Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 67 of 320
Found at i:20323605 original size:18 final size:18
Alignment explanation
Indices: 20323572--20323649 Score: 66
Period size: 18 Copynumber: 4.0 Consensus size: 18
20323562 CAATTAAACC
* *
20323572 ATTTGATTGATATATTTA
1 ATTTGATTTATTTATTTA
*
20323590 ATTTGATTTCTTTATTTA
1 ATTTGATTTATTTATTTA
*
20323608 TAATTGAGTATTATTATATATTTA
1 -ATTTGA-T-TTA-T-T-TATTTA
20323632 ATTTGATTTATTTATTTA
1 ATTTGATTTATTTATTTA
20323650 TAAATAAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
18 21 0.44
19 6 0.12
20 2 0.04
21 5 0.10
22 2 0.04
23 6 0.12
24 6 0.12
ACGTcount: A:0.31, C:0.01, G:0.08, T:0.60
Consensus pattern (18 bp):
ATTTGATTTATTTATTTA
Found at i:20323730 original size:18 final size:18
Alignment explanation
Indices: 20323688--20323724 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20323678 ACAATTTAAA
20323688 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
20323706 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
20323724 A
1 A
20323725 AGTAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:20323851 original size:20 final size:19
Alignment explanation
Indices: 20323806--20323843 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20323796 CATCCAAACA
*
20323806 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAATCATTT
*
20323825 CTAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
20323844 TCCGGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:20323857 original size:14 final size:14
Alignment explanation
Indices: 20323835--20323872 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
20323825 CTAGAAAAGT
*
20323835 AAATCATTTTCCGG
1 AAATTATTTTCCGG
20323849 AAATTATTTTCCGG
1 AAATTATTTTCCGG
*
20323863 AAAATATTTT
1 AAATTATTTT
20323873 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (14 bp):
AAATTATTTTCCGG
Found at i:20323967 original size:6 final size:6
Alignment explanation
Indices: 20323956--20323993 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
20323946 ATATGATTTG
20323956 ATTTTT ATTTTT ATTGATTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATT--TTT ATTTTT ATTTTT ATTTTT
20323994 TCTTCTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 24 0.80
8 6 0.20
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:20323981 original size:20 final size:21
Alignment explanation
Indices: 20323949--20323990 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
20323939 TTCGTGGATA
20323949 TGATTTGATTTTTATTTTTAT
1 TGATTTGATTTTTATTTTTAT
20323970 TGATTT-ATTTTTATTTTTAT
1 TGATTTGATTTTTATTTTTAT
20323990 T
1 T
20323991 TTTTCTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (21 bp):
TGATTTGATTTTTATTTTTAT
Found at i:20324584 original size:17 final size:18
Alignment explanation
Indices: 20324562--20324616 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
20324552 ACACGGGCAT
*
20324562 GCCACACA-GGTATGTGG
1 GCCACACAGGGCATGTGG
20324579 GCCACA-AGGGCATGTGG
1 GCCACACAGGGCATGTGG
* *
20324596 GCC-CACATGAGCATATGG
1 GCCACACA-GGGCATGTGG
20324614 GCC
1 GCC
20324617 CAAAATTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.09
17 18 0.56
18 11 0.34
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.15
Consensus pattern (18 bp):
GCCACACAGGGCATGTGG
Found at i:20324609 original size:18 final size:18
Alignment explanation
Indices: 20324573--20324618 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
20324563 CCACACAGGT
*
20324573 ATGTGGG-CCACAAGGGC
1 ATGTGGGCCCACAAGAGC
*
20324590 ATGTGGGCCCACATGAGC
1 ATGTGGGCCCACAAGAGC
*
20324608 ATATGGGCCCA
1 ATGTGGGCCCA
20324619 AAATTCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (18 bp):
ATGTGGGCCCACAAGAGC
Found at i:20326200 original size:68 final size:66
Alignment explanation
Indices: 20326128--20326289 Score: 234
Period size: 68 Copynumber: 2.4 Consensus size: 66
20326118 GTACACGAAG
* *
20326128 GCTACGAGATACTATATAGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAAACAAA
1 GCTACGAGAGA-TAAAT-GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAAACAAA
20326193 AGA
64 AGA
* *
20326196 GCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAG
1 GCTAC--GAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAAACAAA
20326261 AGA
64 AGA
20326264 GCTACGTGAGAGATAAATGTAGCTAG
1 GCTAC--GAGAGATAAATGTAGCTAG
20326290 ATCGCATGAT
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
68 79 0.90
69 4 0.05
70 5 0.06
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (66 bp):
GCTACGAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAAACAAAAG
A
Found at i:20332598 original size:29 final size:28
Alignment explanation
Indices: 20332562--20332639 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
20332552 TCATGAGATT
20332562 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
20332592 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
20332619 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
20332640 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:20332857 original size:174 final size:174
Alignment explanation
Indices: 20332592--20333093 Score: 968
Period size: 174 Copynumber: 2.9 Consensus size: 174
20332582 AAATTGTACA
*
20332592 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
20332657 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
20332722 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
20332766 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
20332831 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
20332896 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
20332940 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
20333005 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
20333070 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
20333094 ACCTTGAGTT
Statistics
Matches: 323, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 323 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:20338454 original size:29 final size:29
Alignment explanation
Indices: 20338392--20338464 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
20338382 GTCATGAGAT
20338392 TGGCACTAAGTGTGCGGTTTAAATTGTACA
1 TGGCACTAAGTGTGCGGTTTAAA-TGTACA
20338422 --GCACTAAGTGTGCGAGTTTAAA-GTACA
1 TGGCACTAAGTGTGCG-GTTTAAATGTACA
20338449 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
20338465 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 5 0.12
28 14 0.35
29 21 0.52
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGGTTTAAATGTACA
Found at i:20338712 original size:174 final size:174
Alignment explanation
Indices: 20338422--20338923 Score: 968
Period size: 174 Copynumber: 2.9 Consensus size: 174
20338412 AAATTGTACA
*
20338422 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
20338487 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
20338552 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
20338596 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
20338661 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
20338726 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
20338770 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
20338835 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
20338900 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
20338924 ACCTTGAGTT
Statistics
Matches: 323, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 323 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:20342244 original size:93 final size:93
Alignment explanation
Indices: 20342080--20342346 Score: 421
Period size: 93 Copynumber: 2.8 Consensus size: 93
20342070 GTAAGGTGTC
* * * * * * *
20342080 GATGCCATGTCCCAGACATGGTCTTACACGAACTATCATCTC-ATACTCGATG-CATGTCCTAGA
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTATCAATGC-CGATGCCATGTCCCAGA
20342143 CATGTCTTACACTGGCTTACGACCCGAGGCT
63 CATGTCTTACACTGGCTTACGACCCGAGGCT
20342174 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGCCGATGCCATGTCCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGCCGATGCCATGTCCCAGACAT
20342239 GTCTTACACTGGCTTACGACCCGAGGCT
66 GTCTTACACTGGCTTACGACCCGAGGCT
20342267 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGCCGATGCCATGTCCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGCCGATGCCATGTCCCAGACAT
20342332 GATCTTACACTGGCT
66 G-TCTTACACTGGCT
20342347 CTCATAATGT
Statistics
Matches: 163, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
92 22 0.13
93 124 0.76
94 17 0.10
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (93 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGCCGATGCCATGTCCCAGACAT
GTCTTACACTGGCTTACGACCCGAGGCT
Found at i:20342245 original size:47 final size:45
Alignment explanation
Indices: 20342079--20342391 Score: 276
Period size: 46 Copynumber: 6.7 Consensus size: 45
20342069 GGTAAGGTGT
* * * * *
20342079 CGATGCCATGTCCCAGACATGGTCTTACACGAACTATC-ATCTCATAC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGATC-AATGC
* * * * *
20342126 TCGATGCATGTCCTAGACATGTCTTACACTGGCT-TACGACCCGAGGC
1 -CGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CGA-TCAATGC
*
20342173 TGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCG-ATCAATGC
* * * *
20342219 CGATGCCATGTCCCAGACATGTCTTACACTGGCT-TACGACCCGAGGC
1 CGATG-CATGTCCCAGACATGTCTTACACTAGCTCT-CGA-TCAATGC
*
