Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 95 of 190
Found at i:28389509 original size:19 final size:16
Alignment explanation
Indices: 28389484--28389526 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 16
28389474 TAACATATAA
28389484 AATTTATAATTATTTTAT
1 AATTTATAA-T-TTTTAT
28389502 ATATTTATAATTTTTAT
1 A-ATTTATAATTTTTAT
28389519 AATTTATA
1 AATTTATA
28389527 TTTCATAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 2 0.08
19 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTATAATTTTTAT
Found at i:28390212 original size:19 final size:20
Alignment explanation
Indices: 28390174--28390214 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
28390164 TAGAAAAATC
28390174 TTATTATGTATAAATTATAA
1 TTATTATGTATAAATTATAA
28390194 TTATTA-GT-TAAATTTATAA
1 TTATTATGTATAAA-TTATAA
28390213 TT
1 TT
28390215 TCCAGATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTATTATGTATAAATTATAA
Found at i:28390304 original size:22 final size:24
Alignment explanation
Indices: 28390279--28390324 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
28390269 TCAAGTGTAA
28390279 TTTGAACAAA-AAA-AAA-TTATTT
1 TTTGAA-AAATAAATAAATTTATTT
28390301 TTTGAAAAATAAATAAATTTATTT
1 TTTGAAAAATAAATAAATTTATTT
28390325 CCAGTTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 3 0.14
22 9 0.43
23 3 0.14
24 6 0.29
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
TTTGAAAAATAAATAAATTTATTT
Found at i:28391385 original size:22 final size:21
Alignment explanation
Indices: 28391360--28391403 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
28391350 TTTTTTAAAA
28391360 AATATTT-ATATTATTTTTATTT
1 AATATTTAATA-TATTTTT-TTT
28391382 AATATTTAATATATTTTTTTT
1 AATATTTAATATATTTTTTTT
28391403 A
1 A
28391404 CTTATGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 14 0.67
23 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
AATATTTAATATATTTTTTTT
Found at i:28392793 original size:26 final size:26
Alignment explanation
Indices: 28392764--28392815 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
28392754 GCTTCAAGAT
*
28392764 CCAAAATGTATAACTTGTGTCAAATA
1 CCAAAATGCATAACTTGTGTCAAATA
*
28392790 CCAAAATGCATAACTTTTGTCAAATA
1 CCAAAATGCATAACTTGTGTCAAATA
28392816 TAAGTACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (26 bp):
CCAAAATGCATAACTTGTGTCAAATA
Found at i:28396003 original size:16 final size:17
Alignment explanation
Indices: 28395977--28396010 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
28395967 ATTAGTTTTA
28395977 AAAATATAAATATACAT
1 AAAATATAAATATACAT
28395994 AAAA-ATAAATATACAT
1 AAAATATAAATATACAT
28396010 A
1 A
28396011 TATATTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATAAATATACAT
Found at i:28396041 original size:26 final size:27
Alignment explanation
Indices: 28395989--28396041 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
28395979 AATATAAATA
* *
28395989 TACATAAAAATAAATATACATATATAT
1 TACATAAAAATAAAGATACATACATAT
* *
28396016 TACATAAAAA-AAAGATGCATGCATAT
1 TACATAAAAATAAAGATACATACATAT
28396042 GAATATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (27 bp):
TACATAAAAATAAAGATACATACATAT
Found at i:28396054 original size:3 final size:3
Alignment explanation
Indices: 28396046--28396107 Score: 97
Period size: 3 Copynumber: 20.3 Consensus size: 3
28396036 GCATATGAAT
*
28396046 ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
*
28396092 ATA ATA ATA ATG ATA A
1 ATA ATA ATA ATA ATA A
28396108 CAATTTGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28397728 original size:44 final size:44
Alignment explanation
Indices: 28397677--28397786 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
28397667 TTCTGCTCTT
* * *
28397677 TGCAACTTCAGAGAGATAAGATCCA-AGGTTTTAATCCGCTTCAC
1 TGCAACTTCAGGGAGATAAGAT-CATAGGCTTTAATCCGCTCCAC
* * * *
28397721 TGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATCATAGGCTTTAATCCGCTCCAC
*
28397765 TGCAACTTTAGGGAGATAAGAT
1 TGCAACTTCAGGGAGATAAGAT
28397787 TTGCCATATT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 55 0.98
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGATCATAGGCTTTAATCCGCTCCAC
Found at i:28398144 original size:44 final size:43
Alignment explanation
Indices: 28398090--28398639 Score: 525
Period size: 44 Copynumber: 12.7 Consensus size: 43
28398080 GTTATTTTCC
* * *
28398090 ACCTACTCCACTGCTGCTCAGGGAGATAGGGTTCACGATCTTCA
1 ACCTATTCCACTGCTGC-CAGGGAGATAGGATTCACAATCTTCA
*
28398134 ACCTATTCCACTGCTGACCAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTC-ACAATCTTCA
* * * *
28398178 ATCTATTCTACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
*
28398222 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* *
28398266 ACCTATTCTACTGCTGTCTAGGGAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* * *
28398304 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* * *
28398348 GCCTATTCCACTGCTGACCAGGGAGATAGG----GC--TCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* * *
28398386 ATCTATTCCACTGCTGCTCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGC-CAGGGAGATAGGATTCACAATCTTCA
* * *
28398430 ATCTATTCCACTGCTGATCAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTC-ACAATCTTCA
* * *
28398474 ATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGCC-AGGGAGATAGGATTCACAATCTTCA
* * *
28398518 ACCTATTCCATTGCTGACCAGGGAGATAGGATTCAGAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* ** ** *
28398562 ACCTATTCGACTATTGTCCAGGGAGATAGGATTCTTTAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTC-ACAATCTTCA
*
28398607 GCCTATTCCACTGCTGACCAGGGAGATAAGGAT
1 ACCTATTCCACTGCTG-CCAGGGAGAT-AGGAT
28398640 GGGGACATCA
Statistics
Matches: 422, Mismatches: 61, Indels: 44
0.80 0.12 0.08
Matches are distributed among these distances:
37 1 0.00
38 59 0.14
39 2 0.00
40 3 0.01
42 3 0.01
43 5 0.01
44 309 0.73
45 35 0.08
46 5 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (43 bp):
ACCTATTCCACTGCTGCCAGGGAGATAGGATTCACAATCTTCA
Found at i:28398778 original size:88 final size:88
Alignment explanation
Indices: 28398650--28399046 Score: 632
Period size: 88 Copynumber: 4.5 Consensus size: 88
28398640 GGGGACATCA
* * * *
28398650 ATCTGTTTCGCTGTCGGTGTAGGAAGGCAAGATCTACTATTTTTAACCTACTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
*
28398715 GGGAGGCAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTGGTATCTTCG
* * *
28398738 ATCTGCTTCTCTGTCGGTGCAGGAGGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
*
28398803 GGGAGGCAAGGCTAGTATCTTCG
66 GGGAGGCAAGGCTGGTATCTTCG
* *
28398826 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTTCTCCGCTGTAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
28398891 GGGAGGCAAGGTTGTTATCTTCG
66 GGGAGGCAAGGCTGGTATCTTCG
* * *
28398914 ATCTGCTTCACTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGTTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
28398979 GGGAGGCAAGGCTGGTGTCTTTG
66 GGGAGGCAAGGCTGGTATCTTCG
28399002 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
28399047 CTGATCTGCT
Statistics
Matches: 281, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 281 1.00
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.29
Consensus pattern (88 bp):
ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
GGGAGGCAAGGCTGGTATCTTCG
Found at i:28399030 original size:44 final size:44
Alignment explanation
Indices: 28398713--28399041 Score: 155
Period size: 44 Copynumber: 7.5 Consensus size: 44
28398703 CGCTGCAACC
* * * * *
28398713 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCTCTGTCGGTG
1 CAGGAAGGCAAGGCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
* * * * * ****
28398757 CAGGAGGGCAAGATCTGCTAT-TTTTAGCCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTGCTATCTTTGA-TCTGCTTCGCTGTCGGTG
* *
28398801 CAGGGAGGCAAGGCTAG-TATCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCT-GCTATCTTTGATCTGCTTCGCTGTCGGTG
* * * * * * ****
28398845 CAGGAAGGCAAGATCTGCTATTTTTAACCTTCTCCGCTGT-AACC
1 CAGGAAGGCAAG-GCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
* * * * *
28398889 CAGGGAGGCAAGGTTGTTATCTTCGATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGGCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
* * * * * * * ****
28398933 TAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGTTG-CAACC
1 CAGGAAGGCAAG-GCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
* * *
28398977 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
*
28399021 CAGGAAGGCAAGATCTGCTAT
1 CAGGAAGGCAAG-GCTGCTAT
28399042 TTTTACTGAT
Statistics
Matches: 188, Mismatches: 86, Indels: 21
0.64 0.29 0.07
Matches are distributed among these distances:
43 50 0.27
44 85 0.45
45 53 0.28
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
Found at i:28400168 original size:42 final size:42
Alignment explanation
Indices: 28400121--28400223 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 42
28400111 TAGATTACCA
* * *
28400121 CATGCCCCAATCTGATCAAGATTCGAGTTGCTCTAATCACTT
1 CATGCCCCATTCTGATCAAGATTCGAGTCGCTCTAATCACCT
* * ** * *
28400163 CATGCCTCATTTTGATCACTATTTGAGTCGCTCTGATCACCT
1 CATGCCCCATTCTGATCAAGATTCGAGTCGCTCTAATCACCT
*
28400205 CATGTCCCATTCTGATCAA
1 CATGCCCCATTCTGATCAA
28400224 AATTTGAGCC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (42 bp):
CATGCCCCATTCTGATCAAGATTCGAGTCGCTCTAATCACCT
Found at i:28404813 original size:17 final size:17
Alignment explanation
Indices: 28404791--28404827 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 17
28404781 ATATTAGTTT
28404791 TAAAAATATAAATATACA
1 TAAAAA-ATAAATATACA
28404809 TAAAAAATAAATATACA
1 TAAAAAATAAATATACA
28404826 TA
1 TA
28404828 TATATATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAAATAAATATACA
Found at i:28404873 original size:3 final size:3
Alignment explanation
Indices: 28404865--28404907 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
28404855 GCATATGAAT
* * *
28404865 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATT ATA ATG ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28404908 CAATTTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:28404901 original size:15 final size:15
Alignment explanation
Indices: 28404868--28404912 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
28404858 TATGAATATA
* *
28404868 ATAATAATAATAGTA
1 ATAATAATAATAATT
28404883 ATAATAATAATAATT
1 ATAATAATAATAATT
* *
28404898 ATAATGATAACAATT
1 ATAATAATAATAATT
28404913 TATTTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (15 bp):
ATAATAATAATAATT
Found at i:28404940 original size:3 final size:3
Alignment explanation
Indices: 28404934--28404998 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
28404924 ATGAATTACA
28404934 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28404982 AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AA
28404999 ATGCAATTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28409583 original size:13 final size:14
Alignment explanation
Indices: 28409565--28409593 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28409555 TTGTTGCTGA
