Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012064.1 Corchorus olitorius cultivar O-4 contig12097, 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: 31142
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1075 original size:58 final size:58
Alignment explanation
Indices: 977--1086 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
967 ATCATGCCTC
*
977 GGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGACTT
1 GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGACTT
* * *
1035 GGTCCGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA
1087 TTTGATTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 31 0.66
59 16 0.34
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGACTT
Found at i:1642 original size:76 final size:76
Alignment explanation
Indices: 1517--1669 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
1507 TAGAAGAGAA
1517 AGAAAATAAGATGAAAAGAGGAAGGAAACAACCTTAAAAGTATTTATTATTCCCTCCCCATTATG
1 AGAAAATAAGATGAAAAGAGGAAGGAAACAACCTTAAAAGTATTTATTATTCCCTCCCCATTATG
1582 GATTAATTATG
66 GATTAATTATG
1593 AGAAAATAAGATGAAAAGAGGAAGGAAACAACCTTAAAAGTATTTATTATTCCCTCCCCATTATG
1 AGAAAATAAGATGAAAAGAGGAAGGAAACAACCTTAAAAGTATTTATTATTCCCTCCCCATTATG
1658 GATTAATTATG
66 GATTAATTATG
1669 A
1 A
1670 TTAAGTGATT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (76 bp):
AGAAAATAAGATGAAAAGAGGAAGGAAACAACCTTAAAAGTATTTATTATTCCCTCCCCATTATG
GATTAATTATG
Found at i:2666 original size:2 final size:2
Alignment explanation
Indices: 2659--2701 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2649 CTTTAACTAG
2659 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2700 TA
1 TA
2702 GATAGATAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5473 original size:23 final size:23
Alignment explanation
Indices: 5447--5490 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5437 AAATTCTTTA
* *
5447 CTTTATTTTTCGAAAAAAAAATT
1 CTTTACTTTTCCAAAAAAAAATT
5470 CTTTACTTTTCCAAAAAAAAA
1 CTTTACTTTTCCAAAAAAAAA
5491 GGGTTTAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (23 bp):
CTTTACTTTTCCAAAAAAAAATT
Found at i:5497 original size:23 final size:23
Alignment explanation
Indices: 5447--5497 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5437 AAATTCTTTA
* * **
5447 CTTTATTTTTCGAAAAAAAAATT
1 CTTTACTTTTCCAAAAAAAAAGG
5470 CTTTACTTTTCCAAAAAAAAAGG
1 CTTTACTTTTCCAAAAAAAAAGG
*
5493 GTTTA
1 CTTTA
5498 GACCTTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (23 bp):
CTTTACTTTTCCAAAAAAAAAGG
Found at i:5951 original size:22 final size:22
Alignment explanation
Indices: 5926--5969 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5916 TAAATGAAAT
5926 ATTCATATGAAATTATGATAAC
1 ATTCATATGAAATTATGATAAC
* *
5948 ATTCCTATTAAATTATGATAAC
1 ATTCATATGAAATTATGATAAC
5970 CCCTTGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (22 bp):
ATTCATATGAAATTATGATAAC
Found at i:8084 original size:14 final size:14
Alignment explanation
Indices: 8067--8095 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8057 ATTCTGTTCT
8067 TTTAAACATGTTAA
1 TTTAAACATGTTAA
8081 TTTAAACATGTTAA
1 TTTAAACATGTTAA
8095 T
1 T
8096 AGGTTAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTAAACATGTTAA
Found at i:12342 original size:1 final size:1
Alignment explanation
Indices: 12336--12368 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
12326 CATTTTAGGG
*
12336 TTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12369 GTTGTGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:12352 original size:21 final size:21
Alignment explanation
Indices: 12328--12371 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
12318 GTTTTGCTCA
12328 TTTTAGGGTTTTTTTTTTTTG
1 TTTTAGGGTTTTTTTTTTTTG
****
12349 TTTTTTTTTTTTTTTTTTTTG
1 TTTTAGGGTTTTTTTTTTTTG
12370 TT
1 TT
12372 GTGTGTGTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.86
Consensus pattern (21 bp):
TTTTAGGGTTTTTTTTTTTTG
Found at i:13034 original size:2 final size:2
Alignment explanation
Indices: 13029--13061 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13019 TCTCTCTCTC
13029 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
13062 GTATGTATGT
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:13149 original size:2 final size:2
Alignment explanation
Indices: 13137--13171 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13127 AATGAATTCC
13137 AT AT A- 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 AT AT AT
13172 TTTGTCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22384 original size:52 final size:52
Alignment explanation
Indices: 22322--22426 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
22312 ATGCATGTTT
* *
22322 TCCTAATCTCCTTTGGTCTATAACTCTTACCTATTAAAGGATTTTAAATTAC
1 TCCTAATCTCCTTTGGTCTATAACTCCTAACTATTAAAGGATTTTAAATTAC
22374 TCCTAATCTCCTTTGGTCTATAACTCCTAACTATTAAAGGATTTTAAATTAC
1 TCCTAATCTCCTTTGGTCTATAACTCCTAACTATTAAAGGATTTTAAATTAC
22426 T
1 T
22427 TCCTCTATCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.42
Consensus pattern (52 bp):
TCCTAATCTCCTTTGGTCTATAACTCCTAACTATTAAAGGATTTTAAATTAC
Found at i:28795 original size:26 final size:27
Alignment explanation
Indices: 28740--28810 Score: 99
Period size: 26 Copynumber: 2.6 Consensus size: 27
28730 GGTGAATTTC
* *
28740 TGGTCATTTGTACTTCAGGGGGGCATTT
1 TGGTCTTTTGTACTTCA-GGGGGCACTT
*
28768 TGGTCTTTTGTATTTCA-GGGGCACTT
1 TGGTCTTTTGTACTTCAGGGGGCACTT
28794 TGGTCTTTTGTACTTCA
1 TGGTCTTTTGTACTTCA
28811 TTACTAGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 24 0.62
28 15 0.38
ACGTcount: A:0.13, C:0.15, G:0.27, T:0.45
Consensus pattern (27 bp):
TGGTCTTTTGTACTTCAGGGGGCACTT
Found at i:28933 original size:22 final size:22
Alignment explanation
Indices: 28908--28950 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28898 TTATGTTCTC
* *
28908 TTGCATATTTATATTACATTTT
1 TTGCAGATTTATATCACATTTT
*
28930 TTGCAGATTTATCTCACATTT
1 TTGCAGATTTATATCACATTT
28951 GCACTTGCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (22 bp):
TTGCAGATTTATATCACATTTT
Done.