Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020162.1 Corchorus olitorius cultivar O-4 contig20195, 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: 13477
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1219 original size:32 final size:32
Alignment explanation
Indices: 1194--1413 Score: 320
Period size: 32 Copynumber: 6.9 Consensus size: 32
1184 CGTTTGGTAA
* *
1194 TATAGACGCCGCTAAATAAAGGCGTTTTTTTC
1 TATAGACGCCGCTAAATAAGGGCGTTTTGTTC
*
1226 T-TCAGACGCCGCTAAATAAGGGCGTTTTTTTC
1 TAT-AGACGCCGCTAAATAAGGGCGTTTTGTTC
* *
1258 TATAGACGCCGCTAAATAAGGGTGTTTTTTTC
1 TATAGACGCCGCTAAATAAGGGCGTTTTGTTC
1290 TATAGACGCCGCTAAATAAGGGCGTTTTGTTC
1 TATAGACGCCGCTAAATAAGGGCGTTTTGTTC
*
1322 TATAGACGCCGCTAAATAAGGGCATTTTGTTC
1 TATAGACGCCGCTAAATAAGGGCGTTTTGTTC
*
1354 -ATCAGACGCCGCTAAATAAGGGTGTTTTGTTC
1 TAT-AGACGCCGCTAAATAAGGGCGTTTTGTTC
*
1386 -ATCAGACGCCGCTAAATAAAGGCGTTTT
1 TAT-AGACGCCGCTAAATAAGGGCGTTTT
1414 CGTTTCACGC
Statistics
Matches: 176, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
31 3 0.02
32 172 0.98
33 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (32 bp):
TATAGACGCCGCTAAATAAGGGCGTTTTGTTC
Found at i:3797 original size:31 final size:31
Alignment explanation
Indices: 3762--3827 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
3752 TCAGATGCCA
3762 CTATTTAGCGGCGTCTTGTGAGAAAACGCCG
1 CTATTTAGCGGCGTCTTGTGAGAAAACGCCG
*
3793 CTATTTAGCGGCGTCTTTTGAGAAAACGCCG
1 CTATTTAGCGGCGTCTTGTGAGAAAACGCCG
3824 CTAT
1 CTAT
3828 ATATTATAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (31 bp):
CTATTTAGCGGCGTCTTGTGAGAAAACGCCG
Found at i:4122 original size:163 final size:161
Alignment explanation
Indices: 3784--4123 Score: 425
Period size: 162 Copynumber: 2.1 Consensus size: 161
3774 GTCTTGTGAG
* ** * *
3784 AAAACGCCGCTATTTAGCGGCGTCTTTTGAGAAAACGCCGCTATATATTATAGGCGTAGAGTTGG
1 AAAACGCCACTAAATAGCGGCGTCTTATGACAAAACGCCGCTATATATTATAGGCGTAGAGTTGG
* *
3849 AAAATTTATTTGTTTTAGGAGGAGGGAACTTTTCCCTCCAAAAAAAGGGAAACAAAATCTCTCCC
66 AAAATTTATTTGTTTTAGGAGGAGGGAACTTTTCCATCCAAAAAAAGGGAAAAAAAATCTCTCCC
3914 TCCATATATTAAAATAGAGGCGTTTCCTTTTC
131 TCCATATATTAAAATAGAGGCGTTT-CTTTTC
* * * * * *
3946 TAGACGCCACTAAATAGCGGCGTCTTATGTCCAAACGCCGCTATATATTATAGGTGTA-AGTTGT
1 AAAACGCCACTAAATAGCGGCGTCTTATGACAAAACGCCGCTATATATTATAGGCGTAGAGTTGG
* * * *
4010 AAACTTTCTTTGTTTTAGTGGGGAGGGAATTTTTCCAT-CAAAAAAATGGAGAAAAAAAATCTCT
66 AAAATTTATTTGTTTTAG-GAGGAGGGAACTTTTCCATCCAAAAAAA-GG-GAAAAAAAATCTCT
* * *
4074 CCCTCCATATATTAATATGGCGGCGTTT-TTCTGTC
