Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 38
Found at i:3616869 original size:5 final size:5
Alignment explanation
Indices: 3616169--3616867 Score: 975
Period size: 5 Copynumber: 139.8 Consensus size: 5
3616159 ATAACATTAT
*
3616169 AATAT AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
3616219 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
3616269 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* * * *
3616319 AATAC AATAC AATAC AATAC AATAC AATAC AGTAC AACAC AGTAC AGTAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* * * * * * * ** ** *
3616369 AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGCAC AGCAC AGTAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* *** * * * * * * * *
3616419 AGTAC AGCGC ATTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* * * * * * * * *
3616469 AGTAC AGTAC AATAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
*
3616519 AGTAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
3616569 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
3616619 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
3616669 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
3616719 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
3616769 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* * * * * * * *
3616819 AATAC AATAA AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
3616868 TATGTGTGTA
Statistics
Matches: 675, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 675 1.00
ACGTcount: A:0.55, C:0.19, G:0.05, T:0.21
Consensus pattern (5 bp):
AATAC
Found at i:3625323 original size:142 final size:142
Alignment explanation
Indices: 3625067--3625329 Score: 499
Period size: 142 Copynumber: 1.9 Consensus size: 142
3625057 GAAAAATCAT
*
3625067 ATGAAATGACATGTCCTTCACATGCTAATTCTTTATCATTTAGCATTTGAATAATAACTCGTTTT
1 ATGAAATGACATGTCCTTCACATGCTAATTCTTTATCATTTAGCATTTGAATAATAACTCGCTTT
3625132 AACAATTAACCCAATATAACATAGGTGACTATGAATACTCGAATCCTTACAATATCGCCAAATCA
66 AACAATTAACCCAATATAACATAGGTGACTATGAATACTCGAATCCTTACAATATCGCCAAATCA
3625197 GAAAAATCTAAA
131 GAAAAATCTAAA
* *
3625209 ATGAAATGACATGTCCTTCACATGCTAATTCTTTATCTTTTATCATTTGAATAATAACTCGCTTT
1 ATGAAATGACATGTCCTTCACATGCTAATTCTTTATCATTTAGCATTTGAATAATAACTCGCTTT
3625274 AACAATTAACCCAATATAACATAGGTGACTATGAATACTCGAATCCTTACAATATC
66 AACAATTAACCCAATATAACATAGGTGACTATGAATACTCGAATCCTTACAATATC
3625330 CGTCCAACAT
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 118 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (142 bp):
ATGAAATGACATGTCCTTCACATGCTAATTCTTTATCATTTAGCATTTGAATAATAACTCGCTTT
AACAATTAACCCAATATAACATAGGTGACTATGAATACTCGAATCCTTACAATATCGCCAAATCA
GAAAAATCTAAA
Found at i:3631900 original size:25 final size:25
Alignment explanation
Indices: 3631872--3631944 Score: 60
Period size: 25 Copynumber: 2.9 Consensus size: 25
3631862 TTTTGAAATT
*
3631872 TATTTTTTTTAAATATTAAAAATAC
1 TATTTTTTTTAAATATTAAAAACAC
* *
3631897 TATTATATTT--ATATTAAAAAACAC
1 TATTTTTTTTAAATATT-AAAAACAC
* *
3631921 TAATTTTTCTTAAATTATAAAAAA
1 T-ATTTTTTTTAAA-TATTAAAAA
3631945 GCCCCAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
23 5 0.14
24 8 0.22
25 14 0.39
27 6 0.17
28 3 0.08
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTTTTTTTAAATATTAAAAACAC
Found at i:3635216 original size:67 final size:67
Alignment explanation
Indices: 3635132--3635267 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 67
3635122 CCAGATATAT
* * * *
3635132 CATGTGAAATAGACAAAGTAGCTCTACACAAAACCATTGATGGCCATATGATATTTCTCTAATGA
1 CATGTGAAATAAACAAAGTAGCTCTACACAAAACCATTGATGGCCACATGATATATCTCTAAAGA
3635197 GG
66 GG
*
3635199 CATGTGAAATAAACAAAGTAGCTCTACACAAAACCATTGATGGTCACATGATATATCTCTAAAGA
1 CATGTGAAATAAACAAAGTAGCTCTACACAAAACCATTGATGGCCACATGATATATCTCTAAAGA
3635264 GG
66 GG
3635266 CA
1 CA
3635268 GCATAAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (67 bp):
CATGTGAAATAAACAAAGTAGCTCTACACAAAACCATTGATGGCCACATGATATATCTCTAAAGA
GG
Found at i:3639825 original size:22 final size:22
Alignment explanation
Indices: 3639799--3639840 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3639789 CAGATTGCTC
3639799 AGAGGGAACCGATTCCCCCCCA
1 AGAGGGAACCGATTCCCCCCCA
*
3639821 AGAGGGTACCGATTCCCCCC
1 AGAGGGAACCGATTCCCCCC
3639841 TGAATGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (22 bp):
AGAGGGAACCGATTCCCCCCCA
Found at i:3642925 original size:13 final size:13
Alignment explanation
Indices: 3642907--3642932 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3642897 CCATGCTTTG
3642907 CCAAAATATTTTT
1 CCAAAATATTTTT
3642920 CCAAAATATTTTT
1 CCAAAATATTTTT
3642933 GGGCGGAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
CCAAAATATTTTT
Found at i:3645337 original size:21 final size:23
Alignment explanation
Indices: 3645302--3645362 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
3645292 TTGGTGCAGA
*
3645302 GGGAATCGA-TCCCCCCATG-A-
1 GGGAACCGATTCCCCCCATGAAG
* **
3645322 GGGAACCTATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATGAAG
3645345 GGGAACCGATTCCCCCCA
1 GGGAACCGATTCCCCCCA
3645363 CAAGGGAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.23
21 8 0.26
22 1 0.03
23 15 0.48
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.18
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCATGAAG
Found at i:3645375 original size:21 final size:21
Alignment explanation
Indices: 3645301--3645381 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 21
3645291 TTTGGTGCAG
* **
3645301 AGGGAATCGA-TCCCCCCATG
1 AGGGAACCGATTCCCCCCACA
* ***
3645321 AGGGAACCTATTCCCCCTTTGA
1 AGGGAACCGATTCCCCC-CACA
3645343 AGGGGAACCGATTCCCCCCACA
1 A-GGGAACCGATTCCCCCCACA
* *
3645365 AGGGAATCGATACCCCC
1 AGGGAACCGATTCCCCC
3645382 TTGGGGTTCT
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
20 8 0.17
21 20 0.43
22 3 0.07
23 15 0.33
ACGTcount: A:0.26, C:0.36, G:0.22, T:0.16
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCCACA
Found at i:3652283 original size:22 final size:22
Alignment explanation
Indices: 3652258--3652312 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3652248 GAAGGAGTTA
* *
3652258 CAGGAGTTATTTGATTTAATTT
1 CAGGAGTTATATGATATAATTT
* *
3652280 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTT
*
3652302 CGGGAGTTATA
1 CAGGAGTTATA
3652313 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTT
Found at i:3657842 original size:6 final size:6
Alignment explanation
Indices: 3657831--3657867 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
3657821 ACGGATCGGC
* *
3657831 TCGTGG TCGTGG TCGTGG TCATGA TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
3657868 AATACGTGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.05, C:0.16, G:0.43, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:3677572 original size:22 final size:22
Alignment explanation
Indices: 3677545--3677596 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
3677535 GGAGTTACAT
* *
3677545 GAGTTATTTGATTTAATTCCAG
1 GAGTTATATGATATAATTCCAG
* * *
3677567 GGGTTACATGATATAATTTCAG
1 GAGTTATATGATATAATTCCAG
3677589 GAGTTATA
1 GAGTTATA
3677597 ACAACTGAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (22 bp):
GAGTTATATGATATAATTCCAG
Found at i:3681230 original size:20 final size:20
Alignment explanation
Indices: 3681207--3681273 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
3681197 CACGGAATGT
3681207 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
3681227 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
*
3681247 AAGATTACCAGTGAGAATAA
1 AAGATTACCAGTGGGAATAA
3681267 AAGATTA
1 AAGATTA
3681274 TCAGGGAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.21
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:3685278 original size:22 final size:21
Alignment explanation
Indices: 3685253--3685321 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
3685243 GCATACATGC
*
3685253 ATTTGCATTTTATTTGTGTTAT
1 ATTTGCATTTTATTTGTATT-T
3685275 ATTTGCATTATTATATT-TATTT
1 ATTTGCATT-TTAT-TTGTATTT
* *
3685297 ATTTAGCATTTT-TTTGCATTC
1 ATTT-GCATTTTATTTGTATTT
3685318 ATTT
1 ATTT
3685322 TCAAAACTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 2 0.05
21 8 0.20
22 16 0.40
23 12 0.30
24 2 0.05
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62
Consensus pattern (21 bp):
ATTTGCATTTTATTTGTATTT
Found at i:3687725 original size:18 final size:18
Alignment explanation
Indices: 3687702--3687746 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
3687692 ATTAACCCTA
3687702 GGGAAAGGAGCAAAAGCT
1 GGGAAAGGAGCAAAAGCT
*
3687720 GGGAAAGGAGCAAAAGTT
1 GGGAAAGGAGCAAAAGCT
3687738 GGGAAAGGA
1 GGGAAAGGA
3687747 TTAGGAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.42, T:0.07
Consensus pattern (18 bp):
GGGAAAGGAGCAAAAGCT
Found at i:3692087 original size:19 final size:19
Alignment explanation
Indices: 3692063--3692101 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3692053 TACCTAGAAA
*
3692063 GTTTCAATCGTATGAAGAT
1 GTTTCAATCATATGAAGAT
3692082 GTTTCAATCATATGAAGAT
1 GTTTCAATCATATGAAGAT
3692101 G
1 G
3692102 ATCCAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (19 bp):
GTTTCAATCATATGAAGAT
Found at i:3692651 original size:136 final size:135
Alignment explanation
Indices: 3692401--3692846 Score: 617
Period size: 136 Copynumber: 3.3 Consensus size: 135
3692391 CTTAGATAAC
* * * * * *
3692401 CAGACGTCCTTATCACGAAGGAACAATGCCATCTACCGATCAGAACTCTTCATCAAGAATGAGCA
1 CAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCA
*
3692466 AATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAA
66 GATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAA
3692531 GATGG
131 GATGG
* *
3692536 TCAGACGTTCTCATCACGAAGGAATAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGC
1 -CAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGC
* *
3692601 AGCATCA-CCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCATATTATCTCAAATATCTTTA
65 AG-ATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
3692665 AAGATGG
129 AAGATGG
* * *
3692672 CTAGACGTCCTCATCACGAAGGAACAATTTCATCCACTGA-CTAGAACTCCTCATCACGTAGGAG
1 C-AGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATC-AGAACTCCTCATCACGAAGGAG
* * ** * * *
3692736 CCGAGTCATCCTCAGATAATCAGACGTCCTGATCACGAAGGAACCGTGTTATCTCAAATATCTTC
64 CAGA-TCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
3692801 AAAGATGG
128 AAAGATGG
* *
3692809 CCAGACGTCCTCATCATGAAGGAACAATGTCATACACC
1 -CAGACGTCCTCATCACGAAGGAACAATGTCATCCACC
3692847 AGTTGGATCT
Statistics
Matches: 275, Mismatches: 29, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
135 3 0.01
136 179 0.65
137 92 0.33
138 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (135 bp):
CAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCA
GATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAA
GATGG
Found at i:3693014 original size:3 final size:3
Alignment explanation
Indices: 3692999--3693045 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
3692989 GAGACTATCA
*
3692999 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3693046 CAAAATAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3693681 original size:9 final size:10
Alignment explanation
Indices: 3693657--3693684 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3693647 AAGCAAAATA
3693657 GAAAAATGAG
1 GAAAAATGAG
3693667 GAAAAATGAG
1 GAAAAATGAG
3693677 GAAAAATG
1 GAAAAATG
3693685 GCCATTTAAG
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:0.61, C:0.00, G:0.29, T:0.11
Consensus pattern (10 bp):
GAAAAATGAG
Found at i:3694206 original size:2 final size:2
Alignment explanation
Indices: 3694193--3694222 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3694183 ACACATTAAG
*
3694193 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3694223 GAAAAATTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3702796 original size:31 final size:31
Alignment explanation
Indices: 3702758--3702817 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3702748 ATGGATGAGT
*
3702758 GACTAAAATCGAATGGACCGATAACTTTAGA
1 GACTAAAATCGAATGGACCAATAACTTTAGA
* *
3702789 GACTAAAATTGAATGGACTAATAACTTTA
1 GACTAAAATCGAATGGACCAATAACTTTA
3702818 AGGATCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (31 bp):
GACTAAAATCGAATGGACCAATAACTTTAGA
Found at i:3708658 original size:14 final size:15
Alignment explanation
Indices: 3708622--3708664 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
3708612 ACTTTAAGAG
3708622 GAAAATGAGAGAGAA
1 GAAAATGAGAGAGAA
*
3708637 GAAAATGAGAGTGAA
1 GAAAATGAGAGAGAA
3708652 G-AAATGA-AGAGAA
1 GAAAATGAGAGAGAA
3708665 TGAGGTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 5 0.19
14 6 0.23
15 15 0.58
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (15 bp):
GAAAATGAGAGAGAA
Found at i:3709564 original size:14 final size:14
Alignment explanation
Indices: 3709545--3709571 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3709535 TTTTCTTTTA
3709545 TTTATTTATTTATT
1 TTTATTTATTTATT
3709559 TTTATTTATTTAT
1 TTTATTTATTTAT
3709572 CATTAGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:3718522 original size:47 final size:49
Alignment explanation
Indices: 3718454--3718561 Score: 136
Period size: 47 Copynumber: 2.2 Consensus size: 49
3718444 TTATTTTTTC
* *
3718454 TTTAAATTATATATATTATATATAT-ATATATAATTCTAAAA-TTTA-AAA
1 TTTAAATTATATATATTATATA-ATCACATAAAATT-TAAAAGTTTACAAA
3718502 TTTAAATGTATATA-A-TATATAATCACATAAAATTTAAAAGTTTACAAA
1 TTTAAAT-TATATATATTATATAATCACATAAAATTTAAAAGTTTACAAA
3718550 TTTAAATTATAT
1 TTTAAATTATAT
3718562 GCACGAACCA
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
46 7 0.13
47 23 0.43
48 18 0.33
49 6 0.11
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (49 bp):
TTTAAATTATATATATTATATAATCACATAAAATTTAAAAGTTTACAAA
Found at i:3723333 original size:19 final size:19
Alignment explanation
Indices: 3723309--3723356 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 19
3723299 TAGTTTGATG
3723309 AATGCCTCTGCAACAAAGT
1 AATGCCTCTGCAACAAAGT
*
3723328 AATGCCTTTTCTGCCACAAAGT
1 AATGCC---TCTGCAACAAAGT
3723350 AATGCCT
1 AATGCCT
3723357 TTTCTGCCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 7 0.28
22 18 0.72
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (19 bp):
AATGCCTCTGCAACAAAGT
Found at i:3723346 original size:22 final size:22
Alignment explanation
Indices: 3723315--3723367 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
3723305 GATGAATGCC
*
3723315 TCTGCAACAAAGTAATGCCTTT
1 TCTGCCACAAAGTAATGCCTTT
3723337 TCTGCCACAAAGTAATGCCTTT
1 TCTGCCACAAAGTAATGCCTTT
3723359 TCTGCCACA
1 TCTGCCACA
3723368 TGGAGCTGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (22 bp):
TCTGCCACAAAGTAATGCCTTT
Found at i:3725893 original size:14 final size:14
Alignment explanation
Indices: 3725876--3725940 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
3725866 ATTAATATAA
3725876 TAATTTTAAAATAT
1 TAATTTTAAAATAT
3725890 TAATTATTAAAATATT
1 TAATT-TTAAAATA-T
* *
3725906 TAA-TATATAATA-
1 TAATTTTAAAATAT
*
3725918 TAGTTTTAATAATAT
1 TAATTTTAA-AATAT
3725933 TATATTTT
1 TA-ATTTT
3725941 TAATATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
12 2 0.05
13 3 0.08
14 15 0.38
15 11 0.28
16 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TAATTTTAAAATAT
Found at i:3725901 original size:15 final size:15
Alignment explanation
Indices: 3725865--3725905 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
3725855 ATTTATTTAG
* *
3725865 TATTAATATAATAAT
1 TATTAAAATATTAAT
3725880 T-TTAAAATATTAAT
1 TATTAAAATATTAAT
3725894 TATTAAAATATT
1 TATTAAAATATT
3725906 TAATATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTAAAATATTAAT
Found at i:3725941 original size:17 final size:18
Alignment explanation
Indices: 3725904--3725946 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
3725894 TATTAAAATA
3725904 TTTAATATATAATATAGT
1 TTTAATATATAATATAGT
* *
3725922 TTTAATA-ATATTATATT
1 TTTAATATATAATATAGT
3725939 TTTAATAT
1 TTTAATAT
3725947 TTTATTGCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAATATATAATATAGT
Found at i:3726066 original size:32 final size:32
Alignment explanation
Indices: 3726030--3726091 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
3726020 GGTGTAACGC
*
3726030 ACCAAAAAGTACAAAGACCATAGCTGTAGTTT
1 ACCAAAAAGTACAAAGACCAAAGCTGTAGTTT
3726062 ACCAAAAAGTACAAAGACCAAAGCTGTAGT
1 ACCAAAAAGTACAAAGACCAAAGCTGTAGT
3726092 AAATGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (32 bp):
ACCAAAAAGTACAAAGACCAAAGCTGTAGTTT
Found at i:3728073 original size:19 final size:19
Alignment explanation
Indices: 3728008--3728065 Score: 98
Period size: 19 Copynumber: 3.1 Consensus size: 19
3727998 GTAACCCTCT
* *
3728008 AGCTATAAAAGAACTAGAA
1 AGCTATAAAAGAGCTAGGA
3728027 AGCTATAAAAGAGCTAGGA
1 AGCTATAAAAGAGCTAGGA
3728046 AGCTATAAAAGAGCTAGGA
1 AGCTATAAAAGAGCTAGGA
3728065 A
1 A
3728066 TTTATAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.16
Consensus pattern (19 bp):
AGCTATAAAAGAGCTAGGA
Found at i:3728657 original size:13 final size:13
Alignment explanation
Indices: 3728639--3728664 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3728629 GTCATAAATC
3728639 TATGACGCGCATT
1 TATGACGCGCATT
3728652 TATGACGCGCATT
1 TATGACGCGCATT
3728665 GCGCGTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:3728737 original size:85 final size:86
Alignment explanation
Indices: 3728578--3728764 Score: 207
Period size: 85 Copynumber: 2.2 Consensus size: 86
3728568 GACACACAAA
* * **
3728578 TGCGCGTCATTGAAGCCACCGTCATAAATCTCAGATGACATCCAATTGTGTGTCATAAATCTATG
1 TGCGCGTCATTGAAGCCACCGTAAAAAATCGAAGATGACATCCAATTGTGTGTCATAAATCTATG
* * *
3728643 ACGCGCATTTATGACGCGCAT
66 ACGCACATTTACGACGCACAT
* * * *
3728664 TGCGCGTCATTGAAGCCCCCGTAAAAAAT-GAAGATGACA-CACATTTGTGTGTCATAATTTTAT
1 TGCGCGTCATTGAAGCCACCGTAAAAAATCGAAGATGACATC-CAATTGTGTGTCATAAATCTAT
** **
3728727 GACTTACATTTACGACTTACAT
65 GACGCACATTTACGACGCACAT
*
3728749 TGCGTGTCATTGAAGC
1 TGCGCGTCATTGAAGC
3728765 ACACGTCATT
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
84 1 0.01
85 57 0.68
86 26 0.31
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (86 bp):
TGCGCGTCATTGAAGCCACCGTAAAAAATCGAAGATGACATCCAATTGTGTGTCATAAATCTATG
ACGCACATTTACGACGCACAT
Found at i:3728828 original size:2 final size:2
Alignment explanation
Indices: 3728821--3728873 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3728811 TATCATAAAT
3728821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3728863 TA TA TA TA TA T
1 TA TA TA TA TA T
3728874 TGTAGATTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3743380 original size:19 final size:19
Alignment explanation
Indices: 3743345--3743386 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3743335 CCCCCTTTGA
*
3743345 AGGGGAACTGATTCCCCCT
1 AGGGGAACTGATACCCCCT
3743364 AGGGGAA-TCGATACCCCCT
1 AGGGGAACT-GATACCCCCT
3743383 -GGGG
1 AGGGG
3743387 TTCTGGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (19 bp):
AGGGGAACTGATACCCCCT
Found at i:3743515 original size:19 final size:18
Alignment explanation
Indices: 3743473--3743515 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3743463 CTCTACTCTC
