Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 66 of 290
Found at i:20093785 original size:17 final size:17
Alignment explanation
Indices: 20093763--20093795 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20093753 GCCTCTCCTT
20093763 TTTTTTCCTTTTTATTC
1 TTTTTTCCTTTTTATTC
*
20093780 TTTTTTCTTTTTTATT
1 TTTTTTCCTTTTTATT
20093796 ATACGAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCCTTTTTATTC
Found at i:20098383 original size:199 final size:202
Alignment explanation
Indices: 20098027--20098422 Score: 762
Period size: 199 Copynumber: 2.0 Consensus size: 202
20098017 TGAAAGGAAA
20098027 ATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAATGATCAAGCCCGGATGGGTGATCCTATC
1 ATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAATGATCAAGCCCGGA-GGGTGATCCTATC
20098092 CTGATATAGCCCTCCCGAAGAATATGTGTAAAATGGATTTAGCCCGGACGGGTAATCCGAATTAG
65 CTGATATAGCCCTCCCGAAGAATATGTGTAAAATGGATTTAGCCCGGACGGGTAATCCGAATTAG
20098157 GGTCTGAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGGG
130 GGTCTGAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGGG
20098222 GAAAAAGG
195 GAAAAAGG
20098230 ATTCGATGGATC-CTGAAAAGGAATTGACGGTAAAAATGATCAAGCCC-G-GGGTGATCCTATCC
1 ATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAATGATCAAGCCCGGAGGGTGATCCTATCC
20098292 TGATATAGCCCTCCCGAAGAATATGTGTAAAATGGATTTAGCCCGGACGGGTAATCCGAATTAGG
66 TGATATAGCCCTCCCGAAGAATATGTGTAAAATGGATTTAGCCCGGACGGGTAATCCGAATTAGG
20098357 GTCTGAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGGGG
131 GTCTGAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGGGG
20098422 A
196 A
20098423 TTTAGCCTGG
Statistics
Matches: 193, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
199 145 0.75
201 1 0.01
202 35 0.18
203 12 0.06
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (202 bp):
ATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAATGATCAAGCCCGGAGGGTGATCCTATCC
TGATATAGCCCTCCCGAAGAATATGTGTAAAATGGATTTAGCCCGGACGGGTAATCCGAATTAGG
GTCTGAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGGGG
AAAAAGG
Found at i:20102187 original size:27 final size:24
Alignment explanation
Indices: 20102136--20102194 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 24
20102126 GTAAAATGGG
20102136 TTTAAAATAAGGTATATAAAATAA
1 TTTAAAATAAGGTATATAAAATAA
*
20102160 TTTTAAAATAA-GTAATATATAAGTTAA
1 -TTTAAAATAAGGT-ATATA-AA-ATAA
20102187 TTTAAAAT
1 TTTAAAAT
20102195 GTTATATAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.07
25 15 0.50
26 10 0.33
27 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (24 bp):
TTTAAAATAAGGTATATAAAATAA
Found at i:20102460 original size:18 final size:18
Alignment explanation
Indices: 20102433--20102486 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
20102423 ATGTATACAT
* * *
20102433 ATATATAATAGGTAAGGA
1 ATATAAAATAGATAAGAA
* *
20102451 ATATAAAATAAATAATAA
1 ATATAAAATAGATAAGAA
20102469 ATATAAAATAGATCAAGA
1 ATATAAAATAGAT-AAGA
20102487 TAAAATATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 25 0.89
19 3 0.11
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (18 bp):
ATATAAAATAGATAAGAA
Found at i:20104806 original size:16 final size:17
Alignment explanation
Indices: 20104785--20104817 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20104775 TTTAATTATA
20104785 TAAAAATAATAA-AAAT
1 TAAAAATAATAATAAAT
*
20104801 TAAAAATGATAATAAAT
1 TAAAAATAATAATAAAT
20104818 ATTTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
TAAAAATAATAATAAAT
Found at i:20104873 original size:6 final size:6
Alignment explanation
Indices: 20104858--20104886 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
20104848 ATTGATATAC
20104858 AAAA-T AAAATT AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT
20104887 TCAAATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:20109929 original size:3 final size:3
Alignment explanation
Indices: 20109881--20109909 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20109871 AATAAAAGGT
20109881 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20109910 GTTAAGCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20110100 original size:21 final size:21
Alignment explanation
Indices: 20110044--20110090 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
20110034 TAACAAACGT
*
20110044 AATAG-TATAATATTATGATAAC
1 AATAGTTATAATA--ATAATAAC
20110066 AATAGTTATAATAATAATAAC
1 AATAGTTATAATAATAATAAC
20110087 AATA
1 AATA
20110091 TTTTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 5 0.22
23 7 0.30
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (21 bp):
AATAGTTATAATAATAATAAC
Found at i:20110156 original size:3 final size:3
Alignment explanation
Indices: 20110150--20110384 Score: 117
Period size: 3 Copynumber: 79.7 Consensus size: 3
20110140 CCTTAGTAAG
* * * * * *
20110150 AAT AAT AGT AGT AAT AAT AAA AAC AAT AGT AGT AA- ATAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * * *
20110195 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT -AT AGTT AAA AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * * * * * *
20110240 AAT AAT AGT AAT AGT GAT AAT GAT AAT AA- AAA AAT AGT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * * *
20110287 -AT GTT AAAT AAT AAT AGT AA- AA- AAT AGT AAT AGT AAT AAT TAC
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
20110330 AAA AAT GAT AAT GAA- CAT AA- AAT GAT AAT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20110374 AAT AAT AAT AA
1 AAT AAT AAT AA
20110385 ATTATAGGAA
Statistics
Matches: 173, Mismatches: 48, Indels: 22
0.71 0.20 0.09
Matches are distributed among these distances:
2 13 0.08
3 154 0.89
4 6 0.03
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:20112068 original size:88 final size:88
Alignment explanation
Indices: 20111943--20112317 Score: 445
Period size: 88 Copynumber: 4.3 Consensus size: 88
20111933 GTTCCACTGC
* ** * * ** *
20111943 AACTTCAGGGAGATAAGGTTTAGTGGCTTC-AATCGCTCCAATATCATTTCAGGAAGAAGATATT
1 AACTTCAAGGAGATAAGAATT-GTGGCTTCGAACCGCTCCAGTGCCATTTCAGGAAGAAGAGATT
* *
20112007 TGTAACTTCGATCT-CATCCGCTGG
65 TGTAGCTTCGATCTAC-TCCGCTGA
*
20112031 AACTTCAAGGAGATAAGAATTGTGGCTTCGAGCCGCTCCAGTGCCATTTCAAGG-AGAAGAGATT
1 AACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAGTGCCATTTC-AGGAAGAAGAGATT
* ** *
20112095 TGTAGCTTAGATCTACTCCATTAA
65 TGTAGCTTCGATCTACTCCGCTGA
* * ** *
20112119 AACTTCAAGGAGATACGAATTGTGGCTTCGAGCTACTCCAGTGCCATTTCAGGGAGAAGAGATTT
1 AACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAGTGCCATTTCAGGAAGAAGAGATTT
20112184 GTAGC-TCTGATCTACTCCGCTGA
66 GTAGCTTC-GATCTACTCCGCTGA
* * * *
20112207 AACTTCAAGGAGATACGAATTGTGGCTTCGAACTGCTCTAGTGTCATTTCAGGAAGAAGAGATTT
1 AACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAGTGCCATTTCAGGAAGAAGAGATTT
20112272 GTAGCTTCGATCTACTCCGCCTG-
66 GTAGCTTCGATCTACTCCG-CTGA
*
20112295 AACTTCAAGAAGATAAGAATTGT
1 AACTTCAAGGAGATAAGAATTGT
20112318 AATTTTTAGC
Statistics
Matches: 251, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
87 12 0.05
88 230 0.92
89 9 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (88 bp):
AACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAGTGCCATTTCAGGAAGAAGAGATTT
GTAGCTTCGATCTACTCCGCTGA
Found at i:20112318 original size:44 final size:43
Alignment explanation
Indices: 20112006--20112318 Score: 174
Period size: 44 Copynumber: 7.1 Consensus size: 43
20111996 AAGAAGATAT
* *
20112006 TTGTAACTTCGATCT-CATCCGCTGGAACTTCAAGGAGATAAGAA
1 TTGTAGCTTCGATCTAC-TCCG-TGCAACTTCAAGGAGATAAGAA
* * ** * * *
20112050 TTGTGGCTTCGAGCCGCTCCAGTGCCATTTCAAGGAGA-AGAGAT
1 TTGTAGCTTCGATCTACTCC-GTGCAACTTCAAGGAGATA-AGAA
* * ** *
20112094 TTGTAGCTTAGATCTACTCCATTAAAACTTCAAGGAGATACGAA
1 TTGTAGCTTCGATCTACTCC-GTGCAACTTCAAGGAGATAAGAA
* * * * * *
20112138 TTGTGGCTTCGAGCTACTCCAGTGCCATTTCAGGGAGA-AGAGAT
1 TTGTAGCTTCGATCTACTCC-GTGCAACTTCAAGGAGATA-AGAA
* *
20112182 TTGTAGC-TCTGATCTACTCCGCTGAAACTTCAAGGAGATACGAA
1 TTGTAGCTTC-GATCTACTCCG-TGCAACTTCAAGGAGATAAGAA
* * * * * *
20112226 TTGTGGCTTCGAACTGCTCTAGTGTC-ATTTC-AGGAAGA-AGAGAT
1 TTGTAGCTTCGATCTACTC-CGTG-CAACTTCAAGG-AGATA-AGAA
*
20112270 TTGTAGCTTCGATCTACTCCGCCTG-AACTTCAAGAAGATAAGAA
1 TTGTAGCTTCGATCTACTCCG--TGCAACTTCAAGGAGATAAGAA
20112314 TTGTA
1 TTGTA
20112319 ATTTTTAGCC
Statistics
Matches: 197, Mismatches: 54, Indels: 36
0.69 0.19 0.13
Matches are distributed among these distances:
43 10 0.05
44 175 0.89
45 12 0.06
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
TTGTAGCTTCGATCTACTCCGTGCAACTTCAAGGAGATAAGAA
Found at i:20112467 original size:87 final size:87
Alignment explanation
Indices: 20112305--20112585 Score: 420
Period size: 88 Copynumber: 3.2 Consensus size: 87
20112295 AACTTCAAGA
* *
20112305 AGATAAGAAT-TGTAATTTTTAGCCTGTTACCCTACTGCTTTGGGGGTTAAGGCTCACCATCTTC
1 AGATAAG-ATCTGTAATTTTTAGCCTGTTACCCTACTGC-TTAGGGGTTAAGGCTCACCGTCTTC
*
20112369 GATCTGCTCCACTACTGTTTAGGG
64 GATCTGCTCCACTACTGCTTAGGG
* * *
20112393 AGATAAGATCTGTAATTTTCAGACTGTTACCATACTGCTTAGGGGTTAAGGCTCACCGTCTTCGA
1 AGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGTTAAGGCTCACCGTCTTCGA
* * *
20112458 TCTGCTCCACTACTACTTAAGA