20342266 TGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCG-ATCAATGC
*
20342312 CGATGCCATGTCCCAGACATGATCTTACACTGGCTCTC-AT-AATGTGGC
1 CGATG-CATGTCCCAGACATG-TCTTACACTAGCTCTCGATCAA--T-GC
**
20342360 CGATGCATGTCCTTGACATGTCTTACACTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC
20342392 CACCAATAAC
Statistics
Matches: 221, Mismatches: 29, Indels: 32
0.78 0.10 0.11
Matches are distributed among these distances:
45 3 0.01
46 104 0.47
47 86 0.39
48 28 0.13
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGATCAATGC
Found at i:20344445 original size:28 final size:27
Alignment explanation
Indices: 20344388--20344539 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
20344378 TAAATTGTGC
* *
20344388 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
20344415 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
20344443 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
20344470 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
20344498 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
20344525 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20344540 GACTTAATAA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:20344453 original size:55 final size:55
Alignment explanation
Indices: 20344388--20344539 Score: 241
Period size: 55 Copynumber: 2.8 Consensus size: 55
20344378 TAAATTGTGC
* *
20344388 AGCACTAAGTGTGCGAATTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* *
20344443 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* * *
20344498 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
20344540 GACTTAATAA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 90 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
Found at i:20351649 original size:16 final size:16
Alignment explanation
Indices: 20351628--20351660 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20351618 TCTATAAAAA
20351628 AATTTAACTCATTAAT
1 AATTTAACTCATTAAT
20351644 AATTTAACTCATTAAT
1 AATTTAACTCATTAAT
20351660 A
1 A
20351661 CACTACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAACTCATTAAT
Found at i:20364803 original size:9 final size:9
Alignment explanation
Indices: 20364789--20364819 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20364779 TAAACGAATT
20364789 GAGTTATTC
1 GAGTTATTC
*
20364798 GAGTTAATC
1 GAGTTATTC
20364807 GAGTTATTC
1 GAGTTATTC
20364816 GAGT
1 GAGT
20364820 CAACTCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.39
Consensus pattern (9 bp):
GAGTTATTC
Found at i:20366811 original size:19 final size:19
Alignment explanation
Indices: 20366771--20366812 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
20366761 ATTTTAAAAC
* *
20366771 AAAATTGAATTTAGTTTTA
1 AAAATTCAATTTAGTTTAA
20366790 AAAATTCAATTTTA-TTTAA
1 AAAATTCAA-TTTAGTTTAA
20366809 AAAA
1 AAAA
20366813 CAATTTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (19 bp):
AAAATTCAATTTAGTTTAA
Found at i:20367767 original size:24 final size:24
Alignment explanation
Indices: 20367717--20367767 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
20367707 ATCTTTATTT
* * *
20367717 TAAAAAATATTTAATATATGTATA
1 TAAAAAATATTTAAAATATGCAAA
20367741 TAAAAAATATTTACAAATAT-CAAA
1 TAAAAAATATTTA-AAATATGCAAA
20367765 TAA
1 TAA
20367768 TAAGGTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAAAAATATTTAAAATATGCAAA
Found at i:20368388 original size:6 final size:6
Alignment explanation
Indices: 20368379--20368403 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20368369 ATTATATTGC
20368379 ATTTGT ATTTGT ATTTGT ATTTGT A
1 ATTTGT ATTTGT ATTTGT ATTTGT A
20368404 AACTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (6 bp):
ATTTGT
Found at i:20382316 original size:30 final size:30
Alignment explanation
Indices: 20382280--20382340 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
20382270 ATTTTATTGT
*
20382280 TAATTTTTTTATTATTTTAAAGACATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
* *
20382310 TAATTTTGTTATTATTTTAGAGGCATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
20382340 T
1 T
20382341 TATTAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACATTTGC
Found at i:20384469 original size:41 final size:41
Alignment explanation
Indices: 20384410--20384528 Score: 120
Period size: 41 Copynumber: 2.9 Consensus size: 41
20384400 CTTGCTATCA
* * *
20384410 ATGAGCTTTAAC-CATTCACCCAAAATATGATGCTTCTACGT
1 ATGAGCTTAAACTGATTCA-CCAAAATATGATGCTTCTACGC
* ** *
20384451 ATGAGCTTAAATTG-TTCACCAAAATATGGCGC-TCTTAGGC
1 ATGAGCTTAAACTGATTCACCAAAATATGATGCTTC-TACGC
20384491 ATGAGCTTAAACTGATT-ATCCAAAATATGATGCTTCTA
1 ATGAGCTTAAACTGATTCA-CCAAAATATGATGCTTCTA
20384529 AGCACAAGAT
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
39 2 0.03
40 29 0.46
41 30 0.48
42 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (41 bp):
ATGAGCTTAAACTGATTCACCAAAATATGATGCTTCTACGC
Found at i:20385855 original size:13 final size:14
Alignment explanation
Indices: 20385839--20385867 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20385829 AAATTAAACT
20385839 AAAAAG-AAAAGAA
1 AAAAAGAAAAAGAA
20385852 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
20385866 AA
1 AA
20385868 GAGAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:20387439 original size:3 final size:3
Alignment explanation
Indices: 20387431--20387465 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20387421 GCTAACTGTT
20387431 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
20387466 TTTTCCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:20391439 original size:15 final size:15
Alignment explanation
Indices: 20391421--20391450 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20391411 TTCCTGTTCT
*
20391421 TTCTTTTTCTTTTTG
1 TTCTTTTCCTTTTTG
20391436 TTCTTTTCCTTTTTG
1 TTCTTTTCCTTTTTG
20391451 CCTCCTATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.77
Consensus pattern (15 bp):
TTCTTTTCCTTTTTG
Found at i:20393390 original size:21 final size:20
Alignment explanation
Indices: 20393362--20393411 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
20393352 GGAGACTCTA
20393362 AAAATTTTTCGCGAAATTTC
1 AAAATTTTTCGCGAAATTTC
20393382 AAAATTTTTCGCGAAATTTC
1 AAAATTTTTCGCGAAATTTC
20393402 AAAATTTTTC
1 AAAATTTTTC
20393412 CAAAGTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAATTTTTCGCGAAATTTC
Found at i:20397748 original size:2 final size:2
Alignment explanation
Indices: 20397741--20397800 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
20397731 ATTTCAATGT
20397741 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
20397783 CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA
20397801 TATATGATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:20398830 original size:74 final size:74
Alignment explanation
Indices: 20398665--20398831 Score: 203
Period size: 75 Copynumber: 2.2 Consensus size: 74
20398655 AATTATTTTG
* * * * ** *
20398665 ATGGTCACAATTATTTAATTTTTTTATGACTAAATTATTGACACTAAAATTGTAAATAATTACGG
1 ATGGTCACAATTATTCAATTTTCTTAGGACCAAATTATTGACACTAAAATCATAAACAATTA-GG
20398730 ATGAAATTAA
65 ATGAAATTAA
* * *
20398740 ATGGTCACAATTATTCAATTTTCTTGGGACCAAATTATTGACACTAAAATCATAAGCACTT-GTG
1 ATGGTCACAATTATTCAATTTTCTTAGGACCAAATTATTGACACTAAAATCATAAACAATTAG-G
20398804 -TCGAAATTAA
65 AT-GAAATTAA
20398814 ATGGTCACAATTATTCAA
1 ATGGTCACAATTATTCAA
20398832 AGAAATTGGT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
73 2 0.03
74 27 0.34
75 51 0.64
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.37
Consensus pattern (74 bp):
ATGGTCACAATTATTCAATTTTCTTAGGACCAAATTATTGACACTAAAATCATAAACAATTAGGA
TGAAATTAA
Found at i:20401145 original size:31 final size:31
Alignment explanation
Indices: 20401105--20401190 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
20401095 TCAATCTCAG
**
20401105 CATAT-ACTGGGCTGAAGCCTTTACATTATT
1 CATATCACTGGGCCAAAGCCTTTACATTATT
*
20401135 CATATCACTGGGCCAAAGCCTTTTCATTATT
1 CATATCACTGGGCCAAAGCCTTTACATTATT
*
20401166 CATATCACTGTGCCAAAGCCTTTAC
1 CATATCACTGGGCCAAAGCCTTTAC
20401191 TGTAACAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (31 bp):
CATATCACTGGGCCAAAGCCTTTACATTATT
Found at i:20401441 original size:26 final size:25
Alignment explanation
Indices: 20401408--20401479 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
20401398 CTCTTTTAAT
* *
20401408 AACTGGGGTAAAGGCCCTTTTTGATA
1 AACTGGGGCAAA-GCCCTTTTCGATA
20401434 AACTGGGGCAAAAGCCCTTTTCGATA
1 AACTGGGGC-AAAGCCCTTTTCGATA
*
20401460 AATTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
20401480 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 11 0.26
26 28 0.67
27 3 0.07
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:20401643 original size:25 final size:25
Alignment explanation
Indices: 20401615--20401662 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
20401605 ATAATTAAAC
* **
20401615 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
20401640 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
20401663 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:20409200 original size:31 final size:31
Alignment explanation
Indices: 20409160--20409244 Score: 120
Period size: 30 Copynumber: 2.8 Consensus size: 31
20409150 TCAATCTCAG
**
20409160 CATAT-ACTGGGCTGAAGCCTTTACATTATT
1 CATATCACTGGGCCAAAGCCTTTACATTATT
*