28409565 TTTTTCCC-CTTCT
1 TTTTTCCCTCTTCT
28409578 TTTTTCCCTCTTCT
1 TTTTTCCCTCTTCT
28409592 TT
1 TT
28409594 ACTTTGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTCCCTCTTCT
Found at i:28410508 original size:27 final size:27
Alignment explanation
Indices: 28410467--28410690 Score: 200
Period size: 27 Copynumber: 8.3 Consensus size: 27
28410457 AGGAATCATG
* * * *
28410467 GGTAAAATGATCGAATTACCCCCGAAA
1 GGTAAAATTACCGAAATACCCTCGAAA
*
28410494 GGTAAAATTACCGAAACACCCTC-AAA
1 GGTAAAATTACCGAAATACCCTCGAAA
* * *
28410520 GGGTAAAATTATCGAAATACCTTCGAAG
1 -GGTAAAATTACCGAAATACCCTCGAAA
**
28410548 GGTAAAATTACTAAAATACCCTCGAAA
1 GGTAAAATTACCGAAATACCCTCGAAA
* *
28410575 GGTAAAATTACCAAAATACCCTCGAAG
1 GGTAAAATTACCGAAATACCCTCGAAA
*** * *
28410602 GGTAAAATTTTTGAAATACCTTCAAAA
1 GGTAAAATTACCGAAATACCCTCGAAA
* * *
28410629 GATAAAATTACCAAAATACCC-CTGAAG
1 GGTAAAATTACCGAAATACCCTC-GAAA
* * * *
28410656 GGTAAAATTATCGAGATACCCCCGAAG
1 GGTAAAATTACCGAAATACCCTCGAAA
28410683 GGTAAAAT
1 GGTAAAAT
28410691 GATTGTTATT
Statistics
Matches: 158, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
26 4 0.03
27 151 0.96
28 3 0.02
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (27 bp):
GGTAAAATTACCGAAATACCCTCGAAA
Found at i:28410574 original size:81 final size:80
Alignment explanation
Indices: 28410486--28410690 Score: 275
Period size: 81 Copynumber: 2.5 Consensus size: 80
28410476 ATCGAATTAC
* * * * *
28410486 CCCCGAAAGGTAAAATTACCGAAACACCCTCAAAGGGTAAAATTATCGAAATACCTTCGAAGGGT
1 CCCCGAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAAATACCTTCAAAAGAT
*
28410551 AAAATTACTAAAATA
66 AAAATTACCAAAATA
* * *
28410566 CCCTCGAAAGGTAAAATTACCAAAATACCCTCGAAGGGTAAAATTTTTGAAATACCTTCAAAAGA
1 CCC-CGAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAAATACCTTCAAAAGA
28410631 TAAAATTACCAAAATA
65 TAAAATTACCAAAATA
* * * *
28410647 CCCCTGAAGGGTAAAATTATCGAGATACCCCCGAAGGGTAAAAT
1 CCCC-GAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAAT
28410691 GATTGTTATT
Statistics
Matches: 109, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
80 4 0.04
81 105 0.96
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (80 bp):
CCCCGAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAAATACCTTCAAAAGAT
AAAATTACCAAAATA
Found at i:28411122 original size:32 final size:30
Alignment explanation
Indices: 28411048--28411122 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 30
28411038 TAACTGCATT
*
28411048 GTACTGATTACTGTTTTGGGCTAGGGCCCAC
1 GTACTG-TTACTGTTTTGGGCTAGGCCCCAC
28411079 -TCACTGTTACTGTTTTGGGCTTA-GCCCACAC
1 GT-ACTGTTACTGTTTTGGGC-TAGGCCC-CAC
28411110 GGTACTGTTACTG
1 -GTACTGTTACTG
28411123 AATATGGCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
30 18 0.47
31 9 0.24
32 10 0.26
33 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (30 bp):
GTACTGTTACTGTTTTGGGCTAGGCCCCAC
Found at i:28411617 original size:20 final size:20
Alignment explanation
Indices: 28411592--28411632 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28411582 CCAAAATTAG
28411592 GAAACGACTTTTATCAACAA
1 GAAACGACTTTTATCAACAA
*
28411612 GAAACGAGTTTTATCAACAA
1 GAAACGACTTTTATCAACAA
28411632 G
1 G
28411633 TCTAAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (20 bp):
GAAACGACTTTTATCAACAA
Found at i:28416923 original size:20 final size:20
Alignment explanation
Indices: 28416898--28416936 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28416888 TAAACGCAAA
28416898 TGAGCTTAA-AATGAGCTGAT
1 TGAGC-TAAGAATGAGCTGAT
*
28416918 TGAGCTAAGAGTGAGCTGA
1 TGAGCTAAGAATGAGCTGA
28416937 ATGAACTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (20 bp):
TGAGCTAAGAATGAGCTGAT
Found at i:28418871 original size:17 final size:19
Alignment explanation
Indices: 28418839--28418888 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
28418829 GAACACACTC
*
28418839 TCTTCCTTCATCTTTTC-TTT
1 TCTT-CTTC-TCTTTTCAGTT
28418859 TCTTCTT-TCTTTTCAGTT
1 TCTTCTTCTCTTTTCAGTT
28418877 TCTTCTTCTCTT
1 TCTTCTTCTCTT
28418889 GTTGCCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.26
18 9 0.33
19 7 0.26
20 4 0.15
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.66
Consensus pattern (19 bp):
TCTTCTTCTCTTTTCAGTT
Found at i:28419836 original size:27 final size:27
Alignment explanation
Indices: 28419794--28419969 Score: 205
Period size: 27 Copynumber: 6.5 Consensus size: 27
28419784 TACGAATCGT
*
28419794 GGGTAAAATGACTGAAATACCCTCGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
* **
28419821 GGGTAAAATTATTGAAATACCCTTAAA
1 GGGTAAAATTACTGAAATACCCTCGAA
* *
28419848 AGGTAAAATTACTGAAATACACTCGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
**
28419875 GAATAAAATTA-TCGAAATACCCTCGAA
1 GGGTAAAATTACT-GAAATACCCTCGAA
*
28419902 GGGTAAAATTACTGAAATACCC-CTAAA
1 GGGTAAAATTACTGAAATACCCTC-GAA
*
28419929 GGGTAAAATTACTGAGATACCC-CTGAA
1 GGGTAAAATTACTGAAATACCCTC-GAA
*
28419956 GGGTAAAATGACTG
1 GGGTAAAATTACTG
28419970 TTATACCCCT
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.02
27 124 0.98
28 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (27 bp):
GGGTAAAATTACTGAAATACCCTCGAA
Found at i:28419977 original size:81 final size:81
Alignment explanation
Indices: 28419794--28419969 Score: 248
Period size: 81 Copynumber: 2.2 Consensus size: 81
28419784 TACGAATCGT
* *
28419794 GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATTATTGAAATACCCTTAAAAGGTAAAATTA
1 GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTAAAAGGTAAAATTA
28419859 CTGAAATACACTCGAA
66 CTGAAATACACTCGAA
** * *
28419875 GAATAAAATTA-TCGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTAAAGGGTAAAATT
1 GGGTAAAATGACT-GAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTAAAAGGTAAAATT
* *
28419939 ACTGAGATAC-CCCTGAA
65 ACTGAAATACACTC-GAA
28419956 GGGTAAAATGACTG
1 GGGTAAAATGACTG
28419970 TTATACCCCT
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.04
81 77 0.95
82 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (81 bp):
GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTAAAAGGTAAAATTA
CTGAAATACACTCGAA
Found at i:28420202 original size:26 final size:26
Alignment explanation
Indices: 28420147--28420219 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
28420137 ACATATACTG
* ** * *
28420147 TTACTGGCAGCCTTGCTGTATTATTG
1 TTACTGGCAGCTTTGCTGCGTCATTA
28420173 TTACTGGCAGCTTTGCTGCGTCATTA
1 TTACTGGCAGCTTTGCTGCGTCATTA
* *
28420199 TTACTGGTAGCTCTGCTGCGT
1 TTACTGGCAGCTTTGCTGCGT
28420220 TATTGGTGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.40
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCGTCATTA
Found at i:28424868 original size:13 final size:13
Alignment explanation
Indices: 28424852--28424901 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
28424842 TTTAAACCAA
28424852 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
* *
28424865 ACTTCTCAAAAGC
1 ACTTTTCAAAAAC
* *
28424878 ACTTTTCTATAAC
1 ACTTTTCAAAAAC
28424891 ACTTTTCAAAA
1 ACTTTTCAAAA
28424902 GTATTGCCAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:28424891 original size:26 final size:26
Alignment explanation
Indices: 28424852--28424902 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
28424842 TTTAAACCAA
28424852 ACTTTTCAAAAACACTTCTCAAAAGC
1 ACTTTTCAAAAACACTTCTCAAAAGC
* * *
28424878 ACTTTTCTATAACACTTTTCAAAAG
1 ACTTTTCAAAAACACTTCTCAAAAG
28424903 TATTGCCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (26 bp):
ACTTTTCAAAAACACTTCTCAAAAGC
Found at i:28425195 original size:7 final size:7
Alignment explanation
Indices: 28425185--28425220 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
28425175 ATAATTTTCA
28425185 AAAATTT
1 AAAATTT
28425192 AAAATTT
1 AAAATTT
28425199 AAAATTT
1 AAAATTT
28425206 AAAATTT
1 AAAATTT
28425213 AAAATTT
1 AAAATTT
28425220 A
1 A
28425221 GTATTTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAAATTT
Found at i:28429481 original size:50 final size:50
Alignment explanation
Indices: 28429415--28429603 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 50
28429405 ATTATTATCA
* * *
28429415 TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGATCAAACTT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACTT
* * * *
28429465 TTCGGTTCACGTAGTAGCCTGCACATAATACTACACACGTGACCAAAGCCT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAA-CTT
* * * *
28429516 TCCGGTACACATAGTAGACTGCACATAGTACTACACATGTGACCATTA-TCT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-AACT-T
* * *
28429567 ATCGATACACGTAGTAGCCTGCACTTAGTACTACACA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACA
28429604 CGTGTTTATA
Statistics
Matches: 115, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
50 41 0.36
51 73 0.63
52 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACTT
Found at i:28432155 original size:22 final size:20
Alignment explanation
Indices: 28432112--28432150 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28432102 AATTTAAAAA
*
28432112 TATAAAAATTTATTAATATG
1 TATATAAATTTATTAATATG
28432132 TATATAAATTTATTAATAT
1 TATATAAATTTATTAATAT
28432151 ATGTAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATAAATTTATTAATATG
Found at i:28432290 original size:14 final size:14
Alignment explanation
Indices: 28432271--28432308 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
28432261 CTAGAAAAGT
28432271 AAATCATTTTTCAG
1 AAATCATTTTTCAG
*
28432285 AAATCATTTTTCGG
1 AAATCATTTTTCAG
*
28432299 AAAACATTTT
1 AAATCATTTT
28432309 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (14 bp):
AAATCATTTTTCAG
Found at i:28434723 original size:12 final size:12
Alignment explanation
Indices: 28434706--28434731 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28434696 TTAAAATATG
28434706 TTAGTTTTATCA
1 TTAGTTTTATCA
28434718 TTAGTTTTATCA
1 TTAGTTTTATCA
28434730 TT
1 TT
28434732 TATCAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTAGTTTTATCA
Found at i:28436371 original size:6 final size:6
Alignment explanation
Indices: 28436360--28436423 Score: 92
Period size: 6 Copynumber: 10.3 Consensus size: 6
28436350 GAAGTTTAAG
* *
28436360 AAATAA AAATAAA AAATAA AAAAAA ATAAAAA AAATAA AAATAA AAATAA
1 AAATAA AAAT-AA AAATAA AAATAA A-AATAA AAATAA AAATAA AAATAA
28436410 AAATAA AAATAA AA
1 AAATAA AAATAA AA
28436424 GAAATAAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
6 42 0.78
7 12 0.22
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:28436385 original size:12 final size:12
Alignment explanation
Indices: 28436364--28436433 Score: 77
Period size: 12 Copynumber: 5.5 Consensus size: 12
28436354 TTTAAGAAAT
28436364 AAAAATAAAAAA
1 AAAAATAAAAAA
*
28436376 TAAAAAAAAATAAA
1 -AAAAATAAA-AAA
*
28436390 AAAAATAAAAAT
1 AAAAATAAAAAA
*
28436402 AAAAATAAAAAT
1 AAAAATAAAAAA
28436414 AAAAATAAAAGAA
1 AAAAATAAAA-AA
28436427 ATAAAAT
1 A-AAAAT
28436434 CAATGATCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
12 24 0.48
13 18 0.36
14 8 0.16
ACGTcount: A:0.84, C:0.00, G:0.01, T:0.14
Consensus pattern (12 bp):
AAAAATAAAAAA
Found at i:28436403 original size:38 final size:38
