Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 139 of 187
Found at i:41626163 original size:25 final size:25
Alignment explanation
Indices: 41626121--41626170 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41626111 ATCTGATCGA
* * *
41626121 TTTGGGTTTTGAATTTTCATACTTT
1 TTTGAGTTTTGAACTTTCAAACTTT
*
41626146 TTTGAGTTTTGAGCTTTCAAACTTT
1 TTTGAGTTTTGAACTTTCAAACTTT
41626171 ATTTAGACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.10, G:0.16, T:0.56
Consensus pattern (25 bp):
TTTGAGTTTTGAACTTTCAAACTTT
Found at i:41628468 original size:16 final size:16
Alignment explanation
Indices: 41628447--41628485 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
41628437 GATTATAGAA
41628447 ATATATAAAAACATGT
1 ATATATAAAAACATGT
**
41628463 ATATATAAAAGTATGT
1 ATATATAAAAACATGT
41628479 ATATATA
1 ATATATA
41628486 TGTGTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:41630351 original size:19 final size:19
Alignment explanation
Indices: 41630327--41630367 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41630317 ATTTAATCCT
41630327 AATTCTAATCAA-ATTTTAA
1 AATTCTAAT-AAGATTTTAA
*
41630346 AATTCTCATAAGATTTTAA
1 AATTCTAATAAGATTTTAA
41630365 AAT
1 AAT
41630368 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTCTAATAAGATTTTAA
Found at i:41644565 original size:41 final size:41
Alignment explanation
Indices: 41644509--41644783 Score: 460
Period size: 41 Copynumber: 6.7 Consensus size: 41
41644499 CCTTTCGGGG
* ** * *
41644509 CTTTAGCGGCATTTTTATAAAAGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
*
41644550 CTTTAGCGGCGTTTTTGGAGAAGCGCAGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
*
41644591 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCCAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
41644632 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
*
41644673 CTTTAGCGGCGTTTTTTGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
*
41644714 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTAGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
*
41644755 CTTTAGCGGCGTTTTTGGAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGC
41644784 AAAAACATTT
Statistics
Matches: 221, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 221 1.00
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
Found at i:41645318 original size:7 final size:7
Alignment explanation
Indices: 41645303--41645340 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
41645293 TAAATAAGGT
41645303 TTAGGGG
1 TTAGGGG
*
41645310 TTAGTGG
1 TTAGGGG
41645317 TTAGGGG
1 TTAGGGG
*
41645324 TTTGGGG
1 TTAGGGG
41645331 TTAGGGG
1 TTAGGGG
41645338 TTA
1 TTA
41645341 AGAGTTAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.13, C:0.00, G:0.50, T:0.37
Consensus pattern (7 bp):
TTAGGGG
Found at i:41645331 original size:21 final size:22
Alignment explanation
Indices: 41645300--41645340 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41645290 TATTAAATAA
*
41645300 GGTTTAGGGGTTAGTGGTTAGG
1 GGTTTAGGGGTTAGGGGTTAGG
41645322 GGTTT-GGGGTTAGGGGTTA
1 GGTTTAGGGGTTAGGGGTTA
41645341 AGAGTTAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.12, C:0.00, G:0.51, T:0.37
Consensus pattern (22 bp):
GGTTTAGGGGTTAGGGGTTAGG
Found at i:41649619 original size:24 final size:23
Alignment explanation
Indices: 41649591--41649638 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
41649581 AATTTAAAAA
41649591 ATAAAACATAATATAATATTT-ATT
1 ATAAAA-ATAA-ATAATATTTGATT
*
41649615 ATAAAAATAAATATTATTTGATT
1 ATAAAAATAAATAATATTTGATT
41649638 A
1 A
41649639 AAATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAATAATATTTGATT
Found at i:41649711 original size:42 final size:42
Alignment explanation
Indices: 41649652--41649742 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
41649642 TAATTTTTTT
* * ** * *
41649652 TAAAGGTTATGTTTTTAGTGGCGTTTTTGCTAGAATCGCCGC
1 TAAAGGTTATGTTTTTAGCGGCGTTTGTGAAAAAAGCGCCGC
41649694 TAAAGGTT-TGTTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGC
1 TAAAGGTTATGTT-TTTAGCGGCGTTTGTGAAAAAAGCGCCGC
41649736 TAAAGGT
1 TAAAGGT
41649743 AGTGGTCGCG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.35
Consensus pattern (42 bp):
TAAAGGTTATGTTTTTAGCGGCGTTTGTGAAAAAAGCGCCGC
Found at i:41649815 original size:43 final size:43
Alignment explanation
Indices: 41649754--41649944 Score: 283
Period size: 43 Copynumber: 4.4 Consensus size: 43
41649744 GTGGTCGCGT
* *
41649754 TTGTGGGGAAAGTGCCGCTGAAGGTAGTGGTCTTTAGCGGCGC
1 TTGTGGGGAAAGCGCCGCTGAAGGTCGTGGTCTTTAGCGGCGC
41649797 TTGTGGGGAAAGCGCCGCTGAAGGTCGTGGTCTTTAGCGGCGC
1 TTGTGGGGAAAGCGCCGCTGAAGGTCGTGGTCTTTAGCGGCGC
* * *
41649840 TTGTGGGGAAAGCGTCGCTGAAGGTCGTGGTCTTTAGCGACGT
1 TTGTGGGGAAAGCGCCGCTGAAGGTCGTGGTCTTTAGCGGCGC
* * * * *
41649883 TTGTGGGAAAAGCGCCGCTGAAGATCGTGGTCTTTAGCAGTGT
1 TTGTGGGGAAAGCGCCGCTGAAGGTCGTGGTCTTTAGCGGCGC
*
41649926 TTGTGGGAAAAGCGCCGCT
1 TTGTGGGGAAAGCGCCGCT
41649945 AAAGACCATG
Statistics
Matches: 137, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 137 1.00
ACGTcount: A:0.17, C:0.18, G:0.39, T:0.26
Consensus pattern (43 bp):
TTGTGGGGAAAGCGCCGCTGAAGGTCGTGGTCTTTAGCGGCGC
Found at i:41649960 original size:43 final size:43
Alignment explanation
Indices: 41649784--41650012 Score: 167
Period size: 43 Copynumber: 5.3 Consensus size: 43
41649774 AAGGTAGTGG
* * * * ** * *
41649784 TCTTTAGCGGCGCTTGTGGGGAAAGCGCCGCTGAAGGTCGTGG
1 TCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGA
* * * * * ** * *
41649827 TCTTTAGCGGCGCTTGTGGGGAAAGCGTCGCTGAAGGTCGTGG
1 TCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGA
* * * *
41649870 TCTTTAGC-GACGTTTGTGGGAAAAGCGCCGCTGAAGATCGTGG
1 TCTTTAGCAG-CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGA
*
41649913 TCTTTAGCAGTGTTTGTGGGAAAAGCGCCGCTAAAGACCATGA
1 TCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGA
** ** * *
41649956 TCTTTAGTGGCGCTTT-T-CCAAAAACGCCGCTAAAGACCACGA
1 TCTTTAGCAGCG-TTTGTGGGAAAAGCGCCGCTAAAGACCATGA
41649998 TCTTTAGCAGCGTTT
1 TCTTTAGCAGCGTTT
41650013 ATTTCAAAAA
Statistics
Matches: 164, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
41 3 0.02
42 32 0.20
43 125 0.76
44 4 0.02
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (43 bp):
TCTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGA
Found at i:41649960 original size:86 final size:86
Alignment explanation
Indices: 41649784--41649962 Score: 232
Period size: 86 Copynumber: 2.1 Consensus size: 86
41649774 AAGGTAGTGG
* * * * *
41649784 TCTTTAGCGGCGCTTGTGGGGAAAGCGCCGCTGAAGGTCGTGGTCTTTAGCGGCGCTTGTGGGGA
1 TCTTTAGCGACGCTTGTGGGAAAAGCGCCGCTGAAGATCGTGGTCTTTAGCAGCGCTTGTGGGAA
* * ** * *
41649849 AAGCGTCGCTGAAGGTCGTGG
66 AAGCGCCGCTAAAGACCATGA
* * *
41649870 TCTTTAGCGACGTTTGTGGGAAAAGCGCCGCTGAAGATCGTGGTCTTTAGCAGTGTTTGTGGGAA
1 TCTTTAGCGACGCTTGTGGGAAAAGCGCCGCTGAAGATCGTGGTCTTTAGCAGCGCTTGTGGGAA
41649935 AAGCGCCGCTAAAGACCATGA
66 AAGCGCCGCTAAAGACCATGA
41649956 TCTTTAG
1 TCTTTAG
41649963 TGGCGCTTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (86 bp):
TCTTTAGCGACGCTTGTGGGAAAAGCGCCGCTGAAGATCGTGGTCTTTAGCAGCGCTTGTGGGAA
AAGCGCCGCTAAAGACCATGA
Found at i:41649987 original size:42 final size:44
Alignment explanation
Indices: 41649933--41650034 Score: 136
Period size: 42 Copynumber: 2.4 Consensus size: 44
41649923 TGTTTGTGGG
* * ** *
41649933 AAAAGCGCCGCTAAAGACCATGATCTTTAGTGGCG-CT-TTTCC
1 AAAAACGCCGCTAAAGACCACGATCTTTAGCAGCGTCTATTTCA
*
41649975 AAAAACGCCGCTAAAGACCACGATCTTTAGCAGCGTTTATTTCA
1 AAAAACGCCGCTAAAGACCACGATCTTTAGCAGCGTCTATTTCA
41650019 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
41650035 TTAGCGACAC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 31 0.60
43 1 0.02
44 20 0.38
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (44 bp):
AAAAACGCCGCTAAAGACCACGATCTTTAGCAGCGTCTATTTCA
Found at i:41652465 original size:41 final size:41
Alignment explanation
Indices: 41652286--41652696 Score: 191
Period size: 44 Copynumber: 9.7 Consensus size: 41
41652276 TTTTAATCCA
* * * *
41652286 CTCTACTACAACTTCAGGGAGATATGACTCGATGCGATCTA
1 CTCTACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTG
* * * * *** *
41652327 ATCTACTGCAACTTTAGAGAGATAAGATCTGTGTTTTTAATCCG
1 CTCTACTGCAACTTCAGGGAGATAAGA-CTG-G-ATGCGATCTG
* * * * * * *
41652371 CTCCACTGCAATTTTAGGGAGATAGGATTGATTTATTCTG-TCTG
1 CTCTACTGCAACTTCAGGGAGATAAGACTG---GATGC-GATCTG
* * *
41652415 CTCCACTACAACTTCAGGGAGATAAGACTGGATGCGATTTG
1 CTCTACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTG
* * * * * * *
41652456 CTCTACTACAACTTCAGAGAGATAGGATTGGCTTCTTCTG-TTTG
1 CTCTACTGCAACTTCAGGGAGATAAGACTGG---ATGC-GATCTG
* *
41652500 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGCAATCTG
1 CTCTACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTG
* * * * *** *
41652541 TTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCG
1 CTCTACTGCAACTTCAGGGAGATAAGA-C--TGGATGCGATCTG
* * * * * * * *
41652585 CTCCACTGTAACTTTAGGGAGATAGGA-TTGACTTC-TTCTTT
1 CTCTACTGCAACTTCAGGGAGATAAGACTGGA-TGCGATC-TG
41652626 CTGCTTCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTG
1 CT-C-T-ACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTG
*
41652670 CTCTACTGCAACTTCAGAGAGATAAGA
1 CTCTACTGCAACTTCAGGGAGATAAGA
41652697 TCTGTGGTTT
Statistics
Matches: 272, Mismatches: 76, Indels: 44
0.69 0.19 0.11
Matches are distributed among these distances:
40 5 0.02
41 109 0.40
42 5 0.02
43 4 0.01
44 142 0.52
45 7 0.03
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (41 bp):
CTCTACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTG
Found at i:41652495 original size:85 final size:85
Alignment explanation
Indices: 41652389--41652564 Score: 280
Period size: 85 Copynumber: 2.1 Consensus size: 85
41652379 CAATTTTAGG
* * *
41652389 GAGATAGGATTGATTTATTCTGTCTGCTCCACTACAACTTCAGGGAGATAAGACTGGATGCGATT
1 GAGATAGGATTGACTTATTCTGTCTGCTCCACTACAACTTCAGGGAGATAAGACTGGATGCAATC
41652454 TGCTCTACTACAACTTCAGA
66 TGCTCTACTACAACTTCAGA
* * * *
41652474 GAGATAGGATTGGCTTCTTCTGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCAATC
1 GAGATAGGATTGACTTATTCTGTCTGCTCCACTACAACTTCAGGGAGATAAGACTGGATGCAATC
*
41652539 TGTTCTACTACAACTTCAGA
66 TGCTCTACTACAACTTCAGA
41652559 GAGATA
1 GAGATA
41652565 AGATCTGTGG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (85 bp):
GAGATAGGATTGACTTATTCTGTCTGCTCCACTACAACTTCAGGGAGATAAGACTGGATGCAATC
TGCTCTACTACAACTTCAGA
Found at i:41652503 original size:129 final size:129
Alignment explanation
Indices: 41652290--41652523 Score: 303
Period size: 129 Copynumber: 1.8 Consensus size: 129
41652280 AATCCACTCT
* * *
41652290 ACTACAACTTCAGGGAGATATGACTCGATGCGATCTAATCTACTGCAACTTTAGAGAGATAAGAT
1 ACTACAACTTCAGGGAGATAAGACTCGATGCGATCTAATCTACTACAACTTCAGAGAGATAAGAT
* *
41652355 CTGTGTTTTTAATCCGCTCCACTGCAATTTTAGGGAGATAGGATTGATTTATTCTGTCTGCTCC
66 CTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTATTCTGTCTGCTCC
* * ** *
41652419 ACTACAACTTCAGGGAGATAAGACTGGATGCGATTTGCTCTACTACAACTTCAGAGAGATAGGAT
1 ACTACAACTTCAGGGAGATAAGACTCGATGCGATCTAATCTACTACAACTTCAGAGAGATAAGAT
* **
41652484 -TG-GCTTCTTCT-GTTTGCTCCACTGCAACTTCAGGGAGATA
66 CTGTG-TT-TT-TAATCCGCTCCACTGCAACTTCAGGGAGATA
41652524 AGACTGGATG
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
