Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 105 of 210
Found at i:35498275 original size:26 final size:26
Alignment explanation
Indices: 35498246--35498305 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
35498236 ATTACATTAC
*
35498246 ATTAAATTATATATGTAAAATAA-ATA-
1 ATTAAATTACATAT-T-AAATAATATAT
* *
35498272 ATTATATTCCATATTAAATAATATAT
1 ATTAAATTACATATTAAATAATATAT
35498298 ATTAAATT
1 ATTAAATT
35498306 TTTATTTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 6 0.21
25 4 0.14
26 18 0.64
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAAATTACATATTAAATAATATAT
Found at i:35510632 original size:31 final size:29
Alignment explanation
Indices: 35510591--35510666 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
35510581 GGATAAATAT
* *
35510591 CAAAATTATACATGAACTATGGTTTAATGTG
1 CAAATTTATACATGAACTATGATTT--TGTG
* *
35510622 C-AATTGTATACATAAACTTTGATTTTGTG
1 CAAATT-TATACATGAACTATGATTTTGTG
35510651 CAAATTTATACATGAA
1 CAAATTTATACATGAA
35510667 ATTTTGATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 14 0.37
30 7 0.18
31 17 0.45
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (29 bp):
CAAATTTATACATGAACTATGATTTTGTG
Found at i:35510650 original size:29 final size:30
Alignment explanation
Indices: 35510591--35510676 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
35510581 GGATAAATAT
* * *
35510591 CAAAATTATACATG-AACTATGGTTTAATGTG
1 CAAATTTATACATGAAACTTTGATTT--TGTG
35510622 C-AATTGTATACAT-AAACTTTGATTTTGTG
1 CAAATT-TATACATGAAACTTTGATTTTGTG
*
35510651 CAAATTTATACATGAAATTTTGATTT
1 CAAATTTATACATGAAACTTTGATTT
35510677 GATCCGATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
29 12 0.26
30 18 0.38
31 17 0.36
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (30 bp):
CAAATTTATACATGAAACTTTGATTTTGTG
Found at i:35511536 original size:28 final size:28
Alignment explanation
Indices: 35511492--35511578 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
35511482 TCTAGTGTTA
*
35511492 TTTGACTTTAGATTTTTTATTTTTGAAG
1 TTTGACTTTAGAGTTTTTATTTTTGAAG
* *
35511520 TTTGACTTTAGTA-TTTTCATTTTTGAGG
1 TTTGACTTTAG-AGTTTTTATTTTTGAAG
*
35511548 TTTGACTTTAGAGTTTTTATTTTTGGAG
1 TTTGACTTTAGAGTTTTTATTTTTGAAG
35511576 TTT
1 TTT
35511579 ATTTAACTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
27 1 0.02
28 50 0.96
29 1 0.02
ACGTcount: A:0.18, C:0.05, G:0.17, T:0.60
Consensus pattern (28 bp):
TTTGACTTTAGAGTTTTTATTTTTGAAG
Found at i:35521355 original size:33 final size:33
Alignment explanation
Indices: 35521313--35521379 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
35521303 GCCTTTAACT
35521313 CGTTCGGAACCATTCTCGAACAGTTCCCGGGCA
1 CGTTCGGAACCATTCTCGAACAGTTCCCGGGCA
*
35521346 CGTTCGGAACCATTCTCGAACAGTTTCCGGGCA
1 CGTTCGGAACCATTCTCGAACAGTTCCCGGGCA
35521379 C
1 C
35521380 CCTCTATAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.22
Consensus pattern (33 bp):
CGTTCGGAACCATTCTCGAACAGTTCCCGGGCA
Found at i:35522636 original size:15 final size:14
Alignment explanation
Indices: 35522618--35522655 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
35522608 GATGGAAAAA
*
35522618 AATATATGTATATAT
1 AATATAT-TATAGAT
35522633 AATATA-TATAGAT
1 AATATATTATAGAT
35522646 AATATATTAT
1 AATATATTAT
35522656 TGAAGGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 12 0.57
14 3 0.14
15 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (14 bp):
AATATATTATAGAT
Found at i:35523070 original size:21 final size:21
Alignment explanation
Indices: 35523040--35523105 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 21
35523030 CAAATTTTTT
35523040 ATTTTT-AAAAAAATTATAAA
1 ATTTTTCAAAAAAATTATAAA
*
35523060 ATTTTTC-AAAAAATTCTAAAA
1 ATTTTTCAAAAAAATTAT-AAA
* * *
35523081 ATTATACAAAAAAAGTTAAAAA
1 ATTTTTCAAAAAAA-TTATAAA
35523103 ATT
1 ATT
35523106 ATAAAATTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 15 0.41
21 8 0.22
22 12 0.32
23 2 0.05
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
ATTTTTCAAAAAAATTATAAA
Found at i:35523092 original size:22 final size:21
Alignment explanation
Indices: 35523046--35523108 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
35523036 TTTTATTTTT
* *
35523046 AAAAAAA-TTATAAAATTTTTC
1 AAAAAAATTTA-AAAATTATAC
35523067 -AAAAAATTCTAAAAATTATAC
1 AAAAAAATT-TAAAAATTATAC
*
35523088 AAAAAAAGTTAAAAAATTATA
1 AAAAAAA-TTTAAAAATTATA
35523109 AAATTTCTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 6 0.17
21 9 0.26
22 18 0.51
23 2 0.06
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAAAATTTAAAAATTATAC
Found at i:35527002 original size:31 final size:31
Alignment explanation
Indices: 35526967--35527093 Score: 184
Period size: 31 Copynumber: 4.1 Consensus size: 31
35526957 TATAAAATTA
* * *
35526967 TCATTGAACTATTTGAAAGTATTCATTTAAG
1 TCATTGAACTATTCGAAAGTTTTTATTTAAG
* *
35526998 TCATTGGACTATTCGAAGGTTTTTATTTAAG
1 TCATTGAACTATTCGAAAGTTTTTATTTAAG
*
35527029 TCATTGGACTATTCGAAAGTTTTTATTTAAG
1 TCATTGAACTATTCGAAAGTTTTTATTTAAG
35527060 TCATT-AGACTATTCGAAAGTTTTTATTTAAG
1 TCATTGA-ACTATTCGAAAGTTTTTATTTAAG
35527091 TCA
1 TCA
35527094 CTACGCTATT
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (31 bp):
TCATTGAACTATTCGAAAGTTTTTATTTAAG
Found at i:35527114 original size:62 final size:60
Alignment explanation
Indices: 35526982--35527111 Score: 165
Period size: 62 Copynumber: 2.1 Consensus size: 60
35526972 GAACTATTTG
* * * * **
35526982 AAAGTATTCATTTAAGTCATTGGACTATTCGAAGGTTTTTATTTAAGTCATTGGACTATT
1 AAAGTTTTTATTTAAGTCATTAGACTATTCGAAAGTTTTTATTTAAGTCATACGACTATT
35527042 CGAAAGTTTTTATTTAAGTCATTAGACTATTCGAAAGTTTTTATTTAAGTCACTACG-CTATT
1 --AAAGTTTTTATTTAAGTCATTAGACTATTCGAAAGTTTTTATTTAAGTCA-TACGACTATT
35527104 -AAGTTTTT
1 AAAGTTTTT
35527112 TTTTTTGTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
59 8 0.13
62 51 0.84
63 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (60 bp):
AAAGTTTTTATTTAAGTCATTAGACTATTCGAAAGTTTTTATTTAAGTCATACGACTATT
Found at i:35528052 original size:15 final size:15
Alignment explanation
Indices: 35528028--35528058 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35528018 AAAAAATAAA
35528028 TATTGAAAATTTAAG
1 TATTGAAAATTTAAG
35528043 TATTGAAAATTTAAG
1 TATTGAAAATTTAAG
35528058 T
1 T
35528059 GCTGAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (15 bp):
TATTGAAAATTTAAG
Found at i:35528064 original size:15 final size:15
Alignment explanation
Indices: 35528031--35528064 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35528021 AAATAAATAT
*
35528031 TGAAAATTTAAGTAT
1 TGAAAATTTAAGTAC
*
35528046 TGAAAATTTAAGTGC
1 TGAAAATTTAAGTAC
35528061 TGAA
1 TGAA
35528065 TTTAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAAAATTTAAGTAC
Found at i:35530254 original size:25 final size:25
Alignment explanation
Indices: 35530206--35530255 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
35530196 TATGTACACG
*
35530206 TTATAAAAATGTATAAACATATGAA
1 TTATAAAAATGTATAAACAAATGAA
*
35530231 TTATAAAACATG-ATAAATAAATGAA
1 TTATAAAA-ATGTATAAACAAATGAA
35530256 AAACTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (25 bp):
TTATAAAAATGTATAAACAAATGAA
Found at i:35531956 original size:50 final size:50
Alignment explanation
Indices: 35531902--35532671 Score: 408
Period size: 50 Copynumber: 15.5 Consensus size: 50
35531892 CGAGGAAACC
* * *
35531902 AGATCTGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGAGAAGTA
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* ** * * * * * **
35531952 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* * *
35532002 AGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTA
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
** * ** * * * * * **
35532052 AGATCTACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACC
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* * * *
35532102 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGAGAAATA
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* * ** * * * * * **
35532152 AGATCCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACC
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* ** * * *
35532202 AGATCTGCCGTCAT-AGCTTCAATCTACTCCACTGCACCGCCAGGGAAATA
1 AGATCCGCCGTTGTGA-CTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* * * ** * * * * * *
35532252 AGATCCACCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGGGGAAACA
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* ** * * * *
35532302 AGATTCGCCGTTACGACTTCAATCT-ATTCCACTACACCGCCAGGGAAGTA
1 AGATCCGCCGTTGTGACTTCAATCTGCTT-CACTGCACTGCCAGGGAAATA
* * * * * * * * **
35532352 AGATCCGTCGTTGTGGCTTCAATCT-TTTAATTGCAATGTCGGGGAAACC
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* * * * *
35532401 AGATTCGCCGTCGT-AGCTTCAATATGCTCCACT-CACCGCCAGGGAAATA
1 AGATCCGCCGTTGTGA-CTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* * * * * * * * **
35532450 AGATCCGTCGTTGTGGCTTCAATCT-TTTAATTGCAATGTCGGGGAAACC
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* * * * *
35532499 AGATTCGCCGTCGT-AGCTTCAATTTGCTCCACTGCACCGCCAGGGAAATA
1 AGATCCGCCGTTGTGA-CTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* * * * * * * * **
35532549 AGATCCGCCGTTGTGGCTTAAATCT-TTTAATTGCAATGTCGGGGAAACC
1 AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
* * * * *
35532598 AGATTCGCCGTCGT-AGCTTCAATTTGCTCCACTGCACCGCCAGGGAAATA
1 AGATCCGCCGTTGTGA-CTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
*
35532648 AGAT-CGCCGTTGTGGCTTCAATCT
1 AGATCCGCCGTTGTGACTTCAATCT
35532672 TTTTAATTGT
Statistics
Matches: 495, Mismatches: 212, Indels: 27
0.67 0.29 0.04
Matches are distributed among these distances:
48 3 0.01
49 139 0.28
50 353 0.71
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (50 bp):
AGATCCGCCGTTGTGACTTCAATCTGCTTCACTGCACTGCCAGGGAAATA
Found at i:35532005 original size:100 final size:100
Alignment explanation
Indices: 35531850--35532694 Score: 1212
Period size: 100 Copynumber: 8.5 Consensus size: 100
35531840 GCTAAGGAGG
* ** * *
35531850 TAAGACCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGAGGAAACCAGA-TCTGCCGTT
1 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATTC-GCCGTC
* * * *
35531914 GT-GACTTCAATCTGCTTCACTGCACTGCCAGAGAAG
65 GTAG-CTTCAATCTGCTCCACTGCACCGCCAGGGAAA
** * *
35531950 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACCAGATCCGCCGTTG
1 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCG
*
35532015 T-GACTTCAATCTGCTCCACTGCACCGCCAGGGAAG
66 TAG-CTTCAATCTGCTCCACTGCACCGCCAGGGAAA
** *
35532050 TAAGATCTACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGA-TCTGCCGTT
1 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATTC-GCCGTC
*
35532114 GT-GACTTCAATCTGCTCCACTGCACCGCCAGAGAAA
65 GTAG-CTTCAATCTGCTCCACTGCACCGCCAGGGAAA
*
35532150 TAAGATCCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGA-TCTGCCGTC
1 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATTC-GCCGTC
* *
35532214 ATAGCTTCAATCTACTCCACTGCACCGCCAGGGAAA
