Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 126 of 311
Found at i:42404674 original size:95 final size:96
Alignment explanation
Indices: 42404499--42404677 Score: 288
Period size: 95 Copynumber: 1.9 Consensus size: 96
42404489 CATTATAAGA
* * * *
42404499 GCTAGTGTAAGACCATGTCTGAGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCTGAGACATGACATCAGCCACATTATAAGAGCCAGTGTAAGACCACG
42404564 TCTAGGACATGGCATCGGCGTTGCTATGTGT
66 TCTAGGACATGGCATCGGCGTTGCTATGTGT
* * *
42404595 GCTAGTGTAAGACCGTGTCTG-GACATGACATCAGCGACATTATAAGAGCCTGTGTAAGACCACG
1 GCTAGTGTAAGACCATGTCTGAGACATGACATCAGCCACATTATAAGAGCCAGTGTAAGACCACG
42404659 TCTAGGACATGGCATCGGC
66 TCTAGGACATGGCATCGGC
42404678 CTCGACAAGT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
95 56 0.74
96 20 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.23
Consensus pattern (96 bp):
GCTAGTGTAAGACCATGTCTGAGACATGACATCAGCCACATTATAAGAGCCAGTGTAAGACCACG
TCTAGGACATGGCATCGGCGTTGCTATGTGT
Found at i:42404692 original size:48 final size:47
Alignment explanation
Indices: 42404503--42404725 Score: 147
Period size: 48 Copynumber: 4.7 Consensus size: 47
42404493 ATAAGAGCTA
* * * * *
42404503 GTGTAAGACCATGTCTGAGACATGGCATCGGCCAC-ATTATGAGAGCCA
1 GTGTAAGACCATGTCTG-GACATGGCATCGGCCTCGA-CAAGTGAGCCT
* * * *
42404551 GTGTAAGACCATGTCTAGGACATGGCATCGGCGTTG-CTATGTGTG-CT
1 GTGTAAGACCATGTCT-GGACATGGCATCGGCCTCGAC-AAGTGAGCCT
* * *
42404598 AGTGTAAGACCGTGTCTGGACATGACATCAG---CGACATTA-TAAGAGCCT
1 -GTGTAAGACCATGTCTGGACATGGCATCGGCCTCGACA--AGT--GAGCCT
*
42404646 GTGTAAGACCACGTCTAGGACATGGCATCGGCCTCGACAAGTGAGCCAT
1 GTGTAAGACCATGTCT-GGACATGGCATCGGCCTCGACAAGTGAGCC-T
* *
42404695 -TGTAAGACCATATCTGGGATATGGCATCGGC
1 GTGTAAGACCATGTCT-GGACATGGCATCGGC
42404726 AATTTACCCT
Statistics
Matches: 138, Mismatches: 21, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
44 2 0.01
45 2 0.01
47 29 0.21
48 96 0.70
49 3 0.02
50 1 0.01
51 5 0.04
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.23
Consensus pattern (47 bp):
GTGTAAGACCATGTCTGGACATGGCATCGGCCTCGACAAGTGAGCCT
Found at i:42404703 original size:143 final size:144
Alignment explanation
Indices: 42404444--42404725 Score: 383
Period size: 143 Copynumber: 2.0 Consensus size: 144
42404434 AATTGGGTGA
* *
42404444 TATGTGTGCCAGTGTAAGACCATGTCTAGGACATGGCATTAGCCACATTATAAGAGCTAGTGTAA
1 TATGTGTGCCAGTGTAAGACCATGTCTAGGACATGACATCAGCCACATTATAAGAGCTAGTGTAA
* * * *
42404509 GACCATGTCTGAGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTAGGACAT
66 GACCACGTCTGAGACATGGCATCGGCCACATCAAGAGAGCCAGTGTAAGACCATATCTAGGACAT
42404574 GGCATCGGCGTTGC
131 GGCATCGGCGTTGC
* * *
42404588 TATGTGTGCTAGTGTAAGACCGTGTCT-GGACATGACATCAGCGACATTATAAGAGCCT-GTGTA
1 TATGTGTGCCAGTGTAAGACCATGTCTAGGACATGACATCAGCCACATTATAAGAG-CTAGTGTA
* * * *
42404651 AGACCACGTCT-AGGACATGGCATCGGCCTCGA-CAAGTGAGCCATTGTAAGACCATATCTGGGA
65 AGACCACGTCTGA-GACATGGCATCGGCCAC-ATCAAGAGAGCCAGTGTAAGACCATATCTAGGA
*
42404714 TATGGCATCGGC
128 CATGGCATCGGC
42404726 AATTTACCCT
Statistics
Matches: 121, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
142 1 0.01
143 92 0.76
144 28 0.23
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (144 bp):
TATGTGTGCCAGTGTAAGACCATGTCTAGGACATGACATCAGCCACATTATAAGAGCTAGTGTAA
GACCACGTCTGAGACATGGCATCGGCCACATCAAGAGAGCCAGTGTAAGACCATATCTAGGACAT
GGCATCGGCGTTGC
Found at i:42404711 original size:95 final size:95
Alignment explanation
Indices: 42404451--42404711 Score: 283
Period size: 95 Copynumber: 2.7 Consensus size: 95
42404441 TGATATGTGT
* ** * ** * *
42404451 GCCAGTGTAAGACCATGTCTAGGACATGGCATTAGCCACATTATA-AGAGCTAGTGTAAGACCAT
1 GCCAGTGTAAGACCACGTCTAGGACATGGCATCGGCCTCGCTA-AGTGAGCCAGTGTAAGACCAT
* * *
42404515 GTCTGAGACATGGCATCGGCCACATTATGAGA
65 GTCTG-GACATGACATCAGCCACATTATAAGA
* * * * * * *
42404547 GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCGTTGCTATGTGTGCTAGTGTAAGACCGTG
1 GCCAGTGTAAGACCACGTCTAGGACATGGCATCGGCCTCGCTAAGTGAGCCAGTGTAAGACCATG
*
42404612 TCTGGACATGACATCAGCGACATTATAAGA
66 TCTGGACATGACATCAGCCACATTATAAGA
* *
42404642 GCCTGTGTAAGACCACGTCTAGGACATGGCATCGGCCTCGAC-AAGTGAGCCATTGTAAGACCAT
1 GCCAGTGTAAGACCACGTCTAGGACATGGCATCGGCCTCG-CTAAGTGAGCCAGTGTAAGACCAT
*
42404706 ATCTGG
65 GTCTGG
42404712 GATATGGCAT
Statistics
Matches: 138, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
95 80 0.58
96 58 0.42
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (95 bp):
GCCAGTGTAAGACCACGTCTAGGACATGGCATCGGCCTCGCTAAGTGAGCCAGTGTAAGACCATG
TCTGGACATGACATCAGCCACATTATAAGA
Found at i:42411738 original size:16 final size:15
Alignment explanation
Indices: 42411711--42411747 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
42411701 ATAATTCATG
*
42411711 TATAATTATATTTAT
1 TATAATTATATTAAT
42411726 TATAATATATATTAAT
1 TATAAT-TATATTAAT
42411742 TATAAT
1 TATAAT
42411748 CAACTTTATA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:42412459 original size:17 final size:18
Alignment explanation
Indices: 42412430--42412464 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42412420 TTCTCCTAAA
*
42412430 TTTCAATTTTATTTAATT
1 TTTCAATTTTATTGAATT
42412448 TTTCAA-TTTATTGAATT
1 TTTCAATTTTATTGAATT
42412465 GTTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTCAATTTTATTGAATT
Found at i:42414653 original size:5 final size:5
Alignment explanation
Indices: 42414643--42414675 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
42414633 TGCTCGTAAA
42414643 AAAAG AAAAG AAAAG AAAAG AAAA- AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
42414676 AAGAGAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:42418266 original size:27 final size:27
Alignment explanation
Indices: 42418226--42418391 Score: 179
Period size: 27 Copynumber: 6.1 Consensus size: 27
42418216 GGTTGTTATC
42418226 TGACCGTAATACCCCTGTAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* * *
42418253 TGACCGTAACACCCCTGTTGGCTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* **
42418280 TGATCGTAATACCTTTGTAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* * *
42418307 TGATCGTAATACCCTTATAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* * * *
42418334 TCATCGTAATGCCCCGGTAGGGTAAAA
1 TGACCGTAATACCCCTGTAGGGTAAAA
* * * *
42418361 TGACTGTAATACTCCTGTATGGTAACA
1 TGACCGTAATACCCCTGTAGGGTAAAA
42418388 TGAC
1 TGAC
42418392 GATTATGCCT
Statistics
Matches: 115, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (27 bp):
TGACCGTAATACCCCTGTAGGGTAAAA
Found at i:42418566 original size:27 final size:26
Alignment explanation
Indices: 42418526--42418603 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 26
42418516 ATGGAGGAAG
*
42418526 TACTGTACTGGTGGCTATGTCAC-AT
1 TACTGTACTGGTGGCTATGCCACAAT
42418551 TCACTGTTACTGGTGGCTATGCCACAAT
1 T-ACTG-TACTGGTGGCTATGCCACAAT
42418579 TACTGATACTGGTGGC-ATTGCCACA
1 TACTG-TACTGGTGGCTA-TGCCACA
42418604 TTTATTGTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
25 1 0.02
26 5 0.11
27 38 0.81
28 3 0.06
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (26 bp):
TACTGTACTGGTGGCTATGCCACAAT
Found at i:42419870 original size:20 final size:18
Alignment explanation
Indices: 42419832--42419871 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
42419822 ACATGTTATG
*
42419832 TTAATATGTTTAATTTAA
1 TTAATATGCTTAATTTAA
42419850 TTAATATGGCTTAAGTTTAA
1 TTAATAT-GCTTAA-TTTAA
42419870 TT
1 TT
42419872 TTTGTTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (18 bp):
TTAATATGCTTAATTTAA
Found at i:42428015 original size:44 final size:44
Alignment explanation
Indices: 42427955--42428117 Score: 130
Period size: 44 Copynumber: 3.6 Consensus size: 44
42427945 TATACGTGCT
* **
42427955 GATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCA
1 GATGCGTGTCCCAGACACATCTTACACTGGCACAACTCTTAGCA
* * * * * ** *
42427999 GATGTGTGTCCTAGACACATATTACACTGGTTATCATCATCGAAGCT
1 GATGCGTGTCCCAGACACATCTTACACTGG-CA-CAAC-TCTTAGCA
* ** * *
42428046 GATGCATGTCCCAGACATGTCATACACTGGCACAACTCTTAGCC
1 GATGCGTGTCCCAGACACATCTTACACTGGCACAACTCTTAGCA
*
42428090 GATGCGT-ACCCTAGACACATCTTACACT
1 GATGCGTGTCCC-AGACACATCTTACACT
42428118 AGCTATCATC
Statistics
Matches: 87, Mismatches: 28, Indels: 8
0.71 0.23 0.07
Matches are distributed among these distances:
43 3 0.03
44 48 0.55
45 4 0.05
46 4 0.05
47 28 0.32
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (44 bp):
GATGCGTGTCCCAGACACATCTTACACTGGCACAACTCTTAGCA
Found at i:42428072 original size:91 final size:91
Alignment explanation
Indices: 42427952--42428166 Score: 349
Period size: 91 Copynumber: 2.4 Consensus size: 91
42427942 ATATATACGT
* **
42427952 GCTGATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCAGATGTGTGTCCTAGACAC
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCAGATGCGTACCCTAGACAC
* *
42428017 ATATTACACTGGTTATCATCATCGAA
66 ATATTACACTAGCTATCATCATCGAA
* *
42428043 GCTGATGCATGTCCCAGACATGTCATACACTGGCACAACTCTTAGCCGATGCGTACCCTAGACAC
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCAGATGCGTACCCTAGACAC
* *
42428108 ATCTTACACTAGCTATCATCATCGAG
66 ATATTACACTAGCTATCATCATCGAA
42428134 GCTGATGCATGTCCCAGACATGTCTTACACTGG
1 GCTGATGCATGTCCCAGACATGTCTTACACTGG
42428167 TACTCATCTC
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 114 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (91 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCAGATGCGTACCCTAGACAC
ATATTACACTAGCTATCATCATCGAA
Found at i:42428201 original size:47 final size:45
Alignment explanation
Indices: 42427955--42428258 Score: 185
Period size: 47 Copynumber: 6.6 Consensus size: 45
42427945 TATACGTGCT
* * *
42427955 GATGCATGTCCCAGACATGTCTTACACTGG--CACAACTCTTAGCA
1 GATGCATGTCCCAGACATGTCTTACACTGGTACTCATCTC-TAGCC
** * ** * * *
42427999 GATGTGTGTCCTAGACACATATTACACTGGTTA-TCATCATCGAAGCT
1 GATGCATGTCCCAGACATGTCTTACACTGG-TACTCATC-TC-TAGCC
* * *
42428046 GATGCATGTCCCAGACATGTCATACACTGG--CACAACTCTTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGTACTCATCTC-TAGCC
** * * *
42428090 GATGC--GTACCCTAGACACATCTTACACTAGCTA-TCATCATCGAGGCT
1 GATGCATGT-CCC-AGACATGTCTTACACT-GGTACTCATC-TCTA-GCC
42428137 GATGCATGTCCCAGACATGTCTTACACTGGTACTCATCTCTACGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGTACTCATCTCTA-GCC
* * * * *
42428183 GATGCCATGTCCCAGACATGGTCTTATAC-AGTCACTCATAATGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGT-ACTCAT-CTCTAGCC
*
42428231 AATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
42428259 AGCACACAAG
Statistics
Matches: 196, Mismatches: 44, Indels: 37
0.71 0.16 0.13
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 47 0.24
45 4 0.02
46 27 0.14
47 86 0.44
48 23 0.12
49 4 0.02
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGTACTCATCTCTAGCC
Found at i:42434040 original size:47 final size:47
Alignment explanation
Indices: 42433964--42434303 Score: 295
Period size: 47 Copynumber: 7.2 Consensus size: 47
42433954 GTCCCAAAAA
*
42433964 GGTCTTACACT-G-ACACATGTCAAGCCGATGCCATGTCCCAGACAT
1 GGTCTTACACTAGCACACATCTCAAGCCGATGCCATGTCCCAGACAT
* * * *
42434009 GGTCTTACACTAGCTCACATCTCAAGTCGATGCCATGTCCCAGATAA
1 GGTCTTACACTAGCACACATCTCAAGCCGATGCCATGTCCCAGACAT
* * *
42434056 GGTCTTACACT-G-ACTATCATCATCGAGGCCGATG-CGTGTCCTAGACA-
1 GGTCTTACACTAGCAC-A-CATC-TC-AAGCCGATGCCATGTCCCAGACAT
* ***
42434103 CGTCTTACACTAGCACTTGTCTCAATGCCGATGCCATGTCCCAGACAT
1 GGTCTTACACTAGCACACATCTCAA-GCCGATGCCATGTCCCAGACAT
* * * *
42434151 GGTCTTACACAAGCACACATATCTTGAGGCTGATG-CATGTCCCAGACAT
1 GGTCTTACACTAGCACAC--ATC-TCAAGCCGATGCCATGTCCCAGACAT
* * * * * *
42434200 -GTCTTACACTGGCTCTCGTCTCAAAGCCGAAG-CATGTCCCAAACAT
1 GGTCTTACACTAGCACACATCTC-AAGCCGATGCCATGTCCCAGACAT
* * *
42434246 -GTCTTACACTAGCACTCGTCTCAATGCCGATGCCATGTCCTAGACAT
1 GGTCTTACACTAGCACACATCTCAA-GCCGATGCCATGTCCCAGACAT