20409190 CATATCACT-GGCCAAAGCCTTTTCATTATT
1 CATATCACTGGGCCAAAGCCTTTACATTATT
*
20409220 CATATCACTGTGCCAAAGCCTTTAC
1 CATATCACTGGGCCAAAGCCTTTAC
20409245 TGTAACAATG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 32 0.67
31 16 0.33
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (31 bp):
CATATCACTGGGCCAAAGCCTTTACATTATT
Found at i:20409208 original size:30 final size:31
Alignment explanation
Indices: 20409174--20409244 Score: 126
Period size: 30 Copynumber: 2.3 Consensus size: 31
20409164 TACTGGGCTG
20409174 AAGCCTTTACATTATTCATATCACTG-GCCA
1 AAGCCTTTACATTATTCATATCACTGTGCCA
*
20409204 AAGCCTTTTCATTATTCATATCACTGTGCCA
1 AAGCCTTTACATTATTCATATCACTGTGCCA
20409235 AAGCCTTTAC
1 AAGCCTTTAC
20409245 TGTAACAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 25 0.66
31 13 0.34
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (31 bp):
AAGCCTTTACATTATTCATATCACTGTGCCA
Found at i:20409495 original size:26 final size:25
Alignment explanation
Indices: 20409462--20409533 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 25
20409452 CTCTTTTAAT
*
20409462 AACTGGGGCAAAGGCCCTTTTTGATA
1 AACTGGGGCAAA-GCCCTTTTCGATA
20409488 AACTGGGGCAAAAGCCCTTTTCGATA
1 AACTGGGGC-AAAGCCCTTTTCGATA
*
20409514 AATTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
20409534 GCACTTCCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 11 0.26
26 29 0.67
27 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:20409701 original size:25 final size:25
Alignment explanation
Indices: 20409673--20409720 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
20409663 ATAATTAAAC
* **
20409673 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
20409698 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
20409721 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:20422707 original size:24 final size:25
Alignment explanation
Indices: 20422664--20422715 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
20422654 AAACAAATTG
20422664 TATTCCATTTTCATAGTTTAT-TCA
1 TATTCCATTTTCATAGTTTATATCA
*
20422688 TATTCC-TTTTCTATATTTTATATCA
1 TATTCCATTTTC-ATAGTTTATATCA
20422713 TAT
1 TAT
20422716 CATAGTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 5 0.20
24 14 0.56
25 6 0.24
ACGTcount: A:0.25, C:0.15, G:0.02, T:0.58
Consensus pattern (25 bp):
TATTCCATTTTCATAGTTTATATCA
Found at i:20424904 original size:20 final size:20
Alignment explanation
Indices: 20424876--20424919 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
20424866 TACCAACTTG
*
20424876 CAACTTACCATAATCTTTCA
1 CAACATACCATAATCTTTCA
*
20424896 CAACATACCATAGTCTTTCA
1 CAACATACCATAATCTTTCA
20424916 CAAC
1 CAAC
20424920 TTAAACATTG
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:0.32, G:0.02, T:0.30
Consensus pattern (20 bp):
CAACATACCATAATCTTTCA
Found at i:20425041 original size:32 final size:33
Alignment explanation
Indices: 20424998--20425060 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
20424988 CACATAGTAC
*
20424998 CATATCAATGCC-ATATCCCAGATATGGTCTAT
1 CATATCAATGCCAATAGCCCAGATATGGTCTAT
* * *
20425030 CATATCGATGCCAATAGCCTAGCTATGGTCT
1 CATATCAATGCCAATAGCCCAGATATGGTCT
20425061 TAGAAGAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (33 bp):
CATATCAATGCCAATAGCCCAGATATGGTCTAT
Found at i:20434233 original size:50 final size:50
Alignment explanation
Indices: 20434164--20434458 Score: 155
Period size: 50 Copynumber: 5.9 Consensus size: 50
20434154 ACAACTTCAA
* * * *
20434164 TCACGTGTGTAGTACTAAGTGTAAGCTACTACGTATATCAGATGGTTAGG
1 TCACGTGTATAGTACTAAGTGCAAGCTACTACGTATACCAGATAGTTAGG
* * *
20434214 TCACGTGTATGGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGG
1 TCACGTGTATAGTACTAAGTGCAAGCTACTACGTATACCAGATAGTTAGG
* * * * * * * ** * * *
20434264 TCGCATGTGTAGTACTAGGCGCAGGCTACTATGCT-TACCCTACCACTTCA-A
1 TCACGTGTATAGTACTAAGTGCAAGCTACTACG-TATACCAGA-TAGTT-AGG
* * * ** * *
20434315 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGGGTATCAGATGGTTAGG
1 TCACGTGTATAGTACTAAGTGCAAGCTACTACGTATACCAGATAGTTAGG
* * * * * * * * *
20434365 CCACATGTGTAGTACAAAGTGCAAGCTAATACGTGTACCGGATGGTT-GA
1 TCACGTGTATAGTACTAAGTGCAAGCTACTACGTATACCAGATAGTTAGG
** * * * * * *
20434414 TTGCATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATAG
1 TCACGTGTATAGTACTAAGTGCAAGCTACTACGTATACCAGATAG
20434459 CTTCGGTTGC
Statistics
Matches: 187, Mismatches: 53, Indels: 11
0.75 0.21 0.04
Matches are distributed among these distances:
49 37 0.20
50 114 0.61
51 35 0.19
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
TCACGTGTATAGTACTAAGTGCAAGCTACTACGTATACCAGATAGTTAGG
Found at i:20434398 original size:151 final size:150
Alignment explanation
Indices: 20434119--20434451 Score: 450
Period size: 151 Copynumber: 2.2 Consensus size: 150
20434109 GTGAGAACAC
* * *
20434119 GTGTAGTACTAAGTGTAGGCTGCTATACGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGT
1 GTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGT
* * * * * * *
20434184 GTAAGCTACTACGTATATCAGATGGTTAGGTCACGTGTATGGTACTAAGTGCAGGCTACTACGTG
66 GTAAGCTACTACGGATATCAGATGGTTAGGCCACATGTATAGTACAAAGTGCAAGCTAATACGTG
*
20434249 TACCAGATAGTTAGGTCGCAT
131 TACCAGATAGTT-GATCGCAT
* * * * *
20434270 GTGTAGTACTAGGCGCAGGCTACTATGCTTACCCTACCACTTCAATCACGTGTGTAGTACTAAGT
1 GTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGT
* * *
20434335 GTAGGCTACTACGGGTATCAGATGGTTAGGCCACATGTGTAGTACAAAGTGCAAGCTAATACGTG
66 GTAAGCTACTACGGATATCAGATGGTTAGGCCACATGTATAGTACAAAGTGCAAGCTAATACGTG
* * *
20434400 TACCGGATGGTTGATTGCAT
131 TACCAGATAGTTGATCGCAT
*
20434420 GTGTAGTACTAAGTGCAGGCTACTATGTGTAC
1 GTGTAGTACTAAGTGCAGGCTACTATGCGTAC
20434452 TAGATAGCTT
Statistics
Matches: 156, Mismatches: 26, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
150 34 0.22
151 122 0.78
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (150 bp):
GTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGT
GTAAGCTACTACGGATATCAGATGGTTAGGCCACATGTATAGTACAAAGTGCAAGCTAATACGTG
TACCAGATAGTTGATCGCAT
Found at i:20438648 original size:18 final size:20
Alignment explanation
Indices: 20438616--20438653 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
20438606 GTAGATTATG
*
20438616 ATGTTATAGTCATATGTGAT
1 ATGTTATAGTCATATATGAT
20438636 ATGTTAT-GT-ATATATGAT
1 ATGTTATAGTCATATATGAT
20438654 CAAATGACGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (20 bp):
ATGTTATAGTCATATATGAT
Found at i:20453762 original size:14 final size:14
Alignment explanation
Indices: 20453743--20453786 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
20453733 AATTTAAAGA
20453743 TAAAGTTAATGATT
1 TAAAGTTAATGATT
*
20453757 TAAAG-T-AT--TA
1 TAAAGTTAATGATT
20453767 TAAAGTTAATGATT
1 TAAAGTTAATGATT
20453781 TAAAGT
1 TAAAGT
20453787 ATTAGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 6 0.25
11 1 0.04
12 4 0.17
13 1 0.04
14 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (14 bp):
TAAAGTTAATGATT
Found at i:20453774 original size:24 final size:24
Alignment explanation
Indices: 20453742--20453798 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
20453732 CAATTTAAAG
20453742 ATAAAGTTAATGATTTAAAGTATT
1 ATAAAGTTAATGATTTAAAGTATT
20453766 ATAAAGTTAATGATTTAAAGTATT
1 ATAAAGTTAATGATTTAAAGTATT
*
20453790 AGAAA-TTAA
1 ATAAAGTTAA
20453799 AAATAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (24 bp):
ATAAAGTTAATGATTTAAAGTATT
Found at i:20456026 original size:46 final size:46
Alignment explanation
Indices: 20455976--20456147 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
20455966 TGGTTGAGCA
* *
20455976 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
* * *
20456022 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA-A--CG
* *
20456068 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
*
20456114 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
20456148 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 6 0.06
46 86 0.80
47 2 0.02
48 1 0.01
49 6 0.06
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
Found at i:20456130 original size:92 final size:92
Alignment explanation
Indices: 20455973--20456142 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 92
20455963 GGATGGTTGA
* *
20455973 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCCAACTCGTTGAGT
20456038 TGAGTCCGAGTTCGTGAGATGTAACAG
66 TGAGTCCGAGTTCGTGAGATGTAACAG
* **
20456065 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGTGAACG-CCCAAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCCAA-CTCGTTGAG
20456129 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
20456143 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
91 4 0.06
92 68 0.94
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACAG
Found at i:20471123 original size:34 final size:34
Alignment explanation
Indices: 20471085--20471193 Score: 146
Period size: 34 Copynumber: 3.2 Consensus size: 34
20471075 ACGCTAGTTA
*
20471085 GATAAACCGACGAATGTGTGCCCAGCACTAGTCG
1 GATAAACTGACGAATGTGTGCCCAGCACTAGTCG
* *
20471119 GATAAACTGATGAATGTGTGCCCAGCACTAGTCA
1 GATAAACTGACGAATGTGTGCCCAGCACTAGTCG
* * * *
20471153 GCTAAATTGACGAAAGTTGTGCCCAGCGCTAGTCG
1 GATAAACTGACGAATG-TGTGCCCAGCACTAGTCG
20471188 GATAAA
1 GATAAA
20471194 TCAACGAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
34 43 0.67
35 21 0.33
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (34 bp):
