Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 136 of 438
Found at i:40459108 original size:26 final size:26
Alignment explanation
Indices: 40459051--40459108 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
40459041 TACGTGGGAG
40459051 CCTGAAGATGCTCTGAGACAACAATA
1 CCTGAAGATGCTCTGAGACAACAATA
**
40459077 TATGAAGATGCTCTGAGACAACAATA
1 CCTGAAGATGCTCTGAGACAACAATA
40459103 CCTGAA
1 CCTGAA
40459109 TATGTGAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (26 bp):
CCTGAAGATGCTCTGAGACAACAATA
Found at i:40460304 original size:44 final size:44
Alignment explanation
Indices: 40460235--40460398 Score: 133
Period size: 43 Copynumber: 3.8 Consensus size: 44
40460225 TCCGATATGT
*
40460235 GATTTCGTGTAAGACCACATCTGGGACGTTGGCATCA-ATTTGA
1 GATTTCGTGTAAGACCACATCTGGGACATTGGCATCATATTTGA
** * *
40460278 GATTTACGTGTAAGACCATGTTTGGGACATTGGCTTCATATTT--
1 GATTT-CGTGTAAGACCACATCTGGGACATTGGCATCATATTTGA
* * * * * *
40460321 GATTTCATGTAAGACC-CTGTCTGTGACAGTGGTATCGATAATT--
1 GATTTCGTGTAAGACCAC-ATCTGGGACATTGGCATC-ATATTTGA
* * *
40460364 GATTACATGTAAGACCACATCTGGGACGTTGGCAT
1 GATTTCGTGTAAGACCACATCTGGGACATTGGCAT
40460399 TGTACGAGCT
Statistics
Matches: 97, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
42 23 0.24
43 42 0.43
44 28 0.29
45 4 0.04
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (44 bp):
GATTTCGTGTAAGACCACATCTGGGACATTGGCATCATATTTGA
Found at i:40466685 original size:40 final size:40
Alignment explanation
Indices: 40466603--40466820 Score: 248
Period size: 40 Copynumber: 5.5 Consensus size: 40
40466593 AAGCCAAGTA
* * * *
40466603 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCACACAAATG
* *
40466641 CCTTCGGGACATAGCCCGGATATAGTAACTCACACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
*
40466681 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* **
40466721 CCTTCGGGACTTAGCCCGGATATAATAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* * *
40466761 CCTTTGGGACTTAGCCCGGA-ACTAGTCACT-AGCGCAAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCA-CAC-AAATG
40466802 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40466821 TTATCATCCA
Statistics
Matches: 157, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
38 12 0.08
39 17 0.11
40 105 0.67
41 23 0.15
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
Found at i:40466736 original size:80 final size:79
Alignment explanation
Indices: 40466603--40466820 Score: 273
Period size: 80 Copynumber: 2.7 Consensus size: 79
40466593 AAGCCAAGTA
* * * * *
40466603 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTC-AATGCCTTCGGGACATAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAA
*
40466666 TAACTCACACCAATG
65 TAACTCACACAAATG
40466681 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAA
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAA
**
40466746 TAACTCGTACAAATG
65 TAACTCACACAAATG
*
40466761 CCTTTGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACT--CGCACAAATGCCTTCGGGACTTAGCCCGG
40466821 TTATCATCCA
Statistics
Matches: 124, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
78 13 0.10
79 18 0.15
80 65 0.52
81 24 0.19
82 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAAT
AACTCACACAAATG
Found at i:40470413 original size:40 final size:40
Alignment explanation
Indices: 40470368--40470471 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
40470358 TGAATGATAC
* ** *
40470368 CCGGGCTAAGTCTTGAAGGCATTTATGCTA-ATGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATG-TTATAT
** *
40470408 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGTTATAT
40470448 CCGGGCTAAGACCCGAAGGCATTT
1 CCGGGCTAAGACCCGAAGGCATTT
40470472 GTGCAAGTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 53 0.96
41 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGTTATAT
Found at i:40470530 original size:40 final size:40
Alignment explanation
Indices: 40470402--40470535 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 40
40470392 ATGCTAATGA
*
40470402 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG
1 TTATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTTG
* *
40470442 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTA
1 TTATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTG
** * * * ** *
40470482 CCAAATCCGGGTTAAGACCTGAAGGCAATTGTGCTTGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTG
40470522 TTATATCC-GGCTAA
1 TTATATCCGGGCTAA
40470536 ATTCCGAAGA
Statistics
Matches: 76, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
39 5 0.07
40 69 0.91
41 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTG
Found at i:40472619 original size:39 final size:40
Alignment explanation
Indices: 40472507--40472636 Score: 158
Period size: 40 Copynumber: 3.3 Consensus size: 40
40472497 GACTATCTCA
* *
40472507 AATGCCTTCGGGAC-AAACCC-CAGTTATAGTAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-TT-TAGTAACTCGCACG
* *
40472547 AATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* * *
40472587 AATTCCTTTGGG-CTTAACCCGGATTTATTAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
40472626 AATGCCTTCGG
1 AATGCCTTCGG
40472637 ATCTTAGTCC
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 33 0.43
40 37 0.48
41 7 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
Found at i:40481836 original size:39 final size:40
Alignment explanation
Indices: 40481724--40481930 Score: 249
Period size: 40 Copynumber: 5.2 Consensus size: 40
40481714 TGAATGATAC
* * *
40481724 CCGGGCTAAGTCCCGAAGGCATTTATGCTA-ATGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTG-TTATAT
*
40481764 CCGGGCTAAGACCCGAAGGCATTCGTGCTAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
* *
40481804 CCGGGCTAAGACCC-AAGGCATTTGTACGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
* *** *
40481843 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
* * * *
40481883 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
40481923 CC-GGCTAA
1 CCGGGCTAA
40481931 ATTCCGAAGA
Statistics
Matches: 142, Mismatches: 23, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
39 41 0.29
40 99 0.70
41 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
Found at i:40481939 original size:79 final size:80
Alignment explanation
Indices: 40481724--40481930 Score: 256
Period size: 79 Copynumber: 2.6 Consensus size: 80
40481714 TGAATGATAC
* * * *
40481724 CCGGGCTAAGTCCCGAAGGCATTTATGCTAATGATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
* *** *
40481789 TGCTAGTTGTTATAT
66 TGCAAGTTACCAAAT
* * * *
40481804 CCGGGCTAAGACCC-AAGGCATTTGTACGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
40481868 TGCAAGTTACCAAAT
66 TGCAAGTTACCAAAT
* * *
40481883 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAA
40481931 ATTCCGAAGA
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
79 72 0.67
80 35 0.33
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCG
TGCAAGTTACCAAAT
Found at i:40487975 original size:39 final size:36
Alignment explanation
Indices: 40487941--40488009 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
40487931 GTAACAGTCT
* *
40487941 AGTATTAGTGTGGGCCTTAGCCCATTACAAT-A-AC
1 AGTATCAGCGTGGGCCTTAGCCCATTACAATAACAC
*
40487975 AGTATCAGCGTGAGCCTTAGCCCATTACAATAACA
1 AGTATCAGCGTGGGCCTTAGCCCATTACAATAACA
40488010 ATAAAAGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 28 0.93
35 1 0.03
36 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (36 bp):
AGTATCAGCGTGGGCCTTAGCCCATTACAATAACAC
Found at i:40491412 original size:43 final size:43
Alignment explanation
Indices: 40491358--40491542 Score: 217
Period size: 43 Copynumber: 4.3 Consensus size: 43
40491348 CATAGGATTT
*
40491358 TCGATATGTGATTATGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
** * * *
40491401 TCGATCGGTGATTACGTGTAAGACCACATTTGGGATGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
* ** * *
40491444 TTGATATGTGATTACGTGTAAGACCACGTCTAAGACATTAGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
* * * ***
40491487 TCGATATGTGATTACGAGTAAGACCATGTTTAATACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
40491530 TCGATATGTGATT
1 TCGATATGTGATT
40491543 CCGATATGTG
Statistics
Matches: 119, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 119 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:40491574 original size:56 final size:56
Alignment explanation
Indices: 40491488--40491677 Score: 301
Period size: 56 Copynumber: 3.4 Consensus size: 56
40491478 ACATTAGCAT
* *
40491488 CGATATGTGAT-TACGAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTC
1 CGATATGTG-TGTGCGAGTAAGACCATGTTTAATATGTTGGCATCGATATGTGATTC
* *
40491544 CGATATGTGTGTGCGACTAAGACCACGTTTAATATGTTGGCATCGATATGTGATTC
1 CGATATGTGTGTGCGAGTAAGACCATGTTTAATATGTTGGCATCGATATGTGATTC
40491600 CGATATGTGTGTGCGAGTAAGACCATGTTTAATATGTTGGCATCGATATGTGATTC
1 CGATATGTGTGTGCGAGTAAGACCATGTTTAATATGTTGGCATCGATATGTGATTC
* * *
40491656 TGATATGTGTTTACGAGTAAGA
1 CGATATGTGTGTGCGAGTAAGA
40491678 ACCTGTCTAG
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
55 1 0.01
56 123 0.99
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (56 bp):
CGATATGTGTGTGCGAGTAAGACCATGTTTAATATGTTGGCATCGATATGTGATTC
Found at i:40491697 original size:56 final size:56
Alignment explanation
Indices: 40491488--40491705 Score: 226
Period size: 56 Copynumber: 3.9 Consensus size: 56
40491478 ACATTAGCAT
* * * *
40491488 CGATATGTGAT-TACGAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTC
1 CGATATGTG-TGTACGAGTAAGACCATGTCTAAGATGATGGCATCGATATGTGATTC
* * * * * *
40491544 CGATATGTGTGTGCGACTAAGACCACGTTTAATATGTTGGCATCGATATGTGATTC
1 CGATATGTGTGTACGAGTAAGACCATGTCTAAGATGATGGCATCGATATGTGATTC
* * * *
40491600 CGATATGTGTGTGCGAGTAAGACCATGTTTAATATGTTGGCATCGATATGTGATTC
1 CGATATGTGTGTACGAGTAAGACCATGTCTAAGATGATGGCATCGATATGTGATTC
* * * *
40491656 TGATATGTGTTTACGAGTAAGAACC-TGTCTAGGA-GAATGGCATCAATATG
1 CGATATGTGTGTACGAGTAAG-ACCATGTCTAAGATG-ATGGCATCGATATG
40491706 CAATTACATG
Statistics
Matches: 145, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
55 2 0.01
56 140 0.97
57 3 0.02
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (56 bp):
CGATATGTGTGTACGAGTAAGACCATGTCTAAGATGATGGCATCGATATGTGATTC
Found at i:40491697 original size:112 final size:112
Alignment explanation
Indices: 40491488--40491705 Score: 280
Period size: 112 Copynumber: 1.9 Consensus size: 112
40491478 ACATTAGCAT
40491488 CGATATGTGATTACGAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTG
1 CGATATGTGATTACGAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTG
* * * * *
40491553 TGTGCGACTAAGACCACGTTTAATATGTTGGCATCGATATGTGATTC
66 TGTACGACTAAGACCACGTCTAAGATGATGGCATCAATATGTGATTC
* * *
40491600 CGATATGTG-TGTGCGAGTAAGACCATGTTTAATATGTTGGCATCGATATGTGATTCTGATATGT
1 CGATATGTGAT-TACGAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTCCGATATGT
* * * *
40491664 GTTTACGAGTAAGAACC-TGTCTAGGA-GAATGGCATCAATATG
65 GTGTACGACTAAG-ACCACGTCTAAGATG-ATGGCATCAATATG
40491706 CAATTACATG
