Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011711.1 Corchorus olitorius cultivar O-4 contig11744, 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, 709
Length: 1183
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Found at i:285 original size:153 final size:154
Alignment explanation
Indices: 1--1183 Score: 1765
Period size: 153 Copynumber: 7.7 Consensus size: 154
*
1 CAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAAC
1 CAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
*
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAGA--GAAGACGATTCAAAAC-GTCACTAA-TGAGC
65 AATGGAAAGAAAAGCATTGAGGGTTGCCAA-ATCGAAGACGATTCAAAACAG-AACTAATTG-GC
*
127 TCCGATAGGCCCAAAATAAAAATTGTTC
127 TCCGATAGGCCCAAAATAAAAAGTGTTC
* *
155 CAAATGAGCTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGATTATAGTTAGGGCATAAACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* * * *
220 ATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACAATTC-AAACAAAACTAATTGGCCCCG
66 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAGAACTAATTGGCTCCG
* *
284 ATAGGTCCAAAATAACAAGTGTTC
131 ATAGGCCCAAAATAAAAAGTGTTC
*
308 CAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* * * *
373 ATGGAAAGAAAAGCATTGCGGGTTGCC-AATCGAAGACGATTCAAAACAGAACTAATGGGCACAG
66 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAGAACTAATTGGCTCCG
437 ATAGGCCC-AAATAAAAAGTGTTC
131 ATAGGCCCAAAATAAAAAGTGTTC
*
460 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* *
525 ATGGAAAGAAAAGCATTGAGGGTTGCC-AATAGAAGACGATTCAAAAC-GTCACTAA-TGAGCTC
66 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATTG-GCTC
*
587 CGATAGGCCCAAAATAAAAATTGTTC
129 CGATAGGCCCAAAATAAAAAGTGTTC
*
613 CAAATGAGCTAAAAACTTACACAGTGGACTAAACTCACC-AAATAGATTATAGTTAGGCCATAAA
1 CAAATGAGCTAAAAACTT-CACAGTGGACTAATCTCACCAAAAT-GATTATAGTTAGGCCATAAA
* * * *
677 CAATGG-AAGAAAAGCATTGCGGGTTGCC-AATCGAAGACGATTCAAAACTGAACTAATGGGCAC
64 CAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAGAACTAATTGGCTC
*
740 AGATAGGCCC-AAATAAAAAGTGTTC
129 CGATAGGCCCAAAATAAAAAGTGTTC
*
765 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* *
830 ATGGAAAGAAAAGCATTGAGGGTTGCCAAGA--GAAGACGATTCAAAA-TGTCACTAA-TGAGCT
66 ATGGAAAGAAAAGCATTGAGGGTTGCCAA-ATCGAAGACGATTCAAAACAG-AACTAATTG-GCT
*
891 CCGATAGGCCCAAAATAAAAATTGTTC
128 CCGATAGGCCCAAAATAAAAAGTGTTC
* * *
918 AAAATGAGCTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGATTATAGTTAGGGCAT-AACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* * *
982 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
66 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAGAACTAATTGGCTCCG
* *
1047 ATAGGCCCAATATAACAAGTGTTC
131 ATAGGCCCAAAATAAAAAGTGTTC
* *
1071 CAAATGAGCCAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
*
1136 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACTATTCAAAAC
66 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
Statistics
Matches: 939, Mismatches: 66, Indels: 48
0.89 0.06 0.05
Matches are distributed among these distances:
151 50 0.05
152 276 0.29
153 491 0.52
154 122 0.13
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAGAACTAATTGGCTCCG
ATAGGCCCAAAATAAAAAGTGTTC
Found at i:601 original size:305 final size:305
Alignment explanation
Indices: 1--1183 Score: 1876
Period size: 305 Copynumber: 3.9 Consensus size: 305
* *
1 CAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAAC
1 CAAATGAGCT-AAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAAC
** * * * *
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAGAGAAGACGATTCAAAACGTCACTAATGAGCTCCG
65 AATGGAAAGAAAAGCATTGAGGGTTGCCAATCGAAGACGATTCAAAACG-AACTAATGGGCACAG
* *
131 ATAGGCCCAAAATAAAAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGAGTAATCTCACCAAA
129 ATAGGCCC-AAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
* * * *
196 ATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACAAT
193 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATAGAAGACGAT
*** * * * *
261 TC-AAACAAAACTAATTG-GCCCCGATAGGTCCAAAATAACAAGTGTTC
258 TCAAAACGTCACTAA-TGAGCTCCGATAGGCCCAAAATAAAAATTGTTC
308 CAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACA
*
373 ATGGAAAGAAAAGCATTGCGGGTTGCCAATCGAAGACGATTCAAAACAGAACTAATGGGCACAGA
66 ATGGAAAGAAAAGCATTGAGGGTTGCCAATCGAAGACGATTCAAAAC-GAACTAATGGGCACAGA
438 TAGGCCCAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
130 TAGGCCCAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
*
503 TATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC-AATAGAAGACGATTC
195 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATAGAAGACGATTC
567 AAAACGTCACTAATGAGCTCCGATAGGCCCAAAATAAAAATTGTTC
260 AAAACGTCACTAATGAGCTCCGATAGGCCCAAAATAAAAATTGTTC
613 CAAATGAGCTAAAAACTTACACAGTGGACTAAACTCACC-AAATAGATTATAGTTAGGCCATAAA
1 CAAATGAGCTAAAAACTT-CACAGTGGACTAAACTCACCAAAAT-GATTATAGTTAGGCCATAAA
*
677 CAATGG-AAGAAAAGCATTGCGGGTTGCCAATCGAAGACGATTCAAAACTGAACTAATGGGCACA
64 CAATGGAAAGAAAAGCATTGAGGGTTGCCAATCGAAGACGATTCAAAAC-GAACTAATGGGCACA
741 GATAGGCCCAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
