Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 46 of 210
Found at i:16182632 original size:21 final size:20
Alignment explanation
Indices: 16182608--16182652 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16182598 TAACTCAAGG
16182608 GAAACAATCTTAAAATCGAGT
1 GAAACAAT-TTAAAATCGAGT
* * *
16182629 GAAACAGTTTTAAATCGATT
1 GAAACAATTTAAAATCGAGT
16182649 GAAA
1 GAAA
16182653 ATTTTTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (20 bp):
GAAACAATTTAAAATCGAGT
Found at i:16184188 original size:14 final size:13
Alignment explanation
Indices: 16184165--16184197 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
16184155 TTTAAAAAAA
16184165 TTTT-AAATTTTAT
1 TTTTAAAATTTT-T
16184178 TTTTAAAATTTTT
1 TTTTAAAATTTTT
16184191 TTTTAAA
1 TTTTAAA
16184198 TCGTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTAAAATTTTT
Found at i:16185891 original size:30 final size:30
Alignment explanation
Indices: 16185832--16185905 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
16185822 ATCAACGAGG
* * *
16185832 CCCAGACAATCACCCGGCCCATCATCAGCA
1 CCCAGACAATCACCAGGCCCAGCAACAGCA
* *
16185862 CCCATACAATCACCAGGCCTAGCAACAGCA
1 CCCAGACAATCACCAGGCCCAGCAACAGCA
* *
16185892 CCGAGACAGTCACC
1 CCCAGACAATCACC
16185906 TAACCCAGCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.43, G:0.15, T:0.09
Consensus pattern (30 bp):
CCCAGACAATCACCAGGCCCAGCAACAGCA
Found at i:16187672 original size:95 final size:95
Alignment explanation
Indices: 16187378--16187650 Score: 363
Period size: 94 Copynumber: 2.9 Consensus size: 95
16187368 CCTAAACCTC
* *
16187378 AAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTA
1 AAACCCTAATTTATTT-AATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAA-TTTTTA
16187443 AAAATTTATAATTAATTTACTCAAGTAACCCT
64 AAAATTTATAATTAATTTACTCAAGTAACCCT
* * * *
16187475 GAACCCTAATTTATTTAATTTTTTCATAAAAACCCTTAACTCTAAACCCTAATCTAATTTTTAAA
1 AAACCCTAATTTATTTAATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTAAA
* *
16187540 AAATT-TAATTAAATTACTCAAGTAACCCT
66 AATTTATAATTAATTTACTCAAGTAACCCT
* * ** * *
16187569 AAACCCTAATTTAATTACTTTTTTCTTAAAAAACAATAAACACGAAA-CCTAAT-TCAATTTTGA
1 AAACCCTAATTTATTTAATTTTTTCTT-AAAAACCCTAAACACTAAACCCTAATCT-AATTTTTA
16187632 AAAATTTATAATTAATTTA
64 AAAATTTATAATTAATTTA
16187651 ATTGGCAAAC
Statistics
Matches: 153, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
93 1 0.01
94 65 0.42
95 36 0.24
96 36 0.24
97 15 0.10
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (95 bp):
AAACCCTAATTTATTTAATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTAAA
AATTTATAATTAATTTACTCAAGTAACCCT
Found at i:16187764 original size:27 final size:29
Alignment explanation
Indices: 16187708--16187766 Score: 95
Period size: 27 Copynumber: 2.1 Consensus size: 29
16187698 TTTTCTCTAA
16187708 AACCCTAAACCTAAAAACACCAAAACCCT
1 AACCCTAAACCTAAAAACACCAAAACCCT
*
16187737 AACCCTAAACC-AATAAC-CCAAAACCCT
1 AACCCTAAACCTAAAAACACCAAAACCCT
16187764 AAC
1 AAC
16187767 TGCAGGACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 13 0.45
28 5 0.17
29 11 0.38
ACGTcount: A:0.51, C:0.39, G:0.00, T:0.10
Consensus pattern (29 bp):
AACCCTAAACCTAAAAACACCAAAACCCT
Found at i:16188103 original size:14 final size:14
Alignment explanation
Indices: 16188084--16188123 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
16188074 TTGATTGGCA
16188084 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
16188098 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
16188112 GGAAAATGTTTT
1 GTAAAATGTTTT
16188124 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:16188136 original size:34 final size:35
Alignment explanation
Indices: 16188092--16188158 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
16188082 CAGTAAAATG
* *
16188092 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
16188126 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
16188159 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:16188145 original size:20 final size:20
Alignment explanation
Indices: 16188107--16188146 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16188097 CGTAAAATGA
**
16188107 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
16188127 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
16188147 GGAAAATATT
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:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:16194823 original size:16 final size:16
Alignment explanation
Indices: 16194799--16194830 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16194789 ATCAAGAAAG
*
16194799 TAGATGAGGAAAAACA
1 TAGAGGAGGAAAAACA
16194815 TAGAGGAGGAAAAACA
1 TAGAGGAGGAAAAACA
16194831 GCAGAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.28, T:0.09
Consensus pattern (16 bp):
TAGAGGAGGAAAAACA
Found at i:16196277 original size:3 final size:3
Alignment explanation
Indices: 16196269--16196293 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16196259 ACTAAAATCC
16196269 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
16196294 GGAGATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16199387 original size:128 final size:129
Alignment explanation
Indices: 16199149--16199405 Score: 507
Period size: 128 Copynumber: 2.0 Consensus size: 129
16199139 GTAATTTAAT
16199149 TTATACAAGTTTTTTTAATACAAGGATCGTATTTTAAAATCTTTGCACATTCTTGATATTAAGAC
1 TTATACAAGTTTTTTTAATACAAGGATCGTATTTTAAAATCTTTGCACATTCTTGATATTAAGAC
16199214 ACTAATTAATCAACTAGGTACCAATTTTGGGCGTATCGAGGATGCTCATCCTTCCTCGTGCGTA
66 ACTAATTAATCAACTAGGTACCAATTTTGGGCGTATCGAGGATGCTCATCCTTCCTCGTGCGTA
16199278 TTATACAAG-TTTTTTAATACAAGGATCGTATTTTAAAATCTTTGCACATTCTTGATATTAAGAC
1 TTATACAAGTTTTTTTAATACAAGGATCGTATTTTAAAATCTTTGCACATTCTTGATATTAAGAC
16199342 ACTAATTAATCAACTAGGTACCAATTTTGGGCGTATCGAGGATGCTCATCCTTCCTCGTGCGTA
66 ACTAATTAATCAACTAGGTACCAATTTTGGGCGTATCGAGGATGCTCATCCTTCCTCGTGCGTA
16199406 ACCGACTCCC
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 119 0.93
129 9 0.07
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (129 bp):
TTATACAAGTTTTTTTAATACAAGGATCGTATTTTAAAATCTTTGCACATTCTTGATATTAAGAC
ACTAATTAATCAACTAGGTACCAATTTTGGGCGTATCGAGGATGCTCATCCTTCCTCGTGCGTA
Found at i:16200634 original size:36 final size:36
Alignment explanation
Indices: 16200594--16200662 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
16200584 TTATTTAATA
*
16200594 TTAGAGTTTTAATTGTATACAGCTTCTAATTATGTC
1 TTAGAGTTCTAATTGTATACAGCTTCTAATTATGTC
*
16200630 TTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TTAGAGTTCTAATTGTATACAGCTTCTAATTAT
16200663 AGCCTTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (36 bp):
TTAGAGTTCTAATTGTATACAGCTTCTAATTATGTC
Found at i:16207164 original size:36 final size:36
Alignment explanation
Indices: 16207123--16207193 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
16207113 GATTATTTAA
*
16207123 TCTTAGAGTTTTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
16207159 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTAT
16207194 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:16214677 original size:14 final size:14
Alignment explanation
Indices: 16214658--16214689 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
16214648 CTTTGTGGCG
16214658 AACTCTGAAAGAAT
1 AACTCTGAAAGAAT
16214672 AACTCTGAAAGAAT
1 AACTCTGAAAGAAT
16214686 AACT
1 AACT
16214690 TTTGCGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (14 bp):
AACTCTGAAAGAAT
Found at i:16214768 original size:11 final size:11
Alignment explanation
Indices: 16214752--16214777 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16214742 CCTTTGTCAC
16214752 GAACTCTAAAA
1 GAACTCTAAAA
16214763 GAACTCTAAAA
1 GAACTCTAAAA
16214774 GAAC
1 GAAC
16214778 GACTCTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.15
Consensus pattern (11 bp):
GAACTCTAAAA
Found at i:16218660 original size:18 final size:19
Alignment explanation
Indices: 16218637--16218677 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
16218627 CAATTTCCCA
*
16218637 AAATAAATATTACTT-ATT
1 AAATAAATATTAATTAATT
*
16218655 AAATAAATTTTAATTAATT
1 AAATAAATATTAATTAATT
16218674 AAAT
1 AAAT
16218678 TTTCAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAAATATTAATTAATT
Found at i:16218687 original size:16 final size:16
Alignment explanation
Indices: 16218652--16218696 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
16218642 AATATTACTT
16218652 ATTAAATAAATTTT-A
1 ATTAAATAAATTTTCA
*
16218667 ATTAATTAAATTTTCA
1 ATTAAATAAATTTTCA
16218683 ATTAAAT-AATTTTC
1 ATTAAATAAATTTTC
16218697 TCAATCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAATAAATTTTCA
Found at i:16229954 original size:14 final size:14
Alignment explanation
Indices: 16229935--16229961 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16229925 CAATTCTTGG
16229935 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
16229949 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
16229962 ACTAGACCAC
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:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:16232216 original size:24 final size:24
Alignment explanation
Indices: 16232167--16232213 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
16232157 TATCAATTTA
*
16232167 TTTATTACATAAATTATTATTAAT
1 TTTATTAAATAAATTATTATTAAT
16232191 TTTATTTAAATAAA-TATTGATTA
1 TTTA-TTAAATAAATTATT-ATTA
16232214 TTTAATTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTATTAAATAAATTATTATTAAT
Found at i:16233732 original size:22 final size:22
Alignment explanation
Indices: 16233695--16233759 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 22
16233685 AACTAATCCT
*
16233695 CTCTCAAATTTTCTCTCAATTTC
1 CTCTCAAA-TTTCTCTCAAATTC
16233718 CTCTC-AATTTGCTCTCAAATTC
1 CTCTCAAATTT-CTCTCAAATTC
16233740 CT-TCCAAATTTCTCTCAAAT
1 CTCT-CAAATTTCTCTCAAAT
16233760 CCATATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 4 0.11
22 24 0.63
23 10 0.26
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.43
Consensus pattern (22 bp):
CTCTCAAATTTCTCTCAAATTC
Found at i:16233758 original size:11 final size:11
Alignment explanation
Indices: 16233694--16233759 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
16233684 AAACTAATCC
16233694 TCTCTCAAATTT
1 TCTCTCAAA-TT
16233706 TCTCTC-AATT
1 TCTCTCAAATT
16233716 TCCTCTC-AATT
1 T-CTCTCAAATT
16233727 TGCTCTCAAATT
1 T-CTCTCAAATT
*
16233739 CCT-TCCAAATT
1 TCTCT-CAAATT
16233750 TCTCTCAAAT
1 TCTCTCAAAT
16233760 CCATATTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
10 4 0.09
11 32 0.68
12 11 0.23
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:16233779 original size:51 final size:51
Alignment explanation
Indices: 16233719--16233818 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
16233709 CTCAATTTCC
16233719 TCTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * * *
16233770 TCTCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTT
16233819 TTNNNNNNNN
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.03, T:0.44
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:16235239 original size:328 final size:328
Alignment explanation
Indices: 16234642--16235399 Score: 1507
Period size: 328 Copynumber: 2.3 Consensus size: 328
16234632 GTTGCTGAAA
16234642 CTTGAAGATATACGACTTCTATTAGACCAACAGTCGGAAGCACATGTAAGTATTAAATAAAATTG
1 CTTGAAGATATACGACTTCTATTAGACCAACAGTCGGAAGCACATGTAAGTATTAAATAAAATTG
16234707 ATATTTCCATCATTCGCTAGTAGATTGGTATTTAGTAAAGCAAAAATCGAAGGTTGCCTGTCACT
66 ATATTTCCATCATTCGCTAGTAGATTGGTATTTAGTAAAGCAAAAATCGAAGGTTGCCTGTCACT
16234772 ACTGCAGTCATGGGCACAGTTTCGCTTTCCATTTCTACGTCCTCGAGTGGACCACCCATATACAT
131 ACTGCAGTCATGGGCACAGTTTCGCTTTCCATTTCTACGTCCTCGAGTGGACCACCCATATACAT
16234837 TTCCACTCATAACGAGGTAAATTTTATATTATATTTTACAATTATTATGTAGATTTTTAGAAATA
196 TTCCACTCATAACGAGGTAAATTTTATATTATATTTTACAATTATTATGTAGATTTTTAGAAATA
