Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 45 of 206
Found at i:12834377 original size:52 final size:52
Alignment explanation
Indices: 12834306--12834555 Score: 395
Period size: 52 Copynumber: 4.9 Consensus size: 52
12834296 ATCAAGTGAC
*
12834306 AAAGTGATAGGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
12834358 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
12834410 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC------
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
12834456 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
** *
12834508 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
12834556 AGTGATAAGT
Statistics
Matches: 184, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
46 44 0.24
52 140 0.76
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:12834477 original size:46 final size:46
Alignment explanation
Indices: 12834410--12834566 Score: 224
Period size: 46 Copynumber: 3.3 Consensus size: 46
12834400 TGACAAGTGG
*
12834410 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
*
12834456 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
**
12834502 AAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
12834554 AAAGTGATAAGTG
1 AAAGTGATAAGTG
12834567 GCTACACTTA
Statistics
Matches: 100, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
46 57 0.57
52 43 0.43
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
Found at i:12834477 original size:98 final size:98
Alignment explanation
Indices: 12834298--12834566 Score: 421
Period size: 98 Copynumber: 2.7 Consensus size: 98
12834288 TACTTCTGAT
* *
12834298 CAAGTGACAAAGTGATAGGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGGAAAGT
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC------AAAGT
12834363 GATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
59 GATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
12834403 CAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
12834468 GATAGCTTCGGCTACACTTATCTGATCAAGTGA
66 GATAGCTTCGGCTACACTTATCTGATCAAGTGA
**
12834501 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
12834566 G
66 G
12834567 GCTACACTTA
Statistics
Matches: 156, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
98 107 0.69
104 43 0.28
105 6 0.04
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (98 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
GATAGCTTCGGCTACACTTATCTGATCAAGTGA
Found at i:12837008 original size:2 final size:2
Alignment explanation
Indices: 12837001--12837027 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12836991 TTTCTCCGTT
12837001 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12837028 CATGATGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12840914 original size:2 final size:2
Alignment explanation
Indices: 12840902--12840933 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12840892 TTAAAACAGA
12840902 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12840934 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12840938 original size:2 final size:2
Alignment explanation
Indices: 12840933--12840976 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12840923 ATATATATAT
12840933 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12840975 AG
1 AG
12840977 TCTTATTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12849120 original size:126 final size:125
Alignment explanation
Indices: 12848839--12849113 Score: 408
Period size: 126 Copynumber: 2.2 Consensus size: 125
12848829 GGCCAAATAG
* * * *
12848839 GAACTACTGTAGCAAAAGAGTGTCCACATGGGAGATTCTTTCAGTACTTTAGCTGACATTACATC
1 GAACTACTGTAGCAAAAGAGCGTCCACGTGAGAGATTCTTTCAGTACTTTAGCTGACAATACATC
*
12848904 CTGCTTGAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCA
66 CTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCA
* * *
12848964 GAAACTACTGTAGCAAAAGAACGTCCACGTGAGA-ACTTCTTTCAGTACTTTTGCTGACAATGCA
1 G-AACTACTGTAGCAAAAGAGCGTCCACGTGAGAGA-TTCTTTCAGTACTTTAGCTGACAATACA
* * * *
12849028 TTCTGCTTAAAGCGTTTTTGACATTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTCA
64 TCCTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCA
12849090 TGAACTACTGTAGCAAAAGAGCGT
1 -GAACTACTGTAGCAAAAGAGCGT
12849114 TTACGTGGGA
Statistics
Matches: 134, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
125 2 0.01
126 131 0.98
127 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (125 bp):
GAACTACTGTAGCAAAAGAGCGTCCACGTGAGAGATTCTTTCAGTACTTTAGCTGACAATACATC
CTGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCA
Found at i:12849334 original size:89 final size:91
Alignment explanation
Indices: 12849207--12849552 Score: 448
Period size: 97 Copynumber: 3.7 Consensus size: 91
12849197 AAAACCTTAA
* * *
12849207 ACACTAAACCCTAATCTATTTTTTTTAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAA
1 ACACTAAACCCTAATCTAATTTTTTAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAA
12849272 TTTATTTGATTTTTTTCTT-AAAA-C
66 TTTATTTGATTTTTTTCTTAAAAACC
*
12849296 -C-CTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTCACTCAAGTAACCCTAAACCCT
1 ACACTAAACCCTAATCTAA-TTTTTT-AAATTTATAATTAATTTACTCAAGTAACCCTAAACCCT
12849359 AATTTATTTGATTTTTTTCCTTAAAAACCC
64 AATTTATTTGATTTTTTT-CTTAAAAA-CC
* *
12849389 TAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAATCCTAGACC
1 ---ACACTAAACCCTAATCTAATTTTTT-AAATTTATAATTAATTTACTCAAGTAACCCTAAACC
*
12849454 CTAATTTATTTGATTTTTTCCTTAAAAACC
62 CTAATTTATTTGATTTTTTTCTTAAAAACC
* * * * *
12849484 ATAAACACTAAACCCTAATCTAATTTCTTAAATTTATAATTAATTTAATTAAGAAACCTTAAACC
1 ----ACACTAAACCCTAATCTAATTTTTTAAATTTATAATTAATTTACTCAAGTAACCCTAAACC
12849549 CTAA
62 CTAA
12849553 ACCCTTATTT
Statistics
Matches: 230, Mismatches: 15, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
87 15 0.07
88 7 0.03
89 53 0.23
90 3 0.01
91 4 0.02
93 1 0.00
95 36 0.16
96 35 0.15
97 60 0.26
98 16 0.07
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.40
Consensus pattern (91 bp):
ACACTAAACCCTAATCTAATTTTTTAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAA
TTTATTTGATTTTTTTCTTAAAAACC
Found at i:12849443 original size:186 final size:184
Alignment explanation
Indices: 12849165--12849552 Score: 514
Period size: 186 Copynumber: 2.1 Consensus size: 184
12849155 GTAACCTTGG
* *
12849165 ACCCCAAACCCTAATTTATTTAAATTTTCCTTAAAACCTTAAACACTAAACCCTAATCTATTTTT
1 ACCCTAAACCCTAATTTATTTAAATTTTCCTTAAAACCCTAAACACTAAACCCTAATCTATTTTT
** *
12849230 TTTAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTGATTTTTTTCTT-AAA
66 TAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTGATTTTTTCCTTAAAA
* * *
12849294 A-C-C-CTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTCACTCAAGTA
131 ACCACACTAAACCCTAATCTAA-TTTCTT-AAATTTATAATTAATTCAATCAAGAA
**
12849347 ACCCTAAACCCTAATTTATTTGATTTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAAT
1 ACCCTAAACCCTAATTTATTT-A-AATTTTCCTT-AAAACCCTAAACACTAAACCCTAATCT-AT
* * *
12849412 TTTTTAAAATTTATAATTAATTTACTCAAGTAATCCTAGACCCTAATTTATTTGATTTTTTCCTT
62 TTTTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTGATTTTTTCCTT
* *
12849477 AAAAACCATAAACACTAAACCCTAATCTAATTTCTTAAATTTATAATTAATTTAATTAAGAA
127 AAAAACC----ACACTAAACCCTAATCTAATTTCTTAAATTTATAATTAATTCAATCAAGAA
*
12849539 ACCTTAAACCCTAA
1 ACCCTAAACCCTAA
12849553 ACCCTTATTT
Statistics
Matches: 178, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
182 20 0.11
183 1 0.01
184 8 0.04
185 26 0.15
186 61 0.34
187 4 0.02
188 1 0.01
192 35 0.20
193 6 0.03
194 16 0.09
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (184 bp):
ACCCTAAACCCTAATTTATTTAAATTTTCCTTAAAACCCTAAACACTAAACCCTAATCTATTTTT
TAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTGATTTTTTCCTTAAAA
ACCACACTAAACCCTAATCTAATTTCTTAAATTTATAATTAATTCAATCAAGAA
Found at i:12855325 original size:10 final size:10
Alignment explanation
Indices: 12855311--12855462 Score: 195
Period size: 10 Copynumber: 16.5 Consensus size: 10
12855301 AAACTCTCAT
* *
12855311 TCTCTCGCTT
1 TCTCTCTCTC
12855321 TCTCTCTCTC
1 TCTCTCTCTC
12855331 TCTCTCTCTC
1 TCTCTCTCTC
12855341 TCTCTCTCTC
1 TCTCTCTCTC
12855351 TCTCTCTCTC
1 TCTCTCTCTC
12855361 TCTCTCTCTC
1 TCTCTCTCTC
12855371 TCTCTCTCTC
1 TCTCTCTCTC
12855381 TCTCT-TCT-
1 TCTCTCTCTC
12855389 TCT-TCT-TC
1 TCTCTCTCTC
12855397 T-TCT-TCT-
1 TCTCTCTCTC
12855404 TCT-TCT-TC
1 TCTCTCTCTC
12855412 T-TCT-TCT-
1 TCTCTCTCTC
12855419 TCT-TCTCTC
1 TCTCTCTCTC
12855428 TCTCTCTCTC
1 TCTCTCTCTC
12855438 TCTCTCTCTC
1 TCTCTCTCTC
12855448 TCTCTCTCTC
1 TCTCTCTCTC
12855458 TCTCT
1 TCTCT
12855463 TTCTTCACAA
Statistics
Matches: 127, Mismatches: 2, Indels: 26
0.82 0.01 0.17
Matches are distributed among these distances:
7 11 0.09
8 16 0.13
9 6 0.05
10 94 0.74
ACGTcount: A:0.00, C:0.45, G:0.01, T:0.55
Consensus pattern (10 bp):
TCTCTCTCTC
Found at i:12855330 original size:6 final size:6
Alignment explanation
Indices: 12855311--12855462 Score: 195
Period size: 6 Copynumber: 27.5 Consensus size: 6
12855301 AAACTCTCAT
* *
12855311 TCTCTC GCTTTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
12855359 TCTCTC TCTCTC TCTCTC TCTCTC TCT-TC T-TCT- TCT-TC T-TCT-
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
12855401 TCT-TC T-TCT- TCT-TC T-TCT- TCT-TC TCTCTC TCTCTC TCTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
12855442 TCTCTC TCTCTC TCTCTC TCT
1 TCTCTC TCTCTC TCTCTC TCT
12855463 TTCTTCACAA
Statistics
Matches: 129, Mismatches: 4, Indels: 26
0.81 0.03 0.16
Matches are distributed among these distances:
4 12 0.09
5 17 0.13
6 100 0.78
ACGTcount: A:0.00, C:0.45, G:0.01, T:0.55
Consensus pattern (6 bp):
TCTCTC
Found at i:12855391 original size:3 final size:3
Alignment explanation
Indices: 12855383--12855424 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
