Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 30
Found at i:5360215 original size:41 final size:42
Alignment explanation
Indices: 5360113--5360225 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
5360103 TTCACAATTT
* * * *
5360113 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
* * *
5360155 TTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
* *
5360196 ATATGTCCTTCGGGCCATCTATAAGACCTT
1 ATAAGTCCTTCGGGCCATCTGTAAG-CCTT
5360226 CGGTAGGATG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
41 20 0.34
42 38 0.66
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
Found at i:5360234 original size:215 final size:215
Alignment explanation
Indices: 5359147--5360670 Score: 2486
Period size: 214 Copynumber: 7.1 Consensus size: 215
5359137 GTGAAGCAAA
* * *
5359147 CCATCCATAAAACCTTCAGTTAGGATGTTTTCACAA-GAATTTGAAAATGAAAAAATGATG---T
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCA-AATGAATTTGAAAATGAAAAAATGATGTTTT
*
5359208 -------TGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCATTC
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTC
* * *
5359266 GGGCCATCAGTAAGTCTTTCGAGCATGACGCTTAAATCCTTCGGGTCATCCGTAAGGCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
* *
5359331 TAGGATGATAAGTCCTTCGGG
195 CAAGATGATAAGTCCTTCGGG
* *
5359352 TCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTAAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
5359416 AGAAGATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAACTTTCACGATTTGTAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
* * *
5359481 GGCCATTAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGTCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
5359546 AAGATTATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
* * * *
5359566 CCATCCATAAGACCTTCGGGTATGATGCTTTCAAATCAATTTAAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
5359630 AGAAGATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTGTAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
* * * *
5359695 GGCCATTAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTTGGGTCATCTGTAAGTCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
5359760 AAGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
* * * *
5359780 CCATCCATAAAACCATCGGGTAAGATGTTTTCAAATGAATTTAAAAAT-AAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
5359844 AGAAGATGGAATTTTTGAAAACAAAGAATGCGCTTTTC-AAATGTTCACGATTTGTAAGTCCTTC
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAAT-TTCACGATTTGTAAGTCCTTC
*
5359908 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
5359973 CAAGATGATAAGTCCTTCGGG
195 CAAGATGATAAGTCCTTCGGG
5359994 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
5360059 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCACAATTTATAAGTCCTTC
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TTTCACGATTTGTAAGTCCTTC
5360124 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
*
5360189 CAAGATGATATGTCCTTCGGG
195 CAAGATGATAAGTCCTTCGGG
*
5360210 CCATCTATAAGACCTTC-GGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAAATGATGTTTT
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATG-AAAAAATGATGTTTT
* * *
5360274 AAGAAGATGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTC
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTC
5360339 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
5360404 CAAGATGATAAGTCCTTCGGG
195 CAAGATGATAAGTCCTTCGGG
5360425 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
*
5360490 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCA
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
*
5360555 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
5360620 AGGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
* *
5360640 TCATCCATAAGACCTTCGGGCAGGATGTTTT
1 CCATCCATAAGACCTTCGGGTAGGATGTTTT
5360671 TAACCAGGAT
Statistics
Matches: 1243, Mismatches: 58, Indels: 26
0.94 0.04 0.02
Matches are distributed among these distances:
204 12 0.01
205 41 0.03
207 1 0.00
213 4 0.00
214 579 0.47
215 395 0.32
216 210 0.17
217 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (215 bp):
CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGGG
Found at i:5360394 original size:42 final size:41
Alignment explanation
Indices: 5360328--5360429 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
5360318 TTCACAATTT
* * * *
5360328 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
5360369 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
*
5360411 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
5360430 CATAAGACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:5360640 original size:41 final size:42
Alignment explanation
Indices: 5360544--5360655 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 42
5360534 TCACGATTTG
* * * * * * *
5360544 TAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCGGGTCATCCGTAAGCCTTTAGAGCAGGATGCA
*
5360586 TAAATCCTTCGGGTCATCCGTAAGCCTTTAGAGCAGGATG-A
1 TAAGTCCTTCGGGTCATCCGTAAGCCTTTAGAGCAGGATGCA
*
5360627 TAAGTCCTTCGGGTCATCCATAAGACCTT
1 TAAGTCCTTCGGGTCATCCGTAAG-CCTT
5360656 CGGGCAGGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 22 0.37
42 37 0.63
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (42 bp):
TAAGTCCTTCGGGTCATCCGTAAGCCTTTAGAGCAGGATGCA
Found at i:5390698 original size:27 final size:25
Alignment explanation
Indices: 5390647--5390700 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
5390637 ACTCTTCAAG
*
5390647 AAAATAAATTATTTTTAAAAAAAAT
1 AAAATAAATTATATTTAAAAAAAAT
* *
5390672 AAAATAAAATTATAATTTATAATAAAT
1 AAAAT-AAATTAT-ATTTAAAAAAAAT
5390699 AA
1 AA
5390701 TTTAACCACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 7 0.29
27 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAATAAATTATATTTAAAAAAAAT
Found at i:5393842 original size:3 final size:3
Alignment explanation
Indices: 5393834--5393934 Score: 163
Period size: 3 Copynumber: 34.7 Consensus size: 3
5393824 TTTTTATCCA
5393834 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
5393881 TA- TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT CAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5393927 TAT TAT TA
1 TAT TAT TA
5393935 AATTATATAT
Statistics
Matches: 93, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
2 6 0.06
3 87 0.94
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5393847 original size:26 final size:27
Alignment explanation
Indices: 5393817--5393933 Score: 118
Period size: 26 Copynumber: 4.4 Consensus size: 27
5393807 AAACTGAAGA
5393817 TATTAATT-TTTTATCCA-TATTATTAT
1 TATTAATTATTTTAT-CATTATTATTAT
*
5393843 TATTATATTATTATTATTATTATTATTAT
1 TATTA-ATTATT-TTATCATTATTATTAT
* *
5393872 TATT-ATTATTATATTATTATTATTAT
1 TATTAATTATTTTATCATTATTATTAT
* * *
5393898 TATT-ATTATTTTATTATCATCATTAT
1 TATTAATTATTTTATCATTATTATTAT
5393924 TATT-ATTATT
1 TATTAATTATT
5393934 AAATTATATA
Statistics
Matches: 82, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
26 53 0.65
27 9 0.11
28 3 0.04
29 17 0.21
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTAATTATTTTATCATTATTATTAT
Found at i:5393940 original size:26 final size:24
Alignment explanation
Indices: 5393836--5393930 Score: 131
Period size: 23 Copynumber: 4.0 Consensus size: 24
5393826 TTTATCCATA
*
5393836 TTATTATTATTA-TATTATTATTA
1 TTATTATTATTATTATTATTATTT
5393859 TTATTATTATTATTATTATTATTAT
1 TTATTATTATTATTATTATTATT-T
5393884 ATTATTATTATTATTATTATTA-TT
1 -TTATTATTATTATTATTATTATTT
* *
5393908 TTATTATCATCATTATTATTATT
1 TTATTATTATTATTATTATTATT
5393931 ATTAAATTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
23 31 0.48
24 12 0.18
25 1 0.02
26 21 0.32
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTATTATTATTATTATTATTT
Found at i:5403124 original size:17 final size:18
Alignment explanation
Indices: 5403090--5403125 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5403080 GCAATCATTC
*
5403090 TTTACATTTTATTAAATT
1 TTTACATTTCATTAAATT
5403108 TTTACATTTCA-TAAATT
1 TTTACATTTCATTAAATT
5403125 T
1 T
5403126 ACTATATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTACATTTCATTAAATT
Found at i:5407883 original size:83 final size:83
Alignment explanation
Indices: 5407685--5408156 Score: 724
Period size: 83 Copynumber: 5.7 Consensus size: 83
5407675 AACAATTAAA
* * *
5407685 TGAAAGATGAATTTGCCAATAGCATCTTCTGTAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGA
1 TGAAAGATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-
*
5407749 CAGAA-CAATCATTGAGTT
65 CAGAACCAATCATTGAATT
*
5407767 T-AGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TGA-AAGATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
5407831 CAGAACCAATCATTGAATT
65 CAGAACCAATCATTGAATT
5407850 TGAAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TGAAAGATGAATGTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
5407914 CAGAACCAATCATTGAATT
65 CAGAACCAATCATTGAATT
*
5407933 TGGAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TGAAAGATGAATGTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
* *
5407997 CAGAACCAATCAGTGAGTT
65 CAGAACCAATCATTGAATT
* *
5408016 T-AGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TGA-AAGATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
5408080 CAGAACCAATCATTGAATT
65 CAGAACCAATCATTGAATT
* * *
5408099 CGGAACATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 TGAAAGATGAATGTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
5408157 ATTCAGTAGG
Statistics
Matches: 364, Mismatches: 17, Indels: 17
0.91 0.04 0.04
Matches are distributed among these distances:
81 1 0.00
82 61 0.17
83 298 0.82
84 4 0.01
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
TGAAAGATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
AGAACCAATCATTGAATT
Found at i:5408125 original size:249 final size:248
Alignment explanation
Indices: 5407703--5408156 Score: 829
Period size: 249 Copynumber: 1.8 Consensus size: 248
5407693 GAATTTGCCA
* *
5407703 ATAGCATCTTCTGTAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTT
*
