Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 37 of 203
Found at i:12247367 original size:322 final size:323
Alignment explanation
Indices: 12246387--12247442 Score: 967
Period size: 322 Copynumber: 3.2 Consensus size: 323
12246377 AACAGACATT
* *
12246387 AAAAATAGAAATTGAAAACAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
** * ** * **
12246452 TTGA----TTTTTTG-AAACTTAA-CTTGAAAAGCAGATTTTGAAAATACCTCGATATGTGACTG
66 TTGATTTTTTTTTTGAAAACAGAATC-TGAAAAACAGAAATTGAAAATACCTCGACATGTGACCC
* * * ** * *
12246511 GAGGTTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATAGAAATT-AAAAGACTCA
130 GAGGCTCAACTCACATCTCACAATACAAGTTAATTTTTTTGAAAAACAGAAATTGAAAA-A-T-A
* ** *
12246573 ACTCAACTCTCGCAGAAAT-TAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGA
192 CCTCAA---T-GC-GTGATCT--AAAGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGA
* * * * ** *
12246635 AAAATAGAAATTAAAAGACTCAACTCAACTCTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCG
250 AAAACAGAAATTGAAA-A-T--A--C--CTC-AGCACG---TGAGCAGGCTCAACTCACCTCTCG
12246699 CAATATGAGTTGAATTTTTTTG
303 CAATATGAGTTG-ATTTTTTTG
* * * *
12246721 AAAAAAAAAAGAAATTGAAAATAGCTCAGCACGTGAGCTAAGGCTCAACTCACTTCTCGCAATAT
1 ---AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
* **
12246786 GAGTT-A----ATTTTTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGAC
63 GAGTTGATTTTTTTTTTGAAAACAGAATCTGAAAAACAGAAATTGAAAATACCTCGACATGTGAC
* ** * *
12246846 CCGAGGCTCAACTCACATCTCGCAATGTAAGTTAATTTTTTTGAAAAATATAAATTGAAAAAATA
128 CCGAGGCTCAACTCACATCTCACAATACAAGTTAATTTTTTTGAAAAACAGAAATTG-AAAAATA
* *
12246911 CCTCAATGTGTGATCTAAAGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAGACAG
192 CCTCAATGCGTGATCTAAAGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAG
* *
12246976 AAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
257 AAATTGAAAATACCTCAGCACGTGAG-C-AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
12247041 TTTG
320 TTTG
*
12247045 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* * * *
12247110 TTGATTTTTTTTTTGAAAGGCAGAAAT-TGAAAAACAGAAATTGAAAATACCTTGGCGTGTGACC
66 TTGATTTTTTTTTTGAAA-ACAG-AATCTGAAAAACAGAAATTGAAAATACCTCGACATGTGACC
* * * * * * *
12247174 TGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG-AAATTACC
129 CGAGGCTCAACTCACATCTCACAATACAAGTTAATTTTTTTGAAAAACAGAAATTGAAAAATACC
* *
12247237 TC-A-GCGTG-TCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGA
194 TCAATGCGTGAT-CTAAAGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGA
* ** ** *
12247299 AATTGAAAATACCTCAGCATGTTTTG-AGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTT
258 AATTGAAAATACCTCAGCACG-TGAGCAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT
12247363 TTTG
320 TTTG
* * * * * *
12247367 AAAAACAGAAATTGAAAATACCTCGGCGTGTGA-CCTAAGGCTCAACTCGCCGCTCGCAATACGA
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGA
12247431 GTTGATTTTTTT
65 GTTGATTTTTTT
12247443 GACAACAGAA
Statistics
Matches: 619, Mismatches: 76, Indels: 63
0.82 0.10 0.08
Matches are distributed among these distances:
320 29 0.05
321 65 0.11
322 146 0.24
323 5 0.01
324 18 0.03
325 32 0.05
326 23 0.04
327 69 0.11
328 3 0.00
330 1 0.00
332 33 0.05
333 4 0.01
334 22 0.04
335 1 0.00
336 7 0.01
337 130 0.21
338 7 0.01
339 19 0.03
340 1 0.00
341 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (323 bp):
AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTTTTTGAAAACAGAATCTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCG
AGGCTCAACTCACATCTCACAATACAAGTTAATTTTTTTGAAAAACAGAAATTGAAAAATACCTC
AATGCGTGATCTAAAGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAAT
TGAAAATACCTCAGCACGTGAGCAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
Found at i:12247564 original size:164 final size:166
Alignment explanation
Indices: 12247364--12247767 Score: 659
Period size: 164 Copynumber: 2.4 Consensus size: 166
12247354 TGATTTTTTT
* * *
12247364 TTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCTAAGGCTCAACTCGCCGCTCGCAATAC
1 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATAC
* *
12247429 GAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGTATGTCCTGAGGCTCAACTCACCTC
66 GAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTCCTAAGGCTCAACTCACCTC
*
12247494 TCGCAATATGAG-TCAATTTTTTTGAAAGGCAGAAA
131 TCGCAATATGAGTTCAATTTTTTTGAAAGACAGAAA
12247529 TTGAAAAACGGAAATTG-AAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATAC
1 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATAC
*
12247593 GAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTC
66 GAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTCCTAAGGCTCAACTCACCTC
* *
12247658 TCGCAATATGAGTTGATTTTTTTTGAAAGACAGAAA
131 TCGCAATATGAGTTCAATTTTTTTGAAAGACAGAAA
* * * * * *
12247694 TTGAAAAATGGAAATTGAAAATACCTTGACGTGTGACTTGAGGCTCAACTCACCTCTCGCAATAC
1 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATAC
12247759 GAGTTGATT
66 GAGTTGATT
12247768 CTTTCAAAAA
Statistics
Matches: 222, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
164 119 0.54
165 52 0.23
166 51 0.23
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (166 bp):
TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATAC
GAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTCCTAAGGCTCAACTCACCTC
TCGCAATATGAGTTCAATTTTTTTGAAAGACAGAAA
Found at i:12247626 original size:392 final size:396
Alignment explanation
Indices: 12246849--12247700 Score: 1238
Period size: 392 Copynumber: 2.1 Consensus size: 396
12246839 ATGTGACCCG
* * * * * *
12246849 AGGCTCAACTCACATCTCGCAATGTAAGTTAATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG--AAAATACCT
* *
12246914 CAATGTGTGATCTAAAGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAA
64 CAATGTGT-ATCTAAAGCTCAACTCACATCTCACAATATGAGTTGATTTTTTTGAAAAACAGAAA
* * *
12246979 TTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
128 TTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTTTTT
* *
12247044 GAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGA
193 GAAAGACAGAAATTGAAAATACCTCA-CGCATGAGCCAAGGCTCAACTCACCTCTCGCAATATGA
* * *
12247109 GTTGATTTTTTTTTTGAAAGGCAGAAATTGAAAAACAGAAATTGAAAATACCTTGGCGTGTGACC
257 GTTCA-TATTTTTTTGAAAGGCAGAAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACC
*
12247174 TGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTC
321 TGAGGCTCAACTCGCCACTCACAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTC
12247239 AGCGTGTCCTA
386 AGCGTGTCCTA
12247250 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCA
* * **
12247315 GCATGT-T-T-TGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTTGAAAAACAGAA
66 --ATGTGTATCTAAAGCTCAACTCACATCTCACAATATGAGTTGA--TTTTTTTGAAAAACAGAA
* * *
12247377 ATTGAAAATACCTCGGCGTGTGA-CCTAAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTTT
127 ATTGAAAATACCTCAGCGCGTGAGCC-AAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTTT
* * * * *
12247441 TTGACA-ACAGAAATTGAAATTACCTCA-GTATG-TCCTGAGGCTCAACTCACCTCTCGCAATAT
191 TTGAAAGACAGAAATTGAAAATACCTCACGCATGAGCC-AAGGCTCAACTCACCTCTCGCAATAT
*
12247503 GAG-TCA-ATTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG-AAATACCTCGGCGTGTGAC
255 GAGTTCATATTTTTTTGAAAGGCAGAAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGAC
*
12247565 CTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
320 CTGAGGCTCAACTCGCCACTCACAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
12247630 CAGCGTGTCCTA
385 CAGCGTGTCCTA
*
12247642 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGACAGAAATTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTGAAAA
12247701 ATGGAAATTG
Statistics
Matches: 412, Mismatches: 32, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
392 125 0.30
393 60 0.15
395 4 0.01
396 31 0.08
397 29 0.07
398 22 0.05
399 88 0.21
400 1 0.00
401 52 0.13
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (396 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCA
ATGTGTATCTAAAGCTCAACTCACATCTCACAATATGAGTTGATTTTTTTGAAAAACAGAAATTG
AAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTTTTTGAA
AGACAGAAATTGAAAATACCTCACGCATGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTC
ATATTTTTTTGAAAGGCAGAAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGG
CTCAACTCGCCACTCACAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGT
GTCCTA
Found at i:12247661 original size:74 final size:76
Alignment explanation
Indices: 12247529--12247699 Score: 231
Period size: 74 Copynumber: 2.3 Consensus size: 76
12247519 AAGGCAGAAA
* * * * *
12247529 TTGAAAAACGGAAATTGAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACG
1 TTGAAAGACAGAAATTGAAATACCTCAGCGTGT-ACCTAAGGCTCAACTCACCACTCGCAATACG
12247594 AGTTGA-TTTTT
65 AGTTGATTTTTT
* * *
12247605 TTGACA-ACAGAAATTGAAATTACCTCAGCGTGT-CCTAAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAGACAGAAATTGAAA-TACCTCAGCGTGTACCTAAGGCTCAACTCACCACTCGCAATACG
12247668 AGTTGATTTTTT
65 AGTTGATTTTTT
12247680 TTGAAAGACAGAAATTGAAA
1 TTGAAAGACAGAAATTGAAA
12247700 AATGGAAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
74 32 0.38
75 22 0.26
76 30 0.36
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (76 bp):
TTGAAAGACAGAAATTGAAATACCTCAGCGTGTACCTAAGGCTCAACTCACCACTCGCAATACGA
GTTGATTTTTT
Found at i:12247936 original size:14 final size:14
Alignment explanation
Indices: 12247917--12247951 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12247907 TGATTTTTTT
*
12247917 TTGAAAGACAGAAA
1 TTGAAAAACAGAAA
12247931 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
12247945 TTGAAAA
1 TTGAAAA
12247952 TACCTCGGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:12248177 original size:72 final size:73
Alignment explanation
Indices: 12248022--12248221 Score: 219
Period size: 72 Copynumber: 2.8 Consensus size: 73
12248012 TAGAAATTAA
* * ** * * * * *
12248022 AAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAGATTACCTCAT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAAACAAAAATTGAAAATACCTCAG
* *
12248087 CGTGTCCT
66 CGTGCCCC
12248095 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-AATT-AAAACACAAAAATTGAAAATACCTCA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAA-ACAAAAATTGAAAATACCTCA
12248158 GCGTGCCCC
65 GCGTGCCCC
* ** * *
12248167 GAGGCTCAACTCACCTCTAACAATATGAGTTGAT-TTTGAAAAATAAAAATT-AAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAAACAAAAATTGAAAA
12248222 GGCTTAACTC
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
71 7 0.06
72 66 0.61
73 35 0.32
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (73 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAAACAAAAATTGAAAATACCTCAG
CGTGCCCC
Found at i:12248231 original size:53 final size:53
Alignment explanation
Indices: 12248168--12248359 Score: 163
Period size: 53 Copynumber: 3.5 Consensus size: 53
12248158 GCGTGCCCCG
12248168 AGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATAAAAATTAAA
1 AGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATAAAAATTAAA
* ** * *** *** ****
12248221 AGGCTTAACTCACCTCTCGCAATATGAG-TCAAACT-AAAAATACCTCAGCGTGCCCCG
1 AGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATA----AAAAT--TAAA
12248278 AGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATAAAAATTAAA
1 AGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATAAAAATTAAA
* **
12248331 AGGCTTAACTCACCTCTCGCAATATGAGT
1 AGGCTCAACTCACCTCTAACAATATGAGT
12248360 CAAACTAAAA
Statistics
Matches: 100, Mismatches: 31, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
51 7 0.07
52 3 0.03
53 51 0.51
55 4 0.04
57 25 0.25
58 3 0.03
59 7 0.07
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.26
Consensus pattern (53 bp):
AGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATAAAAATTAAA
Found at i:12248290 original size:57 final size:57
Alignment explanation
Indices: 12248221--12248416 Score: 179
Period size: 57 Copynumber: 3.5 Consensus size: 57
12248211 AAAAATTAAA
*
12248221 AGGCTTAACTCACCTCTCGCAATATGAGTCAAACTAAAAATACCTCAGCGTGCCCCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAAACTAAAAATACCTCAGCGTGCCCCG
** * *** *** ****
12248278 AGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATA----AAAAT--TAAA
1 AGGCTCAACTCACCTCTCGCAATATGAG-TCAAACT-AAAAATACCTCAGCGTGCCCCG
*
12248331 AGGCTTAACTCACCTCTCGCAATATGAGTCAAACTAAAAATACCTCAGCGTGCCCCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAAACTAAAAATACCTCAGCGTGCCCCG
* *
12248388 AGGCTCAACTCACTTCTTGCAATATGAGT
1 AGGCTCAACTCACCTCTCGCAATATGAGT
12248417 TGATTTTGAA
Statistics
Matches: 100, Mismatches: 31, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
51 7 0.07
52 3 0.03
53 25 0.25
55 4 0.04
57 51 0.51
58 3 0.03
59 7 0.07
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (57 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAAACTAAAAATACCTCAGCGTGCCCCG
Found at i:12248340 original size:110 final size:110
Alignment explanation
Indices: 12248147--12248428 Score: 537
Period size: 110 Copynumber: 2.6 Consensus size: 110
12248137 ACAAAAATTG
12248147 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATA
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATA
12248212 AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAACTA
66 AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAACTA
12248257 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATA
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATA
12248322 AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAACTA
66 AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAACTA
* **
12248367 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTTGCAATATGAGTTGATTTTGAAAA
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAA
12248429 CAACAATTAA
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 169 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.25
Consensus pattern (110 bp):
AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAACAATATGAGTTGATTTTGAAAAATA
AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAAACTA
Found at i:12248646 original size:74 final size:77
Alignment explanation
Indices: 12248510--12248683 Score: 228
Period size: 76 Copynumber: 2.3 Consensus size: 77
12248500 AAGGCAGAAA
* * * **
12248510 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTTGCCACTCGCAATAC
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAATAC
12248575 GAGTTGA-TTTTT
65 GAGTTGATTTTTT
* * * *
12248587 TTGACA-ACAGAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACG
12248650 AGTTGATTTTTTT
66 AGTTGA-TTTTTT
12248663 TTGAAAGACAGAAATTGAAAA
1 TTGAAAGACAGAAATTGAAAA
12248684 ACAGAAATTG
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
74 32 0.38
76 34 0.40
77 18 0.21
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (77 bp):
TTGAAAGACAGAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACG
AGTTGATTTTTT
Found at i:12248682 original size:14 final size:14
Alignment explanation
Indices: 12248663--12248697 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12248653 TGATTTTTTT
*
12248663 TTGAAAGACAGAAA
1 TTGAAAAACAGAAA
12248677 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
12248691 TTGAAAA
1 TTGAAAA
12248698 TACCTCGGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:12248708 original size:167 final size:167
Alignment explanation
Indices: 12248419--12248901 Score: 556
Period size: 167 Copynumber: 2.9 Consensus size: 167
12248409 ATATGAGTTG
* * * * *
12248419 ATTTTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTATCGCAATAT
1 ATTTTGAAAACAA-AATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
* * *
12248484 CAGTTGATTTTTTTT-AAAGGCAGAAATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACC
65 GAGTTGATTTTTTTTGAAAGACAGAAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACC
*
12248548 TGAGGCTCAACTTGCCACTCGCAATACGAGTTGA-TTT
130 TGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTTT
* *
12248585 -TTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
1 ATTTTGAAAACA-AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
12248649 GAGTTGATTTTTTTTTGAAAGACAGAAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGAC
65 GAGTTGA-TTTTTTTTGAAAGACAGAAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGAC
* *
12248714 TTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTCTTT
129 CTGAGGCTCAACTCGCCACTCGCAATACGAGTTGA-T-TTT
* *
12248755 CAAAAATATAATAATGAAAACAAAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACTCACCT
1 -----AT-T--T--TGAAAAC-AAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCT
* * *
12248820 CTCGCAATATGAGTTGA---TTCTTGAACA-A-TGTAAATTG-AAAACAGAAATTGAAAGTACCT
55 CTCGCAATATGAGTTGATTTTTTTTGAA-AGACAG-AAATTGAAAAACAGAAATTGAAAATACCT
*
12248879 CAGC--GTGACCTGAGGCTCAACTC
118 CGGCGTGTGACCTGAGGCTCAACTC
12248902 ATCTCTCGTA
Statistics
Matches: 275, Mismatches: 22, Indels: 32
0.84 0.07 0.10
Matches are distributed among these distances:
165 61 0.22
166 9 0.03
167 78 0.28
170 3 0.01
174 18 0.07
176 26 0.09
177 15 0.05
178 1 0.00
179 1 0.00
181 62 0.23
182 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (167 bp):
ATTTTGAAAACAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTTTGAAAGACAGAAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCT
GAGGCTCAACTCGCCACTCGCAATACGAGTTGATTTT
Found at i:12248828 original size:181 final size:174
Alignment explanation
Indices: 12248592--12248924 Score: 445
Period size: 181 Copynumber: 1.9 Consensus size: 174
12248582 TTTTTTTGAC
* * *
12248592 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
* * *
12248657 TTTTTTTTGAA-AGACAG-AAATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACTTGAGG
65 ---TTCTTGAACA-A-AGTAAATTG-AAAACAGAAATTGAAAATACCTCAGC--GTGACCTGAGG
* *
12248720 CTCAACTCGCCTCTCGCAATACGAGTTGATTCTTTCAAAAATATAATAATGAA
122 CTCAACTCACCTCTCGCAATACGAGCTGATTCTTTCAAAAATATAATAATGAA
*
12248773 AACAAAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
12248838 TCTTGAACAATGTAAATTGAAAACAGAAATTGAAAGTACCTCAGCGTGACCTGAGGCTCAACTCA
66 TCTTGAACAAAGTAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCA
* * *
12248903 TCTCTCGTAATATGAGCTGATT
131 CCTCTCGCAATACGAGCTGATT
12248925 TTGAAAAAGT
Statistics
Matches: 136, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
174 36 0.26
176 25 0.18
177 14 0.10
178 1 0.01
181 60 0.44
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (174 bp):
AACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TCTTGAACAAAGTAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCA
CCTCTCGCAATACGAGCTGATTCTTTCAAAAATATAATAATGAA
Found at i:12248941 original size:86 final size:86
Alignment explanation
Indices: 12248587--12248945 Score: 418
Period size: 86 Copynumber: 4.1 Consensus size: 86
12248577 GTTGATTTTT
* * *
12248587 TTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
12248652 TTGATTTTTTTTTGAAAGACAGAAA
66 TTGA----TTTTTGAAAAATAGAAA
* * * *
12248677 TTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACTTGAGGCTCAACTCGCCTCTCGCAATAC
1 TTG-AAAACAGAAATTGAAAATACCTCAGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATAT
* *
12248742 GAGTTGATTCTTTCAAAAATATAATA
63 GAGTTGATT-TTTGAAAAATAGAA-A
* * *
12248768 ATGAAAACAAAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
12248833 TTGATTCTTGAACAAT-GTAAA
66 TTGATTTTTGAAAAATAG-AAA
* * *
12248854 TTGAAAACAGAAATTGAAAGTACCTCAGCGTGACCTGAGGCTCAACTCATCTCTCGTAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
12248919 CTGA-TTTTGAAAAAGTAGAAA
66 TTGATTTTTGAAAAA-TAGAAA
12248940 TT-AAAA
1 TTGAAAA
12248946 GGTTCAACCC
Statistics
Matches: 232, Mismatches: 29, Indels: 21
0.82 0.10 0.07
Matches are distributed among these distances:
85 12 0.05
86 69 0.30
87 10 0.04
88 39 0.17
89 2 0.01
90 38 0.16
91 26 0.11
93 36 0.16
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (86 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTGAAAAATAGAAA
Found at i:12249063 original size:142 final size:140
Alignment explanation
Indices: 12248809--12249200 Score: 667
Period size: 142 Copynumber: 2.8 Consensus size: 140
12248799 GACCTGAGGC
* * *
12248809 TCAACTCACCTCTCGCAATATGAGTTGATTCTTGAACAATGTAAATTGAAAACAGAAATTGAAAG
1 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAATTGAAAACAGAAATTGAAAA
* *
12248874 TACCTCAGCGTGACCTGAGGCTCAACTCATCTCTCGTAATATGAGCTGATTTTGAAAAAGTAGAA
66 TACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAA
12248939 ATTAAAAGGT
131 ATTAAAAGGT
* * * *
12248949 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAAAAAACATAATAATGAAGACAGAAATTGAA
1 TCAACCCACCTCTCGCAATATGAGTTGATTCTTG-AACAACGTAA-ATTGAAAACAGAAATTGAA
*
12249014 AATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAG
64 AATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAG
12249079 AAATTAAAAGGT
129 AAATTAAAAGGT
12249091 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAATTGAAAACAGAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAATTGAAAACAGAAATTGAAAA
*
12249156 TACCTCAGCATGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
66 TACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
12249201 TTGAAATTAA
Statistics
Matches: 234, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
140 95 0.41
141 15 0.06
142 124 0.53
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (140 bp):
TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGTAAATTGAAAACAGAAATTGAAAA
TACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAA
ATTAAAAGGT
Found at i:12249137 original size:54 final size:54
Alignment explanation
Indices: 12249037--12249142 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
12249027 GACCTGAGGC
*
12249037 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
12249091 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
12249143 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:12249267 original size:72 final size:71
Alignment explanation
Indices: 12249133--12249298 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
