Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 130 of 141
Found at i:41709559 original size:21 final size:21
Alignment explanation
Indices: 41709535--41709577 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41709525 CAAAGCAAAG
41709535 TCCACTACATAATGAAATGAT
1 TCCACTACATAATGAAATGAT
41709556 TCCACTACATAATGAAATGAT
1 TCCACTACATAATGAAATGAT
41709577 T
1 T
41709578 ATACCATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (21 bp):
TCCACTACATAATGAAATGAT
Found at i:41719630 original size:21 final size:22
Alignment explanation
Indices: 41719599--41719643 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
41719589 TTTCATTTGA
41719599 ATTTTTATGAACTTTTTATTTT
1 ATTTTTATGAACTTTTTATTTT
*
41719621 ATTTTT-TGAATTTTTTATTTT
1 ATTTTTATGAACTTTTTATTTT
41719642 AT
1 AT
41719644 GAATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (22 bp):
ATTTTTATGAACTTTTTATTTT
Found at i:41719636 original size:16 final size:17
Alignment explanation
Indices: 41719617--41719653 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
41719607 GAACTTTTTA
*
41719617 TTTTATTTTTTGAAT-T
1 TTTTATTTTATGAATAT
41719633 TTTTATTTTATGAATAT
1 TTTTATTTTATGAATAT
41719650 TTTT
1 TTTT
41719654 TTATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTATTTTATGAATAT
Found at i:41719664 original size:37 final size:37
Alignment explanation
Indices: 41719601--41719674 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
41719591 TCATTTGAAT
* * *
41719601 TTTTATGAACTTTTTATTTTATTTTTTGAATTTTTTA
1 TTTTATGAACTTTTTATTTTAATTTTTAAATTATTTA
41719638 TTTTATGAA-TATTTT-TTTATAATTTTTAAATTATTTA
1 TTTTATGAACT-TTTTATTT-TAATTTTTAAATTATTTA
41719675 CCGATGTAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (37 bp):
TTTTATGAACTTTTTATTTTAATTTTTAAATTATTTA
Found at i:41728888 original size:5 final size:5
Alignment explanation
Indices: 41728878--41728925 Score: 82
Period size: 5 Copynumber: 10.0 Consensus size: 5
41728868 AAGTTTGTAA
41728878 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-A- TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
41728926 AATTTAAAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 37 0.90
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:41735428 original size:23 final size:25
Alignment explanation
Indices: 41735402--41735454 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
41735392 CATAATATAT
*
41735402 TTTATTTCCT-AAA-ATATTTAGCA
1 TTTATTTACTAAAATATATTTAGCA
*
41735425 TTTA-TTAGTAAAATATATTTAGCA
1 TTTATTTACTAAAATATATTTAGCA
41735449 TTTATT
1 TTTATT
41735455 AGCATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 3 0.12
23 7 0.28
24 14 0.56
25 1 0.04
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTATTTACTAAAATATATTTAGCA
Found at i:41735467 original size:24 final size:24
Alignment explanation
Indices: 41735415--41735468 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
41735405 ATTTCCTAAA
*
41735415 ATATTTAGCATTTATTAGTAAAAT
1 ATATTTAGCATTTATTAGCAAAAT
*
41735439 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCAAAAT
*
41735463 TTATTT
1 ATATTT
41735469 GACGTACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCAAAAT
Found at i:41740256 original size:27 final size:27
Alignment explanation
Indices: 41740211--41740264 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
41740201 TTACCCTGTA
**
41740211 CAATATACTTTATGCAGAAGATATTAG
1 CAATATACTCCATGCAGAAGATATTAG
* *
41740238 CAATATACTCCATGTAGAAGATGTTAG
1 CAATATACTCCATGCAGAAGATATTAG
41740265 GAAGAATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (27 bp):
CAATATACTCCATGCAGAAGATATTAG
Found at i:41742881 original size:19 final size:21
Alignment explanation
Indices: 41742857--41742895 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
41742847 TGTATGCTTT
41742857 CTCGTA-AAACATC-CCAAAA
1 CTCGTACAAACATCTCCAAAA
*
41742876 CTCGTACAAAGATCTCCAAA
1 CTCGTACAAACATCTCCAAA
41742896 GGAACAGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.18
Consensus pattern (21 bp):
CTCGTACAAACATCTCCAAAA
Found at i:41746107 original size:12 final size:13
Alignment explanation
Indices: 41746083--41746112 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
41746073 ATTAGGAAGC
41746083 CCCTTATATATCA
1 CCCTTATATATCA
41746096 CCCTTA-ATATCA
1 CCCTTATATATCA
41746108 CCCTT
1 CCCTT
41746113 CCTTCCTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (13 bp):
CCCTTATATATCA
Found at i:41748057 original size:37 final size:37
Alignment explanation
Indices: 41748003--41748078 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
41747993 TCTTTGGTGT
41748003 AGGAATATCGATACTATTAAACTGGAATTTGATTCCA
1 AGGAATATCGATACTATTAAACTGGAATTTGATTCCA
* * *
41748040 AGGAATA-CTGATCCTATTAGATTGGAATTTGATTCCA
1 AGGAATATC-GATACTATTAAACTGGAATTTGATTCCA
41748077 AG
1 AG
41748079 ACCAAATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (37 bp):
AGGAATATCGATACTATTAAACTGGAATTTGATTCCA
Found at i:41753419 original size:13 final size:13
Alignment explanation
Indices: 41753401--41753427 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41753391 AGCATATTGT
41753401 TCACAATTATAGA
1 TCACAATTATAGA
41753414 TCACAATTATAGA
1 TCACAATTATAGA
41753427 T
1 T
41753428 GAATCTCACA
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:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TCACAATTATAGA
Found at i:41758548 original size:94 final size:94
Alignment explanation
Indices: 41758447--41758628 Score: 355
Period size: 94 Copynumber: 1.9 Consensus size: 94
41758437 TATAAAAGAC
41758447 TAACTAAAACCCATTTTAGGACCGCTCATATTATTTTTAATTTTTTTTAAATATTGATATTATAT
1 TAACTAAAACCCATTTTAGGACCGCTCATATTATTTTTAATTTTTTTTAAATATTGATATTATAT
*
41758512 TATTTTAATATTTAATAATTTTAAAAAAG
66 TATTTTAATATTTAAAAATTTTAAAAAAG
41758541 TAACTAAAACCCATTTTAGGACCGCTCATATTATTTTTAATTTTTTTTAAATATTGATATTATAT
1 TAACTAAAACCCATTTTAGGACCGCTCATATTATTTTTAATTTTTTTTAAATATTGATATTATAT
41758606 TATTTTAATATTTAAAAATTTTA
66 TATTTTAATATTTAAAAATTTTA
41758629 TACATTTATT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (94 bp):
TAACTAAAACCCATTTTAGGACCGCTCATATTATTTTTAATTTTTTTTAAATATTGATATTATAT
TATTTTAATATTTAAAAATTTTAAAAAAG
Found at i:41761253 original size:21 final size:22
Alignment explanation
Indices: 41761228--41761270 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41761218 TGGTTTCAAA
* *
41761228 TTTT-AGTAAAATTAATTTTAT
1 TTTTAAGTAAAATAAAATTTAT
41761249 TTTTAAGTAAAATAAAATTTAT
1 TTTTAAGTAAAATAAAATTTAT
41761271 AAATTTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTAAGTAAAATAAAATTTAT
Found at i:41761295 original size:17 final size:16
Alignment explanation
Indices: 41761273--41761308 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
41761263 AAATTTATAA
41761273 ATTTCAAGTAATATATT
1 ATTTCAAGTAAT-TATT
*
41761290 ATTTCAATTAATTATT
1 ATTTCAAGTAATTATT
41761306 ATT
1 ATT
41761309 ATTGATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTTCAAGTAATTATT
Found at i:41769604 original size:19 final size:19
Alignment explanation
Indices: 41769576--41769612 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41769566 GTTTTTAAAT
*
41769576 AAAATGAAATAAACAAAAG
1 AAAATAAAATAAACAAAAG
*
41769595 AAAATAAAATAAATAAAA
1 AAAATAAAATAAACAAAA
41769613 TAAGGAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAATAAAATAAACAAAAG
Found at i:41770445 original size:171 final size:172
Alignment explanation
Indices: 41770148--41770492 Score: 683
Period size: 171 Copynumber: 2.0 Consensus size: 172
41770138 TATTATTACA
41770148 CTTAACATTTGTTAGTATTTTTAAATTGTTGATAATATATTTATATTTATAATTATATTTCAATT
1 CTTAACATTTGTTAGTATTTTTAAATTGTTGATAATATATTTATATTTATAATTATATTTCAATT
41770213 AAAATTTTATTATCAAAATTATAAAAAAAGAAACGAATGAAATTTAATTAATTAAGGATTGGGTT
66 AAAATTTTATTATCAAAATTATAAAAAAAGAAACGAATGAAATTTAATTAATTAAGGATTGGGTT
41770278 CAGTCCGATGTATTATCAGTTCAGTCAATCACATTTACGTCT
131 CAGTCCGATGTATTATCAGTTCAGTCAATCACATTTACGTCT
41770320 CTTAACATTTG-TAGTATTTTTAAATTGTTGATAATATATTTATATTTATAATTATATTTCAATT
1 CTTAACATTTGTTAGTATTTTTAAATTGTTGATAATATATTTATATTTATAATTATATTTCAATT
41770384 AAAATTTTATTATCAAAATTATAAAAAAAGAAACGAATGAAATTTAATTAATTAAGGATTGGGTT
66 AAAATTTTATTATCAAAATTATAAAAAAAGAAACGAATGAAATTTAATTAATTAAGGATTGGGTT
41770449 CAGTCCGATGTATTATCAGTTCAGTCAATCACATTTACGTCT
131 CAGTCCGATGTATTATCAGTTCAGTCAATCACATTTACGTCT
41770491 CT
1 CT
41770493 ATGTTCTAGA
Statistics
Matches: 173, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
171 162 0.94
172 11 0.06
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.42
Consensus pattern (172 bp):
CTTAACATTTGTTAGTATTTTTAAATTGTTGATAATATATTTATATTTATAATTATATTTCAATT
AAAATTTTATTATCAAAATTATAAAAAAAGAAACGAATGAAATTTAATTAATTAAGGATTGGGTT
CAGTCCGATGTATTATCAGTTCAGTCAATCACATTTACGTCT
Found at i:41778945 original size:24 final size:25
Alignment explanation
Indices: 41778913--41778964 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
41778903 AAATGTATAT
* *
41778913 TTTATATATAAT-TATATTAAATTA
1 TTTAAATATAATCTAAATTAAATTA
* *
41778937 TTTAAATATTATCTAAATTAATTTA
1 TTTAAATATAATCTAAATTAAATTA
41778962 TTT
1 TTT
41778965 TTCATTTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTAAATATAATCTAAATTAAATTA
Found at i:41784631 original size:129 final size:129
Alignment explanation
Indices: 41784399--41784655 Score: 433
Period size: 129 Copynumber: 2.0 Consensus size: 129
41784389 AAAGAAGGGA
* * *
41784399 AGCTTTTCCACCCATGTATTTTTTATCTATAAAACTTAAATCTGAGACCTTACACATTGACATCA
1 AGCTTTTCCACCCATGTATTTTTTATCTACAAAACTTAAATATGAGACCTTACACATAGACATCA
*
41784464 AGCTTTTTAACACTTGATTGAACAAGTGGCAGTCTCTTACGATCGAAAGTTCAAAATTTAAGGC
66 AGCTTTTTAACACTTGATTGAACAAGTGGCAGTCTCTTACGATCGAAAGTTAAAAATTTAAGGC
* *
41784528 AGCTTTTCCACCCTTGTATTTTTTATCTACAAAACTTAAATATGAGACCTTACTCATAGACATCA
1 AGCTTTTCCACCCATGTATTTTTTATCTACAAAACTTAAATATGAGACCTTACACATAGACATCA
* **
41784593 AGCTTTTTAACACTTGATTGAACAAGTGGCAGTTTCTTATTATCGAAAGTTAAAAATTTAAGG
66 AGCTTTTTAACACTTGATTGAACAAGTGGCAGTCTCTTACGATCGAAAGTTAAAAATTTAAGG
41784656 GTAAAATTGT
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 119 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (129 bp):
AGCTTTTCCACCCATGTATTTTTTATCTACAAAACTTAAATATGAGACCTTACACATAGACATCA
AGCTTTTTAACACTTGATTGAACAAGTGGCAGTCTCTTACGATCGAAAGTTAAAAATTTAAGGC
Found at i:41787756 original size:3 final size:3
Alignment explanation
Indices: 41787748--41787777 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
41787738 ATAAATTTCA
*
41787748 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41787778 AATCGTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:41787876 original size:35 final size:35
Alignment explanation
Indices: 41787832--41787902 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
41787822 TACATACACT
* * * * *
41787832 TATACACATACTTTTTTTTGTAATATATATATACA
1 TATAAACATACCTATTTTTATAAAATATATATACA
*
41787867 TATAAACATACCTATTTTTATAAAATATTTATACA
1 TATAAACATACCTATTTTTATAAAATATATATACA
41787902 T
1 T
41787903 GTATATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.46
Consensus pattern (35 bp):
TATAAACATACCTATTTTTATAAAATATATATACA
Found at i:41787952 original size:44 final size:44
Alignment explanation
