Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011329.1 Corchorus capsularis cultivar CVL-1 contig11350, 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: 49124
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--82 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
42 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
83 CCCACCATGA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1364 original size:31 final size:31
Alignment explanation
Indices: 1321--1387 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1311 AAATTCTAAA
* * *
1321 TTGATCCAATTTTTAAACGTTTAGTACCTAT
1 TTGAGCCAATTTTGAAACGTTTAGCACCTAT
*
1352 TTGAGCCAATTTTGAATCGTTTAGCACCTAT
1 TTGAGCCAATTTTGAAACGTTTAGCACCTAT
1383 TTGAG
1 TTGAG
1388 TCCATTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (31 bp):
TTGAGCCAATTTTGAAACGTTTAGCACCTAT
Found at i:1448 original size:19 final size:19
Alignment explanation
Indices: 1392--1457 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
1382 TTTGAGTCCA
* *
1392 TTTAAAAGTATTTAAAAAAT
1 TTTAAAAATATTT-AAAATT
1412 TTTAAAAA-A-TTAAAATT
1 TTTAAAAATATTTAAAATT
*
1429 TTTAAAAATATTTTAAATT
1 TTTAAAAATATTTAAAATT
1448 TTTAAAAATA
1 TTTAAAAATA
1458 AAAAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.32
18 3 0.07
19 18 0.44
20 7 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTAAAAATATTTAAAATT
Found at i:1474 original size:10 final size:10
Alignment explanation
Indices: 1391--1475 Score: 63
Period size: 10 Copynumber: 8.9 Consensus size: 10
1381 ATTTGAGTCC
*
1391 ATTTAAAAGT
1 ATTTAAAAAT
1401 ATTTAAAAA-
1 ATTTAAAAAT
1410 ATTTTAAAAA-
1 A-TTTAAAAAT
1420 A-TT-AAAAT
1 ATTTAAAAAT
*
1428 TTTTAAAAAT
1 ATTTAAAAAT
*
1438 ATTT-TAAAT
1 ATTTAAAAAT
*
1447 TTTTAAAAAT
1 ATTTAAAAAT
***
1457 AAAAAAAAAT
1 ATTTAAAAAT
1467 ATTTAAAAA
1 ATTTAAAAA
1476 GGCCACATAG
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
7 4 0.07
8 2 0.04
9 10 0.18
10 41 0.72
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (10 bp):
ATTTAAAAAT
Found at i:4770 original size:2 final size:2
Alignment explanation
Indices: 4763--4796 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4753 ATCAAATTAG
4763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4797 GTACCAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8740 original size:5 final size:6
Alignment explanation
Indices: 8726--8750 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8716 GCGAAAATCA
8726 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
8751 ATGGCCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:10160 original size:2 final size:2
Alignment explanation
Indices: 10153--10192 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
10143 AAACCCCACT
* *
10153 TA TA TA TA CA TA CA 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
10193 ATAAAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:17475 original size:156 final size:150
Alignment explanation
Indices: 17191--17666 Score: 433
Period size: 156 Copynumber: 3.1 Consensus size: 150
17181 CATCATCTTG
* * * * *
17191 GTTTGGGGTGAGAAACAAACTTCATTATGATAGGGAGTTCAGTTTTACTTAGAATTCTTTCCATA
1 GTTTGGGATGAGAAACAAACTTCACTATGAAAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATA
* * * * *
17256 GTCCTATGGAGATAGTCTAAGTCTCGTGGCCAAATTTCATCTCAATTAGACTTAGTATGAAAAAC
66 GTCTTATGGAGATAGTCTAAGCCTCGTGG-CAAATATCAGCTCAATTAGACTTAGAATGAAAAAC
17321 TTATGCATGTTTTTCAGTTAAGGACA
130 -T-T--A-GTTTTTCAGTTAAGGACA
* *
17347 GTTTGGGATGTGAAACCAACTTCACTATGAAAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATA
1 GTTTGGGATGAGAAACAAACTTCACTATGAAAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATA
*
17412 GTCTTATGGAGATAGTCTAAGCCTACTGATGG-AAA-ATCAGCTTC-ATTGGACTTAGAATGAAA
66 GTCTTATGGAGATAGTCTAAGCCT-C-G-TGGCAAATATCAGC-TCAATTAGACTTAGAATGAAA
*
17474 AACTTAGTTTTTCATTTAAGGACA
127 AACTTAGTTTTTCAGTTAAGGACA
* * * * * * * ** * *
17498 GTTTAGGA-GAGAATCTAAGTTCACCATCAAGGGGAACTCGGTTTTACTTGGAATTTTTTTCATA
1 GTTTGGGATGAGAAACAAACTTCACTATGAAAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATA
* * * * * * * * *
17562 GTCTCATGGAGAGAATCTAAGTCTCTTGCCAAAGTTTCAGCTCAATCAGACTTA-AGGTGAAAAA
66 GTCTTATGGAGATAGTCTAAGCCTCGTGGCAAA-TATCAGCTCAATTAGACTTAGA-ATGAAAAA
*
17626 CTTATGCTAGTTTTTCATTTAAGGACA
129 C---T--TAGTTTTTCAGTTAAGGACA
17653 GTTTGAGG-TGAGAA
1 GTTTG-GGATGAGAA
17667 GTCCAGTTTA
Statistics
Matches: 267, Mismatches: 37, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
147 2 0.01
148 3 0.01
149 4 0.01
150 86 0.32
151 24 0.09
152 1 0.00
153 1 0.00
154 1 0.00
155 25 0.09
156 110 0.41
