Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015173.1 Corchorus olitorius cultivar O-4 contig15206, 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: 40079
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1130 original size:36 final size:36
Alignment explanation
Indices: 1083--1155 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1073 AAAAGAACCT
1083 ATAAAGACAAAAACAAAGCAATCTTTACAAATTCAA
1 ATAAAGACAAAAACAAAGCAATCTTTACAAATTCAA
1119 ATAAAGACAAAAACAAAGCAATCTTTACAAATTCAA
1 ATAAAGACAAAAACAAAGCAATCTTTACAAATTCAA
1155 A
1 A
1156 GGATAGACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.59, C:0.16, G:0.05, T:0.19
Consensus pattern (36 bp):
ATAAAGACAAAAACAAAGCAATCTTTACAAATTCAA
Found at i:2661 original size:31 final size:31
Alignment explanation
Indices: 2555--2653 Score: 159
Period size: 31 Copynumber: 3.3 Consensus size: 31
2545 TTGGCTAAAT
2555 GCTCAATTTGGTCCTAAACCTTTGAGCGAG-C
1 GCTCAATTTGGTCCTAAACCTTTGAGCG-GTC
*
2586 GCTCAATTTGGTCCTAAACCTTTGAAC-GT-
1 GCTCAATTTGGTCCTAAACCTTTGAGCGGTC
2615 GCTCAATTTGGTCCTAAACCTTTGAGCGGTC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGGTC
2646 GCTCAATT
1 GCTCAATT
2654 CAGTCCTATT
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
29 27 0.43
30 2 0.03
31 34 0.54
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (31 bp):
GCTCAATTTGGTCCTAAACCTTTGAGCGGTC
Found at i:5902 original size:21 final size:22
Alignment explanation
Indices: 5878--5924 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5868 AACAATAAAT
5878 GAAATAAAACTC-AAATAGATG
1 GAAATAAAACTCAAAATAGATG
* *
5899 GAAATATAGCTCAAAATAGATG
1 GAAATAAAACTCAAAATAGATG
5921 GAAA
1 GAAA
5925 CATACCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (22 bp):
GAAATAAAACTCAAAATAGATG
Found at i:9154 original size:42 final size:43
Alignment explanation
Indices: 9103--9191 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
9093 GATTTATCAT
9103 TATCCATGTGGC-TTTTTTTTACTTTAAAAATAGCCACGTGGC
1 TATCCATGTGGCTTTTTTTTTACTTTAAAAATAGCCACGTGGC
* *
9145 TATCCATGTGGCTTTTTTTTTACTTTAGAAATTGCCACGTGGC
1 TATCCATGTGGCTTTTTTTTTACTTTAAAAATAGCCACGTGGC
9188 TATC
1 TATC
9192 TTATTGAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 12 0.27
43 32 0.73
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (43 bp):
TATCCATGTGGCTTTTTTTTTACTTTAAAAATAGCCACGTGGC
Found at i:9305 original size:31 final size:30
Alignment explanation
Indices: 9270--9367 Score: 146
Period size: 31 Copynumber: 3.2 Consensus size: 30
9260 AATAGGACTG
9270 AATTGAGTGACCGCTCAAAGGTTTAGGACCA
1 AATTGAG-GACCGCTCAAAGGTTTAGGACCA
*
9301 AATTGAGCA-CGCTCAAAGGTTTAGGACCA
1 AATTGAGGACCGCTCAAAGGTTTAGGACCA
9330 AATTGAGCG-CTCGCTCAAAGGTTTAGGACCA
1 AATTGAG-GAC-CGCTCAAAGGTTTAGGACCA
9361 AATTGAG
1 AATTGAG
9368 CATTTAGCCA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
29 27 0.44
30 1 0.02
31 34 0.55
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (30 bp):
AATTGAGGACCGCTCAAAGGTTTAGGACCA
Found at i:9322 original size:29 final size:29
Alignment explanation
Indices: 9281--9369 Score: 151
Period size: 29 Copynumber: 3.0 Consensus size: 29
9271 ATTGAGTGAC
9281 CGCTCAAAGGTTTAGGACCAAATTGAGCA
1 CGCTCAAAGGTTTAGGACCAAATTGAGCA
*
9310 CGCTCAAAGGTTTAGGACCAAATTGAGCGCT
1 CGCTCAAAGGTTTAGGACCAAATTGA--GCA
9341 CGCTCAAAGGTTTAGGACCAAATTGAGCA
1 CGCTCAAAGGTTTAGGACCAAATTGAGCA
9370 TTTAGCCAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
29 28 0.50
31 28 0.50
