Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 10 of 199
Found at i:3244833 original size:3 final size:3
Alignment explanation
Indices: 3244825--3244885 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
3244815 TAAGTGAGTA
3244825 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3244873 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
3244886 CAAGGTTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3245740 original size:6 final size:6
Alignment explanation
Indices: 3245729--3245766 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
3245719 TAACAAAGAT
3245729 AAATAA AAATAA AAATAA AAATAA AGCAA-AA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A--AATAA AAATAA A
3245767 GAGAGACTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 2 0.07
6 22 0.76
7 3 0.10
8 2 0.07
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (6 bp):
AAATAA
Found at i:3245752 original size:18 final size:18
Alignment explanation
Indices: 3245729--3245766 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3245719 TAACAAAGAT
3245729 AAATAAA-AATAAAAATAA
1 AAATAAACAA-AAAAATAA
3245747 AAATAAAGCAAAAAAATAA
1 AAATAAA-CAAAAAAATAA
3245766 A
1 A
3245767 GAGAGACTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 9 0.50
20 2 0.11
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (18 bp):
AAATAAACAAAAAAATAA
Found at i:3246515 original size:5 final size:5
Alignment explanation
Indices: 3246507--3246535 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3246497 ATAAAATAAA
3246507 ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
3246536 ATAGAGACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:3246935 original size:29 final size:29
Alignment explanation
Indices: 3246875--3246938 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3246865 AATTTTTCAT
* * * *
3246875 ATTTTCTAAAATTTTAAAATATTTTTTGA
1 ATTTTATAAAATTTAAAAATATTATATGA
3246904 ATTTTATAAAACTTTAAAAATATTATAT-A
1 ATTTTATAAAA-TTTAAAAATATTATATGA
3246933 ATTTTA
1 ATTTTA
3246939 GGAAATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (29 bp):
ATTTTATAAAATTTAAAAATATTATATGA
Found at i:3247136 original size:16 final size:17
Alignment explanation
Indices: 3247099--3247138 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3247089 TTCAACTTGT
*
3247099 TTAATTTAAATTTTAAA
1 TTAATTTAAATCTTAAA
*
3247116 ATAATTTAAA-CTTAAA
1 TTAATTTAAATCTTAAA
3247132 TTAATTT
1 TTAATTT
3247139 TACCTCAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTTAAATCTTAAA
Found at i:3249680 original size:21 final size:21
Alignment explanation
Indices: 3249654--3249855 Score: 232
Period size: 21 Copynumber: 9.7 Consensus size: 21
3249644 CCTAAATCAC
* *
3249654 CACCACTACCACCGGTCCACT
1 CACCACCACCACCCGTCCACT
*
3249675 CCCCACC-CCACCACGTCGCACT
1 CACCACCACCACC-CGTC-CACT
*
3249697 C-CCACC-CCACCACGTGCACT
1 CACCACCACCACC-CGTCCACT
3249717 CACCACC-CCACCCGTCCACT
1 CACCACCACCACCCGTCCACT
* *
3249737 CACCACCCCCACCCGTCTACT
1 CACCACCACCACCCGTCCACT
* *
3249758 CACCACCACCACCAGTGCACT
1 CACCACCACCACCCGTCCACT
*
3249779 CACCACCACCACCCGTCTACT
1 CACCACCACCACCCGTCCACT
* *
3249800 CCCCACCACCACCCGTCTACT
1 CACCACCACCACCCGTCCACT
* *
3249821 CCCCACCACCACCCGTCTACT
1 CACCACCACCACCCGTCCACT
3249842 CACCACCACCACCC
1 CACCACCACCACCC
3249856 CCACCCGTCC
Statistics
Matches: 162, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
20 24 0.15
21 133 0.82
22 5 0.03
ACGTcount: A:0.22, C:0.60, G:0.06, T:0.11
Consensus pattern (21 bp):
CACCACCACCACCCGTCCACT
Found at i:3249794 original size:63 final size:62
Alignment explanation
Indices: 3249654--3249855 Score: 259
Period size: 63 Copynumber: 3.2 Consensus size: 62
3249644 CCTAAATCAC
* * *
3249654 CACCACTACCACCGGTCCACTCCCCA-CCCCACCACGTCGCACTCCCACC-CCACCACGTGCACT
1 CACCACCACCACCCGTCCACTCCCCACCCCCACC-CGTC-TACTCCCACCACCACCA-GTGCACT
*
3249717 CACCACC-CCACCCGTCCACTCACCACCCCCACCCGTCTACTCACCACCACCACCAGTGCACT
1 CACCACCACCACCCGTCCACTCCCCACCCCCACCCGTCTACTC-CCACCACCACCAGTGCACT
* * *
3249779 CACCACCACCACCCGTCTACTCCCCACCACCACCCGTCTACTCCCCACCACCACCCGT-CTACT
1 CACCACCACCACCCGTCCACTCCCCACCCCCACCCGTCTACT-CCCACCACCACCAGTGC-ACT
3249842 CACCACCACCACCC
1 CACCACCACCACCC
3249856 CCACCCGTCC
Statistics
Matches: 125, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
61 4 0.03
62 40 0.32
63 80 0.64
64 1 0.01
ACGTcount: A:0.22, C:0.60, G:0.06, T:0.11
Consensus pattern (62 bp):
CACCACCACCACCCGTCCACTCCCCACCCCCACCCGTCTACTCCCACCACCACCAGTGCACT
Found at i:3249874 original size:21 final size:21
Alignment explanation
Indices: 3249656--3249881 Score: 217
Period size: 21 Copynumber: 10.5 Consensus size: 21
3249646 TAAATCACCA
* *
3249656 CCACTACCACCGGTCCACTCC
1 CCACCACCACCCGTCCACTCC
3249677 CCACC-CCACCACGTCGCACT-C
1 CCACCACCACC-CGTC-CACTCC
* *
3249698 CCACC-CCACCACGTGCACTCA
1 CCACCACCACC-CGTCCACTCC
*
3249719 CCACC-CCACCCGTCCACTCA
1 CCACCACCACCCGTCCACTCC
* * *
3249739 CCACCCCCACCCGTCTACTCA
1 CCACCACCACCCGTCCACTCC
* * *
3249760 CCACCACCACCAGTGCACTCA
1 CCACCACCACCCGTCCACTCC
*
3249781 CCACCACCACCCGTCTACTCC
1 CCACCACCACCCGTCCACTCC
*
3249802 CCACCACCACCCGTCTACTCC
1 CCACCACCACCCGTCCACTCC
*
3249823 CCACCACCACCCGTCTACTCACC
1 CCACCACCACCCGTCCACT--CC
3249846 ACCACCACCCCCACCCGTCCACTCC
1 -CCACCA---CCACCCGTCCACTCC
3249871 CCACCACCACC
1 CCACCACCACC
3249882 ACCAGCAGTA
Statistics
Matches: 180, Mismatches: 15, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.13
21 125 0.69
22 4 0.02
23 2 0.01
24 12 0.07
25 2 0.01
27 12 0.07
ACGTcount: A:0.21, C:0.62, G:0.06, T:0.11
Consensus pattern (21 bp):
CCACCACCACCCGTCCACTCC
Found at i:3249898 original size:27 final size:27
Alignment explanation
Indices: 3249823--3249909 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
3249813 CGTCTACTCC
* *
3249823 CCACCACCACCCGT-CTACTCACCACCA
1 CCACCACCACCAGTAC-ACTCCCCACCA
* * *
3249850 CCACCCCCACCCGTCCACTCCCCACCA
1 CCACCACCACCAGTACACTCCCCACCA
* * *
3249877 CCACCACCAGCAGTACAGTCCCCACCC
1 CCACCACCACCAGTACACTCCCCACCA
3249904 CCACCA
1 CCACCA
3249910 GTACAATCTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 50 0.98
28 1 0.02
ACGTcount: A:0.24, C:0.62, G:0.06, T:0.08
Consensus pattern (27 bp):
CCACCACCACCAGTACACTCCCCACCA
Found at i:3249901 original size:21 final size:21
Alignment explanation
Indices: 3249877--3249928 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
3249867 CTCCCCACCA
* *
3249877 CCACCACCAGCAGTACAGTCC
1 CCACCACCACCAGTACAATCC
* *
3249898 CCACCCCCACCAGTACAATCT
1 CCACCACCACCAGTACAATCC
*
3249919 CCACCTCCAC
1 CCACCACCAC
3249929 GAACTCCATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.54, G:0.08, T:0.12
Consensus pattern (21 bp):
CCACCACCACCAGTACAATCC
Found at i:3253350 original size:21 final size:20
Alignment explanation
Indices: 3253320--3253415 Score: 84
Period size: 21 Copynumber: 4.6 Consensus size: 20
3253310 AGCACCGGTT
*
3253320 CCACCTCCACCAGTCCCTTCC
1 CCACCACCACCAGTCCC-TCC
* * *
3253341 CTACCACCACCCGTCCAATCC
1 CCACCACCACCAGTCC-CTCC
*
3253362 CCACCACCACCTGTGCCCTCC
1 CCACCACCACCAGT-CCCTCC
* * *
3253383 CCACCCCCACCCGTCCACTCA
1 CCACCACCACCAGTCC-CTCC
3253404 CCACCACCACCA
1 CCACCACCACCA
3253416 CCGGTTCCTT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.20, C:0.62, G:0.05, T:0.12
Consensus pattern (20 bp):
CCACCACCACCAGTCCCTCC
Found at i:3253366 original size:42 final size:41
Alignment explanation
Indices: 3253320--3253415 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 41
3253310 AGCACCGGTT
*
3253320 CCACCTCCACCAGTCCCTTCCCTACCACCACCCGTCCAATCC
1 CCACCACCACCAGTCCCTTCCC-ACCACCACCCGTCCAATCC
* * * * *
3253362 CCACCACCACCTGTGCCCTCCCCACCCCCACCCGTCCACTCA
1 CCACCACCACCAGT-CCCTTCCCACCACCACCCGTCCAATCC
3253404 CCACCACCACCA
1 CCACCACCACCA
3253416 CCGGTTCCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
42 39 0.85
43 7 0.15
ACGTcount: A:0.20, C:0.62, G:0.05, T:0.12
Consensus pattern (41 bp):
CCACCACCACCAGTCCCTTCCCACCACCACCCGTCCAATCC
Found at i:3256376 original size:21 final size:21
Alignment explanation
Indices: 3256347--3256387 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3256337 AAGCCCGAAG
* *
3256347 GCTATACAGAAGCACATAAGT
1 GCTAAACAGAAACACATAAGT
*
3256368 GCTAAACAGAAACTCATAAG
1 GCTAAACAGAAACACATAAG
3256388 GGTTGAATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:3257822 original size:50 final size:50
Alignment explanation
Indices: 3257708--3257950 Score: 378
Period size: 50 Copynumber: 4.8 Consensus size: 50
3257698 GATAATAACA
* * **
3257708 TGCCAAAGCCATGTCTCAGACATGGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
3257759 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
3257809 TGCCAACGCCATGTACCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
3257859 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
3257909 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
3257951 TTACCCAAAT
Statistics
Matches: 176, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 144 0.82
51 32 0.18
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:3259230 original size:42 final size:41
Alignment explanation
Indices: 3259162--3259248 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
3259152 TTACAGAATG
* *
3259162 AAAACTCATAAGAGCTGTACGAAAACCCATAAGGGTTAAAC
1 AAAACTCAAAAGAGCTGTACCAAAACCCATAAGGGTTAAAC
*
3259203 AAAAGCTCAAAAGAGCTG-ACCAGAAACCCATTAGGGTTAAAC
1 AAAA-CTCAAAAGAGCTGTACCA-AAACCCATAAGGGTTAAAC
3259245 AAAA
1 AAAA
3259249 ACTTATATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
41 7 0.17
42 34 0.83
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.15
Consensus pattern (41 bp):
AAAACTCAAAAGAGCTGTACCAAAACCCATAAGGGTTAAAC
Found at i:3261821 original size:13 final size:14
Alignment explanation
Indices: 3261782--3261827 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
3261772 ATGAGGGTAA
*
3261782 GATTTTATATATCT