65 GTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAA
* * *
35532250 TAAGATCCACCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGGGGAAACAAGATTCGCCGT--
1 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCG
** * *
35532313 TACGACTTCAATCTATTCCACTACACCGCCAGGGAAG
66 TA-G-CTTCAATCTGCTCCACTGCACCGCCAGGGAAA
*
35532350 TAAGATCCGTCGTTGTGGCTTCAATC-TTTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCG
1 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCG
*
35532414 TAGCTTCAATATGCTCCACT-CACCGCCAGGGAAA
66 TAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAA
*
35532448 TAAGATCCGTCGTTGTGGCTTCAATC-TTTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCG
1 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCG
*
35532512 TAGCTTCAATTTGCTCCACTGCACCGCCAGGGAAA
66 TAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAA
*
35532547 TAAGATCCGCCGTTGTGGCTTAAATC-TTTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCG
1 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCG
*
35532611 TAGCTTCAATTTGCTCCACTGCACCGCCAGGGAAA
66 TAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAA
*
35532646 TAAGAT-CGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAA
1 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAA
35532695 TAAAAATCTG
Statistics
Matches: 699, Mismatches: 36, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
98 116 0.17
99 190 0.27
100 387 0.55
101 6 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (100 bp):
TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCG
TAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAA
Found at i:35534551 original size:59 final size:58
Alignment explanation
Indices: 35534472--35534592 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 58
35534462 TGTCTTAGTG
35534472 TAAAGAATTTGAAAAGATTTTAAAATACGATCCTTCCTTTTTATTAATGTTAATTTTA
1 TAAAGAATTTGAAAAGATTTTAAAATACGATCCTTCCTTTTTATTAATGTTAATTTTA
*
35534530 TAAAGGAATTTGAAAATATTTTAAAATACGATCCTTCCTTTTTATTAATGTTAATTTTA
1 TAAA-GAATTTGAAAAGATTTTAAAATACGATCCTTCCTTTTTATTAATGTTAATTTTA
35534589 TAAA
1 TAAA
35534593 AGATGCTTGG
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 4 0.07
59 57 0.93
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (58 bp):
TAAAGAATTTGAAAAGATTTTAAAATACGATCCTTCCTTTTTATTAATGTTAATTTTA
Found at i:35535710 original size:18 final size:19
Alignment explanation
Indices: 35535687--35535748 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
35535677 ATAATCAAAT
35535687 ATAATAAT-GTCAATAACA
1 ATAATAATAGTCAATAACA
*
35535705 ATAATAAATAGT-AATAAAA
1 ATAAT-AATAGTCAATAACA
*
35535724 ATAAAAATAGTCAATTAATCA
1 ATAATAATAGTCAA-TAA-CA
35535745 ATAA
1 ATAA
35535749 ATTAATGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 11 0.31
19 15 0.42
20 5 0.14
21 5 0.14
ACGTcount: A:0.61, C:0.06, G:0.05, T:0.27
Consensus pattern (19 bp):
ATAATAATAGTCAATAACA
Found at i:35537228 original size:67 final size:67
Alignment explanation
Indices: 35537120--35537252 Score: 248
Period size: 67 Copynumber: 2.0 Consensus size: 67
35537110 TTCAATTCAG
35537120 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCA
1 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCA
35537185 AT
66 AT
* *
35537187 AGAGCACACTCCCGCGAACCTCATTTCTTACAGTGGGATTACCAGTCCAGGCTAAATCTCCTGCA
1 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCA
35537252 A
66 A
35537253 CGAAAATTAC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (67 bp):
AGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCA
AT
Found at i:35539180 original size:117 final size:117
Alignment explanation
Indices: 35539048--35539280 Score: 430
Period size: 117 Copynumber: 2.0 Consensus size: 117
35539038 AAAAGAAAAT
* *
35539048 TTTCTTTCTTTCTTCTTCTTCTCATGTTGGTGCATGGGAAAGATGATGAATTCTCTTCATCTTTC
1 TTTCTTTCTTTCTTCTCCTTCTCACGTTGGTGCATGGGAAAGATGATGAATTCTCTTCATCTTTC
35539113 CCCCCTTTTATATTAATCATTTAATAATAAAATAATACTAAAAATCTTAATC
66 CCCCCTTTTATATTAATCATTTAATAATAAAATAATACTAAAAATCTTAATC
*
35539165 TTTCTTTCTTTCTTCTCCTTCTCACGTTGGTTCATGGGAAAGATGATGAATTCTCTTCATCTTTC
1 TTTCTTTCTTTCTTCTCCTTCTCACGTTGGTGCATGGGAAAGATGATGAATTCTCTTCATCTTTC
*
35539230 CTCCCTTTTATATTAATCATTTAATAATAAAATAATACTAAAAATCTTAAT
66 CCCCCTTTTATATTAATCATTTAATAATAAAATAATACTAAAAATCTTAAT
35539281 AAAATATTAA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 112 1.00
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (117 bp):
TTTCTTTCTTTCTTCTCCTTCTCACGTTGGTGCATGGGAAAGATGATGAATTCTCTTCATCTTTC
CCCCCTTTTATATTAATCATTTAATAATAAAATAATACTAAAAATCTTAATC
Found at i:35548345 original size:14 final size:14
Alignment explanation
Indices: 35548328--35548356 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35548318 TTCCTACTTA
35548328 TAAATTCCAAATTC
1 TAAATTCCAAATTC
35548342 TAAATTCCAAATTC
1 TAAATTCCAAATTC
35548356 T
1 T
35548357 CAAACACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATTCCAAATTC
Found at i:35553165 original size:110 final size:111
Alignment explanation
Indices: 35553026--35553252 Score: 438
Period size: 110 Copynumber: 2.0 Consensus size: 111
35553016 TATTAGTTTT
35553026 AAATATAAGTTTTTTTATAAATATTTTTATTACATAAATATTTTTATTTAGATAGTAAATGTACC
1 AAATATAAGTTTTTTTATAAATATTTTTATTACATAAATATTTTTATTTAGATAGTAAATGTACC
35553091 CTAATCTAATTCAATTTTAGTATTGAATTTTAAAAATCAAATAAGA
66 CTAATCTAATTCAATTTTAGTATTGAATTTTAAAAATCAAATAAGA
35553137 AAATATAAG-TTTTTTATAAATATTTTTATTACATAAATATTTTTATTTAGATAGTAAATGTACC
1 AAATATAAGTTTTTTTATAAATATTTTTATTACATAAATATTTTTATTTAGATAGTAAATGTACC
35553201 CTAATCTAATTCAATTTTAGTATTGAATTTTAAAAATCAAATAAGA
66 CTAATCTAATTCAATTTTAGTATTGAATTTTAAAAATCAAATAAGA
35553247 AGAATA
1 A-AATA
35553253 CATTATGCGT
Statistics
Matches: 115, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
110 102 0.89
111 13 0.11
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (111 bp):
AAATATAAGTTTTTTTATAAATATTTTTATTACATAAATATTTTTATTTAGATAGTAAATGTACC
CTAATCTAATTCAATTTTAGTATTGAATTTTAAAAATCAAATAAGA
Found at i:35554180 original size:23 final size:23
Alignment explanation
Indices: 35554154--35554204 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
35554144 TCTGTCCATA
* * * *
35554154 TTATAGTTTTGTTTTTTTAATAT
1 TTATAGTTTTATTTATTAAAAAT
*
35554177 TTATATTTTTATTTATTAAAAAT
1 TTATAGTTTTATTTATTAAAAAT
35554200 TTATA
1 TTATA
35554205 TATAGGCAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (23 bp):
TTATAGTTTTATTTATTAAAAAT
Found at i:35556193 original size:14 final size:13
Alignment explanation
Indices: 35556166--35556200 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
35556156 TATTTCTTTT
*
35556166 TATAAATGTGTTA
1 TATAAATTTGTTA
35556179 TATATAATTTGTTA
1 TATA-AATTTGTTA
35556193 TATAAATT
1 TATAAATT
35556201 CTATAATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
TATAAATTTGTTA
Found at i:35562609 original size:6 final size:6
Alignment explanation
Indices: 35562594--35562641 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
35562584 AAATTATGAT
* *
35562594 GAAAAA -AAAAA GAAAAA GAAAAAA TAAAAA GAAAGAA GAAAAG GAAAA
1 GAAAAA GAAAAA GAAAAA G-AAAAA GAAAAA GAAA-AA GAAAAA GAAAA
35562642 GGAGAGGCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 5 0.14
6 20 0.56
7 11 0.31
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:35562615 original size:13 final size:13
Alignment explanation
Indices: 35562595--35562641 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
35562585 AATTATGATG
35562595 AAAA-AAAAAAGA
1 AAAAGAAAAAAGA
*
35562607 AAAAGAAAAAATA
1 AAAAGAAAAAAGA
*
35562620 AAAAGAAAGAAGA
1 AAAAGAAAAAAGA
*
35562633 AAAGGAAAA
1 AAAAGAAAA
35562642 GGAGAGGCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 4 0.14
13 25 0.86
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:35562617 original size:19 final size:20
Alignment explanation
Indices: 35562595--35562635 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
35562585 AATTATGATG
35562595 AAAAAAAAAAGAAA-AAGAA
1 AAAAAAAAAAGAAAGAAGAA
*
35562614 AAAATAAAAAGAAAGAAGAA
1 AAAAAAAAAAGAAAGAAGAA
35562634 AA
1 AA
35562636 GGAAAAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAGAAAGAAGAA
Found at i:35564316 original size:267 final size:267
Alignment explanation
Indices: 35563810--35564866 Score: 1557
Period size: 267 Copynumber: 4.0 Consensus size: 267
35563800 GCTACAACGG
* * * *
35563810 CGAATCTTATTTCCCTGGCGTTTTAGTAGAGCAGATTGAAGTCACAACGGCGAATCTTATCTCCC
1 CGAATCTTATTTCCCTGGCGTTGTAGCAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCC
* * * *
35563875 TAGCATTAAGGCTTGGATTAGCTGAAGTGGAGCGGATTGAAACTGT-GG-AGTGAATCCTATCTC
66 TGGCGTTAAGGCCTGGATTAGCTGAAGTGGAGCGGATTGAAGCTGTGGGCAGTGAATCCTATCTC
* * * * *
35563938 CTTGGCATTATAGTGGAGCAGATTGAAGCCGTAACGGCGAATCTTAC-TCCCATGGTGGTGTAGT
131 TTTGGCATTACAGTGGAGCAGATTAAAGCCGCAACGGCGAATCTTACTTCCC-TGGCGGTGTAGT
* * * * *
35564002 GGAACAGTTTGAAACTACGACGGTGAATCTTGTTTGCCC-AACATTGCAATTTAAAAGGTTGAAG
195 GGAACAGATTGAAGCTACGACGGCGAATCTTGATT-CCCTAACATTGCAATTTAAAAGATTGAAG
*
35564066 CCGCAATGG
259 CCGCAATGA
* * * * * *
35564075 TGAATCTTATTTCCCTAGAGTTGTAGCGGAGTAGATTGAAGCCACGACGGCGAATCTTATCTGCC
1 CGAATCTTATTTCCCTGGCGTTGTAGCAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCC
* *
35564140 TGGCGTTACGGCCTGGATTAGCTGAAGTGGAGCGGATTGAAGTTGTGGGCAGCT-AATCCTATCT
66 TGGCGTTAAGGCCTGGATTAGCTGAAGTGGAGCGGATTGAAGCTGTGGGCAG-TGAATCCTATCT
*
35564204 CTTTGGCTTTACAGTGGAGCAGATTAAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGT
130 CTTTGGCATTACAGTGGAGCAGATTAAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGT
* * *
35564269 AGAACAGATTGAAGCTACGACGGTGAATCTTAATTCCCTAACATTGCAATTTAAAAGATTGAAGC
195 GGAACAGATTGAAGCTACGACGGCGAATCTTGATTCCCTAACATTGCAATTTAAAAGATTGAAGC
*
35564334 CGCAACGA
260 CGCAATGA
* * *
35564342 CGAATCTTATTTCCCTGGCGTTGTAGCGGAGTAGATTGAAGCCACGACGGCGAATCTTATCTCCT
1 CGAATCTTATTTCCCTGGCGTTGTAGCAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCC
*
35564407 TGGCGTTAAGGCCTGGATTAGCTGAAGTGGAGCGGATTGAAGTTGTGGGCAGTGAATCCTATCTC
66 TGGCGTTAAGGCCTGGATTAGCTGAAGTGGAGCGGATTGAAGCTGTGGGCAGTGAATCCTATCTC
*
35564472 TTTGGCATTACAGTGGAGCAGATTAAAGCCGCAACGGCGAATCTTACTTCCCTGACGGTGTAGTG
131 TTTGGCATTACAGTGGAGCAGATTAAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTG
* * *
35564537 GAACAGATTGAAGCTACGACGGCGAATCTTGATTCCTTAACATTACAATTTAAAAGATTGAAGCT
196 GAACAGATTGAAGCTACGACGGCGAATCTTGATTCCCTAACATTGCAATTTAAAAGATTGAAGCC
35564602 GCAATGA
261 GCAATGA
* *
35564609 CGAATCTTATTTCCCTGGCGTTGTAGCAGAGCATATTGAAGCCACGACGGTGAATCTTATCTCCC
1 CGAATCTTATTTCCCTGGCGTTGTAGCAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCC
** *
35564674 TGGCGTTAAGGCCTGGATTAGCTGAAGTGGAGCACATTGAAGCTGTGGGCAGCGAATCCTATCTC
66 TGGCGTTAAGGCCTGGATTAGCTGAAGTGGAGCGGATTGAAGCTGTGGGCAGTGAATCCTATCTC
* * * *
35564739 TTTGGCATTACAGTAGAACAGATTAAAGTCGCAACGGCGAATCTTACTTCCCCGGCGGTGTAGTG
131 TTTGGCATTACAGTGGAGCAGATTAAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTG
* * * * * *
35564804 GAGCAGATTGAAGCTACGATGGCGAATCTTGTTTGCCTAACATTGTAATTTAAAAGACTGAAG