12249123 TGAACAACGT
* * *
12249133 AAATTGAAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTAGCAATAT
12249198 GAGTTG
66 GAGTTG
* *
12249204 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTAGCAATA
12249269 TGAGTTG
65 TGAGTTG
**
12249276 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
12249299 GGCTTAACTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:12249393 original size:122 final size:124
Alignment explanation
Indices: 12249173--12249419 Score: 383
Period size: 122 Copynumber: 2.0 Consensus size: 124
12249163 GCATGACCTG
* *
12249173 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
*
12249238 TGCCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
* * * *
12249298 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* *
12249360 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
12249419 A
1 A
12249420 ATACCTCAAC
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
121 16 0.14
122 62 0.55
123 7 0.06
124 1 0.01
125 27 0.24
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
Found at i:12249441 original size:71 final size:70
Alignment explanation
Indices: 12249298--12249472 Score: 228
Period size: 71 Copynumber: 2.5 Consensus size: 70
12249288 AAAAATTAAA
* * * * * *
12249298 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCAGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
12249362 CCCCG
66 CCCCG
*
12249367 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
12249432 GTCTTG
65 GCCCCG
12249438 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
12249473 CCCTTGAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
69 26 0.28
70 6 0.06
71 61 0.66
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:12259871 original size:25 final size:26
Alignment explanation
Indices: 12259843--12259912 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 26
12259833 TTTTTTGGGG
12259843 GGGTTAGGTTTTTCTTTTTC-TTTTT
1 GGGTTAGGTTTTTCTTTTTCTTTTTT
12259868 GGGTTAGGTTTTTTCTTTTTCTTTTTTT
1 GGGTTAGG-TTTTTCTTTTTC-TTTTTT
*
12259896 TGGTTAGGTTTTT-TTTT
1 GGGTTAGGTTTTTCTTTT
12259913 GGGGAGGGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
25 8 0.20
26 16 0.39
27 5 0.12
28 12 0.29
ACGTcount: A:0.04, C:0.06, G:0.20, T:0.70
Consensus pattern (26 bp):
GGGTTAGGTTTTTCTTTTTCTTTTTT
Found at i:12259903 original size:28 final size:26
Alignment explanation
Indices: 12259843--12259909 Score: 100
Period size: 28 Copynumber: 2.5 Consensus size: 26
12259833 TTTTTTGGGG
12259843 GGGTTAGG-TTTTTCTTTTTCTTTTT
1 GGGTTAGGTTTTTTCTTTTTCTTTTT
12259868 GGGTTAGGTTTTTTCTTTTTCTTTTTTT
1 GGGTTAGGTTTTTTCTTTTTC--TTTTT
*
12259896 TGGTTAGGTTTTTT
1 GGGTTAGGTTTTTT
12259910 TTTGGGGAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
25 8 0.21
26 12 0.32
28 18 0.47
ACGTcount: A:0.04, C:0.06, G:0.21, T:0.69
Consensus pattern (26 bp):
GGGTTAGGTTTTTTCTTTTTCTTTTT
Found at i:12260960 original size:24 final size:24
Alignment explanation
Indices: 12260933--12261005 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
12260923 ACTATTATAA
**
12260933 AAAATTATAAAATTAAAATTAATT
1 AAAATTATAAAATTAAAATTAAAC
**
12260957 AAAATTACATAAATAAAAAAATTAAAC
1 AAAATT--ATAAA-ATTAAAATTAAAC
* *
12260984 AATATTCTAAAATTAAAATTAA
1 AAAATTATAAAATTAAAATTAA
12261006 CCCTTACCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
24 15 0.39
25 4 0.11
26 5 0.13
27 14 0.37
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAATTATAAAATTAAAATTAAAC
Found at i:12261619 original size:31 final size:32
Alignment explanation
Indices: 12261576--12261641 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
12261566 ATTAAGAAAA
**
12261576 AAAATTCAAATACTTAATTA-ATTATTAATACT
1 AAAATTCAAATACCAAATTATA-TATTAATACT
*
12261608 AAAATT-AAATACCAAATTATATATTAATCCT
1 AAAATTCAAATACCAAATTATATATTAATACT
12261639 AAA
1 AAA
12261642 TTTTGTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 23 0.77
32 7 0.23
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (32 bp):
AAAATTCAAATACCAAATTATATATTAATACT
Found at i:12275782 original size:10 final size:11
Alignment explanation
Indices: 12275758--12275785 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12275748 AGAATACTCT
12275758 AAAACAGATCA
1 AAAACAGATCA
12275769 AAAACAGATCA
1 AAAACAGATCA
12275780 AAAACA
1 AAAACA
12275786 TACCCACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.18, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAACAGATCA
Found at i:12278024 original size:23 final size:24
Alignment explanation
Indices: 12277981--12278025 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
12277971 TTCGCTTAAC
12277981 GTTCACAAACATATAAATGAACAT
1 GTTCACAAACATATAAATGAACAT
12278005 GTTCACAAACAT-TAAATGAAC
1 GTTCACAAACATATAAATGAAC
12278026 CAAGCCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (24 bp):
GTTCACAAACATATAAATGAACAT
Found at i:12281150 original size:59 final size:57
Alignment explanation
Indices: 12281063--12281182 Score: 161
Period size: 57 Copynumber: 2.1 Consensus size: 57
12281053 ACCTTTTTCA
* *
12281063 TATTAAAAGTTTATATAAAAATTAAATGAATTTTTTATTAAAATGATAGAATTAAATGTT
1 TATTAAAAGTTTATATAAAAATAAAATG-ATTTCTTATT-AAATGATAGAATTAAAT-TT
* * *
12281123 TATTAAAATTTTAT-TAAAAATAAAATGATTTCTTATTAAATGGTATAATTAAATTT
1 TATTAAAAGTTTATATAAAAATAAAATGATTTCTTATTAAATGATAGAATTAAATTT
12281179 TATT
1 TATT
12281183 GTTCTAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
56 6 0.11
57 15 0.27
58 9 0.16
59 12 0.22
60 13 0.24
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.46
Consensus pattern (57 bp):
TATTAAAAGTTTATATAAAAATAAAATGATTTCTTATTAAATGATAGAATTAAATTT
Found at i:12283401 original size:86 final size:86
Alignment explanation
Indices: 12283307--12283475 Score: 320
Period size: 86 Copynumber: 2.0 Consensus size: 86
12283297 CTTTGGCCCT
12283307 TTTCAATTTTATATTTCAAAAATTTATCCTAATAAAATGCTCAAATTTAATTTCATTGTTTAATT
1 TTTCAATTTTATATTTCAAAAATTTATCCTAATAAAATGCTCAAATTTAATTTCATTGTTTAATT
12283372 TGATATTTTAATTATTTTATA
66 TGATATTTTAATTATTTTATA
* *
12283393 TTTCAATTTTATATTTCAAAATTTTATCCTAATTAAATGCTCAAATTTAATTTCATTGTTTAATT
1 TTTCAATTTTATATTTCAAAAATTTATCCTAATAAAATGCTCAAATTTAATTTCATTGTTTAATT
12283458 TGATATTTTAATTATTTT
66 TGATATTTTAATTATTTT
12283476 TTCAATTAAG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (86 bp):
TTTCAATTTTATATTTCAAAAATTTATCCTAATAAAATGCTCAAATTTAATTTCATTGTTTAATT
TGATATTTTAATTATTTTATA
Found at i:12283419 original size:15 final size:13
Alignment explanation
Indices: 12283385--12283411 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12283375 TATTTTAATT
12283385 ATTTTATATTTCA
1 ATTTTATATTTCA
12283398 ATTTTATATTTCA
1 ATTTTATATTTCA
12283411 A
1 A
12283412 AATTTTATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTATATTTCA
Found at i:12283873 original size:18 final size:19
Alignment explanation
Indices: 12283850--12283885 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12283840 AACTCAGGTA
12283850 TTAAATTGAA-CATTAAAG
1 TTAAATTGAAGCATTAAAG
*
12283868 TTAAATTTAAGCATTAAA
1 TTAAATTGAAGCATTAAA
12283886 TGATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (19 bp):
TTAAATTGAAGCATTAAAG
Found at i:12290111 original size:85 final size:83
Alignment explanation
Indices: 12289970--12290138 Score: 302
Period size: 85 Copynumber: 2.0 Consensus size: 83
12289960 GTGGCTTTCT
*
12289970 TCTTAAGAAAGGTTTTTTTTTCTTCTTGCAATGAGTTGTATACTTCACCTGTAAAGATATGTACT
1 TCTTAAGAAAGGTTTTTTTTTCTTCTTGCAATGAGTTGTATACTTCACCTGTAAAGATATCTACT
12290035 AGGTGCTTTTATCTTGTA
66 AGGTGCTTTTATCTTGTA
*
12290053 TCTTAAGAAAGGTTTTTTTTTTTCTTCTTGCAATGATTTGTATACTTCACCTGTAAAGATATCTA
1 TCTTAAGAAAGG--TTTTTTTTTCTTCTTGCAATGAGTTGTATACTTCACCTGTAAAGATATCTA
12290118 CTAGGTGCTTTTATCTTGTA
64 CTAGGTGCTTTTATCTTGTA
12290138 T
1 T
12290139 AAAGATGCCT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
83 12 0.15
85 70 0.85
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (83 bp):
TCTTAAGAAAGGTTTTTTTTTCTTCTTGCAATGAGTTGTATACTTCACCTGTAAAGATATCTACT
AGGTGCTTTTATCTTGTA
Found at i:12290164 original size:85 final size:84
Alignment explanation
Indices: 12289990--12290165 Score: 185
Period size: 85 Copynumber: 2.1 Consensus size: 84
12289980 GGTTTTTTTT
*
12289990 TCTTCTTGCAATGAGTTGTATACTTCACCTGTAAAGATATGTACTAGGTGCTTTTATCTTGTATC
1 TCTTCTTGCAATGAGTTGTATACTTCACCTGTAAAGATATCTACTAGGTGCTTTTATCTTGTA-C
* **** *****
12290055 TTAAGAAAGGTTTTTTTTTT
65 TAAAGAAAGGGAAATGGAAC
*
12290075 TCTTCTTGCAATGATTTGTATACTTCACCTGTAAAGATATCTACTAGGTGCTTTTATCTTGTA-T
1 TCTTCTTGCAATGAGTTGTATACTTCACCTGTAAAGATATCTACTAGGTGCTTTTATCTTGTACT
*
12290139 AAAG-ATGCCTGGAAATGGAAC
66 AAAGAAAG---GGAAATGGAAC
12290160 TCTTCT
1 TCTTCT
12290166 ATCTTCAGAA
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
82 2 0.03
83 4 0.05
85 69 0.92
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (84 bp):
TCTTCTTGCAATGAGTTGTATACTTCACCTGTAAAGATATCTACTAGGTGCTTTTATCTTGTACT
AAAGAAAGGGAAATGGAAC
Found at i:12298814 original size:63 final size:63
Alignment explanation
Indices: 12298736--12298935 Score: 364
Period size: 63 Copynumber: 3.2 Consensus size: 63
12298726 ATTGTAGTTT
*
12298736 GAAAGGAAGATCATAAATTTTAGTTGAATTCTGCGAGTATTTACATTTATAGTGTTGCTGATA
1 GAAAGGAAGATCATAAATTTTAGTTGAATTCTGCAAGTATTTACATTTATAGTGTTGCTGATA
*
12298799 GAAAGGAAGATCATAAATTTTAGTTGAATTCTGCCAGTATTTACATTTATAGTGTTGCTGATA
1 GAAAGGAAGATCATAAATTTTAGTTGAATTCTGCAAGTATTTACATTTATAGTGTTGCTGATA
* *
12298862 GAAAGGAAGATCATAAATTTTAGTTGAATTCTGCAAGTATTTACATTTATAATGTTGTTGATA
1 GAAAGGAAGATCATAAATTTTAGTTGAATTCTGCAAGTATTTACATTTATAGTGTTGCTGATA
12298925 GAAAGGAAGAT
1 GAAAGGAAGAT
12298936 AATCCCAAAT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 133 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.37
Consensus pattern (63 bp):
GAAAGGAAGATCATAAATTTTAGTTGAATTCTGCAAGTATTTACATTTATAGTGTTGCTGATA
Found at i:12304347 original size:21 final size:20
Alignment explanation
Indices: 12304323--12304362 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12304313 ACATGCTATT
12304323 TTAAAAAAATTATCAAAAATA
1 TTAAAAAAATTAT-AAAAATA
**
12304344 TTAATTAAATTATAAAAAT
1 TTAAAAAAATTATAAAAAT
12304363 TAAATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAAAAAAATTATAAAAATA
Found at i:12304374 original size:19 final size:18
Alignment explanation
Indices: 12304323--12304386 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
12304313 ACATGCTATT
*
12304323 TTAAAAAAATTATCAAAAATA
1 TTAAATAAATTA--AAAAA-A
* *
12304344 TTAATTAAATTATAAAAA
1 TTAAATAAATTAAAAAAA
12304362 TTAAATAATATTAAAAAAA
1 TTAAATAA-ATTAAAAAAA
*
12304381 TAAAAT
1 TTAAAT
12304387 TAACCCTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 8 0.22
19 18 0.50
21 10 0.28
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAATAAATTAAAAAAA
Found at i:12304378 original size:18 final size:17
Alignment explanation
Indices: 12304337--12304384 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
12304327 AAAAATTATC