157 6 0.02
158 1 0.00
159 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (150 bp):
GTTTGGGATGAGAAACAAACTTCACTATGAAAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATA
GTCTTATGGAGATAGTCTAAGCCTCGTGGCAAATATCAGCTCAATTAGACTTAGAATGAAAAACT
TAGTTTTTCAGTTAAGGACA
Found at i:17602 original size:150 final size:151
Alignment explanation
Indices: 17232--17666 Score: 434
Period size: 150 Copynumber: 2.8 Consensus size: 151
17222 AGGGAGTTCA
* * *
17232 GTTTTACTTAGAATTCTTTCCATAGTC-CTATGGAGATAGTCTAAGTCTCGTGGCCAAATTTCAT
1 GTTTTACTTAGAATTTTTTCCATAGTCTC-ATGGAGATAGTCTAAGTCTC-TTGCCAAATTTCAG
* * * *
17296 CTCAATTAGACTTAGTATGAAAAACTTATGCATGTTTTTCAGTTAAGGACAGTTTGGGATGTGAA
64 CTCAATTAGACTTAGAATGAAAAACTTAT--A-GTTTTTCATTTAAGGACAGTTTAGGA-GAGAA
* * **
17361 ACCAACTTCACTATGAAAGGGAGTTCG
125 ACCAACTTCACCATCAAAGGGAACTCG
* * * *
17388 GTTTTACTTAGAATTTTTTCCATAGTCTTATGGAGATAGTCTAAGCCTACTGATG-GAAA-ATCA
1 GTTTTACTTAGAATTTTTTCCATAGTCTCATGGAGATAGTCTAAGTCT-CT--TGCCAAATTTCA
* *
17451 GCTTC-ATTGGACTTAGAATGAAAAAC-T-TAGTTTTTCATTTAAGGACAGTTTAGGAGAGAATC
63 GC-TCAATTAGACTTAGAATGAAAAACTTATAGTTTTTCATTTAAGGACAGTTTAGGAGAGAAAC
* * *
17513 TAAGTTCACCATCAAGGGGAACTCG
127 CAACTTCACCATCAAAGGGAACTCG
* * * *
17538 GTTTTACTTGGAATTTTTTTCATAGTCTCATGGAGAGAATCTAAGTCTCTTGCCAAAGTTTCAGC
1 GTTTTACTTAGAATTTTTTCCATAGTCTCATGGAGATAGTCTAAGTCTCTTGCCAAA-TTTCAGC
* * *
17603 TCAATCAGACTTA-AGGTGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAA
65 TCAATTAGACTTAGA-ATGAAAAACTTA---TAGTTTTTCATTTAAGGACAGTTT-AGGAGAGAA
17667 GTCCAGTTTA
Statistics
Matches: 231, Mismatches: 32, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
147 2 0.01
148 3 0.01
149 5 0.02
150 86 0.37
151 25 0.11
152 1 0.00
154 1 0.00
155 25 0.11
156 76 0.33
157 6 0.03
158 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (151 bp):
GTTTTACTTAGAATTTTTTCCATAGTCTCATGGAGATAGTCTAAGTCTCTTGCCAAATTTCAGCT
CAATTAGACTTAGAATGAAAAACTTATAGTTTTTCATTTAAGGACAGTTTAGGAGAGAAACCAAC
TTCACCATCAAAGGGAACTCG
Found at i:21676 original size:26 final size:24
Alignment explanation
Indices: 21626--21673 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
21616 GAGGATGTCT
21626 TATATATATTAAGATTATATTAAA
1 TATATATATTAAGATTATATTAAA
*
21650 TATATATA-TATATATTATATTAAA
1 TATATATATTA-AGATTATATTAAA
21674 AATGAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TATATATATTAAGATTATATTAAA
Found at i:22381 original size:2 final size:2
Alignment explanation
Indices: 22374--22409 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
22364 ATATGTAGTG
22374 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
22410 ACGATTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39805 original size:3 final size:3
Alignment explanation
Indices: 39799--39834 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
39789 TTAAAAAAAA
*
39799 AAG AAG AAG AAG AAG AAG ATG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
39835 TTATTCTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:41592 original size:4 final size:4
Alignment explanation
Indices: 41583--41651 Score: 63
Period size: 4 Copynumber: 17.5 Consensus size: 4
41573 TGCTTTATAG
*
41583 TTTA TTTA TTTA --TA TTTA TATA GTATTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -T-TTA TTTA TTTA TTTA TTTA TTTA
* * *
41631 -TTA TTGA TTCA TTTT TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TT
41652 GGTTTGTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
2 2 0.04
3 3 0.06
4 44 0.83
5 2 0.04
6 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:41644 original size:23 final size:23
Alignment explanation
Indices: 41606--41651 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41596 ATTTATATAG
* *
41606 TATTATTTATTTATTTATTTATT
1 TATTATTGATTCATTTATTTATT
*
41629 TATTATTGATTCATTTTTTTATT
1 TATTATTGATTCATTTATTTATT
41652 GGTTTGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TATTATTGATTCATTTATTTATT
Found at i:42912 original size:16 final size:16
Alignment explanation
Indices: 42891--42925 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
42881 GCATTCGAGA
42891 CATGAATATATATACC
1 CATGAATATATATACC
42907 CATGAATATATATACC
1 CATGAATATATATACC
42923 CAT
1 CAT
42926 CGATTGCAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (16 bp):
CATGAATATATATACC
Found at i:43522 original size:2 final size:2
Alignment explanation
Indices: 43515--43545 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43505 TTCTTATCCC
43515 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
43546 AGAAGTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.