Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010448.1 Corchorus capsularis cultivar CVL-1 contig10469, 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: 37014
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5547 original size:22 final size:22
Alignment explanation
Indices: 5522--6149 Score: 207
Period size: 22 Copynumber: 29.0 Consensus size: 22
5512 ATAATCCCAT
5522 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** *** **
5544 TATGAAATTTAAATAATGATAT
1 TATGAAATTTTGATAACCTTCC
* * **
5566 TATGGAATTTTGAAAACCTTTT
1 TATGAAATTTTGATAACCTTCC
*
5588 TAT-AATTATTTT--TAACCTTCT
1 TATGAA--ATTTTGATAACCTTCC
* * *
5609 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
5631 TAAGGAATTTTGA-AGACC-TCAG
1 TATGAAATTTTGATA-ACCTTC-C
5653 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
5675 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
5698 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * * *
5719 ATATGATATATTAATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
5742 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
5763 ATATG-AATTGTT-AGTAATCATAC
1 -TATGAAATT-TTGA-TAACCTTCC
* * * *
5786 TCTGAAATTTTTATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
5808 TATGAAATTTTGATAACC-TCGA
1 TATGAAATTTTGATAACCTTC-C
*
5830 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
5853 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
5876 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
5898 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* * *
5915 TA-CAAATTTTAATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
5936 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
5958 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
*** * *
5980 TATGAAATTTTGATCTGCATAC
1 TATGAAATTTTGATAACCTTCC
* * *
6002 TATGGAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
6024 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
6046 TATGAAATTTTGATATCCTTCC
1 TATGAAATTTTGATAACCTTCC
*
6068 --TGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
6087 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * * *
6111 --T--AA-TTTGGTAATCATAC
1 TATGAAATTTTGATAACCTTCC
6128 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
6150 CAGAAATACC
Statistics
Matches: 439, Mismatches: 124, Indels: 86
0.68 0.19 0.13
Matches are distributed among these distances:
16 10 0.02
17 11 0.03
18 2 0.00
19 4 0.01
20 22 0.05
21 28 0.06
22 273 0.62
23 84 0.19
24 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:5864 original size:23 final size:23
Alignment explanation
Indices: 5834--5913 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
5824 CCTCGATATG
5834 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
5857 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
* * *
5880 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
5902 AAATCTTGATAA
1 AAATTTTGATAA
5914 CTACAAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:5865 original size:45 final size:44
Alignment explanation
Indices: 5807--5914 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 44
5797 TATAATCACA
* *
5807 CTATGAAATTTTGATAACCTCGATATGAAATTTTGATAAATCTTC
1 CTATGAAATTTTGATAACCTCCATATAAAATTTTGATAAAT-TTC
* * *
5852 CTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTC
1 CTATGAAATTTTGAT-AACCTCCATATAAAATTTTGATAAATTTC
* *
5897 TTATGAAATCTTGATAAC
1 CTATGAAATTTTGATAAC
5915 TACAAATTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.06
45 29 0.54
46 22 0.41
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCTCCATATAAAATTTTGATAAATTTC
Found at i:6238 original size:22 final size:22
Alignment explanation
Indices: 6188--6331 Score: 83
Period size: 22 Copynumber: 6.6 Consensus size: 22
6178 TCACATTTTG
* *
6188 AAAA-TTTGATAACCTCTTTCT
1 AAAATTTTGATAACCACTTTAT
* *
6209 GAAATTTTGATAACCGCTTTAT
1 AAAATTTTGATAACCACTTTAT
* * * *
6231 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCACTTTAT
* * *
6253 AAAATTCTGATAATCACATTAT
1 AAAATTTTGATAACCACTTTAT
** * ** *
6275 GTAATTTTGATAACCTCGCTCT
1 AAAATTTTGATAACCACTTTAT
** * *
6297 GGAATTTTGATAACAACATTAT
1 AAAATTTTGATAACCACTTTAT
*
6319 GAAATTTTGATAA