127 1 0.01
128 4 0.04
129 83 0.93
130 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (129 bp):
ACTACAACTTCAGGGAGATAAGACTCGATGCGATCTAATCTACTACAACTTCAGAGAGATAAGAT
CTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTATTCTGTCTGCTCC
Found at i:41652588 original size:85 final size:85
Alignment explanation
Indices: 41652414--41652608 Score: 250
Period size: 85 Copynumber: 2.3 Consensus size: 85
41652404 TATTCTGTCT
* * *
41652414 GCTCCACTACAACTTCAGGGAGATAAGACTGGATGCGATTTGCTCTACTACAACTTCAGAGAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCAATCTGCTCTACTACAACTTCAGAGAGAT
* ** **
41652479 AGGATTGGCTTCTTCTGTTT
66 AAGATTGGCTTCTTCAATCC
*
41652499 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCAATCTGTTCTACTACAACTTCAGAGAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCAATCTGCTCTACTACAACTTCAGAGAGAT
*
41652564 AAGATCTGTGGTT-TT-AATCC
66 AAGAT-TG-GCTTCTTCAATCC
* *
41652584 GCTCCACTGTAACTTTAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
41652609 GGATTGACTT
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
85 89 0.93
86 4 0.04
87 3 0.03
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (85 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCAATCTGCTCTACTACAACTTCAGAGAGAT
AAGATTGGCTTCTTCAATCC
Found at i:41652598 original size:129 final size:129
Alignment explanation
Indices: 41652464--41652749 Score: 466
Period size: 129 Copynumber: 2.2 Consensus size: 129
41652454 TGCTCTACTA
*
41652464 CAACTTCAGAGAGATAGGATTGGCTTCTTCTGTT-TGCTCCACTGCAACTTCAGGGAGATAAGAC
1 CAACTTCAGGGAGATAGGATTGGCTTCTTCT-TTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* *
41652528 TGGATGCAATCTGTTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTG
65 TGGATGCAATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTG
* * * *
41652593 TAACTTTAGGGAGATAGGATTGACTTCTTCTTTCTGCTTCACTGCAACTTCAGGGAGATAAGACT
1 CAACTTCAGGGAGATAGGATTGGCTTCTTCTTTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
* *
41652658 GGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTG
66 GGATGCAATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTG
*
41652722 CAATTTCAGGGAGATAGGATTGGCTTCT
1 CAACTTCAGGGAGATAGGATTGGCTTCT
41652750 GTCTAATTAA
Statistics
Matches: 143, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
128 2 0.01
129 141 0.99
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (129 bp):
CAACTTCAGGGAGATAGGATTGGCTTCTTCTTTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
GGATGCAATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTG
Found at i:41652720 original size:214 final size:214
Alignment explanation
Indices: 41652155--41652737 Score: 679
Period size: 214 Copynumber: 2.8 Consensus size: 214
41652145 ATGATTCATC
* * * *
41652155 GTTTTAATCCGCGCCACTGCAACTTCAGGGAGATAGGATT-A---A-T-AG-CT--TCAACTACA
1 GTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGACTTATTCTGTCTGCTCCACTACA
* * * * * **
41652211 ACTTTAAGGGA-ATAAGGTCT-GATGCGATCTGCTTTACTGCAACTTCAAAAAGATAAGATCCAT
66 AC-TTCAGGGAGATAA-GACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGT
* * * * * *
41652274 CATTTTAATCCACTCTACTACAACTTCAGGGAGATATGACTCGATGCGATCTAATCTACTGCAAC
129 GATTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGACTCGATGCAATCTAATCTACTACAAC
*
41652339 TTTAGAGAGATAAGATCTGTG
194 TTCAGAGAGATAAGATCTGTG
* * *
41652360 TTTTTAATCCGCTCCACTGCAATTTTAGGGAGATAGGATTGATTTATTCTGTCTGCTCCACTACA
1 GTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGACTTATTCTGTCTGCTCCACTACA
* * * *
41652425 ACTTCAGGGAGATAAGACTGGATGCGATTTGCTCTACTACAACTTCAGAGAGATAGGAT-TG-GC
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGA
** *** * **
41652488 TTCTTCTGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCAATCTGTTCTACTACAAC
131 TT-TT-AATCCACTCCACTGCAACTTCAGGGAGATAAGACTCGATGCAATCTAATCTACTACAAC
41652553 TTCAGAGAGATAAGATCTGTG
194 TTCAGAGAGATAAGATCTGTG
* * * * *
41652574 GTTTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTGACTTCTTCTTTCTGCTTCACTGCA
1 GTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGACTTATTCTGTCTGCTCCACTACA
*
41652639 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGA
*
41652704 TTTTAATCCACTCCACTGCAATTTCAGGGAGATA
131 TTTTAATCCACTCCACTGCAACTTCAGGGAGATA
41652738 GGATTGGCTT
Statistics
Matches: 313, Mismatches: 50, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
205 36 0.12
206 1 0.00
209 1 0.00
210 1 0.00
211 1 0.00
212 4 0.01
213 12 0.04
214 250 0.80
215 4 0.01
216 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (214 bp):
GTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGACTTATTCTGTCTGCTCCACTACA
ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGA
TTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGACTCGATGCAATCTAATCTACTACAACTT
CAGAGAGATAAGATCTGTG
Found at i:41652723 original size:85 final size:85
Alignment explanation
Indices: 41652205--41652737 Score: 228
Period size: 85 Copynumber: 6.2 Consensus size: 85
41652195 AATAGCTTCA
* * ** * *
41652205 ACTACAACTTTAAGGGA-ATAAGGTCT-GATGCGATCTGCTTTACTGCAACTTCAAAAAGATAAG
1 ACTACAAC-TTCAGGGAGATAA-GACTGGATGCGATCTGCTCCACTGCAACTTCAGAGAGATAAG
** ** * *
41652268 ATCCATCATTTTAATCCACTCT
64 ATCTGTGGTTTTAATCCGCTCC
* * ** * *
41652290 ACTACAACTTCAGGGAGATATGACTCGATGCGATCTAATCTACTGCAACTTTAGAGAGATAAGAT
1 ACTACAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
*
41652355 CTGTGTTTTTAATCCGCTCC
66 CTGTGGTTTTAATCCGCTCC
* * * * * * * * *
41652375 ACTGCAATTTTAGGGAGATAGGATTGATTTATTCTG-TCTGCTCCACTACAACTTCAGGGAGATA
1 ACTACAACTTCAGGGAGATAAGACTG---GATGC-GATCTGCTCCACTGCAACTTCAGAGAGATA
* *** ** *
41652439 AGA-C--TGGATGCGATTTGCTCT
62 AGATCTGTGGTTTTAATCCGCTCC
* * * * * * *
41652460 ACTACAACTTCAGAGAGATAGGATTGGCTTCTTCTG-TTTGCTCCACTGCAACTTCAGGGAGATA
1 ACTACAACTTCAGGGAGATAAGACTGG---ATGC-GATCTGCTCCACTGCAACTTCAGAGAGATA
* ** * * *
41652524 AGA-C--TGGATGCAATCTGTTCT
62 AGATCTGTGGTTTTAATCCGCTCC
* * *** * * * * *
41652545 ACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGTAACTTTAGGGAGATAG
1 ACTACAACTTCAGGGAGATAAGA-C--TGGATGCGATCTGCTCCACTGCAACTTCAGAGAGATAA
** * *
41652610 GAT-TGACTTCTTCTT--TCTGCTTC
63 GATCTG--TGGTT-TTAATCCGCTCC
* *
41652633 ACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
1 ACTACAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
*
41652698 CTGTGGTTTTAATCCACTCC
66 CTGTGGTTTTAATCCGCTCC
* *
41652718 ACTGCAATTTCAGGGAGATA
1 ACTACAACTTCAGGGAGATA
41652738 GGATTGGCTT
Statistics
Matches: 342, Mismatches: 84, Indels: 44
0.73 0.18 0.09
Matches are distributed among these distances:
83 2 0.01
84 13 0.04
85 263 0.77
86 2 0.01
87 2 0.01
88 57 0.17
89 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (85 bp):
ACTACAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
CTGTGGTTTTAATCCGCTCC
Found at i:41652825 original size:50 final size:50
Alignment explanation
Indices: 41652771--41653651 Score: 498
Period size: 50 Copynumber: 17.7 Consensus size: 50
41652761 TGCAATGTCG
* * * *
41652771 GGGAAGCACGATTCGCCGTTGTAGCTTCAATCTGTCCCACTACACTGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
** * ** * * * *
41652821 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* *
41652871 GGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* ** * ** * * *
41652920 GGGAAGTAAGATTTGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
** * *
41652970 GGGAAGTAAGATTCATCGTTGTAGCTCCAATCTGCTCCACTGCACTGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
** * * ** * * *
41653020 GGGAAGTAAGATTCGCCGTTGCGGCTTTAATCTTTTAAATTGCAATGTC-
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
** * * * *
41653069 GAGGAAACAAGATTCGCCGTCGTAGCTTCATTCTATTCCACTGCACCGCCA
1 G-GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * ** ** * * ** * * * ***
41653120 AGGAAGTAATATTCGATGTTGCGGATTCAATCTTTTAAATTGTAATGTTG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * * *
41653170 GGGAAGTAAGATTCGCCATCGTAGCTTCAATCTGCTCCACTGCACCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * ** * * * ** * * * *
41653220 GAGAAGTAAGATTCACCGTTGCGGCTTTAATATTTTAAATTACAATGTC-
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * * *
41653269 GAGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCA
1 G-GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* ** * * * ** * * *
41653320 GGGAAGTAAGATTCACCGTTGCGGCTTAAATATTTTTAATTGCAATGTC-
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * *
41653369 GAGGAA-TAAGATTCGCTGTTGTAGCTTCAATCTGTTACACTGCACCGCCA
1 G-GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * ** ** * * *
41653419 GAGAAGTAAGATTCGCCATTGCGGCTTCAATC-GTTTAAATTGCAATGTCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTG-TTCCACTGCACTGCCA
* * * * * * *
41653469 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCTA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
* * ** * * ** * * ***
41653519 GGGAAGTAAGATTTGCTGTTGCGGCTTCAATATTTTAAATTGCAATGTTG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
** * * *
41653569 GGGAAACAAGATTCGCCGTTGTAGCTTCAATATATTCCACTGCACCT-CTA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCA-CTGCCA
* *
41653619 GGGAAGTAAGATTCGCTGTTGCAGCTTCAATCT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT
41653652 TTTAAATTAT
Statistics
Matches: 580, Mismatches: 240, Indels: 22
0.69 0.29 0.03
Matches are distributed among these distances:
49 75 0.13
50 502 0.87
51 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCA
Found at i:41653031 original size:100 final size:100
Alignment explanation
Indices: 41652761--41653659 Score: 1183
Period size: 100 Copynumber: 9.0 Consensus size: 100
41652751 TCTAATTAAC
* * *
41652761 TGCAATGTCGGGGAAGCACGATTCGCCGTTGTAGCTTCAATCTG-TCCCACTACACTGCCAGGGA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCT-CCACTGCACCGCCAGGGA
*
41652825 AGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAAT
65 AGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
*
41652861 TGCAATGTCGGGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
*
41652925 GTAAGATTTGCCGTTGCGGCTTCAATCTTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
* * ** * *
41652960 TGCAATGTCAGGGAAGTAAGATTCATCGTTGTAGCTCCAATCTGCTCCACTGCACTGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
*
41653025 GTAAGATTCGCCGTTGCGGCTTTAATCTTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
* * * * ** *
41653060 TGCAATGTCGAGGAAACAAGATTCGCCGTCGTAGCTTCATTCTATTCCACTGCACCGCCAAGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
* ** *
41653125 GTAATATTCGATGTTGCGGATTCAATCTTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
* * * * * *
41653160 TGTAATGTTGGGGAAGTAAGATTCGCCATCGTAGCTTCAATCTGCTCCACTGCACCGCCAGAGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
* * *
41653225 GTAAGATTCACCGTTGCGGCTTTAATATTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
* * *
41653260 TACAATGTCGAGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
* * * *
41653325 GTAAGATTCACCGTTGCGGCTTAAATATTTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
* * * * * *
41653360 TGCAATGTCGAGGAA-TAAGATTCGCTGTTGTAGCTTCAATCTGTTACACTGCACCGCCAGAGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
* *
41653424 GTAAGATTCGCCATTGCGGCTTCAATCGTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
* * * * *
