Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 9 of 297
Found at i:2990551 original size:21 final size:22
Alignment explanation
Indices: 2990518--2990560 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2990508 AACAAATATA
2990518 AAAGGATGAAATT-AATTGAAT
1 AAAGGATGAAATTAAATTGAAT
2990539 AAAGGACTG-AATTGAAATTGAA
1 AAAGGA-TGAAATT-AAATTGAA
2990561 ACGGAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.21, T:0.26
Consensus pattern (22 bp):
AAAGGATGAAATTAAATTGAAT
Found at i:2990723 original size:19 final size:19
Alignment explanation
Indices: 2990699--2990736 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2990689 CTCAGAGGAC
*
2990699 TAAAATGAATTAAAAACAA
1 TAAAATAAATTAAAAACAA
2990718 TAAAATAAATTAAAAACAA
1 TAAAATAAATTAAAAACAA
2990737 AATTATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (19 bp):
TAAAATAAATTAAAAACAA
Found at i:2991405 original size:50 final size:50
Alignment explanation
Indices: 2991330--2991429 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
2991320 AAACGAAAAT
*
2991330 CACCTTTAGGATATTTTATATATTAGATCTTTTTTTTGTTTCGTATTCAA
1 CACCTTTAGGATATTTTATATATTAGATCTCTTTTTTGTTTCGTATTCAA
*
2991380 CACCTTTAGGATATTTTATATATTAGATCTCTTTTTTGTTTTGTATTCAA
1 CACCTTTAGGATATTTTATATATTAGATCTCTTTTTTGTTTCGTATTCAA
2991430 TCTTGTTTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (50 bp):
CACCTTTAGGATATTTTATATATTAGATCTCTTTTTTGTTTCGTATTCAA
Found at i:2992344 original size:46 final size:45
Alignment explanation
Indices: 2992268--2992715 Score: 153
Period size: 44 Copynumber: 9.9 Consensus size: 45
2992258 CTGCAGCTTG
* * * * *
2992268 ATCTATTCCACTGCAACTTCAGGGAAATAAGATTCGTCCGTCTTCA
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATTC-ACCATCTTCA
* * *
2992314 ATCTGCTCCACTGCAATTTTAGGGAGATAAGATTCACTATCTTCA
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATTCACCATCTTCA
* * *
2992359 GTCTACTCCATTGCAACTTTAGGGAGATAAGACTTGTA--A-CTTCA
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGA-TT-CACCATCTTCA
* * * * *** * * * * *
2992403 ACCAATTCCATTGCAA-TTTCAAAAAGATAAGGTTTA-TAGCTTTA
1 ATCTACTCCACTGCAACTTT-AGGGAGATAAGATTCACCATCTTCA
* * * * *
2992447 ATTTAC-CCTACTGCAACTTCAGAGAGATAAGATCTATGACTTATAGCTTCA
1 ATCTACTCC-ACTGCAACTTTAGGGAGATAAGA--T-TCAC-CAT--CTTCA
* * * ** *
2992498 ATCT-GTCCCACTGCAACTTTAGGGACATAAGATTCGCTGTCTTCG
1 ATCTACT-CCACTGCAACTTTAGGGAGATAAGATTCACCATCTTCA
* * * * * * *
2992543 ATTTATTCCACTTCAACCTCAAGGAGATAAGA-TCTA-CAACTTCA
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATTC-ACCATCTTCA
** ** **
2992587 ATCTACTCCACTGTTACTTTAGGGAGATGAA-ATTTTCTTTCTTCA
1 ATCTACTCCACTGCAACTTTAGGGAGAT-AAGATTCACCATCTTCA
* * * * ** ****
2992632 GTCTGCTCCTCTGCAACTTCAGGGAGATAAGGCTC-GTGGCTTCA
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATTCACCATCTTCA
* * *
2992676 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCAT
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATTCACCAT
2992716 AATTTGTAGC
Statistics
Matches: 291, Mismatches: 88, Indels: 47
0.68 0.21 0.11
Matches are distributed among these distances:
42 2 0.01
43 8 0.03
44 112 0.38
45 96 0.33
46 34 0.12
47 5 0.02
48 2 0.01
49 3 0.01
51 27 0.09
52 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (45 bp):
ATCTACTCCACTGCAACTTTAGGGAGATAAGATTCACCATCTTCA
Found at i:2992801 original size:232 final size:231
Alignment explanation
Indices: 2992456--2992996 Score: 712
Period size: 232 Copynumber: 2.3 Consensus size: 231
2992446 AATTTACCCT
* * * * * * * *
2992456 ACTGCAACTTCAGAGAGATAAGA-T-CTATGACTTATAGCTTCAATCTGTCCCACTGCAACTTTA
1 ACTGCAACTTCAGGGAGATAAGATTCCCATAATTTATAGCTTTAATCTGTTCCACTGCAACGTCA
* * * * *
2992519 GGGACATAAGATTCGCTGTCTTCGATTTATTCCACTTCAACCTCAAGGAGATAAGATCTACAACT
66 GGGAAATAAGATTTGCTATCTTCGATCTATTCCACTGCAACCTCAAGGAGATAAGATCTACAACT
* *
2992584 TCAATCTACTCCACTGTTACTTTAGGGAGATGAA-ATTT-TCTTTCTTCAGTCTGCTCCTCTGCA
131 TCAATCTACTCCACTGTTACTTTAGGGAGAT-AAGATTTGT-TGTCTTCAGTCTGCTCCGCTGCA
*
2992647 ACTTCAGGGAGATAAGGCTCGTGGCTTCAATCTGCTCC
194 ACTCCAGGGAGATAAGGCTCGTGGCTTCAATCTGCTCC
*
2992685 ACTGCAACTTCAGGGAGATAAGATTCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGTC
1 ACTGCAACTTCAGGGAGATAAGATTC-CCATAATTTATAGCTTTAATCTGTTCCACTGCAACGTC
* * * *
2992750 AGGGAAATAAGATTTGTTATCTTCGATCTGTTCCACTGCAACTTGAAGGAGATAAGATCTACAAC
65 AGGGAAATAAGATTTGCTATCTTCGATCTATTCCACTGCAACCTCAAGGAGATAAGATCTACAAC
* * * *
2992815 TTCAATCTGCTTCATTGTTACTTTAGGGAGATAAGATTTGTTGTCTTCAGTCTGCTCCGCTGTAA
130 TTCAATCTACTCCACTGTTACTTTAGGGAGATAAGATTTGTTGTCTTCAGTCTGCTCCGCTGCAA
* *
2992880 CTCCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTTC
195 CTCCAGGGAGATAAGGCTCGTGGCTTCAATCTGCTCC
** * * * *
2992917 ACTATAACTTCAAGAAGATAAGATTCTCCATAATTTATAGCTTTAATTTGTTCCACTGCAATGTC
1 ACTGCAACTTCAGGGAGATAAGATTC-CCATAATTTATAGCTTTAATCTGTTCCACTGCAACGTC
*
2992982 AGGGAAGTAAGATTT
65 AGGGAAATAAGATTT
2992997 TCTGTCTTTA
Statistics
Matches: 271, Mismatches: 36, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
229 22 0.08
230 1 0.00
231 2 0.01
232 245 0.90
233 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (231 bp):
ACTGCAACTTCAGGGAGATAAGATTCCCATAATTTATAGCTTTAATCTGTTCCACTGCAACGTCA
GGGAAATAAGATTTGCTATCTTCGATCTATTCCACTGCAACCTCAAGGAGATAAGATCTACAACT
TCAATCTACTCCACTGTTACTTTAGGGAGATAAGATTTGTTGTCTTCAGTCTGCTCCGCTGCAAC
TCCAGGGAGATAAGGCTCGTGGCTTCAATCTGCTCC
Found at i:2992925 original size:44 final size:45
Alignment explanation
Indices: 2992814--2992939 Score: 110
Period size: 44 Copynumber: 2.8 Consensus size: 45
2992804 AGATCTACAA
* * ** ** * *
2992814 CTTCAATCTGCTTCATTGTTACTTTAGGGAGATAAGATTTGTTGT
1 CTTCAATCTGCTTCACTGTAACTCCAGGGAGATAAGAGCTGGTGG
* * *
2992859 CTTCAGTCTGCTCCGCTGTAACTCCAGGGAGATAAG-GCTGGTGG
1 CTTCAATCTGCTTCACTGTAACTCCAGGGAGATAAGAGCTGGTGG
* * * *
2992903 CTTCAATCTGCTTCACTATAACTTCAAGAAGATAAGA
1 CTTCAATCTGCTTCACTGTAACTCCAGGGAGATAAGA
2992940 TTCTCCATAA
Statistics
Matches: 62, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
44 33 0.53
45 29 0.47
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (45 bp):
CTTCAATCTGCTTCACTGTAACTCCAGGGAGATAAGAGCTGGTGG
Found at i:2993052 original size:232 final size:232
Alignment explanation
Indices: 2992487--2993083 Score: 657
Period size: 232 Copynumber: 2.6 Consensus size: 232
2992477 GATCTATGAC
* * * * * * * * * * **
2992487 TTATAGCTTCAATCTGTCCCACTGCAACTTTAGGGACATAAGATTCGCTGTCTTCGATTTATTCC
1 TTATAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGTTATCTTAGATCTGCTCC
* * * *
2992552 ACTTCAACCTCAAGGAGATAAGATCTACAACTTCAATCTACTCCACTGTTACTTTAGGGAGATGA
66 ACTACAACTTCAAGGAGATAAGAGCTACAACTTCAATCTGCTCCACTGTTACTTTAGGGAGAT-A
* * *
2992617 A-ATTTTCTTTCTTCAGTCTGCTCCTCTGCAACTTCAGGGAGATAAGGCTCGTGGCTTCAATCTG
130 AGATTTTCTGTCTTCAGTCTGCTCCGCTGCAACTCCAGGGAGATAAGGCTCGTGGCTTCAATCTG
* * *
2992681 CTCCACTGCAACTTCAGGGAGATAAGATTCGCCATAAT
195 CTCCACTACAACTTCAAGAAGATAAGATTCGCCATAAT
* * *
2992719 TTGTAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGTTATCTTCGATCTGTTCC
1 TTATAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGTTATCTTAGATCTGCTCC
* * * * *
2992784 ACTGCAACTTGAAGGAGATAAGATCTACAACTTCAATCTGCTTCATTGTTACTTTAGGGAGATAA
66 ACTACAACTTCAAGGAGATAAGAGCTACAACTTCAATCTGCTCCACTGTTACTTTAGGGAGATAA
* *
2992849 GATTTGT-TGTCTTCAGTCTGCTCCGCTGTAACTCCAGGGAGATAAGGCTGGTGGCTTCAATCTG
131 GATTT-TCTGTCTTCAGTCTGCTCCGCTGCAACTCCAGGGAGATAAGGCTCGTGGCTTCAATCTG
* * *
2992913 CTTCACTATAACTTCAAGAAGATAAGATTCTCCATAAT
195 CTCCACTACAACTTCAAGAAGATAAGATTCGCCATAAT
* * * *
2992951 TTATAGCTTTAATTTGTTCCACTGCAATGTCAGGGAAGTAAGATTT-TCTGTCTTTAG-TCTGCT
1 TTATAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGT-TATC-TTAGATCTGCT
** * *** * ** *
2993014 CTGCTATAACTTC-AGAGAGATAAG-GCTGATGGCTTCAATATGCTCCACTGCAACTTTAGGAAG
64 CCACTACAACTTCAAG-GAGATAAGAGCT-ACAACTTCAATCTGCTCCACTGTTACTTTAGGGAG
2993077 ATAAGAT
127 ATAAGAT
2993084 CCACCATCTT
Statistics
Matches: 309, Mismatches: 50, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
231 7 0.02
232 298 0.96
233 4 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (232 bp):
TTATAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGTTATCTTAGATCTGCTCC
ACTACAACTTCAAGGAGATAAGAGCTACAACTTCAATCTGCTCCACTGTTACTTTAGGGAGATAA
GATTTTCTGTCTTCAGTCTGCTCCGCTGCAACTCCAGGGAGATAAGGCTCGTGGCTTCAATCTGC
TCCACTACAACTTCAAGAAGATAAGATTCGCCATAAT
Found at i:2993112 original size:232 final size:232
Alignment explanation
Indices: 2992487--2993160 Score: 581
Period size: 232 Copynumber: 2.9 Consensus size: 232
2992477 GATCTATGAC
* * * * * * * * * * **
2992487 TTATAGCTTCAATCTGTCCCACTGCAACTTTAGGGACATAAGATTCGCTGTCTTCGATTTATTCC
1 TTATAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGTTATCTTAGATCTGCTCC
* * * * * ** *
2992552 ACTTCAACCTCAAGGAGATAAGATCTACAACTTCAATCTACTCCACTGTTACTTTAGGGAGATGA
66 ACTACAACTTCAAGGAGATAAGAGCTACAACTTCAATATGCTCCACTGCAACTTTAGGAAGAT-A
*** ** * * *
2992617 A-ATTTTCTTTCTTCAGTCTGCTCCTCTGCAACTTCAGGGAGATAAGGCTCGTGGCTTCAATCTG
130 AGATCCACCATCTTCAGTCTACTCCACTGTAACTTCAGGGAGATAAGGCTCGTGGCTTCAATCTG
* * *
2992681 CTCCACTGCAACTTCAGGGAGATAAGATTCGCCATAAT
195 CTCCACTACAACTTCAAGAAGATAAGATTCGCCATAAT
* * *
2992719 TTGTAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGTTATCTTCGATCTGTTCC
1 TTATAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGTTATCTTAGATCTGCTCC
* * * * * * ** *
2992784 ACTGCAACTTGAAGGAGATAAGATCTACAACTTCAATCTGCTTCATTGTTACTTTAGGGAGATAA
66 ACTACAACTTCAAGGAGATAAGAGCTACAACTTCAATATGCTCCACTGCAACTTTAGGAAGATAA
****** * * * *
2992849 GATTTGTTGTCTTCAGTCTGCTCCGCTGTAACTCCAGGGAGATAAGGCTGGTGGCTTCAATCTGC
131 GATCCACCATCTTCAGTCTACTCCACTGTAACTTCAGGGAGATAAGGCTCGTGGCTTCAATCTGC
* * *
2992914 TTCACTATAACTTCAAGAAGATAAGATTCTCCATAAT
196 TCCACTACAACTTCAAGAAGATAAGATTCGCCATAAT
* * * *
2992951 TTATAGCTTTAATTTGTTCCACTGCAATGTCAGGGAAGTAAGATTT-TCTGTCTTTAG-TCTGCT
1 TTATAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGT-TATC-TTAGATCTGCT
** * ***
2993014 CTGCTATAACTTC-AGAGAGATAAG-GCTGATGGCTTCAATATGCTCCACTGCAACTTTAGGAAG
64 CCACTACAACTTCAAG-GAGATAAGAGCT-ACAACTTCAATATGCTCCACTGCAACTTTAGGAAG
* * *
2993077 ATAAGATCCACCATCTTC-GATCTACTCCACTGTAACTTCAAGGAGATAA-GATC-TACGACTTC
127 ATAAGATCCACCATCTTCAG-TCTACTCCACTGTAACTTCAGGGAGATAAGGCTCGT--GGCTTC
* *
2993139 AATCTGCTCCATTACTACTTCA
189 AATCTGCTCCACTACAACTTCA
2993161 GGGAGATGAG
Statistics
Matches: 365, Mismatches: 69, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
230 1 0.00
231 10 0.03
232 351 0.96
233 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (232 bp):
TTATAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATTTGTTATCTTAGATCTGCTCC
ACTACAACTTCAAGGAGATAAGAGCTACAACTTCAATATGCTCCACTGCAACTTTAGGAAGATAA
GATCCACCATCTTCAGTCTACTCCACTGTAACTTCAGGGAGATAAGGCTCGTGGCTTCAATCTGC
TCCACTACAACTTCAAGAAGATAAGATTCGCCATAAT
Found at i:2994742 original size:40 final size:40
Alignment explanation
Indices: 2994691--2994807 Score: 207
Period size: 40 Copynumber: 2.9 Consensus size: 40
2994681 CGTTTGGAGC
* **
2994691 AAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTAATT
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
2994731 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
2994771 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
2994808 TAGATAACGC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.21
Consensus pattern (40 bp):
AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
Found at i:2994952 original size:112 final size:112
Alignment explanation
Indices: 2994755--2995134 Score: 733
Period size: 112 Copynumber: 3.4 Consensus size: 112
2994745 AGAGTGAGCA
** *
2994755 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
2994820 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
2994867 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
2994932 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
2994979 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
2995044 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
2995091 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAG
2995135 AATTAAAATA
Statistics
Matches: 265, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 265 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (112 bp):
TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
Found at i:2997540 original size:11 final size:11
Alignment explanation
Indices: 2997503--2997542 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
2997493 GAATATCTCA
2997503 AACT-ATGGGT
1 AACTAATGGGT
*
2997513 AACTAGTGGGT
1 AACTAATGGGT
2997524 AACTAATGGGT
1 AACTAATGGGT
2997535 AACTAATG
1 AACTAATG
2997543 TATTATCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:2998910 original size:17 final size:17
Alignment explanation
Indices: 2998885--2999183 Score: 168
Period size: 17 Copynumber: 16.6 Consensus size: 17
2998875 GTTAAATTTA
2998885 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
* *
2998902 TTTCTAAAATAAATTAC
1 TTACTAAAATACATTAC
*
2998919 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
2998942 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
2998959 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
* * *
2998976 TTACATAAATTTGTTTAAATTAA
1 TTAC-TAAA-----ATACATTAC
2998999 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
2999016 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
2999039 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
2999056 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
2999073 TTACTAAAAT---TT-G
1 TTACTAAAATACATTAC
** *
2999086 TT--T-AAATTTATTAA
1 TTACTAAAATACATTAC
*
2999100 TTACTTAAATACATTAC
1 TTACTAAAATACATTAC
*
2999117 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
2999140 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
2999157 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
2999174 TTACTAAAAT
1 TTACTAAAAT
2999184 TTGTTTAAAT
Statistics
Matches: 225, Mismatches: 20, Indels: 74
0.71 0.06 0.23
Matches are distributed among these distances:
10 4 0.02
11 1 0.00
13 4 0.02
14 4 0.02
16 10 0.04
17 138 0.61
18 4 0.02
22 4 0.02
23 47 0.21
24 9 0.04
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:2998966 original size:57 final size:57
Alignment explanation
Indices: 2998876--2999025 Score: 257
Period size: 57 Copynumber: 2.6 Consensus size: 57
2998866 CGATTGAATG
*
2998876 TTAAATTTATTACTAAAATACATTACTTTCTAAAATAAATTACTTAC-TAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACAT-AAATTTGT
*
2998933 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACATAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACATAAATTTGT
*
2998990 TTAAATTAATTACTAAAATACATTACTTACTAAAAT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAAT
2999026 TTGTTTAAAT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
57 88 0.99
58 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.42
Consensus pattern (57 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACATAAATTTGT
Found at i:2999003 original size:40 final size:39
Alignment explanation
Indices: 2998954--2999164 Score: 204
Period size: 40 Copynumber: 5.8 Consensus size: 39
2998944 ACTAAAATAC
*
2998954 ATTACTTACTAAAATACATTACTTACATAAATTTGTTTAA
1 ATTAATTACTAAAATACATTACTTAC-TAAATTTGTTTAA
2998994 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAA
1 ATTAATTACTAAAATACATTACTTACT-AAATTTGTTTAA
* * *
2999034 ATTTATTACTAAAATACATTACTTACTAAA-----ATAC
1 ATTAATTACTAAAATACATTACTTACTAAATTTGTTTAA
* *
2999068 ATTACTTACTAAAAT---TT-GTT--TAAA----TTT--
1 ATTAATTACTAAAATACATTACTTACTAAATTTGTTTAA
*
2999095 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAA
1 ATTAATTACTAAAATACATTACTTACT-AAATTTGTTTAA
*
2999135 ATTTATTACTAAAATACATTACTTACTAAA
1 ATTAATTACTAAAATACATTACTTACTAAA
2999165 ATACATTACT
Statistics
Matches: 143, Mismatches: 13, Indels: 31
0.76 0.07 0.17
Matches are distributed among these distances:
27 13 0.09
28 4 0.03
29 1 0.01
30 4 0.03
31 4 0.03
33 1 0.01
34 18 0.13
38 3 0.02
39 7 0.05
40 88 0.62
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (39 bp):
ATTAATTACTAAAATACATTACTTACTAAATTTGTTTAA
Found at i:2999020 original size:97 final size:97
Alignment explanation
Indices: 2998905--2999216 Score: 518
Period size: 97 Copynumber: 3.2 Consensus size: 97
2998895 ACATTACTTT
*
2998905 CTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
2998970 CATTACTTAC-ATAAATTTGTTTAAATTAATTA
66 CATTACTTACTA-AAATTTGTTTAAATTAATTA
2999002 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
2999067 CATTACTTACTAAAATTTGTTTAAATTTATTAATTA
66 CATTACTTACTAAAATTTGTTT-AA---ATTAATTA
*
2999103 CTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
*
2999168 CATTACTTACTAAAATTTGTTTAAATTTATTA
66 CATTACTTACTAAAATTTGTTTAAATTAATTA
* **
2999200 CTTAAATATGTTACTTA
1 CTAAAATACATTACTTA
2999217 AATTTATTAC
Statistics
Matches: 205, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
97 106 0.52
98 3 0.01
100 2 0.01
101 94 0.46
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (97 bp):
CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
CATTACTTACTAAAATTTGTTTAAATTAATTA
Found at i:2999060 original size:57 final size:60
Alignment explanation
Indices: 2998994--2999126 Score: 218
Period size: 57 Copynumber: 2.2 Consensus size: 60
2998984 ATTTGTTTAA
*
2998994 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAA-T-TT-ATTACTAAAATAC
1 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTATTAATTACTAAAATAC
*
2999051 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTAATTACTTAAATAC
1 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAA-TTATTAATTACTAAAATAC
2999112 ATTACTTACTAAAAT
1 ATTACTTACTAAAAT
2999127 TTGTTTAAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
57 40 0.57
59 1 0.01
60 2 0.03
61 27 0.39
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (60 bp):
ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTATTAATTACTAAAATAC
Found at i:2999119 original size:101 final size:101
Alignment explanation
Indices: 2998905--2999199 Score: 528
Period size: 101 Copynumber: 3.0 Consensus size: 101
2998895 ACATTACTTT
*
2998905 CTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
2998970 CATTACTTAC-ATAAATTTGTTT-AA---ATTAATTA
66 CATTACTTACTA-AAATTTGTTTAAATTTATTAATTA
2999002 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
2999067 CATTACTTACTAAAATTTGTTTAAATTTATTAATTA
66 CATTACTTACTAAAATTTGTTTAAATTTATTAATTA
*
2999103 CTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
2999168 CATTACTTACTAAAATTTGTTTAAATTTATTA
66 CATTACTTACTAAAATTTGTTTAAATTTATTA
2999200 CTTAAATATG
Statistics
Matches: 191, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
97 84 0.44
98 3 0.02
101 104 0.54
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (101 bp):
CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
CATTACTTACTAAAATTTGTTTAAATTTATTAATTA
Found at i:2999165 original size:40 final size:43
Alignment explanation
Indices: 2999051--2999166 Score: 184
Period size: 44 Copynumber: 2.7 Consensus size: 43
2999041 ACTAAAATAC
*
2999051 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAA-TT
*
2999095 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAA-T
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATT
2999137 -TT-ATTACTAAAATACATTACTTACTAAAAT
1 ATTAATTACTAAAATACATTACTTACTAAAAT
2999167 ACATTACTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
40 27 0.39
41 2 0.03
42 1 0.01
44 39 0.57
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (43 bp):
ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATT
Found at i:2999170 original size:57 final size:57
Alignment explanation
Indices: 2999095--2999216 Score: 199
Period size: 57 Copynumber: 2.1 Consensus size: 57
2999085 GTTTAAATTT
* *
2999095 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
1 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
* *
2999152 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTTAAATAT
1 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
*
2999209 GTTACTTA
1 ATTACTTA
2999217 AATTTATTAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (57 bp):
ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
Found at i:2999206 original size:13 final size:13
Alignment explanation
Indices: 2999188--2999258 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
2999178 TAAAATTTGT
2999188 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
2999201 TTAAATATGTTAC
1 TTAAATTTATTAC
2999214 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
2999227 TTAAATATGTTAC
1 TTAAATTTATTAC
2999240 TTAAATTTATTAC
1 TTAAATTTATTAC
2999253 TTAAAT
1 TTAAAT
2999259 AATTATAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (13 bp):
TTAAATTTATTAC
Found at i:2999224 original size:26 final size:26
Alignment explanation
Indices: 2999188--2999259 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
2999178 TAAAATTTGT
2999188 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
2999214 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
2999240 TTAAATTTATTACTTAAATA
1 TTAAATTTATTACTTAAATA
2999260 ATTATAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (26 bp):
TTAAATTTATTACTTAAATATGTTAC
Found at i:2999546 original size:19 final size:19
Alignment explanation
Indices: 2999522--2999748 Score: 100
Period size: 19 Copynumber: 12.5 Consensus size: 19
2999512 TATTAAATAA
2999522 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
*
2999541 TACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
*
2999559 TACAT--T-ACTTACATA-A
1 TACATAATAACTTACA-ACT
2999575 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
2999594 TACATAATACATTTAACTTACAACT
1 TAC---ATA-A--TAACTTACAACT
**
2999619 TACATAAT-ACATT-TGACT
1 TACATAATAAC-TTACAACT
* *
2999637 GACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
* *
2999655 TACA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
2999669 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
* *
2999688 TACATAAT-ACATAATAACT
1 TACATAATAAC-TTACAACT
* *
2999707 TACA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
2999721 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
2999740 TACATAATA
1 TACATAATA
2999749 CATAATAACT
Statistics
Matches: 161, Mismatches: 19, Indels: 56
0.68 0.08 0.24
Matches are distributed among these distances:
14 8 0.05
15 10 0.06
16 14 0.09
17 11 0.07
18 43 0.27
19 52 0.32
21 1 0.01
22 6 0.04
23 1 0.01
25 15 0.09
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.33
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:2999560 original size:18 final size:18
Alignment explanation
Indices: 2999537--2999658 Score: 74
Period size: 18 Copynumber: 6.4 Consensus size: 18
