Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 65 of 199
Found at i:19272652 original size:17 final size:17
Alignment explanation
Indices: 19272625--19272657 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
19272615 AATGTTTCAT
19272625 AAAAAAGAAAGGAAAAAC
1 AAAAAAGAAA-GAAAAAC
19272643 AAAAAA-AAAGAAAAA
1 AAAAAAGAAAGAAAAA
19272658 AAATGAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAGAAAAAC
Found at i:19272658 original size:17 final size:18
Alignment explanation
Indices: 19272625--19272658 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19272615 AATGTTTCAT
*
19272625 AAAAAAGAAAGGAAAAAC
1 AAAAAAGAAAGAAAAAAC
19272643 AAAAAA-AAAGAAAAAA
1 AAAAAAGAAAGAAAAAA
19272659 AATGAGAGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAAC
Found at i:19273663 original size:43 final size:44
Alignment explanation
Indices: 19273544--19273690 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 44
19273534 ATGGCGAATT
* **
19273544 TTATCTCCCTGAAGTTGCAGTGGGGT-AGATTAAAGCCTCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGGGTAAG-TTGAAGCAACAAACC
* * * * * * *
19273588 TTATCTCTCTGAAGCTGCAGTAGAGCATGTTGAAGTAACAAACC
1 TTATCTCCCTGAAGTTGCAGTGGGGTAAGTTGAAGCAACAAACC
* **
19273632 TTATC-CCCTGAAGTTGCAGTGGGGTAAGTTGAAG-ATACCAGTC
1 TTATCTCCCTGAAGTTGCAGTGGGGTAAGTTGAAGCA-ACAAACC
19273675 TTATCTCCCTGAAGTT
1 TTATCTCCCTGAAGTT
19273691 ATAGTGGAGC
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
42 1 0.01
43 32 0.40
44 47 0.58
45 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGGGTAAGTTGAAGCAACAAACC
Found at i:19273709 original size:44 final size:44
Alignment explanation
Indices: 19273661--19273744 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
19273651 TGGGGTAAGT
* * * *
19273661 TGAAGATACCAGTCTTATCTCCCTGAAGTTATAGTGGAGCAGAC
1 TGAAGATACCAATCCTATCTCCCTGAAGTTACAGTAGAGCAGAC
* *
19273705 TGAAGCTACTAATCCTATCTCCCTGAAGTTACAGTAGAGC
1 TGAAGATACCAATCCTATCTCCCTGAAGTTACAGTAGAGC
19273745 GGATTAAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (44 bp):
TGAAGATACCAATCCTATCTCCCTGAAGTTACAGTAGAGCAGAC
Found at i:19274182 original size:51 final size:49
Alignment explanation
Indices: 19273872--19275008 Score: 458
Period size: 45 Copynumber: 24.7 Consensus size: 49
19273862 CATATCAAAC
* * ** * *
19273872 CTTATCTCCCTGAAGTCGCAGTGGAGCAGGTT-AAAAATAAAT-CA-CT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* * *** *
19273918 CTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAG-ACGGGTTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTA-TAATTACAGAT
* * * ** *
19273967 CTTATCTCTCTGAAGTTTCAGTAGAGCAGATTGAAG--CCACT--A-AT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* * * *
19274011 CTTATCCCCCTGAAGTTACAGTGGGGCAGATTG-A-TCAT-ACTA-AG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-ATAATTACAGAT
* * *
19274056 CTTATCTCCTTGAAGTTGTAGTGGAGCAGACTGAAG-AT-A--AC-GAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAG-AT
* * *
19274101 CTTATTTCACTGAAGTTGCAGTGGAACAGATTGAAGCTATAGATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TATA-ATTACAGAT
* *
19274152 CTTATCTCTCTGAAGTTGCAGTAGAGCAGATT--A-TATCAA--AC--A-
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAT-AATTACAGAT
** * ** * *
19274194 -TTATCTCTTTGAAGTTGCAGTGGAGCAGGTT-AAAAATAAAT-CA-AC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* * *** *
19274239 CTTATCTCCCTAAAGTTGCAGTAGAGCAGATTGAAG-ACGGGTTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTA-TAATTACAGAT
* *
19274288 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CT-ACT--A-AT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* * * *
19274332 CTTATCCCCCTGAATTTGCAGTGGGGCAGATTGAA-TA-AATCA-AG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* *
19274377 CTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAG-AT-A--AC-GAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAG-AT
* * *
19274422 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAT-AATTACAGAT
* * * ** *
19274473 CTTATCTCCCTGAAGTTGTAGTGGAGAAAATTGAAG--CCACT--A-AT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* * * * * *
19274517 CTTATCCCCCTGAAGTTGCACTGGGGTAAATTGAA-TA-AATCA-AG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* * *
19274562 CTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAG-AT-A--GC-GAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAG-AT
* * *
19274607 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAT-AATTACAGAT
* * * * * *
19274658 CTTATTTCTCTGAAGTTGTAATAGAGCAGA-T-CA-TATCAA--AC----
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAT-AATTACAGAT
* ** *
19274699 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT-AAAAATAAAT-CA-AT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* * *
19274745 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAG-AT-A--GC-GAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAG-AT
* * * * * * * *
19274790 CTTATTTCCTTGATGTTACAGTAGAACAAATTGAAGCTATAAATTACGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAT-AATTACAGAT
** * * *
19274841 CTTATCTCTTTGAAGTTGCAATAGAGCAGA-T----CAT-ATTA-A-A-
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* * * * ** *
19274881 CATTATCTCCTTGAAATTGCAGTGGAACAGGTT-AAAAATAAAT-CA-AT
1 C-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
* * * * **
19274928 CTTATCTCCTTGAAGTTGTACTGGAGCAGATTGAAG-ACAGGCTAC-GAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATA-ATTACAG-AT
19274977 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
19275009 AAAGCCACAA
Statistics
Matches: 832, Mismatches: 163, Indels: 189
0.70 0.14 0.16
Matches are distributed among these distances:
40 1 0.00
41 76 0.09
42 8 0.01
43 17 0.02
44 103 0.12
45 236 0.28
46 120 0.14
47 33 0.04
48 6 0.01
49 106 0.13
50 2 0.00
51 121 0.15
52 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (49 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTATAATTACAGAT
Found at i:19274199 original size:41 final size:42
Alignment explanation
Indices: 19274153--19274270 Score: 123
Period size: 46 Copynumber: 2.7 Consensus size: 42
19274143 ATTACAGATC
19274153 TTATCTCTCTGAAGTTGCAGTAGAGCAGATT-AT-ATCAAACA
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGATTAATAATC-AACA
* * * *
19274194 TTATCTCTTTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAACC
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGATT---AAT-AATCAACA
* *
19274240 TTATCTCCCTAAAGTTGCAGTAGAGCAGATT
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGATT
19274271 GAAGACGGGT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 28 0.45
45 2 0.03
46 29 0.47
47 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (42 bp):
TTATCTCTCTGAAGTTGCAGTAGAGCAGATTAATAATCAACA
Found at i:19274307 original size:136 final size:137
Alignment explanation
Indices: 19273867--19275134 Score: 410
Period size: 138 Copynumber: 9.2 Consensus size: 137
19273857 CTTATCATAT
* * * * ** * * **
19273867 CAAACCTTATCTCCCTGAAGTCGCAGTGGAGCAGGTTAAAAATAAATCACTCTTATCTCCTTGAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGATCAT-ACTAAGACTTATCTCCTTGAA
* * ** * * * * *
19273932 GTTGCAGTAGAGCAGATTGAAGACGGGTTACAAATCTTATCTCTCTGAAGTTTCAGTAGAGCAGA
65 GTTGCAGTGGAGCAGACT-AA-A--AATAACGAACCTTATCTCACTGAAGTTGCAGTAGAGCAGA
*
19273997 TTGAAG-C--CA
126 TTGAAGACGTTA
* * * * *
19274006 CTAATCTTATCCCCCTGAAGTTACAGTGGGGCAGATTGATCATACTAAGTCTTATCTCCTTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGATCATACTAAGACTTATCTCCTTGAAG
* * * * * * *
19274071 TTGTAGTGGAGCAGACTGAAGATAACGAATCTTATTTCACTGAAGTTGCAGTGGAACAGATTGAA
66 TTGCAGTGGAGCAGACTAAAAATAACGAACCTTATCTCACTGAAGTTGCAGTAGAGCAGATTGAA
*
19274136 GCTATAGATTA
131 G--A-CG-TTA
* * * *
19274147 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT-AT-AT-C-AA-ACATTATCTCTTTGAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGATCATACTAAGAC-TTATCTCCTTGAA
** * *
19274207 GTTGCAGTGGAGCAGGTTAAAAATAAATC-AACCTTATCTCCCTAAAGTTGCAGTAGAGCAGATT
65 GTTGCAGTGGAGCAGACTAAAAAT-AA-CGAACCTTATCTCACTGAAGTTGCAGTAGAGCAGATT
19274271 GAAGACGGGTTA
128 GAAGAC--GTTA
* * * *
19274283 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-TACTAA-TCTTATCCCCCTGAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-ATCATACTAAGACTTATCTCCTTGAA
* * * * * * * *
19274346 TTTGCAGTGGGGCAGATTGAATAAAT--C-AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGAC
65 GTTGCAGTGGAGCAGACT-AA-AAATAACGAA-CCTTATCTCACTGAAGTTGCAGTAGAGCAGAT
*
19274408 TGAAGA--TAA
127 TGAAGACGTTA
* * * * * *
19274417 CGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCC
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-ATC-AT--ACTA-AGA-CTTATCTCC
* * * * ** *** * * * * * * * * *
19274482 CTGAAGTTGTAGTGGAG-AAAATTGAAGCCACTAATCTTATCCCCCTGAAGTTGCACTGGGGTAA
60 TTGAAGTTGCAGTGGAGCAGACTAAAAATAACGAACCTTATCTCACTGAAGTTGCAGTAGAGCAG
* **
19274546 ATTGAATA-AAT-
125 ATTGAAGACGTTA
* * * ** * * * *
19274557 CAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAA-TCTTATTTCCCTGAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGATCATA-CTAAGACTTATCTCCTTGAA
* * * * * * * *
19274621 GTTGCAGTGGAACAGATTAAAGCTATAAATTAC-AGATCTTATTTCTCTGAAGTTGTAATAGAGC
65 GTTGCAGTGGAGCAG-----A-CTAAAAATAACGA-ACCTTATCTCACTGAAGTTGCAGTAGAGC
* *
19274685 AGA-T-CATA---T-
123 AGATTGAAGACGTTA
* * * ** * * * *
19274694 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAA-TCTTATCTCCCTAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGATCAT-ACT-AAGACTTATCTCCTTGA
* * * * * * * * *
19274758 AGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTC-CTTGATGTTACAGTAGAACAAATT
64 AGTTGCAGTGGAGCAGACTAAAAATAACGAACCTTATCTCAC-TGAAGTTGCAGTAGAGCAGATT
**
19274822 GAAGCTATAAATTA
128 GAAG----ACGTTA
** ** * * *
19274836 CGGATCTTATCTCTTTGAAGTTGCAATAGAGC--A--GATCATATTAA-ACATTATCTCCTTGAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGATCATACTAAGAC-TTATCTCCTTGAA
* * ** * * * *
19274896 ATTGCAGTGGAACAGGTTAAAAATAAATC-AATCTTATCTC-CTTGAAGTTGTACTGGAGCAGAT
65 GTTGCAGTGGAGCAGACTAAAAAT-AA-CGAACCTTATCTCAC-TGAAGTTGCAGTAGAGCAGAT
*
19274959 TGAAGACAGGCTA
127 TGAAGAC--GTTA
* * * *
19274972 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-CAC-AA-ACCTTATCT-CTCTG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-GATCATACTAAGA-CTTATCTCCT-TG
* * * ** * * * * *
19275033 AAGTTGCAGTAGATCAG-GTTGAAATAACAAACCTTATCTCCCTAAAGTTGTAGTGGAGCAGATT
63 AAGTTGCAGTGGAGCAGACTAAAAATAACGAACCTTATCTCACTGAAGTTGCAGTAGAGCAGATT
19275097 GAAG-C--TA
128 GAAGACGTTA
* * **
19275104 CTAATCCTATCTCCCTGAAGTTATAGTGGAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAG
19275135 TGAATTAAAA
Statistics
Matches: 860, Mismatches: 201, Indels: 143
0.71 0.17 0.12
Matches are distributed among these distances:
131 1 0.00
132 59 0.07
133 3 0.00
134 104 0.12
135 1 0.00
136 77 0.09
137 143 0.17
138 186 0.22
139 93 0.11
140 78 0.09
141 90 0.10
142 25 0.03
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (137 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGATCATACTAAGACTTATCTCCTTGAAG
TTGCAGTGGAGCAGACTAAAAATAACGAACCTTATCTCACTGAAGTTGCAGTAGAGCAGATTGAA
GACGTTA
Found at i:19274445 original size:321 final size:321
Alignment explanation
Indices: 19273863--19274490 Score: 1046
Period size: 321 Copynumber: 2.0 Consensus size: 321
19273853 GGATCTTATC
* *
19273863 ATATCAAACCTTATCTCCCTGAAGTCGCAGTGGAGCAGGTTAAAAATAAATCACTCTTATCTCCT
1 ATATCAAACATTATCTCCCTGAAGTCGCAGTGGAGCAGGTTAAAAATAAATCACTCTTATCTCCC
* * *
19273928 TGAAGTTGCAGTAGAGCAGATTGAAGACGGGTTACAAATCTTATCTCTCTGAAGTTTCAGTAGAG
66 TAAAGTTGCAGTAGAGCAGATTGAAGACGGGTTACAAATCTTATCTCCCTGAAGTTGCAGTAGAG
*
19273993 CAGATTGAAGCCACTAATCTTATCCCCCTGAAGTTACAGTGGGGCAGATTGATCATACTAAGTCT
131 CAGATTGAAGCCACTAATCTTATCCCCCTGAAGTTACAGTGGGGCAGATTGATAATACTAAGTCT
*
19274058 TATCTCCTTGAAGTTGTAGTGGAGCAGACTGAAGATAACGAATCTTATTTCACTGAAGTTGCAGT
196 TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAACGAATCTTATTTCACTGAAGTTGCAGT
* * *
19274123 GGAACAGATTGAAGCTATAGATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT
261 GGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT
** *
19274184 ATATCAAACATTATCTCTTTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAAC-CTTATCTCC
1 ATATCAAACATTATCTCCCTGAAGTCGCAGTGGAGCAGGTTAAAAATAAATC-ACTCTTATCTCC
*
19274248 CTAAAGTTGCAGTAGAGCAGATTGAAGACGGGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGA
65 CTAAAGTTGCAGTAGAGCAGATTGAAGACGGGTTACAAATCTTATCTCCCTGAAGTTGCAGTAGA
* * *
19274313 GCAGATTGAAGCTACTAATCTTATCCCCCTGAATTTGCAGTGGGGCAGATTGAATAA-A-TCAAG
130 GCAGATTGAAGCCACTAATCTTATCCCCCTGAAGTTACAGTGGGGCAGATTG-ATAATACT-AAG
*
19274376 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGAAGTTGC
193 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAACGAATCTTATTTCACTGAAGTTGC
19274441 AGTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCCTGAAGTTG
258 AGTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCCTGAAGTTG
19274491 TAGTGGAGAA
Statistics
Matches: 286, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
320 1 0.00
321 280 0.98
322 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (321 bp):
ATATCAAACATTATCTCCCTGAAGTCGCAGTGGAGCAGGTTAAAAATAAATCACTCTTATCTCCC
