Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 566 of 770
Found at i:176363695 original size:40 final size:40
Alignment explanation
Indices: 176363616--176363773 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
176363606 TTCGAATGAT
* * * *
176363616 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
176363656 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
176363696 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
176363736 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
176363774 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:176363794 original size:80 final size:80
Alignment explanation
Indices: 176363616--176363803 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
176363606 TTCGAATGAT
* *
176363616 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
176363681 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
176363696 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
176363757 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
176363777 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
176363804 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:176371703 original size:40 final size:40
Alignment explanation
Indices: 176371624--176371781 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
176371614 TTCGAATGAT
* * * *
176371624 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
176371664 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
176371704 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
176371744 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
176371782 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:176371802 original size:80 final size:80
Alignment explanation
Indices: 176371624--176371811 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
176371614 TTCGAATGAT
* *
176371624 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
176371689 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
176371704 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
176371765 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
176371785 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
176371812 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:176378137 original size:40 final size:40
Alignment explanation
Indices: 176378091--176378276 Score: 372
Period size: 40 Copynumber: 4.7 Consensus size: 40
176378081 CTTGCACAAA
176378091 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
176378131 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
176378171 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
176378211 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
176378251 GCCTTCGGGTCTTAGCCCGGATATAT
1 GCCTTCGGGTCTTAGCCCGGATATAT
176378277 TTCCAATGTT
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 146 1.00
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
Found at i:176386306 original size:40 final size:40
Alignment explanation
Indices: 176386198--176386454 Score: 399
Period size: 40 Copynumber: 6.4 Consensus size: 40
176386188 CGGGATTTAA
* * * * *
176386198 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
176386238 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
176386278 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
176386318 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
176386358 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
176386398 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
176386438 CCGGATATATCAACTCG
1 CCGGATATATCAACTCG
176386455 TTCACTATAC
Statistics
Matches: 200, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.00
40 199 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:176388279 original size:29 final size:29
Alignment explanation
Indices: 176388245--176388405 Score: 83
Period size: 29 Copynumber: 5.6 Consensus size: 29
176388235 TACTCGATTT
* * *
176388245 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
176388274 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
176388303 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
* * *** * *
176388332 TGCACACTCAGTGCCATATTTTTCCAGCA
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * * *
176388361 TGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
176388390 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
176388406 ATCTCGTCAC
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
28 1 0.01
29 108 0.98
30 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:176388337 original size:58 final size:59
Alignment explanation
Indices: 176388244--176388405 Score: 195
Period size: 58 Copynumber: 2.8 Consensus size: 59
176388234 ATACTCGATT
** * ** * *
176388244 TCGCACACTTAGTGCCATGCGATTT-AAGCCCGCACACACAGTGCCATACCCTTCGAGC-
1 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTCAGTGCCATACCCTTCCAGCA
***
176388302 TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATTTTTCCAGCA
1 TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATACCCTTCCAGCA
*
176388361 T-GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCA
176388406 ATCTCGTCAC
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
57 4 0.04
58 86 0.95
59 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (59 bp):
TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATACCCTTCCAGCA
Found at i:176393384 original size:2 final size:2
Alignment explanation
Indices: 176393377--176393415 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
176393367 TTGTAAAGAA
176393377 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176393416 GTGATGCCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:176393649 original size:44 final size:44
Alignment explanation
Indices: 176393585--176393744 Score: 132
Period size: 43 Copynumber: 3.7 Consensus size: 44
176393575 TATGTGTTAT
176393585 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGATTTA
* * ** * *
176393629 CGTGTAAGACCATGTTTGGGATATTGGCATCGTATATG-AATTT-
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTTGTGATTTA
* * * * *
176393672 TGTGTAAGACTATGTATGGGACAG-TGGCATCAATATT-TGA-TTA
1 CGTGTAAGACCACGTCTGGGAC-GTTGGCATCGAT-TTGTGATTTA
* * *
176393715 CATGTAAGACCACATCTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
176393745 TGGACGAGCT
Statistics
Matches: 89, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
42 5 0.06
43 48 0.54
44 32 0.36
45 4 0.04
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTTGTGATTTA
Found at i:176402863 original size:30 final size:30
Alignment explanation
Indices: 176402827--176402957 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
176402817 GACAAGATTG
* * * * *
176402827 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
176402857 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
176402885 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
176402915 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
176402944 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
176402958 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:176402918 original size:58 final size:58
Alignment explanation
Indices: 176402827--176402957 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
176402817 GACAAGATTG
* * * * * *
176402827 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
176402885 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
176402944 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
176402958 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:176409024 original size:40 final size:40
Alignment explanation
Indices: 176408922--176409105 Score: 165
Period size: 40 Copynumber: 4.6 Consensus size: 40
176408912 AAATTGAATG
* * * * *
176408922 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
176408962 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
176409002 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * * *
176409042 AAATCCGGGCTAAGACCAGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
176409082 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
176409106 CTTGGTGCGG
Statistics
Matches: 119, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 3 0.03
40 113 0.95
41 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:176421088 original size:30 final size:30
Alignment explanation
Indices: 176421052--176421152 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
176421042 GACAAGATTG
* * *
176421052 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
176421082 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
176421110 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
176421139 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
176421153 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:176421164 original size:29 final size:28
Alignment explanation
Indices: 176421081--176421156 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
176421071 AAAATTGTAC
* *
176421081 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
176421109 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
176421138 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
176421157 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:176423661 original size:79 final size:81
Alignment explanation
Indices: 176423565--176423742 Score: 243
Period size: 79 Copynumber: 2.2 Consensus size: 81
176423555 GCTCGATTGT
* * * * *
176423565 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGCCTT-GGGAATTAGCCCGGATTTAGT
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTAGT
* *
176423629 AAC-TCGCACAAATGC
66 AACTTAGCACAAAAGC
* * *
176423644 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTAGT
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTAGT
*
176423709 CACTTAGCACAAAAGC
66 AACTTAGCACAAAAGC
176423725 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
176423743 ATACCATTCG
