Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 86 of 91
Found at i:19436897 original size:20 final size:20
Alignment explanation
Indices: 19436871--19436943 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
19436861 AATGCAATTA
19436871 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
19436891 TTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
* *
19436911 GTACATCGATGCATCCTACT
1 GTGCATCGATGCATCCTGCT
19436931 GTGCATCGATGCA
1 GTGCATCGATGCA
19436944 CCAAGGCTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:19441674 original size:31 final size:31
Alignment explanation
Indices: 19441639--19441712 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
19441629 ATGGATTTAG
* * *
19441639 TTGGTGACCAAATTATAAGA-TTTTGTAAAGT
1 TTGGTGACCAAAGTATAA-ACTTTGGAAAAGT
19441670 TTGGTGACCAAAGTATAAACTTTGGAAAAGT
1 TTGGTGACCAAAGTATAAACTTTGGAAAAGT
19441701 TTAGG-GACCAAA
1 TT-GGTGACCAAA
19441713 ATGGTAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.03
31 35 0.92
32 2 0.05
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (31 bp):
TTGGTGACCAAAGTATAAACTTTGGAAAAGT
Found at i:19445050 original size:23 final size:21
Alignment explanation
Indices: 19444998--19445059 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
19444988 TTTTGGTGCA
*
19444998 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
19445018 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
19445039 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
19445060 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:19452505 original size:54 final size:54
Alignment explanation
Indices: 19452462--19452800 Score: 396
Period size: 54 Copynumber: 6.3 Consensus size: 54
19452452 TTTCCATATG
* *
19452462 GGCACTAAGTGTGCAACTCACAGAAATCATCATATGTTGATGAACAACTGTTTC
1 GGCACTATGTGTGCAACTCACAGAAATCATCATATGTTGATGAACAACCGTTTC
*
19452516 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACAGAAATCATCATATGTTGATGAACAACCGTTTC
* * *
19452570 GGCACTATGTGTGCAACTCAC-GTAATTCATCATATGTTGATGAACAACCATTTT
1 GGCACTATGTGTGCAACTCACAG-AAATCATCATATGTTGATGAACAACCGTTTC
* * * * * * *
19452624 GACACTATGTGCGCAACTCAC-GAAATTCATTATATGTTCATTAATAACCATTTC
1 GGCACTATGTGTGCAACTCACAGAAA-TCATCATATGTTGATGAACAACCGTTTC
* * * *
19452678 GACACTATGTGTGCAACTTACGGAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACAGAAATCATCATATGTTGATGAACAACCGTTTC
* * * * ** * *
19452732 GGCACTATATGTGCAACCCACA-AAATTCATAATATGTTTATGAATGACCGTATA
1 GGCACTATGTGTGCAACTCACAGAAA-TCATCATATGTTGATGAACAACCGTTTC
*
19452786 GGCACTACGTGTGCA
1 GGCACTATGTGTGCA
19452801 TTTTAACGAA
Statistics
Matches: 246, Mismatches: 35, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
53 5 0.02
54 238 0.97
55 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (54 bp):
GGCACTATGTGTGCAACTCACAGAAATCATCATATGTTGATGAACAACCGTTTC
Found at i:19452551 original size:27 final size:27
Alignment explanation
Indices: 19452470--19452552 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
19452460 TGGGCACTAA
*
19452470 GTGTGCAACTCACAGAAATCATCATAT
1 GTGTGCAACTCACAGAATTCATCATAT
* * * **
19452497 GTTGATG-AAC-AACTG-TTTCGGCACTAT
1 G-TG-TGCAACTCACAGAATTCATCA-TAT
19452524 GTGTGCAACTCACAGAATTCATCATAT
1 GTGTGCAACTCACAGAATTCATCATAT
19452551 GT
1 GT
19452553 TGATGAACAA
Statistics
Matches: 39, Mismatches: 11, Indels: 12
0.63 0.18 0.19
Matches are distributed among these distances:
25 2 0.05
26 9 0.23
27 16 0.41
28 10 0.26
29 2 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (27 bp):
GTGTGCAACTCACAGAATTCATCATAT
Found at i:19452578 original size:27 final size:27
Alignment explanation
Indices: 19452494--19452579 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
19452484 GAAATCATCA
*
19452494 TATGTTGATGAACAACTGTTTCGGCAC
1 TATGTTGATGAACAACAGTTTCGGCAC
* * **
19452521 TATG-TG-TGCAACTCACAGAATTCATCA-
1 TATGTTGATG-AAC-AACAG-TTTCGGCAC
*
19452548 TATGTTGATGAACAACCGTTTCGGCAC
1 TATGTTGATGAACAACAGTTTCGGCAC
19452575 TATGT
1 TATGT
19452580 GTGCAACTCA
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
25 2 0.05
26 10 0.23
27 19 0.44
28 10 0.23
29 2 0.05
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (27 bp):
TATGTTGATGAACAACAGTTTCGGCAC
Found at i:19452605 original size:27 final size:27
Alignment explanation
Indices: 19452521--19452606 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
19452511 GTTTCGGCAC
19452521 TATGTGTGCAACTCACAG-AATTCATCA
1 TATGTGTGCAACTCAC-GTAATTCATCA
* **
19452548 TATGTTGATG-AAC-AACCGT--TTCGGCA
1 TATG-TG-TGCAACTCA-CGTAATTCATCA
19452574 CTATGTGTGCAACTCACGTAATTCATCA
1 -TATGTGTGCAACTCACGTAATTCATCA
19452602 TATGT
1 TATGT
19452607 TGATGAACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
25 2 0.05
26 13 0.30
27 16 0.36
28 11 0.25
29 2 0.05
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (27 bp):
TATGTGTGCAACTCACGTAATTCATCA
Found at i:19452689 original size:162 final size:162
Alignment explanation
Indices: 19452464--19452775 Score: 455
Period size: 162 Copynumber: 1.9 Consensus size: 162
19452454 TCCATATGGG
* * ** *
19452464 CACTAAGTGTGCAACTCACAGAAATCATCATATGTTGATGAACAACTGTTTCGGCACTATGTGTG
1 CACTAAGTGCGCAACTCACAGAAATCATCATATGTTCATGAACAACCATTTCGACACTATGTGTG
* * **
19452529 CAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGCAACTCACGTA
66 CAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATATGTGCAACCCACAAA
*
19452594 ATTCATCATATGTTGATGAACAACCATTTTGA
131 ATTCATAATATGTTGATGAACAACCATTTTGA
* * * *
19452626 CACTATGTGCGCAACTCAC-GAAATTCATTATATGTTCATTAATAACCATTTCGACACTATGTGT
1 CACTAAGTGCGCAACTCACAGAAA-TCATCATATGTTCATGAACAACCATTTCGACACTATGTGT
* *
19452690 GCAACTTACGGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATATGTGCAACCCACAA
65 GCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATATGTGCAACCCACAA
*
19452755 AATTCATAATATGTTTATGAA
130 AATTCATAATATGTTGATGAA
19452776 TGACCGTATA
Statistics
Matches: 132, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
161 4 0.03
162 128 0.97
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (162 bp):
CACTAAGTGCGCAACTCACAGAAATCATCATATGTTCATGAACAACCATTTCGACACTATGTGTG
CAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATATGTGCAACCCACAAA
ATTCATAATATGTTGATGAACAACCATTTTGA
Found at i:19456674 original size:2 final size:2
Alignment explanation
Indices: 19456667--19456751 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
19456657 ACTCATACTT
19456667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19456709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19456751 T
1 T
19456752 TACAAACTTC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19461674 original size:36 final size:36
Alignment explanation
Indices: 19461620--19461931 Score: 381
Period size: 36 Copynumber: 8.7 Consensus size: 36
19461610 CATCTACACG
19461620 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
* * * **
19461656 TCTGATTCAAGTCAAACGGAAGGAGGCGCCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
* * * * *
19461692 TCTGATTCAAGTCAAACGGAATGAGGCATCGGTACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
* * * * * **
19461728 TTCGATTCAAGACGAATGAAAGGAGGCATCAACACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
** *
19461764 TCCGATTCAAGAGGAACGGAAGGAGGCATCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
* *
19461800 TCCGATTCAAGTCGAACAGAAGGAAACATCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
* *
19461836 TCCGATTTATGTCGAACGGAAGGAAGCATCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
* *
19461872 TCTGATTCAAGTCGAATGGAAGGAAGCATCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
*
19461908 TCCGATTCAAGTCGAACAGAAGGA
1 TCCGATTCAAGTCGAACGGAAGGA
19461932 TGTAGCGCAC
Statistics
Matches: 235, Mismatches: 41, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 235 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (36 bp):
TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
Found at i:19463261 original size:36 final size:36
Alignment explanation
Indices: 19463214--19463450 Score: 334
Period size: 36 Copynumber: 6.6 Consensus size: 36
19463204 CTACACGTCC
*
19463214 GATTCAAGTCGAACGGAAGGAAGCATCGGAACTTCT
1 GATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCT
* * * *
19463250 GATTCAAGTCGAACGGAATGAGGCATCGGTACTTCC
1 GATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCT
*
19463286 GATTCAAGTCGAACGGAAGGAGGCATCGGCACTTCT
1 GATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCT
** *
19463322 GATTCAAGAGGAACGGAAGGAGGCATCGGCACTTCCT
1 GATTCAAGTCGAACGGAAGGAAGCATCGGCACTT-CT
19463359 -ATTCAAGTCGAACGGAAGGAAGCATCGGCACTT-T
1 GATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCT
* *
19463393 CGATTCAAGTCGAATGGAAGGAAGCATCGGCACTTCC
1 -GATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCT
*
19463430 GATTCAAGTCGAACAGAAGGA
1 GATTCAAGTCGAACGGAAGGA
19463451 TGTAGCGCAC
Statistics
Matches: 181, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
34 1 0.01
36 178 0.98
37 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (36 bp):
GATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCT
Found at i:19463328 original size:72 final size:72
Alignment explanation
Indices: 19463211--19463450 Score: 374
Period size: 72 Copynumber: 3.3 Consensus size: 72
19463201 CATCTACACG
* *
19463211 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGAACTTCTGATTCAAGTCGAACGGAATGAGGCAT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCTGATTCAAGTCGAACGGAAGGAGGCAT
*
19463276 CGGTACT
66 CGGCACT
* **
19463283 TCCGATTCAAGTCGAACGGAAGGAGGCATCGGCACTTCTGATTCAAGAGGAACGGAAGGAGGCAT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCTGATTCAAGTCGAACGGAAGGAGGCAT
