Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021510.1 Corchorus olitorius cultivar O-4 contig21543, 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: 11395
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:655 original size:178 final size:178
Alignment explanation
Indices: 387--707 Score: 459
Period size: 178 Copynumber: 1.8 Consensus size: 178
377 CGATTAAGGT
* *
387 GATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGAGTCGAAAACTAA
1 GATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAA
* * * ***
452 ATTTAATGTTTCAAGCATCAAAAATGCTTCCGAAA-AATTTGCTGTTTCGGTTAACGGGAATAGA
66 ATTTAATGTTTCAAGCATAAAAAATGCTTCC-AAAGAATTAGCTGTTTCAGTTAACAAAAATAGA
*
516 CGGTCCACTTAATATTATATAACTTTTGCTCCAGATGTTTGATTGAGAC
130 CAGTCCACTTAATATTATATAACTTTTGCTCCAGATGTTTGATTGAGAC
* * * *
565 GATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGGAGGACTC-AAAAGCTA
1 GATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAA-CTA
* *
629 AATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCAGTTAACAAAAATAG
65 AATTTAATGTTTCAA-GCATAAAAAATGCTTCCAAAGAATTAGCTGTTTCAGTTAACAAAAATAG
693 ACAGTCCACTTAATA
129 ACAGTCCACTTAATA
708 CATAATTTGT
Statistics
Matches: 125, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
177 12 0.10
178 113 0.90
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (178 bp):
GATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAA
ATTTAATGTTTCAAGCATAAAAAATGCTTCCAAAGAATTAGCTGTTTCAGTTAACAAAAATAGAC
AGTCCACTTAATATTATATAACTTTTGCTCCAGATGTTTGATTGAGAC
Found at i:5241 original size:21 final size:21
Alignment explanation
Indices: 5215--5255 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5205 TTGAAGCCCT
5215 ATTGGATAC-AAGTGGTACTAA
1 ATTGGAT-CTAAGTGGTACTAA
5236 ATTGGATCTAAGTGGTACTA
1 ATTGGATCTAAGTGGTACTA
5256 GGGTTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (21 bp):
ATTGGATCTAAGTGGTACTAA
Found at i:6387 original size:66 final size:66
Alignment explanation
Indices: 6310--6436 Score: 202
Period size: 66 Copynumber: 1.9 Consensus size: 66
6300 AGTAATTCTG
6310 AACCTAATTTGAGTGTTGTTTACAATGACA-TGAAATCTGTTTTAGATGTTGTTAGTGATGATAG
1 AACCTAATTTGAGTGTTGTTTACAATGACACT-AAATCTGTTTTAGATGTTGTTAGTGATGATAG
6374 TA
65 TA
* * * *
6376 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGA
1 AACCTAATTTGAGTGTTGTTTACAATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGA
6437 AACAAATTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
66 55 0.98
67 1 0.02
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.42
Consensus pattern (66 bp):
AACCTAATTTGAGTGTTGTTTACAATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGATAGT
A
Found at i:6403 original size:33 final size:33
Alignment explanation
Indices: 6310--6405 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 33
6300 AGTAATTCTG
* *
6310 AACCTAATTTGAGTGTTGTTTACAATGACATGA
1 AACCTAATTTGAGTGTTGTTTGCGATGACATGA
* * * * * *
6343 AATCT-GTTTTAGATGTTGTTAGTGATGATA-GTA
1 AACCTAATTTGAG-TGTTGTTTGCGATGACATG-A
6376 AACCTAATTTGAGTGTTGTTTGCGATGACA
1 AACCTAATTTGAGTGTTGTTTGCGATGACA
6406 CTAAATCTGT
Statistics
Matches: 46, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
32 6 0.13
33 35 0.76
34 5 0.11
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (33 bp):
AACCTAATTTGAGTGTTGTTTGCGATGACATGA
Found at i:6425 original size:33 final size:33
Alignment explanation
Indices: 6322--6451 Score: 104
Period size: 33 Copynumber: 3.9 Consensus size: 33
6312 CCTAATTTGA
* *
6322 GTGTTGTTTACAATGACA-TGAAATCTGTTTTAG
1 GTGTTGTTTGCGATGACACT-AAATCTGTTTTAG
* * * * * * **
6355 ATGTTGTTAGTGATGATAGTAAACCTAATTT-G
1 GTGTTGTTTGCGATGACACTAAATCTGTTTTAG
6387 AGTGTTGTTTGCGATGACACTAAATCTGTTTTAG
1 -GTGTTGTTTGCGATGACACTAAATCTGTTTTAG
* *
6421 GTGTTGTTTGTGATGAAAC-AAATTCTGTTTT
1 GTGTTGTTTGCGATGACACTAAA-TCTGTTTT
6452 GGATGCTAAT
Statistics
Matches: 74, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
32 4 0.05
33 68 0.92
34 2 0.03
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (33 bp):
GTGTTGTTTGCGATGACACTAAATCTGTTTTAG
Found at i:10836 original size:29 final size:30
Alignment explanation
Indices: 10776--10855 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
10766 GCTAAATACC
* *
10776 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
10807 CAAAATAATCCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
* *
10836 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
10856 CAAAAATGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:11053 original size:32 final size:30
Alignment explanation
Indices: 10979--11074 Score: 138
Period size: 30 Copynumber: 3.1 Consensus size: 30
10969 TAGGGACTGA
10979 TTTGTCCCAAAAGAAAAACATAAGGGATTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTT
*
11009 TTTATCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGA-TTT
* *
11040 TTTGTCCCTAAAAGAAAAATATAAGAGAATTT
1 TTTGTCCC-AAAAGAAAAACATAAG-GGATTT
11072 TTT
1 TTT
11075 AGTATTTAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.44
31 10 0.17
32 21 0.36
33 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTT
Done.