1 GATTTTGTATATCT
*
3261796 -ATTTTGTACATCT
1 GATTTTGTATATCT
3261809 GATTTTG-ATATCT
1 GATTTTGTATATCT
3261822 GTATTT
1 G-ATTT
3261828 GTTAAGGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.57
Consensus pattern (14 bp):
GATTTTGTATATCT
Found at i:3267069 original size:29 final size:27
Alignment explanation
Indices: 3267008--3267069 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
3266998 TTGGTATCCG
*
3267008 AGTTTTTTCAATTTAACACTTGAGTTT
1 AGTTTTTTCAATTTAACACTTAAGTTT
**
3267035 TCTTTTGTCTCAATTTAACACTTAAGTTT
1 AGTTTT-T-TCAATTTAACACTTAAGTTT
3267064 AGTTTT
1 AGTTTT
3267070 AATATTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 4 0.14
28 1 0.04
29 23 0.82
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (27 bp):
AGTTTTTTCAATTTAACACTTAAGTTT
Found at i:3267175 original size:18 final size:18
Alignment explanation
Indices: 3267149--3267183 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3267139 CACATATCAA
* *
3267149 TTAAGTACCTAATTAAAC
1 TTAAATACCAAATTAAAC
3267167 TTAAATACCAAATTAAA
1 TTAAATACCAAATTAAA
3267184 TATTAAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (18 bp):
TTAAATACCAAATTAAAC
Found at i:3270400 original size:26 final size:26
Alignment explanation
Indices: 3270371--3270443 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
3270361 CCCGTTATGT
*
3270371 GGCTCTTCGTAAGCTTCCTGATTAAA
1 GGCTCTTCGTGAGCTTCCTGATTAAA
* *
3270397 GGCTCTTCGTGAGCTTTCTGATTAAT
1 GGCTCTTCGTGAGCTTCCTGATTAAA
* *
3270423 GGCACTCCG-GAGCTTCCTGAT
1 GGCTCTTCGTGAGCTTCCTGAT
3270444 ATGGCTCACT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
25 11 0.27
26 30 0.73
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCTGATTAAA
Found at i:3271441 original size:88 final size:88
Alignment explanation
Indices: 3271223--3271570 Score: 423
Period size: 88 Copynumber: 4.0 Consensus size: 88
3271213 TCGAAAGCAA
* * *
3271223 AGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTACCTTCCTA-CATGG
1 AGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCC-AGCATAG
* * **
3271287 ACAGCGAAGCAAATCGAA-AACAA
65 ACAGCGAAGCAGATCGAAGACCCC
* * *
3271310 AGCCTTGCCTCCATCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGATCTTGCCCTCCAGCATAAA
1 AGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCAGCATAGA
3271375 CAGCGAAGCAGATCGAAGACCCC
66 CAGCGAAGCAGATCGAAGACCCC
* ** * * * *
3271398 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAAATTGAAGATAGCATATCTTGCCTTCCTGCGTAGA
1 AGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCAGCATAGA
* *
3271463 CAGCGAAGTAGATCGAAGACACC
66 CAGCGAAGCAGATCGAAGACCCC
* * * * *
3271486 AGCCTCGCCTCCCTCGGTTGCAGTAGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGTACT-G
1 AGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCAGCA-TAG
* *
3271550 ACGGCAAAGCAGATCGAAGAC
65 ACAGCGAAGCAGATCGAAGAC
3271571 GGCAAATCTT
Statistics
Matches: 226, Mismatches: 32, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
86 1 0.00
87 74 0.33
88 150 0.66
89 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (88 bp):
AGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCAGCATAGA
CAGCGAAGCAGATCGAAGACCCC
Found at i:3271769 original size:44 final size:45
Alignment explanation
Indices: 3271704--3271795 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 45
3271694 GCATCAGGTT
* * *
3271704 TTATCTCCCTGAGGTTACAATGGAGCAGACTGAGAA-AGCAAGTC
1 TTATCCCCCTGAAGTTACAATGGAGCAGACTGAGAATAGCAAATC
* * *
3271748 TTATCCCCCTGAAGTTGCAATGGGGCAGATTGAGAATAGCAAATC
1 TTATCCCCCTGAAGTTACAATGGAGCAGACTGAGAATAGCAAATC
3271793 TTA
1 TTA
3271796 CTACCCAAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 31 0.76
45 10 0.24
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (45 bp):
TTATCCCCCTGAAGTTACAATGGAGCAGACTGAGAATAGCAAATC
Found at i:3272178 original size:13 final size:13
Alignment explanation
Indices: 3272160--3272186 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3272150 CAATAAAGTC
3272160 CAATTACAATGGG
1 CAATTACAATGGG
3272173 CAATTACAATGGG
1 CAATTACAATGGG
3272186 C
1 C
3272187 CAAATTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (13 bp):
CAATTACAATGGG
Found at i:3272767 original size:27 final size:27
Alignment explanation
Indices: 3272729--3272784 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
3272719 AGGGGGAAGG
3272729 GTTTAGAAACTTTACCTGGTTCGGCGT
1 GTTTAGAAACTTTACCTGGTTCGGCGT
*
3272756 GTTTAGAAACTTTACCTGGTTCGGTGT
1 GTTTAGAAACTTTACCTGGTTCGGCGT
3272783 GT
1 GT
3272785 CGCCGAATCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (27 bp):
GTTTAGAAACTTTACCTGGTTCGGCGT
Found at i:3275353 original size:2 final size:2
Alignment explanation
Indices: 3275346--3275375 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3275336 TTGATACAAG
3275346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3275376 GGGGTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3286446 original size:14 final size:13
Alignment explanation
Indices: 3286422--3286471 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
3286412 ATTTGAAAGA
*
3286422 TTAAAAAAATTAT
1 TTAAGAAAATTAT
3286435 TTATAGAAAATT-T
1 TTA-AGAAAATTAT
3286448 TTAAAGAACAATTAT
1 TT-AAGAA-AATTAT
3286463 TTAAGAAAA
1 TTAAGAAAA
3286472 GAACATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 12 0.38
14 17 0.53
15 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (13 bp):
TTAAGAAAATTAT
Found at i:3289935 original size:23 final size:23
Alignment explanation
Indices: 3289879--3289935 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
3289869 AATAGAAAAC
3289879 ATAAATTAATTTTAAAAAATAAA
1 ATAAATTAATTTTAAAAAATAAA
* *
3289902 ATATATTTAATTTT-AAAACTAAA
1 ATA-AATTAATTTTAAAAAATAAA
3289925 ATAAATGTAAT
1 ATAAAT-TAAT
3289936 CAAAATTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 2 0.07
23 18 0.62
24 9 0.31
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
ATAAATTAATTTTAAAAAATAAA
Found at i:3294684 original size:218 final size:212
Alignment explanation
Indices: 3294354--3294760 Score: 597
Period size: 218 Copynumber: 1.9 Consensus size: 212
3294344 TTCAAAAGAT
* * *
3294354 GGGAGCTTCTAAAGTCCACTAAGGAAATGTTTTATCATTTTGGTCTTGAGAAATCAACCCCTTAA
1 GGGAGCGTCTAAAGTCCACCAAGGAAATGTTTTATCATTTTGGTCTTGAGAAACCAACCCCTTAA
* *
3294419 GCGGTTTTAATGGGTAAGAACACTACCCCTTAGGGAGAAATTGTCTTTCTTATTGAGAGAAGCCT
66 GCGGTTTTAATGGGTAAGAACACTACCCCTTAGGGAGAAACTGTCTTTCTTATTGAAAGAAGCCT
*
3294484 TTGAAGTG-TGTCT-TTTAAGTAAGCAATTCAAACCTCAAACAGTTGGTATGAGGAGAGCCAAAA
131 TTGAAGTGTTGT-TATTTAAGTAAGCAATTCAAACCTCAAACAGTTGGTATGAGAAGAGCCAAAA
3294547 GGATTCATGGAGCTTATC
195 GGATTCATGGAGCTTATC
*
3294565 GGGAGCGTCTAAGGTCCACCAAGGAAATGTTTTATCATTTTGGTCTTGATGGGATTCGAACCAAC
1 GGGAGCGTCTAAAGTCCACCAAGGAAATGTTTTATCATTTTGGTCTTGA---GA----AACCAAC
* *
3294630 TCCTTAAGCGGTTTTAATGGGTAAGAACACTA-CCCTGTAAGGG-GGAACTGTCTTTCTTATTGA
59 CCCTTAAGCGGTTTTAATGGGTAAGAACACTACCCCT-T-AGGGAGAAACTGTCTTTCTTATTGA
* *
3294693 AAGAAGCCTTTGAAGTGTTGTTATTTGAGTAGGCAATTCAAACCTCAAACAGTTGGTATGAGAAG
122 AAGAAGCCTTTGAAGTGTTGTTATTTAAGTAAGCAATTCAAACCTCAAACAGTTGGTATGAGAAG
3294758 AGC
187 AGC
3294761 TCAATGAATT
Statistics
Matches: 174, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
211 46 0.26
214 2 0.01
217 4 0.02
218 73 0.42
219 49 0.28
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (212 bp):
GGGAGCGTCTAAAGTCCACCAAGGAAATGTTTTATCATTTTGGTCTTGAGAAACCAACCCCTTAA
GCGGTTTTAATGGGTAAGAACACTACCCCTTAGGGAGAAACTGTCTTTCTTATTGAAAGAAGCCT
TTGAAGTGTTGTTATTTAAGTAAGCAATTCAAACCTCAAACAGTTGGTATGAGAAGAGCCAAAAG
GATTCATGGAGCTTATC
Found at i:3304084 original size:2 final size:2
Alignment explanation
Indices: 3304077--3304107 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3304067 ACTTGGTATT
3304077 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3304108 TTTGACCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3308161 original size:37 final size:37
Alignment explanation
Indices: 3308109--3308200 Score: 130
Period size: 37 Copynumber: 2.5 Consensus size: 37
3308099 ACATCATCAC
** *
3308109 TTTCATAGATGATTGTATTTGGAAGACATGGAGCTAT
1 TTTCATAGATGATTGTATTCAGAAGACAAGGAGCTAT
* * *
3308146 TTTCATAGATCATTGTAGTCAGAAGACAAGGATCTAT
1 TTTCATAGATGATTGTATTCAGAAGACAAGGAGCTAT
3308183 TTTCATAGATGATTGTAT
1 TTTCATAGATGATTGTAT
3308201 CAACCCTAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.38
Consensus pattern (37 bp):
TTTCATAGATGATTGTATTCAGAAGACAAGGAGCTAT
Found at i:3313572 original size:20 final size:19
Alignment explanation
Indices: 3313547--3313592 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3313537 AATTTATATT
* *
3313547 TAAAAAAATATTAATTACTA
1 TAAAAAAATATT-AGTACGA
*
3313567 TAAAAAATTATTAGTACGA
1 TAAAAAAATATTAGTACGA
3313586 TAAAAAA
1 TAAAAAA
3313593 TCTAAATAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (19 bp):
TAAAAAAATATTAGTACGA
Found at i:3314158 original size:18 final size:20
Alignment explanation
Indices: 3314119--3314163 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
3314109 AAAATTTATA
3314119 ATATT-TTTTTATAAATAAAT
1 ATATTATTTTTATAAAT-AAT
3314139 ATATTATTTTTAT-AAT-AT
1 ATATTATTTTTATAAATAAT
3314157 ATATTAT
1 ATATTAT
3314164 GGACTCGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
20 8 0.33
21 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTATTTTTATAAATAAT
Found at i:3317645 original size:20 final size:20
Alignment explanation
Indices: 3317617--3317656 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3317607 AAAAATTCAG
*
3317617 AAAATATAAAAATTATTAAA
1 AAAACATAAAAATTATTAAA
3317637 AAAACATAAAAATTATTAAA
1 AAAACATAAAAATTATTAAA
3317657 TATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAACATAAAAATTATTAAA
Found at i:3325036 original size:16 final size:16
Alignment explanation
Indices: 3325015--3325045 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3325005 ACCATTAAAC