Indices: 41787904--41788005 Score: 98
Period size: 44 Copynumber: 2.3 Consensus size: 44
41787894 TTTATACATG
* * *
41787904 TATATATTTATAATACACGCACATATTTCCT-ATTTTTATAAACC
1 TATATATATAT-ATACACACACATATTTCATAATTTTTATAAACC
* ** *
41787948 TATATGTATATATACTTACACATATTTCATAATTTTTATATATATC
1 TATATATATATATACACACACATATTTCATAATTTTTATA-A-ACC
*
41787994 TATGTATATATA
1 TATATATATATA
41788006 CATATTTTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
43 15 0.33
44 18 0.39
45 1 0.02
46 12 0.26
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (44 bp):
TATATATATATATACACACACATATTTCATAATTTTTATAAACC
Found at i:41788006 original size:44 final size:43
Alignment explanation
Indices: 41787923--41788006 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
41787913 ATAATACACG
* *
41787923 CACATATTTCCTATTTTTATAAACCTATATGTATATATACTTA
1 CACATATTTCATATTTTTATAAACATATATGTATATATACTTA
* * *
41787966 CACATATTTCATAATTTTTATATATATCTATGTATATATAC
1 CACATATTTCAT-ATTTTTATAAACATATATGTATATATAC
41788007 ATATTTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 11 0.31
44 24 0.69
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (43 bp):
CACATATTTCATATTTTTATAAACATATATGTATATATACTTA
Found at i:41788144 original size:37 final size:40
Alignment explanation
Indices: 41788059--41788146 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 40
41788049 ATTCTATATA
*
41788059 ATAATTTTAAATATATACTTACATATATTTTTCATATTTCC
1 ATAATTTTATATATATAC-TACATATATTTTTCATATTTCC
* * * *
41788100 ATTATTTTATATATATA-TATATATCTTTTTCAT-TTT-T
1 ATAATTTTATATATATACTACATATATTTTTCATATTTCC
41788137 ATAATTTTAT
1 ATAATTTTAT
41788147 TCATTTTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 9 0.22
38 3 0.07
39 14 0.34
41 15 0.37
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (40 bp):
ATAATTTTATATATATACTACATATATTTTTCATATTTCC
Found at i:41788716 original size:288 final size:288
Alignment explanation
Indices: 41788200--41788775 Score: 1127
Period size: 288 Copynumber: 2.0 Consensus size: 288
41788190 TAGTTTTTTT
41788200 TTTTTATATATTTGCTTATTTATTTGTTATTATGTATACATGATTGACTTGTCTTTTATATTTAT
1 TTTTTATATATTTGCTTATTTATTTGTTATTATGTATACATGATTGACTTGTCTTTTATATTTAT
41788265 TTCATTTTTATGATTGTTCGTATTATTCATACTTACATTACCGAATTCATTATATTAACATCATG
66 TTCATTTTTATGATTGTTCGTATTATTCATACTTACATTACCGAATTCATTATATTAACATCATG
41788330 TTTTATTTTTACCATTTTGTGTTAAAATTGTCTTTGTTCAATGTATTAAAGTAGACTTTTTGAAT
131 TTTTATTTTTACCATTTTGTGTTAAAATTGTCTTTGTTCAATGTATTAAAGTAGACTTTTTGAAT
41788395 AAACAAAATTTCGAGTTTAGATTTGAGAAAGTCGTGCCCTAACTTATTGGGTTTTGATTTTCACA
196 AAACAAAATTTCGAGTTTAGATTTGAGAAAGTCGTGCCCTAACTTATTGGGTTTTGATTTTCACA
41788460 ATAAATCTAAACACGTGAGTCTTTTCAG
261 ATAAATCTAAACACGTGAGTCTTTTCAG
41788488 TTTTTATATATTTGCTTATTTATTTGTTATTATGTATACATGATTGACTTGTCTTTTATATTTAT
1 TTTTTATATATTTGCTTATTTATTTGTTATTATGTATACATGATTGACTTGTCTTTTATATTTAT
41788553 TTCATTTTTATGATTGTTCGTATTATTCATACTTACATTACCGAATTCATTATATTAACATCATG
66 TTCATTTTTATGATTGTTCGTATTATTCATACTTACATTACCGAATTCATTATATTAACATCATG
*
41788618 TTTTATTTTTACCATTTTGTGTTAAAATTGTCTTTGTTCAATGTA-TAAATTATGACTTTTTGAA
131 TTTTATTTTTACCATTTTGTGTTAAAATTGTCTTTGTTCAATGTATTAAAGTA-GACTTTTTGAA
41788682 TAAACAAAATTTCGAGTTTAGATTTGAGAAAGTCGTGCCCTAACTTATTGGGTTTTGATTTTCAC
195 TAAACAAAATTTCGAGTTTAGATTTGAGAAAGTCGTGCCCTAACTTATTGGGTTTTGATTTTCAC
41788747 AATAAATCTAAACACGTGAGTCTTTTCAG
260 AATAAATCTAAACACGTGAGTCTTTTCAG
41788776 ACTCAAGTTT
Statistics
Matches: 286, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
287 6 0.02
288 280 0.98
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.48
Consensus pattern (288 bp):
TTTTTATATATTTGCTTATTTATTTGTTATTATGTATACATGATTGACTTGTCTTTTATATTTAT
TTCATTTTTATGATTGTTCGTATTATTCATACTTACATTACCGAATTCATTATATTAACATCATG
TTTTATTTTTACCATTTTGTGTTAAAATTGTCTTTGTTCAATGTATTAAAGTAGACTTTTTGAAT
AAACAAAATTTCGAGTTTAGATTTGAGAAAGTCGTGCCCTAACTTATTGGGTTTTGATTTTCACA
ATAAATCTAAACACGTGAGTCTTTTCAG
Found at i:41790378 original size:19 final size:20
Alignment explanation
Indices: 41790338--41790381 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
41790328 GTCTCTTTAG
* *
41790338 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
41790357 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
41790376 GCATTA
1 GCATTA
41790382 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:41790735 original size:46 final size:46
Alignment explanation
Indices: 41790668--41790760 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
41790658 TAATGAAGGT
41790668 CCTGCATATCTTTCAAATTTTACTCCAACCGACATCCAAGCACAAC
1 CCTGCATATCTTTCAAATTTTACTCCAACCGACATCCAAGCACAAC
*
41790714 CCTGCATATCTTTCAGATTTTACTCCAACCGACATCCAAGCACAAC
1 CCTGCATATCTTTCAAATTTTACTCCAACCGACATCCAAGCACAAC
41790760 C
1 C
41790761 AAACACATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.35, G:0.08, T:0.26
Consensus pattern (46 bp):
CCTGCATATCTTTCAAATTTTACTCCAACCGACATCCAAGCACAAC
Found at i:41792493 original size:7 final size:7
Alignment explanation
Indices: 41792480--41792565 Score: 61
Period size: 7 Copynumber: 12.0 Consensus size: 7
41792470 TCAAAAAAAT
41792480 TAAAAAA
1 TAAAAAA
41792487 -AATAAAA
1 TAA-AAAA
*
41792494 TCAAAAA
1 TAAAAAA
*
41792501 T-CAAAA
1 TAAAAAA
41792507 TCAAAAAAA
1 T--AAAAAA
41792516 TCAAAAAA
1 T-AAAAAA
*
41792524 TCAAAAA
1 TAAAAAA
41792531 TAAAAAA
1 TAAAAAA
*
41792538 T-CAAAA
1 TAAAAAA
41792544 TCAAAAAA
1 T-AAAAAA
*
41792552 TCAAAAA
1 TAAAAAA
41792559 TAAAAAA
1 TAAAAAA
41792566 AAATCAAAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
6 12 0.19
7 32 0.52
8 13 0.21
9 5 0.08
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAAAAA
Found at i:41792506 original size:22 final size:21
Alignment explanation
Indices: 41792474--41792565 Score: 96
Period size: 22 Copynumber: 4.2 Consensus size: 21
41792464 TCAGAATCAA
*
41792474 AAAAATTAAAAAAAATAAAATC
1 AAAAATCAAAAAAAA-AAAATC
*
41792496 AAAAATCAAAATCAAAAAAATC
1 AAAAATCAAAA-AAAAAAAATC
*
41792518 AAAAAATCAAAAATAAAAAATC
1 -AAAAATCAAAAAAAAAAAATC
* *
41792540 -AAAATCAAAAAATCAAAAATA
1 AAAAATCAAAAAA-AAAAAATC
41792561 AAAAA
1 AAAAA
41792566 AAATCAAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
20 11 0.19
21 6 0.10
22 28 0.47
23 14 0.24
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAAATCAAAAAAAAAAAATC
Found at i:41792512 original size:28 final size:27
Alignment explanation
Indices: 41792474--41792564 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
41792464 TCAGAATCAA
*
41792474 AAAAATTAAAAAAAATAAAATCAAAAAT
1 AAAAATCAAAAAAAA-AAAATCAAAAAT
*
41792502 CAAAATCAAAAAAATCAAAAAATCAAAAAT
1 AAAAATC-AAAAAA--AAAAAATCAAAAAT
**
41792532 AAAAAATCAAAATCAAAAAATCAAAAAT
1 -AAAAATCAAAAAAAAAAAATCAAAAAT
41792560 AAAAA
1 AAAAA
41792565 AAAATCAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
27 5 0.09
28 19 0.35
29 6 0.11
30 16 0.30
31 8 0.15
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (27 bp):
AAAAATCAAAAAAAAAAAATCAAAAAT
Found at i:41792513 original size:14 final size:14
Alignment explanation
Indices: 41792483--41792581 Score: 88
Period size: 14 Copynumber: 7.4 Consensus size: 14
41792473 AAAAAATTAA
41792483 AAAAAAT-AAAATC
1 AAAAAATCAAAATC
41792496 -AAAAATCAAAATC
1 AAAAAATCAAAATC
41792509 ---AAA--AAAATC
1 AAAAAATCAAAATC
41792518 AAAAAATCAAAAAT-
1 AAAAAATC-AAAATC
41792532 AAAAAATCAAAATC
1 AAAAAATCAAAATC
*
41792546 AAAAAATCAAAAATAAA
1 AAAAAATC-AAAAT--C
*
41792563 AAAAAATCAAAGTC
1 AAAAAATCAAAATC
41792577 AAAAA
1 AAAAA
41792582 TAGGAGAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 21
0.75 0.03 0.22
Matches are distributed among these distances:
9 6 0.08
11 3 0.04
12 9 0.12
13 11 0.15
14 21 0.29
15 10 0.14
16 4 0.06
17 8 0.11
ACGTcount: A:0.76, C:0.10, G:0.01, T:0.13
Consensus pattern (14 bp):
AAAAAATCAAAATC
Found at i:41792565 original size:28 final size:27
Alignment explanation
Indices: 41792490--41792568 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 27
41792480 TAAAAAAAAT
41792490 AAAATCAAAAATCAAAATCAAAAAAATCAA
1 AAAATCAAAAAT-AAAA--AAAAAAATCAA
*
41792520 AAAATCAAAAATAAAAAATCAAAATCAA
1 AAAATCAAAAATAAAAAA-AAAAATCAA
41792548 AAAATCAAAAATAAAAAAAAA
1 AAAATCAAAAATAAAAAAAAA
41792569 TCAAAGTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
27 4 0.09
28 26 0.57
29 4 0.09
30 12 0.26
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (27 bp):
AAAATCAAAAATAAAAAAAAAAATCAA
Found at i:41792567 original size:37 final size:37
Alignment explanation
Indices: 41792468--41792567 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
41792458 ATGAGTTCAG
* * *
41792468 AATCAAAAAAATTAAAAAAAATAAAATCAAAAATCAA
1 AATCAAAAAAATCAAAAAAAAAAAAATAAAAAATCAA
**
41792505 AATCAAAAAAATCAAAAAATCAAAAATAAAAAATCAA
1 AATCAAAAAAATCAAAAAAAAAAAAATAAAAAATCAA
41792542 AATC-AAAAAATCAAAAATAAAAAAAA
1 AATCAAAAAAATCAAAAA-AAAAAAAA
41792568 ATCAAAGTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 13 0.24
37 42 0.76
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (37 bp):
AATCAAAAAAATCAAAAAAAAAAAAATAAAAAATCAA
Found at i:41792579 original size:37 final size:37
Alignment explanation
Indices: 41792468--41792580 Score: 119
Period size: 37 Copynumber: 3.1 Consensus size: 37
41792458 ATGAGTTCAG
* *
41792468 AATCAAAAAAAT-TAAAA-AAAATAAAATCAAAAATCAA
1 AATCAAAAAAATCAAAAATAAAAAAAAATC--AAATCAA
*
41792505 AATCAAAAAAATCAAAAAATCAAAAATAAA--AAATCAA
1 AATCAAAAAAATC-AAAAAT-AAAAAAAAATCAAATCAA
41792542 AATC-AAAAAATCAAAAATAAAAAAAAATCAAAGTCAA
1 AATCAAAAAAATCAAAAATAAAAAAAAATCAAA-TCAA
41792579 AA
1 AA
41792581 ATAGGAGAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
34 8 0.12
35 6 0.09
36 11 0.17
37 29 0.45
39 4 0.06
41 7 0.11
ACGTcount: A:0.75, C:0.10, G:0.01, T:0.14
Consensus pattern (37 bp):
AATCAAAAAAATCAAAAATAAAAAAAAATCAAATCAA
Found at i:41792581 original size:17 final size:17
Alignment explanation
Indices: 41792474--41792573 Score: 74
Period size: 17 Copynumber: 6.2 Consensus size: 17
41792464 TCAGAATCAA
*
41792474 AAAAATTAAAAAAAAT-
1 AAAAATAAAAAAAAATC
41792490 -AAAATCAAAAATCAAAATC
1 AAAAAT-AAAAA--AAAATC
*
41792509 AAAAA-AATCAAAAAATC
1 AAAAATAA-AAAAAAATC
41792526 AAAAAT---AAAAAATC
1 AAAAATAAAAAAAAATC
*
41792540 -AAAAT--CAAAAAATC
1 AAAAATAAAAAAAAATC
41792554 AAAAATAAAAAAAAATC
1 AAAAATAAAAAAAAATC
41792571 AAA
1 AAA
41792574 GTCAAAAATA
Statistics
Matches: 70, Mismatches: 3, Indels: 21
0.74 0.03 0.22
Matches are distributed among these distances:
13 5 0.07
14 16 0.23
15 10 0.14
16 4 0.06
17 22 0.31
18 7 0.10
19 2 0.03
20 4 0.06
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAAAAAATC
Found at i:41792595 original size:6 final size:6
Alignment explanation
Indices: 41792586--41792625 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
41792576 CAAAAATAGG
41792586 AGAAAA AGAAAGA AGAAAAA AGAAAA AGAAAA AGAAAA AG
1 AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA AG
41792626 GAGAGGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 23 0.72
7 6 0.19
8 3 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:41792624 original size:7 final size:7
Alignment explanation
Indices: 41792588--41792624 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