Alignment explanation
Indices: 28436360--28436433 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
28436350 GAAGTTTAAG
*
28436360 AAATAAAAATAAAAAATAAAAA-AAAATAAAAAAAATAA
1 AAATAAAAAT-AAAAATAAAAATAAAAGAAAAAAAATAA
*
28436398 AAATAAAAATAAAAATAAAAATAAAAGAAATAAAAT
1 AAATAAAAATAAAAATAAAAATAAAAGAAAAAAAAT
28436434 CAATGATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.84, C:0.00, G:0.01, T:0.15
Consensus pattern (38 bp):
AAATAAAAATAAAAATAAAAATAAAAGAAAAAAAATAA
Found at i:28436433 original size:32 final size:32
Alignment explanation
Indices: 28436357--28436432 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 32
28436347 AAAGAAGTTT
28436357 AAGAAATAAAAATAAAAAATAAAAAAAAATAA
1 AAGAAATAAAAATAAAAAATAAAAAAAAATAA
*
28436389 AAAAAATAAAAAT-AAAAATAAAAATAAAAATAA
1 AAGAAATAAAAATAAAAAAT-AAAA-AAAAATAA
28436422 AAGAAATAAAA
1 AAGAAATAAAA
28436433 TCAATGATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 6 0.15
32 16 0.40
33 18 0.45
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (32 bp):
AAGAAATAAAAATAAAAAATAAAAAAAAATAA
Found at i:28444959 original size:29 final size:29
Alignment explanation
Indices: 28444927--28444995 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
28444917 GCCACAAAGC
* *
28444927 CTCACATATATCAAATTTCT-CCACTAGAG
1 CTCACATATA-AAAAATTCTGCCACTAGAG
* * *
28444956 CTCATATATAAAAAATTCTGCCACTGGGG
1 CTCACATATAAAAAATTCTGCCACTAGAG
28444985 CTCACATATAA
1 CTCACATATAA
28444996 TAGAAAAGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (29 bp):
CTCACATATAAAAAATTCTGCCACTAGAG
Found at i:28467450 original size:50 final size:50
Alignment explanation
Indices: 28467396--28467494 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
28467386 AGGATTAATC
* *
28467396 AAGATGCAAACTAAATAAACAAATGAGTTACGTAATGCATAACATAATTT
1 AAGATGCAAACTAAATAAACAAAGGAGTTACATAATGCATAACATAATTT
* * * *
28467446 AAGATGCAAACTTAATTAACATAGGAGTTACATAATGCATGACATAATT
1 AAGATGCAAACTAAATAAACAAAGGAGTTACATAATGCATAACATAATT
28467495 AAAACACAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.27
Consensus pattern (50 bp):
AAGATGCAAACTAAATAAACAAAGGAGTTACATAATGCATAACATAATTT
Found at i:28495547 original size:29 final size:29
Alignment explanation
Indices: 28495506--28495564 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
28495496 TCCTTTCTCC
*
28495506 TCCTCCTTGCTATTCTGTCTTTCTATTTT
1 TCCTCCTTGCTATTCTGTCTATCTATTTT
28495535 TCCTCCTTGCTATTCTGTCTATCTATTTT
1 TCCTCCTTGCTATTCTGTCTATCTATTTT
28495564 T
1 T
28495565 TCTATTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.08, C:0.27, G:0.07, T:0.58
Consensus pattern (29 bp):
TCCTCCTTGCTATTCTGTCTATCTATTTT
Found at i:28496513 original size:1 final size:1
Alignment explanation
Indices: 28496507--28496534 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
28496497 TTTGATCTCC
28496507 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
28496535 GCCTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28514644 original size:39 final size:39
Alignment explanation
Indices: 28514590--28514759 Score: 250
Period size: 39 Copynumber: 4.4 Consensus size: 39
28514580 GACGGCAAAA
*
28514590 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCATGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
* * * * * *
28514629 AAGTGTGATTAGGGGTACCGAAGTACAATAAGGACACAT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
* *
28514668 AAGTGCGATCAGGGGTATCGAAGTACAATAGGGGCACGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
*
28514707 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCATGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
28514746 AAGTGCGATCAGGG
1 AAGTGCGATCAGGG
28514760 TATAATTATA
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 115 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.17
Consensus pattern (39 bp):
AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
Found at i:28514710 original size:19 final size:19
Alignment explanation
Indices: 28514688--28514749 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
28514678 AGGGGTATCG
28514688 AAGTACAATAGGGGCACGT
1 AAGTACAATAGGGGCACGT
* * *
28514707 AAGTGCGATCAGGGGTACCG-
1 AAGTACAAT-AGGGGCA-CGT
* *
28514727 AAGTACAACAGGGGCATGT
1 AAGTACAATAGGGGCACGT
28514746 AAGT
1 AAGT
28514750 GCGATCAGGG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 12 0.38
21 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (19 bp):
AAGTACAATAGGGGCACGT
Found at i:28514730 original size:20 final size:20
Alignment explanation
Indices: 28514590--28514730 Score: 76
Period size: 20 Copynumber: 7.2 Consensus size: 20
28514580 GACGGCAAAA
28514590 AAGTGCGATCAGGGGTACCG
1 AAGTGCGATCAGGGGTACCG
* * * *
28514610 AAGTAC-AACAGGGGCA-TG
1 AAGTGCGATCAGGGGTACCG
* *
28514628 TAAGTGTGATTAGGGGTACCG
1 -AAGTGCGATCAGGGGTACCG
* * * ** **
28514649 AAGTACAAT-AAGGACACAT
1 AAGTGCGATCAGGGGTACCG
*
28514668 AAGTGCGATCAGGGGTATCG
1 AAGTGCGATCAGGGGTACCG
* * *
28514688 AAGTACAAT-AGGGGCA-CG
1 AAGTGCGATCAGGGGTACCG
28514706 TAAGTGCGATCAGGGGTACCG
1 -AAGTGCGATCAGGGGTACCG
28514727 AAGT
1 AAGT
28514731 ACAACAGGGG
Statistics
Matches: 82, Mismatches: 32, Indels: 14
0.64 0.25 0.11
Matches are distributed among these distances:
18 3 0.04
19 37 0.45
20 39 0.48
21 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.34, T:0.18
Consensus pattern (20 bp):
AAGTGCGATCAGGGGTACCG
Found at i:28523824 original size:17 final size:17
Alignment explanation
Indices: 28523804--28523836 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28523794 TAGAATTAGG
28523804 TTGAGAAAATAATTTAA
1 TTGAGAAAATAATTTAA
28523821 TTGAGAAAATAATTTA
1 TTGAGAAAATAATTTA
28523837 GTTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
TTGAGAAAATAATTTAA
Found at i:28526624 original size:249 final size:250
Alignment explanation
Indices: 28525986--28526985 Score: 1215
Period size: 249 Copynumber: 4.0 Consensus size: 250
28525976 TATTCGTTTG
* *
28525986 TAAACTTGTAATTTTTTTTGAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATAC
1 TAAACTTGTAA-TTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATAC
* * * * **
28526051 TTTGTATGATTGTCCTCGTACGGTTTTTGCACGCAAAGCAAAATGGAAGCAAATGTTGGTCATTG
65 TTTTTATGATTTTCCTCGTACGGTTTTTGCACACAAAGAAAAATGGAAGCAAATGTTACTCATTG
** * * * *
28526116 GTTGTCTAAAATTTAAACTAATACTAAGC-AGTATTATATGGCCGGATTGTAATACAGAAAGACA
130 GTTGTCTAACGTTTAAACTAATACTAATCGA-TATTACATGGCCGGATCGTAATACAGAAAAACA
* * * * *
28526180 ACTTACATTACTCGATGAAACTTAACATGTCCTTAGTCTAATCGAAAACGAGCAAAC
194 ACTTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCAAAC
* *
28526237 TAAAATTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATCCATGGATTACATTAATATA-T
1 TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
* * ** * * *
28526301 TTTGTATGACTTTCCTTGTATAGTTTTTGCAGGA-AAAGAAAAATGGAAGAAAATGTTGCTCATT
66 TTT-TATGATTTTCCTCGTACGGTTTTTGCA-CACAAAGAAAAATGGAAGCAAATGTTACTCATT
* * ** *
28526365 GGTTGTCTAACGTTTAAACTAATACTAATCGACATTACATGACTAGATCGTAATATAGAAAAACA
129 GGTTGTCTAACGTTTAAACTAATACTAATCGATATTACATGGCCGGATCGTAATACAGAAAAACA
* * *
28526430 ACTTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCAGAAATGAGCAAAA
194 ACTTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCAAAC
*
28526487 TAAACTTGTAA-TTTTTCAAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
1 TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
* * * * * *
28526551 TTTTACGATTTTCCTCATACGGTTTTTGCATACAAAGGAAAATGGAAGCAAATGCTACTTATTGG
66 TTTTATGATTTTCCTCGTACGGTTTTTGCACACAAAGAAAAATGGAAGCAAATGTTACTCATTGG
* * * *
28526616 TTGTCTAACGTTTAAACTAATACTAAGT-GGTATTACATGGCCGGATTGTAATATAGAAAGACAA
131 TTGTCTAACGTTTAAACTAATACTAA-TCGATATTACATGGCCGGATCGTAATACAGAAAAACAA
* * * * * *
28526680 CTTATATTAGTAGACGGAACTTAACATGTCCTTAACCCAATTGGAAATGAGCAAAC
195 CTTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCAAAC
* * *
28526736 TAAACTTGTAATTTTTTTTTTGAAAAGATTAAATAATAAATA-AAATTCTTGGATTACATTAATA
1 TAAACTTGTAA---TTTTTTCGAAAAGATTGAATAATAAA-ACAAATTCATGGATTACATTAATA
* * * *
28526800 TACATTTTATGATTTTCCTTGTACGGTTTTTGCACGCAAAGAAAAATGAAAGCAAATGTTACTCA
62 TACTTTTTATGATTTTCCTCGTACGGTTTTTGCACACAAAGAAAAATGGAAGCAAATGTTACTCA
* * * *
28526865 TTGGTTGTCTAACGTTTAAACTAATACTAAACGGTATTAAATGGCTGGATCGTAATACA-AAAAG
127 TTGGTTGTCTAACGTTTAAACTAATACTAATCGATATTACATGGCCGGATCGTAATACAGAAAA-
* * * * * *
28526929 ACAACTAATATTAGTA-TTCGAAACTAAACATGACTTTAGTCTAATCGGAAACGAGCA
191 ACAACTTATATTAGTAGAT-GAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCA
28526986 TACCGATTGA
Statistics
Matches: 640, Mismatches: 95, Indels: 26
0.84 0.12 0.03
Matches are distributed among these distances:
248 1 0.00
249 215 0.34
250 214 0.33
251 11 0.02
252 3 0.00
253 195 0.30
254 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (250 bp):
TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
TTTTATGATTTTCCTCGTACGGTTTTTGCACACAAAGAAAAATGGAAGCAAATGTTACTCATTGG
TTGTCTAACGTTTAAACTAATACTAATCGATATTACATGGCCGGATCGTAATACAGAAAAACAAC
TTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCAAAC
Found at i:28526750 original size:499 final size:501
Alignment explanation
Indices: 28525986--28526985 Score: 1355
Period size: 499 Copynumber: 2.0 Consensus size: 501
28525976 TATTCGTTTG
**
28525986 TAAACTTGTAATTTTTTTTGAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATAC
1 TAAACTTGTAA-TTTTTTCAAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATAC
* * * * **
28526051 TTTGTATGATTGTCCTCGTACGGTTTTTGCACGCAAAGCAAAATGGAAGCAAATGTTGGTCATTG
65 TTTGTACGATTGTCCTCATACGGTTTTTGCACACAAAGCAAAATGGAAGCAAATGCTACTCATTG
*
28526116 GTTGTCTAAAATTTAAACTAATACTAAGCAGTATTATATGGCCGGATTGTAATACAGAAAGACAA
130 GTTGTCTAAAATTTAAACTAATACTAAGCAGTATTACATGGCCGGATTGTAATACAGAAAGACAA
* * ** *
28526181 CTTACATTACTCGATGAAACTTAACATGTCCTTAGTCTAATCGAAAACGAGCAAACTAAAATTGT
195 CTTACATTACTAGACGAAACTTAACATGTCCTTAACCCAATCGAAAACGAGCAAACTAAAATTGT
* *
28526246 AA-TTTTTTCGAAAAGATTGAATAATAAA-ACAAATCCATGGATTACATTAATATA-TTTTGTAT
260 AATTTTTTTCGAAAAGATTAAATAATAAATA-AAATCCATGGATTACATTAATATACATTT-TAT
* * * *
28526308 GACTTTCCTTGTATAGTTTTTGCAGGAAAAGAAAAATGGAAGAAAATGTTGCTCATTGGTTGTCT
323 GACTTTCCTTGTACAGTTTTTGCACGAAAAGAAAAATGAAAGAAAATGTTACTCATTGGTTGTCT
* * * *
28526373 AACGTTTAAACTAATACTAATCGACATTACATGACTAGATCGTAATATAGAAAA-ACAACTTATA
388 AACGTTTAAACTAATACTAAACGACATTAAATGACTAGATCGTAATACA-AAAAGACAACTAATA
* * *
28526437 TTAGTAGAT-GAAACTTAACATGTCCTTAATCTAATCAGAAATGAGCAAAA
452 TTAGTA-ATCGAAACTAAACATGACCTTAATCTAATCAGAAACGAGCAAAA
*
28526487 TAAACTTGTAA-TTTTTCAAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
1 TAAACTTGTAATTTTTTCAAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATACT
* * * * *
28526551 TTTTACGATTTTCCTCATACGGTTTTTGCATACAAAGGAAAATGGAAGCAAATGCTACTTATTGG
66 TTGTACGATTGTCCTCATACGGTTTTTGCACACAAAGCAAAATGGAAGCAAATGCTACTCATTGG
** ** *
28526616 TTGTCTAACGTTTAAACTAATACTAAGTGGTATTACATGGCCGGATTGTAATATAGAAAGACAAC
131 TTGTCTAAAATTTAAACTAATACTAAGCAGTATTACATGGCCGGATTGTAATACAGAAAGACAAC
* * * * * * *
28526681 TTATATTAGTAGACGGAACTTAACATGTCCTTAACCCAATTGGAAATGAGCAAACTAAACTTGTA
196 TTACATTACTAGACGAAACTTAACATGTCCTTAACCCAATCGAAAACGAGCAAACTAAAATTGTA
