Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013423.1 Corchorus olitorius cultivar O-4 contig13456, 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: 31182
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:3934 original size:38 final size:37
Alignment explanation
Indices: 3828--3936 Score: 148
Period size: 36 Copynumber: 2.9 Consensus size: 37
3818 AAGAAGTTGA
*
3828 AAAAAAAAAAACTGGGCCTAAAACAGAAAGAGGT-TG
1 AAAAAAAAAAACTGGGCCTAAAACAGAAAGAGGTCGG
* * *
3864 AAAAACAAAACCAGGGCCTAAAACAGAAAGAGGTCGG
1 AAAAAAAAAAACTGGGCCTAAAACAGAAAGAGGTCGG
* *
3901 AAAAGAAAAAAACTGGACCTAAAACAGAGAGAGGTC
1 AAAA-AAAAAAACTGGGCCTAAAACAGAAAGAGGTC
3937 ATAAAAACTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 31 0.50
37 5 0.08
38 26 0.42
ACGTcount: A:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (37 bp):
AAAAAAAAAAACTGGGCCTAAAACAGAAAGAGGTCGG
Found at i:3950 original size:38 final size:36
Alignment explanation
Indices: 3828--3950 Score: 131
Period size: 38 Copynumber: 3.3 Consensus size: 36
3818 AAGAAGTTGA
*
3828 AAAAAAAAAAACTGGGCCTAAAACAGAAAGAGGT-T
1 AAAAACAAAAACTGGGCCTAAAACAGAAAGAGGTCT
* * *
3863 GAAAAACAAAACCAGGGCCTAAAACAGAAAGAGGTCGG
1 -AAAAACAAAAACTGGGCCTAAAACAGAAAGAGGTC-T
* * *
3901 AAAAGAAAAAAACTGGACCTAAAACAGAGAGAGGTCAT
1 AAAA-ACAAAAACTGGGCCTAAAACAGAAAGAGGTC-T
3939 AAAAACTAAAAA
1 AAAAAC-AAAAA
3951 GGAGGGGTTC
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
36 31 0.44
37 5 0.07
38 35 0.49
ACGTcount: A:0.57, C:0.14, G:0.20, T:0.09
Consensus pattern (36 bp):
AAAAACAAAAACTGGGCCTAAAACAGAAAGAGGTCT
Found at i:5045 original size:57 final size:58
Alignment explanation
Indices: 4768--5275 Score: 682
Period size: 59 Copynumber: 8.8 Consensus size: 58
4758 TCAGAATTCC
* *
4768 CTTATCTCGTTTTAAAATCCTGTTCGAGGTCTCTGTTGGAGAGTTTTCAATTCAAAAT
1 CTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* *
4826 TTTATCTTGTTTTTAAAAATCCTGTTCGAGGTCTCTGTTATAGAGTTTTCAATTCAAAAT
1 CTTATCTTG-TTTT-AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
*
4886 CTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGGGTTTTCAATTCAAAAT
1 CTTATCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* * * **
4945 CTAACCTTGCTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAAAACAAAAT
1 CTTATCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* * *
5004 CTCATCTCG-TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTTAAAAT
1 CTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* * * *
5061 CTTACCCTGTTTT--AATCCTGTTAGAGGTCTCTGTTACAGAGTTTTCAATTCAAAAT
1 CTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* ** *
5117 CTCATCTTGTCCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTTAAAAT
1 CTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* * ** *
5175 CTTACCCTGTTTT-TGATCCTGTTCGAGGTCTTTGTTAGAGAGTTTTCAATTCAAAAT
1 CTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
* * * *
5232 TTTATCTTGTTTTAAACTCCTGGTCGAGGTCTCTGTTTGAGAGT
1 CTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
5276 CTATATTTCA
Statistics
Matches: 390, Mismatches: 54, Indels: 12
0.86 0.12 0.03
Matches are distributed among these distances:
56 48 0.12
57 99 0.25
58 82 0.21
59 105 0.27
60 56 0.14
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (58 bp):
CTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
Found at i:5196 original size:171 final size:172
Alignment explanation
Indices: 4780--5268 Score: 667
Period size: 171 Copynumber: 2.8 Consensus size: 172
4770 TATCTCGTTT
* * *
4780 TAAAATCCTGTTCGAGGTCTCTGTTGGAGAGTTTTCAATTCAAAATTTTATCTTGTTTTTAAAAA
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA-CCTGTTTTT---AA
*
4845 TCCTGTTCGAGGTCTCTGTTATAGAGTTTTCAATTCAAAATCTTATCTTGTTTTTAAAATCCTGT
62 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTG-TTTT-AAATCCTGT
* * *
4910 TCGAGGTCTCTGTTAGAGGGTTTTCAATTCAAAATCTAACCTTGCTTC
125 TCGAGGTCTCTGTTACAGAGTTTTCAATTCAAAATCTAACCTTGCTCC
** * * **
4958 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAAAACAAAATCTCATCTCGTTTAAAATCC
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCT-GTTTTTAATCC
* * * *
5023 TGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTTAAAATCTTACCCTGTTTT-AATCCTGTTAGAG
65 TGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAATCCTGTTCGAG
* *
5087 GTCTCTGTTACAGAGTTTTCAATTCAAAATCTCATCTTG-TCC
130 GTCTCTGTTACAGAGTTTTCAATTCAAAATCTAACCTTGCTCC
* *
5129 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTTAAAATCTTACCCTGTTTTTGATCC
1 TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA-CCTGTTTTTAATCC
* * *
5194 TGTTCGAGGTCTTTGTTAGAGAGTTTTCAATTCAAAATTTTATCTTGTTTTAAACTCCTGGTCGA
65 TGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAA-TCCTGTTCGA
5259 GGTCTCTGTT
129 GGTCTCTGTT
5269 TGAGAGTCTA
Statistics
Matches: 273, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
171 102 0.37
172 51 0.19
173 18 0.07
174 4 0.01
175 48 0.18
177 1 0.00
178 49 0.18
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (172 bp):
TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTGTTTTTAATCCT
GTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAATCCTGTTCGAGG
TCTCTGTTACAGAGTTTTCAATTCAAAATCTAACCTTGCTCC
Found at i:5553 original size:29 final size:29
Alignment explanation
Indices: 5521--5772 Score: 235
Period size: 29 Copynumber: 8.7 Consensus size: 29
5511 CGCATGCTCA
* ** *
5521 GGGGAATTTTGGTCATTTTTGCATATATG
1 GGGGCATTTTGGTCATTTTCACATATCTG
*
5550 GGGGCATTTTGGTCATTTCCACATATCTG
1 GGGGCATTTTGGTCATTTTCACATATCTG
* * *
5579 GGGGCAGTTCTGGTCATTTTCGCATATTCGG
1 GGGGCA-TTTTGGTCATTTTCACATA-TCTG
*
5610 GGGGCATTTTGGTCATTTCCACATATCTG
1 GGGGCATTTTGGTCATTTTCACATATCTG
*
5639 GGGGCATTCTGGTCATTTTCACATAT-TCG
1 GGGGCATTTTGGTCATTTTCACATATCT-G
** * *
5668 GGGGCATTTTGGTCATTTTTGCACATCTA
1 GGGGCATTTTGGTCATTTTCACATATCTG
* * **
5697 GGAGCATTTTGGTCATTCTCGA-ATATCCA
1 GGGGCATTTTGGTCATTTTC-ACATATCTG
*
5726 GGGGCATTTCGGTCATCTTTACACAT-TCT-
1 GGGGCATTTTGGTCAT-TTT-CACATATCTG
*
5755 GGGGCAGTTTGGT-ATTTT
1 GGGGCATTTTGGTCATTTT
5773 TTGCATACTC
Statistics
Matches: 183, Mismatches: 32, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
27 3 0.02
28 3 0.02
29 127 0.69
30 38 0.21
31 12 0.07
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTCACATATCTG
Found at i:5649 original size:59 final size:58
Alignment explanation
Indices: 5521--5758 Score: 264
Period size: 58 Copynumber: 4.1 Consensus size: 58
5511 CGCATGCTCA
* * *
5521 GGGGAATTTTGGTCATTTTTGCATATAT-GGGGGCATTTTGGTCATTTCCACATATCTG
