Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398127.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_143.0, 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: 30850
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.24
Warning! 10206 characters in sequence are not A, C, G, or T
Found at i:2430 original size:171 final size:161
Alignment explanation
Indices: 2188--2522 Score: 359
Period size: 171 Copynumber: 2.0 Consensus size: 161
2178 ATTCAAATTC
* * * *
2188 AAATCAATTTGGAGATTATAAAACCATTTGAAGTGACTAATAAGGTTTTTGAAGGAATGGGTGAC
1 AAATCAATTTGGAGATTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGAAATGGGTGAA
* *** * * * * *
2253 TATAAATGGACTTTTCTTGTTAATGAATGCCTATTTCTTTACGTTTCTTAAGGTAAATATTGAAT
66 TATAAATGAACTTTTCTTACCAATGAATGCCTATTTCTTCACGTTTCCTAAGGCAAACATTCAAT
* *
2318 TATAGTTTGTTTTAACCAAAAATGTAAAANNNNNNNNNNTA
131 TATAATATGTTTTAACCAAAAATGTAAAA----------TA
* * * * *
2359 AAATTAATTTTGAGATTATAACACCATTTAAATTGAGTAATAAGGCTTTTG-AGAAAATGGGTGA
1 AAATCAATTTGGAGATTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAG-AAATGGGTGA
* *
2423 ATATAAATGAACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCCTAAGGCAGACATTCAA
65 ATATAAATGAACTTTTCTTACCAATGAATGCCTATTTCTTCACGTTTCCTAAGGCAAACATTCAA
2488 TTATAATATGTTTTAACCAAAAATGTAAAA-A
130 TTATAATATGTTTTAACCAAAAATGTAAAATA
2519 AAAT
1 AAAT
2523 TGAACTAAAA
Statistics
Matches: 141, Mismatches: 22, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
160 5 0.04
170 2 0.01
171 134 0.95
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.36
Consensus pattern (161 bp):
AAATCAATTTGGAGATTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGAAATGGGTGAA
TATAAATGAACTTTTCTTACCAATGAATGCCTATTTCTTCACGTTTCCTAAGGCAAACATTCAAT
TATAATATGTTTTAACCAAAAATGTAAAATA
Found at i:3514 original size:171 final size:172
Alignment explanation
Indices: 3181--3516 Score: 374
Period size: 171 Copynumber: 2.0 Consensus size: 172
3171 NNNNNNNNNN
* *
3181 TGAATGCCTTTTTCTTTATGTTTCTCGAGATAGACATTCAATTATAGTCTGTTTTAATCAAAATT
1 TGAATGCCTTTTTCTTTATGTTTCTCGAGATAGACATTCAATTATAGTATGTTTTAATCAAAAAT
* *
3246 ATAAAAACAATTCAACTTAAAATCAATTATGACATTAGAAAATTATTTAAAGCGAGTAATAAGAC
66 ATAAAAACAATTCAACTTAAAATCAATTATGACATTAGAAAACTATTTAAAGCAAGTAATAAGAC
********** *
3311 TTTTGAAGGNNNNNNNNNNTATAAATGGACTTTTCTTATTAA
131 TTTTGAAGGCTTGAGTGGCTATAAAAGGACTTTTCTTATTAA
* *
3353 TGAATGCCTTTTT-TTTCATGTTTCTTGATG-TAGACATTCAATTCTAGTATGTTTTAA-CTAAA
1 TGAATGCCTTTTTCTTT-ATGTTTCTCGA-GATAGACATTCAATTATAGTATGTTTTAATC-AAA
* * * * ** * *
3415 AATGTAAAAA-AGTTCAACTTAAAATTAATTATTAGTTTATAAAACTATTTAAAGTAAGTAATAA
63 AATATAAAAACAATTCAACTTAAAATCAATTATGACATTAGAAAACTATTTAAAGCAAGTAATAA
**
3479 GGTTTTTGAAGGCTTGAGTGGCTATAAAAGGACTTTTC
128 GACTTTTGAAGGCTTGAGTGGCTATAAAAGGACTTTTC
3517 ATGCCAATGG
Statistics
Matches: 134, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
171 74 0.55
172 59 0.44
173 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.39
Consensus pattern (172 bp):
TGAATGCCTTTTTCTTTATGTTTCTCGAGATAGACATTCAATTATAGTATGTTTTAATCAAAAAT
ATAAAAACAATTCAACTTAAAATCAATTATGACATTAGAAAACTATTTAAAGCAAGTAATAAGAC
TTTTGAAGGCTTGAGTGGCTATAAAAGGACTTTTCTTATTAA
Found at i:4603 original size:172 final size:170
Alignment explanation
Indices: 4389--4999 Score: 543
Period size: 171 Copynumber: 3.6 Consensus size: 170
4379 GAATTTAAAT
* * *
4389 TAAAATCAATTTTGAGATTATAAAACCATTTTAAGTGAGTAATAAGGCTTTGAAGGAAT-AGGTA
1 TAAAATCAATTATGAGATTATAAAACCATTTTAAGAGAGTAATAAGGCTTTGAAGGAATGA-GTG
* * * *
4453 ACTATAAATAGACTTTTCCTGTCAATAAATACATTTTTCTTCACATTTCCCAGGGCAAACATTCA
65 ACTATAAATAGACTTTTCCT-TCAATGAATACATTTTTCTTCACATTTCCTAAGGCAGACATTCA
4518 ATTATAATCTATTCTAACCAAAAAATATAAAAAAAATCCAATC
129 ATTATAATCTATTCTAACC-AAAAATATAAAAAAAATCCAATC
* * *
4561 TAAAATCAATTATGAGATTATAAAGCCA-TTTAATGAGAGTAATAGGGTTTTTGAAGGAATGAGT
1 TAAAATCAATTATGAGATTATAAAACCATTTTAA-GAGAGTAATAAGG-CTTTGAAGGAATGAGT
* * * * * * *
4625 GACTATATATGGGCTTTTCCTTCTAGTGAATACCTTTTTCTTCACATTTCCTATGACAGACATTC
64 GACTATAAATAGACTTTTCCTTC-AATGAATACATTTTTCTTCACATTTCCTAAGGCAGACATTC
* * * * *
4690 AATTATAATCTGTTCTAACTAAAAATGT-AAAAAAATTCAACC
128 AATTATAATCTATTCTAACCAAAAATATAAAAAAAATCCAATC
* ********** * * * *
4732 CANNNNNNNNNNTGAGATTATAAAACCATTTAAAGCA-AGTAATAAGCCCTTTAAAGGAATGGGT
1 TAAAATCAATTATGAGATTATAAAACCATTTTAAG-AGAGTAATAAG-GCTTTGAAGGAATGAGT
* * * * ** ** *
4796 GACAATAAATAGATTTTTCTTATCAATGAATGCATTTTTCTTCATGTTTTTTAAGGTAGACATTC
64 GACTATAAATAGACTTTTCCT-TCAATGAATACATTTTTCTTCACATTTCCTAAGGCAGACATTC
* * * * * *
