Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014792.1 Corchorus olitorius cultivar O-4 contig14825, 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: 23737
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:200 original size:31 final size:29
Alignment explanation
Indices: 134--213 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
124 CTCATTTTTG
* * *
134 AAACGTAAGGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
163 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
194 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
214 GGTATTTAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:1531 original size:15 final size:16
Alignment explanation
Indices: 1496--1534 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1486 AACCGAAAAC
1496 GACCCAACCCAGAATT
1 GACCCAACCCAGAATT
1512 GACCCGAACCCA-AA-T
1 GACCC-AACCCAGAATT
1527 GACCCAAC
1 GACCCAAC
1535 ATTTGAGCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 6 0.27
16 7 0.32
17 6 0.27
ACGTcount: A:0.38, C:0.41, G:0.13, T:0.08
Consensus pattern (16 bp):
GACCCAACCCAGAATT
Found at i:8365 original size:20 final size:21
Alignment explanation
Indices: 8340--8379 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
8330 ATTTTCTTCT
*
8340 TCTCCATA-TTCTATTATCTC
1 TCTCCATACTTCAATTATCTC
8360 TCTCCATACTTCAATTATCT
1 TCTCCATACTTCAATTATCT
8380 ACTCCCTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (21 bp):
TCTCCATACTTCAATTATCTC
Found at i:8384 original size:20 final size:20
Alignment explanation
Indices: 8341--8384 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
8331 TTTTCTTCTT
* *
8341 CTCCATATTCTATTATCTCT
1 CTCCATATTCAATTATCTCA
8361 CTCCATACTTCAATTATCT-A
1 CTCCATA-TTCAATTATCTCA
8381 CTCC
1 CTCC
8385 CTTGCTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (20 bp):
CTCCATATTCAATTATCTCA
Found at i:10402 original size:21 final size:22
Alignment explanation
Indices: 10361--10403 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
10351 CTGAAAAAGG
* *
10361 AGAAAACCCTAGTCTCTTCAAA
1 AGAAAACCCTAGCCTCCTCAAA
10383 AGAAAA-CCTAGCCTCCTCAAA
1 AGAAAACCCTAGCCTCCTCAAA
10404 GATTCCAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (22 bp):
AGAAAACCCTAGCCTCCTCAAA
Found at i:13719 original size:18 final size:18
Alignment explanation
Indices: 13698--13732 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13688 AAAATTACCT
*
13698 TGAGTCTAAACTAGAAAA
1 TGAGACTAAACTAGAAAA
*
13716 TGAGACTAAATTAGAAA
1 TGAGACTAAACTAGAAA
13733 GAAAAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAGACTAAACTAGAAAA
Found at i:15989 original size:46 final size:46
Alignment explanation
Indices: 15922--16019 Score: 187
Period size: 46 Copynumber: 2.1 Consensus size: 46
15912 AGCACATCCA
*
15922 GCCAAGAAGCCGATGCTGAGGTAGAGGGCGATGAATAATCAACCCC
1 GCCAAGAAACCGATGCTGAGGTAGAGGGCGATGAATAATCAACCCC
15968 GCCAAGAAACCGATGCTGAGGTAGAGGGCGATGAATAATCAACCCC
1 GCCAAGAAACCGATGCTGAGGTAGAGGGCGATGAATAATCAACCCC
16014 GCCAAG
1 GCCAAG
16020 TAGCTGCTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.34, C:0.24, G:0.30, T:0.12
Consensus pattern (46 bp):
GCCAAGAAACCGATGCTGAGGTAGAGGGCGATGAATAATCAACCCC
Found at i:16179 original size:64 final size:64
Alignment explanation
Indices: 16074--16209 Score: 229
Period size: 64 Copynumber: 2.1 Consensus size: 64
16064 TCTGGACACG
*
16074 ATTGGGAGCCATGAACGGTGGATTGCTTTGAATGTGTTAGCCAAGTACGTG-GAAGAAATCATGA
1 ATTGGGAGCCATGAACGGTGGATTGCTTTGAATGTGTTAGCCAAGTACG-GAGAAAAAATCATGA
* *
16138 ATTTGGAGCCATGAATGGTGGATTGCTTTGAATGTGTTAGCCAAGTACGGAGAAAAAATCATGA
1 ATTGGGAGCCATGAACGGTGGATTGCTTTGAATGTGTTAGCCAAGTACGGAGAAAAAATCATGA
16202 ATTGGGAG
1 ATTGGGAG
16210 TCATCATCAC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 1 0.01
64 66 0.99
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (64 bp):
ATTGGGAGCCATGAACGGTGGATTGCTTTGAATGTGTTAGCCAAGTACGGAGAAAAAATCATGA
Found at i:21933 original size:68 final size:67
Alignment explanation
Indices: 21824--21958 Score: 243
Period size: 68 Copynumber: 2.0 Consensus size: 67
21814 TATGGTGTTT
21824 GGAATTGAATTTGAAGTGAGAAAAAATGAAATAAAATTAAGATTGGAGTTGTTTTGGCATTGCCG
1 GGAATTGAATTTGAAGTGAGAAAAAATGAAATAAAATTAAGATTGGAGTTG-TTTGGCATTGCCG
21889 GAA
65 GAA
* *
21892 GGAATTGAATTTGAAGTGAGAAAAAATGAAATACAATTAAGATTGGAGTTGTTTGGCCTTGCCGG
1 GGAATTGAATTTGAAGTGAGAAAAAATGAAATAAAATTAAGATTGGAGTTGTTTGGCATTGCCGG
21957 AA
66 AA
21959 TCTGGAAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 15 0.23
68 50 0.77
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.29
Consensus pattern (67 bp):
GGAATTGAATTTGAAGTGAGAAAAAATGAAATAAAATTAAGATTGGAGTTGTTTGGCATTGCCGG
AA
Found at i:22077 original size:9 final size:8
Alignment explanation
Indices: 22046--22076 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
22036 GGCCTGGCCC
*
22046 AAAAGAAG
1 AAAAAAAG
22054 AAAAAAAG
1 AAAAAAAG
22062 AAAAAAAG
1 AAAAAAAG
22070 AAAAAAA
1 AAAAAAA
22077 AAAGGAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:22091 original size:19 final size:19
Alignment explanation
Indices: 22046--22112 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
22036 GGCCTGGCCC
*
22046 AAAAGAAGAAAAAAAGAAA
1 AAAAGAAAAAAAAAAGAAA
*
22065 AAAAGAAAAAAAAAAGGAA
1 AAAAGAAAAAAAAAAGAAA
* *
22084 ACAGGAAAAGGAAATAAAGAAA
1 AAAAGAAAA--AAA-AAAGAAA
*
22106 ATAAGAA
1 AAAAGAA
22113 TTTTGGAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 24 0.63
21 3 0.08
22 11 0.29
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAAGAAAAAAAAAAGAAA
Found at i:23341 original size:13 final size:12
Alignment explanation
Indices: 23323--23367 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
23313 ATTTTATTAC
23323 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
23336 TGTTTTATAAAT
1 TGTTTTATAAAT
*
23348 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
23362 TGTTTT
1 TGTTTT
23368 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Done.