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 14 of 91
Found at i:2806819 original size:9 final size:9
Alignment explanation
Indices: 2806805--2806848 Score: 63
Period size: 10 Copynumber: 4.8 Consensus size: 9
2806795 TATTATACTT
2806805 GAAAAAAAG
1 GAAAAAAAG
2806814 G-AAAAAAG
1 GAAAAAAAG
2806822 GAGAAAAAAGG
1 GA-AAAAAA-G
2806833 GAAAAAAAG
1 GAAAAAAAG
2806842 GAAAAAA
1 GAAAAAA
2806849 TTGAACCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.25
9 9 0.28
10 12 0.38
11 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (9 bp):
GAAAAAAAG
Found at i:2806827 original size:10 final size:9
Alignment explanation
Indices: 2806805--2806848 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
2806795 TATTATACTT
*
2806805 GAAAAAAAG
1 GAAAAAAGG
2806814 GAAAAAAGG
1 GAAAAAAGG
2806823 AGAAAAAAGG
1 -GAAAAAAGG
*
2806833 GAAAAAAAG
1 GAAAAAAGG
2806842 GAAAAAA
1 GAAAAAA
2806849 TTGAACCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 23 0.72
10 9 0.28
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (9 bp):
GAAAAAAGG
Found at i:2807383 original size:32 final size:32
Alignment explanation
Indices: 2807347--2807409 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2807337 GTCAGACACA
2807347 AGAAGTATCTCTATC-AGATGAGCATAACAACG
1 AGAAGTATCTCTA-CAAGATGAGCATAACAACG
2807379 AGAAGTATCTCTACAAGATGAGCATAACAAC
1 AGAAGTATCTCTACAAGATGAGCATAACAAC
2807410 CATTTCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.03
32 29 0.97
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:2809763 original size:76 final size:75
Alignment explanation
Indices: 2809670--2809916 Score: 309
Period size: 75 Copynumber: 3.3 Consensus size: 75
2809660 TAACAAGAAG
* * * *
2809670 CAAATGTTGGGGTATGCTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCTTGAATG
1 CAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATTTTGAACG
** *
2809735 TTTATATCAT
66 TTCGTATCAA
* * * *
2809745 CAAAATGCTGGGGCATGCTGAAAGCCCCTTTT-AATAAGAATGAAGAATGTTGATGTATTTTGAA
1 C-AAATGTTGGGGCATGCTGAAA-ACCCTTTTCAATCAGAATCAAGAATGTTGATGTATTTTGAA
2809809 CGTTCGTATCAA
64 CGTTCGTATCAA
* * *
2809821 CAATTGATGGGGCATGCTG-AAAGCCTATTTCAATCAGAATCAAGAATGTTGATGTATTTTGAAC
1 CAAATGTTGGGGCATGCTGAAAACCCT-TTTCAATCAGAATCAAGAATGTTGATGTATTTTGAAC
*
2809885 GTTCGTATCAG
65 GTTCGTATCAA
*
2809896 CAATTGTTGGGGCATGCTGAA
1 CAAATGTTGGGGCATGCTGAA
2809917 GGCCCATATC
Statistics
Matches: 148, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
73 3 0.02
74 5 0.03
75 76 0.51
76 57 0.39
77 7 0.05
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (75 bp):
CAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATTTTGAACG
TTCGTATCAA
Found at i:2811857 original size:113 final size:113
Alignment explanation
Indices: 2811642--2812549 Score: 1127
Period size: 113 Copynumber: 8.0 Consensus size: 113
2811632 TAGCAAAGAT
* * *
2811642 TCAAATCCATCAC--AATGGATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* *
2811704 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTTTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
2811753 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCGTCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
2811818 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACATTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
2811866 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
2811931 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
** * * * *
2811979 TTGAATTCATCATTTGATGGATCAGCATTACCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* * * * *
2812043 AAGAAGGAAGAATAAATTCATAATGAGAAGAATTTATTTAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * * * *
2812092 TCGAATTCATCACTCGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTAA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
2812157 AGAA-GAAAAATAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * **
2812204 AT-GACTCTATCACAGAAGGATATATATCATCATCAGCATTTCC--AG-AAGTTCATAATGAGAA
1 -TCAAATCCATCAC-------T-T-GAT--GGATCAGCATTTCCAGAGAAAGTTCATAATGAGAA
*
2812265 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
2812325 TCAAATCCATCACTTGATGGATCCGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
2812390 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
** * * * *
2812438 TTGAATTCATCATTTGATGGATCAGCATTGCCA-A-AAGTGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTG
*
2812501 AAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
2812550 ATAACTCTAT
Statistics
Matches: 694, Mismatches: 80, Indels: 45
0.85 0.10 0.05
Matches are distributed among these distances:
110 11 0.02
111 15 0.02
112 121 0.17
113 452 0.65
114 3 0.00
119 1 0.00
120 31 0.04
121 51 0.07
123 9 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:2812393 original size:346 final size:347
Alignment explanation
Indices: 2811642--2812636 Score: 1346
Period size: 346 Copynumber: 2.9 Consensus size: 347
2811632 TAGCAAAGAT
* *
2811642 TCAAATCCATCAC--AATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* * *
2811705 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTTTTCAACCTTTTGCTCAAATCCATCACTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGA-ATTTTTCAACCTTTTGCTCGAATTCATCACTTGA
* *
2811770 TGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCGTCTGAAGAAGGAAGAAGAAGTT
130 TGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * * * * **
2811835 CATAATGAGAAGAGCTTGTTCAACATTTTGC-TCAAATCCATCAC-------T-T-GAT--GGAT
195 CATAATGAGAAGAACTTGTTCAACCTTTTGCAT-AACTCTATCACAGAAGGATATATATCATCAT
*
2811888 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
259 CAGCATTTCC--AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
* *
2811953 TGAGAAGAATTTGTTCAACCTTTTGT
322 TGAGAAGAACTTGTTCAACCTTTTGC
** * * *
2811979 TTGAATTCATCATTTGATGGATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* * * *
2812044 AGAAGGAAGAATAAATTCATAATGAGAAGAATTTATTTAACCTTTTGCTCGAATTCATCACTCGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT-TTCAACCTTTTGCTCGAATTCATCACTTGA
* * * * * *
2812109 TGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTAAAGAA-GAAAAATAAGTT
130 TGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* *
2812173 CATAATAAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGATATATATCATCATC
195 CATAATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGATATATATCATCATC
2812238 AGCATTTCCAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
260 AGCATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
2812302 GAAGAGCTTGTTCAACCTTTTGC
325 GAAGAACTTGTTCAACCTTTTGC
* *
2812325 TCAAATCCATCACTTGATGGATCCGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
* * * *
2812389 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT-TTCAACCTTTTGCTCGAATTCATCACTTG
* * * *
2812454 ATGGATCAGCATTGCCA-A-AAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAG
129 ATGGATCAGCTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
*
2812517 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATATATCATCA
193 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGATATATATCATCA
2812582 TCAGCATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAG
258 TCAGCATTTCCAGAA--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
2812637 TTCATAAGGA
Statistics
Matches: 573, Mismatches: 64, Indels: 31
0.86 0.10 0.05
Matches are distributed among these distances:
337 9 0.02
338 49 0.09
339 148 0.26
344 2 0.00
345 30 0.05
346 280 0.49
347 6 0.01
348 7 0.01
349 42 0.07
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (347 bp):
TCAAATCCATCACTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTTTCAACCTTTTGCTCGAATTCATCACTTGAT
GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGATATATATCATCATCA
GCATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTTTGC
Found at i:2812689 original size:120 final size:123
Alignment explanation
Indices: 2812458--2812693 Score: 306
Period size: 120 Copynumber: 1.9 Consensus size: 123
2812448 CATTTGATGG
*
2812458 ATCAGCATTGCCAAAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATA
1 ATCAGCATTGCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATA
* * *
2812523 ATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATATATCATC
66 AGGAGAAGAACTTATTCAACCTTTTGCATAACTCTATCACAAAAGGAGATATATCATC
* *
2812581 ATCAGCATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-A-A-GAAGTTCAT
1 ATCAGCATTGCCA-AAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCAT
* * *
2812642 AAGGAGGAGAATTTATTC-ACCTTTTTGC-TAGATTAC-ATCACAAAAGGAGATA
65 AAGGAGAAGAACTTATTCAACC-TTTTGCATA-ACT-CTATCACAAAAGGAGATA
2812694 AATTGTCATC
Statistics
Matches: 100, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
119 5 0.05
120 46 0.46
121 2 0.02
122 1 0.01
123 13 0.13
124 33 0.33
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (123 bp):
ATCAGCATTGCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATA
AGGAGAAGAACTTATTCAACCTTTTGCATAACTCTATCACAAAAGGAGATATATCATC
Found at i:2812703 original size:120 final size:123
Alignment explanation
Indices: 2812458--2812734 Score: 304
Period size: 120 Copynumber: 2.3 Consensus size: 123
2812448 CATTTGATGG
*
2812458 ATCAGCATTGCCAAAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATA
1 ATCAGCATTGCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATA
* * * *
2812523 ATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATATATCATC
66 AGGAGAAGAACTTATTCAACCTTTTGCATAACTCTATCACAAAAGGAGATAAATCATC
* *
2812581 ATCAGCATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-A-A-GAAGTTCAT
1 ATCAGCATTGCCA-AAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCAT
* * * **
2812642 AAGGAGGAGAATTTATTC-ACCTTTTTGC-TAGATTAC-ATCACAAAAGGAGATAAATTGTC
65 AAGGAGAAGAACTTATTCAACC-TTTTGCATA-ACT-CTATCACAAAAGGAGATAAATCATC
** * *
2812701 ATCCCCAGTG--GAAA-AGTTCATAATGAGAAGAACT
1 ATCAGCATTGCCAAAAGAGTTCATAATGAGAAGAACT
2812735 AATCCCAAAG
Statistics
Matches: 132, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
116 20 0.15
117 2 0.02
119 5 0.04
120 56 0.42
121 2 0.02
122 1 0.01
123 13 0.10
124 33 0.25
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (123 bp):
ATCAGCATTGCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATA
AGGAGAAGAACTTATTCAACCTTTTGCATAACTCTATCACAAAAGGAGATAAATCATC
Found at i:2812748 original size:346 final size:340
Alignment explanation
Indices: 2811678--2812752 Score: 923
Period size: 346 Copynumber: 3.1 Consensus size: 340
2811668 TTCCAGGTAG
* * * *
2811678 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTT-TT
1 AGTTCATAATGAGAAGAACTAATC---ACAA-GAAGAAGAAGTTCATAATAAGAAGA-ATTTATT
* * * * * * *
2811742 CAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAG
61 CAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAG
* * * * * * *
2811807 AACTCGTCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACATTTTGC-TCAAA
126 AACTCATCTAAAGAA-GAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCAT-AAC
* ** *
2811871 TCCATCAC---------T-TGAT--GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
189 TCTATCACAGAAGGAGATAT-ATCATCATCAGCATTTCC--AG-AAGTTCATAATGAGAAGAACT
* * * * ** *
2811924 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCAT
250 CATCT--AGAAGGAAGAAGAAGTTCATAAGGAGAAGAACTTATTCAACCTTTTGCTCAAATACAT
