Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 82 of 199
Found at i:24684219 original size:133 final size:133
Alignment explanation
Indices: 24683912--24684514 Score: 634
Period size: 133 Copynumber: 4.5 Consensus size: 133
24683902 TAGTTTCTTC
* * ** *
24683912 GATCTACTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTAACTTCAATCTA
1 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTCGATCTA
* * * *** * * * *
24683977 CTCCACCACCAGTATGGGGAGACAAGATCTGTTGTCTTTGATCTACTTCACGCCCTATACATGAA
66 CTTCA-CGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCACG-CCAATACATGAA
24684042 GACAA
129 GACAA
*
24684047 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGAC-AGTATCTGCTTTCTTCGATCT
1 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAG-ATCTGCTTTCTTCGATCT
*
24684111 ACTTTACGCCAATACATGAAGACAAGATCT-TCTTTCTTCGATCTACTTCACGCCAATACATGAA
65 ACTTCACGCCAATACATGAAGACAAGATCTGT-TTTCTTCGATCTACTTCACGCCAATACATGAA
*
24684175 GTCAA
129 GACAA
* *
24684180 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTGTCTTTGATCTA
1 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTCGATCTA
* * ***
24684245 CTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCACCACCAGTATGGGAAG
66 CTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCA-CGCCAATACATGAAG
24684310 ACAA
130 ACAA
* * * *** *
24684314 GATCTGCTATCTTTGATCTACTTCA-CGCCAGTACATGAAGAC-AGATCTGCTTTTCTTTGATCT
1 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC-TTTCTTCGATCT
* * *
24684377 ACTTCACGCCAGTACATGAAGACAAGATCTGCATTTT-TT-GATCTACTT--CGCCACTAGTATG
65 ACTTCACGCCAATACATGAAGACAAGATCTG--TTTTCTTCGATCTACTTCACGCCAATA-CAT-
*
24684438 GGAAGATAA
126 -GAAGACAA
* * *** *
24684447 GATCTG-TTATCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCATTT-TCCGATC
1 GATCTGCTT-TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC-TTTCTTCGATC
24684509 TACTTC
64 TACTTC
24684515 GCCACCAATA
Statistics
Matches: 412, Mismatches: 43, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
130 6 0.01
131 1 0.00
132 9 0.02
133 241 0.58
134 90 0.22
135 65 0.16
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (133 bp):
GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTCGATCTA
CTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCACGCCAATACATGAAGA
CAA
Found at i:24684351 original size:222 final size:221
Alignment explanation
Indices: 24683912--24684540 Score: 888
Period size: 222 Copynumber: 2.8 Consensus size: 221
24683902 TAGTTTCTTC
* * *** ** *
24683912 GATCTACTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTAACTTCAATCTA
1 GATCTACTTTCTTCGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
* * *
24683977 CTCCACCACCAGTATGGGGAGACAAGATCTGTTGTCTTTGATCTACTTCACGCCCTATACATGAA
65 CTTCACCACCAGTATGGGAAGACAAGATCTGTTGTCTTTGATCTACTTCACG-CCAATACATGAA
* *
24684042 GACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGAC-AGTATCTGCTTTCTTC
129 GACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG-ATCTGCTATCTTC
*
24684106 GATCTACTTTACGCCAATACATGAAGACAA
193 GATCTACTTCACGCCAATACATGAAGAC-A
* * *
24684136 GATCTTCTTTCTTCGATCTACTTCACGCCAATACATGAAGTCAAGATCTGCTTTCTTCGATCTAC
1 GATCTACTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTAC
*
24684201 TTCACCACCAGTATGGGAAGACAAGATCTGCTGTCTTTGATCTACTTCACGCCAATACATGAAGA
66 TTCACCACCAGTATGGGAAGACAAGATCTGTTGTCTTTGATCTACTTCACGCCAATACATGAAGA
* *
24684266 CAAGATCTGTTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGAT
131 CAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGAT
*
24684331 CTACTTCACGCCAGTACATGAAGACA
196 CTACTTCACGCCAATACATGAAGACA
* * *
24684357 GATCTGCTTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCATTT-TTTGATCT
1 GATCTAC-TTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-TTTCTTCGATCT
* * * * *
24684421 ACTTCGCCACTAGTATGGGAAGATAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAA
64 ACTTCACCACCAGTATGGGAAGACAAGATCTGTTGTCTTTGATCTACTTCACGCCAATACATGAA
*
24684486 GACAAGATCTGCATTTTC--CGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
129 GACAAGATCTG--TTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT
24684541 ACTGCTACTC
Statistics
Matches: 366, Mismatches: 34, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
221 7 0.02
222 247 0.67
223 84 0.23
224 28 0.08
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (221 bp):
GATCTACTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTAC
TTCACCACCAGTATGGGAAGACAAGATCTGTTGTCTTTGATCTACTTCACGCCAATACATGAAGA
CAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGAT
CTACTTCACGCCAATACATGAAGACA
Found at i:24685820 original size:14 final size:14
Alignment explanation
Indices: 24685801--24685850 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
24685791 CCTTAGCCTC
24685801 TCCATTTTACTTTT
1 TCCATTTTACTTTT
*
24685815 TCCATTTTTCATTTT
1 TCCATTTTAC-TTTT
*
24685830 TTC-TTTTCAC-TTT
1 TCCATTTT-ACTTTT
24685843 TCCATTTT
1 TCCATTTT
24685851 TTTTCATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 5 0.17
14 17 0.59
15 7 0.24
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (14 bp):
TCCATTTTACTTTT
Found at i:24686819 original size:19 final size:19
Alignment explanation
Indices: 24686795--24686834 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
24686785 AATTTGGCAG
24686795 AAAAAATCAG-AAAGAATGA
1 AAAAAATC-GTAAAGAATGA
24686814 AAAAAATCGTAAAGAATGA
1 AAAAAATCGTAAAGAATGA
24686833 AA
1 AA