41792578 AAAATAGGAG
41792588 AAAAAGA
1 AAAAAGA
*
41792595 AAGAAGA
1 AAAAAGA
41792602 AAAAAG-
1 AAAAAGA
41792608 AAAAAG-
1 AAAAAGA
41792614 AAAAAGA
1 AAAAAGA
41792621 AAAA
1 AAAA
41792625 GGAGAGGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:41793401 original size:6 final size:7
Alignment explanation
Indices: 41793383--41793434 Score: 61
Period size: 7 Copynumber: 7.0 Consensus size: 7
41793373 TTGAGTCAAA
41793383 AAAAATG
1 AAAAATG
41793390 AAAAAATG
1 -AAAAATG
41793398 AAAAATG
1 AAAAATG
41793405 AAAAATG
1 AAAAATG
41793412 AAAAAAATG
1 --AAAAATG
41793421 AAAAA-G
1 AAAAATG
41793427 TAAAAATG
1 -AAAAATG
41793435 GAGAGGCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 24 0.60
8 8 0.20
9 7 0.17
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:41793401 original size:7 final size:8
Alignment explanation
Indices: 41793382--41793425 Score: 65
Period size: 7 Copynumber: 5.6 Consensus size: 8
41793372 TTTGAGTCAA
41793382 AAAAAATG
1 AAAAAATG
41793390 AAAAAATG
1 AAAAAATG
41793398 -AAAAATG
1 AAAAAATG
41793405 -AAAAATG
1 AAAAAATG
41793412 AAAAAAATG
1 -AAAAAATG
41793421 AAAAA
1 AAAAA
41793426 GTAAAAATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.41
8 13 0.38
9 7 0.21
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:41793417 original size:23 final size:22
Alignment explanation
Indices: 41793383--41793434 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
41793373 TTGAGTCAAA
41793383 AAAAATGAAAAAATGAAAAA-T
1 AAAAATGAAAAAATGAAAAAGT
41793404 GAAAAATGAAAAAAATGAAAAAGT
1 -AAAAATG-AAAAAATGAAAAAGT
41793428 AAAAATG
1 AAAAATG
41793435 GAGAGGCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.25
23 20 0.71
24 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (22 bp):
AAAAATGAAAAAATGAAAAAGT
Found at i:41794713 original size:43 final size:43
Alignment explanation
Indices: 41794666--41794803 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 43
41794656 AAAACAAAGC
41794666 CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
1 CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
* * * * * ** * *
41794709 CTTGCCTTC-CTGCGTTAACAGTGAAGCAGATCGAA-AA-CAAAGC
1 CTTGCCTTCATTG-GTT-GCAGTGGAGCTGGTTAAAGAAGCAGA-T
* *
41794752 CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAGGTAGAT
1 CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
41794795 CTTGCCTTC
1 CTTGCCTTC
41794804 CTGCGTTAAC
Statistics
Matches: 69, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
42 17 0.25
43 36 0.52
44 16 0.23
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (43 bp):
CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
Found at i:41794752 original size:86 final size:86
Alignment explanation
Indices: 41794607--41795392 Score: 812
Period size: 86 Copynumber: 9.1 Consensus size: 86
41794597 AGAACATACA
** *
41794607 GGTTAAAGAATTAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
1 GGTTAAAGAAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
* *
41794672 TTCATTGGTTG-CAGTGGAGCT
66 TTCATCGGTTGTGA-TGGAGCT
** * *
41794693 GGTTAAAGAAGCAGATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAAAGCCTTGCC
1 GGTTAAAGAAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
* *
41794758 TTCATTGGTTG-CAGTGGAGCT
66 TTCATCGGTTGTGA-TGGAGCT
*** * * *
41794779 GGTTAAAGAGGTAGATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAA-TAAGCCTTGCC
1 GGTTAAAGAAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
* **
41794843 TTCATTGGTT-ACAGTGGAGCT
66 TTCATCGGTTGTGA-TGGAGCT
*** *
41794864 GGTTAAAGAGGTAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AAGCCTTGCC
1 GGTTAAAGAAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
41794928 TCTC-TCGGTTGTGATGGAGCT
66 T-TCATCGGTTGTGATGGAGCT
* * *
41794949 GGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CGTT
1 GGTTAAAGA-AAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTT
* * *
41795013 GCC-TCTTTCGATTGTGATGGAGTT
63 GCCTTC-ATCGGTTGTGATGGAGCT
* * * *
41795037 GATTGAAGACAAAAGATCTTGCTTTCTTGCATTAACAGCGAAGCAGATCGAAAAC-AAGCCTTGC
1 GGTTAAAGA-AAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGC
41795101 CTCTC-TCGGTTGTGATGGAGCT
65 CT-TCATCGGTTGTGATGGAGCT
* * *
41795123 GGTTGAAGACAAAAGATCTTGCCTTCTTGCATTAACAGCGAAGCAGATCGAAAAC-AAGCATTGC
1 GGTTAAAGA-AAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGC
41795187 CTTCATCGGTTGTGATGGAGCT
65 CTTCATCGGTTGTGATGGAGCT
* * * * * *
41795209 GGTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAACAGGTCGAAGATACAAA-CCTT
1 GGTTAAAGA-AAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTT
41795273 GCCTCTC-TCGGTTGTGATGGAGCT
63 GCCT-TCATCGGTTGTGATGGAGCT
* * * * * * * *
41795297 GGTTGAAGACAAGAGATCTTGCATTCTTGCATTGACAGCGAAGCAGGTCGAAGACAAA-CCTTAC
1 GGTTAAAGA-AAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGC
* *
41795361 CTCTC-TCAGTTAT-AGTGGAGCT
65 CT-TCATCGGTTGTGA-TGGAGCT
*
41795383 GGTTGAAGAA
1 GGTTAAAGAA
41795393 TTTCAGATCT
Statistics
Matches: 634, Mismatches: 47, Indels: 39
0.88 0.07 0.05
Matches are distributed among these distances:
85 119 0.19
86 360 0.57
87 3 0.00
88 146 0.23
89 6 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (86 bp):
GGTTAAAGAAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
TTCATCGGTTGTGATGGAGCT
Found at i:41794845 original size:42 final size:42
Alignment explanation
Indices: 41794623--41794928 Score: 128
Period size: 43 Copynumber: 7.2 Consensus size: 42
41794613 AGAATTAGAT
*
41794623 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAA-TAAGC
* * * * * * ** ** *
41794666 CTTGCCTTCATTG-GTT-GCAGTGGAGCTGGTTAAAGAAGCAGAT
1 CTTGCCTTC-CTGCGTTAACAGCGAAGCAGATCGAA-AATAAG-C
* *
41794709 CTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAA-TAAGC
* * * * * * * *
41794752 CTTGCCTTCATTG-GTT-GCAGTGGAGCTGGT-TAAAGAGGT-AGAT
1 CTTGCCTTC-CTGCGTTAACAGCGAAGCAGATCGAAA-A--TAAG-C
*
41794795 CTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAATAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAGC
* * * * * * *
41794837 CTTGCCTTCATTG-GTT-ACAGTGGAGCTGGT-TAAAGAGGT-AGAT
1 CTTGCCTTC-CTGCGTTAACAGCGAAGCAGATCGAAA-A--TAAG-C
*
41794880 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAGC
41794922 CTTGCCT
1 CTTGCCT
41794929 CTCTCGGTTG
Statistics
Matches: 185, Mismatches: 55, Indels: 47
0.64 0.19 0.16
Matches are distributed among these distances:
40 3 0.02
41 13 0.07
42 54 0.29
43 71 0.38
44 38 0.21
45 6 0.03
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (42 bp):
CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAGC
Found at i:41795090 original size:174 final size:172
Alignment explanation
Indices: 41794619--41795392 Score: 902
Period size: 174 Copynumber: 4.5 Consensus size: 172
41794609 TTAAAGAATT
*
41794619 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTG-
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAA-CCTTGCCTTCATTGGTTGT
* * *
41794683 CAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACA
65 CAGTGGAGCTGGTTAAAGAAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAAC-
* * * ***
41794748 AAGCCTTGCCT-TCATTGGTTG-CAGTGGAGCTGGTTAAAGA-GGT
129 AAGCCTTGCCTCTC-TCGGTTGTGA-TGGAGCTGGTTGAAGACAAA
* * * * *
41794791 AGATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAAATAAGCCTTGCCTTCATTGGTT-AC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAACCTTGCCTTCATTGGTTGTC
*** *
41794855 AGTGGAGCTGGTTAAAGAGGTAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAA
66 AGTGGAGCTGGTTAAAGAAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAA
41794920 GCCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
131 GCCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
* * * *
41794962 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACGTTGCC-TCTTTCGATT
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAACCTTGCCTTCATT-GGTT
* * * * * * *
41795026 GTGA-TGGAGTTGATTGAAGACAAAAGATCTTGCTTTCTTGCATTAACAGCGAAGCAGATCGAAA
63 GTCAGTGGAGCTGGTTAAAGA-AACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAA
41795090 ACAAGCCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
127 ACAAGCCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
* * * * *
41795136 AGATCTTGCCTTCTTGCATTAACAGCGAAGCAGATCGAAAACAAGCATTGCCTTCATCGGTTGTG
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAACCTTGCCTTCATTGGTTGTC
* * * * *
41795201 A-TGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAACAGGTCGAAGATA
66 AGTGGAGCTGGTTAAAGA-AACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-A
* *
41795265 CAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAG
128 CAAGCCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
* * * * * * ** *
41795310 AGATCTTGCATTCTTGCATTGACAGCGAAGCAGGTCGAAGACAAACCTTACCTCTC-TCAGTTAT
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAACCTTGCCT-TCATTGGTTGT
*
41795374 -AGTGGAGCTGGTTGAAGAA
65 CAGTGGAGCTGGTTAAAGAA
41795393 TTTCAGATCT
Statistics
Matches: 530, Mismatches: 58, Indels: 27
0.86 0.09 0.04
Matches are distributed among these distances:
170 32 0.06
171 117 0.22
172 114 0.22
173 32 0.06
174 233 0.44
175 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (172 bp):
AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAACCTTGCCTTCATTGGTTGTC
AGTGGAGCTGGTTAAAGAAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAA
GCCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
Found at i:41795198 original size:260 final size:257
Alignment explanation
Indices: 41794619--41795392 Score: 963
Period size: 260 Copynumber: 3.0 Consensus size: 257
41794609 TTAAAGAATT
*
41794619 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTG-
1 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AAGCCTTGCCTTCATCGGTTGT
* * * * * *
41794683 CAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAA-AA
65 GA-TGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGAA
* * * *** * *
41794746 CAAAGCCTTGCCTTCATT-GGTTG-CAGTGGAGCTGGTTAAAGA-GGTAGATCTTGCCTTCCTGC
129 CAAA-CCTTGCC-TCTTTCGGTTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCATTCTTGC
* * * * * *
41794808 GTTAACAACGAAGCAGATCGAAAATAAGCCTTGCCT-TCATTGGTTACAGTGGAGCTGGTTAAAG
191 ATTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTCTC-TCGGTT-TAGTGGAGCTGGTTGAAG
***
41794872 AGGT
254 AAAA
41794876 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTCTC-TCGGTTGT
1 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCT-TCATCGGTTGT
*
41794940 GATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACA
65 GATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGA-A
* * * * *
41795005 CAAACGTTGCCTCTTTCGATTGTGATGGAGTTGATTGAAGACAAAAGATCTTGCTTTCTTGCATT
129 CAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCATTCTTGCATT
41795070 AACAGCGAAGCAGATCGAAAACAAGCCTTGCCTCTCTCGGTTGT-GATGGAGCTGGTTGAAGACA
194 AACAGCGAAGCAGATCGAAAACAAGCCTTGCCTCTCTCGGTT-TAG-TGGAGCTGGTTGAAGA-A
41795134 AA
256 AA
* * *
41795136 AGATCTTGCCTTCTTGCATTAACAGCGAAGCAGATCGAAAACAAGCATTGCCTTCATCGGTTGTG
1 AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATCGGTTGTG
* * *
41795201 ATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAACAGGTCGAAGATAC
66 ATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGA-AC
* * *
41795266 AAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAGAGATCTTGCATTCTTGCATTG
130 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCATTCTTGCATTA
* * * * *
41795331 ACAGCGAAGCAGGTCGAAGACAAACCTTACCTCTCTCAGTTATAGTGGAGCTGGTTGAAGAA
195 ACAGCGAAGCAGATCGAAAACAAGCCTTGCCTCTCTCGGTT-TAGTGGAGCTGGTTGAAGAA
41795393 TTTCAGATCT
Statistics
Matches: 452, Mismatches: 52, Indels: 24
0.86 0.10 0.05
Matches are distributed among these distances:
256 32 0.07
257 86 0.19
258 25 0.06
259 77 0.17
260 231 0.51
261 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (257 bp):
AGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATCGGTTGTG
ATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGAACA
AACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCATTCTTGCATTAA
CAGCGAAGCAGATCGAAAACAAGCCTTGCCTCTCTCGGTTTAGTGGAGCTGGTTGAAGAAAA
Found at i:41795503 original size:44 final size:44
Alignment explanation
Indices: 41795397--41796204 Score: 285
Period size: 44 Copynumber: 18.3 Consensus size: 44
41795387 GAAGAATTTC
* * * * *
41795397 AGATCTTATCTCCCTCAGATTACAGCGGAGTAGATTG-AAGACA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAAA
** * *
41795440 CTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTGAAATAAA
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATAAA
* ** * * *
41795484 AGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCATTAGATTGAAGCT
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTG-A--A-A-T-AA--A
* * * *
41795536 GGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 AG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAAA
* * ** * * * *
41795582 TGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCG-CAT--C
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATAAA
* * * * ** ***
41795623 AGGTCTTATTTCCCTGAGATTGCAGTGGAACAGACCGAAGAATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-AATAAA
* * * **
41795669 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTTAAGCTAGT
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-ATAAA
* *
41795714 A-ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAAA
* * * * * * *
41795757 TGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCACAT--C
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATAAA
* * * * ** ***
41795798 AGGTCTTATTTCCCTGAGATTGCAGTGGAACAGACCGAAGAATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-AATAAA
* * * **
41795844 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTTAAGCTAGT
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-ATAAA
* *
41795889 A-ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAAA
* * * * * * *
41795932 TGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCACAT--C
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATAAA
* * * * ** ***
41795973 AGGTCTTATTTCCCTGAGATTGCAGTGGAACAGACCGAAGAATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-AATAAA
* * * *
41796019 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCG-AAGACA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAAA
** * *
41796062 CTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTGAAATAAA
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATAAA
* ** * * * *
41796106 AGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCG-CAT--C
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATAAA
* * ** ***
41796147 AGGTCTTATTTCCCTGAGATTACAGTGGAATAGATTGAAAATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-AAATAAA
41796192 AGATCTTATCTCC
1 AGATCTTATCTCC
41796205 TAAGGTGGAG
Statistics
Matches: 556, Mismatches: 164, Indels: 88
0.69 0.20 0.11
Matches are distributed among these distances:
41 101 0.18
42 6 0.01
43 82 0.15
44 217 0.39
45 19 0.03
46 93 0.17
47 1 0.00
48 3 0.01
49 2 0.00
50 3 0.01
51 1 0.00
52 1 0.00
53 1 0.00
54 25 0.04
55 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAAA
Found at i:41795752 original size:175 final size:175
Alignment explanation
Indices: 41795525--41796204 Score: 1161
Period size: 175 Copynumber: 3.9 Consensus size: 175
41795515 AGATCGCATT
*
41795525 AGATTGAAGCTGGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTA
1 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTA
*
41795590 TCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATTTCCCTGAGATTGCAGTGGAACA
66 TCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATTTCCCTGAGATTGCAGTGGAACA
41795655 GACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGC
131 GACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGC
* *
41795700 AGATTTAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTA
1 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTA
*
41795765 TCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGGTCTTATTTCCCTGAGATTGCAGTGGAACA
66 TCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATTTCCCTGAGATTGCAGTGGAACA
41795830 GACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGC
131 GACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGC
* *
41795875 AGATTTAAGCTAGTAATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTA
1 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTA
*
41795940 TCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGGTCTTATTTCCCTGAGATTGCAGTGGAACA
66 TCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATTTCCCTGAGATTGCAGTGGAACA
41796005 GACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGC
131 GACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGC
* * * *
41796050 AGATCGAAGAC-ACT-ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTGAAATAAAAGATCT
1 AGATTGAAG-CTAGTAATCCTATCTCCCTGAGA-TTACAGTGGAGCGGATTAAAATAAATGATCT
* *
41796112 TATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATTTCCCTGAGATTACAGTGGAA
64 TATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATTTCCCTGAGATTGCAGTGGAA
* **
41796177 TAGATTGAA-AATTTCAGATCTTATCTCC
129 CAGACCGAAGAATTTCAGATCTTATCTCC
41796205 TAAGGTGGAG
Statistics
Matches: 486, Mismatches: 17, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
173 20 0.04
174 111 0.23
175 354 0.73
176 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (175 bp):
AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTA
TCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGGTCTTATTTCCCTGAGATTGCAGTGGAACA
GACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGC
Found at i:41799453 original size:8 final size:9
Alignment explanation
Indices: 41799298--41799515 Score: 80
Period size: 9 Copynumber: 24.0 Consensus size: 9
41799288 AATGAATACC
*
41799298 TATAGTTTT
1 TATAATTTT
41799307 TCATAATTTT
1 T-ATAATTTT
41799317 TA-AATTTT
1 TATAATTTT
41799325 TAT--TTCTT
1 TATAATT-TT
**
41799333 TCATAATTCA
1 T-ATAATTTT
41799343 TATAATTTTTT
1 TATAA--TTTT
* *
41799354 TATGATTTA
1 TATAATTTT
*
41799363 TATAATTCT
1 TATAATTTT
41799372 T-TAATTTGT
1 TATAATTT-T
*
41799381 TTTAATTTT
1 TATAATTTT
*
41799390 T-TGCACTTTT
1 TAT--AATTTT
41799400 CTAT-ATTTT
1 -TATAATTTT
41799409 TATGATATTTT
1 TAT-A-ATTTT
*
41799420 AAATAATTTT
1 -TATAATTTT
*
41799430 CATAATTTT
1 TATAATTTT
*
41799439 TACAATTTT
1 TATAATTTT
*
41799448 T-TAATTTA
1 TATAATTTT
*
41799456 TAT-ATTTG
1 TATAATTTT
41799464 T-T-ATTTT
1 TATAATTTT
*
41799471 AATAATTTT
1 TATAATTTT
** *
41799480 TGCAGTTTT
1 TATAATTTT
41799489 TAATAATTTT
1 T-ATAATTTT
*
41799499 TATAATTTG
1 TATAATTTT
41799508 TAT-ATTTT
1 TATAATTTT
41799516 ATGATTTTAA
Statistics
Matches: 156, Mismatches: 31, Indels: 45
0.67 0.13 0.19
Matches are distributed among these distances:
7 7 0.04
8 36 0.23
9 64 0.41
10 31 0.20
11 15 0.10
12 3 0.02
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (9 bp):
TATAATTTT
Found at i:41806041 original size:19 final size:20
Alignment explanation
Indices: 41806009--41806046 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
41805999 CATTTTCTTC
*
41806009 CTGAAAAAA-TTAAATTCAA
1 CTGAAAAAACTAAAATTCAA
*
41806028 CTGAAAATACTAAAATTCA
1 CTGAAAAAACTAAAATTCA
41806047 GGAGAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (20 bp):
CTGAAAAAACTAAAATTCAA
Found at i:41812780 original size:26 final size:27
Alignment explanation
Indices: 41812728--41812780 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
41812718 TCTAGAGAGA
* *
41812728 AATATTAGATTGATTGATCTGAGAATT
1 AATATTAGATTGATTGAACCGAGAATT
*
41812755 AATA-TAGATTGATTGAACCGATAATT
1 AATATTAGATTGATTGAACCGAGAATT
41812781 GAACTAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (27 bp):
AATATTAGATTGATTGAACCGAGAATT
Found at i:41816239 original size:118 final size:118
Alignment explanation
Indices: 41816107--41816342 Score: 472
Period size: 118 Copynumber: 2.0 Consensus size: 118
41816097 AAAAAATTAC
41816107 ATTTCTTCTAATATCTTTATTATTTAATTATTTTATAAACAAATTCATCAACTATATTAAAATAT
1 ATTTCTTCTAATATCTTTATTATTTAATTATTTTATAAACAAATTCATCAACTATATTAAAATAT
41816172 TGGACTCACTTGTTAAAACTTTAATTTTTTTTTAAAAAGGAAAACTTTAATCA
66 TGGACTCACTTGTTAAAACTTTAATTTTTTTTTAAAAAGGAAAACTTTAATCA
41816225 ATTTCTTCTAATATCTTTATTATTTAATTATTTTATAAACAAATTCATCAACTATATTAAAATAT
1 ATTTCTTCTAATATCTTTATTATTTAATTATTTTATAAACAAATTCATCAACTATATTAAAATAT
41816290 TGGACTCACTTGTTAAAACTTTAATTTTTTTTTAAAAAGGAAAACTTTAATCA
66 TGGACTCACTTGTTAAAACTTTAATTTTTTTTTAAAAAGGAAAACTTTAATCA
41816343 TTGAAGTTTT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (118 bp):
ATTTCTTCTAATATCTTTATTATTTAATTATTTTATAAACAAATTCATCAACTATATTAAAATAT
TGGACTCACTTGTTAAAACTTTAATTTTTTTTTAAAAAGGAAAACTTTAATCA
Found at i:41821149 original size:20 final size:21
Alignment explanation
Indices: 41821105--41821159 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
41821095 ATGCGTATAC
41821105 ATATAAAAAT-TATTTATTTAAA
1 ATATAAAAATATATTTA--TAAA
41821127 ATATAAAAATATATTTA-AAA
1 ATATAAAAATATATTTATAAA
41821147 ATAATAAATAATA
1 AT-ATAAA-AATA
41821160 AAATATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.17
21 5 0.17
22 14 0.47
23 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAAAATATATTTATAAA
Found at i:41826724 original size:32 final size:32
Alignment explanation
Indices: 41826683--41826746 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
41826673 TTGGTACGAC
41826683 CGGTCTGGTTCTCTGTTTCAAGTTTCAACAAG
1 CGGTCTGGTTCTCTGTTTCAAGTTTCAACAAG
* *
41826715 CGGTCTGGTTCTTTGTTTCGAGTTTCAACAAG
1 CGGTCTGGTTCTCTGTTTCAAGTTTCAACAAG
41826747 TAGTGGATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.39
Consensus pattern (32 bp):
CGGTCTGGTTCTCTGTTTCAAGTTTCAACAAG
Found at i:41833216 original size:4 final size:4
Alignment explanation
Indices: 41833207--41833240 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
41833197 AATATAATGG
* *
41833207 ATAA ATAA ATAA GTAA ATAA ATAA ATGA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
41833241 GAATCAAGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:41833810 original size:13 final size:13
Alignment explanation
Indices: 41833794--41833841 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
41833784 TAATTAAAAT
41833794 AATAATAATAATA
1 AATAATAATAATA
41833807 AATAATAATAA-A
1 AATAATAATAATA
*
41833819 AGATGATAATACATTA
