Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 106 of 172
Found at i:30621705 original size:20 final size:21
Alignment explanation
Indices: 30621682--30621729 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
30621672 GTGTTAGAGA
30621682 TTGAGTTTAGGG-TTTAAGGT
1 TTGAGTTTAGGGTTTTAAGGT
*
30621702 TTGAGTTTAGGGTTTTAGGGT
1 TTGAGTTTAGGGTTTTAAGGT
30621723 TT-AGTTT
1 TTGAGTTT
30621730 GGAAATTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (21 bp):
TTGAGTTTAGGGTTTTAAGGT
Found at i:30621879 original size:7 final size:6
Alignment explanation
Indices: 30621861--30621935 Score: 51
Period size: 7 Copynumber: 11.0 Consensus size: 6
30621851 CAAAAAATAT
*
30621861 GGTTTA GGTTTA CGGTTTA GGGTTTA TGGTTTA GAGTTTTA GGTTTGG
1 GGTTTA GGTTTA -GGTTTA -GGTTTA -GGTTTA G-G-TTTA GGTTT-A
*
30621909 GGTTTA GGATTTA TGATTTAA GGTTTA
1 GGTTTA GG-TTTA -GGTTT-A GGTTTA
30621936 TGGTATATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
6 13 0.23
7 36 0.64
8 7 0.12
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (6 bp):
GGTTTA
Found at i:30621886 original size:14 final size:13
Alignment explanation
Indices: 30621861--30621935 Score: 62
Period size: 14 Copynumber: 5.5 Consensus size: 13
30621851 CAAAAAATAT
30621861 GGTTTA-GGTTTA
1 GGTTTAGGGTTTA
30621873 CGGTTTAGGGTTTA
1 -GGTTTAGGGTTTA
*
30621887 TGGTTTAGAGTTTTA
1 -GGTTTAG-GGTTTA
*
30621902 GGTTTGGGGTTTA
1 GGTTTAGGGTTTA
* *
30621915 GGATTTATGATTTAA
1 GG-TTTAGGGTTT-A
30621930 GGTTTA
1 GGTTTA
30621936 TGGTATATTG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
13 13 0.25
14 30 0.59
15 8 0.16
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (13 bp):
GGTTTAGGGTTTA
Found at i:30622516 original size:115 final size:114
Alignment explanation
Indices: 30622387--30622624 Score: 397
Period size: 115 Copynumber: 2.1 Consensus size: 114
30622377 CGCTTCATAA
* * *
30622387 AAAAACGCCGCTAAAGGTGATATATTACCGGCGTTTT-CTGAAGAAACGCCGCAAATTTCCTTTA
1 AAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTAC-GAAGAAACGCCACAAATTTCCTTTA
30622451 ACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCCTTTAGTGGCGCATTT
65 ACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCCTTTAGTGGCGCATTT
*
30622501 GAAAAACGCCGCTAAAAGTGATATCTTACCAGCGTTTTACGAAGAAACGCCACAAATTTCCTTTA
1 -AAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCACAAATTTCCTTTA
* *
30622566 ACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGTATTT
65 ACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCCTTTAGTGGCGCATTT
30622616 AAAAACGCC
1 AAAAACGCC
30622625 ACAAATATTT
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
114 9 0.08
115 106 0.91
116 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (114 bp):
AAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCACAAATTTCCTTTAA
CTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCCTTTAGTGGCGCATTT
Found at i:30622937 original size:261 final size:260
Alignment explanation
Indices: 30622487--30623016 Score: 871
Period size: 261 Copynumber: 2.0 Consensus size: 260
30622477 TTGTTTTCCT
* *
30622487 TTAGTGGCGCATTTGAAAAACGCCGCTAAAAGTGATATCTTACCAGCGTTTTACGAAGAAACGCC
1 TTAGTGGCGCATATGAAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCC
*
30622552 ACAAATTTCCTTTAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGTATTTA
66 ACAAATTTCCTTTAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTA
* * *
30622617 AAAACGCCACAAATATTTATTACGAGCTGAGGAAACGGTGTCGTTTCCTATTTTTATTAGTGGCG
131 AAAACGCCACAAATATTTACTACGAGCTGAGGAAACGGCGCCGTTTCCTATTTTTATTAGTGGCG
* * * *
30622682 CTTTAGCTAAAGCGCCGCAAAAATGTTTAATGCTACCTTATAACGGTGCCGTTTTGTCCTTGTTA
196 CTTTAGATAAAGCGCCGCAAAAATGTTGAATGCTACCTTATAACGATGCCGTTTTGTCCGTGTTA
* *
30622747 TTAGTGGCGCATATGAAAAACGCCGCTAAAGGTGATATATTACCGGCGTTTTACGAAGAAACGCC
1 TTAGTGGCGCATATGAAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCC
* * *
30622812 ACAAATTTCCTTTAACTGTAACGAAGACGGTGCTGTTTTGTTTTTTTCTTTTAGTGGCGCATTTT
66 ACAAATTTCCTTTAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCA-TTT
*
30622877 AAAAACGCCACAAATATTTACTACGAGCTGAGGAAATGGCGCCGTTTCCTATTTTTATTAGTGGC
130 AAAAACGCCACAAATATTTACTACGAGCTGAGGAAACGGCGCCGTTTCCTATTTTTATTAGTGGC
* * * *
30622942 GCTTTAGATAAAGCGCCGCAAAAATGTTGAATGTTATCTTATGACGATGTCGTTTTGTCCGTGTT
195 GCTTTAGATAAAGCGCCGCAAAAATGTTGAATGCTACCTTATAACGATGCCGTTTTGTCCGTGTT
30623007 A
260 A
30623008 TTAGTGGCG
1 TTAGTGGCG
30623017 TTTTTACTCT
Statistics
Matches: 249, Mismatches: 20, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
260 118 0.47
261 131 0.53
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (260 bp):
TTAGTGGCGCATATGAAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCC
ACAAATTTCCTTTAACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTA
AAAACGCCACAAATATTTACTACGAGCTGAGGAAACGGCGCCGTTTCCTATTTTTATTAGTGGCG
CTTTAGATAAAGCGCCGCAAAAATGTTGAATGCTACCTTATAACGATGCCGTTTTGTCCGTGTTA
Found at i:30625815 original size:9 final size:9
Alignment explanation
Indices: 30625801--30626183 Score: 342
Period size: 9 Copynumber: 43.2 Consensus size: 9
30625791 CACAAATTAA
30625801 ATAACTTAC
1 ATAACTTAC
30625810 ATAACTTAC
1 ATAACTTAC
* * *
30625819 AAAAATTAA
1 ATAACTTAC
30625828 ATAACTTAC
1 ATAACTTAC
30625837 ATAACTTAC
1 ATAACTTAC
* *
30625846 ATAAATTAA
1 ATAACTTAC
30625855 ATAACTTAC
1 ATAACTTAC
30625864 ATAACTTAC
1 ATAACTTAC
*
30625873 ATAAATTA-
1 ATAACTTAC
* *
30625881 AGTAAATTAA
1 A-TAACTTAC
*
30625891 ATAAGTTAC
1 ATAACTTAC
30625900 ATAACTTAC
1 ATAACTTAC
*
30625909 ATAAATTA-
1 ATAACTTAC
* *
30625917 AGTAAATTAA
1 A-TAACTTAC
30625927 ATAACTTAC
1 ATAACTTAC
30625936 ATAACTTAC
1 ATAACTTAC
*
30625945 ATTAA-TTAA
1 A-TAACTTAC
30625954 ATAACTTAC
1 ATAACTTAC
30625963 ATAACTTAC
1 ATAACTTAC
* *
30625972 ATAAATTAA
1 ATAACTTAC
*
30625981 ATATCTTAC
1 ATAACTTAC
30625990 ATAACTTAC
1 ATAACTTAC
*
30625999 ATAAATTA-
1 ATAACTTAC
* *
30626007 AGTAAATTAA
1 A-TAACTTAC
30626017 ATAACTTAC
1 ATAACTTAC
30626026 ATAACTTAC
1 ATAACTTAC
*
30626035 ATAAATTAC
1 ATAACTTAC
30626044 ATAACTTAC
1 ATAACTTAC
* *
30626053 ATAAATTAA
1 ATAACTTAC
30626062 ATAACTTAC
1 ATAACTTAC
30626071 ATAACTTAC
1 ATAACTTAC
*
30626080 ATAAATTA-
1 ATAACTTAC
30626088 AGTAACTTAC
1 A-TAACTTAC
*
30626098 ATTA--TAC
1 ATAACTTAC
30626105 ATAACCTT-C
1 ATAA-CTTAC
*
30626114 TTAACTTAC
1 ATAACTTAC
30626123 ATAA--TAC
1 ATAACTTAC
*
30626130 ATTACTTAC
1 ATAACTTAC
*
30626139 ATAGCTTAC
1 ATAACTTAC
*
30626148 ATTACTTAC
1 ATAACTTAC
*
30626157 ATTA--TAC
1 ATAACTTAC
30626164 ATAACCTT-C
1 ATAA-CTTAC
*
30626173 TTAACTTAC
1 ATAACTTAC
30626182 AT
1 AT
30626184 TATACACAAC
Statistics
Matches: 306, Mismatches: 48, Indels: 40
0.78 0.12 0.10
Matches are distributed among these distances:
7 18 0.06
8 13 0.04
9 266 0.87
10 9 0.03
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (9 bp):
ATAACTTAC
Found at i:30625825 original size:27 final size:27
Alignment explanation
Indices: 30625794--30626099 Score: 396
Period size: 27 Copynumber: 11.7 Consensus size: 27
30625784 TAGGTATCAC
*
30625794 AAATTAAATAACTTACATAACTTACAA
1 AAATTAAATAACTTACATAACTTACAT
30625821 AAATTAAATAACTTACATAACTTACAT
1 AAATTAAATAACTTACATAACTTACAT
30625848 AAATTAAATAACTTACATAACTTACAT
1 AAATTAAATAACTTACATAACTTACAT
* *
30625875 AAA-T---TAA-GT--A-AA-TTAAAT
1 AAATTAAATAACTTACATAACTTACAT
* * * **
30625893 AAGTTACATAACTTACATAAATTAAGT
1 AAATTAAATAACTTACATAACTTACAT
30625920 AAATTAAATAACTTACATAACTTACAT
1 AAATTAAATAACTTACATAACTTACAT
*
30625947 TAATTAAATAACTTACATAACTTACAT
1 AAATTAAATAACTTACATAACTTACAT
*
30625974 AAATTAAATATCTTACATAACTTACAT
1 AAATTAAATAACTTACATAACTTACAT
* * *
30626001 AAATTAAGTAAATTAAATAACTTACAT
1 AAATTAAATAACTTACATAACTTACAT
* * *
30626028 AACTTACATAAATTACATAACTTACAT
1 AAATTAAATAACTTACATAACTTACAT
30626055 AAATTAAATAACTTACATAACTTACAT
1 AAATTAAATAACTTACATAACTTACAT
*
30626082 AAATTAAGTAACTTACAT
1 AAATTAAATAACTTACAT
30626100 TATACATAAC
Statistics
Matches: 244, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
18 7 0.03
19 3 0.01
20 1 0.00
22 4 0.02
23 4 0.02
25 1 0.00
26 3 0.01
27 221 0.91
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.34
Consensus pattern (27 bp):
AAATTAAATAACTTACATAACTTACAT
Found at i:30626137 original size:59 final size:59
Alignment explanation
Indices: 30626068--30626201 Score: 189
Period size: 59 Copynumber: 2.3 Consensus size: 59
30626058 TTAAATAACT
30626068 TACATAACTTACATAAATTA-AGTAACTTACATTATACATAACCTTCTTAACTTACATAA
1 TACATAACTTACATAAATTACA-TAACTTACATTATACATAACCTTCTTAACTTACATAA
* ** * *
30626127 TACATTACTTACATAGCTTACATTACTTACATTATACATAACCTTCTTAACTTACATTA
1 TACATAACTTACATAAATTACATAACTTACATTATACATAACCTTCTTAACTTACATAA
* *
30626186 TACACAACTCACATAA
1 TACATAACTTACATAA
30626202 TGATGTAGTA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
59 64 0.98
60 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (59 bp):
TACATAACTTACATAAATTACATAACTTACATTATACATAACCTTCTTAACTTACATAA
Found at i:30626146 original size:25 final size:23
Alignment explanation
Indices: 30626115--30626248 Score: 83
Period size: 25 Copynumber: 5.4 Consensus size: 23
30626105 ATAACCTTCT
30626115 TAACTTACATAATACATTACTTACA
1 TAACTTACATAATACATTA--TACA
* *
30626140 TAGCTTACATTACTTACATTATACA
1 TAACTTACA-TA-ATACATTATACA
*
30626165 TAACCTT-CTTAACTTACATTATACA
1 TAA-CTTACATAA--TACATTATACA
* * *
30626190 CAACTCACATAAT-GATGTAGTACA
1 TAACTTACATAATACAT-TA-TACA
*
30626214 CAACTTACATAATACATTACTTACA
1 TAACTTACATAATACATTA--TACA
*
30626239 TAGCTTACAT
1 TAACTTACAT
30626249 TACTTACATG
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
22 2 0.02
23 3 0.04
24 22 0.26
25 46 0.54
26 5 0.06
27 7 0.08
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.35
Consensus pattern (23 bp):
TAACTTACATAATACATTATACA
Found at i:30626181 original size:34 final size:34
Alignment explanation
Indices: 30625807--30626257 Score: 201
Period size: 36 Copynumber: 12.9 Consensus size: 34
30625797 TTAAATAACT
* * * *
30625807 TACATAACTTACAAAAATTAAATAACTTACATAA
1 TACATAACTTACATAACTTACATTACTTACATAA
* * *
30625841 CTTACATAAATTAAATAACTTACATAACTTACATAAA
1 --TACATAACTTACATAACTTACATTACTTACAT-AA
* * * *
30625878 TTA-AGTAAATTAAATAAGTTACATAACTTACATAAA
1 -TACA-TAACTTACATAACTTACATTACTTACAT-AA
* * *
30625914 TTA-AGTAAATTAAATAACTTACATAACTTACATTAA
1 -TACA-TAACTTACATAACTTACATTACTTACA-TAA
* * * * *
30625950 TTAAATAACTTACATAACTTACATAAATTAAATATCT
1 -TACATAACTTACATAACTTACATTACTTACATA--A
* * * *
30625987 TACATAACTTACATAAATTA-AGTAAATTAAATAA
1 TACATAACTTACATAACTTACA-TTACTTACATAA
* *
30626021 CTTACATAACTTACATAAATTACATAACTTACATAAA
1 --TACATAACTTACATAACTTACATTACTTACAT-AA
* * *
30626058 TTAAATAACTTACATAACTTACATAAATTA-AGTAA
1 -TACATAACTTACATAACTTACATTACTTACA-TAA
*
30626093 CTTACATTA--TACATAACCTT-C-TTAACTTACATAA
1 --TACATAACTTACATAA-CTTACATT-ACTTACATAA
* * *
30626127 TACATTACTTACATAGCTTACATTACTTACATTA
1 TACATAACTTACATAACTTACATTACTTACATAA
* *
30626161 TACATAACCTT-CTTAACTTACATTA--TACACAA
1 TACATAA-CTTACATAACTTACATTACTTACATAA
* ** * **
30626193 CTCACATAA-TGATGT-A-GTACACAACTTACATAA
1 -T-ACATAACTTACATAACTTACATTACTTACATAA
* *
30626226 TACATTACTTACATAGCTTACATTACTTACAT
1 TACATAACTTACATAACTTACATTACTTACAT
30626258 GGGGCATACA
Statistics
Matches: 340, Mismatches: 46, Indels: 60
0.76 0.10 0.13
Matches are distributed among these distances:
31 10 0.03
32 18 0.05
33 12 0.04
34 67 0.20
35 16 0.05
36 210 0.62
37 7 0.02
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (34 bp):
TACATAACTTACATAACTTACATTACTTACATAA
Found at i:30628060 original size:21 final size:21
Alignment explanation
Indices: 30628034--30628079 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
30628024 CTACAACTTA
30628034 AAGCAAAGGCGGAAGCGAGGG
1 AAGCAAAGGCGGAAGCGAGGG
* * *
30628055 AAGCAACGGCTGCAGCGAGGG
1 AAGCAAAGGCGGAAGCGAGGG
30628076 AAGC
1 AAGC
30628080 GGAGGCTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.43, T:0.02
Consensus pattern (21 bp):
AAGCAAAGGCGGAAGCGAGGG
Found at i:30628516 original size:42 final size:42
Alignment explanation
Indices: 30628438--30628703 Score: 408
Period size: 42 Copynumber: 6.3 Consensus size: 42
30628428 CGCTAAAGAA
*
30628438 TTCTTTAGCGGCGCTTAGAAAAAAGACGCCGCTAAAGACCATG
1 TTCTTTAGCGGCGCTTAGAAAAAA-ACGCCGCTAAAGAACATG
*
30628481 TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATG
1 TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
*
30628523 TTCTTTAGCGGCGCATAGAAAAAAACGCCGCTAAAGAACATG
1 TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
* * *
30628565 CTCTTTAGAGGCGCTTAGAAAAAAACGCAGCTAAAGAACATG
1 TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
* *
30628607 TTCTTTAGAGGCGTTTAGAAAAAAACGCCGCTAAAGAACATG
1 TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
* **
30628649 TTCTTTAGAGGCGCACA-AACAAAAACGCCGCTAAAGAACATG
1 TTCTTTAGCGGCGCTTAGAA-AAAAACGCCGCTAAAGAACATG
30628691 TTCTTTAGCGGCG
1 TTCTTTAGCGGCG
30628704 TTTTTGTTTG
Statistics
Matches: 209, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
41 2 0.01
42 183 0.88
43 24 0.11
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (42 bp):
TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
Found at i:30631052 original size:16 final size:16
Alignment explanation
Indices: 30631031--30631065 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30631021 TATGAATATA
* *
30631031 AATGTGTAAATGTGAT
1 AATGTGCAAATATGAT
30631047 AATGTGCAAATATGAT
1 AATGTGCAAATATGAT
30631063 AAT
1 AAT
30631066 TGGATATTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (16 bp):
AATGTGCAAATATGAT
Found at i:30632493 original size:18 final size:18
Alignment explanation
Indices: 30632466--30632511 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
30632456 GTACAACTAT
30632466 TATA-TATATACTATCAA
1 TATATTATATACTATCAA
*
30632483 TATATTATATACTATTAA