196 GAACAGATTGAAGCTACGACGGCGAATCTTGATTCCCTAACATTGCAATTTAAAAGATTGAAG
35564867 ATGGCGAATC
Statistics
Matches: 719, Mismatches: 67, Indels: 10
0.90 0.08 0.01
Matches are distributed among these distances:
265 95 0.13
266 6 0.01
267 613 0.85
268 5 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (267 bp):
CGAATCTTATTTCCCTGGCGTTGTAGCAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCC
TGGCGTTAAGGCCTGGATTAGCTGAAGTGGAGCGGATTGAAGCTGTGGGCAGTGAATCCTATCTC
TTTGGCATTACAGTGGAGCAGATTAAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTG
GAACAGATTGAAGCTACGACGGCGAATCTTGATTCCCTAACATTGCAATTTAAAAGATTGAAGCC
GCAATGA
Found at i:35565052 original size:45 final size:46
Alignment explanation
Indices: 35565001--35565163 Score: 181
Period size: 45 Copynumber: 3.6 Consensus size: 46
35564991 TATCGCATCT
* *
35565001 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACCT-AAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTCAAGAAAGCA
35565046 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTCAAGAAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTCAAGAAAGCA
* * * * * *
35565091 AGTCTTATCCCCCTAAAATTGCAGTGGGGCAGA-CTAAATAAA-CA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTCAAGAAAGCA
* * * * *
35565135 AATCCTGTCTCCCTAAAGTTGTAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
35565164 TGGATTAGAG
Statistics
Matches: 102, Mismatches: 15, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
44 26 0.25
45 76 0.75
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (46 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCTCAAGAAAGCA
Found at i:35565672 original size:13 final size:14
Alignment explanation
Indices: 35565646--35565674 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
35565636 TAAAACAGAT
35565646 GCCCAAATCCAGTG
1 GCCCAAATCCAGTG
35565660 GCCCAAA-CCAGTG
1 GCCCAAATCCAGTG
35565673 GC
1 GC
35565675 AGAAACCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.38, G:0.24, T:0.10
Consensus pattern (14 bp):
GCCCAAATCCAGTG
Found at i:35565952 original size:40 final size:40
Alignment explanation
Indices: 35565897--35565981 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
35565887 TAAAAAGGAT
*
35565897 AAAAAAAACAATCAATAAGAAAAATAATTATTTTCACAGC
1 AAAAAAAAAAATCAATAAGAAAAATAATTATTTTCACAGC
35565937 AAAAAAAAAAATCAATAAGAAAAATAATTATTTTCACAGC
1 AAAAAAAAAAATCAATAAGAAAAATAATTATTTTCACAGC
35565977 AAAAA
1 AAAAA
35565982 GACAGTTCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.64, C:0.11, G:0.05, T:0.21
Consensus pattern (40 bp):
AAAAAAAAAAATCAATAAGAAAAATAATTATTTTCACAGC
Found at i:35566928 original size:28 final size:29
Alignment explanation
Indices: 35566873--35566929 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
35566863 TCTACATATA
*
35566873 TATATTTATATTTTTTATGAATATTTTTC
1 TATATTTATATTTTTTATAAATATTTTTC
35566902 TATATTT-TATTTTTTAATAAATATTTTT
1 TATATTTATATTTTTT-ATAAATATTTTT
35566930 GTATTTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (29 bp):
TATATTTATATTTTTTATAAATATTTTTC
Found at i:35567326 original size:15 final size:15
Alignment explanation
Indices: 35567303--35567335 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35567293 TTTTTATGCC
35567303 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
35567318 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
35567333 ATT
1 ATT
35567336 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:35570793 original size:26 final size:26
Alignment explanation
Indices: 35570745--35570794 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
35570735 TAACGAGAAG
*
35570745 CTCACAAAGAGCCTTTAATTGGGAAA
1 CTCACAAAGAGCCTATAATTGGGAAA
*
35570771 CTCACGAAGAGCCATATAA-TGGGA
1 CTCACAAAGAGCC-TATAATTGGGA
35570795 TGCTTATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (26 bp):
CTCACAAAGAGCCTATAATTGGGAAA
Found at i:35577860 original size:21 final size:21
Alignment explanation
Indices: 35577835--35577876 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35577825 ATTTTTAATT
35577835 AATTTACTACCAAAACGTTAA
1 AATTTACTACCAAAACGTTAA
* * *
35577856 AATTTTCTACCGAAACTTTAA
1 AATTTACTACCAAAACGTTAA
35577877 TACTACTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
AATTTACTACCAAAACGTTAA
Found at i:35579111 original size:38 final size:39
Alignment explanation
Indices: 35579022--35579123 Score: 125
Period size: 38 Copynumber: 2.6 Consensus size: 39
35579012 ATATAATCCG
* * * *
35579022 AGAATCTGCAACGAATGCTAGATCACGTTAAATAACCCG
1 AGAATCTGCAACAAATGCTAGATCTCATTAAATAACCCA
* * * *
35579061 AGAACCTACAAC-AAGGCTAGATCTCATTAAATAACCTA
1 AGAATCTGCAACAAATGCTAGATCTCATTAAATAACCCA
35579099 AGAATCTGCAACAAATGCTAGATCT
1 AGAATCTGCAACAAATGCTAGATCT
35579124 TGTTATAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 31 0.60
39 21 0.40
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (39 bp):
AGAATCTGCAACAAATGCTAGATCTCATTAAATAACCCA
Found at i:35581065 original size:17 final size:16
Alignment explanation
Indices: 35581015--35581071 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
35581005 CAAATCATGA
*
35581015 TTCTATTCTTTTTTCA-
1 TTCTTTTCTTTTTT-AT
*
35581031 TT-TTTT-TTGTTTAT
1 TTCTTTTCTTTTTTAT
35581045 TTCTTTTCTTTTTTAT
1 TTCTTTTCTTTTTTAT
35581061 CTTCTTTTCTT
1 -TTCTTTTCTT
35581072 CTTCTTCTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 1 0.03
14 7 0.21
15 7 0.21
16 9 0.26
17 10 0.29
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (16 bp):
TTCTTTTCTTTTTTAT
Found at i:35581601 original size:26 final size:26
Alignment explanation
Indices: 35581566--35581615 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
35581556 CTATAGCTTT
35581566 TTTTCTTTTGTATTTTCATTATTTAC
1 TTTTCTTTTGTATTTTCATTATTTAC
35581592 TTTTCTTTTGTATTTTCATTATTT
1 TTTTCTTTTGTATTTTCATTATTT
35581616 TCCAATGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTTCTTTTGTATTTTCATTATTTAC
Found at i:35586851 original size:24 final size:24
Alignment explanation
Indices: 35586728--35586854 Score: 72
Period size: 24 Copynumber: 5.3 Consensus size: 24
35586718 CTCTTTCATG
35586728 AGCTTCCTGA-TATGGCTCGCTT-GA
1 AGCTTCCTGATTATGGCT--CTTAGA
* * *
35586752 A-CTTCCTGATATATGGCTATTCGG
1 AGCTTCCTGAT-TATGGCTCTTAGA
*
35586776 AGCTT-CTCG-TTAATGGCTCTTCGA
1 AGCTTCCT-GATT-ATGGCTCTTAGA
* *
35586800 AGCTACCCG-TTATTGGCT-TGTATG-
1 AGCTTCCTGATTA-TGGCTCT-TA-GA
35586824 AGCTTCCTGATTATGGCTCTTAGA
1 AGCTTCCTGATTATGGCTCTTAGA
35586848 AGCTTCC
1 AGCTTCC
35586855 AGTTATATAG
Statistics
Matches: 81, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
23 14 0.17
24 50 0.62
25 17 0.21
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (24 bp):
AGCTTCCTGATTATGGCTCTTAGA
Found at i:35589866 original size:24 final size:24
Alignment explanation
Indices: 35589839--35589888 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
35589829 TATTATATCT
35589839 CATGATTTACAATTTCATTACTTA
1 CATGATTTACAATTTCATTACTTA
35589863 CATGATTTACAATTTCATTACTTA
1 CATGATTTACAATTTCATTACTTA
35589887 CA
1 CA
35589889 CCGTTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.44
Consensus pattern (24 bp):
CATGATTTACAATTTCATTACTTA
Found at i:35592622 original size:17 final size:17
Alignment explanation
Indices: 35592588--35592623 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
35592578 GAAGAAAAGG
*
35592588 AAAATTAAAAATTAAAA
1 AAAATTAAAAAATAAAA
35592605 AAAATTAAAAAAATAAAA
1 AAAATT-AAAAAATAAAA
35592623 A
1 A
35592624 TATAGGGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAATTAAAAAATAAAA
Found at i:35600694 original size:142 final size:142
Alignment explanation
Indices: 35600237--35600813 Score: 688
Period size: 142 Copynumber: 4.0 Consensus size: 142
35600227 ACTCGGTACG
* * ** * * *
35600237 ATAGACTAGAAAAATAAACTGCTTTTGA-TACAAGTTACATTCATGCCTCCACTCATCGAGCCAA
1 ATAGACTAGAAAAATAAACAGC-ATACACTATAAGTTACATACATGCCTCCACTCATCGACCCAA
* * * *
35600301 ACGTTAAATGTAAATAATGTAACTTTTTAGTCCTTTAAGTGATCAGCATTTATCCATGCCTTAAC
65 ACATTAAATGTAAATAATGTAAC-TTTTAGTCCTTCATGTGATCACCATTTATCCATGCCTTAAC
35600366 ATTTTAAACCAAAT
129 ATTTTAAACCAAAT
* * *
35600380 ATAGACTAAAAAAATAAACAGTATACACTATAAGTTACATTCATCATGCCTCCACTCATCGACCT
1 ATAGACTAGAAAAATAAACAGCATACACTATAAGTTACA-T-A-CATGCCTCCACTCATCGACCC
* * * ** * * ** ** *
35600445 GAATATGAAACCTAAAGATTGTAACTTATTAACCCTTCATGTGATCACCATTTAGGCATACACCT
63 AAACATTAAATGTAAATAATGTAACTT-TTAGTCCTTCATGTGATCACCATTTATCCAT--GCCT
35600510 TAACATTTTAAACCAAAT
125 TAACATTTTAAACCAAAT
* * * ** *
35600528 ATAGACTAGAAAAAAAAACAGCATATATTATAAGTTACATACATGCCTTGACCCATCGACCCAAA
1 ATAGACTAGAAAAATAAACAGCATACACTATAAGTTACATACATGCCTCCACTCATCGACCCAAA
35600593 CATTAAATGTAAATAATGTAACTTTTAGTCCTTCATGTGATCACCATTTATCCATGCCTTAACAT
66 CATTAAATGTAAATAATGTAACTTTTAGTCCTTCATGTGATCACCATTTATCCATGCCTTAACAT
35600658 TTTAAACCAAAT
131 TTTAAACCAAAT
* * * * * * *
35600670 ATAGACTAGAAACATACACGGCATACACTATAAGTTACATTCACGCCTCCACTCATAGACCCAAT
1 ATAGACTAGAAAAATAAACAGCATACACTATAAGTTACATACATGCCTCCACTCATCGACCCAAA
* * *
35600735 CATTAAATGTAAATAATGTAAATTTTTAGTCCTACATGTGATCACCATTTATTCATGCCTTAACA
66 CATTAAATGTAAATAATGT-AACTTTTAGTCCTTCATGTGATCACCATTTATCCATGCCTTAACA
35600800 TTTTAAACCAAAT
130 TTTTAAACCAAAT
35600813 A
1 A
35600814 CATGGAAATA
Statistics
Matches: 363, Mismatches: 63, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
142 94 0.26
143 85 0.23
144 28 0.08
145 39 0.11
146 61 0.17
147 1 0.00
148 55 0.15
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (142 bp):
ATAGACTAGAAAAATAAACAGCATACACTATAAGTTACATACATGCCTCCACTCATCGACCCAAA
CATTAAATGTAAATAATGTAACTTTTAGTCCTTCATGTGATCACCATTTATCCATGCCTTAACAT
TTTAAACCAAAT
Found at i:35605963 original size:37 final size:37
Alignment explanation
Indices: 35605908--35605980 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
35605898 TATATATGGT
35605908 GGCTTAATGTGATATGATCAATGGAACGGTTATATAC
1 GGCTTAATGTGATATGATCAATGGAACGGTTATATAC
* *
35605945 GGCTTACTGTGATTTGATCAATGGAACGGTTATATA
1 GGCTTAATGTGATATGATCAATGGAACGGTTATATA
35605981 AAAAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (37 bp):
GGCTTAATGTGATATGATCAATGGAACGGTTATATAC
Found at i:35609538 original size:24 final size:25
Alignment explanation
Indices: 35609504--35609552 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
35609494 ATTCCTAGAC
*
35609504 TAATAATAGTTTAATTGGGAAAAGA
1 TAATAATAGTTTAACTGGGAAAAGA
*
35609529 TAAT-ATAGTTTAACTGGGAGAAGA
1 TAATAATAGTTTAACTGGGAAAAGA
35609553 AACCCGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.22, T:0.31
Consensus pattern (25 bp):
TAATAATAGTTTAACTGGGAAAAGA
Found at i:35614894 original size:29 final size:28
Alignment explanation
Indices: 35614828--35614894 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
35614818 AAATTTTAAT
*
35614828 TTTTAAATAA-TAAAAGTAGAGGATTAAA
1 TTTTAAA-AACTAAAAGTAGAGGACTAAA
**
35614856 TTTTTGAAACTAAAAGCTGAGAGG-CTAAA
1 TTTTAAAAACTAAAAG-T-AGAGGACTAAA
35614885 TTTTAAAAAC
1 TTTTAAAAAC
35614895 CCGAAGTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.06