128 CCCTCCATATATTAAAATAGAGGCGTTTCTT-T-TC
4109 AAAACGCCACTAAAT
1 AAAACGCCACTAAAT
4124 GGCTATAGTC
Statistics
Matches: 151, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
161 31 0.21
162 67 0.44
163 53 0.35
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (161 bp):
AAAACGCCACTAAATAGCGGCGTCTTATGACAAAACGCCGCTATATATTATAGGCGTAGAGTTGG
AAAATTTATTTGTTTTAGGAGGAGGGAACTTTTCCATCCAAAAAAAGGGAAAAAAAATCTCTCCC
TCCATATATTAAAATAGAGGCGTTTCTTTTC
Found at i:5966 original size:106 final size:106
Alignment explanation
Indices: 5781--5981 Score: 348
Period size: 106 Copynumber: 1.9 Consensus size: 106
5771 GGCAACTATT
*
5781 CAACTTGATCATGATGAGGTGGAGGATATTATGGATATAAAGCATAACGGATTCGATTTTTCGGA
1 CAACTTGATCATGATGAGGTGGAGGATATTATGGATATAAAGCATAAAGGATTCGATTTTTCGGA
*
5846 CGGTATTGGAAACCATGACAAATAGTTATGAGTTATGCGAC
66 CGGGATTGGAAACCATGACAAATAGTTATGAGTTATGCGAC
* *
5887 CAACTTGATCCTGATGAGGTGGAGGATATTATGGATATAAAGCATAAATGATTCGATTTTTCGGA
1 CAACTTGATCATGATGAGGTGGAGGATATTATGGATATAAAGCATAAAGGATTCGATTTTTCGGA
* *
5952 TGGGATTGGAAACCATGATAAATAGTTATG
66 CGGGATTGGAAACCATGACAAATAGTTATG
5982 CAACCAAGTA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 89 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (106 bp):
CAACTTGATCATGATGAGGTGGAGGATATTATGGATATAAAGCATAAAGGATTCGATTTTTCGGA
CGGGATTGGAAACCATGACAAATAGTTATGAGTTATGCGAC
Found at i:11371 original size:19 final size:19
Alignment explanation
Indices: 11334--11372 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
11324 CTCACTTCCA
*
11334 CTTCATCTTCTCCAGCCTT
1 CTTCATCTTCTCCAACCTT
* *
11353 CTTCATCTTTTTCAACCTT
1 CTTCATCTTCTCCAACCTT
11372 C
1 C
11373 CACTCATCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.38, G:0.03, T:0.46
Consensus pattern (19 bp):
CTTCATCTTCTCCAACCTT
Found at i:13181 original size:54 final size:54
Alignment explanation
Indices: 12998--13271 Score: 263
Period size: 54 Copynumber: 5.0 Consensus size: 54
12988 TACTTCTTGA
* * *
12998 TTAACTTAATTACTCTGAATTAAGCTAATTACTATTGATT-GC-TTTTTTACTTCTTGA
1 TTAACTTAATTACTCTGAATTAAGCCAA-T--TATTGATTACCATTTTTTAC-TCTT-T
* * *
13055 TTAACTTAATTGCTCTGAATGAAGCTAATTCTATTGATTA-C-TTTTTTACTTCTTT
1 TTAACTTAATTACTCTGAATTAAGCCAA-T-TATTGATTACCATTTTTTAC-TCTTT
* * * * *
13110 TAAACTTAATAATTCTGAATTAAGCCCATTATTGATCACCATTTTTTACTCTTT
1 TTAACTTAATTACTCTGAATTAAGCCAATTATTGATTACCATTTTTTACTCTTT
* *
13164 TTAACTTAATTACTCTGAATTAAACCAATTACTGATTACCATTTTTTACTC-TT
1 TTAACTTAATTACTCTGAATTAAGCCAATTATTGATTACCATTTTTTACTCTTT
* * * * * *