12855373 TCTCTCTCTC
12855383 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12855425 CTCTCTCTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:12861781 original size:29 final size:29
Alignment explanation
Indices: 12861723--12861781 Score: 66
Period size: 31 Copynumber: 2.0 Consensus size: 29
12861713 ACTCAACTTT
* *
12861723 TAAAAAATAACAAAACAGTCACTAATATTA
1 TAAAAAATAACAAAACAATCACT-AGATTA
*
12861753 TAAAAAAGTGACAAAACAATCACT-GATTA
1 TAAAAAA-TAACAAAACAATCACTAGATTA
12861782 ACTGTTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 4 0.16
30 7 0.28
31 14 0.56
ACGTcount: A:0.58, C:0.14, G:0.07, T:0.22
Consensus pattern (29 bp):
TAAAAAATAACAAAACAATCACTAGATTA
Found at i:12863741 original size:21 final size:20
Alignment explanation
Indices: 12863717--12863764 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
12863707 TTCTTTTAAC
12863717 ATTTTTTATATATTCTTTAGA
1 ATTTTTTATATATT-TTTAGA
* * *
12863738 ATTTTATTTTTTATTTTTATA
1 ATTTT-TTATATATTTTTAGA
12863759 ATTTTT
1 ATTTTT
12863765 AAAAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 15 0.65
22 7 0.30
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTTTTTATATATTTTTAGA
Found at i:12863797 original size:18 final size:17
Alignment explanation
Indices: 12863774--12863817 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
12863764 TAAAAAAATA
*
12863774 TATAAATTGTTGAATTTT
1 TATAAATT-TGGAATTTT
12863792 TATAAATATTGGAATTTT
1 TATAAAT-TTGGAATTTT
12863810 TATAAATT
1 TATAAATT
12863818 ACTTTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
TATAAATTTGGAATTTT
Found at i:12864991 original size:2 final size:2
Alignment explanation
Indices: 12864986--12865010 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12864976 ATATATATAT
12864986 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
12865011 TTCTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12867714 original size:20 final size:21
Alignment explanation
Indices: 12867689--12867739 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
12867679 AAGTTTTATA
* *
12867689 ATATATATTCATTA-TAACAT
1 ATATATATACAATAGTAACAT
*
12867709 ATATATGTACAATAGTTAACAT
1 ATATATATACAATAG-TAACAT
12867731 ATATATATA
1 ATATATATA
12867740 TATATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 11 0.44
22 14 0.56
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (21 bp):
ATATATATACAATAGTAACAT
Found at i:12875042 original size:47 final size:47
Alignment explanation
Indices: 12874983--12875073 Score: 157
Period size: 47 Copynumber: 1.9 Consensus size: 47
12874973 CTTTTCCTAA
*
12874983 TTTTTTTATTTATTTGTCCTTT-TTTGTTTTTTATTTACTTTTTCAGT
1 TTTTTTTATTTATTTCTCCTTTATTTGTTTTTTATTT-CTTTTTCAGT
12875030 TTTTTTTATTTATTTCTCCTTTATTTGTTTTTTATTTCTTTTTC
1 TTTTTTTATTTATTTCTCCTTTATTTGTTTTTTATTTCTTTTTC
12875074 TTTATTTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
47 28 0.67
48 14 0.33
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.76
Consensus pattern (47 bp):
TTTTTTTATTTATTTCTCCTTTATTTGTTTTTTATTTCTTTTTCAGT
Found at i:12875076 original size:25 final size:26
Alignment explanation
Indices: 12874984--12875087 Score: 103
Period size: 25 Copynumber: 4.2 Consensus size: 26
12874974 TTTTCCTAAT
*
12874984 TTTTTTATTTATTTGTCCTTT-TTTG
1 TTTTTTATTTATTTCTCCTTTATTTG
* * *
12875009 TTTTTTATTTACTT-T--TTCAGTT-
1 TTTTTTATTTATTTCTCCTTTATTTG
12875031 TTTTTTATTTATTTCTCCTTTATTTG
1 TTTTTTATTTATTTCTCCTTTATTTG
* * *
12875057 TTTTTTATTTCTTT-TTCTTTATTTC
1 TTTTTTATTTATTTCTCCTTTATTTG
12875082 TTTTTT
1 TTTTTT
12875088 TCTGCTTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 15 0.23
23 3 0.05
24 1 0.02
25 33 0.51
26 13 0.20
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.77
Consensus pattern (26 bp):
TTTTTTATTTATTTCTCCTTTATTTG
Found at i:12875079 original size:14 final size:14
Alignment explanation
Indices: 12875060--12875086 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12875050 TTATTTGTTT
12875060 TTTATTTCTTTTTC
1 TTTATTTCTTTTTC
12875074 TTTATTTCTTTTT
1 TTTATTTCTTTTT
12875087 TTCTGCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTCTTTTTC
Found at i:12875095 original size:25 final size:25
Alignment explanation
Indices: 12875048--12875097 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
12875038 TTTATTTCTC
* *
12875048 CTTTATTTGTTTTTTATTTCTTTTT
1 CTTTATTTCTTTTTTATTGCTTTTT
12875073 CTTTATTTCTTTTTT-TCTGCTTTTT
1 CTTTATTTCTTTTTTAT-TGCTTTTT
12875098 TATTTGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (25 bp):
CTTTATTTCTTTTTTATTGCTTTTT
Found at i:12883385 original size:132 final size:131
Alignment explanation
Indices: 12883225--12883911 Score: 606
Period size: 132 Copynumber: 5.2 Consensus size: 131
12883215 CTCTGAGTTT
*
12883225 GCAGTGAAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGCAGCAGATCAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTG-AGCAGATCAAAGAC
* * *
12883290 GGTGAATCTTATCTTCCCAATGTAGTAGGGAAGCAGATTTAAGCCACCAGGCCTATCTCCCTAAG
65 GGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAG
12883355 CA
130 CA
* * * * * *
12883357 GCAGTGGAGTAGGTTAAAGATTGTAGATCATGTCTCCTTAAGCAGTGGTTGAGCAGATCGAAGGC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG-TGAGCAGATCAAAGAC
* * * **** * * * *
12883422 AGCGAATCATATC-TCTTTGGCGTTA-CAGTGGAA-CAGATTAAAGCTA-AAGGTAGCGAATCTT
65 GGTGAATCTTATCTTCCCAAG-G-TAGTAG-GGAAGCAGATTTAAGCCACCA-GT--C----C-T
* * *
12883483 GTTTCCCTG-GCGTT
119 ATCTCCCTGAGC--A
* * * ** * * * * * * *
12883497 GCAGCGGAGTAGATTAAAGCTGAAGGCAGCTAATCTTATCTCCCT-GGC-CT--T-A-AAGCT-A
1 GCAGTGGAGTAGGTTGAA---GATTGTAG---ATCCTGTCTCCCTAAGCAGTAGTGAGCAGATCA
** * * *
12883555 AAGATAGTGAATCTTATTTTCCCAAGGTAGTAGGGAAGTAGATTTAAGCCACCAGTCTTATCTCC
60 AAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
12883620 CTGAGCA
125 CTGAGCA
* * *
12883627 ACAGCGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGT-GAGCAGATCAAAGAC
*
12883692 GGTGAATCTTATCTTCTCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAG
65 GGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAG
12883757 CA
130 CA
* * *
12883759 GCAGTAGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAAATCAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG-TGAGCAGATCAAAGAC
* *
12883824 GGTGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTTCCTGAG
65 GGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAG
*
12883889 CG
130 CA
* *
12883891 GCAGTAGAGCAGGTTGAAGAT
1 GCAGTGGAGTAGGTTGAAGAT
12883912 ACCAACTTTA
Statistics
Matches: 438, Mismatches: 83, Indels: 68
0.74 0.14 0.12
Matches are distributed among these distances:
124 11 0.03
125 2 0.00
126 1 0.00
127 5 0.01
128 1 0.00
130 16 0.04
131 13 0.03
132 292 0.67
133 8 0.02
134 1 0.00
136 1 0.00
137 6 0.01
138 31 0.07
139 14 0.03
140 17 0.04
141 1 0.00
143 5 0.01
144 1 0.00
145 2 0.00
146 10 0.02
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (131 bp):
GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGAGCAGATCAAAGACG
GTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGC
A
Found at i:12883494 original size:51 final size:51
Alignment explanation
Indices: 12883417--12883544 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 51
12883407 GAGCAGATCG
* ** *
12883417 AAGGCAGCGAATCATATCTCTTTGGCGTTACAGTGGAACAGATTAAAGCTA
1 AAGGCAGCGAATCTTATCTCCCTGGCGTTACAGCGGAACAGATTAAAGCTA
* * * * ** *
12883468 AAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGCGGAGTAGATTAAAGCTG
1 AAGGCAGCGAATCTTATCTCCCTGGCGTTACAGCGGAACAGATTAAAGCTA
*
12883519 AAGGCAGCTAATCTTATCTCCCTGGC
1 AAGGCAGCGAATCTTATCTCCCTGGC
12883545 CTTAAAGCTA
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (51 bp):
AAGGCAGCGAATCTTATCTCCCTGGCGTTACAGCGGAACAGATTAAAGCTA
Found at i:12883945 original size:44 final size:44
Alignment explanation
Indices: 12883891--12884032 Score: 178
Period size: 44 Copynumber: 3.2 Consensus size: 44
12883881 TTCCTGAGCG
*
12883891 GCAGTAGAGCAGGTTGAAGATACCAACTTTATCTCCTTGAAGTT
1 GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCTTGAAGTT
*
12883935 GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCATGAAGTT
1 GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCTTGAAGTT
* * * ** * *
12883979 GCAATGGAGCAGATTGAAGCTATTAA-TCCTATCACCTTGAAGTT
1 GCAGTGGAGCAGGTTGAAGATACCAACT-TTATCTCCTTGAAGTT
*
12884023 GAAGTGGAGC
1 GCAGTGGAGC
12884033 GGATTAAAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 1 0.01
44 84 0.99
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
GCAGTGGAGCAGGTTGAAGATACCAACTTTATCTCCTTGAAGTT
Found at i:12885268 original size:3 final size:3
Alignment explanation
Indices: 12885250--12885332 Score: 94
Period size: 3 Copynumber: 27.0 Consensus size: 3
12885240 CAAATTTTGG
* * * * * *
12885250 ATT ATC ATT GTT ATT ATT ATT GTT ATT GTT GTT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12885298 ATT ATT ATT ATT ATT ATT ATT ATTT ATT AGTT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT
12885333 TATTTTCCTT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
3 64 0.91
4 6 0.09
ACGTcount: A:0.27, C:0.01, G:0.07, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12888622 original size:23 final size:22
Alignment explanation
Indices: 12888595--12888666 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 22
12888585 TTTAAAAATA
*
12888595 ATTTAAAAAAATTATATTTAAT
1 ATTTTAAAAAATTATATTTAAT
*
12888617 ATTTTAAAAAATT-TAATT-A-
1 ATTTTAAAAAATTATATTTAAT
*
12888636 ATTTTAAAAAATTATATTTTAAA
1 ATTTTAAAAAATTATA-TTTAAT
12888659 ATTTTAAA
1 ATTTTAAA
12888667 TTTTAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.30
20 3 0.07
21 6 0.14
22 13 0.30
23 8 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTTAAAAAATTATATTTAAT
Found at i:12888656 original size:15 final size:15
Alignment explanation
