Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 116 of 235
Found at i:39621702 original size:30 final size:30
Alignment explanation
Indices: 39621668--39621728 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39621658 TCCTTAACTC
39621668 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
39621698 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
39621728 A
1 A
39621729 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:39623995 original size:5 final size:5
Alignment explanation
Indices: 39623985--39624039 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
39623975 TAAGCATAAT
39623985 AAATA AAATA AAATA AAATAA AAATAA AAATAA AAATA AAA-A TAAAT-
1 AAATA AAATA AAATA AAAT-A AAAT-A AAAT-A AAATA AAATA -AAATA
39624032 AAATA AAA
1 AAATA AAA
39624040 ATACAAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
4 5 0.11
5 24 0.52
6 17 0.37
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:39624010 original size:6 final size:6
Alignment explanation
Indices: 39623980--39624048 Score: 81
Period size: 6 Copynumber: 11.5 Consensus size: 6
39623970 ATTAATAAGC
39623980 ATAATAA AT-AAA AT-AAA AT-AAA ATAAAA ATAAAA ATAAAA ATAAAA
1 ATAA-AA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
*
39624026 ATAAATAA ATAAAA ATACAA ATA
1 AT-AA-AA ATAAAA ATAAAA ATA
39624049 TTAAGGGCCA
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
5 14 0.24
6 34 0.59
7 6 0.10
8 4 0.07
ACGTcount: A:0.78, C:0.01, G:0.00, T:0.20
Consensus pattern (6 bp):
ATAAAA
Found at i:39631036 original size:21 final size:20
Alignment explanation
Indices: 39631006--39631044 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39630996 TAGAAATATT
39631006 AAATTAAGAAATAAGCATACA
1 AAATTAAG-AATAAGCATACA
*
39631027 AAATTGAGAATAAGCATA
1 AAATTAAGAATAAGCATA
39631045 AAGTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (20 bp):
AAATTAAGAATAAGCATACA
Found at i:39643538 original size:21 final size:20
Alignment explanation
Indices: 39643514--39643552 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39643504 ACTCATCATG
*
39643514 TTATGTTATGTTATTTATTGT
1 TTATGTTAT-TTATATATTGT
39643535 TTATGTTATTTATATATT
1 TTATGTTATTTATATATT
39643553 ACTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (20 bp):
TTATGTTATTTATATATTGT
Found at i:39663160 original size:22 final size:22
Alignment explanation
Indices: 39663091--39663161 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 22
39663081 TATGTATATA
*
39663091 ATAAAATAACCTAATATAAATAAT
1 ATAAAAT-A-CTAAAATAAATAAT
* **
39663115 AAATAAAAAAC-AAAATGATTTAAT
1 --ATAAAATACTAAAAT-AAATAAT
39663139 ATAAAATACTAAAATAAATAAT
1 ATAAAATACTAAAATAAATAAT
39663161 A
1 A
39663162 AATAAATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
22 14 0.39
23 9 0.25
24 6 0.17
25 1 0.03
26 6 0.17
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (22 bp):
ATAAAATACTAAAATAAATAAT
Found at i:39670155 original size:17 final size:17
Alignment explanation
Indices: 39670128--39670174 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
39670118 GTTGACCTCT
*
39670128 AAAAGACAAAAAATAAAAA
1 AAAAGA-AAAAAA-AAAGA
*
39670147 AAAAGAAAAAAAAAAGG
1 AAAAGAAAAAAAAAAGA
39670164 AAAAGAAAAAA
1 AAAAGAAAAAA
39670175 GGCTGAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 14 0.54
18 6 0.23
19 6 0.23
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAGA
Found at i:39670157 original size:12 final size:12
Alignment explanation
Indices: 39670142--39670175 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39670132 GACAAAAAAT
39670142 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
39670154 AAAAAAAAGGAA
1 AAAAAAAAAGAA
*
39670166 AAGAAAAAAG
1 AAAAAAAAAG
39670176 GCTGAAGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:39670175 original size:13 final size:12
Alignment explanation
Indices: 39670142--39670176 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
39670132 GACAAAAAAT
39670142 AAAAAAAAA-GA
1 AAAAAAAAAGGA
39670153 AAAAAAAAAGGA
1 AAAAAAAAAGGA
39670165 AAAGAAAAAAGG
1 AAA-AAAAAAGG
39670177 CTGAAGATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.41
12 5 0.23
13 8 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGGA
Found at i:39677289 original size:82 final size:81
Alignment explanation
Indices: 39677136--39677293 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 81
39677126 CTCTTGCCAC
* * * * *
39677136 CTCAGAGAGATAAGGTTGGTGGTAAAATCTGTTTCATTGCCAATACATAGAAATAAGATTCACTA
1 CTCAGAGAGATAAGGTTAGTGGTAAAATCTGTTCCATTGCCAATACATAGAAACAACATTCACCA
*
39677201 TTTTCGATCTGATCCA
66 TCTTCGATCTGATCCA
* * * *
39677217 CTCAGAGAGATAAGGTTAGTGGCTAAAATCTGTTCCATTGCCAATACGTGGAGACAACATTCGCC
1 CTCAGAGAGATAAGGTTAGTGG-TAAAATCTGTTCCATTGCCAATACATAGAAACAACATTCACC
39677282 ATCTTCGATCTG
65 ATCTTCGATCTG
39677294 TTCCGCTACT
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 21 0.32
82 45 0.68
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (81 bp):
CTCAGAGAGATAAGGTTAGTGGTAAAATCTGTTCCATTGCCAATACATAGAAACAACATTCACCA
TCTTCGATCTGATCCA
Found at i:39677528 original size:176 final size:175
Alignment explanation
Indices: 39677217--39677861 Score: 690
Period size: 176 Copynumber: 3.6 Consensus size: 175
39677207 ATCTGATCCA
* * * * * * * *
39677217 CTCAGAGAGATAAGGTTAGTGGCTAAAATCTGTTCCATTGCCAATACGTGGAGACAACATTCGCC
1 CTCAGAGAGATAAGGCTGGTGG-TAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACC
* * * * * * **
39677282 ATCTTCGATCTGTTCCGCTACTGCTT-AGGGAAATAAGATCTTCAATCTTCAGTGTGCTTTCTCA
65 ATCTTCAATCTGCTCCACTACAG-TTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTCTTG
39677346 CTACCTCAGAAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTAC
129 CTACCTCAGAAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTAC
* * *
39677393 CTCAGAGAGATAAGGCTTGG-GGCTTAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGC
1 CTCAGAGAGATAAGGC-TGGTGG-TAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
* * *
39677457 C-TCTTTCAATCTGCTCCACTACTGTTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTT
64 CATC-TTCAATCTGCTCCACTACAGTTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTCTT
* *
39677521 GCTACCTCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTAC
128 GCTACCTCAGAAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTAC
* * * * *
39677569 CTCAGAGAGATGAGGCTGGTGGTAAAACCTGCTCCATTGTCGATGCATAGAGATAAGATTCACCA
1 CTCAGAGAGATAAGGCTGGTGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCA
* * * ** * *
39677634 TCTGCGAAGCTTTACTCCGTTGCAATCTCAGGGAGAT-AGAATCTTCAAT-TCTCAGTCTGCTTT
66 TCTTC-AA--TCTGCTCCACTACAGT-TCAGGGAGATAAG-ATCTTCAATCT-TCAGTCTGCTTT
* * *
39677697 CTTGCTACATCA-AGAAGATAAGACTTACTCTTCAACCTGCTCTCTTGCTAC
125 CTTGCTACCTCAGA-AAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTAC
* * * * * *
39677748 CTCAGAGAGATGAGGCTGGTGGTAAAATCTGCTCCACTGCTGATACAAGGAGAAAAGATTTACCA
1 CTCAGAGAGATAAGGCTGGTGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCA
* * * *
39677813 TTTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTTCAATCTT
66 TCTTCAATCTGCTCCACTAC-AGTTCAGGGAGATAAGATCTTCAATCTT
39677862 TACCAATGTC
Statistics
Matches: 396, Mismatches: 58, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
175 44 0.11
176 198 0.50
177 7 0.02
178 13 0.03
179 134 0.34
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (175 bp):
CTCAGAGAGATAAGGCTGGTGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCA
TCTTCAATCTGCTCCACTACAGTTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTCTTGCT
ACCTCAGAAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTAC
Found at i:39677558 original size:43 final size:45
Alignment explanation
Indices: 39677488--39677573 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 45
39677478 CTGTTTAGGG
**
39677488 AGATAAGATCTTCAATCTTCAGTCTGCT-TCCTTGCTACCTCAGGA
1 AGATAAGATCTTCAATCTTCAACCTGCTCT-CTTGCTACCTCAGGA
*
39677533 AGATAAGA-C-TCATTCTTCAACCTGCTCTCTTGCTACCTCAG
1 AGATAAGATCTTCAATCTTCAACCTGCTCTCTTGCTACCTCAG
39677574 AGAGATGAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 27 0.73
44 2 0.05
45 8 0.22
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (45 bp):
AGATAAGATCTTCAATCTTCAACCTGCTCTCTTGCTACCTCAGGA
Found at i:39677719 original size:179 final size:175
Alignment explanation
Indices: 39677308--39677861 Score: 618
Period size: 179 Copynumber: 3.1 Consensus size: 175
39677298 GCTACTGCTT
* * **
39677308 AGGGAAATAAGATCTTCAATCTTCAGTGTGCTTTCTCACTACCTC-AGAAAGATAAGACTCAATC
1 AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTCTTGCTACCTCAAG-AAGATAAGACTCAATC
* *
39677372 TTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGG-GGCTTAAATCTGCTCCATTACCG
65 TTCAACCTGCTCTCTTGCTACCTCAGAGAGATGAGGC-TGGTGG-TAAAATCTGCTCCATTACCG
* * * * ** *
39677436 ATACATGGAGATAAGATTCGCCTCTTTCAATCTGCTCCACTACTGTTT
128 ATACATAGAGATAAGATTCACCTCTTGCAATCTACTCCACTACAATTC
* * *
39677484 AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCT
1 AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTCTTGCTACCTCAAGAAGATAAGACTCAATCT
* ** *
39677549 TCAACCTGCTCTCTTGCTACCTCAGAGAGATGAGGCTGGTGGTAAAACCTGCTCCATTGTCGATG
66 TCAACCTGCTCTCTTGCTACCTCAGAGAGATGAGGCTGGTGGTAAAATCTGCTCCATTACCGATA
* ** *
39677614 CATAGAGATAAGATTCACCATC-TGCGAAGCTTTACTCCGTTGCAATCTC
131 CATAGAGATAAGATTCACC-TCTTGC-AA--TCTACTCCACTACAAT-TC
* * *
39677663 AGGGAGAT-AGAATCTTCAAT-TCTCAGTCTGCTTTCTTGCTACATCAAGAAGATAAGACTTACT
1 AGGGAGATAAG-ATCTTCAATCT-TCAGTCTGCTTTCTTGCTACCTCAAGAAGATAAGACTCAAT
* * *
39677726 CTTCAACCTGCTCTCTTGCTACCTCAGAGAGATGAGGCTGGTGGTAAAATCTGCTCCACTGCTGA
64 CTTCAACCTGCTCTCTTGCTACCTCAGAGAGATGAGGCTGGTGGTAAAATCTGCTCCATTACCGA
* * * * * *
39677791 TACA-AGGAGAAAAGATTTACCAT-TTTCGATCTGCTCCACTGCAACTTC
129 TACATA-GAGATAAGATTCACC-TCTTGCAATCTACTCCACTACAA-TTC
39677839 AGGGAGATAAGATCTTCAATCTT
1 AGGGAGATAAGATCTTCAATCTT
39677862 TACCAATGTC
Statistics
Matches: 322, Mismatches: 42, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
175 40 0.12
176 128 0.40
177 5 0.02
178 14 0.04
179 135 0.42
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (175 bp):
AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTTCTTGCTACCTCAAGAAGATAAGACTCAATCT
TCAACCTGCTCTCTTGCTACCTCAGAGAGATGAGGCTGGTGGTAAAATCTGCTCCATTACCGATA
CATAGAGATAAGATTCACCTCTTGCAATCTACTCCACTACAATTC
Found at i:39688303 original size:17 final size:17
Alignment explanation
Indices: 39688281--39688313 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39688271 TGATATGTAC
39688281 TAAAAT-TATTAAAAAAT
1 TAAAATATA-TAAAAAAT
39688298 TAAAATATATAAAAAA
1 TAAAATATATAAAAAA
39688314 AATCAGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATATATAAAAAAT
Found at i:39688314 original size:18 final size:17
Alignment explanation
Indices: 39688281--39688314 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39688271 TGATATGTAC
*
39688281 TAAAATTATTAAAAAAT
1 TAAAATTATAAAAAAAT
39688298 TAAAATATATAAAAAAA
1 TAAAAT-TATAAAAAAA
39688315 ATCAGGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATTATAAAAAAAT
Found at i:39688387 original size:19 final size:19
Alignment explanation
Indices: 39688363--39688447 Score: 140
Period size: 19 Copynumber: 4.6 Consensus size: 19
39688353 GAAAACCAAT
39688363 ATTGCATATCATATCTAAG
1 ATTGCATATCATATCTAAG
39688382 ATTGCA-ATCATATCTAAG
1 ATTGCATATCATATCTAAG
39688400 ATTG--TATCATATCTAAG
1 ATTGCATATCATATCTAAG
*
39688417 AGTGCATATCATATCTAAG
1 ATTGCATATCATATCTAAG
39688436 ATTGCATATCAT
1 ATTGCATATCAT
39688448 TGAATATTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
17 15 0.25
18 16 0.26
19 30 0.49
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (19 bp):
ATTGCATATCATATCTAAG
Found at i:39688415 original size:35 final size:36
Alignment explanation
Indices: 39688369--39688439 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
39688359 CAATATTGCA
*
39688369 TATCATATCTAAGATTGCA-ATCATATCTAAGATTG
1 TATCATATCTAAGAGTGCATATCATATCTAAGATTG
39688404 TATCATATCTAAGAGTGCATATCATATCTAAGATTG
1 TATCATATCTAAGAGTGCATATCATATCTAAGATTG
39688440 CATATCATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 18 0.53
36 16 0.47
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (36 bp):
TATCATATCTAAGAGTGCATATCATATCTAAGATTG
Found at i:39691353 original size:39 final size:40
Alignment explanation
Indices: 39691258--39691519 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
39691248 TTGAATGATG
*
39691258 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
39691296 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
39691337 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
39691376 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
39691415 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
39691454 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
39691493 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
39691520 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:39699369 original size:39 final size:40
Alignment explanation
Indices: 39699274--39699496 Score: 273
Period size: 39 Copynumber: 5.7 Consensus size: 40
39699264 TTGAATGATG
*
39699274 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
39699312 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
39699353 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
39699392 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
39699431 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
39699470 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
39699497 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
39 93 0.56
40 61 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:39699460 original size:79 final size:81
Alignment explanation
Indices: 39699274--39699496 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
39699264 TTGAATGATG
* * *
39699274 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATATCCGGGCTAAGACCCGAAGGCA
*
39699335 TTTGTGCGAGATACTAAT
64 TTTGTGCGAGATACTAAA
39699353 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
*
39699415 TGTGCGAGTTACTAAA
66 TGTGCGAGATACTAAA
* * * * *
39699431 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
39699495 TG
66 TG
39699497 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:39699518 original size:79 final size:79
Alignment explanation
Indices: 39699274--39699529 Score: 224
Period size: 79 Copynumber: 3.3 Consensus size: 79
39699264 TTGAATGATG
* * * *
39699274 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
39699335 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
39699353 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
39699417 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
39699431 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATT
*
39699495 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
39699511 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
39699530 TACGTGATTT
Statistics
Matches: 153, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
77 1 0.01
78 45 0.29
79 70 0.46
80 36 0.24
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:39704103 original size:14 final size:14
Alignment explanation
Indices: 39704084--39704115 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39704074 TCAAATCACC
39704084 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
39704098 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
39704112 GGGC
1 GGGC
39704116 GAAATGACCT
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:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:39709229 original size:14 final size:14
Alignment explanation
Indices: 39709210--39709241 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39709200 TCAAATCACC
39709210 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
39709224 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
39709238 GGGC
1 GGGC
39709242 TAAATGACCT
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:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:39711544 original size:12 final size:12
Alignment explanation
Indices: 39711521--39711562 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
39711511 GATGACGTTA
39711521 AAATG-ATAAAT
1 AAATGAATAAAT
*
39711532 AAATGAATGAAT
1 AAATGAATAAAT
*
39711544 AAATAAATAAAT
1 AAATGAATAAAT
*
39711556 AGATGAA
1 AAATGAA
39711563 GAAACATAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (12 bp):
AAATGAATAAAT
Found at i:39711547 original size:16 final size:15
Alignment explanation
Indices: 39711522--39711551 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39711512 ATGACGTTAA
39711522 AATGATAAATAAATG
1 AATGATAAATAAATG
39711537 AATGAATAAATAAAT
1 AATG-ATAAATAAAT
39711552 AAATAGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (15 bp):
AATGATAAATAAATG
Found at i:39720767 original size:44 final size:44
Alignment explanation
Indices: 39720719--39720867 Score: 109
Period size: 44 Copynumber: 3.4 Consensus size: 44
39720709 GTATTGGCAA
* * * * *
39720719 TGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAAGTTGCAG
1 TGGAGCAGACTCAAGACACAAGCCTTATCTCCCTGAAGATGCAG
* * *
39720763 TGGAGCAGGCTCAAGATACAAGTCTTATCTCCCTGAAGATGCAG
1 TGGAGCAGACTCAAGACACAAGCCTTATCTCCCTGAAGATGCAG
* * * * * * * * * * *
39720807 CGGAGCAAAATGAAAATGACAGGTCTTGTCTCCCTGAAGTTGTAG
1 TGGAGCAGACTCAAGA-CACAAGCCTTATCTCCCTGAAGATGCAG
*
39720852 TGGAGCAGACTGAAGA
1 TGGAGCAGACTCAAGA
39720868 TAGCGAATCT
Statistics
Matches: 81, Mismatches: 23, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
44 46 0.57
45 35 0.43
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (44 bp):
TGGAGCAGACTCAAGACACAAGCCTTATCTCCCTGAAGATGCAG
Found at i:39720823 original size:177 final size:178
Alignment explanation
Indices: 39720471--39720880 Score: 434
Period size: 177 Copynumber: 2.3 Consensus size: 178
39720461 GGTGAATTCG
* * * ** * * *
