Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020411.1 Corchorus olitorius cultivar O-4 contig20444, 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: 50623
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:75 original size:31 final size:32
Alignment explanation
Indices: 37--116 Score: 146
Period size: 31 Copynumber: 2.6 Consensus size: 32
27 ACAAATATTC
37 AATTAAAACTTATATTTTTTTTGGCC-AAAAA
1 AATTAAAACTTATATTTTTTTTGGCCAAAAAA
68 AATTAAAACTTATA-TTTTTTTGGCCAAAAAA
1 AATTAAAACTTATATTTTTTTTGGCCAAAAAA
99 AATTAAAACTTATATTTT
1 AATTAAAACTTATATTTT
117 AAATAATTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
30 11 0.23
31 33 0.70
32 3 0.06
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (32 bp):
AATTAAAACTTATATTTTTTTTGGCCAAAAAA
Found at i:880 original size:16 final size:16
Alignment explanation
Indices: 859--889 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
849 ATTTTATACT
859 TCATTACATATGGAAC
1 TCATTACATATGGAAC
875 TCATTACATATGGAA
1 TCATTACATATGGAA
890 TTCTAGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (16 bp):
TCATTACATATGGAAC
Found at i:12783 original size:136 final size:136
Alignment explanation
Indices: 12528--13006 Score: 807
Period size: 136 Copynumber: 3.5 Consensus size: 136
12518 TATAGAGACA
* * * * * **
12528 TGTTAGATAAGGTGTGGAAGAGATAAGGATTCAATCAAATGGCCACATTTGAATCTTACTTTTAA
1 TGTTGGATAAGGTGTGGAAGAGATAAGGATTCAATCTAACGGTCATATTTGAATCCCACTTTTAA
* * * * *
12593 TCCAACGGTTGGATAA-ACTAAAGATAGATTCTCTGCAAGTGATTGGATAATGTGTTAGATTGTC
66 TCCAACCGTTGGATAAGA-TAAAGATAGATTCTCTGCAAGTGATTGGACATTGTGTTGGATTTTC
12657 TGACTTT
130 TGACTTT
*
12664 TGTTGGATAAGTTGTGGAAGAGATAAGGATTCAATCTAACGGTCATATTTGAATCCCACTTTTAA
1 TGTTGGATAAGGTGTGGAAGAGATAAGGATTCAATCTAACGGTCATATTTGAATCCCACTTTTAA
12729 TCCAACCGTTGGATAAGATAAAGATAGATTCTCTGCAAGTGATTGGACATTGTGTTGGATTTTCT
66 TCCAACCGTTGGATAAGATAAAGATAGATTCTCTGCAAGTGATTGGACATTGTGTTGGATTTTCT
12794 GACTTT
131 GACTTT
12800 TGTTGGATAAGGTGTGGAAGAGATAAGGATTCAATCTAACGGTCATATTTGAATCCCACTTTTAA
1 TGTTGGATAAGGTGTGGAAGAGATAAGGATTCAATCTAACGGTCATATTTGAATCCCACTTTTAA
12865 TCCAACCGTTGGATAAGATAAAGATAGATTCTCTGCAAGTGATTGGACATTGTGTTGGATTTTCT
66 TCCAACCGTTGGATAAGATAAAGATAGATTCTCTGCAAGTGATTGGACATTGTGTTGGATTTTCT
12930 GACTTT
131 GACTTT
* *
12936 TGTTGGATAAGGTGTGGAAGAGATAAGGATTCAATCCAACAGTCATATTTGAATCCCACTTTTAA
1 TGTTGGATAAGGTGTGGAAGAGATAAGGATTCAATCTAACGGTCATATTTGAATCCCACTTTTAA
13001 TCCAAC
66 TCCAAC
13007 GATTTGTAGT
Statistics
Matches: 326, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
136 325 1.00
137 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (136 bp):
TGTTGGATAAGGTGTGGAAGAGATAAGGATTCAATCTAACGGTCATATTTGAATCCCACTTTTAA
TCCAACCGTTGGATAAGATAAAGATAGATTCTCTGCAAGTGATTGGACATTGTGTTGGATTTTCT
GACTTT
Found at i:17456 original size:21 final size:22
Alignment explanation
Indices: 17430--17470 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
17420 GGAATGGCGA
17430 TGGCATGG-GCATGGCCGGTGG
1 TGGCATGGTGCATGGCCGGTGG
*
17451 TGGCATGGTGTATGGCCGGT
1 TGGCATGGTGCATGGCCGGT
17471 AATAGCCGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.10, C:0.17, G:0.49, T:0.24
Consensus pattern (22 bp):
TGGCATGGTGCATGGCCGGTGG
Found at i:20451 original size:15 final size:16
Alignment explanation
Indices: 20431--20460 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20421 ACAGAAACAA
20431 TTTTTTTT-ACGCAAT
1 TTTTTTTTGACGCAAT
20446 TTTTTTTTGACGCAA
1 TTTTTTTTGACGCAA
20461 AACACAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (16 bp):