5407768 AGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
66 AGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
* *
5407833 GAACCAATCATTGAATTTGAAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
131 GAACCAATCATTGAATTCGAAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
5407898 ATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATGAATGTGTTC
196 ATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATGAATGTGTTC
5407951 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCAGTGAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAA-CAATCAGTGAGT
5408015 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
64 TTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
*
5408080 CAGAACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAG
129 CAGAACCAATCATTGAATTCGAAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAG
5408145 TTATCTGATCTG
194 TTATCTGATCTG
5408157 ATTCAGTAGG
Statistics
Matches: 198, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
248 45 0.23
249 153 0.77
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (248 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTT
AGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
GAACCAATCATTGAATTCGAAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
ATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATGAATGTGTTC
Found at i:5409106 original size:114 final size:113
Alignment explanation
Indices: 5408789--5409428 Score: 917
Period size: 114 Copynumber: 5.6 Consensus size: 113
5408779 ATTCAAATCT
** *
5408789 ATCATTTGAAAGATCAGCTTTTCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
5408853 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* *
5408901 ATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
5408966 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAGTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * *
5409014 ATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGA
1 ATC-ATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
**
5409079 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* *
5409128 ATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-ATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
5409193 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * * *
5409242 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* * * *
5409306 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
62 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* ** * *
5409358 ATCATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-
1 ATCATTTGATGGATCATCTTTTCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
5409422 AGAAGAA
65 AGAAGAA
5409429 TTTATTCAAT
Statistics
Matches: 490, Mismatches: 30, Indels: 15
0.92 0.06 0.03
Matches are distributed among these distances:
112 31 0.06
113 125 0.26
114 226 0.46
115 2 0.00
116 87 0.18
117 17 0.03
118 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
ATCATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:5409253 original size:227 final size:227
Alignment explanation
Indices: 5408800--5409428 Score: 924
Period size: 227 Copynumber: 2.8 Consensus size: 227
5408790 TCATTTGAAA
* *
5408800 GATCAGCTTTTCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCAACTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCA
* * *
5408864 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAGCTTTTCCAGAG
66 TAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCATTTGATGGATCATCTTTTCCAGAG
*
5408929 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
131 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
5408994 TCAACCTTTTACCTGAAGTCATCAAATTGATG
196 TCAACCTTTTACCTGAAGTCATCAAATTGATG
* *
5409026 GATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCAACTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCA
* * *
5409091 TAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAATTGATGGATTATCTTTTCCAGA
66 TAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATC-ATTTGATGGATCATCTTTTCCAGA
*
5409156 GAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
130 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * *
5409221 TTCAATCTTTTGCTTGAATTCATC-ATTTGATG
195 TTCAACCTTTTACCTGAAGTCATCAAATTGATG
* * *
5409253 GATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAG
1 GATCAACTTTTCCAGAGAAG-GTTCATAATGAGAAGAAC-C--CATCTGAAGAAGGAAGAAGAAG
* * * * * **
5409317 TTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCATCCCC
62 TTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCATTTGATGGATCATCTTTTCC
*
5409382 AGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
127 AG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
5409429 TTTATTCAAT
Statistics
Matches: 363, Mismatches: 33, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
226 20 0.06
227 117 0.32
228 105 0.29
229 25 0.07
230 96 0.26
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (227 bp):
GATCAACTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCA
TAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCATTTGATGGATCATCTTTTCCAGAG
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTACCTGAAGTCATCAAATTGATG
Found at i:5409488 original size:341 final size:339
Alignment explanation
Indices: 5408806--5409492 Score: 839
Period size: 341 Copynumber: 2.0 Consensus size: 339
5408796 GAAAGATCAG
5408806 CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * *
5408871 AAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
66 AAGAACTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTC
*
5408936 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCT
131 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
* * ** *
5409001 TTTACCTGAAGTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCC
196 TTTACCTGAAGTCATCAAATTGATGGATCATCATCCCCAGAGAAAGTTCATAATGAGAAGAACCC
* * ** * **** ** *
5409066 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATC
261 ATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAACAATTTAATCAA-CGTGAAGCCAAATGCATC
***
5409131 AAATTGATGGATTAT
325 AAAAAAATGGATTAT
5409146 CTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * *
5409211 GAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGT
65 GAAGAACTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAACATTGCCAGAG-AAAGT
5409275 TCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
129 TCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
5409340 AATCTTTTGCTTGAATTCATC-ATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAA
191 AACCTTTTACCTGAAGTCATCAAATTGATGGATCATCATCCCCAG-AGAAAGTTCATAATGAGAA
* * *** *
5409404 GAACTCATCTGAAGAAAG-AGAAGAA-TTTATTCAAT-ATCTCCATTATAATCAA-GTGAAGCCA
255 GAACCCATCTGAAGAAAGAAGAAGAAGTTCA-T-AATGAGAACAATT-TAATCAACGTGAAGCCA
* **
5409465 AATGGAT-AAAAAAATTTATTAT
317 AATGCATCAAAAAAATGGATTAT
5409487 CTTTTC
1 CTTTTC
5409493 ATCTTTGCCC
Statistics
Matches: 294, Mismatches: 44, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
340 14 0.05
341 135 0.46
342 10 0.03
343 31 0.11
344 104 0.35
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (339 bp):
CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTC
ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
TTTACCTGAAGTCATCAAATTGATGGATCATCATCCCCAGAGAAAGTTCATAATGAGAAGAACCC
ATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAACAATTTAATCAACGTGAAGCCAAATGCATCA
AAAAAATGGATTAT
Found at i:5409572 original size:3 final size:3
Alignment explanation
Indices: 5409564--5409638 Score: 132
Period size: 3 Copynumber: 24.7 Consensus size: 3
5409554 TTTTTACCCA
5409564 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5409612 TAT TAT CAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TA
5409639 AATATATATT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 66 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5409667 original size:14 final size:15
Alignment explanation
Indices: 5409637--5409671 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
5409627 TATTATTTAT
5409637 TAAATATATATTAAA
1 TAAATATATATTAAA
*
5409652 TAAATTTATA-TAAA
1 TAAATATATATTAAA
5409666 TAAATA
1 TAAATA
5409672 ATTACAGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:5413538 original size:23 final size:22
Alignment explanation
Indices: 5413504--5413562 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
5413494 CTTTGAATAA
* *
5413504 AAAAACTTTGTTTACCAAAACTG
1 AAAAACTCTGTTTACCAAAAC-C
* * *
5413527 AAAAACTCTGTTTATCAGAGCC
1 AAAAACTCTGTTTACCAAAACC
5413549 AAAAACTCTGTTTA
1 AAAAACTCTGTTTA
5413563 TCAGAGCCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (22 bp):
AAAAACTCTGTTTACCAAAACC
Found at i:5413555 original size:22 final size:23
Alignment explanation
Indices: 5413527--5413584 Score: 100
Period size: 22 Copynumber: 2.6 Consensus size: 23
5413517 ACCAAAACTG
5413527 AAAAACTCTGTTTATCAGAGCC-
1 AAAAACTCTGTTTATCAGAGCCA
5413549 AAAAACTCTGTTTATCAGAGCCA
1 AAAAACTCTGTTTATCAGAGCCA
*
5413572 AAAAATTCTGTTT
1 AAAAACTCTGTTT
5413585 CTACATGGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 22 0.65
23 12 0.35
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (23 bp):
AAAAACTCTGTTTATCAGAGCCA
Found at i:5418640 original size:23 final size:22
Alignment explanation
Indices: 5418590--5418641 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
5418580 ACCAAAACCG
* * *
5418590 GAAAACTTTGTTTACCAGTGTT
1 GAAAACTATGTTTACCAGAGTA
5418612 GAAAAACTATGTTTACCAGAGCTA
1 G-AAAACTATGTTTACCAGAG-TA
5418636 GAAAAC
1 GAAAAC
5418642 ACTGTTTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 22 0.88
24 2 0.08
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (22 bp):
GAAAACTATGTTTACCAGAGTA
Found at i:5427196 original size:65 final size:65
Alignment explanation
Indices: 5427063--5427222 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
5427053 TGGACCCTTA
* * *
5427063 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAACCACAGTGCATCGATGCATGGCTG
*
5427127 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AACCTCAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAACCACAGTGCATCGATGCATGGCT
*
5427190 AT
65 -G