GATAAACTGACGAATGTGTGCCCAGCACTAGTCG
Found at i:20486288 original size:27 final size:27
Alignment explanation
Indices: 20486258--20486309 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
20486248 ATATACTTGT
*
20486258 TCTGGTGGCCTAGCCACAATATCTGTA
1 TCTGGTGACCTAGCCACAATATCTGTA
* * *
20486285 TCTGGTGACTTTGTCACAATATCTG
1 TCTGGTGACCTAGCCACAATATCTG
20486310 GCAGCCTCGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (27 bp):
TCTGGTGACCTAGCCACAATATCTGTA
Found at i:20500964 original size:27 final size:26
Alignment explanation
Indices: 20500926--20500985 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
20500916 ACATATATAT
* *
20500926 ATATATGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
20500952 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
20500979 ATATCTG
1 ATATCTG
20500986 GCAGCCTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:20508572 original size:49 final size:50
Alignment explanation
Indices: 20508517--20508762 Score: 316
Period size: 49 Copynumber: 4.9 Consensus size: 50
20508507 ATCTATTGTG
*
20508517 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
20508567 -GGTCACATGTGTAGTACTAAGTGCATGCTACTATGAGTACCCGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * **
20508617 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
**
20508667 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
20508717 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
20508763 GCTTTGGCTA
Statistics
Matches: 166, Mismatches: 28, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
49 81 0.49
50 47 0.28
51 38 0.23
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:20508653 original size:28 final size:28
Alignment explanation
Indices: 20508622--20508705 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
20508612 AACTTCGATC
20508622 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
20508650 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
20508672 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
20508700 ACGTGT
1 ACGTGT
20508706 ACTGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:20522797 original size:27 final size:27
Alignment explanation
Indices: 20522767--20522964 Score: 234
Period size: 27 Copynumber: 7.3 Consensus size: 27
20522757 TACTGAAATG
** *
20522767 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * *
20522794 CCCTCGATTTATAGAATTACTGTTTCA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
20522821 CCCTCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * **
20522848 CCCTCGAATTATAGAATTACAATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
20522875 CCCTCGATTTACAGAATTATCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * *
20522902 CCCTCAATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * *
20522929 CCCTCAATTTACAAAATTACTGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
20522956 CCCTCGATT
1 CCCTCGATT
20522965 GTGAAATTAC
Statistics
Matches: 146, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 146 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.39
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCGTTTTA
Found at i:20522853 original size:81 final size:81
Alignment explanation
Indices: 20522767--20522964 Score: 272
Period size: 81 Copynumber: 2.4 Consensus size: 81
20522757 TACTGAAATG
* * * *
20522767 CCCTCGATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTA-CTGTTTCACCCTCGATTT
1 CCCTCGATTTATAGAATTACAATTTTACCCTCGATTTACAGAATTATC-GTTTCACCCTCAATTT
*
20522831 ACAAAATTACCGTTTTA
65 ACAAAATTACCATTTTA
* *
20522848 CCCTCGAATTATAGAATTACAATTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCAATTTA
1 CCCTCGATTTATAGAATTACAATTTTACCCTCGATTTACAGAATTATCGTTTCACCCTCAATTTA
20522913 CAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* * * **
20522929 CCCTCAATTTACAAAATTACTGTTTTACCCTCGATT
1 CCCTCGATTTATAGAATTACAATTTTACCCTCGATT
20522965 GTGAAATTAC
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 102 0.99
82 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.39
Consensus pattern (81 bp):
CCCTCGATTTATAGAATTACAATTTTACCCTCGATTTACAGAATTATCGTTTCACCCTCAATTTA
CAAAATTACCATTTTA
Found at i:20523026 original size:27 final size:27
Alignment explanation
Indices: 20522996--20523172 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
20522986 TATAGAATAG
20522996 AATTACCAAAATACCTCTAGTTTATAA
1 AATTACCAAAATACCTCTAGTTTATAA
* *
20523023 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCTCTAGTTTATAA
*
20523050 AATTACCAAAATACCCCTAGTTTATAA
1 AATTACCAAAATACCTCTAGTTTATAA
* * * * * *
20523077 AATTACCGAAACACCACTGGTTTGTGA
1 AATTACCAAAATACCTCTAGTTTATAA
* * * *
20523104 AATTATCGAAATACCT-TCAATTTGTAA
1 AATTACCAAAATACCTCT-AGTTTATAA
*
20523131 AATTACCAAAATACCTCT-GATTTACAA
1 AATTACCAAAATACCTCTAG-TTTATAA
20523158 AATTA-CAGAAATACC
1 AATTACCA-AAATACC
20523173 CTTGACTCTC
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
26 3 0.02
27 122 0.97
28 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCTCTAGTTTATAA
Found at i:20523035 original size:54 final size:53
Alignment explanation
Indices: 20522968--20523145 Score: 153
Period size: 54 Copynumber: 3.3 Consensus size: 53
20522958 CTCGATTGTG
** * *
20522968 AAATTACTGAAATACCCCTA-TAGAATAGAATTACCAAAATACCTCTAGTTTATA
1 AAATTACCAAAATACCCCTAGTAG--TAAAATTACCAAAATACCCCTAGTTTATA
*
20523022 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTATA
1 AAATTACCAAAATACCCCTAG-TAGTAAAATTACCAAAATACCCCTAGTTTATA
* * * * * * * * * * *
20523076 AAATTACCGAAACACCACTGGTTTGTGAAATTATCGAAATA-CCTTCAATTTGTA
1 AAATTACCAAAATACCCCTAG-TAGTAAAATTACCAAAATACCCCT-AGTTTATA
20523130 AAATTACCAAAATACC
1 AAATTACCAAAATACC
20523146 TCTGATTTAC
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
53 3 0.03
54 99 0.95
56 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (53 bp):
AAATTACCAAAATACCCCTAGTAGTAAAATTACCAAAATACCCCTAGTTTATA
Found at i:20523320 original size:27 final size:27
Alignment explanation
Indices: 20523277--20523350 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
20523267 AAATGACTAA
*
20523277 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
20523304 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
20523331 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
20523351 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:20523354 original size:27 final size:27
Alignment explanation
Indices: 20523290--20523354 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
20523280 ACCCCTAATA
*
20523290 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
20523317 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
20523344 GGTAAAATGAC
1 GGTAAAATGAC
20523355 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:20524203 original size:25 final size:24
Alignment explanation
Indices: 20524163--20524232 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
20524153 AGGAAGTGCT
* *
20524163 AAAAGGGCTCTACCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
20524187 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
20524212 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
20524233 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:20524245 original size:24 final size:23
Alignment explanation
Indices: 20524163--20524259 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 23
20524153 AGGAAGTGCT
* * *
20524163 AAAAGGGCTCTACCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAG-TTATC
20524187 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAG-TTATC
*
20524212 AGAAAGGGCTTTGCCCCAGTTATT
1 A-AAAGGGCTTTGCCCCAGTTATC
**
20524236 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAG-GGCTTTGCC-CCAGTTAT
20524260 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.06
24 13 0.21
25 46 0.73
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCCAGTTATC
Found at i:20524439 original size:42 final size:42
Alignment explanation
Indices: 20524380--20524471 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
20524370 TAGTCTCCCC
* *
20524380 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
20524422 AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
20524464 AAATGGGC
1 AAATGGGC
20524472 CTAAGGGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
Found at i:20524599 original size:30 final size:31
Alignment explanation
Indices: 20524495--20524608 Score: 187
Period size: 31 Copynumber: 3.7 Consensus size: 31
20524485 CGTTTACAGT
20524495 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
20524526 AAAGGCTTCGACCCAGTGATATGATTTGTGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
20524557 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
20524588 AAAGG-TTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
20524609 TCAAGACTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 5 0.06
30 11 0.14
31 62 0.79
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:20535269 original size:42 final size:43
Alignment explanation
Indices: 20535168--20535331 Score: 133
Period size: 43 Copynumber: 3.8 Consensus size: 43
20535158 CAATGGCAAC
* * *
20535168 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAAACATGGTCTTACATGAAATCAAATATCGATGCCACT
* * *
20535211 GTCCCATACA-GTGTCTTACATGAAATCCAATA-CGATGCTGA-T
1 GTCCCAAACATG-GTCTTACATGAAATCAAATATCGATGC-CACT
* * * *