42434293 GGTCTTACACT
1 GGTCTTACACT
42434304 GGCTCTCATT
Statistics
Matches: 236, Mismatches: 41, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
45 16 0.07
46 59 0.25
47 78 0.33
48 50 0.21
49 23 0.10
50 8 0.03
51 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (47 bp):
GGTCTTACACTAGCACACATCTCAAGCCGATGCCATGTCCCAGACAT
Found at i:42434301 original size:94 final size:92
Alignment explanation
Indices: 42433953--42434310 Score: 323
Period size: 96 Copynumber: 3.8 Consensus size: 92
42433943 GTTGATACTG
* *
42433953 TGTCCCAAAAAGGTCTTACACTGACACATGTCAA-GCCGATGCCATGTCCCAGACATGGTCTTAC
1 TGTCCCAAACAGGTCTTACACTGACACATCTCAAGGCCGATG-CATGTCCCAGACATGGTCTTAC
* * *
42434017 ACTAGCTCACATCTC-AAGTCGATGCCA
65 ACTAGCTCTCGTCTCAAAGCCGATGCCA
* * * *
42434044 TGTCCCAGATA-AGGTCTTACACTGACTATCATCATCGAGGCCGATGCGTGTCCTAGACA-CGTC
1 TGTCCCA-A-ACAGGTCTTACACTGAC-A-CATC-TCAAGGCCGATGCATGTCCCAGACATGGTC
* * *
42434107 TTACACTAGCACTTGTCTCAATGCCGATGCCA
61 TTACACTAGCTCTCGTCTCAAAGCCGATGCCA
* * ** *
42434139 TGTCCCAGACATGGTCTTACACAAGCACACATATCTTGAGGCTGATGCATGTCCCAGACAT-GTC
1 TGTCCCAAACA-GGTCTTACAC-TG-ACAC--ATCTCAAGGCCGATGCATGTCCCAGACATGGTC
* *
42434203 TTACACTGGCTCTCGTCTCAAAGCCGAAG-CA
61 TTACACTAGCTCTCGTCTCAAAGCCGATGCCA
* * * * *
42434234 TGTCCCAAACATGTCTTACACTAGCACTCGTCTCAATGCCGATGCCATGTCCTAGACATGGTCTT
1 TGTCCCAAACAGGTCTTACACT-G-ACACATCTCAAGGCCGATG-CATGTCCCAGACATGGTCTT
*
42434299 ACACTGGCTCTC
63 ACACTAGCTCTC
42434311 ATTATGTGGT
Statistics
Matches: 218, Mismatches: 32, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
91 7 0.03
92 26 0.12
93 16 0.07
94 53 0.24
95 54 0.25
96 57 0.26
97 5 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (92 bp):
TGTCCCAAACAGGTCTTACACTGACACATCTCAAGGCCGATGCATGTCCCAGACATGGTCTTACA
CTAGCTCTCGTCTCAAAGCCGATGCCA
Found at i:42434364 original size:142 final size:141
Alignment explanation
Indices: 42433953--42434364 Score: 426
Period size: 142 Copynumber: 2.9 Consensus size: 141
42433943 GTTGATACTG
* * * * *
42433953 TGTCCCAAAAAGGTCTTACACT-G-ACACATGTCAA-GCCGATGCCATGTCCCAGACATGGTCTT
1 TGTCCCAAACACGTCTTACACTAGCACTCGTCTCAATGCCGATGCCATGTCCCAGACATGGTCTT
* * * * * * *
42434015 ACACTAGCTCACA-TCTCAAGTCGATGCCATGTCCCAGATAAGGTCTTACACTGA-CTATCATCA
66 ACACTAGCTCACATTATGAGGTTGATG-CATGTCCCAGA-CATGTCTTACACTGAGCCATCATC-
* * * *
42434078 TCGAGGCCGATGCG
128 TCAAAGCCGAAGCA
* * *
42434092 TGTCCTAGACACGTCTTACACTAGCACTTGTCTCAATGCCGATGCCATGTCCCAGACATGGTCTT
1 TGTCCCAAACACGTCTTACACTAGCACTCGTCTCAATGCCGATGCCATGTCCCAGACATGGTCTT
* * * * *
42434157 ACACAAGCACACATATCTTGAGGCTGATGCATGTCCCAGACATGTCTTACACTG-GCTC-TCGTC
66 ACACTAGCTCACAT-T-ATGAGGTTGATGCATGTCCCAGACATGTCTTACACTGAGC-CATCATC
42434220 TCAAAGCCGAAGCA
128 TCAAAGCCGAAGCA
* *
42434234 TGTCCCAAACATGTCTTACACTAGCACTCGTCTCAATGCCGATGCCATGTCCTAGACATGGTCTT
1 TGTCCCAAACACGTCTTACACTAGCACTCGTCTCAATGCCGATGCCATGTCCCAGACATGGTCTT
* * * *
42434299 ACACTGGCTCTCATTATGTGGTTGATGCATGTCCCAGACATGTCTAACACTGGAGCACAT-ATCT
66 ACACTAGCTCACATTATGAGGTTGATGCATGTCCCAGACATGTCTTACACT-GAGC-CATCATCT
42434363 CA
129 CA
42434365 TGTATTGCCA
Statistics
Matches: 224, Mismatches: 38, Indels: 19
0.80 0.14 0.07
Matches are distributed among these distances:
139 18 0.08
140 33 0.15
141 9 0.04
142 127 0.57
143 18 0.08
144 12 0.05
145 7 0.03
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (141 bp):
TGTCCCAAACACGTCTTACACTAGCACTCGTCTCAATGCCGATGCCATGTCCCAGACATGGTCTT
ACACTAGCTCACATTATGAGGTTGATGCATGTCCCAGACATGTCTTACACTGAGCCATCATCTCA
AAGCCGAAGCA
Found at i:42439760 original size:142 final size:140
Alignment explanation
Indices: 42439560--42439915 Score: 378
Period size: 142 Copynumber: 2.5 Consensus size: 140
42439550 GTCGATGCCG
* * * * * * * * *
42439560 TGTCCCAAACAGGTATTACACT-G-ACACATGTCAA-GCCGATGCCATGTCCCAAACATGGTCTT
1 TGTCCCAGACACGTCTTACACTAGCACTCATCTCAATGCCAATGCCACGGCCCAGACATGGTCTT
* *
42439622 ACACTAGCTCACATCTCAAGTC-GATGCCATGTCCCAGATATGGTCTTACACTGACTATCATCAT
66 ACACTAGCTCACATCTCAAGGCAGATG-CATGTCCCAGACAT-GTCTTACACTGACTATCATC-T
* *
42439686 CGAGGCCGATGCA
128 CAAAGCCGATGCA
* * *
42439699 TGTCCTAGACACGTCTTACACTAGCACTCATCTCAATGTCAATGCCACGGCCCAGATATGGTCTT
1 TGTCCCAGACACGTCTTACACTAGCACTCATCTCAATGCCAATGCCACGGCCCAGACATGGTCTT
* * * * * *
42439764 ACACTAGCACGCATATCTCGAGGCAGATGTATGTCCCAGACATGTCTTACACTGGCTCTCATCTC
66 ACACTAG--CTCACATCTCAAGGCAGATGCATGTCCCAGACATGTCTTACACTGACTATCATCTC
42439829 AAAGCCGATGCA
129 AAAGCCGATGCA
* * * * * *
42439841 TGTCCCAGACATGTCTTACACTAGCACTCGTCTCTATGCCGATGCCATGTCCCAGACATGGTCTT
1 TGTCCCAGACACGTCTTACACTAGCACTCATCTCAATGCCAATGCCACGGCCCAGACATGGTCTT
*
42439906 ACACTGGCTC
66 ACACTAGCTC
42439916 TCATTATGTG
Statistics
Matches: 178, Mismatches: 33, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
139 18 0.10
140 3 0.02
141 9 0.05
142 103 0.58
143 18 0.10
144 23 0.13
145 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (140 bp):
TGTCCCAGACACGTCTTACACTAGCACTCATCTCAATGCCAATGCCACGGCCCAGACATGGTCTT
ACACTAGCTCACATCTCAAGGCAGATGCATGTCCCAGACATGTCTTACACTGACTATCATCTCAA
AGCCGATGCA
Found at i:42439767 original size:48 final size:46
Alignment explanation
Indices: 42439560--42439919 Score: 295
Period size: 47 Copynumber: 7.7 Consensus size: 46
42439550 GTCGATGCCG
* * * *
42439560 TGTCCCAAACA-GGTATTACACT-G-ACACATGTCAAGCCGATGCCA
1 TGTCCCAGACATGGTCTTACACTAGCACTCATCTCAAGCCGATG-CA
* * * *
42439604 TGTCCCAAACATGGTCTTACACTAGCTCACATCTCAAGTCGATGCCA
1 TGTCCCAGACATGGTCTTACACTAGCACTCATCTCAAGCCGATG-CA
* *
42439651 TGTCCCAGATATGGTCTTACACT-G-ACTATCATCATCGAGGCCGATGCA
1 TGTCCCAGACATGGTCTTACACTAGCAC--TCATC-TC-AAGCCGATGCA
* * * *
42439699 TGTCCTAGACA-CGTCTTACACTAGCACTCATCTCAATGTCAATGCCA
1 TGTCCCAGACATGGTCTTACACTAGCACTCATCTCAA-GCCGATG-CA
* * * * * * *
42439746 CGGCCCAGATATGGTCTTACACTAGCACGCATATCTCGAGGCAGATGTA
1 TGTCCCAGACATGGTCTTACACTAGCACTC--ATCTC-AAGCCGATGCA
* *
42439795 TGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCAAAGCCGATGCA
1 TGTCCCAGACATGGTCTTACACTAGCACTCATCTC-AAGCCGATGCA
* *
42439841 TGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCTATGCCGATGCCA
1 TGTCCCAGACATGGTCTTACACTAGCACTCATCTC-AAGCCGATG-CA
* *
42439888 TGTCCCAGACATGGTCTTACACTGGCTCTCAT
1 TGTCCCAGACATGGTCTTACACTAGCACTCAT
42439920 TATGTGGTGG
Statistics
Matches: 254, Mismatches: 45, Indels: 30
0.77 0.14 0.09
Matches are distributed among these distances:
44 11 0.04
45 12 0.05
46 61 0.24
47 81 0.32
48 60 0.24
49 19 0.07
50 9 0.04
51 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (46 bp):
TGTCCCAGACATGGTCTTACACTAGCACTCATCTCAAGCCGATGCA
Found at i:42439905 original size:94 final size:95
Alignment explanation
Indices: 42439594--42439919 Score: 369
Period size: 96 Copynumber: 3.4 Consensus size: 95
42439584 CACATGTCAA
* *
42439594 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATCTC-AAGTCGATGCCATGTCCCA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAAAGTCGATGCCATGTCCCA
42439658 GATATGGTCTTACACT-G-ACTATCATCATCGAG
65 GATATGGTCTTACACTAGCAC--TCATC-TCGAG
* * * * * * *
42439690 GCCGATGCATGTCCTAGACA-CGTCTTACACTAGCACTCATCTCAATGTCAATGCCACGGCCCAG
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAAAGTCGATGCCATGTCCCAG
*
42439754 ATATGGTCTTACACTAGCACGCATATCTCGAG
66 ATATGGTCTTACACTAGCACTC--ATCTCGAG
* * * *
42439786 GCAGATGTATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCAAAGCCGATG-CATGTCCCAG
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAAAGTCGATGCCATGTCCCAG
* * * *
42439849 ACAT-GTCTTACACTAGCACTCGTCTCTAT
66 ATATGGTCTTACACTAGCACTCATCTCGAG
*
42439878 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCTCTCAT
42439920 TATGTGGTGG
Statistics
Matches: 195, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
92 11 0.06
93 13 0.07
94 55 0.28
95 54 0.28
96 57 0.29
97 5 0.03
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (95 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAAAGTCGATGCCATGTCCCAG
ATATGGTCTTACACTAGCACTCATCTCGAG
Found at i:42439971 original size:142 final size:142
Alignment explanation
Indices: 42439690--42439965 Score: 349
Period size: 142 Copynumber: 2.0 Consensus size: 142
42439680 CATCATCGAG
* *
42439690 GCCGATGCATGTCCTAGACACGTCTTACACTAGCACTCATCTCAATGTCAATGCCACGGCCCAGA
1 GCCGATGCATGTCCCAGACACGTCTTACACTAGCACTCATCTCAATGCCAATGCCACGGCCCAGA
* * * * *
42439755 TATGGTCTTACACTAGCACGCATATCTCGAGGCAGATGTATGTCCCAGACATGTCTTACACTGGC
66 CATGGTCTTACACTAGCACGCATATATCGAGGCAGATGCATGTCCCAAACATGTCTAACACTGGC
* *
42439820 TCTCATCTCAAA
131 GCACATCTCAAA
* * * * * *
42439832 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCTATGCCGATGCCATGTCCCAGA
1 GCCGATGCATGTCCCAGACACGTCTTACACTAGCACTCATCTCAATGCCAATGCCACGGCCCAGA
* * * * **
42439897 CATGGTCTTACACTGGCTCTCAT-TAT-GTGGTGGATGCATGTCCCAAACATGTCTAACACTGGC
66 CATGGTCTTACACTAGCACGCATATATCGAGGCAGATGCATGTCCCAAACATGTCTAACACTGGC
42439960 GCACAT
131 GCACAT
42439966 ATCTCATGTA
Statistics
Matches: 113, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
140 35 0.31
141 2 0.02
142 76 0.67
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (142 bp):
GCCGATGCATGTCCCAGACACGTCTTACACTAGCACTCATCTCAATGCCAATGCCACGGCCCAGA
CATGGTCTTACACTAGCACGCATATATCGAGGCAGATGCATGTCCCAAACATGTCTAACACTGGC
GCACATCTCAAA
Found at i:42443358 original size:5 final size:5
Alignment explanation
Indices: 42443350--42443378 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
42443340 AAAATAAAAA
42443350 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
42443379 GGTTGGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:42443368 original size:14 final size:14
Alignment explanation
Indices: 42443349--42443378 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42443339 AAAAATAAAA
42443349 ATTTATTTTATTTT
1 ATTTATTTTATTTT
42443363 ATTTATTTTATTTT
1 ATTTATTTTATTTT
42443377 AT
1 AT
42443379 GGTTGGTATC
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:42446639 original size:21 final size:21
Alignment explanation
Indices: 42446615--42446659 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42446605 AACATGGTCG
*
42446615 TGTGGCTACTCCACACTCCCA
1 TGTGGCTACTCCACACACCCA
* *
42446636 TGTGTCTACTTCACACACCCA
1 TGTGGCTACTCCACACACCCA
42446657 TGT
1 TGT
42446660 ACGCAGACCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.38, G:0.13, T:0.29
Consensus pattern (21 bp):
TGTGGCTACTCCACACACCCA
Found at i:42450116 original size:43 final size:43
Alignment explanation
Indices: 42449958--42450114 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 43
42449948 TGTGATTCCG
* * * *
42449958 TGTAAAACCATGTCTGGGACGTTGGCATCGACT-TGA-GATCTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGA-TAT-ATGAT-TACA
* * *
42450002 TGTAAGACCATGTCTGGGACATAGGCATCG-TATATGATTTCA
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATATGATTACA
** * * *
42450044 TGTAAGACC-CTGTCTATGACAGTGGCATTGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGATATATGATTACA
42450087 TGTAAGACCACGTCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
42450115 TGTACGAGCT
Statistics
Matches: 92, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
42 27 0.29
43 37 0.40
44 28 0.30
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATATATGATTACA
Found at i:42452506 original size:17 final size:16
Alignment explanation
Indices: 42452479--42452510 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42452469 TGATAGATCT
42452479 CCGATGAGCTTCCAAC
1 CCGATGAGCTTCCAAC
42452495 CCGATCGAGCTTCCAA
1 CCGAT-GAGCTTCCAA
42452511 TAATTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.25, C:0.38, G:0.19, T:0.19
Consensus pattern (16 bp):
CCGATGAGCTTCCAAC
Found at i:42453499 original size:13 final size:13
Alignment explanation
Indices: 42453474--42453507 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
42453464 CAACACACCA
*