2999527 AATAACTTAC
2999537 AACTTACATAATACATTT
1 AACTTACATAATACATTT
*
2999555 AACTTACATTACTTACA--T
1 AACTTACA-TA-ATACATTT
*
2999573 AA--TACATAATA-ACTTAC
1 AACTTACATAATACA-TT-T
2999590 AACTTACATAATACATTTAACTT
1 AACTTACATAATACA--T---TT
2999613 ACAACTTACATAATACATTT
1 --AACTTACATAATACATTT
* *
2999633 GACTGACATAATACATTT
1 AACTTACATAATACATTT
2999651 AACTTACA
1 AACTTACA
2999659 ACTTACACAA
Statistics
Matches: 80, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
13 1 0.01
14 2 0.03
15 2 0.03
16 4 0.05
17 2 0.03
18 33 0.41
19 11 0.14
20 7 0.09
21 1 0.01
23 1 0.01
24 1 0.01
25 15 0.19
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:2999601 original size:26 final size:26
Alignment explanation
Indices: 2999518--2999923 Score: 579
Period size: 26 Copynumber: 16.1 Consensus size: 26
2999508 ATTTTATTAA
2999518 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
2999544 ATAATACAT-TTAACTTACATTACTTAC
1 ATAATACATAATAACTTACA--ACTTAC
2999571 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
2999597 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
2999622 ATAATAC---AT---TT--GACTGAC
1 ATAATACATAATAACTTACAACTTAC
*
2999640 ATAATACATT-TAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
2999665 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
2999691 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
2999717 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
2999743 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
2999769 ATAATACAT-TTAACTTGCAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
2999794 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
2999820 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
2999846 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
2999871 ACAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
2999896 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
2999922 AT
1 AT
2999924 TTAACTTACA
Statistics
Matches: 343, Mismatches: 23, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
18 12 0.03
20 3 0.01
23 3 0.01
25 113 0.33
26 188 0.55
27 15 0.04
28 9 0.03
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (26 bp):
ATAATACATAATAACTTACAACTTAC
Found at i:2999769 original size:19 final size:19
Alignment explanation
Indices: 2999695--2999825 Score: 65
Period size: 19 Copynumber: 7.5 Consensus size: 19
2999685 ACTTACATAA
2999695 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
* * *
2999714 TACACAAT-ACATAATAACT
1 TACATAATAAC-TTACAACT
*
2999733 TAC-----AACTTACATA-A
1 TACATAATAACTTACA-ACT
2999747 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
*
2999766 TACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
* * *
2999784 TGCA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
2999798 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
2999817 TACATAATA
1 TACATAATA
2999826 CATAATAACT
Statistics
Matches: 81, Mismatches: 14, Indels: 34
0.63 0.11 0.26
Matches are distributed among these distances:
14 9 0.11
15 7 0.09
16 2 0.02
17 6 0.07
18 14 0.17
19 43 0.53
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.31
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:2999799 original size:77 final size:76
Alignment explanation
Indices: 2999642--2999923 Score: 492
Period size: 77 Copynumber: 3.7 Consensus size: 76
2999632 TGACTGACAT
* * *
2999642 AATACATTTAACTTACAACTTACACAATACATAATAACTTACAACTTACATAATACATAATAACT
1 AATACATATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACAT-TTAACT
2999707 TACAACTTACAC
65 TACAACTTACAC
2999719 AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
1 AATACAT-ATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
*
2999784 TGCAACTTACAC
65 TACAACTTACAC
2999796 AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
1 AATACAT-ATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
2999861 TACAACTTACAC
65 TACAACTTACAC
*
2999873 AATACATTTAACTTACAACTTACATAATACATAATAACTTACAACTTACAT
1 AATACATATAACTTACAACTTACATAATACATAATAACTTACAACTTACAT
2999924 TTAACTTACA
Statistics
Matches: 198, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
76 43 0.22
77 106 0.54
78 49 0.25
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (76 bp):
AATACATATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACTT
ACAACTTACAC
Found at i:2999931 original size:11 final size:10
Alignment explanation
Indices: 2999915--2999968 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
2999905 AATAACTTAC
2999915 AACTTACATTT
1 AACTTACA-TT
2999926 AACTTACA-T
1 AACTTACATT
2999935 AA--TACATTT
1 AACTTACA-TT
2999944 AACTTACA-T
1 AACTTACATT
2999953 AACTTACA-T
1 AACTTACATT
2999962 AACTTAC
1 AACTTAC
2999969 CATTGCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:2999952 original size:18 final size:18
Alignment explanation
Indices: 2999889--2999954 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
2999879 TTTAACTTAC
*
2999889 AACTTACATAATACATAAT
1 AACTTACATAATACAT-TT
*
2999908 AACTTACA-ACTTACATTT
1 AACTTACATA-ATACATTT
2999926 AACTTACATAATACATTT
1 AACTTACATAATACATTT
2999944 AACTTACATAA
1 AACTTACATAA
2999955 CTTACATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:2999964 original size:18 final size:18
Alignment explanation
Indices: 2999804--2999968 Score: 69
Period size: 18 Copynumber: 9.5 Consensus size: 18
2999794 ACAATACATA
2999804 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
*
2999820 ATAATACATA-ATAACTTAC
1 AT-A-ACTTACATAACTTAC
2999839 --AACTTACATAA--TAC
1 ATAACTTACATAACTTAC
2999853 ATTTAACTTAC--AACTTAC
1 A--TAACTTACATAACTTAC
*
2999871 ACAA--TACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
*
2999889 --AACTTACATAATACATA-
1 ATAACTTACAT-A-ACTTAC
2999906 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
2999922 ATTTAACTTACATAA--TAC
1 A--TAACTTACATAACTTAC
2999940 ATTTAACTTACATAACTTAC
1 A--TAACTTACATAACTTAC
2999960 ATAACTTAC
1 ATAACTTAC
2999969 CATTGCAATT
Statistics
Matches: 116, Mismatches: 5, Indels: 54
0.66 0.03 0.31
Matches are distributed among these distances:
14 6 0.05
15 8 0.07
16 16 0.14
17 2 0.02
18 64 0.55
19 14 0.12
20 6 0.05
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:3005445 original size:21 final size:21
Alignment explanation
Indices: 3005419--3005489 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
3005409 CTACAACTTA
* *
3005419 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
3005440 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
3005461 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
3005482 AAGCAGAG
1 AAGCAGAG
3005490 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:3005916 original size:84 final size:83
Alignment explanation
Indices: 3005799--3006017 Score: 224
Period size: 84 Copynumber: 2.6 Consensus size: 83
3005789 CCAAAATAGT
* * * * * *
3005799 GGCGTTTTTGTATAAAAGCGCCACTAAAGAACATGTTCTTTCGTGGCGTTTGTAAAAAATGCCAC
1 GGCGTTTTTTTCT-AAA-CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAACGCCAC
*
3005864 TAAAGAACATGGTCTTTAAC
64 TAAAGAACATGATCTTTAAC
* * * *** * *
3005884 GGCATTTTTTT-TACAAACGCCGCTAAAGAACATGTTCTTTAGCGACGTTTTTTTCTAAGCGCCG
1 GGCGTTTTTTTCT--AAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAAAAAACGCCA
*
3005948 CTAAAGAACATGATCTTTAGC
63 CTAAAGAACATGATCTTTAAC
* *
3005969 GGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
1 GGCGTTTTTTTCTAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTT
3006018 TTGTTTGTAA
Statistics
Matches: 111, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
83 3 0.03
84 57 0.51
85 50 0.45
86 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (83 bp):
GGCGTTTTTTTCTAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAACGCCACTA
AAGAACATGATCTTTAAC
Found at i:3005948 original size:42 final size:42
Alignment explanation
Indices: 3005863--3006019 Score: 235
Period size: 42 Copynumber: 3.7 Consensus size: 42
3005853 AAAAATGCCA
* * *
3005863 CTAAAGAACATGGTCTTTAACGGCATTTTTTT-TACAAACGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT--AAGCGCCG
* *
3005906 CTAAAGAACATGTTCTTTAGCGACGTTTTTTTCTAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCG
*
3005948 CTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCG
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCG
3005990 CTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 CTAAAGAACATGGTCTTTAGCGGCGTTTTT
3006020 GTTTGTAAAC
Statistics
Matches: 105, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
42 76 0.72
43 28 0.27
44 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (42 bp):
CTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCG
Found at i:3018626 original size:41 final size:40
Alignment explanation
Indices: 3018571--3018762 Score: 163
Period size: 41 Copynumber: 4.7 Consensus size: 40
3018561 GCAAAAATTA
* * *
3018571 TAAAACACGGAGCAATAGCGGCGTTTTACAAAAAAACACCGC
1 TAAAA-ACAGAGCAATAGCGGCGTTTT-CGATAAAACACCGC
* * *
3018613 TAAAAACAGAGCAATAGCGGTGTTTTTTGTTAAAACACCGC
1 TAAAAACAGAGCAATAGCGGCG-TTTTCGATAAAACACCGC
* * *
3018654 TAAAAACAGAGCAATAGTGGCG-TTTCTGGTAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGTTTTC-GATAAAACACCGC
* * ***
3018694 TAAAAACCAGAGCATTAGCGGCGCTTTTGGA-AAAATGTCGC
1 TAAAAA-CAGAGCAATAGCGGCG-TTTTCGATAAAACACCGC
*
3018735 TAAAAACCAGAGCATTAGCGGCGCTTTT
1 TAAAAA-CAGAGCAATAGCGGCG-TTTT
3018763 GGTAAAAGAA
Statistics
Matches: 128, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 3 0.02
40 17 0.13
41 95 0.74
42 10 0.08
43 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.21
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGTTTTCGATAAAACACCGC
Found at i:3018763 original size:41 final size:41
Alignment explanation
Indices: 3018603--3018769 Score: 196
Period size: 41 Copynumber: 4.1 Consensus size: 41
3018593 GTTTTACAAA
* * * * *
3018603 AAAACACCGCTAAAAA-CAGAGCAATAGCGGTGTTTTTTGTT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCG-CTTTTGGT
* * *
3018644 AAAACACCGCTAAAAA-CAGAGCAATAGTGGCG-TTTCTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTT-TGGT
*
3018684 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* *
3018725 AAAATGTCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
3018766 AAAA
1 AAAA
3018770 GAATTATGGA
Statistics
Matches: 113, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
39 3 0.03
40 18 0.16
41 89 0.79
42 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:3024158 original size:43 final size:42
Alignment explanation
Indices: 3024048--3024193 Score: 186
Period size: 43 Copynumber: 3.4 Consensus size: 42
3024038 ATATATATGG
* *
3024048 TCTTTAGTGGCGTTTTTGGGGAAAGCGTCGCTAAAGATCATG-
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAG-TCATGA
* * *
3024090 TCTTTTGTGGCGTTTTTGGGAAAAGCGCCGCTAAATGTCATGA
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAA-GTCATGA
* * *
3024133 CCTTTAGCGGTGTTTTTGGGGAAAGCGCCACTAAAGGTCATGA
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAA-GTCATGA
3024176 TCTTTAGCGGCGTTTTTG
1 TCTTTAGCGGCGTTTTTG
3024194 AGAAAAAAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 37 0.41
43 53 0.59
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.34
Consensus pattern (42 bp):
TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGTCATGA
Found at i:3025680 original size:20 final size:20
Alignment explanation
Indices: 3025655--3025693 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3025645 TGTATTAATA
* *
3025655 AAATTTTAGAATTTTTCATC
1 AAATTTTACAACTTTTCATC
3025675 AAATTTTACAACTTTTCAT
1 AAATTTTACAACTTTTCAT
3025694 TTTAGTCCCT
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:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (20 bp):
AAATTTTACAACTTTTCATC
Found at i:3026404 original size:43 final size:43
Alignment explanation
Indices: 3026345--3026442 Score: 142
Period size: 43 Copynumber: 2.3 Consensus size: 43
3026335 TTATGAAAAT
* *
3026345 AACGCCGCTATAGAACATGATCTTTAGCAACGTTTTTCCCAAA
1 AACGCCGCTAAAGAACATGATCTTTAGCAACGCTTTTCCCAAA
* ** *
3026388 AATGCCGCTAAAGAACATGATCTTTAGCAGTGCTTTTCCCACA
1 AACGCCGCTAAAGAACATGATCTTTAGCAACGCTTTTCCCAAA
3026431 AACGCCGCTAAA
1 AACGCCGCTAAA
3026443 ACGCCGCTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.26
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGATCTTTAGCAACGCTTTTCCCAAA
Found at i:3026477 original size:54 final size:54
Alignment explanation
Indices: 3026386--3026490 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 54
3026376 GTTTTTCCCA
* *
3026386 AAAATGCCGCTAAAGAACATGATCTTTAGCAGTGCTTTTCCCACAAACGCCGCT
1 AAAACGCCGCTAAAGAACATGATCTTTAGCAGCGCTTTTCCCACAAACGCCGCT
**
3026440 AAAACGCCGCTAAAGAACATGA-CTTTTAGC-GACGCTTTTCCTGCAAACGCC
1 AAAACGCCGCTAAAGAACATGATC-TTTAGCAG-CGCTTTTCCCACAAACGCC
3026491 ACTATAGAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
53 2 0.04
54 43 0.96
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (54 bp):
AAAACGCCGCTAAAGAACATGATCTTTAGCAGCGCTTTTCCCACAAACGCCGCT
Found at i:3026512 original size:42 final size:43
Alignment explanation
Indices: 3026441--3026591 Score: 152
Period size: 42 Copynumber: 3.6 Consensus size: 43
3026431 AACGCCGCTA
* * * *
3026441 AAACGCCGCTAAAGAACATGACTTTTAGCGACGCTTTTCCTGC
1 AAACGCCACTAAAGAATATGACCTTTAGCGACGCTTTTCCTAC
* *
3026484 AAACGCCACTATAGAATA-GACCTTTAGCGGCGCTTTTGCC-AC
1 AAACGCCACTAAAGAATATGACCTTTAGCGACGCTTTT-CCTAC
*
3026526 AAACGCCACTATAA-AATA-GACCTTT-G-GTAGCGCTTTTCTTAC
1 AAACGCCACTA-AAGAATATGACCTTTAGCG-A-CGCTTTTCCTAC
*
3026568 AAACGCCGCTAAAGAATATGACCT
1 AAACGCCACTAAAGAATATGACCT
3026592 GTAAAAAAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
40 1 0.01
41 4 0.04
42 63 0.69
43 23 0.25
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCACTAAAGAATATGACCTTTAGCGACGCTTTTCCTAC
Found at i:3026626 original size:21 final size:21
Alignment explanation
Indices: 3026602--3026658 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
3026592 GTAAAAAAAT
3026602 TATTTTATTTTAATTAAATAA
1 TATTTTATTTTAATTAAATAA
* *
3026623 TA-TTTATTTCTATGTTAAATAT
1 TATTTTATTT-TA-ATTAAATAA
*
3026645 TATATTATCTTTAA
1 TATTTTAT-TTTAA
3026659 ACTATATACT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
20 7 0.25
21 4 0.14
22 9 0.32
23 6 0.21
24 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
TATTTTATTTTAATTAAATAA
Found at i:3031353 original size:93 final size:93
Alignment explanation
Indices: 3031241--3031412 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
3031231 CGCCCATAAG
* *
3031241 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3031306 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
3031334 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3031399 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
3031413 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:3031409 original size:46 final size:46
Alignment explanation
Indices: 3031234--3031409 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
3031224 TGTAACCCGC
* * *
3031234 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
3031280 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
3031330 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
3031373 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
3031410 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:3038878 original size:46 final size:46
Alignment explanation
Indices: 3038811--3039163 Score: 652
Period size: 46 Copynumber: 7.7 Consensus size: 46
3038801 TGTAACCCGC
* * * * * *
3038811 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
3038857 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
3038903 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
3038949 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
3038995 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
3039041 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
3039087 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
3039133 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
3039164 AACCCTAGGT
Statistics
Matches: 301, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 301 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:3040632 original size:6 final size:7
Alignment explanation
Indices: 3040615--3040655 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
3040605 AATTTTAAGT
*
3040615 TTTTTAT
1 TTTTTAA
3040622 TTTTTAA
1 TTTTTAA
3040629 TTTTTAA
1 TTTTTAA
3040636 -TTTTAA
1 TTTTTAA
3040642 TTTTTAA
1 TTTTTAA
*
3040649 ATTTTAA
1 TTTTTAA
3040656 AGTTTTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTAA
Found at i:3040639 original size:20 final size:20
Alignment explanation
Indices: 3040616--3040655 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3040606 ATTTTAAGTT
* *
3040616 TTTTATTTTTTAATTTTTAA
1 TTTTAATTTTTAAATTTTAA
3040636 TTTTAATTTTTAAATTTTAA
1 TTTTAATTTTTAAATTTTAA
3040656 AGTTTTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTAATTTTTAAATTTTAA
Found at i:3040651 original size:14 final size:14
Alignment explanation
Indices: 3040604--3040655 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
3040594 TTAAATATTA
3040604 AAATTTTAAGTTTTTT
1 AAATTTTAA--TTTTT
**
3040620 ATTTTTTAATTTTT
1 AAATTTTAATTTTT
3040634 -AATTTTAATTTTT
1 AAATTTTAATTTTT
3040647 AAATTTTAA
1 AAATTTTAA
3040656 AGTTTTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.35
14 13 0.42
16 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
AAATTTTAATTTTT
Found at i:3040687 original size:8 final size:8
Alignment explanation
Indices: 3040601--3040687 Score: 58
Period size: 8 Copynumber: 10.9 Consensus size: 8
3040591 ATATTAAATA
*
3040601 TTAAAATT
1 TTAAATTT
*
3040609 TTAAGTTT
1 TTAAATTT
*
3040617 TT-TATTT
1 TTAAATTT
*
3040624 TTTAATTT
1 TTAAATTT
3040632 TT-AA-TT
1 TTAAATTT
3040638 TT-AATTT
1 TTAAATTT
3040645 TTAAA-TT
1 TTAAATTT
3040652 TTAAAGTTTT
1 TTAAA--TTT
3040662 TTGAAGATTT
1 TT-AA-ATTT
3040672 TTATAATTT
1 TTA-AATTT
3040681 TTAAATT
1 TTAAATT
3040688 AACATATAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
6 6 0.09
7 18 0.28
8 20 0.31
9 8 0.12
10 10 0.15
11 2 0.03
12 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (8 bp):
TTAAATTT
Found at i:3041451 original size:50 final size:50
Alignment explanation
Indices: 3041387--3041488 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
3041377 GGGACAAAAG
3041387 TAATTAAAAAAGAATCTTATTACTTACCTAAACCCTAAAACAAATTAGTT
1 TAATTAAAAAAGAATCTTATTACTTACCTAAACCCTAAAACAAATTAGTT
* *
3041437 TAATTAAAAAAGAATCTTATTGCTTACCTAAACTCTAAAACAAATTAGTT
1 TAATTAAAAAAGAATCTTATTACTTACCTAAACCCTAAAACAAATTAGTT
3041487 TA
1 TA
3041489 TTGTCATTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (50 bp):
TAATTAAAAAAGAATCTTATTACTTACCTAAACCCTAAAACAAATTAGTT
Found at i:3041950 original size:40 final size:40
Alignment explanation
Indices: 3041886--3042014 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
3041876 AACTTTTTGT
* * * * *
3041886 GGCGTTTTTCAGAAAGAGCTGCTAATGGTCAACCTATAGC
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAGC
* * *
3041926 GGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGT
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAGC
* *
3041966 GGCGTTTTTCAAAAAGCGCCGCCAATGCTCTATCTATAGC
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAGC
3042006 -GCTGTTTTT
1 GGC-GTTTTT
3042015 TATCCAAATG
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
39 2 0.03
40 74 0.97
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (40 bp):
GGCGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAGC
Found at i:3041993 original size:154 final size:153
Alignment explanation
Indices: 3041616--3041993 Score: 499
Period size: 154 Copynumber: 2.5 Consensus size: 153
3041606 AATATTTTTT
* *
3041616 GCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGTCGCT
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGCCGCT
* ** * * *
3041681 AATGCCACTAAAGATCAACATAGAACGTGACATTGTGGTTAATTTTTTTACGGTGTTTTTCAGAA
66 AATGCCACTAAAGATCAACATAAAACGACACATTGTGCTTAATTTTTGTA-GGCGTTTTTCAGAA
* *
3041746 AGCAACGCGAATGGTCGACCTGTA
130 AGCAACGCGAATGGTCAACCTATA
* * * * * *
3041770 GCGACGTTTTTTAAAAAGTGCAGCTAATGCTCGATCTATAGCGGTGATTTTCAAAAAGTGCCACT
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGCCGCT
* *
3041835 AATGCCACTAAAGCTCAACATAAAACGACAGCGTTGTGCTTAACTTTTTGT-GGCGTTTTTCAGA
66 AATGCCACTAAAGATCAACATAAAACGACA-CATTGTGCTTAA-TTTTTGTAGGCGTTTTTCAGA
* *
3041899 AAG-AGCTGCTAATGGTCAACCTATA
129 AAGCAAC-GCGAATGGTCAACCTATA
* * *
3041924 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCGTTTTTCAAAAAGCGCCGCC
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGCCGCT
3041989 AATGC
66 AATGC
3041994 TCTATCTATA
Statistics
Matches: 192, Mismatches: 29, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
153 2 0.01
154 174 0.91
155 10 0.05
156 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (153 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGTGCCGCT
AATGCCACTAAAGATCAACATAAAACGACACATTGTGCTTAATTTTTGTAGGCGTTTTTCAGAAA
GCAACGCGAATGGTCAACCTATA
Found at i:3042406 original size:27 final size:27
Alignment explanation
Indices: 3042375--3042431 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
3042365 TAAAAGCCTA
3042375 TTGTCTCAAATTTTAGTAAAATTAGTT
1 TTGTCTCAAATTTTAGTAAAATTAGTT
3042402 TTGTCTCAAATTTTAGTAAAATTAGTT
1 TTGTCTCAAATTTTAGTAAAATTAGTT
3042429 TTG
1 TTG
3042432 GTCCTAACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (27 bp):
TTGTCTCAAATTTTAGTAAAATTAGTT
Found at i:3042579 original size:43 final size:43
Alignment explanation
Indices: 3042518--3042601 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
3042508 CGTTTGTATA
3042518 CTTGTAATTTTTTCGAACAGATTGGTTTAATAAAATTATTCAT
1 CTTGTAATTTTTTCGAACAGATTGGTTTAATAAAATTATTCAT
3042561 CTTGTAATTTTTTCGAACAGATTGGTTTAATAAAATTATTC
1 CTTGTAATTTTTTCGAACAGATTGGTTTAATAAAATTATTC
3042602 TTGAACTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (43 bp):
CTTGTAATTTTTTCGAACAGATTGGTTTAATAAAATTATTCAT
Found at i:3046351 original size:40 final size:39
Alignment explanation
Indices: 3046320--3046529 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
3046310 GGACTAAGAT
* *
3046320 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
3046360 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
3046400 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
3046440 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
3046480 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
3046519 CCGAAGGCATT
1 CCGAAGGCATT
3046530 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:3046483 original size:120 final size:120