20535253 GTCTCAAACATGGTCTTACACGTAAATCTCAAAT-T-GA-GTCAAT
1 GTCCCAAACATGGTCTTACATG-AAA--TCAAATATCGATGCCACT
* *
20535296 GTCCCAAACGTGGTCTTACATGAAATCACATATCGA
1 GTCCCAAACATGGTCTTACATGAAATCAAATATCGA
20535332 AAATCCTATG
Statistics
Matches: 96, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
40 5 0.05
41 1 0.01
42 31 0.32
43 52 0.54
44 2 0.02
45 5 0.05
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
GTCCCAAACATGGTCTTACATGAAATCAAATATCGATGCCACT
Found at i:20541179 original size:64 final size:64
Alignment explanation
Indices: 20541098--20541282 Score: 196
Period size: 67 Copynumber: 2.9 Consensus size: 64
20541088 AGACATTATG
* *
20541098 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
20541162 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
20541227 AA
63 AA
* * * *
20541229 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGCT
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGCT
20541283 GAACTATATG
Statistics
Matches: 99, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 20 0.20
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.31
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:20541881 original size:13 final size:13
Alignment explanation
Indices: 20541863--20541889 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20541853 AATTAGAGAC
20541863 TCAAAATTATATT
1 TCAAAATTATATT
20541876 TCAAAATTATATT
1 TCAAAATTATATT
20541889 T
1 T
20541890 TTAAAATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAAAATTATATT
Found at i:20550208 original size:56 final size:56
Alignment explanation
Indices: 20550122--20550233 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
20550112 TTTAAATGCT
20550122 AAAATAAGTTTAGTAATGTCTCATGCTCGACTCCGGCGACGGTATAGGGTAAGTGG
1 AAAATAAGTTTAGTAATGTCTCATGCTCGACTCCGGCGACGGTATAGGGTAAGTGG
20550178 AAAATAAGTTTAGTAATGTCTCATGCTCGACTCCGGCGACGGTATAGGGTAAGTGG
1 AAAATAAGTTTAGTAATGTCTCATGCTCGACTCCGGCGACGGTATAGGGTAAGTGG
20550234 GCATTACAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (56 bp):
AAAATAAGTTTAGTAATGTCTCATGCTCGACTCCGGCGACGGTATAGGGTAAGTGG
Found at i:20562593 original size:21 final size:21
Alignment explanation
Indices: 20562569--20562608 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20562559 TTTCTAGGAC
*
20562569 ATGAATTGAATTAAATTGAGT
1 ATGAAATGAATTAAATTGAGT
*
20562590 ATGAAATGGATTAAATTGA
1 ATGAAATGAATTAAATTGA
20562609 TGTTAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (21 bp):
ATGAAATGAATTAAATTGAGT
Found at i:20563128 original size:25 final size:24
Alignment explanation
Indices: 20563086--20563138 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
20563076 CACAAATGCA
*
20563086 GCTCTTTATGAACGTCCTGATATAG
1 GCTCTTTATGAACGTCCTAATAT-G
* * *
20563111 GCTCTTTGTGAGCTTCCTAATATG
1 GCTCTTTATGAACGTCCTAATATG
20563135 GCTC
1 GCTC
20563139 GCATTAACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
GCTCTTTATGAACGTCCTAATATG
Found at i:20565413 original size:53 final size:53
Alignment explanation
Indices: 20565233--20565437 Score: 218
Period size: 55 Copynumber: 3.8 Consensus size: 53
20565223 AGGGTTTAAG
* * * *
20565233 GATACCATGTAAGACCATGCTAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGG-CATTGGTAA-G-TTCATAAGGCAAT
* * * *
20565288 GAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAT
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC-AAT
* *
20565344 G-T-CTCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAT
1 GATAC-CATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGCAAT
* *
20565396 GATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
20565438 TTAAAAGGAT
Statistics
Matches: 125, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
52 6 0.05
53 43 0.34
54 9 0.07
55 64 0.51
56 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (53 bp):
GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGCAAT
Found at i:20565436 original size:108 final size:110
Alignment explanation
Indices: 20565238--20565437 Score: 298
Period size: 108 Copynumber: 1.8 Consensus size: 110
20565228 TTAAGGATAC
* *
20565238 CATGTAAGACCATGCTAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGAC
1 CATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC
*
20565303 CATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAATGTCT
66 CATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAATGTCT
* * * *
20565348 CATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAATGATACCATGTAAGA
1 CATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGA
*
20565410 CCATGTCAAGACATGGCAATGGTAAGTT
65 CCATGTCAAGACATGGCAATGATAAGTT
20565438 TTAAAAGGAT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.58
109 7 0.09
110 24 0.30
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (110 bp):
CATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC
CATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAATGTCT
Found at i:20565696 original size:16 final size:16
Alignment explanation
Indices: 20565675--20565705 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20565665 ATACATTTGA
20565675 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
20565691 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
20565706 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:20572623 original size:28 final size:27
Alignment explanation
Indices: 20572591--20572686 Score: 103
Period size: 28 Copynumber: 3.6 Consensus size: 27
20572581 AAAAATCAAA
*
20572591 TATATAATATACTAAAACTATAAAAC-
1 TATATAATATAATAAAACTATAAAACT
*
20572617 --T-TAATATAATAAAACTTTAAAACGT
1 TATATAATATAATAAAACTATAAAAC-T
*
20572642 TATGTAATATAATAAAACTATAAAACT
1 TATATAATATAATAAAACTATAAAACT
20572669 TGACT-TAATATAATAAAA
1 T-A-TATAATATAATAAAA
20572687 GTTTACGTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
23 20 0.33
24 1 0.02
27 3 0.05
28 35 0.58
29 1 0.02
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.33
Consensus pattern (27 bp):
TATATAATATAATAAAACTATAAAACT
Found at i:20572730 original size:16 final size:16
Alignment explanation
Indices: 20572709--20572743 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20572699 TCTTAATATA
*
20572709 ATAATACTAAATTAAG
1 ATAATACTAAACTAAG
*
20572725 ATAATACTCAACTAAG
1 ATAATACTAAACTAAG
20572741 ATA
1 ATA
20572744 TTATATCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (16 bp):
ATAATACTAAACTAAG
Found at i:20572861 original size:25 final size:27
Alignment explanation
Indices: 20572828--20572884 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
20572818 ATCATGATAA
* *
20572828 TATTCATTAA-AAAAAGTTTACCCTG-
1 TATTAATTAAGAAAAAGTTTACCATGT
*
20572853 TATTAATTAAGATAAAGTTTACCATGT
1 TATTAATTAAGAAAAAGTTTACCATGT
20572880 TATTA
1 TATTA
20572885 TGTTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 9 0.33
26 13 0.48
27 5 0.19
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (27 bp):
TATTAATTAAGAAAAAGTTTACCATGT
Found at i:20575704 original size:29 final size:29
Alignment explanation
Indices: 20575671--20575727 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
20575661 TTTGTACGAG
20575671 GATCTTAGACATGGATAATTCATTTCAAA
1 GATCTTAGACATGGATAATTCATTTCAAA
20575700 GATCTTAGACATGGATAATTCATTTCAA
1 GATCTTAGACATGGATAATTCATTTCAA
20575728 TTACTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (29 bp):
GATCTTAGACATGGATAATTCATTTCAAA
Found at i:20576903 original size:31 final size:31
Alignment explanation
Indices: 20576867--20576928 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
20576857 CAGGTACATA
20576867 ACCAATGAATTTTCATACATAAGATTTCTCT
1 ACCAATGAATTTTCATACATAAGATTTCTCT
* *
20576898 ACCAATGATTTTTCATACATAAGTTTTCTCT
1 ACCAATGAATTTTCATACATAAGATTTCTCT
20576929 TTTACAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (31 bp):
ACCAATGAATTTTCATACATAAGATTTCTCT
Found at i:20576924 original size:15 final size:16
Alignment explanation
Indices: 20576876--20576924 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
20576866 AACCAATGAA
20576876 TTTTCATACATAAGAT
1 TTTTCATACATAAGAT
* *
20576892 TTCTC-TACCA-ATGAT
1 TTTTCATA-CATAAGAT
20576907 TTTTCATACATAAG-T
1 TTTTCATACATAAGAT
20576922 TTT
1 TTT
20576925 CTCTTTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (16 bp):
TTTTCATACATAAGAT
Found at i:20583757 original size:18 final size:18
Alignment explanation
Indices: 20583736--20583813 Score: 57
Period size: 18 Copynumber: 4.0 Consensus size: 18
20583726 CAGTTAAACC
20583736 ATTTGATTAATATATTTA
1 ATTTGATTAATATATTTA
* *
20583754 ATTTGATTTATTTATTTATA
1 ATTTGATTAATATA-TT-TA
*
20583774 ATTGAGTATTATTATATATTTA
1 ATT-TG-ATTA--ATATATTTA
* *
20583796 ATTTGATTTATTTATTTA
1 ATTTGATTAATATATTTA
20583814 TAAATAAATC
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
18 20 0.43
19 2 0.04
20 8 0.17
21 2 0.04
22 8 0.17
23 2 0.04
24 4 0.09
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
ATTTGATTAATATATTTA
Found at i:20583866 original size:16 final size:16
Alignment explanation
Indices: 20583847--20583889 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
20583837 TAAAAATAAT
20583847 TTAAAATATAAATTTA
1 TTAAAATATAAATTTA
*
20583863 TTAATATATATAAATTTG
1 TTAA-A-ATATAAATTTA
*
20583881 TTAATATAT
1 TTAAAATAT
20583890 GTAAAAACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 8 0.35
17 1 0.04
18 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TTAAAATATAAATTTA
