Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012843.1 Corchorus capsularis cultivar CVL-1 contig12864, 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: 25695
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:141 original size:2 final size:2
Alignment explanation
Indices: 129--159 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
119 ACTATCTTAG
129 AT AT A- 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 AT
160 TATTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1156 original size:87 final size:88
Alignment explanation
Indices: 1021--1186 Score: 262
Period size: 87 Copynumber: 1.9 Consensus size: 88
1011 TTCCCTAACC
*
1021 CTGCGTATGCCCTTGGACAAAGATAACAATAGAGTGCAACATAGAGATTCAAAAGCTCTA-TTTC
1 CTGCGTATGCCCTTGCACAAAGATAACAATAGAGTGCAACATAGAGATTCAAAAGCTCTATTTTC
1085 AACAGGGGTGAGGTTCCCTGATT
66 AACAGGGGTGAGGTTCCCTGATT
** ** *
1108 CTGCGTATGCCCTTGCATGAAGATAACGGTAGAGTGCAGCATAGAGATTCAAAAGCTCTATTTTC
1 CTGCGTATGCCCTTGCACAAAGATAACAATAGAGTGCAACATAGAGATTCAAAAGCTCTATTTTC
*
1173 AGCAGGGGTGAGGT
66 AACAGGGGTGAGGT
1187 CTTCTCCTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 54 0.76
88 17 0.24
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (88 bp):
CTGCGTATGCCCTTGCACAAAGATAACAATAGAGTGCAACATAGAGATTCAAAAGCTCTATTTTC
AACAGGGGTGAGGTTCCCTGATT
Found at i:2202 original size:24 final size:24
Alignment explanation
Indices: 2156--2202 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2146 GACTTTAGAG
* * *
2156 TGGCTAACCAAGGAGTTTTGAAAA
1 TGGCCAACCAAGGAGTGTCGAAAA
*
2180 TGGCCAACCCAGGAGTGTCGAAA
1 TGGCCAACCAAGGAGTGTCGAAA
2203 TCTGGAGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (24 bp):
TGGCCAACCAAGGAGTGTCGAAAA
Found at i:2997 original size:20 final size:20
Alignment explanation
Indices: 2969--3007 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2959 GTAGCGGTGT
*
2969 GATTTACACTGGTTAGGTAC
1 GATTGACACTGGTTAGGTAC
*
2989 GATTGACACTGTTTAGGTA
1 GATTGACACTGGTTAGGTA
3008 TTGTACAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (20 bp):
GATTGACACTGGTTAGGTAC
Found at i:7886 original size:28 final size:29
Alignment explanation
Indices: 7826--7886 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
7816 TTCGTGTGTT
* * *
7826 GAAATTACCGTTTTGCCCCTACTAGGCTA
1 GAAATTACAGTTTTGCCCCTACGAGGCCA
7855 -AAATTACAGTTTTGCCCCTA-GAGGCCA
1 GAAATTACAGTTTTGCCCCTACGAGGCCA
7882 GAAAT
1 GAAAT
7887 GATTAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (29 bp):
GAAATTACAGTTTTGCCCCTACGAGGCCA
Found at i:8066 original size:13 final size:13
Alignment explanation
Indices: 8035--8077 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
8025 GTCTGACTGT
*
8035 TTTGGTTGATTA-
1 TTTGGTTTATTAC
8047 TTCTGGTTTATTAC
1 TT-TGGTTTATTAC
*
8061 TTTGGTTTATAAC
1 TTTGGTTTATTAC
8074 TTTG
1 TTTG
8078 ATTATGATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 2 0.07
13 23 0.85
14 2 0.07
ACGTcount: A:0.16, C:0.07, G:0.19, T:0.58
Consensus pattern (13 bp):
TTTGGTTTATTAC
Found at i:13960 original size:20 final size:21
Alignment explanation
Indices: 13935--13983 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
13925 ACCTTTCTTC
13935 CAAAGAAGCACTGC-ATA-TAA
1 CAAAGAAGCAC-GCTATAGTAA
13955 CAAAGAAG-ACGCTATAGTAA
1 CAAAGAAGCACGCTATAGTAA
*
13975 AAAAGAAGC
1 CAAAGAAGC
13984 GCCCTAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 5 0.20
20 18 0.72
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.12
Consensus pattern (21 bp):
CAAAGAAGCACGCTATAGTAA
Found at i:15119 original size:2 final size:2
Alignment explanation
Indices: 15112--15142 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15102 ATTTATGTGC
15112 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15143 GATGATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20474 original size:29 final size:29
Alignment explanation
Indices: 20429--20489 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
20419 AATGCTTCTT
*
20429 TCAGTTTCCTCTTAGAAA-ATTCCTTTACC
1 TCAGTTTCCTCTCAGAAATA-TCCTTTACC
20458 TCAGTTTCCTCTCAGAAATATCCTTTACC
1 TCAGTTTCCTCTCAGAAATATCCTTTACC
20487 TCA
1 TCA
20490 ATATTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.25, C:0.30, G:0.07, T:0.39
Consensus pattern (29 bp):
TCAGTTTCCTCTCAGAAATATCCTTTACC
Done.