Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023918.1 Corchorus olitorius cultivar O-4 contig23951, 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: 21828
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2758 original size:27 final size:25
Alignment explanation
Indices: 2700--2774 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 25
2690 TAGGGTCACC
*
2700 TAGGGGCATTTTGGTCATTTTTGCACA
1 TAGGGGCATTTTGGTCA--TTTGCAAA
2727 TAGGGGCATTTTGGTCATTTGCATAA
1 TAGGGGCATTTTGGTCATTTGCA-AA
*
2753 TAAGGGGGAATTTTGGTCATTT
1 T-A-GGGGCATTTTGGTCATTT
2775 AAAGTTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
25 6 0.14
26 2 0.05
27 18 0.42
28 17 0.40
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40
Consensus pattern (25 bp):
TAGGGGCATTTTGGTCATTTGCAAA
Found at i:3024 original size:34 final size:34
Alignment explanation
Indices: 2986--3054 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
2976 TCCCTTGTTA
2986 TTAAGTTTGTCCAATTTAGTTGATCGCATTCATT
1 TTAAGTTTGTCCAATTTAGTTGATCGCATTCATT
*
3020 TTAAGTTTGTCCAATTTAGTTGATCTCATTCATT
1 TTAAGTTTGTCCAATTTAGTTGATCGCATTCATT
3054 T
1 T
3055 CCCATTAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.49
Consensus pattern (34 bp):
TTAAGTTTGTCCAATTTAGTTGATCGCATTCATT
Found at i:7018 original size:17 final size:18
Alignment explanation
Indices: 6998--7033 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6988 AAAGGGTAAT
6998 TAAAAA-AAATGTTTTCA
1 TAAAAAGAAATGTTTTCA
*
7015 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAATGTTTTCA
7033 T
1 T
7034 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
TAAAAAGAAATGTTTTCA
Found at i:7915 original size:19 final size:18
Alignment explanation
Indices: 7891--7926 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7881 TGAAGATTTA
7891 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
7910 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
7927 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:11886 original size:11 final size:11
Alignment explanation
Indices: 11870--11895 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11860 CTCATCTCGA
11870 ATTCTCCCTGC
1 ATTCTCCCTGC
11881 ATTCTCCCTGC
1 ATTCTCCCTGC
11892 ATTC
1 ATTC
11896 CTTTGTGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.12, C:0.42, G:0.08, T:0.38
Consensus pattern (11 bp):
ATTCTCCCTGC
Found at i:18291 original size:119 final size:119
Alignment explanation
Indices: 18048--18398 Score: 454
Period size: 119 Copynumber: 2.9 Consensus size: 119
18038 GAGTTCAAGG
* ** * * * *
18048 TTAAGTAACCTAAAACTTAATATTTAATTAAGCAATTACAATCTTTAGTTGATAAATGTTGGTAA
1 TTAAGTAACCTAAAATTTAAGGTTTAATTAAGTAATTACAACCTTTAGTTAATAAAT-TTGGGAA
* * *
18113 TTTTCATAATTTATGTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGG
65 TTTTCATAATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGA
18168 TTAAGTAACCTAAAATTTAAGGTTTAATTAAGTAATTACAACCTTTAGTTAATAAATTTGGGAAT
1 TTAAGTAACCTAAAATTTAAGGTTTAATTAAGTAATTACAACCTTTAGTTAATAAATTTGGGAAT
*
18233 TTTCATAATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTGAAATTAAGA
66 TTTCATAATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGA
* * * * * *
18287 TTAAGTAACCCAAACCTTT-AGGTTTAATTAAGTGATTAAAACCTATAATTAATAAACTTTGGGA
1 TTAAGTAACCTAAA-ATTTAAGGTTTAATTAAGTAATTACAACCTTTAGTTAATAAA-TTTGGG-
* * * * *
18351 AACTTTCATAATTCTTTTAAGA-TTAAATAAATCATTAATTGAATTTGA
63 AATTTTCATAATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTGA
18399 TAAGTTTGGA
Statistics
Matches: 206, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
119 103 0.50
120 83 0.40
121 20 0.10
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.40
Consensus pattern (119 bp):
TTAAGTAACCTAAAATTTAAGGTTTAATTAAGTAATTACAACCTTTAGTTAATAAATTTGGGAAT
TTTCATAATTCATTTAAGATTTAAGTGAATCTTTAATTGAATTTGAAACTAAGA
Found at i:19564 original size:44 final size:44
Alignment explanation
Indices: 19499--19624 Score: 225
Period size: 44 Copynumber: 2.9 Consensus size: 44
19489 GGAATCGAGA
* *
19499 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATGAAAG
1 TTATCAAAATTTTATAATGTGGTTATCAAAATTTCATATGAAAG
19543 TTATCAAAATTTTATAATGTGGTTATCAAAATTTCATATGAAAG
1 TTATCAAAATTTTATAATGTGGTTATCAAAATTTCATATGAAAG
*
19587 TGATCAAAATTTTATAATGTGGTTATCAAAATTTCATA
1 TTATCAAAATTTTATAATGTGGTTATCAAAATTTCATA
19625 AGGATATTTA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 79 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTTTATAATGTGGTTATCAAAATTTCATATGAAAG
Found at i:19625 original size:22 final size:22
Alignment explanation
Indices: 19499--19625 Score: 150
Period size: 22 Copynumber: 5.8 Consensus size: 22
19489 GGAATCGAGA
*
19499 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAATGTGG
**
19521 TTATCAAAATTTCAT-ATGAAAG
1 TTATCAAAATTTCATAATG-TGG
*
19543 TTATCAAAATTTTATAATGTGG
1 TTATCAAAATTTCATAATGTGG
**
19565 TTATCAAAATTTCAT-ATGAAAG
1 TTATCAAAATTTCATAATG-TGG
* *
19587 TGATCAAAATTTTATAATGTGG
1 TTATCAAAATTTCATAATGTGG
19609 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
19626 GGATATTTAA
Statistics
Matches: 86, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.06
22 75 0.87
23 6 0.07
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGTGG
Done.