16234902 AAAGTATGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTCATACTCGATTACCTACC
261 AAAGTATGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTCATACTCGATTACCTACC
16234967 TCT
326 TCT
16234970 CTTGAAGATATACGACTTCTATTAGACCAACAGTCGGAAGCACATGTAAGTATTAAATAAAATTG
1 CTTGAAGATATACGACTTCTATTAGACCAACAGTCGGAAGCACATGTAAGTATTAAATAAAATTG
16235035 ATATTTCCATCATTCGCTAGTAGATTGGTATTTAGTAAAGCAAAAATCGAAGGTTGCCTGTCACT
66 ATATTTCCATCATTCGCTAGTAGATTGGTATTTAGTAAAGCAAAAATCGAAGGTTGCCTGTCACT
16235100 ACTGCAGTCATGGGCACAGTTTCGCTTTCCATTTCTACGTCCTCGAGTGGACCACCCATATACAT
131 ACTGCAGTCATGGGCACAGTTTCGCTTTCCATTTCTACGTCCTCGAGTGGACCACCCATATACAT
16235165 TTCCACTCATAACGAGGTAAATTTTATATTATATTTTACAATTATTATGTAGATTTTTAGAAATA
196 TTCCACTCATAACGAGGTAAATTTTATATTATATTTTACAATTATTATGTAGATTTTTAGAAATA
16235230 AAAGTATGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTCATACTCGATTACCTACC
261 AAAGTATGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTCATACTCGATTACCTACC
16235295 TCT
326 TCT
16235298 CTTGAAGATATACGACTTCTATTAGACCAACAGTCGGAAGCACATGTAAGTATTAAATAAAATTG
1 CTTGAAGATATACGACTTCTATTAGACCAACAGTCGGAAGCACATGTAAGTATTAAATAAAATTG
*
16235363 ATATTTCCATCATTCGCTAGTCGATTGGTATTTAGTA
66 ATATTTCCATCATTCGCTAGTAGATTGGTATTTAGTA
16235400 TTTAGTATTA
Statistics
Matches: 429, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
328 429 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (328 bp):
CTTGAAGATATACGACTTCTATTAGACCAACAGTCGGAAGCACATGTAAGTATTAAATAAAATTG
ATATTTCCATCATTCGCTAGTAGATTGGTATTTAGTAAAGCAAAAATCGAAGGTTGCCTGTCACT
ACTGCAGTCATGGGCACAGTTTCGCTTTCCATTTCTACGTCCTCGAGTGGACCACCCATATACAT
TTCCACTCATAACGAGGTAAATTTTATATTATATTTTACAATTATTATGTAGATTTTTAGAAATA
AAAGTATGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTCATACTCGATTACCTACC
TCT
Found at i:16236086 original size:18 final size:18
Alignment explanation
Indices: 16236059--16236098 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16236049 CAGGTGCGTT
* *
16236059 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
16236077 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
16236095 TCCT
1 TCCT
16236099 TTTCCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:16236657 original size:21 final size:21
Alignment explanation
Indices: 16236633--16236993 Score: 308
Period size: 21 Copynumber: 16.0 Consensus size: 21
16236623 TTTAATTGGC
16236633 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* *
16236654 AAACCATAACACCTTAACCTAAAA
1 AAACCCTAAC-CCTTAA-CT-TAA
16236678 ACCCTAACCCTAACCCTTAACTTAA
1 A----AACCCTAACCCTTAACTTAA
*
16236703 AAACCCTAACACCTTAACCTAAAA
1 AAACCCTAAC-CCTTAA-CT-TAA
*
16236727 ACCCCAACCCTAACCGTTAACTTAA
1 A----AACCCTAACCCTTAACTTAA
* *
16236752 AACCCCTAACCCCTTAACCTAAAA
1 AAACCCTAA-CCCTTAA-CT-TAA
16236776 ACCCTAACCCTAACCCTTAACTTAA
1 A----AACCCTAACCCTTAACTTAA
*
16236801 AAACCCTAACCCCTTAACCTAA
1 AAACCCTAA-CCCTTAACTTAA
* *
16236823 AAATCCTAACCCTTAACTTTA
1 AAACCCTAACCCTTAACTTAA
*
16236844 AAACCGTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
* *
16236865 AAACCCTAAACCCTTTACTTTA
1 AAACCCT-AACCCTTAACTTAA
** *
16236887 AAACTGTAACCCTTAAATTAA
1 AAACCCTAACCCTTAACTTAA
* *
16236908 AAAACCTAAACCCTTAACTTTA
1 AAACCCT-AACCCTTAACTTAA
* * *
16236930 AAACCGTAACCCTTAAATAAA
1 AAACCCTAACCCTTAACTTAA
*
16236951 AAACCCTAACACTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
*
16236972 AAACCCTTACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
16236993 A
1 A
16236994 TATAATTTGA
Statistics
Matches: 273, Mismatches: 43, Indels: 48
0.75 0.12 0.13
Matches are distributed among these distances:
21 130 0.48
22 71 0.26
23 6 0.02
24 9 0.03
25 9 0.03
26 6 0.02
27 18 0.07
28 24 0.09
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:16236680 original size:43 final size:43
Alignment explanation
Indices: 16236633--16236993 Score: 334
Period size: 49 Copynumber: 8.0 Consensus size: 43
16236623 TTTAATTGGC
*
16236633 AAACCCTAACCCTTAACTTAAAAACCATAACACCTTAACCTAAAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAAC-CCTTAACCT-AAA
16236678 ACCCTAACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAA
1 A----AACCCTAACCCTTAACTTAAAAACCCTAAC-CCTTAACCT-AAA
* *
16236727 ACCCCAACCCTAACCGTTAACTTAAAACCCCTAACCCCTTAACCTAAAA
1 A----AACCCTAACCCTTAACTTAAAAACCCTAA-CCCTTAACCT-AAA
16236776 ACCCTAACCCTAACCCTTAACTTAAAAACCCTAACCCCTTAACCT-AA
1 A----AACCCTAACCCTTAACTTAAAAACCCTAA-CCCTTAACCTAAA
* * * *
16236823 AAATCCTAACCCTTAACTTTAAAACCGTAACCCTTAA-CTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAA
* * ** **
16236865 AAACCCTAAACCCTTTACTTTAAAACTGTAACCCTTAAATTAAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACCTAAA
* * *
16236909 AAA-CCTAAACCCTTAACTTTAAAACCGTAACCCTTAA-ATAAA
1 AAACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACCTAAA
* * *
16236951 AAACCCTAACACTTAACTTAAAAACCCTTACCCTTAACTTAAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAA
16236994 TATAATTTGA
Statistics
Matches: 283, Mismatches: 23, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
41 2 0.01
42 48 0.17
43 93 0.33
44 6 0.02
45 1 0.00
47 3 0.01
49 129 0.46
50 1 0.00
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (43 bp):
AAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAA
Found at i:16236703 original size:27 final size:27
Alignment explanation
Indices: 16236634--16236812 Score: 190
Period size: 27 Copynumber: 7.2 Consensus size: 27
16236624 TTAATTGGCA
*
16236634 AACCCTAACCCTTAACTTAAAAACCAT
1 AACCCTAACCCTTAACTTAAAAACCCT
*
16236661 AA--C--A-CCTTAACCTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCT
16236683 AACCCTAACCCTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCT
* *
16236710 AA--C--A-CCTTAACCTAAAAACCCC
1 AACCCTAACCCTTAACTTAAAAACCCT
* *
16236732 AACCCTAACCGTTAACTTAAAACCCCT
1 AACCCTAACCCTTAACTTAAAAACCCT
*
16236759 AA--C---CCCTTAACCTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCT
16236781 AACCCTAACCCTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCT
16236808 AACCC
1 AACCC
16236813 CTTAACCTAA
Statistics
Matches: 124, Mismatches: 13, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
22 54 0.44
23 2 0.02
24 3 0.02
25 3 0.02
26 2 0.02
27 60 0.48
ACGTcount: A:0.42, C:0.38, G:0.01, T:0.20
Consensus pattern (27 bp):
AACCCTAACCCTTAACTTAAAAACCCT
Found at i:16236706 original size:49 final size:49
Alignment explanation
Indices: 16236634--16236878 Score: 351
Period size: 49 Copynumber: 5.1 Consensus size: 49
16236624 TTAATTGGCA
*
16236634 AACCCTAACCCTTAACTTAAAAACCATAACACCTTAACCTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCT
*
16236683 AACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCC
1 AACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCT
* * *
16236732 AACCCTAACCGTTAACTTAAAACCCCTAACCCCTTAACCTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCT
*
16236781 AACCCTAACCCTTAACTTAAAAACCCTAACCCCTTAACCTAAAAA---T
1 AACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCT
* * *
16236827 ---CCTAACCCTTAACTTTAAAACCGTAAC-CCTTAACTTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCT
16236872 AAACCCT
1 -AACCCT
16236879 TTACTTTAAA
Statistics
Matches: 178, Mismatches: 11, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
42 13 0.07
43 25 0.14
45 1 0.01
46 1 0.01
49 138 0.78
ACGTcount: A:0.42, C:0.36, G:0.01, T:0.21
Consensus pattern (49 bp):
AACCCTAACCCTTAACTTAAAAACCCTAACACCTTAACCTAAAAACCCT
Found at i:16236924 original size:86 final size:86
Alignment explanation
Indices: 16236781--16236987 Score: 278
Period size: 86 Copynumber: 2.4 Consensus size: 86
16236771 TAAAAACCCT
* *
16236781 AACCCT-AACCCTTAACTTAAAAACCCTAACCCCTTAACCTAAAAATCCTAACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCCTTAAACTAAAAAACCTAACCCTTAACTTTAA
* *
16236845 AACCGTAACCCTTAACTTAAA
66 AACCGTAACCCTTAAATAAAA
* * ** *
16236866 AACCCTAAACCCTTTACTTTAAAACTGTAA-CCCTTAAATTAAAAAACCTAAACCCTTAACTTTA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCCTTAAACTAAAAAACCT-AACCCTTAACTTTA
16236930 AAACCGTAACCCTTAAATAAAA
65 AAACCGTAACCCTTAAATAAAA
* *
16236952 AACCCT-AACACTTAACTTAAAAACCCTTA-CCCTTAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCCTTAA
16236988 CTTAAATATA
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
85 46 0.44
86 59 0.56
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.26
Consensus pattern (86 bp):
AACCCTAAACCCTTAACTTAAAAACCCTAACCCCTTAAACTAAAAAACCTAACCCTTAACTTTAA
AACCGTAACCCTTAAATAAAA
Found at i:16237818 original size:126 final size:126
Alignment explanation
Indices: 16237593--16238180 Score: 928
Period size: 126 Copynumber: 4.7 Consensus size: 126
16237583 TTAGAAGCGA
* * * *
16237593 TTTTATACTGTTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAGGACCTATTGTAGCAAAAG
1 TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAG
*
16237658 CGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGCTTGCAGCGTTG
66 CGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTTG
* *
16237719 TTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTATTGTAGCAAAAG
1 TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAG
* **
16237784 CGTGTCCACGAGGGCGTAATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTTG
66 CGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTTG
* *
16237845 TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTACGAGGACCTACTGTAGCAAAAG
1 TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAG
*
16237910 CGCGTCCACGAGGGAGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTTG
66 CGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTTG
* * *
16237971 TTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACAGTAGCAAAA
1 TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCTACTGTAGCAAAA
* * * * *
16238036 GCGCCTCCACGAGGGCACGATTTCAAAAATTCTTCTCATAA-AGCATCCTGCTTGAAGCGAT-
65 GCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTGCAGCGTTG
*
16238097 TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAG
1 TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAG
* *
16238162 CGCGTACACGTGGGCGCGA
66 CGCGTCCACGAGGGCGCGA
16238181 CTTAAAAAAT
Statistics
Matches: 425, Mismatches: 35, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
125 37 0.09
126 315 0.74
127 71 0.17
128 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (126 bp):
TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAG
CGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGCGTTG
Found at i:16238670 original size:6 final size:7
Alignment explanation
Indices: 16238643--16238667 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16238633 CGTCATTCTT
16238643 AAAAAGA
1 AAAAAGA
16238650 AAAAAGA
1 AAAAAGA
16238657 AAAAAGA
1 AAAAAGA
16238664 AAAA
1 AAAA
16238668 GAAGAGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:16239629 original size:27 final size:27
Alignment explanation
Indices: 16239597--16239651 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
16239587 GTTTATAAAT
* *
16239597 TTTTAAAATTTGTATTTTAATGTGTAA
1 TTTTAAAATTTATATTTTAATGTATAA
* *
16239624 TTTTAAATTTTATGTTTTAATGTATAA
1 TTTTAAAATTTATATTTTAATGTATAA
16239651 T
1 T
16239652 GATTGAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (27 bp):
TTTTAAAATTTATATTTTAATGTATAA
Found at i:16240104 original size:11 final size:11
Alignment explanation
Indices: 16240065--16240105 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
16240055 ACAATAACAA
16240065 CAAAATAGTAG
1 CAAAATAGTAG
* *
16240076 CAACATAATAG
1 CAAAATAGTAG
*
16240087 TAAAATAGTAG
1 CAAAATAGTAG
16240098 CAAAATAG
1 CAAAATAG
16240106 AGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:16240113 original size:22 final size:22
Alignment explanation
Indices: 16240066--16240113 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
16240056 CAATAACAAC
* *
16240066 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
16240088 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
16240110 AAAA
1 AAAA