41653459 TGCAATGTCAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCTAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
* * *
41653524 GTAAGATTTGCTGTTGCGGCTTCAATATTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
* * * ** * *
41653559 TGCAATGTTGGGGAAACAAGATTCGCCGTTGTAGCTTCAATATATTCCACTGCACCTCTAGGGAA
1 TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
* *
41653624 GTAAGATTCGCTGTTGCAGCTTCAATCTTTTAAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
41653659 T
1 T
41653660 ATAACCTCAG
Statistics
Matches: 695, Mismatches: 101, Indels: 6
0.87 0.13 0.01
Matches are distributed among these distances:
99 176 0.25
100 519 0.75
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (100 bp):
TGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
GTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAAT
Found at i:41654955 original size:18 final size:17
Alignment explanation
Indices: 41654930--41654995 Score: 82
Period size: 16 Copynumber: 3.9 Consensus size: 17
41654920 TTCTTTATGC
41654930 TTTTTTTATTGTTTTTA
1 TTTTTTTATTGTTTTTA
*
41654947 TTATTTTTATTATTTTTA
1 TT-TTTTTATTGTTTTTA
*
41654965 TTGTTTTATTG-TTTTA
1 TTTTTTTATTGTTTTTA
*
41654981 TTGTTTT-TTGTTTTT
1 TTTTTTTATTGTTTTT
41654996 GCCTCCACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
15 3 0.07
16 16 0.36
17 9 0.20
18 16 0.36
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (17 bp):
TTTTTTTATTGTTTTTA
Found at i:41654991 original size:23 final size:23
Alignment explanation
Indices: 41654947--41654994 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
41654937 ATTGTTTTTA
*
41654947 TTATTTTTATTATTTTTATTGTT
1 TTATTGTTATTATTTTTATTGTT
*
41654970 TTATTGTT-TTATTGTTTTTTGTT
1 TTATTGTTATTATT-TTTATTGTT
41654993 TT
1 TT
41654995 TGCCTCCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.79
Consensus pattern (23 bp):
TTATTGTTATTATTTTTATTGTT
Found at i:41654995 original size:8 final size:9
Alignment explanation
Indices: 41654932--41654988 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
41654922 CTTTATGCTT
41654932 TTTTTATTG
1 TTTTTATTG
*
41654941 TTTTTATTA
1 TTTTTATTG
*
41654950 TTTTTATTA
1 TTTTTATTG
41654959 TTTTTATTG
1 TTTTTATTG
41654968 -TTTTATTG
1 TTTTTATTG
41654976 -TTTTATTG
1 TTTTTATTG
41654984 TTTTT
1 TTTTT
41654989 TGTTTTTGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
8 16 0.36
9 29 0.64
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (9 bp):
TTTTTATTG
Found at i:41657725 original size:24 final size:25
Alignment explanation
Indices: 41657698--41657751 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
41657688 GGGTTTTTTC
*
41657698 ATGAAATTTAATGCAAATG-ATGCA
1 ATGAAATGTAATGCAAATGAATGCA
* *
41657722 ATGAAATGTAATGCAGATGAATGGA
1 ATGAAATGTAATGCAAATGAATGCA
41657747 ATGAA
1 ATGAA
41657752 TGCAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (25 bp):
ATGAAATGTAATGCAAATGAATGCA
Found at i:41663232 original size:43 final size:43
Alignment explanation
Indices: 41663168--41663271 Score: 172
Period size: 43 Copynumber: 2.4 Consensus size: 43
41663158 GCGTCGCTAA
*
41663168 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCACGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAC
*
41663211 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAC
* *
41663254 CTATAGCGGCGGTTTTCC
1 CTTTAGCGGCGCTTTTCC
41663272 ACAGACCACG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAC
Found at i:41663280 original size:30 final size:30
Alignment explanation
Indices: 41663244--41663301 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
41663234 ACGCCGCTAA
*
41663244 AGACCACGATCTATAGCGGCGGTTTTCCAC
1 AGACCACGATCTATAGCGGCGCTTTTCCAC
41663274 AGACCACGATCTATAGCGGCGCTTTTCC
1 AGACCACGATCTATAGCGGCGCTTTTCC
41663302 CACAAACGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (30 bp):
AGACCACGATCTATAGCGGCGCTTTTCCAC
Found at i:41663296 original size:73 final size:73
Alignment explanation
Indices: 41663201--41663344 Score: 261
Period size: 73 Copynumber: 2.0 Consensus size: 73
41663191 ACGCCGCTAA
* *
41663201 AGACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGATCTATAGCGGCGG
1 AGACCACGACCTATAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGATCTATAGCGGCGC
41663266 TTTTCCAC
66 TTTTCCAC
*
41663274 AGACCACGATCTATAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGATCTATAGCGGCGC
1 AGACCACGACCTATAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGATCTATAGCGGCGC
41663339 TTTTCC
66 TTTTCC
41663345 CACAAACGCC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (73 bp):
AGACCACGACCTATAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGATCTATAGCGGCGC
TTTTCCAC
Found at i:41663306 original size:116 final size:116
Alignment explanation
Indices: 41663171--41663387 Score: 362
Period size: 116 Copynumber: 1.9 Consensus size: 116
41663161 TCGCTAACTT
* *
41663171 TAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCCACAAAC
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACCTATAGCGGCGCTTTTCCCACAAAC
* *
41663236 GCCGCTAAAGACCACGATCTATAGCGGCGGTTTTCCACAGACCACGATCTA
66 GCCGCTAAAGACCACGAGCTATAACGGCGGTTTTCCACAGACCACGATCTA
*
41663287 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGATCTATAGCGGCGCTTTTCCCACAAAC
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACCTATAGCGGCGCTTTTCCCACAAAC
* * *
41663352 GCCGCTAGAGACCACGAGCTTTAACGGCGTTTTTCC
66 GCCGCTAAAGACCACGAGCTATAACGGCGGTTTTCC
41663388 CACAAACGCC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
116 93 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (116 bp):
TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACCTATAGCGGCGCTTTTCCCACAAAC
GCCGCTAAAGACCACGAGCTATAACGGCGGTTTTCCACAGACCACGATCTA
Found at i:41663335 original size:43 final size:43
Alignment explanation
Indices: 41663274--41663445 Score: 220
Period size: 43 Copynumber: 4.0 Consensus size: 43
41663264 GGTTTTCCAC
41663274 AGACCACGATCTATAGCGGCGCTTTTCCCACAAACGCCGCTAA
1 AGACCACGATCTATAGCGGCGCTTTTCCCACAAACGCCGCTAA
*
41663317 AGACCACGATCTATAGCGGCGCTTTTCCCACAAACGCCGCTAG
1 AGACCACGATCTATAGCGGCGCTTTTCCCACAAACGCCGCTAA
* * * *
41663360 AGACCACGAGCTTTAACGGCGTTTTTCCCACAAACGCCGCTAA
1 AGACCACGATCTATAGCGGCGCTTTTCCCACAAACGCCGCTAA
* * * * * ** *
41663403 AGAACA-AACCTTTAGCGGCGCTTCTAGCAAAAACGCCGCTAA
1 AGACCACGATCTATAGCGGCGCTTTTCCCACAAACGCCGCTAA
41663445 A
1 A
41663446 AACATAATCT
Statistics
Matches: 114, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
42 29 0.25
43 85 0.75
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.19
Consensus pattern (43 bp):
AGACCACGATCTATAGCGGCGCTTTTCCCACAAACGCCGCTAA
Found at i:41664219 original size:23 final size:23
Alignment explanation
Indices: 41664169--41664220 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
41664159 GTTAGGTGTC
* *
41664169 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
41664192 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
41664215 AGTATG
1 AGTATG
41664221 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:41668103 original size:15 final size:15
Alignment explanation
Indices: 41668082--41668113 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
41668072 ATAAATGAAA
41668082 AATATATA-T-AATT
1 AATATATATTAAATT
41668095 AATATATATTAAATT
1 AATATATATTAAATT
41668110 AATA
1 AATA
41668114 ATAATGCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATATATTAAATT
Found at i:41668800 original size:7 final size:7
Alignment explanation
Indices: 41668788--41668920 Score: 56
Period size: 7 Copynumber: 18.7 Consensus size: 7
41668778 ACTAGTTAAT
41668788 CTAAACC
1 CTAAACC
41668795 CTAAACC
1 CTAAACC
*
41668802 ATAAA-C
1 CTAAACC
*
41668808 CTAAATC
1 CTAAACC
*
41668815 CTAAAATC
1 CT-AAACC
41668823 CTAAACC
1 CTAAACC
* *
41668830 CTTAACA
1 CTAAACC
41668837 C-ATAACC
1 CTA-AACC
41668844 TCTAAACC
1 -CTAAACC
*
41668852 TTAAACC
1 CTAAACC
*
41668859 C-CAACC
1 CTAAACC
*
41668865 TTTAAACC
1 -CTAAACC
*
41668873 ATAAACC
1 CTAAACC
* *
41668880 ATAAATC
1 CTAAACC
* *
41668887 ATAACCC
1 CTAAACC
41668894 CTAAACC
1 CTAAACC
*
41668901 CATAATCC
1 C-TAAACC
*
41668909 ATAAACC
1 CTAAACC
*
41668916 TTAAA
1 CTAAA
41668921 ATAGTAACTC
Statistics
Matches: 96, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
6 9 0.09
7 65 0.68
8 21 0.22
9 1 0.01
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:41668808 original size:14 final size:14
Alignment explanation
Indices: 41668788--41668978 Score: 70
Period size: 14 Copynumber: 13.4 Consensus size: 14
41668778 ACTAGTTAAT
*
41668788 CTAAACCCTAAACC
1 CTAAACCATAAACC
* *
41668802 ATAAACC-TAAATC
1 CTAAACCATAAACC
41668815 CTAAAATCC-TAAACC
1 CT-AAA-CCATAAACC
*
41668830 CTTAACACAT-AACC
1 CTAAAC-CATAAACC
*
41668844 TCTAAACCTTAAACC
1 -CTAAACCATAAACC
* *
41668859 C-CAACCTTTAAACC
1 CTAAACC-ATAAACC
* *
41668873 ATAAACCATAAATC
1 CTAAACCATAAACC
* * *
41668887 ATAACCCCTAAACC
1 CTAAACCATAAACC
*
41668901 CATAATCCATAAACC
1 C-TAAACCATAAACC
*
41668916 TTAAA--ATAGTAACTC
1 CTAAACCATA--AAC-C
** *
41668931 CTAAACTTTAAACT
1 CTAAACCATAAACC
*
41668945 CTAAACCATATACC
1 CTAAACCATAAACC
* *
41668959 CTAAACTAAAAACC
1 CTAAACCATAAACC
*
41668973 TTAAAC
1 CTAAAC
41668979 TATAGTGATA
Statistics
Matches: 132, Mismatches: 31, Indels: 28
0.69 0.16 0.15
Matches are distributed among these distances:
12 3 0.02
13 11 0.08
14 74 0.56
15 42 0.32
17 2 0.02
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.23
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:41668864 original size:21 final size:21
Alignment explanation
Indices: 41668840--41668879 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41668830 CTTAACACAT
*
41668840 AACCTCTAAACCTTAAACCCC
1 AACCTCTAAACCATAAACCCC
*
41668861 AACCTTTAAACCATAAACC
1 AACCTCTAAACCATAAACC
41668880 ATAAATCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCTCTAAACCATAAACCCC
Found at i:41669335 original size:41 final size:41
Alignment explanation
Indices: 41669276--41669473 Score: 242
Period size: 41 Copynumber: 4.9 Consensus size: 41
41669266 AATATTTTTT
*
41669276 GCGGCGCTT-TTCCAAAAACGCCGCTAAAG-CCCTGAGCATTA
1 GCGGCGCTTATT-CAAAAACGCCGCTAAAGACCC-AAGCATTA
* **
41669317 GTGGCGCTTCCTCAAAAACGCCGCTAAAGACCCAAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGACCCAAGCATTA
* *
41669358 GCGGCGCTTCTTCAAAAACGCCACTAAAGACCCAAGCA-TA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGACCCAAGCATTA
*
41669398 GCGGCGCTTATTCAAAAACGCCGCTAAAG-CCCTGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGACCC-AAGCATTA
* * * *
41669439 GCGGCACTTATTCAAAAACGCTGGTAAAGTCCCAA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGACCCAA
41669474 AAACTAACAA
Statistics
Matches: 139, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
39 3 0.02
40 33 0.24
41 96 0.69
42 7 0.05
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTATTCAAAAACGCCGCTAAAGACCCAAGCATTA
Found at i:41669436 original size:81 final size:81
Alignment explanation
Indices: 41669276--41669459 Score: 239
Period size: 81 Copynumber: 2.2 Consensus size: 81
41669266 AATATTTTTT
* * * *
41669276 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGTGGCGCTTCCTCAAAAACGCCGC
1 GCGGCGCTTTT-CAAAAACGCCACTAAAGCCCTAAGCATTAGCGGCGCTTACTCAAAAACGCCGC
41669341 TAAAGACCCAAGCATTA
65 TAAAGACCCAAGCATTA
*
41669358 GCGGCGCTTCTTCAAAAACGCCACTAAAGACCC-AAGCA-TAGCGGCGCTTATTCAAAAACGCCG