1 A-ATAATAATA-A-TA
41833835 AATAATA
1 AATAATA
41833842 CGGGGTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 2 0.07
13 19 0.66
14 1 0.03
15 5 0.17
16 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:41834428 original size:12 final size:12
Alignment explanation
Indices: 41834411--41834436 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41834401 ACACAAATCA
41834411 AAATAAAAAAAT
1 AAATAAAAAAAT
41834423 AAATAAAAAAAT
1 AAATAAAAAAAT
41834435 AA
1 AA
41834437 CAATGAACAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:41836544 original size:718 final size:709
Alignment explanation
Indices: 41835160--41836595 Score: 2228
Period size: 718 Copynumber: 2.0 Consensus size: 709
41835150 CATTGACTTC
41835160 TAAGGGTGACTTGGAGAACTTCTACTAGGCTCCAAAAAAATTGATTCATTGTTGTTGCCTCGGCA
1 TAAGGGTGACTTGGAGAACTTCTACTAGGCTCCAAAAAAATTGATTCATTGTTGTTGCCTCGGCA
*
41835225 ACAGTGTTGCTGGTGCTTTCTTTGGCACCTCAGCTCGCTCTCAGCCTACCAGCAACCTCCTTAGC
66 ACAGTGTTGCTGGTGCTTCCTTTGGCACCTCAGCTCGCTCTCAGCCTACCAGCAACCTCCTTAGC
* *
41835290 CTCTCGTCAGTAGGTGAAGTGTATAATTTCAAAAGCTCAAGGATCAAGTTTGGATTTTTTTCAAC
131 CTCTCGTCAGTAGGTGAAGTGAATAATTTCAAAAGCTCAAGGATCAAGCTTGGATTTTTTTCAAC
* * *
41835355 TTCAAAGAGATTTTCTTGGAAATACAATGTAATATTTGAGAAGAAGAGAAAGAGAGAAGTGTTTT
196 TTCAAAGAGATTTTCTTGAAAATACAAGGCAATATTTGAGAAGAAGAGAAAGAGAGAA-----TT
41835420 GATGGTAGGACCAGTCAGAGAAGGCCATGGATGGCGGCAACTCATGATGGTAGCGGCTAAGGTTA
256 GATGGTAGGACCAGTCAGAGAAGGCCATGGATGGCGGCAACTCATGATGGTAGCGGCTAAGGTTA
* *
41835485 GAAGAAGAAGAATAAAGGATAGAAAGAAGAATAAGAAACGAAATAAAAAAAAATGAAAAGAGGAA
321 GAAGAAGAAGAATAAAGGAAAGAAAGAAGAATAAGAAAAGAAATAAAAAAAAATGAAAAGAGGAA
* * *
41835550 TGGAATCGTGATTTGTTCCGGATGAAAGATAATTTTTTTATACATTTTTGTAGTTTTTTAAAATT
386 TGGAATCATGA-TTGTTCCGGATGAAAGAGAAATTTTTTATACATTTTTGTAGTTTTTTAAAATT
41835615 TGTAATATATTTTTTATTTATTCGTTATTATATATATATTTAAATTTATTAATAGTTTTTTTAAT
450 TGTAATATATTTTTTATTTATTCGTTATTATATATATATTTAAATTTATTAATAGTTTTTTTAAT
* *
41835680 TTTGAGATGATGACATCATTTTGATGTTATTAATGTCACGTGTCGTTGTCTAATATTGCCATATG
515 TTTGAGATGACGACATCATTTTGATGTTATTAATGACACGTGTCGTTGTCTAATATTGCCATATG
* *
41835745 TCCCAAATTTAATGGTGCTAAAAAAATTATCAAACTAGTTGACTGAAAAAAAGTTTGGGTACTAA
580 TCCCAAAATTAATGGTGCTAAAAAAAGTATCAAACTAGTTGACTGAAAAAAAGTTTGGGTACTAA
*
41835810 TATGAGACAAAAAAAAAACCCCTTAGTACTAATTTGATAAAAGTGAACAAGTTCAAGTACCAAAT
645 TATGAGAC-AAAAAAAAA--CCTTAGTACTAATTTGAGAAAAGTGAACAAGTTCAAGTACCAAAT
41835875 TTA
707 TTA
41835878 TAAGGGTGACTTGGAGAACTTCTACTAGGCTCCAAAAAAATTGATTCATTGTTGTTGCC-CTGGC
1 TAAGGGTGACTTGGAGAACTTCTACTAGGCTCCAAAAAAATTGATTCATTGTTGTTGCCTC-GGC
* * * *
41835942 AACGGTGTTGCTGGTGCTTCCTTTGGCTCCTCAGCTCGCTCTCAGCCTACCGGCAACCTTCTTAG
65 AACAGTGTTGCTGGTGCTTCCTTTGGCACCTCAGCTCGCTCTCAGCCTACCAGCAACCTCCTTAG
*
41836007 CCTCTCGTCAGTAGGTGAAGTGAATAATTTCAAAAGCTCAAGGATCAAGCTTGGATTTTTTTCGA
130 CCTCTCGTCAGTAGGTGAAGTGAATAATTTCAAAAGCTCAAGGATCAAGCTTGGATTTTTTTCAA
*
41836072 CTTCAAAGAGATTTTCTTGAAAATACAAGGCAATGTTTGAGAAGAAGAGAAAGAGAG-A-TGATG
195 CTTCAAAGAGATTTTCTTGAAAATACAAGGCAATATTTGAGAAGAAGAGAAAGAGAGAATTGATG
41836135 GTAGGACCAGTTC-GAGAAGGCCATGGATGGCGGCAACTCATGATGGTAGCGGCTAAGGTTAGAA
260 GTAGGACCAG-TCAGAGAAGGCCATGGATGGCGGCAACTCATGATGGTAGCGGCTAAGGTTAGAA
* * *
41836199 GAAGAGGAA-GAGGGAGAAG-AAGAAGAATAAAGGATAGAAAGAAGAATAAGAAAAAAAATGAAA
324 GAAGAAGAATAAAGGA-AAGAAAGAAGAAT-AA-G--A-AAAG-A-AAT-A-AAAAAAAATGAAA
41836262 AGAGGAATGGAATCATG-TTGTTCCGGATGAAAGAGAAATTTTTTATACATTTTTGTAGTTTTTT
379 AGAGGAATGGAATCATGATTGTTCCGGATGAAAGAGAAATTTTTTATACATTTTTGTAG--TTTT
* *
41836326 TTAAATTTTGTAATATATATTTTTATTTATTTGTTA-T-TATATATATTTAAATTTATTAATAAC
442 TTAAAATTTGTAATATAT-TTTTTATTTATTCGTTATTATATATATATTTAAATTTATTAAT-A-
*
41836389 TTTTTATTTAATTTTGAGATGACGACATCATTTTGATGTTATTAATGACACGTGTCGTTGTCTAA
504 GTTTT-TTTAATTTTGAGATGACGACATCATTTTGATGTTATTAATGACACGTGTCGTTGTCTAA
* * *
41836454 TATTGCCATATGTCTCAAAATTAATGGTGCTAAAAAAAGTATCAAATTAGTTGAC-GGAAAAAAG
568 TATTGCCATATGTCCCAAAATTAATGGTGCTAAAAAAAGTATCAAACTAGTTGACTGAAAAAAAG
* * * * *
41836518 TTTGGGTACTAATATGGGAC-AAAAAAAACTTTAGTACTAATTTGGGAAAAGTGGACGAGTTCAA
633 TTTGGGTACTAATATGAGACAAAAAAAAACCTTAGTACTAATTTGAGAAAAGTGAACAAGTTCAA
41836582 GTACCAAATTTA
698 GTACCAAATTTA
41836594 TA
1 TA
41836596 TTTACGAATT
Statistics
Matches: 664, Mismatches: 36, Indels: 38
0.90 0.05 0.05
Matches are distributed among these distances:
710 13 0.02
711 78 0.12
712 3 0.00
714 1 0.00
715 3 0.00
716 46 0.07
717 44 0.07
718 269 0.41
719 52 0.08
720 47 0.07
721 108 0.16
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (709 bp):
TAAGGGTGACTTGGAGAACTTCTACTAGGCTCCAAAAAAATTGATTCATTGTTGTTGCCTCGGCA
ACAGTGTTGCTGGTGCTTCCTTTGGCACCTCAGCTCGCTCTCAGCCTACCAGCAACCTCCTTAGC
CTCTCGTCAGTAGGTGAAGTGAATAATTTCAAAAGCTCAAGGATCAAGCTTGGATTTTTTTCAAC
TTCAAAGAGATTTTCTTGAAAATACAAGGCAATATTTGAGAAGAAGAGAAAGAGAGAATTGATGG
TAGGACCAGTCAGAGAAGGCCATGGATGGCGGCAACTCATGATGGTAGCGGCTAAGGTTAGAAGA
AGAAGAATAAAGGAAAGAAAGAAGAATAAGAAAAGAAATAAAAAAAAATGAAAAGAGGAATGGAA
TCATGATTGTTCCGGATGAAAGAGAAATTTTTTATACATTTTTGTAGTTTTTTAAAATTTGTAAT
ATATTTTTTATTTATTCGTTATTATATATATATTTAAATTTATTAATAGTTTTTTTAATTTTGAG
ATGACGACATCATTTTGATGTTATTAATGACACGTGTCGTTGTCTAATATTGCCATATGTCCCAA
AATTAATGGTGCTAAAAAAAGTATCAAACTAGTTGACTGAAAAAAAGTTTGGGTACTAATATGAG
ACAAAAAAAAACCTTAGTACTAATTTGAGAAAAGTGAACAAGTTCAAGTACCAAATTTA
Found at i:41838207 original size:18 final size:18
Alignment explanation
Indices: 41838171--41838218 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
41838161 TAAGTCTATT
*
41838171 AATTATAT-ATAT-TATA
1 AATTATATAATATGTAAA
41838187 AATTATATAATATGTAAA
1 AATTATATAATATGTAAA
* *
41838205 AATAATTTAATATG
1 AATTATATAATATG
41838219 ATATATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 8 0.30
17 4 0.15
18 15 0.56
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
AATTATATAATATGTAAA
Found at i:41843492 original size:21 final size:21
Alignment explanation
Indices: 41843466--41843507 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
41843456 TTTTATTTCT
41843466 TTCTTTTTTTAGGATGAAGTG
1 TTCTTTTTTTAGGATGAAGTG
41843487 TTCTTTTTTTAGGATGAAGTG
1 TTCTTTTTTTAGGATGAAGTG
41843508 ATTATAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.24, T:0.52
Consensus pattern (21 bp):
TTCTTTTTTTAGGATGAAGTG
Found at i:41853216 original size:29 final size:30
Alignment explanation
Indices: 41853176--41853232 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
41853166 GGTTAAATGT
* *
41853176 TAACATTTCAAAA-TGGTCATATAAAGACC
1 TAACATTTCAAAAGTGCTCAAATAAAGACC
41853205 TAAC-TTTACAAAAGTGCTCAAATAAAGA
1 TAACATTT-CAAAAGTGCTCAAATAAAGA
41853233 ATTTTTACGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 9 0.38
30 12 0.50
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (30 bp):
TAACATTTCAAAAGTGCTCAAATAAAGACC
Found at i:41854692 original size:13 final size:13
Alignment explanation
Indices: 41854676--41854713 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
41854666 TAAACCAAAG
41854676 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
41854689 TTTTCCACAA-CAC
1 TTTT-CAAAAGCAC
41854702 TTTTCAAAAGCA
1 TTTTCAAAAGCA
41854714 ATGAAGAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 4 0.19
13 13 0.62
14 4 0.19
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:41858614 original size:31 final size:31
Alignment explanation
Indices: 41858576--41858677 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
41858566 CAAGTTAATC
*
41858576 CCTGAACTTGACAATTGTTCTCACATTGAGG
1 CCTGAACTTGATAATTGTTCTCACATTGAGG
* * *
41858607 CCTGAACTTAATGATTGTT-TCCACATTGGGG
1 CCTGAACTTGATAATTGTTCT-CACATTGAGG
* * * *
41858638 CTTGAGCTTGATAATTGTTCCCACATTAAGG
1 CCTGAACTTGATAATTGTTCTCACATTGAGG
*
41858669 CCTAAACTT
1 CCTGAACTT
41858678 TATGGTTTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
30 1 0.02
31 54 0.98
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (31 bp):
CCTGAACTTGATAATTGTTCTCACATTGAGG
Found at i:41863809 original size:44 final size:43
Alignment explanation
Indices: 41863716--41863918 Score: 282
Period size: 44 Copynumber: 4.5 Consensus size: 43
41863706 TTTGAGTACT
*
41863716 TCTGATCAAGGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAGGGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
41863759 TCTGATCAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGGGACAAGTGATAAGTGGTAGC-TTAGCTACACTTA
41863803 TCTGATCAGCGG-CAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAG-GGACAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
41863847 TCTGATCAGTGACAAGCGGCAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCA--G----G-GACAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
41863897 TCTGATCAAGGACAAGTGATAA
1 TCTGATCAGGGACAAGTGATAA
41863919 ATGATCAAAC
Statistics
Matches: 146, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
43 40 0.27
44 62 0.42
45 2 0.01
46 1 0.01
49 1 0.01
50 22 0.15
51 18 0.12
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
TCTGATCAGGGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:41863911 original size:50 final size:51
Alignment explanation
Indices: 41863810--41863912 Score: 183
Period size: 50 Copynumber: 2.0 Consensus size: 51
41863800 TTATCTGATC
41863810 AGCGGCAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAGTGACA
1 AGCGGCAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAGTGACA
41863861 AGCGGCAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAG-GACA
1 AGCGGCAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATC-AGTGACA
41863911 AG
1 AG
41863913 TGATAAATGA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
50 26 0.51
51 25 0.49
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (51 bp):
AGCGGCAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAGTGACA
Found at i:41871563 original size:13 final size:12
Alignment explanation
Indices: 41871530--41871565 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
41871520 ATATATATTT
*
41871530 AAAAATTATATA
1 AAAAATAATATA
41871542 AAAAATAATATA
1 AAAAATAATATA
41871554 AAAAAGTAATAT
1 AAAAA-TAATAT
41871566 GGGCAGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:41873406 original size:30 final size:30
Alignment explanation
Indices: 41873345--41873406 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
41873335 GGAGGGGACG
** **
41873345 GGAGTAAAAGTTTTGGGGGGAAGTGGGAAA
1 GGAGTAAAAGTTTTGGGGAAAAGTGAAAAA
41873375 GGAGTAAAAGTTTTGAGGGAAAAGT-AAAAA
1 GGAGTAAAAGTTTTG-GGGAAAAGTGAAAAA
41873405 GG
1 GG
41873407 TTTGGGAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGGGGAAAAGTGAAAAA
Found at i:41873462 original size:9 final size:9
Alignment explanation
Indices: 41873448--41873484 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41873438 TATATTTTGA
41873448 TATTCGAAT
1 TATTCGAAT
41873457 TATTCGAAT
1 TATTCGAAT
*
41873466 TATTCGAGT
1 TATTCGAAT
41873475 TATTCGAAT
1 TATTCGAAT
41873484 T
1 T
41873485 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41880969 original size:29 final size:28
Alignment explanation
Indices: 41880922--41880979 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
41880912 CCGTTTTTTT
** *
41880922 AATTAATTAGGCATTTAGGCCCGTTTTAA