16240114 CAAATAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:16240690 original size:6 final size:7
Alignment explanation
Indices: 16240663--16240687 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16240653 CGTCATTCTT
16240663 AAAAAGA
1 AAAAAGA
16240670 AAAAAGA
1 AAAAAGA
16240677 AAAAAGA
1 AAAAAGA
16240684 AAAA
1 AAAA
16240688 GAAGAGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:16241649 original size:27 final size:27
Alignment explanation
Indices: 16241617--16241671 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
16241607 GTTTATAAAT
* *
16241617 TTTTAAAATTTGTATTTTAATGTGTAA
1 TTTTAAAATTTATATTTTAATGTATAA
* *
16241644 TTTTAAATTTTATGTTTTAATGTATAA
1 TTTTAAAATTTATATTTTAATGTATAA
16241671 T
1 T
16241672 GATTGAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (27 bp):
TTTTAAAATTTATATTTTAATGTATAA
Found at i:16242124 original size:11 final size:11
Alignment explanation
Indices: 16242085--16242125 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
16242075 ACAATAACAA
16242085 CAAAATAGTAG
1 CAAAATAGTAG
* *
16242096 CAACATAATAG
1 CAAAATAGTAG
*
16242107 TAAAATAGTAG
1 CAAAATAGTAG
16242118 CAAAATAG
1 CAAAATAG
16242126 AGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:16242133 original size:22 final size:22
Alignment explanation
Indices: 16242086--16242133 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
16242076 CAATAACAAC
* *
16242086 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
16242108 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
16242130 AAAA
1 AAAA
16242134 CAAATAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:16262193 original size:17 final size:18
Alignment explanation
Indices: 16262162--16262195 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16262152 TTATATTTAT
16262162 TTTTACTATCAATAATAG
1 TTTTACTATCAATAATAG
*
16262180 TTTT-CTATCTATAATA
1 TTTTACTATCAATAATA
16262196 ACAATAGTGA
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:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTACTATCAATAATAG
Found at i:16274966 original size:14 final size:15
Alignment explanation
Indices: 16274947--16274993 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
16274937 GATAAATAAC
*
16274947 AAAAAAATATACAGTT
1 AAAAATATATA-AGTT
16274963 AAAAATATATAAGTT
1 AAAAATATATAAGTT
16274978 AAAAA-A-ATAA-TT
1 AAAAATATATAAGTT
16274990 AAAA
1 AAAA
16274994 TAATATCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 6 0.20
13 4 0.13
14 1 0.03
15 9 0.30
16 10 0.33
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (15 bp):
AAAAATATATAAGTT
Found at i:16274977 original size:15 final size:14
Alignment explanation
Indices: 16274948--16274999 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
16274938 ATAAATAACA
16274948 AAAAAATATACAGTT
1 AAAAAATATA-AGTT
16274963 AAAAATATATAAGTT
1 AAAAA-ATATAAGTT
16274978 AAAAAA-ATAA-TT
1 AAAAAATATAAGTT
16274990 AAAATAATAT
1 AAAA-AATAT
16275000 CAAAATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.18
13 6 0.18
14 3 0.09
15 14 0.41
16 5 0.15
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (14 bp):
AAAAAATATAAGTT
Found at i:16275004 original size:11 final size:9
Alignment explanation
Indices: 16274981--16275031 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
16274971 ATAAGTTAAA
16274981 AAAATAATT
1 AAAATAATT
16274990 AAAATAATAT
1 AAAATAAT-T
16275000 CAAAATTAATT
1 -AAAA-TAATT
*
16275011 AAATTAATT
1 AAAATAATT
16275020 -AAATAAATT
1 AAAAT-AATT
16275029 AAA
1 AAA
16275032 CCTGTGTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 3 0.09
9 17 0.49
10 6 0.17
11 5 0.14
12 4 0.11
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATAATT
Found at i:16277973 original size:390 final size:391
Alignment explanation
Indices: 16277254--16278023 Score: 1073
Period size: 390 Copynumber: 2.0 Consensus size: 391
16277244 TAACTAATCC
** *
16277254 TGAGCATCCCTGGGACTCTCACTCGATCTTGCTATTTCTTTGACTTTTCCCTTGACGATCGACCT
1 TGAGCATCCCCAGGACTCTCACTCGATCTTGCTATTCCTTTGACTTTTCCCTTGACGATCGACCT
* * * **
16277319 TTTGTAAGATAATCTGAGTCGGTCGCTCAGTTTACGGATGATGGAGGCCCCCGTGGATGGTTGTA
66 TTTGTAAGACAATCTGAGTCGATCGCTCAGTTTACGAATGAAAGAGGCCCCCGTGGATGGTTGTA
* * * * * *
16277384 CGAGCACGAACACATCTTATAGATCATCGTGATAGGGCTCAAAGTTGTCATCCTTCGTAGCCTCG
131 CAAGCACAAACACATCTTATAGATAATCATGATAGGGCTCAAAGTCGTCATCCTTCGTAGCCTCA
* * ** *
16277449 TCATCATCCTCCTCTCCTGCTTCATATTCTTTCTATTCCTCCTAGGATACGTTGTCCTCAGATGA
196 TCATCATCCTCCTCTCCTACTTCATATTCTTTCTATTCCTCCTAGGATACATTACCCTCAGATAA
16277514 ATCACTCAATTTGTCAGGCCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACACC
261 ATCACTCAATTTGTCAGGCCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACACC
* *
16277579 CCAACATC-A-GCGAATCCGAGCAAAAGGGTAACTAGGCATG-ATGTTACCTGTTTTAACTTTGC
326 CCAACATCGATG-G-ATCCGAGCAAAAAGGTAACTAGGCATGCATGTTACATGTTTTAACTTTGC
16277641 CCT
389 CCT
*
16277644 TGAGCATCCCCAGGACTCTCACTCGATCTTGTTATTCCTTTGACTTTTCCCTTGACGATCGACCT
1 TGAGCATCCCCAGGACTCTCACTCGATCTTGCTATTCCTTTGACTTTTCCCTTGACGATCGACCT
* *
16277709 TTTGTAAGACAGTTTGAGTCGATCGCTCAGTTTACGAATGACAAG-GGCCCCCGTGGATGGTTGT
66 TTTGTAAGACAATCTGAGTCGATCGCTCAGTTTACGAATGA-AAGAGGCCCCCGTGGATGGTTGT
* * * ** *
16277773 GCAAGCTCAAACACATCTTATATATAATCATGATAGGGCTTGAAGTCGTCAT-CTTCTTTAGCCT
130 ACAAGCACAAACACATCTTATAGATAATCATGATAGGGCTCAAAGTCGTCATCCTTC-GTAGCCT
* * ** * * *
16277837 CATCATCGTCCTCCTCTCTTACTTTGTCTTCTTTCTATTCCTCCTTGGCTACATTACCCTCAGAT
194 CATCATCATCCTCCTCTCCTACTTCATATTCTTTCTATTCCTCCTAGGATACATTACCCTCAGAT
** * * *
16277902 AAATCACTTGATTTTTTAGGTCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACA
259 AAATCACTCAATTTGTCAGGCCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACA
* *
16277967 CCCCAACATCGATGGATCTGAGGAAAAAGGTAACTAGGCATGCATGTTACATGTTTT
324 CCCCAACATCGATGGATCCGAGCAAAAAGGTAACTAGGCATGCATGTTACATGTTTT
16278024 GGTGCATAAT
Statistics
Matches: 331, Mismatches: 44, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
389 4 0.01
390 310 0.94
391 16 0.05
392 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (391 bp):
TGAGCATCCCCAGGACTCTCACTCGATCTTGCTATTCCTTTGACTTTTCCCTTGACGATCGACCT
TTTGTAAGACAATCTGAGTCGATCGCTCAGTTTACGAATGAAAGAGGCCCCCGTGGATGGTTGTA
CAAGCACAAACACATCTTATAGATAATCATGATAGGGCTCAAAGTCGTCATCCTTCGTAGCCTCA
TCATCATCCTCCTCTCCTACTTCATATTCTTTCTATTCCTCCTAGGATACATTACCCTCAGATAA
ATCACTCAATTTGTCAGGCCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACACC
CCAACATCGATGGATCCGAGCAAAAAGGTAACTAGGCATGCATGTTACATGTTTTAACTTTGCCC
T
Found at i:16278929 original size:21 final size:21
Alignment explanation
Indices: 16278883--16278963 Score: 51
Period size: 21 Copynumber: 3.8 Consensus size: 21
16278873 TTTACAACAC
*
16278883 AAAAATAACATATTTTAAAAA
1 AAAAATAACATATTTAAAAAA
* *
16278904 GAAAATAGCATA-TTAAAAATA
1 AAAAATAACATATTTAAAAA-A
* * *
16278925 AAAAAGT-ATATTTGATTAAAAAT
1 AAAAA-TAACATAT--TTAAAAAA
16278948 AAAAATAA-ATATTTAA
1 AAAAATAACATATTTAA
16278964 TATATAATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
20 10 0.22
21 17 0.38
22 5 0.11
23 6 0.13
24 7 0.16
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAATAACATATTTAAAAAA
Found at i:16278935 original size:19 final size:19
Alignment explanation
Indices: 16278897--16278936 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16278887 ATAACATATT
*
16278897 TTAAAAAGAAAATAGCATA
1 TTAAAAAGAAAAAAGCATA
* *
16278916 TTAAAAATAAAAAAGTATA
1 TTAAAAAGAAAAAAGCATA
16278935 TT
1 TT
16278937 TGATTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (19 bp):
TTAAAAAGAAAAAAGCATA
Found at i:16278959 original size:24 final size:24
Alignment explanation
Indices: 16278915--16278961 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16278905 AAAATAGCAT
*
16278915 ATTAAAAATAAAAAAGTATATTTG
1 ATTAAAAATAAAAAAGAATATTTG
16278939 ATTAAAAATAAAAATA-AATATTT
1 ATTAAAAATAAAAA-AGAATATTT
16278962 AATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
ATTAAAAATAAAAAAGAATATTTG
Found at i:16289029 original size:25 final size:24
Alignment explanation
Indices: 16289001--16289056 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
16288991 AGGAAGAAAG
*
16289001 TAAACAACAAAACT-AAAATCTAACC
1 TAAA-AACAAAA-TGAAAATCTAAAC
*
16289026 TAAAAAGAAAATGGAAAATCTAAAC
1 TAAAAACAAAAT-GAAAATCTAAAC
16289051 TAAAAA
1 TAAAAA
16289057 TGAAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 6 0.22
25 20 0.74
ACGTcount: A:0.64, C:0.14, G:0.05, T:0.16
Consensus pattern (24 bp):
TAAAAACAAAATGAAAATCTAAAC
Found at i:16289068 original size:25 final size:25
Alignment explanation
Indices: 16289015--16289068 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
16289005 CAACAAAACT
* *
16289015 AAAATCTAACCTAAAAAGAAAATGG
1 AAAATCTAAACTAAAAAGAAAATGA
16289040 AAAATCTAAACTAAAAATGAAAA-GA
1 AAAATCTAAACTAAAAA-GAAAATGA
16289065 AAAA
1 AAAA
16289069 GAAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.15
Consensus pattern (25 bp):
AAAATCTAAACTAAAAAGAAAATGA
Found at i:16290973 original size:13 final size:13
Alignment explanation
Indices: 16290957--16291008 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
16290947 TTTAAACCAA
16290957 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
*
16290970 ACTTCTCAAAAAGT
1 ACTTTTC-AAAAGT
* *
16290984 ACTTTTCCATAA-C
1 ACTTTT-CAAAAGT
16290997 ACTTTTCAAAAG
1 ACTTTTCAAAAG
16291009 CAATGAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 4 0.13
13 12 0.39
14 14 0.45
15 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:16302758 original size:23 final size:22
Alignment explanation
Indices: 16302715--16302757 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16302705 ATGATGATTG
16302715 ATATGATGAGATTGATATTTTC
1 ATATGATGAGATTGATATTTTC
*
16302737 ATATGTATGTGATT-ATATTTT
1 ATATG-ATGAGATTGATATTTT
16302758 TTTTATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.51
Consensus pattern (22 bp):
ATATGATGAGATTGATATTTTC
Found at i:16320497 original size:248 final size:249
Alignment explanation
Indices: 16320048--16320544 Score: 987
Period size: 248 Copynumber: 2.0 Consensus size: 249
16320038 ACTGGTAAGT
16320048 ATTCCGAGGATTGTACCCAAGAGATTGCAGATTGGAGAAACTATTATTAAATTAATTATAGAAAA
1 ATTCCGAGGATTGTACCCAAGAGATTGCAGATTGGAGAAACTATTATTAAATTAATTATAGAAAA
16320113 TAATTAATAATCTAATCGAGTCACGAATTAATAGTGTGAATCCAAATTAATATATTAATTAAACT
66 TAATTAATAATCTAATCGAGTCACGAATTAATAGTGTGAATCCAAATTAATATATTAATTAAACT
16320178 AATTAAATTAATTAACCTAACTAACCTAATGGACTTTCCTATTCTTAGTGTAGACAATGCCAGCC
131 AATTAAATTAATTAACCTAACTAACCTAATGGACTTTCCTATTCTTAGTGTAGACAATGCCAGCC
16320243 TCTAGCTTATGATTGATTAAATCCCTAATTATCTAATTAACTAATTAATTATCC
196 TCTAGCTTATGATTGATTAAATCCCTAATTATCTAATTAACTAATTAATTATCC
16320297 ATTCCGAGGA-TGTACCCAAGAGATTGCAGATTGGAGAAACTATTATTAAATTAATTATAGAAAA
1 ATTCCGAGGATTGTACCCAAGAGATTGCAGATTGGAGAAACTATTATTAAATTAATTATAGAAAA
16320361 TAATTAATAATCTAATCGAGTCACGAATTAATAGTGTGAATCCAAATTAATATATTAATTAAACT
66 TAATTAATAATCTAATCGAGTCACGAATTAATAGTGTGAATCCAAATTAATATATTAATTAAACT
16320426 AATTAAATTAATTAACCTAACTAACCTAATGGACTTTCCTATTCTTAGTGTAGACAATGCCAGCC
131 AATTAAATTAATTAACCTAACTAACCTAATGGACTTTCCTATTCTTAGTGTAGACAATGCCAGCC
16320491 TCTAGCTTATGATTGATTAAATCCCTAATTATCTAATTAACTAATTAATTATCC
196 TCTAGCTTATGATTGATTAAATCCCTAATTATCTAATTAACTAATTAATTATCC
16320545 TAGATTAAGT
Statistics
Matches: 248, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
248 238 0.96
249 10 0.04
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (249 bp):
ATTCCGAGGATTGTACCCAAGAGATTGCAGATTGGAGAAACTATTATTAAATTAATTATAGAAAA
TAATTAATAATCTAATCGAGTCACGAATTAATAGTGTGAATCCAAATTAATATATTAATTAAACT
AATTAAATTAATTAACCTAACTAACCTAATGGACTTTCCTATTCTTAGTGTAGACAATGCCAGCC
TCTAGCTTATGATTGATTAAATCCCTAATTATCTAATTAACTAATTAATTATCC
Found at i:16324976 original size:39 final size:39
Alignment explanation
Indices: 16324721--16324973 Score: 364
Period size: 39 Copynumber: 6.5 Consensus size: 39
16324711 CATGTTTTTA
* *
16324721 AGTATTGTGATATATGCTTGAATGTTATATGATTATATA