*
3743473 TCAAATCAACATTTTGCA
1 TCAAATCAACATTTTGAA
*
3743491 TCAAATCAACATTTTTAA
1 TCAAATCAACATTTTGAA
3743509 TCGAAAT
1 TC-AAAT
3743516 TCTCTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.35
Consensus pattern (18 bp):
TCAAATCAACATTTTGAA
Found at i:3745885 original size:22 final size:22
Alignment explanation
Indices: 3745841--3745885 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3745831 ATTTTCAATC
*
3745841 TTAAAATAATTTCAAAACGATT
1 TTAAAATAATTTCAAAACCATT
*
3745863 TTAAAATATATTTC-GAACCATT
1 TTAAAATA-ATTTCAAAACCATT
3745885 T
1 T
3745886 CAAAGCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (22 bp):
TTAAAATAATTTCAAAACCATT
Found at i:3746845 original size:81 final size:81
Alignment explanation
Indices: 3746710--3747818 Score: 1468
Period size: 81 Copynumber: 13.6 Consensus size: 81
3746700 CATTTAACTT
* * * * *
3746710 TTCATCTAACTTGCATGATTGATA-CTTTCCTGCCAAATGCACAGTTAGGTCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTT-CTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* *
3746774 TAAACGGTCATTAACCG
65 TCAACGGTCTTTAACCG
*
3746791 TTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* *
3746856 CAACAGTCTTTAACTG
66 CAACGGTCTTTAACCG
*
3746872 TTCATCTAACTGGCATAATCGACACCATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACC-TTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* *
3746937 TCAAAGGTCTTTAACTG
65 TCAACGGTCTTTAACCG
* * * * *
3746954 TTCATCTAACTGACATAATTGACACATTTCTGCCATATGCACAACTAGGTCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
*
3747019 CAATGGTCTTTAACCG
66 CAACGGTCTTTAACCG
* * *
3747035 CTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGACCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
*
3747100 CAACGGTCTTTAACTG
66 CAACGGTCTTTAACCG
* * * * * * *
3747116 TTCATCTAACTTGTATAAATTGACACATTTCTGTCAAATGCACAGTTAGGCCATTTATATTTTGC
1 TTCATCTAACTGGCAT-AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
*
3747181 TCAACGGTCTTTAACTG
65 TCAACGGTCTTTAACCG
*
3747198 TTCATCTAACTAGCATAAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCAT-AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* * *
3747263 TCAATGATCTTTAACTG
65 TCAACGGTCTTTAACCG
* * * * * *
3747280 TTCATCTAACTGGAATAAATGATACATTTATGCCAAATACACAGCTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* *
3747345 CATA-AGCCTTTAACCG
66 CA-ACGGTCTTTAACCG
* * * *
3747361 TTCATCTAACTAGCATAAATTGACACCTTTCTGCCAAATACACAACTAGGCCATTTATGTTTTAC
1 TTCATCTAACTGGCAT-AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
**
3747426 TCAACGACCTTTAACCG
65 TCAACGGTCTTTAACCG
* * * *
3747443 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATACAAAGCTAGACCAATTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
*
3747508 CAACGGTCTTTAACCA
66 CAACGGTCTTTAACCG
* * * * * *
3747524 TTCATCTAATTGGCATAAATTAACACCTTTATACCAAATGCACAACTAGGCCATTTATGTTTTAC
1 TTCATCTAACTGGCAT-AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
**
3747589 TCAACGGTCTTTAACAT
65 TCAACGGTCTTTAACCG
* *
3747606 TTCATCTAACTGGTATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTGTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
3747671 CAACGGTCTTTAACCG
66 CAACGGTCTTTAACCG
* * * *
3747687 TTCATAT-ACTTGGCATAATTGACACATTTCTGCCAAATGTACAGCTAGGACATTTATCTTTTAC
1 TTCATCTAAC-TGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
3747751 TCAACGGTCTTTAACCG
65 TCAACGGTCTTTAACCG
* * * * *
3747768 TTCATTTGATTGGCATAATTGACACCTTTATGCCAAATGCACAGTTAGGCC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCC
3747819 TCAAAGGCAC
Statistics
Matches: 903, Mismatches: 116, Indels: 18
0.87 0.11 0.02
Matches are distributed among these distances:
80 2 0.00
81 537 0.59
82 364 0.40
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
CAACGGTCTTTAACCG
Found at i:3746929 original size:163 final size:162
Alignment explanation
Indices: 3746710--3747818 Score: 1468
Period size: 163 Copynumber: 6.8 Consensus size: 162
3746700 CATTTAACTT
* * * * *
3746710 TTCATCTAACTTGCATGATTGATA-CTTTCCTGCCAAATGCACAGTTAGGTCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTT-CTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* * *
3746774 TAAACGGTCATTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAG
65 TCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAG
* *
3746839 GCCATTTATCTTTTACTCAACAGTCTTTAACTG
130 GCCATTTATCTTTTACTCAACGGTCTTTAACCG
*
3746872 TTCATCTAACTGGCATAATCGACACCATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACC-TTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* * * * * *
3746937 TCAAAGGTCTTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCATATGCACAACTAG
65 TCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAG
* *
3747002 GTCATTTATCTTTTACTCAATGGTCTTTAACCG
130 GCCATTTATCTTTTACTCAACGGTCTTTAACCG
* * *
3747035 CTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGACCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* * * * * *
3747100 CAACGGTCTTTAACTGTTCATCTAACTTGTATAAATTGACACATTTCTGTCAAATGCACAGTTAG
66 CAACGGTCTTTAACCGTTCATCTAACTGGCAT-AATTGACACCTTTCTGCCAAATGCACAGCTAG
* * *
3747165 GCCATTTATATTTTGCTCAACGGTCTTTAACTG
130 GCCATTTATCTTTTACTCAACGGTCTTTAACCG
*
3747198 TTCATCTAACTAGCATAAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCAT-AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* * * * * * * * *
3747263 TCAATGATCTTTAACTGTTCATCTAACTGGAATAAATGATACATTTATGCCAAATACACAGCTAG
65 TCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAG
* *
3747328 GCCATTTATCTTTTACTCATA-AGCCTTTAACCG
130 GCCATTTATCTTTTACTCA-ACGGTCTTTAACCG
* * * *
3747361 TTCATCTAACTAGCATAAATTGACACCTTTCTGCCAAATACACAACTAGGCCATTTATGTTTTAC
1 TTCATCTAACTGGCAT-AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
** * *
3747426 TCAACGACCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATACAAAGCTAG
65 TCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAG
* * *
3747491 ACCAATTATCTTTTACTCAACGGTCTTTAACCA
130 GCCATTTATCTTTTACTCAACGGTCTTTAACCG
* * * * * *
3747524 TTCATCTAATTGGCATAAATTAACACCTTTATACCAAATGCACAACTAGGCCATTTATGTTTTAC
1 TTCATCTAACTGGCAT-AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
** *
3747589 TCAACGGTCTTTAACATTTCATCTAACTGGTATAATTGACACCTTTCTGCCAAATGCACAGCTAG
65 TCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAG
*
3747654 GCCATTTATCTTGTACTCAACGGTCTTTAACCG
130 GCCATTTATCTTTTACTCAACGGTCTTTAACCG
* * * *
3747687 TTCATAT-ACTTGGCATAATTGACACATTTCTGCCAAATGTACAGCTAGGACATTTATCTTTTAC
1 TTCATCTAAC-TGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* * * * *
3747751 TCAACGGTCTTTAACCGTTCATTTGATTGGCATAATTGACACCTTTATGCCAAATGCACAGTTAG
65 TCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAG
3747816 GCC
130 GCC
3747819 TCAAAGGCAC
Statistics
Matches: 833, Mismatches: 107, Indels: 14
0.87 0.11 0.01
Matches are distributed among these distances:
162 187 0.22
163 567 0.68
164 79 0.09
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (162 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
CAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGG
CCATTTATCTTTTACTCAACGGTCTTTAACCG
Found at i:3747147 original size:244 final size:243
Alignment explanation
Indices: 3746702--3747818 Score: 1463
Period size: 244 Copynumber: 4.6 Consensus size: 243
3746692 CACAAAGACA
* * * * *
3746702 TTTAACTTTTCATCTAACTTG-CATGATTGATAC-TTTCCTGCCAAATGCACAGTTAGGTCATTT
1 TTTAACTGTTCATCTAAC-TGACATAATTGACACATTT-CTGCCAAATGCACAGCTAGGCCATTT
* * * *
3746765 ATCTTTTACTAAACGGTCATTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATG
64 ATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATACCAAATG
*
3746830 CACAGCTAGGCCATTTATCTTTTACTCAACAGTCTTTAACTGTTCATCTAACTGGCATAATCGAC
129 CACAGCTAGGCCATTTATCTTTTACTCAACAGTCTTTAACTGTTCATCTAACTGGCATAATTGAC
*
3746895 ACCATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAAAGGTC
194 A-CATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTC
* * *
3746946 TTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCATATGCACAACTAGGTCATTTAT
1 TTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTAT
* * *
3747011 CTTTTACTCAATGGTCTTTAACCGCTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCA
66 CTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATACCAAATGCA
* * * *
3747076 CAGCTAGACCATTTATCTTTTACTCAACGGTCTTTAACTGTTCATCTAACTTGTATAAATTGACA
131 CAGCTAGGCCATTTATCTTTTACTCAACAGTCTTTAACTGTTCATCTAACTGGCAT-AATTGACA
* * * *
3747141 CATTTCTGTCAAATGCACAGTTAGGCCATTTATATTTTGCTCAACGGTC
195 CATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTC
*
3747190 TTTAACTGTTCATCTAACT-AGCATAAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTT
1 TTTAACTGTTCATCTAACTGA-CAT-AATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTT
* * * * * * * * *
3747254 ATCTTTTACTCAATGATCTTTAACTGTTCATCTAACTGGAATAAATGATACATTTATGCCAAATA
64 ATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATACCAAATG
* * *
3747319 CACAGCTAGGCCATTTATCTTTTACTCATA-AGCCTTTAACCGTTCATCTAACTAGCATAAATTG
129 CACAGCTAGGCCATTTATCTTTTACTCA-ACAGTCTTTAACTGTTCATCTAACTGGCAT-AATTG
* * * * **
3747383 ACACCTTTCTGCCAAATACACAACTAGGCCATTTATGTTTTACTCAACGACC
192 ACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTC
* * * * * * *
3747435 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATACAAAGCTAGACCAATTAT
1 TTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTAT
* * *
3747500 CTTTTACTCAACGGTCTTTAACCATTCATCTAATTGGCATAAATTAACACCTTTATACCAAATGC
66 CTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCAT-AATTGACACCTTTATACCAAATGC
* * * *
3747565 ACAACTAGGCCATTTATGTTTTACTCAACGGTCTTTAACAT-TTCATCTAACTGGTATAATTGAC