Indices: 12888615--12888674 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
12888605 ATTATATTTA
12888615 ATATTTTAAAAAATTT
1 ATATTTTAAAAAA-TT
12888631 AATTAATTTTAAAAAATT
1 -A-T-ATTTTAAAAAATT
**
12888649 ATATTTTAAAATTTT
1 ATATTTTAAAAAATT
*
12888664 AAATTTTAAAA
1 ATATTTTAAAA
12888675 TATACATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
15 21 0.55
16 1 0.03
17 2 0.05
18 3 0.08
19 11 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTTTAAAAAATT
Found at i:12888675 original size:15 final size:15
Alignment explanation
Indices: 12888635--12888692 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
12888625 AAATTTAATT
*
12888635 AATTTTAAAAAATTA
1 AATTTTAAAATATTA
* *
12888650 TATTTTAAAATTTTA
1 AATTTTAAAATATTA
12888665 AATTTTAAAATA-TA
1 AATTTTAAAATATTA
*
12888679 CA-TTTAAAATATTA
1 AATTTTAAAATATTA
12888693 TAAAACAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
13 9 0.25
14 5 0.14
15 22 0.61
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTTAAAATATTA
Found at i:12888793 original size:22 final size:21
Alignment explanation
Indices: 12888772--12888900 Score: 113
Period size: 22 Copynumber: 6.0 Consensus size: 21
12888762 AAATTTATAT
12888772 TTTAAAATTTAAAAAATAATA
1 TTTAAAATTTAAAAAATAATA
* *
12888793 TTTAAATTTTTAAAAAATAACA
1 TTTAAA-ATTTAAAAAATAATA
12888815 TTTAAAA-TTAAAAAATAA-A
1 TTTAAAATTTAAAAAATAATA
**
12888834 TTTAATTTTTTTAAAAAATAATA
1 TTTAA--AATTTAAAAAATAATA
* *
12888857 TTATAAAAAATTTAAAATAT-ACA
1 TT-T--AAAATTTAAAAAATAATA
12888880 TTTAAAATTTTAAAAAA-AATA
1 TTTAAAA-TTTAAAAAATAATA
12888901 ATAAACAAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
19 6 0.07
20 15 0.17
21 16 0.18
22 31 0.36
23 7 0.08
24 10 0.11
26 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAAAATTTAAAAAATAATA
Found at i:12888845 original size:42 final size:43
Alignment explanation
Indices: 12888772--12888896 Score: 148
Period size: 42 Copynumber: 2.9 Consensus size: 43
12888762 AAATTTATAT
12888772 TTTAAAATTTAAAAAATAATATTTAAATTTTTAAAAAATAACA
1 TTTAAAATTTAAAAAATAATATTTAAATTTTTAAAAAATAACA
* *
12888815 TTTAAAA-TTAAAAAATAA-ATTTAATTTTTTTAAAAAATAATA
1 TTTAAAATTTAAAAAATAATATTTAA-ATTTTTAAAAAATAACA
* * *
12888857 TTATAAAAAATTTAAAATAT-ACATTTAAAATTTTAAAAAA
1 TT-T--AAAATTTAAAAAATAATATTTAAATTTTTAAAAAA
12888897 AATAATAAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
41 6 0.08
42 28 0.39
43 8 0.11
45 15 0.21
46 14 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (43 bp):
TTTAAAATTTAAAAAATAATATTTAAATTTTTAAAAAATAACA
Found at i:12888938 original size:15 final size:14
Alignment explanation
Indices: 12888918--12888973 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
12888908 AATAAAAGAG
*
12888918 AAATAAAGGATAAAT
1 AAATAAA-GAAAAAT
*
12888933 AAATAATTGAAAAAGT
1 AAATAA-AGAAAAA-T
*
12888949 AAATAAAGAAAAAC
1 AAATAAAGAAAAAT
12888963 AAATAAA-AAAA
1 AAATAAAGAAAA
12888974 CGAAAAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 4 0.11
14 7 0.20
15 17 0.49
16 7 0.20
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (14 bp):
AAATAAAGAAAAAT
Found at i:12890080 original size:29 final size:29
Alignment explanation
Indices: 12890047--12890106 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
12890037 TCCTCTAACT
12890047 TTACAAAAAAAAAATATTTTAACTTTTCA
1 TTACAAAAAAAAAATATTTTAACTTTTCA
**
12890076 TTACAAAAAAAATTTATTTTAACTTTTCA
1 TTACAAAAAAAAAATATTTTAACTTTTCA
12890105 TT
1 TT
12890107 TAGTTTTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (29 bp):
TTACAAAAAAAAAATATTTTAACTTTTCA
Found at i:12890972 original size:15 final size:16
Alignment explanation
Indices: 12890952--12890983 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12890942 AGATGTTGTA
12890952 TGTAATTCATCT-ATT
1 TGTAATTCATCTGATT
12890967 TGTAATTCATCTGATT
1 TGTAATTCATCTGATT
12890983 T
1 T
12890984 AGTAGCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (16 bp):
TGTAATTCATCTGATT
Found at i:12891698 original size:23 final size:22
Alignment explanation
Indices: 12891671--12891733 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
12891661 AGAAAAAGAC
12891671 AGATGAACAATGAAGATTCTCT
1 AGATGAACAATGAAGATTCTCT
* * *
12891693 ACGATGAATAGT-AAAATTCTCT
1 A-GATGAACAATGAAGATTCTCT
12891715 AGCATGAACAATGAAGATT
1 AG-ATGAACAATGAAGATT
12891734 TTCCGTAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.03
22 18 0.56
23 13 0.41
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (22 bp):
AGATGAACAATGAAGATTCTCT
Found at i:12891864 original size:19 final size:19
Alignment explanation
Indices: 12891827--12891865 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12891817 AATATTTTTA
*
12891827 TTTAAAATTTTTATGATTT
1 TTTAAAATTTTTATAATTT
12891846 TTTAATAATTTTT-TAATTT
1 TTTAA-AATTTTTATAATTT
12891865 T
1 T
12891866 AAAAGGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTAAAATTTTTATAATTT
Found at i:12893224 original size:2 final size:2
Alignment explanation
Indices: 12893217--12893267 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
12893207 ACTCAACATA
* *
12893217 AT AT AT AT AT AT AT AT AT AT AT CAA AC AGT AT -T A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT A-T AT AT AT AT AT AT AT
12893259 AT AT AT AT A
1 AT AT AT AT A
12893268 AAAAAAAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:12899416 original size:15 final size:15
Alignment explanation
Indices: 12899396--12899427 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12899386 TATTTCACTA
*
12899396 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
12899411 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
12899426 TT
1 TT
12899428 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:12900394 original size:22 final size:21
Alignment explanation
Indices: 12900368--12900682 Score: 308
Period size: 22 Copynumber: 14.2 Consensus size: 21
12900358 AGAAATTATC
*
12900368 CAACATTCAGACAACATTTAAT
1 CAACATT-GGACAACATTTAAT
*
12900390 TAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
*
12900412 CAACAATTGGACAACATTCAAT
1 CAAC-ATTGGACAACATTTAAT
*
12900434 TAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
*
12900456 CAACAATTGGACAACATTCAAT
1 CAAC-ATTGGACAACATTTAAT
*
12900478 CAATATTATTTGGACAACATTTAAT
1 C-A-A-CA-TTGGACAACATTTAAT
*
12900503 CAACAATTGGACAACATTAAAT
1 CAAC-ATTGGACAACATTTAAT
12900525 CAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
* * * * *
12900547 AAAAAATTGGATAGCATTCAAT
1 -CAACATTGGACAACATTTAAT
*
12900569 CAATATTTGGACAACATTTAAT
1 CAACA-TTGGACAACATTTAAT
*
12900591 CAACAATTGGACAACATTAAAT
1 CAAC-ATTGGACAACATTTAAT
**
12900613 CAACATTTGGACAGTATTTAAT
1 CAACA-TTGGACAACATTTAAT
12900635 CAACAATTGGACAACA-TTAAT
1 CAAC-ATTGGACAACATTTAAT
* *
12900656 CAATATTTGGACAGCATTTAAT
1 CAACA-TTGGACAACATTTAAT
12900678 CAACA
1 CAACA
12900683 ATTTTTACTT
Statistics
Matches: 243, Mismatches: 33, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.00
21 23 0.09
22 188 0.77
23 12 0.05
24 3 0.01
25 16 0.07
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.30
Consensus pattern (21 bp):
CAACATTGGACAACATTTAAT
Found at i:12900405 original size:11 final size:11
Alignment explanation
Indices: 12900391--12900543 Score: 57
Period size: 11 Copynumber: 13.6 Consensus size: 11
12900381 ACATTTAATT
12900391 AACATTTGGAC
1 AACATTTGGAC
*
12900402 AACATTT-AATC
1 AACATTTGGA-C
*
12900413 AACAATTGGAC
1 AACATTTGGAC
** *
12900424 AACA-TTCAATT
1 AACATTTGGA-C
12900435 AACATTTGGAC
1 AACATTTGGAC
*
12900446 AACATTT-AATC
1 AACATTTGGA-C
*
12900457 AACAATTGGAC
1 AACATTTGGAC
**
12900468 AACA-TTCAATC
1 AACATTTGGA-C
*
12900479 AATATTATTTGGAC
1 -A-A-CATTTGGAC
*
12900493 AACATTT-AATC
1 AACATTTGGA-C
*
12900504 AACAATTGGAC
1 AACATTTGGAC
**
12900515 AACA-TTAAATC
1 AACATTTGGA-C
12900526 AACATTTGGAC
1 AACATTTGGAC
12900537 AACATTT
1 AACATTT
12900544 AATAAAAAAT
Statistics
Matches: 102, Mismatches: 25, Indels: 30
0.65 0.16 0.19
Matches are distributed among these distances:
10 12 0.12
11 72 0.71
12 11 0.11
13 2 0.02
14 2 0.02
15 3 0.03
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (11 bp):
AACATTTGGAC
Found at i:12900425 original size:44 final size:44
Alignment explanation
Indices: 12900377--12900685 Score: 449
Period size: 44 Copynumber: 7.0 Consensus size: 44
12900367 CCAACATTCA
* *
12900377 GACAACATTTAATTAACATTTGGACAACATTTAATCAACAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
*
12900421 GACAACATTCAATTAACATTTGGACAACATTTAATCAACAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
*
12900465 GACAACATTCAATCAATATTATTTGGACAACATTTAATCAACAATTG
1 GACAACATTCAATC-A-A-CATTTGGACAACATTTAATCAACAATTG
* * *
12900512 GACAACATTAAATCAACATTTGGACAACATTTAATAAAAAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
* * *
12900556 GATAGCATTCAATCAATATTTGGACAACATTTAATCAACAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
* **
12900600 GACAACATTAAATCAACATTTGGACAGTATTTAATCAACAATTG
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
* *
12900644 GACAACATT-AATCAATATTTGGACAGCATTTAATCAACAATT
1 GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATT
12900686 TTTACTTCAA
Statistics
Matches: 241, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
43 31 0.13
44 166 0.69
45 2 0.01
46 2 0.01
47 40 0.17
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (44 bp):
GACAACATTCAATCAACATTTGGACAACATTTAATCAACAATTG
Found at i:12900447 original size:66 final size:66
Alignment explanation
Indices: 12900377--12900685 Score: 386
Period size: 66 Copynumber: 4.7 Consensus size: 66
12900367 CCAACATTCA
* * *
12900377 GACAACATTTAATTAACATTTGGACAACATTTAATCAACAATTGGACAACATTCAATTAACATTT
1 GACAACATTTAATCAACATTTGGACAACATTTAATCAACAATTGGACAACATTCAATCAACAATT
12900442 G
66 G
* * * *
12900443 GACAACATTTAATCAACAATTGGACAACATTCAATCAATATTATTTGGACAACATTTAATCAACA
