Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023036.1 Corchorus olitorius cultivar O-4 contig23069, 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: 41505
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:10312 original size:20 final size:21
Alignment explanation
Indices: 10276--10321 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
10266 ACTCAACATG
*
10276 TATCAGAGAACTTACTTGAGA
1 TATCAAAGAACTTACTTGAGA
10297 TATCAAAGAA-TTACTTGAGA
1 TATCAAAGAACTTACTTGAGA
10317 TATCA
1 TATCA
10322 GTTCCTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
TATCAAAGAACTTACTTGAGA
Found at i:15915 original size:22 final size:22
Alignment explanation
Indices: 15874--15951 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
15864 TATTTTTATG
15874 AAATTTTGATAACTACCCTA-A
1 AAATTTTGATAACTACCCTATA
*
15895 TAAATTTTGATAATTTA-CCTATA
1 -AAATTTTGATAA-CTACCCTATA
* * *
15918 AAATTGTGATAAACT-CCATATG
1 AAATTTTGAT-AACTACCCTATA
*
15940 AAACTTTGATAA
1 AAATTTTGATAA
15952 GCTAACTATG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
21 2 0.04
22 38 0.84
23 5 0.11
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACTACCCTATA
Found at i:16043 original size:22 final size:20
Alignment explanation
Indices: 15979--16047 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
15969 AATAAATTTT
*
15979 CCTATGAAATTTTGTAACCTT
1 CCTATG-AATTTTGTAACCTC
* *
16000 CCTATGATTTTTAATAACCTC
1 CCTATGAATTTT-GTAACCTC
*
16021 CCTATGAGATTTTGTTAATCTC
1 CCTATGA-ATTTTG-TAACCTC
16043 CCTAT
1 CCTAT
16048 ATCTTTTGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.13
21 19 0.49
22 15 0.38
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (20 bp):
CCTATGAATTTTGTAACCTC
Found at i:21194 original size:23 final size:24
Alignment explanation
Indices: 21164--21247 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 24
21154 TATAGTATAG
21164 ATAATA-TATATATTAATAAATAA
1 ATAATAGTATATATTAATAAATAA
*
21187 ATAATA-TATATTTTAA-ATAATAA
1 ATAATAGTATATATTAATA-AATAA
*
21210 ATAATGAGT-TA-A-AAATAAATAA
1 ATAAT-AGTATATATTAATAAATAA
*
21232 ATAAATATTATATATT
1 AT-AATAGTATATATT
21248 TAATTATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
22 12 0.25
23 31 0.65
24 4 0.08
25 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAATAGTATATATTAATAAATAA
Found at i:22039 original size:1 final size:1
Alignment explanation
Indices: 22033--22058 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
22023 GAAAGAAAGC
22033 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
22059 GCCAACTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32696 original size:214 final size:215
Alignment explanation
Indices: 32326--32717 Score: 714
Period size: 214 Copynumber: 1.8 Consensus size: 215
32316 TCAACTGAAT
*
32326 ATACAGATTACATTTGTAATAAAAGAAAGAAAGAAAAACTTGTTTAGGTACTGATAAGCCTTTTA
1 ATACAGATTACATTTGTAATAAAAGAAAGAAAGAAAAACTTCTTTAGGTACTGATAAGCCTTTTA
* *
32391 CTTGTCCACTAAAAGAAGTCCTTTTTTTTTCTTTTATGAAATTCTCAGTATTCAGTAGTTACATT
66 CTTGTCCACTAAAAGAAGTCCTTTTTTTTTCTTTTATGAAATTCGCAGTATTCAATAGTTACATT
32456 GAATCTCTGAATAATTCAGAGTCAAGTTGCGTTGGACCTCAATTGAGGGAATTAGATACAATCAT
131 GAATCTCTGAATAATTCAGAGTCAAGTTGCGTTGGACCTCAATTGAGGGAATTAGATACAATCAT
32521 ACAAATATCAATATTGATTG
196 ACAAATATCAATATTGATTG
* *
32541 ATACAGATTACATTTGTAATAAAAGAAAGAAA-AAAAATTTCTTTAGGTATTGATAAGCCTTTTA
1 ATACAGATTACATTTGTAATAAAAGAAAGAAAGAAAAACTTCTTTAGGTACTGATAAGCCTTTTA
*
32605 CTTGTCCACTAAAAGAAGTTCTTTTTTTTTCTTTTATGAAATTCGCAGTATTCAATAGTTACATT
66 CTTGTCCACTAAAAGAAGTCCTTTTTTTTTCTTTTATGAAATTCGCAGTATTCAATAGTTACATT
*
32670 GAATCTCTGAATAATTCAGAGTCAAGTTGCGTTGGATCTCAATTGAGG
131 GAATCTCTGAATAATTCAGAGTCAAGTTGCGTTGGACCTCAATTGAGG
32718 AGAGATCTCA
Statistics
Matches: 170, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
214 138 0.81
215 32 0.19
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (215 bp):
ATACAGATTACATTTGTAATAAAAGAAAGAAAGAAAAACTTCTTTAGGTACTGATAAGCCTTTTA
CTTGTCCACTAAAAGAAGTCCTTTTTTTTTCTTTTATGAAATTCGCAGTATTCAATAGTTACATT
GAATCTCTGAATAATTCAGAGTCAAGTTGCGTTGGACCTCAATTGAGGGAATTAGATACAATCAT
ACAAATATCAATATTGATTG
Done.