1 TATATTATATACTATCAA
30632501 TATATTATATA
1 TATATTATATA
30632512 TTATATGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTATATACTATCAA
Found at i:30632543 original size:5 final size:5
Alignment explanation
Indices: 30632484--30632546 Score: 56
Period size: 5 Copynumber: 12.6 Consensus size: 5
30632474 TACTATCAAT
* * * * * *
30632484 ATATT ATATA CTATTA ATATA TTAT- ATATT ATATG ATATA ATATA ATATT
1 ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
30632534 ATATA ATATA ATA
1 ATATA ATATA ATA
30632547 GGAGGGTTAG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 3 0.06
5 40 0.85
6 4 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (5 bp):
ATATA
Found at i:30632543 original size:15 final size:15
Alignment explanation
Indices: 30632484--30632546 Score: 67
Period size: 15 Copynumber: 4.2 Consensus size: 15
30632474 TACTATCAAT
*
30632484 ATATTATATACTATTA
1 ATATTATATAATA-TA
*
30632500 ATA-TAT-TATATATT
1 ATATTATATA-ATATA
*
30632514 ATATGATATAATATA
1 ATATTATATAATATA
30632529 ATATTATATAATATA
1 ATATTATATAATATA
30632544 ATA
1 ATA
30632547 GGAGGGTTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 6 0.15
15 28 0.72
16 5 0.13
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATTATATAATATA
Found at i:30632932 original size:20 final size:19
Alignment explanation
Indices: 30632909--30632956 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
30632899 ATGTGATATA
30632909 ATATTATATAATGAAATAAT
1 ATATTATATAA-GAAATAAT
* * *
30632929 ATATTTTATAAGTATTAAT
1 ATATTATATAAGAAATAAT
30632948 ATA-TATATA
1 ATATTATATA
30632957 TGTATAACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 5 0.21
19 9 0.38
20 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATTATATAAGAAATAAT
Found at i:30632968 original size:24 final size:23
Alignment explanation
Indices: 30632923--30632988 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
30632913 TATATAATGA
* *
30632923 AATA-ATATATTTTATAAGTATT
1 AATATATATATATTATAACTATT
30632945 AATATATATATATGTATAACTATT
1 AATATATATATAT-TATAACTATT
*
30632969 ATTATATTATATATTATAAC
1 AATATA-TATATATTATAAC
30632989 AAAAGATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 4 0.11
23 7 0.18
24 20 0.53
25 7 0.18
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (23 bp):
AATATATATATATTATAACTATT
Found at i:30633111 original size:18 final size:18
Alignment explanation
Indices: 30633088--30633125 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30633078 TATTTTAATA
30633088 TTTTAA-TAAAATATTATT
1 TTTTAACTAAAATA-TATT
*
30633106 TTTTAACTAAATTATATT
1 TTTTAACTAAAATATATT
30633124 TT
1 TT
30633126 GATTTGGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAACTAAAATATATT
Found at i:30635082 original size:31 final size:32
Alignment explanation
Indices: 30635020--30635084 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
30635010 GGCAAATTAC
*
30635020 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACACTTTA
30635052 AAGAGTAATTGAATCCTAAT-AAAACACTTTA
1 AAGAGTAATTGAATCCTAATAAAAACACTTTA
30635083 AA
1 AA
30635085 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.29
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACACTTTA
Found at i:30640487 original size:15 final size:15
Alignment explanation
Indices: 30640467--30640502 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
30640457 ATGTCAACAA
* *
30640467 AAAATTCAATGTTTT
1 AAAATTAAATATTTT
30640482 AAAATTAAATATTTT
1 AAAATTAAATATTTT
30640497 AAAATT
1 AAAATT
30640503 TACTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
AAAATTAAATATTTT
Found at i:30640658 original size:17 final size:18
Alignment explanation
Indices: 30640636--30640671 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30640626 ATTCTATATG
30640636 AGTTTA-AAAGTATAAAA
1 AGTTTAGAAAGTATAAAA
*
30640653 AGTTTAGAAATTATAAAA
1 AGTTTAGAAAGTATAAAA
30640671 A
1 A
30640672 ATTATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (18 bp):
AGTTTAGAAAGTATAAAA
Found at i:30642052 original size:12 final size:12
Alignment explanation
Indices: 30642035--30642060 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30642025 TGATCAACTC
30642035 GAGCAATTATTT
1 GAGCAATTATTT
30642047 GAGCAATTATTT
1 GAGCAATTATTT
30642059 GA
1 GA
30642061 AGTGTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (12 bp):
GAGCAATTATTT
Found at i:30644462 original size:26 final size:25
Alignment explanation
Indices: 30644415--30644470 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
30644405 AATTGTGACT
* *
30644415 ATTAAATATATTAATTTATTAAAAGA
1 ATTAAATAAATTAACTTATTAAAA-A
*
30644441 ATTAAATAAATTTAACTT-TTAATAA
1 ATTAAATAAA-TTAACTTATTAAAAA
30644466 ATTAA
1 ATTAA
30644471 TATTTATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 6 0.23
26 14 0.54
27 6 0.23
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTAAATAAATTAACTTATTAAAAA
Found at i:30651667 original size:14 final size:15
Alignment explanation
Indices: 30651650--30651678 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30651640 ATTTAATAAA
30651650 ATTTTTATG-ATTTT
1 ATTTTTATGAATTTT
30651664 ATTTTTATGAATTTT
1 ATTTTTATGAATTTT
30651679 TAATTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
ATTTTTATGAATTTT
Found at i:30658070 original size:25 final size:25
Alignment explanation
Indices: 30658025--30658073 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
30658015 ATATAGTTTT
*
30658025 TATATTAATTATAAATGTTATAATA
1 TATATTAATTATAAATATTATAATA
30658050 TATATTATATTAT-AATATTATAAT
1 TATATTA-ATTATAAATATTATAAT
30658074 TAAACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TATATTAATTATAAATATTATAATA
Found at i:30659283 original size:41 final size:41
Alignment explanation
Indices: 30659220--30659340 Score: 143
Period size: 41 Copynumber: 2.9 Consensus size: 41
30659210 ACTAATCTGA
* * *
30659220 TTTATTGCCAGTGAAATAATTCAGACTTTATGTCTAGCAGGC
1 TTTA-TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
*
30659262 TTTATGCCGGTGAAATTATTCAGACTATACGTCTAGCAGGC
1 TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
* * * * * *
30659303 TTAATGCCGGTGATACATTTCGGACTATAAGTCTAGCA
1 TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCA
30659341 AGCTAAAAGC
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 64 0.94
42 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (41 bp):
TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
Found at i:30665353 original size:25 final size:25
Alignment explanation
Indices: 30665308--30665356 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
30665298 ATATAGTTTT
*
30665308 TATATTAATTATAAATGTTATAATA
1 TATATTAATTATAAATATTATAATA
30665333 TATATTATATTAT-AATATTATAAT
1 TATATTA-ATTATAAATATTATAAT
30665357 TAAACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TATATTAATTATAAATATTATAATA
Found at i:30666566 original size:41 final size:41
Alignment explanation
Indices: 30666503--30666627 Score: 151
Period size: 41 Copynumber: 3.0 Consensus size: 41
30666493 ACTAATTTGA
* * *
30666503 TTTATTGCCAGTGAAATAATTCAGACTTTATGTCTAGCAGGC
1 TTTA-TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
*
30666545 TTTATGCCGGTGAAATTATTCAGACTATACGTCTAGCAGGC
1 TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
* * * * * *
30666586 TTAATGCCGGTGATACATTTCGGACTATAAGTCTAGCAGGC
1 TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
30666627 T
1 T
30666628 AAAAGCCGGT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 68 0.94
42 4 0.06
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (41 bp):
TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
Found at i:30669458 original size:47 final size:47
Alignment explanation
Indices: 30669398--30669513 Score: 162
Period size: 47 Copynumber: 2.4 Consensus size: 47
30669388 ATATATATAA
* * *
30669398 ATATATTTTTTATGCATGAAAATGAATTAATCTATAGCTGAATGTAT
1 ATATATTTGTTATGCATGAAAATGAATTAAACTATAGCCGAATGTAT
* *
30669445 ATATAATTGTTATGCA-GAGAAATGAATTAAACTATGGCCGAATGTAT
1 ATATATTTGTTATGCATGA-AAATGAATTAAACTATAGCCGAATGTAT
30669492 ATATATTTGTTATGCATTGAAA
1 ATATATTTGTTATGCA-TGAAA
30669514 TAAATTATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
46 2 0.03
47 54 0.90
48 2 0.03
49 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (47 bp):
ATATATTTGTTATGCATGAAAATGAATTAAACTATAGCCGAATGTAT
Found at i:30669585 original size:161 final size:163
Alignment explanation
Indices: 30669381--30669683 Score: 504
Period size: 161 Copynumber: 1.9 Consensus size: 163
30669371 AAATTAACTA
* *
30669381 CGAATGTATATATATAAATATATTTTTTATGCATGAAAATGAATTAATCTATAGCTGAATGTATA
1 CGAATGTATATATAT-AATATATTTGTTATACATGAAAATGAATTAATCTATAGCTGAATGTATA
* *
30669446 TATAATTGTTATGCAGAGAAATGAATTAAACTATGGCCGAATG-TATATATATTTGTTATGCATT
65 TATAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATGATATATATATTTGTTATACATT
30669510 GAAATAAATTATTTGAAATTACATAGGTTATGGC
130 GAAATAAATTATTTGAAATTACATAGGTTATGGC
30669544 CGAATGTATATATAT-ATATATTTGTTATACATTG-AAATGAATTAATCTATAGCTGAATGTATA
1 CGAATGTATATATATAATATATTTGTTATACA-TGAAAATGAATTAATCTATAGCTGAATGTATA
*
30669607 TGTAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATGTATATATATATTTGTTATACAT
65 TATAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATG-ATATATATATTTGTTATACAT
*
30669672 TGAAATGAATTA
129 TGAAATAAATTA
30669684 ATCTATAGCT
Statistics
Matches: 131, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
161 84 0.64
162 2 0.02
163 45 0.34
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.39
Consensus pattern (163 bp):
CGAATGTATATATATAATATATTTGTTATACATGAAAATGAATTAATCTATAGCTGAATGTATAT
ATAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATGATATATATATTTGTTATACATTG
AAATAAATTATTTGAAATTACATAGGTTATGGC
Found at i:30669799 original size:98 final size:96
Alignment explanation
Indices: 30669554--30669875 Score: 576
Period size: 96 Copynumber: 3.4 Consensus size: 96
30669544 CGAATGTATA
30669554 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
1 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
30669619 GCAGAGAAATAAATTAAACTATGGCCGAATG
66 GCAGAGAAATAAATTAAACTATGGCCGAATG
*
30669650 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATTTAATTGTTAT
1 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
30669715 GCAGAGAAATAAATTAAACTATGGCCGAATG
66 GCAGAGAAATAAATTAAACTATGGCCGAATG
30669746 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
1 --TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
*
30669811 ATGCAGAGAAATGAATTAAACTATGGCCGAATG
64 ATGCAGAGAAATAAATTAAACTATGGCCGAATG
* *
30669844 --TATATATATTTGTTATGCATTGAAATAAATTA
1 TATATATATATTTGTTATACATTGAAATGAATTA
30669876 TTTGAAGTTA
Statistics
Matches: 219, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
94 30 0.14
96 95 0.43
98 94 0.43
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (96 bp):
TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
GCAGAGAAATAAATTAAACTATGGCCGAATG
Found at i:30669869 original size:47 final size:47
Alignment explanation
Indices: 30669556--30669875 Score: 343
Period size: 47 Copynumber: 6.7 Consensus size: 47
30669546 AATGTATATA
* * *
30669556 TATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
1 TATATATATTTGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
* * ** * *
30669603 TATATGTAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATG
1 TATATATATTTGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
* * *
30669650 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
1 --TATATATATTTGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
* * ** * *
30669699 TATATTTAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATG
1 TATATATATTTGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
* * *
30669746 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
1 ----TATATATATTTGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
* * ** *
30669797 TATATGTAATTGTTATGCAGAGAAATGAATTAAACTATGGCCGAATG
1 TATATATATTTGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
*
30669844 TATATATATTTGTTATGCATTGAAATAAATTA
1 TATATATATTTGTTATGCATTGAAATGAATTA
30669876 TTTGAAGTTA
Statistics
Matches: 218, Mismatches: 49, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
47 142 0.65
49 38 0.17
51 38 0.17
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (47 bp):
TATATATATTTGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
Found at i:30670036 original size:41 final size:41
Alignment explanation
Indices: 30669981--30670135 Score: 238
Period size: 41 Copynumber: 3.8 Consensus size: 41
30669971 TTGTAAGTTT
*
30669981 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATT
1 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
*
30670022 GGGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGTATC
1 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
*
30670063 AGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
1 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
* * * * *
30670104 GGGCTTTGTGTCTGGCAGGCTTTATGCCGGTG
1 GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTG
30670136 TTTTATATAA
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 104 1.00
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.31
Consensus pattern (41 bp):
GGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATC
Found at i:30670149 original size:82 final size:82
Alignment explanation
Indices: 30669982--30670154 Score: 229
Period size: 82 Copynumber: 2.1 Consensus size: 82
30669972 TGTAAGTTTG
* *
30669982 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATTGGGCTTTATGCCTAGCAAGCTCTGT
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCGGGCTTTATGCCTAGCAAGCTCTAT
* *
30670047 GCCGGTGAAATGTATCA
66 GCCGGTGAAATATATAA
* * * * *
