Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009955.1 Corchorus capsularis cultivar CVL-1 contig09976, 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: 27162
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:8927 original size:21 final size:21
Alignment explanation
Indices: 8878--8941 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
8868 TCGGTGAGAG
*
8878 TAAAATTGGTTACTGTACATG-
1 TAAAATTTGTTACTGTACA-GA
* *
8899 TTAGATTTGTTACTGTACAGA
1 TAAAATTTGTTACTGTACAGA
*
8920 TAAAATTTGTTGCTGTACAGA
1 TAAAATTTGTTACTGTACAGA
8941 T
1 T
8942 GAGAATATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (21 bp):
TAAAATTTGTTACTGTACAGA
Found at i:9942 original size:27 final size:27
Alignment explanation
Indices: 9904--9957 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9894 TCAAATGTTT
9904 GACAAAATTATTAGTTACGTACTTAAA
1 GACAAAATTATTAGTTACGTACTTAAA
9931 GACAAAATTATTAGTTACGTACTTAAA
1 GACAAAATTATTAGTTACGTACTTAAA
9958 TTCTCAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (27 bp):
GACAAAATTATTAGTTACGTACTTAAA
Found at i:20316 original size:38 final size:37
Alignment explanation
Indices: 20252--20331 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 37
20242 AATTTGCCTT
20252 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
** *
20289 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTTTGTC
20327 TTTGT
1 TTTGT
20332 CTCCGATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 11 0.28
38 28 0.72
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.59
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
Found at i:20927 original size:22 final size:22
Alignment explanation
Indices: 20870--21050 Score: 127
Period size: 22 Copynumber: 8.3 Consensus size: 22
20860 TGTCTCTATG
*
20870 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* * *
20892 TAGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* *
20915 -GGTTATCAAAATTCCATAGTA
1 TGGTTATCAAAATTTCATAGGA
* * * *
20936 TGGTTACCGAAATTTCAAATGA
1 TGGTTATCAAAATTTCATAGGA
** *
20958 AAGTTATCAAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGGA
*
20980 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
21002 TCAGGTAATTAAAATTT-ATA--T
1 T--GGTTATCAAAATTTCATAGGA
** *
21023 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
21045 TGGTTA
1 TGGTTA
21051 ATTATCACAA
Statistics
Matches: 119, Mismatches: 33, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
19 12 0.10
20 3 0.03
21 4 0.03
22 83 0.70
23 6 0.05
24 11 0.09
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:20985 original size:66 final size:66
Alignment explanation
Indices: 20870--20999 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
20860 TGTCTCTATG
* * * * *
20870 TGGTTATCAAAATTTCATAAGATAGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCATAGT
1 TGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCATAGT
20935 A
66 A
* * *
20936 TGGTTACCGAAATTTCA-AATGAAAGTTATCAAAATTTCAT-AGTATGGTTACCAAAATTTCATA
1 TGGTTACCAAAATTTCATAA-GAAAGTTATCAAAATTTCATGAGGA-GGTTACCAAAATTCCATA
20999 G
64 G
21000 GATCAGGTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 5 0.09
66 49 0.91
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (66 bp):
TGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCATAGT
A
Found at i:21132 original size:22 final size:21
Alignment explanation
Indices: 21086--21199 Score: 77
Period size: 22 Copynumber: 5.2 Consensus size: 21
21076 ATCAAAGAGA
* * *
21086 TTATCAAAATGTCATAGCGATG
1 TTAT-AAAATTTCATAGTGAGG
*
21108 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAGTGAGG
*
21130 TTAACAAAATTTCATTAG-GAGG
1 TT-ATAAAATTTCA-TAGTGAGG
* * *
21152 TTACTAATATTTCATGGGGAGG
1 TTA-TAAAATTTCATAGTGAGG
* *