19463348 CGGCACT
66 CGGCACT
* * *
19463355 TCCTATTCAAGTCGAACGGAAGGAAGCATCGGCACTT-TCGATTCAAGTCGAATGGAAGGAAGCA
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCT-GATTCAAGTCGAACGGAAGGAGGCA
19463419 TCGGCACT
65 TCGGCACT
*
19463427 TCCGATTCAAGTCGAACAGAAGGA
1 TCCGATTCAAGTCGAACGGAAGGA
19463451 TGTAGCGCAC
Statistics
Matches: 153, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
71 1 0.01
72 152 0.99
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (72 bp):
TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCTGATTCAAGTCGAACGGAAGGAGGCAT
CGGCACT
Found at i:19464101 original size:14 final size:14
Alignment explanation
Indices: 19464084--19464117 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
19464074 TGGAAGCGTT
19464084 TTGGTTTTTTTTTC
1 TTGGTTTTTTTTTC
19464098 TTGG-TTTTTTTTC
1 TTGGTTTTTTTTTC
19464111 TTGGTTT
1 TTGGTTT
19464118 GGTTTCAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.00, C:0.06, G:0.18, T:0.76
Consensus pattern (14 bp):
TTGGTTTTTTTTTC
Found at i:19464783 original size:36 final size:36
Alignment explanation
Indices: 19464736--19464939 Score: 329
Period size: 36 Copynumber: 5.7 Consensus size: 36
19464726 CATCTACACA
*
19464736 TCCGATTCAAGTCGAACGGAAGGAAGCATCGACACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
*
19464772 TCCGATTCAAGTCGAACGGAAGGAGGCATCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
** *
19464808 TCCGATTCAAGAGGAACGGAAGG-AGTTATCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAG-CATCGGCACT
19464844 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
* *
19464880 TTCGATTCAAGTTGAACGGAAGGAAGCATCGGCACT
1 TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
19464916 TCCGATTCAAGTCGAACGGAAGGA
1 TCCGATTCAAGTCGAACGGAAGGA
19464940 TGTAGCGCAC
Statistics
Matches: 153, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
35 1 0.01
36 150 0.98
37 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (36 bp):
TCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACT
Found at i:19472213 original size:161 final size:158
Alignment explanation
Indices: 19471994--19472385 Score: 415
Period size: 161 Copynumber: 2.5 Consensus size: 158
19471984 AAAAAGGGAC
* * * *
19471994 TCAAAAT-AAGGATGAGGTGAAGAAATAAGGAAATTATGAAAAAA-TGAGGGACTAAATTGAAAA
1 TCAAAATAAAGGATGA-ATGAAGAAATATGAAAATTATAAAAAAATTGAGGGACTAAATTGAAAA
* * * *
19472057 ATATAAAATTTGTTAACAAAAAGATGAATTTAAAACG-CATATGTATTCTATGATGGT-TTAGGA
65 ATAAAAAATTTGTTAACAAAAAGA-GAAATTAAAA-GACATATGTATTCTACGATGGTCCTAGGA
19472120 GCATGTGATTCAAA-ATTGATAAAAAAAAATAGA-T
128 GCATGTGATTCAAATATTG-T---AAAAAA-AGACT
* * *
19472154 TCAAAATAAAGGATGAATCGAACAAATATGAAAATTAT-AAAAAATTGAGGGATTAAATTGACAA
1 TCAAAATAAAGGATGAAT-GAAGAAATATGAAAATTATAAAAAAATTGAGGGACTAAATTGAAAA
* * * *
19472218 ATAGAAATTTTGTTATCAAAAAGAGAAATTGAAAGTACATATGTATTCTACGATGGTCCTAGGAG
65 ATAAAAAATTTGTTAACAAAAAGAGAAATTAAAAG-ACATATGTATTCTACGATGGTCCTAGGAG
* * * *
19472283 CATGTGGTTCAAATTTTGTAGAAAACGACT
129 CATGTGATTCAAATATTGTAAAAAAAGACT
* * *
19472313 T-AAAATAAAAGATGAATTGAAGAAATAT-AGAAATTATAAAAAAATTGGGGGACTAAATTGAAG
1 TCAAAATAAAGGATGAA-TGAAGAAATATGA-AAATTATAAAAAAATTGAGGGACTAAATTGAAA
19472376 AATAAAAAAT
64 AATAAAAAAT
19472386 ATATTATCGA
Statistics
Matches: 196, Mismatches: 25, Indels: 23
0.80 0.10 0.09
Matches are distributed among these distances:
157 1 0.01
158 32 0.16
159 38 0.19
160 22 0.11
161 81 0.41
162 19 0.10
163 3 0.02
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (158 bp):
TCAAAATAAAGGATGAATGAAGAAATATGAAAATTATAAAAAAATTGAGGGACTAAATTGAAAAA
TAAAAAATTTGTTAACAAAAAGAGAAATTAAAAGACATATGTATTCTACGATGGTCCTAGGAGCA
TGTGATTCAAATATTGTAAAAAAAGACT
Found at i:19472505 original size:159 final size:156
Alignment explanation
Indices: 19472011--19472505 Score: 478
Period size: 159 Copynumber: 3.1 Consensus size: 156
19472001 AAGGATGAGG
* * *
19472011 TGAAGAAATAAGGAAATTATGAAAAAA-TGAGGGACTAAATTGAAAAATATAAAATTTGTTAACA
1 TGAAGAAAT-ATGAAATTAT-AAAAAATTGAGGGACTAAATTG-AAAATAAAAAATTTGTTATCA
* * * * * *
19472075 AAAAGATGAATTTAAAACG-CATATGTATTCTATGATGGTTTAGGAGCATGTGATTCAAAATTGA
63 AAAAGAGGAA-TTGAAA-GTAATATGTATTCTAAGATGGTTTAGGAGCATGTGGTTCAAATTTGA
* * *
19472139 TAAAAAAAAATAGATTCAAAATAAAGGATGAAT
126 T--AAAAAAACAGATTTAAAATAAAAGATGAAT
* * * * *
19472172 CGAACAAATATGAAAATTATAAAAAATTGAGGGATTAAATTGACAAATAGAAATTTTGTTATCAA
1 TGAAGAAATATG-AAATTATAAAAAATTGAGGGACTAAATTGA-AAATAAAAAATTTGTTATCAA
* * *
19472237 AAAGAGAAATTGAAAGTACATATGTATTCTACGATGGTCCTAGGAGCATGTGGTTCAAATTTTG-
64 AAAGAGGAATTGAAAGTA-ATATGTATTCTAAGATGGT-TTAGGAGCATGTGGTTCAAA-TTTGA
* *
19472301 T-AGAAAAC-GACTTAAAATAAAAGATGAAT
126 TAAAAAAACAGATTTAAAATAAAAGATGAAT
* * * *
19472330 TGAAGAAATATAGAAATTATAAAAAAATTGGGGGACTAAATTGAAGAATAAAAAATATATTATCG
1 TGAAGAAATAT-GAAATTAT-AAAAAATTGAGGGACTAAATTGAA-AATAAAAAATTTGTTATCA
* * * ** * *
19472395 AAAAGAGGAATTGAGAGTAATTTGAATTCTAAGATAATTTAGGAGCATGCGGTTTAAATTTGATA
63 AAAAGAGGAATTGAAAGTAATATGTATTCTAAGATGGTTTAGGAGCATGTGGTTCAAATTTGATA
* * *
19472460 ATAAAACAGATTTAAAAGAAATGATGAAT
128 AAAAAACAGATTTAAAATAAAAGATGAAT
*
19472489 TGAAGTAATAATGAAAT
1 TGAAGAAAT-ATGAAAT
19472506 CAGGTACTAA
Statistics
Matches: 276, Mismatches: 44, Indels: 30
0.79 0.13 0.09
Matches are distributed among these distances:
156 4 0.01
157 18 0.07
158 55 0.20
159 90 0.33
160 16 0.06
161 71 0.26
162 19 0.07
163 3 0.01
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.28
Consensus pattern (156 bp):
TGAAGAAATATGAAATTATAAAAAATTGAGGGACTAAATTGAAAATAAAAAATTTGTTATCAAAA
AGAGGAATTGAAAGTAATATGTATTCTAAGATGGTTTAGGAGCATGTGGTTCAAATTTGATAAAA
AAACAGATTTAAAATAAAAGATGAAT
Found at i:19474383 original size:41 final size:41
Alignment explanation
Indices: 19474338--19474421 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
19474328 CCAGGGGATT
*
19474338 TTTGAATTTATGGTTTTTCTTTCTATGCTGATTCCAAGTTG
1 TTTGAATCTATGGTTTTTCTTTCTATGCTGATTCCAAGTTG
*
19474379 TTTGAATCTATGGTTTTTCTTTCTATGCTGATTTCAAGTTG
1 TTTGAATCTATGGTTTTTCTTTCTATGCTGATTCCAAGTTG
19474420 TT
1 TT
19474422 CTTTTTCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.55
Consensus pattern (41 bp):
TTTGAATCTATGGTTTTTCTTTCTATGCTGATTCCAAGTTG
Found at i:19481604 original size:16 final size:16
Alignment explanation
Indices: 19481565--19481607 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
19481555 GACCCAAACC
* *
19481565 GTTGAATTTAACCAGA
1 GTTGACTTTGACCAGA
* *
19481581 GTTAACTTTGACCAGG
1 GTTGACTTTGACCAGA
19481597 GTTGACTTTGA
1 GTTGACTTTGA
19481608 ACCGAAAAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (16 bp):
GTTGACTTTGACCAGA
Found at i:19485839 original size:16 final size:16
Alignment explanation
Indices: 19485818--19485862 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
19485808 GACCCGACCC
19485818 GTTGACTTTGACC-AG
1 GTTGACTTTGACCAAG
*
19485833 AGTTGACTTTGACTAAG
1 -GTTGACTTTGACCAAG
19485850 GTTGACTTTGACC
1 GTTGACTTTGACC
19485863 CCAAAAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 24 0.92
17 2 0.08
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (16 bp):
GTTGACTTTGACCAAG
Found at i:19496954 original size:20 final size:20
Alignment explanation
Indices: 19496890--19496960 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
19496880 AGAAATATCT
*
19496890 AGTATCGATACTC-AG-GAA
1 AGTATCGATACTCAAGCTAA
* *
19496908 AGTATCAATAC-CATAAACTAGA
1 AGTATCGATACTC--AAGCTA-A
19496930 AGTATCGATACTCAAGCTAA
1 AGTATCGATACTCAAGCTAA
19496950 AGTATCGATAC
1 AGTATCGATAC
19496961 CAGTACTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
17 1 0.02
18 10 0.24
20 13 0.31
21 6 0.14
22 11 0.26
23 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (20 bp):
AGTATCGATACTCAAGCTAA
Found at i:19497022 original size:20 final size:20
Alignment explanation
Indices: 19496997--19497043 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
19496987 AGTCAGTAGC
*
19496997 ATCGATACCTAGAGGTTAGT
1 ATCGATACCTAGAGGTCAGT
19497017 ATCGATACCTAGAGGTCAGT
1 ATCGATACCTAGAGGTCAGT
*
19497037 ATTGATA
1 ATCGATA
19497044 TTGAGGGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
ATCGATACCTAGAGGTCAGT
Found at i:19502768 original size:20 final size:20
Alignment explanation
Indices: 19502743--19502787 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
19502733 AACAAGTCAA
19502743 TAGTATCGATACCCAGAGGT
1 TAGTATCGATACCCAGAGGT
19502763 TAGTATCGATACCCAGAGGT
1 TAGTATCGATACCCAGAGGT
*
19502783 CAGTA
1 TAGTA
19502788 CTGATGCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (20 bp):
TAGTATCGATACCCAGAGGT
Found at i:19504056 original size:21 final size:21
Alignment explanation
Indices: 19504015--19504063 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
19504005 AAGGCGAGTG
*
19504015 TCGATACTCAAGTGGATGGTA
1 TCGATACTCAAGTGGAGGGTA
*
19504036 TCGATACTCTAG-GGTAGGGTA
1 TCGATACTCAAGTGG-AGGGTA
*
19504057 TCAATAC
1 TCGATAC
19504064 CATTAGGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (21 bp):
TCGATACTCAAGTGGAGGGTA
Found at i:19507044 original size:18 final size:18
Alignment explanation
Indices: 19507021--19507062 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
19507011 ACTTGTGCTC
19507021 TTTTAGACCCACTAAATT
1 TTTTAGACCCACTAAATT
**
19507039 TTTTAGTTCCACTAAATT
1 TTTTAGACCCACTAAATT
19507057 TTTTAG
1 TTTTAG
19507063 TTCACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.48
Consensus pattern (18 bp):
TTTTAGACCCACTAAATT
Found at i:19507068 original size:17 final size:18
Alignment explanation
Indices: 19507029--19507065 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19507019 TCTTTTAGAC
19507029 CCACTAAATTTTTTAGTT