Found at i:20583873 original size:18 final size:18
Alignment explanation
Indices: 20583852--20583894 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
20583842 ATAATTTAAA
20583852 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
20583870 ATATAAATTTGTTAATAT
1 ATATAAATTTATTAATAT
*
20583888 ATGTAAA
1 ATATAAA
20583895 AACAGCTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:20584015 original size:20 final size:19
Alignment explanation
Indices: 20583970--20584007 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20583960 CATCCAAACA
20583970 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAATTATTT
20583989 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAATTATTT
20584008 TCTAGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
CCAGAAAAGTAAATTATTT
Found at i:20590338 original size:24 final size:25
Alignment explanation
Indices: 20590291--20590338 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
20590281 TTAGGTCTCA
* * *
20590291 TGAGCTTCCTGCTTAATGGTTCTTG
1 TGAGCTTCCCGCTTAATAGCTCTTG
20590316 TGAGCTTCCCG-TTAATAGCTCTT
1 TGAGCTTCCCGCTTAATAGCTCTT
20590339 CCAAGCACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (25 bp):
TGAGCTTCCCGCTTAATAGCTCTTG
Found at i:20593495 original size:20 final size:20
Alignment explanation
Indices: 20593470--20593514 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
20593460 AGGGACTAAA
*
20593470 ATGAAAAGTTGT-AAATTTT
1 ATGAAAAATTGTGAAATTTT
*
20593489 GATGAAAAATTTTGAAATTTT
1 -ATGAAAAATTGTGAAATTTT
20593510 ATGAA
1 ATGAA
20593515 TACATGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (20 bp):
ATGAAAAATTGTGAAATTTT
Found at i:20596480 original size:46 final size:45
Alignment explanation
Indices: 20596421--20596545 Score: 130
Period size: 48 Copynumber: 2.7 Consensus size: 45
20596411 ATCTCATAGC
* *
20596421 CGATGTATGTCCCA-ACATGTCTTACACTAGCTCTCGTCTTAA-T-GT
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCT--T-ATAAGTGGT
* *
20596466 CGATGCCATGTCCCATACATGGTCTTACACTGGCTCTTATAATGTGGT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTTATAA-GTGGT
*
20596514 CGATGCATGTCCTAGACATGTCTTACACTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC
20596546 ACACAAATAA
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
45 8 0.12
46 21 0.31
47 17 0.25
48 22 0.32
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.33
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTTATAAGTGGT
Found at i:20602341 original size:27 final size:27
Alignment explanation
Indices: 20602152--20602350 Score: 245
Period size: 27 Copynumber: 7.4 Consensus size: 27
20602142 GGATAAGTTC
* *
20602152 TAGAATTATCGAAATACCCCTGTAAGG
1 TAGAATTACCGAAATACCCCTGTAGGG
20602179 TAGAATTACCGAAATACCCCTGTAGGG
1 TAGAATTACCGAAATACCCCTGTAGGG
**
20602206 TAGAATTATTGAAATACCCCTGTAGGG
1 TAGAATTACCGAAATACCCCTGTAGGG
** *
20602233 TAGAATTACTAAAATACCCCTGTAGGA
1 TAGAATTACCGAAATACCCCTGTAGGG
* * *
20602260 TAGAATTACTGAAATACCCTTGTAGAG
1 TAGAATTACCGAAATACCCCTGTAGGG
* * *
20602287 TAGAAATACTGAAATACCCCTGCAGGG
1 TAGAATTACCGAAATACCCCTGTAGGG
* * *
20602314 TAGAATTACCGAGATACCCTTGTGGGG
1 TAGAATTACCGAAATACCCCTGTAGGG
*
20602341 TAAAATTACC
1 TAGAATTACC
20602351 ATTTTGCCCT
Statistics
Matches: 150, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 150 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
TAGAATTACCGAAATACCCCTGTAGGG
Found at i:20609121 original size:27 final size:27
Alignment explanation
Indices: 20609079--20609251 Score: 202
Period size: 27 Copynumber: 6.4 Consensus size: 27
20609069 TGGATAAGTT
*
20609079 GTAGAATTATCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
***
20609106 GTAGAATTATTAAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
20609133 TTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
20609160 ATAGAATTACCAAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
20609187 GTAGAAATACCGAAATACCCATGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
20609214 GTAGAATTACCGAGATACCCTTGTTGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
20609241 TTATAATTACC
1 GTAGAATTACC
20609252 ATTTTTCCCG
Statistics
Matches: 125, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 125 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:20613483 original size:57 final size:57
Alignment explanation
Indices: 20613388--20613745 Score: 518
Period size: 57 Copynumber: 6.2 Consensus size: 57
20613378 GATCTCATTT
* * * *
20613388 CACACACTTAGTGCCCCAACAACCGATCTTGCACACACAGTGCTTGGTTACAGAACTCG
1 CACACAC--AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
20613447 CACACACAGTGCCTCAACAACTGATCTCGCATACACAGTGCTTGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
20613504 CACACATAGTGCCTCAACAACCAATCTCGCACACACAGTGCTTGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
20613561 CACACACAGTGCCTCAATAACCGATCTCGCACAGACATTGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
**
20613618 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTATAGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * * **
20613675 CACACACAGTGCCTCAACAACCAATCTCACACACACAGTGCTCGATTACGGAACTTA
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
20613732 CACACACAGTGCCT
1 CACACACAGTGCCT
20613746 ATGTTTTCTT
Statistics
Matches: 272, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
57 265 0.97
59 7 0.03
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (57 bp):
CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
Found at i:20613736 original size:28 final size:28
Alignment explanation
Indices: 20613418--20613743 Score: 215
Period size: 28 Copynumber: 11.5 Consensus size: 28
20613408 AACCGATCTT
* * *
20613418 GCACACACAGTGCTTGGTTACAGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
20613446 GCACACACAGTGCCTCAACAACTGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
* * *
20613475 GCATACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* * ** *
20613503 GCACACATAGTGCCTCAACAAC-CAATCTC
1 GCACACACAGTG-CTCGATTACGGAA-CTC
* *
20613532 GCACACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* * * *
20613560 GCACACACAGTGCCTCAATAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
* * *
20613589 GCACAGACATTGCTCGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
20613617 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
* **
20613646 GCACACACAGTGCTCGGTTATAGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** *
20613674 GCACACACAGTGCCTCAACAAC-CAATCTC
1 GCACACACAGTG-CTCGATTACGGAA-CTC
* *
20613703 ACACACACAGTGCTCGATTACGGAACTT
1 GCACACACAGTGCTCGATTACGGAACTC
*
20613731 ACACACACAGTGC
1 GCACACACAGTGC
20613744 CTATGTTTTC
Statistics
Matches: 219, Mismatches: 70, Indels: 18
0.71 0.23 0.06
Matches are distributed among these distances:
28 117 0.53
29 102 0.47
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (28 bp):
GCACACACAGTGCTCGATTACGGAACTC
Found at i:20614261 original size:26 final size:26
Alignment explanation
Indices: 20614232--20614284 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
20614222 ACTTTTCATA
20614232 CACACGTATATTATCCTTTAATCAGG
1 CACACGTATATTATCCTTTAATCAGG
20614258 CACACGTATATTATCCTTTAATCAGG
1 CACACGTATATTATCCTTTAATCAGG
20614284 C
1 C
20614285 TTACAAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (26 bp):
CACACGTATATTATCCTTTAATCAGG
Found at i:20615781 original size:28 final size:28
Alignment explanation
Indices: 20615750--20615812 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
20615740 TCGATATTTT
*
20615750 GCACACTAAGAGTCATTCTCAATATCTC
1 GCACACTAAGAGCCATTCTCAATATCTC
* *
20615778 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGAGCCATTCTCAATATCTC
*
20615806 GTACACT
1 GCACACT
20615813 GAGTACCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (28 bp):
GCACACTAAGAGCCATTCTCAATATCTC
Found at i:20615821 original size:28 final size:28
Alignment explanation
Indices: 20615750--20615821 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
20615740 TCGATATTTT
*
20615750 GCACACTAAG-AGTCATTCTCAATATCTC
1 GCACACTAAGTA-CCATTCTCAATATCTC
* *
20615778 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTACCATTCTCAATATCTC
* *
20615806 GTACACTGAGTACCAT
1 GCACACTAAGTACCAT
20615822 ATTTGATTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (28 bp):
GCACACTAAGTACCATTCTCAATATCTC
Found at i:20622736 original size:20 final size:20
Alignment explanation
Indices: 20622711--20622755 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20622701 ATGAACTAAA
* *
20622711 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTATAAAATTTG
*
20622731 ATGAAAAATTATAAAATTTT
1 ATGAAAAATTATAAAATTTG
20622751 ATGAA
1 ATGAA
20622756 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTATAAAATTTG
Found at i:20625760 original size:40 final size:40
Alignment explanation
Indices: 20625676--20625859 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
20625666 TTGAATGCTG
* * * *
20625676 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
20625715 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
20625756 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
20625796 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
20625836 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
20625860 GTATGAGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:20625813 original size:80 final size:81
