Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 66 of 226
Found at i:25481691 original size:167 final size:167
Alignment explanation
Indices: 25481463--25481789 Score: 539
Period size: 167 Copynumber: 2.0 Consensus size: 167
25481453 GTTCCACTGT
*
25481463 AATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATCCGCTCCACTTCAACTAATCCAAGCC
1 AATGCCAAAGAGATAGGACTCGCTGCCCACAGCTTCAATCCGCTCCACTTCAACTAATCCAAGCC
* * *
25481528 TTAACGCCAGGGAGATAAGATACGCCGTCGTGGCTTCAATCTGCTCCGCTGCA-ATGCCAGGAAA
66 TTAACACCAGGGAGAAAAGATACGCCGTCGTGGCTTCAATCTGCTCCGCTG-AGACGCCAGGAAA
25481592 ATAAGACCCGCCATTGTGGCTTCAATCTTTTTAATTAC
130 ATAAGACCCGCCATTGTGGCTTCAATCTTTTTAATTAC
* * * *
25481630 AATGCCAAAGAGATAGGACTCGCTGCCCACAGCTTTAATCTGCTCCACTTCAGCTAATCCAAGTC
1 AATGCCAAAGAGATAGGACTCGCTGCCCACAGCTTCAATCCGCTCCACTTCAACTAATCCAAGCC
*
25481695 TTAACACCAGGGAGAAAAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTGAGACGCCAGGAAAA
66 TTAACACCAGGGAGAAAAGATACGCCGTCGTGGCTTCAATCTGCTCCGCTGAGACGCCAGGAAAA
* *
25481760 TAAGATCCGCCATTGTGGCTTCAGTCTTTT
131 TAAGACCCGCCATTGTGGCTTCAATCTTTT
25481790 CCATTGCAAC
Statistics
Matches: 148, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
166 1 0.01
167 147 0.99
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (167 bp):
AATGCCAAAGAGATAGGACTCGCTGCCCACAGCTTCAATCCGCTCCACTTCAACTAATCCAAGCC
TTAACACCAGGGAGAAAAGATACGCCGTCGTGGCTTCAATCTGCTCCGCTGAGACGCCAGGAAAA
TAAGACCCGCCATTGTGGCTTCAATCTTTTTAATTAC
Found at i:25481938 original size:88 final size:88
Alignment explanation
Indices: 25481817--25481993 Score: 232
Period size: 88 Copynumber: 2.0 Consensus size: 88
25481807 CGATAAGACG
* * * *
25481817 GGTATCTTCGATCTGCTTCGCTACCAGTACAGGAAGGCAAGATCTG-TCATTTTCAACCTACTCC
1 GGTATCTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTGCT-ATTTTCAACCTACTCC
25481881 ACTACTACCT-AGGGAGACAAGGCT
65 ACTACT-CCTCAGGGAGACAAGGCT
* * *
25481905 GGTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTTAACCTATTCCA
1 GGTATCTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCA
* * *
25481970 CTGCTGCTCAGGGAGATAAGGCT
66 CTACTCCTCAGGGAGACAAGGCT
25481993 G
1 G
25481994 AAGTTTCACC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
87 2 0.03
88 74 0.96
89 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (88 bp):
GGTATCTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCA
CTACTCCTCAGGGAGACAAGGCT
Found at i:25483238 original size:13 final size:13
Alignment explanation
Indices: 25483222--25483259 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
25483212 CCATTTTTAC
25483222 TTTTTCATTTTCA
1 TTTTTCATTTTCA
25483235 TTTTTCATTTTCA
1 TTTTTCATTTTCA
25483248 TCTTTTCATTTT
1 T-TTTTCATTTT
25483260 TTCACATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:25483263 original size:8 final size:7
Alignment explanation
Indices: 25483213--25483260 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
25483203 TTAGCCTCTC
25483213 CATTTTT
1 CATTTTT
25483220 -ACTTTTT
1 CA-TTTTT
25483227 CA-TTTT
1 CATTTTT
25483233 CATTTTT
1 CATTTTT
25483240 CA-TTTT
1 CATTTTT
25483246 CATCTTTT
1 CAT-TTTT
25483254 CATTTTT
1 CATTTTT
25483261 TCACATCACT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
6 13 0.36
7 15 0.42
8 8 0.22
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:25487922 original size:2 final size:2
Alignment explanation
Indices: 25487915--25487950 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25487905 ATGCTAATGC
25487915 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
25487951 TCAAAATCAT
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:25488130 original size:23 final size:24
Alignment explanation
Indices: 25488104--25488149 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
25488094 ATAGTGTATG
25488104 AATATATATATATAT-TATAAAAA
1 AATATATATATATATGTATAAAAA
*
25488127 AATATGTATATATATGTATAAAA
1 AATATATATATATATGTATAAAA
25488150 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
AATATATATATATATGTATAAAAA
Found at i:25488132 original size:29 final size:29
Alignment explanation
Indices: 25488100--25488183 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
25488090 TTGAATAGTG
25488100 TATGAATATATATATATATTATAAAAAAA
1 TATGAATATATATATATATTATAAAAAAA
* * **
25488129 TATGTATATATATGTATAAAAT-AAAAAA
1 TATGAATATATATATATATTATAAAAAAA
* * * *
25488157 TATAAAAAATATATAAATGTTATAAAA
1 TAT-GAATATATATATATATTATAAAA
25488184 TATAAATGGA
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
28 9 0.22
29 29 0.71
30 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
TATGAATATATATATATATTATAAAAAAA
Found at i:25494667 original size:27 final size:28
Alignment explanation
Indices: 25494612--25494676 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 28
25494602 ATAAAAAATA
*
25494612 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
25494640 ACCAAAATATTATAA-ATTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
25494667 ACCAAAATAT
1 ACCAAAATAT
25494677 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 21 0.58
28 15 0.42
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAACATTTTTTTATTT
Found at i:25494873 original size:12 final size:12
Alignment explanation
Indices: 25494858--25494884 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25494848 GAAAGAAAAA
25494858 AAGAAAGGAAGG
1 AAGAAAGGAAGG
25494870 AAGAAAGGAAGG
1 AAGAAAGGAAGG
25494882 AAG
1 AAG
25494885 GACGGAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AAGAAAGGAAGG
Found at i:25494915 original size:39 final size:37
Alignment explanation
Indices: 25494872--25495054 Score: 86
Period size: 39 Copynumber: 5.0 Consensus size: 37
25494862 AAGGAAGGAA
25494872 GAAAGGAAGGAAGGACGGAGAGGAAAGAAGAAAAAGAAG
1 GAAAGGAAGGAAGGA-GGAGAGGAAA-AAGAAAAAGAAG
* * *
25494911 GAAAGAAAAGGAAAGGAGAAGA-GAAAAA-AAAAAGAAA
1 GAAAG-GAAGG-AAGGAGGAGAGGAAAAAGAAAAAGAAG
*
25494948 G-AA-GAAGAAGAGGAAAGGAGAGGAAAAAAGAAAGAA-AAG
1 GAAAGGAAGGA-AGG--AGGAGAGG-AAAAAGAAA-AAGAAG
* ** *
25494987 GAAATG-A-GAA-GA-GA-AAAAAAAAGAAGAAG-AG
1 GAAAGGAAGGAAGGAGGAGAGGAAAAAGAAAAAGAAG
* * *
25495018 GGAAGGAAGGAAGGAAGGA-A-AAAAAAGAAAAAAAAG
1 GAAAGGAAGGAAGG-AGGAGAGGAAAAAGAAAAAGAAG
25495054 G
1 G
25495055 TAATTTTTAT
Statistics
Matches: 111, Mismatches: 15, Indels: 39
0.67 0.09 0.24
Matches are distributed among these distances:
31 8 0.07
32 9 0.08
33 5 0.05
34 9 0.08
35 13 0.12
36 13 0.12
37 11 0.10
38 8 0.07
39 16 0.14
40 13 0.12
41 6 0.05
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.01
Consensus pattern (37 bp):
GAAAGGAAGGAAGGAGGAGAGGAAAAAGAAAAAGAAG
Found at i:25494943 original size:37 final size:36
Alignment explanation
Indices: 25494888--25494983 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 36
25494878 AAGGAAGGAC
*
25494888 GGAGAGGAAAGAAGAAAAAGAAGGA-AAGAAAAGGAAA
1 GGAGAGGAAA-AA-AAAAAGAAGAAGAAGAAAAGGAAA
*
25494925 GGAGAAGAGAAAAAAAAAAGAAAGAAGAAGAAGAGGAAA
1 GGAG-AG-GAAAAAAAAAAG-AAGAAGAAGAAAAGGAAA
*
25494964 GGAGAGGAAAAAAGAAAGAA
1 GGAGAGGAAAAAAAAAAGAA
25494984 AAGGAAATGA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
36 2 0.04
37 21 0.40
38 10 0.19
39 19 0.37
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (36 bp):
GGAGAGGAAAAAAAAAAGAAGAAGAAGAAAAGGAAA
Found at i:25494981 original size:66 final size:64
Alignment explanation
Indices: 25494890--25495048 Score: 193
Period size: 66 Copynumber: 2.5 Consensus size: 64
25494880 GGAAGGACGG
*
25494890 AGAGGAAA-GAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAAAGAAGA-
1 AGAGGAAAGGAAGGAAAA-AA-GAAAGAAAAGGAAAGGAGAAGAG-AAAAAAAAAG-AAGAAGAG
25494953 AGA
62 AGA
* *
25494956 AGAGGAAAGGAGAGGAAAAAAGAAAGAAAAGGAAATGAGAAGAGAAAAAAAAAGAAGAAGAGGGA
1 AGAGGAAAGGA-AGGAAAAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAGAAGAGAGA
25495021 AGGAAGG-AAGGAAGG-AAAAA-AAAGAAAA
1 A-G-AGGAAAGGAAGGAAAAAAGAAAGAAAA
25495049 AAAAGGTAAT
Statistics
Matches: 85, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
63 8 0.09
64 12 0.14
65 16 0.19
66 36 0.42
67 7 0.08
68 6 0.07
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (64 bp):
AGAGGAAAGGAAGGAAAAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAGAAGAGAGA
Found at i:25494982 original size:27 final size:29
Alignment explanation
Indices: 25494943--25495013 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 29
25494933 GAAAAAAAAA
*
25494943 AGAAAGAAG-AAGAAGAGGAAAGGAG-AG
1 AGAAAAAAGAAAGAAGAGGAAAGGAGAAG
* *
25494970 -GAAAAAAGAAAGAAAAGGAAATGAGAAG
1 AGAAAAAAGAAAGAAGAGGAAAGGAGAAG
25494998 AGAAAAAA-AAAGAAGA
1 AGAAAAAAGAAAGAAGA
25495014 AGAGGGAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 7 0.19
27 14 0.38
28 9 0.24
29 7 0.19
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (29 bp):
AGAAAAAAGAAAGAAGAGGAAAGGAGAAG
Found at i:25494984 original size:37 final size:39
Alignment explanation
Indices: 25494854--25494984 Score: 121
Period size: 39 Copynumber: 3.4 Consensus size: 39
25494844 GAAAGAAAGA
* *
25494854 AAAAAAGAAAGGAAGGAA-GAAAGGAAGGAAGG-ACGGAGAGG
1 AAAAAAGAAA-GAAAGAAGGAAA-GAA--AAGGAAAGGAGAGG
*
25494895 AAAGAAG-AA-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAG
1 AAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAG-AG-G
* *
25494934 AAAAAAAAAAGAAAGAA-G-AAGAAGAGGAAAGGAGAGG
1 AAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAGG
25494971 AAAAAAGAAAGAAA
1 AAAAAAGAAAGAAA
25494985 AGGAAATGAG
Statistics
Matches: 77, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
36 4 0.05
37 19 0.25
38 12 0.16
39 25 0.32
40 5 0.06
41 12 0.16
ACGTcount: A:0.66, C:0.01, G:0.34, T:0.00
Consensus pattern (39 bp):
AAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAGG
Found at i:25496353 original size:19 final size:18
Alignment explanation
Indices: 25496316--25496354 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
25496306 ATGAATCAAG
* *
25496316 TTATTCGAGTTAATCGAA
1 TTATTCGAATCAATCGAA
25496334 TTATTCGAATCAACTCGAA
1 TTATTCGAATCAA-TCGAA
25496353 TT
1 TT
25496355 TTTTTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (18 bp):
TTATTCGAATCAATCGAA
Found at i:25496651 original size:38 final size:41
Alignment explanation
Indices: 25496608--25496687 Score: 121
Period size: 38 Copynumber: 2.0 Consensus size: 41
25496598 TAAACATTAA
*
25496608 AAAAGTATTTTAAAAATAAAAA-AATAA-AAAAATAT-TTT
1 AAAAGTATTTTAAAAATAAAAATAAAAATAAAAATATATTT
*
25496646 AAAAGTGTTTTAAAAATAAAAATAAAAATAAAAATATATTT
1 AAAAGTATTTTAAAAATAAAAATAAAAATAAAAATATATTT
25496687 A
1 A
25496688 TTATATTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 21 0.57
39 4 0.11
40 8 0.22
41 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (41 bp):
AAAAGTATTTTAAAAATAAAAATAAAAATAAAAATATATTT
Found at i:25496672 original size:5 final size:6
Alignment explanation
Indices: 25496656--25496681 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25496646 AAAAGTGTTT
25496656 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
25496682 TATTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:25497151 original size:18 final size:18
Alignment explanation
Indices: 25497128--25497187 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
25497118 TTATTTATAT
