Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014399.1 Corchorus olitorius cultivar O-4 contig14432, 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: 43798
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1719 original size:24 final size:25
Alignment explanation
Indices: 1673--1721 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1663 ATTGGAGTAT
*
1673 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
1698 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
1722 ATGTTCACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:3178 original size:13 final size:13
Alignment explanation
Indices: 3160--3197 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3150 AAACATCTTC
3160 TAAACATAATTTG
1 TAAACATAATTTG
3173 TAAACATCAA-TTG
1 TAAACAT-AATTTG
*
3186 TAAATATAATTT
1 TAAACATAATTT
3198 CTTAAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 2 0.09
13 18 0.82
14 2 0.09
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (13 bp):
TAAACATAATTTG
Found at i:4681 original size:40 final size:40
Alignment explanation
Indices: 4626--4706 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
4616 AATTAATTAC
* *
4626 TGTTGATGCTTCAAAGGACTTTAAAAGCTAATTGACCGGG
1 TGTTGATGCCTCAAAGGACTTTAAAAGCCAATTGACCGGG
4666 TGTTGATGCCTCAAAGGACTTTAAAAGCCAATTGACCGGG
1 TGTTGATGCCTCAAAGGACTTTAAAAGCCAATTGACCGGG
4706 T
1 T
4707 ATCACTGCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (40 bp):
TGTTGATGCCTCAAAGGACTTTAAAAGCCAATTGACCGGG
Found at i:5884 original size:26 final size:26
Alignment explanation
Indices: 5854--5905 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5844 GCTCTGAAAA
5854 ACATTCTGTTGAACTCATTTCTAGTT
1 ACATTCTGTTGAACTCATTTCTAGTT
5880 ACATTCTGTTGAACTCATTTCTAGTT
1 ACATTCTGTTGAACTCATTTCTAGTT
5906 TATTATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (26 bp):
ACATTCTGTTGAACTCATTTCTAGTT
Found at i:11713 original size:16 final size:16
Alignment explanation
Indices: 11692--11731 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
11682 AGAGATTAAC
11692 TTACACCCGGTGTAAG
1 TTACACCCGGTGTAAG
11708 TTACACCCGGTGTAAG
1 TTACACCCGGTGTAAG
11724 TTACACCC
1 TTACACCC
11732 TTTCTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (16 bp):
TTACACCCGGTGTAAG
Found at i:27885 original size:65 final size:65
Alignment explanation
Indices: 27781--27910 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
27771 GCTTGCTATT
* * *
27781 GATTCCAACTTTCTGCACTAGGCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCAAGGGTTGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCAAGGGTAGGAC
*
27846 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCAAGGGTAGGAC
27911 CAGTTTTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.32, T:0.20
Consensus pattern (65 bp):
GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCAAGGGTAGGAC
Found at i:36544 original size:65 final size:65
Alignment explanation
Indices: 36435--36564 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
36425 GGAAAAACTG
* * * *
36435 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCATGCCTGGGCTAGTGCAGAAAGTTTGAATC
1 GTCCAACCCATACATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
*
36500 GTCCAACCCATACATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGTAGAAAGTTGGAATC
1 GTCCAACCCATACATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
36565 AATAGCAAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (65 bp):
GTCCAACCCATACATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
Found at i:36780 original size:21 final size:21
Alignment explanation
Indices: 36754--36795 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
36744 GCATCTTAGG
*
36754 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
36775 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
36796 TTCTTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:36930 original size:30 final size:30
Alignment explanation
Indices: 36894--36952 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
36884 TTGATGTCCT
36894 TGATAAGCCCTT-GGCGCATCATTCCCTCCA
1 TGATAAG-CCTTGGGCGCATCATTCCCTCCA
36924 TGATAAGCCTTGGGCGCATCATTCCCTCC
1 TGATAAGCCTTGGGCGCATCATTCCCTCC
36953 CCCTTGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.27
Consensus pattern (30 bp):
TGATAAGCCTTGGGCGCATCATTCCCTCCA
Found at i:37343 original size:33 final size:33
Alignment explanation
Indices: 37306--37410 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
37296 ATTTGCATCC
*
37306 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTATCATCACAAACAACACCT
* * *
37339 AAAACAGATTTAGTGTCTTCACAAACAACACTT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
** * * *
37372 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
37405 AAAACA
1 AAAACA
37411 CTCTTTGCAA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
32 4 0.07
33 54 0.93
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.27
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACCT
Done.