Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold141
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: 2772588
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 118404 characters in sequence are not A, C, G, or T
File 3 of 18
Found at i:378465 original size:21 final size:21
Alignment explanation
Indices: 378439--378507 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 21
378429 GTCCTATATT
*
378439 GATACATTTCAGACATGTGTC
1 GATACATTTCACACATGTGTC
**
378460 GATACA-TTCACTTATGTGTC
1 GATACATTTCACACATGTGTC
** *
378480 GATACA-TTCACTTATGTATC
1 GATACATTTCACACATGTGTC
378500 GATACATT
1 GATACATT
378508 CACTTATTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 36 0.84
21 7 0.16
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
GATACATTTCACACATGTGTC
Found at i:378476 original size:20 final size:20
Alignment explanation
Indices: 378453--378514 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
378443 CATTTCAGAC
378453 ATGTGTCGATACATTCACTT
1 ATGTGTCGATACATTCACTT
378473 ATGTGTCGATACATTCACTT
1 ATGTGTCGATACATTCACTT
*
378493 ATGTATCGATACATTCACTT
1 ATGTGTCGATACATTCACTT
378513 AT
1 AT
378515 TGTATCGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTGTCGATACATTCACTT
Found at i:378968 original size:17 final size:19
Alignment explanation
Indices: 378946--378983 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
378936 TCAATAAGGT
378946 TTAAATT-A-AAAATCATG
1 TTAAATTCATAAAATCATG
378963 TTAAATTCCATAAAATCATG
1 TTAAATT-CATAAAATCATG
378983 T
1 T
378984 AGGTTATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (19 bp):
TTAAATTCATAAAATCATG
Found at i:380142 original size:13 final size:13
Alignment explanation
Indices: 380121--380151 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
380111 CGATACATGG
*
380121 TACAATGTATCGA
1 TACATTGTATCGA
380134 TACATTGTATCGA
1 TACATTGTATCGA
380147 TACAT
1 TACAT
380152 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:380147 original size:33 final size:32
Alignment explanation
Indices: 380105--380171 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
380095 CTATCACTAT
380105 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
380138 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
380171 T
1 T
380172 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:380230 original size:19 final size:20
Alignment explanation
Indices: 380206--380243 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
380196 ATAATTTTAA
*
380206 ATGAA-TGTATCGGTACATT
1 ATGAATTGTATCGATACATT
380225 ATGAATTGTATCGATACAT
1 ATGAATTGTATCGATACAT
380244 GGCTACGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (20 bp):
ATGAATTGTATCGATACATT
Found at i:381758 original size:3 final size:3
Alignment explanation
Indices: 381750--381779 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
381740 TGAAGAGAAA
*
381750 GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
381780 TCGGATGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:386182 original size:19 final size:19
Alignment explanation
Indices: 386156--386196 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
386146 TTGATGTTTG
386156 TTATGTTGTATGAT-TGAA
1 TTATGTTGTATGATATGAA
*
386174 TTATGGTTGTTTGATATGAA
1 TTAT-GTTGTATGATATGAA
386194 TTA
1 TTA
386197 GGGTCTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 9 0.45
20 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (19 bp):
TTATGTTGTATGATATGAA
Found at i:386514 original size:20 final size:22
Alignment explanation
Indices: 386470--386516 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
386460 AATTTTCAAC
386470 AAAT-TTTCACTTTTTCACTTCA
1 AAATCTTTCACTTTTTCAC-TCA
386492 AAATCTTTCA-TTTTTCA-TCA
1 AAATCTTTCACTTTTTCACTCA
386512 AAATC
1 AAATC
386517 ATCAACAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.33
22 11 0.46
23 5 0.21
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATCTTTCACTTTTTCACTCA
Found at i:388227 original size:21 final size:22
Alignment explanation
Indices: 388188--388238 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
388178 GACAATAAAT
*
388188 TTTTTATAAAAAGGGGGAGAAAA
1 TTTTTAT-AAAAGGAGGAGAAAA
*
388211 TTTTTAT-AAAGGAGGAGATAA
1 TTTTTATAAAAGGAGGAGAAAA
388232 TTGTTTA
1 TT-TTTA
388239 AGGGGGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 14 0.56
22 4 0.16
23 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (22 bp):
TTTTTATAAAAGGAGGAGAAAA
Found at i:388257 original size:20 final size:20
Alignment explanation
Indices: 388219--388269 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
388209 AATTTTTATA
* *
388219 AAGGAGGAG-ATAATTGTTT
1 AAGGGGGAGAATAATCGTTT
388238 AAGGGGGAGAATAATCGTTT
1 AAGGGGGAGAATAATCGTTT
*
388258 AAGGGGGTGAAT
1 AAGGGGGAGAAT
388270 TTTTTTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.35, C:0.02, G:0.37, T:0.25
Consensus pattern (20 bp):
AAGGGGGAGAATAATCGTTT
Found at i:388857 original size:13 final size:13
Alignment explanation
Indices: 388839--388863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
388829 CATGCTGCTT
388839 TGTATCGATACAA
1 TGTATCGATACAA
388852 TGTATCGATACA
1 TGTATCGATACA
388864 TGTTCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:388860 original size:33 final size:32
Alignment explanation
Indices: 388818--388882 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
388808 ACACACCCAG
* *
388818 ATGTATCGATACATGCTGCTTTGTATCGATACA
1 ATGTATCGATACATG-TGCATTATATCGATACA
*
388851 ATGTATCGATACATGTTCATTATATCGATACA
1 ATGTATCGATACATGTGCATTATATCGATACA
388883 TGGACAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (32 bp):
ATGTATCGATACATGTGCATTATATCGATACA
Found at i:388878 original size:19 final size:20
Alignment explanation
Indices: 388854--388904 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
388844 CGATACAATG
**
388854 TATCGATACATGTTC-ATTA
1 TATCGATACATGGACAATTA
*
388873 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTA
388893 TATCGATACATG
1 TATCGATACATG
388905 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTA
Found at i:388898 original size:20 final size:20
Alignment explanation
Indices: 388848--388904 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
388838 TTGTATCGAT
*
388848 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
388867 TC-ATTATATCGATACATGG
1 ACAATTGTATCGATACATGG
388886 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
388905 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:389820 original size:20 final size:20
Alignment explanation
Indices: 389795--389850 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
389785 AACAATAAGA
389795 GAATGTATCGATACATGCAT
1 GAATGTATCGATACATGCAT
* * **
389815 GAATGTATCAATATATGTTT
1 GAATGTATCGATACATGCAT
389835 GAAATGTATCGATACA
1 G-AATGTATCGATACA
389851 AGACTATGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
GAATGTATCGATACATGCAT
Found at i:389942 original size:51 final size:52
Alignment explanation
Indices: 389887--390006 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 52
389877 TCTGGAAAGA
* *
389887 AAATGGATTGATACATTTCTCATTGT-TTCAATACATTCTAGGTTT-TAACCC
1 AAATGGATCGATACATTTCTCATTATATT-AATACATTCTAGGTTTCTAACCC
* * * * *
389938 AAATGGATCAATACATTTTTTATTATATTGATACATTCTGGGTTTCTAACCC
1 AAATGGATCGATACATTTCTCATTATATTAATACATTCTAGGTTTCTAACCC
*
389990 AAATGTATCGATACATT
1 AAATGGATCGATACATT
390007 GAAAAATATA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 35 0.60
52 23 0.40
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (52 bp):
AAATGGATCGATACATTTCTCATTATATTAATACATTCTAGGTTTCTAACCC
Found at i:390017 original size:52 final size:51
Alignment explanation
Indices: 389917--390025 Score: 128
Period size: 52 Copynumber: 2.1 Consensus size: 51
389907 CATTGTTTCA
**** * *
389917 ATACATTCTAGGTTTTAACCCAAATGGATCAATACATTTTTTATTATATTG
1 ATACATTCTAGGTTTTAACCCAAATGGATCAATACATTGAAAAATATATCG
* * *
389968 ATACATTCTGGGTTTCTAACCCAAATGTATCGATACATTGAAAAATATATCG
1 ATACATTCTAGGTTT-TAACCCAAATGGATCAATACATTGAAAAATATATCG
390020 ATACAT
1 ATACAT
390026 GCAGGCAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
51 14 0.29
52 34 0.71
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (51 bp):
ATACATTCTAGGTTTTAACCCAAATGGATCAATACATTGAAAAATATATCG
Found at i:392546 original size:80 final size:81
Alignment explanation
Indices: 392435--392741 Score: 311
Period size: 80 Copynumber: 3.8 Consensus size: 81
392425 ATTTTTTTTT
* * * * * * *
392435 ATCTTTGGGGAAACTCCAACTCCACTATCTCTGAAG-GGATATTCTAACCCCGTTTTTACTTTCA
1 ATCTTAGGGGATACTCCAACCCCACCATCTCTGAAGAGGATACTCCAACCCCATTTTTACTTTCA
* *
392499 AAATGTTGAATTTCTC
66 AAATGTCGAATTTATC
* * * *
392515 ATCTTTGGGGATACTCTAACCCCACCATCTCT-TAGAGGATACTCCAACCTCATTTTTAC-TTCT
1 ATCTTAGGGGATACTCCAACCCCACCATCTCTGAAGAGGATACTCCAACCCCATTTTTACTTTC-
* * *
392578 GAAATGTCAAATTTTTC
65 AAAATGTCGAATTTATC
* * ** *
392595 AACTTAGGGGATACTCCAACCCCACTATCT-TGGAAG-GGATACTCCAAATCCATTTTTACTTCC
1 ATCTTAGGGGATACTCCAACCCCACCATCTCT-GAAGAGGATACTCCAACCCCATTTTTACTTTC
392658 AAAATGTCGAATTTATC
65 AAAATGTCGAATTTATC
** * * * *
392675 ATCTTAGGGGATACTTTAACCCCACCATCTATG-AGAGAATACTCCAATCCCGTTTTTACTTTCA
1 ATCTTAGGGGATACTCCAACCCCACCATCTCTGAAGAGGATACTCCAACCCCATTTTTACTTTCA
392739 AAA
66 AAA
392742 CATTAAATTT
Statistics
Matches: 186, Mismatches: 34, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
79 8 0.04
80 173 0.93
81 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (81 bp):
ATCTTAGGGGATACTCCAACCCCACCATCTCTGAAGAGGATACTCCAACCCCATTTTTACTTTCA
AAATGTCGAATTTATC
Found at i:392633 original size:160 final size:160
Alignment explanation
Indices: 392391--392735 Score: 417
Period size: 160 Copynumber: 2.1 Consensus size: 160
392381 CAAAAAAGGG
* * * * * *
392391 TACTCC-ATCCCTATTGTTACTTCTAAAATGCCAAATTTTTTTTTATCTTTGGGGAAACTCCAAC
1 TACTCCAATCCC-ATTTTTACTTCTGAAATGTCAAA---TTTTTCAACTTAGGGGAAACTCCAAC
* * * * * * * *
392455 TCCACTATCTCTGAAGGGATATTCTAACCCCGTTTTTACTTTCAAAATGTTGAATTTCTCATCTT
