Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 122 of 333
Found at i:39441675 original size:10 final size:10
Alignment explanation
Indices: 39441660--39441726 Score: 68
Period size: 10 Copynumber: 6.9 Consensus size: 10
39441650 CAATGTTCAA
39441660 AATTTTTTTC
1 AATTTTTTTC
39441670 AATTTTTTT-
1 AATTTTTTTC
*
39441679 AA-TTTTTTG
1 AATTTTTTTC
*
39441688 AACTTTTTTTT
1 AA-TTTTTTTC
39441699 AATTTTTTTC
1 AATTTTTTTC
* *
39441709 -GTTTTTTTT
1 AATTTTTTTC
39441718 AATTTTTTT
1 AATTTTTTT
39441727 GAAACTTACT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
8 6 0.12
9 11 0.23
10 23 0.48
11 8 0.17
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (10 bp):
AATTTTTTTC
Found at i:39441677 original size:9 final size:9
Alignment explanation
Indices: 39441660--39441726 Score: 71
Period size: 9 Copynumber: 7.0 Consensus size: 9
39441650 CAATGTTCAA
39441660 AATTTTTTT
1 AATTTTTTT
39441669 CAATTTTTTT
1 -AATTTTTTT
*
39441679 AATTTTTTG
1 AATTTTTTT
39441688 AACTTTTTTTT
1 AA--TTTTTTT
39441699 AATTTTTTT
1 AATTTTTTT
**
39441708 CGTTTTTTTT
1 -AATTTTTTT
39441718 AATTTTTTT
1 AATTTTTTT
39441727 GAAACTTACT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
9 24 0.50
10 16 0.33
11 8 0.17
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (9 bp):
AATTTTTTT
Found at i:39441682 original size:19 final size:19
Alignment explanation
Indices: 39441660--39441726 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
39441650 CAATGTTCAA
39441660 AATTTTTTTCAATTTTTTT
1 AATTTTTTTCAATTTTTTT
*
39441679 AA-TTTTTTGAACTTTTTTTT
1 AATTTTTTTCAA--TTTTTTT
**
39441699 AATTTTTTTCGTTTTTTTT
1 AATTTTTTTCAATTTTTTT
39441718 AATTTTTTT
1 AATTTTTTT
39441727 GAAACTTACT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 9 0.22
21 6 0.15
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (19 bp):
AATTTTTTTCAATTTTTTT
Found at i:39442906 original size:63 final size:65
Alignment explanation
Indices: 39442839--39442962 Score: 148
Period size: 67 Copynumber: 1.9 Consensus size: 65
39442829 ACTAACACTT
*
39442839 ATGCATCA-T-TTAATCC-AGCAACTAATTTAATTAATAGAAGCAT-TATTAAATGAAATTTAAC
1 ATGCATCACTATT-ATCCTAGCAACTAATTTAATTAA-AGAAGCATCTATTAAATCAAATTTAAC
39442900 TC
64 TC
* * *
39442902 ATGCATCACTAAATTATCCTAGTAACTAGTTTATTTAAAGAAGCATCTATTAAATCAAATT
1 ATGCATCACT--ATTATCCTAGCAACTAATTTAATTAAAGAAGCATCTATTAAATCAAATT
39442963 CATAAAAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
63 8 0.16
64 1 0.02
66 12 0.24
67 30 0.59
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (65 bp):
ATGCATCACTATTATCCTAGCAACTAATTTAATTAAAGAAGCATCTATTAAATCAAATTTAACTC
Found at i:39455080 original size:24 final size:24
Alignment explanation
Indices: 39455048--39455102 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
39455038 GTTAGGACAT
*
39455048 ATTAAATTCATCCACCAGAAGCTC
1 ATTAAATTCATCAACCAGAAGCTC
* *
39455072 ATTAAATTCGTCAACCAGTAGCTC
1 ATTAAATTCATCAACCAGAAGCTC
39455096 ATTAAAT
1 ATTAAAT
39455103 CTGTCCAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (24 bp):
ATTAAATTCATCAACCAGAAGCTC
Found at i:39457192 original size:20 final size:19
Alignment explanation
Indices: 39457169--39457226 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
39457159 AGCTCAAACG
39457169 AGCTAAAGTAAGCTAAATTA
1 AGCTAAAGT-AGCTAAATTA
39457189 AGCTCAAACG-AGCTAAATTA
1 AGCT-AAA-GTAGCTAAATTA
* *
39457209 AGCTCATGTGAGCTAAAT
1 AGCTAAAGT-AGCTAAAT
39457227 CGAGCTGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 26 0.81
21 3 0.09
22 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (19 bp):
AGCTAAAGTAGCTAAATTA
Found at i:39471079 original size:27 final size:27
Alignment explanation
Indices: 39471048--39471127 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
39471038 AAGGGGGTGG
39471048 TCCATCGAGATAGTAAACATGTGGTAA
1 TCCATCGAGATAGTAAACATGTGGTAA
* *
39471075 TCCATC-ATGACAGTAAACATGTGGTAT
1 TCCATCGA-GATAGTAAACATGTGGTAA
* *
39471102 TCTATCG-GTATAGTAAACACGTGGTA
1 TCCATCGAG-ATAGTAAACATGTGGTA
39471128 GTTTGTCGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.04
27 43 0.96
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (27 bp):
TCCATCGAGATAGTAAACATGTGGTAA
Found at i:39471167 original size:27 final size:27
Alignment explanation
Indices: 39471137--39471201 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
39471127 AGTTTGTCGA
* * *
39471137 GACATTAAACATAAGGTAGTCTACTGG
1 GACAATAAACATAAGGTAGTCCACCGG
* * **
39471164 GACAGTAAAAATGTGGTAGTCCACCGG
1 GACAATAAACATAAGGTAGTCCACCGG
39471191 GACAATAAACA
1 GACAATAAACA
39471202 CAAGAATGTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (27 bp):
GACAATAAACATAAGGTAGTCCACCGG
Found at i:39477809 original size:6 final size:6
Alignment explanation
Indices: 39477795--39477837 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
39477785 ATAAGGTCTC
* *
39477795 TTTAAT TTTATT TTTATT TTCATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT T
39477838 GGGGATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:39478608 original size:19 final size:20
Alignment explanation
Indices: 39478584--39478641 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
39478574 TACCGATCAT
39478584 ATGAAT-AAGCTA-TGTTGAA
1 ATGAATGAA-CTATTGTTGAA
*
39478603 ATGAATGAATTATTGTTGAA
1 ATGAATGAACTATTGTTGAA
* *
39478623 ATGAATGAATTACTGTTGA
1 ATGAATGAACTATTGTTGA
39478642 TACAGATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 8 0.23
20 27 0.77
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (20 bp):
ATGAATGAACTATTGTTGAA
Found at i:39478621 original size:20 final size:20
Alignment explanation
Indices: 39478596--39478641 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
39478586 GAATAAGCTA
*
39478596 TGTTGAAATGAATGAATTAT
1 TGTTGAAATGAATGAATTAC
39478616 TGTTGAAATGAATGAATTAC
1 TGTTGAAATGAATGAATTAC
39478636 TGTTGA
1 TGTTGA
39478642 TACAGATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (20 bp):
TGTTGAAATGAATGAATTAC
Found at i:39478653 original size:20 final size:19
Alignment explanation
Indices: 39478630--39478703 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
39478620 GAAATGAATG
39478630 AATTACTGTTGATACAGATA
1 AATTACTGTT-ATACAGATA
* *
39478650 AATTACTGTTATTACTGATG
1 AATTACTGTTA-TACAGATA
*
39478670 AATTACTGGTTATACAGATG
1 AATTACT-GTTATACAGATA
*
39478690 AACTACTAGTTATA
1 AATTACT-GTTATA
39478704 TGAATGAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.89
21 4 0.09
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (19 bp):
AATTACTGTTATACAGATA
Found at i:39478654 original size:40 final size:39
Alignment explanation
Indices: 39478622--39478711 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 39
39478612 TTATTGTTGA
39478622 AATGAATGAATTACT-GTTGATACAGATAAATTACTGTTATT
1 AATG-ATGAATTACTGGTT-ATACAGATAAATTACTGTTA-T
* * *
39478663 ACTGATGAATTACTGGTTATACAGATGAACTACTAGTTAT
1 AATGATGAATTACTGGTTATACAGATAAATTACT-GTTAT
39478703 -ATGAATGAA
1 AATG-ATGAA
39478712 GTTATATGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
39 2 0.05
40 30 0.71
41 10 0.24
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (39 bp):
AATGATGAATTACTGGTTATACAGATAAATTACTGTTAT
Found at i:39482291 original size:37 final size:37
Alignment explanation
Indices: 39482241--39482319 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
39482231 TTATTACGAA
* *
39482241 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTCT-CACACGAAGTCATCGG
*
39482278 GTCTTACCCGGACAAAATTCTCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCTCACACGAAGTCATCGG
39482315 GTCTT
1 GTCTT
39482320 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 35 0.92
38 3 0.08
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCTCACACGAAGTCATCGG
Found at i:39482516 original size:47 final size:47
Alignment explanation
Indices: 39482438--39482958 Score: 880
Period size: 47 Copynumber: 11.1 Consensus size: 47
39482428 CCCTTCGGGA
* * * * * * *
39482438 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
39482485 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39482532 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39482579 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39482626 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39482673 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39482720 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39482767 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39482814 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39482861 CTTATCACACATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39482908 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39482955 CTTA
1 CTTA
39482959 CTATCATTTC
Statistics
Matches: 449, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 449 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39492005 original size:11 final size:11
Alignment explanation
Indices: 39491989--39492013 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39491979 ATATCTAGAA
39491989 TTCTCTTCATT
1 TTCTCTTCATT
39492000 TTCTCTTCATT
1 TTCTCTTCATT
39492011 TTC
1 TTC
39492014 ATTAACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:39493973 original size:10 final size:10
Alignment explanation
Indices: 39493958--39493985 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
39493948 ATATTACATG
39493958 TTTACTTTGT
1 TTTACTTTGT
39493968 TTTACTTTGT
1 TTTACTTTGT
39493978 TTTACTTT
1 TTTACTTT
39493986 TTCTCCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Found at i:39494743 original size:44 final size:44
Alignment explanation
Indices: 39494642--39494733 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
39494632 TGTTCAAGAA
*
39494642 TACTTCGACCTT-GAGTCGATGAGGCACTATAAGTGTCGTACTGT
1 TACTTCGA-CTTCGAGTCGATGAGGCACTATAAGTGTCGTACTGC
**
39494686 TACTTCGACTTCGAGTCGATGAGGCACCT-TGTGTGTCGTACTGC
1 TACTTCGACTTCGAGTCGATGAGGCA-CTATAAGTGTCGTACTGC
39494730 TACT
1 TACT
39494734 GTTACTTCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 3 0.07
44 38 0.88
45 2 0.05
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (44 bp):
TACTTCGACTTCGAGTCGATGAGGCACTATAAGTGTCGTACTGC
Found at i:39495053 original size:21 final size:22
Alignment explanation
Indices: 39495012--39495106 Score: 108
Period size: 21 Copynumber: 4.5 Consensus size: 22
39495002 AGGCACTTTA
*
39495012 TGTGTCGTATTTCAGGAACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
39495035 TGTGTCGTATT-AGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
39495056 TGTGTCGT-TTCAGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