28 11 0.35
29 13 0.42
30 5 0.16
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (28 bp):
TTTTAAAAACTAAAAGTAGAGGACTAAA
Found at i:35618549 original size:21 final size:21
Alignment explanation
Indices: 35618519--35618575 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
35618509 TACTTAAATT
*
35618519 TTATTGAAAATTAG-AAAAAGAA
1 TTATTAAAAATT-GTAAAAA-AA
*
35618541 TTA-TAAAAATTGTCAAAAAA
1 TTATTAAAAATTGTAAAAAAA
35618561 TTATTAAAAATTGTA
1 TTATTAAAAATTGTA
35618576 CGGGGTATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 6 0.20
21 21 0.70
22 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (21 bp):
TTATTAAAAATTGTAAAAAAA
Found at i:35619057 original size:16 final size:16
Alignment explanation
Indices: 35619019--35619058 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35619009 CCACACACTT
*
35619019 ATATTATAATAATTTA
1 ATATTATAATAATGTA
* *
35619035 TTTTTATAATAATGTA
1 ATATTATAATAATGTA
35619051 ATATTATA
1 ATATTATA
35619059 TATTTTTTTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATTATAATAATGTA
Found at i:35637520 original size:21 final size:21
Alignment explanation
Indices: 35637477--35637516 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
35637467 ATGTCTCTTG
* *
35637477 TTAGGGTTTTGGGTTTTTGGT
1 TTAGGGTTTAGGGTTTTGGGT
35637498 TTAGGG-TTAGGGTTTTGGG
1 TTAGGGTTTAGGGTTTTGGG
35637517 GTTTTTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.07, C:0.00, G:0.42, T:0.50
Consensus pattern (21 bp):
TTAGGGTTTAGGGTTTTGGGT
Found at i:35640542 original size:9 final size:9
Alignment explanation
Indices: 35640466--35640541 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
35640456 GTAGTGATTC
*
35640466 AATTTGGTT
1 AATTCGGTT
35640475 AATTCGGTT
1 AATTCGGTT
*
35640484 AATTCGGGT
1 AATTCGGTT
*
35640493 AATTCGGGT
1 AATTCGGTT
*
35640502 AATTCGGGT
1 AATTCGGTT
35640511 AATTCGGTT
1 AATTCGGTT
35640520 AATTCGGTT
1 AATTCGGTT
*
35640529 AATTTGGTT
1 AATTCGGTT
35640538 AATT
1 AATT
35640542 TTTAACCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 63 1.00
ACGTcount: A:0.24, C:0.08, G:0.25, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:35642768 original size:20 final size:19
Alignment explanation
Indices: 35642723--35642768 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
35642713 CGTTCAATTG
35642723 ATCTATTTGCAATCTTGACA
1 ATCT-TTTGCAATCTTGACA
*
35642743 ACTCTTTTGCAAATCTTGTCA
1 A-TCTTTTGC-AATCTTGACA
35642764 ATCTT
1 ATCTT
35642769 GACATCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (19 bp):
ATCTTTTGCAATCTTGACA
Found at i:35643426 original size:22 final size:21
Alignment explanation
Indices: 35643401--35643466 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
35643391 GTATGTCTAC
35643401 TGTTAATGATGAACTGAGTACA
1 TGTTAATGATGAA-TGAGTACA
**
35643423 TGTTAA--A--AATGTCTAC-
1 TGTTAATGATGAATGAGTACA
35643439 TGTTAATGATGAATTGAGTACA
1 TGTTAATGATGAA-TGAGTACA
35643461 TGTTAA
1 TGTTAA
35643467 ACATTTCTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
16 6 0.18
17 5 0.15
18 3 0.09
20 3 0.09
21 5 0.15
22 12 0.35
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (21 bp):
TGTTAATGATGAATGAGTACA
Found at i:35643435 original size:38 final size:38
Alignment explanation
Indices: 35643393--35643481 Score: 151
Period size: 38 Copynumber: 2.3 Consensus size: 38
35643383 CATGATAAGT
35643393 ATGTCTACTGTTAATGATGAACTGAGTACATGTTAAAA
1 ATGTCTACTGTTAATGATGAACTGAGTACATGTTAAAA
* *
35643431 ATGTCTACTGTTAATGATGAATTGAGTACATGTTAAAC
1 ATGTCTACTGTTAATGATGAACTGAGTACATGTTAAAA
*
35643469 ATTTCTACTGTTA
1 ATGTCTACTGTTA
35643482 GTGCTAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (38 bp):
ATGTCTACTGTTAATGATGAACTGAGTACATGTTAAAA
Found at i:35643492 original size:38 final size:38
Alignment explanation
Indices: 35643396--35643515 Score: 150
Period size: 38 Copynumber: 3.2 Consensus size: 38
35643386 GATAAGTATG
* * *
35643396 TCTACTGTTAATGATGAACTGAGTACATGTTAAAAATG
1 TCTACTGTTAATGATGAATTGAGTACATGTTAAACATA
*
35643434 TCTACTGTTAATGATGAATTGAGTACATGTTAAACATT
1 TCTACTGTTAATGATGAATTGAGTACATGTTAAACATA
* * * * * *
35643472 TCTACTGTTAGTGCTAAATTGAGTATATGCTATACATA
1 TCTACTGTTAATGATGAATTGAGTACATGTTAAACATA
35643510 TCTACT
1 TCTACT
35643516 ACTAGTGTTG
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (38 bp):
TCTACTGTTAATGATGAATTGAGTACATGTTAAACATA
Found at i:35643530 original size:38 final size:38
Alignment explanation
Indices: 35643410--35643530 Score: 98
Period size: 38 Copynumber: 3.2 Consensus size: 38
35643400 CTGTTAATGA
* * * * ** * *
35643410 TGAACTGAGTACATGTTAAAAATGTCTACTGTTAATGA
1 TGAATTGAGTACATGCTAAACATATCTACTACTAGTGC
* * **
35643448 TGAATTGAGTACATGTTAAACATTTCTACTGTTAGTGC
1 TGAATTGAGTACATGCTAAACATATCTACTACTAGTGC
* * * *
35643486 TAAATTGAGTATATGCTATACATATCTACTACTAGTGT
1 TGAATTGAGTACATGCTAAACATATCTACTACTAGTGC
35643524 TGAATTG
1 TGAATTG
35643531 TTCTATTATA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 69 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (38 bp):
TGAATTGAGTACATGCTAAACATATCTACTACTAGTGC
Found at i:35643803 original size:44 final size:44
Alignment explanation
Indices: 35643688--35643832 Score: 150
Period size: 44 Copynumber: 3.3 Consensus size: 44
35643678 AGTGGCAGAC
* * *
35643688 TTATCTGCGAATTTTGCTATATACCCACAGA-TCAGTGGCAGA-T
1 TTATCTGCGAATTTTGCTATGTACCCACA-ACTTAGTGGCAAATT
* * *
35643731 TTATCTGCAAATTTTACTGTGTACCCACAACTTAGTGGCAAATT
1 TTATCTGCGAATTTTGCTATGTACCCACAACTTAGTGGCAAATT
* * * * * *
35643775 TTATCTACGAATTTTGTTATGTATCCACATCTTAATGGAAAATT
1 TTATCTGCGAATTTTGCTATGTACCCACAACTTAGTGGCAAATT
*
35643819 TTATATGCGAATTT
1 TTATCTGCGAATTT
35643833 GTTGTGTATC
Statistics
Matches: 83, Mismatches: 17, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
42 1 0.01
43 34 0.41
44 48 0.58
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (44 bp):
TTATCTGCGAATTTTGCTATGTACCCACAACTTAGTGGCAAATT
Found at i:35643877 original size:43 final size:44
Alignment explanation
Indices: 35643633--35643953 Score: 219
Period size: 43 Copynumber: 7.4 Consensus size: 44
35643623 CCCATAGCTA
* * *
35643633 AGTGGCAG-TTTTCATCTACAAAATTTTGTTGTGTATCCATAGCCC
1 AGTGGCAGATTTT-ATCTGC-AAATTTTGTTGTGTATCCACAGCCT
* * * * * * *
35643678 AGTGGCAGA-CTTATCTGCGAATTTTGCTATATACCCACAG-AT
1 AGTGGCAGATTTTATCTGCAAATTTTGTTGTGTATCCACAGCCT
** * * *
35643720 CAGTGGCAGA-TTTATCTGCAAATTTTACTGTGTACCCACAACTT
1 -AGTGGCAGATTTTATCTGCAAATTTTGTTGTGTATCCACAGCCT
* * * * * *
35643764 AGTGGCAAATTTTATCTACGAATTTTGTTATGTATCCACATCTT
1 AGTGGCAGATTTTATCTGCAAATTTTGTTGTGTATCCACAGCCT
* * * * *
35643808 AATGGAAAATTTTATATGCGAA-TTTGTTGTGTATCCACAGCCT
1 AGTGGCAGATTTTATCTGCAAATTTTGTTGTGTATCCACAGCCT
** *
35643851 AGTGATAGA-TTTATCTGCAAATTTTGTTGTGTAATCCACTGTCC-
1 AGTGGCAGATTTTATCTGCAAATTTTGTTGTGT-ATCCACAG-CCT
* * * * *
35643895 AGTGGTAGATTTTATCTGCAAATTTTGCTGTGCATCTACAGCCC
1 AGTGGCAGATTTTATCTGCAAATTTTGTTGTGTATCCACAGCCT
*
35643939 AATGGCA-A-TTTATCT
1 AGTGGCAGATTTTATCT
35643954 AAAAACAAGT
Statistics
Matches: 221, Mismatches: 46, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
42 17 0.08
43 94 0.43
44 77 0.35
45 33 0.15
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (44 bp):
AGTGGCAGATTTTATCTGCAAATTTTGTTGTGTATCCACAGCCT
Found at i:35649237 original size:24 final size:25
Alignment explanation
Indices: 35649183--35649241 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
35649173 GAAAATTTTC
* *
35649183 TCTTTTCTGCTGTGTTTTCTGTTAT
1 TCTTTGCTGCTGTGTGTTCTGTTAT
*
35649208 TCTTTGCTGCTGTGTGTT-TGTTTT
1 TCTTTGCTGCTGTGTGTTCTGTTAT
*
35649232 TGTTTGCTGC
1 TCTTTGCTGC
35649242 AGGTACGGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.02, C:0.15, G:0.22, T:0.61
Consensus pattern (25 bp):
TCTTTGCTGCTGTGTGTTCTGTTAT
Found at i:35650829 original size:20 final size:19
Alignment explanation
Indices: 35650785--35650870 Score: 61
Period size: 18 Copynumber: 4.5 Consensus size: 19
35650775 AAAATTAAAA
*
35650785 AAAAT-ATTTTTACAATTTT
1 AAAATAATTTTTA-ATTTTT
*
35650804 ACAATAATTTTTAATTTTT
1 AAAATAATTTTTAATTTTT
35650823 CAAAATAAATTATTTAATTTTT
1 -AAAAT-AATT-TTTAATTTTT
* * **
35650845 TAAAT-TTTTTTAAAATTT
1 AAAATAATTTTTAATTTTT
35650863 AAAA-AATT
1 AAAATAATT
35650871 AATTAATTAC
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
18 13 0.25
19 11 0.21
20 11 0.21
21 8 0.15
22 10 0.19
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (19 bp):
AAAATAATTTTTAATTTTT
Found at i:35650849 original size:21 final size:19
Alignment explanation
Indices: 35650800--35650849 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 19
35650790 ATTTTTACAA
35650800 TTTTACAATAATTTTTAATT
1 TTTTA-AATAATTTTTAATT
*
35650820 TTTCAAAATAAATTATTTAATT
1 TTT-TAAAT-AATT-TTTAATT
35650842 TTTTAAAT
1 TTTTAAAT
35650850 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 6 0.24
21 9 0.36
22 10 0.40
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAAATAATTTTTAATT
Found at i:35657363 original size:18 final size:18
Alignment explanation
Indices: 35657340--35657374 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35657330 ATAAAAAATT
35657340 TAAAAA-AAACTTTAAAAA
1 TAAAAATAAA-TTTAAAAA
35657358 TAAAAATAAATTTAAAA
1 TAAAAATAAATTTAAAA
35657375 GTTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAATAAATTTAAAAA
Found at i:35660654 original size:43 final size:41
Alignment explanation
Indices: 35660557--35660655 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 41
35660547 GAAAGAAAGC
*
35660557 ACGCCCAGTTGGAAGCATTTTTTGCTAACATGTCGGGGAAA
1 ACGCCCAGTTGGAAGCATTTTTTGCTAACATGTCAGGGAAA
* * * *
35660598 ACACACCAGGTTGGAAGCATTTTTTGTTGACATGTTAGGGAAA
1 ACGC-CCA-GTTGGAAGCATTTTTTGCTAACATGTCAGGGAAA
*
35660641 ATGTGCCCAGTTGGA
1 A--CGCCCAGTTGGA
35660656 CGCGTTTTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
41 3 0.06
42 3 0.06
43 37 0.79
44 3 0.06
45 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (41 bp):
ACGCCCAGTTGGAAGCATTTTTTGCTAACATGTCAGGGAAA
Found at i:35662666 original size:31 final size:32
Alignment explanation
Indices: 35662631--35662697 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
35662621 ATACTTTTTA
* * *
35662631 ATAATTAGTAAATTAT-TTTAAA-ATTTTAAAT
1 ATAATTAATAAATAATATTTAAATAATTT-AAT
35662662 ATAA-TAATAAATAATATTTAAATAATTTAAT
1 ATAATTAATAAATAATATTTAAATAATTTAAT
35662693 ATAAT
1 ATAAT
35662698 GATACATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 9 0.30
31 17 0.57
32 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
ATAATTAATAAATAATATTTAAATAATTTAAT
Found at i:35671841 original size:5 final size:5
Alignment explanation
Indices: 35671831--35671867 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
35671821 TTCATCCCCC
35671831 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
35671868 TCAGCAAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:35671936 original size:27 final size:27
Alignment explanation
Indices: 35671898--35671950 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
35671888 TATGGGCATG