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 36 0.42
80 22 0.26
81 27 0.32
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (81 bp):
CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTAGT
AACTTAGCACAAAAGC
Found at i:176423672 original size:40 final size:40
Alignment explanation
Indices: 176423565--176423744 Score: 211
Period size: 40 Copynumber: 4.5 Consensus size: 40
176423555 GCTCGATTGT
* * * *
176423565 CTTCGGGACATAGCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGC
*
176423605 CTT-GGGAATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * *
176423644 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * * *
176423684 CTTCGGGAATTAACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAGCCCGGATTTAGTAAC-TCGCACAAATGC
176423725 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACTTAGCCCGGAT
176423745 ACCATTCGAA
Statistics
Matches: 120, Mismatches: 17, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
39 31 0.26
40 61 0.51
41 28 0.23
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:176429397 original size:28 final size:27
Alignment explanation
Indices: 176429334--176429403 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
176429324 ATAGTGAGTC
176429334 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
* *
176429361 CGTACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
176429389 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
176429404 GTACAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:176432520 original size:40 final size:40
Alignment explanation
Indices: 176432465--176432688 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
176432455 TATTCGGATG
*
176432465 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
176432505 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
176432548 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
176432588 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** *
176432628 ATATCCGGGCTAAGACCCGAAGGCATTTGTGTGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
176432668 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
176432689 ATACTTGGGT
Statistics
Matches: 165, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.08
40 114 0.69
41 1 0.01
43 37 0.22
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:176432608 original size:83 final size:80
Alignment explanation
Indices: 176432469--176432688 Score: 295
Period size: 83 Copynumber: 2.7 Consensus size: 80
176432459 CGGATGATAT
* * * *
176432469 CCGGGCTAAGTCTCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTA
176432534 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
176432552 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTA
*
176432617 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* *
176432632 CCGGGCTAAGACCCGAAGGCATTTGTG-TGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AG-TGACTATATCCGGGCTAAGTCCCGAAG
176432689 ATACTTGGGT
Statistics
Matches: 127, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
79 17 0.13
80 44 0.35
81 2 0.02
83 64 0.50
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTA
TGCTAGTGACTATAC
Found at i:176434452 original size:234 final size:234
Alignment explanation
Indices: 176434043--176434467 Score: 787
Period size: 234 Copynumber: 1.8 Consensus size: 234
176434033 GGGCATTACA
* *
176434043 GATACAAATGAAGAATGTCACGTTGTTGAGATTGTTAACACAATAGTTCTAGAAGAATTTGTAGA
1 GATACAAATGAAGAATGTCACGTTGTTGAGATTGTTAACACAATAGTTCAAGAAGAATTTGCAGA
* *
176434108 ATTTTATCACAATAATTCTTATGATGATGTAGACTCATTTGAGTTAATTGAAGCAGAAATGATTG
66 ATTTTATCACAATAATTCTAATGATAATGTAGACTCATTTGAGTTAATTGAAGCAGAAATGATTG
176434173 AAGAGCATGGTGAATTGATGGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTTTGATAAG
131 AAGAGCATGGTGAATTGATGGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTTTGATAAG
176434238 CAGATAACCTTTAATGTTTTCGATGCTATGAAGTGTTCT
196 CAGATAACCTTTAATGTTTTCGATGCTATGAAGTGTTCT
*
176434277 GATACAAATGAAGAATGTCACGTTGTTTAGATTGTTAACACAATAGTTCAAGAAGAATTTGCAGA
1 GATACAAATGAAGAATGTCACGTTGTTGAGATTGTTAACACAATAGTTCAAGAAGAATTTGCAGA
*
176434342 ATTTTATCATAATAATTCTAATGATAATGTAGACTCATTTGAGTTAATTGAAGCAGAAATGATTG
66 ATTTTATCACAATAATTCTAATGATAATGTAGACTCATTTGAGTTAATTGAAGCAGAAATGATTG
*
176434407 AAGAGCTTGGTGAATTGATGGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTTTGA
131 AAGAGCATGGTGAATTGATGGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTTTGA
176434468 ATTATTAAAT
Statistics
Matches: 184, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
234 184 1.00
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (234 bp):
GATACAAATGAAGAATGTCACGTTGTTGAGATTGTTAACACAATAGTTCAAGAAGAATTTGCAGA
ATTTTATCACAATAATTCTAATGATAATGTAGACTCATTTGAGTTAATTGAAGCAGAAATGATTG
AAGAGCATGGTGAATTGATGGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTTTGATAAG
CAGATAACCTTTAATGTTTTCGATGCTATGAAGTGTTCT
Found at i:176435914 original size:93 final size:93
Alignment explanation
Indices: 176435807--176435977 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
176435797 GCCCCTAAGT
* *
176435807 GAACTCAGACTCAACTCAACGAGCTAGGGCTTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTAGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
176435872 CGAGTTCGGATGCCGAGTTACATCTCAC
66 CGAGTTCGGATGCCGAGTTACATCTCAC
* * *
176435900 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTAGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
176435965 CGAGTTCGGATGC
66 CGAGTTCGGATGC
176435978 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTAGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCGAGTTACATCTCAC
Found at i:176435974 original size:46 final size:46
Alignment explanation
Indices: 176435802--176435974 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
176435792 AACCCGCCCC
* * * *
176435802 TAAGTGAACTCAGACTCAACTCAACGAGCTAGGGCTTTCACATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCACATCCA
*
176435848 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCGAGTT-ACAT-C-
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA---C-A-TTCACATCCA
* * *
176435896 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCACATCCA
*
176435941 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
176435975 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 58 0.55
47 28 0.26
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCACATCCA
Found at i:176443062 original size:93 final size:91
Alignment explanation
Indices: 176442905--176443073 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 91
176442895 GCCCCTAAGT
*
176442905 GAACTCGGACTCAACTCAACGAGCTCGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACGAGCTCGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
176442970 AGTTCGGATGCCTAGTTACATCTCAC
66 AGTTCGGATGCCTAGTTACATCTCAC
*
176442996 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTC-G-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
176443061 CGAGTTCGGATGC
64 CGAGTTCGGATGC
176443074 TCAACCATCC
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 25 0.34
92 1 0.01
93 48 0.65
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:176443089 original size:46 final size:44
Alignment explanation
Indices: 176442900--176443081 Score: 183
Period size: 44 Copynumber: 4.0 Consensus size: 44
176442890 AACCCGCCCC
* * *
176442900 TAAGTGAACTCGGACTCAACTCAACGAGCTCGCG-TTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG-GATGCGCAACCA
176442944 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCGC-A---ACCA
* * * *
176442990 TCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCGCAACCA
*
176443037 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCGCAACCA
176443081 T
1 T
176443082 CCTAGTGACA
Statistics
Matches: 114, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
43 2 0.02
44 43 0.38
45 2 0.02
46 30 0.26
47 30 0.26
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (44 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCGCAACCA
Found at i:176447581 original size:40 final size:40
Alignment explanation
Indices: 176447515--176447681 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
176447505 AAATTGAATG
* * *
176447515 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
176447554 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
176447594 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
176447634 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
176447674 ATATCCGG
1 ATATCCGG
176447682 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:176461128 original size:40 final size:40
Alignment explanation
Indices: 176461002--176461129 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
176460992 AAATTGAATG
* * *
176461002 ATATCCGGGCTAA-ATCCCGAAGACAATTATGCTGGAA--ATT
1 ATATCCGGGCTAAGA-CCCGAAGGCAATTGTGCT--AATGGTT
* * *
176461042 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAATGGTT
* *
176461082 ACATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTA-ATGGTT
176461122 ATATCCGG
1 ATATCCGG
176461130 TTATATTCCG
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 69 0.96
41 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAATGGTT
Found at i:176465591 original size:40 final size:40
Alignment explanation
Indices: 176465546--176465684 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
176465536 GGATATAACG
176465546 ACTCGCTCAAATGCCTTCGGGAC-AAAGCCCG-GTTATAGTA
1 ACTCGCTCAAATGCCTTCGGGACTAAA-CCCGAGTT-TAGTA
* *
176465586 ACTCGCTCGAATGCCTTCGGGACTTAACCCGAGTTTAGTA
1 ACTCGCTCAAATGCCTTCGGGACTAAACCCGAGTTTAGTA
* * * * *
176465626 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGAATTTATTA
1 ACTCGCTCAAATGCCTTCGGGACTAAACCCGAGTTTAGTA
* * *
176465665 ACTCGCACGAACGCCTTCGG
1 ACTCGCTCAAATGCCTTCGG
176465685 ATCTTAGTCC
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 33 0.38
40 50 0.57
41 5 0.06