* * **
39495077 TGTGTTGT-TTCAAGCA-CTTA
1 TGTGTCGTATTCAGGCACCTCG
39495097 TGTGTCGTAT
1 TGTGTCGTAT
39495107 ACTGATTAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.17
21 42 0.66
22 2 0.03
23 9 0.14
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:39496001 original size:22 final size:22
Alignment explanation
Indices: 39495975--39496044 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
39495965 TCTTTGATTG
*
39495975 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCTGT
*
39495997 TTAGCACATCT-GTGCTATCTGT
1 TTAGCACAT-TAGTGCTCTCTGT
* * *
39496019 ATAACACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
39496041 TTAG
1 TTAG
39496045 TAGTGCATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:39497975 original size:11 final size:11
Alignment explanation
Indices: 39497959--39497983 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39497949 ATATCTAGAA
39497959 TTCTCTTCATT
1 TTCTCTTCATT
39497970 TTCTCTTCATT
1 TTCTCTTCATT
39497981 TTC
1 TTC
39497984 ATTAACAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:39499266 original size:25 final size:25
Alignment explanation
Indices: 39499237--39499288 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
39499227 AAGAATAATT
**
39499237 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
39499262 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
39499287 TG
1 TG
39499289 TTAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:39501794 original size:24 final size:24
Alignment explanation
Indices: 39501767--39501813 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39501757 ATTGAAATGG
39501767 ATTG-ATTTATTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
39501791 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
39501814 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:39502018 original size:41 final size:39
Alignment explanation
Indices: 39501973--39502108 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 39
39501963 CGACTTCGAG
*
39501973 TCGATGAGGCACTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATGAGGCACTGGGTGTCAA-TTACTACTTCGAATT-AT
* *
39502014 TCGATGAGGCACTGGGTGCCAATT--TACTTC-AATTTAG
1 TCGATGAGGCACTGGGTGTCAATTACTACTTCGAA-TTAT
* **
39502051 TCGATGAGACACAAGGTGTCAAATTACTACTTCGAATTAT
1 TCGATGAGGCACTGGGTGTC-AATTACTACTTCGAATTAT
*
39502091 CCGATGAGGCACTGGGTG
1 TCGATGAGGCACTGGGTG
39502109 CCAAACTGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
37 18 0.23
38 12 0.15
40 25 0.32
41 23 0.29
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (39 bp):
TCGATGAGGCACTGGGTGTCAATTACTACTTCGAATTAT
Found at i:39508031 original size:48 final size:48
Alignment explanation
Indices: 39507975--39508073 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
39507965 TCTAGTCGTT
39507975 ATTCTCACACAAATTGATAACAACCTATGAATTCTATAAAATGTCAGA
1 ATTCTCACACAAATTGATAACAACCTATGAATTCTATAAAATGTCAGA
*
39508023 ATTCTCACACAAATTGGTAACAACCTATGAATTCTATAAAATGTCAGA
1 ATTCTCACACAAATTGATAACAACCTATGAATTCTATAAAATGTCAGA
39508071 ATT
1 ATT
39508074 TTCCATAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (48 bp):
ATTCTCACACAAATTGATAACAACCTATGAATTCTATAAAATGTCAGA
Found at i:39512069 original size:18 final size:19
Alignment explanation
Indices: 39512025--39512073 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
39512015 AGGCATTTTC
39512025 CAACCTTAACATACAAAAT
1 CAACCTTAACATACAAAAT
* *
39512044 AAATCTTAACATAC-AAAT
1 CAACCTTAACATACAAAAT
39512062 CAACCTTAACAT
1 CAACCTTAACAT
39512074 TCATCACATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (19 bp):
CAACCTTAACATACAAAAT
Found at i:39518203 original size:24 final size:24
Alignment explanation
Indices: 39518176--39518221 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
39518166 AAAGTTACTT
39518176 GTAAAACTAAAATTACATGCATAA
1 GTAAAACTAAAATTACATGCATAA
*
39518200 GTAAGACTAAAATTACATGCAT
1 GTAAAACTAAAATTACATGCAT
39518222 GTAGTTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (24 bp):
GTAAAACTAAAATTACATGCATAA
Found at i:39519463 original size:27 final size:27
Alignment explanation
Indices: 39519431--39519483 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
39519421 TACAATCTAT
39519431 AGTTTGCTTGTTTCCTTAGAAACAATG
1 AGTTTGCTTGTTTCCTTAGAAACAATG
39519458 AGTTTGCTTGTTTCCTTAGAAACAAT
1 AGTTTGCTTGTTTCCTTAGAAACAAT
39519484 CATTGGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (27 bp):
AGTTTGCTTGTTTCCTTAGAAACAATG
Found at i:39531345 original size:61 final size:61
Alignment explanation
Indices: 39531250--39531419 Score: 174
Period size: 61 Copynumber: 2.9 Consensus size: 61
39531240 TTATTATTAA
** * * * *
39531250 ATTTTAATAGGATTATAATTAAATGTAATTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATAAC
**
39531311 ATTTTAATATAATTATTATTAAATATAATTTAAT---AAT---AATGTATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATAAC
* *
39531366 ATTCTTAATGTAATTATTATTAAAATATGAA-TTAATAAAAATAAAAATACATAA
1 ATT-TTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAAAAATAAATAA
39531420 GATTAGAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
55 17 0.19
56 16 0.18
57 11 0.12
58 5 0.06
60 3 0.03
61 30 0.34
63 7 0.08
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (61 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATAAC
Found at i:39531346 original size:55 final size:57
Alignment explanation
Indices: 39531287--39531410 Score: 164
Period size: 55 Copynumber: 2.2 Consensus size: 57
39531277 ATTTAATAAA
* *
39531287 AATAAAAATAAATAATTTAATCATATT-TTAATATAATTATTATT-AAATAT-AATTT
1 AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAA-TT
* ** *
39531342 AATAATAATGTATAATTTAATAACATTCTTAATGTAATTATTATTAAAATATGAATT
1 AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAATT
39531399 AATAAAAATAAA
1 AATAAAAATAAA
39531411 AATACATAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
55 22 0.39
56 16 0.28
57 17 0.30
58 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (57 bp):
AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAATT
Found at i:39534606 original size:14 final size:14
Alignment explanation
Indices: 39534587--39534613 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39534577 TATACTTCAC
39534587 GGTGTAAGTGAAAT
1 GGTGTAAGTGAAAT
39534601 GGTGTAAGTGAAA
1 GGTGTAAGTGAAA
39534614 GAAAGAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (14 bp):
GGTGTAAGTGAAAT
Found at i:39539355 original size:20 final size:20
Alignment explanation
Indices: 39539297--39539355 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
39539287 TATTCTATGA
39539297 TATTATA-TAAATTAACGAA-
1 TATTATATTAAATTAAC-AAT
* * **
39539316 -AATATATTTAATTATTAAT
1 TATTATATTAAATTAACAAT
39539335 TATTATATTAAATTAACAAT
1 TATTATATTAAATTAACAAT
39539355 T
1 T
39539356 GCGTATCTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
18 7 0.24
19 6 0.21
20 16 0.55
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (20 bp):
TATTATATTAAATTAACAAT
Found at i:39543179 original size:21 final size:21
Alignment explanation
Indices: 39543155--39543219 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
39543145 AAATCTAACT
39543155 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
** *
39543176 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACG
39543194 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
*
39543215 AAAGC
1 GAAGC
39543220 CCGAAGGCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 8 0.24
19 7 0.21
20 7 0.21
21 12 0.35
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:39543192 original size:39 final size:39
Alignment explanation
Indices: 39543137--39543237 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
39543127 ATCGCGATCT
**
39543137 GAAGCCCGAAATCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
39543176 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
39543215 AAAGCCCGAAGGCTAACTAAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
39543238 TCATCAGAGC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:39546586 original size:31 final size:31
Alignment explanation
Indices: 39546551--39546668 Score: 173
Period size: 31 Copynumber: 3.8 Consensus size: 31
39546541 CTTGTCACTT
*
39546551 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
39546582 GTAGCCGGAGCTACCACTTTTCACTAACCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
39546613 GTAGCAGAAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
39546644 GTAGTCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
39546669 TGTCATTTGT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:39546636 original size:62 final size:62
Alignment explanation
Indices: 39546551--39546668 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
39546541 CTTGTCACTT
* * *
39546551 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCGGAGCTACCACTTTTCACTAACCAG
1 GTAGCAGAAGCTACCACTATTCACTGATCAAGTAGCCGAAGCTACCACTTTTCACTAACCAG
* *
39546613 GTAGCAGAAGCTACCACTTTTCACTGATCAAGTAGTCGAAGCTACCACTTTTCACT
1 GTAGCAGAAGCTACCACTATTCACTGATCAAGTAGCCGAAGCTACCACTTTTCACT
39546669 TGTCATTTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (62 bp):
GTAGCAGAAGCTACCACTATTCACTGATCAAGTAGCCGAAGCTACCACTTTTCACTAACCAG
Found at i:39546744 original size:50 final size:51
Alignment explanation
Indices: 39546644--39546772 Score: 179
Period size: 50 Copynumber: 2.5 Consensus size: 51
39546634 CACTGATCAA
* * * *
39546644 GTAGTCGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCATTGATCAGATAAGT
* * *
39546695 GTAGCCGAAGTTATCACTTATCACTT-TCACTTGTCCTTGATCAGTTAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCATTGATCAGATAAGT
*
39546745 GTAGCCGAAGCTATTACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
39546773 TGCCATGGTC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 45 0.66
51 23 0.34
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCATTGATCAGATAAGT
Found at i:39548087 original size:39 final size:39
Alignment explanation
Indices: 39548025--39548125 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
39548015 ATCGTGATCT
** * *
39548025 GAAGCCCGAAATCTAGCTAAAGCACATAAGTGCTAAACA
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
**
39548064 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
39548103 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
39548126 TCATCAGAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
Found at i:39554937 original size:93 final size:93
Alignment explanation
Indices: 39554825--39554997 Score: 319
Period size: 93 Copynumber: 1.9 Consensus size: 93