25497128 TATTGAATTGTTTAGTCA
1 TATTGAATTGTTTAGTCA
*
25497146 TATTGAA-TATTTA-T-A
1 TATTGAATTGTTTAGTCA
25497161 TTATTGAATTGTTTAGTCA
1 -TATTGAATTGTTTAGTCA
25497180 TATTGAAT
1 TATTGAAT
25497188 ATTTATACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 1 0.03
16 8 0.22
17 10 0.28
18 16 0.44
19 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (18 bp):
TATTGAATTGTTTAGTCA
Found at i:25497162 original size:34 final size:34
Alignment explanation
Indices: 25497119--25497194 Score: 152
Period size: 34 Copynumber: 2.2 Consensus size: 34
25497109 TATTTTATAT
25497119 TATTTATATTATTGAATTGTTTAGTCATATTGAA
1 TATTTATATTATTGAATTGTTTAGTCATATTGAA
25497153 TATTTATATTATTGAATTGTTTAGTCATATTGAA
1 TATTTATATTATTGAATTGTTTAGTCATATTGAA
25497187 TATTTATA
1 TATTTATA
25497195 CTAAAATTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.54
Consensus pattern (34 bp):
TATTTATATTATTGAATTGTTTAGTCATATTGAA
Found at i:25503406 original size:27 final size:26
Alignment explanation
Indices: 25503368--25503461 Score: 91
Period size: 27 Copynumber: 3.5 Consensus size: 26
25503358 AACACGAGTA
*
25503368 GTGCCGTCAATCAGTATGGCACCATTG
1 GTGCCGCCAATCAGT-TGGCACCATTG
** *
25503395 GTGCCGCCAATCTCCTTGACACCATTG
1 GTGCCGCCAATC-AGTTGGCACCATTG
* *
25503422 GTGCCGCCAATGGC-TTTGGCACCTTTG
1 GTGCCGCCAAT--CAGTTGGCACCATTG
25503449 GTGCCGCCAATCA
1 GTGCCGCCAATCA
25503462 CCTTGGCCTG
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
25 1 0.02
27 53 0.95
28 1 0.02
29 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.24, T:0.26
Consensus pattern (26 bp):
GTGCCGCCAATCAGTTGGCACCATTG
Found at i:25503467 original size:27 final size:27
Alignment explanation
Indices: 25503384--25503468 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
25503374 TCAATCAGTA
*
25503384 TGGCACCATTGGTGCCGCCAATCTCCT
1 TGGCACCATTGGTGCCGCCAATCACCT
* ** *
25503411 TGACACCATTGGTGCCGCCAATGGCTT
1 TGGCACCATTGGTGCCGCCAATCACCT
*
25503438 TGGCACCTTTGGTGCCGCCAATCACCT
1 TGGCACCATTGGTGCCGCCAATCACCT
25503465 TGGC
1 TGGC
25503469 CTGACCAGGG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.15, C:0.34, G:0.25, T:0.26
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATCACCT
Found at i:25505875 original size:15 final size:16
Alignment explanation
Indices: 25505855--25505885 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25505845 AATGATCATC
25505855 TTTCTTA-TTTTCTTT
1 TTTCTTACTTTTCTTT
25505870 TTTCTTACTTTTCTTT
1 TTTCTTACTTTTCTTT
25505886 CCAACCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTACTTTTCTTT
Found at i:25507202 original size:44 final size:46
Alignment explanation
Indices: 25507119--25507207 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 46
25507109 ACTATAATGG
25507119 ATAGAGCTGTAATAAGTAATTCAATTGTTTGGTTGAATGGAATGAA
1 ATAGAGCTGTAATAAGTAATTCAATTGTTTGGTTGAATGGAATGAA
*
25507165 ATAGAGCTGTAATAA-T-ATTC-TTGTGTTTGGTTGAATGGAATGA
1 ATAGAGCTGTAATAAGTAATTCAAT-TGTTTGGTTGAATGGAATGA
25507208 TGTTGTAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
43 1 0.02
44 24 0.59
45 1 0.02
46 15 0.37
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (46 bp):
ATAGAGCTGTAATAAGTAATTCAATTGTTTGGTTGAATGGAATGAA
Found at i:25512274 original size:31 final size:30
Alignment explanation
Indices: 25512233--25512303 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
25512223 GATAATGTGA
*
25512233 TATAGTTTAGATAT-AATTTTAAACAACGAAG
1 TATAATTTAGATATCAATTTTAAA-AACG-AG
* *
25512264 TATAATTTAGATATCCATTTTTAAAAATGAG
1 TATAATTTAGATAT-CAATTTTAAAAACGAG
25512295 TATAATTTA
1 TATAATTTA
25512304 AAGGGTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 24 0.69
32 3 0.09
33 8 0.23
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.41
Consensus pattern (30 bp):
TATAATTTAGATATCAATTTTAAAAACGAG
Found at i:25513153 original size:3 final size:3
Alignment explanation
Indices: 25513145--25513170 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25513135 TTCTTCAATT
25513145 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
25513171 CATTTTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:25525752 original size:50 final size:50
Alignment explanation
Indices: 25525676--25525776 Score: 150
Period size: 50 Copynumber: 2.0 Consensus size: 50
25525666 TAAACCAGGC
* *
25525676 TGCACAAGTAGAATCCGTATAGAACTACTCTT-ATTCTATTTGACATTGAT
1 TGCACAAGTAAAATCCGTATAAAACTACT-TTCATTCTATTTGACATTGAT
* *
25525726 TGCACAAGTAAAATCCTTATAAAACTACTTTCCTTCTATTTGACATTGAT
1 TGCACAAGTAAAATCCGTATAAAACTACTTTCATTCTATTTGACATTGAT
25525776 T
1 T
25525777 AAAATAAGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 2 0.04
50 44 0.96
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (50 bp):
TGCACAAGTAAAATCCGTATAAAACTACTTTCATTCTATTTGACATTGAT
Found at i:25528412 original size:14 final size:14
Alignment explanation
Indices: 25528365--25528420 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
25528355 ATAATTATTC
25528365 ATTTAATATTATAA
1 ATTTAATATTATAA
* *
25528379 CTATTTAA-ATAATATT
1 --ATTTAATATTATA-A
25528395 ATTTAATATTATAA
1 ATTTAATATTATAA
25528409 ATTTAATATTAT
1 ATTTAATATTAT
25528421 TTAAATAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 18 0.53
15 10 0.29
16 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAATATTATAA
Found at i:25534722 original size:20 final size:20
Alignment explanation
Indices: 25534697--25534735 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25534687 TTTCAATATT
25534697 GAACACCAAAACTAAATTGG
1 GAACACCAAAACTAAATTGG
*
25534717 GAACACCAAAAGTAAATTG
1 GAACACCAAAACTAAATTG
25534736 AAACTACGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
GAACACCAAAACTAAATTGG
Found at i:25547541 original size:16 final size:16
Alignment explanation
Indices: 25547522--25547552 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25547512 AATGAAATGC
*
25547522 TGCTATAACAGTATGT
1 TGCTATAACAATATGT
25547538 TGCTATAACAATATG
1 TGCTATAACAATATG
25547553 AAATGGTTAC
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:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (16 bp):
TGCTATAACAATATGT
Found at i:25552813 original size:16 final size:16
Alignment explanation
Indices: 25552782--25552829 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
25552772 AATATTATGA
*
25552782 AAAAGAAAAGGGGAAG
1 AAAAGAAAAGAGGAAG
*
25552798 AAAAGAAAAGATGAAG
1 AAAAGAAAAGAGGAAG
25552814 ATATAGAGAAAAGAGG
1 A-A-A-AGAAAAGAGG
25552830 GAGTAATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 15 0.58
17 1 0.04
18 1 0.04
19 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAGAGGAAG
Found at i:25554380 original size:2 final size:2
Alignment explanation
Indices: 25554375--25554412 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25554365 GAACTACTTT
25554375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25554413 AAAGCATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25555969 original size:33 final size:31
Alignment explanation
Indices: 25555910--25555970 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 31
25555900 AAATAATAAA
*
25555910 ATAAAATAACTAAAATGTACTAAAATAACTT
1 ATAAAATAACTAAAATCTACTAAAATAACTT
25555941 ATAAAATAAACTAAAATCCTACTAAAATAA
1 ATAAAAT-AACTAAAAT-CTACTAAAATAA
25555971 TAGACAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 7 0.26
32 9 0.33
33 11 0.41
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.26
Consensus pattern (31 bp):
ATAAAATAACTAAAATCTACTAAAATAACTT
Found at i:25555980 original size:32 final size:31
Alignment explanation
Indices: 25555912--25555981 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
25555902 ATAATAAAAT
* *
25555912 AAAAT-AACTAAAATGTACTAAAATAACTTAT
1 AAAATAAACTAAAATCTACTAAAATAAC-TAG
25555943 AAAATAAACTAAAATCCTACTAAAATAA-TAG
1 AAAATAAACTAAAAT-CTACTAAAATAACTAG
25555974 ACAAATAA
1 A-AAATAA
25555982 CTCTAAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 8 0.24
32 15 0.44
33 11 0.32
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.24
Consensus pattern (31 bp):
AAAATAAACTAAAATCTACTAAAATAACTAG
Found at i:25558394 original size:48 final size:50
Alignment explanation
Indices: 25558342--25558441 Score: 136
Period size: 49 Copynumber: 2.0 Consensus size: 50
25558332 AGCCATGAAC
*
25558342 CGGGAAGCTTATA-AGAGTTAT-AATCGGGAAGTT-CAAACGAGCCAA-TAT
1 CGGGAAGCTT-TAGAGAGCTATAAATCGGGAAGTTCCAAA-GAGCCAATTAT
*
25558390 CGGGAAGCTTTAGAGAGCTATAAATTGGGAAGTTCCAAAGAGCCAATTAT
1 CGGGAAGCTTTAGAGAGCTATAAATCGGGAAGTTCCAAAGAGCCAATTAT
25558440 CG
1 CG
25558442 AAAAGCTCCG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
47 2 0.04
48 17 0.37
49 18 0.39
50 9 0.20
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (50 bp):
CGGGAAGCTTTAGAGAGCTATAAATCGGGAAGTTCCAAAGAGCCAATTAT
Found at i:25558468 original size:49 final size:49
Alignment explanation
Indices: 25558367--25558470 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 49
25558357 AGTTATAATC
** ** *
25558367 GGGAAGTTCAAACGAGCCAATATCGGGAAGCTTTAGAGAGCTATAAATT
1 GGGAAGTTCAAACGAGCCAATATCGAAAAGCTCCAGAGAGCCATAAATT
*
25558416 GGGAAGTTCCAAA-GAGCCAATTATCGAAAAGCTCCGGAGAGCCATAAA-T
1 GGGAAGTT-CAAACGAGCCAA-TATCGAAAAGCTCCAGAGAGCCATAAATT
25558465 GGGAAG
1 GGGAAG
25558471 CTCGCAAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 22 0.47
50 25 0.53
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.18
Consensus pattern (49 bp):
GGGAAGTTCAAACGAGCCAATATCGAAAAGCTCCAGAGAGCCATAAATT
Found at i:25561400 original size:29 final size:30
Alignment explanation
Indices: 25561363--25561424 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
25561353 ATTTCAAGTG
* *
25561363 TATAGTTACAC-TAAATTAAAGTTTATATA
1 TATAATTACACATAAATCAAAGTTTATATA
*
25561392 TATAATTACACATTAAATCAAAGTTTATCTA
1 TATAATTACACA-TAAATCAAAGTTTATATA
25561423 TA
1 TA
25561425 ATTTTAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.36
31 18 0.64
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (30 bp):
TATAATTACACATAAATCAAAGTTTATATA
Found at i:25563180 original size:91 final size:89
Alignment explanation
Indices: 25563016--25563195 Score: 204
Period size: 91 Copynumber: 2.0 Consensus size: 89
25563006 AGTGTTGTAG
* * **
25563016 GTTAATACGGTGTCAGTAGTTTTGAATGCACAACAGGTTTGCATATAAAAGCTGTAGTAAAAGTT
1 GTTAATACGCTGTCAGTAGTTGTGAATGCACAACAGGTTTGCATATAAAAGC-GTACCAAAAGTT
*
25563081 GTAGGTAAACCACCAATGCTTGCAT
65 GGAGGTAAACCACCAATGCTTGCAT
* *
25563106 GTTAATACGCTTTTAGTAGGTTGTGAATGCACAAC-GAGTTTGCATATAAAAGC-TACCAATAAG
1 GTTAATACGCTGTCAGTA-GTTGTGAATGCACAACAG-GTTTGCATATAAAAGCGTACCAA-AAG
* *
25563169 TTTGCGA-GTAAACCATCAATGTTTGCA
63 -TTG-GAGGTAAACCACCAATGCTTGCA
25563196 GATAAATTGT
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
89 4 0.05
90 19 0.25
91 52 0.68
92 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (89 bp):
GTTAATACGCTGTCAGTAGTTGTGAATGCACAACAGGTTTGCATATAAAAGCGTACCAAAAGTTG
GAGGTAAACCACCAATGCTTGCAT
Found at i:25564705 original size:34 final size:34
Alignment explanation
Indices: 25564667--25564740 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
25564657 CAAGCATGTC
25564667 ATTTGCAACTAAATC-AATATGTTATAAGCATAAT
1 ATTTGCAACTAAATCGAAT-TGTTATAAGCATAAT