42453474 AACA-GAGAGTAT
1 AACATGAGAATAT
42453486 AACATGAGAATAT
1 AACATGAGAATAT
42453499 AACATGAGA
1 AACATGAGA
42453508 GTTCGCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.18
Consensus pattern (13 bp):
AACATGAGAATAT
Found at i:42456355 original size:41 final size:41
Alignment explanation
Indices: 42456310--42456654 Score: 276
Period size: 41 Copynumber: 8.4 Consensus size: 41
42456300 CTTCATGCCG
* *
42456310 GTGTATTATATCAAGCTTTGTGCCTAGCAAGTTTCGTGCTA
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGTTTCGTGCTA
* * *
42456351 GTGTATTATATCAGGCTTTATTCCTAGCAGGCTTT-GTGCCA
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGG-TTTCGTGCTA
* * * * * *
42456392 ATGTATTATATCAGGCTTTGTGCTTAGCAAGCTTCATG-TC
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGTTTCGTGCTA
* * * *
42456432 GATGTATTATATCAGGCCTTTATGCCTAGTAGGCTTCATGCTA
1 G-TGTATTATATCAGG-CTTTGTGCCTAGCAGGTTTCGTGCTA
* * * * * *
42456475 GTGTATTATATCAAGCTTTATTCTTAGCAGGCTTCGTG-TCG
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGTTTCGTGCT-A
* ** * *
42456516 GTGTATTATATTAGGAGTTGTGCCTTGTAGGTTTCGTGCTA
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGTTTCGTGCTA
*
42456557 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTT-GTG-TC
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGG-TTTCGTGCTA
* * * *
42456597 GATGTATTATATCAAGATTTGTGCCTTGTAGGCTTT-GTGCT-
1 G-TGTATTATATCAGGCTTTGTGCCTAGCAGG-TTTCGTGCTA
42456638 G-GT-TTATTATCAGGCTT
1 GTGTATTA-TATCAGGCTT
42456655 CATGCAAGTG
Statistics
Matches: 244, Mismatches: 49, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
38 3 0.01
39 10 0.04
40 5 0.02
41 184 0.75
42 40 0.16
43 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (41 bp):
GTGTATTATATCAGGCTTTGTGCCTAGCAGGTTTCGTGCTA
Found at i:42456414 original size:82 final size:82
Alignment explanation
Indices: 42456310--42456647 Score: 365
Period size: 82 Copynumber: 4.1 Consensus size: 82
42456300 CTTCATGCCG
* * *
42456310 GTGTATTATATCAAGCTTTGTGCCTAGCAAGTTTCGTG-CTAGTGTATTATATCAGGCTTTATTC
1 GTGTATTATATCAAGCTTTGTGCCTAGCAAGCTTCGTGTCGA-TGTATTATATCAGGCTTTATGC
* *
42456374 CTAGCAGGCTTTGTGCCA
65 CTAGTAGGCTTTGTGCTA
* * * *
42456392 ATGTATTATATCAGGCTTTGTGCTTAGCAAGCTTCATGTCGATGTATTATATCAGGCCTTTATGC
1 GTGTATTATATCAAGCTTTGTGCCTAGCAAGCTTCGTGTCGATGTATTATATCAGG-CTTTATGC
**
42456457 CTAGTAGGCTTCATGCTA
65 CTAGTAGGCTTTGTGCTA
* * * * * * ** *
42456475 GTGTATTATATCAAGCTTTATTCTTAGCAGGCTTCGTGTCGGTGTATTATATTAGGAGTTGTGCC
1 GTGTATTATATCAAGCTTTGTGCCTAGCAAGCTTCGTGTCGATGTATTATATCAGGCTTTATGCC
*
42456540 TTGTAGG-TTTCGTGCTA
66 TAGTAGGCTTT-GTGCTA
* * * * * *
42456557 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTTGTGTCGATGTATTATATCAAGATTTGTGCC
1 GTGTATTATATCAAGCTTTGTGCCTAGCAAGCTTCGTGTCGATGTATTATATCAGGCTTTATGCC
* *
42456622 TTGTAGGCTTTGTGCTG
66 TAGTAGGCTTTGTGCTA
*
42456639 GTTTATTAT
1 GTGTATTAT
42456648 CAGGCTTCAT
Statistics
Matches: 216, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
81 2 0.01
82 140 0.65
83 74 0.34
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (82 bp):
GTGTATTATATCAAGCTTTGTGCCTAGCAAGCTTCGTGTCGATGTATTATATCAGGCTTTATGCC
TAGTAGGCTTTGTGCTA
Found at i:42456569 original size:165 final size:165
Alignment explanation
Indices: 42456297--42456610 Score: 407
Period size: 165 Copynumber: 1.9 Consensus size: 165
42456287 TAAGTCCTGC
* * *
42456297 AGGCTTCATGCCGGTGTATTATATCAAGCTTTGTGCCTAGCAAGTTTCGTGCTAGTGTATTATAT
1 AGGCTTCATGCCAGTGTATTATATCAAGCTTTATGCCTAGCAAGCTTCGTGCTAGTGTATTATAT
** * *
42456362 CAGGCTTTATTCCTAGCAGGCTTTGTGCCAATGTATTATATCAGGCTTTGTGCTTAGCAAGCTTC
66 CAGGAGTTATGCCTAGCAGGCTTTGTGCCAATGTATTATATCAGGCTTTGTGCCTAGCAAGCTTC
42456427 ATGTCGATGTATTATATCAGGCCTTTATGCCTAGT
131 ATGTCGATGTATTATATCAGGCCTTTATGCCTAGT
* * * * *
42456462 AGGCTTCATGCTAGTGTATTATATCAAGCTTTATTCTTAGCAGGCTTCGTG-TCGGTGTATTATA
1 AGGCTTCATGCCAGTGTATTATATCAAGCTTTATGCCTAGCAAGCTTCGTGCT-AGTGTATTATA
* * * * * * *
42456526 TTAGGAGTTGTGCCTTGTAGG-TTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAGCAGGCT
65 TCAGGAGTTATGCCTAGCAGGCTTT-GTGCCAATGTATTATATCAGGCTTTGTGCCTAGCAAGCT
**
42456590 TTGTGTCGATGTATTATATCA
129 TCATGTCGATGTATTATATCA
42456611 AGATTTGTGC
Statistics
Matches: 126, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
164 4 0.03
165 122 0.97
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.39
Consensus pattern (165 bp):
AGGCTTCATGCCAGTGTATTATATCAAGCTTTATGCCTAGCAAGCTTCGTGCTAGTGTATTATAT
CAGGAGTTATGCCTAGCAGGCTTTGTGCCAATGTATTATATCAGGCTTTGTGCCTAGCAAGCTTC
ATGTCGATGTATTATATCAGGCCTTTATGCCTAGT
Found at i:42456707 original size:41 final size:41
Alignment explanation
Indices: 42456648--42456914 Score: 243
Period size: 41 Copynumber: 6.5 Consensus size: 41
42456638 GGTTTATTAT
* *
42456648 CAGGCTTCATGCAAGTGTATTATATCAGGCTTTGTGCCTAG
1 CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAG
* * * *
42456689 CAGGCTTTGTGCTGGTGTATTATATCAAGCTTTAG-GCTTAG
1 CAGGCTTCGTGCTAGTGTATTATATCAGGCTTT-GTGCCTAG
* *
42456730 CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTCTGACTAG
1 CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAG
* * * * *
42456771 TAGGCTTTGTG-TCAGTGTATTATATTAAGCTTTGTGCCTAA
1 CAGGCTTCGTGCT-AGTGTATTATATCAGGCTTTGTGCCTAG
* * * * * * * *
42456812 AAAGCTTTGTTCTGGTGTGTTATATCAGACTTTGAGCCTAG
1 CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAG
* * * * * *
42456853 TAGGCTTCGTG-TCAGTGTGTTATATCAGGTTTTGAGCTTAA
1 CAGGCTTCGTGCT-AGTGTATTATATCAGGCTTTGTGCCTAG
42456894 CAGGCTTCGTGCTAGTGTATT
1 CAGGCTTCGTGCTAGTGTATT
42456915 GTATTAGGTA
Statistics
Matches: 180, Mismatches: 40, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
40 2 0.01
41 175 0.97
42 3 0.02
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (41 bp):
CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAG
Found at i:42456742 original size:105 final size:107
Alignment explanation
Indices: 42456556--42456761 Score: 298
Period size: 105 Copynumber: 1.9 Consensus size: 107
42456546 GTTTCGTGCT
42456556 AGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTTGTGTCGATGTATTATATCAAGATTTGTGC
1 AGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTTGTGTCGATGTATTATATCAAGATTTGTGC
* *
42456621 CTTGTAGGCTTTGTGCT-G-GT-TTATTATCAGGCTTCATGCA
66 CTTGCAGGCTTCGTGCTAGTGTATTA-TATCAGGCTTCATGCA
* *
42456661 AGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTTGTG-CTGGTGTATTATATCAAGCTTTAG-
1 AGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTTGTGTC-GATGTATTATATCAAGATTT-GT
42456724 G-CTTAGCAGGCTTCGTGCTAGTGTATTATATCAGGCTT
64 GCCTT-GCAGGCTTCGTGCTAGTGTATTATATCAGGCTT
42456762 TCTGACTAGT
Statistics
Matches: 91, Mismatches: 4, Indels: 10
0.87 0.04 0.10
Matches are distributed among these distances:
104 4 0.04
105 70 0.77
106 2 0.02
107 12 0.13
108 3 0.03
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (107 bp):
AGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTTGTGTCGATGTATTATATCAAGATTTGTGC
CTTGCAGGCTTCGTGCTAGTGTATTATATCAGGCTTCATGCA
Found at i:42456774 original size:146 final size:146
Alignment explanation
Indices: 42456516--42456781 Score: 349
Period size: 146 Copynumber: 1.8 Consensus size: 146
42456506 CTTCGTGTCG
* * * *
42456516 GTGTATTATATTAGGAGTTGTGCCTTGTAGGTTTCGTGCTAGTGTATTATATCAGGCTTTGTGCC
1 GTGTATTATATCAGGAGTTGTGCCTAGCAGGTTTCGTGCTAGTGTATTATATCAAGCTTTGTGCC
* * * * *
42456581 TAGCAGGCTTTGTGTCGATGTATTATATCAAGATTTGTGCCTTGTAGGCTTTGTGCTGGTTTATT
66 TAGCAGGCTTCGTGTAGATGTATTATATCAAGATTTCTGACTAGTAGGCTTTGTGCTGGTTTATT
42456646 ATCAGGCTTCATGCAA
131 ATCAGGCTTCATGCAA
** *
42456662 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTT-GTGCTGGTGTATTATATCAAGCTTTAG-G
1 GTGTATTATATCAGGAGTTGTGCCTAGCAGG-TTTCGTGCTAGTGTATTATATCAAGCTTT-GTG
* * *
42456725 CTTAGCAGGCTTCGTGCTAG-TGTATTATATCAGGCTTTCTGACTAGTAGGCTTTGTG
64 CCTAGCAGGCTTCGTG-TAGATGTATTATATCAAGATTTCTGACTAGTAGGCTTTGTG
42456782 TCAGTGTATT
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
146 96 0.94
147 6 0.06
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (146 bp):
GTGTATTATATCAGGAGTTGTGCCTAGCAGGTTTCGTGCTAGTGTATTATATCAAGCTTTGTGCC
TAGCAGGCTTCGTGTAGATGTATTATATCAAGATTTCTGACTAGTAGGCTTTGTGCTGGTTTATT
ATCAGGCTTCATGCAA
Found at i:42456778 original size:187 final size:186
Alignment explanation
Indices: 42456462--42456809 Score: 479
Period size: 187 Copynumber: 1.9 Consensus size: 186
42456452 TATGCCTAGT
* * *
42456462 AGGCTTCATGCTAGTGTATTATATCAAGCTTTATTCTTAGCAGGCTTCGTGTCGGTGTATTATAT
1 AGGCTTCATGCAAGTGTATTATATCAAGCTTTATGCCTAGCAGGCTTCGTGTCGGTGTATTATAT
* * * * *
42456527 TAGGAGTTGTGCCTTGTAGGTTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTT
66 CA-GAGTTGTGCCTTGCAGGCTTCGTGCTAGTGTATTATATCAGGCTTTCTGACTAGCAGGCTTT
42456592 GTGTC-GATGTATTATATCAAGATTTGTGCCTTGTAGGCTTTGTGCTGGTTTATTATC
130 GTGTCAG-TGTATTATATCAAGATTTGTGCCTTGTAGGCTTTGTGCTGGTTTATTATC
* * *
42456649 AGGCTTCATGCAAGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTTGTG-CTGGTGTATTATA
1 AGGCTTCATGCAAGTGTATTATATCAAGCTTTATGCCTAGCAGGCTTCGTGTC-GGTGTATTATA
* *
42456713 TCA-AGCTT-TAGGCTTAGCAGGCTTCGTGCTAGTGTATTATATCAGGCTTTCTGACTAGTAGGC
65 TCAGAG-TTGT-GCCTT-GCAGGCTTCGTGCTAGTGTATTATATCAGGCTTTCTGACTAGCAGGC
* *
42456776 TTTGTGTCAGTGTATTATATTAAGCTTTGTGCCT
127 TTTGTGTCAGTGTATTATATCAAGATTTGTGCCT
42456810 AAAAAGCTTT
Statistics
Matches: 141, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
185 3 0.02
186 7 0.05
187 130 0.92
188 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (186 bp):
AGGCTTCATGCAAGTGTATTATATCAAGCTTTATGCCTAGCAGGCTTCGTGTCGGTGTATTATAT
CAGAGTTGTGCCTTGCAGGCTTCGTGCTAGTGTATTATATCAGGCTTTCTGACTAGCAGGCTTTG
TGTCAGTGTATTATATCAAGATTTGTGCCTTGTAGGCTTTGTGCTGGTTTATTATC
Found at i:42456789 original size:82 final size:82
Alignment explanation
Indices: 42456648--42456914 Score: 304
Period size: 82 Copynumber: 3.3 Consensus size: 82
42456638 GGTTTATTAT
* * * *
42456648 CAGGCTTCATGCAAGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTTGTG-CTGGTGTATTAT
1 CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAGTAGGCTTTGTGTC-AGTGTATTAT
*
42456712 ATCAAGCTTT-AGGCTTAG
65 ATCAAGCTTTGA-GCTTAA
* *
42456730 CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTCTGACTAGTAGGCTTTGTGTCAGTGTATTATA
1 CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAGTAGGCTTTGTGTCAGTGTATTATA
* * *
42456795 TTAAGCTTTGTGCCTAA
66 TCAAGCTTTGAGCTTAA
* * * * * * * * * *
42456812 AAAGCTTTGTTCTGGTGTGTTATATCAGACTTTGAGCCTAGTAGGCTTCGTGTCAGTGTGTTATA
1 CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAGTAGGCTTTGTGTCAGTGTATTATA
* *
42456877 TCAGGTTTTGAGCTTAA
66 TCAAGCTTTGAGCTTAA
42456894 CAGGCTTCGTGCTAGTGTATT
1 CAGGCTTCGTGCTAGTGTATT
42456915 GTATTAGGTA
Statistics
Matches: 150, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
82 149 0.99
83 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (82 bp):
CAGGCTTCGTGCTAGTGTATTATATCAGGCTTTGTGCCTAGTAGGCTTTGTGTCAGTGTATTATA
TCAAGCTTTGAGCTTAA
Found at i:42456899 original size:123 final size:123
Alignment explanation
Indices: 42456648--42456920 Score: 306
Period size: 123 Copynumber: 2.2 Consensus size: 123
42456638 GGTTTATTAT
* * * * ** *
42456648 CAGGCTTCATGCAAGTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTTGTGCTGGTGTATTATA
1 CAGGCTTCGTGCTAGTGTATTATATTAAGCTTTGTGCCTAAAAAGCTTTGTGCTGGTGTATTATA
* *
42456713 TCAAGCTTTAGGCTTAGCAGGCTTCGTGCTAGTGTATTATATCAGGCTTTCTGACTAG
66 TCAAGCTTTAGGCCTAGCAGGCTTCGTGCTAGTGTATTATATCAGGCTTTCTGACTAA
* * * *
42456771 TAGGCTTTGTG-TCAGTGTATTATATTAAGCTTTGTGCCTAAAAAGCTTTGTTCTGGTGTGTTAT
1 CAGGCTTCGTGCT-AGTGTATTATATTAAGCTTTGTGCCTAAAAAGCTTTGTGCTGGTGTATTAT
* *
42456835 ATC-AGACTTT-GAGCCTAGTAGGCTTCGTG-TCAGTGTGTTATATCAGG-TTT-TGAGCTTAA
65 ATCAAG-CTTTAG-GCCTAGCAGGCTTCGTGCT-AGTGTATTATATCAGGCTTTCTGA-C-TAA
*