**** * * ** *
2811989 CATTTGATGGATCAGCATTACCAG-GTAG
313 CACAAAAGGGATCCGCATCCCCAGAG-AA
* * * * * *
2812017 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAATTTATTT
1 AGTTCATAATGAGAAGAACTAATC---ACAA-GAAGAAGAAGTTCATAATAAGAAGAATTTATTC
* * *
2812082 AACCTTTTGCTCGAATTCATCACTCGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
62 AACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGA
* * *
2812147 ACTTATCTAAAGAAGAAAAATAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATGACTCT
127 ACTCATCTAAAGAAGAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATAACTCT
*
2812212 ATCACAGAAGGATATATATCATCATCAGCATTTCCAGAAGTTCATAATGAGAAGAACTCATCTGA
192 ATCACAGAAGGAGATATATCATCATCAGCATTTCCAGAAGTTCATAATGAGAAGAACTCATCT--
* * * * ***
2812277 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGA
255 AGAAGGAAGAAGAAGTTCATAAGGAGAAGAACTTATTCAACCTTTTGCTCAAATACATCACAAAA
* **
2812342 TGGATCCGCATTTCCAGAGAA
320 GGGATCCGCATCCCCAGAGAA
* * *
2812363 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTAATC---ACAA-GAAGAAGAAGTTCATAATAAGAAGAATTTATTC
* * * * * *
2812428 AACCTTTTGTTTGAATTCATCATTTGATGGATCAGCATTGCCA-A-AAGTGTTCATAATGAGAAG
62 AACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGAGAA-AGTTCATAATGAGAAG
* * * *
2812491 AACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATAACT
126 AACTCATCTAAAGAA-GAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATAACT
2812556 CTATCACAGAAGGAGATATATCATCATCAGCATTTCCAGAAGGAGTTCATAATGAGAAGAACTCA
190 CTATCACAGAAGGAGATATATCATCATCAGCATTTCCAG-A--AGTTCATAATGAGAAGAACTCA
* * *
2812621 TCT-GAA-GAAGAAGAAGTTCATAAGGAGGAGAATTTATTC-ACCTTTTTGCT-AGATTACATCA
252 TCTAGAAGGAAGAAGAAGTTCATAAGGAGAAGAACTTATTCAACC-TTTTGCTCA-AATACATCA
** *
2812682 CAAAAGGAGATAAATTGTCATCCCCAGTGGAAA
315 CAAAAGG-GAT---CCG-CATCCCCAG-AG-AA
*
2812715 AGTTCATAATGAGAAGAACTAATCCCAAAGAAGAAGAA
1 AGTTCATAATGAGAAGAACTAATCAC-AAGAAGAAGAA
2812753 CTTGTTCAAT
Statistics
Matches: 631, Mismatches: 75, Indels: 50
0.83 0.10 0.07
Matches are distributed among these distances:
338 49 0.08
339 128 0.20
344 6 0.01
345 74 0.12
346 285 0.45
347 7 0.01
348 1 0.00
349 46 0.07
350 9 0.01
351 1 0.00
352 25 0.04
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (340 bp):
AGTTCATAATGAGAAGAACTAATCACAAGAAGAAGAAGTTCATAATAAGAAGAATTTATTCAACC
TTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTC
ATCTAAAGAAGAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCA
CAGAAGGAGATATATCATCATCAGCATTTCCAGAAGTTCATAATGAGAAGAACTCATCTAGAAGG
AAGAAGAAGTTCATAAGGAGAAGAACTTATTCAACCTTTTGCTCAAATACATCACAAAAGGGATC
CGCATCCCCAGAGAA
Found at i:2812748 original size:459 final size:452
Alignment explanation
Indices: 2811823--2812752 Score: 1194
Period size: 459 Copynumber: 2.0 Consensus size: 452
2811813 TCTGAAGAAG
2811823 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACATTTTGCTCAAATCCATCACTTGATGGAT
1 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACATTTTGCTCAAATCCATCACTTGATGGAT
*
2811888 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
66 CAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
* **
2811953 TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAGCATTACCAGGTAGA
131 TAAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAGCATTACCAGAAAGA
* * *
2812018 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAATTTATTTA
196 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTATTCA
* * *
2812083 ACCTTTTGCTCGAATTCATCACTCGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA
261 ACCTTTTGCTC-AACTCATCACTAGAGGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA
* * * *
2812148 CTTATCTAAAGAAGAAAAATAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATGACTCTA
325 CTCATCT--AGAAGAAAAAGAAGTTCATAAGAAGAAGAACTTATTCAACCTTTTGCATGACTCTA
* * * * * * *
2812213 TCACAGAAGGATATATATCATCATCAGCATTTCCAGAAGTTCATAATGAGAAGAACTCATCTGAA
388 TCACAAAAGGAGATAAATCATCATCACCATGTCCAAAAGTTCATAATGAGAAGAACTAATC---A
*
2812278 GAA
450 CAA
*
2812281 GGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGA
1 -GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACATTTTGCTCAAATCCATCACTTGATGGA
*
2812346 TCCGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
65 TCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
2812411 ATAAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAGCATTGCCA-AAAG
130 ATAAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAGCATTACCAGAAAG
* * * *
2812475 TGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTC
195 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTATTC
*
2812540 AACCTTTTGCAT-AACTCTATCAC-AGAAGGAGATATATCATCATCAGCATTTCCAGA-AGGAGT
260 AACCTTTTGC-TCAACTC-ATCACTAG-AGG-GAT-TA--A-C-T-----TTTCCAGAGA-AAGT
* * * *
2812602 TCATAATGAGAAGAACTCATCT-GAAGAAGAAGAAGTTCATAAGGAGGAGAATTTATTC-ACCTT
310 TCATAATGAGAAGAACTCATCTAGAAGAAAAAGAAGTTCATAAGAAGAAGAACTTATTCAACC-T
* ** * **
2812665 TTTGC-TAGATTAC-ATCACAAAAGGAGATAAATTGTCATCCCCA-GTGGAAAAGTTCATAATGA
374 TTTGCAT-GACT-CTATCACAAAAGGAGATAAATCATCATCACCATGTCCAAAAGTTCATAATGA
*
2812727 GAAGAACTAATCCCAAA
437 GAAGAACTAATCAC-AA
2812744 GAAGAAGAA
1 GAAGAAGAA
2812753 CTTGTTCAAT
Statistics
Matches: 411, Mismatches: 41, Indels: 35
0.84 0.08 0.07
Matches are distributed among these distances:
457 5 0.01
458 77 0.19
459 188 0.46
460 2 0.00
462 10 0.02
463 3 0.01
464 1 0.00
465 30 0.07
466 61 0.15
467 1 0.00
468 1 0.00
469 32 0.08
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (452 bp):
GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACATTTTGCTCAAATCCATCACTTGATGGAT
CAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
TAAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAGCATTACCAGAAAGA
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTATTCA
ACCTTTTGCTCAACTCATCACTAGAGGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
TCATCTAGAAGAAAAAGAAGTTCATAAGAAGAAGAACTTATTCAACCTTTTGCATGACTCTATCA
CAAAAGGAGATAAATCATCATCACCATGTCCAAAAGTTCATAATGAGAAGAACTAATCACAA
Found at i:2812912 original size:18 final size:18
Alignment explanation
Indices: 2812891--2812928 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2812881 ATTTCATTTG
2812891 TTTT-ATTTATTATTATTA
1 TTTTGATTTATTA-TATTA
*
2812909 TTTTGTTTTATTATATTA
1 TTTTGATTTATTATATTA
2812927 TT
1 TT
2812929 ATATCATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTGATTTATTATATTA
Found at i:2814298 original size:2 final size:2
Alignment explanation
Indices: 2814291--2814316 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2814281 TATTATTATT
2814291 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
2814317 ATAAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2814518 original size:20 final size:19
Alignment explanation
Indices: 2814493--2814534 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2814483 CTATTTTATA
2814493 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
2814513 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
2814532 AAT
1 AAT
2814535 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:2814618 original size:116 final size:114
Alignment explanation
Indices: 2814395--2814606 Score: 268
Period size: 115 Copynumber: 1.9 Consensus size: 114
2814385 AATAATCATA
* *
2814395 TTTTAATATATATTTATTTTTCAATATTAAGAAAAGGACTGTCTTAAAGCATCTAGAAGTCCGTT
1 TTTTAATATATATTTATTTTTCAATATGAAGAAAAGGACTGTCTTAAAGCACCTAGAAGTCCGTT
* * ** *
2814460 TTATGATATTTTTACTAAATATCCTATTTTATAAATTATATATTAATTG
66 TTATGATATTTTAAATAAATATAATATTTTATAAATAATATATTAATTG
* * *
2814509 TTTTAATTATTTATTTATTTTTTAATATCGAAGAAAA-GAGCTGTCTTAAGGCACCTAGAAGTCC
1 TTTTAA-TATATATTTATTTTTCAATAT-GAAGAAAAGGA-CTGTCTTAAAGCACCTAGAAGTCC
*
2814573 -TTTTCTGATATTTCTAAATAAATA-AATATTTTAT
63 GTTTTATGATATTT-TAAATAAATATAATATTTTAT
2814607 TTATAAATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
114 6 0.07
115 41 0.49
116 37 0.44
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.46
Consensus pattern (114 bp):
TTTTAATATATATTTATTTTTCAATATGAAGAAAAGGACTGTCTTAAAGCACCTAGAAGTCCGTT
TTATGATATTTTAAATAAATATAATATTTTATAAATAATATATTAATTG
Found at i:2814623 original size:29 final size:30
Alignment explanation
Indices: 2814590--2814647 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2814580 ATATTTCTAA
2814590 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTTATTTCATAAATATAT
* * *
2814619 ATAAATTAATATTTTTTTTCATAATTATA
1 ATAAATAAATATTTTATTTCATAAATATA
2814648 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATAAATAAATATTTTATTTCATAAATATAT
Found at i:2819658 original size:24 final size:24
Alignment explanation
Indices: 2819631--2819718 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 24
2819621 GATATCTGAA
*
2819631 ATCAAAACAGAATTCAGAACATAT
1 ATCAAAACAAAATTCAGAACATAT
* * * *
2819655 ATCATAACAAAATCCAGATA-AGAA
1 ATCAAAACAAAATTCAGA-ACATAT
* * ** *
2819679 ATCAGAACATAATTCAGGTCATGT
1 ATCAAAACAAAATTCAGAACATAT
2819703 ATCAAAACAAAATTCA
1 ATCAAAACAAAATTCA
2819719 AGTCGAAAAT
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
24 46 0.98
25 1 0.02
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATTCAGAACATAT
Found at i:2827895 original size:21 final size:21
Alignment explanation
Indices: 2827869--2827916 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2827859 TATGTTGATG
*
2827869 ACATGCTTGTTGTAGGTTCAA
1 ACATGCTTGTTGCAGGTTCAA
*
2827890 ACATGCTTGTTGCAGGTTCAG
1 ACATGCTTGTTGCAGGTTCAA
2827911 ACATGC
1 ACATGC
2827917 AAGAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (21 bp):
ACATGCTTGTTGCAGGTTCAA
Found at i:2831115 original size:12 final size:12
Alignment explanation
Indices: 2831084--2831128 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2831074 CTTTCTTAAT
2831084 ATTTAAAAACATA
1 ATTTAAAAA-ATA
2831097 A-TT--AAAATA
1 ATTTAAAAAATA
2831106 ATTTAAAAAATA
1 ATTTAAAAAATA
*
2831118 ATTTATAAAAT
1 ATTTAAAAAAT
2831129 TTATAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
9 4 0.14
10 5 0.18
12 18 0.64
13 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
ATTTAAAAAATA
Found at i:2831129 original size:21 final size:21
Alignment explanation
Indices: 2831084--2831137 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
2831074 CTTTCTTAAT
2831084 ATTTAAAAACATAATTAAAATA
1 ATTTAAAAA-ATAATTAAAATA
*
2831106 ATTTAAAAAATAATTTATAA-A
1 ATTTAAAAAATAA-TTAAAATA
2831127 ATTTATAAAAA
1 ATTTA-AAAAA
2831138 GGATTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTTAAAAAATAATTAAAATA
Found at i:2832846 original size:138 final size:139
Alignment explanation
Indices: 2832623--2832947 Score: 431
Period size: 138 Copynumber: 2.3 Consensus size: 139
2832613 CTAGAAAAAA
* * *
2832623 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACGTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * *
2832688 CTCCTTCTGGAAATGCTGATCTTCAAAAGAGGGAT-TT-GTTGATTCAACTCCATATGTGATGAA
66 CTCCTTCTGAAAATACTGATCCTCAAAAGA-GGATCTTCGTTCATTCAACTCCATAGGAGATGAA
* *
2832751 TTAAGGTAAG
130 TCAAGGCAAG
*
2832761 GTTGAACAAATTCTTCTTATTATGAACGTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACGTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
2832826 CTTCC-TCTGAAAATATTGATCCTCAAATGAGGTTCTTCTTTCATTCAATTCCATAGGAGATGAA
66 C-TCCTTCTGAAAATACTGATCCTCAAAAGAGGATCTTCGTTCATTCAACTCCATAGGAGATGAA
*
2832890 TCAATGCAAG