130 ACAGCTAGGCCATTTATCTTTTACTCAACAGTCTTTAAC-TGTTCATCTAACTGGCATAATTGAC
* *
3747629 ACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTGTACTCAACGGTC
194 ACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTC
* * * * *
3747679 TTTAACCGTTCATAT-ACTTGGCATAATTGACACATTTCTGCCAAATGTACAGCTAGGACATTTA
1 TTTAACTGTTCATCTAAC-TGACATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTA
* * * *
3747743 TCTTTTACTCAACGGTCTTTAACCGTTCATTTGATTGGCATAATTGACACCTTTATGCCAAATGC
65 TCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATACCAAATGC
*
3747808 ACAGTTAGGCC
130 ACAGCTAGGCC
3747819 TCAAAGGCAC
Statistics
Matches: 766, Mismatches: 96, Indels: 23
0.87 0.11 0.03
Matches are distributed among these distances:
243 36 0.05
244 444 0.58
245 285 0.37
246 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (243 bp):
TTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTAT
CTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATACCAAATGCA
CAGCTAGGCCATTTATCTTTTACTCAACAGTCTTTAACTGTTCATCTAACTGGCATAATTGACAC
ATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTC
Found at i:3747859 original size:68 final size:68
Alignment explanation
Indices: 3747778--3748023 Score: 411
Period size: 68 Copynumber: 3.6 Consensus size: 68
3747768 TTCATTTGAT
* *
3747778 TGGCATAATTGACACCTTTATGCCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCT
1 TGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCT
3747843 AAC
66 AAC
* * *
3747846 TGGCATAATTGACACCTTTCTGTCAAATGCACAATTAGGCCTTAAAGGCACTTAGCCTTTCATCC
1 TGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCT
3747911 AAC
66 AAC
* * * *
3747914 TGACATAATTGACACATTTTTGTCAAATGCACAGTTAGGCCTTAAAGGCACTTAACCTTTCATCT
1 TGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCT
3747979 AAC
66 AAC
3747982 TGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCT
1 TGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCT
3748024 ATTAATCTTT
Statistics
Matches: 164, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 164 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (68 bp):
TGGCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCT
AAC
Found at i:3748293 original size:54 final size:55
Alignment explanation
Indices: 3748234--3748401 Score: 230
Period size: 55 Copynumber: 3.0 Consensus size: 55
3748224 ACATATATTT
*
3748234 CCCATACGGAAATTCATACACTTAGTACGGATTTCTTAG-TTTGCACACATAGTG
1 CCCATACGGAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACATAGTG
* * * * *
3748288 CCCATAGGGAAGTTCATACACTTAGTATGAATTTCTTAGTTTTGCACTCAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACATAGTG
* * *
3748343 TCCATACAGAAATTCATACACTTAGTATGGATTTCTTAAGTTTTTGCACACTTAGTG
1 CCCATACGGAAATTCATACACTTAGTATGGATTTCTT-AG-TTTTGCACACATAGTG
3748400 CC
1 CC
3748402 ATTTGGTAAT
Statistics
Matches: 96, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
54 35 0.36
55 45 0.47
56 2 0.02
57 14 0.15
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (55 bp):
CCCATACGGAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACATAGTG
Found at i:3751295 original size:18 final size:18
Alignment explanation
Indices: 3751229--3751295 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
3751219 TTAAAGGAGT
3751229 TAGTTTAATT-AATGAAC
1 TAGTTTAATTGAATGAAC
* * *
3751246 CAATTTAAATGAATGAAC
1 TAGTTTAATTGAATGAAC
*
3751264 TAGTTTAATT-AATGGAC
1 TAGTTTAATTGAATGAAC
3751281 TAGCTTT-ATTGAATG
1 TAG-TTTAATTGAATG
3751296 TTCCAACATA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
17 19 0.47
18 21 0.52
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (18 bp):
TAGTTTAATTGAATGAAC
Found at i:3754037 original size:20 final size:20
Alignment explanation
Indices: 3754012--3754065 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
3754002 TGTCAAGGGA
3754012 TGCATCGATGCATGGTGTAG
1 TGCATCGATGCATGGTGTAG
3754032 TGCATCGATGCATGGTGTAG
1 TGCATCGATGCATGGTGTAG
3754052 TGCATCGATGCATG
1 TGCATCGATGCATG
3754066 CCTTCATTAA
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:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (20 bp):
TGCATCGATGCATGGTGTAG
Found at i:3758457 original size:23 final size:23
Alignment explanation
Indices: 3758424--3758491 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
3758414 CATCTTGTAT
*
3758424 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
3758447 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
3758470 GGAACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
3758492 AGTTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:3760190 original size:11 final size:14
Alignment explanation
Indices: 3760160--3760196 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
3760150 ATGATGTCTT
3760160 ATATATTATTTTAA
1 ATATATTATTTTAA
3760174 ATATATTA-TTTAA
1 ATATATTATTTTAA
*
3760187 ATATCTTATT
1 ATATATTATT
3760197 CATACGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATATTATTTTAA
Found at i:3763405 original size:20 final size:21
Alignment explanation
Indices: 3763380--3763472 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
3763370 TTTTCCCAAT
*
3763380 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3763400 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
3763421 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3763441 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3763462 TCGCAATGCGA
1 TCGCAATGCGA
3763473 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3763425 original size:41 final size:41
Alignment explanation
Indices: 3763380--3763472 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3763370 TTTTCCCAAT
3763380 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3763421 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3763462 TCGCAATGCGA
1 TCGCAATGCGA
3763473 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:3763485 original size:41 final size:41
Alignment explanation
Indices: 3763399--3763533 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
3763389 GAATAAGTAA
* *
3763399 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
3763440 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
3763481 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
3763522 TTCGCAACGCGA
1 ATCGCAACGCGA
3763534 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:3763486 original size:20 final size:20
Alignment explanation
Indices: 3763461--3763555 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
3763451 AATTGGGAAA
*
3763461 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
3763481 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
3763502 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
3763522 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3763542 TTCGCAACGCGATA
1 ATCGCAACGCGATA
3763556 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3763771 original size:22 final size:22
Alignment explanation
Indices: 3763743--3763786 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3763733 CACTCTCTCA
*
3763743 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
3763765 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
3763787 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:3764075 original size:20 final size:20
Alignment explanation
Indices: 3764050--3764087 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3764040 CGATTCTCTC
3764050 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
3764070 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
3764088 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:3765419 original size:18 final size:18
Alignment explanation
Indices: 3765398--3765442 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3765388 TCCACTTCGG
**
3765398 GAGCCATCACCTTGCCCA
1 GAGCCATCACCTCACCCA
*
3765416 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3765434 GAGCCATCA
1 GAGCCATCA
3765443 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3765943 original size:20 final size:20
Alignment explanation
Indices: 3765918--3765963 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3765908 TAGTTTACTT
3765918 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
3765938 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
3765958 TCGCAA
1 TCGCAA
3765964 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:3765972 original size:19 final size:20
Alignment explanation
Indices: 3765929--3765973 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3765919 CGCAACACGA
3765929 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
3765949 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
3765968 AAATGA
1 AAATGA
3765974 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:3765979 original size:19 final size:19
Alignment explanation
Indices: 3765937--3766052 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
3765927 GAAAATGACT
***
3765937 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
3765957 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3765976 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3765990 ATCGCAACGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
3766008 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3766022 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3766041 ATCGCAATGCGA
1 ATCGCAATGCGA
3766053 TTTTGTCGTT
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 6 0.08
17 2 0.03
18 11 0.14
19 27 0.35
20 10 0.13
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3765992 original size:14 final size:14
Alignment explanation