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* * *
16324760 AGAATTGT-AGTATATGCTTGAATTTTATATGATTATATG
1 AGTATTGTGA-TATATGCTTGAATGTTATGTGATTATATG
16324799 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
16324838 AGTATTGCGATATATTCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* * * *
16324877 AGTATTGCGATATGTGCTTGAACGTTATGTAATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
*
16324916 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
16324955 TGTAATGTGATATATGCTT
1 AGTATTGTGATATATGCTT
16324974 AAAAGTGAAC
Statistics
Matches: 193, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 1 0.01
39 191 0.99
40 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
Found at i:16344311 original size:28 final size:27
Alignment explanation
Indices: 16344284--16344371 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
16344274 AGAGTAGCCT
*
16344284 TTGTGGCAAACTCTTGAATGATTGGCC
1 TTGTGGAAAACTCTTGAATGATTGGCC
** * ** *
16344311 TTGTGGTGAATTC-TGAAAAATGTAGCC
1 TTGTGGAAAACTCTTGAATGAT-TGGCC
*
16344338 TTTGTGGAAAACTCTTGAATGAATGGCC
1 -TTGTGGAAAACTCTTGAATGATTGGCC
16344366 TTGTGG
1 TTGTGG
16344372 TGAATTCTGA
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
26 6 0.13
27 20 0.44
28 14 0.31
29 5 0.11
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (27 bp):
TTGTGGAAAACTCTTGAATGATTGGCC
Found at i:16344324 original size:55 final size:55
Alignment explanation
Indices: 16344245--16344422 Score: 268
Period size: 55 Copynumber: 3.2 Consensus size: 55
16344235 GCGCACTCTT
*
16344245 ATGAATCGCCCTTGTGGTGAATTCTGAAAAGAGTAGCCTTTGTGGCAAACTCTTGA
1 ATGAAT-GGCCTTGTGGTGAATTCTGAAAAGAGTAGCCTTTGTGGCAAACTCTTGA
* *
16344301 ATGATTGGCCTTGTGGTGAATTCTGAAAA-ATGTAGCCTTTGTGGAAAACTCTTGA
1 ATGAATGGCCTTGTGGTGAATTCTGAAAAGA-GTAGCCTTTGTGGCAAACTCTTGA
* * * *
16344356 ATGAATGGCCTTGTGGTGAATTCTGAAAAGAGTAACTTTTATGGCAAATTCTTGA
1 ATGAATGGCCTTGTGGTGAATTCTGAAAAGAGTAGCCTTTGTGGCAAACTCTTGA
16344411 ATGAATGGCCTT
1 ATGAATGGCCTT
16344423 TTGGCGATAA
Statistics
Matches: 111, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
54 1 0.01
55 104 0.94
56 6 0.05
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (55 bp):
ATGAATGGCCTTGTGGTGAATTCTGAAAAGAGTAGCCTTTGTGGCAAACTCTTGA
Found at i:16344472 original size:110 final size:110
Alignment explanation
Indices: 16344254--16344472 Score: 255
Period size: 110 Copynumber: 2.0 Consensus size: 110
16344244 TATGAATCGC
* * * *
16344254 CCTTGTGGTGAATTCTGAAAAGAGTAGCCTTTGTGGCAAACTCTTGAATGATTGGCCTTGTGGTG
1 CCTTGTGGTGAATTCTGAAAAGAGTAACCTTTATGGCAAACTCTTGAATGAATGGCCTTGTGGCG
* * ** * * *
16344319 AATTCTGAAAAATGTAGCCTTTGTGGAAAACTCTTGAATGAATGG
66 AAATATGAAAAATAAAGACTTTGTGGAAAACTCTTAAAGGAATGG
* * *
16344364 CCTTGTGGTGAATTCTGAAAAGAGTAACTTTTATGGCAAATTCTTGAATGAATGGCCTTTTGGCG
1 CCTTGTGGTGAATTCTGAAAAGAGTAACCTTTATGGCAAACTCTTGAATGAATGGCCTTGTGGCG
*
16344429 ATAATATGAAAAGA-AAAGACTTTGTGGCGAAA-TC-TAAAGGAATG
66 A-AATATGAAAA-ATAAAGACTTTGTGG-AAAACTCTTAAAGGAATG
16344473 ATCTTTGTAG
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
110 67 0.74
111 20 0.22
112 4 0.04
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (110 bp):
CCTTGTGGTGAATTCTGAAAAGAGTAACCTTTATGGCAAACTCTTGAATGAATGGCCTTGTGGCG
AAATATGAAAAATAAAGACTTTGTGGAAAACTCTTAAAGGAATGG
Found at i:16346055 original size:23 final size:23
Alignment explanation
Indices: 16345996--16346084 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 23
16345986 ATATCATACT
* * *
16345996 GAAGTTCTAGTAACAGAAGCACC
1 GAAGTACTAGTAATAGAAGTACC
* *
16346019 GCAGTGCTAGTAATAGAAGTACC
1 GAAGTACTAGTAATAGAAGTACC
* * *
16346042 GAAGTACTAATAATAAAATTACC
1 GAAGTACTAGTAATAGAAGTACC
*
16346065 AAAGTACTAGTAATAGAAGT
1 GAAGTACTAGTAATAGAAGT
16346085 CCCCTGTGGG
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (23 bp):
GAAGTACTAGTAATAGAAGTACC
Found at i:16346587 original size:17 final size:18
Alignment explanation
Indices: 16346562--16346598 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
16346552 TCAATTTTCA
*
16346562 ATTTTCATATTATGG-TT
1 ATTTCCATATTATGGCTT
16346579 ATTTCCATATTATGGCTT
1 ATTTCCATATTATGGCTT
16346597 AT
1 AT
16346599 ATAGACTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (18 bp):
ATTTCCATATTATGGCTT
Found at i:16348053 original size:103 final size:103
Alignment explanation
Indices: 16347929--16348136 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 103
16347919 TGAGGGGTTT
16347929 TAGGTTTCTCATGTATTAAGTCCAATTATATGTACTTCTTGGAATTTTAACCCTACACTTTATAA
1 TAGGTTTCTCATGTATTAAGTCCAATTATATGTACTTCTTGGAATTTTAACCCTACACTTTATAA
16347994 TTTAATCCAACCCAATACATGTTTTTCATTTCTCAAAA
66 TTTAATCCAACCCAATACATGTTTTTCATTTCTCAAAA
*
16348032 TAGGTTTCTCATGTATTAAGTCCAATTATATGTACTTCTTGGAATTTTAATCCTACACTTTATAA
1 TAGGTTTCTCATGTATTAAGTCCAATTATATGTACTTCTTGGAATTTTAACCCTACACTTTATAA
16348097 TTTAATCCAACCCAATACATGTTTTTCATTTCTCAAAA
66 TTTAATCCAACCCAATACATGTTTTTCATTTCTCAAAA
16348135 TA
1 TA
16348137 AATATTATTT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (103 bp):
TAGGTTTCTCATGTATTAAGTCCAATTATATGTACTTCTTGGAATTTTAACCCTACACTTTATAA
TTTAATCCAACCCAATACATGTTTTTCATTTCTCAAAA
Found at i:16352090 original size:9 final size:9
Alignment explanation
Indices: 16352076--16352121 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
16352066 CTTATTCCTA
16352076 ACCAAATTG
1 ACCAAATTG
*
16352085 ACCAAATTT
1 ACCAAATTG
**
16352094 ATAAAATTG
1 ACCAAATTG
16352103 ACCAAATTG
1 ACCAAATTG
16352112 ACCAAATTG
1 ACCAAATTG
16352121 A
1 A
16352122 TATAAGATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (9 bp):
ACCAAATTG
Found at i:16360068 original size:41 final size:41
Alignment explanation
Indices: 16360016--16360098 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
16360006 TTCTATTATC
*
16360016 TAAGACATTTGTTACGTGATTTATTTAAGAATAAAAATCTA
1 TAAGACATTTGTTACCTGATTTATTTAAGAATAAAAATCTA
16360057 TAAGACATTTGTTACCTGATTTATTTAAGAATAAAAATCTA
1 TAAGACATTTGTTACCTGATTTATTTAAGAATAAAAATCTA
16360098 T
1 T
16360099 CTTCATATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (41 bp):
TAAGACATTTGTTACCTGATTTATTTAAGAATAAAAATCTA
Found at i:16364708 original size:41 final size:41
Alignment explanation
Indices: 16364538--16364701 Score: 204
Period size: 41 Copynumber: 4.0 Consensus size: 41
16364528 ACACACCAAT
* *
16364538 CTGGCACCTCAGTGCATCATCGGATAAACCAAAGTAAATATA
1 CTGGCACAT-AGTGCATCATCGAATAAACCAAAGTAAATATA
**
16364580 CTGGCACATAGTATATCATCGAATAAA-CAGAAGTAAATATA
1 CTGGCACATAGTGCATCATCGAATAAACCA-AAGTAAATATA
* * *
16364621 CTAGCACATAGTGTATCATCGAATAAACCGAAGTAAATATA
1 CTGGCACATAGTGCATCATCGAATAAACCAAAGTAAATATA
* ** *
16364662 TTGGCACATAGTGCATCATCGGTTACACCAAAGTAAATAT
1 CTGGCACATAGTGCATCATCGAATAAACCAAAGTAAATAT
16364702 GATGGCATAA
Statistics
Matches: 106, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
40 2 0.02
41 95 0.90
42 9 0.08
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (41 bp):
CTGGCACATAGTGCATCATCGAATAAACCAAAGTAAATATA
Found at i:16364729 original size:82 final size:81
Alignment explanation
Indices: 16364550--16364737 Score: 200
Period size: 82 Copynumber: 2.3 Consensus size: 81
16364540 GGCACCTCAG
* *
16364550 TGCATCATCGGATAAACCAAAGTAAATATACTGGCACATAGTATATCATCGAATAAACAGAAGTA
1 TGCATCATC-GATAAACCGAAGTAAATATACTGGCACATAGTACATCATCGAATAAACAGAAGTA
* *
16364615 AATATACTAGCACATAG
65 AATATACTAGCACAAAA
* * * ** *
16364632 TGTATCATCGAATAAACCGAAGTAAATATATTGGCACATAGTGCATCATCGGTTACACCA-AAGT
1 TGCATCATCG-ATAAACCGAAGTAAATATACTGGCACATAGTACATCATCGAATA-AACAGAAGT
* *
16364696 AAATATGA-TGGCATAAAA
64 AAATAT-ACTAGCACAAAA
*
16364714 TGCATAATCAGATAAACCGAAGTA
1 TGCATCATC-GATAAACCGAAGTA
16364738 TAAACTCGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
81 1 0.01
82 82 0.93
83 5 0.06
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (81 bp):
TGCATCATCGATAAACCGAAGTAAATATACTGGCACATAGTACATCATCGAATAAACAGAAGTAA
ATATACTAGCACAAAA
Found at i:16364737 original size:41 final size:41
Alignment explanation
Indices: 16364550--16364737 Score: 112
Period size: 41 Copynumber: 4.6 Consensus size: 41
16364540 GGCACCTCAG
* * * * * *
16364550 TGCATCATCGGATAAACCAAAGTAAATATACTGGCACATAG
1 TGCATAATCAGATAAACCGAAGTAAATATATTGGCACAAAA
** * * * * * *
16364591 TATATCATC-GAATAAACAGAAGTAAATATACTAGCACATAG
1 TGCATAATCAG-ATAAACCGAAGTAAATATATTGGCACAAAA
* * * *
16364632 TGTATCATC-GAATAAACCGAAGTAAATATATTGGCACATAG
1 TGCATAATCAG-ATAAACCGAAGTAAATATATTGGCACAAAA
* * * * * *
16364673 TGCATCATCGGTTACACCAAAGTAAATATGA-TGGCATAAAA
1 TGCATAATCAGATAAACCGAAGTAAATAT-ATTGGCACAAAA
16364714 TGCATAATCAGATAAACCGAAGTA
1 TGCATAATCAGATAAACCGAAGTA
16364738 TAAACTCGTA
Statistics
Matches: 123, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
40 1 0.01
41 120 0.98
42 2 0.02
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (41 bp):
TGCATAATCAGATAAACCGAAGTAAATATATTGGCACAAAA
Found at i:16364865 original size:7 final size:7
Alignment explanation
Indices: 16364853--16364889 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
16364843 ATACCATTTT
16364853 CATATCA
1 CATATCA
16364860 CATATCA
1 CATATCA
16364867 CATATCA
1 CATATCA
*
16364874 TATATCA
1 CATATCA
16364881 CA-ATCA
1 CATATCA
16364887 CAT
1 CAT
16364890 TTCATGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (7 bp):
CATATCA
Found at i:16367677 original size:16 final size:16
Alignment explanation
Indices: 16367640--16367677 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16367630 GTGAGAGTTC
*
16367640 TTAATTTTTATTATCA
1 TTAATTTTTATTATAA
16367656 TTAATTTTTATT-TAA
1 TTAATTTTTATTATAA
16367671 TTCAATT
1 TT-AATT
16367678 GGGGGGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
TTAATTTTTATTATAA
Found at i:16370222 original size:67 final size:67
Alignment explanation
Indices: 16370114--16370250 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
16370104 AGCACTACAC
16370114 CACTGAAAACTAGCTATCTATATGTATATAATATCCCCCCCCCCCTTTCTCTCATTAGGACGATG
1 CACTGAAAACTAGCTATCTATATGTATATAATATCCCCCCCCCCCTTTCTCTCATTAGGACGATG
16370179 AA
66 AA
16370181 CACTGAAAACTAGCTATCTATATGTATATAATATCCCCCCCCCCCTTTCTCTCATTAGGACGATG
1 CACTGAAAACTAGCTATCTATATGTATATAATATCCCCCCCCCCCTTTCTCTCATTAGGACGATG
16370246 AA
66 AA
16370248 CAC
1 CAC
16370251 ACAGGAAACA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.30, C:0.31, G:0.10, T:0.29
Consensus pattern (67 bp):
CACTGAAAACTAGCTATCTATATGTATATAATATCCCCCCCCCCCTTTCTCTCATTAGGACGATG
AA
Found at i:16377082 original size:16 final size:16
Alignment explanation
Indices: 16377051--16377084 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16377041 AGTAGTAATA
*
16377051 AATTGAAATAGCGTAT
1 AATTGAAATAACGTAT
*
16377067 AATTGAAATAATGTAT
1 AATTGAAATAACGTAT
16377083 AA
1 AA
16377085 AAGTAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32
Consensus pattern (16 bp):
AATTGAAATAACGTAT
Found at i:16382572 original size:30 final size:30
Alignment explanation
Indices: 16382549--16382843 Score: 448
Period size: 30 Copynumber: 9.7 Consensus size: 30
16382539 GTATATGTTT
* *
16382549 TATATATTGCCGAATTGA-TTGTATATGGG
1 TATACATTGCCGAATTGATTTGTATATGGA
16382578 TATACATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
16382608 TATACATTGCAGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
16382638 TATACATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
16382668 TATACGTTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
16382698 TATACATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
16382728 TATACATTGCCGAATTGACTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
** *
16382758 TATACATTGCTTAATTGATTTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
16382788 TATACGTTGCCGAATTGATTTGTATATGTATACA
1 TATACATTGCCGAATTGATTTGTATATG----GA
*
16382822 TATATATTGCCGAATTGATTTG
1 TATACATTGCCGAATTGATTTG
16382844 AGCATTGGAT
Statistics
Matches: 243, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
29 17 0.07
30 205 0.84
34 21 0.09