30670064 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCGGGCTTTGTGTCTGGCAGGCTTTAT
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCGGGCTTTATGCCTAGCAAGCTCTAT
***
30670129 GCCGGTGTTTTATATAA
66 GCCGGTGAAATATATAA
*
30670146 GGCTCTATG
1 GGCTTTATG
30670155 TTTAACAAGT
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (82 bp):
GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCGGGCTTTATGCCTAGCAAGCTCTAT
GCCGGTGAAATATATAA
Found at i:30673744 original size:49 final size:49
Alignment explanation
Indices: 30673671--30673773 Score: 131
Period size: 49 Copynumber: 2.1 Consensus size: 49
30673661 AGCCCTTAAG
* * *
30673671 TTGAAAACCATTGTTGTCGAGCTATCTGGGATGGTA-AGATATGTC-TATA
1 TTGAAAACAATCGTTGTCGAGCTATCTAGGATGGTAGA-ATAT-TCATATA
30673720 TTGAAAACAATCGTTGTC-AGGCTATCTAGGATGGTAGAATATTCATATA
1 TTGAAAACAATCGTTGTCGA-GCTATCTAGGATGGTAGAATATTCATATA
30673769 TTGAA
1 TTGAA
30673774 TGCCATCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
48 3 0.06
49 44 0.92
50 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (49 bp):
TTGAAAACAATCGTTGTCGAGCTATCTAGGATGGTAGAATATTCATATA
Found at i:30678086 original size:18 final size:20
Alignment explanation
Indices: 30678049--30678088 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
30678039 TTGCTATAAC
*
30678049 TTTCAAAAATTGAGCCTCAA
1 TTTCAAAAATCGAGCCTCAA
30678069 TTTC-AAAATCGA-CCTCAA
1 TTTCAAAAATCGAGCCTCAA
30678087 TT
1 TT
30678089 ACATCCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (20 bp):
TTTCAAAAATCGAGCCTCAA
Found at i:30680517 original size:72 final size:72
Alignment explanation
Indices: 30680361--30680564 Score: 176
Period size: 72 Copynumber: 2.8 Consensus size: 72
30680351 GGATTTCATG
* * ** * * *
30680361 ATCGATGGCTTGAGATCCAACATTTGTTGCGGATTCTCTGAAGCTTGTGTGAGCAACATTGAATC
1 ATCGATGGCTTGAGATTCAGCACGTGTTACGGATTCTCTGAAGCTTGTATGAGCAACATCGAATC
* **
30680426 CTTGATT
66 ATCCATT
* * * *
30680433 ATCGATGACTTGAGATTCAGCACGTGTTACGGATTCTTTGAAGCTTGTATGAGCAACGTCGAATT
1 ATCGATGGCTTGAGATTCAGCACGTGTTACGGATTCTCTGAAGCTTGTATGAGCAACATCGAATC
*
30680498 ATCCTTT
66 ATCCATT
** * ** * * * *
30680505 A-CTGATGGCTTGAGATTTGGCACGTGCTGTGAATTCTCTAAAGCTTGTGTGAGCAGCATC
1 ATC-GATGGCTTGAGATTCAGCACGTGTTACGGATTCTCTGAAGCTTGTATGAGCAACATC
30680565 AAGTAAAGCT
Statistics
Matches: 104, Mismatches: 27, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
71 1 0.01
72 103 0.99
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (72 bp):
ATCGATGGCTTGAGATTCAGCACGTGTTACGGATTCTCTGAAGCTTGTATGAGCAACATCGAATC
ATCCATT
Found at i:30689425 original size:13 final size:13
Alignment explanation
Indices: 30689407--30689437 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30689397 TTCCAGCAAC
30689407 TATGAATTTATTT
1 TATGAATTTATTT
30689420 TATGAATTTATTT
1 TATGAATTTATTT
*
30689433 GATGA
1 TATGA
30689438 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:30689645 original size:50 final size:50
Alignment explanation
Indices: 30689532--30689879 Score: 491
Period size: 50 Copynumber: 6.8 Consensus size: 50
30689522 ATTTGGGTAA
*
30689532 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
*
30689588 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
*
30689638 AGAGGTCCCATGTAAGA-CATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
30689687 AGAGGTCCCATGTAAGACCATGTCTGGGACATTGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
30689737 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * * *
30689787 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** * *
30689837 AGAACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30689880 TGTTATTATC
Statistics
Matches: 271, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
49 47 0.17
50 143 0.53
51 34 0.13
52 1 0.00
53 4 0.01
55 2 0.01
56 40 0.15
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:30693583 original size:23 final size:24
Alignment explanation
Indices: 30693557--30693601 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
30693547 TATTTTTAAT
30693557 ATTTACATCTTTTT-GTTAAATTG
1 ATTTACATCTTTTTAGTTAAATTG
** *
30693580 ATTTTTATTTTTTTAGTTAAAT
1 ATTTACATCTTTTTAGTTAAAT
30693602 CAGTATTTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (24 bp):
ATTTACATCTTTTTAGTTAAATTG
Found at i:30706080 original size:23 final size:23
Alignment explanation
Indices: 30706054--30706099 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
30706044 GATTTAAACG
*
30706054 GTTGTTAAATTATGTTTTA-AATA
1 GTTGTT-AACTATGTTTTACAATA
*
30706077 GTTGTTGACTATGTTTTACAATA
1 GTTGTTAACTATGTTTTACAATA
30706100 TCATTATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.50
Consensus pattern (23 bp):
GTTGTTAACTATGTTTTACAATA
Found at i:30706326 original size:20 final size:20
Alignment explanation
Indices: 30706303--30706341 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30706293 TATTTTTAAA
*
30706303 ATTTAAAATATATTTTATAT
1 ATTTAAAATAAATTTTATAT
*
30706323 ATTTAAATTAAATTTTATA
1 ATTTAAAATAAATTTTATA
30706342 AACAATTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTAAAATAAATTTTATAT
Found at i:30708334 original size:39 final size:37
Alignment explanation
Indices: 30708267--30708400 Score: 101
Period size: 39 Copynumber: 3.5 Consensus size: 37
30708257 ACCAGAATGG
* *
30708267 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGA-AATCCGAAG-AATAGTTGA
* *
30708306 CACCCAGTGTCTCATCGGCAAATCCGAAGAA-AGTTGG
1 CACCCAGTGCCTCATCGG-AAATCCGAAGAATAGTTGA
* * *
30708343 TACCCAGTACCTCATCGAAACTATCCGAAGAAATAAAG-TGA
1 CACCCAGTGCCTCATCGGAA--ATCCGAAG-AAT--AGTTGA
* *
30708384 CATCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
30708401 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
36 2 0.03
37 19 0.25
38 10 0.13
39 26 0.35
40 1 0.01
41 15 0.20
42 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAATCCGAAGAATAGTTGA
Found at i:30708563 original size:37 final size:36
Alignment explanation
Indices: 30708492--30708564 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 36
30708482 GTCTCCAAAT
* *
30708492 TCACATTTCAATTCAATTTCACTTTTTCACTTTCAA
1 TCACATTTCAATTCAAATTCACTTTTCCACTTTCAA
* *
30708528 TCACATTTCGATTCAAAATTCACTTTTCCATTTTCAA
1 TCACATTTCAATTC-AAATTCACTTTTCCACTTTCAA
30708565 GTCAATATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.29, C:0.25, G:0.01, T:0.45
Consensus pattern (36 bp):
TCACATTTCAATTCAAATTCACTTTTCCACTTTCAA
Found at i:30708820 original size:3 final size:3
Alignment explanation
Indices: 30708812--30708841 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30708802 AATCTCACTC
30708812 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30708842 CTTATACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30709784 original size:14 final size:17
Alignment explanation
Indices: 30709765--30709802 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
30709755 ATTTATTTCT
30709765 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
30709779 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
30709796 TAATATA
1 TAATATA
30709803 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:30709810 original size:12 final size:11
Alignment explanation
Indices: 30709782--30709825 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
30709772 ATATTTATAA
30709782 TATAATTAATT
1 TATAATTAATT
*
30709793 TAATAATATACTT
1 T-ATAAT-TAATT
30709806 TATAATTAATT
1 TATAATTAATT
30709817 TATATATTA
1 TATA-ATTA
30709826 TATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:30709829 original size:20 final size:23
Alignment explanation
Indices: 30709777--30709839 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
30709767 ATATAATATT
30709777 TATA-ATATAATTAATTTAATAA
1 TATATATATAATTAATTTAATAA
* *
30709799 TATACTTTATAATTAATTTATATAT
1 TATA-TATATAATTAATTTA-ATAA
* *
30709824 TATATAAATAAATAAT
1 TATATATATAATTAAT
30709840 ATAAATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATAATTAATTTAATAA
Found at i:30709841 original size:20 final size:20
Alignment explanation
Indices: 30709794--30709842 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
30709784 TAATTAATTT
*
30709794 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* *
30709814 ATTTATATA-TTATATAAATA
1 AATAATATACTT-TATAAATA
30709834 AATAATATA
1 AATAATATA
30709843 AATATCTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:30724463 original size:29 final size:28
Alignment explanation
Indices: 30724401--30724476 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
30724391 AGACTTTTTT
*
30724401 TTTTTTTAATTAATTAGGGTTTTAGGTCG
1 TTTTTTTAATTAATTA-GGTTTTAGGTAG
*
30724430 TTTTTTTAATTAATTAGTTCTTTAGGTTAG
1 TTTTTTTAATTAATTAGGT-TTTAGG-TAG
**
30724460 -TTTTAAAATTAATTAGG
1 TTTTTTTAATTAATTAGG
30724477 GAAACAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 36 0.90
30 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.55
Consensus pattern (28 bp):
TTTTTTTAATTAATTAGGTTTTAGGTAG
Found at i:30724703 original size:9 final size:9
Alignment explanation
Indices: 30724658--30724705 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
30724648 CATCCATCTT
30724658 TCAACTCTC
1 TCAACTCTC
*
30724667 GCAACTCTC
1 TCAACTCTC
* *
30724676 TCAAACCCTT
1 TC-AACTCTC
*
30724686 TCAAGTCTC
1 TCAACTCTC
30724695 TCAACTCTC
1 TCAACTCTC
30724704 TC
1 TC
30724706 GTTTTAAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.23, C:0.42, G:0.04, T:0.31
Consensus pattern (9 bp):
TCAACTCTC
Found at i:30726851 original size:38 final size:38
Alignment explanation
Indices: 30726800--30726889 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 38
30726790 CACCGGCAAT
* *
30726800 AAGCCTGAATAACACCGGCATTAAGCCAGCTAGGCACA
1 AAGCCTGAATAACACCGACACTAAGCCAGCTAGGCACA
**
30726838 AAGCCTGAATAACACCGACACTAAGCTTGCTAGGCACA
1 AAGCCTGAATAACACCGACACTAAGCCAGCTAGGCACA
30726876 AAGCCTGAATAACA
1 AAGCCTGAATAACA
30726890 GTATGATTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.39, C:0.28, G:0.19, T:0.14
Consensus pattern (38 bp):
AAGCCTGAATAACACCGACACTAAGCCAGCTAGGCACA
Found at i:30733859 original size:13 final size:13
Alignment explanation
Indices: 30733841--30733868 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30733831 TGATTATGGC
30733841 ATCAATCTTATGT
1 ATCAATCTTATGT
30733854 ATCAATCTTATGT
1 ATCAATCTTATGT
30733867 AT
1 AT
30733869 AGGGCCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (13 bp):
ATCAATCTTATGT
Found at i:30736275 original size:18 final size:17
Alignment explanation
Indices: 30736252--30736295 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
30736242 AATTGAGTAC
30736252 TCCATTTCTCATTCCATT
1 TCCATTTCTCATT-CATT
*
30736270 TCCATTTTTCATTCATT
1 TCCATTTCTCATTCATT
30736287 TGCCATTTC
1 T-CCATTTC
30736296 AACATTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.16, C:0.30, G:0.02, T:0.52
Consensus pattern (17 bp):
TCCATTTCTCATTCATT
Found at i:30736639 original size:2 final size:2
Alignment explanation
Indices: 30736632--30736689 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
30736622 CATTTCATTT
30736632 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
30736674 CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA
30736690 TATATATCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:30741915 original size:17 final size:18
Alignment explanation
Indices: 30741878--30741915 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
30741868 ATTGCTTCTC
* *
30741878 AAAAGTGCTTTTGGGCTA
1 AAAAGTACTTTTGAGCTA
30741896 AAAAGTACTTTTGAGC-A
1 AAAAGTACTTTTGAGCTA
30741913 AAA
1 AAA
30741916 GCTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (18 bp):
AAAAGTACTTTTGAGCTA
Found at i:30743289 original size:18 final size:19
Alignment explanation
Indices: 30743266--30743312 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
30743256 AAAAACAAAC
30743266 TTAATTTAAT-ATATATTT
1 TTAATTTAATAATATATTT
*
30743284 TTAATTATTTATAATATATTT
1 TTAA-T-TTAATAATATATTT
*
30743305 ATAATTTA
1 TTAATTTA
30743313 TGATATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.17
19 3 0.13
20 5 0.22
21 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATTTAATAATATATTT
Found at i:30743305 original size:11 final size:11
Alignment explanation
Indices: 30743276--30743309 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
30743266 TTAATTTAAT
*
30743276 ATATATTTTTA
1 ATATATTTATA
30743287 AT-TATTTATA
1 ATATATTTATA
30743297 ATATATTTATA
1 ATATATTTATA
30743308 AT
1 AT
30743310 TTATGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATATATTTATA
Found at i:30743313 original size:18 final size:19
Alignment explanation
Indices: 30743267--30743320 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
30743257 AAAACAAACT
*
30743267 TAATTTAATATATATTTTTAA
1 TAATTT-ATA-ATATATTTAA
*
30743288 TTATTTATAATATATTT-A
1 TAATTTATAATATATTTAA
*
30743306 TAATTTATGATATAT
1 TAATTTATAATATAT
30743321 AAACTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 14 0.48
19 7 0.24
20 3 0.10
21 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TAATTTATAATATATTTAA
Found at i:30748078 original size:20 final size:22
Alignment explanation
Indices: 30748053--30748095 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
30748043 TAGCACATTT
30748053 TTGAC-AATTC-TAAGAAAAAA
1 TTGACAAATTCATAAGAAAAAA
*
30748073 TTGACAAATTCATAATAAAAAA
1 TTGACAAATTCATAAGAAAAAA
30748095 T
1 T
30748096 AAAATAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (22 bp):
TTGACAAATTCATAAGAAAAAA
Found at i:30752722 original size:18 final size:18
Alignment explanation
Indices: 30752695--30752730 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30752685 TATATATAAT
*
30752695 TATATTTTAAAATCAAAA
1 TATATATTAAAATCAAAA
*
30752713 TATATATTAAAATTAAAA
1 TATATATTAAAATCAAAA
30752731 ACACTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TATATATTAAAATCAAAA