62 CCCACTATCTCTGAAGGGATACTCCAAACCCATTTTTACTTCCAAAATGTCGAATTTATCATCTT
* * * *
392520 TGGGGATACTCTAACCCCACCATCTCTTAGAGGA
127 AGGGGATACTCTAACCCCACCATCTATGAGAGAA
*
392554 TACTCCAA-CCTCATTTTTACTTCTGAAATGTCAAATTTTTCAACTTAGGGGATACTCCAACCCC
1 TACTCCAATCC-CATTTTTACTTCTGAAATGTCAAATTTTTCAACTTAGGGGAAACTCCAACCCC
*
392618 ACTATCT-TGGAAGGGATACTCCAAATCCATTTTTACTTCCAAAATGTCGAATTTATCATCTTAG
65 ACTATCTCT-GAAGGGATACTCCAAACCCATTTTTACTTCCAAAATGTCGAATTTATCATCTTAG
*
392682 GGGATACTTTAACCCCACCATCTATGAGAGAA
129 GGGATACTCTAACCCCACCATCTATGAGAGAA
*
392714 TACTCCAATCCCGTTTTTACTT
1 TACTCCAATCCCATTTTTACTT
392736 TCAAAACATT
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
159 1 0.01
160 123 0.79
161 2 0.01
163 28 0.18
164 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.36
Consensus pattern (160 bp):
TACTCCAATCCCATTTTTACTTCTGAAATGTCAAATTTTTCAACTTAGGGGAAACTCCAACCCCA
CTATCTCTGAAGGGATACTCCAAACCCATTTTTACTTCCAAAATGTCGAATTTATCATCTTAGGG
GATACTCTAACCCCACCATCTATGAGAGAA
Found at i:392776 original size:80 final size:79
Alignment explanation
Indices: 392429--392776 Score: 274
Period size: 80 Copynumber: 4.4 Consensus size: 79
392419 TGCCAAATTT
* * * * * * * * *
392429 TTTTTTATCTTTGGGGAAACTCCAACTCCACTATCTCTGA-AGGGATATTCTAACCCCGTTTTTA
1 TTTTTCATCTTAGGGGATACTCCAACCCCACCATCT-TGAGA-GGATACTCCAATCCCATTTTTA
* *
392493 CTTTCAAAATGTTGAA
64 CTTTCAAAATATTAAA
* * * *
392509 TTTCTCATCTTTGGGGATACTCTAACCCCACCATCTCTTAGAGGATACTCCAA-CCTCATTTTTA
1 TTTTTCATCTTAGGGGATACTCCAACCCCACCATCT-TGAGAGGATACTCCAATCC-CATTTTTA
* * *
392573 C-TTCTGAAATGTCAAA
64 CTTTC-AAAATATTAAA
* *
392589 TTTTTCAACTTAGGGGATACTCCAACCCCACTATCTTG-GAAGGGATACTCCAAAT-CCATTTTT
1 TTTTTCATCTTAGGGGATACTCCAACCCCACCATCTTGAG-A-GGATACTCC-AATCCCATTTTT
* * **
392652 ACTTCCAAAATGTCGAA
63 ACTTTCAAAATATTAAA
* ** * *
392669 TTTATCATCTTAGGGGATACTTTAACCCCACCATCTATGAGAGAATACTCCAATCCCGTTTTTAC
1 TTTTTCATCTTAGGGGATACTCCAACCCCACCATCT-TGAGAGGATACTCCAATCCCATTTTTAC
*
392734 TTTCAAAACATTAAA
65 TTTCAAAATATTAAA
* ** *
392749 TTTTTCATTTTTTGGGATATTCCAACCC
1 TTTTTCATCTTAGGGGATACTCCAACCC
392777 TACCGTCTCC
Statistics
Matches: 216, Mismatches: 41, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
78 1 0.00
79 10 0.05
80 195 0.90
81 9 0.04
82 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (79 bp):
TTTTTCATCTTAGGGGATACTCCAACCCCACCATCTTGAGAGGATACTCCAATCCCATTTTTACT
TTCAAAATATTAAA
Found at i:392800 original size:160 final size:160
Alignment explanation
Indices: 392441--392801 Score: 386
Period size: 160 Copynumber: 2.3 Consensus size: 160
392431 TTTTATCTTT
* * * * * * ** * * *
392441 GGGGAAACTCCAACTCCACTATCTCTGAAGGGATATTCTAACCCCGTTTTTACTTTCAAAATGTT
1 GGGGATACTCCAACCCCACCATCTCCGAAGGGATACTCCAAATCCATTTTTACTTCCAAAATGTC
* * * * *
392506 GAATTTCTCATCTTTGGGGATACTCTAACCCCACCATCTCTTAGAGGATACTCCAACCTCATTTT
66 GAATTTATCATCTTAGGGGATACTCTAACCCCACCATCTATGAGAGAATACTCCAACCTCATTTT
**
392571 TACTTCTGAAATGTCAAATTTTTCAACTTA
131 TACTTCAAAAATGTCAAATTTTTCAACTTA
* **
392601 GGGGATACTCCAACCCCACTATCTTGGAAGGGATACTCCAAATCCATTTTTACTTCCAAAATGTC
1 GGGGATACTCCAACCCCACCATCTCCGAAGGGATACTCCAAATCCATTTTTACTTCCAAAATGTC
* *
392666 GAATTTATCATCTTAGGGGATACTTTAACCCCACCATCTATGAGAGAATACTCCAATCC-CGTTT
66 GAATTTATCATCTTAGGGGATACTCTAACCCCACCATCTATGAGAGAATACTCCAA-CCTCATTT
** *
392730 TTACTTTCAAAACAT-T-AAATTTTTCATTTTT
130 TTAC-TTCAAAA-ATGTCAAATTTTTCAACTTA
* * * * * *
392761 TGGGATATTCCAACCCTACCGTCTCCGAGGGGCTACTCCAA
1 GGGGATACTCCAACCCCACCATCTCCGAAGGGATACTCCAA
392802 CCCTGATTTT
Statistics
Matches: 166, Mismatches: 32, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
160 156 0.94
161 8 0.05
162 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (160 bp):
GGGGATACTCCAACCCCACCATCTCCGAAGGGATACTCCAAATCCATTTTTACTTCCAAAATGTC
GAATTTATCATCTTAGGGGATACTCTAACCCCACCATCTATGAGAGAATACTCCAACCTCATTTT
TACTTCAAAAATGTCAAATTTTTCAACTTA
Found at i:395469 original size:21 final size:19
Alignment explanation
Indices: 395445--395497 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
395435 TGATTTTTCT
395445 AAATATTATTATATGATATCA
1 AAATATTATTAT-TGAT-TCA
* *
395466 AAATTATAATTCATTGGTTCA
1 AAA-TATTATT-ATTGATTCA
395487 AAATATTATTA
1 AAATATTATTA
395498 AATGTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.04
20 6 0.22
21 9 0.33
22 9 0.33
23 2 0.07
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (19 bp):
AAATATTATTATTGATTCA
Found at i:396620 original size:10 final size:10
Alignment explanation
Indices: 396605--396704 Score: 53
Period size: 10 Copynumber: 10.0 Consensus size: 10
396595 ACTTTGAAAA
396605 GTTCTAGAAT
1 GTTCTAGAAT
396615 GTTCTAGAAT
1 GTTCTAGAAT
* * *
396625 -ATCGTGGAAG
1 GTTC-TAGAAT
* * *
396635 GCTCTGGAAG
1 GTTCTAGAAT
396645 GTTCTAGAAT
1 GTTCTAGAAT
396655 GTTCTAGAAT
1 GTTCTAGAAT
* * *
396665 -ATCGTGGAAG
1 GTTC-TAGAAT
* *
396675 GCTCT-GAAA
1 GTTCTAGAAT
396684 GATTCTAGAAT
1 G-TTCTAGAAT
396695 GTTCTAGAAT
1 GTTCTAGAAT
396705 ATTGTGGAAG
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
9 8 0.11
10 54 0.77
11 8 0.11
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (10 bp):
GTTCTAGAAT
Found at i:396649 original size:40 final size:40
Alignment explanation
Indices: 396605--396723 Score: 211
Period size: 40 Copynumber: 3.0 Consensus size: 40
396595 ACTTTGAAAA
396605 GTTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAG
1 GTTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAG
*
396645 GTTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGAAAG
1 GTTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAG
* *
396685 ATTCTAGAATGTTCTAGAATATTGTGGAAGGCTCTGGAA
1 GTTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAA
396724 CTTTATGGAG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (40 bp):
GTTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAG
Found at i:406974 original size:73 final size:73
Alignment explanation
Indices: 406890--407048 Score: 255
Period size: 73 Copynumber: 2.2 Consensus size: 73
406880 TGTCAGTTTC
* *
406890 ATGTATTGATACAATTCAATGGTATATCAATACAATGAACATGTATCTAAGCAACGTATCGATAC
1 ATGTATCGATACAATTCAATGGTATATCAATACAATGAACATGTATCTAAACAACGTATCGATAC
*
406955 CAAGCAAA
66 CAAGAAAA
* * * *
406963 ATGTATCGATACAATTCAATGGTGTATCGATACAATGAACATGTATCTAAATAATGTATCGATAC
1 ATGTATCGATACAATTCAATGGTATATCAATACAATGAACATGTATCTAAACAACGTATCGATAC
407028 CAAGAAAA
66 CAAGAAAA
407036 ATGTATCGATACA
1 ATGTATCGATACA
407049 TCTGGGTGTG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (73 bp):
ATGTATCGATACAATTCAATGGTATATCAATACAATGAACATGTATCTAAACAACGTATCGATAC
CAAGAAAA
Found at i:411112 original size:80 final size:79
Alignment explanation
Indices: 410990--411170 Score: 227
Period size: 80 Copynumber: 2.3 Consensus size: 79
410980 TTTTCTTTTT
* *
410990 ATCTTTGGGGATACTCCAACCTCACTATCTCTGAGGGAATACTCTAACCCCACTTTTACTTTCAA
1 ATCTTT-GGGATACTCCAACCTCACCATCTCTGAGGGAATACTCTAACCCCACTTTTACTTCCAA
*
411055 AATGCTAAATTTCTC
65 AAAGCTAAATTTCTC
* * * * * * *
411070 ATCTTTGGGAATACTCCAATCTCACCATCTTTGAGGGGATACTCTTATCTCATTTTTACTTCCAA
1 ATCTTTGGG-ATACTCCAACCTCACCATCTCTGAGGGAATACTCTAACCCCACTTTTACTTCCAA
*
411135 AAAGCTAAATTTTTC
65 AAAGCTAAATTTCTC
*
411150 ATCTTAGAGGATACTCCAACC
1 ATCTTTG-GGATACTCCAACC
411171 CCATTTTTAC
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
79 3 0.03
80 81 0.94
81 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (79 bp):
ATCTTTGGGATACTCCAACCTCACCATCTCTGAGGGAATACTCTAACCCCACTTTTACTTCCAAA
AAGCTAAATTTCTC
Found at i:411163 original size:52 final size:51
Alignment explanation
Indices: 411105--411223 Score: 141
Period size: 52 Copynumber: 2.3 Consensus size: 51
411095 CATCTTTGAG
* * *
411105 GGGATACTCTTATCTCATTTTTACTTCCAAAA-AGCTAAATTTTTCATCTTA
1 GGGATACTCTAACCCCATTTTTACTTCCAAAACAGC-AAATTTTTCATCTTA
* * * *
411156 GAGGATACTCCAACCCCATTTTTACTTCCAAAACATCGAATTTTTCATTTTA
1 G-GGATACTCTAACCCCATTTTTACTTCCAAAACAGCAAATTTTTCATCTTA
411208 GGGAATACTCTAACCC
1 GGG-ATACTCTAACCC
411224 TACCATCTCC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
51 3 0.05
52 52 0.91
53 2 0.04
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (51 bp):
GGGATACTCTAACCCCATTTTTACTTCCAAAACAGCAAATTTTTCATCTTA
Found at i:412189 original size:25 final size:25
Alignment explanation
Indices: 412155--412229 Score: 141
Period size: 25 Copynumber: 3.0 Consensus size: 25
412145 AGAAAATGGG
412155 CAACCCATATGTATCTCGTAATTGT
1 CAACCCATATGTATCTCGTAATTGT
412180 CAACCCATATGTATCTCGTAATTGT
1 CAACCCATATGTATCTCGTAATTGT
*
412205 CAACCCATATGTATCTCGTATTTGT
1 CAACCCATATGTATCTCGTAATTGT
412230 TCTCGATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (25 bp):
CAACCCATATGTATCTCGTAATTGT
Found at i:426595 original size:30 final size:30
Alignment explanation
Indices: 426561--426621 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
426551 CTCGATAATG
*
426561 AGACCTCAGGGTTTTAAAGAAGAATAGATA
1 AGACCTCAGGGTGTTAAAGAAGAATAGATA
*
426591 AGACCTCAGGGTGTTAATGAAGAATAGATA
1 AGACCTCAGGGTGTTAAAGAAGAATAGATA
426621 A
1 A
426622 AGCTAAGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.23
Consensus pattern (30 bp):
AGACCTCAGGGTGTTAAAGAAGAATAGATA
Found at i:429526 original size:24 final size:24
Alignment explanation
Indices: 429499--429546 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
429489 GAGGTTGATA
429499 AATCGAAGGTAGATGTTGTTAGAG
1 AATCGAAGGTAGATGTTGTTAGAG
429523 AATCGAAGGTAGATGTTGTTAGAG
1 AATCGAAGGTAGATGTTGTTAGAG
429547 CCTTACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.29
Consensus pattern (24 bp):
AATCGAAGGTAGATGTTGTTAGAG
Found at i:431431 original size:13 final size:13
Alignment explanation
Indices: 431413--431437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
431403 CAATTCAAGT
431413 ATGTATCGATACA
1 ATGTATCGATACA
431426 ATGTATCGATAC
1 ATGTATCGATAC
431438 TGAGTGAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:435946 original size:20 final size:20
Alignment explanation
Indices: 435873--435943 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
435863 TACCCAGATC