TAAAGTTGCAGTAGAGCAGATTGAAGACGGGTTACAAATCTTATCTCCCTGAAGTTGCAGTAGAG
CAGATTGAAGCCACTAATCTTATCCCCCTGAAGTTACAGTGGGGCAGATTGATAATACTAAGTCT
TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAACGAATCTTATTTCACTGAAGTTGCAGT
GGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT
Found at i:19274498 original size:185 final size:181
Alignment explanation
Indices: 19274280--19275013 Score: 788
Period size: 185 Copynumber: 4.0 Consensus size: 181
19274270 TGAAGACGGG
* *
19274280 TTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAATCTTATCCCCCTGA
1 TTACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGA-T-AA--TACTAATCTTATCCCCCTGA
* * * *
19274345 ATTTGCAGTGGGGCAGATT-GAATAAATCAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACT
62 AGTTGCAGTGGAGCAGATTAAAATAAATCAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
*
19274409 GAAGATAACGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAA
126 GAAGATAACGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAA
* * * * * *
19274465 TTACAAATCTTATCTCCCTGAAGTTGTAGTGGAGAAAATTGAAGCCACTAATCTTATCCCCCTGA
1 TTACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGA-T-AA--TACTAATCTTATCCCCCTGA
* * * * * *
19274530 AGTTGCACTGGGGTAAATT-GAATAAATCAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACT
62 AGTTGCAGTGGAGCAGATTAAAATAAATCAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
*
19274594 GAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAA
126 GAAGATAACGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAA
* * * * * * * *
19274650 TTACAGATCTTATTTCTCTGAAGTTGTAATAGAGCAGATCATATCAAACCTTATCTCCCTGAAGT
1 TTACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATAATA-CTAATCTTATCCCCCTGAAGT
* *
19274715 TGCAGTGGAGCAGGTTAAAAATAAATCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAA
65 TGCAGTGGAGCAGATT-AAAATAAATCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
* * * * * * *
19274780 GATAGCGAATCTTATTTCCTTGATGTTACAGTAGAACAAATTGAAGCTATAAA
129 GATAACGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAA
** ** * * * * * *
19274833 TTACGGATCTTATCTCTTTGAAGTTGCAATAGAGCAGATCATATTAAACATTATCTCCTTGAAAT
1 TTACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATAATACTAATC-TTATCCCCCTGAAGT
* * * * * *
19274898 TGCAGTGGAACAGGTTAAAAATAAATCAATCTTATCTCCTTGAAGTTGTACTGGAGCAGATTGAA
65 TGCAGTGGAGCAGATT-AAAATAAATCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
* * *
19274963 GACAGGCTACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
129 GATA----ACGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGC
19275014 CACAAACCTT
Statistics
Matches: 478, Mismatches: 63, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
181 1 0.00
182 32 0.07
183 196 0.41
184 11 0.02
185 204 0.43
187 34 0.07
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (181 bp):
TTACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATAATACTAATCTTATCCCCCTGAAGTT
GCAGTGGAGCAGATTAAAATAAATCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
TAACGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAA
Found at i:19274578 original size:45 final size:44
Alignment explanation
Indices: 19274150--19275134 Score: 475
Period size: 44 Copynumber: 21.6 Consensus size: 44
19274140 TAGATTACAG
* *
19274150 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT--AT--ATCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAATCA
* ** * *
19274190 AACATTATCTCTTTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCA
1 ATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATT--GAATAAATCA
* * * * **
19274237 ACCTTATCTCCCTAAAGTTGCAGTAGAGCAGATTGAAGACGGGTTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATA---AAT-C-A
*
19274286 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT-ACT-A
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA--TAAATCA
* * *
19274330 ATCTTATCCCCCTGAATTTGCAGTGGGGCAGATTGAATAAATCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAATCA
* * *
19274374 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAA-CGA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATA-AATC-A
* *
19274420 ATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-A---ATAAA-T-C-A
* * * ***
19274471 ATCTTATCTCCCTGAAGTTGTAGTGGAGAAAATTGAAGCCA-CTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAATC-A
* * * * *
19274515 ATCTTATCCCCCTGAAGTTGCACTGGGGTAAATTGAATAAATCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAATCA
* * * * *
19274559 AGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAATC-A
* * *
19274605 ATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G-AATAAA-T-CA
* * * * * *
19274655 GATCTTATTTCTCTGAAGTTGTAATAGAGCAGA-T-CAT--ATCAA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAATC-A
* * *
19274697 ACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--GAATAAATCA
* * * * *
19274743 ATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAATC-A
* * * * * * * *
19274788 ATCTTATTTCCTTGATGTTACAGTAGAACAAATTGAAGCTATAAATTACGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-A---ATAAA-T-C-A
** * * *
19274839 ATCTTATCTCTTTGAAGTTGCAATAGAGCAGATCAT-ATTAAA-C-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT--TGAATAAATCA
* * * * *
19274882 A--TTATCTCCTTGAAATTGCAGTGGAACAGGTTAAAAATAAATCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--GAATAAATCA
* * * * *
19274926 ATCTTATCTCCTTGAAGTTGTACTGGAGCAGATTGAAGACAGGCTACGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATA-A--AT-C-A
* ***
19274975 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAATC-A
* * * * *
19275019 ACCTTATCTCTCTGAAGTTGCAGTAGATCAGGTTGAA-ATAA-CAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATA-AATC-A
* * * *
19275063 ACCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCT-ACT-A
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA--TAAATCA
* **
19275107 ATCCTATCTCCCTGAAGTTATAGTGGAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG
19275135 TGAATTAAAA
Statistics
Matches: 721, Mismatches: 155, Indels: 134
0.71 0.15 0.13
Matches are distributed among these distances:
39 1 0.00
40 2 0.00
41 78 0.11
42 9 0.01
43 5 0.01
44 179 0.25
45 162 0.22
46 91 0.13
47 14 0.02
48 9 0.01
49 78 0.11
50 3 0.00
51 89 0.12
53 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAATCA
Found at i:19274722 original size:92 final size:92
Alignment explanation
Indices: 19274422--19274916 Score: 312
Period size: 92 Copynumber: 5.4 Consensus size: 92
19274412 GATAACGAAT
* * * *
19274422 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCCTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
* * * * * * * *
19274487 GTTGTAGTGGAGAAAATTGA-AGCCACTAAT
66 GTTGCAATAGAGCAGA-TCATA-TCA--AAC
* * *** * * * *
19274517 CTTATCCCCCTGAAGTTGCACTGGGGTAAATT---G-AATAAATCA-AG-TCTTATCTCCCTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
* * * * *
19274576 GTTGCAATGGAGCAGACTGAAGATAGCGAAT
66 GTTGCAATAGAGCAGA-T---CATATCAAAC
* *
19274607 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATTTCTCTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
*
19274672 GTTGTAATAGAGCAGATCATATCAAAC
66 GTTGCAATAGAGCAGATCATATCAAAC
* * * * *
19274699 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAA--AATAAA-T-CA-ATCTTATCTCCCTAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
* * * * * *
19274759 GTTGCAGTGGAGCAGACTGAAGATAGCGAAT
66 GTTGCAATAGAGCAGA-T---CATATCAAAC
* * * * * * * * *
19274790 CTTATTTCCTTGATGTTACAGTAGAACAAATTGAAGCTATAAATTACGGATCTTATCTCTTTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
*
19274855 GTTGCAATAGAGCAGATCATATTAAAC
66 GTTGCAATAGAGCAGATCATATCAAAC
* * * *
19274882 ATTATCTCCTTGAAATTGCAGTGGAACAGGTTAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAA
19274917 AATAAATCAA
Statistics
Matches: 303, Mismatches: 78, Indels: 41
0.72 0.18 0.10
Matches are distributed among these distances:
87 26 0.09
88 3 0.01
89 29 0.10
90 34 0.11
91 39 0.13
92 73 0.24
93 7 0.02
94 8 0.03
95 30 0.10
96 54 0.18
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (92 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAA
GTTGCAATAGAGCAGATCATATCAAAC
Found at i:19274829 original size:183 final size:182
Alignment explanation
Indices: 19274332--19275013 Score: 803
Period size: 183 Copynumber: 3.7 Consensus size: 182
19274322 AGCTACTAAT
* * * *
19274332 CTTATCCCCCTGAATTTGCAGTGGGGCAGATTGAATAAATCAAGTCTTATCTCCCTGAAGTTGTA
1 CTTATCCCCCTGAAGTTGCAGTGGAGCAGATTAAATAAATCAAGTCTTATCTCCCTGAAGTTGCA
*
19274397 GTGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAT
66 GTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAT
* * * * * * * * *
19274462 AAATTACAAATCTTATCTCCCTGAAGTTGTAGTGGAGAAAATTGA-AGCCACTAAT
131 AAATTACAGATCTTATCTCTCTGAAGTTGTAATAGAGCAGA-TCATA-TCA--AAC
* * * * *
19274517 CTTATCCCCCTGAAGTTGCACTGGGGTAAATTGAATAAATCAAGTCTTATCTCCCTGAAGTTGCA
1 CTTATCCCCCTGAAGTTGCAGTGGAGCAGATTAAATAAATCAAGTCTTATCTCCCTGAAGTTGCA
* *
19274582 ATGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTAT
66 GTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAT
*
19274647 AAATTACAGATCTTATTTCTCTGAAGTTGTAATAGAGCAGATCATATCAAAC
131 AAATTACAGATCTTATCTCTCTGAAGTTGTAATAGAGCAGATCATATCAAAC
* * *
19274699 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAA-TCTTATCTCCCTAAAGTTG
1 CTTATCCCCCTGAAGTTGCAGTGGAGCAGATT--AAATAAATCAAGTCTTATCTCCCTGAAGTTG
* * * * *
19274763 CAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCTTGATGTTACAGTAGAACAAATTGAAGCT
64 CAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCT
* * * *
19274828 ATAAATTACGGATCTTATCTCTTTGAAGTTGCAATAGAGCAGATCATATTAAAC
129 ATAAATTACAGATCTTATCTCTCTGAAGTTGTAATAGAGCAGATCATATCAAAC
* * * * * * *
19274882 ATTATCTCCTTGAAATTGCAGTGGAACAGGTTAAAAATAAATCAA-TCTTATCTCCTTGAAGTTG
1 CTTATCCCCCTGAAGTTGCAGTGGAGCAGATT--AAATAAATCAAGTCTTATCTCCCTGAAGTTG
* * * * * * *
19274946 TACTGGAGCAGATTGAAGACAGGCTACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA
64 CAGTGGAGCAGACTGAAGATA-G---CGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGA
19275011 AGC
125 AGC
19275014 CACAAACCTT
Statistics
Matches: 434, Mismatches: 56, Indels: 12
0.86 0.11 0.02
Matches are distributed among these distances:
182 28 0.06
183 200 0.46
184 15 0.03
185 157 0.36
187 34 0.08
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (182 bp):
CTTATCCCCCTGAAGTTGCAGTGGAGCAGATTAAATAAATCAAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAT
AAATTACAGATCTTATCTCTCTGAAGTTGTAATAGAGCAGATCATATCAAAC
Found at i:19274931 original size:506 final size:497
Alignment explanation
Indices: 19273860--19275040 Score: 1433
Period size: 506 Copynumber: 2.3 Consensus size: 497
19273850 AGCGGATCTT
* * * *
19273860 ATCATATCAAACCTTATCTCCCTGAAGTCGCAGTGGAGCAGGTTAAAAATAAATCACTCTTATCT
1 ATCATATTAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAATCTTATCT
* * *
19273925 CCTTGAAGTTGCAGTAGAGCAGATTGAAGACGGGTTACAAATCTTATCTCTCTGAAGTT-TCAGT
66 CCTTGAAGTTGCAGTGGAGCAGATTGAAGACAGGTTACAAATCTTATCTCCCTGAAGTTGT-AGT
* * * * *
19273989 AGAGCAGATTGAAGCCACTAATCTTATCCCCCTGAAGTTACAGTGGGGCAGATTGATCATACTAA
130 GGAGCAGATTGAAGCCACTAATCTTATCCCCCTGAAGTTGCACTGGGGCAAATTGATAATACTAA
* * *
19274054 GTCTTATCTCCTTGAAGTTGTAGTGGAGCAGACTGAAGATAACGAATCTTATTTCACTGAAGTTG
195 GTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAACGAATCTTATTTCACTGAAGTTG
* * * *
19274119 CAGTGGAACAGATTGAAGCTATAGATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT
260 CAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATC
**
19274184 ATATCAAACATTATCTCTTTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAACCTTATCTCCC
325 ATATCAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAACCTTATCTCCC
* * * *
19274249 TAAAGTTGCAGTAGAGCAGATTGAAGACGGGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAG
390 TAAAGTTGCAGTAGAGCAGACTGAAGA---G-TACAAATCTTATCTCCCTGAAGTTACAGTAGAA
* * * * *
19274314 CAGATTGAAGCTACTAATCTTATCCCCCTGAATTTGCAGTGGGGCAG
451 CAAATTGAAGCTACTAATCTTATCCCCCTGAAGTTGCAATAGAGCAG
* * ** * *
19274361 AT--TGAATAAATCAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGAT-AA-CGAAT
1 ATCAT-ATTAAA-C-A---TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATC-AAT
* * * * **
19274422 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCCTGAA
59 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAG--ACAGGTTACAAATCTTATCTCCCTGAA
* * *
19274487 GTTGTAGTGGAGAAAATTGAAGCCACTAATCTTATCCCCCTGAAGTTGCACTGGGGTAAATTGAA
122 GTTGTAGTGGAGCAGATTGAAGCCACTAATCTTATCCCCCTGAAGTTGCACTGGGGCAAATTG-A
*
19274552 TAA-A-TCAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTATTTC
186 TAATACT-AAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAACGAATCTTATTTC
* * *
19274615 CCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATTTCTCTGAAGTTGTAAT
250 ACTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAAT
* *
19274680 AGAGCAGATCATATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAAT
315 AGAGCAGATCATATCAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAAC
* * * * *
19274745 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGA-TAGCGAATCTTATTTCCTTGATGTTAC
380 CTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAAGAGTA-CAAATCTTATCTCCCTGAAGTTAC