66 TCTGCTCCACTACTGCTTAGGG
* *
20112480 AGATAAGATCTGTAATTTTTAGCCTATTACCCTACTGCTTAGGGGGTTAAGGTTCACCGTCTTCG
1 AGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTA-GGGGTTAAGGCTCACCGTCTTCG
20112545 ATCTGCTCCACTACTGCTTAGGG
65 ATCTGCTCCACTACTGCTTAGGG
20112568 AGATAAGATCTGTGAATT
1 AGATAAGATCTGT-AATT
20112586 CACCGACGTT
Statistics
Matches: 173, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
87 82 0.47
88 87 0.50
89 4 0.02
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (87 bp):
AGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGTTAAGGCTCACCGTCTTCGA
TCTGCTCCACTACTGCTTAGGG
Found at i:20117182 original size:26 final size:26
Alignment explanation
Indices: 20117153--20117212 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
20117143 TCCCTTTGAA
* * *
20117153 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
20117179 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
20117207 CCATTC
1 TCATTC
20117213 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:20117198 original size:28 final size:28
Alignment explanation
Indices: 20117167--20117229 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
20117157 TCGATATTTT
*
20117167 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
20117195 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
20117223 GTACACT
1 GCACACT
20117230 GAGTACTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:20121330 original size:3 final size:3
Alignment explanation
Indices: 20121322--20121579 Score: 104
Period size: 3 Copynumber: 87.3 Consensus size: 3
20121312 AACAATAGTT
* * * * *
20121322 ATA ATA ATA AAA ATA ATA GTA GTA A-A TATA ATA ACA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
* * * * *
20121367 ACA ATA ACA ATA ATA AT- ATA GTTA AAA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
20121412 GTG ATA ATA ATA ATA A-A A-A ATA GTA ATA ATA GT- ATG TTAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * * * * * *
20121455 ATA ATA GTA A-A A-A ATA GTA ATA GTA ATA ATT ACA AAA ATG ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * * * * *
20121502 A-C ATA A-A ATC ATA ATA ATA CTA ATG TTA ATA GTA ATAA ATA AGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
* *
20121546 ATA GTA ATA ATA GTA A-A TATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA A
20121580 ATTATAGGAA
Statistics
Matches: 181, Mismatches: 60, Indels: 28
0.67 0.22 0.10
Matches are distributed among these distances:
2 16 0.09
3 155 0.86
4 10 0.06
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:20121439 original size:37 final size:37
Alignment explanation
Indices: 20121375--20121580 Score: 120
Period size: 37 Copynumber: 5.4 Consensus size: 37
20121365 TAACAATAAC
* *
20121375 AATAATAATATAGTTAAAAATAATAATAATAGTAATAG-T-
1 AATAATAATA-A-TAAAAAATAGTAATAATAGT-AT-GTTA
*
20121414 GATAATAATAATAAAAAATAGTAATAATAGTATGTTA
1 AATAATAATAATAAAAAATAGTAATAATAGTATGTTA
* * * *
20121451 AATAATAATAGTAAAAAATAGTAATAGTAATA-ATTA
1 AATAATAATAATAAAAAATAGTAATAATAGTATGTTA
* * *
20121487 CAAAAATGATAATGAACATAAAATCA-TAATAATACTAATGTT-
1 -AATAATAATAAT--A-A-AAAAT-AGTAATAATAGT-ATGTTA
* * **
20121529 AATAGTAATAA-ATAAGAATAGTAATAATAGTA-AATA
1 AATAATAATAATA-AAAAATAGTAATAATAGTATGTTA
20121565 TAATAATAATAATAAA
1 -AATAATAATAATAAA
20121581 TTATAGGAAT
Statistics
Matches: 130, Mismatches: 23, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
35 2 0.02
36 8 0.06
37 80 0.62
38 4 0.03
39 10 0.08
40 1 0.01
41 21 0.16
42 2 0.02
43 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (37 bp):
AATAATAATAATAAAAAATAGTAATAATAGTATGTTA
Found at i:20123942 original size:87 final size:86
Alignment explanation
Indices: 20123785--20123945 Score: 207
Period size: 87 Copynumber: 1.9 Consensus size: 86
20123775 TACATGCATA
* * ** **
20123785 AGGTTGAGTTCTTACTCTTAATGAATTCATATCTTAGGTTTTAGGTGGTCTTATTGAGATGGACT
1 AGGTTGAGTTCTTACTCTTAATGAATTCATATCTCAGATTTTAGGTGGTCCCATTGAGAAAGACT
20123850 AGATGAATTCATTAACATGTG
66 AGATGAATTCATTAACATGTG
* * *
20123871 AGGTTGAGTTTCTTACTCTTAATGAGTTCATAT-TCCAGATTTTGGGTGGTCCCATTTAGAAAGA
1 AGGTTGAG-TTCTTACTCTTAATGAATTCATATCT-CAGATTTTAGGTGGTCCCATTGAGAAAGA
*
20123935 CTTGATGAATT
64 CTAGATGAATT
20123946 AACGAATTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
86 9 0.14
87 54 0.86
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (86 bp):
AGGTTGAGTTCTTACTCTTAATGAATTCATATCTCAGATTTTAGGTGGTCCCATTGAGAAAGACT
AGATGAATTCATTAACATGTG
Found at i:20125775 original size:28 final size:28
Alignment explanation
Indices: 20125743--20125802 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
20125733 TTTATAATTC
* * * *
20125743 ATAATTTTTTATATTATTAATTTTTTTT
1 ATAATTCTCTATATAATAAATTTTTTTT
20125771 ATAATTCTCTATATAATAAATTTTTTTT
1 ATAATTCTCTATATAATAAATTTTTTTT
20125799 ATAA
1 ATAA
20125803 ATAATTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
ATAATTCTCTATATAATAAATTTTTTTT
Found at i:20128104 original size:25 final size:27
Alignment explanation
Indices: 20128067--20128119 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
20128057 TCAAACATGC
20128067 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
20128093 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
20128119 A
1 A
20128120 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:20129626 original size:32 final size:32
Alignment explanation
Indices: 20129589--20129653 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
20129579 AATGCTTACC
20129589 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
20129621 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
20129653 A
1 A
20129654 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:20135371 original size:26 final size:24
Alignment explanation
Indices: 20135341--20135390 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
20135331 AAATAAAAAA
*
20135341 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
20135367 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
20135391 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:20135410 original size:21 final size:21
Alignment explanation
Indices: 20135361--20135419 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
20135351 ATAATAAATC
*
20135361 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
20135381 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
20135403 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
20135420 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:20135496 original size:15 final size:16
Alignment explanation
Indices: 20135466--20135498 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20135456 AAATGGTTAT
20135466 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
20135483 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
20135498 A
1 A
20135499 AAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:20136712 original size:25 final size:27
Alignment explanation
Indices: 20136675--20136727 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
20136665 TCAAACATGC
20136675 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
20136701 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
20136727 A
1 A
20136728 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:20138252 original size:32 final size:32
Alignment explanation
Indices: 20138215--20138276 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
20138205 GCTTATCATA
20138215 CCCATCATCCATTAACTATTAAAATGCTAATG
1 CCCATCATCCATTAACTATTAAAATGCTAATG
20138247 CCCATCATCCATTAACTATTAAAATGCTAA
1 CCCATCATCCATTAACTATTAAAATGCTAA
20138277 AATGCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.31
Consensus pattern (32 bp):
CCCATCATCCATTAACTATTAAAATGCTAATG
Found at i:20139651 original size:27 final size:27
Alignment explanation
Indices: 20139579--20139682 Score: 95
Period size: 27 Copynumber: 3.9 Consensus size: 27
20139569 AAGTCCTTAT
* *
20139579 TACAGAATATGCCACAAAGG-TGTTCCA
1 TACAGAGTATGCCACAAAGGCTATT-CA
* ** *
20139606 TATAGAGTACACCATAAAGGCTATAT-A
1 TACAGAGTATGCCACAAAGGCTAT-TCA
*
20139633 TACAGAGTATGCCACAAAGGCGATTCA
1 TACAGAGTATGCCACAAAGGCTATTCA
* *
20139660 TTCAGTGTATGCCACAAAGGCTA
1 TACAGAGTATGCCACAAAGGCTA
20139683 ACAGGATCCC
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.02
27 56 0.93
28 2 0.03
29 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (27 bp):
TACAGAGTATGCCACAAAGGCTATTCA
Found at i:20141481 original size:71 final size:71
Alignment explanation
Indices: 20141365--20141530 Score: 298
Period size: 71 Copynumber: 2.4 Consensus size: 71
20141355 ATGCTTTATG
* * *
20141365 AAATTAGTGTTACTTTGTTAGATTTTAAGTTTAGACATGAAAAAACAAGACTAATTTATAATAAA
1 AAATTGGTGTTAATTTGTTAGATTTTAAGCTTAGACATGAAAAAACAAGACTAATTTATAATAAA
20141430 AGGACT
66 AGGACT
20141436 AAATTGGTGTTAATTTGTTAGATTTTAAGCTTAGACATGAAAAAACAAGACTAATTTATAATAAA
1 AAATTGGTGTTAATTTGTTAGATTTTAAGCTTAGACATGAAAAAACAAGACTAATTTATAATAAA
20141501 AGGACT
66 AGGACT
20141507 AAATTGGTGTT-ATTTGTTAGATTT
1 AAATTGGTGTTAATTTGTTAGATTT
20141531 CAAGACGAAT
Statistics
Matches: 92, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 13 0.14