* * *
25564701 ATTTGCCACTGAATCGAATTGTTATAAGGATAAT
1 ATTTGCAACTAAATCGAATTGTTATAAGCATAAT
*
25564735 AATTGC
1 ATTTGC
25564741 TACCGTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 32 0.91
35 3 0.09
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (34 bp):
ATTTGCAACTAAATCGAATTGTTATAAGCATAAT
Found at i:25564988 original size:45 final size:45
Alignment explanation
Indices: 25564912--25564998 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
25564902 CTACACCGTT
* * * * *
25564912 TGAGTGGTTTATCCACACTGTATCAGTAGCTTTTATTTGCAACAA
1 TGAGTGGTTTAACCACACTATATCAGCAGCTTTAATATGCAACAA
*
25564957 TGAGTGGTTTAACTACACTATA-CTAGCAGCTTTAATATGCAA
1 TGAGTGGTTTAACCACACTATATC-AGCAGCTTTAATATGCAA
25564999 ACATGTTGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (45 bp):
TGAGTGGTTTAACCACACTATATCAGCAGCTTTAATATGCAACAA
Found at i:25565111 original size:18 final size:19
Alignment explanation
Indices: 25565088--25565139 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 19
25565078 TTTTATTACT
*
25565088 AGTGGTTTATCC-GCAATG
1 AGTGGTTTATCCAACAATG
*
25565106 AGTGGTTCATCCACAACAATG
1 AGTGGTTTAT-C-CAACAATG
25565127 AGTGGTTTATCCA
1 AGTGGTTTATCCA
25565140 CAACGTTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.32
19 3 0.11
20 2 0.07
21 14 0.50
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (19 bp):
AGTGGTTTATCCAACAATG
Found at i:25565127 original size:21 final size:21
Alignment explanation
Indices: 25565101--25565143 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
25565091 GGTTTATCCG
25565101 CAATGAGTGGTTCATCCACAA
1 CAATGAGTGGTTCATCCACAA
*
25565122 CAATGAGTGGTTTATCCACAA
1 CAATGAGTGGTTCATCCACAA
25565143 C
1 C
25565144 GTTGTGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
CAATGAGTGGTTCATCCACAA
Found at i:25567369 original size:20 final size:20
Alignment explanation
Indices: 25567344--25567382 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25567334 CAGACTGAGT
* *
25567344 TTATTCTGTTTACTGTCTGA
1 TTATTCTGTGTACTATCTGA
25567364 TTATTCTGTGTACTATCTG
1 TTATTCTGTGTACTATCTG
25567383 TTTGTTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (20 bp):
TTATTCTGTGTACTATCTGA
Found at i:25575350 original size:9 final size:9
Alignment explanation
Indices: 25575333--25575369 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
25575323 TGAGTTTTCG
25575333 AATTCGAAT
1 AATTCGAAT
*
25575342 AACTCGAAT
1 AATTCGAAT
25575351 AATTCGAAT
1 AATTCGAAT
25575360 AATTCGAAT
1 AATTCGAAT
25575369 A
1 A
25575370 TCAAACTATA
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:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:25585003 original size:26 final size:27
Alignment explanation
Indices: 25584974--25585044 Score: 110
Period size: 26 Copynumber: 2.7 Consensus size: 27
25584964 ACACCAATAT
25584974 CGCAGCAAAGCTGCCAGTAAT-AGTAA
1 CGCAGCAAAGCTGCCAGTAATGAGTAA
*
25585000 CGCAGCAAAGCTGCCAGT-ATGAGTAT
1 CGCAGCAAAGCTGCCAGTAATGAGTAA
*
25585026 CGCAGCAAAGCTGCTAGTA
1 CGCAGCAAAGCTGCCAGTA
25585045 CAGTATACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
25 2 0.05
26 39 0.95
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (27 bp):
CGCAGCAAAGCTGCCAGTAATGAGTAA
Found at i:25586642 original size:15 final size:15
Alignment explanation
Indices: 25586622--25586656 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
25586612 ACAAGGTCAT
* *
25586622 CGATGATATTAATGA
1 CGATGACATGAATGA
25586637 CGATGACATGAATGA
1 CGATGACATGAATGA
25586652 CGATG
1 CGATG
25586657 GAAACATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (15 bp):
CGATGACATGAATGA
Found at i:25588855 original size:62 final size:62
Alignment explanation
Indices: 25588754--25588986 Score: 319
Period size: 62 Copynumber: 3.7 Consensus size: 62
25588744 CAATGTACCT
25588754 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
* * *
25588816 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTGTATTACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
*
25588878 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TGTAATGTTGCA-ATTAATC
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAAT-TT--ATA-TAA-C
*
25588941 -T
61 AA
** *
25588942 AATTTATGACCACAAATTTTGTTCCAAGTTTTAATGTTGTAATGT
1 AATTTAT-ATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT
25588987 TATAATGCTA
Statistics
Matches: 154, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
61 5 0.03
62 104 0.68
63 1 0.01
64 9 0.06
65 35 0.23
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.47
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
Found at i:25588973 original size:65 final size:63
Alignment explanation
Indices: 25588754--25589059 Score: 304
Period size: 62 Copynumber: 4.8 Consensus size: 63
25588744 CAATGTACCT
**
25588754 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTT--ATATAACAA
1 AATTTATACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTGAAT-TAACAA
** * *
25588816 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTGTATT-ACAA
1 AATTTATACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTGAATTAACAA
** *
25588878 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TGTAATGTTGCAATTAATC-
1 AATTTATACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAAT-TTG-AATTAA-CA
*
25588941 T
63 A
* * **
25588942 AATTTATGACCACAAATTTTGTTCCAAGTTTTAATGTTGTAATGT-TATAATGCTACAATTAATC
1 AATTTAT-ACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAAT--TTGAATTAA-C
*
25589006 -T
62 AA
* * *
25589007 AATTTATGACCACAAAGTTAGTTCAAAGTTTTAATGTTGCAAT-TAATTTAATT
1 AATTTAT-ACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-ATTTAATT
25589060 AAATAAATAC
Statistics
Matches: 217, Mismatches: 17, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
61 5 0.02
62 102 0.47
63 4 0.02
64 12 0.06
65 88 0.41
66 6 0.03
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (63 bp):
AATTTATACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTGAATTAACAA
Found at i:25588981 original size:57 final size:60
Alignment explanation
Indices: 25588916--25589045 Score: 167
Period size: 65 Copynumber: 2.1 Consensus size: 60
25588906 TTTAATGTTG
* * *
25588916 TAATGTTGTAATG-T-TG-CAATTAATCTAATTTATGACCACAAATTTTGTTCCAAGTTT
1 TAATGTTGTAATGTTATGACAATTAATCTAATTTATGACCACAAAGTTAGTTCAAAGTTT
25588973 TAATGTTGTAATGTTATAATGCTACAATTAATCTAATTTATGACCACAAAGTTAGTTCAAAGTTT
1 TAATGTTGTAATG-T-T-ATG--ACAATTAATCTAATTTATGACCACAAAGTTAGTTCAAAGTTT
25589038 TAATGTTG
1 TAATGTTG
25589046 CAATTAATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
57 13 0.21
60 1 0.02
62 2 0.03
65 46 0.74
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (60 bp):
TAATGTTGTAATGTTATGACAATTAATCTAATTTATGACCACAAAGTTAGTTCAAAGTTT
Found at i:25591922 original size:5 final size:5
Alignment explanation
Indices: 25591912--25591936 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25591902 TTCTTTCTTT
25591912 TTCCC TTCCC TTCCC TTCCC TTCCC
1 TTCCC TTCCC TTCCC TTCCC TTCCC
25591937 GCCCTCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TTCCC
Found at i:25592226 original size:13 final size:13
Alignment explanation
Indices: 25592208--25592233 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25592198 CAATGACAGC
25592208 GGGTCAGGTTTTT
1 GGGTCAGGTTTTT
25592221 GGGTCAGGTTTTT
1 GGGTCAGGTTTTT
25592234 TTTGTATACG
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:0.08, C:0.08, G:0.38, T:0.46
Consensus pattern (13 bp):
GGGTCAGGTTTTT
Found at i:25605883 original size:12 final size:12
Alignment explanation
Indices: 25605862--25605890 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25605852 TATTTCAGAA
25605862 GATG-AAAACTT
1 GATGAAAAACTT
25605873 GATGAAAAACTT
1 GATGAAAAACTT
25605885 GATGAA
1 GATGAA
25605891 TGAATGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (12 bp):
GATGAAAAACTT
Found at i:25607396 original size:31 final size:31
Alignment explanation
Indices: 25607358--25607423 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
25607348 TTTTTAAACT
*
25607358 AATTTGACCATCAGCCTTTTA-AAACGAGTTG
1 AATTTGACCATCAACCTTTTAGAAA-GAGTTG
* *
25607389 AATTTGACTATTAACCTTTTAGAAAGAGTTG
1 AATTTGACCATCAACCTTTTAGAAAGAGTTG
25607420 AATT
1 AATT
25607424 GTTTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (31 bp):
AATTTGACCATCAACCTTTTAGAAAGAGTTG
Found at i:25608859 original size:16 final size:16
Alignment explanation
Indices: 25608838--25608868 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25608828 TACTTAAAAG
25608838 TTAAAACTAATTGTTA
1 TTAAAACTAATTGTTA
*
25608854 TTAAAATTAATTGTT
1 TTAAAACTAATTGTT
25608869 GTTGAATTTA
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:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:25608972 original size:25 final size:25
Alignment explanation
Indices: 25608942--25608989 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
25608932 AAGATTACTT
25608942 ATTTGAATTTAATTACAAACAATTA
1 ATTTGAATTTAATTACAAACAATTA
25608967 ATTTGAATTTAATTACAAACAAT
1 ATTTGAATTTAATTACAAACAAT
25608990 CAAATCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTGAATTTAATTACAAACAATTA
Found at i:25609073 original size:7 final size:8
Alignment explanation
Indices: 25609055--25609079 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25609045 ATTTAATTCC
25609055 TTTTAACT
1 TTTTAACT
25609063 TTTTAACT
1 TTTTAACT
25609071 TTTTAACT
1 TTTTAACT
25609079 T
1 T
25609080 AAATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTAACT
Found at i:25609633 original size:13 final size:13
Alignment explanation
Indices: 25609615--25609748 Score: 94
Period size: 13 Copynumber: 10.2 Consensus size: 13
25609605 AATTTAAAAG
*
25609615 TTAAAACATTATA
1 TTAAAACAGTATA
*
25609628 TTAAAACAATATAA
1 TTAAAACAGTAT-A
*
25609642 TTATAACAGTATA
1 TTAAAACAGTATA
*
25609655 TTAAAACAATATA
1 TTAAAACAGTATA
*
25609668 TTAAAAAAGTATA
1 TTAAAACAGTATA
* *
25609681 TTTATAATAGTATA
1 -TTAAAACAGTATA
* *
25609695 TTAAAATAATATA
1 TTAAAACAGTATA
* * *
25609708 TTATAA-ATTTTA
1 TTAAAACAGTATA
*
25609720 -TAACAATA-TATTA
1 TTAA-AACAGTA-TA
25609733 TTAAAACAGTATA
1 TTAAAACAGTATA
25609746 TTA
1 TTA
25609749 TATTTAAAAT
Statistics
Matches: 97, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
11 2 0.02
12 7 0.07
13 61 0.63
14 27 0.28
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (13 bp):
TTAAAACAGTATA
Found at i:25609660 original size:40 final size:40
Alignment explanation
Indices: 25609615--25609710 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
25609605 AATTTAAAAG
*
25609615 TTAAAACATTATATTAAAACAA-TATAATTATAACAGTATA
1 TTAAAACAATATATTAAAA-AAGTATAATTATAACAGTATA
* *
25609655 TTAAAACAATATATTAAAAAAGTATATTTATAATAGTATA
1 TTAAAACAATATATTAAAAAAGTATAATTATAACAGTATA
*
25609695 TTAAAATAATATATTA
1 TTAAAACAATATATTA
25609711 TAAATTTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 2 0.04
40 49 0.96
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (40 bp):
TTAAAACAATATATTAAAAAAGTATAATTATAACAGTATA
Found at i:25611461 original size:29 final size:30
Alignment explanation
Indices: 25611424--25611519 Score: 79
Period size: 38 Copynumber: 3.0 Consensus size: 30
25611414 CACAACCATT
*