Found at i:30756129 original size:10 final size:10
Alignment explanation
Indices: 30756114--30756138 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30756104 AATTGAATTG
30756114 ATTTTTTTCT
1 ATTTTTTTCT
30756124 ATTTTTTTCT
1 ATTTTTTTCT
30756134 ATTTT
1 ATTTT
30756139 CATTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
ATTTTTTTCT
Found at i:30761810 original size:20 final size:20
Alignment explanation
Indices: 30761785--30761824 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30761775 CGTAAAATGG
*
30761785 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
30761805 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
30761825 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:30761814 original size:34 final size:35
Alignment explanation
Indices: 30761770--30761836 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
30761760 CAGTAAAATA
* *
30761770 TTTTCCGTAAAATGGTTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
30761804 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
30761837 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:30761939 original size:20 final size:20
Alignment explanation
Indices: 30761914--30761965 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
30761904 GAAAAAGTTG
30761914 TTTTTACATATATTAATAAT-
1 TTTTTACATATATTAA-AATA
* *
30761934 TTTTT--ATATTTTAAATTA
1 TTTTTACATATATTAAAATA
30761952 TTTTTACATATATT
1 TTTTTACATATATT
30761966 GCAATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.08
18 13 0.50
20 11 0.42
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTACATATATTAAAATA
Found at i:30768254 original size:60 final size:60
Alignment explanation
Indices: 30768133--30768261 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 60
30768123 ACTAATATTA
* * * *
30768133 TTTGTACTTCGGTGTCTCTGTATACACTTTGGTGTCTCTATTTGCACATCTGTGCCCCTG
1 TTTGCACTTCGGTGTCTCTGTATACACTTCGGTGTCCCTATTTGCACATCTATGCCCCTG
* * *
30768193 TTTGCACTTCGGTGGTCT-TGTATACACTTCGGTGTCCCTATTTGCACGTCTATGGCTCTG
1 TTTGCACTTCGGT-GTCTCTGTATACACTTCGGTGTCCCTATTTGCACATCTATGCCCCTG
*
30768253 TTCGCACTT
1 TTTGCACTT
30768262 TGGTACCCCT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 56 0.93
61 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.42
Consensus pattern (60 bp):
TTTGCACTTCGGTGTCTCTGTATACACTTCGGTGTCCCTATTTGCACATCTATGCCCCTG
Found at i:30768695 original size:23 final size:23
Alignment explanation
Indices: 30768665--30768712 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
30768655 ATTTACATTG
30768665 TGAAATTCTTTTCACGATATGAA
1 TGAAATTCTTTTCACGATATGAA
30768688 TGAAATTCTTTTCACGATATGAA
1 TGAAATTCTTTTCACGATATGAA
30768711 TG
1 TG
30768713 TGTAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (23 bp):
TGAAATTCTTTTCACGATATGAA
Found at i:30781008 original size:22 final size:23
Alignment explanation
Indices: 30780983--30781040 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
30780973 AATGTTGAAG
30780983 TGTCTTGAGACGTTAAAGTC-CA
1 TGTCTTGAGACGTTAAAGTCTCA
** *
30781005 TGTCTCAAGAC--TAAAGTCTTCT
1 TGTCTTGAGACGTTAAAGTC-TCA
30781027 TGTCTTGAGACGTT
1 TGTCTTGAGACGTT
30781041 TTTTTTCCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
20 7 0.26
22 19 0.70
24 1 0.04
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (23 bp):
TGTCTTGAGACGTTAAAGTCTCA
Found at i:30786059 original size:3 final size:3
Alignment explanation
Indices: 30786051--30786118 Score: 52
Period size: 3 Copynumber: 23.3 Consensus size: 3
30786041 TAAATTAGTG
* * * * *
30786051 AAT AAT AAT AAT AAT AAT AAC ATT AAT GAT -GT AAT -AT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
30786097 AAT AAT ATT AA- AAT AATT AAT A
1 AAT AAT AAT AAT AAT AA-T AAT A
30786119 TAGAAATAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
2 5 0.10
3 42 0.84
4 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:30787791 original size:44 final size:43
Alignment explanation
Indices: 30787703--30788083 Score: 179
Period size: 44 Copynumber: 8.8 Consensus size: 43
30787693 TCATTGTGTT
* * * * *
30787703 AATCTGCTCCACTGCAACTTCAAGGAGGTAGGATTAGTAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTATCTTC
* *
30787747 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTATCTTC
* * * * * *
30787791 AACCCGCTTCACTGCGACTTTAGGGAGATAAGGTT-TATTACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTA-T-CTTC
* * ** * * *
30787835 AACCTACTTTACTGCAACTTCAGAGAGATAAGGTT-TGAT-AT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGT-ATCTTC
* * * * * * *
30787876 GATCTGCTCTACTGCAACTTTAGAGG-TATATGATT-CATCGTTTT
1 AATCTGCTCCACTGCAACTTCAG-GGAGATAAGATTGTATC--TTC
** * * * *
30787920 AATCCACTTCACTGCAACTTCAGGGAGATAGGATTAATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTATCTTC
* * *
30787964 AGTCTGCTCCACTGCAACTTCAGGGAGACAAGACTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-TATCTTC
* * * * *
30788009 AGTTTGCCCCACTGCAACTTCA-GGAGGATAAGACCTG-AT-AT-
1 AATCTGCTCCACTGCAACTTCAGGGA-GATAAGA-TTGTATCTTC
* * *
30788050 GATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
30788084 CGGTAATTTA
Statistics
Matches: 257, Mismatches: 64, Indels: 36
0.72 0.18 0.10
Matches are distributed among these distances:
40 2 0.01
41 48 0.19
42 7 0.03
43 8 0.03
44 152 0.59
45 38 0.15
46 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (43 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTATCTTC
Found at i:30788024 original size:45 final size:44
Alignment explanation
Indices: 30787929--30788032 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 44
30787919 TAATCCACTT
* * * *
30787929 CACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAGTCTGCTC
1 CACTGCAACTTCAGGGAGACAAGATCAATAGCTTCAGTCTGCCC
** * *
30787973 CACTGCAACTTCAGGGAGACAAGACTCGCTATCTTCAGTTTGCCC
1 CACTGCAACTTCAGGGAGACAAGA-TCAATAGCTTCAGTCTGCCC
30788018 CACTGCAACTTCAGG
1 CACTGCAACTTCAGG
30788033 AGGATAAGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 22 0.43
45 29 0.57
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (44 bp):
CACTGCAACTTCAGGGAGACAAGATCAATAGCTTCAGTCTGCCC
Found at i:30788223 original size:50 final size:50
Alignment explanation
Indices: 30788166--30788666 Score: 376
Period size: 50 Copynumber: 10.0 Consensus size: 50
30788156 CTGTAATGTT
* * * *
30788166 AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTACACTGCC
1 AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
* * * * * * *
30788216 AGAGAAGTAAGACTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC
1 AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
* * * * *
30788266 GGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTTCACCT-CC
1 AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCA-ATGCC
* * * * * * * * *
30788316 AGGGAATTAAAACTCGCCGTTGTGGCTTCAATATTTTTAATTGCAATGTC
1 AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
** * * * ** *
30788366 AGGGAAACAAGATTCGCCGTTGCAGCTTCAATCTATTCCACTATATTGCC
1 AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
* * * * * **
30788416 AGGGAAGTAAGACTT-GCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTT
1 AGGGAAGTAAGA-TTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
** * * * * **
30788466 AGGGAAACAAGATTCGCTGTTGTAGTTTCAATTTGTTCCACTGCACCGCC
1 AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
* * * * * * *
30788516 AGGGAAGTAAGATTCACCTTTGTGGCTTCAATCTTTTTAATTGCAATGTC
1 AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
* * * ** **
30788566 GGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTCACTATACCGCC
1 AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
* * * *
30788616 AGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCC
1 AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
30788666 A
1 A
30788667 AAGAGATATG
Statistics
Matches: 330, Mismatches: 117, Indels: 8
0.73 0.26 0.02
Matches are distributed among these distances:
49 3 0.01
50 324 0.98
51 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (50 bp):
AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCAATGCC
Found at i:30788279 original size:100 final size:100
Alignment explanation
Indices: 30788160--30788663 Score: 704
Period size: 100 Copynumber: 5.0 Consensus size: 100
30788150 AATTGACTGT
* * * *
30788160 AATGTTAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTACACTGCCAGAGAAGTA
1 AATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTA
30788225 AGACTCGCCGTTGTGGCTTCAATCTTTTTAATTGC
66 AGACTCGCCGTTGTGGCTTCAATCTTTTTAATTGC
* * *
30788260 AATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTTCACCT-CCAGGGAATT
1 AATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACA-CTGCCAGGGAAGT
* *
30788324 AAAACTCGCCGTTGTGGCTTCAATATTTTTAATTGC
65 AAGACTCGCCGTTGTGGCTTCAATCTTTTTAATTGC
* * * * *
30788360 AATGTCAGGGAAACAAGATTCGCCGTTGCAGCTTCAATCTATTCCACTATATTGCCAGGGAAGTA
1 AATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTA
* *
30788425 AGACTTGCCGTTGTGGCTTCAATCTTTTTAATTGT
66 AGACTCGCCGTTGTGGCTTCAATCTTTTTAATTGC
* * * * * * *
30788460 AATGTTAGGGAAACAAGATTCGCTGTTGTAGTTTCAATTTGTTCCACTGCACCGCCAGGGAAGTA
1 AATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTA
* * *
30788525 AGATTCACCTTTGTGGCTTCAATCTTTTTAATTGC
66 AGACTCGCCGTTGTGGCTTCAATCTTTTTAATTGC
* * * * *
30788560 AATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTCACTATACCGCCAGGGAAGTA
1 AATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTA
*
30788625 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGC
66 AGACTCGCCGTTGTGGCTTCAATCTTTTTAATTGC
30788660 AATG
1 AATG
30788664 CCAAAGAGAT
Statistics
Matches: 354, Mismatches: 48, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
99 1 0.00
100 351 0.99
101 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (100 bp):
AATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTA
AGACTCGCCGTTGTGGCTTCAATCTTTTTAATTGC
Found at i:30790073 original size:15 final size:16
Alignment explanation
Indices: 30790053--30790084 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
30790043 CCTTAGCCTC
30790053 TCCTTTTTCT-TCTTT
1 TCCTTTTTCTCTCTTT
30790068 TCCTTTTTCTCTCTTT
1 TCCTTTTTCTCTCTTT
30790084 T
1 T
30790085 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TCCTTTTTCTCTCTTT
Found at i:30795750 original size:23 final size:24
Alignment explanation
Indices: 30795724--30795769 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
30795714 AAAAGATAGT
*
30795724 AAAATATAAA-AATAAAATAAAAC
1 AAAATATAAACAAAAAAATAAAAC
30795747 AAAATATAAACAAAAAAATAAAA
1 AAAATATAAACAAAAAAATAAAA
30795770 AATAATAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.15
Consensus pattern (24 bp):
AAAATATAAACAAAAAAATAAAAC
Found at i:30796349 original size:12 final size:11
Alignment explanation
Indices: 30796316--30796347 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
30796306 GCTTGGACAA
30796316 AAAATACTTTT
1 AAAATACTTTT
30796327 AAAATACTTTT
1 AAAATACTTTT
30796338 AAAATA-TTTT
1 AAAATACTTTT
30796348 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAATACTTTT
Found at i:30798022 original size:129 final size:129
Alignment explanation
Indices: 30797746--30798892 Score: 1381
Period size: 129 Copynumber: 8.8 Consensus size: 129
30797736 CAACAGTTTT
* * * * **
30797746 CTCCACTACATCTTTAGGGAGATAAGACTAGATGCGATCTGCTCTACTGCAACTGCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATA
* * * * * * *
30797811 AGTTTTGTGGTTTTAAT-CACTCTACTACAACTTCAGGGAGGTAGAATTGGCTTT-TTCTGTCTG
66 AGATCTGTGGTTTTAATCCACTCCACTATAACTTCAGGGAGATAGGATTGG-TTTCTTTTGTCTG
* * *
30797874 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGAT-TAGCTCTACTACAA-TTTCAGATAGA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCT-GCTCTACTGCAACTTT-AGAGAGA
* * * * *
30797937 TAAGATCTGTGATTTTAATCCACTCTACTACAACTTTAGGGAGATAGGCTTGGTTTCTTTTGTCT
64 TAAGATCTGTGGTTTTAATCCACTCCACTATAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCT
30798002 G
129 G
* * * *
30798003 CTCCACTGCAACTTTAGGGAGATAAGACTGGATGCGATCTGAT-TCACTGCAACTTCAGGGAGAT
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCT-ACTGCAACTTTAGAGAGAT
* * * *
30798067 AAGATCTGTGGTTTTAATCCACTCCACTGTAACTTCAGAGTGATAGGATTGGTTTCTTCTGTCTG
65 AAGATCTGTGGTTTTAATCCACTCCACTATAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTG
* *
30798132 CTCCACTGCAACTTCGGGGAGATAAGACTGGATGCGATCTACTCTACTGCAACTTTAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATA
* * * * *
30798197 AGATTTGTGGTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTTTTTTGTCTG
66 AGATCTGTGGTTTTAATCCACTCCACTATAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTG
30798261 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATA
* * * *
30798326 AAATCTGTTGTTTTAATCCGCTCCACTGAT-ACTTTAGGGAGATAGGATTGGTTTCTTTTGTCTG
66 AGATCTGTGGTTTTAATCCACTCCACT-ATAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTG
*
30798390 CTCCACTGCAACTTCAGGGAGATAAGACTGGATACGATCTGCTCTACTGCAACTTTAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATA
* * * * *
30798455 AGATATGTGGTTTTAATCCGCTCCACTATAACTTTAGGGAGATAGGATTAGTTTCTTTTATCTG
66 AGATCTGTGGTTTTAATCCACTCCACTATAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTG
* * * *
30798519 CTCCGCTGCAACTTCAGGAAGATAAGACTGGATGTGATCTGCTCTACTACAACTTTAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATA
* * * * * * *
30798584 AGATCTGTGGCTTTCATCCTCTCCACTGTAACTTCAGGGAGATAGGATTGGCTTCTTTTTTCTT
66 AGATCTGTGGTTTTAATCCACTCCACTATAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTG
* * * * * * *
30798648 CTCAACTGTAACATCAGGGAGATAAGACTAGATGTGATCTGCTCTACTGTAACTTCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATA
* ** *
30798713 AGATCTGTGGTTTTAATCCTCTCCACTGCAACTTCAGGGAGATAGGATTCGTTTCTTTTGTCTAT
66 AGATCTGTGGTTTTAATCCACTCCACTATAACTTCAGGGAGATAGGATTGGTTTCTTTTG----T