71 79 0.86
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (71 bp):
AAATTGGTGTTAATTTGTTAGATTTTAAGCTTAGACATGAAAAAACAAGACTAATTTATAATAAA
AGGACT
Found at i:20144270 original size:38 final size:38
Alignment explanation
Indices: 20144219--20144321 Score: 145
Period size: 38 Copynumber: 2.7 Consensus size: 38
20144209 GTTATATCGT
* *
20144219 TATTCAAGCTTTGTGCCTA-CTAGGCTTAGTGCTAGTGA
1 TATTCAGGCTTTGTGCCTAGC-AGGCTTAGTGCCAGTGA
* *
20144257 TATTCAGGCTTTGTGCCTAGCATGCTTAGTGCCAGTGT
1 TATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGA
*
20144295 TATTCAGGCTTAGTGCCTAGCAGGCTT
1 TATTCAGGCTTTGTGCCTAGCAGGCTT
20144322 CTTACCGGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 57 0.98
39 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (38 bp):
TATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGA
Found at i:20145368 original size:15 final size:16
Alignment explanation
Indices: 20145333--20145375 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
20145323 TCGAGGACTC
20145333 GATTTAGGTATGATAT
1 GATTTAGGTATGATAT
*
20145349 G-TTTATGTATGAT-T
1 GATTTAGGTATGATAT
20145363 GATTTAGGATATG
1 GATTTAGG-TATG
20145376 TCTAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
GATTTAGGTATGATAT
Found at i:20148951 original size:17 final size:17
Alignment explanation
Indices: 20148924--20148965 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
20148914 TTATACCATG
*
20148924 CATATCATGTAAATTTT
1 CATACCATGTAAATTTT
*
20148941 CCTACCATGTAAATTTT
1 CATACCATGTAAATTTT
20148958 CATACCAT
1 CATACCAT
20148966 TTCATTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (17 bp):
CATACCATGTAAATTTT
Found at i:20149438 original size:19 final size:20
Alignment explanation
Indices: 20149396--20149444 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
20149386 TCATGCTTTC
*
20149396 TATTCACATTTTCATATTCA
1 TATTCACATTTTCATAATCA
20149416 -ATTCACATTTTCA-AATCA
1 TATTCACATTTTCATAATCA
20149434 TATTCCACATT
1 TATT-CACATT
20149445 CACATTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 6 0.23
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTCACATTTTCATAATCA
Found at i:20150635 original size:22 final size:20
Alignment explanation
Indices: 20150603--20150643 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
20150593 TTCTGTTTCT
20150603 TTTTAGCTTTGTTTCTTTTG
1 TTTTAGCTTTGTTTCTTTTG
20150623 TTTTATGCTTTTGTTTCTTTT
1 TTTTA-GC-TTTGTTTCTTTT
20150644 ATTTCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.73
Consensus pattern (20 bp):
TTTTAGCTTTGTTTCTTTTG
Found at i:20153000 original size:19 final size:18
Alignment explanation
Indices: 20152976--20153011 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20152966 TTTTTTTTAC
*
20152976 TTTTAATATTTGTTTAAAT
1 TTTTAATA-ATGTTTAAAT
20152995 TTTTAATAATGTTTAAA
1 TTTTAATAATGTTTAAA
20153012 GCTTCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
TTTTAATAATGTTTAAAT
Found at i:20161648 original size:96 final size:96
Alignment explanation
Indices: 20161483--20161678 Score: 231
Period size: 96 Copynumber: 2.0 Consensus size: 96
20161473 AATTTTAGAG
* * ** *
20161483 TTTTAAGGAAAAAATTTAAATAAATTAGGGTTTAGTGTTTGTTAATTAAATTAATTACTAATTTT
1 TTTTAAGGAAAAAATTCAAATAAATTAGGG-TTAGGGTTACTTAAGTAAATTAATTACTAATTTT
* *
20161548 AAAAAATTAGATTATGG-TTTAGTGTTTATGGT
65 AAAAAATTAGATTA-GGATTTAGGGTTTAGGGT
*
20161580 TTTTAAGGAAAAAA-TCAAATAAATTA-GG-TAGGGTTACTTGAGTAAATTAATTA-TAAATTTT
1 TTTTAAGGAAAAAATTCAAATAAATTAGGGTTAGGGTTACTTAAGTAAATTAATTACT-AATTTT
20161641 AAAAAAAATTAGATTAGGATTTTAGGGTTTAGGGT
65 --AAAAAATTAGATTAGGA-TTTAGGGTTTAGGGT
20161676 TTT
1 TTT
20161679 AGGGTATTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
92 1 0.01
93 26 0.30
94 2 0.02
95 16 0.19
96 27 0.31
97 14 0.16
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.42
Consensus pattern (96 bp):
TTTTAAGGAAAAAATTCAAATAAATTAGGGTTAGGGTTACTTAAGTAAATTAATTACTAATTTTA
AAAAATTAGATTAGGATTTAGGGTTTAGGGT
Found at i:20161678 original size:15 final size:15
Alignment explanation
Indices: 20161654--20161683 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20161644 AAAAATTAGA
20161654 TTAGGATTTTAGGGT
1 TTAGGATTTTAGGGT
*
20161669 TTAGGGTTTTAGGGT
1 TTAGGATTTTAGGGT
20161684 ATTTAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (15 bp):
TTAGGATTTTAGGGT
Found at i:20161983 original size:126 final size:125
Alignment explanation
Indices: 20161759--20162048 Score: 429
Period size: 126 Copynumber: 2.3 Consensus size: 125
20161749 TAATTTAAAA
* *
20161759 AAGCTTCTACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAATAAATTTGAGAAGACGTGTC
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTAAAAAATAAATTTGAGAAGACGTGTC
* *
20161824 TGCGTAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTATTGAAAG
66 TGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
*
20161884 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTAAAAAAATAATTTTGAGAAGACGTGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCT-AAAAAATAAATTTGAGAAGACGTGT
* * * * *
20161949 CTGTGCAAATAGTGGT-AAAAACGCTTTAAGCAGGATGCATTTTCAGCAAAATTACTGGAAG
65 CTGCGCAAATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* * * *
20162010 AAACTCCCACGTTGACGCTCTTTTGCTACAGTGGTCTCT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCT
20162049 GAAATAACTT
Statistics
Matches: 149, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
125 38 0.26
126 109 0.73
127 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (125 bp):
AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTAAAAAATAAATTTGAGAAGACGTGTC
TGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
Found at i:20165141 original size:55 final size:55
Alignment explanation
Indices: 20165082--20165519 Score: 208
Period size: 54 Copynumber: 7.7 Consensus size: 55
20165072 TACATGAAAT
* **
20165082 AATATAAAAACATTCAAAATATTTTTTTATTTAAAATAATTTTCATTTTATTAAA
1 AATATAAAAAAATTCAAAATATTACTTTATTTAAAATAATTTTCATTTTATTAAA
* * *
20165137 AATATAAAAGTAAATT--ATA-ATTACTTTATTTAAAACAACCTTTT-ATATTATCACATGAAA
1 AATATAAAA--AAATTCAAAATATTACTTTATTTAAAATAA--TTTTCAT-TT-T---ATTAAA
* * * *
20165197 TAATATAAAAATATTCAAAATGTTACCTTATTTAAAATAATTTCCATTTTATTAAA
1 -AATATAAAAAAATTCAAAATATTACTTTATTTAAAATAATTTTCATTTTATTAAA
* *
20165253 AATATAAAAGTAAATTGC---A-ATTACTTTATTTAAAACAACCTTTT-ATCTAATTACATGAAA
1 AATATAAAA--AAATT-CAAAATATTACTTTATTTAAAATAA--TTTTCAT-T--TT--ATTAAA
* * * **
20165313 TAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAA-TTTCAATTTTATTAAA
1 -AATATAAAAAAATTCAAAATATTACTTTATTTAAAATAATTTTC-ATTTTATTAAA
* * *
20165369 AATATAAAAGTAAATT--ACA-ATTACTTTATTTAAAACAACCTTTT-ATCTAATTACATGAAA
1 AATATAAAA--AAATTCAAAATATTACTTTATTTAAAATAA--TTTTCAT-T--TT--ATTAAA
* * * ** *
20165429 TAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTAAA
1 -AATATAAAAAAATTCAAAATATTACTTTATTTAAAATAATTTTCATTTTATTAAA
*
20165485 AATATAAAAGTAAATT--ACA-ATTACTTTATTTAAAA
1 AATATAAAA--AAATTCAAAATATTACTTTATTTAAAA
20165520 CAACATTTTA
Statistics
Matches: 286, Mismatches: 49, Indels: 97
0.66 0.11 0.22
Matches are distributed among these distances:
54 58 0.20
55 49 0.17
56 26 0.09
57 20 0.07
58 10 0.03
59 16 0.06
60 25 0.09
61 38 0.13
62 44 0.15
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.40
Consensus pattern (55 bp):
AATATAAAAAAATTCAAAATATTACTTTATTTAAAATAATTTTCATTTTATTAAA
Found at i:20165245 original size:116 final size:116
Alignment explanation
Indices: 20165070--20165565 Score: 848
Period size: 116 Copynumber: 4.3 Consensus size: 116
20165060 TTTATATTTT
* * **** *
20165070 ATTACATGAAATAATATAAAAACATTCAAAATATTTTTTTATTTAAAATAATTTTCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
* * *
20165135 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATATT
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
* * *
20165186 ATCACATGAAATAATATAAAAATATTCAAAATGTTACCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
*
20165251 AAAATATAAAAGTAAATTGCAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
*
20165302 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCAATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
20165367 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
20165418 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
*
20165483 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACATTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
20165534 ATTACATGAAATAATATAAAAATATTCAAAAT
1 ATTACATGAAATAATATAAAAATATTCAAAAT
20165566 ATTTGTACAA
Statistics
Matches: 362, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 362 1.00
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (116 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
Found at i:20165987 original size:18 final size:18
Alignment explanation
Indices: 20165960--20165997 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20165950 GAAAAAGGAA
*
20165960 ACATATAAGGGCTACGAT
1 ACATAAAAGGGCTACGAT
*
20165978 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTACGAT
20165996 AC
1 AC
20165998 GTACCTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (18 bp):
ACATAAAAGGGCTACGAT