39720471 CAGATCTTATCTCCATGAGGTAGCAGTGGAGCAGGTTGAAGATGGTGAATCTTATCTTTCCGAGG
1 CAGATCTTATCTCCCTGAAGTAGTAGTGGAGCAGACTGAAGATAGCGAATCTTATC--TCC-ATG
** * * *
39720536 TA---GCAGGGGAACAGATTTTAGCCACCAGCCTTATCTCCCTGAAGTTACTGTAGAGCAGGCTC
63 TATTGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTTACAGTAGAGCAGGCTC
* * * * * * * * * *
39720598 AATATATAAGTCTTGTTTTCCTAAAGTTGCAGTAGAGCAGACTGAAAATTA
128 AAGATACAAGTCTTATCTCCCTAAAGATGCAGCAGAGCAAAATGAAAATGA
* * * *
39720649 TAGATCTTATCTCCCT-AAGTAGTAGTGGAGTAGA-TCGAATATGGCGAATCTTATCTCCATGTA
1 CAGATCTTATCTCCCTGAAGTAGTAGTGGAGCAGACT-GAAGATAGCGAATCTTATCTCCATGTA
* * *
39720712 TTGGCAATGGAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTCAA
65 TTGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTTACAGTAGAGCAGGCTCAA
* *
39720777 GATACAAGTCTTATCTCCCTGAAGATGCAGCGGAGCAAAATGAAAATGA
130 GATACAAGTCTTATCTCCCTAAAGATGCAGCAGAGCAAAATGAAAATGA
* * *
39720826 CAGGTCTTGTCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCGAATCTTAT
1 CAGATCTTATCTCCCTGAAGTAGTAGTGGAGCAGACTGAAGATAGCGAATCTTAT
39720881 TTCACTGAAG
Statistics
Matches: 190, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
174 4 0.02
175 3 0.02
176 1 0.01
177 135 0.71
178 46 0.24
179 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (178 bp):
CAGATCTTATCTCCCTGAAGTAGTAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCATGTAT
TGGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTTACAGTAGAGCAGGCTCAAG
ATACAAGTCTTATCTCCCTAAAGATGCAGCAGAGCAAAATGAAAATGA
Found at i:39720857 original size:45 final size:44
Alignment explanation
Indices: 39720742--39720858 Score: 135
Period size: 44 Copynumber: 2.6 Consensus size: 44
39720732 AGCCACTAGC
*** *
39720742 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTCAAGATACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAAATCAAAATACAAGT
* * * *
39720786 CTTATCTCCCTGAAGATGCAGCGGAGCAAAATGAAAATGACAGGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAAATCAAAAT-ACAAGT
* *
39720831 CTTGTCTCCCTGAAGTTGTAGTGGAGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCA
39720859 GACTGAAGAT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
44 31 0.52
45 29 0.48
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAAAATCAAAATACAAGT
Found at i:39721121 original size:182 final size:181
Alignment explanation
Indices: 39720835--39721166 Score: 479
Period size: 182 Copynumber: 1.8 Consensus size: 181
39720825 ACAGGTCTTG
* * *
39720835 TCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCACTGAAGTTACAGTGG
1 TCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCACTGAAGATACAGTGC
* * * ** * *
39720900 AACAGATGAAGCTATAAATAAATAGATCTTATTTCTCTGAAGTTGTAGTAGAGTAGATCA-TAGC
66 AACAGATAAAGCTATAAATAAACAGATCATACCTCTCTGAAGTTGCAGTAGAGTAGATCATTACC
39720964 AAA-CCTTATCTCCATGAAGTAGCAGTGGAGTAGGCTGAAGTTAAAGTCCTA
131 AAATCC-TATCTCCATGAAGTAGCAGTGGAGTAGGCTGAAGTTAAAGTCCTA
* * * *
39721015 TCTCCCTGAAGTTGCAGTGGAGCAGACATGAAGTTAGTGAATCTTATTTCCCTGAAGATGCAGTG
1 TCTCCCTGAAGTTGCAGTGGAGCAGAC-TGAAGATAGCGAATCTTATTTCACTGAAGATACAGTG
*
39721080 CAACATATTAAAGCTATAAATAAACAGATCATACCTCTCTGAAGTTGCAGTAGAGTAGATCATTA
65 CAACAGA-TAAAGCTATAAATAAACAGATCATACCTCTCTGAAGTTGCAGTAGAGTAGATCATTA
*
39721145 CCAAATCCTATCTCCCTGAAGT
129 CCAAATCCTATCTCCATGAAGT
39721167 TACAGTTTGA
Statistics
Matches: 132, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
180 26 0.20
181 37 0.28
182 48 0.36
183 19 0.14
184 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (181 bp):
TCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCACTGAAGATACAGTGC
AACAGATAAAGCTATAAATAAACAGATCATACCTCTCTGAAGTTGCAGTAGAGTAGATCATTACC
AAATCCTATCTCCATGAAGTAGCAGTGGAGTAGGCTGAAGTTAAAGTCCTA
Found at i:39722156 original size:12 final size:12
Alignment explanation
Indices: 39722139--39722171 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39722129 TCCCCTATAA
*
39722139 AATAGTGAAAAT
1 AATAGTAAAAAT
39722151 AATAGTAAAAAT
1 AATAGTAAAAAT
39722163 AATAGTAAA
1 AATAGTAAA
39722172 GGGGAAGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (12 bp):
AATAGTAAAAAT
Found at i:39723091 original size:10 final size:10
Alignment explanation
Indices: 39723072--39723120 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
39723062 TGAAATTCTA
39723072 AAAGATAAAT
1 AAAGATAAAT
39723082 ACAA-ATAAAT
1 A-AAGATAAAT
39723092 AAAGATAAAT
1 AAAGATAAAT
*
39723102 AAAGATAAAG
1 AAAGATAAAT
39723112 AAA-ATAAAT
1 AAAGATAAAT
39723121 CCTAGAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 7 0.20
10 26 0.74
11 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.18
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:39723391 original size:14 final size:14
Alignment explanation
Indices: 39723372--39723403 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39723362 AGGTCATTTA
39723372 GCCCAACCAAACTG
1 GCCCAACCAAACTG
39723386 GCCCAACCAAACTG
1 GCCCAACCAAACTG
39723400 GCCC
1 GCCC
39723404 GGTGATTTGA
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:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:39723754 original size:155 final size:155
Alignment explanation
Indices: 39723509--39723871 Score: 726
Period size: 155 Copynumber: 2.3 Consensus size: 155
39723499 GACTTAACCC
39723509 GAATCAAGGTGGTCTTTTGTTCTGTTTTCCATTTCCTTTGCAAGTTTATTTTCCAAATTAGTAGG
1 GAATCAAGGTGGTCTTTTGTTCTGTTTTCCATTTCCTTTGCAAGTTTATTTTCCAAATTAGTAGG
39723574 ATCATACTCAAAATAAGCATGCAATTAGCACATAAAATATGTCGTTCTAGAGTATTATCAAAAAG
66 ATCATACTCAAAATAAGCATGCAATTAGCACATAAAATATGTCGTTCTAGAGTATTATCAAAAAG
39723639 ATAGGAATCGAATAGGAAAAAAAGG
131 ATAGGAATCGAATAGGAAAAAAAGG
39723664 GAATCAAGGTGGTCTTTTGTTCTGTTTTCCATTTCCTTTGCAAGTTTATTTTCCAAATTAGTAGG
1 GAATCAAGGTGGTCTTTTGTTCTGTTTTCCATTTCCTTTGCAAGTTTATTTTCCAAATTAGTAGG
39723729 ATCATACTCAAAATAAGCATGCAATTAGCACATAAAATATGTCGTTCTAGAGTATTATCAAAAAG
66 ATCATACTCAAAATAAGCATGCAATTAGCACATAAAATATGTCGTTCTAGAGTATTATCAAAAAG
39723794 ATAGGAATCGAATAGGAAAAAAAGG
131 ATAGGAATCGAATAGGAAAAAAAGG
39723819 GAATCAAGGTGGTCTTTTGTTCTGTTTTCCATTTCCTTTGCAAGTTTATTTTC
1 GAATCAAGGTGGTCTTTTGTTCTGTTTTCCATTTCCTTTGCAAGTTTATTTTC
39723872 GAATATAGCA
Statistics
Matches: 208, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 208 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (155 bp):
GAATCAAGGTGGTCTTTTGTTCTGTTTTCCATTTCCTTTGCAAGTTTATTTTCCAAATTAGTAGG
ATCATACTCAAAATAAGCATGCAATTAGCACATAAAATATGTCGTTCTAGAGTATTATCAAAAAG
ATAGGAATCGAATAGGAAAAAAAGG
Found at i:39724970 original size:2 final size:2
Alignment explanation
Indices: 39724965--39725001 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
39724955 TTTAATGTTT
* *
39724965 TA TA TA TA TA TA TA CA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39725002 TGTCCATTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39727572 original size:35 final size:37
Alignment explanation
Indices: 39727501--39727598 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
39727491 GTAATCTTCA
39727501 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
39727539 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
39727574 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
39727599 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:39727598 original size:17 final size:19
Alignment explanation
Indices: 39727501--39727591 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
39727491 GTAATCTTCA
39727501 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
39727520 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
39727539 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
39727556 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
39727574 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
39727592 AGATATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:39727617 original size:22 final size:22
Alignment explanation
Indices: 39727570--39727614 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
39727560 TTGCAATCTT
*
39727570 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
39727592 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
39727615 GATTTAATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:39727828 original size:18 final size:19
Alignment explanation
Indices: 39727788--39727829 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
39727778 TCCCGCTTAC
39727788 GTTCTTATTTTATACGGTTT
1 GTTCTTATTTTATAC-GTTT
*
39727808 GTTCTTATTTTATTC-TTT
1 GTTCTTATTTTATACGTTT
39727826 GTTC
1 GTTC
39727830 ATCTTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (19 bp):
GTTCTTATTTTATACGTTT
Found at i:39736554 original size:195 final size:195
Alignment explanation
Indices: 39736211--39736602 Score: 658
Period size: 195 Copynumber: 2.0 Consensus size: 195
39736201 TGTTTACACT
39736211 GAAGCAAATCCAAGATGATTTAACATCTCTGTATTGTCAGAGAACAAATCAAAGAAACAGATTTG
1 GAAGCAAATCCAAGATGATTTAACATCTCTGTATTGTCAGAGAACAAATCAAAGAAACAGATTTG
* * *
39736276 GCATCTCCATATTCAACGGAGAGCAGATCGAAGACATAATAGATCTAACCTTCGAATGTTTTCAC