1 CCACTAAATTTTTTAGTT
19507047 CCACTAAATTTTTTAGTT
1 CCACTAAATTTTTTAGTT
19507065 C
1 C
19507066 ACTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (18 bp):
CCACTAAATTTTTTAGTT
Found at i:19507241 original size:17 final size:17
Alignment explanation
Indices: 19507221--19507254 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19507211 ACTTAAAATA
*
19507221 AATTCATTTTTAATTAT
1 AATTCATTTTAAATTAT
*
19507238 AATTTATTTTAAATTAT
1 AATTCATTTTAAATTAT
19507255 TTCAATGACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTCATTTTAAATTAT
Found at i:19507960 original size:35 final size:35
Alignment explanation
Indices: 19507911--19508104 Score: 237
Period size: 35 Copynumber: 5.5 Consensus size: 35
19507901 TAGTAAACCA
* * ** *
19507911 TCCGTTCTAGTTGAATCGAAAGTGCGACACCTCCT
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCTTCCT
* *
19507946 TCCGTTCGACTTGAATC-AGAAGTGTGATGCTTCCT
1 TCCGTTCAACTTGAATCGA-AAGTGCGATGCTTCCT
* *
19507981 TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCT
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCTTCCT
* * *
19508016 TCCTTTCAACTTGAATCGGAAGTGCGATGCTTTCT
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCTTCCT
*
19508051 TCCGTTCAACTTGAATCGGAAGTGCGATGCTTCCT
1 TCCGTTCAACTTGAATCGAAAGTGCGATGCTTCCT
* *
19508086 TCCATTCGACTTGAATCGA
1 TCCGTTCAACTTGAATCGA
19508105 TGCAAACTTT
Statistics
Matches: 138, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
34 1 0.01
35 136 0.99
36 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (35 bp):
TCCGTTCAACTTGAATCGAAAGTGCGATGCTTCCT
Found at i:19508103 original size:70 final size:70
Alignment explanation
Indices: 19507911--19508103 Score: 278
Period size: 70 Copynumber: 2.8 Consensus size: 70
19507901 TAGTAAACCA
* ** * * *
19507911 TCCGTTCTAGTTGAATCGAAAGTGCGACACCTCCTTCCGTTCGACTTGAATCAGAAGTGTGATGC
1 TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCTTCCATTCGACTTGAATCGGAAGTGCGATGC
19507976 TTCCT
66 TTCCT
* *
19507981 TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCTTCCTTTCAACTTGAATCGGAAGTGCGATGC
1 TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCTTCCATTCGACTTGAATCGGAAGTGCGATGC
*
19508046 TTTCT
66 TTCCT
* * *
19508051 TCCGTTCAACTTGAATCGGAAGTGCGATGCTTCCTTCCATTCGACTTGAATCG
1 TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCTTCCATTCGACTTGAATCG
19508104 ATGCAAACTT
Statistics
Matches: 110, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 110 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (70 bp):
TCCGTTCTACTTGAATCGAAAGTGCGATGCCTCCTTCCATTCGACTTGAATCGGAAGTGCGATGC
TTCCT
Found at i:19513996 original size:26 final size:24
Alignment explanation
Indices: 19513955--19514003 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 24
19513945 ACTATTTTAG
19513955 GTTATAATTAAGTATCGATACTTA
1 GTTATAATTAAGTATCGATACTTA
19513979 GTTATAATACTAAGTATCGATACTT
1 GTTATAAT--TAAGTATCGATACTT
19514004 TTCGTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.35
26 15 0.65
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (24 bp):
GTTATAATTAAGTATCGATACTTA
Found at i:19514111 original size:148 final size:149
Alignment explanation
Indices: 19513840--19514130 Score: 372
Period size: 148 Copynumber: 2.0 Consensus size: 149
19513830 ATAATACCTA
* * ** *
19513840 TAAGTATCTATATTTGTCATGAAATAAGTGTTGAATCGTATTTAACATTTTAAGTTATAATAAAA
1 TAAGTATCGATATTTGTCATGAAATAAGTATTGAATCACATTTAACATTTTAAGTTACAATAAAA
* * *
19513905 AAATATGACCAAATATATAACATTTTAGGTTAGATTGGATACTATTTTAGGTTATAATTAAGTAT
66 AAATATGACCAAAGATATAACATTTTAGGTTAGACTGGATACTATTTTAGGTTATAATTAAATAT
*
19513970 CGATACTTAGTTATAATAC
131 AGATACTTAGTTATAATAC
* * * **
19513989 TAAGTATCGATACTTT-TCGTGAAATAAGTATTGCATCACATTTAACATTTTAGGTTACAAT-CG
1 TAAGTATCGATA-TTTGTCATGAAATAAGTATTGAATCACATTTAACATTTTAAGTTACAATAAA
* * * * *
19514052 AAAATGTTACCAAAGCTATAACATTTTAGGTTGGACTGGATAAC-ATTTTAGGTTGTAATTAAAT
65 AAAATATGACCAAAGATATAACATTTTAGGTTAGACTGGAT-ACTATTTTAGGTTATAATTAAAT
19514116 ATAGATACTTAGTTA
129 ATAGATACTTAGTTA
19514131 CAACTATTGA
Statistics
Matches: 121, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
148 67 0.55
149 51 0.42
150 3 0.02
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (149 bp):
TAAGTATCGATATTTGTCATGAAATAAGTATTGAATCACATTTAACATTTTAAGTTACAATAAAA
AAATATGACCAAAGATATAACATTTTAGGTTAGACTGGATACTATTTTAGGTTATAATTAAATAT
AGATACTTAGTTATAATAC
Found at i:19515410 original size:24 final size:24
Alignment explanation
Indices: 19515383--19515430 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19515373 GTCTACATTG
19515383 TATTTTGACCCTCAAGAAAGTCAT
1 TATTTTGACCCTCAAGAAAGTCAT
19515407 TATTTTGACCCTCAAGAAAGTCAT
1 TATTTTGACCCTCAAGAAAGTCAT
19515431 ACTCAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (24 bp):
TATTTTGACCCTCAAGAAAGTCAT
Found at i:19524685 original size:21 final size:22
Alignment explanation
Indices: 19524643--19524693 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
19524633 TACTCAAGAC
*
19524643 AGTATCGATACAACATACTAGA
1 AGTATCGATACAACAAACTAGA
*
19524665 AGTATCGATAC-TCAAACTAGA
1 AGTATCGATACAACAAACTAGA
19524686 A-TATCGAT
1 AGTATCGAT
19524694 GCTACCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (22 bp):
AGTATCGATACAACAAACTAGA
Found at i:19531586 original size:18 final size:17
Alignment explanation
Indices: 19531547--19531589 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
19531537 ATTATATGGA
19531547 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
19531563 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
19531581 TATTATTAT
1 TATTATTAT
19531590 ACGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:19531884 original size:20 final size:20
Alignment explanation
Indices: 19531852--19531904 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
19531842 TATATATATA
19531852 TATATTATTTTTATT-ATTAT
1 TATATT-TTTTTATTCATTAT
*
19531872 TTTCATTTTTTTATTCATTAT
1 TAT-ATTTTTTTATTCATTAT
19531893 TATATTTTTTTA
1 TATATTTTTTTA
19531905 AAACCTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TATATTTTTTTATTCATTAT
Found at i:19532161 original size:38 final size:36
Alignment explanation
Indices: 19532067--19532162 Score: 92
Period size: 38 Copynumber: 2.7 Consensus size: 36
19532057 AGTGAGAGGG
*
19532067 TAGCTTTTCT-ATTTTTAAATA-TTTGTTATATATA
1 TAGCTTTTTTCATTTTTAAATATTTTGTTATATATA
* *
19532101 TAGCTTATTT-ATTTTATTAATATTTTGATGTATATATA
1 TAGCTTTTTTCATTTT-TAAATATTTTG-T-TATATATA
*
19532139 TA-TTTTTTTCATTTTTCAAATATT
1 TAGCTTTTTTCATTTTT-AAATATT
19532163 ACTATATATA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
34 13 0.26
35 5 0.10
36 4 0.08
37 7 0.14
38 21 0.42
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (36 bp):
TAGCTTTTTTCATTTTTAAATATTTTGTTATATATA
Found at i:19532217 original size:9 final size:9
Alignment explanation
Indices: 19532205--19532229 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19532195 CCTTATCTTA
19532205 TTTATTTAT
1 TTTATTTAT
19532214 TTTATTTAT
1 TTTATTTAT
19532223 TTTATTT
1 TTTATTT
19532230 TTTCCCTTTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Found at i:19533202 original size:4 final size:4
Alignment explanation
Indices: 19533193--19533217 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19533183 CATCCTTTTA
19533193 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
19533218 TACTAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:19536630 original size:16 final size:16
Alignment explanation
Indices: 19536604--19536666 Score: 74
Period size: 16 Copynumber: 3.8 Consensus size: 16
19536594 AGATTCAATC
19536604 AAGAA-CAAAAAAGAA
1 AAGAAGCAAAAAAGAA
19536619 AAGAAGCAAAAAAGAAA
1 AAGAAGCAAAAAAG-AA
*
19536636 ACACAAGAACAAAAAAGAA
1 A-AGAAG--CAAAAAAGAA
19536655 AAGAAGCAAAAA
1 AAGAAGCAAAAA
19536667 TCAAAAGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 5 0.12
16 14 0.34
17 3 0.07
18 8 0.20
19 3 0.07
20 8 0.20
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAAGCAAAAAAGAA
Found at i:19536650 original size:20 final size:19
Alignment explanation
Indices: 19536603--19536656 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
19536593 AAGATTCAAT
19536603 CAAGAACAAAAAAG-AAAA
1 CAAGAACAAAAAAGAAAAA
*
19536621 GAAG--CAAAAAAGAAAACA
1 CAAGAACAAAAAAGAAAA-A
19536639 CAAGAACAAAAAAGAAAA
1 CAAGAACAAAAAAGAAAA
19536657 GAAGCAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.27
17 3 0.10
18 7 0.23
20 12 0.40
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (19 bp):
CAAGAACAAAAAAGAAAAA
Found at i:19536672 original size:16 final size:15
Alignment explanation
Indices: 19536633--19536675 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
19536623 AGCAAAAAAG
*
19536633 AAAACACAAGAACAA
1 AAAACAAAAGAACAA
*
19536648 AAAAGAAAAGAAGCAA
1 AAAACAAAAGAA-CAA
*
19536664 AAATCAAAAGAA
1 AAAACAAAAGAA
19536676 AAAGGGACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.74, C:0.12, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAACAAAAGAACAA
Found at i:19538302 original size:37 final size:37
Alignment explanation
Indices: 19538248--19538321 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
19538238 CTCACCATTA
* *
19538248 TCTCTTTTGAGATAATTTCCCTT-GAAAACAAACTTTG
1 TCTCTCTTGAGACAATTTCCCTTGGAAAA-AAACTTTG
*
19538285 TCTCTCTTGAGACAATTTCCCTTGGAAAAAACCTTTG
1 TCTCTCTTGAGACAATTTCCCTTGGAAAAAAACTTTG
19538322 AAATTGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 28 0.85
38 5 0.15
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (37 bp):
TCTCTCTTGAGACAATTTCCCTTGGAAAAAAACTTTG
Found at i:19539305 original size:106 final size:106
Alignment explanation
Indices: 19539078--19539945 Score: 1107