Found at i:20167752 original size:15 final size:15
Alignment explanation
Indices: 20167734--20167764 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20167724 TTTTTATTTT
*
20167734 AAAAAATAAATTTAG
1 AAAAAATAAAATTAG
20167749 AAAAAATAAAATTAG
1 AAAAAATAAAATTAG
20167764 A
1 A
20167765 GCTTTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AAAAAATAAAATTAG
Found at i:20167803 original size:22 final size:22
Alignment explanation
Indices: 20167791--20167840 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
20167781 TAATGAGAGT
20167791 TTTGAGAGGAATTTAAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
*
20167813 TTTGAGA-G-ATTTGAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
20167833 TTTGAGAG
1 TTTGAGAG
20167841 AATATTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 18 0.69
21 1 0.04
22 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
TTTGAGAGGAATTTAAGAGAAA
Found at i:20167814 original size:11 final size:11
Alignment explanation
Indices: 20167791--20167842 Score: 72
Period size: 11 Copynumber: 4.9 Consensus size: 11
20167781 TAATGAGAGT
*
20167791 TTTGAGAGGAA
1 TTTGAGAGAAA
*
20167802 TTTAAGAGAAA
1 TTTGAGAGAAA
20167813 TTTGAGAG--A
1 TTTGAGAGAAA
20167822 TTTGAGAGAAA
1 TTTGAGAGAAA
20167833 TTTGAGAGAA
1 TTTGAGAGAA
20167843 TATTGAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 9 0.25
11 27 0.75
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:20167826 original size:31 final size:31
Alignment explanation
Indices: 20167784--20167842 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
20167774 AAACAATTAA
* *
20167784 TGAGAGTTTTGAGAGGAATTTAAGAGAAATT
1 TGAGAGATTTGAGAGAAATTTAAGAGAAATT
*
20167815 TGAGAGATTTGAGAGAAATTTGAGAGAA
1 TGAGAGATTTGAGAGAAATTTAAGAGAA
20167843 TATTGAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.29
Consensus pattern (31 bp):
TGAGAGATTTGAGAGAAATTTAAGAGAAATT
Found at i:20167854 original size:31 final size:31
Alignment explanation
Indices: 20167791--20167854 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
20167781 TAATGAGAGT
* *
20167791 TTTGAGAGGAATTTAAGAGAAATTTGAGAGA
1 TTTGAGAGAAATTTAAGAGAAATTTGAAAGA
*
20167822 TTTGAGAGAAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAGAAATTTAAGAGAAAT-TTGAAAGA
20167853 TT
1 TT
20167855 GAATATTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (31 bp):
TTTGAGAGAAATTTAAGAGAAATTTGAAAGA
Found at i:20170891 original size:11 final size:11
Alignment explanation
Indices: 20170851--20170926 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
20170841 ATTCCAAAAA
*
20170851 TAATATTATTT
1 TAATATTAATT
20170862 TAATAGTTTAATAT
1 TAATA--TTAAT-T
20170876 TAATATTAATT
1 TAATATTAATT
20170887 TAATACTT-ATCT
1 TAATA-TTAAT-T
*
20170899 TAATAAT-ATT
1 TAATATTAATT
20170909 T--TATTAATT
1 TAATATTAATT
20170918 TAATATTAA
1 TAATATTAA
20170927 AATAATTATC
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.07
10 2 0.04
11 22 0.41
12 13 0.24
13 4 0.07
14 6 0.11
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Found at i:20178557 original size:16 final size:16
Alignment explanation
Indices: 20178513--20178586 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 16
20178503 TGTACTCTTA
20178513 TAACATATAATCCATG
1 TAACATATAATCCATG
*
20178529 TAAAATTTATAATCCATG
1 TAACA--TATAATCCATG
*
20178547 TAACATATAATTCATG
1 TAACATATAATCCATG
* *
20178563 TAAAGTATATAATTCATG
1 T-AA-CATATAATCCATG
20178581 TAACAT
1 TAACAT
20178587 GTACTTCATA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
16 17 0.35
17 4 0.08
18 28 0.57
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (16 bp):
TAACATATAATCCATG
Found at i:20178595 original size:34 final size:34
Alignment explanation
Indices: 20178513--20178595 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
20178503 TGTACTCTTA
* *
20178513 TAACATATAATCCATGTAAAATTTATAATCCATG
1 TAACATATAATTCATGTAAAATATATAATCCATG
* *
20178547 TAACATATAATTCATGTAAAGTATATAATTCATG
1 TAACATATAATTCATGTAAAATATATAATCCATG
* *
20178581 TAACATGTACTTCAT
1 TAACATATAATTCAT
20178596 ATTTCATATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.37
Consensus pattern (34 bp):
TAACATATAATTCATGTAAAATATATAATCCATG
Found at i:20179787 original size:23 final size:23
Alignment explanation
Indices: 20179705--20179791 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
20179695 CCTGATCAGT
*
20179705 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
20179727 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
20179747 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
20179770 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
20179792 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:20181262 original size:16 final size:17
Alignment explanation
Indices: 20181227--20181262 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
20181217 CCTAATTCTC
20181227 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
20181243 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
20181258 CCTTC
1 CCTTC
20181263 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:20192805 original size:23 final size:23
Alignment explanation
Indices: 20192753--20192878 Score: 91
Period size: 22 Copynumber: 5.6 Consensus size: 23
20192743 TTGAGCCGAT
* * *
20192753 AAACAGTAAGCTCAATTGAGCT-
1 AAACGGTAAGCTCCATAGAGCTG
*
20192775 AAACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
*
20192798 AAACGGTAAGC-CCCTA-AGGACTG
1 AAACGGTAAGCTCCATAGA-G-CTG
* * * *
20192821 AAACAGTAAGCTCTAAAAAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
* *
20192844 -AATGGTAAGCT-CATAAGAGCTA
1 AAACGGTAAGCTCCAT-AGAGCTG
20192866 AAACGGTAAGCTC
1 AAACGGTAAGCTC
20192879 ATACGAACTG
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
21 2 0.03
22 37 0.46
23 37 0.46
24 3 0.04
25 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:20192879 original size:23 final size:22
Alignment explanation
Indices: 20192752--20192881 Score: 88
Period size: 23 Copynumber: 5.8 Consensus size: 22
20192742 CTTGAGCCGA
* *
20192752 TAAACAGTAAGCTCA-ATTGAGC
1 TAAACGGTAAGCTCATA-AGAGC
*
20192774 TAAACGGTAAGCTCCGT-AGAGC
1 TAAACGGTAAGCT-CATAAGAGC
* *
20192796 TGAAACGGTAAGCCCCTAAG-GAC
1 T-AAACGGTAAGCTCATAAGAG-C
* *
20192819 TGAAACAGTAAGCTC-TAAAAAGC
1 T-AAACGGTAAGCTCAT-AAGAGC
* *
20192842 TGAATGGTAAGCTCATAAGAGC
1 TAAACGGTAAGCTCATAAGAGC
20192864 TAAAACGGTAAGCTCATA
1 T-AAACGGTAAGCTCATA
20192882 CGAACTGTGG
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
22 37 0.44
23 47 0.55
24 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (22 bp):
TAAACGGTAAGCTCATAAGAGC
Found at i:20208014 original size:12 final size:11
Alignment explanation
Indices: 20207981--20208019 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
20207971 AAACATAATT
20207981 TTCAACAAATAA
1 TTCAACAAA-AA
**
20207993 TTTGACAAAAA
1 TTCAACAAAAA
20208004 TTCAACAAAAA
1 TTCAACAAAAA
20208015 TTCAA
1 TTCAA
20208020 AATGAGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (11 bp):
TTCAACAAAAA
Found at i:20209675 original size:64 final size:64
Alignment explanation
Indices: 20209544--20209675 Score: 147
Period size: 64 Copynumber: 2.1 Consensus size: 64
20209534 GAGCATCCCA
* * * * * * ** * *
20209544 ATCGGTATTGATCCTGCATGTGTTGCGGACATACCGCAGCCCTTTGTGAGCGTCTTGTTATATG
1 ATCGGTATTGACCCTGCATGTATTGCGGACAAACCGCAGCCCTTTATAAGCATCCCGATATAGG
* * *
20209608 ATCGGTATTGACCCTGCATGTATTGCGGATAAACTGCAGCTCTTTATAAGCATCCCGATATAGG
1 ATCGGTATTGACCCTGCATGTATTGCGGACAAACCGCAGCCCTTTATAAGCATCCCGATATAGG
20209672 ATCG
1 ATCG
20209676 CTTGAACTTC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (64 bp):
ATCGGTATTGACCCTGCATGTATTGCGGACAAACCGCAGCCCTTTATAAGCATCCCGATATAGG
Found at i:20212460 original size:30 final size:30
Alignment explanation
Indices: 20212426--20212483 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
20212416 ATTTTCGGGC
* *
20212426 CTAGGGGTAAAATGGTCATTTTGTCAAAGT
1 CTAGGGGCAAAATGGTCATTTTATCAAAGT
20212456 CTAGGGGCAAAATGGTCATTTTATCAAA
1 CTAGGGGCAAAATGGTCATTTTATCAAA
20212484 AATATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (30 bp):
CTAGGGGCAAAATGGTCATTTTATCAAAGT
Found at i:20216265 original size:12 final size:13
Alignment explanation
Indices: 20216248--20216276 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20216238 CGTGAAATAA
20216248 AAAAAATCAA-TT
1 AAAAAATCAATTT
20216260 AAAAAATCAATTT
1 AAAAAATCAATTT
20216273 AAAA
1 AAAA
20216277 TATTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATCAATTT
Found at i:20217378 original size:5 final size:5
Alignment explanation
Indices: 20217368--20217418 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
20217358 TTTGTTTTAG
*
20217368 ATTTT ATTTT ATTTT ATTTTT ATTTG ATTTT -TTATT -TTTCT ATTTT
1 ATTTT ATTTT ATTTT A-TTTT ATTTT ATTTT ATT-TT ATTT-T ATTTT
20217414 ATTTT
1 ATTTT
20217419 TGGAAGTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 3 0.08
5 29 0.73
6 8 0.20
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:20218094 original size:21 final size:21
Alignment explanation
Indices: 20218066--20218126 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