42456894 CAGGCTTCGTGCTAGTGTATTGTATTA
1 CAGGCTTCGTGCTAGTGTATTATATTA
42456921 GGTAAGTTGT
Statistics
Matches: 125, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
121 3 0.02
122 8 0.06
123 113 0.90
124 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (123 bp):
CAGGCTTCGTGCTAGTGTATTATATTAAGCTTTGTGCCTAAAAAGCTTTGTGCTGGTGTATTATA
TCAAGCTTTAGGCCTAGCAGGCTTCGTGCTAGTGTATTATATCAGGCTTTCTGACTAA
Found at i:42458470 original size:47 final size:47
Alignment explanation
Indices: 42458419--42458511 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
42458409 CCTTAGGCTC
42458419 GATTTAAGGCTCGTAAAAGTATTTATGCTATACTCAAGTTATGTTAG
1 GATTTAAGGCTCGTAAAAGTATTTATGCTATACTCAAGTTATGTTAG
*
42458466 GATTTAAGGCTCGTAAAAGTATTTATGCTATATTCAAGTTATGTTA
1 GATTTAAGGCTCGTAAAAGTATTTATGCTATACTCAAGTTATGTTA
42458512 TCGAATGTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (47 bp):
GATTTAAGGCTCGTAAAAGTATTTATGCTATACTCAAGTTATGTTAG
Found at i:42469623 original size:18 final size:18
Alignment explanation
Indices: 42469592--42469638 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
42469582 AATTGAAAGT
**
42469592 ATATATAATTTATTATAAA
1 ATATATAAAATATTA-AAA
*
42469611 A-ATATGAAATATTAAAA
1 ATATATAAAATATTAAAA
42469628 ATATATAAAAT
1 ATATATAAAAT
42469639 TACATAAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.17
18 18 0.78
19 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATATAAAATATTAAAA
Found at i:42471322 original size:18 final size:18
Alignment explanation
Indices: 42471299--42471334 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42471289 GATAGCAAAA
*
42471299 TTTTTTGTA-TTTTTCTT
1 TTTTTTTTATTTTTTCTT
42471316 TTTTTTTTATTTTTTCTT
1 TTTTTTTTATTTTTTCTT
42471334 T
1 T
42471335 CGGCTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.86
Consensus pattern (18 bp):
TTTTTTTTATTTTTTCTT
Found at i:42476294 original size:3 final size:3
Alignment explanation
Indices: 42476282--42476316 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
42476272 TAATCAAAAC
*
42476282 ATA A-A ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42476317 TCGAATGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:42478118 original size:51 final size:51
Alignment explanation
Indices: 42478058--42478324 Score: 175
Period size: 51 Copynumber: 5.4 Consensus size: 51
42478048 GACTTTGACT
* *
42478058 TGCTCTACTGCTACTTCAGAGAGATAAGATCCGTAACTTATAGCTTCAATC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCCGTAACTTATAGCTTCAATC
* * * * *
42478109 TGCTCTACTGCAACTTCAGGGAAATAAGAT---TCAC-TAT--CTTTAGTA
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCCGTAACTTATAGCTTCAATC
* *
42478154 TGCTCCTACTGCAACTTCAGGGAGATAAGA-CTCGCAACTTTTAGCTTCAATC
1 TGCT-CTACTGCAACTTCAGGGAGATAAGATC-CGTAACTTATAGCTTCAATC
* * * * ** *
42478206 TGCTCCACGGCAATTTCAGGGAAATAAGAT---TTGC-TAT--CTTCAGTC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCCGTAACTTATAGCTTCAATC
* ** * * * *
42478251 TACTCTTACTATAACTTCGGGGAGATAAGA-CTCGCAACTTGTAGCTTCAATT
1 TGCTC-TACTGCAACTTCAGGGAGATAAGATC-CGTAACTTATAGCTTCAATC
* *
42478303 TACTCTACTGCAACTTTAGGGA
1 TGCTCTACTGCAACTTCAGGGA
42478325 AATGATATTC
Statistics
Matches: 158, Mismatches: 41, Indels: 34
0.68 0.18 0.15
Matches are distributed among these distances:
45 20 0.13
46 41 0.26
47 5 0.03
48 4 0.03
49 3 0.02
50 4 0.03
51 61 0.39
52 20 0.13
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (51 bp):
TGCTCTACTGCAACTTCAGGGAGATAAGATCCGTAACTTATAGCTTCAATC
Found at i:42478183 original size:97 final size:97
Alignment explanation
Indices: 42478058--42478375 Score: 390
Period size: 97 Copynumber: 3.3 Consensus size: 97
42478048 GACTTTGACT
* * *
42478058 TGCT-CTACTGCTACTTCAGAGAGATAAGA-TCCGTAACTTATAGCTTCAATCTGCTCTACTGCA
1 TGCTCCTACTGCAACTTCAGGGAGATAAGACT-CGCAACTTATAGCTTCAATCTGCTCTACTGCA
* * *
42478121 ACTTCAGGGAAATAAGATTCACTATCTTTAGTA
65 ACTTCAGGGAAATAAGATTCGCTATCTTCAGTC
* * *
42478154 TGCTCCTACTGCAACTTCAGGGAGATAAGACTCGCAACTTTTAGCTTCAATCTGCTCCACGGCAA
1 TGCTCCTACTGCAACTTCAGGGAGATAAGACTCGCAACTTATAGCTTCAATCTGCTCTACTGCAA
* *
42478219 TTTCAGGGAAATAAGATTTGCTATCTTCAGTC
66 CTTCAGGGAAATAAGATTCGCTATCTTCAGTC
* * ** * * * *
42478251 TACTCTTACTATAACTTCGGGGAGATAAGACTCGCAACTTGTAGCTTCAATTTACTCTACTGCAA
1 TGCTCCTACTGCAACTTCAGGGAGATAAGACTCGCAACTTATAGCTTCAATCTGCTCTACTGCAA
* * *
42478316 CTTTAGGGAAATGATATTCGCTATCTTCAGTC
66 CTTCAGGGAAATAAGATTCGCTATCTTCAGTC
* *
42478348 TGCTTC-GCTGCAACTTCAGGGAGATAAG
1 TGCTCCTACTGCAACTTCAGGGAGATAAG
42478376 GCTGGTGGCT
Statistics
Matches: 187, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
96 22 0.12
97 164 0.88
98 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (97 bp):
TGCTCCTACTGCAACTTCAGGGAGATAAGACTCGCAACTTATAGCTTCAATCTGCTCTACTGCAA
CTTCAGGGAAATAAGATTCGCTATCTTCAGTC
Found at i:42478197 original size:46 final size:45
Alignment explanation
Indices: 42478109--42478194 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
42478099 AGCTTCAATC
* *
42478109 TGCTCTACTGCAACTTCAGGGAAATAAGATTCACTATCTTTAGTA
1 TGCTCTACTGCAACTTCAGGGAAATAAGACTCACAATCTTTAGTA
* *
42478154 TGCTCCTACTGCAACTTCAGGGAGATAAGACTCGCAA-CTTT
1 TGCT-CTACTGCAACTTCAGGGAAATAAGACTCACAATCTTT
42478195 TAGCTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 8 0.22
46 28 0.78
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (45 bp):
TGCTCTACTGCAACTTCAGGGAAATAAGACTCACAATCTTTAGTA
Found at i:42478467 original size:143 final size:143
Alignment explanation
Indices: 42478309--42478857 Score: 706
Period size: 143 Copynumber: 3.8 Consensus size: 143
42478299 AATTTACTCT
* * * * * *
42478309 ACTGCAACTTTAGGGAAATGATATTCGCTATCTTCAGTCTGCTTCGCTGCAACTTCAGGGAGATA
1 ACTGCAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATA
* *
42478374 AGGCTGGTGGCTTTAATCTGCTCCACTACAACTTCAAGAAGATAAGATTCGCCATAATTTGTAGC
66 AGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGC
*
42478439 TTTAATTTGTTCC
131 TTTAATCTGTTCC
* * * * *
42478452 ACTGCAACGTCAGGGAAATAAGATTTGCTGTCTTTAGTCTGCTTCGCTGCAATTTCGGGGAGATA
1 ACTGCAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATA
* ** * *
42478517 AGGCTGATGGCTTCAATCTGCTCCACTGTAATTTCAGGAAGATAAGA-TCTGTCATAATTTGTAG
66 AGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTC-GCCATAATTTGTAG
42478581 CTTTAATCTGTTCC
130 CTTTAATCTGTTCC
* * ** * * *
42478595 ACTACAACATCAAAGAAATAAGATTCACTGTCTTCAGTCTGCTCCGCTGCAACTTTAGAGAGATA
1 ACTGCAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATA
*
42478660 AGGCTAGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATAT-GCCATAATTTGTAG
66 AGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGAT-TCGCCATAATTTGTAG
*
42478724 CTTTAATCTGTTCT
130 CTTTAATCTGTTCC
* * * * * *
42478738 ACTGTAACGTCAGGGAAATAAGATTCGTTGTCTTCAGTCTACTCCGTTGTAACTTCAAGGAGATA
1 ACTGCAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATA
* * * * * *
42478803 AGGCTGGTGGATTCAATTTGCTCAACTGCAACTTTAGGAAGATAAGATCCGCCAT
66 AGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCAT
42478858 CTTCGATCTA
Statistics
Matches: 346, Mismatches: 56, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
142 2 0.01
143 343 0.99
145 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (143 bp):
ACTGCAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATA
AGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGC
TTTAATCTGTTCC
Found at i:42484892 original size:3 final size:3
Alignment explanation
Indices: 42484863--42484928 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
42484853 GTTCTAATTC
* *
42484863 TAA TAT TAA TAA TCAA AACA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
42484909 TAA TAA TGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
42484929 TCGAATGATG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.89
4 4 0.07
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:42504392 original size:20 final size:20
Alignment explanation
Indices: 42504353--42504393 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42504343 CAATACCAAT
* *
42504353 TCATTTATACATTCAGAAGA
1 TCATGTATACATTCACAAGA
*
42504373 TCATGTATACATTTACAAGA
1 TCATGTATACATTCACAAGA
42504393 T
1 T
42504394 TAAATAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTATACATTCACAAGA
Found at i:42506511 original size:50 final size:50
Alignment explanation
Indices: 42506455--42506787 Score: 373
Period size: 50 Copynumber: 6.8 Consensus size: 50
42506445 GACGCTAGGT
*
42506455 ATATATGAGAGCTAGTGTAAGACCGTGTCTGGGACATGGCATC-AGCCTCG
1 ATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-CCTCG
* * *
42506505 ATATATGAGAGCTAGTGTAAGACTATGTCTGGTACATGGCATCG-GCTCG
1 ATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCG
* *
42506554 --ATATGTG-TC-AGTGTAAGACCATGTCTGGGACATGGCATCGACAC-CG
1 ATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-CTCG
* * *
42506600 ATATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGACATCGGAAC-CG
1 ATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACCTCG
* * * *
42506650 ATAGATGAGAGCCAGTGTAAGAGCATGTCTGGGACATGGCATCGACCTCA
1 ATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCG
* * * *
42506700 ATATACGAGAG-TCAGTGTAAGACCATGTCTCGGACATGGCATCGACTTTG
1 ATATATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACCTCG
* * *
42506750 ATGTCT--GAGCCAGTGTAAGACCATGTCTGGGACATGGC
1 ATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGC
42506788 GTCGGCACCC
Statistics
Matches: 238, Mismatches: 34, Indels: 24
0.80 0.11 0.08
Matches are distributed among these distances:
45 29 0.12
46 3 0.01
47 7 0.03
48 35 0.15
49 8 0.03
50 154 0.65
51 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
ATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCG
Found at i:42510512 original size:55 final size:53
Alignment explanation
Indices: 42510426--42510671 Score: 245
Period size: 55 Copynumber: 4.6 Consensus size: 53
42510416 CATTAGGGTT
*
42510426 CAAGGATACCATGAAAGACCATGCCAAGACATGGCAATTGGAAAGGTTTCTAAGG
1 CAAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGAAA-GTTTCTAAGG
* * * *
42510481 CAAGGATATCATGTAAGACCATGTCAGGACATGGCATT-GATAAGTTACTATAAGG
1 CAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGA-AAGTT--TCTAAGG
* * **
42510536 CAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGG
1 C-AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGAAAGTTTC-TAAGG
* * *
42510589 CAAGGATACCATGTAAGACCATGTCAAGACATGGCAGTGGTAAGTTTC-AA--
1 CAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGAAAGTTTCTAAGG
* * *
42510639 -AAGGATACCACGTAAGACCATGACAAGCCATGG
1 CAAGGATACCATGTAAGACCATGCCAAGACATGG
42510672 AAATGGTAAG
Statistics
Matches: 162, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
49 30 0.19
52 7 0.04
53 44 0.27
54 9 0.06
55 67 0.41
56 5 0.03
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (53 bp):
CAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGAAAGTTTCTAAGG
Found at i:42510633 original size:108 final size:110
Alignment explanation
Indices: 42510434--42510634 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
42510424 TTCAAGGATA
*
42510434 CCATGAAAGACCATGCCAAGACATGGCAATTGGAAAGGTTTCTAAGGCAAGGATATCATGTAAGA
1 CCATGAAAGACCATGCCAAGACATGGCAATTGGAAAGGTTTCTAAGGCAAGGATACCATGTAAGA
* *
42510499 CCATGTCAGGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAGTGATAAGTTACTATAAGGCAAAGGTC
* * **
42510544 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGAAAGACCATGCCAAGACATGGCAATTGGAAAGGTTTC-TAAGGCAAGGATACCATGTAAG
*
42510606 ACCATGTCAAGACATGGCAGTGGTAAGTT
65 ACCATGTCAAGACATGGCAGTGATAAGTT
42510635 TCAAAAGGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.59
109 6 0.07
110 25 0.30
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (110 bp):
CCATGAAAGACCATGCCAAGACATGGCAATTGGAAAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCATGTCAAGACATGGCAGTGATAAGTTACTATAAGGCAAAGGTC