1 GCGGCGCTT-TTCAAAAACGCCACTAAAG-CCCTAAGCATTAGCGGCGCTTACTCAAAAACGCCG
*
41669421 CTAAAG-CCCTGAGCATTA
64 CTAAAGACCC-AAGCATTA
*
41669439 GCGGCACTTATTCAAAAACGC
1 GCGGCGCTT-TTCAAAAACGC
41669460 TGGTAAAGTC
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
80 3 0.03
81 54 0.59
82 29 0.32
83 5 0.05
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (81 bp):
GCGGCGCTTTTCAAAAACGCCACTAAAGCCCTAAGCATTAGCGGCGCTTACTCAAAAACGCCGCT
AAAGACCCAAGCATTA
Found at i:41669597 original size:40 final size:40
Alignment explanation
Indices: 41669506--41669640 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
41669496 TGGGCTTAGG
* * * *
41669506 TTTTT-GCGGCGCTTTCTGGAAAA-CGCCACTAATGGTT-A
1 TTTTTAGCGGCG-TTTTTAGAAAAGCGCCGCTAATGATTGA
*
41669544 TTTTTAGCAGCGTTTTTAGAAAAGCGCCGCTAAT-ACTTGA
1 TTTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGA-TTGA
* **
41669584 TTTGTAGCGGCGTTTTTCTAAAAGCGCCGCTAATGATTGA
1 TTTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGATTGA
*
41669624 TTTTTAGCGGGGTTTTT
1 TTTTTAGCGGCGTTTTT
41669641 TATCCAAACG
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
38 14 0.17
39 16 0.20
40 50 0.62
41 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGATTGA
Found at i:41672093 original size:24 final size:24
Alignment explanation
Indices: 41672061--41672109 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41672051 ATATAATCCC
41672061 TATACAGCCAACATTTATCAATTT
1 TATACAGCCAACATTTATCAATTT
41672085 TATACAGCCAACATTTATCAATTT
1 TATACAGCCAACATTTATCAATTT
41672109 T
1 T
41672110 TCACAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACAGCCAACATTTATCAATTT
Found at i:41673714 original size:27 final size:28
Alignment explanation
Indices: 41673684--41673737 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
41673674 GATTTAAGAT
*
41673684 ACATATATATTTA-TATA-TAATTATTTA
1 ACATATATAATTAGTATAGT-ATTATTTA
41673711 ACATATATAATTAGTATAGTATTATTT
1 ACATATATAATTAGTATAGTATTATTT
41673738 TATAACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
28 11 0.46
29 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (28 bp):
ACATATATAATTAGTATAGTATTATTTA
Found at i:41682497 original size:31 final size:32
Alignment explanation
Indices: 41682461--41682525 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
41682451 CTTAGATGAT
41682461 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
41682492 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
41682524 TT
1 TT
41682526 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:41683068 original size:12 final size:12
Alignment explanation
Indices: 41683051--41683093 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
41683041 CTTATTCTTT
*
41683051 AAAAAGAATAGC
1 AAAAAGAAAAGC
41683063 AAAAAGAAAAAG-
1 AAAAAG-AAAAGC
41683075 AAAAAGAAGAAGC
1 AAAAAGAA-AAGC
41683088 AAAAAG
1 AAAAAG
41683094 CGCAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 2 0.07
12 15 0.56
13 10 0.37
ACGTcount: A:0.74, C:0.05, G:0.19, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAGC
Found at i:41687995 original size:31 final size:32
Alignment explanation
Indices: 41687959--41688021 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
41687949 CTTAGATAAT
41687959 TTTAAAG-AGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAAGTTTTATTAGGATTCAATTACTC
*
41687990 TTTAAAGAATTTTTATTAGGATTCAATTACTC
1 TTTAAAGAAGTTTTATTAGGATTCAATTACTC
41688022 CTGTAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 7 0.23
32 23 0.77
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (32 bp):
TTTAAAGAAGTTTTATTAGGATTCAATTACTC
Found at i:41696893 original size:30 final size:30
Alignment explanation
Indices: 41696857--41696915 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
41696847 CTTAACAAGC
41696857 AAATGTCTCTAAAATAATAACAAAATTAAT
1 AAATGTCTCTAAAATAATAACAAAATTAAT
*
41696887 AAATGTCTTTAAAATAATAACAAAATTAA
1 AAATGTCTCTAAAATAATAACAAAATTAA
41696916 CAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATGTCTCTAAAATAATAACAAAATTAAT
Found at i:41697347 original size:16 final size:16
Alignment explanation
Indices: 41697326--41697372 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
41697316 CGTTGTATTA
*
41697326 GAATAGAGGCATAATG
1 GAATAGAGGCGTAATG
41697342 GAATAGAGGCGTAATG
1 GAATAGAGGCGTAATG
*
41697358 CAATAGAGGCGTAAT
1 GAATAGAGGCGTAAT
41697373 AGCAAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.32, T:0.19
Consensus pattern (16 bp):
GAATAGAGGCGTAATG
Found at i:41697624 original size:16 final size:16
Alignment explanation
Indices: 41697587--41697628 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41697577 TTAATCATAT
*
41697587 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
41697603 TT-AAATATATTATAA
1 TTAAAATATATTATAA
41697618 TTAAAATATAT
1 TTAAAATATAT
41697629 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:41697635 original size:14 final size:15
Alignment explanation
Indices: 41697596--41697637 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41697586 TTTAAACATA
*
41697596 ATTATTATTAAATAT
1 ATTATAATTAAATAT
41697611 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
41697625 A-TATAATTTAATA
1 ATTATAATTAAATA
41697638 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:41697688 original size:61 final size:61
Alignment explanation
Indices: 41697622--41697929 Score: 230
Period size: 61 Copynumber: 5.1 Consensus size: 61
41697612 TTATAATTAA
41697622 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
41697683 AATATATGATACT-ATAAAA-T-ATAATTTAA-C-ATAATTATGAT-TAAATATA-TTATAATTA
1 AATATATAAT-TTAATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTCA-AATCA
*
41697741 A
61 T
*
41697742 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * ** * * * * *
41697803 AATATATGATACT-ATAAAA--GATAATTTAA-C-ATAATTATTAT-TAAATATA-TTATAATTA
1 AATATATAAT-TTAATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTCA-AATCA
*
41697861 A
61 T
*
41697862 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
41697923 AATATAT
1 AATATAT
41697930 GATACTATAA
Statistics
Matches: 181, Mismatches: 42, Indels: 48
0.67 0.15 0.18
Matches are distributed among these distances:
58 6 0.03
59 66 0.36
60 30 0.17
61 73 0.40
62 6 0.03
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:41697746 original size:16 final size:16
Alignment explanation
Indices: 41697702--41697748 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
41697692 TACTATAAAA
*
41697702 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
41697718 TATGATT-AAATATAT
1 TATAATTAAAATATAT
41697733 TATAATTAAAATATAT
1 TATAATTAAAATATAT
41697749 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:41697803 original size:120 final size:121
Alignment explanation
Indices: 41697585--41697981 Score: 710
Period size: 120 Copynumber: 3.3 Consensus size: 121
41697575 ATTTAATCAT
41697585 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
41697650 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
*
41697706 ATTT-AACATAATTATGATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
41697770 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
41697826 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
41697890 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
* * *
41697946 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAA
41697982 TATTAAATAA
Statistics
Matches: 266, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
120 260 0.98
121 6 0.02
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
Found at i:41697866 original size:16 final size:16
Alignment explanation
Indices: 41697823--41697868 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
41697813 ACTATAAAAG
*
41697823 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
41697839 ATTATT-AAATATATT
1 ATAATTAAAATATATT
41697854 ATAATTAAAATATAT
1 ATAATTAAAATATAT
41697869 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:41697875 original size:14 final size:15
Alignment explanation
Indices: 41697823--41697877 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
41697813 ACTATAAAAG
41697823 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
41697839 ATTATTAAATATATT
1 ATAATTAAATATATT
41697854 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
41697867 ATAATTTAATA
1 ATAATTAAATA
41697878 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:41702878 original size:64 final size:64
Alignment explanation
Indices: 41702777--41702906 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
41702767 GCACCTGCAA
41702777 GACGTGGTGAAGCAAAATGTTGAGCTCAAAATGGGCCTATCTTGTGAATATTTTAGCCCAACAC
1 GACGTGGTGAAGCAAAATGTTGAGCTCAAAATGGGCCTATCTTGTGAATATTTTAGCCCAACAC
41702841 GACGTGGTGAAGCAAAATGTTGAGCTCAAAATGGGCCTATCTTGTGAATATTTTAGCCCAACAC
1 GACGTGGTGAAGCAAAATGTTGAGCTCAAAATGGGCCTATCTTGTGAATATTTTAGCCCAACAC
41702905 GA
1 GA
41702907 AACTATTTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (64 bp):
GACGTGGTGAAGCAAAATGTTGAGCTCAAAATGGGCCTATCTTGTGAATATTTTAGCCCAACAC
Found at i:41706733 original size:11 final size:11
Alignment explanation
Indices: 41706717--41706743 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41706707 ATTTTTATCC
41706717 TTTTTATTTTA
1 TTTTTATTTTA
41706728 TTTTTATTTTA
1 TTTTTATTTTA
41706739 TTTTT
1 TTTTT
41706744 TTACATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:41707534 original size:2 final size:2
Alignment explanation
Indices: 41707527--41707551 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41707517 TTATCCCATT
41707527 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
41707552 TCTCTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41712515 original size:5 final size:5
Alignment explanation
Indices: 41712497--41712535 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
41712487 TACTTCAATT
* *
41712497 GAAAA AAAAA GAAAC GAAAA GAAAAA GAAAA GAAAA GAA
1 GAAAA GAAAA GAAAA GAAAA G-AAAA GAAAA GAAAA GAA
41712536 GAGCGAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:41712523 original size:16 final size:16
Alignment explanation
Indices: 41712497--41712535 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
41712487 TACTTCAATT
*
41712497 GAAAA-AAAAAGAAAC
1 GAAAAGAAAAAGAAAA
41712512 GAAAAGAAAAAGAAAA
1 GAAAAGAAAAAGAAAA
41712528 GAAAAGAA
1 GAAAAGAA
41712536 GAGCGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAAAGAAAA
Found at i:41713583 original size:45 final size:45
Alignment explanation
Indices: 41713489--41713862 Score: 389
Period size: 45 Copynumber: 8.4 Consensus size: 45
41713479 GGAGTAGGCT
* * * * ** * *
41713489 GAAGATAGCAGATCTTGTC-TCCCGGAGTAGCAATGGAGTAGGTC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
41713533 GAAGATTGTAGATCTTGTTTTCCTGTATTAGCAGCGAAATAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
41713578 AAAGATAGCA-AGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-C
1 GAAGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
41713622 TGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGGTC
1 -GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
41713668 GAAGATAGCAGATCTTGTCTTCTTGTATTGGCAACGAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *** * * *