1 AATTAATTAGGCAAATAGG-CCGATTTAA
*
41880951 AATTAATTAGGGAAATAGGCCGATTTAA
1 AATTAATTAGGCAAATAGGCCGATTTAA
41880979 A
1 A
41880980 TAGAAAGCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (28 bp):
AATTAATTAGGCAAATAGGCCGATTTAA
Found at i:41881159 original size:9 final size:9
Alignment explanation
Indices: 41881140--41881192 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
41881130 TTTACATCCA
*
41881140 TCTCTTAAC
1 TCTCTCAAC
*
41881149 TCTCTCGAC
1 TCTCTCAAC
41881158 TCTCTCAAAC
1 TCTCTC-AAC
*
41881168 CCTCTCAAC
1 TCTCTCAAC
*
41881177 TCTTTCAAC
1 TCTCTCAAC
41881186 TCTCTCA
1 TCTCTCA
41881193 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
9 29 0.81
10 7 0.19
ACGTcount: A:0.21, C:0.42, G:0.02, T:0.36
Consensus pattern (9 bp):
TCTCTCAAC
Found at i:41883473 original size:77 final size:78
Alignment explanation
Indices: 41883380--41883535 Score: 305
Period size: 77 Copynumber: 2.0 Consensus size: 78
41883370 ATATTAAGGG
41883380 TATTCTCATCAGTTTAAATTTTTTTTGAATCCGTGTTTTTATAAATAGAGATTATAAATATCACA
1 TATTCTCATCAGTTTAAATTTTTTTTGAATCCGTGTTTTTATAAATAGAGATTATAAATATCACA
41883445 TAATATTTATTTT
66 TAATATTTATTTT
41883458 TATTCTCATC-GTTTAAATTTTTTTTGAATCCGTGTTTTTATAAATAGAGATTATAAATATCACA
1 TATTCTCATCAGTTTAAATTTTTTTTGAATCCGTGTTTTTATAAATAGAGATTATAAATATCACA
41883522 TAATATTTATTTT
66 TAATATTTATTTT
41883535 T
1 T
41883536 TAAATTTTAT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 68 0.87
78 10 0.13
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.51
Consensus pattern (78 bp):
TATTCTCATCAGTTTAAATTTTTTTTGAATCCGTGTTTTTATAAATAGAGATTATAAATATCACA
TAATATTTATTTT
Found at i:41885804 original size:17 final size:16
Alignment explanation
Indices: 41885782--41885820 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41885772 CCTTATTCAC
41885782 ATGAAAAATATTATTCG
1 ATGAAAAA-ATTATTCG
* *
41885799 ATGAAAGAGTTATTCG
1 ATGAAAAAATTATTCG
41885815 ATGAAA
1 ATGAAA
41885821 GAGTTGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (16 bp):
ATGAAAAAATTATTCG
Found at i:41885813 original size:16 final size:16
Alignment explanation
Indices: 41885792--41885825 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41885782 ATGAAAAATA
41885792 TTATTCGATGAAAGAG
1 TTATTCGATGAAAGAG
41885808 TTATTCGATGAAAGAG
1 TTATTCGATGAAAGAG
41885824 TT
1 TT
41885826 GAGGATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (16 bp):
TTATTCGATGAAAGAG
Found at i:41887024 original size:47 final size:47
Alignment explanation
Indices: 41886950--41887043 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
41886940 ATACATACAC
41886950 CTTTTTAGATCAATATGATAGAAATATTGAACCGATTTTAAAAATTT
1 CTTTTTAGATCAATATGATAGAAATATTGAACCGATTTTAAAAATTT
*
41886997 CTTTTTAGATCAATATGATAGAGATATTGAACCGATTTTAAAAATTT
1 CTTTTTAGATCAATATGATAGAAATATTGAACCGATTTTAAAAATTT
41887044 ACATGCATGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (47 bp):
CTTTTTAGATCAATATGATAGAAATATTGAACCGATTTTAAAAATTT
Found at i:41894385 original size:14 final size:15
Alignment explanation
Indices: 41894368--41894402 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41894358 ACAAGTGTTG
41894368 AAAAATT-AAGTATT
1 AAAAATTAAAGTATT
*
41894382 AAAAATTAAATTATT
1 AAAAATTAAAGTATT
41894397 AAAAAT
1 AAAAAT
41894403 ATTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAAATTAAAGTATT
Found at i:41894963 original size:23 final size:25
Alignment explanation
Indices: 41894939--41894992 Score: 78
Period size: 23 Copynumber: 2.2 Consensus size: 25
41894929 ATAACACATT
41894939 TTATAAATTTATA-A-TAT-ATATTT
1 TTATAAATTTATATACTATAAT-TTT
41894962 TTATAAATTTATATACTATAATTTT
1 TTATAAATTTATATACTATAATTTT
41894987 TTATAA
1 TTATAA
41894993 TACATACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 13 0.46
24 1 0.04
25 12 0.43
26 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATAAATTTATATACTATAATTTT
Found at i:41896648 original size:14 final size:15
Alignment explanation
Indices: 41896631--41896665 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41896621 ACAAGTGTTG
41896631 AAAAATT-AAGTATT
1 AAAAATTAAAGTATT
*
41896645 AAAAATTAAATTATT
1 AAAAATTAAAGTATT
41896660 AAAAAT
1 AAAAAT
41896666 ATTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAAATTAAAGTATT
Found at i:41900780 original size:53 final size:53
Alignment explanation
Indices: 41900723--41900827 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
41900713 TAAAAAAATG
41900723 AAAAATCTTTACACTACAAAATGATGTATATCTAGATAAATCATTGATAGAAGA
1 AAAAATC-TTACACTACAAAATGATGTATATCTAGATAAATCATTGATAGAAGA
41900777 AAAAATCTTACACTACAAAATGATGTATATCTAGATAAATCATTGATAGAA
1 AAAAATCTTACACTACAAAATGATGTATATCTAGATAAATCATTGATAGAA
41900828 AAACAAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 44 0.86
54 7 0.14
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (53 bp):
AAAAATCTTACACTACAAAATGATGTATATCTAGATAAATCATTGATAGAAGA
Found at i:41904190 original size:22 final size:23
Alignment explanation
Indices: 41904150--41904195 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
41904140 TCTAAAAAAA
*
41904150 TTATATACTTGTTTGTTTTGAAT
1 TTATATACTTGTTTGTTTTAAAT
41904173 TTATATACTCT-TTT-TTTTAAAT
1 TTATATACT-TGTTTGTTTTAAAT
41904195 T
1 T
41904196 AGTTACGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 12 0.57
24 1 0.05
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (23 bp):
TTATATACTTGTTTGTTTTAAAT
Found at i:41905724 original size:5 final size:6
Alignment explanation
Indices: 41905703--41905739 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
41905693 TAAATTTAAA
41905703 TTTTAGT TTTTAT TTTTAT TTTTATT TTTTAT TTTTA
1 TTTTA-T TTTTAT TTTTAT TTTTA-T TTTTAT TTTTA
41905740 AATTTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:41905731 original size:19 final size:19
Alignment explanation
Indices: 41905703--41905739 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41905693 TAAATTTAAA
41905703 TTTTAGTTTTTATTTTTAT
1 TTTTAGTTTTTATTTTTAT
*
41905722 TTTTATTTTTTATTTTTA
1 TTTTAGTTTTTATTTTTA
41905740 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (19 bp):
TTTTAGTTTTTATTTTTAT
Found at i:41905745 original size:13 final size:13
Alignment explanation
Indices: 41905697--41905746 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
41905687 AAAGGGTAAA
41905697 TTTAAATTTTAGTT
1 TTTAAATTTTA-TT
*
41905711 TTT-ATTTTTATT
1 TTTAAATTTTATT
**
41905723 TTTATTTTTTATT
1 TTTAAATTTTATT
41905736 TTTAAATTTTA
1 TTTAAATTTTA
41905747 AATTTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 5 0.16
13 23 0.74
14 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTAAATTTTATT
Found at i:41914702 original size:25 final size:26
Alignment explanation
Indices: 41914644--41914703 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
41914634 CCATGTCAAC
41914644 AATTAATT-AATTTTTGTAAAAGTTAA
1 AATT-ATTAAATTTTTGTAAAAGTTAA
*
41914670 AATT-TTAAATTTTT-TAAAA-TATAT
1 AATTATTAAATTTTTGTAAAAGT-TAA
41914694 AATTATTAAA
1 AATTATTAAA
41914704 AAAACACGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.03
24 13 0.43
25 12 0.40
26 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
AATTATTAAATTTTTGTAAAAGTTAA
Found at i:41915040 original size:55 final size:55
Alignment explanation
Indices: 41914979--41915089 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
41914969 TAAATATATT
* *
41914979 TAATATTTTTATAATTTATTTTATTCGAGTTAAGAGTAATATTCAGATAAACCTC
1 TAATATTTTTATAATTTATTTTATTCAAATTAAGAGTAATATTCAGATAAACCTC
41915034 TAATATTTTTATAATTTATTTTATTCAAATTAAGAGTAATATTCAGATAAACCTC
1 TAATATTTTTATAATTTATTTTATTCAAATTAAGAGTAATATTCAGATAAACCTC
41915089 T
1 T
41915090 GTCGAATTCG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (55 bp):
TAATATTTTTATAATTTATTTTATTCAAATTAAGAGTAATATTCAGATAAACCTC
Found at i:41919448 original size:24 final size:24
Alignment explanation
Indices: 41919416--41919464 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41919406 ACTTAATACC
41919416 TCTTTATTCCGTCGTTTGGTTCAA
1 TCTTTATTCCGTCGTTTGGTTCAA
41919440 TCTTTATTCCGTCGTTTGGTTCAA
1 TCTTTATTCCGTCGTTTGGTTCAA
41919464 T
1 T
41919465 GTGTTTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.51
Consensus pattern (24 bp):
TCTTTATTCCGTCGTTTGGTTCAA
Found at i:41919631 original size:11 final size:11
Alignment explanation
Indices: 41919615--41919640 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41919605 CGCCTCTTCT
41919615 TTCGTTCTACC
1 TTCGTTCTACC
41919626 TTCGTTCTACC
1 TTCGTTCTACC
41919637 TTCG
1 TTCG
41919641 CCTCCCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.35, G:0.12, T:0.46
Consensus pattern (11 bp):
TTCGTTCTACC
Found at i:41922108 original size:7 final size:7
Alignment explanation
Indices: 41922096--41922131 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
41922086 AAGAGAACCC
41922096 CTTATTT
1 CTTATTT
41922103 CTTATTT
1 CTTATTT
*
41922110 ATTATTT
1 CTTATTT
41922117 ACTTATTT
1 -CTTATTT
41922125 CTTATTT
1 CTTATTT
41922132 ATTGTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.69
Consensus pattern (7 bp):
CTTATTT
Found at i:41922133 original size:11 final size:11
Alignment explanation
Indices: 41922097--41922134 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
41922087 AGAGAACCCC
41922097 TTATTTCTTAT
1 TTATTTCTTAT
*
41922108 TTATTAT-TTAC
1 TTATT-TCTTAT
41922119 TTATTTCTTAT
1 TTATTTCTTAT
41922130 TTATT
1 TTATT
41922135 GTTAAAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.04
11 21 0.91
12 1 0.04
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTCTTAT
Found at i:41925403 original size:31 final size:31
Alignment explanation
Indices: 41925368--41925441 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
41925358 CACATTAGTA
*
41925368 GTCACCCAACTATTTATAAATTTAT-TTTTTG
1 GTCACCCAACTAATTA-AAATTTATCTTTTTG
* *
41925399 GTCACCCAACTAATTAAATTTTGTCTTTTTG
1 GTCACCCAACTAATTAAAATTTATCTTTTTG
*
41925430 GTCA-TCAACTAA
1 GTCACCCAACTAA
41925442 CTAACGTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 13 0.34
31 25 0.66
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (31 bp):
GTCACCCAACTAATTAAAATTTATCTTTTTG
Found at i:41925853 original size:6 final size:6
Alignment explanation
Indices: 41925808--41925847 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
41925798 TTCATGTAAT
41925808 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
41925848 AGAAAATCCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:41925853 original size:18 final size:17
Alignment explanation
Indices: 41925805--41925854 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 17
41925795 TTTTTCATGT
*
41925805 AATAAAATAAAAATAAA
1 AATAAAAAAAAAATAAA
41925822 AATAAAAATAAAAATAAA
1 AATAAAAA-AAAAATAAA
41925840 AATAAAAAAGAAAAT
1 AATAAAAAA-AAAAT
41925855 CCGTTTCTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (17 bp):
AATAAAAAAAAAATAAA
Found at i:41929436 original size:2 final size:2
Alignment explanation
Indices: 41929429--41929494 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
41929419 CAACCTTCTG
* *
41929429 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