130 TCAAGGCAAG
* *
2832900 GTTGAACAAGTTCTTCTCATTATGAACGTTTTCTTCCTCTTCAGATGA
1 GTTGAACAAATTCTTCTCATTATGAACGTCTTCTTCCTCTTCAGATGA
2832948 ACTTCACCTG
Statistics
Matches: 163, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
137 3 0.02
138 84 0.52
139 76 0.47
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (139 bp):
GTTGAACAAATTCTTCTCATTATGAACGTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTCCTTCTGAAAATACTGATCCTCAAAAGAGGATCTTCGTTCATTCAACTCCATAGGAGATGAAT
CAAGGCAAG
Found at i:2833502 original size:74 final size:73
Alignment explanation
Indices: 2833370--2833543 Score: 258
Period size: 74 Copynumber: 2.4 Consensus size: 73
2833360 GAGGTCTTAT
* * *
2833370 CATCTTGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGACTT
1 CATCATGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCCCCCGAAGAC-T
*
2833435 TTTTGAAAA
65 TTTTAAAAA
* * * *
2833444 CATCATGCATTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAATAAGCCCCCGAAGGCTT
1 CATCATGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCCCCCGAAGACTT
2833509 TTTAAAAA
66 TTTAAAAA
*
2833517 CATCATGCACTGGAGGGCTTACAGATG
1 CATCATGCACTGTAGGGCTTACAGATG
2833544 TGGGAAATAG
Statistics
Matches: 89, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
73 33 0.37
74 56 0.63
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (73 bp):
CATCATGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCCCCCGAAGACTT
TTTAAAAA
Found at i:2834702 original size:53 final size:54
Alignment explanation
Indices: 2834607--2834763 Score: 192
Period size: 54 Copynumber: 2.9 Consensus size: 54
2834597 TAACTAGTTC
* * * * * * *
2834607 GTAAAACATTTGATAACATATTCATCATCTCATATGGTTTCTGC-TCAGATGTTT
1 GTAAAACATTTGACAACACATTCATCCTTTTATGTGGATTCTGCAT-AGATGTTT
2834661 GTAAAA-ATTTGACAACACATTCATCCTTTTATGTGGATTCTGCATAGATGTTT
1 GTAAAACATTTGACAACACATTCATCCTTTTATGTGGATTCTGCATAGATGTTT
* * * *
2834714 GTAAAACATTTGGCAATACATTCATCCATTTCTGTGGATTCTGCATAGAT
1 GTAAAACATTTGACAACACATTCATCCTTTTATGTGGATTCTGCATAGAT
2834764 TTATGATCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 44 0.49
54 46 0.51
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCCTTTTATGTGGATTCTGCATAGATGTTT
Found at i:2838836 original size:7 final size:7
Alignment explanation
Indices: 2838824--2838878 Score: 65
Period size: 7 Copynumber: 7.6 Consensus size: 7
2838814 CTTGATTCAA
2838824 TTTTTCT
1 TTTTTCT
2838831 TTTTTCT
1 TTTTTCT
2838838 TTTTTCCT
1 TTTTT-CT
*
2838846 TTTTCCT
1 TTTTTCT
*
2838853 TTTTCCT
1 TTTTTCT
*
2838860 TTTTCCTT
1 TTTTTC-T
2838868 TTTTTCT
1 TTTTTCT
2838875 TTTT
1 TTTT
2838879 ATGACTTCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
7 32 0.73
8 12 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:2838843 original size:14 final size:14
Alignment explanation
Indices: 2838824--2838878 Score: 74
Period size: 15 Copynumber: 3.8 Consensus size: 14
2838814 CTTGATTCAA
*
2838824 TTTTTCTTTTTTCT
1 TTTTTCTTTTTCCT
2838838 TTTTTCCTTTTTCCT
1 TTTTT-CTTTTTCCT
*
2838853 TTTTCCTTTTTCCTT
1 TTTTTCTTTTTCC-T
2838868 TTTTTCTTTTT
1 TTTTTCTTTTT
2838879 ATGACTTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.36
15 23 0.64
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTTCCT
Found at i:2838848 original size:21 final size:21
Alignment explanation
Indices: 2838824--2838870 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2838814 CTTGATTCAA
* *
2838824 TTTTTCTTTTTTCTTTTTTCC
1 TTTTTCCTTTTTCCTTTTTCC
2838845 TTTTTCCTTTTTCCTTTTTCC
1 TTTTTCCTTTTTCCTTTTTCC
2838866 TTTTT
1 TTTTT
2838871 TTCTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTCCTTTTTCCTTTTTCC
Found at i:2841610 original size:30 final size:30
Alignment explanation
Indices: 2841576--2841638 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2841566 GCTTATGGGT
*
2841576 CATATTGCTTGTCTGGACTACAACTTCTTC
1 CATATTGCTTATCTGGACTACAACTTCTTC
*
2841606 CATATTGCTTATCTGGACTGCAACTTCTTC
1 CATATTGCTTATCTGGACTACAACTTCTTC
2841636 CAT
1 CAT
2841639 GACATTCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.40
Consensus pattern (30 bp):
CATATTGCTTATCTGGACTACAACTTCTTC
Found at i:2842963 original size:28 final size:26
Alignment explanation
Indices: 2842908--2842965 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
2842898 AAGCATTAAT
*
2842908 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
2842934 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
2842962 AAAA
1 AAAA
2842966 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:2843699 original size:11 final size:11
Alignment explanation
Indices: 2843685--2843718 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2843675 AACATAATTA
2843685 AAATAATTTAT
1 AAATAATTTAT
2843696 AAATAATTTAT
1 AAATAATTTAT
2843707 -AA-AATTTAT
1 AAATAATTTAT
2843716 AAA
1 AAA
2843719 AAGGATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.32
10 4 0.18
11 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAATAATTTAT
Found at i:2843703 original size:20 final size:20
Alignment explanation
Indices: 2843678--2843718 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2843668 ATTTAAAAAC
2843678 ATAA-TTAAAATAATTTATAA
1 ATAATTTAAAA-AATTTATAA
*
2843698 ATAATTTATAAAATTTATAA
1 ATAATTTAAAAAATTTATAA
2843718 A
1 A
2843719 AAGGATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAATTTAAAAAATTTATAA
Found at i:2844861 original size:16 final size:16
Alignment explanation
Indices: 2844840--2844870 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2844830 ATAAATAAAT
2844840 GAACATAAACGAACAC
1 GAACATAAACGAACAC
2844856 GAACATAAACGAACA
1 GAACATAAACGAACA
2844871 AAATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:2844952 original size:10 final size:10
Alignment explanation
Indices: 2844937--2845011 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
2844927 ATTTAATAAA
2844937 ATAAACGAAC
1 ATAAACGAAC
2844947 ATAAACGAAC
1 ATAAACGAAC
2844957 ----ACGAAC
1 ATAAACGAAC
*
2844963 ATAAACAAAC
1 ATAAACGAAC
** *
2844973 ACGAAC-ATAA
1 ATAAACGA-AC
2844983 ATGAACACGAAC
1 AT-AA-ACGAAC
2844995 ATAAACGAAC
1 ATAAACGAAC
2845005 ATAAACG
1 ATAAACG
2845012 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2844962 original size:16 final size:16
Alignment explanation
Indices: 2844941--2845005 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
2844931 AATAAAATAA
2844941 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2844957 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
2844973 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2844989 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2845005 A
1 A
2845006 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2845227 original size:12 final size:12
Alignment explanation
Indices: 2845210--2845240 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2845200 TATTGATTCA
2845210 AGCTCGATTCCG
1 AGCTCGATTCCG
2845222 AGCTCGATTCCG
1 AGCTCGATTCCG
2845234 AGCTCGA
1 AGCTCGA
2845241 CATTGCCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (12 bp):
AGCTCGATTCCG
Found at i:2846131 original size:14 final size:14
Alignment explanation
Indices: 2846114--2846166 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
2846104 GAACATAAAT
2846114 GAACATAACCGAAC
1 GAACATAACCGAAC
2846128 GAACAT-A---AAC
1 GAACATAACCGAAC
2846138 GAACATAACCGAAC
1 GAACATAACCGAAC
2846152 GAACATAACCGAAC
1 GAACATAACCGAAC
2846166 G
1 G
2846167 TTCACGAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.51, C:0.26, G:0.15, T:0.08
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:2846176 original size:24 final size:24
Alignment explanation
Indices: 2846104--2846165 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
2846094 ATAAATGAAT
*
2846104 GAACATAAATGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
2846128 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
2846152 GAACATAACCGAAC
1 GAACATAAACGAAC
2846166 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.24, G:0.13, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:2860311 original size:24 final size:24
Alignment explanation
Indices: 2860284--2860356 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
2860274 CGTTCATTTA
2860284 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
2860308 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * *
2860332 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
2860356 C
1 C
2860357 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.10, C:0.15, G:0.26, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:2860313 original size:14 final size:14
Alignment explanation
Indices: 2860294--2860349 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
2860284 CGTTCGTGAA
2860294 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2860308 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2860322 CG-T---TTATGTT
1 CGTTCGGTTATGTT
2860332 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2860346 CGTT
1 CGTT
2860350 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:2860369 original size:24 final size:24
Alignment explanation
Indices: 2860295--2860356 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
2860285 GTTCGTGAAC
*
2860295 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
2860319 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
2860343 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
2860357 ATTCATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:2861407 original size:16 final size:16
Alignment explanation
Indices: 2861386--2861430 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
2861376 GGGTCTCCAA
2861386 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
2861402 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
2861418 CGTTTATGTTCGT
1 CGTTTATGTTCGT
2861431 TTATTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.07, C:0.13, G:0.24, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:2861521 original size:16 final size:16
Alignment explanation
Indices: 2861500--2861532 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2861490 AAAAAAATTT
2861500 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2861516 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2861532 T
1 T
2861533 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2865049 original size:17 final size:19
Alignment explanation
Indices: 2865016--2865050 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2865006 GTTTGAGTTA
2865016 AATTTATAATATAATAATT
1 AATTTATAATATAATAATT
2865035 AATTTA-AAT-TAATAAT
1 AATTTATAATATAATAAT
2865051 CATTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTTATAATATAATAATT
Found at i:2873280 original size:19 final size:19
Alignment explanation
Indices: 2873253--2873290 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2873243 AAAACGAATA
*
2873253 TTTTTGGCTTGAGTTTTAC
1 TTTTCGGCTTGAGTTTTAC
2873272 TTTTCGGCTTGAGTTTTAC
1 TTTTCGGCTTGAGTTTTAC
2873291 GGCCCTGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.13, G:0.21, T:0.55
Consensus pattern (19 bp):
TTTTCGGCTTGAGTTTTAC
Found at i:2881404 original size:16 final size:17
Alignment explanation
Indices: 2881376--2881410 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2881366 CGTATCGCCG
2881376 ACAAAATTTTACTATTC
