Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017266.1 Corchorus olitorius cultivar O-4 contig17299, 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: 43103
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:6400 original size:20 final size:18
Alignment explanation
Indices: 6351--6402 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
6341 AAATAAGCAT
*
6351 GGAGCTTGGTTTTTTGCGC
1 GGAGC-TGGTTTTTAGCGC
**
6370 GGAGCAAGTTTTTAGCTGC
1 GGAGCTGGTTTTTAGC-GC
6389 AGGAGCTGGTTTTT
1 -GGAGCTGGTTTTT
6403 GAGATGAGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 8 0.31
19 7 0.27
20 11 0.42
ACGTcount: A:0.13, C:0.13, G:0.35, T:0.38
Consensus pattern (18 bp):
GGAGCTGGTTTTTAGCGC
Found at i:7174 original size:34 final size:34
Alignment explanation
Indices: 7108--7174 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
7098 TCATGAATTT
* *****
7108 ATAAGACTATAATCATTCTTTTTTTTTTTGAAAA
1 ATAAGACTATAATCATTCTATTTGAACATGAAAA
7142 ATAAGACTATAATCATTCTATTTGAACATGAAA
1 ATAAGACTATAATCATTCTATTTGAACATGAAA
7175 TGTATAATTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (34 bp):
ATAAGACTATAATCATTCTATTTGAACATGAAAA
Found at i:11740 original size:15 final size:15
Alignment explanation
Indices: 11720--11748 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11710 TAAGACTTTT
11720 TCTAATTAGTATTTG
1 TCTAATTAGTATTTG
11735 TCTAATTAGTATTT
1 TCTAATTAGTATTT
11749 TGTTATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (15 bp):
TCTAATTAGTATTTG
Found at i:11784 original size:13 final size:12
Alignment explanation
Indices: 11764--11810 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
11754 TCATTTTCGG
11764 AAAAAAAAAAGA
1 AAAAAAAAAAGA
*
11776 GAAATAAAAAAGA
1 -AAAAAAAAAAGA
11789 AAAAAAGAAAAGA
1 AAAAAA-AAAAGA
*
11802 AAAGAAAAA
1 AAAAAAAAA
11811 CTATTTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 8 0.27
13 22 0.73
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:13489 original size:15 final size:15
Alignment explanation
Indices: 13469--13502 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13459 GGTCAAGAAC
* *
13469 AAAAAAAGAGAAGAT
1 AAAAAAAAAGAAGAG
13484 AAAAAAAAAGAAGAG
1 AAAAAAAAAGAAGAG
13499 AAAA
1 AAAA
13503 GCCATACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGAAGAG
Found at i:31076 original size:17 final size:17
Alignment explanation
Indices: 31051--31086 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31041 GTTTTCCTGT
* *
31051 TTTTTGTTTTTGTTTCG
1 TTTTCGTTTTTGTTGCG
31068 TTTTCGTTTTTGTTGCG
1 TTTTCGTTTTTGTTGCG
31085 TT
1 TT
31087 GTCAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.19, T:0.72
Consensus pattern (17 bp):
TTTTCGTTTTTGTTGCG
Found at i:33467 original size:5 final size:6
Alignment explanation
Indices: 33452--33476 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33442 ATTGCGTTAA
33452 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
33477 ATTTGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:39176 original size:30 final size:30
Alignment explanation
Indices: 39142--39200 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
39132 AAGTTCGTGT
*
39142 TTGAAGACTTATTGAA-AATAATTTGAAGAA
1 TTGAAGAC-TATTGAAGAATAATTTCAAGAA
*
39172 TTGAAGACTATTGAAGAATCATTTCAAGA
1 TTGAAGACTATTGAAGAATAATTTCAAGA
39201 GGCAAGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (30 bp):
TTGAAGACTATTGAAGAATAATTTCAAGAA
Found at i:41340 original size:57 final size:57
Alignment explanation
Indices: 41252--41366 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
41242 ATTTATCTGC
* *
41252 ATATGAACTCAAATATGCATATCTCCATATAAATTTTGTTTAAAAAGTGCTCACTGG
1 ATATGAACCCAAATATGCATATCTCCATATAAATTTGGTTTAAAAAGTGCTCACTGG
* * *
41309 ATATGAACCCAAATGTGCATATCTCCATATAAATTTGGTTTCAAAAGTGCTCATTGG
1 ATATGAACCCAAATATGCATATCTCCATATAAATTTGGTTTAAAAAGTGCTCACTGG
41366 A
1 A
41367 AATAAAGAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (57 bp):
ATATGAACCCAAATATGCATATCTCCATATAAATTTGGTTTAAAAAGTGCTCACTGG
Found at i:43065 original size:2 final size:2
Alignment explanation
Indices: 43058--43097 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
43048 AAGAGATAAC
43058 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43098 CAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.