Alignment explanation
Indices: 20625676--20625856 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 81
20625666 TTGAATGCTG
* *
20625676 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
20625740 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
20625756 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
20625817 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
20625836 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
20625857 ATTGTATGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 4 0.04
80 77 0.86
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:20632200 original size:23 final size:23
Alignment explanation
Indices: 20632170--20632216 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
20632160 CAAAGATCAC
20632170 TACTAATAATATGTATACATACA
1 TACTAATAATATGTATACATACA
20632193 TACTAATAATATGTATACATACA
1 TACTAATAATATGTATACATACA
20632216 T
1 T
20632217 TTCCTGCGTT
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:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (23 bp):
TACTAATAATATGTATACATACA
Found at i:20633776 original size:43 final size:43
Alignment explanation
Indices: 20633724--20633835 Score: 206
Period size: 43 Copynumber: 2.6 Consensus size: 43
20633714 TCGGCATTAC
*
20633724 GCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
20633767 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
20633810 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
20633836 TAATACCAGT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.30, C:0.33, G:0.26, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:20633893 original size:38 final size:38
Alignment explanation
Indices: 20633833--20633935 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
20633823 GAAGGCCCGA
** * * *
20633833 ATATAATACCAGTGCTAGGCCTGCGGGATTTATCCCAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCAG
* *
20633871 ATATAATACCAGCACGAAGCCTGCGCGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCAG
**
20633909 ATATTTTACCAGCACGAAGCCTGCGGG
1 ATATAATACCAGCACGAAGCCTGCGGG
20633936 TCTTTAAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCAG
Found at i:20637705 original size:7 final size:7
Alignment explanation
Indices: 20637681--20637721 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
20637671 TAGTCTTAAA
20637681 ATAAAAT
1 ATAAAAT
*
20637688 A-AAAGT
1 ATAAAAT
*
20637694 A-AAAAC
1 ATAAAAT
20637700 ATAAAAT
1 ATAAAAT
20637707 ATAAAAT
1 ATAAAAT
20637714 ATAAAAT
1 ATAAAAT
20637721 A
1 A
20637722 AAAGTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 9 0.31
7 20 0.69
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (7 bp):
ATAAAAT
Found at i:20658119 original size:55 final size:55
Alignment explanation
Indices: 20658060--20658195 Score: 139
Period size: 55 Copynumber: 2.5 Consensus size: 55
20658050 TGCGACATGG
* * * * ***
20658060 CCGTGGGTGAACCTGCCAAAACAACATGGGCGTGCGACATGCCCGTGCTTGGAAA
1 CCGTGGGTGAACCTGCCAAAACAACACGGGCGTGAGACACGCCCATGCCAAGAAA
* * ** *
20658115 CCGTGGCTGAACCTGTCAAATTAACACGGGCGTGAGACACGCCCATGCCAAGCAA
1 CCGTGGGTGAACCTGCCAAAACAACACGGGCGTGAGACACGCCCATGCCAAGAAA
**
20658170 CCGT-GGCAAACCTGCCAAAACAACAC
1 CCGTGGGTGAACCTGCCAAAACAACAC
20658196 CGACGTGGAC
Statistics
Matches: 63, Mismatches: 18, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
54 16 0.25
55 47 0.75
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (55 bp):
CCGTGGGTGAACCTGCCAAAACAACACGGGCGTGAGACACGCCCATGCCAAGAAA
Found at i:20661727 original size:16 final size:16
Alignment explanation
Indices: 20661706--20661736 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20661696 TAAAATGCTC
20661706 AACTTGGAATGTGTGA
1 AACTTGGAATGTGTGA
20661722 AACTTGGAATGTGTG
1 AACTTGGAATGTGTG
20661737 GGGGTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (16 bp):
AACTTGGAATGTGTGA
Found at i:20675297 original size:49 final size:49
Alignment explanation
Indices: 20675225--20675399 Score: 224
Period size: 49 Copynumber: 3.5 Consensus size: 49
20675215 TGAGGTCACG
* *
20675225 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGGTAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * * * * *
20675274 TGTGTAGTATTAAGTGTAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCGCA
*
20675325 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
*
20675374 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
20675400 TGCATACCAG
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 62 0.59
50 4 0.04
51 39 0.37
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:20675395 original size:100 final size:100
Alignment explanation
Indices: 20675220--20675412 Score: 314
Period size: 100 Copynumber: 1.9 Consensus size: 100
20675210 TATTGTGAGG
* * * *
20675220 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGGTAATTGGTCGCATGTGTAGTATT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTACT
* * *
20675285 AAGTGTAGGCTACTATGCGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTATGCATACCAGATAACTTCGA
20675320 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTACT
*
20675385 ATGTGCAGGCTACTATGCATACCAGATA
66 AAGTGCAGGCTACTATGCATACCAGATA
20675413 GCTTTGGATA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCATACCAGATAACTTCGA
Found at i:20678023 original size:24 final size:24
Alignment explanation
Indices: 20677953--20678023 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
20677943 TAGCTCAAAA
* * * *
20677953 GAGCATCCCGATATTAGCTCTCAT
1 GAGCTTCCCGTTAATAGCTCTTAT
* * *
20677977 GAGCTTCCTGTTTAATGGTTCTTAT
1 GAGCTTCCCG-TTAATAGCTCTTAT
20678002 GAGCTTCCCGTTAATAGCTCTT
1 GAGCTTCCCGTTAATAGCTCTT
20678024 CGGAGCATCC
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (24 bp):
GAGCTTCCCGTTAATAGCTCTTAT
Found at i:20678135 original size:26 final size:24
Alignment explanation
Indices: 20678080--20678147 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 24
20678070 CTTAGCTTTT
20678080 ATGAGCTTCCCGATTATGACTCTTC
1 ATGAGCTTCCC-ATTATGACTCTTC
* *
20678105 ATGAGCTTCCCATTAATTGGCTCTTT
1 ATGAGCTTCCCATT-A-TGACTCTTC
* *
20678131 GTGAGCTTCCCAATATG
1 ATGAGCTTCCCATTATG
20678148 GCTCACTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.14
25 13 0.35
26 19 0.51
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (24 bp):
ATGAGCTTCCCATTATGACTCTTC
Found at i:20679012 original size:52 final size:52
Alignment explanation
Indices: 20678949--20679054 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
20678939 ATATAACATG
20678949 GTTAATATATGTGTTCTTGGTATGGTTAGATTGAATTATATTAAACATATAT
1 GTTAATATATGTGTTCTTGGTATGGTTAGATTGAATTATATTAAACATATAT
20679001 GTTAATATATGTGTTCTTGGTATGGTTAGATTGAATTATATTAAACATATAT
1 GTTAATATATGTGTTCTTGGTATGGTTAGATTGAATTATATTAAACATATAT
20679053 GT
1 GT
20679055 CTTACAAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (52 bp):
GTTAATATATGTGTTCTTGGTATGGTTAGATTGAATTATATTAAACATATAT
Found at i:20688996 original size:20 final size:20
Alignment explanation
Indices: 20688971--20689011 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20688961 ATTGTTTATA
20688971 CAAAAGCCGCAGACAATGGC
1 CAAAAGCCGCAGACAATGGC
20688991 CAAAAGCCGCAGACAATGGC
1 CAAAAGCCGCAGACAATGGC
20689011 C
1 C
20689012 CATAGTAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.32, G:0.24, T:0.05
Consensus pattern (20 bp):
CAAAAGCCGCAGACAATGGC
Found at i:20692102 original size:48 final size:48
Alignment explanation
Indices: 20691948--20692095 Score: 206
Period size: 48 Copynumber: 3.1 Consensus size: 48
20691938 ATATATACAC
* * * **
20691948 ATCTCATATATATTTCACATTAGCCATTTGCCTTTACCACATATGCAT
1 ATCTCATACATATTTCACATTAGCCATTCGACTTTACCACATATATAT
** *
20691996 GGCTCATACATATTTCACATTAGCCTTTCGACTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGACTTTACCACATATATAT
* *
20692044 ATCTCATACATATTTTACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGACTTTACCACATATATAT
20692092 ATCT
1 ATCT
20692096 TGTACATCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGACTTTACCACATATATAT
Found at i:20703686 original size:14 final size:15
Alignment explanation
Indices: 20703669--20703697 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20703659 TCACGAAAAT
20703669 TTCACACAT-ATAAA
1 TTCACACATAATAAA
20703683 TTCACACATAATAAA
1 TTCACACATAATAAA
20703698 CATTGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:20706198 original size:37 final size:37
Alignment explanation
Indices: 20706148--20706226 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
20706138 TTATTACGAA
* *
20706148 GTCTTACCCGGACATAATCACCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCACCACACGAAGTCATCGG
* *
20706185 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCACCACACGAAGTCATCGG
20706222 GTCTT
1 GTCTT
20706227 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCACCACACGAAGTCATCGG
Found at i:20706423 original size:47 final size:47
Alignment explanation
Indices: 20706345--20707795 Score: 1926
Period size: 47 Copynumber: 29.9 Consensus size: 47
20706335 CCCTTCGGGA
* * * * * *
20706345 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