Indices: 3765973--3766030 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3765963 ATGCGAAATG
3765973 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3765987 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3766003 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3766019 AAAATCGCAACG
1 AAAATCGCAACG
3766031 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3766015 original size:32 final size:33
Alignment explanation
Indices: 3765957--3766047 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3765947 GGAAATGGCT
*
3765957 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3765990 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3766022 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
3766048 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:3766122 original size:18 final size:19
Alignment explanation
Indices: 3766071--3766124 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3766061 TTGCGATTTT
*
3766071 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3766090 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3766110 CATTT-GTGTTGCGAT
1 CATTTCGCGTTGCGAT
3766125 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.29
19 5 0.16
20 17 0.55
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3768013 original size:14 final size:14
Alignment explanation
Indices: 3767994--3768027 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3767984 TGTTTAATTT
3767994 ATTTGTAAAAGATG
1 ATTTGTAAAAGATG
* *
3768008 ATTTGTAAATGTTG
1 ATTTGTAAAAGATG
3768022 ATTTGT
1 ATTTGT
3768028 TTAATTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGATG
Found at i:3768166 original size:19 final size:19
Alignment explanation
Indices: 3768144--3768211 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
3768134 ATCGCAACGA
3768144 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
3768163 GAAAATCACAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3768182 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
3768196 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
3768212 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.64
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:3768287 original size:20 final size:20
Alignment explanation
Indices: 3768230--3768287 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
3768220 TCGCATTGCG
* *
3768230 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
3768250 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
3768270 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
3768288 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:3769580 original size:12 final size:12
Alignment explanation
Indices: 3769563--3769587 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3769553 ATATAATCCT
3769563 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3769575 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3769587 G
1 G
3769588 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3771914 original size:33 final size:33
Alignment explanation
Indices: 3771871--3771993 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
3771861 ATTACTATCA
3771871 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
* ** *
3771904 CAATGAGAAATGAAAATCGCAACGCTA-ATTTCG
1 CAATGCGAAATGAAAATCGCAACGAGAGA-ATCG
*
3771937 CAATGCGAAATGAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
3771970 CAATGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
3771994 CGAATTTAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 77 0.97
34 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:3771923 original size:19 final size:19
Alignment explanation
Indices: 3771871--3771925 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
3771861 ATTACTATCA
*
3771871 CAATGCGAAATGAAAATCG
1 CAATGAGAAATGAAAATCG
*
3771890 CAACGAG--A-G--AATCG
1 CAATGAGAAATGAAAATCG
3771904 CAATGAGAAATGAAAATCG
1 CAATGAGAAATGAAAATCG
3771923 CAA
1 CAA
3771926 CGCTAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
14 11 0.39
16 2 0.07
17 2 0.07
19 13 0.46
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.13
Consensus pattern (19 bp):
CAATGAGAAATGAAAATCG
Found at i:3771980 original size:66 final size:66
Alignment explanation
Indices: 3771871--3772000 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
3771861 ATTACTATCA
*
3771871 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGAGAAATGAAAATCGCAACGCTAATTTC
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGAGAAATGAAAATCGCAACGCGAATTTC
3771936 G
66 G
* *
3771937 CAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGAGAAATGAAAATCGCAACGCGAATTT
3772001 AATTTCACGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (66 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGAGAAATGAAAATCGCAACGCGAATTTC
G
Found at i:3772015 original size:19 final size:20
Alignment explanation
Indices: 3771993--3772035 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3771983 AAATCGCAAC
3771993 GCGAATTT-AATTTCACGTT
1 GCGAATTTCAATTTCACGTT
* * *
3772012 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCACGTT
3772032 GCGA
1 GCGA
3772036 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCACGTT
Found at i:3772195 original size:14 final size:14
Alignment explanation
Indices: 3772176--3772212 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3772166 CATCAATTAA
3772176 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3772190 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3772204 ACAAATCAA
1 ACAAATCAA
3772213 TTAAACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3775750 original size:33 final size:33
Alignment explanation
Indices: 3775698--3775819 Score: 136
Period size: 33 Copynumber: 3.5 Consensus size: 33
3775688 AGATAATGAG
*
3775698 AATCGCAATGCGGAAATGACTATCGCAACGAGAA
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAA
* * *
3775732 AATCGCAACGCGAAATGACTATCGCGACCAGAC
1 AATCGCAACGCGAAATGACTATCGCAACGAGAA
** *
3775765 AATCGCAACGCGAAATGAAAATCGCAACTGCGAATGA
1 AATCGCAACGCGAAATGACTATCGCAAC-GAG-A--A
3775802 AATCGCAACGCGAAATGA
1 AATCGCAACGCGAAATGA
3775820 AATTTTTATT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
33 44 0.59
34 11 0.15
35 1 0.01
37 18 0.24
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAA
Found at i:3775787 original size:19 final size:19
Alignment explanation
Indices: 3775677--3775821 Score: 98
Period size: 19 Copynumber: 8.1 Consensus size: 19
3775667 TGGTTGAAAG
*
3775677 AAATCGCAACGAGATAATGA
1 AAATCGCAACGCGA-AATGA
* *
3775697 GAATCGCAATGCGGAAATGA
1 AAATCGCAACGC-GAAATGA
**
3775717 CTATCGCAA--CG--A-GA
1 AAATCGCAACGCGAAATGA
3775731 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
** *
3775750 CTATCGCGAC-C---A-GA
1 AAATCGCAACGCGAAATGA
*
3775764 CAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
3775783 AAATCGCAACTGCG-AATG-
1 AAATCGCAAC-GCGAAATGA
3775801 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
3775820 AA
1 AA
3775822 TTTTTATTTC
Statistics
Matches: 98, Mismatches: 13, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
14 19 0.19
15 3 0.03
16 2 0.02
17 4 0.04
18 18 0.18
19 26 0.27
20 24 0.24
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
AAATCGCAACGCGAAATGA
Found at i:3775806 original size:18 final size:18
Alignment explanation
Indices: 3775672--3775822 Score: 99
Period size: 20 Copynumber: 8.6 Consensus size: 18
3775662 TCTTTTGGTT
*
3775672 GAAA-GAAATCGCAACGA
1 GAAATGAAATCGCAACGC
*
3775689 GATAATGAGAATCGCAATGC
1 GA-AATGA-AATCGCAACGC
*
3775709 GGAAATGACTATCGCAA--C
1 -GAAATGA-AATCGCAACGC
*
3775727 GAGA--AAATCGCAACGC
1 GAAATGAAATCGCAACGC
* *
3775743 GAAATGACTATCGCGAC-C
1 GAAATGA-AATCGCAACGC
3775761 ---A-GACAATCGCAACGC
1 GAAATGA-AATCGCAACGC
3775776 GAAATGAAAATCGCAACTGC
1 GAAATG-AAATCGCAAC-GC
3775796 G-AATGAAATCGCAACGC
1 GAAATGAAATCGCAACGC
3775813 GAAATGAAAT
1 GAAATGAAAT
3775823 TTTTATTTCG
Statistics
Matches: 106, Mismatches: 11, Indels: 33
0.71 0.07 0.22
Matches are distributed among these distances:
14 17 0.16
15 3 0.03
16 4 0.04
17 8 0.08
18 24 0.23
19 23 0.22
20 25 0.24
21 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAATGAAATCGCAACGC
Found at i:3776177 original size:20 final size:20
Alignment explanation
Indices: 3776152--3776204 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3776142 GCGCTATGTA
3776152 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
3776172 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
3776192 TATCTCGTTGCGA
1 AATCGCGTTGCGA
3776205 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:3776238 original size:20 final size:20
Alignment explanation
Indices: 3776213--3776266 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3776203 GATTTTGTAT
3776213 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
3776233 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
3776253 TATCGCATTGCGAT
1 TATCGCATTGCGAT
3776267 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:3776251 original size:61 final size:61
Alignment explanation
Indices: 3776153--3776269 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
3776143 CGCTATGTAA
* * * * *
3776153 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
3776214 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
3776270 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:3776285 original size:61 final size:61
Alignment explanation
Indices: 3776153--3776287 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
3776143 CGCTATGTAA
* * * * * ** *
3776153 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