Period size: 106 Copynumber: 8.1 Consensus size: 106
19539068 ATATCACGCC
* * *
19539078 ACTCGAGATAATACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCACTTT-T
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAA-CACTTTCC
* * *
19539142 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
65 CA--AT--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
19539188 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAATCA-TTACC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAA-CACTTTCC
19539252 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
19539294 ACTCGAGACAACACAAGTTCAACTTCATAACGAATGGACGGCTGGTTGTCAACAAACCACTTT-T
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAA-CACTTTCC
* * *
19539358 CAGTTTCATTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTGG
65 CA--AT--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
19539404 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTAGTTGTCAACAAAATAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAAC-AAACACTTTCC
* * *
19539469 CAGTTTTAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
19539511 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGAGACGACTGGTTTTCAACAAACCACTTT-T
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAA-CACTTTCC
* *
19539575 CAATTTTAGAGCCAATTTCAACGTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
19539617 ACTCAAGGCAACACAAGTTCAACTTCACAACGAAGGGACGACTAGTTGTTAGCAAACACTTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACACTTTCCC
19539682 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
19539723 ACTCAAGACGACAAAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACACTTTCCC
*
19539788 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
19539829 ACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACACTTTCCC
* * * *
19539894 AGTTCCGGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
*
19539935 ACTCGAAACAA
1 ACTCGAGACAA
19539946 TAATACCCAC
Statistics
Matches: 673, Mismatches: 74, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
105 7 0.01
106 422 0.63
107 90 0.13
108 2 0.00
109 3 0.00
110 144 0.21
111 5 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACACTTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:19540945 original size:13 final size:13
Alignment explanation
Indices: 19540927--19540951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19540917 ATTACGCACA
19540927 CAAAGAAAATACC
1 CAAAGAAAATACC
19540940 CAAAGAAAATAC
1 CAAAGAAAATAC
19540952 GCAAGAAGCC
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:0.64, C:0.20, G:0.08, T:0.08
Consensus pattern (13 bp):
CAAAGAAAATACC
Found at i:19541267 original size:18 final size:17
Alignment explanation
Indices: 19541228--19541270 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
19541218 ATTATATGGA
19541228 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
19541244 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
19541262 TATTATTAT
1 TATTATTAT
19541271 ACGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:19541326 original size:2 final size:2
Alignment explanation
Indices: 19541321--19541345 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19541311 TATATTTTAT
19541321 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 T
19541346 TTCTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19541582 original size:19 final size:19
Alignment explanation
Indices: 19541541--19541582 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
19541531 TATATATTAT
* *
19541541 TTTTATTATTATTTTCATT
1 TTTTATTATTATTATCATA
19541560 TTTTATTCATTATTAT-ATA
1 TTTTATT-ATTATTATCATA
19541579 TTTT
1 TTTT
19541583 TTAAAAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATTATTATTATCATA
Found at i:19541845 original size:42 final size:40
Alignment explanation
Indices: 19541752--19541854 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 40
19541742 GAGAGGGTAG
*
19541752 CTTTTTTATTTTTAAATATTTGTTGTATATATATATATAA
1 CTTTTTTATTTTTAAATATTTGATGTATATATATATATAA
* * *
19541792 CTTATTTATTTTATTAATATTTTGATGTATATATATATAT-T
1 CTTTTTTATTTT-TAAATA-TTTGATGTATATATATATATAA
*
19541833 TTTTTTTCATTTTTCAAATATT
1 CTTTTTT-ATTTTT-AAATATT
19541855 ACTATATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
40 11 0.21
41 13 0.25
42 28 0.54
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (40 bp):
CTTTTTTATTTTTAAATATTTGATGTATATATATATATAA
Found at i:19541909 original size:9 final size:9
Alignment explanation
Indices: 19541897--19541921 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19541887 CCTTATCTTA
19541897 TTTATTTAT
1 TTTATTTAT
19541906 TTTATTTAT
1 TTTATTTAT
19541915 TTTATTT
1 TTTATTT
19541922 TTTCCCTTTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Found at i:19552768 original size:17 final size:18
Alignment explanation
Indices: 19552746--19552780 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19552736 AACCTTTACT
19552746 TTTAAA-ATATAGTTGAA
1 TTTAAACATATAGTTGAA
*
19552763 TTTAAACATATATTTGAA
1 TTTAAACATATAGTTGAA
19552781 ATAAAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (18 bp):
TTTAAACATATAGTTGAA
Found at i:19553329 original size:2 final size:2
Alignment explanation
Indices: 19553322--19553351 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19553312 TATAACAAAA
19553322 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
19553352 CGTCAACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19553527 original size:24 final size:24
Alignment explanation
Indices: 19553483--19553528 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
19553473 TTGTATAAAT
* *
19553483 TGCACCGAAGTGCCGCGTAGAATA
1 TGCACCGAAGTGCCACATAGAATA
19553507 TGCACCGAAGTGCCACATAGAA
1 TGCACCGAAGTGCCACATAGAA
19553529 ATGTCCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (24 bp):
TGCACCGAAGTGCCACATAGAATA
Found at i:19553572 original size:23 final size:23
Alignment explanation
Indices: 19553521--19553581 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
19553511 CCGAAGTGCC
* * * *
19553521 ACATAGAAATGTCCCGAATGATT
1 ACATAGTATTGTCCCGAAGGACT
*
19553544 ATATAGTATTGTCCCGAAGGACT
1 ACATAGTATTGTCCCGAAGGACT
19553567 ACATAGTATTGTCCC
1 ACATAGTATTGTCCC
19553582 AAATAACCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (23 bp):
ACATAGTATTGTCCCGAAGGACT
Found at i:19553617 original size:23 final size:23
Alignment explanation
Indices: 19553553--19553620 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 23
19553543 TATATAGTAT
* * * *
19553553 TGTCCCGAAGGACTACATAGTAT
1 TGTCCCGAAGGACCACGTAGAAA
* ** *
19553576 TGTCCCAAATAACCCCGTAGAAA
1 TGTCCCGAAGGACCACGTAGAAA
19553599 TGTCCCGAAGGACCACGTAGAA
1 TGTCCCGAAGGACCACGTAGAA
19553621 CCCTCGACTC
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAA
Found at i:19553760 original size:31 final size:30
Alignment explanation
Indices: 19553709--19553777 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
19553699 TATTTTCATG
*
19553709 TAATCACATAGTTCAATATCACATAGACATA
1 TAATCACATAGGTCAATATCACATAG-CATA
** * *
19553740 TAATCACATAGGTCCTTATCACGTAGCTTA
1 TAATCACATAGGTCAATATCACATAGCATA
19553770 T-ATCACAT
1 TAATCACAT
19553778 TTTCATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 7 0.21
30 4 0.12
31 22 0.67
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.32
Consensus pattern (30 bp):
TAATCACATAGGTCAATATCACATAGCATA
Found at i:19553776 original size:45 final size:45
Alignment explanation
Indices: 19553736--19553863 Score: 157
Period size: 45 Copynumber: 2.8 Consensus size: 45
19553726 ATCACATAGA
** * *
19553736 CATATAATCACATAGGTCCTTATCACGTAGCTTATATCACATTTT
1 CATATAATCACATAGGTCAATAACACATAGCTTATATCACATTTT
* * *
19553781 CATATAATCGCTTAGGTCAATAACACATAGCTTATATCATATTTT
1 CATATAATCACATAGGTCAATAACACATAGCTTATATCACATTTT
* ** *
19553826 CATGTAATCACATAGGTCAATCTCACATATCTTATATC
1 CATATAATCACATAGGTCAATAACACATAGCTTATATC
19553864 TTGTTCACAT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.37
Consensus pattern (45 bp):
CATATAATCACATAGGTCAATAACACATAGCTTATATCACATTTT
Found at i:19559497 original size:18 final size:18
Alignment explanation
Indices: 19559471--19559506 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19559461 GAATATTTTT
19559471 TGAAAGAATTAAAATCTG
1 TGAAAGAATTAAAATCTG
* *
19559489 TGAAGGAATTGAAATCTG
1 TGAAAGAATTAAAATCTG
19559507 AATCTGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (18 bp):
TGAAAGAATTAAAATCTG
Found at i:19560073 original size:28 final size:28
Alignment explanation
Indices: 19560023--19560088 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
19560013 CCTAAACCCG
* *
19560023 AACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCAAATATCAAACTTAAAAA
* *
19560051 AACTCGACCCAAATATTAAACTTAAAAA
1 AACCCGACCCAAATATCAAACTTAAAAA
*
19560079 AGCCCGACCC
1 AACCCGACCC
19560089 GAACCCGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.45, C:0.32, G:0.08, T:0.15
Consensus pattern (28 bp):
AACCCGACCCAAATATCAAACTTAAAAA
Found at i:19560173 original size:33 final size:33
Alignment explanation
Indices: 19560131--19560207 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
19560121 TCCCAAAATT
* * **
19560131 TTAAAAAAACCCGATCCGACCCGAATATCACGC
1 TTAAAAAAACCCGACCCAACCCGAATATCAAAC
19560164 TTAAAAAAACCCGACCCAACCCGAATATCAAAC
1 TTAAAAAAACCCGACCCAACCCGAATATCAAAC
19560197 TTAAAAAAACC
1 TTAAAAAAACC
19560208 AACCCGAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.47, C:0.31, G:0.08, T:0.14
Consensus pattern (33 bp):
TTAAAAAAACCCGACCCAACCCGAATATCAAAC
Found at i:19560252 original size:120 final size:119
Alignment explanation
