Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023279.1 Corchorus olitorius cultivar O-4 contig23312, 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: 43301
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1387 original size:30 final size:29
Alignment explanation
Indices: 1322--1389 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1312 GCGTTTGGAC
*
1322 GTTTTGCCCCTGAAATTCAATTTCGTATA
1 GTTTTGCCCCTGAAATTCAATTTCGGATA
* *
1351 -TTTTGCCTCCTGAACTTCAATTTTGGGA-A
1 GTTTTGCC-CCTGAAATTCAA-TTTCGGATA
1380 GTTTTGCCCC
1 GTTTTGCCCC
1390 CTCAACCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 7 0.21
29 14 0.42
30 12 0.36
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (29 bp):
GTTTTGCCCCTGAAATTCAATTTCGGATA
Found at i:7678 original size:19 final size:17
Alignment explanation
Indices: 7648--7691 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
7638 GGAGGAGATA
* * *
7648 AGAACAGAGAAGAAGGG
1 AGAAGAGAGAGGAAGAG
7665 A-AAGAGAGAGGAAGAG
1 AGAAGAGAGAGGAAGAG
7681 AGAAGAGAGAG
1 AGAAGAGAGAG
7692 AATTAGTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.55, C:0.02, G:0.43, T:0.00
Consensus pattern (17 bp):
AGAAGAGAGAGGAAGAG
Found at i:19127 original size:33 final size:33
Alignment explanation
Indices: 19084--19162 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
19074 GTTTTAGATT
* *
19084 TTGTTAGTGATGATACTAAACCTAATTTAAGTG
1 TTGTTTGTGATGACACTAAACCTAATTTAAGTG
** ** *
19117 TTGTTTGTGATGACACTAAATTTGTTTTAGGTG
1 TTGTTTGTGATGACACTAAACCTAATTTAAGTG
19150 TTGTTTGTGATGA
1 TTGTTTGTGATGA
19163 AACAAATTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (33 bp):
TTGTTTGTGATGACACTAAACCTAATTTAAGTG
Found at i:19176 original size:33 final size:33
Alignment explanation
Indices: 19109--19210 Score: 111
Period size: 33 Copynumber: 3.1 Consensus size: 33
19099 CTAAACCTAA
* *
19109 TTTAAGTGTTGTTTGTGATGACACTAAATT-TGT
1 TTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGT
19142 TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
1 TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
* **
19175 TTT-GGATGCTAATTGTGATGAAAACAAA-TCTGT
1 TTTAGG-TGTTGTTTGTGATG-AAACAAATTCTGT
19208 TTT
1 TTT
19211 GGTTGATCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
32 7 0.11
33 47 0.77
34 7 0.11
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.45
Consensus pattern (33 bp):
TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
Found at i:29952 original size:29 final size:31
Alignment explanation
Indices: 29919--29981 Score: 103
Period size: 29 Copynumber: 2.1 Consensus size: 31
29909 GCCCTCTGAT
29919 CCTGAACTTCAATTTT-GGACATTTTGCC-C
1 CCTGAACTTCAATTTTGGGACATTTTGCCAC
*
29948 CCTGAACTTCAATTTTGGGACGTTTTGCCAC
1 CCTGAACTTCAATTTTGGGACATTTTGCCAC
29979 CCT
1 CCT
29982 CAGCCTAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 16 0.52
30 11 0.35
31 4 0.13
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.37
Consensus pattern (31 bp):
CCTGAACTTCAATTTTGGGACATTTTGCCAC
Found at i:31645 original size:21 final size:22
Alignment explanation
Indices: 31619--31665 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
31609 AATAATTTTA
31619 AAAAATTGAATTGAATTA-AAT
1 AAAAATTGAATTGAATTAGAAT
* *
31640 AAAAATTGAGTTTAATTAGAAT
1 AAAAATTGAATTGAATTAGAAT
31662 AAAA
1 AAAA
31666 CTGTAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (22 bp):
AAAAATTGAATTGAATTAGAAT
Found at i:32422 original size:117 final size:116
Alignment explanation
Indices: 32262--32496 Score: 332
Period size: 117 Copynumber: 2.0 Consensus size: 116
32252 AATCTACCAC
32262 TATACCCTTATTTTTCTAACATATCTCTAAACTCACATTGTTTAAACTATTATAGTTTTACTCTA
1 TATACCCTTATTTTTCTAACATATCTCTAAACTCACATTGTTTAAACTATTATAGTTTTACTCTA
* * * *
32327 CT-AAAAACTCTATTTTTAAATAA-TAAATCTAAATCTTTATAAATATTTTATT
66 CTAAAAAAATATATTTTT---TAACTAAATCTAAATCCTTACAAATATTTTATT
* * * *
32379 TATACCCTTATTTTTCTAATATATTTCTAAACTGC-CATTGTTTAAACTGTTATAGTTTTAGTCT
1 TATACCCTTATTTTTCTAACATATCTCTAAACT-CACATTGTTTAAACTATTATAGTTTTACTCT
32443 ACTAAAAAAAATATATTTTTTAACTAAATCTAAATCCTTACAAATATTTTATT
65 ACT-AAAAAAATATATTTTTTAACTAAATCTAAATCCTTACAAATATTTTATT
32496 T
1 T
32497 TTACTATTTT
Statistics
Matches: 106, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
116 3 0.03
117 89 0.84
118 1 0.01
119 13 0.12
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.46
Consensus pattern (116 bp):
TATACCCTTATTTTTCTAACATATCTCTAAACTCACATTGTTTAAACTATTATAGTTTTACTCTA
CTAAAAAAATATATTTTTTAACTAAATCTAAATCCTTACAAATATTTTATT
Done.