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCTCAAATGCCTTCGGGACTAAACCCGAGTTTAGTA
Found at i:176465667 original size:79 final size:80
Alignment explanation
Indices: 176465521--176465735 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 80
176465511 AATCACGTAT
*** * ** *
176465521 CTTCGGAAT-TTAA-CCGGATATAACGACTCGCTCAAATGCCTTCGGGACAAAGCCCGGTTATAG
1 CTTCGG-ATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGATTATAG
* *
176465584 TAACTCGCTCGAATGC
65 TAACTCGCACGAACGC
*
176465600 CTTCGGGA-CTTAACCC-GAGTTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGAATT-T
1 CTTC-GGATCTTAACCCGGA-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG-ATTAT
*
176465661 ATTAACTCGCACGAACGC
63 AGTAACTCGCACGAACGC
** * *
176465679 CTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CTTCGGATCTTAACCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
176465736 GACATCATTC
Statistics
Matches: 111, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
78 3 0.03
79 60 0.54
80 48 0.43
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
CTTCGGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGATTATAGT
AACTCGCACGAACGC
Found at i:176468208 original size:40 final size:40
Alignment explanation
Indices: 176468149--176468366 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
176468139 TGGATGATAA
* * *
176468149 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
176468189 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
176468229 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
176468269 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
176468309 CCGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
176468349 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
176468367 TACTTGGCTT
Statistics
Matches: 163, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 16 0.10
40 147 0.90
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:176472012 original size:14 final size:14
Alignment explanation
Indices: 176471993--176472023 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
176471983 GAGATGAAAG
176471993 CTAGACCTACGTTC
1 CTAGACCTACGTTC
176472007 CTAGACCTACGTTC
1 CTAGACCTACGTTC
176472021 CTA
1 CTA
176472024 TAAGAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.13, T:0.29
Consensus pattern (14 bp):
CTAGACCTACGTTC
Found at i:176475506 original size:40 final size:40
Alignment explanation
Indices: 176475439--176475658 Score: 347
Period size: 40 Copynumber: 5.5 Consensus size: 40
176475429 CATTTGAATG
176475439 ATATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
176475478 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
176475518 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
176475558 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * * * * *
176475598 ATGTCCGGGTTAAGACCCGAAGGCAATTGGGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
176475638 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
176475659 AAACTTGGGT
Statistics
Matches: 169, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
38 1 0.01
39 26 0.15
40 142 0.84
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:176483564 original size:40 final size:40
Alignment explanation
Indices: 176483505--176483685 Score: 231
Period size: 40 Copynumber: 4.5 Consensus size: 40
176483495 CATTTGAATG
* * *
176483505 ATATCTGGGCAAAGCCCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
176483545 ATATCCGGGCTAAGACCCGAAGACATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* *
176483585 ATATCCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * * * * *
176483625 ATGTCCGGGTTAAGACCCGAAGGCAATTGGGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
176483665 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
176483686 AAACTTGGGT
Statistics
Matches: 123, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
38 1 0.01
39 12 0.10
40 110 0.89
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:176486083 original size:40 final size:40
Alignment explanation
Indices: 176485921--176486101 Score: 165
Period size: 40 Copynumber: 4.6 Consensus size: 40
176485911 CGAATGATGT
* * * *
176485921 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAAC
* * * * *
176485961 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT
1 CCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAAC
*
176486001 CCGGGCTAA-TCCCGAAGGC-TTTGTGCAAGTTACTAAAC
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAC
* **
176486039 CCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTCGCTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AAC
**
176486079 CCGGGCTTCGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
176486102 TGAGTGAGTC
Statistics
Matches: 115, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
38 24 0.21
39 18 0.16
40 64 0.56
41 9 0.08
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAC
Found at i:176486085 original size:78 final size:79
Alignment explanation
Indices: 176485920--176486071 Score: 200
Period size: 78 Copynumber: 1.9 Consensus size: 79
176485910 TCGAATGATG
* * *
176485920 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAA-TCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
* *
176485985 GTGCGAGTTAATAAA
65 GTGCAAGTCAATAAA
* **
176486000 TCCGGGCTAATCCCGAAGGCTTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATTC
1 TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATTC
176486063 GTGCAAGTC
65 GTGCAAGTC
176486072 GCTATAACCG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.02
78 35 0.56
79 17 0.27
80 10 0.16
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTCG
TGCAAGTCAATAAA
Found at i:176488245 original size:29 final size:29
Alignment explanation
Indices: 176488212--176488343 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
176488202 GTGACGAGAT
*
176488212 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* *
176488241 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * ***
176488270 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * * *
176488299 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ACA
176488328 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
176488344 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATACA
Found at i:176501053 original size:40 final size:40
Alignment explanation
Indices: 176500994--176501162 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
176500984 CGGGACTTTA
* * *
176500994 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
176501034 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
176501074 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
176501114 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
176501154 CCCGGATAT
1 CCCGGATAT
176501163 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:176503287 original size:73 final size:73
Alignment explanation
Indices: 176503154--176503346 Score: 302
Period size: 73 Copynumber: 2.6 Consensus size: 73
176503144 GCTTTATCAT
*
176503154 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCA-AAATCCC-TTTTAATAACTGGGGCAT
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAA-CCCTTTTTAATAACTGGGGCAT
*
176503216 AAGCCCTTTTG
63 AAGCCCTTTTA
176503227 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAACCCTTTTTAATAACTGGGGCATAAG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAACCCTTTTTAATAACTGGGGCATAAG
176503292 CCCTTTTA
66 CCCTTTTA
* *
176503300 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAACCCTTTT
176503347 GCACTTCCTC
Statistics
Matches: 113, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
72 25 0.22
73 88 0.78
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (73 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAACCCTTTTTAATAACTGGGGCATAAG
CCCTTTTA
Found at i:176503347 original size:24 final size:24
Alignment explanation
Indices: 176503154--176503346 Score: 298
Period size: 24 Copynumber: 8.0 Consensus size: 24
176503144 GCTTTATCAT
*
176503154 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
176503179 ATAACTGGGGCAAAATCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
176503203 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
176503227 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
176503251 ATAACTGGGGCATAAACCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTA
176503276 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
176503300 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
176503324 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
176503347 GCACTTCCTC
Statistics
Matches: 156, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
24 122 0.78
25 34 0.22
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:176503477 original size:20 final size:20
Alignment explanation
Indices: 176503396--176503470 Score: 122
Period size: 20 Copynumber: 4.0 Consensus size: 20
176503386 TATGAATACA
176503396 TCATGTGCATATCAT--A--
1 TCATGTGCATATCATACATG
176503412 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
176503432 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
176503452 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
176503471 ACCATGTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
16 15 0.27
18 1 0.02
20 39 0.71
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:176503541 original size:25 final size:25
Alignment explanation
Indices: 176503513--176503560 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
176503503 ATATATAAAC
* * *
176503513 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
176503538 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
176503561 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:176508688 original size:47 final size:47
Alignment explanation
Indices: 176508574--176508751 Score: 190
Period size: 46 Copynumber: 3.9 Consensus size: 47