4861 GATTATAATC-AGTTTTAACCGAAAATATACAAAGAATTCAAAT-
128 AATTATAATCTA-TTCTAACCAAAAATATA-AAAAAAATCCAATC
* *
4904 TAAAATCAATTCTGAGATTATAAAACCATTTTAAGTGAGTAATAAGGCTTTAGAAGGAATGAGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTTAAGAGAGTAATAAGGCTTT-GAAGGAATGAGTG
* *
4969 ACTACAATTAGACTTTT-CTTGCCAATGAATA
65 ACTATAAATAGACTTTTCCTT--CAATGAATA
5000 TCTTTTTNNN
Statistics
Matches: 336, Mismatches: 88, Indels: 30
0.74 0.19 0.07
Matches are distributed among these distances:
170 1 0.00
171 127 0.38
172 117 0.35
173 90 0.27
174 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.33
Consensus pattern (170 bp):
TAAAATCAATTATGAGATTATAAAACCATTTTAAGAGAGTAATAAGGCTTTGAAGGAATGAGTGA
CTATAAATAGACTTTTCCTTCAATGAATACATTTTTCTTCACATTTCCTAAGGCAGACATTCAAT
TATAATCTATTCTAACCAAAAATATAAAAAAAATCCAATC
Found at i:4822 original size:21 final size:21
Alignment explanation
Indices: 4798--4837 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4788 GAATGGGTGA
4798 CAATAAATAG-ATTTTTCTTAT
1 CAATAAAT-GCATTTTTCTTAT
*
4819 CAATGAATGCATTTTTCTT
1 CAATAAATGCATTTTTCTT
4838 CATGTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (21 bp):
CAATAAATGCATTTTTCTTAT
Found at i:4836 original size:171 final size:170
Alignment explanation
Indices: 4390--4999 Score: 458
Period size: 172 Copynumber: 3.5 Consensus size: 170
4380 AATTTAAATT
* * * * * *
4390 AAAATCAATTTTGAGATTATAAAACCATTTTAAGTGAGTAATAAGGCTTTGAAGGAATAGGTAAC
1 AAAATCAATTATGAGATTATAAAACCATTTAAAG-AAGTAATAAGCCTTTGAAGGAATGGGTGAC
* *
4455 TATAAATAGACTTTTCCTGTCAATAAATACATTTTTCTTCACATTTCCCAGGGCAAACATTCAAT
65 TATAAATAGACTTTTCCT-TCAATGAATACATTTTTCTTCACATTTCCCAGGACAAACATTCAAT
* *
4520 TATAATCTATTCTAACCAAAAAATATAAAAAAAATCCAATCT
129 TATAATCTATTCTAACCAAAAAATATAAAAAAAATCCAACCC
* * * ** *
4562 AAAATCAATTATGAGATTATAAAGCCATTTAATGAGAGTAATAGGGTTTTTGAAGGAATGAGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGA-AGTAATA-AGCCTTTGAAGGAATGGGTGA
* * * * * * * *
4627 CTATATATGGGCTTTTCCTTCTAGTGAATACCTTTTTCTTCACATTTCCTATGACAGACATTCAA
64 CTATAAATAGACTTTTCCTTC-AATGAATACATTTTTCTTCACATTTCCCAGGACAAACATTCAA
* * * *
4692 TTATAATCTGTTCTAA-CTAAAAATGT-AAAAAAATTCAACCC
128 TTATAATCTATTCTAACCAAAAAATATAAAAAAAATCCAACCC
********** *
4733 ANNNNNNNNNNTGAGATTATAAAACCATTTAAAGCAAGTAATAAGCCCTTTAAAGGAATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAG-AAGTAATAAG-CCTTTGAAGGAATGGGTGA
* * * * ** *** * * *
4798 CAATAAATAGATTTTTCTTATCAATGAATGCATTTTTCTTCATGTTTTTTAAGG-TAGACATTCG
64 CTATAAATAGACTTTTCCT-TCAATGAATACATTTTTCTTCA-CATTTCCCAGGACAAACATTCA
* * * * * ***
4862 ATTATAATC-AGTTTTAACC-GAAAATATACAAAGAATTCAAATT
127 ATTATAATCTA-TTCTAACCAAAAAATATAAAAAAAATCCAACCC
* * * * *
4905 AAAATCAATTCTGAGATTATAAAACCATTTTAAGTGAGTAATAAGGCTTTAGAAGGAATGAGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAG-AAGTAATAAGCCTTT-GAAGGAATGGGTGA
* *
4970 CTACAATTAGACTTTT-CTTGCCAATGAATA
64 CTATAAATAGACTTTTCCTT--CAATGAATA
5000 TCTTTTTNNN
Statistics
Matches: 333, Mismatches: 92, Indels: 26
0.74 0.20 0.06
Matches are distributed among these distances:
170 2 0.01
171 119 0.36
172 130 0.39
173 82 0.25
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.33
Consensus pattern (170 bp):
AAAATCAATTATGAGATTATAAAACCATTTAAAGAAGTAATAAGCCTTTGAAGGAATGGGTGACT
ATAAATAGACTTTTCCTTCAATGAATACATTTTTCTTCACATTTCCCAGGACAAACATTCAATTA
TAATCTATTCTAACCAAAAAATATAAAAAAAATCCAACCC
Found at i:5412 original size:170 final size:168
Alignment explanation
Indices: 5107--5576 Score: 519
Period size: 170 Copynumber: 2.8 Consensus size: 168
5097 NNNNNNNTTT
* * *
5107 CAATGAATATCTTTTTCTCTACGTTTTCAAGATAGACATTCAATTATAATCTGTTCTAAGTAAAA
1 CAATGAATGTCTTTTT-TC-ACGTTTTCAAGATAGACATTCAATTATAATTTGTTCTAACTAAAA
********** * * *
5172 ATGTAAAAAAATTCAANNNNNNNNNNATTATGAGACTATAAAAATATTTAAAGCGAGTAATAACG
64 ATGTAAAAAAATTCAAACTAAAATCAATTTTGAGATTATAAAAATATTTAAAGTGAGTAATAACG
* *
5237 CTTTTAAAAAAATGGCTGATTATAAATAGACTTTTATTGG
129 CTTTTAAAAAAATGGCTGACTATAAATAGACTTTTATTGC
5277 CAATGAATGTCTTTTTTCACGTTTCTCAAGATAGACATTCAATTATAATTTGTTCTAACTAAAAA
1 CAATGAATGTCTTTTTTCACGTTT-TCAAGATAGACATTCAATTATAATTTGTTCTAACTAAAAA
* * * * *
5342 TGTAGAAAGAATTCAAACTAAAATCAATTTTGACATTATAAAATTATTTAAAGTGACTAATAAGG
65 TGTA-AAAAAATTCAAACTAAAATCAATTTTGAGATTATAAAAATATTTAAAGTGAGTAATAACG
* * *
5407 CTTTTAAAAAAATGGGTGACTATAAATATACTTTTCTTGC
129 CTTTTAAAAAAATGGCTGACTATAAATAGACTTTTATTGC
* * * * * * * *
5447 CAATGAATGTATTTTTCTTCACATTTTTCAAGGTAAACATTTAATTATAATTTTTTTTAACAAAA
1 CAATGAATGT-CTTTT-TTCAC-GTTTTCAAGATAGACATTCAATTATAATTTGTTCTAACTAAA
* * *