*
12304337 AAAAATATTAATTAAATT
1 AAAAA-ATTAAATAAATT
12304355 ATAAAAATTAAATAATATT
1 A-AAAAATTAAATAA-ATT
*
12304374 AAAAAAATAAA
1 AAAAAATTAAA
12304385 ATTAACCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAAATTAAATAAATT
Found at i:12315750 original size:14 final size:14
Alignment explanation
Indices: 12315731--12315760 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12315721 CTTGTTTTTC
*
12315731 TTTTTCCTTTTCCT
1 TTTTTCCTTTACCT
12315745 TTTTTCCTTTACCT
1 TTTTTCCTTTACCT
12315759 TT
1 TT
12315761 AATCTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTCCTTTACCT
Found at i:12316075 original size:3 final size:3
Alignment explanation
Indices: 12316060--12316133 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
12316050 AAAACACCAG
* * *
12316060 TCT TCT GCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
12316108 TCT TCT TCT TTT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
12316134 CACTATCTGC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:12325581 original size:18 final size:19
Alignment explanation
Indices: 12325554--12325591 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12325544 ATAACTTTCA
*
12325554 GAAAATAATTAT-TTTTTT
1 GAAAAAAATTATATTTTTT
12325572 GAAAAAAATTATATTTTTT
1 GAAAAAAATTATATTTTTT
12325591 G
1 G
12325592 GTATTTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (19 bp):
GAAAAAAATTATATTTTTT
Found at i:12326177 original size:19 final size:18
Alignment explanation
Indices: 12326155--12326237 Score: 58
Period size: 18 Copynumber: 4.3 Consensus size: 18
12326145 AGAAAACTTT
12326155 TAAAAATTTATTGAAAATA
1 TAAAAATTTATT-AAAATA
** *
12326174 TAAAAAAATATTAAAATC
1 TAAAAATTTATTAAAATA
* **
12326192 TAAAAATTAAAGAAAATTA
1 TAAAAATTTATTAAAA-TA
*
12326211 TTAAAAATATTCATAAAAATA
1 -TAAAAAT-TT-ATTAAAATA
12326232 TAAAAA
1 TAAAAA
12326238 AACATTTAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
18 16 0.33
19 11 0.23
20 13 0.27
21 3 0.06
22 5 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAAAATTTATTAAAATA
Found at i:12326183 original size:10 final size:11
Alignment explanation
Indices: 12326168--12326269 Score: 52
Period size: 10 Copynumber: 9.1 Consensus size: 11
12326158 AAATTTATTG
12326168 AAAATA-TAAA
1 AAAATATTAAA
12326178 AAAATATTAAA
1 AAAATATTAAA
*
12326189 ATCTAAAAATTAAA
1 A---AAATATTAAA
12326203 GAAAATTATT--A
1 -AAAA-TATTAAA
*
12326214 AAAATATTCATA
1 AAAATATT-AAA
12326226 AAAATA-TAAA
1 AAAATATTAAA
* *
12326236 AAAACATTTAA
1 AAAATATTAAA
*
12326247 AAATTA-TAAA
1 AAAATATTAAA
*
12326257 AATATATTTAAA
1 AAAATA-TTAAA
12326269 A
1 A
12326270 TTATTATAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 22
0.69 0.10 0.22
Matches are distributed among these distances:
9 4 0.06
10 24 0.34
11 14 0.20
12 15 0.21
13 3 0.04
14 9 0.13
15 1 0.01
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:12326228 original size:21 final size:20
Alignment explanation
Indices: 12326204--12326282 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 20
12326194 AAAATTAAAG
12326204 AAAATTATTAAAAATATTCAT
1 AAAATTATTAAAAATATT-AT
* * *
12326225 AAAAATATAAAAAAACATT-T
1 AAAATTAT-TAAAAATATTAT
*
12326245 AAAAATTA-TAAAAATATATTT
1 -AAAATTATTAAAAATAT-TAT
12326266 AAAATTATTATAAAATA
1 AAAATTATTA-AAAATA
12326283 CAAATAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
19 7 0.15
20 9 0.20
21 16 0.35
22 14 0.30
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTATTAAAAATATTAT
Found at i:12326247 original size:20 final size:21
Alignment explanation
Indices: 12326224--12326280 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
12326214 AAAATATTCA
12326224 TAAAAA-TATAAAAAAACATT
1 TAAAAATTATAAAAAAACATT
* *
12326244 TAAAAATTATAAAAATATATT
1 TAAAAATTATAAAAAAACATT
12326265 TAAAATTATTATAAAA
1 TAAAA--ATTATAAAA
12326281 TACAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 6 0.19
21 17 0.53
23 9 0.28
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAATTATAAAAAAACATT
Found at i:12331706 original size:6 final size:6
Alignment explanation
Indices: 12331695--12331736 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
12331685 ATAGCAGCCT
12331695 ACACCA ACACCA ACACCA ACACCA ACACCA ACACCA ACACCA
1 ACACCA ACACCA ACACCA ACACCA ACACCA ACACCA ACACCA
12331737 TTTCTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
ACACCA
Found at i:12339311 original size:24 final size:24
Alignment explanation
Indices: 12339284--12339334 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
12339274 GAAAAATCAT
12339284 ATATATTGTTTTTATTCATTTTCA
1 ATATATTGTTTTTATTCATTTTCA
12339308 ATATATTGTTTTTATTCATTTTCA
1 ATATATTGTTTTTATTCATTTTCA
12339332 ATA
1 ATA
12339335 CCTGTTTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (24 bp):
ATATATTGTTTTTATTCATTTTCA
Found at i:12340676 original size:40 final size:40
Alignment explanation
Indices: 12340621--12340696 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
12340611 TTGGAGCTAA
12340621 CCCTCAAATAATGATTATATCCAAAGATTTACCTTCAAAT
1 CCCTCAAATAATGATTATATCCAAAGATTTACCTTCAAAT
12340661 CCCTCAAATAATGATTATATCCAAAGATTTACCTTC
1 CCCTCAAATAATGATTATATCCAAAGATTTACCTTC
12340697 TATTTGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (40 bp):
CCCTCAAATAATGATTATATCCAAAGATTTACCTTCAAAT
Found at i:12343139 original size:42 final size:42
Alignment explanation
Indices: 12343065--12343234 Score: 234
Period size: 42 Copynumber: 4.0 Consensus size: 42
12343055 TTCAGGTGCA
* **
12343065 TCTTCGGAAACAGCAGCATCATTGGT-TCCATCAGCTGCCAAT
1 TCTTCAGAAACAGCAGCATCATTGGTCT-CATCAGCCACCAAT
* *
12343107 TCTTGAGAAACAGCAGCATCATAGGTCTCATCAGCCACCAAT
1 TCTTCAGAAACAGCAGCATCATTGGTCTCATCAGCCACCAAT
* * *
12343149 TCTTCAGAAACAACAGCATCGTTGGTCTCATCAGCCAACAAT
1 TCTTCAGAAACAGCAGCATCATTGGTCTCATCAGCCACCAAT
* *
12343191 TCTTCAGATACAGCAGCATCATTGGTCTCATCAGCTACCAAT
1 TCTTCAGAAACAGCAGCATCATTGGTCTCATCAGCCACCAAT
12343233 TC
1 TC
12343235 CTCATTCGGC
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
42 111 0.99
43 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (42 bp):
TCTTCAGAAACAGCAGCATCATTGGTCTCATCAGCCACCAAT
Found at i:12345704 original size:31 final size:28
Alignment explanation
Indices: 12345669--12345726 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 28
12345659 AAATGTGATA
12345669 TTAGTCCCTATACTTAGACAAAAATTAAAAT
1 TTAGTCCCTATACTT--A-AAAAATTAAAAT
* *
12345700 TTAGTCTCTGTACTTAAAAAATTAAAA
1 TTAGTCCCTATACTTAAAAAATTAAAA
12345727 ATTAACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 1 0.04
31 13 0.52
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (28 bp):
TTAGTCCCTATACTTAAAAAATTAAAAT
Found at i:12348793 original size:50 final size:49
Alignment explanation
Indices: 12348739--12348859 Score: 111
Period size: 51 Copynumber: 2.4 Consensus size: 49
12348729 ATCAGCCTTA
* * **
12348739 TTAAAATTTTAAAAATTCAAAAAAAATT-ATAAAATTTGTTTTTAA-ATTTT
1 TTAAAATTTTAAAAATT--AAAAAAATTAAAAAAAATACTTTTTAATA-TTT
* * *
12348789 TTAAATAATTTAAATTATTAAAAATATTAAAAAAAATACTTTTTAATATTT
1 TTAAA-ATTTTAAA-AATTAAAAAAATTAAAAAAAATACTTTTTAATATTT
*
12348840 TTAAAATTTTAAAAAATAAA
1 TTAAAATTTTAAAAATTAAA
12348860 TTAAATGCTA
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
49 5 0.09
50 20 0.35
51 28 0.49
52 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (49 bp):
TTAAAATTTTAAAAATTAAAAAAATTAAAAAAAATACTTTTTAATATTT
Found at i:12350853 original size:15 final size:16
Alignment explanation
Indices: 12350833--12350865 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12350823 GTTCCAATAA
12350833 ACTTTTAA-TTTATAT
1 ACTTTTAAGTTTATAT
12350848 ACTTTTAAGTTTTATAT
1 ACTTTTAAG-TTTATAT
12350865 A
1 A
12350866 ATGTAAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
ACTTTTAAGTTTATAT
Found at i:12356343 original size:24 final size:23
Alignment explanation
Indices: 12356316--12356375 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
12356306 CAAATTCGTC
*
12356316 AAAGGGAATAATTATATTCATTAA
1 AAAGGGAATAAGTATATTC-TTAA
12356340 AAAGGGAATAAGTATATTCTTAA
1 AAAGGGAATAAGTATATTCTTAA
* *
12356363 AAAAGGAAAAAGT
1 AAAGGGAATAAGT
12356376 GTGGCATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (23 bp):
AAAGGGAATAAGTATATTCTTAA
Found at i:12356370 original size:23 final size:24
Alignment explanation
Indices: 12356320--12356375 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
12356310 TTCGTCAAAG
* *
12356320 GGAATAATTATATTCATTAAAAAG
1 GGAATAAGTATATTCATTAAAAAA
12356344 GGAATAAGTATATTC-TTAAAAAA
1 GGAATAAGTATATTCATTAAAAAA
*
12356367 GGAAAAAGT
1 GGAATAAGT
12356376 GTGGCATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.29
Consensus pattern (24 bp):
GGAATAAGTATATTCATTAAAAAA
Found at i:12359679 original size:18 final size:16
Alignment explanation
Indices: 12359656--12359690 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12359646 AATAGCTTTG
12359656 AAAAGTATATTATAAAAT
1 AAAAGT-TATTA-AAAAT
12359674 AAAAGTTATTAAAAAT
1 AAAAGTTATTAAAAAT
12359690 A
1 A
12359691 TGTTATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAAGTTATTAAAAAT
Found at i:12365603 original size:23 final size:23
Alignment explanation
Indices: 12365569--12365632 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
12365559 AAGGTCAAAA
*
12365569 TATAATTTTATCATTTATTAATT
1 TATAATTTTATCATTTATTAACT
*
12365592 TATGATTTTATCAGTTT-TTAACT
1 TATAATTTTATCA-TTTATTAACT
*
12365615 TATAATTTCATCATTTAT
1 TATAATTTTATCATTTAT
12365633 GAAAGGACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.09
23 29 0.83
24 3 0.09
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (23 bp):
TATAATTTTATCATTTATTAACT
Found at i:12368435 original size:219 final size:219
Alignment explanation
Indices: 12368068--12368671 Score: 782
Period size: 229 Copynumber: 2.7 Consensus size: 219
12368058 AAATGCCGTA
* *
12368068 AATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCGCTTTCTATA
1 AATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCGCTTTTTGTA
* * * * * *
12368133 AAACGCCACTAAATGTTAGGTAATAGCGGCGTACGTAAACAAACGCCGCAAAAAAGTTGATCAAA
66 AAACGCCGCTAAAGGTTAGGTGATAGCGGCGAATGTAAACAAACGCTG--AAAAAGTTGATCAAA
* *
12368198 ACGACAGCGTTTTATTTCTTCGCTTTACTTGATTTAGT-G-AAAACGCCT-CAACTTTCGTTCTT
129 ACGGCAGCGTTTTATTTCTTCGCTTTACTTGATTTAGTGGTAAAACG-CTACAACTTTCGGTCTT
*
12368260 TACCGGCGCTTTTCCAAAAGTGCCGCT
193 TACCGGCGCTTTTCCAAAAGCGCCGCT
* * *
12368287 AGTAAGTAAAGCAAAACGACGTTGTTTTCTGTTGATGTATAGGGACATTAGCGGCGCTTTTTGTA
1 AATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCGCTTTTTGTA
* *
12368352 AAACGCCGCTAAAGGTTAGGTGATAGCGGCAAATGTAAACAAACGCTGTATAAAGTTGATCAAAA
66 AAACGCCGCTAAAGGTTAGGTGATAGCGGCGAATGTAAACAAACGCTG-AAAAAGTTGATC-AAA
* *
12368417 ACGGCAGTGTTCTATTTCTTCGCTTTACTTGATTTAGTGGCGATTTTTAAAAACGCTACAACTTT
129 ACGGCAGCGTTTTATTTCTTCGCTTTACTTGATTTAGT-G-G-----T-AAAACGCTACAACTTT
* *
12368482 CGGTCTTTACCGGCGCTTTTCCATAAGCGCCGTT
186 CGGTCTTTACCGGCGCTTTTCCAAAAGCGCCGCT
* *
12368516 AATAAGTTAAGCAAAATGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCACTTTTTGTA
1 AATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCGCTTTTTGTA
* * * * * *
12368581 AAACGCCGCTAAAGGTTAAGTGTTAGCGGCGCATATAAACAAACGTTGCAAATATGTTGATCAAA
66 AAACGCCGCTAAAGGTTAGGTGATAGCGGCGAATGTAAACAAACGCTG-AAA-AAGTTGATCAAA
* *
12368646 ATGGAAGCGTTTTATTTCTTCGCTTT
129 ACGGCAGCGTTTTATTTCTTCGCTTT
12368672 GCTAATAAGT
Statistics
Matches: 333, Mismatches: 39, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
218 11 0.03
219 139 0.42
222 1 0.00
228 2 0.01
229 172 0.52
230 8 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (219 bp):
AATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCGCTTTTTGTA
AAACGCCGCTAAAGGTTAGGTGATAGCGGCGAATGTAAACAAACGCTGAAAAAGTTGATCAAAAC
GGCAGCGTTTTATTTCTTCGCTTTACTTGATTTAGTGGTAAAACGCTACAACTTTCGGTCTTTAC
CGGCGCTTTTCCAAAAGCGCCGCT
Found at i:12369084 original size:14 final size:14
Alignment explanation
Indices: 12369062--12369307 Score: 69
Period size: 14 Copynumber: 17.1 Consensus size: 14
12369052 TTTATGAGTC
*
12369062 AAGGTTTAGGGTTT
1 AAGGGTTAGGGTTT
12369076 ACA-GGTTAGGGGTTT
1 A-AGGGTTA-GGGTTT
*
12369091 AAGGGTTATGGTTTGT
1 AAGGGTTA-GGGTT-T
* * *
12369107 GCATGGGTTATGGTTC
1 --AAGGGTTAGGGTTT
*
12369123 AAGGGTTGGGGTTT
1 AAGGGTTAGGGTTT
*
12369137 AA-GGTTAATGGTTT
1 AAGGGTT-AGGGTTT
*
12369151 -AGGGTTTAATGG-TT
1 AAGGG-TT-AGGGTTT
* *
12369165 -AGAGTTTAAGGTTT
1 AAG-GGTTAGGGTTT
*
12369179 -AGAGGTTAGGGATT
1 AAG-GGTTAGGGTTT
*
12369193 AAGGGATATGGGTTT
1 AAGGGTTA-GGGTTT
* *
12369208 AGGGGTTAGGGTAT
1 AAGGGTTAGGGTTT
12369222 AAGGGTT-GGGTTTT
1 AAGGGTTAGGG-TTT
* **
12369236 AA-GGTTTGTGGACT
1 AAGGGTTAG-GGTTT
* *
12369250 AAAGATTATGGGTTT
1 AAGGGTTA-GGGTTT
* *
12369265 AAGGATTGGGGTTT
1 AAGGGTTAGGGTTT
* *
12369279 AGGGGTT-GGGGTT
1 AAGGGTTAGGGTTT
* *
12369292 AAGGTTTAGAGTTT
1 AAGGGTTAGGGTTT
12369306 AA
1 AA
12369308 TTGTTAAAAA
Statistics
Matches: 173, Mismatches: 40, Indels: 38
0.69 0.16 0.15
Matches are distributed among these distances:
13 25 0.14
14 84 0.49
15 52 0.30
16 2 0.01
17 3 0.02
18 7 0.04
ACGTcount: A:0.22, C:0.02, G:0.39, T:0.37
Consensus pattern (14 bp):
AAGGGTTAGGGTTT
Found at i:12369155 original size:21 final size:21
Alignment explanation
Indices: 12369131--12369186 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
12369121 TCAAGGGTTG
12369131 GGGTTTAAGGTTAATG-GTTTA
1 GGGTTTAAGGTTAA-GAGTTTA
12369152 GGGTTTAATGGTT-AGAGTTTA
1 GGGTTTAA-GGTTAAGAGTTTA
*
12369173 AGGTTTAGAGGTTA
1 GGGTTTA-AGGTTA
12369187 GGGATTAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.03
21 24 0.80
22 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (21 bp):
GGGTTTAAGGTTAAGAGTTTA
Found at i:12369187 original size:21 final size:21
Alignment explanation
Indices: 12369147--12369196 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
12369137 AAGGTTAATG
*
12369147 GTTTAGGGTTTAATGGTTAGA
1 GTTTAAGGTTTAATGGTTAGA
*
12369168 GTTTAAGGTTTAGA-GGTTAGG
1 GTTTAAGGTTTA-ATGGTTAGA
*
12369189 GATTAAGG
1 GTTTAAGG
12369197 GATATGGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (21 bp):
GTTTAAGGTTTAATGGTTAGA
Found at i:12369206 original size:29 final size:27
Alignment explanation
Indices: 12369174--12369234 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
12369164 TAGAGTTTAA
12369174 GGTTTAGAGGTTAGGG-ATTAAGGGATATG
1 GGTTTAGAGGTTAGGGTA-TAAGGG-T-TG
*
12369203 GGTTTAGGGGTTAGGGTATAAGGGTTG
1 GGTTTAGAGGTTAGGGTATAAGGGTTG
12369230 GGTTT
1 GGTTT
12369235 TAAGGTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.23
28 1 0.03
29 21 0.70
30 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.34
Consensus pattern (27 bp):
GGTTTAGAGGTTAGGGTATAAGGGTTG
Found at i:12369227 original size:22 final size:22
Alignment explanation
Indices: 12369184--12369228 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12369174 GGTTTAGAGG
*
12369184 TTAGGGATTAAGGGATATGGGT
1 TTAGGGATTAAGGGATAAGGGT
*
12369206 TTAGGGGTT-AGGGTATAAGGGT
1 TTAGGGATTAAGGG-ATAAGGGT
12369228 T
1 T
12369229 GGGTTTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (22 bp):
TTAGGGATTAAGGGATAAGGGT
Found at i:12371712 original size:3 final size:3
Alignment explanation
Indices: 12371704--12371728 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12371694 AGAATCCATG
12371704 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
12371729 CAACATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12374152 original size:55 final size:55
Alignment explanation
Indices: 12374092--12374202 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
12374082 ACATCAAAGA
*
12374092 TGAAGTTAAATGGCTTTCCCAAGGTCCAAATCGAGTGGTTAAAAGATATAGTGCG
1 TGAAGTTAAATGGCTCTCCCAAGGTCCAAATCGAGTGGTTAAAAGATATAGTGCG
12374147 TGAAGTTAAATGGCTCTCCCAAGGTCCAAATCGAGTGGTTAAAAGATATAGTGCG
1 TGAAGTTAAATGGCTCTCCCAAGGTCCAAATCGAGTGGTTAAAAGATATAGTGCG
12374202 T
1 T
12374203 TCCTCATCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (55 bp):
TGAAGTTAAATGGCTCTCCCAAGGTCCAAATCGAGTGGTTAAAAGATATAGTGCG
Found at i:12376554 original size:66 final size:66
Alignment explanation
Indices: 12376448--12376617 Score: 243
Period size: 66 Copynumber: 2.6 Consensus size: 66
12376438 AGCAAATTAC
* *
12376448 ACAACTTAAAGCAGAGGCAGCATCGAGAGAAGTTGAGGTTCA-AAGAAGATATGAAGAACTCCAA
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGTTGAGGTTCAGAAGAAG-TATGAAGAACTCCAA
12376512 CT
65 CT
* *
12376514 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGTTGAGGTTCAGAGGAAGTATGAAGAACTCCAGC
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGTTGAGGTTCAGAAGAAGTATGAAGAACTCCAAC
12376579 T
66 T
* * * * *
12376580 GCAGCTTAAAGCAGATGCGGCAGCGAGGGAAGTAGAGG
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGTTGAGG
12376618 CAGCAGCGAA
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
66 89 0.95
67 5 0.05
ACGTcount: A:0.38, C:0.16, G:0.30, T:0.15
Consensus pattern (66 bp):
ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGTTGAGGTTCAGAAGAAGTATGAAGAACTCCAAC
T
Found at i:12376625 original size:21 final size:21
Alignment explanation
Indices: 12376599--12376658 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
12376589 AGCAGATGCG
12376599 GCAGCGAGGGAAGTAGAGGCA
1 GCAGCGAGGGAAGTAGAGGCA
** * * *
12376620 GCAGCGAAAGAAGCAAAGGCT
1 GCAGCGAGGGAAGTAGAGGCA
12376641 GCAGCGAGGGAAGTAGAG
1 GCAGCGAGGGAAGTAGAG
12376659 CAGAGCAGAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.43, T:0.05
Consensus pattern (21 bp):
GCAGCGAGGGAAGTAGAGGCA
Found at i:12377027 original size:31 final size:31
Alignment explanation
Indices: 12376992--12377058 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
12376982 AAGCGTCGCT
*
12376992 AAAAGTCAT-GATCTATAGCGGCGTTTATGGA
1 AAAAG-CATCGATCTATAGCGGCATTTATGGA
* *
12377023 AAAAGCATCGCTCTATAGCGGCATTTGTGGA
1 AAAAGCATCGATCTATAGCGGCATTTATGGA
12377054 AAAAG
1 AAAAG
12377059 AACCGCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGCATCGATCTATAGCGGCATTTATGGA
Found at i:12377095 original size:43 final size:43
Alignment explanation
Indices: 12377034--12377134 Score: 157
Period size: 43 Copynumber: 2.3 Consensus size: 43
12377024 AAAGCATCGC
12377034 TCTATAGCGGCATTTGTGGAAAAAGAACCGCTAAAGGTCATGG
1 TCTATAGCGGCATTTGTGGAAAAAGAACCGCTAAAGGTCATGG
* * **
12377077 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
1 TCTATAGCGGCATTTGTGGAAAAAGAACCGCTAAAGGTCATGG
*
12377120 TCTATAGCGGAATTT
1 TCTATAGCGGCATTT
12377135 TTCTGGAAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (43 bp):
TCTATAGCGGCATTTGTGGAAAAAGAACCGCTAAAGGTCATGG
Found at i:12381890 original size:20 final size:20
Alignment explanation
Indices: 12381865--12381964 Score: 64
Period size: 21 Copynumber: 5.0 Consensus size: 20
12381855 GAAAAAATAA
12381865 AAAAAATCA-ATAAAATTTATT
1 AAAAAAT-ATATAAAA-TTATT
*
12381886 TAAAAATATATAAAATTATT
1 AAAAAATATATAAAATTATT
*
12381906 -AAAAATTTAT-AAATGTATAT
1 AAAAAATATATAAAAT-TAT-T
* * * *
12381926 AAATATTATAAAAAATTGTT
1 AAAAAATATATAAAATTATT
*
12381946 -AAAAATATAAAAAAATTAT
1 AAAAAATAT-ATAAAATTAT
12381965 CAAATATAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
18 4 0.06
19 18 0.29
20 17 0.27
21 20 0.32
22 4 0.06
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAAATATATAAAATTATT
Found at i:12381909 original size:19 final size:19
Alignment explanation
Indices: 12381874--12381964 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 19
12381864 AAAAAAATCA
12381874 ATAAAATTTATTTAAAAATAT
1 ATAAAA-TTA-TTAAAAATAT
*
12381895 ATAAAATTATTAAAAATTT
1 ATAAAATTATTAAAAATAT
*
12381914 AT-AAATGTATATAAATATTAT
1 ATAAAAT-TAT-TAAA-AATAT
* *
12381935 AAAAAATTGTTAAAAATAT
1 ATAAAATTATTAAAAATAT
*
12381954 AAAAAAATTAT
1 -ATAAAATTAT
12381965 CAAATATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
18 4 0.07
19 18 0.31
20 20 0.34
21 12 0.21
22 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAATTATTAAAAATAT
Found at i:12381924 original size:27 final size:28
Alignment explanation
Indices: 12381883--12381982 Score: 73
Period size: 27 Copynumber: 3.5 Consensus size: 28
12381873 AATAAAATTT
12381883 ATTTAAAAATATATA-AAATTATTA-AAA
1 ATTTAAAAATATATATAAA-TATTATAAA
* *
12381910 ATTTATAAATGTATATAAATATTATAAAAA
1 ATTTAAAAATATATATAAATATTAT--AAA
* *
12381940 ATTGTTAAAAATATA-A-AAAAATTATCAA
1 A-T-TTAAAAATATATATAAATATTATAAA
* *
12381968 ATATAAAAAAATATA
1 ATTTAAAAATATATA
12381983 ATTTCTAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
26 9 0.16
27 20 0.34
28 6 0.10
30 12 0.21
31 2 0.03
32 9 0.16
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (28 bp):
ATTTAAAAATATATATAAATATTATAAA
Found at i:12381964 original size:30 final size:29
Alignment explanation
Indices: 12381857--12381964 Score: 85
Period size: 30 Copynumber: 3.7 Consensus size: 29
12381847 ATGCGGTGGA
* **
12381857 AAAAATA-AAAAAAATCAATAAAATTTATTT
1 AAAAATATAAAAAAAT-TATAAAAAAT-TTT
* *
12381887 AAAAATAT-ATAAAATTATTAAAAATTTAT
1 AAAAATATAAAAAAATTATAAAAAATTT-T
** * *
12381916 AAATGTATATAAATATTATAAAAAATTGTT
1 AAAAATATAAAAAAATTATAAAAAATT-TT
12381946 AAAAATATAAAAAAATTAT
1 AAAAATATAAAAAAATTAT
12381965 CAAATATAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
28 2 0.03
29 13 0.22
30 43 0.73
31 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAAATATAAAAAAATTATAAAAAATTTT
Found at i:12381977 original size:20 final size:20
Alignment explanation
Indices: 12381935--12381978 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
12381925 TAAATATTAT
* * *
12381935 AAAAAATTGTTAAAAATATA
1 AAAAAATTATCAAAAATAAA
*
12381955 AAAAAATTATCAAATATAAA
1 AAAAAATTATCAAAAATAAA
12381975 AAAA
1 AAAA
12381979 TATAATTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAATTATCAAAAATAAA
Found at i:12382461 original size:21 final size:19
Alignment explanation
Indices: 12382382--12382469 Score: 58
Period size: 20 Copynumber: 4.4 Consensus size: 19
12382372 TTTTTAATAA
*
12382382 ATTTCTATAATTTAC-ATAT
1 ATTTTTATAATTT-CTATAT
12382401 ACTTTTCCTAT-ATTTCT-TAT
1 A-TTTT--TATAATTTCTATAT
*
