Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024355.1 Corchorus olitorius cultivar O-4 contig24388, 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, 612
Length: 1020
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Found at i:285 original size:154 final size:153
Alignment explanation
Indices: 1--1017 Score: 1516
Period size: 154 Copynumber: 6.6 Consensus size: 153
* *
1 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAGAGCATTGAGGTTTGCTAAATCGAAGA
1 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
* ** * *
66 CGATTCAATACGTCACTAATGGGCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGATAAA
66 CGATTCAAAACGGAACTAATGGG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
*
131 AAGTTCACAGTGGACTAATCTCAC
130 AACTTCACAGTGGACTAATCTCAC
*
155 CAAAATGATTATAGTTAGGCCATTAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
1 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
* * *
220 CGATTCAAAACGGAACTAATGAGCCCAAATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAA
66 CGATTCAAAACGGAACTAATGGGCCC-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
285 AACTTCACAGTGGACTAATCTCAC
130 AACTTCACAGTGGACTAATCTCAC
* **
309 TAAAATGATTATAGTTAGG-C-TAAACAATGGAAAGAAAAGGTTTGAGGTTTGCCAAATCGAAGA
1 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
372 CGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
66 CGATTCAAAACGGAACTAATGGGCC-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
*
437 AATTTCACAGTGGACTAATCTCAC
130 AACTTCACAGTGGACTAATCTCAC
461 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
1 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
* *
526 CGATTCAAAACGGAACTAATGAGTCCAGATAGGCCCAAAATAACAAGTGTTCCAAAATGAGCTAA
66 CGATTCAAAACGGAACTAATG-GGCCCGATAGGCCCAAAATAACAAGTGTTCC-AAATGAGCT-A
591 AAAACTTCACAGTGGACTAATCTCAC
128 AAAACTTCACAGTGGACTAATCTCAC
* *
617 TAAAATGATTATAGTTAGG-C-TAAACAATCGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAG
1 CAAAATGATTATAGTTAGGCCATAAACAAT-GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
680 ACGATTACAAAACGGAACTAATAGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGAC
65 ACGATT-CAAAACGGAACTAAT-GGGCC-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAG-C
*
745 T-AAAA-TTCACAGTGGACTATTCTCAC
126 TAAAAACTTCACAGTGGACTAATCTCAC
*
771 C-AAATGATTATAGTTAGG-CATAAACAATGG-AAGAAAA-CATTGAGGTTTGCCAAATCGAAGT
1 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
* *
832 CGATTC-AAACGGAACTAATGAGCCTCGATAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAA
66 CGATTCAAAACGGAACTAATGGGCC-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* * * *
896 AACCTCAAAGTGGACTAATCTAAA
130 AACTTCACAGTGGACTAATCTCAC
* * * *
920 CAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAATTCGAAGA
1 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
* * **
985 AGATTCAATACGTCACTAATGGGCCCCGATAGG
66 CGATTCAAAACGGAACTAATGGG-CCCGATAGG
1018 ACC
Statistics
Matches: 791, Mismatches: 51, Indels: 42
0.89 0.06 0.05
Matches are distributed among these distances:
147 2 0.00
148 42 0.05
149 30 0.04
150 17 0.02
151 39 0.05
152 154 0.19
153 52 0.07
154 299 0.38
155 58 0.07
156 69 0.09
157 29 0.04
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (153 bp):
CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
CGATTCAAAACGGAACTAATGGGCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAGTGGACTAATCTCAC
Found at i:576 original size:306 final size:306
Alignment explanation
Indices: 2--1017 Score: 1577
Period size: 306 Copynumber: 3.3 Consensus size: 306
1 C
* *
2 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAGAGCATTGAGGTTTGCTAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* ** * *
67 GATTCAATACGTCACTAATGGGCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGATAAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
132 AGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATTAACAATGGAAAGAAAAGC
131 A-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* *
197 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCAAATAGGTCCAAAATA
195 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAG-CCAGATAGGCCCAAAATA
262 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACT
259 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACT
**
310 AAAATGATTATAGTTAGG-C-TAAACAATGGAAAGAAAAGGTTTGAGGTTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
*
373 GATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
438 ATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
131 A-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
503 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGTCCAGATAGGCCCAAAATA
195 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAG-CCAGATAGGCCCAAAATA
568 ACAAGTGTTCCAAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACT
259 ACAAGTGTTCC-AAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACT
*
618 AAAATGATTATAGTTAGG-C-TAAACAATCGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGA
1 AAAATGATTATAGTTAGGCCATAAACAAT-GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
*
681 CGATTACAAAACGGAACTAATAGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGACT
65 CGATT-CAAAACGGAACTAAT-GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG-CT
*
746 -AAAATTCACAGTGGACTATTCTCACC-AAATGATTATAGTTAGG-CATAAACAATGG-AAGAAA
127 AAAAATTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
* *
807 A-CATTGAGGTTTGCCAAATCGAAGTCGATTC-AAACGGAACTAATGAGCCTCGATAGGCCCAAA
192 AGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCC-AGATAGGCCCAAA
* * * *
870 ATAACAAGTGTTCAAAATGAGCTAAAAACCTCAAAGTGGACTAATCTAAAC-
256 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT-CACT
* * * * *
921 AAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAATTCGAAGAA
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* **
986 GATTCAATACGTCACTAATGGGCCCCGATAGG
66 GATTCAAAACGGAACTAATGGGCCCCGATAGG
1018 ACC
Statistics
Matches: 665, Mismatches: 33, Indels: 26
0.92 0.05 0.04
Matches are distributed among these distances:
302 12 0.02
303 51 0.08
304 49 0.07
305 49 0.07
306 264 0.40
307 17 0.03
308 85 0.13
309 56 0.08
310 36 0.05
311 44 0.07
312 2 0.00
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (306 bp):
AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ATTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCAGATAGGCCCAAAATAAC
AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACT
Done.