1 ACAAAATTTTACTATTC
2881393 ACAAAA-TTTACTATTC
1 ACAAAATTTTACTATTC
2881409 AC
1 AC
2881411 GTGAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (17 bp):
ACAAAATTTTACTATTC
Found at i:2883781 original size:24 final size:24
Alignment explanation
Indices: 2883735--2883781 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2883725 TCGAATACCT
*
2883735 AAAAATATCTTTTAAAAATAAATA
1 AAAAATATCTTTTAAAAACAAATA
*
2883759 AAAAATTAT-TTTTAAAGACAAAT
1 AAAAA-TATCTTTTAAAAACAAAT
2883782 TGGTCTGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (24 bp):
AAAAATATCTTTTAAAAACAAATA
Found at i:2884340 original size:2 final size:2
Alignment explanation
Indices: 2884333--2884389 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2884323 TGATAGGAGC
2884333 AT AT AT AT 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 AT AT AT AT
2884375 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2884390 AATTAGTGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2886252 original size:80 final size:80
Alignment explanation
Indices: 2886092--2887086 Score: 1116
Period size: 80 Copynumber: 12.5 Consensus size: 80
2886082 TTTGAGCTAA
* * * * * * * *
2886092 AAGTTATTCTCATTATGAACTCCTTCT-TT-GAAAATGTTGATCCATCACTTTTTGTGATTGAAT
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAG-AAATGTCGATCCAACTCCTTCTGTGATGGAAT
*
2886155 CTG-GCGAAGGTTGAAC
65 C-GAGCAAAGGTTGAAC
* * * * ** *
2886171 AAGTTCTTCTCATTATGAACTTCTTCTCTTGGAAATGTCAATCCATCTCCTTTTACGATGGAATT
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGTCGATCCAACTCCTTCTGTGATGGAATC
2886236 GAGCAAAGGTTGAAC
66 GAGCAAAGGTTGAAC
* * * * *
2886251 AAGTTTTTCTCATTATGAACTTATTTTCTTTGAAATGTTGATCCAACTCCTTCTGTGATGGAATC
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGTCGATCCAACTCCTTCTGTGATGGAATC
2886316 GAGCAAAGGTTGAAC
66 GAGCAAAGGTTGAAC
* * ** * * * *
2886331 AAGTTCTTCTCATTATAAACTTTTTCTCTCGGCAATGTTGATCCAACTCCATCTATGATGGAATC
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGTCGATCCAACTCCTTCTGTGATGGAATC
2886396 GAGCAAAGGTTGAAC
66 GAGCAAAGGTTGAAC
* * * * * *
2886411 AAGTTCTTCTCATTCTGAACTTATTCTCGT-GAAAATATCGATCCACCTCCTTATGTGATGGAAT
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAG-AAATGTCGATCCAACTCCTTCTGTGATGGAAT
*
2886475 TGAGCAAAGGTTGAAC
65 CGAGCAAAGGTTGAAC
* * * * *
2886491 AAGTTATTCTCATTACGAACTTCTTCTCTAAGAAAT-ACTAGTCCAACTCCTTCTGTGATGGAAT
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGTCGA-TCCAACTCCTTCTGTGATGGAAT
2886555 CGAGCAAAGGTTGAAC
65 CGAGCAAAGGTTGAAC
* * * * *
2886571 AAGTTCTTCTCATTATGAACTTCTTCTC-TAAAAAT-ACTGGTCCAACTCATTCTATGATGGAAT
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGTC-GATCCAACTCCTTCTGTGATGGAAT
2886634 CGAG-AAACGGTTGAAC
65 CGAGCAAA-GGTTGAAC
* * * **
2886650 AAGTTCTTCTCATTATGAACTTCTTCTCTT-GAAAATGTCGATCCACCTCCTTATGTGCTAAAAT
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAG-AAATGTCGATCCAACTCCTTCTGTGATGGAAT
* *
2886714 TGAGCAAAGGTTAAAC
65 CGAGCAAAGGTTGAAC
* * * *
2886730 AAGTTCTTCTCATTATAAACTTCTTCTCTAAGAAATGTTGGTCCAACTCCTTCTGTGATGGAATC
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGTCGATCCAACTCCTTCTGTGATGGAATC
**
2886795 GAGCAAACATTGAAC
66 GAGCAAAGGTTGAAC
* * * * *
2886810 AAGTTCTTCTCATTATGAACTTCTTCTCTAACAAATATTGGTCCAACTCCTTCTGTGATGGAATC
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGTCGATCCAACTCCTTCTGTGATGGAATC
2886875 GAGCAACA-GTTGAAC
66 GAGCAA-AGGTTGAAC
* * * * *
2886890 AAGTTCTTCTCATTATGAACTTCTTCTCTAACAAAT-ACTGGTCCAACTCCTTCTGTTATGGAAT
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGTC-GATCCAACTCCTTCTGTGATGGAAT
**
2886954 TAAGCAAAGGTTGAAC
65 CGAGCAAAGGTTGAAC
* * *
2886970 AAGTTTTTCTCATTATGAACTTCTTCTCTAAGAAATGAT-GGTCCAACTCCTTCTGTGATGGAAT
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATG-TCGATCCAACTCCTTCTGTGATGGAAT
*
2887034 CGAGAAAAGGTTGAAC
65 CGAGCAAAGGTTGAAC
* *
2887050 AAGTTCTCCTCATTATGAACTTCTTCTC-TGGAAATGT
1 AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGT
2887087 TACTCTTTAA
Statistics
Matches: 790, Mismatches: 108, Indels: 37
0.84 0.12 0.04
Matches are distributed among these distances:
78 4 0.01
79 104 0.13
80 674 0.85
81 8 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (80 bp):
AAGTTCTTCTCATTATGAACTTCTTCTCTTAGAAATGTCGATCCAACTCCTTCTGTGATGGAATC
GAGCAAAGGTTGAAC
Found at i:2886995 original size:479 final size:479
Alignment explanation
Indices: 2886163--2887078 Score: 1392
Period size: 479 Copynumber: 1.9 Consensus size: 479
2886153 ATCTGGCGAA
* * *
2886163 GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGGAAATGTCAATCCATCTCCTTTTACG
1 GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGAAAATGTCAATCCACCTCCTTATACG
** * * * * **
2886228 ATGGAATTGAGCAAAGGTTGAACAAGTTTTTCTCATTATGAACTTATTTTCTTTGAAATGTTGAT
66 ATAAAATTGAGCAAAGGTTAAACAAGTTCTTCTCATTATAAACTTATTCTCTAAGAAATGTTGAT
** *
2886293 CCAACTCCTTCTGTGATGGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATAAACTTTTTCT
131 CCAACTCCTTCTGTGATGGAATCGAGCAAACATTGAACAAGTTCTTCTCATTATAAACTTCTTCT
** *
2886358 CTCGGCAATGTTGATCCAACTCCATCTATGATGGAATCGAGCAAAGGTTGAACAAGTTCTTCTCA
196 CTCAACAATATTGATCCAACTCCATCTATGATGGAATCGAGCAAAGGTTGAACAAGTTCTTCTCA
* * * *
2886423 TTCTGAACTTATTCTCGTGAAAATATCGATCCACCTCCTTATGTGATGGAATTGAGCAAAGGTTG
261 TTATGAACTTATTCTCGTAAAAATATCGATCCAACTCCTTATGTGATGGAATTAAGCAAAGGTTG
2886488 AACAAGTTATTCTCATTACGAACTTCTTCTCTAAGAAAT-ACTAGTCCAACTCCTTCTGTGATGG
326 AACAAGTTATTCTCATTACGAACTTCTTCTCTAAGAAATGA-TAGTCCAACTCCTTCTGTGATGG
* *
2886552 AATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTAAAAATACTGGTCCAAC
390 AATCGAGAAAAGGTTGAACAAGTTCTCCTCATTATGAACTTCTTCTCTAAAAATACTGGTCCAAC
2886617 TCATTCTATGATGGAATCGAGAAAC
455 TCATTCTATGATGGAATCGAGAAAC
* **
2886642 GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGAAAATGTCGATCCACCTCCTTATGTG
1 GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGAAAATGTCAATCCACCTCCTTATACG
* * *
2886707 CTAAAATTGAGCAAAGGTTAAACAAGTTCTTCTCATTATAAACTTCTTCTCTAAGAAATGTTGGT
66 ATAAAATTGAGCAAAGGTTAAACAAGTTCTTCTCATTATAAACTTATTCTCTAAGAAATGTTGAT
*
2886772 CCAACTCCTTCTGTGATGGAATCGAGCAAACATTGAACAAGTTCTTCTCATTATGAACTTCTTCT
131 CCAACTCCTTCTGTGATGGAATCGAGCAAACATTGAACAAGTTCTTCTCATTATAAACTTCTTCT
* * *
2886837 CT-AACAAATATTGGTCCAACTCCTTCTGTGATGGAATCGAGCAACA-GTTGAACAAGTTCTTCT
196 CTCAAC-AATATTGATCCAACTCCATCTATGATGGAATCGAGCAA-AGGTTGAACAAGTTCTTCT
* * * *
2886900 CATTATGAACTTCTTCTC-TAACAAATA-CTGGTCCAACTCCTTCTGTTATGGAATTAAGCAAAG
259 CATTATGAACTTATTCTCGTAA-AAATATC-GATCCAACTCCTTATGTGATGGAATTAAGCAAAG
* * *
2886963 GTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCTAAGAAATGATGGTCCAACTCCTTCTGTGA
322 GTTGAACAAGTTATTCTCATTACGAACTTCTTCTCTAAGAAATGATAGTCCAACTCCTTCTGTGA
2887028 TGGAATCGAGAAAAGGTTGAACAAGTTCTCCTCATTATGAACTTCTTCTCT
387 TGGAATCGAGAAAAGGTTGAACAAGTTCTCCTCATTATGAACTTCTTCTCT
2887079 GGAAATGTTA
Statistics
Matches: 392, Mismatches: 40, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
478 4 0.01
479 386 0.98
480 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (479 bp):
GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGAAAATGTCAATCCACCTCCTTATACG
ATAAAATTGAGCAAAGGTTAAACAAGTTCTTCTCATTATAAACTTATTCTCTAAGAAATGTTGAT
CCAACTCCTTCTGTGATGGAATCGAGCAAACATTGAACAAGTTCTTCTCATTATAAACTTCTTCT
CTCAACAATATTGATCCAACTCCATCTATGATGGAATCGAGCAAAGGTTGAACAAGTTCTTCTCA
TTATGAACTTATTCTCGTAAAAATATCGATCCAACTCCTTATGTGATGGAATTAAGCAAAGGTTG
AACAAGTTATTCTCATTACGAACTTCTTCTCTAAGAAATGATAGTCCAACTCCTTCTGTGATGGA
ATCGAGAAAAGGTTGAACAAGTTCTCCTCATTATGAACTTCTTCTCTAAAAATACTGGTCCAACT
CATTCTATGATGGAATCGAGAAAC
Found at i:2888811 original size:3 final size:3
Alignment explanation
Indices: 2888805--2888842 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
2888795 TTTATTTATT
2888805 ATA ATA ATAA ATA ATA A-A TATA ATA ATA ATA ATA ATA A
1 ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA ATA ATA A
2888843 AATGGTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.03
3 27 0.84
4 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2889522 original size:151 final size:151
Alignment explanation
Indices: 2889242--2889536 Score: 369
Period size: 151 Copynumber: 2.0 Consensus size: 151
2889232 TTTAATTTAA
*
2889242 TCTCTTAACTTTTAATGATTTTCTAATTTCTTAAATTCATCATTTATTTTAAATCTATTTTCACC
1 TCTCTTAACTTTGAATGATTTTCTAATTTCTTAAATTCATCATTTATTTTAAATCTATTTTCACC
* *
2889307 AAATTTGAACCACATGCTCCTCTACTACTATAGAATATATATGTAACTTCAATTCCTATTTTTAA
66 AAATTTGAACCACATGCTCCTCTACCACTATAGAATATATATGTAAATTCAATTCCTATTTTTAA
*
2889372 TTATAATTTTTTTTAAATCAG
131 CTATAATTTTTTTTAAATCAG
* * * * * * *
2889393 TCTCTTAACTTTGCATGA-TTTCATCATTTCTTCAGTTCATCATTTATTTTAAGTCTATTTTTAT
1 TCTCTTAACTTTGAATGATTTTC-TAATTTCTTAAATTCATCATTTATTTTAAATCTATTTTCAC
* * * * * ** ** *
2889457 CAAATTTTAACCTCATGTTCCTCTACCACTATAGAATGTCTATG-AAATTGTATTTTTTTTATTT
65 CAAATTTGAACCACATGCTCCTCTACCACTATAGAATATATATGTAAATTCAATTCCTATT-TTT
2889521 AACTATAATTTTTTTT
129 AACTATAATTTTTTTT
2889537 CAATTTAATA
Statistics
Matches: 121, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
150 14 0.12
151 107 0.88
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (151 bp):
TCTCTTAACTTTGAATGATTTTCTAATTTCTTAAATTCATCATTTATTTTAAATCTATTTTCACC
AAATTTGAACCACATGCTCCTCTACCACTATAGAATATATATGTAAATTCAATTCCTATTTTTAA
CTATAATTTTTTTTAAATCAG
Found at i:2889542 original size:22 final size:19
Alignment explanation
Indices: 2889508--2889548 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 19
2889498 ATGAAATTGT
2889508 ATTTTTTTTATTTAACTATA
1 ATTTTTTTTATTTAA-TATA
2889528 ATTTTTTTTCAATTTAATATA
1 ATTTTTTTT--ATTTAATATA
2889549 TTAACTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTTTATTTAATATA
Found at i:2901259 original size:15 final size:15
Alignment explanation
Indices: 2901241--2901273 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2901231 GACCTTGACA
2901241 CAATCCCCTCCAATC
1 CAATCCCCTCCAATC
2901256 CAATCCCCTCCAATC
1 CAATCCCCTCCAATC
2901271 CAA
1 CAA
2901274 GTAATGGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.52, G:0.00, T:0.18
Consensus pattern (15 bp):
CAATCCCCTCCAATC
Found at i:2909415 original size:24 final size:20
Alignment explanation
Indices: 2909362--2909419 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
2909352 TTCCCCTTGA
*
2909362 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
2909382 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
2909405 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2909420 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2909494 original size:64 final size:64
Alignment explanation
Indices: 2909407--2909567 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 64
2909397 TCTTTAACAT
* *
2909407 GTGCATCGATGCACTACC-CATGCATCGATACACTAATTACCTTCAATGTTTT-CA-TTTTAAGG
1 GTGCATCGATGCACT-CCTTATGCATCGATACACTAATTACATTCAAT-TTTTCCATTTTTAA-G
2909469 GG
63 GG
* * *
2909471 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTACATTCGATTTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACTAATTACATTCAATTTTTCCATTTTTAAGGG
* *
2909535 GTGCATCGATACAC-CTCTTGTGCATCGATACAC
1 GTGCATCGATGCACTC-CTTATGCATCGATACAC
2909568 ACTGAACAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
63 7 0.08
64 72 0.85
65 6 0.07
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACTAATTACATTCAATTTTTCCATTTTTAAGGG
