Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006648.1 Corchorus capsularis cultivar CVL-1 contig06669, 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, 637
Length: 1062
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Found at i:221 original size:113 final size:111
Alignment explanation
Indices: 19--224 Score: 340
Period size: 113 Copynumber: 1.8 Consensus size: 111
9 CTACTAGGCG
* *
19 CCGAAAGGCCCGAAATAAAAGTGTTCTGAATGAGCTAAAAACTTCACATTGGACTAATCTCATCA
1 CCGAAAGGCCCGAAATAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCA
84 AAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGTGGGCC
66 AAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGTGGGCC
*
130 CCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAAACTTCACAATGGACTATTCTCAC
1 CCGAAAGGCCCGAAAT-AAAAGTGTTCTGAATGAGCT-AAAAACTTCACAATGGACTAATCTCAC
* * *
195 CAAAATGATTATAGTTAGGTCGTAAACAAT
64 CAAAATAATTATAGTTAGGCCATAAACAAT
225 TAGAAGAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 16 0.18
112 20 0.23
113 51 0.59
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (111 bp):
CCGAAAGGCCCGAAATAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCA
AAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGTGGGCC
Found at i:767 original size:307 final size:306
Alignment explanation
Indices: 124--1062 Score: 1440
Period size: 307 Copynumber: 3.1 Consensus size: 306
114 AAAGAAAAAG
*
124 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAAACTTCACAATGGACTAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCT-AAAAACTTCACAATGGACTAA
* *
189 TCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTAGAAGAAAAGCTTTCTTGG-TTGCCAAA
65 TCTCATCAAAATGATTATAGTTAGGTCGTAAACAATTAGAAGAAAAGCTTT-GTGGTTTGCCAAA
* * * * *
253 TTGAAGCCGATTTAAAACAGCACTACTGGGCCCCGAAAGGCCCGAAATAAAAAATGTTCTGAATG
129 TCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATG
* *
318 AGATAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGTCGTAAACAATGGAA
194 AGCTAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAGTTAGGTCGTAAACAATGGAA
* * *
383 AGAAAAGCTTTCTTGGTTGCCAAATTGAAGCCGATTTAAAACAGCACTAC
259 A-AAAAGCTTTGTT-GTTGCCAAATAGAAGACGATTTAAAACAGCACTAC
*
433 TGAGCCCCGAAAGGCCCG-AAT-AAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
* *
496 CTCATCAAAATGATTATAGTTAGGTCGT-AACATATTTGAATGAAATGCTTTGTGGTTTGCCAAA
66 CTCATCAAAATGATTATAGTTAGGTCGTAAACA-ATTAGAA-GAAAAGCTTTGTGGTTTGCCAAA
* *
560 TCGTAGACGATTCAAAACAGCACTAATGGGCCCCGAACGGCCCGAAATAAAAAGTGTTCTGAATG
129 TCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATG
* *
625 AGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATCGAA
194 AGCTAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAGTTAGGTCGTAAACAATGGAA
* * *
690 AAAAAGATTTGTTGATGCCAAATAGAAGACGATTTAAAACAGCACTAA
259 AAAAAGCTTTGTTGTTGCCAAATAGAAGACGATTTAAAACAGCACTAC
738 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
* * * *
803 CTCATCAAAATAATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCTTTGTGGTTTGCCAAAT
66 CTCATCAAAATGATTATAGTTAGGTCGTAAACAATTAG-AAGAAAAGCTTTGTGGTTTGCCAAAT
867 CGAAGACGATTCAAAACAGCACTAATGGG-CCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGA
130 CGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGA
* * *
931 GCTAAAAACTTCACAATAGACTAATCTCATCAAAATGATTATAGTTAGGTCGTAAATATTTGGAA
