Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020556.1 Corchorus olitorius cultivar O-4 contig20589, 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: 23753
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4022 original size:51 final size:52
Alignment explanation
Indices: 3921--4022 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 52
3911 GTTCTTCAAA
* *
3921 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTATAGTGTTT
*
3973 TTCT-CTTGTTTCA-ATCTTGTCTCCA-GACATACAAACACT-GTATACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCT-CAGGACAAACAAACACTCGTATA-GTGTT
4023 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
50 3 0.07
51 34 0.77
52 7 0.16
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.41
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTATAGTGTTT
Found at i:8089 original size:31 final size:32
Alignment explanation
Indices: 8010--8089 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 32
8000 ATAAACAGTC
*
8010 AAAA-CGTTTTGCCCTTT-TTTGAAAATTCCG
1 AAAATCGTTTTGCCCTTTATTTGAAAATTACG
8040 AAAAT-GTTTTGCCC-TTATTTGTAAAA-TACG
1 AAAATCGTTTTGCCCTTTATTTG-AAAATTACG
8070 -AAATCGTTTTGCCCTTTATT
1 AAAATCGTTTTGCCCTTTATT
8090 GATCATATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
29 6 0.14
30 29 0.66
31 9 0.20
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (32 bp):
AAAATCGTTTTGCCCTTTATTTGAAAATTACG
Found at i:9075 original size:22 final size:21
Alignment explanation
Indices: 9050--9133 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 21
9040 TATATATATA
9050 TATATATATTAATAAATTTTCC
1 TATATATATTAATAAATTTT-C
* *
9072 TATAT-TAAT-ATAAAATTT-
1 TATATATATTAATAAATTTTC
* * *
9090 AATATATATTAATATATTTATA
1 TATATATATTAATAAATTT-TC
9112 TATATATATTAATAAAATTTTC
1 TATATATATTAAT-AAATTTTC
9134 CTAATTTGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.08
19 3 0.06
20 14 0.29
21 4 0.08
22 18 0.38
23 5 0.10
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATATATTAATAAATTTTC
Found at i:9103 original size:10 final size:10
Alignment explanation
Indices: 9072--9125 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
9062 TAAATTTTCC
9072 TATATTAATA
1 TATATTAATA
*
9082 TAAAATTTAATA
1 T-ATA-TTAATA
9094 TATATTAATA
1 TATATTAATA
*
9104 TATTTATATATA
1 TATAT-TA-ATA
9116 TATATTAATA
1 TATATTAATA
9126 AAATTTTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 14 0.39
11 8 0.22
12 14 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TATATTAATA
Found at i:10772 original size:17 final size:17
Alignment explanation
Indices: 10750--10785 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
10740 TGATTTGTAA
10750 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
10767 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
10784 AG
1 AG
10786 CTCTTTATAT
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:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:13363 original size:18 final size:18
Alignment explanation
Indices: 13340--13399 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
13330 TACAAAATAT
13340 TGTTCCACTACTGCAGGA
1 TGTTCCACTACTGCAGGA
*
13358 TGTTCCACTACTGCAGAA
1 TGTTCCACTACTGCAGGA
* * * *
13376 TGTTGCATTGCCGCAGGA
1 TGTTCCACTACTGCAGGA
13394 TGTTCC
1 TGTTCC
13400 GCTGCCGCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (18 bp):
TGTTCCACTACTGCAGGA
Found at i:13405 original size:18 final size:18
Alignment explanation
Indices: 13340--13408 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
13330 TACAAAATAT
* *
13340 TGTTCCACTACTGCAGGA
1 TGTTCCACTGCCGCAGGA
* * *
13358 TGTTCCACTACTGCAGAA
1 TGTTCCACTGCCGCAGGA
* *
13376 TGTTGCATTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
*
13394 TGTTCCGCTGCCGCA
1 TGTTCCACTGCCGCA
13409 AGAACCTTTG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.28
Consensus pattern (18 bp):
TGTTCCACTGCCGCAGGA
Found at i:20022 original size:28 final size:29
Alignment explanation
Indices: 19991--20048 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