25611424 AACAGCATTAACA-ACAAAATCAAAATCAG
1 AACACCATTAACACACAAAATCAAAATCAG
25611453 AACACCATTAACAGCATTAACAGCAAAATCAAAATCAG
1 AACACCATT-A-A-C----ACA-CAAAATCAAAATCAG
*
25611491 AACACCATTAACAGTA-AAAATCAAAATCA
1 AACACCATTAACA-CACAAAATCAAAATCA
25611520 CAACCAACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
29 8 0.15
30 14 0.25
31 2 0.04
32 2 0.04
35 1 0.02
36 2 0.04
37 2 0.04
38 24 0.44
ACGTcount: A:0.56, C:0.22, G:0.06, T:0.16
Consensus pattern (30 bp):
AACACCATTAACACACAAAATCAAAATCAG
Found at i:25611469 original size:38 final size:38
Alignment explanation
Indices: 25611418--25611504 Score: 165
Period size: 38 Copynumber: 2.3 Consensus size: 38
25611408 AAAAAACACA
25611418 ACCATTAACAGCATTAACAACAAAATCAAAATCAGAAC
1 ACCATTAACAGCATTAACAACAAAATCAAAATCAGAAC
*
25611456 ACCATTAACAGCATTAACAGCAAAATCAAAATCAGAAC
1 ACCATTAACAGCATTAACAACAAAATCAAAATCAGAAC
25611494 ACCATTAACAG
1 ACCATTAACAG
25611505 TAAAAATCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.53, C:0.24, G:0.07, T:0.16
Consensus pattern (38 bp):
ACCATTAACAGCATTAACAACAAAATCAAAATCAGAAC
Found at i:25611513 original size:30 final size:29
Alignment explanation
Indices: 25611462--25611519 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
25611452 GAACACCATT
* *
25611462 AACAGCATTAACAGCAAAATCAAAATCAG
1 AACACCATTAACAGAAAAATCAAAATCAG
25611491 AACACCATTAACAGTAAAAATCAAAATCA
1 AACACCATTAACAG-AAAAATCAAAATCA
25611520 CAACCAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.16
Consensus pattern (29 bp):
AACACCATTAACAGAAAAATCAAAATCAG
Found at i:25614369 original size:3 final size:3
Alignment explanation
Indices: 25614354--25614401 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
25614344 AATTAAAAAG
* *
25614354 ATA ATA ATG ATA ATA ATA ATA TTA ATA ATA AT- ATGA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT-A ATA
25614400 AT
1 AT
25614402 CTAGAGTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.82
4 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:25614371 original size:12 final size:11
Alignment explanation
Indices: 25614354--25614401 Score: 62
Period size: 12 Copynumber: 4.2 Consensus size: 11
25614344 AATTAAAAAG
25614354 ATAATAATGATA
1 ATAATAAT-ATA
25614366 ATAATAATATTA
1 ATAATAATA-TA
25614378 ATAATAATATGA
1 ATAATAATAT-A
25614390 ATAATAA-ATA
1 ATAATAATATA
25614400 AT
1 AT
25614402 CTAGAGTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.09
11 4 0.12
12 27 0.79
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
ATAATAATATA
Found at i:25614434 original size:18 final size:18
Alignment explanation
Indices: 25614413--25614459 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
25614403 TAGAGTTTGA
*
25614413 AAATATATAAAAAGATAT
1 AAATAAATAAAAAGATAT
*
25614431 AAATAAATAAAACGATAT
1 AAATAAATAAAAAGATAT
25614449 -AATAAAATAAA
1 AAAT-AAATAAA
25614460 TGTATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAAAGATAT
Found at i:25615394 original size:5 final size:6
Alignment explanation
Indices: 25615374--25615409 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
25615364 CCAGTAAGCG
25615374 TTTATTT TTTATT TTTATT TTTATT TTATATT TTTA
1 TTTA-TT TTTATT TTTATT TTTATT TT-TATT TTTA
25615410 AAAAATAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.64
7 10 0.36
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:25615962 original size:44 final size:44
Alignment explanation
Indices: 25615908--25617238 Score: 253
Period size: 44 Copynumber: 29.5 Consensus size: 44
25615898 CGAAATTGGG
* * *
25615908 CCACTACAACTTCAGGGAGATAGGATTAATAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAACCTGCT
** * *
25615952 CCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAACCTGCT
** ** * *
25615996 CCACTGCAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATT--AATAGCTTCAACCTGCT
* * ** * * *
25616042 CCACTGCAACTTCAAGGAGATAAGGTTTGTGGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAACCTGCT
* ** ** * **
25616086 ---CTGTAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTATT
1 CCACTGCAACTTCAGGGAGATAAGATT--AATAGCTTCAACCTGCT
* * * * * *
25616129 CCACTGCAGCTTTAGGGAGATAAGGTT--T-GATAT-GATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAGCT-TCAACCTGCT
* * * * *
25616170 CTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATGGCTTTAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGA--T-TAA--TA--GCTTCAACCTGCT
* * * ** * ** *
25616221 CCACTGCAACTTCAAGGAAATGAGATTCGTTATCTTCAGTCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAACCTGCT
* * * *
25616266 CCA-TACAGCTTCAGGGAGATAAGACTT-GTAACTTCAACCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTAATAGCTTCAACCTGCT
* * * * *
25616309 CCACTACAACTTCAGGGAGATAAGGTT--T-GCTACGATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAACCTGCT
* * * ** *
25616350 CTACTGCAACTTTAGAGAGATAAGATCTACAATTTATAGCTTCAATTTGTT
1 CCACTGCAACTTCAGGGAGATAAGAT-T---A---ATAGCTTCAACCTGCT
* * ** ** ** *
25616401 CCACTGCAACTTCAAGGAAATAAGATTCCCTATATTCAGTCAGCT
1 CCACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAACCTGCT
** ** * **
25616446 CCACTGCAACTTCCA-GGAGATAAGATTGGTTTATTTTTAACCTATT
1 CCACTGCAACTT-CAGGGAGATAAGATT--AATAGCTTCAACCTGCT
* * * * * * * *
25616492 GCACTACAGCTTCAGTGAGATAAGGTTTGATATG-ATCTA-CT-CT
1 CCACTGCAACTTCAGGGAGATAA-GATTAATA-GCTTCAACCTGCT
* * * * *
25616535 --ACTGCAACTTTAGAGAGATAAGATCTGTAATTTATAGCTTTAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGA--T-T-A---ATAGCTTCAACCTGCT
* * ** * * ** **
25616584 CCACTGCAACTTCAGTGAAATAAGATTCGCTATCTCCAGTCTATT
1 CCACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAACCTGCT
* * * *
25616629 CCACTGCAGCTTTAGGGAGATAAGACTT-GTAACTTCAACCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTAATAGCTTCAACCTGCT
* ** * * * *
25616673 CCACTGTAACTTTTGGGAGATAAGGTT--T-TCTAT-GATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAGCT-TCAACCTGCT
* * * * * * *
25616714 CTACTGTAACTTTAGAGAGTTAAGATCTGCAATTTATAGCTTCAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGAT-T---A---ATAGCTTCAACCTGCT
* * * ** * **
25616765 CCATTGCAACTTTAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAACCTGCT
* * * * * * *
25616810 CCACTGTAACCTCATGGAGATAAGACTAGTGGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAACCTGCT
* * * * * *
25616854 CTACTACAACTTCAGGGAGATAAGGTT--T-GCTAT-GATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAGCT-TCAACCTGCT
* * * *
25616895 CTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA--T-T-A---ATAGCTTCAACCTGCT
* * * ** * **
25616946 CCATTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAACCTGCT
* * * * *
25616991 CCACTGCAACTTTAGGGAGATAAGACTT-GTAACTTCAACATACT
1 CCACTGCAACTTCAGGGAGATAAGA-TTAATAGCTTCAACCTGCT
* *
25617035 CCACTGCAACTTCAGGGAGATAAGATT--T-GCTAT-GATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAGCT-TCAACCTGCT
* * * *
25617076 CTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGAT-T---A---ATAGCTTCAACCTGCT
* * ** * **
25617127 CCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAACCTGCT
** * * *
25617172 CCACTATAACTTCAGGAAGATAAGACTAAT-GACTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAATAG-CTTCAACCTGCT
*
25617216 CCATTGCAACTTCAGGGAGATAA
1 CCACTGCAACTTCAGGGAGATAA
25617239 AATTCGCCAT
Statistics
Matches: 940, Mismatches: 259, Indels: 176
0.68 0.19 0.13
Matches are distributed among these distances:
40 1 0.00
41 183 0.19
42 13 0.01
43 34 0.04
44 241 0.26
45 182 0.19
46 89 0.09
47 10 0.01
48 6 0.01
49 4 0.00
50 11 0.01
51 166 0.18
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAACCTGCT
Found at i:25616055 original size:46 final size:46
Alignment explanation
Indices: 25615908--25616332 Score: 260
Period size: 44 Copynumber: 9.5 Consensus size: 46
25615898 CGAAATTGGG
* * ** * * * *
25615908 CCACTACAACTTCAGGGAGATAGGATT--AATAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTT
*
25615952 CCACTGCAACTTCAGGGAGATAAGATTGG--TATCTTCAACCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTT
*
25615996 CCACTGCAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTT
* * * ** *
25616042 CCACTGCAACTTCAAGGAGATAAGGTT--TGTGGCTTTAATCTG--
1 CCACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTT
* * * *
25616084 -CTCTGTAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTATT
1 CCACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTT
* * * * * *
25616129 CCACTGCAGCTTTAGGGAGAT-A-A--GGTTTGA--TATGATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTGGTTT-ATCTTTAACCTGTT
* * * *
25616170 CTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATGGCTTTAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGAT-TG--GTTTAT--CTTTAACCTGTT
* * * * * **
25616221 CCACTGCAACTTCAAGGAAATGAGATTCG-TTATCTTCAGTCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTT
* * * * *
25616266 CCA-TACAGCTTCAGGGAGATAAGACTT-G--TAACTTCAACCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTGGTTTATCTTTAACCTGTT
*
25616309 CCACTACAACTTCAGGGAGATAAG
1 CCACTGCAACTTCAGGGAGATAAG
25616333 GTTTGCTACG
Statistics
Matches: 298, Mismatches: 60, Indels: 46
0.74 0.15 0.11
Matches are distributed among these distances:
41 45 0.15
42 6 0.02
43 25 0.08
44 113 0.38
45 16 0.05
46 55 0.18
47 5 0.02
48 3 0.01
50 1 0.00
51 29 0.10
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (46 bp):
CCACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTT
Found at i:25616181 original size:87 final size:88
Alignment explanation
Indices: 25615998--25617101 Score: 437
Period size: 92 Copynumber: 12.3 Consensus size: 88
25615988 AACCTGTTCC
*
25615998 ACTGCAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTTCCACTGCAACTTCAAGGAGAT
1 ACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTTCCACTGCAACTTCAAGGAGAT
* * * *
25616063 AAGGTTTGTGGCTTTAATCTG--CT
66 AAGG-TTCT-GATATGATCTGCTCT
* * * * * *
25616086 -CTGTAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTATTCCACTGCAGCTTTAGGGAGAT
1 ACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTTCCACTGCAACTTCAAGGAGAT
25616150 AAGGTT-TGATATGATCTGCTCT
66 AAGGTTCTGATATGATCTGCTCT
* * *
25616172 ACTGCAACTTCAGAGAGATAAGATCTGTAATTTATGGCTTTAATCTGTTCCACTGCAACTTCAAG
1 ACTGCAACTTCAGGGAGATAAGAT-TG--GTTTAT--CTTTAACCTGTTCCACTGCAACTTCAAG
* * * * * * * *
25616237 GAAATGAGATTCGTTATCTTCAGTCTGTTCC
61 GAGATAAGGTTC-TGAT-ATGA-TCTGCTCT
* * * * * * *
25616268 A-TACAGCTTCAGGGAGATAAGACTT-G--TAACTTCAACCTGCTCCACTACAACTTCAGGGAGA
1 ACTGCAACTTCAGGGAGATAAGA-TTGGTTTATCTTTAACCTGTTCCACTGCAACTTCAAGGAGA
* *
25616329 TAAGGTT-TGCTACGATCTGCTCT
65 TAAGGTTCTGATATGATCTGCTCT
* * ** * **
25616352 ACTGCAACTTTAGAGAGATAAGATCTACAATTTATAGCTTCAATTTGTTCCACTGCAACTTCAAG
1 ACTGCAACTTCAGGGAGATAAGAT-T--GGTTTAT--CTTTAACCTGTTCCACTGCAACTTCAAG
* * * * *
25616417 GAAATAAGATTCCCT-ATATTCAGTCAGCTCC
61 GAGATAAGGTT--CTGATA-TGA-TCTGCTCT
* * * * *
25616448 ACTGCAACTTCCA-GGAGATAAGATTGGTTTATTTTTAACCTATTGCACTACAGCTTC-AGTGAG
1 ACTGCAACTT-CAGGGAGATAAGATTGGTTTATCTTTAACCTGTTCCACTGCAACTTCAAG-GAG
*
25616511 ATAAGGTT-TGATATGATCTACTCT
64 ATAAGGTTCTGATATGATCTGCTCT
* * * *
25616535 ACTGCAACTTTAGAGAGATAAGATCTGTAATTTATAGCTTTAATCTGTTCCACTGCAACTTC-AG