20218056 GGTTACACAA
20218066 CCTA-TTCACACGGTCGTGTC
1 CCTACTTCACACGGTCGTGTC
20218086 CCTACTTCACACAGG-CGTGTC
1 CCTACTTCACAC-GGTCGTGTC
20218107 CCT-CTGTCACACGGTCGTGT
1 CCTACT-TCACACGGTCGTGT
20218127 GCTACCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.22
21 27 0.73
22 2 0.05
ACGTcount: A:0.15, C:0.36, G:0.21, T:0.28
Consensus pattern (21 bp):
CCTACTTCACACGGTCGTGTC
Found at i:20220296 original size:22 final size:21
Alignment explanation
Indices: 20220250--20220293 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
20220240 TTTAAAACCC
20220250 AATGAGTATCAATACTTTTTA
1 AATGAGTATCAATACTTTTTA
*
20220271 AATGAGTATCAATATTTTTTA
1 AATGAGTATCAATACTTTTTA
20220292 AA
1 AA
20220294 ATGTATCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (21 bp):
AATGAGTATCAATACTTTTTA
Found at i:20221896 original size:22 final size:22
Alignment explanation
Indices: 20221870--20221916 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
20221860 GGTTTTCTTG
20221870 TTTAT-TTCTGTTT-TTGTTTTAT
1 TTTATCTTCT-TTTATT-TTTTAT
20221892 TTTATCTTCTTTTATTTTTTAT
1 TTTATCTTCTTTTATTTTTTAT
20221914 TTT
1 TTT
20221917 TTTTAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTATCTTCTTTTATTTTTTAT
Found at i:20221911 original size:27 final size:27
Alignment explanation
Indices: 20221880--20221932 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20221870 TTTATTTCTG
* *
20221880 TTTTTGTTTTATTTTATCTT-CTTTTAT
1 TTTTTATTTT-TTTTAACTTACTTTTAT
20221907 TTTTTATTTTTTTTAACTTACTTTTA
1 TTTTTATTTTTTTTAACTTACTTTTA
20221933 AACATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTTTATTTTTTTTAACTTACTTTTAT
Found at i:20224249 original size:16 final size:17
Alignment explanation
Indices: 20224216--20224249 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20224206 CGCATAATAT
*
20224216 AATAAGCATTTTTAAAA
1 AATAAACATTTTTAAAA
20224233 AATAAACATTTTTAAAA
1 AATAAACATTTTTAAAA
20224250 TTTTAATTTT
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:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (17 bp):
AATAAACATTTTTAAAA
Found at i:20240410 original size:20 final size:20
Alignment explanation
Indices: 20240385--20240424 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20240375 AATATTTTTC
*
20240385 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
20240405 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
20240425 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:20240426 original size:34 final size:35
Alignment explanation
Indices: 20240373--20240439 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
20240363 CAAACACCAG
* *
20240373 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
20240408 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
20240440 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:20240431 original size:14 final size:14
Alignment explanation
Indices: 20240408--20240447 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
20240398 ACAGAAAAGT
*
20240408 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
20240422 AAATCATTTTACGG
1 AAAACATTTTACAG
20240436 AAAACATTTTAC
1 AAAACATTTTAC
20240448 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:20246967 original size:17 final size:18
Alignment explanation
Indices: 20246945--20246984 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
20246935 CAAAACGTGT
20246945 TTTTTAATAATTTTAT-A
1 TTTTTAATAATTTTATAA
20246962 TTTTT-ATAATTTTATAA
1 TTTTTAATAATTTTATAA
20246979 TTTTTA
1 TTTTTA
20246985 TTTCTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTAATAATTTTATAA
Found at i:20246968 original size:8 final size:8
Alignment explanation
Indices: 20246945--20247017 Score: 69
Period size: 8 Copynumber: 9.0 Consensus size: 8
20246935 CAAAACGTGT
20246945 TTTTTAATA
1 TTTTT-ATA
*
20246954 ATTTTATA
1 TTTTTATA
20246962 TTTTTATA
1 TTTTTATA
*
20246970 ATTTTATAA
1 TTTTTAT-A
20246979 TTTTTAT-
1 TTTTTATA
20246986 TTCTTTATA
1 TT-TTTATA
* *
20246995 TTTATATT
1 TTTTTATA
20247003 TTTTTAT-
1 TTTTTATA
20247010 TTTTTATA
1 TTTTTATA
20247018 AATGTATATA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
7 9 0.17
8 31 0.58
9 13 0.25
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTATA
Found at i:20246983 original size:25 final size:25
Alignment explanation
Indices: 20246946--20247121 Score: 77
Period size: 25 Copynumber: 7.1 Consensus size: 25
20246936 AAAACGTGTT
20246946 TTTTAATAA-TTTTATATTTTTATAA
1 TTTT-ATAATTTTTATATTTTTATAA
20246971 TTTTATAATTTTTAT-TTCTTTAT-A
1 TTTTATAATTTTTATATT-TTTATAA
*
20246995 -TTTAT-ATTTTTTTATTTTTTATAA
1 TTTTATAATTTTTATA-TTTTTATAA
* * *
20247019 ATGTATATATTATATT-T-TTCTTTCAAAA
1 TTTTATA-ATT-T-TTATATT-TTT-ATAA
* **
20247047 TATTATTTTTTTTATA-TTTT-TAA
1 TTTTATAATTTTTATATTTTTATAA
* * *
20247070 TTCTACTTA-CTTTATATTTTTATAA
1 TTTTA-TAATTTTTATATTTTTATAA
* *
20247095 ATTTATATTTTTTATATATTTT-TAA
1 TTTTATAATTTTTATAT-TTTTATAA
20247120 TT
1 TT
20247122 CTACTTACTT
Statistics
Matches: 113, Mismatches: 19, Indels: 38
0.66 0.11 0.22
Matches are distributed among these distances:
22 7 0.06
23 21 0.19
24 17 0.15
25 41 0.36
26 9 0.08
27 8 0.07
28 8 0.07
29 2 0.02
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (25 bp):
TTTTATAATTTTTATATTTTTATAA
Found at i:20246985 original size:17 final size:16
Alignment explanation
Indices: 20246945--20247116 Score: 72
Period size: 16 Copynumber: 10.8 Consensus size: 16
20246935 CAAAACGTGT
20246945 TTTTTAATAATTTTATA
1 TTTTT-ATAATTTTATA
20246962 TTTTTATAATTTTATAA
1 TTTTTATAATTTTAT-A
*
20246979 TTTTTAT-TTCTTTATA
1 TTTTTATAAT-TTTATA
* **
20246995 TTTATATTTTTTTAT-
1 TTTTTATAATTTTATA
* *
20247010 TTTTTATAAATGTATA
1 TTTTTATAATTTTATA
*
20247026 -TATTAT-ATTTT-T-
1 TTTTTATAATTTTATA
* * * *
20247038 CTTTCAAAATATTAT-
1 TTTTTATAATTTTATA
*
20247053 TTTTTTTATATTTT-TA
1 TTTTTATA-ATTTTATA
* * * *
20247069 ATTCTACTTACTTTATA
1 TTTTTA-TAATTTTATA
*
20247086 TTTTTATAAATTTATA
1 TTTTTATAATTTTATA
20247102 TTTTTTATATATTTT
1 -TTTTTATA-ATTTT
20247117 TAATTCTACT
Statistics
Matches: 113, Mismatches: 29, Indels: 25
0.68 0.17 0.15
Matches are distributed among these distances:
13 4 0.04
14 7 0.06
15 21 0.19
16 42 0.37
17 35 0.31
18 4 0.04
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (16 bp):
TTTTTATAATTTTATA
Found at i:20247008 original size:33 final size:31
Alignment explanation
Indices: 20246956--20247016 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
20246946 TTTTAATAAT
*
20246956 TTTATATTTTTATAATTTTATAATTTTTATTTC
1 TTTATATTTATATAATTTTAT--TTTTTATTTC
**
20246989 TTTATATTTATATTTTTTTATTTTTTAT
1 TTTATATTTATATAATTTTATTTTTTAT
20247017 AAATGTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 7 0.28
33 18 0.72
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (31 bp):
TTTATATTTATATAATTTTATTTTTTATTTC
Found at i:20247087 original size:23 final size:23
Alignment explanation
Indices: 20247057--20247138 Score: 85
Period size: 23 Copynumber: 3.4 Consensus size: 23
20247047 TATTATTTTT
20247057 TTTATATTTTTAATTCTACTTAC
1 TTTATATTTTTAATTCTACTTAC
* **
20247080 TTTATATTTTTATAAATT-TATATTTT
1 TTTATA-TTTT-T-AATTCTA-CTTAC
20247106 TTATATATTTTTAATTCTACTTAC
1 TT-TATATTTTTAATTCTACTTAC
20247130 TTTATATTT
1 TTTATATTT
20247139 GTATAAATGC
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
23 13 0.28
24 12 0.26
25 6 0.13
26 12 0.26
27 4 0.09
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATATTTTTAATTCTACTTAC
Found at i:20247121 original size:50 final size:50
Alignment explanation
Indices: 20247050--20247165 Score: 182
Period size: 50 Copynumber: 2.4 Consensus size: 50
20247040 TTCAAAATAT
* * **
20247050 TATTTTTTTTATATTTTTAATTCTACTTACTTTATATTTTTATAAATTTA
1 TATTTTTTATATATTTTTAATTCTACTTACTTTATATTTGTATAAATGCA
20247100 TATTTTTTATATATTTTTAATTCTACTTACTTTATATTTGTATAAATGCA
1 TATTTTTTATATATTTTTAATTCTACTTACTTTATATTTGTATAAATGCA
20247150 TA--TTTTATATATTTTT
1 TATTTTTTATATATTTTT
20247166 CAAAATAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 14 0.23
50 48 0.77
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (50 bp):
TATTTTTTATATATTTTTAATTCTACTTACTTTATATTTGTATAAATGCA
Found at i:20247133 original size:25 final size:25
Alignment explanation
Indices: 20247059--20247136 Score: 90
Period size: 25 Copynumber: 3.1 Consensus size: 25
20247049 TTATTTTTTT
20247059 TATATTTTTAATTCTACTTACTTTA
1 TATATTTTTAATTCTACTTACTTTA
**
20247084 TAT-TTTTATAAATT-TA-TATTTTTTA
1 TATATTTT-T-AATTCTACT-TACTTTA
20247109 TATATTTTTAATTCTACTTACTTTA
1 TATATTTTTAATTCTACTTACTTTA
20247134 TAT
1 TAT
20247137 TTGTATAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
24 9 0.21
25 25 0.58
26 9 0.21
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (25 bp):
TATATTTTTAATTCTACTTACTTTA
Found at i:20249741 original size:137 final size:137
Alignment explanation
Indices: 20249495--20249781 Score: 493
Period size: 137 Copynumber: 2.1 Consensus size: 137
20249485 CATTGGGCCT
** * * *
20249495 AAGCCCATTCAGGTAATAGTGGTACTGGGCCAGAGCCCTTTTTAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTT
* *
20249560 AGACCCTTATTCAGATAACAGTATGGCCCATAGGCCTATCTCAAAATACATGCAATATCAGTAAA