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:16383537 original size:38 final size:38
Alignment explanation
Indices: 16383486--16383559 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
16383476 AGACTATGGC
16383486 TAATTTTGAATTGTATATAAGTTGCCATACGAAATGAT
1 TAATTTTGAATTGTATATAAGTTGCCATACGAAATGAT
*
16383524 TAATTTTGAATTGTATATAAGTTGCCATGCGAAATG
1 TAATTTTGAATTGTATATAAGTTGCCATACGAAATG
16383560 GTTTGTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (38 bp):
TAATTTTGAATTGTATATAAGTTGCCATACGAAATGAT
Found at i:16401478 original size:135 final size:135
Alignment explanation
Indices: 16401236--16401774 Score: 919
Period size: 135 Copynumber: 4.0 Consensus size: 135
16401226 TAGAAAAACG
*
16401236 AATTATATACTTTCCAAAAGAATATTAATTTTATCTTTTATATTTTGACCAAAATTAATTAATAT
1 AATTATATTCTTTCCAAAAGAATATTAATTTTATCTTTTATATTTTGACCAAAATTAATTAATAT
16401301 AACTATTTATATTAATAAATTTGATAAAATATATACAATTAATAATATGTATGAATCAAATTCAT
66 AACTATTTATATTAATAAATTTGATAAAATATATACAATTAATAATATGTATGAATCAAATTCAT
16401366 ATATT
131 ATATT
16401371 AATTATATTCTTTCCAAAAGAATATTAATTTTATCTTTTATATTTTGACCAAAATTAATTAATAT
1 AATTATATTCTTTCCAAAAGAATATTAATTTTATCTTTTATATTTTGACCAAAATTAATTAATAT
16401436 AACTATTTATATTAATAAATTTGATAAAATATATACAATTAATAATATGTATGAATCAAATTCAT
66 AACTATTTATATTAATAAATTTGATAAAATATATACAATTAATAATATGTATGAATCAAATTCAT
16401501 ATATT
131 ATATT
16401506 AATTATATTCTTTCCAAAAGAATATTAATTTTATCTTTTATATTTTGACCAAAATTAATTAATAT
1 AATTATATTCTTTCCAAAAGAATATTAATTTTATCTTTTATATTTTGACCAAAATTAATTAATAT
16401571 AACTATTTATATTAATAAATTTGATAAAATATATACAATTAATAATATGTATGAATCAAATTCAT
66 AACTATTTATATTAATAAATTTGATAAAATATATACAATTAATAATATGTATGAATCAAATTCAT
16401636 ATATT
131 ATATT
*
16401641 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCTAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTT-A--TCTTTTATATTTTGACCAAAATTAATTAA
* * * * * * * *
16401706 TATAATTGTTTATA-T--T---TTCGGTAAAATATATACAGTTAATATTTTGTATTAATCAAATT
63 TATAACTATTTATATTAATAAATTTGATAAAATATATACAATTAATAATATGTATGAATCAAATT
16401765 CATATATT
128 CATATATT
16401773 AA
1 AA
16401775 GTATTTATAC
Statistics
Matches: 391, Mismatches: 10, Indels: 9
0.95 0.02 0.02
Matches are distributed among these distances:
132 47 0.12
135 302 0.77
136 1 0.00
137 1 0.00
138 40 0.10
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (135 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTATCTTTTATATTTTGACCAAAATTAATTAATAT
AACTATTTATATTAATAAATTTGATAAAATATATACAATTAATAATATGTATGAATCAAATTCAT
ATATT
Found at i:16408658 original size:138 final size:138
Alignment explanation
Indices: 16407965--16408640 Score: 1016
Period size: 138 Copynumber: 4.9 Consensus size: 138
16407955 AAAAAGAAAC
* **
16407965 TATATTCTTTCCAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACAAAAATTAATTAATAT
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
* * * * *
16408030 AATTATTTATGTTAATAAATTCGGTAAAATATATACAATTATTATTTTGTATGAATCAAATTCAT
66 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCAT
16408095 ATATTAAT
131 ATATTAAT
*
16408103 TATATTCTTTCCAAAAGAATACTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
* *
16408168 AACTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAAGTCAT
66 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCAT
16408233 ATATTAAT
131 ATATTAAT
* * * *
16408241 TATTTTCTTTCC-AAAGAATTTTAATTTCCATGT-TTTTCATATTTTGACCAAAATTAATTAATG
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTT-ATATTTTGACCGAAATTAATTAATA
* * * *
16408304 TAATTTTTTATATTAATAAATTTGGTAAAACATATACAATTAGTATTTTGTATGAATCAAATTCA
65 TAATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCA
16408369 TATATTAAT
130 TATATTAAT
* * * * * **
16408378 TATTTTCTTTGC-AAAGAATATCAATTTTCACGTCTTTTATATTTTGACCGAAATTAATTAATGC
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
* * * *
16408442 AATTGTTTATATTAATAAATTTGATAAAATATATAAAATTAATATTTTGTATTAATCAAATTCAT
66 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCAT
16408507 ATATTAAT
131 ATATTAAT
* * * *
16408515 TACATTCTTTCCAAAAGAATATTAATTCCCATTTCTTTTAAATTTTGACCGAAATTAATTAATAT
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
16408580 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAAT
66 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAAT
16408641 AGAGAACATA
Statistics
Matches: 485, Mismatches: 50, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
136 4 0.01
137 238 0.49
138 243 0.50
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (138 bp):
TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCAT
ATATTAAT
Found at i:16409651 original size:42 final size:42
Alignment explanation
Indices: 16409604--16409686 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
16409594 TGCATTATTG
16409604 TTGTCCAATCCCACAATAATACTTAACTAAGGACCTTTTAAA
1 TTGTCCAATCCCACAATAATACTTAACTAAGGACCTTTTAAA
16409646 TTGTCCAATCCCACAATAATACTTAACTAAGGACCTTTTAA
1 TTGTCCAATCCCACAATAATACTTAACTAAGGACCTTTTAA
16409687 GAATAATCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (42 bp):
TTGTCCAATCCCACAATAATACTTAACTAAGGACCTTTTAAA
Found at i:16417737 original size:31 final size:33
Alignment explanation
Indices: 16417687--16417747 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
16417677 GAAAAAAGAC
16417687 AAAAAAAAACTTGATTAGTTGAGAGACTAATTG
1 AAAAAAAAACTTGATTAGTTGAGAGACTAATTG
* *
16417720 AAAAAAAAA-TTTA-TAGTTGAGTGACTAA
1 AAAAAAAAACTTGATTAGTTGAGAGACTAA
16417748 AAGAGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 14 0.54
32 3 0.12
33 9 0.35
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (33 bp):
AAAAAAAAACTTGATTAGTTGAGAGACTAATTG
Found at i:16420733 original size:5 final size:5
Alignment explanation
Indices: 16420714--16420748 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
16420704 ATTTTATAGC
*
16420714 TTTTA TTAT- TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
16420749 AGTTTTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 3 0.11
5 24 0.89
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:16420852 original size:476 final size:483
Alignment explanation
Indices: 16420239--16421141 Score: 1225
Period size: 476 Copynumber: 1.9 Consensus size: 483
16420229 TTTAGTGCTA
*
16420239 TTTTATTATTTTGTTATTTTATTTTCTAGTTTTTACTACTCTTTTCTTTTTCACTTTCTCCATCT
1 TTTTATTATTTTGTTATTTTATTTTATAGTTTTTACTACTCTTTTC-TTTTCACTTTCTCCATCT
* *
16420304 CCTTTGTTTGTTTTTTTTTTCTTTTTTTTCTTTTGGGAAACAGTTTTGCTTGCAGATTTCAAAGA
65 CATTTGTTTGTTTTATTTTTC-----TTTCTTTTGGGAAACAGTTTTGCTTGCAGATTTCAAAGA
* *
16420369 GCTTCGCTCCTTTGTCGTCAAGTCGGTGTTTGGACATCATTGATCACGAATCAGGTGTGGGTTCT
125 GCTTCGCTCCTTTGTCATCAAGTCGGTGTCTGGACATCATTGATCACGAATCAGGTGTGGGTTCT
* * * * * *
16420434 GAATTTATTTTACTTTGTTTGTGAATTCTTGAGTTGATTCTGTGAAAGTTAGCATTTCA-CGTGT
190 GAATCTATTCTACTTTGTTTGCGAACTCTTGAGTTGATTCTGTGAAAGTCAACATTTCAGCGTGT
* **
16420498 GTGTATGT-T-TG-T-AACCGGTTATTTACGATGCTGCAGTATTGTTTTATGCTTAGACCTTGTT
255 GTGTATGTGTGTGTTCAACCGGTTATTTACGATGCTGCAGTATTGTTTTATGCTTAAAAATTGTT
* *
16420559 CAATTTGGTATGATTTCAGGTTATCGAGGGATGGGAAATGTTTCAAGTGCGAAAGCACAATTTTT
320 CAATTTGGTATGATTTCAGGTTATCGAGGGATGGGAAATGTTTCAAGTGCAAAACCACAATTTTT
* *
16420624 TAGGCTATTTTAGGGTGGTTTCACGACCACACGGACGGTCCACACGGTCGTGTTGAATTGGGAGT
385 TAGGCTATTTTAGGGCGATTTCACGACCACACGGACGGTCCACACGGTCGTGTTGAATTGGGAGT
16420689 TAGGATTCCGAGCCAATTTTATAGCTTTTATTAT
450 TAGGATTCCGAGCCAATTTTATAGCTTTTATTAT
* *
16420723 TTTTATT-TTATT-TTATTTTATTTTATAGTTTTTACTGCTCTTTTC-TTTCACTTTCTCCCTCT
1 TTTTATTATT-TTGTTATTTTATTTTATAGTTTTTACTACTCTTTTCTTTTCACTTTCTCCATCT
*
16420785 CATTTGTTTGCTTTTATTTTTC-TTCTTTTGGGAAACAGTTTTGCTTG-TGAATTTCAGAA-AGC
65 CATTTGTTTG-TTTTATTTTTCTTTCTTTTGGGAAACAGTTTTGCTTGCAG-ATTTCA-AAGAGC
** * * **
16420847 TTCGCTCCTTTGTCATTGAGTTGGTGTCTGTACATCATTGATCGTGAATCAGGTGTGGGTTCTGA
127 TTCGCTCCTTTGTCATCAAGTCGGTGTCTGGACATCATTGATCACGAATCAGGTGTGGGTTCTGA
* * *
16420912 ATCTCTTCTATTTTGTTTGCGAACTCTTGAGTTGATTCTGTGAAAGTCAACATTTCATGTGTGTG
192 ATCTATTCTACTTTGTTTGCGAACTCTTGAGTTGATTCTGTGAAAGTCAACATTTCA-GCGTGTG
* ** * * * *
16420977 TGTGTGTGTGTGTTTGCAACTTGTTATTTGCGATGTTGCAGTGTTGTTTTATGCTTAAAAATTTT
256 TGTATGTGTGTG-TT-CAACCGGTTATTTACGATGCTGCAGTATTGTTTTATGCTTAAAAATTGT
* * *
16421042 TCAATTTGGTATGATTTCAGGTTATCGAGGGTTGGGAAGTGTTTCGAGTGCAAAACCACAATTTT
319 TCAATTTGGTATGATTTCAGGTTATCGAGGGATGGGAAATGTTTCAAGTGCAAAACCACAATTTT
* * *
16421107 TTGGGTTATTTTAGGGCGATTTCGCGACCACACGG
384 TTAGGCTATTTTAGGGCGATTTCACGACCACACGG
16421142 GTGGCCATAT
Statistics
Matches: 364, Mismatches: 43, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
475 1 0.00
476 140 0.38
477 2 0.01
478 11 0.03
479 1 0.00
480 2 0.01
481 25 0.07
482 11 0.03
483 33 0.09
484 138 0.38
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.46
Consensus pattern (483 bp):
TTTTATTATTTTGTTATTTTATTTTATAGTTTTTACTACTCTTTTCTTTTCACTTTCTCCATCTC
ATTTGTTTGTTTTATTTTTCTTTCTTTTGGGAAACAGTTTTGCTTGCAGATTTCAAAGAGCTTCG
CTCCTTTGTCATCAAGTCGGTGTCTGGACATCATTGATCACGAATCAGGTGTGGGTTCTGAATCT
ATTCTACTTTGTTTGCGAACTCTTGAGTTGATTCTGTGAAAGTCAACATTTCAGCGTGTGTGTAT
GTGTGTGTTCAACCGGTTATTTACGATGCTGCAGTATTGTTTTATGCTTAAAAATTGTTCAATTT
GGTATGATTTCAGGTTATCGAGGGATGGGAAATGTTTCAAGTGCAAAACCACAATTTTTTAGGCT
ATTTTAGGGCGATTTCACGACCACACGGACGGTCCACACGGTCGTGTTGAATTGGGAGTTAGGAT
TCCGAGCCAATTTTATAGCTTTTATTAT
Found at i:16427153 original size:21 final size:20
Alignment explanation
Indices: 16427129--16427168 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
16427119 GATGGCATGA
16427129 TTAATT-AGATATTAATTTAGG
1 TTAATTAAGAT-TT-ATTTAGG
16427150 TTAATTAAGATTTATTTAG
1 TTAATTAAGATTTATTTAG
16427169 TAAAAACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (20 bp):
TTAATTAAGATTTATTTAGG
Found at i:16430439 original size:29 final size:29
Alignment explanation
Indices: 16430402--16430657 Score: 171
Period size: 29 Copynumber: 8.8 Consensus size: 29
16430392 CAATGGTTGT
* *
16430402 AACCGTCCCTTTTCATATTCGATGGTCAA
1 AACCATCCCTTTTCATATTCGATGGTCGA
* * *
16430431 AACCATCCCTTTTCATTAATCGATGGTTGT
1 AACCATCCCTTTTCA-TATTCGATGGTCGA
* *
16430461 CACCATCCCTTTTCATAGTT-GATGGTCGT
1 AACCATCCCTTTTCATA-TTCGATGGTCGA
* * *
16430490 CACCATCCCTTTTCATTAATCGATAGTCGA
1 AACCATCCCTTTTCA-TATTCGATGGTCGA
* * ** *
16430520 AGCTATCATTTTTCATATTCGATAGTCGA
1 AACCATCCCTTTTCATATTCGATGGTCGA
* * * * *
16430549 AGCTATCCCTTTTCACACTCGATGGTCGT
1 AACCATCCCTTTTCATATTCGATGGTCGA
* *
16430578 CACCATCCCTTTTCATAGTT-GATGATC-A
1 AACCATCCCTTTTCATA-TTCGATGGTCGA
* * *
16430606 TCACCATCCC-TTTCATAATT-GATAGCCGA
1 -AACCATCCCTTTTCAT-ATTCGATGGTCGA
* * *
16430635 AGCTATCTCTTTTCATATTCGAT
1 AACCATCCCTTTTCATATTCGAT
16430658 AGCCGAAGCT
Statistics
Matches: 180, Mismatches: 37, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
28 20 0.11
29 115 0.64
30 45 0.25
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (29 bp):
AACCATCCCTTTTCATATTCGATGGTCGA
Found at i:16430486 original size:59 final size:59
Alignment explanation
Indices: 16430394--16430657 Score: 209
Period size: 59 Copynumber: 4.5 Consensus size: 59
16430384 GTGCTAAACA
* *
16430394 ATGGTTGTAACCGTCCCTTTTCATATTCGATGGTCAAAACCATCCCTTTTCATTAATCG
1 ATGGTCGTAACCATCCCTTTTCATATTCGATGGTCAAAACCATCCCTTTTCATTAATCG
* * ***
16430453 ATGGTTGTCACCATCCCTTTTCATAGTT-GATGGTCGTCACCATCCCTTTTCATTAATCG
1 ATGGTCGTAACCATCCCTTTTCATA-TTCGATGGTCAAAACCATCCCTTTTCATTAATCG
* * ** * * * * * *
16430512 ATAGTCG-AAGCTATCATTTTTCATATTCGATAGTCGAAGCTATCCCTTTTCA-CACTCG
1 ATGGTCGTAA-CCATCCCTTTTCATATTCGATGGTCAAAACCATCCCTTTTCATTAATCG
* * ** *
16430570 ATGGTCGTCACCATCCCTTTTCATAGTT-GATGATCATCACCATCCC-TTTCA-TAATTG
1 ATGGTCGTAACCATCCCTTTTCATA-TTCGATGGTCAAAACCATCCCTTTTCATTAATCG
* * * *
16430627 ATAGCCG-AAGCTATCTCTTTTCATATTCGAT
1 ATGGTCGTAA-CCATCCCTTTTCATATTCGAT
16430658 AGCCGAAGCT
Statistics
Matches: 160, Mismatches: 38, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
56 3 0.02
57 29 0.18
58 36 0.22
59 90 0.56
60 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.38
Consensus pattern (59 bp):
ATGGTCGTAACCATCCCTTTTCATATTCGATGGTCAAAACCATCCCTTTTCATTAATCG
