Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020982.1 Corchorus olitorius cultivar O-4 contig21015, 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: 10179
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:241 original size:29 final size:29
Alignment explanation
Indices: 199--391 Score: 188
Period size: 29 Copynumber: 6.3 Consensus size: 29
189 GGAGTAACTG
* * *
199 AAATACCCCTAGATGTGTAAAAATGACTA
1 AAATGCCCCTAGATATGCAAAAATGACTA
* *
228 AAATGCCCCTAGATATGCGAAGATGACTA
1 AAATGCCCCTAGATATGCAAAAATGACTA
*
257 AAATGCCCCTGGATATGCAAAAATGACTA
1 AAATGCCCCTAGATATGCAAAAATGACTA
* *
286 AAATGCCCCTGGATATGCAAAAGTGACTA
1 AAATGCCCCTAGATATGCAAAAATGACTA
* *
315 AAATGTCCCTGGATATGCAAAAGTGCAAAAGTGACTA
1 AAATGCCCCTAGATATGC---A----AAAA-TGACTA
* * *
352 AAATGTCCCCTGGATGTGCAAAAATGACCA
1 AAATG-CCCCTAGATATGCAAAAATGACTA
382 AAATGCCCCT
1 AAATGCCCCT
392 TTAAGTGACC
Statistics
Matches: 141, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
29 100 0.71
30 10 0.07
31 4 0.03
32 1 0.01
35 1 0.01
36 3 0.02
37 11 0.08
38 11 0.08
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (29 bp):
AAATGCCCCTAGATATGCAAAAATGACTA
Found at i:343 original size:37 final size:38
Alignment explanation
Indices: 301--374 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 38
291 CCCCTGGATA
301 TGCAAAAGTGACTAAAATGT-CCCTGGATATGCAAAAG
1 TGCAAAAGTGACTAAAATGTCCCCTGGATATGCAAAAG
*
338 TGCAAAAGTGACTAAAATGTCCCCTGGATGTGCAAAA
1 TGCAAAAGTGACTAAAATGTCCCCTGGATATGCAAAA
375 ATGACCAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 20 0.57
38 15 0.43
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (38 bp):
TGCAAAAGTGACTAAAATGTCCCCTGGATATGCAAAAG
Found at i:4304 original size:13 final size:13
Alignment explanation
Indices: 4288--4312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4278 TTAACCCTTC
4288 TCTTTAGATTTTA
1 TCTTTAGATTTTA
4301 TCTTTAGATTTT
1 TCTTTAGATTTT
4313 GATCATTCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (13 bp):
TCTTTAGATTTTA
Found at i:8785 original size:13 final size:14
Alignment explanation
Indices: 8763--8798 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
8753 TTATTTTAAG
*
8763 AATATAATTATATT
1 AATATAATTATATA
8777 AAT-TAATTATATA
1 AATATAATTATATA
8790 AATATAATT
1 AATATAATT
8799 GTAAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATAATTATATA
Found at i:8991 original size:11 final size:11
Alignment explanation
Indices: 8975--9013 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
8965 GTTTCCTTAA
8975 TCGGGCCGGGC
1 TCGGGCCGGGC
8986 TCGGGCCGGGC
1 TCGGGCCGGGC
8997 TCGGGCCGGGC
1 TCGGGCCGGGC
9008 TCGGGC
1 TCGGGC
9014 TTTTACTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.54, T:0.10
Consensus pattern (11 bp):
TCGGGCCGGGC
Found at i:9001 original size:6 final size:6
Alignment explanation
Indices: 8975--9014 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
8965 GTTTCCTTAA
8975 TCGGGC -CGGGC TCGGGC -CGGGC TCGGGC -CGGGC TCGGGC T
1 TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC T
9015 TTTACTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 15 0.48
6 16 0.52
ACGTcount: A:0.00, C:0.35, G:0.53, T:0.12
Consensus pattern (6 bp):
TCGGGC
Found at i:9359 original size:24 final size:24
Alignment explanation
Indices: 9327--9375 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
9317 AAGTGATTGG
*
9327 GATTACAAACATACAGGAAGACCC
1 GATTACAAACACACAGGAAGACCC
* *
9351 GATTACAAACGCACATGAAGACCC
1 GATTACAAACACACAGGAAGACCC
9375 G
1 G
9376 TTGGGATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.27, G:0.18, T:0.12
Consensus pattern (24 bp):
GATTACAAACACACAGGAAGACCC
Done.