39554815 CGCTCATAAG
* *
39554825 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
39554890 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
39554918 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
39554983 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
39554998 CAAACATCAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:39554993 original size:46 final size:46
Alignment explanation
Indices: 39554819--39554993 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
39554809 GTAACCCGCT
* * *
39554819 CATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATC
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATC
* *
39554865 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTTA
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--TC
***
39554911 CATCTCTCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATC
1 CATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATC
*
39554958 CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
39554994 TGCCCAAACA
Statistics
Matches: 109, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 67 0.61
47 33 0.30
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATC
Found at i:39555012 original size:46 final size:46
Alignment explanation
Indices: 39554826--39555012 Score: 170
Period size: 46 Copynumber: 4.0 Consensus size: 46
39554816 GCTCATAAGC
* * * *
39554826 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT-A-AGT
1 GAACTCGGACTCAACTCAACGAGCTC-GG-ATGCCCATACATCATAGT
* *
39554872 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATC-T-CT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCCA--TACATCATAGT
* * *
39554918 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT-A-AGT
1 -GAACTCGGACTCAACTCAACGAGCTCGG--ATGCCCATACATCATAGT
* *
39554965 GAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCATAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCCATACATCATAGT
39555011 GA
1 GA
39555013 CATGTCACTT
Statistics
Matches: 114, Mismatches: 16, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
44 11 0.10
45 3 0.03
46 63 0.55
47 33 0.29
49 4 0.04
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGCCCATACATCATAGT
Found at i:39557158 original size:18 final size:18
Alignment explanation
Indices: 39557135--39557175 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
39557125 CCTAGATGGC
39557135 ACTTGATGTTCAGCATTA
1 ACTTGATGTTCAGCATTA
39557153 ACTTGATGTTCAGCATTA
1 ACTTGATGTTCAGCATTA
39557171 ACTTG
1 ACTTG
39557176 CTGACAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (18 bp):
ACTTGATGTTCAGCATTA
Found at i:39562382 original size:28 final size:28
Alignment explanation
Indices: 39562350--39562850 Score: 172
Period size: 28 Copynumber: 17.6 Consensus size: 28
39562340 CCTTTAACAG
39562350 GTTTT-CCACAAAGGTCTA-CTTTCTAGA
1 GTTTTGCCACAAAGG-CTACCTTTCTAGA
* * * *
39562377 GTTTTTCCATAAAGGCTATCCTTT-AACA
1 GTTTTGCCACAAAGGCTA-CCTTTCTAGA
* * *
39562405 GGTTCGCTACAAAGGCTTACCTTTCTAGA
1 GTTTTGCCACAAAGGC-TACCTTTCTAGA
* * *
39562434 GTTTTGCCACAAAGGCTCTCCTTT-AACA
1 GTTTTGCCACAAAGGCT-ACCTTTCTAGA
* *
39562462 GGTTTGCCACAAAGGCTTACATTTCTAGA
1 GTTTTGCCACAAAGGC-TACCTTTCTAGA
* * *
39562491 GTTTTGCCCCAAAGGCTATCCTTT-AATA
1 GTTTTGCCACAAAGGCTA-CCTTTCTAGA
* *
39562519 -TGTTTGCCACAAAGGTTTACCTTTCCAGA
1 GT-TTTGCCACAAAGG-CTACCTTTCTAGA
* *
39562548 GTTTTTCCACAAAGGCTATCATTTAAC-A-A
1 GTTTTGCCACAAAGGCTA-CCTTT--CTAGA
* * * *
39562577 G-TTCGCCATATAGGCTTACCTTTTTAGA
1 GTTTTGCCACAAAGGC-TACCTTTCTAGA
* ** * *
39562605 GTTTTTCCATGAAGTCTATCCTTTAATAG-
1 GTTTTGCCACAAAGGCTA-CCTTT-CTAGA
* * * *
39562634 G-TGTGCCATAAAGGCTTACCTTTCCAGT
1 GTTTTGCCACAAAGGC-TACCTTTCTAGA
*
39562662 GTTTTGCCACAAAGGCTATCCTTTAATAG-
1 GTTTTGCCACAAAGGCTA-CCTTT-CTAGA
** * *
39562691 G-TTCACCACATAGGCTTAACTTTCTAGA
1 GTTTTGCCACAAAGGC-TACCTTTCTAGA
** * * * *
39562719 GTTTTGTGATAAAGACTATCCTTT-AACA
1 GTTTTGCCACAAAGGCTA-CCTTTCTAGA
* ** * *
39562747 GGTTCACCACAAAGGCTTACATTTCCAGA
1 GTTTTGCCACAAAGGC-TACCTTTCTAGA
* * * * *
39562776 GTTTTTCCAAAAAAGGTTGTCCTTTAATAG-
1 GTTTTGCC-ACAAAGGCT-ACCTTT-CTAGA
*
39562806 GTTTT-CCACATAGGCTTACCTTTCTAGA
1 GTTTTGCCACAAAGGC-TACCTTTCTAGA
39562834 GTTTTGCCGA-AAAGGCT
1 GTTTTGCC-ACAAAGGCT
39562851 TTTCTTCTCC
Statistics
Matches: 339, Mismatches: 95, Indels: 79
0.66 0.19 0.15
Matches are distributed among these distances:
27 18 0.05
28 156 0.46
29 139 0.41
30 23 0.07
31 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (28 bp):
GTTTTGCCACAAAGGCTACCTTTCTAGA
Found at i:39562449 original size:57 final size:57
Alignment explanation
Indices: 39562340--39562850 Score: 535
Period size: 57 Copynumber: 9.0 Consensus size: 57
39562330 CAAAAGATGC
** * *
39562340 CCTTTAACAGGTTTTCCACAAAGG-TCTA-CTTTCTAGAGTTTTTCCATAAAGGCTAT
1 CCTTTAACAGGTTCGCCACAAAGGCT-TACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* *
39562396 CCTTTAACAGGTTCGCTACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTCT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * *
39562453 CCTTTAACAGGTTTGCCACAAAGGCTTACATTTCTAGAGTTTTGCCCCAAAGGCTAT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * * *
39562510 CCTTTAATATGTTTGCCACAAAGGTTTACCTTTCCAGAGTTTTTCCACAAAGGCTAT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * * * ** *
39562567 CATTTAACAAGTTCGCCATATAGGCTTACCTTTTTAGAGTTTTTCCATGAAGTCTAT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * *
39562624 CCTTTAATAGGTGT-GCCATAAAGGCTTACCTTTCCAGTGTTTTGCCACAAAGGCTAT
1 CCTTTAACAGGT-TCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * ** * *
39562681 CCTTTAATAGGTTCACCACATAGGCTTAACTTTCTAGAGTTTTGTGATAAAGACTAT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * * * *
39562738 CCTTTAACAGGTTCACCACAAAGGCTTACATTTCCAGAGTTTTTCCAAAAAAGGTTGT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCC-ACAAAGGCTAT
* ** *
39562796 CCTTTAATAGGTTTTCCACATAGGCTTACCTTTCTAGAGTTTTGCCGA-AAAGGCT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCC-ACAAAGGCT
39562851 TTTCTTCTCC
Statistics
Matches: 378, Mismatches: 72, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
56 24 0.06
57 306 0.81
58 48 0.13
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (57 bp):
CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
Found at i:39562564 original size:171 final size:170
Alignment explanation
Indices: 39562340--39562850 Score: 621
Period size: 171 Copynumber: 3.0 Consensus size: 170
39562330 CAAAAGATGC
* * *
39562340 CCTTTAACAGGTTTTCCACAAAGGTCTACTTTCTAGAGTTTTTCCATAAAGGCTATCCTTTAACA
1 CCTTTAATAGGTTTACCACAAAGGTTTACTTTCTAGAGTTTTTCCATAAAGGCTATCCTTTAACA
* * * * *
39562405 GGTTCGCTACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTCTCCTTTAACAGGTTTGCC
66 GGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTTCCAAAAAGGCTATCCTTTAATAGGTTTGCC
* *
39562470 ACAAAGGCTTACATTTCTAGAGTTTTGCCCCAAAGGCTAT
131 ACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * *
39562510 CCTTTAATATGTTTGCCACAAAGGTTTACCTTTCCAGAGTTTTTCCACAAAGGCTATCATTTAAC
1 CCTTTAATAGGTTTACCACAAAGGTTTA-CTTTCTAGAGTTTTTCCATAAAGGCTATCCTTTAAC
* * * * ** * *
39562575 AAGTTCGCCATATAGGCTTACCTTTTTAGAGTTTTTCCATGAAGTCTATCCTTTAATAGGTGTGC
65 AGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTTCCAAAAAGGCTATCCTTTAATAGGTTTGC
* * *
39562640 CATAAAGGCTTACCTTTCCAGTGTTTTGCCACAAAGGCTAT
130 CACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * *
39562681 CCTTTAATAGGTTCACCACATAGGCTTAACTTTCTAGAGTTTTGT-GATAAAGACTATCCTTTAA
1 CCTTTAATAGGTTTACCACAAAGG-TTTACTTTCTAGAGTTTT-TCCATAAAGGCTATCCTTTAA
* * * * *
39562745 CAGGTTCACCACAAAGGCTTACATTTCCAGAGTTTTTCCAAAAAAGGTTGTCCTTTAATAGGTTT
64 CAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTTCC-AAAAAGGCTATCCTTTAATAGGTTT
* *
39562810 TCCACATAGGCTTACCTTTCTAGAGTTTTGCCGA-AAAGGCT
128 GCCACAAAGGCTTACCTTTCTAGAGTTTTGCC-ACAAAGGCT
39562851 TTTCTTCTCC
Statistics
Matches: 284, Mismatches: 52, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
170 24 0.08
171 202 0.71
172 57 0.20
173 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (170 bp):
CCTTTAATAGGTTTACCACAAAGGTTTACTTTCTAGAGTTTTTCCATAAAGGCTATCCTTTAACA
GGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTTCCAAAAAGGCTATCCTTTAATAGGTTTGCC
ACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
Found at i:39563052 original size:53 final size:53
Alignment explanation
Indices: 39562970--39563072 Score: 172
Period size: 53 Copynumber: 1.9 Consensus size: 53
39562960 TCCTTAAAAT
39562970 TTTCCATATGATGCCATAACCCACCAGTTA-GGATCTTACACGATATGGTCTTC
1 TTTCCATATGATGCCATAACCCACCAGTTATGG-TCTTACACGATATGGTCTTC
* *
39563023 TTTCCATATGATGTCATAACCCACTAGTTATGGTCTTACACGATATGGTC
1 TTTCCATATGATGCCATAACCCACCAGTTATGGTCTTACACGATATGGTC
39563073 GTTTAGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 45 0.96
54 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (53 bp):
TTTCCATATGATGCCATAACCCACCAGTTATGGTCTTACACGATATGGTCTTC
Found at i:39564676 original size:17 final size:18
Alignment explanation
Indices: 39564616--39564676 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
39564606 ACCCTCCTAC
39564616 TATATTATAT-GATGTTATA
1 TATATTATATAG-T-TTATA
* *
39564635 TCATACTATATAGTATATAA
1 T-ATATTATATAGTTTAT-A
39564655 TATATTA-ATAGTTTATA
1 TATATTATATAGTTTATA
39564672 TATAT
1 TATAT
39564677 GCTGCAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.17
18 8 0.23
19 9 0.26
20 11 0.31
21 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (18 bp):
TATATTATATAGTTTATA
Found at i:39564852 original size:5 final size:5
Alignment explanation
Indices: 39564846--39564879 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
39564836 TCTACTATAC
* *
39564846 AATAC AATAC AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA
39564880 ATAGTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (5 bp):
AATAT
Found at i:39579895 original size:17 final size:17
Alignment explanation
Indices: 39579873--39579906 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39579863 TTGCTTGTAC
*
39579873 ATGAATAAATGAATAAA
1 ATGAATAAATAAATAAA
*
39579890 ATGAATACATAAATAAA
1 ATGAATAAATAAATAAA
39579907 GGCTCAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.24
Consensus pattern (17 bp):
ATGAATAAATAAATAAA
Found at i:39582150 original size:43 final size:44
Alignment explanation
Indices: 39582102--39582313 Score: 254
Period size: 43 Copynumber: 4.9 Consensus size: 44
39582092 TTCCGAGATA
* * *
39582102 TGATTACATGTAAGACGATGTCTGGGAAATTGGCATTGTAT-TG
1 TGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTATATG
39582145 TGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTAT-TG
1 TGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTATATG
* *
39582188 TGATTACGTGTAAGACGATGTCTAGGACATTGGCATCGT-TATA
1 TGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTATATG
* * **
39582231 TGATTTCGTGTAAGACCATGTCTAGGACATTGGCA-TAAATATG
1 TGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTATATG
* * * * * *
39582274 TGATAACATGTAAGACCATATCTAGGATA-TGACATTGTAT
1 TGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTAT
39582314 TATCTATATA
Statistics
Matches: 147, Mismatches: 19, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
42 5 0.03
43 142 0.97
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (44 bp):
TGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTATATG
Found at i:39585255 original size:35 final size:35
Alignment explanation
Indices: 39585164--39585330 Score: 165
Period size: 35 Copynumber: 4.6 Consensus size: 35
39585154 CATGGCAAAG
* *
39585164 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
39585199 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
* *
39585234 TGTGAAATATAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGC
*** * * *
39585274 TAACAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGC
**
39585309 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
39585331 TCAATGAGGA
Statistics
Matches: 113, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 81 0.72
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 27 0.24
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
Found at i:39585283 original size:75 final size:75
Alignment explanation
Indices: 39585164--39585334 Score: 203
Period size: 75 Copynumber: 2.4 Consensus size: 75
39585154 CATGGCAAAG
*** *
39585164 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATT-TC
*
39585223 CCATACTGAGC
65 CCATACCGAGC
*
39585234 TGTGAAATATAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATTTCC
*
39585299 CATACCGAGT
66 CATACCGAGC
**
39585309 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
39585335 TGAGGAAAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
70 17 0.20
73 4 0.05
74 5 0.06
75 59 0.69
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:39592744 original size:35 final size:35
Alignment explanation
Indices: 39592653--39592819 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
39592643 CATGGCAAAG
*
39592653 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
*
39592688 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
39592723 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGT
*** * *
39592763 TAACAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGT
**
39592798 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
39592820 TCAATGAGGA
Statistics
Matches: 115, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
34 1 0.01
35 82 0.71
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 28 0.24
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
Found at i:39592773 original size:75 final size:75
Alignment explanation
Indices: 39592653--39592823 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
39592643 CATGGCAAAG
*** *
39592653 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATT-TC
*
39592712 CCATACTGAGC
65 CCATACCGAGC
39592723 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATTTCC
*
39592788 CATACCGAGT
66 CATACCGAGC
**
39592798 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
39592824 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:39597727 original size:12 final size:12
Alignment explanation
Indices: 39597710--39597739 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39597700 ACAAAATCCG
39597710 AATTTAATTTCC
1 AATTTAATTTCC
*
39597722 AATTTAATTTCT
1 AATTTAATTTCC
39597734 AATTTA
1 AATTTA
39597740 TTTAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:39600596 original size:29 final size:28
Alignment explanation
Indices: 39600532--39600598 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
39600522 AGGTGCATTG
*
39600532 AACATAATCAGCCACAAGGACTCTCATA
1 AACAGAATCAGCCACAAGGACTCTCATA
* * *
39600560 TATAGAATCAGCTACAAAGG-CTCTCATAA
1 AACAGAATCAGCCAC-AAGGACTCTCAT-A
39600589 AACAGAATCA
1 AACAGAATCA
39600599 ACCATAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (28 bp):
AACAGAATCAGCCACAAGGACTCTCATA
Found at i:39601730 original size:19 final size:20
Alignment explanation
Indices: 39601706--39601745 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
39601696 AGGGGGAAAG
* *
39601706 TGGGAGAGAGTAAAAA-TTT
1 TGGGAGAAAATAAAAAGTTT
39601725 TGGGAGAAAATAAAAAGTTT
1 TGGGAGAAAATAAAAAGTTT
39601745 T
1 T
39601746 ACAGGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (20 bp):
TGGGAGAAAATAAAAAGTTT
Found at i:39604639 original size:10 final size:10
Alignment explanation
Indices: 39604626--39604655 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
39604616 TTAGTTTAGG
39604626 TTTAGTTTTC
1 TTTAGTTTTC
39604636 TTTAGGTTTTC
1 TTTA-GTTTTC
39604647 TTTAGTTTT
1 TTTAGTTTT
39604656 TCTCCGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.10, C:0.07, G:0.13, T:0.70
Consensus pattern (10 bp):
TTTAGTTTTC
Found at i:39606806 original size:38 final size:38
Alignment explanation
Indices: 39606755--39606831 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
39606745 ATTGATTCAT
39606755 TAACGTGGTGCTAAGTAGATATACCACGATTAAACATG
1 TAACGTGGTGCTAAGTAGATATACCACGATTAAACATG
* * * *
39606793 TAACGTGGTGCTAAGTGGATATGCCACGGTTATACATG
1 TAACGTGGTGCTAAGTAGATATACCACGATTAAACATG
39606831 T
1 T
39606832 TAATTTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTAGATATACCACGATTAAACATG
Found at i:39615538 original size:17 final size:17
Alignment explanation
Indices: 39615516--39615560 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
39615506 TTTTTATCAT
39615516 TTATCATTTATCGAGCA
1 TTATCATTTATCGAGCA
*
39615533 TTATCATTTATCGGGCA
1 TTATCATTTATCGAGCA
39615550 TTATCATTTAT
1 TTATCATTTAT
39615561 TTCAAGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (17 bp):
TTATCATTTATCGAGCA
Found at i:39616951 original size:22 final size:22
Alignment explanation
Indices: 39616906--39616961 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
39616896 TTGTCCGAGA
39616906 TATCGCGATATCCTCTTCTAGG
1 TATCGCGATATCCTCTTCTAGG
*
39616928 TATCGCAATATCCTCTTC-AGGG
1 TATCGCGATATCCTCTTCTA-GG
*
39616950 TATTGCGATATC
1 TATCGCGATATC
39616962 ACCTAAGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (22 bp):
TATCGCGATATCCTCTTCTAGG
Found at i:39617614 original size:43 final size:43
Alignment explanation
Indices: 39617559--39617657 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
39617549 TTATTTGAAA
* *
39617559 AAACGCCGCTAAAGGTCATGGCCTTTAGCAGCGCTTTTCCAAC
1 AAACACCGCTAAAGGTCACGGCCTTTAGCAGCGCTTTTCCAAC
* * *
39617602 AAACACGGCTAAAGGTCACGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACACCGCTAAAGGTCACGGCCTTTAGCAGCGCTTTTCCAAC
*
39617645 AAACGCCGCTAAA
1 AAACACCGCTAAA
39617658 CGCCGCTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.20
Consensus pattern (43 bp):
AAACACCGCTAAAGGTCACGGCCTTTAGCAGCGCTTTTCCAAC
Found at i:39617900 original size:19 final size:19
Alignment explanation
Indices: 39617855--39617901 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
39617845 ATCAAATTAA
*
39617855 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
39617874 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
39617893 AATAAAAAT
1 AATAAAAAT
39617902 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:39620258 original size:40 final size:39
Alignment explanation
Indices: 39620227--39620436 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
39620217 GGACTAAGAT
* *
39620227 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
39620267 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
39620307 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
39620347 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
39620387 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
39620426 CCGAAGGCATT
1 CCGAAGGCATT
39620437 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:39620390 original size:120 final size:120
Alignment explanation
Indices: 39620174--39620436 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
39620164 TTGAATGCTG
* *
39620174 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
39620238 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
39620294 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
39620357 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
39620413 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
39620437 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:39620456 original size:79 final size:80
Alignment explanation
Indices: 39620175--39620471 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
39620165 TGAATGCTGT
* ** * * * **
39620175 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
39620238 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
39620255 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
39620319 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
39620335 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
39620399 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
39620414 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
39620472 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:39637287 original size:16 final size:16
Alignment explanation
Indices: 39637266--39637299 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
39637256 AATGCTTAAG
39637266 TAATTA-TATTATATGT
1 TAATTATTATT-TATGT
39637282 TAATTATTATTTATGT
1 TAATTATTATTTATGT
39637298 TA
1 TA
39637300 TGAATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TAATTATTATTTATGT
Found at i:39637790 original size:13 final size:13
Alignment explanation
Indices: 39637772--39637849 Score: 68
Period size: 13 Copynumber: 5.8 Consensus size: 13
39637762 AAAAAAATGA
39637772 TATATGAAATGGT
1 TATATGAAATGGT
* *
39637785 TATATGAATTGAT
1 TATATGAAATGGT
39637798 TATATGGAAAAATGG-
1 TATAT-G--AAATGGT
* *
39637813 TATACGAAAGGGT
1 TATATGAAATGGT
*
39637826 TATATGAATTGGT
1 TATATGAAATGGT
39637839 TATATGGAAAT
1 TATAT-GAAAT
39637850 AGATATTTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
12 5 0.10
13 31 0.62
14 6 0.12
15 4 0.08
16 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.23, T:0.36
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:39637842 original size:41 final size:41
Alignment explanation
