTTTATGGTT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTG-AAGAAAAGCTTTGTGGTT
*
1003 TCCCAAATCGAAGCCGATTCAAAACAGC
65 TGCCAAATCGAAGCCGATTCAAAACAGC
Statistics
Matches: 800, Mismatches: 53, Indels: 39
0.90 0.06 0.04
Matches are distributed among these distances:
152 5 0.01
153 37 0.05
154 274 0.34
155 168 0.21
156 108 0.14
157 51 0.06
158 55 0.07
159 8 0.01
161 11 0.01
162 30 0.04
163 52 0.06
164 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (153 bp):
TGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTGAAGAAAAGCTTTGTGGTTT
GCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCGAAAGACCCGAAATAACAAGTGTTC
TGAATGAGCTAAAAACTTCACAA
Found at i:922 original size:309 final size:308
Alignment explanation
Indices: 1--1030 Score: 1706
Period size: 309 Copynumber: 3.3 Consensus size: 308
*
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGACAGAAAAGCTTTGTGGTT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGTGGTT
66 TGCCCAAATCGAAGCCGATTCAAAACAGCACGTAACTAGGGCCCCGAAAAGGACCCAAAATAACA
66 T-CCCAAATCGAAGCCGATTCAAAACAGCAC-TAA-T-GGGCCCCG-AAAGG-CCCAAAATAACA
131 AGTGTTCTGAATAGAGCTAAAAACTTCACAACGGACTAATACTACACCAAAATGATTATAGTTAG
125 AGTGTTCTGAAT-GAGCTAAAAACTTCACAACGGACTAAT-CT-CACCAAAATGATTATAGTTAG
196 GTCGTAAACAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTA
187 GTCGTAAACAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTA
* *
261 ACGGGCCCCGAAACGACCCGAAATAACAAGTGTTCTGAATGACCGAAAAACTTCACAG
252 ACGGGCCCCGAAA-GACCCGAAATAACAAGTGTTCTGAATGAGCGAAAAACTTCACAA
* * *
319 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAAAATTGAAAGAAAAGCATTGTGCTT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGTGGTT
* * *
384 TCCCAACTCGAAGCCCGATTCAAAACAGCACTAATGGGACCCCGAAAGGCCCGAAATAACAAGTT
66 TCCCAAATCGAAG-CCGATTCAAAACAGCACTAATGGG-CCCCGAAAGGCCCAAAATAACAAGTG
*
449 TTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACC-AAAT-ATTATAGTTAGGTCGT-A
129 TTCTGAATGAGCTAAAAACTTCACAACGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAA
* * * * *
511 ACAATTAGAAGAAAAGCTATGTGGTTTGCCAAATCGAAGCTGATTAGAAAACGAGCACTAATGGG
194 ACAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATT-CAAAAC-AGCACTAACGGG
*
576 ACCCCGAAAGACCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAA
257 -CCCCGAAAGACCCGAAATAACAAGTGTTCTGAATGAGCGAAAAACTTCACAA
*
629 TGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTGAAAGAAAAGTCTTTGTGGT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAG-CTTTGTGGT
* *
694 TTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCTGAAAGGCCCAAAATAACAAGTGT
65 TTCCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGT
759 TCTGAATGAGCTAAAAACTTCACAACGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAA
130 TCTGAATGAGCTAAAAACTTCACAACGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAA
824 CAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCC
195 CAATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCC
889 CGAAAGACCCGAAATAACAAGTGTTCTGAATGAGCGAAAAACTTCACAA
260 CGAAAGACCCGAAATAACAAGTGTTCTGAATGAGCGAAAAACTTCACAA
* *
938 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGTTTTATGGTT
1 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGTGGTT
1003 TCCCAAATCGAAGCCGATTCAAAACAGC
66 TCCCAAATCGAAGCCGATTCAAAACAGC
Statistics
Matches: 667, Mismatches: 36, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
308 78 0.12
309 189 0.28
310 148 0.22
311 52 0.08
312 45 0.07
313 26 0.04
314 22 0.03
315 8 0.01
316 6 0.01
317 14 0.02
318 79 0.12
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (308 bp):
TGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGCTTTGTGGTT
TCCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTT
CTGAATGAGCTAAAAACTTCACAACGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAAC
AATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCCC
GAAAGACCCGAAATAACAAGTGTTCTGAATGAGCGAAAAACTTCACAA
Done.