35671898 ACTATTGCCTCGACAGAAATTTTGTTC
1 ACTATTGCCTCGACAGAAATTTTGTTC
35671925 ACTATTGCCTCGACAGAAATTTTGTT
1 ACTATTGCCTCGACAGAAATTTTGTT
35671951 TATAGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (27 bp):
ACTATTGCCTCGACAGAAATTTTGTTC
Found at i:35675443 original size:28 final size:29
Alignment explanation
Indices: 35675411--35675474 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
35675401 TAAATATTTT
35675411 TATTTTTT-ATTTTTTTAATTTTAAAATA
1 TATTTTTTAATTTTTTTAATTTTAAAATA
*
35675439 TATTTTTTAATTTTTTTATTTTTAAAATA
1 TATTTTTTAATTTTTTTAATTTTAAAATA
*
35675468 AATTTTT
1 TATTTTT
35675475 GGTGTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 8 0.24
29 25 0.76
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (29 bp):
TATTTTTTAATTTTTTTAATTTTAAAATA
Found at i:35694521 original size:28 final size:27
Alignment explanation
Indices: 35694471--35694532 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
35694461 ATGTATACTG
35694471 TATAAAAGAATGCCTATATATATATAT
1 TATAAAAGAATGCCTATATATATATAT
* * * *
35694498 TATAAAAGTCATGCGTATGTATATGTAT
1 TATAAAAG-AATGCCTATATATATATAT
*
35694526 CATAAAA
1 TATAAAA
35694533 AACAATGCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.35
Consensus pattern (27 bp):
TATAAAAGAATGCCTATATATATATAT
Found at i:35695838 original size:28 final size:27
Alignment explanation
Indices: 35695788--35695849 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
35695778 ATGTATACTG
35695788 TATAAAAGAATGCCTATATATATATAT
1 TATAAAAGAATGCCTATATATATATAT
* * * *
35695815 TATAAAAGTCATGCGTATGTATATGTAT
1 TATAAAAG-AATGCCTATATATATATAT
*
35695843 CATAAAA
1 TATAAAA
35695850 AACAATGCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.35
Consensus pattern (27 bp):
TATAAAAGAATGCCTATATATATATAT
Found at i:35696148 original size:17 final size:17
Alignment explanation
Indices: 35696115--35696148 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35696105 TCACAAAAAA
*
35696115 AAATAAAAATAAAAAGG
1 AAATAAAAACAAAAAGG
*
35696132 AAATAAAAACAAGAAGG
1 AAATAAAAACAAAAAGG
35696149 GAGCAGATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.09
Consensus pattern (17 bp):
AAATAAAAACAAAAAGG
Found at i:35702927 original size:42 final size:42
Alignment explanation
Indices: 35702844--35703243 Score: 567
Period size: 42 Copynumber: 9.5 Consensus size: 42
35702834 GCACTAAATC
* ***
35702844 TCATGTTCTTTAGTGGCGCTACCG-AAAAACGCCGCTAAAGA
1 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
35702885 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
1 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
35702927 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
1 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
35702969 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
1 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
35703011 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
1 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
35703053 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
1 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
* *
35703095 TCATGTTCTTTAGCAGCGCTTAGGAAGAAAACGCCGCTAAAAGA
1 TCATGTTCTTTAGCGGCGCTTGGGAA-AAAACGCCGCT-AAAGA
* * *
35703139 -AATGTTCTGTAGCGGCGCTTGGTAAAAAACGCCGCTAAA-A
1 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
* * **** *
35703179 GTAATGTTCTTTACCGGCGCTTCATCTACAAACGCCGCTAAA-A
1 -TCATGTTCTTTAGCGGCGCTT-GGGAAAAAACGCCGCTAAAGA
35703222 GT-AGTGTTCTTTAGCGGCGCTT
1 -TCA-TGTTCTTTAGCGGCGCTT
35703244 ATTTCACAAA
Statistics
Matches: 333, Mismatches: 19, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
40 1 0.00
41 23 0.07
42 239 0.72
43 65 0.20
44 5 0.02
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.25
Consensus pattern (42 bp):
TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGA
Found at i:35703657 original size:12 final size:12
Alignment explanation
Indices: 35703636--35703671 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
35703626 TGAACCTCTA
*
35703636 CTTCTATCGCTG
1 CTTCTCTCGCTG
35703648 CTTCTCTCGCTG
1 CTTCTCTCGCTG
*
35703660 CTTCTCTTGCTG
1 CTTCTCTCGCTG
35703672 TGGCCTCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.36, G:0.17, T:0.44
Consensus pattern (12 bp):
CTTCTCTCGCTG
Found at i:35703681 original size:21 final size:21
Alignment explanation
Indices: 35703657--35703725 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
35703647 GCTTCTCTCG
* * *
35703657 CTGCTTCTCTTGCTGTGGCCT
1 CTGCTTCTCTCGCTGTAGCAT
35703678 CTGCTTCTCTCGCTGTAGCAT
1 CTGCTTCTCTCGCTGTAGCAT
**
35703699 CTGCTT-TCCTCGCTGCCGCAT
1 CTGCTTCT-CTCGCTGTAGCAT
35703720 CTGCTT
1 CTGCTT
35703726 TAAGTTGTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.04, C:0.36, G:0.20, T:0.39
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGTAGCAT
Found at i:35704380 original size:18 final size:18
Alignment explanation
Indices: 35704357--35704392 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
35704347 ATTGAATTTT
35704357 AATT-AATATAAATAAACA
1 AATTAAATATAAA-AAACA
35704375 AATTAAATATAAAAAACA
1 AATTAAATATAAAAAACA
35704393 TATAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AATTAAATATAAAAAACA
Found at i:35704400 original size:18 final size:19
Alignment explanation
Indices: 35704361--35704400 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
35704351 AATTTTAATT
*
35704361 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
35704380 AATATAAA-AAACATATAA
1 AATATAAATAAACAAATAA
35704398 AAT
1 AAT
35704401 GATTTTGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:35704766 original size:113 final size:112
Alignment explanation
Indices: 35704498--35705154 Score: 554
Period size: 113 Copynumber: 5.8 Consensus size: 112
35704488 TCGAGAAAAG
* * * ** * *
35704498 CGCCGCTAATACTATGC-TTCAGCAGCGTTTTCCTGTGTGCGCCACTAATTCCAGTATACATCAA
1 CGCCGCTAATACTATACATT-AGCGGCGTTTTCC-ATAAGCGCCACTAATTCTAATATACATCAA
* * * * * *
35704562 GAACTAAACGCTGTGTTTTCGTTAATAT-CTTTTGGCGGCGCTTACCAAAAA
64 G-ACCAAACTCTGCGTTTTGGTTAAGATAC-TTT-GCGGCGCTTACCACAAA
* * * ** * *
35704613 GCGCCGCAAATAGTA-AGCATTAGCTGCGTTTTGAAGTAAGCGCCACTAACTCTAATATACGTCA
1 -CGCCGCTAATACTATA-CATTAGCGGCGTTTTCCA-TAAGCGCCACTAATTCTAATATACATCA
* *
35704677 AGGCCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCCACAAA
63 AGACCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTACCACAAA
* * *
35704727 CGCCGCTACTACTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCAAG
1 CGCCGCTAATACTATACATTAGCGGCGTTTTCC-ATAAGCGCCACTAATTCTAATATACATCAAG
* * *
35704792 ACCAAACTCCGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAA
65 ACCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTACCA-CAAA
* * * * ** * * * * *
35704841 CGCTGCTATTACTATGCTTTAATGGCGTTTTCCTTAAACTCCACTAATTATAGTATACATCAAGA
1 CGCCGCTAATACTATACATTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
* * ** * *
35704906 CCAAAACGCTGCATTTTGGTTAAGATGTTTTGCGGCG-TTGAACGCTC-AG
66 CC-AAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTT--AC-CACAAA
* *
35704955 CGCCGCTAATACTATACATTAGCGGCGTTTTCTTTATAAGCGCCACTAATTGTAATATACATCAA
1 CGCCGCTAATACTATACATTAGCGGCGTTTTC--CATAAGCGCCACTAATTCTAATATACATCAA
* * ** * *
35705020 GACCAAACTCTGCGTTTTGGTTAACA-CCTTTTGCGGCGCTTTTGC-TAAG
64 GACCAAACTCTGCGTTTTGGTTAAGATAC-TTTGCGGCGC-TTACCACAAA
* * * *
35705069 CGCCGCTAATACTATGCATTACCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAG
1 CGCCGCTAATACTATACATTAGCGGCGTTT-TCCATAAGCGCCACTAATTCTAATATACATCAAG
* *
35705134 ACCAGAACGCTGCGTGTTGGT
65 ACCA-AACTCTGCGTTTTGGT
35705155 CTTGAGATTT
Statistics
Matches: 441, Mismatches: 81, Indels: 40
0.78 0.14 0.07
Matches are distributed among these distances:
113 154 0.35
114 150 0.34
115 55 0.12
116 78 0.18
117 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (112 bp):
CGCCGCTAATACTATACATTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
CCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTACCACAAA
Found at i:35704931 original size:114 final size:113
Alignment explanation
Indices: 35704498--35705173 Score: 549
Period size: 114 Copynumber: 5.9 Consensus size: 113
35704488 TCGAGAAAAG
* * *** * *
35704498 CGCCGCTAATACTATGC-TTCAGCAGCGTTTTCCTGTGTGCGCCACTAATTCCAGTATACATCAA
1 CGCCGCTAATACTATACATT-AGCGGCGTTTTCCT-TAAACGCCACTAATTCTAATATACATCAA
* * * * * * *
35704562 GAACTAAACGCTGTGTTTTCGTTAATATCTTTTGGCGGCGCTTACCA-AAAA
64 G-ACCAAACTCTGCGTTTTGGTTAAGATATTTT-GCGGCGCTTACCACCAAA
* * * *** * * *
35704613 GCGCCGCAAATAGTA-AGCATTAGCTGCGTTTTGAAGTAAGCGCCACTAACTCTAATATACGTCA
1 -CGCCGCTAATACTATA-CATTAGCGGCGTTTT-CCTTAAACGCCACTAATTCTAATATACATCA
* * *
35704677 AGGCCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCCA-CAAA
63 AGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTACCACCAAA
* * * * *
35704727 CGCCGCTACTACTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCAAG
1 CGCCGCTAATACTATACATTAGCGGCGTTTTCC-TTAAACGCCACTAATTCTAATATACATCAAG
* *
35704792 ACCAAACTCCGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAA
65 ACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTACCACCAAA
* * * * ** * * *
35704841 CGCTGCTATTACTATGCTTTAATGGCGTTTTCCTTAAACTCCACTAATTATAGTATACATCAAGA
1 CGCCGCTAATACTATACATTAGCGGCGTTTTCCTTAAACGCCACTAATTCTAATATACATCAAGA
* * * * * *
35704906 CCAAAACGCTGCATTTTGGTTAAGATGTTTTGCGGCG-TTGAACGCTC-AG
66 CC-AAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT-ACCAC-CAAA
* *
35704955 CGCCGCTAATACTATACATTAGCGGCGTTTTCTTTATAAGCGCCACTAATTGTAATATACATCAA
1 CGCCGCTAATACTATACATTAGCGGCGTTTTCCTTA-AA-CGCCACTAATTCTAATATACATCAA
* ** *** * *
35705020 GACCAAACTCTGCGTTTTGGTTAACACCTTTTGCGGCGCTT-TTGCTAAG
64 GACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTACCACCAAA
* * * * *
35705069 CGCCGCTAATACTATGCATTACCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAG
1 CGCCGCTAATACTATACATTAGCGGCGTTT-TCCTTAAACGCCACTAATTCTAATATACATCAAG
* * * *
35705134 ACCAGAACGCTGCGTGTTGGTCT-TGAGATTTTGCGGCGCT
65 ACCA-AACTCTGCGTTTTGGT-TAAGATATTTTGCGGCGCT
35705174 GTGTAGTAAA
Statistics
Matches: 456, Mismatches: 88, Indels: 34
0.79 0.15 0.06
Matches are distributed among these distances:
113 150 0.33
114 170 0.37
115 59 0.13
116 75 0.16
117 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (113 bp):
CGCCGCTAATACTATACATTAGCGGCGTTTTCCTTAAACGCCACTAATTCTAATATACATCAAGA
CCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTACCACCAAA
Found at i:35705037 original size:229 final size:228
Alignment explanation
Indices: 35704496--35705146 Score: 573
Period size: 229 Copynumber: 2.8 Consensus size: 228
35704486 TTTCGAGAAA
* * ** ** * *
35704496 AGCGCCGCTAATACTATGC-TTCAGCAGCGTTTTCCTGTGTGCGCCACTAATTCCAGTATACATC
1 AGCGCCGCTAATACTATACATT-AGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACATC
* * * * * * * * *
35704560 AAGAACTAAACGCTGTGTTTTCGTTAATATC-TTTTGGCGGCGCTTACCA-AAAAGCGCCGCAAA
65 AAG-ACCAAACTCCGCGTTTTGGTTAACA-CATTTT-GAGGCGCTT-CCACCAAA-CGCCGCTAA
* * * * ** * * * * *
