Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002884.1 Corchorus capsularis cultivar CVL-1 contig02892, 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: 2742
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:1001 original size:27 final size:29
Alignment explanation
Indices: 970--1046 Score: 104
Period size: 27 Copynumber: 2.7 Consensus size: 29
960 AAAATGGACT
* *
970 AAAAATGACCAAAATGCCCCTTTAATGCA
1 AAAAATGACCAAAATGCCCCTTGAATGTA
* *
999 AAAAAAGACCAAAATACCCC-TGAATGT-
1 AAAAATGACCAAAATGCCCCTTGAATGTA
1026 AAAAATGACCAAAATGCCCCT
1 AAAAATGACCAAAATGCCCCT
1047 ATGTGACCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 18 0.44
28 5 0.12
29 18 0.44
ACGTcount: A:0.48, C:0.25, G:0.10, T:0.17
Consensus pattern (29 bp):
AAAAATGACCAAAATGCCCCTTGAATGTA
Found at i:1605 original size:64 final size:63
Alignment explanation
Indices: 1267--1693 Score: 480
Period size: 63 Copynumber: 7.0 Consensus size: 63
1257 AACTCTTGAG
*
1267 CAAGATTTTAG-ATTGAAAC-AGAAACTCTC-AGCTAGAGACCTCAAGCAGGATTTAAAATGAAA
1 CAAGA-TTTAGAATTGAAACAAGAAACTCTCGA-CTAGAGACCTCAAGCAGGATTTGAAATGAAA
* ** * *
1329 CAAGATTTTGGGTTG-----A-AAACTCTCGATTAGAGACCTCGAGCAGG-TTTGAAAATGAAA
1 CAAGATTTAGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTG-AAATGAAA
* * * * *
1386 CAGGACTTAGAATTG-----A-TAACTCTCGACTAAAGACCTCAAGCAGGATTTAAAATGAAA
1 CAAGATTTAGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAA
* * * * ** *
1443 CAAGATTTTGGATTGAAATAAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGGAA-G--A
1 CAAGATTTAGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAA
*
1503 CAAGATTTAAAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAA
1 CAAGATTTAGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAA
1566 CAAGACTTTAGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AA
1 CAAGA-TTTAGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAA
* *
1629 CATGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAA
1 CAAGA-TTTAGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAA
1693 C
1 C
1694 TCTCCAACAG
Statistics
Matches: 312, Mismatches: 38, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
56 3 0.01
57 86 0.28
58 5 0.02
60 51 0.16
61 5 0.02
62 10 0.03
63 95 0.30
64 57 0.18
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (63 bp):
CAAGATTTAGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAA
Found at i:1683 original size:187 final size:180
Alignment explanation
Indices: 1267--1684 Score: 487
Period size: 187 Copynumber: 2.3 Consensus size: 180
1257 AACTCTTGAG
* **
1267 CAAGATTTTAGATTGAAAC-AGAAACTCTC-AGCTAGAGACCTCAAGCAGGATTTAAAATGAAAC
1 CAAGATTTTGGATTGAAACAAGAAACTCTCGA-CTAGAGACCTCAAGCAGGATTTGGAA-G--AC
**** * * *
1330 AAGATTTTGGGTTG-----A-AAACTCTCGATTAGAGACCTCGAGCAGGTTTGAAAATGAAACAG
62 AAGATTTAAAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGTTTGAAAATGAAACAA
*
1389 GACTTAGAATTGATAACTCTCGACTAAAGACCTCAAGCAGGATTTAAAATGAAA
127 GACTTAGAATTGAAAACTCTCGACTAAAGACCTCAAGCAGGATTTAAAATGAAA
* * **
1443 CAAGATTTTGGATTGAAATAAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGGAAGACAAGA
1 CAAGATTTTGGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGGAAGACAAGA
1508 TTTAAAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTG-AAATGAAACAAGAC
66 TTTAAAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGG-TTTGAAAATGAAACAAGAC
* *
1572 TTTAGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AA
130 -TTAGAATTG-----A-AAACTCTCGACTAAAGACCTCAAGCAGGATTTAAAATGAAA
*
1629 CATGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTG
1 CAAGATTTTGG-ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTG
1685 AAATGAAACT
Statistics
Matches: 203, Mismatches: 22, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
174 12 0.06
176 18 0.09
177 31 0.15
178 1 0.00
179 1 0.00
180 39 0.19
181 13 0.06
186 13 0.06
187 75 0.37
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.23
Consensus pattern (180 bp):
CAAGATTTTGGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGGAAGACAAGA
TTTAAAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGTTTGAAAATGAAACAAGACT
TAGAATTGAAAACTCTCGACTAAAGACCTCAAGCAGGATTTAAAATGAAA
Found at i:1725 original size:127 final size:126
Alignment explanation
Indices: 1403--1693 Score: 381
Period size: 127 Copynumber: 2.3 Consensus size: 126
1393 TAGAATTGAT
* * **** * *
1403 AACTCTCGACTAAAGACCTCAAGCAGGATTTAAAATGAAACAAGA-TTTTGGATTGAAATAAGAA
1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACAACAGAATTGAAACAAGAA
* ** *
1467 ACTCTCGACTAGAGACCTCGATTAGGATTTGGAA-G-ACAAGATTTAAAATTGAAACAAGA
66 ACTCTCGACTAGAGACCTCAAACAGGATTTGAAATGAACAAGATTTAAAATTGAAACAAGA
***
1526 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACTTTAGAATTGAAACAAGAA
1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACAACAGAATTGAAACAAGAA
* * **
1591 ACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACATGATTTTGGAATTGAAACAAGA
66 ACTCTCGACTAGAGACCTCAAACAGGATTTGAAATGAACAAGA-TTTAAAATTGAAACAAGA