66 GCATCTCCATATTCAACGGAGAGCAGATCGAAGACATAACAGATCTAACATTCGAATGTCTTCAC
* *
39736341 ATCGAAGTAGATCCAAGATGATTTGGCATCTTTGCGTTGACAAGGAGCAGATCGAAGACATAGCA
131 ATCGAAATAGATCCAAGATGATTTGGCATCCTTGCGTTGACAAGGAGCAGATCGAAGACATAGCA
* * * *
39736406 GAAGCAGATCTAAGATGATTTAACATCTCTGTATTGTTAGAGAACAAATCGAAGAAACAGATTTG
1 GAAGCAAATCCAAGATGATTTAACATCTCTGTATTGTCAGAGAACAAATCAAAGAAACAGATTTG
* *
39736471 GCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACATTCGAATGTCTTCAC
66 GCATCTCCATATTCAACGGAGAGCAGATCGAAGACATAACAGATCTAACATTCGAATGTCTTCAC
* * *
39736536 ATCGAAATAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAGTAGATCGAAGACATAGCA
131 ATCGAAATAGATCCAAGATGATTTGGCATCCTTGCGTTGACAAGGAGCAGATCGAAGACATAGCA
39736601 GA
1 GA
39736603 TTTGGCTTTC
Statistics
Matches: 183, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
195 183 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (195 bp):
GAAGCAAATCCAAGATGATTTAACATCTCTGTATTGTCAGAGAACAAATCAAAGAAACAGATTTG
GCATCTCCATATTCAACGGAGAGCAGATCGAAGACATAACAGATCTAACATTCGAATGTCTTCAC
ATCGAAATAGATCCAAGATGATTTGGCATCCTTGCGTTGACAAGGAGCAGATCGAAGACATAGCA
Found at i:39736815 original size:78 final size:77
Alignment explanation
Indices: 39736686--39736979 Score: 392
Period size: 78 Copynumber: 3.8 Consensus size: 77
39736676 GAAAAAACAA
** * * *
39736686 ATTTGGCATCTCCATATTCGACGGAGAGCAAATCGAAGACATAGCAGATCTGACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGAGGGA-AGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
*
39736751 CACATCCAAGATG
65 CAGATCCAAGATG
* *
39736764 ATTTGGCATCTCTGTATTAGATGGGAAGCAGATCGAAAACACAGCAGATCTGACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGA-GGGAAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
39736829 CAGATCCAAGATG
65 CAGATCCAAGATG
* * *
39736842 ATTTGGCATCTCTGTATTAGAAGGGGAGCAGATCGAAGACATAACAGGT-TGGACCTTCATTGAA
1 ATTTGGCATCTCTGTATTAG-AGGGAAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGAA
*
39736906 ACAGATCCAAGATG
64 GCAGATCCAAGATG
* * * *
39736920 ATTTGGCATCTTTGTATTAGACGGGGAGCAGATTGAAGACATAGCAGATCTAACCTTCAT
1 ATTTGGCATCTCTGTATTAGA-GGGAAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
39736980 GTGTTTACAT
Statistics
Matches: 192, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
77 2 0.01
78 185 0.96
79 5 0.03
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (77 bp):
ATTTGGCATCTCTGTATTAGAGGGAAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAGC
AGATCCAAGATG
Found at i:39737143 original size:89 final size:88
Alignment explanation
Indices: 39737011--39737177 Score: 253
Period size: 89 Copynumber: 1.9 Consensus size: 88
39737001 CAAGATGAAA
*
39737011 GATTTGGCATCTCTGTATTAGACGGGAGCAAATCGGAGATAACAGATTTGGCATCTCTGTATTAG
1 GATTTGGCATCTCTGTATTAGACGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTAG
*
39737076 ACGGGGAGCAGATTGAAGAAGCT
66 ACAGGGAGCAGATTGAAGAAGCT
** * * *
39737099 GATTTGGTGTCTCTGTATTAGATGGGGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTA
1 GATTTGGCATCTCTGTATTAGA-CGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTA
*
39737164 GATAGGGAGCAGAT
65 GACAGGGAGCAGAT
39737178 CAAAGATAGC
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 20 0.29
89 50 0.71
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (88 bp):
GATTTGGCATCTCTGTATTAGACGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATTAG
ACAGGGAGCAGATTGAAGAAGCT
Found at i:39737163 original size:45 final size:45
Alignment explanation
Indices: 39736996--39737191 Score: 236
Period size: 44 Copynumber: 4.4 Consensus size: 45
39736986 ACATCGAAGT
* *
39736996 AGATCCAAGATGAA-AGATTTGGCATCTCTGTATTAGA-CGGGAGC
1 AGATCGAAGAT-AACAGATTTGGCATCTCTGTATTAGATGGGGAGC
* * *
39737040 AAATCGGAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGC
1 AGATCGAAGATAACAGATTTGGCATCTCTGTATTAGATGGGGAGC
* * * **
39737085 AGATTGAAGA-AGCTGATTTGGTGTCTCTGTATTAGATGGGGAGC
1 AGATCGAAGATAACAGATTTGGCATCTCTGTATTAGATGGGGAGC
* *
39737129 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTAGATAGGGAGC
1 AGATCGAAGATAACAGATTTGGCATCTCTGTATTAGATGGGGAGC
* *
39737174 AGATCAAAGATAGCAGAT
1 AGATCGAAGATAACAGAT
39737192 ATCGCCTTCC
Statistics
Matches: 130, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
43 2 0.02
44 69 0.53
45 59 0.45
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (45 bp):
AGATCGAAGATAACAGATTTGGCATCTCTGTATTAGATGGGGAGC
Found at i:39737612 original size:35 final size:37
Alignment explanation
Indices: 39737541--39737638 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
39737531 GTAATCTTCA
39737541 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
39737579 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
39737614 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
39737639 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:39737638 original size:17 final size:19
Alignment explanation
Indices: 39737541--39737631 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
39737531 GTAATCTTCA
39737541 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
39737560 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
39737579 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
39737596 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
39737614 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
39737632 AGATATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:39737657 original size:22 final size:22
Alignment explanation
Indices: 39737541--39737654 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 22
39737531 GTAATCTTCA
39737541 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
39737560 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
39737579 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
39737596 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
39737614 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
39737636 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
39737655 GATTTAATTT
Statistics
Matches: 86, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
17 16 0.19
18 16 0.19
19 34 0.40
22 8 0.09
23 12 0.14
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:39737944 original size:18 final size:17
Alignment explanation
Indices: 39737921--39737955 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39737911 TGTTTCCCTG
*
39737921 ATTTTTTTATATATTTTA
1 ATTTTTTAATAT-TTTTA
39737939 ATTTTTTAATATTTTTA
1 ATTTTTTAATATTTTTA
39737956 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTAATATTTTTA
Found at i:39741835 original size:17 final size:16
Alignment explanation
Indices: 39741815--39741850 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39741805 TTGGTTGCAT
*
39741815 TTTATTTTTGTTTTTAG
1 TTTATTTTT-TTTCTAG
39741832 TTTATTTTTTTTCTAG
1 TTTATTTTTTTTCTAG
39741848 TTT
1 TTT
39741851 TTCTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTATTTTTTTTCTAG
Found at i:39751885 original size:17 final size:16
Alignment explanation
Indices: 39751865--39751900 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39751855 TTGGTTGCAT
*
39751865 TTTATTTTTGTTTTTAG
1 TTTATTTTT-TTTCTAG
39751882 TTTATTTTTTTTCTAG
1 TTTATTTTTTTTCTAG
39751898 TTT
1 TTT
39751901 TTCTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTATTTTTTTTCTAG
Found at i:39761748 original size:19 final size:20
Alignment explanation
Indices: 39761711--39761748 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
39761701 AGAGGGACAA
*
39761711 TATGATTAAATTATGATGTG
1 TATGATTAAATGATGATGTG
*
39761731 TATG-TTAAATGATTATGT
1 TATGATTAAATGATGATGT
39761749 AATGTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (20 bp):
TATGATTAAATGATGATGTG
Found at i:39763692 original size:25 final size:25
Alignment explanation
Indices: 39763664--39763716 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
39763654 ATAACTAGAG
39763664 AATGTGTACATAAAAGTAAAGTTAT
1 AATGTGTACATAAAAGTAAAGTTAT
39763689 AATGTGTACATAAAAGTAAAGTTAT
1 AATGTGTACATAAAAGTAAAGTTAT
39763714 AAT
1 AAT
39763717 ATTGATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (25 bp):
AATGTGTACATAAAAGTAAAGTTAT
Found at i:39765444 original size:38 final size:38
Alignment explanation
Indices: 39765398--39765510 Score: 219
Period size: 38 Copynumber: 3.0 Consensus size: 38
39765388 AATGCAAAGT
39765398 ACGT-GGCAAAGAAGAAATTTTCATCACATAGATCACA
1 ACGTGGGCAAAGAAGAAATTTTCATCACATAGATCACA
39765435 ACGTGGGCAAAGAAGAAATTTTCATCACATAGATCACA
1 ACGTGGGCAAAGAAGAAATTTTCATCACATAGATCACA
39765473 ACGTGGGCAAAGAAGAAATTTTCATCACATAGATCACA
1 ACGTGGGCAAAGAAGAAATTTTCATCACATAGATCACA
39765511 CAAACGAGAA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
37 4 0.05
38 71 0.95
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (38 bp):
ACGTGGGCAAAGAAGAAATTTTCATCACATAGATCACA
Found at i:39767521 original size:25 final size:24
Alignment explanation
Indices: 39767476--39767522 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