12382421 ATTTTATAATAATTTTTATAT
1 ATTTT-T-ATAATTTCTATAT
12382442 ATTCTTTATAACTTTCTATA-
1 ATT-TTTATAA-TTTCTATAT
12382462 ATTTTTAT
1 ATTTTTAT
12382470 TTTTAACAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
18 1 0.02
19 12 0.21
20 20 0.36
21 18 0.32
22 5 0.09
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTATAATTTCTATAT
Found at i:12385823 original size:18 final size:18
Alignment explanation
Indices: 12385797--12385834 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12385787 ATTTGGTCTT
12385797 AATTCTAAAAAAATGTAA
1 AATTCTAAAAAAATGTAA
* *
12385815 AATTTTAAAAAATTGTAA
1 AATTCTAAAAAAATGTAA
12385833 AA
1 AA
12385835 AAAATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (18 bp):
AATTCTAAAAAAATGTAA
Found at i:12390523 original size:26 final size:26
Alignment explanation
Indices: 12390464--12390524 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
12390454 AGCCATATCG
**
12390464 GGAAGCTCACAAAGAGCCAATTAATG
1 GGAAGCTCACAAAGAGCCAATTAACA
12390490 GGAAGCTCACAAAGAGCC-ATATAACA
1 GGAAGCTCACAAAGAGCCAAT-TAACA
*
12390516 GGATGCTCA
1 GGAAGCTCA
12390525 TAAGAGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 2 0.06
26 29 0.94
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCAATTAACA
Found at i:12394564 original size:14 final size:14
Alignment explanation
Indices: 12394528--12394561 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12394518 TCATCATTTG
*
12394528 CCTACAACCAAAAC
1 CCTATAACCAAAAC
12394542 CCTATAACCAAAAC
1 CCTATAACCAAAAC
12394556 CC-ATAA
1 CCTATAA
12394562 ACCCATACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:12396736 original size:19 final size:19
Alignment explanation
Indices: 12396712--12396764 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
12396702 AACATGAAAA
*
12396712 TTTTGAAACATGAGATTTT-
1 TTTTGAAACACGA-ATTTTC
12396731 TTTTGAAACACGAATTTTC
1 TTTTGAAACACGAATTTTC
*
12396750 TTTTTTAAACACGAA
1 -TTTTGAAACACGAA
12396765 AATTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 12 0.40
20 13 0.43
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTTGAAACACGAATTTTC
Found at i:12396776 original size:17 final size:16
Alignment explanation
Indices: 12396750--12396785 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
12396740 ACGAATTTTC
*
12396750 TTTTTTAAACACGAAAA
1 TTTTTAAAACAC-AAAA
12396767 TTTTTAAAACACAAAA
1 TTTTTAAAACACAAAA
12396783 TTT
1 TTT
12396786 GTTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTTTAAAACACAAAA
Found at i:12396798 original size:38 final size:37
Alignment explanation
Indices: 12396730--12396808 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
12396720 CATGAGATTT
* * * * *
12396730 TTTTTGAAACACGAATTTTCTTTTTTAAACACGAAAA
1 TTTTTAAAACACAAAATTTCTTTTTAAAACACAAAAA
* *
12396767 TTTTTAAAACACAAAATTTGTTTTTGAAAACATAAAAA
1 TTTTTAAAACACAAAATTTCTTTTT-AAAACACAAAAA
12396805 TTTT
1 TTTT
12396809 GATAAAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 21 0.62
38 13 0.38
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (37 bp):
TTTTTAAAACACAAAATTTCTTTTTAAAACACAAAAA
Found at i:12396807 original size:22 final size:20
Alignment explanation
Indices: 12396767--12396807 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
12396757 AACACGAAAA
*
12396767 TTTTTAAAACACAAAATTTG
1 TTTTTAAAACAAAAAATTTG
12396787 TTTTTGAAAACATAAAAATTT
1 TTTTT-AAAACA-AAAAATTT
12396808 TGATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTTTAAAACAAAAAATTTG
Found at i:12396853 original size:20 final size:20
Alignment explanation
Indices: 12396820--12396951 Score: 55
Period size: 21 Copynumber: 6.8 Consensus size: 20
12396810 ATAAAAAATG
**
12396820 AAACACGAGGATTTTTTTTA
1 AAACACGAAAATTTTTTTTA
*
12396840 AAACACGAAAA---TTTAT-
1 AAACACGAAAATTTTTTTTA
* ** *
12396856 GAACACGGTCAATTTTTTTGA
1 AAACAC-GAAAATTTTTTTTA
* *
12396877 AAACATGAAAA---TTTTTG
1 AAACACGAAAATTTTTTTTA
* *
12396894 AAAGACGAGAATTTTTTTTGTA
1 AAACACGA-AAATTTTTTT-TA
12396916 AAACAC-AGAAATTTTTTTTGA
1 AAACACGA-AAATTTTTTTT-A
*
12396937 AAACAAGAAAATTTT
1 AAACACGAAAATTTT
12396952 CAAAATACGG
Statistics
Matches: 79, Mismatches: 21, Indels: 23
0.64 0.17 0.19
Matches are distributed among these distances:
16 5 0.06
17 17 0.22
18 2 0.03
20 16 0.20
21 32 0.41
22 7 0.09
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (20 bp):
AAACACGAAAATTTTTTTTA
Found at i:12396893 original size:18 final size:18
Alignment explanation
Indices: 12396870--12397074 Score: 83
Period size: 17 Copynumber: 11.6 Consensus size: 18
12396860 ACGGTCAATT
12396870 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACATGAAAA
**
12396888 TTTTTGAAAGACGA-GAATTT
1 TTTTTGAAA-AC-ATGAA-AA
* *
12396908 TTTTTGTAAAACACAGAAATTT
1 TTTTTG-AAAACA-TGAAA--A
*
12396930 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACATGAAAA
* * * **
12396948 -TTTTCAAAATACGGGAA
1 TTTTTGAAAACATGAAAA
*
12396965 TTTTTGAAAACACT----T
1 TTTTTGAAAACA-TGAAAA
*
12396980 TTTTTTAAAACATGAAAA
1 TTTTTGAAAACATGAAAA
*
12396998 TTTTTG-AAACACTG-GAA
1 TTTTTGAAAACA-TGAAAA
* *
12397015 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACATGAAAA
* *
12397032 TTTTTG-AAACGTGAGAA
1 TTTTTGAAAACATGAAAA
*
12397049 TTTTTGAAAACACG-AAA
1 TTTTTGAAAACATGAAAA
12397066 TTTTT-AAAA
1 TTTTTGAAAA
12397075 AAAACAAAAA
Statistics
Matches: 141, Mismatches: 27, Indels: 40
0.68 0.13 0.19
Matches are distributed among these distances:
14 1 0.01
15 11 0.08
16 10 0.07
17 45 0.32
18 35 0.25
19 6 0.04
20 14 0.10
21 12 0.09
22 7 0.05
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (18 bp):
TTTTTGAAAACATGAAAA
Found at i:12396910 original size:38 final size:38
Alignment explanation
Indices: 12396817--12396926 Score: 120
Period size: 37 Copynumber: 2.9 Consensus size: 38
12396807 TTGATAAAAA
*
12396817 ATGAAACACGAGGATTTTTTTT-AAAACACGAAAATTT
1 ATGAAACACGAGAATTTTTTTTGAAAACACGAAAATTT
*
12396854 ATG-AACACG-GTCAA-TTTTTTTGAAAACATGAAAATTT
1 ATGAAACACGAG--AATTTTTTTTGAAAACACGAAAATTT
* *
12396891 TTGAAAGACGAGAATTTTTTTTGTAAAACACAGAAA
1 ATGAAACACGAGAATTTTTTTTG-AAAACAC-GAAA
12396927 TTTTTTTTGA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
35 1 0.02
36 13 0.22
37 22 0.37
38 13 0.22
39 7 0.12
40 4 0.07
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (38 bp):
ATGAAACACGAGAATTTTTTTTGAAAACACGAAAATTT
Found at i:12396931 original size:22 final size:20
Alignment explanation
Indices: 12396868--12396951 Score: 84
Period size: 21 Copynumber: 4.2 Consensus size: 20
12396858 ACACGGTCAA
*
12396868 TTTTTTTGAAAACATGAAA-
1 TTTTTTTGAAAACAAGAAAT
* *
12396887 -ATTTTTGAAAGACGAG-AAT
1 TTTTTTTGAAA-ACAAGAAAT
12396906 TTTTTTTGTAAAACACAGAAAT
1 TTTTTTTG-AAAACA-AGAAAT
12396928 TTTTTTTGAAAACAAGAAAAT
1 TTTTTTTGAAAACAAG-AAAT
12396949 TTT
1 TTT
12396952 CAAAATACGG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
18 11 0.21
19 3 0.06
20 10 0.19
21 18 0.34
22 11 0.21
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (20 bp):
TTTTTTTGAAAACAAGAAAT
Found at i:12396938 original size:60 final size:51
Alignment explanation
Indices: 12396868--12397026 Score: 153
Period size: 60 Copynumber: 3.0 Consensus size: 51
12396858 ACACGGTCAA
12396868 TTTTTTTGAAAACATGAAAATTTTTGAAAGACGAGAATTTTTTTTGTAAAACACAGAAAT
1 TTTTTTTGAAAACATGAAAATTTTTGAAAGACGAGAA---TTTTTG-AAAACAC-----T
* ** * *
12396928 TTTTTTTGAAAACAAGAAAATTTTCAAAATACGGGAATTTTTGAAAACACT
1 TTTTTTTGAAAACATGAAAATTTTTGAAAGACGAGAATTTTTGAAAACACT
*
12396979 TTTTTTT-AAAACATGAAAATTTTTGAAACACTG-GAA-TTTTGAAAACAC
1 TTTTTTTGAAAACATGAAAATTTTTGAAAGAC-GAGAATTTTTGAAAACAC
12397027 GAAGATTTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
49 12 0.13
50 23 0.26
51 9 0.10
56 7 0.08
57 6 0.07
60 32 0.36
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (51 bp):
TTTTTTTGAAAACATGAAAATTTTTGAAAGACGAGAATTTTTGAAAACACT
Found at i:12396983 original size:50 final size:49
Alignment explanation
Indices: 12396928--12397026 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 49
12396918 ACACAGAAAT
*
12396928 TTTTTTTGAAAACAAGAAAATTTTCAAAATACGGGAATTTTTGAAAACAC
1 TTTTTTTGAAAACAAGAAAATTTTCAAAACACGGGAA-TTTTGAAAACAC
* * ** *
12396978 TTTTTTTTAAAACATGAAAATTTTTGAAACACTGGAATTTTGAAAACAC
1 TTTTTTTGAAAACAAGAAAATTTTCAAAACACGGGAATTTTGAAAACAC
12397027 GAAGATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 12 0.28
50 31 0.72
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (49 bp):
TTTTTTTGAAAACAAGAAAATTTTCAAAACACGGGAATTTTGAAAACAC
Found at i:12397035 original size:34 final size:34
Alignment explanation
Indices: 12396980--12397070 Score: 114
Period size: 34 Copynumber: 2.6 Consensus size: 34
12396970 GAAAACACTT
* *
12396980 TTTTTTAAAACATGAAAATTTTTGAAACACTG-GAA
1 TTTTTGAAAACACG-AAATTTTTGAAAC-CTGAGAA
*
12397015 -TTTTGAAAACACGAAGATTTTTGAAACGTGAGAA
1 TTTTTGAAAACACGAA-ATTTTTGAAACCTGAGAA
12397049 TTTTTGAAAACACGAAATTTTT
1 TTTTTGAAAACACGAAATTTTT
12397071 AAAAAAAACA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
33 4 0.08
34 31 0.62
35 15 0.30
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (34 bp):
TTTTTGAAAACACGAAATTTTTGAAACCTGAGAA
Found at i:12397378 original size:21 final size:21
Alignment explanation
Indices: 12397352--12397391 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12397342 AAAAAGCTCA
12397352 AAAATACGAGATTGACCGATC
1 AAAATACGAGATTGACCGATC
*
12397373 AAAATACGAGCTTGACCGA
1 AAAATACGAGATTGACCGA
12397392 GAGGGTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (21 bp):
AAAATACGAGATTGACCGATC
Found at i:12397428 original size:7 final size:7
Alignment explanation
Indices: 12397416--12397495 Score: 81
Period size: 7 Copynumber: 11.1 Consensus size: 7
12397406 TCGAGCCTTC
12397416 CTTTTTT
1 CTTTTTT
12397423 CTTTTTT
1 CTTTTTT
*
12397430 C-TTTTC
1 CTTTTTT
*
12397436 CTTTTTCC
1 CTTTTT-T
12397444 CTTTTTTT
1 C-TTTTTT
*
12397452 TTTCTTTT
1 CTT-TTTT
12397460 CTTTTTT
1 CTTTTTT
12397467 CTTTTTT
1 CTTTTTT
*
12397474 CTGTTTT
1 CTTTTTT
*
12397481 CTGTTTT
1 CTTTTTT
12397488 CTTTTTT
1 CTTTTTT
12397495 C
1 C
12397496 CTTCTTTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
6 5 0.08
7 45 0.71
8 8 0.13
9 5 0.08
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.79
Consensus pattern (7 bp):
CTTTTTT
Found at i:12397440 original size:12 final size:12
Alignment explanation
Indices: 12397419--12397509 Score: 78
Period size: 12 Copynumber: 7.2 Consensus size: 12
12397409 AGCCTTCCTT
12397419 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
12397431 TTTTCCTTTTTCCC
1 TTTT-CTTTTT-TC
12397445 TTTT-TTTTTTC
1 TTTTCTTTTTTC
12397456 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
12397468 TTTTTTCTGTTTTCTG
1 --TTTTCT-TTTT-TC
12397484 TTTTCTTTTTTC
1 TTTTCTTTTTTC
* *
12397496 -CTTCTTTTTCC
1 TTTTCTTTTTTC
12397507 TTT
1 TTT
12397510 GGCCTGCTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
11 14 0.22
12 18 0.28
13 10 0.16
14 17 0.27
15 4 0.06
16 1 0.02
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:12397501 original size:32 final size:31
