Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 151 of 335
Found at i:44386652 original size:50 final size:50
Alignment explanation
Indices: 44386593--44386691 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
44386583 GTTTTATGAC
*
44386593 ATGCTGATCATTTATTTACCTACGGCAACATCAAATTCCCACTCTAACAG
1 ATGCTGATCATTTATTTACCTACGACAACATCAAATTCCCACTCTAACAG
44386643 ATGCTGATCATTTATTTACCTACGACAACATCAAATTCCCACTCTAACA
1 ATGCTGATCATTTATTTACCTACGACAACATCAAATTCCCACTCTAACA
44386692 TGTACTTATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.30
Consensus pattern (50 bp):
ATGCTGATCATTTATTTACCTACGACAACATCAAATTCCCACTCTAACAG
Found at i:44388044 original size:17 final size:16
Alignment explanation
Indices: 44388022--44388056 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
44388012 GTTTGTTTCT
44388022 ATTAAAAAAAGAAATAA
1 ATTAAAAAAA-AAATAA
*
44388039 ATTAAAAAGAAAATAA
1 ATTAAAAAAAAAATAA
44388055 AT
1 AT
44388057 ATTACCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (16 bp):
ATTAAAAAAAAAATAA
Found at i:44388047 original size:15 final size:16
Alignment explanation
Indices: 44388027--44388056 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44388017 TTTCTATTAA
44388027 AAAAAG-AAATAAATT
1 AAAAAGAAAATAAATT
44388042 AAAAAGAAAATAAAT
1 AAAAAGAAAATAAAT
44388057 ATTACCATAT
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:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (16 bp):
AAAAAGAAAATAAATT
Found at i:44389969 original size:33 final size:33
Alignment explanation
Indices: 44389925--44389999 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
44389915 AATTCCACAG
*
44389925 GCTCGTCTGGCCCACACGGCCCAAACCAGTCTA
1 GCTCGTGTGGCCCACACGGCCCAAACCAGTCTA
* *
44389958 GCTCGTGTGGCCCACAGGGCCCAAATCAGTCTA
1 GCTCGTGTGGCCCACACGGCCCAAACCAGTCTA
44389991 GCTCGTGTG
1 GCTCGTGTG
44390000 TCACGCATGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.19, C:0.36, G:0.27, T:0.19
Consensus pattern (33 bp):
GCTCGTGTGGCCCACACGGCCCAAACCAGTCTA
Found at i:44395678 original size:17 final size:17
Alignment explanation
Indices: 44395656--44395694 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
44395646 GCAGTCTCTA
*
44395656 TCAGTTTTGCTACAGTC
1 TCAGTTTTACTACAGTC
*
44395673 TCAGTTTTACTACAGTT
1 TCAGTTTTACTACAGTC
44395690 TCAGT
1 TCAGT
44395695 ATACATTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (17 bp):
TCAGTTTTACTACAGTC
Found at i:44395840 original size:35 final size:35
Alignment explanation
Indices: 44395794--44395872 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
44395784 GTTTTAGAAT
*
44395794 ACATAC-AAGATCGACACCGGAGACTCGGTGTACC
1 ACATACTAAGATCGACACCGAAGACTCGGTGTACC
* *
44395828 ACATACTAAGATCGGCGCCGAAGACTCGGTGTACC
1 ACATACTAAGATCGACACCGAAGACTCGGTGTACC
44395863 ACATACTAAG
1 ACATACTAAG
44395873 TTAAATCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 6 0.15
35 35 0.85
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (35 bp):
ACATACTAAGATCGACACCGAAGACTCGGTGTACC
Found at i:44396619 original size:35 final size:35
Alignment explanation
Indices: 44396553--44396619 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
44396543 GTAGCAGTTT
* * * *
44396553 GGGCCTTAGCCTAGTTCAGTATCAGTTATGCACTA
1 GGGCCTTAGCCCAGTTCAATAACAGTCATGCACTA
44396588 GGGCCTTAGCCCA-TTACAATAACAGTCATGCA
1 GGGCCTTAGCCCAGTT-CAATAACAGTCATGCA
44396620 TACAGTAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.07
35 25 0.93
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (35 bp):
GGGCCTTAGCCCAGTTCAATAACAGTCATGCACTA
Found at i:44398502 original size:15 final size:15
Alignment explanation
Indices: 44398461--44398504 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
44398451 ATCATATTTT
*
44398461 ATTTTTTT-AGATTA
1 ATTTTTTTAAAATTA
44398475 ATTTTTATTTAAAATTA
1 A-TTTT-TTTAAAATTA
44398492 ATTTTTTTAAAAT
1 ATTTTTTTAAAAT
44398505 ATAGTACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.04
15 12 0.46
16 7 0.27
17 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
ATTTTTTTAAAATTA
Found at i:44398622 original size:42 final size:40
Alignment explanation
Indices: 44398575--44398664 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 40
44398565 TAAAAAGTAT
* *
44398575 TTATATTAAAAAAATACTACCATAAATATAATAAATGTCTTA
1 TTATATTAAAAAAATAC-A-AATAAATATAATAAATATCTTA
*
44398617 TTATATT--AAAAATACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAAATACAAATAAATATAATAAATATCTTA
*
44398655 TTGTATTAAA
1 TTATATTAAA
44398665 TATAATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
38 25 0.60
39 1 0.02
40 9 0.21
42 7 0.17
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAAAATACAAATAAATATAATAAATATCTTA
Found at i:44401893 original size:20 final size:20
Alignment explanation
Indices: 44401868--44401909 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
44401858 CACAAGCTCC
44401868 TGTGGCTTGGAACACGCCCG
1 TGTGGCTTGGAACACGCCCG
44401888 TGTGGCTTGGAACACGCCCG
1 TGTGGCTTGGAACACGCCCG
44401908 TG
1 TG
44401910 CAGTCATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21
Consensus pattern (20 bp):
TGTGGCTTGGAACACGCCCG
Found at i:44404071 original size:40 final size:40
Alignment explanation
Indices: 44403943--44404055 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
44403933 TGCTGGAAAT
* * * *
44403943 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
* * *
44403983 TATATCCGGGCTAAGGCCCGAAGGCATTCGTGCGAGTTAC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
*
44404023 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGC
44404056 ACGTGATTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
Found at i:44412319 original size:2 final size:2
Alignment explanation
Indices: 44412312--44412347 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
44412302 ATTAAGAAAC
44412312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44412348 TGAAAAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44412617 original size:17 final size:17
Alignment explanation
Indices: 44412597--44412635 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
44412587 AATATTTTTA
*
44412597 AAAAATTA-ATAATATAT
1 AAAAATTAGAAAATA-AT
44412614 AAAAATTAGAAAATAAT
1 AAAAATTAGAAAATAAT
44412631 AAAAA
1 AAAAA
44412636 AAATATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATTAGAAAATAAT
Found at i:44412618 original size:18 final size:18
Alignment explanation
Indices: 44412595--44412636 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
44412585 AAAATATTTT
*
44412595 TAAAAAATTA-ATAAT-A
1 TAAAAAATTAGAAAATAA
44412611 TATAAAAATTAGAAAATAA
1 TA-AAAAATTAGAAAATAA
44412630 TAAAAAA
1 TAAAAAA
44412637 AATATGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 8 0.36
18 9 0.41
19 3 0.14
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
TAAAAAATTAGAAAATAA
Found at i:44416466 original size:20 final size:20
Alignment explanation
Indices: 44416428--44416466 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44416418 TTCTTAGATT
*
44416428 TTTAACCCAACACATTATTA
1 TTTAACCCAACACAATATTA
* *
44416448 TTTAATCCAACTCAATATT
1 TTTAACCCAACACAATATT
44416467 TGTTTTCTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAACCCAACACAATATTA
Found at i:44416692 original size:14 final size:13
Alignment explanation
Indices: 44416646--44416698 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
44416636 TCATAATGAC
44416646 TAATTAATTTAATT
1 TAATT-ATTTAATT
* *
44416660 TCATTATTGAATT
1 TAATTATTTAATT
44416673 TCAATTATTTAATT
1 T-AATTATTTAATT
*
44416687 ATAATTACTTAA
1 -TAATTATTTAA
44416699 ATAATAATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 8 0.25
14 23 0.72
15 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.53
Consensus pattern (13 bp):
TAATTATTTAATT
Found at i:44418007 original size:23 final size:23
Alignment explanation
Indices: 44417977--44418021 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
44417967 GGGTAGGATC
44417977 TGAATCTGTATCTGTTATGCATG
1 TGAATCTGTATCTGTTATGCATG
44418000 TGAATCTGTATCTGTTATGCAT
1 TGAATCTGTATCTGTTATGCAT
44418022 TGATGTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (23 bp):
TGAATCTGTATCTGTTATGCATG