176508564 TGTAACCCGC
* * * * *
176508574 CCATAAGTGAACTC-GACTCAACTCAACGAGCTCGG-CG-TTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGCAT
*
176508618 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG---CAT
* * *
176508668 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGCAT
*
176508711 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC
176508752 CAAATATCCC
Statistics
Matches: 113, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
43 3 0.03
44 15 0.13
45 22 0.19
46 34 0.30
47 33 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (47 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGCAT
Found at i:176508746 original size:93 final size:91
Alignment explanation
Indices: 176508582--176508751 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 91
176508572 GCCCATAAGT
*
176508582 GAACTCGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 GAACTCGACTCAACTCAACGAGCTCGGCGCTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
176508647 AGTTCGGATGCCTAGTTACATCTCAC
66 AGTTCGGATGCCTAGTTACATCTCAC
*
176508673 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTC-GACTCAACTCAACGAGCTCGG-CGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
176508738 CGAGTTCGGATGCC
64 CGAGTTCGGATGCC
176508752 CAAATATCCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 6 0.08
92 20 0.27
93 49 0.65
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (91 bp):
GAACTCGACTCAACTCAACGAGCTCGGCGCTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:176508766 original size:46 final size:45
Alignment explanation
Indices: 176508623--176508766 Score: 148
Period size: 46 Copynumber: 3.1 Consensus size: 45
176508613 CGCATCCATA
* *
176508623 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---ACATCCC
* * * * *
176508671 A-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTC-GCATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCC--C
*
176508716 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AACATCCC
176508762 AGTGA
1 AGTGA
176508767 CATGTCACTT
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
43 4 0.05
45 1 0.01
46 37 0.47
47 31 0.40
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCCC
Found at i:176511174 original size:30 final size:30
Alignment explanation
Indices: 176511130--176511218 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
176511120 CAAAGATAAC
176511130 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
176511159 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
176511189 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
176511219 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:176511178 original size:15 final size:15
Alignment explanation
Indices: 176511130--176511209 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
176511120 CAAAGATAAC
*
176511130 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
176511144 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
176511159 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
176511174 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
176511189 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
176511204 AAGAAA
1 AAGAAA
176511210 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:176511218 original size:15 final size:15
Alignment explanation
Indices: 176511141--176511218 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
176511131 AGAAAACCGA
176511141 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
176511156 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
176511170 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
176511185 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
176511201 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
176511216 ATA
1 ATA
176511219 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:176513335 original size:27 final size:28
Alignment explanation
Indices: 176513274--176513343 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
176513264 AAATTTGTAC
* *
176513274 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
176513302 AGCACTAAGTGTGCGAG-CTGAATATAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
*
176513329 GGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
176513344 TGATCGAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGAATATAT
Found at i:176520996 original size:27 final size:28
Alignment explanation
Indices: 176520935--176521004 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
176520925 AAATTTGTAC
* *
176520935 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
176520963 AGCACTAAGTGTGCGAG-CTGAATATAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
*
176520990 GGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
176521005 TGATCGAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGAATATAT
Found at i:176524844 original size:93 final size:93
Alignment explanation
Indices: 176524732--176524903 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
176524722 GCCCATAAGT
* *
176524732 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
176524797 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
176524825 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
176524890 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
176524904 CAAATATCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:176524899 original size:46 final size:46
Alignment explanation
Indices: 176524724--176524899 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
176524714 TGTAACCCGC
* * *
176524724 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
176524770 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
176524820 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
176524863 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
176524900 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:176526164 original size:26 final size:26
Alignment explanation
Indices: 176526133--176526184 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
176526123 TTCTATCTCG
176526133 GATTTTGTGGTCACGAAACCACTATT
1 GATTTTGTGGTCACGAAACCACTATT
176526159 GATTTTGTGGTCACGAAACCACTATT
1 GATTTTGTGGTCACGAAACCACTATT
176526185 CCGACTAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
GATTTTGTGGTCACGAAACCACTATT
Found at i:176526386 original size:17 final size:17
Alignment explanation
Indices: 176526366--176526399 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
176526356 GACTAAGCCA
176526366 TAAAGCTTAGTAAGCTC
1 TAAAGCTTAGTAAGCTC
176526383 TAAAGCTTAGTAAGCTC
1 TAAAGCTTAGTAAGCTC
176526400 ATATAGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (17 bp):
TAAAGCTTAGTAAGCTC
Found at i:176530947 original size:71 final size:71
Alignment explanation
Indices: 176530863--176531026 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
176530853 CGATTTGTCT
176530863 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
176530928 CTTTCA
66 CTTTCA
* *
176530934 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
176530999 CTTTCA
66 CTTTCA
176531005 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
176531027 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:176542446 original size:80 final size:80
Alignment explanation
Indices: 176542362--176542510 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
176542352 TATGGTAACC
* * * *
176542362 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
176542426 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
176542442 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
176542507 CCGG
66 CCGG
176542511 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:176542452 original size:40 final size:38
Alignment explanation
Indices: 176542403--176542510 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
176542393 ATCACGATTT
*
176542403 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
176542443 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
176542483 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
176542511 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:176544550 original size:14 final size:14
Alignment explanation
Indices: 176544531--176544558 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
176544521 CAAATTACAT
176544531 GTTAGAATAGTATC
1 GTTAGAATAGTATC
176544545 GTTAGAATAGTATC
1 GTTAGAATAGTATC
176544559 ATTGGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:176545661 original size:12 final size:12
Alignment explanation
Indices: 176545644--176545669 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
176545634 TATATCTTAT
176545644 AAATTCCAACTC
1 AAATTCCAACTC
176545656 AAATTCCAACTC
1 AAATTCCAACTC
176545668 AA
1 AA
176545670 TGGTCCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATTCCAACTC
Found at i:176546147 original size:49 final size:50
Alignment explanation
Indices: 176546064--176546187 Score: 214
Period size: 49 Copynumber: 2.5 Consensus size: 50
176546054 TCACAAATTC
*
176546064 CAAATAAATTACATAAAAAAATAAATCTAATAAACCTAAAACACACATGA
1 CAAATAAATTACATAAAAAAATAAATCTAATAAACCTAAAACACACAAGA
* *
176546114 CAAATAACTTACAT-AAAAAATAAATTTAATAAACCTAAAACACACAAGA
1 CAAATAAATTACATAAAAAAATAAATCTAATAAACCTAAAACACACAAGA
176546163 CAAATAAATTACATAAAAAAATAAA
1 CAAATAAATTACATAAAAAAATAAA
176546188 ACATTCTTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
49 46 0.67
50 23 0.33
ACGTcount: A:0.64, C:0.15, G:0.02, T:0.20
Consensus pattern (50 bp):
CAAATAAATTACATAAAAAAATAAATCTAATAAACCTAAAACACACAAGA
Found at i:176546614 original size:25 final size:24
Alignment explanation
Indices: 176546528--176546615 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 24
176546518 ACTTCTTCTC
* *
176546528 TTTCCCTTTCTCCTTTCCTTTTCTATT
1 TTTCCC-TTCT-CTTTTCTTCTCT-TT
* *
176546555 TTTCCCTTCCCTTCTCTTCTCTTT
1 TTTCCCTTCTCTTTTCTTCTCTTT
* * *
176546579 ATTCAACTTCTATTTTCTTCTCTTT