1 GACAACATTTAATCAACATTTGGACAACATTTAATCAACA--A-TTGGACAACATTCAATCAACA
12900508 ATTG
63 ATTG
* * * * * * *
12900512 GACAACATTAAATCAACATTTGGACAACATTTAATAAAAAATTGGATAGCATTCAATCAATATTT
1 GACAACATTTAATCAACATTTGGACAACATTTAATCAACAATTGGACAACATTCAATCAACAATT
12900577 G
66 G
* * * ** *
12900578 GACAACATTTAATCAACAATTGGACAACATTAAATCAACATTTGGACAGTATTTAATCAACAATT
1 GACAACATTTAATCAACATTTGGACAACATTTAATCAACAATTGGACAACATTCAATCAACAATT
12900643 G
66 G
* *
12900644 GACAACA-TTAATCAATATTTGGACAGCATTTAATCAACAATT
1 GACAACATTTAATCAACATTTGGACAACATTTAATCAACAATT
12900686 TTTACTTCAA
Statistics
Matches: 207, Mismatches: 33, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
65 30 0.14
66 118 0.57
67 1 0.00
68 1 0.00
69 57 0.28
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (66 bp):
GACAACATTTAATCAACATTTGGACAACATTTAATCAACAATTGGACAACATTCAATCAACAATT
G
Found at i:12900873 original size:2 final size:2
Alignment explanation
Indices: 12900866--12900897 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12900856 TAATCATACC
12900866 AT 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 AT
12900898 CTTTACATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12901594 original size:42 final size:42
Alignment explanation
Indices: 12901488--12901643 Score: 145
Period size: 43 Copynumber: 3.6 Consensus size: 42
12901478 TCATACAATA
* * * * * *
12901488 CCAACGTCCCAGACATGGTCTTTCATGTAATCAAACAACGATG
1 CCAATGTCCCAGACATGGTCTTACACGTAATCATA-AACTACG
* *
12901531 CCACTGTCCCAGACA-GAGTCTTACACGTAATCATATACTACG
1 CCAATGTCCCAGACATG-GTCTTACACGTAATCATAAACTACG
* * *
12901573 CCAATGTCCCAGATATGGTCTTACACGTAAATC-TCAAATTGAGG
1 CCAATGTCCCAGACATGGTCTTACACGT-AATCAT-AAACT-ACG
*
12901617 CCAATGTCCCAGACGTGGTCTTACACG
1 CCAATGTCCCAGACATGGTCTTACACG
12901644 ATGTCACATT
Statistics
Matches: 93, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 30 0.32
43 36 0.39
44 27 0.29
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
CCAATGTCCCAGACATGGTCTTACACGTAATCATAAACTACG
Found at i:12904405 original size:28 final size:28
Alignment explanation
Indices: 12904373--12904445 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
12904363 ATAAGATTTA
*
12904373 ATATTAAATTTAATCTAATATTAAATTG
1 ATATTAAATTTAATATAATATTAAATTG
* * *
12904401 ATATTAGATTAAATTTAATATTAAATTG
1 ATATTAAATTTAATATAATATTAAATTG
12904429 --ATTAAATTTAATATAAT
1 ATATTAAATTTAATATAAT
12904446 TGAACTCTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 14 0.36
28 25 0.64
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (28 bp):
ATATTAAATTTAATATAATATTAAATTG
Found at i:12909022 original size:23 final size:22
Alignment explanation
Indices: 12908969--12909057 Score: 106
Period size: 23 Copynumber: 3.7 Consensus size: 22
12908959 GAGCCATGAT
12908969 CGGTAAGCTCATTCCGAGCTGATAAA
1 CGGTAAGCTCA-T-CGAGCTG--AAA
12908995 CGGTAAGCTCTATCGAGCTGAAA
1 CGGTAAGCTC-ATCGAGCTGAAA
*
12909018 CGGTAAGCTCCATAGAGCTGAAA
1 CGGTAAGCT-CATCGAGCTGAAA
12909041 CGGTAAGCTCATACGAG
1 CGGTAAGCTCAT-CGAG
12909058 TTGTGGTGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
22 3 0.05
23 35 0.60
24 1 0.02
25 7 0.12
26 11 0.19
27 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.20
Consensus pattern (22 bp):
CGGTAAGCTCATCGAGCTGAAA
Found at i:12912716 original size:41 final size:41
Alignment explanation
Indices: 12912477--12912717 Score: 299
Period size: 41 Copynumber: 5.9 Consensus size: 41
12912467 TTGTATAAAA
* * * * * *
12912477 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATAT-ATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATT
* * * *
12912517 CCACCGGCA-CAAAGCCTGCTAGACATAAGGTCTGATACATTT
1 -CACCGGCATC-AAGCCTGCTAGACATAAAGTCTGAAATAATT
*
12912559 CACCGGCA-CTAAGCCTGCTAGACATAAAGTCTGAAGTAATT
1 CACCGGCATC-AAGCCTGCTAGACATAAAGTCTGAAATAATT
* *
12912600 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAGTAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATT
*
12912641 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATT
*
12912682 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAA
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAA
12912718 CATCTTATTT
Statistics
Matches: 181, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 178 0.98
42 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (41 bp):
CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATT
Found at i:12913389 original size:16 final size:17
Alignment explanation
Indices: 12913368--12913402 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12913358 ATCTAATAAT
12913368 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
12913384 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
12913401 TT
1 TT
12913403 CGACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:12917292 original size:24 final size:25
Alignment explanation
Indices: 12917255--12917307 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
12917245 TCTTTTTGCA
*
12917255 TTCATTCCATTCATCTGCATTACAT
1 TTCATTCCATTCATCTGCATTAAAT
* * *
12917280 TTCATTGCA-TCATTTGTATTAAAT
1 TTCATTCCATTCATCTGCATTAAAT
12917304 TTCA
1 TTCA
12917308 CGAAAGAGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (25 bp):
TTCATTCCATTCATCTGCATTAAAT
Found at i:12920451 original size:9 final size:9
Alignment explanation
Indices: 12920437--12920492 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
12920427 ACAAAAATAA
12920437 AAGAAAAAG
1 AAGAAAAAG
*
12920446 AAGAAAAAA
1 AAGAAAAAG
*
12920455 AAGAAAAAAAT
1 AAG--AAAAAG
12920466 AAGAAAAAG
1 AAGAAAAAG
12920475 AAG-AAAA-
1 AAGAAAAAG
12920482 AAGAAAAAG
1 AAGAAAAAG
12920491 AA
1 AA
12920493 ATAAAAGGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 3 0.08
8 8 0.20
9 21 0.52
11 8 0.20
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:12920463 original size:20 final size:20
Alignment explanation
Indices: 12920440--12920483 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
12920430 AAAATAAAAG
12920440 AAAAAGAAGAAAAAAAAGAA
1 AAAAAGAAGAAAAAAAAGAA
* *
12920460 AAAAATAAGAAAAAGAAGAA
1 AAAAAGAAGAAAAAAAAGAA
12920480 AAAA
1 AAAA
12920484 GAAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAGAAGAAAAAAAAGAA
Found at i:12920471 original size:29 final size:29
Alignment explanation
Indices: 12920429--12920496 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
12920419 AATATTCTAC
*
12920429 AAAAATAA-AAGAAAAAGAAGAAAAAA-A
1 AAAAAAAATAAGAAAAAGAAGAAAAAAGA
12920456 AGAAAAAAATAAGAAAAAGAAGAAAAAAGA
1 A-AAAAAAATAAGAAAAAGAAGAAAAAAGA
*
12920486 AAAAGAAATAA
1 AAAAAAAATAA
12920497 AAGGAGAGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 1 0.03
28 6 0.17
29 27 0.75
30 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (29 bp):
AAAAAAAATAAGAAAAAGAAGAAAAAAGA
Found at i:12920472 original size:16 final size:16
Alignment explanation
Indices: 12920435--12920498 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 16
12920425 CTACAAAAAT
*
12920435 AAAAGAAAAAGAAGAAAA
1 AAAAGAAAAA-AA-AAGA
12920453 AAAAGAAAAAAATAAGA
1 AAAAGAAAAAAA-AAGA
*
12920470 AAAAGAAGAAAAAAGA
1 AAAAGAAAAAAAAAGA
12920486 AAAAGAAATAAAA
1 AAAAGAAA-AAAA
12920499 GGAGAGGCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
16 11 0.27
17 20 0.49
18 10 0.24
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAAAAGA
Found at i:12920498 original size:9 final size:8
Alignment explanation
Indices: 12920435--12920499 Score: 60
Period size: 9 Copynumber: 7.6 Consensus size: 8
12920425 CTACAAAAAT
12920435 AAAAGAAA
1 AAAAGAAA
12920443 AAGAAGAAAA
1 AA-AAG-AAA
12920453 AAAAGAAA
1 AAAAGAAA
*
12920461 AAAATAAGA
1 AAAAGAA-A
12920470 AAAAGAAGA
1 AAAAGAA-A
*
12920479 AAAA-AGA
1 AAAAGAAA
12920486 AAAAGAAA
1 AAAAGAAA
12920494 TAAAAG
1 -AAAAG
12920500 GAGAGGCTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
7 5 0.10
8 14 0.29
9 24 0.50
10 5 0.10
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAAAGAAA
Found at i:12921439 original size:50 final size:50
Alignment explanation
Indices: 12921383--12922385 Score: 603
Period size: 50 Copynumber: 20.2 Consensus size: 50
12921373 GCAGTTAAAA
* *
12921383 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTAGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* **** * * * ** * * ** *
12921433 AAATTGAAGCTACAATTATGAATCTTGCTCCCCCGATATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * *
12921483 AGATTGAAGCTACAACAGTGAATTTTACTTCCCTGGCGGTGCAGT-GAAGC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAA-C
* * * * * ** *
12921533 AGATTGAAACTACAACGGCGAATCTTGCTTCGCC-GAC-TTGGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTC-CCTGGCAGT-GCAGTGGAAC
* * * * *
12921583 AGATTGAAGCCACAACTGTGAATCTTACTTCCCTGGC-GATACAGTGGAGC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAG-TGCAGTGGAAC
* * * * * * * * ** *
12921633 AGTTTAAAGCTACAACGGCTAATCTTACTTCCCCGACATTACAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* ** * *
12921683 AGATTGAAGCTACAACAGTAAATCTTACTTCTCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* *** * * * * * ** *
12921733 AGATTGAAGCTATAACAATGAATCTTGCTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * ** *
12921783 AGATTGAAGCCACAACGACGAATCTTACTTCTCTGGTGGTGCAGTGGAGC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
** ** * * ** *
12921833 AGATTGAAGCTACAACGGATAATCTTGTTTTCCC-GACATTGCAGTTAAAA
1 AGATTGAAGCTACAACGGCGAATCTT-ACTTCCCTGGCAGTGCAGTGGAAC
* * * *
12921883 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTACAGTGGAAT
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * * ** *
12921933 AGATTGAAGCTACAACGGTGAATATTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * *
12921983 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAGC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * *
12922033 AGATTGAAGCCACAACGGCGAATCTTACTTCTCAGGCGGTGCAGTGGAAT