Indices: 39637744--39637848 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
39637734 AGAAAAATGA
* ** * *
39637744 TATATGAATTGGTTACATAAAAAAATGATATATGAAATGGT
1 TATATGAATTGGTTATATGGAAAAATGATATACGAAAGGGT
* *
39637785 TATATGAATTGATTATATGGAAAAATGGTATACGAAAGGGT
1 TATATGAATTGGTTATATGGAAAAATGATATACGAAAGGGT
39637826 TATATGAATTGGTTATATGGAAA
1 TATATGAATTGGTTATATGGAAA
39637849 TAGATATTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (41 bp):
TATATGAATTGGTTATATGGAAAAATGATATACGAAAGGGT
Found at i:39642488 original size:37 final size:38
Alignment explanation
Indices: 39642391--39642541 Score: 178
Period size: 38 Copynumber: 4.2 Consensus size: 38
39642381 TCGACAAGAT
*
39642391 CGAA-GCATTG-G-GAG-TACTATAT-CTGGCTAAGTC
1 CGAAGGCATTGTGCGAGTTACTATATCCGGGCTAAGTC
39642424 CTGAAGGCATTGTGCGAGTTACTATATCCGGGC-AAGTC
1 C-GAAGGCATTGTGCGAGTTACTATATCCGGGCTAAGTC
39642462 CGAAGGCATTTGTGCGAGTTAC-ATATCCGGGCTAAGTCC
1 CGAAGGCA-TTGTGCGAGTTACTATATCCGGGCTAAGT-C
* *
39642501 CGAAGGCATTGTGCGAG-TGCTA-ATCC-GGCTAAATC
1 CGAAGGCATTGTGCGAGTTACTATATCCGGGCTAAGTC
39642536 CGAAGG
1 CGAAGG
39642542 TACTGGTTTG
Statistics
Matches: 105, Mismatches: 3, Indels: 18
0.83 0.02 0.14
Matches are distributed among these distances:
33 1 0.01
34 3 0.03
35 13 0.12
36 8 0.08
37 26 0.25
38 41 0.39
39 13 0.12
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (38 bp):
CGAAGGCATTGTGCGAGTTACTATATCCGGGCTAAGTC
Found at i:39647792 original size:41 final size:41
Alignment explanation
Indices: 39647737--39647837 Score: 152
Period size: 41 Copynumber: 2.4 Consensus size: 41
39647727 AGACATGGTC
*
39647737 TAGCGGCAGCTTTCCCACAAACGCCGCTATTAGT-CATGGCTT
1 TAGCGGC-GCTTTCCCAAAAACGCCGCTA-TAGTCCATGGCTT
39647779 TAGCGGC-CTTTTCCCAAAAACGCCGCTATAGTCCATGGCTT
1 TAGCGGCGC-TTTCCCAAAAACGCCGCTATAGTCCATGGCTT
39647820 TAGCGGCGCTTTCCCAAA
1 TAGCGGCGCTTTCCCAAA
39647838 CATACCCGTA
Statistics
Matches: 55, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
40 5 0.09
41 42 0.76
42 8 0.15
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (41 bp):
TAGCGGCGCTTTCCCAAAAACGCCGCTATAGTCCATGGCTT
Found at i:39651199 original size:3 final size:3
Alignment explanation
Indices: 39651191--39651215 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39651181 GTTGGAGCTC
39651191 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
39651216 TGCAGTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:39654197 original size:3 final size:3
Alignment explanation
Indices: 39654179--39654243 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
39654169 ATATAATACC
* * * *
39654179 AAT AGT AAT AAT -AT AAT AAT GAC AA- AAGT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
39654223 AAT AAT AAT -AT CAAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT
39654244 GATGATGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
2 6 0.12
3 40 0.80
4 4 0.08
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:39656020 original size:89 final size:90
Alignment explanation
Indices: 39655920--39656167 Score: 276
Period size: 89 Copynumber: 2.8 Consensus size: 90
39655910 TGCCCTACTA
* *
39655920 CAACTTCAGGGAGGTAAGGTTTGTTTTGATCTACTCCACTGTAACTTC-GAGAGATAAGATCTGT
1 CAACTTCAGGGAGATAAGGTTTGTTTTGATCTACTCCACTGCAACTTCAGAGAGATAAGATCTGT
* *
39655984 GATTTAACTTCAATCTATTCCACTG
66 GATTTAACTTCAACCTACTCCACTG
* * * * * *
39656009 TAACTTTAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGA-
1 CAACTTCAGGGAGATAAGGTTTG-T-T-TTGA-TCTACTCCACTGCAACTTCAGAGAGATAAGAT
* * *
39656073 CT-CG---TAATTTCAACCTGCTCCACTG
62 CTGTGATTTAACTTCAACCTACTCCACTG
*
39656098 CAACTTCAGGGAGATAAGG-TTGTTTTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGT
1 CAACTTCAGGGAGATAAGGTTTGTTTTGATCTACTCCACTGCAACTTCAGAGAGATAAGATCTGT
*
39656162 AATTTA
66 GATTTA
39656168 GCTTTAAACT
Statistics
Matches: 127, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
84 29 0.23
85 5 0.04
86 1 0.01
87 1 0.01
88 3 0.02
89 52 0.41
90 1 0.01
91 1 0.01
92 4 0.03
93 19 0.15
94 11 0.09
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (90 bp):
CAACTTCAGGGAGATAAGGTTTGTTTTGATCTACTCCACTGCAACTTCAGAGAGATAAGATCTGT
GATTTAACTTCAACCTACTCCACTG
Found at i:39656098 original size:44 final size:42
Alignment explanation
Indices: 39655992--39656566 Score: 298
Period size: 45 Copynumber: 12.9 Consensus size: 42
39655982 GTGATTTAAC
** * * * *
39655992 TTCAATCTATTCCACTGTAACTTTAGGGAAATAAGATTTGCTAT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTG-TAT
* *
39656036 CTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGTAAT
1 -TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGT-AT
* * *
39656081 TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTGT-T
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAT
* * *
39656122 TT-GATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAAT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGT-AT
* * * * * *
39656165 TTAGCTTTAAACTGTTTCACTGCAATTTTAG-GTAAATAAGATTTGCTAT
1 TT--C---AATCTGCTCCACTGCAACTTCAGAG-AGATAAGA-TTG-TAT
* * * * * *
39656214 CTTTAGTCTGCTCCACTGCAACTCCAGGGAGATGAGACTTGT-G
1 -TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGTAT
* **
39656257 TT-GATCTGCTCTGCTGCAACTTCAGAGAGATAAGATCTGTAATTT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGT-A--T
* * * *
39656302 AGCTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTAT
1 ---TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTG-TAT
* *
39656349 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAT
1 -TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGTAT
* * *
39656393 CTTCGACCTGCTCTACTGCAACTTCAGAGAGATAAGATT-TAT
1 -TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAT
** * *
39656435 TTTGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTGTAAT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGT-AT
* * * * * *
39656479 TTAGCTTTAATCCGTTCCAGTGTAACTTCAGGGAAATAAGATTTGCTAT
1 TT--C---AATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTG-TAT
* * *
39656528 CTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGATT
1 -TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATT
39656567 TTTGACTTCA
Statistics
Matches: 407, Mismatches: 86, Indels: 75
0.72 0.15 0.13
Matches are distributed among these distances:
40 29 0.07
41 69 0.17
42 6 0.01
43 9 0.02
44 75 0.18
45 120 0.29
46 1 0.00
47 1 0.00
48 4 0.01
49 83 0.20
50 10 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (42 bp):
TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAT
Found at i:39656164 original size:84 final size:84
Alignment explanation
Indices: 39655902--39656469 Score: 267
Period size: 89 Copynumber: 6.4 Consensus size: 84
39655892 GAATTTATTG
* * *
39655902 TTTCAATCTGC-CCTACTACAACTTCAGGGAGGTAAGGTTTGTTTTGATCTACTCCACTGTAACT
1 TTTCAATCTGCTCC-ACTGCAACTTCAGGGAGATAAGG-TTGTTTTGATCTACTCCACTGCAACT
39655966 TC-GAGAGATAAGATCTGTGATTTAA
64 TCAGAGAGATAAGATC--TG---TAA
* ** * * * * * *
39655991 CTTCAATCTATTCCACTGTAACTTTAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCA
1 TTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG-GTTG-T-T-TTGA-TCTACTCCACTGCA
39656056 ACTTCAGAGAGATAAGA-CTCGTAA
61 ACTTCAGAGAGATAAGATCT-GTAA
* *
39656080 TTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTGTTTTGATCTACTCTACTGCAACTTC
1 TTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTGTTTTGATCTACTCCACTGCAACTTC
39656145 AGAGAGATAAGATCTGTAA
66 AGAGAGATAAGATCTGTAA
* * * * * * * * * *
39656164 TTTAGCTTTAAACTGTTTCACTGCAATTTTAGGTAAATAAGATTTGCTATCTTTAGTCTGCTCCA
1 TTT--C---AATCTGCTCCACTGCAACTTCAGGGAGATAAG-GTTG-T-T-TTGA-TCTACTCCA
* * *
39656229 CTGCAACTCCAGGGAGATGAGA-CTTGT--
56 CTGCAACTTCAGAGAGATAAGATC-TGTAA
* * ** * * **
39656256 GTT-GATCTGCTCTGCTGCAACTTCAGAGAGATAAGATCTGTAATTTAGCTTCAATCTGTTCCAC
1 TTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGT-TGT--TTT-G-----ATCTACTCCAC
* * * *
39656320 TGCAACTTTAGGGAAATAAGATTTGCT-A
57 TGCAACTTCAGAGAGATAAGATCTG-TAA
* * * * *
39656348 TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCGACCTGCTCTACTGCA
1 T-TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG-GTTGT-T-TT-GATCTACTCCACTGCA
39656413 ACTTCAGAGAGATAAGAT-T-T-A
61 ACTTCAGAGAGATAAGATCTGTAA
** * **
39656434 TTTTGATCTGCTCTACTGCAACTTCAAAGAGATAAG
1 TTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
39656470 ATCTGTAATT
Statistics
Matches: 367, Mismatches: 77, Indels: 74
0.71 0.15 0.14
Matches are distributed among these distances:
84 36 0.10
85 38 0.10
86 30 0.08
87 1 0.00
88 4 0.01
89 112 0.31
90 34 0.09
91 5 0.01
92 7 0.02
93 26 0.07
94 73 0.20
95 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (84 bp):
TTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTGTTTTGATCTACTCCACTGCAACTTC
AGAGAGATAAGATCTGTAA
Found at i:39656204 original size:178 final size:178
Alignment explanation
Indices: 39655902--39656252 Score: 508
Period size: 178 Copynumber: 2.0 Consensus size: 178
39655892 GAATTTATTG
* * *
39655902 TTTCAATCTGCCCTACTACAACTTCAGGGAGGTAAGGTTTGTTTTGATCTACTCCACTGTAACTT
1 TTTCAACCTGCCCTACTACAACTTCAGGGAGATAAGGTTTGTTTTGATCTACTCCACTGCAACTT
* * *
39655967 CGAGAGATAAGATCTGTGATTTAACTTCAATCTATTCCACTGTAACTTTAGGGAAATAAGATTTG
66 CGAGAGATAAGATCTGTAATTTAACTTCAAACTATTCCACTGCAACTTTAGGGAAATAAGATTTG
*
39656032 CTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGTAA
131 CTATCTTCAGTCTGCTCCACTGCAACTCCAGAGAGATAAGACTCGTAA
* *
39656080 TTTCAACCTGCTCC-ACTGCAACTTCAGGGAGATAAGG-TTGTTTTGATCTACTCTACTGCAACT
1 TTTCAACCTGC-CCTACTACAACTTCAGGGAGATAAGGTTTGTTTTGATCTACTCCACTGCAACT
* * * * * *
39656143 TCAGAGAGATAAGATCTGTAATTTAGCTTTAAACTGTTTCACTGCAATTTTAGGTAAATAAGATT
65 TC-GAGAGATAAGATCTGTAATTTAACTTCAAACTATTCCACTGCAACTTTAGGGAAATAAGATT
* * *
39656208 TGCTATCTTTAGTCTGCTCCACTGCAACTCCAGGGAGATGAGACT
129 TGCTATCTTCAGTCTGCTCCACTGCAACTCCAGAGAGATAAGACT
39656253 TGTGTTGATC
Statistics
Matches: 153, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
177 26 0.17
178 125 0.82
179 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (178 bp):
TTTCAACCTGCCCTACTACAACTTCAGGGAGATAAGGTTTGTTTTGATCTACTCCACTGCAACTT
CGAGAGATAAGATCTGTAATTTAACTTCAAACTATTCCACTGCAACTTTAGGGAAATAAGATTTG
CTATCTTCAGTCTGCTCCACTGCAACTCCAGAGAGATAAGACTCGTAA
Found at i:39656289 original size:135 final size:135
Alignment explanation
Indices: 39656087--39656430 Score: 528
Period size: 135 Copynumber: 2.5 Consensus size: 135
39656077 TAATTTCAAC
* * *
39656087 CTGCTCCACTGCAACTTCAGGGAGATAAG-GTTGTTTTGATCTACTCTACTGCAACTTCAGAGAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCTTGATCTGCTCTACTGCAACTTCAGAGAG