39767466 TTTATGGAAT
*
39767476 TTATTTGAATGTGAAATTGTATTC
1 TTATTTGAATGTGAAAGTGTATTC
39767500 TTATTATGAAT-TGAAAAGTGTAT
1 TTATT-TGAATGTG-AAAGTGTAT
39767523 GTGTAGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (24 bp):
TTATTTGAATGTGAAAGTGTATTC
Found at i:39774107 original size:34 final size:34
Alignment explanation
Indices: 39774067--39774135 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
39774057 TATATTATAA
39774067 ATGAAGAGGCATCTGCTCAAATCGATGTAAAATT
1 ATGAAGAGGCATCTGCTCAAATCGATGTAAAATT
39774101 ATGAAGAGGCATCTGCTCAAATCGATGTAAAATT
1 ATGAAGAGGCATCTGCTCAAATCGATGTAAAATT
39774135 A
1 A
39774136 GAGTGGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (34 bp):
ATGAAGAGGCATCTGCTCAAATCGATGTAAAATT
Found at i:39781626 original size:13 final size:13
Alignment explanation
Indices: 39781608--39781663 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
39781598 TAACTTTTTC
39781608 CTAAATATTATCA
1 CTAAATATTATCA
39781621 CTAAATA--ATC-
1 CTAAATATTATCA
*
39781631 CTAACTATTATCA
1 CTAAATATTATCA
*
39781644 CTAAATATAATCA
1 CTAAATATTATCA
39781657 CTAAATA
1 CTAAATA
39781664 ATTCAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 6 0.16
11 3 0.08
12 3 0.08
13 25 0.68
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:39781633 original size:23 final size:23
Alignment explanation
Indices: 39781606--39781650 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
39781596 GCTAACTTTT
39781606 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
39781629 TCCTAACTATTATCACTAAATA
1 TCCTAAATATTATCACTAAATA
39781651 TAATCACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:39782523 original size:9 final size:9
Alignment explanation
Indices: 39782506--39782563 Score: 57
Period size: 10 Copynumber: 6.2 Consensus size: 9
39782496 AAATTGAAAA
39782506 AATATTTTTT
1 AATA-TTTTT
39782516 AATATTTTT
1 AATATTTTT
39782525 -ATACTATTTT
1 AATA-T-TTTT
*
39782535 AATAATTTT
1 AATATTTTT
39782544 AATAATTTTT
1 AAT-ATTTTT
39782554 AAT-TTTTT
1 AATATTTTT
39782562 AA
1 AA
39782564 AAAATTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
8 10 0.24
9 13 0.31
10 16 0.38
11 3 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (9 bp):
AATATTTTT
Found at i:39782536 original size:19 final size:18
Alignment explanation
Indices: 39782511--39782562 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
39782501 GAAAAAATAT
*
39782511 TTTTTAATATTTTTATAC
1 TTTTTAATATTTTTATAA
*
39782529 TATTTTAATAATTTTAATAA
1 T-TTTTAAT-ATTTTTATAA
39782549 TTTTTAAT-TTTTTA
1 TTTTTAATATTTTTA
39782563 AAAAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 5 0.17
18 1 0.03
19 14 0.48
20 9 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTAATATTTTTATAA
Found at i:39782569 original size:28 final size:28
Alignment explanation
Indices: 39782512--39782566 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
39782502 AAAAAATATT
*
39782512 TTTTAATATTTTTATACTATTTTAATAA
1 TTTTAATATTTTTATACTATTTTAAAAA
*
39782540 TTTTAATAATTTTTA-A-TTTTTTAAAAA
1 TTTTAAT-ATTTTTATACTATTTTAAAAA
39782567 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.38
28 8 0.33
29 7 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTAATATTTTTATACTATTTTAAAAA
Found at i:39787079 original size:6 final size:6
Alignment explanation
Indices: 39787068--39787140 Score: 146
Period size: 6 Copynumber: 12.2 Consensus size: 6
39787058 CATACATACG
39787068 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
39787116 TACATA TACATA TACATA TACATA T
1 TACATA TACATA TACATA TACATA T
39787141 CGGCATTTCT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:39805657 original size:46 final size:46
Alignment explanation
Indices: 39805592--39805865 Score: 345
Period size: 46 Copynumber: 6.0 Consensus size: 46
39805582 TTATCTTTGA
* * * * *
39805592 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGT
** **
39805638 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGT
* * **
39805685 CATGTTGCAAT-GTATCTTTCAACCATGGTTTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
* * *
39805730 CACGTTGCCATGGTTTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
* *
39805776 CATATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
*
39805822 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
39805866 TTCAGAGAGC
Statistics
Matches: 204, Mismatches: 22, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
45 15 0.07
46 177 0.87
47 12 0.06
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
Found at i:39808260 original size:17 final size:18
Alignment explanation
Indices: 39808224--39808265 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
39808214 ACACCTTTAA
*
39808224 TTTTCCCTTTTCTTCTTTC
1 TTTTCTCTTTTC-TCTTTC
39808243 TTTTCTCTTTTC-CTTTC
1 TTTTCTCTTTTCTCTTTC
39808260 TTTTCT
1 TTTTCT
39808266 TCCCCTACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
19 11 0.50
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTCTCTTTTCTCTTTC
Found at i:39808331 original size:12 final size:12
Alignment explanation
Indices: 39808294--39808337 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
39808284 ATTTGCTTTG
*
39808294 TTTCTTCATTTC
1 TTTCTTTATTTC
* *
39808306 TATCTTTTTTTC
1 TTTCTTTATTTC
39808318 TTTCTTTATTTC
1 TTTCTTTATTTC
39808330 TTT-TTTAT
1 TTTCTTTAT
39808338 ATATATATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTCTTTATTTC
Found at i:39808531 original size:18 final size:19
Alignment explanation
Indices: 39808482--39808531 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
39808472 TATAATATAA
39808482 TTATTTAATTAATAAATATC
1 TTATTTAA-TAATAAATATC
39808502 TT-TTATAAAATAATAAATAT-
1 TTATT-T--AATAATAAATATC
39808522 TTATTTAATA
1 TTATTTAATA
39808532 TCTAATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 4 0.15
19 2 0.08
20 6 0.23
21 12 0.46
22 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTTAATAATAAATATC
Found at i:39811054 original size:24 final size:24
Alignment explanation
Indices: 39811022--39811071 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
39811012 TCACTAAAGA
39811022 TTCACTCAAATCACTCGAGGTGTT
1 TTCACTCAAATCACTCGAGGTGTT
39811046 TTCACTCAAATCACTCGAGGTGTT
1 TTCACTCAAATCACTCGAGGTGTT
39811070 TT
1 TT
39811072 AAAGACAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (24 bp):
TTCACTCAAATCACTCGAGGTGTT
Found at i:39821443 original size:25 final size:25
Alignment explanation
Indices: 39821404--39821472 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 25
39821394 GCGGATTCTT
*
39821404 TGAAGCTAGTATTAGCAGCAT-TGAAC
1 TGAAGCTAGTGTTAGCA--ATCTGAAC
*
39821430 T-AAGCTAGTGTTAGCAATCCTGATC
1 TGAAGCTAGTGTTAGCAAT-CTGAAC
39821455 TGAAGCTAGTGTTAGCAA
1 TGAAGCTAGTGTTAGCAA
39821473 CTCAAATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 2 0.05
25 19 0.50
26 17 0.45
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (25 bp):
TGAAGCTAGTGTTAGCAATCTGAAC
Found at i:39826958 original size:21 final size:21
Alignment explanation
Indices: 39826906--39826946 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
39826896 AGAGCTAAAC
39826906 GGAAACCCATAAGGGTTGAAA
1 GGAAACCCATAAGGGTTGAAA
39826927 GGAAACCCATAAGGGTTGAA
1 GGAAACCCATAAGGGTTGAA
39826947 CAGAAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
GGAAACCCATAAGGGTTGAAA
Found at i:39827723 original size:30 final size:30
Alignment explanation
Indices: 39827689--39827754 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
39827679 AGGATATCAT
39827689 AAAACCCCTAATAAAATAGAAATTTAATAC
1 AAAACCCCTAATAAAATAGAAATTTAATAC
*
39827719 AAAACCCTTAATAAAATAGAAATTTAATAC
1 AAAACCCCTAATAAAATAGAAATTTAATAC
*
39827749 CAAACC
1 AAAACC
39827755 ATAATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.56, C:0.18, G:0.03, T:0.23
Consensus pattern (30 bp):
AAAACCCCTAATAAAATAGAAATTTAATAC
Found at i:39830933 original size:23 final size:22
Alignment explanation
Indices: 39830896--39830968 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 22
39830886 CGAACACACC
* * *
39830896 ATAGCTCGCAAGAGCGTCCTGAT
1 ATAGCTCACATGAGCAT-CTGAT
39830919 ATAGCTCACATGAGCATCTCGAT
1 ATAGCTCACATGAGCATCT-GAT
* * *
39830942 ATAAGCTCTCTTGAGCTTTCTGAT
1 AT-AGCTCACATGAGC-ATCTGAT
39830966 ATA
1 ATA
39830969 TGGTTCTTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.05
23 20 0.49
24 16 0.39
25 3 0.07
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (22 bp):
ATAGCTCACATGAGCATCTGAT
Found at i:39830966 original size:24 final size:23
Alignment explanation
Indices: 39830914--39830968 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
39830904 CAAGAGCGTC
39830914 CTGATAT-AGCTCACATGAGCAT
1 CTGATATAAGCTCACATGAGCAT
* * *
39830936 CTCGATATAAGCTCTCTTGAGCTTT
1 CT-GATATAAGCTCACATGAGC-AT
39830961 CTGATATA
1 CTGATATA
39830969 TGGTTCTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.07
23 5 0.19
24 17 0.63
25 3 0.11