30798778 CTG
127 CTG
* * * * * * * * * * *
30798781 TTCCACTGTAACTTTAGGGAGATAGGATTGGTTTCTTTTG-TCTGCTCCACTGCAACTTAAAAAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGC----GATCTGCTCTACTGCAACTTTAGAGA
* * **
30798845 GATAGGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
62 GATAAGATCTGTGGTTTTAATCCACTCCACTATAACTTCAGGGAGATA
30798893 AGACTGGATG
Statistics
Matches: 894, Mismatches: 107, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
127 2 0.00
128 74 0.08
129 719 0.80
130 5 0.01
133 28 0.03
136 65 0.07
137 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (129 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATA
AGATCTGTGGTTTTAATCCACTCCACTATAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTG
Found at i:30798092 original size:85 final size:85
Alignment explanation
Indices: 30797746--30799031 Score: 510
Period size: 85 Copynumber: 14.9 Consensus size: 85
30797736 CAACAGTTTT
* * * * * * * *
30797746 CTCCACTACATCTTTAGGGAGATAAGACTAGATGCGATCTGCTCTACTGCAACTGCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATTCGATCTGCTCCACTGCAACTTCAGGGAGATA
* * *
30797811 AGTTTTGTGGTTTTAATC-A
66 AGATCTGTGGTTTTAATCTG
* * * * *
30797830 CTCTACTACAACTTCAGGGAGGT-AGAATTGGCTTTTTCTG-TCTGCTCCACTGCAACTTCAGGG
1 CTCCACTGCAACTTCAGGGAGATAAG-ACTGG---ATTC-GATCTGCTCCACTGCAACTTCAGGG
*
30797893 AGATAAGA-CTAGATGCG-ATT-A---G
61 AGATAAGATCT-G-TG-GTTTTAATCTG
* * * ** ** ** * * *
30797915 CTCTACTACAATTTCAGATAGATAAGATCTGTGATTTTAATCCACTCTACTACAACTTTAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CTG-GA-TTCGATCTGCTCCACTGCAACTTCAGGGAG
* **
30797980 AT-AG-GCT-TGGTTTCTTTTGTCTG
63 ATAAGATCTGTGG--T-TTTAATCTG
* * * *
30798003 CTCCACTGCAACTTTAGGGAGATAAGACTGGATGCGATCTGATTCACTGCAACTTCAGGGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATTCGATCTGCTCCACTGCAACTTCAGGGAGATA
**
30798068 AGATCTGTGGTTTTAATCCA
66 AGATCTGTGGTTTTAATCTG
* * * * * * *
30798088 CTCCACTGTAACTTCAGAGTGATAGGATTGGTTTCTTCTG-TCTGCTCCACTGCAACTTCGGGGA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGG---ATTC-GATCTGCTCCACTGCAACTTCAGGGA
* *** *
30798152 GATAAGA-C--TGGATGCGATCTA
62 GATAAGATCTGTGGTTTTAATCTG
* * * * * ** * *
30798173 CTCTACTGCAACTTTAGAGAGATAAGATTTGTGGTTTTAATCCGCTCCACTGTAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGA---CTGGATTCGATCTGCTCCACTGCAACTTCAGGGAG
* ** **
30798238 ATAGGAT-TGATTTTTTTTGTCTG
63 ATAAGATCTG-TGGTTTTAATCTG
* * * *
30798261 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATTCGATCTGCTCCACTGCAACTTCAGGGAGATA
* * *
30798326 AAATCTGTTGTTTTAATCCG
66 AGATCTGTGGTTTTAATCTG
* * * *
30798346 CTCCACTG-ATACTTTAGGGAGATAGGATTGGTTTCTTTTG-TCTGCTCCACTGCAACTTCAGGG
1 CTCCACTGCA-ACTTCAGGGAGATAAGACTGGATTC----GATCTGCTCCACTGCAACTTCAGGG
* ***
30798409 AGATAAGA-C--TGGATACGATCTG
61 AGATAAGATCTGTGGTTTTAATCTG
* * * * * ** * ** *
30798431 CTCTACTGCAACTTTAGAGAGATAAGATATGTGGTTTTAATCCGCTCCACTATAACTTTAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAG--A-CTGGATTCGATCTGCTCCACTGCAACTTCAGGGAG
* * *
30798496 ATAGGAT-TAGT-TTCTTTTATCTG
63 ATAAGATCT-GTGGT-TTTAATCTG
* * * * * *
30798519 CTCCGCTGCAACTTCAGGAAGATAAGACTGGATGT-GATCTGCTCTACTACAACTTTAGAGAGAT
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGAT-TCGATCTGCTCCACTGCAACTTCAGGGAGAT
* *
30798583 AAGATCTGTGGCTTTCATCCT-
65 AAGATCTGTGGTTTTAAT-CTG
* * * * ** * * * *
30798604 CTCCACTGTAACTTCAGGGAGATAGGATTGGCTTCTTTTTTCTTCTCAACTGTAACATCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATTC---GATCTGCTCCACTGCAACTTCAGGGAG
* * * *
30798669 ATAAGA-C--TAGATGTGATCTG
63 ATAAGATCTGTGGTTTTAATCTG
* * * * **
30798689 CTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCT-CTCCACTGCAACTTCAGGGA
1 CTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATTCGAT-CTGCTCCACTGCAACTTCAGGGA
* * ** *
30798753 GATAGGATTCGTTTCTTTTGTCTATCTG
62 GATAAGA-TC-TGTGGTTT-T-AATCTG
* * * * * * * ***
30798781 TTCCACTGTAACTTTAGGGAGATAGGATTGGTTTCTTTTG-TCTGCTCCACTGCAACTTAAAAAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATTC----GATCTGCTCCACTGCAACTTCAGGGA
* *
30798845 GATAGGATCTGTGGTTTTAATCCG
62 GATAAGATCTGTGGTTTTAATCTG
* * * * * **
30798869 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTTCTCTACAGCAAGTTCAAAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATTCGATCTGCTCCACTGCAACTTCAGGGAGATA
**
30798934 AGATCTGTGGTTTTAATCCA
66 AGATCTGTGGTTTTAATCTG
* * * * * * **
30798954 TTCCACTACAACTTCAGGGAGATAGGACTGGATACGATCTGTTCTACTGCAACTTCAAAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGATTCGATCTGCTCCACTGCAACTTCAGGGAGATA
*
30799019 AGATTTGTGGTTT
66 AGATCTGTGGTTT
30799032 ATAGCTTTAA
Statistics
Matches: 892, Mismatches: 231, Indels: 157
0.70 0.18 0.12
Matches are distributed among these distances:
80 1 0.00
81 2 0.00
83 2 0.00
84 33 0.04
85 505 0.57
86 20 0.02
87 42 0.05
88 214 0.24
89 10 0.01
90 7 0.01
91 5 0.01
92 51 0.06
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (85 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTGGATTCGATCTGCTCCACTGCAACTTCAGGGAGATA
AGATCTGTGGTTTTAATCTG
Found at i:30798892 original size:44 final size:44
Alignment explanation
Indices: 30797782--30798977 Score: 472
Period size: 44 Copynumber: 27.7 Consensus size: 44
30797772 ACTAGATGCG
* * * * *
30797782 ATCTGCTCTACTGCAACTGCAGAGAGATAAGTTTTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * * * * *
30797826 ATC-ACTCTACTACAACTTCAGGGAGGT-AGAAT-TG-GCTTTTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAG-ATCTGTG-GTTTT-A
* *
30797869 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTAGATGCG-ATT-
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-G-TG-GTTTTA
* * * ** *
30797913 A---GCTCTACTACAATTTCAGATAGATAAGATCTGTGATTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
** * * * * *
30797954 ATCCACTCTACTACAACTTTAGGGAGAT-AG-GCT-TGGTTTCTTTT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGG--T-TTTA
* * * ***
30797998 GTCTGCTCCACTGCAACTTTAGGGAGATAAGA-C--TGGATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* *
30798039 ATCTGATTCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
** * * * * * *
30798083 ATCCACTCCACTGTAACTTCAGAGTGATAGGAT-TG-GTTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTT-TT-A
* * * ***
30798127 GTCTGCTCCACTGCAACTTCGGGGAGATAAGA-C--TGGATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * * * *
30798168 ATCTACTCTACTGCAACTTTAGAGAGATAAGATTTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * * ** *
30798212 ATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-TGATTTTTTTT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TGGTTTTA
* * ***
30798256 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * * * *
30798297 ATCTGCTCTACTGCAACTTTAGAGAGATAAAATCTGTTGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * * * *
30798341 ATCCGCTCCACTG-ATACTTTAGGGAGATAGGAT-TG-GTTTCTTTT
1 ATCTGCTCCACTGCA-ACTTCAGGGAGATAAGATCTGTG-GT-TTTA
* * ***
30798385 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATACG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * * *
30798426 ATCTGCTCTACTGCAACTTTAGAGAGATAAGATATGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* ** * * * *
30798470 ATCCGCTCCACTATAACTTTAGGGAGATAGGAT-TAGT-TTCTTTT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGGT-TTTA
* * * * *
30798514 ATCTGCTCCGCTGCAACTTCAGGAAGATAAGA-C--TGGATGTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * * * * *
30798555 ATCTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGGCTTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * * *
30798599 ATCCT-CTCCACTGTAACTTCAGGGAGATAGGAT-TG-GCTTCTTTT
1 AT-CTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTG-GT-TTTA
* * * * * * * * *
30798643 TTCTTCTCAACTGTAACATCAGGGAGATAAGA-C--TAGATGTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * *
30798684 ATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * ** *
30798728 ATCCT-CTCCACTGCAACTTCAGGGAGATAGGATTCGTTTCTTTTGTCT
1 AT-CTGCTCCACTGCAACTTCAGGGAGATAAGA-TC-TGTGGTTT-T-A
* * * * * *
30798776 ATCTGTTCCACTGTAACTTTAGGGAGATAGGAT-TG-GTTTCTTTT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTG-GT-TTTA
* * *** *
30798820 GTCTGCTCCACTGCAACTTAAAAAAGATAGGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * ***
30798864 ATCCGCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
* * * * **
30798905 ATCTTCTCTACAGCAAGTTCAAAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
*** *
30798949 ATCCATTCCACTACAACTTCAGGGAGATA
1 ATCTGCTCCACTGCAACTTCAGGGAGATA
30798978 GGACTGGATA
Statistics
Matches: 833, Mismatches: 246, Indels: 146
0.68 0.20 0.12
Matches are distributed among these distances:
40 4 0.00
41 228 0.27
42 21 0.03
43 45 0.05
44 473 0.57
45 20 0.02
46 10 0.01
47 6 0.01
48 26 0.03
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTA
Found at i:30799167 original size:50 final size:50
Alignment explanation
Indices: 30799035--30799706 Score: 369
Period size: 50 Copynumber: 13.4 Consensus size: 50
30799025 GTGGTTTATA
* * * ** *
30799035 GCTTTAATCTTTTTAACTGCAATGT-AGGGGAAGCAAGATTCGCTATTGTT
1 GCTTCAATCTTTTTAATTGCAATGTCA-GGGAAGTAAGATTCGCCGTTGTG
** ** * ** * * *
30799085 GCTTCAATCTGCTCCACTGCACCGCCAAGGAAGTAAGATTCGTCGTTGTG
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
* * * * *
30799135 GCTTCAATCTTTTTAATTGTAATGTCGGGGAAGCAAGATTCACCGTTGTA
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
* ** * * ** * * *
30799185 GCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCACCGTTGCG
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
* * * * * * * * *
30799235 GCTACAATCTTTTTAATTACAATGTCGGGGAAGCAATATTCACTGTTATA
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
* *** * ** * * *
30799285 GCTTCAATCTGTCCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGCG
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
* * * * * * * * *
30799335 GCTACAATCTTTTTAATTACAATGTCGGGGAAGCAATATTCACTGTTATA
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
* *** * * ** * *
30799385 GCTTCAATCTGTCCCACTGTACCG-CAAGGGAAGTAAGACTCGCCATTGTG
1 GCTTCAATCTTTTTAATTGCAATGTC-AGGGAAGTAAGATTCGCCGTTGTG
* ** *
30799435 GCTTCAATCTTTTTAATTGCAATGTTAGGGAAACAAGATTCGTCGTTGTG
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
* * ** * * * *
30799485 GCTTCAATCTTTCTAATTGCAATGTCGGGGAAACAAGATTTGTCGTTATT
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
* * ** * * * * *
30799535 GCTTCAATATGTTCCACTACACTGCCAGGGTAGTAAGACTT-GCCGTTGTG
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGA-TTCGCCGTTGTG
* * *
30799585 GCTTCAACCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTA
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
* * ** ** * * *
30799635 GCTTTAATCTGTTCCATTGCACCGCCAGGGAAGTAAGATTCACCATTGTG
1 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
*
30799685 GCTTTAATCTTTTTAATTGCAA
1 GCTTCAATCTTTTTAATTGCAA
30799707 CCTCAGGGGT
Statistics
Matches: 443, Mismatches: 174, Indels: 10
0.71 0.28 0.02
Matches are distributed among these distances:
49 3 0.01
50 437 0.99
51 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (50 bp):
GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTG
Found at i:30799516 original size:100 final size:100
Alignment explanation
Indices: 30799040--30799475 Score: 577
Period size: 100 Copynumber: 4.4 Consensus size: 100
30799030 TTATAGCTTT
* * * * * * *
30799040 AATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCGCTATTGTTGCTTCAATCTG-CTCCACTG
1 AATCTTTTTAATTACAATGTCGGGGAAGCAAGATTCACTGTTATAGCTTCAATCTGTC-CCACTG
* ** * *
30799104 CACCGCCAAGGAAGTAAGATTCGTCGTTGTGGCTTC
65 CACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTAC
** * * * *
30799140 AATCTTTTTAATTGTAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTAC
1 AATCTTTTTAATTACAATGTCGGGGAAGCAAGATTCACTGTTATAGCTTCAATCTGTCCCACTGC
30799205 ACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTAC
66 ACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTAC
*
30799240 AATCTTTTTAATTACAATGTCGGGGAAGCAATATTCACTGTTATAGCTTCAATCTGTCCCACTGC
1 AATCTTTTTAATTACAATGTCGGGGAAGCAAGATTCACTGTTATAGCTTCAATCTGTCCCACTGC
30799305 ACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTAC
66 ACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTAC
* *
30799340 AATCTTTTTAATTACAATGTCGGGGAAGCAATATTCACTGTTATAGCTTCAATCTGTCCCACTGT
1 AATCTTTTTAATTACAATGTCGGGGAAGCAAGATTCACTGTTATAGCTTCAATCTGTCCCACTGC
* * * * * *
30799405 ACCGCAAGGGAAGTAAGACTCGCCATTGTGGCTTC
66 ACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTAC
* ** *
30799440 AATCTTTTTAATTGCAATGTTAGGGAAACAAGATTC
1 AATCTTTTTAATTACAATGTCGGGGAAGCAAGATTC
30799476 GTCGTTGTGG
Statistics
Matches: 302, Mismatches: 33, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
100 302 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (100 bp):
AATCTTTTTAATTACAATGTCGGGGAAGCAAGATTCACTGTTATAGCTTCAATCTGTCCCACTGC
ACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTAC
Found at i:30799633 original size:150 final size:150
Alignment explanation
Indices: 30799310--30799644 Score: 411
Period size: 150 Copynumber: 2.2 Consensus size: 150
30799300 ACTGCACCGC
* * * * * *
30799310 CAGGGAAGTAAGATTCACCGTTGCGGCTACAATCTTTTTAATTACAATGTCGGGGAAGCAATATT
1 CAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTCTAATTACAATGTCGGGGAAACAAGATT
* **
30799375 CACTGTTATAGCTTCAATCTGTCCCACTGTACCGCAAGGGAAGTAAGACTCGCCATTGTGGCTTC
66 CACTGTTATAGCTTCAATATGTCCCACTACACCGCAAGGGAAGTAAGACTCGCCATTGTGGCTTC
*
30799440 AATCTTTTTAATTGCAATGT
131 AACCTTTTTAATTGCAATGT
* ** * *
30799460 TAGGGAAACAAGATTCGTCGTTGTGGCTTCAATCTTTCTAATTGCAATGTCGGGGAAACAAGATT
1 CAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTCTAATTACAATGTCGGGGAAACAAGATT
** * * * * * * *
30799525 -TGTCGTTATTGCTTCAATATGTTCCACTACACTGCCAGGGTAGTAAGACTTGCCGTTGTGGCTT
