Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 34 of 106
Found at i:13088263 original size:43 final size:42
Alignment explanation
Indices: 13088215--13088389 Score: 147
Period size: 43 Copynumber: 4.1 Consensus size: 42
13088205 CACCATCCCA
* **
13088215 TCATCATCGACTCATGTGCTCTCCCTACTCGCACAT-GGCTAGG
1 TCATCATCGGCT-ATGTGCTCTCCCTACTCGCACATAACCTA-G
* * * *
13088258 TCATCACCGGTTTATGCGCACTCCCTACTCGCACATAACCTAG
1 TCATCATCGG-CTATGTGCTCTCCCTACTCGCACATAACCTAG
* *
13088301 TCATCATCGGCT-TATGCATACTCCCTACTCGCACATAACCGAG
1 TCATCATCGGCTATGTGC-T-CTCCCTACTCGCACATAACCTAG
* ** * * *
13088344 TCATCATCGGCTTATGCGAACTCTCTACTCGCACATAGCCGAG
1 TCATCATCGGC-TATGTGCTCTCCCTACTCGCACATAACCTAG
13088387 TCA
1 TCA
13088390 ATATCATTAC
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 96 0.90
44 5 0.05
45 2 0.02
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (42 bp):
TCATCATCGGCTATGTGCTCTCCCTACTCGCACATAACCTAG
Found at i:13099863 original size:13 final size:13
Alignment explanation
Indices: 13099845--13099869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13099835 TTTCAGAAAA
13099845 TTTATAAAATCAT
1 TTTATAAAATCAT
13099858 TTTATAAAATCA
1 TTTATAAAATCA
13099870 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:13103072 original size:19 final size:19
Alignment explanation
Indices: 13103048--13103084 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13103038 AGAAGAAGGA
*
13103048 GAAGAAGCTGCTGGAGAAT
1 GAAGAAGATGCTGGAGAAT
13103067 GAAGAAGATGCTGGAGAA
1 GAAGAAGATGCTGGAGAA
13103085 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.38, T:0.14
Consensus pattern (19 bp):
GAAGAAGATGCTGGAGAAT
Found at i:13104499 original size:15 final size:16
Alignment explanation
Indices: 13104477--13104524 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
13104467 ACTTCTCTTT
13104477 AGGTTTATATATTATA
1 AGGTTTATATATTATA
*
13104493 A-GTTTATATA-AATAA
1 AGGTTTATATATTAT-A
*
13104508 AGGTATATATATTATA
1 AGGTTTATATATTATA
13104524 A
1 A
13104525 TTAATAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 11 0.42
17 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (16 bp):
AGGTTTATATATTATA
Found at i:13104767 original size:344 final size:341
Alignment explanation
Indices: 13104255--13104949 Score: 961
Period size: 344 Copynumber: 2.0 Consensus size: 341
13104245 ATATATATAT
* * *
13104255 ATATATACACTAAAAGTATTTCAATATATATAATAGCAATTATATTCCTCATAAATGAACCTAAT
1 ATATATATACTAAAAATATTTCAATATATATAATAGCAATTATATTCCTCATAAATGAAAC-AAT
* * *
13104320 ATATATAAAGTATATATATTAAAAGACATTACAAGTTAATTAAAAATTATAGTTTCATGAATTAA
65 ATATATAAACTATATATATTAAAAGACATTACAAGTTAATGAAAAATCATAGTTTCATGAATTAA
* *
13104385 TTTAATTAACTATATGAGTTTGTCCTTAATTACATGAAATTTTAAAAAACTAACTAGGTTTCAAA
130 TTTAATTAACTATATGAGTTTGTCCTTAATTACATGAAA--TTAAAAAAATAACTAGGTTCCAAA
* * * * * *
13104450 ACTATTCTAATCTCACAA-CTTCTCTTT-AG-GTTTATATATTATAAGTTTATATAAATAAAGGT
193 ACTATTCCAATCTCAAAAGCTT-TCTTTAAGTGTATATATATTATAAGGTTATACAAACAAAGGT
** * *
13104512 ATATATATTATAATTAATAATTTTTATAAGCTGTAATTTTTGTAATGTTAACACAAAATAGAAAG
257 ATATATATTATAATTAATAA-TTTTATAAGCTACAATGTTTGTAATATTAACACAAAATAGAAAG
* *
13104577 TAAATATGTTTATATTTAAAGC
321 TAAATATATTAATA-TTAAAGC
* * ** * *
13104599 ATATATATACTAAAAATATTTTAGTATATATATAATAGTAATTATATTTTTTATAAATTAAGAC-
1 ATATATATACTAAAAATATTTCA--ATATATATAATAGCAATTATATTCCTCATAAATGAA-ACA
*
13104663 A-ATATATAAACTATATATATTAAAAGACATTACAAGTTAATGAATAATCATAGTTTCATGAATT
63 ATATATATAAACTATATATATTAAAAGACATTACAAGTTAATGAAAAATCATAGTTTCATGAATT
* **
13104727 AATTTAATTAACTATATG-GATTTGTCCTTAATTTCATGAAATTAAAAAAATAGTTAGGTTCCAA
128 AATTTAATTAACTATATGAG-TTTGTCCTTAATTACATGAAATTAAAAAAATAACTAGGTTCCAA
*
13104791 AACTATTCCAATCTCAAAAGCTTTCTTTAAGTGTATATATATTATAAGGTTATACAAACAATGGT
192 AACTATTCCAATCTCAAAAGCTTTCTTTAAGTGTATATATATTATAAGGTTATACAAACAAAGGT
*
13104856 ATATATATTATAATTAATAATTTTATAAGTTACAATGTTTGTAATATTAACACAAAATAGAAAGT
257 ATATATATTATAATTAATAATTTTATAAGCTACAATGTTTGTAATATTAACACAAAATAGAAAGT
*
13104921 AAATATATTAATATTAAAGT
322 AAATATATTAATATTAAAGC
13104941 ATATATATA
1 ATATATATA
13104950 ATAGTAATTA
Statistics
Matches: 311, Mismatches: 33, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
342 56 0.18
343 57 0.18
344 165 0.53
345 1 0.00
346 31 0.10
347 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (341 bp):
ATATATATACTAAAAATATTTCAATATATATAATAGCAATTATATTCCTCATAAATGAAACAATA
TATATAAACTATATATATTAAAAGACATTACAAGTTAATGAAAAATCATAGTTTCATGAATTAAT
TTAATTAACTATATGAGTTTGTCCTTAATTACATGAAATTAAAAAAATAACTAGGTTCCAAAACT
ATTCCAATCTCAAAAGCTTTCTTTAAGTGTATATATATTATAAGGTTATACAAACAAAGGTATAT
ATATTATAATTAATAATTTTATAAGCTACAATGTTTGTAATATTAACACAAAATAGAAAGTAAAT
ATATTAATATTAAAGC
Found at i:13105384 original size:32 final size:32
Alignment explanation
Indices: 13105348--13105430 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
13105338 ATTGCCATCC
* *
13105348 TTATACTAAAACACATCAACTTCTTAATAAAG
1 TTATACTAAAACATATCAACTTCCTAATAAAG
* * * *
13105380 TTATATTAAAACATATTAAGTTCCTAATAGAG
1 TTATACTAAAACATATCAACTTCCTAATAAAG
* *
13105412 ATACACTAAAACATATCAA
1 TTATACTAAAACATATCAA
13105431 TAAACAATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (32 bp):
TTATACTAAAACATATCAACTTCCTAATAAAG
Found at i:13114850 original size:19 final size:19
Alignment explanation
Indices: 13114826--13114863 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13114816 CCATTTGACT
*
13114826 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
13114845 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
13114864 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:13115696 original size:10 final size:10
Alignment explanation
Indices: 13115681--13115709 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
13115671 TTTATTTGAG
13115681 GAATTATGAT
1 GAATTATGAT
13115691 GAATTATGAT
1 GAATTATGAT
13115701 GAATTATGA
1 GAATTATGA
13115710 GCCTAGAAAA
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:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (10 bp):
GAATTATGAT
Found at i:13127685 original size:35 final size:35
Alignment explanation
Indices: 13127619--13127867 Score: 261
Period size: 35 Copynumber: 7.1 Consensus size: 35
13127609 AACTTGATTA
*
13127619 AAATTGTTTAATTAAG---TTGTGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
13127651 AAATTGTTTAATTAAATCATTGAGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
13127686 AGATTATTTAATTAAGTCATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*** * * *
13127721 AAATTAAATAATTAAGTTATTGGACCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*
13127756 AAATTTGTTTAATTAAGTCATTGGGCCTAATTGATT
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * ** *
13127792 AAAATTTTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * * **
13127828 AAATTTTTTAATTAAGTTATTGAGCCTAATCGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
13127863 AAATT
1 AAATT
13127868 AAACAATTAA
Statistics
Matches: 183, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
32 15 0.08
35 112 0.61
36 53 0.29
37 3 0.02
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:13127855 original size:142 final size:139
Alignment explanation
Indices: 13127612--13127888 Score: 376
Period size: 142 Copynumber: 2.0 Consensus size: 139
13127602 TCTCAACAAC
*
13127612 TTGATTAAAATTGTTTAATTAAGTTGTGCCTAATTAATTAAATTGTTTAATTAAATCATTGAGCC
1 TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTGTTTAATTAAATCATTGAGCC
* * * *
13127677 TAATTAATTAGATTATTTAATTAAGTCATTGGGCCTAATTAATTAAATTAAATAATTAAGTT-AT
66 TAATTAATTAAATTATTTAATTAAGTCATTGAGCCTAATCAATTAAATTAAACAATTAAGTTAAT
13127741 TGGACCTAA
131 TGGACCTAA
* * * **
13127750 TTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTTTTTAATTAAATTGTTG
1 TTGATTAAAATTGTTTAATTAAG---TTGGGCCTAATTAATT-AAATTGTTTAATTAAATCATTG
* * * * *
13127815 GGCTTAATTAATTAAATTTTTTAATTAAGTTATTGAGCCTAATCGATTAAATTAAACAATTAAGT
62 AGCCTAATTAATTAAATTATTTAATTAAGTCATTGAGCCTAATCAATTAAATTAAACAATTAAGT
13127880 TAATTGGAC
127 TAATTGGAC
13127889 TTCTTAAGGA
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
138 22 0.18
141 14 0.12
142 76 0.64
143 7 0.06
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (139 bp):
TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTGTTTAATTAAATCATTGAGCC
TAATTAATTAAATTATTTAATTAAGTCATTGAGCCTAATCAATTAAATTAAACAATTAAGTTAAT
TGGACCTAA
Found at i:13127886 original size:107 final size:106
Alignment explanation
Indices: 13127660--13127886 Score: 242
Period size: 107 Copynumber: 2.1 Consensus size: 106
13127650 TAAATTGTTT
* * * * *
13127660 AATTAAATCATTGAGCCTAATTAATTAGATTATTTAATTAAGTCATTGGGCCTAATTAATTAAAT
1 AATTAAGTAATTGGGCCTAATTAATTAAATTATTTAATTAAATCATTGGGCCTAATTAATTAAAT
* ****
13127725 TAAATAATTAAGTTATTGGACCTAATTGATTAAATTTGTTT
66 TAAATAATTAAGTTATTGGACCTAATCGATTAAATTTAAAC
* * * ** *
13127766 AATTAAGTCATTGGGCCTAATTGATTAAAATTTTTTAATTAAATTGTTGGGCTTAATTAATTAAA
1 AATTAAGTAATTGGGCCTAATTAATT-AAATTATTTAATTAAATCATTGGGCCTAATTAATTAAA
***
13127831 TTTTTTAATTAAGTTATT-GAGCCTAATCGATTAAA-TTAAAC
65 TTAAATAATTAAGTTATTGGA-CCTAATCGATTAAATTTAAAC
13127872 AATTAAGTTAATTGG
1 AATTAAG-TAATTGG
13127887 ACTTCTTAAG
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