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
111 2 0.02
112 86 0.95
113 3 0.03
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (112 bp):
CGATATGTGATTACGAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTG
TGTACGACTAAGACCACGTCTAAGATGATGGCATCAATATGTGATTC
Found at i:40494769 original size:42 final size:44
Alignment explanation
Indices: 40494664--40494790 Score: 134
Period size: 44 Copynumber: 2.9 Consensus size: 44
40494654 ATGTGTTATT
* * * * *
40494664 GTGTAAGACCACGTCTGGGACATTGGCATCAAT-TCGTGATTTAC
1 GTGTAAGACCATGTCTGGGACAATGGTATCGATAT-ATGATTTAC
*
40494708 GTGTAAGACCATGTCTGGGACATTGGTATCG-TATATGATTT-C
1 GTGTAAGACCATGTCTGGGACAATGGTATCGATATATGATTTAC
* * * *
40494750 GTGTAAGACCTTGTTTGGGACAATGGTGTCGATATTTGATT
1 GTGTAAGACCATGTCTGGGACAATGGTATCGATATATGATT
40494791 ACATGTCAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
42 28 0.39
43 15 0.21
44 29 0.40
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (44 bp):
GTGTAAGACCATGTCTGGGACAATGGTATCGATATATGATTTAC
Found at i:40495885 original size:19 final size:20
Alignment explanation
Indices: 40495861--40495898 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40495851 GGTACCACCA
40495861 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
40495880 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
40495899 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:40496190 original size:45 final size:44
Alignment explanation
Indices: 40496126--40496290 Score: 165
Period size: 45 Copynumber: 3.7 Consensus size: 44
40496116 CGCCCCTAAG
* * *
40496126 TGAACTCAGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCAT-AA
* * *
40496171 TGAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTTACATCTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--TCCA--TAA
* * *
40496218 CGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAG
1 TGAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCATCCATAA
40496263 TGAACTC-GACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGTTCGG
40496291 ATGCTCAACC
Statistics
Matches: 98, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
43 1 0.01
44 23 0.23
45 34 0.35
46 3 0.03
47 31 0.32
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (44 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCATAA
Found at i:40501705 original size:19 final size:20
Alignment explanation
Indices: 40501681--40501718 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40501671 GGTACCACCA
40501681 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
40501700 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
40501719 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:40502011 original size:46 final size:45
Alignment explanation
Indices: 40501944--40502109 Score: 187
Period size: 46 Copynumber: 3.7 Consensus size: 45
40501934 CCCCCCTAAG
* *
40501944 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCAT-AA
* * *
40501990 TGAACTCGGACTCAACTCAACGAGTTCGATGCCTAGTT-ACAT-C-TCA
1 TGAACTCGGACTCAACTCAACGAGTTCG--GAC--GTTCGCATCCATAA
* * *
40502036 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAA
40502081 TGAACTC-GACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA
40502110 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 11, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 25 0.25
45 7 0.07
46 55 0.54
47 1 0.01
48 3 0.03
49 3 0.03
50 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAA
Found at i:40502059 original size:92 final size:91
Alignment explanation
Indices: 40501945--40502112 Score: 275
Period size: 92 Copynumber: 1.8 Consensus size: 91
40501935 CCCCCTAAGT
* *
40501945 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT-AATGAACTC-GACTCAACTCAA
40502010 CGAGTTC-GATGCCTAGTTACATCTCAC
64 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
40502037 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGTGAACTCGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAATGAACTCGACTCAACTCAACG
40502102 AGTTCGGATGC
66 AGTTCGGATGC
40502113 TCAACCATCC
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
90 19 0.27
91 13 0.18
92 39 0.55
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAATGAACTCGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:40509276 original size:42 final size:43
Alignment explanation
Indices: 40509203--40509338 Score: 148
Period size: 43 Copynumber: 3.2 Consensus size: 43
40509193 GTCTGGAACG
* * * *
40509203 TTGGCATCAATTTGTGATTTACGTGTAAGACCATGTCTGGGACA
1 TTGGCATCGATATATGATTT-CGTGTAAGACCATGTCTGGGATA
* * *
40509247 TTGGTATCG-TATATGATTTCGTGTAAGACCCTGTTTGGGATA
1 TTGGCATCGATATATGATTTCGTGTAAGACCATGTCTGGGATA
* * * * *
40509289 GTGGCATCGATATTTGATTACATGTAAGACCACGTCTGGGATA
1 TTGGCATCGATATATGATTTCGTGTAAGACCATGTCTGGGATA
40509332 TTGGCAT
1 TTGGCAT
40509339 TGTACGAGCT
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
42 27 0.36
43 41 0.55
44 7 0.09
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (43 bp):
TTGGCATCGATATATGATTTCGTGTAAGACCATGTCTGGGATA
Found at i:40511323 original size:47 final size:47
Alignment explanation
Indices: 40511216--40511326 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 47
40511206 CTTTTGTTAT
* * * * * *
40511216 GCCATGGTATAGGAATTCAAAGAGGAGTTACCTTTATTTGGCTATGG
1 GCCATGGTATAGGTACTCAAAGAGAAGTTACCTTGATTTAGCTACGG
* * *
40511263 GCCATGGTATAGGTACTCAAGGATAAGTTACCTTGATTTAGTTACGG
1 GCCATGGTATAGGTACTCAAAGAGAAGTTACCTTGATTTAGCTACGG
40511310 GCCATGGTATAGGTACT
1 GCCATGGTATAGGTACT
40511327 TATCAAGAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (47 bp):
GCCATGGTATAGGTACTCAAAGAGAAGTTACCTTGATTTAGCTACGG
Found at i:40511962 original size:12 final size:12
Alignment explanation
Indices: 40511945--40511983 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
40511935 TTGGTTAAAA
*
40511945 GAGAGATTAGAG
1 GAGAGATTTGAG
*
40511957 GAGAGATTTGGG
1 GAGAGATTTGAG
40511969 GAGAGATTTGAG
1 GAGAGATTTGAG
40511981 GAG
1 GAG
40511984 TGGATCAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.46, T:0.21
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:40519836 original size:12 final size:12
Alignment explanation
Indices: 40519819--40519857 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40519809 TTGGTTGATG
*
40519819 GAGAGATTAGAA
1 GAGAGATTTGAA
**
40519831 GAGAGATTTGGG
1 GAGAGATTTGAA
40519843 GAGAGATTTGAA
1 GAGAGATTTGAA
40519855 GAG
1 GAG
40519858 TGGATCAAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (12 bp):
GAGAGATTTGAA
Found at i:40529241 original size:68 final size:68
Alignment explanation
Indices: 40529095--40529250 Score: 158
Period size: 68 Copynumber: 2.2 Consensus size: 68
40529085 AGCCGATTTG
* * * *
40529095 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACATA
*
40529160 TATC
65 TATA
* *
40529164 TCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTAC-
40529226 ATATAGTA
62 ATATA-TA
40529234 TCTCGTAGC-CTTCTTGT
1 TCTCGTAGCTC-TCTTGT
40529251 ACACATGATG
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
67 1 0.01
68 34 0.46
69 7 0.09
70 6 0.08
71 26 0.35
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACATAT
ATA
Found at i:40533986 original size:24 final size:25
Alignment explanation
Indices: 40533938--40533986 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
40533928 TTAATTAAAG
40533938 TTTGGTCCATTAATTTTTTCGATTT
1 TTTGGTCCATTAATTTTTTCGATTT
40533963 TTTGGTCCATTAATTTTTTC-ATTT
1 TTTGGTCCATTAATTTTTTCGATTT
40533987 GGATAGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.16, C:0.12, G:0.10, T:0.61
Consensus pattern (25 bp):
TTTGGTCCATTAATTTTTTCGATTT
Found at i:40539794 original size:40 final size:39
Alignment explanation
Indices: 40539739--40539901 Score: 177
Period size: 40 Copynumber: 4.1 Consensus size: 39
40539729 TGAATGATAC
* * *
40539739 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTG-TTATAT
*
40539779 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGTTATAT
* * *
40539819 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGT-TACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGT--TATAT
* * *
40539859 CCGGGTTAAGACCTGAAGGCAATTGTGCTTGTGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGTTATAT
40539898 CCGG
1 CCGG
40539902 TTAAATCCAG
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
38 1 0.01
39 10 0.10
40 87 0.84
41 6 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGTTATAT
Found at i:40542948 original size:43 final size:43
Alignment explanation
Indices: 40542880--40543038 Score: 200
Period size: 43 Copynumber: 3.7 Consensus size: 43
40542870 ATAGCTCGTA
*
40542880 CAATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATAT
1 CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAT
* *
40542923 CAATGCC-ACTGTCCCAGACAG-GGTCTTACATGAAATCATATAT
1 CAATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCAAATAT
* * *
40542966 -AATGCCAATGTCCCAGACATGGTCTTACAAGTAAATCACAA-AT
1 CAATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCA-AATAT
40543009 CAATGCCAACGTCCCAGACGTGGTCTTACA
1 CAATGCCAACGTCCCAGACGTGGTCTTACA
40543039 GGATAACACA
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
42 27 0.27
43 43 0.43
44 29 0.29
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAT
Found at i:40543025 original size:86 final size:85
Alignment explanation
Indices: 40542881--40543038 Score: 223
Period size: 86 Copynumber: 1.8 Consensus size: 85
40542871 TAGCTCGTAC
* * *
40542881 AATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATATCAATGCCACTGTCCCAGACAG-G
1 AATGCCAACGTCCCAGACATGGTCTTACAAGTAATCAAATATCAATGCCACTGTCCCAGAC-GTG
40542945 GTCTTACATGAAATCATATAT
65 GTCTTACATGAAATCATATAT
*
40542966 AATGCCAATGTCCCAGACATGGTCTTACAAGTAAATCACAA-ATCAATGCCAAC-GTCCCAGACG
1 AATGCCAACGTCCCAGACATGGTCTTACAAGT-AATCA-AATATCAATGCC-ACTGTCCCAGACG
40543029 TGGTCTTACA
63 TGGTCTTACA
40543039 GGATAACACA
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
85 29 0.45
86 32 0.49
87 4 0.06
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (85 bp):
AATGCCAACGTCCCAGACATGGTCTTACAAGTAATCAAATATCAATGCCACTGTCCCAGACGTGG
TCTTACATGAAATCATATAT
Found at i:40557936 original size:23 final size:23
Alignment explanation
Indices: 40557909--40557955 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
40557899 ATATCGCTAC
40557909 ATAGCCATTATCAAATTGATGCT
1 ATAGCCATTATCAAATTGATGCT
40557932 ATAGCCATTATCAAATTGATGCT
1 ATAGCCATTATCAAATTGATGCT
40557955 A
1 A
40557956 AATGGTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (23 bp):
ATAGCCATTATCAAATTGATGCT
Found at i:40562409 original size:40 final size:40
Alignment explanation
Indices: 40562350--40562491 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
40562340 AAATTGAATG
* * *
40562350 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
40562390 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
40562430 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
40562470 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