*
5427192 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
5427223 CAATTTAATT
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 29 0.33
65 55 0.63
66 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAACCACAGTGCATCGATGCATGGCTG
Found at i:5427261 original size:65 final size:64
Alignment explanation
Indices: 5427063--5427272 Score: 225
Period size: 65 Copynumber: 3.2 Consensus size: 64
5427053 TGGACCCTTA
* * * *
5427063 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGC-CAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAACTCAG-GTGCATCGATGCATGGTTG
*
5427127 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAAACCTCA-GTGCATCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAT-ATAA-CTCAGGTGCATCGATGCATGGT
5427190 AT-
63 -TG
* * * *
5427192 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCAAGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAACTCA-GGTGCATCGATGCATGG-TT
5427256 G
64 G
5427257 GTGCATC-AGTGCATCA
1 GTGCATCGA-TGCATCA
5427273 CTTTGAAAAA
Statistics
Matches: 124, Mismatches: 11, Indels: 21
0.79 0.07 0.13
Matches are distributed among these distances:
62 3 0.02
63 5 0.04
64 48 0.39
65 64 0.52
66 2 0.02
67 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAACTCAGGTGCATCGATGCATGGTTG
Found at i:5433819 original size:22 final size:21
Alignment explanation
Indices: 5433777--5433816 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5433767 GAGTTTATTT
*
5433777 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5433798 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5433817 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5435894 original size:65 final size:65
Alignment explanation
Indices: 5435761--5435920 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
5435751 TGCACTAAGA
* * * * *
5435761 GTGCATTGATGCATCAAGTGCATTCGATG-TTTCAAAATATCTAGAGTCCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAACCTACAGTCCATCGATGCATGACTG
*
5435825 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAACCT-CAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAAAACCTACAGTCCATCGATGCAT-G-A
5435889 -T-
63 CTG
*
5435890 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
5435921 CAATTTAATT
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 27 0.32
65 49 0.58
66 8 0.09
67 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAACCTACAGTCCATCGATGCATGACTG
Found at i:5441209 original size:26 final size:26
Alignment explanation
Indices: 5441186--5441245 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
5441176 ATATAAAAGA
5441186 GATTTAATTT-CTCTTTTATTAAAAAT
1 GATTT-ATTTCCTCTTTTATTAAAAAT
*
5441212 GATTTATTTCCTCTTTTATTAGAATAT
1 GATTTATTTCCTCTTTTATTA-AAAAT
5441239 -ATTTATT
1 GATTTATT
5441246 AGCTCTTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 4 0.13
26 23 0.74
27 4 0.13
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (26 bp):
GATTTATTTCCTCTTTTATTAAAAAT
Found at i:5441251 original size:26 final size:26
Alignment explanation
Indices: 5441196--5441253 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
5441186 GATTTAATTT
*
5441196 CTCTTTTATTAAAAATGATTTATTTC
1 CTCTTTTATTAAAAATGATTTATTAC
* *
5441222 CTCTTTTATTAGAATAT-ATTTATTAG
1 CTCTTTTATTA-AAAATGATTTATTAC
5441248 CTCTTT
1 CTCTTT
5441254 CAGTCCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (26 bp):
CTCTTTTATTAAAAATGATTTATTAC
Found at i:5445290 original size:19 final size:21
Alignment explanation
Indices: 5445252--5445291 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5445242 TAGTCTTTAT
5445252 TTATTTAATTTAGTTTATCTTG
1 TTATTTAA-TTAGTTTATCTTG
5445274 TTATTTAA-TAG-TTATCTT
1 TTATTTAATTAGTTTATCTT
5445292 TTTGTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
22 8 0.44
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (21 bp):
TTATTTAATTAGTTTATCTTG
Found at i:5451483 original size:16 final size:16
Alignment explanation
Indices: 5451462--5451501 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5451452 CATGATTCAA
*
5451462 TTTTTTTTCTTTTTTC
1 TTTTTTTTCTTTTTCC
*
5451478 TTTTTTTCCTTTTTCC
1 TTTTTTTTCTTTTTCC
5451494 TTTTTTTT
1 TTTTTTTT
5451502 GAGTATATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTTCTTTTTCC
Found at i:5453925 original size:22 final size:22
Alignment explanation
Indices: 5453876--5453930 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
5453866 TATAAATGAG
*
5453876 AAAATGCATAA-ATGAAAAAAT
1 AAAATGCAAAATATGAAAAAAT
* *
5453897 AAGAATGCAAAATATGCAAATAT
1 AA-AATGCAAAATATGAAAAAAT
5453920 AAAATG-AAAAT
1 AAAATGCAAAAT
5453931 GTAAATACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 10 0.34
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAATGCAAAATATGAAAAAAT
Found at i:5457986 original size:3 final size:3
Alignment explanation
Indices: 5457980--5458051 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
5457970 AAAATTTATT
* * *
5457980 TAA TAA TAA TAA TAA TAA TAA -AA TTA TTA TAG TAA TAA TAA -AA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5458025 TAA TAA AAA AAA TAAA TAA TAAA TAA T
1 TAA TAA TAA TAA T-AA TAA T-AA TAA T
5458052 GAGTAATGGA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 6 0.10
3 46 0.79
4 6 0.10
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5458015 original size:29 final size:29
Alignment explanation
Indices: 5457963--5458032 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
5457953 TTTGGATCTG
5457963 AAATAATAAAATTTATTTAATAATAATAA
1 AAATAATAAAATTTATTTAATAATAATAA
* *
5457992 TAATAATAAAA-TTATTATAGTAATAATAA
1 AAATAATAAAATTTATT-TAATAATAATAA
5458021 AATATAATAAAA
1 AA-ATAATAAAA
5458033 AAAATAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.14
29 22 0.61
30 9 0.25
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (29 bp):
AAATAATAAAATTTATTTAATAATAATAA
Found at i:5461550 original size:35 final size:35
Alignment explanation
Indices: 5461499--5461577 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
5461489 TGTTTGGGAT
5461499 TGAATGTCAAGCTGCTAATCTGAAGCAA-GACAATA
1 TGAATGTCAAGCTGCTAATCTGAAG-AAGGACAATA
*
5461534 TGAATGTCAAGTTGCTAATCTGAAGAAGGACAATA
1 TGAATGTCAAGCTGCTAATCTGAAGAAGGACAATA
*
5461569 TAAATGTCA
1 TGAATGTCA
5461578 CCCAGTATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 2 0.05
35 39 0.95
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (35 bp):
TGAATGTCAAGCTGCTAATCTGAAGAAGGACAATA
Found at i:5467594 original size:29 final size:29
Alignment explanation
Indices: 5467518--5467607 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 29
5467508 CAAAATATCC
* * *
5467518 AACTTTTAAAAATTAGACTTTGGTC-CTTA
1 AACTTTCAAAATTTATACTTTGGTCAC-TA
*
5467547 AACTTTTTCAAACTTTATACTTTGGTCACTA
1 AAC--TTTCAAAATTTATACTTTGGTCACTA
*
5467578 AACTTTCAAAATTTATATTTTGGTCACTA
1 AACTTTCAAAATTTATACTTTGGTCACTA
5467607 A
1 A
5467608 TCAAAATTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
29 28 0.54
31 23 0.44
32 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (29 bp):
AACTTTCAAAATTTATACTTTGGTCACTA
Found at i:5468961 original size:18 final size:18
Alignment explanation
Indices: 5468940--5468981 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5468930 GTCCCAAAGG
5468940 ACCACTATATCCCGAAGA
1 ACCACTATATCCCGAAGA
* *
5468958 ACCACTATGTCCCGAAGG
1 ACCACTATATCCCGAAGA
5468976 ACCACT
1 ACCACT
5468982 GATTATCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.36, G:0.14, T:0.17
Consensus pattern (18 bp):
ACCACTATATCCCGAAGA
Found at i:5473787 original size:18 final size:18
Alignment explanation
Indices: 5473764--5473799 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5473754 GCGTAGAATT
5473764 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
*
5473782 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
5473800 ATAATCCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:5479096 original size:12 final size:12
Alignment explanation
Indices: 5479081--5479118 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
5479071 GTTATTTAAA
5479081 CGGGTATTGGGC
1 CGGGTATTGGGC
*
5479093 CGGGTATTGGGT
1 CGGGTATTGGGC
5479105 CGGGTATTGGGC
1 CGGGTATTGGGC
5479117 CG
1 CG
5479119 AGAATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:5479108 original size:24 final size:24
Alignment explanation
Indices: 5479081--5479135 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
5479071 GTTATTTAAA
* * *
5479081 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
5479105 CGGGTATTGGGCCGAGAATCGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
5479129 CGGGTAT
1 CGGGTAT
5479136 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGT
Found at i:5479288 original size:13 final size:13
Alignment explanation
Indices: 5479232--5479275 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
5479222 TTTAATATTT
*
5479232 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
5479244 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
5479257 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
5479270 ATCGGG
1 ATCGGG
5479276 TAATCGGGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.14, C:0.16, G:0.52, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:5479344 original size:6 final size:6
Alignment explanation
Indices: 5479333--5479357 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5479323 AAATGGGTTT
5479333 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
5479358 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:5489275 original size:35 final size:36
Alignment explanation
Indices: 5489228--5489298 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
5489218 AATATTGATA
5489228 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
*
5489264 ATGCT-AAATTAGGTTATCCCACTAGTATTGGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
5489299 GACGATTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 29 0.85
36 5 0.15
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (36 bp):
ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
Found at i:5493717 original size:19 final size:19
Alignment explanation