* * **
19274809 AGTAGAACAAATTGAAGCTATAAATTACGGATCTTATCTCTTTGAAGTTGCAATAGAGCAG
444 AGTAGAACAAATTGAAGC--T--ACTA---ATCTTATCCCCCTGAAGTTGCAATAGAGCAG
* * *
19274870 ATCATATTAAACATTATCTCCTTGAAATTGCAGTGGAACAGGTTAAAAATAAATCAATCTTATCT
1 ATCATATTAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAATCTTATCT
* * * * *
19274935 CCTTGAAGTTGTACTGGAGCAGATTGAAGACAGGCTACGAATCTTATCTCCCTGAAGTTGCAGTG
66 CCTTGAAGTTGCAGTGGAGCAGATTGAAGACAGGTTACAAATCTTATCTCCCTGAAGTTGTAGTG
* * * * *
19275000 GAGCAGATTAAAGCCACAAACCTTATCTCTCTGAAGTTGCA
131 GAGCAGATTGAAGCCACTAATCTTATCCCCCTGAAGTTGCA
19275041 GTAGATCAGG
Statistics
Matches: 569, Mismatches: 87, Indels: 45
0.81 0.12 0.06
Matches are distributed among these distances:
499 1 0.00
500 4 0.01
501 5 0.01
502 34 0.06
503 1 0.00
504 101 0.18
505 61 0.11
506 323 0.57
507 5 0.01
508 1 0.00
509 27 0.05
510 5 0.01
511 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (497 bp):
ATCATATTAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAATCTTATCT
CCTTGAAGTTGCAGTGGAGCAGATTGAAGACAGGTTACAAATCTTATCTCCCTGAAGTTGTAGTG
GAGCAGATTGAAGCCACTAATCTTATCCCCCTGAAGTTGCACTGGGGCAAATTGATAATACTAAG
TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAACGAATCTTATTTCACTGAAGTTGC
AGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCA
TATCAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAATCAACCTTATCTCCCT
AAAGTTGCAGTAGAGCAGACTGAAGAGTACAAATCTTATCTCCCTGAAGTTACAGTAGAACAAAT
TGAAGCTACTAATCTTATCCCCCTGAAGTTGCAATAGAGCAG
Found at i:19275072 original size:183 final size:179
Alignment explanation
Indices: 19274365--19275089 Score: 696
Period size: 183 Copynumber: 3.9 Consensus size: 179
19274355 GGGCAGATTG
* * *
19274365 AATAAATCAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAACGAATCTTATTTC
1 AATAAATCAA-TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTATTTC
* * * *
19274430 CCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCCCTGAAGTTGTAGT
65 CCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAA-TAC--A-CTTATCTCTCTGAAGTTGCAAT
* * * * * * * * *
19274495 GGAGAAAATTGA-AGCCACTAATCTTATCCCCCTGAAGTTGCACTGG----GG-TAAA
126 AGAGCAGA-TCATA-TCA--AACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAA
19274547 TTGAATAAATCAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTAT
1 ---AATAAATCAA-TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTAT
* *
19274612 TTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATTTCTCTGAAGTTGT
62 TTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAA-TAC--A-CTTATCTCTCTGAAGTTGC
* *
19274677 AATAGAGCAGATCATATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAA
123 AATAGAGCAGATCATATCAAACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAA
* *
19274734 AATAAATCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCC
1 AATAAATCAATCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTATTTCC
* * * * * * *
19274799 TTGATGTTACAGTAGAACAAATTGAAGCTATAAATTACGGATCTTATCTCTTTGAAGTTGCAATA
66 CTGAAGTTGCAGTGGAACAGATTAAAGCTATAAA-TAC--A-CTTATCTCTCTGAAGTTGCAATA
* * *
19274864 GAGCAGATCATATTAAACATTATCTCCTTGAAATTGCAGTGGAACAGGTTAAA
127 GAGCAGATCATATCAAACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAA
* * * * *
19274917 AATAAATCAATCTTATCTCCTTGAAGTTGTACTGGAGCAGATTGAAGACAGGCTACGAATCTTAT
1 AATAAATCAATCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATA-G---CGAATCTTAT
* * * * *
19274982 CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CAA-AC-CTTATCTCTCTGAAGTTGCAGTA
62 TTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATACACTTATCTCTCTGAAGTTGCAATA
* * * * *
19275044 GATCAGGTTGAAATAACAAACCTTATCTCCCT-AAAGTTGTAGTGGA
127 GAGCA-GAT--CATATCAAACCTTATCTCCCTGAAA-TTGCAGTGGA
19275090 GCAGATTGAA
Statistics
Matches: 467, Mismatches: 59, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
180 25 0.05
181 2 0.00
182 27 0.06
183 225 0.48
184 17 0.04
185 128 0.27
186 4 0.01
187 39 0.08
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (179 bp):
AATAAATCAATCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAATCTTATTTCC
CTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATACACTTATCTCTCTGAAGTTGCAATAGAGC
AGATCATATCAAACCTTATCTCCCTGAAATTGCAGTGGAACAGGTTAAA
Found at i:19276736 original size:18 final size:18
Alignment explanation
Indices: 19276671--19276751 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
19276661 TTATTTTTTC
*
19276671 TTATTATTAA-TACTATTA
1 TTATTA-TAATTACAATTA
* * * *
19276689 ATATTATTATTGCCATTA
1 TTATTATAATTACAATTA
*
19276707 TTATTATAATTATAATTA
1 TTATTATAATTACAATTA
* * *
19276725 TTATTTTCATTACCATTA
1 TTATTATAATTACAATTA
19276743 TTATATATA
1 TTAT-TATA
19276752 TTTAGTTATT
Statistics
Matches: 46, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
17 2 0.04
18 42 0.91
19 2 0.04
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (18 bp):
TTATTATAATTACAATTA
Found at i:19276746 original size:3 final size:3
Alignment explanation
Indices: 19276562--19276729 Score: 87
Period size: 3 Copynumber: 57.3 Consensus size: 3
19276552 AATTTTGTCC
* **
19276562 TAT TAT TAT TAT TAT TAT TAT TAT CAGT T-T TAT TGC TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * * * * * * *
19276606 TAC TAT TAA CAT CAT TAT TAG AAT TAT TAT TAA TGT TAT TAC TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * * *
19276652 TAT T-T TAT T-T TAT T-T T-T TCT TAT TAT TAA TAC TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * * *
19276696 TAT TGC CAT TAT TAT TAT AAT TAT AAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
19276730 TTCATTACCA
Statistics
Matches: 120, Mismatches: 38, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
2 12 0.10
3 105 0.88
4 3 0.03
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:19278882 original size:44 final size:44
Alignment explanation
Indices: 19278832--19278922 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
19278822 GGTGAAATAA
* * * *
19278832 AATAGAAGTTGTGGTAATTATGCATTTAAAACA-AATTGTAATTT
1 AATAGAAGTTCTGATAATTACGCATTTAAAA-ATAATTATAATTT
*
19278876 AATAGAAGTTCTGATAATTACGTATTTAAAAATAATTATAATTT
1 AATAGAAGTTCTGATAATTACGCATTTAAAAATAATTATAATTT
19278920 AAT
1 AAT
19278923 TTACATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (44 bp):
AATAGAAGTTCTGATAATTACGCATTTAAAAATAATTATAATTT
Found at i:19280628 original size:19 final size:19
Alignment explanation
Indices: 19280592--19280666 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
19280582 ACTTATTGGT
*
19280592 TAGGATACAC-CTCATGTGC
1 TAGGATACACTCT-GTGTGC
*
19280611 CAGGATACACTCTGTGTGC
1 TAGGATACACTCTGTGTGC
* * * **
19280630 TAGAATGCACTTTGTACGC
1 TAGGATACACTCTGTGTGC
*
19280649 TAGGATACACTTTGTGTG
1 TAGGATACACTCTGTGTG
19280667 TCAAGATGCG
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 41 0.95
20 2 0.05
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (19 bp):
TAGGATACACTCTGTGTGC
Found at i:19282202 original size:12 final size:12
Alignment explanation
Indices: 19282184--19282215 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19282174 GTTATTTGTT
19282184 ATTTATTAATTA
1 ATTTATTAATTA
*
19282196 GTTTATTAATTA
1 ATTTATTAATTA
19282208 ATTTATTA
1 ATTTATTA
19282216 TTATTATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
ATTTATTAATTA
Found at i:19282252 original size:18 final size:18
Alignment explanation
Indices: 19282208--19282253 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
19282198 TTATTAATTA
*
19282208 ATTTATTATTATTATCAT
1 ATTTATTATTATAATCAT
19282226 AGTTT-TTATTACTAAT-AT
1 A-TTTATTATTA-TAATCAT
19282244 ATTTATTATT
1 ATTTATTATT
19282254 GATATGGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 15 0.62
19 6 0.25
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTATTATTATAATCAT
Found at i:19293223 original size:30 final size:31
Alignment explanation
Indices: 19293188--19293318 Score: 137
Period size: 30 Copynumber: 4.4 Consensus size: 31
19293178 AATTAATTAA
*
19293188 AAAATTATATTTTAACCCCTAAACTTTTCT-
1 AAAATTACATTTTAACCCCTAAACTTTTCTC
* *
19293218 AAAATTACATTTTGACCCCTAAAATTTT-TC
1 AAAATTACATTTTAACCCCTAAACTTTTCTC
* *
19293248 AAAATTACATTTCAACCCCTTAA-TTTT-TC
1 AAAATTACATTTTAACCCCTAAACTTTTCTC
* * * * *
19293277 TAAATTACTTTTTAAACACTACAC-TTTCTC
1 AAAATTACATTTTAACCCCTAAACTTTTCTC
19293307 AAAATTACATTT
1 AAAATTACATTT
19293319 CGGCCCCAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
29 26 0.31
30 57 0.69
ACGTcount: A:0.37, C:0.21, G:0.01, T:0.42
Consensus pattern (31 bp):
AAAATTACATTTTAACCCCTAAACTTTTCTC
Found at i:19293314 original size:59 final size:60
Alignment explanation
Indices: 19293188--19293319 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 60
19293178 AATTAATTAA
* * * * * *
19293188 AAAATTATATTTTAACCCCTAAACTTTTCTAAAATTACATTTTGACCCCTAAAATTTTTC
1 AAAATTACATTTCAACCCCTAAACTTTTCTAAAATTACATTTTAAACACTAAAATTTCTC
* * * * *
19293248 AAAATTACATTTCAACCCCTTAATTTTTCT-AAATTACTTTTTAAACACTACACTTTCTC
1 AAAATTACATTTCAACCCCTAAACTTTTCTAAAATTACATTTTAAACACTAAAATTTCTC
19293307 AAAATTACATTTC
1 AAAATTACATTTC
19293320 GGCCCCAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 35 0.57
60 26 0.43
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.42
Consensus pattern (60 bp):
AAAATTACATTTCAACCCCTAAACTTTTCTAAAATTACATTTTAAACACTAAAATTTCTC
Found at i:19293677 original size:21 final size:21
Alignment explanation
Indices: 19293653--19293710 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
19293643 AAGCAAAGAC
*
19293653 ACAAAAAATAAAAAAAAGCAA
1 ACAAAAAAGAAAAAAAAGCAA
*
19293674 ACAAAAAAGAAAAAATAGCAA
1 ACAAAAAAGAAAAAAAAGCAA
*
19293695 AGAAAGAAAAGAAAAA
1 A-CAA-AAAAGAAAAA
19293711 GAAGAAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 20 0.62
22 2 0.06
23 10 0.31
ACGTcount: A:0.79, C:0.07, G:0.10, T:0.03
Consensus pattern (21 bp):
ACAAAAAAGAAAAAAAAGCAA
Found at i:19293811 original size:13 final size:13
Alignment explanation
Indices: 19293793--19293866 Score: 77
Period size: 13 Copynumber: 6.0 Consensus size: 13
19293783 GGGCTCATCG
19293793 AGAAAGAAGAAAA
1 AGAAAGAAGAAAA
19293806 AGAAAGAAG-AAA
1 AGAAAGAAGAAAA
**
19293818 AG-GGGAAGAAGAA
1 AGAAAGAAGAA-AA
19293831 AG-AAGAA-AAAA
1 AGAAAGAAGAAAA
19293842 AGAAA-AAGAAAA
1 AGAAAGAAGAAAA
*
19293854 AGAAAAAAGAAAA
1 AGAAAGAAGAAAA
19293867 TAACTTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.19
12 19 0.37
13 23 0.44
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAAGAAGAAAA
Found at i:19293815 original size:7 final size:6
Alignment explanation
Indices: 19293793--19293866 Score: 62
Period size: 6 Copynumber: 12.0 Consensus size: 6
19293783 GGGCTCATCG
*** *
19293793 AGAAAGA AGAAAA AGAAAGA AG-AAA AGGGGA AGAAGAA AGAAGA A-AAAA
1 AGAAA-A AGAAAA AGAAA-A AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA
19293842 AGAAAA AGAAAA AGAAAAA AGAAAA
1 AGAAAA AGAAAA AG-AAAA AGAAAA
19293867 TAACTTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
5 7 0.13
6 29 0.53
7 19 0.35
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:19293850 original size:21 final size:21
Alignment explanation
Indices: 19293799--19293866 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
19293789 ATCGAGAAAG
*
19293799 AAGAAAAAGAAAGAAGAAAAG
1 AAGAAAAAGAAAGAAGAAAAA
** *
19293820 GGGAAGAAGAAAGAAGAAAAA
1 AAGAAAAAGAAAGAAGAAAAA
19293841 AAGAAAAAGAAA-AAG-AAAA
1 AAGAAAAAGAAAGAAGAAAAA
19293860 AAGAAAA
1 AAGAAAA
19293867 TAACTTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 11 0.28
20 3 0.08
21 26 0.65
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
AAGAAAAAGAAAGAAGAAAAA
Found at i:19294550 original size:20 final size:20
Alignment explanation
Indices: 19294508--19294551 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
19294498 GTAAATATTC
**
19294508 AAAAATTCTCGTGTTTTTTT
1 AAAAATTCTCGTGTTTTAAT
19294528 AAAAATTCTCGTGTTTTAAT
1 AAAAATTCTCGTGTTTTAAT
19294548 AAAA
1 AAAA
19294552 TCACGATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (20 bp):
AAAAATTCTCGTGTTTTAAT
Found at i:19294821 original size:35 final size:35
Alignment explanation
Indices: 19294708--19295115 Score: 268
Period size: 35 Copynumber: 11.5 Consensus size: 35
19294698 ATTTTCGTGC
*
19294708 TTTCGTGTTTTCAAAATTTTC-ATGTTTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCGATGTTTCAAAAAT
* * ***
19294742 CCTTT--TGTTTTCCAAAATTCCGGCATTTCAAAAAAAT
1 --TTTCGTGTTTTCAAAAATTTCGATGTTTC--AAAAAT
* *
19294779 TTTCGTGTTTTCAAGAATTTCGATGATTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCGATGTTTCAAAAAT
* * * *
19294814 TTCCGTGTTTTCAAGAATTTTC-ACGTTTTTATAAAAT
1 TTTCGTGTTTTCAA-AAATTTCGATG-TTTCA-AAAAT
* * *
19294851 TTTCGTGTTTTTAAAAAATTCCCG-TGTTTTAAAGATAAAT
1 TTTCGTG-TTTTCAAAAATT-TCGATG-TTT-CA-A-AAAT
* * *
19294891 TTTTGTGTTTTCGAAAATTTTC-TTGTTTCAAAAAT
1 TTTCGTGTTTTC-AAAAATTTCGATGTTTCAAAAAT
** * * *
19294926 CCTCTTGTTTTCAAAAATTCCGGTGTTTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCGATGTTTCAAAAAT
* *
19294961 CTTCGTGTTTTCAAAAATTTCGATGATTCAAAAAAT
1 TTTCGTGTTTTCAAAAATTTCGATGTTTC-AAAAAT
19294997 TTTCGTGTTTTCAAAAATTTCTCG-TGTTTCAAAAAT
1 TTTCGTGTTTTCAAAAA-TT-TCGATGTTTCAAAAAT
*
19295033 TTT--T-TTTTC-AAAATGTTCG-TGTTTTCAACAAT
1 TTTCGTGTTTTCAAAAAT-TTCGATG-TTTCAAAAAT
