Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015703.1 Corchorus capsularis cultivar CVL-1 contig15724, 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: 13119
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:932 original size:38 final size:38
Alignment explanation
Indices: 881--958 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
871 TTTCAACAAA
881 TTCAACAATCTTACATTCTTACTTAATACTTT-ACATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGA-ATTT
919 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
957 TT
1 TT
959 GGTAATTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 38 0.97
39 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.01, T:0.49
Consensus pattern (38 bp):
TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
Found at i:3764 original size:6 final size:6
Alignment explanation
Indices: 3753--3782 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3743 AAAGTTAGTA
3753 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
3783 TTTAGAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:6778 original size:22 final size:22
Alignment explanation
Indices: 6625--6795 Score: 113
Period size: 22 Copynumber: 8.0 Consensus size: 22
6615 TATTTTACTT
* * *
6625 TTATCAAAACTTCATAGTGTGG
1 TTATCAAAATTTCATAGGGAGG
* *
6647 TTATCAAAATTTCATAGAGATG
1 TTATCAAAATTTCATAGGGAGG
* * **
6669 TCATCAAAATGTCATATAGAGG
1 TTATCAAAATTTCATAGGGAGG
* * *
6691 TTATCAAAATTTCATTGTGTGG
1 TTATCAAAATTTCATAGGGAGG
*
6713 TTATC-AAA--T--TAGGAAGG
1 TTATCAAAATTTCATAGGGAGG
* * *
6730 TTAT-TAAATTTTATTGTGGA-G
1 TTATCAAAATTTCATAG-GGAGG
*
6751 TAATCAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
6773 TTATCAACATTTCATAAGGAGG
1 TTATCAAAATTTCATAGGGAGG
6795 T
1 T
6796 CATTGTTAGT
Statistics
Matches: 114, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
17 11 0.10
19 2 0.02
21 12 0.11
22 89 0.78
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:6876 original size:22 final size:22
Alignment explanation
Indices: 6849--7032 Score: 134
Period size: 22 Copynumber: 8.5 Consensus size: 22
6839 TAGTATCTAG
6849 ATCAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
* *
6871 AGCAAAATTTCATAACG-AGGTT
1 ATCAAAATTTCAT-AGGAAGGTT
* * *
6893 ATCAAAGA-ATCATAGGGATGTT
1 ATCAAA-ATTTCATAGGAAGGTT
* *
6915 GTCAAAA-TT--T--G-TGGTT
1 ATCAAAATTTCATAGGAAGGTT
*
6931 ATCAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
6953 ATCAAAATTTCATA-GATAGGTTT
1 ATCAAAATTTCATAGGA-AGG-TT
* **
6976 ATCAAAATTTTATAGGAAAATTT
1 ATCAAAATTTCATAGG-AAGGTT
*
6999 ATCAAAATTTCATAGTAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
* *
7021 ATTACAATTTCA
1 ATCAAAATTTCA
7033 CAGTGTGATT
Statistics
Matches: 128, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.07
17 3 0.02
19 2 0.02
21 7 0.05
22 70 0.55
23 34 0.27
24 2 0.02
25 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGAAGGTT
Found at i:6944 original size:38 final size:38
Alignment explanation
Indices: 6889--6962 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
6879 TTCATAACGA
* * * *
6889 GGTTATCAAAGAATCATAGGGATGTTGTCAAAATTTGT
1 GGTTATCAAAGAATCATAAGAAGGTTATCAAAATTTGT
*
6927 GGTTATCAAA-ATTTCATAAGAAGGTTATCAAAATTT
1 GGTTATCAAAGA-ATCATAAGAAGGTTATCAAAATTT
6963 CATAGATAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 1 0.03
38 29 0.97
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (38 bp):
GGTTATCAAAGAATCATAAGAAGGTTATCAAAATTTGT
Found at i:6981 original size:23 final size:22
Alignment explanation
Indices: 6929--7020 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 22
6919 AAATTTGTGG
6929 TTATCAAAATTTCATAAGAAGG-
1 TTATCAAAATTTCAT-AGAAGGT
6951 TTATCAAAATTTCATAGATAGGT
1 TTATCAAAATTTCATAGA-AGGT
* **
6974 TTATCAAAATTTTATAGGAAAAT
1 TTATCAAAATTTCATA-GAAGGT
6997 TTATCAAAATTTCATAGTAAGGT
1 TTATCAAAATTTCATAG-AAGGT
7020 T
1 T
7021 ATTACAATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.05
22 19 0.32
23 36 0.60
24 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAAGGT
Found at i:7072 original size:22 final size:22
Alignment explanation
Indices: 7019--7072 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
7009 CATAGTAAGG
* *
7019 TTATTACAATTTCACAGTGTGA
1 TTATTAAAATTTCACAATGTGA
*
7041 -T-TCAAAATTTCACAATGTGA
1 TTATTAAAATTTCACAATGTGA
7061 TTATTAAAATTT
1 TTATTAAAATTT
7073 TATATGGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 2 0.08
22 8 0.31
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
TTATTAAAATTTCACAATGTGA
Found at i:7179 original size:43 final size:43
Alignment explanation
Indices: 7125--7206 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
7115 TACACATAGA
* *
7125 GGTTATAAAAATTTTATACTGTGATTAAGAAAATTTCATTGAT
1 GGTTATAAAAATTTCATACTGAGATTAAGAAAATTTCATTGAT
* * * *
7168 GGTTATCAAAATTTCATAGTGAGGTTAATAAAATTTCAT
1 GGTTATAAAAATTTCATACTGAGATTAAGAAAATTTCAT
7207 AACAAGATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (43 bp):
GGTTATAAAAATTTCATACTGAGATTAAGAAAATTTCATTGAT
Found at i:7200 original size:22 final size:21
Alignment explanation
Indices: 7119--7207 Score: 69
Period size: 22 Copynumber: 4.2 Consensus size: 21
7109 CAACATTACA
7119 CATA-GAGGTTATAAAAATTT
1 CATATGAGGTTATAAAAATTT
* * *
7139 TATACTGTGATTA-AGAAAATTT
1 CATA-TGAGGTTATA-AAAATTT
*
7161 CAT-TGATGGTTATCAAAATTT
1 CATATGA-GGTTATAAAAATTT
7182 CATAGTGAGGTTA-ATAAAATTT
1 CATA-TGAGGTTATA-AAAATTT
7204 CATA
1 CATA
7208 ACAAGATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
20 5 0.09
21 15 0.28
22 30 0.57
23 3 0.06
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (21 bp):
CATATGAGGTTATAAAAATTT
Found at i:9643 original size:24 final size:23
Alignment explanation
Indices: 9597--9650 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
9587 TTAGCTTTTT
*
9597 TTTTTTTTTTTTTTGAGTGAAGC
1 TTTTTTTTTTTTTTGAGTAAAGC
*
9620 GTTTTTTTTTTTTTT-ACTTAAAGC
1 -TTTTTTTTTTTTTTGA-GTAAAGC
9644 TTTTTTT
1 TTTTTTT
9651 ACTACATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.13, C:0.06, G:0.11, T:0.70
Consensus pattern (23 bp):
TTTTTTTTTTTTTTGAGTAAAGC
Done.