128 GATAGGCCCAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
* *
806 ATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC-AAGAGAAGACGAT
193 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATAGAAGACGAT
*
870 TCAAAATGTCACTAATGAGCTCCGATAGGCCCAAAATAAAAATTGTTC
258 TCAAAACGTCACTAATGAGCTCCGATAGGCCCAAAATAAAAATTGTTC
* * * *
918 AAAATGAGCTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGATTATAGTTAGGGCAT-AACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACA
* *
982 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
66 ATGGAAAGAAAAGCATTGAGGGTTGCC-AATCGAAGACGATTCAAAAC-GAACTAATGGGCACAG
* * *
1047 ATAGGCCCAATATAACAAGTGTTCCAAATGAGCCAAAAACTTCACAGTGGACTAAACTCACCAAA
129 ATAGGCCCAA-ATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
* *
1112 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACTAT
193 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATAGAAGACGAT
1177 TCAAAAC
258 TCAAAAC
Statistics
Matches: 824, Mismatches: 42, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
303 8 0.01
304 70 0.08
305 456 0.55
306 263 0.32
307 27 0.03
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (305 bp):
CAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACA
ATGGAAAGAAAAGCATTGAGGGTTGCCAATCGAAGACGATTCAAAACGAACTAATGGGCACAGAT
AGGCCCAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATAGAAGACGATTCA
AAACGTCACTAATGAGCTCCGATAGGCCCAAAATAAAAATTGTTC
Found at i:909 original size:458 final size:459
Alignment explanation
Indices: 1--1183 Score: 1912
Period size: 458 Copynumber: 2.6 Consensus size: 459
1 CAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAAC
1 CAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAAC
*
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAGAGAAGACGATTCAAAACGTCACTAATGAGCTCCG
65 AATGGAAAGAAAAGCATTGAGGGTTGCCAATAGAAGACGATTCAAAACGTCACTAATGAGCTCCG
* *
131 ATAGGCCCAAAATAAAAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGAGTAATCTCACCAAA
130 ATAGGCCCAAAATAAAAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAA
* *
196 ATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACAAT
195 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAAT
* * * *
261 TC-AAACAAAACTAATTGGCCCCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
260 TCAAAACAAAACTAATGGGCACAGATAGGTCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
325 TCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
325 TCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
* ** *
390 GCGGGTTGCCAATCGAAGACGATTCAAAACAGAACTAATGGGCACAGATAGGCCCAAATAAAAAG
390 GAGGGTTGCCAAGAGAAGACGATTCAAAACAGAACTAATGAGCACAGATAGGCCCAAATAAAAAG
455 TGTTC
455 TGTTC
460 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACA
525 ATGGAAAGAAAAGCATTGAGGGTTGCCAATAGAAGACGATTCAAAACGTCACTAATGAGCTCCGA
66 ATGGAAAGAAAAGCATTGAGGGTTGCCAATAGAAGACGATTCAAAACGTCACTAATGAGCTCCGA
590 TAGGCCCAAAATAAAAATTGTTCCAAATGAGCTAAAAACTTACACAGTGGACTAAACTCACC-AA
131 TAGGCCCAAAATAAAAATTGTTCCAAATGAGCTAAAAACTT-CACAGTGGACTAAACTCACCAAA
* *
654 ATAGATTATAGTTAGGCCATAAACAATGG-AAGAAAAGCATTGCGGGTTGCC-AATCGAAGACGA
195 AT-GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAA
** *
717 TTCAAAACTGAACTAATGGGCACAGATAGG-CCCAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
259 TTCAAAACAAAACTAATGGGCACAGATAGGTCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
* *
781 TTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
324 TTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* * * *
846 TGAGGGTTGCCAAGAGAAGACGATTCAAAA-TGTCACTAATGAGCTCCGATAGGCCCAAAATAAA
389 TGAGGGTTGCCAAGAGAAGACGATTCAAAACAG-AACTAATGAGCACAGATAGGCCC-AAATAAA
*
910 AATTGTTC
452 AAGTGTTC
* * * *
918 AAAATGAGCTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGATTATAGTTAGGGCAT-AACA
1 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACA
* ** * *
982 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
66 ATGGAAAGAAAAGCATTGAGGGTTGCC-AATAGAAGACGATTCAAAACGTCACTAATGAGCTCCG
* * * *
1047 ATAGGCCCAATATAACAAGTGTTCCAAATGAGCCAAAAACTTCACAGTGGACTAAACTCACCAAA
130 ATAGGCCCAAAATAAAAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAA
*
1112 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACTAT
195 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAAT
1177 TCAAAAC
260 TCAAAAC
Statistics
Matches: 675, Mismatches: 40, Indels: 18
0.92 0.05 0.02
Matches are distributed among these distances:
456 1 0.00
457 232 0.34
458 370 0.55
459 72 0.11
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (459 bp):
CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACA
ATGGAAAGAAAAGCATTGAGGGTTGCCAATAGAAGACGATTCAAAACGTCACTAATGAGCTCCGA
TAGGCCCAAAATAAAAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAA
TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATT
CAAAACAAAACTAATGGGCACAGATAGGTCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTT
CACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
AGGGTTGCCAAGAGAAGACGATTCAAAACAGAACTAATGAGCACAGATAGGCCCAAATAAAAAGT
GTTC
Done.