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (29 bp):
CGCTCAAAGGTTTAGGACCAAATTGAGCA
Found at i:9368 original size:31 final size:31
Alignment explanation
Indices: 9281--9368 Score: 153
Period size: 31 Copynumber: 2.9 Consensus size: 31
9271 ATTGAGTGAC
9281 CGCTCAAAGGTTTAGGACCAAATTGA--GCA
1 CGCTCAAAGGTTTAGGACCAAATTGAGCGCA
*
9310 CGCTCAAAGGTTTAGGACCAAATTGAGCGCT
1 CGCTCAAAGGTTTAGGACCAAATTGAGCGCA
9341 CGCTCAAAGGTTTAGGACCAAATTGAGC
1 CGCTCAAAGGTTTAGGACCAAATTGAGC
9369 ATTTAGCCAG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 26 0.46
31 30 0.54
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (31 bp):
CGCTCAAAGGTTTAGGACCAAATTGAGCGCA
Found at i:9588 original size:11 final size:11
Alignment explanation
Indices: 9574--9611 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9564 ATTCATAACA
9574 AATTTATAATT
1 AATTTATAATT
9585 AATTTATAATT
1 AATTTATAATT
9596 -ATTTGATAATT
1 AATTT-ATAATT
*
9607 TATTT
1 AATTT
9612 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:9788 original size:25 final size:22
Alignment explanation
Indices: 9755--9837 Score: 71
Period size: 25 Copynumber: 3.6 Consensus size: 22
9745 GATCTTGCTC
9755 ATAA-AATTAATAGTAGGTTTAATA
1 ATAATAATTAATA-TA--TTTAATA
*
9779 ATAATAATTAATATAAATATAAATA
1 ATAATAATTAATAT--AT-TTAATA
*
9804 TTAATAATTAATATA-TTAATA
1 ATAATAATTAATATATTTAATA
*
9825 TTAATAATTAATA
1 ATAATAATTAATA
9838 ATAAAGCGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
21 18 0.35
23 1 0.02
24 6 0.12
25 26 0.50
26 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (22 bp):
ATAATAATTAATATATTTAATA
Found at i:12041 original size:44 final size:44
Alignment explanation
Indices: 11978--12066 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
11968 TGAGTGGAAA
11978 TGATTCATTTTTCAAGGTTTTCTTACTATTTCTTTGGTTAATTT
1 TGATTCATTTTTCAAGGTTTTCTTACTATTTCTTTGGTTAATTT
12022 TGATTCATTTTTCAAGGTTTTCTTACTATTTCTTTGGTTAATTT
1 TGATTCATTTTTCAAGGTTTTCTTACTATTTCTTTGGTTAATTT
12066 T
1 T
12067 TTTTGGTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (44 bp):
TGATTCATTTTTCAAGGTTTTCTTACTATTTCTTTGGTTAATTT
Found at i:16445 original size:3 final size:3
Alignment explanation
Indices: 16393--16421 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16383 ATAATAAATA
16393 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16422 ATTAGGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16465 original size:3 final size:3
Alignment explanation
Indices: 16459--16501 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
16449 TTATTCTTAG
16459 TAA TAA TAA -AA -AA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
16502 TATTATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.84
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16508 original size:3 final size:3
Alignment explanation
Indices: 16502--16528 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16492 AATAATAATA
16502 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
16529 ATTTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:21240 original size:72 final size:72
Alignment explanation
Indices: 21154--21298 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
21144 TTTTAGGGTG
21154 GTCATATATGATATATGTGAATAGAAAAATGTTTGGAAGTATTTGCTTCGGCATTGTATCCCACC
1 GTCATATATGATATATGTGAATAGAAAAATGTTTGGAAGTATTTGCTTCGGCATTGTATCCCACC
21219 ACTACTT
66 ACTACTT
*
21226 GTCATATATGATATATGTGAATAGAAAAATGTTTGTAAGTATTTGCTTCGGCATTGTATCCCACC
1 GTCATATATGATATATGTGAATAGAAAAATGTTTGGAAGTATTTGCTTCGGCATTGTATCCCACC
