Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011545.1 Corchorus olitorius cultivar O-4 contig11578, 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: 3041
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Found at i:31 original size:21 final size:21
Alignment explanation
Indices: 1--56 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
*
1 CCAAGTTCATTGGAGAAGGTT
1 CCAAGATCATTGGAGAAGGTT
22 CCAAGATCATTGGAGAAGGTT
1 CCAAGATCATTGGAGAAGGTT
* *
43 TCAAGCTCATTGGA
1 CCAAGATCATTGGA
57 AATGCCTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (21 bp):
CCAAGATCATTGGAGAAGGTT
Found at i:1609 original size:21 final size:21
Alignment explanation
Indices: 1583--1695 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
1573 TGCTAGAAGT
1583 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
1604 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
1625 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
1646 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
1667 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
1688 TCATTGGA
1 TCATTGGA
1696 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:2777 original size:154 final size:153
Alignment explanation
Indices: 2497--3041 Score: 823
Period size: 154 Copynumber: 3.6 Consensus size: 153
2487 ATTCGTATCA
* *
2497 TGTTCCAAATGGGCTAAAAACTTCTCAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * * *
2562 AAACAATGGAAAGAAAAG-ACTTTAGAGTTGCCAAATCGGAGATGATTCAAAACGGAACTAATGG
66 AAACAATGGAAAGAAAAGCA-TTGAGATTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGG
*
2626 GCCCCGGTAGGCCCAAAATAACAAG
129 GCCCCGATAGGCCCAAAATAACAAG
**
2651 TGTTCCAAATTTGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* *
2716 AAACAATGGAAAGAAACGCATGGAGATTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGG
66 AAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGG
2781 CCCCGATAGGCCCAAAATAACAAG
130 CCCCGATAGGCCCAAAATAACAAG
* * * *
2805 TGTTCCGAATGAGCTAAAAACTTACACAATGGACTAATCTCACCAAAATGAATATAGTTAGGTCA
1 TGTTCCAAATGAGCTAAAAACTT-CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* * * *
2870 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACTATTCAAAACGGACTAATGAG
65 TAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGG
2935 -CCCGATAGGCCCAAAAT-ACAAG
130 CCCCGATAGGCCCAAAATAACAAG
* *
2957 TGTTCCGAATGAGCT-AAAACATCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
3020 -AACAATGGAAAGAAAAGCATTG
66 AAACAATGGAAAGAAAAGCATTG
Statistics
Matches: 362, Mismatches: 27, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
148 22 0.06
149 19 0.05
150 19 0.05
151 6 0.02
152 20 0.06
153 17 0.05
154 170 0.47
155 89 0.25
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (153 bp):
TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
AAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGC
CCCGATAGGCCCAAAATAACAAG
Done.