24686835 GAACATTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.68, C:0.05, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAAAATCGTAAAGAATGA
Found at i:24688729 original size:19 final size:20
Alignment explanation
Indices: 24688705--24688744 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
24688695 AACCGTGTTT
* *
24688705 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
24688724 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
24688744 A
1 A
24688745 TGCGAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:24688796 original size:13 final size:13
Alignment explanation
Indices: 24688778--24688803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24688768 GTTTAATTTT
24688778 TTTACTAGAAAAC
1 TTTACTAGAAAAC
24688791 TTTACTAGAAAAC
1 TTTACTAGAAAAC
24688804 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:24691633 original size:18 final size:16
Alignment explanation
Indices: 24691603--24691651 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
24691593 ATTTTATACG
*
24691603 AAAAAAATGAAAAAAT
1 AAAAAAATAAAAAAAT
*
24691619 AAAAGAAAATAAAAACAT
1 -AAA-AAAATAAAAAAAT
*
24691637 AAATAAATAAAAAAA
1 AAAAAAATAAAAAAA
24691652 CGGACACTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.37
17 6 0.22
18 11 0.41
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.12
Consensus pattern (16 bp):
AAAAAAATAAAAAAAT
Found at i:24699426 original size:31 final size:29
Alignment explanation
Indices: 24699388--24699464 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
24699378 TTAATGACTC
*
24699388 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
***
24699419 AGTGACTAAAATGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
24699448 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
24699465 CTGAGGCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 23 0.55
30 1 0.02
31 18 0.43
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:24699592 original size:15 final size:17
Alignment explanation
Indices: 24699567--24699599 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
24699557 TGCATTTTGT
24699567 ATTATATTTTAAA-AAA
1 ATTATATTTTAAATAAA
24699583 ATTA-ATTTTAAATAAA
1 ATTATATTTTAAATAAA
24699599 A
1 A
24699600 AGTAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATATTTTAAATAAA
Found at i:24711059 original size:46 final size:46
Alignment explanation
Indices: 24710982--24711140 Score: 158
Period size: 46 Copynumber: 3.4 Consensus size: 46
24710972 CAACCTAGCA
* * ** **
24710982 GGTGACCAGGCACTATTCTCCGATTAATGTAGGTTTAACCTTAATG
1 GGTGACCAGACACTATTATCTTATTCGTGTAGGTTTAACCTTAATG
* * *
24711028 GGTGACCAGGCACTATTATCTTATTCGTGTAGGTTCAACCCTT-ACG
1 GGTGACCAGACACTATTATCTTATTCGTGTAGGTTTAA-CCTTAATG
* * *
24711074 GTTGACCAGACACTATGATTCATTATTCGTGTAGGTTTAACCTAAATG
1 GGTGACCAGACACTATTA-TC-TTATTCGTGTAGGTTTAACCTTAATG
* *
24711122 GGTAACCAAACACTATTAT
1 GGTGACCAGACACTATTAT
24711141 TTTCACCTGT
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
46 49 0.53
47 10 0.11
48 33 0.36
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (46 bp):
GGTGACCAGACACTATTATCTTATTCGTGTAGGTTTAACCTTAATG
Found at i:24711135 original size:48 final size:45
Alignment explanation
Indices: 24711009--24711137 Score: 141
Period size: 48 Copynumber: 2.8 Consensus size: 45
24710999 CTCCGATTAA
* *
24711009 TGTAGGTTTAACCTTAATGGGTGACCAGGCACTATTATCTTATTCG
1 TGTAGGTTTAACC-TAATGGGTGACCAGACACTATGATCTTATTCG
* * * *
24711055 TGTAGGTTCAACCCTTACGGTTGACCAGACACTATGATTCATTATTCG
1 TGTAGGTTTAA-CCTAATGGGTGACCAGACACTATGA-TC-TTATTCG
* *
24711103 TGTAGGTTTAACCTAAATGGGTAACCAAACACTAT
1 TGTAGGTTTAACCT-AATGGGTGACCAGACACTAT
24711138 TATTTTCACC
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
46 28 0.42
47 7 0.10
48 32 0.48
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (45 bp):
TGTAGGTTTAACCTAATGGGTGACCAGACACTATGATCTTATTCG
Found at i:24712227 original size:182 final size:182
Alignment explanation
Indices: 24711914--24712283 Score: 641
Period size: 182 Copynumber: 2.0 Consensus size: 182
24711904 TATAAACTTG
* * * *
24711914 GGTTTCTGGTAAGCAAATGTTATAATTGGCATTCTTAAAATTGTGAATTTAGATGGTTAAAACAT
1 GGTTTGTGGTAAGAAAATGTTATAATTGGAATTCTTAAAATTGTGAATTTAGATGGATAAAACAT
24711979 ATTTGGTTGTTGATTTGAATTGATGAATTGTTGGTACCAATGAGGGCATATTCGTTGTATGTTTA
66 ATTTGGTTGTTGATTTGAATTGATGAATTGTTGGTACCAATGAGGGCATATTCGTTGTATGTTTA
*
24712044 AATGATTAGGTAAATTGGTTTTTTGGCTTTGAAATATGTATGTTTTGGTGTT
131 AATGATTAGGTAAATTGGTTTTTTGGCTTTGAAATATGTAGGTTTTGGTGTT
*
24712096 GGTTTGTGGTAAGAAAATGTTATAATTGGAATTCTTGAAATTGTGAATTTAGATGGATAAAACAT
1 GGTTTGTGGTAAGAAAATGTTATAATTGGAATTCTTAAAATTGTGAATTTAGATGGATAAAACAT
* * *
24712161 ATTTGGTTGTTGATTTGAATTGATGAATTGTTGGTGCCAATGATGGCATATTGGTTGTATGTTTA
66 ATTTGGTTGTTGATTTGAATTGATGAATTGTTGGTACCAATGAGGGCATATTCGTTGTATGTTTA
* *
24712226 AATGGTTAGGTGAATTGGTTTTTTGGCTTTGAAATATGTAGGTTTTGGTGTT
131 AATGATTAGGTAAATTGGTTTTTTGGCTTTGAAATATGTAGGTTTTGGTGTT
24712278 GGTTTG
1 GGTTTG
24712284 AATAACAAAA
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
182 177 1.00
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.44
Consensus pattern (182 bp):
GGTTTGTGGTAAGAAAATGTTATAATTGGAATTCTTAAAATTGTGAATTTAGATGGATAAAACAT
ATTTGGTTGTTGATTTGAATTGATGAATTGTTGGTACCAATGAGGGCATATTCGTTGTATGTTTA
AATGATTAGGTAAATTGGTTTTTTGGCTTTGAAATATGTAGGTTTTGGTGTT
Found at i:24726166 original size:25 final size:25
Alignment explanation