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * *
12922083 AGATTGAAACTACAACGGCGAATCTTGCTTCCC---C-G-ACA-TTG--T
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * *
12922125 A-ATTAAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* ** ** * * * * ** *
12922174 AGATTAAAGCTACAACAACGAATCTTGTTTCCCCGACATTACAGTTAAAT
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * * * *
12922224 AGATTAAAGCTACTACGACAAATCTTACTTCCCTGGCGGTGTAGTGGAAT
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * ** * * * ** *
12922274 AGATTGAAGCTACGACGGTGAATCTTGTTTCCCCGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
** * *
12922324 AGATTGAAGCTACAACAACGAATCTTACTTCCCTGGCGGTACAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* *
12922374 ATATTAAAGCTA
1 AGATTGAAGCTA
12922386 TAAATTACTG
Statistics
Matches: 699, Mismatches: 236, Indels: 36
0.72 0.24 0.04
Matches are distributed among these distances:
41 26 0.04
42 2 0.00
44 3 0.00
45 3 0.00
46 3 0.00
47 3 0.00
49 11 0.02
50 639 0.91
51 9 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
Found at i:12922106 original size:100 final size:100
Alignment explanation
Indices: 12921371--12922115 Score: 846
Period size: 100 Copynumber: 7.5 Consensus size: 100
12921361 ACCCCTAAGG
* * *
12921371 TTGCAGTTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTAGCGGTGCAGTGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
**** * * *
12921436 TTGAAGCTACAATTATGAATCTTGCTCCCCCGATA
66 TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * *
12921471 TTGCAATTAAAAAGATTGAAGCTACAACAGTGAATTTTACTTCCCTGGCGGTGCAGT-GAAGCAG
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAA-CAG
* * *
12921535 ATTGAAACTACAACGGCGAATCTTGCTTCGCCGAC-
65 ATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * * *
12921570 TTGGCAATTAAAAAGATTGAAGCCACAACTGTGAATCTTACTTCCCTGGCGATACAGTGGAGCAG
1 TT-GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAG
* * *
12921635 TTTAAAGCTACAACGGCTAATCTTACTTCCCCGACA
65 ATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * ** *
12921671 TTACAATTAAAAAGATTGAAGCTACAACAGTAAATCTTACTTCTCTGGCGGTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* *** *
12921736 TTGAAGCTATAACAATGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * *
12921771 TTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCTCTGGTGGTGCAGTGGAGCAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
** ** *
12921836 TTGAAGCTACAACGGATAATCTTGTTTTCCCGACA
66 TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * *
12921871 TTGCAGTTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTACAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* * *
12921936 TTGAAGCTACAACGGTGAATATTACTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * *
12921971 TTGCAATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAGCAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* * * * *
12922036 TTGAAGCCACAACGGCGAATCTTACTTCTCAGGCG
66 TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * ** * * *
12922071 GTGCAGTGGAATAGATTGAAACTACAACGGCGAATCTTGCTTCCC
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCC
12922116 CGACATTGTA
Statistics
Matches: 544, Mismatches: 97, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
99 5 0.01
100 535 0.98
101 4 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
TTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
Found at i:12922196 original size:91 final size:91
Alignment explanation
Indices: 12922039--12922213 Score: 262
Period size: 91 Copynumber: 1.9 Consensus size: 91
12922029 GAGCAGATTG
* * * **
12922039 AAGCCACAACGGCGAATCTTACTTCTCAGGCGGTGCAGTGGAATAGATTGAAACTACAACGGCGA
1 AAGCCACAACGGCGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGATTGAAACTACAACAACGA
12922104 ATCTTGCTTCCCCGACATTGTAATTA
66 ATCTTGCTTCCCCGACATTGTAATTA
* *
12922130 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATT-AAAGCTACAACAACG
1 AAGCCACAACGGCGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGATTGAAA-CTACAACAACG
*
12922194 AATCTTGTTTCCCCGACATT
65 AATCTTGCTTCCCCGACATT
12922214 ACAGTTAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
90 3 0.04
91 72 0.96
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (91 bp):
AAGCCACAACGGCGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGATTGAAACTACAACAACGA
ATCTTGCTTCCCCGACATTGTAATTA
Found at i:12922248 original size:141 final size:141
Alignment explanation
Indices: 12921989--12922256 Score: 349
Period size: 141 Copynumber: 1.9 Consensus size: 141
12921979 AAAAAGATTG
* * **
12921989 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAGCAGATTGAAGCCACAACGGCGA
1 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACAACGA
* * * * * * * *
12922054 ATCTTACTTCTCAGGCGGTGCAGTGGAATAGATTGAAACTACAACGGCGAATCTTGCTTCCCCGA
66 ATCTTACTTCCCAGACAGTACAGTGAAATAGATTGAAACTACAACGACAAATCTTACTTCCCCGA
12922119 CATTGTAATTA
131 CATTGTAATTA
*
12922130 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAACGA
1 AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACAACGA
** * * * *
12922195 ATCTTGTTTCCCCGACATTACAGTTAAATAGATT-AAAGCTACTACGACAAATCTTACTTCCC
66 ATCTTACTTCCCAGACAGTACAGTGAAATAGATTGAAA-CTACAACGACAAATCTTACTTCCC
12922257 TGGCGGTGTA
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
140 3 0.03
141 104 0.97
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (141 bp):
AAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACAACGA
ATCTTACTTCCCAGACAGTACAGTGAAATAGATTGAAACTACAACGACAAATCTTACTTCCCCGA
CATTGTAATTA
Found at i:12922327 original size:241 final size:241
Alignment explanation
Indices: 12921902--12922356 Score: 550
Period size: 241 Copynumber: 1.9 Consensus size: 241
12921892 CTACAACAGC
* * * *** *
12921902 GAATCTTACTTCCCTGGCGGTACAGTGGAATAGATTGAAGCTACAACGGTGAATATTACTTCCCT
1 GAATCTTACTTCCCTGGCAGTACAGTGGAACAGATTAAAGCTACAACAACGAATATTACTTCCCC
* * *** *
12921967 GACATTGCAATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAG
66 GACATTACAATTAAAAAGATTAAAGCCACAACGACAAATCTTACTTCCCTGGCAGTGCAGTGGAA
* * * *
12922032 CAGATTGAAGCCACAACGGCGAATCTTACTTCTCAGGCGGTGCAGTGGAATAGATTGAAACTACA
131 CAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACAGTGCAGTGAAATAGATTGAAACTACA
** *
12922097 ACGGCGAATCTTGCTTCCCCGACATTGTAATTAAAGCCACAACGGT
196 ACAACGAATCTTACTTCCCCGACATTGTAATTAAAGCCACAACGGT
* * **
12922143 GAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAACGAATCTTGTTTCCCC
1 GAATCTTACTTCCCTGGCAGTACAGTGGAACAGATTAAAGCTACAACAACGAATATTACTTCCCC
* * * * * *
12922208 GACATTACAGTTAAATAGATTAAAGCTACTACGACAAATCTTACTTCCCTGGCGGTGTAGTGGAA
66 GACATTACAATTAAAAAGATTAAAGCCACAACGACAAATCTTACTTCCCTGGCAGTGCAGTGGAA
* * * * ** * * * *
12922273 TAGATTGAAGCTACGACGGTGAATCTTGTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACA
131 CAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACAGTGCAGTGAAATAGATTGAAACTACA
12922338 ACAACGAATCTTACTTCCC
196 ACAACGAATCTTACTTCCC
12922357 TGGCGGTACA
Statistics
Matches: 174, Mismatches: 40, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
241 174 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (241 bp):
GAATCTTACTTCCCTGGCAGTACAGTGGAACAGATTAAAGCTACAACAACGAATATTACTTCCCC
GACATTACAATTAAAAAGATTAAAGCCACAACGACAAATCTTACTTCCCTGGCAGTGCAGTGGAA
CAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACAGTGCAGTGAAATAGATTGAAACTACA
ACAACGAATCTTACTTCCCCGACATTGTAATTAAAGCCACAACGGT
Found at i:12922541 original size:45 final size:44
Alignment explanation
Indices: 12922484--12922601 Score: 130
Period size: 45 Copynumber: 2.7 Consensus size: 44
12922474 ATTTGAAATA
*
12922484 ACAAACCTTATCTCTCTGAAGTTGCAGTGAAGCAGGTTAAAGAT
1 ACAAATCTTATCTCTCTGAAGTTGCAGTGAAGCAGGTTAAAGAT
* * * * *
12922528 ACCCAATCTTATCTC-CTTGAAGTTGCTGTGAAGCAGATTGAAGCT
1 A-CAAATCTTATCTCTC-TGAAGTTGCAGTGAAGCAGGTTAAAGAT
* * *
12922573 ACTAATCATATCTCCCTGAAGTTGCAGTG
1 ACAAATCTTATCTCTCTGAAGTTGCAGTG
12922602 GAGCGGATTA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
44 25 0.40
45 37 0.60
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
ACAAATCTTATCTCTCTGAAGTTGCAGTGAAGCAGGTTAAAGAT
Found at i:12931121 original size:25 final size:25
Alignment explanation
Indices: 12931080--12931136 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
12931070 ACAATCCATG
** * *
12931080 TAAATCATGTATCTCATGTAACTTT
1 TAAATCATGTAAATCATATAACATT
12931105 TAAATCATGTAAATCATATAACATT
1 TAAATCATGTAAATCATATAACATT
*
12931130 TATATCA
1 TAAATCA
12931137 ATTCTTTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACATT
Found at i:12931233 original size:20 final size:20
Alignment explanation
Indices: 12931185--12931234 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
12931175 TAACAAAAAT
*
12931185 TTATCCGTATCAACCGTAAA
1 TTATCCATATCAACCGTAAA
* *
12931205 TTATACATATCAACGGT-AA
1 TTATCCATATCAACCGTAAA
12931224 TTCATCCATAT
1 TT-ATCCATAT
12931235 AATTACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (20 bp):
TTATCCATATCAACCGTAAA
Found at i:12931439 original size:23 final size:23
Alignment explanation
Indices: 12931406--12931474 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
12931396 CCGAGTTGAT
*
12931406 AAACGGTAAGCTCTATCA-AGCTG
1 AAACGGTAAGCTCCAT-AGAGCTG
*
12931429 AAACGGAAAGCTCCATAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
12931452 AAACGGTAAGCT-CATATGAGCTG
1 AAACGGTAAGCTCCATA-GAGCTG
12931475 TGGTGAGTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
22 5 0.12
23 36 0.88
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:12933779 original size:15 final size:15
Alignment explanation
Indices: 12933759--12933787 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12933749 TGCTTTCATA
12933759 CACAACCATCAATTC
1 CACAACCATCAATTC
12933774 CACAACCATCAATT
1 CACAACCATCAATT
