Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399946.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3175.0, 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: 10646
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 1520 characters in sequence are not A, C, G, or T
Found at i:670 original size:170 final size:170
Alignment explanation
Indices: 532--857 Score: 467
Period size: 170 Copynumber: 1.9 Consensus size: 170
522 NNNNNNNNNN
* * *
532 ACCATTTAAAGCAAGTAGTAAGGCTTTCGAAGGAATGGATGACTATAAATGGACTTTTCTTA-CT
1 ACCATTTAAAACAAGTAATAAGGCTTTCGAAGGAATGGATGACTATAAATGCACTTTTCTTATC-
* * * * *
596 AGTGAATGGTTTT-TCTTCATGTTTCCCAAGATAAACATTTAACTATAATCTCTTTTAACGAAAC
65 AATGAATGGTTTTCTCTTCATGTTTCCCAAGATAAACATTGAA-TATAATCTATTTTAACAAAAA
*
660 ATATAAAAAAATTCAACTTAAAATTAATTATGGGATTATAAA
129 ATATAAAAAAATTCAACTTAAAATCAATTATGGGATTATAAA
** *
702 ACCATTTAAAATGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAATGCACTTTTCTTATCA
1 ACCATTTAAAACAAGTAATAAGGCTTTCGAAGGAATGGATGACTATAAATGCACTTTTCTTATCA
* * *
767 ATGAATGGTTTTCTCTTCATGTTTCCTAAGGTATACATTGAATATAATCTATTTTAACAAAAAAT
66 ATGAATGGTTTTCTCTTCATGTTTCCCAAGATAAACATTGAATATAATCTATTTTAACAAAAAAT
**
832 ATAAAAAAATTTTACTTAAAATCAAT
131 ATAAAAAAATTCAACTTAAAATCAAT
858 GGATGGAGTG
Statistics
Matches: 137, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
170 111 0.81
171 26 0.19
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (170 bp):
ACCATTTAAAACAAGTAATAAGGCTTTCGAAGGAATGGATGACTATAAATGCACTTTTCTTATCA
ATGAATGGTTTTCTCTTCATGTTTCCCAAGATAAACATTGAATATAATCTATTTTAACAAAAAAT
ATAAAAAAATTCAACTTAAAATCAATTATGGGATTATAAA
Found at i:1650 original size:170 final size:169
Alignment explanation
Indices: 1365--1885 Score: 537
Period size: 171 Copynumber: 3.1 Consensus size: 169
1355 AATTATTCAA
* * * * *
1365 CTTGCCAATGAATGGATTTTT-CATCATATTTCCTGAGGTACACATTCAATTATAATCTATTTGA
1 CTTGCCAATGAAT-GATTTTTGCCTCACATTTCCTAAGGCA-ACATTCAATTATAATCTATTTTA
* * *
1429 ACTG-AAAATGCAAAAAAATTCAACTTCAAATTAACTATGAGATTATAAAACCATTTAAAGTGAG
64 A-TGAAAAATG-TAAAAAATTCAACTTCAAATTAATTATGAGATTATAAAACCATTTAAAGTAAG
** *
1493 TAATAAGGCTTTCGAAGGCTTCAGTGAGTATAAATGGACTTTT
127 TAATAAGGCTTTCGAAGGAATCAGTGACTATAAATGGACTTTT
* * * * *
1536 -TGTGCCAATGGATGGTTTTTGCTTCACATTTCTCTAA-GCAGACATTCAATTATAGTATATTTT
1 CT-TGCCAATGAATGATTTTTGCCTCACATTTC-CTAAGGCA-ACATTCAATTATAATCTATTTT
* * *
1599 AATGAAAAATGTAAAAAATTCAACTTCAAATGAATTATGAGATTATAAAACCATTTAAAGCAAGC
63 AATGAAAAATGTAAAAAATTCAACTTCAAATTAATTATGAGATTATAAAACCATTTAAAGTAAGT
* **
1664 AATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT
128 AATAAGGCTTTCGAAGGAATCAGTGACTATAAATGGACTTTT
* * * * ** * * * *
1706 CTTGCTAGTGAATTATTTTTTCCTCATGTTTCCTAAGGTAAGCATTCAAATGTAATCTGTTTTAA
1 CTTGCCAATGAATGATTTTTGCCTCACATTTCCTAAGGCAA-CATTCAATTATAATCTATTTTAA
** * * * *
1771 CCAAAAATATTAAAAAATTTAACTTAAAATTAATTATGAGATTATAAAACTATTTAAAGTAAGTA
65 TGAAAAAT-GTAAAAAATTCAACTTCAAATTAATTATGAGATTATAAAACCATTTAAAGTAAGTA