Indices: 5493690--5493744 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
5493680 ATGCATTGGC
5493690 CTATGAATATGAAATTAAG
1 CTATGAATATGAAATTAAG
*
5493709 CTATAAATATGAAATTAAG
1 CTATGAATATGAAATTAAG
*
5493728 CTATGAATTTGAAATTA
1 CTATGAATATGAAATTA
5493745 TGAATTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.35
Consensus pattern (19 bp):
CTATGAATATGAAATTAAG
Found at i:5493748 original size:14 final size:14
Alignment explanation
Indices: 5493729--5493758 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5493719 GAAATTAAGC
5493729 TATGAATTTGAAAT
1 TATGAATTTGAAAT
5493743 TATGAATTTGAAAT
1 TATGAATTTGAAAT
5493757 TA
1 TA
5493759 AGTTATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TATGAATTTGAAAT
Found at i:5493766 original size:19 final size:19
Alignment explanation
Indices: 5493691--5493810 Score: 81
Period size: 19 Copynumber: 6.6 Consensus size: 19
5493681 TGCATTGGCC
* *
5493691 TATGAATATGAAATTAAGC
1 TATGAATTTGAAATTAAGT
* * *
5493710 TATAAATATGAAATTAAGC
1 TATGAATTTGAAATTAAGT
5493729 TATGAATTTG--A--AA-T
1 TATGAATTTGAAATTAAGT
5493743 TATGAATTTGAAATTAAGT
1 TATGAATTTGAAATTAAGT
* * *
5493762 TATGAATCTAAAAGTAAGT
1 TATGAATTTGAAATTAAGT
* * *
5493781 TTTGAATATGGAAA-TAGGT
1 TATGAAT-TTGAAATTAAGT
*
5493800 TTTGAATTTGA
1 TATGAATTTGA
5493811 GAATGAATTC
Statistics
Matches: 82, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
14 10 0.12
15 2 0.02
16 1 0.01
17 1 0.01
18 5 0.06
19 60 0.73
20 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.38
Consensus pattern (19 bp):
TATGAATTTGAAATTAAGT
Found at i:5493861 original size:13 final size:13
Alignment explanation
Indices: 5493841--5493898 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
5493831 AAGTACTGGT
5493841 TATGAAAATAAAA
1 TATGAAAATAAAA
* *
5493854 TGTGAAAAT-GAA
1 TATGAAAATAAAA
*
5493866 TATGAAAGTAAAA
1 TATGAAAATAAAA
* *
5493879 GATGAAAATGAAA
1 TATGAAAATAAAA
5493892 TATGAAA
1 TATGAAA
5493899 GTTCTTAAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 9 0.26
13 26 0.74
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.22
Consensus pattern (13 bp):
TATGAAAATAAAA
Found at i:5493877 original size:25 final size:26
Alignment explanation
Indices: 5493841--5493900 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 26
5493831 AAGTACTGGT
*
5493841 TATGAAAATAAAATG-TGAAAATG-AA
1 TATGAAAGTAAAA-GATGAAAATGAAA
5493866 TATGAAAGTAAAAGATGAAAATGAAA
1 TATGAAAGTAAAAGATGAAAATGAAA
5493892 TATGAAAGT
1 TATGAAAGT
5493901 TCTTAAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 1 0.03
25 20 0.62
26 11 0.34
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.23
Consensus pattern (26 bp):
TATGAAAGTAAAAGATGAAAATGAAA
Found at i:5495119 original size:18 final size:17
Alignment explanation
Indices: 5495086--5495119 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5495076 TATATTAAAT
*
5495086 TAATAAAAAAACATATG
1 TAATAAAAAAAAATATG
5495103 TAATAAAAAAATAATAT
1 TAATAAAAAAA-AATAT
5495120 ACATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
TAATAAAAAAAAATATG
Found at i:5495964 original size:45 final size:45
Alignment explanation
Indices: 5495915--5496039 Score: 232
Period size: 45 Copynumber: 2.8 Consensus size: 45
5495905 TTTGTTTATA
*
5495915 CATCCTTTTATGCCTTTTATACACCATTATACATTTCATTTATGG
1 CATCCTTTCATGCCTTTTATACACCATTATACATTTCATTTATGG
5495960 CATCCTTTCATGCCTTTTATACACCATTATACATTTCATTTATGG
1 CATCCTTTCATGCCTTTTATACACCATTATACATTTCATTTATGG
*
5496005 CATCCTTTCATGCCTTTTATACACCATTATGCATT
1 CATCCTTTCATGCCTTTTATACACCATTATACATT
5496040 GCTATCGATC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.24, C:0.25, G:0.06, T:0.45
Consensus pattern (45 bp):
CATCCTTTCATGCCTTTTATACACCATTATACATTTCATTTATGG
Found at i:5496403 original size:55 final size:55
Alignment explanation
Indices: 5496279--5496842 Score: 645
Period size: 55 Copynumber: 10.3 Consensus size: 55
5496269 TTTATTAAGA
* ** * * **
5496279 TGCACACGTAGT--CTATACGG-TAGTTCATTTACCCATGATGAATTTCG-GGGGT
1 TGCACACATAGTGCCTATACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATT
* *
5496331 TGCACACATCGTGCCTATATGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
5496386 TGCACACATAGTGCCTATACGGTTATTCATTAACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * *
5496441 TGCACACATAGTGTCTATAAGGTTATTCATTAACTCATGATTAATTCCATGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
** * * ***
5496496 TGCACACATAGTGAATGTACTGTTATTCATCAACTCATGATGAATTATATGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
** * * **
5496551 TGCACACATAGTGTTTGTACTGTTATTCATCAACTCATGATGAATTCATTGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * *
5496606 TGCACATATAGTGCCTGTACGGTTATTAATCAACTCATGATGAATTACGTGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
5496661 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * *
5496716 TACACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * * * *
5496771 TGCACACTTAATGCCGAAACAGTTATTCATCCACAT-ATGATGAATTCCGTGGA-A
1 TGCACACATAGTGCCTATACGGTTATTCATCAAC-TCATGATGAATTCCGTGGATT
*
5496825 TGCACACTTAGTGCCTAT
1 TGCACACATAGTGCCTAT
5496843 TTGGTAATCA
Statistics
Matches: 447, Mismatches: 60, Indels: 8
0.87 0.12 0.02
Matches are distributed among these distances:
52 10 0.02
54 42 0.09
55 394 0.88
56 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (55 bp):
TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:5497206 original size:22 final size:22
Alignment explanation
Indices: 5497174--5497233 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 22
5497164 GTATCGATAC
* *
5497174 CCATACCATGGTATCGATATTA
1 CCATACTATGGTATCGATAATA
5497196 CCATACTATGGTA-C-A-AATA
1 CCATACTATGGTATCGATAATA
* *
5497215 CTATGCTATGGTATCGATA
1 CCATACTATGGTATCGATA
5497234 CCTTCCCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 14 0.45
20 2 0.06
21 2 0.06
22 13 0.42
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (22 bp):
CCATACTATGGTATCGATAATA
Found at i:5502074 original size:46 final size:46
Alignment explanation
Indices: 5502005--5502237 Score: 360
Period size: 46 Copynumber: 5.1 Consensus size: 46
5501995 ACCACTATGT
* * *
5502005 ATTTTCATTTGTGGCATCCTTTCATGCCAATTATGCACTGTTATAA
1 ATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGTTATAC
* * *
5502051 ATTTTCATTTATGACATCATTTCATGCTAATTACGCACTGTTATAC
1 ATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGTTATAC
5502097 ATTTTCATTTAT-ATCATCCTTTCATGCCAATTATGCACTGTTATAC
1 ATTTTCATTTATGA-CATCCTTTCATGCCAATTATGCACTGTTATAC
5502143 ATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGTTATAC
1 ATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGTTATAC
* ** *
5502189 ATTTTCATTTATGGCATCCTTTCATAACAATTATGCATTGTTATAC
1 ATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGTTATAC
5502235 ATT
1 ATT
5502238 AGTGTTATCC
Statistics
Matches: 172, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 1 0.01
46 170 0.99
47 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.45
Consensus pattern (46 bp):
ATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGTTATAC
Found at i:5502559 original size:54 final size:54
Alignment explanation
Indices: 5502491--5502619 Score: 143
Period size: 54 Copynumber: 2.4 Consensus size: 54
5502481 TATAGGTTCA
* ** * *
5502491 TTCATCAACCTATGATGAATTCC-TAGGGTTGCACACATAATGTCGAAACGGTTG
1 TTCATCAACATATGATGAATTCCATA-AATTACACACATAATGACGAAACGGTTG
* * * * * *
5502545 TTTATTAACATATGATTAATTCCATAAATTACACACTTAGTGACGAAATGGTTG
1 TTCATCAACATATGATGAATTCCATAAATTACACACATAATGACGAAACGGTTG
5502599 TTCATCAACATATGATGAATT
1 TTCATCAACATATGATGAATT
5502620 TCGTGTTGGG
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
54 58 0.97
55 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTCCATAAATTACACACATAATGACGAAACGGTTG
Found at i:5506504 original size:19 final size:19
Alignment explanation
Indices: 5506461--5506498 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5506451 TAAGTATTCT
5506461 TCACCTCGATCTGATCGAA
1 TCACCTCGATCTGATCGAA
5506480 TCACCTCGATCTGATCGAA
1 TCACCTCGATCTGATCGAA
5506499 GTACCTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (19 bp):
TCACCTCGATCTGATCGAA
Found at i:5509996 original size:2 final size:2
Alignment explanation
Indices: 5509989--5510013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5509979 TTATTCCGAA
5509989 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5510014 AATTAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5511199 original size:54 final size:54
Alignment explanation
Indices: 5511084--5511475 Score: 568
Period size: 54 Copynumber: 7.4 Consensus size: 54
5511074 TCTAACATTT
5511084 CGTGAATTGCACACTTAGTGCCGAAACGGTTG-T--TCAACATATGATGAATTC
1 CGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTC
* *
5511135 CGTGAATTGCACACATAGTGCCGAAATGGTTGTTCATCAACATATGATGAATTC
1 CGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTC
*
5511189 CGTGAATTGCACA-TTCAGTGCCAAAACGGTTG-T--TCAACATATGATGAATTC
1 CGTGAATTGCACACTT-AGTGCCGAAACGGTTGTTCATCAACATATGATGAATTC
* **
5511240 TGTGAATTGCACACTTAGT-TTGAAACGGTTGTTCATCAACATATGATGAATTC
1 CGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTC
* * * *
5511293 CATGAATTGTACACTTACTGCCGAAACGGTTGTTCATCAACATATGATGAATTT
1 CGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTC
* * *
5511347 CATGAATTGCACACTTAGTGCTGAAACAGTTGTTCATCAACATATGATGAATTC
1 CGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTC
* * *
5511401 CGTGAATTACACACTTAGTACCGAAACGGTTGTTCATCAATATATGATGAATTC
1 CGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTC
5511455 CGTG-ATTGCACACTTAGTGCC
1 CGTGAATTGCACACTTAGTGCC
5511476 TATTTGGTAA
Statistics
Matches: 303, Mismatches: 29, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
50 9 0.03
51 64 0.21
52 3 0.01
53 50 0.17
54 177 0.58
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (54 bp):
CGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTC
Found at i:5516449 original size:45 final size:46
Alignment explanation
Indices: 5516290--5516475 Score: 293
Period size: 46 Copynumber: 4.1 Consensus size: 46
5516280 ACCACTATGT
* *
5516290 ATTTTCATTTGTGGCATCATTTCATGCCAATTATGCACTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