Found at i:2912849 original size:20 final size:21
Alignment explanation
Indices: 2912808--2912849 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
2912798 TTATCACACT
2912808 AACATATAATTCATACCTACAAC
1 AACATATAATTCATA-C-ACAAC
2912831 AACATATAATTCATA-ACAA
1 AACATATAATTCATACACAA
2912850 ACACATGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
23 15 0.79
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (21 bp):
AACATATAATTCATACACAAC
Found at i:2913174 original size:20 final size:20
Alignment explanation
Indices: 2913149--2913186 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2913139 TTCCCCTTGA
2913149 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
2913169 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
2913187 TTAACCTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:2913346 original size:64 final size:64
Alignment explanation
Indices: 2913194--2913354 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
2913184 TCTTTAACCT
* * * * *
2913194 GTGCATCGATGCACTACCCATGCACCGATACACTAATCACCTTTGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACTAATCACATTCGATGTTTTCATTTTAAGGGG
* ** *
2913258 GTGCATCGATGCAC-TCCTTATGCATCGATGCACTAATTGCATTCGATG-TTTCAATTTTTAA-T
1 GTGCATCGATGCACTTCC-TATGCATCGATACACTAATCACATTCGATGTTTTC-A-TTTTAAGG
2913320 GG
63 GG
* *
2913322 GTGCATCGATGCACTTCCTGTGCATCAATACAC
1 GTGCATCGATGCACTTCCTATGCATCGATACAC
2913355 ACTAGACAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
63 6 0.07
64 66 0.81
65 9 0.11
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTTCCTATGCATCGATACACTAATCACATTCGATGTTTTCATTTTAAGGGG
Found at i:2917234 original size:21 final size:21
Alignment explanation
Indices: 2917210--2917253 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2917200 TTCACCTTCT
2917210 TCCTCCACTTCAAATTGTTCA
1 TCCTCCACTTCAAATTGTTCA
* *
2917231 TCCTCTACTTCAACTTGTTCA
1 TCCTCCACTTCAAATTGTTCA
2917252 TC
1 TC
2917254 TTGTTCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.34, G:0.05, T:0.41
Consensus pattern (21 bp):
TCCTCCACTTCAAATTGTTCA
Found at i:2917258 original size:30 final size:30
Alignment explanation
Indices: 2917224--2917282 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2917214 CCACTTCAAA
2917224 TTGTTCATCCTCTACT-TCAACTTGTTCATC
1 TTGTTCATCCTCTACTAT-AACTTGTTCATC
2917254 TTGTTCATCCTCTACTATAACTTGTTCAT
1 TTGTTCATCCTCTACTATAACTTGTTCAT
2917283 TGTTTGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.19, C:0.27, G:0.07, T:0.47
Consensus pattern (30 bp):
TTGTTCATCCTCTACTATAACTTGTTCATC
Found at i:2918020 original size:13 final size:13
Alignment explanation
Indices: 2917963--2918027 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 13
2917953 CCTAAAACGA
*
2917963 TGTTTATAGATAT
1 TGTTTATACATAT
*
2917976 T-ATTATACATAT
1 TGTTTATACATAT
* *
2917988 TGTTTTATAGATAA
1 TG-TTTATACATAT
*
2918002 TATTTATACATAT
1 TGTTTATACATAT
*
2918015 TGTTTATATATAT
1 TGTTTATACATAT
2918028 ATATATATAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
12 10 0.25
13 21 0.52
14 9 0.22
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (13 bp):
TGTTTATACATAT
Found at i:2918026 original size:2 final size:2
Alignment explanation
Indices: 2918019--2918053 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
2918009 ACATATTGTT
2918019 TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
2918054 CTATTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2918041 original size:27 final size:26
Alignment explanation
Indices: 2917963--2918053 Score: 96
Period size: 27 Copynumber: 3.5 Consensus size: 26
2917953 CCTAAAACGA
*
2917963 TGTTTATAGATAT-TATTATACATAT
1 TGTTTATATATATATATTATACATAT
*
2917988 TGTTT-TATAGATAATATTTATACATAT
1 TGTTTATATATAT-ATA-TTATACATAT
*
2918015 TGTTTATATATATATATATATATATAT
1 TGTTTATATATATATAT-TATACATAT
* *
2918042 AGTATATATATA
1 TGTTTATATATA
2918054 CTATTTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
24 5 0.09
25 5 0.09
26 3 0.05
27 36 0.65
28 6 0.11
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (26 bp):
TGTTTATATATATATATTATACATAT
Found at i:2918382 original size:38 final size:38
Alignment explanation
Indices: 2918337--2918425 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
2918327 TTCCATGAAT
* *
2918337 AACCCTAAAAAACTCCCTCATTATGAATACATATTAAAA
1 AACCCTAAAAAACTCACTCATTATGAAT-CAGATTAAAA
* * * *
2918376 AA-CCTAAGAAAACTCATTCATTTTGAATCGGGTTAAAA
1 AACCCTAA-AAAACTCACTCATTATGAATCAGATTAAAA
2918414 AACCCTAAAAAA
1 AACCCTAAAAAA
2918426 ACCTTTCACT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
38 18 0.43
39 24 0.57
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.25
Consensus pattern (38 bp):
AACCCTAAAAAACTCACTCATTATGAATCAGATTAAAA
Found at i:2918901 original size:24 final size:23
Alignment explanation
Indices: 2918869--2918914 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
2918859 TTTTCCAAAG
2918869 TTAATAAAATGATTTTAATTCAT
1 TTAATAAAATGATTTTAATTCAT
*
2918892 TTAATTAAAATGGTTTTAATTCA
1 TTAA-TAAAATGATTTTAATTCA
2918915 CTTCATGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (23 bp):
TTAATAAAATGATTTTAATTCAT
Found at i:2927310 original size:2 final size:2
Alignment explanation
Indices: 2927303--2927340 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2927293 ACAAAATACA
2927303 AT AT 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 AT AT
2927341 GTTTACAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2927774 original size:22 final size:22
Alignment explanation
Indices: 2927749--2927820 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
2927739 CACCACAACT
2927749 CATAATTTGTACCGAAGTGCCA
1 CATAATTTGTACCGAAGTGCCA
* * * *
2927771 CATAA-TTGTCCCAAATTACCA
1 CATAATTTGTACCGAAGTGCCA
** *
2927792 CATAGGTTGCACCGAAGTGCCA
1 CATAATTTGTACCGAAGTGCCA
2927814 CATAATT
1 CATAATT
2927821 GTCCCAGATA
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
21 16 0.43
22 21 0.57
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (22 bp):
CATAATTTGTACCGAAGTGCCA
Found at i:2927792 original size:21 final size:20
Alignment explanation
Indices: 2927768--2927859 Score: 78
Period size: 21 Copynumber: 4.3 Consensus size: 20
2927758 TACCGAAGTG
2927768 CCACATAATTGTCCCAAATTA
1 CCACATAATTGTCCCAAA-TA
* * *
2927789 CCACATAGGTTG-CACCGAAGTG
1 CCACATA-ATTGTC-CC-AAATA
*
2927811 CCACATAATTGTCCCAGATA
1 CCACATAATTGTCCCAAATA
*
2927831 GCCACATAATTGTCCCAAAAGA
1 -CCACATAATTGTCCC-AAATA
2927853 CCACATA
1 CCACATA
2927860 GACCCTCGAC
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
20 2 0.04
21 35 0.62
22 17 0.30
23 2 0.04
ACGTcount: A:0.36, C:0.29, G:0.13, T:0.22
Consensus pattern (20 bp):
CCACATAATTGTCCCAAATA
Found at i:2928036 original size:20 final size:21
Alignment explanation
Indices: 2927993--2928039 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2927983 ATAGAGTATA
*
2927993 TTCATATTCACTGATTCGAAG
1 TTCATATTCACTGATTCAAAG
*
2928014 TTCATATTCACTTA-TCAAAG
1 TTCATATTCACTGATTCAAAG
2928034 TTCATA
1 TTCATA
2928040 ACACATAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (21 bp):
TTCATATTCACTGATTCAAAG
Found at i:2928462 original size:53 final size:55
Alignment explanation
Indices: 2928378--2928515 Score: 199
Period size: 54 Copynumber: 2.5 Consensus size: 55
2928368 ATAACAGGGA
* * *
2928378 GTATCGATACACTCCTCAGTGTACCGATACACAAATTGCATTCGATG-TTTGAGG
1 GTATCGATACACTCCTCAGTGTACAGATACACAAATGGAATTCGATGTTTTGAGG
* * *
2928432 GTATCGATACACTACT-AGTGTACATATACACAAATGGAATTCGATGTTTTGAGT
1 GTATCGATACACTCCTCAGTGTACAGATACACAAATGGAATTCGATGTTTTGAGG
*
2928486 GTATCGATACACTCCTCAGTGTACCGATAC
1 GTATCGATACACTCCTCAGTGTACAGATAC
2928516 CACTCATACA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
53 26 0.36
54 36 0.49
55 11 0.15
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (55 bp):
GTATCGATACACTCCTCAGTGTACAGATACACAAATGGAATTCGATGTTTTGAGG
Found at i:2932762 original size:12 final size:12
Alignment explanation
Indices: 2932745--2932778 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2932735 TTGATTTCTT
*
2932745 CCTCTTCCTTGA
1 CCTCTTCCTCGA
2932757 CCTCTTCCTCGA
1 CCTCTTCCTCGA
2932769 CCTCTTCCTC
1 CCTCTTCCTC
2932779 TTACTGGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.50, G:0.06, T:0.38
Consensus pattern (12 bp):
CCTCTTCCTCGA
Found at i:2934666 original size:22 final size:22
Alignment explanation
Indices: 2934640--2934709 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
2934630 CCACAACTCG
*
2934640 TAATTTGCACCAAAGTGCCACA
1 TAATTTGCACCGAAGTGCCACA
2934662 TAA-TTGTC-CCGAA-TGACCACA
1 TAATTTG-CACCGAAGTG-CCACA
**
2934683 TAGGTTGCACCGAAGTGCCACA
1 TAATTTGCACCGAAGTGCCACA
2934705 TAATT
1 TAATT
2934710 ATCCCGGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 2 0.05
21 15 0.38
22 20 0.51
23 2 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (22 bp):
TAATTTGCACCGAAGTGCCACA
Found at i:2934682 original size:21 final size:21
Alignment explanation
Indices: 2934657--2934748 Score: 73
Period size: 21 Copynumber: 4.3 Consensus size: 21
2934647 CACCAAAGTG
*
2934657 CCACATAATTGTCCCGAATGA
1 CCACATAATTATCCCGAATGA
* *
2934678 CCACATAGGTT-GCACCGAAGTG-
1 CCACATA-ATTATC-CCGAA-TGA
* *
2934700 CCACATAATTATCCCGGAGGA
1 CCACATAATTATCCCGAATGA
*
2934721 CCACATAATTATCCCAAAAT-A
1 CCACATAATTATCCC-GAATGA
2934742 CCACATA
1 CCACATA
2934749 GACCCTCAAC
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
20 1 0.02
21 37 0.66
22 16 0.29
23 2 0.04
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (21 bp):
CCACATAATTATCCCGAATGA
Found at i:2934705 original size:43 final size:43
Alignment explanation
Indices: 2934644--2934727 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
2934634 AACTCGTAAT
* *
2934644 TTGCACCAAAGTGCCACATAATTGTCCCGAATGACCACATAGG
1 TTGCACCAAAGTGCCACATAATTATCCCGAAGGACCACATAGG
* *
2934687 TTGCACCGAAGTGCCACATAATTATCCCGGAGGACCACATA
1 TTGCACCAAAGTGCCACATAATTATCCCGAAGGACCACATA
2934728 ATTATCCCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (43 bp):
TTGCACCAAAGTGCCACATAATTATCCCGAAGGACCACATAGG
Found at i:2935325 original size:54 final size:54
Alignment explanation
Indices: 2935215--2935326 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
2935205 AAGGGTATTC
* *
2935215 CTCAGTGTACAGATACACAAATTGCATTCGATGTTTGAGGATATCGATACACTA
1 CTCAGTGTACAGATACACAAATTGCATTCGATGTTTAAGGATAACGATACACTA
* * *
2935269 CTCAGTGTACCGATACATAAA-TGACATTCGATATTTTAAGTG-TAACGATACA-TA
1 CTCAGTGTACAGATACACAAATTG-CATTCGAT-GTTTAAG-GATAACGATACACTA
2935323 CTCA
1 CTCA
2935327 TACAATTACA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
53 2 0.04
54 33 0.66
55 14 0.28
56 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (54 bp):
CTCAGTGTACAGATACACAAATTGCATTCGATGTTTAAGGATAACGATACACTA
Found at i:2936983 original size:31 final size:31
Alignment explanation
Indices: 2936945--2937016 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
2936935 TTAAAGTCTT
* * *
2936945 AGGGACCATTATATA-GTAAATTGATAATGTC
1 AGGGACCATTATATACG-AAATAGATAACGTA
2936976 AGGGACCATTATATACGAAATAGATAACGTA
1 AGGGACCATTATATACGAAATAGATAACGTA
2937007 AGGGACCATT
1 AGGGACCATT
2937017 TACCCTTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (31 bp):
AGGGACCATTATATACGAAATAGATAACGTA
Found at i:2937649 original size:3 final size:3