* * ** *
1836 ATAAGGCTTTCAAAGCAATGGGTGACAATAAATGGACTTTT
129 ATAAGGCTTTCGAAGGAATCAGTGACTATAAATGGACTTTT
*
1877 CTTACCAAT
1 CTTGCCAAT
1886 AATCTCCCTC
Statistics
Matches: 289, Mismatches: 53, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
169 5 0.02
170 140 0.48
171 141 0.49
172 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (169 bp):
CTTGCCAATGAATGATTTTTGCCTCACATTTCCTAAGGCAACATTCAATTATAATCTATTTTAAT
GAAAAATGTAAAAAATTCAACTTCAAATTAATTATGAGATTATAAAACCATTTAAAGTAAGTAAT
AAGGCTTTCGAAGGAATCAGTGACTATAAATGGACTTTT
Found at i:3741 original size:171 final size:171
Alignment explanation
Indices: 3227--5517 Score: 1754
Period size: 171 Copynumber: 13.4 Consensus size: 171
3217 TAAACTGACA
* * * * * *
3227 AAAACCATTAAAAGCGAGTAATAAGGCTTTTGAAGACGT-AGGTGACTATAAATGGACTTTACTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGA-GTGACTATAAATAGACTTTTCTT
* * * ** * * * * *
3291 GCTAGTGAAT-TATTTTTTCTTCAC-ATTCTCT-AAGGTAAACATTCAAATATAATATATTTTAA
65 ACCAATGAATGGCTTTTGTCTTCACGTTTC-CTGAA-GTAGACATTCAATTATAATATGTTTTAA
* *
3353 CTAAAAATATAAAAAAATTCAACTTAAAATGAATTATGAGACTAT
128 -TAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * **
3398 AAAACTATTTAAAACAAGTAATAAGGCTTTCAAAGAAATGAGTGACTATAAATAGAC-TTT-TTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * * * * *
3461 TCAATAAATGG-TTTTGTCTTGACGTTTCC-CAAGGTAGACATTTAA-TATAATTTGTTTGAACT
66 CCAATGAATGGCTTTTGTCTTCACGTTTCCTGAA-GTAGACATTCAATTATAATATGTTTTAA-T
** *
3523 AAAAATAT-AAAAAATTCAACTTAAAATCAAAAATGAAATTAT
129 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
3565 AAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGCTTGAGTTACTATAAACAAACTTTTCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * *
3630 CCAATGGATGGCTTTTGT-TTCATGTTTCCTGAAGTAGACATTCAATTATAATATATTTTAATGA
66 CCAATGAATGGCTTTTGTCTTCACGTTTCCTGAAGTAGACATTCAATTATAATATGTTTTAAT-A
* * * ** *
3694 AAAATGTAAAACAATTCAACTCAAAATCAATTAAAAAATTAT
130 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
** ** * * ** * *
3736 AAAACCATTTAAAGTTAGTAATAAGGCTTTCGAACACATGGGTGACTATAAATTGTGTTTTATTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * * * ** * * *
3801 TCAATGAATGCCTTTT-TTTTCACGTTT-CTCGAGGTAGGCATTCAATTATTTTCTGTTTCAACC
66 CCAATGAATGGCTTTTGTCTTCACGTTTCCT-GAAGTAGACATTCAATTATAATATGTTTTAA-T
* * * * *
3864 AAAAATATGACAAAATTTAACTTAAAATTAATTATGAGATTAG
129 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* ** * * * * *
3907 AAAACTATTTAGGGCGAGTAATAAGCCTTTCGACGGCTTGAGTGACTATAAGTGGACTTTTCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * * * * * * * *
3972 GCAATGGATAGCCTTTG-CTTCACATTTCCTAAAGTAAACATTCAATTACAGTATATTTTAATGA
66 CCAATGAATGGCTTTTGTCTTCACGTTTCCTGAAGTAGACATTCAATTATAATATGTTTTAAT-A
*** * **
4036 AAAACGCAAAAAAAGTCAACTTAAAATCAATTATGTCATTAT
130 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * *
4078 AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGCTTGAGTGACTATAAAT-GAACTTTT-TA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAG-ACTTTTCT-