Found at i:44431400 original size:7 final size:7
Alignment explanation
Indices: 44431390--44431416 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
44431380 GTGTTTTAAT
44431390 TTTTTTA
1 TTTTTTA
44431397 TTTTTTA
1 TTTTTTA
44431404 TTTTTTA
1 TTTTTTA
44431411 TTTTTT
1 TTTTTT
44431417 GGTTGGGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:44439139 original size:15 final size:15
Alignment explanation
Indices: 44439119--44439148 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44439109 CGGGCTGGCA
44439119 CATGGGTGTGTGGTC
1 CATGGGTGTGTGGTC
44439134 CATGGGTGTGTGGTC
1 CATGGGTGTGTGGTC
44439149 AACCGTGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.13, G:0.47, T:0.33
Consensus pattern (15 bp):
CATGGGTGTGTGGTC
Found at i:44440284 original size:14 final size:15
Alignment explanation
Indices: 44440261--44440290 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
44440251 AAATCAAAAT
44440261 AAAATCAAAAATAAA
1 AAAATCAAAAATAAA
44440276 AAAAT-AAAAATAAA
1 AAAATCAAAAATAAA
44440290 A
1 A
44440291 TAAGACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAATCAAAAATAAA
Found at i:44443317 original size:19 final size:20
Alignment explanation
Indices: 44443295--44443336 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
44443285 TGCGCCAAGG
44443295 TGCACCTCATGTGCCAGA-A
1 TGCACCTCATGTGCCAGATA
* *
44443314 TGCACTTCGTGTGCCAGATA
1 TGCACCTCATGTGCCAGATA
44443334 TGC
1 TGC
44443337 GCTTTGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCACCTCATGTGCCAGATA
Found at i:44444292 original size:22 final size:23
Alignment explanation
Indices: 44444267--44444313 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
44444257 TTAAGCTTTC
*
44444267 ATTTTAGTTATATTTT-TAAAAA
1 ATTTTACTTATATTTTGTAAAAA
*
44444289 A-TTTACTTTTATTTTGTAAAAA
1 ATTTTACTTATATTTTGTAAAAA
44444311 ATT
1 ATT
44444314 AAATTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
21 12 0.57
22 8 0.38
23 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTTTACTTATATTTTGTAAAAA
Found at i:44444320 original size:22 final size:21
Alignment explanation
Indices: 44444277--44444320 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
44444267 ATTTTAGTTA
* *
44444277 TATTTTTAAAAAATTTACTTT
1 TATTTTTAAAAAATTAAATTT
44444298 TATTTTGTAAAAAATTAAATTT
1 TATTTT-TAAAAAATTAAATTT
44444320 T
1 T
44444321 TACAAAAAAT
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:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTTTTAAAAAATTAAATTT
Found at i:44444327 original size:18 final size:19
Alignment explanation
Indices: 44444306--44444341 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
44444296 TTTATTTTGT
44444306 AAAAAATTAAATT-TTTAC
1 AAAAAATTAAATTATTTAC
44444324 AAAAAATTAAATTATTTA
1 AAAAAATTAAATTATTTA
44444342 ATTGTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAAATTAAATTATTTAC
Found at i:44446395 original size:32 final size:34
Alignment explanation
Indices: 44446349--44446413 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
44446339 TAATAGTGGT
* *
44446349 ACTGGGCCAGAG-CCCTT-TTTAGATTACAATAA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
**
44446381 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATA
44446414 TGGCCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 10 0.37
33 5 0.19
34 12 0.44
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (34 bp):
ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
Found at i:44446758 original size:25 final size:27
Alignment explanation
Indices: 44446721--44446773 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
44446711 TCAAACATGC
44446721 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
44446747 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
44446773 A
1 A
44446774 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:44448283 original size:26 final size:26
Alignment explanation
Indices: 44448252--44448359 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
44448242 TGAAATTCCC
44448252 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
44448278 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
44448304 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
44448330 ATCATGGAACATTTACCT-AACTCATT
1 ATCATGGAACATTTACCTAAAC-CATT
44448356 ATCA
1 ATCA
44448360 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 2 0.03
26 74 0.97
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:44448765 original size:2 final size:2
Alignment explanation
Indices: 44448754--44448783 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
44448744 AATATAAATC
44448754 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44448784 CAAAGCACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44460742 original size:42 final size:43
Alignment explanation
Indices: 44460674--44460783 Score: 145
Period size: 42 Copynumber: 2.6 Consensus size: 43
44460664 GCCCTGTTTT
* * * *
44460674 CACACAGCCTG-TGACACAGGCGTGTCTGGTGGCCGTGTGATG
1 CACACGGCCTGTTGACACGGGCATGTCTGGTGGCCGTGTGAGG
44460716 CACACGG-CT-TATGACACGGGCATGTCTGGTGGCCGTGTGAGG
1 CACACGGCCTGT-TGACACGGGCATGTCTGGTGGCCGTGTGAGG
*
44460758 CACACGGCCTGTTTACACGGGCATGT
1 CACACGGCCTGTTGACACGGGCATGT
44460784 GACCCTTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
41 2 0.03
42 41 0.69
43 15 0.25
44 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.35, T:0.22
Consensus pattern (43 bp):
CACACGGCCTGTTGACACGGGCATGTCTGGTGGCCGTGTGAGG
Found at i:44464077 original size:29 final size:29
Alignment explanation
Indices: 44464035--44464094 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
44464025 GAGGTTTCAA
*
44464035 AGCCTCTTCATATTCTTCCTCATCATCAT
1 AGCCTCTTCATATTCTTCATCATCATCAT
44464064 AGCCTCTTCATATTCTTCATCATCATCAT
1 AGCCTCTTCATATTCTTCATCATCATCAT
44464093 AG
1 AG
44464095 TCATAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.40
Consensus pattern (29 bp):
AGCCTCTTCATATTCTTCATCATCATCAT
Found at i:44466210 original size:21 final size:24
Alignment explanation
Indices: 44466163--44466220 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
44466153 ATATGATCTA
*
44466163 AAAAGACGAAATAAACAAATTTAGT
1 AAAAGAAGAAATAAACAAA-TTAGT
*
44466188 AATA-AAGAAATAAA-AAA-TAGT
1 AAAAGAAGAAATAAACAAATTAGT
44466209 AAAAGAAGAAAT
1 AAAAGAAGAAAT
44466221 TTGAGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.24
22 7 0.24
23 3 0.10
24 9 0.31
25 3 0.10
ACGTcount: A:0.67, C:0.03, G:0.12, T:0.17
Consensus pattern (24 bp):
AAAAGAAGAAATAAACAAATTAGT
Found at i:44478844 original size:29 final size:30
Alignment explanation
Indices: 44478798--44478856 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
44478788 ATCTTTTAGG
*
44478798 CCCACATGGCCAGACACACAGGCGTGTGGC
1 CCCACACGGCCAGACACACAGGCGTGTGGC
* * *
44478828 CCCACACGGCTAG-CACACGGGCTTGTGGC
1 CCCACACGGCCAGACACACAGGCGTGTGGC
44478857 TTAGTTGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.20, C:0.37, G:0.31, T:0.12
Consensus pattern (30 bp):
CCCACACGGCCAGACACACAGGCGTGTGGC
Found at i:44479554 original size:66 final size:66
Alignment explanation
Indices: 44479448--44479581 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
44479438 CCGAATTGGT
*
44479448 AACACCGAGTGCTAATCCAATTAGTACTCACTAACCTAACATTGAGCGGAGTAATACTGAGGGAA
1 AACACCAAGTGCTAATCCAATTAGTACTCACTAACCTAACATTGAGCGGAGTAATACTGAGGGAA
44479513 G
66 G
44479514 AACACCAAGTGCTAATCCAATTAGTACTCACTAACCTAACATTGAGCGGAGTAATACTGAGGGAA
1 AACACCAAGTGCTAATCCAATTAGTACTCACTAACCTAACATTGAGCGGAGTAATACTGAGGGAA
44479579 G
66 G
44479580 AA
1 AA
44479582 GTGACTCACA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (66 bp):
AACACCAAGTGCTAATCCAATTAGTACTCACTAACCTAACATTGAGCGGAGTAATACTGAGGGAA
G
Found at i:44479659 original size:21 final size:21
Alignment explanation
Indices: 44479633--44479674 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
44479623 CATGTTGCAG
44479633 GAACTACATTCGCTACAGCAT
1 GAACTACATTCGCTACAGCAT
44479654 GAACTACATTCGCTACAGCAT
1 GAACTACATTCGCTACAGCAT
44479675 CTGTACCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (21 bp):
GAACTACATTCGCTACAGCAT
Found at i:44487823 original size:33 final size:33
Alignment explanation
