Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019022.1 Corchorus olitorius cultivar O-4 contig19055, 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: 10998
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3178 original size:8 final size:9
Alignment explanation
Indices: 3141--3179 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
3131 TTAAAATTAC
3141 TTATGGAAA
1 TTATGGAAA
*
3150 TTTAAGGAAA
1 -TTATGGAAA
3160 TTATGGAAA
1 TTATGGAAA
3169 TTAT-GAAA
1 TTATGGAAA
3177 TTA
1 TTA
3180 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 7 0.26
9 12 0.44
10 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (9 bp):
TTATGGAAA
Found at i:4528 original size:49 final size:47
Alignment explanation
Indices: 4454--4596 Score: 148
Period size: 49 Copynumber: 3.0 Consensus size: 47
4444 TCCAAGCAAT
*
4454 CATTTACTTTTCAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAA
1 CATTTA-TTTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAA
* *
4502 CATTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGAT
1 CATTTATTTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAA
* * * *
4551 CTTTTAATTTT-CATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 CATTTATTTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
4597 TTGGCACGCT
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
47 16 0.20
48 26 0.32
49 39 0.48
50 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (47 bp):
CATTTATTTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAA
Found at i:4680 original size:22 final size:25
Alignment explanation
Indices: 4655--4711 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 25
4645 GCGCGAACAA
*
4655 GATCAAACCATTTTT-TT-T-AAAG
1 GATCCAACCATTTTTGTTATGAAAG
4677 GATCCAACCATTTTTGTTATGAAAG
1 GATCCAACCATTTTTGTTATGAAAG
4702 GATCCAACCA
1 GATCCAACCA
4712 AATTTGGTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 14 0.45
23 2 0.06
24 1 0.03
25 14 0.45
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (25 bp):
GATCCAACCATTTTTGTTATGAAAG
Found at i:5424 original size:178 final size:180
Alignment explanation
Indices: 5020--5469 Score: 498
Period size: 178 Copynumber: 2.5 Consensus size: 180
5010 TTTCAGAAAC
* * * * *
5020 TTTTTGATACTTGAAACATCAAATTTAGCTTTGGAATCCTTCATGAAAGTTGTAGATTATGCAAC
1 TTTTT-ATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGTAGATAATGGAAC
* * * *
5085 AACCTTTTAATAGACATTTGAATCA-CTTCAATCGGACATCTGGAGCAAAAATTATGCAATATTT
65 AACCTTTTAATAGACACTTGAATCACCTTCAATCAGACATCTGGAACAAAAATTAAGCAATATTT
* * * **
5149 AAGTACACCGTCCATTTCCGTTAACCGAAACAACTATTTTCTTGAATCGTT
130 AAGTACACCGTCCATTCCCGTTAACCGAAACAACTATTTTCTGGAAGCGAA
* * *
5200 TTTTTATATTTGGAACATTAAA-TTAGCTTTCGAGTCCTTAATGAAAGTTGTAGATAATGGAACA
1 TTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGTAGATAATGGAACA
* * * * * ***
5264 ATCTTTTAAGAGACACTTGAATCACCTT-AATTAGACATGTGGAACAAAAGTTAAGTGTTA-TTA
66 ACCTTTTAATAGACACTTGAATCACCTTCAATCAGACATCTGGAACAAAAATTAAGCAATATTTA
** * *
5327 AGTGGAGCGTCTATTCCCGTTAACCGAAACAACTAATTTT-TCGGAAGC-AA
131 AGTACACCGTCCATTCCCGTTAACCGAAACAACT-ATTTTCT-GGAAGCGAA
* * * * * *
5377 TTTTTATACTTGAAACATTAAATTTAGTTTTTGAGTTCTTCATGAAAGTTGTAGATCATGGGATA
1 TTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGTAGATAATGGAACA
* *
5442 ACCTTTAAATAGACACTCGAATCACCTT
66 ACCTTTTAATAGACACTTGAATCACCTT
5470 GATCGGATAT
Statistics
Matches: 224, Mismatches: 42, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
177 53 0.24
178 149 0.67
179 17 0.08
180 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (180 bp):
TTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGTAGATAATGGAACA
ACCTTTTAATAGACACTTGAATCACCTTCAATCAGACATCTGGAACAAAAATTAAGCAATATTTA
AGTACACCGTCCATTCCCGTTAACCGAAACAACTATTTTCTGGAAGCGAA
Found at i:8227 original size:28 final size:28
Alignment explanation
Indices: 8171--8234 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
8161 AATTAAATTA
* * * * *
8171 AATTTTTTTTTTCTTTTTTTTCTTTCTC
1 AATTTTCTTTTTCTTCTTCTTCCTCCTC
8199 AATTTTCTTTTTCTTCTTCTTCCTCCTC
1 AATTTTCTTTTTCTTCTTCTTCCTCCTC
8227 -ATTTTCTT
1 AATTTTCTT
8235 CCCTCTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (28 bp):
AATTTTCTTTTTCTTCTTCTTCCTCCTC
Found at i:10397 original size:18 final size:19
Alignment explanation
Indices: 10357--10400 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
10347 TCATACTACT
10357 GAAACT-AACTGACTCAAA
1 GAAACTGAACTGACTCAAA
* *
10375 CAAACTGAATTGACTC-AA
1 GAAACTGAACTGACTCAAA
10393 GAAACTGA
1 GAAACTGA
10401 CTAAACCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (19 bp):
GAAACTGAACTGACTCAAA
Done.