41713713 GAAGATAGCAGATCTTATCTCCCTG-AGCAGCAGTGGAGTAGGTC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
41713757 GAAGATTGTAGATCTTGTCTTCCTGTATTAGCAGCGAGGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
41713802 GAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-C
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
41713846 TGAAGATAACAGATCTT
1 -GAAGATAGCAGATCTT
41713863 ATCTCTCTGA
Statistics
Matches: 270, Mismatches: 53, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
44 51 0.19
45 217 0.80
46 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:41713999 original size:129 final size:129
Alignment explanation
Indices: 41713856--41714104 Score: 399
Period size: 129 Copynumber: 1.9 Consensus size: 129
41713846 TGAAGATAAC
* * * *
41713856 AGATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGTA
1 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTAAAGTTGCA
* * *
41713921 GTGAAGTAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAT
66 ATGAAGTAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAAATAT
* *
41713985 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCTCTAAAGTTGCA
1 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTAAAGTTGCA
* *
41714050 ATGGAGTAGATAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTAGAGCAGAT
66 ATGAAGTAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTAGAGCAGAT
41714105 CGCATCCAGT
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 109 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (129 bp):
AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTAAAGTTGCA
ATGAAGTAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAAATAT
Found at i:41714156 original size:129 final size:129
Alignment explanation
Indices: 41714042--41714493 Score: 656
Period size: 129 Copynumber: 3.5 Consensus size: 129
41714032 TATCTCTCTA
* * * * * *
41714042 AAGTTGCAATGGAGTAGATAGAAGAAAC-CA-ATCCTATCTCCCTAAAGTTGCAGTAGAGCAGAT
1 AAGTTGCAGTGGAGCAGAT-TAA-AAACACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
* * * *
41714105 CGCATCCAGTCTAATCTCCCTAAAGTTGCAGTGGAGCAGACAGAAGAATCCAATCCTATCTTCCT
64 CGCATCCAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTTCCT
41714170 G
129 G
* * * *
41714171 AAGTTGTAGTGGAGCGGATTAAAAACACAGATCTTATCTCTCTAAAGTTACAGTAGAGCAGATCG
1 AAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCG
* *
41714236 CATCCAGTCTTGTCTCACTGAAGTTGCAGTGGAGCAGAAAGAAGAAACCAATCCTATCTTCCTG
66 CATCCAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTTCCTG
* *
41714300 AAGTTGCAGTAGAGAAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCG
1 AAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCG
* * *
41714365 CATCTAGTCTTATCTCACTGAAGTTGCAGTGGAGTAGACGGAAGAAACCAATCCTATCTTCCTG
66 CATCCAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTTCCTG
* * *
41714429 AATTTGCAGTGGAGCGGATTAAAAACACAGATCTTATCTCTCTGAAGCTGCAGTAGAGCAGATCG
1 AAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCG
41714494 TATCAGACTT
Statistics
Matches: 291, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
127 4 0.01
128 4 0.01
129 283 0.97
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (129 bp):
AAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCG
CATCCAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTTCCTG
Found at i:41714160 original size:214 final size:214
Alignment explanation
Indices: 41713862--41714318 Score: 680
Period size: 214 Copynumber: 2.1 Consensus size: 214
41713852 TAACAGATCT
* * * * * *
41713862 TATCTCTCTGAAGTTGTAGTAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGTAGTGAAG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTAATCTCCCTAAAGTTGCAGTGAAG
* * *
41713927 TAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATATAGATCTT
66 CAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTT
* * * *
41713992 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCTCTAAAGTTGCAATGGAGT
131 ATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCCAGTCTTATCTCACTAAAGTTGCAATGGAGC
*
41714057 AGATAGAAGAAACCAATCC
196 AGAAAGAAGAAACCAATCC
* * *
41714076 TATCTCCCTAAAGTTGCAGTAGAGCAGATCGCATCCAGTCTAATCTCCCTAAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTAATCTCCCTAAAGTTGCAGTGAAG
* * * *
41714141 CAGACAGAAGAATCCAATCCTATCTTCCTGAAGTTGTAGTGGAGCGGATTAAAAACACAGATCTT
66 CAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTT
* * *
41714206 ATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCCAGTCTTGTCTCACTGAAGTTGCAGTGGAGC
131 ATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCCAGTCTTATCTCACTAAAGTTGCAATGGAGC
41714271 AGAAAGAAGAAACCAATCC
196 AGAAAGAAGAAACCAATCC
* *
41714290 TATCTTCCTGAAGTTGCAGTAGAGAAGAT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGAT
41714319 TAAAAACACA
Statistics
Matches: 216, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
214 216 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (214 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTAATCTCCCTAAAGTTGCAGTGAAG
CAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTT
ATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCCAGTCTTATCTCACTAAAGTTGCAATGGAGC
AGAAAGAAGAAACCAATCC
Found at i:41714423 original size:85 final size:85
Alignment explanation
Indices: 41713991--41714443 Score: 357
Period size: 85 Copynumber: 5.3 Consensus size: 85
41713981 ATATAGATCT
*
41713991 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCTCTAAAGTTGCAATGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCTCTAAAGTTGCAGTGGAG
*
41714056 TAGATAGAAGAAACCAATCC
66 TAGACAGAAGAAACCAATCC
* * * *
41714076 TATCTCCCTAAAGTTGCAGTAGAGCAGATCGCATCCAGTCTAATCTCCCTAAAGTTGCAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCTCTAAAGTTGCAGTGGAG
* *
41714141 CAGACAGAAGAATCCAATCC
66 TAGACAGAAGAAACCAATCC
* * * *** * *
41714161 TATCT-TCCTGAAGTTGTAGTGGAGCGGATTAAAAACACAGATCTTATCTCTCTAAAGTTACAGT
1 TATCTCT-CTGAAGTTGCAGTAGAGCAGA-TCGCATC-CAG-TCTTATCTCTCTAAAGTTGCAGT
* * * * *
41714225 --AG-AG-CAGATCGCATCCAGTCT
62 GGAGTAGACAGA-AGAAACCAATCC
* * * ** * * * * *
41714246 TGTCTCACTGAAGTTGCAGTGGAGCAGAAAGAAGAAACCAATCCTATCT-TCCTGAAGTTGCAGT
1 TATCTCTCTGAAGTTGCAGTAGAGCAG--A-TCGCATCCAGTCTTATCTCT-CTAAAGTTGCAGT
* * ** *
41714310 AGAGAAGA-TTAA-AAACACAGATCT
62 GGAGTAGACAGAAGAAAC-CA-ATCC
* * *
41714334 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCACTGAAGTTGCAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCTCTAAAGTTGCAGTGGAG
*
41714399 TAGACGGAAGAAACCAATCC
66 TAGACAGAAGAAACCAATCC
* *
41714419 TATCT-TCCTGAATTTGCAGTGGAGC
1 TATCTCT-CTGAAGTTGCAGTAGAGC
41714444 GGATTAAAAA
Statistics
Matches: 290, Mismatches: 59, Indels: 38
0.75 0.15 0.10
Matches are distributed among these distances:
84 6 0.02
85 203 0.70
86 14 0.05
87 17 0.06
88 50 0.17
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (85 bp):
TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCTCTAAAGTTGCAGTGGAG
TAGACAGAAGAAACCAATCC
Found at i:41714467 original size:44 final size:43
Alignment explanation
Indices: 41713855--41714491 Score: 322
Period size: 44 Copynumber: 14.8 Consensus size: 43
41713845 CTGAAGATAA
* * * * * *
41713855 CAGATCTTATCTCTCTGAAGTTGTAGTAGAGCAGA-TCACATC
1 CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAAAC
* * * * * **
41713897 TAG-TCTTATCTCCCTGAAGTTGTAGTGAAGTAGACAGAAGAAAC
1 CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGA-TTAA-AAAC
* * *
41713941 CA-ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATA
1 CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAAA-C
* * * *** *
41713984 TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATC
1 CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAAAC
* * * * *
41714026 CAG-TCTTATCTCTCTAAAGTTGCAATGGAGTAGATAGAAGAAAC
1 CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGAT-TAA-AAAC
* * * * *** *
41714070 CA-ATCCTATCTCCCTAAAGTTGCAGTAGAGCAGA-TCGCATC
1 CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAAAC
* * * *
41714111 CAG-TCTAATCTCCCTAAAGTTGCAGTGGAGCAGA-CAGAAGAATC
1 CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTA-AA-AA-C
* * *
41714155 CA-ATCCTATCTTC-CTGAAGTTGTAGTGGAGCGGATTAAAAAC
1 CAGATCTTATC-TCACTGAAGTTGCAGTGGAGCAGATTAAAAAC
* * * * *** *
41714197 ACAGATCTTATCTCTCTAAAGTTACAGTAGAGCAGA-TCGCATC
1 -CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAAAC
* **
41714240 CAG-TCTTGTCTCACTGAAGTTGCAGTGGAGCAGAAAGAAGAAAC
1 CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAG-ATTAA-AAAC
* * *
41714284 CA-ATCCTATCTTC-CTGAAGTTGCAGTAGAGAAGATTAAAAAC
1 CAGATCTTATC-TCACTGAAGTTGCAGTGGAGCAGATTAAAAAC
* * *** *
41714326 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATC
1 -CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAAAC
* * **
41714369 TAG-TCTTATCTCACTGAAGTTGCAGTGGAGTAGACGGAAGAAAC
1 CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGA-TTAA-AAAC
* * *
41714413 CA-ATCCTATCTTC-CTGAATTTGCAGTGGAGCGGATTAAAAAC
1 CAGATCTTATC-TCACTGAAGTTGCAGTGGAGCAGATTAAAAAC
* * *
41714455 ACAGATCTTATCTCTCTGAAGCTGCAGTAGAGCAGAT
1 -CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGAT
41714492 CGTATCAGAC
Statistics
Matches: 446, Mismatches: 113, Indels: 70
0.71 0.18 0.11
Matches are distributed among these distances:
41 139 0.31
42 22 0.05
43 32 0.07
44 246 0.55
45 7 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
CAGATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAAAC
Found at i:41715462 original size:5 final size:5
Alignment explanation
Indices: 41715452--41715480 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
41715442 TTTTTATCCT
41715452 TTTTA TTTTA TTTTA TTTTA TTTT- TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
41715481 CATATTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:41716490 original size:17 final size:17
Alignment explanation
Indices: 41716468--41716501 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41716458 ATTTAAATTG
41716468 TTTATATTGTTTATTTC
1 TTTATATTGTTTATTTC
*
41716485 TTTATATTTTTTATTTC
1 TTTATATTGTTTATTTC
41716502 AAAAATGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTATATTGTTTATTTC
Found at i:41723166 original size:11 final size:12
Alignment explanation
Indices: 41723150--41723178 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41723140 CCCCTAATTA
41723150 AAAGTG-TTGAG
1 AAAGTGATTGAG
41723161 AAAGTGATTGAG
1 AAAGTGATTGAG
41723173 AAAGTG
1 AAAGTG
41723179 GTGTTCAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.24
Consensus pattern (12 bp):
AAAGTGATTGAG
Found at i:41728587 original size:44 final size:44
Alignment explanation
Indices: 41728524--41728611 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
41728514 TGCATTTGAT
*
41728524 CATTTTAACTAGGTTTAATTTAATAACAAGCCTTCAAATTATAA
1 CATTTTAACTAGGTTTAATTTAATAACAAGCCTTCAAAATATAA
41728568 CATTTTAACTAGGTTTAATTTAATAACAAGCCTTCAAAATATAA
1 CATTTTAACTAGGTTTAATTTAATAACAAGCCTTCAAAATATAA
41728612 TTTTATTATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.38
Consensus pattern (44 bp):
CATTTTAACTAGGTTTAATTTAATAACAAGCCTTCAAAATATAA
Found at i:41735456 original size:59 final size:59
Alignment explanation
Indices: 41735393--41735563 Score: 163
Period size: 60 Copynumber: 2.9 Consensus size: 59
41735383 TGTCTGATTC
* *
41735393 TGTTATATGTGAAGCATTTGTGGC-GAAATATGTTATTTGAGA-GCCTTTGTGGTGGAATA
