Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020047.1 Corchorus olitorius cultivar O-4 contig20080, 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, 669
Length: 1116
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:292 original size:154 final size:154
Alignment explanation
Indices: 1--1109 Score: 1649
Period size: 154 Copynumber: 7.2 Consensus size: 154
* * *
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATCGAAA-AAAAGCATTGCGATTTGCCAAAT
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
*
65 CGAAGACGATTCAAAACGTCACTAAT-AGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
66 CGAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
*
129 GCTACAAACTTCACAGTGGACTAA
131 GCTAAAAACTTCACAGTGGACTAA
* * * * *
153 TTTCACGAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGGGGTTTGCCAAAT
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
* **
218 CGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
66 CGAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
283 GCTAAAAACTTCACAGTGGACTAA
131 GCTAAAAACTTCACAGTGGACTAA
* *
307 TCTCACCAAAATGATTATAGTTAGGCAATAAACGAATGGAAAAAAAAAAGCATTGAGGTTTGCCA
1 TCTCACCAAAATGATTATAGTTAGGCCATAAAC-AATGG--AAAGAAAAGCATTGAGGTTTGCCA
* * *
372 AATCGAAGACGATTCAAAAACGTCATTAATGGACCCCAAAAGGCCCAAAAATAACAAGTGTTCCA
63 AATCGAAGACGATTC-AAAACGTCACTAATGGGCCCCGAAAGGCCC-AAAATAACAAGTGTTCCA
437 AATGAGCTAAAAACTTCACAGTGGACTAA
126 AATGAGCTAAAAACTTCACAGTGGACTAA
* *
466 TCTCACCTAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAAGCATTGAGGTTTGCCAAA
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG-AAAGAAAAGCATTGAGGTTTGCCAAA
* *
531 TCGAAGACGATTCAAAACAG-AACTAATGGGCCCCGAAAGGCCCAGAATAACAAGTGTTCCAAAT
65 TCGAAGACGATTCAAAAC-GTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
* *
595 GAGCTAAACACTTCACATTGGACTAA
129 GAGCTAAAAACTTCACAGTGGACTAA
* * *
621 TCTCACCAAAAGGATTATAGTTAGGCCATTAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
* * *
686 CGAAGATGATTCAAAACGTCACCAATGGGCCCC-AATAGGTCCAAAATAACAAGTGTTCCAAATG
66 CGAAGACGATTCAAAACGTCACTAATGGGCCCCGAA-AGGCCCAAAATAACAAGTGTTCCAAATG
* *
750 AGTTAAAAACTTCACTGTGGACTAA
130 AGCTAAAAACTTCACAGTGGACTAA
*
775 TCTCACCAAAATGATTATAGTTAGGCCATAAACTATGGAAA-AAAATG-ATTGAGGTTTGCCAAA
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA-GCATTGAGGTTTGCCAAA
** *
838 TCGAAGA-GTATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAAT
65 TCGAAGACG-ATTCAAAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
*
902 GAGCTAAACACTTCACAGTGGACTAA
129 GAGCTAAAAACTTCACAGTGGACTAA
* * * * *
928 TCTCACCAAAAGGATTATAGTTAGGCCATTAATAATGGAAAGAAAAGCCTTGTGGTTTGCCAAAT
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
* * **
993 CGAAGATGATTCAAAACGTCACTAATGGGCACC-AATAGATCCAAAATAACAAGTGTTCCAAATG
66 CGAAGACGATTCAAAACGTCACTAATGGGCCCCGAA-AGGCCCAAAATAACAAGTGTTCCAAATG
1057 AGCTAAAAACTTCACAGTGGACTAA
130 AGCTAAAAACTTCACAGTGGACTAA
1082 TCTCACCAAAATGATTATAGTTAGGCCA
1 TCTCACCAAAATGATTATAGTTAGGCCA
1110 CTGAGAC
Statistics
Matches: 866, Mismatches: 74, Indels: 32
0.89 0.08 0.03
Matches are distributed among these distances:
152 38 0.04
153 182 0.21
154 353 0.41
155 85 0.10
156 24 0.03
157 77 0.09
158 29 0.03
159 78 0.09
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
CGAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
GCTAAAAACTTCACAGTGGACTAA