Indices: 19560016--19560245 Score: 286
Period size: 120 Copynumber: 1.9 Consensus size: 119
19560006 TTTTCATCCT
* *
19560016 AAACCCGAACCCGACCCGAATATCACACTTAAAAAAACTCGACCCAAATATTAAACTTAAAAAAG
1 AAACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCGACCCAAATATCAAACTTAAAAAAG
* * *
19560081 CCCGACCCGAACCCGTTTTTTTAAAAAAAATCCGACCCAATCCCAAAATTTTAAAA
66 ACCAACCCGAA--CGTTTTTTTAAAAAAAATACGACCCAATCCCAAAATTTTAAAA
* *
19560137 AAACCCG-ATCCGACCCGAATATCACGCTTAAAAAAACCCGACCCAACCCGAATATCAAACTTAA
1 AAACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCGACCC-A----AATATCAAACTTAA
* * *
19560201 AAAA-ACCAACCCGAA-TTTTTTTTAAAAAAAATATGACCCGATCCC
61 AAAAGACCAACCCGAACGTTTTTTTAAAAAAAATACGACCCAATCCC
19560246 GAATTTTTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
120 34 0.36
121 34 0.36
124 9 0.10
125 17 0.18
ACGTcount: A:0.44, C:0.30, G:0.08, T:0.19
Consensus pattern (119 bp):
AAACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCGACCCAAATATCAAACTTAAAAAAG
ACCAACCCGAACGTTTTTTTAAAAAAAATACGACCCAATCCCAAAATTTTAAAA
Found at i:19594635 original size:2 final size:2
Alignment explanation
Indices: 19594628--19594692 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
19594618 TCTAGTCCTT
19594628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19594670 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
19594693 TATGGTTTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19599192 original size:18 final size:18
Alignment explanation
Indices: 19599169--19599206 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19599159 CATATGTTTT
19599169 TTATTTTATT-TTATTCTA
1 TTATTTT-TTATTATTCTA
*
19599187 TTATTTTTTATTATTTTA
1 TTATTTTTTATTATTCTA
19599205 TT
1 TT
19599207 TTAATTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTTTATTATTCTA
Found at i:19610126 original size:104 final size:104
Alignment explanation
Indices: 19609941--19610193 Score: 346
Period size: 104 Copynumber: 2.4 Consensus size: 104
19609931 CTTTAAATTA
* * * * * * *
19609941 TCCAGATTGACCCAACTTCCTCAATGAGAAGGAACAACATCATATGAAAGTGGTCAAAACTCTTC
1 TCCAGATTGACCCGACTTCCTCAACGAGAAGGAACAACGTCATCTAAAAGCGGCCAAAACTCTTC
* *
19610006 AACATGGATGAGCAGTGTCGTCTTCAAC-CCTAGATTATC
66 AACATGGATGAGCAGTGTCATATTCAACACC-AGATTATC
* * * *
19610045 TCCAAATTGACTCGACTTCCTCAACAAGAAGGAACAACGTCATCTAAAAGCGGCCAGAACTCTTC
1 TCCAGATTGACCCGACTTCCTCAACGAGAAGGAACAACGTCATCTAAAAGCGGCCAAAACTCTTC
19610110 AACATGGATGAGCAGTGTCATATTCAACACCAGATTATC
66 AACATGGATGAGCAGTGTCATATTCAACACCAGATTATC
* * *
19610149 TTCAGATTGACCCGACTTCCTTAACGAGAAGGAACATCGTCATCT
1 TCCAGATTGACCCGACTTCCTCAACGAGAAGGAACAACGTCATCT
19610194 TCAACAAACA
Statistics
Matches: 129, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
104 127 0.98
105 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (104 bp):
TCCAGATTGACCCGACTTCCTCAACGAGAAGGAACAACGTCATCTAAAAGCGGCCAAAACTCTTC
AACATGGATGAGCAGTGTCATATTCAACACCAGATTATC
Found at i:19611810 original size:16 final size:16
Alignment explanation
Indices: 19611784--19611821 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19611774 TATGTATGTA
*
19611784 TATATATATATATTATG
1 TATATAGATATA-TATG
19611801 T-TATAGATATATATG
1 TATATAGATATATATG
19611816 TATATA
1 TATATA
19611822 TTTATGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 13 0.68
17 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (16 bp):
TATATAGATATATATG
Found at i:19614984 original size:17 final size:16
Alignment explanation
Indices: 19614952--19614985 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
19614942 TTACTATTCA
19614952 TGTGAATAGTAAATTT
1 TGTGAATAGTAAATTT
*
19614968 TGTGAATAGTAAAATT
1 TGTGAATAGTAAATTT
19614984 TG
1 TG
19614986 GTCTGCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (16 bp):
TGTGAATAGTAAATTT
Found at i:19624100 original size:50 final size:50
Alignment explanation
Indices: 19623970--19624100 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
19623960 CACCCGTAAC
* * * * * *
19623970 AGTAAAGCGTGCCCCCTGAACTGCGCTCTAAGCTGATTTGGCGTCACGTG
1 AGTATAGCGCGCCCCCTGATCCGCGCTATACGCTGATTTGGCGTCACGTG
* * * * *
19624020 GGTATAGCACGCCCCCTG-TCCTGCGATATACGGTGATTTGGCGTCACTTG
1 AGTATAGCGCGCCCCCTGATCC-GCGCTATACGCTGATTTGGCGTCACGTG
19624070 AGTATAGCGCGCCCCCTGATCCGCGCTATAC
1 AGTATAGCGCGCCCCCTGATCCGCGCTATAC
19624101 CTGGGTATCT
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.02
50 61 0.94
51 3 0.05
ACGTcount: A:0.18, C:0.31, G:0.27, T:0.24
Consensus pattern (50 bp):
AGTATAGCGCGCCCCCTGATCCGCGCTATACGCTGATTTGGCGTCACGTG
Found at i:19624320 original size:17 final size:18
Alignment explanation
Indices: 19624283--19624323 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
19624273 CTATTATGTA
*
19624283 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
19624301 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
19624318 TTTACT
1 TTTACT
19624324 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:19624579 original size:111 final size:111
Alignment explanation
Indices: 19624385--19624717 Score: 585
Period size: 111 Copynumber: 3.0 Consensus size: 111
19624375 TGGAAATCAT
* *
19624385 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
19624450 TATTTAGTTTATTTATTTAATGCATGATTATTAGATTAAAAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
19624496 ATATCTCGACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
19624561 TAATTAGTTGATTTATTTAATGCATGATTATTTGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
19624607 ATATCTTGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
19624672 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
19624718 TTTTTGTAAT
Statistics
Matches: 211, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 211 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:19626610 original size:9 final size:9
Alignment explanation
Indices: 19626598--19626647 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
19626588 ACCTGCTCAG
*
19626598 GATGATGAC
1 GATGACGAC
19626607 GATGACGAC
1 GATGACGAC
*
19626616 GATGACGAT
1 GATGACGAC
*
19626625 GGTGACGAC
1 GATGACGAC
*
19626634 GACGACGAC
1 GATGACGAC
19626643 GATGA
1 GATGA
19626648 TGATGACAGC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (9 bp):
GATGACGAC
Found at i:19628896 original size:21 final size:21
Alignment explanation
Indices: 19628845--19628903 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
19628835 TAAAATTGTT
*
19628845 CTGAAGGACCTCATATATGTC
1 CTGAAGGACCACATATATGTC
*
19628866 CCGAAGGACCACATATATGTC
1 CTGAAGGACCACATATATGTC
* * *
19628887 TTGAATGACCATATATA
1 CTGAAGGACCACATATA
19628904 ACCCTCGACT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (21 bp):
CTGAAGGACCACATATATGTC
Found at i:19633632 original size:30 final size:30
Alignment explanation
Indices: 19633598--19633654 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
19633588 TTCAACCTAA
19633598 ACTTTAGATAAAATATTAATTTAACCATTG
1 ACTTTAGATAAAATATTAATTTAACCATTG
*
19633628 ACTTTAGATAAAATATTAATTTGACCA
1 ACTTTAGATAAAATATTAATTTAACCA
19633655 CTAATCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (30 bp):
ACTTTAGATAAAATATTAATTTAACCATTG
Found at i:19633732 original size:31 final size:31
Alignment explanation
Indices: 19633690--19633773 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
19633680 AACTGAATTC
* *
19633690 AAGAGTCAAATTTATATTTTATCTAAAATCT
1 AAGAGTTAAATTAATATTTTATCTAAAATCT
* *
19633721 ATG-GATTAAATTAATATTTTATCTAAAATTT
1 AAGAG-TTAAATTAATATTTTATCTAAAATCT
19633752 AAGAGTTAAATTAATATTTTAT
1 AAGAGTTAAATTAATATTTTAT
19633774 TTTATGTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 1 0.02
31 44 0.96
32 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (31 bp):
AAGAGTTAAATTAATATTTTATCTAAAATCT
Found at i:19633765 original size:36 final size:35
Alignment explanation
Indices: 19633725--19633796 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
19633715 AAATCTATGG
19633725 ATTAA-ATTAATATTTTATCTAAAATTTAAGAGTTAA
1 ATTAATATT-ATATTTTATCTAAAATTT-AGAGTTAA
* * * *
19633761 ATTAATATTTTATTTTATGTAAAGTTTAGGGTTAA
1 ATTAATATTATATTTTATCTAAAATTTAGAGTTAA
19633796 A
1 A
19633797 GTCCTAAGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 8 0.26
36 20 0.65
37 3 0.10
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (35 bp):
ATTAATATTATATTTTATCTAAAATTTAGAGTTAA
Found at i:19643092 original size:18 final size:18
Alignment explanation
Indices: 19643069--19643103 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19643059 GTTTGATAGC
*
19643069 TATAATTTATTTTCCTAA
1 TATAATTCATTTTCCTAA
19643087 TATAATTCATTTTCCTA
1 TATAATTCATTTTCCTA
19643104 GTTCATTTGT
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:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (18 bp):
TATAATTCATTTTCCTAA
Found at i:19643294 original size:22 final size:18
Alignment explanation
Indices: 19643269--19643316 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 18
19643259 TACAAAAATA
19643269 TTTAATATAAATATAATATAAT
1 TTTAATATAAAT-T-ATAT--T
19643291 TTTAATA-AAATTATATT
1 TTTAATATAAATTATATT
19643308 TTTAATATA
1 TTTAATATA
19643317 TTATTAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.32
18 1 0.04
19 4 0.16
20 1 0.04
21 4 0.16
22 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATATAAATTATATT
Found at i:19643403 original size:58 final size:56
Alignment explanation
Indices: 19643300--19643425 Score: 141
Period size: 58 Copynumber: 2.2 Consensus size: 56
19643290 TTTTAATAAA
* *
19643300 ATTATATTTTT-AATATATTATTAGTATATACTCATATATATTATAATAATATATGAT
1 ATTATATTTTTAAATAAATTATTAATATATACTCATATATATTATAATAATAT-T-AT
* *
