Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013811.1 Corchorus olitorius cultivar O-4 contig13844, 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: 12706
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2763 original size:2 final size:2
Alignment explanation
Indices: 2756--2813 Score: 54
Period size: 2 Copynumber: 31.5 Consensus size: 2
2746 TATTATACAC
* * *
2756 TA TA TA TA T- TA T- TA TA TA TA TA -A TA TC TT TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2795 TA TA TA TA TA -A TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA T
2814 CTTTACATAC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
1 5 0.11
2 41 0.89
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2814 original size:32 final size:33
Alignment explanation
Indices: 2751--2822 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 33
2741 AATTATATTA
2751 TACACTATATATATTATTATATATATAATATCTT
1 TACA-TATATATATTATTATATATATAATATCTT
2785 TACATATATATA-TA-TATATAATATAATATCTT
1 TACATATATATATTATTATAT-ATATAATATCTT
2817 TACATA
1 TACATA
2823 CATACATAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
31 5 0.14
32 20 0.54
33 8 0.22
34 4 0.11
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (33 bp):
TACATATATATATTATTATATATATAATATCTT
Found at i:6402 original size:2 final size:2
Alignment explanation
Indices: 6348--6386 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6338 AGGAGAAAGT
6348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6387 CTAATTCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9092 original size:33 final size:33
Alignment explanation
Indices: 9050--9168 Score: 168
Period size: 33 Copynumber: 3.6 Consensus size: 33
9040 TTCGGTGTCA
9050 CCCTAGGAGGGCGGCAAGCCGTGCTGAGTGCCG
1 CCCTAGGAGGGCGGCAAGCCGTGCTGAGTGCCG
*
9083 CCCTAGGAGGGCGACAAGCCGTGCTGAGTGCCG
1 CCCTAGGAGGGCGGCAAGCCGTGCTGAGTGCCG
* * *
9116 CCCTAGGAGGGCGGCATGCCATGGTTG-GTGCCG
1 CCCTAGGAGGGCGGCAAGCCGT-GCTGAGTGCCG
**
9149 CCCTCCGAGGGCGGCAAGCC
1 CCCTAGGAGGGCGGCAAGCC
9169 ATGGTTATGC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
33 74 0.96
34 3 0.04
ACGTcount: A:0.15, C:0.32, G:0.40, T:0.13
Consensus pattern (33 bp):
CCCTAGGAGGGCGGCAAGCCGTGCTGAGTGCCG
Found at i:9170 original size:33 final size:33
Alignment explanation
Indices: 9050--9184 Score: 166
Period size: 33 Copynumber: 4.1 Consensus size: 33
9040 TTCGGTGTCA
*
9050 CCCTAGGAGGGCGGCAAGCCGTGCTGAGTGCCG
1 CCCTAGGAGGGCGGCAAGCCATGCTGAGTGCCG
* *
9083 CCCTAGGAGGGCGACAAGCCGTGCTGAGTGCCG
1 CCCTAGGAGGGCGGCAAGCCATGCTGAGTGCCG
* *
9116 CCCTAGGAGGGCGGCATGCCATGGTTG-GTGCCG
1 CCCTAGGAGGGCGGCAAGCCAT-GCTGAGTGCCG
** * *
9149 CCCTCCGAGGGCGGCAAGCCATGGTTA-TGCCG
1 CCCTAGGAGGGCGGCAAGCCATGCTGAGTGCCG
9181 CCCT
1 CCCT
9185 CAGCACCAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
32 11 0.12
33 76 0.84
34 3 0.03
ACGTcount: A:0.15, C:0.32, G:0.39, T:0.15
Consensus pattern (33 bp):
CCCTAGGAGGGCGGCAAGCCATGCTGAGTGCCG
Found at i:11231 original size:21 final size:21
Alignment explanation
Indices: 11205--11246 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
11195 TTCAACAGAC
11205 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
11226 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
11247 TCTGATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGAGTTGT
Found at i:11257 original size:71 final size:70
Alignment explanation
Indices: 11132--11326 Score: 257
Period size: 71 Copynumber: 2.8 Consensus size: 70
11122 TTTTTCCGCT
* * * * *
11132 ACAAGTCCTGGGCAAGAATTGTCCAAGTCCTGGACAGGACTTGTTCTAAATTTTCTTCCGTCTTT
1 ACAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGATTTTTCTTCCGTCTTT
11197 CAACAG
65 CAACAG
*
11203 ACCAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTT
1 A-CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGATTTTTCTTCCGTCTTT
11268 CAACAG
65 CAACAG
* * ** *
11274 ACAAGATCCTAGGCAGTAGTTGTCAAAACCTGGGCAGGACTTGTCCTG-TTTTT
1 ACAAG-TCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGATTTTT
11327 AGCCTTCAAT
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
70 9 0.08
71 82 0.75
72 19 0.17
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (70 bp):
ACAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGATTTTTCTTCCGTCTTTC
AACAG
Done.