66 AGACCCTTATTCAGATAACAGTATGGCCCATAGGCCCATCTCAAAATACATGCAACATCAGTAAA
20249625 CATATGC
131 CATATGC
20249632 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTT
* *
20249697 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGACCCTTATTCAGATAACAGTATGGCCCATAGGCCCATCTCAAAATACATGCAACATCAGTAAA
20249762 CATATGC
131 CATATGC
20249769 AAGCCCATTTGGG
1 AAGCCCATTTGGG
20249782 GAGACTACTC
Statistics
Matches: 141, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
137 141 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTT
AGACCCTTATTCAGATAACAGTATGGCCCATAGGCCCATCTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:20251563 original size:26 final size:26
Alignment explanation
Indices: 20251532--20251639 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
20251522 TGAAATGCCC
20251532 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
20251558 ATCATGGAACATTTATCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
* *
20251584 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
20251610 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
20251636 ATCA
1 ATCA
20251640 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
25 4 0.05
26 66 0.90
27 3 0.04
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:20251610 original size:52 final size:52
Alignment explanation
Indices: 20251532--20251639 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
20251522 TGAAATGCCC
* * *
20251532 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTATCTAACCTATT
1 ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATT
* *
20251584 ATCATGGAATATTTACCTAATCCATTATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATT
20251636 ATCA
1 ATCA
20251640 ATTTGTACCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATT
Found at i:20253856 original size:30 final size:30
Alignment explanation
Indices: 20253820--20253883 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
20253810 TCAATTAGAC
**
20253820 TAAGGACATGTGTAGGTTTGTCTACTAATA
1 TAAGGACATGTGTAGGTTCATCTACTAATA
* *
20253850 TAAGGACATGTTTAGGTTCATTTACTAATA
1 TAAGGACATGTGTAGGTTCATCTACTAATA
20253880 TAAG
1 TAAG
20253884 TTGTCTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (30 bp):
TAAGGACATGTGTAGGTTCATCTACTAATA
Found at i:20257007 original size:38 final size:38
Alignment explanation
Indices: 20256956--20257034 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
20256946 GAATTAAGGC
20256956 TTAGTGCCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
1 TTAGTGCCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
*
20256994 TTAGTGTCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
1 TTAGTGCCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
20257032 TTA
1 TTA
20257035 AGTATTCAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.14, C:0.27, G:0.10, T:0.49
Consensus pattern (38 bp):
TTAGTGCCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
Found at i:20263000 original size:23 final size:22
Alignment explanation
Indices: 20262953--20263012 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
20262943 TTTTTATTAA
* *
20262953 AAAATTTAAAAATTAAAATTAT
1 AAAATTTATAAATTAAAAGTAT
20262975 AAAATTTATAAATATAAAAGGT-T
1 AAAATTTATAAAT-TAAAA-GTAT
20262998 -AAATTTATTAAATTA
1 AAAATTTA-TAAATTA
20263013 TTTAGAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 21 0.64
23 11 0.33
24 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (22 bp):
AAAATTTATAAATTAAAAGTAT
Found at i:20264844 original size:2 final size:2
Alignment explanation
Indices: 20264837--20264864 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20264827 CATCTCAATA
20264837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20264865 GCATACTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20268058 original size:17 final size:17
Alignment explanation
Indices: 20268036--20268069 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20268026 GCTACAAAAT
*
20268036 CAAATCTTCTAATATTA
1 CAAATCTTCTAAGATTA
20268053 CAAATCTTCTAAGATTA
1 CAAATCTTCTAAGATTA
20268070 GTTTTCATAT
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:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
CAAATCTTCTAAGATTA
Found at i:20268866 original size:21 final size:21
Alignment explanation
Indices: 20268824--20268866 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20268814 ACAAACACAA
* **
20268824 CTCTGCCTCTGTCACCTGCGC
1 CTCTGCCTCTGCCACCAACGC
*
20268845 CTCTTCCTCTGCCACCAACGC
1 CTCTGCCTCTGCCACCAACGC
20268866 C
1 C
20268867 ACGCCTGTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.09, C:0.51, G:0.14, T:0.26
Consensus pattern (21 bp):
CTCTGCCTCTGCCACCAACGC
Found at i:20271180 original size:4 final size:4
Alignment explanation
Indices: 20271171--20271212 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
20271161 TATGACGTAG
20271171 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
20271213 GTTGCTTGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:20272043 original size:43 final size:43
Alignment explanation
Indices: 20271974--20272158 Score: 244
Period size: 43 Copynumber: 4.3 Consensus size: 43
20271964 TATTTGAAAA
* * * *
20271974 AAACGCCGCTAAAGAACATGAGCTTTAGCCGCACTTTAACCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCACCAC
* * * *
20272017 AAACGCCGCTAAAGTATATGACCTTTAGCGGTGCTTTCACCAG
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCACCAC
* * *
20272060 AAACGCCGTTAAAGACCATGACCTTTAGCGGCGCTTTCACCAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCACCAC
* * *
20272103 AAACGCCGCTAAAGAACATCACCTTTAGTGGCGTTTTCACCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCACCAC
20272146 AAACGCCGCTAAA
1 AAACGCCGCTAAA
20272159 AGTAGCGTTC
Statistics
Matches: 122, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 122 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCACCAC
Found at i:20272906 original size:13 final size:14
Alignment explanation
Indices: 20272880--20272908 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20272870 ACTAATGACA
20272880 AATTAAACCATTAT
1 AATTAAACCATTAT
20272894 AATTAAA-CATTAT
1 AATTAAACCATTAT
20272907 AA
1 AA
20272909 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:20274055 original size:31 final size:31
Alignment explanation
Indices: 20274017--20274079 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
20274007 TGAACAATAC
20274017 TTAGATTTCGTAATCTTCTTCTAGGCATTTT
1 TTAGATTTCGTAATCTTCTTCTAGGCATTTT
20274048 TTAGATTTCGTAATCTTCTTCTAGGCATTTT
1 TTAGATTTCGTAATCTTCTTCTAGGCATTTT
20274079 T
1 T
20274080 CCTACAAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (31 bp):
TTAGATTTCGTAATCTTCTTCTAGGCATTTT
Found at i:20276251 original size:12 final size:12
Alignment explanation
Indices: 20276234--20276259 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20276224 TTCACCTTCT
20276234 TCATCAGATTCA
1 TCATCAGATTCA
20276246 TCATCAGATTCA
1 TCATCAGATTCA
20276258 TC
1 TC
20276260 TCTCGATCTT
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:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:20278001 original size:5 final size:5
Alignment explanation
Indices: 20277991--20278023 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
20277981 TTATGTAAAT
20277991 TATGA TATGA TATGA TATGA TATGA TATGA TAT
1 TATGA TATGA TATGA TATGA TATGA TATGA TAT
20278024 CTATTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (5 bp):
TATGA
Found at i:20278049 original size:9 final size:9
Alignment explanation
Indices: 20278035--20278154 Score: 120
Period size: 9 Copynumber: 13.6 Consensus size: 9
20278025 TATTTATGTA
20278035 TTATGTAAG
1 TTATGTAAG
*
20278044 TTATGTGAG
1 TTATGTAAG
*
20278053 TTATGTAAC
1 TTATGTAAG
20278062 TTATGTAAG
1 TTATGTAAG
20278071 TTATGTAAG
1 TTATGTAAG
* *
20278080 TAATGTGAG
1 TTATGTAAG
20278089 TTATGTAAG
1 TTATGTAAG
*
20278098 TTATGGTATG
1 TTAT-GTAAG
* * *
20278108 ATATAT-AT
1 TTATGTAAG
*
20278116 TTATAT-A-
1 TTATGTAAG
20278123 TTATGTAAG
1 TTATGTAAG
*
20278132 TTATGTAAA
1 TTATGTAAG
20278141 TTATGTAAG
1 TTATGTAAG
20278150 TTATG
1 TTATG
20278155 AAATTTAAAC
Statistics
Matches: 91, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
7 5 0.05
8 7 0.08
9 72 0.79
10 7 0.08
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:20278259 original size:20 final size:20
Alignment explanation
Indices: 20278235--20278273 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20278225 TCTATTTTGG
20278235 TTATA-ATATGTTT-TGAAT
1 TTATATATATGTTTATGAAT
*
20278253 TTATATATATTTTTATGAAT
1 TTATATATATGTTTATGAAT
20278273 T
1 T
20278274 AAATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TTATATATATGTTTATGAAT
Found at i:20279648 original size:19 final size:19
Alignment explanation
Indices: 20279624--20279661 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20279614 ATATTAGTAT
20279624 TAATTATACCAAATATATC
1 TAATTATACCAAATATATC
20279643 TAATTATACCAAATATATC
1 TAATTATACCAAATATATC
20279662 ATATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATTATACCAAATATATC
Found at i:20280355 original size:38 final size:39