* * *
19295065 TCTCGTG-TTTCTAAAATTCTC-ATGTTTCCAAAAT
1 TTTCGTGTTTTCAAAAATT-TCGATGTTTCAAAAAT
*
19295099 TTTCGTGTTTTAAAAAA
1 TTTCGTGTTTTCAAAAA
19295116 AATTTGTTTC
Statistics
Matches: 292, Mismatches: 52, Indels: 57
0.73 0.13 0.14
Matches are distributed among these distances:
31 6 0.02
32 16 0.05
33 5 0.02
34 41 0.14
35 92 0.32
36 43 0.15
37 46 0.16
38 18 0.06
39 9 0.03
40 16 0.05
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (35 bp):
TTTCGTGTTTTCAAAAATTTCGATGTTTCAAAAAT
Found at i:19294832 original size:18 final size:18
Alignment explanation
Indices: 19294773--19295114 Score: 170
Period size: 18 Copynumber: 19.3 Consensus size: 18
19294763 GGCATTTCAA
*
19294773 AAAAATTTTCGTGTTTTC
1 AAAAATTTCCGTGTTTTC
* *
19294791 AAGAATTT-CGATG-ATTC
1 AAAAATTTCCG-TGTTTTC
19294808 AAAAATTTCCGTGTTTTC
1 AAAAATTTCCGTGTTTTC
*
19294826 AAGAATTTTCACGT-TTTT-
1 AA-AAATTTC-CGTGTTTTC
* *
19294844 ATAAAATTTTCGTGTTTTTA
1 A-AAAATTTCCGTG-TTTTC
* *
19294864 AAAAATTCCCGTGTTTTAA
1 AAAAATTTCCGTGTTTT-C
**
19294883 AGATAAATTTTTGTGTTTTC
1 A-A-AAATTTCCGTGTTTTC
* * *
19294903 GAAAATTTTCTTG-TTTC
1 AAAAATTTCCGTGTTTTC
* *
19294920 AAAAA-TCCTCTTGTTTTC
1 AAAAATTTC-CGTGTTTTC
19294938 AAAAA-TTCCG-GTGTTTC
1 AAAAATTTCCGTGT-TTTC
19294955 AAAAATCTT-CGTGTTTTC
1 AAAAAT-TTCCGTGTTTTC
*
19294973 AAAAATTT-CGATG-ATTC
1 AAAAATTTCCG-TGTTTTC
*
19294990 AAAAAATTTTCGTGTTTTC
1 -AAAAATTTCCGTGTTTTC
19295009 AAAAATTTCTCGTG-TTTC
1 AAAAATTTC-CGTGTTTTC
*
19295027 AAAAATTT---TTTTTTC
1 AAAAATTTCCGTGTTTTC
19295042 -AAAATGTT-CGTGTTTTC
1 AAAAAT-TTCCGTGTTTTC
*
19295059 AACAA-TTCTCGTG-TTTC
1 AAAAATTTC-CGTGTTTTC
* *
19295076 TAAAA-TTCTCATG-TTTC
1 AAAAATTTC-CGTGTTTTC
* *
19295093 CAAAATTTTCGTGTTTT-
1 AAAAATTTCCGTGTTTTC
19295110 AAAAA
1 AAAAA
19295115 AAATTTGTTT
Statistics
Matches: 258, Mismatches: 34, Indels: 65
0.72 0.10 0.18
Matches are distributed among these distances:
14 6 0.02
15 6 0.02
16 5 0.02
17 81 0.31
18 102 0.40
19 41 0.16
20 5 0.02
21 12 0.05
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (18 bp):
AAAAATTTCCGTGTTTTC
Found at i:19294851 original size:19 final size:19
Alignment explanation
Indices: 19294808--19294870 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
19294798 TCGATGATTC
*
19294808 AAAAA-TTTC-CGTGTTTTC
1 AAAAATTTTCACGT-TTTTA
*
19294826 AAGAATTTTCACGTTTTTA
1 AAAAATTTTCACGTTTTTA
* **
19294845 TAAAATTTTCGTGTTTTTA
1 AAAAATTTTCACGTTTTTA
19294864 AAAAATT
1 AAAAATT
19294871 CCCGTGTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 4 0.11
19 29 0.81
20 3 0.08
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (19 bp):
AAAAATTTTCACGTTTTTA
Found at i:19294876 original size:19 final size:19
Alignment explanation
Indices: 19294838--19294880 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
19294828 GAATTTTCAC
* **
19294838 GTTTTTATAAAATTTTCGT
1 GTTTTTAAAAAATTCCCGT
19294857 GTTTTTAAAAAATTCCCGT
1 GTTTTTAAAAAATTCCCGT
19294876 GTTTT
1 GTTTT
19294881 AAAGATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (19 bp):
GTTTTTAAAAAATTCCCGT
Found at i:19294919 original size:17 final size:17
Alignment explanation
Indices: 19294887--19295114 Score: 178
Period size: 17 Copynumber: 13.2 Consensus size: 17
19294877 TTTTAAAGAT
* *
19294887 AAATTTTTGTGTTTTCGA
1 AAATTTTCGTG-TTTCAA
*
19294905 AAATTTTCTTGTTTCAA
1 AAATTTTCGTGTTTCAA
** *
19294922 AAATCCTCTTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
*
19294940 AAA-TTCCGGTGTTTCAA
1 AAATTTTC-GTGTTTCAA
*
19294957 AAATCTTCGTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
*
19294975 AAA-TTTCGATGATTCAAA
1 AAATTTTCG-TGTTTC-AA
19294993 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
19295011 AAATTTCTCGTGTTTCAA
1 AAATTT-TCGTGTTTCAA
*
19295029 AAATTTT--TTTTTC-A
1 AAATTTTCGTGTTTCAA
*
19295043 AAATGTTCGTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
* * *
19295061 CAATTCTCGTGTTTCTA
1 AAATTTTCGTGTTTCAA
* * *
19295078 AAATTCTCATGTTTCCA
1 AAATTTTCGTGTTTCAA
*
19295095 AAATTTTCGTGTTTTAA
1 AAATTTTCGTGTTTCAA
19295112 AAA
1 AAA
19295115 AAATTTGTTT
Statistics
Matches: 169, Mismatches: 28, Indels: 27
0.75 0.12 0.12
Matches are distributed among these distances:
14 7 0.04
15 5 0.03
16 1 0.01
17 74 0.44
18 69 0.41
19 13 0.08
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:19296840 original size:4 final size:4
Alignment explanation
Indices: 19296827--19296861 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
19296817 GCATGACTGA
19296827 CATT CA-T CATT CATT CATT CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT
19296862 GCATGTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
CATT
Found at i:19302001 original size:157 final size:152
Alignment explanation
Indices: 19301726--19302630 Score: 1144
Period size: 157 Copynumber: 5.9 Consensus size: 152
19301716 TGTTTTTTGT
*
19301726 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTTAC--GCTGAGGTATTTTTCAAT
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTTCAAT
* * *
19301789 TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGG
66 TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGG
*
19301854 TATTTCTTTTAAATTTCT-ATTTTC
131 TA--T-TTTTAAATTTCTCTTTTTC
* *
19301878 AAAAATCAACTCATATTGTGAGAGGTGAGCTGAGCCTCGGGTCACATGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTA-TT-TTTCA
* * *
19301943 AGTTTCTGTTTTTAAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTG
64 A-TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
*
19302008 AGGTATTTTTCAATTTCTGTCTTTTTC
128 AGGTATTTTTAAATTTC--TCTTTTTC
* * * ** * * *
19302035 AAAAATCAACTCATTTTGCT-AGAAGTGAGTTTAGTTTCGGGTCACATGCCGAGGCATTTCTTTT
1 AAAAATCAACTCATATTG-TGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTA-TT-TTTC
* *
19302099 AAGTTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCT
63 AA-TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCT
* * * *
19302164 GATGTATTTTTCAATTTATGTCCTTTTC
127 GAGGTATTTTT-AAATT-TCTCTTTTTC
* * * * * *
19302192 AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGTTGAGGTA-TTTTAAAT
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTTCAAT
*
19302256 TT-TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
66 TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGG
*
19302320 TA-TTTTAAATTTCTGTTTTTC
131 TATTTTTAAATTTCTCTTTTTC
* *
19302341 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAAG-TCGAGGTATTTTTCAA
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATGCT-GAGGTATTTTTCAA
* * * *
19302405 TTTCTGTTTTTCAAAAATCAACTCATGTTACGAGAGGTGAGTTGAGTCTCGAGTCACACGCTGAG
65 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAG
* *
19302470 GTATTTTTCAATTTCTGTTTTTTC
130 GTATTTTTAAATTTCT-CTTTTTC
*
19302494 AAAAAATCAACTCATATTGCT-AGAGGTGAGTTGAGCCTCGGGTCGCATGCTGAGGTATTATTTT
1 -AAAAATCAACTCATATTG-TGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTA-T-TTTT
* * * *
19302558 CAATTTCTGTTTTTCAAAAATCAACTCATATTACGATAGGTGAGTTGAGCCTCGGGTCGCACGCC
62 CAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCT
*
19302623 GAGTTATT
127 GAGGTATT
19302631 CTCGATTTCT
Statistics
Matches: 665, Mismatches: 66, Indels: 40
0.86 0.09 0.05
Matches are distributed among these distances:
148 1 0.00
149 58 0.09
150 13 0.02
151 63 0.09
152 114 0.17
153 9 0.01
154 74 0.11
155 6 0.01
156 76 0.11
157 246 0.37
158 4 0.01
159 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (152 bp):
AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTTTCAAT
TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGG
TATTTTTAAATTTCTCTTTTTC
Found at i:19302008 original size:79 final size:76
Alignment explanation
Indices: 19301702--19302650 Score: 1187
Period size: 78 Copynumber: 12.3 Consensus size: 76
19301692 TTTCACAAAT
* *
19301702 TATTTTTCAATCTT-TGTTTTTTGTAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGG
1 TATTTTTCAAT-TTCTG-TTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
*
19301766 GT--TACGCTGAGG
63 GTCACACGCTGAGG
*
19301778 TATTTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
19301843 ACATGCCGAGG
66 ACACGCTGAGG
* * * *
19301854 TATTTCTTTTAAATTTCT-ATTTTCAAAAATCAACTCATATTGTGAGAGGTGAGCTGAGCCTCGG
1 TA--T-TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
*
19301918 GTCACATGCTGAGG
63 GTCACACGCTGAGG
* * * *
19301932 TATTTCTTTTAAGTTTCTGTTTTTAAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGG
1 TA-TT-TTTCAA-TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
19301997 GTCACACGCTGAGG
63 GTCACACGCTGAGG
* * * * **
19302011 TATTTTTCAATTTCTGTCTTTTTCAAAAATCAACTCATTTTGCTAGAAGTGAGTTTAGTTTCGGG
1 TATTTTTCAATTTCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* *
19302076 TCACATGCCGAGG
64 TCACACGCTGAGG
* * * *
19302089 CATTTCTTTTAAGTTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGG
1 TA-TT-TTTCAA-TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
*
19302154 GTCACACGCTGATG
63 GTCACACGCTGAGG
* *
19302168 TATTTTTCAATTTATGTCCTTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGT--TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* *
19302233 TCGCACGTTGAGG
64 TCACACGCTGAGG
*
19302246 TA-TTTTAAATTT-TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
19302309 GCACGCTGAGG
66 ACACGCTGAGG
*
19302320 TA-TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
19302384 ACAAG-TCGAGG
66 ACACGCT-GAGG
* * * *
19302395 TATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATGTTACGAGAGGTGAGTTGAGTCTCGAGTC
1 TATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
19302460 ACACGCTGAGG
66 ACACGCTGAGG
*
19302471 TATTTTTCAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTG-TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* *
19302536 TCGCATGCTGAGG
64 TCACACGCTGAGG
* *
19302549 TATTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTACGATAGGTGAGTTGAGCCTCGGG
1 TA-T-TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * *
19302614 TCGCACGCCGAGT
64 TCACACGCTGAGG
* * *
19302627 TA-TTCTCGATTTCTGCTTTTCAAA
1 TATTTTTCAATTTCTGTTTTTCAAA
19302651 TAAAAAGAAA
Statistics
Matches: 777, Mismatches: 72, Indels: 49
0.87 0.08 0.05
Matches are distributed among these distances:
74 111 0.14
75 85 0.11
76 119 0.15
77 33 0.04
78 276 0.36
79 129 0.17
80 18 0.02
81 6 0.01
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (76 bp):
TATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
ACACGCTGAGG
Found at i:19302873 original size:29 final size:29
Alignment explanation
Indices: 19302797--19302920 Score: 176
Period size: 29 Copynumber: 4.2 Consensus size: 29
19302787 AATTAATTAA
19302797 AAAATTACATTTTGACCCCTAAACTTTTC
1 AAAATTACATTTTGACCCCTAAACTTTTC
19302826 TAAAATTACATTTTGACCCCTAAACTTTTC
1 -AAAATTACATTTTGACCCCTAAACTTTTC
** *
19302856 AAAATTACATTTCAACCCCTTAACTTTTC
1 AAAATTACATTTTGACCCCTAAACTTTTC
* * *
19302885 TAAATTACATTTTGATCCCTACACTTTCTC
1 AAAATTACATTTTGACCCCTAAACTTT-TC
19302915 AAAATT
1 AAAATT
19302921 GCGTTTCTAC
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 47 0.57
30 36 0.43
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAAACTTTTC
Found at i:19302933 original size:59 final size:59
Alignment explanation
Indices: 19302797--19302920 Score: 187
Period size: 59 Copynumber: 2.1 Consensus size: 59
19302787 AATTAATTAA
**
19302797 AAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTTTC
1 AAAATTACATTTCAACCCCTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTTTC
* * *
19302856 AAAATTACATTTCAACCCCTTAACTTTTCT-AAATTACATTTTGATCCCTACACTTTCTC
1 AAAATTACATTTCAACCCCTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTT-TC
19302915 AAAATT
1 AAAATT
19302921 GCGTTTCTAC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 24 0.41
59 35 0.59
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (59 bp):
AAAATTACATTTCAACCCCTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTTTC
Found at i:19303297 original size:17 final size:18
Alignment explanation
Indices: 19303272--19303318 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
19303262 ACAAAAAAAT
*
19303272 AAAAA-AAAAGCA-AGCA
1 AAAAAGAAAAGAATAGCA
19303288 AAAAAGAAAA-AATAGCA
1 AAAAAGAAAAGAATAGCA
19303305 AAGAAAGAAAAGAA
1 AA-AAAGAAAAGAA
19303319 AAAGAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.23
17 10 0.38
18 8 0.31
19 2 0.08
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAATAGCA
Found at i:19303297 original size:21 final size:23
Alignment explanation
Indices: 19303273--19303331 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
19303263 CAAAAAAATA
*
19303273 AAAAAAAAGC-AAGCAA-AAAAG
1 AAAAAAAAGCAAAGAAAGAAAAG
*
19303294 AAAAAATAGCAAAGAAAGAAAAG
1 AAAAAAAAGCAAAGAAAGAAAAG
* *
19303317 AAAAAGAAGAAAAGA
1 AAAAAAAAGCAAAGA
19303332 GGGGAGAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 9 0.29
22 5 0.16
23 17 0.55
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAAAAAAGCAAAGAAAGAAAAG
Found at i:19303424 original size:7 final size:7
Alignment explanation
Indices: 19303414--19303503 Score: 58
Period size: 7 Copynumber: 12.4 Consensus size: 7
19303404 GGGAAAGAAG
19303414 AAAAAGA
1 AAAAAGA
19303421 AAAAAGA
1 AAAAAGA
* *
19303428 AGAGAGA
1 AAAAAGA
19303435 AAGAAAGAA
1 AA-AAAG-A