*
435873 TATCGATACATATTTTAATG
1 TATCGATACATATTTCAATG
* * *
435893 TATCGATACATGTATGAATG
1 TATCGATACATATTTCAATG
*
435913 TATTGATACAT-TCTTCAATG
1 TATCGATACATAT-TTCAATG
435933 TATCGATACAT
1 TATCGATACAT
435944 TCTGTCTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
TATCGATACATATTTCAATG
Found at i:449888 original size:13 final size:13
Alignment explanation
Indices: 449870--449894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
449860 CAAAGATCAG
449870 TGTATCGATACAA
1 TGTATCGATACAA
449883 TGTATCGATACA
1 TGTATCGATACA
449895 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:449975 original size:19 final size:19
Alignment explanation
Indices: 449947--450011 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
449937 AACTGTACAT
*
449947 TGTATAGATACAAAACTTA
1 TGTATCGATACAAAACTTA
449966 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
449979 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
449998 TGTATTGATACAAA
1 TGTATCGATACAAA
450012 TCGTTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
16 2 0.05
18 1 0.03
19 22 0.59
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:449983 original size:32 final size:32
Alignment explanation
Indices: 449942--450009 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
449932 TTCGTAACTG
449942 TACATTGTATAGATACAAAACTTATGTATCGA
1 TACATTGTATAGATACAAAACTTATGTATCGA
* * *
449974 TACATTGTATCGATACAACACTTATGTATTGA
1 TACATTGTATAGATACAAAACTTATGTATCGA
450006 TACA
1 TACA
450010 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATAGATACAAAACTTATGTATCGA
Found at i:449984 original size:13 final size:13
Alignment explanation
Indices: 449966--449990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
449956 ACAAAACTTA
449966 TGTATCGATACAT
1 TGTATCGATACAT
449979 TGTATCGATACA
1 TGTATCGATACA
449991 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:453538 original size:10 final size:10
Alignment explanation
Indices: 453523--453600 Score: 76
Period size: 9 Copynumber: 7.9 Consensus size: 10
453513 TCCTTCATAC
453523 CCAAAAAAAA
1 CCAAAAAAAA
453533 CCAAAAAAAA
1 CCAAAAAAAA
453543 --AAGAAAAAA
1 CCAA-AAAAAA
453552 CCAAAAAAATA
1 CCAAAAAAA-A
453563 -C-AAAAAAA
1 CCAAAAAAAA
453571 -CAAAAAAAA
1 CCAAAAAAAA
453580 CCAATAAAAATA
1 CCAA-AAAAA-A
*
453592 ACAAAAAAA
1 CCAAAAAAA
453601 GAGAAACGGG
Statistics
Matches: 59, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
8 4 0.07
9 19 0.32
10 19 0.32
11 13 0.22
12 4 0.07
ACGTcount: A:0.81, C:0.14, G:0.01, T:0.04
Consensus pattern (10 bp):
CCAAAAAAAA
Found at i:453551 original size:19 final size:18
Alignment explanation
Indices: 453525--453579 Score: 76
Period size: 19 Copynumber: 3.0 Consensus size: 18
453515 CTTCATACCC
453525 AAAAAAAACCAAAAAAAA
1 AAAAAAAACCAAAAAAAA
453543 AAGAAAAAACCAAAAAAATA
1 AA-AAAAAACCAAAAAAA-A
*
453563 CAAAAAAA-CAAAAAAAA
1 AAAAAAAACCAAAAAAAA
453580 CCAATAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
19 21 0.62
20 2 0.06
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (18 bp):
AAAAAAAACCAAAAAAAA
Found at i:453555 original size:29 final size:28
Alignment explanation
Indices: 453523--453600 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
453513 TCCTTCATAC
453523 CCAAAAAAA-ACCAAAAAAAAAAGAAAAAA
1 CCAAAAAAATA-CAAAAAAAAAA-AAAAAA
*
453552 CCAAAAAAATACAAAAAAACAAAAAAAA
1 CCAAAAAAATACAAAAAAAAAAAAAAAA
453580 CCAATAAAAATAACAAAAAAA
1 CCAA-AAAAAT-ACAAAAAAA
453601 GAGAAACGGG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 10 0.22
29 25 0.56
30 10 0.22
ACGTcount: A:0.81, C:0.14, G:0.01, T:0.04
Consensus pattern (28 bp):
CCAAAAAAATACAAAAAAAAAAAAAAAA
Found at i:453588 original size:19 final size:17
Alignment explanation
Indices: 453526--453599 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 17
453516 TTCATACCCA
*
453526 AAAAAAACCAAAAAAAAA
1 AAAAAAA-CAAAAAAAAC
453544 AGAAAAAACCAAAAAAATAC
1 A-AAAAAA-CAAAAAAA-AC
453564 AAAAAAACAAAAAAAACC
1 AAAAAAACAAAAAAAA-C
*
453582 AATAAAAATAACAAAAAA
1 AA-AAAAACAA-AAAAAA
453600 AGAGAAACGG
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.02
18 12 0.24
19 28 0.57
20 8 0.16
ACGTcount: A:0.82, C:0.12, G:0.01, T:0.04
Consensus pattern (17 bp):
AAAAAAACAAAAAAAAC
Found at i:454854 original size:28 final size:28
Alignment explanation
Indices: 454822--455312 Score: 696
Period size: 28 Copynumber: 17.5 Consensus size: 28
454812 CGTTCATCTC
* ***
454822 TTCAAAGCCCACAAGTCAGTGGTAAATT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
454850 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
454879 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
454907 TTCAAAGCCCACAAGTCAGTGGCATTCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
454935 TTCAAATCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
454963 TTCAAAGCCCA-AAGTCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
454991 TTCAAAGCCCAAAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
455019 TTCAAAGCCCACAAGTAAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
455047 TTCAAAGCCCACAAGTAAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
455075 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
455103 TTCAAAGGCCACAAGTCAGTGACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
455131 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
455159 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
455187 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
455215 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
455243 TTCAAAGCCCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
455271 TTCAAAGCCCACAAGTCAATAGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
455300 TTCAAAGCCCACA
1 TTCAAAGCCCACA
455313 CGAGTCGGTG
Statistics
Matches: 419, Mismatches: 40, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
27 11 0.03
28 357 0.85
29 51 0.12
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:457179 original size:20 final size:21
Alignment explanation
Indices: 457148--457186 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
457138 AGCCTTTGAC
*
457148 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTAATATGTTT
457169 CATGC-TTTTTTAATATGT
1 CATGCATTTTTTAATATGT
457187 CCAGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (21 bp):
CATGCATTTTTTAATATGTTT
Found at i:459847 original size:13 final size:13
Alignment explanation
Indices: 459829--459861 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
459819 CAATTTCCTT
459829 ATGTATCGATACA
1 ATGTATCGATACA
459842 ATGTATCGATACA
1 ATGTATCGATACA
*
459855 TTGTATC
1 ATGTATC
459862 ATGTATCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:459948 original size:19 final size:19
Alignment explanation
Indices: 459904--459959 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
459894 CTGGCAATCT
*
459904 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
459924 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
459943 CATGTATCGATACAATG
1 CATGTATCGATACAATG
459960 TATCAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:462386 original size:13 final size:13
Alignment explanation
Indices: 462368--462392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
462358 ATTGTACCCA
462368 ATGTATCGATACC
1 ATGTATCGATACC
462381 ATGTATCGATAC
1 ATGTATCGATAC
462393 AAGGAATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACC
Found at i:464122 original size:13 final size:13
Alignment explanation
Indices: 464104--464160 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
464094 TTCAACAATT
464104 TGTATCGATACAA
1 TGTATCGATACAA
464117 TGTATCGATACATAA
1 TGTATCGATAC--AA
464132 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
464149 TGTATCGATACA
1 TGTATCGATACA
464161 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:464141 original size:19 final size:18
Alignment explanation
Indices: 464117--464177 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
464107 ATCGATACAA
464117 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
464136 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
464149 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
464168 TGTATCGATA
1 TGTATCGATA
464178 TAATGTATCG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.31
15 2 0.06
17 2 0.06
19 21 0.58
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:464144 original size:32 final size:32
Alignment explanation
Indices: 464103--464192 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
464093 TTTCAACAAT
464103 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
464135 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
464167 TTGTATCGATATAATGTATCGCTACA
1 TTGTATCGATACAATGTATCGATACA
464193 AAGCTACTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:464249 original size:13 final size:13
Alignment explanation
Indices: 464231--464256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
464221 CATTATTCCA
464231 TGTATCGATACAT
1 TGTATCGATACAT
464244 TGTATCGATACAT
1 TGTATCGATACAT
464257 GGATTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:470126 original size:200 final size:200
Alignment explanation
Indices: 469783--470182 Score: 791
Period size: 200 Copynumber: 2.0 Consensus size: 200
469773 TACTCCCGAA
469783 TATGAAGAATGGAAACTTCGCCACATCAACGATGCATTACCACCACCCAATTTTGGGACACTGCA
1 TATGAAGAATGGAAACTTCGCCACATCAACGATGCATTACCACCACCCAATTTTGGGACACTGCA
469848 AATCCCAATCGAAGAGCCTCCTTCTGAGATCGAGTTGCTTAGGAGGGAATTTGAACAAGAAAAGA
66 AATCCCAATCGAAGAGCCTCCTTCTGAGATCGAGTTGCTTAGGAGGGAATTTGAACAAGAAAAGA
469913 CATCCTTTGCAACAGAAATTGCTCGGCTAAAGGAGGACAAGAGCCAATTGAAGATGGATATCTAT
131 CATCCTTTGCAACAGAAATTGCTCGGCTAAAGGAGGACAAGAGCCAATTGAAGATGGATATCTAT
469978 CTTAG
196 CTTAG
469983 TATGAAGAATGGAAACTTCGCCACATCAACGATGCATTACCACCACCCAATTTTGGGACACTGCA
1 TATGAAGAATGGAAACTTCGCCACATCAACGATGCATTACCACCACCCAATTTTGGGACACTGCA
*
470048 AATCCCAATCGAAGAGCCTCCTTTTGAGATCGAGTTGCTTAGGAGGGAATTTGAACAAGAAAAGA
