Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011780.1 Corchorus olitorius cultivar O-4 contig11813, 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, 780
Length: 1300
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Found at i:392 original size:154 final size:153
Alignment explanation
Indices: 1--811 Score: 1239
Period size: 154 Copynumber: 5.3 Consensus size: 153
* * *
1 AGTGGACTAATGTCACCAAAATGATTATAGATAGGCCATAAACAATGGAAAGAAAAGCCTTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTA-GCCATAAACAATGGAAAGAAAAGCATTGAGG
* * *
66 TTTGCCAAATCGAAGACGATACAAAATGTCACTAATGGGCCCCGATAGGCCCAAAGTAACAAGTG
65 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
* *
131 ATCCAAACGAGCTAAAAAACTTCAC
130 TTCCAAATGAGCT-AAAAACTTCAC
* * *
156 AGAGGACTAATCTCACCAAATTGATTATAGTTACGCCATAAACCATGGAAAGAAAAGCATTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTA-GCCATAAACAATGGAAAGAAAAGCATTGAGG
*
221 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCGCGATAGGCCCAAAATAACAAGTG
65 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
286 TTCCAAATGAGCTAAAAACTTCAC
130 TTCCAAATGAGCTAAAAACTTCAC
* * *
310 AGTGGACTAATCTCACCAAAATGATTATATTTAGTCCATAAACAGTGGAAAGAAAAGCATTGAAG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAG-CCATAAACAATGGAAAGAAAAGCATTGAGG
* ** *
375 TTTGCCAAATCGAAGACGATTTAAATTGTCACTAATGTGCCCCGATAGGCCCAAAATAACAAGT-
65 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
439 TATCCAAATGAGCTAAAAACTTCAC
130 T-TCCAAATGAGCTAAAAACTTCAC
*
464 AGTGGACTAATCTCACCAAATTGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTA-GCCATAAACAATGGAAAGAAAAGCATTGAGG
* *
529 TTTGCCAAATCGAAGACGATTCAAAA-GTCACTAATGGGCCGCGATAGGGCCAAAATAACAAGTG
65 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
593 TTCCAAATGAGCTAAAAACTTCAC
130 TTCCAAATGAGCTAAAAACTTCAC
*
617 AGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATAGAAAGAAAAGCATTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAG-CCATAAACAATGGAAAGAAAAGCATTGAGG
** ** *
682 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTAGATAGGCCCAAAATAACAAGTA
65 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
* * *
747 TTCCAATTGAGCTAAGAACTTCAT
130 TTCCAAATGAGCTAAAAACTTCAC
* *
771 AGTGGACTAATCTCATCAAAATGATTATAGGTAGGCCATAA
1 AGTGGACTAATCTCACCAAAATGATTATAGTTA-GCCATAA
812 TGATGCGCCA
Statistics
Matches: 603, Mismatches: 46, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
152 1 0.00
153 146 0.24
154 324 0.54
155 132 0.22
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (153 bp):
AGTGGACTAATCTCACCAAAATGATTATAGTTAGCCATAAACAATGGAAAGAAAAGCATTGAGGT
TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
TCCAAATGAGCTAAAAACTTCAC
Found at i:656 original size:307 final size:308
Alignment explanation
Indices: 1--811 Score: 1320
Period size: 307 Copynumber: 2.6 Consensus size: 308
* * * *
1 AGTGGACTAATGTCACCAAAATGATTATAGATAGGCCATAAACAATGGAAAGAAAAGCCTTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGG
* * *
66 TTTGCCAAATCGAAGACGATACAAAATGTCACTAATGGGCCCCGATAGGCCCAAAGTAACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTT
* *
131 ATCCAAACGAGCTAAAAAACTTCACAGAGGACTAATCTCACCAAATTGATTATAGTTACGCCATA
131 ATCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTACGCCATA
*
196 AACCATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGC
195 AACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGC
261 CGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
260 CGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* * *
310 AGTGGACTAATCTCACCAAAATGATTATATTTAGTCCATAAACAGTGGAAAGAAAAGCATTGAAG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGG
* * *
375 TTTGCCAAATCGAAGACGATTTAAATTGTCACTAATGTGCCCCGATAGGCCCAAAATAACAAGTT
66 TTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTT
440 ATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTACGCCATAA
131 ATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTACGCCATAA
505 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA-GTCACTAATGGGCC
196 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
*
569 GCGATAGGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
261 GCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
*
617 AGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATAGAAAGAAAAGCATTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGG
* ** **
682 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTAGATAGGCCCAAAATAACAAG-T
66 TTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTT
* * * * * * *
746 ATTCCAATTGAGCTAAGAACTTCATAGTGGACTAATCTCATCAAAATGATTATAGGTAGGCCATA
131 A-TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTACGCCATA
811 A
195 A
812 TGATGCGCCA
Statistics
Matches: 465, Mismatches: 36, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
306 2 0.00
307 234 0.50
308 100 0.22
309 129 0.28
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (308 bp):
AGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGG
TTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTT
ATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTACGCCATAA
ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
GCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
Found at i:938 original size:21 final size:21
Alignment explanation
Indices: 914--988 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
904 AAGATGCTAG
914 AAGTTCATTGGAGAAGGTTCC
1 AAGTTCATTGGAGAAGGTTCC
935 AAGTTCATTGGAGAAGGTTCC
1 AAGTTCATTGGAGAAGGTTCC
** *
956 AAAATCATTGGAGAAGGTTTC
1 AAGTTCATTGGAGAAGGTTCC
*
977 AAGCTCATTGGA
1 AAGTTCATTGGA
989 ATTGCCTAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (21 bp):
AAGTTCATTGGAGAAGGTTCC
Done.