Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015547.1 Corchorus olitorius cultivar O-4 contig15580, 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: 30285
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6901 original size:2 final size:2
Alignment explanation
Indices: 6889--6950 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
6879 TACTATTAAC
* * *
6889 TA TA GA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T- TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6930 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
6951 TAATTGAAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:10899 original size:35 final size:35
Alignment explanation
Indices: 10853--10919 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
10843 GACTTAACCC
* * *
10853 GTAGAGTGCAAGCACAACACTCCACAATCGCGTCT
1 GTAGACTGCAAGCACAACACTACACAAACGCGTCT
*
10888 GTAGACTGCAAGCACAATACTACACAAACGCG
1 GTAGACTGCAAGCACAACACTACACAAACGCG
10920 CACACCCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (35 bp):
GTAGACTGCAAGCACAACACTACACAAACGCGTCT
Found at i:12796 original size:22 final size:20
Alignment explanation
Indices: 12766--12808 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
12756 AAGAAATAAA
12766 AATAACTTATACCATAACTTTC
1 AATAACTTA-ACCAT-ACTTTC
* *
12788 AATATCTTAATCATACTTTC
1 AATAACTTAACCATACTTTC
12808 A
1 A
12809 TAGCTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAACTTAACCATACTTTC
Found at i:14788 original size:18 final size:17
Alignment explanation
Indices: 14767--14800 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
14757 TAGTAATTTT
14767 TTTTTTGAGAACTAAATA
1 TTTTTT-AGAACTAAATA
14785 TTTTTTAGAACTAAAT
1 TTTTTTAGAACTAAAT
14801 GTATAAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
TTTTTTAGAACTAAATA
Found at i:17131 original size:4 final size:4
Alignment explanation
Indices: 17117--17151 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
17107 AAAAAGAAGG
*
17117 TAAA T-AA TAAA TAAA TAAT TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
17152 AGTCGTGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:17141 original size:12 final size:11
Alignment explanation
Indices: 17086--17151 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
17076 GACTTTGGGA
17086 AAATAAT-AAT
1 AAATAATAAAT
17096 AAA-AATTAAAT
1 AAATAA-TAAAT
* *
17107 AAA-AAGAAGGT
1 AAATAATAA-AT
17118 AAATAATAAAT
1 AAATAATAAAT
17129 AAATAATTAAAT
1 AAATAA-TAAAT
17141 AAATAAATAAA
1 AAAT-AATAAA
17152 AGTCGTGGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
9 2 0.04
10 6 0.13
11 19 0.41
12 17 0.37
13 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:18132 original size:20 final size:20
Alignment explanation
Indices: 18107--18165 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
18097 TTAAAATTGG
*
18107 TATTCAATTGCAATATAATA
1 TATTCAATTACAATATAATA
18127 TATTCAATTACAATATAATA
1 TATTCAATTACAATATAATA
18147 TATTCAATTACAATATAAT
1 TATTCAATTACAATATAAT
18166 CAATATCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (20 bp):
TATTCAATTACAATATAATA
Found at i:19429 original size:12 final size:12
Alignment explanation
Indices: 19408--19449 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
19398 AGGCATGGTC
19408 AAAA-TATAAAT
1 AAAATTATAAAT
19419 AAAATTATAAAT
1 AAAATTATAAAT
*
19431 AATAAATATAAAT
1 AA-AATTATAAAT
19444 ATAAAT
1 A-AAAT
19450 AAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 9 0.35
13 12 0.46
14 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTATAAAT
Found at i:19437 original size:19 final size:19
Alignment explanation
Indices: 19409--19459 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
19399 GGCATGGTCA
19409 AAAT-ATAAATA-AAATTAT
1 AAATAATAAATATAAA-TAT
19427 AAATAATAAATATAAATAT
1 AAATAATAAATATAAATAT
19446 AAAT-A-AAATATAAA
1 AAATAATAAATATAAA
19460 GTAAGAACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.29
18 5 0.16
19 14 0.45
20 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATAATAAATATAAATAT
Found at i:19443 original size:6 final size:6
Alignment explanation
Indices: 19409--19459 Score: 70
Period size: 6 Copynumber: 8.5 Consensus size: 6
19399 GGCATGGTCA
19409 AAATAT AAATA- AAATTAT AAATAAT AAATAT AAATAT AAATA- AAATAT
1 AAATAT AAATAT AAA-TAT AAAT-AT AAATAT AAATAT AAATAT AAATAT
19457 AAA
1 AAA
19460 GTAAGAACGT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 8 0.20
6 24 0.59
7 9 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATAT
Done.