Alignment explanation
Indices: 3046267--3046529 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
3046257 TTGAATGCTG
* *
3046267 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
3046331 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
3046387 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
3046450 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
3046506 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
3046530 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:3046549 original size:79 final size:80
Alignment explanation
Indices: 3046268--3046564 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
3046258 TGAATGCTGT
* ** * * * **
3046268 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
3046331 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
3046348 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
3046412 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
3046428 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
3046492 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
3046507 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
3046565 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:3054294 original size:40 final size:40
Alignment explanation
Indices: 3054211--3054553 Score: 485
Period size: 40 Copynumber: 8.6 Consensus size: 40
3054201 TTGAATGCTG
* * * * * *
3054211 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
3054251 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
3054291 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
3054331 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
3054371 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
3054411 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
3054451 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
3054491 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
3054530 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3054554 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:3058194 original size:20 final size:20
Alignment explanation
Indices: 3058157--3058194 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3058147 TGTTGTTTGG
*
3058157 CCCATCTTTCTTTTCTCTTA
1 CCCATCTTTCTTTCCTCTTA
3058177 CCCATCTTAT-TTTCCTCT
1 CCCATCTT-TCTTTCCTCT
3058195 CTTGTATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.11, C:0.37, G:0.00, T:0.53
Consensus pattern (20 bp):
CCCATCTTTCTTTCCTCTTA
Found at i:3059121 original size:10 final size:10
Alignment explanation
Indices: 3059108--3059138 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3059098 AAAAAAAATT
3059108 AAAATTTAAA
1 AAAATTTAAA
3059118 AAAATTT-AA
1 AAAATTTAAA
3059127 AAAATTTAAA
1 AAAATTTAAA
3059137 AA
1 AA
3059139 TTTATCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:3059148 original size:10 final size:9
Alignment explanation
Indices: 3059108--3059142 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
3059098 AAAAAAAATT
3059108 AAAATTTAAA
1 AAAATTT-AA
3059118 AAAATTTAA
1 AAAATTTAA
3059127 AAAATTT-A
1 AAAATTTAA
3059135 AAAATTTA
1 AAAATTTA
3059143 TCAAAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 9 0.38
10 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAATTTAA
Found at i:3062400 original size:33 final size:33
Alignment explanation
Indices: 3062340--3062456 Score: 137
Period size: 33 Copynumber: 3.5 Consensus size: 33
3062330 AGTACATCAT
*
3062340 CAATCCAACCAAACACACCAGATGCTCACT-AGAGC
1 CAATCCAACC-ATCACACCA-ATGCTCA-TAAGAGC
* *
3062375 CAATCCATCCATCGCACCAATGCTCATAAGAGC
1 CAATCCAACCATCACACCAATGCTCATAAGAGC
* *
3062408 TAATCCAACCATCACACCAATGCTCATAAAAGC
1 CAATCCAACCATCACACCAATGCTCATAAGAGC
* *
3062441 TAAACCAACCATCACA
1 CAATCCAACCATCACA
3062457 TCAAATAGAG
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 1 0.01
33 56 0.77
34 7 0.10
35 9 0.12
ACGTcount: A:0.40, C:0.36, G:0.09, T:0.15
Consensus pattern (33 bp):
CAATCCAACCATCACACCAATGCTCATAAGAGC
Found at i:3074900 original size:45 final size:45
Alignment explanation
Indices: 3074846--3075059 Score: 205
Period size: 45 Copynumber: 4.6 Consensus size: 45
3074836 GTTAAGAATA
3074846 CCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATC
1 CCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATC
* * * * * **
3074891 CCGTGTAAGACCATGCTAAGACATGGCATCGGCATTGATTAAGGA-C
1 CCATGTAAGACCATGTTAAGACATGGCATTGGTA-AG-GCAAGGATC
* * ** ** ** *
3074937 TCCATGTAAGACCATATCAAGATGTACCATTGGCACTAAGAAAAGGATA
1 -CCATGTAAGACCATGTTAAGACATGGCATTGG---TAAGGCAAGGATC
3074986 CCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATC
1 CCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATC
* *
3075031 CCGTGTAAGACCATGCTAAGACATGGCAT
1 CCATGTAAGACCATGTTAAGACATGGCAT
3075060 CGGCATTGAT
Statistics
Matches: 130, Mismatches: 32, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
45 67 0.52
46 2 0.02
47 28 0.22
48 31 0.24
49 1 0.01
50 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (45 bp):
CCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATC
Found at i:3074991 original size:48 final size:47
Alignment explanation
Indices: 3074843--3075139 Score: 164
Period size: 45 Copynumber: 6.4 Consensus size: 47
3074833 AAGGTTAAGA
* * ** **
3074843 ATACCATGTAAGACCATGTTAAGACATGGCATTGG--TAAGGCAAGG
1 ATACCATGTAAGACCATATCAAGACATACCATTGGCATAAGAAAAGG
* * * ** * * *
3074888 ATCCCGTGTAAGACCAT-GCTAAGACATGGCATCGGCAT-TGATTAAGG
1 ATACCATGTAAGACCATATC-AAGACATACCATTGGCATAAGA-AAAGG
**
3074935 ACT-CCATGTAAGACCATATCAAGATGTACCATTGGCACTAAGAAAAGG
1 A-TACCATGTAAGACCATATCAAGACATACCATTGGCA-TAAGAAAAGG
* * ** **
3074983 ATACCATGTAAGACCATGTTAAGACATGGCATTGG--TAAGGCAAGG
1 ATACCATGTAAGACCATATCAAGACATACCATTGGCATAAGAAAAGG
* * * ** * * *
3075028 ATCCCGTGTAAGACCAT-GCTAAGACATGGCATCGGCAT-TGATTAAGG
1 ATACCATGTAAGACCATATC-AAGACATACCATTGGCATAAGA-AAAGG
**
3075075 ACT-CCATGTAAGACCATATCAAGATGTACCATTGGCACTAAGAAAAGG
1 A-TACCATGTAAGACCATATCAAGACATACCATTGGCA-TAAGAAAAGG
3075123 ATACCATGTAAGACCAT
1 ATACCATGTAAGACCAT
3075140 GCCAAGGCAT
Statistics
Matches: 192, Mismatches: 42, Indels: 33
0.72 0.16 0.12
Matches are distributed among these distances:
45 66 0.34
46 2 0.01
47 64 0.33
48 56 0.29
49 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (47 bp):
ATACCATGTAAGACCATATCAAGACATACCATTGGCATAAGAAAAGG
Found at i:3075016 original size:140 final size:140
Alignment explanation
Indices: 3074843--3075161 Score: 602
Period size: 140 Copynumber: 2.3 Consensus size: 140
3074833 AAGGTTAAGA
3074843 ATACCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCATGCT
1 ATACCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCATGCT
3074908 AAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCATATCAAGATGTACCATTGGCAC
66 AAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCATATCAAGATGTACCATTGGCAC
3074973 TAAGAAAAGG
131 TAAGAAAAGG
3074983 ATACCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCATGCT
1 ATACCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCATGCT
3075048 AAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCATATCAAGATGTACCATTGGCAC
66 AAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCATATCAAGATGTACCATTGGCAC
3075113 TAAGAAAAGG
131 TAAGAAAAGG
** * *
3075123 ATACCATGTAAGACCATGCCAAGGCATGGCATTGATAAG
1 ATACCATGTAAGACCATGTTAAGACATGGCATTGGTAAG
3075162 TTCTATAAGG
Statistics
Matches: 175, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 175 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (140 bp):
ATACCATGTAAGACCATGTTAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCATGCT
AAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCATATCAAGATGTACCATTGGCAC
TAAGAAAAGG
Found at i:3075235 original size:50 final size:49
Alignment explanation
Indices: 3075141--3075242 Score: 143
Period size: 50 Copynumber: 2.1 Consensus size: 49
3075131 TAAGACCATG
*
3075141 CCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGA
1 CCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGA
* **
3075190 CCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGG-TCTCATGTAAGA
1 CCAAGACATGGCATTGATAAGTT-CTATAAGGC-AAGGAAATCATGTAAGA
3075240 CCA
1 CCA
3075243 TGCCAAGGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
49 21 0.45
50 22 0.47
51 4 0.09
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.23
Consensus pattern (49 bp):
CCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGA
Found at i:3075253 original size:50 final size:49
Alignment explanation
Indices: 3075127--3075253 Score: 130
Period size: 50 Copynumber: 2.5 Consensus size: 49
3075117 AAAAGGATAC
3075127 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAAT
1 CATGTAAGACCATGCC-A---A-GGCATTGATAAGTTCTATAAGGCAAGGAAAT
* * * * **
3075181 CATGTAAGACCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGG-TCT
1 CATGTAAGACCATGCCAAGGCATTGATAAGTT-CTATAAGGC-AAGGAAAT
3075231 CATGTAAGACCATGCCAAGGCAT
1 CATGTAAGACCATGCCAAGGCAT
3075254 GACATTGGTG
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
49 13 0.21
50 30 0.48
51 4 0.06
53 1 0.02
54 14 0.23
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (49 bp):
CATGTAAGACCATGCCAAGGCATTGATAAGTTCTATAAGGCAAGGAAAT
Found at i:3094895 original size:33 final size:33
Alignment explanation
Indices: 3094868--3094952 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
3094858 TGCTCACTCA
* *
3094868 AGCCAATCCATCCATCATAGCAATGCTCATAAG
1 AGCCAATCCAACCATCACAGCAATGCTCATAAG
*
3094901 AGCTAATCCAACCATCACAGCAATGCTCATAAG
1 AGCCAATCCAACCATCACAGCAATGCTCATAAG
* *
3094934 AGCTAAACCAACCATCACA
1 AGCCAATCCAACCATCACA
3094953 TCAAATAGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.40, C:0.32, G:0.11, T:0.18
Consensus pattern (33 bp):
AGCCAATCCAACCATCACAGCAATGCTCATAAG
Found at i:3096865 original size:53 final size:53
Alignment explanation
Indices: 3096798--3097063 Score: 249
Period size: 53 Copynumber: 5.0 Consensus size: 53
3096788 TTTTGTAGCG
*
3096798 TATCTGAAGA-GGAAGCCTTTGTAGCAATCTATGAAATAGAAGCCTTTGTAGTGA
1 TATCTGAA-ATGGAAGCCTTTGTGGCAATCTATGAAATAGAAGCCTTTGT-GTGA
* * * **
3096852 -ATTTGAAATGGAAGCTTTTGTGGCAATCTATGAAACAGAAGCCTTCATG-GCA
1 TATCTGAAATGGAAGCCTTTGTGGCAATCTATGAAATAGAAGCCTTTGTGTG-A
* * * * * * *
3096904 TATTTGAAATGGAGGTCTTTGTAGCAATCTATGAAAAAAAAGCCTTCGTGGTGA
1 TATCTGAAATGGAAGCCTTTGTGGCAATCTATGAAATAGAAGCCTTTGT-GTGA
* *
3096958 -ATCTGAAATGGAAGCCTTTGTGGCAATCT-TGAAA-CGAAAGCCTTTATG-GCA
1 TATCTGAAATGGAAGCCTTTGTGGCAATCTATGAAATAG-AAGCCTTTGTGTG-A
* * * *
3097009 TATCTGAAATGTAAGCCTTTGTGGCAATCAATGAAATGGAAGCGTTTGTGGTGA
1 TATCTGAAATGGAAGCCTTTGTGGCAATCTATGAAATAGAAGCCTTTGT-GTGA
3097063 T
1 T
3097064 CTATAGAAAG
Statistics
Matches: 174, Mismatches: 26, Indels: 24
0.78 0.12 0.11
Matches are distributed among these distances:
50 1 0.01
51 3 0.02
52 43 0.25
53 119 0.68
54 6 0.03
55 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (53 bp):
TATCTGAAATGGAAGCCTTTGTGGCAATCTATGAAATAGAAGCCTTTGTGTGA
Found at i:3096968 original size:106 final size:105
Alignment explanation
Indices: 3096798--3097044 Score: 336
Period size: 106 Copynumber: 2.3 Consensus size: 105
3096788 TTTTGTAGCG
* * * *
3096798 TATCTGAAGA-GGAAGCCTTTGTAGCAATCTATGAAATAGAAGCCTTTGTAGTGAATTTGAAATG
1 TATCTGAA-ATGGAAGCCTTTGTAGCAATCTATGAAAAAAAAGCCTTCGTAGTGAATCTGAAATG
*
