Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011335.1 Corchorus olitorius cultivar O-4 contig11368, 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: 2195
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Found at i:519 original size:154 final size:154
Alignment explanation
Indices: 1--1326 Score: 2088
Period size: 154 Copynumber: 8.6 Consensus size: 154
* * *
1 ATAGTTAGGCCATAAAACAACT-TAAAGAAAAGC-TTCGAGGATTGCCAAATCGAAGATGATTCA
1 ATAGTTAGGCCAT-AAACAA-TGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGACGATTCA
* *
64 AAACGGAACCAATGGGCCCCCGATAGGCCCTAAAAATAACAAGTGTTCCAAATGAGTTAAAAACT
63 AAACGGAACTAATGGG-CCCCGATAGGCCC--AAAATAACAAGTGTTCCAAATGAGCTAAAAACT
*
129 TCACAGTGGACTAATCTCTCCAAAATGATT
125 TCACAGTGGACTAATCTCACCAAAATGATT
*
159 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCTAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
* * *
224 CGGAACTAATTGGCCCCGATAGGCCCAAAATAAACAAGTAGTTCCAAATGAGTTAAAAACTTCTC
66 CGGAACTAATGGGCCCCGATAGGCCCAAAAT-AACAAGT-GTTCCAAATGAGCTAAAAACTTCAC
289 AGTGGACTAATCTCACCAAAATGATT
129 AGTGGACTAATCTCACCAAAATGATT
*
315 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCGAATCGAAGACGATTCAAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
* * *
380 AGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTTAAAACTTCACAG
66 CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
*
445 TGGACTAATCTCACCATAATGATT
131 TGGACTAATCTCACCAAAATGATT
* * *
469 GTAGTTAGGCCAGAAACAATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGAAGACGATTCAAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
* *
534 CGGAATTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAA
66 CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
*
599 TCGACTAATCTCACCAAAATGATT
131 TGGACTAATCTCACCAAAATGATT
* * * *
623 ATAGTTAGGCCGTAAACAACT-TAAAGAAAAGC-TTCGAGGATTGCCAAATCGAAGATGATTCAA
1 ATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGACGATTCAA
*
686 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCAC
64 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
751 AGTGGACTAATCTCACCAAAATGATT
129 AGTGGACTAATCTCACCAAAATGATT
* * * * *
777 ATAGTTAGGCCATAAACAATGGAAAGAAATGCATTTAGGTTTGCCAAATGGAAGACAATGCAAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
842 CGGAACTAAT-GGCCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
66 CGGAACTAATGGGCCCC-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
*
906 GTGGACTAATCTCACCATAATGATT
130 GTGGACTAATCTCACCAAAATGATT
*
931 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGAAGACGATTCAAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
*
996 CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCAAAAAACTTCACAG
66 CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* * *
1061 TCGACTAATCTCACCAAATTAATT
131 TGGACTAATCTCACCAAAATGATT
*
1085 ATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
*
1150 CGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG-TCAAAAACTTCACA
66 CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCACA
* *
1214 GTGGACTAATCTCACCATATTGATT
130 GTGGACTAATCTCACCAAAATGATT
* * **
1239 ATAGTTAGGCCATAAACAATGGAAAGAAAAGTAGTGAGGTTTGCCAAAATTTAAGACGATTCAAA
1 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC-AAATCGAAGACGATTCAAA
1304 ACGGAACTAATGGGCCCCGATAG
65 ACGGAACTAATGGGCCCCGATAG
1327 TGATGCGCCA
Statistics
Matches: 1084, Mismatches: 72, Indels: 27
0.92 0.06 0.02
Matches are distributed among these distances:
153 9 0.01
154 790 0.73
155 62 0.06
156 154 0.14
157 54 0.05
158 15 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
TGGACTAATCTCACCAAAATGATT
Found at i:1459 original size:21 final size:21
Alignment explanation
Indices: 1433--1545 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
1423 TGCTAGAAGT
1433 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
1454 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
1475 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
1496 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
1517 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
1538 TCATTGGA
1 TCATTGGA
1546 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
Done.