1 ACTGCAACTTCAGGGAGATAAGAT-TG--GTTTAT--CTTTAACCTGTTCCACTGCAACTTCAAG
* * * * ** *
25616599 TGAAATAAGATTC-GCTATCTCCAGTCTATTCC
61 -GAGATAAGGTTCTG--ATAT-GA-TCTGCTCT
* * * * * * ***
25616631 ACTGCAGCTTTAGGGAGATAAGACTT-G--TAACTTCAACCTGCTCCACTGTAACTTTTGGGAGA
1 ACTGCAACTTCAGGGAGATAAGA-TTGGTTTATCTTTAACCTGTTCCACTGCAACTTCAAGGAGA
**
25616693 TAAGGTT-TTCTATGATCTGCTCT
65 TAAGGTTCTGATATGATCTGCTCT
* * * * * * * * * *
25616716 ACTGTAACTTTAGAGAGTTAAGATCTGCAATTTATAGCTTCAATCTGTTCCATTGCAACTTTAGG
1 ACTGCAACTTCAGGGAGATAAGAT-TG--GTTTAT--CTTTAACCTGTTCCACTGCAACTTCAAG
* * * * *
25616781 GAAATAAGATTC-GCTATCTTCAGTCTGCTCC
61 GAGATAAGGTTCTG--AT-ATGA-TCTGCTCT
* * * * * ** * * * * * *
25616812 ACTGTAACCTCATGGAGATAAGACTAG--TGGCTTCAATCTGCTCTACTACAACTTCAGGGAGAT
1 ACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTTCCACTGCAACTTCAAGGAGAT
* *
25616875 AAGGTT-TGCTATGATCTACTCT
66 AAGGTTCTGATATGATCTGCTCT
* * * * * * *
25616897 ACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAATCTGCTCCATTACAACTTCAGG
1 ACTGCAACTTCAGGGAGATAAGAT-TG--GTTTAT--CTTTAACCTGTTCCACTGCAACTTCAAG
* * * * *
25616962 GAAATAAGATTC-GCTATCTTCAGTCTGCTCC
61 GAGATAAGGTTCTG--AT-ATGA-TCTGCTCT
* * * * ** *
25616993 ACTGCAACTTTAGGGAGATAAGACTT-G--TAACTTCAACATACTCCACTGCAACTTCAGGGAGA
1 ACTGCAACTTCAGGGAGATAAGA-TTGGTTTATCTTTAACCTGTTCCACTGCAACTTCAAGGAGA
* *
25617055 TAAGATT-TGCTATGATCTGCTCT
65 TAAGGTTCTGATATGATCTGCTCT
*
25617078 ACTGCAACTTCAGAGAGATAAGAT
1 ACTGCAACTTCAGGGAGATAAGAT
25617102 CTGCAATTTA
Statistics
Matches: 753, Mismatches: 191, Indels: 148
0.69 0.17 0.14
Matches are distributed among these distances:
84 18 0.02
85 98 0.13
86 13 0.02
87 113 0.15
88 38 0.05
89 98 0.13
90 20 0.03
91 31 0.04
92 161 0.21
93 5 0.01
94 10 0.01
95 30 0.04
96 115 0.15
97 3 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (88 bp):
ACTGCAACTTCAGGGAGATAAGATTGGTTTATCTTTAACCTGTTCCACTGCAACTTCAAGGAGAT
AAGGTTCTGATATGATCTGCTCT
Found at i:25616755 original size:181 final size:181
Alignment explanation
Indices: 25615908--25617238 Score: 1477
Period size: 181 Copynumber: 7.4 Consensus size: 181
25615898 CGAAATTGGG
* * * * *
25615908 CCACTACAACTTCAGGGAGATAGGA-TTAATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
1 CCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGA
* * * * * * * * *
25615972 TAA-GATTGGTATCTTCAACCTGTTCCACTGCAACTTCAGGGAGATAAGAT-TG--GTTTAT--T
65 TAAGGTTTGCTA---T-GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGC
* * * * * * ** * *
25616031 TTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGGTTTG-TGGCTTTAATCTGCT
126 TTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
* ** * ** * *
25616086 ---CTGTAACTTCAGGGAGATAAGA-TTGGTTTATTTTTAACCTATTCCACTGCAGCTTTAGGGA
1 CCACTGCAACTTCAGGGAGATAAGACTT-G--TAACTTCAACCTGCTCCACTGCAACTTCAGGGA
* * *
25616147 GATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATGGCTT
63 GATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTT
* * * * *
25616212 TAATCTGTTCCACTGCAACTTCAAGGAAATGAGATTCGTTATCTTCAGTCTGTT
128 CAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
* * *
25616266 CCA-TACAGCTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAGAT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGAT
* * *
25616330 AAGGTTTGCTACGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTACAATTTATAGCTTCAA
66 AAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAA
* * * * *
25616395 TTTGTTCCACTGCAACTTCAAGGAAATAAGATTCCCTATATTCAGTCAGCT
131 TCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
** * ** * * * *
25616446 CCACTGCAACTTCCA-GGAGATAAGA-TTGGTTTATTTTTAACCTATTGCACTACAGCTTCAGTG
1 CCACTGCAACTT-CAGGGAGATAAGACTT-G--TAACTTCAACCTGCTCCACTGCAACTTCAGGG
* * * *
25616509 AGATAAGGTTTGATATGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTGTAATTTATAGCT
62 AGATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCT
* * * **
25616574 TTAATCTGTTCCACTGCAACTTCAGTGAAATAAGATTCGCTATCTCCAGTCTATT
127 TCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
* * * **
25616629 CCACTGCAGCTTTAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGTAACTTTTGGGAGAT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGAT
* * * *
25616694 AAGGTTTTCTATGATCTGCTCTACTGTAACTTTAGAGAGTTAAGATCTGCAATTTATAGCTTCAA
66 AAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAA
* *
25616759 TCTGTTCCATTGCAACTTTAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
131 TCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
* * * * ** * * *
25616810 CCACTGTAACCTCATGGAGATAAGACTAGTGGCTTCAATCTGCTCTACTACAACTTCAGGGAGAT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGAT
* * *
25616875 AAGGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTTAA
66 AAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAA
* * *
25616940 TCTGCTCCATTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
131 TCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
* * *
25616991 CCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACATACTCCACTGCAACTTCAGGGAGAT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGAT
*
25617056 AAGATTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAA
66 AAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAA
*
25617121 TCTGTTCCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
131 TCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
** * ** * * *
25617172 CCACTATAACTTCAGGAAGATAAGACTAATGACTTCAATCTGCTCCATTGCAACTTCAGGGAGAT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGAT
25617237 AA
66 AA
25617239 AATTCGCCAT
Statistics
Matches: 971, Mismatches: 162, Indels: 37
0.83 0.14 0.03
Matches are distributed among these distances:
174 29 0.03
175 24 0.02
177 35 0.04
178 6 0.01
179 35 0.04
180 145 0.15
181 520 0.54
182 22 0.02
183 153 0.16
184 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (181 bp):
CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGAT
AAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAA
TCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCT
Found at i:25617055 original size:362 final size:360
Alignment explanation
Indices: 25616142--25617238 Score: 1629
Period size: 362 Copynumber: 3.0 Consensus size: 360
25616132 CTGCAGCTTT
*
25616142 AGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTAT
1 AGGGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTAT
* * * * *
25616207 GGCTTTAATCTGTTCCACTGCAACTTCAAGGAAATGAGATTCGTTATCTTCAGTCTGTTCCA-TA
66 AGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGTTCCACTG
* *
25616271 CAGCTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGTT
131 CAGCTTTAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTT
* * *
25616336 TGCTACGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTACAATTTATAGCTTCAATTTGTT
196 TGCTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGCAATTTATAGCTTCAATCTGTT
* * * * * *
25616401 CCACTGCAACTTCAAGGAAATAAGATTCCCTATATTCAGTCAGCTCCACTGCAACTTCCAGGAGA
261 CCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGTAACTT-CAGGAGA
* * * * * * ** *
25616466 TAAGATTGGTTTATTTTTAACCTATTGCACTACAGCTTC
325 TAAGACTAG-TGA-CTTCAATCTGCT-CACTACAACTTC
* *
25616505 AGTGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTGTAATTTAT
1 AGGGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTAT
* * *
25616570 AGCTTTAATCTGTTCCACTGCAACTTCAGTGAAATAAGATTCGCTATCTCCAGTCTATTCCACTG
66 AGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGTTCCACTG
* **
25616635 CAGCTTTAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGTAACTTTTGGGAGATAAGGTT
131 CAGCTTTAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTT
* * *
25616700 TTCTATGATCTGCTCTACTGTAACTTTAGAGAGTTAAGATCTGCAATTTATAGCTTCAATCTGTT
196 TGCTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGCAATTTATAGCTTCAATCTGTT
* *
25616765 CCATTGCAACTTTAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGTAACCTCATGGAGA
261 CCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGTAACTTCA-GGAGA
*
25616830 TAAGACTAGTGGCTTCAATCTGCTCTACTACAACTTC
325 TAAGACTAGTGACTTCAATCTGCTC-ACTACAACTTC
*
25616867 AGGGAGATAAGGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTAT
1 AGGGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTAT
* * * *
25616932 AGCTTTAATCTGCTCCATTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTG
66 AGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGTTCCACTG
* * * *
25616997 CAACTTTAGGGAGATAAGACTTGTAACTTCAACATACTCCACTGCAACTTCAGGGAGATAAGATT
131 CAGCTTTAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTT
*
25617062 TGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAATCTGTT
196 TGCTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGCAATTTATAGCTTCAATCTGTT
*
25617127 CCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTATAACTTCAGGAAGA
261 CCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGTAACTTCAGG-AGA
* * *
25617192 TAAGACTAATGACTTCAATCTGCTCCATTGCAACTTC
325 TAAGACTAGTGACTTCAATCTGCT-CACTACAACTTC
25617229 AGGGAGATAA
1 AGGGAGATAA
25617239 AATTCGCCAT
Statistics
Matches: 661, Mismatches: 68, Indels: 11
0.89 0.09 0.01
Matches are distributed among these distances:
361 3 0.00
362 356 0.54
363 121 0.18
364 181 0.27
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (360 bp):
AGGGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTAT
AGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGTTCCACTG
CAGCTTTAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTT
TGCTATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGCAATTTATAGCTTCAATCTGTT
CCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGTAACTTCAGGAGAT
AAGACTAGTGACTTCAATCTGCTCACTACAACTTC
Found at i:25621225 original size:17 final size:17
Alignment explanation
Indices: 25621203--25621235 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
25621193 ATTTATTTTA
25621203 TAAAAAAATCATAATTG
1 TAAAAAAATCATAATTG
25621220 TAAAAAAATCATAATT
1 TAAAAAAATCATAATT
25621236 AATCATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (17 bp):
TAAAAAAATCATAATTG
Found at i:25621376 original size:16 final size:15
Alignment explanation
Indices: 25621340--25621377 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
25621330 TTATTTTTTC
25621340 ATAAAT-ATTTTTAA
1 ATAAATAATTTTTAA
25621354 A-AAATAATTTTTCAA
1 ATAAATAATTTTT-AA
25621369 ATAAATAAT
1 ATAAATAAT
25621378 AAATAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
14 7 0.33
15 3 0.14
16 7 0.33
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATAATTTTTAA
Found at i:25630664 original size:23 final size:23
Alignment explanation
Indices: 25630637--25630681 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
25630627 GAAAAATATT
25630637 AAATATATATA-TTTTTATTTTTA
1 AAATATA-ATAGTTTTTATTTTTA
25630660 AAATATAATAGTTTTTTATTTT
1 AAATATAATAG-TTTTTATTTT
25630682 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 7 0.35
24 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATATAATAGTTTTTATTTTTA
Found at i:25630792 original size:9 final size:9
Alignment explanation
Indices: 25630778--25630805 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
25630768 TTTTGTTACA
25630778 ACAATTAAT
1 ACAATTAAT