Found at i:42513532 original size:180 final size:179
Alignment explanation
Indices: 42513209--42513787 Score: 820
Period size: 180 Copynumber: 3.2 Consensus size: 179
42513199 TCCATTTTCA
* * * * *
42513209 ATCTGCTCCACTGCAAGTTCAGGGAAATAAAATCTTCAATTCTCAATCTGCTTCCTTGTTATCTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAAATCTTCAATTCTCAGTCTGCTTCCTTGCTACCTC
* **
42513274 AGGAAGATAAGACTCATTCTTCAACCTGCTCTTTTGCTACCTCAGAGAGATAAGGCTTGGTAATA
66 AGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGGTGGT-
* * *
42513339 AAATCTACTCCATTGCCAATACATGGAGATAAGATTCACCATCTGTGAAG
130 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGCGAAG
42513389 ATCTGCTCCACTGCAACTTCAGGGAGATAAAATCTTCAATTCTCAGTCTGCTTCCTTGCTACCTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAAATCTTCAATTCTCAGTCTGCTTCCTTGCTACCTC
* * * *
42513454 AGGAAGATAAGACTCATTCTTCATCCTGCTCTCTTGCTATCTCAGAGAGATAAGGTTTGATGGTA
66 AGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGGTGGTA
* * *
42513519 ACATCTGCTCCATTGCTGATACATGGAGATAAGATTCACCATC-ACAAAG
131 A-ATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGCGAAG
* * * * * *
42513568 ATATACTCCGCTGCAACTTCAGAGAGATAATATCCTCAATTCTCAGTCTGCTTCCTTGCTACCTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAAATCTTCAATTCTCAGTCTGCTTCCTTGCTACCTC
* * ** *
42513633 AGAAAGATAAGACTCATTCTTTAACCTATTCTCTTGCTACCTCAGAGAGACAAGGCTTGGTGGTG
66 AGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGGTGGT-
42513698 AAATCTGCTCCATTGCCGATACATGGAGATAA-ATTTCACCATCTGCGAAG
130 AAATCTGCTCCATTGCCGATACATGGAGATAAGA-TTCACCATCTGCGAAG
* * *
42513748 ATCTGCTCCGCTGCAACTTCAAGGAGATAAGATCTTCAAT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAAATCTTCAAT
42513788 CTTTACCAAT
Statistics
Matches: 353, Mismatches: 42, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
178 1 0.00
179 157 0.44
180 195 0.55
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (179 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAAATCTTCAATTCTCAGTCTGCTTCCTTGCTACCTC
AGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGGTGGTA
AATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGCGAAG
Found at i:42523586 original size:46 final size:46
Alignment explanation
Indices: 42523536--42523707 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
42523526 TGAGCATCCA
42523536 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * *
42523582 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG
* *
42523629 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * *
42523675 AGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42523708 GCAGGTTACA
Statistics
Matches: 106, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 58 0.55
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:42523688 original size:93 final size:93
Alignment explanation
Indices: 42523529--42523700 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
42523519 GGATGATTGA
* *
42523529 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42523594 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
42523622 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
42523687 TGAGTCTGAGTTCG
66 TGAGTCCGAGTTCG
42523701 CTTATGGGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42538993 original size:26 final size:26
Alignment explanation
Indices: 42538964--42539071 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
42538954 TGGTACAAAT
*
42538964 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
42538990 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
42539016 TGATAATGGGTTAGGTAAACATTCTA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
42539042 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
42539068 TGAT
1 TGAT
42539072 GGGCATTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:42540264 original size:8 final size:8
Alignment explanation
Indices: 42540251--42540280 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
42540241 AGATCGGCAC
42540251 AAGCCGAA
1 AAGCCGAA
42540259 AAGCCGAA
1 AAGCCGAA
*
42540267 ATGCCGAA
1 AAGCCGAA
42540275 AAGCCG
1 AAGCCG
42540281 GTATTTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.27, G:0.27, T:0.03
Consensus pattern (8 bp):
AAGCCGAA
Found at i:42548073 original size:29 final size:29
Alignment explanation
Indices: 42548040--42548098 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
42548030 TATAACAGAG
* **
42548040 TAAGTTCTGTATATTATGTGTTAATATGC
1 TAAGTTCGGTATATTACATGTTAATATGC
*
42548069 TAAGTTCGGTATGTTACATGTTAATATGC
1 TAAGTTCGGTATATTACATGTTAATATGC
42548098 T
1 T
42548099 TAGAAACATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (29 bp):
TAAGTTCGGTATATTACATGTTAATATGC
Found at i:42548481 original size:21 final size:21
Alignment explanation
Indices: 42548455--42548494 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42548445 ATTTTCTCTG
*
42548455 ATATGATATA-TGTTTCTGAAT
1 ATATGAAATATTG-TTCTGAAT
42548476 ATATGAAATATTGTTCTGA
1 ATATGAAATATTGTTCTGA
42548495 TAATTACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
ATATGAAATATTGTTCTGAAT
Found at i:42552270 original size:2 final size:2
Alignment explanation
Indices: 42552263--42552287 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42552253 AACTTTAAAT
42552263 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42552288 GATCAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42569044 original size:46 final size:46
Alignment explanation
Indices: 42568977--42569107 Score: 156
Period size: 46 Copynumber: 2.8 Consensus size: 46
42568967 AATCTCACCT
* * * *
42568977 ATAATGAACTCAGAATGCAACTCAACGAGCTCGGGTG-TTCGCATCC
1 ATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTT-GCATCC
* * *
42569023 ATAATGAACTCGGAACACAACTCAATGAGTTTGGATGCTTGCATCC
1 ATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTGCATCC
* *
42569069 ATAGGTGAACTCGGAACGTAACTCAACGAGTTCGGATGC
1 ATA-ATGAACTCGGAACGCAACTCAACGAGTTCGGATGC
42569108 CTCATAATTC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
46 39 0.55
47 32 0.45
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (46 bp):
ATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTGCATCC
Found at i:42571763 original size:45 final size:45
Alignment explanation
Indices: 42571665--42571823 Score: 175
Period size: 45 Copynumber: 3.6 Consensus size: 45
42571655 CCGGTATTTT
* * * *
42571665 GCCTGCTAGGCTC-GAGGCCCG-ATA-TCATTTCACTGGCACTATA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGT-ATCTCACTGACATTATA
*
42571708 GCCTGCTAGGCTCGAAA-GCCCGAATAGTATCTCA-TCGATATTATA
1 GCCTGCTAGGCTC-AAAGGCCCGAATAGTATCTCACT-GACATTATA
* * *
42571753 GCCTGCTAGGCTCAAAGGCCCGAATAGTATTTCACTGGCATCATA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACTGACATTATA
*
42571798 GCCTGCTAGGCACAAAGGCCCGAATA
1 GCCTGCTAGGCTCAAAGGCCCGAATA
42571824 CACATCACCG
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
43 13 0.13
44 9 0.09
45 75 0.76
46 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (45 bp):
GCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACTGACATTATA
Found at i:42571859 original size:43 final size:43
Alignment explanation
Indices: 42571752--42571978 Score: 262
Period size: 43 Copynumber: 5.2 Consensus size: 43
42571742 TCGATATTAT
* * ** * *
42571752 AGCCTGCTAGGCTCAAAGGCCCGAATAGTATTTCACTGGCATC-A
1 AGCCTGCTAGGCACAAAGGCCCGAATA-CACATCACCGG-AACGA
42571796 TAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGAACGA
1 -AGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGAACGA
* *
42571840 AGCCTGCTAGGCA-AGAAGGCTCGAATACACATCACCAGCAA-GA
1 AGCCTGCTAGGCACA-AAGGCCCGAATACACATCACC-GGAACGA
* * * *
42571883 AGCCTACTAGGCACGAAGGCCCGAATACACATCACCAGCACGA
1 AGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGAACGA
* *
42571926 AGCCTGCTAGGCACAAAGGCCTGAATACACATCACCGGCACGA
1 AGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGAACGA
42571969 AGCCTGCTAG
1 AGCCTGCTAG
42571979 ATTTAACCCG
Statistics
Matches: 159, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
42 2 0.01
43 120 0.75
44 11 0.07
45 26 0.16
ACGTcount: A:0.33, C:0.31, G:0.23, T:0.14
Consensus pattern (43 bp):
AGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGAACGA
Found at i:42576837 original size:39 final size:40
Alignment explanation
Indices: 42576743--42576851 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 40
42576733 ACACACCAGG
* * ** *
42576743 CAGAAACTCATAAGAGCTAATCCAATTGAAATACGCTAAA
1 CAGAAGCTCATAAGAGCTAGTCCACCTGAAACACGCTAAA
* *
42576783 TAGAAGCTCAGAAGAGCTAGTCCACCTGAAACACGC-AAA
1 CAGAAGCTCATAAGAGCTAGTCCACCTGAAACACGCTAAA
* *
42576822 CAGAAGCTCATAAGAGTTGGTCCACCTGAA
1 CAGAAGCTCATAAGAGCTAGTCCACCTGAA
42576852 TCATTCCAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
39 29 0.50
40 29 0.50
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.17
Consensus pattern (40 bp):
CAGAAGCTCATAAGAGCTAGTCCACCTGAAACACGCTAAA
Found at i:42585037 original size:22 final size:22
Alignment explanation
Indices: 42585009--42585055 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
42584999 TTTGGAATGT
42585009 CATCTCTAAATAAATACCAAAA
1 CATCTCTAAATAAATACCAAAA
42585031 CATCTCTAAATAAATACCAAAA
1 CATCTCTAAATAAATACCAAAA
42585053 CAT
1 CAT
42585056 TTCACCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (22 bp):
CATCTCTAAATAAATACCAAAA
Found at i:42592854 original size:46 final size:45
Alignment explanation
Indices: 42592801--42592970 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 45
42592791 TTGAGCATCT
42592801 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATTGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA-TGATGCGAATGTCC
* * * *
42592847 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-AATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAA-T--G--TCC
* * *
42592894 GAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAATGTCC
* *
42592940 GAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
42592971 GGGGCGGGTT
Statistics
Matches: 101, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 56 0.55
47 28 0.28
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAATGTCC
Found at i:42592954 original size:93 final size:93
Alignment explanation
Indices: 42592795--42592965 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
42592785 GGATGGTTGA
* * * *
42592795 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATTGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42592860 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
42592888 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
42592953 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
42592966 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:42595677 original size:104 final size:104
Alignment explanation
Indices: 42595488--42595753 Score: 430
Period size: 104 Copynumber: 2.6 Consensus size: 104
42595478 TTGTATATAA
** *
42595488 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATGGTGGTGCTATGTGCG-TGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGAT-ATCCACCATATCTT
42595552 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
42595592 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCGATATCCACCATATCTT
42595657 TGAAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
42595696 AGGGGTTGCTAAGTGCTGATT-CCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCGATATCCACCA
42595754 ATAACGGTTA
Statistics
Matches: 152, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
103 33 0.22
104 79 0.52
105 39 0.26
106 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGATATCCACCATATCTTT
GAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:42657782 original size:44 final size:41