40562492 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:40562515 original size:40 final size:39
Alignment explanation
Indices: 40562388--40562517 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
40562378 ATGCTGGAAA
* * *
40562388 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-AAT-GC
* *
40562429 -TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAATG-C
*
40562467 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGC
1 -TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA-ATGC
40562508 TTATATCCGG
1 TTATATCCGG
40562518 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 70 0.93
41 2 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAATGC
Found at i:40570426 original size:40 final size:40
Alignment explanation
Indices: 40570360--40570510 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
40570350 AAATTGAATG
* * *
40570360 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
40570399 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
40570439 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
40570479 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
40570511 ACATGTTATA
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
39 16 0.17
40 75 0.81
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:40572947 original size:31 final size:31
Alignment explanation
Indices: 40572904--40573049 Score: 249
Period size: 31 Copynumber: 4.7 Consensus size: 31
40572894 TTAGTCTTGA
40572904 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
40572934 CATATCACTGGGCCGAAACCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
40572965 CATATCACTGGGACGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
40572996 CATATCACTGGGTCAAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
40573027 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
40573050 ACTGTAAACG
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 5 0.05
31 103 0.95
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:40573120 original size:42 final size:42
Alignment explanation
Indices: 40573073--40573206 Score: 241
Period size: 42 Copynumber: 3.2 Consensus size: 42
40573063 TGGCCCTTAG
* *
40573073 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTTAATGAATGTATGCAA
*
40573115 GCCCATTTCAATATCACATGTAATGTTAATGAATGTATGCAT
1 GCCCATTTCAATATCACATGTAATGTTAATGAATGTATGCAA
40573157 GCCCATTTCAATATCACATGTAATGTTAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTTAATGAATGTATGCAA
40573199 GCCCATTT
1 GCCCATTT
40573207 GGGGAGACTA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTTAATGAATGTATGCAA
Found at i:40573382 original size:25 final size:25
Alignment explanation
Indices: 40573354--40573423 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
40573344 CTCTTTTAAT
40573354 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
40573379 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
40573404 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
40573424 ACACTTCCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 38 0.90
26 4 0.10
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:40574261 original size:27 final size:27
Alignment explanation
Indices: 40574231--40574295 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
40574221 GGGCATATTT
40574231 GTCATTTTACCATACAAGGG-TATTACA
1 GTCATTTTACCATACAAGGGCT-TTACA
* * * *
40574258 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACA
*
40574285 GTCTTTTTACC
1 GTCATTTTACC
40574296 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACA
Found at i:40574379 original size:27 final size:27
Alignment explanation
Indices: 40574349--40574456 Score: 89
Period size: 27 Copynumber: 4.0 Consensus size: 27
40574339 GTAAATCTAC
40574349 AAACCAAGGGTATTT-TAGTAATTTTGT
1 AAACCAAGGGTATTTCTAGTAATTTT-T
* *
40574376 AAACTAATGGTATTTCTA-TAATTTTT
1 AAACCAAGGGTATTTCTAGTAATTTTT
*
40574402 AAAAAGTCAAGGGTATTTCT-GTAATTTTTT
1 --AAA-CCAAGGGTATTTCTAGTAA-TTTTT
* * *
40574432 AAATCAGGGGTATTT-TGGTAATTTT
1 AAACCAAGGGTATTTCTAGTAATTTT
40574457 ACAAATTGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
26 6 0.09
27 35 0.51
28 8 0.12
29 14 0.21
30 5 0.07
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.44
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTAGTAATTTTT
Found at i:40574419 original size:29 final size:27
Alignment explanation
Indices: 40574353--40574446 Score: 93
Period size: 27 Copynumber: 3.4 Consensus size: 27
40574343 ATCTACAAAC
*
40574353 CAAGGGTATTT-TAGTAATTTTGTAAACT
1 CAAGGGTATTTCTA-TAATTTT-TAAAAT
*
40574381 -AATGGTATTTCTATAATTTTTAAAAAGT
1 CAAGGGTATTTCTATAATTTTT-AAAA-T
* *
40574409 CAAGGGTATTTCTGTAATTTTTTAAAT
1 CAAGGGTATTTCTATAATTTTTAAAAT
*
40574436 CAGGGGTATTT
1 CAAGGGTATTT
40574447 TGGTAATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
26 1 0.02
27 30 0.54
28 6 0.11
29 19 0.34
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (27 bp):
CAAGGGTATTTCTATAATTTTTAAAAT
Found at i:40574462 original size:27 final size:27
Alignment explanation
Indices: 40574398--40574535 Score: 111
Period size: 27 Copynumber: 5.1 Consensus size: 27
40574388 TTTCTATAAT
* *
40574398 TTTTAAAAAGTCAAGGGTATTTCT-GTAA
1 TTTTACAAA-TCAGGGGTATTT-TGGTAA
**
40574426 TTTTTTAAATCAGGGGTATTTTGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
* * *
40574453 TTTTACAAAT-TGAAGGTATTTCGGTAA
1 TTTTACAAATCAG-GGGTATTTTGGTAA
* * ** *
40574480 TTTCACAAACCAGTAGTATTTCGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
40574507 TTTTACAAA-CTAGGGGTATTTTGGTAA
1 TTTTACAAATC-AGGGGTATTTTGGTAA
40574534 TT
1 TT
40574536 CTATCCTACA
Statistics
Matches: 89, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
26 3 0.03
27 78 0.88
28 8 0.09
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (27 bp):
TTTTACAAATCAGGGGTATTTTGGTAA
Found at i:40574603 original size:27 final size:27
Alignment explanation
Indices: 40574571--40574683 Score: 147
Period size: 27 Copynumber: 4.2 Consensus size: 27
40574561 TTTCACAATT
40574571 GAGGGTAAAATGGTAATTTTGTAAA-C
1 GAGGGTAAAATGGTAATTTTGTAAATC
* *
40574597 TGAGGGTAAAATAGTAATTTTGTAAGTC
1 -GAGGGTAAAATGGTAATTTTGTAAATC
* *
40574625 GAGGGTAAAACGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTTTGTAAATC
* **
40574652 GAGGGTAAAATGGTAATTCTACAAATC
1 GAGGGTAAAATGGTAATTTTGTAAATC
40574679 GAGGG
1 GAGGG
40574684 CATTTCAATA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
27 75 0.99
28 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.28
Consensus pattern (27 bp):
GAGGGTAAAATGGTAATTTTGTAAATC
Found at i:40576691 original size:15 final size:15
Alignment explanation
Indices: 40576671--40576700 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40576661 CAACACTTGT
40576671 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
40576686 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
40576701 AATACATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:40580360 original size:40 final size:41
Alignment explanation
Indices: 40580313--40580556 Score: 340
Period size: 40 Copynumber: 6.1 Consensus size: 41
40580303 CGGGCTTTAA
* *
40580313 CCGGATA-TAGCCACTCGCTCAAATGCCTTCGGGACTTAGC
1 CCGGATATTAGTCACTCGCACAAATGCCTTCGGGACTTAGC
*
40580353 CCGGATA-TAGT-AGTTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATTAGTCA-CTCGCACAAATGCCTTCGGGACTTAGC
*
40580393 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATTAGTCACTCGCACAAATGCCTTCGGGACTTAGC
* * *
40580433 CCGGA-ATTAGTAACTCGCACAAATGCCTTCTGAACTTAGC
1 CCGGATATTAGTCACTCGCACAAATGCCTTCGGGACTTAGC
* *
40580473 CAGG-TATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATTAGTCACTCGCACAAATGCCTTCGGGACTTAGC
*
40580513 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATTAGTCACTCGCACAAATGCCTTCGGGACTTAGC
40580553 CCGG
1 CCGG
40580557 TTATCATCCG
Statistics
Matches: 187, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
39 2 0.01
40 184 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (41 bp):
CCGGATATTAGTCACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40584839 original size:21 final size:21
Alignment explanation
Indices: 40584813--40584852 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40584803 ATAAAAATCC
*
40584813 CACACGGGCGTGTGAGACCCT
1 CACACGGGCGTGTCAGACCCT
*
40584834 CACACGGTCGTGTCAGACC
1 CACACGGGCGTGTCAGACC
40584853 TGTACCTTAT
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:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (21 bp):
CACACGGGCGTGTCAGACCCT
Found at i:40584955 original size:22 final size:21
Alignment explanation
Indices: 40584893--40584960 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
40584883 AGTTACACAG
40584893 CCTGTCCACACGGGCGTGTGCC
1 CCTGT-CACACGGGCGTGTGCC
* ** *
40584915 TCTGTCACACGACCATGTGCTAC
1 CCTGTCACACGGGCGTGTGC--C
*
40584938 CCT-TCACACGGGCGTGTGGC
1 CCTGTCACACGGGCGTGTGCC
40584958 CCT
1 CCT
40584961 ATCTCGCCAA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
20 4 0.11
21 12 0.34
22 16 0.46
23 3 0.09
ACGTcount: A:0.13, C:0.38, G:0.26, T:0.22
Consensus pattern (21 bp):
CCTGTCACACGGGCGTGTGCC
Found at i:40585937 original size:25 final size:26
Alignment explanation
Indices: 40585886--40585946 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
40585876 CATATTGATA
* *
40585886 TTCG-ACTGAAATGTCTGATTGATTG
1 TTCGAACTGAAATGTCTGATTAACTG
*
40585911 TTC-AACTGAAATGTTTGATTAACTG
1 TTCGAACTGAAATGTCTGATTAACTG
40585936 TTCGAA-TGAAA
1 TTCGAACTGAAA
40585947 GGCACTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (26 bp):
TTCGAACTGAAATGTCTGATTAACTG
Found at i:40592737 original size:46 final size:45
Alignment explanation
Indices: 40592685--40592888 Score: 197
Period size: 46 Copynumber: 4.5 Consensus size: 45
40592675 GTCGATGCCG
* * *
40592685 TGTCCCAGACAGGTCTTACACTGA-CACATGTAACCGT-GCTGACGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATCT---CGTAGCCGACGCA
40592731 TGTCCCAGACATGTCTTACACT-AGCACATCTCGTAGCCGACGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATCTCGTAGCCGACGCA
* *
40592775 TGTCCCAGACATGTCTGACACTG-GCTATCATCTCG-AGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGAGC-A-CATCTCGTA-GCCGACGCA
* * * *
40592821 TGTCCCAGACATGTCTTACACTG-GCTC-TCATACTGTGGCTGATGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATC-T-C-GTAGCCGACGCA
40592867 TGTCCCAGACATGTCTTACACT
1 TGTCCCAGACATGTCTTACACT
40592889 AGCCCTCGTC
Statistics
Matches: 139, Mismatches: 9, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.04
44 33 0.24
45 4 0.03
46 97 0.70
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTGAGCACATCTCGTAGCCGACGCA
Found at i:40592908 original size:92 final size:91
Alignment explanation
Indices: 40592728--40592944 Score: 249
Period size: 92 Copynumber: 2.4 Consensus size: 91
40592718 CCGTGCTGAC
*
40592728 GCATGTCCCAGACATGTCTTACACTAG-CACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
1 GCATGTCCCAGACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
* * *
40592792 ACACTGGCTATCATCTCGAGGCCGAT
66 ACACTAGCCATCATCTCAAGGCCGAT
