Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024878.1 Corchorus olitorius cultivar O-4 contig24911, 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: 44662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4191 original size:54 final size:52
Alignment explanation
Indices: 4133--4239 Score: 178
Period size: 54 Copynumber: 2.0 Consensus size: 52
4123 AACCAAGCAA
*
4133 ATCCTAAATATTTGAATCTTAATAAAAAAGATTGAGCTTTCACCAACAAAATAT
1 ATCCTAAATATTTGAATCTTAAT-AAAAAGATTGAACTTTCACCAAC-AAATAT
*
4187 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACTAACAAATAT
1 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACCAACAAATAT
4239 A
1 A
4240 CTATTGTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 7 0.14
53 21 0.41
54 23 0.45
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (52 bp):
ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACCAACAAATAT
Found at i:6091 original size:31 final size:31
Alignment explanation
Indices: 6054--6191 Score: 159
Period size: 31 Copynumber: 4.5 Consensus size: 31
6044 ACGGTGTCTG
*
6054 ACGTGGCATGCCACGTATACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * *
6085 ATGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
** * *
6116 ACGTATCACGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * * **
6147 ATGTGGCATACCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
6178 ACGTGGCATGCCAC
1 ACGTGGCATGCCAC
6192 ATGCACAAAA
Statistics
Matches: 88, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:17703 original size:11 final size:11
Alignment explanation
Indices: 17689--17717 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
17679 TTATATTTCC
17689 TTTTCCTTTTT
1 TTTTCCTTTTT
17700 TTTT-CTTTTT
1 TTTTCCTTTTT
17710 TTTTCCTT
1 TTTTCCTT
17718 CTCTTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCCTTTTT
Found at i:17722 original size:16 final size:15
Alignment explanation
Indices: 17701--17746 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
17691 TTCCTTTTTT
17701 TTTCTTTTTTTTTCC
1 TTTCTTTTTTTTTCC
* *
17716 TTCTCTTCTCTTTTCC
1 TT-TCTTTTTTTTTCC
17732 TTTCTTTTTTATTTC
1 TTTCTTTTTT-TTTC
17747 AATTAGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTTTTTTTTCC
Found at i:17727 original size:21 final size:21
Alignment explanation
Indices: 17689--17729 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17679 TTATATTTCC
* * *
17689 TTTTCCTTTTTTTTTCTTTTT
1 TTTTCCTTCTCTTCTCTTTTT
17710 TTTTCCTTCTCTTCTCTTTT
1 TTTTCCTTCTCTTCTCTTTT
17730 CCTTTCTTTT
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:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCCTTCTCTTCTCTTTTT
Found at i:17735 original size:21 final size:21
Alignment explanation
Indices: 17684--17735 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
17674 TTCTTTTATA
* * *
17684 TTTCCTTTTCCTTTTTTTTTCT
1 TTTCC-TTTCCTTCTCTTCTCT
**
17706 TTTTTTTTCCTTCTCTTCTCT
1 TTTCCTTTCCTTCTCTTCTCT
17727 TTTCCTTTC
1 TTTCCTTTC
17736 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTCCTTTCCTTCTCTTCTCT
Found at i:18816 original size:21 final size:20
Alignment explanation
Indices: 18788--18828 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
18778 GGGTGAGTGT
* *
18788 GAGTGAGAGTGAGACTGAGA
1 GAGTGAGAGAGAGACAGAGA
18808 GAGTAGAGAGAGAGACAGAGA
1 GAGT-GAGAGAGAGACAGAGA
18829 ATTCAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.05, G:0.44, T:0.10
Consensus pattern (20 bp):
GAGTGAGAGAGAGACAGAGA
Found at i:21528 original size:18 final size:18
Alignment explanation
Indices: 21505--21583 Score: 122
Period size: 18 Copynumber: 4.4 Consensus size: 18
21495 GGAACAGAAT
*
21505 CTGTGTTCGGTGCTGGAA
1 CTGTGTTCGGTGCTGGGA
*
21523 CTGTGTTCGGTGCTGGGG
1 CTGTGTTCGGTGCTGGGA
21541 CTGTGTTCGGTGCTGGGA
1 CTGTGTTCGGTGCTGGGA
* *
21559 TTGTGTTCAGTGCTGGGA
1 CTGTGTTCGGTGCTGGGA
21577 CTGTGTT
1 CTGTGTT
21584 AACAGGTTGA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.06, C:0.15, G:0.42, T:0.37
Consensus pattern (18 bp):
CTGTGTTCGGTGCTGGGA
Found at i:27315 original size:2 final size:2
Alignment explanation
