Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005006.1 Corchorus capsularis cultivar CVL-1 contig05024, 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: 33255
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4816 original size:17 final size:18
Alignment explanation
Indices: 4775--4818 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
4765 TTCAGAGTGT
* *
4775 ATGAAGAATGATGAAATAG
1 ATGAAG-ATGAGGAAACAG
4794 ATGAAGATGAGGAAACA-
1 ATGAAGATGAGGAAACAG
4811 ATGAAGAT
1 ATGAAGAT
4819 CATTAGCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 9 0.39
19 6 0.26
ACGTcount: A:0.52, C:0.02, G:0.27, T:0.18
Consensus pattern (18 bp):
ATGAAGATGAGGAAACAG
Found at i:7144 original size:1 final size:1
Alignment explanation
Indices: 7138--7172 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
7128 TGCGCTACAT
7138 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7173 CTTTGTAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10223 original size:3 final size:3
Alignment explanation
Indices: 10215--10239 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10205 TGTGCTATAC
10215 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
10240 TTCCTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11065 original size:52 final size:52
Alignment explanation
Indices: 10993--11096 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
10983 ATCCCTTTTG
10993 TTCCTTTCATTTCTTCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCT
1 TTCCTTTCATTTCTTCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCT
11045 TTCCTTTCATTTCTTCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCT
1 TTCCTTTCATTTCTTCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCT
11097 CTCCATATAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (52 bp):
TTCCTTTCATTTCTTCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCT
Found at i:11117 original size:52 final size:52
Alignment explanation
Indices: 11007--11118 Score: 156
Period size: 52 Copynumber: 2.2 Consensus size: 52
10997 TTTCATTTCT
* * * *
11007 TCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCTTTCCTTTCATTTCT
1 TCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCTCTCCTTACAGTTCA
11059 TCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCTCTCCATATACAGTT-A
1 TCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCTCTCC-T-TACAGTTCA
11112 T-CTTCCA
1 TCCTTCCA
11119 TCGATCTTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
52 47 0.87
53 2 0.04
54 5 0.09
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (52 bp):
TCCTTCCAAGAAACCACTTTCAATGGAGTCTGGATCCTCTCCTTACAGTTCA
Found at i:12169 original size:27 final size:27
Alignment explanation
Indices: 12139--12192 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
12129 ATTTGGTTTG
12139 GGCCCTCTTTATGAGAAGCGGCCAACT
1 GGCCCTCTTTATGAGAAGCGGCCAACT
* * * *
12166 GGCCCTGTTTGTGAGATGTGGCCAACT
1 GGCCCTCTTTATGAGAAGCGGCCAACT
12193 AATGCTGTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (27 bp):
GGCCCTCTTTATGAGAAGCGGCCAACT
Found at i:26150 original size:17 final size:17
Alignment explanation
Indices: 26128--26182 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
26118 ACTGAAAATG
26128 GCAAAAAGATACTATAA
1 GCAAAAAGATACTATAA
* * *
26145 GCAAAACTGA-A-AAT-G
1 GCAAAA-AGATACTATAA
26160 GCAAAAAGATACTATAA
1 GCAAAAAGATACTATAA
26177 GCAAAA
1 GCAAAA
26183 CAGTTAGCAG
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 2 0.07
15 7 0.25
16 4 0.14
17 13 0.46
18 2 0.07
ACGTcount: A:0.58, C:0.13, G:0.15, T:0.15
Consensus pattern (17 bp):
GCAAAAAGATACTATAA
Found at i:26154 original size:32 final size:32
Alignment explanation
Indices: 26118--26183 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
26108 GGAGCCGGTT
26118 ACTGAAAATGGCAAAAAGATACTATAAGCAAA
1 ACTGAAAATGGCAAAAAGATACTATAAGCAAA
26150 ACTGAAAATGGCAAAAAGATACTATAAGCAAA
1 ACTGAAAATGGCAAAAAGATACTATAAGCAAA
26182 AC
1 AC
26184 AGTTAGCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.56, C:0.14, G:0.15, T:0.15
Consensus pattern (32 bp):
ACTGAAAATGGCAAAAAGATACTATAAGCAAA
Found at i:26576 original size:15 final size:15
Alignment explanation
Indices: 26556--26585 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
26546 GGTTTCTTTC
26556 AAAAAGATGGAAAAA
1 AAAAAGATGGAAAAA
26571 AAAAAGATGGAAAAA
1 AAAAAGATGGAAAAA
26586 CGGACCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
AAAAAGATGGAAAAA
Found at i:30875 original size:15 final size:14
Alignment explanation
Indices: 30857--30910 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
30847 ATGGAAATCC
30857 TGGATATGGATAGTG
1 TGGATATGGATA-TG
30872 TGGATATGGATATTG
1 TGGATATGGATA-TG
* *
30887 TGGAAATGGATCATA
1 TGGATATGGAT-ATG
30902 TGGATATGG
1 TGGATATGG
30911 GGGAATATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 33 0.97
16 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.35, T:0.33
Consensus pattern (14 bp):
TGGATATGGATATG
Found at i:30915 original size:24 final size:25
Alignment explanation
Indices: 30875--30921 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
30865 GATAGTGTGG
* *
30875 ATATGGATATTGTGGAA-ATGGATC
1 ATATGGATATGGGGGAATATGGATC
30899 ATATGGATATGGGGGAATATGGA
1 ATATGGATATGGGGGAATATGGA
30922 AGTTATTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.34, C:0.02, G:0.34, T:0.30
Consensus pattern (25 bp):
ATATGGATATGGGGGAATATGGATC
Done.