Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022668.1 Corchorus olitorius cultivar O-4 contig22701, 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: 26414
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:6054 original size:22 final size:22
Alignment explanation
Indices: 6009--6061 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
5999 TGCTTTCTGA
**
6009 TTAATTGTTTTCTTTAATTTTC
1 TTAATTGTTTTCTTTAATAGTC
*
6031 TTGATTGTTTTC-TTAGATAGTC
1 TTAATTGTTTTCTTTA-ATAGTC
6053 TTAATTGTT
1 TTAATTGTT
6062 AGTTTGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62
Consensus pattern (22 bp):
TTAATTGTTTTCTTTAATAGTC
Found at i:6606 original size:17 final size:17
Alignment explanation
Indices: 6581--6637 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
6571 TAAAAAACTG
* *
6581 GGCCTAAAACAGAGAGA
1 GGCCAAAAACAGAAAGA
*
6598 GGCCAAAAAACA-AAAAA
1 GGCC-AAAAACAGAAAGA
*
6615 GGACCTAAAACAGAAAGA
1 GG-CCAAAAACAGAAAGA
6633 GGCCA
1 GGCCA
6638 GGGAAGGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.54, C:0.19, G:0.23, T:0.04
Consensus pattern (17 bp):
GGCCAAAAACAGAAAGA
Found at i:6649 original size:35 final size:36
Alignment explanation
Indices: 6567--6637 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
6557 AAAAGGAGCT
* * *
6567 AAAATAAAAAACTGGGCCTAAAACAGAGAGAGGCCAA
1 AAAACAAAAAAC-GGACCTAAAACAGAAAGAGGCCAA
6604 AAAACAAAAAA-GGACCTAAAACAGAAAGAGGCCA
1 AAAACAAAAAACGGACCTAAAACAGAAAGAGGCCA
6638 GGGAAGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 21 0.68
37 10 0.32
ACGTcount: A:0.58, C:0.17, G:0.20, T:0.06
Consensus pattern (36 bp):
AAAACAAAAAACGGACCTAAAACAGAAAGAGGCCAA
Found at i:6671 original size:37 final size:36
Alignment explanation
Indices: 6573--6680 Score: 103
Period size: 37 Copynumber: 3.0 Consensus size: 36
6563 AGCTAAAATA
* *
6573 AAAAACTGGGCCTAAAACAGAGAGAGGCCAAAAAAC
1 AAAAACTGGACCTAAAACAAAGAGAGGCCAAAAAAC
* ** **
6609 AAAAA-AGGACCTAAAACAGAA-AGAGGCCAGGGAAGG
1 AAAAACTGGACCTAAAACA-AAGAGAGGCCA-AAAAAC
*
6645 AAAAACTGGACCTAAAACAAAGAGAGGTCATAAAAA
1 AAAAACTGGACCTAAAACAAAGAGAGGCCA-AAAAA
6681 TTAAAAAGGA
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
35 19 0.35
36 15 0.27
37 21 0.38
ACGTcount: A:0.55, C:0.16, G:0.23, T:0.06
Consensus pattern (36 bp):
AAAAACTGGACCTAAAACAAAGAGAGGCCAAAAAAC
Found at i:7567 original size:59 final size:57
Alignment explanation
Indices: 7500--7942 Score: 553
Period size: 59 Copynumber: 7.6 Consensus size: 57
7490 TTTTTGGTTG
* *
7500 TAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTGTTTCAATTCAAAACCTTATTTTGTTT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT-TTTCAATTCAAAA-CTTATCTTGTTT
* * * *
7559 TAAAATCCTATTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATTCTATCTCGTTTT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAACT-TATCTTG-TTT
* * * * *
7618 TAAAATCCTGTTCGAGGTCTCTATTAGAGAGTTTTTATTTCAAAATTCTATCTCGTTTT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAACT-TATCTTG-TTT
7677 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAA-CTTATCTTGTTT
* * *
7735 TAAAATCCTGTTTGAGGTCTCTGTTAGAGTGTGTTTCAATTCAAAACCTTATTTTGTTT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT-TTTCAATTCAAAA-CTTATCTTGTTT