1 TTTC-CCTTCTCTTTTCTTCTCTTT
176546604 TTTCCCTT-TCTT
1 TTTCCCTTCTCTT
176546616 CCCTTCCCGC
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
23 3 0.06
24 8 0.17
25 28 0.58
26 3 0.06
27 6 0.12
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTCCCTTCTCTTTTCTTCTCTTT
Found at i:176547176 original size:20 final size:21
Alignment explanation
Indices: 176547140--176547195 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
176547130 AAGGCAACAG
176547140 AAAAATT--TAAAAATTATTT
1 AAAAATTAATAAAAATTATTT
* *
176547159 -TAAATTAATAAAAGTTATTT
1 AAAAATTAATAAAAATTATTT
176547179 AAAAAATTAATAAAAAT
1 -AAAAATTAATAAAAAT
176547196 ATTACAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 5 0.17
20 11 0.38
22 13 0.45
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAATTAATAAAAATTATTT
Found at i:176547965 original size:26 final size:26
Alignment explanation
Indices: 176547931--176547983 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
176547921 AAACTATTAA
176547931 TAATGTTAAATATATTTTATTAATTT
1 TAATGTTAAATATATTTTATTAATTT
*
176547957 TAATTTTAAATATATTTTATTAATTT
1 TAATGTTAAATATATTTTATTAATTT
176547983 T
1 T
176547984 TGAAGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TAATGTTAAATATATTTTATTAATTT
Found at i:176559876 original size:49 final size:49
Alignment explanation
Indices: 176559796--176560177 Score: 598
Period size: 49 Copynumber: 8.1 Consensus size: 49
176559786 GTACATAATA
*
176559796 ATATATGTGATAA-GCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
176559844 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTG-AAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
176559892 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
*
176559941 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
176559990 ATATATGTGATAAGGCCTAATGG-C--CGTGATGAATGTG-AAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
*
176560035 ATATATGTGATAAGGCC---T-------GTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
* *
176560074 ATATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
*
176560123 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
176560172 ATATAT
1 ATATAT
176560178 ATGTGGTAAA
Statistics
Matches: 313, Mismatches: 8, Indels: 25
0.90 0.02 0.07
Matches are distributed among these distances:
38 12 0.04
39 24 0.08
42 2 0.01
45 24 0.08
46 13 0.04
48 62 0.20
49 176 0.56
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.31
Consensus pattern (49 bp):
ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
Found at i:176560066 original size:38 final size:39
Alignment explanation
Indices: 176560011--176560091 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
176560001 AAGGCCTAAT
176560011 GGCC-GTGATGAATGTGAAA-TGTATATATATGTGATAA
1 GGCCTGTGATGAATGTGAAAGTGTATATATATGTGATAA
176560048 GGCCTGTGATGAATGTGAAAGTGTATATATATGTGATAA
1 GGCCTGTGATGAATGTGAAAGTGTATATATATGTGATAA
176560087 GGCCT
1 GGCCT
176560092 AATGGCTGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 4 0.10
38 15 0.36
39 23 0.55
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.32
Consensus pattern (39 bp):
GGCCTGTGATGAATGTGAAAGTGTATATATATGTGATAA
Found at i:176560068 original size:84 final size:86
Alignment explanation
Indices: 176559969--176560140 Score: 303
Period size: 84 Copynumber: 2.0 Consensus size: 86
176559959 AATGGCCGAC
176559969 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGC-CGTGATGAATGTG-AAATG
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCACGTGATGAATGTGAAAATG
176560032 TATATATATGTGATAAGGCCT
66 TATATATATGTGATAAGGCCT
*
176560053 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTGAAAA
1 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGC--ACGTGATGAATGTGAAAA
176560118 TGTATATATATGTGATAAGGCCT
64 TGTATATATATGTGATAAGGCCT
176560141 AATGGCCGAC
Statistics
Matches: 83, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
84 45 0.54
87 12 0.14
88 26 0.31
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (86 bp):
GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCACGTGATGAATGTGAAAATG
TATATATATGTGATAAGGCCT
Found at i:176560078 original size:133 final size:137
Alignment explanation
Indices: 176559796--176560177 Score: 594
Period size: 133 Copynumber: 2.7 Consensus size: 137
176559786 GTACATAATA
176559796 ATATATGTGATAA-GCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATGTGATAAGGC
176559860 CTAATGGCCGACGTGATGAATGTGAAATGTATATATATGTGATAAGGCCTAATGGCCGACGTGAT
66 CTAATGGCC-ACGTGATGAATGTGAAATGTATATATATGTGATAAGGCC--AT------CGTGAT
176559925 GAATGTGAAAATGTAT
122 GAATGTGAAAATGTAT
* *
176559941 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATGTGATAAGGC
176560006 CTAATGG-C-CGTGATGAATGTGAAATGTATATATATGTGATAAGGCC-T-GTGATGAATGTGAA
66 CTAATGGCCACGTGATGAATGTGAAATGTATATATATGTGATAAGGCCATCGTGATGAATGTGAA
*
176560067 AGTGTAT
131 AATGTAT
*
176560074 ATATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTGAAAATGTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATGTGATAAGGC
176560139 CTAATGGCCGACGTGATGAATGTGAAAGTGTATATATAT
66 CTAATGGCC-ACGTGATGAATGTGAAA-TGTATATATAT
176560178 ATGTGGTAAA
Statistics
Matches: 226, Mismatches: 6, Indels: 18
0.90 0.02 0.07
Matches are distributed among these distances:
133 89 0.39
134 1 0.00
136 16 0.07
137 11 0.05
140 1 0.00
143 38 0.17
145 14 0.06
146 56 0.25
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.31
Consensus pattern (137 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATGTGATAAGGC
CTAATGGCCACGTGATGAATGTGAAATGTATATATATGTGATAAGGCCATCGTGATGAATGTGAA
AATGTAT
Found at i:176560301 original size:37 final size:36
Alignment explanation
Indices: 176560246--176560332 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
176560236 AACTTGGAAA
176560246 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGT-AGACCCGATGACTACGTGTGGAGAT
176560284 TATGTCCGGGTACGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTA-GACCCGATGACTACGTGTGGAGAT
176560321 TATGTCCGGGTA
1 TATGTCCGGGTA
176560333 AGACTTCGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 43 0.90
38 4 0.08
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (36 bp):
TATGTCCGGGTAGACCCGATGACTACGTGTGGAGAT
Found at i:176569421 original size:25 final size:25
Alignment explanation
Indices: 176569392--176569439 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
176569382 TTATACCATG
* * *
176569392 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
176569417 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
176569440 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:176569542 original size:20 final size:20
Alignment explanation
Indices: 176569482--176569542 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
176569472 ATAAATATGG
*
176569482 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
176569502 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
176569522 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
176569542 T
1 T
176569543 GTAATCATAA
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:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:176569659 original size:46 final size:48
Alignment explanation
Indices: 176569592--176569709 Score: 161
Period size: 46 Copynumber: 2.5 Consensus size: 48
176569582 GAGGAAGTGA
176569592 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATG-CCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
176569638 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
176569686 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
176569710 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
46 34 0.53
47 8 0.12
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:176569705 original size:25 final size:24
Alignment explanation
Indices: 176569592--176569709 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
176569582 GAGGAAGTGA
*
176569592 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
176569616 AAAAGGGCTTATG-CCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
176569638 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
176569662 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
176569686 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
176569710 ATGATAAAGC
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
22 13 0.15
23 16 0.19
24 44 0.52
25 11 0.13
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:176569946 original size:30 final size:31
Alignment explanation
Indices: 176569901--176569994 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
176569891 CGTTTACAGT
176569901 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
176569932 AAAGGCTT-GGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
176569962 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
176569993 AA
1 AA
176569995 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
30 30 0.49
31 31 0.51
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:176577370 original size:15 final size:15
Alignment explanation
Indices: 176577331--176577409 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
176577321 GTATCTTGGG
*
176577331 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
176577346 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
176577361 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
176577375 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
176577390 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
176577404 TTTCTT
1 TTTCTT
176577410 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:176577394 original size:29 final size:29
Alignment explanation
Indices: 176577322--176577408 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
176577312 CATAGTATCG
* * * *
176577322 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
176577352 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