* * * *
40592818 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACT-GTGGCTGATGCATGTCCCAGACATGTC
1 GCATGTCCCAGACATGTCTTACACTGGC-CACAT-CTCGTAGCCGACGCATGTCCCAGACATGTC
* * * *
40592882 TTACACTAGCCCTCGTCTCAATGCCGAT
64 TGACACTAGCCATCATCTCAAGGCCGAT
* *
40592910 GCCATGTCTCATACATGGTCTTACACTGGCACACA
1 G-CATGTCCCAGACAT-GTCTTACACTGGC-CACA
40592945 AATCTCATGT
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
90 26 0.25
92 50 0.47
93 14 0.13
94 16 0.15
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.26
Consensus pattern (91 bp):
GCATGTCCCAGACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
ACACTAGCCATCATCTCAAGGCCGAT
Found at i:40592911 original size:46 final size:44
Alignment explanation
Indices: 40592728--40592936 Score: 190
Period size: 46 Copynumber: 4.6 Consensus size: 44
40592718 CCGTGCTGAC
*
40592728 GCATGTCCCAGACATGTCTTACACTAGCACATC-TCGTA-GCCGAC
1 GCATGTCCCAGACATGTCTTACACTAGC-CATCATC-TATGCCGAT
* * * *
40592772 GCATGTCCCAGACATGTCTGACACTGGCTATCATCTCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATCATCT--ATGCCGAT
* * *
40592818 GCATGTCCCAGACATGTCTTACACTGGCTC-TCATACTGTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTAGC-CATCAT-CTAT-GCCGAT
* *
40592864 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATCATCT--ATGCCGAT
* *
40592910 GCCATGTCTCATACATGGTCTTACACT
1 G-CATGTCCCAGACAT-GTCTTACACT
40592937 GGCACACAAA
Statistics
Matches: 138, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
43 4 0.03
44 28 0.20
45 4 0.03
46 77 0.56
47 15 0.11
48 10 0.07
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.27
Consensus pattern (44 bp):
GCATGTCCCAGACATGTCTTACACTAGCCATCATCTATGCCGAT
Found at i:40598721 original size:13 final size:13
Alignment explanation
Indices: 40598703--40598727 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40598693 GGTCATATAA
40598703 AAATTTTGTTAAG
1 AAATTTTGTTAAG
40598716 AAATTTTGTTAA
1 AAATTTTGTTAA
40598728 TTGCATGCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
AAATTTTGTTAAG
Found at i:40599775 original size:40 final size:40
Alignment explanation
Indices: 40599714--40599901 Score: 182
Period size: 40 Copynumber: 4.7 Consensus size: 40
40599704 GATAATTATA
40599714 CCTGAATTGCACATACATGCCCCTGTTGTACTTCAG-TACC
1 CCTGAATTGCACATACATGCCCCTGTTGTACTT-AGATACC
* * * * * *
40599754 CCTAAATTGCACATACGTGCCCCTATTGTACTTTGTTATC
1 CCTGAATTGCACATACATGCCCCTGTTGTACTTAGATACC
* * * *
40599794 CCTGAATTGCATATACATGCCCCTATTTTACTTTGATACC
1 CCTGAATTGCACATACATGCCCCTGTTGTACTTAGATACC
* * * *
40599834 CTTGAATTGCACATACATGTCTCTGTTTGTACTTCAG-TAGC
1 CCTGAATTGCACATACATGCCCCTG-TTGTACTT-AGATACC
* * *
40599875 CCTGAATAGCACTTACGTGCCCCTGTT
1 CCTGAATTGCACATACATGCCCCTGTT
40599902 CACACTCCGG
Statistics
Matches: 120, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
39 1 0.01
40 89 0.74
41 29 0.24
42 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.35
Consensus pattern (40 bp):
CCTGAATTGCACATACATGCCCCTGTTGTACTTAGATACC
Found at i:40608256 original size:27 final size:27
Alignment explanation
Indices: 40608222--40608338 Score: 123
Period size: 27 Copynumber: 4.4 Consensus size: 27
40608212 CCATAAAATA
*
40608222 GGTAAAAT-AACAGTAATGCCCCTATAG
1 GGTAAAATGAAC-GTAATGCCCCTGTAG
* *
40608249 GGTAAAATGATCGTAATG-CCTTGTAG
1 GGTAAAATGAACGTAATGCCCCTGTAG
*
40608275 GGTAAAATGATCGTAATGCCCCTGTAG
1 GGTAAAATGAACGTAATGCCCCTGTAG
* * *
40608302 GGTAAAATG-ACTGTAATACCTCTGTAT
1 GGTAAAATGAAC-GTAATGCCCCTGTAG
*
40608329 TGTAAAATGA
1 GGTAAAATGA
40608339 CGATTATGTC
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
26 25 0.32
27 50 0.65
28 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (27 bp):
GGTAAAATGAACGTAATGCCCCTGTAG
Found at i:40608303 original size:53 final size:54
Alignment explanation
Indices: 40608234--40608338 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 54
40608224 TAAAATAACA
*
40608234 GTAATGCCCCTATAGGGTAAAATGA-TCGTAATGCCT-TGTAGGGTAAAATGATC
1 GTAATGCCCCTATAGGGTAAAATGACT-GTAATACCTCTGTAGGGTAAAATGATC
* **
40608287 GTAATGCCCCTGTAGGGTAAAATGACTGTAATACCTCTGTATTGTAAAATGA
1 GTAATGCCCCTATAGGGTAAAATGACTGTAATACCTCTGTAGGGTAAAATGA
40608339 CGATTATGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
53 32 0.70
54 14 0.30
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (54 bp):
GTAATGCCCCTATAGGGTAAAATGACTGTAATACCTCTGTAGGGTAAAATGATC
Found at i:40608339 original size:27 final size:27
Alignment explanation
Indices: 40608234--40608338 Score: 133
Period size: 27 Copynumber: 3.9 Consensus size: 27
40608224 TAAAATAACA
* *
40608234 GTAATGCCCCTATAGGGTAAAATGATC
1 GTAATGCCTCTGTAGGGTAAAATGATC
40608261 GTAATGCCT-TGTAGGGTAAAATGATC
1 GTAATGCCTCTGTAGGGTAAAATGATC
*
40608287 GTAATGCCCCTGTAGGGTAAAATGA-C
1 GTAATGCCTCTGTAGGGTAAAATGATC
* **
40608313 TGTAATACCTCTGTATTGTAAAATGA
1 -GTAATGCCTCTGTAGGGTAAAATGA
40608339 CGATTATGTC
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 25 0.36
27 44 0.64
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (27 bp):
GTAATGCCTCTGTAGGGTAAAATGATC
Found at i:40618975 original size:40 final size:38
Alignment explanation
Indices: 40618935--40619143 Score: 175
Period size: 40 Copynumber: 5.2 Consensus size: 38
40618925 ATTATTCCTA
* * *
40618935 AATTGCACATACGTTCCCTTATTGTACTCTAGTACCCCTA
1 AATTGCACATACGTGCCC-TGTTGTACT-TAGTACCCCTG
40618975 AATTGCACATACGTGGCCCTGTTGTACTTCAGTACCCCTG
1 AATTGCACATACGT-GCCCTGTTGTACTT-AGTACCCCTG
* * * * *
40619015 AATTGCTCATATGTGCCACTGTTGTACTTTGGTATCCTTG
1 AATTGCACATACGTGCC-CTGTTGTAC-TTAGTACCCCTG
* * * *
40619055 AATTGCCCATACCTACCCTCGTTGTACTTCGGTACCCCTG
1 AATTGCACATACGTGCCCT-GTTGTACTT-AGTACCCCTG
* * *
40619095 AATTGTACATACGTGCCCCTATTTGTACTTTAGTACCCATG
1 AATTGCACATACGTG-CCCT-GTTGTAC-TTAGTACCCCTG
*
40619136 AATAGCAC
1 AATTGCAC
40619144 TTATGTAGCC
Statistics
Matches: 137, Mismatches: 24, Indels: 15
0.78 0.14 0.09
Matches are distributed among these distances:
39 8 0.06
40 98 0.72
41 29 0.21
42 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (38 bp):
AATTGCACATACGTGCCCTGTTGTACTTAGTACCCCTG
Found at i:40623850 original size:18 final size:17
Alignment explanation
Indices: 40623827--40623860 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
40623817 CTTAGGCCAT
40623827 AATGGGCCAAATGGGCCG
1 AATGGGCC-AATGGGCCG
40623845 AATGGGCCAATGGGCC
1 AATGGGCCAATGGGCC
40623861 CGTGGGCCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.24, G:0.38, T:0.12
Consensus pattern (17 bp):
AATGGGCCAATGGGCCG
Found at i:40623858 original size:8 final size:9
Alignment explanation
Indices: 40623821--40623860 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
40623811 CATGGGCTTA
40623821 GGCCATAATG
1 GGCCA-AATG
40623831 GGCCAAATG
1 GGCCAAATG
*
40623840 GGCCGAATG
1 GGCCAAATG
40623849 GGCC-AATG
1 GGCCAAATG
40623857 GGCC
1 GGCC
40623861 CGTGGGCCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.28
9 16 0.55
10 5 0.17
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (9 bp):
GGCCAAATG
Found at i:40632349 original size:30 final size:30
Alignment explanation
Indices: 40632313--40632370 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40632303 TATAATTTCA
* *
40632313 TTTTATTTTTATTTTAATTTGGTCCTAACC
1 TTTTATTTTTATTTCAATTTAGTCCTAACC
*
40632343 TTTTATTTTTGTTTCAATTTAGTCCTAA
1 TTTTATTTTTATTTCAATTTAGTCCTAA
40632371 TGGCTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (30 bp):
TTTTATTTTTATTTCAATTTAGTCCTAACC
Found at i:40632546 original size:29 final size:28
Alignment explanation
Indices: 40632507--40632576 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
40632497 TAAAGTTTTA
* *
40632507 TTTTTATTTAAATTTTTTTATATATAAT
1 TTTTTATTTAAAATGTTTTATATATAAT
*
40632535 TTATTTATTTAAAATGTTTTATATATCAT
1 TT-TTTATTTAAAATGTTTTATATATAAT
40632564 TTTTTATTATAAA
1 TTTTTATT-TAAA
40632577 CATTATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.22
29 29 0.78
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
TTTTTATTTAAAATGTTTTATATATAAT
Found at i:40632568 original size:14 final size:14
Alignment explanation
Indices: 40632507--40632575 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
40632497 TAAAGTTTTA
*
40632507 TTTTTATTTA-AATT
1 TTTTTATATATAA-T
40632521 TTTTTATATATAAT
1 TTTTTATATATAAT
* *
40632535 TTATTTATTTAAAAT
1 TT-TTTATATATAAT
* *
40632550 GTTTTATATATCAT
1 TTTTTATATATAAT
40632564 TTTTTAT-TATAA
1 TTTTTATATATAA
40632576 ACATTATTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
13 4 0.09
14 27 0.61
15 13 0.30
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (14 bp):
TTTTTATATATAAT
Found at i:40632595 original size:19 final size:20
Alignment explanation
Indices: 40632573--40632612 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
40632563 TTTTTTATTA
*
40632573 TAAACATTATT-TATACATT
1 TAAAAATTATTATATACATT
*
40632592 TAAAAATTATTATATATATT
1 TAAAAATTATTATATACATT
40632612 T
1 T
40632613 TTATTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAAATTATTATATACATT
Found at i:40632612 original size:20 final size:19
Alignment explanation
Indices: 40632568--40632612 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
40632558 TATCATTTTT
*
40632568 TATTATAAACATTATTTATA
1 TATT-TAAAAATTATTTATA
*
40632588 CATTTAAAAATTATTATATA
1 TATTTAAAAATTATT-TATA
40632608 TATTT
1 TATTT
40632613 TTATTTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTAAAAATTATTTATA
Found at i:40632656 original size:12 final size:12
Alignment explanation
Indices: 40632636--40632683 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
40632626 ATTTGTTATA
40632636 TTATT-TATATT
1 TTATTATATATT
40632647 TTATTATATATT
1 TTATTATATATT
40632659 TTATTTATATATT
1 TTA-TTATATATT
*
40632672 TTGTTATATATT
1 TTATTATATATT
40632684 AAATCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 5 0.15
12 18 0.53
13 11 0.32
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTATTATATATT
Found at i:40632679 original size:35 final size:36
Alignment explanation
Indices: 40632634--40632707 Score: 59
Period size: 34 Copynumber: 2.2 Consensus size: 36
40632624 TTATTTGTTA
* * *
40632634 TATTATTTATATTTTATTATATATTTTA-TTTATA-
1 TATTATGTATATATTATTATATATTTTATTATATAT
* *
40632668 TATTTTGT-TATA-TATTAAATCATTTTATTATATA-
1 TATTATGTATATATTATTATAT-ATTTTATTATATAT
40632702 TATTAT
1 TATTAT
40632708 TCATTTCTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
32 7 0.22
33 9 0.28
34 16 0.50
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (36 bp):
TATTATGTATATATTATTATATATTTTATTATATAT
Found at i:40632708 original size:25 final size:23
Alignment explanation
Indices: 40632598--40632767 Score: 88
Period size: 23 Copynumber: 7.1 Consensus size: 23
40632588 CATTTAAAAA
40632598 TTATTATATATATT-TTTAT-TT
1 TTATTATATATATTATTTATATT
*
40632619 ATGTATTATTTGTTATATTATTTATATT
1 -T-TATTA--T-ATATATTATTTATATT
*
40632647 TTATTATATATTTTATTTATATAT
1 TTATTATATATATTATTTATAT-T
*
40632671 TT-TGT-TATATATTA--AATCATT
1 TTAT-TATATATATTATTTAT-ATT
*
40632692 TTATTATATATATTATTCAT-TT
1 TTATTATATATATTATTTATATT
*
