Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009582.1 Corchorus capsularis cultivar CVL-1 contig09603, 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: 13509
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:2243 original size:14 final size:14
Alignment explanation
Indices: 2193--2243 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
2183 AATTTACTTT
*
2193 ATTAAAAAATTATAA
1 ATTACAAAA-TATAA
* *
2208 TTTACAAATTATAA
1 ATTACAAAATATAA
*
2222 ATGA-AAAATATAA
1 ATTACAAAATATAA
2235 ATTACAAAA
1 ATTACAAAA
2244 ATTAGATTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 11 0.39
14 11 0.39
15 6 0.21
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (14 bp):
ATTACAAAATATAA
Found at i:4923 original size:15 final size:16
Alignment explanation
Indices: 4899--4932 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4889 CTTAGGGACT
4899 AAATTAAAATAA-TTA
1 AAATTAAAATAATTTA
*
4914 AAATTTAAATAATTTA
1 AAATTAAAATAATTTA
4930 AAA
1 AAA
4933 AATGGACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTAAAATAATTTA
Found at i:5049 original size:24 final size:24
Alignment explanation
Indices: 5021--5083 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
5011 TAGAATTATC
*
5021 TATATATTTATTATATGTATGTAT
1 TATATATTTATTATATATATGTAT
5045 TATATATTTATTATATATATGTAT
1 TATATATTTATTATATATATGTAT
*
5069 TATATATTTAATATA
1 TATATATTTATTATA
5084 GGATTAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (24 bp):
TATATATTTATTATATATATGTAT
Found at i:5058 original size:11 final size:11
Alignment explanation
Indices: 5016--5083 Score: 73
Period size: 11 Copynumber: 5.7 Consensus size: 11
5006 CCATATAGAA
5016 TTATCTATATAT
1 TTAT-TATATAT
5028 TTATTATATGTAT
1 TTATTATA--TAT
*
5041 GTATTATATAT
1 TTATTATATAT
5052 TTATTATATAT
1 TTATTATATAT
5063 ATGTATTATATAT
1 -T-TATTATATAT
*
5076 TTAATATA
1 TTATTATA
5084 GGATTAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
11 23 0.47
12 6 0.12
13 20 0.41
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (11 bp):
TTATTATATAT
Found at i:5074 original size:13 final size:13
Alignment explanation
Indices: 5021--5075 Score: 78
Period size: 13 Copynumber: 4.4 Consensus size: 13
5011 TAGAATTATC
*
5021 TATATATTTATTA
1 TATATATGTATTA
*
5034 TATGTATGTATTA
1 TATATATGTATTA
5047 TATAT-T-TATTA
1 TATATATGTATTA
5058 TATATATGTATTA
1 TATATATGTATTA
5071 TATAT
1 TATAT
5076 TTAATATAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 10 0.27
12 2 0.05
13 25 0.68
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (13 bp):
TATATATGTATTA
Found at i:5237 original size:10 final size:10
Alignment explanation
Indices: 5224--5259 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5214 CATTTCTAAC
5224 AACTTCTTCA
1 AACTTCTTCA
*
5234 AACTTGTTCA
1 AACTTCTTCA
*
5244 AACTTGTTCA
1 AACTTCTTCA
5254 AACTTC
1 AACTTC
5260 ATTTCTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (10 bp):
AACTTCTTCA
Found at i:5335 original size:26 final size:26
Alignment explanation
Indices: 5299--5365 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
5289 CTTCATTTTA
5299 TAATCATAAACTAATTAAATACTAAT
1 TAATCATAAACTAATTAAATACTAAT
*
5325 TAATCATAAACTAATTAAATACTGAT
1 TAATCATAAACTAATTAAATACTAAT
*
5351 TAAACATAAACTAAT
1 TAATCATAAACTAAT
5366 AAACTAAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (26 bp):
TAATCATAAACTAATTAAATACTAAT
Found at i:5337 original size:15 final size:15
Alignment explanation
Indices: 5299--5342 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
5289 CTTCATTTTA
5299 TAATCATAAACTAAT
1 TAATCATAAACTAAT
5314 TAA--AT--ACTAAT
1 TAATCATAAACTAAT
5325 TAATCATAAACTAAT
1 TAATCATAAACTAAT
5340 TAA
1 TAA
5343 ATACTGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.36
13 4 0.16
15 12 0.48
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATCATAAACTAAT
Found at i:6201 original size:13 final size:13
Alignment explanation
Indices: 6179--6212 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
6169 AATTTTGTTG
*
6179 TTTTATTATTTAT
1 TTTTAATATTTAT
6192 TTTTAATATTTAT
1 TTTTAATATTTAT
6205 TATTTAAT
1 T-TTTAAT
6213 TTGCAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTAATATTTAT
Found at i:6224 original size:20 final size:20
Alignment explanation
Indices: 6180--6222 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6170 ATTTTGTTGT
**
6180 TTTATTATTTATTTTTAATA
1 TTTATTATTTATTTGCAATA
6200 TTTATTATTTAATTTGCAATA
1 TTTATTATTT-ATTTGCAATA
6221 TT
1 TT
6223 ATCCTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTATTATTTATTTGCAATA
Found at i:6456 original size:22 final size:22
Alignment explanation
Indices: 6414--6458 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
6404 TCGATTCCAT
**
6414 GTCCGAATCACCGGATTGACCG
1 GTCCGAATCACCGGACGGACCG
6436 GTCCG-ATCACCGGACCGGACCG
1 GTCCGAATCACCGGA-CGGACCG
6458 G
1 G
6459 GTTTAATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.20, C:0.36, G:0.31, T:0.13
Consensus pattern (22 bp):
GTCCGAATCACCGGACGGACCG
Found at i:9870 original size:27 final size:27
Alignment explanation
Indices: 9839--9890 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
9829 GCTGCTGGGA
9839 CTTCAAATGGTGGGGATAAGGCTGGAC
1 CTTCAAATGGTGGGGATAAGGCTGGAC
* *
9866 CTTCAAATGTTGGGGATGAGGCTGG
1 CTTCAAATGGTGGGGATAAGGCTGG
9891 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.38, T:0.25
Consensus pattern (27 bp):
CTTCAAATGGTGGGGATAAGGCTGGAC
Found at i:11759 original size:10 final size:10
Alignment explanation
Indices: 11744--11770 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
11734 AACTTCCTGC
11744 AAAATTCCAG
1 AAAATTCCAG
11754 AAAATTCCAG
1 AAAATTCCAG
11764 AAAATTC
1 AAAATTC
11771 TAGAGTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (10 bp):
AAAATTCCAG
Done.