5512 AATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTA-AAAAACCATTTAAAGTGAGTAATA
63 AATGTA-AAAAAATTCAAACTAAAATCAATTTTGAGATTATAAAAA-TATTTAAAGTGAGTAATA
5576 A
126 A
5577 NNNNNNNNNN
Statistics
Matches: 252, Mismatches: 42, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
168 6 0.02
169 44 0.17
170 102 0.40
171 8 0.03
172 89 0.35
173 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.36
Consensus pattern (168 bp):
CAATGAATGTCTTTTTTCACGTTTTCAAGATAGACATTCAATTATAATTTGTTCTAACTAAAAAT
GTAAAAAAATTCAAACTAAAATCAATTTTGAGATTATAAAAATATTTAAAGTGAGTAATAACGCT
TTTAAAAAAATGGCTGACTATAAATAGACTTTTATTGC
Found at i:5565 original size:172 final size:170
Alignment explanation
Indices: 5217--5576 Score: 477
Period size: 172 Copynumber: 2.1 Consensus size: 170
5207 CTATAAAAAT
* * *
5217 ATTTAAAGCGAGTAATAACGCTTTTAAAAAAATGGCTGATTATAAATAGACTTTTATTGGCAATG
1 ATTTAAAGTGAGTAATAACGCTTTTAAAAAAATGGCTGACTATAAATAGACTTTTATTGCCAATG
* * * *
5282 AATGTCTTTTTTCACGTTTCTCAAGATAGACATTCAATTATAATTTGTTCTAACTAAAAATGTAG
66 AATGTCTTTTTTCACATTTCTCAAGATAAACATTCAATTATAATTTGTTCTAACAAAAAATGTAC
* * **
5347 AAAGAATTCAAACTAAAATCAATTTTGACATTATAAAATT
131 AAAAAATTCAAACTAAAATCAATTTTGACATTAAAAAACC
* * * * *
5387 ATTTAAAGTGACTAATAAGGCTTTTAAAAAAATGGGTGACTATAAATATACTTTTCTTGCCAATG
1 ATTTAAAGTGAGTAATAACGCTTTTAAAAAAATGGCTGACTATAAATAGACTTTTATTGCCAATG
* * * * * *
5452 AATGTATTTTTCTTCACATTTTTCAAGGTAAACATTTAATTATAATTTTTTTTAACAAAAAATGT
66 AATGT-CTTTT-TTCACATTTCTCAAGATAAACATTCAATTATAATTTGTTCTAACAAAAAATGT
* * *
5517 ACAAAAAATTCAAATTTAAATCAATTTTGAGATTAAAAAACC
129 ACAAAAAATTCAAACTAAAATCAATTTTGACATTAAAAAACC
5559 ATTTAAAGTGAGTAATAA
1 ATTTAAAGTGAGTAATAA
5577 NNNNNNNNNN
Statistics
Matches: 162, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
170 62 0.38
171 4 0.02
172 96 0.59
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (170 bp):
ATTTAAAGTGAGTAATAACGCTTTTAAAAAAATGGCTGACTATAAATAGACTTTTATTGCCAATG
AATGTCTTTTTTCACATTTCTCAAGATAAACATTCAATTATAATTTGTTCTAACAAAAAATGTAC
AAAAAATTCAAACTAAAATCAATTTTGACATTAAAAAACC
Found at i:6165 original size:172 final size:162
Alignment explanation
Indices: 5980--6299 Score: 329
Period size: 172 Copynumber: 1.9 Consensus size: 162
5970 ATGGGTGACT
* * **
5980 ATAAATGGACTTTTCTTGCCAATAAATGCATTTTACATCGCGATTCTCAA-GGTAGATGTTCAAT
1 ATAAATAGACTTTTCTTGCCAATAAATACATTTTACATCGCGATTC-CAATGGTAGACATTCAAT
* **
6044 TATAATCTGTTTCAACAAAAAATGTACAAAG-AATTGAAACTAAAATCAATTTTGGGATTAGAAA
65 TATAATCTATTTCAACAAAAAATGTA-AAAGAAATTGAAACTAAAATCAATTTTAAGATTAGAAA
* *
6108 ACTATTTAAAGTAAGTAATAAGGCTTTTAAAGGA
129 ACCATTTAAAGCAAGTAATAAGGCTTTTAAAGGA
* * * * * *
6142 ATNNNNNNNNNNAAATAGACTTTTCTTGCCAATGAATACCTTTTTCTTCGTGTTTCCAATGGTAG
1 AT----------AAATAGACTTTTCTTGCCAATAAATACATTTTACATCGCGATTCCAATGGTAG
* * **
6207 ACATTCAATTATAATCTATTTTAACAAAACATGTAAAAGAAATTGAATTTAAAATCAATTTTAAG
56 ACATTCAATTATAATCTATTTCAACAAAAAATGTAAAAGAAATTGAAACTAAAATCAATTTTAAG
* *
6272 ATTATAAAACCATTTAAAGCGAGTAATA
121 ATTAGAAAACCATTTAAAGCAAGTAATA
6300 NNNNNNNNNN
Statistics
Matches: 125, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
162 2 0.02
171 7 0.06
172 116 0.93
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.33
Consensus pattern (162 bp):
ATAAATAGACTTTTCTTGCCAATAAATACATTTTACATCGCGATTCCAATGGTAGACATTCAATT
ATAATCTATTTCAACAAAAAATGTAAAAGAAATTGAAACTAAAATCAATTTTAAGATTAGAAAAC
CATTTAAAGCAAGTAATAAGGCTTTTAAAGGA
Found at i:7298 original size:171 final size:171
Alignment explanation
Indices: 6603--7461 Score: 634
Period size: 170 Copynumber: 5.0 Consensus size: 171
6593 NNNNNNNNNN
* * * *
6603 AGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGACTTTTCTTGCCAATAAATGA-ATTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAAT-ACCTTT
* * *
6667 TTCTTTCTA--TTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAAGC-AAAAATGTACAAAG
65 TTC-TTC-ACGTTTCCCAAGGTAGACATTCAATTATAATCTGTTCTAA-CAAAAAATGT-CAAAA
* * * * **********
6729 AATTCAAAATAAAATCAATTTTGAGATTATGANNNNNNNNNNAGTG
126 AATTCAAACTCAAATCAATTATGAGATTATAAAACCATTTAAAGTG
* * *
6775 AGTAATAAGGTTTTTGAAGTAATTG-GTGA-TGATAAATGGAC-TTTCATGCCAATG---ACCTT
1 AGTAATAAGGCTTTTGAAGGAA-TGAGTGACT-ATAAATGGACTTTTCTTGCCAATGAATACCTT
* * * ** * * *
6834 TTTCTTCAAGTTTCCCAAGGCAAACATTTGATTATAATCTTTTCTGACTAAAAATGT-AAAAAAT
64 TTTCTTCACGTTTCCCAAGGTAGACATTCAATTATAATCTGTTCTAACAAAAAATGTCAAAAAAT
* *******
6898 TC-AA-TGCAAAGTCAATTATGAGATTATAAAGCCATTNNNNNNN
129 TCAAACT-CAAA-TCAATTATGAGATTATAAAACCATTTAAAGTG
*** * * * * * *
6941 NNNAATAAGGCTTTTGAAAGAATGGGTGGCTATAAATGGGCTTTTCTTGCTAATGAATACCCTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT
** * ** * * * *
7006 TCTTCACGTCACCTAAGACAAACATTCAATTATAATATGCTCTAACCAAAAATGT-AAAAAATTC
66 TCTTCACGTTTCCCAAGGTAGACATTCAATTATAATCTGTTCTAACAAAAAATGTCAAAAAATTC
* * * *
7070 AATCTAAAATCAGTTATGAGATTATAAAGA-CATTTAATGTG
131 AAACTCAAATCAATTATGAGATTATAAA-ACCATTTAAAGTG
* * * *
7111 AGTAATAAGGCTTTTGAAGGATTGAGTGACAATAAATGGACCTTTCTTGCTAATGAATACCTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT
* * *
7176 TCTTTACGTTTCCCAAGGTAGACAATCAATTATAATCTGTTCTAACAAAAAAGGTCAAAAAATTC
66 TCTTCACGTTTCCCAAGGTAGACATTCAATTATAATCTGTTCTAACAAAAAATGTCAAAAAATTC
* * *
7241 AACCTCAAATCAATTATGAAATTATAAAATCATTTAAAGTG
131 AAACTCAAATCAATTATGAGATTATAAAACCATTTAAAGTG
********** * *
7282 AGTAATAAGGCTTTTGANNNNNNNNNNGACTATAAATGGAGTTTTCTTGCCAATGAATGCCTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT
* * * * * * * *
7347 TCTTCACATTT-CTAGAGATAGACATTCAATTATATTTTATTTTAATAAAAAATGTGCAAAAAAT
66 TCTTCACGTTTCCCA-AGGTAGACATTCAATTATAATCTGTTCTAACAAAAAATGT-CAAAAAAT
* * *
7411 TTAAATTCAAATCAATTTTGAGATTATAAAACCATTTAAAGTG
129 TCAAACTCAAATCAATTATGAGATTATAAAACCATTTAAAGTG
*
7454 ACTAATAA
1 AGTAATAA
7462 NNNNNNNNNN
Statistics
Matches: 541, Mismatches: 125, Indels: 42
0.76 0.18 0.06
Matches are distributed among these distances:
164 1 0.00
165 7 0.01
166 56 0.10
167 17 0.03
168 43 0.08
170 180 0.33
171 150 0.28
172 85 0.16
173 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT
TCTTCACGTTTCCCAAGGTAGACATTCAATTATAATCTGTTCTAACAAAAAATGTCAAAAAATTC
AAACTCAAATCAATTATGAGATTATAAAACCATTTAAAGTG
Found at i:9313 original size:172 final size:171
Alignment explanation
Indices: 8957--9317 Score: 476
Period size: 172 Copynumber: 2.1 Consensus size: 171
8947 NNNNNNAAAG
** * *
8957 TCCATTTATAGTCACTAATTTCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCA
1 TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAACTTTAAATAGTTTTATAATCTCA
* * *
9022 AAATTAGATTTAAGTTGGATTTTATTACATTTTTTCTTAAAACAAACTATAATTGAATGTTTACC
66 AAATTAGATTTAAGTTGAATTTTATTACATTTTTTATTAAAACAAACTATAATTGAATGTCTACC
* * * *
9087 TCGAGAAACATAAAGAAATAGGCATTCATTGACAAGACAAG
131 TAGAGAAACATAAAGAAAAAGGCATTCATTGACAAGAAAAC
* *
9128 TCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTAGTAACTTTAAAT-GTTTTTATAATCTC
1 TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAACTTTAAATAG-TTTTATAATCTC
* * * * * *
9192 AAAATT-GATTTGAATTTGAATTTTTTATATATTTTTTATTAAAATAGAGTATAATTGAATGTCT
65 AAAATTAGATTT-AAGTTGAATTTTAT-TACATTTTTTATTAAAACAAACTATAATTGAATGTCT
* *
9256 GCCTAGAGAAACATGAAA-AAAAAGGCATTCATTGGCAAGAAAAC
128 ACCTAGAGAAACAT-AAAGAAAAAGGCATTCATTGACAAGAAAAC
9300 TCCATTTATAGTCACCCA
1 TCCATTTATAGTCACCCA
9318 NNNNNNNNNN
Statistics
Matches: 164, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
170 6 0.04
171 73 0.45
172 82 0.50
173 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (171 bp):
TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAACTTTAAATAGTTTTATAATCTCA
AAATTAGATTTAAGTTGAATTTTATTACATTTTTTATTAAAACAAACTATAATTGAATGTCTACC
TAGAGAAACATAAAGAAAAAGGCATTCATTGACAAGAAAAC
Found at i:9528 original size:28 final size:28
Alignment explanation
Indices: 9496--9555 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
9486 TGAATGTCTG
9496 CTTTAGGAAACATGAAGAAAAAAACATT
1 CTTTAGGAAACATGAAGAAAAAAACATT
9524 CTTTAGGAAACATGAAGAAAAAAACATT
1 CTTTAGGAAACATGAAGAAAAAAACATT
9552 CTTT
1 CTTT
9556 GGCAAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (28 bp):
CTTTAGGAAACATGAAGAAAAAAACATT
Found at i:11338 original size:171 final size:170
Alignment explanation
Indices: 10938--11491 Score: 584
Period size: 171 Copynumber: 3.2 Consensus size: 170
10928 NNNNNNGAGA
* * * *
10938 TTATAAAACCATTTAAAGCGAGTATTAAGGCTTTTAAAGGTATGGGTGACTATAAATAAGCTTTT
1 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGAGCTTTT
*
11003 CTTATCAATGAATGCCTATTTCTTTATGTTTCTCA-AGGTAGACATTCAATTCTA-TCTTGCTTT
66 CTTACCAATGAATGCCT-TTTCTTTATGTTTCT-ATAGGTAGACATTCAATTCTAGTC-TGCTTT
** * * * * *
11066 AATGAAACATGTACAAAGAATTTAAAT-TTAAATCAATTTTGAGA
128 AACCAAAAATGTA-AAA-AAATTAAATCTAAAATCAATTATGAGT
* * * * *
11110 TTATAAAACTATTTAGAGTGAGTAATAAGGCTTTTGACGGAATGGGTGACTATAAATGGGCTTTT
1 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGAGCTTTT
* * * *
11175 CTT-GCAAGTGAATGCCTTCTTCTTTATGTTT-TATGAGTTAGACATTCAATTATAGTCTGTTTT
66 CTTACCAA-TGAATGCCTT-TTCTTTATGTTTCTAT-AGGTAGACATTCAATTCTAGTCTGCTTT
* * *
11238 AACCAAAAATATAAAAAAATTCAATCTAAAATCAATTATGACT
128 AACCAAAAATGTAAAAAAATTAAATCTAAAATCAATTATGAGT