* * *
28526746 ATTTTTTTTTTGAAAAGATTAAATAATAAATAAAATTCTTGGATTACATTAATATACATTTTATG
261 A--TTTTTTTCGAAAAGATTAAATAATAAATAAAATCCATGGATTACATTAATATACATTTTATG
* * * *
28526811 ATTTTCCTTGTACGGTTTTTGCACGCAAAGAAAAATGAAAGCAAATGTTACTCATTGGTTGTCTA
324 ACTTTCCTTGTACAGTTTTTGCACGAAAAGAAAAATGAAAGAAAATGTTACTCATTGGTTGTCTA
** * *
28526876 ACGTTTAAACTAATACTAAACGGTATTAAATGGCTGGATCGTAATACAAAAAGACAACTAATATT
389 ACGTTTAAACTAATACTAAACGACATTAAATGACTAGATCGTAATACAAAAAGACAACTAATATT
* * * *
28526941 AGTATTCGAAACTAAACATGACTTTAGTCTAATCGGAAACGAGCA
454 AGTAATCGAAACTAAACATGACCTTAATCTAATCAGAAACGAGCA
28526986 TACCGATTGA
Statistics
Matches: 432, Mismatches: 60, Indels: 13
0.86 0.12 0.03
Matches are distributed among these distances:
499 217 0.50
501 16 0.04
502 195 0.45
503 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (501 bp):
TAAACTTGTAATTTTTTCAAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATACT
TTGTACGATTGTCCTCATACGGTTTTTGCACACAAAGCAAAATGGAAGCAAATGCTACTCATTGG
TTGTCTAAAATTTAAACTAATACTAAGCAGTATTACATGGCCGGATTGTAATACAGAAAGACAAC
TTACATTACTAGACGAAACTTAACATGTCCTTAACCCAATCGAAAACGAGCAAACTAAAATTGTA
ATTTTTTTCGAAAAGATTAAATAATAAATAAAATCCATGGATTACATTAATATACATTTTATGAC
TTTCCTTGTACAGTTTTTGCACGAAAAGAAAAATGAAAGAAAATGTTACTCATTGGTTGTCTAAC
GTTTAAACTAATACTAAACGACATTAAATGACTAGATCGTAATACAAAAAGACAACTAATATTAG
TAATCGAAACTAAACATGACCTTAATCTAATCAGAAACGAGCAAAA
Found at i:28530134 original size:46 final size:46
Alignment explanation
Indices: 28530046--28530216 Score: 283
Period size: 46 Copynumber: 3.8 Consensus size: 46
28530036 TGGAATGAAA
* *
28530046 GTATGGTATTTTAGTAAAG--AACCATACTCAGTTGTGAAAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
*
28530090 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAGAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
*
28530136 GTATGGTATTTCAGTAACGAAAACCATACTGAGTTGTGAAAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
*
28530182 GTATGGTATTTCAGTGAAGAAAACCATACTGAGTT
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
28530217 ATAGCATTGT
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
44 18 0.15
46 100 0.85
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (46 bp):
GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
Found at i:28547345 original size:132 final size:132
Alignment explanation
Indices: 28547123--28547382 Score: 389
Period size: 132 Copynumber: 2.0 Consensus size: 132
28547113 AAAATAAAGA
* *
28547123 GACTTTTATTCTCTAAAAATTAAATATATTTTCCGGAATAACTATTCTATCGGTTTCTATTTGAG
1 GACTTTTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATCGGTTTCTATTTAAG
*
28547188 AAAAGAATTTTTCTTTTCACTTCAAAAGAAAAGAAAACTATTTCTAATTTCTGTGTTTGATTCAA
66 AAAAGAATTTTTCTTTTCACCTCAAAAGAAAAGAAAACTATTTCTAATTTCTGTGTTTGATTCAA
28547253 AT
131 AT
* * *
28547255 GACTTTTATTCTCTAAGAATTAAATATATTTTTCGGAATAACGATTCTATCTGTCTT-TATTTAA
1 GACTTTTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATCGGT-TTCTATTTAA
* * * * *
28547319 GAAGAGAA-TTTTCATTTTCACCTCAAAAGAAAATAAAGCTATTTCTAGTTTTTGTGTTTGATTC
65 GAAAAGAATTTTTC-TTTTCACCTCAAAAGAAAAGAAAACTATTTCTAATTTCTGTGTTTGATTC
28547383 GATTTGATTG
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
131 5 0.04
132 108 0.94
133 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (132 bp):
GACTTTTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATCGGTTTCTATTTAAG
AAAAGAATTTTTCTTTTCACCTCAAAAGAAAAGAAAACTATTTCTAATTTCTGTGTTTGATTCAA
AT
Found at i:28552153 original size:18 final size:18
Alignment explanation
Indices: 28552132--28552190 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
28552122 GAAACCCATA
28552132 TTATTATGCGAACCTTTG
1 TTATTATGCGAACCTTTG
* *
28552150 TTATTATGC-AAACTTACG
1 TTATTATGCGAACCTT-TG
* * *
28552168 TTTTTATGTGAACCTATG
1 TTATTATGCGAACCTTTG
28552186 TTATT
1 TTATT
28552191 TTCCGAACCC
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
17 5 0.16
18 22 0.71
19 4 0.13
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (18 bp):
TTATTATGCGAACCTTTG
Found at i:28552217 original size:36 final size:36
Alignment explanation
Indices: 28552123--28552217 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 36
28552113 TCTTTTTTCG
** * *
28552123 AAACCCATATTATTATGCGAACCTTTGTTATTATGC
1 AAACCCACGTTATTATGCGAACCTATGTTATTATCC
** * * *
28552159 AAACTTACGTTTTTATGTGAACCTATGTTATTTTCC
1 AAACCCACGTTATTATGCGAACCTATGTTATTATCC
* *
28552195 GAACCCACGTTATTGTGCGAACC
1 AAACCCACGTTATTATGCGAACC
28552218 CTAACATTAA
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (36 bp):
AAACCCACGTTATTATGCGAACCTATGTTATTATCC
Found at i:28554750 original size:44 final size:42
Alignment explanation
Indices: 28554700--28554812 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 42
28554690 GGTGCTTCGG
* *** *
28554700 TGGCATTCTATTAACCTTTATGGTGTATTTTGATTTGGCCTTTA
1 TGGCATTCTATTAGCCTTTATGGCACATTTT-A-TTAGCCTTTA
*
28554744 TGGCATTCTGATCTAGCCTTTGTGGCACATTTTATTAGCCTTTA
1 TGGCATTCT-AT-TAGCCTTTATGGCACATTTTATTAGCCTTTA
* *
28554788 TGGCATTCTACTAGCCTTTGTGGCA
1 TGGCATTCTATTAGCCTTTATGGCA
28554813 TGTTCTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 14 0.23
43 1 0.02
44 27 0.45
45 3 0.05
46 15 0.25
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (42 bp):
TGGCATTCTATTAGCCTTTATGGCACATTTTATTAGCCTTTA
Found at i:28554762 original size:22 final size:21
Alignment explanation
Indices: 28554737--28554813 Score: 86
Period size: 20 Copynumber: 3.6 Consensus size: 21
28554727 TTTTGATTTG
28554737 GCCTTTATGGCATTCTGATCTA
1 GCCTTTATGGCATTCT-ATCTA
* *
28554759 GCCTTTGTGGCACATTTTAT-TA
1 GCCTTTATGG--CATTCTATCTA
28554781 GCCTTTATGGCATTCTA-CTA
1 GCCTTTATGGCATTCTATCTA
*
28554801 GCCTTTGTGGCAT
1 GCCTTTATGGCAT
28554814 GTTCTATATG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
20 20 0.43
22 20 0.43
23 2 0.04
24 5 0.11
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (21 bp):
GCCTTTATGGCATTCTATCTA
Found at i:28556855 original size:19 final size:19
Alignment explanation
Indices: 28556831--28556870 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
28556821 ACATAAAATA
*
28556831 AACTAAGTAAAAACTTAAG
1 AACTAAATAAAAACTTAAG
28556850 AACTAAATAAAAACTTAAG
1 AACTAAATAAAAACTTAAG
28556869 AA
1 AA
28556871 TCAATCCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (19 bp):
AACTAAATAAAAACTTAAG
Found at i:28560558 original size:12 final size:12
Alignment explanation
Indices: 28560541--28560575 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
28560531 TTGGCCCGCC
28560541 TATATTAATTTT
1 TATATTAATTTT
*
28560553 TATATTATTTTT
1 TATATTAATTTT
28560565 TATA-TAATTTT
1 TATATTAATTTT
28560576 AAAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:28560733 original size:30 final size:30
Alignment explanation
Indices: 28560699--28560760 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
28560689 CTTAACAAGA
*
28560699 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAAGAACAAAATTAAC
* *
28560729 AAATGTCTTTAAAATAAGAACAAAATTAAC
1 AAATGCCTCTAAAATAAGAACAAAATTAAC
28560759 AA
1 AA
28560761 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.24
Consensus pattern (30 bp):
AAATGCCTCTAAAATAAGAACAAAATTAAC
Found at i:28562725 original size:69 final size:69
Alignment explanation
Indices: 28562595--28562736 Score: 178
Period size: 69 Copynumber: 2.1 Consensus size: 69
28562585 ACTGCCTTTG
* ****
28562595 GTTTCCTCCTTTCGTCTCTACTCAGCTGCTACACTCTATTGTTGCCTTTGGATCTCTACACCATT
1 GTTTCCTCCTTTCGTCCCTACTCAGCTGCTACACTCTATTGTTGCCTCCAAATCTCTACACCATT
28562660 TAGA
66 TAGA
* * * *
28562664 GTTTCCTCCTTTCGTCCCTACTCAGTTGCTACCCTTTATTGTTGCCTCCAAATCT-TCACACCCT
1 GTTTCCTCCTTTCGTCCCTACTCAGCTGCTACACTCTATTGTTGCCTCCAAATCTCT-ACACCAT
*
28562728 TTAGG
65 TTAGA
28562733 GTTT
1 GTTT
28562737 TTCCTCTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
68 1 0.02
69 61 0.98
ACGTcount: A:0.15, C:0.32, G:0.13, T:0.41
Consensus pattern (69 bp):
GTTTCCTCCTTTCGTCCCTACTCAGCTGCTACACTCTATTGTTGCCTCCAAATCTCTACACCATT
TAGA
Found at i:28564821 original size:26 final size:26
Alignment explanation
Indices: 28564785--28564849 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
28564775 TTACATCAAC
28564785 GCTCACACGAGCTATGAAATGGGTCT
1 GCTCACACGAGCTATGAAATGGGTCT
28564811 GCTCACACGAGCTATGAAATGGGTCT
1 GCTCACACGAGCTATGAAATGGGTCT
28564837 GCTCACACGAGCT
1 GCTCACACGAGCT
28564850 GTGGGTCGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (26 bp):
GCTCACACGAGCTATGAAATGGGTCT
Found at i:28570359 original size:23 final size:22
Alignment explanation
Indices: 28570315--28570647 Score: 332
Period size: 23 Copynumber: 14.9 Consensus size: 22
28570305 AGGATGCTAG
28570315 TTAAGGGTTTAGGG-TTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
28570336 TTCAAGGGTTTAGGGTTTTTAAT
1 TT-AAGGGTTTAGGGTTTTTAAT
* **** *
28570359 TAAATTAAATTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
28570382 TTAAGGGCTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
28570405 TTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
28570427 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
28570450 TTAAGGGCTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
28570473 TTAAGGGTTTA-GGTTTTATAAT
1 TTAAGGGTTTAGGGTTTT-TAAT
* *
28570495 TTAAGGG-TTAGAGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
* *
28570516 TTAAGGG-TTAAGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
* *
28570537 TTAAGGATTTAGTGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
28570560 TTAAGGGTTTAGGATTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
28570582 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
28570605 TTAAAGGTTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
28570628 TTAAGGATTTAGGGTTTTTA
1 TTAAGGGTTTAGGGTTTTTA
28570648 GGTAATAACT
Statistics
Matches: 255, Mismatches: 45, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
21 33 0.13
22 94 0.37
23 128 0.50
ACGTcount: A:0.27, C:0.01, G:0.24, T:0.48
Consensus pattern (22 bp):
TTAAGGGTTTAGGGTTTTTAAT
Found at i:28570421 original size:68 final size:68
Alignment explanation
Indices: 28570313--28570559 Score: 328
Period size: 68 Copynumber: 3.7 Consensus size: 68
28570303 GCAGGATGCT
* *
28570313 AGTTAAGGGTTTAGGG-TTTTAATTTCAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTT
1 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTT
28570377 TTA
66 TTA
**
28570380 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAGGGTTT
1 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTT
28570445 TTA
66 TTA
* * *
28570448 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTA-GG-TTTT-A-TAATTTAAGGGTTAGAGT
1 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAA--ATTAGGGT
28570509 TTTTA
64 TTTTA
* * * *
28570514 AGTTAAGGG-TTAAGGTTTTTAA-GTTAAGGATTTAGTGTTTTTAATT
1 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATT
28570560 TTAAGGGTTT
Statistics
Matches: 161, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
64 16 0.10
65 14 0.09
66 28 0.17
67 18 0.11
68 85 0.53
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (68 bp):
AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTT
TTA
Found at i:28570639 original size:45 final size:44
Alignment explanation
Indices: 28570315--28570647 Score: 316
Period size: 45 Copynumber: 7.5 Consensus size: 44
28570305 AGGATGCTAG
* *
28570315 TTAAGGGTTTAGGG-TTTTAATTTCAAGGGTTTAGGGTTTTTAAT
1 TTAAGGATTTAGGGTTTTTAAGTT-AAGGGTTTAGGGTTTTTAAT
* ** * *
28570359 TAAATTAAATTAGGGTTTTTAAGTTAAGGGCTTAGGGTTTTTAATT
1 TTAA-GGATTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAA-T
* ** *
28570405 TTAAGGGTTTAGGGTTTTTAA-TTAAATTAGTTTAGGGTTTTTAAG
1 TTAAGGATTTAGGGTTTTTAAGTT-AA-GGGTTTAGGGTTTTTAAT
** *
28570450 TTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTA-GGTTTTATAAT
1 TTAAGGATTTAGGGTTTTTAA-GTTAAGGGTTTAGGGTTTT-TAAT
* * * *
28570495 TTAAGG-GTTAGAGTTTTTAAGTTAAGGG-TTAAGGTTTTTAAG
1 TTAAGGATTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAT
* * *
28570537 TTAAGGATTTAGTGTTTTTAATTTTAAGGGTTTAGGATTTTTAAT
1 TTAAGGATTTAGGGTTTTTAA-GTTAAGGGTTTAGGGTTTTTAAT
* ** *
28570582 TAAATTAGTTTAGGGTTTTTAAGTTAAAGGTTTAGGGTTTTTAATT
1 TTAAGGA-TTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAA-T
28570628 TTAAGGATTTAGGGTTTTTA
1 TTAAGGATTTAGGGTTTTTA
28570648 GGTAATAACT
Statistics
Matches: 235, Mismatches: 40, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
42 12 0.05
43 25 0.11
44 30 0.13
45 120 0.51
46 46 0.20
47 2 0.01
ACGTcount: A:0.27, C:0.01, G:0.24, T:0.48
Consensus pattern (44 bp):
TTAAGGATTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAT
Found at i:28570840 original size:21 final size:21
Alignment explanation
Indices: 28570816--28570862 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
28570806 TTGTCCAGCT
*
28570816 TCCGGCGGCGATTGTGGTTCC
1 TCCGGCGGCGATTCTGGTTCC
* *
28570837 TCCGGCGGGGATTCTGGTTCT
1 TCCGGCGGCGATTCTGGTTCC
28570858 TCCGG
1 TCCGG
28570863 TACAACATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.28, G:0.38, T:0.30
Consensus pattern (21 bp):
TCCGGCGGCGATTCTGGTTCC
Found at i:28571144 original size:18 final size:18
Alignment explanation
Indices: 28571118--28571160 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28571108 GACTCGGAAA
* *
28571118 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
28571136 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
28571154 AGGAAAC
1 AGGAAAC
28571161 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:28571817 original size:7 final size:7
Alignment explanation
Indices: 28571807--28571832 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28571797 TTATATACAT
28571807 AATACTA
1 AATACTA
28571814 AATACTA
1 AATACTA
28571821 AATACTA
1 AATACTA
28571828 AATAC
1 AATAC
28571833 CAATCAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:28572039 original size:20 final size:20
Alignment explanation
Indices: 28572002--28572039 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28571992 TTTATTTTTA
*
28572002 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
28572022 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
28572040 TTCCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:28580931 original size:23 final size:23
Alignment explanation
Indices: 28580905--28581134 Score: 142
Period size: 23 Copynumber: 10.1 Consensus size: 23
28580895 ACAAATATTG
* * *
28580905 AATACGCTACATAGGCATTATAA
1 AATACGCCACAAAGGCATTACAA
* * ** *
28580928 AATACACCACAAAAGCATTGTAG
1 AATACGCCACAAAGGCATTACAA
* *
28580951 AATAAGCCACATAA-GCATTGCAA
1 AATACGCCACA-AAGGCATTACAA
* ** * *
28580974 AATACACCACAAAGAAAATACAT
1 AATACGCCACAAAGGCATTACAA
* * * *
28580997 AATAAGCCACATAGGCATTGCAT
1 AATACGCCACAAAGGCATTACAA
* *
28581020 AATATGCCACAAATGCATTACAA
1 AATACGCCACAAAGGCATTACAA
* * ** *
28581043 AATATGCCACATAGGCATTGTAG
1 AATACGCCACAAAGGCATTACAA
* *
28581066 AATACACCATAAAGGCATTACAA
1 AATACGCCACAAAGGCATTACAA
* * * *
28581089 AATATGCTACAAAGGCATTATAG
1 AATACGCCACAAAGGCATTACAA
28581112 AATACGCCACAAAGGC-TT-CAA
1 AATACGCCACAAAGGCATTACAA
28581133 AA
1 AA
28581135 GTAACTTACC
Statistics
Matches: 154, Mismatches: 51, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
21 3 0.02
22 4 0.03
23 145 0.94
24 2 0.01
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (23 bp):
AATACGCCACAAAGGCATTACAA
Found at i:28580976 original size:46 final size:46
Alignment explanation
Indices: 28580913--28581107 Score: 185
Period size: 46 Copynumber: 4.2 Consensus size: 46
28580903 TGAATACGCT
** ** *
28580913 ACATAGGCATTATAAAATACACCACAAAAGCATTGTAGAATAAGCC
1 ACATAGGCATTGCAAAATACACCACAAAAGCATTACAAAATAAGCC
* * * *
28580959 ACATAAGCATTGCAAAATACACCAC-AAAGAAAATACATAATAAGCC
1 ACATAGGCATTGCAAAATACACCACAAAAG-CATTACAAAATAAGCC
* ** * *
28581005 ACATAGGCATTGCATAATATGCCACAAATGCATTACAAAATATGCC
1 ACATAGGCATTGCAAAATACACCACAAAAGCATTACAAAATAAGCC
* * * * * *
28581051 ACATAGGCATTGTAGAATACACCATAAAGGCATTACAAAATATGCT
1 ACATAGGCATTGCAAAATACACCACAAAAGCATTACAAAATAAGCC
*
28581097 ACAAAGGCATT
1 ACATAGGCATT
28581108 ATAGAATACG
Statistics
Matches: 122, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
45 4 0.03
46 115 0.94
47 3 0.02
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.21
Consensus pattern (46 bp):
ACATAGGCATTGCAAAATACACCACAAAAGCATTACAAAATAAGCC
Found at i:28581113 original size:46 final size:46
Alignment explanation
Indices: 28580917--28581134 Score: 172
Period size: 46 Copynumber: 4.8 Consensus size: 46
28580907 TACGCTACAT
* * ** * *
28580917 AGGCATTATAAAATACACCACAAAAGCATTGTAGAATAAGCCACATA
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACA-A
** * ** * * * *
28580964 A-GCATTGCAAAATACACCACAAAGAAAATACATAATAAGCCACAT
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACAA
** * ** * *
28581009 AGGCATTGCATAATATGCCACAAATGCATTACAAAATATGCCACAT
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACAA
* * *
28581055 AGGCATTGTAGAATACACCATAAAGGCATTACAAAATATGCTACAA
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACAA
*
28581101 AGGCATTATAGAATACGCCACAAAGGC-TT-CAAAA
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAA
28581135 GTAACTTACC
Statistics
Matches: 140, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
44 5 0.04
45 3 0.02
46 131 0.94
47 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (46 bp):
AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACAA
Found at i:28581121 original size:92 final size:92
Alignment explanation
Indices: 28580905--28581124 Score: 233
Period size: 92 Copynumber: 2.4 Consensus size: 92
28580895 ACAAATATTG
* * ** *
28580905 AATACGCTACATAGGCATTATAAAATACACCACAAAAGCATTGTAGAATAAGCCACATAAGCATT
1 AATAAGCTACATAGGCATTATAAAATACGCCACAAAAGCATTACAAAATAAGCCACATAAGCATT
*
28580970 GCAAAATACACCACAAAGAAAATACAT
66 GCAAAATACACCACAAAGAAAATACAA
* ** * * * * *
28580997 AATAAGCCACATAGGCATTGCATAATATGCCACAAATGCATTACAAAATATGCCACATAGGCATT
1 AATAAGCTACATAGGCATTATAAAATACGCCACAAAAGCATTACAAAATAAGCCACATAAGCATT
* * * ** *
28581062 GTAGAATACACCATAAAGGCATTACAA
66 GCAAAATACACCACAAAGAAAATACAA
* * *
28581089 AATATGCTACAAAGGCATTATAGAATACGCCACAAA
1 AATAAGCTACATAGGCATTATAAAATACGCCACAAA
28581125 GGCTTCAAAA
Statistics
Matches: 101, Mismatches: 27, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
92 101 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (92 bp):
AATAAGCTACATAGGCATTATAAAATACGCCACAAAAGCATTACAAAATAAGCCACATAAGCATT
GCAAAATACACCACAAAGAAAATACAA
Found at i:28599211 original size:23 final size:23
Alignment explanation
Indices: 28599131--28599264 Score: 117
Period size: 23 Copynumber: 5.8 Consensus size: 23
28599121 TGAGTACACT
* * *
28599131 ACATAGGTATTGCAGAATTCACC
1 ACATAGGCATTGCAGAATACGCC
* * * *
28599154 ACAAAGGCATTACAAAATACGCT
1 ACATAGGCATTGCAGAATACGCC
*
28599177 ACAAAGGCATTGCAGAATACGCC
1 ACATAGGCATTGCAGAATACGCC
* * * * *
28599200 ATATAGGTATTGTAGAATATGTC
1 ACATAGGCATTGCAGAATACGCC
* *
28599223 AC-TAAGGCATTACATAATACGCC
1 ACAT-AGGCATTGCAGAATACGCC
28599246 ACATAGGCATTGCAGAATA
1 ACATAGGCATTGCAGAATA
28599265 TGCTAAAAGT
Statistics
Matches: 84, Mismatches: 25, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
22 1 0.01
23 82 0.98
24 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (23 bp):
ACATAGGCATTGCAGAATACGCC
Found at i:28606805 original size:28 final size:28
Alignment explanation
Indices: 28606723--28606855 Score: 160
Period size: 28 Copynumber: 4.6 Consensus size: 28
28606713 CAGCCCTATT
28606723 CAATGACAGTAA-AGTGTGGGCCTTAGCC
1 CAAT-ACAGTAACAGTGTGGGCCTTAGCC
*
28606751 TAATACAGTAACAGTACAGTGTGGGCCTTAGCC
1 CAATACAGT---A--ACAGTGTGGGCCTTAGCC
* *
28606784 CAATATAGTAACAGTGTAGGCCTTAGCC
1 CAATACAGTAACAGTGTGGGCCTTAGCC
* *
28606812 CAATACAGTAACAATGTGGGCTTTAGCC
1 CAATACAGTAACAGTGTGGGCCTTAGCC
28606840 CAATACAGTAACAGTG
1 CAATACAGTAACAGTG
28606856 CAGTGCAATA
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
27 5 0.06
28 59 0.66
30 2 0.02
32 1 0.01
33 23 0.26
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (28 bp):
CAATACAGTAACAGTGTGGGCCTTAGCC
Found at i:28606854 original size:56 final size:59
Alignment explanation
Indices: 28606723--28606855 Score: 175
Period size: 61 Copynumber: 2.3 Consensus size: 59
28606713 CAGCCCTATT
* *
28606723 CAATGACAGTAA-AGTGTGGGCCTTAGCCTAATACAGTAACAGTACAGTGTGGGCCTTAGCC
1 CAAT-ACAGTAACAGTGTAGGCCTTAGCCCAATACAGTAACA--ACAGTGTGGGCCTTAGCC
* *
28606784 CAATATAGTAACAGTGTAGGCCTTAGCCCAATACAGTAAC-A-A-TGTGGGCTTTAGCC
1 CAATACAGTAACAGTGTAGGCCTTAGCCCAATACAGTAACAACAGTGTGGGCCTTAGCC
28606840 CAATACAGTAACAGTG
1 CAATACAGTAACAGTG
28606856 CAGTGCAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
56 28 0.42
57 1 0.02
58 1 0.02
60 6 0.09
61 30 0.45
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (59 bp):
CAATACAGTAACAGTGTAGGCCTTAGCCCAATACAGTAACAACAGTGTGGGCCTTAGCC
Found at i:28607369 original size:81 final size:79
Alignment explanation
Indices: 28607234--28607469 Score: 287
Period size: 81 Copynumber: 2.9 Consensus size: 79
28607224 TTATCTCCTA
** * *
28607234 GGGGTATAACAGTTATTTTACCTTATGGGGATATTTCGATCATTTTACCCTATAGGGGTATTTCG
1 GGGGTATTTCAGTCATTTTACCTTATGGGG-TATTTCGGTCATTTTACCCTATAGGGGTATTTCG
28607299 ATCAATTTTCCCTATG
65 ATC-ATTTTCCCTATG
* *
28607315 GGGGTATTT-TGATCATTTTAGCC-TATGAGGGTATTTCGGTCATTTTACCCTATAGGAGTATTT
1 GGGGTATTTCAG-TCATTTTA-CCTTATG-GGGTATTTCGGTCATTTTACCCTATAGGGGTATTT
*
28607378 CGATCATTTTAACCTATG
63 CGATCATTTT-CCCTATG
* * * * *
28607396 GGTGTATTTCAGTTATTTTACCTTATGGGGGTATTTTGGTCATTTTACACTATGGGGGTATTTCG
1 GGGGTATTTCAGTCATTTTACCTTAT-GGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
28607461 ATCATTTTC
65 ATCATTTTC
28607470 ATCTATTAGG
Statistics
Matches: 133, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
80 8 0.06
81 118 0.89
82 7 0.05
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (79 bp):
GGGGTATTTCAGTCATTTTACCTTATGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGA
TCATTTTCCCTATG
Found at i:28607475 original size:27 final size:26
Alignment explanation
Indices: 28607248--28607468 Score: 246
Period size: 27 Copynumber: 8.2 Consensus size: 26
28607238 TATAACAGTT
*
28607248 ATTTTACCTTATGGGGATATTTCGATC
1 ATTTTACC-TATGGGGGTATTTCGATC
*
28607275 ATTTTACCCTATAGGGGTATTTCGATC