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (23 bp):
CTGATATAAGCTCACATGAGCAT
Found at i:39836763 original size:25 final size:26
Alignment explanation
Indices: 39836735--39836786 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
39836725 AAGTTGTAAA
39836735 TAAAACAATATCTCTAGA-AATTTTC
1 TAAAACAATATCTCTAGATAATTTTC
* * *
39836760 TAAAATAATTTCTTTAGATAATTTTC
1 TAAAACAATATCTCTAGATAATTTTC
39836786 T
1 T
39836787 CTCCACAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (26 bp):
TAAAACAATATCTCTAGATAATTTTC
Found at i:39836968 original size:59 final size:61
Alignment explanation
Indices: 39836895--39837012 Score: 168
Period size: 62 Copynumber: 2.0 Consensus size: 61
39836885 ATCACTATAA
* * *
39836895 TATTAAATTGATATAATACTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAGTCT
1 TATTAAATTAATATAATACTTACTACAAGATAAATATTAAAATAAATTTAATATTAAGTCT
* *
39836954 TATTAAATTAATATAATATTTATCTACAAGATAAATATTAAAATAATTTTAATATTAAG
1 TATTAAATTAATATAATACTTA-CTACAAGATAAATATTAAAATAAATTTAATATTAAG
39837013 ATAATAACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 20 0.39
61 1 0.02
62 30 0.59
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (61 bp):
TATTAAATTAATATAATACTTACTACAAGATAAATATTAAAATAAATTTAATATTAAGTCT
Found at i:39838707 original size:15 final size:16
Alignment explanation
Indices: 39838687--39838716 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39838677 GAAAATTGCC
39838687 AAAATTGG-CTAAATA
1 AAAATTGGACTAAATA
39838702 AAAATTGGACTAAAT
1 AAAATTGGACTAAAT
39838717 TGGAATGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (16 bp):
AAAATTGGACTAAATA
Found at i:39843379 original size:14 final size:14
Alignment explanation
Indices: 39843355--39843387 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39843345 AATTTGTGTG
39843355 TTTTTTATTTTAT-
1 TTTTTTATTTTATA
39843368 TTTTTTATTTTTATA
1 TTTTTTA-TTTTATA
39843383 TTTTT
1 TTTTT
39843388 CACAAATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTATTTTATA
Found at i:39847445 original size:26 final size:26
Alignment explanation
Indices: 39847409--39847459 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
39847399 AGCACTGCCA
39847409 TGTGCAGAGGGGACAGTTTCTGGTTT
1 TGTGCAGAGGGGACAGTTTCTGGTTT
*
39847435 TGTGCGGAGGGGACAGTTTCTGGTT
1 TGTGCAGAGGGGACAGTTTCTGGTT
39847460 CTGGGTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.14, C:0.12, G:0.41, T:0.33
Consensus pattern (26 bp):
TGTGCAGAGGGGACAGTTTCTGGTTT
Found at i:39850817 original size:7 final size:7
Alignment explanation
Indices: 39850801--39850907 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
39850791 AATAAATGAA
*
39850801 ATAATTT
1 ATAATAT
39850808 ATAATAT
1 ATAATAT
39850815 ATAATAT
1 ATAATAT
*
39850822 A-AAAAT
1 ATAATAT
* *
39850828 GTAAGTTT
1 ATAA-TAT
*
39850836 TTAA-A-
1 ATAATAT
*
39850841 ATAATGT
1 ATAATAT
39850848 ATAATAT
1 ATAATAT
*
39850855 A-AATAA
1 ATAATAT
39850861 ATAAATAT
1 AT-AATAT
39850869 ATAAGATAT
1 AT-A-ATAT
39850878 ATAAGT-T
1 ATAA-TAT
39850885 A-AA-AT
1 ATAATAT
39850890 ATAATAT
1 ATAATAT
39850897 ATAATA-
1 ATAATAT
39850903 ATAAT
1 ATAAT
39850908 TTACAAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
5 5 0.06
6 18 0.23
7 34 0.44
8 14 0.18
9 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:39850871 original size:21 final size:21
Alignment explanation
Indices: 39850839--39850903 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
39850829 TAAGTTTTTA
*
39850839 AAAT-AATGTATAATATAAAT
1 AAATAAATATATAATATAAAT
* *
39850859 AAATAAATATATAAGATATAT
1 AAATAAATATATAATATAAAT
*
39850880 AAGTTAAA-ATATAATATATAAT
1 AA-ATAAATATATAATATA-AAT
39850902 AA
1 AA
39850904 TAATTTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 24 0.67
22 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATAAATATATAATATAAAT
Found at i:39850872 original size:28 final size:29
Alignment explanation
Indices: 39850841--39850901 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
39850831 AGTTTTTAAA
39850841 ATAATGTATAATATAA-AT-AAATA-AATAT
1 ATAATG-AT-ATATAAGATAAAATATAATAT
*
39850869 ATAA-GATATATAAGTTAAAATATAATAT
1 ATAATGATATATAAGATAAAATATAATAT
39850897 ATAAT
1 ATAAT
39850902 AATAATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 6 0.21
28 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
ATAATGATATATAAGATAAAATATAATAT
Found at i:39850942 original size:12 final size:13
Alignment explanation
Indices: 39850923--39850953 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
39850913 AATTTTGAAA
39850923 ATATAAATAATAT
1 ATATAAATAATAT
39850936 A-ATAAATAATAT
1 ATATAAATAATAT
39850948 ATATAA
1 ATATAA
39850954 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:39850951 original size:16 final size:15
Alignment explanation
Indices: 39850928--39850958 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
39850918 TGAAAATATA
39850928 AATAATATAATAAAT
1 AATAATATAATAAAT
39850943 AATATATATAATAAAT
1 AATA-ATATAATAAAT
39850959 TAAAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATAATAAAT
Found at i:39851314 original size:17 final size:18
Alignment explanation
Indices: 39851261--39851367 Score: 146
Period size: 17 Copynumber: 5.9 Consensus size: 18
39851251 AATCATATCT
*
39851261 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
39851280 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
39851298 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
39851315 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
39851333 TTTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
39851350 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
39851368 TGAAGATTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
17 31 0.40
18 31 0.40
19 16 0.21
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:39851319 original size:35 final size:35
Alignment explanation
Indices: 39851261--39851367 Score: 178
Period size: 35 Copynumber: 3.0 Consensus size: 35
39851251 AATCATATCT
39851261 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
39851298 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
39851333 TTTAAGATTGTATCATATCTAAGATTGCATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
39851368 TGAAGATTAT
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
35 53 0.78
36 5 0.07
37 10 0.15
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:39861226 original size:12 final size:13
Alignment explanation
Indices: 39861209--39861237 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39861199 TTTTGAAAAT
39861209 ATAAATAATATA-
1 ATAAATAATATAC
39861221 ATAAATAATATAC
1 ATAAATAATATAC
39861234 ATAA
1 ATAA
39861238 TAAATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAATAATATAC
Found at i:39861246 original size:21 final size:20
Alignment explanation
Indices: 39861136--39861250 Score: 64
Period size: 21 Copynumber: 5.8 Consensus size: 20
39861126 AAAATAATGT
*
39861136 ATAATATAAATAAATATATAA
1 ATAATAT-AATAAAAATATAA
*
39861157 GAT-ATATAAGTTAAAATAT-A
1 -ATAATATAA-TAAAAATATAA
* * *
39861177 AT-ATATAATAATAATTTAC
1 ATAATATAATAAAAATATAA
* *
39861196 A-AAT-T-TTGAAAATATAA
1 ATAATATAATAAAAATATAA
*
39861213 ATAATATAATAAATAATATAC
1 ATAATATAATAAA-AATATAA
39861234 ATAATA-AATTAAAAATA
1 ATAATATAA-TAAAAATA
39861251 AGTTTAAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
17 8 0.11
18 10 0.14
19 12 0.17
20 12 0.17
21 27 0.38
22 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (20 bp):
ATAATATAATAAAAATATAA
Found at i:39861581 original size:18 final size:17
Alignment explanation
Indices: 39861545--39861677 Score: 176
Period size: 18 Copynumber: 7.5 Consensus size: 17
39861535 AATCATATCT
39861545 TCTAAGATTGTATATCATA
1 TCTAAGATTG-A-ATCATA
39861564 TCTAAGATTGCAATCATA
1 TCTAAGATTG-AATCATA
*
39861582 TCTAAGATTGTATCATA
1 TCTAAGATTGAATCATA
*
39861599 TCTAATATTGCAATCATA
1 TCTAAGATTG-AATCATA
*
39861617 TCTAAGATTGTATCATA
1 TCTAAGATTGAATCATA
39861634 TCTAAGATTGCAATCATA
1 TCTAAGATTG-AATCATA
* *
39861652 TTTAAGATTGTATCATA
1 TCTAAGATTGAATCATA
39861669 TCTAAGATT
1 TCTAAGATT
39861678 ACATATCATT
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
17 45 0.44
18 46 0.45
19 11 0.11
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (17 bp):
TCTAAGATTGAATCATA
Found at i:39861603 original size:35 final size:35
Alignment explanation
Indices: 39861545--39861686 Score: 230
Period size: 35 Copynumber: 4.0 Consensus size: 35
39861535 AATCATATCT
39861545 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
*
39861582 TCTAAGATTGTATCATATCTAATATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
39861617 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* *
39861652 TTTAAGATTGTATCATATCTAAGATTACATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
39861687 TGAAGATTAT
Statistics
Matches: 100, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
35 85 0.85
36 5 0.05
37 10 0.10
