Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015743.1 Corchorus olitorius cultivar O-4 contig15776, 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, 806
Length: 1344
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:642 original size:155 final size:154
Alignment explanation
Indices: 7--1344 Score: 1936
Period size: 155 Copynumber: 8.7 Consensus size: 154
1 ACAAAA
7 GGACTAATCTCACCAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGCATTGAGGT
1 GGACTAATCTCACC-AAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGGT
* * * * *
72 TTGCCAAACCGAAGACAATTCAAAAC-TGAACTAATGGGCCTCGATAGGCACAAAATAACAACGT
64 TTGCCAAATCGAAGACGATTCAAAACGT-CACTAATGGGCCCCGATAGGCCCAAAATAACAA-GT
*
136 GTTCCAAATGAGCTAAAATCTTCACAGT
127 GTTCCAAATGAGCTAAAAACTTCACAGT
* *
164 GGACAAATCTCATC-AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
1 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
* * * * * *
228 GCGAAACCGAAGACAATTCAAAAC-TGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGTT
66 GCCAAATCGAAGACGATTCAAAACGT-CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
292 CCAAATGAGCTAAAAACTTCACAGT
130 CCAAATGAGCTAAAAACTTCACAGT
* *
317 GGACTAATCTCACCAAAATGATTAT--TTAGGCCATAGACAATGGAAA-AAAAGAATTGAGGTTT
1 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
* * ** *
379 GCCAAATCGAAGACGATTCAAAACGTCACTATTGGGCCTCGATAGGAACATAATAACAAGTGTTC
66 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
444 CAAATGAGCTAAAAACTTCACAGT
131 CAAATGAGCTAAAAACTTCACAGT
*
468 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTT
1 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
* *
533 GCCAAATCGAAGACGATTCAAAACGTCACTGATTGCGCCCCGATAGGCCCAAAATAACAAGTGTT
66 GCCAAATCGAAGACGATTCAAAACGTCACT-AATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
*
598 CCAAATGAGCAAAAAACTTCACAGT
130 CCAAATGAGCTAAAAACTTCACAGT
* * *
623 GGACAAATCTCACCAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAATCATTGAGGTTT
1 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
* *
688 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCTCCGATAGGACCCAAAATAACAAGTGTT
66 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGG-CCCAAAATAACAAGTGTT
753 CCAAATGAGCTAAAAACTTCACAGT
130 CCAAATGAGCTAAAAACTTCACAGT
778 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGTTT
1 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
* * *
842 GCCAAGTCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTTTTC
66 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
907 CAAATGAGCTAAAAACTTCACAGT
131 CAAATGAGCTAAAAACTTCACAGT
*
931 GGACTAATCTCACC-AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAAGGTT
1 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTT
* * *
995 T-CCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGAG--CAAAAT-ACAAATGC
65 TGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAG-GCCCAAAATAACAAGTGT
1055 TCCAAATGAGCTAAAAAACTTCACAGT
129 TCCAAATGAGCT-AAAAACTTCACAGT
** * * *
1082 GGACTAATCTCATGAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAGGCATCGAAGG-T
1 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTT
* * *
1146 TGCGAAATACGAAGACGATTCAAAACGTACACTAATGGTCCCCGACTTGGCCCAAAATAATCAAG
65 TGCCAAAT-CGAAGACGATTCAAAACGT-CACTAATGGGCCCCGA-TAGGCCCAAAATAA-CAAG
* *
1211 TTTTACAAATGAGCTAAAAACTTCACAGT
126 TGTTCCAAATGAGCTAAAAACTTCACAGT
* *
1240 GGACTAATCTCACC-AAATGATTATTGTTAGGCCATAAACAATGG-AAGAAAAGACATCGAAGG-
1 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTG-AGGT
* *
1302 TTGTCAAATCGAAGACGATTCAAAAACGTCACTAATGGTCCCC
64 TTGCCAAATCGAAGACGATTC-AAAACGTCACTAATGGGCCCC
Statistics
Matches: 1095, Mismatches: 63, Indels: 47
0.91 0.05 0.04
Matches are distributed among these distances:
150 17 0.02
151 154 0.14
152 123 0.11
153 167 0.15
154 206 0.19
155 282 0.26
156 35 0.03
157 69 0.06
158 27 0.02
159 15 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
CAAATGAGCTAAAAACTTCACAGT