* *
5516336 ATTTTCATTTATGTCATCCTTTCATGCCAATTTTGCACTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
* *
5516382 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACAGTTACAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
* *
5516428 A-TTTCATTTATGGCATACTTTCATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
5516473 ATT
1 ATT
5516476 AGTGTTATCC
Statistics
Matches: 127, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 41 0.32
46 86 0.68
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
Found at i:5516461 original size:22 final size:22
Alignment explanation
Indices: 5516390--5516461 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
5516380 ACATTTTCAT
*
5516390 TTATGGCATCCTTTCATGCCAA
1 TTATGGCATACTTTCATGCCAA
* * * ** *
5516412 TTAT-GCACAGTTACACATTTCAT
1 TTATGGCATACTT--TCATGCCAA
5516435 TTATGGCATACTTTCATGCCAA
1 TTATGGCATACTTTCATGCCAA
5516457 TTATG
1 TTATG
5516462 CATTGTTATA
Statistics
Matches: 34, Mismatches: 13, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
21 5 0.15
22 14 0.41
23 9 0.26
24 6 0.18
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.39
Consensus pattern (22 bp):
TTATGGCATACTTTCATGCCAA
Found at i:5516803 original size:54 final size:53
Alignment explanation
Indices: 5516710--5517132 Score: 482
Period size: 54 Copynumber: 7.9 Consensus size: 53
5516700 TAGTGCCTAT
* * ** * *
5516710 ACGGTCGTTCATCAACCTATGATGAATTATGT-AGGTTGCACACATAGTGCGAAA
1 ACGGTTGTTCATCAACATATGATGAATTCCGTGA-ATTGCACACTTAGTGCG-AA
* * * *
5516764 ACGGTTGTTCATCAACATATGATGAATTTCGTAAATTGCACACTTTGTGCCAAA
1 ACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTG-CGAA
* * * *
5516818 ATGGTTTTTCAT-AACATATGATGAATTCCTTGAATTGCACA-TTCAGTGCCAAA
1 ACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTT-AGTG-CGAA
* *
5516871 ACAGTTGTT--T-AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAA
1 ACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTG-CGAA
* * *
5516922 ACGGTTG-TCATCCACATATAATGAATTCCGTGAATTGTACACTTAGTGCTGAA
1 ACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGC-GAA
*
5516975 ACGGTTGTTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCCGAA
1 ACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTG-CGAA
* * *
5517029 ATGGTTGTTCATCAACAAATGATGAATTCCGTGAATTGTACACTTAGTGCTGAA
1 ACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGC-GAA
* * *
5517083 ATGATTGTTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGC
1 ACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGC
5517133 CTATTTGGTA
Statistics
Matches: 321, Mismatches: 37, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.00
51 42 0.13
52 6 0.02
53 83 0.26
54 186 0.58
55 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (53 bp):
ACGGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCGAA
Found at i:5517015 original size:158 final size:160
Alignment explanation
Indices: 5516720--5517133 Score: 516
Period size: 158 Copynumber: 2.6 Consensus size: 160
5516710 ACGGTCGTTC
* * * *
5516720 ATCAACCTATGATGAATTATGT-AGGTTGCACACATAGTG-CGAAAACGGTTGTTCATCAACATA
1 ATCAACATATGATGAATTCTGTGA-ATTGCACACTTAGTGCCG-AAACGGTTGTTCATCAACATA
* * * * * *
5516783 TGATGAATTTCGTAAATTGCACACTTTGTGCCAAAATGGTTTTTCATAACATATGATGAATTCCT
64 TGATGAATTCCGTGAATTGCACACTTAGTGCCAAAACGGTTGTTCATAACATATGATGAATTCCA
5516848 TGAATTGCACA-TTCAGTGCCAAAACAGTTGTT
129 TGAATTGCACACTT-AGTGCCAAAACAGTTGTT
* *
5516880 -T-AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTG-TCATCCACATATA
1 ATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATG
* **
5516942 ATGAATTCCGTGAATTGTACACTTAGTGCTGAAACGGTTGTTCATCAACATATGATGAATTCCAT
66 ATGAATTCCGTGAATTGCACACTTAGTGCCAAAACGGTTGTTCAT-AACATATGATGAATTCCAT
* **
5517007 GAATTGCACACTTAGTGCCGAAATGGTTGTT
130 GAATTGCACACTTAGTGCCAAAACAGTTGTT
* * * * * *
5517038 CATCAACAAATGATGAATTCCGTGAATTGTACACTTAGTGCTGAAATGATTGTTCATCAACATAT
1 -ATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATAT
*
5517103 GATGAATTCCATGAATTGCACACTTAGTGCC
65 GATGAATTCCGTGAATTGCACACTTAGTGCC
5517134 TATTTGGTAA
Statistics
Matches: 217, Mismatches: 29, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
157 48 0.22
158 82 0.38
159 6 0.03
160 1 0.00
161 42 0.19
162 38 0.18
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (160 bp):
ATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATG
ATGAATTCCGTGAATTGCACACTTAGTGCCAAAACGGTTGTTCATAACATATGATGAATTCCATG
AATTGCACACTTAGTGCCAAAACAGTTGTT
Found at i:5518595 original size:66 final size:65
Alignment explanation
Indices: 5518432--5518652 Score: 166
Period size: 66 Copynumber: 3.4 Consensus size: 65
5518422 GGGATAATGG
** ** *
5518432 TTTCAAGAGAAACTGACTCAAAGA-TGATACTTCAAGAGAAGA-TATCTCAA-GAGAGAC-AAAT
1 TTTCAAGAGAAACAAACTCAAAGATTG-TGTTTCAAGAGAA-ACCATCTCAAGGA-AGACAAAAT
**
5518493 TCG
63 TTA
* * * *
5518496 TTTCAAGGGAAAC-GACTCAAAGATATGTTTTTCAAGGGAAACCATCTCAATGG-AGACAAAATT
1 TTTCAAGAGAAACAAACTCAAAGAT-TGTGTTTCAAGAGAAACCATCTCAA-GGAAGACAAAATT
5518559 TA
64 TA
* * *** *
5518561 TTTCAAGAGAATCAAACTCAAAGATTGGTGTTTCATGAGAAATTGTCTCAAGGAAGACAAGATTT
1 TTTCAAGAGAAACAAACTCAAAGATT-GTGTTTCAAGAGAAACCATCTCAAGGAAGACAAAATTT
*
5518626 G
65 A
**
5518627 TTTCAAGAGAAACATTCTCAAAGATT
1 TTTCAAGAGAAACAAACTCAAAGATT
5518653 ATAACTTTTG
Statistics
Matches: 127, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
63 11 0.09
64 33 0.26
65 21 0.17
66 62 0.49
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (65 bp):
TTTCAAGAGAAACAAACTCAAAGATTGTGTTTCAAGAGAAACCATCTCAAGGAAGACAAAATTTA
Found at i:5518894 original size:32 final size:32
Alignment explanation
Indices: 5518853--5518916 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
5518843 TTCACATCAG
*
5518853 GATGTTGAATAC-CCAAAGATGCCCCAACATTC
1 GATGTTGAAT-CTCCAAAGATGACCCAACATTC
*
5518885 GATGTTGAATCTCCAAAGATGACCCATCATTC
1 GATGTTGAATCTCCAAAGATGACCCAACATTC
5518917 ATCGTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGACCCAACATTC
Found at i:5528291 original size:25 final size:24
Alignment explanation
Indices: 5528241--5528291 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
5528231 TTTTCTTTGA
5528241 TTTTTTCTTCTTTGCTCTTTGTTT
1 TTTTTTCTTCTTTGCTCTTTGTTT
*
5528265 TTTTCTTCTTCTTCTTCTCTTTGTTT
1 TTTT-TTCTTCTT-TGCTCTTTGTTT
5528291 T
1 T
5528292 GATTGAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 4 0.17
25 8 0.33
26 12 0.50
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.75
Consensus pattern (24 bp):
TTTTTTCTTCTTTGCTCTTTGTTT
Found at i:5537384 original size:20 final size:19
Alignment explanation
Indices: 5537361--5537414 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
5537351 AATTTCTCTC
5537361 TTAACTTTTAACTTTCATT
1 TTAACTTTTAACTTTCATT
* **
5537380 ATTAATTTTTCTCTTTCATT
1 -TTAACTTTTAACTTTCATT
*
5537400 TTAACTTTTACCTTT
1 TTAACTTTTAACTTT
5537415 TCTCTTTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAACTTTTAACTTTCATT
Found at i:5541084 original size:20 final size:20
Alignment explanation
Indices: 5541059--5541109 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5541049 CACGTGAGGA
5541059 TTATTTTCTTCTTAT-TTTAT
1 TTATTTTCTT-TTATATTTAT
* *
5541079 TTATTTTATTTTTTATTTAT
1 TTATTTTCTTTTATATTTAT
*
5541099 TTATTGTCTTT
1 TTATTTTCTTT
5541110 ACCATTTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (20 bp):
TTATTTTCTTTTATATTTAT
Found at i:5544346 original size:71 final size:71
Alignment explanation
Indices: 5544230--5544371 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
5544220 TAGCTGAAAT
5544230 CAAGGCTTAAACTCGGTTATGCCTCTTCATTTGCCTTACTTCTCTTTGCAGCCCACGAGAGAAAG
1 CAAGGCTTAAACTCGGTTATGCCTCTTCATTTGCCTTACTTCTCTTTGCAGCCCACGAGAGAAAG
5544295 AGAGAA
66 AGAGAA
*
5544301 CAAGGCTTAAACTCGGTTATGCCTCTTCATTTGCCTTACTTCTCTTTGCATCCCACGAGAGAAAG
1 CAAGGCTTAAACTCGGTTATGCCTCTTCATTTGCCTTACTTCTCTTTGCAGCCCACGAGAGAAAG
5544366 AGAGAA
66 AGAGAA
5544372 ACAATCTCTC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (71 bp):
CAAGGCTTAAACTCGGTTATGCCTCTTCATTTGCCTTACTTCTCTTTGCAGCCCACGAGAGAAAG
AGAGAA
Found at i:5545697 original size:21 final size:21
Alignment explanation
Indices: 5545671--5545745 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
5545661 GTTTCCAAAT
* *
5545671 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
5545692 TCGCAATGCGAACTTGGATTA
1 TCGCAATGCGAACTTGGACTA
5545713 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
5545734 TCGCAATGCGAA
1 TCGCAATGCGAA
5545746 TATGTAAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:5545786 original size:21 final size:21
Alignment explanation
Indices: 5545760--5545868 Score: 118
Period size: 21 Copynumber: 5.3 Consensus size: 21
5545750 TAAATCGCAA
5545760 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
*
5545781 TACGATAGTCGAAGTT--CGT
1 TGCGATAGTCGAAGTTCGCGT
*
5545800 TGTGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
* * * *
5545821 TGCGATTTATTCTAAATT--CAT
1 TGCGA--TAGTCGAAGTTCGCGT
5545842 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
5545863 TGCGAT
1 TGCGAT
5545869 TTATTCCAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
19 25 0.36
21 37 0.53
23 8 0.11
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.34
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:5545806 original size:19 final size:19
Alignment explanation
Indices: 5545762--5545817 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
5545752 AATCGCAATG
5545762 CGATAGTCGAAGTTCGCGTTA
1 CGATAGTCGAAGTT--CGTTA
*
5545783 CGATAGTCGAAGTTCGTTG
1 CGATAGTCGAAGTTCGTTA
*
5545802 TGATAGTCGAAGTTCG
1 CGATAGTCGAAGTTCG
5545818 CGTTGCGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
CGATAGTCGAAGTTCGTTA
Found at i:5545862 original size:42 final size:42
Alignment explanation
Indices: 5545760--5545892 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
5545750 TAAATCGCAA
* * * *
5545760 TGCGATAGTCGAAGTTCGCGTTACGA--TAGTCGAAGTTCGT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
* * *
5545800 TGTGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCAT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