1 ATTTTA-CCTATGGGGGTATTTCGATC
* *
28607302 AATTTTCCCTATGGGGGTATTTTGATC
1 -ATTTTACCTATGGGGGTATTTCGATC
* *
28607329 ATTTTAGCCTATGAGGGTATTTCGGTC
1 ATTTTA-CCTATGGGGGTATTTCGATC
* *
28607356 ATTTTACCCTATAGGAGTATTTCGATC
1 ATTTTA-CCTATGGGGGTATTTCGATC
* *
28607383 ATTTTAACCTATGGGTGTATTTC-AGTT
1 ATTTT-ACCTATGGGGGTATTTCGA-TC
* *
28607410 ATTTTACCTTATGGGGGTATTTTGGTC
1 ATTTTACC-TATGGGGGTATTTCGATC
28607437 ATTTTACACTATGGGGGTATTTCGATC
1 ATTTTAC-CTATGGGGGTATTTCGATC
28607464 ATTTT
1 ATTTT
28607469 CATCTATTAG
Statistics
Matches: 163, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
26 9 0.06
27 145 0.89
28 9 0.06
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.44
Consensus pattern (26 bp):
ATTTTACCTATGGGGGTATTTCGATC
Found at i:28610212 original size:28 final size:27
Alignment explanation
Indices: 28610168--28610366 Score: 254
Period size: 28 Copynumber: 7.1 Consensus size: 27
28610158 CTATTCAGTG
*
28610168 ACAGTACAGTGTGGGCCTTAGCCCAAT
1 ACAGAACAGTGTGGGCCTTAGCCCAAT
* * *
28610195 ATAGTTACAATGTGGGCCTTAGCCCAAT
1 ACAG-AACAGTGTGGGCCTTAGCCCAAT
* * *
28610223 ACAGTAATAATGTGGGCCTTAGCCTAAT
1 ACAG-AACAGTGTGGGCCTTAGCCCAAT
28610251 ACAGAATCAGTGTGGGCCTTAGCCCAAT
1 ACAGAA-CAGTGTGGGCCTTAGCCCAAT
* *
28610279 ACAGAATCAGTGGGGGCCTTAGCTCAAT
1 ACAGAA-CAGTGTGGGCCTTAGCCCAAT
28610307 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAG-AACAGTGTGGGCCTTAGCCCAAT
*
28610335 ACAGAATCGGTGTGGGCCTTAGCCCAAT
1 ACAGAA-CAGTGTGGGCCTTAGCCCAAT
28610363 ACAG
1 ACAG
28610367 TAATAGTGCA
Statistics
Matches: 154, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.05
28 145 0.94
29 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (27 bp):
ACAGAACAGTGTGGGCCTTAGCCCAAT
Found at i:28610244 original size:56 final size:56
Alignment explanation
Indices: 28610174--28610374 Score: 289
Period size: 56 Copynumber: 3.6 Consensus size: 56
28610164 AGTGACAGTA
* * *
28610174 CAGTGTGGGCCTTAGCCCAATATAGTTACAATGTGGGCCTTAGCCCAATACAGTAAT
1 CAGTGTGGGCCTTAGCCCAATACAGTAACAGTGTGGGCCTTAGCCCAATACAG-AAT
* *
28610231 -AATGTGGGCCTTAGCCTAATACAG-AATCAGTGTGGGCCTTAGCCCAATACAGAAT
1 CAGTGTGGGCCTTAGCCCAATACAGTAA-CAGTGTGGGCCTTAGCCCAATACAGAAT
* *
28610286 CAGTGGGGGCCTTAGCTCAATACAGTAACAGTGTGGGCCTTAGCCCAATACAGAAT
1 CAGTGTGGGCCTTAGCCCAATACAGTAACAGTGTGGGCCTTAGCCCAATACAGAAT
* *
28610342 CGGTGTGGGCCTTAGCCCAATACAGTAATAGTG
1 CAGTGTGGGCCTTAGCCCAATACAGTAACAGTG
28610375 CAGCGCAATA
Statistics
Matches: 128, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
55 4 0.03
56 122 0.95
57 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (56 bp):
CAGTGTGGGCCTTAGCCCAATACAGTAACAGTGTGGGCCTTAGCCCAATACAGAAT
Found at i:28610321 original size:84 final size:84
Alignment explanation
Indices: 28610174--28610374 Score: 289
Period size: 84 Copynumber: 2.4 Consensus size: 84
28610164 AGTGACAGTA
* * * * *
28610174 CAGTGTGGGCCTTAGCCCAATATAG-TTACAATGTGGGCCTTAGCCCAATACAGTAATAATGTGG
1 CAGTGTGGGCCTTAGCCCAATACAGAAT-CAGTGGGGGCCTTAGCCCAATACAGTAACAATGTGG
*
28610238 GCCTTAGCCTAATACAGAAT
65 GCCTTAGCCCAATACAGAAT
* *
28610258 CAGTGTGGGCCTTAGCCCAATACAGAATCAGTGGGGGCCTTAGCTCAATACAGTAACAGTGTGGG
1 CAGTGTGGGCCTTAGCCCAATACAGAATCAGTGGGGGCCTTAGCCCAATACAGTAACAATGTGGG
28610323 CCTTAGCCCAATACAGAAT
66 CCTTAGCCCAATACAGAAT
*
28610342 CGGTGTGGGCCTTAGCCCAATACAGTAAT-AGTG
1 CAGTGTGGGCCTTAGCCCAATACAG-AATCAGTG
28610375 CAGCGCAATA
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
84 102 0.96
85 4 0.04
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (84 bp):
CAGTGTGGGCCTTAGCCCAATACAGAATCAGTGGGGGCCTTAGCCCAATACAGTAACAATGTGGG
CCTTAGCCCAATACAGAAT
Found at i:28610535 original size:26 final size:26
Alignment explanation
Indices: 28610481--28610556 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
28610471 ACCAATATCA
* * * **
28610481 CAGCAAAGCTGCTAGTAATAGCACCG
1 CAGCAAAGCTGCCAGTAACAGTATTG
* *
28610507 CAGCAGAGCTGCCAGTATCAGTATTG
1 CAGCAAAGCTGCCAGTAACAGTATTG
*
28610533 CAGCAAAGTTGCCAGTAACAGTAT
1 CAGCAAAGCTGCCAGTAACAGTAT
28610557 ATGTGCCAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGTAACAGTATTG
Found at i:28611183 original size:27 final size:27
Alignment explanation
Indices: 28610788--28611173 Score: 363
Period size: 27 Copynumber: 14.4 Consensus size: 27
28610778 GGGTATAATA
* * *
28610788 GTCATTTTACCCTCTAGGCGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * **
28610815 ATTATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
28610842 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
*
28610869 GTCATTTTA-CCT-T-GGGGTATTTTT
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
28610893 GTCATTTTACCTTAT-GGTGGTATTTTT
1 GTCATTTTACCCTATAGG-GGTATTTTG
* *
28610920 TTCATTTTACCCTAT-GGGGAATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * *
28610946 GCCATTTTATCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * *
28610973 CTCATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATAGGGGTATTTTG
28611000 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
28611027 CTCATTTTACCCTAT-GGGAGTATTTCG
1 GTCATTTTACCCTATAGGG-GTATTTTG
* * **
28611054 GTCATTTTACCTTATGGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTTG
* **
28611081 GTCATTTTACCCTATAGGGGTATGTCA
1 GTCATTTTACCCTATAGGGGTATTTTG
* *** *
28611108 GTCATTTT-CATCTATTAGGGGTAAAATA
1 GTCATTTTAC-CCTA-TAGGGGTATTTTG
* *
28611136 GACATTTTACCCTTTAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
28611163 GTCATTTTACC
1 GTCATTTTACC
28611174 TATTTGGGGT
Statistics
Matches: 302, Mismatches: 48, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
24 18 0.06
25 3 0.01
26 29 0.10
27 230 0.76
28 21 0.07
29 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTTG
Found at i:28619062 original size:25 final size:26
Alignment explanation
Indices: 28619033--28619088 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
28619023 TTAATTAGTA
*
28619033 TAAAATATT-AATAATTCAAT-AAAT
1 TAAAATATTAAATAATTAAATAAAAT
28619057 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATTAAATAATTAAATAAAAT
28619083 TAAAAT
1 TAAAAT
28619089 TTGGGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATATTAAATAATTAAATAAAAT
Found at i:28619477 original size:22 final size:19
Alignment explanation
Indices: 28619438--28619479 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
28619428 TGCAAAGCTG
28619438 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
28619457 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
28619479 A
1 A
28619480 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:28626951 original size:6 final size:6
Alignment explanation
Indices: 28626928--28626968 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
28626918 TATTTAACCC
*
28626928 AAATT- AAATT- AGATTA AAATTA AAATTA AAATTA AAATTA A
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA A
28626969 TTATATTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (6 bp):
AAATTA
Found at i:28630986 original size:21 final size:21
Alignment explanation
Indices: 28630962--28631008 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
28630952 AGGTTAACAG
*
28630962 AATGCCATAAAAGCCATACAA
1 AATGCCACAAAAGCCATACAA
* *
28630983 AATGCCACAAAGGCCATACAG
1 AATGCCACAAAAGCCATACAA
28631004 AATGC
1 AATGC
28631009 ATTATAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.13
Consensus pattern (21 bp):
AATGCCACAAAAGCCATACAA
Found at i:28637633 original size:3 final size:3
Alignment explanation
Indices: 28637619--28637648 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28637609 TTGTATTTAA
*
28637619 TGT TGT TAT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
28637649 CTACATTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.30, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:28639379 original size:27 final size:27
Alignment explanation
Indices: 28639349--28639437 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 27
28639339 TGTAAACACG
*
28639349 TCATGAAAGAAATGTCTTTGTGGTGAA
1 TCATGAAAGAAATGCCTTTGTGGTGAA
*
28639376 TCATGAAAGAAATGCCTTTGTGGCGAA
1 TCATGAAAGAAATGCCTTTGTGGTGAA
* *
28639403 TCATGAAAGAAAAGCCTTGGTGGTGAA
1 TCATGAAAGAAATGCCTTTGTGGTGAA
*
28639430 TTATGAAA
1 TCATGAAA
28639438 AGAATTTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (27 bp):
TCATGAAAGAAATGCCTTTGTGGTGAA
Found at i:28642316 original size:27 final size:27
Alignment explanation
Indices: 28642284--28642341 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
28642274 AGGTTGTTCT
28642284 TTTCATACTTCACCACAAAGGCATCCA
1 TTTCATACTTCACCACAAAGGCATCCA
** * *
28642311 TTTCATGGTTCACCACAAAGGCTTTCA
1 TTTCATACTTCACCACAAAGGCATCCA
28642338 TTTC
1 TTTC
28642342 CTGACATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (27 bp):
TTTCATACTTCACCACAAAGGCATCCA
Found at i:28645690 original size:21 final size:22
Alignment explanation
Indices: 28645666--28645714 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
28645656 GGATCAATTT
28645666 GAAACAAA-ATAGAAAATTTTG
1 GAAACAAATATAGAAAATTTTG
* * *
28645687 GAAA-AAATTTTGAATATTTTG
1 GAAACAAATATAGAAAATTTTG
28645708 GAAACAA
1 GAAACAA
28645715 GGGTCACACG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.13
21 18 0.78
22 2 0.09
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (22 bp):
GAAACAAATATAGAAAATTTTG
Found at i:28657937 original size:45 final size:45
Alignment explanation
Indices: 28657888--28658315 Score: 402
Period size: 45 Copynumber: 9.4 Consensus size: 45
28657878 AGACCACAAC
** *
28657888 TGAAAGATGCTATGGCATCATTATTC-AAA-TGAGTAAGACCATAGT
1 TGAAAGACACTATGGCATCA-TA-TCGAAAGTGAATAAGACCATAGT
** * *
28657933 TGAAAGATGCTATGGCATCATGATTC-AGA-TGAGTAAGACCATAGT
1 TGAAAGACACTATGGCATCAT-A-TCGAAAGTGAATAAGACCATAGT
* *
28657978 TGAAAGACAGTATGGCATCATATCGGAAAGTGAATAAGAGCATAGT
1 TGAAAGACACTATGGCATCATATC-GAAAGTGAATAAGACCATAGT
* * * ** * *
28658024 T-AAAGACATTATGGAATCCTATAAAAAATGGATAAGACCATAGT
1 TGAAAGACACTATGGCATCATATCGAAAGTGAATAAGACCATAGT
* * *
28658068 TGAAAGACACTATGGCATTATATCAAAAAGTGAATAAGACCATAAT
1 TGAAAGACACTATGGCATCATATC-GAAAGTGAATAAGACCATAGT
* * * *
28658114 TGAAAGACACTATGGCAACCTATCGAAAATGGATAAGACCATAGT
1 TGAAAGACACTATGGCATCATATCGAAAGTGAATAAGACCATAGT
* *
28658159 TGAAAGACACTATGGCATCATATCAGAAACTGAATAAGACCATGGT
1 TGAAAGACACTATGGCATCATATC-GAAAGTGAATAAGACCATAGT
* * *
28658205 TAAAAGAAACTTATGGCATCATATCGGAAAGTGAATAAGACCATGGT
1 TGAAAGACAC-TATGGCATCATATC-GAAAGTGAATAAGACCATAGT
** * * * *
28658252 TGAAATTCATTATGGCATCA-AGTCGAGAA-TAAATAAGATCATGGT
1 TGAAAGACACTATGGCATCATA-TCGA-AAGTGAATAAGACCATAGT
28658297 TGAAAGACACTATGGCATC
1 TGAAAGACACTATGGCATC
28658316 CTTCAATCAT
Statistics
Matches: 324, Mismatches: 49, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
43 2 0.01
44 20 0.06
45 169 0.52
46 94 0.29
47 39 0.12
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (45 bp):
TGAAAGACACTATGGCATCATATCGAAAGTGAATAAGACCATAGT
Found at i:28658166 original size:91 final size:91
Alignment explanation
Indices: 28657966--28658313 Score: 389
Period size: 91 Copynumber: 3.8 Consensus size: 91
28657956 TTCAGATGAG
* ** *