3776214 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
3776276 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
3776288 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:3776410 original size:20 final size:19
Alignment explanation
Indices: 3776385--3776448 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
3776375 CAACGCGAAT
*
3776385 TTGCGATAATGGAGATCGCG
1 TTGCGA-AATAGAGATCGCG
* *
3776405 TTGCGAATTAGCGATCGCG
1 TTGCGAAATAGAGATCGCG
* * *
3776424 TTGCGAATTAGCGATCGCA
1 TTGCGAAATAGAGATCGCG
3776443 TTGCGA
1 TTGCGA
3776449 TTTTGTTGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 34 0.85
20 6 0.15
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (19 bp):
TTGCGAAATAGAGATCGCG
Found at i:3776422 original size:19 final size:19
Alignment explanation
Indices: 3776398--3776448 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
3776388 CGATAATGGA
3776398 GATCGCGTTGCGAATTAGC
1 GATCGCGTTGCGAATTAGC
3776417 GATCGCGTTGCGAATTAGC
1 GATCGCGTTGCGAATTAGC
*
3776436 GATCGCATTGCGA
1 GATCGCGTTGCGA
3776449 TTTTGTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (19 bp):
GATCGCGTTGCGAATTAGC
Found at i:3777514 original size:18 final size:18
Alignment explanation
Indices: 3777487--3777532 Score: 69
Period size: 16 Copynumber: 2.7 Consensus size: 18
3777477 TTTTTGGAGA
3777487 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGTGAAGG
*
3777505 AATTGAAATC--TGAAGG
1 AATTGGAATCTGTGAAGG
3777521 AATTGGAATCTG
1 AATTGGAATCTG
3777533 AATATGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 15 0.62
18 9 0.38
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (18 bp):
AATTGGAATCTGTGAAGG
Found at i:3778161 original size:39 final size:40
Alignment explanation
Indices: 3778106--3778196 Score: 148
Period size: 39 Copynumber: 2.3 Consensus size: 40
3778096 TTCACCCTAA
* *
3778106 ACCCGAACCCGGCCCGAATATCACACTT-AAAAAAACCCG
1 ACCCGAACCCGACCCGAATATCAAACTTAAAAAAAACCCG
*
3778145 ACCCGACCCCGACCCGAATATCAAACTTAAAAAAAACCCG
1 ACCCGAACCCGACCCGAATATCAAACTTAAAAAAAACCCG
3778185 ACCCGAACCCGA
1 ACCCGAACCCGA
3778197 AATTTTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 25 0.53
40 22 0.47
ACGTcount: A:0.40, C:0.40, G:0.12, T:0.09
Consensus pattern (40 bp):
ACCCGAACCCGACCCGAATATCAAACTTAAAAAAAACCCG
Found at i:3778210 original size:30 final size:31
Alignment explanation
Indices: 3778174--3778253 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 31
3778164 ATCAAACTTA
*
3778174 AAAAAAACCCGACCCGAACCCGAA-ATTTTT
1 AAAAAAATCCGACCCGAACCCGAATATTTTT
* * *
3778204 AAAAAAATCCGACCCGATCCTGAATTGTTTTT
1 AAAAAAATCCGACCCGAACCCGAA-TATTTTT
*
3778236 AAAAATATCCGACCCGAA
1 AAAAAAATCCGACCCGAA
3778254 TACCAAAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 21 0.50
32 21 0.50
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.21
Consensus pattern (31 bp):
AAAAAAATCCGACCCGAACCCGAATATTTTT
Found at i:3779137 original size:257 final size:252
Alignment explanation
Indices: 3778557--3779175 Score: 779
Period size: 257 Copynumber: 2.4 Consensus size: 252
3778547 CTTATTCATA
* *
3778557 TATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATAT-TCGGGTTGG
1 TATTGAATAAAAATATTTTTTTTATTATTTTGGGTCGGGTTTCTAATTCATATATATCGGGTCGG
* * * *
3778621 GTCGGGTGAAACTTTATTTTGGTCAGGTCGGGTCGATTTTTTTAATTGTGATATTCGGGTCGGGT
66 GTCTGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGT
** * *
3778686 CGAGTTTGGGTTTAGGGTGAAAAATACTCAACCCGAAAATATATATAATTTTACCTTATATATTT
131 CGAGTTCAGGTTTAGGGTGAAAAATACCCAACCCGAAAAAATATATAATTTTACCTTATATATTT
3778751 AGGAATAAATTACAATAATACCCCTCTATATATATTTTTTTTCCAATTAAGTCACTGTTTT
196 AGGAATAAATTACAATAATACCCCTCTATATATA----TTTTCCAATTAAGTCACTGTTTT
* *
3778812 TATTGAAT--AAAT-TTTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTAATATAT-TCGG
1 TATTGAATAAAAATATTTTTTTTATTATTT----T-GGGTCGGGTTTCTAATTCATATATATCGG
* * *
3778873 GTCGGGTCTGGTGAAACTTTATTTTGGTTGGGTCGAGTCGGTTTTGTTTAAGTGTGATTTTCGGG
61 GTCGGGTCTGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTT-TTTAAGTGTGATATTCGGG
* * *
3778938 TCGGGTCGGGTTCAGGTTTAGGGTGAAAAATACCCGACCTGACCTAAAAAATATATAATTTTACC
125 TCGGGTCGAGTTCAGGTTTAGGGTGAAAAATACCC-AAC---CCGAAAAAATATATAATTTTACC
*
3779003 TTATATATTTAGGAAT-AATTACAGTAATA-CCC-CTATATATA-TTTCCAATTAAGTCACTGTT
186 TTATATATTTAGGAATAAATTACAATAATACCCCTCTATATATATTTTCCAATTAAGTCACTGTT
3779064 TT
251 TT
* *
3779066 TATTGAATAAAAATAATTTTTTTATTATTTTGGGTTGGGTTTCTAATTCATATATTCGAGTCGGG
1 TATTGAATAAAAATATTTTTTTTATTATTTTGGGTCGGGTTTCTAATTCATATA-T--A-TCGGG
3779131 TCGGGTCGAGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGG
62 TCGGGTC---T--GGTGAAACTTTATTTTGGTCGGGTCGGGTCGG
3779176 ATCGGGTGGA
Statistics
Matches: 316, Mismatches: 25, Indels: 39
0.83 0.07 0.10
Matches are distributed among these distances:
252 35 0.11
253 6 0.02
254 30 0.09
255 8 0.03
256 4 0.01
257 91 0.29
258 48 0.15
259 11 0.03
260 4 0.01
261 12 0.04
262 67 0.21
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (252 bp):
TATTGAATAAAAATATTTTTTTTATTATTTTGGGTCGGGTTTCTAATTCATATATATCGGGTCGG
GTCTGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGT
CGAGTTCAGGTTTAGGGTGAAAAATACCCAACCCGAAAAAATATATAATTTTACCTTATATATTT
AGGAATAAATTACAATAATACCCCTCTATATATATTTTCCAATTAAGTCACTGTTTT
Found at i:3779485 original size:17 final size:17
Alignment explanation
Indices: 3779463--3779509 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
3779453 TATGGAATTT
*
3779463 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
3779480 GATTCCAATTACTTCACA
1 GATTCCAATT-CCTCACA
*
3779498 GACTCCAATTCC
1 GATTCCAATTCC
3779510 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.30
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:3783966 original size:24 final size:24
Alignment explanation
Indices: 3783939--3783996 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
3783929 ACCGCAGCTT
3783939 CCACCACCTTCTGCGCTTCCACTA
1 CCACCACCTTCTGCGCTTCCACTA
3783963 CCACCACCTTCTGCGCTTCCACTA
1 CCACCACCTTCTGCGCTTCCACTA
3783987 CCACCACCTT
1 CCACCACCTT
3783997 TGTCTAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.17, C:0.52, G:0.07, T:0.24
Consensus pattern (24 bp):
CCACCACCTTCTGCGCTTCCACTA
Found at i:3784860 original size:14 final size:15
Alignment explanation
Indices: 3784841--3784873 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3784831 CAATAATCAC
*
3784841 TTTTTT-AAATGTGA
1 TTTTTTAAAATATGA
3784855 TTTTTTAAAATATGA
1 TTTTTTAAAATATGA
3784870 TTTT
1 TTTT
3784874 CTTTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (15 bp):
TTTTTTAAAATATGA
Found at i:3786507 original size:19 final size:20
Alignment explanation
Indices: 3786465--3786508 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3786455 AATAAAGTAT
* *
3786465 TATTGAATTTTAAGATTTTA
1 TATTCAATTTTAAGATTATA
3786485 TATTCAATTTTAA-ATTATA
1 TATTCAATTTTAAGATTATA
3786504 TATTC
1 TATTC
3786509 GATTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTCAATTTTAAGATTATA
Found at i:3792580 original size:273 final size:273
Alignment explanation
Indices: 3792093--3792641 Score: 1098
Period size: 273 Copynumber: 2.0 Consensus size: 273
3792083 TCAAAAGGGA
3792093 AAGTTGACACTATATTGTTTTTAAAGAGAAAAGGTAAAGATTTATTAGTAGTTCAAATTTATGTT
1 AAGTTGACACTATATTGTTTTTAAAGAGAAAAGGTAAAGATTTATTAGTAGTTCAAATTTATGTT
3792158 GATGATATAATATTTGGTTCTACTAATGATGCTCTTTGCCAAGAATTTTCTAAGCTAATGTAGAG
66 GATGATATAATATTTGGTTCTACTAATGATGCTCTTTGCCAAGAATTTTCTAAGCTAATGTAGAG
3792223 TGAATTTAAGATGAGCATGATGGGGGAGCTTTCATTTTTCTTGGGACTCCAAATCAAGCAAAGAA
131 TGAATTTAAGATGAGCATGATGGGGGAGCTTTCATTTTTCTTGGGACTCCAAATCAAGCAAAGAA
3792288 AAGATGGCATCTTCATCAATCAAGCAAAATACATCAAGGATATGCTCAAGAAGTTCAACTTGGAA
196 AAGATGGCATCTTCATCAATCAAGCAAAATACATCAAGGATATGCTCAAGAAGTTCAACTTGGAA
3792353 AATGTCAAACCCC
261 AATGTCAAACCCC
3792366 AAGTTGACACTATATTGTTTTTAAAGAGAAAAGGTAAAGATTTATTAGTAGTTCAAATTTATGTT
1 AAGTTGACACTATATTGTTTTTAAAGAGAAAAGGTAAAGATTTATTAGTAGTTCAAATTTATGTT
3792431 GATGATATAATATTTGGTTCTACTAATGATGCTCTTTGCCAAGAATTTTCTAAGCTAATGTAGAG
66 GATGATATAATATTTGGTTCTACTAATGATGCTCTTTGCCAAGAATTTTCTAAGCTAATGTAGAG
3792496 TGAATTTAAGATGAGCATGATGGGGGAGCTTTCATTTTTCTTGGGACTCCAAATCAAGCAAAGAA
131 TGAATTTAAGATGAGCATGATGGGGGAGCTTTCATTTTTCTTGGGACTCCAAATCAAGCAAAGAA
3792561 AAGATGGCATCTTCATCAATCAAGCAAAATACATCAAGGATATGCTCAAGAAGTTCAACTTGGAA
196 AAGATGGCATCTTCATCAATCAAGCAAAATACATCAAGGATATGCTCAAGAAGTTCAACTTGGAA
3792626 AATGTCAAACCCC
261 AATGTCAAACCCC
3792639 AAG
1 AAG
3792642 CTACTCCAAT
Statistics
Matches: 276, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
273 276 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (273 bp):
AAGTTGACACTATATTGTTTTTAAAGAGAAAAGGTAAAGATTTATTAGTAGTTCAAATTTATGTT
GATGATATAATATTTGGTTCTACTAATGATGCTCTTTGCCAAGAATTTTCTAAGCTAATGTAGAG
TGAATTTAAGATGAGCATGATGGGGGAGCTTTCATTTTTCTTGGGACTCCAAATCAAGCAAAGAA
AAGATGGCATCTTCATCAATCAAGCAAAATACATCAAGGATATGCTCAAGAAGTTCAACTTGGAA
AATGTCAAACCCC
Found at i:3793696 original size:15 final size:12
Alignment explanation
Indices: 3793661--3793685 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3793651 TCGATACCTC
3793661 CTCACTATGTAT
1 CTCACTATGTAT
3793673 CTCACTATGTAT
1 CTCACTATGTAT
3793685 C
1 C
3793686 GATACACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (12 bp):
CTCACTATGTAT
Found at i:3793704 original size:21 final size:20
Alignment explanation
Indices: 3793680--3793736 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 20
3793670 TATCTCACTA
3793680 TGTATCGATACACTATGAATG
1 TGTATCGATACACT-TGAATG
*
3793701 TGTATCGTTACATTCCTTGAATG
1 TGTATCGATACA---CTTGAATG