5545842 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
5545884 TGCGATAGT
1 TGCGATAGT
5545893 ATTGCATTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 24 0.29
42 58 0.71
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (42 bp):
TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
Found at i:5545884 original size:21 final size:21
Alignment explanation
Indices: 5545818--5545889 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
5545808 TCGAAGTTCG
*
5545818 CGTTGCGATTTATTCTAAATT
1 CGTTGCGATTTATTCCAAATT
* * * *
5545839 CATTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
5545858 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
5545881 CGTTGCGAT
1 CGTTGCGAT
5545890 AGTATTGCAT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 8 0.21
21 23 0.59
23 8 0.21
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:5545974 original size:6 final size:6
Alignment explanation
Indices: 5545967--5546011 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
5545957 CGTATTACCA
* * *
5545967 CGACCA CGACCC CCACCA CGACCC CGACCC CGACCC CGACCC CGA
1 CGACCC CGACCC CGACCC CGACCC CGACCC CGACCC CGACCC CGA
5546012 GACAAGACGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.22, C:0.62, G:0.16, T:0.00
Consensus pattern (6 bp):
CGACCC
Found at i:5546008 original size:18 final size:18
Alignment explanation
Indices: 5545963--5546011 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
5545953 GACACGTATT
*
5545963 ACCACGACCACGACCCCC
1 ACCACGACCCCGACCCCC
*
5545981 ACCACGACCCCGACCCCG
1 ACCACGACCCCGACCCCC
*
5545999 ACCCCGACCCCGA
1 ACCACGACCCCGA
5546012 GACAAGACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.61, G:0.14, T:0.00
Consensus pattern (18 bp):
ACCACGACCCCGACCCCC
Found at i:5546510 original size:5 final size:5
Alignment explanation
Indices: 5546496--5546526 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5546486 CCGCCGCCGC
5546496 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
5546527 GGTCGGGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:5546551 original size:6 final size:6
Alignment explanation
Indices: 5546540--5546566 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5546530 CGGGTGATCG
5546540 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
5546567 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:5549567 original size:34 final size:34
Alignment explanation
Indices: 5549528--5549634 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
5549518 TTAGGTTGAA
* * *
5549528 TTTAATGTTAAATTTTGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
* * *
5549562 TTTAATTTTAAATTTCAAATAATATTATTTGTAT
1 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
5549596 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
5549630 TTTAA
1 TTTAA
5549635 AAACATTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATACTATAATTTGTAT
Found at i:5550118 original size:21 final size:21
Alignment explanation
Indices: 5550088--5550133 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5550078 TATGGTATAA
* *
5550088 AACCTTGCGGGCTAGGCATGT
1 AACCTGGCGGGCTAGGAATGT
5550109 AACCTGGCGGGCTAGGAATGT
1 AACCTGGCGGGCTAGGAATGT
5550130 AACC
1 AACC
5550134 CTGCGGAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.20
Consensus pattern (21 bp):
AACCTGGCGGGCTAGGAATGT
Found at i:5550139 original size:21 final size:21
Alignment explanation
Indices: 5550088--5550139 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5550078 TATGGTATAA
* *
5550088 AACCTTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
5550109 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
5550130 AACCCTGCGG
1 AACCCTGCGG
5550140 AGATGACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 22 0.81
22 3 0.11
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:5551978 original size:27 final size:27
Alignment explanation
Indices: 5551922--5552008 Score: 94
Period size: 26 Copynumber: 3.4 Consensus size: 27
5551912 ATTAGCACAA
*
5551922 AAAATAAATAATTA-ATAAA-TTTAAAT
1 AAAAT-AATAATTATATAAATTTTTAAT
5551948 -AAATAATAATTATATAAATTTTTAAT
1 AAAATAATAATTATATAAATTTTTAAT
* *
5551974 AAAATAATATTTATAT-AATTATTAAT
1 AAAATAATAATTATATAAATTTTTAAT
*
5552000 ATAA-AATAA
1 AAAATAATAA
5552009 AAACTTTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
24 8 0.15
25 13 0.25
26 18 0.34
27 14 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AAAATAATAATTATATAAATTTTTAAT
Found at i:5551991 original size:16 final size:15
Alignment explanation
Indices: 5551935--5551991 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
5551925 ATAAATAATT
*
5551935 AATAA-ATTTAAATA
1 AATAATATTTATATA
*
5551949 AATAATAATTATATA
1 AATAATATTTATATA
5551964 AAT--T-TTTA-ATAA
1 AATAATATTTATAT-A
5551976 AATAATATTTATATA
1 AATAATATTTATATA
5551991 A
1 A
5551992 TTATTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
11 2 0.06
12 7 0.21
13 1 0.03
14 6 0.18
15 16 0.47
16 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAATATTTATATA
Found at i:5553932 original size:25 final size:26
Alignment explanation
Indices: 5553887--5553941 Score: 94
Period size: 25 Copynumber: 2.1 Consensus size: 26
5553877 ACATCCTTTT
5553887 AGCGGGTCTAGAGGCATCCTAACAGCA
1 AGCGGGTCTA-AGGCATCCTAACAGCA
5553914 AGCGGGTCT-AGGCATCCTAACAGCA
1 AGCGGGTCTAAGGCATCCTAACAGCA
5553939 AGC
1 AGC
5553942 AAGAGTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 19 0.68
27 9 0.32
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.15
Consensus pattern (26 bp):
AGCGGGTCTAAGGCATCCTAACAGCA
Found at i:5556248 original size:76 final size:77
Alignment explanation
Indices: 5556117--5556305 Score: 278
Period size: 76 Copynumber: 2.5 Consensus size: 77
5556107 TTGCTAAGAA
** *
5556117 GAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGGTTTTGGCCCCGAGATTTCCAG
1 GAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAG
5556181 AATGCTCGGAGG
66 AATGCTCGGAGG
*
5556193 GAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTT-GCTCCGAGAATTCCAG
1 GAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAG
*
5556257 TATGCTCGGAGG
66 AATGCTCGGAGG
* *
5556269 GAACCGA-TCCCTCCCA-AGGGGGTACCGATTCCCCCCT
1 GAACCGATTCCC-CCCATAGGAGGAACCGATTCCCCCCT
5556306 TGTACAACGG
Statistics
Matches: 104, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
75 23 0.22
76 67 0.64
77 14 0.13
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.20
Consensus pattern (77 bp):
GAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAG
AATGCTCGGAGG
Found at i:5557370 original size:15 final size:15
Alignment explanation
Indices: 5557347--5557376 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5557337 GACGAACTGA
5557347 AATTACAACAACAAC
1 AATTACAACAACAAC
*
5557362 AATTCCAACAACAAC
1 AATTACAACAACAAC
5557377 TATAAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:5562899 original size:28 final size:27
Alignment explanation
Indices: 5562841--5562899 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
5562831 TTAAAACATT
* *
5562841 ATTATTTTATATATTTAATATTAATAT
1 ATTATTTTATATATTTAATATTAAAAA
*
5562868 ATTATTTTAATATCATTTTA-ATTAAAAA
1 ATTATTTT-ATAT-ATTTAATATTAAAAA
5562896 ATTA
1 ATTA
5562900 ATTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.30
28 14 0.52
29 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTATTTTATATATTTAATATTAAAAA
Found at i:5562946 original size:26 final size:28
Alignment explanation
Indices: 5562917--5562980 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
5562907 AATTATATTT
5562917 ATTAATATT-TTTAATAATAT-ATAAAA
1 ATTAATATTATTTAATAATATCATAAAA
* *
5562943 ATTAATATTATTTATTAATTTCATAAAA
1 ATTAATATTATTTAATAATATCATAAAA
5562971 A--AATATTATT
1 ATTAATATTATT
5562981 AAATTATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 18 0.53
27 9 0.26
28 7 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTAATATTATTTAATAATATCATAAAA
Found at i:5563049 original size:8 final size:8
Alignment explanation
Indices: 5563033--5563065 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
5563023 ATAATATTCT
5563033 TATTTTAA
1 TATTTTAA
*
5563041 TATTATAA
1 TATTTTAA
5563049 T-TTTTAA
1 TATTTTAA
5563056 TATTTTAA
1 TATTTTAA
5563064 TA
1 TA
5563066 ATATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTTAA
Found at i:5563055 original size:15 final size:15
Alignment explanation
Indices: 5563035--5563064 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5563025 AATATTCTTA
5563035 TTTTAATATTATAAT
1 TTTTAATATTATAAT
*
5563050 TTTTAATATTTTAAT
1 TTTTAATATTATAAT
5563065 AATATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAATATTATAAT
Found at i:5563061 original size:23 final size:22
Alignment explanation
Indices: 5563018--5563079 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
5563008 TCTTTAAAAT
* **
5563018 ATAATATAATATTCTTATTTTA
1 ATAATATAATTTTAATATTTTA
*
5563040 ATATTATAATTTTTAATATTTTA
1 ATAATATAA-TTTTAATATTTTA
*
5563063 ATAATATTATTTTAATA
1 ATAATATAATTTTAATA
5563080 AATAATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATAATATAATTTTAATATTTTA
Found at i:5563099 original size:42 final size:39
Alignment explanation
Indices: 5563022--5563162 Score: 101
Period size: 37 Copynumber: 3.6 Consensus size: 39
5563012 TAAAATATAA
* * * * *
5563022 TATAATATTCTTATTTTAAT--ATTATAATTTTTAATAT
1 TATAATAATATTATTTTAATAAATAATAAATATTAATAT
* *
5563059 TTTAATAATATTATTTTAATAAATAATAAAAATAATTAATAA
1 TATAATAATATTATTTTAATAAATAAT--AAAT-ATTAATAT
* * * * * *
5563101 GATATTATTCTCATTTTAATAAATAATTAATA-TAAT-T
1 TATAATAATATTATTTTAATAAATAATAAATATTAATAT
*
5563138 TATAATAATTTTATTTTAATAAATA
1 TATAATAATATTATTTTAATAAATA
5563163 TAATAATCGT
Statistics
Matches: 79, Mismatches: 20, Indels: 10
0.72 0.18 0.09
Matches are distributed among these distances:
37 37 0.47
38 4 0.05
39 5 0.06
40 3 0.04
41 3 0.04
42 27 0.34
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (39 bp):
TATAATAATATTATTTTAATAAATAATAAATATTAATAT
Found at i:5563524 original size:15 final size:15
Alignment explanation
Indices: 5563486--5563529 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
5563476 GTCTAGACTT
*