28657966 TAAGACCATAGTTGAAAGACAGTATGGCATCATATCGGAAAGTGAATAAGAGCATAGTT-AAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAAGTGAATAAGACCATAGTTGAAAGA
* **
28658030 CATTATGG-AATCCTATAAAAAATGGA
66 CACTATGGCAA-CCTATCGAAAATGGA
* *
28658056 TAAGACCATAGTTGAAAGACACTATGGCATTATATCAAAAAGTGAATAAGACCATAATTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAAGTGAATAAGACCATAGTTGAAAGA
28658121 CACTATGGCAACCTATCGAAAATGGA
66 CACTATGGCAACCTATCGAAAATGGA
* * * *
28658147 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAGAAACTGAATAAGACCATGGTTAAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAAGTGAATAAGACCATAGTTGAAAGA
* * * * *
28658212 AACTTATGGCATCATATCGGAAAGTGAA
66 CAC-TATGGCAACCTATC-GAAAATGGA
* ** * * * * * *
28658240 TAAGACCATGGTTGAAATTCATTATGGCATCA-AGTCGAGAA-TAAATAAGATCATGGTTGAAAG
1 TAAGACCATAGTTGAAAGACACTATGGCATCATA-TCAAAAAGTGAATAAGACCATAGTTGAAAG
28658303 ACACTATGGCA
65 ACACTATGGCA
28658314 TCCTTCAATC
Statistics
Matches: 222, Mismatches: 31, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
90 53 0.24
91 93 0.42
92 37 0.17
93 39 0.18
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (91 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCATATCAAAAAGTGAATAAGACCATAGTTGAAAGA
CACTATGGCAACCTATCGAAAATGGA
Found at i:28662512 original size:14 final size:14
Alignment explanation
Indices: 28662495--28662522 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28662485 TGATGCCTTG
28662495 AAGATGCAATTATT
1 AAGATGCAATTATT
28662509 AAGATGCAATTATT
1 AAGATGCAATTATT
28662523 TCCTTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
AAGATGCAATTATT
Found at i:28666348 original size:25 final size:25
Alignment explanation
Indices: 28666316--28666399 Score: 123
Period size: 25 Copynumber: 3.4 Consensus size: 25
28666306 AGCTGTAAAT
28666316 GGTAAGCTCCTCCGAGCTGAATAAC
1 GGTAAGCTCCTCCGAGCTGAATAAC
* *
28666341 GGTAAGCTCTTCTGAGCTGAATAAC
1 GGTAAGCTCCTCCGAGCTGAATAAC
* * *
28666366 GGTAAACTCCTCCAAGCTGAATAAT
1 GGTAAGCTCCTCCGAGCTGAATAAC
28666391 GGTAAGCTC
1 GGTAAGCTC
28666400 ATACAAGCTA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (25 bp):
GGTAAGCTCCTCCGAGCTGAATAAC
Found at i:28666406 original size:25 final size:25
Alignment explanation
Indices: 28666297--28666427 Score: 106
Period size: 25 Copynumber: 5.3 Consensus size: 25
28666287 GTACATGTAT
*
28666297 GCTCATACGAGCTGTA-AATGGTAA
1 GCTCATACGAGCTGAATAATGGTAA
* * *
28666321 GCTCCTCCGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAATGGTAA
* *
28666346 GCTC-TTCTGAGCTGAATAACGGTAA
1 GCTCATAC-GAGCTGAATAATGGTAA
* * * *
28666371 ACTCCTCCAAGCTGAATAATGGTAA
1 GCTCATACGAGCTGAATAATGGTAA
* **
28666396 GCTCATACAAGCT-AAGCATCGGTAA
1 GCTCATACGAGCTGAATAAT-GGTAA
28666421 GCTCATA
1 GCTCATA
28666428 TGAGTTGAGC
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
24 19 0.21
25 68 0.76
26 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAATGGTAA
Found at i:28666438 original size:25 final size:25
Alignment explanation
Indices: 28666391--28666452 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
28666381 GCTGAATAAT
28666391 GGTAAGCTCATACAAGCTAAGCATC
1 GGTAAGCTCATACAAGCTAAGCATC
** * *
28666416 GGTAAGCTCATATGAGTTGAGCATC
1 GGTAAGCTCATACAAGCTAAGCATC
28666441 GGTAAGCTCATA
1 GGTAAGCTCATA
28666453 AGAGCCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (25 bp):
GGTAAGCTCATACAAGCTAAGCATC
Found at i:28674147 original size:14 final size:14
Alignment explanation
Indices: 28674128--28674159 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
28674118 TGCTCATACG
28674128 AGCTGTGAACGGTA
1 AGCTGTGAACGGTA
28674142 AGCTGTGAACGGTA
1 AGCTGTGAACGGTA
28674156 AGCT
1 AGCT
28674160 CCTCTGAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.16, G:0.34, T:0.22
Consensus pattern (14 bp):
AGCTGTGAACGGTA
Found at i:28674181 original size:25 final size:25
Alignment explanation
Indices: 28674149--28674231 Score: 114
Period size: 25 Copynumber: 3.3 Consensus size: 25
28674139 GTAAGCTGTG
28674149 AACGGTAAGCTCCTCTGAGCTGAAT
1 AACGGTAAGCTCCTCTGAGCTGAAT
* *
28674174 AAAGGTAAGCTCCTCCGAGCT-AGAT
1 AACGGTAAGCTCCTCTGAGCTGA-AT
* *
28674199 AACGGTAAGCTCGTCTAAGCTGAAT
1 AACGGTAAGCTCCTCTGAGCTGAAT
28674224 AACGGTAA
1 AACGGTAA
28674232 CCTCATACGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.02
25 48 0.96
26 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (25 bp):
AACGGTAAGCTCCTCTGAGCTGAAT
Found at i:28674243 original size:50 final size:50
Alignment explanation
Indices: 28674149--28674244 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
28674139 GTAAGCTGTG
* * * *
28674149 AACGGTAAGCTCCTCTGAGCTGAATAAAGGTAAGCTCCTCCGAGCTAGAT
1 AACGGTAAGCTCCTCTAAGCTGAATAAAGGTAACCTCATACGAGCTAGAT
* *
28674199 AACGGTAAGCTCGTCTAAGCTGAATAACGGTAACCTCATACGAGCT
1 AACGGTAAGCTCCTCTAAGCTGAATAAAGGTAACCTCATACGAGCT
28674245 GAGCATCAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (50 bp):
AACGGTAAGCTCCTCTAAGCTGAATAAAGGTAACCTCATACGAGCTAGAT
Found at i:28674244 original size:25 final size:24
Alignment explanation
Indices: 28674149--28674246 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 24
28674139 GTAAGCTGTG
*
28674149 AACGGTAAGCTCCTCTGAGCTGAAT
1 AACGGTAAGCTCATC-GAGCTGAAT
* *
28674174 AAAGGTAAGCTCCTCCGAGCT-AGAT
1 AACGGTAAGCTCAT-CGAGCTGA-AT
* *
28674199 AACGGTAAGCTCGTCTAAGCTGAAT
1 AACGGTAAGCTCATC-GAGCTGAAT
*
28674224 AACGGTAACCTCATACGAGCTGA
1 AACGGTAAGCTCAT-CGAGCTGA
28674247 GCATCAGTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
24 2 0.03
25 56 0.92
26 3 0.05
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (24 bp):
AACGGTAAGCTCATCGAGCTGAAT
Found at i:28674257 original size:50 final size:49
Alignment explanation
Indices: 28674153--28674260 Score: 119
Period size: 50 Copynumber: 2.2 Consensus size: 49
28674143 GCTGTGAACG
* * * * *
28674153 GTAAGCTCCTCTGAGCTGAATAAAGGTAAGCTCCTCCGAGCTAGATAACG
1 GTAAGCTCCTCTAAGCTGAATAAAGGTAACCTCATACGAGCTAGAT-ACA
* *
28674203 GTAAGCTCGTCTAAGCTGAATAACGGTAACCTCATACGAGCTGAGCAT-CA
1 GTAAGCTCCTCTAAGCTGAATAAAGGTAACCTCATACGAGCT-AG-ATACA
28674253 GTAAGCTC
1 GTAAGCTC
28674261 ATAAGAGCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
50 45 0.92
51 2 0.04
52 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (49 bp):
GTAAGCTCCTCTAAGCTGAATAAAGGTAACCTCATACGAGCTAGATACA
Found at i:28682739 original size:21 final size:21
Alignment explanation
Indices: 28682714--28682766 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
28682704 GTTGTTGAGA
*
28682714 AGGAAGTTGCTGCTGTAGAAG
1 AGGAAGTTGCTGCTGAAGAAG
*
28682735 AGGAAGTTGTTGCTGAAGAAG
1 AGGAAGTTGCTGCTGAAGAAG
*
28682756 AAGAAGTTGCT
1 AGGAAGTTGCT
28682767 AAAAATGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.36, T:0.25
Consensus pattern (21 bp):
AGGAAGTTGCTGCTGAAGAAG
Found at i:28683218 original size:49 final size:49
Alignment explanation
Indices: 28683159--28683257 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
28683149 TATTTTTAGC
28683159 TTTAGTTGTAGTATCCATGCATTACATGTAGCTGTAAGTTTTATTTGGA
1 TTTAGTTGTAGTATCCATGCATTACATGTAGCTGTAAGTTTTATTTGGA
*
28683208 TTTAGTTGTAGTATCCATGCATTATATGTAGCTGTAAGTTTTATTTGGA
1 TTTAGTTGTAGTATCCATGCATTACATGTAGCTGTAAGTTTTATTTGGA
28683257 T
1 T
28683258 AAGTATACAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.46
Consensus pattern (49 bp):
TTTAGTTGTAGTATCCATGCATTACATGTAGCTGTAAGTTTTATTTGGA
Found at i:28689282 original size:46 final size:45
Alignment explanation
Indices: 28689000--28689482 Score: 473
Period size: 45 Copynumber: 10.7 Consensus size: 45
28688990 TTCAGATGAG
* * * *
28689000 TAAGACCATAGTTGAAAGACGCTATGGCCTCATTAATC--AAGCGAG
1 TAAGACCATAGTTGAAAGACACTATGGCATCA-T-ATCGAAAGTGAA
* * * ** * * *
28689045 TAATACAATAGCTGAAAGATGCTATGGTATCATGATTC-AGA-TGAG
1 TAAGACCATAGTTGAAAGACACTATGGCATCAT-A-TCGAAAGTGAA
* * *
28689090 TAAGACCATAGTTGAAAGACATTATGGCATCTTATCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCGAAAGTGAA
* *
28689135 TAAGACCAGAGTTGAAA-ACATTATGGCATCATATCAGAAAGTGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATC-GAAAGTGAA
* * *
28689180 TAAGGCCATAGTT-AAAGACACTATGGCATCCTATCGAATA-TGGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCGAA-AGTGAA
* *
28689224 TAAGACCATAGTTGAAAGACGCCATGGCATCATATCTGAAAGTGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATC-GAAAGTGAA
** *
28689270 TAAGACCATAGTTGAAAGACACTATACCATTC-TATCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCA-TCATATCGAAAGTGAA
* *
28689315 TAAGACCATAGTTGAAAGACACTATGGCATCATATTGGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATA-TCGAAAGTGAA
* *
28689361 TAAGACCATGGTTGAAAGACACTATGGCATCATGTCGGAAAGTGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATC-GAAAGTGAA
* * * *
28689407 TAAGACCATGGTTGAAAGACATTATGGCTTCA-AGTCGAGAA-TAAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATA-TCGA-AAGTGAA
* *
28689452 TAAGACCATGGTTGAAAGACATTATGGCATC
1 TAAGACCATAGTTGAAAGACACTATGGCATC
28689483 CTTTAATCAT
Statistics
Matches: 373, Mismatches: 49, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
43 2 0.01
44 45 0.12
45 204 0.55
46 120 0.32
47 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCATATCGAAAGTGAA
Found at i:28689285 original size:22 final size:22
Alignment explanation
Indices: 28689260--28689332 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
28689250 GCATCATATC
28689260 TGAAAGTGAATAAGACCATAGT
1 TGAAAGTGAATAAGACCATAGT
** * * **
28689282 TGAAAGACACT-ATACCATTCT
1 TGAAAGTGAATAAGACCATAGT
*
28689303 ATCGAAAATGAATAAGACCATAGT
1 -T-GAAAGTGAATAAGACCATAGT
28689327 TGAAAG
1 TGAAAG
28689333 ACACTATGGC
Statistics
Matches: 34, Mismatches: 14, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
21 7 0.21
22 13 0.38
23 7 0.21
24 7 0.21
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (22 bp):
TGAAAGTGAATAAGACCATAGT
Found at i:28689328 original size:91 final size:91
Alignment explanation
Indices: 28689090--28689482 Score: 485
Period size: 91 Copynumber: 4.3 Consensus size: 91
28689080 TTCAGATGAG
* * *
28689090 TAAGACCATAGTTGAAAGACATTATGGCATCTTATCGAAAATGAATAAGACCAGAGTTGAAA-AC
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCGAAAATGAATAAGACCATAGTTGAAAGAC
* *
28689154 ATTATGGCATCATATCAGAAAGTGAA
66 ACTATGGCATCATATCTGAAAGTGAA
* * * *
28689180 TAAGGCCATAGTT-AAAGACACTATGGCATCCTATCGAATATGGATAAGACCATAGTTGAAAGAC
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATCGAAAATGAATAAGACCATAGTTGAAAGAC
* *
28689244 GCCATGGCATCATATCTGAAAGTGAA
66 ACTATGGCATCATATCTGAAAGTGAA
**
28689270 TAAGACCATAGTTGAAAGACACTATACCATTC-TATCGAAAATGAATAAGACCATAGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCA-TCATATCGAAAATGAATAAGACCATAGTTGAAAGA
*
28689334 CACTATGGCATCATAT-TGGAAAATGAA
65 CACTATGGCATCATATCT-GAAAGTGAA
* * * *
28689361 TAAGACCATGGTTGAAAGACACTATGGCATCATGTCGGAAAGTGAATAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATC-GAAAATGAATAAGACCATAGTTGAAAGA
* * *
28689426 CATTATGGCTTCA-AGTC-GAGAA-TAAA
65 CACTATGGCATCATA-TCTGA-AAGTGAA
* *
28689452 TAAGACCATGGTTGAAAGACATTATGGCATC
1 TAAGACCATAGTTGAAAGACACTATGGCATC
28689483 CTTTAATCAT
Statistics
Matches: 266, Mismatches: 28, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