41929471 CT CT CT CT CT CT CT CT CT CC CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT
41929495 ATTTATATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:41932357 original size:17 final size:17
Alignment explanation
Indices: 41932335--41932369 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41932325 TGGTAGAACA
41932335 TTTATT-TTATTGTTAAT
1 TTTATTATTATT-TTAAT
41932352 TTTATTATTATTTTAAT
1 TTTATTATTATTTTAAT
41932369 T
1 T
41932370 GTAACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTATTATTATTTTAAT
Found at i:41941169 original size:14 final size:14
Alignment explanation
Indices: 41941150--41941179 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41941140 CTTATTTAGG
41941150 TATGAATTAAATGT
1 TATGAATTAAATGT
41941164 TATGAATTAAATGT
1 TATGAATTAAATGT
41941178 TA
1 TA
41941180 GGATTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TATGAATTAAATGT
Found at i:41945135 original size:58 final size:57
Alignment explanation
Indices: 41944992--41945135 Score: 147
Period size: 58 Copynumber: 2.5 Consensus size: 57
41944982 TAATTTTGGT
*
41944992 TTCAATGTTTAATTTGGTACCTG-A-TTTTTTCCCCCAAATTAGTACATGAGTTGGC
1 TTCAATGTTTAATTTGGTACCTGAATTTTTTTCCCCCAAATTAGTACATGAGTTGAC
** *
41945047 TTCAATGTTTAATTTGAG-ACCT-AAGTTTTTTTCGTCC-AATCT-GATACCTGAGTTTGAC
1 TTCAATGTTTAATTTG-GTACCTGAA-TTTTTTTCCCCCAAAT-TAG-TACATGAG-TTGAC
* *
41945105 TTCAATATTTACTTTGGTACCTGAATTTTTT
1 TTCAATGTTTAATTTGGTACCTGAATTTTTT
41945136 CAATTTGATA
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
55 21 0.28
56 5 0.07
57 18 0.24
58 28 0.38
59 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.45
Consensus pattern (57 bp):
TTCAATGTTTAATTTGGTACCTGAATTTTTTTCCCCCAAATTAGTACATGAGTTGAC
Found at i:41951903 original size:11 final size:12
Alignment explanation
Indices: 41951876--41951903 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41951866 TAAAAATTAA
41951876 AAAAAGTATTTT
1 AAAAAGTATTTT
41951888 AAAAAGTATTTT
1 AAAAAGTATTTT
41951900 AAAA
1 AAAA
41951904 TTAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (12 bp):
AAAAAGTATTTT
Found at i:41951917 original size:27 final size:27
Alignment explanation
Indices: 41951885--41951949 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
41951875 AAAAAAGTAT
*
41951885 TTTAAAAAGTATTTTAAAATTAAAAAA
1 TTTAAAAAATATTTTAAAATTAAAAAA
41951912 TTTAAAAAATATTTTAAAATTAAAAAA
1 TTTAAAAAATATTTTAAAATTAAAAAA
*
41951939 ATTAAAAAATA
1 TTTAAAAAATA
41951950 AATATATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
TTTAAAAAATATTTTAAAATTAAAAAA
Found at i:41968691 original size:2 final size:2
Alignment explanation
Indices: 41968684--41968730 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
41968674 ATTCAGATGC
*
41968684 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41968726 AT AT A
1 AT AT A
41968731 GAAACTTGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41971275 original size:31 final size:31
Alignment explanation
Indices: 41971236--41971306 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
41971226 CAAGTTAGTC
*
41971236 CCTAAACTTGGCAATTGCTCCTACATT-GAG
1 CCTAAACTTGGCAATTGCTCCCACATTAGAG
* * *
41971266 TCCTGAACTTGGCAGTTGTTCCCACATTAGAG
1 -CCTAAACTTGGCAATTGCTCCCACATTAGAG
41971298 CCTAAACTT
1 CCTAAACTT
41971307 TAGGATTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (31 bp):
CCTAAACTTGGCAATTGCTCCCACATTAGAG
Found at i:41972411 original size:126 final size:126
Alignment explanation
Indices: 41972186--41972437 Score: 488
Period size: 126 Copynumber: 2.0 Consensus size: 126
41972176 ACATCTGAAA
41972186 CAGGCACTTCCTTTGGAAAGGTCGGTGGAAACTCCAAAAATCATATCTGTTGCACAATTTCGTCC
1 CAGGCACTTCCTTTGGAAAGGTCGGTGGAAACTCCAAAAATCATATCTGTTGCACAATTTCGTCC
41972251 CGAGAAGGTGCACATACTTACATAGACCTTCAAGCTAAATTTTTAATGGTTCCGGTGTTTC
66 CGAGAAGGTGCACATACTTACATAGACCTTCAAGCTAAATTTTTAATGGTTCCGGTGTTTC
41972312 CAGGCACTTCCTTTGGAAAGGTCGGTGGAAACTCCAAAAATCATATCTGTTGCACAATTTTCGTC
1 CAGGCACTTCCTTTGGAAAGGTCGGTGGAAACTCCAAAAATCATATCTGTTGCACAA-TTTCGTC
41972377 CCG-GAAGGTGCACATACTTACATAGACCTTCAAGCTAAATTTTTAATGGTTCCGGTGTTTC
65 CCGAGAAGGTGCACATACTTACATAGACCTTCAAGCTAAATTTTTAATGGTTCCGGTGTTTC
41972438 GGTTTTGGAA
Statistics
Matches: 125, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
126 115 0.92
127 10 0.08
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (126 bp):
CAGGCACTTCCTTTGGAAAGGTCGGTGGAAACTCCAAAAATCATATCTGTTGCACAATTTCGTCC
CGAGAAGGTGCACATACTTACATAGACCTTCAAGCTAAATTTTTAATGGTTCCGGTGTTTC
Found at i:41974612 original size:9 final size:9
Alignment explanation
Indices: 41974595--41974653 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
41974585 GTTAACAAAT
*
41974595 AATTTTAAA
1 AATTATAAA
41974604 AATTATAAA
1 AATTATAAA
41974613 ATATT-TAAA
1 A-ATTATAAA
41974622 AA-TA-AATA
1 AATTATAA-A
41974630 AATTATAAAA
1 AATTAT-AAA
*
41974640 AATCATAAA
1 AATTATAAA
41974649 AATTA
1 AATTA
41974654 GCAACAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
9 23 0.56
10 9 0.22
11 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
AATTATAAA
Found at i:41986459 original size:20 final size:19
Alignment explanation
Indices: 41986425--41986474 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
41986415 TAAAATTTAC
*
41986425 AAATATAATTTCATTCATT
1 AAATATAATTTCATTCAAT
*
41986444 AAATATTATATTCATTCAAT
1 AAATATAAT-TTCATTCAAT
41986464 AAAATATAATT
1 -AAATATAATT
41986475 AATAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 8 0.31
20 10 0.38
21 8 0.31
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATATAATTTCATTCAAT
Found at i:41986499 original size:19 final size:19
Alignment explanation
Indices: 41986477--41986513 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
41986467 ATATAATTAA
41986477 TAAAT-TTTTATATAAAATT
1 TAAATGTTTTAT-TAAAATT
41986496 TAAATGTTTTATTAAAAT
1 TAAATGTTTTATTAAAAT
41986514 AATATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TAAATGTTTTATTAAAATT
Found at i:41987898 original size:31 final size:31
Alignment explanation
Indices: 41987857--41988245 Score: 522
Period size: 31 Copynumber: 12.7 Consensus size: 31
41987847 ATCCAATGCT
* *
41987857 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
41987887 CGAATCAAATTCGGCAATGAATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
41987918 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
41987948 CAAATCAACTTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
41987979 CAAATCAAATTCAGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
41988010 CAAATC-AATTCAGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
41988040 CAAATCAAATTCGGTAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
41988071 CAAATCAAATTCGACAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
41988102 CAAATC-AATTCGGCAATGTACATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
41988132 CAATTCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
41988163 CAAATC-AATTTGGCAATGTATATCTATA-A
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
41988192 GCAAATCAAATTCGGCAATGTATATCTTTATA
1 -CAAATCAAATTCGGCAATGTATATCTATATA
*
41988224 CAAA-CCAATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
41988246 AAACATATAC
Statistics
Matches: 320, Mismatches: 32, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
29 1 0.00
30 133 0.42
31 185 0.58
32 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:41987954 original size:61 final size:61
Alignment explanation
Indices: 41987857--41988245 Score: 539
Period size: 61 Copynumber: 6.4 Consensus size: 61
41987847 ATCCAATGCT
* * *
41987857 CAAATCAATTCGGCAATATATATCCATATACGAATCAAATTCGGCAATGAATATCTATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATA
* * *
41987918 CAAATCAATTCGGCAATGTATATCCATATACAAATCAACTTCGGCAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATA
* * * *
41987979 CAAATCAAATTCAGCAATGTATATCTATATACAAATC-AATTCAGCAATGTATATCCATATA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATA
* * * *
41988040 CAAATCAAATTCGGTAATGTATAACCATATACAAATCAAATTCGACAATGTATATCTATAAA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATA
* * * *
41988102 CAAATCAATTCGGCAATGTACATCTATAAACAATTCAAATTCGGCAATGTATATCTATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATA
* * *
41988163 CAAATCAATTTGGCAATGTATATCTATA-AGCAAATCAAATTCGGCAATGTATATCTTTATA
1 CAAATCAATTCGGCAATGTATATCCATATA-CAAATCAAATTCGGCAATGTATATCTATATA
*
41988224 CAAACCAATTCGGCAATGTATA
1 CAAATCAATTCGGCAATGTATA
41988246 AAACATATAC
Statistics
Matches: 292, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
60 1 0.00
61 237 0.81
62 54 0.18
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (61 bp):
CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATA
Found at i:41987985 original size:92 final size:91
Alignment explanation
Indices: 41987857--41988256 Score: 552
Period size: 92 Copynumber: 4.4 Consensus size: 91
41987847 ATCCAATGCT
* * * *
41987857 CAAATCAATTCGGCAATATATATCCATATACGAATCAAATTCGGCAATGAATATCTATATACAAA
1 CAAATCAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
41987922 TCAATTCGGCAATGTATATCCATATA
66 TCAATTCGGCAATGTATATCCATATA
*
41987948 CAAATCAACTTCGGCAATGTATAACCATATACAAATCAAATTCAGCAATGTATATCTATATACAA
1 CAAATCAA-TTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
*
41988013 ATCAATTCAGCAATGTATATCCATATA
65 ATCAATTCGGCAATGTATATCCATATA
* * *
41988040 CAAATCAAATTCGGTAATGTATAACCATATACAAATCAAATTCGACAATGTATATCTATAAACAA
1 CAAATC-AATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* * *
41988105 ATCAATTCGGCAATGTACATCTATAAA
65 ATCAATTCGGCAATGTATATCCATATA
* * * *
41988132 CAATTCAAATTCGGCAATGTATATCTATATACAAATC-AATTTGGCAATGTATATCTATA-AGCA
1 CAAATC-AATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATA-CA
**
41988195 AATCAAATTCGGCAATGTATATCTTTATA
64 AATC-AATTCGGCAATGTATATCCATATA
* *
41988224 CAAACCAATTCGGCAATGTATAAAACATATACA
1 CAAATCAATTCGGCAATGTAT-AACCATATACA
41988257 TTTAAATTCA
Statistics
Matches: 276, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
90 1 0.00
91 49 0.18
92 224 0.81
93 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (91 bp):
CAAATCAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
TCAATTCGGCAATGTATATCCATATA
Found at i:41988871 original size:60 final size:60
Alignment explanation
Indices: 41988782--41988896 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
41988772 ATAAAATTAA
* * * *
41988782 TATTTTAACTTTAGATTTGTAGTCTCGAAACCAGTATTCTGATTTGACCCAAAAAAATAT
1 TATTTTAACTTCAGATTTGTAGTCCCGAAACCACTATTCCGATTTGACCCAAAAAAATAT
* * * *
41988842 TATTTTAACTTCGGATTTGTGGTCCCGAAATCACTATTCCGGTTTGACCCAAAAA
1 TATTTTAACTTCAGATTTGTAGTCCCGAAACCACTATTCCGATTTGACCCAAAAA
41988897 TGGGCTGTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (60 bp):
TATTTTAACTTCAGATTTGTAGTCCCGAAACCACTATTCCGATTTGACCCAAAAAAATAT
Found at i:41990057 original size:31 final size:31
Alignment explanation
Indices: 41990022--41990081 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
41990012 AACAACTAGT
*
41990022 GACTTAAATAAAAACTTTTG-AATAGTTCAAC
1 GACTTAAATAAAAA-TATTGAAATAGTTCAAC
* *
41990053 GACTTGAATGAAAATATTGAAATAGTTCA
1 GACTTAAATAAAAATATTGAAATAGTTCA
41990082 GTGACCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (31 bp):