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:39865702 original size:43 final size:43
Alignment explanation
Indices: 39865641--39865745 Score: 165
Period size: 43 Copynumber: 2.4 Consensus size: 43
39865631 TTTAAATTTT
39865641 ATGACCTTTAGCGGCGTTTGAGGGAAAAGCGCCGCTAAAGGTC
1 ATGACCTTTAGCGGCGTTTGAGGGAAAAGCGCCGCTAAAGGTC
* * * *
39865684 ATGACCTTTAACGACGTTTGTGGGAAAAGTGCCGCTAAAGGTC
1 ATGACCTTTAGCGGCGTTTGAGGGAAAAGCGCCGCTAAAGGTC
*
39865727 ATGCCCTTTAGCGGCGTTT
1 ATGACCTTTAGCGGCGTTT
39865746 TTTTAAATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.26
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGTTTGAGGGAAAAGCGCCGCTAAAGGTC
Found at i:39865849 original size:31 final size:34
Alignment explanation
Indices: 39865793--39865854 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 34
39865783 ATAGCGGCGT
*
39865793 TTTTTGCGGCGCTTGTAAAAACGTCG-TAAATAG
1 TTTTAGCGGCGCTTGTAAAAACGTCGCTAAATAG
*
39865826 TTTTAGCGGCGC-T-TAAAAGCGTCGCTAAA
1 TTTTAGCGGCGCTTGTAAAAACGTCGCTAAA
39865855 GACCTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 10 0.38
32 5 0.19
33 11 0.42
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (34 bp):
TTTTAGCGGCGCTTGTAAAAACGTCGCTAAATAG
Found at i:39874907 original size:13 final size:13
Alignment explanation
Indices: 39874889--39874913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39874879 CTTCAATTTC
39874889 AGTATTTTCCAAA
1 AGTATTTTCCAAA
39874902 AGTATTTTCCAA
1 AGTATTTTCCAA
39874914 CTCTTATCTG
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:0.08, T:0.40
Consensus pattern (13 bp):
AGTATTTTCCAAA
Found at i:39880820 original size:175 final size:175
Alignment explanation
Indices: 39880529--39880878 Score: 700
Period size: 175 Copynumber: 2.0 Consensus size: 175
39880519 TTGCCCCTCG
39880529 TGCGTAAATGACTAACTTGTGTGATGATTGGGTTAGTTGACGTGGATTTATGTTTTATCATTAAT
1 TGCGTAAATGACTAACTTGTGTGATGATTGGGTTAGTTGACGTGGATTTATGTTTTATCATTAAT
39880594 CCGTAAGTCTAATGTGTTAGTGATCGATTATAGGATTATCGCGTGGGAGATATCGTCATAAATCA
66 CCGTAAGTCTAATGTGTTAGTGATCGATTATAGGATTATCGCGTGGGAGATATCGTCATAAATCA
39880659 TCATCAACCAGGTGTGTAAACGACACCCTCCCTTAGACTAAATCC
131 TCATCAACCAGGTGTGTAAACGACACCCTCCCTTAGACTAAATCC
39880704 TGCGTAAATGACTAACTTGTGTGATGATTGGGTTAGTTGACGTGGATTTATGTTTTATCATTAAT
1 TGCGTAAATGACTAACTTGTGTGATGATTGGGTTAGTTGACGTGGATTTATGTTTTATCATTAAT
39880769 CCGTAAGTCTAATGTGTTAGTGATCGATTATAGGATTATCGCGTGGGAGATATCGTCATAAATCA
66 CCGTAAGTCTAATGTGTTAGTGATCGATTATAGGATTATCGCGTGGGAGATATCGTCATAAATCA
39880834 TCATCAACCAGGTGTGTAAACGACACCCTCCCTTAGACTAAATCC
131 TCATCAACCAGGTGTGTAAACGACACCCTCCCTTAGACTAAATCC
39880879 GTAAAAGCTG
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 175 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (175 bp):
TGCGTAAATGACTAACTTGTGTGATGATTGGGTTAGTTGACGTGGATTTATGTTTTATCATTAAT
CCGTAAGTCTAATGTGTTAGTGATCGATTATAGGATTATCGCGTGGGAGATATCGTCATAAATCA
TCATCAACCAGGTGTGTAAACGACACCCTCCCTTAGACTAAATCC
Found at i:39883481 original size:21 final size:21
Alignment explanation
Indices: 39883442--39883481 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39883432 CTGTGTTCAG
* *
39883442 AGGTTCGACAGTCTTGATGCA
1 AGGTTCGACAGTATCGATGCA
39883463 AGGTTCGACAGTATCGATG
1 AGGTTCGACAGTATCGATG
39883482 AAACTTTGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
AGGTTCGACAGTATCGATGCA
Found at i:39883585 original size:6 final size:6
Alignment explanation
Indices: 39883574--39883636 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
39883564 AGTCCACTTA
* *
39883574 TTTTAT TTTTAT TTTTAT TTTTAT CTTT-C TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
39883621 CTTT-C TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTA
39883637 AAAACTTATG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
5 6 0.13
6 41 0.87
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:39883606 original size:23 final size:23
Alignment explanation
Indices: 39883580--39883636 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
39883570 CTTATTTTAT
39883580 TTTTATTTTTATTTTTATCTTTC
1 TTTTATTTTTATTTTTATCTTTC
39883603 TTTTATTTTTATTTTTATCTTTC
1 TTTTATTTTTATTTTTATCTTTC
39883626 TTTTATTTTTA
1 TTTTATTTTTA
39883637 AAAACTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTATTTTTATTTTTATCTTTC
Found at i:39884613 original size:4 final size:4
Alignment explanation
Indices: 39884606--39884651 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
39884596 CTTAAAAAAA
* *
39884606 ATAC ATAC ATAT ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
39884652 TTTAGTGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:39884623 original size:12 final size:12
Alignment explanation
Indices: 39884606--39884651 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
39884596 CTTAAAAAAA
39884606 ATACATACATAT
1 ATACATACATAT
39884618 ATACATACATAT
1 ATACATACATAT
*
39884630 ATACATACATAC
1 ATACATACATAT
39884642 ATACATACAT
1 ATACATACAT
39884652 TTTAGTGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (12 bp):
ATACATACATAT
Found at i:39888837 original size:44 final size:44
Alignment explanation
Indices: 39888774--39888862 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
39888764 AGATGCAAGC
*
39888774 AGTTCTTGCGTAGATGGATCTGAAGGATGCCCTGCTAAGGATAG
1 AGTTCTTGCGCAGATGGATCTGAAGGATGCCCTGCTAAGGATAG
* *
39888818 AGTTCTTGCGCAGATGGATCTGGAGGATGCCCTGCTAGGGATAG
1 AGTTCTTGCGCAGATGGATCTGAAGGATGCCCTGCTAAGGATAG
39888862 A
1 A
39888863 TAAGATGCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.26
Consensus pattern (44 bp):
AGTTCTTGCGCAGATGGATCTGAAGGATGCCCTGCTAAGGATAG
Found at i:39890911 original size:11 final size:11
Alignment explanation
Indices: 39890891--39890920 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39890881 TCCTCTGTTT
39890891 CTTCACCGTCC
1 CTTCACCGTCC
*
39890902 CTTCATCGTCC
1 CTTCACCGTCC
39890913 CTTCACCG
1 CTTCACCG
39890921 CCGTCTACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.10, C:0.50, G:0.10, T:0.30
Consensus pattern (11 bp):
CTTCACCGTCC
Found at i:39891004 original size:17 final size:17
Alignment explanation
Indices: 39890984--39891031 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
39890974 TTTTTTGTTG
39890984 TATTTTATTTTATTTAA
1 TATTTTATTTTATTTAA
* *
39891001 TATTATATTTGT-TTTAT
1 TATTTTATTT-TATTTAA
39891018 TATTTTATTTTATT
1 TATTTTATTTTATT
39891032 ATTATGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
TATTTTATTTTATTTAA
Found at i:39894981 original size:8 final size:8
Alignment explanation
Indices: 39894968--39894998 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
39894958 TTTATTTTAT
39894968 TTTATTTC
1 TTTATTTC
39894976 TTTATTTC
1 TTTATTTC
39894984 TTTATTTC
1 TTTATTTC
39894992 TTTATTT
1 TTTATTT
39894999 GTTTGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTATTTC
Found at i:39895251 original size:9 final size:9
Alignment explanation
Indices: 39895209--39895251 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
39895199 ATTAATCTAT
*
39895209 TTTTTATTA
1 TTTTTATTG
39895218 TTTGTTCATTG
1 TTT-TT-ATTG
39895229 TTTTTATTG
1 TTTTTATTG
*
39895238 CTTTTATTG
1 TTTTTATTG
39895247 TTTTT
1 TTTTT
39895252 GTTCTTAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 19 0.66
10 4 0.14
11 6 0.21
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTTATTG
Found at i:39896385 original size:17 final size:17
Alignment explanation
Indices: 39896365--39896397 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39896355 CAACTCGCTC
39896365 GACACTTCAATCTTCTT
1 GACACTTCAATCTTCTT
*
39896382 GACACTTCGATCTTCT
1 GACACTTCAATCTTCT
39896398 CAACACACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.39
Consensus pattern (17 bp):
GACACTTCAATCTTCTT
Found at i:39901368 original size:22 final size:21
Alignment explanation
Indices: 39901343--39901386 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
39901333 TTCCAGTTCA
*
39901343 TTAATTATTAATTTTTATTTAT
1 TTAATTATTAATTATT-TTTAT
*
39901365 TTAATTTTTAATTATTTTTAT
1 TTAATTATTAATTATTTTTAT
39901386 T
1 T
39901387 ACTGATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTAATTATTAATTATTTTTAT
Found at i:39901370 original size:15 final size:15
Alignment explanation
Indices: 39901343--39901381 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
39901333 TTCCAGTTCA
39901343 TTAATTA-TTAATTT
1 TTAATTATTTAATTT
*
39901357 TTATTTATTTAATTT
1 TTAATTATTTAATTT
39901372 TTAATTATTT
1 TTAATTATTT
39901382 TTATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTAATTATTTAATTT
Found at i:39901413 original size:15 final size:16
Alignment explanation
Indices: 39901375--39901413 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
39901365 TTAATTTTTA
39901375 ATTATTTTTATTACTG
1 ATTATTTTTATTACTG
39901391 ATTA-TTTTATTACT-
1 ATTATTTTTATTACTG
39901405 ATTATTTTT
1 ATTATTTTT
39901414 TTAATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTATTTTTATTACTG
Found at i:39903047 original size:6 final size:6