Alignment explanation
Indices: 2937643--2937707 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
2937633 TTCATTTGAA
* *
2937643 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAA TAT TAT TAT TAT TA-
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2937687 TAT ATAT TAT TAT TAT TAT TA
1 TAT -TAT TAT TAT TAT TAT TA
2937708 AAAAAATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 3 0.06
3 47 0.87
4 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2937666 original size:18 final size:18
Alignment explanation
Indices: 2937643--2937706 Score: 92
Period size: 18 Copynumber: 3.4 Consensus size: 18
2937633 TTCATTTGAA
2937643 TATTATTTATATTATTAT
1 TATTATTTATATTATTAT
2937661 TATTATTATAAATATTATTAT
1 TATTATT-T--ATATTATTAT
*
2937682 TATTATATATATTATTAT
1 TATTATTTATATTATTAT
2937700 TATTATT
1 TATTATT
2937707 AAAAAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 23 0.56
19 1 0.02
20 1 0.02
21 16 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATTTATATTATTAT
Found at i:2937667 original size:21 final size:20
Alignment explanation
Indices: 2937643--2937707 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 20
2937633 TTCATTTGAA
2937643 TATTATT-TA-TATTATTAT
1 TATTATTATATTATTATTAT
*
2937661 TATTATTATAAATATTATTAT
1 TATTATTAT-ATTATTATTAT
2937682 TATTATATATATTATTATTAT
1 TATTAT-TATATTATTATTAT
2937703 TATTA
1 TATTA
2937708 AAAAAATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 7 0.17
19 1 0.02
20 1 0.02
21 30 0.71
22 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATTATATTATTATTAT
Found at i:2938996 original size:12 final size:12
Alignment explanation
Indices: 2938979--2939043 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
2938969 TTAATTCCTT
2938979 TTATTTTAATTA
1 TTATTTTAATTA
*
2938991 TTATTTGCAA-TA
1 TTATTT-TAATTA
2939003 TTATTTTATTATTA
1 TTATTTTA--ATTA
*
2939017 TTACTTTTTATTA
1 TTA-TTTTAATTA
2939030 TTATTCTT-ATTA
1 TTATT-TTAATTA
2939042 TT
1 TT
2939044 TATATAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 1 0.02
12 22 0.50
13 12 0.27
14 5 0.11
15 4 0.09
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:2939007 original size:3 final size:3
Alignment explanation
Indices: 2939001--2939043 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
2938991 TTATTTGCAA
* *
2939001 TAT TAT T-T TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
2939044 TATATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:2939027 original size:16 final size:15
Alignment explanation
Indices: 2939006--2939043 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
2938996 TGCAATATTA
2939006 TTTTATTATTATTACT
1 TTTTATTATTATT-CT
2939022 TTTTATTATTATTCT
1 TTTTATTATTATTCT
*
2939037 TATTATT
1 TTTTATT
2939044 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTATTATTCT
Found at i:2939046 original size:16 final size:15
Alignment explanation
Indices: 2939001--2939043 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 15
2938991 TTATTTGCAA
2939001 TATTATT-TTATTAT
1 TATTATTCTTATTAT
*
2939015 TATTA--CTTTTTAT
1 TATTATTCTTATTAT
2939028 TATTATTCTTATTAT
1 TATTATTCTTATTAT
2939043 T
1 T
2939044 TATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 5 0.21
15 8 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTCTTATTAT
Found at i:2939067 original size:18 final size:16
Alignment explanation
Indices: 2939044--2939078 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2939034 TCTTATTATT
2939044 TATATA-AATAAATATA
1 TATATATAATAAATA-A
2939060 TATATATAATAAATAA
1 TATATATAATAAATAA
2939076 TAT
1 TAT
2939079 TTTTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATAATAAATAA
Found at i:2939274 original size:19 final size:19
Alignment explanation
Indices: 2939227--2939276 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2939217 ATAAATATCC
2939227 TATTTTTTAAATGATATATT
1 TATTTTTT-AATGATATATT
* * * *
2939247 AATTGTTTAATTATTTATT
1 TATTTTTTAATGATATATT
2939266 TATTTTTTAAT
1 TATTTTTTAAT
2939277 ATCAAAGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TATTTTTTAATGATATATT
Found at i:2941382 original size:8 final size:7
Alignment explanation
Indices: 2941358--2941399 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2941348 TTTTCATACA
2941358 TGCA-TT
1 TGCATTT
2941364 TGCATTT
1 TGCATTT
2941371 TGCATCTT
1 TGCAT-TT
2941379 TGCATTT
1 TGCATTT
* *
2941386 TTCATTG
1 TGCATTT
2941393 TGCATTT
1 TGCATTT
2941400 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:2941382 original size:15 final size:14
Alignment explanation
Indices: 2941358--2941399 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2941348 TTTTCATACA
2941358 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
2941371 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
2941386 TTCATTGTGCATTT
1 TGCATTTTGCATTT
2941400 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:2941469 original size:12 final size:12
Alignment explanation
Indices: 2941452--2941477 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2941442 ACATTCACAT
2941452 ATTTACATTTGC
1 ATTTACATTTGC
2941464 ATTTACATTTGC
1 ATTTACATTTGC
2941476 AT
1 AT
2941478 ATTTCCATAA
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:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:2947742 original size:54 final size:54
Alignment explanation
Indices: 2947660--2947817 Score: 289
Period size: 54 Copynumber: 2.9 Consensus size: 54
2947650 AGAAATCTTG
2947660 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
2947714 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* * *
2947768 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACAAACAT
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACAT
2947818 GCTATTCTGA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (54 bp):
GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
Found at i:2948214 original size:22 final size:22
Alignment explanation
Indices: 2948183--2948237 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2948173 ATCTACACTC
2948183 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGATAGATTCCCTT
* *
2948205 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCCCTT
2948227 TTCAAAGATGA
1 TTCAAAGATGA
2948238 AAGCTTTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCCCTT
Found at i:2948835 original size:113 final size:114
Alignment explanation
Indices: 2948637--2948921 Score: 434
Period size: 113 Copynumber: 2.5 Consensus size: 114
2948627 TTAGCAAAGC
*
2948637 TCAAATCCATCACTTGATGGATCAGCATTACCAG-GTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTACCAGAGTAGAGTTCATAATGAGAAGAACTCATCTG
2948701 AAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGA
66 AAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGA
* * * *
2948750 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTACCAGAGTAGAGTTCATAATGAGAAGAACTCATCTG
*
2948814 AAGAAGGAAA-AAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGT
66 AAGAA-GAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGA
* * * * *
2948863 TTAAATTCATCATTTGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTC
1 TCAAATCCATCACTTGATGGATCAGCATTACCAGAGTAGAGTTCATAATGAGAAGAACTC
2948922 GTTATCTGAA
Statistics
Matches: 155, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
112 2 0.01
113 148 0.95
114 5 0.03
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (114 bp):
TCAAATCCATCACTTGATGGATCAGCATTACCAGAGTAGAGTTCATAATGAGAAGAACTCATCTG
AAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGA
Found at i:2949031 original size:95 final size:93
Alignment explanation
Indices: 2948847--2949035 Score: 247
Period size: 95 Copynumber: 2.0 Consensus size: 93
2948837 TGAGAAGAGC
* *
2948847 TTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAAGTAGAGTTCATAATG
1 TTGTTCAACCTTTTGTTTAAATTCATCATTCGATGGATCAACATTCCCAAGTAGAGTTCATAATG
2948912 AGAAGAACTCGTTATCTGAAAAAGAAGAAT
66 AGAAGAACTC--TATCTGAAAAAGAAGAAT
* * ** *
2948942 TTGTTTAACCTTTTGTTTGAATTCATCATTCGATGGATCATTA-TCCCCAGTGAAAGAGTTCATA
1 TTGTTCAACCTTTTGTTTAAATTCATCATTCGATGGATCAACATTCCCAAGT---AGAGTTCATA
2949006 ATGAGAAGAACTC-ATCTGAAGAAAGAAGAA
63 ATGAGAAGAACTCTATCTGAA-AAAGAAGAA
2949036 GAAGTTCATA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
94 13 0.16
95 47 0.57
97 23 0.28
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (93 bp):
TTGTTCAACCTTTTGTTTAAATTCATCATTCGATGGATCAACATTCCCAAGTAGAGTTCATAATG
AGAAGAACTCTATCTGAAAAAGAAGAAT
Found at i:2949147 original size:113 final size:113
Alignment explanation
Indices: 2948934--2949652 Score: 889
Period size: 113 Copynumber: 6.3 Consensus size: 113
2948924 TATCTGAAAA
* * * *
2948934 AGAAGAATTTGTTTAACCTTTTGTTTGAATTCATCA-TTCGATGGATCA--TTATCCCCAGTGAA
1 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTT-GATGGATCAGCTT-T-GCCA--GAA
*
2948996 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
61 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
** * * *
2949049 AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCTTTGCCAGAAAGAGT
*
2949114 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * * **
2949162 AGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTTAATGGATCAGCATCCCCAGTGAAAGA
1 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCTTTGCCA--GAAAGA
2949227 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
64 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* ***
2949277 AGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATCATTTGATGGATCAG-TATTGCCAGGGCGA
1 AGAAGAACTTGTTCAACCTTTT-GCTTGAATTCATCACTTGATGGATCAGCT-TTGCCAGAAAGA
* *
2949340 GTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
64 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* ***
2949390 AGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATCA-TTCGATGGATCAGCATTGCCAGGGCGA
1 AGAAGAACTTGTTCAACCTTTT-GCTTGAATTCATCACTT-GATGGATCAGCTTTGCCAGAAAGA
* *
2949453 GTTCATAATAAGAAGAACTCATCTGAAGAAAGG-AGAAGAAGTTCATAATT
64 GTTCATAATGAGAAGAACTCATCTGAAG-AAGGAAGAAGAAGTTCATAATG
* * * * * * * *
2949503 AGAAGAATTTATTCAACTTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCTTTGCCAGAAAGAGT
2949568 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* *
2949616 AGAAGAACTTGTTCAATCTTTTGATTG-ATTCTATCAC
1 AGAAGAACTTGTTCAACCTTTTGCTTGAATTC-ATCAC
2949653 AGAAGGAGAT
Statistics
Matches: 534, Mismatches: 56, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
112 10 0.02
113 367 0.69
114 12 0.02
115 140 0.26
116 3 0.01
117 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCTTTGCCAGAAAGAGT
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
Found at i:2949345 original size:228 final size:226
Alignment explanation
Indices: 2948934--2949637 Score: 1018
Period size: 228 Copynumber: 3.1 Consensus size: 226
2948924 TATCTGAAAA
* * * **
2948934 AGAAGAATTTGTTTAACCTTTTGTTTGAATTCATCATTCGATGGATCATTATCCCCAGTGAAAGA
1 AGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTCGATGGATCAGCATCCCCAGTGAAAGA
*
2948999 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
66 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * *
2949064 ACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA
131 A-CTTTTGCTCGAATTCATCACTTGATGGATCAG-TTTTCCAGAGAGAGTTCATAATGAGAAGAA
*
2949129 CTCATCTGAAGAAGGAAGAAGAAATTCATAATG