66 CACT-GTTATAGCTTCAATATGTCCCACTACACCGCAAGGGAAGTAAGACTCGCCATTGTGGCTT
30799589 CAACCTTTTTAATTGCAATGT
130 CAACCTTTTTAATTGCAATGT
* * *
30799610 CGGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCT
1 CAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
30799645 GTTCCATTGC
Statistics
Matches: 153, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
149 1 0.01
150 152 0.99
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (150 bp):
CAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTCTAATTACAATGTCGGGGAAACAAGATT
CACTGTTATAGCTTCAATATGTCCCACTACACCGCAAGGGAAGTAAGACTCGCCATTGTGGCTTC
AACCTTTTTAATTGCAATGT
Found at i:30801094 original size:12 final size:12
Alignment explanation
Indices: 30801073--30801115 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
30801063 ACATGATTGG
30801073 TTTATTTTTTTA
1 TTTATTTTTTTA
* *
30801085 TTTATCTTTTCA
1 TTTATTTTTTTA
30801097 -TTATTTTTTTA
1 TTTATTTTTTTA
30801108 TTT-TTTTT
1 TTTATTTTT
30801116 GTGCTTGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 14 0.54
12 12 0.46
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:30806284 original size:50 final size:50
Alignment explanation
Indices: 30806225--30807048 Score: 239
Period size: 50 Copynumber: 16.7 Consensus size: 50
30806215 GCAATTAAAA
* *
30806225 AGATTGAAGCCACAACAGCGAGTCTTACTTCTCTGGCAGTACAGTGGAAC
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* * ** * * ** * ** ** *
30806275 AGATTGAAGCTATAACGGTAAATTTTGTTTCCCCGATATTGTA-A-TTAAAA
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCA--GTACAGTGGAAC
*
30806325 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCGGTACAGTGGAAC
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* ** * ** * * * * * ** *
30806375 AGATTGAAGCTACAACGATGAATCTTGTTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* * ** *
30806425 AGATTGAAGCCACAATGGCGAGTCTTACTTCCCTAGTGGTGCAGTGGAAC
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* * * * *
30806475 AAATTGAAGCTACAACGACGA-----A--T-CCTGGC-GATGCAGTGGAAT
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAG-TACAGTGGAAC
* * * * * * ** *
30806517 AGATTAAAGCTACAACGGCAAATCTTA-TTTCCTCGACATTGTA-A-TTAAAA
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCT-GGCA--GTACAGTGGAAC
* ** * ** * *
30806567 AGATTGAA-CACATAACGATGAATCTTACTTCCCTGGTGGTGCACTGGAAC
1 AGATTGAAGC-CACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* *** * ** * * ** *
30806617 AGATTGAAGCTACAACTATGAATCTTGTTTCCCCGACATTGTA-A-TTAAAA
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCA--GTACAGTGGAAC
* * * *
30806667 AGATTGATGCCATAACAGCGAGTCTTACTTCCCCGGCAGTACAGTGGAAC
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* * * * * * * * * * ** *
30806717 AGATTGAAGCTACAAGGGTGAATCTT-GTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* * * * *
30806766 AGATTGAAGCCACAGCGGTGAGTTTTACTTCCCTGGCAGTGCAGTGGGAC
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* * * * * * * ** *
30806816 AGATTGAAGCTACAACGGCGAATTTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* * * * * *
30806866 AGATTGAAGCCACAATGGGGAATCTTACTTTCCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* * * ** * * * ** *
30806916 AGATTGAAGCTACAACGGCGTA-TCTT-GTTTCCTCGATATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCG-AGTCTTACTTCCCT-GGCAGTACAGTGGAAC
* * * * ** *
30806966 ATATTGAAGCCACAACGACAAATCTTACTTCCCTGGCAGTGTAGTGGAGC
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
* * * *
30807016 AGATTGAAGCTACAACAGCGAATCTTGCTTCCC
1 AGATTGAAGCCACAACGGCGAGTCTTACTTCCC
30807049 CAACATTGCA
Statistics
Matches: 540, Mismatches: 204, Indels: 60
0.67 0.25 0.07
Matches are distributed among these distances:
41 1 0.00
42 31 0.06
43 1 0.00
45 1 0.00
47 1 0.00
48 9 0.02
49 50 0.09
50 424 0.79
51 15 0.03
52 6 0.01
53 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTACAGTGGAAC
Found at i:30806403 original size:100 final size:100
Alignment explanation
Indices: 30806213--30806498 Score: 437
Period size: 100 Copynumber: 2.9 Consensus size: 100
30806203 ACCCCTGAGG
* * *
30806213 TTGCAATTAAAAAGATTGAAGCCACAACAGCGAGTCTTACTTCTCTGGCAGTACAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCGGTACAGTGGAACAGA
* * * * *
30806278 TTGAAGCTATAACGGTAAATTTTGTTTCCCCGATA
66 TTGAAGCTACAACGATGAATCTTGTTTCCCCGACA
*
30806313 TTGTAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCGGTACAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCGGTACAGTGGAACAGA
30806378 TTGAAGCTACAACGATGAATCTTGTTTCCCCGACA
66 TTGAAGCTACAACGATGAATCTTGTTTCCCCGACA
* * * * *
30806413 TTGCAATTAAAAAGATTGAAGCCACAATGGCGAGTCTTACTTCCCTAGTGGTGCAGTGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCGGTACAGTGGAACAGA
*
30806478 TTGAAGCTACAACGACGAATC
66 TTGAAGCTACAACGATGAATC
30806499 CTGGCGATGC
Statistics
Matches: 170, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 170 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCGGTACAGTGGAACAGA
TTGAAGCTACAACGATGAATCTTGTTTCCCCGACA
Found at i:30806640 original size:142 final size:142
Alignment explanation
Indices: 30806356--30806632 Score: 376
Period size: 142 Copynumber: 2.0 Consensus size: 142
30806346 GTCTTACTTC
* * ** *
30806356 CCTGGCGGTACAGTGGAACAGATTGAAGCTACAACGATGAATCTTGTTTCCCCGACATTGCAATT
1 CCTGGCGATACAGTGGAACAGATTAAAGCTACAACGACAAATCTTATTTCCCCGACATTGCAATT
* * * *
30806421 AAAAAGATTGAAGCCACAATGGCGAGTCTTACTTCCCTAGTGGTGCAGTGGAACAAATTGAAGCT
66 AAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGTGGTGCACTGGAACAAATTGAAGCT
30806486 ACAACGACGAAT
131 ACAACGACGAAT
* * * * *
30806498 CCTGGCGATGCAGTGGAATAGATTAAAGCTACAACGGCAAATCTTATTTCCTCGACATTGTAATT
1 CCTGGCGATACAGTGGAACAGATTAAAGCTACAACGACAAATCTTATTTCCCCGACATTGCAATT
* * * *
30806563 AAAAAGATTGAA-CACATAACGATGAATCTTACTTCCCTGGTGGTGCACTGGAACAGATTGAAGC
66 AAAAAGATTGAAGC-CACAACGACGAATCTTACTTCCCTAGTGGTGCACTGGAACAAATTGAAGC
30806627 TACAAC
130 TACAAC
30806633 TATGAATCTT
Statistics
Matches: 116, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
141 1 0.01
142 115 0.99
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (142 bp):
CCTGGCGATACAGTGGAACAGATTAAAGCTACAACGACAAATCTTATTTCCCCGACATTGCAATT
AAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGTGGTGCACTGGAACAAATTGAAGCT
ACAACGACGAAT
Found at i:30806691 original size:242 final size:242
Alignment explanation
Indices: 30806266--30806731 Score: 673
Period size: 242 Copynumber: 1.9 Consensus size: 242
30806256 TCTGGCAGTA
* * * * * *
30806266 CAGTGGAACAGATTGAAGCTATAACGGTAAATTTTGTTTCCCCGATATTGTAATTAAAAAGATTG
1 CAGTGGAACAGATTAAAGCTACAACGGCAAATCTTATTTCCCCGACATTGTAATTAAAAAGATTG
* * *
30806331 AAGCCACAACGGCGAGTCTTACTTCCCTGGCGGTACAGTGGAACAGATTGAAGCTACAACGATGA
66 AAGCCACAACGACGAATCTTACTTCCCTGGCGGTACACTGGAACAGATTGAAGCTACAACGATGA
** *
30806396 ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAATGGCGAGTCTTACTTCCCTAG
131 ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACAGCGAGTCTTACTTCCCCAG
** *
30806461 TGGTGCAGTGGAACAAATTGAAGCTACAACGACGAATCCTGGCGATG
196 CAGTACAGTGGAACAAATTGAAGCTACAACGACGAATCCTGGCGATG
* *
30806508 CAGTGGAATAGATTAAAGCTACAACGGCAAATCTTATTTCCTCGACATTGTAATTAAAAAGATTG
1 CAGTGGAACAGATTAAAGCTACAACGGCAAATCTTATTTCCCCGACATTGTAATTAAAAAGATTG
* * * * *
30806573 AA-CACATAACGATGAATCTTACTTCCCTGGTGGTGCACTGGAACAGATTGAAGCTACAACTATG
66 AAGC-CACAACGACGAATCTTACTTCCCTGGCGGTACACTGGAACAGATTGAAGCTACAACGATG
* * * *
30806637 AATCTTGTTTCCCCGACATTGTAATTAAAAAGATTGATGCCATAACAGCGAGTCTTACTTCCCCG
130 AATCTTGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACAGCGAGTCTTACTTCCCCA
*
30806702 GCAGTACAGTGGAACAGATTGAAGCTACAA
195 GCAGTACAGTGGAACAAATTGAAGCTACAA
30806732 GGGTGAATCT
Statistics
Matches: 196, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
241 1 0.01
242 195 0.99
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (242 bp):
CAGTGGAACAGATTAAAGCTACAACGGCAAATCTTATTTCCCCGACATTGTAATTAAAAAGATTG
AAGCCACAACGACGAATCTTACTTCCCTGGCGGTACACTGGAACAGATTGAAGCTACAACGATGA
ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACAGCGAGTCTTACTTCCCCAG
CAGTACAGTGGAACAAATTGAAGCTACAACGACGAATCCTGGCGATG
Found at i:30807070 original size:50 final size:50
Alignment explanation
Indices: 30806617--30807177 Score: 315
Period size: 50 Copynumber: 11.2 Consensus size: 50
30806607 GCACTGGAAC
* * * *
30806617 AGATTGAAGCTACAACTA-TGAATCTTGTTTCCCCGACATTGTAATTAAAA
1 AGATTGAAGCTACAAC-AGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * ** *
30806667 AGATTGATGCCATAACAGCGAGTCTTACTTCCCCGGCAGTACAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
** * *
30806717 AGATTGAAGCTACAAGGGTGAATCTTG-TTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * * * *** *
30806766 AGATTGAAGCCACAGCGGTGAGTTTTACTTCCCTGGCAGTGCAGTGGGAC
1 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * *
30806816 AGATTGAAGCTACAACGGCGAATTTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* ** * * * * * ** ** *
30806866 AGATTGAAGCCACAATGGGGAATCTTACTTTCCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * *
30806916 AGATTGAAGCTACAACGGCGTATCTTGTTTCCTCGATATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * ** **
30806966 ATATTGAAGCCACAAC-GACAAATCTTACTTCCCTGGCAGTGTAGTGGAGC
1 AGATTGAAGCTACAACAG-CGAATCTTGCTTCCCCGACATTGCAGTTAAAA
*
30807016 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCAACATTGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * ** *
30807066 AGATTGAAGCTACAACAGCAAATC-TGACTTCCCTGGCGGTGTAG--AAGAA
1 AGATTGAAGCTACAACAGCGAATCTTG-CTTCCCCGACATTGCAGTTAA-AA
* * *
30807115 CTGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
1 -AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
*
30807166 AGATTAAAGCTA
1 AGATTGAAGCTA
30807178 TAAACCACAA
Statistics
Matches: 369, Mismatches: 132, Indels: 20
0.71 0.25 0.04
Matches are distributed among these distances:
48 2 0.01
49 42 0.11
50 318 0.86
51 5 0.01
52 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:30807177 original size:100 final size:100
Alignment explanation
Indices: 30806498--30807175 Score: 729
Period size: 100 Copynumber: 6.8 Consensus size: 100
30806488 AACGACGAAT
* * * * ** * *
30806498 CCTGGC-GATGCAGTGGAATAGATTAAAGCTACAACGGCAAATCTTATTTCCTCGACATTGTAAT
1 CCTGGCAG-TGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAAT
* *
30806562 TAAAAAGATTGAA-CACATAAC-GATGAATCTTACTTC
65 TAAAAAGATTGAAGC-CACAACAG-CGAATCTTACTTC
** * * * *
30806598 CCTGGTGGTGCACTGGAACAGATTGAAGCTACAACTA-TGAATCTTGTTTCCCCGACATTGTAAT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAAC-AGCGAATCTTGCTTCCCCGACATTGCAAT
* * *
30806662 TAAAAAGATTGATGCCATAACAGCGAGTCTTACTTC
65 TAAAAAGATTGAAGCCACAACAGCGAATCTTACTTC
* * ** *
30806698 CCCGGCAGTACAGTGGAACAGATTGAAGCTACAAGGGTGAATCTTG-TTCCCCGACATTGCAATT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
* * * * *
30806762 AAAAAGATTGAAGCCACAGCGGTGAGTTTTACTTC
66 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTC
* * * * *
30806797 CCTGGCAGTGCAGTGGGACAGATTGAAGCTACAACGGCGAATTTTACTTCCCTGACATTGCAATT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
** * *
30806862 AAAAAGATTGAAGCCACAATGGGGAATCTTACTTT
66 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTC
* * * * * *
30806897 CCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGTATCTTGTTTCCTCGATATTGCAATT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
* *
30806962 AAAAATATTGAAGCCACAAC-GACAAATCTTACTTC
66 AAAAAGATTGAAGCCACAACAG-CGAATCTTACTTC
* * * *
30806997 CCTGGCAGTGTAGTGGAGCAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCAACATTGCAGTT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
* * *
30807062 AAAAAGATTGAAGCTACAACAGCAAATCTGACTTC
66 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTC
* * ** * *
30807097 CCTGGCGGTGTAGAAGAACTGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
*
30807162 AAAAAGATTAAAGC
66 AAAAAGATTGAAGC
30807176 TATAAACCAC
Statistics
Matches: 494, Mismatches: 76, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
99 86 0.17
100 404 0.82
101 4 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (100 bp):
CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
AAAAAGATTGAAGCCACAACAGCGAATCTTACTTC
Found at i:30807490 original size:85 final size:84
Alignment explanation
Indices: 30807400--30807814 Score: 282
Period size: 85 Copynumber: 4.8 Consensus size: 84
30807390 CTACAGATCT
* * * *
30807400 TATCTCTCTGAAATTGCAGTAGAGCAGATCACATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
30807465 CAGACAAAAGAAACCAATCC
66 CAGAC-AAAGAAACCAATCC
*** * * * ** **
30807485 TATCTCCCTGAAGTCATAGTAGAGCGGATTAAAACCACAGATCTTATCTCTTTGAAGTTGCAGCA
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TCAAATC-CAG-TCTTATCTCCCTGAAGTTGCAGTG
* * * * *
30807550 AAGCAGATC---GCATCCAGTCT
63 GAGCAGA-CAAAGAAACCAATCC
* * * * *
30807570 TATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACCAATCCTATCTCCCTAAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATC---A-AATCCAGTCTTATCTCCCTGAAGTTGCAGT
** ** * *
30807634 GGAGTGGATTAA-AATCACATATCT
62 GGAGCAGACAAAGAAAC-CA-ATCC
* * * * *
30807658 TATCTCTCTGAAGTTACAGTAGAGCAGATCACATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
30807723 CAGACAGAAGAAACCAATCC
66 CAGACA-AAGAAACCAATCC
* * * * * * *
30807743 TACCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TCAAATC-CAG-TCTTATCTCCCTGAAGTTGCAGTG
30807808 GAGCAGA
63 GAGCAGA
30807815 TCGCATCTAG
Statistics
Matches: 244, Mismatches: 67, Indels: 35
0.71 0.19 0.10
Matches are distributed among these distances:
85 130 0.53
86 19 0.08
87 13 0.05
88 80 0.33
89 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
CAGACAAAGAAACCAATCC
Found at i:30807498 original size:44 final size:43
Alignment explanation
Indices: 30807440--30807814 Score: 228