Indices: 27308--27351 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
27298 TAATATTTAG
*
27308 TA TA TA TA TT TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27351 T
1 T
27352 TTCAACCCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28827 original size:21 final size:21
Alignment explanation
Indices: 28803--28846 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
28793 CAGATTAATC
* *
28803 ATGTTCAATATGATAATTCTT
1 ATGTCCAATATGATAATCCTT
28824 ATGTCCAATATGATAATCCTT
1 ATGTCCAATATGATAATCCTT
28845 AT
1 AT
28847 TTAGAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (21 bp):
ATGTCCAATATGATAATCCTT
Found at i:32569 original size:21 final size:19
Alignment explanation
Indices: 32544--32597 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
32534 GCTGCTCTAA
32544 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
32565 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
32584 TAATCTCATCTGTA
1 TAATCTCATCTGTA
32598 TAGTTGCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:35655 original size:63 final size:64
Alignment explanation
Indices: 35571--35725 Score: 169
Period size: 65 Copynumber: 2.5 Consensus size: 64
35561 CCTTCCCTCT
* * *
35571 AGAGATCCTCCTCA-AAGTACCTGC-AGCGGCGGAAGCCG-TAGCCAGTGATGAAGACCTCCTGC
1 AGAGATCCTCCTCAGAA-TACCTGCAAACAGC-GAAGCAGATAGCCAGTGATGAAGACCTCCTGC
35633 G
64 G
* ** *
35634 AGAGATCCTCCTCAGAATACCTGCCAAACATCTCATCAGATAGCCAGTGATGAAGACCTCCTGCG
1 AGAGATCCTCCTCAGAATACCTG-CAAACAGCGAAGCAGATAGCCAGTGATGAAGACCTCCTGCG
35699 AGAGA---TCCTCAGAATACCTGCCAAACA
1 AGAGATCCTCCTCAGAATACCTG-CAAACA
35726 TCTCATCAGA
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
62 22 0.27
63 20 0.25
64 6 0.07
65 33 0.41
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (64 bp):
AGAGATCCTCCTCAGAATACCTGCAAACAGCGAAGCAGATAGCCAGTGATGAAGACCTCCTGCG
Found at i:35694 original size:65 final size:62
Alignment explanation
Indices: 35609--35736 Score: 229
Period size: 62 Copynumber: 2.0 Consensus size: 62
35599 GCGGAAGCCG
35609 TAGCCAGTGATGAAGACCTCCTGCGAGAGATCCTCCTCAGAATACCTGCCAAACATCTCATCAGA
1 TAGCCAGTGATGAAGACCTCCTGCGAGAGA---TCCTCAGAATACCTGCCAAACATCTCATCAGA
35674 TAGCCAGTGATGAAGACCTCCTGCGAGAGATCCTCAGAATACCTGCCAAACATCTCATCAGA
1 TAGCCAGTGATGAAGACCTCCTGCGAGAGATCCTCAGAATACCTGCCAAACATCTCATCAGA
35736 T
1 T
35737 CAAAATGCGT
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
62 33 0.52
65 30 0.48
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (62 bp):
TAGCCAGTGATGAAGACCTCCTGCGAGAGATCCTCAGAATACCTGCCAAACATCTCATCAGA
Found at i:35797 original size:19 final size:19
Alignment explanation
Indices: 35773--35811 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
35763 TCTCTAATCT
35773 CCAGTTCCGAATTCTGCCG
1 CCAGTTCCGAATTCTGCCG
35792 CCAGTTCCGAATTCTGCCG
1 CCAGTTCCGAATTCTGCCG
35811 C
1 C
35812 TCCCACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.38, G:0.21, T:0.26
Consensus pattern (19 bp):
CCAGTTCCGAATTCTGCCG
Found at i:39942 original size:20 final size:20
Alignment explanation
Indices: 39917--39968 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
39907 ATTTACCTAG
*
39917 AGGCAGGCATCAGCATTGAT
1 AGGCAGCCATCAGCATTGAT
39937 AGGCAGCCATCAGCATTGAT
1 AGGCAGCCATCAGCATTGAT
39957 AGGCAGCCATCA
1 AGGCAGCCATCA
39969 TATCAGCCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (20 bp):
AGGCAGCCATCAGCATTGAT
Found at i:43269 original size:21 final size:21
Alignment explanation
Indices: 43228--43270 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
43218 AGATTGAGTG
*
43228 ATATAATTTAACTAAATCTAA
1 ATATAATTTAAATAAATCTAA
*
43249 ATATGATTTAAATCAAA-CTAA
1 ATATAATTTAAAT-AAATCTAA
43270 A
1 A
43271 ATTAAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATAATTTAAATAAATCTAA
Found at i:43746 original size:8 final size:8
Alignment explanation
Indices: 43733--43757 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43723 ACTATTATTG
43733 TTTGTTTA
1 TTTGTTTA
43741 TTTGTTTA
1 TTTGTTTA
43749 TTTGTTTA
1 TTTGTTTA
43757 T
1 T
43758 ATATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (8 bp):
TTTGTTTA
Done.