106 34 0.34
107 66 0.66
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (106 bp):
AATTAAGTAATTGGGCCTAATTAATTAAATTATTTAATTAAATCATTGGGCCTAATTAATTAAAT
TAAATAATTAAGTTATTGGACCTAATCGATTAAATTTAAAC
Found at i:13129780 original size:91 final size:91
Alignment explanation
Indices: 13129625--13129805 Score: 344
Period size: 91 Copynumber: 2.0 Consensus size: 91
13129615 CATGGATGCA
*
13129625 ACCGCTTTATGGAAAGAGGTTGTTTGTTGGAGAAATTGGACACTCAATGATCAGGAAGGATTCTT
1 ACCGCTTTATGGAAAGAGGTTGTTTGTTGAAGAAATTGGACACTCAATGATCAGGAAGGATTCTT
*
13129690 TCCTTGGCTGATCATTGACTCCTAAT
66 TCCTTAGCTGATCATTGACTCCTAAT
13129716 ACCGCTTTATGGAAAGAGGTTGTTTGTTGAAGAAATTGGACACTCAATGATCAGGAAGGATTCTT
1 ACCGCTTTATGGAAAGAGGTTGTTTGTTGAAGAAATTGGACACTCAATGATCAGGAAGGATTCTT
13129781 TCCTTAGCTGATCATTGACTCCTAA
66 TCCTTAGCTGATCATTGACTCCTAA
13129806 ATATTAGGGA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (91 bp):
ACCGCTTTATGGAAAGAGGTTGTTTGTTGAAGAAATTGGACACTCAATGATCAGGAAGGATTCTT
TCCTTAGCTGATCATTGACTCCTAAT
Found at i:13131773 original size:23 final size:23
Alignment explanation
Indices: 13131745--13131789 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13131735 GTTATGAAAT
13131745 ATAACTTAAAAGAACAAATAAAA
1 ATAACTTAAAAGAACAAATAAAA
* *
13131768 ATAACTTGAAAGAACAACTAAA
1 ATAACTTAAAAGAACAAATAAA
13131790 GAAAGAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.64, C:0.11, G:0.07, T:0.18
Consensus pattern (23 bp):
ATAACTTAAAAGAACAAATAAAA
Found at i:13132007 original size:16 final size:17
Alignment explanation
Indices: 13131980--13132011 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13131970 GGATTAAATC
13131980 CTAATGTTAAATCTAAT
1 CTAATGTTAAATCTAAT
13131997 CTAAT-TTAAATCTAA
1 CTAATGTTAAATCTAA
13132012 ATTTAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (17 bp):
CTAATGTTAAATCTAAT
Found at i:13134348 original size:35 final size:35
Alignment explanation
Indices: 13134282--13134348 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
13134272 AAGTATTCAC
*
13134282 TTTTATTCTTATCAGTATTTTTAATTCCATTGATA
1 TTTTATTCTTATCAGTATTTATAATTCCATTGATA
* ** * *
13134317 TTTTATTGTTATTTGTATTTATATTTTCATTG
1 TTTTATTCTTATCAGTATTTATAATTCCATTG
13134349 CTGTTTTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (35 bp):
TTTTATTCTTATCAGTATTTATAATTCCATTGATA
Found at i:13136097 original size:27 final size:28
Alignment explanation
Indices: 13136050--13136113 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
13136040 AGTTCTTAAA
* *
13136050 AAAAATAACTTTTTTTAAAAAACAAGTTT
1 AAAAA-AACTTTTTTTAAAAAAAAAGCTT
13136079 AAAAAAA-TTTTTTTAAAAAAAAAGCTT
1 AAAAAAACTTTTTTTAAAAAAAAAGCTT
13136106 AAAGAAAA
1 AAA-AAAA
13136114 GCTCCAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 21 0.66
28 6 0.19
29 5 0.16
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (28 bp):
AAAAAAACTTTTTTTAAAAAAAAAGCTT
Found at i:13139348 original size:251 final size:251
Alignment explanation
Indices: 13138837--13139521 Score: 941
Period size: 251 Copynumber: 2.7 Consensus size: 251
13138827 CGTAAAGCAA
** ** * *
13138837 TAAGAATTGACAAAAAAACTCGTAAAGGTAGAATAACTAAATTTAAAATCTTAACGTAAATGTGT
1 TAAGAATTGACGTAAAAACTTATAAAGTTAGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
* * * *
13138902 AAAAGTTAACGTAACAAGTCAATTAAA-GAAAAAATTTTAATTTTAATATAAAATAAATATTTAA
66 GAAAGTTAACGTAACAAGTCAATTAAATAAAAAAAATCTAATTTTAATA-AAAATAAATATTTAA
*
13138966 ATTTATATTCTCGGACTAAAATTAG-TTAACGATATACAAATTTTAA-TTTTAAATAAAAAATAA
130 ATTTATATTCTCGGACTAAAAGT-GTTTAACGATATACAAATTTTAATTTTTAAATAAAAAATAA
* * * *
13139029 TAAAGATAAAAGTAATTATAGTTCAAAATTGATATAAATAAGTCTTTACGTAAAACTG
194 TAAAGATAAAAATAATTATAGTTCAAAATTGACATAAATAAGTCTTGAAGTAAAACTG
* *
13139087 TAACAATTGACGTAAAAACTTATAAAGTTAGAATAACTAAATTTTAAATCTTAACGTAAATATGT
1 TAAGAATTGACGTAAAAACTTATAAAGTTAGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
** * *
13139152 GAAAGTTAATATAACAAGTCAATTAAATAAAAAAAATCTAATTTTAATGAAAAACAAACATTTAA
66 GAAAGTTAACGTAACAAGTCAATTAAATAAAAAAAATCTAATTTTAAT-AAAAATAAATATTTAA
* ** * * * *
13139217 ATTTATACTCTTAGATTATAAGTGTTTAACAATATACAAATTTTAATTTTTAAATAAACAATAAT
130 ATTTATATTCTCGGACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAAAATAAT
*
13139282 AAAGATAAAAATAATTATAGTTC-AAATTGACATAGAA-AAGTCTTGAAGTTAAACTG
195 AAAGATAAAAATAATTATAGTTCAAAATTGACATA-AATAAGTCTTGAAGTAAAACTG
* * * *
13139338 TGAGAATTGACGTAAAAACTTATAAA-TGTGGAATAACTAAATTTTTAATCTTAACGTAAACGTG
1 TAAGAATTGACGTAAAAACTTATAAAGT-TAGAATAACTAAATTTTAAATCTTAACGTAAATGTG
* * *
13139402 TGAAAGTTAACGTAACAAGTTAATTAAGTAAAAAAAATTCTAATTTTAGTAAAAAATAAATATTT
65 TGAAAGTTAACGTAACAAGTCAATTAAATAAAAAAAA-TCTAATTTTAAT-AAAAATAAATATTT
13139467 AAATTTATATTCTCGGACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAA
128 AAATTTATATTCTCGGACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAA
13139522 GTTTTGACAT
Statistics
Matches: 379, Mismatches: 49, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
250 83 0.22
251 182 0.48
252 114 0.30
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.34
Consensus pattern (251 bp):
TAAGAATTGACGTAAAAACTTATAAAGTTAGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
GAAAGTTAACGTAACAAGTCAATTAAATAAAAAAAATCTAATTTTAATAAAAATAAATATTTAAA
TTTATATTCTCGGACTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAAAATAATA
AAGATAAAAATAATTATAGTTCAAAATTGACATAAATAAGTCTTGAAGTAAAACTG
Found at i:13146130 original size:19 final size:20
Alignment explanation
Indices: 13146095--13146132 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
13146085 ATTTAAAATC
*
13146095 TTAACGTAAATATGTGATAG
1 TTAACGTAAATAAGTGATAG
13146115 TTAACGT-AATAAGTGATA
1 TTAACGTAAATAAGTGATA
13146133 ATAATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.34
Consensus pattern (20 bp):
TTAACGTAAATAAGTGATAG
Found at i:13149416 original size:1 final size:1
Alignment explanation
Indices: 13149410--13149439 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
13149400 CATATTCCCC
*
13149410 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13149440 GAAACCCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:13149440 original size:8 final size:8
Alignment explanation
Indices: 13149410--13149443 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
13149400 CATATTCCCC
13149410 AAAAAAA-
1 AAAAAAAG
*
13149417 AAAAAAAA
1 AAAAAAAG
13149425 AAAAAAAG
1 AAAAAAAG
13149433 AAAAAAAG
1 AAAAAAAG
13149441 AAA
1 AAA
13149444 CCCCTAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:13150006 original size:21 final size:21
Alignment explanation
Indices: 13149980--13150023 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13149970 TTAGCTGTCT
*
13149980 GAAAGCTGAGATGAAA-GAAGC
1 GAAAGC-GAGACGAAAGGAAGC
*
13150001 GAAAGCGTGACGAAAGGAAGC
1 GAAAGCGAGACGAAAGGAAGC
13150022 GA
1 GA
13150024 TAACGCATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.45, C:0.11, G:0.36, T:0.07
Consensus pattern (21 bp):
GAAAGCGAGACGAAAGGAAGC
Found at i:13151300 original size:4 final size:4
Alignment explanation
Indices: 13151291--13151350 Score: 75
Period size: 4 Copynumber: 15.0 Consensus size: 4
13151281 AAATGACGAG
* * * *
13151291 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
13151339 ATAT GTAT ATAT
1 ATAT ATAT ATAT
13151351 GTTTGTCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:13151302 original size:6 final size:6
Alignment explanation
Indices: 13151291--13151350 Score: 75
Period size: 6 Copynumber: 10.0 Consensus size: 6
13151281 AAATGACGAG
* * * *
13151291 ATATAT ATATAT ATATAT ATATAT ATATAT ATGTAT GTATGT ATATGT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
13151339 ATATGT ATATAT
1 ATATAT ATATAT
13151351 GTTTGTCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:13153237 original size:11 final size:10
Alignment explanation
Indices: 13153212--13153236 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13153202 TGAACTTCTC
13153212 TTTTTCTTTT
1 TTTTTCTTTT
13153222 TTTTTCTTTT
1 TTTTTCTTTT
13153232 TTTTT
1 TTTTT
13153237 TGACATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:13153331 original size:37 final size:37
Alignment explanation
Indices: 13153267--13153339 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
13153257 TTCATCCAAA
13153267 GAAATTTTAAACATTATATATATATATATATATACTNT
1 GAAATTTTAAACATTATATATATATATATATATACT-T
13153305 GAAATTTTAAACA-TATATATATATATATATATACT
1 GAAATTTTAAACATTATATATATATATATATATACT
13153340 AATTATCTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 22 0.63
38 13 0.37
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (37 bp):
GAAATTTTAAACATTATATATATATATATATATACTT
Found at i:13160723 original size:23 final size:24
Alignment explanation
Indices: 13160697--13160747 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
13160687 TCAATATATT
* *
13160697 CACACAAAAACTACCACA-CATGG
1 CACACAAAAACAACCACATCATCG
13160720 CACACAAAAACAACCACATCATCG
1 CACACAAAAACAACCACATCATCG
13160744 CACA
1 CACA
13160748 TAAATATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.49, C:0.37, G:0.06, T:0.08
Consensus pattern (24 bp):
CACACAAAAACAACCACATCATCG
Found at i:13162922 original size:110 final size:110