Indices: 24726137--24726187 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
24726127 CTTTTAAACA
*
24726137 TATAACACTTTATATACAATCATAT
1 TATAACACTTTACATACAATCATAT
24726162 TATAACACTTTACATACAATCATAT
1 TATAACACTTTACATACAATCATAT
24726187 T
1 T
24726188 TAGAGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (25 bp):
TATAACACTTTACATACAATCATAT
Found at i:24728796 original size:19 final size:19
Alignment explanation
Indices: 24728760--24728797 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
24728750 ATTGCAAAAA
*
24728760 TTCATATATTCTTGTATTT
1 TTCATATATACTTGTATTT
24728779 TTCACTATATACTT-TATTT
1 TTCA-TATATACTTGTATTT
24728798 ATTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.61
Consensus pattern (19 bp):
TTCATATATACTTGTATTT
Found at i:24728952 original size:51 final size:51
Alignment explanation
Indices: 24728892--24729009 Score: 202
Period size: 51 Copynumber: 2.3 Consensus size: 51
24728882 TTTATTTCAC
24728892 ATTTC-ATTTAATTCACATAATTAATTCTACTATCTCATTTTTCACATCAA
1 ATTTCTATTTAATTCACATAATTAATTCTACTATCTCATTTTTCACATCAA
*
24728942 ATTTCTATTTAATTCACATAATTAATTCTACTATTTCATTTTTCACATCAA
1 ATTTCTATTTAATTCACATAATTAATTCTACTATCTCATTTTTCACATCAA
* *
24728993 ATTTCTATGTATTTCAC
1 ATTTCTATTTAATTCAC
24729010 TTGTATTATT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
50 5 0.08
51 59 0.92
ACGTcount: A:0.32, C:0.19, G:0.01, T:0.48
Consensus pattern (51 bp):
ATTTCTATTTAATTCACATAATTAATTCTACTATCTCATTTTTCACATCAA
Found at i:24729433 original size:144 final size:144
Alignment explanation
Indices: 24729173--24729461 Score: 517
Period size: 144 Copynumber: 2.0 Consensus size: 144
24729163 AGTTCATGGG
* *
24729173 TACTTCCTCTTTTTCTATGAAAATCTCTTCCTTTTTACTTCTCCTACCACTTGAATCTTTTTCTC
1 TACTTCCTCTTTTTCTATCAAAATCTCTTCCGTTTTACTTCTCCTACCACTTGAATCTTTTTCTC
24729238 AACTTTTCTATTCATCGACATGTCAAAATACAATATTTCCCCATGAGAAACCTTTACTTTAACAC
66 AACTTTTCTATTCATCGACATGTCAAAATACAATATTTCCCCATGAGAAACCTTTACTTTAACAC
24729303 CATATTTATGATTT
131 CATATTTATGATTT
*
24729317 TACTTCCTCTTTTTCTATCAAAATCTCTTCCGTTTTACTTCTCCTACCACTTGACTCTTTTTCTC
1 TACTTCCTCTTTTTCTATCAAAATCTCTTCCGTTTTACTTCTCCTACCACTTGAATCTTTTTCTC
*
24729382 AACTTTTCTCTTCATC-AGCATGTCAAAATACAATATTTCCCCATGAGAAACCTTTACTTTAACA
66 AACTTTTCTATTCATCGA-CATGTCAAAATACAATATTTCCCCATGAGAAACCTTTACTTTAACA
*
24729446 CCATATTTATGTTTT
130 CCATATTTATGATTT
24729461 T
1 T
24729462 TTTTCTATCA
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
143 1 0.01
144 138 0.99
ACGTcount: A:0.25, C:0.26, G:0.05, T:0.44
Consensus pattern (144 bp):
TACTTCCTCTTTTTCTATCAAAATCTCTTCCGTTTTACTTCTCCTACCACTTGAATCTTTTTCTC
AACTTTTCTATTCATCGACATGTCAAAATACAATATTTCCCCATGAGAAACCTTTACTTTAACAC
CATATTTATGATTT
Found at i:24729676 original size:4 final size:4
Alignment explanation
Indices: 24729664--24729694 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
24729654 TAAAATTAGT
24729664 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
24729695 AAGGATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:24730091 original size:31 final size:31
Alignment explanation
Indices: 24729998--24730093 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
24729988 GGCAAATTAC
*
24729998 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
24730029 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
24730061 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
24730092 AA
1 AA
24730094 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:24739590 original size:32 final size:32
Alignment explanation
Indices: 24739554--24739624 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
24739544 TTTACGTATA
*
24739554 ATCATTTAAGCATAACCTTACAACATTTATCC
1 ATCATTTAAGCACAACCTTACAACATTTATCC
24739586 ATCATTTAAGCACAACCTTACAACATTTATCC
1 ATCATTTAAGCACAACCTTACAACATTTATCC
24739618 ATCATTT
1 ATCATTT
24739625 CCATTTCAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (32 bp):
ATCATTTAAGCACAACCTTACAACATTTATCC
Found at i:24746394 original size:43 final size:43
Alignment explanation
Indices: 24746092--24746404 Score: 301
Period size: 43 Copynumber: 7.3 Consensus size: 43
24746082 TTATGTGAAA
* * * *
24746092 AAACGCCGCTATAGAACATGAACTTTAGCGGCACTTTTATAAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
* *
24746135 AAACACCGCTAAAGAACATAACCTTTAGCGGCAC-TTTACTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTA-TCAC
* *
24746178 AAACGCCGCTAAAGAACATGATCTTTAGTGGCACTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
* **
24746221 AAACGCCACTAAAGAACATGACC-TTAGCGGTGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
* * * **
24746263 AAGCGCCGCTAAAGAGCATGACCTTTAACGGTTCTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
* * * ** * *
24746306 AAACGCCACTATAGAGA-ATG-CCTTTTAACGGCTTTTTTTTTAC
1 AAACGCCGCTAAAGA-ACATGACC-TTTAGCGGCACTTTTATCAC
* * * * * *
24746349 AAACACTGTTAAACAACATGATCTTTAGTGGCACTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
*
24746392 AAACGCTGCTAAA
1 AAACGCCGCTAAA
24746405 AGCACCGTTC
Statistics
Matches: 220, Mismatches: 43, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
42 43 0.20
43 172 0.78
44 5 0.02
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCAC
Found at i:24751219 original size:22 final size:23
Alignment explanation
Indices: 24751194--24751270 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 23
24751184 ATACAAAAAT
24751194 AAACCCTAAACCTTAAAACTC-A
1 AAACCCTAAACCTTAAAACTCTA
*
