Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019032.1 Corchorus olitorius cultivar O-4 contig19065, 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: 46748
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2668 original size:29 final size:31
Alignment explanation
Indices: 2630--2711 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
2620 AGATTTTGAT
*
2630 AGGTTTAGGACCAATTTGAGCAAGT-AT-AA
1 AGGTTTAGGACCAAATTGAGCAAGTCATCAA
*
2659 AGGTTTAGGACCAAATTGAGC-ATTCCATCAA
1 AGGTTTAGGACCAAATTGAGCAAGT-CATCAA
2690 AGGTTTAGGACCAAATTGAGCA
1 AGGTTTAGGACCAAATTGAGCA
2712 TTTAGCCAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.04
29 20 0.43
30 2 0.04
31 23 0.49
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (31 bp):
AGGTTTAGGACCAAATTGAGCAAGTCATCAA
Found at i:4134 original size:19 final size:19
Alignment explanation
Indices: 4110--4149 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4100 TTTACAGCTG
4110 AGATTTAGAGTACAAGATC
1 AGATTTAGAGTACAAGATC
4129 AGATTTAGAGTACAAGATC
1 AGATTTAGAGTACAAGATC
4148 AG
1 AG
4150 TTAGAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (19 bp):
AGATTTAGAGTACAAGATC
Found at i:4159 original size:17 final size:18
Alignment explanation
Indices: 4114--4159 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
4104 CAGCTGAGAT
4114 TTAGAGTACAAGATCAGA
1 TTAGAGTACAAGATCAGA
4132 TTTAGAGTACAAGATCAG-
1 -TTAGAGTACAAGATCAGA
*
4150 TTAGAATACA
1 TTAGAGTACA
4160 TAAGTAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
19 17 0.65
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (18 bp):
TTAGAGTACAAGATCAGA
Found at i:4587 original size:18 final size:18
Alignment explanation
Indices: 4564--4599 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4554 GTTCAGCTGC
4564 GGTATTGGCCAATGCTTT
1 GGTATTGGCCAATGCTTT
4582 GGTATTGGCCAATGCTTT
1 GGTATTGGCCAATGCTTT
4600 ATACTCTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (18 bp):
GGTATTGGCCAATGCTTT
Found at i:6534 original size:30 final size:30
Alignment explanation
Indices: 6498--6561 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
6488 TTGATGTGGA
6498 AGAAATTTGAGAGGACAAGGAAGAGATGGT
1 AGAAATTTGAGAGGACAAGGAAGAGATGGT
* *
6528 AGAAATTTGAGAGGACGAGGAAGAGGTGGT
1 AGAAATTTGAGAGGACAAGGAAGAGATGGT
6558 AGAA
1 AGAA
6562 GATAGTGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.39, T:0.16
Consensus pattern (30 bp):
AGAAATTTGAGAGGACAAGGAAGAGATGGT
Found at i:6720 original size:19 final size:19
Alignment explanation
Indices: 6696--6735 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
6686 TTTATAGCTG
6696 AGATTTAGAGTACAAGATC
1 AGATTTAGAGTACAAGATC
6715 AGATTTAGAGTACAAGATC
1 AGATTTAGAGTACAAGATC
6734 AG
1 AG
6736 TTAGAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (19 bp):
AGATTTAGAGTACAAGATC
Found at i:6745 original size:17 final size:18
Alignment explanation
Indices: 6700--6745 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
6690 TAGCTGAGAT
6700 TTAGAGTACAAGATCAGA
1 TTAGAGTACAAGATCAGA
6718 TTTAGAGTACAAGATCAG-
1 -TTAGAGTACAAGATCAGA
*
6736 TTAGAATACA
1 TTAGAGTACA
6746 TAAGTAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
19 17 0.65
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (18 bp):
TTAGAGTACAAGATCAGA
Found at i:20883 original size:24 final size:24
Alignment explanation
Indices: 20855--20906 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
20845 GCGTGCTAGG
20855 CCAGGCACGCGGGCCAGCGCAGGC