25630787 ACAATTAAT
1 ACAATTAAT
25630796 ACAATTAAT
1 ACAATTAAT
25630805 A
1 A
25630806 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:25630827 original size:68 final size:68
Alignment explanation
Indices: 25630748--25630958 Score: 390
Period size: 68 Copynumber: 3.1 Consensus size: 68
25630738 TCAAGTTTGT
*
25630748 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
25630813 AAA
66 AAA
25630816 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
25630881 AAA
66 AAA
25630884 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
25630947 AAT
66 AAA
25630950 TTTACTAAT
1 TTTACTAAT
25630959 AATTAATTTT
Statistics
Matches: 141, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 28 0.20
67 1 0.01
68 112 0.79
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:25630858 original size:9 final size:9
Alignment explanation
Indices: 25630846--25630873 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
25630836 TTTTATTACA
25630846 ACAATTAAT
1 ACAATTAAT
25630855 ACAATTAAT
1 ACAATTAAT
25630864 ACAATTAAT
1 ACAATTAAT
25630873 A
1 A
25630874 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:25630967 original size:16 final size:16
Alignment explanation
Indices: 25630946--25630987 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
25630936 AATAATTTGA
* *
25630946 TAATTTTACTAATAAT
1 TAATTTTAATAACAAT
25630962 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
25630978 TAGTTTTAAT
1 TAATTTTAAT
25630988 TTTATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:25631000 original size:28 final size:28
Alignment explanation
Indices: 25630969--25631026 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
25630959 AATTAATTTT
*
25630969 AATAACAATTAGTTTTAATTTT-ATTAAA
1 AATAA-AATTAATTTTAATTTTAATTAAA
**
25630997 AATAATTTTAATTTTAATTTTAATTAAA
1 AATAAAATTAATTTTAATTTTAATTAAA
25631025 AA
1 AA
25631027 CGGGTCGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
AATAAAATTAATTTTAATTTTAATTAAA
Found at i:25631007 original size:21 final size:22
Alignment explanation
Indices: 25630961--25631014 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
25630951 TTACTAATAA
* *
25630961 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAACAAATAATT
*
25630983 TTAATTTTATTAA-AAATAATT
1 TTAATTTTAATAACAAATAATT
25631004 TTAATTTTAAT
1 TTAATTTTAAT
25631015 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTAATTTTAATAACAAATAATT
Found at i:25631501 original size:27 final size:26
Alignment explanation
Indices: 25631453--25631527 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 26
25631443 ATTCTAAAAT
* *
25631453 ATATATT-TATAAATTTTAAAAAAACCA
1 ATATATTATATAAA-ATTGAAAAAA-CA
* *
25631480 ATATATTATATAAAATTGAAAATATA
1 ATATATTATATAAAATTGAAAAAACA
*
25631506 A-AAATTATATAAAAATTGAAAA
1 ATATATTATAT-AAAATTGAAAA
25631528 TTTATCATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 8 0.20
26 13 0.32
27 14 0.34
28 6 0.15
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (26 bp):
ATATATTATATAAAATTGAAAAAACA
Found at i:25631780 original size:9 final size:8
Alignment explanation
Indices: 25631737--25631793 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
25631727 TATTTTGATT
25631737 TTTTTAAA
1 TTTTTAAA
*
25631745 -ATTTAAA
1 TTTTTAAA
* *
25631752 TTTATATA
1 TTTTTAAA
25631760 TTTTTAAA
1 TTTTTAAA
25631768 TTTTTAAA
1 TTTTTAAA
25631776 TTTTTTAAA
1 -TTTTTAAA
25631785 CTTTTTAAA
1 -TTTTTAAA
25631794 AAATTTGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
7 6 0.15
8 18 0.45
9 16 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
TTTTTAAA
Found at i:25662379 original size:23 final size:23
Alignment explanation
Indices: 25662353--25662398 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
25662343 AAAGAAAGAT
*
25662353 ATACTATC-TAATGAAGACACCAA
1 ATACAATCATAATGAAGA-ACCAA
*
25662376 ATACAATCATAATTAAGAACCAA
1 ATACAATCATAATGAAGAACCAA
25662399 TAATTTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.52, C:0.20, G:0.07, T:0.22
Consensus pattern (23 bp):
ATACAATCATAATGAAGAACCAA
Found at i:25667875 original size:33 final size:31
Alignment explanation
Indices: 25667829--25667976 Score: 111
Period size: 33 Copynumber: 4.8 Consensus size: 31
25667819 TTAACCGTTA
*
25667829 TCGGTGGATTCAGCACTTAGCAACCACCAGTAAT
1 TCGG-GGAATCAGCACTTAGCAACC-CCA-TAAT
*
25667863 TCGGGGAATCAGCACTTAGCAACCCCTTTTACAT
1 TCGGGGAATCAGCACTTAGCAACCCC--ATA-AT
25667897 TC----AA--AGCACTTAGCAACCACCAATGAA-
1 TCGGGGAATCAGCACTTAGCAACC-CC-AT-AAT
25667924 TCGGGGAATCAGCACTTAGCAACCCC----T
1 TCGGGGAATCAGCACTTAGCAACCCCATAAT
*
25667951 TGGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
25667977 CTTCACATTT
Statistics
Matches: 97, Mismatches: 5, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
27 27 0.28
28 16 0.16
29 3 0.03
30 2 0.02
31 2 0.02
32 4 0.04
33 35 0.36
34 8 0.08
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (31 bp):
TCGGGGAATCAGCACTTAGCAACCCCATAAT
Found at i:25668037 original size:100 final size:102
Alignment explanation
Indices: 25667901--25668154 Score: 422
Period size: 100 Copynumber: 2.5 Consensus size: 102
25667891 TTACATTCAA
25667901 AGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCAC
1 AGCACTTAGCAA-CACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCAC
25667966 TTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATC
65 TTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATC
25668004 AGCACTTAGC-A-ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACT
1 AGCACTTAGCAACACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACT
* *
25668067 TAGCAACCCCCTTTATATTTAAAGATACGGTGGAATC
66 TAGCAACCCCCTTCACATTTAAAGATACGGTGGAATC
* * **
25668104 AGCAGTTAGCAACCACCAATGAGTTAGGGAATCAGCACTTAGCAACCCCTT
1 AGCACTTAGCAA-CACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
25668155 CATATTCAAT
Statistics
Matches: 142, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
100 96 0.68
101 1 0.01
102 1 0.01
103 44 0.31
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (102 bp):
AGCACTTAGCAACACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACT
TAGCAACCCCCTTCACATTTAAAGATACGGTGGAATC
Found at i:25668064 original size:27 final size:28
Alignment explanation
Indices: 25667998--25668076 Score: 106
Period size: 27 Copynumber: 2.8 Consensus size: 28
25667988 AAGATACGGT
**
25667998 GGAATCAGCACTTAGCAACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCCCT--ATCGG
*
25668028 GGAATCAGCACTTAGCAACCCCT-TGGG
1 GGAATCAGCACTTAGCAACCCCTATCGG
25668055 GGAATCAGCACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
25668077 CTTTATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.54
30 21 0.46
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.16
Consensus pattern (28 bp):
GGAATCAGCACTTAGCAACCCCTATCGG
Found at i:25669243 original size:11 final size:12
Alignment explanation
Indices: 25669215--25669248 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
25669205 GCCCAAACGT
25669215 CGAAATTTTTGAA
1 CGAAATTTTT-AA
25669228 CGAAATTTTT-A
1 CGAAATTTTTAA
25669239 CGAAATTTTT
1 CGAAATTTTT
25669249 CCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:25672092 original size:22 final size:23
Alignment explanation
Indices: 25672060--25672105 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
25672050 TCATTTAATA
* *
25672060 TTTTTATAAATTT-TAATAATTT
1 TTTTTACAAATTTATAAAAATTT
25672082 TTTTTACAAATTTATAAAAATTT
1 TTTTTACAAATTTATAAAAATTT
25672105 T
1 T
25672106 AAAAAACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTTACAAATTTATAAAAATTT
Found at i:25676233 original size:33 final size:32
Alignment explanation
Indices: 25676190--25676253 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
25676180 TTCATTCGCA
*
25676190 AACCTCAACTTGGAAAACTATGCCTAGTCTGCG
1 AACCTCAACTTGGAAAACTATGCATA-TCTGCG
* *
25676223 AACCTTAACTTGGCAAACTATGCATATCTGC
1 AACCTCAACTTGGAAAACTATGCATATCTGC
25676254 TAATGCTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (32 bp):
AACCTCAACTTGGAAAACTATGCATATCTGCG
Found at i:25676728 original size:13 final size:13
Alignment explanation
Indices: 25676710--25676734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25676700 ACAAACTTTT
25676710 TATTTTTAATATA
1 TATTTTTAATATA
25676723 TATTTTTAATAT
1 TATTTTTAATAT
25676735 TTTATCTTAT
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:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTTAATATA
Found at i:25679729 original size:15 final size:15
Alignment explanation
Indices: 25679709--25679748 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
25679699 TGGGACTACC
25679709 ACGATGACAACAATG
1 ACGATGACAACAATG
* * *
25679724 ACGATGACGATAGTG
1 ACGATGACAACAATG
25679739 ACGATGACAA
1 ACGATGACAA
25679749 TGATGAGGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.15
Consensus pattern (15 bp):
ACGATGACAACAATG
Found at i:25679788 original size:27 final size:27
Alignment explanation
Indices: 25679739--25679790 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
25679729 GACGATAGTG
* *
25679739 ACGATGACAATGATGAGGCTGGCGGAA
1 ACGACGACAATGATGAGGATGGCGGAA
* *
25679766 ACGACGACAATGATTATGATGGCGG
1 ACGACGACAATGATGAGGATGGCGG
25679791 CAGTGACAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.35, T:0.17
Consensus pattern (27 bp):
ACGACGACAATGATGAGGATGGCGGAA
Found at i:25679798 original size:24 final size:24
Alignment explanation
Indices: 25679771--25679821 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
25679761 CGGAAACGAC
**
25679771 GACAATGATTATGATGGCGGCAGT
1 GACAATGACGATGATGGCGGCAGT
* *
25679795 GACAATGACGATGATGGTGGTAGT
1 GACAATGACGATGATGGCGGCAGT
25679819 GAC
1 GAC
25679822 CATAGCGCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.35, T:0.24
Consensus pattern (24 bp):
GACAATGACGATGATGGCGGCAGT
Found at i:25686356 original size:49 final size:47
Alignment explanation
Indices: 25686315--25686452 Score: 143
Period size: 48 Copynumber: 2.9 Consensus size: 47
25686305 GCCATGCAAC
* *
25686315 GGGAAGCTCATACGAGCCA-ATATCGGGAAGCTCCGGAGAGCCATTAATT
1 GGGAAGCTCATA-GAGCCAGATATCGGGAAGCTCAGAAGAGCCA-TAA-T
* * *
25686364 AGGAAGCTCATAAGAGCCAGTTATCGGGAAGCTCATAAGAGCCATAAT
1 GGGAAGCTCAT-AGAGCCAGATATCGGGAAGCTCAGAAGAGCCATAAT
* * * *
25686412 GGGAAGCTCCAGAGAGCCATATATCGGGATGCTCATAAGAG
1 GGGAAGCT-CATAGAGCCAGATATCGGGAAGCTCAGAAGAG
25686453 TTGCGGTGTG
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
48 34 0.45
49 21 0.28
50 21 0.28
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.18
Consensus pattern (47 bp):
GGGAAGCTCATAGAGCCAGATATCGGGAAGCTCAGAAGAGCCATAAT
Found at i:25686369 original size:74 final size:73
Alignment explanation
Indices: 25686278--25686452 Score: 205
Period size: 74 Copynumber: 2.4 Consensus size: 73
25686268 ACTTTCTTTC
** *
25686278 GAGCCATATAATAGGAAGCTCATGTGAGCCA-TGCAACGGGAAGCTCATACGAGCCA-ATATCGG
1 GAGCCATATAATAGGAAGCTCATAAGAGCCAGT-CAACGGGAAGCTCATAAGAGCCATA-AT-GG
*
25686341 GAAGCTCCGGA
63 GAAGCTCCAGA
* *
25686352 GAGCCAT-TAATTAGGAAGCTCATAAGAGCCAGTTATCGGGAAGCTCATAAGAGCCATAATGGGA
1 GAGCCATATAA-TAGGAAGCTCATAAGAGCCAGTCAACGGGAAGCTCATAAGAGCCATAATGGGA
25686416 AGCTCCAGA
65 AGCTCCAGA