66 AATCCCAATCGAAGAGCCTCCTTCTGAGATCGAGTTGCTTAGGAGGGAATTTGAACAAGAAAAGA
470113 CATCCTTTGCAACAGAAATTGCTCGGCTAAAGGAGGACAAGAGCCAATTGAAGATGGATATCTAT
131 CATCCTTTGCAACAGAAATTGCTCGGCTAAAGGAGGACAAGAGCCAATTGAAGATGGATATCTAT
470178 CTTAG
196 CTTAG
470183 GCGCGGTGAA
Statistics
Matches: 199, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 199 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (200 bp):
TATGAAGAATGGAAACTTCGCCACATCAACGATGCATTACCACCACCCAATTTTGGGACACTGCA
AATCCCAATCGAAGAGCCTCCTTCTGAGATCGAGTTGCTTAGGAGGGAATTTGAACAAGAAAAGA
CATCCTTTGCAACAGAAATTGCTCGGCTAAAGGAGGACAAGAGCCAATTGAAGATGGATATCTAT
CTTAG
Found at i:478373 original size:1 final size:1
Alignment explanation
Indices: 478367--478444 Score: 57
Period size: 1 Copynumber: 78.0 Consensus size: 1
478357 CATCCTCCGC
* * * * * * * * *
478367 AAAAAAAAAAAAAGAAAAGAAAAGAAAGAAGAAAAAAAAGAAAAAAAGAAAACAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
478432 AAACAACAAAAAA
1 AAAAAAAAAAAAA
478445 GGTCCGGATG
Statistics
Matches: 55, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:478384 original size:9 final size:9
Alignment explanation
Indices: 478367--478445 Score: 65
Period size: 9 Copynumber: 8.7 Consensus size: 9
478357 CATCCTCCGC
478367 AAAAA-AAA
1 AAAAAGAAA
478375 AAAAAGAAA
1 AAAAAGAAA
478384 AGAAAAG--A
1 A-AAAAGAAA
*
478392 AAGAAGAAA
1 AAAAAGAAA
478401 AAAAAGAAA
1 AAAAAGAAA
*
478410 AAAAGAAAACA
1 AAAA-AGAA-A
*
478421 AAAAACAAA
1 AAAAAGAAA
*
478430 AAAAACAACA
1 AAAAAGAA-A
478440 AAAAAG
1 AAAAAG
478446 GTCCGGATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
7 4 0.07
8 7 0.12
9 26 0.44
10 17 0.29
11 5 0.08
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:478401 original size:29 final size:29
Alignment explanation
Indices: 478368--478443 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
478358 ATCCTCCGCA
* * * *
478368 AAAAAAAAAAAAGAAAAGAAAAGAAAGAAG
1 AAAAAAAAGAAA-AAAAGAAAACAAAAAAC
478398 AAAAAAAAGAAAAAAAGAAAACAAAAAAC
1 AAAAAAAAGAAAAAAAGAAAACAAAAAAC
*
478427 AAAAAAAACAACAAAAA
1 AAAAAAAAGAA-AAAAA
478444 AGGTCCGGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 24 0.60
30 16 0.40
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (29 bp):
AAAAAAAAGAAAAAAAGAAAACAAAAAAC
Found at i:478407 original size:21 final size:19
Alignment explanation
Indices: 478367--478433 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
478357 CATCCTCCGC
478367 AAAAAAA-AAAAAAGAAAAG
1 AAAAAAAGAAAAAA-AAAAG
478386 AAAAGAAAGAAGAAAAAAAAG
1 AAAA-AAAGAA-AAAAAAAAG
*
478407 AAAAAAAGAAAACAAAAAAC
1 AAAAAAAGAAAA-AAAAAAG
478427 AAAAAAA
1 AAAAAAA
478434 ACAACAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
19 6 0.14
20 22 0.51
21 11 0.26
22 4 0.09
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAAAG
Found at i:478439 original size:19 final size:20
Alignment explanation
Indices: 478366--478444 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
478356 GCATCCTCCG
478366 CAAAAAAA-AAAA-AAGAAAA
1 CAAAAAAAGAAAACAA-AAAA
*
478385 GAAAAGAAAGAAGAA-AAAAAA
1 CAAAA-AAAGAA-AACAAAAAA
*
478406 GAAAAAAAGAAAACAAAAAA
1 CAAAAAAAGAAAACAAAAAA
*
478426 CAAAAAAA-ACAACAAAAAA
1 CAAAAAAAGAAAACAAAAAA
478445 GGTCCGGATG
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
19 16 0.30
20 22 0.42
21 11 0.21
22 4 0.08
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (20 bp):
CAAAAAAAGAAAACAAAAAA
Found at i:480234 original size:13 final size:13
Alignment explanation
Indices: 480216--480240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
480206 TTCAACAATT
480216 TGTATCGATACAA
1 TGTATCGATACAA
480229 TGTATCGATACA
1 TGTATCGATACA
480241 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:480329 original size:13 final size:13
Alignment explanation
Indices: 480311--480336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
480301 CATTATTCCA
480311 TGTATCGATACAT
1 TGTATCGATACAT
480324 TGTATCGATACAT
1 TGTATCGATACAT
480337 GGATTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:480902 original size:10 final size:10
Alignment explanation
Indices: 480887--480913 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
480877 CCTTCCCATA
480887 AAAACACCTC
1 AAAACACCTC
480897 AAAACACCTC
1 AAAACACCTC
480907 AAAACAC
1 AAAACAC
480914 TTCCTCCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.37, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAACACCTC
Found at i:488327 original size:20 final size:19
Alignment explanation
Indices: 488302--488353 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
488292 CAATCTCATA
* *
488302 TATCGATACAGTTGTCCATG
1 TATCGATACA-ATGACCATG
*
488322 TATCGATACAATGAGCATG
1 TATCGATACAATGACCATG
488341 TATCGATACAATG
1 TATCGATACAATG
488354 TATCAATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (19 bp):
TATCGATACAATGACCATG
Found at i:492437 original size:79 final size:79
Alignment explanation
Indices: 492340--492674 Score: 410
Period size: 79 Copynumber: 4.3 Consensus size: 79
492330 AAACGAGGTC
*
492340 GGAGTA-CCCCTTCGAAAATAACAAGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAA
1 GGAGTATCCCC-TCGAAAATAACAAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAA
* * *
492404 AATAAGACTAGAGCT
65 AATAAAACCAGAGTT
** *
492419 GGAGTATCCCCTCGAAAATAATGAGGTTGGAGTATCCCCGATTGTG--AAATTGGTGTTTTAAAA
1 GGAGTATCCCCTCGAAAATAACAAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAA
* *
492482 ATAAAACCGGGGTT
66 ATAAAACCAGAGTT
* * *
492496 GGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTT-AGA
1 GGAGTATCCCCTCGAAAATAACAAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGA-A
*
492560 AATAAAA-CTGAGGTT
65 AATAAAACCAGA-GTT
*** * * * *
492575 GGAGTATCCCCTCGAAAATAATGGGGTTGAAGTATCCTCGATTGTGAAGAATTGGTGTTTTGAGA
1 GGAGTATCCCCTCGAAAATAACAAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAA
*
492640 ATAAAACCAGGGTT
66 ATAAAACCAGAGTT
*
492654 GGAGTATCCCCTCGGAAATAA
1 GGAGTATCCCCTCGAAAATAA
492675 AAACATGAAT
Statistics
Matches: 222, Mismatches: 27, Indels: 14
0.84 0.10 0.05
Matches are distributed among these distances:
77 66 0.30
78 3 0.01
79 146 0.66
80 7 0.03
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (79 bp):
GGAGTATCCCCTCGAAAATAACAAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAA
ATAAAACCAGAGTT
Found at i:492603 original size:156 final size:158
Alignment explanation
Indices: 492326--492666 Score: 485
Period size: 156 Copynumber: 2.2 Consensus size: 158
492316 TATTTTAGAG
* * * * *
492326 ATAAAAACGAGGTCGGAGTA-CCCCTTCGAAAATAACAAGGTTAGAGTATCCCCGATTGTGAAAA
1 ATAAAACCGGGGTTGGAGTATCCCC-TCAAAAATAACAAGGTTAGAGTATCCCCAATTGTGAAAA
* *
492390 ATTGGTGTTTTGAAAATAAGACTAGAGCTGGAGTATCCCCTCGAAAATAATGAGGTTGGAGTATC
65 ATTGGTGTTTTGAAAATAAAACTAGAGCTGGAGTATCCCCTCGAAAATAATGAGGTTGAAGTATC
492455 CCCGATTGTG-A-AATTGGTGTTTTAAAA
130 CCCGATTGTGAAGAATTGGTGTTTTAAAA
* *
492482 ATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCCCAATTGTGAAAAA
* *
492547 TTGGTGTTTT-AGAAATAAAACT-GAGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGAAGTAT
66 TTGGTGTTTTGA-AAATAAAACTAGA-GCTGGAGTATCCCCTCGAAAATAATGAGGTTGAAGTAT
* * *
492610 CCTCGATTGTGAAGAATTGGTGTTTTGAGA
129 CCCCGATTGTGAAGAATTGGTGTTTTAAAA
*
492640 ATAAAACCAGGGTTGGAGTATCCCCTC
1 ATAAAACCGGGGTTGGAGTATCCCCTC
492667 GGAAATAAAA
Statistics
Matches: 165, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
155 3 0.02
156 117 0.71
157 5 0.03
158 40 0.24
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (158 bp):
ATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCCCAATTGTGAAAAA
TTGGTGTTTTGAAAATAAAACTAGAGCTGGAGTATCCCCTCGAAAATAATGAGGTTGAAGTATCC
CCGATTGTGAAGAATTGGTGTTTTAAAA
Found at i:495071 original size:50 final size:50
Alignment explanation
Indices: 495007--495141 Score: 175
Period size: 50 Copynumber: 2.7 Consensus size: 50
494997 AAAAATGCTT
*
495007 GAATGTATCAATACATTGAGA-AATGTATCGATACATCTGTG-TAAAACCCA
1 GAATGTATCGATACATTGA-ACAATGTATCGATACATCTG-GATAAAACCCA
* * *
495057 GAATGTTTCGATACATTGAACAATGTATCGATATATCTGGATAAAATCCA
1 GAATGTATCGATACATTGAACAATGTATCGATACATCTGGATAAAACCCA
* * *
495107 AAATGTATCGATACAATGAATAATGTATCGATACA
1 GAATGTATCGATACATTGAACAATGTATCGATACA
495142 AATTGTGGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
49 2 0.03
50 72 0.97
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (50 bp):
GAATGTATCGATACATTGAACAATGTATCGATACATCTGGATAAAACCCA
Found at i:495805 original size:81 final size:81
Alignment explanation
Indices: 495656--495881 Score: 206
Period size: 82 Copynumber: 2.7 Consensus size: 81
495646 AGGGGCATTT
* * ** *
495656 TGCTCTTTGAGGATAAAGGAAAAGAAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAGA
1 TGCTCTTTGAGGATAAAGGAAAAGAAGGAAATGAAATGCGCCCTAATCTTTGAGGACAAAAGAGA
495721 AAAGGAAAAGACGTCC
66 AAAGGAAAAGACGTCC
* * *
495737 TGCTCTTTGAGGACTAAGGGAAAAGAAGGAAAT-AAGGTGCGCCCTAATCTTTGAGGATAAAAGA
1 TGCTCTTTGAGGA-TAAAGGAAAAGAAGGAAATGAA-ATGCGCCCTAATCTTTGAGGACAAAAGA
*
495801 -AAAAGGAAAA-AAGTGCATC
64 GAAAAGGAAAAGACGT-C--C
* * * * * ** *
495820 TTGCTCTTTGAAGACAAAAGAGAAAAGAAGAAAAAGAAGTGCATCCTATTCTTTGAGGACAA
1 -TGCTCTTTGAGGA-TAAAG-GAAAAGAAGGAAATGAAATGCGCCCTAATCTTTGAGGACAA
495882 TGGGACAAGA
Statistics
Matches: 119, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
80 3 0.03
81 26 0.22
82 39 0.33
83 1 0.01
84 16 0.13
85 32 0.27
86 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (81 bp):
TGCTCTTTGAGGATAAAGGAAAAGAAGGAAATGAAATGCGCCCTAATCTTTGAGGACAAAAGAGA
AAAGGAAAAGACGTCC
Found at i:495839 original size:40 final size:44
Alignment explanation
Indices: 495784--495864 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 44
495774 TGCGCCCTAA
* *
495784 TCTTTGAGGATAAAAGA-AAAAG-G-AAAA-AAGTGCATCTTGC
1 TCTTTGAAGACAAAAGAGAAAAGAGAAAAAGAAGTGCATCTTGC
495824 TCTTTGAAGACAAAAGAGAAAAGAAGAAAAAGAAGTGCATC
1 TCTTTGAAGACAAAAGAGAAAAG-AGAAAAAGAAGTGCATC
495865 CTATTCTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 15 0.44
41 5 0.15
43 1 0.03
44 4 0.12
45 9 0.26
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.19