Alignment explanation
Indices: 42657716--42657907 Score: 205
Period size: 43 Copynumber: 4.6 Consensus size: 41
42657706 TTCACGTCAA
*
42657716 TGCCTTCGGGACTTAGCTCGGTTATAGTAACTCGCACAAATT
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA-T
*
42657758 TGCCGTTCGGGACTTTAGCCCGGTTATACCTAACTCGCAC-AAT
1 TGCC-TTCGGGAC-TTAGCCCGGTTATA-GTAACTCGCACAAAT
* * *
42657801 TCCCATTCGGGACTTGGCCCAGTTATATAGTAACTGCGCACAAA-
1 TGCC-TTCGGGACTTAGCCC-GGT-TATAGTAACT-CGCACAAAT
* * *
42657845 TGCCTTC-GGACTTAGCCCGGATATAGT-ACTCACACAAAG
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAAT
42657884 TGCCTTCGGG-CTTAGCCCGGTTAT
1 TGCCTTCGGGACTTAGCCCGGTTAT
42657908 CAATCAAATA
Statistics
Matches: 128, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
38 7 0.05
39 23 0.18
40 8 0.06
41 1 0.01
42 20 0.16
43 30 0.23
44 27 0.21
45 12 0.09
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (41 bp):
TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAAT
Found at i:42663412 original size:29 final size:28
Alignment explanation
Indices: 42663374--42663494 Score: 99
Period size: 29 Copynumber: 4.2 Consensus size: 28
42663364 TTAATTGTAC
42663374 AGCACT-AGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
42663401 AGCACTTAAGTGTG-GAGTTTGGATT-TGAT
1 AGCAC-TAAGTGTGCGAGCTT-GATTATG-T
42663430 AGTGCACTAAGTGTGCGAG-TT-ATTATGGT
1 A--GCACTAAGTGTGCGAGCTTGATTAT-GT
* * *
42663459 AGCACTGAGTGGGCGATCTTGAATTATGT
1 AGCACTAAGTGTGCGAGCTTG-ATTATGT
*
42663488 CGCACTA
1 AGCACTA
42663495 GCTTGATGAG
Statistics
Matches: 76, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
27 18 0.24
28 13 0.17
29 22 0.29
30 16 0.21
31 7 0.09
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATGT
Found at i:42666737 original size:46 final size:45
Alignment explanation
Indices: 42666644--42666729 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
42666634 TACATTTCAC
* *
42666644 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCAGACTCAACTCAACGAGTTCGGA-ATGCGCAACCATAAGT
* *
42666690 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GAACTCAGACTCAACTCAACGAGTTCGGAATGCGCAACCAT
42666730 CCTAGTGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 9 0.25
46 27 0.75
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (45 bp):
GAACTCAGACTCAACTCAACGAGTTCGGAATGCGCAACCATAAGT
Found at i:42667166 original size:30 final size:30
Alignment explanation
Indices: 42667132--42667191 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
42667122 ATTTAATACG
42667132 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
42667162 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
42667192 GGCTCGGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:42678966 original size:10 final size:10
Alignment explanation
Indices: 42678951--42679009 Score: 66
Period size: 10 Copynumber: 5.9 Consensus size: 10
42678941 TAATTTTACT
42678951 TTTATCTTTA
1 TTTATCTTTA
*
42678961 TTTATCCTTA
1 TTTATCTTTA
42678971 TTTATCTTTA
1 TTTATCTTTA
*
42678981 ATTATCTTTAA
1 TTTATCTTT-A
* *
42678992 TTAAT-TTTG
1 TTTATCTTTA
42679001 TTTATCTTT
1 TTTATCTTT
42679010 TAGAATTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
9 4 0.10
10 32 0.80
11 4 0.10
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:42687425 original size:12 final size:13
Alignment explanation
Indices: 42687389--42687453 Score: 55
Period size: 13 Copynumber: 4.9 Consensus size: 13
42687379 AACCCAACCT
42687389 TTATTTT-TGTTTA
1 TTATTTTAT-TTTA
*
42687402 TTTTTCTTATTTTA
1 TTATT-TTATTTTA
42687416 -TATTTTATTTTA
1 TTATTTTATTTTA
42687428 TTATTTGT-TATTTA
1 TTATTT-TAT-TTTA
*
42687442 TTACTTTATTTT
1 TTATTTTATTTT
42687454 TGGATATTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 8 0.19
13 17 0.40
14 17 0.40
15 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:42687441 original size:26 final size:27
Alignment explanation
Indices: 42687389--42687453 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
42687379 AACCCAACCT
42687389 TTATTTT-TGTTTATTTTTCTTATTTTA
1 TTATTTTAT-TTTATTTTTCTTATTTTA
*
42687416 -TATTTTATTTTATTATTTGTTA-TTTA
1 TTATTTTATTTTATT-TTTCTTATTTTA
*
42687442 TTACTTTATTTT
1 TTATTTTATTTT
42687454 TGGATATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (27 bp):
TTATTTTATTTTATTTTTCTTATTTTA
Found at i:42690071 original size:16 final size:16
Alignment explanation
Indices: 42690047--42690077 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42690037 AGTAATAAGA
*
42690047 AGAAGAAGAAAAAAAT
1 AGAAAAAGAAAAAAAT
42690063 AGAAAAAGAAAAAAA
1 AGAAAAAGAAAAAAA
42690078 GTGATGTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (16 bp):
AGAAAAAGAAAAAAAT
Found at i:42690724 original size:10 final size:10
Alignment explanation
Indices: 42690709--42690767 Score: 75
Period size: 10 Copynumber: 5.9 Consensus size: 10
42690699 AATTTTAGCT
42690709 TTTATCTTTA
1 TTTATCTTTA
*
42690719 TTTATCCTTA
1 TTTATCTTTA
42690729 TTTATCTTTA
1 TTTATCTTTA
*
42690739 ATTATCTTTA
1 TTTATCTTTA
*
42690749 TTTAAT-TGTA
1 TTT-ATCTTTA
42690759 TTTATCTTT
1 TTTATCTTT
42690768 TAGAATTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
9 2 0.05
10 37 0.90
11 2 0.05
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:42693968 original size:22 final size:24
Alignment explanation
Indices: 42693940--42693984 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
42693930 ATTTTGTTCA
42693940 ATTTTAACTT-TTAT-TCAAAACC
1 ATTTTAACTTGTTATATCAAAACC
*
42693962 ATTTTAATTTGTTATATCAAAAC
1 ATTTTAACTTGTTATATCAAAAC
42693985 ATATTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 7 0.35
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTTTAACTTGTTATATCAAAACC
Found at i:42695841 original size:20 final size:19
Alignment explanation
Indices: 42695796--42695843 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
42695786 TTTAAAATAG
*
42695796 TTTAACTTTGATTGAAAAAT
1 TTTAAC-TTAATTGAAAAAT
* *
42695816 TCTAACTTAATTGAAACTAT
1 TTTAACTTAATTGAAA-AAT
42695836 TTTAACTT
1 TTTAACTT
42695844 GGTTGATTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (19 bp):
TTTAACTTAATTGAAAAAT
Found at i:42698293 original size:27 final size:27
Alignment explanation
Indices: 42698251--42698334 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
42698241 AAGCTTTTTA
* *
42698251 TGGAAATCTATTAAAAGGAAGCCTTTG
1 TGGAGATCTATGAAAAGGAAGCCTTTG
** ** *
42698278 TGGCTATCTATGAAAAGGAAATCTTTC
1 TGGAGATCTATGAAAAGGAAGCCTTTG
*
42698305 TGGAGATCTATG-AAGGGAATGCCTTTG
1 TGGAGATCTATGAAAAGGAA-GCCTTTG
42698332 TGG
1 TGG
42698335 TGCACTTTAA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
26 6 0.14
27 38 0.86
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (27 bp):
TGGAGATCTATGAAAAGGAAGCCTTTG
Found at i:42701089 original size:31 final size:31
Alignment explanation
Indices: 42701051--42701109 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
42701041 TATTTGAGTT
42701051 AATTAAGTTATTTGGATCAACTCGAATAAAA
1 AATTAAGTTATTTGGATCAACTCGAATAAAA
* * *
42701082 AATTAAGTTTTTTGGTTTAACTCGAATA
1 AATTAAGTTATTTGGATCAACTCGAATA
42701110 TGAATTACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (31 bp):
AATTAAGTTATTTGGATCAACTCGAATAAAA
Found at i:42703727 original size:32 final size:32
Alignment explanation
Indices: 42703686--42703750 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
42703676 TTGAAAGAGT
42703686 AAGTTTATTTTATGTGTGTAAATAGTAAGATG
1 AAGTTTATTTTATGTGTGTAAATAGTAAGATG
42703718 AAGTTTATTTTATGTGTGTAAATAGTAAGATG
1 AAGTTTATTTTATGTGTGTAAATAGTAAGATG
42703750 A
1 A
42703751 GGAAGTAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (32 bp):
AAGTTTATTTTATGTGTGTAAATAGTAAGATG
Found at i:42704511 original size:53 final size:53
Alignment explanation
Indices: 42704428--42704549 Score: 140
Period size: 53 Copynumber: 2.3 Consensus size: 53
42704418 GAACACACCA
* **
42704428 GAAAAAGAAGCATTT-TGGCGATCTACGAAAAGGAAGACTTTGTGGTGATCTAT
1 GAAAAAGAAGC-TTTGTGGCGATCTACGAAAAGAAAGACTTTGTGGCAATCTAT
* * *
42704481 -AAAAAGAAGTCTTTGTGGCGATTTATGAAAAGAAAGCCTTTGTGGCAATCTAT
1 GAAAAAGAAG-CTTTGTGGCGATCTACGAAAAGAAAGACTTTGTGGCAATCTAT
*
42704534 GAAACAGAAGCCTTTG
1 GAAAAAGAAG-CTTTG
42704550 CAGGGATCTA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
52 12 0.21
53 33 0.57
54 13 0.22
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (53 bp):
GAAAAAGAAGCTTTGTGGCGATCTACGAAAAGAAAGACTTTGTGGCAATCTAT
Found at i:42704534 original size:27 final size:26
Alignment explanation
Indices: 42704430--42704580 Score: 144
Period size: 27 Copynumber: 5.7 Consensus size: 26
42704420 ACACACCAGA
* *
42704430 AAAAGAAGCATTT-TGGCGATCTACG
1 AAAAGAAGCCTTTGTGGCGATCTATG
* * *
42704455 AAAAGGAAGACTTTGTGGTGATCTATA
1 AAAA-GAAGCCTTTGTGGCGATCTATG
* *
42704482 AAAAGAAGTCTTTGTGGCGATTTATG
1 AAAAGAAGCCTTTGTGGCGATCTATG
*
42704508 AAAAGAAAGCCTTTGTGGCAATCTATG
1 AAAAG-AAGCCTTTGTGGCGATCTATG
*
42704535 AAACAGAAGCCTTTGCAGG-GATCTATG
1 AAA-AGAAGCCTTTG-TGGCGATCTATG
**
42704562 AAGGGAATGCCTTTGTGGC
1 AAAAGAA-GCCTTTGTGGC
42704581 ACACTCTAAA
Statistics
Matches: 102, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
25 4 0.04
26 35 0.34
27 59 0.58
28 4 0.04
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.27
Consensus pattern (26 bp):
AAAAGAAGCCTTTGTGGCGATCTATG
Found at i:42711526 original size:39 final size:39
Alignment explanation
Indices: 42711460--42711535 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
42711450 GGTATCAATT
*
42711460 TCACATTTTATCTTTAAAATAAATTTT-ATTTAAAAAAA
1 TCACATTTTATATTTAAAATAAATTTTAATTTAAAAAAA
* ** *
42711498 TCACATTTTTATATTTAATATATTTTTTAATTTCAAAA
1 TCACA-TTTTATATTTAAAATAAATTTTAATTTAAAAA
42711536 TACATGTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 5 0.16
39 18 0.58
40 8 0.26
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (39 bp):
TCACATTTTATATTTAAAATAAATTTTAATTTAAAAAAA
Found at i:42714607 original size:50 final size:52
Alignment explanation
Indices: 42714544--42714644 Score: 145
Period size: 50 Copynumber: 2.0 Consensus size: 52
42714534 TACAAATAGT
* *
42714544 AAGAAAGTATTATTAAATTATTT-AATTTTAATCACTTAATTATT-TGATGTG
1 AAGAAAATATTATTAAATTATTTAAATTTAAAT-ACTTAATTATTATGATGTG
*
42714595 AAGAAAAT-TTATTAAATTATTTAAATTTAAATAGTTAATTATTATGATGT
1 AAGAAAATATTATTAAATTATTTAAATTTAAATACTTAATTATTATGATGT
42714645 TTAGATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
50 24 0.53
51 21 0.47
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (52 bp):
AAGAAAATATTATTAAATTATTTAAATTTAAATACTTAATTATTATGATGTG
Found at i:42716428 original size:126 final size:125
Alignment explanation
Indices: 42716234--42716563 Score: 303
Period size: 126 Copynumber: 2.6 Consensus size: 125
42716224 ACAACACACA
* * * * * * * **
42716234 CAATCATTCCAC-ACATCTACACTTTCAACTCTGGTTTATTTTTCACAAGCACCTCAGCACGCGT
1 CAATCATTCC-CTACATCAACAC-ATCAACACTAGTTTATTTTACACAAGCACCACAACACGCAC
* * * *
42716298 AATCATTCCCTGCA-TGAACACATACAACAAC-ATTTTATTTTTCACAAGCACC-TCAACATGTG
64 AATCATTCCTTGCATTG-ACACATACAAC-ACTAGTTTATTTTACACAAGCACCAT-AACACGTG
* * *
42716360 TAATCATTCCCTACATCAACACATACAACACTAGTTTATTTTCCACAAGCACCACAACATGCACA
1 CAATCATTCCCTACATCAACACAT-CAACACTAGTTTATTTTACACAAGCACCACAACACGCACA
* * * * * *
42716425 ATCATTCATTACATTGACACATTCATCACTAGTTTATTTTACATAAGCACCATAGCACGTG
65 ATCATTCCTTGCATTGACACATACAACACTAGTTTATTTTACACAAGCACCATAACACGTG
* * **
42716486 CAATCATTCCCTACA-CTAACACAGTCATCA-TCACTTTATTTTACACAAGCACCACAACACGTT
1 CAATCATTCCCTACATC-AACACA-TCAACACT-AGTTTATTTTACACAAGCACCACAACACGCA
42716549 CAATCATTCCTTGCA
63 CAATCATTCCTTGCA
42716564 CCGACACCTT
Statistics
Matches: 166, Mismatches: 30, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
125 6 0.04
126 156 0.94
127 4 0.02
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.29
Consensus pattern (125 bp):