*** * * * * * * *
4141 TGGTAATGGATGGCTTTTG-CTTCACGTTTCCCT-AGGGACACATTCAATTACAGTATATTTTAA
64 TACCAATGAATGGCTTTTGTCTTCACGTTT-CCTGAAGTAGACATTCAATTATAATATGTTTTAA
** * * * * *
4204 TGGCAAACACAAAAAAAATCTACTTAAAATCAATTATGACATTAT
128 T-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* *
4249 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATAGACTTTACTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * * * * *
4314 -CAAGTGAATTG--TTTGTTCTTCACGTTT-CTTATGGTAAACATTCAAATATAATCTGTTTGAA
66 CCAA-TGAATGGCTTTTG-TCTTCACGTTTCCTGA-AGTAGACATTCAATTATAATATGTTTTAA
*
4375 CTAAAAGTATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
128 -TAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * * *
4420 GAAACTATTTAGAA-CGAGTAATAAGGCTTTCCAAGGAATGAGTGACCATAAATGGGCTTTTCTT
1 AAAACCATTTA-AAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTT
* * * * * * * * *
4484 ATCAATAAAT-GATTCTATCTTCACCTTTCC-CAAGTTAGACATTCAA-TATAATCTGTTTGAAC
65 ACCAATGAATGGCTTTTGTCTTCACGTTTCCTGAAG-TAGACATTCAATTATAATATGTTTTAA-
* * ** *
4546 T-AAAATATAAAAAAATTCAATTTAAAATAAACAAAGACG-TTAT
128 TAAAAATATAAAAAAATTCAACTTAAAATCAATTATGA-GATTAT
* * * * * *
4589 AAAACCATTTAAAGTGAATAATAAGGCTTTCGAAGGCTTGAATGACTATAAATAAACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * *
4654 CCAATGGATGGCTTTTG-CTTTACGTTTCCTGAAGTAGAAATTCAATTATAATATATTTTAATTA
66 CCAATGAATGGCTTTTGTCTTCACGTTTCCTGAAGTAGACATTCAATTATAATATGTTTTAA-TA
* * * *
4718 AAAATACAAAAAAATTTAACTCAAAATTAATTATGAGATTAT
130 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * ** *
4760 AAAACTATTTAGAGTGAGTAATAAGGCTTTCGAAATCATG-GATGACTATAAATGGACTTTTCTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAG-TGACTATAAATAGACTTTTCTT
* ** * * * * ** *
4824 GCCAATGAATACCTTTT-TGTTCATGTTT-CTCGAGGTAGGCATTCAATTATTTTCTGTTTTAAC
65 ACCAATGAATGGCTTTTGTCTTCACGTTTCCT-GAAGTAGACATTCAATTATAATATGTTTTAA-
* * * * *
4887 CAAAAATGTGATAAAATTCAACTTAAAATCAATTATGAAATTAT
128 TAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
4931 AAAACCATTTAAGGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATGGGCTTTACTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * * * * **
4996 GCAATGGATAGCTTTTG-CTTCACATTTCCCT-ACA-CAGACATTCAATTATAGTA-AATTTAAT
66 CCAATGAATGGCTTTTGTCTTCACGTTT-CCTGA-AGTAGACATTCAATTATAATATGTTTTAAT
* * * *
5057 AAAAAATTTAAAAAAATTCAATTTAACATCTATTATGAGATTAT
129 -AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
5101 AAAACCATTTAAAGCAAGCAATAAGGCCTTCGAAGGAATGGGTGACTATAAATAGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * * ** * * * * *
5166 CTAGTGAATTG-TTTTTTCTTCGTGTTT-CTTAAGGTAGACATTCAAATATAATATGCTTCAACC
66 CCAATGAATGGCTTTTGTCTTCACGTTTCCTGAA-GTAGACATTCAATTATAATATGTTTTAA-T
*
5229 AAAAATATAAAAAAAAGTT-GACTTAAAATCAATTATGAGATTAT
129 AAAAATAT-AAAAAAA-TTCAACTTAAAATCAATTATGAGATTAT
* * * * * * *
