Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013368.1 Corchorus olitorius cultivar O-4 contig13401, 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: 8518
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:1659 original size:135 final size:135
Alignment explanation
Indices: 1417--1672 Score: 386
Period size: 135 Copynumber: 1.9 Consensus size: 135
1407 GTTTTTGCCT
* * ** *
1417 TAAGGATGGTGGCGTTTTTAAGTACAAACGCTGACACACTAACAATTATTAGGGTGTTTCCAATA
1 TAAGGATGGCGGCGTTTTTAAGTACAAACGCCGACACACTAACAACAATTACGGTGTTTCCAATA
* * *
1482 ACAAACGATGTTATAGTTAATTTTCAGCTAATATTCCAATTTTGCGCTAAAAAAAAGAGGGAAAC
66 ACAAACGACGTTACAGTTAATTTTCAGCTAATATTCCAATTTTGCGCGAAAAAAAAGAGGGAAAC
1547 CAAAA
131 CAAAA
* *
1552 TAAGGATGGCGTCGTTTTTAAGTACAAACGCCGCCACACTAACAACAATTACGGTGTTTCCAATA
1 TAAGGATGGCGGCGTTTTTAAGTACAAACGCCGACACACTAACAACAATTACGGTGTTTCCAATA
* * * *
1617 ACAAATGCCGTTACAGTTAATTTTCAGCTAATTTTCTAATTTTGCGCGAAAAAAAA
66 ACAAACGACGTTACAGTTAATTTTCAGCTAATATTCCAATTTTGCGCGAAAAAAAA
1673 AGAAAAAAAT
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
135 107 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (135 bp):
TAAGGATGGCGGCGTTTTTAAGTACAAACGCCGACACACTAACAACAATTACGGTGTTTCCAATA
ACAAACGACGTTACAGTTAATTTTCAGCTAATATTCCAATTTTGCGCGAAAAAAAAGAGGGAAAC
CAAAA
Found at i:2126 original size:9 final size:9
Alignment explanation
Indices: 2112--2136 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2102 AGAGACCTCA
2112 TCCATGTCC
1 TCCATGTCC
2121 TCCATGTCC
1 TCCATGTCC
2130 TCCATGT
1 TCCATGT
2137 ATCTGGTCTT
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:0.12, C:0.40, G:0.12, T:0.36
Consensus pattern (9 bp):
TCCATGTCC
Found at i:4984 original size:78 final size:78
Alignment explanation
Indices: 4850--5010 Score: 295
Period size: 78 Copynumber: 2.1 Consensus size: 78
4840 GTTTTCTACT
* *
4850 TAAAATAGTAAAATGGTAAACTGAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
4915 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
4928 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
4993 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
5006 TAAAA
1 TAAAA
5011 CTATAAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.34
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
GTTTTTAGTTGAG
Found at i:5118 original size:6 final size:6
Alignment explanation
Indices: 5101--5137 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
5091 GTACTTTTTA
5101 ATATAG -TATAG ATATAG --ATAG ATATAG ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
5138 TTTAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.14
5 5 0.18
6 19 0.68
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:5123 original size:10 final size:10
Alignment explanation
Indices: 5101--5130 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
5091 GTACTTTTTA
5101 ATATAGTATAG
1 ATATAG-ATAG
5112 ATATAGATAG
1 ATATAGATAG
5122 ATATAGATA
1 ATATAGATA
5131 TAGATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (10 bp):
ATATAGATAG
Found at i:5128 original size:16 final size:15
Alignment explanation
Indices: 5103--5136 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
5093 ACTTTTTAAT
5103 ATAGTATAGATATAG
1 ATAGTATAGATATAG
5118 ATAGATATAGATATAG
1 ATAG-TATAGATATAG
5134 ATA
1 ATA
5137 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (15 bp):
ATAGTATAGATATAG
Found at i:6281 original size:44 final size:44
Alignment explanation
Indices: 6219--6316 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 44
6209 GCTAAAACAT
*
6219 AAGAATATAAATATTAATCCATTAAAATTAATATAAAGAAATAAG
1 AAGAA-ATAAATACTAATCCATTAAAATTAATATAAAGAAATAAG
6264 AAGAAATAAATACTAATCCATTAAAATTAATATAAAGAAATAAG
1 AAGAAATAAATACTAATCCATTAAAATTAATATAAAGAAATAAG
6308 AAGAAATAA
1 AAGAAATAA
6317 TCAAGTTAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 47 0.90
45 5 0.10
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26
Consensus pattern (44 bp):
AAGAAATAAATACTAATCCATTAAAATTAATATAAAGAAATAAG
Found at i:7206 original size:112 final size:112
Alignment explanation
Indices: 7054--7265 Score: 286
Period size: 112 Copynumber: 1.9 Consensus size: 112
7044 AGAAACGCCG
* *
7054 CCATTTAAGGAAATGGAGGGAGAATTTTCCTCCGGAAATAATTA-TTAAAAACTACAAAAAGAAA
1 CCATTTAAAGAAACGGAGGGAGAATTTTCCTCCGGAAATAATTATTTAAAAACTACAAAAA-AAA
*
7118 TTTCC-AAAATTTAAAATAAATTAGCGGCGTTTATGGAGCCAAACGCTA
65 -TTCCTAAAATATAAAATAAATTAGCGGCGTTTATGGAGCCAAACGCTA
* * * * *
7166 CCATTTAAAGAAACGGTGTGAG-ATTTTACCTCTGGGAATAATTATTTAAAAACTTCAAAAAAAA
1 CCATTTAAAGAAACGGAGGGAGAATTTT-CCTCCGGAAATAATTATTTAAAAACTACAAAAAAAA
* *
7230 TTCCTAAAATATAAAATATATTAGTGGCGTTTATGG
65 TTCCTAAAATATAAAATAAATTAGCGGCGTTTATGG
7266 CTAATAAACG
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
111 9 0.10
112 63 0.72
113 15 0.17
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (112 bp):
CCATTTAAAGAAACGGAGGGAGAATTTTCCTCCGGAAATAATTATTTAAAAACTACAAAAAAAAT
TCCTAAAATATAAAATAAATTAGCGGCGTTTATGGAGCCAAACGCTA
Found at i:7918 original size:4 final size:4
Alignment explanation
Indices: 7909--7934 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
7899 AATATTAATG
7909 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
7935 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:7939 original size:2 final size:2
Alignment explanation
Indices: 7932--7956 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7922 ACATACATAC
7932 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
7957 CTAGTCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.