* *
25686425 GAGCCATAT-ATCGGGATGCTCATAAGAG
1 GAGCCATATAAT-AGGAAGCTCATAAGAG
25686453 TTGCGGTGTG
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
72 1 0.01
73 37 0.42
74 48 0.55
75 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (73 bp):
GAGCCATATAATAGGAAGCTCATAAGAGCCAGTCAACGGGAAGCTCATAAGAGCCATAATGGGAA
GCTCCAGA
Found at i:25686452 original size:25 final size:25
Alignment explanation
Indices: 25686278--25686452 Score: 139
Period size: 25 Copynumber: 7.1 Consensus size: 25
25686268 ACTTTCTTTC
* **
25686278 GAGCCATATAAT-AGGAAGCTCATGT
1 GAGCCATAT-ATCGGGAAGCTCATAA
** * *
25686303 GAGCCATGCAACGGGAAGCTCATAC
1 GAGCCATATATCGGGAAGCTCATAA
***
25686328 GAGCCA-ATATCGGGAAGCTCCGGA
1 GAGCCATATATCGGGAAGCTCATAA
**
25686352 GAGCCAT-TAATTAGGAAGCTCATAA
1 GAGCCATAT-ATCGGGAAGCTCATAA
25686377 GAGCCAGT-TATCGGGAAGCTCATAA
1 GAGCCA-TATATCGGGAAGCTCATAA
*
25686402 GAGCCATA-AT-GGGAAGCTCCA-GA
1 GAGCCATATATCGGGAAGCT-CATAA
*
25686425 GAGCCATATATCGGGATGCTCATAA
1 GAGCCATATATCGGGAAGCTCATAA
25686450 GAG
1 GAG
25686453 TTGCGGTGTG
Statistics
Matches: 118, Mismatches: 23, Indels: 18
0.74 0.14 0.11
Matches are distributed among these distances:
23 17 0.14
24 28 0.24
25 71 0.60
26 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (25 bp):
GAGCCATATATCGGGAAGCTCATAA
Found at i:25686567 original size:105 final size:105
Alignment explanation
Indices: 25686413--25686601 Score: 243
Period size: 105 Copynumber: 1.8 Consensus size: 105
25686403 AGCCATAATG
* * * * * **
25686413 GGAAGCTCCAGAGAGCCATATATCGGGATGCTCATAAGAGTTGCGGTGTGTCCGTAACACATGCA
1 GGAAGCTCCAGAGAGCCAAATATCGAGATGCTCATAAGAGCTACAGTGTGTCCACAACACATGCA
25686478 GGATCAGAACCAATCGGGATGCTCCGAAGAGCTATTAACA
66 GGATCAGAACCAATCGGGATGCTCCGAAGAGCTATTAACA
** * * * *
25686518 GGAAGCTCGTGAGAGCCAAATATCGAGATTCTCGTAAGAGCTATAGTGTGTGCACAACACATGCA
1 GGAAGCTCCAGAGAGCCAAATATCGAGATGCTCATAAGAGCTACAGTGTGTCCACAACACATGCA
* *
25686583 GGATCATAGCCAATCGGGA
66 GGATCAGAACCAATCGGGA
25686602 ACCCTGTATC
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
105 69 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (105 bp):
GGAAGCTCCAGAGAGCCAAATATCGAGATGCTCATAAGAGCTACAGTGTGTCCACAACACATGCA
GGATCAGAACCAATCGGGATGCTCCGAAGAGCTATTAACA
Found at i:25686908 original size:21 final size:21
Alignment explanation
Indices: 25686882--25686921 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25686872 TATACGAATG
25686882 AATTTAACA-TAAATTTAATAC
1 AATTT-ACATTAAATTTAATAC
*
25686903 AATTTACATTCAATTTAAT
1 AATTTACATTAAATTTAAT
25686922 CAAATTCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTACATTAAATTTAATAC
Found at i:25689774 original size:17 final size:18
Alignment explanation
Indices: 25689745--25690005 Score: 108
Period size: 17 Copynumber: 14.1 Consensus size: 18
25689735 ACACAATAAT
25689745 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
25689763 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
25689780 AATTTTTTGAAAACACGGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
25689800 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
25689818 AATTTTCG-ATACATGAGA
1 AATTTTTGAAAACACGA-A
*
25689836 ATTTTTTG---ACACGAA
1 AATTTTTGAAAACACGAA
* *
25689851 AAATTTTGAAAACA-AAA
1 AATTTTTGAAAACACGAA
* * *
25689868 AAATTTCGAAAACATG--
1 AATTTTTGAAAACACGAA
* *
25689884 AATTTCTTTAAAACATGAA
1 AATTT-TTGAAAACACGAA
** *
25689903 TTTTTTTTAAAAAACACGAGA
1 -AATTTTT-GAAAACACGA-A
25689924 AATTTTTTGAAAACACGAAA
1 AA-TTTTTGAAAACACG-AA
*
25689944 ACATGAAAATTTTGAAACCACGAA
1 A-AT-----TTTTGAAAACACGAA
*
25689968 AATTTTTG-AAATACGAGA
1 AATTTTTGAAAACACGA-A
* *
25689986 ATTTTTTGAACACACGAA
1 AATTTTTGAAAACACGAA
25690004 AA
1 AA
25690006 CACGAAAAAA
Statistics
Matches: 182, Mismatches: 37, Indels: 48
0.68 0.14 0.18
Matches are distributed among these distances:
15 7 0.04
16 9 0.05
17 45 0.25
18 45 0.25
19 26 0.14
20 25 0.14
21 8 0.04
23 2 0.01
24 3 0.02
25 12 0.07
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:25689787 original size:19 final size:18
Alignment explanation
Indices: 25689729--25690005 Score: 97
Period size: 18 Copynumber: 14.8 Consensus size: 18
25689719 ACACGAGAAC
25689729 TTTGAAACAC-AATAATAATT
1 TTTGAAACACGAA-AAT--TT
*
25689749 TTTGAAAACACGAAGA-TT
1 TTTG-AAACACGAAAATTT
25689767 TTTGAAACACGAAAATTT
1 TTTGAAACACGAAAATTT
* *
25689785 TTTGAAAACACGGAATTTT
1 TTTG-AAACACGAAAATTT
* *
25689804 TTTGAAAACAAGGAAA-TT
1 TTTG-AAACACGAAAATTT
* * * *
25689822 TTCGATACATGAGAATTT
1 TTTGAAACACGAAAATTT
*
25689840 TTTG--ACACGAAAA-AT
1 TTTGAAACACGAAAATTT
* **
25689855 TTTGAAA-ACAAAAAAAT
1 TTTGAAACACGAAAATTT
* *
25689872 TTCGAAA-AC-ATGAATTT
1 TTTGAAACACGA-AAATTT
* * **
25689889 CTTTAAAACATGAATTTTT
1 -TTTGAAACACGAAAATTT
*
25689908 TTTAAAAAACACGAGAAATTT
1 TTT--GAAACACGA-AAATTT
*
25689929 TTTGAAAACACGAAAACATGAAAAT
1 TTTG-AAACACG-AAA-AT----TT
25689954 TTTGAAACCACGAAAA-TT
1 TTTGAAA-CACGAAAATTT
* *
25689972 TTTGAAATACGAGAATTT
1 TTTGAAACACGAAAATTT
25689990 TTTGAACACACGAAAA
1 TTTGAA-ACACGAAAA
25690006 CACGAAAAAA
Statistics
Matches: 196, Mismatches: 36, Indels: 51
0.69 0.13 0.18
Matches are distributed among these distances:
15 5 0.03
16 14 0.07
17 37 0.19
18 46 0.23
19 37 0.19
20 22 0.11
21 17 0.09
22 2 0.01
23 1 0.01
24 6 0.03
25 9 0.05
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (18 bp):
TTTGAAACACGAAAATTT
Found at i:25689792 original size:36 final size:38
Alignment explanation
Indices: 25689729--25689814 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
25689719 ACACGAGAAC
25689729 TTTGAAACACAATAATAATTTTTGAAAACAC-GAAGATT
1 TTTGAAACACAATAAT-ATTTTTGAAAACACGGAAGATT
**
25689767 TTTGAAACACGAA-AAT-TTTTTGAAAACACGGAATTTT
1 TTTGAAACAC-AATAATATTTTTGAAAACACGGAAGATT
25689804 TTTGAAA-ACAA
1 TTTGAAACACAA
25689815 GGAAATTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 15 0.34
37 12 0.27
38 13 0.30
39 2 0.05
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (38 bp):
TTTGAAACACAATAATATTTTTGAAAACACGGAAGATT
Found at i:25690010 original size:44 final size:43
Alignment explanation
Indices: 25689957--25690049 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 43
25689947 TGAAAATTTT
* * * *
25689957 GAAACCACG-AAAATTTTTGAAATACGAGAATTTTTTGAACACAC
1 GAAAACACGAAAAAATTTT-AAACACGAGAA-TTTTTGAAAACAC
*
25690001 GAAAACACGAAAAAAATTTTAAACACGGGAATTTTTGAAAACAC
1 GAAAACACG-AAAAAATTTTAAACACGAGAATTTTTGAAAACAC
25690045 GAAAA
1 GAAAA
25690050 TTTTTTATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 25 0.60
45 9 0.21
46 8 0.19
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (43 bp):
GAAAACACGAAAAAATTTTAAACACGAGAATTTTTGAAAACAC
Found at i:25690079 original size:17 final size:17
Alignment explanation
Indices: 25690017--25690087 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
25690007 ACGAAAAAAA
*
25690017 TTTT-AAACACGGGAAT
1 TTTTGAAACACGAGAAT
*
25690033 TTTTGAAAACACGAAAAT
1 TTTTG-AAACACGAGAAT
* **
25690051 TTTTTATTCACGAGAAT
1 TTTTGAAACACGAGAAT
25690068 TTTTGAAACACG-GAAT
1 TTTTGAAACACGAGAAT
25690084 TTTT
1 TTTT
25690088 TTTTAAAGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
16 12 0.27
17 18 0.41
18 14 0.32
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (17 bp):
TTTTGAAACACGAGAAT
Found at i:25690088 original size:17 final size:16
Alignment explanation
Indices: 25690017--25690087 Score: 63
Period size: 16 Copynumber: 4.2 Consensus size: 16
25690007 ACGAAAAAAA
*
25690017 TTTTAAACACGGGAAT
1 TTTTAAACACGAGAAT
*
25690033 TTTTGAAAACACGAAAATT
1 TTTT--AAACACGAGAA-T
**
25690052 TTTTATTCACGAGAAT
1 TTTTAAACACGAGAAT
25690068 TTTTGAAACACG-GAAT
1 TTTT-AAACACGAGAAT
25690084 TTTT
1 TTTT
25690088 TTTTAAAGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
16 17 0.39
17 13 0.30
18 9 0.20
19 5 0.11
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (16 bp):
TTTTAAACACGAGAAT
Found at i:25690090 original size:35 final size:35
Alignment explanation
Indices: 25690001--25690089 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
25689991 TTGAACACAC
** ** *
25690001 GAAAACACGAAAAAAATTTTAAACACGGGAATTTTT
1 GAAAACACG-AAAATTTTTTATTCACGAGAATTTTT
25690037 GAAAACACGAAAATTTTTTATTCACGAGAATTTTT
1 GAAAACACGAAAATTTTTTATTCACGAGAATTTTT
* *
25690072 G-AAACACGGAATTTTTTT
1 GAAAACACGAAAATTTTTT
25690090 TTAAAGAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
34 15 0.33
35 22 0.48
36 9 0.20
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (35 bp):
GAAAACACGAAAATTTTTTATTCACGAGAATTTTT
Found at i:25690341 original size:20 final size:20
Alignment explanation
Indices: 25690312--25690349 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25690302 GGGATTCTAA
25690312 TAAAACACGAGAATTTTTAT
1 TAAAACACGAGAATTTTTAT
* *
25690332 TAAAATACGAGGATTTTT
1 TAAAACACGAGAATTTTT
25690350 GAATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAACACGAGAATTTTTAT
Found at i:25690826 original size:19 final size:19
Alignment explanation
Indices: 25690786--25690847 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
25690776 TGGGCTGCTG
* *
25690786 TTTTTATTTT-TTTTACTAC
1 TTTTTATTTTCTTTT-TTTC
25690805 TTTTTATTTTCTTTTTTTC
1 TTTTTATTTTCTTTTTTTC
25690824 TTTCTT-TTTTCTCTCTTTTTC
1 TTT-TTATTTTCT-T-TTTTTC
25690845 TTT
1 TTT
25690848 CTCCTTTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 21 0.57
20 7 0.19
21 9 0.24
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTATTTTCTTTTTTTC
Found at i:25690844 original size:21 final size:20
Alignment explanation
Indices: 25690811--25690866 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
25690801 CTACTTTTTA
*
25690811 TTTTCTT-TTTTTCTTTCTT
1 TTTTCTTCTTTTTCTTTCTC
25690830 TTTTCTCTCTTTTTCTTTCTC
1 TTTTCT-TCTTTTTCTTTCTC
* *
25690851 CTTTCTTCTTCTTCTT
1 TTTTCTTCTTTTTCTT
25690867 CTTCCCTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.19
20 10 0.31
21 16 0.50
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCTTCTTTTTCTTTCTC
Found at i:25690850 original size:12 final size:12
Alignment explanation
Indices: 25690812--25690860 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
25690802 TACTTTTTAT
*
25690812 TTTCTTTTTTTC
1 TTTCTCTTTTTC
25690824 TTTCT-TTTTTC
1 TTTCTCTTTTTC
25690835 --TCTCTTTTTC
1 TTTCTCTTTTTC
25690845 TTTCTCCTTTCTTC
1 TTTCT-CTTT-TTC
25690859 TT
1 TT
25690861 CTTCTTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 3 0.09
10 6 0.19
11 6 0.19
12 8 0.25
13 4 0.12
14 5 0.16
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTCTTTTTC
Found at i:25691056 original size:21 final size:21
Alignment explanation
Indices: 25691031--25691074 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
25691021 TCGTTTTTTT
*
25691031 TTTGCTACTCTTTTTGTTTGC
1 TTTGCTACTCTTTTTGGTTGC
**
25691052 TTTGCTTTTCTTTTTGGTTGC
1 TTTGCTACTCTTTTTGGTTGC
25691073 TT
1 TT
25691075 GCAACTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.16, G:0.16, T:0.66
Consensus pattern (21 bp):
TTTGCTACTCTTTTTGGTTGC
Found at i:25691652 original size:29 final size:29
Alignment explanation
Indices: 25691571--25691667 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 29
25691561 GGCCAAAACA
* *
25691571 TAATTTTAAGAAAGTTTAGGGGTCAAAGTG