3325015 CATAACTTCATATACA
1 CATAACTTCATATACA
*
3325031 CATAACTTTATATAC
1 CATAACTTCATATAC
3325046 CAAATTTGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (16 bp):
CATAACTTCATATACA
Found at i:3325896 original size:42 final size:42
Alignment explanation
Indices: 3325815--3325998 Score: 190
Period size: 42 Copynumber: 4.3 Consensus size: 42
3325805 AAGACGAATA
* * * * *
3325815 AATTATACTGGCATGCGTAGTGCATCATCGAATAAACCAAAGC
1 AATTATACTAGCACGC-AAGTGCATCATCGGATATACCAAAGC
* * * *
3325858 AATTATGCTAGCACGTAAGTGCATCAAT-GGATGTACCAAAGA
1 AATTATACTAGCACGCAAGTGCATC-ATCGGATATACCAAAGC
* * * *
3325900 AAATATATTTGCACGCAAGTGCATCATCGGATATACCGAAGC
1 AATTATACTAGCACGCAAGTGCATCATCGGATATACCAAAGC
* *
3325942 AATTATACTAGCACACACAATGCATCATCGGATATACCAAAGC
1 AATTATACTAGCACGCA-AGTGCATCATCGGATATACCAAAGC
*
3325985 AATTATACTGGCAC
1 AATTATACTAGCAC
3325999 ACACGGTGCA
Statistics
Matches: 114, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
41 2 0.02
42 62 0.54
43 50 0.44
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (42 bp):
AATTATACTAGCACGCAAGTGCATCATCGGATATACCAAAGC
Found at i:3325999 original size:43 final size:42
Alignment explanation
Indices: 3325833--3326020 Score: 189
Period size: 42 Copynumber: 4.4 Consensus size: 42
3325823 TGGCATGCGT
* * * **
3325833 AGTGCATCATCGAATAAACCAAAGCAATTATGCTAGCACGTA
1 AGTGCATCATCGGATATACCAAAGCAATTATACTAGCACACA
* * * * * *
3325875 AGTGCATCAAT-GGATGTACCAAAGAAAATATATTTGCACGCA
1 AGTGCATC-ATCGGATATACCAAAGCAATTATACTAGCACACA
*
3325917 AGTGCATCATCGGATATACCGAAGCAATTATACTAGCACACA
1 AGTGCATCATCGGATATACCAAAGCAATTATACTAGCACACA
* *
3325959 CAATGCATCATCGGATATACCAAAGCAATTATACTGGCACACA
1 -AGTGCATCATCGGATATACCAAAGCAATTATACTAGCACACA
* * *
3326002 CGGTGCAACATCAGATATA
1 -AGTGCATCATCGGATATA
3326021 TCGAAGTATA
Statistics
Matches: 120, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
41 2 0.02
42 62 0.52
43 56 0.47
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (42 bp):
AGTGCATCATCGGATATACCAAAGCAATTATACTAGCACACA
Found at i:3326461 original size:35 final size:35
Alignment explanation
Indices: 3326415--3326484 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3326405 CGGGTCAATG
3326415 TTAGCCACGAATAATCACAAAACATATAGTACTAT
1 TTAGCCACGAATAATCACAAAACATATAGTACTAT
3326450 TTAGCCACGAATAATCACAAAACATATAGTACTAT
1 TTAGCCACGAATAATCACAAAACATATAGTACTAT
3326485 CAATTTCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (35 bp):
TTAGCCACGAATAATCACAAAACATATAGTACTAT
Found at i:3329727 original size:84 final size:84
Alignment explanation
Indices: 3329627--3329945 Score: 584
Period size: 84 Copynumber: 3.8 Consensus size: 84
3329617 AGGATCCCGG
*
3329627 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCGACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
3329692 TTCACAATCAAGGATACGA
66 TTCACAATCAAGGATACGA
3329711 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
3329776 TTCACAATCAAGGATACGA
66 TTCACAATCAAGGATACGA
* *
3329795 CGGAATCAGCACTTAGCAACCACCTTATAATCAACGATACGGGGAATCAGCACATAGCAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
*
3329860 TTCACAATCAAGGATACGG
66 TTCACAATCAAGGATACGA
* *
3329879 TGGAATCAACACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCTCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
3329944 TT
66 TT
3329946 TTGATCAATG
Statistics
Matches: 227, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 227 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (84 bp):
TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
TTCACAATCAAGGATACGA
Found at i:3329769 original size:41 final size:41
Alignment explanation
Indices: 3329579--3329986 Score: 428
Period size: 41 Copynumber: 9.7 Consensus size: 41
3329569 CAACCGTTAC
* **
3329579 ACGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGAT
1 ACGG-GGAATCAGCACTTAGCAACCACCTTATAATC-AAGGAT
* *
3329622 CCCGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 -ACGG-GGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
* * *
3329665 ACGGGGAATCAGCACATAGCGACC-CCTTTCACAATCAAGGAT
1 ACGGGGAATCAGCACTTAGCAACCACC-TT-ATAATCAAGGAT
* *
3329707 ACGATGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 ACG-GGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
* *
3329749 ACGGGGAATCAGCACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGGGAATCAGCACTTAGCAACCACC-TT-ATAATCAAGGAT
* *
3329791 ACGACGGAATCAGCACTTAGCAACCACCTTATAATCAACGAT
1 ACG-GGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
* *
3329833 ACGGGGAATCAGCACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGGGAATCAGCACTTAGCAACCACC-TT-ATAATCAAGGAT
* *
3329875 ACGGTGGAATCAACACTTAGCAACCACCTTATAATCAATGAT
1 ACGG-GGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
* * * * * *
3329917 ACGGGGAATCAGCACATAGCAACCTCTTTTTGATCAATGAT
1 ACGGGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
** *
3329958 TTGGGGAATCTGCACTTAGCAACC-CCTTA
1 ACGGGGAATCAGCACTTAGCAACCACCTTA
3329987 CATTAAAAGA
Statistics
Matches: 309, Mismatches: 43, Indels: 28
0.81 0.11 0.07
Matches are distributed among these distances:
40 9 0.03
41 113 0.37
42 83 0.27
43 66 0.21
44 38 0.12
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (41 bp):
ACGGGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
Found at i:3331270 original size:21 final size:20
Alignment explanation
Indices: 3331235--3331276 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3331225 ATTGGATGTA
*
3331235 AATAAATTAATAATATTATT
1 AATAAATTAATAATAATATT
*
3331255 AATATATTAGATAATAATATT
1 AATAAATTA-ATAATAATATT
3331276 A
1 A
3331277 TTAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AATAAATTAATAATAATATT
Found at i:3334939 original size:25 final size:25
Alignment explanation
Indices: 3334891--3334949 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
3334881 TTTGGCTCTC
*
3334891 ACGAGCTTCCCGTTAAATGGTTCTT
1 ACGAGCTTCCCGTTAAATAGTTCTT
* *
3334916 ACGAGCTTCTCGTTAAATATTTCTT
1 ACGAGCTTCCCGTTAAATAGTTCTT
**
3334941 GTGAGCTTC
1 ACGAGCTTC
3334950 GGAGCATCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (25 bp):
ACGAGCTTCCCGTTAAATAGTTCTT
Found at i:3335051 original size:25 final size:26
Alignment explanation
Indices: 3335023--3335091 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 26
3335013 CCCGATATAT
3335023 GGCTTTTCGGAGCTTCCTGAT-TAAA
1 GGCTTTTCGGAGCTTCCTGATATAAA
* * **
3335048 GGCTCTCTCATGAGCTTCCTGATATTTA
1 GGCT-TTTC-GGAGCTTCCTGATATAAA
3335076 -GCTTTTCGGAGCTTCC
1 GGCTTTTCGGAGCTTCC
3335092 CGATGTTGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 12 0.34
26 6 0.17
27 15 0.43
28 2 0.06
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (26 bp):
GGCTTTTCGGAGCTTCCTGATATAAA
Found at i:3337014 original size:33 final size:32
Alignment explanation
Indices: 3336977--3337045 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
3336967 ATTTGTTATG
3336977 AAAATGAACATGTTATATGGAAATATGATAAGA
1 AAAATGAACATGTTATATGGAAATATGATAA-A
*
3337010 AAAATGTACATGTTATATGGAAATATGATAAA
1 AAAATGAACATGTTATATGGAAATATGATAAA
3337042 AAAA
1 AAAA
3337046 GTATATGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 5 0.14
33 30 0.86
ACGTcount: A:0.54, C:0.03, G:0.16, T:0.28
Consensus pattern (32 bp):
AAAATGAACATGTTATATGGAAATATGATAAA
Found at i:3340512 original size:36 final size:37
Alignment explanation
Indices: 3340433--3340556 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 37
3340423 ATCTTTTGGC
*
3340433 GATATAAAACGTAAGAG-GTGTGAAACCA-TTCATTGAT
1 GATATAAAATGTAAGAGAGTGT-AAACCACTT-ATTGAT
**** *
3340470 GATATAAAATGTAAGA-AGTGTAAATTGTTTGTTGAT
1 GATATAAAATGTAAGAGAGTGTAAACCACTTATTGAT
* *
3340506 GATATAAAATGGAA-AGAGTGTAAACCACTTATTGGT
1 GATATAAAATGTAAGAGAGTGTAAACCACTTATTGAT
3340542 GATATAAAATGTAAG
1 GATATAAAATGTAAG
3340557 CAACATATAT
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
35 1 0.01
36 48 0.69
37 21 0.30
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (37 bp):
GATATAAAATGTAAGAGAGTGTAAACCACTTATTGAT
Found at i:3348139 original size:33 final size:33
Alignment explanation
Indices: 3348102--3348205 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 33
3348092 TATATACATA
3348102 TGCATAAAATAATAATATTTAAGTGCAAGCAAC
1 TGCATAAAATAATAATATTTAAGTGCAAGCAAC
* * * ** * **
3348135 TGCATTACATGAA-AAAAAATAAATATATA-CATA-
1 TGCATAAAAT-AATAATATTTAAGTGCA-AGCA-AC
3348168 TGCATAAAATAATAATATTTAAGTGCAAGCAAC
1 TGCATAAAATAATAATATTTAAGTGCAAGCAAC
3348201 TGCAT
1 TGCAT
3348206 TACAATCGTG
Statistics
Matches: 49, Mismatches: 16, Indels: 12
0.64 0.21 0.16
Matches are distributed among these distances:
32 4 0.08
33 41 0.84
34 4 0.08
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.28
Consensus pattern (33 bp):
TGCATAAAATAATAATATTTAAGTGCAAGCAAC
Found at i:3348160 original size:66 final size:66
Alignment explanation
Indices: 3348081--3348209 Score: 258
Period size: 66 Copynumber: 2.0 Consensus size: 66
3348071 ATTAAATATG
3348081 AAAAAAATAAATATATACATATGCATAAAATAATAATATTTAAGTGCAAGCAACTGCATTACATG
1 AAAAAAATAAATATATACATATGCATAAAATAATAATATTTAAGTGCAAGCAACTGCATTACATG
3348146 A
66 A
3348147 AAAAAAATAAATATATACATATGCATAAAATAATAATATTTAAGTGCAAGCAACTGCATTACA
1 AAAAAAATAAATATATACATATGCATAAAATAATAATATTTAAGTGCAAGCAACTGCATTACA
3348210 ATCGTGATAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.53, C:0.11, G:0.09, T:0.27
Consensus pattern (66 bp):
AAAAAAATAAATATATACATATGCATAAAATAATAATATTTAAGTGCAAGCAACTGCATTACATG
A
Found at i:3355265 original size:4 final size:4
Alignment explanation
Indices: 3355256--3355312 Score: 87
Period size: 4 Copynumber: 14.2 Consensus size: 4
3355246 GTGCCCCCGT
* * *
3355256 TACA TACA TACA TACC TACA TACA TACA TACG TACA TACA TACG TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
3355304 TACA TACA T
1 TACA TACA T
3355313 GCTACTCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.44, C:0.26, G:0.04, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:3357385 original size:2 final size:2
