Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015822.1 Corchorus capsularis cultivar CVL-1 contig15843, 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: 16942
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Found at i:5296 original size:30 final size:30
Alignment explanation
Indices: 5260--5319 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
5250 CAAGGGGGAG
5260 GGAATGATGCGCCCAAGG-CTTA-TCATGGAC
1 GGAATGATGCG-CCAAGGACTTACT-ATGGAC
5290 GGAATGATGCGCCAAGGACTTACTATGGAC
1 GGAATGATGCGCCAAGGACTTACTATGGAC
5320 TTGAAGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 6 0.21
30 21 0.75
31 1 0.04
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTACTATGGAC
Found at i:6567 original size:12 final size:12
Alignment explanation
Indices: 6550--6577 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6540 CGCAACACCT
6550 GCCACATGACCG
1 GCCACATGACCG
6562 GCCACATGACCG
1 GCCACATGACCG
6574 GCCA
1 GCCA
6578 TCGCATGCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.43, G:0.25, T:0.07
Consensus pattern (12 bp):
GCCACATGACCG
Found at i:9112 original size:30 final size:30
Alignment explanation
Indices: 9072--9129 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
9062 TGTCTTCAAG
9072 TCCATAATAAGTCCTT-GGCGCATAATTCCT
1 TCCATAATAAG-CCTTGGGCGCATAATTCCT
* *
9102 TCCATGATAAGCCTTGGGCGCATCATTC
1 TCCATAATAAGCCTTGGGCGCATAATTC
9130 ACTCCCCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATAATTCCT
Found at i:9509 original size:33 final size:33
Alignment explanation
Indices: 9472--9588 Score: 180
Period size: 33 Copynumber: 3.5 Consensus size: 33
9462 TTCTTTTCAC
* ** *
9472 CCAAAACAAAATTTTTTTTAATGCTATAATCAA
1 CCAAAACAGAATTTTTTGCAATGCTATGATCAA
*
9505 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTTTTTGCAATGCTATGATCAA
9538 CCAAAACAGAATTTTTTGCAATGCTATGATCAA
1 CCAAAACAGAATTTTTTGCAATGCTATGATCAA
9571 CCAAAACAGAATTGTTTT
1 CCAAAACAGAATT-TTTT
9589 CATCACAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
33 73 0.95
34 4 0.05
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (33 bp):
CCAAAACAGAATTTTTTGCAATGCTATGATCAA
Found at i:9608 original size:66 final size:66
Alignment explanation
Indices: 9472--9613 Score: 169
Period size: 66 Copynumber: 2.2 Consensus size: 66
9462 TTCTTTTCAC
* ** * * *
9472 CCAAAACAAAATTTTTTTTAATGCTATAATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTTTTTGCAATGCTATAATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
9537 A
66 A
* * * *
9538 CCAAAACAGAATTTTTTGCAATGCTATGATCAACCAAAACAGAATTGTTTTC-ATCACAATTAGC
1 CCAAAACAGAATTTTTTGCAATGCTATAATCAACCAAAACAGAATTATTTGCAAT-ACAATGAGC
*
9602 AT
65 AA
9604 CCAAAACAGA
1 CCAAAACAGA
9614 TTTAGTATCA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 2 0.03
66 62 0.97
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (66 bp):
CCAAAACAGAATTTTTTGCAATGCTATAATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
A
Found at i:9643 original size:33 final size:33
Alignment explanation
Indices: 9606--9710 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
9596 ATTAGCATCC
9606 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCACAAACAACACTT
* * ** *
9639 AAAACAAATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCACAAACAACACTT
** * *
9672 AAATTAGGTTTAGTATCATCCCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCACAAACAACACT-T