Alignment explanation
Indices: 20280313--20280422 Score: 107
Period size: 38 Copynumber: 2.8 Consensus size: 39
20280303 TTAGATAGTT
* **
20280313 CGAAGCAAAGTTGACACCCAGTGTCTCATCGGCT-TAGC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAATCTAGC
** ** *
20280351 CGAAGTAAAG-TGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAATCTAGC
*
20280389 CGAAGTAATAGTATGACGCCCAGTGTCTCATCGA
1 CGAAGTAA-AGT-TGACACCCAGTGTCTCATCGA
20280423 CTCGAGGTCG
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
37 17 0.31
38 20 0.36
39 2 0.04
41 16 0.29
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (39 bp):
CGAAGTAAAGTTGACACCCAGTGTCTCATCGAATCTAGC
Found at i:20280896 original size:38 final size:38
Alignment explanation
Indices: 20280861--20280938 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
20280851 ATTTAAAATT
20280861 AATACGTAATAATAAATAACTTGAATTATAGTAAAACA
1 AATACGTAATAATAAATAACTTGAATTATAGTAAAACA
* * *
20280899 AATACTTAATAATAAATAACTTGAATTATAATAATACA
1 AATACGTAATAATAAATAACTTGAATTATAGTAAAACA
20280937 AA
1 AA
20280939 CCCGAATTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (38 bp):
AATACGTAATAATAAATAACTTGAATTATAGTAAAACA
Found at i:20280929 original size:19 final size:19
Alignment explanation
Indices: 20280869--20280932 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
20280859 TTAATACGTA
20280869 ATAATAAATAACTTGAATT
1 ATAATAAATAACTTGAATT
* ** *
20280888 ATAGTAAA-ACAAAT-ACTT
1 ATAATAAATA-ACTTGAATT
20280906 AATAATAAATAACTTGAATT
1 -ATAATAAATAACTTGAATT
20280926 ATAATAA
1 ATAATAA
20280933 TACAAACCCG
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
18 4 0.12
19 25 0.76
20 4 0.12
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAATAAATAACTTGAATT
Found at i:20281508 original size:12 final size:12
Alignment explanation
Indices: 20281493--20281523 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20281483 TCTCTTTTAT
20281493 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
20281505 TTTTTCTTTCTC
1 TTTTTCTTTCCC
20281517 TTTTTCT
1 TTTTTCT
20281524 CCCCTACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:20283431 original size:26 final size:26
Alignment explanation
Indices: 20283395--20283478 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
20283385 TGATACAAAT
20283395 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
20283421 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
20283447 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
20283473 TGATAA
1 TGATAA
20283479 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:20286660 original size:2 final size:2
Alignment explanation
Indices: 20286653--20286679 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20286643 TTGATTCTTT
20286653 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 T
20286680 TTCCAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20287882 original size:19 final size:18
Alignment explanation
Indices: 20287854--20287892 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
20287844 ACTATTAATT
*
20287854 TTTAAAAATTCAACAAAA
1 TTTAAAAATTCAAAAAAA
*
20287872 TTTATAAAATTTAAAAAAA
1 TTTA-AAAATTCAAAAAAA
20287891 TT
1 TT
20287893 GATCAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAAAAATTCAAAAAAA
Found at i:20288614 original size:41 final size:40
Alignment explanation
Indices: 20288550--20288656 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 40
20288540 TTTTTTGCAG
*
20288550 CGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAG-GTA
1 CGTTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCG-A
* * *
20288590 CGTTTTTTCAAAAAGCACCACTAATGCTCGATCTATAGCGG
1 CG-TTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCGA
20288631 CGTTTTTCAAAAAGCACCGCTAATGC
1 CGTTTTTCAAAAAGCACCGCTAATGC
20288657 CACTAAAGCT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
40 25 0.42
41 34 0.57
42 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCGA
Found at i:20288648 original size:40 final size:40
Alignment explanation
Indices: 20288549--20288810 Score: 166
Period size: 40 Copynumber: 6.7 Consensus size: 40
20288539 TTTTTTTGCA
* *
20288549 GCGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAG-G
1 GCGTTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCG
* *
20288588 TACGTTTTTTCAAAAAGCACCACTAATGCTCGATCTATAGCG
1 -GCG-TTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCG
*
20288630 GCGTTTTTCAAAAAGCACCGCTAATGC-C-A-CTAAAGC-
1 GCGTTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCG
* **** * * ** ** * * *
20288666 TC-AACAT-AAAACG-A-CGTGTTGTGCTTAATTTTTTTGCG
1 GCGTTTTTCAAAAAGCACCG-CTAATGCTCGA-TCTATAGCG
* *
20288704 GCGTTTTTCAAAAAG-AGCCGCTAATGCTCGATCTGTAGTG
1 GCGTTTTTCAAAAAGCA-CCGCTAATGCTCGATCTATAGCG
* * *
20288744 GCGTTTTTTAAAAAGCGCCACTAATGCTCGATCTATAGCG
1 GCGTTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCG
* * *
20288784 ACGTTTTTAAAAAAGCACTGCTAATGC
1 GCGTTTTTCAAAAAGCACCGCTAATGC
20288811 CACTAAAGCT
Statistics
Matches: 163, Mismatches: 46, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
32 2 0.01
33 5 0.03
34 5 0.03
35 2 0.01
36 1 0.01
37 9 0.06
38 2 0.01
39 2 0.01
40 92 0.56
41 40 0.25
42 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (40 bp):
GCGTTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCG
Found at i:20288810 original size:154 final size:153
Alignment explanation
Indices: 20288529--20288957 Score: 581
Period size: 147 Copynumber: 2.8 Consensus size: 153
20288519 AAATTGCGGC
* *
20288529 TTGTGCTTAATTTTTTTGCAGCGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAGGTACGTT
1 TTGTGCTTAATTTTTTTGC-GCGTTTTTCAAAAAGAGCCGCTAATGCTCAATCTATAGG-GCGTT
* *
20288594 TTTTCAAAAAGCACCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCCA
64 TTTT-AAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCACAGCTAATGCCA
20288659 CTAAAGCTCAACATAAAACGAC-GTG
128 CTAAAGCTCAACATAAAACGACGGTG
* *
20288684 TTGTGCTTAATTTTTTTGCGGCGTTTTTCAAAAAGAGCCGCTAATGCTCGATCTGTAGTGGCGTT
1 TTGTGCTTAATTTTTTTGC-GCGTTTTTCAAAAAGAGCCGCTAATGCTCAATCTATAG-GGCGTT
* * *
20288749 TTTTAAAAAGCGCCACTAATGCTCGATCTATAGCGACGTTTTTAAAAAAGCACTGCTAATGCCAC
64 TTTTAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCACAGCTAATGCCAC
20288814 TAAAGCTCAACATAAAACGACGGTG
129 TAAAGCTCAACATAAAACGACGGTG
* *
20288839 TTGTGCTTAA--TTTTT-----TTTTGCAAAAA-ATGCCGCTAATGCTCAACCTATAGCGGCGTT
1 TTGTGCTTAATTTTTTTGCGCGTTTTTCAAAAAGA-GCCGCTAATGCTCAATCTATAG-GGCGTT
* * * *
20288896 TTTCATAAAGCGCCGCTAATGCTCGATCCT-TAGCGGCGTTTTTCAAAAAGCGCAGCTAATGC
64 TTTTAAAAAGCGCCACTAATGCTCGAT-CTATAGCGGCGTTTTTCAAAAAGCACAGCTAATGC
20288958 TCGATCTACA
Statistics
Matches: 249, Mismatches: 21, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
146 1 0.00
147 87 0.35
148 2 0.01
153 5 0.02
154 78 0.31
155 75 0.30
156 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (153 bp):
TTGTGCTTAATTTTTTTGCGCGTTTTTCAAAAAGAGCCGCTAATGCTCAATCTATAGGGCGTTTT
TTAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCACAGCTAATGCCACTA
AAGCTCAACATAAAACGACGGTG
Found at i:20288911 original size:40 final size:40
Alignment explanation
Indices: 20288853--20288978 Score: 155
Period size: 40 Copynumber: 3.1 Consensus size: 40
20288843 GCTTAATTTT
**
20288853 TTTTTGCAAAAAATGCCGCTAATGCTCAACCTATAGCGGCG
1 TTTTT-CAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCG
* *
20288894 TTTTTCATAAAGCGCCGCTAATGCTCGATCCT-TAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTC-AACCTATAGCGGCG
* * * *
20288934 TTTTTCAAAAAGCGCAGCTAATGCTCGATCTACAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCG
20288974 TTTTT
1 TTTTT
20288979 TATCCAGGCG
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.03
40 62 0.85
41 9 0.12
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCG
Found at i:20288995 original size:41 final size:40
Alignment explanation
Indices: 20288867--20288978 Score: 163
Period size: 40 Copynumber: 2.8 Consensus size: 40
20288857 TGCAAAAAAT
* *
20288867 GCCGCTAATGCTCAACCTATAGCGGCGTTTTTCATAAAGC
1 GCCGCTAATGCTCGATCTATAGCGGCGTTTTTCATAAAGC
*
20288907 GCCGCTAATGCTCGATCCT-TAGCGGCGTTTTTCAAAAAGC
1 GCCGCTAATGCTCGAT-CTATAGCGGCGTTTTTCATAAAGC
* *
20288947 GCAGCTAATGCTCGATCTACAGCGGCGTTTTT
1 GCCGCTAATGCTCGATCTATAGCGGCGTTTTT
20288979 TATCCAGGCG
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.03
40 61 0.94
41 2 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (40 bp):
GCCGCTAATGCTCGATCTATAGCGGCGTTTTTCATAAAGC
Found at i:20290687 original size:22 final size:21
Alignment explanation
Indices: 20290662--20290704 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
20290652 TAAAGTATAT
20290662 ACATAATATATATGAAA-ACATA
1 ACATAATAT-TA-GAAATACATA
*
20290684 ACATAGTATTAGAAATACATA
1 ACATAATATTAGAAATACATA
20290705 TTAGAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (21 bp):
ACATAATATTAGAAATACATA
Found at i:20291060 original size:24 final size:24
Alignment explanation
Indices: 20290999--20291062 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 24
20290989 ATATACACGA
*
20290999 AATAGTATAAAAAATATATATAACT
1 AATAATATAAAAAA-ATATATAACT
*
20291024 AATAATAT--TAAAATATAT-ACAT