5273 AAAACTATTTAAAACGAGTAATAAAGCTTTTGAAAGAATGAGCGACTATAAATAGACTTTTCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * *
5338 CCAATAAATGG-TTTTGTCTTCACATTTTCC-AAAGTAGACATTCAA-TATTAA-CTGTTTTAAC
66 CCAATGAATGGCTTTTGTCTTCAC-GTTTCCTGAAGTAGACATTCAATTA-TAATATGTTTTAA-
*
5399 CAAAAATATAAAAAAAATAT-AACTTAAAATCAATTATGAGATTAT
128 TAAAAATAT-AAAAAAAT-TCAACTTAAAATCAATTATGAGATTAT
* *** * * * * * *
5444 GAAACCATTTAAAATAAGCAACAAGACTTTCGAAGGAATGGGTGACTATAAATAGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
*
5509 CCAGTGAAT
66 CCAATGAAT
5518 TATTGTTTCC
Statistics
Matches: 1682, Mismatches: 376, Indels: 124
0.77 0.17 0.06
Matches are distributed among these distances:
167 75 0.04
168 30 0.02
169 183 0.11
170 209 0.12
171 1044 0.62
172 131 0.08
173 9 0.01
174 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (171 bp):
AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTA
CCAATGAATGGCTTTTGTCTTCACGTTTCCTGAAGTAGACATTCAATTATAATATGTTTTAATAA
AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
Found at i:4015 original size:342 final size:339
Alignment explanation
Indices: 3227--5585 Score: 2010
Period size: 342 Copynumber: 6.9 Consensus size: 339
3217 TAAACTGACA
* * * * * *
3227 AAAACCATTAAAAGCGAGTAATAAGGCTTTTGAAGACGT-AGGTGACTATAAATGGACTTTACTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGA-GTGACTATAAATAGACTTTTCTT
* * * * * *
3291 -GCTAGTGAATTA-TTTTTTCTTCACA-TTCTCTAAGGTAAACATTCAAATATAATATATTTTAA
65 AGC-AATGGA-TAGCTTTTGCTTCACATTTC-CTAAAGTAAACATTCAATTATAATATATTTTAA
* * * *
3353 CTAAAAATATAAAAAAATTCAACTTAAAATGAATTATGAGACTATAAAACTATTTAAAACAAGTA
127 -TAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTA
* * * * * *
3418 ATAAGGCTTTCAAAGAAATGAGTGACTATAAATAGAC-TTT-TTATCAATAAATGGTTTTGTCTT
191 ATAAGGCTTTCGAAG-AATGGGTGACTATAAATTGACTTTTCTTGTCAATGAATGCTTTT-TCTT
* * * *
3481 GACGTTTCCCAAGGTAGACATTTAA-TATAATT-TGTTTGAACTAAAAATAT-AAAAAATTCAAC
254 CACGTTTCCCAAGGTAGACATTCAATTAT-ATTCTGTTTCAACCAAAAATATAAAAAAATTCAAC
** *
3543 TTAAAATCAAAAATGAAATTAT
318 TTAAAATCAATTATGAGATTAT
* * * *
3565 AAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGCTTGAGTTACTATAAACAAACTTTTCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTTCTTA
* * * ** * *
3630 CCAATGGATGGCTTTTGTTTCATGTTTCCTGAAGTAGACATTCAATTATAATATATTTTAATGAA
66 GCAATGGATAGCTTTTGCTTCACATTTCCTAAAGTAAACATTCAATTATAATATATTTTAAT-AA
* * * ** * **
3695 AAATGTAAAACAATTCAACTCAAAATCAATTAAAAAATTATAAAACCATTTAAAGTTAGTAATAA
130 AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAA
* ** * *
3760 GGCTTTCGAACACATGGGTGACTATAAATTGTGTTTTATTGTCAATGAATGCCTTTTTTTTCACG
195 GGCTTTCGAAGA-ATGGGTGACTATAAATTGACTTTTCTTGTCAATGAATG-CTTTTTCTTCACG
* * * * * * *
3825 TTTCTCGAGGTAGGCATTCAATTATTTTCTGTTTCAACCAAAAATATGACAAAATTTAACTTAAA
258 TTTCCCAAGGTAGACATTCAATTATATTCTGTTTCAACCAAAAATATAAAAAAATTCAACTTAAA
* *
3890 ATTAATTATGAGATTAG
323 ATCAATTATGAGATTAT
* ** * * * *
3907 AAAACTATTTAGGGCGAGTAATAAGCCTTTCGACGGCTTGAGTGACTATAAGTGGACTTTTCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTTCTTA
* * *
3972 GCAATGGATAGCCTTTGCTTCACATTTCCTAAAGTAAACATTCAATTACAGTATATTTTAATGAA
66 GCAATGGATAGCTTTTGCTTCACATTTCCTAAAGTAAACATTCAATTATAATATATTTTAAT-AA
*** * ** *
4037 AAACGCAAAAAAAGTCAACTTAAAATCAATTATGTCATTATAAAACCATTTAAAGCGAGTAATAA
130 AAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAA
* ** * * *
4102 GGCTTTCAAAAGCTTGAGTGACTATAAA-TGAACTTTT-TATGGT-AATGGATGGCTTTTGCTTC
195 GGCTTTC-GAAGAATGGGTGACTATAAATTG-ACTTTTCT-T-GTCAATGAAT-GCTTTTTCTTC
* * * * * * * * * * * *
4164 ACGTTTCCCTAGGGACACATTCAATTACAGTATATTTTAATGGCAAACACA-AAAAAAA-TCTAC
255 ACGTTTCCCAAGGTAGACATTCAATTATATTCTGTTTCAA--CCAAAAATATAAAAAAATTCAAC
*
4227 TTAAAATCAATTATGACATTAT
318 TTAAAATCAATTATGAGATTAT
* * *
4249 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATAGACTTTACTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTTCTTA
* * * * * ** * * * *
4314 -CAAGTGAATTG-TTTGTTCTTCACGTTTCTTATGGTAAACATTCAAATATAATCTGTTTGAACT
66 GCAA-TGGATAGCTTT-TGCTTCACATTTCCTAAAGTAAACATTCAATTATAATATATTTTAA-T
* * * *
4377 AAAAGTATAAAAAAATTCAACTTAAAATCAATTATGAGATTATGAAACTATTTAGAA-CGAGTAA
128 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA-AAGCAAGTAA
* * * * * * * * *
4441 TAAGGCTTTCCAAGGAATGAGTGACCATAAATGGGCTTTTCTTATCAATAAATGATTCTATCTTC
192 TAAGGCTTTCGAA-GAATGGGTGACTATAAATTGACTTTTCTTGTCAATGAATGCTT-TTTCTTC
* * * * * *
4506 ACCTTTCCCAAGTTAGACATTCAA-TATAATCTGTTTGAA-CTAAAATATAAAAAAATTCAATTT
255 ACGTTTCCCAAGGTAGACATTCAATTATATTCTGTTTCAACCAAAAATATAAAAAAATTCAACTT
* ** *
4569 AAAATAAACAAAGACG-TTAT
320 AAAATCAATTATGA-GATTAT
* * * *
4589 AAAACCATTTAAAGTGAATAATAAGGCTTTCGAAGGCTTGAATGACTATAAATAAACTTTTCTT-
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTTCTTA
* * * *
4653 GCCAATGGATGGCTTTTGCTTTACGTTTCCTGAAGTAGAA-ATTCAATTATAATATATTTTAATT
66 G-CAATGGATAGCTTTTGCTTCACATTTCCTAAAGTA-AACATTCAATTATAATATATTTTAA-T
* * * * * * **
4717 AAAAATACAAAAAAATTTAACTCAAAATTAATTATGAGATTATAAAACTATTTAGAGTGAGTAAT
128 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAAT
* * * * *
4782 AAGGCTTTCGAA-ATCATGGATGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTGTTC
193 AAGGCTTTCGAAGA--ATGGGTGACTATAAATTGACTTTTCTTGTCAATGAAT-GCTTTTTCTTC
* * * * * * * * *
4846 ATGTTTCTCGAGGTAGGCATTCAATTATTTTCTGTTTTAACCAAAAATGTGATAAAATTCAACTT
255 ACGTTTCCCAAGGTAGACATTCAATTATATTCTGTTTCAACCAAAAATATAAAAAAATTCAACTT
*
4911 AAAATCAATTATGAAATTAT
320 AAAATCAATTATGAGATTAT
* * * * *
4931 AAAACCATTTAAGGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATGGGCTTTACTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTTCTTA
* * * * *
4996 GCAATGGATAGCTTTTGCTTCACATTTCCCTACA-CAGACATTCAATTATAGTA-AATTTAATAA
66 GCAATGGATAGCTTTTGCTTCACATTT-CCTAAAGTAAACATTCAATTATAATATATTTTAAT-A
* * * * *
5059 AAAATTTAAAAAAATTCAATTTAACATCTATTATGAGATTATAAAACCATTTAAAGCAAGCAATA
129 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* * * * *