* * *
11281 TTATAAAA-TCATTTAAAGCGAGTAATAAGACTTTTGAAGGTATGGGTGGCTATAAATGAACTTT
1 TTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGAGCTTT
* * * * * *
11345 TTTTACCAATGAATACTTTTTTCTTCATGTTTCT-TAGGGTAGATATTCAATTCTAGTTTGCTTT
65 TCTTACCAATGAATGC-CTTTTCTTTATGTTTCTATA-GGTAGACATTCAATTCTAGTCTGCTTT
* * * *
11409 AACCAAAAATGTTAAAAAATTTAA-CTTAAAATAAATTATTAGT
128 AACCAAAAATGTAAAAAAATTAAATC-TAAAATCAATTATGAGT
* * *
11452 TTATAAAACTATTTAAAGCAAGCAATAAGGCTTTCGAAGG
1 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGG
11492 CTTGNNNNNN
Statistics
Matches: 318, Mismatches: 51, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
170 11 0.03
171 187 0.59
172 118 0.37
173 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (170 bp):
TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGAGCTTTT
CTTACCAATGAATGCCTTTTCTTTATGTTTCTATAGGTAGACATTCAATTCTAGTCTGCTTTAAC
CAAAAATGTAAAAAAATTAAATCTAAAATCAATTATGAGT
Found at i:12097 original size:171 final size:161
Alignment explanation
Indices: 11909--12218 Score: 298
Period size: 171 Copynumber: 1.9 Consensus size: 161
11899 TCAAAATTTG
* * * *
11909 TTTTAAGTTGGATTTTTTTATATTTTTGCTTAAAACAAACTATAATTGATTGTTTACC-AAGAGA
1 TTTTAAGTTGAATTTTTTTACATTTTTGCTTAAAACAAACTATAATTGATGGTCTACCTAAG-GA
* * * *
11973 AACATAAAGAAATAGGCATTCGTTGATAAGACAAGTCCATTTATAGTCACCCATTCTTTCAAAAG
65 AACATAAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAG
12038 CCTTATTACNNNNNNNNNNTAGTTTTATAATCTCATACTTGA
130 CCTTATTAC----------TAGTTTTATAATCTCATACTTGA
* * * * * * * * *
12080 TTTTAGGTTGAATTTTTTTACCTTTTTGGTTAGAACAGATTGTAATTGATGGTCTGCCTTAGGAA
1 TTTTAAGTTGAATTTTTTTACATTTTTGCTTAAAACAAACTATAATTGATGGTCTACCTAAGGAA
** ** * * *
12145 ATGTGGAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCATTTTTTCAAAAGC
66 ACATAAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGC
12210 CTTATTACT
131 CTTATTACT
12219 CNNNNNNNNN
Statistics
Matches: 114, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
161 1 0.01
171 111 0.97
172 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.38
Consensus pattern (161 bp):
TTTTAAGTTGAATTTTTTTACATTTTTGCTTAAAACAAACTATAATTGATGGTCTACCTAAGGAA
ACATAAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGC
CTTATTACTAGTTTTATAATCTCATACTTGA
Found at i:12825 original size:171 final size:172
Alignment explanation
Indices: 12408--12828 Score: 415
Period size: 171 Copynumber: 2.5 Consensus size: 172
12398 GAGAAATTGG
* * * * *
12408 CATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAACTTTATTAGTCACTTT
1 CATTCATTGGCAAGAAAACTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTT
*
12473 AAATGGTTTTACAATCTCCAAATTGATTTGAATTTGAATTTTCTGTACATTTTTAGTTAAAACAA
66 AAATGGTTTTATAATCTCCAAATTGATTTGAATTTGAATTTTCTGTACATTTTTAGTTAAAACAA
* * * * *
12538 ATTATAATTTAATATCTGCCTGGAGAAACATGAAGAGAAAGG
131 ATTATAATTTAATATCTACCTAGAGAAACAAGAAGAAAAAGA
* **********
12580 CATTCATTGGCAAGAAAACACCATTTATAGTCACCCATTCTTTCAAAAGCCTTANNNNNNNNNNT
1 CATTCATTGGCAAGAAAACTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTT
* * * * *
12645 AATTGGTTTTATAATCT-CATAATTGATTTTAGA-TTGAATATTT-T-TACGTTTTTTGTTAGAA
66 AAATGGTTTTATAATCTCCA-AATTGATTTGA-ATTTGAAT-TTTCTGTACATTTTTAGTTAAAA
* *
12706 CAGAA-TAT-ATTTGAATGTTTACCTTAG-GAAACAAGAAGAAAAAGA
128 CA-AATTATAATTT-AATATCTACC-TAGAGAAACAAGAAGAAAAAGA
* * * * * * *
12751 TATTCATTGGTAAGAAAATTTCATTTGTAGTCACCTATTCCTTCAAAAGCCTTATTACTCACTTT
1 CATTCATTGGCAAGAAAACTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTT
12816 AAATGGTTTTATA
66 AAATGGTTTTATA
12829 NNNNNNNNNN
Statistics
Matches: 196, Mismatches: 47, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
170 4 0.02
171 102 0.52
172 86 0.44
173 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.37
Consensus pattern (172 bp):
CATTCATTGGCAAGAAAACTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTT
AAATGGTTTTATAATCTCCAAATTGATTTGAATTTGAATTTTCTGTACATTTTTAGTTAAAACAA
ATTATAATTTAATATCTACCTAGAGAAACAAGAAGAAAAAGA
Found at i:13629 original size:171 final size:171
Alignment explanation
Indices: 13337--14090 Score: 698
Period size: 171 Copynumber: 4.4 Consensus size: 171
13327 NNNNNNNGGC
* * * * ** * *
13337 TATAATTGACTGTCTACCTTAGGAAACGTGAAGTAAAAG-CTAAACTATTGACACG-AAAGTCCA
1 TATAATTGAATGTCTACCTTGGGAAACGTAAAGAAAAAGAC-ATTC-ATTAACAAGAAAAGTCCA
* ** * *
13400 TTTATAGTCACCCATTCTTTCAAAACCCTTATTACTCACGATAAATAGTTTTATAATCTCATAAT
64 TTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAAT
* * * *
13465 TGATTTTAGGTTGGATTTTTTGACTTTTTTGATTAGAACAAAT
