Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006912.1 Corchorus capsularis cultivar CVL-1 contig06933, 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: 12935
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:360 original size:49 final size:49
Alignment explanation
Indices: 304--406 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 49
294 GAAGCTTTTT
**
304 GTAAAAATGCCATCTTTG-GAT-AGAAGATTGAATTTTTAGTAATTAGTAA
1 GTAAAAATGCCATCTTTGAG-TGA-AAGATTGAAACTTTAGTAATTAGTAA
* *
353 GTAAAAATGTCATCTTTGAGTGAAAGATTGAAACTTTAGTGATTAGTAA
1 GTAAAAATGCCATCTTTGAGTGAAAGATTGAAACTTTAGTAATTAGTAA
402 GTAAA
1 GTAAA
407 GATGTCACCT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 46 0.96
50 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (49 bp):
GTAAAAATGCCATCTTTGAGTGAAAGATTGAAACTTTAGTAATTAGTAA
Found at i:412 original size:49 final size:49
Alignment explanation
Indices: 327--432 Score: 140
Period size: 49 Copynumber: 2.2 Consensus size: 49
317 CTTTGGATAG
** * * **
327 AAGATTGAATTTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGAGTGA
1 AAGATTGAAACTTTAGTAATTAGTAAGTAAAAATGTCACCTTAGAGCAA
* *
376 AAGATTGAAACTTTAGTGATTAGTAAGTAAAGATGTCACCTTAGAGCAA
1 AAGATTGAAACTTTAGTAATTAGTAAGTAAAAATGTCACCTTAGAGCAA
425 AAGATTGA
1 AAGATTGA
433 TTTTTAGAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.33
Consensus pattern (49 bp):
AAGATTGAAACTTTAGTAATTAGTAAGTAAAAATGTCACCTTAGAGCAA
Found at i:1361 original size:55 final size:54
Alignment explanation
Indices: 1302--1672 Score: 589
Period size: 55 Copynumber: 6.7 Consensus size: 54
1292 CAATCCGAAC
*
1302 AGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAGGTAAT
1 AGTAATCAGTAAATCAGTAGTTAAGT-AAAAGAGATTAATCAGAGTCAAGGTAAT
*
1357 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT
1 AGTAATCAGTAAATCAGTAGTTAAGTAA-AAGAGATTAATCAGAGTCAAGGTAAT
* *
1412 AGTAATCAGTAAATCAGTAGTCAAGTAAAAAGAGATTAATCAAAGTCAAGGTAAT
1 AGTAATCAGTAAATCAGTAGTTAAGT-AAAAGAGATTAATCAGAGTCAAGGTAAT
* * *
1467 AGTAATCAATAAATCAGTAATTAAGTAAAACGAGATTAATCAGAGTCAAAGTAAT
1 AGTAATCAGTAAATCAGTAGTTAAGTAAAA-GAGATTAATCAGAGTCAAGGTAAT
* *
1522 AGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAAT
1 AGTAATCAGTAAATCAGTAGTTAAGT-AAAAGAGATTAATCAGAGTCAAGGTAAT
*
1577 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT
1 AGTAATCAGTAAATCAGTAGTTAAGTAA-AAGAGATTAATCAGAGTCAAGGTAAT
1632 AGTAATCAGTAAATCAGTAGTTAAGTAAGAAGAGATTAATC
1 AGTAATCAGTAAATCAGTAGTTAAGTAA-AAGAGATTAATC
1673 GGTAAATTGA
Statistics
Matches: 298, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
54 8 0.03
55 284 0.95
56 6 0.02
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (54 bp):
AGTAATCAGTAAATCAGTAGTTAAGTAAAAGAGATTAATCAGAGTCAAGGTAAT
Found at i:1697 original size:71 final size:72
Alignment explanation
Indices: 1622--1758 Score: 204
Period size: 71 Copynumber: 1.9 Consensus size: 72
1612 TTAATCAGAG
* * * * *
1622 TCAAGGTAATAGTAATCAGTAAATCAGTAGTTAAGTAAGAAGAGATTAATCGGTAAATTGA-TAA
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGAGAGTAATCAGTAAATTGAGTAA
1686 TTAAGAA
66 TTAAGAA
* *
1693 TCAAGGTAATAGTAATCAGTAAATCAGTAATCAGGTAAAAAGATAGTAATCAGTAAATTGAGTAA
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGAGAGTAATCAGTAAATTGAGTAA
1758 T
66 T
1759 CAGTAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
71 54 0.93
72 4 0.07