13217 TTAACTTAATTACTTTGAATTGAGCCCATTACTGATTATCA-TTTTTACTTTTT
1 TTAACTTAATTACTCTGAATTAAGCCAATTATTGATTACCATTTTTTACTCTTT
13270 TT
1 TT
13272 TTTTCAACTT
Statistics
Matches: 189, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
52 8 0.04
53 50 0.26
54 51 0.27
55 29 0.15
56 23 0.12
57 28 0.15
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (54 bp):
TTAACTTAATTACTCTGAATTAAGCCAATTATTGATTACCATTTTTTACTCTTT
Found at i:13260 original size:107 final size:108
Alignment explanation
Indices: 12976--13271 Score: 291
Period size: 107 Copynumber: 2.7 Consensus size: 108
12966 ATCTTACTAA
** * **
12976 TGATTACCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACT-ATTGATTGC
1 TGATTACTTTTTTACTTCTT--TTAACTTAATTACTTTGAATTAAGCCCATTACTGATT-A-T-C
* * * * *
13040 -TTTTTTACTTCTTGATTAACTTAATTGCTCTGAATGAAGCTAATTCTAT
61 ATTTTTTAC-TCTT-TTTAACTTAATTACTCTGAATGAAACCAATTCTAC
* * * *
13089 TGATTACTTTTTTACTTCTTTTAAACTTAA-TAATTCTGAATTAAGCCCATTATTGATCACCATT
1 TGATTACTTTTTTACTTCTTTT-AACTTAATTACTT-TGAATTAAGCCCATTACTGATTATCATT
*
13153 TTTTACTCTTTTTAACTTAATTACTCTGAATTAAACCAA-T-TAC
64 TTTTACTCTTTTTAACTTAATTACTCTGAATGAAACCAATTCTAC
*
13196 TGATTACCATTTTTTAC-TCTTTTAACTTAATTACTTTGAATTGAGCCCATTACTGATTATCA-T
1 TGATTA-C-TTTTTTACTTCTTTTAACTTAATTACTTTGAATTAAGCCCATTACTGATTATCATT
*
13259 TTTTACTTTTTTT
64 TTTTACTCTTTTT
13272 TTTTCAACTT
Statistics
Matches: 155, Mismatches: 21, Indels: 21
0.79 0.11 0.11
Matches are distributed among these distances:
106 13 0.08
107 37 0.24
108 12 0.08
109 32 0.21
110 5 0.03
111 13 0.08
112 23 0.15
113 20 0.13
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.49
Consensus pattern (108 bp):
TGATTACTTTTTTACTTCTTTTAACTTAATTACTTTGAATTAAGCCCATTACTGATTATCATTTT
TTACTCTTTTTAACTTAATTACTCTGAATGAAACCAATTCTAC
Found at i:13379 original size:32 final size:30
Alignment explanation
Indices: 13334--13455 Score: 124
Period size: 32 Copynumber: 3.9 Consensus size: 30
13324 ATTACCAGTT
*
13334 TTTGAATTGAATTACTGATTTCCATTTTCC
1 TTTGAATTTAATTACTGATTTCCATTTTCC
*
13364 TTATAGAACTTAATTACTGATTAT-CATTACTT--
1 TT-T-GAATTTAATTACTGATT-TCCATT--TTCC
*
13396 TTTGAATTTACTTACTGATTTCCATTTTACTC
1 TTTGAATTTAATTACTGATTTCCATTTT-C-C
*
13428 TTTGAATTTAATTACTGATTCCCATTTT
1 TTTGAATTTAATTACTGATTTCCATTTT
13456 TACTCTTCGA
Statistics
Matches: 76, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
28 2 0.03
29 1 0.01
30 21 0.28
31 2 0.03
32 47 0.62
33 1 0.01
34 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (30 bp):
TTTGAATTTAATTACTGATTTCCATTTTCC
Done.