194 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* **
2949162 AGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTTAATGGATCAGCATCCCCAGTGAAAGA
1 AGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTCGATGGATCAGCATCCCCAGTGAAAGA
2949227 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
66 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * * *
2949292 ACTTTTCGCTTGAATTCATCATTTGATGGATCAGTATTGCCAGGGCGAGTTCATAATAAGAAGAA
131 ACTTTT-GCTCGAATTCATCACTTGATGGATCAGT-TTTCCAGAGAGAGTTCATAATGAGAAGAA
*
2949357 CTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
194 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * ** **
2949390 AGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAG-G-GCGA
1 AGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTCGATGGATCAGCATCCCCAGTGAAAGA
* * * *
2949453 GTTCATAATAAGAAGAACTCATCTGAAGAAAGG-AGAAGAAGTTCATAATTAGAAGAATTTATTC
66 GTTCATAATGAGAAGAACTCATCTGAAG-AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
2949517 AACTTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGA
130 AAC-TTTTGCTCGAATTCATCACTTGATGGATC-AGTTTTCCAGAGAGAGTTCATAATGAGAAGA
2949582 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
193 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
2949616 AGAAGAACTTGTTCAATCTTTT
1 AGAAGAACTTGTTCAA-CTTTT
2949638 GATTGATTCT
Statistics
Matches: 429, Mismatches: 41, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
226 155 0.36
227 22 0.05
228 252 0.59
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (226 bp):
AGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTCGATGGATCAGCATCCCCAGTGAAAGA
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACTTTTGCTCGAATTCATCACTTGATGGATCAGTTTTCCAGAGAGAGTTCATAATGAGAAGAACT
CATCTGAAGAAGGAAGAAGAAGTTCATAATG
Found at i:2949375 original size:341 final size:341
Alignment explanation
Indices: 2948934--2949651 Score: 1009
Period size: 341 Copynumber: 2.1 Consensus size: 341
2948924 TATCTGAAAA
* * * *
2948934 AGAAGAATTTGTTTAACCTTTTGTTTGAATTCATCATTCGATGGATCATTATCCCCAGTGAAAGA
1 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAGTATCCCCAGTGAAAGA
*
2948999 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
66 GTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
2949064 ACCTTTT-GCTCAAATCCATCACTT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG
131 A-CTTTTCGCTCAAATCCATCA-TTCGATGGATCAGCATTGCCAGAAAAAGTTCATAATAAGAAG
* * *
2949127 AACTCATCTGAAG-AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAA
194 AACTCATCTGAAGAAAGG-AGAAGAAATTCATAATGAGAAGAATTTATTCAACTTTTTGCTCGAA
* * *
2949191 TTCATCATTTAATGGATCAGCATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
258 TTCATCACTCAATGGATCAACATCCCCA--GAAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
2949256 AGGAAGAAGAAGTTCATAATG
321 AGGAAGAAGAAGTTCATAATG
* ** **
2949277 AGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATCATTTGATGGATCAGTATTGCCAG-G-GCG
1 AGAAGAACTTGTTCAACCTTTT-GCTTGAATTCATCATTCGATGGATCAGTATCCCCAGTGAAAG
2949339 AGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
65 AGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
** * ****
2949404 AACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGA
130 AACTTTTCGCTCAAATCCATCATTCGATGGATCAGCATTGCCAGAAAAAGTTCATAATAAGAAGA
* *
2949469 ACTCATCTGAAGAAAGGAGAAGAAGTTCATAATTAGAAGAATTTATTCAACTTTTTGCTCGAATT
195 ACTCATCTGAAGAAAGGAGAAGAAATTCATAATGAGAAGAATTTATTCAACTTTTTGCTCGAATT
* * ** *
2949534 CATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
260 CATCACTCAATGGATCAACATCCCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
2949599 AGAAGAAGTTCATAATG
325 AGAAGAAGTTCATAATG
* *
2949616 AGAAGAACTTGTTCAATCTTTTGATTG-ATTCTATCA
1 AGAAGAACTTGTTCAACCTTTTGCTTGAATTC-ATCA
2949652 CAGAAGGAGA
Statistics
Matches: 335, Mismatches: 34, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
338 4 0.01
339 79 0.24
340 12 0.04
341 185 0.55
342 10 0.03
343 45 0.13
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (341 bp):
AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAGTATCCCCAGTGAAAGA
GTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACTTTTCGCTCAAATCCATCATTCGATGGATCAGCATTGCCAGAAAAAGTTCATAATAAGAAGAA
CTCATCTGAAGAAAGGAGAAGAAATTCATAATGAGAAGAATTTATTCAACTTTTTGCTCGAATTC
ATCACTCAATGGATCAACATCCCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATG
Found at i:2949905 original size:3 final size:3
Alignment explanation
Indices: 2949899--2949959 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
2949889 TTCATTTGAA
2949899 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TA- TAT TA- TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2949942 ATAT TAT TAT TAT TAT TA
1 -TAT TAT TAT TAT TAT TA
2949960 AAAAAATAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 5 0.09
3 44 0.83
4 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2951254 original size:3 final size:3
Alignment explanation
Indices: 2951248--2951289 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
2951238 TTATTTGCAA
* *
2951248 TAT TAT T-T TAT TAT TAT TAT TTT TAT TAT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2951290 TATATAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:2951306 original size:13 final size:13
Alignment explanation
Indices: 2951290--2951316 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2951280 TCTTATTATT
2951290 TATATAATAAATA
1 TATATAATAAATA
2951303 TATATAATAAATA
1 TATATAATAAATA
2951316 T
1 T
2951317 TTGTTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATAATAAATA
Found at i:2951471 original size:106 final size:107
Alignment explanation
Indices: 2951361--2951581 Score: 263
Period size: 106 Copynumber: 2.1 Consensus size: 107
2951351 TACTTTTAAT
* * *
2951361 AATCATATTTTAA-TATATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAA
1 AATCATATATTAATTATATA-TTA-TTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAA
* * * *
2951423 CTGGATGTCCATTTTCTGATATTTTTAAATAAAT-ATATTTTTTA
64 CTAGAAGT-CATTTTCTGATATTTCTAAATAAATAATATTTTATA
* * * * * *
2951467 AATCATATATTAATTGTTTATTATTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGACACCT
1 AATCATATATTAATTATATATTATTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACT
2951532 AGAAGTCATTTTCTGATATTTCTAAATAAATAATATTTTATA
66 AGAAGTCATTTTCTGATATTTCTAAATAAATAATATTTTATA
2951574 AAT-ATATA
1 AATCATATA
2951582 AATTAATTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
105 13 0.13
106 47 0.48
107 38 0.39
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (107 bp):
AATCATATATTAATTATATATTATTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACT
AGAAGTCATTTTCTGATATTTCTAAATAAATAATATTTTATA
Found at i:2954069 original size:14 final size:12
Alignment explanation
Indices: 2954039--2954072 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
2954029 TATATATTTG
2954039 TATATATTTTAA
1 TATATATTTTAA
2954051 TATATAGTTTTAA
1 TATATA-TTTTAA
2954064 TGATATATT
1 T-ATATATT
2954073 ACTATATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (12 bp):
TATATATTTTAA
Found at i:2955563 original size:20 final size:20
Alignment explanation
Indices: 2955538--2955849 Score: 303
Period size: 20 Copynumber: 15.5 Consensus size: 20
2955528 GATTTTCCAT
* *
2955538 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCTGTA
*
2955558 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-TGTA
*
2955578 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCTGTA
* * * *
2955597 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCTGT-A
* *
2955619 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCTGTA
2955639 AATCGCAACGAC-AATAC-GTAA
1 AATCGCAACG-CGAAT-CTGT-A
* *
2955660 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCTGTA
*
2955680 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCTGTA
*
2955700 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCTGTA
*
2955720 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGCGAAT-CTGTA
* * *
2955740 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCTGTA
*
2955760 AATCGCAATGCGAATAC-GTA
1 AATCGCAACGCGAAT-CTGTA
*
2955780 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATCTGTA
* *
2955800 AATCGCAATGCGAATCTATA
1 AATCGCAACGCGAATCTGTA
*
2955820 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATCTGTA
2955840 AATCGCAACG
1 AATCGCAACG
2955850 AGATTCTGAC
Statistics
Matches: 250, Mismatches: 28, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.01
20 209 0.84
21 37 0.15
22 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCTGTA
Found at i:2959178 original size:20 final size:21
Alignment explanation
Indices: 2959153--2959207 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
2959143 AGACATTCAT
*
2959153 TTGACTATCGCAATGC-GAAA
1 TTGACTATCGCAACGCAGAAA
2959173 TTGACTATCGCAACGCAGAAA
1 TTGACTATCGCAACGCAGAAA
*
2959194 -TGACTATAGCAACG
1 TTGACTATCGCAACG
2959208 AGAGAATCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (21 bp):
TTGACTATCGCAACGCAGAAA
Found at i:2959284 original size:53 final size:54
Alignment explanation
Indices: 2959159--2959353 Score: 252
Period size: 53 Copynumber: 3.7 Consensus size: 54
2959149 TCATTTGACT
* ** ** * **
2959159 ATCGCAATGCGAAATTGACTATCGCAACGCAGAAATGACTATAGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGACTGA
* *
2959213 ATCGTAATGC-AAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGACTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGACTGA
* *
2959265 ATCACAATGCGAAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGACTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGACTGA
*
2959318 ATCGCAATGCGAAAATGAAAATCGCAACGCGGAAAT
1 ATCGCAATGCGAAAATGAAAATCGCAACGCAGAAAT
2959354 TTCGCATTGC
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
52 26 0.21
53 85 0.68
54 14 0.11
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.16
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGCAGAAATGAAAATCGCAACGACTGA
Found at i:2959353 original size:20 final size:19
Alignment explanation
Indices: 2959212--2959344 Score: 133
Period size: 19 Copynumber: 7.4 Consensus size: 19
2959202 GCAACGAGAG
* *
2959212 AATCGTAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
2959231 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2959250 AATCGCAA--CG-ACTG--
1 AATCGCAATGCGAAATGAA
*
2959264 AATCACAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
2959284 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2959303 AATCGCAA--CG-ACTG--
1 AATCGCAATGCGAAATGAA
2959317 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
2959337 AATCGCAA
1 AATCGCAA
2959345 CGCGGAAATT
Statistics
Matches: 94, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 4 0.04
18 6 0.06
19 40 0.43
20 19 0.20
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2959418 original size:19 final size:19
Alignment explanation
Indices: 2959352--2959495 Score: 208
Period size: 19 Copynumber: 7.8 Consensus size: 19
2959342 CAACGCGGAA
2959352 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
2959371 ATTTTCACATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
2959389 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2959405 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2959424 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2959443 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