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (72 bp):
TCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGAGAGTAATCAGTAAATTGAGTAA
TTAAGAA
Found at i:1758 original size:16 final size:15
Alignment explanation
Indices: 1703--1764 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 15
1693 TCAAGGTAAT
*
1703 AGTAATCAGTAAATC
1 AGTAATCAGTAAATG
*
1718 AGTAATCAGGTAAAAAG
1 AGTAATCA-GT-AAATG
1735 ATAGTAATCAGTAAATTG
1 --AGTAATCAGTAAA-TG
1753 AGTAATCAGTAA
1 AGTAATCAGTAA
1765 TTAAAGAGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.21
16 14 0.36
17 6 0.15
18 3 0.08
19 8 0.21
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (15 bp):
AGTAATCAGTAAATG
Found at i:2117 original size:22 final size:23
Alignment explanation
Indices: 2027--2119 Score: 81
Period size: 22 Copynumber: 4.2 Consensus size: 23
2017 ATCTGAAAGG
* *
2027 GTAAAATGGTAATTAGTA-AAGA
1 GTAAAATAGTAATCAGTACAAGA
* *
2049 GTAAAATAGTAATCACTA-AAAA
1 GTAAAATAGTAATCAGTACAAGA
*
2071 GTAAGAA-GGTAAATCA--ACAAGA
1 GTAA-AATAGT-AATCAGTACAAGA
2093 GTAAAATAGTAATCAGTACAA-A
1 GTAAAATAGTAATCAGTACAAGA
2115 GTAAA
1 GTAAA
2120 GAATAATCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
21 8 0.14
22 39 0.67
23 11 0.19
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.22
Consensus pattern (23 bp):
GTAAAATAGTAATCAGTACAAGA
Found at i:8494 original size:11 final size:11
Alignment explanation
Indices: 8478--8507 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
8468 TGATCTTCAA
8478 GTCTTCAAATT
1 GTCTTCAAATT
8489 GTCTTCAAATT
1 GTCTTCAAATT
8500 GTCTTCAA
1 GTCTTCAA
8508 GAAATCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (11 bp):
GTCTTCAAATT
Found at i:10035 original size:24 final size:26
Alignment explanation
Indices: 9983--10095 Score: 180
Period size: 24 Copynumber: 4.5 Consensus size: 26
9973 TGTGCCGTAA
*
9983 TCATGGCAACCAAATCCCCACATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
10009 TCATGGCAACCAAGT-CCC-CATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
10033 TCATGGCAACCAAGTCCCCACATGGC
1 TCATGGCAACCAAGTCCCCACATGGC
*
10059 TCATGGCAACCAAGT-CCC-CATAGC
1 TCATGGCAACCAAGTCCCCACATGGC
10083 TCATGGCAACCAA
1 TCATGGCAACCAA
10096 AAATAGGTCT
Statistics
Matches: 83, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
24 39 0.47
25 9 0.11
26 35 0.42
ACGTcount: A:0.29, C:0.37, G:0.18, T:0.16
Consensus pattern (26 bp):
TCATGGCAACCAAGTCCCCACATGGC
Found at i:10058 original size:50 final size:50
Alignment explanation
Indices: 9983--10096 Score: 210
Period size: 50 Copynumber: 2.3 Consensus size: 50
9973 TGTGCCGTAA
*
9983 TCATGGCAACCAAATCCCCACATGGCTCATGGCAACCAAGTCCCCATGGC
1 TCATGGCAACCAAATCCCCACATGGCTCATGGCAACCAAGTCCCCATAGC
*
10033 TCATGGCAACCAAGTCCCCACATGGCTCATGGCAACCAAGTCCCCATAGC
1 TCATGGCAACCAAATCCCCACATGGCTCATGGCAACCAAGTCCCCATAGC
10083 TCATGGCAACCAAA
1 TCATGGCAACCAAA
10097 AATAGGTCTG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.30, C:0.37, G:0.18, T:0.16
Consensus pattern (50 bp):
TCATGGCAACCAAATCCCCACATGGCTCATGGCAACCAAGTCCCCATAGC
Found at i:12377 original size:19 final size:18
Alignment explanation
Indices: 12344--12379 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12334 TTGAAATAAT
12344 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
12362 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
12380 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.