19643357 ATTATATTTTTAAATAAATTATTAATATTTA-TC-TATTATTTTTATAATAATATTAT
1 ATTATATTTTTAAATAAATTATTAATATATACTCATA-TA-TATTATAATAATATTAT
* *
19643413 ATTAAATTATTAA
1 ATTATATTTTTAA
19643426 TAATGAGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
56 15 0.25
57 16 0.27
58 29 0.48
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (56 bp):
ATTATATTTTTAAATAAATTATTAATATATACTCATATATATTATAATAATATTAT
Found at i:19643860 original size:30 final size:30
Alignment explanation
Indices: 19643757--19643860 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 30
19643747 CCCGAAAAAT
* *
19643757 GTAATTTATTTTACATAAAACAG-TTTTAG
1 GTAATTCATTTTACGTAAAACAGTTTTTAG
*** * * *
19643786 GTAATTCATTTTTTTTAAAATAGTTTTCAT
1 GTAATTCATTTTACGTAAAACAGTTTTTAG
*
19643816 ATAATTCATTTTACGTAAAACAGTTTTTAG
1 GTAATTCATTTTACGTAAAACAGTTTTTAG
19643846 GTAA-TCTATTTTACG
1 GTAATTC-ATTTTACG
19643861 CAAATTATTT
Statistics
Matches: 58, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
29 20 0.34
30 38 0.66
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.48
Consensus pattern (30 bp):
GTAATTCATTTTACGTAAAACAGTTTTTAG
Found at i:19644405 original size:15 final size:15
Alignment explanation
Indices: 19644385--19644414 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19644375 AGACTCCATT
19644385 GATGTTCCACTTTGC
1 GATGTTCCACTTTGC
*
19644400 GATGTTTCACTTTGC
1 GATGTTCCACTTTGC
19644415 AATTGTGGAC
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:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (15 bp):
GATGTTCCACTTTGC
Found at i:19645347 original size:12 final size:12
Alignment explanation
Indices: 19645332--19645368 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
19645322 GGAGAGTTTG
19645332 GTCTTATTTGTT
1 GTCTTATTTGTT
19645344 GTCTTATTTG-T
1 GTCTTATTTGTT
19645355 GTCTTATTTGTT
1 GTCTTATTTGTT
19645367 GT
1 GT
19645369 TGCCTTGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.08, C:0.08, G:0.19, T:0.65
Consensus pattern (12 bp):
GTCTTATTTGTT
Found at i:19645359 original size:11 final size:11
Alignment explanation
Indices: 19645328--19645365 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
19645318 TGGTGGAGAG
19645328 TTTG-GTCTTA
1 TTTGTGTCTTA
19645338 TTTGTTGTCTTA
1 TTTG-TGTCTTA
19645350 TTTGTGTCTTA
1 TTTGTGTCTTA
19645361 TTTGT
1 TTTGT
19645366 TGTTGCCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 4 0.15
11 12 0.46
12 10 0.38
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.66
Consensus pattern (11 bp):
TTTGTGTCTTA
Found at i:19645695 original size:30 final size:30
Alignment explanation
Indices: 19645659--19645748 Score: 105
Period size: 29 Copynumber: 3.0 Consensus size: 30
19645649 GGAGGCTAAT
19645659 CATGTTCACTAGCATG-AACAATTATAACCA
1 CATGTTCACTAGCATGAAACAATTATAA-CA
*
19645689 CATGTTCACTAGCATGCAAACAAGTAT-A-A
1 CATGTTCACTAGCATG-AAACAATTATAACA
* *
19645718 CATGTTCACCAACATGCAAACAATTATAACA
1 CATGTTCACTAGCATG-AAACAATTATAACA
19645749 TTTTACCTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 25 0.48
30 17 0.33
31 2 0.04
32 8 0.15
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.24
Consensus pattern (30 bp):
CATGTTCACTAGCATGAAACAATTATAACA
Found at i:19647578 original size:15 final size:15
Alignment explanation
Indices: 19647530--19647580 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
19647520 ACTTTATTCA
*
19647530 TTTCAGCAGCACCAC
1 TTTCAGCAGCATCAC
***
19647545 TTTCAGCTTTATTCA-
1 TTTCAGCAGCA-TCAC
19647560 TTTCAGCAGCATCAC
1 TTTCAGCAGCATCAC
19647575 TTTCAG
1 TTTCAG
19647581 TACTACCCAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
14 3 0.11
15 22 0.81
16 2 0.07
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (15 bp):
TTTCAGCAGCATCAC
Found at i:19647580 original size:30 final size:30
Alignment explanation
Indices: 19647463--19647579 Score: 162
Period size: 30 Copynumber: 3.9 Consensus size: 30
19647453 ACTATCAGAC
* * * *
19647463 TTATCCATTTCAGTAGCACAACTTTCAACA
1 TTATTCATTTCAGCAGCACCACTTTCAACT
* *
19647493 TTATTTATTTTAGCAGCACCACTTTCAACT
1 TTATTCATTTCAGCAGCACCACTTTCAACT
*
19647523 TTATTCATTTCAGCAGCACCACTTTCAGCT
1 TTATTCATTTCAGCAGCACCACTTTCAACT
*
19647553 TTATTCATTTCAGCAGCATCACTTTCA
1 TTATTCATTTCAGCAGCACCACTTTCA
19647580 GTACTACCCA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.38
Consensus pattern (30 bp):
TTATTCATTTCAGCAGCACCACTTTCAACT
Found at i:19648193 original size:20 final size:20
Alignment explanation
Indices: 19648157--19648214 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
19648147 ACACTCACAA
*
19648157 TATCATATA-TCACATATAAT
1 TATCATAAAGTCA-ATATAAT
*
19648177 TATCATAGAGTCAATAT-AT
1 TATCATAAAGTCAATATAAT
*
19648196 CACTCATAAAGTCAATATA
1 TA-TCATAAAGTCAATATA
19648215 TCATACATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
TATCATAAAGTCAATATAAT
Found at i:19648227 original size:22 final size:20
Alignment explanation
Indices: 19648179--19648217 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19648169 CATATAATTA
*
19648179 TCATAGAGTCAATATATCAC
1 TCATAAAGTCAATATATCAC
19648199 TCATAAAGTCAATATATCA
1 TCATAAAGTCAATATATCA
19648218 TACATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (20 bp):
TCATAAAGTCAATATATCAC
Found at i:19651973 original size:18 final size:18
Alignment explanation
Indices: 19651950--19651984 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19651940 GTTTGATAGC
*
19651950 TATAATTTATTTTCCTAA
1 TATAATTCATTTTCCTAA
19651968 TATAATTCATTTTCCTA
1 TATAATTCATTTTCCTA
19651985 GTTCATTTGT
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:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (18 bp):
TATAATTCATTTTCCTAA
Found at i:19652175 original size:22 final size:18
Alignment explanation
Indices: 19652150--19652197 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 18
19652140 TACAAAAATA
19652150 TTTAATATAAATATAATATAAT
1 TTTAATATAAAT-T-ATAT--T
19652172 TTTAATA-AAATTATATT
1 TTTAATATAAATTATATT
19652189 TTTAATATA
1 TTTAATATA
19652198 TTATTAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.32
18 1 0.04
19 4 0.16
20 1 0.04
21 4 0.16
22 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATATAAATTATATT
Found at i:19652197 original size:11 final size:11
Alignment explanation
Indices: 19652183--19652303 Score: 56
Period size: 11 Copynumber: 11.2 Consensus size: 11
19652173 TTAATAAAAT
*
19652183 TATATTTTTAA
1 TATATTATTAA
*
19652194 TATATTATTAG
1 TATATTATTAA
* *
19652205 TATA-TACTCA
1 TATATTATTAA
19652215 TATATTA-TAA
1 TATATTATTAA
* *
19652225 TATA-TATGAT
1 TATATTATTAA
*
19652235 TATATTTTTAAA
1 TATATTATT-AA
*
19652247 TAAATTATTAA
1 TATATTATTAA
*
19652258 TAT-TTATCTAT
1 TATATTAT-TAA
*
19652269 TAT-TTTTATAA
1 TATATTAT-TAA
*
19652280 TAATATTA-TAT
1 T-ATATTATTAA
*
19652291 TAAATTATTAA
1 TATATTATTAA
19652302 TA
1 TA
19652304 ATGAGTAATA
Statistics
Matches: 80, Mismatches: 22, Indels: 16
0.68 0.19 0.14
Matches are distributed among these distances:
9 2 0.03
10 27 0.34
11 39 0.49
12 10 0.12
13 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TATATTATTAA
Found at i:19652733 original size:30 final size:30
Alignment explanation
Indices: 19652633--19652736 Score: 113
Period size: 30 Copynumber: 3.5 Consensus size: 30
19652623 CCCGAAAAAT
* *
19652633 GTAATTTATTTTACATAAAACAG-TTTTAG
1 GTAATTCATTTTACGTAAAACAGTTTTTAG
** * * *
19652662 GTAATTCATTTTATTTAAAATAGTTTTCAT
1 GTAATTCATTTTACGTAAAACAGTTTTTAG
*
19652692 ATAATTCATTTTACGTAAAACAGTTTTTAG
1 GTAATTCATTTTACGTAAAACAGTTTTTAG
19652722 GTAA-TCTATTTTACG
1 GTAATTC-ATTTTACG
19652737 CAAATTATTT
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.35
30 39 0.65
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.47
Consensus pattern (30 bp):
GTAATTCATTTTACGTAAAACAGTTTTTAG
Found at i:19653282 original size:15 final size:15
Alignment explanation
Indices: 19653262--19653291 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19653252 AGACTCCATT
19653262 GATGTTCCACTTTGC
1 GATGTTCCACTTTGC
*
19653277 GATGTTTCACTTTGC
1 GATGTTCCACTTTGC
19653292 AATTGTGGAC
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:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (15 bp):
GATGTTCCACTTTGC
Found at i:19654223 original size:12 final size:12
Alignment explanation
Indices: 19654208--19654241 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
19654198 GAGAGTTTGG
19654208 TCTTATTTGTTA
1 TCTTATTTGTTA
*
19654220 TCTTATTTG-TG
1 TCTTATTTGTTA
19654231 TCTTATTTGTT
1 TCTTATTTGTT
19654242 GTTGCCTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.68
Consensus pattern (12 bp):
TCTTATTTGTTA
Found at i:19654236 original size:11 final size:11
Alignment explanation
Indices: 19654203--19654240 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19654193 TGGTGGAGAG
19654203 TTTG-GTCTTA
1 TTTGTGTCTTA
*
19654213 TTTGTTATCTTA
1 TTTG-TGTCTTA
19654225 TTTGTGTCTTA
1 TTTGTGTCTTA
19654236 TTTGT
1 TTTGT
19654241 TGTTGCCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 4 0.17
11 11 0.46
12 9 0.38
ACGTcount: A:0.11, C:0.08, G:0.16, T:0.66
Consensus pattern (11 bp):
TTTGTGTCTTA
Found at i:19654318 original size:54 final size:54
Alignment explanation
Indices: 19654237--19654339 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
19654227 TGTGTCTTAT
* * * *
19654237 TTGTTGTTGCCTTGGAGTTGGCTGTTGGAGA-GTTTGGTTAGGAGCATGTTGAGG
1 TTGTTGCTACCTTAGAGTTGGCTGTTGG-GATGGTTGGTTAGGAGCATGTTGAGG
* *
19654291 TTGTTGCTACCTTAGAGTTGGTTGTTGGGATGGTTGGTTAGGTGCATGT
1 TTGTTGCTACCTTAGAGTTGGCTGTTGGGATGGTTGGTTAGGAGCATGT
19654340 CGAGCTTCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 2 0.05
54 40 0.95