1 AAAATTTTGATAA
6332 TCTTCCTATA
Statistics
Matches: 92, Mismatches: 30, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
21 3 0.03
22 89 0.97
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
AAAATTTTGATAACCACTTTAT
Found at i:6308 original size:44 final size:44
Alignment explanation
Indices: 6164--6354 Score: 165
Period size: 44 Copynumber: 4.4 Consensus size: 44
6154 AATACCACTG
* * *
6164 TGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTC
1 TGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCTCTCTC
* * * * * * * *
6208 TGAAATTTTGATAACCGCTTTATAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCTCTC
* * * *
6252 TAAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCTC
1 TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCTCTC
* *
6296 TGGAATTTTGATAA-CAACATTATGAAATTTTGATAATCT-TC-C
1 TGAAATTTTGATAATC-ACATTATGAAATTTTGATAACCTCTCTC
*
6338 TATAAATTTTGATAATC
1 T-GAAATTTTGATAATC
6355 TGATCTCTAT
Statistics
Matches: 112, Mismatches: 31, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
42 2 0.02
43 18 0.16
44 92 0.82
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (44 bp):
TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCTCTC
Found at i:6341 original size:88 final size:87
Alignment explanation
Indices: 6175--6354 Score: 200
Period size: 88 Copynumber: 2.1 Consensus size: 87
6165 GAAATTTTTG
* ** ** *
6175 TAATCACATTTTGAAAATTTGATAACCTCTTTCTGAAATTTTGATAACCGCTTTATAAAATTTTG
1 TAATCACATTATGAAAATTTGATAACCTCGCTCTGAAATTTTGATAACAACATTATAAAATTTTG
* *
6240 TTGACCCCTCTATAAAATTCTGA
66 ATAACCCCTCTAT-AAATTCTGA
* * * *
6263 TAATCACATTATGTAATTTTGATAACCTCGCTCTGGAATTTTGATAACAACATTATGAAATTTTG
1 TAATCACATTATGAAAATTTGATAACCTCGCTCTGAAATTTTGATAACAACATTATAAAATTTTG
* * *
6328 ATAA-TCTTCCTATAAATTTTGA
66 ATAACCCCT-CTATAAATTCTGA
6350 TAATC
1 TAATC
6355 TGATCTCTAT
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
87 15 0.20
88 61 0.80
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (87 bp):
TAATCACATTATGAAAATTTGATAACCTCGCTCTGAAATTTTGATAACAACATTATAAAATTTTG
ATAACCCCTCTATAAATTCTGA
Found at i:6346 original size:21 final size:23
Alignment explanation
Indices: 6316--6404 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 23
6306 ATAACAACAT
6316 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAATCTTCTC
6338 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATCT--TCTC
* * *
6362 TATGGAATTTCGATAATC-ACTC
1 TATGAAATTTTGATAATCTTCTC
*
6384 TATGAGA-TTTGATAATCTTCT
1 TATGAAATTTTGATAATCTTCT
6405 ATTAAATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
21 24 0.44
22 13 0.24
23 2 0.04
24 4 0.07
25 12 0.22
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (23 bp):
TATGAAATTTTGATAATCTTCTC
Found at i:6387 original size:22 final size:21
Alignment explanation
Indices: 6345--6400 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
6335 TCCTATAAAT
6345 TTTGATAATCTGATCTCTATG-GAA
1 TTTGATAATC--A-CTCTATGAG-A
6369 TTTCGATAATCACTCTATGAGA
1 TTT-GATAATCACTCTATGAGA
6391 TTTGATAATC
1 TTTGATAATC
6401 TTCTATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 7 0.23
22 11 0.37
23 2 0.07
24 3 0.10
25 7 0.23
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (21 bp):
TTTGATAATCACTCTATGAGA
Found at i:6415 original size:21 final size:22
Alignment explanation
Indices: 6316--6415 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 22
6306 ATAACAACAT
6316 TATGAAATTTTGATAATC-TTCC
1 TATGAAATTTTGATAATCATT-C
6338 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATC--AT-TC
* * *
6362 TATGGAATTTCGATAATCACTC
1 TATGAAATTTTGATAATCATTC
*
6384 TATGAGA-TTTGATAATC-TTC
1 TATGAAATTTTGATAATCATTC
*
6404 TATTAAATTTTG
1 TATGAAATTTTG
6416 GTACTCCTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 7 0.11
21 27 0.43
22 10 0.16
23 1 0.02
24 5 0.08
25 13 0.21
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (22 bp):
TATGAAATTTTGATAATCATTC
Found at i:6467 original size:22 final size:21
Alignment explanation
Indices: 6438--6795 Score: 146
Period size: 22 Copynumber: 16.5 Consensus size: 21
6428 AAATTGAGAC
*
6438 TTTT-ATAACCTTCGTATGAAA
1 TTTTGATAACC-TCCTATGAAA