129 TGATTTTAAGTTGAATTTTTTGACTTTTTTGCTTAAAACAAAT
* * * **
13508 TATAATTGAATGTCTGCCTTGGGAAACATGAAGAAAAAGGTATTCATTAACAAGAAAAGTCCATT
1 TATAATTGAATGTCTACCTTGGGAAACGTAAAGAAAAAGACATTCATTAACAAGAAAAGTCCATT
* * **********
13573 TATAGTCACCAATT-TCCTCAAAAGCCTTATTACTCACTTTNNNNNNNNNNATAATCTCAAAATT
66 TATAGTCACCCATTCT-TTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATT
* * * *
13637 -AGTTTTAAGTTGGATTTTTTTACATTTTTGCTTAAAACAAAC
130 GA-TTTTAAGTTGAATTTTTTGACTTTTTTGCTTAAAACAAAT
* * * * *
13679 TATAGTTGAATGT-TCACC-TGGAGAAACGTAAAGAAATAGACATTCATTGACAAGACAAGTTCA
1 TATAATTGAATGTCT-ACCTTGG-GAAACGTAAAGAAAAAGACATTCATTAACAAGAAAAGTCCA
* * *
13742 TTTATAGTCACCCATTCTTTCAAAAGCCTTATTAGTCACTTCAAATGGTTTTATAATTTCAAAAT
64 TTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAAT
* * * * * * *
13807 TGATTTAAATTTAAATTTTTTATACATTTTTTG-TTAAAATAGAG
129 TGATTTTAAGTTGAATTTTTT-GAC-TTTTTTGCTTAAAACAAAT
** * * *
13851 TATAATTGAATGTCTACCTTAAGAAACGTGAAG-AAAAGACATTCATTAACAAGAAAACTCTATT
1 TATAATTGAATGTCTACCTTGGGAAACGTAAAGAAAAAGACATTCATTAACAAGAAAAGTCCATT
* * * * *
13915 TATAGTCTCCCATTCTTTCAAAAGCCTTACTACTCACTTTAAATGTTTTTATAATCTCATAATTT
66 TATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTG
* * *
13980 ATTTTAGGTTGAATTTTTTGACCTTTTTT-CTTAGAACAGAT
131 ATTTTAAGTTGAATTTTTTGA-CTTTTTTGCTTAAAACAAAT
* * ** * ***
14021 TATAATTGAATGTCTACCTTGCGAAACGTAAAGGAAAAGGTATTTATTGGTAAGAAAAGTCCATT
1 TATAATTGAATGTCTACCTTGGGAAACGTAAAGAAAAAGACATTCATTAACAAGAAAAGTCCATT
14086 TATAG
66 TATAG
14091 NNNNNNNNNN
Statistics
Matches: 466, Mismatches: 102, Indels: 30
0.78 0.17 0.05
Matches are distributed among these distances:
170 58 0.12
171 362 0.78
172 38 0.08
173 8 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.37
Consensus pattern (171 bp):
TATAATTGAATGTCTACCTTGGGAAACGTAAAGAAAAAGACATTCATTAACAAGAAAAGTCCATT
TATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTG
ATTTTAAGTTGAATTTTTTGACTTTTTTGCTTAAAACAAAT
Found at i:13998 original size:342 final size:341
Alignment explanation
Indices: 13383--14090 Score: 773
Period size: 342 Copynumber: 2.1 Consensus size: 341
13373 AAGCTAAACT
*
13383 ATTGACACGAAAGTCCATTTATAGTCACCCATTCTTTCAAAACCCTTATTACTCACGATAAATAG
1 ATTGACAAGAAAGTCCATTTATAGTCACCCATTCTTTCAAAACCCTTATTACTCACGATAAATAG
* * * ** * *
13448 TTTTATAATCTCATAATTGATTTTAGGTTGGATTTTTTGACTTTTTTGATTAGAACAAATTATAA
66 TTTTATAATCTCAAAATTGATTTAAAGTTAAATTTTTTGACTTTTTTGATTAAAACAAAGTATAA
* ** ** *
13513 TTGAATGTCTGCCTTGGGAAACATGAAGAAAAAGGTATTCATTAACAAGAAAAGTCCATTTATAG
131 TTGAATGTCTACCTTAAGAAACATGAAGAAAAAGACATTCATTAACAAGAAAACTCCATTTATAG
* **********
13578 TCACCAATTTCCTCAAAAGCCTTATTACTCACTTTNNNNNNNNNNATAATCTCAAAATTAGTTTT
196 TCACCAATTTCCTCAAAAGCCTTACTACTCACTTTAAATGTTTTTATAATCTCAAAATTAGTTTT
* * *
13643 AAGTTGGATTTTTTTACATTTTTGCTTAAAACAAACTATAGTTGAATGT-TCACCTGGAGAAACG
261 AAGTTGAATTTTTTGACATTTTTGCTTAAAACAAACTATAATTGAATGTCT-ACCTGGAGAAACG
13707 TAAAGAAATAGACATTC
325 TAAAGAAATAGACATTC
* * * *
13724 ATTGACAAGACAAGTTCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTAGTCAC-TTCAAAT
1 ATTGACAAGA-AAGTCCATTTATAGTCACCCATTCTTTCAAAACCCTTATTACTCACGAT-AAAT
* * * * * *
13788 GGTTTTATAATTTCAAAATTGATTTAAATTTAAATTTTTTATACATTTTTTG-TTAAAATAGAGT
64 AGTTTTATAATCTCAAAATTGATTTAAAGTTAAATTTTTT-GAC-TTTTTTGATTAAAACAAAGT
* *
13852 ATAATTGAATGTCTACCTTAAGAAACGTGAAG-AAAAGACATTCATTAACAAGAAAACTCTATTT
127 ATAATTGAATGTCTACCTTAAGAAACATGAAGAAAAAGACATTCATTAACAAGAAAACTCCATTT
* * * *
13916 ATAGTCTCCCA-TTCTTTCAAAAGCCTTACTACTCACTTTAAATGTTTTTATAATCTCATAATTT
192 ATAGTCACCAATTTC-CTCAAAAGCCTTACTACTCACTTTAAATGTTTTTATAATCTCA-AAATT
* * * * * * * *
13980 A-TTTTAGGTTGAATTTTTTGACCTTTTTTCTTAGAACAGATTATAATTGAATGTCTACCTTGCG
255 AGTTTTAAGTTGAATTTTTTGACATTTTTGCTTAAAACAAACTATAATTGAATGTCTACCTGGAG
** *
14044 AAACGTAAAGGAAA-AGGTATTT
320 AAACGTAAA-GAAATAGACATTC
**
14066 ATTGGTAAGAAAAGTCCATTTATAG
1 ATTGACAAG-AAAGTCCATTTATAG
14091 NNNNNNNNNN
Statistics
Matches: 300, Mismatches: 58, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
341 13 0.04
342 231 0.77
343 49 0.16
344 7 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.37
Consensus pattern (341 bp):
ATTGACAAGAAAGTCCATTTATAGTCACCCATTCTTTCAAAACCCTTATTACTCACGATAAATAG
TTTTATAATCTCAAAATTGATTTAAAGTTAAATTTTTTGACTTTTTTGATTAAAACAAAGTATAA
TTGAATGTCTACCTTAAGAAACATGAAGAAAAAGACATTCATTAACAAGAAAACTCCATTTATAG
TCACCAATTTCCTCAAAAGCCTTACTACTCACTTTAAATGTTTTTATAATCTCAAAATTAGTTTT
AAGTTGAATTTTTTGACATTTTTGCTTAAAACAAACTATAATTGAATGTCTACCTGGAGAAACGT
AAAGAAATAGACATTC
Found at i:15094 original size:172 final size:171