* * * *
39656151 ATAAGATCTGTAATTTAGCTTTAAACTGTTTCACTGCAATTTTAGGTAAATAAGATTTGCTATCT
66 ATAAGATCTGTAATTTAGCTTCAAACTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCT
*
39656216 TTAGT
131 TCAGT
* * * *
39656221 CTGCTCCACTGCAACTCCAGGGAGATGAGACTTGTGTTGATCTGCTCTGCTGCAACTTCAGAGAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCTTGATCTGCTCTACTGCAACTTCAGAGAG
*
39656286 ATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCT
66 ATAAGATCTGTAATTTAGCTTCAAACTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCT
39656351 TCAGT
131 TCAGT
*
39656356 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCGACCTGCTCTACTGCAACTTCAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG--TCTT-GATCTGCTCTACTGCAACTTCAGA
39656421 GAGATAAGAT
63 GAGATAAGAT
39656431 TTATTTTGAT
Statistics
Matches: 189, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
134 27 0.14
135 127 0.67
137 3 0.02
138 32 0.17
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (135 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCTTGATCTGCTCTACTGCAACTTCAGAGAG
ATAAGATCTGTAATTTAGCTTCAAACTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCT
TCAGT
Found at i:39656382 original size:94 final size:94
Alignment explanation
Indices: 39656261--39656565 Score: 351
Period size: 94 Copynumber: 3.3 Consensus size: 94
39656251 CTTGTGTTGA
**
39656261 TCTGCTCTGCTGCAACTTCAGAGAGATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAAC
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAAC
*
39656326 TTTAGGGAAATAAGATTTGCTATCTTCAG
66 TTCAGGGAAATAAGATTTGCTATCTTCAG
* * * * *
39656355 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTGT-A--T--CTTCGACCTGCTCTACTGCAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATC-TGTAATTTAGCTTCAATCTGTTCCACTGCAA
* * * *
39656414 CTTCAGAGAGATAAGA-TT--TATTTTGA-
65 CTTCAGGGAAATAAGATTTGCTATCTTCAG
* * * * * *
39656440 TCTGCTCTACTGCAACTTCAAAGAGATAAGATCTGTAATTTAGCTTTAATCCGTTCCAGTGTAAC
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAAC
39656505 TTCAGGGAAATAAGATTTGCTATCTTCAG
66 TTCAGGGAAATAAGATTTGCTATCTTCAG
* *
39656534 TCTGCTCCGCTGCAACTTCAGGGAGATAAGAT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGAT
39656566 TTTTGACTTC
Statistics
Matches: 169, Mismatches: 31, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
85 31 0.18
86 8 0.05
88 3 0.02
89 30 0.18
90 27 0.16
91 3 0.02
93 8 0.05
94 59 0.35
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (94 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAAC
TTCAGGGAAATAAGATTTGCTATCTTCAG
Found at i:39656446 original size:179 final size:179
Alignment explanation
Indices: 39656221--39656564 Score: 553
Period size: 179 Copynumber: 1.9 Consensus size: 179
39656211 TATCTTTAGT
* * * * *
39656221 CTGCTCCACTGCAACTCCAGGGAGATGAGACTTGTGTTGATCTGCTCTGCTGCAACTTCAGAGAG
1 CTGCTCCACTGCAACTCCAGAGAGATAAGACTTATGTTGATCTGCTCTACTGCAACTTCAAAGAG
* *
39656286 ATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCT
66 ATAAGATCTGTAATTTAGCTTCAATCCGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCT
39656351 TCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCGAC
131 TCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCGAC
* * * *
39656400 CTGCTCTACTGCAACTTCAGAGAGATAAGATTTATTTTGATCTGCTCTACTGCAACTTCAAAGAG
1 CTGCTCCACTGCAACTCCAGAGAGATAAGACTTATGTTGATCTGCTCTACTGCAACTTCAAAGAG
* * *
39656465 ATAAGATCTGTAATTTAGCTTTAATCCGTTCCAGTGTAACTTCAGGGAAATAAGATTTGCTATCT
66 ATAAGATCTGTAATTTAGCTTCAATCCGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCT
*
39656530 TCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGA
131 TCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
39656565 TTTTTGACTT
Statistics
Matches: 150, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
179 150 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (179 bp):
CTGCTCCACTGCAACTCCAGAGAGATAAGACTTATGTTGATCTGCTCTACTGCAACTTCAAAGAG
ATAAGATCTGTAATTTAGCTTCAATCCGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCT
TCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCGAC
Found at i:39656696 original size:68 final size:68
Alignment explanation
Indices: 39656587--39657529 Score: 1354
Period size: 68 Copynumber: 13.9 Consensus size: 68
39656577 ATCTACTCCG
* * * ** ***
39656587 CTGAAAGTTCAAGGAGATCTACTATGGCTTCGAGCCGCTCCAATATCATTTCAGGGAGAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
39656652 CCA
66 CCA
* * * * * *
39656655 CTGAAACTTCAAGGAGATCTGTTATGGCTTCTAGCCACTCCAATGCCATTTCAGGAAGAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
39656720 CCA
66 CCA
* * *
39656723 CTGAAACTTCAAGGAGATCTACTATGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
39656788 CCA
66 CCA
* * * *
39656791 CTGAAACTTCAAGGAGATCTGTTGTGACTTTTAGCCGCTCCAACGCTATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
*
39656856 CCG
66 CCA
* * *
39656859 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGTCGCTCCAACGCCATTTCAGGAAGAAGAAAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
*
39656924 CCG
66 CCA
* * *
39656927 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGTCATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
*
39656992 CCG
66 CCA
* * * *
39656995 CTAAAACCTCAAGGAGATCTACTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
39657060 CCA
66 CCA
*
39657063 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACTCCATTTCAGGG-GAGAGAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGA-AGAGA
*
39657127 TCCT
65 TCCA
* * *
39657131 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCACTTCAACGCCATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
39657196 CCA
66 CCA
*
39657199 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACTCCATTTCAGGG-GAGAGAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGA-AGAGA
*
39657263 TCCT
65 TCCA
* * * *
39657267 CTGAAACTTCAAGAAGATCTGCTGTGGCTTTTAGCCACTCCAATGCCATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
39657332 CCA
66 CCA
* * *
39657335 CTGAAACTTCAAGAAGATCTGCTGTGGCTTTTAGCCACTCCAACGCCATTTTAGGG-GAAAGAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAG-AAGAGA
39657399 TCCA
65 TCCA
* *
39657403 CTGAAACTTCAAGTAGATCTGCTGTGGTTTTTAGCCGCTCCAACGCCATTTCAGGG-GAAAGAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAG-AAGAGA
*
39657467 TCCT
65 TCCA
*
39657471 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGAGAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGA
39657530 GGGGATTGGT
Statistics
Matches: 796, Mismatches: 73, Indels: 12
0.90 0.08 0.01
Matches are distributed among these distances:
67 2 0.00
68 791 0.99
69 3 0.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (68 bp):
CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
CCA
Found at i:39665115 original size:63 final size:65
Alignment explanation
Indices: 39665033--39665169 Score: 251
Period size: 63 Copynumber: 2.1 Consensus size: 65
39665023 TCTGTAGTTT
*
39665033 AAAAGAAAACTATGTAAAGGATATAAATAAATAAAATGATAATAACAAGAATAAAATACGT-AAA
1 AAAATAAAACTATGTAAAGGATATAAATAAATAAAATGATAATAACAAGAATAAAATACGTAAAA
39665097 AAAATAAAA-TATGTAAAGGATATAAATAAATAAAATGATAATAACAAGAATAAAATACGTAAAA
1 AAAATAAAACTATGTAAAGGATATAAATAAATAAAATGATAATAACAAGAATAAAATACGTAAAA
39665161 AAAATAAAA
1 AAAATAAAA
39665170 GTAACATTAA
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
63 51 0.72
64 20 0.28
ACGTcount: A:0.66, C:0.04, G:0.09, T:0.20
Consensus pattern (65 bp):
AAAATAAAACTATGTAAAGGATATAAATAAATAAAATGATAATAACAAGAATAAAATACGTAAAA
Found at i:39665165 original size:33 final size:33
Alignment explanation
Indices: 39665060--39665165 Score: 98
Period size: 33 Copynumber: 3.3 Consensus size: 33
39665050 AGGATATAAA
*
39665060 TAAATAAAATGATAATAACAAGAATAAAATACG
1 TAAAAAAAATGATAATAACAAGAATAAAATACG
* * *
39665093 T-AAAAAAAT-AAAATATGTA-AAGGATATAA-A--
1 TAAAAAAAATGATAATA---ACAAGAATAAAATACG
*
39665123 TAAATAAAATGATAATAACAAGAATAAAATACG
1 TAAAAAAAATGATAATAACAAGAATAAAATACG
39665156 TAAAAAAAAT
1 TAAAAAAAAT
39665166 AAAAGTAACA
Statistics
Matches: 55, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
29 1 0.02
30 9 0.16
31 13 0.24
32 13 0.24
33 18 0.33
34 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.22
Consensus pattern (33 bp):
TAAAAAAAATGATAATAACAAGAATAAAATACG
Found at i:39665322 original size:3 final size:3
Alignment explanation
Indices: 39665304--39665365 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
39665294 ATATAATACC
* *
39665304 AAT AGT AAT AAT -AT AAT AAT GAA- AA- AAGT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA-T AAT AAT AAT AAT AAT
39665348 AAT AAT -AT CAAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT
39665366 TATGATGATG
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
2 8 0.16
3 35 0.71
4 6 0.12
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:39665342 original size:21 final size:21
Alignment explanation
Indices: 39665316--39665365 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
39665306 TAGTAATAAT
39665316 ATAATAATGAA-AA-AAGTAACA
1 ATAATAAT-AATAATAA-TAACA
*
39665337 ATAATAATAATAATAATATCA
1 ATAATAATAATAATAATAACA
39665358 ATAATAAT
1 ATAATAAT
39665366 TATGATGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (21 bp):
ATAATAATAATAATAATAACA
Found at i:39667380 original size:3 final size:3
Alignment explanation
Indices: 39667374--39667423 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
39667364 TTTTTCTCTT
39667374 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39667422 TT
1 TT
39667424 TTTTACTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39668437 original size:15 final size:14
Alignment explanation
Indices: 39668418--39668457 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
39668408 CCATGGCCAT
39668418 TAAACCTTAAACCA
1 TAAACCTTAAACCA
*
39668432 TAAAACCCTAAACCA
1 T-AAACCTTAAACCA
*
39668447 TAGACCTTAAA
1 TAAACCTTAAA
39668458 TATTAAACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.20
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:39668635 original size:16 final size:15
Alignment explanation
Indices: 39668580--39668636 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 15
39668570 ATATGATGTT
* *
39668580 TTTTGGGGTTTAAGG
1 TTTTAGGGTTTATGG
* *
39668595 TTTTAGGGGTTATAG
1 TTTTAGGGTTTATGG
*
39668610 -TTTAGTGTTTATGG
1 TTTTAGGGTTTATGG
39668624 TTTTTAGGGTTTA
1 -TTTTAGGGTTTA
39668637 GGGGTTATAG
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
14 11 0.34
15 11 0.34
16 10 0.31
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.53
Consensus pattern (15 bp):