Indices: 44487761--44487827 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
44487751 TCCGTGTATT
* * * *
44487761 TATGGCGTAAAAATCTGTCTGCTTTAGTGGTTA
1 TATGGCATAAAAATCCGTCTACTTCAGTGGTTA
*
44487794 TATGGCATAAACATCCGTCTACTTCAGTGGTTA
1 TATGGCATAAAAATCCGTCTACTTCAGTGGTTA
44487827 T
1 T
44487828 GTGTTCTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (33 bp):
TATGGCATAAAAATCCGTCTACTTCAGTGGTTA
Found at i:44489183 original size:18 final size:18
Alignment explanation
Indices: 44489158--44489207 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
44489148 TTGGGCCATA
*
44489158 TGGG-CCACAAGGGCATG
1 TGGGCCCACACGGGCATG
44489175 TGGGCCCACACGGGCATG
1 TGGGCCCACACGGGCATG
44489193 TGGGCCCACACGGGC
1 TGGGCCCACACGGGC
44489208 GAACATTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 4 0.13
18 27 0.87
ACGTcount: A:0.18, C:0.32, G:0.40, T:0.10
Consensus pattern (18 bp):
TGGGCCCACACGGGCATG
Found at i:44494132 original size:10 final size:10
Alignment explanation
Indices: 44494109--44494161 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
44494099 TTAGTTTTTC
*
44494109 AAATAATTAAA
1 AAAT-ATTATA
44494120 AAATATTATA
1 AAATATTATA
44494130 AAATATTATA
1 AAATATTATA
*
44494140 AAA-ATTTTA
1 AAATATTATA
44494149 AAA-ATTATTA
1 AAATATTA-TA
44494159 AAA
1 AAA
44494162 ATAATATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
9 11 0.29
10 23 0.61
11 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATATTATA
Found at i:44494133 original size:21 final size:19
Alignment explanation
Indices: 44494109--44494162 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
44494099 TTAGTTTTTC
44494109 AAATAATTAAAAAATATTATA
1 AAAT-ATTAAAAAATATTA-A
*
44494130 AAATATTATAAAAATTTTAA
1 AAATATTA-AAAAATATTAA
44494150 AAATTATTAAAAA
1 AAA-TATTAAAAA
44494163 TAATATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATTAAAAAATATTAA
Found at i:44494160 original size:19 final size:21
Alignment explanation
Indices: 44494109--44494164 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
44494099 TTAGTTTTTC
44494109 AAATAATTA-AAAAATATTATA
1 AAAT-ATTATAAAAATATTATA
44494130 AAATATTATAAAAAT-TT-TA
1 AAATATTATAAAAATATTATA
44494149 AAA-ATTATTAAAAATA
1 AAATATTA-TAAAAATA
44494165 ATATTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.12
19 12 0.38
20 6 0.19
21 10 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATATTATAAAAATATTATA
Found at i:44494569 original size:30 final size:30
Alignment explanation
Indices: 44494533--44494608 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 30
44494523 AATTAATTTT
*
44494533 TAATTTTAATATTTTTTTTGTAATT-TTAAA
1 TAATTTTAATATTTTTTTTATAATTCTT-AA
44494563 TAATTTTAATA--TTTTTTATAATTCTTAA
1 TAATTTTAATATTTTTTTTATAATTCTTAA
44494591 TAATTTTTAATCATTTTT
1 TAA-TTTTAAT-ATTTTT
44494609 CATAATTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 16 0.40
29 9 0.22
30 12 0.30
32 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (30 bp):
TAATTTTAATATTTTTTTTATAATTCTTAA
Found at i:44494578 original size:19 final size:21
Alignment explanation
Indices: 44494556--44494600 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
44494546 TTTTTTGTAA
44494556 TTTTAAATAATT-TTAAT-AT
1 TTTTAAATAATTCTTAATAAT
*
44494575 TTTT-TATAATTCTTAATAAT
1 TTTTAAATAATTCTTAATAAT
44494595 TTTTAA
1 TTTTAA
44494601 TCATTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 6 0.29
19 9 0.43
20 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAAATAATTCTTAATAAT
Found at i:44494608 original size:10 final size:10
Alignment explanation
Indices: 44494553--44494615 Score: 67
Period size: 10 Copynumber: 6.5 Consensus size: 10
44494543 ATTTTTTTTG
*
44494553 TAATTTTAAA
1 TAATTTTTAA
44494563 TAA-TTTTAA
1 TAATTTTTAA
*
44494572 T-ATTTTTTA
1 TAATTTTTAA
*
44494581 TAATTCTTAA
1 TAATTTTTAA
44494591 TAATTTTTAA
1 TAATTTTTAA
* *
44494601 TCATTTTTCA
1 TAATTTTTAA
44494611 TAATT
1 TAATT
44494616 ACTTGAAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
8 1 0.02
9 12 0.28
10 30 0.70
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:44494705 original size:19 final size:17
Alignment explanation
Indices: 44494677--44494719 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
44494667 TTCAAATAAT
44494677 TATTAAAAAAATTTGTTTA
1 TATT-AAAAAATTT-TTTA
*
44494696 TATTATAAAATTTTTTA
1 TATTAAAAAATTTTTTA
*
44494713 TTTTAAA
1 TATTAAA
44494720 GTTATTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
18 8 0.38
19 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TATTAAAAAATTTTTTA
Found at i:44506685 original size:17 final size:19
Alignment explanation
Indices: 44506643--44506686 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
44506633 ACGAAATTTT
*
44506643 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
44506662 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
44506680 AA-TATTA
1 AATTATTA
44506687 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:44506796 original size:15 final size:15
Alignment explanation
Indices: 44506778--44506806 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44506768 ATATTTATAA
44506778 AATTATTATTATTAT
1 AATTATTATTATTAT
44506793 AATTATTATTATTA
1 AATTATTATTATTA
44506807 GATAGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATTATTATTAT
Found at i:44509108 original size:20 final size:20
Alignment explanation
Indices: 44509065--44509112 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
44509055 GTTGTTTTGT
44509065 TATGGGCCAACTGTATTGAA
1 TATGGGCCAACTGTATTGAA
*
44509085 -ATGGGCCCAACTGTGTT-AA
1 TATGGG-CCAACTGTATTGAA
44509104 TAT-GGCCAA
1 TATGGGCCAA
44509113 GGCCCAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (20 bp):
TATGGGCCAACTGTATTGAA
Found at i:44509179 original size:60 final size:59
Alignment explanation
Indices: 44509103--44509241 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 59
44509093 AACTGTGTTA
* * * *
44509103 ATATGGCCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATATACTCT-GA-TATATAA-AGGGCTACGGCCCAGATTAATACTG
* * *
44509163 ATATGGGCTAGGCCCAATATACTCTGATACTATAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATACTCTGATA-TATAAAGGGCTACGGCCCAGATTAATACTG
*
44509223 ATATGGGCTAAAGCCCAAT
1 ATATGGGCT-AGGCCCAAT
44509242 TAACACTGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
59 1 0.01
60 51 0.76
61 15 0.22
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAATATACTCTGATATATAAAGGGCTACGGCCCAGATTAATACTG
Found at i:44512303 original size:13 final size:13
Alignment explanation
Indices: 44512299--44512323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44512289 CAATTACCCA
44512299 ACCCAACCCAATT
1 ACCCAACCCAATT
44512312 ACCCAACCCAAT
1 ACCCAACCCAAT
44512324 CATAAAAATT
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:44512308 original size:18 final size:18
Alignment explanation
Indices: 44512285--44512322 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
44512275 AATATATATT
44512285 AACCCAATTACCCAACCC
1 AACCCAATTACCCAACCC
44512303 AACCCAATTACCCAACCC
1 AACCCAATTACCCAACCC
44512321 AA
1 AA
44512323 TCATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.47, G:0.00, T:0.11
Consensus pattern (18 bp):
AACCCAATTACCCAACCC
Found at i:44512387 original size:5 final size:6
Alignment explanation
Indices: 44512348--44512395 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
44512338 ATAATTTAAT
*
44512348 AAATAA AAATAA GAATATAA AACTAA AAATAA AAATAA AAATTAA AAA
1 AAATAA AAATAA -AA-ATAA AAATAA AAATAA AAATAA AAA-TAA AAA
44512396 ATATATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
6 23 0.62
7 10 0.27
8 4 0.11
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:44512398 original size:14 final size:13
Alignment explanation
Indices: 44512348--44512395 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
44512338 ATAATTTAAT
44512348 AAATAAAAATAAGA
1 AAATAAAAATAA-A
* *
44512362 ATATAAAACT-AA
1 AAATAAAAATAAA
44512374 AAATAAAAATAAA
1 AAATAAAAATAAA
*
44512387 AATTAAAAA
1 AAATAAAAA
44512396 ATATATATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 9 0.32
13 11 0.39
14 8 0.29
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:44512398 original size:20 final size:20