Consensus pattern (44 bp):
TCTTTGAAGACAAAAGAGAAAAGAGAAAAAGAAGTGCATCTTGC
Found at i:495873 original size:45 final size:40
Alignment explanation
Indices: 495779--495881 Score: 107
Period size: 45 Copynumber: 2.5 Consensus size: 40
495769 TAAGGTGCGC
*
495779 CCTAATCTTTGAGGATAAAAGAAAAAGGAAAAAAGTGCAT
1 CCTAATCTTTGAGGACAAAAGAAAAAGGAAAAAAGTGCAT
* ** *
495819 CTTGCTCTTTGAAGACAAAAGAGAAAAGAAGAAAAAGAAGTGCAT
1 CCTAATCTTTGAGGACAAAAGA-AAAAG--G-AAAA-AAGTGCAT
*
495864 CCTATTCTTTGAGGACAA
1 CCTAATCTTTGAGGACAA
495882 TGGGACAAGA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
40 17 0.35
41 5 0.10
43 1 0.02
44 4 0.08
45 22 0.45
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (40 bp):
CCTAATCTTTGAGGACAAAAGAAAAAGGAAAAAAGTGCAT
Found at i:496027 original size:61 final size:61
Alignment explanation
Indices: 495931--496328 Score: 540
Period size: 60 Copynumber: 6.6 Consensus size: 61
495921 GACAAAGGAG
* * ** * *
495931 AAAAGGAAAAAGTGTCCTATTCTTTGCGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* **
495992 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGATTGG-AAGTGCCACCAACTTGTGCAGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
496052 AAAAGGAAAAGGCATCTTGCTCTTTGAGAACT-GAAAGTGCCATCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
*
496112 AAAAGGAAAAGACGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
*
496172 AAAAGGAAAAGACGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
496233 AAAAGGAAAAGGCGTCCTGCTCTTTGAAGACTAGAAGGTGCTACCAACTTGTGTGGGTTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
496294 GAAAGGAAAA--TGT-CTGGCTCTTTGAGGACT-GAAAG
1 AAAAGGAAAAGGCGTCCT-GCTCTTTGAGGACTGGAAAG
496329 GATAAAAGGT
Statistics
Matches: 303, Mismatches: 31, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
58 6 0.02
59 16 0.05
60 161 0.53
61 120 0.40
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (61 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:497306 original size:12 final size:12
Alignment explanation
Indices: 497289--497323 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
497279 TTAAGCAGGT
497289 TCTTTTCTTTTC
1 TCTTTTCTTTTC
*
497301 TCTTTTTTTTTC
1 TCTTTTCTTTTC
*
497313 TTTTTTCTTTT
1 TCTTTTCTTTT
497324 TTCTAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TCTTTTCTTTTC
Found at i:497313 original size:17 final size:17
Alignment explanation
Indices: 497291--497325 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
497281 AAGCAGGTTC
497291 TTTTCTTTTCTCTTTTT
1 TTTTCTTTTCTCTTTTT
*
497308 TTTTCTTTTTTCTTTTT
1 TTTTCTTTTCTCTTTTT
497325 T
1 T
497326 CTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTCTTTTCTCTTTTT
Found at i:509687 original size:28 final size:28
Alignment explanation
Indices: 509653--509725 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
509643 TAAAGATAAA
509653 AATGGGGTCAGAGTA-CCCCTTCAAAAAT
1 AATGGGGTCAGAGTATCCCC-TCAAAAAT
** *
509681 AATGGGGTTGGAGTATCCCCTCGAAAAT
1 AATGGGGTCAGAGTATCCCCTCAAAAAT
**
509709 AATGGGGTTGGAGTATC
1 AATGGGGTCAGAGTATC
509726 TGATTGTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 37 0.90
29 4 0.10
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (28 bp):
AATGGGGTCAGAGTATCCCCTCAAAAAT
Found at i:509844 original size:79 final size:77
Alignment explanation
Indices: 509683--509870 Score: 229
Period size: 79 Copynumber: 2.4 Consensus size: 77
509673 TCAAAAATAA
* * * ** *
509683 TGGGGTTGGAGTATCCCCT-CGAAAATAATGGGGTTGGAGTATCTGATTGTGAAAAATTGGTGTT
1 TGGGGTTAGAGTATCCTCTCCG-AAATAACGGGGTTGGAGTATCCAATTGTGAAAAATTAGTGTT
509747 TTGAAAATAAAAC
65 TTGAAAATAAAAC
* *
509760 CGGGGTTAGAGTATCCTCTCCGAAATAACGGGGTTGGAGTATCCCCAATTGTGGAAAATTAGTGT
1 TGGGGTTAGAGTATCCTCTCCGAAATAACGGGGTTGGAGTAT--CCAATTGTGAAAAATTAGTG-
509825 TTTTG-AAATAAAAC
63 TTTTGAAAATAAAAC
*
509839 TGGGGTTAGAGTAT-CTGCTCAGAAATAACGGG
1 TGGGGTTAGAGTATCCT-CTCCGAAATAACGGG
509871 CCCCGATTGT
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
77 35 0.36
78 4 0.04
79 52 0.54
80 5 0.05
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.29
Consensus pattern (77 bp):
TGGGGTTAGAGTATCCTCTCCGAAATAACGGGGTTGGAGTATCCAATTGTGAAAAATTAGTGTTT
TGAAAATAAAAC
Found at i:509933 original size:69 final size:69
Alignment explanation
Indices: 509802--509935 Score: 164
Period size: 69 Copynumber: 1.9 Consensus size: 69
509792 GTTGGAGTAT
* ** *
509802 CCCCAATTGTGGAAAATTAGTGTTTTTGAAATAAAACTGGGGTTAGAGTATCTGCTCAGAAATAA
1 CCCCAATTGTGAAAAATTAGTGTTTTTGAAATAAAACCAGGGTTAGAGTATCTCCTCAGAAATAA
509867 CGGG
66 CGGG
* * * *
509871 CCCCGATTGTGAAAAATTGGTG-TTTTGAGAATAAAACCAGGTTTAGAGTATC-CCTTCGGAAAT
1 CCCCAATTGTGAAAAATTAGTGTTTTTGA-AATAAAACCAGGGTTAGAGTATCTCC-TCAGAAAT
509934 AA
64 AA
509936 AAACATGAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
68 7 0.13
69 48 0.87
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (69 bp):
CCCCAATTGTGAAAAATTAGTGTTTTTGAAATAAAACCAGGGTTAGAGTATCTCCTCAGAAATAA
CGGG
Found at i:512284 original size:51 final size:51
Alignment explanation
Indices: 512238--512373 Score: 159
Period size: 50 Copynumber: 2.7 Consensus size: 51
512228 AAAAAAGCTT
* * * *
512238 GAATGTATCGATACATTGAGA-AATGTATCGATACATTTGGGTAAAAACCCA
1 GAATATATCGATACAATGA-ACAATGTATCGATACATCTAGGTAAAAACCCA
*
512289 GAATATATCGATACAATGAACAATGTATCGATACATCTAGGT-AAAATCCA
1 GAATATATCGATACAATGAACAATGTATCGATACATCTAGGTAAAAACCCA
* * * * *
512339 AAATGTATTGATATAATGAACAATGTATTGATACA
1 GAATATATCGATACAATGAACAATGTATCGATACA
512374 AATTGTGAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
50 38 0.51
51 36 0.49
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (51 bp):
GAATATATCGATACAATGAACAATGTATCGATACATCTAGGTAAAAACCCA
Found at i:513166 original size:21 final size:21
Alignment explanation
Indices: 513142--513189 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
513132 TATCAACTTG
513142 TAATTCAATTATTTTCTTTTC
1 TAATTCAATTATTTTCTTTTC
*
513163 TAATTCATTTATTTTCTTTTC
1 TAATTCAATTATTTTCTTTTC
513184 TAATTC
1 TAATTC
513190 TTCCTCTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATTCAATTATTTTCTTTTC
Found at i:513199 original size:21 final size:21
Alignment explanation
Indices: 513142--513203 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
513132 TATCAACTTG
513142 TAATTCAATT-ATTTTCTTTTC
1 TAATTC-ATTCATTTTCTTTTC
*
513163 TAATTCATTTATTTTCTTTTC
1 TAATTCATTCATTTTCTTTTC
*
513184 TAATTC-TTCCTCTTTCTTTT
1 TAATTCATTCAT-TTTCTTTT
513204 TAAGCACATC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.16
21 31 0.84
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (21 bp):
TAATTCATTCATTTTCTTTTC
Found at i:515009 original size:20 final size:21
Alignment explanation
Indices: 514984--515032 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
514974 GGGCACAATA
*
514984 TATCGATACATTTCAA-CATG
1 TATCGATACAATTCAAGCATG
*
515004 TATCGATACAATTCAAGTATG
1 TATCGATACAATTCAAGCATG
515025 TATCGATA
1 TATCGATA
515033 TAATGTATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (21 bp):
TATCGATACAATTCAAGCATG
Found at i:515101 original size:20 final size:19
Alignment explanation
Indices: 515076--515125 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
515066 ACCAGTTTTA
* *
515076 TGTATCGATACTTTTCAAGG
1 TGTATCGATAC-TATCAACG
* *
515096 TGTATCAATACTATGAACG
1 TGTATCGATACTATCAACG
515115 TGTATCGATAC
1 TGTATCGATAC
515126 AATGTATCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTATCGATACTATCAACG
Found at i:515133 original size:13 final size:13
Alignment explanation
Indices: 515115--515171 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 13
515105 ACTATGAACG
515115 TGTATCGATACAA
1 TGTATCGATACAA
515128 TGTATCGATACTAAGCAAA
1 TGTATCG--A-T-A-C-AA
515147 TTGTATCGATACAA
1 -TGTATCGATACAA
515161 TGTATCGATAC
1 TGTATCGATAC
515172 TAAGCAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 18 0.49
14 2 0.05
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 2 0.05
20 7 0.19
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:515153 original size:20 final size:20
Alignment explanation
Indices: 515128--515191 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
515118 ATCGATACAA
515128 TGTATCGATACTAAGCAAAT
1 TGTATCGATACTAAGCAAAT
515148 TGTATCG--A-T-A-C-AA-
1 TGTATCGATACTAAGCAAAT
515161 TGTATCGATACTAAGCAAAT
1 TGTATCGATACTAAGCAAAT
515181 TGTATCGATAC
1 TGTATCGATAC
515192 ATCTAGGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 7 0.19
14 2 0.05
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 2 0.05
20 18 0.49
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
TGTATCGATACTAAGCAAAT
Found at i:515157 original size:33 final size:33
Alignment explanation
Indices: 515115--515192 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
515105 ACTATGAACG
515115 TGTATCGATACAATGTATCGATACTAAGCAAAT
1 TGTATCGATACAATGTATCGATACTAAGCAAAT
515148 TGTATCGATACAATGTATCGATACTAAGCAAAT
1 TGTATCGATACAATGTATCGATACTAAGCAAAT
515181 TGTATCGATACA
1 TGTATCGATACA
515193 TCTAGGTGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACTAAGCAAAT
Found at i:520350 original size:10 final size:10
Alignment explanation
Indices: 520335--520371 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
520325 TAAAAATATA
520335 ATTTTAAAAT
1 ATTTTAAAAT
520345 ATTTTAAAAT
1 ATTTTAAAAT
*
520355 -TTATAAAA-
1 ATTTTAAAAT
520363 ATTTTAAAA
1 ATTTTAAAA
520372 AAATTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 14 0.58
10 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:520366 original size:18 final size:18
Alignment explanation
Indices: 520334--520371 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
520324 ATAAAAATAT
520334 AATTTTAAAATATTTTAA
1 AATTTTAAAATATTTTAA
520352 AATTTATAAAA-ATTTTAA
1 AATTT-TAAAATATTTTAA
520370 AA
1 AA
520372 AAATTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTTTAAAATATTTTAA
Found at i:520399 original size:13 final size:13
Alignment explanation
Indices: 520381--520405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