ACGTcount: A:0.13, C:0.08, G:0.39, T:0.41
Consensus pattern (54 bp):
TTGTTGCTACCTTAGAGTTGGCTGTTGGGATGGTTGGTTAGGAGCATGTTGAGG
Found at i:19654569 original size:30 final size:30
Alignment explanation
Indices: 19654533--19654622 Score: 105
Period size: 29 Copynumber: 3.0 Consensus size: 30
19654523 GGAGGCTAAT
19654533 CATGTTCACTAGCATG-AACAATTATAACCA
1 CATGTTCACTAGCATGAAACAATTATAA-CA
*
19654563 CATGTTCACTAGCATGCAAACAAGTAT-A-A
1 CATGTTCACTAGCATG-AAACAATTATAACA
* *
19654592 CATGTTCACCAACATGCAAACAATTATAACA
1 CATGTTCACTAGCATG-AAACAATTATAACA
19654623 TTTTACCTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 25 0.48
30 17 0.33
31 2 0.04
32 8 0.15
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.24
Consensus pattern (30 bp):
CATGTTCACTAGCATGAAACAATTATAACA
Found at i:19656384 original size:30 final size:30
Alignment explanation
Indices: 19656336--19656450 Score: 158
Period size: 30 Copynumber: 3.8 Consensus size: 30
19656326 ACTATCAGAC
* * *
19656336 TTATCCATTTCAGTAGCACCACTTTCAACA
1 TTATTCATTTCAGCAGCACCACTTTCAACT
* *
19656366 TTATTTATTTTAGCAGCACCACTTTCAACT
1 TTATTCATTTCAGCAGCACCACTTTCAACT
*
19656396 TTATTCATTTCAGCAGCACCACTTTCAGCT
1 TTATTCATTTCAGCAGCACCACTTTCAACT
* *
19656426 TTATTCATTTCAGTAGCATCACTTT
1 TTATTCATTTCAGCAGCACCACTTT
19656451 TAGTACTACC
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (30 bp):
TTATTCATTTCAGCAGCACCACTTTCAACT
Found at i:19657066 original size:20 final size:20
Alignment explanation
Indices: 19657030--19657067 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19657020 ACACTCACAA
*
19657030 TATCATATATCACATATAAT
1 TATCATAGATCACATATAAT
19657050 TATCATAGAGTCA-ATATA
1 TATCATAGA-TCACATATA
19657068 TCACTCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (20 bp):
TATCATAGATCACATATAAT
Found at i:19658512 original size:19 final size:18
Alignment explanation
Indices: 19658471--19658512 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
19658461 CAAAACTATC
*
19658471 AGTTTTAAAAAATATTAA
1 AGTTTTAAAAAATATGAA
*
19658489 CGTTTTGAAAAAATATGAA
1 AGTTTT-AAAAAATATGAA
19658508 AGTTT
1 AGTTT
19658513 AGTTACTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (18 bp):
AGTTTTAAAAAATATGAA
Found at i:19661053 original size:16 final size:16
Alignment explanation
Indices: 19661032--19661064 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19661022 ATTTTTTAAG
19661032 AATTTGATTAATAATT
1 AATTTGATTAATAATT
*
19661048 AATTTGATTCATAATT
1 AATTTGATTAATAATT
19661064 A
1 A
19661065 GTTAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
AATTTGATTAATAATT
Found at i:19661171 original size:18 final size:19
Alignment explanation
Indices: 19661119--19661174 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
19661109 CCCAAACTCA
*
19661119 TTTAAAACTAAATTAATAT
1 TTTAAACCTAAATTAATAT
19661138 TTTAAGATCC--AA-TAAT-T
1 TTTAA-A-CCTAAATTAATAT
19661155 TTTAAACCTAAATTAATAT
1 TTTAAACCTAAATTAATAT
19661174 T
1 T
19661175 AATTAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
15 2 0.07
16 1 0.03
17 8 0.27
18 8 0.27
19 9 0.30
20 1 0.03
21 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (19 bp):
TTTAAACCTAAATTAATAT
Found at i:19662468 original size:39 final size:38
Alignment explanation
Indices: 19662386--19662472 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 38
19662376 TTGTGCCAAC
* *
19662386 AGTATCGATATTAACGCTTGGGTATTAATACTCGGGCAT
1 AGTATCGATACTAACCCTTGGGTATTAATACTCGGG-AT
*
19662425 AGTATCGATACTGACCCTTGGGTA-TAGATACTCAGGG-T
1 AGTATCGATACTAACCCTTGGGTATTA-ATACTC-GGGAT
19662463 GAGTATCGAT
1 -AGTATCGAT
19662473 GCTAGAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 3 0.07
39 36 0.86
40 3 0.07
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (38 bp):
AGTATCGATACTAACCCTTGGGTATTAATACTCGGGAT
Found at i:19663297 original size:21 final size:22
Alignment explanation
Indices: 19663264--19663304 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19663254 GGTTAAAATA
19663264 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
19663286 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
19663305 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:19669786 original size:15 final size:15
Alignment explanation
Indices: 19669766--19669829 Score: 101
Period size: 15 Copynumber: 4.3 Consensus size: 15
19669756 TTCCTCTTGT
* *
19669766 TCTTCCTGATATGTG
1 TCTTCCTGATGTGCG
19669781 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
*
19669796 TCTTCCTGATGTGCA
1 TCTTCCTGATGTGCG
19669811 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
19669826 TCTT
1 TCTT
19669830 TTTTTGCTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (15 bp):
TCTTCCTGATGTGCG
Found at i:19672300 original size:76 final size:75
Alignment explanation
Indices: 19672184--19672331 Score: 208
Period size: 76 Copynumber: 2.0 Consensus size: 75
19672174 TTATAAATCC
* * *
19672184 TAATTAAAATACTAAAACCTATTTAAACTGAAATACAAAGATAAAGATAAAAT-ATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAAATAAAATAAAAAGATAAA-ATAAAATGATAAAAATAAT
19672248 ATCCTAAAACT
65 ATCCTAAAACT
* * * *
19672259 TAATTAAAATACTAAAAACCTATTTAAAATAAAATAAAAAGATAAAATATAATGTTTAAAATATT
1 TAATTAAAATACT-AAAACCTATTTAAAATAAAATAAAAAGATAAAATAAAATGATAAAAATAAT
19672324 ATCCTAAA
65 ATCCTAAA
19672332 TTTGAGTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
75 19 0.30
76 45 0.70
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (75 bp):
TAATTAAAATACTAAAACCTATTTAAAATAAAATAAAAAGATAAAATAAAATGATAAAAATAATA
TCCTAAAACT
Found at i:19678942 original size:475 final size:477
Alignment explanation
Indices: 19678026--19678957 Score: 1530
Period size: 475 Copynumber: 2.0 Consensus size: 477
19678016 TTGATTCTAG
* *
19678026 AAATAACTTCGATGTTTTGAAAATAACTTGGTATTGATACCCCTATAGGGAGTATTGATACTCCC
1 AAATAACTTCGATATTTTGAAAATAACTTGATATTGATACCCCTATAGGGAGTATTGATACTCCC
19678091 ATAAGTATCGATAACAAAGTTGGCTACTGGAATCCTAAACTTGCCACCGGTATCGATACCAACCC
66 ATAAGTATCGATAACAAAGTTGGCTACTGGAATCCTAAACTTGCCACCGGTATCGATACCAACCC
19678156 TTGAGTATCGAGACCAAACCAAGTATCGATACTCCTTGAGGGAGTATCGATACTACACTCAAAAA
131 TTGAGTATCGAGACCAAACCAAGTATCGATACTCCTTGAGGGAGTATCGATACTACACTCAAAAA
* *
19678221 TTATCATTGTTTTTACACTACATGAAGAACAATATCGATACTGTTCTTCCAATACCCTATTTTGG
196 TTATCATTGTTTTTACACTACACGAAGAACAATATCGATACTGTTCTTCCAAGACCCTATTTTGG
* * * * * *
19678286 GCACGAAATTTGTATCTCAACTCAGACATTCACTCCCCTAAGGCTAACAAATATTATCAAATTCT
261 GAACAAAATTTGTATCTCAACTCACACATTCACTCCCATAAGGCTAACAAATATTACCAAATACT
* *
19678351 TAGTTAGGTTCATAGAGGTCGAAAGGAGTAATATTTCTTGCTTTAAAACATCAAACATAGAATTT
326 TAGTTAGGTTCATAGAGGTCGAAAGGAGTAATATTTCATGCTTAAAAACATCAAACATAGAATTT
*
19678416 ACCATGGATTACTCTAGCATGCTTCATGAACTTAACTAACCATTTATGCATATATAATGATCTAC
391 ACCATGGATTACTCTAGCATGCTTCATGAACTTAACTAACCATATATGCATATATAATGATCTAC
19678481 ATAGGGTGAGTATCGATACCAT
456 ATAGGGTGAGTATCGATACCAT
* * *
19678503 AAATAACTTTGATATTTTGAAAATAACTCT-ATATTGATATCCCTATGGGGAGTATTGATACTCC
1 AAATAACTTCGATATTTTGAAAATAACT-TGATATTGATACCCCTATAGGGAGTATTGATACTCC
* * *
19678567 CATAATTATCGGTAACAAAGTTGGCTACT-GAATCCTAAACTTGCCACTGGTATCGATACC-ACC
65 CATAAGTATCGATAACAAAGTTGGCTACTGGAATCCTAAACTTGCCACCGGTATCGATACCAACC
* *
19678630 ACTTGAGTATCGAGACCAGACCAAGTATCGATACTCCTTGAGGGAGTATCGATACTACACTCACA
130 -CTTGAGTATCGAGACCAAACCAAGTATCGATACTCCTTGAGGGAGTATCGATACTACACTCAAA
* * * * * *
19678695 AATTATCCTTGTTTTTATACTACACGAAGAACAATATCGGTATTGTTCTTGCAGGACCCTATTTT
194 AATTATCATTGTTTTTACACTACACGAAGAACAATATCGATACTGTTCTTCCAAGACCCTATTTT
* *
19678760 GGGAACAAAATTT-TATCTCAACTCACCCATTCACTCCCATAAGGCTAACAAATATTACCAGATA
259 GGGAACAAAATTTGTATCTCAACTCACACATTCACTCCCATAAGGCTAACAAATATTACCAAATA
* * *
19678824 CTTAGTTAGGTTCTTAGAGGTCGAAAGGAGTCATCTTTCATGCTTAAAAACATCAAACATAGAAT
324 CTTAGTTAGGTTCATAGAGGTCGAAAGGAGTAATATTTCATGCTTAAAAACATCAAACATAGAAT
19678889 TTACCATGGATTACTCTAGCATGCTTCATGAACTTAACTAACCATATATGCATATATAATGATCT
389 TTACCATGGATTACTCTAGCATGCTTCATGAACTTAACTAACCATATATGCATATATAATGATCT
19678954 ACAT
454 ACAT
19678958 GTGGTATGGA
Statistics
Matches: 421, Mismatches: 32, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
475 176 0.42
476 160 0.38
477 84 0.20
478 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (477 bp):
AAATAACTTCGATATTTTGAAAATAACTTGATATTGATACCCCTATAGGGAGTATTGATACTCCC
ATAAGTATCGATAACAAAGTTGGCTACTGGAATCCTAAACTTGCCACCGGTATCGATACCAACCC
TTGAGTATCGAGACCAAACCAAGTATCGATACTCCTTGAGGGAGTATCGATACTACACTCAAAAA
TTATCATTGTTTTTACACTACACGAAGAACAATATCGATACTGTTCTTCCAAGACCCTATTTTGG
GAACAAAATTTGTATCTCAACTCACACATTCACTCCCATAAGGCTAACAAATATTACCAAATACT
TAGTTAGGTTCATAGAGGTCGAAAGGAGTAATATTTCATGCTTAAAAACATCAAACATAGAATTT
ACCATGGATTACTCTAGCATGCTTCATGAACTTAACTAACCATATATGCATATATAATGATCTAC
ATAGGGTGAGTATCGATACCAT
Found at i:19680176 original size:19 final size:21
Alignment explanation
Indices: 19680149--19680188 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
19680139 TTAGGCGTAA
19680149 ATTATAATTTTAGTT-ATTTT
1 ATTATAATTTTAGTTCATTTT
19680169 ATTA-AATTTTAGTTCATTTT
1 ATTATAATTTTAGTTCATTTT
19680189 GATTCTGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTATAATTTTAGTTCATTTT
Found at i:19684783 original size:76 final size:75
Alignment explanation
Indices: 19684670--19684876 Score: 310
Period size: 76 Copynumber: 2.8 Consensus size: 75
19684660 TCGTTATGAG
* * *
19684670 ATGGGGGTATCAGTA-CCTCCTGGGGGTATCGGTACCCTCCGAGAAATCTGTTATTTCTCGGAGT
1 ATGGGGGTATCGGTACCCTCTTGGGGGTATCGGTACCCTCCGAGAAATCTGTTATTTCTCGGAGC
19684734 CAAATCTTAC
66 CAAATCTTAC
* * * *
19684744 ATGGGGGTATCGGTACCCTCTTGGGGGGTATCTGTACCCTTCGAGCAATTTGTTATTTCTCGGAG
1 ATGGGGGTATCGGTACCCTCTT-GGGGGTATCGGTACCCTCCGAGAAATCTGTTATTTCTCGGAG
19684809 CCAAATCTTAC