1 TAATTTT-AGAAAGTTTAAGGGTCAAAATG
* * *
25691601 CAATTGTGAGAAAGTCTAAGGGTCAAAATG
1 TAATT-TTAGAAAGTTTAAGGGTCAAAATG
**
25691631 TAATTTTAGAAAGTTTTTGGGTCAAAATG
1 TAATTTTAGAAAGTTTAAGGGTCAAAATG
25691660 TAAATTTT
1 T-AATTTT
25691668 GAAGAGTACA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 21 0.38
30 33 0.60
31 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (29 bp):
TAATTTTAGAAAGTTTAAGGGTCAAAATG
Found at i:25692103 original size:76 final size:76
Alignment explanation
Indices: 25691887--25693248 Score: 1799
Period size: 76 Copynumber: 17.6 Consensus size: 76
25691877 CTCGGCGTGC
* * * * *
25691887 GACCCGAGACTCAACTCACTTCTAGCGA-TATGAGTTGATTTTTGAAAAAC-ATGAA-TT-GAA-
1 GACCCGAGGCTCAACTCACCTCT-G-TATTATGAGTTGATTTTTGAAAAACGA-AAATTTAAAAG
** *
25691947 AAATACCTTAGCGT
63 AAATACCTCGGCAT
* * * * *
25691961 GACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTGAAACAC-ATAAATTTAAAAG
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTGAAAAACGA-AAATTTAAAAG
25692025 AAATACCTCGGCAT
63 AAATACCTCGGCAT
**
25692039 GGTCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
25692104 TACCTCGGCAT
66 TACCTCGGCAT
*
25692115 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
25692180 TACCTCGGCAT
66 TACCTCGGCAT
*
25692191 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
25692256 TACCTCGGCAT
66 TACCTCGGCAT
*
25692267 GACCCGAGGCTCAACTCA-CTCTGTATTATGAGTTGATTTTTGAAAAACAAAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
25692331 TACCTCGGCAT
66 TACCTCGGCAT
* * *
25692342 GACCCCAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGAAATTTAAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAACG-A-AAATTTAAAAG
* *
25692407 AAATACCTCAGCGT
63 AAATACCTCGGCAT
*
25692421 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
25692486 TACCTCGGCAT
66 TACCTCGGCAT
*
25692497 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGAAATTTAAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAACG-A-AAATTT---AA
* * *
25692562 AAAAAATACCTCAGCGT
60 AAGAAATACCTCGGCAT
*
25692579 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
25692644 TACCTCGGCAT
66 TACCTCGGCAT
**
25692655 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGCAGATATTTTTAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTG-AAAAA-C-GA-AAATTTAAA
* * *
25692720 AAAAATACCTCAGCGT
61 AGAAATACCTCGGCAT
*
25692736 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
25692801 TACCTCGGCAT
66 TACCTCGGCAT
* *
25692812 GACCCAAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
25692877 TACCTCGGCAT
66 TACCTCGGCAT
25692888 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
25692953 TACCTCGGCAT
66 TACCTCGGCAT
* * *
25692964 GACCCAAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAC-AAAAATT-GAAG--
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAACGAAAATTTAAAAGAA
25693025 ATACCTCAGG-ATGT
65 ATACCTC-GGCA--T
* * **
25693039 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTCAAAA-GCAGAAATTT---
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTTTGAAAAACG-A-AAATTTAAA
25693100 A-AAATACCTCAGG-ATGT
61 AGAAATACCTC-GGCA--T
*
25693117 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTCTTTTGAAAAAACAGAAATTAAATT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA--T-TTTTG-AAAAAC-G-AA--AATTT
* *
25693182 AAAA-AAATACCTCAGCGT
58 AAAAGAAATACCTCGGCAT
25693200 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAA
25693249 AAAACAGAAT
Statistics
Matches: 1168, Mismatches: 78, Indels: 78
0.88 0.06 0.06
Matches are distributed among these distances:
73 9 0.01
74 32 0.03
75 113 0.10
76 558 0.48
77 82 0.07
78 92 0.08
79 85 0.07
80 13 0.01
81 76 0.07
82 59 0.05
83 38 0.03
84 1 0.00
85 10 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (76 bp):
GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGAAAATTTAAAAGAAA
TACCTCGGCAT
Found at i:25694602 original size:1 final size:1
Alignment explanation
Indices: 25694596--25694694 Score: 54
Period size: 1 Copynumber: 99.0 Consensus size: 1
25694586 TTCATCTTGA
* * * * * * * * * * *
25694596 TTTTTTTTCTTTTCTTTGTTTTTTTGTTTTTGTTTTTTATTTTTTTGTTTTGTCTATTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
25694661 GTTTTTTTGTTTTTTTCTATTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25694695 AAGCATAATA
Statistics
Matches: 66, Mismatches: 32, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.04, C:0.05, G:0.07, T:0.84
Consensus pattern (1 bp):
T
Found at i:25694617 original size:14 final size:13
Alignment explanation
Indices: 25694596--25694694 Score: 67
Period size: 13 Copynumber: 7.5 Consensus size: 13
25694586 TTCATCTTGA
25694596 TTTTTTTTCTTTT-
1 TTTTTTTT-TTTTG
* *
25694609 CTTTGTTTTTTTG
1 TTTTTTTTTTTTG
* *
25694622 TTTTTGTTTTTTA
1 TTTTTTTTTTTTG
*
25694635 TTTTTTTGTTTTG
1 TTTTTTTTTTTTG
* *
25694648 TCTATTTTTTTCTG
1 T-TTTTTTTTTTTG
25694662 TTTTTTTGTTTTT-
1 TTTTTTT-TTTTTG
* * *
25694675 TTCTATTTTTTTA
1 TTTTTTTTTTTTG
25694688 TTTTTTT
1 TTTTTTT
25694695 AAGCATAATA
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
12 9 0.14
13 41 0.64
14 14 0.22
ACGTcount: A:0.04, C:0.05, G:0.07, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:25694617 original size:18 final size:18
Alignment explanation
Indices: 25694596--25694694 Score: 71
Period size: 18 Copynumber: 5.4 Consensus size: 18
25694586 TTCATCTTGA
*
25694596 TTTTTTTTCTTTTCTTTG
1 TTTTTTTTCTTTTTTTTG
25694614 TTTTTTTGT-TTTTGTTTT-
1 TTTTTTT-TCTTTT-TTTTG
* * *
25694632 TTATTTTTT-TGTTTTGTC
1 TT-TTTTTTCTTTTTTTTG
25694650 TATTTTTTTCTGTTTTTTTG
1 T-TTTTTTTCT-TTTTTTTG
*
25694670 -TTTTTTTCTATTTTTTTA
1 TTTTTTTTCT-TTTTTTTG
25694688 TTTTTTT
1 TTTTTTT
25694695 AAGCATAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
17 3 0.05
18 40 0.62
19 17 0.26
20 5 0.08
ACGTcount: A:0.04, C:0.05, G:0.07, T:0.84
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTTTG
Found at i:25694621 original size:8 final size:8
Alignment explanation
Indices: 25694597--25694676 Score: 69
Period size: 8 Copynumber: 9.9 Consensus size: 8
25694587 TCATCTTGAT
*
25694597 TTTTTTTC
1 TTTTTTTG
25694605 TTTTCTTTG
1 TTTT-TTTG
25694614 TTTTTTTG
1 TTTTTTTG
25694622 --TTTTTG
1 TTTTTTTG
*
25694628 -TTTTTTA
1 TTTTTTTG
25694635 TTTTTTTG
1 TTTTTTTG
25694643 TTTTGTCTAT-
1 TTTT-T-T-TG
25694653 TTTTTTCTG
1 TTTTTT-TG
25694662 TTTTTTTG
1 TTTTTTTG
25694670 TTTTTTT
1 TTTTTTT
25694677 CTATTTTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
6 6 0.10
7 5 0.08
8 29 0.48
9 15 0.25
10 5 0.08
11 1 0.02
ACGTcount: A:0.03, C:0.05, G:0.09, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:25699690 original size:17 final size:18
Alignment explanation
Indices: 25699661--25699923 Score: 137
Period size: 18 Copynumber: 14.1 Consensus size: 18
25699651 ACACAATAAT
25699661 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
25699679 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
25699696 AATTTTTTGAAAACACAGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
25699716 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
25699734 AATTTTCG-ATACA-TAA
1 AATTTTTGAAAACACGAA
25699750 GAATTTTTTG---ACACGAA
1 -AA-TTTTTGAAAACACGAA
*
25699767 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
25699785 AA-TTTCGAAAACATGAA
1 AATTTTTGAAAACACGAA
** * *
25699802 TTTTTTTTTAAAACATGAA
1 -AATTTTTGAAAACACGAA
** *
25699821 TTTTTTTAAAAAAACACGAGA
1 AATTTTT--GAAAACACGA-A
25699842 AATTTTTTGAAAACACGAAA
1 AA-TTTTTGAAAACACG-AA
*
25699862 ACATGAAAATTTTGAAACCACGAA
1 A-AT-----TTTTGAAAACACGAA
25699886 AATTTTTG-AAACACGAGA
1 AATTTTTGAAAACACGA-A
*
25699904 ATTTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
25699922 AA
1 AA
25699924 CACGAAAAAA
Statistics
Matches: 191, Mismatches: 30, Indels: 48
0.71 0.11 0.18
Matches are distributed among these distances:
15 5 0.03
16 6 0.03
17 38 0.20
18 56 0.29
19 39 0.20
20 22 0.12
21 3 0.02
22 5 0.03
23 2 0.01
24 3 0.02
25 12 0.06
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:25699703 original size:19 final size:17
Alignment explanation
Indices: 25699645--25699730 Score: 68
Period size: 18 Copynumber: 4.7 Consensus size: 17
25699635 ACACGAGAAC
25699645 TTTGAAACACAATAATAATT
1 TTTGAAACACAA-AAT--TT
*
25699665 TTTGAAAACACGAAGA-TT
1 TTTG-AAACAC-AAAATTT
25699683 TTTGAAACACGAAAATTT
1 TTTGAAACAC-AAAATTT
*
25699701 TTTGAAAACACAGAATTTT
1 TTTG-AAACACA-AAATTT
25699720 TTTGAAA-ACAA
1 TTTGAAACACAA
25699731 GGAAATTTTC
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
16 1 0.02
17 13 0.22
18 16 0.28
19 15 0.26
20 4 0.07
21 7 0.12
22 2 0.03
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (17 bp):
TTTGAAACACAAAATTT
Found at i:25699739 original size:19 final size:19
Alignment explanation
Indices: 25699663--25699739 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 19
25699653 ACAATAATAA
*
25699663 TTTTTGAAAAC-ACGAAGA-
1 TTTTTGAAAACAAGGAA-AT
* *
25699681 TTTTTG-AAACACGAAAAT
1 TTTTTGAAAACAAGGAAAT
*
25699699 TTTTTGAAAACACA-GAATT
1 TTTTTGAAAACA-AGGAAAT
25699718 TTTTTGAAAACAAGGAAAT
1 TTTTTGAAAACAAGGAAAT
25699737 TTT
1 TTT
25699740 CGATACATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
17 5 0.11
18 15 0.32
19 27 0.57
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (19 bp):
TTTTTGAAAACAAGGAAAT
Found at i:25699833 original size:19 final size:19
Alignment explanation
Indices: 25699792--25699833 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
25699782 GAAAATTTCG
**
25699792 AAAACATGAATTTTTTTTT
1 AAAACATGAATTTTTTTAA
25699811 AAAACATGAATTTTTTTAA
1 AAAACATGAATTTTTTTAA
25699830 AAAA
1 AAAA
25699834 ACACGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
AAAACATGAATTTTTTTAA
Found at i:25699928 original size:44 final size:43
Alignment explanation
Indices: 25699875--25699967 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 43
25699865 TGAAAATTTT
* *
25699875 GAAACCACG-AAAATTTTTGAAACACGAGAATTTTTTGAAAACAC
1 GAAAACACGAAAAAATTTT-AAACACGAGAA-TTTTTGAAAACAC
*
25699919 GAAAACACGAAAAAAATTTTAAACACGGGAATTTTTGAAAACAC
1 GAAAACACG-AAAAAATTTTAAACACGAGAATTTTTGAAAACAC
*
25699963 AAAAA
1 GAAAA
25699968 TTTTTTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 25 0.58
45 10 0.23
46 8 0.19
ACGTcount: A:0.52, C:0.14, G:0.13, T:0.22
Consensus pattern (43 bp):
GAAAACACGAAAAAATTTTAAACACGAGAATTTTTGAAAACAC
Found at i:25699952 original size:62 final size:62
Alignment explanation
Indices: 25699831--25699973 Score: 184
Period size: 61 Copynumber: 2.3 Consensus size: 62
25699821 TTTTTTTAAA
*
25699831 AAAACACGAGAAATTTTTTGAAAACACGAAAACATGAAAATTTTGAAACCACGAAAATTTTTG
1 AAAACACGAG-AATTTTTTGAAAACACGAAAACACGAAAATTTTGAAACCACGAAAATTTTTG
**
25699894 -AAACACGAGAATTTTTTGAAAACACGAAAACACGAAAAAAATTTT-AAA-CACGGGAATTTTTG
1 AAAACACGAGAATTTTTTGAAAACACGAAAACACG---AAAATTTTGAAACCACGAAAATTTTTG
* *
25699956 AAAACACAAAAATTTTTT
1 AAAACACGAGAATTTTTT
25699974 ATTCACGAGA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
61 24 0.34
62 21 0.30
63 18 0.25
64 8 0.11
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.26
Consensus pattern (62 bp):
AAAACACGAGAATTTTTTGAAAACACGAAAACACGAAAATTTTGAAACCACGAAAATTTTTG
Done.