Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011914.1 Corchorus capsularis cultivar CVL-1 contig11935, 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: 23171
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:1865 original size:65 final size:65
Alignment explanation
Indices: 1785--1922 Score: 276
Period size: 65 Copynumber: 2.1 Consensus size: 65
1775 TTTGGCCAAA
1785 ATAAAAGTTTAGGGGCTTATTTGACGGTTCAATGTAAGTTCAAGGGCCTTTTCGCTCATTAAACC
1 ATAAAAGTTTAGGGGCTTATTTGACGGTTCAATGTAAGTTCAAGGGCCTTTTCGCTCATTAAACC
1850 ATAAAAGTTTAGGGGCTTATTTGACGGTTCAATGTAAGTTCAAGGGCCTTTTCGCTCATTAAACC
1 ATAAAAGTTTAGGGGCTTATTTGACGGTTCAATGTAAGTTCAAGGGCCTTTTCGCTCATTAAACC
1915 ATAAAAGT
1 ATAAAAGT
1923 GGTTATTTTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 73 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (65 bp):
ATAAAAGTTTAGGGGCTTATTTGACGGTTCAATGTAAGTTCAAGGGCCTTTTCGCTCATTAAACC
Found at i:3195 original size:13 final size:13
Alignment explanation
Indices: 3177--3233 Score: 66
Period size: 12 Copynumber: 4.5 Consensus size: 13
3167 GATATTGACA
3177 GATATATCGAATG
1 GATATATCGAATG
*
3190 GATATATTGACA--
1 GATATATCGA-ATG
3202 GATATATCGAATG
1 GATATATCGAATG
*
3215 GATATATCG-ACG
1 GATATATCGAATG
3227 GATATAT
1 GATATAT
3234 TGATATATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 1 0.03
12 18 0.47
13 18 0.47
14 1 0.03
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (13 bp):
GATATATCGAATG
Found at i:3199 original size:25 final size:25
Alignment explanation
Indices: 3168--3233 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
3158 TTTAATCCAG
3168 ATATTGACAGATATATCGAATGGAT
1 ATATTGACAGATATATCGAATGGAT
3193 ATATTGACAGATATATCGAATGGAT
1 ATATTGACAGATATATCGAATGGAT
* *
3218 ATATCGACGGATATAT
1 ATATTGACAGATATAT
3234 TGATATATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (25 bp):
ATATTGACAGATATATCGAATGGAT
Found at i:3207 original size:12 final size:12
Alignment explanation
Indices: 3165--3233 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 12
3155 GGGTTTAATC
3165 CAGATAT-T-GA
1 CAGATATATCGA
3175 CAGATATATCGA
1 CAGATATATCGA
*
3187 -ATGGATATATTGA
1 CA--GATATATCGA
3200 CAGATATATCGA
1 CAGATATATCGA
3212 -ATGGATATATCGA
1 CA--GATATATCGA
*
3225 CGGATATAT
1 CAGATATAT
3234 TGATATATTG
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
10 7 0.15
11 3 0.06
12 18 0.38
13 19 0.40
14 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.30
Consensus pattern (12 bp):
CAGATATATCGA
Found at i:9671 original size:15 final size:15
Alignment explanation
Indices: 9651--9708 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 15
9641 GCCAAATCAG
9651 ATATTTTATT-AAAAA
1 ATATTTT-TTCAAAAA
9666 ATATTTTTTCAAAAA
1 ATATTTTTTCAAAAA
9681 ATAAATTTTTTACTAAAAGA
1 AT--ATTTTTT-C-AAAA-A
9701 ATATTTTT
1 ATATTTTT
9709 AACATTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.05
15 14 0.38
17 7 0.19
18 7 0.19
19 4 0.11
20 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATTTTTTCAAAAA
Found at i:9681 original size:17 final size:18
Alignment explanation
Indices: 9661--9708 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
9651 ATATTTTATT
9661 AAAAAATATTTTTT-CAA
1 AAAAAATATTTTTTACAA
*
9678 AAAATAA-ATTTTTTACTA
1 AAAA-AATATTTTTTACAA
*
9696 AAAGAATATTTTT
1 AAAAAATATTTTT
9709 AACATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAAAATATTTTTTACAA
Found at i:10328 original size:36 final size:37
Alignment explanation
Indices: 10254--10347 Score: 154
Period size: 36 Copynumber: 2.6 Consensus size: 37
10244 AAAATGCTGG
10254 CGCAGTAAGGAGAGCTCTGCGGTAAATAGGGTGCTAT
1 CGCAGTAAGGAGAGCTCTGCGGTAAATAGGGTGCTAT
* * *
10291 CGTAGTAAGAAGAGCTTTGCGGTAAA-AGGGTGCTAT
1 CGCAGTAAGGAGAGCTCTGCGGTAAATAGGGTGCTAT
10327 CGCAGTAAGGAGAGCTCTGCG
1 CGCAGTAAGGAGAGCTCTGCG
10348 ATGAAGAGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 28 0.55
37 23 0.45
ACGTcount: A:0.28, C:0.16, G:0.35, T:0.21
Consensus pattern (37 bp):
CGCAGTAAGGAGAGCTCTGCGGTAAATAGGGTGCTAT
Found at i:11902 original size:19 final size:20
Alignment explanation
Indices: 11858--11896 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11848 GGGAAAAGAG
*
11858 ATGTATTAGGCCTCTTTTTC
1 ATGTATTAGGCCTATTTTTC
*
11878 ATGTATTGGGCCTATTTTT
1 ATGTATTAGGCCTATTTTT
11897 GTGTATGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
ATGTATTAGGCCTATTTTTC
Found at i:20978 original size:5 final size:5
Alignment explanation
Indices: 20968--21001 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
20958 GATACTGTAG
20968 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
21002 GCCAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
ATTTT
Done.