Alignment explanation
Indices: 13162788--13163007 Score: 404
Period size: 110 Copynumber: 2.0 Consensus size: 110
13162778 AGTGAGTTTT
13162788 ATTTGCTATTTAATTTTAGTTTTAATTTATTAGTTTTAATTATTCTTTTTTATTGTTTGGATAAA
1 ATTTGCTATTTAATTTTAGTTTTAATTTATTAGTTTTAATTATTCTTTTTTATTGTTTGGATAAA
* * *
13162853 ATTAGAGTGTTATAATTTTAGTCGTTAATCGTAGGAATTAAACAA
66 ATTAGAGTATTATAATTTTAGTAGTTAATAGTAGGAATTAAACAA
13162898 ATTTGCTATTTAATTTTAGTTTTAATTTATTAGTTTTAATTATTCTTTTTTATTGTTTGGATAAA
1 ATTTGCTATTTAATTTTAGTTTTAATTTATTAGTTTTAATTATTCTTTTTTATTGTTTGGATAAA
*
13162963 ATTAGGGTATTATAATTTTAGTAGTTAATAGTAGGAATTAAACAA
66 ATTAGAGTATTATAATTTTAGTAGTTAATAGTAGGAATTAAACAA
13163008 TTCTCCGTGA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 106 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.52
Consensus pattern (110 bp):
ATTTGCTATTTAATTTTAGTTTTAATTTATTAGTTTTAATTATTCTTTTTTATTGTTTGGATAAA
ATTAGAGTATTATAATTTTAGTAGTTAATAGTAGGAATTAAACAA
Found at i:13167677 original size:14 final size:14
Alignment explanation
Indices: 13167658--13167685 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13167648 CATCATCATT
13167658 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
13167672 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
13167686 AAATAGGTGT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:13169891 original size:21 final size:22
Alignment explanation
Indices: 13169874--13169914 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13169864 ATTTAAAACA
13169874 AATTTTTGGA-AACATAAAAAG
1 AATTTTTGGATAACATAAAAAG
* *
13169895 TATTTTTGTATAACATAAAA
1 AATTTTTGGATAACATAAAA
13169915 TTTATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (22 bp):
AATTTTTGGATAACATAAAAAG
Found at i:13173706 original size:3 final size:3
Alignment explanation
Indices: 13173698--13173722 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13173688 AATTACGAAT
13173698 GCA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA G
13173723 AGAGCTGCAG
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:0.32, C:0.32, G:0.36, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:13177109 original size:66 final size:66
Alignment explanation
Indices: 13177001--13177142 Score: 198
Period size: 66 Copynumber: 2.2 Consensus size: 66
13176991 TATAAAAACA
* * **
13177001 TATTACACGTCATGATTAAATTGTTACACATCATGTACAAAAATATGTGATAAGTCATGGTTAGG
1 TATTACACGCCATGATTAAATTGTTACACATCATGTACAAAAATATGTGATAAGCCATAATTAGG
13177066 T
66 T
* *
13177067 TGTTACACGCCATGGA-TAAATTGTTACAC-GCTATGTACAAAAATATGTGATAAGCCATAATTA
1 TATTACACGCCAT-GATTAAATTGTTACACATC-ATGTACAAAAATATGTGATAAGCCATAATTA
13177130 GGT
64 GGT
13177133 TATTACACGC
1 TATTACACGC
13177143 TATGTTGAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
65 1 0.01
66 64 0.96
67 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (66 bp):
TATTACACGCCATGATTAAATTGTTACACATCATGTACAAAAATATGTGATAAGCCATAATTAGG
T
Found at i:13177358 original size:27 final size:29
Alignment explanation
Indices: 13177285--13177360 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
13177275 CCAGTTGAAA
* *
13177285 AAAAAATATTGTTGTTACACGTCATATTG
1 AAAAAATATTATTGTTACACGACATATTG
*
13177314 AAAAAATATTATTATTACACGACATATT-
1 AAAAAATATTATTGTTACACGACATATTG
* *
13177342 CAAAAACATT-TTGTTACAC
1 AAAAAATATTATTGTTACAC
13177361 TTTAATATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 8 0.20
28 8 0.20
29 25 0.61
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (29 bp):
AAAAAATATTATTGTTACACGACATATTG
Found at i:13199041 original size:2 final size:2
Alignment explanation
Indices: 13199034--13199102 Score: 56
Period size: 2 Copynumber: 36.5 Consensus size: 2
13199024 AAATTTATGA
** * *
13199034 AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T GC AT AA AC AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
13199073 AT AT AT AT AT AT AT AT TT A- AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13199103 AGCATTACTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
1 4 0.08
2 49 0.92
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13199298 original size:17 final size:17
Alignment explanation
Indices: 13199278--13199318 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
13199268 TAATAAAGTA
13199278 ATATA-TTATATATATAC
1 ATATATTTA-ATATATAC
*
13199295 ATATATTTAATTTATAC
1 ATATATTTAATATATAC
13199312 ATA-ATTT
1 ATATATTT
13199319 GTTTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 3 0.14
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATTTAATATATAC
Found at i:13199573 original size:15 final size:16
Alignment explanation
Indices: 13199550--13199583 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
13199540 TATATACTTA
*
13199550 TTAATAAGTCAAATAT
1 TTAATAAGTAAAATAT
13199566 TTAA-AAGTAAAATAT
1 TTAATAAGTAAAATAT
13199581 TTA
1 TTA
13199584 TGATGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (16 bp):
TTAATAAGTAAAATAT
Found at i:13200049 original size:16 final size:17
Alignment explanation
Indices: 13200028--13200063 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
13200018 ACCCTTTTAA
13200028 TTATGTATTTATTTT-T
1 TTATGTATTTATTTTGT
*
13200044 TTATGTTTTTATTTTGT
1 TTATGTATTTATTTTGT
13200061 TTA
1 TTA
13200064 ATATTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (17 bp):
TTATGTATTTATTTTGT
Found at i:13214715 original size:16 final size:18
Alignment explanation
Indices: 13214693--13214735 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
13214683 TTCTTTTTTA
13214693 ATATATATTAA-AAATAT
1 ATATATATTAATAAATAT
* *
13214710 -TATATATCAATATATAT
1 ATATATATTAATAAATAT
13214727 ATATATATT
1 ATATATATT
13214736 TGCAAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 9 0.43
17 5 0.24
18 7 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATATATTAATAAATAT
Found at i:13215416 original size:72 final size:71
Alignment explanation
Indices: 13215154--13215418 Score: 347
Period size: 70 Copynumber: 3.7 Consensus size: 71
13215144 TGTTTTTAAC
* * * *
13215154 AAATGAAAAATATTTGGAATTTATTTAAAATATTGAAAATTCAAATTCAAATTAGAAGTCAAATG
1 AAATAAAAAATATTTGAAATTTATTTAAAATATTGAAAACTCAAATT-GAATTAGAAGTCAAATG
*
13215219 TGGATAT
65 TAGATAT
* * *
13215226 AAATAAAAAATATAT-AAATTTATTT-AAATAATCGAAAACTCAAATTGAATTAAAAGTCAAATG
1 AAATAAAAAATATTTGAAATTTATTTAAAAT-ATTGAAAACTCAAATTGAATTAGAAGTCAAATG
13215289 TAGATAT
65 TAGATAT
**
13215296 AAATAAAAAA-ATTCAAAATTTATTTAAAATATTGAAAACTCAAATTGAATTAGAAGTCAAATGT
1 AAATAAAAAATATTTGAAATTTATTTAAAATATTGAAAACTCAAATTGAATTAGAAGTCAAATGT
* *
13215360 ATATAAA
66 AGAT-AT
* * *
13215367 AAATAAAAAACATTTGGAATTTATTTAAAATGTTGAAAACTCAAATTGAATT
1 AAATAAAAAATATTTGAAATTTATTTAAAATATTGAAAACTCAAATTGAATT
13215419 TAGTGTGTAA
Statistics
Matches: 170, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
69 2 0.01
70 80 0.47
71 38 0.22
72 50 0.29
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (71 bp):
AAATAAAAAATATTTGAAATTTATTTAAAATATTGAAAACTCAAATTGAATTAGAAGTCAAATGT
AGATAT
Found at i:13215744 original size:28 final size:28
Alignment explanation
Indices: 13215713--13215766 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
13215703 TATTACAAAC
13215713 AAATAAATTACATCAAATATAAATAAGT
1 AAATAAATTACATCAAATATAAATAAGT
*
13215741 AAATAAATTATATCAAATATAAATAA
1 AAATAAATTACATCAAATATAAATAA
13215767 AATTTCAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.30
Consensus pattern (28 bp):
AAATAAATTACATCAAATATAAATAAGT
Found at i:13231294 original size:23 final size:23
Alignment explanation
Indices: 13231253--13231328 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
13231243 AACTTAAAAC
*
13231253 ATATAAATAAATAGT-ATAAATAA
1 ATATAAATAAA-AATAATAAATAA
13231276 ATATAAATAAAAATAATAATATAA
1 ATATAAATAAAAATAATAA-ATAA
* *
13231300 AT-TAAA-AGAAAAAAATAAAAAA
1 ATATAAATA-AAAATAATAAATAA
*
13231322 ATTTAAA
1 ATATAAA
13231329 ATTGAGTGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
22 8 0.17
23 32 0.70
24 6 0.13
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (23 bp):
ATATAAATAAAAATAATAAATAA
Found at i:13235329 original size:14 final size:14
Alignment explanation
Indices: 13235310--13235337 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13235300 TATAGTTGAT
13235310 AACTCTATTTCATA
1 AACTCTATTTCATA
13235324 AACTCTATTTCATA
1 AACTCTATTTCATA
13235338 GAGTTATTTG
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:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (14 bp):
AACTCTATTTCATA
Found at i:13235709 original size:17 final size:17
Alignment explanation
Indices: 13235678--13235718 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
13235668 ATTTTATGAT
13235678 GTTTTATTCTAAGTTTA
1 GTTTTATTCTAAGTTTA
13235695 GTTATTATT-TAAGTTTA
1 GTT-TTATTCTAAGTTTA
13235712 GTTTTAT
1 GTTTTAT
13235719 GTTTTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 14 0.61
18 5 0.22
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.61
Consensus pattern (17 bp):
GTTTTATTCTAAGTTTA
Found at i:13241351 original size:26 final size:27
Alignment explanation
Indices: 13241321--13241377 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
13241311 TTAAATTAGT
*
13241321 TATTAAGA-AATAAATTATATAAGTAA