Found at i:16430618 original size:117 final size:116
Alignment explanation
Indices: 16430410--16430679 Score: 373
Period size: 115 Copynumber: 2.3 Consensus size: 116
16430400 GTAACCGTCC
* * * * * *
16430410 CTTTTCATATTCGATGGTCAAAACCATCCCTTTTCATTAATCGATGGTTGTCACCATCCCTTTTC
1 CTTTTCATATTCGATAGTCGAAGCTATCCCTTTTCATCAATCGATGGTCGTCACCATCCCTTTTC
* * *
16430475 ATAGTTGATGGTCGTCACCATCCCTTTTCATTAATCGATAGTCGAAGCTATCAT
66 ATAGTTGATGATCATCACCATCCC-TTTCA-TAATCGATAGCCGAAGCTATC-T
*
16430529 -TTTTCATATTCGATAGTCGAAGCTATCCCTTTTCA-CACTCGATGGTCGTCACCATCCCTTTTC
1 CTTTTCATATTCGATAGTCGAAGCTATCCCTTTTCATCAATCGATGGTCGTCACCATCCCTTTTC
*
16430592 ATAGTTGATGATCATCACCATCCCTTTCATAATTGATAGCCGAAGCTATCT
66 ATAGTTGATGATCATCACCATCCCTTTCATAATCGATAGCCGAAGCTATCT
* **
16430643 CTTTTCATATTCGATAGCCGAAGCTATCTTTTTTCAT
1 CTTTTCATATTCGATAGTCGAAGCTATCCCTTTTCAT
16430680 TGGTCGATGA
Statistics
Matches: 135, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
114 1 0.01
115 51 0.38
116 5 0.04
117 47 0.35
118 31 0.23
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (116 bp):
CTTTTCATATTCGATAGTCGAAGCTATCCCTTTTCATCAATCGATGGTCGTCACCATCCCTTTTC
ATAGTTGATGATCATCACCATCCCTTTCATAATCGATAGCCGAAGCTATCT
Found at i:16430658 original size:29 final size:29
Alignment explanation
Indices: 16430498--16430679 Score: 106
Period size: 29 Copynumber: 6.3 Consensus size: 29
16430488 GTCACCATCC
* *
16430498 CTTTTCATTAATCGATAGTCGAAGCTATCAT
1 CTTTTCA-TATTCGATAGCCGAAGCTATC-T
* *
16430529 -TTTTCATATTCGATAGTCGAAGCTATCC
1 CTTTTCATATTCGATAGCCGAAGCTATCT
* * * * * * *
16430557 CTTTTCACACTCGATGGTCGTCA-CCATCC
1 CTTTTCATATTCGATAGCCG-AAGCTATCT
* *** *
16430586 CTTTTCATAGTT-GATGATCATCA-CCATC-
1 CTTTTCATA-TTCGAT-AGCCGAAGCTATCT
*
16430614 CCTTTCATAATT-GATAGCCGAAGCTATCT
1 CTTTTCAT-ATTCGATAGCCGAAGCTATCT
16430643 CTTTTCATATTCGATAGCCGAAGCTATCT
1 CTTTTCATATTCGATAGCCGAAGCTATCT
*
16430672 TTTTTCAT
1 CTTTTCAT
16430680 TGGTCGATGA
Statistics
Matches: 121, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
27 3 0.02
28 19 0.16
29 91 0.75
30 8 0.07
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (29 bp):
CTTTTCATATTCGATAGCCGAAGCTATCT
Found at i:16430678 original size:115 final size:117
Alignment explanation
Indices: 16430411--16430670 Score: 364
Period size: 117 Copynumber: 2.2 Consensus size: 117
16430401 TAACCGTCCC
* * * * * * * *
16430411 TTTTCATATTCGATGGTCAAAACCATCCCTTTTCATTAATCGATGGTTGTCACCATCCCTTTTCA
1 TTTTCATATTCGATAGCCGAAGCTATCCCTTTTCA-CACTCGATGGTCGTCACCATCCCTTTTCA
* * *
16430476 TAGTTGATGGTCGTCACCATCCCTTTTCATTAATCGATAGTCGAAGCTATCAT
65 TAGTTGATGATCATCACCATCCCTTTTCATTAATCGATAGCCGAAGCTATCAT
*
16430529 TTTTCATATTCGATAGTCGAAGCTATCCCTTTTCACACTCGATGGTCGTCACCATCCCTTTTCAT
1 TTTTCATATTCGATAGCCGAAGCTATCCCTTTTCACACTCGATGGTCGTCACCATCCCTTTTCAT
*
16430594 AGTTGATGATCATCACCATCCC-TTTCA-TAATTGATAGCCGAAGCTATC-T
66 AGTTGATGATCATCACCATCCCTTTTCATTAATCGATAGCCGAAGCTATCAT
16430643 CTTTTCATATTCGATAGCCGAAGCTATC
1 -TTTTCATATTCGATAGCCGAAGCTATC
16430671 TTTTTTCATT
Statistics
Matches: 129, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
114 1 0.01
115 45 0.35
116 5 0.04
117 47 0.36
118 31 0.24
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (117 bp):
TTTTCATATTCGATAGCCGAAGCTATCCCTTTTCACACTCGATGGTCGTCACCATCCCTTTTCAT
AGTTGATGATCATCACCATCCCTTTTCATTAATCGATAGCCGAAGCTATCAT
Found at i:16451080 original size:21 final size:20
Alignment explanation
Indices: 16451048--16451086 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
16451038 TATTTATTTG
16451048 TATTTTTTTTC-TCTTTTTT
1 TATTTTTTTTCTTCTTTTTT
16451067 TATTTTTTCCTTCTTCTTTT
1 TATTTTTT--TTCTTCTTTT
16451087 CCTAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (20 bp):
TATTTTTTTTCTTCTTTTTT
Found at i:16463553 original size:58 final size:57
Alignment explanation
Indices: 16463448--16463557 Score: 125
Period size: 58 Copynumber: 1.9 Consensus size: 57
16463438 TTTGATATAA
* * * *
16463448 TATTACAAATTATAATAATATATATTATGTATTCTTAGTATAGCATATGATATAGTAT
1 TATTACAAATTATAATAATATATATTATATATTATTAATAAAGCATAT-ATATAGTAT
* *
16463506 TATTACATAA-TATAATAATATATTTTATAT-TTATTAATACAATCATATATAT
1 TATTACA-AATTATAATAATATATATTATATATTATTAATA-AAGCATATATAT
16463558 GACTATTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
57 11 0.25
58 31 0.70
59 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (57 bp):
TATTACAAATTATAATAATATATATTATATATTATTAATAAAGCATATATATAGTAT
Found at i:16463944 original size:21 final size:21
Alignment explanation
Indices: 16463905--16463944 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16463895 AACTCTTAAT
* * *
16463905 ATATTATATTATATGATATGG
1 ATATAATATTACATAATATGG
16463926 ATATAATATTACATAATAT
1 ATATAATATTACATAATAT
16463945 AATATAACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATAATATTACATAATATGG
Found at i:16470910 original size:58 final size:57
Alignment explanation
Indices: 16470805--16470914 Score: 125
Period size: 58 Copynumber: 1.9 Consensus size: 57
16470795 TTTGATATAA
* * * *
16470805 TATTACAAATTATAATAATATATATTATGTATTCTTAGTATAGCATATGATATAGTAT
1 TATTACAAATTATAATAATATATATTATATATTATTAATAAAGCATAT-ATATAGTAT
* *
16470863 TATTACATAA-TATAATAATATATTTTATAT-TTATTAATACAATCATATATAT
1 TATTACA-AATTATAATAATATATATTATATATTATTAATA-AAGCATATATAT
16470915 GACTATTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
57 11 0.25
58 31 0.70
59 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (57 bp):
TATTACAAATTATAATAATATATATTATATATTATTAATAAAGCATATATATAGTAT
Found at i:16484952 original size:3 final size:3
Alignment explanation
Indices: 16484946--16484982 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16484936 AACAGTTTAA
16484946 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
16484983 GAACAGGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16491145 original size:9 final size:9
Alignment explanation
Indices: 16491127--16491185 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
16491117 TTTGGTTAAA
16491127 AATTAACCG
1 AATTAACCG
*
16491136 AATTACCCG
1 AATTAACCG
16491145 AATTAACCG
1 AATTAACCG
*
16491154 ACTTAACCG
1 AATTAACCG
*
16491163 AATTACCCG
1 AATTAACCG
**
16491172 AATTGCCCG
1 AATTAACCG
16491181 AATTA
1 AATTA
16491186 TATGTTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:16491150 original size:18 final size:18
Alignment explanation
Indices: 16491127--16491185 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
16491117 TTTGGTTAAA
16491127 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
* *
16491145 AATTAACCGACTTAACCG
1 AATTAACCGAATTACCCG
* *
16491163 AATTACCCGAATTGCCCG
1 AATTAACCGAATTACCCG
16491181 AATTA
1 AATTA
16491186 TATGTTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:16495725 original size:22 final size:23
Alignment explanation
Indices: 16495699--16495743 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
16495689 TGTGATGAGG
**
16495699 TTATCTTATGAATATGTT-AAAT
1 TTATCTTAAAAATATGTTGAAAT
16495721 TTATCTTAAAAATATGTTGAAAT
1 TTATCTTAAAAATATGTTGAAAT
16495744 GGATTGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (23 bp):
TTATCTTAAAAATATGTTGAAAT
Found at i:16496644 original size:21 final size:21
Alignment explanation
Indices: 16496614--16496653 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16496604 ATGAACTTAA
*
16496614 ATTTTTTATTAAAAAATATAC
1 ATTTTATATTAAAAAATATAC
* *
16496635 ATTTTATATTTAAATATAT
1 ATTTTATATTAAAAAATAT
16496654 TTGGTCTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTATATTAAAAAATATAC
Found at i:16498974 original size:23 final size:23
Alignment explanation
Indices: 16498923--16498975 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
16498913 ATTTCTAAAA
*
16498923 TTTTAATAAATATATTTATATTT
1 TTTTATTAAATATATTTATATTT
**
16498946 AATTATTAAA-ATATTTAATATTT
1 TTTTATTAAATATATTT-ATATTT
16498969 TTTTATT
1 TTTTATT
16498976 TATCGAAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTATTAAATATATTTATATTT
Found at i:16510474 original size:26 final size:25
Alignment explanation
Indices: 16510443--16510496 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
16510433 TCATCCCAAA
*
16510443 TTTACCCTAG-TAAAATTTTTGACAAT
1 TTTACCC-AGATAAAA-TTTTAACAAT
*
16510469 TTTACCCCGATAAAATTTTAACAAT
1 TTTACCCAGATAAAATTTTAACAAT
16510494 TTT
1 TTT
16510497 GCCCCCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.43
Consensus pattern (25 bp):
TTTACCCAGATAAAATTTTAACAAT
Found at i:16510502 original size:26 final size:25
Alignment explanation
Indices: 16510443--16510512 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
16510433 TCATCCCAAA
* * *
16510443 TTTACCCTAGTAAAATTTTTGACAAT
1 TTTACCCCAATAAAA-TTTTAACAAT
*
16510469 TTTACCCCGATAAAATTTTAACAAT
1 TTTACCCCAATAAAATTTTAACAAT
*
16510494 TTTGCCCCCAATAAAATTT
1 TTT-ACCCCAATAAAATTT
16510513 CGAGAAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 12 0.32
26 25 0.68
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.39
Consensus pattern (25 bp):
TTTACCCCAATAAAATTTTAACAAT
Found at i:16518153 original size:9 final size:9
Alignment explanation
Indices: 16518119--16518188 Score: 61
Period size: 9 Copynumber: 7.6 Consensus size: 9
16518109 AGATATTTTG
16518119 ATTTTTTATA
1 ATTTTTTA-A
*
16518129 TATTTTTGAA
1 -ATTTTTTAA
* *
16518139 AGTTTTTAT
1 ATTTTTTAA
*
16518148 ATTTTTTGA
1 ATTTTTTAA
*
16518157 ATTTTTTGA
1 ATTTTTTAA
16518166 A-TTTTTAA
1 ATTTTTTAA
16518174 ATTTTATTAA
1 ATTTT-TTAA
16518184 ATTTT
1 ATTTT
16518189 ATTATTTGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
8 7 0.14
9 25 0.51
10 10 0.20
11 7 0.14
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:16518170 original size:17 final size:18
Alignment explanation
Indices: 16518150--16518188 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
16518140 GTTTTTATAT
* *
16518150 TTTTTGAATTTT-TTGAA
1 TTTTTAAATTTTATTAAA
16518167 TTTTTAAATTTTATTAAA
1 TTTTTAAATTTTATTAAA
16518185 TTTT
1 TTTT
16518189 ATTATTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTTAAATTTTATTAAA
Found at i:16532791 original size:21 final size:21
Alignment explanation
Indices: 16532755--16532816 Score: 94
Period size: 19 Copynumber: 3.1 Consensus size: 21
16532745 ATTACAAAAC
*
16532755 ATATCATA-CCAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
16532775 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
16532794 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
16532815 AT
1 AT
16532817 CCTTGAAGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
19 19 0.50
20 8 0.21
21 11 0.29
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:16532909 original size:44 final size:45
Alignment explanation
Indices: 16532882--16533001 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 45
16532872 CTACCATTTC
* *
16532882 CAACCTATTCCATTACTGACCAGGGAGAT-AGTATTCTCAATCTT
1 CAACCTAATCCACTACTGACCAGGGAGATAAGTATTCTCAATCTT
* * * *
16532926 CAACCTAATCCACTGCTGACCAGGGAGAT-AGGAATCACAATCTT
1 CAACCTAATCCACTACTGACCAGGGAGATAAGTATTCTCAATCTT
* * * * *
16532970 CAACCTATTTCACTGCTGTCTAGGGAGATAAG
1 CAACCTAATCCACTACTGACCAGGGAGATAAG
16533002 AATAGTGGCT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
44 63 0.97
45 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (45 bp):
CAACCTAATCCACTACTGACCAGGGAGATAAGTATTCTCAATCTT
Found at i:16533086 original size:44 final size:44
Alignment explanation
Indices: 16533038--16533651 Score: 232
Period size: 44 Copynumber: 14.2 Consensus size: 44
16533028 CTCCTGGGGA
* * *
16533038 AGATAAGATTTGCCGTCTTCGATCTACTCCACTACTGCTTAGGG
1 AGATAAGATTTGCAGTCTTCAACCTACTCCACTACTGCTTAGGG
* * * * *
16533082 AGATAAGATCTGCTA-TTTTCAACCTATTCCACTGCTGAC-CAGGG
1 AGATAAGATTTGC-AGTCTTCAACCTACTCCACTACTG-CTTAGGG
* * * * *
16533126 AGATAGGATTCT-CAATCTTCAACCTATTCCAC-AGCTG-TCCAGAG
1 AGATAAGATT-TGCAGTCTTCAACCTACTCCACTA-CTGCT-TAGGG
* * * * * * * * * *
16533170 AGATAGGACTAG-TGGCTTAAATCTGCTTCC-CTACT-CCTGGGG
1 AGATAAGATTTGCAGTCTTCAACCTAC-TCCACTACTGCTTAGGG