3096862 GAAGCTTTTGTGGCAATCTATGAAAC-AGAAGCCTTCATGGCA
65 GAAGCCTTTGTGGCAATCT-TGAAACGA-AAGCCTTCATGGCA
* * * *
3096904 TATTTGAAATGGAGGTCTTTGTAGCAATCTATGAAAAAAAAGCCTTCGTGGTGAATCTGAAATGG
1 TATCTGAAATGGAAGCCTTTGTAGCAATCTATGAAAAAAAAGCCTTCGTAGTGAATCTGAAATGG
*
3096969 AAGCCTTTGTGGCAATCTTGAAACGAAAGCCTTTATGGCA
66 AAGCCTTTGTGGCAATCTTGAAACGAAAGCCTTCATGGCA
* * *
3097009 TATCTGAAATGTAAGCCTTTGTGGCAATCAATGAAA
1 TATCTGAAATGGAAGCCTTTGTAGCAATCTATGAAA
3097045 TGGAAGCGTT
Statistics
Matches: 123, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
105 50 0.41
106 73 0.59
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (105 bp):
TATCTGAAATGGAAGCCTTTGTAGCAATCTATGAAAAAAAAGCCTTCGTAGTGAATCTGAAATGG
AAGCCTTTGTGGCAATCTTGAAACGAAAGCCTTCATGGCA
Found at i:3097058 original size:27 final size:25
Alignment explanation
Indices: 3096780--3097059 Score: 177
Period size: 26 Copynumber: 10.6 Consensus size: 25
3096770 CACACAGAAG
* * *
3096780 ATGGAAGCTTTTGTAGCGTATCTGAA
1 ATGGAAGCCTTTGTGGC-AATCTGAA
*
3096806 GA-GGAAGCCTTTGTAGCAATCTATGAA
1 -ATGGAAGCCTTTGTGGCAATC--TGAA
* *
3096833 ATAGAAGCCTTTGTAGTG-AATTTGAA
1 ATGGAAGCCTTTGT-G-GCAATCTGAA
*
3096859 ATGGAAGCTTTTGTGGCAATCTATGAA
1 ATGGAAGCCTTTGTGGCAATC--TGAA
** ** *
3096886 ACAGAAGCCTTCATGGCATATTTGAA
1 ATGGAAGCCTTTGTGGCA-ATCTGAA
* * *
3096912 ATGGAGGTCTTTGTAGCAATCTATGAA
1 ATGGAAGCCTTTGTGGCAATC--TGAA
*** * *
3096939 AAAAAAGCCTTCGTGGTGAATCTGAA
1 ATGGAAGCCTTTGTGG-CAATCTGAA
3096965 ATGGAAGCCTTTGTGGCAATCTTGAA
1 ATGGAAGCCTTTGTGGCAATC-TGAA
* * *
3096991 ACGAAAGCCTTTATGGCATATCTGAA
1 ATGGAAGCCTTTGTGGCA-ATCTGAA
*
3097017 ATGTAAGCCTTTGTGGCAATCAATGAA
1 ATGGAAGCCTTTGTGGCAATC--TGAA
*
3097044 ATGGAAGCGTTTGTGG
1 ATGGAAGCCTTTGTGG
3097060 TGATCTATAG
Statistics
Matches: 194, Mismatches: 43, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
24 1 0.01
25 16 0.08
26 100 0.52
27 67 0.35
28 9 0.05
29 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (25 bp):
ATGGAAGCCTTTGTGGCAATCTGAA
Found at i:3101561 original size:30 final size:30
Alignment explanation
Indices: 3101525--3101584 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
3101515 TTCCCGAGCC
*
3101525 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
3101555 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
3101585 CGTATTAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:3109933 original size:21 final size:21
Alignment explanation
Indices: 3109907--3109948 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3109897 CCCCTGTAAT
*
3109907 TTAAATTTTTCTAAAT-TTTTC
1 TTAAATGTTTC-AAATGTTTTC
3109928 TTAAATGTTTCAAATGTTTTC
1 TTAAATGTTTCAAATGTTTTC
3109949 GATTTAGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57
Consensus pattern (21 bp):
TTAAATGTTTCAAATGTTTTC
Found at i:3113610 original size:26 final size:28
Alignment explanation
Indices: 3113573--3113631 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
3113563 TTTAGCCTTT
* * *
3113573 ATACTAATTACTGGTAGC-TTTGCTGTG
1 ATACTAATTACTGGAAACTTTTGCTGCG
3113600 ATACT-ATTACTGGAAACTTTTGCTGCG
1 ATACTAATTACTGGAAACTTTTGCTGCG
3113627 ATACT
1 ATACT
3113632 GATATTGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (28 bp):
ATACTAATTACTGGAAACTTTTGCTGCG
Found at i:3120787 original size:21 final size:21
Alignment explanation
Indices: 3120763--3120808 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3120753 CTAAGATGTG
*
3120763 AATTGAATTCAATTGA-GTATA
1 AATTGAATTAAATTGATGT-TA
3120784 AATTGAATTAAATTGATGTTA
1 AATTGAATTAAATTGATGTTA
3120805 AATT
1 AATT
3120809 CATTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.41
Consensus pattern (21 bp):
AATTGAATTAAATTGATGTTA
Found at i:3122440 original size:30 final size:30
Alignment explanation
Indices: 3122406--3122502 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
3122396 CCATACGGGT
** *
3122406 TGACACACGGGCGTGTGTCTCAAAGGTGAG
1 TGACACACGGGCGTGTGTCTCAACCGTGTG
*
3122436 TGACACACGGGTGTGTGTCTCAACCGTGTG
1 TGACACACGGGCGTGTGTCTCAACCGTGTG
* * *
3122466 TGACACATGGGCTTGTGTCTCAACTGTGTG
1 TGACACACGGGCGTGTGTCTCAACCGTGTG
3122496 TGACACA
1 TGACACA
3122503 TGGGTATGTG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.26
Consensus pattern (30 bp):
TGACACACGGGCGTGTGTCTCAACCGTGTG
Found at i:3137873 original size:75 final size:75
Alignment explanation
Indices: 3137750--3137900 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
3137740 CGGCTGCGTC
**
3137750 AATCATCTATCGAGTCGAAGGATTCAGGCCATTGTGAAATGTTTGAACCTGTAGCCAGAGTGGTA
1 AATCATCTATCGAGTCGAAGGATTCAGGCCATTGTGAAACATTTGAACCTGTAGCCAGAGTGGTA
3137815 ACCCATGGTG
66 ACCCATGGTG
3137825 AATCATCTATCGAGTCGAAGGATTCAGGCCATTGTGAAACATTTGAACCTGTAGCCAGAGTGGTA
1 AATCATCTATCGAGTCGAAGGATTCAGGCCATTGTGAAACATTTGAACCTGTAGCCAGAGTGGTA
3137890 ACCCATGGTG
66 ACCCATGGTG
3137900 A
1 A
3137901 GGGCACCTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (75 bp):
AATCATCTATCGAGTCGAAGGATTCAGGCCATTGTGAAACATTTGAACCTGTAGCCAGAGTGGTA
ACCCATGGTG
Found at i:3142168 original size:27 final size:27
Alignment explanation
Indices: 3142138--3142315 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
3142128 ATATTGAGTC
* *
3142138 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
3142165 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
3142192 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
3142220 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
3142247 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
3142274 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
3142301 CGCACACTTAATGCT
1 CGCACACTTAGTGCT
3142316 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:3142277 original size:82 final size:81
Alignment explanation
Indices: 3142159--3142310 Score: 225
Period size: 82 Copynumber: 1.9 Consensus size: 81
3142149 TGCTATATAA
* *
3142159 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
3142224 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
3142241 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
3142305 CACTTA
65 CACTTA
3142311 ATGCTGTACA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 12 0.19
82 51 0.81
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:3142298 original size:54 final size:54
Alignment explanation
Indices: 3142138--3142310 Score: 197
Period size: 54 Copynumber: 3.2 Consensus size: 54
3142128 ATATTGAGTC
* * * *
3142138 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
3142192 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
3142247 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
3142301 CGCACACTTA
1 CGCACACTTA
3142311 ATGCTGTACA
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
52 1 0.01
54 53 0.53
55 45 0.45
56 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:3142817 original size:12 final size:12
Alignment explanation
Indices: 3142800--3142826 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3142790 ATGGCATACT
3142800 TATGTATATATA
1 TATGTATATATA
3142812 TATGTATATATA
1 TATGTATATATA
3142824 TAT
1 TAT
3142827 ACTTCGGAAT
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:3147530 original size:12 final size:12
Alignment explanation
Indices: 3147513--3147538 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3147503 ATAGAGTTAC
3147513 GATACCAGTGAT
1 GATACCAGTGAT
3147525 GATACCAGTGAT
1 GATACCAGTGAT
3147537 GA
1 GA
3147539 ACATTAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (12 bp):
GATACCAGTGAT
Found at i:3156150 original size:93 final size:93
Alignment explanation
Indices: 3156038--3156209 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
3156028 GCCCATAAGT
* *
3156038 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3156103 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
3156131 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3156196 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
3156210 CAAATATCCT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:3156205 original size:46 final size:46
Alignment explanation
Indices: 3156030--3156205 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
3156020 TGTAACCCGC
* * *
3156030 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
3156076 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
3156126 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
3156169 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
3156206 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:3166590 original size:11 final size:10
Alignment explanation
Indices: 3166567--3166609 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
3166557 GTACATCTGC
*
3166567 TCTTTTTTGT
1 TCTTTTTTTT
3166577 TCTTTTTGTTT
1 TCTTTTT-TTT
*
3166588 TCTTTTGTTT
1 TCTTTTTTTT
*
3166598 TCCTTTTTTT
1 TCTTTTTTTT
3166608 TC
1 TC
3166610 ATGAGCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:3166591 original size:21 final size:20
Alignment explanation
Indices: 3166567--3166609 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3166557 GTACATCTGC
*
3166567 TCTTTT-TTGTTCTTTTTGTTT
1 TCTTTTGTT-TTCCTTTT-TTT
3166588 TCTTTTGTTTTCCTTTTTTT
1 TCTTTTGTTTTCCTTTTTTT
3166608 TC
1 TC
3166610 ATGAGCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 13 0.65
22 2 0.10
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (20 bp):
TCTTTTGTTTTCCTTTTTTT
Found at i:3169314 original size:20 final size:20
Alignment explanation
Indices: 3169277--3169314 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3169267 GAACTTCCTC
*
3169277 TCTCTCTTGAGCTACAACAG
1 TCTCTCTTGAACTACAACAG
3169297 TCTCATCTTGAACT-CAAC
1 TCTC-TCTTGAACTACAAC
3169315 CATCTTGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (20 bp):
TCTCTCTTGAACTACAACAG
Found at i:3179121 original size:26 final size:26
Alignment explanation
Indices: 3179092--3179151 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
3179082 TCCCTTTGAA
* * *
3179092 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
3179118 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
3179146 CCATTC
1 TCATTC
3179152 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:3179137 original size:28 final size:28
Alignment explanation
Indices: 3179106--3179177 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
3179096 TCGATATTTT
*
3179106 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
3179134 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
3179162 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
3179178 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:3181997 original size:49 final size:49
Alignment explanation
Indices: 3181925--3182020 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
3181915 ATTTGTGTTC
*
3181925 TGAGAAATCCAAAATTAATTCAAATGATTCTGAGTGAAGCTCACAGTTT
1 TGAGAAATCCAAAATTAATTCAAATGATTCTAAGTGAAGCTCACAGTTT
3181974 TGAGAAATCCAAAATTAATTCAAATGATTCTAAGTGAAGCTCACAGT
1 TGAGAAATCCAAAATTAATTCAAATGATTCTAAGTGAAGCTCACAGT
3182021 AGTCGTTTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.29
Consensus pattern (49 bp):
TGAGAAATCCAAAATTAATTCAAATGATTCTAAGTGAAGCTCACAGTTT
Found at i:3198153 original size:44 final size:44
Alignment explanation
Indices: 3198081--3198168 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
3198071 ATTACATGTA
* * * *
3198081 TCGCATCCATTATGAACTCTGACCAACTCCACGAGTTCGAATGC