9705 AAAACA
1 AAAACA
9711 CTCTTTGCAA
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
32 1 0.02
33 55 0.98
ACGTcount: A:0.47, C:0.21, G:0.08, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACTT
Found at i:10159 original size:33 final size:33
Alignment explanation
Indices: 10085--10160 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 33
10075 GGCGCGAGTG
* ** * *
10085 ACCGGCCATGCGACTTGGAGAAGCCCTGCTAAC
1 ACCGGCCACGCGACCCGGAGAAGCCCGGCCAAC
* * *
10118 ACCAGCCACGCGACCCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACCCGGAGAAGCCCGGCCAAC
10151 ACCGGCCACG
1 ACCGGCCACG
10161 TGATATGGAC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.22, C:0.41, G:0.28, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACCCGGAGAAGCCCGGCCAAC
Found at i:11249 original size:33 final size:33
Alignment explanation
Indices: 11166--11256 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
11156 CGCCAAATGA
* * **
11166 TGGCCGGT-TGTGGCCGGACATGTCCTTGTCGCG
1 TGGCCGGTGT-TGGCCGGGCATCTCCGGGTCGCG
*
11199 TGGCCGGTGATGGCCGGGCATCTCCGGGTCGCG
1 TGGCCGGTGTTGGCCGGGCATCTCCGGGTCGCG
*
11232 TGGCCGGTGTTGGCCGGGCTTCTCC
1 TGGCCGGTGTTGGCCGGGCATCTCC
11257 AAATCGCATG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.04, C:0.30, G:0.42, T:0.24
Consensus pattern (33 bp):
TGGCCGGTGTTGGCCGGGCATCTCCGGGTCGCG
Found at i:11269 original size:33 final size:33
Alignment explanation
Indices: 11194--11272 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
11184 CATGTCCTTG
***
11194 TCGCGTGGCCGGTGATGGCCGGGCATCTCCGGG
1 TCGCGTGGCCGGTGATGGCCGGGCATCTCCAAA
* *
11227 TCGCGTGGCCGGTGTTGGCCGGGCTTCTCCAAA
1 TCGCGTGGCCGGTGATGGCCGGGCATCTCCAAA
*
11260 TCGCATGGCCGGT
1 TCGCGTGGCCGGT
11273 CACTCGCGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.08, C:0.30, G:0.41, T:0.22
Consensus pattern (33 bp):
TCGCGTGGCCGGTGATGGCCGGGCATCTCCAAA
Found at i:14969 original size:8 final size:8
Alignment explanation
Indices: 14941--14974 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
14931 GAATCGGCTA
14941 TGAATTTT
1 TGAATTTT
*
14949 TGAAGTTTC
1 TGAA-TTTT
14958 TGAATTTT
1 TGAATTTT
14966 TGAATTTT
1 TGAATTTT
14974 T
1 T
14975 CAAGAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:15981 original size:33 final size:31
Alignment explanation
Indices: 15934--16016 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 31
15924 CGCCAAACGA
* *
15934 TGGCCGGTTGTGGCCGGACATGTTC-ATGTCGCG
1 TGGCCGG-TGTGGCCGG-CATCTCCGA-GTCGCG
15967 TGGCCGGTGATGGCCAGGCATCTCCGAGTCGCG
1 TGGCCGGTG-TGGCC-GGCATCTCCGAGTCGCG
*
16000 TGGCCTGTGTTGGCCGG
1 TGGCCGGTG-TGGCCGG
16017 GCTTCTCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
32 4 0.09
33 36 0.84
34 3 0.07
ACGTcount: A:0.08, C:0.27, G:0.41, T:0.24
Consensus pattern (31 bp):
TGGCCGGTGTGGCCGGCATCTCCGAGTCGCG
Found at i:16024 original size:33 final size:33
Alignment explanation
Indices: 15961--16024 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
15951 ACATGTTCAT
15961 GTCGCGTGGCCGGTGATGGCCAGGCATCTCCGA
1 GTCGCGTGGCCGGTGATGGCCAGGCATCTCCGA
* * * *
15994 GTCGCGTGGCCTGTGTTGGCCGGGCTTCTCC
1 GTCGCGTGGCCGGTGATGGCCAGGCATCTCC
16025 AAATCGCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.06, C:0.31, G:0.39, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTGATGGCCAGGCATCTCCGA
Done.