Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 61 of 145
Found at i:20954124 original size:22 final size:23
Alignment explanation
Indices: 20954078--20954144 Score: 98
Period size: 25 Copynumber: 2.8 Consensus size: 23
20954068 TTTTTGCAAT
20954078 TTATTTATTTTAAAATTTTTATA
1 TTATTTATTTTAAAATTTTTATA
* *
20954101 TTATTTGTTTTAAATTATTTTATTA
1 TTATTTATTTTAAAAT-TTTTA-TA
20954126 TTATTTATTTTAAAATTTT
1 TTATTTATTTTAAAATTTT
20954145 CACATATTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 14 0.37
24 8 0.21
25 16 0.42
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (23 bp):
TTATTTATTTTAAAATTTTTATA
Found at i:20954422 original size:23 final size:23
Alignment explanation
Indices: 20954390--20954437 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
20954380 TGGTTATTTA
* * *
20954390 TTTTAATTTGCTTTGTATGTTAT
1 TTTTAATTTGCGTTGCATATTAT
*
20954413 TTTTATTTTGCGTTGCATATTAT
1 TTTTAATTTGCGTTGCATATTAT
20954436 TT
1 TT
20954438 ACTTTGAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.12, T:0.65
Consensus pattern (23 bp):
TTTTAATTTGCGTTGCATATTAT
Found at i:20954471 original size:24 final size:25
Alignment explanation
Indices: 20954429--20954487 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
20954419 TTTGCGTTGC
* ** *
20954429 ATATTATTTACTTTGAATTG-CTTT
1 ATATTATTTACCTCAAATTGTCTAT
20954453 ATATTATTTACCTCAAATTGTTCTAT
1 ATATTATTTACCTCAAATTG-TCTAT
20954479 ATATTATTT
1 ATATTATTT
20954488 CGTTTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 17 0.59
26 12 0.41
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (25 bp):
ATATTATTTACCTCAAATTGTCTAT
Found at i:20964027 original size:3 final size:3
Alignment explanation
Indices: 20964019--20964066 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
20964009 TACTAGCATA
20964019 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
20964067 AATAATAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:20964071 original size:3 final size:3
Alignment explanation
Indices: 20964065--20964094 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20964055 GATGATGATG
20964065 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20964095 TGTGTACAAG
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:20964215 original size:18 final size:17
Alignment explanation
Indices: 20964163--20964215 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
20964153 TAAATAGATG
20964163 AGTAAATGATAATAAAAT
1 AGTAAAT-ATAATAAAAT
* * *
20964181 AATAATAGATGATAAAAT
1 AGTAA-ATATAATAAAAT
20964199 AGTAAATATAATGAAAA
1 AGTAAATATAAT-AAAA
20964216 CGTAAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 5 0.19
18 21 0.78
19 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.26
Consensus pattern (17 bp):
AGTAAATATAATAAAAT
Found at i:20965567 original size:24 final size:24
Alignment explanation
Indices: 20965535--20965580 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20965525 TTTTGGGTCT
20965535 GTTTGGGTTAGGTTT-AGTTTGGTG
1 GTTTGGGTT-GGTTTGAGTTTGGTG
*
20965559 GTTTTGGTTGGTTTGAGTTTGG
1 GTTTGGGTTGGTTTGAGTTTGG
20965581 GTTGGGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.07, C:0.00, G:0.41, T:0.52
Consensus pattern (24 bp):
GTTTGGGTTGGTTTGAGTTTGGTG
Found at i:20966216 original size:239 final size:242
Alignment explanation
Indices: 20965776--20966258 Score: 742
Period size: 239 Copynumber: 2.0 Consensus size: 242
20965766 CCACTTCAGG
*
20965776 GAAATAAGATCGTTAGTCTGCTCCACCTCAACTTCAGGGAGATAAGACTCGTAACTTCAACCTGC
1 GAAATAAGATCGTTAGTCTGCTCCACCTCAACTTCAGGGAAATAAGACTCGTAACTT--ACC-GC
* * *
20965841 CCACTACAATTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCTACTATAACTTCAGAGAGAT
63 CCACTACAATTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTCAGAGAGAA
* * *
20965906 AAGATTCGCTATCTTCCAAGAGATAATATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGG
128 AAGATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGG
20965971 AGTTCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAAA
193 AGTTCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAAA
* *
20966021 GAAATAATATCGTTAGTCTGCTCCACTTCAACTTCAGGGAAATAAGACTCGTAAC-T-CC-CCCA
1 GAAATAAGATCGTTAGTCTGCTCCACCTCAACTTCAGGGAAATAAGACTCGTAACTTACCGCCCA
* * * *
20966083 CTACAACTTT-AGGGATATAAGGTTTATAGCTTTAATCTGCCCTACTGCAACTTTAGAGAGAAAA
66 CTACAA-TTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTCAGAGAGAAAA
* *
20966147 GATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTGCAA-TTTCAGGAA
130 GATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGG-A
*
20966211 GTTCAGATTTGTAACTTATAGCCTTAATCTGTTCCACTGTAACTTCAA
194 GTTCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAA
20966259 GGTTGATGCT
Statistics
Matches: 220, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
238 6 0.03
239 156 0.71
240 3 0.01
241 2 0.01
244 1 0.00
245 52 0.24
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (242 bp):
GAAATAAGATCGTTAGTCTGCTCCACCTCAACTTCAGGGAAATAAGACTCGTAACTTACCGCCCA
CTACAATTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTCAGAGAGAAAAG
ATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGGAGT
TCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAAA
Found at i:20966444 original size:11 final size:10
Alignment explanation
Indices: 20966430--20966495 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
20966420 GGCCTCTCCT
20966430 TTTTCTTTTTC
1 TTTT-TTTTTC
*
20966441 TTTTCTTTTCC
1 TTTT-TTTTTC
* *
20966452 TTATTTTTCC
1 TTTTTTTTTC
20966462 TTATTTTTTTC
1 TT-TTTTTTTC
*
20966473 TTATTTTTTC
1 TTTTTTTTTC
*
20966483 -TTATTTTTC
1 TTTTTTTTTC
20966492 TTTT
1 TTTT
20966496 ATGAAACATT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
9 7 0.16
10 17 0.38
11 21 0.47
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:20966468 original size:9 final size:10
Alignment explanation
Indices: 20966446--20966491 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
20966436 TTTTCTTTTC
20966446 TTTTCCTTAT
1 TTTTCCTTAT
20966456 TTTTCCTTATT
1 TTTTCCTTA-T
*
20966467 TTTTTCTTAT
1 TTTTCCTTAT
*
20966477 TTTTTCTTAT
1 TTTTCCTTAT
20966487 TTTTC
1 TTTTC
20966492 TTTTATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTCCTTAT
Found at i:20966470 original size:21 final size:21
Alignment explanation
Indices: 20966446--20966490 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
20966436 TTTTCTTTTC
20966446 TTTTCCTTATTTTTCCTTATT
1 TTTTCCTTATTTTTCCTTATT
* *
20966467 TTTTTCTTATTTTTTCTTATT
1 TTTTCCTTATTTTTCCTTATT
20966488 TTT
1 TTT
20966491 CTTTTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCCTTATTTTTCCTTATT
Found at i:20966489 original size:8 final size:9
Alignment explanation
Indices: 20966435--20966493 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 9
20966425 CTCCTTTTTC
*
20966435 TTTTTCTTT
1 TTTTTCTTA
20966444 TCTTTTCCTTA
1 T-TTTT-CTTA
20966455 TTTTTCCTTA
1 TTTTT-CTTA
20966465 TTTTTTTCTTA
1 --TTTTTCTTA
20966476 TTTTTTCTTA
1 -TTTTTCTTA
20966486 TTTTTCTT
1 TTTTTCTT
20966494 TTATGAAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
9 9 0.20
10 23 0.51
11 8 0.18
12 5 0.11
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTCTTA
Found at i:20966497 original size:21 final size:21
Alignment explanation
Indices: 20966435--20966497 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
20966425 CTCCTTTTTC
* *
20966435 TTTTTCTTTTCTTTTC-CTTAT
1 TTTTTCTTAT-TTTTCTTTTAT
*
20966456 TTTTCCTTATTTTT-TTCTTAT
1 TTTTTCTTATTTTTCTT-TTAT
20966477 TTTTTCTTATTTTTCTTTTAT
1 TTTTTCTTATTTTTCTTTTAT
20966498 GAAACATTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 29 0.83
22 2 0.06
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTCTTATTTTTCTTTTAT
Found at i:20973239 original size:44 final size:44
Alignment explanation
Indices: 20973189--20974118 Score: 660
Period size: 44 Copynumber: 20.6 Consensus size: 44
20973179 TTTGAACCTA
*
20973189 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* ** * * *
20973233 CCCCACTATAACTTCAGGGAGATAAGATTTTTAGCTTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * *
20973277 TTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * *
20973321 CTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * *
20973365 CTCCACTGTAACTTCAGGTAGATAAGATTTTTAGCTTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * *
20973409 TTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAACCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * * *
20973453 CTCCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGT-A----T--CTTCAATCTG
* * * *
20973504 TTCCATTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTG
* * * *
20973549 CTCCACTGCAACTTTAGGGAAATAAGATTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* ** * *
20973593 CTCCACTGCAACTTCAGGGAGATAAGGTTTAAAACTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * *
20973637 CTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTG
* *
20973682 CTCCACTGCAACTTTAGGGAGATAAGACTTGTATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * *
20973726 CCCCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTT-AATCTG
1 CTCCACTGCAACTTCAGGGAGAT---A-AG--ATTTGTA-TCTTCAATCTG
* * * * ** * * *
20973776 TTCCACTGCAACTTTAAGGAAATAAGATTCACTATATTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-TGTATCTTCAATCTG
* * * * ** * * *
20973821 CTCCATTGCAACTTTAGGGAGATAAAACTCATAACTTAAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * ** * * *
20973865 CCCCACTGCAACTTAAAGGG-GATCCGATTTGTATTTTGTAGCCTTGATATG
1 CTCCACTGCAACTT-CAGGGAGATAAGATTTGTA-TCT-T---C--AATCTG
* * * ** **
20973916 TTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-TGTATCTTCAATCTG
* * * * * *
20973961 CTCCATTGCAACTTTAGGGATATAAGACTTGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * * *
20974005 C-CCTACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTA
1 CTCC-ACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * *
20974049 CTCTAATACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTG
* *
20974094 CTCCACTACAACTTTAGGGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAA
20974119 AATTCGTCAT
Statistics
Matches: 685, Mismatches: 170, Indels: 61
0.75 0.19 0.07
Matches are distributed among these distances:
43 2 0.00
44 414 0.60
45 167 0.24
46 2 0.00
47 4 0.01
48 1 0.00
50 33 0.05
51 59 0.09
52 3 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
Found at i:20973388 original size:132 final size:133
Alignment explanation
Indices: 20973183--20974118 Score: 789
Period size: 133 Copynumber: 6.9 Consensus size: 133
20973173 ATGTAATTTG
* * * * **
20973183 AACCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTGCCCCACTATAACTTC
1 AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTC
* * *
20973248 AGGGAGATAAGATTT-TTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
66 AGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
20973312 TTC
131 TTC
* * *
20973315 AACCTGCTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGTAACTTC
1 AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTC
* * * *
20973380 AGGTAGATAAGATTT-TTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
66 AGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
20973444 TTC
131 TTC
* * * * * * *
20973447 AACCCGCTCCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTTAATCTGTTCCATTG
1 AACCTGCTCCACTGCAACTTCAGGGAGAT-AAG---GT---TTGTAGCTTTAATCTGCTCCACTG
* * * * *
20973512 CAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAAATAAGAT
59 CAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
20973577 TTGTAGCTTT
124 TTGTAGCTTC
* ** * *
20973587 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTAAAACTTTAATCTGCTCTACTGCAACTTC
1 AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTC
* * * * * *
20973652 AGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTATC
66 AGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
20973717 TTC
131 TTC
* * * * * * * *
20973720 AATCTGCCCCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTTAATCTGTTCCACTGC
1 AACCTGCTCCACTGCAACTTCAGGGAGAT---A-AG--GTTTGTAGCTTTAATCTGCTCCACTGC
* * * ** ** * * * * * *
20973785 AACTTTAAGGAAATAAGATTCACTATATTTAGTCTGCTCCATTGCAACTTTAGGGAGATAAAACT
60 AACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
** * *
20973850 CATAACTTA
125 TGTAGCTTC
* * ** * * * * * *
20973859 AACCTGCCCCACTGCAACTTAAAGGGGATCCGATTTGTATTTTGTAGCCTTGATATGTTCCACCG
1 AACCTGCTCCACTGCAACTT-CA-GGGA---GATAAG--GTTTGTAGCTTTAATCTGCTCCACTG
* ** * ** * * * *
20973924 CAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTGCTCCATTGCAACTTTAGGGATATAAGAC
59 CAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
20973989 TTGTAACTTC
124 TTGTAGCTTC
* * * * * *
20973999 AACCTGC-CCTACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTACTCTAATACAACTT
1 AACCTGCTCC-ACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTT
* * * * *
20974063 CAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTACAACTTTAGGGAGATAA
65 CAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
20974119 AATTCGTCAT
Statistics
Matches: 672, Mismatches: 112, Indels: 39
0.82 0.14 0.05
Matches are distributed among these distances:
132 151 0.22
133 182 0.27
135 4 0.01
136 4 0.01
137 1 0.00
138 4 0.01
139 143 0.21
140 177 0.26
141 3 0.00
144 3 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (133 bp):
AACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTC
AGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
TTC
Found at i:20973766 original size:272 final size:268
Alignment explanation
Indices: 20973191--20974118 Score: 866
Period size: 272 Copynumber: 3.4 Consensus size: 268
20973181 TGAACCTACT
* * * * *
20973191 CCACTGCAACTTCAGGGAGAT-A-AG--ATTTGTATCTTTAATCTGCCCCACTATAACTTCAGGG
1 CCACTGTAACTTCAGGGAGATGATTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGG
* * * * * * *
20973252 AGATAAGATTT-TTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCA
66 AAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTAA
* *
20973316 ACCTGCTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGTAACTTCA
131 ACCTGCTCCACTGCAACTTAAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGCAACTTCA
* * * * * * * *
20973381 GGTAGATAAGATTTTTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTT
196 GG-AGATAAGATTTCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTT
* *
20973446 CAACCCGCT
260 CAACCTGCC
* * * * * * *
20973455 CCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTTAATCTGTTCCATTGCAACTTTA
1 CCACTGTAACTTCAGGGAGATGA---TTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCA
*
20973520 GGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAAATAAGATTTGTAGCT
63 GGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCT
* * * * ** * *
20973585 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTAAAACTTTAATCTGCTCTACTGCAACT
128 TAAACCTGCTCCACTGCAACTTAAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGCAACT
20973650 TCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTA
193 TCAG-GAGATAAGATTT-CTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTA
* *
20973715 TCTTCAATCTGCC
256 ACTTCAACCTGCC
** * * * * * *
20973728 CCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTTAATCTGTTCCACTGCAACTTTAA
1 CCACTGTAACTTCAGGGAGAT--GATTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCAG
** * * * * * * ** *
20973793 GGAAATAAGATTCACTATATTTAGTCTGCTCCATTGCAACTTTAGGGAGATAAAACTCATAACTT
64 GGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTT
* ** * * * * * *
20973858 AAACCTGCCCCACTGCAACTTAAAGGGGATCCGATTTGTATTTTGTAGCCTTGATATGTTCCACC
129 AAACCTGCTCCACTGCAACTT-AA-GGGA---GATAAG--CTTTGTAGCTTTAATCTGCTCCACT
* * * * *
20973923 GCAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTGCTCCATTGCAACTTTAGGGATATAAGA
187 GCAACTTCA-GGAGATAAGATT-TCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGA
20973988 CTTGTAACTTCAACCTGCC
250 CTTGTAACTTCAACCTGCC
* * * * * * *
20974007 CTACTGTAACTTCAGGGAGAT-A-AG--GTTTATAGCTTTAATCTACTCTAATACAACTTCAGGG
1 CCACTGTAACTTCAGGGAGATGATTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGG
* * * *
20974068 AGATAAGATTTGCTATCTTCAGTTTGCTCCACTACAACTTTAGGGAGATAA
66 AAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAA
20974119 AATTCGTCAT
Statistics
Matches: 537, Mismatches: 106, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
264 18 0.03
265 1 0.00
269 1 0.00
271 39 0.07
272 222 0.41
273 137 0.26
274 4 0.01
275 3 0.01
276 1 0.00
277 4 0.01
279 106 0.20
280 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (268 bp):
CCACTGTAACTTCAGGGAGATGATTGTAATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGG
AAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTAA
ACCTGCTCCACTGCAACTTAAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGCAACTTCA
GGAGATAAGATTTCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTC
AACCTGCC
Found at i:20973963 original size:412 final size:405
Alignment explanation
Indices: 20973174--20974118 Score: 1061
Period size: 412 Copynumber: 2.3 Consensus size: 405
20973164 GTATAGGAAA
* * * * * * * *
20973174 TGTAATTTGAACCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTGCCCCAC
1 TGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAACTTTAATCTGCTCTAC
* * * * * *
20973239 TATAACTTCAGGGAGATAAGATTT-TTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAG
66 TACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAG
* * * * * *
20973303 ATTTGTAGCTTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTGCTC
131 ACTTGTAGCTTCAACCTGCCCCACTACAACTTCAGGGAGATAAGATTTGTAGCCTTAATCTGCTC
* * * ** * * *
20973368 CACTGTAACTTCAGGTAGATAAGATTTTTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATA
196 CACTGCAACTTAAGGTAAATAAGATTACTAGATTCAATCTGCTCCACTGCAACTTCAGGGAGATA
* * ** * * * * * * * * *
20973433 AGATTTGTAGCTTCAACCCGCTCCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTT
261 AAACTCATAACTTAAACCCGCCCCACTGCAACTTAAGGGAGATCAGATTTGTAACTTGTAGCCTT
* ** * **
20973498 AATCTGTTCCATTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
326 AATATGTTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCACTGCAACTT
*
20973563 TAGGGAAATAAGATT
391 TAGGGAAATAAGACT
* * * *
20973578 TGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTAAAACTTTAATCTGCTCTAC
1 TGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAACTTTAATCTGCTCTAC
* * *
20973643 TGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAG
66 TACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAG
* * * *
20973708 ACTTGTATCTTCAATCTGCCCCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTTAAT
131 ACTTGTAGCTTCAACCTGCCCCACTACAACTTCAGGGAGAT---A-AG--ATTTGTAGCCTTAAT
* * * * * *
20973773 CTGTTCCACTGCAACTTTAAGG-AAATAAGATTCACTATATTTAGTCTGCTCCATTGCAACTTTA
190 CTGCTCCACTGCAAC-TTAAGGTAAATAAGATT-ACTAGATTCAATCTGCTCCACTGCAACTTCA
* * **
20973837 GGGAGATAAAACTCATAACTTAAACCTGCCCCACTGCAACTTAAAGGG-GATCCGATTTGTATTT
253 GGGAGATAAAACTCATAACTTAAACCCGCCCCACTGCAACTT-AAGGGAGATCAGATTTGTAACT
* **
20973901 TGTAGCCTTGATATGTTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTGCTCCA
317 TGTAGCCTTAATATGTTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCA
* *
20973966 TTGCAACTTTAGGGATATAAGACT
382 CTGCAACTTTAGGGAAATAAGACT
* * *
20973990 TGTAACTTCAACCTGC-CCTACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTACTCTA
1 TGTAACTTCAACCTGCTCC-ACTGCAACTTCAGGGAGATAAGGTTTATAACTTTAATCTGCTCTA
* *
20974054 ATACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTACAACTTTAGGGAGATAA
65 CTACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAA
20974119 AATTCGTCAT
Statistics
Matches: 445, Mismatches: 85, Indels: 14
0.82 0.16 0.03
Matches are distributed among these distances:
404 75 0.17
405 68 0.15
408 1 0.00
409 1 0.00
411 37 0.08
412 259 0.58
413 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (405 bp):
TGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATAACTTTAATCTGCTCTAC
TACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAG
ACTTGTAGCTTCAACCTGCCCCACTACAACTTCAGGGAGATAAGATTTGTAGCCTTAATCTGCTC
CACTGCAACTTAAGGTAAATAAGATTACTAGATTCAATCTGCTCCACTGCAACTTCAGGGAGATA
AAACTCATAACTTAAACCCGCCCCACTGCAACTTAAGGGAGATCAGATTTGTAACTTGTAGCCTT
AATATGTTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCACTGCAACTT
TAGGGAAATAAGACT
Found at i:20977098 original size:21 final size:23
Alignment explanation
Indices: 20977074--20977116 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20977064 CAACACAACT
20977074 TCTCA-ATT-AGTGAATATCTTG
1 TCTCATATTAAGTGAATATCTTG
*
20977095 TCTCATATTAAGTGAATTTCTT
1 TCTCATATTAAGTGAATATCTT
20977117 ACTGAGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.47
Consensus pattern (23 bp):
TCTCATATTAAGTGAATATCTTG
Found at i:20977650 original size:41 final size:42
Alignment explanation
Indices: 20977533--20977659 Score: 175
Period size: 43 Copynumber: 3.0 Consensus size: 42
20977523 GCCCCAAAAG
*
20977533 TACATTTTGCTAGATTGAGCTTCAGTTGGAATTTTCTCAATC
1 TACATTTTGCTAGATTGAGCTTCAGCTGGAATTTTCTCAATC
* * * *
20977575 TACATTTTTGTTGGATTAAGCTTCAGCTAGAATTTTCTCAATC
1 TACA-TTTTGCTAGATTGAGCTTCAGCTGGAATTTTCTCAATC
* *
20977618 TACATTTTACT-GAATGAGCTTCAGCTGGAATTTTCTCAATC
1 TACATTTTGCTAGATTGAGCTTCAGCTGGAATTTTCTCAATC
20977659 T
1 T
20977660 CAAGAACAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
41 28 0.38
42 9 0.12
43 37 0.50
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (42 bp):
TACATTTTGCTAGATTGAGCTTCAGCTGGAATTTTCTCAATC
Found at i:20982343 original size:19 final size:20
Alignment explanation
Indices: 20982312--20982365 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
20982302 GGTCTTTTTC
* *
20982312 TGAAATTTAATGCATATG-A
1 TGAAATGTAATGCAAATGCA
*
20982331 TGCAATGTAATGCAAATGCA
1 TGAAATGTAATGCAAATGCA
20982351 TGAAATG-AATGCAAA
1 TGAAATGTAATGCAAA
20982366 AAGAGGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGCA
Found at i:20984333 original size:30 final size:31
Alignment explanation
Indices: 20984294--20984353 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
20984284 AGAGGTGGGA
*
20984294 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
20984325 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
20984354 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:20984591 original size:18 final size:18
Alignment explanation
Indices: 20984568--20984602 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20984558 TAGTTTGATA
20984568 TTCGAGTTATTCGAATTG
1 TTCGAGTTATTCGAATTG
*
20984586 TTCGAGTTATTCTAATT
1 TTCGAGTTATTCGAATT
20984603 TGAAAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (18 bp):
TTCGAGTTATTCGAATTG
Found at i:20994748 original size:41 final size:41
Alignment explanation
Indices: 20994691--20994796 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 41
20994681 GGAAGTTATC
*
20994691 TGAAAAGGTTAAAAAGGACAATATCCGACAAA-GATACCAAA
1 TGAAAAGGTTGAAAAGGACAATATCCGA-AAAGGATACCAAA
*
20994732 TGAAAAGGTTGAAAAGGACAATATCCGAAAAGGATATCAAA
1 TGAAAAGGTTGAAAAGGACAATATCCGAAAAGGATACCAAA
* * *
20994773 TGAATAGGTTGAAAATGACGATAT
1 TGAAAAGGTTGAAAAGGACAATAT
20994797 TTGAAGAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 3 0.05
41 56 0.95
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (41 bp):
TGAAAAGGTTGAAAAGGACAATATCCGAAAAGGATACCAAA
Found at i:21001841 original size:29 final size:29
Alignment explanation
Indices: 21001809--21001872 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
21001799 CTGAAGTAGG
21001809 AAAGTCTTATGGGACTATTTTATGAGTAC
1 AAAGTCTTATGGGACTATTTTATGAGTAC
21001838 AAAGTCTTATGGGACTATTTTATGAGTAC
1 AAAGTCTTATGGGACTATTTTATGAGTAC
21001867 -AAGTCT
1 AAAGTCT
21001873 GCAAAGAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (29 bp):
AAAGTCTTATGGGACTATTTTATGAGTAC
Found at i:21017852 original size:14 final size:14
Alignment explanation
Indices: 21017833--21017881 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
21017823 TCATTTTTTA
21017833 AATTTTTACATTCT
1 AATTTTTACATTCT
21017847 AATTTTTACATTCT
1 AATTTTTACATTCT
*
21017861 AATTCTTT-TATTCT
1 AATT-TTTACATTCT
21017875 AATTTTT
1 AATTTTT
21017882 TTATTTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 3 0.09
14 27 0.82
15 3 0.09
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTTTACATTCT
Found at i:21017883 original size:14 final size:14
Alignment explanation
Indices: 21017842--21017886 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
21017832 AAATTTTTAC
**
21017842 ATTCTAATTTTTAC
1 ATTCTAATTTTTTT
*
21017856 ATTCTAATTCTTTT
1 ATTCTAATTTTTTT
21017870 ATTCTAATTTTTTT
1 ATTCTAATTTTTTT
21017884 ATT
1 ATT
21017887 TTCTTCTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTCTAATTTTTTT
Found at i:21021057 original size:5 final size:5
Alignment explanation
Indices: 21021047--21021077 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
21021037 ACCCTAGCTC
21021047 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG T
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG T
21021078 CTTCTTCCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:21021616 original size:4 final size:4
Alignment explanation
Indices: 21021599--21021633 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
21021589 TTACCTTATT
*
21021599 TTTA TTTG TTTA TTTA TTTA TTTA -TTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
21021634 GTTTCTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:21021616 original size:12 final size:12
Alignment explanation
Indices: 21021599--21021633 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
21021589 TTACCTTATT
*
21021599 TTTATTTGTTTA
1 TTTATTTATTTA
21021611 TTTATTTATTTA
1 TTTATTTATTTA
21021623 -TTATTTATTTA
1 TTTATTTATTTA
21021634 GTTTCTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTATTTATTTA
Found at i:21021956 original size:3 final size:3
Alignment explanation
Indices: 21021948--21021983 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
21021938 TTTTATTTTC
*
21021948 TAT TAT TAT TAT TAT TAT T-T TAT TAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21021984 CTTCTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:21021972 original size:17 final size:17
Alignment explanation
Indices: 21021950--21021983 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21021940 TTATTTTCTA
*
21021950 TTATTATTATTATTATT
1 TTATTAGTATTATTATT
21021967 TTATTAGTATTATTATT
1 TTATTAGTATTATTATT
21021984 CTTCTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTAGTATTATTATT
Found at i:21023169 original size:6 final size:6
Alignment explanation
Indices: 21023158--21023221 Score: 56
Period size: 6 Copynumber: 9.8 Consensus size: 6
21023148 TTTGTTTCTC
* * *
21023158 TTTTTA TTTTTA TTTTTTTA TGTTTA TGTTTA ATTTTA TTTTTA GTTGTTTTA
1 TTTTTA TTTTTA --TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA --T-TTTTA
21023211 TTTTTA TTTTT
1 TTTTTA TTTTT
21023222 TTAGACTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
6 36 0.73
7 1 0.02
8 7 0.14
9 5 0.10
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:21023219 original size:26 final size:25
Alignment explanation
Indices: 21023143--21023220 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 25
21023133 GGATCAGTGA
*
21023143 TTTTATTTGTTTCTCTTTTTATTTTTAT
1 TTTTA-TTGTTT-TATTTTTA-TTTTAT
* *
21023171 TTTT-TTATGTTTATGTTTAATTTTAT
1 TTTTATTGT-TTTAT-TTTTATTTTAT
21023197 TTTTAGTTGTTTTATTTTTATTTT
1 TTTTA-TTGTTTTATTTTTATTTT
21023221 TTTAGACTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 23 0.56
27 11 0.27
28 7 0.17
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (25 bp):
TTTTATTGTTTTATTTTTATTTTAT
Found at i:21037150 original size:16 final size:16
Alignment explanation
Indices: 21037131--21037172 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
21037121 TTCATTAGGA
*
21037131 TAATATTTTTATTTTC
1 TAATATTTTTATCTTC
21037147 TAATA-TTTTATCTTC
1 TAATATTTTTATCTTC
21037162 TAATTATTTTT
1 TAA-TATTTTT
21037173 GGATAACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 12 0.52
16 7 0.30
17 4 0.17
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATATTTTTATCTTC
Found at i:21041954 original size:27 final size:27
Alignment explanation
Indices: 21041917--21041971 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
21041907 TTCACTCCTA
21041917 TAAAAATGTTTATTCATATTTCTATAC
1 TAAAAATGTTTATTCATATTTCTATAC
*
21041944 TAAAAATGTTTATTCATGTTTCTATAC
1 TAAAAATGTTTATTCATATTTCTATAC
21041971 T
1 T
21041972 TAGGAGAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (27 bp):
TAAAAATGTTTATTCATATTTCTATAC
Found at i:21046791 original size:21 final size:21
Alignment explanation
Indices: 21046765--21046805 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21046755 ATGCGGCAAG
21046765 TTAACTGGCCACATCAGCTAA
1 TTAACTGGCCACATCAGCTAA
**
21046786 TTAACTGGCCATGTCAGCTA
1 TTAACTGGCCACATCAGCTA
21046806 TCCCATTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
TTAACTGGCCACATCAGCTAA
Found at i:21047984 original size:24 final size:24
Alignment explanation
Indices: 21047940--21048008 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
21047930 TTTCCAAAAT
* *
21047940 ATTTAGTATTTATTAGTATAATAA
1 ATTTAGCATTTATTAGCATAATAA
* *
21047964 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATTAGCATAATAA
*
21047988 ACTT-GACATTTATTAGCATAA
1 ATTTAG-CATTTATTAGCATAA
21048009 AAGTATTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAA
Found at i:21050319 original size:24 final size:23
Alignment explanation
Indices: 21050259--21050319 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