Alignment explanation
Indices: 44512351--44512395 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
44512341 ATTTAATAAA
*
44512351 TAAAAATAAGAATATAAAAC
1 TAAAAATAAAAATATAAAAC
*
44512371 TAAAAATAAAAATA-AAAAT
1 TAAAAATAAAAATATAAAAC
44512390 TAAAAA
1 TAAAAA
44512396 ATATATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (20 bp):
TAAAAATAAAAATATAAAAC
Found at i:44512434 original size:9 final size:9
Alignment explanation
Indices: 44512420--44512456 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44512410 TACAAATAAC
44512420 TCGGTTAAT
1 TCGGTTAAT
44512429 TCGGTTAAT
1 TCGGTTAAT
*
44512438 TCGATTAAT
1 TCGGTTAAT
44512447 TCGGTTAAT
1 TCGGTTAAT
44512456 T
1 T
44512457 TTATACTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (9 bp):
TCGGTTAAT
Found at i:44514669 original size:16 final size:16
Alignment explanation
Indices: 44514639--44514669 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44514629 TAAATATAAA
*
44514639 TTATTCTATTTATATT
1 TTATTCTATATATATT
44514655 TTATTCTATATATAT
1 TTATTCTATATATAT
44514670 ATAAATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTCTATATATATT
Found at i:44515924 original size:60 final size:60
Alignment explanation
Indices: 44515834--44515986 Score: 186
Period size: 60 Copynumber: 2.6 Consensus size: 60
44515824 TTGGACCAAT
** * * *
44515834 AAAAGTTCAAATCTTGATGTGGAAACAATTACCAAATTTA-GAAGTTAATTTGGACAAAAA
1 AAAAGTTCAAATCTCAATGTGAAAACAATTACCAAATTTATGAA-TTAACTTAGACAAAAA
* **
44515894 AAAAGTTCAAATCTCAATGTGAAAATAATTATTAAATTTATGAATTAACTTAGACAAAAA
1 AAAAGTTCAAATCTCAATGTGAAAACAATTACCAAATTTATGAATTAACTTAGACAAAAA
*
44515954 AAAAATTCAAA-CATCAATGT-AAAACAATTACCA
1 AAAAGTTCAAATC-TCAATGTGAAAACAATTACCA
44515987 TTAAGATTTC
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
59 11 0.14
60 65 0.82
61 3 0.04
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (60 bp):
AAAAGTTCAAATCTCAATGTGAAAACAATTACCAAATTTATGAATTAACTTAGACAAAAA
Found at i:44520566 original size:15 final size:16
Alignment explanation
Indices: 44520547--44520590 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
44520537 TAATATCAAT
*
44520547 TACATTAATAATAAAA
1 TACATTATTAATAAAA
*
44520563 -ACATTATTAGTAAAA
1 TACATTATTAATAAAA
44520578 TA-ATTATTAATAA
1 TACATTATTAATAA
44520591 TTTGTTATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 23 0.96
16 1 0.04
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (16 bp):
TACATTATTAATAAAA
Found at i:44520795 original size:19 final size:18
Alignment explanation
Indices: 44520753--44520789 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
44520743 ATTTTTATTC
44520753 TATTTA-AAATAAAATAT
1 TATTTATAAATAAAATAT
44520770 TATTTATAAATAAAA-AT
1 TATTTATAAATAAAATAT
44520787 TAT
1 TAT
44520790 ATTTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATTTATAAATAAAATAT
Found at i:44520809 original size:13 final size:13
Alignment explanation
Indices: 44520793--44520818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44520783 AAATTATATT
44520793 TATTTAATTAAAA
1 TATTTAATTAAAA
44520806 TATTTAATTAAAA
1 TATTTAATTAAAA
44520819 AACTTGGTTT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTTAATTAAAA
Found at i:44521509 original size:18 final size:18
Alignment explanation
Indices: 44521488--44521527 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
44521478 AAAATATTTA
*
44521488 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
44521506 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
44521524 TTTT
1 TTTT
44521528 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:44521559 original size:12 final size:12
Alignment explanation
Indices: 44521529--44521561 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
44521519 TATATTTTTT
44521529 AAAATT-ATATA
1 AAAATTAATATA
44521540 AAAA-TAATATA
1 AAAATTAATATA
44521551 AAAATTAATAT
1 AAAATTAATAT
44521562 GGAATGGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:44522196 original size:14 final size:13
Alignment explanation
Indices: 44522161--44522200 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
44522151 TAAAACACAT
*
44522161 AAAAATTATAAAC
1 AAAAATTATAAAA
*
44522174 AAAATTTATAAAA
1 AAAAATTATAAAA
44522187 AAAAAGTTATAAAA
1 AAAAA-TTATAAAA
44522201 TTTTTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (13 bp):
AAAAATTATAAAA
Found at i:44522341 original size:18 final size:17
Alignment explanation
Indices: 44522305--44522339 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
44522295 TTATTTTTAA
*
44522305 TAAAAAATTTATAGCTT
1 TAAAAAATTTATAACTT
44522322 TAAAAAATTTATAACTT
1 TAAAAAATTTATAACTT
44522339 T
1 T
44522340 TATTTATAAT
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:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAAAAATTTATAACTT
Found at i:44529656 original size:26 final size:26
Alignment explanation
Indices: 44529597--44529656 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
44529587 TCAATTAATA
* *
44529597 AAGTTCTCTTTGAGTTTTCTTTTTAAG
1 AAGTTTTC-TTGAGTTTTCTTTTAAAG
*
44529624 AATTTTTCTTGAGTTTTCTTTTAAA-
1 AAGTTTTCTTGAGTTTTCTTTTAAAG
44529649 AGAGTTTT
1 A-AGTTTT
44529657 AACAATCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.04
26 21 0.75
27 6 0.21
ACGTcount: A:0.22, C:0.08, G:0.13, T:0.57
Consensus pattern (26 bp):
AAGTTTTCTTGAGTTTTCTTTTAAAG
Found at i:44530610 original size:26 final size:26
Alignment explanation
Indices: 44530565--44530614 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
44530555 ACTTTTTCTT
*
44530565 AAAGAAAACTCAAGAGAAATTTTAAA
1 AAAGAAAACTCAAGAAAAATTTTAAA
44530591 AAAGAAAACTCAA-ATAAAATTTTA
1 AAAGAAAACTCAAGA-AAAATTTTA
44530615 TTAATTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.22
Consensus pattern (26 bp):
AAAGAAAACTCAAGAAAAATTTTAAA
Found at i:44532856 original size:62 final size:62
Alignment explanation
Indices: 44532752--44532906 Score: 177
Period size: 62 Copynumber: 2.5 Consensus size: 62
44532742 CATAGCTGAG
* * * *
44532752 TAACTCACTATTTTGAAGTTAGAGTCACATGAGCCAGAGACACAGATGTGTGTCTAGGCTGTA
1 TAACTCACTATTTGGAA-TTAGAGTCACACGAGCCAGAGACACAGACGTGTGTCTAGGCCGTA
* * * * *
44532815 TAACTCACTATTTGGAATTAGAGTCACACGGGCCA-AGGACACGGGCGTGTGTTTAGGCCGTG
1 TAACTCACTATTTGGAATTAGAGTCACACGAGCCAGA-GACACAGACGTGTGTCTAGGCCGTA
* *
44532877 TAACTCACTGTTTTGGAATTAGAGACACAC
1 TAACTCACT-ATTTGGAATTAGAGTCACAC
44532907 AGACCAAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
61 1 0.01
62 44 0.56
63 34 0.43
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (62 bp):
TAACTCACTATTTGGAATTAGAGTCACACGAGCCAGAGACACAGACGTGTGTCTAGGCCGTA
Found at i:44532929 original size:63 final size:62
Alignment explanation
Indices: 44532751--44532942 Score: 179
Period size: 63 Copynumber: 3.1 Consensus size: 62
44532741 ACATAGCTGA
* * * * * *** *
44532751 GTAACTCACTATTTTGAAGTTAGAGTCACA-TGAGCCAGAGACACAGATGTGTGTCTAGGCTGT
1 GTAACTCACTATTTGGAA-TTAGAGACACACAGA-CCAAAGACACGGGCATGTGTCTAGGCCGT
* * * * * * *
44532814 ATAACTCACTATTTGGAATTAGAGTCACACGGGCCAAGGACACGGGCGTGTGTTTAGGCCGT
1 GTAACTCACTATTTGGAATTAGAGACACACAGACCAAAGACACGGGCATGTGTCTAGGCCGT
* * *
44532876 GTAACTCACTGTTTTGGAATTAGAGACACACAGACCAAAGACATGGGCATGTGTCCAGGCCGT
1 GTAACTCACT-ATTTGGAATTAGAGACACACAGACCAAAGACACGGGCATGTGTCTAGGCCGT
44532939 GTAA
1 GTAA
44532943 GATATATTTT
Statistics
Matches: 106, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
62 42 0.40
63 64 0.60
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25
Consensus pattern (62 bp):
GTAACTCACTATTTGGAATTAGAGACACACAGACCAAAGACACGGGCATGTGTCTAGGCCGT
Found at i:44533122 original size:108 final size:108
Alignment explanation
Indices: 44532985--44533195 Score: 287
Period size: 108 Copynumber: 2.0 Consensus size: 108
44532975 GTGTTGAACT
* *
44532985 GTGTGCTAAACCGTTTAACTCAATATTTTGAGCCACATGGACGTGTGTTAGGACATGTGACAGGT
1 GTGTGCTAAACCGTGTAACTCAATATTTTGAGCCACATGGACGTGTATTAGGACATGTGACAGGT
* * *
44533050 CATGTGTGACACTGAGGTAGGCCACACTGGTATGTGCTGGGTC
66 CATGTGCGACACTAAGGTAGGCCACACGGGTATGTGCTGGGTC
* * * * * * *
44533093 GTGTGCTATACCGTGTAACTTACTGTTTTGAGCCACATGGGCGTGTATTAGGCCATGTGATAGGT
1 GTGTGCTAAACCGTGTAACTCAATATTTTGAGCCACATGGACGTGTATTAGGACATGTGACAGGT
* * *