TTTTAGGGTTTATGG
Found at i:39668637 original size:37 final size:39
Alignment explanation
Indices: 39668588--39668678 Score: 141
Period size: 37 Copynumber: 2.4 Consensus size: 39
39668578 TTTTTTGGGG
* *
39668588 TTTAAGGTTTTAGGGGTTATAGTTTAGTGTTTATG-GTT
1 TTTAAGGGTTTAGGGGTTATAGATTAGTGTTTATGAGTT
*
39668626 TTT-AGGGTTTAGGGGTTATAGATTAGTGTTTATGATTT
1 TTTAAGGGTTTAGGGGTTATAGATTAGTGTTTATGAGTT
39668664 TTTAAGGGTTTAGGG
1 TTTAAGGGTTTAGGG
39668679 TTTTAGGGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
37 29 0.60
38 8 0.17
39 11 0.23
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (39 bp):
TTTAAGGGTTTAGGGGTTATAGATTAGTGTTTATGAGTT
Found at i:39668792 original size:40 final size:40
Alignment explanation
Indices: 39668718--39668891 Score: 267
Period size: 41 Copynumber: 4.3 Consensus size: 40
39668708 TTTTGACCAT
* *
39668718 AAACGCTGCTATTGCTCTGGTTTTTAGCGGCGTTTTTGGTA
1 AAACGCCGCTATTGCTCT-ATTTTTAGCGGCGTTTTTGGTA
* *
39668759 AAACGCTGCTATTGCTCTGTTTTTAGCGGCGTTTTTGGTAA
1 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGGT-A
* *
39668800 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTGTTTGCTA
1 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGGTA
39668840 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGGATA
1 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGG-TA
39668881 AAACGCCGCTA
1 AAACGCCGCTA
39668892 AAAACACTGC
Statistics
Matches: 125, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 58 0.46
41 67 0.54
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (40 bp):
AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGGTA
Found at i:39668857 original size:81 final size:82
Alignment explanation
Indices: 39668697--39668891 Score: 272
Period size: 81 Copynumber: 2.4 Consensus size: 82
39668687 GTTATATGAC
* * * * *
39668697 TTTTAGCGGCG-TTTT-GACCATAAACGCTGCTATTGCTCTGGTTTTTAGCGGCGTTTTTGGTAA
1 TTTTAGCGGCGTTTTTGGA-TA-AAACGCCGCTATTGCTCTGATTTTTAGCGGCGTGTTTGCTAA
* *
39668760 AACGCTGCTATTGCTCTGT
64 AACGCCGCTATTGCTCTAT
39668779 TTTTAGCGGCGTTTTTGG-TAAAAACGCCGCTATTGCTCT-ATTTTTAGCGGCGTGTTTGCTAAA
1 TTTTAGCGGCGTTTTTGGAT-AAAACGCCGCTATTGCTCTGATTTTTAGCGGCGTGTTTGCTAAA
39668842 ACGCCGCTATTGCTCTAT
65 ACGCCGCTATTGCTCTAT
39668860 TTTTAGCGGCGTTTTTGGATAAAACGCCGCTA
1 TTTTAGCGGCGTTTTTGGATAAAACGCCGCTA
39668892 AAAACACTGC
Statistics
Matches: 102, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
81 67 0.66
82 29 0.28
83 5 0.05
84 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (82 bp):
TTTTAGCGGCGTTTTTGGATAAAACGCCGCTATTGCTCTGATTTTTAGCGGCGTGTTTGCTAAAA
CGCCGCTATTGCTCTAT
Found at i:39675005 original size:56 final size:56
Alignment explanation
Indices: 39674907--39675178 Score: 204
Period size: 56 Copynumber: 4.9 Consensus size: 56
39674897 TCCCTTTCAA
* * * * * * * *
39674907 AGATAGCCACAAAGGCTTCATTTTACAAATATCGCAACAAAGGCTTCCTTTAACAG
1 AGATCGCCACAAAGGCTTCCTTTAATAGAGATCACCACAAAGGCTTCCTTTAACAG
* * * ** *
39674963 AGAACGCCACGAATGCTTCCTTTAATAGAGATCACCGA-AAAGGAATCCTTTAACAA
1 AGATCGCCACAAAGGCTTCCTTTAATAGAGATCACC-ACAAAGGCTTCCTTTAACAG
* * * * * * *
39675019 AGCTCGCTACAAAGGCTTCTTTTAACAGCGATCATCACAAAGGCTTTCTTTAACAG
1 AGATCGCCACAAAGGCTTCCTTTAATAGAGATCACCACAAAGGCTTCCTTTAACAG
* * * * * * * *
39675075 AGATCACCACAAAGGCTTCCATTAATGGAGGTCGCTACAAAAGATTCCTTTAACAG
1 AGATCGCCACAAAGGCTTCCTTTAATAGAGATCACCACAAAGGCTTCCTTTAACAG
* * * * * * *
39675131 AGATCACCACAAAAGATTCCTTTAACAAATATTACCACAAAGGCTTCC
1 AGATCGCCACAAAGGCTTCCTTTAATAGAGATCACCACAAAGGCTTCC
39675179 CTTTTCTTGG
Statistics
Matches: 159, Mismatches: 55, Indels: 4
0.73 0.25 0.02
Matches are distributed among these distances:
55 1 0.01
56 157 0.99
57 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (56 bp):
AGATCGCCACAAAGGCTTCCTTTAATAGAGATCACCACAAAGGCTTCCTTTAACAG
Found at i:39675031 original size:84 final size:84
Alignment explanation
Indices: 39674938--39675173 Score: 231
Period size: 84 Copynumber: 2.8 Consensus size: 84
39674928 TTTACAAATA
* * * * *
39674938 TCGCAACAAAGGCTTCCTTTAACAGAGAACGCCACGAATGCTTCCTTTAATAGAGATCACCGA-A
1 TCGCTACAAAGGCTTCCTTTAACAGAGAACACCACAAAGGCTTCCTTTAACAGAGATCACC-ACA
*
39675002 AAGGAATCCTTTAACAAAGC
65 AAGGAATCCATTAACAAAGC
* * * * *
39675022 TCGCTACAAAGGCTTCTTTTAACAGCGATCATCACAAAGGCTTTCTTTAACAGAGATCACCACAA
1 TCGCTACAAAGGCTTCCTTTAACAGAGAACACCACAAAGGCTTCCTTTAACAGAGATCACCACAA
** *** *
39675087 AGGCTTCCATTAATGGAGG
66 AGGAATCCATTAACAAAGC
* * * * * * * *
39675106 TCGCTACAAAAGATTCCTTTAACAGAGATCACCACAAAAGATTCCTTTAACAAATATTACCACAA
1 TCGCTACAAAGGCTTCCTTTAACAGAGAACACCACAAAGGCTTCCTTTAACAGAGATCACCACAA
39675171 AGG
66 AGG
39675174 CTTCCCTTTT
Statistics
Matches: 123, Mismatches: 28, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
83 1 0.01
84 122 0.99
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (84 bp):
TCGCTACAAAGGCTTCCTTTAACAGAGAACACCACAAAGGCTTCCTTTAACAGAGATCACCACAA
AGGAATCCATTAACAAAGC
Found at i:39675058 original size:28 final size:29
Alignment explanation
Indices: 39674913--39675182 Score: 166
Period size: 28 Copynumber: 9.6 Consensus size: 29
39674903 TCAAAGATAG
* * *
39674913 CCACAAAGGCTTCAT-TTT-ACAAATATCG
1 CCACAAAGGCTTC-TCTTTAACAGAGATCA
* * *
39674941 CAACAAAGGCTTC-CTTTAACAGAGAACG
1 CCACAAAGGCTTCTCTTTAACAGAGATCA
* * *
39674969 CCACGAATGCTTC-CTTTAATAGAGATCA
1 CCACAAAGGCTTCTCTTTAACAGAGATCA
** * * *
39674997 CCGA-AAAGGAATC-CTTTAACAAAGCTCG
1 CC-ACAAAGGCTTCTCTTTAACAGAGATCA
* *
39675025 CTACAAAGGCTTCT-TTTAACAGCGATCA
1 CCACAAAGGCTTCTCTTTAACAGAGATCA
*
39675053 TCACAAAGGCTT-TCTTTAACAGAGATCA
1 CCACAAAGGCTTCTCTTTAACAGAGATCA
* ** * *
39675081 CCACAAAGGCTTC-CATTAATGGAGGTCG
1 CCACAAAGGCTTCTCTTTAACAGAGATCA
* * *
39675109 CTACAAAAGATTC-CTTTAACAGAGATCA
1 CCACAAAGGCTTCTCTTTAACAGAGATCA
* * * * *
39675137 CCACAAAAGATTC-CTTTAACAAATATTA
1 CCACAAAGGCTTCTCTTTAACAGAGATCA
*
39675165 CCACAAAGGCTTCCCTTT
1 CCACAAAGGCTTCTCTTT
39675183 TCTTGGTGAT
Statistics
Matches: 186, Mismatches: 48, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
27 5 0.03
28 176 0.95
29 5 0.03
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (29 bp):
CCACAAAGGCTTCTCTTTAACAGAGATCA
Found at i:39675387 original size:53 final size:53
Alignment explanation
Indices: 39675300--39675447 Score: 152
Period size: 53 Copynumber: 2.8 Consensus size: 53
39675290 AAATATTTCC
** * *
39675300 ATATGATGTCATAACCCACCAGTTACAGTCTTACACGATATGGTCTTCTTTTT
1 ATATGATACCATAACCCACCAGTTACAATCTTACACGATATGATCTTCTTTTT
* * * * ***
39675353 ATATGATACCATACCCCACCAGTTATAATTTTACATGATATGATCTTCTTCCC
1 ATATGATACCATAACCCACCAGTTACAATCTTACACGATATGATCTTCTTTTT
** * * *
39675406 ATATGATGTCATAACCCACCAATTACGATCTTACACAATATG
1 ATATGATACCATAACCCACCAGTTACAATCTTACACGATATG
39675448 GTCCATTAGT
Statistics
Matches: 75, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
53 75 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (53 bp):
ATATGATACCATAACCCACCAGTTACAATCTTACACGATATGATCTTCTTTTT
Found at i:39678136 original size:25 final size:24
Alignment explanation
Indices: 39678101--39678152 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
39678091 ACAAACACAA
39678101 CTCTTTATGAGCGTCCTGATATAGG
1 CTCTTTATGAGCGTCCTGATAT-GG
* *
39678126 CTCTTTTTGAGCTTCCTGATATGG
1 CTCTTTATGAGCGTCCTGATATGG
39678150 CTC
1 CTC
39678153 GCTTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (24 bp):
CTCTTTATGAGCGTCCTGATATGG
Found at i:39682052 original size:54 final size:54
Alignment explanation
Indices: 39681932--39682060 Score: 147
Period size: 54 Copynumber: 2.4 Consensus size: 54
39681922 AGTTTGTATA
* *
39681932 AGATATTATAA-TTATTTAATTTTATTTTTACCTAATTAATATTCAGTTATACTT
1 AGATATT-TAATTTATTAAATTTTATTTTTACCTAATTAATATTCAGTTATAATT
* * * *
39681986 AGATATTAAATTTATTAAATTTTATTTTTA-TTAAATTAATATTTAGATTCTAATT
1 AGATATTTAATTTATTAAATTTTATTTTTACCT-AATTAATATTCAG-TTATAATT
*
39682041 TG-TATTTAATTTATTAAATT
1 AGATATTTAATTTATTAAATT
39682061 AAACTAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
53 3 0.05
54 54 0.84
55 7 0.11
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (54 bp):
AGATATTTAATTTATTAAATTTTATTTTTACCTAATTAATATTCAGTTATAATT
Found at i:39682433 original size:19 final size:19
Alignment explanation
Indices: 39682409--39682449 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
39682399 ATCTTTATGA
*
39682409 GAAACACACTTCAGTTGGT
1 GAAACACACTTCAGTTGAT
39682428 GAAACACACTTCAGTTGAT
1 GAAACACACTTCAGTTGAT
39682447 GAA
1 GAA
39682450 CTTTTCTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (19 bp):
GAAACACACTTCAGTTGAT
Found at i:39690102 original size:23 final size:23
Alignment explanation
Indices: 39690047--39690093 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39690037 TTGGCTAATG
39690047 TGGCCTATATGTCTTATGTTGTT
1 TGGCCTATATGTCTTATGTTGTT
39690070 TGGCCTATATGTCTTATGTTGTT
1 TGGCCTATATGTCTTATGTTGTT
39690093 T
1 T
39690094 TGGTTATATA
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:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (23 bp):
TGGCCTATATGTCTTATGTTGTT
Found at i:39691116 original size:44 final size:44
Alignment explanation
Indices: 39691016--39691160 Score: 179
Period size: 43 Copynumber: 3.3 Consensus size: 44
39691006 CGTTTATTTA
* * * * *
39691016 AAAAACACCGCTAAAGATCATGACATTTAGCGACGTTTTTTCC-
1 AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTCCT
* *
39691059 ACAAACGCTGCTAAAGATCACGACCTTTAGCGGCGCTTTTTCCT
1 AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTCCT
* *
39691103 ATAAACGCCGCTAAAGATCACGACCTTTAGCGGCAC-TTTT-CT
1 AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTCCT
39691145 CAAAAACGCCGCTAAA
1 -AAAAACGCCGCTAAA
39691161 AGTCATGAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
42 2 0.02
43 54 0.61
44 33 0.37
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (44 bp):
AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTCCT
Found at i:39695886 original size:18 final size:19
Alignment explanation
Indices: 39695860--39695903 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
39695850 CTAATCTCTA
39695860 TTTTATATTTTA-TTTTAT
1 TTTTATATTTTATTTTTAT
*
39695878 TTTTGTATTTTATTTTTAT
1 TTTTATATTTTATTTTTAT
39695897 TTATTAT
1 TT-TTAT
39695904 CAATGTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.50
19 8 0.36
20 3 0.14
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTATATTTTATTTTTAT
Found at i:39695888 original size:13 final size:12
Alignment explanation
Indices: 39695858--39695898 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
39695848 CACTAATCTC
*
39695858 TATTTTATATTT
1 TATTTTATTTTT
39695870 TATTTTATTTTT
