Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 17 of 427
Found at i:4694547 original size:13 final size:13
Alignment explanation
Indices: 4694529--4694556 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4694519 TATGCACTCG
4694529 AAAAAAAAAAACA
1 AAAAAAAAAAACA
4694542 AAAAAAAAAAACA
1 AAAAAAAAAAACA
4694555 AA
1 AA
4694557 TGAGAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:4698689 original size:17 final size:17
Alignment explanation
Indices: 4698652--4698692 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4698642 AGAAAGGAAA
4698652 AAGA-GGAGGGGAGAGG
1 AAGAGGGAGGGGAGAGG
*
4698668 GAGAGGGAGGGGA-AGTG
1 AAGAGGGAGGGGAGAG-G
4698685 AAGAGGGA
1 AAGAGGGA
4698693 AAAAGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.37, C:0.00, G:0.61, T:0.02
Consensus pattern (17 bp):
AAGAGGGAGGGGAGAGG
Found at i:4715037 original size:19 final size:19
Alignment explanation
Indices: 4715013--4715050 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4715003 ATCCATGTAA
4715013 GCATTTAACTGAGTTTCAT
1 GCATTTAACTGAGTTTCAT
4715032 GCATTTAACTGAGTTTCAT
1 GCATTTAACTGAGTTTCAT
4715051 CCCACTCATA
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:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (19 bp):
GCATTTAACTGAGTTTCAT
Found at i:4721812 original size:13 final size:14
Alignment explanation
Indices: 4721794--4721824 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
4721784 ATGTATGAAT
4721794 ATATACATATA-TA
1 ATATACATATATTA
4721807 ATATACATATATTA
1 ATATACATATATTA
4721821 ATAT
1 ATAT
4721825 TGATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATACATATATTA
Found at i:4721891 original size:22 final size:21
Alignment explanation
Indices: 4721864--4721908 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4721854 AATCATTAGT
4721864 AATAA-TAATAC--TAAAAAA
1 AATAATTAATACATTAAAAAA
*
4721882 AATAATTAATACATTAACAAA
1 AATAATTAATACATTAAAAAA
4721903 AATAAT
1 AATAAT
4721909 AGTAACAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 6 0.26
21 12 0.52
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAATTAATACATTAAAAAA
Found at i:4723785 original size:71 final size:71
Alignment explanation
Indices: 4723694--4723825 Score: 210
Period size: 71 Copynumber: 1.9 Consensus size: 71
4723684 ATTTAATAGG
* * *
4723694 AATTGAAATTACCTCAACGTGCCCCGAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAATTACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGA
4723759 AACATA
66 AACATA
* **
4723765 AATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
1 AATTGAAATTACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
4723826 CCTTGGAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (71 bp):
AATTGAAATTACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGA
AACATA
Found at i:4723958 original size:160 final size:160
Alignment explanation
Indices: 4723711--4724238 Score: 1004
Period size: 160 Copynumber: 3.3 Consensus size: 160
4723701 ATTACCTCAA
*
4723711 CGTGCCCCGAGG-TTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATT
1 CGTGCCCTGAGGCTT-AACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATT
4723775 ACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTCCTTGGAAAACATG
65 ACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTCCTTGGAAAACATG
4723840 AATTAAAAAGCAGAAATTGAAAATACCTGGG
130 AATTAAAAAGCAGAAATTGAAAATACCTGGG
4723871 CGTGCCCTGAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTA
1 CGTGCCCTGAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTA
*
4723936 CCTCAACGTGTCTTGAGGCTCAACTTACCTCTCGCAATATGAGCTGATTTCCTTGGAAAACATGA
66 CCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTCCTTGGAAAACATGA
4724001 ATTAAAAAGCAGAAATTGAAAATACCTGGG
131 ATTAAAAAGCAGAAATTGAAAATACCTGGG
4724031 CGTGCCCTGAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTA
1 CGTGCCCTGAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTA
4724096 CCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTCCTTGGAAAACATGA
66 CCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTCCTTGGAAAACATGA
4724161 ATTAAAAAGCAGAAATTGAAAATACCTGGG
131 ATTAAAAAGCAGAAATTGAAAATACCTGGG
*
4724191 CGTGCCCTGAGGCTTAACTTCATTTCTCGCAATATGAGTTGATTTTTG
1 CGTGCCCTGAGGCTTAAC-TCACTTCTCGCAATATGAGTTGATTTTTG
4724239 GAGAAAACAA
Statistics
Matches: 362, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
160 332 0.92
161 30 0.08
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (160 bp):
CGTGCCCTGAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTA
CCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTCCTTGGAAAACATGA
ATTAAAAAGCAGAAATTGAAAATACCTGGG
Found at i:4725236 original size:13 final size:13
Alignment explanation
Indices: 4725220--4725246 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4725210 GATCCCTTCC
4725220 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
4725233 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
4725246 T
1 T
4725247 TAGATGCCCT
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:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:4726926 original size:21 final size:21
Alignment explanation
Indices: 4726900--4726942 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4726890 AAGAAGTTCA
4726900 GTCTTGCGGTGAACGGATAAT
1 GTCTTGCGGTGAACGGATAAT
4726921 GTCTTGCGGTGAACGGATAAT
1 GTCTTGCGGTGAACGGATAAT
4726942 G
1 G
4726943 ATTCCCGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.35, T:0.28
Consensus pattern (21 bp):
GTCTTGCGGTGAACGGATAAT
Found at i:4737064 original size:13 final size:14
Alignment explanation
Indices: 4737046--4737076 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
4737036 ATGTATGAAT
4737046 ATATACATATA-TA
1 ATATACATATATTA
4737059 ATATACATATATTA
1 ATATACATATATTA
4737073 ATAT
1 ATAT
4737077 TGATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATACATATATTA
Found at i:4737143 original size:22 final size:21
Alignment explanation
Indices: 4737116--4737160 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4737106 AATCATTAGT
4737116 AATAA-TAATAC--TAAAAAA
1 AATAATTAATACATTAAAAAA
*
4737134 AATAATTAATACATTAACAAA
1 AATAATTAATACATTAAAAAA
4737155 AATAAT
1 AATAAT
4737161 AGTAACAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 6 0.26
21 12 0.52
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAATTAATACATTAAAAAA
Found at i:4737801 original size:12 final size:12
Alignment explanation
Indices: 4737784--4737822 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
4737774 TAAAAAACTC
4737784 TTTTTTTTTTGT
1 TTTTTTTTTTGT
4737796 TTTTTTTTTTGT
1 TTTTTTTTTTGT
*
4737808 TTTTTTTTATGT
1 TTTTTTTTTTGT
4737820 TTT
1 TTT
4737823 AATACATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:4738980 original size:2 final size:2
Alignment explanation
Indices: 4738973--4739005 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4738963 ATTGTGATTC
4738973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4739006 AAACTTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4742143 original size:51 final size:51
Alignment explanation
Indices: 4742081--4742192 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
4742071 TTTATATAAT
* * **
4742081 AACAAATTTAGCCCTCAA-AGTTTATACATTTTGTCAATTTGGTTTTAATTG
1 AACAAATTTAGCCCACAATA-TTTATACATCTTGTCAATTTGGTCCTAATTG
* * *
4742132 AACAAATTTAGCTCACAATATTTATACATCTTGTCAATTTGGTCCTGATTT
1 AACAAATTTAGCCCACAATATTTATACATCTTGTCAATTTGGTCCTAATTG
4742183 AACAAATTTA
1 AACAAATTTA
4742193 ACTTGCAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 52 0.98
52 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (51 bp):
AACAAATTTAGCCCACAATATTTATACATCTTGTCAATTTGGTCCTAATTG
Found at i:4742206 original size:51 final size:50
Alignment explanation
Indices: 4742081--4742220 Score: 136
Period size: 51 Copynumber: 2.7 Consensus size: 50
4742071 TTTATATAAT
* * * * **
4742081 AACAAATTTAGCCCTCAAAGTTTATACATTTTGTCAATTTGGTTTTAATTG
1 AACAAATTTAACTCACAAAATTTATACA-TTTGTCAATTTGGTCCTAATTG
* * * *
4742132 AACAAATTTAGCTCACAATATTTATACATCTTGTCAATTTGGTCCTGATTT
1 AACAAATTTAACTCACAAAATTTATACAT-TTGTCAATTTGGTCCTAATTG
** *
4742183 AACAAATTTAACTTGCAAAATTTACACATTCTGTCAAT
1 AACAAATTTAACTCACAAAATTTATACATT-TGTCAAT
4742221 ATTTACACAA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
50 2 0.03
51 72 0.97
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.40
Consensus pattern (50 bp):
AACAAATTTAACTCACAAAATTTATACATTTGTCAATTTGGTCCTAATTG
Found at i:4748695 original size:16 final size:16
Alignment explanation
Indices: 4748676--4748714 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4748666 GTTTGGTTCA
4748676 CTGTAATGGAATA-AGG
1 CTGTAATGGAATAGA-G
*
4748692 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
4748708 CTGTAAT
1 CTGTAAT
4748715 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:4749127 original size:18 final size:17
Alignment explanation
Indices: 4749049--4749123 Score: 66
Period size: 18 Copynumber: 4.4 Consensus size: 17
4749039 TTGAAATTTG
4749049 TAATATTATAATTAAATA
1 TAATATTATAATT-AATA
*
4749067 TAATAATT-TAA-TAACA
1 TAAT-ATTATAATTAATA
* *
4749083 T-ATATTATAAATATATC
1 TAATATTATAATTA-ATA
*
4749100 TAATAGTATAATTAATA
1 TAATATTATAATTAATA
4749117 TAATATT
1 TAATATT
4749124 TATACCCAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