* * * *
7794 TAAAATCCTGTTCAAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATTCTATCTCGTTTT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAACT-TATCTTG-TTT
* **
7853 TAAAATCCTGTTCGAGGTCTCTATTAGAGAGTTTTCAATTCAAAATCTCGTCTTGTTT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAA-CTTATCTTGTTT
** * *
7911 TAAAATTGTGGTCGAGGTCTCTGTTTGAGAGT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
7943 CTATATTTCA
Statistics
Matches: 340, Mismatches: 37, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.01
58 97 0.29
59 239 0.70
60 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (57 bp):
TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAACTTATCTTGTTT
Found at i:7797 original size:176 final size:176
Alignment explanation
Indices: 7500--7942 Score: 665
Period size: 176 Copynumber: 2.5 Consensus size: 176
7490 TTTTTGGTTG
* * *
7500 TAAAATCCTGGTCGAGGTCTCTGTTAGAGAGTGTTTCAATTCAAAACCTTATTTTGTTTTAAAAT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT-TTTCAATTCAAAATCTTATCTTGTTTTAAAAT
* * *
7565 CCTATTCGAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATTCTATCTCGTTTTTAAAATCCTGTT
65 CCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAACTCTATCTCGTTTTTAAAATCCTGTT
* *
7630 CGAGGTCTCTATTAGAGAGTTTTTATTTCAAAATTCTATCTCGTTTT
130 CAAGGTCTCTATTAGAGAGTTTTCATTTCAAAATTCTATCTCGTTTT
7677 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAAATC
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAAATC
* * * *
7742 CTGTTTGAGGTCTCTGTTAGAGTGTGTTTCAATTCAAAAC-CTTATTTTG-TTTTAAAATCCTGT
66 CTGTTCGAGGTCTCTGTTAGAGAGT-TTTCAATTCAAAACTC-TATCTCGTTTTTAAAATCCTGT
*
7805 TCAAGGTCTCTGTTAGAGAGTTTTCATTTCAAAATTCTATCTCGTTTT
129 TCAAGGTCTCTATTAGAGAGTTTTCATTTCAAAATTCTATCTCGTTTT
* ** *
7853 TAAAATCCTGTTCGAGGTCTCTATTAGAGAGTTTTCAATTCAAAATCTCGTCTTGTTTTAAAATT
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAAATC
* * *
7918 GTGGTCGAGGTCTCTGTTTGAGAGT
66 CTGTTCGAGGTCTCTGTTAGAGAGT
7943 CTATATTTCA
Statistics
Matches: 242, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
176 194 0.80
177 48 0.20
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (176 bp):
TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAAATC
CTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAACTCTATCTCGTTTTTAAAATCCTGTTC
AAGGTCTCTATTAGAGAGTTTTCATTTCAAAATTCTATCTCGTTTT
Found at i:8223 original size:29 final size:29
Alignment explanation
Indices: 8189--8404 Score: 183
Period size: 29 Copynumber: 7.6 Consensus size: 29
8179 GCTCTCCCAG
*
8189 GGGCATTTTGGTCATTTTTGCAAATCTAA
1 GGGCATTTTGGTCATTTTTGCATATCTAA
** * *
8218 AAGCATCTTGATCATTTTTGCATATCTAA
1 GGGCATTTTGGTCATTTTTGCATATCTAA
* * * *
8247 GAGCATCTTGATCATCTTTGCATATCTAA
1 GGGCATTTTGGTCATTTTTGCATATCTAA
* * * * * *
8276 GAGCATCTAGATCATTTTTGCATATCCAG
1 GGGCATTTTGGTCATTTTTGCATATCTAA
* *
8305 GGGTATTTTGGTCATTTTT-CATGTCT-A
1 GGGCATTTTGGTCATTTTTGCATATCTAA
* *
8332 GGGCATTTTGGTCA-TTTTGCA-AGTCCAG
1 GGGCATTTTGGTCATTTTTGCATA-TCTAA
* *
8360 GGGCATTTTGGTCA-TTTTACA-AGTCTAG
1 GGGCATTTTGGTCATTTTTGCATA-TCTAA
8388 GGGCATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
8405 GCACATTCAG
Statistics