24751216 AAACCTTAAACCTTAAAACTCTA
1 AAACCCTAAACCTTAAAACTCTA
** * *
24751239 AAACTTTAAA-CTTTAAACCCTA
1 AAACCCTAAACCTTAAAACTCTA
*
24751261 AAATCCTAAA
1 AAACCCTAAA
24751271 ACTCTAAACC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 37 0.79
23 10 0.21
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (23 bp):
AAACCCTAAACCTTAAAACTCTA
Found at i:24751243 original size:30 final size:30
Alignment explanation
Indices: 24751193--24751314 Score: 126
Period size: 30 Copynumber: 4.1 Consensus size: 30
24751183 TATACAAAAA
* *
24751193 TAAACCCTAAACCT-TAAAACTCAAAACCT
1 TAAACCCTAAAACTCTAAAACTCTAAACCT
* * *
24751222 TAAACCTTAAAACTCTAAAACTTTAAACTT
1 TAAACCCTAAAACTCTAAAACTCTAAACCT
24751252 TAAACCCTAAAA-TCCTAAAACTCTAAACCT
1 TAAACCCTAAAACT-CTAAAACTCTAAACCT
* * *
24751282 TACACCCTAAAA-TCATAAACCT-TAAACCC
1 TAAACCCTAAAACTC-TAAAACTCTAAACCT
24751311 TAAA
1 TAAA
24751315 ATAAAATATT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
29 23 0.29
30 55 0.71
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.25
Consensus pattern (30 bp):
TAAACCCTAAAACTCTAAAACTCTAAACCT
Found at i:24751290 original size:22 final size:22
Alignment explanation
Indices: 24751265--24751316 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
24751255 ACCCTAAAAT
*
24751265 CCTAAAACTC-TAAACCTTACAC
1 CCTAAAA-TCATAAACCTTAAAC
24751287 CCTAAAATCATAAACCTTAAAC
1 CCTAAAATCATAAACCTTAAAC
24751309 CCTAAAAT
1 CCTAAAAT
24751317 AAAATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (22 bp):
CCTAAAATCATAAACCTTAAAC
Found at i:24751648 original size:84 final size:84
Alignment explanation
Indices: 24751461--24751695 Score: 299
Period size: 84 Copynumber: 2.8 Consensus size: 84
24751451 GGGGCTAAGA
* * * * **
24751461 AAACGACGCCATTTAAATCAAATTGGTATTGCAATTTTGCGGCGTTTTTAGGGCAAACGCCACTA
1 AAACAACGCCGTTTAAGTCAAATTGGTATTGCAATTTTGCGGCG--TTTATGAAAAACGCCACT-
*
24751526 AAAAACTTAATTCCCTATAGTG
63 AAAAACTTAATTCCATATAGTG
* * *
24751548 AAACAACGACGTTTAAGTCAAATTGGTATCGCAATTTTGCGACGTTTATGAAAAACGCCACTAAA
1 AAACAACGCCGTTTAAGTCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACGCCACTAAA
* *
24751613 AACTTAATTCCATGTCGTG
66 AACTTAATTCCATATAGTG
* * * *
24751632 AAACAACGCCGTTTAAGTCAAATTGGTATTGTATTTTTGTGGCGTTTATGAAAAATGCCACTAA
1 AAACAACGCCGTTTAAGTCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACGCCACTAA
24751696 TGTATAACCT
Statistics
Matches: 129, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
84 76 0.59
85 15 0.12
87 38 0.29
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (84 bp):
AAACAACGCCGTTTAAGTCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACGCCACTAAA
AACTTAATTCCATATAGTG
Found at i:24751819 original size:124 final size:123
Alignment explanation
Indices: 24751599--24752008 Score: 518
Period size: 124 Copynumber: 3.3 Consensus size: 123
24751589 ACGTTTATGA
* * * *
24751599 AAAACGCCACTAAAAACTTAATTCCATGTCGTGAAACAACGCCGTTTAAGTCAAATTGGTATTGT
1 AAAACGCCACTAAAAATTTAATTCCCTGTAGTGAAACGACGCCGTTTAAGTC-AATTGGTATTGT
* * * *
24751664 ATTTTTGTGGCGTTTATGAAAAATGCCACTAATGTATAACCTTTGAGGCATTTTCGGTC
65 AATTTTGCGGCGTTTATGAAAAACGCCACTAATGTATAACCTTTGAGGCATTTTCAGTC
*
24751723 AAAACGCCACTAAAAATTTAATTCCCTATAGTGAAACGACGCCGTTTAAGTCAATTTGGTATTGT
1 AAAACGCCACTAAAAATTTAATTCCCTGTAGTGAAACGACGCCGTTTAAGTCAA-TTGGTATTGT
* * * *
24751788 AATTTTACGGCGTTTATGAAAAACCCCACTAACGTATAACCTTT-ACGGCTTTTTCAGTC
65 AATTTTGCGGCGTTTATGAAAAACGCCACTAATGTATAACCTTTGA-GGCATTTTCAGTC
* * * * * *
24751847 AAAATGCCACTAAAAGTTTAATGCTCTGTAGTGAAACGACGACGTTTAAGTCGAATTGGTATTGC
1 AAAACGCCACTAAAAATTTAATTCCCTGTAGTGAAACGACGCCGTTTAAGTC-AATTGGTATTGT
* * * *
24751912 AATTTTGCGGTGTTTATAAAAAACGCCACTAATGTATCACCTTTGAGGCATTTTCAATC
65 AATTTTGCGGCGTTTATGAAAAACGCCACTAATGTATAACCTTTGAGGCATTTTCAGTC
* * * *
24751971 AAAACGACACTAAAAAAATT-ATTTCCTGTAGTGGAACG
1 AAAACGCCACT-AAAAATTTAATTCCCTGTAGTGAAACG
24752009 GTGTCGTTTT
Statistics
Matches: 245, Mismatches: 36, Indels: 10
0.84 0.12 0.03
Matches are distributed among these distances:
123 3 0.01
124 233 0.95
125 9 0.04
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (123 bp):
AAAACGCCACTAAAAATTTAATTCCCTGTAGTGAAACGACGCCGTTTAAGTCAATTGGTATTGTA
ATTTTGCGGCGTTTATGAAAAACGCCACTAATGTATAACCTTTGAGGCATTTTCAGTC
Found at i:24754788 original size:16 final size:15
Alignment explanation
Indices: 24754767--24754799 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
24754757 TCATGGTTTT
24754767 TTTATAATTTTTATAA
1 TTTATAATTTTTA-AA
24754783 TTTATAATTTTTAAA
1 TTTATAATTTTTAAA
24754798 TT
1 TT
24754800 ATTTGTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTATAATTTTTAAA
Found at i:24757993 original size:7 final size:7
Alignment explanation
Indices: 24757977--24758017 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
24757967 GTCCAAAAAG
*
24757977 TATATTA
1 TATATAA
24757984 TATATAA
1 TATATAA
24757991 TATATAA
1 TATATAA
24757998 TATATAA
1 TATATAA
24758005 TATATAA
1 TATATAA
24758012 TATATA
1 TATATA
24758018 TTATTTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TATATAA
Found at i:24758002 original size:21 final size:21
Alignment explanation
Indices: 24757977--24758025 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
24757967 GTCCAAAAAG
24757977 TATATTATATATAATATATAA
1 TATATTATATATAATATATAA
* *
24757998 TATATAATATATAATATATAT
1 TATATTATATATAATATATAA
24758019 TAT-TTAT
1 TATATTAT
24758026 TTTGATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATTATATATAATATATAA
Found at i:24761120 original size:28 final size:29
Alignment explanation
Indices: 24761072--24761126 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
24761062 ATGTTGCCAT
* *
24761072 TGATGAAATTTGTGATTTTAGATGTTAAG
1 TGATGAAATTTGAGATATTAGATGTTAAG
*
24761101 TGATG-AATTTGAGATATTAGTTGTTA
1 TGATGAAATTTGAGATATTAGATGTTA
24761127 TGTAAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (29 bp):
TGATGAAATTTGAGATATTAGATGTTAAG
Found at i:24781577 original size:14 final size:14
Alignment explanation
Indices: 24781558--24781584 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24781548 TCGGTTAAAG
24781558 TTAGTGAAGTTTAT
1 TTAGTGAAGTTTAT
24781572 TTAGTGAAGTTTA
1 TTAGTGAAGTTTA
24781585 AAGGAGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (14 bp):
TTAGTGAAGTTTAT
Found at i:24782320 original size:46 final size:46
Alignment explanation
Indices: 24782253--24782345 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
24782243 GTGGAGCATC
24782253 TGTATTATCAAAAATTGATCTCCGTTCTGAGTACCATCAGCTCAAG
1 TGTATTATCAAAAATTGATCTCCGTTCTGAGTACCATCAGCTCAAG
24782299 TGTATTATCAAAAATTGATCTCCGTTCTGAGTACCATCAGCTCAAG
1 TGTATTATCAAAAATTGATCTCCGTTCTGAGTACCATCAGCTCAAG
24782345 T
1 T
24782346 TTAAGGAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (46 bp):
TGTATTATCAAAAATTGATCTCCGTTCTGAGTACCATCAGCTCAAG
Found at i:24791141 original size:18 final size:20
Alignment explanation
Indices: 24791118--24791166 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 20
24791108 TGACATATGG
24791118 TAAAAAAATTATAA-AAG-A
1 TAAAAAAATTATAATAAGTA
*
24791136 T-AAAAAATAATAATAAGTA
1 TAAAAAAATTATAATAAGTA
24791155 TAAAAAATATTA
1 TAAAAAA-ATTA
24791167 AATTTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 11 0.44
18 4 0.16
19 2 0.08
20 5 0.20
21 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
TAAAAAAATTATAATAAGTA
Found at i:24791151 original size:20 final size:19
Alignment explanation
Indices: 24791120--24791163 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
24791110 ACATATGGTA
*
24791120 AAAAAATTATAA-AAG-AT
1 AAAAAATAATAATAAGTAT
24791137 AAAAAATAATAATAAGTAT
1 AAAAAATAATAATAAGTAT
24791156 AAAAAATA
1 AAAAAATA
24791164 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.46
18 3 0.12
19 10 0.42
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAAATAATAATAAGTAT
Found at i:24791157 original size:19 final size:17
Alignment explanation
Indices: 24791120--24791168 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 17
24791110 ACATATGGTA
*
24791120 AAAAAATTATAAAAGAT
1 AAAAAATAATAAAAGAT
24791137 AAAAAATAATAATAAGTAT
1 AAAAAATAATAA-AAG-AT
*
24791156 AAAAAATATTAAA
1 AAAAAATAATAAA
24791169 TTTTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 11 0.39
18 4 0.14
19 13 0.46
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (17 bp):
AAAAAATAATAAAAGAT
Found at i:24791185 original size:28 final size:29
Alignment explanation
Indices: 24791143--24791208 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
24791133 AGATAAAAAA
*
24791143 TAATAATAAGTATAAAAAATATT-AAATTT
1 TAATAA-AAATATAAAAAATATTAAAATTT
* *
24791172 TAATAAAAATATAAAAAGTTTTAAAATTT
1 TAATAAAAATATAAAAAATATTAAAATTT
*
24791201 TATTAAAA
1 TAATAAAA
24791209 GGTAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
TAATAAAAATATAAAAAATATTAAAATTT
Found at i:24791216 original size:29 final size:28
Alignment explanation
Indices: 24791143--24791225 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
24791133 AGATAAAAAA
* * *
24791143 TAATAATAAGTATAAAAAATATTAAATTT
1 TAATAA-AAATATAAAAATTATAAAATTT
*
24791172 TAATAAAAATATAAAAAGTTTTAAAATTT
1 TAATAAAAATATAAAAA-TTATAAAATTT
* *
24791201 TATTAAAAGGTA-AAAAATTATAAAA
1 TAATAAAA-ATATAAAAATTATAAAA
24791226 ACCCTAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 17 0.38
29 26 0.58
30 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (28 bp):
TAATAAAAATATAAAAATTATAAAATTT
Found at i:24791283 original size:75 final size:74
Alignment explanation
Indices: 24791128--24791283 Score: 163
Period size: 75 Copynumber: 2.1 Consensus size: 74
24791118 TAAAAAAATT
* ** * *
24791128 ATAAAAGATAAAAAATAATAATAAGTATAAAAAATATTAAATTTTAATAAAAATATAAAAAGTTT
1 ATAAAAGATAAAAAATAATAAAAACCATAAAAAATATTAAATTTTAATAAAAATATAAAAAATTA
**
24791193 TAAAATTTT
66 TAAAATTAC
* * * *
24791202 ATTAAAAGGTAAAAAATTATAAAAACCCTAAAAAAT-TGTAAATTTTTATAAAAATTATAAAAAA
1 A-TAAAAGATAAAAAATAATAAAAACCATAAAAAATAT-TAAATTTTAATAAAAA-TAT-AAAAA
24791266 ATTATAAAA-TAC
62 ATTATAAAATTAC
24791278 ATAAAA
1 ATAAAA
24791284 AAATTCTCAT
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
74 2 0.03
75 48 0.72
76 5 0.07
77 12 0.18
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (74 bp):
ATAAAAGATAAAAAATAATAAAAACCATAAAAAATATTAAATTTTAATAAAAATATAAAAAATTA
TAAAATTAC
Found at i:24793361 original size:18 final size:18
Alignment explanation
Indices: 24793338--24793375 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
24793328 AAAAACCCCT
*
24793338 AACCCTAGG-AAGAAATAG
1 AACCCT-GGAAAGAAACAG
24793356 AACCCTGGAAAGAAACAG
1 AACCCTGGAAAGAAACAG
24793374 AA
1 AA
24793376 AGCGCGTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.53, C:0.18, G:0.21, T:0.08
Consensus pattern (18 bp):
AACCCTGGAAAGAAACAG
Found at i:24794564 original size:22 final size:22
Alignment explanation
Indices: 24794536--24794577 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