14 3 0.07
15 5 0.11
16 6 0.13
17 11 0.24
18 17 0.38
19 3 0.07
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TAATATTATAATTAATA
Found at i:4749413 original size:2 final size:2
Alignment explanation
Indices: 4749408--4749451 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
4749398 TCTTTGGTTA
* * *
4749408 TC TC TC TC TC TC TC TC TC TC CC TC TC TC CC TC TC CC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4749450 TC
1 TC
4749452 ACACCTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (2 bp):
TC
Found at i:4750711 original size:25 final size:25
Alignment explanation
Indices: 4750683--4750731 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
4750673 ATATATATCA
4750683 TAAA-ATAGCATATAAAAGAAATAAT
1 TAAACATAGCATATAAAA-AAATAAT
4750708 TAAACATAGCATATAAAAAAATAA
1 TAAACATAGCATATAAAAAAATAA
4750732 AACTATGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.22
Consensus pattern (25 bp):
TAAACATAGCATATAAAAAAATAAT
Found at i:4750732 original size:21 final size:23
Alignment explanation
Indices: 4750682--4750731 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 23
4750672 AATATATATC
4750682 ATAAAATAGCATATAAAAGAAATA
1 ATAAAATAGCATAT-AAAGAAATA
*
4750706 ATTAAACATAGCATATAAAAAAATA
1 A-TAAA-ATAGCATATAAAGAAATA
4750731 A
1 A
4750732 AACTATGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 1 0.04
25 13 0.57
26 9 0.39
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (23 bp):
ATAAAATAGCATATAAAGAAATA
Found at i:4751247 original size:22 final size:21
Alignment explanation
Indices: 4751212--4751255 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4751202 AAAGGATATC
4751212 TACAAATTAAATCTCCAAGAT
1 TACAAATTAAATCTCCAAGAT
* *
4751233 TACAAGATTATATCTTCAAGAT
1 TACAA-ATTAAATCTCCAAGAT
4751255 T
1 T
4751256 GCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (21 bp):
TACAAATTAAATCTCCAAGAT
Found at i:4751274 original size:19 final size:19
Alignment explanation
Indices: 4751250--4751317 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
4751240 TTATATCTTC
4751250 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCT
4751269 AAGATTG--TATCATATCT
1 AAGATTGCATATCATATCT
4751286 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCT
4751305 AAGATTGCATATC
1 AAGATTGCATATC
4751318 CTTAAAGATT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.36
19 30 0.64
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (19 bp):
AAGATTGCATATCATATCT
Found at i:4751326 original size:36 final size:35
Alignment explanation
Indices: 4751242--4751327 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 35
4751232 TTACAAGATT
4751242 ATATCTTCAAGATTGCATATCATATCTAAGATTGTATC
1 ATATCTT-AAGATTGCATATCATATCTAAGATTG--TC
4751280 ATATC-TAAGATTGCATATCATATCTAAGATTG-C
1 ATATCTTAAGATTGCATATCATATCTAAGATTGTC
4751313 ATATCCTTAAAGATT
1 ATAT-CTT-AAGATT
4751328 ATATTTCCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
33 5 0.11
34 1 0.02
35 1 0.02
36 32 0.71
37 1 0.02
38 5 0.11
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (35 bp):
ATATCTTAAGATTGCATATCATATCTAAGATTGTC
Found at i:4751877 original size:18 final size:18
Alignment explanation
Indices: 4751854--4751899 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
4751844 GGGTGAAACA
4751854 AGTTTCCTTTAAAAGTTG
1 AGTTTCCTTTAAAAGTTG
4751872 AGTTTCCTTTAAAAGTTG
1 AGTTTCCTTTAAAAGTTG
* *
4751890 GGTTTTCTTT
1 AGTTTCCTTT
4751900 TTTGGGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (18 bp):
AGTTTCCTTTAAAAGTTG
Found at i:4755960 original size:19 final size:19
Alignment explanation
Indices: 4755912--4755960 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
4755902 TTTGCTGTTT
*
4755912 TTTTC-TGTTTTCTTGCTT
1 TTTTCTTGTTTTCTTGCTA
* * *
4755930 TTTTATTATTTTGTTGCTA
1 TTTTCTTGTTTTCTTGCTA
4755949 TTTTCTTGTTTT
1 TTTTCTTGTTTT
4755961 TTTTACTATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.06, C:0.10, G:0.10, T:0.73
Consensus pattern (19 bp):
TTTTCTTGTTTTCTTGCTA
Found at i:4756028 original size:14 final size:14
Alignment explanation
Indices: 4755991--4756028 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
4755981 TTCACAATTA
4755991 TGTTGTTATTATTT
1 TGTTGTTATTATTT
**
4756005 TGTTACTATTATTT
1 TGTTGTTATTATTT
4756019 TGTTGTTATT
1 TGTTGTTATT
4756029 GTATAACTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.16, C:0.03, G:0.13, T:0.68
Consensus pattern (14 bp):
TGTTGTTATTATTT
Found at i:4762262 original size:19 final size:19
Alignment explanation
Indices: 4762227--4762263 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4762217 TCGCTTTTCC
* *
4762227 ATTGTTTTTTTTTCATTTT
1 ATTGTTTTTCTTCCATTTT
4762246 ATTGTTTTTCTTCCATTT
1 ATTGTTTTTCTTCCATTT
4762264 CATAAAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.73
Consensus pattern (19 bp):
ATTGTTTTTCTTCCATTTT
Found at i:4762498 original size:17 final size:16
Alignment explanation
Indices: 4762462--4762497 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
4762452 AAATGAAAAG
4762462 AAAATAAATTATTAGT
1 AAAATAAATTATTAGT
4762478 AAAATAAATGTATTA-T
1 AAAATAAAT-TATTAGT
4762494 AAAA
1 AAAA
4762498 AGGAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AAAATAAATTATTAGT
Found at i:4765634 original size:99 final size:100
Alignment explanation
Indices: 4765463--4765663 Score: 316
Period size: 99 Copynumber: 2.0 Consensus size: 100
4765453 ATGAATCATC
* * * *
4765463 GTATAAAAGCCTTGTTTTATATAAGCTTTGTTAAGTAATACAAGCTATAGCATTCTCTTACACTC
1 GTATAAAAGCCTTGTTGTACATAAGCCTTGTTAAGTAATACAAGCTATAACATTCTCTTACACTC
*
4765528 ACTTTCTTTGCATATTAAG-T-CTTGTATTTGGTTT
66 ACTTTCTTTGCATATT-AGCTCCTTGTATTTCGTTT
* *
4765562 GTATAAAAGCCTTGTTGTACATAAGCCTTGTTGAGTAATACAAGCTATAACATTGTCTTACACTC
1 GTATAAAAGCCTTGTTGTACATAAGCCTTGTTAAGTAATACAAGCTATAACATTCTCTTACACTC
4765627 ACTTTCTTTGCATATTAGCTCCTTGTATTTCGTTT
66 ACTTTCTTTGCATATTAGCTCCTTGTATTTCGTTT
4765662 GT
1 GT
4765664 TTGAGTGCCT
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
98 2 0.02
99 76 0.82
100 15 0.16
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (100 bp):
GTATAAAAGCCTTGTTGTACATAAGCCTTGTTAAGTAATACAAGCTATAACATTCTCTTACACTC
ACTTTCTTTGCATATTAGCTCCTTGTATTTCGTTT
Found at i:4767371 original size:74 final size:74
Alignment explanation
Indices: 4767245--4767465 Score: 320
Period size: 74 Copynumber: 3.0 Consensus size: 74
4767235 AATCCACGTC
* * * * * *
4767245 CTCCTACATTAGCAACAATGCCTATGCTAATCGAGCTAAAGGCTGAAACGGCTTAATGACTAATT
1 CTCCTACATTAGTAACAATGCCTATACCAATCGAGCTAAAGACTCAATCGGCTTAATGACTAATT
4767310 TTCTTTATT
66 TTCTTTATT
* *
4767319 CTCCTACATTAGTAACAATGCCTATACCAATTGAGCTAAAGACTCAATCGGCTTAATGCCTAATT
1 CTCCTACATTAGTAACAATGCCTATACCAATCGAGCTAAAGACTCAATCGGCTTAATGACTAATT
4767384 TTCTTTATT
66 TTCTTTATT
* * *
4767393 CTCCTACATTAGTAACAATGCCCATACCAATCGAG-TTAAGACTCAATCGGCTCAAT-ACCTAAT
1 CTCCTACATTAGTAACAATGCCTATACCAATCGAGCTAAAGACTCAATCGGCTTAATGA-CTAAT
4767456 TTTCTTTATT
65 TTTCTTTATT
4767466 TACCATTCCT
Statistics
Matches: 133, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
73 34 0.26
74 99 0.74
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (74 bp):
CTCCTACATTAGTAACAATGCCTATACCAATCGAGCTAAAGACTCAATCGGCTTAATGACTAATT
TTCTTTATT
Found at i:4767608 original size:2 final size:2
Alignment explanation
Indices: 4767601--4767628 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4767591 TTTAAATACC
4767601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4767629 AATTTGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4768940 original size:15 final size:15
Alignment explanation
Indices: 4768920--4768948 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4768910 TGTCCTATTG
4768920 ATCCTGGAGGAGGAT
1 ATCCTGGAGGAGGAT
4768935 ATCCTGGAGGAGGA
1 ATCCTGGAGGAGGA
4768949 GGAGGAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.41, T:0.17
Consensus pattern (15 bp):
ATCCTGGAGGAGGAT
Found at i:4777613 original size:21 final size:21
Alignment explanation
Indices: 4777589--4777630 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4777579 AAGGACTTGG
4777589 GGAGAAAAAGGAAGAAGAAGA
1 GGAGAAAAAGGAAGAAGAAGA
* * *
4777610 GGAGCAAGAGGAGGAAGAAGA
1 GGAGAAAAAGGAAGAAGAAGA
4777631 TGATGATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.43, T:0.00
Consensus pattern (21 bp):
GGAGAAAAAGGAAGAAGAAGA
Found at i:4777653 original size:3 final size:3
Alignment explanation
Indices: 4777647--4777694 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
4777637 TGATGAGGAT
* *
4777647 GAA GAA GAA GAA GAA GAA GAG GAA GAA GAA GAA GGAA -AA GAA GGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA
4777692 GAA
1 GAA
4777695 AATGGGGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4780342 original size:43 final size:43
Alignment explanation
Indices: 4780250--4780350 Score: 134
Period size: 43 Copynumber: 2.3 Consensus size: 43
4780240 GGTAGCCCTC
4780250 TCTTATAACTACCATTAGTGTGCCTTAATTGGACATATAGCGT
1 TCTTATAACTACCATTAGTGTGCCTTAATTGGACATATAGCGT
** * *
4780293 GGTTATAATTACCATTAGTGTTG-CTTAATTGGACATTTAAG-GT
1 TCTTATAACTACCATTAGTG-TGCCTTAATTGGACATAT-AGCGT
4780336 TCTTATAACTACCAT
1 TCTTATAACTACCAT
4780351 CAAACTTTCC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 45 0.92
44 4 0.08
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (43 bp):