1 TATTAAGATAATAAATTATATAAATAA
* *
13241347 TATT-AGATAATAATTTATTTAAATAA
1 TATTAAGATAATAAATTATATAAATAA
13241373 -ATTAA
1 TATTAA
13241378 TTAAGAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (27 bp):
TATTAAGATAATAAATTATATAAATAA
Found at i:13245868 original size:52 final size:51
Alignment explanation
Indices: 13245774--13245872 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 51
13245764 CATACATATA
*
13245774 TATACATACATATTAATTCTCTAGCCTAGGCATCATTATCTAGGCATACCT
1 TATACACACATATTAATTCTCTAGCCTAGGCATCATTATCTAGGCATACCT
* * * *
13245825 TATACACACATATATAGTTTTCTAGCCTAGG-TTCATCTGTCTAGGCAT
1 TATACACACATAT-TAATTCTCTAGCCTAGGCATCAT-TATCTAGGCAT
13245873 GTATCTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 16 0.39
52 25 0.61
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (51 bp):
TATACACACATATTAATTCTCTAGCCTAGGCATCATTATCTAGGCATACCT
Found at i:13247968 original size:42 final size:43
Alignment explanation
Indices: 13247856--13248011 Score: 226
Period size: 42 Copynumber: 3.7 Consensus size: 43
13247846 CAGCTCATGT
* * *
13247856 GCACTCCCTACTCGCACATAGCTAGGTCAGTAGCGGCTTATGC
1 GCACTCCCTACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
* * *
13247899 GCACTCCCTACTCGCACATAGCAGGGTCAGCATCGGCTGATGT
1 GCACTCCCTACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
*
13247942 GCACTCCC-ACTCGCAGATAGCTGGGTCAGCATCGGCTTATGC
1 GCACTCCCTACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
*
13247984 GCACT-CCTACTCGCACATAGCCGGGTCA
1 GCACTCCCTACTCGCACATAGCTGGGTCA
13248012 ATATCATCAT
Statistics
Matches: 100, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 2 0.02
42 53 0.53
43 45 0.45
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.21
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
Found at i:13247970 original size:85 final size:85
Alignment explanation
Indices: 13247843--13248011 Score: 259
Period size: 85 Copynumber: 2.0 Consensus size: 85
13247833 CTCCCATCAT
*
13247843 CATCAGCTCATGTGCACTCCCTACTCGCACATAGCTAGGTCAGTAGCGGCTTATGCGCACTCCCT
1 CATCAGCTCATGTGCACTCCCTACTCGCACATAGCTAGGTCAGCAGCGGCTTATGCGCACT-CCT
13247908 ACTCGCACATAGCAGGGTCAG
65 ACTCGCACATAGCAGGGTCAG
* * * * *
13247929 CATCGGCTGATGTGCACTCCC-ACTCGCAGATAGCTGGGTCAGCATCGGCTTATGCGCACTCCTA
1 CATCAGCTCATGTGCACTCCCTACTCGCACATAGCTAGGTCAGCAGCGGCTTATGCGCACTCCTA
*
13247993 CTCGCACATAGCCGGGTCA
66 CTCGCACATAGCAGGGTCA
13248012 ATATCATCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
84 22 0.29
85 35 0.46
86 19 0.25
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.22
Consensus pattern (85 bp):
CATCAGCTCATGTGCACTCCCTACTCGCACATAGCTAGGTCAGCAGCGGCTTATGCGCACTCCTA
CTCGCACATAGCAGGGTCAG
Found at i:13248061 original size:2 final size:2
Alignment explanation
Indices: 13248056--13248129 Score: 60
Period size: 2 Copynumber: 37.5 Consensus size: 2
13248046 CATATATTCG
* * * * * *
13248056 TA TA TA TA TA TG TA TA CA TA TA TA TA TG TA CA TA TA CA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
13248098 TA TG TA CA TA TA TA TA TA TA TA T- TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13248130 CAACATAACG
Statistics
Matches: 53, Mismatches: 18, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (2 bp):
TA
Found at i:13248117 original size:18 final size:18
Alignment explanation
Indices: 13248056--13248118 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
13248046 CATATATTCG
13248056 TATATATATATGT--ATA
1 TATATATATATGTACATA
*
13248072 CATATATATATGTACATA
1 TATATATATATGTACATA
* *
13248090 TACATGTATATGTACATA
1 TATATATATATGTACATA
13248108 TATATATATAT
1 TATATATATAT
13248119 ATTATGTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 12 0.31
18 27 0.69
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
TATATATATATGTACATA
Found at i:13252487 original size:79 final size:79
Alignment explanation
Indices: 13252339--13252487 Score: 194
Period size: 79 Copynumber: 1.9 Consensus size: 79
13252329 TTGACTAATT
* * * *
13252339 AAAATTTACTTATGCGTCATCCATTTTATCTCTAAAAAAAATTAAGATAATTAGAGATAATACCT
1 AAAATTTACCTATGAGTCATCCAATTTATCTCTAAAAAAAATTAAGATAATTAGAGATAAAACCT
13252404 AAATTAGATCAATC
66 AAATTAGATCAATC
* * * *
13252418 AAAATTTACCTGTGAGTTATCCAATTTATCTCT-AAATAAATTATGATAATTTAGAGATAAAATC
1 AAAATTTACCTATGAGTCATCCAATTTATCTCTAAAAAAAATTAAGATAA-TTAGAGATAAAA-C
13252482 C-AAATT
64 CTAAATT
13252488 TGGTCATCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
78 14 0.23
79 44 0.73
80 2 0.03
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (79 bp):
AAAATTTACCTATGAGTCATCCAATTTATCTCTAAAAAAAATTAAGATAATTAGAGATAAAACCT
AAATTAGATCAATC
Found at i:13252500 original size:57 final size:56
Alignment explanation
Indices: 13252436--13252549 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 56
13252426 CCTGTGAGTT
* *
13252436 ATCCAATTTATC-TCTAAATAAATTATGATAATTTAGAGATAAAATCCAAATTTGGTC
1 ATCCAATTTATCAT-TAAATAAATTAAGATAATTTAAAGATAAAAT-CAAATTTGGTC
*
13252493 ATCCAATTTATCATTAAATAAATTAAGATAATTTAAAGCTAAAATCAAATTTGGTC
1 ATCCAATTTATCATTAAATAAATTAAGATAATTTAAAGATAAAATCAAATTTGGTC
13252549 A
1 A
13252550 ATCAAAATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 12 0.23
57 40 0.75
58 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (56 bp):
ATCCAATTTATCATTAAATAAATTAAGATAATTTAAAGATAAAATCAAATTTGGTC
Found at i:13253583 original size:18 final size:17
Alignment explanation
Indices: 13253555--13253588 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13253545 TTTAGTTTAA
13253555 TTTTAAAAATTATTATT
1 TTTTAAAAATTATTATT
*
13253572 TTTTATAAAATTTTTAT
1 TTTTA-AAAATTATTAT
13253589 AATAACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAAATTATTATT
Found at i:13253697 original size:22 final size:22
Alignment explanation
Indices: 13253672--13253715 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13253662 TCTTCCAAAC
13253672 CATTTGACACACAATTAAAAAA
1 CATTTGACACACAATTAAAAAA
* *
13253694 CATTTGATACACAGTTAAAAAA
1 CATTTGACACACAATTAAAAAA
13253716 GAAAAGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (22 bp):
CATTTGACACACAATTAAAAAA
Found at i:13260559 original size:32 final size:32
Alignment explanation
Indices: 13260521--13260600 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
13260511 CCTAATAGAC
** *
13260521 ATACTAAAACACATTAACTTTTTAATAGAGTT
1 ATACTAAAACACATTAACTTCCTAATAAAGTT
* ** *
13260553 ATACTAAAACATACCAAGTTCCTAATAAAGTT
1 ATACTAAAACACATTAACTTCCTAATAAAGTT
13260585 ATACTAAAACACATTA
1 ATACTAAAACACATTA
13260601 GCAAACAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.31
Consensus pattern (32 bp):
ATACTAAAACACATTAACTTCCTAATAAAGTT
Found at i:13264626 original size:33 final size:35
Alignment explanation
Indices: 13264559--13264625 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
13264549 TCAATAATTA
*
13264559 TCTTAATAAATATTTTCTAGTTAAGACAATTTTTG
1 TCTTAATAAATATTTTCTAATTAAGACAATTTTTG
13264594 TCTTAA-AAATA-TTTCTATATTAAGACAATTTT
1 TCTTAATAAATATTTTCTA-ATTAAGACAATTTT
13264626 GACTTGCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 6 0.20
34 18 0.60
35 6 0.20
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (35 bp):
TCTTAATAAATATTTTCTAATTAAGACAATTTTTG
Found at i:13269257 original size:39 final size:40
Alignment explanation
Indices: 13269200--13269278 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 40
13269190 CATTGTGAAG
* *
13269200 ACACTAATTATGGTGAGGTTAG-AAACCCCACTAAGGTGA
1 ACACCAATTATGGCGAGGTTAGAAAACCCCACTAAGGTGA
* * *
13269239 ACACCAATTTTGGCGAGGTTCGAAAACCCCTCTAAGGTGA
1 ACACCAATTATGGCGAGGTTAGAAAACCCCACTAAGGTGA
13269279 GAAATAGCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 18 0.53
40 16 0.47
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (40 bp):
ACACCAATTATGGCGAGGTTAGAAAACCCCACTAAGGTGA
Found at i:13274208 original size:39 final size:40
Alignment explanation
Indices: 13274154--13274230 Score: 122
Period size: 39 Copynumber: 1.9 Consensus size: 40
13274144 CATTGTGAAG
*
13274154 ACACTAACTATGGCGATGTTAG-AAACCCCACTAAGGTCA
1 ACACTAACTATGGCGAGGTTAGAAAACCCCACTAAGGTCA
13274193 ACACTAATCT-TGGCGAGGTTAGAAAACCCCACTAAGGT
1 ACACTAA-CTATGGCGAGGTTAGAAAACCCCACTAAGGT
13274231 TAAAATTAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 18 0.51
40 17 0.49
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (40 bp):
ACACTAACTATGGCGAGGTTAGAAAACCCCACTAAGGTCA
Found at i:13279119 original size:2 final size:2
Alignment explanation
Indices: 13279112--13279160 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
13279102 AATTAAATTA
13279112 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13279154 AG AG AG A
1 AG AG AG A
13279161 TAAGATTTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13279288 original size:16 final size:17
Alignment explanation
Indices: 13279263--13279295 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13279253 TTTATTGCGA
*
13279263 TTTAGTTTTATTTAATT
1 TTTAGTTTTAATTAATT
13279280 TTTAG-TTTAATTAATT
1 TTTAGTTTTAATTAATT
13279296 GATTTCGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTAGTTTTAATTAATT
Found at i:13280232 original size:24 final size:24
Alignment explanation
Indices: 13280200--13280248 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