1 TCGCATCCATAATGAACCCAGACCAACTCAACGAGTTCGAATGC
* * *
3198125 TCGCATCCATAATGAACCCAGACTAACTCAATGAGTTCGGATGC
1 TCGCATCCATAATGAACCCAGACCAACTCAACGAGTTCGAATGC
3198169 CTCATATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (44 bp):
TCGCATCCATAATGAACCCAGACCAACTCAACGAGTTCGAATGC
Found at i:3201709 original size:161 final size:161
Alignment explanation
Indices: 3201444--3201765 Score: 644
Period size: 161 Copynumber: 2.0 Consensus size: 161
3201434 AAAAACGGGG
3201444 ATTGGAGCACTTATAATCAAGCTTGAAATGTTGAACAAAACCCTAGCTATGGCTATTGGAAATTT
1 ATTGGAGCACTTATAATCAAGCTTGAAATGTTGAACAAAACCCTAGCTATGGCTATTGGAAATTT
3201509 CGGCTAGCACTTGAGAAGATAAGCTCATTTTTGCTTTGATTTTCCCTTTTTATTCTTTTAATTAC
66 CGGCTAGCACTTGAGAAGATAAGCTCATTTTTGCTTTGATTTTCCCTTTTTATTCTTTTAATTAC
3201574 CAAATGACCAAAATGCTCTTAGGGTCTTTCT
131 CAAATGACCAAAATGCTCTTAGGGTCTTTCT
3201605 ATTGGAGCACTTATAATCAAGCTTGAAATGTTGAACAAAACCCTAGCTATGGCTATTGGAAATTT
1 ATTGGAGCACTTATAATCAAGCTTGAAATGTTGAACAAAACCCTAGCTATGGCTATTGGAAATTT
3201670 CGGCTAGCACTTGAGAAGATAAGCTCATTTTTGCTTTGATTTTCCCTTTTTATTCTTTTAATTAC
66 CGGCTAGCACTTGAGAAGATAAGCTCATTTTTGCTTTGATTTTCCCTTTTTATTCTTTTAATTAC
3201735 CAAATGACCAAAATGCTCTTAGGGTCTTTCT
131 CAAATGACCAAAATGCTCTTAGGGTCTTTCT
3201766 TTCAAATTTT
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 161 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (161 bp):
ATTGGAGCACTTATAATCAAGCTTGAAATGTTGAACAAAACCCTAGCTATGGCTATTGGAAATTT
CGGCTAGCACTTGAGAAGATAAGCTCATTTTTGCTTTGATTTTCCCTTTTTATTCTTTTAATTAC
CAAATGACCAAAATGCTCTTAGGGTCTTTCT
Found at i:3203061 original size:18 final size:18
Alignment explanation
Indices: 3203038--3203074 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3203028 GTTTTATGTC
* *
3203038 TGTTTATTTTTGTTTTTA
1 TGTTTATTTGTGTGTTTA
3203056 TGTTTATTTGTGTGTTTA
1 TGTTTATTTGTGTGTTTA
3203074 T
1 T
3203075 TTTTTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.16, T:0.73
Consensus pattern (18 bp):
TGTTTATTTGTGTGTTTA
Found at i:3205154 original size:43 final size:44
Alignment explanation
Indices: 3205096--3205246 Score: 182
Period size: 43 Copynumber: 3.5 Consensus size: 44
3205086 GATTGCTGAG
* *
3205096 ATGTGAATACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * *
3205140 -TGTGATTACGTGTAAGACCATGTTTTGGACATTGGCATCGT-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * *
3205182 ATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCAACG-AT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* *
3205225 GTGTGATAACATGTAAGACCAT
1 ATGTGATTACATGTAAGACCAT
3205247 TTTGGGATAT
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
42 1 0.01
43 89 0.99
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:3208000 original size:10 final size:10
Alignment explanation
Indices: 3207972--3208001 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3207962 TAGTTTTAAG
3207972 TTTAGTTTTC
1 TTTAGTTTTC
3207982 TTTAGGTTTTC
1 TTTA-GTTTTC
3207993 TTTAGTTTT
1 TTTAGTTTT
3208002 TCTCTGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.10, C:0.07, G:0.13, T:0.70
Consensus pattern (10 bp):
TTTAGTTTTC
Found at i:3208496 original size:183 final size:181
Alignment explanation
Indices: 3208190--3208545 Score: 559
Period size: 183 Copynumber: 2.0 Consensus size: 181
3208180 TAGTTAAATT
* *
3208190 TATTTCAGTTTATTTTACTTCAAATGTGTTAAAGCTTGTTCCTTTTATGTTTCTTGCTTTAGATT
1 TATTTCAGTTTATTTTACGTCAAATATGTTAAAGCTTGTTCCTTTTATGTTTCTTGCTTTAGATT
*
3208255 TCTTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTAGTGCTTAAAAATCTCAACTTTCAC
66 TCTTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTAGTGCATAAAAATCTCAACTTTCAC
*
3208320 ATTTTTCGTAAGCTTTACTTTCATAGCTTCTTTGTTTCCTATTTTTGTATG
131 ATTTTTCGTAACCTTTACTTTCATAGCTTCTTTGTTTCCTATTTTTGTATG
* ** * * *
3208371 TATTTCAGTTTATTTTAGGTCAAATATGTTAAATTTTGTTCCTTTTATGTTTTTTTTTCTTTATA
1 TATTTCAGTTTATTTTACGTCAAATATGTTAAAGCTTGTTCCTTTTATG--TTTCTTGCTTTAGA
** *
3208436 TTTCTTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTGCATAAAAGTCTCAACTTTC
64 TTTCTTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTAGTGCATAAAAATCTCAACTTTC
* *
3208501 ACATTTTTCTTAACCTTTACTTTCATGGCTTCTTTGTTTCCTATT
129 ACATTTTTCGTAACCTTTACTTTCATAGCTTCTTTGTTTCCTATT
3208546 GTTTTGTTTA
Statistics
Matches: 158, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 44 0.28
183 114 0.72
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (181 bp):
TATTTCAGTTTATTTTACGTCAAATATGTTAAAGCTTGTTCCTTTTATGTTTCTTGCTTTAGATT
TCTTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTAGTGCATAAAAATCTCAACTTTCAC
ATTTTTCGTAACCTTTACTTTCATAGCTTCTTTGTTTCCTATTTTTGTATG
Found at i:3211053 original size:49 final size:49
Alignment explanation
Indices: 3211000--3211122 Score: 223
Period size: 47 Copynumber: 2.6 Consensus size: 49
3210990 TTAGGATTCT
*
3211000 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATATGAGATAAGGCCTAATGGCCG
3211049 ATGTGATGAATGTGAAAGTG--TATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATATGAGATAAGGCCTAATGGCCG
3211096 ATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGATGAATGTGAAAGTGTATATAT
3211123 NNNNNNNNNN
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
47 46 0.65
49 25 0.35
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (49 bp):
ATGTGATGAATGTGAAAGTGTATATATATGAGATAAGGCCTAATGGCCG
Found at i:3213223 original size:40 final size:40
Alignment explanation
Indices: 3213163--3213495 Score: 481
Period size: 40 Copynumber: 8.4 Consensus size: 40
3213153 NNNNNNNNNN
* *
3213163 ATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAGGAGC
1 ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
* * *
3213203 ATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAGGAGC
1 ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
*
3213243 ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGC
1 ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
* * * *
3213283 ATTCGAGTTGGTGTTATATCCGGGCTAAGTCTCGAAGAGC
1 ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
*
3213323 ATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGC
1 ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
* *
3213363 ATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGC
1 ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
* * *
3213403 ATTCGAGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGC
1 ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
* *
3213443 ATTCGAGCTGGTG-T-TATCCGGGCTAAGTCTCGAAGAGC
1 ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
*
3213481 ATTCATGCTGGTGAT
1 ATTCGTGCTGGTGAT
3213496 GTGTATTCGG
Statistics
Matches: 271, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
38 33 0.12
39 2 0.01
40 236 0.87
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (40 bp):
ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
Found at i:3213517 original size:8 final size:8
Alignment explanation
Indices: 3213504--3213530 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3213494 ATGTGTATTC
3213504 GGCCATTA
1 GGCCATTA
3213512 GGCCATTA
1 GGCCATTA
3213520 GGCCATTA
1 GGCCATTA
3213528 GGC
1 GGC
3213531 TGAAGTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (8 bp):
GGCCATTA
Found at i:3214530 original size:47 final size:47
Alignment explanation
Indices: 3214461--3214651 Score: 310
Period size: 47 Copynumber: 4.1 Consensus size: 47
3214451 GTTTGTATCA
3214461 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
3214508 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
*
3214555 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAC
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
* * * * * * *
3214602 AGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGAT
1 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
3214649 AAG
1 AAG
3214652 TCCCGAAGGG
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 134 1.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.27
Consensus pattern (47 bp):
AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
Found at i:3214826 original size:37 final size:37
Alignment explanation
Indices: 3214770--3214848 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
3214760 CCGAGCTCTA
* * *
3214770 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
3214807 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
3214844 AAGAC
1 AAGAC
3214849 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:3217008 original size:18 final size:18
Alignment explanation
Indices: 3216985--3217028 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
3216975 AAACACACGG
3216985 AGTAAGCTTTGAAAGCTT
1 AGTAAGCTTTGAAAGCTT
3217003 AGTAAGCTTTGAAAGCTT
1 AGTAAGCTTTGAAAGCTT
3217021 AGTAAGCT
1 AGTAAGCT
3217029 CGTATCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (18 bp):
AGTAAGCTTTGAAAGCTT
Found at i:3217027 original size:9 final size:9
Alignment explanation
Indices: 3216985--3217028 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
3216975 AAACACACGG
3216985 AGTAAGCTT
1 AGTAAGCTT
* *
3216994 TGAAAGCTT
1 AGTAAGCTT
3217003 AGTAAGCTT
1 AGTAAGCTT
* *
3217012 TGAAAGCTT
1 AGTAAGCTT
3217021 AGTAAGCT
1 AGTAAGCT
3217029 CGTATCTTAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (9 bp):
AGTAAGCTT
Found at i:3222825 original size:27 final size:28
Alignment explanation
Indices: 3222788--3223001 Score: 268
Period size: 27 Copynumber: 8.0 Consensus size: 28
3222778 AAACATACAT
* **
3222788 CACATAGGGGCAAAA-CAGTCATTTTGC
1 CACATAAGGGCAAAATCAGTCATTTTAA
*
3222815 CACATAAGGGCAAAATC-GTCATTTTAT
1 CACATAAGGGCAAAATCAGTCATTTTAA
* *
3222842 CATATAAGGG-AAAATC-GTTATTTTAA
1 CACATAAGGGCAAAATCAGTCATTTTAA
*
3222868 CACATAAGGGCAAAATCA-TCAATTTAA
1 CACATAAGGGCAAAATCAGTCATTTTAA
*
3222895 CACATAAGGGCAAAAT-AGTCATTTTAC
1 CACATAAGGGCAAAATCAGTCATTTTAA
*
3222922 CACATAAGGGCAAAA-CTA-TCATTTTAT
1 CACATAAGGGCAAAATC-AGTCATTTTAA
3222949 CACATAAGGGCAAAATC-GTCATTTTAA
1 CACATAAGGGCAAAATCAGTCATTTTAA
3222976 CACATAAGGGCAAAAT-AGTCATTTTA
1 CACATAAGGGCAAAATCAGTCATTTTA
3223002 CCCTATAGGG
Statistics
Matches: 165, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
26 24 0.15
27 138 0.84
28 3 0.02
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (28 bp):
CACATAAGGGCAAAATCAGTCATTTTAA
Found at i:3222979 original size:81 final size:80
Alignment explanation
Indices: 3222786--3223003 Score: 298
Period size: 81 Copynumber: 2.7 Consensus size: 80
3222776 ATAAACATAC
* ** * * *
3222786 ATCACATAGGGGCAAAA-CAGTCATTTTGCCACATAAGGGCAAAATCGTCATTTTATCATATAAG
1 ATCACATAAGGGCAAAATC-GTCATTTTAACACATAAGGGCAAAATAGTCATTTTACCACATAAG
3222850 GGAAAATCGTTATTTT
65 GGAAAATCGTTATTTT
* * *
3222866 AACACATAAGGGCAAAATCATCAATTTAACACATAAGGGCAAAATAGTCATTTTACCACATAAGG
1 ATCACATAAGGGCAAAATCGTCATTTTAACACATAAGGGCAAAATAGTCATTTTACCACATAAGG
3222931 GCAAAA-C-TATCATTTT
66 G-AAAATCGT-T-ATTTT
3222947 ATCACATAAGGGCAAAATCGTCATTTTAACACATAAGGGCAAAATAGTCATTTTACC
1 ATCACATAAGGGCAAAATCGTCATTTTAACACATAAGGGCAAAATAGTCATTTTACC
3223004 CTATAGGGGT
Statistics
Matches: 122, Mismatches: 12, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
79 1 0.01
80 57 0.47
81 64 0.52
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (80 bp):
ATCACATAAGGGCAAAATCGTCATTTTAACACATAAGGGCAAAATAGTCATTTTACCACATAAGG
GAAAATCGTTATTTT
Found at i:3223023 original size:27 final size:26