GACTTAAATAAAAATATTGAAATAGTTCAAC
Found at i:41991171 original size:5 final size:6
Alignment explanation
Indices: 41991144--41991169 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41991134 NNNNATATAT
41991144 AAACAA AAACAA AAACAA AAACAA AA
1 AAACAA AAACAA AAACAA AAACAA AA
41991170 CACCCTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:41991528 original size:34 final size:34
Alignment explanation
Indices: 41991488--41991555 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
41991478 TCATGTCCAC
41991488 TTATAGAAAATAAAATGTTACTATAAAACAAAGG
1 TTATAGAAAATAAAATGTTACTATAAAACAAAGG
41991522 TTATAGAAAATAAAATGTTACTATAAAACAAAGG
1 TTATAGAAAATAAAATGTTACTATAAAACAAAGG
41991556 ATTGTTACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (34 bp):
TTATAGAAAATAAAATGTTACTATAAAACAAAGG
Found at i:41991541 original size:17 final size:17
Alignment explanation
Indices: 41991488--41991541 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
41991478 TCATGTCCAC
41991488 TTATAGAAAATAAAATG
1 TTATAGAAAATAAAATG
* * *
41991505 TTACTATAAAA-CAAAGG
1 TTA-TAGAAAATAAAATG
41991522 TTATAGAAAATAAAATG
1 TTATAGAAAATAAAATG
41991539 TTA
1 TTA
41991542 CTATAAAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 6 0.21
17 17 0.59
18 6 0.21
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.30
Consensus pattern (17 bp):
TTATAGAAAATAAAATG
Found at i:41998830 original size:13 final size:13
Alignment explanation
Indices: 41998812--41998836 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41998802 GGGTGTCAGA
41998812 AAAAGTATTTACC
1 AAAAGTATTTACC
41998825 AAAAGTATTTAC
1 AAAAGTATTTAC
41998837 TTTTTTCATT
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:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (13 bp):
AAAAGTATTTACC
Found at i:41999166 original size:15 final size:16
Alignment explanation
Indices: 41999146--41999182 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41999136 ACAAAATCAA
41999146 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
41999161 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
41999177 ATAAAA
1 ATAAAA
41999183 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:41999536 original size:19 final size:19
Alignment explanation
Indices: 41999535--41999692 Score: 79
Period size: 19 Copynumber: 7.7 Consensus size: 19
41999525 CATACAAAAT
41999535 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
41999554 TACAAAA-TACTA-ATCCAA
1 TACAAAATTACAATATTC-A
* * *
41999572 AACTATAAA-TACAAAATTAA
1 TAC-A-AAATTACAATATTCA
*
41999592 TTATAAAATAATTACAATATTCA
1 -TACAAAAT--T-ACAATATTCA
*
41999615 TACAAAATTATAATATTCA
1 TACAAAATTACAATATTCA
*
41999634 TATAAAATTACAAAATTACAATATTCA
1 TACAAAA-T-------TACAATATTCA
41999661 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
41999680 TGCAAAATTACAA
1 TACAAAATTACAA
41999693 AATTACAATA
Statistics
Matches: 106, Mismatches: 16, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
17 3 0.03
18 7 0.07
19 49 0.46
20 11 0.10
21 3 0.03
22 8 0.08
23 8 0.08
26 1 0.01
27 16 0.15
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:41999547 original size:27 final size:27
Alignment explanation
Indices: 41999509--41999867 Score: 171
Period size: 27 Copynumber: 14.0 Consensus size: 27
41999499 NNNNNNNNNN
*
41999509 ACAATATTACAATATTCATACAAAATT
1 ACAAAATTACAATATTCATACAAAATT
41999536 ACAAAATTACAATATTCATACAAAA-T
1 ACAAAATTACAATATTCATACAAAATT
* * * **
41999562 AC-TAATCCAAAACTATAAATACAAAATT
1 ACAAAAT-TACAA-TATTCATACAAAATT
** * * *
41999590 A-ATTA-TAAAATAAT--TACAATATTCAT
1 ACAAAATTACAATATTCATACAA-AAT--T
* *
41999616 ACAAAATTATAATATTCATATAAAATT
1 ACAAAATTACAATATTCATACAAAATT
41999643 ACAAAATTACAATA-T--T-C---A-T
1 ACAAAATTACAATATTCATACAAAATT
*
41999662 ACAAAATTACAATATTCATGCAAAATT
1 ACAAAATTACAATATTCATACAAAATT
*
41999689 ACAAAATTACAATATTCGTACAAAA-T
1 ACAAAATTACAATATTCATACAAAATT
* * * **
41999715 AC-TAATCCAAAACTATAAATACAAAATT
1 ACAAAAT-TACAA-TATTCATACAAAATT
** * * *
41999743 A-ATTA-TAAAATAAT--TACAATATTCAT
1 ACAAAATTACAATATTCATACAA-AAT--T
* *
41999769 ACAAAATTATAATATTCATATAAAATT
1 ACAAAATTACAATATTCATACAAAATT
41999796 ACAAAATTACAATA-T--T-C---A-T
1 ACAAAATTACAATATTCATACAAAATT
*
41999815 ACAAAATTACAATATTCATGCAAAATT
1 ACAAAATTACAATATTCATACAAAATT
*
41999842 ACAAAATTACAATATTCGTACAAAAT
1 ACAAAATTACAATATTCATACAAAAT
41999868 ACTAATCCAA
Statistics
Matches: 252, Mismatches: 42, Indels: 76
0.68 0.11 0.21
Matches are distributed among these distances:
19 30 0.12
20 4 0.02
22 2 0.01
23 12 0.05
24 6 0.02
25 10 0.04
26 28 0.11
27 126 0.50
28 22 0.09
29 4 0.02
30 8 0.03
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.31
Consensus pattern (27 bp):
ACAAAATTACAATATTCATACAAAATT
Found at i:41999650 original size:8 final size:8
Alignment explanation
Indices: 41999637--41999700 Score: 56
Period size: 8 Copynumber: 7.2 Consensus size: 8
41999627 ATATTCATAT
41999637 AAAATTAC
1 AAAATTAC
41999645 AAAATTAC
1 AAAATTAC
*
41999653 AATATTCATAC
1 AA-AAT--TAC
41999664 AAAATTAC
1 AAAATTAC
*
41999672 AATATTCATGC
1 AAAATT-A--C
41999683 AAAATTAC
1 AAAATTAC
41999691 AAAATTAC
1 AAAATTAC
41999699 AA
1 AA
41999701 TATTCGTACA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
8 29 0.63
9 3 0.07
10 3 0.07
11 11 0.24
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (8 bp):
AAAATTAC
Found at i:41999656 original size:46 final size:46
Alignment explanation
Indices: 41999601--41999867 Score: 227
Period size: 46 Copynumber: 5.9 Consensus size: 46
41999591 ATTATAAAAT
* *
41999601 AATTACAATATTCATACAAAATTATAATATTCATATAAAATTACAA
1 AATTACAATATTCATACAAAATTACAATATTCATACAAAATTACAA
*
41999647 AATTACAATATTCATACAAAATTACAATATTCATGCAAAATTACAA
1 AATTACAATATTCATACAAAATTACAATATTCATACAAAATTACAA
* * * *
41999693 AATTACAATATTCGTACAAAA-TACTA-ATCCAAAACTATAAA-TACAA
1 AATTACAATATTCATACAAAATTACAATATTC-ATAC-A-AAATTACAA
* *
41999739 AATT---A-ATT-ATAAAATAATTACAATATTCATACAAAATTATAA
1 AATTACAATATTCATACAA-AATTACAATATTCATACAAAATTACAA
* **
41999781 TATT-C-ATATAAAATTACAAAATTACAATATTCATACAAAATTACAA
1 AATTACAATAT-TCA-TACAAAATTACAATATTCATACAAAATTACAA
* * *
41999827 TATTCATGCAA-AAT--TACAAAATTACAATATTCGTACAAAAT
1 AATT-A--CAATATTCATACAAAATTACAATATTCATACAAAAT
41999868 ACTAATCCAA
Statistics
Matches: 183, Mismatches: 21, Indels: 34
0.77 0.09 0.14
Matches are distributed among these distances:
41 7 0.04
42 13 0.07
43 9 0.05
44 8 0.04
45 6 0.03
46 130 0.71
47 7 0.04
50 2 0.01
51 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (46 bp):
AATTACAATATTCATACAAAATTACAATATTCATACAAAATTACAA
Found at i:41999710 original size:19 final size:19
Alignment explanation
Indices: 41999601--41999971 Score: 110
Period size: 19 Copynumber: 17.3 Consensus size: 19
41999591 ATTATAAAAT
41999601 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
*
41999620 AATTATAATATTCATATAAAATTACAA
1 AATTACAATATTC-------A-TACAA
41999647 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
41999666 AATTACAATATTCATGCAAAATTACAA
1 AATTACAATA-T--T-C---A-TACAA
*
41999693 AATTACAATATTCGTACAA
1 AATTACAATATTCATACAA
* * *
41999712 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
41999732 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
41999753 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
*
41999773 AATTATAATATTCATATAAAATTACAA
1 AATTACAATATTC-------A-TACAA
41999800 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
41999819 AATTACAATATTCATGCAAAATTACAA
1 AATTACAATA-T--T-C---A-TACAA
*
41999846 AATTACAATATTCGTACAA
1 AATTACAATATTCATACAA
* * *
41999865 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
41999885 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
41999906 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
*
41999926 AATTATAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
*
41999947 AATTACAATATACATACAA
1 AATTACAATATTCATACAA
41999966 AATTAC
1 AATTAC
41999972 CCATTGGCAC
Statistics
Matches: 269, Mismatches: 27, Indels: 112
0.66 0.07 0.27
Matches are distributed among these distances:
17 6 0.02
18 12 0.04
19 100 0.37
20 28 0.10
21 23 0.09
22 10 0.04
23 14 0.05
24 2 0.01
25 4 0.01
26 6 0.02
27 64 0.24
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.31
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:41999792 original size:153 final size:153
Alignment explanation
Indices: 41999509--41999946 Score: 840
Period size: 153 Copynumber: 2.9 Consensus size: 153
41999499 NNNNNNNNNN
* * *
41999509 ACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAATACTAATCCAAAA
1 ACAAAATTACAATATTCATGCAAAATTACAAAATTACAATATTCGTACAAAATACTAATCCAAAA
41999574 CTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATTATAATATTCATATAA
66 CTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATTATAATATTCATATAA
41999639 AATTACAAAATTACAATATTCAT
131 AATTACAAAATTACAATATTCAT
41999662 ACAAAATTACAATATTCATGCAAAATTACAAAATTACAATATTCGTACAAAATACTAATCCAAAA
1 ACAAAATTACAATATTCATGCAAAATTACAAAATTACAATATTCGTACAAAATACTAATCCAAAA
41999727 CTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATTATAATATTCATATAA
66 CTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATTATAATATTCATATAA
41999792 AATTACAAAATTACAATATTCAT
131 AATTACAAAATTACAATATTCAT
41999815 ACAAAATTACAATATTCATGCAAAATTACAAAATTACAATATTCGTACAAAATACTAATCCAAAA
1 ACAAAATTACAATATTCATGCAAAATTACAAAATTACAATATTCGTACAAAATACTAATCCAAAA
*
41999880 CTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATTATAATATTCATACAA
66 CTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATTATAATATTCATATAA
41999945 AA
131 AA
41999947 AATTACAATA
Statistics
Matches: 281, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 281 1.00
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (153 bp):
ACAAAATTACAATATTCATGCAAAATTACAAAATTACAATATTCGTACAAAATACTAATCCAAAA
CTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATTATAATATTCATATAA
AATTACAAAATTACAATATTCAT
Found at i:41999803 original size:8 final size:8
Alignment explanation
Indices: 41999790--41999853 Score: 56
Period size: 8 Copynumber: 7.2 Consensus size: 8
41999780 ATATTCATAT
41999790 AAAATTAC
1 AAAATTAC
41999798 AAAATTAC
1 AAAATTAC
*
41999806 AATATTCATAC
1 AA-AAT--TAC
41999817 AAAATTAC
1 AAAATTAC
*
41999825 AATATTCATGC
1 AAAATT-A--C
41999836 AAAATTAC
1 AAAATTAC
41999844 AAAATTAC
1 AAAATTAC
41999852 AA
1 AA
41999854 TATTCGTACA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
8 29 0.63
9 3 0.07
10 3 0.07
11 11 0.24
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (8 bp):
AAAATTAC
Found at i:41999957 original size:21 final size:21
Alignment explanation
Indices: 41999902--41999967 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
41999892 AATTAATTAT
41999902 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
*
41999924 --AAAATTATAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
41999943 AAAAAATTACAATATACATAC
1 AAAAAATTACAATATTCATAC
41999964 AAAA
1 AAAA
41999968 TTACCCATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
19 16 0.41
20 2 0.05
21 21 0.54
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Done.