Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018409.1 Corchorus olitorius cultivar O-4 contig18442, 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, 739
Length: 1233
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Found at i:1034 original size:153 final size:154
Alignment explanation
Indices: 500--1233 Score: 1100
Period size: 154 Copynumber: 4.8 Consensus size: 154
490 GAAACAACTT
* *
500 AAAGAAAAGCTTTGAGGTTTGCCAAATCGAAAACGATTCAAAAACGTCACTAATGGGC-CCAGAT
1 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC-AAAACGTCACTAATGGGCACC-GAT
* * * *
564 AGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACATCACAGTGGACTAATCTCACCAAATT
64 AGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
*
629 GATCACAGTTAGTCCATAAATAATGG
129 GATCACAGTTAGTCCATAAACAATGG
* ** * * *
655 AAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACCAATGGGCCCCGATTG
1 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCACCGATAG
720 GTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
66 GTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* *
785 TTAGAGTTAGTCCATAAACAATGG
131 TCACAGTTAGTCCATAAACAATGG
*
809 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCCCTAATGGGCACCGATAG
1 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCACCGATAG
* * * *
874 G-CCAAGATTAACAAGTGTTTCAAATGAGCTAAAAACTTCGCAGTGGACTAATCTCATCAAAATG
66 GTCCAA-AATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
* * *
938 ATTATAGTTAGTCCATAAA-AATGA
130 ATCACAGTTAGTCCATAAACAATGG
*
962 AAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCACCGATAG
1 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCACCGATAG
* * * * *
1027 G-CCAAGATAACAAGTGTTCCAATTGAGCTAAAAACATCATAGTGGACTAATCTCACCAAATTGA
66 GTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1091 TCACAGTTAGT-CATAAACAATGG
131 TCACAGTTAGTCCATAAACAATGG
* ** * *
1114 AAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACCAATGGGCCCCGATAG
1 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCACCGATAG
1179 GTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
66 GTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
Statistics
Matches: 524, Mismatches: 51, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
151 6 0.01
152 123 0.23
153 125 0.24
154 232 0.44
155 38 0.07
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCACCGATAG
GTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
TCACAGTTAGTCCATAAACAATGG
Done.