35704623 TAGTAAGCATTAGCTGCGTTT-TGAAGTAAGCGCCACTAACTCTAATATACGTCAAGGCC-AAAC
125 TACTATGCATTAACGGCGTTTGT-CCGTAAACGCCACTAATTATAATATACATCAAGACCAAAAC
* * ** * *
35704686 TCTGCGTTTTGGTTAAGATACTTTGCGGCGCTT--TC-CAC
189 GCTGCATTTTGGTTAAGATGTTTTGCGGCG-TTGAACGCTC
* * * *
35704724 AAACGCCGCTACTACTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTC
1 -AGCGCCGCTAATACTATACATTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACATC
* * * *
35704789 AAGACCAAACTCCGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAACGCTGCTATTACT
65 AAGACCAAACTCCGCGTTTTGGTTAACACATTTTGAGGCGCTT-CCACCAAACGCCGCTAATACT
* * * * *
35704854 ATGCTTTAATGGCGTTT-TCCTTAAACTCCACTAATTATAGTATACATCAAGACCAAAACGCTGC
129 ATGCATTAACGGCGTTTGTCCGTAAACGCCACTAATTATAATATACATCAAGACCAAAACGCTGC
35704918 ATTTTGGTTAAGATGTTTTGCGGCGTTGAACGCTC
194 ATTTTGGTTAAGATGTTTTGCGGCGTTGAACGCTC
** *
35704953 AGCGCCGCTAATACTATACATTAGCGGCGTTTTCTTTATAAGCGCCACTAATTGTAATATACATC
1 AGCGCCGCTAATACTATACATTAGCGGCGTTTTC-CAATAAGCGCCACTAATTCTAATATACATC
* * * *** * *
35705018 AAGACCAAACTCTGCGTTTTGGTTAACACCTTTTGCGGCGCTTTTGCTAAGCGCCGCTAATACTA
65 AAGACCAAACTCCGCGTTTTGGTTAACACATTTTGAGGCGCTTCCACCAAACGCCGCTAATACTA
* * * * *
35705083 TGCATTACCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAGACCAGAACGCTGC
130 TGCATTAACGGCGTTTGTCCGTAAACGCCACTAATTATAATATACATCAAGACCAAAACGCTGC
35705147 GTGTTGGTCT
Statistics
Matches: 339, Mismatches: 74, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
226 28 0.08
227 64 0.19
228 86 0.25
229 159 0.47
230 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (228 bp):
AGCGCCGCTAATACTATACATTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACATCA
AGACCAAACTCCGCGTTTTGGTTAACACATTTTGAGGCGCTTCCACCAAACGCCGCTAATACTAT
GCATTAACGGCGTTTGTCCGTAAACGCCACTAATTATAATATACATCAAGACCAAAACGCTGCAT
TTTGGTTAAGATGTTTTGCGGCGTTGAACGCTC
Found at i:35709145 original size:22 final size:22
Alignment explanation
Indices: 35709118--35709177 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
35709108 CCCGAGAACT
35709118 AAAATAAAATATCGTGGAAACA
1 AAAATAAAATATCGTGGAAACA
* * *
35709140 AAAATAAACA-CTC-TGGGAACT
1 AAAATAAA-ATATCGTGGAAACA
*
35709161 TAAATAAAATATCGTGG
1 AAAATAAAATATCGTGG
35709178 CTTACTGCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
22 13 0.43
23 1 0.03
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.22
Consensus pattern (22 bp):
AAAATAAAATATCGTGGAAACA
Found at i:35724620 original size:20 final size:20
Alignment explanation
Indices: 35724595--35724635 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
35724585 TCGAATAATC
35724595 TATAATCATACGAAGATGAT
1 TATAATCATACGAAGATGAT
*
35724615 TATAATCATATGAAGATGAT
1 TATAATCATACGAAGATGAT
35724635 T
1 T
35724636 CTCAATGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (20 bp):
TATAATCATACGAAGATGAT
Found at i:35729493 original size:25 final size:25
Alignment explanation
Indices: 35729437--35729508 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 25
35729427 TTACCGAATC
* ** *
35729437 CAGCTCTTATGAGCTTATTGATACT
1 CAGCTCGTATGAGCTTACCGTTACT
* *
35729462 CAACTCGTATGAGCTTACCGTTATT
1 CAGCTCGTATGAGCTTACCGTTACT
* *
35729487 CAGCTCGGAGGAGCTTACCGTT
1 CAGCTCGTATGAGCTTACCGTT
35729509 TATCACTTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACCGTTACT
Found at i:35731090 original size:26 final size:26
Alignment explanation
Indices: 35731061--35731114 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
35731051 ACGTGAAATG
35731061 TATGATTGTTTGATTTATAAGTCTGA
1 TATGATTGTTTGATTTATAAGTCTGA
35731087 TATGATTGTTTGATTTATAAGTCTGA
1 TATGATTGTTTGATTTATAAGTCTGA
35731113 TA
1 TA
35731115 ATACTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.50
Consensus pattern (26 bp):
TATGATTGTTTGATTTATAAGTCTGA
Found at i:35743673 original size:7 final size:7
Alignment explanation
Indices: 35743663--35743739 Score: 52
Period size: 7 Copynumber: 10.6 Consensus size: 7
35743653 ATAGATTATA
35743663 ATATAAT
1 ATATAAT
35743670 ATATAAT
1 ATATAAT
35743677 ATTACATAAT
1 A-T--ATAAT
35743687 ATATAAT
1 ATATAAT
*
35743694 ATCTAAT
1 ATATAAT
35743701 CAT-TAAT
1 -ATATAAT
*
35743708 ACAT-AT
1 ATATAAT
35743714 ATATAA-
1 ATATAAT
35743720 AGTATTAAT
1 A-TA-TAAT
*
35743729 ATATTAT
1 ATATAAT
35743736 ATAT
1 ATAT
35743740 TATTTGATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
6 7 0.12
7 34 0.60
8 8 0.14
9 2 0.04
10 6 0.11
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:35743690 original size:24 final size:25
Alignment explanation
Indices: 35743663--35743716 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
35743653 ATAGATTATA
35743663 ATATAATATATAAT-ATTACATA-AT
1 ATATAATATATAATCATTA-ATACAT
*
35743687 ATATAATATCTAATCATTAATACAT
1 ATATAATATATAATCATTAATACAT
35743712 ATATA
1 ATATA
35743717 TAAAGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (25 bp):
ATATAATATATAATCATTAATACAT
Found at i:35748221 original size:15 final size:14
Alignment explanation
Indices: 35748200--35748235 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
35748190 ATAATCCTTA
*
35748200 ATAATTATCTTAAT
1 ATAATTATCCTAAT
35748214 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
35748229 ATAATTA
1 ATAATTA
35748236 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:35748818 original size:23 final size:23
Alignment explanation
Indices: 35748787--35748842 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
35748777 AGTCCTCAAA
* *
35748787 TTATTTTTTTCTTT-TTTATTTAT
1 TTATATTTTTATTTATTTA-TTAT
35748810 TT-TGATTTTTATTTATTTATTAT
1 TTAT-ATTTTTATTTATTTATTAT
35748833 TTATATTTTT
1 TTATATTTTT
35748843 TATGCTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 22 0.79
24 5 0.18
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (23 bp):
TTATATTTTTATTTATTTATTAT
Found at i:35748834 original size:11 final size:11
Alignment explanation
Indices: 35748786--35748836 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
35748776 TAGTCCTCAA
*
35748786 ATTATTTTTTT
1 ATTATTTATTT
* *
35748797 CTTTTTTATTT
1 ATTATTTATTT
*
35748808 ATT-TTGATTT
1 ATTATTTATTT
35748818 -TTATTTATTT
1 ATTATTTATTT
35748828 ATTATTTAT
1 ATTATTTAT
35748837 ATTTTTTATG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 2 0.06
10 12 0.38
11 18 0.56
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (11 bp):
ATTATTTATTT
Found at i:35748844 original size:20 final size:19
Alignment explanation
Indices: 35748798--35748845 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
35748788 TATTTTTTTC
*
35748798 TTTTTTATTTATTTTGATT
1 TTTTTTATTTATTTTGATA
*
35748817 TTTATTTATTTATTATTTATA
1 TTT-TTTATTTATT-TTGATA
35748838 TTTTTTAT
1 TTTTTTAT
35748846 GCTTTAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 15 0.60
21 7 0.28
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTTTATTTATTTTGATA
Found at i:35750019 original size:4 final size:4
Alignment explanation
Indices: 35750005--35750090 Score: 83
Period size: 4 Copynumber: 21.5 Consensus size: 4
35749995 CCAAATAAGT
*
35750005 AATA AAT- AATA AATA AA-A TAATA AATA AATA AAGTA AAGAA AATA AA-A
1 AATA AATA AATA AATA AATA -AATA AATA AATA AA-TA AA-TA AATA AATA
35750053 TAATA AATA AATA AATA AATA AA-A AAGTA AA-A AATA AA
1 -AATA AATA AATA AATA AATA AATA AA-TA AATA AATA AA
35750091 AATTGGGTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
3 11 0.15
4 47 0.66
5 13 0.18
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:35750031 original size:30 final size:30
Alignment explanation
Indices: 35749997--35750090 Score: 113
Period size: 30 Copynumber: 3.1 Consensus size: 30
35749987 ATTAATATCC
*
35749997 AAATAAGT-AATAAATAATAAATAAAATAAT
1 AAATAAATAAATAAATAA-AAATAAAATAAT
*
35750027 AAATAAATAAAGTAAA-GAAAATAAAATAAT
1 AAATAAATAAA-TAAATAAAAATAAAATAAT
35750057 AAATAAATAAATAAATAAAAAAGTAAAA-AAT
1 AAATAAATAAATAAAT-AAAAA-TAAAATAAT
35750088 AAA
1 AAA
35750091 AATTGGGTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
29 4 0.07
30 30 0.54
31 13 0.23
32 9 0.16
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (30 bp):
AAATAAATAAATAAATAAAAATAAAATAAT
Found at i:35753692 original size:270 final size:270
Alignment explanation
Indices: 35753211--35753742 Score: 893
Period size: 270 Copynumber: 2.0 Consensus size: 270
35753201 AAATAAAAAT
*
35753211 AGAATTAAGAATATTGAATCAAAAATTCGAGAAATTAAAAATAGAGTTGAAAGAAAGGAAATTCT
1 AGAATTAAGAATATTGAATCAAAAATTCGAGAAATTAAAAATAGAGTTGAAAGAAAGAAAATTCT
* *** * *
35753276 TTTGGGAGGTTCCAGCCTCCAGTTGTCTCGTTGTGCCTTGGGTTCAATCCTCGCCTTTAGATGAT
66 TATGGGAGGTTCCAGCCTCCAGTTGTCTCGTTCCACCTTAGGTTCAATCCTCGACTTTAGATGAT
* * *
35753341 CCTTCCCAAATCGAATAAGCCAGTTATAGTCGAAGAGGACGCCTACGACCACCAGCTTCAAGGAT
131 CCTTCCCAAACCGAATAAGCCAGTTATAGTCGAAGAGGACGCCTACGACCACCAACTCCAAGGAT
*
35753406 TTAGACTTACGATTTAGTGGAACCTGACTCTAGCCAACAATCGCTTCTGTGGGATCATCTTATGC
196 TTAGACTTACGATTTAGTGAAACCTGACTCTAGCCAACAATCGCTTCTGTGGGATCATCTTATGC
35753471 TAAAAATAAC
261 TAAAAATAAC
* * *
35753481 AGAATTAAGAATATTGAATCGAAAATTTGAGAAATTAAAAATAGAGTTGAGAGAAAGAAAATTCT
1 AGAATTAAGAATATTGAATCAAAAATTCGAGAAATTAAAAATAGAGTTGAAAGAAAGAAAATTCT
*
35753546 TATGGGAGGTTCCAGCCTCCAGTTGTCTCGTTCCATCTTAGGTTCAATCCTCGACTTTAGATGAT
66 TATGGGAGGTTCCAGCCTCCAGTTGTCTCGTTCCACCTTAGGTTCAATCCTCGACTTTAGATGAT
* * *
35753611 CCTTCCCAAACCGAATAAGCCAGTTATAGTGGAAGAGGACGCCTATGACCACCAACTCCAATGAT
131 CCTTCCCAAACCGAATAAGCCAGTTATAGTCGAAGAGGACGCCTACGACCACCAACTCCAAGGAT
*
35753676 TTAGACTTACGATTTAGTGAAACCTGACTCTAGCCAACAATCGCTTCTGTGGGATCGTCTTATGC
196 TTAGACTTACGATTTAGTGAAACCTGACTCTAGCCAACAATCGCTTCTGTGGGATCATCTTATGC
35753741 TA
261 TA
35753743 GATCAACACT
Statistics
Matches: 243, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
270 243 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (270 bp):
AGAATTAAGAATATTGAATCAAAAATTCGAGAAATTAAAAATAGAGTTGAAAGAAAGAAAATTCT
TATGGGAGGTTCCAGCCTCCAGTTGTCTCGTTCCACCTTAGGTTCAATCCTCGACTTTAGATGAT
CCTTCCCAAACCGAATAAGCCAGTTATAGTCGAAGAGGACGCCTACGACCACCAACTCCAAGGAT
TTAGACTTACGATTTAGTGAAACCTGACTCTAGCCAACAATCGCTTCTGTGGGATCATCTTATGC
TAAAAATAAC
Found at i:35754306 original size:15 final size:14
Alignment explanation
Indices: 35754263--35754320 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
35754253 ATAAAATAAA
* *
35754263 ATCCTAAAATAAATA
1 ATCCTAATAT-AATT
*
35754278 ATCCTTA-ATAATT
1 ATCCTAATATAATT
*
35754291 ATCTTAATATTAATT
1 ATCCTAATA-TAATT
35754306 ATCCTAATATAATT
1 ATCCTAATATAATT
35754320 A
1 A
35754321 AAATAGAGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 8 0.22
14 9 0.25
15 19 0.53
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (14 bp):
ATCCTAATATAATT
Found at i:35754990 original size:34 final size:34
Alignment explanation
Indices: 35754923--35754997 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
35754913 AGACACGGTT
* *
35754923 GTGTGGAGATCTCACATGCTCGTGTGGCCAGGCC
1 GTGTGGAGATCTCACATGCCCATGTGGCCAGGCC
* *
35754957 GTGTGGAGATCTCACATGCCCATGTTGCTAGGCC
1 GTGTGGAGATCTCACATGCCCATGTGGCCAGGCC
*
35754991 TTGTGGA
1 GTGTGGA
