Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012306.1 Corchorus capsularis cultivar CVL-1 contig12327, 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: 19360
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:473 original size:19 final size:18
Alignment explanation
Indices: 439--476 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
429 CTTGAAATAT
439 TTCTTCAATGATCTTCAA
1 TTCTTCAATGATCTTCAA
*
457 TTCTTCAAATTATCTTCAA
1 TTCTTC-AATGATCTTCAA
476 T
1 T
477 AAATCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (18 bp):
TTCTTCAATGATCTTCAA
Found at i:1279 original size:71 final size:71
Alignment explanation
Indices: 1163--1303 Score: 264
Period size: 71 Copynumber: 2.0 Consensus size: 71
1153 TAAATAATGT
*
1163 TATGTTAGACTTAGGAGCTTCATTAATAGTTATGCCTTATACCACTTATTCTGCTTTGAATCTTG
1 TATGTTAGACTTAGGAGCTTCATTAAGAGTTATGCCTTATACCACTTATTCTGCTTTGAATCTTG
1228 GACCTC
66 GACCTC
*
1234 TATGTTAGACTTAGGAGCTTCATTAAGAGTTATTCCTTATACCACTTATTCTGCTTTGAATCTTG
1 TATGTTAGACTTAGGAGCTTCATTAAGAGTTATGCCTTATACCACTTATTCTGCTTTGAATCTTG
1299 GACCT
66 GACCT
1304 TTGAAATTAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (71 bp):
TATGTTAGACTTAGGAGCTTCATTAAGAGTTATGCCTTATACCACTTATTCTGCTTTGAATCTTG
GACCTC
Found at i:4307 original size:30 final size:29
Alignment explanation
Indices: 4234--4311 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
4224 TTGCTTATTT
* * *
4234 TATCTTTCAATTG-TTGATTTGAATTGCCA
1 TATCTTGCTATTGATTGA-TTGAATTGCAA
4263 TATCTTGCTATTGATTGATTGAATTGCAA
1 TATCTTGCTATTGATTGATTGAATTGCAA
*
4292 TTAT-TTGTTAGTTGATTGAT
1 -TATCTTGCTA-TTGATTGAT
4312 AGATTGTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 26 0.62
30 16 0.38
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (29 bp):
TATCTTGCTATTGATTGATTGAATTGCAA
Found at i:10804 original size:19 final size:19
Alignment explanation
Indices: 10772--10811 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
10762 ACCCGAATAA
*
10772 TAAATAAATTAATTAAAAT
1 TAAATAAATAAATTAAAAT
*
10791 TAAATGAATAAATTAAAAT
1 TAAATAAATAAATTAAAAT
10810 TA
1 TA
10812 TCTTGTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAATAAATAAATTAAAAT
Found at i:10938 original size:19 final size:20
Alignment explanation
Indices: 10899--10934 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
10889 ATTTTTAAGT
10899 AAAAATATAATATATAAATA
1 AAAAATATAATATATAAATA
10919 AAAAAT-TAATAT-TAAA
1 AAAAATATAATATATAAA
10935 ATAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATATAATATATAAATA
Found at i:12344 original size:6 final size:6
Alignment explanation
Indices: 12335--12362 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12325 TAAAGCAAAG
12335 TAAATC TAAATC TAAATC TAAATC TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAA
12363 GCAGATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (6 bp):
TAAATC
Found at i:12374 original size:12 final size:13
Alignment explanation
Indices: 12359--12403 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
12349 AATCTAAATC
12359 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
12371 TAAAGCAAATTAA
1 TAAAGCAGATTAA
12384 TAAAGCAGATTAA
1 TAAAGCAGATTAA
12397 TAAAGCA
1 TAAAGCA
12404 AACATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:15584 original size:10 final size:10
Alignment explanation
Indices: 15564--15615 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
15554 CGGATAGCTT
15564 GGCATTGGCCG
1 GGCA-TGGCCG
15575 GGCATGGCCG
1 GGCATGGCCG
*
15585 GGCTGAAGGCGCG
1 GGC--ATGGC-CG
*
15598 GACATGGCCG
1 GGCATGGCCG
15608 GGCATGGC
1 GGCATGGC
15616 TTGGTGACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 18 0.53
11 8 0.24
12 4 0.12
13 4 0.12
ACGTcount: A:0.13, C:0.27, G:0.48, T:0.12
Consensus pattern (10 bp):
GGCATGGCCG
Found at i:19086 original size:35 final size:36
Alignment explanation
Indices: 19047--19129 Score: 91
Period size: 35 Copynumber: 2.3 Consensus size: 36
19037 TAAATAAAAA
* * *
19047 TTAAAAGCAGAAACAG-AAAATAAAAA-TATTTTTTT
1 TTAAAAG-AAAAACAGAAAAAGAAAAATTAATTTTTT
*
19082 TTAAAAAGAAAAACGGAAAAAGAAAAATTAATTTTTT
1 TT-AAAAGAAAAACAGAAAAAGAAAAATTAATTTTTT
19119 TT-AAAGAAAAA
1 TTAAAAGAAAAA
19130 TCGGAAACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 17 0.41
36 14 0.34
37 10 0.24
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.28
Consensus pattern (36 bp):
TTAAAAGAAAAACAGAAAAAGAAAAATTAATTTTTT
Found at i:19108 original size:36 final size:36
Alignment explanation
Indices: 19063--19136 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
19053 GCAGAAACAG
* *
19063 AAAATAAAAA-TATTTTTTTTTAAAAAGAAAAA-CGGA
1 AAAAGAAAAATTAATTTTTTTT--AAAGAAAAATCGGA
19099 AAAAGAAAAATTAATTTTTTTTAAAGAAAAATCGGA
1 AAAAGAAAAATTAATTTTTTTTAAAGAAAAATCGGA
19135 AA
1 AA
19137 CCCTAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 9 0.26
36 15 0.44
37 10 0.29
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (36 bp):
AAAAGAAAAATTAATTTTTTTTAAAGAAAAATCGGA
Done.