Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013994.1 Corchorus olitorius cultivar O-4 contig14027, 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: 17545
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Found at i:3283 original size:60 final size:59
Alignment explanation
Indices: 3069--3371 Score: 441
Period size: 59 Copynumber: 5.1 Consensus size: 59
3059 TTTTAAGAAA
* * *
3069 AAAAACAAGATAACACTTTGAAATGAAAACTCTCTAACAGAGACCTCGATCAGGA-TTT
1 AAAAACAAGATAAGATTTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGATTTT
*
3127 AGAAAACAAGATAAGATTTTGAAATGAAAACTCTCGAACAGAGACCTCGAACAGGATTTTTT
1 A-AAAACAAGATAAGATTTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGA--TTTT
*
3189 AAAAAACAAGATAAGATGTTGAAATG-AAACTCTCTAACAGAGACCTCGAACAGGATTTTT
1 -AAAAACAAGATAAGATTTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGA-TTTT
3249 AAAAACAAGATAAGATTTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGA-TTT
1 AAAAACAAGATAAGATTTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGATTTT
* * * *
3307 AGAAAACAAGACAAGGTTTTTAATTGAAACACTCTCTAACAGAGACCTCGAACAGGATTTT
1 A-AAAACAAGATAAGATTTTGAAATGAAA-ACTCTCTAACAGAGACCTCGAACAGGATTTT
3368 AAAA
1 AAAA
3372 CAGAAAAAGG
Statistics
Matches: 225, Mismatches: 11, Indels: 16
0.89 0.04 0.06
Matches are distributed among these distances:
58 5 0.02
59 97 0.43
60 64 0.28
61 32 0.14
62 26 0.12
63 1 0.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (59 bp):
AAAAACAAGATAAGATTTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGATTTT
Found at i:3354 original size:120 final size:119
Alignment explanation
Indices: 3068--3371 Score: 436
Period size: 121 Copynumber: 2.5 Consensus size: 119
3058 TTTTTAAGAA
* * *
3068 AAAAAACAAGATAACACT-TTGAAATGAAAACTCTCTAACAGAGACCTCGATCAGGA-TTTAGAA
1 AAAAAACAAGACAAGA-TGTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTA-AA
3131 AACAAGATAAGATTTTGAAATGAAAACTCTCGAACAGAGACCTCGAACAGGATTTTTT
64 AACAAGATAAGATTTTGAAATGAAAACTCTCGAACAGAGACCTCGAACAGGA--TTTT
*
3189 AAAAAACAAGATAAGATGTTGAAATG-AAACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAA
1 AAAAAACAAGACAAGATGTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAA
*
3253 ACAAGATAAGATTTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGA-TTT
65 ACAAGATAAGATTTTGAAATGAAAACTCTCGAACAGAGACCTCGAACAGGATTTT
* * * * *
3307 AGAAAACAAGACAAGGTTTTTAATTGAAACACTCTCTAACAGAGACCTCGAACAGGATTTTAAAA
1 AAAAAACAAGACAAGATGTTGAAATGAAA-ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAA
3372 CAGAAAAAGG
Statistics
Matches: 169, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
118 23 0.14
119 10 0.06
120 56 0.33
121 76 0.45
122 4 0.02
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (119 bp):
AAAAAACAAGACAAGATGTTGAAATGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAA
CAAGATAAGATTTTGAAATGAAAACTCTCGAACAGAGACCTCGAACAGGATTTT
Found at i:3862 original size:2 final size:2
Alignment explanation
Indices: 3855--3883 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3845 TTGACAAAGA
3855 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3884 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3888 original size:2 final size:2
Alignment explanation
Indices: 3883--3908 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3873 ACACACACAC
3883 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3909 GAAAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4319 original size:38 final size:37
Alignment explanation
Indices: 4251--4372 Score: 140
Period size: 36 Copynumber: 3.3 Consensus size: 37
4241 TTTTTATTTA
* * * *
4251 TTTTCTTTTTTTCTGACCTCTCTCTGTTTTAGG-CCAAG
1 TTTTTTTTTTTTC-AACCTCTTTCTATTTTAGGTCC-AG
4289 TTTTTTTTCTTTTCAACCTCTTTCTATTTTAGGTCCAG
1 TTTTTTTT-TTTTCAACCTCTTTCTATTTTAGGTCCAG
** *
4327 -TTTTCCTTTTTCGACCTCTTTCTATTTTAGGTCCAG
1 TTTTTTTTTTTTCAACCTCTTTCTATTTTAGGTCCAG
4363 TTTTTTTTTT
1 TTTTTTTTTT
4373 AGGCTCCTTC
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
36 28 0.39
37 12 0.17
38 25 0.35
39 7 0.10
ACGTcount: A:0.11, C:0.21, G:0.10, T:0.58
Consensus pattern (37 bp):
TTTTTTTTTTTTCAACCTCTTTCTATTTTAGGTCCAG
Found at i:14420 original size:11 final size:11
Alignment explanation
Indices: 14406--14439 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
14396 TAAAGGAAAA
14406 AGCTAGGAAGG
1 AGCTAGGAAGG
14417 AGCTAGGAAGG
1 AGCTAGGAAGG
14428 AGCTAGGAAGG
1 AGCTAGGAAGG
14439 A
1 A
14440 TCCTACTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09
Consensus pattern (11 bp):
AGCTAGGAAGG
Found at i:16672 original size:33 final size:31
Alignment explanation
Indices: 16634--16738 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 31
16624 GCTATGATCA
** *
16634 ACCAAAACAGATTTGTTCTCATCACAATTAGC
1 ACCAAAACAGATTTGTT-TCATCACAAACAAC
*
16666 ATCCAAAACAGAATTTGTTTCATCAAAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
16699 ACCTAAAACAGATTTGGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
16732 ACTCAAA
1 AC-CAAA
16739 TTAGGTTTAG
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
32 7 0.11
33 47 0.76
34 8 0.13
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.24
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Done.