Alignment explanation
Indices: 12397419--12397504 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
12397409 AGCCTTCCTT
* *
12397419 TTTTCTTTTTTCTTTTCCTTTTTCCCTTTTTT
1 TTTTCTTTTTTC-TTTCTTTTTTCCCTTTTTG
* **
12397451 TTTTCTTTTCTTTTTTCTTTTTTCTGTTTTCTG
1 TTTTCTTTT-TTCTTTCTTTTTTCCCTTTT-TG
*
12397484 TTTTCTTTTTTCCTTCTTTTT
1 TTTTCTTTTTTCTTTCTTTTT
12397505 CCTTTGGCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
32 33 0.73
33 12 0.27
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (31 bp):
TTTTCTTTTTTCTTTCTTTTTTCCCTTTTTG
Found at i:12397793 original size:18 final size:18
Alignment explanation
Indices: 12397772--12397815 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
12397762 GTTTGGGTTG
12397772 CGGGTCGGGTCACCGGAT
1 CGGGTCGGGTCACCGGAT
* *
12397790 CGGGTCGTGTCGCCGGAT
1 CGGGTCGGGTCACCGGAT
12397808 CGGGTCGG
1 CGGGTCGG
12397816 TTTGACCCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.27, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCACCGGAT
Found at i:12397869 original size:6 final size:6
Alignment explanation
Indices: 12397859--12397939 Score: 65
Period size: 6 Copynumber: 13.3 Consensus size: 6
12397849 ATTTTTTATT
* **
12397859 TTTTTCC TTTTTC -TTTTC TTTTTC TTTTTC TTTTTTC TTCTTC TCCTTC
1 TTTTT-C TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
* * * * *
12397908 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
12397940 CNNNNNNNNN
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
5 5 0.07
6 53 0.77
7 11 0.16
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:12397893 original size:13 final size:13
Alignment explanation
Indices: 12397859--12397902 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
12397849 ATTTTTTATT
*
12397859 TTTTTCCTTTTTC
1 TTTTTCTTTTTTC
12397872 -TTTTC-TTTTTC
1 TTTTTCTTTTTTC
12397883 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
*
12397896 TTCTTCT
1 TTTTTCT
12397903 CCTTCTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 6 0.21
12 10 0.36
13 12 0.43
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:12397901 original size:3 final size:3
Alignment explanation
Indices: 12397869--12397940 Score: 96
Period size: 3 Copynumber: 25.0 Consensus size: 3
12397859 TTTTTCCTTT
* * *
12397869 TTC TT- TTC TTT TTC TTT TTC TT- TT- TTC TTC TTC TCC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12397914 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
12397941 NNNNNNNNNN
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 6 0.10
3 55 0.90
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:12414763 original size:3 final size:3
Alignment explanation
Indices: 12414757--12414802 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
12414747 TTTTCTTTCT
*
12414757 TTC TTC TTC CTC TT- TTC TTC TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TT-C TTC TTC TTC TTC
12414803 AAAGTCTAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:12414786 original size:10 final size:10
Alignment explanation
Indices: 12414771--12414799 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
12414761 TCTTCCTCTT
12414771 TTCTTCTTCC
1 TTCTTCTTCC
12414781 TTCTTCTTCC
1 TTCTTCTTCC
12414791 TTCTTCTTC
1 TTCTTCTTC
12414800 TTCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:12414787 original size:13 final size:13
Alignment explanation
Indices: 12414757--12414802 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
12414747 TTTTCTTTCT
12414757 TTCTTCTTCC-TC
1 TTCTTCTTCCTTC
12414769 TT-TTCTT-CTTCC
1 TTCTTCTTCCTT-C
12414781 TTCTTCTTCCTTC
1 TTCTTCTTCCTTC
12414794 TTCTTCTTC
1 TTCTTCTTC
12414803 AAAGTCTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 6 0.20
12 5 0.17
13 15 0.50
14 3 0.10
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TTCTTCTTCCTTC
Found at i:12414893 original size:10 final size:10
Alignment explanation
Indices: 12414858--12414907 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
12414848 ACGCCGGTAC
12414858 TCTT-TCTTT
1 TCTTCTCTTT
* *
12414867 TCTTCTCCTC
1 TCTTCTCTTT
12414877 T-TTCTCTTT
1 TCTTCTCTTT
12414886 TCTTCTCTTT
1 TCTTCTCTTT
*
12414896 TCTTCTTTTT
1 TCTTCTCTTT
12414906 TC
1 TC
12414908 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:12414905 original size:19 final size:19
Alignment explanation
Indices: 12414862--12414904 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
12414852 CGGTACTCTT
12414862 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
12414881 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
12414898 TTCTTTT
1 -TCTTTT
12414905 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:12415188 original size:29 final size:29
Alignment explanation
Indices: 12415155--12415271 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
12415145 TGTAATTTTT
*
12415155 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
12415184 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
12415214 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
12415243 GGAAAAGTTTAGGTGTCAAAATGCAATTT
1 AGAAAA-TTTAGG-GTTAAAATGAAATTT
12415272 TTATTTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 16 0.22
30 54 0.75
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.31
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:12415210 original size:30 final size:30
Alignment explanation
Indices: 12415170--12415271 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
12415160 ATTTAGGATT
*
12415170 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
12415200 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
12415230 AAAATGAAATTT-AGGAAAAGTTTAGGTGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
12415260 AAAATGCAATTT
1 AAAATGAAATTT
12415272 TTATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:12415646 original size:22 final size:22
Alignment explanation
Indices: 12415618--12415662 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12415608 CCCAAAGTCG
12415618 AGCGGGCCACCCGACCATGGAC
1 AGCGGGCCACCCGACCATGGAC
12415640 AGCGGGCCACCCGACCATGGAC
1 AGCGGGCCACCCGACCATGGAC
12415662 A
1 A
12415663 TCTCTAGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.40, G:0.31, T:0.04
Consensus pattern (22 bp):
AGCGGGCCACCCGACCATGGAC
Found at i:12416650 original size:2 final size:2
Alignment explanation
Indices: 12416643--12416668 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12416633 TAATTGCTTT
12416643 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
12416669 GTTTTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12423466 original size:28 final size:28
Alignment explanation
Indices: 12423435--12423495 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
12423425 TATGAACTAA
* * *
12423435 GTGTTGTTTTATAAACTCGAAAATTTAG
1 GTGTTGTTTAATAAACTAGAAAATTAAG
12423463 GTGTTGTTTAATAAACTAGAAAATTAAG
1 GTGTTGTTTAATAAACTAGAAAATTAAG
12423491 G-GTTG
1 GTGTTG
12423496 AAAATCTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (28 bp):
GTGTTGTTTAATAAACTAGAAAATTAAG
Found at i:12427226 original size:124 final size:124
Alignment explanation
Indices: 12426776--12427243 Score: 407
Period size: 124 Copynumber: 3.8 Consensus size: 124
12426766 TAAAAAGGAA
* * * ** * ** *
12426776 CATAAAACTTAGCTTCAATGCATGCAGTCCTTTGAATCTCGAAATATCGAATGA-TACGATCATA
1 CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATC-AAACATTTCGATCATA
* * *
12426840 T-AA-AAATCTACTATTTACTTGGGAAGCAAGAAACAATCAGACATCAATCTAAGAAACCAG
65 TCAACAAA--TACTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAG
* * * * * *
12426900 CATACAACTTGGCTTCAATGCCTGCAATCAGTTGATTCTCGAAATATCAAACATTTCGATCACAT
1 CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATCAAACATTTCGATCATAT
* ** * *
12426965 CAAC--AT-CT-CTTACTTGCTAAACAAGCAAGCATCAATCA-ACCAT-GAATC-AGAAAAACTC
66 CAACAAATACTATTTACTTGGGAAACAAG-AA--A-CAATCAGA-CATCG-ATCTA-AGAAACTA
12427023 G
124 G
* * * *
12427024 CATACAGCTTAGCTTCGATGCATGCAGTCAGTTGAATCTTAAAATATCAAACATTTTGATCATAT
1 CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATCAAACATTTCGATCATAT
* * ** *
12427089 TAGCATCTGCTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAG
66 CAACAAATACTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAG
* * * * * **
12427148 AATACAACCTAGCTTCGATGCCTGTAGTCAGTTAAATCTCAAAATTTTGAACATTTCGATCATAT
1 CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATCAAACATTTCGATCATAT
* *
12427213 CAACAAATACTATTTACTTAGGAAGCAAGAA
66 CAACAAATACTATTTACTTGGGAAACAAGAA
12427244 TCAGCATTAA
Statistics
Matches: 272, Mismatches: 55, Indels: 34
0.75 0.15 0.09
Matches are distributed among these distances:
120 13 0.05
121 4 0.01
122 1 0.00
123 6 0.02
124 223 0.82
125 6 0.02
126 1 0.00
127 4 0.01
128 14 0.05
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (124 bp):
CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATCAAACATTTCGATCATAT
CAACAAATACTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAG
Found at i:12427241 original size:248 final size:248
Alignment explanation
Indices: 12426783--12427246 Score: 563
Period size: 248 Copynumber: 1.9 Consensus size: 248
12426773 GAACATAAAA
** * **
12426783 CTTAGCTTCAATGCATGCAGTCCTTTGAATCTCGAAATATCGAATGATACGATCATATAAAAATC
1 CTTAGCTTCAATGCATGCAGTCAGTTGAATCTCAAAATATCGAAACATACGATCATATAAAAATC
* * * *
12426848 TACTATTTACTTGGGAAGCAAGAAACAATCAGACATCAATCTAAGAAACCAGCATACAACTTGGC
66 TACTATTTACTTGGGAAACAAGAAACAATCAGACATCAATCTAAGAAACCAGAATACAACCTAGC
* * * **
12426913 TTCAATGCCTGCAATCAGTTGATTCTCGAAATATCAAACATTTCGATCACATCAACATCTCTTAC
131 TTCAATGCCTGCAATCAGTTAAATCTCAAAATATCAAACATTTCGATCACATCAACAAATCTTAC
* *
12426978 TTGCTAAACAAGCAAGCATCAATCAACCATGAATCAGAAAAACTCGCATACAG
196 TTACTAAACAAGCAAGAATCAATCAACCATGAATCAGAAAAACTCGCATACAG
* * ** * **
12427031 CTTAGCTTCGATGCATGCAGTCAGTTGAATCTTAAAATATC-AAACATTTTGATCATATTAGCAT
1 CTTAGCTTCAATGCATGCAGTCAGTTGAATCTCAAAATATCGAAACA-TACGATCATATAAAAAT
* * *
12427095 CTGCTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAGAATACAACCTAG
65 CTACTATTTACTTGGGAAACAAGAAACAATCAGACATCAATCTAAGAAACCAGAATACAACCTAG
* * * * ** *
12427160 CTTCGATGCCTGTAGTCAGTTAAATCTCAAAATTTTGAACATTTCGATCATATCAACAAATAC-T
130 CTTCAATGCCTGCAATCAGTTAAATCTCAAAATATCAAACATTTCGATCACATCAACAAAT-CTT
* * **
12427224 ATTTACTTAGGAAGCAAGAATCA
194 ACTTACTAAACAAGCAAGAATCA
12427247 GCATTAAATC
Statistics
Matches: 177, Mismatches: 37, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
247 3 0.02
248 173 0.98
249 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (248 bp):
CTTAGCTTCAATGCATGCAGTCAGTTGAATCTCAAAATATCGAAACATACGATCATATAAAAATC
TACTATTTACTTGGGAAACAAGAAACAATCAGACATCAATCTAAGAAACCAGAATACAACCTAGC
TTCAATGCCTGCAATCAGTTAAATCTCAAAATATCAAACATTTCGATCACATCAACAAATCTTAC
TTACTAAACAAGCAAGAATCAATCAACCATGAATCAGAAAAACTCGCATACAG
Found at i:12427299 original size:115 final size:121
Alignment explanation
Indices: 12427157--12427382 Score: 288
Period size: 120 Copynumber: 1.9 Consensus size: 121
12427147 GAATACAACC
