Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009041.1 Corchorus capsularis cultivar CVL-1 contig09062, 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: 35349
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Found at i:1980 original size:15 final size:14
Alignment explanation
Indices: 1955--1991 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
1945 CTTCCTTGCC
*
1955 TTTTGATTAATTTT
1 TTTTTATTAATTTT
1969 TTTTATATTAATTTT
1 TTTT-TATTAATTTT
1984 TTTTTATT
1 TTTTTATT
1992 TTTGTTCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTTATTAATTTT
Found at i:1986 original size:16 final size:15
Alignment explanation
Indices: 1960--1991 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1950 TTGCCTTTTG
1960 ATTAATTTTTTTTAT
1 ATTAATTTTTTTTAT
1975 ATTAATTTTTTTT-T
1 ATTAATTTTTTTTAT
1989 ATT
1 ATT
1992 TTTGTTCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTAATTTTTTTTAT
Found at i:2762 original size:15 final size:15
Alignment explanation
Indices: 2742--2770 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2732 TTGAAATTCA
2742 GGTGAAGCTCTCTCG
1 GGTGAAGCTCTCTCG
2757 GGTGAAGCTCTCTC
1 GGTGAAGCTCTCTC
2771 ACCTTGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (15 bp):
GGTGAAGCTCTCTCG
Found at i:13617 original size:70 final size:71
Alignment explanation
Indices: 13461--13639 Score: 200
Period size: 70 Copynumber: 2.5 Consensus size: 71
13451 GATTAAGAAG
* * * * *
13461 AATTAAGAAATGAAAGTATAGTCAAGGTCCTAATTTGGATAATTAAGAAGAGTAAAGTCTTAATT
1 AATTAAGAAAAGAAAGCACAGTCAAGGTCCTAATTTGGACAATCAAGAAGAGTAAAGTCTTAATT
*
13526 CTGGGT
66 CAGGGT
*** * * * * *
13532 AATTAAGAGGGGAAAGCACAATCAAGGTCTTAATTTGG-CAATCAAGAATAGTAAATTCTTAGTT
1 AATTAAGAAAAGAAAGCACAGTCAAGGTCCTAATTTGGACAATCAAGAAGAGTAAAGTCTTAATT
13596 CAGGGT
66 CAGGGT
*
13602 AATTAAGAAAAGAAAGTC-CAGTCAAGGCCCTAATTTGG
1 AATTAAGAAAAGAAAG-CACAGTCAAGGTCCTAATTTGG
13640 GTAGTTAAGG
Statistics
Matches: 88, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
70 56 0.64
71 32 0.36
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (71 bp):
AATTAAGAAAAGAAAGCACAGTCAAGGTCCTAATTTGGACAATCAAGAAGAGTAAAGTCTTAATT
CAGGGT
Found at i:13750 original size:40 final size:40
Alignment explanation
Indices: 13699--13789 Score: 173
Period size: 40 Copynumber: 2.3 Consensus size: 40
13689 CATAGTTGAG
13699 GACTTAATTCATAGAAATTAAGTAAAAACAGTAGTCAAAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAGTAGTCAAAA
*
13739 GACTTAATTCATAGAAATTCAGTAAAAACAGTAGTCAAAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAGTAGTCAAAA
13779 GACTTAATTCA
1 GACTTAATTCA
13790 GTGGAAGCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.26
Consensus pattern (40 bp):
GACTTAATTCATAGAAATTAAGTAAAAACAGTAGTCAAAA
Found at i:13916 original size:74 final size:71
Alignment explanation
Indices: 13833--14072 Score: 324
Period size: 74 Copynumber: 3.2 Consensus size: 71
13823 CAATTAAGTA
13833 AGGTAAA-AGAAGACTGACTTAATTTC-AAGGAAATTAGGTAAA-AGAAGACTGACTTAATTTCA
1 AGGTAAAGA-AAGACTGACTTAATTTCAAAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTCA
13895 AGGAAATT
64 AGGAAATT
*
13903 CGGTAAAAGAAAGACTGACTTAATTTCGAAAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTT
1 AGGT-AAAGAAAGACTGACTTAATTTC---AAAGGAAATTAGGTAAAGAAAGACTGACTTAATTT
13968 CAAGGAAATT
62 CAAGGAAATT
*
13978 AGGTAAAGATAGACTGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTC
1 AGGTAAAGAAAGACTGACTTAATTTC---AAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTC
14043 AAGGAAGGAAATT
63 ----AAGGAAATT
14056 AGGTAAAGAAAGACTGA
1 AGGTAAAGAAAGACTGA
14073 GGCACATGCT
Statistics
Matches: 153, Mismatches: 6, Indels: 14
0.88 0.03 0.08
Matches are distributed among these distances:
70 3 0.02
71 20 0.13
72 1 0.01
74 58 0.38
75 45 0.29
76 1 0.01
78 25 0.16
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (71 bp):
AGGTAAAGAAAGACTGACTTAATTTCAAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAG
GAAATT
Found at i:13951 original size:39 final size:35
Alignment explanation
Indices: 13833--14072 Score: 313
Period size: 39 Copynumber: 6.5 Consensus size: 35
13823 CAATTAAGTA
13833 AGGTAAA-AGAAGACTGACTTAATTTCAAGGAAATT
1 AGGTAAAGA-AAGACTGACTTAATTTCAAGGAAATT
13868 AGGTAAA-AGAAGACTGACTTAATTTCAAGGAAATT
1 AGGTAAAGA-AAGACTGACTTAATTTCAAGGAAATT
*
13903 CGGTAAAAGAAAGACTGACTTAATTTCGAAAAAGGAAATT
1 AGGT-AAAGAAAGACTGACTTAATTTC----AAGGAAATT
13943 AGGTAAAGAAAGACTGACTTAATTTCAAGGAAATT
1 AGGTAAAGAAAGACTGACTTAATTTCAAGGAAATT
*
13978 AGGTAAAGATAGACTGACTTAATTTCAAGAAAGGAAATT
1 AGGTAAAGAAAGACTGACTTAATTTC----AAGGAAATT
14017 AGGTAAAGAAAGACTGACTTAATTTCAAGGAAGGAAATT
1 AGGTAAAGAAAGACTGACTTAATTTC----AAGGAAATT
14056 AGGTAAAGAAAGACTGA
1 AGGTAAAGAAAGACTGA
14073 GGCACATGCT
Statistics
Matches: 190, Mismatches: 5, Indels: 16
0.90 0.02 0.08
Matches are distributed among these distances:
35 72 0.38
36 20 0.11
37 1 0.01
39 85 0.45
40 12 0.06
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (35 bp):
AGGTAAAGAAAGACTGACTTAATTTCAAGGAAATT
Found at i:20408 original size:23 final size:23
Alignment explanation
Indices: 20365--20410 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
20355 GTCATCGAAT
**
20365 ACTTTCTTTCATATTTCCCTTTC
1 ACTTTCTTTCATAACTCCCTTTC
20388 ACTTTCTTT-ATAACTCTCCTTTC
1 ACTTTCTTTCATAACTC-CCTTTC
20411 TTTCCTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.54
Consensus pattern (23 bp):
ACTTTCTTTCATAACTCCCTTTC
Found at i:21197 original size:16 final size:16
Alignment explanation
Indices: 21176--21209 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
21166 TGGCATTAAG
21176 AAAAAAGGAAAATATT
1 AAAAAAGGAAAATATT
21192 AAAAAAGGAAAATATT
1 AAAAAAGGAAAATATT
21208 AA
1 AA
21210 TCAATATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAAAGGAAAATATT
Found at i:31953 original size:31 final size:32
Alignment explanation
Indices: 31918--31987 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
31908 TTGGTGCTAG
31918 ACGCCGCGAAATAGCAGCGTCTACTTT-ACAA
1 ACGCCGCGAAATAGCAGCGTCTACTTTGACAA
* * *
31949 ACGCCGCGAAATAGCGGCGTCTTCTTTGTCAA
1 ACGCCGCGAAATAGCAGCGTCTACTTTGACAA
31981 ACGCCGC
1 ACGCCGC
31988 TATTTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 25 0.71
32 10 0.29
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (32 bp):
ACGCCGCGAAATAGCAGCGTCTACTTTGACAA
Found at i:32076 original size:195 final size:193
Alignment explanation
Indices: 31788--32182 Score: 612
Period size: 195 Copynumber: 2.0 Consensus size: 193
31778 AAATAAGAAG
* *
31788 ACGCCGCCATATTAATATGTGGAGGGAGAGATTTTTTTTTCCTTTTTTTGGAGGGAAAAATTTCC
1 ACGCCGCCATATTAATATATGGAGGGAGAGATTTTTTTTTCCTTTTTTTGGAGGGAAAAATTCCC
31853 TCCCCTAAAACAAAGAAAAATATACAACTACACGGCTATAAAATATAGCGGCGTCTTGGTGCTAG
