Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009986.1 Corchorus capsularis cultivar CVL-1 contig10007, 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: 21132
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:110 original size:33 final size:33
Alignment explanation
Indices: 55--121 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
45 ATCGCAAATA
*
55 TTTTTTTTTTAGAAAAATCGGAAAAAGGAAAAAC
1 TTTTTTTTTTAGAAAAATCGGAAAAA-CAAAAAC
89 TTTTTTTTTTAGAAAAA-CGGAAAAACAAAAAC
1 TTTTTTTTTTAGAAAAATCGGAAAAACAAAAAC
121 T
1 T
122 AATTCTTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 7 0.22
33 8 0.25
34 17 0.53
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (33 bp):
TTTTTTTTTTAGAAAAATCGGAAAAACAAAAAC
Found at i:3191 original size:40 final size:41
Alignment explanation
Indices: 3138--3283 Score: 224
Period size: 41 Copynumber: 3.6 Consensus size: 41
3128 CTTGAGAAAC
*
3138 ACTTCTGGTGTCAAATGTAATTTTAATTTACCAAAGTGACA
1 ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA
*
3179 ACTTCTGG-GTCAAAGGTAATTTTAATTTACCAAGGTGACA
1 ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA
* * *
3219 ACTTCTAGTGTCAGTA-GTAATTTTAATTTACCCAAGTGACA
1 ACTTCTGGTGTCA-AAGGTAATTTTAATTTACCAAAGTGACA
3260 ACTTCTGGTGTCAAAGGTAATTTT
1 ACTTCTGGTGTCAAAGGTAATTTT
3284 CAATATTATT
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
40 38 0.40
41 55 0.59
42 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (41 bp):
ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA
Found at i:3698 original size:13 final size:13
Alignment explanation
Indices: 3660--3699 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3650 TCTCCAGATA
* *
3660 ATCTTCAGTTGAA
1 ATCTTCTGTTGAT
*
3673 ATCTTCTGATGAT
1 ATCTTCTGTTGAT
3686 ATCTTCTGTTGAT
1 ATCTTCTGTTGAT
3699 A
1 A
3700 ATATTCTCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (13 bp):
ATCTTCTGTTGAT
Found at i:4112 original size:19 final size:19
Alignment explanation
Indices: 4088--4143 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
4078 GCCGTCATAT
4088 AATTTTTTCGAAATCACTA
1 AATTTTTTCGAAATCACTA
* *
4107 AATTTTTTTGAAA--AATGA
1 AATTTTTTCGAAATCACT-A
*
4125 AATTTTTTCAAAATCACTA
1 AATTTTTTCGAAATCACTA
4144 TATCTGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.07
18 12 0.41
19 13 0.45
20 2 0.07
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (19 bp):
AATTTTTTCGAAATCACTA
Found at i:4307 original size:24 final size:24
Alignment explanation
Indices: 4280--4366 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
4270 AAAGCATATT
*
4280 GCGGCGTCCGGACGCCCCTATTTG
1 GCGGCGTCCAGACGCCCCTATTTG
*
4304 GCGGCGTCTA-ACGCCCCTATTTG
1 GCGGCGTCCAGACGCCCCTATTTG
* * *
4327 GCGGCGTCCATACGACACTATTTG
1 GCGGCGTCCAGACGCCCCTATTTG
*
4351 GGGGCGTCCAGACGCC
1 GCGGCGTCCAGACGCC
4367 GCTACCTGCA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 22 0.41
24 32 0.59
ACGTcount: A:0.14, C:0.34, G:0.31, T:0.21
Consensus pattern (24 bp):
GCGGCGTCCAGACGCCCCTATTTG
Found at i:4468 original size:32 final size:32
Alignment explanation
Indices: 4417--4546 Score: 199
Period size: 32 Copynumber: 4.1 Consensus size: 32
4407 TAAATATAGC
*
4417 GGCG-TTTGTTTCTTTAGACGCCTCTATATAAG
