Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006621.1 Corchorus capsularis cultivar CVL-1 contig06642, 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: 2449
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 16--2125 Score: 2995
Period size: 154 Copynumber: 13.7 Consensus size: 154
6 AAACTACTGG
* *
16 AAGAAAAGCTTTGNGGTTTGCCAAATCGAAGACGATTCAAAACAGCAGTAATGGGCCCCGAAAGG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
*
81 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAAGAAT
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAAT
* * *
146 TATAGTTAGGCCATAAACTATGGA
131 TATAGTTAGGCCGTAAACAATTGA
* *
170 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCAGTAATGGTCCCCGAAAGG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
* *
235 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTTACAATGGACTAATCTCATCAAAATAAC
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAAT
*
300 TATAGTTAGGTCGTAAACAATTGA
131 TATAGTTAGGCCGTAAACAATTGA
** * * * * ** *
324 AAGAAAAGCTTTGTGGTTTGCCAAATTTAAGCCGATTCAAAACAACACTATTCGGCCTTGAAAAG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
* *
389 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAGA-GGACTAATCTCACCAAAATGA
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACA-ATGGACTAATCTCATCAAAATAA
453 TTATAGTTAGGCCGTAAACAATTGA
130 TTATAGTTAGGCCGTAAACAATTGA
* * * *
478 AAGAAATGCTTTGTGGTTTGCCAAATTGAAGGCGATTCAAAACAGCACTAATGGGCCCTGAAAGG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
*
543 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATTAT
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAAT
*
608 TATAGTTAGGTCGTAAACAATTGA
131 TATAGTTAGGCCGTAAACAATTGA
* *
632 CAGAAAAGCTTTGTGGTTTGCTAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
* * * * * * *
697 CTCGAAATTATAAGTTTTCTGAATGAGATAGAAACTTCACCAA-AGACTAATCTCATCAAAATAA
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCA-CAATGGACTAATCTCATCAAAATAA
* * *
761 TTATAGTTAGGCCATAAACTATGGA
130 TTATAGTTAGGCCGTAAACAATTGA
* * *
786 AGGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCAGTAATGGGCCTCGAAAGG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
* * * * *
851 CCAGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTTACAATGGACTAATCTCATAAAAATAAC
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAAT
*
916 TATAGTTAGGTCGTAAACAATTGA
131 TATAGTTAGGCCGTAAACAATTGA
* * *
940 AAGAAAAGCTTTGTGGTTTGCTAAATCGAAGACGATTCAAAACAGCAGTAATGGGCCCCAAAAGG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
*
1005 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAAGAAT
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAAT
* * *
1070 TATAGTTAGGCCATAAACTATGGA
131 TATAGTTAGGCCGTAAACAATTGA
* * * *
1094 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCAGTAATTGGCCCCAAAAGA
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
* * * *
1159 CCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTTAAAATGGTCTAATCTCATCAAAATAAT
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAAT
* *
1224 TATGGTTAGGTCGTAAACAATTGA
131 TATAGTTAGGCCGTAAACAATTGA
* * * * ** * *
1248 AAGAAAAGCTTTGTGGTTTGCCAAATTGAAGCCGATTTAAAACAGCAATTTTCGGCCTCGAAAGG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