Alignment explanation
Indices: 14619--15324 Score: 515
Period size: 172 Copynumber: 4.1 Consensus size: 171
14609 NNNNNNTTGT
* * * *
14619 AAGAAAAG-TCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCGATCTAAATGGTTTT
1 AAGAAAAGCT-CATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTT
* * ** * * *
14683 ATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTATGTGTTTCA-TTAAAGCAAGCTAGAATT
65 ATAATCTCAAAATTGATTTAAATTTAAATT-TTTTTAAAT-TTTTAGTTAAAACAAGCTATAATT
* * * *
14747 GAATGTCTATCC-TGAGAAATATAAAGAAATAGGCATTCATTAGC
128 GAATGTCTA-CCTTGAAAAACATAAAAAAATAGGAATTCATTAGC
* * *
14791 AAGAGAAGCTTATTTATAGTCACCCATACCTTTAAAAGCCTTATTACTCGCTTT-AATGGTTTTA
1 AAGAAAAGCTCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTA
* * * * * *
14855 TAATGTCATAATTGGTTTTAAGTTAAATTTTTTTAAAATTTTTAGTTAAAACAAACTATAATTGA
66 TAATCTCAAAATTGATTTAAATTTAAATTTTTTT-AAATTTTTAGTTAAAACAAGCTATAATTGA
* *
14920 ATGTTTACCTTGAAAAACGTAAAAAAATAGGAATTCATTAGC
130 ATGTCTACCTTGAAAAACATAAAAAAATAGGAATTCATTAGC
* * * **********
14962 AAGAAAAG-TCCGTTTATAGTCACCTATTCCTTCAAAAGCCTNNNNNNNNNNTTTAAATGGTTTT
1 AAGAAAAGCT-CATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTT
* * *
15026 ATAATCTCAAAATTTATTTAAATTTAAATTTTTTATACATTTTTAGTTAAAACAAGTTATAATTG
65 ATAATCTCAAAATTGATTTAAATTTAAATTTTTT-TAAATTTTTAGTTAAAACAAGCTATAATTG
* * * * * *
15091 AATGTCTACCTTAAAAAAGATGAAGAACAA-A-GCATTTATT-GAT
129 AATGTCTACCTTGAAAAACAT-AA-AAAAATAGGAATTCATTAG-C
* ** * * ** *
15134 AAGAAAAG-TCCATTTATAGAT-ACCCATTCCTTTGAAGGCCGTATTACTTACTTTAAATAGTTT
1 AAGAAAAGCT-CATTTATAG-TCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* * * * * * * * *
15197 TATAAACT-AGTAATTGATTTTAAGTTGATTTTGTTTTACATTTTTGGCTAAAAC-AGACT-TGA
64 TATAATCTCA-AAATTGATTTAAATTTAAATTT-TTTTAAATTTTTAGTTAAAACAAG-CTAT-A
* * * * *
15259 ATTAAATATCTACCTTGAGAAACATAAAAAAAATA-GCATTCATTGGC
125 ATTGAATGTCTACCTTGAAAAACAT-AAAAAAATAGGAATTCATTAGC
15306 AAGAAAAG-TCCATTTATAG
1 AAGAAAAGCT-CATTTATAG
15325 CTNNNNNNNN
Statistics
Matches: 422, Mismatches: 95, Indels: 34
0.77 0.17 0.06
Matches are distributed among these distances:
170 11 0.03
171 130 0.31
172 267 0.63
173 10 0.02
174 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (171 bp):
AAGAAAAGCTCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTA
TAATCTCAAAATTGATTTAAATTTAAATTTTTTTAAATTTTTAGTTAAAACAAGCTATAATTGAA
TGTCTACCTTGAAAAACATAAAAAAATAGGAATTCATTAGC
Found at i:21319 original size:171 final size:169
Alignment explanation
Indices: 20972--22719 Score: 1046
Period size: 171 Copynumber: 10.2 Consensus size: 169
20962 NNNNNNNNNN
*
20972 ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCATTTTAAAT-GATTTTATAATCTCATAATT-
1 ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATAG-TTTTATAATCTCATAATTG
* * * * * * * *
21035 CTTTTAAGTTAAATTTTTTACATTTTTGGGTAAAAAAGGCTATACTTGAATGTATGCCTTGGGAA
65 ATTTTAAGTTGAATTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTGCCTTAGGAA
* * ** *
21100 ACGTGAAGTAAAAGCTAAACTATTGACACGAAAAGTCCATTT
130 ACATGAAG-AAAAGGTATTC-ATTGACAAGAAAAGTCCATTT
* * * *
21142 ATAGTCACTCATTCTTTCAAAAGCCTTATTACTCACTATAAATAGTTTTATAATTTCAGAATTGA
1 ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGA
* * * * *
21207 TTTTAGGTTGAATTTTTTAACCTTTTTGATTAGAACAGATTATAATTGAATGTCTGCCTTAGGAA
66 TTTTAAGTTGAATTTTTT-ACATTTTTGGTTAAAACAGACTATAATTGAATGTCTGCCTTAGGAA
* * *
21272 ACATAAAGAGAAAGGTAGTCATTGACAAGAAAAGTCTATTT
130 ACATGAAGA-AAAGGTATTCATTGACAAGAAAAGTCCATTT
* * * * *
21313 ATAGTCACCAATT-TCCTCAAAAGCCTTATTACTCACTTGAAATGGTTTTATAATCTCAAAATT-
1 ATAGTCACCCATTCT-TTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTG
* * * * * *
21376 AGTTTTAAGTTAGATTTTTTTACATGTTTGGTTAAAACAAACTATAATTGAACGT-T-CACCTCG
65 A-TTTTAAGTT-GAATTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTGC-CTTAG
** * *
21439 AGAAACAT-ATAGAAATAGGCCTTCATTGACAAGACAAGTCTATTT
127 -GAAACATGA-AGAAA-AGGTATTCATTGACAAGAAAAGTCCATTT
* * * * **********
21484 ATAGTCACTCATCCCTTCAAAAGCCTTATTAATCACTTTAAATAGTTTTATNNNNNNNNNNTTGA
1 ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGA
* * * ** * * * *
21549 TTTGAATTTAAATTTTTTGTACATTTTTTATTAAAATAGAGTATAATTGAATGTCTGCCTCAAGA
66 TTTTAAGTTGAA-TTTTT-TACATTTTTGGTTAAAACAGACTATAATTGAATGTCTGCCTTAGGA
* ** * * *
21614 AACGTGAAGAAAAAGACATTCGTTGACAAGAAAACTCCTTTT
129 AACATGAAG-AAAAGGTATTCATTGACAAGAAAAGTCCATTT
* ********** *
21656 ATAGTCACCCATTCTTTCAAAAGCCTTACTACTCACNNNNNNNNNNTTTATAATCTCATAATTTA
1 ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGA
* * * * * * *