1 GGCGCTTTG-TTCTTTAGACGCCGCTATATAAG
* *
4449 GGCGCTTTGTTATTCAGACGCCGCTATATAAG
1 GGCGCTTTGTTCTTTAGACGCCGCTATATAAG
* *
4481 GGCACTTTGTTCTTTAGATGCCGCTATATAAG
1 GGCGCTTTGTTCTTTAGACGCCGCTATATAAG
4513 GGCGCTTTGTTCTTTAGACGCCGCTATATAAG
1 GGCGCTTTGTTCTTTAGACGCCGCTATATAAG
4545 GG
1 GG
4547 TATACCCCAA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 84 0.95
33 4 0.05
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (32 bp):
GGCGCTTTGTTCTTTAGACGCCGCTATATAAG
Found at i:4949 original size:6 final size:6
Alignment explanation
Indices: 4911--4949 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
4901 TCTCCATCGT
*
4911 CACCGC CACCGC CACAGC CACCGC CACCGC CACCGC CAC
1 CACCGC CACCGC CACCGC CACCGC CACCGC CACCGC CAC
4950 TAGTATTCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.21, C:0.64, G:0.15, T:0.00
Consensus pattern (6 bp):
CACCGC
Found at i:7006 original size:27 final size:27
Alignment explanation
Indices: 6968--7055 Score: 140
Period size: 27 Copynumber: 3.3 Consensus size: 27
6958 ACCCGAGGCA
6968 AAGTGGGAGGATCCACTACTGGGGTCG
1 AAGTGGGAGGATCCACTACTGGGGTCG
* *
6995 AAGTGGGAGGATCCACTGCTTGGGTCG
1 AAGTGGGAGGATCCACTACTGGGGTCG
* *
7022 CAGTGGGAGGATCCACTTCTGGGGTCG
1 AAGTGGGAGGATCCACTACTGGGGTCG
7049 AAGTGGG
1 AAGTGGG
7056 GAGGGCCGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.19, C:0.18, G:0.42, T:0.20
Consensus pattern (27 bp):
AAGTGGGAGGATCCACTACTGGGGTCG
Found at i:7114 original size:24 final size:24
Alignment explanation
Indices: 7082--7136 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
7072 ACATCCTCTC
7082 CATTTGCAGCCTCAATGGGGTCGT
1 CATTTGCAGCCTCAATGGGGTCGT
*
7106 CATTTGCAGCCTCAATTGGGTCGT
1 CATTTGCAGCCTCAATGGGGTCGT
7130 CATTTGC
1 CATTTGC
7137 TGCTAAATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (24 bp):
CATTTGCAGCCTCAATGGGGTCGT
Found at i:8544 original size:13 final size:13
Alignment explanation
Indices: 8526--8551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8516 CATCGAACGG
8526 AAGGAAAGGAGAA
1 AAGGAAAGGAGAA
8539 AAGGAAAGGAGAA
1 AAGGAAAGGAGAA
8552 CAGACGGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (13 bp):
AAGGAAAGGAGAA
Found at i:8635 original size:25 final size:27
Alignment explanation
Indices: 8601--8662 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 27
8591 ACTTACTCTT
8601 GAGGAGAAGGGCGC-G-AATCGAAGGA
1 GAGGAGAAGGGCGCTGAAATCGAAGGA
8626 GAGGAGAAGGGCGCTGCAAATCGAAGGA
1 GAGGAGAAGGGCGCTG-AAATCGAAGGA
8654 GAGGAGAAG
1 GAGGAGAAG
8663 AGAGAGCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.41
26 1 0.03
28 19 0.56
ACGTcount: A:0.37, C:0.11, G:0.47, T:0.05
Consensus pattern (27 bp):
GAGGAGAAGGGCGCTGAAATCGAAGGA
Found at i:21086 original size:2 final size:2
Alignment explanation
Indices: 21063--21126 Score: 62
Period size: 2 Copynumber: 33.0 Consensus size: 2
21053 GAGATGATGA
* * *
21063 AT AT AC AT AT -T AT AT TT AT AT AT AGT AT -T AT -T TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
21103 AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
21127 TTATTG
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
1 3 0.06
2 46 0.90
3 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (2 bp):
AT
Done.