44533158 CATGTGCGACATTAAGGTAGGCCATACGGGTGTGTGCT
66 CATGTGCGACACTAAGGTAGGCCACACGGGTATGTGCT
44533196 AGGCTGTGTG
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
108 88 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (108 bp):
GTGTGCTAAACCGTGTAACTCAATATTTTGAGCCACATGGACGTGTATTAGGACATGTGACAGGT
CATGTGCGACACTAAGGTAGGCCACACGGGTATGTGCTGGGTC
Found at i:44533483 original size:52 final size:52
Alignment explanation
Indices: 44533405--44533511 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
44533395 ATGAAATATG
44533405 ATAAGTAAGTGTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
1 ATAAGTAAGTGTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
44533457 ATAAGTAAGTGTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
1 ATAAGTAAGTGTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
44533509 ATA
1 ATA
44533512 CGTATATCTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (52 bp):
ATAAGTAAGTGTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
Found at i:44533524 original size:52 final size:52
Alignment explanation
Indices: 44533405--44533524 Score: 197
Period size: 52 Copynumber: 2.3 Consensus size: 52
44533395 ATGAAATATG
*
44533405 ATAAGTAAGTGTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
1 ATAAGTAAGTCTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
*
44533457 ATAAGTAAGTGTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
1 ATAAGTAAGTCTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
*
44533509 ATACGTATA-TCTGATA
1 ATAAGTA-AGTCTGATA
44533525 TCTATTAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
52 64 0.98
53 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (52 bp):
ATAAGTAAGTCTGATAGCATAACATGAGCATGATCTGAATTTGTACTACTAT
Found at i:44543575 original size:36 final size:35
Alignment explanation
Indices: 44543474--44543578 Score: 90
Period size: 33 Copynumber: 3.0 Consensus size: 35
44543464 CTATGGCAGT
* * *
44543474 TTTTTAGACGCAAGACCATGGTTGGACCATGTCAA
1 TTTTTAGACGTAAGACCATGGTTGGACCATGACAG
* * *** *
44543509 TGTTT--ATGTAAGACCATAGCAAGG-CTATGACAG
1 TTTTTAGACGTAAGACCAT-GGTTGGACCATGACAG
44543542 TTTTTCAGACGTAAGACCATGGTTGGACCATGACAG
1 TTTTT-AGACGTAAGACCATGGTTGGACCATGACAG
44543578 T
1 T
44543579 GTATATATAT
Statistics
Matches: 50, Mismatches: 15, Indels: 9
0.68 0.20 0.12
Matches are distributed among these distances:
33 20 0.40
34 3 0.06
35 7 0.14
36 20 0.40
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (35 bp):
TTTTTAGACGTAAGACCATGGTTGGACCATGACAG
Found at i:44543587 original size:2 final size:2
Alignment explanation
Indices: 44543580--44543606 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44543570 CATGACAGTG
44543580 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
44543607 GTAAGACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44554872 original size:29 final size:29
Alignment explanation
Indices: 44554782--44554941 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
44554772 ACTCGATTTC
* * **
44554782 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
44554811 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
44554839 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
44554869 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
44554898 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
44554927 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
44554942 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:44560815 original size:29 final size:29
Alignment explanation
Indices: 44560725--44560884 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
44560715 ACTCGATTTC
* * **
44560725 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
44560754 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
44560782 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
44560812 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
44560841 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
44560870 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
44560885 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:44568870 original size:29 final size:29
Alignment explanation
Indices: 44568780--44568939 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
44568770 ACTCGATTTC
* * **
44568780 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
44568809 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
44568837 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
44568867 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
44568896 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
44568925 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
44568940 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:44571118 original size:21 final size:21
Alignment explanation
Indices: 44571090--44571175 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
44571080 CCTGATCAGT
* *
44571090 ATACGACACATAAAGTGCCTA
1 ATACGACACACAAAGTGCCTG
* * *
44571111 AAACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
* *
44571132 ATACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
*
44571153 ATACGACACATAAAGTGCCTG
1 ATACGACACACAAAGTGCCTG
44571174 AT
1 AT
44571176 CGATAAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (21 bp):
ATACGACACACAAAGTGCCTG
Found at i:44572644 original size:16 final size:17
Alignment explanation
Indices: 44572609--44572644 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
44572599 CCTAATTCTC
44572609 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
44572625 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
44572640 CCTTC
1 CCTTC
44572645 CCCTGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:44577693 original size:18 final size:17
Alignment explanation
Indices: 44577670--44577712 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
44577660 CGTAAGATTC
44577670 TTCTTCTCCAGTATGCAT
1 TTCTTCTCCAGTAT-CAT
44577688 TTCTTCAT-CAGTATCAT
1 TTCTTC-TCCAGTATCAT
*
44577705 TTATTCTC
1 TTCTTCTC
44577713 TCATCCGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 1 0.05
17 8 0.36
18 12 0.55
19 1 0.05
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.49
Consensus pattern (17 bp):
TTCTTCTCCAGTATCAT
Found at i:44578992 original size:21 final size:21
Alignment explanation
Indices: 44578964--44579049 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
44578954 CCTGATCAGT
* *
44578964 ATACGACACATAAAGTGCCTA
1 ATACGACACACAAAGTGCCTG
* * *
44578985 AAACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
* *
44579006 ATACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
*
44579027 ATACGACACATAAAGTGCCTG
1 ATACGACACACAAAGTGCCTG
44579048 AT
1 AT
44579050 CGATAAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (21 bp):
ATACGACACACAAAGTGCCTG
Found at i:44580508 original size:15 final size:16
Alignment explanation
Indices: 44580485--44580515 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
44580475 ATTCTCCCTT
44580485 TTTCTTTTCTTTCTTC
1 TTTCTTTTCTTTCTTC
44580501 TTTC-TTTCTTTCTTC
1 TTTCTTTTCTTTCTTC
44580516 CCCTGTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTTCTTTCTTC
Found at i:44582261 original size:7 final size:7
Alignment explanation
Indices: 44582245--44582317 Score: 85
Period size: 7 Copynumber: 10.4 Consensus size: 7
44582235 TCCCTTCCTA
*
44582245 TTCCAAT
1 TTCCAGT
44582252 TTCCAGT
1 TTCCAGT
44582259 TTCCAG-
1 TTCCAGT
44582265 TTCCTAGT
1 TTCC-AGT
* *
44582273 TTCTACT
1 TTCCAGT
*
44582280 TTCTAGT
1 TTCCAGT
44582287 TTCCAGT
1 TTCCAGT
44582294 TTCCAGT
1 TTCCAGT
44582301 TTCCAGT
1 TTCCAGT
*
44582308 TTCCATT
1 TTCCAGT
44582315 TTC
1 TTC
44582318 TTTTCTTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
6 4 0.07
7 51 0.88
8 3 0.05
ACGTcount: A:0.15, C:0.27, G:0.10, T:0.48
Consensus pattern (7 bp):
TTCCAGT
Found at i:44584843 original size:21 final size:22
Alignment explanation
Indices: 44584825--44584869 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
44584815 GAGAAAAAGT
44584825 TTTGGGGGAAAAAGTAAAAATA
1 TTTGGGGGAAAAAGTAAAAATA
* *
44584847 TTTGGGGTAAAATGT-AAAATA
1 TTTGGGGGAAAAAGTAAAAATA
44584868 TT
1 TT