21721 TTTTAGGTTGAATTTTTTTCCTTTTTTGGTTAGAGCAGATTATAATTGAATGTCTACCTT-GTGA
66 TTTTAAGTTGAA-TTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTGCCTTAG-GA
* * **
21785 AATATGAAGAAAAAGATATTCATTGGTAAGAAAAGTCCATTT
129 AACATGAAG-AAAAGGTATTCATTGACAAGAAAAGTCCATTT
** * * * * * * *
21827 GGAGTCACCTATT-TTCTCAAAAGCTTTATTACTCGCCCTCAAA-GGTTTTATAATCTCAAAATT
1 ATAGTCACCCATTCTT-TCAAAAGCCTTATTACTC-ACTTTAAATAGTTTTATAATCTCATAATT
* ** * * * * * * *
21890 AATTTTAAGTTGAAATTTTTTACATTTTTCATTAAAAAAGGCTACAATTTAGTGTTTGCCTTGGG
64 GATTTTAAGTTG-AATTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTGCCTTAGG
* * **
21955 GAACATGAAGCAAAAGCTAGCCATTGGTAC-A-AAAAGTCCATTT
128 AAACATGAAG-AAAAGGTATTCATT-G-ACAAGAAAAGTCCATTT
* ** * * * * * *
21998 ATAGTCACTCAAGCCTTC-AAAGTCTTATTGCTTACTTTAAATAGTTTTATAAAT-TAATAATTC
1 ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTAT-AATCTCATAATTG
* * ** * *
22061 ATTTTAAGTTGAATTTTTTTACATTTTTGGTTCAAGAA-A-ACAAGAATTGAACATCTACCTTAA
65 ATTTTAAGTTGAA-TTTTTTACATTTTTGGTT-AA-AACAGACTATAATTGAATGTCTGCCTTAG
* * *
22124 GAAACGTGAAGAAAAAGTATTCATTCACAAGAAAAGTCCATTT
127 GAAACATGAAGAAAAGGTATTCATTGACAAGAAAAGTCCATTT
** * * * *
22167 ATAACCACCCATACCTTCAAAAGTCTTATTACTCATTTTAAATAGTTTTATAA-CATCATAATTG
1 ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC-TCATAATTG
********** ** * *
22231 ATTTTAAGTTGAATTATTTTACATTTNNNNNNNNNNCAGACTATAATTGAATGTCTAACTCATGA
65 ATTTTAAGTTGAATT-TTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTGCCTTAGGA
* * *
22296 AACATAAAGAAGAAGGCATTCATTTG-TAAGAAAAGTCCATTT
129 AACATGAAGAA-AAGGTATTCA-TTGACAAGAAAAGTCCATTT
* ** * * * **********
22338 ATTGTCATTCATTCCTTT-AAAAGCTTTATTACTCACTCTAAATGGTTTTATNNNNNNNNNNTTG
1 ATAGTCACCCATT-CTTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTG
* * * * ** * * * ** *
22402 ATTTAAATTTGAATTCTTTGTATATGTTTCATTGAAGCA-AGCTAGAATTGAATGT-TTACTTTG
65 ATTTTAAGTTGAATT-TTT-TACATTTTTGGTTAAAACAGA-CTATAATTGAATGTCTGCCTTAG
* * * * *
22465 AAAAACATAAAGAATTAGGCATTCATTGACAAGAAAAG-CTTATTT
127 -GAAACATGAAGAA-AAGGTATTCATTGACAAGAAAAGTC-CATTT
* * * * *
22510 ATAGTCAACCATACCTTCAAAAGCCTTATTACTCGCTTTAAAT-GGTTT-TAATCTCATAATTGA
1 ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGA
* * ** * * *
22573 TTTTAAGCTT-AATTTTTTACATTTTT-GTGTAAAAAAGGCTATAATTGAACATCTGCTTTCGGG
66 TTTTAAG-TTGAATTTTTTACATTTTTGGT-TAAAACAGACTATAATTGAATGTCTGCCTTAGGA
* * ** * *
22636 AACGTGAAGTAAAAGTTAAACTATTGGCACGAAAAGTCCATTT
129 AACATGAAG-AAAAGGTATTC-ATTGACAAGAAAAGTCCATTT
*
22679 AGAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAA
1 ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAA
22720 NNNNNNNNNN
Statistics
Matches: 1174, Mismatches: 347, Indels: 115
0.72 0.21 0.07
Matches are distributed among these distances:
167 3 0.00
168 34 0.03
169 109 0.09
170 243 0.21
171 511 0.44
172 267 0.23
173 6 0.01
174 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.37
Consensus pattern (169 bp):
ATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGA
TTTTAAGTTGAATTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTGCCTTAGGAAA
CATGAAGAAAAGGTATTCATTGACAAGAAAAGTCCATTT
Found at i:25004 original size:172 final size:161
Alignment explanation
Indices: 24813--25140 Score: 313
Period size: 172 Copynumber: 2.0 Consensus size: 161
24803 AAAGGAATGG
* *
24813 GTAACTACAAATGGACTTTTCTTGCAAATAAATGCCTT-TGTCTTCACT-TTT-GTGAAGGTAAA
1 GTAACTACAAATAGACTTTTCTTGCAAATAAATGCCTTCT-TCTTCA-TGTTTCATG-AGGTAAA
* * * * *
24875 CATTCTATTATATTCTGTTTTAACAAAAAATGTACAACGAAATGAAATTTAAATC-AAATTTGAG
63 CATTCAATTATATTCTGTTTTAACAAAAAATGTA-AA-AAAATCAAACTTAAAACTAAATTTGAG
*
24939 ATTATAAAATCATTTAAAGTGAGTAATAAGGTTTTT
126 ATTATAAAACCATTTAAAGTGAGTAATAAGGTTTTT
* * ** *
24975 NNNNNNNNNNGTAACTATAAATAGACTTTTCTTGCTAATGTATGCCTTCTTCTTTATGTTTCATG
1 ----------GTAACTACAAATAGACTTTTCTTGCAAATAAATGCCTTCTTCTTCATGTTTCATG
* * * * * *
25040 AGTTAGACATTCAATTATATTCTGTTTTAACCAAATATGTAAAAAAATCCAACTTAAAACTAATT
56 AGGTAAACATTCAATTATATTCTGTTTTAACAAAAAATGTAAAAAAATCAAACTTAAAACTAAAT
*
25105 TTGAGATTATTAAACCATTTAAAGTGAGTAATAAGG
121 TTGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
25141 CNNNNNNNNN
Statistics
Matches: 132, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
170 12 0.09
171 40 0.30
172 77 0.58
173 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.37
Consensus pattern (161 bp):
GTAACTACAAATAGACTTTTCTTGCAAATAAATGCCTTCTTCTTCATGTTTCATGAGGTAAACAT
TCAATTATATTCTGTTTTAACAAAAAATGTAAAAAAATCAAACTTAAAACTAAATTTGAGATTAT
AAAACCATTTAAAGTGAGTAATAAGGTTTTT
Done.