19303444 GAAAAAGA
1 -AAAAAGA
19303452 AAGAAA-A
1 AA-AAAGA
** *
19303459 AAAGGGG
1 AAAAAGA
*
19303466 AAGAAGA
1 AAAAAGA
*
19303473 AAGAAGA
1 AAAAAGA
19303480 AAAAA-A
1 AAAAAGA
19303486 GAAAAAGA
1 -AAAAAGA
19303494 AAAAAGA
1 AAAAAGA
19303501 AAA
1 AAA
19303504 TAATTTTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
6 2 0.03
7 47 0.73
8 8 0.12
9 5 0.08
10 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:19303443 original size:31 final size:34
Alignment explanation
Indices: 19303407--19303496 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 34
19303397 GCTGATCGGG
*
19303407 AAAGAAGAAAAAGAAAAAAGAAGA-GAG-A-AAG
1 AAAGAAGAAAAAGAAAAAAGAAAAGGAGAAGAAG
*
19303438 AAAGAAGAAAAAGAAAGAAA-AAAAGGGGAAGAAG
1 AAAGAAGAAAAAGAAA-AAAGAAAAGGAGAAGAAG
*
19303472 AAAGAAGAAAAAAAGAAAAAGAAAA
1 AAAGAAGAAAAAGA-AAAAAGAAAA
19303497 AAGAAAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
31 19 0.38
32 5 0.10
33 1 0.02
34 19 0.38
35 6 0.12
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (34 bp):
AAAGAAGAAAAAGAAAAAAGAAAAGGAGAAGAAG
Found at i:19303456 original size:21 final size:21
Alignment explanation
Indices: 19303406--19303502 Score: 81
Period size: 21 Copynumber: 4.6 Consensus size: 21
19303396 GGCTGATCGG
* *
19303406 GAAAGAAGAAAAAGAAAAAAGAA
1 GAAAGAA-AGAAAGAAGAAA-AA
*
19303429 GAGAGAAAGAAAGAAGAAAAA
1 GAAAGAAAGAAAGAAGAAAAA
* ** *
19303450 GAAAGAAAAAAAGGGGAAGAA
1 GAAAGAAAGAAAGAAGAAAAA
*
19303471 GAAAG-AAGAAAAAAAGAAAAA
1 GAAAGAAAG-AAAGAAGAAAAA
19303492 GAAA-AAAGAAA
1 GAAAGAAAGAAA
19303503 ATAATTTTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 5 0.08
21 38 0.64
22 10 0.17
23 6 0.10
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAGAAAAA
Found at i:19303470 original size:42 final size:42
Alignment explanation
Indices: 19303424--19303503 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
19303414 AAAAAGAAAA
* *
19303424 AAGAAGAGAGAA-AGAAAGAAGAAAAAGAAAGAAA-AAAAGGGG
1 AAGAAGAAAGAAGA-AAAAAAGAAAAAGAAA-AAAGAAAAGGGG
19303466 AAGAAGAAAGAAGAAAAAAAGAAAAAGAAAAAAGAAAA
1 AAGAAGAAAGAAGAAAAAAAGAAAAAGAAAAAAGAAAA
19303504 TAATTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 3 0.09
42 30 0.88
43 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (42 bp):
AAGAAGAAAGAAGAAAAAAAGAAAAAGAAAAAAGAAAAGGGG
Found at i:19303499 original size:24 final size:24
Alignment explanation
Indices: 19303411--19303501 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
19303401 ATCGGGAAAG
* *
19303411 AAGAAAAAGAAAAAAGAAGAGAGA
1 AAGAAAAAGAAAAAAGAAGAAAAA
19303435 AAGAAAGAAG-AAAAAGAAAGAAAAA
1 AAGAAA-AAGAAAAAAG-AAGAAAAA
*** *
19303460 AAGGGGAAGAAGAAAGAAGAAAAA
1 AAGAAAAAGAAAAAAGAAGAAAAA
19303484 AAGAAAAAGAAAAAAGAA
1 AAGAAAAAGAAAAAAGAA
19303502 AATAATTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 37 0.69
25 17 0.31
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (24 bp):
AAGAAAAAGAAAAAAGAAGAAAAA
Found at i:19303501 original size:31 final size:31
Alignment explanation
Indices: 19303406--19303501 Score: 97
Period size: 34 Copynumber: 3.0 Consensus size: 31
19303396 GGCTGATCGG
* *
19303406 GAAAGAAGAAAAAGA-AAAAAGAAGAGAGAAA
1 GAAAGAAGAAAAAAAGAAAAAGAAGAAAG-AA
*
19303437 GAAAGAAGAAAAAGAAAGAAAAA-AAGGGGAAGAA
1 GAAAGAAG-AAAA-AAAGAAAAAGAA--GAAAGAA
*
19303471 GAAAGAAGAAAAAAAGAAAAAGAAAAAAGAA
1 GAAAGAAGAAAAAAAGAAAAAGAAGAAAGAA
19303502 AATAATTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
31 13 0.24
32 13 0.24
33 10 0.19
34 15 0.28
35 3 0.06
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (31 bp):
GAAAGAAGAAAAAAAGAAAAAGAAGAAAGAA
Found at i:19303751 original size:10 final size:11
Alignment explanation
Indices: 19303736--19303772 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
19303726 GAGGCAGGCC
19303736 AGAAAAAAA-A
1 AGAAAAAAAGA
19303746 AGAAAAAAAGA
1 AGAAAAAAAGA
*
19303757 AGAAAGAAAGA
1 AGAAAAAAAGA
19303768 A-AAAA
1 AGAAAA
19303773 TGTTCAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 12 0.50
11 12 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:19304337 original size:35 final size:33
Alignment explanation
Indices: 19304290--19304410 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 33
19304280 CGTGCTTTCG
19304290 TGTTTTCAAAATTTTCA-TGTTTCAAAAATCCTTT
1 TGTTTTCAAAA-TTTCAGTGTTTCAAAAAT-CTTT
* * *
19304324 TGTTTTCCAAAATTCCAGCGTTTCAAAAATTTTTT
1 TGTTTT-CAAAATTTCAGTGTTTCAAAAA-TCTTT
*
19304359 GTGTTTTCAAGAATTTCAGTGATTCAAAAAAT-TTCT
1 -TGTTTTCAA-AATTTCAGTGTTTC-AAAAATCTT-T
19304395 ATGTTTTCAAGAATTT
1 -TGTTTTCAA-AATTT
19304411 TCACGTTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
34 10 0.14
35 23 0.32
36 35 0.48
37 5 0.07
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (33 bp):
TGTTTTCAAAATTTCAGTGTTTCAAAAATCTTT
Found at i:19304368 original size:19 final size:18
Alignment explanation
Indices: 19304344--19304682 Score: 214
Period size: 18 Copynumber: 18.5 Consensus size: 18
19304334 AATTCCAGCG
*
19304344 TTTCAAAAATTTTTTGTGT
1 TTTCAAAAA-TTTTCGTGT
*
19304363 TTTCAAGAA-TTTCAGTG-
1 TTTCAAAAATTTTC-GTGT
* * *
19304380 ATTCAAAAAATTTCTATGT
1 TTTCAAAAATTTTC-GTGT
* *
19304399 TTTCAAGAATTTTCACGTTT
1 TTTCAAAAATTTT--CGTGT
* *
19304419 TTTTATAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* * *
19304437 TTTTAAAAAATTCCGGTGTT
1 TTTCAAAAATTTTC-GTG-T
*
19304457 TTTAAAGATAAATTTTCGTGT
1 TTT-CA-A-AAATTTTCGTGT
*
19304478 TTTCAAAAATTTTCTTGT
1 TTTCAAAAATTTTCGTGT
** *
19304496 TTT-AAAAATCCTCCTGT
1 TTTCAAAAATTTTCGTGT
*
19304513 TTTCAAAAA-TTCCG-GT
1 TTTCAAAAATTTTCGTGT
*
19304529 GTTTCAAAAATCTTCGTGT
1 -TTTCAAAAATTTTCGTGT
19304548 TTTCAAAAA-TTTCG-GT
1 TTTCAAAAATTTTCGTGT
*
19304564 GATTCAAAAAATTTTCGTGT
1 -TTTC-AAAAATTTTCGTGT
19304584 TTTCAAAAATTTCTCGTG-
1 TTTCAAAAATTT-TCGTGT
* *
19304602 TTTCAAAAATTTTCTTTTTTT
1 TTTCAAAAATTTTC---GTGT
*
19304623 TTTC-AAAATGTTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
19304640 TTTCAACAATTCTCGTG-
1 TTTCAAAAATTTTCGTGT
*
19304657 TTTCAAAAATTTCCGTGT
1 TTTCAAAAATTTTCGTGT
19304675 TTT-AAAAA
1 TTTCAAAAA
19304683 AAATTTGCTT
Statistics
Matches: 249, Mismatches: 46, Indels: 52
0.72 0.13 0.15
Matches are distributed among these distances:
16 4 0.02
17 68 0.27
18 92 0.37
19 37 0.15
20 28 0.11
21 10 0.04
22 4 0.02
23 6 0.02
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.47
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:19304674 original size:35 final size:36
Alignment explanation
Indices: 19304287--19304683 Score: 212
Period size: 35 Copynumber: 10.9 Consensus size: 36
19304277 TTTCGTGCTT
* * *
19304287 TCGTGTTTTC-AAAATTTTCATG-TTTCAAAAATCC
1 TCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAATTC
** * * *
19304321 TTTTGTTTTCCAAAA-TTCCAGCG-TTTCAAAAATTTT
1 TCGTGTTTTCAAAAATTTCC-GTGTTTTCAAAAA-TTC
* * * *
19304357 TTGTGTTTTCAAGAATTTCAGTG-ATTCAAAAAATT-
1 TCGTGTTTTCAAAAATTTCCGTGTTTTC-AAAAATTC
* * * * * *
19304392 TCTATGTTTTCAAGAATTTTCACGTTTTTTTATAAATTT
1 TC-GTGTTTTCAA-AAATTTC-CGTGTTTTCAAAAATTC
* * * *
19304431 TCGTGTTTTTAAAAAATTCCGGTGTTTTTAAAGATAAATTT
1 TCGTGTTTTCAAAAATTTCC-GTG-TTTT-CA-A-AAATTC
* * *
19304472 TCGTGTTTTCAAAAATTTTCTTGTTTT-AAAAATCC
1 TCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAATTC
*
19304507 TCCTGTTTTCAAAAA-TTCCG-GTGTTTCAAAAA-TC
1 TCGTGTTTTCAAAAATTTCCGTGT-TTTCAAAAATTC
* * *
19304541 TTCGTGTTTTCAAAAATTTCGGTG-ATTCAAAAAATTT
1 -TCGTGTTTTCAAAAATTTCCGTGTTTTC-AAAAATTC
19304578 TCGTGTTTTCAAAAATTTCTCGTG-TTTCAAAAATTTTC
1 TCGTGTTTTCAAAAATTTC-CGTGTTTTCAAAAA--TTC
** * *
19304616 TTTTTTTTTTC-AAAATGTT-CGTGTTTTCAACAATTC
1 -TCGTGTTTTCAAAAAT-TTCCGTGTTTTCAAAAATTC
*
19304652 TCGTG-TTTCAAAAATTTCCGTGTTTTAAAAAA
1 TCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAA
19304684 AATTTGCTTC
Statistics
Matches: 278, Mismatches: 55, Indels: 59
0.71 0.14 0.15
Matches are distributed among these distances:
33 2 0.01
34 24 0.09
35 74 0.27
36 67 0.24
37 33 0.12
38 35 0.13
39 18 0.06
40 2 0.01
41 23 0.08
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (36 bp):
TCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAATTC
Found at i:19306752 original size:44 final size:44
Alignment explanation
Indices: 19306657--19307040 Score: 295
Period size: 44 Copynumber: 8.8 Consensus size: 44
19306647 AGATGGCAAA
* ** * *
19306657 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAACCAATAAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGTAACAAG
*
19306702 TC-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAAG
* * * *
19306745 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGAAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAACAAG
* * * *** *
19306790 TCTTATC-CCCTGAAGTTGTAGTAGG-GCAGACTGAAGATGGTAAA
1 TCTTATCTCCCTGAAGTTGCAGT-GGAGCAGATTAAAG-TAACAAG
* * * *
19306834 TCTTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAATTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAAG
* * *
19306878 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAA-CAAG
** * * * * * *
19306923 TCTTATC-CTTTGAAGTTGTAGTGGGGCAAACTGAAGATGACGAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAAC-AAG
* * *
19306967 TCTTGTCTCCCTGAAGTTGCAGT-G-G-AG---AAAGTGACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAAG
* *
19307005 TCTTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
19307041 ATGATTGATC
Statistics
Matches: 273, Mismatches: 50, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
37 2 0.01
38 26 0.10
39 4 0.01
40 1 0.00
41 1 0.00
42 1 0.00
43 9 0.03
44 167 0.61
45 62 0.23
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAAG
Found at i:19306849 original size:133 final size:133
Alignment explanation
Indices: 19306704--19307032 Score: 472
Period size: 133 Copynumber: 2.5 Consensus size: 133
19306694 CCAATAATTC
*
19306704 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTG
* **
19306769 GAGCAGACTGAAGAAAACAAGTCTTATCCCCTGAAGTTGTAGTAGGGCAGACTGAAGATGGTAAA
66 GAGCAGACTGAAGAAAACAAGTCTTATCCCCTGAAGTTGTAGTAGGGCAAACTGAAGATGACAAA
19306834 TCT
131 TCT
* * *
19306837 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAATTTACAAGTCTTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTG
* ** * *
19306902 GAGCAGACTGAAGAAAGCAAGTCTTATCCTTTGAAGTTGTAGTGGGGCAAACTGAAGATGACGAA
66 GAGCAGACTGAAGAAAACAAGTCTTATCCCCTGAAGTTGTAGTAGGGCAAACTGAAGATGACAAA
19306967 TCT
131 TCT
* * * *
19306970 TGTCTCCCTGAAGTTGCAGT-G-G-AG---AAAGTGACAAATCTTATCTCCCTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTG
19307029 GAGC
66 GAGC
19307033 GGATTAAAAT
Statistics
Matches: 177, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
127 35 0.20
130 1 0.01
131 1 0.01
132 1 0.01
133 139 0.79
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (133 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTG
GAGCAGACTGAAGAAAACAAGTCTTATCCCCTGAAGTTGTAGTAGGGCAAACTGAAGATGACAAA
TCT
Found at i:19306958 original size:177 final size:172
Alignment explanation
Indices: 19306644--19307040 Score: 453
Period size: 177 Copynumber: 2.3 Consensus size: 172
19306634 GATGGATTGA
* * * *
19306644 AGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAACCAATAATTCTATCT
1 AGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAACCAACAAGTCTATCT
* **
19306709 CCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCA
65 CCCTGAAGTTGCAGTGGAGCAGACTAAAGAAACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCA
* *
19306774 GACTGAAGAAAAC-AAGTCTTATC-CCCTGAAGTTGTAGTAGGGCAG
130 AACTGAAGAAAACGAA-TCTTATCTCCCTGAAGTTGCAGT--GG-AG
* * ***
19306819 ACTGAAGATGGTAAATCTTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAATTTACAAGTCTTAT
1 A--GAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAACCAACAAGTC-TAT
* ** * * *
19306884 CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCTTATC-CTTTGAAGTTGTAGTGGG
63 CTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAA-CAAGTCTTATCTCCCTAAAGTTGCAGTGGA
** *
19306948 GCAAACTGAAGATGACGAATCTTGTCTCCCTGAAGTTGCAGTGGAG
127 GCAAACTGAAGAAAACGAATCTTATCTCCCTGAAGTTGCAGTGGAG
* *
19306994 A-AAG-TGACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAA
1 AGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
19307041 ATGATTGATC
Statistics
Matches: 189, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
171 39 0.21
172 3 0.02
175 4 0.02
176 10 0.05
177 106 0.56
178 27 0.14
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (172 bp):
AGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAACCAACAAGTCTATCTC
CCTGAAGTTGCAGTGGAGCAGACTAAAGAAACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAA
ACTGAAGAAAACGAATCTTATCTCCCTGAAGTTGCAGTGGAG
Found at i:19308536 original size:12 final size:12
Alignment explanation
Indices: 19308521--19308558 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
19308511 TTATTTTTTA
19308521 TTTATTAATTAT
1 TTTATTAATTAT
19308533 TTTATTAAATTAT
1 TTTATT-AATTAT
19308546 TATTATT-ATTAT
1 T-TTATTAATTAT
19308558 T
1 T
19308559 GCCATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.50
13 7 0.29
14 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTATTAATTAT
Found at i:19313975 original size:37 final size:37
Alignment explanation
Indices: 19313855--19313978 Score: 98