2959462 ATTTCGCTTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
2959481 ATTTCACATTGCGAT
1 ATTTCGCATTGCGAT
2959496 AGTCTGTTTT
Statistics
Matches: 112, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
14 6 0.05
16 6 0.05
17 3 0.03
18 4 0.04
19 81 0.72
20 12 0.11
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:2959616 original size:14 final size:14
Alignment explanation
Indices: 2959597--2959633 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2959587 CATCAATTAA
2959597 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2959611 ACAAATCATCTTTT
1 ACAAATCAACATTT
2959625 ACAAATCAA
1 ACAAATCAA
2959634 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2963063 original size:33 final size:33
Alignment explanation
Indices: 2963026--2963118 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2963016 TTGAAATGAA
* **
2963026 AATCGCAACGCGGAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
2963059 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
2963092 AATCGCAACGCGAAATAAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2963119 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:2963065 original size:14 final size:14
Alignment explanation
Indices: 2963046--2963101 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2963036 CGGAATGACT
2963046 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2963060 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
2963079 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
2963093 ATCGCAACG
1 ATCGCAACG
2963102 CGAAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2963083 original size:19 final size:19
Alignment explanation
Indices: 2963018--2963123 Score: 79
Period size: 19 Copynumber: 6.1 Consensus size: 19
2963008 TCTTTTGGTT
2963018 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* **
2963037 GGAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2963054 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2963070 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2963087 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
2963103 GAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2963122 GA
1 GA
2963124 TTTTGGGTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
14 19 0.28
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 36 0.54
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2963170 original size:21 final size:21
Alignment explanation
Indices: 2963144--2963188 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2963134 CGCGTTGCGA
**
2963144 TTCTCTCATTGCGATCTTCAT
1 TTCTCTCATTGCGATAGTCAT
*
2963165 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCATTGCGATAGTCAT
2963186 TTC
1 TTC
2963189 GTGTTGCGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (21 bp):
TTCTCTCATTGCGATAGTCAT
Found at i:2963213 original size:20 final size:19
Alignment explanation
Indices: 2963152--2963221 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
2963142 GATTCTCTCA
*
2963152 TTGCGATCTTCATTTCTCTCG
1 TTGCGATTTTCATTT-TCT-G
**
2963173 TTGCGATAGTCA-TTTCGTG
1 TTGCGATTTTCATTTTC-TG
2963192 TTGCGATTTTCATTTTCATG
1 TTGCGATTTTCATTTTC-TG
2963212 TTGCGATTTT
1 TTGCGATTTT
2963222 AAGTTAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
19 13 0.31
20 19 0.45
21 10 0.24
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTTCTG
Found at i:2963802 original size:20 final size:20
Alignment explanation
Indices: 2963777--2963970 Score: 194
Period size: 20 Copynumber: 9.6 Consensus size: 20
2963767 CTTTAAAAAT
2963777 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2963797 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* * *
2963817 TGTCGTTGCGATTTACGTATT
1 CG-CGTTGCGATTTACGGATA
* * *
2963838 CTCGTTGTGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
2963858 CGCGTTACGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
2963878 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2963898 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2963918 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
2963939 CACGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
2963960 CTCGTTGCGAT
1 CGCGTTGCGAT
2963971 ACTCAGAATC
Statistics
Matches: 142, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
20 91 0.64
21 51 0.36
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2963869 original size:40 final size:41
Alignment explanation
Indices: 2963777--2964031 Score: 238
Period size: 41 Copynumber: 6.3 Consensus size: 41
2963767 CTTTAAAAAT
* * * *
2963777 CGCGTTGCGA-TTTACGGATACGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGA-TTTACGGATA
* * *
2963817 TGTCGTTGCGA-TTTACGTATTCTCGTTGTGATTTACAGATA
1 CG-CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
*
2963858 CGCGTTACGA-TTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
*
2963898 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* * * * *
2963939 CACGTTGCGATTTTACGGATACTCGTTGCGATACT-CAGA-A
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGAT-TTACGGATA
* * ** *
2963979 TCGCGTTGCGATTTATA--TATTCGCGTTGCGATTTTCATATT
1 -CGCGTTGCGATTT-TACGTATTCTCGTTGCGATTTACGGATA
2964020 CGCGTTGCGATT
1 CGCGTTGCGATT
2964032 ATGGAAAATT
Statistics
Matches: 181, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 80 0.44
41 97 0.54
42 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:2964002 original size:20 final size:20
Alignment explanation
Indices: 2963979--2964031 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
2963969 ATACTCAGAA
2963979 TCGCGTTGCGATTTAT-ATAT
1 TCGCGTTGCGATTT-TCATAT
2963999 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
2964019 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2964032 ATGGAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:2965922 original size:32 final size:32
Alignment explanation
Indices: 2965884--2965972 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 32
2965874 CTTTATTTTG
2965884 TTCGGGTCGGGTCGGATTTTTTAAATGTGATA
1 TTCGGGTCGGGTCGGATTTTTTAAATGTGATA
* *
2965916 TTCGGGTCGAGTCGGGTCAATTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTC-GG---A-TTTTTTAAATGTGATA
2965953 TTCGGGTCGGGTTCGGATTT
1 TTCGGGTCGGG-TCGGATTT
2965973 AGGGTGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
32 12 0.25
33 5 0.10
34 1 0.02
36 1 0.02
37 27 0.56
38 2 0.04
ACGTcount: A:0.16, C:0.11, G:0.33, T:0.40
Consensus pattern (32 bp):
TTCGGGTCGGGTCGGATTTTTTAAATGTGATA
Found at i:2969333 original size:25 final size:24
Alignment explanation
Indices: 2969272--2969322 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
2969262 TTCTTCTTTT
2969272 TGTGACCTCATTTCAATTTTTTCA
1 TGTGACCTCATTTCAATTTTTTCA
2969296 TGTGACCTCATTTCAATTTTTTCA
1 TGTGACCTCATTTCAATTTTTTCA
2969320 TGT
1 TGT
2969323 TCCACTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (24 bp):
TGTGACCTCATTTCAATTTTTTCA
Found at i:2974280 original size:2 final size:2
Alignment explanation
Indices: 2974267--2974299 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
2974257 TGCTATTGTC
2974267 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
2974300 AAATATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2975546 original size:20 final size:21
Alignment explanation
Indices: 2975521--2975560 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2975511 CAACTTACAA
*
2975521 TGCATTAT-GAACTATTATTT
1 TGCATTATACAACTATTATTT
2975541 TGCATTATACAACTATTATT
1 TGCATTATACAACTATTATT
2975561 AGTTGCATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (21 bp):
TGCATTATACAACTATTATTT
Found at i:2979023 original size:43 final size:42
Alignment explanation
Indices: 2978953--2979073 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 42
2978943 GCTAAAGTTC
2978953 GCGGCGTTTGTTAACGAAAAACGCCGCAATAGGTGACGATATATA
1 GCGGCGTTTGTT-A--AAAAACGCCGCAATAGGTGACGATATATA
** * *
2978998 GCGGCGTTTGTTGAAAAAACGCCGCAATAGGTGTTGCTATTTA
1 GCGGCGTTTGTT-AAAAAACGCCGCAATAGGTGACGATATATA
*
2979041 GCGGCGTTTGTCTTAAAAACGCCGCAATAGGTG
1 GCGGCGTTTGT-TAAAAAACGCCGCAATAGGTG
2979074 TTGTCGTTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
43 55 0.80
44 1 0.01
45 13 0.19
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (42 bp):
GCGGCGTTTGTTAAAAAACGCCGCAATAGGTGACGATATATA
Found at i:2979074 original size:43 final size:43
Alignment explanation
Indices: 2978969--2979266 Score: 219
Period size: 43 Copynumber: 6.9 Consensus size: 43
2978959 TTTGTTAACG
** * *
2978969 AAAAACGCCGCAATAGGTGACGATATATAGCGGCGTTTGT-TGA
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCT-C
* *
2979012 AAAAACGCCGCAATAGGTGTTGCTATTTAGCGGCGTTTGTCTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
* * * *
2979055 AAAAACGCCGCAATAGGTGTTG-TCGTTTAGCGGTGTTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGAT-ATTTAGCGGCGTTTGTCTC
** * * * * * * *
2979098 CCAAACGCCGCAGTAGGTATCGTTGTTTAGCGGCGTTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
* * * *
2979141 AAAAATGCCGCAATAGGTGTTGTTGTTTAGCGGTGTTT-T-TC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
* * * * *
2979182 AAACAAGCGCCGCAATAAGCGTTGAGATTTAGCGGCGTTTTTATC
1 AAA-AA-CGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
* * * * *
2979227 GAAAACACCGCTACATGT-TATGATATTTAGCGGCGTTTGT
1 AAAAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTGT
2979267 GGTAAAAAAA
Statistics
Matches: 208, Mismatches: 39, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
41 4 0.02
42 5 0.02
43 190 0.91
44 5 0.02
45 4 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
Found at i:2979104 original size:86 final size:86
Alignment explanation
Indices: 2978969--2979221 Score: 258
Period size: 86 Copynumber: 2.9 Consensus size: 86
2978959 TTTGTTAACG
** * * * *
2978969 AAAAACGCCGCAATAGGTGACGAT-ATATAGCGGCGTTTGTTGAAA-AAACGCCGCAATAGGTGT
1 AAAAACGCCGCAATAGGTGTTG-TCGTTTAGCGGTGTTT-TTCAAACAAACGCCGCAATAGGTGT
* **
2979032 TGCTATTTAGCGGCGTTTGTCTT
64 TGATATTTAGCGGCGTTTGTCCC
*** * * *
2979055 AAAAACGCCGCAATAGGTGTTGTCGTTTAGCGGTGTTTTTCCCCCAAACGCCGCAGTAGGTATCG
1 AAAAACGCCGCAATAGGTGTTGTCGTTTAGCGGTGTTTTTCAAACAAACGCCGCAATAGGTGTTG
* * *
2979120 TTGTTTAGCGGCGTTTTTCCC
66 ATATTTAGCGGCGTTTGTCCC
* * * * *
2979141 AAAAATGCCGCAATAGGTGTTGTTGTTTAGCGGTGTTTTTCAAACAAGCGCCGCAATAAGCGTTG
1 AAAAACGCCGCAATAGGTGTTGTCGTTTAGCGGTGTTTTTCAAACAAACGCCGCAATAGGTGTTG
*
2979206 AGATTTAGCGGCGTTT
66 ATATTTAGCGGCGTTT
2979222 TTATCGAAAA
Statistics
Matches: 134, Mismatches: 31, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
85 3 0.02
86 131 0.98
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (86 bp):
AAAAACGCCGCAATAGGTGTTGTCGTTTAGCGGTGTTTTTCAAACAAACGCCGCAATAGGTGTTG
ATATTTAGCGGCGTTTGTCCC
Found at i:2981015 original size:22 final size:22
Alignment explanation
Indices: 2980987--2981033 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2980977 GCTTTACAAA
2980987 AAGTAAACATTCAAGGATCAAG
1 AAGTAAACATTCAAGGATCAAG
2981009 AAGTAAACATTCAAGGATCAAG
1 AAGTAAACATTCAAGGATCAAG
2981031 AAG
1 AAG
2981034 GCTTTACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.13, G:0.19, T:0.17
Consensus pattern (22 bp):
AAGTAAACATTCAAGGATCAAG
Done.