24794526 TTAGAAAGGT
24794536 GCTAGCTAAGTTTTGTTATTGA
1 GCTAGCTAAGTTTTGTTATTGA
24794558 GCTAGCTAAGTTTTGTTATT
1 GCTAGCTAAGTTTTGTTATT
24794578 AAGTTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (22 bp):
GCTAGCTAAGTTTTGTTATTGA
Found at i:24799590 original size:22 final size:22
Alignment explanation
Indices: 24799562--24799612 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
24799552 GAATAAAAAG
24799562 TGAGCTAGCTAAGTTCTGTTAT
1 TGAGCTAGCTAAGTTCTGTTAT
24799584 TGAGCTAGCTAAGTTCTGTTAT
1 TGAGCTAGCTAAGTTCTGTTAT
*
24799606 TAAGCTA
1 TGAGCTA
24799613 AGTTTGTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (22 bp):
TGAGCTAGCTAAGTTCTGTTAT
Found at i:24799613 original size:18 final size:20
Alignment explanation
Indices: 24799568--24799621 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
24799558 AAAGTGAGCT
24799568 AGCTAAGTTCTGTTATTGAGC
1 AGCTAAGTTCTGTTATTGA-C
24799589 TAGCTAAGTTCTGTTATT-A-
1 -AGCTAAGTTCTGTTATTGAC
24799608 AGCTAAGTT-TGTTA
1 AGCTAAGTTCTGTTA
24799622 GTTTGTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.16
18 9 0.28
21 1 0.03
22 17 0.53
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (20 bp):
AGCTAAGTTCTGTTATTGAC
Found at i:24803145 original size:18 final size:18
Alignment explanation
Indices: 24803122--24803157 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
24803112 AACTAGTTTT
24803122 AACGATGCTGATGTGGCA
1 AACGATGCTGATGTGGCA
*
24803140 AACGATGCTGATTTGGCA
1 AACGATGCTGATGTGGCA
24803158 TCCCACACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.25
Consensus pattern (18 bp):
AACGATGCTGATGTGGCA
Found at i:24806073 original size:17 final size:16
Alignment explanation
Indices: 24806048--24806082 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
24806038 AATATTTTCT
24806048 AAAAATACAAAAATTA
1 AAAAATACAAAAATTA
24806064 AAAAACTACAAAAATTA
1 AAAAA-TACAAAAATTA
24806081 AA
1 AA
24806083 TTAAATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAATACAAAAATTA
Found at i:24806990 original size:55 final size:55
Alignment explanation
Indices: 24806929--24807039 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
24806919 CCCGCGTGCG
24806929 CGCCTTCGCACGTGCGCCACCGCTGCTTGTTGTGCCTCCATACACGCCACGTCCC
1 CGCCTTCGCACGTGCGCCACCGCTGCTTGTTGTGCCTCCATACACGCCACGTCCC
24806984 CGCCTTCGCACGTGCGCCACCGCTGCTTGTTGTGCCTCCATACACGCCACGTCCC
1 CGCCTTCGCACGTGCGCCACCGCTGCTTGTTGTGCCTCCATACACGCCACGTCCC
24807039 C
1 C
24807040 AGCCCTGCTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.11, C:0.46, G:0.22, T:0.22
Consensus pattern (55 bp):
CGCCTTCGCACGTGCGCCACCGCTGCTTGTTGTGCCTCCATACACGCCACGTCCC
Found at i:24808185 original size:18 final size:18
Alignment explanation
Indices: 24808155--24808189 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24808145 TATATGCATG
24808155 TACATTACTTTATTTTAT
1 TACATTACTTTATTTTAT
24808173 TACA-TACTGTTATTTTA
1 TACATTACT-TTATTTTA
24808190 ATTCTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (18 bp):
TACATTACTTTATTTTAT
Found at i:24819638 original size:44 final size:43
Alignment explanation
Indices: 24819567--24819688 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 43
24819557 GAAGATGGCA
* * * *
24819567 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* * * *
24819611 AATCCTATATCCCTGAAGTTGTAGTGGAGAAGATTAAAGTAAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
*
24819654 AGATCCTATCCCCCTGAAGTTGCAGTGGAGCAGAT
1 A-ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
24819689 CAAAATGATC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 3 0.05
44 62 0.95
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (43 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
Found at i:24821637 original size:18 final size:18
Alignment explanation
Indices: 24821607--24821641 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24821597 TATATGCATG
24821607 TACATTACTTTATTTTAT
1 TACATTACTTTATTTTAT
24821625 TACA-TACTGTTATTTTA
1 TACATTACT-TTATTTTA
24821642 ATTCTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (18 bp):
TACATTACTTTATTTTAT
Found at i:24822036 original size:23 final size:21
Alignment explanation
Indices: 24822010--24822057 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
24822000 TTTATTTAAA
24822010 TTAATAAAT-ATATGTTATTTTCT
1 TTAAT-AATGATAT-TTATTTT-T
*
24822033 TTAATTATGATATTTATTTTT
1 TTAATAATGATATTTATTTTT
24822054 TTAA
1 TTAA
24822058 ATTTATTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 5 0.22
22 9 0.39
23 9 0.39
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TTAATAATGATATTTATTTTT
Found at i:24826136 original size:20 final size:20
Alignment explanation
Indices: 24826111--24826162 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
24826101 TGTATATTAT
24826111 ATATTTATATTTTATTTTTA
1 ATATTTATATTTTATTTTTA
* *
24826131 ATATTTAGATTTAATTTTTA
1 ATATTTATATTTTATTTTTA
*
24826151 AGA-TTATATTTT
1 ATATTTATATTTT
24826163 TGTTTGTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
ATATTTATATTTTATTTTTA
Found at i:24829678 original size:40 final size:40
Alignment explanation
Indices: 24829605--24829794 Score: 209
Period size: 40 Copynumber: 4.8 Consensus size: 40
24829595 GAGTTACTGG
* * ** * *
24829605 AGTATAAATAGGGGCACAAAAGTGCATTTAGGGGTACCGA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTACCGA
* **
24829645 AGTACAAACAGAGGCACGTAAGTGCAATCAGGGGTACTAA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTACCGA
* **
24829685 AGTACAAACAGGAGCACGTAAGTGCAATCAGGGGTATTGA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTACCGA
* * *
24829725 GGTACAAACAGGGGCATGTAAGTGCAATCAGAGGTACCGA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTACCGA
* * * *
24829765 GGTACAAATAGGGGCACATAAGTTCAATCA
1 AGTACAAACAGGGGCACGTAAGTGCAATCA
24829795 TTCAATAATT
Statistics
Matches: 127, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 127 1.00
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.17
Consensus pattern (40 bp):
AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTACCGA
Found at i:24829696 original size:20 final size:19
Alignment explanation
Indices: 24829634--24829738 Score: 66
Period size: 20 Copynumber: 5.3 Consensus size: 19
24829624 AAGTGCATTT
*
24829634 AGGGGTACCGAAGTACAAAC
1 AGGGGTA-CTAAGTACAAAC
* * * *
24829654 AGAGGCACGTAAGTGCAATC
1 AGGGGTAC-TAAGTACAAAC
24829674 AGGGGTACTAAAGTACAAAC
1 AGGGGTACT-AAGTACAAAC
* * * *
24829694 AGGAGCACGTAAGTGCAATC
1 AGGGGTAC-TAAGTACAAAC
* *
24829714 AGGGGTATTGAGGTACAAAC
1 AGGGGTACT-AAGTACAAAC
24829734 AGGGG
1 AGGGG
24829739 CATGTAAGTG
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
19 3 0.05
20 58 0.94
21 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.32, T:0.14
Consensus pattern (19 bp):
AGGGGTACTAAGTACAAAC
Found at i:24830391 original size:113 final size:113
Alignment explanation
Indices: 24830264--24830489 Score: 443
Period size: 113 Copynumber: 2.0 Consensus size: 113
24830254 AATACAATAA
24830264 TCAAAGCTTCAAACACATGGTTATCATAAAAAAACCTTCAAGATTCATCAATGAAAACTTCTAAA
1 TCAAAGCTTCAAACACATGGTTATCATAAAAAAACCTTCAAGATTCATCAATGAAAACTTCTAAA
24830329 ATTTTTAACAGATTCAAAAACAAAGGTACGAGCTAGCTGAACCTAGGT
66 ATTTTTAACAGATTCAAAAACAAAGGTACGAGCTAGCTGAACCTAGGT
*
24830377 TCAAAGCTTCAAACACATGGTTATCATAAAAAAACCTTCAAGATTTATCAATGAAAACTTCTAAA
1 TCAAAGCTTCAAACACATGGTTATCATAAAAAAACCTTCAAGATTCATCAATGAAAACTTCTAAA
24830442 ATTTTTAACAGATTCAAAAACAAAGGTACGAGCTAGCTGAACCTAGGT
66 ATTTTTAACAGATTCAAAAACAAAGGTACGAGCTAGCTGAACCTAGGT
24830490 GCAACGATCT
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.26
Consensus pattern (113 bp):
TCAAAGCTTCAAACACATGGTTATCATAAAAAAACCTTCAAGATTCATCAATGAAAACTTCTAAA
ATTTTTAACAGATTCAAAAACAAAGGTACGAGCTAGCTGAACCTAGGT
Found at i:24840399 original size:45 final size:45
Alignment explanation
Indices: 24840305--24840413 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
24840295 AGGAAATGGT
* *
24840305 TAAGACCATAGTTGAAAGACACTATGACACAATATCGAAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACACAATACCGAAAACAAA
* * * *
24840350 TAAGACCATAGTTGAAAGACACTATGGCACCATACC-AGAAACGAG
1 TAAGACCATAGTTGAAAGACACTATGACACAATACCGA-AAACAAA
**
24840395 TAAGACCATAACTGAAAGA
1 TAAGACCATAGTTGAAAGA
24840414 TGTTATGGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 1 0.02
45 54 0.98
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGACACAATACCGAAAACAAA
Found at i:24840476 original size:45 final size:45
Alignment explanation
Indices: 24840391--24840516 Score: 128
Period size: 45 Copynumber: 2.8 Consensus size: 45
24840381 ATACCAGAAA
* * **
24840391 CGAGTAAGACCATAACTGAAAGATGTTATGGA-ATTGTGATTCCAT
1 CGAGTAAGACCATAACTGAAAGACGCTAT-GACATCATGATTCCAT
* * **
24840436 CGAGTAAGACTATAACTGAAAGACGGTATGACATCATGATTTTAT
1 CGAGTAAGACCATAACTGAAAGACGCTATGACATCATGATTCCAT
* ** *
24840481 CGAGTAAAACCATAGTTGAAAGACGCTATGGCATCA
1 CGAGTAAGACCATAACTGAAAGACGCTATGACATCA
24840517 CGAATCAAAC
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 2 0.03
45 65 0.97
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.26
Consensus pattern (45 bp):
CGAGTAAGACCATAACTGAAAGACGCTATGACATCATGATTCCAT
Found at i:24840592 original size:46 final size:45
Alignment explanation
Indices: 24840485--24840597 Score: 138
Period size: 45 Copynumber: 2.5 Consensus size: 45
24840475 TTTTATCGAG
* *
24840485 TAAAACCATAGTTGAAAGACGCTATGGCATCACGAATCAAACAAA
1 TAAAACCATAGTTGAAAGACACTATGGCAACACGAATCAAACAAA
* * * *
24840530 TAAGACCATAGTTGAAAGGCACTATGGCAACACGATTGAAA-ATGAA
1 TAAAACCATAGTTGAAAGACACTATGGCAACACGAATCAAACA--AA
*
24840576 TAAAACCATGGTTGAAAGACAC
1 TAAAACCATAGTTGAAAGACAC
24840598 CATGACACCC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 35 0.61
46 21 0.37
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.19
Consensus pattern (45 bp):
TAAAACCATAGTTGAAAGACACTATGGCAACACGAATCAAACAAA
Found at i:24846340 original size:26 final size:26
Alignment explanation
Indices: 24846311--24846360 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
24846301 TTAGATAAAA
24846311 AGGGGTTGCTAAGTGCAGATTCCTCG
1 AGGGGTTGCTAAGTGCAGATTCCTCG
**
24846337 AGGGGTTGCTAAGTGTTGATTCCT
1 AGGGGTTGCTAAGTGCAGATTCCT
24846361 TGAATTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCAGATTCCTCG
Found at i:24846482 original size:41 final size:41
Alignment explanation
Indices: 24846380--24846565 Score: 169
Period size: 43 Copynumber: 4.4 Consensus size: 41
24846370 GATTCTAAGG
* * * *
24846380 GTGGTTGTTAAGTGCTGATTCCACCGTAT-ATTTGATTGTGAAA
1 GTGGTTGCTAAGTGCTGATTCC-CCGTATCA-CTGAATAT-AAA
*
24846423 -TGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAA
1 GT-GGTTGCTAAGTGCTGATTCCCCGTATCACTGAATATAAA
* ** * *
24846464 GTGGTTGCTAAGTACTGATTCCACCGTATCTTTGATTGTGAAA
1 GTGGTTGCTAAGTGCTGATTCC-CCGTATCACTGAATAT-AAA
* * * * *
24846507 GGGGTTCCTATGTGCTGATTCCCCGTATCACTGAATTTAAG