Period size: 37 Copynumber: 3.4 Consensus size: 37
19313845 AATAAATTTA
* * *
19313855 ATATTAAATTTAATTTAATACTTATCTTA-ATAGTATT
1 ATATTAAATTAAATATAATATTTATCTTATA-AGTATT
* * *
19313892 TTATT-AATTTAATATTAAAATGATTATC-T-TAA-TATT
1 ATATTAAATTAAATA-TAATAT--TTATCTTATAAGTATT
*
19313928 AAATTAAATTAAATATAATATTTATCTTGATAAGTATT
1 ATATTAAATTAAATATAATATTTATCTT-ATAAGTATT
19313966 ATATT-AATTAAAT
1 ATATTAAATTAAAT
19313979 TTTAAAGTGA
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
34 5 0.07
35 1 0.01
36 20 0.29
37 28 0.41
38 10 0.14
39 5 0.07
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (37 bp):
ATATTAAATTAAATATAATATTTATCTTATAAGTATT
Found at i:19313990 original size:74 final size:74
Alignment explanation
Indices: 19313852--19313991 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 74
19313842 TTTAATAAAT
* * * *
19313852 TTAATATTAAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAATGATT
1 TTAATATTAAATTAAATATAATACTTATCTTAATAGTATTATATTAATTAAATATTAAAATGATT
19313917 ATCTTAATA
66 ATCTTAATA
* * * *
19313926 TTAA-ATTAAATTAAATATAATATTTATCTTGATAAGTATTATATTAATTAAATTTTAAAGTGAT
1 TTAATATTAAATTAAATATAATACTTATCTTAAT-AGTATTATATTAATTAAATATTAAAATGAT
19313990 TA
65 TA
19313992 AGTTTAATCA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 25 0.44
74 32 0.56
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (74 bp):
TTAATATTAAATTAAATATAATACTTATCTTAATAGTATTATATTAATTAAATATTAAAATGATT
ATCTTAATA
Found at i:19316520 original size:25 final size:27
Alignment explanation
Indices: 19316448--19316527 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 27
19316438 ATAAATCTTA
19316448 AAATTATATATAATTTT-AGTTTAGTATGT
1 AAATTATATATAATTTTGA-TTT-G-ATGT
*
19316477 AAATTATACATGAATTTTGATTTGA-GT
1 AAATTATATAT-AATTTTGATTTGATGT
19316504 -AATTATATATAATTTTGATTTGAT
1 AAATTATATATAATTTTGATTTGAT
19316528 TCAATTCTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
25 13 0.28
26 9 0.20
27 2 0.04
28 1 0.02
29 11 0.24
30 9 0.20
31 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.50
Consensus pattern (27 bp):
AAATTATATATAATTTTGATTTGATGT
Found at i:19318481 original size:50 final size:50
Alignment explanation
Indices: 19318422--19318601 Score: 184
Period size: 51 Copynumber: 3.6 Consensus size: 50
19318412 AAAGTGATGG
* *
19318422 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATACT-AT-GA
* * * * * *
19318472 TCGCATGTGTAGTACTATGTGCAAGATACTATGCGTACCGGATACTTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATACTAT-GA
** * * * *
19318523 TCATGTGTGTAGTACTATGTGCAGGGTACTACGTGTATCGGATAGTAATGT
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATACT-ATGA
19318574 TCACATGTGTAGTACTATGTGCAGGCTA
1 TCACATGTGTAGTACTATGTGCAGGCTA
19318602 TTGTGTGAAC
Statistics
Matches: 104, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
50 36 0.35
51 66 0.63
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATACTATGA
Found at i:19318664 original size:45 final size:45
Alignment explanation
Indices: 19318615--19318700 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
19318605 TGTGAACCGA
* *
19318615 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCATCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCATCGG
19318660 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
19318701 CTGAGTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCATCGG
Found at i:19323383 original size:2 final size:2
Alignment explanation
Indices: 19323376--19323415 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
19323366 GGAGTTGTCC
19323376 AT AT AT AT AT 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 AT AT AT AT AT
19323416 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19323523 original size:2 final size:2
Alignment explanation
Indices: 19323516--19323567 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
19323506 NNNNNNNNNN
19323516 AT AT AT AT AT AT 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 AT AT AT AT AT AT
*
19323558 AT AA AT AT AT
1 AT AT AT AT AT
19323568 TTGTTTTTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19324398 original size:7 final size:7
Alignment explanation
Indices: 19324386--19324414 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
19324376 TTAAGGGTAA
19324386 ATTAGCC
1 ATTAGCC
19324393 ATTAGCC
1 ATTAGCC
19324400 ATTAGCC
1 ATTAGCC
19324407 ATTAGCC
1 ATTAGCC
19324414 A
1 A
19324415 ATAGGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (7 bp):
ATTAGCC
Found at i:19326657 original size:25 final size:25
Alignment explanation
Indices: 19326614--19326663 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
19326604 AGCCAATGAG
*
19326614 GATTTTTTTTATATTTTC-GTTGTT
1 GATTTTTTTGATATTTTCGGTTGTT
*
19326638 GATTTTATTTGATGTTTTCGGTTGTT
1 GATTTT-TTTGATATTTTCGGTTGTT
19326664 AATCGAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 10 0.45
26 6 0.27
ACGTcount: A:0.12, C:0.04, G:0.18, T:0.66
Consensus pattern (25 bp):
GATTTTTTTGATATTTTCGGTTGTT
Found at i:19327606 original size:3 final size:3
Alignment explanation
Indices: 19327598--19327654 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
19327588 CGAGTATATG
19327598 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19327646 TAT TAT TAT
1 TAT TAT TAT
19327655 GTTTATCTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19327748 original size:11 final size:11
Alignment explanation
Indices: 19327734--19327786 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
19327724 ATTCAATGGT
19327734 TATTTTAATTC
1 TATTTTAATTC
* *
19327745 TATTTTGAGTC
1 TATTTTAATTC
19327756 TATTTTGAATTC
1 TATTTT-AATTC
19327768 ATATATTTAATT-
1 -TAT-TTTAATTC
19327780 TATTTTA
1 TATTTTA
19327787 GAACTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (11 bp):
TATTTTAATTC
Found at i:19332526 original size:15 final size:14
Alignment explanation
Indices: 19332506--19332539 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
19332496 GATCCTTTCA
*
19332506 AAAAAAATCAAAAT
1 AAAAAAATAAAAAT
19332520 CAAAAAAATAAAAAT
1 -AAAAAAATAAAAAT
19332535 AAAAA
1 AAAAA
19332540 TAAGAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:19334902 original size:44 final size:45
Alignment explanation
Indices: 19334850--19335062 Score: 116
Period size: 44 Copynumber: 4.6 Consensus size: 45
19334840 GATTGAAGCT
*
19334850 AGAAATCTTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAA
1 AGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAA
* * * * *
19334895 AG-GATCTTATCTCTCTGAAG-TTACAGTAGAGTAGATCACATCAGATTGAA
1 AGAAATCTTATCTCCCT-AAGATTACAGTGGAGCAGATTA-A--A-A-T-AA
* * **
19334945 GCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--
1 ---AGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATT-AAAATAA
* * * **
19334992 AGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAA
1 AGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAA
*
19335037 ATG--ATCTTATCTCTCTGAAG-TTACAG
1 A-GAAATCTTATCTCCCT-AAGATTACAG
19335063 CAGAGTAGAT
Statistics
Matches: 126, Mismatches: 25, Indels: 35
0.68 0.13 0.19
Matches are distributed among these distances:
43 3 0.02
44 76 0.60
45 9 0.07
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 3 0.02
53 4 0.03
54 26 0.21
55 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
AGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAA
Found at i:19335017 original size:98 final size:97
Alignment explanation
Indices: 19334838--19335024 Score: 234
Period size: 98 Copynumber: 1.9 Consensus size: 97
19334828 ATTTAAGCCA
* * * * *
19334838 CAGATTGAAGCTAGAAATCTTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTAAAAT-AAGAATCCT
*
19334903 ATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
65 ATCTCCCTGAAGTTACAGTAGAGTAGATCACAT
* **
19334936 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCC
1 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATT-AAAATAAG-AATCC
*
19335000 TATCTCCCTG-AGATTACAGTGGAGT
64 TATCTCCCTGAAG-TTACAGTAGAGT
19335025 GGATTAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
97 4 0.05
98 69 0.91
99 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (97 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTAAAATAAGAATCCTA
TCTCCCTGAAGTTACAGTAGAGTAGATCACAT
Found at i:19335179 original size:23 final size:23
Alignment explanation
Indices: 19335149--19335195 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
19335139 TGGCGATGCA
19335149 GTGGAGCAGATTAAAGCCACATC
1 GTGGAGCAGATTAAAGCCACATC
19335172 GTGGAGCAGATTAAAGCCACATC
1 GTGGAGCAGATTAAAGCCACATC
19335195 G
1 G
19335196 GTAAATCTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (23 bp):
GTGGAGCAGATTAAAGCCACATC
Found at i:19335262 original size:50 final size:49
Alignment explanation
Indices: 19335179--19335536 Score: 225
Period size: 50 Copynumber: 7.2 Consensus size: 49
19335169 ATCGTGGAGC
* * ** **
19335179 AGATTAAAGCCACATCGGTAAATCTCGCTTCCCTGACACTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGACA-TGCAGTTAAAA
* * * * ** **
19335229 ATATTAAAGCTACAACAGCGAATCTTACCTCCCTGGCGATGCAGTGGAGT
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGAC-ATGCAGTTAAAA
* * * * * *
19335279 AGATTAAAGCCACATCGGTGAA-CTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGACA-TGCAGTTAAAA
* * ** *
19335328 AGATTAAAGCCACAACAGCAAATCTTACCTCCCTGACGATGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGAC-ATGCAGTTAAAA
* * * * *
19335378 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGACA-TGCAGTTAAAA
* * * * * * * ** *
19335428 GGATTAAAGCTACAATAGCGAATCTTACTTCCCAGGCGGTGTAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGAC-ATGCAGTTAAAA
* * * * *
19335478 AGATTGAAGCTACAACAGCGAATCTTGCTT-CCTCGACATCACAGTTAAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCT-GACAT-GCAGTTAAAA
19335528 AGATTAAAG
1 AGATTAAAG
19335537 TTGCGAGTTA
Statistics
Matches: 225, Mismatches: 75, Indels: 16
0.71 0.24 0.05
Matches are distributed among these distances:
48 1 0.00
49 38 0.17
50 184 0.82
51 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (49 bp):
AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGACATGCAGTTAAAA
Found at i:19335474 original size:100 final size:100
Alignment explanation
Indices: 19335172--19335536 Score: 480
Period size: 100 Copynumber: 3.7 Consensus size: 100
19335162 AAGCCACATC
* * * * * *
19335172 GTGGAGCAGATTAAAGCCACATCGGTAAATCTCGCTTCCCTGACACTGCAGTTAAAAATATTAAA
1 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
19335237 GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
66 GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
** *
19335272 GTGGAGTAGATTAAAGCCACATCGGTGAA-CTTGCTTCCCCGACATTGTAGTTAAAAAGATTAAA
1 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
* * *
19335336 GCCACAACAGCAAATCTTACCTCCCTGACGATGCA
66 GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
*
19335371 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAGGATTAAA
1 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
* * * * *
19335436 GCTACAATAGCGAATCTTACTTCCCAGGCGGTGTA
66 GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
* * * * * * ** *
19335471 GTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCTCGACATCACAGTTAAACAGATTAAA
1 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
19335536 G
66 G
19335537 TTGCGAGTTA
Statistics
Matches: 232, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
99 89 0.38
100 143 0.62
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (100 bp):
GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
Found at i:19337077 original size:15 final size:15
Alignment explanation
Indices: 19337041--19337082 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
19337031 TTTAATCGAG
19337041 TATATGTATTATTAT
1 TATATGTATTATTAT
*
19337056 TATTATGT-TTATCTTT
1 TA-TATGTATTAT-TAT
19337072 TATATGTATTA
1 TATATGTATTA
19337083 AGCTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (15 bp):
TATATGTATTATTAT
Found at i:19337155 original size:11 final size:11
Alignment explanation
Indices: 19337141--19337193 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
19337131 ATTCAATGGT
19337141 TATTTTAATTC
1 TATTTTAATTC
* *
19337152 TATTTTGAGTC
1 TATTTTAATTC
19337163 TATTTTGAATTC
1 TATTTT-AATTC
19337175 ATATATTTAATT-
1 -TAT-TTTAATTC
19337187 TATTTTA
1 TATTTTA
19337194 GAACTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (11 bp):
TATTTTAATTC
Found at i:19342517 original size:43 final size:43
Alignment explanation
Indices: 19342466--19342617 Score: 177
Period size: 43 Copynumber: 3.6 Consensus size: 43
19342456 TGTGTTTTTG
* * *
19342466 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACA
* * * * *
19342509 TGTAAGACCATGTCTGGGACATTGGCATTG-TATTTAATT-CA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACA
19342550 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTACA
*
19342593 TGTAAGAACACGTCTGGGACGTTGG
1 TGTAAGACCACGTCTGGGACGTTGG
19342618 TATTGTACGA
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
41 26 0.29
42 13 0.15
43 49 0.55
44 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACA
Found at i:19342608 original size:84 final size:84
Alignment explanation