44584870 ATAGTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.31
Consensus pattern (22 bp):
TTTGGGGGAAAAAGTAAAAATA
Found at i:44585247 original size:2 final size:2
Alignment explanation
Indices: 44585240--44585278 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
44585230 TATTGAACAA
*
44585240 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44585279 GCACCTGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:44586302 original size:41 final size:41
Alignment explanation
Indices: 44586245--44586326 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
44586235 TTGGTGGAAC
*
44586245 ACTGGTATAATCATAAGGCATCAAGGGTTTCCTAGGACAAT
1 ACTGGTATAATCATAAGGCATCAAGGGTATCCTAGGACAAT
44586286 ACTGGTATAATCATAAGGCATCAAGGGTATCCTAGGACAAT
1 ACTGGTATAATCATAAGGCATCAAGGGTATCCTAGGACAAT
44586327 CATTTGTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (41 bp):
ACTGGTATAATCATAAGGCATCAAGGGTATCCTAGGACAAT
Found at i:44587196 original size:14 final size:15
Alignment explanation
Indices: 44587172--44587200 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
44587162 ATTAAATCTT
44587172 TAATATAAAATATTA
1 TAATATAAAATATTA
44587187 TAATAT-AAATATTA
1 TAATATAAAATATTA
44587201 AAAAAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATATAAAATATTA
Found at i:44588556 original size:26 final size:26
Alignment explanation
Indices: 44588521--44588785 Score: 229
Period size: 26 Copynumber: 10.2 Consensus size: 26
44588511 AAAGAAAACG
*
44588521 AAATAAATAATATATAAAACAATTTG
1 AAATAAATAATATATAAAACAATTTA
* *
44588547 AATTAGAT-A-ATATAAAACAATTTA
1 AAATAAATAATATATAAAACAATTTA
* * *
44588571 AAGTAAATAATATGTAAAACAAATTA
1 AAATAAATAATATATAAAACAATTTA
** **
44588597 AAATAAATAATATACGAAGGAATTTA
1 AAATAAATAATATATAAAACAATTTA
44588623 AAATAAATAATATATATGAAA-AATTTA
1 AAATAAATAATATATA--AAACAATTTA
* *
44588650 AAAT-AAT-ATGTA-AAAAGAAGTTTA
1 AAATAAATAATATATAAAACAA-TTTA
* *
44588674 AAATAAATAATATACAAAACAGTTTAA
1 AAATAAATAATATATAAAACAATTT-A
* *
44588701 AAATAAATGATATATAAAAAAATAATTCA
1 AAATAAATAATATATAAAACAAT--TT-A
** *
44588730 AAATAAATAATATATATGACAGTTTAA
1 AAATAAATAATATATAAAACAATTT-A
*
44588757 AAATAAATAATATATGAAA-AATTTA
1 AAATAAATAATATATAAAACAATTTA
44588782 AAAT
1 AAAT
44588786 GGATAATAGT
Statistics
Matches: 191, Mismatches: 36, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
22 3 0.02
23 2 0.01
24 29 0.15
25 14 0.07
26 66 0.35
27 54 0.28
28 2 0.01
29 21 0.11
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (26 bp):
AAATAAATAATATATAAAACAATTTA
Found at i:44588564 original size:24 final size:24
Alignment explanation
Indices: 44588521--44588863 Score: 168
Period size: 26 Copynumber: 13.6 Consensus size: 24
44588511 AAAGAAAACG
*
44588521 AAATAAATAATATATAAAACAATTTG
1 AAATAAAT-A-ATATAAAACAATTTA
* *
44588547 AATTAGATAATATAAAACAATTTA
1 AAATAAATAATATAAAACAATTTA
* *
44588571 AAGTAAATAATATGTAAAACAAATTA
1 AAATAAATAATA--TAAAACAATTTA
**
44588597 AAATAAATAATATACGAAGGAATTTA
1 AAATAAATAATATA--AAACAATTTA
*
44588623 AAATAAATAATATATATGAAAAATTTA
1 AAATAAATAATATA-A--AACAATTTA
* *
44588650 AAAT-AAT-ATGTAAAAAGAAGTTTA
1 AAATAAATAATAT-AAAACAA-TTTA
*
44588674 AAATAAATAATATACAAAACAGTTTAA
1 AAATAAATAATAT--AAAACAATTT-A
*
44588701 AAATAAATGATATATAAAAAAATAATTCA
1 AAATAAAT-A-ATATAAAACAAT--TT-A
* *
44588730 AAATAAATAATATATATGACAGTTTAA
1 AAATAAATAATATA-A-AACAATTT-A
44588757 AAATAAATAATATATGAAA-AATTTA
1 AAATAAATAATATA--AAACAATTTA
* * * * *
44588782 AAATGGATAATAGTTTGAAATAGTTTA
1 AAAT--A-AATAATATAAAACAATTTA
* *
44588809 AAAT--AT-GTAGAAAAC---TTA
1 AAATAAATAATATAAAACAATTTA
44588827 AAATAAAT-A-ATAAAACAATTTAA
1 AAATAAATAATATAAAACAATTT-A
44588850 AAATAAATAATATA
1 AAATAAATAATATA
44588864 TGAGAAAAAG
Statistics
Matches: 247, Mismatches: 39, Indels: 63
0.71 0.11 0.18
Matches are distributed among these distances:
18 7 0.03
19 6 0.02
20 2 0.01
21 5 0.02
22 4 0.02
23 13 0.05
24 35 0.14
25 17 0.07
26 66 0.27
27 64 0.26
28 10 0.04
29 18 0.07
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (24 bp):
AAATAAATAATATAAAACAATTTA
Found at i:44588589 original size:50 final size:51
Alignment explanation
Indices: 44588521--44588785 Score: 191
Period size: 50 Copynumber: 5.1 Consensus size: 51
44588511 AAAGAAAACG
* * * *
44588521 AAATAAATAATATATAAAACAATTTGAATTAGATAATATA-AAACAATTTA
1 AAATAAATAATATATAAAACAAATTAAAATAAATAATATACAAACAATTTA
* * **
44588571 AAGTAAATAATATGTAAAACAAATTAAAATAAATAATATACGAAGGAATTTA
1 AAATAAATAATATATAAAACAAATTAAAATAAATAATATAC-AAACAATTTA
* * * *
44588623 AAATAAATAATATATATGAAA-AATTTAAAAT-AAT-ATGTAAAAAGAAGTTTA
1 AAATAAATAATATATA--AAACAAATTAAAATAAATAATATACAAACAA-TTTA
* ** *
44588674 AAATAAATAATATACAAAACAGTTTAAAAATAAATGATATATA-AAAAAATAATTCA
1 AAATAAATAATATATAAAACAAATT-AAAATAAAT-A-ATATACAAACAAT--TT-A
** ** *
44588730 AAATAAATAATATATATGACAGTTTAAAAATAAATAATATATGAAA-AATTTA
1 AAATAAATAATATATAAAACAAATT-AAAATAAATAATATA-CAAACAATTTA
44588782 AAAT
1 AAAT
44588786 GGATAATAGT
Statistics
Matches: 178, Mismatches: 21, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
49 3 0.02
50 43 0.24
51 28 0.16
52 33 0.19
53 12 0.07
54 13 0.07
55 10 0.06
56 36 0.20
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (51 bp):
AAATAAATAATATATAAAACAAATTAAAATAAATAATATACAAACAATTTA
Found at i:44588633 original size:76 final size:75
Alignment explanation
Indices: 44588521--44588785 Score: 216
Period size: 76 Copynumber: 3.4 Consensus size: 75
44588511 AAAGAAAACG
* * * * *
44588521 AAATAAATAATATATAAAACAATTTGAATTAGATAATATAAAACAATTTAAAGTAAATAATATGT
1 AAATAAATAATATACAAAACAATTTAAAATAAATAATATAAAAAAATTTAAA-TAAATAATATGT
44588586 AAAACAAATTA
65 AAAACAAATTA
* **
44588597 AAATAAATAATATACGAAGGAATTTAAAATAAATAATATATATGAAAAATTT--A-AAATAATAT
1 AAATAAATAATATACAAAACAATTTAAAATAAATAATATA-A--AAAAATTTAAATAAATAATAT
44588659 GTAAAA-AGAAGTTTA
63 GTAAAACA-AA--TTA
*
44588674 AAATAAATAATATACAAAACAGTTTAAAAATAAATGATATATAAAAAAATAATTCAAAATAAATA
1 AAATAAATAATATACAAAACAATTT-AAAATAAAT-A-ATATAAAAAAAT--TT--AAATAAATA
* ** **
44588739 ATATATATGACAGTTTAA
59 ATATGTAAAACAAATT-A
**
44588757 AAATAAATAATATATGAAA-AATTTAAAAT
1 AAATAAATAATATACAAAACAATTTAAAAT
44588786 GGATAATAGT
Statistics
Matches: 151, Mismatches: 20, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
74 1 0.01
75 17 0.11
76 33 0.22
77 32 0.21
78 9 0.06
79 11 0.07
80 5 0.03
81 5 0.03
82 6 0.04
83 19 0.13
84 12 0.08
85 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (75 bp):
AAATAAATAATATACAAAACAATTTAAAATAAATAATATAAAAAAATTTAAATAAATAATATGTA
AAACAAATTA
Found at i:44588681 original size:103 final size:108
Alignment explanation
Indices: 44588521--44588785 Score: 257
Period size: 103 Copynumber: 2.5 Consensus size: 108
44588511 AAAGAAAACG
* * *
44588521 AAATAAATAATATATA--AAACAATTTGAATTAGATAATATAAAACAATTTAAAGTAAATAATAT
1 AAATAAATAATATATATGAAACAATTTAAAATAGATAATATAAAACAATTTAAAATAAATAATAT
** ** * *
44588584 GTAAAACAAATT-AAAATAAAT-A-ATAT-ACGAAGGAATTTA
66 ACAAAACAAATTAAAAATAAATGATATATAAAAAAAGAATTCA
* *
44588623 AAATAAATAATATATATGAAA-AATTTAAAATA-AT-ATGTAAAAAGAAGTTTAAAATAAATAAT
1 AAATAAATAATATATATGAAACAATTTAAAATAGATAATAT-AAAACAA-TTTAAAATAAATAAT
** *
44588685 ATACAAAACAGTTTAAAAATAAATGATATATAAAAAAATAATTCA
64 ATACAAAACAAATTAAAAATAAATGATATATAAAAAAAGAATTCA
* *
44588730 AAATAAATAATATATATG--ACAGTTTAAAAATAAATAATATATGAAA-AATTTAAAAT
1 AAATAAATAATATATATGAAACAATTT-AAAATAGATAATATA--AAACAATTTAAAAT
44588786 GGATAATAGT
Statistics
Matches: 133, Mismatches: 16, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
101 3 0.02
102 24 0.18
103 33 0.25
104 12 0.09
105 2 0.02
106 8 0.06
107 32 0.24
108 11 0.08
109 5 0.04
110 3 0.02
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (108 bp):
AAATAAATAATATATATGAAACAATTTAAAATAGATAATATAAAACAATTTAAAATAAATAATAT
ACAAAACAAATTAAAAATAAATGATATATAAAAAAAGAATTCA
Found at i:44588721 original size:29 final size:27
Alignment explanation
Indices: 44588622--44588784 Score: 103
Period size: 27 Copynumber: 6.1 Consensus size: 27
44588612 GAAGGAATTT
*
44588622 AAAATAAATAATATATATGAAAAA-TTT-
1 AAAATAAAT-ATATATA-AAAAAAGTTTA
* *
44588649 AAAAT-AATATGTA-AAAAGAAGTTT-
1 AAAATAAATATATATAAAAAAAGTTTA
*
44588673 AAAATAAATA-ATATACAAAACAGTTTA
1 AAAATAAATATATATA-AAAAAAGTTTA