40632714 CTTATTTTATTATATATTATGTTATCTT
1 -TTA--TTA-TATATATTAT-TTATATT
*
40632742 ATTATT-TAT-TATTATATATAATT
1 -TTATTATATATATTATTTAT-ATT
40632765 TTA
1 TTA
40632768 AAATTTACAA
Statistics
Matches: 118, Mismatches: 10, Indels: 40
0.70 0.06 0.24
Matches are distributed among these distances:
21 6 0.05
22 21 0.18
23 38 0.32
24 10 0.08
25 4 0.03
26 23 0.19
27 9 0.08
28 7 0.06
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TTATTATATATATTATTTATATT
Found at i:40632743 original size:20 final size:20
Alignment explanation
Indices: 40632715--40632753 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40632705 TATTCATTTC
*
40632715 TTATTTTATTATATATTATG
1 TTATCTTATTATATATTATG
*
40632735 TTATCTTATTATTTATTAT
1 TTATCTTATTATATATTAT
40632754 TATATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTATCTTATTATATATTATG
Found at i:40632746 original size:28 final size:26
Alignment explanation
Indices: 40632634--40632760 Score: 101
Period size: 25 Copynumber: 5.0 Consensus size: 26
40632624 TTATTTGTTA
40632634 TATT-ATTTA-TATTTTATTATATAT
1 TATTCATTTATTATTTTATTATATAT
*
40632658 T-TT-ATTTATATATTTTGTTATATAT
1 TATTCATTTAT-TATTTTATTATATAT
*
40632683 TAAATCA-TT-TTA--TTA-TATATAT
1 T-ATTCATTTATTATTTTATTATATAT
*
40632705 TATTCATTTCTTATTTTATTATATAT
1 TATTCATTTATTATTTTATTATATAT
*
40632731 TATGTTATCTTATTATTTATTATTATATAT
1 TAT-TCAT-TTATTA-TT-TTATTATATAT
40632761 AATTTTAAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
21 4 0.05
22 10 0.12
23 12 0.14
24 1 0.01
25 20 0.24
26 11 0.13
27 6 0.07
28 6 0.07
29 2 0.02
30 11 0.13
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (26 bp):
TATTCATTTATTATTTTATTATATAT
Found at i:40641877 original size:41 final size:41
Alignment explanation
Indices: 40641832--40641949 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
40641822 TGAAAGATAA
40641832 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
40641873 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
40641903 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
40641944 ATGTAG
1 ATGTAG
40641950 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:40641888 original size:71 final size:71
Alignment explanation
Indices: 40641800--40641963 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
40641790 GAGATGTATC
40641800 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
40641865 AGGACA
66 AGGACA
40641871 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
40641936 AGGACA
66 AGGACA
40641942 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
40641964 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:40649061 original size:40 final size:40
Alignment explanation
Indices: 40648998--40649170 Score: 226
Period size: 40 Copynumber: 4.4 Consensus size: 40
40648988 ATGCTAATGA
40648998 TTATATCC-GGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
40649037 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * *
40649077 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
** * * ** *
40649117 CCAAATCCGGGTTAAGACCCGAAGGCAATT-GTGCTTGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG
40649157 TTATATCC-GGCTAA
1 TTATATCCGGGCTAA
40649171 ATTCCGAAGA
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 13 0.11
40 101 0.86
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:40649125 original size:80 final size:79
Alignment explanation
Indices: 40648965--40649170 Score: 236
Period size: 80 Copynumber: 2.6 Consensus size: 79
40648955 TGAATGATAC
* * * * * *
40648965 CCGGGCTAAG-TCCGAAGGCATTTATGCTAATGATTATATCCGGCTAAGACCCGAAGGCATTCGT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGGTTATATCCGGCTAAGACCCGAAGGCATTCGT
* *** *
40649029 GCGAGTTGTTATAT
66 GCAAGTTACCAAAT
* *
40649043 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGGTTATATCC-GGCTAAGACCCGAAGGCATTC
40649107 GTGCAAGTTACCAAAT
64 GTGCAAGTTACCAAAT
* **
40649123 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCCGGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGGTTATATCCGGCTAA
40649171 ATTCCGAAGA
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
78 12 0.11
79 27 0.25
80 65 0.61
81 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGGTTATATCCGGCTAAGACCCGAAGGCATTCGT
GCAAGTTACCAAAT
Found at i:40657137 original size:40 final size:39
Alignment explanation
Indices: 40657077--40657262 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 39
40657067 TGAATGATAC
* * *
40657077 CCGGGCTAAG-TCCGAAGGCATTTATGCTAATGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAATG-TTATAT
* *
40657116 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGTTATAT
* *
40657156 CCGGGCTAAGA-CCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGTTATAT
*
40657195 CCGGGCTAAGACCCGAAGGCATTTGTGC-AA-GTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAATGTT---ATAT
* *
40657235 CCGGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGCTAAGACCCGAAGGCATTTGTGC
40657263 TTGTGGTTAT
Statistics
Matches: 131, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
37 3 0.02
39 50 0.38
40 76 0.58
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAATGTTATAT
Found at i:40657277 original size:40 final size:40
Alignment explanation
Indices: 40657110--40657282 Score: 226
Period size: 40 Copynumber: 4.4 Consensus size: 40
40657100 ATGCTAATGA
40657110 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
40657150 TTATATCCGGGCTAAGA-CCGAAGGCATTCGTGCGAGTTG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * *
40657189 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
** * * ** *
40657229 CCAAATCCGGGTTAAGACCCGAAGGCAATT-GTGCTTGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG
40657269 TTATATCC-GGCTAA
1 TTATATCCGGGCTAA
40657283 ATTCCGAAGA
Statistics
Matches: 116, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
39 44 0.38
40 69 0.59
41 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:40657291 original size:79 final size:79
Alignment explanation
Indices: 40657077--40657282 Score: 236
Period size: 79 Copynumber: 2.6 Consensus size: 79
40657067 TGAATGATAC
* ** * * *
40657077 CCGGGCTAAGTCCGAAGGCATTTATGCTAATGATTATATCCGGGCTAAGACCCGAAGGCATTCGT
1 CCGGGCTAAGACCGAAGGCATTCGTGCGAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCGT
* *** *
40657142 GCGAGTTGTTATAT
66 GCAAGTTACCAAAT
* *
40657156 CCGGGCTAAGACCGAAGGCATTCGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTGT
1 CCGGGCTAAGACCGAAGGCATTCGTGCGAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCGT
40657221 GCAAGTTACCAAAT
66 GCAAGTTACCAAAT
* **
40657235 CCGGGTTAAGACCCGAAGGCAATT-GTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGA-CCGAAGGC-ATTCGTGCGAGTGGTTATATCCGGGCTAA
40657283 ATTCCGAAGA
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
79 82 0.76
80 23 0.21
81 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGACCGAAGGCATTCGTGCGAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTCGT
GCAAGTTACCAAAT
Found at i:40663645 original size:40 final size:40
Alignment explanation
Indices: 40663566--40663787 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
40663556 CCAAACCAAG
* * * * *
40663566 TGCCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAA
40663605 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
40663645 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
* * *
40663685 TGCCTTCGGGATTTAGCCCGGATATAGTAGCTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
* * *
40663725 TGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAA
* *
40663764 TGCCTTCGGGACATAGCCCTGTTA
1 TGCCTTCGGGACTTAGCCCGGTTA
40663788 CCATCCAAAT
Statistics
Matches: 162, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
38 1 0.01
39 47 0.29
40 113 0.70
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
Found at i:40663781 original size:119 final size:119
Alignment explanation
Indices: 40663566--40663787 Score: 324
Period size: 119 Copynumber: 1.9 Consensus size: 119
40663556 CCAAACCAAG
* * *
40663566 TGCCTTCGGAATTTAGCCGGATATAGCTACTTGCTCAAATGCCTTCGGGACTTAGCCCGGTTATA
1 TGCCTTCGGAATTTAGCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
* *
40663631 GTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
66 GTAACTAGCACAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAA
*
40663685 TGCCTTCGGGATTTAGCCCGGATATAG-TAGCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA-A
1 TGCCTTCGGAATTTAG-CCGGATATAGCTA-CTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
* *
40663747 TTAGTCACTAGCACAAATGCCTTCGGGACATAGCCCTGTTA
64 -TAGTAACTAGCACAAATGCCTTCGGGACATAGCCCGGTTA
40663788 CCATCCAAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
118 1 0.01
119 63 0.68
120 28 0.30
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (119 bp):
TGCCTTCGGAATTTAGCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
GTAACTAGCACAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAA
Found at i:40668244 original size:90 final size:90
Alignment explanation
Indices: 40668143--40668726 Score: 979
Period size: 90 Copynumber: 6.5 Consensus size: 90
40668133 CGGGGAACAA
* * * * * *
40668143 ATCGAAGATGACAGATTTGGCATCTCTATATTAGACAGGGACCAGATCGAAGATAGAAGATTTGA
1 ATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGA
*
40668208 CATTCGTGTGTTTACATCGAAGCAA
66 CATTCGTGTGTTTACATCGAAGCAG
* *
40668233 ATCGAAAATGACAGGTTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGA
1 ATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGA
40668298 CATTCGTGTGTTTACATCGAAGCAG
66 CATTCGTGTGTTTACATCGAAGCAG
* *
40668323 ATCGAAGATGATAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGAACTGA
1 ATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGA
* *
40668388 CATTCATGTGTTTATATCGAAGCAG
66 CATTCGTGTGTTTACATCGAAGCAG
* *
40668413 ATCAAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGA
1 ATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGA
40668478 CATTCGTGTGTTTACATCGAAGCAG
66 CATTCGTGTGTTTACATCGAAGCAG
* *
40668503 ATCGAAGATGACAGATTTGGCGTATCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGA
1 ATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGA
40668568 CATTCGTGTGTTTACATCGAAGCAG
66 CATTCGTGTGTTTACATCGAAGCAG
*
40668593 ATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCCAAGATAGCAGATCTGA
1 ATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGA
* *
40668658 CATTCGTGTGTTTACATTGAAGTAG
66 CATTCGTGTGTTTACATCGAAGCAG
*
40668683 ATCGAAGATGACATATTTGGCGTCTCTGTATTAGACGGGGAGCA
1 ATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCA
40668727 TGTGACAGCC
Statistics
Matches: 465, Mismatches: 29, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 465 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (90 bp):
ATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGA
CATTCGTGTGTTTACATCGAAGCAG
Found at i:40668685 original size:45 final size:45
Alignment explanation
Indices: 40668185--40668691 Score: 289
Period size: 45 Copynumber: 11.3 Consensus size: 45
40668175 AGACAGGGAC
* *