195 GCTAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAGTTAGGTCGTAAACA-ATGGAA
* * * * *
996 GAAAAGCTTTGTTGTTTGCCTAATCGAAGATGATTCAAAACAGCACTAC
259 AAAAAGCTTTGTTG-TTGCCAAATAGAAGACGATTTAAAACAGCACTAC
1045 TGGGCCCCGAAAGGCCCG
1 TGGGCCCCGAAAGGCCCG
Statistics
Matches: 577, Mismatches: 44, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
305 141 0.24
306 139 0.24
307 273 0.47
308 7 0.01
309 17 0.03
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (306 bp):
TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
CTCATCAAAATGATTATAGTTAGGTCGTAAACAATTAGAAGAAAAGCTTTGTGGTTTGCCAAATC
GAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAG
CTAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAGTTAGGTCGTAAACAATGGAAAA
AAAGCTTTGTTGTTGCCAAATAGAAGACGATTTAAAACAGCACTAC
Found at i:958 original size:153 final size:153
Alignment explanation
Indices: 124--1062 Score: 1388
Period size: 153 Copynumber: 6.1 Consensus size: 153
114 AAAGAAAAAG
*
124 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAAACTTCACAATGGACTAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCT-AAAAACTTCACAATGGACTAA
* * *
189 TCTCACCAAAATGATTATAGTTAGGTCGTAAACAAT-TAGAAGAAAAGCTTTCTTGGTTGCCAAA
65 TCTCATCAAAATGATTATAGTTAGGTCGTAAACAATGGA-AAGAAAAGCTTT-GTGGTTGCCAAA
* * * *
253 TTGAAGCCGATTTAAAACAGCACTAC
128 TCGAAGACGATTCAAAACAGCACTAA
* *
279 TGGGCCCCGAAAGGCCCGAAATAAAAAATGTTCTGAATGAGATAAAAACTTCACAATGGACTAAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
* * *
344 CTCATCAAAATAATTATAGTTAGGTCGTAAACAATGGAAAGAAAAGCTTTCTTGGTTGCCAAATT
66 CTCATCAAAATGATTATAGTTAGGTCGTAAACAATGGAAAGAAAAGCTTT-GTGGTTGCCAAATC
* * *
409 GAAGCCGATTTAAAACAGCACTAC
130 GAAGACGATTCAAAACAGCACTAA
*
433 TGAGCCCCGAAAGGCCCG-AAT-AAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
* * *
496 CTCATCAAAATGATTATAGTTAGGTCGT-AACATATTTGAATGAAATGCTTTGTGGTTTGCCAAA
66 CTCATCAAAATGATTATAGTTAGGTCGTAAACA-A-TGGAAAGAAAAGCTTTGTGG-TTGCCAAA
*
560 TCGTAGACGATTCAAAACAGCACTAA
128 TCGAAGACGATTCAAAACAGCACTAA
*
586 TGGGCCCCGAACGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
* * * * * *
651 CTCACCAAAATGATTATAGTTAGGTCGTAAACAATCGAAA-AAAAGATTTGTTGATGCCAAATAG
66 CTCATCAAAATGATTATAGTTAGGTCGTAAACAATGGAAAGAAAAGCTTTGTGGTTGCCAAATCG
*
715 AAGACGATTTAAAACAGCACTAA
131 AAGACGATTCAAAACAGCACTAA
738 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
* * *
803 CTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATC
66 CTCATCAAAATGATTATAGTTAGGTCGTAAACAATGGAAAGAAAAGCTTTGTGG-TTGCCAAATC
868 GAAGACGATTCAAAACAGCACTAA
130 GAAGACGATTCAAAACAGCACTAA
*
892 TGGG-CCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATAGACTAAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
* * * *
956 CTCATCAAAATGATTATAGTTAGGTCGTAAATATTTGG-AAGAAAAGCTTTGTTGTTTGCCTAAT
66 CTCATCAAAATGATTATAGTTAGGTCGTAAACA-ATGGAAAGAAAAGCTTTG-TGGTTGCCAAAT
* *
1020 CGAAGATGATTCAAAACAGCACTAC
129 CGAAGACGATTCAAAACAGCACTAA
1045 TGGGCCCCGAAAGGCCCG
1 TGGGCCCCGAAAGGCCCG
Statistics
Matches: 720, Mismatches: 52, Indels: 25
0.90 0.07 0.03
Matches are distributed among these distances:
151 4 0.01
152 200 0.28
153 218 0.30
154 182 0.25
155 112 0.16
156 4 0.01
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (153 bp):
TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAAT
CTCATCAAAATGATTATAGTTAGGTCGTAAACAATGGAAAGAAAAGCTTTGTGGTTGCCAAATCG
AAGACGATTCAAAACAGCACTAA