5563486 TTTTTTAAAATAAAATA
1 TTTTTT-AAA-AATATA
*
5563503 TTATTTAAAAATATA
1 TTTTTTAAAAATATA
5563518 TTTTTTAAAAAT
1 TTTTTTAAAAAT
5563530 CTGGTCACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 16 0.67
16 3 0.12
17 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTTTAAAAATATA
Found at i:5570326 original size:11 final size:12
Alignment explanation
Indices: 5570294--5570340 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
5570284 TAACTTTAAA
*
5570294 ATCTTTAATTCC
1 ATCTTTGATTCC
*
5570306 ATATTTGATTCC
1 ATCTTTGATTCC
5570318 ATC-TTGATTCC
1 ATCTTTGATTCC
5570329 ATCTTTGATTCC
1 ATCTTTGATTCC
5570341 TTGATCCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.21, C:0.23, G:0.06, T:0.49
Consensus pattern (12 bp):
ATCTTTGATTCC
Found at i:5574103 original size:104 final size:104
Alignment explanation
Indices: 5573914--5574103 Score: 290
Period size: 104 Copynumber: 1.8 Consensus size: 104
5573904 AGTATGATGA
* * * * * *
5573914 TTATCGATCGATTTTGTTTGATGCATATGTTGTATTTTCGTATAAGTACCTTTGTGTACTTTCGG
1 TTATCAATCAATTTTGTTTAATACATATGTTGCATTTTCATATAAGTACCTTTGTGTACTTTCGG
* *
5573979 CACTATGTTTACATTGATGGTGTTCATAATGAGCACTTG
66 CACTATGTGTACATTCATGGTGTTCATAATGAGCACTTG
*
5574018 TTATCAATCAATTTTGTTTAATACATATGTTGCATTTTCATATCAGTACCTTTGTGTACTTTCGG
1 TTATCAATCAATTTTGTTTAATACATATGTTGCATTTTCATATAAGTACCTTTGTGTACTTTCGG
*
5574083 CACTATGTGTGCATTCATGGT
66 CACTATGTGTACATTCATGGT
5574104 ATTTAAATGA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
104 76 1.00
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (104 bp):
TTATCAATCAATTTTGTTTAATACATATGTTGCATTTTCATATAAGTACCTTTGTGTACTTTCGG
CACTATGTGTACATTCATGGTGTTCATAATGAGCACTTG
Found at i:5575472 original size:21 final size:22
Alignment explanation
Indices: 5575440--5575486 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
5575430 ATCATAAAAC
5575440 AATTTATAAATA-CAAAAATAA
1 AATTTATAAATATCAAAAATAA
*
5575461 AATTTA-ACAATATTCAGAAATAA
1 AATTTATA-AATA-TCAAAAATAA
5575484 AAT
1 AAT
5575487 AGATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.05
21 10 0.45
23 11 0.50
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (22 bp):
AATTTATAAATATCAAAAATAA
Found at i:5576592 original size:96 final size:96
Alignment explanation
Indices: 5576425--5576611 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 96
5576415 TAGTAACCAA
* * * * * * * *
5576425 TAGATTTCATGATCCATAAATCAGGAACGATCATATTTTCCAGTGAAAAAAGGAAGCCATATAAC
1 TAGATTCCATGATCCATAAATCAGGAAAGATAATATTTTACAATGAAAAAAGGAAACCAGAGAAC
*
5576490 ACATTTCAGGTAACCATAGTTCATAATCTAG
66 ACATTTCAAGTAACCATAGTTCATAATCTAG
* ** *
5576521 TAGATTCCATGATCCATAAATCAGGAAAGATAATATTTTATAATGAGCACA-GACAACCAGAGAA
1 TAGATTCCATGATCCATAAATCAGGAAAGATAATATTTTACAATGAAAAAAGGA-AACCAGAGAA
*
5576585 CATATTTCAAGTAACCATAGTTCATAA
65 CACATTTCAAGTAACCATAGTTCATAA
5576612 ACCAATAAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
95 2 0.03
96 74 0.97
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (96 bp):
TAGATTCCATGATCCATAAATCAGGAAAGATAATATTTTACAATGAAAAAAGGAAACCAGAGAAC
ACATTTCAAGTAACCATAGTTCATAATCTAG
Found at i:5578598 original size:15 final size:15
Alignment explanation
Indices: 5578578--5578618 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
5578568 TCAAAGTCAA
5578578 TGGGTTGACTCAATT
1 TGGGTTGACTCAATT
*
5578593 TGGGTTGACTCAGTT
1 TGGGTTGACTCAATT
5578608 TGGGTTGACTC
1 TGGGTTGACTC
5578619 GTTCGGATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.32, T:0.39
Consensus pattern (15 bp):
TGGGTTGACTCAATT
Found at i:5586594 original size:104 final size:104
Alignment explanation
Indices: 5586414--5586613 Score: 265
Period size: 104 Copynumber: 1.9 Consensus size: 104
5586404 TATGATGGTT
* * * *
5586414 ATCGATCGATTTTGTTTATTGCATATGTTGCATTTTCGTACCAGTACTTTTATGTACTTTCGACA
1 ATCGATCGATTTTCTTTAATGCATATGTTGCATTTTCATACCAGTACCTTTATGTACTTTCGACA
** * *
5586479 CTATGTGTGCATTGATGGTGTTCATAATGAGCACTTTTA
66 CTATCAGTGCATTCATGGTATTCATAATGAGCACTTTTA
* ** * * **
5586518 ATCGATCGATTTTCTTTAATGCATATGTTGTATTTTCATATTAGTACCTTTGTGTACTTTTGGTA
1 ATCGATCGATTTTCTTTAATGCATATGTTGCATTTTCATACCAGTACCTTTATGTACTTTCGACA
5586583 CTATCAGTGCATTCATGGTATTCATAATGAG
66 CTATCAGTGCATTCATGGTATTCATAATGAG
5586614 TTTGTGAATT
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
104 81 1.00
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.45
Consensus pattern (104 bp):
ATCGATCGATTTTCTTTAATGCATATGTTGCATTTTCATACCAGTACCTTTATGTACTTTCGACA
CTATCAGTGCATTCATGGTATTCATAATGAGCACTTTTA
Found at i:5592794 original size:8 final size:8
Alignment explanation
Indices: 5592781--5592808 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5592771 GACTAATTTC
5592781 AAAGAATG
1 AAAGAATG
5592789 AAAGAATG
1 AAAGAATG
5592797 AAAGAATG
1 AAAGAATG
5592805 AAAG
1 AAAG
5592809 GGGTATTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (8 bp):
AAAGAATG
Found at i:5594013 original size:54 final size:54
Alignment explanation
Indices: 5593928--5594262 Score: 467
Period size: 54 Copynumber: 6.2 Consensus size: 54
5593918 CTATGTGTAC
5593928 TATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCAC-ATAATTCATCATATGTTGATGAACAACCG
*
5593982 TATAGGCACTAAGTGTGCAACCCACATAATTCATTATATGTTGATGAACAACTC-
1 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAAC-CG
* *
5594036 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTAATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCG
* * **
5594090 TAAAGGCACTGAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCG
* * *
5594144 TATAGGCATTAAGTGTGCAATCCACGTAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCG
* * * * * * **
5594198 TATAGGCAGTATGTGTACAAACCACATAATTCATAATATGTTTATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCG
*
5594252 TATGGGCACTA
1 TATAGGCACTA
5594263 CGAGTGCATC
Statistics
Matches: 253, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
53 2 0.01
54 250 0.99
55 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCG
Found at i:5594905 original size:54 final size:54
Alignment explanation
Indices: 5594823--5595096 Score: 365
Period size: 54 Copynumber: 5.1 Consensus size: 54
5594813 GCATATTTAT
* * *
5594823 TGTGCAACCCACGTAATTCATTATATGTTGATGAACAAACATATAGGCACTAAG
1 TGTGCAACCCACGAAATTCATCATATGTTGATGAACAAACGTATAGGCACTAAG
5594877 TGTGCAACCCACGAAATTCATCATATGTTGATGAAC-AACTGTATAGGCACTAAG
1 TGTGCAACCCACGAAATTCATCATATGTTGATGAACAAAC-GTATAGGCACTAAG
* *
5594931 TGTGAAACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTAAG
1 TGTGCAACCCACGAAATTCATCATATGTTGATGAACAAACGTATAGGCACTAAG
* * *
5594985 TGTGCAACCCAC-AGAATTCATCATATGTTGATGAACAACCGTATAGGCAGTATG
1 TGTGCAACCCACGA-AATTCATCATATGTTGATGAACAAACGTATAGGCACTAAG
* * * * ** *
5595039 TGTGCGAA-CCATGAAATTCATAATATATTTATGAATGAACGTATAGGCACTATG
1 TGTGC-AACCCACGAAATTCATCATATGTTGATGAACAAACGTATAGGCACTAAG
5595093 TGTG
1 TGTG
5595097 AATCTCAACG
Statistics
Matches: 199, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
53 4 0.02
54 190 0.95
55 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (54 bp):
TGTGCAACCCACGAAATTCATCATATGTTGATGAACAAACGTATAGGCACTAAG
Found at i:5597272 original size:18 final size:19
Alignment explanation
Indices: 5597243--5597280 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5597233 TCCTTTCTTT
5597243 ATTTTCAGATTCATAACTC
1 ATTTTCAGATTCATAACTC
*
5597262 ATTTT-AGATTCATAGCTC
1 ATTTTCAGATTCATAACTC
5597280 A
1 A
5597281 ATGTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (19 bp):
ATTTTCAGATTCATAACTC
Found at i:5597484 original size:19 final size:19
Alignment explanation
Indices: 5597456--5597574 Score: 193
Period size: 19 Copynumber: 6.3 Consensus size: 19
5597446 TCACTCCACC
* *
5597456 TCATAGCTCATTTTTAGAT
1 TCATAACTCATTTTCAGAT
5597475 TCATAACTCATTTTCAGAT
1 TCATAACTCATTTTCAGAT
*
5597494 TCATAAATCATTTTCAGAT
1 TCATAACTCATTTTCAGAT
5597513 TCATAACTCATTTTCAGAT
1 TCATAACTCATTTTCAGAT
*
5597532 TCATAGCTCATTTTCAGAT
1 TCATAACTCATTTTCAGAT
*
5597551 TCATAACTCATTTTTAGAT
1 TCATAACTCATTTTCAGAT
5597570 TCATA
1 TCATA
5597575 GCCTGTTGAG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 93 1.00
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (19 bp):
TCATAACTCATTTTCAGAT
Found at i:5598389 original size:19 final size:20
Alignment explanation
Indices: 5598343--5598395 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
5598333 AAAAACCTGA
*
5598343 GTGCATCGATGCATGGTCTT
1 GTGCATCGATGCATGGTCAT
5598363 GTGCATCGATGCATGGT-AT
1 GTGCATCGATGCATGGTCAT
*
5598382 GTGTATCGATGCAT
1 GTGCATCGATGCAT
5598396 AAAATGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (20 bp):
GTGCATCGATGCATGGTCAT
Found at i:5598452 original size:20 final size:20
Alignment explanation
Indices: 5598423--5598460 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5598413 TGAAAAATTA
*
5598423 ATTGGTGCATCGATGCATGG
1 ATTGGAGCATCGATGCATGG
*
5598443 ATTGGAGCATCGGTGCAT
1 ATTGGAGCATCGATGCAT
5598461 TACTTTGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (20 bp):
ATTGGAGCATCGATGCATGG
Found at i:5605105 original size:22 final size:21
Alignment explanation
Indices: 5605063--5605102 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5605053 GAGTTTATTT
*
5605063 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5605084 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5605103 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5607113 original size:20 final size:20
Alignment explanation
Indices: 5607088--5607141 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
5607078 AAAAACCTGA
5607088 GTGCATCGATGCATGGTCTT
1 GTGCATCGATGCATGGTCTT
5607108 GTGCATCGATGCATGGTCTT
1 GTGCATCGATGCATGGTCTT
5607128 GTGCATCGATGCAT
1 GTGCATCGATGCAT
5607142 CAAATGCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (20 bp):
GTGCATCGATGCATGGTCTT
Found at i:5607239 original size:20 final size:20
Alignment explanation
Indices: 5607214--5607251 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5607204 TGAAAAATTA
5607214 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
* *
5607234 ATTGGTTCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