176577381 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
176577409 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:176579810 original size:46 final size:46
Alignment explanation
Indices: 176579760--176579935 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
176579750 TGGTTGAGCA
176579760 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
176579806 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
176579851 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
176579899 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
176579936 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:176579916 original size:93 final size:93
Alignment explanation
Indices: 176579757--176579927 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
176579747 GGATGGTTGA
* *
176579757 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
176579822 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
176579850 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
176579915 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
176579928 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:176582921 original size:15 final size:15
Alignment explanation
Indices: 176582882--176582961 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
176582872 GTATCTTGGG
*
176582882 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
176582897 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
176582912 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
176582927 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
176582942 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
176582956 TTTCTT
1 TTTCTT
176582962 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:176582951 original size:30 final size:30
Alignment explanation
Indices: 176582873--176582960 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
176582863 CATAGTATCG
* * *
176582873 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
176582903 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
176582933 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
176582961 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:176585388 original size:46 final size:46
Alignment explanation
Indices: 176585338--176585513 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
176585328 TGGTTGAGCA
176585338 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
176585384 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
176585429 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
176585477 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
176585514 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:176585494 original size:93 final size:93
Alignment explanation
Indices: 176585335--176585505 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
176585325 GGATGGTTGA
* *
176585335 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
176585400 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
176585428 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
176585493 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
176585506 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:176592302 original size:40 final size:41
Alignment explanation
Indices: 176592247--176592414 Score: 184
Period size: 40 Copynumber: 4.2 Consensus size: 41
176592237 TGAATGATAC
* *
176592247 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
* * *
176592287 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
* ** *
176592327 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGCT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
* * * *
176592367 CCGGGTTAAGACCCGAAGGCAATTGTGCTTG-TGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
176592407 CC-GGCTAA
1 CCGGGCTAA
176592415 ATTCCGAAGA
Statistics
Matches: 106, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
39 6 0.06
40 98 0.92
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (41 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
Found at i:176592380 original size:80 final size:80
Alignment explanation
Indices: 176592247--176592414 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
176592237 TGAATGATAC
* * ** *
176592247 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGC-ATTC
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATT-
*
176592311 GTGCGAGTTGTTATAT
65 GTGCGAGTGGTTATAT
* *
176592327 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGCT-ACCAAATCCGGGTTAAGACCCGAAGGCAATT
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAG-TGACCAAATCCGGGCTAAGACCCGAAGGCAATT
**
176592391 GTGCTTGTGGTTATAT
65 GTGCGAGTGGTTATAT
176592407 CC-GGCTAA
1 CCGGGCTAA
176592415 ATTCCGAAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
79 6 0.08
80 66 0.87
81 4 0.05
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATTG
TGCGAGTGGTTATAT
Found at i:176598759 original size:20 final size:19
Alignment explanation
Indices: 176598734--176598786 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
176598724 TATTTTATGT
*
176598734 ATTTAATGTGTCTTGAGTCC
1 ATTTAATATGTCTT-AGTCC
176598754 ATTTAATATGT-TCTAG-CC
1 ATTTAATATGTCT-TAGTCC
176598772 ATTTAATATGTCTTA
1 ATTTAATATGTCTTA
176598787 AGTTTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 15 0.50
19 4 0.13
20 11 0.37
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (19 bp):
ATTTAATATGTCTTAGTCC
Found at i:176598785 original size:38 final size:38
Alignment explanation
Indices: 176598734--176598807 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
176598724 TATTTTATGT
* *
176598734 ATTTAATGTGTCTTGAGTCCATTTAATATGTTCTAGCC
1 ATTTAATATGTCTTAAGTCCATTTAATATGTTCTAGCC
** *
176598772 ATTTAATATGTCTTAAGTTTATTTAATGTGTTCTAG
1 ATTTAATATGTCTTAAGTCCATTTAATATGTTCTAG
176598808 TTAATATAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.49
Consensus pattern (38 bp):
ATTTAATATGTCTTAAGTCCATTTAATATGTTCTAGCC
Found at i:176600115 original size:28 final size:28
Alignment explanation
Indices: 176600004--176600115 Score: 100
Period size: 28 Copynumber: 4.0 Consensus size: 28
176599994 ACCTATATAT
* *
176600004 ATATGGCCCACTAGGCCCAATCTCTTTC
1 ATATGGCCCACTAGGCCCAATCACATTC
* * *
176600032 ATATGGCCCATTAGGCCCATTCACATTT
1 ATATGGCCCACTAGGCCCAATCACATTC
* ** * * *
176600060 ATGTGAACCATTAGGCGCAAATCGCATTC
1 ATATGGCCCACTAGGC-CCAATCACATTC
176600089 ATATGG-CCACTAGGCCCAAATCACATT
1 ATATGGCCCACTAGGCCC-AATCACATT
176600116 TACTGTCATG
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
27 1 0.02
28 52 0.80
29 12 0.18
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (28 bp):
ATATGGCCCACTAGGCCCAATCACATTC
Found at i:176601872 original size:40 final size:39
Alignment explanation
Indices: 176601796--176602018 Score: 288
Period size: 39 Copynumber: 5.6 Consensus size: 39
176601786 GCTACTCGTT
*
176601796 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
176601835 CAAATGCCTTCGGGACTTAACCCGGATTTAGTGACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCA
*
176601875 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
176601914 CCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
176601953 CAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
176601994 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
176602019 CATCATTCGA
Statistics
Matches: 163, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
39 85 0.52
40 65 0.40
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:176601898 original size:79 final size:79
Alignment explanation
Indices: 176601796--176602018 Score: 308
Period size: 79 Copynumber: 2.8 Consensus size: 79
176601786 GCTACTCGTT
* *
176601796 CAAATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
* *
176601861 TTTAGTGACTCGCA
66 ATTAGTAACTCGCA
* *
176601875 CAAATGCCTTCGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
176601938 AATTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * * *
176601953 CAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
176602017 GA
64 GA
176602019 CATCATTCGA
Statistics
Matches: 127, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
78 37 0.29
79 70 0.55
80 20 0.16
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:176601978 original size:118 final size:119
Alignment explanation
Indices: 176601798--176602018 Score: 306
Period size: 118 Copynumber: 1.9 Consensus size: 119
176601788 TACTCGTTCA
* *
176601798 AATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
* *
176601863 TAGTGAC-TCGCACAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCACC
66 TAGTCACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
176601916 AATGCCTTCGGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
*
176601979 TATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 TATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
176602019 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
117 4 0.04
118 65 0.72
119 21 0.23
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (119 bp):
AATGCCTTCGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
TAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:176610070 original size:119 final size:120
Alignment explanation
Indices: 176609888--176610110 Score: 319
Period size: 119 Copynumber: 1.9 Consensus size: 120
176609878 TACTCGTTCA
*
176609888 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* * *
176609953 TTAGTGAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTCACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* **
176610008 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
*
176610070 ATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
176610111 CATCATTCGA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
118 4 0.04
119 68 0.74
120 20 0.22
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:176610110 original size:40 final size:40
Alignment explanation