CAATCATTCCCTACATCAACACATCAACACTAGTTTATTTTACACAAGCACCACAACACGCACAA
TCATTCCTTGCATTGACACATACAACACTAGTTTATTTTACACAAGCACCATAACACGTG
Found at i:42716547 original size:63 final size:63
Alignment explanation
Indices: 42716234--42716558 Score: 273
Period size: 63 Copynumber: 5.2 Consensus size: 63
42716224 ACAACACACA
* * * * * * * * *
42716234 CAATCATTCCAC-ACATCTACACTTTCAACTCTGGTTTATTTTTCACAAGCACCTCAGCACGCG
1 CAATCATTCC-CTACATCAACACATACAACACTAGTTTATTTTACACAAGCACCACAACACGTG
* * * * * * *
42716297 TAATCATTCCCTGCATGAACACATACAACAAC-ATTTTATTTTTCACAAGCACCTCAACATGTG
1 CAATCATTCCCTACATCAACACATACAAC-ACTAGTTTATTTTACACAAGCACCACAACACGTG
* * * **
42716360 TAATCATTCCCTACATCAACACATACAACACTAGTTTATTTTCCACAAGCACCACAACATGCA
1 CAATCATTCCCTACATCAACACATACAACACTAGTTTATTTTACACAAGCACCACAACACGTG
** ** * * * * *
42716423 CAATCATTCATTACATTGACACATTCATCACTAGTTTATTTTACATAAGCACCATAGCACGTG
1 CAATCATTCCCTACATCAACACATACAACACTAGTTTATTTTACACAAGCACCACAACACGTG
* *
42716486 CAATCATTCCCTACA-CTAACACAGT-CATCA-TCACTTTATTTTACACAAGCACCACAACACGT
1 CAATCATTCCCTACATC-AACACA-TACAACACT-AGTTTATTTTACACAAGCACCACAACACGT
*
42716548 T
63 G
42716549 CAATCATTCC
1 CAATCATTCC
42716559 TTGCACCGAC
Statistics
Matches: 214, Mismatches: 42, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
62 4 0.02
63 208 0.97
64 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.29
Consensus pattern (63 bp):
CAATCATTCCCTACATCAACACATACAACACTAGTTTATTTTACACAAGCACCACAACACGTG
Found at i:42718582 original size:16 final size:16
Alignment explanation
Indices: 42718553--42718596 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
42718543 ATCTTCATTG
*
42718553 AATCCTTAAAATCTTCA
1 AATCCTT-AAATCTTAA
42718570 AATCCTTAAATCTTAA
1 AATCCTTAAATCTTAA
*
42718586 AATCCCTAAAT
1 AATCCTTAAAT
42718597 TGTTAGCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (16 bp):
AATCCTTAAATCTTAA
Found at i:42718992 original size:117 final size:117
Alignment explanation
Indices: 42718784--42718994 Score: 305
Period size: 117 Copynumber: 1.8 Consensus size: 117
42718774 TTTGATTTGT
* * * * * * *
42718784 TGGTTATTTGTGATTCATTATTGCAATTTTAGTGCCATAGTGTAGGGTTTGTTTTGTTAATTTGT
1 TGGTTATTTGTGATTCATTATTGCAATTTCAGTACCACAATGTAAGGTCTGTTTTATTAATTTGT
* *
42718849 AATGCAAAAGTGGTCTCGATGTTGTTGATAAAACTGTTGTTAAAATTGTAGA
66 AATGCAAAAGTGGTCCCGATGATGTTGATAAAACTGTTGTTAAAATTGTAGA
* *
42718901 TGGTTATTTGTGATTTATTATTGCAATTTCAGTACCACAATGTAAGGTCTGTTTTATTGATTTGT
1 TGGTTATTTGTGATTCATTATTGCAATTTCAGTACCACAATGTAAGGTCTGTTTTATTAATTTGT
* *
42718966 AATGCGACAGTGGTCCCGATGATGTTGAT
66 AATGCAAAAGTGGTCCCGATGATGTTGAT
42718995 TTCTATTACC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
117 81 1.00
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.44
Consensus pattern (117 bp):
TGGTTATTTGTGATTCATTATTGCAATTTCAGTACCACAATGTAAGGTCTGTTTTATTAATTTGT
AATGCAAAAGTGGTCCCGATGATGTTGATAAAACTGTTGTTAAAATTGTAGA
Found at i:42719943 original size:51 final size:51
Alignment explanation
Indices: 42719864--42719964 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
42719854 AAGTTGCTGC
* * *
42719864 TGATGAATACGCTGGTGATTTTGCAACATCAAATGGAGTAGATAATGTTGT
1 TGATGAATACACTGGTGATTTTGAAACATCAAATAGAGTAGATAATGTTGT
* * * *
42719915 TGATGAATATACTGGTGATTTTGAAACATCAGATAGATTGGATAATGTTG
1 TGATGAATACACTGGTGATTTTGAAACATCAAATAGAGTAGATAATGTTG
42719965 CTGCTACACG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.35
Consensus pattern (51 bp):
TGATGAATACACTGGTGATTTTGAAACATCAAATAGAGTAGATAATGTTGT
Found at i:42724252 original size:20 final size:18
Alignment explanation
Indices: 42724202--42724253 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
42724192 CTACAAGATA
42724202 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
42724219 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
42724239 AATATTAAATTAATA
1 AATATTAAATTAATA
42724254 AATTACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:42727469 original size:49 final size:47
Alignment explanation
Indices: 42727330--42727503 Score: 133
Period size: 48 Copynumber: 3.6 Consensus size: 47
42727320 TGATGTGTGT
* *
42727330 GCTAGTGTAAGACCTGCTAGGGACATGGCATCAGCACTGATAG-ATGAGA
1 GCTAGTGTAAGACCTGTTTGGGACATGGCATC-G-ACTGAT-GTATGAGA
** * *
42727379 GCTAGTGTAAGA-CTGTTTGGGACACAGCATTGGCCTCGATGTATG-GAA
1 GCTAGTGTAAGACCTGTTTGGGACATGGCA-TCGACT-GATGTATGAG-A
*
42727427 GTTAGTGTAAGACCTGTTTGGGACATGGCATCGACTTAGATG--TGAGA
1 GCTAGTGTAAGACCTGTTTGGGACATGGCATCGAC-T-GATGTATGAGA
* * * *
42727474 GCCAGGGTAAGACCATGTTTAGAACATGGC
1 GCTAGTGTAAGACC-TGTTTGGGACATGGC
42727504 GTCGGCATCG
Statistics
Matches: 100, Mismatches: 17, Indels: 17
0.75 0.13 0.13
Matches are distributed among these distances:
47 18 0.18
48 49 0.49
49 33 0.33
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.25
Consensus pattern (47 bp):
GCTAGTGTAAGACCTGTTTGGGACATGGCATCGACTGATGTATGAGA
Found at i:42728296 original size:30 final size:30
Alignment explanation
Indices: 42728260--42728317 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
42728250 TAGACACACG
*
42728260 GTCAACCCAATGGGCGTGTTGTCTGGTCGT
1 GTCAACCCAATGGGCGTATTGTCTGGTCGT
42728290 GTCAACCCAATGGGCGTATTGTCTGGTC
1 GTCAACCCAATGGGCGTATTGTCTGGTC
42728318 ATGTATCCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (30 bp):
GTCAACCCAATGGGCGTATTGTCTGGTCGT
Found at i:42728788 original size:22 final size:21
Alignment explanation
Indices: 42728763--42728804 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
42728753 GTCAAGAAGG
42728763 CCACACGAGCGTGTCGCCCCTT
1 CCACACGAGCGTGT-GCCCCTT
* *
42728785 CCACACGGGTGTGTGCCCCT
1 CCACACGAGCGTGTGCCCCT
42728805 GTTTTAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.12, C:0.43, G:0.26, T:0.19
Consensus pattern (21 bp):
CCACACGAGCGTGTGCCCCTT
Found at i:42730057 original size:2 final size:2
Alignment explanation
Indices: 42730052--42730077 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42730042 AGATAAAAGA
42730052 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
42730078 TACAAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42752820 original size:115 final size:115
Alignment explanation
Indices: 42752618--42752880 Score: 409
Period size: 115 Copynumber: 2.3 Consensus size: 115
42752608 ACAGTATATT
* * **
42752618 AAAATGACAAAATGCCAATTTGATATCAATACCAATATACAATATCGATACTTATCTTCAAAGAT
1 AAAATGGCTAAATGCCAAAATGATATCAATACCAATATACAATATCGATACTTATCTTCAAAGAT
* *
42752683 TGATACTTTATAAAGGTATCGATACAGGTTGACTTGTGTCAAAATTTTTG
66 CGATACTTTATAAAGGTATCGATACAGGTTGACTTATGTCAAAATTTTTG
* * *
42752733 AAAATGGCTAAATGCCAAAATGATATCAATACCAATATACAGTATTGATACTTATCTTGAAAGAT
1 AAAATGGCTAAATGCCAAAATGATATCAATACCAATATACAATATCGATACTTATCTTCAAAGAT
* *
42752798 CGATACTTTATAAAGGTATCGATATAGGTTGACTTATGTCCAAATTTTTG
66 CGATACTTTATAAAGGTATCGATACAGGTTGACTTATGTCAAAATTTTTG
**
42752848 AAAATGGCTAAATGCCAAAACAATATCAATACC
1 AAAATGGCTAAATGCCAAAATGATATCAATACC
42752881 CAATTTGGTA
Statistics
Matches: 135, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 135 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (115 bp):
AAAATGGCTAAATGCCAAAATGATATCAATACCAATATACAATATCGATACTTATCTTCAAAGAT
CGATACTTTATAAAGGTATCGATACAGGTTGACTTATGTCAAAATTTTTG
Found at i:42754416 original size:14 final size:14
Alignment explanation
Indices: 42754397--42754426 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42754387 CTCTACTCGT
*
42754397 AATATTGTATAAAA
1 AATATTATATAAAA
42754411 AATATTATATAAAA
1 AATATTATATAAAA
42754425 AA
1 AA
42754427 AAGAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
AATATTATATAAAA
Found at i:42754774 original size:9 final size:9
Alignment explanation
Indices: 42754760--42754787 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
42754750 TACTCCACTT
42754760 AACCACTCC
1 AACCACTCC
42754769 AACCACTCC
1 AACCACTCC
42754778 AACCACTCC
1 AACCACTCC
42754787 A
1 A
42754788 CTACACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.54, G:0.00, T:0.11
Consensus pattern (9 bp):
AACCACTCC
Found at i:42754807 original size:13 final size:13
Alignment explanation
Indices: 42754785--42754849 Score: 77
Period size: 13 Copynumber: 5.3 Consensus size: 13
42754775 TCCAACCACT
*
42754785 CCACTACACTAAA
1 CCACTCCACTAAA
42754798 CCACTCCACTAAA
1 CCACTCCACTAAA
42754811 CCAC-CC-C--AA
1 CCACTCCACTAAA
42754820 CCAC-CCTACTAAA
1 CCACTCC-ACTAAA
42754833 CCACTCCACTAAA
1 CCACTCCACTAAA
42754846 CCAC
1 CCAC
42754850 CTCAACCACT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
9 8 0.17
11 2 0.04
12 2 0.04
13 32 0.70
14 2 0.04
ACGTcount: A:0.38, C:0.49, G:0.00, T:0.12
Consensus pattern (13 bp):
CCACTCCACTAAA
Found at i:42754836 original size:35 final size:35
Alignment explanation
Indices: 42754792--42754858 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
42754782 ACTCCACTAC
42754792 ACTAAACCACTCCACTAAACCACCCCAACCACCCT
1 ACTAAACCACTCCACTAAACCACCCCAACCACCCT
*
42754827 ACTAAACCACTCCACTAAACCACCTCAACCAC
1 ACTAAACCACTCCACTAAACCACCCCAACCAC
42754859 TCCACTTGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.39, C:0.49, G:0.00, T:0.12
Consensus pattern (35 bp):
ACTAAACCACTCCACTAAACCACCCCAACCACCCT
Found at i:42755266 original size:3 final size:3
Alignment explanation
Indices: 42755234--42755363 Score: 52
Period size: 3 Copynumber: 43.3 Consensus size: 3
42755224 GGAGAGAGTG
* * * * *
42755234 TTA TTT TTA ATA TTG TTA TTA TTT TCTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* ** * * * * *
42755280 ATA CCA CTA TTA TCA TCA TTA TTA CTA TTA -TA TTA -TA ATA CCTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA --TTA
* * *
42755324 TTCA TTA TTA TTA CTA TT- GTG TTA TTA TTA TTA TTA TTA T
1 TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
42755364 ATTTCCTTTT
Statistics
Matches: 95, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
2 7 0.07
3 83 0.87
4 4 0.04
5 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:42755271 original size:19 final size:18
Alignment explanation
Indices: 42755234--42755275 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
42755224 GGAGAGAGTG
*
42755234 TTATTTTTAATATTGTTA
1 TTATTTTTAATATTATTA
*
42755252 TTATTTTCTATTATTATTA
1 TTATTTT-TAATATTATTA
42755271 TTATT
1 TTATT
42755276 ACTAATACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTAATATTATTA
Found at i:42755334 original size:33 final size:39
Alignment explanation
Indices: 42755260--42755341 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 39
42755250 TATTATTTTC
*
42755260 TATTATTATTATTATTACTAATACCACTATTATCATCAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
*
42755299 TATTACTATTA-TATTA-TAATA-C-CT-TT-TCATTAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
42755332 TATTACTATT
1 TATTACTATT
42755342 GTGTTATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 16 0.39
34 2 0.05
35 2 0.05
36 1 0.02
37 5 0.12
38 5 0.12
39 10 0.24
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.52
Consensus pattern (39 bp):
TATTACTATTATTATTACTAATACCACTATTATCATCAT
Found at i:42757432 original size:126 final size:126
Alignment explanation
Indices: 42757205--42757716 Score: 637
Period size: 126 Copynumber: 4.0 Consensus size: 126
42757195 CATTTTTGGG
** * * * * * * * *
42757205 CGACACTTTTTTAAGTGTTAGGATAGACTTGTCGATATACGTTTTGACCAACTATTTGTGTAAGA
1 CGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTATATAAGA
42757270 GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTATGC
66 GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTATGC
* *
42757331 CGACACTTTCCTAAGTGTTGGGATAGACTTGCCGATATACACTTTGGCCAACTCTTTATATAAGA
1 CGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTATATAAGA
* * * *
42757396 GTTGGGATATGCATGCCTAAGACAACGCTTATATAAGAGTCGGCTTTGTTCAACACTACGC
66 GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTATGC
* * * * * *
42757457 CGACACTTTTCTAAGTGTTGGGGTAGACTTGTCGGCATACGTTTTGGCCAACTCTTTGTATAAGA
1 CGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTATATAAGA
* *
42757522 GTTGGTATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTCCAACACTATGCCGAC
66 GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTAT---G-C
* *
42757587 ACTTTTAGGCCAACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATATGCTTTGGTCAACTCT
1 -C------G---ACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCT
* * *
42757652 TTATATAAGGGTTGGGATATACATGCCTAAGGCAACGCTTAAATAAGAGTCGGTTTTGTCCAACA
56 TTATATAAGAGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACA
42757717 TTCTGCCAAC
Statistics
Matches: 331, Mismatches: 41, Indels: 14
0.86 0.11 0.04
Matches are distributed among these distances:
126 222 0.67
129 1 0.00
130 1 0.00
131 1 0.00
137 1 0.00
140 105 0.32
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (126 bp):
CGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTATATAAGA
GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTATGC
Found at i:42757651 original size:140 final size:140
Alignment explanation
Indices: 42757459--42757716 Score: 399
Period size: 140 Copynumber: 1.8 Consensus size: 140
42757449 CACTACGCCG
* * * * * *
42757459 ACACTTTTCTAAGTGTTGGGGTAGACTTGTCGGCATACGTTTTGGCCAACTCTTTGTATAAGAGT
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTATATAAGAGT
* *
42757524 TGGTATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTCCAACACTATGCCGACAC
66 TGGGATATACATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTCCAACACTATGCCGACAC
42757589 TTTTAGGCCA
131 TTTTAGGCCA
* * *
42757599 ACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATATGCTTTGGTCAACTCTTTATATAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTATATAAGAGT
* *
42757664 TGGGATATACATGCCTAAGGCAACGCTTAAATAAGAGTCGGTTTTGTCCAACA
66 TGGGATATACATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTCCAACA
42757717 TTCTGCCAAC
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
140 105 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (140 bp):
ACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTATATAAGAGT
TGGGATATACATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTCCAACACTATGCCGACAC
TTTTAGGCCA
Found at i:42759333 original size:14 final size:14
Alignment explanation
Indices: 42759316--42759389 Score: 67
Period size: 14 Copynumber: 5.3 Consensus size: 14
42759306 ATCTAATTAA
* *
42759316 TTTAGGGTTTAAGG
1 TTTATGGTTTAGGG
*
42759330 TTTATGATTTAGGG
1 TTTATGGTTTAGGG
* *
42759344 TTTGTGGTTTAGGA
1 TTTATGGTTTAGGG
* * * *
42759358 TTTAAGGATTATGA
1 TTTATGGTTTAGGG
42759372 TTTATGGTTTAGGG
1 TTTATGGTTTAGGG
42759386 TTTA
1 TTTA
42759390 AAATTTTAGG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.49
Consensus pattern (14 bp):
TTTATGGTTTAGGG
Found at i:42759339 original size:21 final size:21
Alignment explanation
Indices: 42759315--42759390 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
42759305 TATCTAATTA
42759315 ATTTAGGGTTTAAGGTTTATG
1 ATTTAGGGTTTAAGGTTTATG
** *
42759336 ATTTAGGGTTTGTGGTTTAGG
1 ATTTAGGGTTTAAGGTTTATG
* * * *
42759357 ATTTAAGGATTATGATTTATG
1 ATTTAGGGTTTAAGGTTTATG
*
42759378 GTTTAGGGTTTAA
1 ATTTAGGGTTTAA
42759391 AATTTTAGGT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (21 bp):
ATTTAGGGTTTAAGGTTTATG
Found at i:42759422 original size:21 final size:21
Alignment explanation
Indices: 42759394--42759444 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
42759384 GGTTTAAAAT
* * *
42759394 TTTA-GGTTTTGGGTTTTGAG
1 TTTAGGGTTTTGGATGTAGAG
*
42759414 TTTAGGGTTTTGGATGTAGTG
1 TTTAGGGTTTTGGATGTAGAG
42759435 TTTAGGGTTT
1 TTTAGGGTTT
42759445 AAGGAAGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (21 bp):
TTTAGGGTTTTGGATGTAGAG
Found at i:42761090 original size:31 final size:31
Alignment explanation
Indices: 42761052--42761115 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
42761042 CCTTTTCATA
42761052 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
42761083 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
42761114 TT
1 TT
42761116 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:42761384 original size:23 final size:23
Alignment explanation
Indices: 42761309--42761420 Score: 163
Period size: 23 Copynumber: 4.7 Consensus size: 23
42761299 ACTTTATCAT
*
42761309 ATAACTGGAGGCCT-AGCCTCTTTGA
1 ATAACTGG-GGCATAAGCC-CTTT-A
*
42761334 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCC-TTTA
42761358 ATAACTGGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTA
42761381 ATAACTGGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTA
42761404 ATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGC
42761421 AATTTTTCAC
Statistics
Matches: 82, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
23 44 0.54
24 23 0.28
25 15 0.18
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (23 bp):
ATAACTGGGGCATAAGCCCTTTA
Found at i:42761501 original size:20 final size:20
Alignment explanation
Indices: 42761476--42761536 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
42761466 TTATGATTAC
42761476 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
42761496 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
42761516 GTCATGTGTATATCATACAT
1 ATCATGTGCATATCATACAT
42761536 A
1 A
42761537 CCGTGTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:42761624 original size:24 final size:25
Alignment explanation
Indices: 42761579--42761625 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
42761569 ATACATAAAC
* *
42761579 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGTAAAACGGTCATTTTTA
42761604 CCTAGGGG-AAAACGGTCATTTT
1 CCTAGGGGTAAAACGGTCATTTT
42761626 CATGTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (25 bp):
CCTAGGGGTAAAACGGTCATTTTTA
Found at i:42762197 original size:20 final size:20
Alignment explanation
Indices: 42762172--42762209 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42762162 ATTTTGGGAT
*
42762172 TTATTTTTAATTATCTTTAA
1 TTATTTGTAATTATCTTTAA
*
42762192 TTATTTGTATTTATCTTT
1 TTATTTGTAATTATCTTT
42762210 TAGAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (20 bp):
TTATTTGTAATTATCTTTAA
Found at i:42763771 original size:40 final size:40
Alignment explanation
Indices: 42763697--42763832 Score: 168
Period size: 40 Copynumber: 3.5 Consensus size: 40
42763687 GAGCATAAAT
* * * *
42763697 AGGGGCACGAAAGTG-AATCA-CGGTACCAACGTACAAAC
1 AGGGGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAC
*
42763735 AGGGGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAT
1 AGGGGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAC
* * * * *
42763775 AGAGACATGTATATGCAATCAGGGGTACCGAAGTACAAAC
1 AGGGGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAC
42763815 AGGGGCACGTATGTGCAA
1 AGGGGCACGTATGTGCAA
42763833 ACAAATACTA
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 13 0.16
39 5 0.06
40 63 0.78
ACGTcount: A:0.37, C:0.19, G:0.29, T:0.15
Consensus pattern (40 bp):
AGGGGCACGTATGTGCAATCAGGGGTACCAAAGTACAAAC
Found at i:42763833 original size:20 final size:20
Alignment explanation
Indices: 42763730--42763835 Score: 61
Period size: 20 Copynumber: 5.3 Consensus size: 20
42763720 TACCAACGTA
42763730 CAAACAGGGGCACGTATGTG
1 CAAACAGGGGCACGTATGTG
* * ** * *
42763750 CAATCAGGGGTACCAAAGTA
1 CAAACAGGGGCACGTATGTG
* * * * *
42763770 CAAATAGAGACATGTATATG
1 CAAACAGGGGCACGTATGTG
* * * *
42763790 CAATCAGGGGTACCG-AAGTA
1 CAAACAGGGGCA-CGTATGTG
42763810 CAAACAGGGGCACGTATGTG
1 CAAACAGGGGCACGTATGTG
42763830 CAAACA
1 CAAACA
42763836 AATACTAATT
Statistics
Matches: 54, Mismatches: 30, Indels: 4
0.61 0.34 0.05
Matches are distributed among these distances:
19 2 0.04
20 51 0.94
21 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (20 bp):
CAAACAGGGGCACGTATGTG
Found at i:42765096 original size:23 final size:23
Alignment explanation
Indices: 42765048--42765096 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
42765038 TCGTCCTCGG
42765048 CTCCTTCTTCCTTCAAGTGTAGCT
1 CTCCTTCTTCCTTCAAGTGTA-CT
42765072 CTCC-TCTTCCCTTCATAGTGT-CT
1 CTCCTTCTT-CCTTCA-AGTGTACT
42765095 CT
1 CT
42765097 GAAGCCTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 8 0.35
24 10 0.43
25 5 0.22
ACGTcount: A:0.10, C:0.37, G:0.10, T:0.43
Consensus pattern (23 bp):
CTCCTTCTTCCTTCAAGTGTACT
Found at i:42766088 original size:53 final size:53
Alignment explanation
Indices: 42766029--42766140 Score: 136
Period size: 53 Copynumber: 2.1 Consensus size: 53
42766019 CAAATTGGAC
* * *
42766029 AACATCCAATACTCAAATGATATGCT-TTAAAGTGATATGACAACAGGGTTGAA
1 AACATCCAATAC-CAAATGATAAGCTATTAAAGTGATATAACAAAAGGGTTGAA
* * * * *
42766082 AACATCCAGTACCCAATGATAAGCTATTCATGTGATATAACAAAAGGGTTGAC
1 AACATCCAATACCAAATGATAAGCTATTAAAGTGATATAACAAAAGGGTTGAA
42766135 AACATC
1 AACATC
42766141 TATTATCCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
52 11 0.22
53 39 0.78
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (53 bp):
AACATCCAATACCAAATGATAAGCTATTAAAGTGATATAACAAAAGGGTTGAA
Found at i:42773157 original size:20 final size:20
Alignment explanation
Indices: 42773112--42773158 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
42773102 TTTTGAAAAT
*
42773112 TAAAAAT-TTTAAAAATATT
1 TAAAAATATTTAAAAATATA
42773131 TAAAAATATTTAAAAATATA
1 TAAAAATATTTAAAAATATA
*
42773151 TATAAATA
1 TAAAAATA
42773159 ATAAACTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATATTTAAAAATATA
Found at i:42773158 original size:10 final size:10
Alignment explanation
Indices: 42773111--42773149 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
42773101 TTTTTGAAAA
42773111 TTAAAAAT-T
1 TTAAAAATAT
42773120 TTAAAAATAT
1 TTAAAAATAT
42773130 TTAAAAATAT
1 TTAAAAATAT
42773140 TTAAAAATAT
1 TTAAAAATAT
42773150 ATATAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:42773418 original size:20 final size:20
Alignment explanation
Indices: 42773391--42773436 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
42773381 AATGAAATAA
42773391 AATTTTTTTAAA-ACATTCT
1 AATTTTTTTAAATACATTCT
* *
42773410 AATTTTTTTAAATACTTTTT
1 AATTTTTTTAAATACATTCT
42773430 AATTTTT
1 AATTTTT
42773437 AGTAAATGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTTTTAAATACATTCT
Found at i:42778899 original size:45 final size:45
Alignment explanation
Indices: 42778835--42778925 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
42778825 TATCGTCTAC
42778835 ACCGATCACAAAAGCCTCAAATATCTCCTTACTCAGAAAGAGTTG
1 ACCGATCACAAAAGCCTCAAATATCTCCTTACTCAGAAAGAGTTG
* * *
42778880 ACCGATCATAAAGGCCTCAAATATCTCCTTACTCAGAAGGAGTTG
1 ACCGATCACAAAAGCCTCAAATATCTCCTTACTCAGAAAGAGTTG
42778925 A
1 A
42778926 ATCTTAGACA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.23
Consensus pattern (45 bp):
ACCGATCACAAAAGCCTCAAATATCTCCTTACTCAGAAAGAGTTG
Found at i:42783422 original size:16 final size:16
Alignment explanation
Indices: 42783403--42783441 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
42783393 ATGAAAACTG
42783403 CAAGTTTTGAAAGTGA
1 CAAGTTTTGAAAGTGA
42783419 CAAGTTTTGAAAGTGA
1 CAAGTTTTGAAAGTGA
42783435 CAA-TTTT
1 CAAGTTTT
42783442 CTCCAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (16 bp):
CAAGTTTTGAAAGTGA
Found at i:42788868 original size:30 final size:30
Alignment explanation
Indices: 42788809--42788868 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
42788799 ATTTACGACC
*
42788809 CTAGAGGTAAAATCGTAATTTTGTAAAAAT
1 CTAGAGGTAAAATCGTAATTTTGCAAAAAT
* * * *
42788839 CTAGGGGTAAAATGGTCATTTTGCCAAAAT
1 CTAGAGGTAAAATCGTAATTTTGCAAAAAT
42788869 ATGAATTATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (30 bp):
CTAGAGGTAAAATCGTAATTTTGCAAAAAT
Done.