Period size: 44 Copynumber: 8.7 Consensus size: 43
30807430 ACATCCAGTT
30807440 TTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGAC-AAAGAAACCAATC
* *** * * ** *
30807484 CTATCTCCCTGAAGTCATAGTAGAGCGGATTAA-AACCACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAGAAAC-CA-ATC
** *** * * *
30807528 TTATCTCTTTGAAGTTGCAGCAAAGCAGATC---GCATCCAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAGAAACCAATC
30807569 TTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGAC-AAAGAAACCAATC
* * ** ** *
30807613 CTATCTCCCTAAAGTTGCAGTGGAGTGGATTAA-AATCACATATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAGAAAC-CA-ATC
* * * * * * *
30807657 TTATCTCTCTGAAGTTACAGTAGAGCAGATC--A-CATCTAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAGAAACCAATC
*
30807698 TTATCTCCTTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACA-AAGAAACCAATC
* * ** *
30807742 CTACCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AACCACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAGAAAC-CA-ATC
* * *
30807786 TTATCTCTCTAAAGTTGCAGTAGAGCAGA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA
30807815 TCGCATCTAG
Statistics
Matches: 247, Mismatches: 67, Indels: 34
0.71 0.19 0.10
Matches are distributed among these distances:
40 2 0.01
41 53 0.21
42 12 0.05
43 19 0.08
44 161 0.65
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAGAAACCAATC
Found at i:30807567 original size:129 final size:129
Alignment explanation
Indices: 30807230--30807856 Score: 816
Period size: 129 Copynumber: 4.9 Consensus size: 129
30807220 TCGCATCTAG
* * * * * * * *
30807230 TCCTATCTTCCTAAAATTACAGTAGAGCGGGTTAAAACCACAGATCTTATCTCTTTGAAGTTACA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* * * * * * *
30807295 GTATAACAGATCGCATTCAGTTTTATCTCTCTAAAGTTGCAGTGGAGCAGACAAAAGAAACAAA
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * *
30807359 TTCTATCTCCCT---G-T--AGTGGAGCGGATTAAAACTACAGATCTTATCTCTCTGAAATTGCA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* *
30807418 GTAGAGCAGATCACATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
*** * *
30807482 TCCTATCTCCCTGAAGTCATAGTAGAGCGGATTAAAACCACAGATCTTATCTCTTTGAAGTTGCA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* *
30807547 GCAAAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * * * *
30807611 TCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCACATATCTTATCTCTCTGAAGTTACA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* * * *
30807676 GTAGAGCAGATCACATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAA
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * *
30807740 TCCTACCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* * * * *
30807805 GTAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGATGTAGTGGAACAGAC
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
30807857 TGTTGATAGC
Statistics
Matches: 436, Mismatches: 56, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
123 107 0.25
125 1 0.00
126 1 0.00
129 327 0.75
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (129 bp):
TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
Found at i:30809229 original size:19 final size:19
Alignment explanation
Indices: 30809189--30809235 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
30809179 AATGAAGTTT
*
30809189 TTTTTA-AAAAAAAATTGG
1 TTTTTATAAAAAAAATTGA
30809207 TTTTTATAAAAAAAATAT-A
1 TTTTTATAAAAAAAAT-TGA
*
30809226 TTTTTTTAAA
1 TTTTTATAAA
30809236 TTTGACCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.24
19 18 0.72
20 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TTTTTATAAAAAAAATTGA
Found at i:30825604 original size:19 final size:20
Alignment explanation
Indices: 30825580--30825623 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
30825570 CGGATACATG
30825580 TTTATTTTT-GATCTCATAA
1 TTTATTTTTGGATCTCATAA
30825599 TTTATTTTTGGATCTCATAA
1 TTTATTTTTGGATCTCATAA
30825619 TTTAT
1 TTTAT
30825624 CCTTTCACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTATTTTTGGATCTCATAA
Found at i:30826086 original size:25 final size:25
Alignment explanation
Indices: 30826013--30826086 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
30826003 TTCCTGAAAC
30826013 TTGTTCTCCTTGTTGATGTCAAAAA
1 TTGTTCTCCTTGTTGATGTCAAAAA
* * * *
30826038 TTGTCCTCCTTG-CG-T-T--TAAC
1 TTGTTCTCCTTGTTGATGTCAAAAA
*
30826058 TTGTTCTCCTTGTTGATGTCAAAAT
1 TTGTTCTCCTTGTTGATGTCAAAAA
30826083 TTGT
1 TTGT
30826087 CTTCATGAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 13 0.36
21 1 0.03
22 2 0.06
23 2 0.06
24 1 0.03
25 17 0.47
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (25 bp):
TTGTTCTCCTTGTTGATGTCAAAAA
Found at i:30833057 original size:42 final size:42
Alignment explanation
Indices: 30833011--30833141 Score: 117
Period size: 42 Copynumber: 3.1 Consensus size: 42
30833001 AAGAACGGAA
* * *
30833011 CTTTTAGTAGCGTTT-TCGATAAAAGCGTCGCTAAAGGTCATG-
1 CTTTTAGCAGCATTTGT-GATAAAAGCG-CGCTAAAGATCATGT
*
30833053 CTTTTAGCGGCATTTGTGATAAAAGCGCGCTAAAGATCATGT
1 CTTTTAGCAGCATTTGTGATAAAAGCGCGCTAAAGATCATGT
* * * *
30833095 C-TTTAGCGGCATTTTTGGGT-AAAGCGCCGCTAAAGGTCATGTT
1 CTTTTAGCAGCATTTGT-GATAAAAGCG-CGCTAAAGATCATG-T
30833138 CTTT
1 CTTT
30833142 AGCGACGTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
41 33 0.43
42 38 0.50
43 3 0.04
44 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (42 bp):
CTTTTAGCAGCATTTGTGATAAAAGCGCGCTAAAGATCATGT
Found at i:30833100 original size:41 final size:43
Alignment explanation
Indices: 30833028--30833145 Score: 154
Period size: 41 Copynumber: 2.8 Consensus size: 43
30833018 TAGCGTTTTC
*
30833028 GATAAAAGCGTCGCTAAAGGTCATG-CTTTTAGCGGCATTTGT-
1 GATAAAAGCGCCGCTAAAGGTCATGTC-TTTAGCGGCATTTGTG
* *
30833070 GATAAAAGCG-CGCTAAAGATCATGTCTTTAGCGGCATTTTTG
1 GATAAAAGCGCCGCTAAAGGTCATGTCTTTAGCGGCATTTGTG
*
30833112 GGT-AAAGCGCCGCTAAAGGTCATGTTCTTTAGCG
1 GATAAAAGCGCCGCTAAAGGTCATG-TCTTTAGCG
30833146 ACGTTTTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
41 33 0.49
42 26 0.38
43 9 0.13
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
GATAAAAGCGCCGCTAAAGGTCATGTCTTTAGCGGCATTTGTG
Found at i:30833437 original size:11 final size:11
Alignment explanation
Indices: 30833421--30833445 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30833411 ATTTGGGAGT
30833421 AAAATGAGTGA
1 AAAATGAGTGA
30833432 AAAATGAGTGA
1 AAAATGAGTGA
30833443 AAA
1 AAA
30833446 TCGGAAAATC
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:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (11 bp):
AAAATGAGTGA
Found at i:30834557 original size:7 final size:7
Alignment explanation
Indices: 30834545--30834603 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
30834535 TAATTTAGCC
30834545 ATTTTTA
1 ATTTTTA
30834552 ATTTTTA
1 ATTTTTA
30834559 A--TTTA
1 ATTTTTA
*
30834564 ATATTTTT
1 AT-TTTTA
30834572 ATTTTTA
1 ATTTTTA
30834579 A--TTTA
1 ATTTTTA
30834584 ATTTTT-
1 ATTTTTA
30834590 ATATTTTA
1 AT-TTTTA
30834598 ATTTTT
1 ATTTTT
30834604 TGTTTGTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
5 10 0.23
6 2 0.05
7 24 0.56
8 7 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTA
Found at i:30834575 original size:20 final size:18
Alignment explanation
Indices: 30834545--30834601 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 18
30834535 TAATTTAGCC
30834545 ATTTTTAATTTTTAATTTAA
1 ATTTTT-ATTTTTAATTT-A
30834565 TATTTTTATTTTTAATTTA
1 -ATTTTTATTTTTAATTTA
30834584 ATTTTTATATTTTAATTT
1 ATTTTTAT-TTTTAATTT
30834602 TTTGTTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.23
19 10 0.29
20 11 0.31
21 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTATTTTTAATTTA
Found at i:30839281 original size:171 final size:171
Alignment explanation
Indices: 30838996--30839307 Score: 597
Period size: 171 Copynumber: 1.8 Consensus size: 171
30838986 CCTAGATTTC
*
30838996 CTCCTCCTAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
1 CTCCTCCAAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
*
30839061 TTATCCAGTAGAGTTTTAGCCAAACTCCACCTCTCTCACCACAAAGAAATAAAATAAATATCCTT
66 TTATCCAGTAAAGTTTTAGCCAAACTCCACCTCTCTCACCACAAAGAAATAAAATAAATATCCTT
30839126 TTGCATTCCATTTTGAATTCCTAGATTTCCTCCTCCTAATT
131 TTGCATTCCATTTTGAATTCCTAGATTTCCTCCTCCTAATT
30839167 CTCCTCCAAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
1 CTCCTCCAAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
*
30839232 TTATCCAGTAAAGTTTTAGCCAAACTCCACCTTTCTCACCACAAAGAAATAAAATAAATATCCTT
66 TTATCCAGTAAAGTTTTAGCCAAACTCCACCTCTCTCACCACAAAGAAATAAAATAAATATCCTT
30839297 TTGCATTCCAT
131 TTGCATTCCAT
30839308 GAGATTCGAA
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 138 1.00
ACGTcount: A:0.31, C:0.34, G:0.06, T:0.29
Consensus pattern (171 bp):
CTCCTCCAAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
TTATCCAGTAAAGTTTTAGCCAAACTCCACCTCTCTCACCACAAAGAAATAAAATAAATATCCTT
TTGCATTCCATTTTGAATTCCTAGATTTCCTCCTCCTAATT
Found at i:30840678 original size:24 final size:24
Alignment explanation
Indices: 30840634--30840680 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
30840624 TAAAAAAATT
*
30840634 GAAAAAAATAAAAAATTTTGAAAA
1 GAAAAAAATAAAAAATATTGAAAA
*
30840658 GAAAAAATTCAAAAAA-ATTGAAA
1 GAAAAAAAT-AAAAAATATTGAAA
30840681 TTGTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (24 bp):
GAAAAAAATAAAAAATATTGAAAA
Found at i:30842817 original size:21 final size:21
Alignment explanation
Indices: 30842791--30842843 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
30842781 CAATTTTCAT
* *
30842791 ACGGGCATGTGCCTTGGCCAC
1 ACGGGCATGTGCCCTAGCCAC
* *
30842812 ACGGGCGTGTCCCCTAGCCAC
1 ACGGGCATGTGCCCTAGCCAC
*
30842833 ATGGGCATGTG
1 ACGGGCATGTG
30842844 AGATTTCTAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.32, G:0.34, T:0.19
Consensus pattern (21 bp):
ACGGGCATGTGCCCTAGCCAC
Found at i:30851342 original size:16 final size:17
Alignment explanation
Indices: 30851316--30851359 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
30851306 TGTATGTATG
* * *
30851316 TATATATGTATATAAAT
1 TATATAAGTATAAAAAA
30851333 TATA-AAGTATAAAAAA
1 TATATAAGTATAAAAAA
30851349 TATATAAGTAT
1 TATATAAGTAT
30851360 GTATATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (17 bp):
TATATAAGTATAAAAAA
Found at i:30851370 original size:27 final size:26
Alignment explanation
Indices: 30851340--30851395 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
30851330 AATTATAAAG
30851340 TATAAA-AAATATATAAGTATGTATATA
1 TATAAACAAATATAT--GTATGTATATA
30851367 TATAAATCAAATATATGTATGTATATA
1 TATAAA-CAAATATATGTATGTATATA
30851394 TA
1 TA
30851396 ATTAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 19 0.70
29 8 0.30
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (26 bp):
TATAAACAAATATATGTATGTATATA
Found at i:30851415 original size:29 final size:27
Alignment explanation
Indices: 30851356--30851415 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
30851346 AAATATATAA
* *
30851356 GTATGTATATATATAAATCAAATATAT
1 GTATGTATATATATAAATCAAATAAAG
30851383 GTATGTATATATAATTAAATCTAAA-AAAG
1 GTATGTATATAT-A-TAAATC-AAATAAAG
30851412 GTAT
1 GTAT
30851416 AAATGAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.43
28 1 0.04
29 12 0.43
30 3 0.11
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (27 bp):
GTATGTATATATATAAATCAAATAAAG
Found at i:30856518 original size:13 final size:14
Alignment explanation
Indices: 30856500--30856533 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
30856490 AGTCAAACAA
30856500 AAAAATGAAAAA-T
1 AAAAATGAAAAAGT
30856513 AAAAATGAAAAAGT
1 AAAAATGAAAAAGT
30856527 AAAAATG
1 AAAAATG
30856534 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (14 bp):
AAAAATGAAAAAGT
Found at i:30858436 original size:50 final size:50
Alignment explanation
Indices: 30857755--30858618 Score: 484
Period size: 50 Copynumber: 17.3 Consensus size: 50
30857745 ATTGCAGTTC
* ** * * *
30857755 AAAAGATTGAAGCTACAACAGCAAATCTCACCTCCCTA-GCGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCC-AGGAGATGCAGTGG
* * * * * * **
30857805 AACAGATTGAAGCTACGACGGCGAATCTCACTTCCC-CGACATTGCAATTC
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGA-TGCAGTGG
* * * * * * *
30857855 AAAAGATTGAAGCTACAACAGCGAATCTCACCTCCCTGGCGATGTAGCGG
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGATGCAGTGG
* * * **
30857905 AACAA-ATTGAAGCTACAACGGTGAATCTCACTTCCC-CGACATTGCAATTT
1 AA-AAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGA-TGCAGTGG
* ** * * *
30857955 AAAAGATTGAAGCTACAACAGCAAATCTCAAC-TCCCTGGTGATGCAG-CG
1 AAAAGATTGAAGCTACAACGGTGAATCTC-ACTTCCCAGGAGATGCAGTGG
* * * * * *
30858004 AAACAGATCGAAGCTACAACGGCGAATCTCACTTCCC-TGACATTGCAAT-T
1 AAA-AGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGA-TGCAGTGG
* * * * * *
30858054 CAAAGATTGAAGCCACAACGGTGAATCTTAC-TCCTAGGCGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGATGCAGTGG
** * * * * * **
30858103 AGCAGATTGAAGCTATAACGGTAAATCTCACTTCCC-CGACATTGCAATTC
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGA-TGCAGTGG
* * * * * * *
30858153 AAAAGATTTAAGCCACAACGGTGAATCTTACTTTCCAGGCGATGTAGCGG
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGATGCAGTGG
** * * * * **
30858203 AGTAGATTGAAGCTGCAACGGTGAATCTCACTTCCC-CGACATTGCAATTC
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGA-TGCAGTGG
* * * *
30858253 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGTGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGATGCAGTGG
** * * **
30858303 AGCAGATTGAAGCTACAACGGTGAATCTCACTTCCCCA--ACATTGCAATTC
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTT-CCCAGGAGA-TGCAGTGG
* * * * * *
30858353 AAAAGATTTAAGCCACAACGGCGAATCTTACTTCCCAGGTGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGATGCAGTGG
** * * * **
30858403 AGCAGATTGAAGCTACAACGGCGAATCTCACTTCCTC--GACATTGCAATTC
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCC-CAGGAGA-TGCAGTGG
* * * *
30858453 AAAAGATTTAAGCCACAACGGTGAATCTTACTTCCCAGGTGATGCAGTGG
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGATGCAGTGG
** * * * **
30858503 AGCAGATTGAAACTACAACGGTGAATCTCACTTCCTC--GACATTGCAATTC
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCC-CAGGAGA-TGCAGTGG
* * * * * *
30858553 AAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCAGGCGATGTAGTGG
1 AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGATGCAGTGG
* *
30858603 AATAGGTTGAAGCTAC
1 AAAAGATTGAAGCTAC
30858619 GATAGCGAAT
Statistics
Matches: 591, Mismatches: 192, Indels: 62
0.70 0.23 0.07
Matches are distributed among these distances:
48 7 0.01
49 78 0.13
50 483 0.82
51 23 0.04
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAACGGTGAATCTCACTTCCCAGGAGATGCAGTGG
Found at i:30858642 original size:100 final size:100
Alignment explanation
Indices: 30857745--30858596 Score: 1181
Period size: 100 Copynumber: 8.5 Consensus size: 100
30857735 AAAACCATAG
* * * * * * *
30857745 ATTGCAGTTCAAAAGATTGAAGCTACAACAGCAAATCTCACCTCCCTA-GCGATGCAGCGGAACA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCC-AGGCGATGCAGCGGAGCA
* *
30857809 GATTGAAGCTACGACGGCGAATCTCACTTCCCCGAC
65 GATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
* * * * * * * *
30857845 ATTGCAATTCAAAAGATTGAAGCTACAACAGCGAATCTCACCTCCCTGGCGATGTAGCGGAACAA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
30857910 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
* * * * * * * * *
30857945 ATTGCAATTTAAAAGATTGAAGCTACAACAGCAAATCTCAAC-TCCCTGGTGATGCAGCGAAACA
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCT-TACTTCCCAGGCGATGCAGCGGAGCA
* * *
30858009 GATCGAAGCTACAACGGCGAATCTCACTTCCCTGAC
65 GATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
* *
30858045 ATTGCAATTC-AAAGATTGAAGCCACAACGGTGAATCTTAC-TCCTAGGCGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
* *
30858108 ATTGAAGCTATAACGGTAAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
* * * * *
30858143 ATTGCAATTCAAAAGATTTAAGCCACAACGGTGAATCTTACTTTCCAGGCGATGTAGCGGAGTAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
*
30858208 ATTGAAGCTGCAACGGTGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
* *
30858243 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGTGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
*
30858308 ATTGAAGCTACAACGGTGAATCTCACTTCCCCAAC
66 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
* *
30858343 ATTGCAATTCAAAAGATTTAAGCCACAACGGCGAATCTTACTTCCCAGGTGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
* *
30858408 ATTGAAGCTACAACGGCGAATCTCACTTCCTCGAC
66 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
* * * *
30858443 ATTGCAATTCAAAAGATTTAAGCCACAACGGTGAATCTTACTTCCCAGGTGATGCAGTGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
* *
30858508 ATTGAAACTACAACGGTGAATCTCACTTCCTCGAC
66 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
*
30858543 ATTGCAATTCAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCAGGCGATG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATG
30858597 TAGTGGAATA
Statistics
Matches: 687, Mismatches: 61, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
98 60 0.09
99 52 0.08
100 573 0.83
101 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (100 bp):
ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC
Found at i:30859072 original size:13 final size:13
Alignment explanation
Indices: 30859054--30859078 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30859044 TCTAGCCCGA
30859054 CGCCGCCTCCATG
1 CGCCGCCTCCATG
30859067 CGCCGCCTCCAT
1 CGCCGCCTCCAT
30859079 CAGTGCAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.56, G:0.20, T:0.16
Consensus pattern (13 bp):
CGCCGCCTCCATG
Found at i:30864161 original size:46 final size:46
Alignment explanation
Indices: 30864094--30864622 Score: 806
Period size: 46 Copynumber: 11.4 Consensus size: 46
30864084 CTAGAAGCAA
30864094 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
* *
30864140 CAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATTGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
* *
30864186 CAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
*
30864232 CAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
* * * *
30864278 CAGATCTTGCCTTCCTGTATTTGGCAGTGAAGTAGATCGAAGATGG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
* * * *
30864324 CAGATCTTATCTTCTTGTATTTGGCAGTGGACTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
* * *
30864370 CAGATCTTGTCTTCCTGTATTTGGCAACAGAGTAGATCTAAGAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATC-GA-AGATAG
* * *
30864418 CAGATCTTATCTTCCTGTATTTGGCAGCAGAGTAGATCTAAGATATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAG--ATAG
*
30864466 CAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
30864512 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
* *
30864558 CAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGACCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
* *
30864604 CAGATCTTATCTTCTTGTA
1 CAGATCTTGTCTTCCTGTA
30864623 CTGACAGTGG
Statistics
Matches: 440, Mismatches: 39, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
46 354 0.80
47 2 0.00
48 84 0.19
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (46 bp):
CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAG
Found at i:30864880 original size:44 final size:44
Alignment explanation
Indices: 30864746--30864882 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 44
30864736 CGGATTTTAC
* * *
30864746 CTCCCTAAGATTACAGTGGAGTACATTGAAGCCAGTAGTCCT-T
1 CTCCCTGAGATTACAGTGGAGTACATTGAAGCTAGTAGTTCTAT
* * ** * * * *
30864789 GCCTCCCTCG-G-TTGCAGTGGAGCAGGTTGATGGT-GGA-TTCTAC
1 --CTCCCT-GAGATTACAGTGGAGTACATTGAAGCTAGTAGTTCTAT
30864832 CTCCCTGAGATTACAGTGGAGTACATTGAAGCTAGTAGTTCTAT
1 CTCCCTGAGATTACAGTGGAGTACATTGAAGCTAGTAGTTCTAT
30864876 CTCCCTG
1 CTCCCTG
30864883 GGCAGCAGTG
Statistics
Matches: 67, Mismatches: 19, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
40 1 0.01
41 7 0.10
42 20 0.30
43 4 0.06
44 28 0.42
45 7 0.10
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (44 bp):
CTCCCTGAGATTACAGTGGAGTACATTGAAGCTAGTAGTTCTAT
Found at i:30864917 original size:19 final size:19
Alignment explanation
Indices: 30864893--30864932 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
30864883 GGCAGCAGTG
30864893 GAATAGATTGAAGATTACA
1 GAATAGATTGAAGATTACA
30864912 GAATAGATTGAAGATTACA
1 GAATAGATTGAAGATTACA
30864931 GA
1 GA
30864933 TCTTATCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.25
Consensus pattern (19 bp):
GAATAGATTGAAGATTACA
Found at i:30865136 original size:43 final size:44
Alignment explanation
Indices: 30865086--30865193 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
30865076 CTAAGATTAC
* *
30865086 AGTGGAGTACATTGAAGCCGGTAG-TCCTATCTCCCTAAGTAGT
1 AGTGGAGTACATTGAAGACGGTAGATCCTATCTCCCTAAGCAGT
** ** *
30865129 AGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTACATTGAAGACGGTAGATCCTATCTCCCTAAGCAGT
* * *
30865173 AGTGGAGCAGATCGAAGACGG
1 AGTGGAGTACATTGAAGACGG
30865194 CGAATCTTAT
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
43 19 0.37
44 33 0.63
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (44 bp):
AGTGGAGTACATTGAAGACGGTAGATCCTATCTCCCTAAGCAGT
Found at i:30865269 original size:43 final size:43
Alignment explanation
Indices: 30865241--30865618 Score: 194
Period size: 40 Copynumber: 8.9 Consensus size: 43
30865231 AAGCCACTAG
30865241 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
* * * * **
30865284 TCTTATCTCCCTAAGCAGTAGTGGAGCGGATC-ACATCAA--G-
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACTGA
* * * * *
30865324 TCTTATCTCCCTAAGCAATAGTGGAGCATACAAAAGAAACCGA
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
* * * * **
30865367 TCTTATCTCCCTAAGCAGTAGTGGAGCGGATC-ACATCAA--G-
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACTGA
* *
30865407 TCTTATCTCCCTAAGCACTAAGCAATAGTGGAGCAGACAAAAGAAACCGA
1 CCTTATCTCCCTAAG---T-AG---TAGTGGAGCAGACAAAAGAAACTGA
* * * **
30865457 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA--G-
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACTGA
** * * *
30865497 TTTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGA
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
* * * * * **
30865540 TCTTATCTCCCTAAGCAGTAGTGAAGCGGATC-ACATCAA--G-
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACTGA
* * *
30865580 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAA
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAA
30865619 ATGATGAATC
Statistics
Matches: 266, Mismatches: 45, Indels: 51
0.73 0.12 0.14
Matches are distributed among these distances:
39 3 0.01
40 109 0.41
41 4 0.02
42 2 0.01
43 108 0.41
44 6 0.02
46 3 0.01
47 15 0.06
49 1 0.00
50 15 0.06
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (43 bp):
CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
Found at i:30865339 original size:40 final size:40
Alignment explanation
Indices: 30865242--30865609 Score: 303
Period size: 43 Copynumber: 8.7 Consensus size: 40
30865232 AGCCACTAGC
* * **
30865242 CTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACTGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA--G-T
*
30865285 CTTATCTCCCTAAGCAGTAGTGGAGCGGATCACATCAAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGT
* * * **
30865325 CTTATCTCCCTAAGCAATAGTGGAGCATA-CAAAAGAAACCGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA--G-T
*
30865368 CTTATCTCCCTAAGCAGTAGTGGAGCGGATCACATCAAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGT
* **
30865408 CTTATCTCCCTAAGCACTAAGCAATAGTGGAGCAGA-CAAAAGAAACCGAT
1 CTTATCTCCCTAAG--C--AG---TAGTGGAGCAGATC-ACATCAA--G-T
30865458 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGT
* * * **
30865498 TTTATCTCCCTAAGCAATAGTGGAGCAGA-CAAAAGAAACCGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA--G-T
* *
30865541 CTTATCTCCCTAAGCAGTAGTGAAGCGGATCACATCAAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGT
*
30865581 CTTATCTCCCTAAGCAATAGTGGAGCAGA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGA
30865610 CAAAAGAAAA
Statistics
Matches: 263, Mismatches: 39, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
39 2 0.01
40 105 0.40
41 4 0.02
42 3 0.01
43 108 0.41
44 6 0.02
46 3 0.01
47 15 0.06
48 1 0.00
49 1 0.00
50 15 0.06
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (40 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGT
Found at i:30865346 original size:83 final size:83
Alignment explanation
Indices: 30865242--30865618 Score: 628
Period size: 83 Copynumber: 4.5 Consensus size: 83
30865232 AGCCACTAGC
* * *
30865242 CTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGATCTTATCTCCCTAAGCAGTAGTG
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
30865307 GAGCGGATCACATCAAGT
66 GAGCGGATCACATCAAGT
*
30865325 CTTATCTCCCTAAGCAATAGTGGAGCATACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
30865390 GAGCGGATCACATCAAGT
66 GAGCGGATCACATCAAGT
30865408 CTTATCTCCCTAAGCACTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGC
1 CTTATCT--C----C-CTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGC
*
30865473 AGTAGTGGAGCAGATCACATCAAGT
59 AGTAGTGGAGCGGATCACATCAAGT
*
30865498 TTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
*
30865563 AAGCGGATCACATCAAGT
66 GAGCGGATCACATCAAGT
30865581 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAA
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAA
30865619 ATGATGAATC
Statistics
Matches: 277, Mismatches: 10, Indels: 14
0.92 0.03 0.05
Matches are distributed among these distances:
83 195 0.70
84 1 0.00
85 1 0.00
88 1 0.00
89 1 0.00
90 78 0.28
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (83 bp):
CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
GAGCGGATCACATCAAGT
Found at i:30865461 original size:173 final size:173
Alignment explanation
Indices: 30865259--30865596 Score: 631
Period size: 173 Copynumber: 2.0 Consensus size: 173
30865249 CCCTAAGTAG
* *
30865259 TAGTGGAGCAGACAAAAGAAACTGATCTTATCTCCCTAAGCAGTAGTGGAGCGGATCACATCAAG
1 TAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
*
30865324 TCTTATCTCCCTAAGCAATAGTGGAGCATACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGT
66 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGT
*
30865389 GGAGCGGATCACATCAAGTCTTATCTCCCTAAGCACTAAGCAA
131 GAAGCGGATCACATCAAGTCTTATCTCCCTAAGCACTAAGCAA
30865432 TAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
1 TAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
*
30865497 TTTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGT
66 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGT
30865562 GAAGCGGATCACATCAAGTCTTATCTCCCTAAGCA
131 GAAGCGGATCACATCAAGTCTTATCTCCCTAAGCA
30865597 ATAGTGGAGC
Statistics
Matches: 160, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
173 160 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (173 bp):
TAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
TCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGT
GAAGCGGATCACATCAAGTCTTATCTCCCTAAGCACTAAGCAA
Found at i:30867950 original size:16 final size:16
Alignment explanation
Indices: 30867912--30867955 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
30867902 TTACATACTT
* *
30867912 ATACATATATGTATAT
1 ATACATATATATATAC
* *
30867928 TTTCATATATATATAC
1 ATACATATATATATAC
30867944 ATACATATATAT
1 ATACATATATAT
30867956 TTACTTACTC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (16 bp):
ATACATATATATATAC
Done.