65 CCAAATCTTAC
*
19684820 ATGGGGGTATAGGTACCCTCTTGGGGGTATCGGTACCCTCCGA-ACAATCTGTTATTT
1 ATGGGGGTATCGGTACCCTCTTGGGGGTATCGGTACCCTCCGAGA-AATCTGTTATTT
19684877 TTGTTTAAGA
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
74 14 0.12
75 35 0.30
76 69 0.58
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (75 bp):
ATGGGGGTATCGGTACCCTCTTGGGGGTATCGGTACCCTCCGAGAAATCTGTTATTTCTCGGAGC
CAAATCTTAC
Found at i:19684846 original size:20 final size:20
Alignment explanation
Indices: 19684821--19684859 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19684811 AAATCTTACA
19684821 TGGGGGTATAGGTACCCTCT
1 TGGGGGTATAGGTACCCTCT
*
19684841 TGGGGGTATCGGTACCCTC
1 TGGGGGTATAGGTACCCTC
19684860 CGAACAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.36, T:0.28
Consensus pattern (20 bp):
TGGGGGTATAGGTACCCTCT
Found at i:19687598 original size:22 final size:23
Alignment explanation
Indices: 19687555--19687608 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
19687545 CGTAGAGGGT
*
19687555 ATCGGTACCTACTCAAAGGGGGG
1 ATCGGTACCCACTCAAAGGGGGG
* *
19687578 ATCGGTACCCATTC-AAGGGGGT
1 ATCGGTACCCACTCAAAGGGGGG
*
19687600 ATCGATACC
1 ATCGGTACC
19687609 TCTTGCACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (23 bp):
ATCGGTACCCACTCAAAGGGGGG
Found at i:19692903 original size:21 final size:21
Alignment explanation
Indices: 19692877--19692932 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
19692867 GGAGTGTTGG
*
19692877 GGGTATCGGTACCCCTGTATA
1 GGGTATCGGTACCCCTGCATA
19692898 GGGTATCGGTACCCCTGCATA
1 GGGTATCGGTACCCCTGCATA
*
19692919 GGGTATCGATACCC
1 GGGTATCGGTACCC
19692933 TACTATGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.25
Consensus pattern (21 bp):
GGGTATCGGTACCCCTGCATA
Found at i:19693053 original size:21 final size:20
Alignment explanation
Indices: 19693025--19693085 Score: 86
Period size: 21 Copynumber: 3.0 Consensus size: 20
19693015 AAATCTTACA
*
19693025 TGGGGGTATCAGTACCCTCT
1 TGGGGGTATCGGTACCCTCT
19693045 TGGGTGGTATCGGTACCCTCT
1 TGGG-GGTATCGGTACCCTCT
*
19693066 TGGGGGGTATCGGCACCCTC
1 T-GGGGGTATCGGTACCCTC
19693086 CGAGCAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 4 0.11
21 30 0.81
22 3 0.08
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.28
Consensus pattern (20 bp):
TGGGGGTATCGGTACCCTCT
Found at i:19693137 original size:97 final size:96
Alignment explanation
Indices: 19692971--19693157 Score: 338
Period size: 97 Copynumber: 1.9 Consensus size: 96
19692961 GTTATAAGAT
* *
19692971 GGGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAATCTTACATGGGGGTATCA
1 GGGGGTATCGGCACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAATCTTACATAGGGGTATCA
19693036 GTACCCTCTTGGGTGGTATCGGTACCCTCTTG
66 GTACCCTCTTGGG-GGTATCGGTACCCTCTTG
*
19693068 GGGGGTATCGGCACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAATCTTACATAGGGGTATCG
1 GGGGGTATCGGCACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAATCTTACATAGGGGTATCA
19693133 GTACCCTCTTGGGGGTATCGGTACC
66 GTACCCTCTTGGGGGTATCGGTACC
19693158 ATCCGAGCAA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
96 12 0.14
97 75 0.86
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (96 bp):
GGGGGTATCGGCACCCTCCGAGCAATCTGTTATTTCTCGGAGCCAAATCTTACATAGGGGTATCA
GTACCCTCTTGGGGGTATCGGTACCCTCTTG
Found at i:19700634 original size:24 final size:24
Alignment explanation
Indices: 19700604--19700653 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
19700594 TAAAAGAGAG
*
19700604 ACAAAAAATGAAA-AATAATAATAAT
1 ACAAAAAA-GAAACAAAAATAA-AAT
19700629 ACAAAAAAGAAACAAAAATAAAAT
1 ACAAAAAAGAAACAAAAATAAAAT
19700653 A
1 A
19700654 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (24 bp):
ACAAAAAAGAAACAAAAATAAAAT
Found at i:19700644 original size:36 final size:38
Alignment explanation
Indices: 19700571--19700646 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 38
19700561 GAAGTTAACT
* * * *
19700571 AAATTAAAAATAAATAAATAAAATAAAAGAGAGACAAA
1 AAATGAAAAATAAATAAATAAAACAAAAAAGAAACAAA
*
19700609 AAATGAAAAAT-AAT-AATAATACAAAAAAGAAACAAA
1 AAATGAAAAATAAATAAATAAAACAAAAAAGAAACAAA
19700645 AA
1 AA
19700647 TAAAATAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 20 0.61
37 3 0.09
38 10 0.30
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (38 bp):
AAATGAAAAATAAATAAATAAAACAAAAAAGAAACAAA
Found at i:19700758 original size:3 final size:3
Alignment explanation
Indices: 19700750--19700804 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
19700740 ATATATATTT
19700750 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19700798 ATA ATA A
1 ATA ATA A
19700805 AGGACTAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19701902 original size:13 final size:12
Alignment explanation
Indices: 19701875--19701955 Score: 58
Period size: 13 Copynumber: 6.7 Consensus size: 12
19701865 ACAATATGTA
19701875 ATAATATATTGAT
1 ATAATATATT-AT
19701888 ATAATATA-TAT
1 ATAATATATTAT
* *
19701899 ATATTTATGTTAT
1 ATA-ATATATTAT
*
19701912 ATAATTATAGTAT
1 ATAA-TATATTAT
* * *
19701925 ACAACATAATAT
1 ATAATATATTAT
*
19701937 GT-ATATATTAT
1 ATAATATATTAT
19701948 ATAATATA
1 ATAATATA
19701956 ATACATATAC
Statistics
Matches: 51, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
11 13 0.25
12 15 0.29
13 23 0.45
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (12 bp):
ATAATATATTAT
Found at i:19701962 original size:30 final size:31
Alignment explanation
Indices: 19701878--19701964 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
19701868 ATATGTAATA
* *
19701878 ATATATTGATATAATAT-ATATATATTTATGT
1 ATATATT-ATATAATATAATACATATATATGT
* *
19701909 -TATATAATTATAGTATACA-ACATA-ATATGT
1 ATATATTA-TATAATATA-ATACATATATATGT
19701939 ATATATTATATAATATAATACATATA
1 ATATATTATATAATATAATACATATA
19701965 CCCTATATAC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
29 2 0.05
30 30 0.68
31 11 0.25
32 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (31 bp):
ATATATTATATAATATAATACATATATATGT
Found at i:19701964 original size:23 final size:23
Alignment explanation
Indices: 19701886--19701964 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 23
19701876 TAATATATTG
*
19701886 ATATAATATATATATATT-TATG
1 ATATAATATATATATATTATATA
* * *
19701908 TTAT-ATA-AT-TATAGTATACA
1 ATATAATATATATATATTATATA
* *
19701928 ACATAATATGTATATATTATATA
1 ATATAATATATATATATTATATA
*
19701951 ATATAATACATATA
1 ATATAATATATATA
19701965 CCCTATATAC
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
19 5 0.12
20 6 0.15
21 6 0.15
22 4 0.10
23 20 0.49
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (23 bp):
ATATAATATATATATATTATATA
Found at i:19706918 original size:44 final size:44
Alignment explanation
Indices: 19706768--19707010 Score: 218
Period size: 44 Copynumber: 5.5 Consensus size: 44
19706758 TCGATGTTGT
* * * *
19706768 TCCAACTCCTTATGCGATGGAAACAAGTGAAATGGTGATGCTGA
1 TCCAACTCCTTATGTGATGGAATCAGGCGAAATGGTGATGCTGA
* * ** * * *
19706812 TACAATTCCTTATGTGACAGAATCTA-GCAAAAAGGTCGATGCTGC
1 TCCAACTCCTTATGTGATGGAATC-AGGCGAAATGGT-GATGCTGA
* * * * * * *
19706857 TCCAAATCCGTATGTGATAGAAACAGGCAAAATGTTGATGTTGA
1 TCCAACTCCTTATGTGATGGAATCAGGCGAAATGGTGATGCTGA
*
19706901 TCCAATTCCTTATGTGATGGAATCAGGCGAAATGGTGATGCTGA
1 TCCAACTCCTTATGTGATGGAATCAGGCGAAATGGTGATGCTGA
* * *** **
19706945 TCCAACTCATTATGTGATGGAATCGGGCGAAACAATGATATTGA
1 TCCAACTCCTTATGTGATGGAATCAGGCGAAATGGTGATGCTGA
19706989 TCCAACTCCTTTATGTGATGGA
1 TCCAACTCC-TTATGTGATGGA
19707011 TGAACCAAGG
Statistics
Matches: 160, Mismatches: 35, Indels: 7
0.79 0.17 0.03
Matches are distributed among these distances:
44 113 0.71
45 47 0.29
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (44 bp):
TCCAACTCCTTATGTGATGGAATCAGGCGAAATGGTGATGCTGA
Found at i:19706924 original size:89 final size:88
Alignment explanation
Indices: 19706797--19707010 Score: 214
Period size: 89 Copynumber: 2.4 Consensus size: 88
19706787 GAAACAAGTG
* * * ** *
19706797 AAATGGTGATGCTGATACAATTCCTTATGTGACAGAATCTA-GCAAAAAGGTCGATGCTGCTCCA
1 AAATGATGATGTTGATCCAATTCCTTATGTGATGGAATC-AGGCAAAAAGGT-GATGCTGATCCA
*
19706861 AATCCGTATGTGATAGAAACAGGCA
64 AATCAGTATGTGATAGAAACAGGCA
* * * *
19706886 AAATGTTGATGTTGATCCAATTCCTTATGTGATGGAATCAGGCGAAATGGTGATGCTGATCCAAC
1 AAATGATGATGTTGATCCAATTCCTTATGTGATGGAATCAGGCAAAAAGGTGATGCTGATCCAAA
* * * * *
19706951 TCATTATGTGATGGAATCGGGCG
66 TCAGTATGTGATAGAAACAGGCA
** * *
19706974 AAACAATGATATTGATCCAACTCCTTTATGTGATGGA
1 AAATGATGATGTTGATCCAATTCC-TTATGTGATGGA
19707011 TGAACCAAGG
Statistics
Matches: 103, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
88 49 0.48
89 54 0.52
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (88 bp):
AAATGATGATGTTGATCCAATTCCTTATGTGATGGAATCAGGCAAAAAGGTGATGCTGATCCAAA
TCAGTATGTGATAGAAACAGGCA
Found at i:19707434 original size:23 final size:23
Alignment explanation
Indices: 19707408--19707460 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
19707398 AGGATAAAAG
19707408 TAAAAAAGATTTATTTATTTCAT
1 TAAAAAAGATTTATTTATTTCAT
* *
19707431 TAAAAGAGATTTATTTATTTTAT
1 TAAAAAAGATTTATTTATTTCAT
19707454 TAAAAAA
1 TAAAAAA
19707461 ATATTTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (23 bp):
TAAAAAAGATTTATTTATTTCAT
Found at i:19708122 original size:16 final size:16
Alignment explanation
Indices: 19708081--19708123 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
19708071 AGGTACCCAG
* *
19708081 TTGCCTTGACAATTAG
1 TTGCCTCGACAATTAC
* *
19708097 TTGTCACGACAATTAC
1 TTGCCTCGACAATTAC
19708113 TTGCCTCGACA
1 TTGCCTCGACA
19708124 GCCTGTTGCC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (16 bp):
TTGCCTCGACAATTAC
Done.