Indices: 19342466--19342624 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
19342456 TGTGTTTTTG
* * * * *
19342466 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGAACACGTCTGGGACAT
19342531 TGGCATTGTATTTAATTCA
66 TGGCATTGTATTTAATTCA
19342550 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTACATGTAAGAACACGTCTGGGAC
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTACATGTAAGAACACGTCTGGGAC
* *
19342613 GTTGGTATTGTA
64 ATTGGCATTGTA
19342625 CGAGCCTTCC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
83 1 0.02
84 64 0.97
85 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (84 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGAACACGTCTGGGACAT
TGGCATTGTATTTAATTCA
Found at i:19343594 original size:27 final size:28
Alignment explanation
Indices: 19343556--19343609 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
19343546 AAGAGTATGT
19343556 TATATGACTGTTTTGGTTGAT-TGCTTC
1 TATATGACTGTTTTGGTTGATATGCTTC
19343583 TATATGACTGTTTTGGTTGATATGCTT
1 TATATGACTGTTTTGGTTGATATGCTT
19343610 GCTTGAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.17, C:0.09, G:0.22, T:0.52
Consensus pattern (28 bp):
TATATGACTGTTTTGGTTGATATGCTTC
Found at i:19347106 original size:37 final size:39
Alignment explanation
Indices: 19347065--19347202 Score: 100
Period size: 40 Copynumber: 3.5 Consensus size: 39
19347055 TTATCTACAT
* *
19347065 TACTGGTGGTTTGTCCACA-T-TGGCAGTTTATCTGTAA
1 TACTGGTAGCTTGTCCACATTATGGCAGTTTATCTGTAA
* * *
19347102 TACTGGTAGCTTGTCTACATTACTGGCAGTTTATCTGCAT
1 TACTGGTAGCTTGTCCACATTA-TGGCAGTTTATCTGTAA
* * * * * * *
19347142 TATTGATGGCTTGTCCATATTACTGGCAGCTTGTCTGCAA
1 TACTGGTAGCTTGTCCACATTA-TGGCAGTTTATCTGTAA
** *
19347182 TTTTGGTAGTTTCGTCCACAT
1 TACTGGTAGCTT-GTCCACAT
19347203 ATATTGGAGT
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
37 16 0.20
38 1 0.01
40 55 0.70
41 7 0.09
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (39 bp):
TACTGGTAGCTTGTCCACATTATGGCAGTTTATCTGTAA
Found at i:19347127 original size:20 final size:20
Alignment explanation
Indices: 19347102--19347177 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
19347092 TTATCTGTAA
*
19347102 TACTGGTAGCTTGTCTACAT
1 TACTGGCAGCTTGTCTACAT
* * *
19347122 TACTGGCAGTTTATCTGCAT
1 TACTGGCAGCTTGTCTACAT
* *** * *
19347142 TATTGATGGCTTGTCCATAT
1 TACTGGCAGCTTGTCTACAT
19347162 TACTGGCAGCTTGTCT
1 TACTGGCAGCTTGTCT
19347178 GCAATTTTGG
Statistics
Matches: 38, Mismatches: 18, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (20 bp):
TACTGGCAGCTTGTCTACAT
Found at i:19347154 original size:40 final size:40
Alignment explanation
Indices: 19347045--19347180 Score: 143
Period size: 40 Copynumber: 3.5 Consensus size: 40
19347035 AAGGAGGAAG
* * *
19347045 TACTGGCAATTTATCTACATTACTGGTGGTTTGTCCACA-
1 TACTGGCAGTTTATCTGCATTACTGGTGGCTTGTCCACAT
* * * *
19347084 T--TGGCAGTTTATCTGTAATACTGGTAGCTTGTCTACAT
1 TACTGGCAGTTTATCTGCATTACTGGTGGCTTGTCCACAT
* * *
19347122 TACTGGCAGTTTATCTGCATTATTGATGGCTTGTCCATAT
1 TACTGGCAGTTTATCTGCATTACTGGTGGCTTGTCCACAT
* *
19347162 TACTGGCAGCTTGTCTGCA
1 TACTGGCAGTTTATCTGCA
19347181 ATTTTGGTAG
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
37 29 0.37
38 1 0.01
39 1 0.01
40 47 0.60
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (40 bp):
TACTGGCAGTTTATCTGCATTACTGGTGGCTTGTCCACAT
Found at i:19350692 original size:12 final size:13
Alignment explanation
Indices: 19350665--19350697 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
19350655 TTAAAAACCC
*
19350665 TTTCATTTATTTT
1 TTTCCTTTATTTT
19350678 TTTCCTTTA-TTT
1 TTTCCTTTATTTT
19350690 TTTCCTTT
1 TTTCCTTT
19350698 GAAATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCCTTTATTTT
Found at i:19351999 original size:22 final size:22
Alignment explanation
Indices: 19351960--19352001 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19351950 TGAATAAACC
* * *
19351960 AAATAAATTTTATTTCTGTAGA
1 AAATAAACTTAATATCTGTAGA
19351982 AAATAAACTTAATATCTGTA
1 AAATAAACTTAATATCTGTA
19352002 AACTGAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATAAACTTAATATCTGTAGA
Found at i:19354211 original size:2 final size:2
Alignment explanation
Indices: 19354204--19354236 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19354194 AAGATAATAG
*
19354204 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19354237 TTATCCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19360153 original size:6 final size:6
Alignment explanation
Indices: 19360142--19360169 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19360132 AGGATTACAA
19360142 ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTT
19360170 TTAGAAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTCC
Found at i:19369625 original size:79 final size:79
Alignment explanation
Indices: 19369494--19369651 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
19369484 GATAAGTTGA
19369494 AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACAATAAGCATGCACAAAGGCGTGAAACTCAT
1 AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACAATAAGCATGCACAAAGGCGTGAAACTCAT
19369559 TTTTACAGCATTCC
66 TTTTACAGCATTCC
*
19369573 AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACTATAAGCATGCACAAAGGCGTGAAACTCAT
1 AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACAATAAGCATGCACAAAGGCGTGAAACTCAT
19369638 TTTTACAGCATTCC
66 TTTTACAGCATTCC
19369652 TTCGTTTATA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.23
Consensus pattern (79 bp):
AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACAATAAGCATGCACAAAGGCGTGAAACTCAT
TTTTACAGCATTCC
Found at i:19377650 original size:31 final size:30
Alignment explanation
Indices: 19377582--19377650 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
19377572 TGGTTTCAAT
19377582 TCAGTCACTTAACTTTCAAAAAATGAAAAA
1 TCAGTCACTTAACTTTCAAAAAATGAAAAA
* * * *
19377612 TCGGTCAC-TAACGTTATCGAAAAGTGACAAA
1 TCAGTCACTTAAC-TT-TCAAAAAATGAAAAA
19377643 TCAGTCAC
1 TCAGTCAC
19377651 CCACTAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 4 0.12
30 9 0.28
31 19 0.59
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (30 bp):
TCAGTCACTTAACTTTCAAAAAATGAAAAA
Found at i:19377785 original size:3 final size:3
Alignment explanation
Indices: 19377779--19377814 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
19377769 CTAATAACAA
*
19377779 AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG -AG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
19377815 GACTGTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19379532 original size:36 final size:36
Alignment explanation
Indices: 19379475--19379568 Score: 127
Period size: 35 Copynumber: 2.6 Consensus size: 36
19379465 AAATTTTTTT
* *
19379475 AAAAATTAATTGAATTAGGTTTTAGGAGTTTT-AAG
1 AAAAATTAATTAAATTAGGTTTTAGGAGTTTTAAAA
* * *
19379510 TAAAATTAATTAAATTAGGGTTTAGGATTTTTAAAA
1 AAAAATTAATTAAATTAGGTTTTAGGAGTTTTAAAA
19379546 AAAAATTAATTAAATTAAGGTTT
1 AAAAATTAATTAAATT-AGGTTT
19379569 AGTTTTTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 28 0.56
36 17 0.34
37 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (36 bp):
AAAAATTAATTAAATTAGGTTTTAGGAGTTTTAAAA
Found at i:19379576 original size:35 final size:36
Alignment explanation
Indices: 19379475--19379582 Score: 130
Period size: 36 Copynumber: 3.0 Consensus size: 36
19379465 AAATTTTTTT
* * *
19379475 AAAAATTAATTGAATT-AGGTTTTAGGAGTTTT-AAG
1 AAAAATTAATTAAATTAAGG-TTTAGGATTTTTAAAA
* *
19379510 TAAAATTAATTAAATTAGGGTTTAGGATTTTTAAAA
1 AAAAATTAATTAAATTAAGGTTTAGGATTTTTAAAA
**
19379546 AAAAATTAATTAAATTAAGGTTTAGTTTTTTTAAAA
1 AAAAATTAATTAAATTAAGGTTTAGGATTTTTAAAA
19379582 A
1 A
19379583 TAATTTTGTG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
35 25 0.40
36 37 0.60
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (36 bp):
AAAAATTAATTAAATTAAGGTTTAGGATTTTTAAAA
Found at i:19379894 original size:124 final size:124
Alignment explanation
Indices: 19379669--19379991 Score: 452
Period size: 124 Copynumber: 2.6 Consensus size: 124
19379659 GAATTTTGTT
* * *
19379669 TTTTTCTATAGTAGTTCTTGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAA
1 TTTTTCTATAGTAGTTCTTG-AAAA-TAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAA
*
19379734 ACGCTTTAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAAGCTCCCACGTGGACGCTA
64 ACGCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTG-AAAAAAGCTCCCACGTGGACGCTA
*
19379796 TTTTTCTACAGTAGTTCTTGAAAA-AATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAAC
1 TTTTTCTATAGTAGTTCTTGAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAAC
* * * * *
19379860 TCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGATGCTC
66 GCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTA
* * * *
19379919 TTTTTCTATAGTAGTTCTTGAGAAAATAAATTTGAGAAGACGGTTAC-GTAAAAATAGTGTCAAT
1 TTTTTCTATAGTAGTTCTT--GAAAATAATTTTGAGAAGACGGTT-CTGAAAAAATAGTGTAAAA
19379983 AACGCTTCA
63 AACGCTTCA
19379992 CGGCATACTT
Statistics
Matches: 176, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
123 39 0.22
124 69 0.39
125 5 0.03
126 43 0.24
127 20 0.11
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (124 bp):
TTTTTCTATAGTAGTTCTTGAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAAC
GCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTA
Found at i:19381829 original size:24 final size:24
Alignment explanation
Indices: 19381779--19381829 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
19381769 AAAAAAGAAT
* * *
19381779 GCGGAGGTGTTTGCATCACCCATG
1 GCGGAGGTGTTTGAATCACACAAG
* *
19381803 GCGGAGGTGTTTGAATCTCATAAG
1 GCGGAGGTGTTTGAATCACACAAG
19381827 GCG
1 GCG
19381830 ATGGGGACTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (24 bp):
GCGGAGGTGTTTGAATCACACAAG
Found at i:19385326 original size:16 final size:16
Alignment explanation
Indices: 19385305--19385361 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
19385295 TTTGGTTCGC
*
19385305 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
19385321 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
19385337 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
19385353 TGTAATGGA
1 TGTAATGGA
19385362 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:19385628 original size:18 final size:17
Alignment explanation
Indices: 19385607--19385641 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19385597 TTATTATTAA
*
19385607 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
19385625 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
19385642 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19389288 original size:12 final size:12
Alignment explanation
Indices: 19389273--19389302 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19389263 AATACAAACA
19389273 ACAGAAGCTGCT
1 ACAGAAGCTGCT
19389285 ACAGAAGCTGCT
1 ACAGAAGCTGCT
*
19389297 AAAGAA
1 ACAGAA
19389303 ATTAACCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (12 bp):
ACAGAAGCTGCT
Found at i:19389570 original size:14 final size:14
Alignment explanation
Indices: 19389551--19389581 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
19389541 AAAATATTAA
19389551 CAACAAATAGTTCC
1 CAACAAATAGTTCC
19389565 CAACAAATAGTTCC
1 CAACAAATAGTTCC
19389579 CAA
1 CAA
19389582 TTGCCAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (14 bp):
CAACAAATAGTTCC
Found at i:19392123 original size:139 final size:139
Alignment explanation
Indices: 19391873--19392151 Score: 558
Period size: 139 Copynumber: 2.0 Consensus size: 139
19391863 AGGCGTCATG
19391873 TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
1 TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
19391938 CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
66 CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
19392003 TTTTTACTT
131 TTTTTACTT
19392012 TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
1 TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
19392077 CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
66 CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
19392142 TTTTTACTT
131 TTTTTACTT
19392151 T
1 T
19392152 GATTCTAATG
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (139 bp):
TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
TTTTTACTT
Found at i:19392807 original size:28 final size:29
Alignment explanation
Indices: 19392726--19392821 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
19392716 AAGATATAAC
* * *
19392726 AATTTTTACTAT-TTTTAAATTTTTTAAAT
1 AATTTTTACAATATTTTAAAATTTCT-AAT
*
19392755 AATTTTTTACAATCTTTTAAAATTTCTAAT
1 AA-TTTTTACAATATTTTAAAATTTCTAAT
* *
19392785 AATTTTTACAGTATTTT-CAATTTCTAAT
1 AATTTTTACAATATTTTAAAATTTCTAAT
19392813 ATATTTTTA
1 A-ATTTTTA
19392822 AATTTGCAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.19
29 22 0.38
30 14 0.24
31 11 0.19
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (29 bp):
AATTTTTACAATATTTTAAAATTTCTAAT
Found at i:19395808 original size:2 final size:2
Alignment explanation
Indices: 19395796--19395834 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
19395786 TTGAAAAATT
*
19395796 TA TA TA AA 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
