Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021928.1 Corchorus olitorius cultivar O-4 contig21961, 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: 21271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3092 original size:7 final size:7
Alignment explanation
Indices: 3080--3120 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
3070 ATTTACGTTA
3080 TATATAC
1 TATATAC
3087 TATATAC
1 TATATAC
3094 TATATAC
1 TATATAC
3101 TATATAC
1 TATATAC
3108 TA-ATAC
1 TATATAC
3114 TAATATA
1 T-ATATA
3121 TACTAAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 5 0.16
7 24 0.75
8 3 0.09
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (7 bp):
TATATAC
Found at i:3126 original size:16 final size:15
Alignment explanation
Indices: 3081--3126 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
3071 TTTACGTTAT
*
3081 ATATACTATATACT-
1 ATATAATATATACTA
*
3095 ATATACTATATACTA
1 ATATAATATATACTA
3110 ATACTAATATATACTA
1 ATA-TAATATATACTA
3126 A
1 A
3127 ATGTTATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 14 0.48
15 3 0.10
16 12 0.41
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATAATATATACTA
Found at i:4237 original size:110 final size:111
Alignment explanation
Indices: 4040--4259 Score: 334
Period size: 110 Copynumber: 2.0 Consensus size: 111
4030 GAATTTGCTA
* * * *
4040 ACCACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAAAACTCTATAACTAAAATGATTT
1 ACCACCTACTCACATATATGATAAGAACCAAAAGAAAAAAAAAAACTCTAAAACTAAAATAATTT
** * * *
4105 GCTATGCACATATCAAGAATGCTCGACTCGCCAGCGCGAGCCGATG
66 GCTAACCACAAATCAAGAATGCTCAACGCGCCAGCGCGAGCCGATG
*
4151 ACCACCTACTCACATATATGATAAGAACCAAAAG-AAAAAAAAAACTCTAAAATTAAAATAATTT
1 ACCACCTACTCACATATATGATAAGAACCAAAAGAAAAAAAAAAACTCTAAAACTAAAATAATTT
*
4215 GCTAACCACAAATCAAGAATGCTCAACGCGCCAGCGTGAGCCGAT
66 GCTAACCACAAATCAAGAATGCTCAACGCGCCAGCGCGAGCCGAT
4260 CAACTTGTAT
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
110 66 0.67
111 32 0.33
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (111 bp):
ACCACCTACTCACATATATGATAAGAACCAAAAGAAAAAAAAAAACTCTAAAACTAAAATAATTT
GCTAACCACAAATCAAGAATGCTCAACGCGCCAGCGCGAGCCGATG
Found at i:4605 original size:178 final size:174
Alignment explanation
Indices: 4291--4637 Score: 511
Period size: 178 Copynumber: 2.0 Consensus size: 174
4281 ATACCCTCTG
* *
4291 GAAATTACTAAAGGTTCCCATCAACTTTTAATGTGGAGAACCTTTTCACCCCGTTTTGGTCTTTT
1 GAAATTACTAAAGGTCCCCATCAACTTTTAATGTGGAGAACCTTATCACCCCGTTTTGGTCTTTT
* * *
4356 CTCATGTGGTTGATTACTGAAATATCCCCTCAGCCTAACATGTTTTCTTTAGATCCATTGTCTTT
66 CTCACGTGGTTGATTACTGAAATATCCCCTAAGCCTAACATGTTTTCTTCAGATCCATTGTCTTT
*
4421 GTGTGTAATTTGG-CTATTGAGTTCTAATAAATGTTGTTCCCACT
131 GTGTGTAATTTGGTC-ATTGAGTTCTAATAAATGATGTTCCCACT
* *
4465 GAAATTTACTAAAGGATCCCCCATCAACTTTTAATGTGGAGTGACCTTATCGCCCCGTTTTGGTC
1 GAAA-TTACTAAAGG-T-CCCCATCAACTTTTAATGTGGAG-AACCTTATCACCCCGTTTTGGTC
*
4530 TTTTCTCACGTGGTTGATTACTGAAATA-CCCCTTAAGCCTAACATGTTTTCTTCAGATCCGTTG
62 TTTTCTCACGTGGTTGATTACTGAAATATCCCC-TAAGCCTAACATGTTTTCTTCAGATCCATT-
* *
4594 GT-TTTGTGTGTAATTTGGTCATTGAGTTCTGATAAGTGATGTTC
125 GTCTTTGTGTGTAATTTGGTCATTGAGTTCTAATAAATGATGTTC
4638 TCACCATAAT
Statistics
Matches: 155, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
174 4 0.03
175 10 0.06
176 1 0.01
177 26 0.17
178 111 0.72
179 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (174 bp):
GAAATTACTAAAGGTCCCCATCAACTTTTAATGTGGAGAACCTTATCACCCCGTTTTGGTCTTTT
CTCACGTGGTTGATTACTGAAATATCCCCTAAGCCTAACATGTTTTCTTCAGATCCATTGTCTTT
GTGTGTAATTTGGTCATTGAGTTCTAATAAATGATGTTCCCACT
Found at i:5238 original size:18 final size:19
Alignment explanation
Indices: 5196--5238 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5186 TATATAAATT
*
5196 CTTTTTACATGAACTGATT
1 CTTTTTACATGAACTGATG
* *
5215 CTTTTTACATGGATTGATG
1 CTTTTTACATGAACTGATG
5234 CTTTT
1 CTTTT
5239 GCTTTTCCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (19 bp):
CTTTTTACATGAACTGATG
Found at i:10272 original size:16 final size:17