Alignment explanation
Indices: 3357380--3357409 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3357370 AAAAAAAAAA
3357380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3357410 TCACGAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3357749 original size:17 final size:17
Alignment explanation
Indices: 3357727--3357769 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3357717 CTTTTCTTTC
3357727 TTTCTTTCCTTTTTCTT
1 TTTCTTTCCTTTTTCTT
*
3357744 TTTCTTTCGTTTTTCTT
1 TTTCTTTCCTTTTTCTT
3357761 TTTCTTTCC
1 TTTCTTTCC
3357770 GCTTTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTCTTTCCTTTTTCTT
Found at i:3357775 original size:17 final size:17
Alignment explanation
Indices: 3357727--3357775 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
3357717 CTTTTCTTTC
*
3357727 TTTCTTTCCTTTTTCTT
1 TTTCTTTCCGTTTTCTT
3357744 TTTCTTT-CGTTTTTCTT
1 TTTCTTTCCG-TTTTCTT
*
3357761 TTTCTTTCCGCTTTC
1 TTTCTTTCCGTTTTC
3357776 AAAATGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 25 0.89
18 2 0.07
ACGTcount: A:0.00, C:0.24, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTCTTTCCGTTTTCTT
Found at i:3359819 original size:3 final size:3
Alignment explanation
Indices: 3359811--3359837 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3359801 CCTCCTAAAC
3359811 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
3359838 ATTTTACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:3363034 original size:26 final size:27
Alignment explanation
Indices: 3363005--3363055 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3362995 ATGTTGTAAT
3363005 ATATAATATTA-AAAAATAAAAGAAGA
1 ATATAATATTATAAAAATAAAAGAAGA
* *
3363031 ATATCATATTATAAAATTAAAAGAA
1 ATATAATATTATAAAAATAAAAGAA
3363056 AGGATTGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (27 bp):
ATATAATATTATAAAAATAAAAGAAGA
Found at i:3364072 original size:125 final size:126
Alignment explanation
Indices: 3363729--3364081 Score: 478
Period size: 126 Copynumber: 2.8 Consensus size: 126
3363719 TAATTTCGAG
** * *
3363729 TTGACGTTTCTGATAAAATAATATAAAATCGCTTCTAGCAGGATGGTATTTGAGAAAAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
3363794 AAATCGCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
* * * * * *
3363855 TTCACGTTTCTGAGCAAATAGTATAAAATCGGTTCTAGCAGGACGCTATTTAAAAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * *
3363920 AAATTGCGGCCTTGT-CAGCGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATT-TTTTT
66 AAATCGCGCCCTTGTGGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
* * *
3363980 TTGATGTTTCTGAGCAAATAATATAAAATCACTTATA-CTAGGATGCTATTTGAGAAGAATTTGT
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGC-AGGATGCTATTTGAGAAGAATTTGT
* **
3364044 GAAATCGCGCCCTCGTGGACGCAATTTTGCTACAGTAG
65 GAAATCGCGCCCTTGTGGACGCGCTTTTGCTACAGTAG
3364082 CATGTTTGGG
Statistics
Matches: 194, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
124 1 0.01
125 89 0.46
126 104 0.54
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (126 bp):
TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
Found at i:3367296 original size:116 final size:116
Alignment explanation
Indices: 3367111--3367443 Score: 605
Period size: 116 Copynumber: 2.9 Consensus size: 116
3367101 TGATAAATTG
*
3367111 TATTAAGTCAAAAAATTGTATTAATGGTTAGT-AAATTATTAAATTATATACAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATACAATTATTAATTGT
* *
3367175 TAGTACCAGTTAAAACATTTTTCCAAATTTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
3367226 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATACAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATACAATTATTAATTGT
3367291 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
* * *
3367342 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATACAATTATTAATTGT
3367407 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
3367444 CGTTAAGGTT
Statistics
Matches: 211, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
115 32 0.15
116 179 0.85
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATACAATTATTAATTGT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
Found at i:3367479 original size:23 final size:23
Alignment explanation
Indices: 3367449--3367724 Score: 260
Period size: 23 Copynumber: 11.7 Consensus size: 23
3367439 CATTACGTTA
3367449 AGGTTAGGGTTTTTAATTGAATTAGGTT
1 AGGTTAGGGTTTTTAATT-AA--A--TT
3367477 AGGGTTAGGGTTTTTAATT-AA--
1 A-GGTTAGGGTTTTTAATTAAATT
*
3367498 GGGTTTAGGGTTTTTAATTGAATTAGGTT
1 AGG-TTAGGGTTTTTAATT-AA--A--TT
3367527 AAGGTTAGGGTTTTTAATTAAATT
1 -AGGTTAGGGTTTTTAATTAAATT
*
3367551 AGGCTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
* *
3367574 AGGTTAGAGTTTTTAATTTAA--
1 AGGTTAGGGTTTTTAATTAAATT
* *
3367595 GGGTTTAGGGTTTTTAATTGAATT
1 AGG-TTAGGGTTTTTAATTAAATT
3367619 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
* *
3367642 AGGCTAGGGTTTTTAATTTAA--
1 AGGTTAGGGTTTTTAATTAAATT
* * *
3367663 GGGTTTAGAGTTTTAAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
3367687 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
3367710 AGGCTAGGGTTTTTA
1 AGGTTAGGGTTTTTA
3367725 TTACATGTCA
Statistics
Matches: 209, Mismatches: 22, Indels: 39
0.77 0.08 0.14
Matches are distributed among these distances:
20 2 0.01
21 19 0.09
22 30 0.14
23 111 0.53
24 6 0.03
25 2 0.01
26 1 0.00
27 1 0.00
28 3 0.01
29 32 0.15
30 2 0.01
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (23 bp):
AGGTTAGGGTTTTTAATTAAATT
Found at i:3367482 original size:29 final size:29
Alignment explanation
Indices: 3367440--3367561 Score: 134
Period size: 29 Copynumber: 4.5 Consensus size: 29
3367430 CAAATCTAAC
* *
3367440 ATTACGTTAAGGTTAGGGTTTTTAATTGA
1 ATTAGGTTAGGGTTAGGGTTTTTAATTGA
3367469 ATTAGGTTAGGGTTAGGGTTTTTAATT--
1 ATTAGGTTAGGGTTAGGGTTTTTAATTGA
*
3367496 A--A-G---GGTTTAGGGTTTTTAATTGA
1 ATTAGGTTAGGGTTAGGGTTTTTAATTGA
* *
3367519 ATTAGGTTAAGGTTAGGGTTTTTAATTAA
1 ATTAGGTTAGGGTTAGGGTTTTTAATTGA
*
3367548 ATTAGGCTAGGGTT
1 ATTAGGTTAGGGTT
3367562 TTTAATTAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
21 17 0.22
23 1 0.01
24 1 0.01
25 2 0.03
26 1 0.01
27 1 0.01
29 54 0.70
ACGTcount: A:0.26, C:0.02, G:0.28, T:0.44
Consensus pattern (29 bp):
ATTAGGTTAGGGTTAGGGTTTTTAATTGA
Found at i:3367519 original size:50 final size:50
Alignment explanation
Indices: 3367452--3367629 Score: 235
Period size: 50 Copynumber: 3.6 Consensus size: 50
3367442 TACGTTAAGG
3367452 TTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGT
1 TTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGT
* *
3367502 TTAGGGTTTTTAATTGAATTAGGTTAAGGTTAGGGTTTTTAATTAAATTAGG-
1 TTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATT-AA--GGGT
* *
3367554 CTAGGGTTTTTAATT-AA--A--TTA-GGTTAGAGTTTTTAATTTAAGGGT
1 TTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAA-TTAAGGGT
3367599 TTAGGGTTTTTAATTGAATTAGGTTAGGGTT
1 TTAGGGTTTTTAATTGAATTAGGTTAGGGTT
3367630 TTTAATTAAA
Statistics
Matches: 111, Mismatches: 6, Indels: 21
0.80 0.04 0.15
Matches are distributed among these distances:
44 2 0.02
45 14 0.13
46 18 0.16
47 5 0.05
48 1 0.01
49 1 0.01
50 46 0.41
51 8 0.07
52 14 0.13
53 2 0.02
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.47
Consensus pattern (50 bp):
TTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGT
Found at i:3367609 original size:68 final size:68
Alignment explanation
Indices: 3367531--3367724 Score: 334
Period size: 68 Copynumber: 2.9 Consensus size: 68
3367521 TAGGTTAAGG
* * *
3367531 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTTAAG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTTAAG
3367596 GGT
66 GGT
*
3367599 TTAGGGTTTTTAATTGAATTAGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTTAAG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTTAAG
3367664 GGT
66 GGT
* *
3367667 TTAGAGTTTTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTA
3367725 TTACATGTCA
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 119 1.00
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.47
Consensus pattern (68 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTTAAG
GGT
Found at i:3367647 original size:91 final size:89
Alignment explanation
Indices: 3367479--3367724 Score: 307
Period size: 91 Copynumber: 2.7 Consensus size: 89
3367469 ATTAGGTTAG
*
3367479 GGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAAGGTTAGGGTTTTTA
1 GGTTAGAGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTG-A--A--TT-AGGTTAGGGTTTTTA
3367543 ATTAAATTAGGCTAGGGTTTTTAATTAAATTA
60 ATTAAATTAGGCTAGGGTTTTTAATTAAA--A
3367575 GGTTAGAGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTTTTAATTAAA
1 GGTTAGAGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTTTTAATTAAA
* *
3367640 TTAGGCTAGGGTTTTTAATTTAAG
66 TTAGGCTAGGGTTTTTAATTAAAA
* * * * *
3367664 GGTTTAGAGTTTTAAATTAAATTAGG-TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTA
1 GG-TTAGAGTTTTTAATTTAA--GGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTTTTA
3367725 TTACATGTCA
Statistics
Matches: 138, Mismatches: 8, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
89 2 0.01
90 16 0.12
91 76 0.55
92 4 0.03
94 1 0.01
96 15 0.11
97 24 0.17
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.46
Consensus pattern (89 bp):
GGTTAGAGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTTTTAATTAAA
TTAGGCTAGGGTTTTTAATTAAAA
Found at i:3368260 original size:18 final size:18
Alignment explanation
Indices: 3368237--3368271 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3368227 CGGAAAAGGA
*
3368237 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
3368255 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
3368272 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:3368934 original size:7 final size:7