21050249 AAGATCTAGT
*
21050259 ATTTATTAGTATAATATATTTAG
1 ATTTATTAGTATAATATATTTAC
* *
21050282 ATTTACTAGCATAATATATTTGAC
1 ATTTATTAGTATAATATATTT-AC
21050306 ATTTATTAGTATAA
1 ATTTATTAGTATAA
21050320 AAATATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (23 bp):
ATTTATTAGTATAATATATTTAC
Found at i:21062954 original size:24 final size:24
Alignment explanation
Indices: 21062925--21063031 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 24
21062915 TTCCACTAGA
21062925 AATAAAAATAAGAACAATGAAA-AT
1 AATAAAAATAA-AACAATGAAATAT
21062949 AATAAAAAT-AAACTAA-GAAATAT
1 AATAAAAATAAAAC-AATGAAATAT
** *
21062972 AGGAATAATAAAACATAT-AAATAT
1 AATAAAAATAAAACA-ATGAAATAT
* *
21062996 AATAACAATAAAAATAATGAAA-AT
1 AATAAAAAT-AAAACAATGAAATAT
21063020 AAT-AAAATAAAA
1 AATAAAAATAAAA
21063032 TAATAGAACA
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
22 11 0.16
23 16 0.24
24 33 0.49
25 8 0.12
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
AATAAAAATAAAACAATGAAATAT
Found at i:21062958 original size:9 final size:9
Alignment explanation
Indices: 21062944--21063026 Score: 50
Period size: 9 Copynumber: 9.3 Consensus size: 9
21062934 AAGAACAATG
21062944 AAAATAATA
1 AAAATAATA
21062953 AAAATAAACTA
1 AAAAT-AA-TA
21062964 AGAAAT-ATA
1 A-AAATAATA
**
21062973 GGAATAATA
1 AAAATAATA
21062982 AAACAT-AT-
1 AAA-ATAATA
21062990 -AAAT-ATA
1 AAAATAATA
* *
21062997 ATAACAATA
1 AAAATAATA
*
21063006 AAAATAATG
1 AAAATAATA
21063015 AAAATAATA
1 AAAATAATA
21063024 AAA
1 AAA
21063027 TAAAATAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
6 4 0.07
7 2 0.04
8 5 0.09
9 33 0.59
10 5 0.09
11 3 0.05
12 4 0.07
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.22
Consensus pattern (9 bp):
AAAATAATA
Found at i:21063006 original size:15 final size:14
Alignment explanation
Indices: 21062988--21063034 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
21062978 AATAAAACAT
21062988 ATAAATATAATAACA
1 ATAAATATAATAA-A
*
21063003 ATAAAAATAATGAAA
1 ATAAATATAAT-AAA
*
21063018 AT-AATAAAATAAA
1 ATAAATATAATAAA
21063031 ATAA
1 ATAA
21063035 TAGAACATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
15 13 0.48
16 2 0.07
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (14 bp):
ATAAATATAATAAA
Found at i:21063044 original size:23 final size:24
Alignment explanation
Indices: 21062925--21063044 Score: 81
Period size: 24 Copynumber: 5.1 Consensus size: 24
21062915 TTCCACTAGA
* * *
21062925 AATAAAAATAAGAACAATGAAAAT
1 AATAACAATAAAAATAATGAAAAT
* *
21062949 AATAAAAAT-AAACTAA-GAAATAT
1 AATAACAATAAAAATAATGAAA-AT
** *
21062972 AGGAATAATAAAACAT-AT-AAATAT
1 AATAACAATAAAA-ATAATGAAA-AT
21062996 AATAACAATAAAAATAATGAAAAT
1 AATAACAATAAAAATAATGAAAAT
*
21063020 AATAA-AAT-AAAATAATAGAACAT
1 AATAACAATAAAAATAAT-GAAAAT
21063043 AA
1 AA
21063045 ACATGAAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
22 12 0.15
23 24 0.31
24 38 0.49
25 4 0.05
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
AATAACAATAAAAATAATGAAAAT
Found at i:21069608 original size:18 final size:17
Alignment explanation
Indices: 21069581--21069614 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21069571 ATTAGAATGT
*
21069581 AAAAATTAAATTAAAAC
1 AAAAATTAAAATAAAAC
21069598 AAAAATATAAAATAAAA
1 AAAAAT-TAAAATAAAA
21069615 TAAACAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATTAAAATAAAAC
Found at i:21077004 original size:15 final size:16
Alignment explanation
Indices: 21076975--21077013 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21076965 TTTTTATTTT
*
21076975 TATTTTTAATCAAATA
1 TATTTTTAATAAAATA
21076991 TATTTTT-ATAAAATA
1 TATTTTTAATAAAATA
21077006 TATATTTT
1 TAT-TTTT
21077014 TTGGACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTTAATAAAATA
Found at i:21077008 original size:45 final size:45
Alignment explanation
Indices: 21076956--21077099 Score: 183
Period size: 45 Copynumber: 3.3 Consensus size: 45
21076946 ATTATATATT
21076956 AAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATA
1 AAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATA
** * * * *
21077001 AAATATATA--TTT-TTTGGACTTTTAATCCGAAT-TA--TATATT
1 AAATATATATTTTTATTTTTATTTTTAAT-CAAATATATTTTTATA
21077041 AAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATA
1 AAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATA
21077086 AAATATATATTTTT
1 AAATATATATTTTT
21077100 TGGACTTTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
40 13 0.16
42 20 0.25
43 20 0.25
45 27 0.34
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (45 bp):
AAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATA
Found at i:21077049 original size:42 final size:42
Alignment explanation
Indices: 21076942--21077140 Score: 183
Period size: 42 Copynumber: 4.7 Consensus size: 42
21076932 CCGGCCCAGC
* ** *
21076942 CCGAATTATATATTAAATATATATTTTTATTTTTATTTTTAAT
1 CCGAATTATATATTAAATATATATATTT-TTTGGACTTTTAAT
* * *
21076985 -C-AAATATATTTTTATAAAATATATATTTTTTGGACTTTTAAT
1 CCGAATTATA-TATTA-AATATATATATTTTTTGGACTTTTAAT
* ** *
21077027 CCGAATTATATATTAAATATATATTTTTATTTTTATTTTTAAT
1 CCGAATTATATATTAAATATATATATTT-TTTGGACTTTTAAT
* * *
21077070 -C-AAATATATTTTTATAAAATATATATTTTTTGGACTTTTAAT
1 CCGAATTATA-TATTA-AATATATATATTTTTTGGACTTTTAAT
21077112 CCGAATTATATATTAAATATATAT-TTTTT
1 CCGAATTATATATTAAATATATATATTTTT
21077141 ATTTTTAATT
Statistics
Matches: 123, Mismatches: 24, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
41 17 0.14
42 51 0.41
43 43 0.35
44 12 0.10
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.55
Consensus pattern (42 bp):
CCGAATTATATATTAAATATATATATTTTTTGGACTTTTAAT
Found at i:21077068 original size:85 final size:85
Alignment explanation
Indices: 21076942--21077147 Score: 403
Period size: 85 Copynumber: 2.4 Consensus size: 85
21076932 CCGGCCCAGC
21076942 CCGAATTATATATTAAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATAAAATAT
1 CCGAATTATATATTAAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATAAAATAT
21077007 ATATTTTTTGGACTTTTAAT
66 ATATTTTTTGGACTTTTAAT
21077027 CCGAATTATATATTAAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATAAAATAT
1 CCGAATTATATATTAAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATAAAATAT
21077092 ATATTTTTTGGACTTTTAAT
66 ATATTTTTTGGACTTTTAAT
21077112 CCGAATTATATATTAAATATATATTTTTTATTTTTA
1 CCGAATTATATATTAAATATATA-TTTTTATTTTTA
21077148 ATTAAATATG
Statistics
Matches: 120, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 108 0.90
86 12 0.10
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.55
Consensus pattern (85 bp):
CCGAATTATATATTAAATATATATTTTTATTTTTATTTTTAATCAAATATATTTTTATAAAATAT
ATATTTTTTGGACTTTTAAT
Found at i:21077089 original size:15 final size:16
Alignment explanation
Indices: 21077060--21077098 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21077050 TTTTTATTTT
*
21077060 TATTTTTAATCAAATA
1 TATTTTTAATAAAATA
21077076 TATTTTT-ATAAAATA
1 TATTTTTAATAAAATA
21077091 TATATTTT
1 TAT-TTTT
21077099 TTGGACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTTAATAAAATA
Found at i:21092967 original size:18 final size:18
Alignment explanation
Indices: 21092943--21092986 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
21092933 CACAGTTTGG
*
21092943 CAAATTAATACAGTTCAC
1 CAAATTAATACAGATCAC
*
21092961 CATATTAATACAGATCAC
1 CAAATTAATACAGATCAC
21092979 CAAATTAA
1 CAAATTAA
21092987 CATAGTTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27
Consensus pattern (18 bp):
CAAATTAATACAGATCAC
Found at i:21100115 original size:16 final size:16
Alignment explanation
Indices: 21100094--21100126 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21100084 AAGGTTGTTG
21100094 AACTGAAATAGAGTTT
1 AACTGAAATAGAGTTT
21100110 AACTGAAATAGAGTTT
1 AACTGAAATAGAGTTT
21100126 A
1 A
21100127 CTCTTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (16 bp):
AACTGAAATAGAGTTT
Found at i:21102371 original size:19 final size:19
Alignment explanation
Indices: 21102349--21102491 Score: 112
Period size: 19 Copynumber: 7.4 Consensus size: 19
21102339 ATGCACCTCA
21102349 TGTGCCAATATGCACTTTG
1 TGTGCCAATATGCACTTTG
* *
21102368 TGTGCCAGTATGCGCTTTG
1 TGTGCCAATATGCACTTTG
** *
21102387 TGCACCAGGA-ATGCGCTTTG
1 TGTGCCA--ATATGCACTTTG
* *
21102407 TGTGCCAAGATGCACTTCG
1 TGTGCCAATATGCACTTTG
** * *
21102426 TGTGCCAGGATGTACTTCG
1 TGTGCCAATATGCACTTTG
21102445 TGTGCCAATAT--ACGTTTCG
1 TGTGCCAATATGCAC-TTT-G
*
21102464 TGTGCCAATAATGCACTTCG
1 TGTGCCAAT-ATGCACTTTG
21102484 TGTGCCAA
1 TGTGCCAA
21102492 GTTGCACATT
Statistics
Matches: 101, Mismatches: 15, Indels: 15
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.02
18 3 0.03
19 66 0.65
20 26 0.26
21 2 0.02
22 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (19 bp):
TGTGCCAATATGCACTTTG
Found at i:21102452 original size:38 final size:39
Alignment explanation
Indices: 21102333--21102498 Score: 122
Period size: 39 Copynumber: 4.3 Consensus size: 39
21102323 CACTTCATAC
* * * * *
21102333 GCCATGATGCACCTCATGTGCCAA-TATGCACTTTGTGT
1 GCCAAGATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
* * ** * * *
21102371 GCC-AGTATGCGCTTTGTGCACCAGGAATGCGCTTTGTGT
1 GCCAAG-ATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
* *
21102410 GCCAAGATGCACTTCGTGTGCC-AGGATGTACTTCGTGT
1 GCCAAGATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
* * ** *
21102448 GCCAATATACGTTTCGTGTGCCAATAATGCACTTCGTGT
1 GCCAAGATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
*
21102487 GCCAAGTTGCAC
1 GCCAAGATGCAC
21102499 ATTATGTGCT
Statistics
Matches: 93, Mismatches: 31, Indels: 7
0.71 0.24 0.05
Matches are distributed among these distances:
37 1 0.01
38 43 0.46
39 47 0.51
40 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (39 bp):
GCCAAGATGCACTTCGTGTGCCAAGAATGCACTTCGTGT