12933788 ATAATATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (15 bp):
CACAACCATCAATTC
Found at i:12938776 original size:22 final size:22
Alignment explanation
Indices: 12938751--12938800 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
12938741 CCTAATCAAC
* *
12938751 TTAAATAATTGGGTTAGTACT-
1 TTAAATAATTGGATCAGTACTG
*
12938772 TTTAATAATTGGATCAGTACTG
1 TTAAATAATTGGATCAGTACTG
12938794 TTAAATA
1 TTAAATA
12938801 GAAAAGGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (22 bp):
TTAAATAATTGGATCAGTACTG
Found at i:12939600 original size:10 final size:10
Alignment explanation
Indices: 12939585--12939627 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
12939575 ATAACTTTAT
12939585 TTAAATATAA
1 TTAAATATAA
12939595 TTAAATAATAA
1 TTAAAT-ATAA
*
12939606 TTAATTATAA
1 TTAAATATAA
*
12939616 ATAAATACTAA
1 TTAAATA-TAA
12939627 T
1 T
12939628 AACTCTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 15 0.56
11 12 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAATATAA
Found at i:12939614 original size:21 final size:21
Alignment explanation
Indices: 12939585--12939627 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12939575 ATAACTTTAT
*
12939585 TTAAATATAATTAAATAATAA
1 TTAAATATAAATAAATAATAA
* *
12939606 TTAATTATAAATAAATACTAA
1 TTAAATATAAATAAATAATAA
12939627 T
1 T
12939628 AACTCTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATATAAATAAATAATAA
Found at i:12940543 original size:24 final size:24
Alignment explanation
Indices: 12940507--12940555 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
12940497 AATTTTTCAA
*
12940507 ATTTAATCTTTAAATTATT-ATTT
1 ATTTAATATTTAAATTATTAATTT
12940530 ATTTAGATATTTAAATTATTAATTT
1 ATTTA-ATATTTAAATTATTAATTT
12940555 A
1 A
12940556 GTCTCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
24 13 0.57
25 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTAATATTTAAATTATTAATTT
Found at i:12946384 original size:9 final size:9
Alignment explanation
Indices: 12946370--12946410 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
12946360 TTTCGAATTT
12946370 GAATAACTC
1 GAATAACTC
* *
12946379 GAATAATTT
1 GAATAACTC
12946388 GAATAACTC
1 GAATAACTC
*
12946397 GAATAATTC
1 GAATAACTC
12946406 GAATA
1 GAATA
12946411 TCAAACTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (9 bp):
GAATAACTC
Found at i:12946388 original size:18 final size:18
Alignment explanation
Indices: 12946365--12946410 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
12946355 TGAGTTTTCG
12946365 AATTTGAATAACTCGAAT
1 AATTTGAATAACTCGAAT
12946383 AATTTGAATAACTCGAAT
1 AATTTGAATAACTCGAAT
*
12946401 AATTCGAATA
1 AATTTGAATA
12946411 TCAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
AATTTGAATAACTCGAAT
Found at i:12947789 original size:2 final size:2
Alignment explanation
Indices: 12947784--12947862 Score: 65
Period size: 2 Copynumber: 40.5 Consensus size: 2
12947774 ACACACACAC
* * *
12947784 AT AT AT AT AT AT AT AT AT AT AT AT AC AT TT GT ACT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
12947825 AT AT TT CT -T AA AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12947863 AGGTACCATT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
1 3 0.05
2 58 0.94
3 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12949046 original size:2 final size:2
Alignment explanation
Indices: 12949039--12949073 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12949029 CAAATTATGC
12949039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12949074 ACCATAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12949388 original size:43 final size:43
Alignment explanation
Indices: 12949327--12949421 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 43
12949317 TTCTAGATAG
* *
12949327 GGTCTTACTTGAAAATACAAGTCGATGCCATCGTCCCAGACGT
1 GGTCTTACATGAAAATACAAGTCGATGCCATCGTCACAGACGT
* *
12949370 GGTCTTACATGAAAATACAAGTTGATGTCATCGTCACAGACGT
1 GGTCTTACATGAAAATACAAGTCGATGCCATCGTCACAGACGT
12949413 GGTCTTACA
1 GGTCTTACA
12949422 CAAAAACACT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (43 bp):
GGTCTTACATGAAAATACAAGTCGATGCCATCGTCACAGACGT
Found at i:12953536 original size:6 final size:6
Alignment explanation
Indices: 12953527--12953558 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12953517 TTCTAGAAAA
*
12953527 CTCTCC CTCTCC CTCTCA CTCTCC CTCTCC CT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CT
12953559 ATACCTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.62, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:12954250 original size:18 final size:19
Alignment explanation
Indices: 12954214--12954251 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12954204 GAAAAAAAGG
*
12954214 AAAGAAAAGTAGAAGGAAA
1 AAAGAAAACTAGAAGGAAA
12954233 AAAGAAAACTAG-AGGAAA
1 AAAGAAAACTAGAAGGAAA
12954251 A
1 A
12954252 GGCTCCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.03, G:0.24, T:0.05
Consensus pattern (19 bp):
AAAGAAAACTAGAAGGAAA
Found at i:12956490 original size:18 final size:18
Alignment explanation
Indices: 12956467--12956509 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
12956457 CCCTCATCAT
*
12956467 CTAAGGGGAAATAGAAAG
1 CTAAGGGGAAATAGAAAA
12956485 CTAAGGGGAAATAGAAAA
1 CTAAGGGGAAATAGAAAA
12956503 CTAAGGG
1 CTAAGGG
12956510 AAAGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.07, G:0.33, T:0.12
Consensus pattern (18 bp):
CTAAGGGGAAATAGAAAA
Found at i:12956519 original size:17 final size:18
Alignment explanation
Indices: 12956467--12956521 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
12956457 CCCTCATCAT
* * *
12956467 CTAAGGGGAAATAGAAAG
1 CTAAGGGGAAAGAAAAAA
* *
12956485 CTAAGGGGAAATAGAAAA
1 CTAAGGGGAAAGAAAAAA
12956503 CTAA-GGGAAAGAAAAAA
1 CTAAGGGGAAAGAAAAAA
12956520 CT
1 CT
12956522 GACTAAGTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.55, C:0.07, G:0.27, T:0.11
Consensus pattern (18 bp):
CTAAGGGGAAAGAAAAAA
Found at i:12965546 original size:27 final size:26
Alignment explanation
Indices: 12965509--12965603 Score: 118
Period size: 27 Copynumber: 3.6 Consensus size: 26
12965499 ACTTACGACC
* *
12965509 GAAGGGCAAAATAACCGAAATACCCT
1 GAAGGGTAAAATGACCGAAATACCCT
*
12965535 CGAAGGGTAAAATGACCGATATACCCT
1 -GAAGGGTAAAATGACCGAAATACCCT
* *
12965562 AAAGGATAAAATGACCGAAATACCCT
1 GAAGGGTAAAATGACCGAAATACCCT
*
12965588 TATAGGGTAAAATGAC
1 GA-AGGGTAAAATGAC
12965604 TGTTATACCC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 24 0.41
27 35 0.59
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (26 bp):
GAAGGGTAAAATGACCGAAATACCCT
Found at i:12965820 original size:26 final size:26
Alignment explanation
Indices: 12965791--12965845 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12965781 TTTGCCACAT
*
12965791 ATACTGTTACTGGCACCTTCGCTGCG
1 ATACTGTTACTAGCACCTTCGCTGCG
* * * *
12965817 ATACTTTTACTAGCAGCTTTGCTGGG
1 ATACTGTTACTAGCACCTTCGCTGCG
12965843 ATA
1 ATA
12965846 TTGGTGTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTAGCACCTTCGCTGCG
Found at i:12965982 original size:28 final size:28
Alignment explanation
Indices: 12965940--12966031 Score: 130
Period size: 28 Copynumber: 3.3 Consensus size: 28
12965930 GTTACATTAT
* *
12965940 CACACTGTTATTGTATCAGGCTAAGGTC
1 CACACTGTTACTGTATCGGGCTAAGGTC
* *
12965968 CACACTGTTACTGTATTGGGCTAAGGCC
1 CACACTGTTACTGTATCGGGCTAAGGTC
* *
12965996 CACACTATTACTATATCGGGCTAAGGTC
1 CACACTGTTACTGTATCGGGCTAAGGTC
12966024 CACACTGT
1 CACACTGT
12966032 ACTATTATTG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (28 bp):
CACACTGTTACTGTATCGGGCTAAGGTC
Found at i:12969260 original size:19 final size:20
Alignment explanation
Indices: 12969221--12969260 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12969211 TAAATTGGGC
*
12969221 CCAAGAGCCCAAAACTGAGA
1 CCAAGAGCCCAAAAATGAGA
*
12969241 CCAAGA-CCCAAAAATTAGA
1 CCAAGAGCCCAAAAATGAGA
12969260 C
1 C
12969261 AAACCAAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.47, C:0.30, G:0.15, T:0.07
Consensus pattern (20 bp):
CCAAGAGCCCAAAAATGAGA
Found at i:12970811 original size:16 final size:16
Alignment explanation
Indices: 12970774--12970813 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12970764 TTAATCAAAT
* *
12970774 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
12970790 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
12970806 TAAAATTA
1 TAAAATTA
12970814 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:12970841 original size:16 final size:16
Alignment explanation
Indices: 12970820--12970861 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
12970810 ATTATCAAAT
12970820 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
12970836 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
*
12970852 AATTAATTGT
1 TATTAATTGT
12970862 ATTAATTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (16 bp):
TATTAATTGTTAATTG
Found at i:12970843 original size:9 final size:9
Alignment explanation
Indices: 12970820--12970870 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
12970810 ATTATCAAAT
12970820 TATTAATTG
1 TATTAATTG
12970829 --TTAATTG
1 TATTAATTG
12970836 TATTAATTG
1 TATTAATTG
12970845 --TTAATTG
1 TATTAATTG
*
12970852 AATTAATTG
1 TATTAATTG
12970861 TATTAATTG
1 TATTAATTG
12970870 T
1 T
12970871 TGTAACAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
7 14 0.38
9 23 0.62
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (9 bp):
TATTAATTG
Found at i:12970863 original size:25 final size:25
Alignment explanation
Indices: 12970822--12970871 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
12970812 TATCAAATTA
12970822 TTAATTG-TTAATTGTATTAATTG-
1 TTAATTGATTAATTGTATTAATTGT
12970845 TTAATTGAATTAATTGTATTAATTGT
1 TTAATTG-ATTAATTGTATTAATTGT
12970871 T
1 T