1 AATAATATAAAAAAATATATAAC-T
*
20291046 GATAATATAAAAAAATA
1 AATAATATAAAAAAATA
20291063 ATATTAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 2 0.06
22 14 0.44
23 3 0.09
24 6 0.19
25 7 0.22
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (24 bp):
AATAATATAAAAAAATATATAACT
Found at i:20291086 original size:23 final size:21
Alignment explanation
Indices: 20291060--20291198 Score: 80
Period size: 23 Copynumber: 6.5 Consensus size: 21
20291050 ATATAAAAAA
20291060 ATAATAT-TAGAAAATATATGTAC
1 ATAATATATA-AAAATATA--TAC
20291083 ATAATATATAAAAATATATAC
1 ATAATATATAAAAATATATAC
20291104 ATAATATAGTATTAAAA-A-AT--
1 ATAATATA-TA--AAAATATATAC
*
20291124 ATAATAT-TAAAATACATATA-
1 ATAATATATAAAA-ATATATAC
*
20291144 AT-ATATGT-AAAATATATAC
1 ATAATATATAAAAATATATAC
*
20291163 ACAATATAGTATTAAAATATATATGC
1 ATAATATA-TA--AAAATATATA--C
20291189 ATAATATATA
1 ATAATATATA
20291199 TAACACATAC
Statistics
Matches: 95, Mismatches: 4, Indels: 32
0.73 0.03 0.24
Matches are distributed among these distances:
16 3 0.03
17 1 0.01
18 9 0.09
19 10 0.11
20 14 0.15
21 12 0.13
22 4 0.04
23 16 0.17
24 16 0.17
25 2 0.02
26 8 0.08
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAATATATAAAAATATATAC
Found at i:20291125 original size:24 final size:21
Alignment explanation
Indices: 20290999--20291126 Score: 59
Period size: 21 Copynumber: 5.9 Consensus size: 21
20290989 ATATACACGA
*
20290999 AATAGTATAAAAAATATATATAACT
1 AATA-TATAAAAAA-ATATA-CA-T
* *
20291024 AATAATATTAAAATATATACAT
1 AAT-ATATAAAAAAATATACAT
*
20291046 GATA-ATATAAAAAA-ATA-AT
1 AATATATA-AAAAAATATACAT
* * *
20291065 -AT-TAGAAAATATATGTACAT
1 AATATATAAAA-AAATATACAT
*
20291085 AATATATAAAAATATATACAT
1 AATATATAAAAAAATATACAT
20291106 AATATAGTATTAAAAAATATA
1 AATATA-TA--AAAAAATATA
20291127 ATATTAAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
17 3 0.04
18 6 0.08
19 4 0.05
20 7 0.09
21 23 0.29
22 11 0.14
23 1 0.01
24 14 0.17
25 10 0.12
26 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (21 bp):
AATATATAAAAAAATATACAT
Found at i:20291144 original size:17 final size:15
Alignment explanation
Indices: 20291106--20291147 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
20291096 ATATATACAT
*
20291106 AATATAGTATTAAAA
1 AATATAATATTAAAA
20291121 AATATAATATTAAAA
1 AATATAATATTAAAA
20291136 TACATATAATAT
1 -A-ATATAATAT
20291148 ATGTAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 1 0.04
17 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
AATATAATATTAAAA
Found at i:20291169 original size:59 final size:60
Alignment explanation
Indices: 20291023--20291185 Score: 194
Period size: 59 Copynumber: 2.7 Consensus size: 60
20291013 TATATATAAC
* * *
20291023 TAATAATATTAAAATATATACATGATA-A-TA-TAAAAAA-ATAATATTAGAAAATATATG
1 TAATAATATTAAAATATATACATAATATAGTATTAAAAAATATAATATTA-AAAATACATA
20291080 TACATAATATATAAAAATATATACATAATATAGTATTAAAAAATATAATATT-AAAATACATA
1 TA-ATAATAT-T-AAAATATATACATAATATAGTATTAAAAAATATAATATTAAAAATACATA
* *
20291142 TAAT-ATATGTAAAATATATACACAATATAGTATTAAAATATATA
1 TAATAATAT-TAAAATATATACATAATATAGTATTAAAAAATATA
20291186 TGCATAATAT
Statistics
Matches: 93, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
57 2 0.02
58 7 0.08
59 33 0.35
60 21 0.23
61 3 0.03
62 12 0.13
63 7 0.08
64 8 0.09
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (60 bp):
TAATAATATTAAAATATATACATAATATAGTATTAAAAAATATAATATTAAAAATACATA
Found at i:20291355 original size:19 final size:20
Alignment explanation
Indices: 20291309--20291356 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
20291299 GAAATACTTA
**
20291309 ATATATAATATTTGAAATAT
1 ATATATAATATTAAAAATAT
**
20291329 ATGCATAATA-TAAAAATAT
1 ATATATAATATTAAAAATAT
20291348 ATATATAAT
1 ATATATAAT
20291357 GTAGTATTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
ATATATAATATTAAAAATAT
Found at i:20291637 original size:26 final size:26
Alignment explanation
Indices: 20291576--20291637 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
20291566 ACATAATGAT
20291576 AATAATAATAATATTGAAATATAAAAAA
1 AATAAT-ATAATA-TGAAATATAAAAAA
* *
20291604 AACAAATATAATA-GAAATATTAAAATA
1 AA-TAATATAATATGAAATA-TAAAAAA
20291631 AATAATA
1 AATAATA
20291638 AAGTAATACC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 10 0.34
27 8 0.28
28 8 0.28
29 3 0.10
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (26 bp):
AATAATATAATATGAAATATAAAAAA
Found at i:20296678 original size:22 final size:24
Alignment explanation
Indices: 20296650--20296693 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
20296640 TATTGTTTTT
20296650 AAAAAAA-TCAAAAGTT-TGTTAA
1 AAAAAAAGTCAAAAGTTGTGTTAA
20296672 AAAAAAAGTCAAAAGTTGTGTT
1 AAAAAAAGTCAAAAGTTGTGTT
20296694 TTGAAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (24 bp):
AAAAAAAGTCAAAAGTTGTGTTAA
Found at i:20300100 original size:2 final size:2
Alignment explanation
Indices: 20300093--20300126 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20300083 TACATCCTCC
20300093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20300127 TAACACAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20308137 original size:26 final size:26
Alignment explanation
Indices: 20308108--20308157 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
20308098 TACATGATCG
20308108 TGCACAGCCCTGACTGATCCCTTTCA
1 TGCACAGCCCTGACTGATCCCTTTCA
20308134 TGCACAGCCCTGACTGATCCCTTT
1 TGCACAGCCCTGACTGATCCCTTT
20308158 TCTTCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.38, G:0.16, T:0.28
Consensus pattern (26 bp):
TGCACAGCCCTGACTGATCCCTTTCA
Found at i:20312455 original size:43 final size:43
Alignment explanation
Indices: 20312408--20312512 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
20312398 AGTATGATTA
* * *
20312408 CTTTGATTTATCTAATGATGCAATAT-GTGTGCCACTATAATTG
1 CTTTGATTCATCCAATGATGCAAT-TCGTGTGCCAATATAATTG
* * *
20312451 CTTTGGTTCATCCAATGATGCACTTCTTGTGCCAATATAATTG
1 CTTTGATTCATCCAATGATGCAATTCGTGTGCCAATATAATTG
* *
20312494 CTTTGGTTCATCCGATGAT
1 CTTTGATTCATCCAATGAT
20312513 ACTCCTCGTG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 53 0.98
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (43 bp):
CTTTGATTCATCCAATGATGCAATTCGTGTGCCAATATAATTG
Found at i:20312530 original size:43 final size:43
Alignment explanation
Indices: 20312434--20312538 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
20312424 GATGCAATAT
* * *
20312434 GTGTGCCACTATAATTGCTTTGGTTCATCCAATGATGCACTTC
1 GTGTGCCAATATAATTGCTTTGGTTCATCCAATGATACACCTC
* * *
20312477 TTGTGCCAATATAATTGCTTTGGTTCATCCGATGATACTCCTC
1 GTGTGCCAATATAATTGCTTTGGTTCATCCAATGATACACCTC
* *
20312520 GTGTGTCAATACAATTGCT
1 GTGTGCCAATATAATTGCT
20312539 CCGACTTGCT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (43 bp):
GTGTGCCAATATAATTGCTTTGGTTCATCCAATGATACACCTC
Found at i:20314098 original size:11 final size:11
Alignment explanation
Indices: 20314082--20314121 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
20314072 AGTTCTTTTG
20314082 TTTTAATATTA
1 TTTTAATATTA
*
20314093 TTTTAAT-TTT
1 TTTTAATATTA
20314103 TTTTAA-A-TA
1 TTTTAATATTA
20314112 TTTTAATATT
1 TTTTAATATT
20314122 TATAATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
9 7 0.29
10 9 0.38
11 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTAATATTA
Found at i:20314113 original size:19 final size:22
Alignment explanation
Indices: 20314077--20314118 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
20314067 CCTTTAGTTC
20314077 TTTTGTTTTAATATTATTTTAA
1 TTTTGTTTTAATATTATTTTAA
20314099 TTTT-TTTTAA-A-TATTTTAA
1 TTTTGTTTTAATATTATTTTAA
20314118 T
1 T
20314119 ATTTATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
21 6 0.30
22 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTGTTTTAATATTATTTTAA
Found at i:20314454 original size:28 final size:28
Alignment explanation
Indices: 20314414--20314469 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
20314404 AAAAAAACAA
* *
20314414 AAACTGTTTAAAAAAATTGATGTGACAG
1 AAACTGTTAAAAAAAACTGATGTGACAG
20314442 AAACTGTTAAAAAAAACTGATGTGACAG
1 AAACTGTTAAAAAAAACTGATGTGACAG
20314470 GGATGGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (28 bp):
AAACTGTTAAAAAAAACTGATGTGACAG
Found at i:20314523 original size:27 final size:27
Alignment explanation
Indices: 20314485--20314548 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
20314475 GAGAGCATGC
**
20314485 CAGAGGCGGCACTGGTGAAGCCTGTGG
1 CAGAGGCGGCACCAGTGAAGCCTGTGG
20314512 CAGAGGCGGCACCAGTGAAGCCTGTGG
1 CAGAGGCGGCACCAGTGAAGCCTGTGG
20314539 CAGAGGCGGC
1 CAGAGGCGGC
20314549 GCCCACTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.44, T:0.11
Consensus pattern (27 bp):
CAGAGGCGGCACCAGTGAAGCCTGTGG
Found at i:20314749 original size:16 final size:16
Alignment explanation
Indices: 20314728--20314766 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20314718 AAATTATTAT
*
20314728 AAAAAATAAAATACTA
1 AAAAAATAAAATACCA
* *
20314744 AAAAAATAATATGCCA
1 AAAAAATAAAATACCA
20314760 AAAAAAT
1 AAAAAAT
20314767 TTCTCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAAATAAAATACCA
Done.