520371 AAAATTAAAT
520381 ATATTTATATCTC
1 ATATTTATATCTC
520394 ATATTTATATCT
1 ATATTTATATCT
520406 AATTTTAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTTATATCTC
Found at i:522429 original size:11 final size:11
Alignment explanation
Indices: 522411--522444 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
522401 ATATGGTATA
522411 AAAAATAAT-T
1 AAAAATAATAT
522421 AAAATATAATAT
1 AAAA-ATAATAT
522433 AAAAATAATAT
1 AAAAATAATAT
522444 A
1 A
522445 TATTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.18
11 13 0.59
12 5 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:523213 original size:15 final size:16
Alignment explanation
Indices: 523193--523222 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
523183 TTTAAATTAT
523193 TTTAAA-TTTAAATCG
1 TTTAAATTTTAAATCG
523208 TTTAAATTTTAAATC
1 TTTAAATTTTAAATC
523223 ATTTCGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTAAATTTTAAATCG
Found at i:523235 original size:16 final size:15
Alignment explanation
Indices: 523183--523226 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
523173 TATTTTTGAG
*
523183 TTTAAATTATTTTAAA
1 TTTAAATCA-TTTAAA
*
523199 TTTAAATCGTTTAAA
1 TTTAAATCATTTAAA
523214 TTTTAAATCATTT
1 -TTTAAATCATTT
523227 CGAATTTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (15 bp):
TTTAAATCATTTAAA
Found at i:524087 original size:13 final size:13
Alignment explanation
Indices: 524069--524094 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
524059 TACAGCAAGT
524069 ATGTATCGATACA
1 ATGTATCGATACA
524082 ATGTATCGATACA
1 ATGTATCGATACA
524095 TAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:644573 original size:14 final size:14
Alignment explanation
Indices: 644554--644617 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 14
644544 TTCTCTTCAA
644554 AAAAAAAAAAAGAG
1 AAAAAAAAAAAGAG
*
644568 -AAAAAAAAAACA-
1 AAAAAAAAAAAGAG
* *
644580 AAAAAAAACAA-AC
1 AAAAAAAAAAAGAG
* *
644593 AAAGAAAAAGAGAG
1 AAAAAAAAAAAGAG
644607 AAAAGAAAAAA
1 AAAA-AAAAAA
644618 CCTACTTAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
12 1 0.03
13 28 0.74
14 4 0.11
15 5 0.13
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAG
Found at i:645668 original size:55 final size:55
Alignment explanation
Indices: 645583--646368 Score: 1161
Period size: 55 Copynumber: 14.3 Consensus size: 55
645573 TCCGCTTTTT
*
645583 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
645638 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
645693 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
645748 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
645803 AGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
645858 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
645913 AGTCCTTAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-T-C
645968 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
646023 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
646078 AGTCCTCAAAGAGCA-GACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
646132 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
646187 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
646242 ATTCC-CAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
646296 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
646351 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
646369 TACAATTTAT
Statistics
Matches: 685, Mismatches: 29, Indels: 34
0.92 0.04 0.05
Matches are distributed among these distances:
53 9 0.01
54 101 0.15
55 560 0.82
56 13 0.02
57 2 0.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:647007 original size:21 final size:21
Alignment explanation
Indices: 646983--647039 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
646973 AAAAAATTTA
646983 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
647004 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
647025 AATGTATCGATACAT
1 AATGTATCGATACAT
647040 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:647119 original size:19 final size:19
Alignment explanation
Indices: 647095--647149 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
647085 AATTCAACAA
647095 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
647114 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
647133 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
647150 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:647207 original size:13 final size:13
Alignment explanation
Indices: 647189--647214 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
647179 CATTTTTCTG
647189 TGTATCGATACAT
1 TGTATCGATACAT
647202 TGTATCGATACAT
1 TGTATCGATACAT
647215 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:647211 original size:33 final size:33
Alignment explanation
Indices: 647169--647235 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
647159 GCCAAGGAAA
***
647169 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
647202 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
647235 T
1 T
647236 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:649760 original size:52 final size:51
Alignment explanation
Indices: 649687--649856 Score: 186
Period size: 52 Copynumber: 3.3 Consensus size: 51
649677 TTATTTTCGA
*
649687 GGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTAT--TTCAAAACACCAATTTTTCCACAATC
* **
649739 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTA-TTTCAAAACACCAATTTTTCC-ACAATC
* *
649791 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATTT-C-AAAACACCAATTTTTCCACAATC
*
649843 GAGGATACTCCAAC
1 GGGGATACTCCAAC
649857 CTCGTTATTT
Statistics
Matches: 100, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
51 14 0.14
52 69 0.69
53 13 0.13
54 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATTTCAAAACACCAATTTTTCCACAATC
Found at i:649876 original size:28 final size:28
Alignment explanation
Indices: 649840--649916 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
649830 ATTTTTCACA
* * *
649840 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
649868 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
649896 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
649917 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:650046 original size:76 final size:78
Alignment explanation
Indices: 649870--650071 Score: 214
Period size: 76 Copynumber: 2.6 Consensus size: 78
649860 GTTATTTCAT
* * * *
649870 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
649935 TGATTTCTCATAAT
65 CGATTTCTCACAAC
** * * * *
649949 TAGGGATACTCCAACCTCGTTATTTTCGAAGGGATACTCCAATCCCGATTT-TT-TC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
650011 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* *
650025 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCCCG
650072 TTATTATCTC
Statistics
Matches: 102, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
75 8 0.08
76 49 0.48
77 2 0.02
78 4 0.04
79 39 0.38
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.28
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:669157 original size:25 final size:25
Alignment explanation
Indices: 669117--669202 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
669107 CAAAAAAATC
**
669117 AAATAAAAAAAGTAAAAAAGATAAGT
1 AAATAAAAAAA-TAAAAAAGATAAAA
*
669143 AAATAAAAAAATAAAAAAGGTAAAA
1 AAATAAAAAAATAAAAAAGATAAAA
* *
669168 AAATAAAAACA-AAAAAACA-AAAA
1 AAATAAAAAAATAAAAAAGATAAAA
*
669191 ACAAGAAAAAAA
1 A-AATAAAAAAA
669203 ACCAAAGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.10
24 14 0.27
25 21 0.41
26 11 0.22
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.09
Consensus pattern (25 bp):
AAATAAAAAAATAAAAAAGATAAAA
Found at i:669182 original size:15 final size:14
Alignment explanation
Indices: 669164--669203 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
669154 TAAAAAAGGT
*
669164 AAAAAAATAAAAAC
1 AAAAAAAAAAAAAC
669178 AAAAAAACAAAAAAC
1 AAAAAAA-AAAAAAC
669193 AAGAAAAAAAA
1 AA-AAAAAAAA
669204 CCAAAGAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 11 0.48
16 5 0.22
ACGTcount: A:0.88, C:0.07, G:0.03, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:669201 original size:18 final size:21
Alignment explanation
Indices: 669178--669221 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
669168 AAATAAAAAC
669178 AAAAAAA-CAAA-AAACAAGA
1 AAAAAAACCAAAGAAACAAGA
669197 AAAAAAACCAAAGAAACAAGA
1 AAAAAAACCAAAGAAACAAGA
669218 AAAA
1 AAAA
669222 TGAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.30
20 4 0.17
21 12 0.52
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAACCAAAGAAACAAGA
Found at i:669226 original size:28 final size:28
Alignment explanation
Indices: 669168--669232 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
669158 AAAGGTAAAA
669168 AAATAAAAACAAAAAAACAAAAAACAAG
1 AAATAAAAACAAAAAAACAAAAAACAAG
* *
669196 AAA-AAAAACCAAAGAAACAAGAAAA-ATG
1 AAATAAAAA-CAAAAAAACAA-AAAACAAG
669224 AAATAAAAA
1 AAATAAAAA
669233 TGAAAAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 5 0.16
28 18 0.56
29 9 0.28
ACGTcount: A:0.80, C:0.09, G:0.06, T:0.05
Consensus pattern (28 bp):
AAATAAAAACAAAAAAACAAAAAACAAG
Found at i:670231 original size:14 final size:14
Alignment explanation
Indices: 670212--670238 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
670202 TATTAGACTT
670212 CACATCATGCATTG
1 CACATCATGCATTG
670226 CACATCATGCATT
1 CACATCATGCATT
670239 CATATTACAA
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:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (14 bp):
CACATCATGCATTG
Found at i:671060 original size:34 final size:33
Alignment explanation
Indices: 670928--671091 Score: 210
Period size: 33 Copynumber: 5.0 Consensus size: 33
670918 GGAGCAACTC
*
670928 TTTTTAAAGCCCACACAAGTTGGTGGCGA-CCTC
1 TTTTTAAAGCCCACACAAGTTGGTGGC-ATCCTT
* * *
670961 TTCTT-AAGTCCACACAAGCTGGTGGCAT-C-T
1 TTTTTAAAGCCCACACAAGTTGGTGGCATCCTT
* *