12970872 GTAACAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.29
25 16 0.67
26 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (25 bp):
TTAATTGATTAATTGTATTAATTGT
Found at i:12970933 original size:68 final size:68
Alignment explanation
Indices: 12970858--12970993 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
12970848 ATTGAATTAA
*
12970858 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAATAAACTTGATGTTTTATTATT
1 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTATT
12970923 ATT
66 ATT
12970926 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTATT
1 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTATT
12970991 ATT
66 ATT
12970994 ATTTTATTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (68 bp):
TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAACAAACTTGATGTTTTATTATT
ATT
Found at i:12971000 original size:14 final size:14
Alignment explanation
Indices: 12970981--12971011 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12970971 AAACTTGATG
12970981 TTTTATTATTATTA
1 TTTTATTATTATTA
*
12970995 TTTTATTTTTATTA
1 TTTTATTATTATTA
12971009 TTT
1 TTT
12971012 AGTAACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:12971272 original size:54 final size:54
Alignment explanation
Indices: 12971207--12971356 Score: 142
Period size: 65 Copynumber: 2.6 Consensus size: 54
12971197 CAAATAAAAA
*
12971207 AAACTTAAAATAAAAAACAATTATAATTTAAAAATAAGGAAATGAAAGTAAATG
1 AAACTTTAAATAAAAAACAATTATAATTTAAAAATAAGGAAATGAAAGTAAATG
***
12971261 AAACTTTAAATAAAAAACTATTAGTTGGATAAATTAGTTGGCCAATAAGGAAATGAAAGTAAATG
1 AAACTTTAAATAAAAAAC-A--A-TT--AT-AA-T--TT-AAAAATAAGGAAATGAAAGTAAATG
*
12971326 AAAC-TTAAATAAAAAACTATTAT-ATTTAAAA
1 AAACTTTAAATAAAAAACAATTATAATTTAAAA
12971357 TATATATATT
Statistics
Matches: 77, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
52 1 0.01
53 2 0.03
54 17 0.22
55 2 0.03
56 1 0.01
57 1 0.01
58 4 0.05
60 4 0.05
61 3 0.04
62 1 0.01
64 15 0.19
65 26 0.34
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.27
Consensus pattern (54 bp):
AAACTTTAAATAAAAAACAATTATAATTTAAAAATAAGGAAATGAAAGTAAATG
Found at i:12978718 original size:29 final size:30
Alignment explanation
Indices: 12978654--12978724 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 30
12978644 AAATTTTTTA
* *
12978654 AATAATTTATTT-AATTAATAATAAAAATT
1 AATATTTTATTTAAATTAATAATAAAAAGT
* *
12978683 AAT-TTTTATTTAAATT-ATAGTAAATAGT
1 AATATTTTATTTAAATTAATAATAAAAAGT
*
12978711 AATATTTTCTTTAA
1 AATATTTTATTTAA
12978725 TTTTTGTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 19 0.54
29 16 0.46
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (30 bp):
AATATTTTATTTAAATTAATAATAAAAAGT
Found at i:12984312 original size:41 final size:41
Alignment explanation
Indices: 12984247--12984416 Score: 157
Period size: 41 Copynumber: 4.2 Consensus size: 41
12984237 CTATCTTTCA
* *
12984247 GGCTTTAGCGGCG-TTTTTAAAAAGCGTCGCTAATGCTCAG
1 GGCTTTAGCGACGCTTTTTAGAAAGCGTCGCTAATGCTCAG
* *
12984287 TGCTTTAGCGACGCTTTTTAGAAAGCGTCGCGAATGCTCAG
1 GGCTTTAGCGACGCTTTTTAGAAAGCGTCGCTAATGCTCAG
* * * *
12984328 GGTTTTATC-A-GCATTTTTGAGAAAGTGCCGCTAATGCTCAG
1 GGCTTTAGCGACGC-TTTTT-AGAAAGCGTCGCTAATGCTCAG
* ** * * * *
12984369 GGCTTTAGCGGCATTTTTTATAAAGCGCCTCGAATGCTCAG
1 GGCTTTAGCGACGCTTTTTAGAAAGCGTCGCTAATGCTCAG
*
12984410 GGATTTA
1 GGCTTTA
12984417 AAATAATTTA
Statistics
Matches: 105, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 17 0.16
41 81 0.77
42 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (41 bp):
GGCTTTAGCGACGCTTTTTAGAAAGCGTCGCTAATGCTCAG
Found at i:12984602 original size:7 final size:7
Alignment explanation
Indices: 12984590--12984773 Score: 52
Period size: 7 Copynumber: 25.7 Consensus size: 7
12984580 TATCACTATA
12984590 GTTTAGG
1 GTTTAGG
12984597 GTTTAGG
1 GTTTAGG
* *
12984604 GTATATG
1 GTTTAGG
*
12984611 GTTTAGA
1 GTTTAGG
12984618 GTTTAAGG
1 GTTT-AGG
12984626 G-TTA-G
1 GTTTAGG
**
12984631 GTGTTACCA
1 GT-TTA-GG
* *
12984640 TTTTAAG
1 GTTTAGG
*
12984647 GTTTATG
1 GTTTAGG
*
12984654 GATTATGG
1 GTTTA-GG
12984662 GTTTAGG
1 GTTTAGG
* *
12984669 GATTATG
1 GTTTAGG
*
12984676 GTTTATG
1 GTTTAGG
**
12984683 GTTTAAA
1 GTTTAGG
** *
12984690 GACTGGG
1 GTTTAGG
*
12984697 GTTTAAG
1 GTTTAGG
12984704 GTTTAGAG
1 GTTTAG-G
*
12984712 G-TTATGT
1 GTTTA-GG
*
12984719 GTTAAGG
1 GTTTAGG
12984726 GTTTATGG
1 GTTTA-GG
*
12984734 TTTTAGG
1 GTTTAGG
*
12984741 GTTTTAAG
1 G-TTTAGG
12984749 GTTTA-G
1 GTTTAGG
* *
12984755 ATTTATG
1 GTTTAGG
12984762 GTTTAGG
1 GTTTAGG
12984769 GTTTA
1 GTTTA
12984774 AATTAACTAG
Statistics
Matches: 125, Mismatches: 40, Indels: 24
0.66 0.21 0.13
Matches are distributed among these distances:
5 2 0.02
6 6 0.05
7 88 0.70
8 28 0.22
9 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:12984666 original size:15 final size:14
Alignment explanation
Indices: 12984646--12984683 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
12984636 ACCATTTTAA
12984646 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
12984660 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
12984675 GGTTTATGG
1 GGTTTATGG
12984684 TTTAAAGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:12984666 original size:22 final size:21
Alignment explanation
Indices: 12984641--12984688 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
12984631 GTGTTACCAT
*
12984641 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
* *
12984663 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
12984684 TTTAA
1 TTTAA
12984689 AGACTGGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:12984999 original size:7 final size:7
Alignment explanation
Indices: 12984976--12985009 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
12984966 AATAATTATA
12984976 TATGGATT
1 TATGGA-T
*
12984984 TAGGGAT
1 TATGGAT
12984991 TATGGAT
1 TATGGAT
12984998 TATGGAT
1 TATGGAT
12985005 TATGG
1 TATGG
12985010 TTTTAGGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.41
Consensus pattern (7 bp):
TATGGAT
Found at i:12985006 original size:14 final size:15
Alignment explanation
Indices: 12984976--12985017 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
12984966 AATAATTATA
12984976 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
*
12984991 TATGGA-TTATGGAT
1 TATGGATTTAGGGAT
*
12985005 TATGGTTTTAGGG
1 TATGGATTTAGGG
12985018 TTGGGATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:12985039 original size:21 final size:21
Alignment explanation
Indices: 12985011--12985080 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
12985001 GGATTATGGT
* *
12985011 TTTA-GGGTTGGGATTTAAGG
1 TTTAGGGGTTAGGAGTTAAGG
*
12985031 TTTAGGGGTTAGGAGTTAGGG
1 TTTAGGGGTTAGGAGTTAAGG
* *
12985052 GTTAGGGGTTAAGAGTTAAGG
1 TTTAGGGGTTAGGAGTTAAGG
12985073 ATTTAGGG
1 -TTTAGGG
12985081 ATTTAAGGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 4 0.10
21 31 0.76
22 6 0.15
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.34
Consensus pattern (21 bp):
TTTAGGGGTTAGGAGTTAAGG
Found at i:12985042 original size:7 final size:7
Alignment explanation
Indices: 12985032--12985062 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12985022 GATTTAAGGT
12985032 TTAGGGG
1 TTAGGGG
*
12985039 TTAGGAG
1 TTAGGGG
12985046 TTAGGGG
1 TTAGGGG
12985053 TTAGGGG
1 TTAGGGG
12985060 TTA
1 TTA
12985063 AGAGTTAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:12989795 original size:43 final size:43
Alignment explanation
Indices: 12989729--12989869 Score: 192
Period size: 43 Copynumber: 3.3 Consensus size: 43
12989719 TTTGCCAAAA
* * * *
12989729 TTAGTGGCGTTTGTTGGTAAAGCGCTGCTAAAGGTCATGTTTT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTTT
* ***
12989772 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGAACATGAGCT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTTT
**
12989815 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGTTTT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTTT
12989858 TTAGCGGCGTTT
1 TTAGCGGCGTTT
12989870 TTTCACATAA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTTT
Found at i:12992347 original size:28 final size:29
Alignment explanation
Indices: 12992308--12992374 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
12992298 TAATATATAT
* * *
12992308 TTTTATTATTTTATAAGATT-AAATTAAA
1 TTTTATTATTTTAAAAAATTAAAATAAAA
12992336 TTTTATCT-TTTTAAAAAATTAAAATAAAA
1 TTTTAT-TATTTTAAAAAATTAAAATAAAA
12992365 TTTTATTATT
1 TTTTATTATT
12992375 ACTAATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTTATTATTTTAAAAAATTAAAATAAAA
Found at i:12995419 original size:35 final size:35
Alignment explanation
Indices: 12995373--12995443 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
12995363 TATTACATTA
12995373 ATATATATTATTAGTACAATAGTATAGACGGATTG
1 ATATATATTATTAGTACAATAGTATAGACGGATTG
12995408 ATATATATTATTAGTACAATAGTATAGACGGATTG
1 ATATATATTATTAGTACAATAGTATAGACGGATTG
12995443 A
1 A
12995444 CAATTTGAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.37
Consensus pattern (35 bp):
ATATATATTATTAGTACAATAGTATAGACGGATTG
Found at i:12996688 original size:28 final size:28
Alignment explanation
Indices: 12996648--12996703 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
12996638 GTAATCATCT
12996648 CATCCAGAGTTACTAAATATATTTGAGA
1 CATCCAGAGTTACTAAATATATTTGAGA
12996676 CATCCAGAGTTACTAAATATATTTGAGA
1 CATCCAGAGTTACTAAATATATTTGAGA
12996704 TAGGGGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (28 bp):
CATCCAGAGTTACTAAATATATTTGAGA
Found at i:12998798 original size:29 final size:29
Alignment explanation
Indices: 12998766--12998833 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
12998756 ATTTAGTACA
*
12998766 TATACTTT-AATTTGATCAAATTTAATCTC
1 TATACTTTGAA-TTGATCAAATTTAATCCC
* *
12998795 TATACTCTTTGAATTGGTCAAGTTTAATCCC