Alignment explanation
Indices: 3368924--3368948 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3368914 ATACATACAT
3368924 AATACTA
1 AATACTA
3368931 AATACTA
1 AATACTA
3368938 AATACTA
1 AATACTA
3368945 AATA
1 AATA
3368949 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:3370207 original size:51 final size:51
Alignment explanation
Indices: 3370092--3370207 Score: 205
Period size: 51 Copynumber: 2.3 Consensus size: 51
3370082 TATTTTAAAA
* *
3370092 AAGGAAATTGAGAAGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
*
3370143 GAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
3370194 AAGGAAATTGAGAG
1 AAGGAAATTGAGAG
3370208 AATTTTGGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (51 bp):
AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
Found at i:3370231 original size:24 final size:22
Alignment explanation
Indices: 3370179--3370230 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
3370169 AAATATAGAT
3370179 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
3370201 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
3370223 TTGAGAGA
1 TTGAGAGA
3370231 GGATTTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:3370236 original size:24 final size:23
Alignment explanation
Indices: 3370179--3370236 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
3370169 AAATATAGAT
3370179 TTGAGAGA-ATTTTGGAAGGAAA
1 TTGAGAGAGATTTTGGAAGGAAA
3370201 TTGAGAGA-ATTTTGGAAGGAAA
1 TTGAGAGAGATTTTGGAAGGAAA
3370223 TTGAGAGAGGATTT
1 TTGAGAGA-GATTT
3370237 GTTTGTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 30 0.88
24 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (23 bp):
TTGAGAGAGATTTTGGAAGGAAA
Found at i:3370744 original size:19 final size:20
Alignment explanation
Indices: 3370722--3370759 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3370712 TTTAGTCCCT
*
3370722 AATTTAATATTT-AATCATA
1 AATTTAAAATTTAAATCATA
3370741 AATTTAAAATTTAAATCAT
1 AATTTAAAATTTAAATCAT
3370760 CTCAACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTAAAATTTAAATCATA
Found at i:3373398 original size:12 final size:13
Alignment explanation
Indices: 3373372--3373403 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3373362 TTATTTCTTC
3373372 AATTT-TCTCTAA
1 AATTTCTCTCTAA
3373384 AATTTCTCTCT-A
1 AATTTCTCTCTAA
3373396 AATTTCTC
1 AATTTCTC
3373404 AAAGCTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTCTCTCTAA
Found at i:3380212 original size:25 final size:25
Alignment explanation
Indices: 3380176--3380225 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3380166 GGTGTTTTTT
3380176 GTATAAGATATAATAATAAATTTAA
1 GTATAAGATATAATAATAAATTTAA
*
3380201 GTATAAGGTATAATAATAAATTTAA
1 GTATAAGATATAATAATAAATTTAA
3380226 CTCTTAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (25 bp):
GTATAAGATATAATAATAAATTTAA
Found at i:3391203 original size:51 final size:49
Alignment explanation
Indices: 3391120--3391324 Score: 207
Period size: 44 Copynumber: 4.3 Consensus size: 49
3391110 ACTTCTGATC
* *
3391120 AGTGACAAGTGATAAGT-AGTAGCTTCAACTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGA-TAGCTTTAGCTACACTTATCTGATCA-TG-CA
*
3391171 AGTGACAAGTGATAAGTGATAGCTTTAGCTACAGTTATCTG---AT-CA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCATGCA
* *
3391216 A-TGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCA-G--
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCATGCA
* * *
3391261 -G-GACATGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCA-TG-CA
*
3391310 AGTGAAAAGTGATAA
1 AGTGACAAGTGATAA
3391325 ATACGATCCG
Statistics
Matches: 131, Mismatches: 10, Indels: 26
0.78 0.06 0.16
Matches are distributed among these distances:
44 76 0.58
45 3 0.02
46 1 0.01
47 2 0.02
48 1 0.01
50 1 0.01
51 46 0.35
52 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (49 bp):
AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCATGCA
Found at i:3391238 original size:44 final size:44
Alignment explanation
Indices: 3391174--3391320 Score: 231
Period size: 44 Copynumber: 3.3 Consensus size: 44
3391164 AGTGACAAGT
* * **
3391174 GACAAGTGATAAGTGATAGCTTTAGCTACAGTTATCTGATCAAT
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGG
*
3391218 GACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGG
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGG
*
3391262 GACATGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGG
1 GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGG
*
3391306 GACAAGTGAAAAGTG
1 GACAAGTGATAAGTG
3391321 ATAAATACGA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 94 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (44 bp):
GACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGG
Found at i:3395368 original size:22 final size:22
Alignment explanation
Indices: 3395340--3395386 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3395330 ATTTATTTGA
3395340 TTAGGTGGAACCATTCGGCGAG
1 TTAGGTGGAACCATTCGGCGAG
3395362 TTAGGTGGAACCATTCGGCGAG
1 TTAGGTGGAACCATTCGGCGAG
3395384 TTA
1 TTA
3395387 TGTTGGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (22 bp):
TTAGGTGGAACCATTCGGCGAG
Found at i:3397243 original size:43 final size:42
Alignment explanation
Indices: 3397177--3397334 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 42
3397167 AGATCGTACA
* * *
3397177 ATGCCAATGTCCCTGAC-GTGGTCTTATATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAATCAAAT-ACG
* *
3397220 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCATATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATACG
* * *
3397262 ATGCTAATGTCCCAGACATGGTCTTACACGCAAATCTCAAAT-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACACG-TAA--TCAAATACG
* **
3397306 ATGCCAACGTTTCAGAC-GTGGTCTTACAC
1 ATGCCAATGTCCCAGACAG-GGTCTTACAC
3397335 AAAATCACAT
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
42 30 0.32
43 34 0.36
44 26 0.27
45 5 0.05
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATACG
Found at i:3397275 original size:42 final size:43
Alignment explanation
Indices: 3397177--3397291 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
3397167 AGATCGTACA
* * *
3397177 ATGCCAATGTCCCTGAC-GTGGTCTTATATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAATCAAATAACG
* *
3397220 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCATAT-ACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATAACG
* *
3397262 ATGCTAATGTCCCAGACATGGTCTTACACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACG
3397292 CAAATCTCAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
42 30 0.48
43 32 0.51
44 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATAACG
Found at i:3398437 original size:13 final size:13
Alignment explanation
Indices: 3398419--3398443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3398409 ACAAACGATA
3398419 AAATTTTCACACG
1 AAATTTTCACACG
3398432 AAATTTTCACAC
1 AAATTTTCACAC
3398444 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:3399741 original size:25 final size:26
Alignment explanation
Indices: 3399713--3399761 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
3399703 AATAAAATAA
*
3399713 AATTTGTTTTTAATA-TTTTAATAGT
1 AATTTATTTTTAATATTTTTAATAGT
*
3399738 AATTTATTTTTTATATTTTTAATA
1 AATTTATTTTTAATATTTTTAATA
3399762 AAATAGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (26 bp):
AATTTATTTTTAATATTTTTAATAGT
Found at i:3403044 original size:126 final size:124
Alignment explanation
Indices: 3402780--3403049 Score: 323
Period size: 126 Copynumber: 2.2 Consensus size: 124
3402770 AAGGGCCAAA
* * * *
3402780 CAGGAACTACTGTGGAAAAAGAGAGTCCATGTGGGAGCTTTTCAATAATTTTGCTGACAGTGTAT
1 CAGGAACTACTGTAGAAAAAGAGAGTCCACGTGGGAGCTTTTCAATAATTTTACTGACAGTGCAT
*
3402845 CCTTCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAAATACTTTTT
66 CCTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAAATACTTTTT
* * * *
3402904 TAGGAACTACTGTAGAAAAATAGTGTCCACGTGGGAGCTTTTTTCAGTAATTTTACTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGAGTCCACGTGGGAGC--TTTTCAATAATTTTACTGACAGTGC
* * * * *
3402969 ATCCTGCTTGGAGCATTTTTTACATTATCTT-TTCAGAA-TCGTTTTCTCAAAATTA-TGTTTT
64 ATCCTGCTTGAAGCATTTTTGACACTAT-TTGTTCAGAACT-GTCTTCTCAAAAATACT-TTTT
*
3403030 CA-GAACCTATTGTAGAAAAA
1 CAGGAA-CTACTGTAGAAAAA
3403050 CAAACAAAAG
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
124 33 0.27
125 5 0.04
126 84 0.68
127 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (124 bp):
CAGGAACTACTGTAGAAAAAGAGAGTCCACGTGGGAGCTTTTCAATAATTTTACTGACAGTGCAT
CCTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAAATACTTTTT
Found at i:3403144 original size:34 final size:30
Alignment explanation
Indices: 3403104--3403183 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 30
3403094 TAAACACAAA
3403104 ATTATTTTAAAAAATAAAATCCTAATTTAATTT
1 ATTA-TTTAAAAAA-AAAA-CCTAATTTAATTT
*
3403137 ATTTATTTAAAACCCAAAAAACCTATTTTAATTT
1 A-TTATTTAAAA---AAAAAACCTAATTTAATTT
3403171 ATTATTTAAAAAA
1 ATTATTTAAAAAA
3403184 CCTTAAACCC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
30 2 0.05
33 18 0.43
34 16 0.38
35 4 0.10
36 2 0.05
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (30 bp):
ATTATTTAAAAAAAAAACCTAATTTAATTT
Found at i:3403192 original size:33 final size:34
Alignment explanation
Indices: 3403119--3403182 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
3403109 TTTAAAAAAT
* *
3403119 AAAATCCTAATTTAATTTATTTATTTAAAACCCA
1 AAAAACCTAATTTAATTTATTTATTTAAAAACCA
*
3403153 AAAAACCTATTTTAATTTA-TTATTTAAAAA
1 AAAAACCTAATTTAATTTATTTATTTAAAAA
3403183 ACCTTAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 10 0.37
34 17 0.63
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (34 bp):
AAAAACCTAATTTAATTTATTTATTTAAAAACCA
Found at i:3405997 original size:13 final size:13