TCTTATAACTACCATTAGTGTGCCTTAATTGGACATATAGCGT
Found at i:4783109 original size:20 final size:20
Alignment explanation
Indices: 4783080--4783121 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4783070 CCGCTGTTGC
*
4783080 TTTAGCAAAAGTTAATGAGG
1 TTTAGCAAAAGTTAACGAGG
*
4783100 TTTAGTAAAAGTTAACGAGG
1 TTTAGCAAAAGTTAACGAGG
4783120 TT
1 TT
4783122 GAAGAAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (20 bp):
TTTAGCAAAAGTTAACGAGG
Found at i:4796985 original size:16 final size:16
Alignment explanation
Indices: 4796964--4797019 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
4796954 GTTTGGTTGC
*
4796964 CTGTAATAGAATAGCG
1 CTGTAATAGAATAGAG
*
4796980 CTGTAATTGAATAGAG
1 CTGTAATAGAATAGAG
*
4796996 GTGTAATAGAATAGAG
1 CTGTAATAGAATAGAG
4797012 CTGTAATA
1 CTGTAATA
4797020 AGTAATTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (16 bp):
CTGTAATAGAATAGAG
Found at i:4797089 original size:44 final size:46
Alignment explanation
Indices: 4797004--4797093 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
4796994 AGGTGTAATA
*
4797004 GAATAGAGCTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
***
4797050 GAATAGAACTGTAAT-AGT-ATTCTTGTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
4797094 ATGTTGTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 23 0.57
45 3 0.08
46 14 0.35
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.36
Consensus pattern (46 bp):
GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
Found at i:4797287 original size:17 final size:17
Alignment explanation
Indices: 4797265--4797297 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4797255 AATTATTATT
4797265 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
4797282 AAATATAATTTAATAA
1 AAATATAATTTAATAA
4797298 CATTCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:4803818 original size:13 final size:15
Alignment explanation
Indices: 4803800--4803838 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
4803790 GAAGATGGAT
4803800 AAATAAA-AAAA-AG
1 AAATAAATAAAATAG
4803813 AAATAAATAAAATAG
1 AAATAAATAAAATAG
4803828 AATATAAATAA
1 AA-ATAAATAA
4803839 GATAAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 4 0.17
15 4 0.17
16 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (15 bp):
AAATAAATAAAATAG
Found at i:4805659 original size:105 final size:105
Alignment explanation
Indices: 4805472--4805683 Score: 370
Period size: 105 Copynumber: 2.0 Consensus size: 105
4805462 TCTCCATTTT
* * *
4805472 TGTCTCACAATTTTGTTTCAAGTTGCTTTGCCTTCAACATACAAATAAAATATAGATGTAAGTGA
1 TGTCTCACAATTTTGTTTCAAATTGCTTCGCCTTCAACATACAAATAAAATATAGATGTAAGTAA
*
4805537 ATATATATAATGGAAATAAAATTTTAATAAAATAAAAAAG
66 ATATATATAATGAAAATAAAATTTTAATAAAATAAAAAAG
* *
4805577 TGTCTCACAATTTTGTTTCAAATTGCTTCGTCTTCAACCTACAAATAAAATATAGATGTAAGTAA
1 TGTCTCACAATTTTGTTTCAAATTGCTTCGCCTTCAACATACAAATAAAATATAGATGTAAGTAA
4805642 ATATATATAATGAAAATAAAATTTTAATAAAATAAAAAAG
66 ATATATATAATGAAAATAAAATTTTAATAAAATAAAAAAG
4805682 TG
1 TG
4805684 AAACCAATTA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (105 bp):
TGTCTCACAATTTTGTTTCAAATTGCTTCGCCTTCAACATACAAATAAAATATAGATGTAAGTAA
ATATATATAATGAAAATAAAATTTTAATAAAATAAAAAAG
Found at i:4807582 original size:153 final size:151
Alignment explanation
Indices: 4807046--4807564 Score: 781
Period size: 153 Copynumber: 3.4 Consensus size: 151
4807036 AAAGGAATGG
* * * * *
4807046 TGATGAAATTCTTACCACTAAGATGAAGACGT-ATCAAAGAGGATAGACCAGAAAGATCACAATG
1 TGATGAAATTGTTACCACTAAGATCAAGATGTCA-CAAAGAGGATAGACCAGAAATATCACTATG
* * *
4807110 AGTATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAAGTAAAGAACATGAAGCTTTGAGA
65 AGTATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAA-TTAAG-ATATCAAGCTTTGAGA
4807175 GTCGAGTAAGAGATGCAGGTATGC
128 GTCGAGTAAGAGATGCAGGTATGC
* * *
4807199 TGATGAAATTGTTACCACTAAGGTCAAGATGACGCAAAGAGGATAGACCAGAAATATCACTATGA
1 TGATGAAATTGTTACCACTAAGATCAAGATGTCACAAAGAGGATAGACCAGAAATATCACTATGA
*
4807264 GTATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAGATTTTCAAGCTTTGAGAG
66 GTATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAAT-TAAGA-TATCAAGCTTTGAGAG
*
4807329 TCGAGTAAGAGATGCATGTATGC
129 TCGAGTAAGAGATGCAGGTATGC
*
4807352 TGATGAAATTGTTACCACTAAGATCAAGATGCCACAAAGAGGATAGACCAGAAATATCACTATGA
1 TGATGAAATTGTTACCACTAAGATCAAGATGTCACAAAGAGGATAGACCAGAAATATCACTATGA
*
4807417 GTATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAATTCAAGATATCCAAGCTTCGAGAG
66 GTATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAATT-AAGATAT-CAAGCTTTGAGAG
4807482 TCGAGTAAGAGATGCAGGTATGC
129 TCGAGTAAGAGATGCAGGTATGC
* * * *
4807505 TGATGAAATTGTTACCACTAAGATCAAGTTTTTC-CAAACAAGATAGACCAGAAATATCAC
1 TGATGAAATTGTTACCACTAAGATCAAG-ATGTCACAAAGAGGATAGACCAGAAATATCAC
4807565 GTGGAATATC
Statistics
Matches: 336, Mismatches: 24, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
152 5 0.01
153 329 0.98
154 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (151 bp):
TGATGAAATTGTTACCACTAAGATCAAGATGTCACAAAGAGGATAGACCAGAAATATCACTATGA
GTATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAATTAAGATATCAAGCTTTGAGAGTC
GAGTAAGAGATGCAGGTATGC
Found at i:4810440 original size:35 final size:35
Alignment explanation
Indices: 4810394--4810463 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
4810384 CAACCAAGTC
4810394 GCTATGAGTAACTGGATATGTCTGACATAGTTTTG
1 GCTATGAGTAACTGGATATGTCTGACATAGTTTTG
*
4810429 GCTATGAGTAACTTGATATGTCTGACATAGTTTTG
1 GCTATGAGTAACTGGATATGTCTGACATAGTTTTG
4810464 CTGATATCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (35 bp):
GCTATGAGTAACTGGATATGTCTGACATAGTTTTG
Found at i:4813864 original size:93 final size:93
Alignment explanation
Indices: 4813750--4813920 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
4813740 GCCCATAAGT
*
4813750 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
4813815 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
4813843 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
4813908 CGAGTTCGGATGC
66 CGAGCTCGGATGC
4813921 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:4813917 original size:46 final size:46
Alignment explanation
Indices: 4813742--4813917 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
4813732 TGTAACCCGC
*
4813742 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
4813788 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* * *
4813838 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
4813881 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
4813918 TGCTCAACCA
Statistics
Matches: 113, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 65 0.58
47 28 0.25
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:4816483 original size:17 final size:17
Alignment explanation
Indices: 4816463--4816595 Score: 167
Period size: 17 Copynumber: 7.5 Consensus size: 17
4816453 AATGATATGT
4816463 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
* *
4816480 AATCTTAAATATGATTGC
1 AATCTTAGATATGA-TAC
4816498 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
*
4816515 AATCTTAGATATGATTGC
1 AATCTTAGATATGA-TAC
*
4816533 AATCTTAGATATGATAT
1 AATCTTAGATATGATAC
*
4816550 AATCTTAGATATGATTGC
1 AATCTTAGATATGA-TAC
*
4816568 AATATTAGATATGATATAC
1 AATCTTAGATATG--ATAC
4816587 AATCTTAGA
1 AATCTTAGA
4816596 AGATATGATT
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
17 44 0.44
18 44 0.44
19 10 0.10
20 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (17 bp):
AATCTTAGATATGATAC
Found at i:4816503 original size:35 final size:35
Alignment explanation
Indices: 4816454--4816595 Score: 221
Period size: 35 Copynumber: 4.0 Consensus size: 35
4816444 ATAATCTTCA
* *
4816454 ATGATATGTAATCTTAGATATGATACAATCTTAAAT
1 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
4816490 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
*
4816525 ATGATTGCAATCTTAGATATGATATAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
*
4816560 ATGATTGCAATATTAGATATGATATACAATCTTAGA
1 ATGATTGCAATCTTAGATATG--ATACAATCTTAGA
4816596 AGATATGATT
Statistics
Matches: 99, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
35 82 0.83
36 5 0.05
37 12 0.12
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (35 bp):
ATGATTGCAATCTTAGATATGATACAATCTTAGAT
Found at i:4817098 original size:17 final size:17
Alignment explanation
Indices: 4817078--4817138 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
4817068 CCAATATATT
4817078 TTATATTTTTTATATAA
1 TTATATTTTTTATATAA
*
4817095 TTAT-TATTCTTATA-AA
1 TTATAT-TTTTTATATAA
4817111 -TATATTTTTTTATTATATA
1 TTATA-TTTTTTA-TATA-A
4817130 TTATATTTT
1 TTATATTTT
4817139 AAATTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
15 3 0.09
16 8 0.23
17 14 0.40
18 1 0.03
19 5 0.14
20 4 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATATTTTTTATATAA
Found at i:4817128 original size:15 final size:15
Alignment explanation
Indices: 4817079--4817131 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
4817069 CAATATATTT
4817079 TATATTTTTTATATAA
1 TATATTTTTT-TATAA
*
4817095 T-TATTATTCTTATAAA
1 TATATT-TTTTTAT-AA
*
4817111 TATATTTTTTTATTA
1 TATATTTTTTTATAA
4817126 TATATT
1 TATATT
4817132 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 14 0.45
16 13 0.42
17 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATTTTTTTATAA
Found at i:4817139 original size:17 final size:17
Alignment explanation
Indices: 4817072--4817139 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 17
4817062 TCTAAACCAA
*
4817072 TATATTTTATATTTT-T
1 TATATATTATATTTTAT
4817088 TATATAATTATTATTCTTAT
1 TATAT-ATTA-TATT-TTAT
*
4817108 AAATATATT-T-TTTTAT
1 -TATATATTATATTTTAT
4817124 TATATATTATATTTTA
1 TATATATTATATTTTA
4817140 AATTTATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
15 7 0.17
16 10 0.24
17 10 0.24
18 5 0.12
19 2 0.05
20 4 0.10
21 4 0.10
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATATTATATTTTAT
Found at i:4817555 original size:23 final size:23
Alignment explanation
Indices: 4817505--4817555 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 23
4817495 TTACACATTA
*
4817505 ATATTTACCATGTTTTTTTTATAT
1 ATATTTA-CATGTTTTATTTATAT
4817529 -TATTTA-ATGTTTTATTTATGAT
1 ATATTTACATGTTTTATTTAT-AT
4817551 ATATT
1 ATATT
4817556 GTATATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 12 0.50
22 2 0.08
23 10 0.42
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (23 bp):
ATATTTACATGTTTTATTTATAT
Found at i:4818526 original size:80 final size:79
Alignment explanation
Indices: 4818425--4818585 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 79
4818415 ACATGTTTGC
* *
4818425 ACTTTGTTGCTCGCACCAGGCTGAGCTTGCACCTTTGACAGGCTCACATTTTTTGCTTACTGTCC
1 ACTTTGCTGCTCGCACCAGGCTAAGCTTGCACCTTTGACAGGCTCACA-TTTTTGCTTACTGTCC
4818490 CTTAAGGTGTCTTCA
65 CTTAAGGTGTCTTCA
* * * *
4818505 ACTTTGCTGTTCGCACTAGGCTAAGCTTGCACCTTTGACAGGCTCGCATTTTTGCTTACTGTCTC
1 ACTTTGCTGCTCGCACCAGGCTAAGCTTGCACCTTTGACAGGCTCACATTTTTGCTTACTGTCCC
4818570 TTAAGGTGTCTTCA
66 TTAAGGTGTCTTCA
4818584 AC
1 AC
4818586 AGGCTCGCAA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
79 32 0.43
80 43 0.57
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (79 bp):
ACTTTGCTGCTCGCACCAGGCTAAGCTTGCACCTTTGACAGGCTCACATTTTTGCTTACTGTCCC
TTAAGGTGTCTTCA
Found at i:4818657 original size:25 final size:25
Alignment explanation
Indices: 4818629--4818689 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
4818619 ATGAACTCAT
*
4818629 AGCTTGCACTTCTCGCTAAGCTTGC
1 AGCTTGCACATCTCGCTAAGCTTGC
*
4818654 AGCTTTG-ACATCTTGCTAAGCTTGC
1 AGC-TTGCACATCTCGCTAAGCTTGC
*
4818679 AACTTGCACAT
1 AGCTTGCACAT
4818690 TGGAAAACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 3 0.10
25 25 0.81
26 3 0.10
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (25 bp):
AGCTTGCACATCTCGCTAAGCTTGC
Found at i:4819623 original size:18 final size:18
Alignment explanation
Indices: 4819600--4819642 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4819590 GTTCAACGTG
4819600 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
4819618 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
4819636 TAATTAA
1 TAATTAA
4819643 AAATCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:4826717 original size:186 final size:186
Alignment explanation
Indices: 4826403--4826775 Score: 728
Period size: 186 Copynumber: 2.0 Consensus size: 186
4826393 CACGAGGCTT
4826403 GGTGCACAAGCTTCCTGTTTTTGCTTGCTGCTTTGTTTCAAGTTCCAACAACGTATTAACTCAAT
1 GGTGCACAAGCTTCCTGTTTTTGCTTGCTGCTTTGTTTCAAGTTCCAACAACGTATTAACTCAAT
*
4826468 TCACTCAATTGACATATCTACGTATATCTCGTTCTCTAATTATTTTCTACTTTCCAAATATTATT
66 TCACTCAATTAACATATCTACGTATATCTCGTTCTCTAATTATTTTCTACTTTCCAAATATTATT
4826533 AAGCTCAAGCTTGACTCAAAATTTAAAGCTTGATATTCAGTTTAAACTAAGCTCAA
131 AAGCTCAAGCTTGACTCAAAATTTAAAGCTTGATATTCAGTTTAAACTAAGCTCAA
4826589 GGTGCACAAGCTTCCTGTTTTTGCTTGCTGCTTTGTTTCAAGTTCCAACAACGTATTAACTCAAT
1 GGTGCACAAGCTTCCTGTTTTTGCTTGCTGCTTTGTTTCAAGTTCCAACAACGTATTAACTCAAT
4826654 TCACTCAATTAACATATCTACGTATATCTCGTTCTCTAATTATTTTCTACTTTCCAAATATTATT
66 TCACTCAATTAACATATCTACGTATATCTCGTTCTCTAATTATTTTCTACTTTCCAAATATTATT
*
4826719 AAGCTTAAGCTTGACTCAAAATTTAAAGCTTGATATTCAGTTTAAACTAAGCTCAA
131 AAGCTCAAGCTTGACTCAAAATTTAAAGCTTGATATTCAGTTTAAACTAAGCTCAA
4826775 G
1 G
4826776 ATATAATCCA
Statistics
Matches: 185, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 185 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (186 bp):
GGTGCACAAGCTTCCTGTTTTTGCTTGCTGCTTTGTTTCAAGTTCCAACAACGTATTAACTCAAT
TCACTCAATTAACATATCTACGTATATCTCGTTCTCTAATTATTTTCTACTTTCCAAATATTATT
AAGCTCAAGCTTGACTCAAAATTTAAAGCTTGATATTCAGTTTAAACTAAGCTCAA
Found at i:4833474 original size:19 final size:18
Alignment explanation
Indices: 4833436--4833493 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
4833426 TGGTTCTATA
* *
4833436 AATTATATGTATAAATAAT
1 AATTATTTGTA-AAAAAAT
*
4833455 AATTTATTTTTAAAAAAAT
1 AA-TTATTTGTAAAAAAAT
*
4833474 AATTATTTGTAAAAACAT
1 AATTATTTGTAAAAAAAT
4833492 AA
1 AA
4833494 AAATACATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 16 0.48
19 10 0.30
20 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (18 bp):
AATTATTTGTAAAAAAAT
Found at i:4835477 original size:44 final size:44
Alignment explanation
Indices: 4835429--4835702 Score: 485
Period size: 44 Copynumber: 6.2 Consensus size: 44
4835419 CTCAAGAACA
4835429 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
*
4835473 CCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
*
4835517 CCCAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
*
4835561 CCAAATCTGCTATCTTCGATTTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
4835605 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAAAGACA
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
4835649 CTAAATCTGCTATCTTTGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
4835693 CCAAATCTGC
1 CCAAATCTGC
4835703 AGGATTTACC
Statistics
Matches: 217, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 217 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (44 bp):
CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
Found at i:4847118 original size:46 final size:46
Alignment explanation
Indices: 4847068--4847243 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
4847058 TGGTTGAGCA
4847068 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4847114 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
4847159 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4847207 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4847244 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:4847224 original size:93 final size:93
Alignment explanation
Indices: 4847065--4847236 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
4847055 GGATGGTTGA
* *
4847065 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
4847130 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
4847158 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
4847223 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
4847237 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:4853362 original size:46 final size:46
Alignment explanation
Indices: 4853312--4853487 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
4853302 TGGTTGAGCA
4853312 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4853358 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
4853403 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4853451 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4853488 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:4853468 original size:93 final size:93
Alignment explanation
Indices: 4853309--4853480 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
4853299 GGATGGTTGA
* *
4853309 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
4853374 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
4853402 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
4853467 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
4853481 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:4857191 original size:3 final size:3
Alignment explanation
Indices: 4857183--4857239 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
4857173 ATATATTACA
4857183 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4857231 AAT AAT AAT
1 AAT AAT AAT
4857240 GTATAACACG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4857334 original size:19 final size:19
Alignment explanation
Indices: 4857281--4857334 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
4857271 TGGTTCTATA
* * *
4857281 AATTATATGTATAAATAAT
1 AATTATTTGTAAAAAAAAT
* *
4857300 AATTTATTTTTTAAAAAAAT
1 AA-TTATTTGTAAAAAAAAT
4857320 AATTATTTGTAAAAA
1 AATTATTTGTAAAAA
4857335 CATAAAAATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
AATTATTTGTAAAAAAAAT
Found at i:4857679 original size:2 final size:2
Alignment explanation
Indices: 4857672--4857727 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
4857662 ACATAAGGTT
4857672 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4857714 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
4857728 CGCGTGGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4862191 original size:141 final size:141
Alignment explanation
Indices: 4861934--4862192 Score: 382
Period size: 141 Copynumber: 1.8 Consensus size: 141
4861924 TTAAGTTTCA
* *
4861934 TGCAATTTGACAATCCAAGAAACTCAAGCTTTGAGAGTCGAGTAAGAGATGCAGGTAGGCTGATG
1 TGCAATTTGACAATCCAAGAAACCCAAGCTTCGAGAGTCGAGTAAGAGATGCAGGTAGGCTGATG
* *
4861999 AAATTGTTACGCTTAAGATCAAGGAATTCCAAAGAGGATAGACCATGAATATCTGCTTCACCAAG