** * * *
16533212 AAGATAAGATTCACCA-TCTTCGATCTCCTCCACTACTGCTTAGGG
1 -AGATAAGATT-TGCAGTCTTCAACCTACTCCACTACTGCTTAGGG
* * * *
16533257 AGATAAGATCTGCAATTTTCAACCTACTCCACTACCGCTTAGGG
1 AGATAAGATTTGCAGTCTTCAACCTACTCCACTACTGCTTAGGG
* * * *
16533301 AGATAAG-TCT--AGTCTTCAACCTATTCCACTGCTG-TCCAGGG
1 AGATAAGATTTGCAGTCTTCAACCTACTCCACTACTGCT-TAGGG
* * * * * ** * *
16533342 AGATAGGGTTTG-TGGCTTAAATATGCTTCC-CTACT-CCTAGGG
1 AGATAAGATTTGCAGTCTTCAACCTAC-TCCACTACTGCTTAGGG
* * * ** *
16533384 AAGATAAGATTCGCCGTCTTCCATTTGCTCCACTACTGCTTAGGG
1 -AGATAAGATTTGCAGTCTTCAACCTACTCCACTACTGCTTAGGG
* * *
16533429 AGATAAGATCTGCAATTTTCAACCTACTCCACTACTGCTTAGGG
1 AGATAAGATTTGCAGTCTTCAACCTACTCCACTACTGCTTAGGG
* *
16533473 AGATAAG----GCTAGTCTTCAACCTATTCCACTACTG-TGCAGGG
1 AGATAAGATTTGC-AGTCTTCAACCTACTCCACTACTGCT-TAGGG
* * * * * * *
16533514 AGATAGGGTTTGTAG-CTTAAATCTACTTCC-CTACT-CCTACGGA
1 AGATAAGATTTGCAGTCTTCAACCTAC-TCCACTACTGCTTA-GGG
* ** * ** *
16533557 AGATAAGATTCGTTGTCTTCGATTTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCAGTCTTCAACCTACTCCACTACTGCTTAGGG
* * * * * * *
16533601 AGATAATATCTGTAATTTTCAACCTACTCCACTACTGCTCAAGG
1 AGATAAGATTTGCAGTCTTCAACCTACTCCACTACTGCTTAGGG
16533645 AGATAAG
1 AGATAAG
16533652 GTCTACAATA
Statistics
Matches: 417, Mismatches: 115, Indels: 76
0.69 0.19 0.12
Matches are distributed among these distances:
40 4 0.01
41 60 0.14
42 9 0.02
43 79 0.19
44 248 0.59
45 17 0.04
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
AGATAAGATTTGCAGTCTTCAACCTACTCCACTACTGCTTAGGG
Found at i:16533417 original size:172 final size:173
Alignment explanation
Indices: 16532903--16533696 Score: 1006
Period size: 172 Copynumber: 4.6 Consensus size: 173
16532893 ATTACTGACC
* * * * *
16532903 AGGGAGAT-AGTATTCT-CAATCTTCAACCTAATCCACTGCTGAC-CAGGGAGATAGGAATCACA
1 AGGGAGATAAG-A-TCTGCAATTTTCAACCTACTCCACTACTG-CTCAGGGAGATA--AGTCTCA
* * * *
16532965 ATCTTCAACCTATTTCACTGCTGTCTAGGGAGATAAGAATAGTGGCTTAAATCTGCTTCCCTACT
61 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACT
* * *
16533030 CCTGGGGAAGATAAGATTTGCCGTCTTCGATCTACTCCACTACTGCTT
126 CCTAGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
* * * *
16533078 AGGGAGATAAGATCTGCTATTTTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCTCAAT
1 AGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTACTG-CTCAGGGAGATA--AGTCTCAAT
* * *
16533142 CTTCAACCTATTCCACAGCTGTCCAGAGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTACTCC
63 CTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTCC
* * * *
16533207 TGGGGAAGATAAGATTCACCATCTTCGATCTCCTCCACTACTGCTT
128 TAGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
* * *
16533253 AGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTACCGCTTAGGGAGATAAGTCT-AGTCTT
1 AGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGTCTCAATCTT
* * *
16533317 CAACCTATTCCACTGCTGTCCAGGGAGATAGGGTTTGTGGCTTAAATATGCTTCCCTACTCCTAG
66 CAACCTATTCCACTGCTGTCCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTCCTAG
* *
16533382 GGAAGATAAGATTCGCCGTCTTCCATTTGCTCCACTACTGCTT
131 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
* * *
16533425 AGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTACTGCTTAGGGAGATAAGGCT-AGTCTT
1 AGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGTCTCAATCTT
* * * * * * *
16533489 CAACCTATTCCACTACTGTGCAGGGAGATAGGGTTTGTAGCTTAAATCTACTTCCCTACTCCTAC
66 CAACCTATTCCACTGCTGTCCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTCCTAG
** *
16533554 GGAAGATAAGATTCGTTGTCTTCGATTTGCTCCACTACTGCTT
131 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
* * * *
16533597 AGGGAGATAATATCTGTAATTTTCAACCTACTCCACTACTGCTCAAGGAGATAAGGTCTACAATA
1 AGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTACTGCTCAGGGAGATAA-GTCT-CAATC
* *
16533662 TTCAACCTATTCCACTGCTATCCATGGAGATAGGA
64 TTCAACCTATTCCACTGCTGTCCAGGGAGATAGGA
16533697 CCAGTAACTT
Statistics
Matches: 556, Mismatches: 57, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
172 312 0.56
173 7 0.01
174 4 0.01
175 231 0.42
176 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (173 bp):
AGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGTCTCAATCTT
CAACCTATTCCACTGCTGTCCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTCCTAG
GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
Found at i:16533666 original size:44 final size:44
Alignment explanation
Indices: 16533583--16533677 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 44
16533573 CTTCGATTTG
* * * ** *
16533583 CTCCACTACTGCTTAGGGAGATAATATCTGTAATTTTCAACCTA
1 CTCCACTACTGCTCAAGGAGATAAGATCTACAATATTCAACCTA
*
16533627 CTCCACTACTGCTCAAGGAGATAAGGTCTACAATATTCAACCTA
1 CTCCACTACTGCTCAAGGAGATAAGATCTACAATATTCAACCTA
*
16533671 TTCCACT
1 CTCCACT
16533678 GCTATCCATG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (44 bp):
CTCCACTACTGCTCAAGGAGATAAGATCTACAATATTCAACCTA
Found at i:16534180 original size:87 final size:87
Alignment explanation
Indices: 16533732--16534661 Score: 1272
Period size: 87 Copynumber: 10.6 Consensus size: 87
16533722 TCAGTACAGG
* * * ** ** *
16533732 AAGGCAAGATCTGTTATTTTCAACTTGCTCCACTGTAAGCCAGGGAGGCAAGGCTGGTGTCTTCG
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAA-ATAGGGAGGCAAGGCTGGTATCTTCG
* *
16533797 ATCTGCTTCGCTGTTG-T-CGGTA
65 ATCTGCTTCGCTGTCGATGCAG-A
* ***
16533819 CAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACGACCCAGGGAGGCAAGGCTGGTATCTTC
1 -AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC-AAATAGGGAGGCAAGGCTGGTATCTTC
* * * *
16533884 GATCTGCTTCACTGTCGGTACAGG
64 GATCTGCTTCGCTGTCGATGCAGA
* **
16533908 AAGGCAAGATCTACTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCG
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAA-ATAGGGAGGCAAGGCTGGTATCTTCG
* * *
16533973 ATCTGCTTCGCTGTCGTTACAGG
65 ATCTGCTTCGCTGTCGATGCAGA
* ** * * *
16533996 AAGGCAAGATCTTCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGGAAGACTGATATCTTCG
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAA-ATAGGGAGGCAAGGCTGGTATCTTCG
* * *
16534061 ATCTGCTTCACTGTC-AGTACAGG
65 ATCTGCTTCGCTGTCGA-TGCAGA
* * *
16534084 AAGGTAAGATATGCTATCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
*
16534149 TCTGTTTCGCTGTCGATGCAGA
66 TCTGCTTCGCTGTCGATGCAGA
*** *
16534171 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAGGCTAGTATCTTCG
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC-AAATAGGGAGGCAAGGCTGGTATCTTCG
* * * * *
16534236 ATTTGCTTCACTGTCGGTACAGG
65 ATCTGCTTCGCTGTCGATGCAGA
*
16534259 AAGGCAAGATCTGCTATCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
16534324 TCTGCTTCGCTGTCGATGCAGA
66 TCTGCTTCGCTGTCGATGCAGA
* *
16534346 AAGGCAAGATCTGCTTTCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
16534411 TCTGCTTCGCTGTCGATGCAGA
66 TCTGCTTCGCTGTCGATGCAGA
* *
16534433 AAGGCAAGATCTGCTTTCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
16534498 TCTGCTTCGCTGTCGATGCAGA
66 TCTGCTTCGCTGTCGATGCAGA
* *
16534520 AAGGCAAGATCTGCTTTCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
16534585 TCTGCTTCGCTGTCGATGCAGA
66 TCTGCTTCGCTGTCGATGCAGA
*
16534607 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCTAGGGAGGCAAGGCT
1 AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAA-ATAGGGAGGCAAGGCT
16534662 TTGTGATTTC
Statistics
Matches: 771, Mismatches: 63, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
87 410 0.53
88 357 0.46
89 2 0.00
90 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (87 bp):
AAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAATAGGGAGGCAAGGCTGGTATCTTCGA
TCTGCTTCGCTGTCGATGCAGA
Found at i:16534502 original size:174 final size:174
Alignment explanation
Indices: 16533726--16534661 Score: 1331
Period size: 175 Copynumber: 5.3 Consensus size: 174
16533716 TTGTCGTCAG
* * * ***
16533726 TACAGGAAGGCAAGATCTGTTATTTTCAACTTGCTCCACTGTA-AGCCAGGGAGGCAAGGCTGGT
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCA-T-TACAAATAGGGAGGCAAGGCTGGT
* * * *
16533790 GTCTTCGATCTGCTTCGCTGTTG-T-CGGTACAAGGCAAGATCTGCTATCTTCAACCTACTCCAC
64 ATCTTCGATCTGCTTCGCTGTCGATGCAG-A-AAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
* *
16533853 TACGACCCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGG
127 TAC-AACCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGA
* * **
16533902 TACAGGAAGGCAAGATCTACTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCATTACAA-ATAGGGAGGCAAGGCTGGTA
* * * *
16533967 TCTTCGATCTGCTTCGCTGTCGTTACAGGAAGGCAAGATCTTCTATCTTCAACCTGCTCCACTAC
65 TCTTCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
* * *
16534032 AACCCAGGGAGGGAAGACTGATATCTTCGATCTGCTTCACTGTC-A
130 AA-CCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGA
* *
16534077 GTACAGGAAGGTAAGATATGCTATCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTA
1 -TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTA
*
16534142 TCTTCGATCTGTTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
65 TCTTCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
* * * *
16534207 GACCCAGGGAGGCAAGGCTAGTATCTTCGATTTGCTTCACTGTCGG
130 -AACCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGA
16534253 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTAT
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTAT
* *
16534318 CTTCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTTTCTTCAACCTGCTCCATTACA
66 CTTCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
** *
16534383 AATAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGA
131 ACCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGA
* * *
16534427 TGCAGAAAGGCAAGATCTGCTTTCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTAT
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTAT
* *
16534492 CTTCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTTTCTTCAACCTGCTCCATTACA
66 CTTCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
** *
16534557 AATAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGA
131 ACCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGA
* * * *
16534601 TGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCTAGGGAGGCAAGGCT
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCATTACAA-ATAGGGAGGCAAGGCT
16534662 TTGTGATTTC
Statistics
Matches: 698, Mismatches: 53, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
174 253 0.36
175 255 0.37
176 187 0.27
177 1 0.00
178 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (174 bp):
TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCATTACAAATAGGGAGGCAAGGCTGGTAT
CTTCGATCTGCTTCGCTGTCGATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
ACCAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGA
Found at i:16536977 original size:133 final size:135
Alignment explanation
Indices: 16536727--16536984 Score: 493
Period size: 133 Copynumber: 1.9 Consensus size: 135
16536717 ATATCTGGGG
16536727 ACCTATGGTAAGTGCAAAAGAATATACAAAAGAATGTGTGAATTTATGAATAATTATTATAAATG
1 ACCTATGGTAAGTGCAAAAGAATATACAAAAGAATGTGTGAATTTATGAATAATTATTATAAATG
16536792 AAAGAATGGAAGAAAATCCAAAAGAATAAAAGAATAATTACTCGCAAAGAATGAAATAATATTGG
66 AAAGAATGGAAGAAAATCCAAAAGAATAAAAGAATAATTACTCGCAAAGAATGAAATAATATTGG
16536857 CTCAA
131 CTCAA
16536862 ACCTATGGT-A-TGCAAAAGAATATACAAAAGAATGTGTGAATTTATGAATAATTATTATAAATG
1 ACCTATGGTAAGTGCAAAAGAATATACAAAAGAATGTGTGAATTTATGAATAATTATTATAAATG
*
16536925 AAAGAATGGAAGAAAATCCAAAAGAATATAAGAATAATTACTCGCAAAGAATGAAATAAT
66 AAAGAATGGAAGAAAATCCAAAAGAATAAAAGAATAATTACTCGCAAAGAATGAAATAAT
16536985 TTTGAACACC
Statistics
Matches: 122, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
133 112 0.92
134 1 0.01
135 9 0.07
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.25
Consensus pattern (135 bp):
ACCTATGGTAAGTGCAAAAGAATATACAAAAGAATGTGTGAATTTATGAATAATTATTATAAATG
AAAGAATGGAAGAAAATCCAAAAGAATAAAAGAATAATTACTCGCAAAGAATGAAATAATATTGG
CTCAA
Found at i:16543236 original size:19 final size:19