35754998 ACCAAAAACC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.16, C:0.24, G:0.33, T:0.27
Consensus pattern (34 bp):
GTGTGGAGATCTCACATGCCCATGTGGCCAGGCC
Found at i:35756617 original size:24 final size:24
Alignment explanation
Indices: 35756479--35756617 Score: 86
Period size: 25 Copynumber: 5.6 Consensus size: 24
35756469 CACACTACAA
* *
35756479 CTCTTATGAGCGTCCCGATATATGA
1 CTCTTATGAGCTTCCCGAT-TATGG
* * * *
35756504 ATCTTCA-GAGCTTCTCAATTAAAGG
1 CTCTT-ATGAGCTTCCCGATT-ATGG
*
35756529 CTCTTTCATGAGCTTCCTGATATATGG
1 CTC-TT-ATGAGCTTCCCGAT-TATGG
* **
35756556 CTTTTCGGAGCTTCCCGA-TATTGG
1 CTCTTATGAGCTTCCCGATTA-TGG
*
35756580 CTCGTT-TGAACTTCCCGATTATGG
1 CTC-TTATGAGCTTCCCGATTATGG
35756604 CTCTTATGAGCTTC
1 CTCTTATGAGCTTC
35756618 TCTTTATATA
Statistics
Matches: 86, Mismatches: 19, Indels: 19
0.69 0.15 0.15
Matches are distributed among these distances:
23 4 0.05
24 29 0.34
25 31 0.36
26 7 0.08
27 14 0.16
28 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (24 bp):
CTCTTATGAGCTTCCCGATTATGG
Found at i:35756665 original size:25 final size:25
Alignment explanation
Indices: 35756609--35756673 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
35756599 TATGGCTCTT
* * *
35756609 ATGAGCTTCTCTTTATATAGCTCGA
1 ATGAGCTTCTCGTTACATAGCTCAA
* * *
35756634 ATAAGCTTCTCGTTACATGGTTCAA
1 ATGAGCTTCTCGTTACATAGCTCAA
*
35756659 ATGAGCTTCCCGTTA
1 ATGAGCTTCTCGTTA
35756674 TATGTCTTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (25 bp):
ATGAGCTTCTCGTTACATAGCTCAA
Found at i:35767688 original size:75 final size:75
Alignment explanation
Indices: 35767565--35767871 Score: 496
Period size: 75 Copynumber: 4.1 Consensus size: 75
35767555 NNNNNNNNNN
* * * * *
35767565 CAACCCCTTTCACATTTAAGATACGGTGGGATCAGCACTTAGCAACCACCAATGAGTT-AGGAAA
1 CAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGA-TTCGGGGAA
*
35767629 TCAGCACTTAA
65 TCAGCACTTAG
*
35767640 CAACCCCCTTCACATTTAAAATACGGTAGAATCAGCACTTAGCAACCACCAATGATTCGGGGAAT
1 CAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAAT
35767705 CAGCACTTAG
66 CAGCACTTAG
*
35767715 CAACCCCCTTCACATTTAAAATACGTTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAAT
1 CAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAAT
35767780 CAGCACTTAG
66 CAGCACTTAG
*
35767790 CAA-CCCCTTCACATTTAAAATACGTTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAAT
1 CAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAAT
35767854 CAGCACTTAG
66 CAGCACTTAG
35767864 --ACCCCCTT
1 CAACCCCCTT
35767872 GGGGGAATCA
Statistics
Matches: 221, Mismatches: 9, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
72 1 0.00
73 6 0.03
74 73 0.33
75 141 0.64
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (75 bp):
CAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAAT
CAGCACTTAG
Found at i:35767710 original size:33 final size:33
Alignment explanation
Indices: 35767668--35767863 Score: 167
Period size: 33 Copynumber: 5.4 Consensus size: 33
35767658 AAATACGGTA
35767668 GAATCAGCACTTAGCAACCACCAATGATTCGGG
1 GAATCAGCACTTAGCAACCACCAATGATTCGGG
* * * *
35767701 GAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGTTG
1 GAATCAGCACTTAGCAA-CCAC--CA-A--T--GATTCG-GG
35767743 GAATCAGCACTTAGCAACCACCAATGATTCGGG
1 GAATCAGCACTTAGCAACCACCAATGATTCGGG
* * * *
35767776 GAATCAGCACTTAGCAACCCCTTCACATTTAAAATACGTTG
1 GAATCAGCACTTAGCAACCAC--CA-A--T--GATTCG-GG
35767817 GAATCAGCACTTAGCAACCACCAATGATTCGGG
1 GAATCAGCACTTAGCAACCACCAATGATTCGGG
35767850 GAATCAGCACTTAG
1 GAATCAGCACTTAG
35767864 ACCCCCTTGG
Statistics
Matches: 130, Mismatches: 16, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
33 53 0.41
34 11 0.08
35 2 0.02
36 5 0.04
37 1 0.01
38 3 0.02
39 5 0.04
40 4 0.03
41 28 0.22
42 18 0.14
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (33 bp):
GAATCAGCACTTAGCAACCACCAATGATTCGGG
Found at i:35767862 original size:149 final size:150
Alignment explanation
Indices: 35767565--35767871 Score: 496
Period size: 149 Copynumber: 2.1 Consensus size: 150
35767555 NNNNNNNNNN
* * *
35767565 CAACCCCTTTCACATTTAAGATACGGTGGGATCAGCACTTAGCAACCACCAATGAGTTAGGAAAT
1 CAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGAGTTAGGAAAT
35767630 CAGCACTTAACAACCCCCTTCACATTTAAAATACGGTAGAATCAGCACTTAGCAACCACCAATGA
66 CAGCACTTAACAACCCCCTTCACATTTAAAATACGGTAGAATCAGCACTTAGCAACCACCAATGA
35767695 TTCGGGGAATCAGCACTTAG
131 TTCGGGGAATCAGCACTTAG
* * *
35767715 CAACCCCCTTCACATTTAAAATACGTTGGAATCAGCACTTAGCAACCACCAATGA-TTCGGGGAA
1 CAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGAGTT-AGGAAA
* * *
35767779 TCAGCACTTAGCAA-CCCCTTCACATTTAAAATACGTTGGAATCAGCACTTAGCAACCACCAATG
65 TCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTAGAATCAGCACTTAGCAACCACCAATG
35767843 ATTCGGGGAATCAGCACTTAG
130 ATTCGGGGAATCAGCACTTAG
35767864 --ACCCCCTT
1 CAACCCCCTT
35767872 GGGGGAATCA
Statistics
Matches: 147, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
147 8 0.05
149 71 0.48
150 68 0.46
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (150 bp):
CAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGAGTTAGGAAAT
CAGCACTTAACAACCCCCTTCACATTTAAAATACGGTAGAATCAGCACTTAGCAACCACCAATGA
TTCGGGGAATCAGCACTTAG
Found at i:35767876 original size:26 final size:27
Alignment explanation
Indices: 35767847--35767899 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
35767837 CCAATGATTC
35767847 GGGGAATCAGCACTTAG-ACCCCCTTG
1 GGGGAATCAGCACTTAGAACCCCCTTG
35767873 GGGGAATCAGCACTTAGCAACCCCCTT
1 GGGGAATCAGCACTTAG-AACCCCCTT
35767900 TATATTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 17 0.68
28 8 0.32
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.19
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGAACCCCCTTG
Found at i:35772163 original size:24 final size:24
Alignment explanation
Indices: 35772136--35772183 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
35772126 AGTCAACAAG
35772136 GTGGAAAAAAATTGAGAATAAAAA
1 GTGGAAAAAAATTGAGAATAAAAA
*
35772160 GTGGAAAAGAATTGAGAATAAAAA
1 GTGGAAAAAAATTGAGAATAAAAA
35772184 CAACACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (24 bp):
GTGGAAAAAAATTGAGAATAAAAA
Found at i:35777961 original size:184 final size:188
Alignment explanation
Indices: 35777717--35778080 Score: 423
Period size: 184 Copynumber: 1.9 Consensus size: 188
35777707 TGTTGCTGCT
* *
35777717 TCATAATCATCATCATCGAGTTTCCACACTTTTACATGTTCACGGCAAAATGAAAAAGTAAATGC
1 TCATAATCATAATCATCGAGTTTCCACACTTTTACATGTTCACGGCAAAAAGAAAAAGTAAATGC
**
35777782 GA-ATATGTACATATGTGTAAC-AG-AAA-AAATGACAAAACCATTAATTGAAATAAGGAAAGAA
66 -ACATATGTACATATGTGTAACAAGAAAACAAACAACAAAACCATTAATTGAAATAAGGAAAGAA
* *
35777843 AAAAAAG-CGTGTAAGTACAGTGAGAGTCGTAGTTGCCGCTGCTTCATGATCATCATCA
130 AAAAAAGAAGTGTAAGTACAGTGAGAGTCGTAATTGCCGCTGCTTCATGATCATCATCA
* * ** * *** *
35777901 TCATCATCATAATCATTGAGTTTTTACAGTTTTACATGTTTGTGGCAAAAAGAAAAAGTAAGTGC
1 TCATAATCATAATCATCGAGTTTCCACACTTTTACATGTTCACGGCAAAAAGAAAAAGTAAATGC
* * ** * *
35777966 ACGTGTGTATGTATGTGTAACAAAAGAAAACAAACAACAAAACCATTAATTGAAATAGGGAAGGA
66 ACATATGTACATATGTGTAAC--AAGAAAACAAACAACAAAACCATTAATTGAAATAAGGAAAGA
* * * * *
35778031 AAAAAATGTAAGTTTAAGTACAGTTAGAGTTGTAATTGTCGCTGCTTCAT
129 AAAAAAAG-AAGTGTAAGTACAGTGAGAGTCGTAATTGCCGCTGCTTCAT
35778081 AATGCACGAA
Statistics
Matches: 146, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
183 1 0.01
184 69 0.47
187 2 0.01
188 3 0.02
189 37 0.25
191 34 0.23
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (188 bp):
TCATAATCATAATCATCGAGTTTCCACACTTTTACATGTTCACGGCAAAAAGAAAAAGTAAATGC
ACATATGTACATATGTGTAACAAGAAAACAAACAACAAAACCATTAATTGAAATAAGGAAAGAAA
AAAAAGAAGTGTAAGTACAGTGAGAGTCGTAATTGCCGCTGCTTCATGATCATCATCA
Found at i:35789366 original size:52 final size:52
Alignment explanation
Indices: 35789245--35789358 Score: 142
Period size: 52 Copynumber: 2.2 Consensus size: 52
35789235 AAAGTCTTTT
** *
35789245 GTCCTCTTATAAATTATTATGCTTTACTTTACTAAAGTATGAGTGAATCATC
1 GTCCTCTTATAAATTATTAAACTTTACTTTACTAAAGTATGAGTGAATCATA
* * *
35789297 GTCCTCTTGTAAATTATTAAACTTTACTTTTGA-TAAAGTTTGA-TGAGTCATA
1 GTCCTCTTATAAATTATTAAACTTTAC-TTT-ACTAAAGTATGAGTGAATCATA
35789349 GTCCTCTTAT
1 GTCCTCTTAT
35789359 GCATTATTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
52 40 0.75
53 12 0.23
54 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (52 bp):
GTCCTCTTATAAATTATTAAACTTTACTTTACTAAAGTATGAGTGAATCATA
Found at i:35791638 original size:50 final size:50
Alignment explanation
Indices: 35791584--35791740 Score: 242
Period size: 50 Copynumber: 3.1 Consensus size: 50
35791574 ACATCAGAGT
* * * *
35791584 TCTCATATAGGTGCCTATGTCATGTCCCAGACATGGTCTTACGGGGGACC
1 TCTCATATCGGTGCCAACGTCATGTCCCAGACATGGTCTTACGTGGGACC
* * *
35791634 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
1 TCTCATATCGGTGCCAACGTCATGTCCCAGACATGGTCTTACGTGGGACC
*
35791684 TCTCATCTCGGTGCCAACGTCATGTCCCAGACATGGTCTTACGTGGGACC
1 TCTCATATCGGTGCCAACGTCATGTCCCAGACATGGTCTTACGTGGGACC
35791734 TCTCATA
1 TCTCATA
35791741 ATCTCAATGA
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 97 1.00
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.27
Consensus pattern (50 bp):
TCTCATATCGGTGCCAACGTCATGTCCCAGACATGGTCTTACGTGGGACC
Found at i:35791670 original size:100 final size:100
Alignment explanation
Indices: 35791558--35791739 Score: 265
Period size: 100 Copynumber: 1.8 Consensus size: 100
35791548 CAATGTCATA
* ** * *
35791558 TCCCAGAGATGGTATTACATCAGAGTTCTCATATAGGTGCCTATGTCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTATTACATCAGACCTCTCATATAGGTGCCAACGTCATGTCCCAGACATGGTCT
35791623 TACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
66 TACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
* ** * *
35791658 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGTCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTATTACATCAGACCTCTCATATAGGTGCCAACGTCATGTCCCAGACATGGTCT
*
35791723 TACGTGGGACCTCTCAT
66 TACGGGGGACCTCTCAT
35791740 AATCTCAATG
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 71 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (100 bp):
TCCCAGACATGGTATTACATCAGACCTCTCATATAGGTGCCAACGTCATGTCCCAGACATGGTCT
TACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
Found at i:35792163 original size:30 final size:30
Alignment explanation
Indices: 35792129--35792192 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
35792119 CCTCGACTCT
* *
35792129 AACTTTTACAAAATTGCGA-TTTTGCCCCTA
1 AACTTTTACAAAATTAC-ACTTTTGCCCCAA
*
35792159 AACTTTTACATAATTACACTTTTGCCCCAA
1 AACTTTTACAAAATTACACTTTTGCCCCAA
35792189 AACT
1 AACT
35792193 CAAAAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (30 bp):
AACTTTTACAAAATTACACTTTTGCCCCAA
Found at i:35799781 original size:60 final size:60
Alignment explanation
Indices: 35799716--35799904 Score: 172
Period size: 60 Copynumber: 3.1 Consensus size: 60
35799706 TTAATTTATA
35799716 TTTATCAAAATATAAATTATCTTAATTCCAAAAACTAAACATTTATATTAATTATTTTAC
1 TTTATCAAAATATAAATTATCTTAATTCCAAAAACTAAACATTTATATTAATTATTTTAC