19395835 GATTAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19395809 original size:10 final size:10
Alignment explanation
Indices: 19395791--19395831 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
19395781 TTGTTTTGAA
*
19395791 AAATTTATAT
1 AAATATATAT
19395801 AAATATATAT
1 AAATATATAT
*
19395811 ATATATATAT
1 AAATATATAT
*
19395821 ATATATATAT
1 AAATATATAT
19395831 A
1 A
19395832 TATGATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AAATATATAT
Found at i:19400572 original size:21 final size:21
Alignment explanation
Indices: 19400546--19400590 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
19400536 CAAAACTTAT
19400546 TAATTATGGTAGTTAAGTGAC
1 TAATTATGGTAGTTAAGTGAC
19400567 TAATTATGGTAGTTAAGTGAC
1 TAATTATGGTAGTTAAGTGAC
19400588 TAA
1 TAA
19400591 ATAGTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (21 bp):
TAATTATGGTAGTTAAGTGAC
Found at i:19403591 original size:7 final size:7
Alignment explanation
Indices: 19403579--19403616 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
19403569 ATGGGTACAT
19403579 ATGTATA
1 ATGTATA
19403586 ATGTATA
1 ATGTATA
19403593 ATGTATA
1 ATGTATA
19403600 ATGTATA
1 ATGTATA
19403607 ATGTATA
1 ATGTATA
19403614 ATG
1 ATG
19403617 CTATTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (7 bp):
ATGTATA
Found at i:19405232 original size:12 final size:12
Alignment explanation
Indices: 19405217--19405241 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19405207 TAATGTTTGA
19405217 GGGATTAATATG
1 GGGATTAATATG
19405229 GGGATTAATATG
1 GGGATTAATATG
19405241 G
1 G
19405242 TGTGTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (12 bp):
GGGATTAATATG
Found at i:19406385 original size:30 final size:29
Alignment explanation
Indices: 19406312--19406385 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
19406302 GAATTAAAAA
*
19406312 TAAATTAATAAATATTTTCATATTTTATC
1 TAAATTAATAAATATTTACATATTTTATC
* *
19406341 TAAATTAAAAAAATATTTAGAT-TTTTCCAT-
1 TAAATT-AATAAATATTTACATATTTT--ATC
19406371 TAAATTAGATAAATA
1 TAAATTA-ATAAATA
19406386 AGATAACAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
29 11 0.30
30 24 0.65
31 2 0.05
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (29 bp):
TAAATTAATAAATATTTACATATTTTATC
Found at i:19408383 original size:32 final size:32
Alignment explanation
Indices: 19408329--19408389 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
19408319 CTTTTAACAA
* * *
19408329 TATTATTTTTAAAATTTAAATTCTATTTTTTT
1 TATTATTTCTAAAATTGAAATTCGATTTTTTT
* *
19408361 TATTGTTTCTAAAATTGGAATTCGATTTT
1 TATTATTTCTAAAATTGAAATTCGATTTT
19408390 CCTTTTAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (32 bp):
TATTATTTCTAAAATTGAAATTCGATTTTTTT
Found at i:19409630 original size:24 final size:24
Alignment explanation
Indices: 19409615--19409666 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
19409605 AATCAATGTC
*
19409615 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
19409639 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
19409663 AAAT
1 AAAT
19409667 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:19409790 original size:29 final size:29
Alignment explanation
Indices: 19409757--19409815 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
19409747 TCCACATTGA
*
19409757 CACGAATTCTCAACGAACAAGTTCTTCAC
1 CACGAACTCTCAACGAACAAGTTCTTCAC
*
19409786 CACGAACTCTCAATGAACAAGTTCTTCAC
1 CACGAACTCTCAACGAACAAGTTCTTCAC
19409815 C
1 C
19409816 TCTTCCACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (29 bp):
CACGAACTCTCAACGAACAAGTTCTTCAC
Found at i:19413307 original size:24 final size:24
Alignment explanation
Indices: 19413292--19413344 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
19413282 AATCAATGTC
19413292 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
** *
19413316 AAATATATTAAACTAATAAAATACT
1 AAATATATTATGCTAAT-AAATGCT
19413341 AAAT
1 AAAT
19413345 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:19414205 original size:17 final size:19
Alignment explanation
Indices: 19414172--19414206 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19414162 TATGCTAATT
19414172 TTATTACTATAAAATAGAG
1 TTATTACTATAAAATAGAG
19414191 TTATTACT-T-AAATAGA
1 TTATTACTATAAAATAGA
19414207 ATTAATAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (19 bp):
TTATTACTATAAAATAGAG
Found at i:19414377 original size:85 final size:85
Alignment explanation
Indices: 19414285--19414458 Score: 348
Period size: 85 Copynumber: 2.0 Consensus size: 85
19414275 ATAATGTTAC
19414285 TTTGCATTAATTACAAGTAAACTATATTGTATGTTGAATATGTTAAAAATGTTTTAATTATTGTT
1 TTTGCATTAATTACAAGTAAACTATATTGTATGTTGAATATGTTAAAAATGTTTTAATTATTGTT
19414350 TGCAATTTTATATTGTAATA
66 TGCAATTTTATATTGTAATA
19414370 TTTGCATTAATTACAAGTAAACTATATTGTATGTTGAATATGTTAAAAATGTTTTAATTATTGTT
1 TTTGCATTAATTACAAGTAAACTATATTGTATGTTGAATATGTTAAAAATGTTTTAATTATTGTT
19414435 TGCAATTTTATATTGTAATA
66 TGCAATTTTATATTGTAATA
19414455 TTTG
1 TTTG
19414459 AACGGATAAG
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (85 bp):
TTTGCATTAATTACAAGTAAACTATATTGTATGTTGAATATGTTAAAAATGTTTTAATTATTGTT
TGCAATTTTATATTGTAATA
Found at i:19416351 original size:16 final size:16
Alignment explanation
Indices: 19416332--19416373 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
19416322 TTATTATTAT
19416332 TATTAATTATATTTAA
1 TATTAATTATATTTAA
*
19416348 TATTAATATAAATTTAA
1 TATTAAT-TATATTTAA
*
19416365 -ATTTATTAT
1 TATTAATTAT
19416374 TATGTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 2 0.09
16 12 0.55
17 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATTATATTTAA
Found at i:19416991 original size:16 final size:17
Alignment explanation
Indices: 19416966--19417005 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
19416956 AAAAACAATA
*
19416966 TAAT-AAATTATTAAT-
1 TAATAAAATTATAAATC
19416981 TAATAAAATTATAAATC
1 TAATAAAATTATAAATC
19416998 T-ATAAAAT
1 TAATAAAAT
19417006 CATTGCATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 17 0.77
17 1 0.05
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATAAAATTATAAATC
Found at i:19417136 original size:22 final size:21
Alignment explanation
Indices: 19417085--19417151 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
19417075 ATAAATATGA
* *
19417085 TTTTATAAAATTAAATATAATA
1 TTTTATAATATTAAA-ATAATT
* *
19417107 ATTAATAATATTAAAATCAATT
1 TTTTATAATATTAAAAT-AATT
*
19417129 TTTTATAATTAATAAAATTAATT
1 TTTTATAA-TATTAAAA-TAATT
19417152 GAGTGAGGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
21 2 0.06
22 21 0.60
23 11 0.31
24 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTATAATATTAAAATAATT
Found at i:19420754 original size:27 final size:25
Alignment explanation
Indices: 19420715--19420769 Score: 58
Period size: 27 Copynumber: 2.1 Consensus size: 25
19420705 TAAATGAGCA
19420715 AAATAAAAAAAAA-ATAATAGAAAACAT
1 AAATAAAAAAAAACAT-ATA-AAAA-AT
* *
19420742 AAATACAACAAAACATATAAAAAAT
1 AAATAAAAAAAAACATATAAAAAAT
19420767 AAA
1 AAA
19420770 GAAAGTACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 5 0.20
26 4 0.16
27 14 0.56
28 2 0.08
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (25 bp):
AAATAAAAAAAAACATATAAAAAAT
Found at i:19420920 original size:50 final size:49
Alignment explanation
Indices: 19420866--19421129 Score: 214
Period size: 50 Copynumber: 5.2 Consensus size: 49
19420856 AAGAAAAATA
19420866 TACATATAGAAATTATAAAATATGGATAGAAAGTATAATACATATATACG
1 TACATATAGAAATTATAAAATATGGATAGAAAGTATAATA-ATATATACG
* * * * **
19420916 TACATATATATAAGTTAATAAATATATAGATCATAAAG-ATAATGATTATATATA
1 TACATATAGA-AA-TT-ATAAA-ATATGGAT-AGAAAGTATAAT-AATATATACG
* *
19420970 TATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATACG
1 TACATATAGAAATTATAAAATATGGATAGAAAGTATAATA-ATATATACG
* * * * *
19421020 TACATATATATATAAGTTAATAAATATATAGATCATAAAG-GTAATGATTATATA--
1 TAC--ATATAGA-AA-TT-ATAAA-ATATGGAT-AGAAAGTATAAT-AATATATACG
* *
19421074 TATATATAGAAATTATAAAATATGTATAGAAAGTATAAT-ATATATACG
1 TACATATAGAAATTATAAAATATGGATAGAAAGTATAATAATATATACG
19421122 TACATATA
1 TACATATA
19421130 TATAAGGTAA
Statistics
Matches: 166, Mismatches: 29, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
46 6 0.04
47 5 0.03
48 17 0.10
49 11 0.07
50 30 0.18
51 9 0.05
52 16 0.10
53 9 0.05
54 30 0.18
55 11 0.07
56 16 0.10
57 6 0.04
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (49 bp):
TACATATAGAAATTATAAAATATGGATAGAAAGTATAATAATATATACG
Found at i:19420997 original size:20 final size:20
Alignment explanation
Indices: 19420969--19421017 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
19420959 GATTATATAT
*
19420969 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
19420989 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
19421009 ATATATATA
1 ATATATATA
19421018 CGTACATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:19421046 original size:16 final size:16
Alignment explanation
Indices: 19421000--19421049 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
19420990 TATGTATAGA
19421000 AAGTATAATATATATAT
1 AAGT-TAATATATATAT
*
19421017 ACG-TACATATATATAT
1 AAGTTA-ATATATATAT
*
19421033 AAGTTAATAAATATAT
1 AAGTTAATATATATAT
19421049 A
1 A
19421050 GATCATAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 2 0.07
16 22 0.79
17 4 0.14
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (16 bp):
AAGTTAATATATATAT
Found at i:19421056 original size:106 final size:104
Alignment explanation
Indices: 19420863--19421177 Score: 503
Period size: 104 Copynumber: 3.0 Consensus size: 104
19420853 ATAAAGAAAA
* * *
19420863 ATATACATATAGAAATTATAAAATATGGATAGAAAGTATAATACATATATACGTACATATATATA
1 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATACGTACATATATATA
19420928 AGTTAATAAATATATAGATCATAAAGATAATGATTATAT
66 AGTTAATAAATATATAGATCATAAAGATAATGATTATAT
19420967 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATACGTACATATATATA
1 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATACGTAC--ATATATA
*
19421032 TAAGTTAATAAATATATAGATCATAAAGGTAATGA-T-TAT
64 TAAGTTAATAAATATATAGATCATAAAGATAATGATTATAT
19421071 ATATATATATAGAAATTATAAAATATGTATAGAAAGTAT-A-ATATATATACGTACATATATATA
1 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATACGTACATATATATA
* * * * *
19421134 AGGTAATAAATATATAAATCATAAAAATAATAATTACAT
66 AGTTAATAAATATATAGATCATAAAGATAATGATTATAT
19421173 ATATA
1 ATATA
19421178 AACTAAAAAA
Statistics
Matches: 197, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
100 37 0.19
101 1 0.01
102 21 0.11
103 1 0.01
104 95 0.48
105 1 0.01
106 41 0.21
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (104 bp):
ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATACGTACATATATATA
AGTTAATAAATATATAGATCATAAAGATAATGATTATAT
Found at i:19421101 original size:20 final size:20
Alignment explanation
Indices: 19421073--19421119 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19421063 ATGATTATAT
*
19421073 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
19421093 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
19421113 ATATATA
1 ATATATA
19421120 CGTACATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:19421745 original size:22 final size:21
Alignment explanation
Indices: 19421710--19421805 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 21
19421700 AAAGGGTATC
* *
19421710 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
19421731 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
19421754 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
19421773 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
19421792 TGCATATCATATCT
1 TACAAATCATATCT
19421806 AAGGTTGCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
17 2 0.03
19 26 0.43
21 7 0.12
22 15 0.25
23 10 0.17
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:19421753 original size:23 final size:22
Alignment explanation
Indices: 19421710--19421767 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
19421700 AAAGGGTATC
* *
19421710 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
19421731 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
19421754 TGCATATCATATCT
1 TACAAATCATATCT
19421768 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:19421770 original size:19 final size:19
Alignment explanation
Indices: 19421746--19421818 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
19421736 AATCATATCT
19421746 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
19421765 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
19421784 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
19421803 TCTAAGGTTGCATATC
1 TCTAAGATTGCATATC
19421819 CTCGAAGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:19428475 original size:19 final size:20
Alignment explanation
Indices: 19428451--19428500 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
19428441 TGATAAACTT
*
19428451 TCTTTATATATTTTT-AGAA
1 TCTTTATATATTTTTGAAAA
19428470 TCTTTA-ATATTTTTGAAAA
1 TCTTTATATATTTTTGAAAA
19428489 T-TTTATA-ATTTT
1 TCTTTATATATTTT
19428501 ACATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (20 bp):
TCTTTATATATTTTTGAAAA
Done.