3793724 TGTATCGATACAC
1 TGTATCGATACAC
3793737 CCAGAGGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 11 0.35
23 17 0.55
24 2 0.06
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
TGTATCGATACACTTGAATG
Found at i:3796100 original size:19 final size:20
Alignment explanation
Indices: 3796058--3796101 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3796048 AATAAAGTAT
* *
3796058 TATTGAATTTTAAGATTTTA
1 TATTCAATTTTAAGATTATA
3796078 TATTCAATTTTAA-ATTATA
1 TATTCAATTTTAAGATTATA
3796097 TATTC
1 TATTC
3796102 GATTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTCAATTTTAAGATTATA
Found at i:3800857 original size:32 final size:32
Alignment explanation
Indices: 3800821--3800906 Score: 172
Period size: 32 Copynumber: 2.7 Consensus size: 32
3800811 AGGAGAATAC
3800821 TTAGTGTTCGAGAGAAACTAAGTAGCTCATCT
1 TTAGTGTTCGAGAGAAACTAAGTAGCTCATCT
3800853 TTAGTGTTCGAGAGAAACTAAGTAGCTCATCT
1 TTAGTGTTCGAGAGAAACTAAGTAGCTCATCT
3800885 TTAGTGTTCGAGAGAAACTAAG
1 TTAGTGTTCGAGAGAAACTAAG
3800907 GAGGATCAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (32 bp):
TTAGTGTTCGAGAGAAACTAAGTAGCTCATCT
Found at i:3812847 original size:23 final size:23
Alignment explanation
Indices: 3812817--3812900 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 23
3812807 CACTGAAGTG
*
3812817 CCACATAGAAATGTCCTAAAGGA
1 CCACATAGAAATGTCCTAAATGA
* * * *
3812840 CCACATAGTATTGTCTTGAATGA
1 CCACATAGAAATGTCCTAAATGA
** *
3812863 CCGGATAGAAATGTCCCAAATGA
1 CCACATAGAAATGTCCTAAATGA
* *
3812886 CCGCGTAGAAATGTC
1 CCACATAGAAATGTC
3812901 TCGAAGGGCC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (23 bp):
CCACATAGAAATGTCCTAAATGA
Found at i:3812915 original size:23 final size:23
Alignment explanation
Indices: 3812868--3812941 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
3812858 AATGACCGGA
* * * *
3812868 TAGAAATGTCCCAAATGACCGCG
1 TAGAAATATCCCGAAGGACCACG
* * *
3812891 TAGAAATGTCTCGAAGGGCCACG
1 TAGAAATATCCCGAAGGACCACG
* *
3812914 TAGAATTATCCCGAAGGACCGCG
1 TAGAAATATCCCGAAGGACCACG
3812937 TAGAA
1 TAGAA
3812942 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.18
Consensus pattern (23 bp):
TAGAAATATCCCGAAGGACCACG
Found at i:3816288 original size:36 final size:36
Alignment explanation
Indices: 3816241--3816374 Score: 148
Period size: 36 Copynumber: 3.8 Consensus size: 36
3816231 CTGCAAGTTA
*
3816241 AACTCTGATCAAGCTGATAATTCCTTATATAGGTTC
1 AACTCTGATCAAGCTGGTAATTCCTTATATAGGTTC
* *
3816277 AACTCTGATCAAGCTGGTAATTCCTTATACAAGTTC
1 AACTCTGATCAAGCTGGTAATTCCTTATATAGGTTC
** * *
3816313 AAAACTGATC-GGTTGGTAATTCCTTATATAGGTT-
1 AACTCTGATCAAGCTGGTAATTCCTTATATAGGTTC
* * *
3816347 TACTACCGATCAA-CTGGTAACTCCTTAT
1 AACT-CTGATCAAGCTGGTAATTCCTTAT
3816375 GGATCTAAGG
Statistics
Matches: 80, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
34 1 0.01
35 38 0.47
36 41 0.51
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (36 bp):
AACTCTGATCAAGCTGGTAATTCCTTATATAGGTTC
Found at i:3817440 original size:17 final size:17
Alignment explanation
Indices: 3817418--3817497 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
3817408 AATGTAGAAA
* *
3817418 TGTTGGTTGTTGCTGCC
1 TGTTGGCTGTTGCTACC
*
3817435 TGTTGGCTGTTGCTGCC
1 TGTTGGCTGTTGCTACC
3817452 TGTTGGCTGTTGCTACC
1 TGTTGGCTGTTGCTACC
3817469 TGTTGGCTGTTGCTACC
1 TGTTGGCTGTTGCTACC
* *
3817486 TGCTGCCTGTTG
1 TGTTGGCTGTTG
3817498 TCGGTTCATG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 59 1.00
ACGTcount: A:0.03, C:0.23, G:0.33, T:0.42
Consensus pattern (17 bp):
TGTTGGCTGTTGCTACC
Found at i:3818112 original size:14 final size:14
Alignment explanation
Indices: 3818080--3818112 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3818070 TTGAAGATTT
*
3818080 ATAACATAAGAATC
1 ATAATATAAGAATC
3818094 ATAATATAAGAATC
1 ATAATATAAGAATC
3818108 ATAAT
1 ATAAT
3818113 TAATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (14 bp):
ATAATATAAGAATC
Found at i:3818118 original size:18 final size:18
Alignment explanation
Indices: 3818095--3818157 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
3818085 ATAAGAATCA
*
3818095 TAATATAAGAATCATAAT
1 TAATATAATAATCATAAT
*
3818113 TAATATAATAATTCTATTCAT
1 TAATATAATAA-TC-A-TAAT
* *
3818134 TAATTTAATTATCATAAT
1 TAATATAATAATCATAAT
3818152 TAATAT
1 TAATAT
3818158 TTTATTATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 18 0.50
19 3 0.08
20 3 0.08
21 12 0.33
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (18 bp):
TAATATAATAATCATAAT
Found at i:3819036 original size:43 final size:43
Alignment explanation
Indices: 3818989--3819571 Score: 407
Period size: 43 Copynumber: 13.2 Consensus size: 43
3818979 TAGAGGCATT
* *
3818989 AATTATAAAGTTAGAAA-TCGAGATTGAAAAAAATAGGGGCCTC
1 AATTATAAAGTTAAAAAGT-GAGATTGAAAAAATTAGGGGCCTC
* * *
3819032 AATTATAAA-TGT-ATAATTGAGATTGAAAAAGCTTAGGGGCCTC
1 AATTATAAAGT-TAAAAAGTGAGATTGAAAAA-ATTAGGGGCCTC
* * *
3819075 AATTATAAAAG-TAAAAATTGAGATTGAAAACACTTAGGGACCTC
1 AATTAT-AAAGTTAAAAAGTGAGATTGAAAA-AATTAGGGGCCTC
* * * *
3819119 AATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGTCTC
1 AATTATAAAGTTAAAAAGTGAGATTGAAAAAA-TTAGGGGCCTC
* *
3819163 AATTATAAAGTTTAAAAAGTGAGATTG-AAAAATTAGGAGTCTC
1 AATTATAAAG-TTAAAAAGTGAGATTGAAAAAATTAGGGGCCTC
* * * * *
3819206 AATTAT-AAGAATAGAAATTGTGATTGAAAAAACTTA-GGGCATC
1 AATTATAAAG-TTAAAAAGTGAGATTGAAAAAA-TTAGGGGCCTC
* * * *
3819249 AATTGTAAAGATAGAAAAGGTAGAAAGTGAATTTGAAAAAACTTAAGGGCATC
1 AATTATAAAGTTA-AAAA-GT-G--A--G-A-TTGAAAAAA-TTAGGGGCCTC
* * *
3819302 AATTATAAAGTTTAAAAGTG-GTATTAAAAAAATTAGGGGCATC
1 AATTATAAAGTTAAAAAGTGAG-ATTGAAAAAATTAGGGGCCTC
* * * * * *
3819345 AATTATAAAGGTAAAAAGTGATACTGAAAAACTTAAGGGTCTC
1 AATTATAAAGTTAAAAAGTGAGATTGAAAAAATTAGGGGCCTC
* * *
3819388 AATTATAAAGTTAAAAAGTGAGATTAAAAAAAATAGAGGCCTC
1 AATTATAAAGTTAAAAAGTGAGATTGAAAAAATTAGGGGCCTC
* * ** * * *
3819431 AACTATAAAGGTAAAAAAACG-GATTGAAAAAATTAGAGACTTC
1 AATTATAAA-GTTAAAAAGTGAGATTGAAAAAATTAGGGGCCTC
** * *
3819474 AATTATAAAAATAAAAAGTGAGATTGAATAAAATTA-AGACCTC
1 AATTATAAAGTTAAAAAGTGAGATTGAA-AAAATTAGGGGCCTC
* * *
3819517 AATTATAAAGATTAAAAA-TAAGATTTTAAAAAAATTTAGAGGCCT-
1 AATTATAAAG-TTAAAAAGTGAGA--TTGAAAAAA-TTAGGGGCCTC
3819562 AATTATAAAG
1 AATTATAAAG
3819572 ATGAAAAAAT
Statistics
Matches: 436, Mismatches: 72, Indels: 62
0.76 0.13 0.11
Matches are distributed among these distances:
42 36 0.08
43 202 0.46
44 118 0.27
45 35 0.08
46 6 0.01
50 2 0.00
51 3 0.01
52 17 0.04
53 17 0.04
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (43 bp):
AATTATAAAGTTAAAAAGTGAGATTGAAAAAATTAGGGGCCTC
Found at i:3819375 original size:139 final size:138
Alignment explanation
Indices: 3819125--3819405 Score: 339
Period size: 139 Copynumber: 2.0 Consensus size: 138
3819115 CCTCAATTAT
*
3819125 AAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGTCTCAATTATAAAGTTTAAAAAGTGAGATTG
1 AAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGTCTCAATTATAAAGTTTAAAAAGTGAGATTA
* *
3819190 AAAAATTAGGAGTCTCAATTATAAGAATAGAAATTGTGATTGAAAAAACTT-AGGG-CATCAATT
66 AAAAATTAGGAGGCTCAATTATAAGAATAGAAATAGTGATTG-AAAAACTTAAGGGTC-TCAATT
*
3819253 GTAAAGATAGA
129 ATAAAGATA-A
3819264 AAAGGTAGAAAGTGA-ATTTGAAAAAACTTAAGGG-CATCAATTATAAAGTTT-AAAAGTG-GTA
1 AAAGGTAGAAAGTGAGA-TTGAAAAAACTTAAGGGTC-TCAATTATAAAGTTTAAAAAGTGAG-A
*
3819325 TTAAAAAAATTAGG-GGCATCAATTATAA-AGGTA-AAA-AGTGATACTGAAAAACTTAAGGGTC
63 TT-AAAAAATTAGGAGGC-TCAATTATAAGA-ATAGAAATAGTGAT--TGAAAAACTTAAGGGTC
*
3819386 TCAATTATAAAGTTAA
123 TCAATTATAAAGATAA
3819402 AAAG
1 AAAG
3819406 TGAGATTAAA
Statistics
Matches: 126, Mismatches: 6, Indels: 21
0.82 0.04 0.14
Matches are distributed among these distances:
137 6 0.05
138 31 0.25
139 88 0.70
140 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (138 bp):
AAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGTCTCAATTATAAAGTTTAAAAAGTGAGATTA
AAAAATTAGGAGGCTCAATTATAAGAATAGAAATAGTGATTGAAAAACTTAAGGGTCTCAATTAT
AAAGATAA
Found at i:3819871 original size:19 final size:19
Alignment explanation
Indices: 3819847--3819884 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3819837 TACTGATTTT
3819847 GTTATTATT-GGACACTTTA
1 GTTATTATTAGG-CACTTTA
*
3819866 GTTATTGTTAGGCACTTTA
1 GTTATTATTAGGCACTTTA
3819885 CCGGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (19 bp):
GTTATTATTAGGCACTTTA
Found at i:3821898 original size:42 final size:42
Alignment explanation
Indices: 3821852--3821956 Score: 167
Period size: 42 Copynumber: 2.5 Consensus size: 42
3821842 TTTTTCATGC
* *
3821852 TTGTTTCAAGTAATTTGTTTTTTGGAAAATGTTTTCCCGTGT
1 TTGTTTCACGTAATTTGTTTTTTGGAAAATATTTTCCCGTGT
*
3821894 TTGTTTCACGTAATTCGTTTTTTGGAAAATATTTTCCCGTGT
1 TTGTTTCACGTAATTTGTTTTTTGGAAAATATTTTCCCGTGT
*
3821936 TTATTTCACGTAA-TTGTTTTT
1 TTGTTTCACGTAATTTGTTTTT
3821957 CCGGAATGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 7 0.12
42 51 0.88
ACGTcount: A:0.19, C:0.11, G:0.16, T:0.53
Consensus pattern (42 bp):
TTGTTTCACGTAATTTGTTTTTTGGAAAATATTTTCCCGTGT
Found at i:3822281 original size:28 final size:28
Alignment explanation
Indices: 3822250--3822313 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
3822240 TTTATTTTAA
3822250 TAATATAT-AATAAAAAAATTTATATATT
1 TAATA-ATGAATAAAAAAATTTATATATT
* **
3822278 TAATAATGAATAATATTATTTATATATT
1 TAATAATGAATAAAAAAATTTATATATT
3822306 TAAATAAT
1 T-AATAAT
3822314 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 23 0.74
29 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TAATAATGAATAAAAAAATTTATATATT
Found at i:3822293 original size:19 final size:19
Alignment explanation
Indices: 3822271--3822323 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
