Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017219.1 Corchorus olitorius cultivar O-4 contig17252, 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: 16390
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:1364 original size:2 final size:2
Alignment explanation
Indices: 1357--1385 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1347 AAGTCTTTAT
1357 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
1386 TCTAGTGCTT
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:1773 original size:19 final size:19
Alignment explanation
Indices: 1749--1785 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1739 GTACGGTAAC
*
1749 TAATCTAATCTGTACAGTG
1 TAATCTAATATGTACAGTG
*
1768 TAATCTCATATGTACAGT
1 TAATCTAATATGTACAGT
1786 TGCTAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATATGTACAGTG
Found at i:2696 original size:29 final size:29
Alignment explanation
Indices: 2663--2727 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2653 TTTTTCTGAT
* *
2663 TTTGTTTAAGTGCAGGTTGTGCACTTGTG
1 TTTGTTTAAGTGCAGGTTGTACACTTGGG
* **
2692 TTTGTTCAAGTGTGGGTTGTACACTTGGG
1 TTTGTTTAAGTGCAGGTTGTACACTTGGG
*
2721 ATTGTTT
1 TTTGTTT
2728 TGAGTGTGGG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.09, G:0.31, T:0.46
Consensus pattern (29 bp):
TTTGTTTAAGTGCAGGTTGTACACTTGGG
Found at i:10678 original size:31 final size:31
Alignment explanation
Indices: 10611--10688 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
10601 TTGCGGCAAA
*
10611 ATGCTCAATTTGGGGCCAAACGTTTGCCGTG
1 ATGCTCAATTTGGGGCCAAACGTTTGCCGGG
* * *
10642 ATGCTCGATTTGGGGCCAAACGTTTTCGGGG
1 ATGCTCAATTTGGGGCCAAACGTTTGCCGGG
* *
10673 CTGCTCAATGTGGGGC
1 ATGCTCAATTTGGGGC
10689 TTTTTCTGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (31 bp):
ATGCTCAATTTGGGGCCAAACGTTTGCCGGG
Found at i:13546 original size:29 final size:29
Alignment explanation
Indices: 13491--13546 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
13481 TTTTTCTAAT
* *
13491 TTTGTTTAAGTGCGGGTTGTGCACTTGTG
1 TTTGTTCAAGTGCGGGTTGTACACTTGTG
* *
13520 TTTGTTCAAGTGTGGGTTGTACGCTTG
1 TTTGTTCAAGTGCGGGTTGTACACTTG
13547 AGATTGTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.11, C:0.11, G:0.34, T:0.45
Consensus pattern (29 bp):
TTTGTTCAAGTGCGGGTTGTACACTTGTG
Found at i:13553 original size:29 final size:29
Alignment explanation
Indices: 13492--13554 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
13482 TTTTCTAATT
* * * *
13492 TTGTTTAAGTGCGGGTTGTGCACTTGTGT
1 TTGTTCAAGTGCGGGTTGTACACTTGAGA
* *
13521 TTGTTCAAGTGTGGGTTGTACGCTTGAGA
1 TTGTTCAAGTGCGGGTTGTACACTTGAGA
13550 TTGTT
1 TTGTT
13555 TTGAGTGTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.13, C:0.10, G:0.33, T:0.44
Consensus pattern (29 bp):
TTGTTCAAGTGCGGGTTGTACACTTGAGA
Found at i:14583 original size:32 final size:31
Alignment explanation
Indices: 14515--14587 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
14505 TCGAACGGAT
*
14515 TCGGGTTCGGGTACTTCAGGTTCGGGTTCTA
1 TCGGGTTCGGGTACTTCAGGTTCGGGTTATA
* *
14546 GCGGGTTCGGGTATTTTC-GGTCTCGGGTTATA
1 TCGGGTTCGGGTA-CTTCAGGT-TCGGGTTATA
14578 TCGGGTTCGG
1 TCGGGTTCGG
14588 TTTCGGATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 15 0.42
32 21 0.58
ACGTcount: A:0.08, C:0.18, G:0.38, T:0.36
Consensus pattern (31 bp):
TCGGGTTCGGGTACTTCAGGTTCGGGTTATA
Found at i:14587 original size:16 final size:16
Alignment explanation
Indices: 14515--14587 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
14505 TCGAACGGAT
14515 TCGGGTTCGGGTACT-
1 TCGGGTTCGGGTACTA
* *
14530 TCAGGTTCGGGTTCTA
1 TCGGGTTCGGGTACTA
* * *
14546 GCGGGTTCGGGTATTT
1 TCGGGTTCGGGTACTA
14562 TC-GGTCTCGGGTTA-TA
1 TCGGGT-TCGGG-TACTA
14578 TCGGGTTCGG
1 TCGGGTTCGG
14588 TTTCGGATAG
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
15 16 0.36
16 24 0.53
17 5 0.11
ACGTcount: A:0.08, C:0.18, G:0.38, T:0.36
Consensus pattern (16 bp):
TCGGGTTCGGGTACTA
Found at i:15802 original size:13 final size:14
Alignment explanation
Indices: 15777--15807 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
15767 AAGTTTATTG
15777 ATAATATATATAAT
1 ATAATATATATAAT
15791 ATAATA-ATATAAT
1 ATAATATATATAAT
15804 ATAA
1 ATAA
15808 CATGATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATATATATAAT
Done.