Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012596.1 Corchorus capsularis cultivar CVL-1 contig12617, 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: 55459
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:114 original size:2 final size:2
Alignment explanation
Indices: 107--135 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
97 ATTCCAAATT
107 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 T
136 TTGAGGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6955 original size:13 final size:13
Alignment explanation
Indices: 6939--7049 Score: 51
Period size: 13 Copynumber: 8.8 Consensus size: 13
6929 AATAAATATA
6939 AATTATATATTAT
1 AATTATATATTAT
6952 AATTATATGTATT-T
1 AATTATA--TATTAT
* *
6966 ACTT-TACATATAT
1 AATTATATAT-TAT
*
6979 AA-TATATATAGAGT
1 AATTATATAT-TA-T
6993 AATTATATATT-T
1 AATTATATATTAT
* *
7005 ACTT-TCTA-TAT
1 AATTATATATTAT
*
7016 ATTTAT-TA-TAT
1 AATTATATATTAT
7027 AAATTATA-ATTAT
1 -AATTATATATTAT
7040 AATTATATAT
1 AATTATATAT
7050 ATTATAATAA
Statistics
Matches: 75, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
10 1 0.01
11 14 0.19
12 20 0.27
13 22 0.29
14 7 0.09
15 11 0.15
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (13 bp):
AATTATATATTAT
Found at i:7037 original size:41 final size:42
Alignment explanation
Indices: 6934--7040 Score: 102
Period size: 41 Copynumber: 2.6 Consensus size: 42
6924 AAAATAATAA
*
6934 ATATAA-AT-TATATATTATAATTATATGTATTTACTTTACAT
1 ATATAATATATATAAATTATAATTATA-GTATTTACTTTACAT
* *
6975 ATATAATATATATAGA--GTAATTATA-TATTTACTTT-C-T
1 ATATAATATATATAAATTATAATTATAGTATTTACTTTACAT
*
7012 ATATATTTATTATATAAATTATAATTATA
1 ATATA-ATA-TATATAAATTATAATTATA
7041 ATTATATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
37 6 0.11
38 3 0.05
39 17 0.31
41 22 0.40
42 2 0.04
43 5 0.09
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (42 bp):
ATATAATATATATAAATTATAATTATAGTATTTACTTTACAT
Found at i:7053 original size:15 final size:15
Alignment explanation
Indices: 6942--7068 Score: 63
Period size: 15 Copynumber: 8.5 Consensus size: 15
6932 AAATATAAAT
6942 TATATATTATAATTA
1 TATATATTATAATTA
* *
6957 TATGTATT-TACTT-
1 TATATATTATAATTA
*
6970 TACATA-TATAA-TA
1 TATATATTATAATTA
*
6983 TATATA-GAGTAATTA
1 TATATATTA-TAATTA
*
6998 TATAT-TTACT--TTC
1 TATATATTA-TAATTA
*
7011 TATATATTTATTATATA
1 TATATA-TTATAAT-TA
*
7028 AATTATAATTATAATTA
1 TA-TAT-ATTATAATTA
*
7045 TATATATTATAATAAA
1 TATATATTATAAT-TA
7061 TATATATT
1 TATATATT
7069 TACTTTTATA
Statistics
Matches: 84, Mismatches: 15, Indels: 25
0.68 0.12 0.20
Matches are distributed among these distances:
12 2 0.02
13 19 0.23
14 8 0.10
15 27 0.32
16 13 0.15
17 5 0.06
18 9 0.11
19 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.51
Consensus pattern (15 bp):
TATATATTATAATTA
Found at i:12237 original size:15 final size:15
Alignment explanation
Indices: 12217--12248 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12207 ATATGTTTAT
*
12217 TTGGTTTGTAGGTAG
1 TTGGTTTATAGGTAG
12232 TTGGTTTATAGGTAG
1 TTGGTTTATAGGTAG
12247 TT
1 TT
12249 ATAGTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (15 bp):
TTGGTTTATAGGTAG
Found at i:28173 original size:2 final size:2
Alignment explanation
Indices: 28162--28190 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28152 CCCTTACATA
28162 AT AT -T 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
28191 TTCTTGTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:29656 original size:2 final size:2
Alignment explanation
Indices: 29649--29680 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29639 CTTCCTCAAC
29649 AT 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 AT
29681 TCAAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33571 original size:21 final size:21
Alignment explanation
Indices: 33545--33588 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33535 TTTAAGGAGG
*
33545 TTGCTAAAT-ACCGTCCTATTT
1 TTGCT-AATCACCGTCCCATTT
*
33566 TTGCTATTCACCGTCCCATTT
1 TTGCTAATCACCGTCCCATTT
33587 TT
1 TT
33589 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (21 bp):
TTGCTAATCACCGTCCCATTT
Found at i:33687 original size:32 final size:32
Alignment explanation
Indices: 33651--33713 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
33641 GCGGAGCCTC
33651 CCCACTAGGACGGCTCTGCCACGGCTAGCCGT
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGT
*
33683 CCCACTAGGACGGCTTTGCCACGGCTAGCCG
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCG
33714 CCCTAGTGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.16, C:0.40, G:0.29, T:0.16
Consensus pattern (32 bp):
CCCACTAGGACGGCTCTGCCACGGCTAGCCGT
Found at i:33848 original size:33 final size:33
Alignment explanation
Indices: 33789--33882 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
33779 TAGTACCGGT
* **
33789 GCCGCCCCAGGG-GGCGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGG
* *
33821 GCCGCCCCAGGGAGGCGGCCTGGCCATGATAGT
1 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGG
*
33854 GCCGCCCCA-GGAGGGCGGCTTGGCCATGG
1 GCCGCCCCAGGGA-GGCGGCCTGGCCATGG
33883 CTCAGCCGCC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 15 0.28
33 38 0.72
ACGTcount: A:0.13, C:0.33, G:0.41, T:0.13
Consensus pattern (33 bp):
GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGG
Found at i:47016 original size:48 final size:48
Alignment explanation
Indices: 46957--47057 Score: 184
Period size: 48 Copynumber: 2.1 Consensus size: 48
46947 GAAGTAATCA
*
46957 AAACAAATAACATGGCATGCGATTTTCATGAATAAATTGATACAAAAC
1 AAACAAATAACATGGCATGCAATTTTCATGAATAAATTGATACAAAAC
*
47005 AAACAAATAACATGGCATGCAATTTTCATTAATAAATTGATACAAAAC
1 AAACAAATAACATGGCATGCAATTTTCATGAATAAATTGATACAAAAC
47053 AAACA
1 AAACA
47058 CGTACAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (48 bp):
AAACAAATAACATGGCATGCAATTTTCATGAATAAATTGATACAAAAC
Found at i:47231 original size:22 final size:22
Alignment explanation
Indices: 47187--47232 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
47177 ACAAATTACC
* *
47187 CAACAAATTTGAGTAATTACAT
1 CAACAAATTTGAGAAAATACAT
47209 CAACAAATTTG-GAAAATAGCAT
1 CAACAAATTTGAGAAAATA-CAT
47231 CA
1 CA
47233 GATTCATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (22 bp):
CAACAAATTTGAGAAAATACAT
Found at i:55134 original size:15 final size:15
Alignment explanation
Indices: 55114--55143 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55104 ATCAGGCTGC
*
55114 CACGATACACGATAT
1 CACGATACACAATAT
55129 CACGATACACAATAT
1 CACGATACACAATAT
55144 TTCAACCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Done.