40668185 CAGATCGAAGATAGAAGATTTGACATTCGTGTGTTTACATCGAAG
1 CAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG
* * * * * * * * *
40668230 CAAATCGAAAAT-GACAGGTTTGGCGTCTC-TGT-ATTAGA-CGGGGAG
1 CAGATCGAAGATAG-CAGATCTGACAT-TCGTGTGTTTACATC--GAAG
40668275 CAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG
1 CAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG
* * * * * * *
40668320 CAGATCGAAGAT-GATAGATTTGGCGTCTC-TGT-ATTAGA-CGGGGAG
1 CAGATCGAAGATAG-CAGATCTGACAT-TCGTGTGTTTACATC--GAAG
* * *
40668365 CAGATCGAAGATAGCAGAACTGACATTCATGTGTTTATATCGAAG
1 CAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG
* * * * * * *
40668410 CAGATCAAAGAT-GACAGATTTGGCGTCTC-TGT-ATTAGA-CGGGGAG
1 CAGATCGAAGATAG-CAGATCTGACAT-TCGTGTGTTTACATC--GAAG
*
40668455 CAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
1 CAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG
* * * * * *
40668500 CAGATCGAAGAT-GACAGATTTGGCGTATC-TGT-ATTAGA-CGGGGAG
1 CAGATCGAAGATAG-CAGATCTGACAT-TCGTGTGTTTACATC--GAAG
*
40668545 CAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
1 CAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG
* * * * * *
40668590 CAGATCGAAGAT-GACAGATTTGGCGTCTC-TGT-ATTAGA-CGGGGAG
1 CAGATCGAAGATAG-CAGATCTGACAT-TCGTGTGTTTACATC--GAAG
* *
40668635 CAGATCCAAGATAGCAGATCTGACATTCGTGTGTTTACATTGAAG
1 CAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG
*
40668680 TAGATCGAAGAT
1 CAGATCGAAGAT
40668692 GACATATTTG
Statistics
Matches: 342, Mismatches: 80, Indels: 80
0.68 0.16 0.16
Matches are distributed among these distances:
43 5 0.01
44 35 0.10
45 263 0.77
46 35 0.10
47 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.27
Consensus pattern (45 bp):
CAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG
Found at i:40670573 original size:40 final size:40
Alignment explanation
Indices: 40670410--40670601 Score: 151
Period size: 40 Copynumber: 4.8 Consensus size: 40
40670400 CGAATGATGT
* * * *
40670410 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC
* * * * *
40670450 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGAT-AATAAAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TCACTAAAC
* * * *
40670490 CTGGGCTAAG-CCCAAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
* *
40670529 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC
** *
40670569 CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTC
40670602 GTTATATCCG
Statistics
Matches: 120, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
38 1 0.01
39 29 0.24
40 80 0.67
41 10 0.08
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
Found at i:40670575 original size:79 final size:81
Alignment explanation
Indices: 40670409--40670593 Score: 202
Period size: 79 Copynumber: 2.3 Consensus size: 81
40670399 TCGAATGATG
* * *
40670409 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
40670473 CGTGCGAGATAATAAA
66 CGTGCGAGATAATAAA
* * * **
40670489 TCTGGGCTAAG-CCCAAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
40670551 TCGTGCGAG-TCACTATAA
65 TCGTGCGAGAT-AATA-AA
**
40670569 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40670594 AGCGAGTCGT
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
78 2 0.02
79 53 0.61
80 32 0.37
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATAATAAA
Found at i:40671895 original size:9 final size:9
Alignment explanation
Indices: 40671881--40671913 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
40671871 AGTCTGGAAA
40671881 ATTTTTTTT
1 ATTTTTTTT
40671890 ATTTTTTTT
1 ATTTTTTTT
40671899 ATTTTTTTT
1 ATTTTTTTT
40671908 -TTTTTT
1 ATTTTTT
40671914 AGGACTGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:40673387 original size:30 final size:30
Alignment explanation
Indices: 40673330--40673387 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40673320 TATAATTTCA
* *
40673330 TTTTATTTTTATTTTAATTTGGCCCTAACC
1 TTTTATTTTTATTTCAATTTAGCCCTAACC
* *
40673360 TTTTATTTTTGTTTCAATTTAGTCCTAA
1 TTTTATTTTTATTTCAATTTAGCCCTAA
40673388 TGGCTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (30 bp):
TTTTATTTTTATTTCAATTTAGCCCTAACC
Found at i:40673695 original size:12 final size:12
Alignment explanation
Indices: 40673675--40673709 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
40673665 ATTTGTTATA
40673675 TTATT-TATATT
1 TTATTATATATT
40673686 TTATTATATATT
1 TTATTATATATT
40673698 TTATTATATATT
1 TTATTATATATT
40673710 AAATCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTATATATT
Found at i:40673744 original size:20 final size:22
Alignment explanation
Indices: 40673687--40673732 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40673677 ATTTATATTT
*
40673687 TATTATAT-ATTTTA-T-TATA
1 TATTAAATCATTTTATTATATA
40673706 TATTAAATCATTTTATTATATA
1 TATTAAATCATTTTATTATATA
40673728 TATTA
1 TATTA
40673733 TTCATTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 6 0.26
21 1 0.04
22 9 0.39
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTAAATCATTTTATTATATA
Found at i:40673769 original size:20 final size:20
Alignment explanation
Indices: 40673741--40673779 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40673731 TATTCATTTC
*
40673741 TTATTTTATTATATATTATG
1 TTATCTTATTATATATTATG
*
40673761 TTATCTTATTATTTATTAT
1 TTATCTTATTATATATTAT
40673780 TATATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTATCTTATTATATATTATG
Found at i:40673822 original size:13 final size:13
Alignment explanation
Indices: 40673804--40673845 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
40673794 AAATTTACAA
*
40673804 ATTATTATTAAAT
1 ATTATTATTATAT
*
40673817 ATTATTTTTATAT
1 ATTATTATTATAT
*
40673830 ATCATTATTATAT
1 ATTATTATTATAT
40673843 ATT
1 ATT
40673846 TAGTATGACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTATTATTATAT
Found at i:40677344 original size:25 final size:24
Alignment explanation
Indices: 40677283--40677349 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
40677273 ACGCGGGATA
*
40677283 ATAATTCTCACACGAGCTATGAAT
1 ATAATGCTCACACGAGCTATGAAT
* *
40677307 ATTATGCTCACACAAGCTATGAAT
1 ATAATGCTCACACGAGCTATGAAT
*
40677331 GTAAATGCTCACACGAGCT
1 AT-AATGCTCACACGAGCT
40677350 GTAGGTTGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 22 0.61
25 14 0.39
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (24 bp):
ATAATGCTCACACGAGCTATGAAT
Found at i:40681473 original size:40 final size:40
Alignment explanation
Indices: 40681428--40681595 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
40681418 CGGAATATAA
*
40681428 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAAC
* * * *
40681468 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAAC
** *
40681508 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAAC
** * * * * * *
40681548 CCGGATATAATTTCAAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAAC
40681588 CCGGATAT
1 CCGGATAT
40681596 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:40684390 original size:29 final size:29
Alignment explanation
Indices: 40684357--40684413 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
40684347 AGAGTAAGTC
*
40684357 TGTTAGGAGTAAATGAACAGTTATATATT
1 TGTTAGGAGTAAATGAACAGTTAGATATT
40684386 TGTTAGGAGTAAATGAACAGTTAGATAT
1 TGTTAGGAGTAAATGAACAGTTAGATAT
40684414 AAGTATAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.35
Consensus pattern (29 bp):
TGTTAGGAGTAAATGAACAGTTAGATATT
Found at i:40703094 original size:27 final size:26
Alignment explanation
Indices: 40703022--40703096 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
40703012 TTGGGTCGTT
* *
40703022 AATACCCACGGTTTGTAAAATTATCGA
1 AATACCC-CGATTTGTAAAATTACCGA
*
40703049 AATACCTCCGGA-TTATAAAATTACCGA
1 AATACC-CC-GATTTGTAAAATTACCGA
40703076 AATACCCGCGATTTGTAAAAT
1 AATACCC-CGATTTGTAAAAT
40703097 GACTGTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
26 3 0.08
27 35 0.88
28 2 0.05
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (26 bp):
AATACCCCGATTTGTAAAATTACCGA
Found at i:40703120 original size:27 final size:26
Alignment explanation
Indices: 40703090--40703313 Score: 191
Period size: 27 Copynumber: 8.4 Consensus size: 26
40703080 CCCGCGATTT
* *
40703090 GTAAAATGACTGTAATTCCTCAGTAGG
1 GTAAAATGACTGTAATACC-CTGTAGG
*
40703117 GTAAAATGACTGTAATACCCCT-AAGG
1 GTAAAATGACTGTAATA-CCCTGTAGG
* * * *
40703143 GTGAAATGACTATAATACCCCTATAAG
1 GTAAAATGACTGTAATA-CCCTGTAGG
* *
40703170 GTAAAATGACCGTAATACCCCTGTAGT
1 GTAAAATGACTGTAATA-CCCTGTAGG
* *
40703197 GTTAAATGACCGTAATACCTCTGTAGG
1 GTAAAATGACTGTAATACC-CTGTAGG
*
40703224 GTAAAATGA-TCGTAATGCCCTGTAGG
1 GTAAAATGACT-GTAATACCCTGTAGG
* ** * *
40703250 ATAAAATGACCATAATGCCCTTTTAGG
1 GTAAAATGACTGTAATACCC-TGTAGG
* *
40703277 GTAAAATGACCGTAATACCCTTGTATG
1 GTAAAATGACTGTAATACCC-TGTAGG
40703304 GTAAAATGAC
1 GTAAAATGAC
40703314 GATTATGCCC
Statistics
Matches: 164, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
26 48 0.29
27 114 0.70
28 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (26 bp):
GTAAAATGACTGTAATACCCTGTAGG
Found at i:40703134 original size:54 final size:53
Alignment explanation
Indices: 40703064--40703313 Score: 161
Period size: 53 Copynumber: 4.7 Consensus size: 53
40703054 CTCCGGATTA
* * * *
40703064 TAAAATTACCGAAATACCCGCGATTTGTAAAATGACTGTAATTCCTCAGTAGGG
1 TAAAATGACCGTAATACCC-CGATGTGTAAAATGACTGTAATACCTCAGTAGGG
* * * * * * * *
40703118 TAAAATGACTGTAATACCCCTAAGGGTGAAATGACTATAATACCCCTA-TAAGG
1 TAAAATGACCGTAATACCCCGATGTGTAAAATGACTGTAATACCTC-AGTAGGG
* * *
40703171 TAAAATGACCGTAATACCCCTG-TAGTGTTAAATGACCGTAATACCTCTGTAGGG
1 TAAAATGACCGTAATACCCC-GAT-GTGTAAAATGACTGTAATACCTCAGTAGGG
* * * ** * **
40703225 TAAAATGATCGTAATGCCCTG-TAG-GATAAAATGACCATAATGCC-CTTTTAGGG
1 TAAAATGACCGTAATACCCCGAT-GTG-TAAAATGACTGTAATACCTC-AGTAGGG
*
40703278 TAAAATGACCGTAATACCCTTGTATG-GTAAAATGAC
1 TAAAATGACCGTAATACCC-CG-ATGTGTAAAATGAC
40703314 GATTATGCCC
Statistics
Matches: 156, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
52 2 0.01
53 84 0.54
54 67 0.43
55 2 0.01
56 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (53 bp):
TAAAATGACCGTAATACCCCGATGTGTAAAATGACTGTAATACCTCAGTAGGG
Found at i:40703173 original size:53 final size:54
Alignment explanation
Indices: 40703113--40703313 Score: 226
Period size: 53 Copynumber: 3.8 Consensus size: 54
40703103 AATTCCTCAG
* * * *
40703113 TAGGGTAAAATGACTGTAATACCCCT-AAGGGTGAAATGACTATAATACCCCTA
1 TAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCATAATACCCCTA
* * * * * *
40703166 TAAGGTAAAATGACCGTAATACCCCTGTAGTGTTAAATGACCGTAATACCTCTG
1 TAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCATAATACCCCTA
* * * * * *
40703220 TAGGGTAAAATGATCGTAAT-GCCCTGTAGGATAAAATGACCATAATGCCCTTT
1 TAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCATAATACCCCTA
* *
40703273 TAGGGTAAAATGACCGTAATACCCTTGTATGGTAAAATGAC
1 TAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGAC
40703314 GATTATGCCC
Statistics
Matches: 121, Mismatches: 25, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
53 67 0.55