21291 ACTACTT
66 ACTACTT
21298 G
1 G
21299 AAAATACTTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (72 bp):
GTCATATATGATATATGTGAATAGAAAAATGTTTGGAAGTATTTGCTTCGGCATTGTATCCCACC
ACTACTT
Found at i:24871 original size:8 final size:8
Alignment explanation
Indices: 24860--24891 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
24850 AAATGGGGAA
24860 AGAAAGGG
1 AGAAAGGG
24868 AGAAAGGG
1 AGAAAGGG
24876 AGAAAGGG
1 AGAAAGGG
24884 AGAAAGGG
1 AGAAAGGG
24892 GCTTGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (8 bp):
AGAAAGGG
Found at i:25141 original size:1 final size:1
Alignment explanation
Indices: 25135--25162 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
25125 AAGGTAAGGG
25135 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
25163 GAAATTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:28916 original size:50 final size:50
Alignment explanation
Indices: 28857--28956 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
28847 ACGGTGGGCC
*
28857 CTCAATAAAACTATGAAGCTCTGAAAAGGAGGGGAAAAGATATTTGATAA
1 CTCAATAAAACTATGAAGCTCTGAAAAGGAGGGGAAAAGATATTCGATAA
*
28907 CTCAATAAAACTATGAAGCTCTGAAAAGGAGTGGAAAAGATATTCGATAA
1 CTCAATAAAACTATGAAGCTCTGAAAAGGAGGGGAAAAGATATTCGATAA
28957 TAGAACAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (50 bp):
CTCAATAAAACTATGAAGCTCTGAAAAGGAGGGGAAAAGATATTCGATAA
Found at i:32120 original size:40 final size:40
Alignment explanation
Indices: 32065--32142 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
32055 ATAACTAGGA
* *
32065 GCTAAACCTGTATTTAATTTCTTGT-CTTAATTATTAGGGG
1 GCTAAACCTGAATTTAATTTATT-TCCTTAATTATTAGGGG
32105 GCTAAACCTGAATTTAATTTATTTCCTTAATTATTAGG
1 GCTAAACCTGAATTTAATTTATTTCCTTAATTATTAGG
32143 AGGGTCAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 1 0.03
40 34 0.97
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (40 bp):
GCTAAACCTGAATTTAATTTATTTCCTTAATTATTAGGGG
Found at i:36562 original size:21 final size:21
Alignment explanation
Indices: 36538--36605 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
36528 TGAATGATGA
36538 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATGGCCGGTGG
* **
36559 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATGGCCGGTGG
* * *
36580 TGGCACGGTGAATGGCTGGTAG
1 TGGCACGG-GCATGGCCGGTGG
36602 TGGC
1 TGGC
36606 TTGGTAGTGG
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 26 0.70
22 11 0.30
ACGTcount: A:0.13, C:0.21, G:0.47, T:0.19
Consensus pattern (21 bp):
TGGCACGGGCATGGCCGGTGG
Found at i:36912 original size:23 final size:21
Alignment explanation
Indices: 36870--36912 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
36860 TGGGCAAGCG
**
36870 GCGCGGATGGCCGGTTGTGGT
1 GCGCGGATGGCCGGGCGTGGT
36891 GCGCGGATGGGTCCGGGCGTGG
1 GCGCGGAT-GG-CCGGGCGTGG
36913 CCAGGAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 2 0.11
23 8 0.44
ACGTcount: A:0.05, C:0.21, G:0.56, T:0.19
Consensus pattern (21 bp):
GCGCGGATGGCCGGGCGTGGT
Found at i:36991 original size:28 final size:28
Alignment explanation
Indices: 36951--37006 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
36941 ATGGCCGGGT
36951 AGGTGACTCGGTGCGGCACGGGTTTGGC
1 AGGTGACTCGGTGCGGCACGGGTTTGGC
36979 AGGTGACTCGGTGCGGCACGGGTTTGGC
1 AGGTGACTCGGTGCGGCACGGGTTTGGC
37007 CGGTTCTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.11, C:0.21, G:0.46, T:0.21
Consensus pattern (28 bp):
AGGTGACTCGGTGCGGCACGGGTTTGGC
Done.