Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011725.1 Corchorus olitorius cultivar O-4 contig11758, 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, 1000
Length: 1751
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Found at i:322 original size:154 final size:154
Alignment explanation
Indices: 1--1741 Score: 2495
Period size: 154 Copynumber: 11.4 Consensus size: 154
* * ** * *
1 AAGCATTGAGGTTTGCTAAATCGAAGACGATTCAATACGTCTCTAATGGGCCTCGATAGGCCCA-
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAATGGACCCCGATAGG-CCAG
* * *
65 AAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGT-GACTAATCACACCAAAATGATTATA
65 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATA
129 GTTAGGCCATAAACAATGGAAAGAA
130 GTTAGGCCATAAACAATGGAAAGAA
* * * *
154 AAGCATTGAGGTTTGCAAAATCGAAGACTATTCAAAACGGAACTAATGGACCCCGATATGCCAGT
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAATGGACCCCGATAGGCCAGA
* *
219 AATAACAAGTGTTCCAAATGAGCTAAGAACTTTAAAGTGGACTAATCTCACCAAAATGATTATAG
66 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAG
284 TTAGGCCATAAACAATGGAAAGAA
131 TTAGGCCATAAACAATGGAAAGAA
* * * *
308 AAGCATTGAGGTTTGTC-AAATCGAAAACGATTCAAAACGTCACAAATGGACCCCGATAGGCCAA
1 AAGCATTGAGGTTTG-CAAAATCGAAGACGATTCAAAACGTAACTAATGGACCCCGATAGGCCAG
* *
372 AAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCACACCAAAATGATTATA
65 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATA
437 GTTAGGCCATAAACAATGGAAAGAA
130 GTTAGGCCATAAACAATGGAAAGAA
* * * *
462 AAGCATTGAGGTTTGCAAAATCGAAGACTATTCAAAACGGAACTAATGGACCCCGATATGCCAGT
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAATGGACCCCGATAGGCCAGA
* *
527 AATAACAAGTGTTCCAAATGAGCTAAGAACTTTAAAGTGGACTAATCTCACCAAAATGATTATAG
66 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAG
592 TTAGGCCATAAACAATGGAAAGAA
131 TTAGGCCATAAACAATGGAAAGAA
* *
616 AAGCATTGAGGTTTGCAAAATCGAAGACGATT-ACAAACGGAACTAATGGACCCCGATATGCCAG
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCA-AAACGTAACTAATGGACCCCGATAGGCCAG
* * * *
680 TAATAACAAGTGTTCCAAATGAGCT-AGAACTTTAAAGTGGACTAATCACACCAAAATGATTATA
65 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATA
744 GTTAGGCCATAAACAATGGAAAG-A
130 GTTAGGCCATAAACAATGGAAAGAA
* *
768 AAGCATTGAGGTTTGCCGAAAATCGGAAAACGATTCAAAACGTACACAAATGGACCCCCGATAGG
1 AAGCATTGAGGTTTG-C-AAAATC-GAAGACGATTCAAAACGTA-ACTAATGGA-CCCCGATAGG
* *
833 CCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAGAGTGGACTAATCTCACCAAAATGAT
61 CCAGAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGAT
898 TATAGTTAGGCCATAAACAATGGAAAGAA
126 TATAGTTAGGCCATAAACAATGGAAAGAA
* * * *
927 AAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCA-
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAATGGACCCCGATAGG-CCAG
* *
991 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCACACGAAAAATGATTAT
65 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCAC-CAAAATGATTAT
*
1056 AGTTAGGCCATAAACAATGGAAGGAA
129 AGTTAGGCCATAAACAATGGAAAGAA
* * * *
1082 AAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAACGTCACAAATGGACCCCGATAGGCCCA-
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAATGGACCCCGATAGG-CCAG
* *
1146 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATCATA
65 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATA
1211 GTTAGGCCATAAACAATGGAAAGAA
130 GTTAGGCCATAAACAATGGAAAGAA
* * * * *
1236 AAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAATAGACCCCGATCGG---G-
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAATGGACCCCGATAGGCCAGA
* * * *
1297 ----CCAA-----CCAAATGAGCTAGAAACTTCAAAGTTGACTAATCTCAGCAAAATGATTATAG