54 54 0.45
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (54 bp):
TAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCATAATACCCCTA
Found at i:40703311 original size:107 final size:107
Alignment explanation
Indices: 40703089--40703313 Score: 276
Period size: 107 Copynumber: 2.1 Consensus size: 107
40703079 ACCCGCGATT
* * * * *
40703089 TGTAAAATGACTGTAATTCCTCAGTAGGGTAAAATGACTGTAATACCCCTAAGGGTGAAATGACT
1 TGTAAAATGACCGTAATACCTCAGTAGGGTAAAATGACTGTAATACCCCTAAGGATAAAATGACC
40703154 ATAATACCCCTATAAGGTAAAATGACCGTAATACCCCTGTAG
66 ATAATACCCCTATAAGGTAAAATGACCGTAATACCCCTGTAG
* * * *
40703196 TGTTAAATGACCGTAATACCTCTGTAGGGTAAAATGA-TCGTAAT-GCCCTGTAGGATAAAATGA
1 TGTAAAATGACCGTAATACCTCAGTAGGGTAAAATGACT-GTAATACCCCT-AAGGATAAAATGA
* * * * *
40703259 CCATAATGCCCTTTTAGGGTAAAATGACCGTAATACCCTTGTA-
64 CCATAATACCCCTATAAGGTAAAATGACCGTAATACCCCTGTAG
40703302 TGGTAAAATGAC
1 T-GTAAAATGAC
40703314 GATTATGCCC
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
106 6 0.06
107 94 0.94
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (107 bp):
TGTAAAATGACCGTAATACCTCAGTAGGGTAAAATGACTGTAATACCCCTAAGGATAAAATGACC
ATAATACCCCTATAAGGTAAAATGACCGTAATACCCCTGTAG
Found at i:40703322 original size:80 final size:80
Alignment explanation
Indices: 40703112--40703324 Score: 227
Period size: 80 Copynumber: 2.7 Consensus size: 80
40703102 TAATTCCTCA
* * * * * *
40703112 GTAGGGTAAAATGACTGTAATACCCCT-AAGGGTGAAATGACTATAATACCCCTATAAGGTAAAA
1 GTAGGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATGACGATAAT-GCCCTATAAGGTAAAA
*
40703176 TGACCGTAATACCCCT
65 TGACCATAATACCCCT
* * *
40703192 GTAGTGTTAAATGACCGTAATA-CCTCTGTAGGGTAAAATGATCG-TAATGCCCTGT-AGGATAA
1 GTAGGGTAAAATGACCGTAATACCCT-TGTAGGGTAAAATGA-CGATAATGCCCTATAAGG-TAA
* *
40703254 AATGACCATAATGCCCTT
63 AATGACCATAATACCCCT
* * *
40703272 TTAGGGTAAAATGACCGTAATACCCTTGTATGGTAAAATGACGATTATGCCCT
1 GTAGGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATGACGATAATGCCCT
40703325 TATGTTTCGT
Statistics
Matches: 110, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
79 7 0.06
80 84 0.76
81 18 0.16
82 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (80 bp):
GTAGGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATGACGATAATGCCCTATAAGGTAAAAT
GACCATAATACCCCT
Found at i:40703499 original size:27 final size:26
Alignment explanation
Indices: 40703450--40703501 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40703440 TGGAGGAAGT
*
40703450 ACTGTACTGGTGACTATGTCACATTC
1 ACTGTACTGGTGACTATGCCACATTC
* *
40703476 ACTGTTACTGGTGGCTTTGCCACATT
1 ACTG-TACTGGTGACTATGCCACATT
40703502 TACTATTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (26 bp):
ACTGTACTGGTGACTATGCCACATTC
Found at i:40710690 original size:45 final size:47
Alignment explanation
Indices: 40710608--40710695 Score: 135
Period size: 45 Copynumber: 1.9 Consensus size: 47
40710598 AGATACTCAG
* *
40710608 AAATCTCGCACTCTAAGTGCCAATAATATAGCCGAAGCTATCTAAAT
1 AAATCTCGCACTCGAAGTGCCAATAACATAGCCGAAGCTATCTAAAT
*
40710655 AAATCTTGCAC-CGAAGTGCCAAT-ACATAGCCGAAGCTATCT
1 AAATCTCGCACTCGAAGTGCCAATAACATAGCCGAAGCTATCT
40710696 CAGCATCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 17 0.45
46 11 0.29
47 10 0.26
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (47 bp):
AAATCTCGCACTCGAAGTGCCAATAACATAGCCGAAGCTATCTAAAT
Found at i:40711202 original size:12 final size:11
Alignment explanation
Indices: 40711185--40711229 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
40711175 AATTGGTCAT
40711185 GGAGGGATTGTA
1 GGAGGGATTG-A
40711197 GGAGGGAGTTGA
1 GGAGGGA-TTGA
*
40711209 GGAGAGATATGA
1 GGAGGGAT-TGA
40711221 GGAGGGATT
1 GGAGGGATT
40711230 TTAGGAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 2 0.07
12 24 0.83
13 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.51, T:0.20
Consensus pattern (11 bp):
GGAGGGATTGA
Found at i:40711235 original size:12 final size:12
Alignment explanation
Indices: 40711185--40711236 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
40711175 AATTGGTCAT
40711185 GGAGGGA-TTGTA
1 GGAGGGATTTG-A
*
40711197 GGAGGGAGTTGA
1 GGAGGGATTTGA
* *
40711209 GGAGAGATATGA
1 GGAGGGATTTGA
*
40711221 GGAGGGATTTTA
1 GGAGGGATTTGA
40711233 GGAG
1 GGAG
40711237 AAAATCAAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 30 0.91
13 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.50, T:0.21
Consensus pattern (12 bp):
GGAGGGATTTGA
Found at i:40712680 original size:27 final size:27
Alignment explanation
Indices: 40712642--40712931 Score: 391
Period size: 27 Copynumber: 10.7 Consensus size: 27
40712632 CGTACCTGAA
* * *
40712642 CCCTTATGTGATAAAATGACAATTTTT
1 CCCTCATGTGATAAAATGACGATTTTG
* *
40712669 CCCTCATATGATAAAATGACGATTTTA
1 CCCTCATGTGATAAAATGACGATTTTG
*
40712696 CCCTTATGTGATAAAATGACGATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
40712723 CCCTCATGTGATAAAATGACGATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
* * *
40712750 CCCTTATATGATAAAATGACAATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
* *
40712777 CCCTCATGTGATAAAATGATGATTTTA
1 CCCTCATGTGATAAAATGACGATTTTG
*
40712804 CCCTCATGTGATAAAATGACAATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
* * *
40712831 CCTTTATGTGATAAAATGACGATTTTT
1 CCCTCATGTGATAAAATGACGATTTTG
* *
40712858 CCTTCATGTGATAAAACGACGATTTTG
1 CCCTCATGTGATAAAATGACGATTTTG
* * *
40712885 CCCTTACGTGATAAAATGACGATTTTA
1 CCCTCATGTGATAAAATGACGATTTTG
*
40712912 CCCTTATGTGATAAAATGAC
1 CCCTCATGTGATAAAATGAC
40712932 TGAAATACCC
Statistics
Matches: 231, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 231 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (27 bp):
CCCTCATGTGATAAAATGACGATTTTG
Found at i:40712727 original size:54 final size:54
Alignment explanation
Indices: 40712641--40712931 Score: 440
Period size: 54 Copynumber: 5.4 Consensus size: 54
40712631 GCGTACCTGA
* *
40712641 ACCCTTATGTGATAAAATGACAATTTTTCCCTCATATGATAAAATGACGATTTT
1 ACCCTTATGTGATAAAATGACAATTTTGCCCTCATGTGATAAAATGACGATTTT
*
40712695 ACCCTTATGTGATAAAATGACGATTTTGCCCTCATGTGATAAAATGACGATTTT
1 ACCCTTATGTGATAAAATGACAATTTTGCCCTCATGTGATAAAATGACGATTTT
* * *
40712749 GCCCTTATATGATAAAATGACAATTTTGCCCTCATGTGATAAAATGATGATTTT
1 ACCCTTATGTGATAAAATGACAATTTTGCCCTCATGTGATAAAATGACGATTTT
* * *
40712803 ACCCTCATGTGATAAAATGACAATTTTGCCTTTATGTGATAAAATGACGATTTT
1 ACCCTTATGTGATAAAATGACAATTTTGCCCTCATGTGATAAAATGACGATTTT
* * * * *
40712857 -TCCTTCATGTGATAAAACGACGATTTTGCCCTTACGTGATAAAATGACGATTTT
1 ACCCTT-ATGTGATAAAATGACAATTTTGCCCTCATGTGATAAAATGACGATTTT
40712911 ACCCTTATGTGATAAAATGAC
1 ACCCTTATGTGATAAAATGAC
40712932 TGAAATACCC
Statistics
Matches: 214, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
53 3 0.01
54 207 0.97
55 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (54 bp):
ACCCTTATGTGATAAAATGACAATTTTGCCCTCATGTGATAAAATGACGATTTT
Found at i:40712953 original size:27 final size:27
Alignment explanation
Indices: 40712923--40712990 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
40712913 CCTTATGTGA
* *
40712923 TAAAATGACTGAAATACCCTCATTGGG
1 TAAAATGACTGAAATACCCCCATAGGG
40712950 TAAAATGA-TCGAAATACCCCCATAGGG
1 TAAAATGACT-GAAATACCCCCATAGGG
*
40712977 TAAAATGACAGAAA
1 TAAAATGACTGAAA
40712991 CACCTTTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCCATAGGG
Found at i:40714976 original size:15 final size:15
Alignment explanation
Indices: 40714956--40714984 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40714946 ATGCACTTAT
40714956 TAATGATTTCCATAC
1 TAATGATTTCCATAC
40714971 TAATGATTTCCATA
1 TAATGATTTCCATA
40714985 AATGTCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (15 bp):
TAATGATTTCCATAC
Found at i:40718797 original size:39 final size:40
Alignment explanation
Indices: 40718730--40718807 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 40
40718720 AATAATTAGA
* * *
40718730 TGATGGCATATACGTGCTCCTATTTGTACTTCAGTACCCC
1 TGATGGCACATACGTGCTCCTATATGTACTTCAATACCCC
*
40718770 TGATTGCACATACGTGC-CCTATATGTACTTCAATACCC
1 TGATGGCACATACGTGCTCCTATATGTACTTCAATACCC
40718808 TTGAACGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 19 0.56
40 15 0.44
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (40 bp):
TGATGGCACATACGTGCTCCTATATGTACTTCAATACCCC
Found at i:40718825 original size:30 final size:30
Alignment explanation
Indices: 40718789--40718850 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
40718779 ATACGTGCCC
40718789 TATATGTACTTCAATACCCTTGAACGCATT
1 TATATGTACTTCAATACCCTTGAACGCATT
*
40718819 TATATGTACTTCAGTACCCTTGAACGCATT
1 TATATGTACTTCAATACCCTTGAACGCATT
40718849 TA
1 TA
40718851 CATGCCTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (30 bp):
TATATGTACTTCAATACCCTTGAACGCATT
Found at i:40724807 original size:40 final size:39
Alignment explanation
Indices: 40724760--40724880 Score: 161
Period size: 40 Copynumber: 3.0 Consensus size: 39
40724750 CGGGCTTTAA
* *
40724760 CCGGATATAGCCACTCGCTCAAATGCCTTCGGGACTTAGC
1 CCGGATATAG-AACTCGCACAAATGCCTTCGGGACTTAGC
** *
40724800 CCGGATATAGTAGTTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAG-AACTCGCACAAATGCCTTCGGGACTTAGC
*
40724840 CCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGC
1 CCGGATATAG-AACTCGCACAAATGCCTTCGGGACTTAGC
40724880 C
1 C
40724881 GGGTTATCAT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (39 bp):
CCGGATATAGAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40730056 original size:71 final size:71
Alignment explanation
Indices: 40729972--40730135 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
40729962 CGATTTGTCT
40729972 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
40730037 CTTTCA
66 CTTTCA
40730043 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
40730108 CTTTCA
66 CTTTCA
40730114 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
40730136 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:40730173 original size:71 final size:70
Alignment explanation
Indices: 40729972--40730169 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
40729962 CGATTTGTCT
* * * *
40729972 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
40730037 CTTTCA
65 CTTTCA
* * * *
40730043 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
40730108 CTTTCA
65 CTTTCA
* *
40730114 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
40730170 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:40743340 original size:40 final size:40
Alignment explanation
Indices: 40743311--40743532 Score: 333
Period size: 40 Copynumber: 5.5 Consensus size: 40
40743301 GCCACTCGCT
* * * *
40743311 CAAATGCCTTCGGGACTTAGCTCGG-ATATAGT-AGTTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTCA-CTAGCA
* *
40743351 CAAATGCCTTCGGGACTTAGCCCGG-ATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCA
*
40743391 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
40743431 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
40743471 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