* * * * *** * * * * * *
35799776 TTTATC-AATTATTGAATCT-TATAAATTTTTAACATTCAACTTATTTGGTTCTTAA-T-TTATA
1 TTTATCAAAATA-TAAAT-TATCTTAATTCCAAAAACTAAAC--ATTT--ATATTAATTATTTTA
35799837 -
60 C
35799837 TTTATCAAAATATAAATTATCTTAATTCCAAAAACTAAACATTTATATTAATTATTTTAC
1 TTTATCAAAATATAAATTATCTTAATTCCAAAAACTAAACATTTATATTAATTATTTTAC
35799897 TTTATCAA
1 TTTATCAA
35799905 TTATTGAAAT
Statistics
Matches: 92, Mismatches: 26, Indels: 22
0.66 0.19 0.16
Matches are distributed among these distances:
57 5 0.05
58 1 0.01
59 12 0.13
60 32 0.35
61 24 0.26
62 12 0.13
63 1 0.01
64 5 0.05
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.47
Consensus pattern (60 bp):
TTTATCAAAATATAAATTATCTTAATTCCAAAAACTAAACATTTATATTAATTATTTTAC
Found at i:35799895 original size:121 final size:121
Alignment explanation
Indices: 35799681--35799928 Score: 480
Period size: 121 Copynumber: 2.0 Consensus size: 121
35799671 TTGAAGTTTA
35799681 TTTTAACATTCAACTTATTTGGTTCTTAATTTATATTTATCAAAATATAAATTATCTTAATTCCA
1 TTTTAACATTCAACTTATTTGGTTCTTAATTTATATTTATCAAAATATAAATTATCTTAATTCCA
35799746 AAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTG-AATCTTATAAAT
66 AAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTGAAATCTTAT-AAT
35799802 TTTTAACATTCAACTTATTTGGTTCTTAATTTATATTTATCAAAATATAAATTATCTTAATTCCA
1 TTTTAACATTCAACTTATTTGGTTCTTAATTTATATTTATCAAAATATAAATTATCTTAATTCCA
35799867 AAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTGAAATCTTATAAT
66 AAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTGAAATCTTATAAT
35799923 TTTTAA
1 TTTTAA
35799929 TTAATAAATA
Statistics
Matches: 126, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
121 118 0.94
122 8 0.06
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.48
Consensus pattern (121 bp):
TTTTAACATTCAACTTATTTGGTTCTTAATTTATATTTATCAAAATATAAATTATCTTAATTCCA
AAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTGAAATCTTATAAT
Found at i:35799923 original size:60 final size:60
Alignment explanation
Indices: 35799738--35799923 Score: 152
Period size: 61 Copynumber: 3.1 Consensus size: 60
35799728 TAAATTATCT
35799738 TAATTCCAAAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTG-AATCTTA
1 TAATTCCAAAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTGAAATCTTA
*** * * * * * * *
35799797 TAAATTTTTAACATTCAACTTATTTGGTTCTTAA-T-TTATA-TTTATCAA-AATAT-AAAT-TA
1 T-AATTCCAAAAACTAAAC--ATTT--ATATTAATTATTTTACTTTATCAATTAT-TGAAATCT-
*
35799856 TCT
59 T-A
35799859 TAATTCCAAAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTGAAATCTTA
1 TAATTCCAAAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTGAAATCTTA
35799919 TAATT
1 TAATT
35799924 TTTAATTAAT
Statistics
Matches: 90, Mismatches: 22, Indels: 29
0.64 0.16 0.21
Matches are distributed among these distances:
57 5 0.06
58 1 0.01
59 9 0.10
60 28 0.31
61 31 0.34
62 10 0.11
63 1 0.01
64 5 0.06
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (60 bp):
TAATTCCAAAAACTAAACATTTATATTAATTATTTTACTTTATCAATTATTGAAATCTTA
Found at i:35801205 original size:21 final size:20
Alignment explanation
Indices: 35801172--35801210 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
35801162 TTATCATTGT
35801172 ACCTAAAATTGAAACCCTAA
1 ACCTAAAATTGAAACCCTAA
*
35801192 ACCTTAAATGTGAAACCCT
1 ACCTAAAAT-TGAAACCCT
35801211 CATGTCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.23
Consensus pattern (20 bp):
ACCTAAAATTGAAACCCTAA
Found at i:35801507 original size:21 final size:21
Alignment explanation
Indices: 35801482--35801521 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35801472 TAAACTTGAT
*
35801482 ATAAATCTTAAACCCTAAATC
1 ATAAATCATAAACCCTAAATC
*
35801503 ATAAATCATAAACTCTAAA
1 ATAAATCATAAACCCTAAA
35801522 CCTCAAACCC
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:0.53, C:0.20, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAAATCATAAACCCTAAATC
Found at i:35811965 original size:21 final size:21
Alignment explanation
Indices: 35811909--35811968 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
35811899 TTCCAAGAGC
*
35811909 TTGGAATTCAAAAGCTCCCAT
1 TTGGAATTCAAAAGTTCCCAT
35811930 TTGGAATTCAAAAGTTCCCAT
1 TTGGAATTCAAAAGTTCCCAT
35811951 TTGGAATTCAAAAGTTCC
1 TTGGAATTCAAAAGTTCC
35811969 AAGAGCTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (21 bp):
TTGGAATTCAAAAGTTCCCAT
Found at i:35813412 original size:104 final size:104
Alignment explanation
Indices: 35813222--35813430 Score: 303
Period size: 104 Copynumber: 2.0 Consensus size: 104
35813212 CCTCAAGATT
* **
35813222 AGTCTAATGAGAGATACAAACAATGGATGGTTTAGTTGTTCCTTGTGCATTCTAAGGATAAGTGC
1 AGTCGAATGAGAGATACAAACAATGGATGGACTAGTTGTTCCTTGTGCATTCTAAGGATAAGTGC
35813287 AAAGAAATAACATGTGAAATCTGGGCTATTTGGGAGGAC
66 AAAGAAATAACATGTGAAATCTGGGCTATTTGGGAGGAC
* * * *
35813326 AGTCGAATGAGAGATACAGATAGTGGATGGACT-GTTTGTTCTTTGTGCATTCTAAGGATAAGTG
1 AGTCGAATGAGAGATACAAACAATGGATGGACTAG-TTGTTCCTTGTGCATTCTAAGGATAAGTG
** * *
35813390 CAGGGAAATAACATGTGTAATCTGGGCTATTTGGGGGGAC
65 CAAAGAAATAACATGTGAAATCTGGGCTATTTGGGAGGAC
35813430 A
1 A
35813431 AAAACAGACA
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
103 1 0.01
104 92 0.99
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (104 bp):
AGTCGAATGAGAGATACAAACAATGGATGGACTAGTTGTTCCTTGTGCATTCTAAGGATAAGTGC
AAAGAAATAACATGTGAAATCTGGGCTATTTGGGAGGAC
Found at i:35815429 original size:24 final size:24
Alignment explanation
Indices: 35815402--35815519 Score: 62
Period size: 24 Copynumber: 5.2 Consensus size: 24
35815392 TATATATGAG
35815402 TTATTTTTTGTGTAAATACATTCA
1 TTATTTTTTGTGTAAATACATTCA
* * *
35815426 TTA----TT-TG-AATTATATATGA
1 TTATTTTTTGTGTAAATACAT-TCA
35815445 GTTATTTTTTGTGTAAATACATTCA
1 -TTATTTTTTGTGTAAATACATTCA
* * *
35815470 TTA----TT-TG-AATTATATATGA
1 TTATTTTTTGTGTAAATACAT-TCA
35815489 GTTATTTTTTGTGTAAATACATTCA
1 -TTATTTTTTGTGTAAATACATTCA
35815514 TTATTT
1 TTATTT
35815520 GAATTATATA
Statistics
Matches: 66, Mismatches: 12, Indels: 32
0.60 0.11 0.29
Matches are distributed among these distances:
18 12 0.18
19 8 0.12
20 10 0.15
24 16 0.24
25 8 0.12
26 12 0.18
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (24 bp):
TTATTTTTTGTGTAAATACATTCA
Found at i:35815442 original size:44 final size:44
Alignment explanation
Indices: 35815379--35815554 Score: 352
Period size: 44 Copynumber: 4.0 Consensus size: 44
35815369 TTTCAAATTA
35815379 TCATTATTTGAATTATATATGAGTTATTTTTTGTGTAAATACAT
1 TCATTATTTGAATTATATATGAGTTATTTTTTGTGTAAATACAT
35815423 TCATTATTTGAATTATATATGAGTTATTTTTTGTGTAAATACAT
1 TCATTATTTGAATTATATATGAGTTATTTTTTGTGTAAATACAT
35815467 TCATTATTTGAATTATATATGAGTTATTTTTTGTGTAAATACAT
1 TCATTATTTGAATTATATATGAGTTATTTTTTGTGTAAATACAT
35815511 TCATTATTTGAATTATATATGAGTTATTTTTTGTGTAAATACAT
1 TCATTATTTGAATTATATATGAGTTATTTTTTGTGTAAATACAT
35815555 GTGAGAGTAT
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 132 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (44 bp):
TCATTATTTGAATTATATATGAGTTATTTTTTGTGTAAATACAT
Found at i:35817086 original size:12 final size:12
Alignment explanation
Indices: 35817071--35817116 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
35817061 ACCTTTTATT
35817071 TTTATTTTTTTA
1 TTTATTTTTTTA
35817083 TTTATTTTTTTA
1 TTTATTTTTTTA
35817095 TGTATATTTGTTTT-
1 T-T-TATTT-TTTTA
35817109 TTTATTTT
1 TTTATTTT
35817117 AAACAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.03
12 18 0.58
13 2 0.06
14 6 0.19
15 4 0.13
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:35817093 original size:26 final size:26
Alignment explanation
Indices: 35817064--35817116 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
35817054 TCCTCAGACC
* *
35817064 TTTTATTTTTATTT-TTTTATTTATTT
1 TTTTATGTATATTTGTTTT-TTTATTT
35817090 TTTTATGTATATTTGTTTTTTTATTT
1 TTTTATGTATATTTGTTTTTTTATTT
35817116 T
1 T
35817117 AAACAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (26 bp):
TTTTATGTATATTTGTTTTTTTATTT
Found at i:35822829 original size:13 final size:13
Alignment explanation
Indices: 35822811--35822865 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
35822801 ATTTGTCCGA
35822811 AAATAGAAATGCT
1 AAATAGAAATGCT
*
35822824 AAATAGAAATGAT
1 AAATAGAAATGCT
35822837 AAAT-GAACA-G--
1 AAATAGAA-ATGCT
35822847 AAATTAGAAATGCT
1 AAA-TAGAAATGCT
35822861 AAATA
1 AAATA
35822866 TAGAACTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
10 3 0.09
11 2 0.06
12 8 0.23
13 19 0.54
14 3 0.09
ACGTcount: A:0.58, C:0.05, G:0.15, T:0.22
Consensus pattern (13 bp):
AAATAGAAATGCT
Found at i:35826895 original size:5 final size:5
Alignment explanation
Indices: 35826885--35826915 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
35826875 CTAAATACCC
*
35826885 AGAAA AGAAA AGAAA AGAAA AGAAA CGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
35826916 ATCAAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:35827935 original size:5 final size:5
Alignment explanation
Indices: 35827925--35827955 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
35827915 CTAAATACCC
*
35827925 AGAAA AGAAA AGAAA AGAAA AGAAA CGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
35827956 ATCAAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:35835499 original size:20 final size:20
Alignment explanation
Indices: 35835476--35835516 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
35835466 TTATTCAAAC
* *
35835476 AATATTACTTGAATAGTTAT
1 AATATTACATGAATAATTAT
*
35835496 AATATTAGATGAATAATTAT
1 AATATTACATGAATAATTAT
35835516 A
1 A
35835517 TGCCTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.41
Consensus pattern (20 bp):
AATATTACATGAATAATTAT
Found at i:35837812 original size:19 final size:18
Alignment explanation
Indices: 35837764--35837804 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
35837754 TAACTTTGTC
35837764 TAAAA-TTTTATACTTTT
1 TAAAATTTTTATACTTTT
35837781 TAAAATTAATTTATA-TTTT
1 TAAAATT--TTTATACTTTT
35837800 TAAAA
1 TAAAA
35837805 GATTTTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 1 0.05
19 9 0.43
20 6 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAAATTTTTATACTTTT
Found at i:35838445 original size:20 final size:19
Alignment explanation
Indices: 35838422--35838461 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
35838412 AAAATCACAA
35838422 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAA-ATTTAT
*
35838442 AAAAAATTCTAAAATTTAT
1 AAAAAATTCAAAAATTTAT
35838461 A
1 A
35838462 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAATTCAAAAATTTAT
Found at i:35844516 original size:35 final size:35
Alignment explanation
Indices: 35844470--35844539 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
35844460 TTCAAAGCTG
* *
35844470 TCTATTCGAGTCACATTCACTGAATTATTTTTACC
1 TCTATTCGAGTCACAGTCACTAAATTATTTTTACC
*
35844505 TCTATTCGAGTCATAGTCACTAAATTATTTTTACC
1 TCTATTCGAGTCACAGTCACTAAATTATTTTTACC
35844540 CAGAGCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (35 bp):
TCTATTCGAGTCACAGTCACTAAATTATTTTTACC
Done.