Alignment explanation
Indices: 3405979--3406008 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3405969 TCCAACAACT
3405979 ATGAATTTATTTC
1 ATGAATTTATTTC
*
3405992 ATGAATTTATTTG
1 ATGAATTTATTTC
3406005 ATGA
1 ATGA
3406009 TGATCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:3406183 original size:50 final size:50
Alignment explanation
Indices: 3406103--3406337 Score: 353
Period size: 50 Copynumber: 4.7 Consensus size: 50
3406093 ATTTGGGTAA
* *
3406103 AGAGGTCTCATGTAAGACCATGTCTTGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
3406153 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
3406203 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
3406253 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCCTGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
3406303 AGAACATCCCATGTAAGACCATGTCTGAGACATGG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGG
3406338 TTTTGGCATG
Statistics
Matches: 169, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 141 0.83
51 28 0.17
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:3415701 original size:79 final size:77
Alignment explanation
Indices: 3415274--3415922 Score: 704
Period size: 78 Copynumber: 8.3 Consensus size: 77
3415264 TTCTGTTTTT
* * * * * *
3415274 TTTTTCCAAAAATCAACTCATATTGCAAGATGTGAGTTGAGCCTCGGACTCACGCCAAGGTATTT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATTT
3415339 CTTTTAAATTTCTG
66 -TTTT-AATTTCTG
*
3415353 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGCTACACGCCGAGGTATT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGC-ACACGCCGAGGTATT
3415417 TTTATTAATTTCTG
65 TTT-TTAATTTCTG
* * * * *
3415431 TTTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTTTGGTCACATGCCGAGATAT
1 -TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCGGGCACACGCCGAGGTAT
3415496 TTCTTTTAAATTTCTG
64 TT-TTTT-AATTTCTG
* * * * *
3415512 TTTTTCAAAAAAATTAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG-TCACGCTGAGGTA--
1 TTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATT
* *
3415574 TTTTAAATTTCTA
65 TTTTTAATTTCTG
*** * * *
3415587 TTTTTTGTAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACGCTGAGATATT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACACGCCGAGGTATT
*
3415652 TTTTTTATTTCTG
65 TTTTTAATTTCTG
* * * *
3415665 TTTTTCAAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGG-TCACGCTGAGGTA--
1 TTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATT
*
3415727 TTTTCAATTTCTG
65 TTTTTAATTTCTG
*** * *
3415740 TTTTTTTTTAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCCAGGTAT
1 -TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACACGCCGAGGTAT
3415805 TTCTTTTAAATTTCTG
64 TT-TTTT-AATTTCTG
*
3415821 TTTTTC--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGATATTT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTA-TT
3415884 TTTTTAAATTTACTTG
65 TTTTT-AATTT-C-TG
*
3415900 TTTTTTCTAAAAATACAACTCAT
1 -TTTTTCAAAAAAT-CAACTCAT
3415923 NNNNNNNNNN
Statistics
Matches: 485, Mismatches: 58, Indels: 50
0.82 0.10 0.08
Matches are distributed among these distances:
74 37 0.08
75 60 0.12
76 19 0.04
77 44 0.09
78 106 0.22
79 77 0.16
80 74 0.15
81 55 0.11
82 5 0.01
83 8 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (77 bp):
TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATTT
TTTTAATTTCTG
Found at i:3415718 original size:153 final size:153
Alignment explanation
Indices: 3415282--3415884 Score: 773
Period size: 153 Copynumber: 3.9 Consensus size: 153
3415272 TTTTTTTCCA
* * * * *
3415282 AAAATCAACTCATATTGCAAGATGTGAGTTGAGCCTC-GGACTCACGCCAAGGTATTTCTTTTAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACGCCGAGATATTTCTTTTAA
* *
3415346 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGCTACACGCCGA
66 ATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG-GGT-CACGCCGA
* *
3415411 GGTATTTTTATTAATTTCTGTTTTTTCAA
129 GGTA-TTTTA--AATTTCTATTTTTT-AT
* ** * *
3415440 AAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTTTGGTCACATGCCGAGATATTTCTTTTAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACGCCGAGATATTTCTTTTAA
* * *
3415505 ATTTCTGTTTTTCAAAAAAATTAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
66 ATTTCTGTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGA
*
3415570 GGTATTTTAAATTTCTATTTTTTGT
129 GGTATTTTAAATTTCTATTTTTTAT
* * *
3415595 AAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACGCTGAGATATTT-TTTT-T
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACGCCGAGATATTTCTTTTAA
* *
3415658 ATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCACGCTGA
66 ATTTCTGTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGA
* * *
3415723 GGTATTTTCAATTTCTGTTTTTTTTT
129 GGTATTTTAAATTTCT-ATTTTTTAT
* * * *
3415749 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCCAGGTATTTCTTTTAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACGCCGAGATATTTCTTTTAA
* *
3415814 ATTTCTGTTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAG
66 ATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-TCACGCCGAG
*
3415878 ATATTTT
130 GTATTTT
3415885 TTTTAAATTT
Statistics
Matches: 395, Mismatches: 43, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
153 115 0.29
154 77 0.19
155 55 0.14
156 26 0.07
158 38 0.10
159 46 0.12
160 2 0.01
161 36 0.09
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (153 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACGCCGAGATATTTCTTTTAA
ATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGG
TATTTTAAATTTCTATTTTTTAT
Found at i:3416044 original size:10 final size:10
Alignment explanation
Indices: 3416029--3416069 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
3416019 NNNNAAGAAG
3416029 AAGAAGGAAA
1 AAGAAGGAAA
*
3416039 AAGAAGAAAA
1 AAGAAGGAAA
3416049 AAGAA-GAAA
1 AAGAAGGAAA
3416058 AA-AAGAGAAA
1 AAGAAG-GAAA
3416068 AA
1 AA
3416070 ATAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 2 0.07
9 5 0.19
10 20 0.74
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAGAAGGAAA
Found at i:3416054 original size:20 final size:19
Alignment explanation
Indices: 3416024--3416069 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3416014 NNNNNNNNNA
*
3416024 AGAAGAAGAAGGAAAAAGAAG
1 AGAAAAAGAA-GAAAAA-AAG
3416045 A-AAAAAGAAGAAAAAAAG
1 AGAAAAAGAAGAAAAAAAG
3416063 AGAAAAA
1 AGAAAAA
3416070 ATAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 11 0.48
20 7 0.30
21 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AGAAAAAGAAGAAAAAAAG
Found at i:3416070 original size:20 final size:22
Alignment explanation
Indices: 3416026--3416070 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
3416016 NNNNNNNAAG
3416026 AAGAAGAAGGAAAAAGAAGAAAA
1 AAGAAGAA-GAAAAAGAAGAAAA
3416049 AAGAAGAA-AAAAAG-AGAAAA
1 AAGAAGAAGAAAAAGAAGAAAA
3416069 AA
1 AA
3416071 TAAAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 6 0.27
23 8 0.36
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (22 bp):
AAGAAGAAGAAAAAGAAGAAAA
Found at i:3416170 original size:21 final size:20
Alignment explanation
Indices: 3416145--3416199 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 20
3416135 AGTCCAATCA
*
3416145 AAAAAAAAAAAGAAATTAAGC
1 AAAAAAAAAAAGAAA-AAAGC
3416166 AAAAAAAAAAGAGAAAAAAGC
1 AAAAAAAAAA-AGAAAAAAGC
3416187 AACACAAAAAAAA
1 AA-A-AAAAAAAA
3416200 AACCAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 16 0.53
22 7 0.23
23 7 0.23
ACGTcount: A:0.80, C:0.07, G:0.09, T:0.04
Consensus pattern (20 bp):
AAAAAAAAAAAGAAAAAAGC
Found at i:3416394 original size:10 final size:10
Alignment explanation
Indices: 3416381--3416482 Score: 70
Period size: 10 Copynumber: 10.5 Consensus size: 10
3416371 AGCCCAGTCC
3416381 AAAAAA-AAA
1 AAAAAAGAAA
* *
3416390 GAAAAAG-AG
1 AAAAAAGAAA
3416399 AAAAAAGAAA
1 AAAAAAGAAA
3416409 AAAAAAGAAA
1 AAAAAAGAAA
* *
3416419 AGAGAAGAAA
1 AAAAAAGAAA
3416429 AGAAAAA-AAA
1 A-AAAAAGAAA
*
3416439 GAAAAAAGGAA
1 -AAAAAAGAAA
* **
3416450 AAAGAAGGGA
1 AAAAAAGAAA
*
3416460 AAAAAAG--G
1 AAAAAAGAAA
3416468 AAAAAAGAAA
1 AAAAAAGAAA
3416478 AAAAA
1 AAAAA
3416483 GGGGCCCAAG
Statistics
Matches: 72, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
8 7 0.10
9 12 0.17
10 47 0.65
11 6 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:3416403 original size:9 final size:9
Alignment explanation
Indices: 3416382--3416483 Score: 76
Period size: 9 Copynumber: 11.8 Consensus size: 9
3416372 GCCCAGTCCA
*
3416382 AAAAAAAAG
1 AAAAAAGAG
3416391 -AAAAAGAG
1 AAAAAAGAG
3416399 AAAAAAGA-
1 AAAAAAGAG
3416407 AAAAAA-A-
1 AAAAAAGAG
*
3416414 AGAAAAGAG
1 AAAAAAGAG
3416423 AAGAAAAGA-
1 AA-AAAAGAG
3416432 AAAAAA-AG
1 AAAAAAGAG
3416440 AAAAAAG-G
1 AAAAAAGAG
*
3416448 AAAAAGAAGGG
1 -AAAA-AAGAG
3416459 AAAAAA-AGG
1 AAAAAAGA-G
*
3416468 AAAAAAGAA
1 AAAAAAGAG
3416477 AAAAAAG
1 AAAAAAG
3416484 GGGCCCAAGT
Statistics
Matches: 77, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
7 7 0.09
8 25 0.32
9 30 0.39
10 14 0.18
11 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:3416454 original size:28 final size:28
Alignment explanation
Indices: 3416401--3416480 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 28
3416391 AAAAAGAGAA
* *
3416401 AAAAGAAAAAAAA-AGAAAA-G-AGAAG
1 AAAAGAAAAAAAAGAAAAAAGGAAAAAG
3416426 AAAAGAAAAAAAAGAAAAAAGGAAAAAG
1 AAAAGAAAAAAAAGAAAAAAGGAAAAAG
** * *
3416454 AAGGGAAAAAAAGGAAAAAAGAAAAAA
1 AAAAGAAAAAAAAGAAAAAAGGAAAAA
3416481 AAGGGGCCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
25 13 0.28
26 5 0.11
27 1 0.02
28 27 0.59
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (28 bp):
AAAAGAAAAAAAAGAAAAAAGGAAAAAG
Found at i:3416480 original size:17 final size:17
Alignment explanation
Indices: 3416381--3416484 Score: 90
Period size: 17 Copynumber: 6.0 Consensus size: 17
3416371 AGCCCAGTCC
3416381 AAAAAA-AAAGAAAAAGAG