66 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAG
*
1353 TTAGGCAATAAACAATGGAAAGAA
131 TTAGGCCATAAACAATGGAAAGAA
* ** * * * *
1377 AAGCATTGAGGTTTGCCAAATCGAAGAAAATTTAATACGTCACTAATGCGA-CCC-ATAGGCCAA
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAATG-GACCCCGATAGGCCAG
*
1440 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCACACCAAAATGATTATA
65 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATA
1505 GTTAGGCCATAAACAATGGAAAGAA
130 GTTAGGCCATAAACAATGGAAAGAA
* *
1530 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCAGT
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAATGGACCCCGATAGGCCAGA
* *
1595 AATAACAAGTGTTCCAAATGAGCTAAGAACTTTAAAGTGGACTAATCTCACCAAAATGATTATAG
66 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAG
*
1660 TTAGGCCATAAACAATTGAAAGAA
131 TTAGGCCATAAACAATGGAAAGAA
* * * * *
1684 AAGCATTGAGGTTTGCCAAATCGAAGATGATTCGAAACGGAAC-AAGTGGGCCCCGATA
1 AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAA-TGGACCCCGATA
1742 TGCCCAAAAT
Statistics
Matches: 1448, Mismatches: 107, Indels: 65
0.89 0.07 0.04
Matches are distributed among these distances:
140 4 0.00
141 117 0.08
142 2 0.00
146 3 0.00
148 3 0.00
152 21 0.01
153 266 0.18
154 715 0.49
155 176 0.12
156 26 0.02
157 41 0.03
158 59 0.04
159 15 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
AAGCATTGAGGTTTGCAAAATCGAAGACGATTCAAAACGTAACTAATGGACCCCGATAGGCCAGA
AATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAG
TTAGGCCATAAACAATGGAAAGAA
Found at i:1417 original size:141 final size:141
Alignment explanation
Indices: 851--1423 Score: 642
Period size: 155 Copynumber: 3.9 Consensus size: 141
841 AACAAGTGTT
* * *
851 CCAAATGAGCTAAAAACTTCAGAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATCATAGTTAGGCAATAAAC
* ** * *
916 AATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGTCACAAATGGACCCC
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAAATTCAAAACGTCACTAATAGACCCC
* *
981 GATAGGCCCAAAATAACAA
131 GATCGG-GC-------CAA
* * * *
1000 GTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCACACGAAAAATGATTATAGTTAGGCC
1 -----CCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCAC-CAAAATGATCATAGTTAGGCA
* * * *
1065 ATAAACAATGGAAGGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAACGTCACAAATG
60 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAAATTCAAAACGTCACTAATA
* *
1130 GACCCCGATAGGCCCAAAATAACAA
125 GACCCCGATCGG-GC-------CAA
* *
1155 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATCATAGTTAGGCCA
1 -----CCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATCATAGTTAGGCAA
*
1220 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACGTCACTAATAG
61 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAAATTCAAAACGTCACTAATAG
1285 ACCCCGATCGGGCCAA
126 ACCCCGATCGGGCCAA
* * * *
1301 CCAAATGAGCTAGAAACTTCAAAGTTGACTAATCTCAGCAAAATGATTATAGTTAGGCAATAAAC
1 CCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATCATAGTTAGGCAATAAAC
* *
1366 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAAATTTAATACGTCACTAAT
66 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAAATTCAAAACGTCACTAAT
1424 GCGACCCATA
Statistics
Matches: 392, Mismatches: 26, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
141 114 0.29
146 3 0.01
153 1 0.00
154 126 0.32
155 148 0.38
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (141 bp):
CCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATCATAGTTAGGCAATAAAC
AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAAATTCAAAACGTCACTAATAGACCCC
GATCGGGCCAA
Done.