Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011524.1 Corchorus olitorius cultivar O-4 contig11557, 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: 2133
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Found at i:388 original size:21 final size:21
Alignment explanation
Indices: 362--495 Score: 191
Period size: 21 Copynumber: 6.4 Consensus size: 21
352 TGCTAGAAGT
362 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
383 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
404 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
425 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
446 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
**
467 TCATTGGAG-AAGGTTTTAAGC
1 TCATTGGAGCAA-GTTCCAAGC
488 TCATTGGA
1 TCATTGGA
496 AATGCCTAAG
Statistics
Matches: 105, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 104 0.99
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:2081 original size:154 final size:154
Alignment explanation
Indices: 1308--2133 Score: 1456
Period size: 155 Copynumber: 5.4 Consensus size: 154
1298 ATTCGTATCA
*
1308 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTTAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
* *
1372 AATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGTCCAAAATAACAAGTGTTCCAAA
66 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
1437 TGAGCTAAAAACTTCACAGTGGAC
131 TGAGCTAAAAACTTCACAGTGGAC
1461 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
*
1526 AATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCCCAAAATAAGCAAGTGTTCCAA
66 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA-CAAGTGTTCCAA
1591 ATGAGCTAAAAACTTCACAGTGGAC
130 ATGAGCTAAAAACTTCACAGTGGAC
* *
1616 TAATCTCACCATAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGATTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC-
* *
1681 AAATTGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA
65 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
1746 ATGAGCTAAAAACTTCACAGTGGAC
130 ATGAGCTAAAAACTTCACAGTGGAC
*
1771 TAATCTCACCATAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC-
*
1836 AAATTGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
65 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
* *
1901 ATGAGCTAAAAACTTCACAATCGAC
130 ATGAGCTAAAAACTTCACAGTGGAC
*
1926 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
* * * *
1991 AATCGAAAACGATTCAAAACGGAACGAATGGTCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAA
66 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
*
2056 TGAGCTAAAAACTTCTCAGTGGAC
131 TGAGCTAAAAACTTCACAGTGGAC
2080 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
Statistics
Matches: 649, Mismatches: 21, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
153 45 0.07
154 205 0.32
155 349 0.54
156 50 0.08
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
TGAGCTAAAAACTTCACAGTGGAC
Done.