Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019352.1 Corchorus olitorius cultivar O-4 contig19385, 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: 18669
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:36 original size:16 final size:16
Alignment explanation
Indices: 15--54 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5 TGGTATGCTG
15 ATGATGATGAAGGAAA
1 ATGATGATGAAGGAAA
* *
31 ATGATGATGAATGATA
1 ATGATGATGAAGGAAA
47 ATGATGAT
1 ATGATGAT
55 CATGTATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (16 bp):
ATGATGATGAAGGAAA
Found at i:320 original size:35 final size:36
Alignment explanation
Indices: 275--355 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 36
265 AGGCCCAAGC
275 GGCCCTAGCGCCCAGGCC-AG-GCGCGGGCCAGCGCAT
1 GGCCC-AGCGCCCAGGCCTAGTGCGCGGGCCAGC-CAT
* *
311 GGCCCAGCGCCCAGGCCTGGTGTGCGGGCCAGCCAT
1 GGCCCAGCGCCCAGGCCTAGTGCGCGGGCCAGCCAT
347 GG-CCAGCGC
1 GGCCCAGCGC
356 TCAAGCTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
35 19 0.46
36 11 0.27
37 11 0.27
ACGTcount: A:0.12, C:0.41, G:0.40, T:0.07
Consensus pattern (36 bp):
GGCCCAGCGCCCAGGCCTAGTGCGCGGGCCAGCCAT
Found at i:1298 original size:28 final size:29
Alignment explanation
Indices: 1240--1303 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
1230 CTTAGGACGT
* * *
1240 TAAAATTA-CATATTTGCCCTTGGTCGGC
1 TAAAATTACCATATTTACCCCTGGTCGAC
*
1268 TAAAATTACCAT-TTTACCCCTGGTTGAC
1 TAAAATTACCATATTTACCCCTGGTCGAC
1296 T-AAATTAC
1 TAAAATTAC
1304 AGTTCTGCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 7 0.23
28 21 0.68
29 3 0.10
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (29 bp):
TAAAATTACCATATTTACCCCTGGTCGAC
Found at i:1742 original size:12 final size:12
Alignment explanation
Indices: 1691--1747 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
1681 CCCGTTGAGG
*
1691 AAATGTTTTATT
1 AAATGTTTTAAT
*
1703 ACA-GTTTTACAT
1 AAATGTTTTA-AT
*
1715 AAATGATTTTTA-
1 AAATG-TTTTAAT
1727 AAATGTTTTAAT
1 AAATGTTTTAAT
1739 AAATGTTTT
1 AAATGTTTT
1748 GGGTGCATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 11 0.31
12 19 0.53
13 2 0.06
14 4 0.11
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (12 bp):
AAATGTTTTAAT
Found at i:2809 original size:25 final size:24
Alignment explanation
Indices: 2773--2819 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
2763 AATACTTACA
2773 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
2797 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
2820 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:3700 original size:36 final size:36
Alignment explanation
Indices: 3646--3715 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
3636 GAGATTTTGG
* *
3646 AGAAATATAATAATCAAAATTACAAAAGATGTAATA
1 AGAAATATAATAACCAAAATCACAAAAGATGTAATA
* *
3682 AGAAATTTGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATAATAACCAAAATCACAAAAGATGTAA
3716 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.23
Consensus pattern (36 bp):
AGAAATATAATAACCAAAATCACAAAAGATGTAATA
Found at i:5089 original size:59 final size:58
Alignment explanation
Indices: 4977--5092 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 58
4967 ATAGCATCAT
*
4977 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATAA
* * *
5035 GCCTTGGTCCGAAAACGTCTTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
1 GCCTCGGTCCGAAAACGTC--TTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATA
5093 TTTGATTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 17 0.33
59 19 0.37
60 16 0.31
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (58 bp):
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATAA
Found at i:9486 original size:11 final size:12
Alignment explanation
Indices: 9466--9490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9456 TGGCAGCTAG
9466 TTTTGTTTTTTT
1 TTTTGTTTTTTT
9478 TTTTGTTTTTTT
1 TTTTGTTTTTTT
9490 T
1 T
9491 AAAAATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:15666 original size:1 final size:1
Alignment explanation
Indices: 15655--15697 Score: 68
Period size: 1 Copynumber: 43.0 Consensus size: 1
15645 GCTTTGATGC
* *
15655 TTTTTTATTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15698 GCGCGGAGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.02, C:0.02, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Done.