Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018052.1 Corchorus olitorius cultivar O-4 contig18085, 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: 42797
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:42 original size:27 final size:27
Alignment explanation
Indices: 1--58 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
1 ATTTGCACATCCAGGGGCATTTTAGTC
1 ATTTGCACATCCAGGGGCATTTTAGTC
* *
28 ATTTGCACATTCAGGGGCATTTTGGTC
1 ATTTGCACATCCAGGGGCATTTTAGTC
55 ATTT
1 ATTT
59 TAAGTTCAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (27 bp):
ATTTGCACATCCAGGGGCATTTTAGTC
Found at i:78 original size:26 final size:26
Alignment explanation
Indices: 37--88 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
27 CATTTGCACA
**
37 TTCAGGGGCATTTTGGTCATTTTAAG
1 TTCAGGGGCACGTTGGTCATTTTAAG
63 TTCAGGGGCACGTTGGTCATTTTAAG
1 TTCAGGGGCACGTTGGTCATTTTAAG
89 CCCACTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.38
Consensus pattern (26 bp):
TTCAGGGGCACGTTGGTCATTTTAAG
Found at i:2605 original size:25 final size:25
Alignment explanation
Indices: 2575--2623 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2565 GACTTTTAAA
* *
2575 TTCCTTGGTGCACTTGGGCCTTTTG
1 TTCCTTGATGCACTTGGACCTTTTG
* *
2600 TTCCTTTATGCATTTGGACCTTTT
1 TTCCTTGATGCACTTGGACCTTTT
2624 ATTTATGTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.08, C:0.22, G:0.20, T:0.49
Consensus pattern (25 bp):
TTCCTTGATGCACTTGGACCTTTTG
Found at i:27747 original size:19 final size:19
Alignment explanation
Indices: 27723--27761 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
27713 AAGTGGACTT
27723 TAAATGACCAAAACGCCCC
1 TAAATGACCAAAACGCCCC
*
27742 TAAATGACCAAAATGCCCC
1 TAAATGACCAAAACGCCCC
27761 T
1 T
27762 GAACATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.33, G:0.10, T:0.15
Consensus pattern (19 bp):
TAAATGACCAAAACGCCCC
Found at i:27837 original size:28 final size:27
Alignment explanation
Indices: 27743--27843 Score: 157
Period size: 27 Copynumber: 3.7 Consensus size: 27
27733 AAACGCCCCT
27743 AAATGACCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
27770 AAATGACCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
*** *
27797 AAATGACCAAAATGCCCCTGGATTTTGA
1 AAATGACCAAAATGCCCCT-GAACATGC
27825 AAATGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
27844 AGTTGATCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
27 46 0.67
28 23 0.33
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:37663 original size:16 final size:15
Alignment explanation
Indices: 37625--37666 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
37615 ACAGAGATTG
*
37625 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
37640 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
37655 ACTAGAAAACAA
1 AC-AGAAAACAA
37667 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:40455 original size:14 final size:15
Alignment explanation
Indices: 40436--40465 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40426 CAATCAAAGC
40436 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
40450 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
40465 A
1 A
40466 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:40848 original size:21 final size:21
Alignment explanation
Indices: 40822--40868 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
40812 GGAATGGCGA
**
40822 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
40843 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
40864 TGGCA
1 TGGCA
40869 TGGTGAATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:41148 original size:21 final size:21
Alignment explanation
Indices: 41111--41150 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41101 CCGGGCATGA
*
41111 GGCGCGGAGGGTAGCACGGAT
1 GGCGCGGAGGGAAGCACGGAT
41132 GGCGCGGA-GGAAGGCACGG
1 GGCGCGGAGGGAA-GCACGG
41151 CTAGCCAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.20, C:0.20, G:0.55, T:0.05
Consensus pattern (21 bp):
GGCGCGGAGGGAAGCACGGAT
Done.