1 AAAAAAGAAA-AAAAAG-G
*
3416399 AAAAAAGAAAAAAAAAG
1 AAAAAAGAAAAAAAAGG
* *
3416416 AAAAGAG-AAGAAAA-G
1 AAAAAAGAAAAAAAAGG
3416431 AAAAAA-AAGAAAAAAGG
1 AAAAAAGAA-AAAAAAGG
*
3416448 AAAAAGAAGGGAAAAAAAGG
1 -AAAA-AA-GAAAAAAAAGG
3416468 AAAAAAGAAAAAAAAGG
1 AAAAAAGAAAAAAAAGG
3416485 GGCCCAAGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
15 7 0.10
16 11 0.15
17 18 0.25
18 17 0.24
19 9 0.13
20 8 0.11
21 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAGG
Found at i:3416481 original size:8 final size:8
Alignment explanation
Indices: 3416383--3416481 Score: 94
Period size: 8 Copynumber: 11.9 Consensus size: 8
3416373 CCCAGTCCAA
3416383 AAAAAAAG
1 AAAAAAAG
*
3416391 AAAAAGAG
1 AAAAAAAG
3416399 -AAAAAAG
1 AAAAAAAG
3416406 AAAAAAA-
1 AAAAAAAG
3416413 AAGAAAAGAG
1 AA-AAAA-AG
*
3416423 AAGAAAAG
1 AAAAAAAG
3416431 AAAAAAAAG
1 -AAAAAAAG
*
3416440 AAAAAAGG
1 AAAAAAAG
3416448 AAAAAGAAGGG
1 AAAAA-AA--G
3416459 AAAAAAAG
1 AAAAAAAG
*
3416467 GAAAAAAG
1 AAAAAAAG
3416475 AAAAAAA
1 AAAAAAA
3416482 AGGGGCCCAA
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
7 8 0.11
8 45 0.60
9 12 0.16
10 4 0.05
11 6 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:3416994 original size:16 final size:15
Alignment explanation
Indices: 3416975--3417026 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
3416965 CGTGTTTTAA
3416975 AAAATTCCGGTGTTTC
1 AAAATTCC-GTGTTTC
3416991 AAAAATT-CGTGTTTTC
1 -AAAATTCCGTG-TTTC
*
3417007 AAAATTCCAGTGATTC
1 AAAATTCC-GTGTTTC
3417023 AAAA
1 AAAA
3417027 AAATTTCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.29
16 13 0.42
17 9 0.29
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (15 bp):
AAAATTCCGTGTTTC
Found at i:3416994 original size:17 final size:16
Alignment explanation
Indices: 3416974--3417274 Score: 77
Period size: 18 Copynumber: 16.9 Consensus size: 16
3416964 TCGTGTTTTA
3416974 AAAAATTCCGGTGTTTC
1 AAAAATTCC-GTGTTTC
3416991 AAAAATT-CGTGTTTTC
1 AAAAATTCCGTG-TTTC
*
3417007 -AAAATTCCAGTGATTC
1 AAAAATTCC-GTGTTTC
* *
3417023 AAAAAAATTTCATGTTTTC
1 --AAAAATTCCGTG-TTTC
3417042 TAAAAATTTCTC-TGTTTC
1 -AAAAA-TTC-CGTGTTTC
*
3417060 AAAAAAATTTTCGTGTTTAC
1 --AAAAA-TTCCGTGTTT-C
* * *
3417080 AAAAATTTTCATATTTTC
1 AAAAA-TTCCGT-GTTTC
*
3417098 AAAAATTTTCGTGTTTTC
1 AAAAA-TTCCGTG-TTTC
*
3417116 AACAATTCTCGTGTTTC
1 AAAAATTC-CGTGTTTC
* * *
3417133 ACAAATTTTCGTGTTTTAA
1 A-AAAATTCCGTG-TTT-C
** *
3417152 AAAAATTTTGTGTTTTAAAA
1 AAAAATTCCGTG-TTT---C
**
3417172 AAAAATTATTGTGTTTC
1 AAAAATT-CCGTGTTTC
*
3417189 AAAAATTGTCGTGTTTC
1 AAAAATT-CCGTGTTTC
**
3417206 AAAAATCTTAGTGTTTTC
1 AAAAAT-TCCGTG-TTTC
* *
3417224 AAAAATTTTCGGTTTTTC
1 AAAAA--TTCCGTGTTTC
*
3417242 AAAAATTCTCGTGATTC
1 AAAAATTC-CGTGTTTC
3417259 AAAAACTTCCGTGTTT
1 AAAAA-TTCCGTGTTT
3417275 TTTTTTAAAA
Statistics
Matches: 226, Mismatches: 31, Indels: 54
0.73 0.10 0.17
Matches are distributed among these distances:
15 9 0.04
16 12 0.05
17 62 0.27
18 89 0.39
19 34 0.15
20 15 0.07
21 5 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (16 bp):
AAAAATTCCGTGTTTC
Found at i:3417011 original size:32 final size:33
Alignment explanation
Indices: 3416964--3417027 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3416954 AAAAAAATCC
* *
3416964 TCGTGTTTTAAAAAATTCCGGTGTTTCAAAAAT
1 TCGTGTTTTAAAAAATTCCAGTGATTCAAAAAT
*
3416997 TCGTGTTTT-CAAAATTCCAGTGATTCAAAAA
1 TCGTGTTTTAAAAAATTCCAGTGATTCAAAAA
3417028 AATTTCATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 19 0.68
33 9 0.32
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (33 bp):
TCGTGTTTTAAAAAATTCCAGTGATTCAAAAAT
Found at i:3417046 original size:18 final size:18
Alignment explanation
Indices: 3417024--3417248 Score: 133
Period size: 18 Copynumber: 12.4 Consensus size: 18
3417014 CAGTGATTCA
*
3417024 AAAAAATTTCATGTTTTC
1 AAAAATTTTCATGTTTTC
3417042 TAAAAATTTCTC-TG-TTTC
1 -AAAAATTT-TCATGTTTTC
* *
3417060 AAAAAAATTTTCGTGTTTAC
1 --AAAAATTTTCATGTTTTC
*
3417080 AAAAATTTTCATATTTTC
1 AAAAATTTTCATGTTTTC
*
3417098 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCATGTTTTC
* * *
3417116 AACAATTCTCGTG-TTTC
1 AAAAATTTTCATGTTTTC
* * *
3417133 ACAAATTTTCGTGTTTTAA
1 AAAAATTTTCATGTTTT-C
* *
3417152 AAAAATTTT-GTGTTTTAA
1 AAAAATTTTCATGTTTT-C
**
3417170 AAAAAAATT-ATTGTGTTTC
1 AAAAATTTTCA-TGT-TTTC
* *
3417189 AAAAATTGTCGTG-TTTC
1 AAAAATTTTCATGTTTTC
*
3417206 AAAAATCTT-AGTGTTTTC
1 AAAAATTTTCA-TGTTTTC
*
3417224 AAAAATTTTC-GGTTTTTC
1 AAAAATTTTCATG-TTTTC
3417242 AAAAATT
1 AAAAATT
3417249 CTCGTGATTC
Statistics
Matches: 165, Mismatches: 28, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
17 28 0.17
18 91 0.55
19 38 0.23
20 8 0.05
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCATGTTTTC
Found at i:3417109 original size:36 final size:34
Alignment explanation
Indices: 3417062--3417263 Score: 165
Period size: 36 Copynumber: 5.6 Consensus size: 34
3417052 TCTGTTTCAA
*
3417062 AAAAATTTTCGTGTTTACAAAAATTTTCATATTTTC
1 AAAAATTTTCGTGTTT-CAAAAATTTTCGT-TTTTC
* * *
3417098 AAAAATTTTCGTGTTTTCAACAATTCTCGTGTTTC
1 AAAAATTTTCGTG-TTTCAAAAATTTTCGTTTTTC
* * *
3417133 ACAAATTTTCGTGTTTTAAAAAAATTTT-GTGTTTTAAAA
1 AAAAATTTTCGTG-TTT-CAAAAATTTTCGT-TTTT---C
* *
3417172 AAAAATTATT-GTGTTTCAAAAATTGTCGTGTTTC
1 AAAAATT-TTCGTGTTTCAAAAATTTTCGTTTTTC
* *
3417206 AAAAATCTTAGTGTTTTCAAAAATTTTCGGTTTTTC
1 AAAAATTTTCGTG-TTTCAAAAATTTTC-GTTTTTC
* *
3417242 AAAAATTCTCGTGATTCAAAAA
1 AAAAATTTTCGTGTTTCAAAAA
3417264 CTTCCGTGTT
Statistics
Matches: 133, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
33 2 0.02
34 9 0.07
35 43 0.32
36 49 0.37
37 14 0.11
38 5 0.04
39 9 0.07
40 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (34 bp):
AAAAATTTTCGTGTTTCAAAAATTTTCGTTTTTC
Found at i:3417246 original size:73 final size:74
Alignment explanation
Indices: 3417023--3417232 Score: 186
Period size: 73 Copynumber: 2.9 Consensus size: 74
3417013 CCAGTGATTC
* * * *
3417023 AAAAAAA-TTTCATGTTTTCTAAAAATTTCTC-TGTTTCAAAAAAATTTTCGTG-TTTACAAAAA
1 AAAAAAATTTTCGTGTTTTC-AAAAA-TTCTCGTGTTTC--AAAAATCTTAGTGTTTTAAAAAAA
* *
3417085 TTTTCATATTTT--
62 TTTT-GTGTTTTAA
* * * * *
3417097 -CAAAAATTTTCGTGTTTTCAACAATTCTCGTGTTTCACAAATTTTCGTGTTTTAAAAAAATTTT
1 AAAAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTCAAAAATCTTAGTGTTTTAAAAAAATTTT
3417161 GTGTTTTAA
66 GTGTTTTAA
* *
3417170 AAAAAAATTATT-GTG-TTTCAAAAATTGTCGTGTTTCAAAAATCTTAGTGTTTT-CAAAAATTT
1 AAAAAAATT-TTCGTGTTTTCAAAAATTCTCGTGTTTCAAAAATCTTAGTGTTTTAAAAAAATTT
3417232 T
65 T
3417233 CGGTTTTTCA
Statistics
Matches: 115, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
71 17 0.15
72 27 0.23
73 48 0.42
74 21 0.18
75 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.45
Consensus pattern (74 bp):
AAAAAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTCAAAAATCTTAGTGTTTTAAAAAAATTTT
GTGTTTTAA
Found at i:3417308 original size:36 final size:37
Alignment explanation
Indices: 3417250--3417319 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 37
3417240 TCAAAAATTC
3417250 TCGTGATTCAAAAACTTCCGTGTTTTTTTTTAAAAAA
1 TCGTGATTCAAAAACTTCCGTGTTTTTTTTTAAAAAA
*
3417287 TCGTGTTTC-AAAA-TTCTCGTGTTTTTTTTTAAA
1 TCGTGATTCAAAAACTTC-CGTGTTTTTTTTTAAA
3417320 TTCTCATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 3 0.10
36 20 0.65
37 8 0.26
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (37 bp):
TCGTGATTCAAAAACTTCCGTGTTTTTTTTTAAAAAA
Found at i:3417332 original size:36 final size:36
Alignment explanation
Indices: 3417260--3417333 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
3417250 TCGTGATTCA
* *
3417260 AAAACTTCCGTGTTTTTTTTTAAAAAATCGTGTTTC
1 AAAACTTCCGTGTTTTTTTTTAAAAAATCATATTTC
***
3417296 AAAA-TTCTCGTGTTTTTTTTTAAATTCTCATATTTC
1 AAAACTTC-CGTGTTTTTTTTTAAAAAATCATATTTC
3417332 AA
1 AA
3417334 TCGGATCACG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 3 0.09
36 29 0.91
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (36 bp):
AAAACTTCCGTGTTTTTTTTTAAAAAATCATATTTC
Found at i:3419052 original size:18 final size:19
Alignment explanation
Indices: 3419019--3419057 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
3419009 TAAATAATTT
3419019 GAGTTATTCGTGTTAA-TC
1 GAGTTATTCGTGTTAACTC
3419037 GAGTTATTCG-GATTAACTC
1 GAGTTATTCGTG-TTAACTC
3419056 GA
1 GA
3419058 ATAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 14 0.74
19 4 0.21
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (19 bp):
GAGTTATTCGTGTTAACTC
Found at i:3419941 original size:18 final size:18
Alignment explanation
Indices: 3419909--3419954 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
3419899 AACAGTTTCG
*
3419909 AAAGAAAGA-AAAAATAA
1 AAAGAAAAATAAAAATAA
*
3419926 AGAGAAAAATAAAAATAA
1 AAAGAAAAATAAAAATAA
*
3419944 AAAGGAAAATA
1 AAAGAAAAATA
3419955 GAACTTGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (18 bp):
AAAGAAAAATAAAAATAA
Found at i:3424499 original size:25 final size:23
Alignment explanation
Indices: 3424449--3424492 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3424439 CTATATATAA
* *
3424449 CTTAATAAAATTTAAAAAATATT
1 CTTAATAAAATTAAAAAAAAATT
3424472 CTTAATAAAATTAAAAAAAAA
1 CTTAATAAAATTAAAAAAAAA
3424493 GTTTCTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (23 bp):
CTTAATAAAATTAAAAAAAAATT
Found at i:3426571 original size:18 final size:17
Alignment explanation
Indices: 3426538--3426576 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
3426528 TTTTCTAAAT
3426538 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
3426556 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
3426573 TGTG
1 TGTG
3426577 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:3426829 original size:23 final size:23
Alignment explanation
Indices: 3426802--3426900 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
3426792 AGTGTTATTG
* *
3426802 ATCAGTGGTAGCTTCAGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
3426825 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
3426848 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
3426871 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3426894 ATCAGTG
1 ATCAGTG
3426901 TTGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:3435585 original size:124 final size:124
Alignment explanation
Indices: 3435363--3435618 Score: 381
Period size: 124 Copynumber: 2.1 Consensus size: 124
3435353 AAATAGTGGG
** * * *
3435363 AAATCGCTTTTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
3435428 TCGCTACAGTGGTCATGTAAGAAATAAT-TTTTTTTGACGTTTTCTAAGCAAATAGTATA
66 TCGCTACAGTGGTCATGTAAGAAATAATATTTTTTTGACG-TTTCTAAGCAAATAGTATA
3435487 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
* * * * *
3435552 TCGCTACAGTTGGTCATGTAGGAAATAA-ATTTTTTTTGACGTTTCTGAGTAAATAGTGTC
66 TCGCTACAG-TGGTCATGTAAGAAATAATA-TTTTTTTGACGTTTCTAAGCAAATAGTATA
3435612 AAATCGC
1 AAATCGC
3435619 GCCCTCGTGG
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
124 69 0.58
125 39 0.33
126 11 0.09
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
TCGCTACAGTGGTCATGTAAGAAATAATATTTTTTTGACGTTTCTAAGCAAATAGTATA
Found at i:3438936 original size:33 final size:32
Alignment explanation
Indices: 3438889--3439039 Score: 150
Period size: 28 Copynumber: 5.0 Consensus size: 32
3438879 AATCCGCTGA
*
3438889 GTTATGTTAGGGTTTTTACATTAATTAAATTAG
1 GTTAGGTTAGGGTTTTTA-ATTAATTAAATTAG
3438922 GTTAGGTTAGGG--TTT--TTAATTAAATTAG
1 GTTAGGTTAGGGTTTTTAATTAATTAAATTAG
3438950 GTTAGGTTAGGGTTTTTAATTAAATT-AA--A-
1 GTTAGGTTAGGGTTTTTAATT-AATTAAATTAG
3438979 -TTAGGTTAGGGTTTTTAATTAAATTAAATTA-
1 GTTAGGTTAGGGTTTTTAATT-AATTAAATTAG
*
3439010 --T--GTTAGGGTTTTTAATTAAGTTAAGTTAG
1 GTTAGGTTAGGGTTTTTAATTAA-TTAAATTAG
3439039 G
1 G
3439040 GTTTTTAATT
Statistics
Matches: 105, Mismatches: 2, Indels: 25
0.80 0.02 0.19
Matches are distributed among these distances:
27 2 0.02
28 73 0.70
29 2 0.02
30 5 0.05
31 4 0.04
32 4 0.04
33 15 0.14
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (32 bp):
GTTAGGTTAGGGTTTTTAATTAATTAAATTAG
Found at i:3438940 original size:28 final size:28
Alignment explanation
Indices: 3438909--3439081 Score: 239
Period size: 28 Copynumber: 6.4 Consensus size: 28
3438899 GGTTTTTACA
*
3438909 TTAATTAAATTAGGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
3438937 TTAATTAAATTAGGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
3438965 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
* *
3438993 TTAATTAAATTAAATTATGTTAGGG--T
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
3439019 TT--TT-AATTAAGTTAAGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
3439044 TTAATTATATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGTTAGGGTTT
*
3439072 TTAATCAAAT
1 TTAATTAAAT
3439082 AATGTCAAAA
Statistics
Matches: 131, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
23 16 0.12
24 2 0.02
25 3 0.02
26 3 0.02
27 2 0.02
28 105 0.80
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (28 bp):
TTAATTAAATTAAGTTAGGTTAGGGTTT
Found at i:3441236 original size:22 final size:22
Alignment explanation
Indices: 3441208--3441261 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3441198 TTTTATAAGA
*
3441208 AAAAATAAATTAATAAATATCT
1 AAAAATAAATTAAAAAATATCT
* *
3441230 AAAAATACATAAAAAAATATCT
1 AAAAATAAATTAAAAAATATCT
*
3441252 -TAAATAAATT
1 AAAAATAAATT
3441262 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAATAAATTAAAAAATATCT
Found at i:3441421 original size:26 final size:26
Alignment explanation
Indices: 3441358--3441408 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
3441348 TTGAAAATAT
3441358 TAAAAATTTTAAAATTATTTTAAAAA
1 TAAAAATTTTAAAATTATTTTAAAAA
3441384 TAAAAATTTTAAAATT-TTCTTAAAA
1 TAAAAATTTTAAAATTATT-TTAAAA
3441409 TAATGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAAAATTTTAAAATTATTTTAAAAA
Found at i:3441484 original size:22 final size:22
Alignment explanation
Indices: 3441449--3441558 Score: 134
Period size: 22 Copynumber: 5.0 Consensus size: 22
3441439 TATGGATTTG
*
3441449 GAGATTTTTTGAAGGAAATTGA
1 GAGAATTTTTGAAGGAAATTGA
* * *
3441471 GAGGATTTTAGAAGGAATTTGA
1 GAGAATTTTTGAAGGAAATTGA
*
3441493 GAGAA-TTTTGAAAGGAATTTGA
1 GAGAATTTTTG-AAGGAAATTGA
3441515 GAGAATTTTTGAACGG-AATTGA
1 GAGAATTTTTGAA-GGAAATTGA
*
3441537 GAGAATTTTTGAAGGATATTGA
1 GAGAATTTTTGAAGGAAATTGA
3441559 TATTGAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.08
22 63 0.83
23 7 0.09
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.34
Consensus pattern (22 bp):
GAGAATTTTTGAAGGAAATTGA
Found at i:3443250 original size:5 final size:5
Alignment explanation
Indices: 3443242--3443267 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3443232 GAGATGGAAT
3443242 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
3443268 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:3443267 original size:26 final size:26
Alignment explanation
Indices: 3443216--3443267 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3443206 TGAAGTTTTC
* * *
3443216 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
3443242 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
3443268 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:3443822 original size:16 final size:16
Alignment explanation
Indices: 3443780--3443831 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 16
3443770 TGGTGAGAAG
3443780 TAAAAGTTTAAGGGGGAAA
1 TAAAAGTTT--GGGGG-AA
3443799 TAAAAAGTTTGGGGGAA
1 T-AAAAGTTTGGGGGAA
*
3443816 TAAAAGTTTGAGGGAA
1 TAAAAGTTTGGGGGAA
3443832 AGTAAATAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 14 0.45
17 3 0.10
18 5 0.16
19 1 0.03
20 8 0.26
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (16 bp):
TAAAAGTTTGGGGGAA
Found at i:3444154 original size:21 final size:20
Alignment explanation
Indices: 3444115--3444154 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3444105 GGGGAAAGTG
* *
3444115 GGAAAGAGTAAAAGTTTTGA
1 GGAAAAAGTAAAAGGTTTGA
3444135 GGAAAAAGTAAAAAGGTTTG
1 GGAAAAAGT-AAAAGGTTTG
3444155 GGAGTTTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (20 bp):
GGAAAAAGTAAAAGGTTTGA
Found at i:3445107 original size:20 final size:22
Alignment explanation
Indices: 3445082--3445125 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3445072 CACGTGGTAT
3445082 AAAATTATA-AA-AATCATAAA
1 AAAATTATACAAGAATCATAAA
*
3445102 AAAATTATACAAGAATTATAAA
1 AAAATTATACAAGAATCATAAA
3445124 AA
1 AA
3445126 TGAATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 2 0.10
22 10 0.48
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATTATACAAGAATCATAAA
Found at i:3445232 original size:34 final size:34
Alignment explanation
Indices: 3445158--3445233 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
3445148 ATAAAAAATC
* * *
3445158 TATTTTTAAAAGGTTAATAAATTTTATATTTTAT
1 TATTTTTAAAAGGATAATAAATTTTAAATATTAT
3445192 TATTTTTAAAAGGATAATAAATTTTTAAAATATT-T
1 TATTTTTAAAAGGATAATAAA-TTTT-AAATATTAT
3445227 T-TTTTTA
1 TATTTTTA
3445234 TTCTTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 26 0.70
35 6 0.16
36 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (34 bp):
TATTTTTAAAAGGATAATAAATTTTAAATATTAT
Found at i:3445955 original size:19 final size:20
Alignment explanation
Indices: 3445931--3445969 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
3445921 ATGGAGGAAG
3445931 TCAGTGTAAAGGG-GGAAAA
1 TCAGTGTAAAGGGAGGAAAA
3445950 TCAGTGTAAAGGGAGGAAAA
1 TCAGTGTAAAGGGAGGAAAA
3445970 AAGAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.44, C:0.05, G:0.36, T:0.15
Consensus pattern (20 bp):
TCAGTGTAAAGGGAGGAAAA
Found at i:3446810 original size:24 final size:22
Alignment explanation
Indices: 3446778--3446839 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 22
3446768 AGTGTATTGT
3446778 ATATTATTATTTTAGATTTATCA
1 ATATTATTATTTTA-ATTTATCA
* *
3446801 TGTTTTATTATTTTTAATTTATCA
1 -ATATTATTA-TTTTAATTTATCA
3446825 ATATTATTATTTTAA
1 ATATTATTATTTTAA
3446840 ATTCATCGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 6 0.18
23 7 0.21
24 15 0.45
25 5 0.15
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (22 bp):
ATATTATTATTTTAATTTATCA
Found at i:3446883 original size:47 final size:46
Alignment explanation
Indices: 3446807--3446898 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 46
3446797 ATCATGTTTT
* * * *
3446807 ATTATTTTTAATTTATCAATATTATTATTTTAAATTCATCGTTAAC
1 ATTATTTTAAATCTATCAATATTATTATTTCAAATTCATCATTAAC
* *
3446853 ATTATTTTAAATCTATC-ATGTATATCTATTTCAAATTTATCATTAA
1 ATTATTTTAAATCTATCAATAT-TAT-TATTTCAAATTCATCATTAA
3446899 TATTTTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
45 3 0.08
46 18 0.47
47 17 0.45
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (46 bp):
ATTATTTTAAATCTATCAATATTATTATTTCAAATTCATCATTAAC
Found at i:3448343 original size:3 final size:3
Alignment explanation
Indices: 3448337--3448383 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
3448327 AATAACGGTG
* *
3448337 ATA ATA ATA ATA ATA ATA A-A TTG ATA ATA ATA ATA GATTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA
3448383 A
1 A
3448384 CATTACTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 1 0.03
3 32 0.86
4 2 0.05
5 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3448365 original size:14 final size:14
Alignment explanation
Indices: 3448337--3448383 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
3448327 AATAACGGTG
3448337 ATAAT-AATA-ATA
1 ATAATAAATAGATA
*
3448349 ATAATAAATTGATA
1 ATAATAAATAGATA
3448363 ATAAT-AATAGATTA
1 ATAATAAATAGA-TA
3448377 ATAATAA
1 ATAATAA
3448384 CATTACTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 5 0.17
13 8 0.28
14 15 0.52
15 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (14 bp):
ATAATAAATAGATA
Done.