13280190 TTTGATGAAG
13280200 TATTATGTCTATTGTGCAACAATC
1 TATTATGTCTATTGTGCAACAATC
13280224 TATTATGTCTATTGTGCAACAATC
1 TATTATGTCTATTGTGCAACAATC
13280248 T
1 T
13280249 TTCATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (24 bp):
TATTATGTCTATTGTGCAACAATC
Found at i:13280584 original size:71 final size:73
Alignment explanation
Indices: 13280423--13280608 Score: 211
Period size: 72 Copynumber: 2.6 Consensus size: 73
13280413 ATAAAATCAA
* ** * * *
13280423 TAAAGTTTTAGTCGACCAAAAGTT-ACTTTAATCGATTAAAACAATTCTGTTTCAAATTAGGGGT
1 TAAAGTTTTAATCGATTAAAA-TTCATTTTAATCGATTAAAACAATTATATTTCAAATTAGGGGT
* *
13280487 TAATGTCAG
65 CAAAGTCAG
*
13280496 TAAAGTTTTAATTGATTAAAATTCA-TTTAA-CTGATTAAAACAATTATATTTCAAA-TA-GGGT
1 TAAAGTTTTAATCGATTAAAATTCATTTTAATC-GATTAAAACAATTATATTTCAAATTAGGGGT
13280557 CCAAAGTCAG
65 -CAAAGTCAG
* *
13280567 TAACGTTTTAATCGATTAAAGTTCATTTTAATCGATTAAAAC
1 TAAAGTTTTAATCGATTAAAATTCATTTTAATCGATTAAAAC
13280609 TATTTTGTGT
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
70 4 0.04
71 32 0.33
72 42 0.43
73 19 0.20
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (73 bp):
TAAAGTTTTAATCGATTAAAATTCATTTTAATCGATTAAAACAATTATATTTCAAATTAGGGGTC
AAAGTCAG
Found at i:13287360 original size:39 final size:39
Alignment explanation
Indices: 13287317--13287400 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
13287307 CAACGAGATT
* * **
13287317 CAGCGAAATTGTGACCCAGAAACAGAATGTTTCTCGTTG
1 CAGCGAAATTGTAACCCAGAAACAGAAAGTTTCTCACTG
*
13287356 CAGCGAAATTGTAACCTAGAAACAGAAAGTTTCTCACTG
1 CAGCGAAATTGTAACCCAGAAACAGAAAGTTTCTCACTG
13287395 CAGCGA
1 CAGCGA
13287401 GAATGAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (39 bp):
CAGCGAAATTGTAACCCAGAAACAGAAAGTTTCTCACTG
Found at i:13287788 original size:43 final size:43
Alignment explanation
Indices: 13287740--13287847 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
13287730 TCACTAGCTC
* *** *
13287740 ATGCGCACTCCCTACTCGCGCATGGTTGGGTCATCAC-CAGG-TT
1 ATGCGCACTCCCTACTCGCACAAAATCGGGTCATC-CTC-GGCTT
*
13287783 ATGCGCATTCCCTACTCGCACAAAATCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACAAAATCGGGTCATCCTCGGCTT
*
13287826 ATGCGCACTCCCTACTTGCACA
1 ATGCGCACTCCCTACTCGCACA
13287848 TAGCCGAGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.05
43 52 0.95
ACGTcount: A:0.19, C:0.35, G:0.20, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACAAAATCGGGTCATCCTCGGCTT
Found at i:13289217 original size:19 final size:19
Alignment explanation
Indices: 13289193--13289230 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
13289183 ACTTATAAAC
13289193 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
13289212 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
13289231 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:13293171 original size:49 final size:49
Alignment explanation
Indices: 13293099--13293218 Score: 152
Period size: 49 Copynumber: 2.4 Consensus size: 49
13293089 CATTCATCAT
* *
13293099 CATAGCTGGGTTATCATCATCATCAGCTTATACACACTCTCTACTCGCA
1 CATAGCTGGGTCATCATCATCATCAGCTTATACACACTCCCTACTCGCA
* *** *
13293148 CATAGCTGGGTCATCATCATCATCGGCTTATGTGCACTCCCTACTTGCA
1 CATAGCTGGGTCATCATCATCATCAGCTTATACACACTCCCTACTCGCA
*
13293197 CATAGCCGGGTCAAT-ATCATCA
1 CATAGCTGGGTC-ATCATCATCA
13293219 CACAACATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 60 0.97
50 2 0.03
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (49 bp):
CATAGCTGGGTCATCATCATCATCAGCTTATACACACTCCCTACTCGCA
Found at i:13293602 original size:41 final size:42
Alignment explanation
Indices: 13293544--13293627 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 42
13293534 TCACACACAC
*
13293544 ACAATATCACTACCAACC-CA-TTGCATAAATACATTTCTAA
1 ACAATATCACTACCAACCTAATTTGCATAAATACATTTCTAA
13293584 ANCAATATCACTACCAACCTAATTTGCATAAATACATTTCTAA
1 A-CAATATCACTACCAACCTAATTTGCATAAATACATTTCTAA
13293627 A
1 A
13293628 AGCTATTTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 1 0.03
41 17 0.43
42 1 0.03
43 21 0.52
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.29
Consensus pattern (42 bp):
ACAATATCACTACCAACCTAATTTGCATAAATACATTTCTAA
Found at i:13296884 original size:18 final size:18
Alignment explanation
Indices: 13296858--13296895 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
13296848 TGAAATTGAG
13296858 AAAAAGAAACAAA-AAAA
1 AAAAAGAAACAAAGAAAA
*
13296875 AAAAAGGAAAGAAAGAAAA
1 AAAAA-GAAACAAAGAAAA
13296894 AA
1 AA
13296896 GAAAAAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAGAAACAAAGAAAA
Found at i:13296887 original size:22 final size:22
Alignment explanation
Indices: 13296860--13296902 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13296850 AAATTGAGAA
13296860 AAAGAAACAAAAAAAAAAAAGG
1 AAAGAAACAAAAAAAAAAAAGG
* *
13296882 AAAGAAAGAAAAAAGAAAAAG
1 AAAGAAACAAAAAAAAAAAAG
13296903 ATTGAAGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAGAAACAAAAAAAAAAAAGG
Found at i:13296902 original size:17 final size:17
Alignment explanation
Indices: 13296858--13296903 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
13296848 TGAAATTGAG
13296858 AAAAAGAAACAA-AAAAA
1 AAAAAGAAA-AAGAAAAA
* *
13296875 AAAAAG-GAAAGAAAGA
1 AAAAAGAAAAAGAAAAA
13296891 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
13296904 TTGAAGTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.08
16 11 0.46
17 11 0.46
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAA
Found at i:13297261 original size:10 final size:10
Alignment explanation
Indices: 13297235--13297278 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
13297225 TTAATTTAAG
*
13297235 TTATTTTAGT
1 TTATTTTACT
13297245 TTAATTTTACT
1 TT-ATTTTACT
*
13297256 TTATTTTGCT
1 TTATTTTACT
*
13297266 TTAATTTACT
1 TTATTTTACT
13297276 TTA
1 TTA
13297279 AGAAAAGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.66
Consensus pattern (10 bp):
TTATTTTACT
Found at i:13297275 original size:20 final size:20
Alignment explanation
Indices: 13297225--13297278 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
13297215 TATTGAGTAA
**
13297225 TTAATTTAAGTTATTTTAGT
1 TTAATTTACTTTATTTTAGT
13297245 TTAATTTTACTTTATTTT-GCT
1 TTAA-TTTACTTTATTTTAG-T
13297266 TTAATTTACTTTA
1 TTAATTTACTTTA
13297279 AGAAAAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (20 bp):
TTAATTTACTTTATTTTAGT
Found at i:13303736 original size:21 final size:21
Alignment explanation
Indices: 13303693--13303747 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
13303683 TTAGTTGGAC
* *
13303693 GAAAGAAGAAAG-GAAAGAAA
1 GAAAGGAGAAAGAAAAAGAAA
*
13303713 GAAAGGAGAAAGAAAAAGAGA
1 GAAAGGAGAAAGAAAAAGAAA
13303734 GAAAGGA-AAA-AAAA
1 GAAAGGAGAAAGAAAA
13303748 GCTTGGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.13
20 14 0.45
21 13 0.42
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
GAAAGGAGAAAGAAAAAGAAA
Found at i:13310439 original size:13 final size:13
Alignment explanation
Indices: 13310421--13310459 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
13310411 CATTACAATA
*
13310421 AGCAAGATGCCAT
1 AGCAAGGTGCCAT
13310434 AGCAAGGTGCCAT
1 AGCAAGGTGCCAT
*
13310447 AGAAAGGTGCCAT
1 AGCAAGGTGCCAT
13310460 GCATTCAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (13 bp):
AGCAAGGTGCCAT
Found at i:13316501 original size:22 final size:21
Alignment explanation
Indices: 13316458--13316502 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
13316448 ATTCTCGATT
* *
13316458 CAGCAAGATTCATTCTCGCTG
1 CAGCAAGATCCATTCTCACTG
*
13316479 CAGCAAGAATCCATTTTCACTG
1 CAGCAAG-ATCCATTCTCACTG
13316501 CA
1 CA
13316503 ACGAGAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (21 bp):
CAGCAAGATCCATTCTCACTG
Found at i:13317846 original size:21 final size:21
Alignment explanation
Indices: 13317816--13317855 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13317806 AGCTTTATAT
*
13317816 GTTGTGTTAA-TTAAGACAAAA
1 GTTGTCTTAACTT-AGACAAAA
13317837 GTTGTCTTAACTTAGACAA
1 GTTGTCTTAACTTAGACAA
13317856 GAATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (21 bp):
GTTGTCTTAACTTAGACAAAA
Found at i:13317869 original size:50 final size:51
Alignment explanation
Indices: 13317811--13318004 Score: 180
Period size: 50 Copynumber: 3.7 Consensus size: 51
13317801 ATGGTAGCTT
* * *
13317811 TATATGTTGTGTTAATT-AAGACAAAAGTTGTCTTAACTTAGACAAGAATT
1 TATATGTTGTCTTAATTAAAGACAAAAGTTGTCTTAATTTAGACAAGAATA
* * *
13317861 TATTTGTTGTCTTAATTTAGACAAGAAAACAAAAGTTATCTTAATTTAGACAA-AGTA
1 TATATGTTGTCTTAA-TT--A-AAG---ACAAAAGTTGTCTTAATTTAGACAAGAATA
* * *
13317918 CATATGTTGTCTTAATTAAATACAAGAGTTGTCTTAATTTAGACAATG-ATA
1 TATATGTTGTCTTAATTAAAGACAAAAGTTGTCTTAATTTAGACAA-GAATA
* * *
13317969 TATATGTTGTCTTAATT-AAGATAAGAGTTGCCTTAA
1 TATATGTTGTCTTAATTAAAGACAAAAGTTGTCTTAA
13318005 ATTAAGATAA
Statistics
Matches: 118, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
50 52 0.44
51 20 0.17
53 2 0.02
54 1 0.01
55 3 0.03
56 2 0.02
57 15 0.13
58 23 0.19
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (51 bp):
TATATGTTGTCTTAATTAAAGACAAAAGTTGTCTTAATTTAGACAAGAATA
Found at i:13317998 original size:21 final size:22
Alignment explanation