Found at i:21103689 original size:27 final size:27
Alignment explanation
Indices: 21103651--21103707 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
21103641 GGCATTACAT
21103651 GGTTGCTGAAAAGTAAACGTGACCACG
1 GGTTGCTGAAAAGTAAACGTGACCACG
21103678 GGTTGCTGAAAAGTAAACGTGACCACG
1 GGTTGCTGAAAAGTAAACGTGACCACG
21103705 GGT
1 GGT
21103708 CATTCATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.19
Consensus pattern (27 bp):
GGTTGCTGAAAAGTAAACGTGACCACG
Found at i:21105690 original size:27 final size:25
Alignment explanation
Indices: 21105673--21105721 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
21105663 ATTTAATTAG
21105673 ATAA-ATATTATTTTATTAATATTTTA
1 ATAAGATATTATTTTATT-AT-TTTTA
*
21105699 ATAAGATATTTTTTTATTATTTT
1 ATAAGATATTATTTTATTATTTT
21105722 ATTTAGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 6 0.29
27 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
ATAAGATATTATTTTATTATTTTTA
Found at i:21105889 original size:13 final size:13
Alignment explanation
Indices: 21105871--21105897 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21105861 AAAAGAATTT
21105871 CCATAGCTACCAA
1 CCATAGCTACCAA
21105884 CCATAGCTACCAA
1 CCATAGCTACCAA
21105897 C
1 C
21105898 AGTGTAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (13 bp):
CCATAGCTACCAA
Found at i:21106218 original size:21 final size:20
Alignment explanation
Indices: 21106180--21106242 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
21106170 ATTCAATTTC
21106180 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
21106197 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
21106218 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
21106237 TGCAAT
1 T-CAAT
21106243 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:21106464 original size:51 final size:50
Alignment explanation
Indices: 21106404--21106541 Score: 154
Period size: 50 Copynumber: 2.7 Consensus size: 50
21106394 ATGTTCGGTT
*
21106404 CACATAGTAGCCTGCACATAGTACTACACACGTGA-TTGAA-ACTATCCAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCT-AACA-T-TCCAGTA
* * * * * * *
21106455 CGCATAGTAGCCTGCACATAGTTCTACAAATGCGACCTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAACATTCCAGTA
*
21106505 CACATAGTAGCCTGTACATAGTACTACACACGTGACC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC
21106542 ATCACTTTCA
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
50 37 0.52
51 32 0.45
52 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAACATTCCAGTA
Found at i:21109475 original size:33 final size:32
Alignment explanation
Indices: 21109426--21109487 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
21109416 CATGGCAATG
* *
21109426 TTTTAATGTAAGACCATAATTGGGCTATGGCA
1 TTTTAATGAAAGACCATAACTGGGCTATGGCA
*
21109458 TTTTAATGAAAAGACCATAACTGGGTTATG
1 TTTTAATG-AAAGACCATAACTGGGCTATG
21109488 ACACCTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (32 bp):
TTTTAATGAAAGACCATAACTGGGCTATGGCA
Found at i:21110668 original size:13 final size:13
Alignment explanation
Indices: 21110650--21110687 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
21110640 TGCAAATGAA
21110650 TCATTTCTCATTT
1 TCATTTCTCATTT
21110663 TCATTTCT-ATTT
1 TCATTTCTCATTT
*
21110675 CCATTTC-CATTT
1 TCATTTCTCATTT
21110687 T
1 T
21110688 GAGAAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:21110739 original size:45 final size:46
Alignment explanation
Indices: 21110688--21110777 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 46
21110678 TTTCCATTTT
* * *
21110688 GAGAAAACTACATTTATTTTCAAAT-TATTTCATTTCTCTATTTCG
1 GAGAAAACCACAATCATTTTCAAATGTATTTCATTTCTCTATTTCG
* * *
21110733 GAGAAAACCATAATCATTTTTAAATGTTTTTCATTTCTCTATTTC
1 GAGAAAACCACAATCATTTTCAAATGTATTTCATTTCTCTATTTC
21110778 TATTCATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.47
Consensus pattern (46 bp):
GAGAAAACCACAATCATTTTCAAATGTATTTCATTTCTCTATTTCG
Found at i:21113683 original size:20 final size:20
Alignment explanation
Indices: 21113658--21113698 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
21113648 TAAGGTATAT
21113658 GTGTATGAAAACTAGTGAAA
1 GTGTATGAAAACTAGTGAAA
21113678 GTGTATGAAAACTAGTGAAA
1 GTGTATGAAAACTAGTGAAA
21113698 G
1 G
21113699 CATTTGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.24
Consensus pattern (20 bp):
GTGTATGAAAACTAGTGAAA
Found at i:21115000 original size:18 final size:17
Alignment explanation
Indices: 21114960--21115001 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
21114950 TACTTTATAA
*
21114960 TTTTTTTTTTGAAGTAT
1 TTTTTTTTTTGAAGAAT
21114977 TATTTTATTTTT-AAGAAT
1 T-TTTT-TTTTTGAAGAAT
21114995 TTTTTTT
1 TTTTTTT
21115002 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 2 0.09
17 5 0.23
18 10 0.45
19 5 0.23
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (17 bp):
TTTTTTTTTTGAAGAAT
Found at i:21120261 original size:44 final size:44
Alignment explanation
Indices: 21120202--21120323 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 44
21120192 GATCATTTTG
* *
21120202 ATCCGCTCCACTACAACTTCAGGGAGATAGGATCTAT-TACTTTA
1 ATCCGCTCCACTACAACTTCAGGGAGATAGGAT-TATCGACTTCA
* *
21120246 ATCCGCTCCAATACAACTTCAGGGAGATAGGATTATCGGCTTCA
1 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGACTTCA
* * * *
21120290 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATT
1 ATCCGCTCCACTACAACTTCAGGGAGATAGGATT
21120324 TGCCATCTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 3 0.04
44 65 0.96
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (44 bp):
ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGACTTCA
Found at i:21131602 original size:16 final size:16
Alignment explanation
Indices: 21131581--21131611 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21131571 AAGCTGTCGA
21131581 AAATAATTTTTTTTAT
1 AAATAATTTTTTTTAT
21131597 AAATAATTTTTTTTA
1 AAATAATTTTTTTTA
21131612 AAAAACAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AAATAATTTTTTTTAT
Found at i:21135865 original size:25 final size:24
Alignment explanation
Indices: 21135831--21135878 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
21135821 ATGTCTTCTC
21135831 CAACAATCAAACAGTGGGAGGCCTT
1 CAACAATCAAACA-TGGGAGGCCTT
* *
21135856 CAACAGTCAAACATTGGAGGCCT
1 CAACAATCAAACATGGGAGGCCT
21135879 CGAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (24 bp):
CAACAATCAAACATGGGAGGCCTT
Found at i:21142230 original size:2 final size:2
Alignment explanation
Indices: 21142225--21142252 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21142215 AATTGAAAAA
21142225 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
21142253 TAGAAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21147675 original size:2 final size:2
Alignment explanation
Indices: 21147628--21147658 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21147618 CCAGTTCTTG
21147628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21147659 GTACCTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21150734 original size:59 final size:60
Alignment explanation
Indices: 21150661--21150778 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 60
21150651 TATACTAGTA
* *
21150661 GTCACTCAACTATTAGTGAATTCCTTTTTT-GACACTCAATTATGAAAAGTTACAAAATG
1 GTCACTCAACTATTAGTAAATTCCTTTTTTAGACACTCAACTATGAAAAGTTACAAAATG
* * * * *
21150720 GTCACTCAATTATTAGTAAATTTCTTTTTTAGTCACTCAACTATTAAAAGTTATAAAAT
1 GTCACTCAACTATTAGTAAATTCCTTTTTTAGACACTCAACTATGAAAAGTTACAAAAT
21150779 TTTTACTCTA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 27 0.53
60 24 0.47
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (60 bp):
GTCACTCAACTATTAGTAAATTCCTTTTTTAGACACTCAACTATGAAAAGTTACAAAATG
Found at i:21151050 original size:19 final size:19
Alignment explanation
Indices: 21151026--21151079 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
21151016 AATCTTCGAG
21151026 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21151045 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
21151064 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
21151080 AGATGTGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:21157830 original size:24 final size:24
Alignment explanation
Indices: 21157795--21157841 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
21157785 TTGAATCAAT
21157795 AGGAAAGAGTAGGCAACATCTTGC
1 AGGAAAGAGTAGGCAACATCTTGC
*
21157819 AGGAAAGGGTAGGCAACATCTTG
1 AGGAAAGAGTAGGCAACATCTTG
21157842 GGGCATTGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.32, T:0.17
Consensus pattern (24 bp):
AGGAAAGAGTAGGCAACATCTTGC
Found at i:21159047 original size:44 final size:45
Alignment explanation
Indices: 21158984--21159456 Score: 446
Period size: 44 Copynumber: 10.7 Consensus size: 45
21158974 NNNNNNNNNN
* * * *
21158984 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGG-CGTGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
*
21159028 AGTAGATCGAAGATAGCAGATCATGTCTTCCTATATTGGTAGTGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
* * * *
21159073 AGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATACTGG-AGGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTA-GTGA
* * * * *
21159117 AGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGG-CGTGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
* * *
21159161 AGTAGATCAAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
* * * * * *
21159205 AGTGGATCGAAGAT-TCAGATCTTATCTTCCCATACTGGTAGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
* * * * *
21159249 AGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGG-CGTGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
* * * *
21159293 AGTAGATCAAAAATAGCAGGTCCTGTCTTCCTATATTGGTAG-GA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
* * * * * *
21159337 AGTGGATCGAAAAT-GCAGATCTTGTCTTCCCATACTGGTGGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