Found at i:908 original size:307 final size:307
Alignment explanation
Indices: 1--1109 Score: 1733
Period size: 307 Copynumber: 3.6 Consensus size: 307
* * * *
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATCGAAA-AAAAGCATTGCGATTTGCCAAAT
1 TCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
*
65 CGAAGACGATTCAAAACGTCACTAAT-AGCCCCGAA-AGGCCCAAAATAACAAGTGTTCCAAATG
66 CGAAGACGATTCAAAACGTCACTAATGGGCCCC-AATAGGCCCAAAATAACAAGTGTTCCAAATG
* * * *
128 AGCTACAAACTTCACAGTGGACTAATTTCACGAAAAGGATTATAGTTAGGCCATAAACAATGGAA
130 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
* *
193 AGAAAAGAATTGGGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGGC
195 A-AAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGC
*
258 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
259 CCAAAATAACAAGTGTTCCAAATGAGCTAAACACTTCACAGTGGACTAA
* * * *
307 TCTCACCAAAATGATTATAGTTAGGCAATAAACGAATGGAAAAAAAAAAGCATTGAGGTTTGCCA
1 TCTCACCAAAAGGATTATAGTTAGGCCATAAAC-AATGG--AAAGAAAAGCATTGTGGTTTGCCA
* * *
372 AATCGAAGACGATTCAAAAACGTCATTAATGGACCCCAAAAGGCCCAAAAATAACAAGTGTTCCA
63 AATCGAAGACGATTC-AAAACGTCACTAATGGGCCCCAATAGGCCC-AAAATAACAAGTGTTCCA
*
437 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCTAAATGATTATAGTTAGGCCATAAACAAT
126 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* *
502 GGAAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
191 GG--AAAAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
* *
567 AAGGCCCAGAATAACAAGTGTTCCAAATGAGCTAAACACTTCACATTGGACTAA
254 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAACACTTCACAGTGGACTAA
*
621 TCTCACCAAAAGGATTATAGTTAGGCCATTAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
1 TCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * *
686 CGAAGATGATTCAAAACGTCACCAATGGGCCCCAATAGGTCCAAAATAACAAGTGTTCCAAATGA
66 CGAAGACGATTCAAAACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGA
* * *
751 GTTAAAAACTTCACTGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACTATGGAAA
131 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
816 AAAATG-ATTGAGGTTTGCCAAATCGAAGA-GTATTCAAAACGGAACTAATGGGCCCCGAAAGGC
196 AAAA-GAATTGAGGTTTGCCAAATCGAAGACG-ATTCAAAACGGAACTAATGGGCCCCGAAAGGC
*
879 CTAAAATAACAAGTGTTCCAAATGAGCTAAACACTTCACAGTGGACTAA
259 CCAAAATAACAAGTGTTCCAAATGAGCTAAACACTTCACAGTGGACTAA
* * *
928 TCTCACCAAAAGGATTATAGTTAGGCCATTAATAATGGAAAGAAAAGCCTTGTGGTTTGCCAAAT
1 TCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
* * **
993 CGAAGATGATTCAAAACGTCACTAATGGGCACCAATAGATCCAAAATAACAAGTGTTCCAAATGA
66 CGAAGACGATTCAAAACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGA
1058 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
131 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
1110 CTGAGAC
Statistics
Matches: 746, Mismatches: 45, Indels: 23
0.92 0.06 0.03
Matches are distributed among these distances:
306 33 0.04
307 286 0.38
308 1 0.00
309 84 0.11
310 58 0.08
311 51 0.07
312 10 0.01
313 85 0.11
314 135 0.18
315 3 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (307 bp):
TCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAAT
CGAAGACGATTCAAAACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGA
GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
AAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCC
AAAATAACAAGTGTTCCAAATGAGCTAAACACTTCACAGTGGACTAA
Done.