1 TGTTATATG-GAAGCATTTGTGGCTG-AATATGTTATATGAGACGCATTTGTGGTGGAATA
* * *
41735452 TGTTATATGGAAGTCA-TTGTGGCTGATTCTGTTATATGTGACGCATTTGTGGTGGAATA
1 TGTTATATGGAAG-CATTTGTGGCTGAATATGTTATATGAGACGCATTTGTGGTGGAATA
* * * * *
41735511 TATTATATGGGAAGGC-TTTGTGGGTGATTCTGTTATATGTGACG-ACTTTGTGG
1 TGTTATAT-GGAA-GCATTTGTGGCTGAATATGTTATATGAGACGCA-TTTGTGG
41735564 CTATCTATAC
Statistics
Matches: 98, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
58 23 0.23
59 36 0.37
60 38 0.39
61 1 0.01
ACGTcount: A:0.22, C:0.08, G:0.30, T:0.40
Consensus pattern (59 bp):
TGTTATATGGAAGCATTTGTGGCTGAATATGTTATATGAGACGCATTTGTGGTGGAATA
Found at i:41735471 original size:29 final size:29
Alignment explanation
Indices: 41735393--41735533 Score: 119
Period size: 29 Copynumber: 4.8 Consensus size: 29
41735383 TGTCTGATTC
* *
41735393 TGTTATATGTGAAGCATTTGTGGCGAAATA
1 TGTTATATG-GAAGCATTTGTGGTGGAATA
* *
41735423 TGTTAT-TTGAGAGCCTTTGTGGTGGAATA
1 TGTTATATGGA-AGCATTTGTGGTGGAATA
* *
41735452 TGTTATATGGAAGTCA-TTGTGGCT-GATTC
1 TGTTATATGGAAG-CATTTGTGG-TGGAATA
*
41735481 TGTTATATGTGACGCATTTGTGGTGGAATA
1 TGTTATATG-GAAGCATTTGTGGTGGAATA
*
41735511 TATTATATGGGAAGGC-TTTGTGG
1 TGTTATAT-GGAA-GCATTTGTGG
41735534 GTGATTCTGT
Statistics
Matches: 89, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
28 2 0.02
29 45 0.51
30 39 0.44
31 3 0.03
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (29 bp):
TGTTATATGGAAGCATTTGTGGTGGAATA
Found at i:41735546 original size:60 final size:59
Alignment explanation
Indices: 41735437--41735563 Score: 193
Period size: 60 Copynumber: 2.1 Consensus size: 59
41735427 ATTTGAGAGC
* *
41735437 CTTTGTGGTGGAATATGTTATATGGAAGTCATTGTGGCTGATTCTGTTATATGTGACG-
1 CTTTGTGGTGGAATATATTATATGGAAGGCATTGTGGCTGATTCTGTTATATGTGACGA
* *
41735495 CATTTGTGGTGGAATATATTATATGGGAAGGCTTTGTGGGTGATTCTGTTATATGTGACGA
1 C-TTTGTGGTGGAATATATTATAT-GGAAGGCATTGTGGCTGATTCTGTTATATGTGACGA
41735556 CTTTGTGG
1 CTTTGTGG
41735564 CTATCTATAC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
58 1 0.02
59 21 0.34
60 39 0.63
61 1 0.02
ACGTcount: A:0.20, C:0.08, G:0.31, T:0.41
Consensus pattern (59 bp):
CTTTGTGGTGGAATATATTATATGGAAGGCATTGTGGCTGATTCTGTTATATGTGACGA
Found at i:41735547 original size:30 final size:30
Alignment explanation
Indices: 41735452--41735563 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 30
41735442 TGGTGGAATA
* * *
41735452 TGTTATAT-GGAAGTCATTGTGGCTGATTC
1 TGTTATATGGGAAGGCTTTGTGGGTGATTC
* * * *
41735481 TGTTATATGTG-ACGCATTTGT-GGTGGAATA
1 TGTTATATGGGAAGGC-TTTGTGGGT-GATTC
*
41735511 TATTATATGGGAAGGCTTTGTGGGTGATTC
1 TGTTATATGGGAAGGCTTTGTGGGTGATTC
* * *
41735541 TGTTATATGTGACGACTTTGTGG
1 TGTTATATGGGAAGGCTTTGTGG
41735564 CTATCTATAC
Statistics
Matches: 62, Mismatches: 16, Indels: 9
0.71 0.18 0.10
Matches are distributed among these distances:
29 12 0.19
30 44 0.71
31 6 0.10
ACGTcount: A:0.21, C:0.08, G:0.30, T:0.41
Consensus pattern (30 bp):
TGTTATATGGGAAGGCTTTGTGGGTGATTC
Found at i:41740844 original size:7 final size:8
Alignment explanation
Indices: 41740831--41740864 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
41740821 AAAAAAGTAC
41740831 AAAAAAAT
1 AAAAAAAT
41740839 AAAAAAAT
1 AAAAAAAT
41740847 AAAAAAATT
1 AAAAAAA-T
*
41740856 TAAAAAAT
1 AAAAAAAT
41740864 A
1 A
41740865 TTCTGTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAAAAAT
Found at i:41745618 original size:16 final size:16
Alignment explanation
Indices: 41745597--41745661 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
41745587 TTCGCTGTAT
41745597 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
41745613 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
41745629 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
* *
41745645 TGTAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
41745661 T
1 T
41745662 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.37, C:0.03, G:0.35, T:0.25
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:41745912 original size:16 final size:16
Alignment explanation
Indices: 41745875--41745916 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41745865 TTAATCATAT
*
41745875 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
41745891 TT-AAATATATTATAA
1 TTAAAATATATTATAA
41745906 TTAAAATATAT
1 TTAAAATATAT
41745917 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:41745923 original size:14 final size:15
Alignment explanation
Indices: 41745884--41745925 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41745874 TTTAAACATA
*
41745884 ATTATTATTAAATAT
1 ATTATAATTAAATAT
41745899 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
41745913 A-TATAATTTAATA
1 ATTATAATTAAATA
41745926 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:41746043 original size:14 final size:15
Alignment explanation
Indices: 41745994--41746045 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41745984 ATAAAATAGA
41745994 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
41746009 TATTAAATATATTAT
1 AATTAAATATATTAT
41746024 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
41746037 AATTTAATA
1 AATTAAATA
41746046 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:41746163 original size:14 final size:15
Alignment explanation
Indices: 41746114--41746165 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41746104 ATAAAAGATA
41746114 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
41746129 TATTAAATATATTAT
1 AATTAAATATATTAT
41746144 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
41746157 AATTTAATA
1 AATTAAATA
41746166 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:41746301 original size:120 final size:120
Alignment explanation
Indices: 41745878--41746290 Score: 738
Period size: 120 Copynumber: 3.4 Consensus size: 120
41745868 ATCATATTTA
*
41745878 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
41745943 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATAGAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
41745998 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
41746063 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
41746118 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
41746183 TATTCTTATATGAATTTAGTCAAATCATAATATATGATACTATAAAAGATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
* * *
41746238 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
41746291 TAAAATAATT
Statistics
Matches: 284, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
120 282 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
Found at i:41746360 original size:26 final size:28
Alignment explanation
Indices: 41746331--41746391 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
41746321 TATGAATTTG
*
41746331 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
41746357 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
41746385 TAAAATT
1 TATAATT
41746392 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:41746401 original size:91 final size:90
Alignment explanation
Indices: 41746306--41746513 Score: 299
Period size: 91 Copynumber: 2.3 Consensus size: 90
41746296 TAATTATAAC
** * * * *
41746306 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTAAACAATTTAAAATAATTAATAATAAATATAATTTAATAAT
*
41746371 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
*
41746397 TAATAAGTTTTCTTATATGAATTTAAACAATTTAAAATAATTAATAATAAATATAATTTAATAAT
1 TAATAA-ATTTCTTATATGAATTTAAACAATTTAAAATAATTAATAATAAATATAATTTAATAAT
*
41746462 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
41746488 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
41746514 CTAAAATCAA
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
91 84 0.81
92 20 0.19
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTAAACAATTTAAAATAATTAATAATAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:41746454 original size:16 final size:16
Alignment explanation
Indices: 41746429--41746472 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
41746419 TTAAACAATT
41746429 TAAA-ATAATTAATAA
1 TAAATATAATTAATAA
41746444 TAAATATAATTTAATAA
1 TAAATATAA-TTAATAA
*
41746461 TGATATATAATT
1 T-AAATATAATT
41746473 TCATAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 4 0.16
16 4 0.16
17 10 0.40
18 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TAAATATAATTAATAA
Found at i:41746470 original size:18 final size:17
Alignment explanation
Indices: 41746429--41746478 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
41746419 TTAAACAATT
41746429 TAAA-ATAA-TTAATAA
1 TAAATATAATTTAATAA
41746444 TAAATATAATTTAATAA
1 TAAATATAATTTAATAA
* *
41746461 TGATATATAATTTCATAA
1 T-AAATATAATTTAATAA
41746479 AATTCTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 8 0.27
18 14 0.47
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATATAATTTAATAA
Found at i:41746473 original size:44 final size:43
Alignment explanation
Indices: 41746287--41746473 Score: 103
Period size: 44 Copynumber: 4.1 Consensus size: 43
41746277 GATTTAATAA
* *
41746287 AATTTAAAATAATTATAACTAATAAAT-T-ATCTTATATGAATTTGTAT
1 AATTTAAAATAA-T-TAA-TAATAAATATAAT-TTA-AT-AATATATAT
* * *
41746334 AATTTAAAATAATTATTATTACATATAATTTAATAATAATATAT
1 AATTTAAAATAATTAATAATAAATATAATTTAATAAT-ATATAT
** * * * * * *
41746378 AATTTCATAAAATTCTTGATAATAAGT-T-TTCTTATATGAATTTAAAC
1 AA-TT--TAAAATAATTAATAATAAATATAAT-TTA-AT-AATATATAT
41746425 AATTTAAAATAATTAATAATAAATATAATTTAATAATGATATAT
1 AATTTAAAATAATTAATAATAAATATAATTTAATAAT-ATATAT
41746469 AATTT
1 AATTT
41746474 CATAAAATTC
Statistics
Matches: 104, Mismatches: 24, Indels: 27
0.67 0.15 0.17
Matches are distributed among these distances:
43 6 0.06
44 40 0.38
45 13 0.12
46 10 0.10
47 32 0.31
48 3 0.03
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (43 bp):
AATTTAAAATAATTAATAATAAATATAATTTAATAATATATAT
Found at i:41746489 original size:44 final size:43
Alignment explanation
Indices: 41746356--41746490 Score: 103
Period size: 44 Copynumber: 3.0 Consensus size: 43
41746346 TTATTATTAC
*
41746356 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGAT-A
1 ATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAATAA
** * * * * **
41746399 ATAAGTTTTCTTATATGAATTTAAACAATTT-AAAATAATTAATAATAA
1 AT-A-TAAT-TTA-AT-AATATATATAATTTCATAA-AATTCTTAATAA
41746447 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAA
1 ATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAATAA
41746491 TAAAATGTTC
Statistics
Matches: 66, Mismatches: 17, Indels: 17
0.66 0.17 0.17
Matches are distributed among these distances:
43 5 0.08
44 21 0.32
45 8 0.12
46 8 0.12
47 18 0.27
48 6 0.09
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (43 bp):
ATATAATTTAATAATATATATAATTTCATAAAATTCTTAATAA
Found at i:41746491 original size:47 final size:47
Alignment explanation
Indices: 41746356--41746494 Score: 128
Period size: 47 Copynumber: 3.0 Consensus size: 47
41746346 TTATTATTAC
* *
41746356 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * * * **
41746403 GT-T--TTCTTAT-ATGAATTTAAACAATT--TAAAATAATTAATAATAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
41746447 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
41746494 A
1 A
41746495 ATGTTCTTAT
Statistics