Indices: 13317974--13318014 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13317964 TGATATATAT
*
13317974 GTTGTCTT-AATTAAGATAAGA
1 GTTGCCTTAAATTAAGATAAGA
13317995 GTTGCCTTAAATTAAGATAA
1 GTTGCCTTAAATTAAGATAA
13318015 TGTTGAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (22 bp):
GTTGCCTTAAATTAAGATAAGA
Found at i:13318019 original size:21 final size:20
Alignment explanation
Indices: 13317972--13318019 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
13317962 AATGATATAT
*
13317972 ATGTTGTCTTAATTAAGATA
1 ATGTTGCCTTAATTAAGATA
*
13317992 AGAGTTGCCTTAAATTAAGATA
1 A-TGTTGCCTT-AATTAAGATA
13318014 ATGTTG
1 ATGTTG
13318020 AAGGACTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 11 0.48
22 11 0.48
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (20 bp):
ATGTTGCCTTAATTAAGATA
Found at i:13323547 original size:107 final size:107
Alignment explanation
Indices: 13323361--13323566 Score: 394
Period size: 107 Copynumber: 1.9 Consensus size: 107
13323351 AGCTCATTGC
* *
13323361 TATATTTGACTATTAGTAGATCGGATATTATCTTTAATGTAAGGTTATATGCTCGATTTTAATCA
1 TATATTTGACTACTAGTAGATCGGATATTAGCTTTAATGTAAGGTTATATGCTCGATTTTAATCA
13323426 TCCTTTAGAGAATCCCAATTAAGTGCAACAAAGAAATGTTGT
66 TCCTTTAGAGAATCCCAATTAAGTGCAACAAAGAAATGTTGT
13323468 TATATTTGACTACTAGTAGATCGGATATTAGCTTTAATGTAAGGTTATATGCTCGATTTTAATCA
1 TATATTTGACTACTAGTAGATCGGATATTAGCTTTAATGTAAGGTTATATGCTCGATTTTAATCA
13323533 TCCTTTAGAGAATCCCAATTAAGTGCAACAAAGA
66 TCCTTTAGAGAATCCCAATTAAGTGCAACAAAGA
13323567 GAATCTTTAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 97 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (107 bp):
TATATTTGACTACTAGTAGATCGGATATTAGCTTTAATGTAAGGTTATATGCTCGATTTTAATCA
TCCTTTAGAGAATCCCAATTAAGTGCAACAAAGAAATGTTGT
Found at i:13324771 original size:35 final size:35
Alignment explanation
Indices: 13324696--13324786 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
13324686 CATACAAGGA
** ** *
13324696 AATATCATTATGTGCACTCCCTACTGGCACATTTC
1 AATATCATCGTGTGCACTCCCTACTCACACACTTC
*
13324731 TATATCATCGTGTGCACTCCCTACTCACACACTTC
1 AATATCATCGTGTGCACTCCCTACTCACACACTTC
*
13324766 AATATCA-CTGTATGCACTCCC
1 AATATCATC-GTGTGCACTCCC
13324787 GCCCACATCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 1 0.02
35 46 0.98
ACGTcount: A:0.25, C:0.33, G:0.10, T:0.32
Consensus pattern (35 bp):
AATATCATCGTGTGCACTCCCTACTCACACACTTC
Found at i:13325520 original size:36 final size:36
Alignment explanation
Indices: 13325480--13325548 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
13325470 GCTTTTATTC
* *
13325480 TTCCTTTCT-CTTTTTTTCTTTCTTCTTCTCCTTCCT
1 TTCCTTTCTCCTTTCTTTCTTTCCT-TTCTCCTTCCT
13325516 TTCCTTTCTCCTTTCTTTCTTTCCTTTCTCCTT
1 TTCCTTTCTCCTTTCTTTCTTTCCTTTCTCCTT
13325549 TCTTCCAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 17 0.57
37 13 0.43
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (36 bp):
TTCCTTTCTCCTTTCTTTCTTTCCTTTCTCCTTCCT
Found at i:13325539 original size:20 final size:20
Alignment explanation
Indices: 13325480--13325552 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
13325470 GCTTTTATTC
*
13325480 TTCCTTTCT-CTTTTTTTCT
1 TTCCTTTCTCCTTTCTTTCT
*
13325499 TTCTTCTTCTCC-TTC---CT
1 TTCCT-TTCTCCTTTCTTTCT
13325516 TTCCTTTCTCCTTTCTTTCT
1 TTCCTTTCTCCTTTCTTTCT
13325536 TTCCTTTCTCCTTTCTT
1 TTCCTTTCTCCTTTCTT
13325553 CCAACCGACC
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 6 0.13
17 9 0.20
19 4 0.09
20 25 0.56
21 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (20 bp):
TTCCTTTCTCCTTTCTTTCT
Found at i:13325552 original size:16 final size:16
Alignment explanation
Indices: 13325494--13325538 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
13325484 TTTCTCTTTT
*
13325494 TTTCTTTCTTCTTCTCC
1 TTTCTTTCCT-TTCTCC
*
13325511 TTCCTTTCCTTTCTCC
1 TTTCTTTCCTTTCTCC
13325527 TTTCTTT-CTTTC
1 TTTCTTTCCTTTC
13325539 CTTTCTCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 5 0.20
16 12 0.48
17 8 0.32
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCTTTCCTTTCTCC
Found at i:13328516 original size:16 final size:17
Alignment explanation
Indices: 13328474--13328516 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
13328464 AATACCTCTA
* *
13328474 CTTTTCTTTTCCTAATT
1 CTTTTCTTTCCCTAATC
13328491 CTTTTCTTTCCCTAATC
1 CTTTTCTTTCCCTAATC
13328508 CTTTT-TTTC
1 CTTTTCTTTC
13328517 TCTCTTTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.09, C:0.28, G:0.00, T:0.63
Consensus pattern (17 bp):
CTTTTCTTTCCCTAATC
Found at i:13332633 original size:30 final size:28
Alignment explanation
Indices: 13332599--13332658 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
13332589 TTTTTGAAAT
* *
13332599 TTACACTTTTGCCCCCATAAAAGTGAAAAA
1 TTACACTTTTG--CCCAAAAAACTGAAAAA
*
13332629 TTACATTTTTGCCCAAAAAACTGAAAAA
1 TTACACTTTTGCCCAAAAAACTGAAAAA
13332657 TT
1 TT
13332659 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 17 0.63
30 10 0.37
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (28 bp):
TTACACTTTTGCCCAAAAAACTGAAAAA
Found at i:13340876 original size:21 final size:21
Alignment explanation
Indices: 13340843--13340882 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13340833 ATATAAACAA
*
13340843 AACAACAACAAAAAAAATACT
1 AACAAAAACAAAAAAAATACT
* *
13340864 AACAAAAAGAAAACAAATA
1 AACAAAAACAAAAAAAATA
13340883 AAGAACGAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.75, C:0.15, G:0.03, T:0.07
Consensus pattern (21 bp):
AACAAAAACAAAAAAAATACT
Found at i:13342193 original size:2 final size:2
Alignment explanation
Indices: 13342186--13342220 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
13342176 TAATATACAA
*
13342186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13342221 ATAAAACTAN
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13345946 original size:323 final size:322
Alignment explanation
Indices: 13345359--13346007 Score: 892
Period size: 323 Copynumber: 2.0 Consensus size: 322
13345349 AAACCAGGGG
* *
13345359 CAACAAAGCCTCCTTAACTGCATTTTCCCTCAAAGAATCCTTTTGGAGAAGAACCCCTCCTTAAA
1 CAACAAAGCCTCCTTAACTCCATTTTCCCTCAAAGAATCCTTTTGGAGAAGAACCACTCCTTAAA
* * * * *
13345424 CAAGCATTGCTAACCCAAATCGTGGCACAAAAAACATAACATTACGAAAAGAGAGGCGAAGAAGC
66 CAAACATTGCTAACCCAAATCATGGCACAAAAAACATAACACTAAGAAAAGAGAGGCAAAGAAGC
* * * *
13345489 TGTTGTGTCACAAAAAAAAAATCCCCGAAGAAACTTAACATGGAACAAAGCAACCTTTCTCCAAG
131 TGTTATGTCACAAAAAAAAAATCCCCAAAGAAACTAAACATGGAACAAAGCAACCTTTCTCAAAG
* * * *
13345554 GAAAGAGGACCTCAAGCTTCATGAGCCCTCCTTATTCCATCAGCACACCACTCACAATCCCAGGA
196 GAAAGAGGACCTCAAGCTTCATAAGCCCTCCTCATTCCATCAACACACCACTCACAATCCCAAGA
*
13345619 ACATATGACCACCTACCTCTTGCCTTAAAAAAGTCAACCCCTTTTCCCCTCAACCCTTATAC
261 ACATATGACCACCTACCTATTGCCTTAAAAAAGTCAACCCCTTTTCCCCTCAACCCTTATAC
* * *
13345681 CAACAAAGCCTTCTTAACTCCTTTTTCCCTCAGAGAATCCTTTT-G-G-AGAACCACTCCTTAAA
1 CAACAAAGCCTCCTTAACTCCATTTTCCCTCAAAGAATCCTTTTGGAGAAGAACCACTCCTTAAA
* * * * *
13345743 CAAACATTGGTGACCCACATCATGGCATAAAAAACATAACACTAAGAAAAGAGAGGCAAAGAAGT
66 CAAACATTGCTAACCCAAATCATGGCACAAAAAACATAACACTAAGAAAAGAGAGGCAAAGAAGC
* * * *
13345808 TGTTATGTCACAAAAAAGACAATCTCTAAAGAAACTCAACAGCATGGAACAAAGCAATCTTTCTC
131 TGTTATGTCACAAAAAA-AAAATCCCCAAAGAAACT-AA-A-CATGGAACAAAGCAACCTTTCTC
*
13345873 AAAAGGAAA-AGGACCTCAAGCTTCATAAGCCCTCCTCGTTCCATCAACACACCACTCACAATCC
192 -AAAGGAAAGAGGACCTCAAGCTTCATAAGCCCTCCTCATTCCATCAACACACCACTCACAATCC
* * * ** * **
13345937 CAAGAACATATGACCACCTCCCTATTGCCTTAAAAAAGTTAGCCTTTTTTCCCTTCGGCCCTTAT
256 CAAGAACATATGACCACCTACCTATTGCCTTAAAAAAGTCAACCCCTTTTCCCCTCAACCCTTAT
13346002 AC
321 AC
13346004 CAAC
1 CAAC
13346008 CCTCACAACC
Statistics
Matches: 285, Mismatches: 37, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
319 86 0.30
320 15 0.05
321 2 0.01
322 41 0.14
323 134 0.47
324 7 0.02
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.22
Consensus pattern (322 bp):
CAACAAAGCCTCCTTAACTCCATTTTCCCTCAAAGAATCCTTTTGGAGAAGAACCACTCCTTAAA
CAAACATTGCTAACCCAAATCATGGCACAAAAAACATAACACTAAGAAAAGAGAGGCAAAGAAGC
TGTTATGTCACAAAAAAAAAATCCCCAAAGAAACTAAACATGGAACAAAGCAACCTTTCTCAAAG
GAAAGAGGACCTCAAGCTTCATAAGCCCTCCTCATTCCATCAACACACCACTCACAATCCCAAGA
ACATATGACCACCTACCTATTGCCTTAAAAAAGTCAACCCCTTTTCCCCTCAACCCTTATAC
Found at i:13347862 original size:40 final size:40
Alignment explanation
Indices: 13347807--13347886 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
13347797 AGCAATGTCG
*
13347807 GAGCATTACTTACAATCTCATACTTTTTCTTAGAAGACAA
1 GAGCATTACTTACAATCTCATACTTTTTCTTAGAAAACAA
*
13347847 GAGCATTACTTACAATCTCATATTTTTTCTTAGAAAACAA
1 GAGCATTACTTACAATCTCATACTTTTTCTTAGAAAACAA
13347887 ACTCATTCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (40 bp):
GAGCATTACTTACAATCTCATACTTTTTCTTAGAAAACAA
Found at i:13354726 original size:28 final size:29
Alignment explanation
Indices: 13354695--13354797 Score: 140
Period size: 29 Copynumber: 3.6 Consensus size: 29
13354685 GGCAGCTTTT
13354695 ACAT-TTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
13354723 ACATGTTTTGTCTTAATTTAGACAAG-AA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* * *
13354751 ACTAT-CTATGTCTCAATTTAGACAAGAAA
1 AC-ATGTTTTGTCTTAATTTAGACAAGAAA
*
13354780 ATATGTTTTGTCTTAATT