1 TATA--CTTTGAATTGATCAAATTTAATCCC
12998826 TATACTTT
1 TATACTTT
12998834 TTAATTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 8 0.24
31 23 0.70
32 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.47
Consensus pattern (29 bp):
TATACTTTGAATTGATCAAATTTAATCCC
Found at i:12998822 original size:31 final size:30
Alignment explanation
Indices: 12998781--12998839 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
12998771 TTTAATTTGA
*
12998781 TCAAATTTAATCTCTATACTCTTTGAATTGG
1 TCAAATTTAATCCCTATACT-TTTGAATTGG
* *
12998812 TCAAGTTTAATCCCTATACTTTTTAATT
1 TCAAATTTAATCCCTATACTTTTGAATT
12998840 TTTAAAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (30 bp):
TCAAATTTAATCCCTATACTTTTGAATTGG
Found at i:13004486 original size:6 final size:6
Alignment explanation
Indices: 13004475--13004506 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
13004465 ATATAGACAA
13004475 GGGAGT GGGAGT GGGAGT GGGAGT GGGAGT GG
1 GGGAGT GGGAGT GGGAGT GGGAGT GGGAGT GG
13004507 AAAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.69, T:0.16
Consensus pattern (6 bp):
GGGAGT
Found at i:13021247 original size:20 final size:21
Alignment explanation
Indices: 13021222--13021264 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
13021212 CACATTAGTG
13021222 AACAAATATGAATAT-AAATA
1 AACAAATATGAATATGAAATA
**
13021242 AACAAATATTTATATGAAATA
1 AACAAATATGAATATGAAATA
13021263 AA
1 AA
13021265 ATAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (21 bp):
AACAAATATGAATATGAAATA
Found at i:13021273 original size:22 final size:20
Alignment explanation
Indices: 13021222--13021278 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
13021212 CACATTAGTG
**
13021222 AACAAATATGAATATAAATA
1 AACAAATATTTATATAAATA
13021242 AACAAATATTTATATGAAATAA
1 AACAAATATTTATAT-AAAT-A
*
13021264 AATAAATATTTATAT
1 AACAAATATTTATAT
13021279 TTAAAATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 13 0.41
21 4 0.12
22 15 0.47
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
AACAAATATTTATATAAATA
Found at i:13021726 original size:20 final size:20
Alignment explanation
Indices: 13021703--13021743 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
13021693 TTAAATCAAT
*
13021703 TTGATTAAAATCAAATAAAA
1 TTGATTAAAATAAAATAAAA
**
13021723 TTGATTGGAATAAAATAAAA
1 TTGATTAAAATAAAATAAAA
13021743 T
1 T
13021744 CAAATAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
TTGATTAAAATAAAATAAAA
Found at i:13021744 original size:30 final size:30
Alignment explanation
Indices: 13021708--13021775 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
13021698 TCAATTTGAT
*
13021708 TAAAATCAAATAAAATTGATTGGAATAAAA
1 TAAAATCAAATAAAATAGATTGGAATAAAA
*
13021738 TAAAATCAAATAAAATAGATTGGAATCAAA
1 TAAAATCAAATAAAATAGATTGGAATAAAA
13021768 TAAAATCA
1 TAAAATCA
13021776 GGATATATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.25
Consensus pattern (30 bp):
TAAAATCAAATAAAATAGATTGGAATAAAA
Found at i:13021754 original size:20 final size:20
Alignment explanation
Indices: 13021731--13021773 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
13021721 AATTGATTGG
13021731 AATAAAATAAAATCAAATAA
1 AATAAAATAAAATCAAATAA
* * **
13021751 AATAGATTGGAATCAAATAA
1 AATAAAATAAAATCAAATAA
13021771 AAT
1 AAT
13021774 CAGGATATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (20 bp):
AATAAAATAAAATCAAATAA
Found at i:13060208 original size:23 final size:23
Alignment explanation
Indices: 13060176--13060220 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13060166 CCGATTTGCT
*
13060176 CCCTCCGTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTG
*
13060199 CCCTCTGTTTATTTTCTTTTCT
1 CCCTCCGTTTATTTTCTTTTCT
13060221 TTTCTACCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.02, C:0.31, G:0.07, T:0.60
Consensus pattern (23 bp):
CCCTCCGTTTATTTTCTTTTCTG
Found at i:13060246 original size:38 final size:39
Alignment explanation
Indices: 13060199--13060272 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
13060189 TTCTTTTCTG
*
13060199 CCCTCTGTTTATTTTC-TTTTCTTTTCTACCGATTTGCT
1 CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTTGCT
* * *
13060237 CCCTTTGTTTCTTCTCATTTTCTTTTCTGCCGATTT
1 CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTT
13060273 CTGAGTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 13 0.42
39 18 0.58
ACGTcount: A:0.07, C:0.27, G:0.08, T:0.58
Consensus pattern (39 bp):
CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTTGCT
Found at i:13060948 original size:16 final size:16
Alignment explanation
Indices: 13060927--13060961 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
13060917 GCATTGGGCC
13060927 GTATTGGATTAGACGT
1 GTATTGGATTAGACGT
*
13060943 GTATTGGATTAGAGGT
1 GTATTGGATTAGACGT
13060959 GTA
1 GTA
13060962 ATAGCAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.34, T:0.37
Consensus pattern (16 bp):
GTATTGGATTAGACGT
Found at i:13061008 original size:16 final size:16
Alignment explanation
Indices: 13060987--13061022 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
13060977 TTTGGTTGAA
13060987 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
13061003 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
13061019 TGTA
1 TGTA
13061023 ATGCTAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:13061967 original size:23 final size:23
Alignment explanation
Indices: 13061941--13061985 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13061931 TCGGTAGAAA
*
13061941 AGAAAAGAAAATAAACAGAGGGC
1 AGAAAAGAAAAGAAACAGAGGGC
*
13061964 AGAAAAGAAAAGAAACGGAGGG
1 AGAAAAGAAAAGAAACAGAGGG
13061986 AGCAAATCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.07, G:0.31, T:0.02
Consensus pattern (23 bp):
AGAAAAGAAAAGAAACAGAGGGC
Found at i:13063514 original size:13 final size:13
Alignment explanation
Indices: 13063496--13063520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13063486 ATTTCATGAG
13063496 GTGAAAAGAAAAC
1 GTGAAAAGAAAAC
13063509 GTGAAAAGAAAA
1 GTGAAAAGAAAA
13063521 AGGAGGCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.24, T:0.08
Consensus pattern (13 bp):
GTGAAAAGAAAAC
Found at i:13065081 original size:32 final size:32
Alignment explanation
Indices: 13065040--13065105 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
13065030 TTTTCTTTGC
13065040 ATTGCAAGTTGTCTCTGGATTATGTATTAATT
1 ATTGCAAGTTGTCTCTGGATTATGTATTAATT
13065072 ATTGCAAGTTGTCTCTGGATTATGTATTAATT
1 ATTGCAAGTTGTCTCTGGATTATGTATTAATT
13065104 AT
1 AT
13065106 CATGCTTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (32 bp):
ATTGCAAGTTGTCTCTGGATTATGTATTAATT
Found at i:13070902 original size:25 final size:25
Alignment explanation
Indices: 13070864--13070914 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
13070854 GACAAGACAA
13070864 CATAGGATGCTTGTTTTAGTACGTT
1 CATAGGATGCTTGTTTTAGTACGTT
*
13070889 CATAGGATGTTTGTTTTAGTACGTT
1 CATAGGATGCTTGTTTTAGTACGTT
13070914 C
1 C
13070915 TTTCTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.45
Consensus pattern (25 bp):
CATAGGATGCTTGTTTTAGTACGTT
Found at i:13073411 original size:20 final size:21
Alignment explanation
Indices: 13073370--13073410 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13073360 TTTGCCCGGG
*
13073370 CCCAAAACTAAATAAATAAAA
1 CCCAAAACTAAAAAAATAAAA
13073391 CCCAAAA-TAAAAAAAATAAA
1 CCCAAAACT-AAAAAAATAAA
13073411 CATTCCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.71, C:0.17, G:0.00, T:0.12
Consensus pattern (21 bp):
CCCAAAACTAAAAAAATAAAA
Found at i:13074772 original size:28 final size:28
Alignment explanation
Indices: 13074700--13074772 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 28
13074690 GTTTAATTTC
*
13074700 TTTATATA-TA-TTATTATT-TTTTAACA
1 TTTATATATTATTTA-TATTATTTTAAAA
*
13074726 TTTTTATATT-TTTAT-TTATTTTAAAA
1 TTTATATATTATTTATATTATTTTAAAA
13074752 TTTATATATTATTTATATTAT
1 TTTATATATTATTTATATTAT
13074773 ACTATTTGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 2 0.05
26 24 0.62
27 9 0.23
28 4 0.10
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTATATATTATTTATATTATTTTAAAA
Found at i:13074853 original size:28 final size:29
Alignment explanation
Indices: 13074808--13074873 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 29
13074798 TTGTTTCACG
* *
13074808 TATTATTTATTTTGAACTGCTT-TATATAT
1 TATTATTTATCTTAAACTG-TTATATATAT
13074837 TATT-TTTATCTTAAACTGTTATATATAT
1 TATTATTTATCTTAAACTGTTATATATAT
13074865 ATATATATT
1 -TAT-TATT
13074874 ATTTATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
28 19 0.61
29 7 0.23
30 1 0.03
31 2 0.06
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.58
Consensus pattern (29 bp):
TATTATTTATCTTAAACTGTTATATATAT
Found at i:13074981 original size:50 final size:50
Alignment explanation
Indices: 13074866--13075081 Score: 172
Period size: 50 Copynumber: 4.3 Consensus size: 50
13074856 TATATATATA
* * *
13074866 TATATATTATTTATTTTAGATTTTTTTACATATTATTTCTTTTAAACTATTT
1 TATATATTATTTATTTTAAATTTTTTTA-A-ATTATTTATTTCAAACTATTT
* * * **
13074918 TATGTAATGTTTATTTTAAATTGCTTTAAATTATTTATTTCAAACTATTT
1 TATATATTATTTATTTTAAATTTTTTTAAATTATTTATTTCAAACTATTT
* * * * * * *
13074968 TATATTTTATTTATGTTAATTTTTTTTACATTGTTTATTTTGAACCT-TTT
1 TATATATTATTTATTTTAAATTTTTTTAAATTATTTA-TTTCAAACTATTT
* * * *
13075018 TTTGTATTATTTATTTTAAA-TTTTTT--ATTATTTACTTT-AAATTTTTT
1 TATATATTATTTATTTTAAATTTTTTTAAATTATTTA-TTTCAAACTATTT
*
13075065 TGTATATTATTTTATTT
1 TATATATTA-TTTATTT
13075082 CATTTGTCTT
Statistics
Matches: 130, Mismatches: 31, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
46 3 0.02
47 20 0.15
48 7 0.05
49 6 0.05
50 64 0.49
51 8 0.06
52 22 0.17
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (50 bp):
TATATATTATTTATTTTAAATTTTTTTAAATTATTTATTTCAAACTATTT
Done.