* * *
1313 CCCGAAATAACAAGTGTTCTGAATAAGCTAAAAACTTCACAGA-GGACTAATCTCACCAAAATGA
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACA-ATGGACTAATCTCATCAAAATAA
1377 TTATAGTTAGGTCC-TAAACAATTG-
130 TTATAGTTAGG-CCGTAAACAATTGA
*
1401 AAG-AATGCTTTGT-G-TTG-C-AATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
* * * * * **
1461 CCCGAAATAATATGTGTTCTGAAGGAGATAGAAACTTCACAAAAGACTAATCTCATCAAAATAAT
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAAT
* * * *
1526 TATACTTAGGCCATAAACTATGGA
131 TATAGTTAGGCCGTAAACAATTGA
* * *
1550 AAGAAAAGCTTTGT-GTTTGGCCAAATCGAAGACGACTCAAAACAGCAGTAATGGTCCCCGAAAG
1 AAGAAAAGCTTTGTGGTTT-GCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAG
*
1614 GCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTTACAATGGACTAATCTCATCAAAATAA
65 GCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAA
* *
1679 CTATAGTTAGGTCGTAAACAATTGA
130 TTATAGTTAGGCCGTAAACAATTGA
* ** * * * ** *
1704 AAGGAAAGCTTTGTGGTTTGCCAAATTTAAGCCGATTCAAAACAACACTAATCGGCCTTGAAAAG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
* * *
1769 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAGA-GGACTAATCTCACCAGAATGA
66 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACA-ATGGACTAATCTCATCAAAATAA
1833 TTATAGTTAGGCCGTAAACAATTGA
130 TTATAGTTAGGCCGTAAACAATTGA
* * *
1858 AAGAAATGCTTTGTGGTTTGCCAAATTGAAGACGATTCAAAACAGCACTAATGGGCCCTGAAAAG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCG-AAAG
*
1923 GCCCGAAAT-ACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGAATAATCTCATCAAAAATA
65 GCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC-AAAATA
*
1987 ATTATAGTTAGGTCGTAAAACAATTTGA
129 ATTATAGTTAGGCCGT-AAACAA-TTGA
* * *
2015 CAGAAAAGCTTTGTGGTTTGCTAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCAAAAGG
1 AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
2080 CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAAACTTCACAATGG
66 CCCGAAATAACAAGTGTTCTGAATGAGCT-AAAAACTTCACAATGG
2126 CCAATTCGAA
Statistics
Matches: 1737, Mismatches: 196, Indels: 42
0.88 0.10 0.02
Matches are distributed among these distances:
147 3 0.00
148 105 0.06
149 4 0.00
150 13 0.01
151 3 0.00
152 10 0.01
153 9 0.01
154 1435 0.83
155 42 0.02
156 19 0.01
157 78 0.04
158 16 0.01
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (154 bp):
AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGG
CCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAAT
TATAGTTAGGCCGTAAACAATTGA
Found at i:2195 original size:91 final size:90
Alignment explanation
Indices: 2040--2215 Score: 307
Period size: 91 Copynumber: 1.9 Consensus size: 90
2030 GTTTGCTAAA
*
2040 TCGAAGACGATTCAAAACAGCACTAATGGGCCCCAAAAGGCCCGAAATAACAAGTGTTCTGAATG
1 TCGAAGACGATTCAAAACAGCACTAATGGGCCACAAAAGGCCCGAAATAACAAGTGTTCTGAATG
2105 AGCTAAAAAACTTCACAATGGCCAAT
66 AGCT-AAAAACTTCACAATGGCCAAT
* *
2131 TCGAAGACGATTCAAAACAGCAGTAATGGGCCACGAAAGGCCCGAAATAACAAGTGTTCTGAATG
1 TCGAAGACGATTCAAAACAGCACTAATGGGCCACAAAAGGCCCGAAATAACAAGTGTTCTGAATG
*
2196 AGCTAAAAACTTTACAATGG
66 AGCTAAAAACTTCACAATGG
2216 ACTAATCTCA
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 15 0.19
91 66 0.81
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.18
Consensus pattern (90 bp):
