Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011753.1 Corchorus olitorius cultivar O-4 contig11786, 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, 751
Length: 1253
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Found at i:589 original size:154 final size:154
Alignment explanation
Indices: 9--1253 Score: 1762
Period size: 154 Copynumber: 8.0 Consensus size: 154
1 GAAACGAA
* * * *
9 CCCAAAATAACTAGTGTTCCAAATGAGCTAAAAACTTCAGAGTGGACTAGTCTCACCAATATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* * * * *
74 TATAGTTAGTGCAATAAACAATGAAAAAAAAAAGCAT-TAGGGTTTGCCGAATCGAAGACGATTC
66 TATAGTTAG-GCCATAAACAATG-GAAAGAAAAGCATCGAGGG-TTGCCAAATCGAAGACGATTC
* * **
138 AAAACATCACTTATGGGCGTCGATAGG
128 AAAACGTCACTAATGGGCCCCGATAGG
* *
165 CCCAAAATAGCAAGTG-TACAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* *
229 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAA
294 ACGTCACTAACTGGGCCCCCGATAGG
131 ACGTCACTAA-TGGG-CCCCGATAGG
320 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAGTGGACTAAATCTCACCAAAATG
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC-AGTGGACT-AATCTCACCAAAATG
* * *
385 ATTATAGTTAGGCCATAAACAATCGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA
64 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCA
450 AAACGTCACTAATGGGCCCCGATAGG
129 AAACGTCACTAATGGGCCCCGATAGG
* * *
476 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTTAGCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* *
541 TATAGTTAGCCCATAAACAGTGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAA
** *
606 ACGGAACTAATGGGCCCCGAAAGG
131 ACGTCACTAATGGGCCCCGATAGG
*
630 CCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* *
695 TATAGTTAGGCCATAAACAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGATGACGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAA
** * **
760 ACGAAACTAATGGCCCCCGGGAGG
131 ACGTCACTAATGGGCCCCGATAGG
* *
784 CCTAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* * *
849 TATAGTTAGGCCATAAACAATCGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAA
914 ACGTCACTAATGGGCCCCGATAGG
131 ACGTCACTAATGGGCCCCGATAGG
*
938 CCCAAATTAACAAGTGTTCCAAATGAGCCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 CCCAAAATAACAAGTGTTCCAAATGAG-CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * *
1003 TTATAGTTCA--CCATAAACAATGGAAACAAAAGCATCGAGGGTTGCGAAATCGATGACGATTCA
65 TTATAGTT-AGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCA
** *
1066 AATACGAAAACTAAATGGCCCCCGGA-ACGGG
129 AA-ACG-TCACT-AATGGGCCCC-GATA--GG
* * * * *
1097 CCTAAAATAAACAAGTGTTCCAAATGAGTTAAAAACTTACACAGTAGACTATTCTCAGCAAAAAT
1 CCCAAAAT-AACAAGTGTTCCAAATGAGCTAAAAACTT-CACAGTGGACTAATCTCA-CCAAAAT
*
1162 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGATGACGATTA
63 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATT-
* *
1227 CAGAGCGTCGACTAATAGGGCCCCGAT
127 CAAAACGTC-ACTAAT-GGGCCCCGAT
Statistics
Matches: 988, Mismatches: 78, Indels: 40
0.89 0.07 0.04
Matches are distributed among these distances:
153 42 0.04
154 473 0.48
155 132 0.13
156 89 0.09
157 22 0.02
158 93 0.09
159 17 0.02
160 36 0.04
161 21 0.02
162 60 0.06
163 3 0.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (154 bp):
CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAA
ACGTCACTAATGGGCCCCGATAGG
Done.