670991 TTTTCAAAGCCTACACAAGTTGGTGGCATCCTT
1 TTTTTAAAGCCCACACAAGTTGGTGGCATCCTT
671024 TTTTTAAAGCCCACACAAGTTGGTGGCATCCTT
1 TTTTTAAAGCCCACACAAGTTGGTGGCATCCTT
* *
671057 TTTTTCCAAGCCCGCACAAGTTGGTGGCATCCTT
1 TTTTT-AAAGCCCACACAAGTTGGTGGCATCCTT
671091 T
1 T
671092 CTCAAAAGCC
Statistics
Matches: 113, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
30 3 0.03
31 22 0.19
32 20 0.18
33 41 0.36
34 27 0.24
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (33 bp):
TTTTTAAAGCCCACACAAGTTGGTGGCATCCTT
Found at i:671078 original size:67 final size:63
Alignment explanation
Indices: 670926--671091 Score: 210
Period size: 67 Copynumber: 2.6 Consensus size: 63
670916 GTGGAGCAAC
* *
670926 TCTTTTT-AAAGCCCACACAAGTTGGTGGCGA-CCTCTTCTTAAGTCCACACAAGCTGGTGGCA
1 TCTTTTTCAAAGCCCACACAAGTTGGTGGC-ATCCTTTTCTTAAGCCCACACAAGCTGGTGGCA
* * *
670988 TCTTTTTCAAAGCCTACACAAGTTGGTGGCATCCTTTTTTTAAAGCCCACACAAGTTGGTGGCA
1 TCTTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTTCTT-AAGCCCACACAAGCTGGTGGCA
* *
671052 TCCTTTTTTTCCAAGCCCGCACAAGTTGGTGGCATCCTTT
1 T-C--TTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTT
671092 CTCAAAAGCC
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
62 8 0.09
63 28 0.31
64 21 0.23
65 1 0.01
67 32 0.36
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (63 bp):
TCTTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTTCTTAAGCCCACACAAGCTGGTGGCA
Found at i:671118 original size:67 final size:67
Alignment explanation
Indices: 670928--671164 Score: 174
Period size: 67 Copynumber: 3.7 Consensus size: 67
670918 GGAGCAACTC
* * *
670928 TTTTT-AAAGCCCACACAAGTTGGTGGCGA-CCTCTTCT--TAAGTCCACACAAG-CTGGTGGCA
1 TTTTTCAAAGCCCACACAAGTTGGTGGC-ATCCT-TTCTCAAAAGCCCACACAAGTC-GATGGCA
670988 T-C--
63 TCCTT
* * ** * *
670990 TTTTTCAAAGCCTACACAAGTTGGTGGCATCCTTTTTTTAAAGCCCACACAAGTTGGTGGCATCC
1 TTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTCGATGGCATCC
671055 TT
66 TT
* * * * * *
671057 TTTTTCCAAGCCCGCACAAGTTGGTGGCATCCTTTCTCAAAAGCCTACGCGAGTCGATGGCAACC
1 TTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTCGATGGCATCC
671122 --
66 TT
* * * * * *
671122 CTTTT-AAAGCCCACATAGGTTAGTGGCAACC-CTCTCAAAAGCC
1 TTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCC
671165 TACGCATGTT
Statistics
Matches: 142, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
62 9 0.06
63 35 0.25
64 40 0.28
65 5 0.04
67 53 0.37
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (67 bp):
TTTTTCAAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTCGATGGCATCC
TT
Found at i:671148 original size:98 final size:97
Alignment explanation
Indices: 670921--671149 Score: 234
Period size: 98 Copynumber: 2.4 Consensus size: 97
670911 CCCTAGTGGA
* * * * *
670921 GCAA-CTCTTTTTAAAGCCCACACAAGTTGGTGGCGA-CCTCTTCTT--AAGTCCACACAAGCTG
1 GCAACCTC-TTTTAAAGCCCACACAAGTTAGTGGC-ATCCTTTTTTTCCAAGCCCGCACAAGCTG
* * *
670982 GTGGCATCTTTTTCAAAGCCTACACAAGTTGGTG
64 GTGGCATCTTTCTCAAAGCCTACACAAGTCGATG
* * * *
671016 GCATCCTTTTTTTAAAGCCCACACAAGTTGGTGGCATCCTTTTTTTCCAAGCCCGCACAAGTTGG
1 GCAACC-TCTTTTAAAGCCCACACAAGTTAGTGGCATCCTTTTTTTCCAAGCCCGCACAAGCTGG
* *
671081 TGGCATCCTTTCTCAAAAGCCTACGCGAGTCGATG
65 TGGCAT-CTTTCTC-AAAGCCTACACAAGTCGATG
* *
671116 GCAACC-CTTTTAAAGCCCACATAGGTTAGTGGCA
1 GCAACCTCTTTTAAAGCCCACACAAGTTAGTGGCA
671150 ACCCTCTCAA
Statistics
Matches: 110, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
95 4 0.04
96 34 0.31
97 1 0.01
98 44 0.40
99 6 0.05
100 21 0.19
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (97 bp):
GCAACCTCTTTTAAAGCCCACACAAGTTAGTGGCATCCTTTTTTTCCAAGCCCGCACAAGCTGGT
GGCATCTTTCTCAAAGCCTACACAAGTCGATG
Found at i:671180 original size:32 final size:31
Alignment explanation
Indices: 671075--671181 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 31
671065 AGCCCGCACA
* *
671075 AGTTGGTGGCATCCTTTCTCAAAAGCCTACGC
1 AGTTGGTGGCAACC-CTCTCAAAAGCCTACGC
* * ** * **
671107 GAGTCGATGGCAACCCT-TTTAAAGCCCACAT
1 -AGTTGGTGGCAACCCTCTCAAAAGCCTACGC
*
671138 AGGTTAGTGGCAACCCTCTCAAAAGCCTACGC
1 A-GTTGGTGGCAACCCTCTCAAAAGCCTACGC
671170 ATGTTGGTGGCA
1 A-GTTGGTGGCA
671182 TCTCCTTTTA
Statistics
Matches: 53, Mismatches: 19, Indels: 5
0.69 0.25 0.06
Matches are distributed among these distances:
30 1 0.02
31 21 0.40
32 20 0.38
33 11 0.21
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (31 bp):
AGTTGGTGGCAACCCTCTCAAAAGCCTACGC
Found at i:671356 original size:50 final size:50
Alignment explanation
Indices: 671188--671644 Score: 251
Period size: 52 Copynumber: 9.0 Consensus size: 50
671178 GGCATCTCCT
* * * *** *
671188 TTTAAGTCCAATGTTGTTGGCCCTGAATCAGCATATCAATAACCTTCATC
1 TTTAAGTCCAACGTTGTTGGCCTTGAATCAGCACATTGGTAACCTTTATC
* * * *
671238 TTTAAGTCCAACG-TGCT-GACTATGAATTAGCACATTGG-CACCTTTATTGTC
1 TTTAAGTCCAACGTTGTTGGCCT-TGAATCAGCACATTGGTAACCTTTA---TC
* * *
671289 TTTAAGTCTAACGTTGTTGGCCTTAAATCAGCACATTGGTAACCTTCATC
1 TTTAAGTCCAACGTTGTTGGCCTTGAATCAGCACATTGGTAACCTTTATC
* ** * * * * *
671339 TTTAAGTCCAACATTGTTGGTGTTGAATCAGTAAATCGGCACCCATATTATC
1 TTTAAGTCCAACGTTGTTGGCCTTGAATCAGCACATTGGTAACC-T-TTATC
* ***** * * * *
671391 TTTAAGTCCAATGTCACCAGCCCTAAATCAGCACACTAGTAACCTTTATC
1 TTTAAGTCCAACGTTGTTGGCCTTGAATCAGCACATTGGTAACCTTTATC
* * * * * *
671441 TTTAAGTCCAACATCGGTGGCCTTGAATCAGCACATTGGCACCCTTGTTGTC
1 TTTAAGTCCAACGTTGTTGGCCTTGAATCAGCACATTGGTAACC-T-TTATC
* * * * * * **
671493 TTTAAGTCCAATGTCGTTAGCCCTAAATCAGTACAACGGTAACCTTTATC
1 TTTAAGTCCAACGTTGTTGGCCTTGAATCAGCACATTGGTAACCTTTATC
* * * *
671543 ATTAGGTCCAA-ATATCGTTGGCCTTGAATCAGCACATTGG-CACCTTTATC
1 TTTAAGTCCAACGT-T-GTTGGCCTTGAATCAGCACATTGGTAACCTTTATC
* * * * * *
671593 ATCTGTAAGTCCAATGTTGCTAGCCATGAATCAGCATATTGG-CACCTTTATC
1 -T-T-TAAGTCCAACGTTGTTGGCCTTGAATCAGCACATTGGTAACCTTTATC
671645 ATCATTAAGT
Statistics
Matches: 300, Mismatches: 90, Indels: 32
0.71 0.21 0.08
Matches are distributed among these distances:
48 8 0.03
49 15 0.05
50 107 0.36
51 36 0.12
52 115 0.38
53 18 0.06
54 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (50 bp):
TTTAAGTCCAACGTTGTTGGCCTTGAATCAGCACATTGGTAACCTTTATC
Found at i:671422 original size:102 final size:102
Alignment explanation
Indices: 671227--671609 Score: 367
Period size: 102 Copynumber: 3.8 Consensus size: 102
671217 AGCATATCAA
* * * * * * *
671227 TAACCTTCATCTTTAAGTCCAAC-GTGCT-GACTATGAATTAGCACATTGGCACCTTTATTGTCT
1 TAACCTTTATCTTTAAGTCCAACATTGTTGGCCT-TGAATCAGCACATTGGCACCCTTATTATCT
* * ***** * *
671290 TTAAGTCTAACGTTGTTGGCCTTAAATCAGCACATTGG
65 TTAAGTCCAATGTCACCAGCCCTAAATCAGCACAATGG
* ** * * * *
671328 TAACCTTCATCTTTAAGTCCAACATTGTTGGTGTTGAATCAGTAAATCGGCACCCATATTATCTT
1 TAACCTTTATCTTTAAGTCCAACATTGTTGGCCTTGAATCAGCACATTGGCACCCTTATTATCTT
* *
671393 TAAGTCCAATGTCACCAGCCCTAAATCAGCACACTAG
66 TAAGTCCAATGTCACCAGCCCTAAATCAGCACAATGG
* * * *
671430 TAACCTTTATCTTTAAGTCCAACATCGGTGGCCTTGAATCAGCACATTGGCACCCTTGTTGTCTT
1 TAACCTTTATCTTTAAGTCCAACATTGTTGGCCTTGAATCAGCACATTGGCACCCTTATTATCTT
*** * *
671495 TAAGTCCAATGTCGTTAGCCCTAAATCAGTACAACGG
66 TAAGTCCAATGTCACCAGCCCTAAATCAGCACAATGG
* * * *
671532 TAACCTTTATCATTAGGTCCAA-ATATCGTTGGCCTTGAATCAGCACATTGGCACCTTTATCATC
1 TAACCTTTATCTTTAAGTCCAACAT-T-GTTGGCCTTGAATCAGCACATTGGCACCCTTATTATC
*
671596 TGTAAGTCCAATGT
64 TTTAAGTCCAATGT
671610 TGCTAGCCAT
Statistics
Matches: 230, Mismatches: 48, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
101 25 0.11
102 158 0.69
103 47 0.20
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (102 bp):
TAACCTTTATCTTTAAGTCCAACATTGTTGGCCTTGAATCAGCACATTGGCACCCTTATTATCTT
TAAGTCCAATGTCACCAGCCCTAAATCAGCACAATGG
Found at i:671538 original size:204 final size:204
Alignment explanation
Indices: 671227--671609 Score: 475
Period size: 204 Copynumber: 1.9 Consensus size: 204
671217 AGCATATCAA
* * *
671227 TAACCTTCATCTTTAAGTCCAACGTGCTGACTATGAATTAGCACATTGGCACCTTTATTGTCTTT
1 TAACCTTCATCTTTAAGTCCAACATGCTGACTATGAATCAGCACATTGGCACCCTTATTGTCTTT
* * * * ** *
671292 AAGTCTAACGTTGTTGGCCTTAAATCAGCACATTGGTAACCTTCATCTTTAAGTCCAACAT-T-G
66 AAGTCCAACGTCGTTAGCCCTAAATCAGCACAACGGTAACCTTCATCATTAAGTCCAA-ATATCG
** * * *
671355 TTGGTGTTGAATCAGTAAATCGGCACCCATATTATCTTTAAGTCCAATGTCACCAGCCCTAAATC
130 TTGGCCTTGAATCAGCAAATCGGCACCCATATCATCTGTAAGTCCAATGTCACCAGCCCTAAATC
671420 AGCACACTAG
195 AGCACACTAG
* * * *
671430 TAACCTTTATCTTTAAGTCCAACATCGGTGGCCT-TGAATCAGCACATTGGCACCCTTGTTGTCT
1 TAACCTTCATCTTTAAGTCCAACAT-GCT-GACTATGAATCAGCACATTGGCACCCTTATTGTCT
* * * *
671494 TTAAGTCCAATGTCGTTAGCCCTAAATCAGTACAACGGTAACCTTTATCATTAGGTCCAAATATC
64 TTAAGTCCAACGTCGTTAGCCCTAAATCAGCACAACGGTAACCTTCATCATTAAGTCCAAATATC
* * **
671559 GTTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTGTAAGTCCAATGT
129 GTTGGCCTTGAATCAGCAAATCGGCACCCATATCATCTGTAAGTCCAATGT
671610 TGCTAGCCAT
Statistics
Matches: 149, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
203 25 0.17
204 79 0.53
205 45 0.30
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (204 bp):
TAACCTTCATCTTTAAGTCCAACATGCTGACTATGAATCAGCACATTGGCACCCTTATTGTCTTT
AAGTCCAACGTCGTTAGCCCTAAATCAGCACAACGGTAACCTTCATCATTAAGTCCAAATATCGT
TGGCCTTGAATCAGCAAATCGGCACCCATATCATCTGTAAGTCCAATGTCACCAGCCCTAAATCA
GCACACTAG
Found at i:671675 original size:52 final size:52
Alignment explanation
Indices: 671260--671688 Score: 193
Period size: 52 Copynumber: 8.3 Consensus size: 52
671250 GTGCTGACTA
* ** * * * * *
671260 TGAATTAGCACATTGGCACCTTTATTGTCTTTAAGTCTAACGTTGTTGGCCT
1 TGAATCAGCACATTGGCACCTTTATCATCTGTAAGTCCAATGTCGTAGGCCT
* * * ** * * **
671312 TAAATCAGCACATTGGTAACC--T-TCATCTTTAAGTCCAACATTGTTGGTGT
1 TGAATCAGCACATTGG-CACCTTTATCATCTGTAAGTCCAATGTCGTAGGCCT
* * * ** * * ** *
671362 TGAATCAGTAAATCGGCACCCATATTATCTTTAAGTCCAATGTCACCA-GCCC
1 TGAATCAGCACATTGGCACCTTTATCATCTGTAAGTCCAATGTC-GTAGGCCT
* * ** **
671414 TAAATCAGCACACTAGTAACCTTTATC-T-T-TAAGTCCAACATCGGT-GGCCT
1 TGAATCAGCACA-TTGGCACCTTTATCATCTGTAAGTCCAATGTC-GTAGGCCT
* * ** * *
671464 TGAATCAGCACATTGGCACCCTTGTTGTCTTTAAGTCCAATGTCGTTA-GCCC
1 TGAATCAGCACATTGGCACCTTTATCATCTGTAAGTCCAATGTCG-TAGGCCT
* * ** * * * *