TTTTTTTTGACGCAAT
Found at i:20513 original size:26 final size:26
Alignment explanation
Indices: 20478--20529 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
20468 AACTCTTTTC
20478 TTTTCTTTTCAAAAACGCAACACAAA
1 TTTTCTTTTCAAAAACGCAACACAAA
*
20504 TTTTTTTTTCAAAAACGCAACACAAA
1 TTTTCTTTTCAAAAACGCAACACAAA
20530 AAATTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (26 bp):
TTTTCTTTTCAAAAACGCAACACAAA
Found at i:40578 original size:41 final size:41
Alignment explanation
Indices: 40518--40596 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
40508 AACTGGATTC
*
40518 TTAATCATTATGCCCCTTAAAATTGTTTCTAATTACAACAT
1 TTAATCATTATGCCACTTAAAATTGTTTCTAATTACAACAT
*
40559 TTAATCATTATGGCACTTAAAATTGTTTCTAATTACAA
1 TTAATCATTATGCCACTTAAAATTGTTTCTAATTACAA
40597 ATTATGCTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (41 bp):
TTAATCATTATGCCACTTAAAATTGTTTCTAATTACAACAT
Found at i:43821 original size:16 final size:16
Alignment explanation
Indices: 43800--43834 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
43790 ACGGATGAAT
43800 GCTTTTAATAATAAAG
1 GCTTTTAATAATAAAG
43816 GCTTTTAATAATAAAG
1 GCTTTTAATAATAAAG
43832 GCT
1 GCT
43835 AAAACACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (16 bp):
GCTTTTAATAATAAAG
Found at i:45128 original size:12 final size:12
Alignment explanation
Indices: 45111--45226 Score: 131
Period size: 12 Copynumber: 10.2 Consensus size: 12
45101 TTACGTGTAG
45111 CCCGGGACAACA
1 CCCGGGACAACA
45123 CCCGGGACAACA
1 CCCGGGACAACA
*
45135 --C-TGA-AACA
1 CCCGGGACAACA
45143 GCCCGGGACAACA
1 -CCCGGGACAACA
*
45156 CCCCGGACAACA
1 CCCGGGACAACA
45168 CCCGGGACAACA
1 CCCGGGACAACA
45180 -CC--GA-AACA
1 CCCGGGACAACA
45188 GCCCGGGACAACA
1 -CCCGGGACAACA
*
45201 CCCCGGACAACA
1 CCCGGGACAACA
45213 CCCGGGACAACA
1 CCCGGGACAACA
45225 CC
1 CC
45227 GAAACAGAAC
Statistics
Matches: 88, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
8 8 0.09
9 4 0.05
10 3 0.03
11 3 0.03
12 62 0.70
13 8 0.09
ACGTcount: A:0.34, C:0.42, G:0.22, T:0.01
Consensus pattern (12 bp):
CCCGGGACAACA
Found at i:45166 original size:45 final size:45
Alignment explanation
Indices: 45115--45233 Score: 229
Period size: 45 Copynumber: 2.6 Consensus size: 45
45105 GTGTAGCCCG
*
45115 GGACAACACCCGGGACAACACTGAAACAGCCCGGGACAACACCCC
1 GGACAACACCCGGGACAACACCGAAACAGCCCGGGACAACACCCC
45160 GGACAACACCCGGGACAACACCGAAACAGCCCGGGACAACACCCC
1 GGACAACACCCGGGACAACACCGAAACAGCCCGGGACAACACCCC
45205 GGACAACACCCGGGACAACACCGAAACAG
1 GGACAACACCCGGGACAACACCGAAACAG
45234 AACGGGCCTA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.37, C:0.39, G:0.23, T:0.01
Consensus pattern (45 bp):
GGACAACACCCGGGACAACACCGAAACAGCCCGGGACAACACCCC
Found at i:45197 original size:33 final size:32
Alignment explanation
Indices: 45152--45214 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
45142 AGCCCGGGAC
*
45152 AACACCCCGGACAACACCCGGGACAACACCGA
1 AACACCCCGGACAACACCCCGGACAACACCGA
*
45184 AACAGCCCGGGACAACACCCCGGACAACACC
1 AACA-CCCCGGACAACACCCCGGACAACACC
45215 CGGGACAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.37, C:0.44, G:0.19, T:0.00
Consensus pattern (32 bp):
AACACCCCGGACAACACCCCGGACAACACCGA
Found at i:47448 original size:12 final size:12
Alignment explanation
Indices: 47431--47459 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
47421 TGGGAATTGT
47431 TGAAACACCTAA
1 TGAAACACCTAA
47443 TGAAACACCTAA
1 TGAAACACCTAA
47455 TGAAA
1 TGAAA
47460 TTACTAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (12 bp):
TGAAACACCTAA
Done.