Alignment explanation
Indices: 3222993--3223310 Score: 365
Period size: 27 Copynumber: 11.9 Consensus size: 26
3222983 GGGCAAAATA
*
3222993 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATCTTACCCTAT-GGGGTATTTCG
* *
3223020 GTCATTTTACCCTATAGGGGTATTTCA
1 GTCATCTTACCCTAT-GGGGTATTTCG
3223047 GTCATCTTACCCTATGGGGGTATTTCG
1 GTCATCTTACCCTAT-GGGGTATTTCG
3223074 GTCAT-TGTACCCTATGGGGGTATTTCG
1 GTCATCT-TACCCTAT-GGGGTATTTCG
* * *
3223101 GTCATTTTACCCTCTAT-GGATATTTTG
1 GTCATCTTA-CC-CTATGGGGTATTTCG
* *
3223128 GTCATTTTACCCTATTGGGGTATTTTG
1 GTCATCTTACCCTA-TGGGGTATTTCG
*
3223155 GTCATCTTACCTTATGGGAGTA-TTCG
1 GTCATCTTACCCTATGGG-GTATTTCG
* *
3223181 ATCATCTTACCCTATGGGGTTATTTCT
1 GTCATCTTACCCTATGGGG-TATTTCG
* *
3223208 GTCTTTTTACCCTATGGGGTATTTCG
1 GTCATCTTACCCTATGGGGTATTTCG
*
3223234 GTCATCTTACCCTATGGGGGTATTTCA
1 GTCATCTTACCCTAT-GGGGTATTTCG
*
3223261 GTCATCTTACCCTAT-GGGCATTTCG
1 GTCATCTTACCCTATGGGGTATTTCG
3223286 GTCATCTTACCCTATGGGGGTATTT
1 GTCATCTTACCCTAT-GGGGTATTT
3223311 TGATCACCAT
Statistics
Matches: 256, Mismatches: 23, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
25 27 0.11
26 48 0.19
27 174 0.68
28 3 0.01
29 4 0.02
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (26 bp):
GTCATCTTACCCTATGGGGTATTTCG
Found at i:3223051 original size:81 final size:82
Alignment explanation
Indices: 3222966--3223136 Score: 177
Period size: 81 Copynumber: 2.1 Consensus size: 82
3222956 GGGCAAAATC
*
3222966 GTCATTTTAACACATA-AGGGCAAAAT-AGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTA
1 GTCATTTTAAC-CATATAGGGCAAAATCAGTCATTGTACCCTATAGGGGTATTTCGGTCATTTTA
*
3223029 CCCTATAGGGGTATTTCA
65 CCCTATAGGGATATTTCA
* * * ** ** * *
3223047 GTCATCTT-ACCCTATGGGGGTATTTCGGTCATTGTACCCTATGGGGGTATTTCGGTCATTTTAC
1 GTCATTTTAACCATATAGGGCAAAATCAGTCATTGTACCCTATAGGGGTATTTCGGTCATTTTAC
* * **
3223111 CCTCTATGGATATTTTG
66 CCTATAGGGATATTTCA
3223128 GTCATTTTA
1 GTCATTTTA
3223137 CCCTATTGGG
Statistics
Matches: 71, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
79 3 0.04
80 7 0.10
81 61 0.86
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (82 bp):
GTCATTTTAACCATATAGGGCAAAATCAGTCATTGTACCCTATAGGGGTATTTCGGTCATTTTAC
CCTATAGGGATATTTCA
Found at i:3225550 original size:17 final size:16
Alignment explanation
Indices: 3225530--3225561 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3225520 CTTCAAAGAC
3225530 ATTAAAAATACAAAAAA
1 ATTAAAAATA-AAAAAA
3225547 ATTAAAAATAAAAAA
1 ATTAAAAATAAAAAA
3225562 CGGGGTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
ATTAAAAATAAAAAAA
Found at i:3229562 original size:26 final size:26
Alignment explanation
Indices: 3229533--3229672 Score: 102
Period size: 27 Copynumber: 5.3 Consensus size: 26
3229523 ATCCCTATTT
* *
3229533 AAAATACTTTAGTTTACCAAATTACC
1 AAAATACATTAGTTTACAAAATTACC
*
3229559 AAAATACCATTGGTTTACAAAATTACC
1 AAAATA-CATTAGTTTACAAAATTACC
** ** *
3229586 AAAATACCCT-GTTTTGTAAAATTACT
1 AAAATACATTAG-TTTACAAAATTACC
* * *
3229612 AAAATACCCTTGGTTTATAAAATTACC
1 AAAATA-CATTAGTTTACAAAATTACC
** **
3229639 AAAATACCCCTAGTTTGTAAAATTACC
1 AAAATA-CATTAGTTTACAAAATTACC
3229666 AAAATAC
1 AAAATAC
3229673 CCCTGATTTG
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
25 1 0.01
26 26 0.27
27 68 0.71
28 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (26 bp):
AAAATACATTAGTTTACAAAATTACC
Found at i:3229582 original size:27 final size:27
Alignment explanation
Indices: 3229551--3229701 Score: 178
Period size: 27 Copynumber: 5.6 Consensus size: 27
3229541 TTAGTTTACC
** *
3229551 AAATTACCAAAATACCATTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
3229578 AAATTACCAAAATA-CCCTGTTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
3229604 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
3229631 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* * *
3229658 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTATA
*
3229685 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
3229702 TCAACCTGTA
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
26 20 0.19
27 86 0.81
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTATA
Found at i:3229608 original size:53 final size:54
Alignment explanation
Indices: 3229551--3229673 Score: 196
Period size: 53 Copynumber: 2.3 Consensus size: 54
3229541 TTAGTTTACC
3229551 AAATTACCAAAATACCATTGGTTTACAAAATTACCAAAATA-CCCT-GTTTTGTA
1 AAATTACCAAAATACCATTGGTTTACAAAATTACCAAAATACCCCTAG-TTTGTA
* * *
3229604 AAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCATTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTA
3229658 AAATTACCAAAATACC
1 AAATTACCAAAATACC
3229674 CCTGATTTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
53 38 0.59
54 25 0.39
55 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCATTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTA
Found at i:3229715 original size:27 final size:27
Alignment explanation
Indices: 3229577--3229756 Score: 168
Period size: 27 Copynumber: 6.7 Consensus size: 27
3229567 ATTGGTTTAC
* *
3229577 AAAATTACCAAAATACCCT-GTTTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* * *
3229603 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACTAAAATACCCTCGATTTGT
* *
3229630 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACTAAAATACCCTCGA-TTTGT
*
3229657 AAAATTACCAAAATACCC-CTGATTTGT
1 AAAATTACTAAAATACCCTC-GATTTGT
* * **
3229684 GAAATTACTAAAATACCCTCAACCTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* *
3229711 AAAATTATTAAAATACCCTCGACTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* * *
3229738 GAAATTACGAAAGTACCCT
1 AAAATTACTAAAATACCCT
3229757 TGATGTACAG
Statistics
Matches: 128, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
26 18 0.14
27 108 0.84
28 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTCGATTTGT
Found at i:3229743 original size:81 final size:81
Alignment explanation
Indices: 3229577--3229760 Score: 201
Period size: 81 Copynumber: 2.3 Consensus size: 81
3229567 ATTGGTTTAC
* *****
3229577 AAAATTACCAAAATA-CCCTGTTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAA
1 AAAATTACCAAAATACCCCTGATTTGTAAAATTACTAAAATACCCTCAACCTATAAAATTACCAA
* *
3229641 AATACCCCTAGTTTGT
66 AATACCCCGAGCTTGT
* * **
3229657 AAAATTACCAAAATACCCCTGATTTGTGAAATTACTAAAATACCCTCAACCTGTAAAATTATTAA
1 AAAATTACCAAAATACCCCTGATTTGTAAAATTACTAAAATACCCTCAACCTATAAAATTACCAA
3229722 AATACCCTCGA-CTTGT
66 AATACCC-CGAGCTTGT
* * * *
3229738 GAAATTACGAAAGTACCCTTGAT
1 AAAATTACCAAAATACCCCTGAT
3229761 GTACAGAATT
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
80 15 0.17
81 69 0.80
82 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (81 bp):
AAAATTACCAAAATACCCCTGATTTGTAAAATTACTAAAATACCCTCAACCTATAAAATTACCAA
AATACCCCGAGCTTGT
Found at i:3229843 original size:35 final size:35
Alignment explanation
Indices: 3229762--3229834 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
3229752 ACCCTTGATG
* *
3229762 TACAGAATTACCGTTTTACCCTCGATTTACAAAAT
1 TACAAAATTACCATTTTACCCTCGATTTACAAAAT
* *
3229797 TACAAAATTACCATTTTACCCTTGATTTATAAAAT
1 TACAAAATTACCATTTTACCCTCGATTTACAAAAT
3229832 TAC
1 TAC
3229835 CATTTTACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (35 bp):
TACAAAATTACCATTTTACCCTCGATTTACAAAAT
Found at i:3230230 original size:27 final size:26
Alignment explanation
Indices: 3230190--3230249 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
3230180 GCATATATAT
* *
3230190 ATATCTATTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
3230216 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
3230243 ATATCTG
1 ATATCTG
3230250 GCAGCCTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:3230377 original size:6 final size:6
Alignment explanation
Indices: 3230368--3230440 Score: 78
Period size: 6 Copynumber: 11.8 Consensus size: 6
3230358 TTGCATTCAC
* *
3230368 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TCACCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
3230418 ATTCTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCT
3230441 CATTTTCATT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
5 3 0.05
6 46 0.81
7 6 0.11
8 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:3230405 original size:25 final size:25
Alignment explanation
Indices: 3230371--3230435 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
3230361 CATTCACATT
*
3230371 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTCACCTGATA
*
3230396 CTGATTCTGATTCTGTCACCTGATT
1 CTGATTCTGATTCTGTCACCTGATA
3230421 CTGATTCTGATTCTG
1 CTGATTCTGATTCTG
3230436 ATTCTCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.45
Consensus pattern (25 bp):
CTGATTCTGATTCTGTCACCTGATA
Found at i:3230406 original size:31 final size:28
Alignment explanation
Indices: 3230368--3230440 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 28
3230358 TTGCATTCAC
3230368 ATTCTGATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTC---TACCTGATACTG
*
3230399 ATTCTGATTCTG--TC-ACCTGATTCTG
1 ATTCTGATTCTGATTCTACCTGATACTG
3230424 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
3230441 CATTTTCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 22 0.58
27 2 0.05
29 2 0.05
31 12 0.32
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.47
Consensus pattern (28 bp):
ATTCTGATTCTGATTCTACCTGATACTG
Found at i:3233039 original size:23 final size:23
Alignment explanation
Indices: 3232986--3233039 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
3232976 AAAAGAACAA
* *
3232986 AAAGAAAAAATAGCTAAAAAAAG
1 AAAGAAAAAAGAGCGAAAAAAAG
* * *
3233009 AAAGGAAAAAAGAGGGAAAAGAAT
1 AAA-GAAAAAAGAGCGAAAAAAAG
3233033 AAAGAAA
1 AAAGAAA
3233040 GTGAAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.06
Consensus pattern (23 bp):
AAAGAAAAAAGAGCGAAAAAAAG
Found at i:3233064 original size:28 final size:28
Alignment explanation
Indices: 3233003--3233069 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
3232993 AAATAGCTAA
*
3233003 AAAAAGAAAG-GAAAAAAGAGGGAAAAG
1 AAAAAGAAAGTGAAAAAAGAGAGAAAAG
*
3233030 AATAAAGAAAGTGAAAAAA-ATGAGAGAAG
1 AA-AAAGAAAGTGAAAAAAGA-GAGAAAAG
3233059 AAAAAGAAAGT
1 AAAAAGAAAGT
3233070 AAAGATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 2 0.06
28 18 0.51
29 15 0.43
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (28 bp):
AAAAAGAAAGTGAAAAAAGAGAGAAAAG
Found at i:3241512 original size:22 final size:22
Alignment explanation
Indices: 3241477--3241530 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
3241467 CGGCCTCTAG
* **
3241477 CACGAGCATG-TCCTAGGGTCA
1 CACGAGCGTGTTCCTAGGACCA
* *
3241498 CACGGGCGTGTTCCTTGGACCA
1 CACGAGCGTGTTCCTAGGACCA
3241520 CACGAGCGTGT
1 CACGAGCGTGT
3241531 GAGCTCCGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.20
Consensus pattern (22 bp):
CACGAGCGTGTTCCTAGGACCA
Found at i:3246020 original size:38 final size:38
Alignment explanation
Indices: 3245969--3246045 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
3245959 TGATGTTTTT
3245969 GGTATTTGAAATATCTAATTTTCCTTCATTTGCCATCA
1 GGTATTTGAAATATCTAATTTTCCTTCATTTGCCATCA
3246007 GGTATTTGAAATATCTAATTTTCCTTCATTTGCCATCA
1 GGTATTTGAAATATCTAATTTTCCTTCATTTGCCATCA
3246045 G
1 G
3246046 CTTCTGCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (38 bp):
GGTATTTGAAATATCTAATTTTCCTTCATTTGCCATCA
Done.