1653 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAAC
1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAAC
1694 TCTCCAACAG
Statistics
Matches: 152, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
123 43 0.28
124 46 0.30
125 1 0.01
126 5 0.03
127 57 0.38
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.22
Consensus pattern (126 bp):
AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACAACAGAATTGAAACAAGAA
ACTCTCGACTAGAGACCTCAAACAGGATTTGAAATGAACAAGATTTAAAATTGAAACAAGA
Found at i:1732 original size:127 final size:128
Alignment explanation
Indices: 1403--1756 Score: 357
Period size: 127 Copynumber: 2.8 Consensus size: 128
1393 TAGAATTGAT
* * **** * *
1403 AACTCTCGACTAAAGACCTCAAGCAGGATTTAAAATGAAACAAGA-TTTTGGATTGAAATAAGAA
1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACAACAGAATTGAAACAAGAA
** ** ** * **
1467 ACTCTCGACTAGAGACCTCGATTAGGA-TTTGGAA-G-ACAAGA-TTTAAAATTGAAACAAGA
66 ACTCTCGACTAGAGACCTAAAACAGGATTTTAAAATGAACATGATTTTGGAATTGAAACAAGA
***
1526 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACTTTAGAATTGAAACAAGAA
1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACAACAGAATTGAAACAAGAA
* * *
1591 ACTCTCGACTAGAGACCTCAAGCAGGA-TTTGAAATGAACATGATTTTGGAATTGAAACAAGA
66 ACTCTCGACTAGAGACCTAAAACAGGATTTTAAAATGAACATGATTTTGGAATTGAAACAAGA
**** * *
1653 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACTCTCCAACAGGATTTTGAATC-A-
1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACAACA-GA-ATTGAAACAAG
1716 AAACTCTCGAGC-AGAGACCTAAAACAGGATTTTAAAATGAA
64 AAACTCTCGA-CTAGAGACCTAAAACAGGATTTTAAAATGAA
1757 ATTCAAAGCA
Statistics
Matches: 199, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
123 43 0.22
124 46 0.23
125 1 0.01
126 5 0.03
127 84 0.42
128 14 0.07
129 6 0.03
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (128 bp):
AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGACAACAGAATTGAAACAAGAA
ACTCTCGACTAGAGACCTAAAACAGGATTTTAAAATGAACATGATTTTGGAATTGAAACAAGA
Found at i:2035 original size:69 final size:69
Alignment explanation
Indices: 1924--2061 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 69
1914 AAGACCACCC
* * *
1924 TGGATCAACTGGAAAAAACTGATGAAAAACCGCCCTAGGTCGACTGAATCGATCGTTCTGACACA
1 TGGATAAACTGGAAAAAACTGAAGAAAAACCGCCCTAGGTCGACTGAATCGATCATTCTGACACA
1989 AACT
66 AACT
* * * *
1993 TGGATAAACTTGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACACA
1 TGGATAAACTGGAAAAAACTGAAGAAAAACCGCCCTAGGTCGACTGAATCGATCATTCTGACACA
2058 AACT
66 AACT
2062 GAAGAAAGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (69 bp):
TGGATAAACTGGAAAAAACTGAAGAAAAACCGCCCTAGGTCGACTGAATCGATCATTCTGACACA
AACT
Found at i:2088 original size:49 final size:49
Alignment explanation
Indices: 2009--2159 Score: 221
Period size: 49 Copynumber: 3.1 Consensus size: 49
1999 AACTTGAAAC
* * *
2009 AACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACACA
1 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTCTGACATA
* *
2058 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCAATCATTCTGTCATA
1 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTCTGACATA
** * *
2107 AACTTTAGAAAGACCACCCTAGGTCAATTGAATCGATCATTCTGACATA
1 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTCTGACATA
2156 AACT
1 AACT
2160 TCGAATAAAC
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 91 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (49 bp):
AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTCTGACATA
Found at i:2280 original size:71 final size:72
Alignment explanation
Indices: 2113--2302 Score: 328
Period size: 71 Copynumber: 2.7 Consensus size: 72
2103 CATAAACTTT
* * *
2113 AGAAAGACCACCCTAGGTCAATTGAATCGATCATTCTGACATAAACTTCGAATAAACTTTGAAAA
1 AGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTTGAAAA
2178 CAACTGA
66 CAACTGA
*
2185 AGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAAC-TTGAAAA
1 AGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTTGAAAA
2249 CAACTGA
66 CAACTGA
*
2256 TGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACT
1 AGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACT
2303 AAAGAAAGGC
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 59 0.53
72 53 0.47
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (72 bp):
AGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTTGAAAA
CAACTGA
Found at i:2379 original size:36 final size:36
Alignment explanation
Indices: 2282--2389 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 36
2272 GTCGACTGAA
* * **
2282 TCGATCATTCTGACATAAACTAAAGAAAGGCGGCCC
1 TCGATCATTCCGACATAAACTAAAGAAAGACCACCC
* * * *
2318 TGGGTCAAT-CGAAATAAACTAAAGAAAGACCACCC
1 TCGATCATTCCGACATAAACTAAAGAAAGACCACCC
* *
2353 TCGATCATTCCGACATAAACTGAAGAAAAACCACCC
1 TCGATCATTCCGACATAAACTAAAGAAAGACCACCC
2389 T
1 T
2390 GGGTCAACTG
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 27 0.47
36 30 0.53
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.18
Consensus pattern (36 bp):
TCGATCATTCCGACATAAACTAAAGAAAGACCACCC
Done.