Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007849.1 Corchorus capsularis cultivar CVL-1 contig07870, 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: 29363
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2268 original size:2 final size:2
Alignment explanation
Indices: 2261--2290 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2251 TATTATATGC
2261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2291 TTCCCTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5595 original size:31 final size:29
Alignment explanation
Indices: 5557--5618 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
5547 TATCTCTATG
*
5557 TTTTTTTTTATCATCAAGTTAAACTTGAATA
1 TTTTTTTTTA--AGCAAGTTAAACTTGAATA
* *
5588 TTTTTTTTTAAGGAAGTTAAATTTGAATA
1 TTTTTTTTTAAGCAAGTTAAACTTGAATA
5617 TT
1 TT
5619 GATTTCGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.64
31 10 0.36
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (29 bp):
TTTTTTTTTAAGCAAGTTAAACTTGAATA
Found at i:6127 original size:23 final size:23
Alignment explanation
Indices: 6100--6149 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
6090 GACAATAGAC
6100 AAAACTCTCACAAAGGAGTCCCA
1 AAAACTCTCACAAAGGAGTCCCA
6123 AAAACTCTCACAAAGGAGTCCCA
1 AAAACTCTCACAAAGGAGTCCCA
6146 AAAA
1 AAAA
6150 AAACAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.48, C:0.28, G:0.12, T:0.12
Consensus pattern (23 bp):
AAAACTCTCACAAAGGAGTCCCA
Found at i:15996 original size:14 final size:14
Alignment explanation
Indices: 15977--16006 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
15967 TTAGTAGTAT
15977 TTTTTTTTCAAGCA
1 TTTTTTTTCAAGCA
15991 TTTTTTTTCAAGCA
1 TTTTTTTTCAAGCA
16005 TT
1 TT
16007 CTTAATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTTTTTTCAAGCA
Found at i:16367 original size:11 final size:12
Alignment explanation
Indices: 16342--16372 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
16332 TTGTTTATTG
16342 TTCGTTTAAATA
1 TTCGTTTAAATA
16354 TTCGTTTAAA-A
1 TTCGTTTAAATA
16365 TTCGTTTA
1 TTCGTTTA
16373 TGATTTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (12 bp):
TTCGTTTAAATA
Found at i:17591 original size:14 final size:14
Alignment explanation
Indices: 17574--17602 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17564 CTCCGAAAAA
17574 AAGTTTATTCATTG
1 AAGTTTATTCATTG
17588 AAGTTTATTCATTG
1 AAGTTTATTCATTG
17602 A
1 A
17603 TGTGTCACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (14 bp):
AAGTTTATTCATTG
Found at i:18953 original size:6 final size:6
Alignment explanation
Indices: 18942--18967 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
18932 CAAAGAAAAG
18942 AAAGGC AAAGGC AAAGGC AAAGGC AA
1 AAAGGC AAAGGC AAAGGC AAAGGC AA
18968 CCATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAGGC
Found at i:24117 original size:16 final size:17
Alignment explanation
Indices: 24093--24138 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
24083 TTGGTTGAGA
*
24093 GAAAAGAAATAGGAA-G
1 GAAAGGAAATAGGAAGG
*
24109 GAAAGGAAATAGTAAGG
1 GAAAGGAAATAGGAAGG
*
24126 GAAGGGAAATAGG
1 GAAAGGAAATAGG
24139 GATGAATGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (17 bp):
GAAAGGAAATAGGAAGG
Found at i:25398 original size:42 final size:42
Alignment explanation
Indices: 25315--25400 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
25305 GACTTAACTG
* *