**
12427157 TAGCTTCGATGCCTGTAGTCAGTTAAATCT-CAAA-AT-TTTGAACA-TTTCGATCATATCAAC-
1 TAGCTTCGATGCC--TAGTCAGTTAAATCTCCAAATATCAATGAACATTTTCGATCATATCAACG
12427217 AAATACTATTTACTTAGGAAGCAAGAATCAGC-ATTAAATCTAAAAAACTGACAGTTTAT
64 AAA-ACTATTTACTTAGGAAGCAAGAATCAGCTA-TAAATCTAAAAAACTGACAGTTTAT
* * *
12427276 TAGCTTCGATGCC-A-TCAGTTAAATCTCCAAATATCGAATGAACATTTTCTATCATATTAACGT
1 TAGCTTCGATGCCTAGTCAGTTAAATCTCCAAATATC-AATGAACATTTTCGATCATATCAACGA
* *
12427339 AAACTATTTACTTATGAAGCAAGAATCAGCTATCAATCTAAAAA
65 AAACTATTTACTTAGGAAGCAAGAATCAGCTATAAATCTAAAAA
12427383 GACTCGCATA
Statistics
Matches: 93, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
115 12 0.13
116 5 0.05
117 2 0.02
119 19 0.20
120 52 0.56
121 3 0.03
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (121 bp):
TAGCTTCGATGCCTAGTCAGTTAAATCTCCAAATATCAATGAACATTTTCGATCATATCAACGAA
AACTATTTACTTAGGAAGCAAGAATCAGCTATAAATCTAAAAAACTGACAGTTTAT
Found at i:12432043 original size:75 final size:74
Alignment explanation
Indices: 12431890--12432044 Score: 177
Period size: 75 Copynumber: 2.1 Consensus size: 74
12431880 TAAAATTATA
** * * *
12431890 TTTTATATTTGTTATCGAATTATTTATTTAACAAAGTATTTTAATAAAACTATTTATTAATTAAT
1 TTTTATATTTCCTATCAAATTATTTATTTAACAAAGTATTTTAATAAAACTATTAATTAATGAAT
* *
12431955 TATATCTTC
66 TAGATCATC
* * ** *
12431964 TTTTATATTTCCTATCAAATTTATTTTTTTAACAAAGTATTTTCATAAGATTTATTAATTTATGA
1 TTTTATATTTCCTATCAAA-TTATTTATTTAACAAAGTATTTTAATAA-AACTATTAATTAATGA
12432029 ATTAGATCAT-
64 ATTAGATCATC
12432039 TTTTAT
1 TTTTAT
12432045 TAGTAATAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
74 16 0.24
75 32 0.48
76 19 0.28
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.54
Consensus pattern (74 bp):
TTTTATATTTCCTATCAAATTATTTATTTAACAAAGTATTTTAATAAAACTATTAATTAATGAAT
TAGATCATC
Found at i:12433875 original size:216 final size:216
Alignment explanation
Indices: 12433495--12434023 Score: 711
Period size: 216 Copynumber: 2.4 Consensus size: 216
12433485 CATAAATTCG
* * * *
12433495 TTGAAGCAGTCGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTCACCCATAATCATTGA
1 TTGAAGCACTTGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTTA-CCATAATTATTGA
* * * * *
12433560 TTTTTAGTGTGCAAAACTGAAAATTTTGTTCATGTACTTATTGTTTGAAGTCAATTATTTACTGA
65 TTTTTAGTGTTCAAAACTGAAAATTCTGTTCATCTACTTATTGTTCGAAGTCAATTACTTACTGA
** * * *
12433625 ATAATTGAATGAGTAAAATTATATATTTTGCTGTCTCTAAAGTTGAA-TTTTTGTTCTTCATCGA
130 ATAATTGAATGAGTAAAACGATACATTGTGCTGTCTCAAAAGTT-AATTTTTTGTTCTTCATCGA
*
12433689 ATTATGTATAAATAGTTT-AGGC
194 ATTATGTATAAATACTTTAAGGC
*
12433711 TTGAAGCACTTGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTTACTCATAATTATTGG
1 TTGAAGCACTTGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTTAC-CATAATTATTGA
* * *
12433776 TTTTTAGTGTTCAAAACTGAGAATTCTGTTTATCTAGTTATTGTTCGAAGTCAATTACTTACTGA
65 TTTTTAGTGTTCAAAACTGAAAATTCTGTTCATCTACTTATTGTTCGAAGTCAATTACTTACTGA
* *
12433841 ATAATTGAATTAGTAAAACGATACATTGTGCTGTCTCAAAAGTTAATTTTTTTTTGTTTTTCATC
130 ATAATTGAATGAGTAAAACGATACATTGTGCTGTCTCAAAAGTTAA---TTTTTTGTTCTTCATC
* *
12433906 GAATTGTGTCTAAATACTTTAAGGC
192 GAATTATGTATAAATACTTTAAGGC
* ** * *
12433931 TTGAAGCACTTGATAACCATCCGTTTTCGCTTTCTGGGTAATTATTATTTACCATCATTGTTGAT
1 TTGAAGCACTTGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTTACCATAATTATTGAT
* *
12433996 TTTTAGTGCTCAAAAACTGAAAAATCTG
66 TTTTAGTGTTC-AAAACTGAAAATTCTG
12434024 CTTATTTTAC
Statistics
Matches: 274, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
215 3 0.01
216 153 0.56
219 51 0.19
220 67 0.24
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (216 bp):
TTGAAGCACTTGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTTACCATAATTATTGAT
TTTTAGTGTTCAAAACTGAAAATTCTGTTCATCTACTTATTGTTCGAAGTCAATTACTTACTGAA
TAATTGAATGAGTAAAACGATACATTGTGCTGTCTCAAAAGTTAATTTTTTGTTCTTCATCGAAT
TATGTATAAATACTTTAAGGC
Found at i:12443417 original size:14 final size:14
Alignment explanation
Indices: 12443382--12443409 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12443372 ATTGGTTTTC
12443382 GAAATGGGTTATTT
1 GAAATGGGTTATTT
12443396 GAAATGGGTTATTT
1 GAAATGGGTTATTT
12443410 TCAATGGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
GAAATGGGTTATTT
Found at i:12443943 original size:27 final size:28
Alignment explanation
Indices: 12443868--12443943 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 28
12443858 ATGAATGAAA
* *
12443868 TTTTTGATAAA-AGGATCAATTTATTCT
1 TTTTTAATAAATAGGATTAATTTATTCT
12443895 TTAATTTAAT-AATAGGAATTAATTTATT-T
1 TT--TTTAATAAATAGG-ATTAATTTATTCT
*
12443924 TTTTTAATAAATAGGGTTAA
1 TTTTTAATAAATAGGATTAA
12443944 ATATAATCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
27 12 0.29
28 8 0.20
29 11 0.27
30 10 0.24
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (28 bp):
TTTTTAATAAATAGGATTAATTTATTCT
Found at i:12456008 original size:21 final size:21
Alignment explanation
Indices: 12455982--12456036 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
12455972 AACAGCGGTG
*
12455982 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
12456003 GCGGTGAGATTAGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
12456024 GCGATGAGATTAG
1 GCGGTGAGATTAG
12456037 AAACAATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:12456994 original size:29 final size:29
Alignment explanation
Indices: 12456952--12457124 Score: 145
Period size: 29 Copynumber: 6.2 Consensus size: 29
12456942 GAATAAACCG
*
12456952 AATACAGTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
12456981 AATACACTACATATATTTTTTTTATTTTTAA
1 AATACACTACATATA--TTTTTTATTTTTAA
* **
12457012 AAT--A-T---T-T-TTTATT-TTTAAAA
1 AATACACTACATATATTTTTTATTTTTAA
* * *
12457032 TACACTAC-AT--ATATTTTTTATTTTTAA
1 AATAC-ACTACATATATTTTTTATTTTTAA
*
12457059 AATACACTACATATTTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
*
12457088 AATACATTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAA
12457118 AATACAC
1 AATACAC
12457125 AAATACAATG
Statistics
Matches: 113, Mismatches: 16, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
20 6 0.05
21 5 0.04
23 1 0.01
24 1 0.01
25 2 0.02
26 7 0.06
27 9 0.08
28 1 0.01
29 44 0.39
30 20 0.18
31 17 0.15
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.54
Consensus pattern (29 bp):
AATACACTACATATATTTTTTATTTTTAA
Found at i:12457021 original size:19 final size:18
Alignment explanation
Indices: 12456998--12457033 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12456988 TACATATATT
12456998 TTTTTTATTTTTAAAATA
1 TTTTTTATTTTTAAAATA
12457016 TTTTTTATTTTTAAAATA
1 TTTTTTATTTTTAAAATA
12457034 CACTACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTATTTTTAAAATA
Found at i:12457036 original size:49 final size:49
Alignment explanation
Indices: 12456964--12457121 Score: 194
Period size: 49 Copynumber: 3.1 Consensus size: 49
12456954 TACAGTACAT
12456964 ATATTTTTTATTTTTAAAATACACTACATATATTTTTTTTATTTTTAAA
1 ATATTTTTTATTTTTAAAATACACTACATATATTTTTTTTATTTTTAAA
*
12457013 ATATTTTTTATTTTTAAAATACACTACATATATTTTTTATT-TTTAAAATACACTA
1 ATATTTTTTATTTTTAAAATACACTACATATATTTTTT-TTATTT---TTA-A--A
*
12457068 CATATTTTTTTTATTTTTAAAATACATTACATATA-TTTTTTTATTTTTAAA
1 -ATA--TTTTTTATTTTTAAAATACACTACATATATTTTTTTTATTTTTAAA
12457119 ATA
1 ATA
12457122 CACAAATACA
Statistics
Matches: 95, Mismatches: 3, Indels: 21
0.80 0.03 0.18
Matches are distributed among these distances:
49 41 0.43
50 5 0.05
51 1 0.01
52 2 0.02
53 2 0.02
54 2 0.02
55 1 0.01
56 5 0.05
57 8 0.08
58 28 0.29
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (49 bp):
ATATTTTTTATTTTTAAAATACACTACATATATTTTTTTTATTTTTAAA
Found at i:12457079 original size:30 final size:29
Alignment explanation
Indices: 12457016--12457124 Score: 191
Period size: 29 Copynumber: 3.7 Consensus size: 29
12457006 TTTTAAAATA
*
12457016 TTTTTTATTTTTAAAATACACTACATATA
1 TTTTTTATTTTTAAAATACACTACATATT
12457045 TTTTTTATTTTTAAAATACACTACATATT
1 TTTTTTATTTTTAAAATACACTACATATT
*
12457074 TTTTTTATTTTTAAAATACATTACATATAT
1 TTTTTTATTTTTAAAATACACTACATAT-T
12457104 TTTTTTATTTTTAAAATACAC
1 TTTTTTATTTTTAAAATACAC
12457125 AAATACAATG
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 55 0.72
30 21 0.28
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTTTTATTTTTAAAATACACTACATATT
Found at i:12457187 original size:21 final size:21
Alignment explanation
Indices: 12457163--12457230 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
12457153 GATTCCCCTC
12457163 TTTCACCGTGCCCTCCTCCCA
1 TTTCACCGTGCCCTCCTCCCA
* * *
12457184 TTTC-CCATTCCCATTTCC-CCTA
1 TTTCACCGTGCCC---TCCTCCCA
*
12457206 TTCCACCGTGCCCTCCTCCCA
1 TTTCACCGTGCCCTCCTCCCA
12457227 TTTC
1 TTTC
12457231 CCCTCTTCCA
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
20 9 0.26
21 10 0.29
22 6 0.18
23 9 0.26
ACGTcount: A:0.10, C:0.50, G:0.06, T:0.34
Consensus pattern (21 bp):
TTTCACCGTGCCCTCCTCCCA
Found at i:12457226 original size:30 final size:31
Alignment explanation
Indices: 12457192--12457263 Score: 101
Period size: 30 Copynumber: 2.3 Consensus size: 31
12457182 CATTTCCCAT
*
12457192 TCCCATTTCCCCTATTCCACCG-TGCCCTCC
1 TCCCATTTCCCCTATTCCACCGATCCCCTCC
* *
12457222 TCCCATTTCCCCTCTTCCATCGATTCCCCTCC
1 TCCCATTTCCCCTATTCCACCGA-TCCCCTCC
12457254 TCCCATTTCC
1 TCCCATTTCC
12457264 TATTCCCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 20 0.54
32 17 0.46
ACGTcount: A:0.10, C:0.53, G:0.04, T:0.33
Consensus pattern (31 bp):
TCCCATTTCCCCTATTCCACCGATCCCCTCC
Found at i:12457234 original size:15 final size:15
Alignment explanation
Indices: 12457216--12457263 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
12457206 TTCCACCGTG
12457216 CCCTCCTCCCATTTC
1 CCCTCCTCCCATTTC
*
12457231 CCCT-CTTCCATCGATTC
1 CCCTCCTCCCAT---TTC
12457248 CCCTCCTCCCATTTC
1 CCCTCCTCCCATTTC
12457263 C
1 C
12457264 TATTCCCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
17 7 0.26
18 6 0.22
ACGTcount: A:0.08, C:0.56, G:0.02, T:0.33
Consensus pattern (15 bp):
CCCTCCTCCCATTTC
Found at i:12458013 original size:19 final size:18
Alignment explanation
Indices: 12457989--12458032 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
12457979 AATTATTAAT
12457989 AAATAAATATTAAAATATA
1 AAATAAAT-TTAAAATATA
*
12458008 AAAT-AATTTAAATTATA
1 AAATAAATTTAAAATATA
12458025 AAA-AAATT
1 AAATAAATT
12458033 AACAATAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 16 0.70
18 3 0.13
19 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAAATTTAAAATATA
Found at i:12458034 original size:16 final size:16
Alignment explanation
Indices: 12457987--12458039 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
12457977 TAAATTATTA
12457987 ATAAATAAATATTAAAAT
1 ATAAA-AAA-ATTAAAAT
* *
12458005 ATAAAATAATTTAAATT
1 ATAAAA-AAATTAAAAT
12458022 ATAAAAAAATTAACAAT
1 ATAAAAAAATTAA-AAT
12458039 A
1 A
12458040 ATCAACCCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 6 0.21
17 16 0.55
18 7 0.24
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAAAAATTAAAAT
Done.