Alignment explanation
Indices: 10239--10272 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10229 AAGAAGATTT
*
10239 AAACATATAGGAAGATA
1 AAACATATAGGAACATA
10256 AAACATATAGG-ACATA
1 AAACATATAGGAACATA
10272 A
1 A
10273 GGAGTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (17 bp):
AAACATATAGGAACATA
Found at i:11689 original size:33 final size:33
Alignment explanation
Indices: 11649--11717 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
11639 TTTAATAATA
* *
11649 AAAGAAAGGTAGAAGGAGGAGATTATGCATGAT
1 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
11682 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
1 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
11715 AAA
1 AAA
11718 TAAACTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.04, G:0.30, T:0.16
Consensus pattern (33 bp):
AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
Found at i:12360 original size:128 final size:127
Alignment explanation
Indices: 12098--12363 Score: 435
Period size: 128 Copynumber: 2.1 Consensus size: 127
12088 ATTCATAACA
* * *
12098 AGAAATTAATTGTAGAAGTGAATCCATATATATAGTCATATATAAAGTATAACGGAAATTACATT
1 AGAAATTAATTATAGAAGTGAATCCATATATATAGTCATATATAAAGTATAAAGGAAATTACAAT
* *
12163 AATTATCGTCATTTAGTATCTTTGATATTTGATATTAAGATAAAAAACAAACCAATAATTAT
66 AATTATCGTCATTTAGTATCATTGATATTTAATATTAAGATAAAAAACAAACCAATAATTAT
12225 AGAAATTAATTATAGAAGTGAATCCATATATATAGTCATATATAAAGTATAAAGGAAATTTACAA
1 AGAAATTAATTATAGAAGTGAATCCATATATATAGTCATATATAAAGTATAAAGGAAA-TTACAA
* * *
12290 TAATTATTGTCATTTATTATCATTGATATTTAATATTAAGATAAAAAACAAACCAATAGTTAT
65 TAATTATCGTCATTTAGTATCATTGATATTTAATATTAAGATAAAAAACAAACCAATAATTAT
12353 A-AGAATTAATT
1 AGA-AATTAATT
12364 TGGCTCAATC
Statistics
Matches: 129, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
127 57 0.44
128 72 0.56
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.36
Consensus pattern (127 bp):
AGAAATTAATTATAGAAGTGAATCCATATATATAGTCATATATAAAGTATAAAGGAAATTACAAT
AATTATCGTCATTTAGTATCATTGATATTTAATATTAAGATAAAAAACAAACCAATAATTAT
Found at i:13869 original size:11 final size:11
Alignment explanation
Indices: 13855--13892 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13845 ATTCATAACA
13855 AATTTATAATT
1 AATTTATAATT
13866 AATTTATAATT
1 AATTTATAATT
13877 -ATTTGATAATT
1 AATTT-ATAATT
*
13888 TATTT
1 AATTT
13893 TATGTAGGAA
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:19312 original size:21 final size:22
Alignment explanation
Indices: 19275--19316 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
19265 AATAATGGGT
19275 ATTAAACTAATTTAGGGTTTAG
1 ATTAAACTAATTTAGGGTTTAG
19297 ATTAAACTAA-TTAGGGTTTA
1 ATTAAACTAATTTAGGGTTTA
19317 TGTAACCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (22 bp):
ATTAAACTAATTTAGGGTTTAG
Found at i:20664 original size:18 final size:18
Alignment explanation
Indices: 20641--20675 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20631 ACAAAAACTG
20641 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
20659 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
20676 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:20715 original size:18 final size:18
Alignment explanation
Indices: 20692--20729 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
20682 AATTCCCTAT
20692 CAAATGAACAAAAACGAA
1 CAAATGAACAAAAACGAA
20710 CAAATGAACAAAAACGAA
1 CAAATGAACAAAAACGAA
20728 CA
1 CA
20730 GAAAAACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.18, G:0.11, T:0.05
Consensus pattern (18 bp):
CAAATGAACAAAAACGAA
Found at i:20737 original size:18 final size:18
Alignment explanation
Indices: 20692--20738 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
20682 AATTCCCTAT
*
20692 CAAATGAACAAAAACGAA
1 CAAATAAACAAAAACGAA
*
20710 CAAATGAACAAAAACGAA
1 CAAATAAACAAAAACGAA
20728 CAGAA-AAACAA
1 CA-AATAAACAA
20739 GAAATGCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.68, C:0.17, G:0.11, T:0.04
Consensus pattern (18 bp):
CAAATAAACAAAAACGAA
Done.