21174 TTATCAAAATTTTATAGTGTGG
1 TTAT-AAAATTTCATAGTGAGG
21196 TTAT
1 TTAT
21200 GAAGGTTATA
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
21 6 0.08
22 60 0.83
23 6 0.08
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:21287 original size:22 final size:23
Alignment explanation
Indices: 21235--21404 Score: 117
Period size: 22 Copynumber: 7.7 Consensus size: 23
21225 TAAGGAATAC
* *
21235 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
21256 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
21277 CGAAATTTCATCGAGATCAGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
* *
21302 CAAAATTT-ATAG-GAAGCTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
21323 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
21345 CAAAATTTCAAAGCG-TGGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
21367 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
*
21389 CAGAATTTCATAGAGA
1 CAAAATTTCATAGAGA
21405 GGTCAACAAA
Statistics
Matches: 118, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
20 10 0.08
21 22 0.19
22 64 0.54
23 6 0.05
24 3 0.03
25 13 0.11
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:21415 original size:44 final size:44
Alignment explanation
Indices: 21323--21444 Score: 102
Period size: 44 Copynumber: 2.8 Consensus size: 44
21313 GGAAGCTTAT
* * * * * *
21323 CAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGTGGTTAT
1 CAAAATTACATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAA
* *
21367 CAAAATTACATAATG-TGATTATCAGAATTTCATAGAGAGGTCAA
1 CAAAATTACATAATGTTG-TTATCAAAATTTCAAAGAGAGGTCAA
** * ** *
21411 CAAAATTTGATAAAGAGGTTATCAAATTTTCAAA
1 CAAAATTACATAATGTTGTTATCAAAATTTCAAA
21445 ATGTTATTAC
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
43 2 0.03
44 58 0.95
45 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (44 bp):
CAAAATTACATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAA
Found at i:21436 original size:22 final size:22
Alignment explanation
Indices: 21298--21442 Score: 89
Period size: 22 Copynumber: 6.6 Consensus size: 22
21288 CGAGATCAGA
* *
21298 TTATCAAAATTT-AT-AGGAAGC
1 TTATCAAAATTTCATAAAG-AGG
** **
21319 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
* *
21341 TTATCAAAATTTCA-AAGCGTGG
1 TTATCAAAATTTCATAA-AGAGG
* * * *
21363 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* *
21385 TTATCAGAATTTCATAGAGAGG
1 TTATCAAAATTTCATAAAGAGG
* * *
21407 TCAACAAAATTTGATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
21429 TTATCAAATTTTCA
1 TTATCAAAATTTCA
21443 AAATGTTATT
Statistics
Matches: 94, Mismatches: 26, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
21 13 0.14
22 78 0.83
23 3 0.03
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:21576 original size:19 final size:20
Alignment explanation
Indices: 21542--21579 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
21532 CTTTTATTAT
21542 GGAGGATATCAAAATTTCAG
1 GGAGGATATCAAAATTTCAG
21562 GGAGGATAT-AAAATTTCA
1 GGAGGATATCAAAATTTCA
21580 TGGTTTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (20 bp):
GGAGGATATCAAAATTTCAG
Found at i:21683 original size:22 final size:22
Alignment explanation
Indices: 21591--21842 Score: 119
Period size: 22 Copynumber: 11.5 Consensus size: 22
21581 GGTTTAGTTT
*
21591 TCAAAATTTTATAA-GAGGGTTA
1 TCAAAATTTCATAAGGA-GGTTA
* * *
21613 TCAAAATTTCAT-AGTATGTAGA
1 TCAAAATTTCATAAGGAGGT-TA
* ** *
21635 TCAAAATATCATTGGGAGATTA
1 TCAAAATTTCATAAGGAGGTTA
* *
21657 ACAAAATTTCATAATGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
** *
21679 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
*
21701 TCAAAATTT--T---TA-GTTA
1 TCAAAATTTCATAAGGAGGTTA
* * *
21717 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATAAGGAGGTTA
* *
21739 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATAAGGAGG-TTA
* *
21762 TCAAAATTTTAT-AGGAAGATTTA
1 TCAAAATTTCATAAGG-AG-GTTA
* *
21785 ACAAAACTTCAT-AGCGAGGTTA
1 TCAAAATTTCATAAG-GAGGTTA
* * *
21807 TCACAATTTCATCATAGTGTGATTA
1 TCAAAATTTCAT-A-AG-GAGGTTA
21832 TCAAAATTTCA
1 TCAAAATTTCA
21843 GAGTGTAATT
Statistics
Matches: 170, Mismatches: 44, Indels: 29
0.70 0.18 0.12
Matches are distributed among these distances:
16 12 0.07
17 1 0.01
18 1 0.01
20 1 0.01
21 4 0.02
22 97 0.57
23 36 0.21
24 1 0.01
25 17 0.10
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAAGGAGGTTA
Found at i:21764 original size:23 final size:23
Alignment explanation
Indices: 21736--21815 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
21726 CATAAGAAAG
21736 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
21759 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* * * *
21782 TTAACAAAACTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
21804 TTATCACAATTT
1 TTATCAAAATTT
21816 CATCATAGTG
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 9 0.20
23 37 0.80
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:21808 original size:45 final size:44
Alignment explanation
Indices: 21713--21818 Score: 113
Period size: 45 Copynumber: 2.4 Consensus size: 44
21703 AAAATTTTTA
* * * * *
21713 GTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAAGAAAGTTAACAAAACTTCATAGCGAG
* * *
21757 GTTTATCAAAATTTTATAGGAAGATTTAACAAAACTTCATAGCGAG
1 G-TTATCAAAATTTCATAAGAA-AGTTAACAAAACTTCATAGCGAG
*
21803 GTTATCACAATTTCAT
1 GTTATCAAAATTTCAT
21819 CATAGTGTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
44 1 0.02
45 30 0.60
46 19 0.38
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (44 bp):
GTTATCAAAATTTCATAAGAAAGTTAACAAAACTTCATAGCGAG
Found at i:21822 original size:25 final size:25
Alignment explanation
Indices: 21793--21842 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21783 TAACAAAACT
* *
21793 TCATAGCGAGGTTATCACAATTTCA
1 TCATAGCGAGATTATCAAAATTTCA
* *
21818 TCATAGTGTGATTATCAAAATTTCA
1 TCATAGCGAGATTATCAAAATTTCA
21843 GAGTGTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (25 bp):
TCATAGCGAGATTATCAAAATTTCA
Found at i:21926 original size:22 final size:23
Alignment explanation
Indices: 21900--21950 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
21890 CGTGGTTATA
*
21900 TATCAATATATCATA-TGGAGGT
1 TATCAACATATCATAGTGGAGGT
* **
21922 TATCAACATCTCATAGTGTTGGT
1 TATCAACATATCATAGTGGAGGT
21945 TATCAA
1 TATCAA
21951 AATTTCATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (23 bp):
TATCAACATATCATAGTGGAGGT
Found at i:22398 original size:46 final size:46
Alignment explanation
Indices: 22306--22401 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
22296 CCGATGGGAG
** *
22306 TGACGTGGCCTACCCTTACCTCTTCAGGAAAATACCACTGTTACCA
1 TGACGTGGCCTACCCTTACCTCTTCAGGAAAATACCACCATCACCA
*
22352 TGACGTGGCTTACCCTTACCTCTTCA-GAATAATACCACCATCACCA
1 TGACGTGGCCTACCCTTACCTCTTCAGGAA-AATACCACCATCACCA
22398 TGAC
1 TGAC
22402 ATACACTTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 3 0.07
46 42 0.93
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.26
Consensus pattern (46 bp):
TGACGTGGCCTACCCTTACCTCTTCAGGAAAATACCACCATCACCA
Found at i:26837 original size:25 final size:25
Alignment explanation
Indices: 26809--26863 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
26799 ATAAATTAAG
26809 GATTTTTTCTTCAAAAAATATCATA
1 GATTTTTTCTTCAAAAAATATCATA
* * *
26834 GATTTTTTTTTGAGAAAATATCATA
1 GATTTTTTCTTCAAAAAATATCATA
*
26859 AATTT
1 GATTT
26864 AATCGCCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (25 bp):
GATTTTTTCTTCAAAAAATATCATA
Done.