Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016100.1 Corchorus capsularis cultivar CVL-1 contig16121, 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: 40417
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:8988 original size:21 final size:21
Alignment explanation
Indices: 8946--8988 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
8936 CTATTATATG
* *
8946 TGGCTAAATTCTATTAATTTA
1 TGGCTAAATTCTAATAAGTTA
* *
8967 TGGCTAAGTTTTAATAAGTTA
1 TGGCTAAATTCTAATAAGTTA
8988 T
1 T
8989 TTCTATTTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (21 bp):
TGGCTAAATTCTAATAAGTTA
Found at i:17354 original size:22 final size:22
Alignment explanation
Indices: 17329--17387 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
17319 CTTAAATACA
*
17329 CTAATTAATTAATTAATTAAGG
1 CTAATTAATTAATTAATTAACG
* *
17351 CTAATGAA-TACACTAATTAACG
1 CTAATTAATTA-ATTAATTAACG
* *
17373 CTAACTACTTAATTA
1 CTAATTAATTAATTA
17388 GCACACCCTA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
21 2 0.07
22 24 0.86
23 2 0.07
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (22 bp):
CTAATTAATTAATTAATTAACG
Found at i:17435 original size:10 final size:10
Alignment explanation
Indices: 17420--17473 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
17410 ACAAATTAGT
*
17420 TAATTAACAG
1 TAATTAACAC
17430 TAATTAACAC
1 TAATTAACAC
17440 TAA-TAAC-C
1 TAATTAACAC
17448 -AATTAACAC
1 TAATTAACAC
*
17457 AAATTAAC-C
1 TAATTAACAC
17466 ATAATTAA
1 -TAATTAA
17474 ATTTAACCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 2 0.05
8 5 0.13
9 6 0.16
10 25 0.66
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.28
Consensus pattern (10 bp):
TAATTAACAC
Found at i:17453 original size:17 final size:18
Alignment explanation
Indices: 17431--17466 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
17421 AATTAACAGT
*
17431 AATTAACACTAA-TAACC
1 AATTAACACAAATTAACC
17448 AATTAACACAAATTAACC
1 AATTAACACAAATTAACC
17466 A
1 A
17467 TAATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (18 bp):
AATTAACACAAATTAACC
Found at i:20116 original size:15 final size:15
Alignment explanation
Indices: 20096--20126 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20086 CTTAATTGAC
20096 TGTGGCAATAAACGT
1 TGTGGCAATAAACGT
20111 TGTGGCAATAAACGT
1 TGTGGCAATAAACGT
20126 T
1 T
20127 ATATCCTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (15 bp):
TGTGGCAATAAACGT
Found at i:20211 original size:15 final size:16
Alignment explanation
Indices: 20187--20219 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20177 TTTAGAAAAG
20187 AAAATAATTTAATTTA
1 AAAATAATTTAATTTA
*
20203 AAAAT-ATTTTATTTA
1 AAAATAATTTAATTTA
20218 AA
1 AA
20220 TAACTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATAATTTAATTTA
Found at i:23981 original size:40 final size:40
Alignment explanation
Indices: 23932--24051 Score: 213
Period size: 40 Copynumber: 3.0 Consensus size: 40
23922 TATCACCTTT
*
23932 GAGAGATTGCCCTTGTGTTATATGTGCTTAGGGACTTTGA
1 GAGAGATTGCCCTTGTGTTATATGTGTTTAGGGACTTTGA
*
23972 GAGAGATTGCCCTTATGTTATATGTGTTTAGGGACTTTGA
1 GAGAGATTGCCCTTGTGTTATATGTGTTTAGGGACTTTGA
*
24012 GAGAGATTGCCCTTGTGTTATATGCGTTTAGGGACTTTGA
1 GAGAGATTGCCCTTGTGTTATATGTGTTTAGGGACTTTGA
24052 TTATTAGGTA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (40 bp):
GAGAGATTGCCCTTGTGTTATATGTGTTTAGGGACTTTGA
Found at i:31395 original size:33 final size:33
Alignment explanation
Indices: 31331--31445 Score: 178
Period size: 33 Copynumber: 3.5 Consensus size: 33
31321 TTCTTTTCAC
* ** *
31331 CCAAAACAGAGTTATTT-TTATGCTATAATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
31363 CCAAAACAAAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
31396 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
31429 CCAAAACAGAATTATTT
1 CCAAAACAGAATTATTT
31446 TCATCACAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 15 0.20
33 61 0.80
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:31466 original size:66 final size:65
Alignment explanation
Indices: 31331--31473 Score: 155
Period size: 66 Copynumber: 2.2 Consensus size: 65
31321 TTCTTTTCAC
* ** * * *
31331 CCAAAACAGAGTTATTTTTATGCTATAATCAACCAAAACAAAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTCAATGCTATAATCAACCAAAACAAAATTATTTGCAATACAATGAGCAA
* * * *
31396 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTTC-ATCACAATTAGC
1 CCAAAACAGAATTATTT-CAATGCTATAATCAACCAAAACAAAATTATTTGCAAT-ACAATGAGC
*
31460 AT
64 AA
31462 CCAAAACA-AATT
1 CCAAAACAGAATT
31474 TGGTATCATC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
65 22 0.34
66 43 0.66
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (65 bp):
CCAAAACAGAATTATTTCAATGCTATAATCAACCAAAACAAAATTATTTGCAATACAATGAGCAA
Found at i:31501 original size:33 final size:33
Alignment explanation
Indices: 31464--31568 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
31454 ATTAGCATCC
* * *
31464 AAAACAAATTTGGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
31497 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
31530 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
31563 AAAACA
1 AAAACA
31569 CTCTTTGCAA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 1 0.02
33 56 0.98
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:33115 original size:11 final size:9
Alignment explanation
Indices: 33082--33106 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
33072 CTGGTCCAAT
33082 TTTTTTTTA
1 TTTTTTTTA
33091 TTTTTTTTA
1 TTTTTTTTA
33100 TTTTTTT
1 TTTTTTT
33107 GATATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Done.