* *
6459 TTTTGATAACCACGCTATAAAA
1 TTTTGATAACCTC-CTATGAAA
*
6481 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CCTATGAAA
*
6503 TATT-AGTAACCTCCTATTGAAA
1 TTTTGA-TAACCTCCTA-TGAAA
*
6525 TTTTGTTAA-CTACACTATGAAA
1 TTTTGATAACCT-C-CTATGAAA
*
6547 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-CTATGAAA
* * *
6569 TTTTGATAATCT-CTTTGGTAACC
1 TTTTGATAACCTCCTAT-G-AA-A
** *
6592 TTTCT-ATAAAAT--TGTGAAA
1 TTT-TGATAACCTCCTATGAAA
* *
6611 --AT--TAACCATTCTATGAAA
1 TTTTGATAACC-TCCTATGAAA
** * *
6629 TTTCAATAACCAACCTAAGAAA
1 TTTTGATAACC-TCCTATGAAA
*
6651 TTTTAATAACCTGATCCTATGAAA
1 TTTTGATAACC---TCCTATGAAA
* * *
6675 TTTTGGTAGCCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
6697 TTTTGATATCTTCCATATGAAA
1 TTTTGATAACCTCC-TATGAAA
* * *
6719 TTTTGGTAACCACGCTATGTAA
1 TTTTGATAACCTC-CTATGAAA
6741 TTTTGATAACCTCCTCATGAAA
1 TTTTGATAACCTCCT-ATGAAA
* * *
6763 TTATAATAACCATCTTATGAAA
1 TTTTGATAACC-TCCTATGAAA
6785 TTTTGATAACC
1 TTTTGATAACC
6796 ACATAGAGAC
Statistics
Matches: 254, Mismatches: 54, Indels: 57
0.70 0.15 0.16
Matches are distributed among these distances:
15 3 0.01
16 2 0.01
18 6 0.02
20 5 0.02
21 19 0.07
22 181 0.71
23 20 0.08
24 18 0.07
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:6796 original size:22 final size:22
Alignment explanation
Indices: 6613--6796 Score: 151
Period size: 22 Copynumber: 8.3 Consensus size: 22
6603 TTGTGAAAAT
* **
6613 TAACCATTCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * *
6635 TAACCAACCTAAGAAATTTTAA
1 TAACCATCCTATGAAATTTTGA
*
6657 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTGA
*
6681 TAGCCA-CACTATGAAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
* * *
6703 T-ATCTTCCATATGAAATTTTGG
1 TAACCATCC-TATGAAATTTTGA
*
6725 TAACCA-CGCTATGTAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
* *
6747 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTGA
*
6769 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
6791 TAACCA
1 TAACCA
6797 CATAGAGACA
Statistics
Matches: 128, Mismatches: 24, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
21 5 0.04
22 100 0.78
23 6 0.05
24 17 0.13
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:6993 original size:19 final size:20
Alignment explanation
Indices: 6962--6999 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6952 TATTGACATT
6962 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
6981 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
7000 ACTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:24510 original size:9 final size:9
Alignment explanation
Indices: 24496--24522 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
24486 GGGACCCTTT
24496 TTCATTTTC
1 TTCATTTTC
24505 TTCATTTTC
1 TTCATTTTC
24514 TTCATTTTC
1 TTCATTTTC
24523 CACATAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (9 bp):
TTCATTTTC
Found at i:30346 original size:35 final size:35
Alignment explanation
Indices: 30274--30347 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
30264 TACATGGACT
* **
30274 AATT-AAATTGATTACTTTTTAGGTACATGAATGA
1 AATTGAAATTGATTACTTTTTAAGTACATGAACAA
*
30308 AATTGAAATTGATTATTTTTTAAGTACATGAACAA
1 AATTGAAATTGATTACTTTTTAAGTACATGAACAA
30343 AATTG
1 AATTG
30348 TTTGTACACT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
34 4 0.11
35 31 0.89
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (35 bp):
AATTGAAATTGATTACTTTTTAAGTACATGAACAA
Found at i:32246 original size:20 final size:20
Alignment explanation
Indices: 32221--32264 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
32211 GTGGAAAAAT
32221 CACAAAGAGAATCCATTAGC
1 CACAAAGAGAATCCATTAGC
32241 CACAAAGAGAATCCATTAGC
1 CACAAAGAGAATCCATTAGC
32261 CACA
1 CACA
32265 GCCTACATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.27, G:0.14, T:0.14
Consensus pattern (20 bp):
CACAAAGAGAATCCATTAGC
Found at i:35103 original size:2 final size:2
Alignment explanation
Indices: 35096--35127 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35086 AAGAACAAAT
35096 TA TA 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
35128 AACAGAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.