1 CCAGGCACGCGGGCCAGCGCAGGC
*
20879 CCAGGCGCGCGGGCCAGCGCAGGC
1 CCAGGCACGCGGGCCAGCGCAGGC
20903 CCAG
1 CCAG
20907 CGGCCTGGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.15, C:0.42, G:0.42, T:0.00
Consensus pattern (24 bp):
CCAGGCACGCGGGCCAGCGCAGGC
Found at i:26138 original size:21 final size:21
Alignment explanation
Indices: 26098--26138 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
26088 CGTGGAGGAG
*
26098 GGCGCGGATGACCGGGCAGGC
1 GGCGCGGATGACCGGACAGGC
* *
26119 GGCGCGGATGGCTGGACAGG
1 GGCGCGGATGACCGGACAGG
26139 TGACTCGGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.54, T:0.07
Consensus pattern (21 bp):
GGCGCGGATGACCGGACAGGC
Found at i:29138 original size:33 final size:29
Alignment explanation
Indices: 29055--29148 Score: 73
Period size: 34 Copynumber: 3.0 Consensus size: 29
29045 TTTTTTTTTC
* *
29055 TTTTTTTTTAGAAAAACGCACAAAACAAA
1 TTTTTTTTTAGAAAAACGCAAAAAAAAAA
*
29084 -TTTTTTTTAAATTAAAGACGCAAAGAAAAATAA
1 TTTTTTTTTAGA--AAA-ACGCAAA-AAAAA-AA
*
29117 TTTTTTTTTCAGAAAAAACGCAGAAAAGAAAA
1 TTTTTTTTT-AG-AAAAACGCA-AAAAAAAAA
29149 GGAAAAACGA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
28 10 0.20
30 3 0.06
31 6 0.12
32 6 0.12
33 11 0.22
34 13 0.25
35 1 0.02
36 1 0.02
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (29 bp):
TTTTTTTTTAGAAAAACGCAAAAAAAAAA
Found at i:29142 original size:31 final size:29
Alignment explanation
Indices: 29055--29143 Score: 74
Period size: 33 Copynumber: 2.9 Consensus size: 29
29045 TTTTTTTTTC
*
29055 TTTTTTTTTAGAAAAACGCACAAAACAAA
1 TTTTTTTTTAGAAAAACGCAGAAAACAAA
*
29084 -TTTTTTTTAAATTAAAGACGCAAAGAAAA-ATAA
1 TTTTTTTTTAGA--AAA-ACGC--AGAAAACA-AA
29117 TTTTTTTTTCAGAAAAAACGCAGAAAA
1 TTTTTTTTT-AG-AAAAACGCAGAAAA
29144 GAAAAGGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
28 10 0.21
30 3 0.06
31 10 0.21
32 1 0.02
33 11 0.23
34 11 0.23
35 1 0.02
36 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (29 bp):
TTTTTTTTTAGAAAAACGCAGAAAACAAA
Found at i:29164 original size:21 final size:20
Alignment explanation
Indices: 29130--29168 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29120 TTTTTTCAGA
* *
29130 AAAAACGCAGAAAAGAAAAGG
1 AAAAACG-AAAAAAAAAAAGG
29151 AAAAACGAAAAAAAAAAA
1 AAAAACGAAAAAAAAAAA
29169 TTTAGATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAACGAAAAAAAAAAAGG
Found at i:35367 original size:6 final size:6
Alignment explanation
Indices: 35356--35394 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
35346 TTTCTAAACC
35356 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
35395 ACTTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:35405 original size:18 final size:18
Alignment explanation
Indices: 35356--35405 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
35346 TTTCTAAACC
*
35356 TTTCTTTTTCTTTTTCTT
1 TTTCTTCTTCTTTTTCTT
*
35374 TTTCTTTTTCTTTTTCTT
1 TTTCTTCTTCTTTTTCTT
35392 TTTACTTCTT-TTTT
1 TTT-CTTCTTCTTTT
35406 CCCAGCTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTCTTCTTCTTTTTCTT
Found at i:43408 original size:27 final size:27
Alignment explanation
Indices: 43368--43426 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
43358 TTCATTATAT
* *
43368 GGGTAAAATCGTAATTTTATCAATCAA
1 GGGTAAAATAGTAAATTTATCAATCAA
* * * *
43395 GGGTAACATAGTAAATTTGTCCATCAC
1 GGGTAAAATAGTAAATTTATCAATCAA
43422 GGGTA
1 GGGTA
43427 TTTTTGGTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (27 bp):
GGGTAAAATAGTAAATTTATCAATCAA
Done.