66 AAATTGTTACGCCTAAGATCAAGGAATTCCAAAGAGGATAAACCATGAATATCTGCTTCACCAAG
4862064 AGTGCAAATGT
131 AGTGCAAATGT
* * *
4862075 TGCAATTTGACAATTCAAGATACCCAAGCTTCGAGAGTCGAGTAAGAGATGCAGGTATGCTGATG
1 TGCAATTTGACAATCCAAGAAACCCAAGCTTCGAGAGTCGAGTAAGAGATGCAGGTAGGCTGATG
*
4862140 AAATTGTTAC-CACTAAGATCAA-G-ATGTATCAAAGAGGATAAACCA-GAAATATC
66 AAATTGTTACGC-CTAAGATCAAGGAAT-T-CCAAAGAGGATAAACCATG-AATATC
4862193 ACGTGGAATA
Statistics
Matches: 106, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
139 2 0.02
140 4 0.04
141 100 0.94
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (141 bp):
TGCAATTTGACAATCCAAGAAACCCAAGCTTCGAGAGTCGAGTAAGAGATGCAGGTAGGCTGATG
AAATTGTTACGCCTAAGATCAAGGAATTCCAAAGAGGATAAACCATGAATATCTGCTTCACCAAG
AGTGCAAATGT
Found at i:4865293 original size:16 final size:16
Alignment explanation
Indices: 4865274--4865312 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4865264 CACATAGGAT
*
4865274 TATAAAATATTATAT-A
1 TATAAAAT-TCATATAA
4865290 TATAAAATTCATATAA
1 TATAAAATTCATATAA
4865306 TATAAAA
1 TATAAAA
4865313 ACTAACAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAAAATTCATATAA
Found at i:4869032 original size:24 final size:23
Alignment explanation
Indices: 4868986--4869034 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
4868976 AATAACAAAG
* **
4868986 ATATTTATACTAATTAATGCTAA
1 ATATTTATACTAATAAAAACTAA
4869009 ATATATTATACTAATAAAAACTAA
1 ATAT-TTATACTAATAAAAACTAA
4869033 AT
1 AT
4869035 CTTCTACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATTTATACTAATAAAAACTAA
Found at i:4871841 original size:30 final size:30
Alignment explanation
Indices: 4871805--4871863 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
4871795 GCTCGCAGTG
*
4871805 CTTCTTCTTTTACGCACTCCCAATGCCTTA
1 CTTCTTCTTCTACGCACTCCCAATGCCTTA
** *
4871835 CTTCTTCTTCTACGTGCTTCCAATGCCTT
1 CTTCTTCTTCTACGCACTCCCAATGCCTT
4871864 GATGCTCTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.14, C:0.36, G:0.08, T:0.42
Consensus pattern (30 bp):
CTTCTTCTTCTACGCACTCCCAATGCCTTA
Found at i:4872710 original size:25 final size:24
Alignment explanation
Indices: 4872682--4872733 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
4872672 ATATGAAAAG
*
4872682 AAATAACAAAGATATTTATGCTAAT
1 AAATAACAAAGATA-TTATACTAAT
** *
4872707 AAATATTAAATATATTATACTAAT
1 AAATAACAAAGATATTATACTAAT
4872731 AAA
1 AAA
4872734 AACTAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAACAAAGATATTATACTAAT
Found at i:4872729 original size:24 final size:24
Alignment explanation
Indices: 4872693--4872744 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4872683 AATAACAAAG
* * *
4872693 ATAT-TTATGCTAATAAATATTAA
1 ATATATTATACTAATAAAAACTAA
4872716 ATATATTATACTAATAAAAACTAA
1 ATATATTATACTAATAAAAACTAA
4872740 ATATA
1 ATATA
4872745 CTAGAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATATTATACTAATAAAAACTAA
Found at i:4880875 original size:19 final size:21
Alignment explanation
Indices: 4880841--4880888 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
4880831 TGGCGCTTGG
4880841 GTACGGA--CTGTACTGG-C-
1 GTACGGAGGCTGTACTGGACA
*
4880858 GTACGGAGGCTGTGCTGGACA
1 GTACGGAGGCTGTACTGGACA
4880879 GTACGGAGGC
1 GTACGGAGGC
4880889 CAGGGTTGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 7 0.27
19 8 0.31
20 1 0.04
21 10 0.38
ACGTcount: A:0.19, C:0.21, G:0.42, T:0.19
Consensus pattern (21 bp):
GTACGGAGGCTGTACTGGACA
Found at i:4884976 original size:2 final size:2
Alignment explanation
Indices: 4884969--4885010 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4884959 ACTATTAACC
4884969 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
4885011 TGTAAGGCCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4886659 original size:2 final size:2
Alignment explanation
Indices: 4886647--4886712 Score: 69
Period size: 2 Copynumber: 32.5 Consensus size: 2
4886637 CAATTATTAT
* * * * * *
4886647 TA TA TA CA TA TA TG TT TA TA GA TA TC TA TA TT TGA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
4886690 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
4886713 TATTAAATCT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
2 51 0.98
3 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4888022 original size:132 final size:131
Alignment explanation
Indices: 4887565--4888010 Score: 406
Period size: 132 Copynumber: 3.4 Consensus size: 131
4887555 ACGGAATAGT
* * * * * *
4887565 TTGCAGTTTCGCGTTTGCTCAAAACAATTGAATATCACTTC-AAATTTCACTCACTCTTTTTAAA
1 TTGCAATTTCTCGTTTGTTCAAAACAATCGAATATCTCTTCAAAATTTCACTCA-TATTTTTAAA
* * * * * *
4887629 ATCCC-TT-GAATGAAGGCAATATGCGATATTTGGCAACTT-GTGGAATCGTTCCCTAACGTGTT
65 AACCCTTTAAAATGAAGGCAATATTCGATATTTGGCAA-TTCGGGGAATAGTACCCTAACGTGTT
4887691 GGG
129 GGG
* * * * * *
4887694 TTATG-AATTTCTCGCTTGCAT-AAAATAATCAAATATCCCCTCAAAATTTCACTCATATATTTT
1 -T-TGCAATTTCTCGTTTG-TTCAAAACAATCGAATATCTCTTCAAAATTTCACTCATAT-TTTT
* * * * * * *
4887757 AAAAATCCTTTAAAAATGAAGGTAATACTCGGTATTTGACAATTC-GGGAATCA-TGCCCTACCG
62 AAAAACCCTTT-AAAATGAAGGCAATATTCGATATTTGGCAATTCGGGGAAT-AGTACCCTAACG
*
4887820 TGCTGGG
125 TGTTGGG
** * * **
4887827 TTGTGATTTCTCGTTTGTTCAAAACAATCGAAGAT-TCCTTCGAAATTTCACTCACGTTTTCTAA
1 TTGCAATTTCTCGTTTGTTCAAAACAATCGAATATCT-CTTCAAAATTTCACTCATATTTT-TAA
* * *
4887891 AAACCCTTTAAAATGAAGGCGATATTCGATGTTTGGCAATTCGGGGAATAGTACCCTATCGTGTT
64 AAACCCTTTAAAATGAAGGCAATATTCGATATTTGGCAATTCGGGGAATAGTACCCTAACGTGTT
4887956 GGG
129 GGG
* *
4887959 TTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCTCTTCAAAATTTCACT
1 TTGCAATTTCTCGTTTGTTCAAAACAATCGAATATCTCTTCAAAATTTCACT
4888011 TGTATTTTCT
Statistics
Matches: 250, Mismatches: 50, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
130 29 0.12
131 59 0.24
132 117 0.47
133 22 0.09
134 23 0.09
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (131 bp):
TTGCAATTTCTCGTTTGTTCAAAACAATCGAATATCTCTTCAAAATTTCACTCATATTTTTAAAA
ACCCTTTAAAATGAAGGCAATATTCGATATTTGGCAATTCGGGGAATAGTACCCTAACGTGTTGG
G
Found at i:4900011 original size:44 final size:44
Alignment explanation
Indices: 4899521--4899997 Score: 564
Period size: 44 Copynumber: 10.8 Consensus size: 44
4899511 GGCGAATCCT
* * *
4899521 GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* **
4899565 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGTAGATCGAATCCTA
1 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAA-GATA
* * * * *
4899610 -CATATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAAATA
1 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* *
4899653 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGTAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
4899697 GCAGATTTGACGTCTCTGTATTGGCAAAGAGTAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * * ** *
4899741 GCAAATTTAGCGTCTTTGTATTGGTGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
4899785 GCAGATTTGGCATCTCTGTGTTGTCAGAGAGCAGATCGAAGAT-
1 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
4899828 GACAGATTTGGCATCTCTGTATTGGCTGAGAGCAGATCGAATATA
1 G-CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * * *
4899873 GCAGATTTGGTGTCTCTGTATTGGCGGAGAACAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
4899917 GCAGATTTAGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGAT-
1 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
4899960 GACAGATTTGACATCTCTGTATTGACAGAGAGCAGATC
1 G-CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATC
4899998 AAAAATAATA
Statistics
Matches: 369, Mismatches: 59, Indels: 10
0.84 0.13 0.02
Matches are distributed among these distances:
43 4 0.01
44 362 0.98
45 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.27
Consensus pattern (44 bp):
GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATA
Found at i:4903143 original size:132 final size:130
Alignment explanation
Indices: 4902676--4903194 Score: 426
Period size: 132 Copynumber: 4.0 Consensus size: 130
4902666 TAAGTATCCA
** * * * * * * * *
4902676 TTTAAAAATTCTTTAAAATGAAGACGAGATCCGATATTTGGCAATCCACGGAATAGTGCCCTAAC
1 TTTAAAAACCCTTTAAAACGAAGGCGATATTCGATGTTTGGCAATTC-GGGAATAGTACCCTAAC
* *
4902741 GTGTTGGGTTGCAATTTCGCGTTTGCTCAAAACAATCGAATATCACTTC-AAATTTCACTCACTC
65 GTGTTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATATCACTTCAAAATTTCACTCACTC
4902805 TT
130 -T
* * * * * * *
4902807 TTTAAAATCCC-TT-GAATGAAGGCGATATGT-GATATTTGGCAACTCGTGGAATCGTGCCCTAA
1 TTTAAAAACCCTTTAAAACGAAGGCGATAT-TCGATGTTTGGCAATTCG-GGAATAGTACCCTAA
* * * * * *
4902869 CGTGTTGGGTTATG-AATTTCTCGCTTGCAT-AAAATAATCAAATATCCCCTCAAAATTTCACTC
64 CGTGTTGGG-T-TGCAATTTCTCGTTTG-TTCAAAACAATCGAATATCACTTCAAAATTTCACTC
*
4902932 ATATCT
126 A-CTCT
* ** * * * *
4902938 TTTAAAAATCCTTTAAAAACGAAGGTAATACTCGGTGTTTGACAATTCGGGAGTCA-TGA-CCTA
1 TTTAAAAACCCTTT-AAAACGAAGGCGATATTCGATGTTTGGCAATTCGGGAAT-AGT-ACCCTA
* * ** * **
4903001 CCGTGCTGGGTTGTGATTTCTCGTTTGTTCAAAACAATCGAAGATTGCTTCAAAATTTCACTCAC
63 ACGTGTTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATATCACTTCAAAATTTCACTCAC
4903066 GT-T
128 -TCT
* *
4903069 TTCTAAAAACCCTTTAAAACGAAGGCGATATTCGATGTTTGGCAATTTGAGGAATAGTACCCTAT
1 TT-TAAAAACCCTTTAAAACGAAGGCGATATTCGATGTTTGGCAATTCG-GGAATAGTACCCTAA
* * ** *
4903134 CGTGTTGGGTTGCAATTTCTCGTTTGTTCAAAATAATTGAATATTTCTTCGAAATTTCACT
64 CGTGTTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATATCACTTCAAAATTTCACT
4903195 TGTATTTTCT
Statistics
Matches: 306, Mismatches: 62, Indels: 39
0.75 0.15 0.10
Matches are distributed among these distances:
129 48 0.16
130 31 0.10
131 69 0.23
132 118 0.39
133 18 0.06
134 22 0.07
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (130 bp):
TTTAAAAACCCTTTAAAACGAAGGCGATATTCGATGTTTGGCAATTCGGGAATAGTACCCTAACG
TGTTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATATCACTTCAAAATTTCACTCACTCT
Found at i:4903800 original size:20 final size:20
Alignment explanation
Indices: 4903751--4903792 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4903741 TAAGTAAAAG
4903751 ATATCTAAAATGATTATTTT
1 ATATCTAAAATGATTATTTT
4903771 ATATCTAAAATGATTATTTT
1 ATATCTAAAATGATTATTTT
4903791 AT
1 AT
4903793 GTGTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
ATATCTAAAATGATTATTTT
Found at i:4905025 original size:19 final size:17
Alignment explanation
Indices: 4905001--4905081 Score: 56
Period size: 19 Copynumber: 4.4 Consensus size: 17
4904991 ATGTCATAAG
4905001 TAAAAAATTACTTAAAAAC
1 TAAAAAATT--TTAAAAAC
* *
4905020 TAAAAAACTCATTAAAATC
1 TAAAAAA-T-TTTAAAAAC
4905039 TAAAAAATATATT-AAAAC
1 TAAAAAAT-T-TTAAAAAC
* *
4905057 TTAGAAAATTTTAAAAAT
1 -TAAAAAATTTTAAAAAC
4905075 TAAAAAA
1 TAAAAAA
4905082 AAAATCATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
17 8 0.16
18 10 0.20
19 30 0.61
20 1 0.02
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.28
Consensus pattern (17 bp):
TAAAAAATTTTAAAAAC
Found at i:4908965 original size:26 final size:26
Alignment explanation
Indices: 4908936--4909071 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
4908926 TGATACAAAT
* *
4908936 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
4908962 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
4908988 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
4909014 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
4909040 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
4909066 TGATAA
1 TGATAA
4909072 GAATATCATA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:4911103 original size:136 final size:137
Alignment explanation
Indices: 4910855--4911140 Score: 511
Period size: 136 Copynumber: 2.1 Consensus size: 137
4910845 GAGTAGTCTC
4910855 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
4910920 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTAAAAAGGGCTTTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTAAAAAGGGCTCTGGCCCAGTACC
4910985 ACTGTTA
131 ACTGTTA
*
4910992 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
4911056 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTAAAAAGGGCTCTGGCCCAGTACC
4911121 ACTGTTA
131 ACTGTTA
**
4911128 CCTGAATGGGCTT
1 CCCAAATGGGCTT
4911141 AGGCCCAATG
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
136 123 0.86
137 20 0.14
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTAAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:4914088 original size:17 final size:16
Alignment explanation
Indices: 4914000--4914114 Score: 64
Period size: 17 Copynumber: 7.2 Consensus size: 16
4913990 CGTTAATTTT
4914000 TATATATACTAAT-AAA
1 TATATATA-TAATAAAA
* *
4914016 TA-ATAGATAATGAAA
1 TATATATATAATAAAA
*
4914031 TAATATGTATAATAAAA
1 T-ATATATATAATAAAA
* * *
4914048 GGA-AGATATTATAAGGAA
1 -TATATATATAATAA--AA
4914066 TA-ATATATAATAAAA
1 TATATATATAATAAAA
*
4914081 TATGATATGTAAT--AA
1 TAT-ATATATAATAAAA
4914096 -ATATATATAATAAAA
1 TATATATATAATAAAA
4914111 TATA
1 TATA
4914115 ATGAAACATA
Statistics
Matches: 75, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
13 8 0.11
14 6 0.08
15 16 0.21
16 14 0.19
17 29 0.39
18 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.09, T:0.33
Consensus pattern (16 bp):
TATATATATAATAAAA
Found at i:4914128 original size:30 final size:30
Alignment explanation
Indices: 4914001--4914120 Score: 86
Period size: 30 Copynumber: 3.9 Consensus size: 30
4913991 GTTAATTTTT
4914001 ATATATACTAAT-AAATAATAGATAATGAAAT-A
1 ATATATA-TAATAAAAT-AT-GAT-ATGAAATAA
* * * * **
4914033 ATATGTATAATAAAAGGAAGATATTATAAGGA
1 ATATATATAATAAAA-TATGATATGA-AATAA
*
4914065 ATAATATATAATAAAATATGATATGTAATAA
1 AT-ATATATAATAAAATATGATATGAAATAA
4914096 ATATATATAATAAAATAT-A-ATGAAA
1 ATATATATAATAAAATATGATATGAAA
4914121 CATAAATACT
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
28 5 0.07
29 1 0.01
30 19 0.27
31 14 0.20
32 19 0.27
33 12 0.17
ACGTcount: A:0.58, C:0.01, G:0.09, T:0.32
Consensus pattern (30 bp):
ATATATATAATAAAATATGATATGAAATAA
Found at i:4914210 original size:24 final size:23
Alignment explanation
Indices: 4914167--4914228 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
4914157 TATTATTCAA
*
4914167 TAATAATAAAAAATTTATACAAT
1 TAATAATAAAAAATTAATACAAT
4914190 TAATGAATAATAAAA-TAATACATAAT
1 TAAT-AATAA-AAAATTAATAC--AAT
*
4914216 TTATAATAAAAAA
1 TAATAATAAAAAA
4914229 ATTTAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 4 0.12
24 14 0.42
25 9 0.27
26 6 0.18
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (23 bp):
TAATAATAAAAAATTAATACAAT
Found at i:4914331 original size:12 final size:12
Alignment explanation
Indices: 4914266--4914331 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
4914256 ATAGTAAAAA
4914266 AATATAATGTAT
1 AATATAATGTAT
*
4914278 AATGA-AATTTAT
1 AAT-ATAATGTAT
*
4914290 AAATAAAATGTAT
1 -AATATAATGTAT
**
4914303 AATAATAA-AAAT
1 AAT-ATAATGTAT
4914315 AATATAATGTAT
1 AATATAATGTAT
4914327 AATAT
1 AATAT
4914332 GTAAATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 4 0.10
12 25 0.60
13 13 0.31
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (12 bp):
AATATAATGTAT
Found at i:4914336 original size:25 final size:25
Alignment explanation
Indices: 4914254--4914336 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
4914244 AAGGAATAAT
4914254 ATATAGTAAAAA-AATATAATGTAT-
1 ATAT-GTAAAAATAATATAATGTATA
* *
4914278 A-ATG-AAATTTATAAATAAAATGTATA
1 ATATGTAAA--AAT-AATATAATGTATA
*
4914304 ATA-ATAAAAATAATATAATGTATA
1 ATATGTAAAAATAATATAATGTATA
4914328 ATATGTAAA
1 ATATGTAAA
4914337 TAAAAACTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
21 3 0.07
22 1 0.02
23 3 0.07
24 16 0.36
25 17 0.38
26 1 0.02
27 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (25 bp):
ATATGTAAAAATAATATAATGTATA
Found at i:4914379 original size:26 final size:25
Alignment explanation
Indices: 4914350--4914420 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
4914340 AAACTATTTT
4914350 ATATAACTAATATTTAAAAATAAATA
1 ATATAA-TAATATTTAAAAATAAATA
*
4914376 ATAT-ATAAAGTATTTAATAAATAAATT
1 ATATAAT-AA-TATTTAA-AAATAAATA
**
4914403 ATGCAATAATATTTAAAA
1 ATATAATAATATTTAAAA
4914421 GGATTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 1 0.03
25 5 0.13
26 18 0.47
27 12 0.32
28 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (25 bp):
ATATAATAATATTTAAAAATAAATA
Found at i:4926146 original size:83 final size:83
Alignment explanation
Indices: 4926047--4926215 Score: 268
Period size: 83 Copynumber: 2.0 Consensus size: 83
4926037 ATAACCCTCT
* * * *
4926047 TCTGGTCTGGTCTGTCAACCAATTTCCAAGTGTCATTCTTATGTATCATCTCCATTTCTGC-TTC
1 TCTGGTCTGGCCTGTCAACCAATTTCCAAGTGACACTCTTATGTATCATCTCCATTTCTACTTTC
4926111 TATGGCCCTATTCCAACAA
66 -ATGGCCCTATTCCAACAA
*
4926130 TCTGGTCTGGCCTGTCAACCAATTTCCAAGTGACACTCTTGTGTATCATCTCCATTTCTACTTTC
1 TCTGGTCTGGCCTGTCAACCAATTTCCAAGTGACACTCTTATGTATCATCTCCATTTCTACTTTC
*
4926195 ATGGCCCTTTTCCAACAA
66 ATGGCCCTATTCCAACAA
4926213 TCT
1 TCT
4926216 TTTCTAGCAG
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
83 76 0.96
84 3 0.04
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.38
Consensus pattern (83 bp):
TCTGGTCTGGCCTGTCAACCAATTTCCAAGTGACACTCTTATGTATCATCTCCATTTCTACTTTC
ATGGCCCTATTCCAACAA
Found at i:4929593 original size:43 final size:43
Alignment explanation
Indices: 4929541--4929724 Score: 217
Period size: 43 Copynumber: 4.3 Consensus size: 43
4929531 TTTTTGAAAA
* *
4929541 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCAC
* * * * ** *
4929584 AAACGCCGCTAAAAACCAGGACTTTTAGCGGCGC-TTTTAAAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCAC
*
4929626 AAACTCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCAC
* * * * * *
4929669 AAACGCCGCCAAATATCATAACCTTTAGCAGCACTTTTCTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCAC
4929712 AAACGCCGCTAAA
1 AAACGCCGCTAAA
4929725 AATAATGATA
Statistics
Matches: 117, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
42 33 0.28
43 84 0.72
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCAC
Found at i:4929653 original size:42 final size:42
Alignment explanation
Indices: 4929532--4929663 Score: 165
Period size: 42 Copynumber: 3.1 Consensus size: 42
4929522 AGTGGCGTTT
4929532 TTTTGAAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCGC
1 TTTT-AAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCGC
**** * * *
4929575 TTTTTTCGCAAACGCCGCTAAAAACCAGGACTTTTAGCGGCGC
1 -TTTTAAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCGC
* *
4929618 TTTTAAAAAAACTCCGCTAAAGACCATGACCTTTAGCGGCAC
1 TTTTAAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCGC
4929660 TTTT
1 TTTT
4929664 TTCACAAACG
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 37 0.51
43 31 0.43
44 4 0.06
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (42 bp):
TTTTAAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCGC
Found at i:4929696 original size:85 final size:86
Alignment explanation
Indices: 4929532--4929724 Score: 244
Period size: 85 Copynumber: 2.3 Consensus size: 86
4929522 AGTGGCGTTT
* * *
4929532 TTTTGAAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGCAAACGCCGCTAAA
1 TTTTGAAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCACAAACGCCGCCAAA
* * * *
4929597 AACCAGGACTTTTAGCGGCGC
66 AACCAGAACCTTTAGCAGCAC
*
4929618 TTTT-AAAAAAACTCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCACAAACGCCGCCAAA
1 TTTTGAAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCACAAACGCCGCCAAA
* * *
4929682 TATCATAACCTTTAGCAGCAC
66 AACCAGAACCTTTAGCAGCAC
*** *
4929703 TTTTCTCACAAACGCCGCTAAA
1 TTTTGAAAAAAACGCCGCTAAA
4929725 AATAATGATA
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
85 74 0.81
86 17 0.19
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (86 bp):
TTTTGAAAAAAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTCACAAACGCCGCCAAA
AACCAGAACCTTTAGCAGCAC
Found at i:4933904 original size:19 final size:17
Alignment explanation
Indices: 4933872--4933911 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
4933862 ATAAGATTAA
4933872 TTTTAAATTTTTTTTAT
1 TTTTAAATTTTTTTTAT
4933889 TTTTAACATATTTTTTTAT
1 TTTTAA-AT-TTTTTTTAT
4933908 TTTT
1 TTTT
4933912 TTCTTTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
19 13 0.62
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTAAATTTTTTTTAT
Found at i:4933995 original size:7 final size:7
Alignment explanation
Indices: 4933970--4934068 Score: 83
Period size: 7 Copynumber: 14.0 Consensus size: 7
4933960 ATATGGACTA
*
4933970 AAATATT
1 AAATTTT
*
4933977 AAATATT
1 AAATTTT
4933984 AAATTTT
1 AAATTTT
4933991 AAATTTTT
1 AAA-TTTT
*
4933999 AAGTTTT
1 AAATTTT
**
4934006 TTATTTT
1 AAATTTT
**
4934013 TTATTTT
1 AAATTTT
*
4934020 -ATTTTT
1 AAATTTT
* *
4934026 TATTTTT
1 AAATTTT
4934033 AAATTTT
1 AAATTTT
4934040 AAATTTT
1 AAATTTT
4934047 AAATTTT
1 AAATTTT
4934054 AAATTTTT
1 AAA-TTTT
4934062 AAATTTT
1 AAATTTT
4934069 GAGTTTATTT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
6 4 0.05
7 63 0.79
8 13 0.16
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (7 bp):
AAATTTT
Found at i:4934021 original size:12 final size:12
Alignment explanation
Indices: 4934004--4934031 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4933994 TTTTTAAGTT
4934004 TTTTATTTTTTA
1 TTTTATTTTTTA
4934016 TTTTATTTTTTA
1 TTTTATTTTTTA
4934028 TTTT
1 TTTT
4934032 TAAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:4934042 original size:56 final size:55
Alignment explanation
Indices: 4933975--4934085 Score: 159
Period size: 55 Copynumber: 2.0 Consensus size: 55
4933965 GACTAAAATA
* * * * *
4933975 TTAAATATTAAATTTTAAATTTTTAAGTTTTTTATTTTTTATTTTATTTTTTATTT
1 TTAAATATTAAATTTTAAA-TTTTAAATTTTTAAATTTTGAGTTTATTTTTTATTT
*
4934031 TTAAATTTTAAATTTTAAATTTTAAATTTTTAAATTTTGAGTTTATTTTTTATTT
1 TTAAATATTAAATTTTAAATTTTAAATTTTTAAATTTTGAGTTTATTTTTTATTT
4934086 CGGTTTAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
55 31 0.63
56 18 0.37
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (55 bp):
TTAAATATTAAATTTTAAATTTTAAATTTTTAAATTTTGAGTTTATTTTTTATTT
Found at i:4934081 original size:49 final size:49
Alignment explanation
Indices: 4933982--4934082 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 49
4933972 ATATTAAATA
* ** * * *
4933982 TTAAATTTTAAATTTTTAAGTTTTTTATTTTTTATTTTATTTTTTATTT
1 TTAAATTTTAAATTTTTAAATTTTAAATTTTTAATTTTAGTTTATATTT
4934031 TTAAATTTTAAA-TTTTAAATTTTAAATTTTTAAATTTTGAGTTTAT-TTT
1 TTAAATTTTAAATTTTTAAATTTTAAATTTTT-AATTTT-AGTTTATATTT
4934080 TTA
1 TTA
4934083 TTTCGGTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
48 16 0.36
49 23 0.52
50 5 0.11
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (49 bp):
TTAAATTTTAAATTTTTAAATTTTAAATTTTTAATTTTAGTTTATATTT
Found at i:4934672 original size:7 final size:7
Alignment explanation
Indices: 4934660--4934723 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
4934650 CCCATGGCCA
4934660 TTAAACC
1 TTAAACC
4934667 TTAAACC
1 TTAAACC
*
4934674 ATAAAACC
1 -TTAAACC
*
4934682 CTAAACC
1 TTAAACC
* *
4934689 ATAAGCC
1 TTAAACC
4934696 TTAAACC
1 TTAAACC
**
4934703 TTAAATA
1 TTAAACC
4934710 TTAAACC
1 TTAAACC
*
4934717 GTAAACC
1 TTAAACC
4934724 AAAAAATAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
7 38 0.86
8 6 0.14
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (7 bp):
TTAAACC
Found at i:4934680 original size:15 final size:15
Alignment explanation
Indices: 4934657--4934707 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
4934647 ATACCCATGG
*
4934657 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
*
4934672 CCATAAAACCCTAAA
1 CCATAAAACCTTAAA
*
4934687 CCAT-AAGCCTTAAA
1 CCATAAAACCTTAAA
*
4934701 CCTTAAA
1 CCATAAA
4934708 TATTAAACCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:4935003 original size:41 final size:41
Alignment explanation
Indices: 4934946--4935230 Score: 335
Period size: 41 Copynumber: 7.0 Consensus size: 41
4934936 GGGGTTATAT
*
4934946 GACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCC
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCC
* *
4934987 GACTTTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCC
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCC
* *
4935028 GACTTTTAGCGGCGTTTTACCAAAAGCGTCGCTATTGCCCC
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCC
* *
4935069 GACTTTTAGCGGCGTATTACCAAAAGCGCCGCTATTGCTCT
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCC
* * *
4935110 G-TTTTTAGCGGCGTTTTAACAAAAGATGCCGCTATTGCT-C
1 GACTTTTAGCGGCGTTTTACCAAAAG-CGCCGCTATTGCTCC
* * * * * * **
4935150 TATTTTTAGCGGCATTTTAACAAAAAACGCCGCTATTACTTT
1 GACTTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTATTGCTCC
* *
4935192 G-TTTTTAGCTGCGTTTTACCCAAAA-CGCCGCTATTGCTC
1 GACTTTTAGCGGCGTTTTA-CCAAAAGCGCCGCTATTGCTC
4935231 TGTGTTTTAC
Statistics
Matches: 213, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
40 34 0.16
41 174 0.82
42 5 0.02
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (41 bp):
GACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCC
Found at i:4937611 original size:159 final size:157
Alignment explanation
Indices: 4937216--4937684 Score: 673
Period size: 153 Copynumber: 3.0 Consensus size: 157
4937206 TCAAAGCAGA
* *
4937216 AATATCACCATGAATATCTGCTTCACCAAGAGTGCAAATGTTGCAATTTGAAAATATAAGATATT
1 AATATCACTATGAATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGAAAATATAAGAT-TT
* * * *
4937281 CAAGCTTGGATAGTCGAGTAAGTGATGCAGGTATGCTGATGAAATTGTTACCATTAAGATCAAGA
65 CAAGCTTCGAGAGTCGAGTAAGAGATGCAGGTATGCTGATGAAATTGTTACCACTAAGATCAAGA
4937346 TGCCTCAAAGAGGATAGACCAG-AA-AT
130 TGCCTCAAAGAGGATAGACCAGAAATAT
* * *
4937372 -ATA--ACTATGAGTATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGATAATGTAAGCAATT
1 AATATCACTATGAATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGAAAATATAAG--ATT
* *
4937434 T-AAGCTTTGAGAGTCGAGTAAGAGATGCAGGTATGCTGATGAAATTGTTACCACTAAGATCGAG
64 TCAAGCTTCGAGAGTCGAGTAAGAGATGCAGGTATGCTGATGAAATTGTTACCACTAAGATCAAG
* *
4937498 ATGACTCAAAGAGGATATACCAGAAATAT
129 ATGCCTCAAAGAGGATAGACCAGAAATAT
* *
4937527 GAATATCACTATGATTATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAGATTT
1 -AATATCACTATGAATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGAAAATATAAGATTT
*
4937592 CCAAGCTTCGAGAGTCGAGTAAGAGATGCA-GTATGCTGATGAAGTTGTTACCACTAAGATCAAG
65 -CAAGCTTCGAGAGTCGAGTAAGAGATGCAGGTATGCTGATGAAATTGTTACCACTAAGATCAAG
* * *
4937656 ACGCCACAAAGTGGATAGACCAGAAATAT
129 ATGCCTCAAAGAGGATAGACCAGAAATAT
4937685 CACGTGGAAT
Statistics
Matches: 280, Mismatches: 23, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
153 128 0.46
154 4 0.01
155 7 0.03
157 7 0.03
158 56 0.20
159 78 0.28
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (157 bp):
AATATCACTATGAATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGAAAATATAAGATTTC
AAGCTTCGAGAGTCGAGTAAGAGATGCAGGTATGCTGATGAAATTGTTACCACTAAGATCAAGAT
GCCTCAAAGAGGATAGACCAGAAATAT
Found at i:4945254 original size:2 final size:2
Alignment explanation
Indices: 4945247--4945281 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4945237 AATTAAAATA
4945247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4945282 CTATCTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4949002 original size:14 final size:15
Alignment explanation
Indices: 4948976--4949006 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4948966 TCCAAGTTCA
4948976 TCAACACATTTTTCT
1 TCAACACATTTTTCT
4948991 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
4949005 TC
1 TC
4949007 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:4952303 original size:18 final size:17
Alignment explanation
Indices: 4952280--4952324 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
4952270 ATGAATTTTT
4952280 TTAAAATAATAAAATACA
1 TTAAAATAATAAAA-ACA
* *
4952298 TTAAAAATATTAAAAATA
1 TT-AAAATAATAAAAACA
4952316 TTAAAATAA
1 TTAAAATAA
4952325 ATATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAATAATAAAAACA
Found at i:4952311 original size:9 final size:9
Alignment explanation
Indices: 4952282--4952321 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
