Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012173.1 Corchorus capsularis cultivar CVL-1 contig12194, 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: 6776
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--50 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
*
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC 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
*
43 CC CT CT CT
1 CT CT CT CT
51 ATGGTCCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:1426 original size:138 final size:141
Alignment explanation
Indices: 1256--1526 Score: 408
Period size: 138 Copynumber: 1.9 Consensus size: 141
1246 CACTTATGAT
*
1256 CATCTCTTTTTACATGGATAATCATGTAAAAAAAAAAGAAAAAATAA-GGGGGAAAACAGTATTT
1 CATCTCTTTTTACATGGATAATCATGT-AAAAAAAAAGAAAAAATAAGGGGGGAAAACAATATTT
* * *
1320 TC-T-ACGAAAACTGA-AAAATCAATCAATCAATTC-ATTCCAAATTACTCCCTATATATTGTCT
65 TCTTAACGAAAACTGATAAAA-CAATCAATCAATTCTATTCCAAATTACTCCCCATATACTATCT
1381 CCAATCTTTTGAC
129 CCAATCTTTTGAC
*
1394 CATCTCTTTTTACATGGATAATCATGTAAAAAAAAAGGAAAAATAAGGGGGGAAAACAATATTTT
1 CATCTCTTTTTACATGGATAATCATGTAAAAAAAAAGAAAAAATAAGGGGGGAAAACAATATTTT
* * * *
1459 CTTAACGAAGATTGATAAAACGATCAATCATTTCTATTCCAAATTACTCCCCATATACTATCTCC
66 CTTAACGAAAACTGATAAAACAATCAATCAATTCTATTCCAAATTACTCCCCATATACTATCTCC
1524 AAT
131 AAT
1527 GAAGTTCACA
Statistics
Matches: 119, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
137 18 0.15
138 45 0.38
139 1 0.01
140 21 0.18
141 34 0.29
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (141 bp):
CATCTCTTTTTACATGGATAATCATGTAAAAAAAAAGAAAAAATAAGGGGGGAAAACAATATTTT
CTTAACGAAAACTGATAAAACAATCAATCAATTCTATTCCAAATTACTCCCCATATACTATCTCC
AATCTTTTGAC
Found at i:2472 original size:14 final size:14
Alignment explanation
Indices: 2453--2488 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2443 AATTGGATAA
2453 GAGATTGGAGTTTG
1 GAGATTGGAGTTTG
2467 GAGATTGGAGTTTG
1 GAGATTGGAGTTTG
*
2481 GAGCTTGG
1 GAGATTGG
2489 TAAGTGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.03, G:0.44, T:0.33
Consensus pattern (14 bp):
GAGATTGGAGTTTG
Found at i:2888 original size:12 final size:13
Alignment explanation
Indices: 2867--2921 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
2857 AAAAGGGGTA
2867 AAAGGAAAAAGAG
1 AAAGGAAAAAGAG
*
2880 AAAGGAAAAGAAAGG
1 AAAGGAAAA-AGA-G
2895 AAA-GAAAAA-A-
1 AAAGGAAAAAGAG
2905 AAAGGAAAAAGA-
1 AAAGGAAAAAGAG
2917 AAAGG
1 AAAGG
2922 GGAAATAGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 3 0.08
11 6 0.16
12 7 0.19
13 10 0.27
14 7 0.19
15 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AAAGGAAAAAGAG
Found at i:2903 original size:15 final size:15
Alignment explanation
Indices: 2872--2912 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2862 GGGTAAAAGG
*
2872 AAAAAGAGAAAGGAAA
1 AAAAAG-GAAAGAAAA
*
2888 AGAAAGGAAAGAAAA
1 AAAAAGGAAAGAAAA
2903 AAAAAGGAAA
1 AAAAAGGAAA
2913 AAGAAAAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAAGGAAAGAAAA
Found at i:2919 original size:15 final size:17
Alignment explanation
Indices: 2884--2920 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
2874 AAAGAGAAAG
2884 GAAAAGAAAGGAAAGAA
1 GAAAAGAAAGGAAAGAA
2901 -AAAA-AAAGGAAA-AA
1 GAAAAGAAAGGAAAGAA
2915 GAAAAG
1 GAAAAG
2921 GGGAAATAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.11
15 12 0.67
16 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAGGAAAGAA
Found at i:3823 original size:20 final size:20
Alignment explanation
Indices: 3786--3825 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3776 TGGTTTTATA
**
3786 ATCTTGGTTTTGGATTGATT
1 ATCTTGGTTTTACATTGATT
*
3806 ATCTTGGTTTTACTTTGATT
1 ATCTTGGTTTTACATTGATT
3826 TATGATCATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.57
Consensus pattern (20 bp):
ATCTTGGTTTTACATTGATT
Found at i:5840 original size:43 final size:44
Alignment explanation
Indices: 5776--5861 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 44
5766 CATGAAGAAG
* *
5776 TTTAATGGGTAACCAACTTAATAGGGAGTAGT-TTTTTTTTTAT
1 TTTAATGGGTAACCAACTTAATAGGGAGCAGTGTTTTTATTTAT
* *
5819 TTTAATGGGTAACTAATTTAATAGGGAGCAGTGTTTTTATTTA
1 TTTAATGGGTAACCAACTTAATAGGGAGCAGTGTTTTTATTTA
5862 AATATAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 29 0.76
44 9 0.24
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (44 bp):
TTTAATGGGTAACCAACTTAATAGGGAGCAGTGTTTTTATTTAT
Done.