* * * *
21159381 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGGCA-TGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
* * *
21159425 AGTAGATCAAAAATAGCA-AGTCTTGCCTTCCT
1 AGTAGATCGAAGATAGCAGA-TCTTGTCTTCCT
21159457 GCACCGATAG
Statistics
Matches: 342, Mismatches: 77, Indels: 20
0.78 0.18 0.05
Matches are distributed among these distances:
43 45 0.13
44 222 0.65
45 75 0.22
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (45 bp):
AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGA
Found at i:21159269 original size:132 final size:132
Alignment explanation
Indices: 21158984--21159456 Score: 768
Period size: 132 Copynumber: 3.6 Consensus size: 132
21158974 NNNNNNNNNN
* * * * *
21158984 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGGCGTGAAGTAGATCGAAGATAGCAGAT
1 AGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAATAGCAGGT
*
21159049 CATGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGG-AG
66 CCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTA-
21159113 GCGA
129 GCGA
*
21159117 AGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGGT
1 AGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAATAGCAGGT
* *
21159182 CCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATTCAGATCTTATCTTCCCATACTGGTAGC
66 CCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTAGC
21159247 GA
131 GA
21159249 AGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAATAGCAGGT
1 AGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAATAGCAGGT
* *
21159314 CCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAAATGCAGATCTTGTCTTCCCATACTGGTGGC
66 CCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTAGC
21159379 GA
131 GA
* * * *
21159381 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGGCATGAAGTAGATCAAAAATAGCAAGT
1 AGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAATAGCAGGT
* *
21159446 CTTGCCTTCCT
66 CCTGTCTTCCT
21159457 GCACCGATAG
Statistics
Matches: 321, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
132 239 0.74
133 82 0.26
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (132 bp):
AGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAATAGCAGGT
CCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTAGC
GA
Found at i:21159652 original size:44 final size:44
Alignment explanation
Indices: 21159578--21159680 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 44
21159568 TGGCAAATTT
* * *
21159578 TATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCC-GATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAACCTG-GAATCC
* *
21159622 TATCTCCCTGAAGTTGCAGT-GAAGCGGATTAAAACCTGGAATCT
1 TATCTCCCTGAAGTTGCAGTGGAA-CAGATTAAAACCTGGAATCC
*
21159666 TATCTCTCTGAAGTT
1 TATCTCCCTGAAGTT
21159681 ACAGAGAGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
43 3 0.06
44 47 0.92
45 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAACCTGGAATCC
Found at i:21159805 original size:128 final size:129
Alignment explanation
Indices: 21159577--21159828 Score: 314
Period size: 128 Copynumber: 2.0 Consensus size: 129
21159567 ATGGCAAATT
* ** * *
21159577 TTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTAAAGTTGCAGTGGAACAGATAAAAAACGATAATCCTATCTCCCTAAAGTTGCAGC
* *
21159642 GAAGCGGATTAAAACCTGGAATCTTATCTCTCTGAAGTTACAG-AGAGCAGAACGCATCTAGTC
66 GAAGCGGATTAAAACATGGAATCTTATCTCTCTGAAATTACAGTAGAGCAGAACGCATCTAGTC
* * *
21159705 TTATCTCTCTAAAGTTGCAGTGGAGCAGACTAAATAAAC-A-AATCCTATCTCCCTAAAGTTGTA
1 TTATCTCCCTAAAGTTGCAGTGGAACAGA-TAAA-AAACGATAATCCTATCTCCCTAAAGTTGCA
* * ** *
21159768 GCGGAGTGGATTAGAATGATGG-ATCTTATCTCTCTGAAATTACAGTAGAGCAGATCGCATC
64 GCGAAGCGGATTA-AAACATGGAATCTTATCTCTCTGAAATTACAGTAGAGCAGAACGCATC
21159829 AAATTCATCT
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
128 80 0.76
129 23 0.22
130 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (129 bp):
TTATCTCCCTAAAGTTGCAGTGGAACAGATAAAAAACGATAATCCTATCTCCCTAAAGTTGCAGC
GAAGCGGATTAAAACATGGAATCTTATCTCTCTGAAATTACAGTAGAGCAGAACGCATCTAGTC
Found at i:21160136 original size:19 final size:19
Alignment explanation
Indices: 21160112--21160187 Score: 82
Period size: 19 Copynumber: 3.8 Consensus size: 19
21160102 AATCTTCGAG
21160112 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATGT
*
21160131 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATGT
*
21160150 GATAT-TAATCTTAGAAGATGT
1 GATATGCAATCTT---AGATGT
*
21160171 GATTTTGCAATCTTAGA
1 GA-TATGCAATCTTAGA
21160188 GATTTAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 23 0.49
20 3 0.06
21 7 0.15
22 2 0.04
23 6 0.13
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATGT
Found at i:21160173 original size:21 final size:22
Alignment explanation
Indices: 21160144--21160187 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
21160134 ATGCAATCTT
21160144 AGATATGATATT-AATCTTAGA
1 AGATATGATATTCAATCTTAGA
* *
21160165 AGATGTGATTTTGCAATCTTAGA
1 AGATATGATATT-CAATCTTAGA
21160188 GATTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (22 bp):
AGATATGATATTCAATCTTAGA
Found at i:21160711 original size:15 final size:15
Alignment explanation
Indices: 21160693--21160742 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
21160683 TTTCTTTATT
21160693 TTTTTATATTAATTA
1 TTTTTATATTAATTA
* **
21160708 TTTTTTTATTTCTT-
1 TTTTTATATTAATTA
21160722 TTTTTATATTTAATTA
1 TTTTTATA-TTAATTA
21160738 TTTTT
1 TTTTT
21160743 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 7 0.26
15 15 0.56
16 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATATTAATTA
Found at i:21160724 original size:29 final size:30
Alignment explanation
Indices: 21160682--21160745 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
21160672 TCCTTTTTCA
*
21160682 TTTTCTTTATTTTTTTATA-TTAATTATTT
1 TTTTATTTATTTTTTTATATTTAATTATTT
*
21160711 TTTTATTTCTTTTTTTATATTTAATTATTT
1 TTTTATTTATTTTTTTATATTTAATTATTT
21160741 TTTTA
1 TTTTA
21160746 AAAATATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTATTTATTTTTTTATATTTAATTATTT
Found at i:21160858 original size:25 final size:25
Alignment explanation
Indices: 21160795--21160858 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
21160785 TTTTTTGTAG
*
21160795 TATA-ATATAATTATTTTTTATTTA
1 TATATATATAATTATTTTTTATCTA
* *
21160819 TTTATATGTAATTATTTTTTATCTA
1 TATATATATAATTATTTTTTATCTA
* *
21160844 TATGTATATATTTAT
1 TATATATATAATTAT
21160859 CTTAGTATAC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 3 0.09
25 29 0.91
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (25 bp):
TATATATATAATTATTTTTTATCTA
Found at i:21164428 original size:38 final size:38
Alignment explanation
Indices: 21164353--21164428 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
21164343 TGGCGACATT
* **
21164353 ATGAAAGTGGTTATCTATAGGCTCTACGCAGTGACACC
1 ATGAAAATGGTTATCTATAGGCTCTACGCAGCAACACC
*
21164391 ATGAAAATGGTTATCTATAGGCTCTACGGAGCAACACC
1 ATGAAAATGGTTATCTATAGGCTCTACGCAGCAACACC
21164429 TTGGAAGAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (38 bp):
ATGAAAATGGTTATCTATAGGCTCTACGCAGCAACACC
Found at i:21175213 original size:12 final size:13
Alignment explanation
Indices: 21175196--21175224 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
21175186 TTTCACATTT
21175196 TTTTATTTTCA-A
1 TTTTATTTTCACA
21175208 TTTTATTTTCACA
1 TTTTATTTTCACA
21175221 TTTT
1 TTTT
21175225 TCTGTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATTTTCACA
Found at i:21189204 original size:2 final size:2
Alignment explanation
Indices: 21189192--21189223 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21189182 TTTATTCTTT
21189192 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21189224 TAGATTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21190578 original size:11 final size:10
Alignment explanation
Indices: 21190559--21190642 Score: 52
Period size: 11 Copynumber: 8.4 Consensus size: 10
21190549 TCAGACGTGG
21190559 TTTTTAATAA
1 TTTTTAATAA
21190569 TTTTTAAATAA
1 TTTTT-AATAA
*
21190580 TTTTT--TTA
1 TTTTTAATAA
*
21190588 TTTTGAA-AA
1 TTTTTAATAA
* *
21190597 TAAATTTGAT-A
1 T--TTTTAATAA
21190608 TTTCTT-ATAA
1 TTT-TTAATAA
21190618 TTTTTAATAA
1 TTTTTAATAA
21190628 TTTTTAAATAA
1 TTTTT-AATAA
21190639 TTTT
1 TTTT
21190643 GTACCAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
8 6 0.11
9 7 0.12
10 20 0.35
11 24 0.42
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:21190642 original size:20 final size:20
Alignment explanation
Indices: 21190560--21190642 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
21190550 CAGACGTGGT
21190560 TTTTAATAATTTTTAAATAA
1 TTTTAATAATTTTTAAATAA
* * *
21190580 TTTT-TTTATTTTGAAAATAA
1 TTTTAATAATTTT-TAAATAA
* *
21190600 ATTTGAT-ATTTCTT--ATAA
1 TTTTAATAATTT-TTAAATAA
21190618 TTTTTAATAATTTTTAAATAA
1 -TTTTAATAATTTTTAAATAA
21190639 TTTT
1 TTTT
21190643 GTACCAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
18 4 0.08
19 13 0.27
20 25 0.52
21 6 0.12
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAATAATTTTTAAATAA
Found at i:21194872 original size:13 final size:13
Alignment explanation
Indices: 21194856--21194901 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
21194846 TTTCTCTTTC
21194856 TATTTCTTATTTT
1 TATTTCTTATTTT
21194869 TATTT-TTATTTT
1 TATTTCTTATTTT
* * *
21194881 TAATTATAATTTT
1 TATTTCTTATTTT
21194894 TATTTCTT
1 TATTTCTT
21194902 TTTAGCACCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTCTTATTTT
Found at i:21194880 original size:6 final size:6
Alignment explanation
Indices: 21194856--21194898 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
21194846 TTTCTCTTTC
* *
21194856 TATTTCT TATTTT TATTTT TATTTT TAATTAT AATTTT TATTT
1 TATTT-T TATTTT TATTTT TATTTT T-ATTTT TATTTT TATTT
21194899 CTTTTTAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 22 0.71
7 9 0.29