1 GGGGCATTCTGGTCATTTTCGCATAT-TCGGGGGCATTTTGGTCATTTCCACATATCTG
5579 GGGGCAGTTCTGGTCATTTTCGCATATTCGGGGGGCATTTTGGTCATTTCCACATATCTG
1 GGGGCA-TTCTGGTCATTTTCGCATATTC-GGGGGCATTTTGGTCATTTCCACATATCTG
* *** * *
5639 GGGGCATTCTGGTCATTTTCACATATTCGGGGGCATTTTGGTCATTTTTGCACATCTA
1 GGGGCATTCTGGTCATTTTCGCATATTCGGGGGCATTTTGGTCATTTCCACATATCTG
* * * * * * * *
5697 GGAGCATTTTGGTCATTCTCGAATATCCAGGGGCATTTCGGTCATCTTTACACAT-TCTG
1 GGGGCATTCTGGTCATTTTCGCATATTCGGGGGCATTTTGGTCA--TTTCCACATATCTG
5756 GGG
1 GGG
5759 CAGTTTGGTA
Statistics
Matches: 152, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
58 67 0.44
59 44 0.29
60 41 0.27
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (58 bp):
GGGGCATTCTGGTCATTTTCGCATATTCGGGGGCATTTTGGTCATTTCCACATATCTG
Found at i:16488 original size:13 final size:12
Alignment explanation
Indices: 16459--16490 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
16449 ATTTCATTAA
16459 GAAAAATGTTTT
1 GAAAAATGTTTT
16471 GAAAAATGTTTT
1 GAAAAATGTTTT
16483 GAAAAATG
1 GAAAAATG
16491 CTCTCATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (12 bp):
GAAAAATGTTTT
Found at i:21884 original size:248 final size:248
Alignment explanation
Indices: 21446--21926 Score: 881
Period size: 248 Copynumber: 1.9 Consensus size: 248
21436 ATAGTAAACT
* * *
21446 ACTCTTCATAACTGGGTCTTCCTCTAACTGGATCAGATCTTGGAGATCTGCTTTGATTGCAATTG
1 ACTCTTCATAAATGGGCCTTCCTCTAACAGGATCAGATCTTGGAGATCTGCTTTGATTGCAATTG
21511 AATTTGAAAAGAAAATAACAATTTGATTTGTTATTTATAGGAGAGAAACACGTGTACAGTGTTTT
66 AATTTGAAAAGAAAATAACAATTTGATTTGTTATTTATAGGAGAGAAACACGTGTACAGTGTTTT
*
21576 GGTGTCCGAAGACAAGATTGAAACAAGAGAAAAACACTAAAAGAGTGTTTAAATGTCCTGAGACA
131 GGTGTCCGAAGACAAGATTGAAACAAGAGAAAAACACTAAAAAAGTGTTTAAATGTCCTGAGACA
21641 AGATCTAAACAAGGAAAATTTGATGAACGAGTAAGAACATGTGATGAACAAGG
196 AGATCTAAACAAGGAAAATTTGATGAACGAGTAAGAACATGTGATGAACAAGG
21694 ACTCTTCATAAATGGGCCTTCCTCTAACAGGATCAGATCTTGGAGATCTGCTTTGATTGCAATTG
1 ACTCTTCATAAATGGGCCTTCCTCTAACAGGATCAGATCTTGGAGATCTGCTTTGATTGCAATTG
*
21759 AATTTGAAAAGAAAATAACAATTTTATTTGTTATTTATAGGAGAGAAACACGTGTACAGTGTTTT
66 AATTTGAAAAGAAAATAACAATTTGATTTGTTATTTATAGGAGAGAAACACGTGTACAGTGTTTT
* * *
21824 GGTGTCCGGAGATAAGATTGAAACAAGAGAAAAACACTAAAAAAGTGTTTGAATGTCCTGAGACA
131 GGTGTCCGAAGACAAGATTGAAACAAGAGAAAAACACTAAAAAAGTGTTTAAATGTCCTGAGACA
*
21889 AGATTTAAACAAGGAAAATTTGATGAACGAGTAAGAAC
196 AGATCTAAACAAGGAAAATTTGATGAACGAGTAAGAAC
21927 TCGGGATGAA
Statistics
Matches: 224, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
248 224 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (248 bp):
ACTCTTCATAAATGGGCCTTCCTCTAACAGGATCAGATCTTGGAGATCTGCTTTGATTGCAATTG
AATTTGAAAAGAAAATAACAATTTGATTTGTTATTTATAGGAGAGAAACACGTGTACAGTGTTTT
GGTGTCCGAAGACAAGATTGAAACAAGAGAAAAACACTAAAAAAGTGTTTAAATGTCCTGAGACA
AGATCTAAACAAGGAAAATTTGATGAACGAGTAAGAACATGTGATGAACAAGG
Found at i:23667 original size:45 final size:45
Alignment explanation
Indices: 23599--23727 Score: 240
Period size: 45 Copynumber: 2.8 Consensus size: 45
23589 TAAATTCTAC
*
23599 TCCATCTCTAGGTTAATTCATCAAAATAAAGCTAATATTCTACTCA
1 TCCATCTCTA-GATAATTCATCAAAATAAAGCTAATATTCTACTCA
23645 TCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTACTCA
1 TCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTACTCA
