Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011151.1 Corchorus capsularis cultivar CVL-1 contig11172, 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: 39801
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2968 original size:18 final size:18
Alignment explanation
Indices: 2945--2982 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
2935 TCTTCTTCTT
2945 CGGCGGCAGC-AACAACGA
1 CGGCGGCAGCTAA-AACGA
2963 CGGCGGCAGCTAAAACGA
1 CGGCGGCAGCTAAAACGA
2981 CG
1 CG
2983 ACGAGATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.32, C:0.32, G:0.34, T:0.03
Consensus pattern (18 bp):
CGGCGGCAGCTAAAACGA
Found at i:10541 original size:2 final size:2
Alignment explanation
Indices: 10534--10563 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10524 TGGAAGAATA
10534 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
10564 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11950 original size:51 final size:51
Alignment explanation
Indices: 11874--11973 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
11864 AAGCTCTATA
* * *
11874 ACTTTCTATATAGATGCTTATTTGATAGTTACATTGAATCTCGAATAATGC
1 ACTTTCTATATAAACGCTTATTTGATAGTTACATTGAATCCCGAATAATGC
*
11925 ACTTTCTGTATAAACGCTTATTTGATAGTTACATTGAATCCCGAATAAT
1 ACTTTCTATATAAACGCTTATTTGATAGTTACATTGAATCCCGAATAAT
11974 ACAGAGTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (51 bp):
ACTTTCTATATAAACGCTTATTTGATAGTTACATTGAATCCCGAATAATGC
Found at i:15700 original size:49 final size:49
Alignment explanation
Indices: 15627--15723 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
15617 CATGGTCTAC
* * *
15627 GTAGGCTGAAACTAAGAGTTCAGTACTTTACTACCAGGTAATAAACTCG
1 GTAGGCTGAAACTAAGAGTCCAGTACTCTACCACCAGGTAATAAACTCG
15676 GTAGGCTGAAACTAAGAGTCCAGTACTCTACCACCAGGTAATAAACTC
1 GTAGGCTGAAACTAAGAGTCCAGTACTCTACCACCAGGTAATAAACTC
15724 ACATTCTGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (49 bp):
GTAGGCTGAAACTAAGAGTCCAGTACTCTACCACCAGGTAATAAACTCG
Found at i:15768 original size:33 final size:33
Alignment explanation
Indices: 15721--15783 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
15711 AGGTAATAAA
* *
15721 CTCACATTCTGTGAGAGTTGAATCTAAGACTAC
1 CTCACATTCCGTGAGAGTTGAACCTAAGACTAC
15754 CTCACATTCCGTGAGAGTTGAACCTAAGAC
1 CTCACATTCCGTGAGAGTTGAACCTAAGAC
15784 CATCCAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (33 bp):
CTCACATTCCGTGAGAGTTGAACCTAAGACTAC
Found at i:15844 original size:57 final size:57
Alignment explanation
Indices: 15751--15862 Score: 215
Period size: 57 Copynumber: 2.0 Consensus size: 57
15741 AATCTAAGAC
15751 TACCTCACATTCCGTGAGAGTTGAACCTAAGACCATCCAATACTCTACCACATTCTG
1 TACCTCACATTCCGTGAGAGTTGAACCTAAGACCATCCAATACTCTACCACATTCTG
*
15808 TACCTCACATTCCGTGAGAGTTGAACCTAAGGCCATCCAATACTCTACCACATTC
1 TACCTCACATTCCGTGAGAGTTGAACCTAAGACCATCCAATACTCTACCACATTC
15863 CGTGAGAGAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (57 bp):
TACCTCACATTCCGTGAGAGTTGAACCTAAGACCATCCAATACTCTACCACATTCTG
Found at i:15923 original size:24 final size:25
Alignment explanation
Indices: 15880--15928 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
15870 GAATGTGAGA
*
15880 GTTGAACCTAAAGACTATCCAATAC
1 GTTGAACCTAAAGACCATCCAATAC
15905 GTTGAACCT-AAGACCATCCAATAC
1 GTTGAACCTAAAGACCATCCAATAC
15929 TCTACCACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (25 bp):
GTTGAACCTAAAGACCATCCAATAC
Found at i:15961 original size:13 final size:13
Alignment explanation
Indices: 15943--15969 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15933 CCACATTCCG
15943 TGAGAGTTGAACC
1 TGAGAGTTGAACC
15956 TGAGAGTTGAACC
1 TGAGAGTTGAACC
15969 T
1 T
15970 AAGACCATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (13 bp):
TGAGAGTTGAACC
Found at i:25976 original size:2 final size:2
Alignment explanation
Indices: 25969--26001 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25959 CTATTATTTC
25969 TA 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 TA T
26002 GATGGTGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33731 original size:11 final size:11
Alignment explanation
Indices: 33711--33754 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
33701 TCTTTCATTA
*
33711 ATTACATTATT
1 ATTATATTATT
*
33722 ATTATGTTATT
1 ATTATATTATT
33733 ATTATATTA-T
1 ATTATATTATT
33743 ATTATA-TATT
1 ATTATATTATT
33753 AT
1 AT
33755 ATTATTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 2 0.07
10 10 0.34
11 17 0.59
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
ATTATATTATT
Found at i:33752 original size:12 final size:12
Alignment explanation
Indices: 33729--33759 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
33719 ATTATTATGT
33729 TATTATTATATTA
1 TATTA-TATATTA
33742 TATTATATATTA
1 TATTATATATTA
33754 TATTAT
1 TATTAT
33760 TCTTTTCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATATATTA
Found at i:33752 original size:17 final size:16
Alignment explanation
Indices: 33716--33759 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
33706 CATTAATTAC
*
33716 ATTATTATTATGTTATT
1 ATTA-TATTATATTATT
33733 ATTATATTATATTATAT
1 ATTATATTATATTAT-T
33750 ATTATATTAT
1 ATTATATTAT
33760 TCTTTTCCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTATATTATATTATT
Done.