Indices: 176609867--176610110 Score: 300
Period size: 40 Copynumber: 6.1 Consensus size: 40
176609857 CGGAATTTAA
** *
176609867 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
176609907 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
176609947 CCGGATTTAGTGACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
176609987 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
176610026 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
176610066 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
176610106 CCGGA
1 CCGGA
176610111 CATCATTCGA
Statistics
Matches: 180, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.18
40 133 0.74
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:176619874 original size:40 final size:40
Alignment explanation
Indices: 176619672--176619860 Score: 315
Period size: 40 Copynumber: 4.7 Consensus size: 40
176619662 ATTCGGATTG
*
176619672 ATAACCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
176619712 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
176619752 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
176619792 ATAACCAGGCTGAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
176619832 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
176619861 AGCTAGTAGC
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 136 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:176619893 original size:39 final size:40
Alignment explanation
Indices: 176619672--176619893 Score: 252
Period size: 40 Copynumber: 5.6 Consensus size: 40
176619662 ATTCGGATTG
* *
176619672 ATAACCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
* * * *
176619712 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
* * * *
176619752 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
* * * *
176619792 ATAACCAGGCTGAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
* *
176619832 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTA-CT
*
176619872 ATATCC-GGCTAAACT-CCGAAGG
1 ATAACCGGGCT-AACTCCCGAAGG
176619894 TACGTGGTTT
Statistics
Matches: 163, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 13 0.08
40 150 0.92
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
Found at i:176627831 original size:40 final size:40
Alignment explanation
Indices: 176627629--176627817 Score: 324
Period size: 40 Copynumber: 4.7 Consensus size: 40
176627619 ATTCGGATTG
176627629 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
176627669 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
176627709 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
176627749 ATAACCGGGCTGAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
176627789 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
176627818 AGCTAGTAGC
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 137 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:176627831 original size:80 final size:80
Alignment explanation
Indices: 176627629--176627840 Score: 329
Period size: 80 Copynumber: 2.7 Consensus size: 80
176627619 ATTCGGATTG
*
176627629 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCAGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
176627694 TTTGTGCGAGTTAAT
66 TTTGTGCGAGTTAAT
* * * *
176627709 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTGAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
*
176627774 TTTGTGCGAGTTACT
66 TTTGTGCGAGTTAAT
* *
176627789 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATATCC-GGCTAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAA
176627841 ACTCCGAAGG
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
79 7 0.06
80 112 0.94
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTAAT
Found at i:176627850 original size:39 final size:40
Alignment explanation
Indices: 176627629--176627850 Score: 252
Period size: 40 Copynumber: 5.6 Consensus size: 40
176627619 ATTCGGATTG
* *
176627629 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
* * * * *
176627669 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAAT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
* * * *
176627709 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
* * *
176627749 ATAACCGGGCTGAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
* *
176627789 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTA-CT
*
176627829 ATATCC-GGCTAAACT-CCGAAGG
1 ATAACCGGGCT-AACTCCCGAAGG
176627851 TATGTGGTTT
Statistics
Matches: 164, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
39 13 0.08
40 151 0.92
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAACTCCCGAAGGCATTTGAGCGAGTTACT
Found at i:176633271 original size:13 final size:13
Alignment explanation
Indices: 176633255--176633301 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
176633245 TTTTCATAAA
*
176633255 ACCATTTCGTTTT
1 ACCATTTCATTTT
* *
176633268 ACCATTTCATATA
1 ACCATTTCATTTT
176633281 ACCATTTCATTTT
1 ACCATTTCATTTT
176633294 ACACATTT
1 AC-CATTT
176633302 AGCACATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 23 0.82
14 5 0.18
ACGTcount: A:0.28, C:0.23, G:0.02, T:0.47
Consensus pattern (13 bp):
ACCATTTCATTTT
Found at i:176633283 original size:26 final size:27
Alignment explanation
Indices: 176633246--176633301 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
176633236 ATACATCTAT
*
176633246 TTTCATAAAACCATTTCGTTTTAC-CA
1 TTTCATAAAACCATTTCATTTTACACA
*
176633272 TTTCATATAACCATTTCATTTTACACA
1 TTTCATAAAACCATTTCATTTTACACA
176633299 TTT
1 TTT
176633302 AGCACATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.46
Consensus pattern (27 bp):
TTTCATAAAACCATTTCATTTTACACA
Found at i:176633315 original size:29 final size:26
Alignment explanation
Indices: 176633254--176633316 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
176633244 ATTTTCATAA
* *
176633254 AACCATTTCGTTTTACCATTTCATAT
1 AACCATTTCATTTTACCATTTCACAT
176633280 AACCATTTCATTTTACACATTTAGCACAT
1 AACCATTTCATTTTAC-CATTT--CACAT
*
176633309 AATCATTT
1 AACCATTT
176633317 TGTATATCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.48
27 5 0.16
29 11 0.35
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (26 bp):
AACCATTTCATTTTACCATTTCACAT
Found at i:176642519 original size:43 final size:42
Alignment explanation
Indices: 176642375--176642545 Score: 139
Period size: 43 Copynumber: 4.0 Consensus size: 42
176642365 CATAAAGCTT
* * *
176642375 ATACAATGCCATATCCCAGATATGGTCTTACATGTTATCAC-
1 ATACAATGCCATATCCCAGACATGGTCTTACACGTAATCACA
* * * * * *
176642416 GTATCGATGCCACTATCCCAGACAAGGACTTACACGAAATCA-T
1 ATA-CAATGCCA-TATCCCAGACATGGTCTTACACGTAATCACA
* * *
176642459 ATAACGATGCCAATGTCCCAGATATGGTCTTACACGTAATCACA
1 AT-ACAATGCC-ATATCCCAGACATGGTCTTACACGTAATCACA
* * * *
176642503 ATACAATGCTAGTGTCCAAGACATGGTCTTACATGTAATCACA
1 ATACAATGCCA-TATCCCAGACATGGTCTTACACGTAATCACA
176642546 TCTCGAAAAT
Statistics
Matches: 103, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.02
42 8 0.08
43 89 0.86
44 4 0.04
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (42 bp):
ATACAATGCCATATCCCAGACATGGTCTTACACGTAATCACA
Found at i:176645886 original size:28 final size:28
Alignment explanation
Indices: 176645854--176645952 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
176645844 GCAATAAGCC
*
176645854 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
176645882 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
176645910 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
176645939 CGCACACTTAGTGC
1 CGCACACTTAGTGC
176645953 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:176653565 original size:28 final size:28
Alignment explanation
Indices: 176653533--176653631 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
176653523 GCAATAAGCC
*
176653533 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
176653561 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
176653589 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
176653618 CGCACACTTAGTGC
1 CGCACACTTAGTGC
176653632 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:176658410 original size:25 final size:24
Alignment explanation
Indices: 176658376--176658488 Score: 113
Period size: 25 Copynumber: 4.6 Consensus size: 24
176658366 TTAAAAGGTC
176658376 CGCACACATAGTGCCATGTAGTTTT
1 CGCACACATAGTGCCATGTA-TTTT
* *
176658401 CACACACATAGTGCCACGT-TTCCTT
1 CGCACACATAGTGCCATGTATT--TT
* * * *
176658426 -GCACACATAGTGCTATATAATCT
1 CGCACACATAGTGCCATGTATTTT
176658449 CGCACACATAGTGCCATGTAGTTTT
1 CGCACACATAGTGCCATGTA-TTTT
*
176658474 TGCACACATAGTGCC
1 CGCACACATAGTGCC
176658489 GCATAACCTC
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
23 3 0.04
24 31 0.44
25 36 0.51
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (24 bp):
CGCACACATAGTGCCATGTATTTT
Found at i:176658433 original size:49 final size:48
Alignment explanation
Indices: 176658377--176658511 Score: 146
Period size: 49 Copynumber: 2.8 Consensus size: 48
176658367 TAAAAGGTCC
* * *
176658377 GCACACATAGTGCCATGTAGTTTTCACACACATAGTGCCACGT-TTCCTT
1 GCACACATAGTGCCATATA-ATCTCACACACATAGTGCCACGTATT-CTT
* * * *
176658426 GCACACATAGTGCTATATAATCTCGCACACATAGTGCCATGTAGTTTTT
1 GCACACATAGTGCCATATAATCTCACACACATAGTGCCACGTA-TTCTT
** *
176658475 GCACACATAGTGCCGCATAACCTCACACACATAGTGC
1 GCACACATAGTGCCATATAATCTCACACACATAGTGC
176658512 TAAAATTTCT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
48 19 0.26
49 51 0.71
50 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (48 bp):
GCACACATAGTGCCATATAATCTCACACACATAGTGCCACGTATTCTT
Found at i:176658453 original size:24 final size:24
Alignment explanation
Indices: 176658376--176658511 Score: 85
Period size: 24 Copynumber: 5.6 Consensus size: 24
176658366 TTAAAAGGTC
* * *
176658376 CGCACACATAGTGCCATGTAGTTTT
1 CGCACACATAGTGCCATATA-ATCT
* ** *
176658401 CACACACATAGTGCCACGT-TTCCT
1 CGCACACATAGTGCCATATAAT-CT