1 ACATGTTTTGTCTTAATT
13354798 AAAGATAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 28 0.44
29 36 0.56
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (29 bp):
ACATGTTTTGTCTTAATTTAGACAAGAAA
Found at i:13361525 original size:19 final size:18
Alignment explanation
Indices: 13361504--13361552 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 18
13361494 AAAAATTAAA
13361504 AAATATTAATATTTAACT
1 AAATATTAATATTTAACT
*
13361522 AAA-A--AAT-GTTAACTT
1 AAATATTAATATTTAAC-T
13361537 AAATATTAATATTTAA
1 AAATATTAATATTTAA
13361553 ATTATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 9
0.69 0.06 0.26
Matches are distributed among these distances:
14 5 0.21
15 7 0.29
16 1 0.04
17 1 0.04
18 6 0.25
19 4 0.17
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
AAATATTAATATTTAACT
Found at i:13365647 original size:38 final size:38
Alignment explanation
Indices: 13365591--13365663 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
13365581 TGAGGTAGAA
* * **
13365591 AATATCACTAGGATTATGTAGCTGATAGTGGGGCAGGG
1 AATACCACTAGAATTATGTAGCCAATAGTGGGGCAGGG
13365629 AATACCACTAGAATTATGTAGCCAATAGTGGGGCA
1 AATACCACTAGAATTATGTAGCCAATAGTGGGGCA
13365664 TTGAAAGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.25
Consensus pattern (38 bp):
AATACCACTAGAATTATGTAGCCAATAGTGGGGCAGGG
Found at i:13368161 original size:30 final size:31
Alignment explanation
Indices: 13368095--13368161 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
13368085 ACATTGTGAA
* *
13368095 AGGTTATACCTTAACCATTAAAAGGTAGTGT
1 AGGTTATACCTTAACCATAAAAAGGTAGAGT
*
13368126 TGGTTATACCTTAACCATAAAAAGGTAGAG-
1 AGGTTATACCTTAACCATAAAAAGGTAGAGT
13368156 AGGTTA
1 AGGTTA
13368162 AACTTGATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (31 bp):
AGGTTATACCTTAACCATAAAAAGGTAGAGT
Found at i:13368520 original size:20 final size:20
Alignment explanation
Indices: 13368495--13368534 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
13368485 ACTCTAACAA
*
13368495 AGACAAGTATCGATACCTAG
1 AGACAAATATCGATACCTAG
*
13368515 AGACAAATATTGATACCTAG
1 AGACAAATATCGATACCTAG
13368535 TGACCGTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (20 bp):
AGACAAATATCGATACCTAG
Found at i:13372586 original size:18 final size:18
Alignment explanation
Indices: 13372565--13372604 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13372555 CAAACACAAC
13372565 CTTTTCTTCAACTTT-ACA
1 CTTTTCTTCAA-TTTAACA
*
13372583 CTTTTCTTCTATTTAACA
1 CTTTTCTTCAATTTAACA
13372601 CTTT
1 CTTT
13372605 ATTTTCTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.20, C:0.25, G:0.00, T:0.55
Consensus pattern (18 bp):
CTTTTCTTCAATTTAACA
Found at i:13375545 original size:20 final size:20
Alignment explanation
Indices: 13375520--13375565 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
13375510 CTTCTAAACC
13375520 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
13375540 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
13375560 TCAAAT
1 TCAAAT
13375566 GGGGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:13382565 original size:43 final size:43
Alignment explanation
Indices: 13382502--13382609 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
13382492 ATATGGACTC
* ** *
13382502 AGTTATGTGCGAGTAAGGAGTGCGTATAAGCCGATGATGACCT
1 AGTTATGTGCGAGTAGGGAGTGCACATAAACCGATGATGACCT
* *
13382545 -GATTATGTGTGAGTAGGGAGTGCACATAAACCGGTGATGACCT
1 AG-TTATGTGCGAGTAGGGAGTGCACATAAACCGATGATGACCT
**
13382588 AGCCATGTGCGAGTAGGGAGTG
1 AGTTATGTGCGAGTAGGGAGTG
13382610 TGCATGAGCT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.02
43 52 0.96
44 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (43 bp):
AGTTATGTGCGAGTAGGGAGTGCACATAAACCGATGATGACCT
Found at i:13386057 original size:13 final size:13
Alignment explanation
Indices: 13386039--13386063 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13386029 GGAAAATGAG
13386039 ATTTTATAAAATA
1 ATTTTATAAAATA
13386052 ATTTTATAAAAT
1 ATTTTATAAAAT
13386064 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:13390640 original size:18 final size:20
Alignment explanation
Indices: 13390603--13390643 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
13390593 ACTCAACTCC
13390603 TTTCATACAACTTCAAGTAA
1 TTTCATACAACTTCAAGTAA
*
13390623 TTTCATAC-A-TTCATGTAA
1 TTTCATACAACTTCAAGTAA
13390641 TTT
1 TTT
13390644 TTTTTCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTCATACAACTTCAAGTAA
Found at i:13398504 original size:20 final size:19
Alignment explanation
Indices: 13398475--13398524 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
13398465 CTTATTTTGT
13398475 TTATTTATTTATATTAAAC
1 TTATTTATTTATATTAAAC
* *
13398494 TTATCTTATTTATCTTAAAT
1 TTAT-TTATTTATATTAAAC
13398514 TTATTT-TTTAT
1 TTATTTATTTAT
13398525 TTTTATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.18
19 6 0.21
20 17 0.61
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTATTTATATTAAAC
Found at i:13399254 original size:18 final size:17
Alignment explanation
Indices: 13399213--13399245 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
13399203 TACTAGAAGT
13399213 AAAAT-AATAAAAAAAG
1 AAAATAAATAAAAAAAG
13399229 AAAATAAATAATAAAAA
1 AAAATAAATAA-AAAAA
13399246 TAATATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATAAATAAAAAAAG
Found at i:13400299 original size:47 final size:47
Alignment explanation
Indices: 13400227--13400572 Score: 194
Period size: 47 Copynumber: 7.2 Consensus size: 47
13400217 CTACACAACT
* * * * *
13400227 TTGGAAAAAACTTTTCATCTTTAAATGTGGCTACACAACTTAAAATAA
1 TTGG-AAAAGCTTTTCAACTCTAAATGAGGCTATACAACTTAAAATAA
* * *
13400275 TTGGAAAAGCTTTTCAGCTCTAAATGAGGCTATAAAACTTAAAATGA
1 TTGGAAAAGCTTTTCAACTCTAAATGAGGCTATACAACTTAAAATAA
* * *
13400322 TTGGAAAAGCTCCTT-AACTCTAAATGAGGCTATGCAATTTAAAATAA
1 TTGGAAAAGCT-TTTCAACTCTAAATGAGGCTATACAACTTAAAATAA
** * * ** **
13400369 TTGGAAAAGCTCATCATCT-TAAAATGAAGCTACGCAACTTAAAAATGC
1 TTGGAAAAGCTTTTCAACTCT-AAATGAGGCTATACAACTT-AAAATAA
* ** * * * ** *
13400417 TTGGAAAAACTCCTCATCTTTAAATGAGACTATACAACTTTTTTTCTTCAATGA
1 TTGGAAAAGCTTTTCAACTCTAAATGAGGCTATACAAC------T-TAAAATAA
* * * * *
13400471 TTTGAAAAGCTCTTT-ATCTCTAAAGGAGGCTATATAACTTAAAATGA
1 TTGGAAAAGCT-TTTCAACTCTAAATGAGGCTATACAACTTAAAATAA
* * ** * * * *
13400518 TTAGAAAATCTCCTCATCTCTAAATGAGGTTATGCAACTTAAAATGA
1 TTGGAAAAGCTTTTCAACTCTAAATGAGGCTATACAACTTAAAATAA
13400565 TTGGAAAA
1 TTGGAAAA
13400573 ACTCATCATT
Statistics
Matches: 236, Mismatches: 48, Indels: 29
0.75 0.15 0.09
Matches are distributed among these distances:
46 4 0.02
47 154 0.65
48 42 0.18
49 1 0.00
54 33 0.14
55 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (47 bp):
TTGGAAAAGCTTTTCAACTCTAAATGAGGCTATACAACTTAAAATAA
Found at i:13413678 original size:20 final size:20
Alignment explanation
Indices: 13413649--13413691 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
13413639 ATTAGGTTCC
13413649 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
13413669 TTTTATGTTATTCCTTTTAA
1 TTTTAAGTTATTCATTTTAA
13413689 TTT
1 TTT
13413692 GGTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:13414761 original size:14 final size:14
Alignment explanation
Indices: 13414742--13414768 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13414732 TTGGTTTTAA
13414742 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
13414756 TTTTAGTTAATTA
1 TTTTAGTTAATTA
13414769 ATAAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:13420438 original size:3 final size:3
Alignment explanation
Indices: 13420432--13420463 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
13420422 TTTTTTTACT
*
13420432 TTA TTA TGA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13420464 TTAATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:13422922 original size:3 final size:3
Alignment explanation
Indices: 13422916--13422940 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13422906 TGTTTTCGAA
13422916 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
13422941 TTTTGAGATA
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):
AAT
Found at i:13425341 original size:14 final size:14
Alignment explanation
Indices: 13425322--13425348 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13425312 TTGGTTTTAA
13425322 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
13425336 TTTTAGTTAATTA
1 TTTTAGTTAATTA
13425349 ATAAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:13426970 original size:2 final size:2
Alignment explanation
Indices: 13426963--13426992 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13426953 CTAGAGAACA
13426963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13426993 CTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13435818 original size:37 final size:37
Alignment explanation
Indices: 13435777--13435863 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
13435767 AAATGTTTAG
*
13435777 TTGATACTACTTGGT-ATTGCTTGATGATGCTTAATGA
1 TTGATAATACTTGGTAATT-CTTGATGATGCTTAATGA
*
13435814 TTGATAATGCTTGGTAATTCTTGATGATGCTTAATGA
1 TTGATAATACTTGGTAATTCTTGATGATGCTTAATGA
* *
13435851 ATGATAATGCTTG
1 TTGATAATACTTG