25315 TGGGTTTCTATTATTGGTTGTTTCTATTTTTCAATAGTTTCA
1 TGGGTTTCTATTATTGGTTGTCTCTATTCTTCAATAGTTTCA
* *
25357 TGGGTTTTTATTATTGGTTGTCTCTATTCTT-AAGTATTTTCA
1 TGGGTTTCTATTATTGGTTGTCTCTATTCTTCAA-TAGTTTCA
25399 TG
1 TG
25401 CCATTGAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.16, C:0.09, G:0.17, T:0.57
Consensus pattern (42 bp):
TGGGTTTCTATTATTGGTTGTCTCTATTCTTCAATAGTTTCA
Found at i:25975 original size:35 final size:35
Alignment explanation
Indices: 25936--26017 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
25926 CTATTTGATT
**
25936 ATTTACTTAATTACACCGAATTAAGCTAATTACTG
1 ATTTACTTAATTACACCGAATTAAGCTAATTACCA
* *
25971 ATTTACTTAATTACACCGAATTAAGTTTATTACCA
1 ATTTACTTAATTACACCGAATTAAGCTAATTACCA
26006 ATTTACTTAATT
1 ATTTACTTAATT
26018 TACCAGTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGCTAATTACCA
Found at i:26022 original size:17 final size:17
Alignment explanation
Indices: 26000--26107 Score: 85
Period size: 17 Copynumber: 6.1 Consensus size: 17
25990 ATTAAGTTTA
26000 TTACCAATTTACTTAAT
1 TTACCAATTTACTTAAT
*
26017 TTACCAGTTTACTTAAT
1 TTACCAATTTACTTAAT
* * *
26034 TGCACCGAATTAAGTTAA-
1 T-TACC-AATTTACTTAAT
26052 TTACCAAACTACTTAACTTAA-
1 TTACC-AA-T--TT-ACTTAAT
*
26073 TTACCAAATTACTTAAT
1 TTACCAATTTACTTAAT
*
26090 TTACCAGTTTACTTAAT
1 TTACCAATTTACTTAAT
26107 T
1 T
26108 GCACCGTATT
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
16 6 0.08
17 40 0.56
18 5 0.07
19 8 0.11
20 3 0.04
21 10 0.14
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (17 bp):
TTACCAATTTACTTAAT
Found at i:26065 original size:35 final size:35
Alignment explanation
Indices: 26025--26166 Score: 142
Period size: 35 Copynumber: 4.0 Consensus size: 35
26015 ATTTACCAGT
26025 TTACTTAATTGCACCGAATTAAGTTAATTACCAAA
1 TTACTTAATTGCACCGAATTAAGTTAATTACCAAA
* ** * * **
26060 CTACTTAACTTAATTACCAAATT-ACTTAATTTACCAGT
1 TTACTTAA-TT--GCACCGAATTAAGTTAA-TTACCAAA
* *
26098 TTACTTAATTGCACCGTATTAAGTTGATTACCAAA
1 TTACTTAATTGCACCGAATTAAGTTAATTACCAAA
* *
26133 TTACTTAATTACACCGAATTAAGTTGATTACCAA
1 TTACTTAATTGCACCGAATTAAGTTAATTACCAA
26167 TTTGCTCTTC
Statistics
Matches: 84, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
35 51 0.61
36 6 0.07
37 7 0.08
38 20 0.24
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (35 bp):
TTACTTAATTGCACCGAATTAAGTTAATTACCAAA
Found at i:26072 original size:21 final size:21
Alignment explanation
Indices: 26043--26088 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
26033 TTGCACCGAA
*
26043 TTAAGTTAATTACCAAACTAC
1 TTAACTTAATTACCAAACTAC
*
26064 TTAACTTAATTACCAAATTAC
1 TTAACTTAATTACCAAACTAC
26085 TTAA
1 TTAA
26089 TTTACCAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAACTTAATTACCAAACTAC
Found at i:26085 original size:73 final size:73
Alignment explanation
Indices: 25999--26140 Score: 248
Period size: 73 Copynumber: 1.9 Consensus size: 73
25989 AATTAAGTTT
*
25999 ATTACCAATTTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTAC
1 ATTACCAAATTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTAC
26064 TTAACTTA
66 TTAACTTA
* * *
26072 ATTACCAAATTACTTAATTTACCAGTTTACTTAATTGCACCGTATTAAGTTGATTACCAAATTAC
1 ATTACCAAATTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTAC
26137 TTAA
66 TTAA
26141 TTACACCGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (73 bp):
ATTACCAAATTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTAC
TTAACTTA
Done.