3822261 AAAAAAATTT
*
3822271 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
3822290 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
3822312 ATAT-TTTAATAA
1 ATATATTTAATAA
3822324 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:3822344 original size:23 final size:23
Alignment explanation
Indices: 3822318--3822362 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3822308 AATAATATTT
3822318 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
3822341 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
3822363 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3822718 original size:20 final size:20
Alignment explanation
Indices: 3822680--3822719 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3822670 TACGAAAAAT
**
3822680 ATTTTCCAGAAATGTAATTC
1 ATTTTCCAGAAATCAAATTC
*
3822700 ATTTTCCAGAATTCAAATTC
1 ATTTTCCAGAAATCAAATTC
3822720 CAGTAATTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (20 bp):
ATTTTCCAGAAATCAAATTC
Found at i:3822729 original size:15 final size:15
Alignment explanation
Indices: 3822693--3822780 Score: 79
Period size: 15 Copynumber: 5.5 Consensus size: 15
3822683 TTCCAGAAAT
**
3822693 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
3822708 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
*
3822722 GTAATTCATTTTCCAGTTCCA
1 GTAATTCA------AATTCCA
3822743 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
*
3822758 ATAATTCAAATTCCA
1 GTAATTCAAATTCCA
3822773 GTAATTCA
1 GTAATTCA
3822781 TTTTCAAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
14 12 0.20
15 34 0.57
21 14 0.23
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:3822750 original size:36 final size:35
Alignment explanation
Indices: 3822703--3822774 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
3822693 GTAATTCATT
* **
3822703 TTCCAGAATTCAAATTCCAGTAATTCATTTTCCAG
1 TTCCAGAATTCAAATTCCAATAATTCAAATTCCAG
3822738 TTCCAGTAATTCAAATTCCAATAATTCAAATTCCAG
1 TTCCAG-AATTCAAATTCCAATAATTCAAATTCCAG
3822774 T
1 T
3822775 AATTCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (35 bp):
TTCCAGAATTCAAATTCCAATAATTCAAATTCCAG
Found at i:3822756 original size:21 final size:21
Alignment explanation
Indices: 3822717--3822757 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3822707 AGAATTCAAA
**
3822717 TTCCAGTAATTCATTTTCCAG
1 TTCCAGTAATTCAAATTCCAG
3822738 TTCCAGTAATTCAAATTCCA
1 TTCCAGTAATTCAAATTCCA
3822758 ATAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.39
Consensus pattern (21 bp):
TTCCAGTAATTCAAATTCCAG
Found at i:3829622 original size:15 final size:15
Alignment explanation
Indices: 3829600--3829638 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3829590 TAAATAAAAA
3829600 TAAT-AAAAATT-AT
1 TAATAAAAAATTAAT
3829613 TAAATAAAAAATTAAT
1 T-AATAAAAAATTAAT
3829629 TAATAAAAAA
1 TAATAAAAAA
3829639 AATAGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 3 0.13
15 16 0.70
16 3 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAATAAAAAATTAAT
Found at i:3829639 original size:16 final size:15
Alignment explanation
Indices: 3829598--3829639 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
3829588 ATTAAATAAA
3829598 AATAATAAAAATTATT
1 AATAA-AAAAATTATT
3829614 AA-ATAAAAAATTAATT
1 AATA-AAAAAATT-ATT
3829630 AATAAAAAAA
1 AATAAAAAAA
3829640 ATAGAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.35
16 14 0.61
17 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAAAAAATTATT
Found at i:3830321 original size:3 final size:3
Alignment explanation
Indices: 3830313--3830351 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3830303 AAATCAATCA
3830313 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3830352 AATGCAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:3832862 original size:10 final size:10
Alignment explanation
Indices: 3832833--3832920 Score: 94
Period size: 10 Copynumber: 9.1 Consensus size: 10
3832823 GCTGCTGGAA
3832833 AACCGGTTTG
1 AACCGGTTTG
*
3832843 -ACCAGTTTTG
1 AACC-GGTTTG
3832853 AACCGGTTTG
1 AACCGGTTTG
*
3832863 -ACCGGTTCG
1 AACCGGTTTG
3832872 AACCGGTTTG
1 AACCGGTTTG
*
3832882 -ACCGGTCTG
1 AACCGGTTTG
3832891 AACCGGTTTG
1 AACCGGTTTG
*
3832901 -ACCGGTCTG
1 AACCGGTTTG
*
3832910 AACCGGGTTG
1 AACCGGTTTG
3832920 A
1 A
3832921 CCCGACCCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 27 0.42
10 34 0.53
11 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:3832876 original size:19 final size:19
Alignment explanation
Indices: 3832833--3832922 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
3832823 GCTGCTGGAA
* *
3832833 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
3832853 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
3832872 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
3832891 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
3832910 AACCGGGTTGACC
1 AACCGGTTTGACC
3832923 CGACCCGACC
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 14 0.21
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:3832946 original size:13 final size:13
Alignment explanation
Indices: 3832924--3832953 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3832914 GGGTTGACCC
3832924 GACC-CGACCGTT
1 GACCGCGACCGTT
3832936 GACCGCGACCGTT
1 GACCGCGACCGTT
3832949 GACCG
1 GACCG
3832954 TTGACTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.17, C:0.40, G:0.30, T:0.13
Consensus pattern (13 bp):
GACCGCGACCGTT
Found at i:3839412 original size:9 final size:9
Alignment explanation
Indices: 3839380--3839452 Score: 83
Period size: 10 Copynumber: 7.7 Consensus size: 9
3839370 CTGCTGGAAA
3839380 ACCGGTTTG
1 ACCGGTTTG
*
3839389 ACCAGTTTTG
1 ACC-GGTTTG
3839399 AACCGGTTTG
1 -ACCGGTTTG
*
3839409 ACCGGTTCG
1 ACCGGTTTG
3839418 AACCGGTTTG
1 -ACCGGTTTG
*
3839428 ACCGGTCTG
1 ACCGGTTTG
3839437 AACCGGTTTG
1 -ACCGGTTTG
3839447 ACCGGT
1 ACCGGT
3839453 CTGAACCGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 25 0.46
10 26 0.48
11 3 0.06
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3839453 original size:19 final size:19
Alignment explanation
Indices: 3839379--3839460 Score: 121
Period size: 19 Copynumber: 4.3 Consensus size: 19
3839369 GCTGCTGGAA
* *
3839379 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
3839399 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
3839418 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
3839437 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
3839456 AACCG
1 AACCG
3839461 ACCCGACCGT
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
18 1 0.02
19 44 0.75
20 14 0.24
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:3839468 original size:19 final size:19
Alignment explanation
Indices: 3839427--3839469 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
3839417 GAACCGGTTT
****
3839427 GACCGGTCTGAACCGGTTT
1 GACCGGTCTGAACCGACCC
3839446 GACCGGTCTGAACCGACCC
1 GACCGGTCTGAACCGACCC
3839465 GACCG
1 GACCG
3839470 TTGACCGCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.30, T:0.16
Consensus pattern (19 bp):
GACCGGTCTGAACCGACCC
Found at i:3839469 original size:38 final size:38
Alignment explanation
Indices: 3839397--3839469 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
3839387 TGACCAGTTT
****
3839397 TGAACCGGTTTGACCGGTTCGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGGTTCGAACCGACCCGACCGGTC
3839435 TGAACCGGTTTGACCGG-TCTGAACCGACCCGACCG
1 TGAACCGGTTTGACCGGTTC-GAACCGACCCGACCG
3839470 TTGACCGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 2 0.07
38 28 0.93
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.22
Consensus pattern (38 bp):
TGAACCGGTTTGACCGGTTCGAACCGACCCGACCGGTC
Found at i:3839482 original size:13 final size:13
Alignment explanation
Indices: 3839460--3839489 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3839450 GGTCTGAACC
3839460 GACC-CGACCGTT
1 GACCGCGACCGTT
3839472 GACCGCGACCGTT
1 GACCGCGACCGTT
3839485 GACCG
1 GACCG
3839490 TTGACTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.17, C:0.40, G:0.30, T:0.13
Consensus pattern (13 bp):
GACCGCGACCGTT
Found at i:3844431 original size:10 final size:11
Alignment explanation
Indices: 3844410--3844439 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
3844400 TCTTAAATAA
3844410 CATTTTTCTCT
1 CATTTTTCTCT
3844421 CATTTTT-TCT
1 CATTTTTCTCT
3844431 CATTTTTCT
1 CATTTTTCT
3844440 GTTTTGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (11 bp):
CATTTTTCTCT
Found at i:3844536 original size:22 final size:22
Alignment explanation
Indices: 3844508--3844581 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
3844498 GGAAGGAGCT
*
3844508 CCGGTCACCGGCCGACTATCGG
1 CCGGTCACCGGTCGACTATCGG
* *
3844530 CCGGTCATCGGTCGACTATCAG
1 CCGGTCACCGGTCGACTATCGG
3844552 CCGGTCACCGGTCGACTATCGG
1 CCGGTCACCGGTCGACTATCGG
*
3844574 TCGGTCAC
1 CCGGTCAC
3844582 TATTTCAGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.15, C:0.36, G:0.30, T:0.19
Consensus pattern (22 bp):
CCGGTCACCGGTCGACTATCGG
Found at i:3844598 original size:22 final size:23
Alignment explanation
Indices: 3844573--3844629 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
3844563 TCGACTATCG
3844573 GTCGGTCACTATTTC-AGCCACC
1 GTCGGTCACTATTTCTAGCCACC
*
3844595 GTCGGTCACTA-TTCTGGCCACC
1 GTCGGTCACTATTTCTAGCCACC
* *
3844617 GTCGATCATTATT
1 GTCGGTCACTATT
3844630 CACTACTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 26 0.87
23 1 0.03
ACGTcount: A:0.18, C:0.32, G:0.19, T:0.32
Consensus pattern (23 bp):
GTCGGTCACTATTTCTAGCCACC
Done.