5607252 CATTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:5611224 original size:29 final size:29
Alignment explanation
Indices: 5611142--5611232 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 29
5611132 CAAAATATAT
* *
5611142 AACTTTTAAAATTTATATTTTTGGTCCA-TG
1 AACTTTCAAAATTTATA-TTTTGG-CCACTA
*
5611172 AACTTTTCCAAAATTTATACTTTGGCCACTA
1 AAC-TTT-CAAAATTTATATTTTGGCCACTA
* *
5611203 AACTTTCAAAATTTACATTTTGGCAACTA
1 AACTTTCAAAATTTATATTTTGGCCACTA
5611232 A
1 A
5611233 CCAAAATTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
29 21 0.40
30 9 0.17
31 12 0.23
32 10 0.19
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (29 bp):
AACTTTCAAAATTTATATTTTGGCCACTA
Found at i:5612060 original size:2 final size:2
Alignment explanation
Indices: 5612055--5612083 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5612045 AAACACACAC
5612055 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5612084 CACCCCCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5612270 original size:24 final size:24
Alignment explanation
Indices: 5612243--5612311 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
5612233 AAATGGAGAT
*
5612243 ATCAGAAATCAAAATAGAATTCAG
1 ATCAGAAATCAAAATAGAATTCAA
* * * *
5612267 ATCAGATATCATAACAGAATCCAA
1 ATCAGAAATCAAAATAGAATTCAA
* *
5612291 ATCAAAAATCAGAATAGAATT
1 ATCAGAAATCAAAATAGAATT
5612312 TAGGTAATGT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.54, C:0.14, G:0.10, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAATAGAATTCAA
Found at i:5612349 original size:24 final size:24
Alignment explanation
Indices: 5612244--5612349 Score: 72
Period size: 24 Copynumber: 4.4 Consensus size: 24
5612234 AATGGAGATA
*
5612244 TCAGAAATCAAAATAGAATTC-AG
1 TCAGAAATCAAAACAGAATTCAAG
* * * *
5612267 ATCAGATATCATAACAGAATCCAAA
1 -TCAGAAATCAAAACAGAATTCAAG
* * * * *
5612292 TCAAAAATCAGAATAGAATTTAGG
1 TCAGAAATCAAAACAGAATTCAAG
* *
5612316 TAATG-TATCAAAACAGAATTCAAG
1 TCA-GAAATCAAAACAGAATTCAAG
5612340 TCAGAAATCA
1 TCAGAAATCA
5612350 GATAAAATAT
Statistics
Matches: 57, Mismatches: 22, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
23 1 0.02
24 55 0.96
25 1 0.02
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (24 bp):
TCAGAAATCAAAACAGAATTCAAG
Found at i:5615291 original size:23 final size:23
Alignment explanation
Indices: 5615261--5615314 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
5615251 TCGGTTCGTC
5615261 GATCGGAGGTCAGACGGCGAGTA
1 GATCGGAGGTCAGACGGCGAGTA
*
5615284 GATCGGAGGTCAGATGGCGAGTA
1 GATCGGAGGTCAGACGGCGAGTA
5615307 GATCGGAG
1 GATCGGAG
5615315 TTGAATTGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.15, G:0.44, T:0.15
Consensus pattern (23 bp):
GATCGGAGGTCAGACGGCGAGTA
Found at i:5619408 original size:19 final size:19
Alignment explanation
Indices: 5619384--5619454 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
5619374 CATTTCTTTG
*
5619384 TTTTCAGATTCATAACTAA
1 TTTTCAGATTCATAACTCA
* *
5619403 TTTTCAGACTCATAGCTCA
1 TTTTCAGATTCATAACTCA
5619422 TTTTCAGATTCATAACTCA
1 TTTTCAGATTCATAACTCA
5619441 TTTTCAGATTCATA
1 TTTTCAGATTCATA
5619455 GTCCAATGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (19 bp):
TTTTCAGATTCATAACTCA
Found at i:5619825 original size:20 final size:20
Alignment explanation
Indices: 5619795--5619834 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5619785 TTCTTACTTG
5619795 AAATCATATATAATTAAAATA
1 AAATCATATATAA-TAAAATA
*
5619816 AAAT-ATATATTATAAAATA
1 AAATCATATATAATAAAATA
5619835 CTTCAGGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATCATATATAATAAAATA
Found at i:5622856 original size:29 final size:30
Alignment explanation
Indices: 5622812--5622873 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
5622802 TTGGTCCATA
*
5622812 AAACTTTCCAAAATTTATACTTTGGCCACT
1 AAACTTTCCAAAATTTACACTTTGGCCACT
* *
5622842 AAACTTT-CAAAATTTACATTTTGGTCACT
1 AAACTTTCCAAAATTTACACTTTGGCCACT
5622871 AAA
1 AAA
5622874 TAAATTTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.37
Consensus pattern (30 bp):
AAACTTTCCAAAATTTACACTTTGGCCACT
Found at i:5622951 original size:10 final size:10
Alignment explanation
Indices: 5622936--5622963 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5622926 TGTGAGGAAG
5622936 CCCTGCCTGA
1 CCCTGCCTGA
5622946 CCCTGCCTGA
1 CCCTGCCTGA
5622956 CCCTGCCT
1 CCCTGCCT
5622964 CTTTCACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.54, G:0.18, T:0.21
Consensus pattern (10 bp):
CCCTGCCTGA
Found at i:5626965 original size:178 final size:177
Alignment explanation
Indices: 5626666--5627021 Score: 703
Period size: 178 Copynumber: 2.0 Consensus size: 177
5626656 TCATTAACAA
5626666 TCGAAAAAGTATCATTCAAGCATTTCCAACACCAAATAAAACAATTTATGGTATGGCAAACATCA
1 TCGAAAAAGTATCATTCAAGCATTTCCAACACCAAATAAAACAATTTATGGTATGGCAAACATCA
5626731 TCCCAAAAGTATTATTTAAATACAAGCCTTTAAATGATATGGAAATGAAGAACAAGAGGAAGAAA
66 TCCCAAAAGTATTATTTAAATACAAGCCTTTAAATGATATGGAAATGAAGAACAAGAGGAAG-AA
5626796 AAACTCCCAGAACAGAGCTATGCCATGACATCAGACCACCACCATGAC
130 AAACTCCCAGAACAGAGCTATGCCATGACATCAGACCACCACCATGAC
5626844 TCGAAAAAGTATCATTCAAGCATTTCCAACACCAAATAAAACAATTTATGGTATGGCAAACATCA
1 TCGAAAAAGTATCATTCAAGCATTTCCAACACCAAATAAAACAATTTATGGTATGGCAAACATCA
5626909 TCCCAAAAGTATTATTTAAATACAAGCCTTTAAATGATATGGAAATGAAGAACAAGAGGAAGAAA
66 TCCCAAAAGTATTATTTAAATACAAGCCTTTAAATGATATGGAAATGAAGAACAAGAGGAAGAAA
5626974 AACTCCCAGAACAGAGCTATGCCATGACATCAGACCACCACCATGAC
131 AACTCCCAGAACAGAGCTATGCCATGACATCAGACCACCACCATGAC
5627021 T
1 T
5627022 GCTCCAGTGG
Statistics
Matches: 178, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
177 51 0.29
178 127 0.71
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (177 bp):
TCGAAAAAGTATCATTCAAGCATTTCCAACACCAAATAAAACAATTTATGGTATGGCAAACATCA
TCCCAAAAGTATTATTTAAATACAAGCCTTTAAATGATATGGAAATGAAGAACAAGAGGAAGAAA
AACTCCCAGAACAGAGCTATGCCATGACATCAGACCACCACCATGAC
Found at i:5630720 original size:64 final size:67
Alignment explanation
Indices: 5630616--5630747 Score: 243
Period size: 64 Copynumber: 2.0 Consensus size: 67
5630606 GGTCTCCACA
5630616 GTGCTTGGATAAGAACAGTTCATTCCAATAATAATGTAATACATCTTGTCTGAACTTTTTCAACC
1 GTGCTTGGATAAGAACAGTTCATTCCAATAATAATGTAATACATCTTGTCTGAACTTTTTCAACC
5630681 CT
66 CT
5630683 GTGCTT-GAT-AGAACAG-TCATTCCAATAATAATGTAATACATCTTGTCTGAACTTTTTCAACC
1 GTGCTTGGATAAGAACAGTTCATTCCAATAATAATGTAATACATCTTGTCTGAACTTTTTCAACC
5630745 CT
66 CT
5630747 G
1 G
5630748 GCAAGATAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
64 49 0.75
65 7 0.11
66 3 0.05
67 6 0.09
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (67 bp):
GTGCTTGGATAAGAACAGTTCATTCCAATAATAATGTAATACATCTTGTCTGAACTTTTTCAACC
CT
Found at i:5633135 original size:90 final size:90
Alignment explanation
Indices: 5632982--5633279 Score: 560
Period size: 90 Copynumber: 3.3 Consensus size: 90
5632972 GTGTGTTTTC
*
5632982 TCTATATCTAATTAATTGGAATTTAATAATCCTTTTATATCCAAGTTACCCTAATCATATTAGGG
1 TCTATATTTAATTAATTGGAATTTAATAATCCTTTTATATCCAAGTTACCCTAATCATATTAGGG
5633047 ATTTTATTATTTCAAATTAATTAAA
66 ATTTTATTATTTCAAATTAATTAAA
5633072 TCTATATTTAATTAATTGGAATTTAATAATCCTTTTATATCCAAGTTACCCTAATCATATTAGGG
1 TCTATATTTAATTAATTGGAATTTAATAATCCTTTTATATCCAAGTTACCCTAATCATATTAGGG
5633137 ATTTTATTATTTCAAATTAATTAAA
66 ATTTTATTATTTCAAATTAATTAAA
*
5633162 TATATATTTAATTAATTGGAATTTAATAATCCTTTTATATCCAAGTTACCCTAATCATATTAGGG
1 TCTATATTTAATTAATTGGAATTTAATAATCCTTTTATATCCAAGTTACCCTAATCATATTAGGG
5633227 ATTTTATTATTTCAAATTAATTAAA
66 ATTTTATTATTTCAAATTAATTAAA
* *
5633252 TCTATATTTAATTAATTGAAATTAAATA
1 TCTATATTTAATTAATTGGAATTTAATA
5633280 TTCGGGATTA
Statistics
Matches: 203, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 203 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.45
Consensus pattern (90 bp):
TCTATATTTAATTAATTGGAATTTAATAATCCTTTTATATCCAAGTTACCCTAATCATATTAGGG
ATTTTATTATTTCAAATTAATTAAA
Found at i:5651091 original size:66 final size:66
Alignment explanation
Indices: 5650985--5651117 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
5650975 GATAGTGAAA
5650985 CTCTATGCATCATTTAATTCGGTGGAATTCTACTCACATCCATGGCATTGCACCCTTTAGTGAGT
1 CTCTATGCATCATTTAATTCGGTGGAATTCTACTCACATCCATGGCATTGCACCCTTTAGTGAGT
5651050 G
66 G
5651051 CTCTATGCATCATTTAATTCGGTGGAATTCTACTCACATCCATGGCATTGCACCCTTTAGTGAGT
1 CTCTATGCATCATTTAATTCGGTGGAATTCTACTCACATCCATGGCATTGCACCCTTTAGTGAGT
5651116 G
66 G
5651117 C
1 C
5651118 AACAAATTTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (66 bp):
CTCTATGCATCATTTAATTCGGTGGAATTCTACTCACATCCATGGCATTGCACCCTTTAGTGAGT
G
Found at i:5663407 original size:16 final size:16
Alignment explanation
Indices: 5663382--5663450 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
5663372 GGTATTACCC
5663382 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
5663398 GACCTATTTTCAACCT
1 GACCTGTTTTCAACCT
*
5663414 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
* * *
5663430 GACATGTTTTTAACAT
1 GACCTGTTTTCAACCT
5663446 GACCT
1 GACCT
5663451 ATAAATTATC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:5663683 original size:16 final size:13
Alignment explanation
Indices: 5663650--5663676 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5663640 GACCTATTAT
5663650 ATAAAATTATTTA
1 ATAAAATTATTTA
5663663 ATAAAATTATTTA
1 ATAAAATTATTTA
5663676 A
1 A
5663677 AAATAAATTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:5663738 original size:14 final size:14
Alignment explanation
Indices: 5663716--5663762 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
5663706 TGCAAAGGAA
*
5663716 AATTAATATAGTTT
1 AATTTATATAGTTT
5663730 AATTTATATA----
1 AATTTATATAGTTT
5663740 AA-TTATATAGTTT
1 AATTTATATAGTTT
5663753 AATTTATATA
1 AATTTATATA
5663763 AAGAAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:5663749 original size:23 final size:24
Alignment explanation
Indices: 5663715--5663764 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
5663705 ATGCAAAGGA
5663715 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
5663739 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
5663762 AAA
1 AAA
5663765 GAAGAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Done.