Found at i:1033 original size:459 final size:462
Alignment explanation
Indices: 124--1062 Score: 1550
Period size: 459 Copynumber: 2.0 Consensus size: 462
114 AAAGAAAAAG
*
124 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAAACTTCACAATGGACTAT
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAAACTTCACAATGGACTAA
* * *
189 TCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTAGAAGAAAAGCTTTCTTGGTTGCCAAAT
66 TCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTAGAAAAAAAGATTTCTTGGATGCCAAAT
* * *
254 TGAAGCCGATTTAAAACAGCACTACTGGGCCCCGAAAGGCCCGAAATAAAAAATGTTCTGAATGA
131 AGAAGACGATTTAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAATGTTCTGAATGA
* *
319 GATAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGTCGTAAACAATGGAAA
196 GATAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAA
* * * * *
384 GAAAAGCTTTCTTGGTTGCCAAATTGAAGCCGATTTAAAACAGCACTACTGAGCCCCGAAAGGCC
261 GAAAAGCTTTCGTGGTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGAGCCCCGAAAGGCC
*
449 CGAATAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATA
326 CGAATAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATAGACTAATCTCATCAAAATGATTATA
* *
514 GTTAGGTCGTAACATATTTGAATGAAATGCTTTGTGGTTTGCCAAATCGTAGACGATTCAAAACA
391 GTTAGGTCGTAACATATTTGAATGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACA
579 GCACTAA
456 GCACTAA
*
586 TGGGCCCCGAACGGCCCGAAATAAAAAGTGTTCTGAATGAGCT-AAAAACTTCACAATGGACTAA
1 TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAAACTTCACAATGGACTAA
* *
650 TCTCACCAAAATGATTATAGTTAGGTCGTAAACAA-TCGAAAAAAAGATTTGTT-GATGCCAAAT
66 TCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTAGAAAAAAAGATTTCTTGGATGCCAAAT
*
713 AGAAGACGATTTAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGA
131 AGAAGACGATTTAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAATGTTCTGAATGA
*
778 GCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAA
196 GATAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAA
*
843 GAAAAGCTTT-GTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATG-GGCCCGAAAGGC
261 GAAAAGCTTTCGTGG-TTGCCAAATCGAAGACGATTCAAAACAGCACTAATGAGCCCCGAAAGGC
906 CCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATAGACTAATCTCATCAAAATGATT
325 CCG-AAT-AAAAGTGTTCTGAATGAGCTAAAAACTTCACAATAGACTAATCTCATCAAAATGATT
* * *
971 ATAGTTAGGTCGTAA-ATATTTGGAA-GAAAAGCTTTGTTGTTTGCCTAATCGAAGATGATTCAA
388 ATAGTTAGGTCGTAACATATTT-GAATGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAA
*
1034 AACAGCACTAC
452 AACAGCACTAA
1045 TGGGCCCCGAAAGGCCCG
1 TGGGCCCCGAAAGGCCCG
Statistics
Matches: 445, Mismatches: 28, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
458 17 0.04
459 243 0.55
460 88 0.20
461 55 0.12
462 42 0.09
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (462 bp):
TGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAAACTTCACAATGGACTAA
TCTCACCAAAATGATTATAGTTAGGTCGTAAACAATTAGAAAAAAAGATTTCTTGGATGCCAAAT
AGAAGACGATTTAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAAAAAATGTTCTGAATGA
GATAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAA
GAAAAGCTTTCGTGGTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGAGCCCCGAAAGGCC
CGAATAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATAGACTAATCTCATCAAAATGATTATA
GTTAGGTCGTAACATATTTGAATGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACA
GCACTAA
Done.