5124 AGGCCTTCGAAGGAATGGGTGACTATAAATAGACTTTTCTTG-CTAGTGAATTGTTTTTTCTTCG
194 AGGCTTTCGAA-GAATGGGTGACTATAAATTGACTTTTCTTGTC-AATGAA-TGCTTTTTCTTCA
* ** * * * * *
5188 TGTTTCTTAAGGTAGACATTCAAATATAATATGCTTCAACCAAAAATATAAAAAAAAGTT-GACT
256 CGTTTCCCAAGGTAGACATTCAATTATATTCTGTTTCAACCAAAAATAT-AAAAAAA-TTCAACT
5252 TAAAATCAATTATGAGATTAT
319 TAAAATCAATTATGAGATTAT
* * * * * ** *
5273 AAAACTATTTAAAACGAGTAATAAAGCTTTTGAAAGAATGAGCGACTATAAATAGACTTTTCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTTCTTA
* ** * * * *
5338 CCAATAAAT-GGTTTTGTCTTCACATTTTCC-AAAGTAGACATTCAA-TATTAA-CTGTTTTAAC
66 GCAATGGATAGCTTTTG-CTTCACA-TTTCCTAAAGTAAACATTCAATTA-TAATATATTTTAA-
* * ** *
5399 CAAAAATATAAAAAAAATAT-AACTTAAAATCAATTATGAGATTATGAAACCATTTAAAATAAGC
127 TAAAAATAT-AAAAAAAT-TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGT
* * * * * ** *
5463 AACAAGACTTTCGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAGTGAATTATTGTTTCC
190 AATAAGGCTTTCGAA-GAATGGGTGACTATAAATTGACTTTTCTTGTCAATGAATGCTT-TTTCT
* * * * * * *
5528 TCATGTTTCCCAAGGTAAACATTCAAATATAATCTGTTTGAATCAAAAATATTAAAAA
253 TCACGTTTCCCAAGGTAGACATTCAATTATATTCTGTTTCAACCAAAAATATAAAAAA
5586 NNNNNNNNNN
Statistics
Matches: 1614, Mismatches: 345, Indels: 120
0.78 0.17 0.06
Matches are distributed among these distances:
337 3 0.00
338 179 0.11
339 16 0.01
340 272 0.17
341 227 0.14
342 740 0.46
343 169 0.10
344 8 0.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (339 bp):
AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTTCTTA
GCAATGGATAGCTTTTGCTTCACATTTCCTAAAGTAAACATTCAATTATAATATATTTTAATAAA
AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAG
GCTTTCGAAGAATGGGTGACTATAAATTGACTTTTCTTGTCAATGAATGCTTTTTCTTCACGTTT
CCCAAGGTAGACATTCAATTATATTCTGTTTCAACCAAAAATATAAAAAAATTCAACTTAAAATC
AATTATGAGATTAT
Found at i:4731 original size:682 final size:676
Alignment explanation
Indices: 3309--5456 Score: 1781
Period size: 682 Copynumber: 3.2 Consensus size: 676
3299 ATTATTTTTT
* * * *
3309 CTTCACA-TTCTCTAAGGTAAACATTCAAATATAATATATTTTAACTAAAAATATAAAAAAATTC
1 CTTCACATTTC-CTAAAGTAAACATTCAATTATAATATATTTTAATTAAAAATACAAAAAAATTC
* * * * *
3373 AACTTAAAATGAATTATGAGACTATAAAACTATTTAAAACAAGTAATAAGGCTTTCAAAGAAATG
65 AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCAAAG-CATG
* *
3438 AGTGACTATAAAT-AGACTTTTTAT-CAATAAATGG-TTTTGTCTTGACGTTTCCCAAGGTAGAC
129 AGTGACTATAAATGA-ACTTTTTATGCAATGAATGGCTTTTG-CTTCACGTTTCCCAAGGTAGAC
* * * **
3500 ATTTAATATAATTTGTTTGAACTAAAAATATAAAAAATTCAACTTAAAATCAAAAATGAAATTAT
192 ATTCAAT-TAATATGTTTTAAC-AAAAATA-AAAAAATTCAACTTAAAATCAATTATGAAATTAT
* * * * *
3565 AAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGCTTGAGTTACTATAAACAAACTTTTCTTA
254 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTACTTA
* * * * *
3630 CCAATGGATGGCTTTTGTTTCATGTTTCCTGAAGTAGACATTCAATTATAATATATTTTAATGAA
319 CCAATGAATGGCTTTTGTTTCACGTTTCCTGAAGTAAACATTCAAATATAATATATTTGAATGAA
* *
3695 AAATGTAAAACAATTCAACTCAAAATCAATTAAAAAATTATAAAACCATTTAAAGTTAGTAATAA