*
44588700 AAAATAAATGATATATAAAAAAA-TAATTC
1 AAAATAAAT-ATATATAAAAAAAGT--TTA
** *
44588729 AAAATAAATA-ATATATATGACAGTTTA
1 AAAATAAATATATATA-AAAAAAGTTTA
*
44588756 AAAATAAATA-ATATATGAAAAA-TTTA
1 AAAATAAATATATATA-AAAAAAGTTTA
44588782 AAA
1 AAA
44588785 TGGATAATAG
Statistics
Matches: 109, Mismatches: 16, Indels: 23
0.74 0.11 0.16
Matches are distributed among these distances:
23 4 0.04
24 11 0.10
25 9 0.08
26 18 0.17
27 40 0.37
28 10 0.09
29 17 0.16
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (27 bp):
AAAATAAATATATATAAAAAAAGTTTA
Found at i:44601447 original size:46 final size:46
Alignment explanation
Indices: 44601395--44601713 Score: 430
Period size: 46 Copynumber: 7.0 Consensus size: 46
44601385 GCTTTCTGAA
*
44601395 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
44601441 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
44601487 ATAAAATGTGCAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
44601533 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
44601579 ATAAAATGTGTAAGACCATGGTTG-AAGATACCATGG-AA-ATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG--AT
*** *
44601624 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
44601670 A-GAAAATGAGTAAGACCATAGTTGAAAGACACAATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
44601714 TCAAAGATAA
Statistics
Matches: 245, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
43 2 0.01
44 2 0.01
45 34 0.14
46 203 0.83
47 2 0.01
48 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:44601685 original size:137 final size:138
Alignment explanation
Indices: 44601398--44601708 Score: 466
Period size: 137 Copynumber: 2.3 Consensus size: 138
44601388 TTCTGAAATG
* *
44601398 AAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGATATGAAATGTGTAAGACCATGGT
1 AAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACAGGATATAAAATGTGTAAGACCATGGT
* * **
44601463 TGAAAGATACCATGGCAACAGGATATAAAATGTGCAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACAGAACATAAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
*
44601528 ATGATATA
131 ATGATAGA
*
44601536 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGTGTAAGACCATGGT
1 AAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACAGGATATAAAATGTGTAAGACCATGGT
*
44601601 TG-AAGATACCATGG-AA-ATGTAACATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCA
66 TGAAAGATACCATGGCAACA-G-AACATAAAATGAACAAGACCATGGTTGAAAGATACCATGGCA
*
44601663 ACCTGATAGA
129 ACATGATAGA
* * *
44601673 AAATGAGTAAGACCATAGTTGAAAGACACAATGGCA
1 AAATGTGTAAGACCATGGTTGAAAGACACCATGGCA
44601709 TCATGTCAAA
Statistics
Matches: 157, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
135 1 0.01
136 3 0.02
137 89 0.57
138 64 0.41
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (138 bp):
AAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACAGGATATAAAATGTGTAAGACCATGGT
TGAAAGATACCATGGCAACAGAACATAAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
ATGATAGA
Found at i:44602015 original size:16 final size:17
Alignment explanation
Indices: 44601994--44602026 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44601984 ATGATGGAGC
44601994 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
44602010 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
44602027 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:44605828 original size:2 final size:2
Alignment explanation
Indices: 44605821--44605853 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44605811 ATAGTATTGT
44605821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44605854 TATGAGTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44609517 original size:6 final size:7
Alignment explanation
Indices: 44609499--44609526 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
44609489 ATGTTACTCC
44609499 CTTTTTT
1 CTTTTTT
44609506 CTTTTTT
1 CTTTTTT
44609513 CTTTTTT
1 CTTTTTT
44609520 CTTTTTT
1 CTTTTTT
44609527 ATGAAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
CTTTTTT
Found at i:44611924 original size:7 final size:7
Alignment explanation
Indices: 44611912--44611936 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44611902 TCAAACGTTG
44611912 TTTCCAT
1 TTTCCAT
44611919 TTTCCAT
1 TTTCCAT
44611926 TTTCCAT
1 TTTCCAT
44611933 TTTC
1 TTTC
44611937 ATTGTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTCCAT
Found at i:44622673 original size:10 final size:11
Alignment explanation
Indices: 44622643--44622675 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
44622633 CGGCCCGCCC
44622643 ATATTAATTTT
1 ATATTAATTTT
44622654 ATATTAATTTT
1 ATATTAATTTT
44622665 ATA-TAATTTT
1 ATATTAATTTT
44622675 A
1 A
44622676 AAAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:44622699 original size:18 final size:18
Alignment explanation
Indices: 44622676--44622720 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
44622666 TATAATTTTA
*
44622676 AAAAATATATAAACCATC
1 AAAAATATATAAAACATC
44622694 AAAAATACTA-AAAACATC
1 AAAAATA-TATAAAACATC
44622712 AAAAA-ATAT
1 AAAAATATAT
44622721 TTCTCAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 19 0.79
19 2 0.08
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATATATAAAACATC
Found at i:44622841 original size:30 final size:30
Alignment explanation
Indices: 44622798--44622855 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
44622788 TTTAACAAGT
* *
44622798 AAATGCCTCTAAAATAGTAACAAAATTAGA
1 AAATGCCTCTAAAATAATAAAAAAATTAGA
* *
44622828 AAATGTCTTTAAAATAATAAAAAAATTA
1 AAATGCCTCTAAAATAATAAAAAAATTA
44622856 ACAATAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.28
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAAAAAAATTAGA
Found at i:44622914 original size:22 final size:22
Alignment explanation
Indices: 44622889--44622931 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
44622879 TATCCAAACA
44622889 ATAACAACAAAATAGTAGCAAT
1 ATAACAACAAAATAGTAGCAAT
* **
44622911 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
44622932 AATAGGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAT
Found at i:44622935 original size:11 final size:11
Alignment explanation
Indices: 44622896--44622936 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
44622886 ACAATAACAA
44622896 CAAAATAGTAG
1 CAAAATAGTAG
* *
44622907 CAATATAATAG
1 CAAAATAGTAG
*
44622918 TAAAATAGTAG
1 CAAAATAGTAG
44622929 CAAAATAG
1 CAAAATAG
44622937 GAAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:44628797 original size:18 final size:19
Alignment explanation
Indices: 44628774--44628812 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
44628764 CTTGGCCTAT
* *
44628774 TACAGTATCA-ATATTCAG
1 TACAGTAACAGATATACAG
44628792 TACAGTAACAGATATACAG
1 TACAGTAACAGATATACAG
44628811 TA
1 TA
44628813 TCAAATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (19 bp):
TACAGTAACAGATATACAG
Found at i:44635053 original size:21 final size:21
Alignment explanation
Indices: 44635024--44635077 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
44635014 TTATATGTTT
*
44635024 AGTATGATCTGTGGTA-AGATA
1 AGTATGATCTGTGATATA-ATA
* *
44635045 AGTACGATCAGTGATATAATA
1 AGTATGATCTGTGATATAATA
44635066 AGTATGATCTGT
1 AGTATGATCTGT
44635078 ATTTGTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.33
Consensus pattern (21 bp):
AGTATGATCTGTGATATAATA
Found at i:44635104 original size:20 final size:20
Alignment explanation
Indices: 44635064--44635105 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
44635054 AGTGATATAA
* * *
44635064 TAAGTATGATCTGTATTTGT
1 TAAGCATGATCTGAATCTGT
44635084 TAAGCATGATCTGAATCTGT
1 TAAGCATGATCTGAATCTGT
44635104 TA
1 TA
44635106 TAAAAGCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (20 bp):
TAAGCATGATCTGAATCTGT
Found at i:44640266 original size:23 final size:21
Alignment explanation
Indices: 44640239--44640280 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
44640229 ATGAATTAGA
44640239 ATGTTGAAATGTTATGTTTAAAT
1 ATGTTGAAATG--ATGTTTAAAT
*
44640262 ATGTTTAAATGATGTTTAA
1 ATGTTGAAATGATGTTTAA
44640281 GTCTCTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.48
Consensus pattern (21 bp):