4952272 GAATTTTTTT
*
4952282 AAAATAATA
1 AAAATATTA
*
4952291 AAATACATTA
1 AAA-ATATTA
4952301 AAAATATTA
1 AAAATATTA
4952310 AAAATATTA
1 AAAATATTA
4952319 AAA
1 AAA
4952322 TAAATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAATATTA
Found at i:4952798 original size:30 final size:30
Alignment explanation
Indices: 4952764--4952831 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
4952754 CAACAAAATT
4952764 AACAATAAAATAAGAGTTATACAATATTCA
1 AACAATAAAATAAGAGTTATACAATATTCA
*
4952794 AACAATAAAATAAGAGTTATATAATATTCA
1 AACAATAAAATAAGAGTTATACAATATTCA
*
4952824 ACCAATAA
1 AACAATAA
4952832 CAACATAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.26
Consensus pattern (30 bp):
AACAATAAAATAAGAGTTATACAATATTCA
Found at i:4954024 original size:32 final size:32
Alignment explanation
Indices: 4953959--4954030 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
4953949 TTGTTCCTTA
* *
4953959 TTGTTTGTTTGGAAAGAAAGAAACATTCATTG
1 TTGTTTGTTTGAAAAGAAAGAAACATTAATTG
4953991 TTGTTTGTTTGAAAAGAAAGAAACA-TAAGTTG
1 TTGTTTGTTTGAAAAGAAAGAAACATTAA-TTG
4954023 TT-TTTGTT
1 TTGTTTGTT
4954031 ACTATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 8 0.22
32 29 0.78
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (32 bp):
TTGTTTGTTTGAAAAGAAAGAAACATTAATTG
Found at i:4958936 original size:16 final size:16
Alignment explanation
Indices: 4958906--4958953 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
4958896 GAAAATTAAT
4958906 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
4958921 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
4958938 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
4958953 A
1 A
4958954 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:4958952 original size:11 final size:11
Alignment explanation
Indices: 4958897--4958967 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
4958887 ATAGCTTAAG
*
4958897 AAAATTAATAT
1 AAAATTAAAAT
4958908 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
4958920 AATAA-T-AATT
1 AA-AATTAAAAT
*
4958930 AAAAAT-AAAT
1 AAAATTAAAAT
4958940 AAAATTAAAAT
1 AAAATTAAAAT
*
4958951 AAACTTAAAAT
1 AAAATTAAAAT
*
4958962 AGAATT
1 AAAATT
4958968 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:4966640 original size:40 final size:40
Alignment explanation
Indices: 4966585--4966664 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
4966575 ACTCTTTTAC
4966585 AACCTTAAAAAATACACTCATTAGATATTAGAACTCATAA
1 AACCTTAAAAAATACACTCATTAGATATTAGAACTCATAA
* *
4966625 AACCTTAGAAAATACACTTATTAGATATTAGAACTCATAA
1 AACCTTAAAAAATACACTCATTAGATATTAGAACTCATAA
4966665 CACATTTAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.29
Consensus pattern (40 bp):
AACCTTAAAAAATACACTCATTAGATATTAGAACTCATAA
Found at i:4966910 original size:2 final size:2
Alignment explanation
Indices: 4966905--4966941 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4966895 GAAAAAAAGT
*
4966905 TA TA TA TA TA TA TA TA TA TA TA GA 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 T
4966942 CCGAAAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4975845 original size:12 final size:12
Alignment explanation
Indices: 4975830--4975862 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4975820 ATTTTTTAGT
4975830 TTATTATATATA
1 TTATTATATATA
4975842 TTATT-TATTATA
1 TTATTATA-TATA
4975854 TTATTATAT
1 TTATTATAT
4975863 TTTCAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.11
12 15 0.79
13 2 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTATATATA
Found at i:4975850 original size:16 final size:15
Alignment explanation
Indices: 4975829--4975860 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
4975819 TATTTTTTAG
4975829 TTTATTATATATATTA
1 TTTATTATAT-TATTA
4975845 TTTATTATATTATTA
1 TTTATTATATTATTA
4975860 T
1 T
4975861 ATTTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTATATTATTA
Found at i:4975928 original size:21 final size:20
Alignment explanation
Indices: 4975836--4975946 Score: 70
Period size: 21 Copynumber: 5.6 Consensus size: 20
4975826 TAGTTTATTA
4975836 TATATATTATTTAT-TATAT
1 TATATATTATTTATATATAT
* *
4975855 TATTATATT-TTCA-AAAT-T
1 TA-TATATTATTTATATATAT
* * *
4975873 TGTAAATTA-TTATTATACAT
1 TATATATTATTTA-TATATAT
* * *
4975893 TATATTTTAACTTATATATCT
1 TATATATT-ATTTATATATAT
*
4975914 TATATATTTATTTATTTATAT
1 TATATA-TTATTTATATATAT
4975935 TATATATTATTT
1 TATATATTATTT
4975947 TAAAAAAACT
Statistics
Matches: 67, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
17 7 0.10
18 2 0.03
19 9 0.13
20 18 0.27
21 26 0.39
22 5 0.07
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (20 bp):
TATATATTATTTATATATAT
Found at i:4975942 original size:7 final size:7
Alignment explanation
Indices: 4975836--4975944 Score: 50
Period size: 7 Copynumber: 15.4 Consensus size: 7
4975826 TAGTTTATTA
4975836 TATATAT
1 TATATAT
*
4975843 TATTTAT
1 TATATAT
4975850 TATATTAT
1 TATA-TAT
*
4975858 TATATTT
1 TATATAT
*
4975865 TCA-AAATT
1 T-ATATA-T
* *
4975873 TGTAAAT
1 TATATAT
4975880 TAT-TAT
1 TATATAT
*
4975886 TATACAT
1 TATATAT
4975893 TATAT-T
1 TATATAT
4975899 T-TA-ACT
1 TATATA-T
4975905 TATATATCT
1 TATATA--T
4975914 TATATATT
1 TATATA-T
*
4975922 TATTTAT
1 TATATAT
4975929 T-TATAT
1 TATATAT
4975935 TATATAT
1 TATATAT
4975942 TAT
1 TAT
4975945 TTTAAAAAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
5 2 0.03
6 14 0.18
7 34 0.44
8 20 0.26
9 8 0.10
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.59
Consensus pattern (7 bp):
TATATAT
Found at i:4977866 original size:30 final size:31
Alignment explanation
Indices: 4977832--4977903 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 31
4977822 TTTTAGGTTA
*
4977832 CTTAAAAGTTAGTAAA-AAAA-ATTTTGG-GCC
1 CTTAAAAGTTA--AAAGAAAATATTTTGGACCC
*
4977862 CTTAAAAGCTAAAAGAAAATATTTTGGAACCC
1 CTTAAAAGTTAAAAGAAAATATTTTGG-ACCC
4977894 CTTAAAAGTT
1 CTTAAAAGTT
4977904 GATAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 3 0.09
29 4 0.11
30 17 0.49
32 11 0.31
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.29
Consensus pattern (31 bp):
CTTAAAAGTTAAAAGAAAATATTTTGGACCC
Found at i:4987093 original size:15 final size:15
Alignment explanation
Indices: 4987050--4987093 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
4987040 ATAATTTACA
* *
4987050 AATAAAATATGTAGT
1 AATAAAATATATAAT
4987065 AATATAAATCATATAAT
1 AATA-AAAT-ATATAAT
4987082 AATAAAATATAT
1 AATAAAATATAT
4987094 GTAATACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.32
16 8 0.32
17 9 0.36
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (15 bp):
AATAAAATATATAAT
Found at i:4987098 original size:17 final size:19
Alignment explanation
Indices: 4987056--4987099 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
4987046 TACAAATAAA
*
4987056 ATATGTAGTAATATAAATC
1 ATATGTAATAATATAAATC
4987075 ATA--TAATAATA-AAAT-
1 ATATGTAATAATATAAATC
4987090 ATATGTAATA
1 ATATGTAATA
4987100 CAATAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
15 3 0.14
16 4 0.18
17 12 0.55
19 3 0.14
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (19 bp):
ATATGTAATAATATAAATC
Found at i:4987180 original size:21 final size:21
Alignment explanation
Indices: 4987156--4987200 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
4987146 TCATATAAAA
*
4987156 ATATAGTAAAATA-ATTAATAT
1 ATATAGGAAAATACA-TAATAT
4987177 ATATAGGAAAATACATAATAT
1 ATATAGGAAAATACATAATAT
4987198 ATA
1 ATA
4987201 CTAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (21 bp):
ATATAGGAAAATACATAATAT
Found at i:4987259 original size:19 final size:19
Alignment explanation
Indices: 4987153--4987265 Score: 55
Period size: 19 Copynumber: 5.4 Consensus size: 19
4987143 TTTTCATATA
*
4987153 AAAATATAGTAAAATAATT
1 AAAATATAGTAAAATAAAT
* *
4987172 AATATATATAGGAAAATACAT
1 AA-A-ATATAGTAAAATAAAT
* * *
4987193 AATATATACTAAATTTTTAAAT
1 AAAATATAGTAAA---ATAAAT
* *
4987215 AAAATTTATAATAATATAATAGAT
1 AAAA--TATAGT-A-A-AATAAAT
4987239 AAAATATAGTAAAATAAAT
1 AAAATATAGTAAAATAAAT
*
4987258 AATATATA
1 AAAATATA
4987266 TATATATATA
Statistics
Matches: 69, Mismatches: 15, Indels: 20
0.66 0.14 0.19
Matches are distributed among these distances:
19 23 0.33
20 2 0.03
21 16 0.23
22 12 0.17
24 13 0.19
25 1 0.01
26 1 0.01
27 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAATATAGTAAAATAAAT
Found at i:4987309 original size:27 final size:27
Alignment explanation
Indices: 4987237--4987315 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
4987227 AATATAATAG
* *
4987237 ATAAAATATAGTAAAATAAATAATATAT
1 ATAAAATATAGTAAAATGAA-AATACAT
*
4987265 ATATATATATA-TAAAATGAAAATACAT
1 ATA-AAATATAGTAAAATGAAAATACAT
* *
4987292 ATAACATATAGTAAAATGCAAATA
1 ATAAAATATAGTAAAATGAAAATA
4987316 TAACAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
26 6 0.14
27 21 0.48
28 11 0.25
29 6 0.14
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (27 bp):
ATAAAATATAGTAAAATGAAAATACAT
Found at i:4987339 original size:16 final size:17
Alignment explanation
Indices: 4987313--4987346 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
4987303 TAAAATGCAA
4987313 ATATAACAAAATATAAT
1 ATATAACAAAATATAAT
4987330 ATATAA-AAAATATAAT
1 ATATAACAAAATATAAT
4987346 A
1 A
4987347 AACAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATAACAAAATATAAT
Done.