384 AAATATAAAAAAATTCAACTCAAAATCAATTAAAAAATTATAAAACCATTTAAAG-TAGTAATAA
* * * * * * * * * *
3760 GGCTTTCGAACACATGGGTGACTATAAATTGTGTTTTATTGTCAATGAATGCCTTTTTTTTCACG
448 GGCTTTCCAACACATGAGTGACCATAAATTGGGTTTTATTATCAATAAATGCATTTATCTTCACC
* * * ** * * *
3825 TTTCTCGAGGTAGGCATTCAATTATTTTCTGTTTCAACCAAAAATATGACAAAATTTAACTTAAA
513 TTTCCCAAGGTAGACATTCAATTATAATCTGTTTCAACCAAAAATATAAAAAAATTCAACTTAAA
* ** * * ** * * *
3890 ATTAATTATGAGATTAGAAAACTATTTAGGGCGAGTAATAAGCCTTTCGACGGCTTGAGTGACTA
578 ATAAACAAAGAGATTAGAAAACCATTTAAAGCGAATAATAAGCCTTTCGAAGGCTTGAATGACTA
* **
3955 TAAGTGGACTTTTCTTAGCAATGGATAGCCTTTG
643 TAAATAAACTTTTCTTAGCAATGGATAGCCTTTG
* * * ** *
3989 CTTCACATTTCCTAAAGTAAACATTCAATTACAGTATATTTTAATGAAAAACGCAAAAAAAGTCA
1 CTTCACATTTCCTAAAGTAAACATTCAATTATAATATATTTTAATTAAAAATACAAAAAAATTCA
** * *
4054 ACTTAAAATCAATTATGTCATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGCTTGA
66 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTC-AAAGCATGA
* * * * *
4119 GTGACTATAAATGAACTTTTTATGGTAATGGATGGCTTTTGCTTCACGTTTCCCTAGGGACACAT
130 GTGACTATAAATGAACTTTTTAT-GCAATGAATGGCTTTTGCTTCACGTTTCCCAAGGTAGACAT
* * * * * *
4184 TCAATTACAGTATATTTTAATGGCAAACACAAAAAAAATCTACTTAAAATCAATTATGACATTAT
194 TCAATTA-A-TATGTTTTAA---CAAAAATAAAAAAATTCAACTTAAAATCAATTATGAAATTAT
* *
4249 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTATAAATAGACTTTACTTA
254 AAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTACTTA
* * * * *
4314 -CAAGTGAATTG--TTTGTTCTTCACGTTT-CTTATGGTAAACATTCAAATATAATCTGTTTGAA
319 CCAA-TGAATGGCTTTTG-T-TTCACGTTTCCTGA-AGTAAACATTCAAATATAATATATTTGAA
* * ** * * *
4375 CT-AAAAGTATAAAAAAATTCAACTTAAAATCAATTATGAGATTATGAAACTATTTAGAACG-AG
380 -TGAAAAATATAAAAAAATTCAACTCAAAATCAATTAAAAAATTATAAAACCATTTA-AA-GTAG
* *
4438 TAATAAGGCTTTCCAAGGA-ATGAGTGACCATAAA-TGGGCTTTTCTTATCAATAAATG-ATTCT
442 TAATAAGGCTTTCCAA-CACATGAGTGACCATAAATTGGG-TTTTATTATCAATAAATGCATT-T
* * *
4500 ATCTTCACCTTTCCCAAGTTAGACATTCAA-TATAATCTGTTTGAA-CTAAAATATAAAAAAATT
504 ATCTTCACCTTTCCCAAGGTAGACATTCAATTATAATCTGTTTCAACCAAAAATATAAAAAAATT
* * * *
4563 CAATTTAAAATAAACAAAGACG-TTATAAAACCATTTAAAGTGAATAATAAGGCTTTCGAAGGCT
569 CAACTTAAAATAAACAAAGA-GATTAGAAAACCATTTAAAGCGAATAATAAGCCTTTCGAAGGCT
* *
4627 TGAATGACTATAAATAAACTTTTCTT-GCCAATGGATGGCTTTTG
633 TGAATGACTATAAATAAACTTTTCTTAG-CAATGGATAGCCTTTG
* * * *
4671 CTTTACGTTTCCTGAAGTAGAA-ATTCAATTATAATATATTTTAATTAAAAATACAAAAAAATTT
1 CTTCACATTTCCTAAAGTA-AACATTCAATTATAATATATTTTAATTAAAAATACAAAAAAATTC
* * * * *
4735 AACTCAAAATTAATTATGAGATTATAAAACTATTTAGAGTGAGTAATAAGGCTTTCGAAATCATG
65 AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTC-AAAGCATG
* ** * * *
4800 -GATGACTATAAATGGACTTTTCT-TGCCAATGAATACCTTTTTG-TTCATGTTTCTCGAGGTAG
129 AG-TGACTATAAATGAACTTTT-TATG-CAATGAATGGC-TTTTGCTTCACGTTTCCCAAGGTAG
* * * * *
4862 GCATTCAATTATTTTCTGTTTTAACCAAAAATGTGATAAAATTCAACTTAAAATCAATTATGAAA