40743511 CAAATGCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
40743533 GGTTATCATC
Statistics
Matches: 175, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
40 172 0.98
41 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCA
Found at i:40747504 original size:46 final size:46
Alignment explanation
Indices: 40747453--40747540 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 46
40747443 TTTTGCTGAT
*
40747453 TTTTTTTCTCCTTAGTCGACC-TATTGCTGCCATTTTCCAGCCCTCA
1 TTTTTTT-TCCTTACTCGACCTTATTGCTGCCATTTTCCAGCCCTCA
** * * *
40747499 TTTTTTTTGTTTACTGGCCCTTTTTGCTGCCATTTTCCAGCC
1 TTTTTTTTCCTTACTCGACCTTATTGCTGCCATTTTCCAGCC
40747541 ATTTGTTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 8 0.23
46 27 0.77
ACGTcount: A:0.10, C:0.30, G:0.12, T:0.48
Consensus pattern (46 bp):
TTTTTTTTCCTTACTCGACCTTATTGCTGCCATTTTCCAGCCCTCA
Found at i:40747845 original size:12 final size:12
Alignment explanation
Indices: 40747828--40747862 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
40747818 ACTCCCAACC
40747828 TGCTGGACAAAA
1 TGCTGGACAAAA
40747840 TGCTGGACAAAA
1 TGCTGGACAAAA
40747852 TGCTGCGACAA
1 TGCTG-GACAA
40747863 TCAGATTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (12 bp):
TGCTGGACAAAA
Found at i:40762957 original size:23 final size:22
Alignment explanation
Indices: 40762906--40762957 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
40762896 TAAAATGACT
40762906 AAAA-AAATTTTTATTTTTAAA
1 AAAATAAATTTTTATTTTTAAA
** *
40762927 AATCTAAACTTTTTCTTTTTAAA
1 AAAATAAA-TTTTTATTTTTAAA
40762950 AAAATAAA
1 AAAATAAA
40762958 AAATTTTCCC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 2 0.08
22 3 0.12
23 19 0.79
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATAAATTTTTATTTTTAAA
Found at i:40763485 original size:12 final size:12
Alignment explanation
Indices: 40763468--40763497 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40763458 TTTACAGGTC
40763468 TAAAAAAGAAAA
1 TAAAAAAGAAAA
40763480 TAAAAAAGAAAA
1 TAAAAAAGAAAA
*
40763492 GAAAAA
1 TAAAAA
40763498 CAAAGGCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (12 bp):
TAAAAAAGAAAA
Found at i:40766714 original size:32 final size:32
Alignment explanation
Indices: 40766673--40766735 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
40766663 AATCAAAGAG
*
40766673 AAGGAGAGGGGGTTAGGAACGACTATGGCAAT
1 AAGGAGAGGGGGTGAGGAACGACTATGGCAAT
40766705 AAGGAGAGGGGGTGAGGAACGACTATGGCAA
1 AAGGAGAGGGGGTGAGGAACGACTATGGCAA
40766736 CTAGAAGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.43, T:0.13
Consensus pattern (32 bp):
AAGGAGAGGGGGTGAGGAACGACTATGGCAAT
Found at i:40768895 original size:48 final size:48
Alignment explanation
Indices: 40768824--40769095 Score: 262
Period size: 48 Copynumber: 5.7 Consensus size: 48
40768814 TATGTGTGCT
* *
40768824 AGTGTAAGACCATGTCGGGGACATGGCATTGGCCA-AGAAATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACA-AAATGAGAGCC
* *
40768872 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACAACATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAAAATGAGAGCC
* * * ** * * * *
40768920 AATGTAAGACCATGTTTGGGACATGGCATCAG-CATTGATATGTGCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CAAAATGAGAGCC
* * * *
40768968 AGTGTAAGACTATGTCGGGGACATGGTATCGGCCACAACATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAAAATGAGAGCC
* * * * * * *
40769016 AGTGTAAGACCATGTTTGGGATATGGCATCAG-CATTAAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CAAAATGAGAGCC
* *
40769064 AGTGTAAGACCATGTCTGGTACATGACATCGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG
40769096 GCTCGACATG
Statistics
Matches: 181, Mismatches: 39, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
47 4 0.02
48 174 0.96
49 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAAAATGAGAGCC
Found at i:40769071 original size:144 final size:144
Alignment explanation
Indices: 40768811--40769093 Score: 399
Period size: 144 Copynumber: 2.0 Consensus size: 144
40768801 GACAGTTGGG
* *
40768811 TGATATGTGTGCTAGTGTAAGACCATGTCGGGGACATGGCATTGGCCAAGAAATGAGAGCCAGTG
1 TGATATGTGCGCTAGTGTAAGACCATGTCGGGGACATGGCATCGGCCAAGAAATGAGAGCCAGTG
* * *
40768876 TAAGACCATGTTTGGGACATGGCATCGGCCACAACATGAGAGCCAATGTAAGACCATGTTTGGGA
66 TAAGACCATGTTTGGGACATGGCATCAGCCACAACACGAGAGCCAATGTAAGACCATGTCTGGGA
*
40768941 CATGGCATCAGCAT
131 CATGACATCAGCAT
* * *
40768955 TGATATGTGCGCTAGTGTAAGACTATGTCGGGGACATGGTATCGGCCACA-ACATGAGAGCCAGT
1 TGATATGTGCGCTAGTGTAAGACCATGTCGGGGACATGGCATCGGCCA-AGAAATGAGAGCCAGT
* * * * *
40769019 GTAAGACCATGTTTGGGATATGGCATCAG-CATTAAGACGAGAGCTAGTGTAAGACCATGTCTGG
65 GTAAGACCATGTTTGGGACATGGCATCAGCCA-CAACACGAGAGCCAATGTAAGACCATGTCTGG
*
40769083 TACATGACATC
129 GACATGACATC
40769094 GGGCTCGACA
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
143 2 0.02
144 119 0.98
145 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.23
Consensus pattern (144 bp):
TGATATGTGCGCTAGTGTAAGACCATGTCGGGGACATGGCATCGGCCAAGAAATGAGAGCCAGTG
TAAGACCATGTTTGGGACATGGCATCAGCCACAACACGAGAGCCAATGTAAGACCATGTCTGGGA
CATGACATCAGCAT
Found at i:40769105 original size:96 final size:96
Alignment explanation
Indices: 40768824--40769130 Score: 339
Period size: 96 Copynumber: 3.2 Consensus size: 96
40768814 TATGTGTGCT
** ** ** * * *
40768824 AGTGTAAGACCATGTCGGGGACATGGCATTGGCCAAGAA-ATGAGAGCCAGTGTAAGACCATGTT
1 AGTGTAAGACCATGTTTGGGACATGGCATCAG-CATTAAGACGAGAGCTAGTGTAAGACCATGTC
40768888 TGGGACATGGCATCGGCCACAACATGAGAGCC
65 TGGGACATGGCATCGGCCACAACATGAGAGCC
* * * * * * * *
40768920 AATGTAAGACCATGTTTGGGACATGGCATCAGCATTGATATGTGCGCTAGTGTAAGACTATGTCG
1 AGTGTAAGACCATGTTTGGGACATGGCATCAGCATTAAGACGAGAGCTAGTGTAAGACCATGTCT
*
40768985 GGGACATGGTATCGGCCACAACATGAGAGCC
66 GGGACATGGCATCGGCCACAACATGAGAGCC
*
40769016 AGTGTAAGACCATGTTTGGGATATGGCATCAGCATTAAGACGAGAGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCAGCATTAAGACGAGAGCTAGTGTAAGACCATGTCT
* * * * * *
40769081 GGTACATGACATCGGGCTCGACATGTA-AGCT
66 GGGACATGGCATCGGCCACAACATG-AGAGCC
* *
40769112 AGCGCAAGACCATGTTTGG
1 AGTGTAAGACCATGTTTGG
40769131 ATAACGGCAT
Statistics
Matches: 176, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
95 3 0.02
96 172 0.98
97 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (96 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCAGCATTAAGACGAGAGCTAGTGTAAGACCATGTCT
GGGACATGGCATCGGCCACAACATGAGAGCC
Found at i:40769113 original size:144 final size:144
Alignment explanation
Indices: 40768821--40769126 Score: 375
Period size: 144 Copynumber: 2.1 Consensus size: 144
40768811 TGATATGTGT
*
40768821 GCTAGTGTAAGACCATGTCGGGGACATGGCATTGGCCAAGAAATGAGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCGGGGACATGGCATCGGCCAAGAAATGAGAGCCAGTGTAAGACCATG
* * * *
40768886 TTTGGGACATGGCATCGGCCACAACATGAGAGCCAATGTAAGACCATGTTTGGGACATGGCATCA
66 TTTGGGACATGGCATCAGCCACAACACGAGAGCCAATGTAAGACCATGTCTGGGACATGACATCA
* * **
40768951 GCATTGATATGTGC
131 GCATCGACATGTAA
* * *
40768965 GCTAGTGTAAGACTATGTCGGGGACATGGTATCGGCCACA-ACATGAGAGCCAGTGTAAGACCAT
1 GCTAGTGTAAGACCATGTCGGGGACATGGCATCGGCCA-AGAAATGAGAGCCAGTGTAAGACCAT
* * * * * *
40769029 GTTTGGGATATGGCATCAG-CATTAAGACGAGAGCTAGTGTAAGACCATGTCTGGTACATGACAT
65 GTTTGGGACATGGCATCAGCCA-CAACACGAGAGCCAATGTAAGACCATGTCTGGGACATGACAT
*
40769093 CGGGC-TCGACATGTAA
129 C-AGCATCGACATGTAA
* *
40769109 GCTAGCGCAAGACCATGT
1 GCTAGTGTAAGACCATGT
40769127 TTGGATAACG
Statistics
Matches: 137, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
143 2 0.01
144 132 0.96
145 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (144 bp):
GCTAGTGTAAGACCATGTCGGGGACATGGCATCGGCCAAGAAATGAGAGCCAGTGTAAGACCATG
TTTGGGACATGGCATCAGCCACAACACGAGAGCCAATGTAAGACCATGTCTGGGACATGACATCA
GCATCGACATGTAA
Found at i:40776725 original size:219 final size:219
Alignment explanation
Indices: 40776346--40777006 Score: 1313
Period size: 219 Copynumber: 3.0 Consensus size: 219
40776336 ATGATTAAAT
40776346 TAGTGAATTTTTATCATTTTAGATCAAGAAATACAAAATCCAGGCCTAGACCGGGGGAAGGCTAA
1 TAGTGAATTTTTATCATTTTAGATCAAGAAATACAAAATCCAGGCCTAGACCGGGGGAAGGCTAA
*
40776411 ACAAGTAGACTAAATTCAACTAGTTGCCACCTTTTTGTATACCGAGGTAAGTTGTACGTAAGTAA
66 ACAAGTAGACTAAATTCAACTAGTTGCCAACTTTTTGTATACCGAGGTAAGTTGTACGTAAGTAA
40776476 GGCAACTTTATCATTATTATGTGTTGAATGATTAATTTTGTGTAATATGGTTGAAATAGCTTATG
131 GGCAACTTTATCATTATTATGTGTTGAATGATTAATTTTGTGTAATATGGTTGAAATAGCTTATG
40776541 AATAATGCATGATGAAATTCAATG
196 AATAATGCATGATGAAATTCAATG
40776565 TAGTGAATTTTTATCATTTTAGATCAAGAAATACAAAATCCAGGCCTAGACCGGGGGAAGGCTAA
1 TAGTGAATTTTTATCATTTTAGATCAAGAAATACAAAATCCAGGCCTAGACCGGGGGAAGGCTAA
40776630 ACAAGTAGACTAAATTCAACTAGTTGCCAACTTTTTGTATACCGAGGTAAGTTGTACGTAAGTAA
66 ACAAGTAGACTAAATTCAACTAGTTGCCAACTTTTTGTATACCGAGGTAAGTTGTACGTAAGTAA
40776695 GGCAACTTTATCATTATTATGTGTTGAATGATTAATTTTGTGTAATATGGTTGAAATAGCTTATG
131 GGCAACTTTATCATTATTATGTGTTGAATGATTAATTTTGTGTAATATGGTTGAAATAGCTTATG
40776760 AATAATGCATGATGAAATTCAATG
196 AATAATGCATGATGAAATTCAATG
40776784 TAGTGAATTTTTATCATTTTAGATCAAGAAATACAAAATCCAGGCCTAGACCGGGGGAAGGCTAA
1 TAGTGAATTTTTATCATTTTAGATCAAGAAATACAAAATCCAGGCCTAGACCGGGGGAAGGCTAA
40776849 ACAAGTAGACTAAATTCAACTAGTTGCCAACTTTTTGTATACCGAGGTAAGTTGTACGTAAGTAA
66 ACAAGTAGACTAAATTCAACTAGTTGCCAACTTTTTGTATACCGAGGTAAGTTGTACGTAAGTAA
40776914 GGCAACTTTATCATTATTATGTGTTGAATGATTAATTTTGTGTAATATGGTTGAAATAGCTTATG
131 GGCAACTTTATCATTATTATGTGTTGAATGATTAATTTTGTGTAATATGGTTGAAATAGCTTATG
40776979 AATAATGCATGATGAAATTCAATG
196 AATAATGCATGATGAAATTCAATG
40777003 TAGT
1 TAGT
40777007 AGAGTCCCAA
Statistics
Matches: 441, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 441 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (219 bp):
TAGTGAATTTTTATCATTTTAGATCAAGAAATACAAAATCCAGGCCTAGACCGGGGGAAGGCTAA
ACAAGTAGACTAAATTCAACTAGTTGCCAACTTTTTGTATACCGAGGTAAGTTGTACGTAAGTAA
GGCAACTTTATCATTATTATGTGTTGAATGATTAATTTTGTGTAATATGGTTGAAATAGCTTATG
AATAATGCATGATGAAATTCAATG
Found at i:40777133 original size:48 final size:48
Alignment explanation
Indices: 40777062--40777295 Score: 265
Period size: 48 Copynumber: 4.9 Consensus size: 48
40777052 ACATTTGGGT
* * *
40777062 GATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCTTCAGCCAC
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC
* *
40777110 GATATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCAC
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC
* * * * *
40777158 AACATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-GGCATT
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCA-C
* * * *
40777206 GATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTC
1 GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC
* * * * *
40777254 GACATGTA-AGCCATTGTAACACCATGTTTGGAACATGGCATC
1 GATATG-AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
40777296 GACAATTCAC
Statistics
Matches: 155, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
47 3 0.02
48 150 0.97
49 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (48 bp):
GATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC
Done.