Matches: 67, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
44 20 0.30
45 12 0.18
46 12 0.18
47 23 0.34
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:41746790 original size:2 final size:2
Alignment explanation
Indices: 41746783--41746815 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41746773 CTGGCATAAA
41746783 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
41746816 TTTTGACAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41747535 original size:15 final size:16
Alignment explanation
Indices: 41747514--41747559 Score: 78
Period size: 15 Copynumber: 3.0 Consensus size: 16
41747504 ATTGACAACA
41747514 TCAAAACAGAACACAT
1 TCAAAACAGAACACAT
41747530 TC-AAACAGAACACA-
1 TCAAAACAGAACACAT
41747544 TCAAAACAGAACACAT
1 TCAAAACAGAACACAT
41747560 GCCGACCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.57, C:0.26, G:0.07, T:0.11
Consensus pattern (16 bp):
TCAAAACAGAACACAT
Found at i:41750901 original size:8 final size:7
Alignment explanation
Indices: 41750860--41750921 Score: 53
Period size: 7 Copynumber: 9.3 Consensus size: 7
41750850 AAAATAAAGC
41750860 ATATAAA
1 ATATAAA
*
41750867 ATAGAAA
1 ATATAAA
41750874 A-AT-AA
1 ATATAAA
41750879 ATATAAA
1 ATATAAA
41750886 ATATAAA
1 ATATAAA
41750893 ATAATAAA
1 AT-ATAAA
*
41750901 AGGA-AAA
1 A-TATAAA
41750908 A-ATAAA
1 ATATAAA
41750914 A-ATAAA
1 ATATAAA
41750920 AT
1 AT
41750922 TGGGTTCCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
5 4 0.09
6 13 0.28
7 22 0.48
8 7 0.15
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (7 bp):
ATATAAA
Found at i:41755239 original size:16 final size:16
Alignment explanation
Indices: 41755214--41755244 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41755204 GTATGCTATT
*
41755214 TTTGACATGCATAGTG
1 TTTGAAATGCATAGTG
41755230 TTTGAAATGCATAGT
1 TTTGAAATGCATAGT
41755245 TATAGCCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (16 bp):
TTTGAAATGCATAGTG
Found at i:41765581 original size:18 final size:18
Alignment explanation
Indices: 41765536--41765595 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 18
41765526 AACAATTGAG
41765536 AGAAAAAGAAAGGAGTAAAG-
1 AGAAAAAGAAA-GA--AAAGA
41765556 AGACAAAAGAAAGAAAAGA
1 AGA-AAAAGAAAGAAAAGA
*
41765575 AGAAAAATCAAGAGAAAAGA
1 AGAAAAA-GAA-AGAAAAGA
41765595 A
1 A
41765596 ATTGAGTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 8 0.23
19 5 0.14
20 14 0.40
21 8 0.23
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.03
Consensus pattern (18 bp):
AGAAAAAGAAAGAAAAGA
Found at i:41766835 original size:20 final size:20
Alignment explanation
Indices: 41766798--41766835 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41766788 ATTCAGCTCC
*
41766798 AATCAGCTCAGTTGAGCTGA
1 AATCAGCTCAGTTAAGCTGA
41766818 AATCAGCTC-GTTTAAGCT
1 AATCAGCTCAG-TTAAGCT
41766836 CAATTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (20 bp):
AATCAGCTCAGTTAAGCTGA
Found at i:41772463 original size:42 final size:43
Alignment explanation
Indices: 41772404--41772508 Score: 176
Period size: 43 Copynumber: 2.5 Consensus size: 43
41772394 ACCCCTTGGG
* * *
41772404 GGAATCAGCACTTAGCAACCCCC-TTCACATTTCAGATGCGGT
1 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGT
41772446 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGT
41772489 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
41772509 ACCAATGAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
42 23 0.39
43 36 0.61
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGT
Found at i:41779051 original size:18 final size:20
Alignment explanation
Indices: 41779028--41779072 Score: 67
Period size: 18 Copynumber: 2.3 Consensus size: 20
41779018 AAAGTTATGT
41779028 AAAAAAATTAAAT-AAA-AC
1 AAAAAAATTAAATGAAATAC
41779046 AAAAAAATTAAATGAAATTAC
1 AAAAAAATTAAATGAAA-TAC
41779067 AAAAAA
1 AAAAAA
41779073 CAAATAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.54
19 3 0.12
21 8 0.33
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAAAAATTAAATGAAATAC
Found at i:41782288 original size:22 final size:22
Alignment explanation
Indices: 41782247--41782288 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
41782237 ACAAAGGTTG
*
41782247 ATATTTTTTTTATTTCATTTTT
1 ATATTTTATTTATTTCATTTTT
41782269 ATATGTTTATTTATTT-ATTT
1 ATAT-TTTATTTATTTCATTT
41782289 ATTAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
ATATTTTATTTATTTCATTTTT
Found at i:41783365 original size:21 final size:21
Alignment explanation
Indices: 41783322--41783365 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41783312 TATTTTCCTT
*
41783322 TATTTTCATAAATACATTATA
1 TATTTTCATAAATAAATTATA
* * *
41783343 TATTTTGATATATAAATTTTA
1 TATTTTCATAAATAAATTATA
41783364 TA
1 TA
41783366 ATTCTAGATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTTTCATAAATAAATTATA
Found at i:41783605 original size:13 final size:14
Alignment explanation
Indices: 41783572--41783608 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
41783562 TTTCTTATGA
41783572 ATATTAGTTTCGTTT
1 ATATTA-TTTCGTTT
41783587 AT-TTATTT-GTTT
1 ATATTATTTCGTTT
41783599 ATATTATTTC
1 ATATTATTTC
41783609 TATGCCATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 3 0.15
15 2 0.10
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (14 bp):
ATATTATTTCGTTT
Found at i:41783635 original size:15 final size:15
Alignment explanation
Indices: 41783615--41783649 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41783605 TTTCTATGCC
41783615 ATTGTTGTATTTATT
1 ATTGTTGTATTTATT
*
41783630 ATTGTTGTATTTGTT
1 ATTGTTGTATTTATT
41783645 ATTGT
1 ATTGT
41783650 GACATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (15 bp):
ATTGTTGTATTTATT
Found at i:41787483 original size:21 final size:21
Alignment explanation
Indices: 41787453--41787512 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
41787443 TGTGGATCAA
* *
41787453 CTCTTTTGAGCTTCTTTTCAG
1 CTCTTATGAGCTTCTGTTCAG
41787474 CTCTTATGAGCTTCTGTTCAG
1 CTCTTATGAGCTTCTGTTCAG
*
41787495 CTCTTATGAGCTTTTGTT
1 CTCTTATGAGCTTCTGTT
41787513 GGCGTGTTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.12, C:0.22, G:0.17, T:0.50
Consensus pattern (21 bp):
CTCTTATGAGCTTCTGTTCAG
Found at i:41796559 original size:26 final size:26
Alignment explanation
Indices: 41796512--41796561 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
41796502 TTCATATTAT
*
41796512 TGAAATTAAAATTTATTGTTAAAATA
1 TGAAATTAAAATTTAATGTTAAAATA
*
41796538 TGAAATTGAAA-TTAATGCTTAAAA
1 TGAAATTAAAATTTAATG-TTAAAA
41796562 CAAGTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (26 bp):
TGAAATTAAAATTTAATGTTAAAATA
Found at i:41796724 original size:33 final size:32
Alignment explanation
Indices: 41796652--41796727 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
41796642 ATGTTTATAT
* *
41796652 GTAAGATCC-TAACTGGGATATGGCATTTTAAT
1 GTAAGA-CCATAACTGGGATATGGCATTTGAAC
* *
41796684 GAAAAGACCATAACTGGGTTATGGCACTTTGAAC
1 G-TAAGACCATAACTGGGATATGGCA-TTTGAAC
41796718 GTAAGACCAT
1 GTAAGACCAT
41796728 GGTTGGACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
32 3 0.08
33 27 0.75
34 6 0.17
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (32 bp):
GTAAGACCATAACTGGGATATGGCATTTGAAC
Found at i:41796793 original size:101 final size:101
Alignment explanation
Indices: 41796618--41796812 Score: 275
Period size: 101 Copynumber: 1.9 Consensus size: 101
41796608 AATTGACGAA
* * *
41796618 TAAGACCATGGTTGGACCATGGCAATGTTTATATGTAAGATCCTAACTGGGATATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGATCCTAACTGGGATATGGCATTCTAA
41796683 TGAAAAGACCATAACTGGGTTATGGCACTTTGAACG
66 TGAAAAGACCATAACTGGGTTATGGCACTTTGAACG
* * * ** *
41796719 TAAGACCATGGTTGGACTATGGTAGTATTTATAAGTAAGA-CCATAGTTGGGCTATGGCATTCTA
1 TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGATCC-TAACTGGGATATGGCATTCTA
* *
41796783 ATGATAAGACCATAATTGGGTTATGGCACT
65 ATGAAAAGACCATAACTGGGTTATGGCACT
41796813 ACAAATCTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 2 0.02
101 80 0.98
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGATCCTAACTGGGATATGGCATTCTAA
TGAAAAGACCATAACTGGGTTATGGCACTTTGAACG
Found at i:41796796 original size:33 final size:33
Alignment explanation
Indices: 41796665--41796812 Score: 111
Period size: 33 Copynumber: 4.4 Consensus size: 33
41796655 AGATCCTAAC
* * * *
41796665 TGGGATATGGCATTTTAATGAAAAGACCATAAC
1 TGGGCTATGGCACTTTAATGATAAGACCATAAT
* * **
41796698 TGGGTTATGGCACTTTGAACG-TAAGACCATGGT
1 TGGGCTATGGCACTTT-AATGATAAGACCATAAT
* * * * * *
41796731 TGGACTATGGTAGTATTTATAAGTAAGACCATAGT
1 TGGGCTATGGCACT-TTAATGA-TAAGACCATAAT
41796766 TGGGCTATGGCA-TTCTAATGATAAGACCATAAT
1 TGGGCTATGGCACTT-TAATGATAAGACCATAAT
*
41796799 TGGGTTATGGCACT
1 TGGGCTATGGCACT
41796813 ACAAATCTAA
Statistics
Matches: 88, Mismatches: 21, Indels: 11
0.73 0.17 0.09
Matches are distributed among these distances:
33 56 0.64
34 11 0.12
35 21 0.24
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (33 bp):
TGGGCTATGGCACTTTAATGATAAGACCATAAT
Found at i:41796828 original size:101 final size:101
Alignment explanation
Indices: 41796618--41796845 Score: 262
Period size: 101 Copynumber: 2.3 Consensus size: 101
41796608 AATTGACGAA
* * *
41796618 TAAGACCATGGTTGGACCATGGCAATGTTTATATGTAAGATCCTAACTGGGATATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGATCCTAACTGGGATATGGCATTCTAA
***
41796683 TGAAAAGACCATAACTGGGTTATGGCACTTTGAACG
66 TGAAAAGACCATAACTGGGTTATGGCACTACAAACG
* * * ** *
41796719 TAAGACCATGGTTGGACTATGGTAGTATTTATAAGTAAGA-CCATAGTTGGGCTATGGCATTCTA
1 TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGATCC-TAACTGGGATATGGCATTCTA
* *
41796783 ATGATAAGACCATAATTGGGTTATGGCACTACAAATC-
65 ATGAAAAGACCATAACTGGGTTATGGCACTACAAA-CG
* * * *
41796820 TAATACCATGGCTGGGCCATGACAAT
1 TAAGACCATGGTTGGACCATGGCAAT
41796846 GCATGTGTAA
Statistics
Matches: 104, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
100 2 0.02
101 101 0.97
102 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGATCCTAACTGGGATATGGCATTCTAA
TGAAAAGACCATAACTGGGTTATGGCACTACAAACG
Found at i:41800453 original size:19 final size:20
Alignment explanation
Indices: 41800407--41800458 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
41800397 GGGTTGGCAT
41800407 TTTGGTGCCTCTGATTGCACA
1 TTTGGTG-CTCTGATTGCACA
41800428 TTT-GTGCTCT-ATCTGCAC-
1 TTTGGTGCTCTGAT-TGCACA
41800446 TTTGGTGCATCTG
1 TTTGGTGC-TCTG
41800459 TTACGCGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 5 0.19
19 13 0.48
20 6 0.22
21 3 0.11
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (20 bp):
TTTGGTGCTCTGATTGCACA
Found at i:41803996 original size:9 final size:9
Alignment explanation
Indices: 41803979--41804045 Score: 116
Period size: 9 Copynumber: 7.4 Consensus size: 9
41803969 TCGAGTTGAT
41803979 TCGAATAAC
1 TCGAATAAC
*
41803988 TCGATTAAC
1 TCGAATAAC
41803997 TCGAATAAC
1 TCGAATAAC
41804006 TCGAATAAC
1 TCGAATAAC
*
41804015 TCGATTAAC
1 TCGAATAAC
41804024 TCGAATAAC
1 TCGAATAAC
41804033 TCGAATAAC
1 TCGAATAAC
41804042 TCGA
1 TCGA
41804046 TTCGTTTAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.25
Consensus pattern (9 bp):
TCGAATAAC
Found at i:41804010 original size:27 final size:27
Alignment explanation
Indices: 41803979--41804047 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