89 43 0.16
90 51 0.19
91 130 0.49
92 42 0.16
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (91 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCATATCGAAAATGAATAAGACCATAGTTGAAAGAC
ACTATGGCATCATATCTGAAAGTGAA
Found at i:28695585 original size:33 final size:34
Alignment explanation
Indices: 28695514--28695593 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 34
28695504 CCTCACTTTT
*
28695514 TCTTGTTTGCTTTCTTCACTCGTTTCTTTTGCAGAC
1 TCTT-TTT-CTTTCTTCACTCGTTTCTTTTGCAAAC
*
28695550 TCTTTTTCTTTC-TCACTCGATTT-TTTTTCAAAC
1 TCTTTTTCTTTCTTCACTCG-TTTCTTTTGCAAAC
*
28695583 TCTCTTTCTTT
1 TCTTTTTCTTT
28695594 TTCTTTTTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 25 0.62
34 8 0.20
35 3 0.08
36 4 0.10
ACGTcount: A:0.10, C:0.25, G:0.07, T:0.57
Consensus pattern (34 bp):
TCTTTTTCTTTCTTCACTCGTTTCTTTTGCAAAC
Found at i:28695631 original size:15 final size:14
Alignment explanation
Indices: 28695584--28695640 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 14
28695574 TTTTCAAACT
28695584 CTCTTTCTTTTT--
1 CTCTTTCTTTTTCA
*
28695596 CTTTTTCTTTTT--
1 CTCTTTCTTTTTCA
*
28695608 CTTTTTCTTTTTCCA
1 CTCTTTCTTTTT-CA
28695623 CTCTTTCTTTTTCA
1 CTCTTTCTTTTTCA
28695637 CTCT
1 CTCT
28695641 AAATTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
12 23 0.57
14 6 0.15
15 11 0.28
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (14 bp):
CTCTTTCTTTTTCA
Found at i:28695635 original size:6 final size:6
Alignment explanation
Indices: 28695587--28695620 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
28695577 TCAAACTCTC
28695587 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
28695621 CACTCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:28695733 original size:11 final size:12
Alignment explanation
Indices: 28695717--28695749 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
28695707 TTTATTGTTC
28695717 TTTTTCTTTC-A
1 TTTTTCTTTCGA
28695728 TTTTTCTTCTCGA
1 TTTTTCTT-TCGA
28695741 TTTTTCTTT
1 TTTTTCTTT
28695750 ACAAGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 3 0.15
13 9 0.45
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTTCTTTCGA
Found at i:28696655 original size:13 final size:13
Alignment explanation
Indices: 28696637--28696669 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
28696627 CACGTACAAA
28696637 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
28696650 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
28696663 TTTTTTT
1 TTTTTTT
28696670 AAATCACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:28699109 original size:27 final size:27
Alignment explanation
Indices: 28699038--28699095 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
28699028 GAATAGGAGG
** * *
28699038 ATTAACACCCTGAACATTTGGATTATT
1 ATTAACACCAGGACCATTTGGATTATC
28699065 ATTAACACCAGGACCATTTGGATTATC
1 ATTAACACCAGGACCATTTGGATTATC
28699092 ATTA
1 ATTA
28699096 TGACTGGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (27 bp):
ATTAACACCAGGACCATTTGGATTATC
Found at i:28705656 original size:11 final size:11
Alignment explanation
Indices: 28705640--28705715 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
28705630 TTCACTCACT
28705640 TTAATATTAAA
1 TTAATATTAAA
28705651 TTAATA--AAA
1 TTAATATTAAA
*
28705660 -TACTATTAAGA
1 TTAATATTAA-A
*
28705671 TAAATATTAAA
1 TTAATATTAAA
28705682 TTTAAT-TTAATA
1 -TTAATATTAA-A
28705694 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
28705707 ATAATATTA
1 TTAATATTA
28705716 TTTTTGGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 2 0.04
11 19 0.37
12 16 0.31
13 3 0.06
14 4 0.08
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:28705693 original size:37 final size:36
Alignment explanation
Indices: 28705646--28705715 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
28705636 CACTTTAATA
*
28705646 TTAAATTAATA-AAATACTATTAAGATAAATATTAAAT
1 TTAAATTAATATAAA-ACTATTAAAAT-AATATTAAAT
* *
28705683 TTAATTTAATATTAAACTATTAAAATAATATTA
1 TTAAATTAATATAAAACTATTAAAATAATATTA
28705716 TTTTTGGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 7 0.24
37 20 0.69
38 2 0.07
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAAATTAATATAAAACTATTAAAATAATATTAAAT
Found at i:28709441 original size:17 final size:17
Alignment explanation
Indices: 28709410--28709442 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28709400 TAACGCAAGG
28709410 GACCTTTTCATGATCCC
1 GACCTTTTCATGATCCC
28709427 GACCTGTTTCA-GATCC
1 GACCT-TTTCATGATCC
28709443 GTCACTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.33
Consensus pattern (17 bp):
GACCTTTTCATGATCCC
Found at i:28712862 original size:13 final size:13
Alignment explanation
Indices: 28712844--28712870 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28712834 ATTTAACAGC
28712844 GCTGTGAAAAAAT
1 GCTGTGAAAAAAT
28712857 GCTGTGAAAAAAT
1 GCTGTGAAAAAAT
28712870 G
1 G
28712871 TTGTTGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (13 bp):
GCTGTGAAAAAAT
Found at i:28715475 original size:19 final size:19
Alignment explanation
Indices: 28715439--28715475 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28715429 AAAGAATTTA
*
28715439 AAAACTAAAACCCTAATCT
1 AAAACTAAAACCCAAATCT
*
28715458 AAAACTAAAACTCAAATC
1 AAAACTAAAACCCAAATC
28715476 AAGGGAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAACTAAAACCCAAATCT
Found at i:28716690 original size:29 final size:29
Alignment explanation
Indices: 28716657--28716712 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
28716647 ATTTAGCAAG
* *
28716657 TAAGTTGTTTTTTGCAAACTATGTTCGTA
1 TAAGTTGTGTTTGGCAAACTATGTTCGTA
* *
28716686 TAAGTTGTGTTTGGCGAACTGTGTTCG
1 TAAGTTGTGTTTGGCAAACTATGTTCG
28716713 CAAGTATGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.20, C:0.11, G:0.25, T:0.45
Consensus pattern (29 bp):
TAAGTTGTGTTTGGCAAACTATGTTCGTA
Found at i:28720150 original size:24 final size:25
Alignment explanation
Indices: 28720098--28720150 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
28720088 CTGAATAATA
* *
28720098 GTAAGCTCATACGAGCTGAGCATCG
1 GTAAGCTCATAAGAGCTGAACATCG
28720123 GTAAGCTCATAAGAGCT-AACATCG
1 GTAAGCTCATAAGAGCTGAACATCG
28720147 GTAA
1 GTAA
28720151 CCCTAATGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (25 bp):
GTAAGCTCATAAGAGCTGAACATCG
Found at i:28721588 original size:69 final size:68
Alignment explanation
Indices: 28721465--28721592 Score: 193
Period size: 69 Copynumber: 1.9 Consensus size: 68
28721455 AGTTTAATAG
* * *
28721465 TAAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAA
1 TAAATTAAATTTAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGATTATCTTAA
28721530 AAT
66 AAT
** *
28721533 TAAATTAAATTTAATGTTTATCTTGATAAATATTATATTAATTTAATATTAAAGTGATTA
1 TAAATTAAATTTAATACTTATCTTAAT-AATATTATATTAATTTAATATTAAAGTGATTA
28721593 AGTTTATCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
68 23 0.43
69 30 0.57
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (68 bp):
TAAATTAAATTTAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGATTATCTTAA
AAT
Found at i:28731479 original size:12 final size:13
Alignment explanation
Indices: 28731456--28731484 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28731446 GATTATTGTC
28731456 ATTTTGGATTGGT
1 ATTTTGGATTGGT
28731469 ATTTT-GATTGGT
1 ATTTTGGATTGGT
28731481 ATTT
1 ATTT
28731485 GAGTTTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (13 bp):
ATTTTGGATTGGT
Found at i:28743185 original size:533 final size:537
Alignment explanation
Indices: 28742171--28743244 Score: 1674
Period size: 533 Copynumber: 2.0 Consensus size: 537
28742161 TGTGACGTAT
* *
28742171 AGATATTCTGGTGTTGCTTTGGAACTCACTAAGTTTTATAAACTTACTCCGTTTATCTTCCCTTC
1 AGATATTCTGATGTTGCTTTGGAACTCACTAAGTTCTATAAACTTACTCCGTTTATCTTCCCTTC
28742236 TCAGGACCATTAAAGAAATAAAGGAACCTTCAAGGACTACGCCAGAGGATATATTATGTGTGAAG
66 TCAGGACCATTAAAGAAATAAAGGAACCTTCAAGGACTACGCCAGAGGATATATTATGTGTGAAG
*
28742301 CTTATAGTGATTTTGTATTATGCATGACAAATGAGATTAGCATCAAGGCTTGAAATATGATAAAC
131 CTTATAGTGATTTTGTATTATGCATG--AAA-GAGA-TAGCATCAAGGCTTGAAATATGAGAAAC
* *
28742366 AATATTTTGTAACTAAAATTGTATCCACCAAATGGCGTCCTTTCCTTAAATCTTCATAATGAACT
192 AATATTTTGTAACTAAAATTGTATCCACCAAATGGCGTCCTCTCCTTAAATCTTCACAATGAACT
* * *
28742431 TTTGTGTTTTAAAGGTGTTTAGGCCCTAAAGTTTAAAAGTTTTATTTATTACTACTATAGCAAAT
257 TTTGTGTTTTAAAGGTGTTTAGGCCCTAAAGTCTAAAAGTTTTATTTACTACTACTATAGCAAAC
* * *
28742496 ACCTTTTGTTCTTTTGTAAACTTGAGATTTCGCCAATTTCGTTACAGTAAGGAAAGGCTTCAAAG
322 ACCTTTTGCTCTTTTGTAAACTTGAGATTCCGCCAATTTCGTAACAGTAAGGAAAGGCTTCAAAG
* ** * *
28742561 TTGCAACACACCACTCCTGGATCCTCCTTAAGGGTCGGGGATGGGGCGCTACAACCGAAAACTTG
387 TTGCAACACACCACTCCTGGATCCTCCTTAAAGGTCAAGGATGAGGCACTACAACCGAAAACTTG
28742626 TAACCTTGCACTTTTTGGATTAGTCACTAACACATGATAGATGAAAAACATGGCCCTCTTGTGTA
452 TAACCTTGCACTTTTTGGATTAGTCACTAACACATGATAGATGAAAAACATGGCCCTCTTGTGTA
28742691 ATCGAAAAGTAATGTGGTCAC
517 ATCGAAAAGTAATGTGGTCAC
*
28742712 AGATATTCTGATGTTGCTTTGGAACTCACTAAGTTCTATGAACTTACTCCGTTTATCTTCCCTTC
1 AGATATTCTGATGTTGCTTTGGAACTCACTAAGTTCTATAAACTTACTCCGTTTATCTTCCCTTC
* * * * *
28742777 TCAGGACCCTTGAAGAAATAAAGGAACCTTTACA-GACTACTCTAGAGGATATATTATGTGT-AA
66 TCAGGACCATTAAAGAAATAAAGGAACCTTCA-AGGACTACGCCAGAGGATATATTATGTGTGAA
* *
28742840 GGCTTATAGTGATTTTGTATTATGCATG-AA-AG-TGGCATCAAGGCTTGAAATCTGAGAAACAA
130 -GCTTATAGTGATTTTGTATTATGCATGAAAGAGATAGCATCAAGGCTTGAAATATGAGAAACAA
* * *
28742902 TATTTTGTAACTAAAATTGTATCCGCCAAAT-TCGTCCTCTCCTTAAATCTTTACAATGAACTTT
194 TATTTTGTAACTAAAATTGTATCCACCAAATGGCGTCCTCTCCTTAAATCTTCACAATGAACTTT
* * * *
28742966 TGTGTTTTAAAGGTGTTTGGGCCCTTAAGTCTAAAAGTTTTATTTACTACTGCTATAGCAAACGC
259 TGTGTTTTAAAGGTGTTTAGGCCCTAAAGTCTAAAAGTTTTATTTACTACTACTATAGCAAACAC
**
28743031 CTTTTGCTCTTTTGTAAACTTGAGATTCCGCCAATTTCGTAATTGTAAGGAAAGGCTTCAAAGTT
324 CTTTTGCTCTTTTGTAAACTTGAGATTCCGCCAATTTCGTAACAGTAAGGAAAGGCTTCAAAGTT
* ** * * **
28743096 GTAATGCACCATTCTTGGATCCTCCTTAAAGGTCAAGGATGAGGCACTACAACCGGGAACTTGTA
389 GCAACACACCACTCCTGGATCCTCCTTAAAGGTCAAGGATGAGGCACTACAACCGAAAACTTGTA
* *
28743161 ACCTTGCACTTTTTGGATTAGTCACTAGCACATGATAGATGGAAAACATGGCCCTCTTGTGTAAT
454 ACCTTGCACTTTTTGGATTAGTCACTAACACATGATAGATGAAAAACATGGCCCTCTTGTGTAAT
28743226 CGAAAAGTAATGTGGTCAC
519 CGAAAAGTAATGTGGTCAC
28743245 GGTCATTTGT
Statistics
Matches: 489, Mismatches: 42, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
533 282 0.58
534 57 0.12
536 2 0.00
538 2 0.00
540 2 0.00
541 143 0.29
542 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (537 bp):
AGATATTCTGATGTTGCTTTGGAACTCACTAAGTTCTATAAACTTACTCCGTTTATCTTCCCTTC
TCAGGACCATTAAAGAAATAAAGGAACCTTCAAGGACTACGCCAGAGGATATATTATGTGTGAAG
CTTATAGTGATTTTGTATTATGCATGAAAGAGATAGCATCAAGGCTTGAAATATGAGAAACAATA
TTTTGTAACTAAAATTGTATCCACCAAATGGCGTCCTCTCCTTAAATCTTCACAATGAACTTTTG
TGTTTTAAAGGTGTTTAGGCCCTAAAGTCTAAAAGTTTTATTTACTACTACTATAGCAAACACCT
TTTGCTCTTTTGTAAACTTGAGATTCCGCCAATTTCGTAACAGTAAGGAAAGGCTTCAAAGTTGC
AACACACCACTCCTGGATCCTCCTTAAAGGTCAAGGATGAGGCACTACAACCGAAAACTTGTAAC
CTTGCACTTTTTGGATTAGTCACTAACACATGATAGATGAAAAACATGGCCCTCTTGTGTAATCG
AAAAGTAATGTGGTCAC
Done.