20706392 CCTGTCACATATATACACTTTCACATTCATCACATCGGACATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20706439 CTTATCAAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20706486 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20706533 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20706582 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20706629 CTTATCACAGATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20706678 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20706727 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20706776 C-TATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20706822 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20706869 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20706916 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20706963 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707010 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707059 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707108 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707155 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20707202 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707249 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * * **** ***
20707295 CTTATCACAT-TCACATCGGCCATT-AGGCCTT-ATCACATATATACACTTTCAC
1 CTTATCACATAT-ATA-C--ACTTTCA--CATTCATCACAT-CGGCCA-TTAGGC
* ** *
20707347 ATTCATCACATCGGCCAT-TAGGC-CTTATCACATATATATACACTTTCACATTCATCACA-TCG
1 CTT-ATCACAT-----ATATA--CACTT-TCAC----AT-T-CA---TCACA-TCGGC-CATTAG
20707409 GC
46 GC
* ** *
20707411 CATTA--AGCCT-TAT-CACATATAT-ACACTT--TCACATTCATCACA-TCGGCCATTAGGC
1 C-TTATCA-CATATATACAC-T-T-TCACA-TTCATCACA-TCGGC-CATTAGG--------C
*
20707466 CTTATCACATATATACACTTTCAGATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707513 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
20707562 CTTATCACATATATACACTTTCATATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707609 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707656 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707703 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707752 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
20707796 CGCCATACTA
Statistics
Matches: 1285, Mismatches: 54, Indels: 130
0.87 0.04 0.09
Matches are distributed among these distances:
45 1 0.00
46 52 0.04
47 750 0.58
48 7 0.01
49 382 0.30
50 5 0.00
51 2 0.00
52 3 0.00
53 9 0.01
54 9 0.01
55 17 0.01
56 12 0.01
57 9 0.01
58 5 0.00
59 2 0.00
60 1 0.00
62 2 0.00
63 2 0.00
64 3 0.00
65 9 0.01
66 3 0.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20706424 original size:25 final size:25
Alignment explanation
Indices: 20706396--20706473 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
20706386 CTCGGCCCTG
20706396 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
*** *** *
20706421 TCACAT-CGGACA-TTAGGCCTT-A
1 TCACATATATACACTTTCACATTCA
*
20706443 TCAAATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
20706468 TCACAT
1 TCACAT
20706474 CGGCCATTAG
Statistics
Matches: 34, Mismatches: 16, Indels: 6
0.61 0.29 0.11
Matches are distributed among these distances:
22 6 0.18
23 8 0.24
24 8 0.24
25 12 0.35
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:20707305 original size:30 final size:29
Alignment explanation
Indices: 20707269--20707332 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 29
20707259 ATATACACTT
20707269 TCACATTCATCACATCGGCCATTA-GCCTTA
1 TCACATT--TCACATCGGCCATTAGGCCTTA
20707299 TCACA-TTCACATCGGCCATTAGGCCTTA
1 TCACATTTCACATCGGCCATTAGGCCTTA
20707327 TCACAT
1 TCACAT
20707333 ATATACACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 15 0.47
28 11 0.34
29 1 0.03
30 5 0.16
ACGTcount: A:0.27, C:0.33, G:0.11, T:0.30
Consensus pattern (29 bp):
TCACATTTCACATCGGCCATTAGGCCTTA
Found at i:20707313 original size:27 final size:28
Alignment explanation
Indices: 20707278--20707332 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
20707268 TTCACATTCA
20707278 TCACATCGGCCATTA-GCCTTATCACAT
1 TCACATCGGCCATTAGGCCTTATCACAT
20707305 TCACATCGGCCATTAGGCCTTATCACAT
1 TCACATCGGCCATTAGGCCTTATCACAT
20707333 ATATACACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.29
Consensus pattern (28 bp):
TCACATCGGCCATTAGGCCTTATCACAT
Found at i:20707313 original size:74 final size:75
Alignment explanation
Indices: 20707231--20707379 Score: 282
Period size: 74 Copynumber: 2.0 Consensus size: 75
20707221 TTCACATTCA
20707231 TCACATCGGCCATTAGACCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
1 TCACATCGGCCATTAGACCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707295 CTTATCACAT
66 CTTATCACAT
*
20707305 TCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 TCACATCGGCCATTAGACCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20707370 CTTATCACAT
66 CTTATCACAT
20707380 ATATATACAC
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 61 0.84
75 12 0.16
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (75 bp):
TCACATCGGCCATTAGACCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
CTTATCACAT
Found at i:20725360 original size:14 final size:15
Alignment explanation
Indices: 20725343--20725371 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20725333 TCAAAAAAAC
20725343 TTCACACAT-ATAAA
1 TTCACACATAATAAA
20725357 TTCACACATAATAAA
1 TTCACACATAATAAA
20725372 CACTGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:20734742 original size:17 final size:17
Alignment explanation
Indices: 20734720--20734755 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
20734710 ACTAAGTCGA
20734720 TCAAATTCAAGGTAAGT
1 TCAAATTCAAGGTAAGT
20734737 TCAAATTCAAGGTAAGT
1 TCAAATTCAAGGTAAGT
20734754 TC
1 TC
20734756 TTAAGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (17 bp):
TCAAATTCAAGGTAAGT
Found at i:20735672 original size:47 final size:47
Alignment explanation
Indices: 20735619--20736771 Score: 1973
Period size: 47 Copynumber: 24.4 Consensus size: 47
20735609 CAGCCACGAC
* * *
20735619 AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20735666 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
20735713 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
20735760 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
20735807 AGTGTATATACGTGATAAGGCCTAATCGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
20735854 AGTGTATATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATA--TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
20735903 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20735950 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20735997 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
20736044 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
20736091 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20736138 AGTGTATATATGTGGTAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
20736185 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
20736232 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20736279 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20736326 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20736375 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
20736424 AGTGTATATGTGTGATAAGGCCTAATAGCTGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
20736471 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20736518 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAACGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20736565 AGTGTATATATGTGATAAGGCCTAATAGTCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
20736612 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20736659 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * * * * * *
20736706 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
20736753 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
20736772 TCCCGAAGGG
Statistics
Matches: 1059, Mismatches: 43, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
47 918 0.87
49 141 0.13
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:20736946 original size:37 final size:37
Alignment explanation
Indices: 20736890--20736968 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
20736880 CCGAGCTCTA
* *
20736890 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
20736927 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
20736964 AAGAC
1 AAGAC
20736969 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:20742414 original size:16 final size:16
Alignment explanation
Indices: 20742372--20742406 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
20742362 TATAATAACC
20742372 TAAACTAAAAAAACTT
1 TAAACTAAAAAAACTT
20742388 TAAACTAAAAAAACTT
1 TAAACTAAAAAAACTT
20742404 TAA
1 TAA
20742407 GATAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAACTAAAAAAACTT
Found at i:20749069 original size:19 final size:19
Alignment explanation
Indices: 20749047--20749122 Score: 82
Period size: 19 Copynumber: 3.8 Consensus size: 19
20749037 CAAGAATGTC
*
20749047 AAAAACAAAAATAAAAGAA
1 AAAAATAAAAATAAAAGAA
* *
20749066 AAAATTAAAAATAAAACAA
1 AAAAATAAAAATAAAAGAA
20749085 AAAAATAGAAAATGAAAATGAA
1 AAAAATA-AAAAT-AAAA-GAA
20749107 AAAAGAT-AAAATAAAA
1 AAAA-ATAAAAATAAAA
20749123 AATATGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 22 0.46
20 9 0.19
21 9 0.19
22 6 0.12
23 2 0.04
ACGTcount: A:0.79, C:0.03, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAATAAAAATAAAAGAA
Done.