41803969 TCGAGTTGAT
41803979 TCGAATAACTCGATTAACTCGAATAAC
1 TCGAATAACTCGATTAACTCGAATAAC
41804006 TCGAATAACTCGATTAACTCGAATAAC
1 TCGAATAACTCGATTAACTCGAATAAC
41804033 TCGAATAACTCGATT
1 TCGAATAACTCGATT
41804048 CGTTTAACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.28
Consensus pattern (27 bp):
TCGAATAACTCGATTAACTCGAATAAC
Found at i:41804178 original size:2 final size:2
Alignment explanation
Indices: 41804171--41804203 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41804161 TCATACATAC
41804171 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 A
41804204 ATAGCAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41807206 original size:29 final size:29
Alignment explanation
Indices: 41807171--41807237 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
41807161 GTGAATGTCT
* * *
41807171 CAACATTGGGATCAGAATGCTCAATGCCG
1 CAACATTGGGATCAAAATGCCCAAGGCCG
* **
41807200 CAACATTGAGATCAAAATGCCCAAGGTTG
1 CAACATTGGGATCAAAATGCCCAAGGCCG
41807229 CAACATTGG
1 CAACATTGG
41807238 CTAGGGAAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (29 bp):
CAACATTGGGATCAAAATGCCCAAGGCCG
Found at i:41809841 original size:4 final size:4
Alignment explanation
Indices: 41809832--41809867 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
41809822 TATTAAATCA
41809832 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
41809868 ATCTATTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:41810906 original size:42 final size:42
Alignment explanation
Indices: 41810852--41811030 Score: 200
Period size: 42 Copynumber: 4.3 Consensus size: 42
41810842 GATTTTAGGC
*
41810852 TTACGACTAGCAGGCTT-ATCGCCAGTGAAACAATATCAGACT
1 TTACGTCTAGCAGGCTTAAT-GCCAGTGAAACAATATCAGACT
* * * * *
41810894 TTACGTCCAGCAGGCCTAATGCCAGTGAAATAATTTTAGACT
1 TTACGTCTAGCAGGCTTAATGCCAGTGAAACAATATCAGACT
* * * * *
41810936 TTAAGTCTAGCAAGCTTAATTCCAGTGAAAGAATATCAAACT
1 TTACGTCTAGCAGGCTTAATGCCAGTGAAACAATATCAGACT
* *
41810978 TTACGTCTAGCAGGCTTAATGCCGGTGAAAC-ATTTCAGACT
1 TTACGTCTAGCAGGCTTAATGCCAGTGAAACAATATCAGACT
* *
41811019 ATATGTCTAGCA
1 TTACGTCTAGCA
41811031 AGCTAAGTGT
Statistics
Matches: 112, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
41 18 0.16
42 92 0.82
43 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (42 bp):
TTACGTCTAGCAGGCTTAATGCCAGTGAAACAATATCAGACT
Found at i:41810999 original size:84 final size:83
Alignment explanation
Indices: 41810873--41811034 Score: 234
Period size: 84 Copynumber: 1.9 Consensus size: 83
41810863 AGGCTTATCG
* * *
41810873 CCAGTGAAACAATATCAGACTTTACGTCCAGCAGGCCTAATGCCAGTGAAATAATTTTAGACTTT
1 CCAGTGAAACAATATCAAACTTTACGTCCAGCAGGCCTAATGCCAGTGAAA-AATTTCAGACTAT
41810938 AAGTCTAGCAAGCTTAATT
65 AAGTCTAGCAAGCTTAATT
* * * * *
41810957 CCAGTGAAAGAATATCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATA
1 CCAGTGAAACAATATCAAACTTTACGTCCAGCAGGCCTAATGCCAGTGAAAAATTTCAGACTATA
*
41811022 TGTCTAGCAAGCT
66 AGTCTAGCAAGCT
41811035 AAGTGTCGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
83 23 0.33
84 46 0.67
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (83 bp):
CCAGTGAAACAATATCAAACTTTACGTCCAGCAGGCCTAATGCCAGTGAAAAATTTCAGACTATA
AGTCTAGCAAGCTTAATT
Found at i:41818184 original size:41 final size:42
Alignment explanation
Indices: 41818056--41818244 Score: 192
Period size: 41 Copynumber: 4.5 Consensus size: 42
41818046 GGCTTAGCGC
* * * *
41818056 CTAGTAGGCTT-ATCGCCAGTGAAATAATTTCAGACTTTACGT
1 CTAGCAGGCTTAAT-GCCGGTGAAACAATATCAGACTTTACGT
*
41818098 CTAGCAGGCTTAATGCCGGTAAAACAATATCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGT
* * *
41818140 CTAGCAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGT
* * * *
41818181 CTAGCAGG-ATAAGTGCCGGTG-TACTAA-ATCAGGCTTTAAGT
1 CTAGCAGGCTTAA-TGCCGGTGAAAC-AATATCAGACTTTACGT
41818222 CTAGCAGGC-TAAGTGCCGGTGAA
1 CTAGCAGGCTTAA-TGCCGGTGAA
41818245 TCTATTTAAA
Statistics
Matches: 125, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
40 5 0.04
41 59 0.47
42 59 0.47
43 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (42 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGT
Found at i:41827021 original size:539 final size:539
Alignment explanation
Indices: 41826004--41827069 Score: 1641
Period size: 539 Copynumber: 2.0 Consensus size: 539
41825994 TTGACCTAAT
* *
41826004 CATCAGTAATAACTTTTGTACCTACAGAAGTGTTAACCTGAACATCTCCCATTCCCTTGGCTTCA
1 CATCAGTAATAACTTTTGTACCTACAGAAGTGCTAACCTAAACATCTCCCATTCCCTTGGCTTCA
* * *
41826069 ATGATCTGGCCATTTCAAACTCTGATTCTCGAACTGAATAATCTATCAATCTCCTTGAACATGCT
66 ATGATCTGGCCATTTCAAACTCTGATTCTCAAACTGAAGAATATATCAATCTCCTTGAACATGCT
* *
41826134 TTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACTAGTTTTTCTTGTCTTGGTTGT
131 TTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACCAGTTTTTCTTATCTTGGTTGT
*
41826199 TGACTGTGAAGCATGAAGCAGTGAATGTGAGCTCCTCCTAAGCTTGATTTTCTTCAGCACTTGAG
196 TGACTGTGAAGCATGAAGCAGTGAATGTGAGCTCCTCCTAAGATTGATTTTCTTCAGCACTTGAG
* * *
41826264 CCTGATTAGACTACTATTGTTGTTACTGTACTTTGTTTTTATAAATTCTAAAATCGTGGCCAAAT
261 CCTGATTAGACTACTATTGTTGCTACTGCACTTTGTTTTTACAAATTCTAAAATCGTGGCCAAAT
* *** * * *
41826329 TGCTTACAGTTTTTACACTGTGCACCAATTTTTATCCAACAAAACTTTTATGAATGACCCATCTT
326 TGCTTACAATTTTTACACTACACACCAAGTCTTATCCAACAAAACTTTTATAAATGACCCATCTT
* * * *
41826394 TTTGCAATTCGATCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTTGCCTTTCTCTTGCTT
391 TTTGCAATCCAAGCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTAGCCTTTCTCTTGCTT
* * * * * *
41826459 GATTCCTTTTCTTCTTGCCTTTGTTTCTTGAAGAGCATGGAGTTTCCTTGTTTCTCGCTTGGTAA
456 GATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGTAA
41826524 GCACCTTCTACGTGAAAGA
521 GCACCTTCTACGTGAAAGA
* *
41826543 CATCAGTAATAACTTTTGTACCTATAGAAGTGCTAACCTAAACGTC-CCCATTTCCCTTGGCTTC
1 CATCAGTAATAACTTTTGTACCTACAGAAGTGCTAACCTAAACATCTCCCA-TTCCCTTGGCTTC
* * * *
41826607 AATGATCTGGCCATTTCCAAGTCTGATTCTCAAACTGAAGGATATGTCAATCTCCTTGAACATGC
65 AATGATCTGGCCATTTCAAACTCTGATTCTCAAACTGAAGAATATATCAATCTCCTTGAACATGC
* * *
41826672 TTTCATCTGAAACCATATGGTTTGTACAACCTCTGTCAATCAACCATTTTTTCTTATCTTGGTTG
130 TTTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACCAGTTTTTCTTATCTTGGTTG
* * * *
41826737 TTGATTTTGAAGCATGAAGTAGTGAAT-TCGAGCTCCTCCTGAGATTGATTTTCTTCAGCACTTG
195 TTGACTGTGAAGCATGAAGCAGTGAATGT-GAGCTCCTCCTAAGATTGATTTTCTTCAGCACTTG
* * *
41826801 AGCCTGATTAGACTGCTATTGTTGCTGCTGCACTTTGTTTTTACAAATTCTAAAATTGTGGCCAA
259 AGCCTGATTAGACTACTATTGTTGCTACTGCACTTTGTTTTTACAAATTCTAAAATCGTGGCCAA
* * * ** *
41826866 ATTGCTTACAATTTTTACGCTACACACCAGGTCTTGTCCAGTAAAACTTTTCTAAATGACCCATC
324 ATTGCTTACAATTTTTACACTACACACCAAGTCTTATCCAACAAAACTTTTATAAATGACCCATC
*
41826931 TTTTTGCAATCCAAGCATGGTGGATACTTTTTCTTTTCACCATCTCTTTTTAGCCTTTCTCTTGC
389 TTTTTGCAATCCAAGCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTAGCCTTTCTCTTGC
41826996 TTGATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGT
454 TTGATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGT
41827061 AAGCACCTT
519 AAGCACCTT
41827070 TTGTGTGCCC
Statistics
Matches: 474, Mismatches: 51, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
538 5 0.01
539 469 0.99
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (539 bp):
CATCAGTAATAACTTTTGTACCTACAGAAGTGCTAACCTAAACATCTCCCATTCCCTTGGCTTCA
ATGATCTGGCCATTTCAAACTCTGATTCTCAAACTGAAGAATATATCAATCTCCTTGAACATGCT
TTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACCAGTTTTTCTTATCTTGGTTGT
TGACTGTGAAGCATGAAGCAGTGAATGTGAGCTCCTCCTAAGATTGATTTTCTTCAGCACTTGAG
CCTGATTAGACTACTATTGTTGCTACTGCACTTTGTTTTTACAAATTCTAAAATCGTGGCCAAAT
TGCTTACAATTTTTACACTACACACCAAGTCTTATCCAACAAAACTTTTATAAATGACCCATCTT
TTTGCAATCCAAGCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTAGCCTTTCTCTTGCTT
GATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGTAA
GCACCTTCTACGTGAAAGA
Found at i:41830541 original size:3 final size:3
Alignment explanation
Indices: 41830533--41830568 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
41830523 TTTAACTTAA
41830533 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41830569 TAAAGTGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41839358 original size:33 final size:32
Alignment explanation
Indices: 41839321--41839382 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
41839311 CAACATTATT
41839321 GTTAGATAGTTTT-ATTTGTTTTAGTCACTCATC
1 GTTAGATAGTTTTCA--TGTTTTAGTCACTCATC
* *
41839354 GTTAGTTTGTTTTCATGTTTTAGTCACTC
1 GTTAGATAGTTTTCATGTTTTAGTCACTC
41839383 GTCATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 14 0.54
33 11 0.42
34 1 0.04
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (32 bp):
GTTAGATAGTTTTCATGTTTTAGTCACTCATC
Found at i:41844441 original size:18 final size:19
Alignment explanation
Indices: 41844402--41844445 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
41844392 TACCATTTGA
41844402 ATTAAATATTAATATTATT
1 ATTAAATATTAATATTATT
*
41844421 ATTAAA-ATTAA-ATTGTAT
1 ATTAAATATTAATATTAT-T
41844439 ATTAAAT
1 ATTAAAT
41844446 GATTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTAAATATTAATATTATT
Found at i:41853001 original size:3 final size:3
Alignment explanation
Indices: 41852993--41853029 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
41852983 CATGGTTGCT
41852993 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41853030 AAGAGTCGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41857416 original size:22 final size:22
Alignment explanation
Indices: 41857388--41857540 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
41857378 TGTTGATAGT
*
41857388 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
41857410 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
41857432 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
41857454 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
41857476 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
41857498 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
41857520 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
41857541 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:41863988 original size:43 final size:43
Alignment explanation
Indices: 41863863--41863989 Score: 159
Period size: 41 Copynumber: 3.0 Consensus size: 43
41863853 ATAGGATCTC
* *
41863863 CGATATGTGTTTACGTGTAAGACCATGTCTGGGACATCGGCAT
1 CGATATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
* * *
41863906 CG-TATTTGATT-CGTGTAAGACCCTGTCTGGGACAATGGCAT
1 CGATATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
* * * *
41863947 CGATATGTGATTACATGTAAGACCAGGTATGGGACGTTGGCAT
1 CGATATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
41863990 TGTACGGGAT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 29 0.41
42 15 0.21
43 26 0.37
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (43 bp):
CGATATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
Found at i:41872759 original size:27 final size:27
Alignment explanation
Indices: 41872723--41872777 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
41872713 ACTTAGATTT
**
41872723 TACATTGGTTAAATACTTAGTGTGAGA
1 TACATTGGTTAAATACCAAGTGTGAGA
41872750 TACATTGGTTAAATACCAAGTGTGAGA
1 TACATTGGTTAAATACCAAGTGTGAGA
41872777 T
1 T
41872778 TTGCATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (27 bp):
TACATTGGTTAAATACCAAGTGTGAGA
Done.