Found at i:1279 original size:309 final size:308
Alignment explanation
Indices: 7--1344 Score: 1931
Period size: 309 Copynumber: 4.3 Consensus size: 308
1 ACAAAA
*
7 GGACTAATCTCACCAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAAGCATTGAGGT
1 GGACTAATCTCACC-AAAATGATTATTGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGGT
* * * *
72 TTGCCAAACCGAAGACAATTCAAAAC-TGAACTAATGGGCCTCGATAGGCA-CAAAATAACAACG
64 TTGCCAAATCGAAGACGATTCAAAACGT-CACTAATGGGCCCCGATAGG-AGCAAAATAACAA-G
* * *
135 TGTTCCAAATGAGCTAAAATCTTCACAGTGGACAAATCTCATC-AAATGATTATAGTTAGGCCAT
126 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * * *
199 AAACAATGGAAAGAAAAGCATTGAGGTTTGCGAAACCGAAGACAATTCAAAAC-TGAACTAATGG
191 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT-CACTAATGG
* * *
263 GCCTCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
255 TCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
* *
317 GGACTAATCTCACCAAAATGATTA-T-TTAGGCCATAGACAATGGAAA-AAAAGAATTGAGGTTT
1 GGACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
* * * *
379 GCCAAATCGAAGACGATTCAAAACGTCACTATTGGGCCTCGATAGGAACATAATAACAAGTGTTC
66 GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGAGCAAAATAACAAGTGTTC
444 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
131 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* *
509 ATGGAAAGAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTGATTGCG-CCC
196 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACT-AATG-GTCCC
*
573 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCAAAAAACTTCACAGT
259 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
* *
623 GGACAAATCTCACCAAAATGATTATAT-TTAGGCCATAAACAATGGAAAGAAAATCATTGAGGTT
1 GGACTAATCTCACCAAAATGATTAT-TGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTT
* * *
687 TGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCTCCGATAGGACCCAAAATAACAAGTGT
65 TGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGA-GCAAAATAACAAGTGT
752 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
129 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
*
817 CAATGGAAAG-AAAGCATTGAGGTTTGCCAAGTCGAAGACGATTCAAAACGTCACTAATGGTCCC
194 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCC
*
881 CGATAGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAAAACTTCACAGT
259 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
* *
931 GGACTAATCTCACC-AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAAGGTT
1 GGACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTT
* * *
995 T-CCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATA-GAGCAAAAT-ACAAATGCT
65 TGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGAGCAAAATAACAAGTGTT
** *
1056 CCAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCATGAAAATGATTATATTTAGGCCATAAA
130 CCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * *
1121 CAATGGAAAGAAAGGCATCGAAGG-TTGCGAAATACGAAGACGATTCAAAACGTACACTAATGGT
194 CAATGGAAAGAAAAGCATTG-AGGTTTGCCAAAT-CGAAGACGATTCAAAACGT-CACTAATGGT
* * *
1185 CCCCGACTTGGCCCAAAATAATCAAGTTTTACAAATGAGCTAAAAACTTCACAGT
256 CCCCGA-TAGGCCCAAAATAA-CAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
*
1240 GGACTAATCTCACC-AAATGATTATTGTTAGGCCATAAACAATGG-AAGAAAAGACATCGAAGG-
1 GGACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAG-CATTG-AGGT
* *
1302 TTGTCAAATCGAAGACGATTCAAAAACGTCACTAATGGTCCCC
64 TTGCCAAATCGAAGACGATTC-AAAACGTCACTAATGGGCCCC
Statistics
Matches: 946, Mismatches: 58, Indels: 47
0.90 0.06 0.04
Matches are distributed among these distances:
303 18 0.02
304 108 0.11
305 154 0.16
306 115 0.12
307 102 0.11
308 117 0.12
309 211 0.22
310 109 0.12
311 12 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (308 bp):
GGACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGAGCAAAATAACAAGTGTTC
CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCG
ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
Done.