66 TCCCCTAAAACAAAGAAAAATATACAACTACACGGCTATAAAATATAGCGGCGTCTTGGTGCTAG
* * *
31918 ACGCCGCGAAATAGCAGCGT-CTACTTTACAAACGCCGCGAAATAGCGGCGTCTTCTTTGTCAA
131 ACGCCGCAAAATAGCAGCGTGCTACTGTA-AAACACCGCGAAATAGCGGCGTCTTCTTTGTCAA
* *
31981 ACGCCGCTATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTTTTGTTGGAGGGAAAAATTC
1 ACGCCGCCATATTAATATATGGAGGGAGAGA-TTTTTTTTTCCTTTTT-TTGGAGGGAAAAATTC
* *
32046 CCTCCCCTAAAACGAAGAAAAATTTACAACTACACGGCTATAAAATATAGCGGCGTCTTGGTGCT
64 CCTCCCCTAAAACAAAGAAAAATATACAACTACACGGCTATAAAATATAGCGGCGTCTTGGTGCT
** * * * * *
32111 AGACGCCGCAAAATAGTGGCGTGTTAGTGTAAGACACCGCGAATTAGCGGCGTCTTCTTTTTCAA
129 AGACGCCGCAAAATAGCAGCGTGCTACTGTAAAACACCGCGAAATAGCGGCGTCTTCTTTGTCAA
32176 ACGCCGC
1 ACGCCGC
32183 GAAATAGCGG
Statistics
Matches: 183, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
193 28 0.15
194 16 0.09
195 134 0.73
196 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (193 bp):
ACGCCGCCATATTAATATATGGAGGGAGAGATTTTTTTTTCCTTTTTTTGGAGGGAAAAATTCCC
TCCCCTAAAACAAAGAAAAATATACAACTACACGGCTATAAAATATAGCGGCGTCTTGGTGCTAG
ACGCCGCAAAATAGCAGCGTGCTACTGTAAAACACCGCGAAATAGCGGCGTCTTCTTTGTCAA
Found at i:32183 original size:32 final size:31
Alignment explanation
Indices: 32147--32213 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 31
32137 GTGTAAGACA
* *
32147 CCGCGAATTAGCGGCGTCTTCTTTTTCAAAC
1 CCGCGAAATAGCGGCGTCTTCTTTGTCAAAC
32178 GCCGCGAAATAGCGGCGTCTTCTTTGTCAAAC
1 -CCGCGAAATAGCGGCGTCTTCTTTGTCAAAC
32210 CCGC
1 CCGC
32214 TATTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 4 0.12
32 29 0.88
ACGTcount: A:0.19, C:0.31, G:0.22, T:0.27
Consensus pattern (31 bp):
CCGCGAAATAGCGGCGTCTTCTTTGTCAAAC
Found at i:32244 original size:226 final size:226
Alignment explanation
Indices: 31916--32330 Score: 690
Period size: 226 Copynumber: 1.8 Consensus size: 226
31906 TCTTGGTGCT
*
31916 AGACGCCGCGAAATAGCAGCGTCTACTTTACAAACGCCGCGAAATAGCGGCGTCTTCTTTGTCAA
1 AGACACCGCGAAATAGCAGCGTCTACTTTACAAACGCCGCGAAATAGCGGCGTCTTCTTTGTCAA
31981 ACGCCGCTATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTTTTGTTGGAGGGAAAAATTC
66 ACGCCGCTATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTTTTGTTGGAGGGAAAAATTC
*
32046 CCTCCCCTAAAACGAAGAAAAATTTACAACTACACGGC-TATAAAATATAGCGGCGTCTTGGTGC
131 CCTCCCCTAAAACAAAGAAAAATTTACAACTACAC-GCATATAAAATATAGCGGCGTCTTGGTGC
32110 TAGACGCCGCAAAATAGTGGCGTGTTAGTGTA
195 TAGACGCCGCAAAATAGTGGCGTGTTAGTGTA
* * * *
32142 AGACACCGCGAATTAGCGGCGTCTTCTTTTTCAAACGCCGCGAAATAGCGGCGTCTTCTTTGTCA
1 AGACACCGCGAAATAGCAGCGTCTAC-TTTACAAACGCCGCGAAATAGCGGCGTCTTCTTTGTCA
32207 AAC-CCGCTATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTTTTGTTGGAGGGAAAAATT
65 AACGCCGCTATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTTTTGTTGGAGGGAAAAATT
* * * * * *
32271 CCCTCCTCTGAAACAAAGTAAATTTTGCAACTACACGCATATAATATATAGCGGCGTCTT
130 CCCTCCCCTAAAACAAAGAAAAATTTACAACTACACGCATATAAAATATAGCGGCGTCTT
32331 TTCTGTATGC
Statistics
Matches: 175, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
225 2 0.01
226 133 0.76
227 40 0.23
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (226 bp):
AGACACCGCGAAATAGCAGCGTCTACTTTACAAACGCCGCGAAATAGCGGCGTCTTCTTTGTCAA
ACGCCGCTATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTTTTGTTGGAGGGAAAAATTC
CCTCCCCTAAAACAAAGAAAAATTTACAACTACACGCATATAAAATATAGCGGCGTCTTGGTGCT
AGACGCCGCAAAATAGTGGCGTGTTAGTGTA
Done.