Matches: 158, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
26 4 0.03
27 17 0.11
28 45 0.28
29 92 0.58
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTTGCATATCTAA
Found at i:8334 original size:28 final size:28
Alignment explanation
Indices: 8287--8431 Score: 154
Period size: 28 Copynumber: 5.2 Consensus size: 28
8277 AGCATCTAGA
*
8287 TCATTTTTGCATA-TCCAGGGGTATTTTGG
1 TCATTTTT-CA-AGTCCAGGGGCATTTTGG
* *
8316 TCATTTTTCATGTCTA-GGGCATTTTGG
1 TCATTTTTCAAGTCCAGGGGCATTTTGG
*
8343 TCATTTTGCAAGTCCAGGGGCATTTTGG
1 TCATTTTTCAAGTCCAGGGGCATTTTGG
* *
8371 TCATTTTACAAGTCTAGGGGCATTTTGG
1 TCATTTTTCAAGTCCAGGGGCATTTTGG
* * *
8399 TCA-TTTGCACA-TTCAGGGGCGTTTTGG
1 TCATTTTTCA-AGTCCAGGGGCATTTTGG
8426 TCATTT
1 TCATTT
8432 AAAGTCTACT
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
27 44 0.44
28 48 0.48
29 8 0.08
ACGTcount: A:0.17, C:0.16, G:0.25, T:0.42
Consensus pattern (28 bp):
TCATTTTTCAAGTCCAGGGGCATTTTGG
Found at i:8343 original size:27 final size:28
Alignment explanation
Indices: 8303--8439 Score: 158
Period size: 27 Copynumber: 5.0 Consensus size: 28
8293 TTGCATATCC
* * *
8303 AGGGGTATTTTGGTCATTTTTCATGTCT
1 AGGGGCATTTTGGTCATTTTACAAGTCT
* *
8331 A-GGGCATTTTGGTCATTTTGCAAGTCC
1 AGGGGCATTTTGGTCATTTTACAAGTCT
8358 AGGGGCATTTTGGTCATTTTACAAGTCT
1 AGGGGCATTTTGGTCATTTTACAAGTCT
* *
8386 AGGGGCATTTTGGTCA-TTTGCACATTC-
1 AGGGGCATTTTGGTCATTTTACA-AGTCT
*
8413 AGGGGCGTTTTGGTCA-TTTA-AAGTCT
1 AGGGGCATTTTGGTCATTTTACAAGTCT
8439 A
1 A
8440 CTTCTAGCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.03
26 2 0.02
27 46 0.48
28 44 0.46
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.40
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTACAAGTCT
Found at i:8372 original size:55 final size:56
Alignment explanation
Indices: 8291--8439 Score: 200
Period size: 55 Copynumber: 2.7 Consensus size: 56
8281 TCTAGATCAT
* * * *
8291 TTTTGCATATCCAGGGGTATTTTGGTCATTTTTCATGTCTA-GGGCATTTTGGTCA
1 TTTTGCACATCCAGGGGCATTTTGGTCATTTTACAAGTCTAGGGGCATTTTGGTCA
8346 TTTTGCA-AGTCCAGGGGCATTTTGGTCATTTTACAAGTCTAGGGGCATTTTGGTCA
1 TTTTGCACA-TCCAGGGGCATTTTGGTCATTTTACAAGTCTAGGGGCATTTTGGTCA
* *
8402 -TTTGCACATTCAGGGGCGTTTTGGTCA-TTTA-AAGTCTA
1 TTTTGCACATCCAGGGGCATTTTGGTCATTTTACAAGTCTA
8440 CTTCTAGCTT
Statistics
Matches: 86, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
53 7 0.08
54 5 0.06
55 59 0.69
56 15 0.17
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (56 bp):
TTTTGCACATCCAGGGGCATTTTGGTCATTTTACAAGTCTAGGGGCATTTTGGTCA
Found at i:11237 original size:21 final size:21
Alignment explanation
Indices: 11211--11250 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11201 CTTTCAATTG
*
11211 CTGCAATTTCACCTGTTTTTA
1 CTGCAATTCCACCTGTTTTTA
*
11232 CTGCAATTCCGCCTGTTTT
1 CTGCAATTCCACCTGTTTT
11251 CTTTCAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.12, T:0.45
Consensus pattern (21 bp):
CTGCAATTCCACCTGTTTTTA
Found at i:12758 original size:32 final size:30
Alignment explanation
Indices: 12713--12795 Score: 94
Period size: 32 Copynumber: 2.7 Consensus size: 30
12703 TTAAGTAAAC
* * * **
12713 TCCAAAAAAAGATTTTGGAAAGTAAGGTTA
1 TCCAAAAGAAGATTTTGGAAAATAAAGAAA
*
12743 TCCCCAAAAGGAGATTTTGGAAAATAAAGAAA