671516 TAAATCAGTACAACGGTAACCTTTATCA--T-TAGGTCCAAATATCGTTGGCCT
1 TGAATCAGCACATTGG-CACCTTTATCATCTGTAAGTCC-AATGTCGTAGGCCT
* *
671567 TGAATCAGCACATTGGCACCTTTATCATCTGTAAGTCCAATGTTGCTA-GCCA
1 TGAATCAGCACATTGGCACCTTTATCATCTGTAAGTCCAATGTCG-TAGGCCT
* * *
671619 TGAATCAGCATATTGGCACCTTTATCATCAT-TAAGTCTAGTGTCGTAGGCCT
1 TGAATCAGCACATTGGCACCTTTATCATC-TGTAAGTCCAATGTCGTAGGCCT
* *
671671 TGAATCTGTACATTGGCA
1 TGAATCAGCACATTGGCA
671689 TATTACATGA
Statistics
Matches: 276, Mismatches: 80, Indels: 42
0.69 0.20 0.11
Matches are distributed among these distances:
49 11 0.04
50 77 0.28
51 29 0.11
52 134 0.49
53 25 0.09
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (52 bp):
TGAATCAGCACATTGGCACCTTTATCATCTGTAAGTCCAATGTCGTAGGCCT
Found at i:672319 original size:20 final size:21
Alignment explanation
Indices: 672282--672327 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
672272 TTTGATAATT
* *
672282 TGTACCAATACAATAAGTGAC
1 TGTATCAATACAATAAGTGAA
672303 TGTATCAATAC-ATAAGTGAA
1 TGTATCAATACAATAAGTGAA
672323 TGTAT
1 TGTAT
672328 AGATACATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCAATACAATAAGTGAA
Found at i:683696 original size:20 final size:19
Alignment explanation
Indices: 683673--683728 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
683663 AGTCAAAAGT
683673 AAAAACACAACAAAAAAAAC
1 AAAAACACAA-AAAAAAAAC
*
683693 AAAAACA-AAAAAAAAACC
1 AAAAACACAAAAAAAAAAC
*
683711 AAACACACAGAAAAAAAA
1 AAAAACACA-AAAAAAAA
683729 GTACAAAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 14 0.44
19 3 0.09
20 15 0.47
ACGTcount: A:0.80, C:0.18, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAACACAAAAAAAAAAC
Found at i:683700 original size:18 final size:18
Alignment explanation
Indices: 683674--683727 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
683664 GTCAAAAGTA
683674 AAAACACAACAAAAAAAAC
1 AAAA-ACAACAAAAAAAAC
683693 AAAAACAA-AAAAAAAAC
1 AAAAACAACAAAAAAAAC
*
683710 -CAAACACACAGAAAAAAA
1 AAAAACA-ACA-AAAAAAA
683728 AGTACAAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 5 0.16
17 10 0.32
18 5 0.16
19 11 0.35
ACGTcount: A:0.80, C:0.19, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAACAACAAAAAAAAC
Found at i:685058 original size:13 final size:13
Alignment explanation
Indices: 685040--685065 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
685030 CAATTTTTTG
685040 TGTATCGATACAT
1 TGTATCGATACAT
685053 TGTATCGATACAT
1 TGTATCGATACAT
685066 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:685077 original size:32 final size:33
Alignment explanation
Indices: 685020--685083 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
685010 TACAAGCCAA
**
685020 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
685053 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
685084 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:685517 original size:25 final size:27
Alignment explanation
Indices: 685489--685538 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
685479 TTGTTGGAAA
*
685489 CAAACCAT-T-ATCTTTCTTGTCAAAT
1 CAAACCATATCATCTTTATTGTCAAAT
685514 CAAACCATATCATCTTTATTGTCAA
1 CAAACCATATCATCTTTATTGTCAA
685539 GCAAGCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.36
26 1 0.05
27 13 0.59
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (27 bp):
CAAACCATATCATCTTTATTGTCAAAT
Found at i:686221 original size:30 final size:30
Alignment explanation
Indices: 686186--686523 Score: 322
Period size: 30 Copynumber: 11.0 Consensus size: 30
686176 TCTTCAAATC
*
686186 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
1 TCTCTTCTCTAAGTCCACGACTCAGTGGCA
*
686216 TCTCTTTTCTAAGTCCACGACTCAGTGGCA
1 TCTCTTCTCTAAGTCCACGACTCAGTGGCA
* * * * *
686246 TCCTTTTCTCCAAAGTCCACAATTTAGTGGCA
1 T-CTCTTCT-CTAAGTCCACGACTCAGTGGCA
* * * *
686278 TCTTTTCTTTAAATTCCACAACTCAGTGGCA
1 TCTCTTCTCT-AAGTCCACGACTCAGTGGCA
* *
686309 TCTCTTTTCTAAGTTCACGACTCAGTGGCA
1 TCTCTTCTCTAAGTCCACGACTCAGTGGCA
* *
686339 TC-CATGTCTTCAAAGTCCACAACTCAGTGGCA
1 TCTC-T-TC-TCTAAGTCCACGACTCAGTGGCA
* * * *
686371 TCCCTTTTCTAACTCCACGACTTAGTGGCA
1 TCTCTTCTCTAAGTCCACGACTCAGTGGCA
*
686401 TCTTTTCTTCTAAGTCCACGACTCAGTGGCA
1 TCTCTTC-TCTAAGTCCACGACTCAGTGGCA
* * * *
686432 TCCCTTTTCTAACTCCACGACTTAGTGGCA
1 TCTCTTCTCTAAGTCCACGACTCAGTGGCA
*
686462 TCTTTTCTTCTAAGTCCACGACTCAGTGGCA
1 TCTCTTC-TCTAAGTCCACGACTCAGTGGCA
* *
686493 TCT-TGTCCCAAAGTCCACGACT-ATGTGGCA
1 TCTCT-TCTCTAAGTCCACGACTCA-GTGGCA
686523 T
1 T
686524 TTTTTTCTTT
Statistics
Matches: 252, Mismatches: 45, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
29 2 0.01
30 118 0.47
31 89 0.35
32 42 0.17
33 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (30 bp):
TCTCTTCTCTAAGTCCACGACTCAGTGGCA
Found at i:686296 original size:31 final size:30
Alignment explanation
Indices: 686196--686903 Score: 290
Period size: 33 Copynumber: 22.7 Consensus size: 30
686186 TCTCTTCTCA
*
686196 AAGTCCACGACTCAGTGGCATCTCTTT-TCT
1 AAGTCCACGACTCAGTGGCATCT-TTTCTTT
**
686226 AAGTCCACGACTCAGTGGCATCCTTTTCTCCA
1 AAGTCCACGACTCAGTGGCAT-CTTTTCT-TT
* * *
686258 AAGTCCACAATTTAGTGGCATCTTTTCTTT
1 AAGTCCACGACTCAGTGGCATCTTTTCTTT
* * *
686288 AAATTCCACAACTCAGTGGCATCTCTTT-TCT
1 -AAGTCCACGACTCAGTGGCATCT-TTTCTTT
* * * *
686319 AAGTTCACGACTCAGTGGCATCCATGTCTTCA
1 AAGTCCACGACTCAGTGGCAT-CTTTTCTT-T
*
686351 AAGTCCACAACTCAGTGGCATCCCTTTTC--T
1 AAGTCCACGACTCAGTGGCAT--CTTTTCTTT
* *
686381 AACTCCACGACTTAGTGGCATCTTTTCTTCT
1 AAGTCCACGACTCAGTGGCATCTTTTCTT-T
686412 AAGTCCACGACTCAGTGGCATCCCTTTTC--T
1 AAGTCCACGACTCAGTGGCAT--CTTTTCTTT
* *
686442 AACTCCACGACTTAGTGGCATCTTTTCTTCT
1 AAGTCCACGACTCAGTGGCATCTTTTCTT-T
* ***
686473 AAGTCCACGACTCAGTGGCATCTTGTCCCA
1 AAGTCCACGACTCAGTGGCATCTTTTCTTT
*
686503 AAGTCCACGACT-ATGTGGCATTTTTTTCTTTT
1 AAGTCCACGACTCA-GTGGCA-TCTTTTC-TTT
* * **
686535 CAAAGTCCACAACTCTGTGGCA-C-CCT-TTT
1 --AAGTCCACGACTCAGTGGCATCTTTTCTTT
* *
686564 AAGTCCACAACTTC-GTGGCACCTTTTTCATTTT
1 AAGTCCACGAC-TCAGTGGCATC-TTTTC--TTT
* * * *
686597 AAAGCCCACAACTCTGTGGCACTTTTTTTCCTTTT
1 -AAGTCCACGACTCAGTGGCA--TCTTTT-C-TTT
* * * **
686632 AAGTCTACAACTTC-GTGGC-GC-CCT-TTT
1 AAGTCCACGAC-TCAGTGGCATCTTTTCTTT
* *
686659 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
1 AAGTCCACGACTCAGTGGCATC-TTTT-C-TTT
* * *
686692 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACGACTCAGTGGCATCTT-TT-C-TTT
* * *
686725 AAGCCCACAACTCCGTGGCACTCATTTTCCTTTT
1 AAGTCCACGACTCAGTGGCA-TC-TTTT-C-TTT
* **
686759 AAGTCCACAACTTCA-TGGCA-C-CCT-TTT
1 AAGTCCACGAC-TCAGTGGCATCTTTTCTTT
*
686786 AAGTCCACAACTCCA-TGGCATCTTTTTCCTTTT
1 AAGTCCACGACT-CAGTGGCATC-TTTT-C-TTT
** *
686819 AAGTCCATAACTCCA-TGGCACCTTGTTCCTTTT
1 AAGTCCACGACT-CAGTGGCATCTT-TT-C-TTT
* * * *
686852 AAGTTCACAACTTC-GTGGCACCTTTTTTTTTT
1 AAGTCCACGAC-TCAGTGGCA--TCTTTTCTTT
*
686884 AAGTCCACGACTCTGTGGCA
1 AAGTCCACGACTCAGTGGCA
686904 CCCTTTTCCC
Statistics
Matches: 540, Mismatches: 78, Indels: 118
0.73 0.11 0.16
Matches are distributed among these distances:
26 3 0.01
27 56 0.10
28 17 0.03
29 4 0.01
30 105 0.19
31 87 0.16
32 64 0.12
33 113 0.21
34 74 0.14
35 16 0.03
36 1 0.00
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (30 bp):
AAGTCCACGACTCAGTGGCATCTTTTCTTT
Found at i:686331 original size:93 final size:91
Alignment explanation
Indices: 686199--686556 Score: 388
Period size: 93 Copynumber: 3.9 Consensus size: 91
686189 CTTCTCAAAG
686199 TCCACGACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTCCAAAGTCC
1 TCCACGACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCT-CAAAGTCC
* *
686264 ACAATTTAGTGGCATCTTTTCTTTAAAT
65 ACAACTTAGTGGCATCTTTTCTTT-AAC
* * * *
686292 TCCACAACTCAGTGGCATCTCTTTTCTAAGTTCACGACTCAGTGGCATCCATGTCTTCAAAGTCC
1 TCCACGACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTC-TCAAAGTCC
*
686357 ACAACTCAGTGGCATCCCTTTTC--TAAC
65 ACAACTTAGTGGCAT--CTTTTCTTTAAC
* * *
686384 TCCACGACTTAGTGGCATCTTTTCTTCTAAGTCCACGACTCAGTGGCATCCCTTTTCT--AACTC
1 TCCACGACTCAGTGGCATCTCTT-TTCTAAGTCCACGACTCAGTGGCAT-CCTTTTCTCAAAGTC
* *
686447 CACGACTTAGTGGCATCTTTTCTTCTAAG
64 CACAACTTAGTGGCATCTTTTCTT-TAAC
** * **
686476 TCCACGACTCAGTGGCATCT-TGTCCCAAAGTCCACGACT-ATGTGGCATTTTTTTCTTTTCAAA
1 TCCACGACTCAGTGGCATCTCT-TTTCTAAGTCCACGACTCA-GTGGCATCCTTTTC---TCAAA
686539 GTCCACAACTCT-GTGGCA
61 GTCCACAACT-TAGTGGCA
686557 CCCTTTTAAG
Statistics
Matches: 224, Mismatches: 25, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
89 6 0.03
90 6 0.03
91 39 0.17
92 45 0.20
93 99 0.44
94 6 0.03
95 22 0.10
96 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (91 bp):
TCCACGACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTCAAAGTCCA
CAACTTAGTGGCATCTTTTCTTTAAC
Found at i:686404 original size:123 final size:122
Alignment explanation
Indices: 686186--686494 Score: 401
Period size: 123 Copynumber: 2.5 Consensus size: 122
686176 TCTTCAAATC
* *
686186 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTT-TTCTAAGTCCACGACTCAGTGGCAT-CC
1 TCTCTTTTCTAAGTCCACGACTCAGTGGCATC-CTTCTTCTAAGTCCACGACTCAGTGGCATCCC
* * *
686249 TTTTCTCCAAAGTCCACAATTTAGTGGCATCTTTTCTT-TAAATTCCACAACTCAGTGGCA
65 TTTTCT-C-AACTCCACAACTTAGTGGCATCTTTTCTTCT-AAGTCCACAACTCAGTGGCA
* * *
686309 TCTCTTTTCTAAGTTCACGACTCAGTGGCATCCATGTCTTCAAAGTCCACAACTCAGTGGCATCC
1 TCTCTTTTCTAAGTCCACGACTCAGTGGCATCC-T-TCTTCTAAGTCCACGACTCAGTGGCATCC
* *
686374 CTTTTCT-AACTCCACGACTTAGTGGCATCTTTTCTTCTAAGTCCACGACTCAGTGGCA
64 CTTTTCTCAACTCCACAACTTAGTGGCATCTTTTCTTCTAAGTCCACAACTCAGTGGCA
* * * *
686432 TCCCTTTTCTAACTCCACGACTTAGTGGCATCTTTTCTTCTAAGTCCACGACTCAGTGGCATC
1 TCTCTTTTCTAAGTCCACGACTCAGTGGCATC-CTTCTTCTAAGTCCACGACTCAGTGGCATC
686495 TTGTCCCAAA
Statistics
Matches: 163, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
122 27 0.17
123 103 0.63
124 2 0.01
125 23 0.14
126 8 0.05
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (122 bp):
TCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTCTTCTAAGTCCACGACTCAGTGGCATCCCT
TTTCTCAACTCCACAACTTAGTGGCATCTTTTCTTCTAAGTCCACAACTCAGTGGCA
Done.