ATGTTGAAATGATGTTTAAAT
Found at i:44640278 original size:11 final size:10
Alignment explanation
Indices: 44640251--44640280 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
44640241 GTTGAAATGT
44640251 TATGTTTAAA
1 TATGTTTAAA
44640261 TATGTTTAAA
1 TATGTTTAAA
44640271 TGATGTTTAA
1 T-ATGTTTAA
44640281 GTCTCTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
TATGTTTAAA
Found at i:44641175 original size:12 final size:12
Alignment explanation
Indices: 44641158--44641183 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44641148 ATATATTTTA
44641158 ATATTTTAAGGT
1 ATATTTTAAGGT
44641170 ATATTTTAAGGT
1 ATATTTTAAGGT
44641182 AT
1 AT
44641184 TTGGAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
ATATTTTAAGGT
Found at i:44641371 original size:2 final size:2
Alignment explanation
Indices: 44641364--44641390 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44641354 TTGATTTGTG
44641364 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
44641391 TTGTATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44641734 original size:20 final size:20
Alignment explanation
Indices: 44641679--44641735 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
44641669 TGCTCCTAAC
*
44641679 AGTACCTTC-GTACTCCTGTT
1 AGTA-CTTCTGTACTCCTGAT
* *
44641699 AGTA-TTATTGTGCTCCTGAT
1 AGTACTT-CTGTACTCCTGAT
44641719 AGTACTTCTGTACTCCT
1 AGTACTTCTGTACTCCT
44641736 ATTAGCACTG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (20 bp):
AGTACTTCTGTACTCCTGAT
Found at i:44647610 original size:15 final size:14
Alignment explanation
Indices: 44647582--44647618 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
44647572 TATTTTTTTT
44647582 AAAATT-ATAT-AA
1 AAAATTAATATAAA
*
44647594 AAATTTAATATAAA
1 AAAATTAATATAAA
44647608 AAAATTAATAT
1 AAAATTAATAT
44647619 GAGTCGAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 5 0.24
13 4 0.19
14 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTAATATAAA
Found at i:44647844 original size:17 final size:17
Alignment explanation
Indices: 44647822--44647856 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
44647812 TTATAAAAGT
* *
44647822 ATCTTTTAAAATTTAAA
1 ATCTTTAAAAATATAAA
44647839 ATCTTTAAAAATATAAA
1 ATCTTTAAAAATATAAA
44647856 A
1 A
44647857 ATGTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
ATCTTTAAAAATATAAA
Found at i:44648265 original size:35 final size:35
Alignment explanation
Indices: 44648226--44648325 Score: 123
Period size: 35 Copynumber: 2.9 Consensus size: 35
44648216 GTCAAAGTCG
* *
44648226 ACCTTAAAGAGGTTGGGATAGACCCGTCTAA-GACA
1 ACCTTAAAAAGGTTGGGATAGACACGTCTAAGGA-A
* * * *
44648261 ACCTTAAAAAAGTTGGGACAAACTCGTCTAAGGAA
1 ACCTTAAAAAGGTTGGGATAGACACGTCTAAGGAA
44648296 ACCTTAAAAAGGTTGGGATAGA-ACGTCTAA
1 ACCTTAAAAAGGTTGGGATAGACACGTCTAA
44648326 TAGGGTAGAC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
34 7 0.13
35 46 0.84
36 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (35 bp):
ACCTTAAAAAGGTTGGGATAGACACGTCTAAGGAA
Found at i:44651729 original size:20 final size:20
Alignment explanation
Indices: 44651704--44651782 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
44651694 ATTATAAAAT
44651704 AATTCAAAATAATTTTTAAA
1 AATTCAAAATAATTTTTAAA
44651724 AATTCAAAATAATTTTT-AA
1 AATTCAAAATAATTTTTAAA
* *
44651743 AATTGAAAAT-ATTTATAAA
1 AATTCAAAATAATTTTTAAA
* *
44651762 AATTAAAAAATATTTTTTAAA
1 AATT-CAAAATAATTTTTAAA
44651783 TTAAAAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.10
19 17 0.33
20 22 0.43
21 7 0.14
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (20 bp):
AATTCAAAATAATTTTTAAA
Found at i:44651752 original size:39 final size:39
Alignment explanation
Indices: 44651704--44651782 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
44651694 ATTATAAAAT
* *
44651704 AATTCAAAATAATTTTTAAAAATT-CAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAAAAATTAAAAAATAATTTTTAA
* *
44651743 AATTGAAAATATTTATAAAAATTAAAAAATATTTTTTAA
1 AATTCAAAATATTTATAAAAATTAAAAAATAATTTTTAA
44651782 A
1 A
44651783 TTAAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 12 0.34
39 23 0.66
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (39 bp):
AATTCAAAATATTTATAAAAATTAAAAAATAATTTTTAA
Found at i:44651783 original size:19 final size:19
Alignment explanation
Indices: 44651709--44651791 Score: 80
Period size: 19 Copynumber: 4.3 Consensus size: 19
44651699 AAAATAATTC
*
44651709 AAAATAATTTTTAAAAATT-C
1 AAAAT-ATTTTT-AAAATTAA
*
44651729 AAAATAATTTTTAAAATT-G
1 AAAAT-ATTTTTAAAATTAA
*
44651748 AAAATATTTATAAAAATTAA
1 AAAATATTT-TTAAAATTAA
*
44651768 AAAATATTTTTTAAATTAA
1 AAAATATTTTTAAAATTAA
44651787 AAAAT
1 AAAAT
44651792 TGGAATAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.07
19 31 0.55
20 21 0.38
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (19 bp):
AAAATATTTTTAAAATTAA
Found at i:44651784 original size:38 final size:39
Alignment explanation
Indices: 44651704--44651789 Score: 104
Period size: 38 Copynumber: 2.2 Consensus size: 39
44651694 ATTATAAAAT
* * *
44651704 AATTCAAAATAATTTTTAAAAATTCAAAATAATTTTTAA
1 AATTAAAAATAATTTATAAAAATTAAAAATAATTTTTAA
* *
44651743 AATTGAAAAT-ATTTATAAAAATTAAAAA-ATATTTTTTA
1 AATTAAAAATAATTTATAAAAATTAAAAATA-ATTTTTAA
44651781 AATTAAAAA
1 AATTAAAAA
44651790 ATTGGAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 1 0.02
38 31 0.76
39 9 0.22
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (39 bp):
AATTAAAAATAATTTATAAAAATTAAAAATAATTTTTAA
Found at i:44660603 original size:3 final size:3
Alignment explanation
Indices: 44660595--44660629 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
44660585 ATTTATTTGT
44660595 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
44660630 CTTTTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:44664237 original size:44 final size:44
Alignment explanation
Indices: 44664150--44664237 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
44664140 ATTACATGTA
* * * ** *
44664150 TCGCATCCATTATGAACTCAGACCAATTCAACGATTTCGGATGC
1 TCGCATCCATAATGAACTCAAACCAACTCAACGAGCTCAGATGC
44664194 TCGCATCCATAATGAACTCAAACCAACTCAACGAGCTCAGATGC
1 TCGCATCCATAATGAACTCAAACCAACTCAACGAGCTCAGATGC
44664238 CTCATATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (44 bp):
TCGCATCCATAATGAACTCAAACCAACTCAACGAGCTCAGATGC
Found at i:44666234 original size:31 final size:31
Alignment explanation
Indices: 44666199--44666260 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
44666189 AATATAAGAC
44666199 TAAATCAACCACAACATGACAATTAAATACA
1 TAAATCAACCACAACATGACAATTAAATACA
44666230 TAAATCAACCACAACATGACAATTAAATACA
1 TAAATCAACCACAACATGACAATTAAATACA
44666261 AATCTCATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.23, G:0.03, T:0.19
Consensus pattern (31 bp):
TAAATCAACCACAACATGACAATTAAATACA
Found at i:44667056 original size:49 final size:47
Alignment explanation
Indices: 44666899--44667223 Score: 255
Period size: 49 Copynumber: 6.7 Consensus size: 47
44666889 TAGGGTACGA
* * *
44666899 TGTCGATGCCATGTTCCAAACATGGTCTTACACTGACTCTCACATCTA
1 TGTCGATGCCATGTCCCAAACA-GGTCTTACACTGACTCTCACATATT
* * * * *
44666947 AGTCAATGCCATGTACCAGACAGGTCTTACACTGACT-TCCACACATT
1 TGTCGATGCCATGTCCCAAACAGGTCTTACACTGACTCT-CACATATT
* * * *
44666994 AGGCCGATGCCATGTCCCAAACAGCTCTTACACTGGCTCTCACTTATATT
1 -TGTCGATGCCATGTCCCAAACAGGTCTTACACTGACTCTCAC--ATATT
*
44667044 TGTCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCACTTATATT
1 TGTCGATGCCATGTCCCAAACAGGTCTTACACTGACTCTCAC--ATATT
* * *
44667093 TGTCGATGCCATGTCCCAGACAGGACTTACACT-AGCT-T-GCATATCT
1 TGTCGATGCCATGTCCCAAACAGGTCTTACACTGA-CTCTCACATAT-T
* * * * * *
44667139 TGAGGCCGATGCCGTGTCCCAGATAGGTCTTACACTGGCTCTCATC-TATC
1 T---GTCGATGCCATGTCCCAAACAGGTCTTACACTGACTCTCA-CATATT
* * *
44667189 GGTGCTGATGCCATGTCCCAGATAGGTCTTACACT
1 TGT-C-GATGCCATGTCCCAAACAGGTCTTACACT
44667224 AGCACACACA
Statistics
Matches: 229, Mismatches: 32, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
45 4 0.02
46 3 0.01
47 22 0.10
48 53 0.23
49 138 0.60
50 5 0.02
51 3 0.01
52 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.29
Consensus pattern (47 bp):
TGTCGATGCCATGTCCCAAACAGGTCTTACACTGACTCTCACATATT
Done.