190 ACATTCAATTA--ATATGTTTTAA-CAAAAA--TAAAAAAATTCAACTTAAAATCAATTATGAAA
* * *
4927 TTATAAAACCATTTAAGGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATGGGCTTTA
250 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTA
** * * * * * * * * *
4992 CTTGGCAATGGATAGCTTTTGCTTCACATTTCCCT-ACA-CAGACATTCAATTATAGTAAATTT-
315 CTTACCAATGAATGGCTTTTGTTTCACGTTT-CCTGA-AGTAAACATTCAAATATAATATATTTG
* * * * * * ** * *
5054 AATAAAAAATTTAAAAAAATTCAATTTAACATCTATTATGAGATTATAAAACCATTTAAAGCAAG
378 AATGAAAAATATAAAAAAATTCAACTCAAAATCAATTAAAAAATTATAAAACCATTTAAAG-TAG
* * * * * * * ** * * * * *
5119 CAATAAGGCCTTCGAAGGA-ATGGGTGACTATAAATAGACTTTTCTT-GCTAGTGAATTG-TTTT
442 TAATAAGGCTTTCCAA-CACATGAGTGACCATAAATTGGGTTTTATTATC-AAT-AAATGCATTT
* *** ** * * *
5181 TTCTTCGTGTTTCTTAAGGTAGACATTCAAATATAATATGCTTCAACCAAAAATATAAAAAAAAG
504 ATCTTCACCTTTCCCAAGGTAGACATTCAATTATAATCTGTTTCAACCAAAAATAT-AAAAAAA-
* * ** * * * * * * *
5246 TT-GACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACGAGTAATAAAG-CTTTTGAAAG
567 TTCAACTTAAAATAAACAAAGAGATTAGAAAACCATTTAAAGCGAATAAT-AAGCCTTTCGAAGG
** ** * * ** **
5309 AATGAGCGACTATAAATAGACTTTTCTTACCAATAAAT-GGTTTTG
631 CTTGAATGACTATAAATAAACTTTTCTTAGCAATGGATAGCCTTTG
* * * ** *
5354 TCTTCACATTTTCC-AAAGTAGACATTCAA-TATTAA-CTGTTTTAACCAAAAATATAAAAAAAA
1 -CTTCACA-TTTCCTAAAGTAAACATTCAATTA-TAATATATTTTAATTAAAAATA-CAAAAAAA
* *
5416 TAT-AACTTAAAATCAATTATGAGATTATGAAACCATTTAAA
62 T-TCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
5457 ATAAGCAACA
Statistics
Matches: 1181, Mismatches: 232, Indels: 106
0.78 0.15 0.07
Matches are distributed among these distances:
679 1 0.00
680 132 0.11
681 126 0.11
682 437 0.37
683 81 0.07
684 382 0.32
685 20 0.02
686 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (676 bp):
CTTCACATTTCCTAAAGTAAACATTCAATTATAATATATTTTAATTAAAAATACAAAAAAATTCA
ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCAAAGCATGAG
TGACTATAAATGAACTTTTTATGCAATGAATGGCTTTTGCTTCACGTTTCCCAAGGTAGACATTC
AATTAATATGTTTTAACAAAAATAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACCA
TTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATAGACTTTACTTACCAATGA
ATGGCTTTTGTTTCACGTTTCCTGAAGTAAACATTCAAATATAATATATTTGAATGAAAAATATA
AAAAAATTCAACTCAAAATCAATTAAAAAATTATAAAACCATTTAAAGTAGTAATAAGGCTTTCC
AACACATGAGTGACCATAAATTGGGTTTTATTATCAATAAATGCATTTATCTTCACCTTTCCCAA
GGTAGACATTCAATTATAATCTGTTTCAACCAAAAATATAAAAAAATTCAACTTAAAATAAACAA
AGAGATTAGAAAACCATTTAAAGCGAATAATAAGCCTTTCGAAGGCTTGAATGACTATAAATAAA
CTTTTCTTAGCAATGGATAGCCTTTG
Found at i:8766 original size:21 final size:21
Alignment explanation
Indices: 8742--8788 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
8732 TTGGAAGCCA
8742 AGAACAAAGCAAGCAAATAAG
1 AGAACAAAGCAAGCAAATAAG
**
8763 AGAATTAAGCAAGCAAATAAG
1 AGAACAAAGCAAGCAAATAAG
8784 AGAAC
1 AGAAC
8789 TGGAGGGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.60, C:0.13, G:0.19, T:0.09
Consensus pattern (21 bp):
AGAACAAAGCAAGCAAATAAG
Done.