13435864 ATGATGCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 43 0.93
38 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (37 bp):
TTGATAATACTTGGTAATTCTTGATGATGCTTAATGA
Found at i:13435848 original size:27 final size:27
Alignment explanation
Indices: 13435818--13435889 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
13435808 TAATGATTGA
* * *
13435818 TAATGCTTGGTAATTCTTGATGATGCT
1 TAATGATTGATAATGCTTGATGATGCT
*
13435845 TAATGAATGATAATGCTTGATGATGCT
1 TAATGATTGATAATGCTTGATGATGCT
13435872 TAATGATTGATAATGCTT
1 TAATGATTGATAATGCTT
13435890 CAAGAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (27 bp):
TAATGATTGATAATGCTTGATGATGCT
Found at i:13435878 original size:37 final size:37
Alignment explanation
Indices: 13435794--13435878 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
13435784 TACTTGGTAT
* *
13435794 TGCTTGATGATGCTTAATGATTGATAATGCTTGGTAA
1 TGCTTGATGATGCTTAATGAATGATAATGCTTGATAA
* *
13435831 TTCTTGATGATGCTTAATGAATGATAATGCTTGATGA
1 TGCTTGATGATGCTTAATGAATGATAATGCTTGATAA
*
13435868 TGCTTAATGAT
1 TGCTTGATGAT
13435879 TGATAATGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.41
Consensus pattern (37 bp):
TGCTTGATGATGCTTAATGAATGATAATGCTTGATAA
Found at i:13436922 original size:408 final size:411
Alignment explanation
Indices: 13436142--13436932 Score: 1247
Period size: 408 Copynumber: 1.9 Consensus size: 411
13436132 GTCTTTTACT
*
13436142 AATTGGTAACTTATTGGTTTCATGATTTCTCTAAAGGGGAGTAAGATTATGCTTTAAAGTGATTA
1 AATTGGAAACTTATTGGTTTCATGATTTCTCTAAAGGGGAGTAAGATTATGCTTTAAAGTGATTA
13436207 TTGTCCATGTCCCTTCTCCTTTTGTTTCATGATTTCCTTTACTAACAATTGATATTAACCTAATG
66 TTGTCCATGTCCCTTCTCCTTTTGTTTCATGATTTCCTTTACTAACAATTGATATTAACCTAATG
* * *
13436272 ATTTTTTAAAAAGGAGTTAATCATTGGCATATATGTTTGCATGAATTCTTTCAATCAAAATTTGT
131 ATTTCTTAAAAAGGAGTCAATCATTGGCACATA-GTTTGCATGAATTCTTTCAATCAAAATTTGT
* * * *
13436337 GTCATTAGCACTTGGTATCTTCAACAATAAGTTTTGATGAGAATCCAATATTTGGTGTCTTTCAT
195 GTCATTAGCACTTGGTATCTTCAACAAAAAATTTTGATGAAAATCCAACATTTGGTGTCTTTCAT
*
13436402 TATTGGTAATATCCTTGAACACCAAATTGATATTGTGCTTTACATAGATACTATGCTTTTCACTT
260 TATTGATAATATCCTTGAACACCAAATTGATATTGTGCTTTACATAGATACTATGCTTTTCACTT
*
13436467 ATGCTTGAATGTTGAAATCAATAATTGATATCAGGTTTTTGAGTTCATTCCAAATATTTATTCTA
325 ATGCTTGAATGTTGAAATCAATAATTGATATCAGATTTTTGAGTTCATTCCAAATATTTATTCTA
13436532 GGCTCATGATTTCTCTCCTAAC
390 GGCTCATGATTTCTCTCCTAAC
* **
13436554 AATTGGAAACTTATTGGTTT-TTGGATTTCT-TTGAGGGAGAGTAAGATTATGCTTTAAAGTGAT
1 AATTGGAAACTTATTGGTTTCAT-GATTTCTCTAAAGGG-GAGTAAGATTATGCTTTAAAGTGAT
* * *
13436617 TAGTT-TCCTTTTCCCTTCTCCTTTTGTTTCATGATTTCCTTTACTAACAATTGATATTGACCTA
64 TA-TTGTCCATGTCCCTTCTCCTTTTGTTTCATGATTTCCTTTACTAACAATTGATATTAACCTA
*** *
13436681 ATGATTTCTTAAGGGGGAGTCAATCATT-G-ACATA-TTTGCATGAATTCTTTTAATCAAAATTT
128 ATGATTTCTTAAAAAGGAGTCAATCATTGGCACATAGTTTGCATGAATTCTTTCAATCAAAATTT
* **
13436743 GTGTCATTATCACTTGGTATCTTCAACAAAAAATTTTGATGAAAATTTAACATTTGGTGTCTTTC
193 GTGTCATTAGCACTTGGTATCTTCAACAAAAAATTTTGATGAAAATCCAACATTTGGTGTCTTTC
*
13436808 ATTATTGATAATATCCTTGAACACTAAATTGATATTGTGCTTTACATAGATACTATGCTTCTT-A
258 ATTATTGATAATATCCTTGAACACCAAATTGATATTGTGCTTTACATAGATACTATGCTT-TTCA
*
13436872 CTTATGCTTGAATGTTGAAATCAATAATTGATATCA-ATTTTCTTAGTTCATTCCAAATATT
322 CTTATGCTTGAATGTTGAAATCAATAATTGATATCAGATTTT-TGAGTTCATTCCAAATATT
13436933 GATATCAAGC
Statistics
Matches: 349, Mismatches: 25, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
407 4 0.01
408 198 0.57
409 2 0.01
410 4 0.01
411 7 0.02
412 132 0.38
413 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (411 bp):
AATTGGAAACTTATTGGTTTCATGATTTCTCTAAAGGGGAGTAAGATTATGCTTTAAAGTGATTA
TTGTCCATGTCCCTTCTCCTTTTGTTTCATGATTTCCTTTACTAACAATTGATATTAACCTAATG
ATTTCTTAAAAAGGAGTCAATCATTGGCACATAGTTTGCATGAATTCTTTCAATCAAAATTTGTG
TCATTAGCACTTGGTATCTTCAACAAAAAATTTTGATGAAAATCCAACATTTGGTGTCTTTCATT
ATTGATAATATCCTTGAACACCAAATTGATATTGTGCTTTACATAGATACTATGCTTTTCACTTA
TGCTTGAATGTTGAAATCAATAATTGATATCAGATTTTTGAGTTCATTCCAAATATTTATTCTAG
GCTCATGATTTCTCTCCTAAC
Found at i:13440040 original size:10 final size:11
Alignment explanation
Indices: 13440013--13440048 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
13440003 TATGGCCGGC
*
13440013 CAAAGCAAGAA
1 CAAAGGAAGAA
13440024 CAAAGGAAGAA
1 CAAAGGAAGAA
13440035 -AAAGGAAGAA
1 CAAAGGAAGAA
13440045 CAAA
1 CAAA
13440049 CCCTAGGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.67, C:0.11, G:0.22, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:13440105 original size:21 final size:21
Alignment explanation
Indices: 13440061--13440105 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13440051 CTAGGTACAC
* *
13440061 AAATTCAAGGGAAAAGTGTGA
1 AAATTCAAGGAAAAAGTGTAA
13440082 AAATTCAAGGAAACAAGT-TAA
1 AAATTCAAGGAAA-AAGTGTAA
13440103 AAA
1 AAA
13440106 AAGTAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.18
Consensus pattern (21 bp):
AAATTCAAGGAAAAAGTGTAA
Found at i:13442983 original size:43 final size:43
Alignment explanation
Indices: 13442922--13443044 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
13442912 CCCATCATCA
* **
13442922 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATGGCTAGG
1 TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAACTAGG
* *
13442965 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACTGGG
1 TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAACTAGG
* * *
13443008 TCAT-TCTAGACTTATGCGCACTCCTTACTCGCACATA
1 TCATCACCAG-CTTATGCGCACTCCCTACTCGCACATA
13443045 GCTTAGTCAA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
42 3 0.04
43 67 0.96
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (43 bp):
TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAACTAGG
Found at i:13448010 original size:37 final size:37
Alignment explanation
Indices: 13447960--13448033 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
13447950 GACACTATAA
13447960 GTATCAATACTTCATTCATCACATGAATAAGGCATTG
1 GTATCAATACTTCATTCATCACATGAATAAGGCATTG
*
13447997 GTATCAATACTTCATTCATCACATGAATAAGGTATTG
1 GTATCAATACTTCATTCATCACATGAATAAGGCATTG
13448034 AGACCCTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (37 bp):
GTATCAATACTTCATTCATCACATGAATAAGGCATTG
Found at i:13449410 original size:2 final size:2
Alignment explanation
Indices: 13449403--13449441 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
13449393 ATTATGTTTG
13449403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13449442 GTTGTGCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13451166 original size:38 final size:39
Alignment explanation
Indices: 13451080--13451186 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 39
13451070 ACTCGGCTCA
*
13451080 TGTACATCCCCCCACATCGTGCACATAGCCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAGG-ACCATCG
* *
13451120 TGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAG-GACCATCG
13451158 TGTACATCCCCCCCACATCGTGCACATAG
1 TGTACAT-CCCCCCACATCGTGCACATAG
13451187 GCACTATCAT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 12 0.20
39 21 0.36
40 26 0.44
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.20
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACATAGCAGGACCATCG
Found at i:13454962 original size:63 final size:63
Alignment explanation
Indices: 13454853--13455013 Score: 232
Period size: 63 Copynumber: 2.6 Consensus size: 63
13454843 ACATCATAGT
** * * *
13454853 CGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTGTCACAACGTTGTCATTCAAT
1 CGGCATGTGCACTGCCCACTCCGCACATGCACGGTCATAATAGTCACAACATTGTCATTCAAC
* * *
13454916 TGGCATATGCACTGCCCACTCCGCACATGCATGGTCATAATAGTCACAACATTGTCATTCAAC
1 CGGCATGTGCACTGCCCACTCCGCACATGCACGGTCATAATAGTCACAACATTGTCATTCAAC
* *
13454979 CGACATGTGTACTGCCCACTCCGCACATGCACGGT
1 CGGCATGTGCACTGCCCACTCCGCACATGCACGGT
13455014 TACATCAATT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 85 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (63 bp):
CGGCATGTGCACTGCCCACTCCGCACATGCACGGTCATAATAGTCACAACATTGTCATTCAAC
Found at i:13458255 original size:13 final size:14
Alignment explanation
Indices: 13458237--13458265 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13458227 ATCAAGAAGT
13458237 TTTCATTAT-CAGA
1 TTTCATTATCCAGA
13458250 TTTCATTATCCAGA
1 TTTCATTATCCAGA
13458264 TT
1 TT
13458266 ATCTTCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (14 bp):
TTTCATTATCCAGA
Found at i:13460227 original size:42 final size:42
Alignment explanation
Indices: 13460168--13460334 Score: 228
Period size: 42 Copynumber: 4.0 Consensus size: 42
13460158 TGTTGATGTG
13460168 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
13460210 GACCCGGCTATGTGCGAGTATGAGTGCACATAAGCCATTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
13460252 GACCCGACTATGTGTGAGT-GGAAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGG-AGTGCACATAAGCCGTTGCT
* * * * * *
13460294 AACCCAGCTATATGCAAGTAGGAGTACGCATAAGCCGTTGC
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
13460335 ATATGAGATG
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.01
42 106 0.97
43 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.22
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Done.