TCGAAGACGATTCAAAACAGCACTAATGGGCCACAAAAGGCCCGAAATAACAAGTGTTCTGAATG
AGCTAAAAACTTCACAATGGCCAAT
Found at i:2341 original size:245 final size:246
Alignment explanation
Indices: 1881--2369 Score: 844
Period size: 245 Copynumber: 2.0 Consensus size: 246
1871 TGGTTTGCCA
1881 AATTGAAGACGATTCAAAACAGCACTAATGGGCCCTGAAAAGGCCCGAAATACAAGTGTTCTGAA
1 AATTGAAGACGATTCAAAACAGCACTAATGGGCCCTGAAAAGGCCCGAAATACAAGTGTTCTGAA
*
1946 TGAGCTAAAAACTTCACAATGGAATAATCTCATCAAAAATAATTATAGTTAGGTCGTAAAACAAT
66 TGAGCTAAAAACTTCACAATGGAATAATCTCATCAAAAATAACTATAGTTAGGTCGTAAAACAAT
* *
2011 TTGACAGAAAAGCTTTGTGGTTTGCTAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCAA
131 TTGAAAGAAAAGCTTTGTGGTTTGCTAAATCGAAGACAATTCAAAACAGCACTAATGGGCCCCAA
2076 AAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAAACTTCACAATGGCC
196 AAGGCCCGAAATAACAAGTGTTCTGAATGAGCT-AAAAACTTCACAATGGCC
*
2128 AATTCGAAGACGATTCAAAACAGCAGTAATGGGCCAC-G-AAAGGCCCGAAATAACAAGTGTTCT
1 AATT-GAAGACGATTCAAAACAGCACTAATGGGCC-CTGAAAAGGCCCGAAAT-ACAAGTGTTCT
* *
2191 GAATGAGCTAAAAACTTTACAATGGACTAATCTCATC-AAAATAACTATAGTTAGGTCGT-AAAC
63 GAATGAGCTAAAAACTTCACAATGGAATAATCTCATCAAAAATAACTATAGTTAGGTCGTAAAAC
2254 AA-TTGAAAGAAAAGCTTTGTGGTTTGCTAAATCGAAGACAATTCAAAACAGCACTAATGGGCCC
128 AATTTGAAAGAAAAGCTTTGTGGTTTGCTAAATCGAAGACAATTCAAAACAGCACTAATGGGCCC
*
2318 CGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
193 CAAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
2370 ACTAATCTCA
Statistics
Matches: 232, Mismatches: 7, Indels: 9
0.94 0.03 0.04
Matches are distributed among these distances:
244 16 0.07
245 95 0.41
246 6 0.03
247 38 0.16
248 76 0.33
249 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (246 bp):
AATTGAAGACGATTCAAAACAGCACTAATGGGCCCTGAAAAGGCCCGAAATACAAGTGTTCTGAA
TGAGCTAAAAACTTCACAATGGAATAATCTCATCAAAAATAACTATAGTTAGGTCGTAAAACAAT
TTGAAAGAAAAGCTTTGTGGTTTGCTAAATCGAAGACAATTCAAAACAGCACTAATGGGCCCCAA
AAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGCC
Found at i:2353 original size:154 final size:154
Alignment explanation
Indices: 2125--2446 Score: 563
Period size: 154 Copynumber: 2.1 Consensus size: 154
2115 CTTCACAATG
* * *
2125 GCCAATTCGAAGACGATTCAAAACAGCAGTAATGGGCCACGAAAGGCCCGAAATAACAAGTGTTC
1 GCCAAATCGAAGACAATTCAAAACAGCACTAATGGGCCACGAAAGGCCCGAAATAACAAGTGTTC
* *
2190 TGAATGAGCTAAAAACTTTACAATGGACTAATCTCATCAAAATAACTATAGTTAGGTCGTAAACA
66 TGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAACTATAGTTAGGCCGTAAACA
*
2255 ATTGAAAGAAAAGCTTTGTGGTTT
131 ATTAAAAGAAAAGCTTTGTGGTTT
* *
2279 GCTAAATCGAAGACAATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTC
1 GCCAAATCGAAGACAATTCAAAACAGCACTAATGGGCCACGAAAGGCCCGAAATAACAAGTGTTC
*
2344 TGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCGTAAACA
66 TGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAACTATAGTTAGGCCGTAAACA
2409 ATTAAAAGAAAAGCTTTGTGGTTT
131 ATTAAAAGAAAAGCTTTGTGGTTT
2433 GCCAAATCGAAGAC
1 GCCAAATCGAAGAC
2447 GAT
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
154 158 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (154 bp):
GCCAAATCGAAGACAATTCAAAACAGCACTAATGGGCCACGAAAGGCCCGAAATAACAAGTGTTC
TGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAACTATAGTTAGGCCGTAAACA
ATTAAAAGAAAAGCTTTGTGGTTT
Done.