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:21198332 original size:23 final size:24
Alignment explanation
Indices: 21198297--21198372 Score: 95
Period size: 23 Copynumber: 3.3 Consensus size: 24
21198287 AATGTTGTTG
* *
21198297 ATCAATGGTAGCTTTAG-CTACAT
1 ATCAGTGGTAGCTTAAGACTACAT
*
21198320 TTCAGTGGTAGC-TAAGACTACAT
1 ATCAGTGGTAGCTTAAGACTACAT
*
21198343 ATCAGTGGTAGCTT-CGACTACAT
1 ATCAGTGGTAGCTTAAGACTACAT
21198366 ATCAGTG
1 ATCAGTG
21198373 TGGCACTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 3 0.07
23 42 0.91
24 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (24 bp):
ATCAGTGGTAGCTTAAGACTACAT
Found at i:21205737 original size:23 final size:23
Alignment explanation
Indices: 21205704--21205779 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
21205694 AGTGTTGTTG
21205704 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
21205727 TTGAGTGGTAGCTACGGCTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
21205750 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
21205773 ATCAGTG
1 ATCAGTG
21205780 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:21207512 original size:23 final size:23
Alignment explanation
Indices: 21207486--21207561 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
21207476 ATAAGTGTCA
* *
21207486 CACTGATATATAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
21207509 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
21207532 CACTG-TAATGTAGCCGTAGCTAC
1 CACTGAT-ATGTAGCCGAAGCTAC
21207555 CACTGAT
1 CACTGAT
21207562 CAATAACACT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
22 1 0.02
23 46 0.96
24 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:21209548 original size:308 final size:308
Alignment explanation
Indices: 21208990--21209607 Score: 1218
Period size: 308 Copynumber: 2.0 Consensus size: 308
21208980 CAATTTTTGG
21208990 GATAGCAACAGTGATGTGAATTTGAAAAATCACCAAAAATAGTAGAAATGGAATTAGAGAGTGAA
1 GATAGCAACAGTGATGTGAATTTGAAAAATCACCAAAAATAGTAGAAATGGAATTAGAGAGTGAA
21209055 TGATATATAGGATTAAAGCTTATCAAGTCTATTTTTACATGAAAGAAACGGCGTAGGAAAAAGAA
66 TGATATATAGGATTAAAGCTTATCAAGTCTATTTTTACATGAAAGAAACGGCGTAGGAAAAAGAA
*
21209120 TTTTATATTTTGAGATATTTGAATTTTAGTGAAATAGGGTCAGAATGGTTTTTTAAGTCCTCTGT
131 TTTTATATTTTGAGATATTTGAATTTTAGTGAAATAGGGTCAGAATGGGTTTTTAAGTCCTCTGT
21209185 TCTGAATTTAGAAATTCATTAAAAATTGTATAGAAAGAATTATGAATCATAATTTATATTTATAG
196 TCTGAATTTAGAAATTCATTAAAAATTGTATAGAAAGAATTATGAATCATAATTTATATTTATAG
21209250 ATTCCTTAGTGAGTCTATTTTCTATAGAAACAAGCAGAAACACCATAT
261 ATTCCTTAGTGAGTCTATTTTCTATAGAAACAAGCAGAAACACCATAT
21209298 GATAGCAACAGTGATGTGAATTTGAAAAATCACCAAAAATAGTAGAAATGGAATTAGAGAGTGAA
1 GATAGCAACAGTGATGTGAATTTGAAAAATCACCAAAAATAGTAGAAATGGAATTAGAGAGTGAA
*
21209363 TGATATATAGGATTAAAGCTTATCAAGTCTATTTTTACATGAAAGAAACGGCGTAGGATAAAGAA
66 TGATATATAGGATTAAAGCTTATCAAGTCTATTTTTACATGAAAGAAACGGCGTAGGAAAAAGAA
21209428 TTTTATATTTTGAGATATTTGAATTTTAGTGAAATAGGGTCAGAATGGGTTTTTAAGTCCTCTGT
131 TTTTATATTTTGAGATATTTGAATTTTAGTGAAATAGGGTCAGAATGGGTTTTTAAGTCCTCTGT
21209493 TCTGAATTTAGAAATTCATTAAAAATTGTATAGAAAGAATTATGAATCATAATTTATATTTATAG
196 TCTGAATTTAGAAATTCATTAAAAATTGTATAGAAAGAATTATGAATCATAATTTATATTTATAG
21209558 ATTCCTTAGTGAGTCTATTTTCTATAGAAACAAGCAGAAACACCATAT
261 ATTCCTTAGTGAGTCTATTTTCTATAGAAACAAGCAGAAACACCATAT
21209606 GA
1 GA
21209608 AATCTGTACA
Statistics
Matches: 308, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
308 308 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.34
Consensus pattern (308 bp):
GATAGCAACAGTGATGTGAATTTGAAAAATCACCAAAAATAGTAGAAATGGAATTAGAGAGTGAA
TGATATATAGGATTAAAGCTTATCAAGTCTATTTTTACATGAAAGAAACGGCGTAGGAAAAAGAA
TTTTATATTTTGAGATATTTGAATTTTAGTGAAATAGGGTCAGAATGGGTTTTTAAGTCCTCTGT
TCTGAATTTAGAAATTCATTAAAAATTGTATAGAAAGAATTATGAATCATAATTTATATTTATAG
ATTCCTTAGTGAGTCTATTTTCTATAGAAACAAGCAGAAACACCATAT
Found at i:21211075 original size:13 final size:13
Alignment explanation
Indices: 21211059--21211084 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21211049 AAGAAAAGAA
21211059 AAGAAGAAGGGGC
1 AAGAAGAAGGGGC
21211072 AAGAAGAAGGGGC
1 AAGAAGAAGGGGC
21211085 TGATCCGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.46, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGGGGC
Found at i:21223144 original size:87 final size:87
Alignment explanation
Indices: 21223043--21223218 Score: 318
Period size: 87 Copynumber: 2.0 Consensus size: 87
21223033 AGAGAAGTCG
*
21223043 GATCATGACAGCTAACACAAAGGCCGAATCACATTGTCGATGGTGAAT-AAATGAGACTTTTCTT
1 GATCATGACAGCTAACACAAAGGCCGAATCACATTGTCGATGGTGAATAAAAGGA-ACTTTTCTT
21223107 TTAAACTAAGAGAAAATGCCCTA
65 TTAAACTAAGAGAAAATGCCCTA
*
21223130 GATCATGACAGCTAACACAAATGCCGAATCACATTGTCGATGGTGAATAAAAGGAACTTTTCTTT
1 GATCATGACAGCTAACACAAAGGCCGAATCACATTGTCGATGGTGAATAAAAGGAACTTTTCTTT
21223195 TAAACTAAGAGAAAATGCCCTA
66 TAAACTAAGAGAAAATGCCCTA
21223217 GA
1 GA
21223219 CAAATATGAC
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
87 81 0.94
88 5 0.06
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (87 bp):
GATCATGACAGCTAACACAAAGGCCGAATCACATTGTCGATGGTGAATAAAAGGAACTTTTCTTT
TAAACTAAGAGAAAATGCCCTA
Found at i:21223514 original size:9 final size:9
Alignment explanation
Indices: 21223500--21223567 Score: 93
Period size: 9 Copynumber: 7.4 Consensus size: 9
21223490 TTTGGTTAAA
21223500 AATTACCCG
1 AATTACCCG
21223509 AATTACCCG
1 AATTACCCG
21223518 AATTACCCG
1 AATTACCCG
*
21223527 AATTAACCG
1 AATTACCCG
21223536 AATTA-CCG
1 AATTACCCG
*
21223544 AAAAATACCCG
1 --AATTACCCG
21223555 AATTACCCG
1 AATTACCCG
21223564 AATT
1 AATT
21223568 TTTTTATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
8 3 0.06
9 43 0.81
10 4 0.08
11 3 0.06
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:21223789 original size:16 final size:16
Alignment explanation
Indices: 21223763--21223802 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
21223753 CTATTGGGTG
*
21223763 GATTATTTCGAGTT-T
1 GATTTTTTCGAGTTAT
21223778 GAGTTTTTTCGAGTTAT
1 GA-TTTTTTCGAGTTAT
21223795 GATTTTTT
1 GATTTTTT
21223803 TAGGTTCGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 17 0.77
17 3 0.14
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.57
Consensus pattern (16 bp):
GATTTTTTCGAGTTAT
Found at i:21224258 original size:12 final size:12
Alignment explanation
Indices: 21224241--21224265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21224231 TGGGTGTAAA
21224241 GCGTCTGTAGGT
1 GCGTCTGTAGGT
21224253 GCGTCTGTAGGT
1 GCGTCTGTAGGT
21224265 G
1 G
21224266 GCTTCAGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.44, T:0.32
Consensus pattern (12 bp):
GCGTCTGTAGGT
Found at i:21242042 original size:13 final size:14
Alignment explanation
Indices: 21242019--21242047 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21242009 GATTTTTGTA
21242019 AAAACTATTTTTTT
1 AAAACTATTTTTTT
21242033 AAAA-TATTTTTTT
1 AAAACTATTTTTTT
21242046 AA
1 AA
21242048 TCAAGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
AAAACTATTTTTTT
Found at i:21249961 original size:47 final size:44
Alignment explanation
Indices: 21249901--21249989 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 44
21249891 GACTCCATGG
21249901 ATTTTGAAATTATA-TATTTTAACATGATTTTTAATATTTTTTAATA
1 ATTTTGAAATTATATTATTTTAA-AT-ATTTTTAA-ATTTTTTAATA
21249947 ATTTTGATAATTATATTTATTTTAAATATTTTTAAATTTTTTA
1 ATTTTGA-AATTATA-TTATTTTAAATATTTTTAAATTTTTTA
21249990 GAATTATTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
46 15 0.38
47 15 0.38
48 2 0.05
49 8 0.20
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (44 bp):
ATTTTGAAATTATATTATTTTAAATATTTTTAAATTTTTTAATA
Found at i:21250896 original size:28 final size:28
Alignment explanation
Indices: 21250843--21250898 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
21250833 GGCATAAGTG
* * *
21250843 TATATATTATAAATTTTTAAAGTTAAAA
1 TATATATTATAAATATTAAAAATTAAAA
21250871 TATATATTAT-AATATTAAAATATTAAAA
1 TATATATTATAAATATTAAAA-ATTAAAA
21250899 GTTAAGTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TATATATTATAAATATTAAAAATTAAAA
Found at i:21250915 original size:5 final size:5
Alignment explanation
Indices: 21250907--21250940 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
21250897 AAGTTAAGTA
21250907 TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
21250941 ATAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:21250922 original size:36 final size:37
Alignment explanation
Indices: 21250843--21250925 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 37
21250833 GGCATAAGTG
* *
21250843 TATATATTATAAATTTTTAAAGTTAAAATATATATTA
1 TATATATTATAAATATTAAAAGTTAAAATATATATTA
*
21250880 TA-ATATTA-AAATATTAAAAGTT-AAGTATATATTA
1 TATATATTATAAATATTAAAAGTTAAAATATATATTA
21250914 TATTATATTATA
1 TA-TATATTATA
21250926 TTATATTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 13 0.32
35 12 0.30
36 12 0.30
37 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (37 bp):
TATATATTATAAATATTAAAAGTTAAAATATATATTA
Found at i:21251713 original size:24 final size:24
Alignment explanation
Indices: 21251686--21251732 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
21251676 ATTGAAATGG
21251686 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
21251710 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
21251733 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:21252309 original size:31 final size:33
Alignment explanation
Indices: 21252274--21252341 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
21252264 CAAATGGTGA
* *
21252274 GAATTGAGTATGGAATGAATGATGT-ATT-TAT
1 GAATTGAATATGGAATGAATAATGTCATTGTAT
* *
21252305 GAATTGAATATTGAATGACTAATGTCATTGTAT
1 GAATTGAATATGGAATGAATAATGTCATTGTAT
21252338 GAAT
1 GAAT
21252342 AAATGTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 21 0.68
32 3 0.10
33 7 0.23