Alignment explanation
Indices: 39903016--39903097 Score: 62
Period size: 6 Copynumber: 13.3 Consensus size: 6
39903006 ATAAGGATCA
* * * *
39903016 TTTA-T TTTATT TATT-TT CTTTTTT TTTATT TTTA-T TTTATG TCTATG
1 TTTATT TTTATT T-TTATT -TTTATT TTTATT TTTATT TTTATT TTTATT
39903063 TTTATT TTTATT TTTAATTGT TTTATT TTTATT TT
1 TTTATT TTTATT TTT-A-T-T TTTATT TTTATT TT
39903098 CTTAGACTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
5 9 0.14
6 42 0.66
7 7 0.11
8 2 0.03
9 4 0.06
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:39903097 original size:5 final size:5
Alignment explanation
Indices: 39903016--39903076 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
39903006 ATAAGGATCA
* * *
39903016 TTTAT TTTA- TTTAT TTTCT TTTTT TTTATT TTTAT TTTAT GTCTAT GTTTATT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT -TTTAT -TTTA-T
39903069 TTTAT TTT
1 TTTAT TTT
39903077 TAATTGTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
4 4 0.09
5 25 0.53
6 17 0.36
7 1 0.02
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:39903135 original size:26 final size:25
Alignment explanation
Indices: 39903063--39903143 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
39903053 TATGTCTATG
*
39903063 TTTATTTTTA-TTT-TT-AA-TTGT
1 TTTATTTTTATTTTCTTAAACTTAT
*
39903084 TTTATTTTTATTTTCTTAGACTTAT
1 TTTATTTTTATTTTCTTAAACTTAT
*
39903109 TTTGTTTATTATTTT-TTAAACTATATT
1 TTTATTT-TTATTTTCTTAAACT-TA-T
39903136 TTTATTTT
1 TTTATTTT
39903144 GATGGTTGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 10 0.21
22 3 0.06
23 2 0.04
24 1 0.02
25 15 0.31
26 10 0.21
27 7 0.15
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTATTTTTATTTTCTTAAACTTAT
Found at i:39905271 original size:102 final size:102
Alignment explanation
Indices: 39905091--39905294 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 102
39905081 ACTAAACTGA
* *
39905091 TAACATTTGCAAACTTTGGGAAACTTGGAAAATTGTCAAACATTTAAGGGTCACATGCCCGTGTG
1 TAACATTTGCAAACTTTGGGAAACTTAGAAAATTATCAAACATTTAAGGGTCACATGCCCGTGTG
39905156 AACAAGCCGTGTGACCAGACACGCCCGTGTCACAGGC
66 AACAAGCCGTGTGACCAGACACGCCCGTGTCACAGGC
39905193 TAACATTTGCAAACTTTGGGAAACTTAGAAAATTATCAAACATTTAAGGGTCACATGCCCGTGTG
1 TAACATTTGCAAACTTTGGGAAACTTAGAAAATTATCAAACATTTAAGGGTCACATGCCCGTGTG
*
39905258 AACAAGATC-TGTGACCAGACACGCCCGTGTCACAGGC
66 AACAAG-CCGTGTGACCAGACACGCCCGTGTCACAGGC
39905295 CATGTGAAAA
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
102 97 0.99
103 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (102 bp):
TAACATTTGCAAACTTTGGGAAACTTAGAAAATTATCAAACATTTAAGGGTCACATGCCCGTGTG
AACAAGCCGTGTGACCAGACACGCCCGTGTCACAGGC
Found at i:39906645 original size:43 final size:43
Alignment explanation
Indices: 39906545--39906699 Score: 127
Period size: 43 Copynumber: 3.6 Consensus size: 43
39906535 CAATGCCATA
* ** * * *
39906545 TCCCAGATATGGTCTTACATGTTATC--ACATATCAATGCCACTA
1 TCCCAGACATGGTCTTACATGAAATCTGA-ATA-CAAGGCCAATG
* * *
39906588 TCCCAGACAGGGTCTTACATGAAATC-GATTAACGAGGCCAATG
1 TCCCAGACATGGTCTTACATGAAATCTGAAT-ACAAGGCCAATG
* * * * *
39906631 TCTCAGATATGGTCTTACACGTAATCTGAATACAATGCCAATG
1 TCCCAGACATGGTCTTACATGAAATCTGAATACAAGGCCAATG
*
39906674 TCCCAGACATGGTCTTACATGCAATC
1 TCCCAGACATGGTCTTACATGAAATC
39906700 AAATCTTGTT
Statistics
Matches: 88, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
43 83 0.94
44 5 0.06
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACATGAAATCTGAATACAAGGCCAATG
Found at i:39909468 original size:12 final size:12
Alignment explanation
Indices: 39909451--39909480 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39909441 AAATAATTAA
39909451 TAAATTAGAAAT
1 TAAATTAGAAAT
*
39909463 TAAATTGGAAAT
1 TAAATTAGAAAT
39909475 TAAATT
1 TAAATT
39909481 TGGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (12 bp):
TAAATTAGAAAT
Found at i:39910859 original size:4 final size:4
Alignment explanation
Indices: 39910850--39910882 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
39910840 AACTTAAGCC
39910850 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
39910883 GTACAAGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:39914784 original size:18 final size:18
Alignment explanation
Indices: 39914761--39914795 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39914751 AGCCTAGAAT
*
39914761 CTCACACGCCCGTGTGGA
1 CTCACACACCCGTGTGGA
*
39914779 CTCACACACTCGTGTGG
1 CTCACACACCCGTGTGG
39914796 CCCACACGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.37, G:0.26, T:0.20
Consensus pattern (18 bp):
CTCACACACCCGTGTGGA
Found at i:39914820 original size:24 final size:24
Alignment explanation
Indices: 39914793--39914847 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
39914783 CACACTCGTG
39914793 TGGCCCACACGGCCCAAATCAGTC
1 TGGCCCACACGGCCCAAATCAGTC
39914817 TGGCCCACACGGCCCAAATCAGTC
1 TGGCCCACACGGCCCAAATCAGTC
39914841 TGGCCCA
1 TGGCCCA
39914848 TGTGTCACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.42, G:0.22, T:0.13
Consensus pattern (24 bp):
TGGCCCACACGGCCCAAATCAGTC
Found at i:39916088 original size:16 final size:16
Alignment explanation
Indices: 39916067--39916100 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39916057 TTGAAACAAC
*
39916067 ATAAATAATTAATTAA
1 ATAAATAATAAATTAA
*
39916083 ATAAATTATAAATTAA
1 ATAAATAATAAATTAA
39916099 AT
1 AT
39916101 TGGAAATTAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAATAATAAATTAA
Found at i:39916873 original size:47 final size:48
Alignment explanation
Indices: 39916819--39916911 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
39916809 TACTGACACA
39916819 TCAAATTGGAAGG-AAAAAAGTAATTCTTATTTAATTCCAAATGAATT
1 TCAAATTGGAAGGAAAAAAAGTAATTCTTATTTAATTCCAAATGAATT
39916866 TCAAATTGGAAGGAAAAAAAGTAATTCTTATTTAATTCCAAATGAA
1 TCAAATTGGAAGGAAAAAAAGTAATTCTTATTTAATTCCAAATGAA
39916912 GTCCAATGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 13 0.29
48 32 0.71
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (48 bp):
TCAAATTGGAAGGAAAAAAAGTAATTCTTATTTAATTCCAAATGAATT
Found at i:39919699 original size:38 final size:38
Alignment explanation
Indices: 39919643--39919720 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
39919633 AGCAACTTCT
39919643 AAATCTGAGAAGGGATTTCGAGAATCTGAAAATGAAAG
1 AAATCTGAGAAGGGATTTCGAGAATCTGAAAATGAAAG
* *
39919681 AAATTTGAGAAGGGATTTCGAGAATTTGAAAATGAAAG
1 AAATCTGAGAAGGGATTTCGAGAATCTGAAAATGAAAG
39919719 AA
1 AA
39919721 GAGGAAACTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (38 bp):
AAATCTGAGAAGGGATTTCGAGAATCTGAAAATGAAAG
Found at i:39925722 original size:23 final size:23
Alignment explanation
Indices: 39925692--39925736 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
39925682 TCTAAATTTG
*
39925692 ATAATTTAGTACAAAATTGTTTA
1 ATAATTTAGTACAAAAATGTTTA
* *
39925715 ATAATTTATTATAAAAATGTTT
1 ATAATTTAGTACAAAAATGTTT
39925737 TATTGATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (23 bp):
ATAATTTAGTACAAAAATGTTTA
Found at i:39925890 original size:20 final size:20
Alignment explanation
Indices: 39925829--39925891 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
39925819 AGAATTTTAT
* *
39925829 GTATTCCCTCATAATTTTTG
1 GTATTCTCTCATTATTTTTG
* * *
39925849 GCACTCTCTCATGT-TTATTG
1 GTATTCTCTCAT-TATTTTTG
39925869 GTATTCTCTCATTATTTTTG
1 GTATTCTCTCATTATTTTTG
39925889 GTA
1 GTA
39925892 CACACCTCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (20 bp):
GTATTCTCTCATTATTTTTG
Found at i:39926396 original size:24 final size:20
Alignment explanation
Indices: 39926343--39926413 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 20
39926333 ACACTCATAC
39926343 TTTTTGGTACTTTCTTATAAT
1 TTTTTGGTA-TTTCTTATAAT
39926364 TTTTT-GTATTCTCTTATAATGT
1 TTTTTGGTATT-TCTTATAA--T
* *
39926386 ATTTTTGGTATTTCGTCATTAT
1 -TTTTTGGTATTTC-TTATAAT
39926408 TTTTTG
1 TTTTTG
39926414 TACTCTCGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
19 2 0.05
20 11 0.26
21 11 0.26
22 2 0.05
23 7 0.17
24 9 0.21
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.63
Consensus pattern (20 bp):
TTTTTGGTATTTCTTATAAT
Found at i:39931750 original size:17 final size:17
Alignment explanation
Indices: 39931728--39931761 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39931718 TTCTGCTTAC
39931728 AATTAAACCTAAACTAT
1 AATTAAACCTAAACTAT
39931745 AATTAAACCTAAACTAT
1 AATTAAACCTAAACTAT
39931762 GTCACTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTAAACCTAAACTAT
Found at i:39941877 original size:10 final size:10
Alignment explanation
Indices: 39941862--39941894 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
39941852 AGAATTTTTT
39941862 TAAAAAATTG
1 TAAAAAATTG
39941872 TAAAAAATT-
1 TAAAAAATTG
39941881 T-AAAAATTG
1 TAAAAAATTG
39941890 TAAAA
1 TAAAA
39941895 TTTTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 7 0.33
9 2 0.10
10 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (10 bp):
TAAAAAATTG
Done.