Alignment explanation
Indices: 16543212--16543279 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
16543202 AATCATATCT
*
16543212 TCCAAGATTGTATATCATA
1 TCCAAGATTATATATCATA
16543231 TCCAAGATTCCATATATCATA
1 TCCAAGATT--ATATATCATA
* **
16543252 TCTAAGACCATATATCATA
1 TCCAAGATTATATATCATA
*
16543271 TCTAAGATT
1 TCCAAGATT
16543280 GCATATCCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 26 0.63
21 15 0.37
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.35
Consensus pattern (19 bp):
TCCAAGATTATATATCATA
Found at i:16543248 original size:21 final size:21
Alignment explanation
Indices: 16543222--16543285 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
16543212 TCCAAGATTG
*
16543222 TATATCATATCCAAGATTCCA
1 TATATCATATCTAAGATTCCA
16543243 TATATCATATCTAAGA--CCA
1 TATATCATATCTAAGATTCCA
*
16543262 TATATCATATCTAAGATTGCA
1 TATATCATATCTAAGATTCCA
16543283 TAT
1 TAT
16543286 CCTTGAAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.49
21 20 0.51
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (21 bp):
TATATCATATCTAAGATTCCA
Found at i:16546151 original size:9 final size:9
Alignment explanation
Indices: 16546055--16546191 Score: 73
Period size: 10 Copynumber: 14.4 Consensus size: 9
16546045 TTCTCTCAAC
16546055 AAAAA-TTA
1 AAAAATTTA
*
16546063 CAAAAATTCA
1 -AAAAATTTA
*
16546073 AAACAATTTC
1 AAA-AATTTA
*
16546083 TAAAATTTA
1 AAAAATTTA
*
16546092 AAATATTTATA
1 AAA-AATT-TA
*
16546103 AAAAAATT-
1 AAAAATTTA
*
16546111 CAAAATTTA
1 AAAAATTTA
***
16546120 AATTTTTTA
1 AAAAATTTA
16546129 AAAAATTATA
1 AAAAATT-TA
16546139 AAAAATTTAA
1 AAAAATTT-A
16546149 AAAAATTCTA
1 AAAAATT-TA
16546159 AAAAATATATA
1 AAAAAT-T-TA
*
16546170 AAGAAAGTTA
1 AA-AAATTTA
16546180 AAAAA-TTA
1 AAAAATTTA
16546188 AAAA
1 AAAA
16546192 TTTTCTAGAA
Statistics
Matches: 98, Mismatches: 20, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
8 13 0.13
9 29 0.30
10 41 0.42
11 12 0.12
12 3 0.03
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTTA
Found at i:16546683 original size:17 final size:18
Alignment explanation
Indices: 16546657--16546706 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
16546647 AAATATTTAA
16546657 AAAAATTATAAAAACACT
1 AAAAATTATAAAAACACT
*
16546675 AAAAA-TATAAAAACATT
1 AAAAATTATAAAAACACT
*
16546692 AAAATTTTATAAAAA
1 AAAA-ATTATAAAAA
16546707 TATAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.54
18 5 0.18
19 8 0.29
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATTATAAAAACACT
Found at i:16552458 original size:33 final size:32
Alignment explanation
Indices: 16552421--16552496 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
16552411 TTACAGGGCC
* * **
16552421 ATGGTCTTACATTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACA-TCAGAATGCCATAACCCAACT
*
16552454 ATGGTCTTATCATCAGAATGCCATAGCCCAACT
1 ATGGTCTTA-CATCAGAATGCCATAACCCAACT
16552487 ATGGTCTTAC
1 ATGGTCTTAC
16552497 GTATAAATGC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 1 0.03
33 34 0.92
34 2 0.05
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (32 bp):
ATGGTCTTACATCAGAATGCCATAACCCAACT
Found at i:16552559 original size:101 final size:101
Alignment explanation
Indices: 16552419--16552632 Score: 293
Period size: 101 Copynumber: 2.1 Consensus size: 101
16552409 TCTTACAGGG
* * *
16552419 CCATGGTCTTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCA
1 CCATGGTCTTACATCCATAGTGCCATAACCCAATCATGGTCTTATCATCAGAATGCCATAGCCCA
* ** *
16552484 ACTATGGTCTTACGTATAAATGCCGCCATGGTCCAA
66 ACTATGGTCTTACATATAAACACCGCCATGGTCAAA
** * *
16552520 CCATGGTCTTATGTCCATAGTGCCATAACCTAATCATGGTCTTATCATCGGAATGCCATAGCCCA
1 CCATGGTCTTACATCCATAGTGCCATAACCCAATCATGGTCTTATCATCAGAATGCCATAGCCCA
* * **
16552585 GCTGTGGTCTTACATATAAACATTGCCATGGTCAAA
66 ACTATGGTCTTACATATAAACACCGCCATGGTCAAA
16552621 CCATGGTCTTAC
1 CCATGGTCTTAC
16552633 GTTTGAATAA
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 97 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (101 bp):
CCATGGTCTTACATCCATAGTGCCATAACCCAATCATGGTCTTATCATCAGAATGCCATAGCCCA
ACTATGGTCTTACATATAAACACCGCCATGGTCAAA
Found at i:16560177 original size:59 final size:59
Alignment explanation
Indices: 16560067--16560179 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
16560057 TAGGGATGAT
* * *
16560067 ATATAACAAAGAAAAGCCACAAAGGCTTCCACATATATGAAATTTAGCCACAAATGCTC
1 ATATAACAAAGAAAAGCCAAAAAGGCTTCCACATATATGAAATTCAACCACAAATGCTC
* * *
16560126 ATATAACAGAGAACAA-CCAAAAAGGCTTTCACATATAAT-AGATTCAACCACAAA
1 ATATAACAAAGAA-AAGCCAAAAAGGCTTCCACATAT-ATGAAATTCAACCACAAA
16560180 GGCATCACTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 42 0.91
60 4 0.09
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (59 bp):
ATATAACAAAGAAAAGCCAAAAAGGCTTCCACATATATGAAATTCAACCACAAATGCTC
Found at i:16560800 original size:21 final size:20
Alignment explanation
Indices: 16560776--16560816 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
16560766 AGAACTAAGA
*
16560776 GTTCTACCGGTACAACTCTGG
1 GTTCTACCGATACAAC-CTGG
*
16560797 GTTCTACTGATACAACCTGG
1 GTTCTACCGATACAACCTGG
16560817 ACTTCTATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (20 bp):
GTTCTACCGATACAACCTGG
Found at i:16561283 original size:177 final size:179
Alignment explanation
Indices: 16560979--16561339 Score: 600
Period size: 177 Copynumber: 2.0 Consensus size: 179
16560969 GCCAATTGCG
* *
16560979 CTCACCTAGACTTAACTAAGTTTTCTTTCAAAAATCTCATCACATAGTGCTTATAATATTCATAT
1 CTCACCTAAACTTAACTAAGTTTTCTTTCAAAAATCACATCACATAGTGC-T-T-ATATTCATAT
16561044 CTTAAGTCAAACATACAAGCCACCATACACACACATTGAATTTGCTAACCTTGACCTCAAACACC
63 CTTAAGTCAAACATACAAGCCACCATACACACACATTGAATTTGCTAACCTTGACCTCAAACACC
*
16561109 ATGCCTAGATCCAAACCAATTACTACCATTCATGATCAAACATTGAGCACAA
128 ATGCCTAGATCCAAACCAATTACTACCACTCATGATCAAACATTGAGCACAA
* * *
16561161 CTCACCTAAACTTAACTAAGTTTTCTTTCAAAATTCACATCACATAGTGC-T-TCTTCATCTCTT
1 CTCACCTAAACTTAACTAAGTTTTCTTTCAAAAATCACATCACATAGTGCTTATATTCATATCTT
* *
16561224 AAGTCAAACATACAAGCCACCATACACACACATTGAATTTGCTTACCTTGACTTCAAACACCATG
66 AAGTCAAACATACAAGCCACCATACACACACATTGAATTTGCTAACCTTGACCTCAAACACCATG
*
16561289 CTTAGATCCAAACCAATTACTACCACTCATGATCAAACATTGAGCACAA
131 CCTAGATCCAAACCAATTACTACCACTCATGATCAAACATTGAGCACAA
16561338 CT
1 CT
16561340 TAAGAGTTAA
Statistics
Matches: 170, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
177 122 0.72
179 1 0.01
182 47 0.28
ACGTcount: A:0.36, C:0.28, G:0.07, T:0.29
Consensus pattern (179 bp):
CTCACCTAAACTTAACTAAGTTTTCTTTCAAAAATCACATCACATAGTGCTTATATTCATATCTT
AAGTCAAACATACAAGCCACCATACACACACATTGAATTTGCTAACCTTGACCTCAAACACCATG
CCTAGATCCAAACCAATTACTACCACTCATGATCAAACATTGAGCACAA
Found at i:16587634 original size:20 final size:20
Alignment explanation
Indices: 16587558--16587633 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
16587548 AAACTTATGC
16587558 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
16587578 TAAGTAAAT-AAA-GTGAAGAG
1 TAAGTAAATGAAATG-GAA-AG
* *
16587598 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGAAATGGAAAG
16587618 TAAGTAAATGAAATGG
1 TAAGTAAATGAAATGG
16587634 TTCATCATCT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
18 1 0.02
19 6 0.12
20 37 0.76
21 4 0.08
22 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:16591446 original size:30 final size:30
Alignment explanation
Indices: 16591411--16591485 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
16591401 ACTTAAATAT
* *
16591411 CCACAAACGCATCCATACATCATTAGATAG
1 CCACAAAGGCATCCACACATCATTAGATAG
***
16591441 CCACAAAGGTGCCCACACATCATTAGATAG
1 CCACAAAGGCATCCACACATCATTAGATAG
* *
16591471 CAACAAGGGCATCCA
1 CCACAAAGGCATCCA
16591486 AATTCATTCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.31, G:0.15, T:0.16
Consensus pattern (30 bp):
CCACAAAGGCATCCACACATCATTAGATAG
Found at i:16591722 original size:61 final size:61
Alignment explanation
Indices: 16591645--16591808 Score: 206
Period size: 61 Copynumber: 2.7 Consensus size: 61
16591635 ACATGTATCC
* * * * *
16591645 GAGAACAACCACAAAGGCTTCCATATATAATATG-TTTCGTCA-ATATGGCTCCCATATAATA
1 GAGAACAACCACAAAGGCTTCCACATATAATA-GATTTAGCCATAAAT-GCTCACATATAATA
*
16591706 GAGAACAACCACAAAGGCTTCCACATATAATAGATTTAGCCATAAATGCTCATATATAATA
1 GAGAACAACCACAAAGGCTTCCACATATAATAGATTTAGCCATAAATGCTCACATATAATA
* * * *
16591767 AAGAATAGCCACAAAGGCTTCCACATATAATAGATTCAGCCA
1 GAGAACAACCACAAAGGCTTCCACATATAATAGATTTAGCCA
16591809 CAAAAACATC
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
60 1 0.01
61 87 0.96
62 3 0.03
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.24
Consensus pattern (61 bp):
GAGAACAACCACAAAGGCTTCCACATATAATAGATTTAGCCATAAATGCTCACATATAATA
Found at i:16591738 original size:32 final size:32
Alignment explanation
Indices: 16591697--16591800 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 32
16591687 ATATGGCTCC
* *
16591697 CATATAATAGAGAACAACCACAAAGGCTTCCA
1 CATATAATAGAGAATAGCCACAAAGGCTTCCA
** * *
16591729 CATATAATAGA-TTTAGCCATAAATGC-T-CA
1 CATATAATAGAGAATAGCCACAAAGGCTTCCA
* *
16591758 TATATAATAAAGAATAGCCACAAAGGCTTCCA
1 CATATAATAGAGAATAGCCACAAAGGCTTCCA
16591790 CATATAATAGA
1 CATATAATAGA
16591801 TTCAGCCACA
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
29 11 0.20
30 12 0.22
31 10 0.18
32 22 0.40
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (32 bp):
CATATAATAGAGAATAGCCACAAAGGCTTCCA
Found at i:16591809 original size:31 final size:31
Alignment explanation
Indices: 16591653--16591812 Score: 118
Period size: 31 Copynumber: 5.2 Consensus size: 31
16591643 CCGAGAACAA
* *
16591653 CCACAAAGGCTTCCATATATAATATGTTTC-G
1 CCACAAAGGCTTCCACATATAATA-GATTCAG
* * ** *
16591684 TCA-ATATGGC-TCC-CATATAATAGAGAACAA
1 CCACA-AAGGCTTCCACATATAATAGA-TTCAG
*
16591714 CCACAAAGGCTTCCACATATAATAGATTTAG
1 CCACAAAGGCTTCCACATATAATAGATTCAG
* * * *
16591745 CCATAAATGC-T-CATATATAATAAAGAAT-AG
1 CCACAAAGGCTTCCACATATAAT--AGATTCAG
16591775 CCACAAAGGCTTCCACATATAATAGATTCAG
1 CCACAAAGGCTTCCACATATAATAGATTCAG
16591806 CCACAAA
1 CCACAAA
16591813 AACATCACTT
Statistics
Matches: 97, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
28 1 0.01
29 18 0.19
30 25 0.26
31 33 0.34
32 20 0.21
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (31 bp):
CCACAAAGGCTTCCACATATAATAGATTCAG
Found at i:16592019 original size:54 final size:54
Alignment explanation
Indices: 16591950--16592076 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 54
16591940 CAAACTAGGT
* * * *
16591950 CTTACACAATGTGGTCTT-TGTTTCCCCATATGATGCCATAGCTT-ATGGCTAGAC
1 CTTACACTATATGGTCTTCT-TTTCCCCATATGATGCCATAG-TTAACGACTAGAC
* * **
16592004 CTTAGACTATATGGTCTTCTTTTCCCCATTTGATGCCATAGTTAACGACTAGGG
1 CTTACACTATATGGTCTTCTTTTCCCCATATGATGCCATAGTTAACGACTAGAC
16592058 CTTACACTATATGGTCTTC
1 CTTACACTATATGGTCTTC
16592077 AATTGCCACT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
53 2 0.03
54 59 0.95
55 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (54 bp):
CTTACACTATATGGTCTTCTTTTCCCCATATGATGCCATAGTTAACGACTAGAC
Found at i:16597963 original size:28 final size:28
Alignment explanation
Indices: 16597911--16597980 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
16597901 TGGTTATACA
* *
16597911 TATATTATATATATGCATGATTTTATCT
1 TATATAATATATATGCATGACTTTATCT
* *
16597939 TATATAATATATATGCATGGCTTTATTT
1 TATATAATATATATGCATGACTTTATCT
* *
16597967 TACATAGTATATAT
1 TATATAATATATAT
16597981 TAATGGATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (28 bp):
TATATAATATATATGCATGACTTTATCT
Found at i:16600315 original size:22 final size:23
Alignment explanation
Indices: 16600290--16600332 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
16600280 TCTTAGGGTA
16600290 CTCACAGAACCCTCA-CTTTTTC
1 CTCACAGAACCCTCATCTTTTTC
* *
16600312 CTCACATAATCCTCATCTTTT
1 CTCACAGAACCCTCATCTTTT
16600333 GTAGCTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.23, C:0.37, G:0.02, T:0.37
Consensus pattern (23 bp):
CTCACAGAACCCTCATCTTTTTC
Done.