Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012289.1 Corchorus olitorius cultivar O-4 contig12322, 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: 30937
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:3752 original size:90 final size:90
Alignment explanation
Indices: 3599--3780 Score: 364
Period size: 90 Copynumber: 2.0 Consensus size: 90
3589 TTGAGTGGAG
3599 CTTTTAGTAAATTTGGTAGGGTTTACAAATTATGTATAGTTTGTATACAACATATTAAACATAAC
1 CTTTTAGTAAATTTGGTAGGGTTTACAAATTATGTATAGTTTGTATACAACATATTAAACATAAC
3664 CTTGTCATGCTAAAAGACTAATAAA
66 CTTGTCATGCTAAAAGACTAATAAA
3689 CTTTTAGTAAATTTGGTAGGGTTTACAAATTATGTATAGTTTGTATACAACATATTAAACATAAC
1 CTTTTAGTAAATTTGGTAGGGTTTACAAATTATGTATAGTTTGTATACAACATATTAAACATAAC
3754 CTTGTCATGCTAAAAGACTAATAAA
66 CTTGTCATGCTAAAAGACTAATAAA
3779 CT
1 CT
3781 AAAAGGTTTC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 92 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (90 bp):
CTTTTAGTAAATTTGGTAGGGTTTACAAATTATGTATAGTTTGTATACAACATATTAAACATAAC
CTTGTCATGCTAAAAGACTAATAAA
Found at i:12201 original size:56 final size:56
Alignment explanation
Indices: 12110--12215 Score: 176
Period size: 56 Copynumber: 1.9 Consensus size: 56
12100 GTGAACTTGG
*
12110 AGGCATCCCCAGGACGCGCCGCCCCATATGGGGAGGCGTCCCTAGCTGGCACCCCC
1 AGGCATCCCCAGGACGCGCCGCCCCATATGGGGAGGCGTCCCCAGCTGGCACCCCC
* * *
12166 AGGCGTCCCCTGGACGCGCCGCCTCATATGGGGAGGCGTCCCCAGCTGGC
1 AGGCATCCCCAGGACGCGCCGCCCCATATGGGGAGGCGTCCCCAGCTGGC
12216 GCCTCCCCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.14, C:0.41, G:0.33, T:0.12
Consensus pattern (56 bp):
AGGCATCCCCAGGACGCGCCGCCCCATATGGGGAGGCGTCCCCAGCTGGCACCCCC
Found at i:12250 original size:33 final size:34
Alignment explanation
Indices: 12213--12285 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
12203 GTCCCCAGCT
*
12213 GGCGCCTCCCCATATGG-GGCGGCGCGATTCGGG
1 GGCGCCTCCCCATATGGTGGCGGCGCGATCCGGG
*
12246 GGCGCCTCCCCATATGGTGGGGGCGCGATCCGGG
1 GGCGCCTCCCCATATGGTGGCGGCGCGATCCGGG
12280 GGCGCC
1 GGCGCC
12286 CTGGGTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 17 0.46
34 20 0.54
ACGTcount: A:0.08, C:0.34, G:0.44, T:0.14
Consensus pattern (34 bp):
GGCGCCTCCCCATATGGTGGCGGCGCGATCCGGG
Found at i:14740 original size:26 final size:25
Alignment explanation
Indices: 14700--14748 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
14690 CACTACAACA
* * *
14700 AAACCAATCAGAAATCATGAACACTC
1 AAACCAAGCAAAAAT-ATAAACACTC
14726 AAACCAAGCAAAAATATAAACAC
1 AAACCAAGCAAAAATATAAACAC
14749 CTACACTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.57, C:0.24, G:0.06, T:0.12
Consensus pattern (25 bp):
AAACCAAGCAAAAATATAAACACTC
Found at i:17054 original size:17 final size:17
Alignment explanation
Indices: 17014--17054 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
17004 TACCCAAAAT
17014 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
17031 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
17047 TTTCGGGT
1 TTTCGGGT
17055 TGGACGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:20237 original size:18 final size:18
Alignment explanation
Indices: 20214--20248 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20204 CCCCTCTTCC
*
20214 TCTTCCCCTTCTCTCTGT
1 TCTTCCCCCTCTCTCTGT
20232 TCTTCCCCCTCTCTCTG
1 TCTTCCCCCTCTCTCTG
20249 GACTCGACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.49, G:0.06, T:0.46
Consensus pattern (18 bp):
TCTTCCCCCTCTCTCTGT
Found at i:21213 original size:17 final size:18
Alignment explanation
Indices: 21191--21226 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21181 AATTTTTAAA
*
21191 TTAACAAA-AATTATATT
1 TTAACAAATAAATATATT
21208 TTAACAAATAAATATATT
1 TTAACAAATAAATATATT
21226 T
1 T
21227 ACTACCTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAACAAATAAATATATT
Found at i:24399 original size:51 final size:50
Alignment explanation
Indices: 24298--24399 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
24288 GTTCTTCATA
* *
24298 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTATAGTGT
* *
24348 TTTTCTCTTGTTTCA-ATCTTGTGTCCGGAC-ATACAAACACT-GTATACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTATA-GTGT
24399 T
1 T
24400 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 10 0.23
51 33 0.75
52 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.43
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTATAGTGT
Found at i:28801 original size:22 final size:21
Alignment explanation
Indices: 28776--28829 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
28766 GAAGTTCGTG
28776 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
28798 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
28817 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
28830 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Done.