23690 TCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 TCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
23728 AATTGTTGCT
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
45 72 0.88
46 10 0.12
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (45 bp):
TCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTACTCA
Found at i:24960 original size:27 final size:27
Alignment explanation
Indices: 24922--24976 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
24912 TACCATTGTT
24922 GGTTTTATATTGACAGTTTCTTTCTCA
1 GGTTTTATATTGACAGTTTCTTTCTCA
24949 GGTTTTATATTGACAGTTTCTTTCTCA
1 GGTTTTATATTGACAGTTTCTTTCTCA
24976 G
1 G
24977 CAATTAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (27 bp):
GGTTTTATATTGACAGTTTCTTTCTCA
Found at i:30603 original size:21 final size:20
Alignment explanation
Indices: 30562--30610 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
30552 GATTATGTAA
**
30562 ATGCAAAATGTGAAATTAAT
1 ATGCAAAATGTGAAACGAAT
*
30582 ATGCGAAAATGTGATACGAAT
1 ATGC-AAAATGTGAAACGAAT
30603 ATGCAAAA
1 ATGCAAAA
30611 GAACATAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.24
Consensus pattern (20 bp):
ATGCAAAATGTGAAACGAAT
Found at i:30773 original size:27 final size:28
Alignment explanation
Indices: 30707--30779 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
30697 GATGAAGTAG
30707 AAATGACCAAAATGCCCCTGGACATGCA
1 AAATGACCAAAATGCCCCTGGACATGCA
* * *
30735 AAATGACTAAAATACCCCT-GA-ATGCGC
1 AAATGACCAAAATGCCCCTGGACATGC-A
30762 AAATGACCAAAATGCCCC
1 AAATGACCAAAATGCCCC
30780 ATAGATGACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.10
27 18 0.46
28 17 0.44
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGCA
Found at i:31084 original size:52 final size:51
Alignment explanation
Indices: 31020--31182 Score: 213
Period size: 52 Copynumber: 3.2 Consensus size: 51
31010 CGATCAATTT
* * *
31020 CTTTGAATTGTCTTCCACTCTAATATATTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAAT-TAATATATTAAAAGGACCGTCTTCCGCTTATC
* * * *
31072 CTTTGAACTGTCTACGAATTCA-ATATTGAAAGGACCGCCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTAATATATTAAAAGGACCGTCTTCCGCTTATC
*
31122 CTTTGAACTGTCTACCAATTCAATCT-TATAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATT-AATATAT-TAAAAGGACCGTCTTCCGCTTATC
31174 CTTTGAACT
1 CTTTGAACT
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
50 45 0.47
51 4 0.04
52 47 0.49
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (51 bp):
CTTTGAACTGTCTACCAATTAATATATTAAAAGGACCGTCTTCCGCTTATC
Found at i:31114 original size:50 final size:50
Alignment explanation
Indices: 31044--31182 Score: 224
Period size: 50 Copynumber: 2.7 Consensus size: 50
31034 CCACTCTAAT
*
31044 ATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACGAATTCA
1 ATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCA
* *
31094 ATATTGAAAGGACCGCCTTCCGCTTATCCTTTGAACTGTCTACCAATTCA
1 ATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCA
*
31144 ATCTTATAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
1 AT-AT-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 49 0.60
51 1 0.01
52 31 0.38
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (50 bp):
ATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCA
Done.