19981 AATATTTTTT
*
19991 ATTTT-TTTTTAAACGCAAAAATAAGAGA
1 ATTTTATTTTAAAACGCAAAAATAAGAGA
*
20019 ATTTTATTTTAAAACGCCAAAATAAGAGA
1 ATTTTATTTTAAAACGCAAAAATAAGAGA
20048 A
1 A
20049 AATTCTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (29 bp):
ATTTTATTTTAAAACGCAAAAATAAGAGA
Found at i:20294 original size:54 final size:55
Alignment explanation
Indices: 20214--20369 Score: 192
Period size: 54 Copynumber: 2.9 Consensus size: 55
20204 TAGACTTATC
* * * * *
20214 TAAACAGTAACTAGTTTAATTCTGGGTAGTTAAACTAAAGAGTAAAAGGAGA-AG
1 TAAACAATAATTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAAAGAG
* * * *
20268 TAAATAGA-AGTTAGTTTAATTTTGGGTAATTAAACTAAATAGT-AAAGAAAAGAG
1 TAAACA-ATAATTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAAAGAG
20322 TAAACAATAATTAGTTTAATTCTGGGTAATTAAACTAAAGAAGTAAAA
1 TAAACAATAATTAGTTTAATTCTGGGTAATTAAACTAAAG-AGTAAAA
20370 ATAAGCAGTA
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
53 7 0.08
54 71 0.85
55 3 0.04
56 3 0.04
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (55 bp):
TAAACAATAATTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAAAGAG
Found at i:21308 original size:50 final size:50
Alignment explanation
Indices: 21148--21422 Score: 354
Period size: 50 Copynumber: 5.5 Consensus size: 50
21138 TAAAACCTGG
* ** * *
21148 TGGGAACTTTCCCAATTTGCAAAAGAGCTAGATTGAATACTTTGAAAACTGA
1 TGGGAACTTTCCCGATTTG-AAAA-ATTTAAATTGAATACTTTGAAGACTGA
* * **
21200 TGGGAACTTTCCCAAGTTGAAAAGAGCTAAATTGAATACTTTGAAGACTGA
1 TGGGAACTTTCCCGATTTGAAAA-ATTTAAATTGAATACTTTGAAGACTGA
* * *
21251 TGGGAACTTTCCCGACTTGAAAAATTTAACTTAAATACTTTGAAGACTGA
1 TGGGAACTTTCCCGATTTGAAAAATTTAAATTGAATACTTTGAAGACTGA
* *
21301 TGGGAACTTTCCCGATGTGAAAAATTTAAATCGAATACTTTGAAGACTGA
1 TGGGAACTTTCCCGATTTGAAAAATTTAAATTGAATACTTTGAAGACTGA
* *
21351 TGGGAACTTTCCCGATTTGAAAAATTTAAATTGAATAC-TTAAAAACTGA
1 TGGGAACTTTCCCGATTTGAAAAATTTAAATTGAATACTTTGAAGACTGA
* *
21400 TGAGAACTTTCCCAATTTGAAAA
1 TGGGAACTTTCCCGATTTGAAAA
21423 CTTAAACCTG
Statistics
Matches: 203, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
49 30 0.15
50 104 0.51
51 51 0.25
52 18 0.09
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (50 bp):
TGGGAACTTTCCCGATTTGAAAAATTTAAATTGAATACTTTGAAGACTGA
Found at i:22991 original size:40 final size:40
Alignment explanation
Indices: 22827--23341 Score: 761
Period size: 40 Copynumber: 13.0 Consensus size: 40
22817 CGGGAATAGG
* * * * ** *
22827 AACAAAACCTCCCGATGAGGAAGGGCAAACTAAGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
* * * * *
22867 GACAACACTTTCCGGTAGGGAAAGACAAACT-GGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
*
22906 AACAACACCTTCCGGTGGGG-AGGGCAAACT-GGTATCTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
22944 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
* * *
22984 GACAACACCTACCGGTGGGGAAGGGCAAATTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
* * *
23024 GACAACACCTTCCGGTGGGGAAGGGTAAACTGGGTTTTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
* *
23064 AATAACACCTTCCGGTGGGGAAGGGCAAATTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
*
23104 GACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
23144 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
23184 AACAACACCTTCCGGTGGGGAAGGGCAAACT-GGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
23223 AACAACACCTTCCGGT-GGGAGAGGGCAAACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGA-AGGGCAAACTGGGTATTTA
* *
23263 GACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATATA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
*
23303 GACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT
23342 GAAATATAGA
Statistics
Matches: 433, Mismatches: 37, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
38 39 0.09
39 67 0.15
40 323 0.75
41 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.20
Consensus pattern (40 bp):
AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
Done.