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (33 bp):
GAATTGAATATGGAATGAATAATGTCATTGTAT
Found at i:21253524 original size:26 final size:26
Alignment explanation
Indices: 21253484--21253536 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
21253474 AGTATTTACT
*
21253484 TAAAGAGGCTTTATGATTGAGGGTGG
1 TAAAGAGGCTATATGATTGAGGGTGG
21253510 TAAAGAGGCTATATGATTGAGGGTGG
1 TAAAGAGGCTATATGATTGAGGGTGG
21253536 T
1 T
21253537 GAATGAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.30
Consensus pattern (26 bp):
TAAAGAGGCTATATGATTGAGGGTGG
Found at i:21254068 original size:6 final size:6
Alignment explanation
Indices: 21254057--21254090 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
21254047 CTTAAAACAC
21254057 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAA
21254091 CACTTTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:21254259 original size:20 final size:20
Alignment explanation
Indices: 21254190--21254259 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
21254180 GTTTCTTTTG
* *
21254190 AATCGATTTTTTATTGTCTTA
1 AATCGATTCTTTGTTGT-TTA
*
21254211 AATTGATTCTTTGTTGTTTA
1 AATCGATTCTTTGTTGTTTA
*
21254231 AATCAATTCTTTGTTGTTTA
1 AATCGATTCTTTGTTGTTTA
*
21254251 ACTCGATTC
1 AATCGATTC
21254260 AAACGTCAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.54
Consensus pattern (20 bp):
AATCGATTCTTTGTTGTTTA
Found at i:21268650 original size:13 final size:13
Alignment explanation
Indices: 21268627--21268659 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21268617 TTGGGCTAGG
21268627 TGTAA-TTGGGTC
1 TGTAATTTGGGTC
*
21268639 TGTAATTTGGGTT
1 TGTAATTTGGGTC
21268652 TGTAATTT
1 TGTAATTT
21268660 TTGCTATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.18, C:0.03, G:0.27, T:0.52
Consensus pattern (13 bp):
TGTAATTTGGGTC
Found at i:21270517 original size:25 final size:24
Alignment explanation
Indices: 21270480--21270614 Score: 80
Period size: 25 Copynumber: 5.5 Consensus size: 24
21270470 AAATTGGTGC
21270480 TTAATTGCTGTCCATTTTTTAGCATA
1 TTAA-TGCTGTCCATTTTTT-GCATA
* * **
21270506 TTAATTCTGTCCAAATTAGTGC-T-
1 TTAATGCTGTCC-ATTTTTTGCATA
*
21270529 TAAATGCTGTCCATTTTTTGGCATA
1 TTAATGCTGTCCATTTTTT-GCATA
* **
21270554 TTAATGCTGTCCAAATTAGTGC-T-
1 TTAATGCTGTCC-ATTTTTTGCATA
* * *
21270577 TAAATGCTGTCCATTTTTTTACAAA
1 TTAATGCTGTCCA-TTTTTTGCATA
*
21270602 TCAATGCTGTCCA
1 TTAATGCTGTCCA
21270615 AATGTTGTTA
Statistics
Matches: 81, Mismatches: 20, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
22 5 0.06
23 27 0.33
24 3 0.04
25 34 0.42
26 12 0.15
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (24 bp):
TTAATGCTGTCCATTTTTTGCATA
Found at i:21270538 original size:23 final size:23
Alignment explanation
Indices: 21270512--21270589 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
21270502 CATATTAATT
21270512 CTGTCCAAATTAGTGCTTAAATG
1 CTGTCCAAATTAGTGCTTAAATG
* ** *
21270535 CTGTCC-ATTTTTTGGCATATTAATG
1 CTGTCCAAATTAGT-GC-T-TAAATG
21270560 CTGTCCAAATTAGTGCTTAAATG
1 CTGTCCAAATTAGTGCTTAAATG
21270583 CTGTCCA
1 CTGTCCA
21270590 TTTTTTTACA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
22 4 0.09
23 20 0.47
24 2 0.05
25 13 0.30
26 4 0.09
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (23 bp):
CTGTCCAAATTAGTGCTTAAATG
Found at i:21270538 original size:48 final size:48
Alignment explanation
Indices: 21270461--21270617 Score: 235
Period size: 48 Copynumber: 3.3 Consensus size: 48
21270451 TGATGATAAG
* * *
21270461 ATGCTATCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTA
* *
21270509 ATTCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTA
* *
21270557 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTA-CAAATCA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCA-TTTTTTAGCATATTA
21270605 ATGCTGTCCAAAT
1 ATGCTGTCCAAAT
21270618 GTTGTTACTG
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 93 0.94
49 6 0.06
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (48 bp):
ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTA
Found at i:21273736 original size:16 final size:17
Alignment explanation
Indices: 21273715--21273747 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21273705 AAAACTAAAA
21273715 AAATA-TTACACTTTCC
1 AAATATTTACACTTTCC
*
21273731 AAATATTTACATTTTCC
1 AAATATTTACACTTTCC
21273748 TATTTTTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTACACTTTCC
Found at i:21283914 original size:3 final size:3
Alignment explanation
Indices: 21283906--21283947 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
21283896 GAGTATTTGT
* * *
21283906 CTG CTG CTG CTG CTG CTG TTG CTG TTG CTG TTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
21283948 AATCTGGAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.26, G:0.33, T:0.40
Consensus pattern (3 bp):
CTG
Found at i:21283923 original size:12 final size:12
Alignment explanation
Indices: 21283906--21283947 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
21283896 GAGTATTTGT
*
21283906 CTGCTGCTGCTG
1 CTGCTGTTGCTG
21283918 CTGCTGTTGCTG
1 CTGCTGTTGCTG
*
21283930 TTGCTGTTGCTG
1 CTGCTGTTGCTG
21283942 CTGCTG
1 CTGCTG
21283948 AATCTGGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.33, T:0.40
Consensus pattern (12 bp):
CTGCTGTTGCTG
Found at i:21290981 original size:82 final size:81
Alignment explanation
Indices: 21290829--21290983 Score: 204
Period size: 82 Copynumber: 1.9 Consensus size: 81
21290819 GCCCTCCCAA
* * * *
21290829 AAAATGAAAATCTTCAATTTAGTCCTCTTATAAATAAAAAAATTATAAATTAATATAAATCGAAA
1 AAAATGAAAATCTTCAATTCAATCCTCTTATAAATAAAAAAATTATAAATAAATATAAATCAAAA
21290894 CTACACTTCACTCCTC
66 CTACACTTCACTCCTC
* * * *
21290910 AAAATGAAAATTTTTCAATTCAATTCTCTTGTAAATAAAGAAATTATAAATAAATATATAAT-AA
1 AAAATGAAAA-TCTTCAATTCAATCCTCTTATAAATAAAAAAATTATAAATAAATATA-AATCAA
*
21290974 AATTACACTT
64 AACTACACTT
21290984 TAACCCCCTA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 10 0.16
82 50 0.79
83 3 0.05
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (81 bp):
AAAATGAAAATCTTCAATTCAATCCTCTTATAAATAAAAAAATTATAAATAAATATAAATCAAAA
CTACACTTCACTCCTC
Found at i:21297712 original size:9 final size:9
Alignment explanation
Indices: 21297698--21297722 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21297688 TTCAAGTGCT
21297698 CTCAAAATG
1 CTCAAAATG
21297707 CTCAAAATG
1 CTCAAAATG
21297716 CTCAAAA
1 CTCAAAA
21297723 AGCCAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (9 bp):
CTCAAAATG
Found at i:21308424 original size:18 final size:18
Alignment explanation
Indices: 21308401--21308435 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21308391 TAAGGCTAAT
21308401 AAAAGAATCTAATCCTGC
1 AAAAGAATCTAATCCTGC
21308419 AAAAGAATCTAATCCTG
1 AAAAGAATCTAATCCTG
21308436 GATTTAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (18 bp):
AAAAGAATCTAATCCTGC
Found at i:21314201 original size:13 final size:13
Alignment explanation
Indices: 21314185--21314209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21314175 AGTACTTCAA
21314185 AAAAAACACTTTG
1 AAAAAACACTTTG
21314198 AAAAAACACTTT
1 AAAAAACACTTT
21314210 TTTTTGGCTA
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:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAAAACACTTTG
Found at i:21315781 original size:28 final size:28
Alignment explanation
Indices: 21315729--21315798 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
21315719 AAATAAAAAA
*
21315729 TTACCAAAAT-TTTATACATTTTTTTAT
1 TTACCAAAATATATATACATTTTTTTAT
21315756 TTACCAAAATATATATA-ATTTTTTTTAT
1 TTACCAAAATATATATACA-TTTTTTTAT
21315784 TTACCAAAATATATA
1 TTACCAAAATATATA
21315799 AAAAACAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 11 0.28
28 29 0.73
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (28 bp):
TTACCAAAATATATATACATTTTTTTAT
Found at i:21315901 original size:27 final size:26
Alignment explanation
Indices: 21315861--21315938 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 26
21315851 TCCCTGGGTG
21315861 AAGGGAACACTGTTGGCGGCACCAAAC
1 AAGGGAAC-CTGTTGGCGGCACCAAAC
21315888 AAGGGAACCTTGTTGGCGGCACCAAAC
1 AAGGGAACC-TGTTGGCGGCACCAAAC
*
21315915 AA-GGATTCCCTGTTGGCGGCACCA
1 AAGGGA--ACCTGTTGGCGGCACCA
21315939 CTCGTGTTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
26 4 0.09
27 41 0.87
28 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.29, T:0.15
Consensus pattern (26 bp):
AAGGGAACCTGTTGGCGGCACCAAAC
Found at i:21317584 original size:57 final size:58
Alignment explanation
Indices: 21317500--21317616 Score: 218
Period size: 57 Copynumber: 2.0 Consensus size: 58
21317490 CCGGACGACC
21317500 ACTCCACCTACAAAAAATAAATATAGCGTTTAGAGTTGGTTGGTAACATTAGTCAATAT
1 ACTCCACCTAC-AAAAATAAATATAGCGTTTAGAGTTGGTTGGTAACATTAGTCAATAT
21317559 ACTCCACCTAC-AAAATAAATATAGCGTTTAGAGTTGGTTGGTAACATTAGTCAATAT
1 ACTCCACCTACAAAAATAAATATAGCGTTTAGAGTTGGTTGGTAACATTAGTCAATAT
21317616 A
1 A
21317617 TTATGACTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
57 47 0.81
59 11 0.19
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (58 bp):
ACTCCACCTACAAAAATAAATATAGCGTTTAGAGTTGGTTGGTAACATTAGTCAATAT
Found at i:21319792 original size:38 final size:38
Alignment explanation
Indices: 21319758--21319866 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 38
21319748 TCTTCTTCTT
*
21319758 CTTCTTTTT-TTT-TTCTCTTCCCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTT-TCCTCCCCTTTCCTTTTCTTTC
*
21319795 CTTATTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTC
*
21319833 CTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTC
1 CTTCTTTTTCTTTCTTTCCTCCCCTTTCCTTTTC
21319867 CTTCTTTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
37 8 0.12
38 56 0.85
39 2 0.03
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (38 bp):
CTTCTTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTC
Done.