1 TATTTTATTTTT
39695882 GTATTTTA-TTTT
1 -TATTTTATTTTT
39695894 TATTT
1 TATTT
39695899 ATTATCAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 15 0.56
13 7 0.26
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TATTTTATTTTT
Found at i:39696750 original size:15 final size:14
Alignment explanation
Indices: 39696730--39696770 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
39696720 ATGTGATGTT
39696730 TTTTAGGGTTTAGTA
1 TTTTAGGGTTTA-TA
*
39696745 TTTTAGGGGTTATA
1 TTTTAGGGTTTATA
*
39696759 GTTTAGGGTTTA
1 TTTTAGGGTTTA
39696771 AGATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (14 bp):
TTTTAGGGTTTATA
Found at i:39696796 original size:54 final size:53
Alignment explanation
Indices: 39696731--39696847 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 53
39696721 TGTGATGTTT
* *
39696731 TTTAGGGTTTAGTATTTT-AGGGGTTATAGTTTAGGGTTTAAGATTTTTTAAGG
1 TTTAGGGTTTAGTATTTTAAGGAG-TATAGATTAGGGTTTAAGATTTTTTAAGG
* * * **
39696784 TTTAGGAGTTTAGTGTTTTAAGGAGTATAGATTAGTGTTTATGATTTTTTGGGG
1 TTTAGG-GTTTAGTATTTTAAGGAGTATAGATTAGGGTTTAAGATTTTTTAAGG
*
39696838 TTTAAGGTTT
1 TTTAGGGTTT
39696848 TAGGGGTTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 10 0.19
54 40 0.74
55 4 0.07
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (53 bp):
TTTAGGGTTTAGTATTTTAAGGAGTATAGATTAGGGTTTAAGATTTTTTAAGG
Found at i:39696850 original size:54 final size:54
Alignment explanation
Indices: 39696731--39696833 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
39696721 TGTGATGTTT
* *
39696731 TTTAGG-GTTTAGTATTTTAGGGGTTATAGTTTAGGGTTTAAGATTTTTTAAGG
1 TTTAGGAGTTTAGTATTTTAGGAGTTATAGATTAGGGTTTAAGATTTTTTAAGG
* * *
39696784 TTTAGGAGTTTAGTGTTTTAAGGAG-TATAGATTAGTGTTTATGATTTTTT
1 TTTAGGAGTTTAGTATTTT-AGGAGTTATAGATTAGGGTTTAAGATTTTTT
39696834 GGGGTTTAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 6 0.14
54 33 0.77
55 4 0.09
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.50
Consensus pattern (54 bp):
TTTAGGAGTTTAGTATTTTAGGAGTTATAGATTAGGGTTTAAGATTTTTTAAGG
Found at i:39697000 original size:40 final size:40
Alignment explanation
Indices: 39696863--39697006 Score: 227
Period size: 41 Copynumber: 3.5 Consensus size: 40
39696853 GTTATATGAT
39696863 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGCC
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTG-C
*
39696904 TTTTAGAGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGC
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GC
*
39696945 TTTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCTAG-
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GC
*
39696985 TTTTAGCGGCGTTTTAACAAAA
1 TTTTAGCGGCGTTTTACCAAAA
39697007 CACCTCTATT
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
40 21 0.22
41 75 0.77
42 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGC
Found at i:39698666 original size:29 final size:29
Alignment explanation
Indices: 39698607--39698666 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
39698597 AGTGATTTGT
* *
39698607 TAAAATTGAATCAAATCAAAATTTCATTA
1 TAAAATTGAATCAAATCAAAAGTTAATTA
39698636 TAAAATTGAA-CGAAATC-AAAGTTAATGTA
1 TAAAATTGAATC-AAATCAAAAGTTAAT-TA
39698665 TA
1 TA
39698667 GTTTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (29 bp):
TAAAATTGAATCAAATCAAAAGTTAATTA
Found at i:39711232 original size:18 final size:18
Alignment explanation
Indices: 39711209--39711301 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
39711199 CCCAACTACT
*
39711209 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
**
39711227 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
*
39711245 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
39711263 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
39711281 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
39711299 GTA
1 GTA
39711302 AACGGTCGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:39711261 original size:36 final size:36
Alignment explanation
Indices: 39711209--39711301 Score: 159
Period size: 36 Copynumber: 2.6 Consensus size: 36
39711199 CCCAACTACT
* *
39711209 GTATACGTGAACAGTACCGTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
39711245 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
39711281 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
39711302 AACGGTCGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:39713447 original size:19 final size:18
Alignment explanation
Indices: 39713414--39713449 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39713404 AAAATTTATT
*
39713414 AAAATAAAAATTATAAAA
1 AAAATAAAAAATATAAAA
39713432 AAAATAAAAAAATATAAA
1 AAAAT-AAAAAATATAAA
39713450 TTATTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAATAAAAAATATAAAA
Found at i:39713533 original size:21 final size:22
Alignment explanation
Indices: 39713483--39713533 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
39713473 TTTTAAATTT
39713483 ATATTTAAAATTTAGAAAATAA
1 ATATTTAAAATTTAGAAAATAA
39713505 AT-TGTTAAAATTATA-AAAA-AA
1 ATAT-TTAAAATT-TAGAAAATAA
39713526 ATATTTAA
1 ATATTTAA
39713534 TTTGTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 9 0.35
22 15 0.58
23 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
ATATTTAAAATTTAGAAAATAA
Found at i:39714354 original size:26 final size:26
Alignment explanation
Indices: 39714317--39714370 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
39714307 AAAGCATAAA
* *
39714317 CATAAACTGAAAAACAATCACGTGTC
1 CATAAACCGAAAAACAATCACGCGTC
39714343 CATAAACCGAAAAACAATCACGCGTC
1 CATAAACCGAAAAACAATCACGCGTC
39714369 CA
1 CA
39714371 AAGCCCCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.28, G:0.11, T:0.15
Consensus pattern (26 bp):
CATAAACCGAAAAACAATCACGCGTC
Found at i:39724954 original size:51 final size:49
Alignment explanation
Indices: 39724842--39724957 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 49
39724832 TTTATAACAA
* *
39724842 CCATGCAAATGTATTTGGATAGGAAAATGTCTCATTTCATTGAAACTGT
1 CCATGCTAATGTATTTGGATAGGAAAATGTCTCATTGCATTGAAACTGT
* *
39724891 CTATGCTAATGTATTTGGTTGAGGAAAAATGTCTTCA-TGCATTTGAAA-TCGT
1 CCATGCTAATGTATTTGGAT-AGG-AAAATGTC-TCATTGCA-TTGAAACT-GT
*
39724943 CCATG-TCATGTATTT
1 CCATGCTAATGTATTT
39724958 AAATGAGATA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
49 17 0.30
50 3 0.05
51 21 0.38
52 15 0.27
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (49 bp):
CCATGCTAATGTATTTGGATAGGAAAATGTCTCATTGCATTGAAACTGT
Found at i:39724996 original size:50 final size:50
Alignment explanation
Indices: 39724942--39725037 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
39724932 TTTGAAATCG
*
39724942 TCCATG-TCATGTATTTAAATGAGATAAACGTCTCTATGCATTGAAAACCA
1 TCCATGATCATGTATTTAAATGACA-AAACGTCTCTATGCATTGAAAACCA
* * * *
39724992 TCCATGATCATGTATTTGAATTACAAAACGTCTTTGTGCATTGAAA
1 TCCATGATCATGTATTTAAATGACAAAACGTCTCTATGCATTGAAA
39725038 TTGTCCATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 25 0.62
51 15 0.38
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (50 bp):
TCCATGATCATGTATTTAAATGACAAAACGTCTCTATGCATTGAAAACCA
Found at i:39725074 original size:20 final size:20
Alignment explanation
Indices: 39725032--39725099 Score: 75
Period size: 19 Copynumber: 3.3 Consensus size: 20
39725022 TCTTTGTGCA
39725032 TTGAAATTGTCCATGTCCCATGC
1 TTGAAATTGTCCA--T-CCATGC
39725055 TTGAAATTGTCCATCCATGC
1 TTGAAATTGTCCATCCATGC
* * *
39725075 TTGAAA-CGTCTATCCTTGC
1 TTGAAATTGTCCATCCATGC
39725094 TTGAAA
1 TTGAAA
39725100 CATTCATCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 16 0.38
20 12 0.29
21 1 0.02
23 13 0.31
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (20 bp):
TTGAAATTGTCCATCCATGC
Found at i:39725094 original size:19 final size:19
Alignment explanation
Indices: 39725049--39725116 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
39725039 TGTCCATGTC
*
39725049 CCATGCTTGAAATTGTCCAT
1 CCATGCTTGAAA-CGTCCAT
*
39725069 CCATGCTTGAAACGTCTAT
1 CCATGCTTGAAACGTCCAT
* * *
39725088 CCTTGCTTGAAACATTCAT
1 CCATGCTTGAAACGTCCAT
*
39725107 CTATGCTTGA
1 CCATGCTTGA
39725117 TGTTTGAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (19 bp):
CCATGCTTGAAACGTCCAT
Found at i:39726405 original size:88 final size:88
Alignment explanation
Indices: 39726301--39726480 Score: 342
Period size: 88 Copynumber: 2.0 Consensus size: 88
39726291 AATTATAAGC
*
39726301 AATTACACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTAACTTAATGGATTTATAAACAAA
1 AATTACACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTAACTTAATAGATTTATAAACAAA
39726366 TTCCTTATAACTGCACCATTAAT
66 TTCCTTATAACTGCACCATTAAT
*
39726389 AATTACACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTACCTTAATAGATTTATAAACAAA
1 AATTACACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTAACTTAATAGATTTATAAACAAA
39726454 TTCCTTATAACTGCACCATTAAT
66 TTCCTTATAACTGCACCATTAAT
39726477 AATT
1 AATT
39726481 CTTAAGTAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.32
Consensus pattern (88 bp):
AATTACACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTAACTTAATAGATTTATAAACAAA
TTCCTTATAACTGCACCATTAAT
Found at i:39728568 original size:14 final size:14
Alignment explanation
Indices: 39728549--39728579 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39728539 ATCCAAACAA
39728549 TAACAATAAAATAG
1 TAACAATAAAATAG
*
39728563 TAACAATATAATAG
1 TAACAATAAAATAG
39728577 TAA
1 TAA
39728580 AACTGTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (14 bp):
TAACAATAAAATAG
Found at i:39728831 original size:19 final size:19
Alignment explanation
Indices: 39728807--39728862 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
39728797 ATATACACAT
39728807 TTGTCATTTACTAATCAAG
1 TTGTCATTTACTAATCAAG
*
39728826 TTGTC----ACCAAT-AA-
1 TTGTCATTTACTAATCAAG
39728839 -TGTCATTTACTAATCAAG
1 TTGTCATTTACTAATCAAG
39728857 TTGTCA
1 TTGTCA
39728863 CCGATAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 4 0.14
14 2 0.07
15 5 0.18
16 5 0.18
17 2 0.07
19 10 0.36
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (19 bp):
TTGTCATTTACTAATCAAG
Found at i:39728843 original size:31 final size:31
Alignment explanation
Indices: 39728808--39728872 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
39728798 TATACACATT
39728808 TGTCATTTACTAATCAAGTTGTCACCAATAA
1 TGTCATTTACTAATCAAGTTGTCACCAATAA
*
39728839 TGTCATTTACTAATCAAGTTGTCACCGATAA
1 TGTCATTTACTAATCAAGTTGTCACCAATAA
39728870 TGT
1 TGT
39728873 AACTTTCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (31 bp):
TGTCATTTACTAATCAAGTTGTCACCAATAA
Done.