1 T--CCAAAAGAAGATTTTGGAAAATAAAGAAA
12775 TCCAAAAGAAGATTTTGGAAA
1 TCCAAAAGAAGATTTTGGAAA
12796 TTAGTAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 20 0.45
32 24 0.55
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (30 bp):
TCCAAAAGAAGATTTTGGAAAATAAAGAAA
Found at i:13095 original size:27 final size:27
Alignment explanation
Indices: 12994--13095 Score: 132
Period size: 27 Copynumber: 3.7 Consensus size: 27
12984 AGGATCAACT
* *
12994 AGGGGCATTTTGGTCATTTTCAAAATC
1 AGGGGCATTTTGGTCATTTGCACAATC
* * *
13021 TAGGGGCATTTTGGCCATTTACACATTC
1 -AGGGGCATTTTGGTCATTTGCACAATC
*
13049 AGGGGCATTTTGGTCATTTGCACAGTC
1 AGGGGCATTTTGGTCATTTGCACAATC
*
13076 AAGGGCATTTTGGTCATTTG
1 AGGGGCATTTTGGTCATTTG
13096 AACCCTTACC
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 43 0.65
28 23 0.35
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACAATC
Found at i:14069 original size:145 final size:145
Alignment explanation
Indices: 13806--14070 Score: 503
Period size: 145 Copynumber: 1.8 Consensus size: 145
13796 ACATAAGGCA
*
13806 ATTCTCAATACAGTGCACAAACAAAGCAGGGGCATATTAAGATCCAATGCATCAGTTCAAATACA
1 ATTCTCAATAAAGTGCACAAACAAAGCAGGGGCATATTAAGATCCAATGCATCAGTTCAAATACA
13871 AAGGCTCATTCATGGAAACCCCTTGCACTTTGGGGACTGAATCTTAAGAAGTTAAGATATTCTTC
66 AAGGCTCATTCATGGAAACCCCTTGCACTTTGGGGACTGAATCTTAAGAAGTTAAGATATTCTTC
13936 GAAGAAAAATAGGAT
131 GAAGAAAAATAGGAT
13951 ATTCTCAATAAAGTGCACAAACAAAGCAGGGGCATATTAAGATCCAATGCATCAGTTCAAATACA
1 ATTCTCAATAAAGTGCACAAACAAAGCAGGGGCATATTAAGATCCAATGCATCAGTTCAAATACA
* *
14016 AGGGCTCATTCATGGAAACCCCTTGCACTTTGGGGATTGAATCTTAAGAAGTTAA
66 AAGGCTCATTCATGGAAACCCCTTGCACTTTGGGGACTGAATCTTAAGAAGTTAA
14071 AACCCAATTC
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
145 117 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (145 bp):
ATTCTCAATAAAGTGCACAAACAAAGCAGGGGCATATTAAGATCCAATGCATCAGTTCAAATACA
AAGGCTCATTCATGGAAACCCCTTGCACTTTGGGGACTGAATCTTAAGAAGTTAAGATATTCTTC
GAAGAAAAATAGGAT
Found at i:16467 original size:22 final size:22
Alignment explanation
Indices: 16442--16483 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
16432 CATATTCTCA
16442 TTCGTTTAAGTTCAATTTGCAT
1 TTCGTTTAAGTTCAATTTGCAT
16464 TTCGTTTAAGTTCAATTTGC
1 TTCGTTTAAGTTCAATTTGC
16484 TTTTGCTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (22 bp):
TTCGTTTAAGTTCAATTTGCAT
Found at i:17889 original size:15 final size:15
Alignment explanation
Indices: 17869--17899 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17859 ACAGAGATTG
*
17869 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
17884 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
17899 A
1 A
17900 TTAGAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:22053 original size:10 final size:10
Alignment explanation
Indices: 22009--22054 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
21999 GAAGTTCGTG
22009 TGAAGACTTAT
1 TGAAGAC-TAT
*
22020 TCAAGACTATT
1 TGAAGACTA-T
22031 TGAAGA-T-T
1 TGAAGACTAT
22039 TGAAGACTAT
1 TGAAGACTAT
22049 TGAAGA
1 TGAAGA
22055 ATAATTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
10 10 0.33
11 12 0.40
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (10 bp):
TGAAGACTAT
Done.