* *
176658425 TGCACACATAGTGCTATATAATCT
1 CGCACACATAGTGCCATATAATCT
* * *
176658449 CGCACACATAGTGCCATGTAGTTTT
1 CGCACACATAGTGCCATATA-ATCT
* ** *
176658474 TGCACACATAGTGCCGCATAACCT
1 CGCACACATAGTGCCATATAATCT
*
176658498 CACACACATAGTGC
1 CGCACACATAGTGC
176658512 TAAAATTTCT
Statistics
Matches: 85, Mismatches: 23, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
23 2 0.02
24 47 0.55
25 36 0.42
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (24 bp):
CGCACACATAGTGCCATATAATCT
Found at i:176658504 original size:73 final size:73
Alignment explanation
Indices: 176658376--176658513 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 73
176658366 TTAAAAGGTC
* ** **
176658376 CGCACACATAGTGCCATGTAGTTTTCACACACATAGTGCCACGTTTCCTTGCACACATAGTGCTA
1 CGCACACATAGTGCCATGTAGTTTTCACACACATAGTGCCACATAACCTCACACACATAGTGCTA
176658441 TATAATCT
66 TATAATCT
** *
176658449 CGCACACATAGTGCCATGTAGTTTTTGCACACATAGTGCCGCATAACCTCACACACATAGTGCTA
1 CGCACACATAGTGCCATGTAGTTTTCACACACATAGTGCCACATAACCTCACACACATAGTGCTA
176658514 AAATTTCTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (73 bp):
CGCACACATAGTGCCATGTAGTTTTCACACACATAGTGCCACATAACCTCACACACATAGTGCTA
TATAATCT
Found at i:176670082 original size:50 final size:50
Alignment explanation
Indices: 176669949--176670114 Score: 208
Period size: 50 Copynumber: 3.3 Consensus size: 50
176669939 GCGATCAATA
* * * *
176669949 TTGTATATTTGGCTATAAAGGTATGCACAAATGTGATATTATATTTGAAT-
1 TTGTATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTG-ATC
* * *
176669999 TTGGTATATTCGGCCATATAAGTAAGCACATATGTGATGTTATATTTGATC
1 TT-GTATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGATC
* * * *
176670050 TTGCATATTTGGCCACATAGGTATGCATATATGTGATATTATATTTGATC
1 TTGTATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGATC
176670100 TTGTATATTCGGCCA
1 TTGTATATTCGGCCA
176670115 AATGAGTGAT
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 58 0.59
51 40 0.41
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (50 bp):
TTGTATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGATC
Found at i:176674709 original size:17 final size:18
Alignment explanation
Indices: 176674667--176674715 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
176674657 AGTTGAAAAG
176674667 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
176674686 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
176674703 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
176674716 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:176675604 original size:40 final size:39
Alignment explanation
Indices: 176675538--176675703 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 39
176675528 AAATTGAATG
* * *
176675538 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGG-TATT
* * **
176675577 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT
176675616 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-G-TATT
* * **
176675656 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGT-ATT
176675696 ATATCCGG
1 ATATCCGG
176675704 TTATATTCCG
Statistics
Matches: 105, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
38 3 0.03
39 43 0.41
40 57 0.54
41 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT
Found at i:176682666 original size:17 final size:18
Alignment explanation
Indices: 176682624--176682672 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
176682614 AGTTGAAAAG
176682624 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
176682643 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
176682660 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
176682673 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:176683561 original size:40 final size:39
Alignment explanation
Indices: 176683495--176683660 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 39
176683485 AAATTGAATG
* * *
176683495 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGG-TATT
* * **
176683534 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT
176683573 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-G-TATT
* * **
176683613 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGT-ATT
176683653 ATATCCGG
1 ATATCCGG
176683661 TTATATTCCG
Statistics
Matches: 105, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
38 3 0.03
39 43 0.41
40 57 0.54
41 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT
Found at i:176690207 original size:41 final size:41
Alignment explanation
Indices: 176690162--176690279 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
176690152 TGAAAGATAA
176690162 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
176690203 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
176690233 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
176690274 ATGTAG
1 ATGTAG
176690280 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:176690218 original size:71 final size:71
Alignment explanation
Indices: 176690130--176690293 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
176690120 GAGATGTATC
176690130 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
176690195 AGGACA
66 AGGACA
176690201 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
176690266 AGGACA
66 AGGACA
176690272 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
176690294 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:176694959 original size:40 final size:40
Alignment explanation
Indices: 176694914--176695080 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 40
176694904 CGGAATATAA
*
176694914 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * * *
176694954 CCGGATAGAGTAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
176694994 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * ** *
176695034 CCGGATATAATTTCCAGCATAGTTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
176695073 CCGGATAT
1 CCGGATAT
176695081 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 14 0.14
40 89 0.86
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:176700024 original size:27 final size:28
Alignment explanation
Indices: 176699987--176700126 Score: 166
Period size: 27 Copynumber: 5.2 Consensus size: 28
176699977 AGCATGGCTG
* *
176699987 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
176700013 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
*
176700041 CTAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
176700068 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* * *
176700095 CCAGAT-TAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
176700122 CCAGA
1 CCAGA
176700127 ACGCTTCCTC
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.05
27 82 0.80
28 16 0.16
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:176701777 original size:26 final size:26
Alignment explanation
Indices: 176701741--176701850 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
176701731 CATTAAATTC
176701741 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
176701767 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
176701793 TTATCATGAAATATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
176701819 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
176701845 TTATCA
1 TTATCA
176701851 ATTTGTACCA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:176708115 original size:2 final size:2
Alignment explanation
Indices: 176708108--176708137 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
176708098 TTATTATAGA
176708108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176708138 GATTTACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176708912 original size:18 final size:19
Alignment explanation
Indices: 176708863--176708905 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
176708853 TAAATGGATA
*
176708863 ATTATCTAATT-AAT-TTT
1 ATTATTTAATTAAATATTT
176708880 ATTATTTAATTAAATATTT
1 ATTATTTAATTAAATATTT
176708899 ATT-TTTA
1 ATTATTTA
176708906 GATAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 7 0.30
19 6 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATTTAATTAAATATTT
Found at i:176710367 original size:26 final size:29
Alignment explanation
Indices: 176710337--176710400 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 29
176710327 AAGCAATAGG
*
176710337 TAATAATAAATATAATAAT-AG-A-AATA
1 TAATAATAAAGATAATAATAAGTATAATA
* *
176710363 TAATATTAAAGATAATACTAAGTATAATA
1 TAATAATAAAGATAATAATAAGTATAATA
176710392 TAATAATAA
1 TAATAATAA
176710401 TAATGTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 16 0.52
27 2 0.06
28 1 0.03
29 12 0.39
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (29 bp):
TAATAATAAAGATAATAATAAGTATAATA
Found at i:176710409 original size:14 final size:14
Alignment explanation
Indices: 176710337--176710412 Score: 59
Period size: 14 Copynumber: 5.3 Consensus size: 14
176710327 AAGCAATAGG
176710337 TAATAATAAATATAA
1 TAATAAT-AATATAA
176710352 TAATAGA-AATATAA
1 TAATA-ATAATATAA
* *
176710366 TATTAA-AGATAATAC
1 TAATAATA-AT-ATAA
176710381 TAAGT-ATAATATAA
1 TAA-TAATAATATAA
*
176710395 TAATAATAATGTAA
1 TAATAATAATATAA
176710409 TAAT
1 TAAT
176710413 GATAGTAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.06
14 31 0.62
15 13 0.26
16 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.34
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:176711137 original size:14 final size:14
Alignment explanation
Indices: 176711118--176711165 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
176711108 AAAAGAGAAG
176711118 AAAGAGAAGGGAGAA
1 AAAGAGAAGGGAG-A
*
176711133 AAGAGAGAAGGGAGG
1 AA-AGAGAAGGGAGA
* *
176711148 AAAGAGAGGGGGGA
1 AAAGAGAAGGGAGA
176711162 AAAG
1 AAAG
176711166 GGGAGAGCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 13 0.46
15 4 0.14
16 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (14 bp):
AAAGAGAAGGGAGA
Done.