1 GTGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATATAAA
24846548 GTGGTTGCTAAGTGCTGA
1 GTGGTTGCTAAGTGCTGA
24846566 ATCCACCAAG
Statistics
Matches: 115, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
41 38 0.33
42 37 0.32
43 40 0.35
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
GTGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATATAAA
Found at i:24846482 original size:84 final size:84
Alignment explanation
Indices: 24846380--24846572 Score: 314
Period size: 84 Copynumber: 2.3 Consensus size: 84
24846370 GATTCTAAGG
* * *
24846380 GTGGTTGTTAAGTGCTGATTCCACCGTATATTTGATTGTGAAATGGGTTGCTATGTGCTGATTCC
1 GTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTCCTATGTGCTGATTCC
24846445 CCGTATCACTGAATATAAA
66 CCGTATCACTGAATATAAA
* *
24846464 GTGGTTGCTAAGTACTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTCCTATGTGCTGATTCC
1 GTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTCCTATGTGCTGATTCC
* *
24846529 CCGTATCACTGAATTTAAG
66 CCGTATCACTGAATATAAA
*
24846548 GTGGTTGCTAAGTGCTGAATCCACC
1 GTGGTTGCTAAGTGCTGATTCCACC
24846573 AAGTAACGAA
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 100 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (84 bp):
GTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTCCTATGTGCTGATTCC
CCGTATCACTGAATATAAA
Found at i:24849016 original size:22 final size:21
Alignment explanation
Indices: 24848982--24849036 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
24848972 AATTAGTAAT
* * *
24848982 TTTTTGTTTTGTTTGTTTTTG
1 TTTTTGTTATGTTAGTTCTTG
24849003 TTTTTGTCTATGTTAGTTCTTG
1 TTTTTGT-TATGTTAGTTCTTG
*
24849025 -TTTTGTTTTGTT
1 TTTTTGTTATGTT
24849037 CAATTACGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 5 0.17
21 13 0.45
22 11 0.38
ACGTcount: A:0.04, C:0.04, G:0.18, T:0.75
Consensus pattern (21 bp):
TTTTTGTTATGTTAGTTCTTG
Found at i:24857279 original size:29 final size:29
Alignment explanation
Indices: 24857243--24857338 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
24857233 TCAAAGTGTC
* * *
24857243 GCCACAAAGGCATCCTTTTAACAGTGATT
1 GCCACAAAGACATCCTTTTAACAGAGATA
* * * ** *
24857272 GCCACAAAGTCTTTCTTTTAGTAGAAATA
1 GCCACAAAGACATCCTTTTAACAGAGATA
*
24857301 GCCACAAAGACATCCTTTTAACAAAGATA
1 GCCACAAAGACATCCTTTTAACAGAGATA
24857330 GCCACAAAG
1 GCCACAAAG
24857339 CTTTCCTTTT
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (29 bp):
GCCACAAAGACATCCTTTTAACAGAGATA
Found at i:24857357 original size:29 final size:30
Alignment explanation
Indices: 24857220--24857358 Score: 101
Period size: 29 Copynumber: 4.8 Consensus size: 30
24857210 TTCTGAAAGG
* * *
24857220 AAAGACTTTCCTTTCAA-AGTG-TCGCCAC
1 AAAGACTTTCCTTTTAATAGAGATAGCCAC
* * * * *
24857248 AAAGGC-ATCCTTTTAACAGTGATTGCCAC
1 AAAGACTTTCCTTTTAATAGAGATAGCCAC
* * *
24857277 AAAGTCTTT-CTTTTAGTAGAAATAGCCAC
1 AAAGACTTTCCTTTTAATAGAGATAGCCAC
* * *
24857306 AAAGAC-ATCCTTTTAACAAAGATAGCCAC
1 AAAGACTTTCCTTTTAATAGAGATAGCCAC
*
24857335 AAAG-CTTTCCTTTTAATTGAGATA
1 AAAGACTTTCCTTTTAATAGAGATA
24857359 ACCGAAAAGG
Statistics
Matches: 85, Mismatches: 21, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
27 8 0.09
28 11 0.13
29 65 0.76
30 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (30 bp):
AAAGACTTTCCTTTTAATAGAGATAGCCAC
Found at i:24857375 original size:58 final size:58
Alignment explanation
Indices: 24857244--24857405 Score: 166
Period size: 58 Copynumber: 2.8 Consensus size: 58
24857234 CAAAGTGTCG
** * * *
24857244 CCACAAAGGCATCCTTTTAACAGTGATTGCCACAAAGTCTTTCTTTTAGTAGAAATAG
1 CCACAAAGGCATCCTTTTAACAAAGATAGCCACAAAGTCTTTCTTTTAATAGAAATAA
* * *
24857302 CCACAAAGACATCCTTTTAACAAAGATAGCCACAAAG-CTTTCCTTTTAATTGAGATAA
1 CCACAAAGGCATCCTTTTAACAAAGATAGCCACAAAGTCTTT-CTTTTAATAGAAATAA
* * * * * *
24857360 CCGA-AAAGGCTTCCTTTAAACAAATATAGCCATAAAGGCATTCTTT
1 CC-ACAAAGGCATCCTTTTAACAAAGATAGCCACAAAGTCTTTCTTT
24857406 CAAAGATAGC
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
57 4 0.05
58 79 0.91
59 4 0.05
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (58 bp):
CCACAAAGGCATCCTTTTAACAAAGATAGCCACAAAGTCTTTCTTTTAATAGAAATAA
Found at i:24860528 original size:25 final size:25
Alignment explanation
Indices: 24860439--24860533 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 25
24860429 CGTTTCGACC
* *
24860439 CACAGCTCGTATTAGCATATCGATT
1 CACAGCTCGTATGAGCATACCGATT
*** *
24860464 TGTAGCTCGTGA-GAGCATACCTATT
1 CACAGCTCGT-ATGAGCATACCGATT
*
24860489 TACAGCTCG-AGTGAGCATACCGATT
1 CACAGCTCGTA-TGAGCATACCGATT
24860514 CACAGCTCGTATGAGCATAC
1 CACAGCTCGTATGAGCATAC
24860534 ATGTACATGA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
23 1 0.02
25 53 0.95
26 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (25 bp):
CACAGCTCGTATGAGCATACCGATT
Found at i:24861661 original size:20 final size:20
Alignment explanation
Indices: 24861628--24861666 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
24861618 GCCATATGGT
24861628 TTAGCTTGTGTTATGGTATC
1 TTAGCTTGTGTTATGGTATC
24861648 TTAG-TTGTGATTATGGTAT
1 TTAGCTTGTG-TTATGGTAT
24861667 TTTCAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.18, C:0.05, G:0.26, T:0.51
Consensus pattern (20 bp):
TTAGCTTGTGTTATGGTATC
Found at i:24879624 original size:167 final size:167
Alignment explanation
Indices: 24879346--24879655 Score: 458
Period size: 167 Copynumber: 1.9 Consensus size: 167
24879336 GCGTTATAGT
* *
24879346 GGAGCAGATTAAAGCCACGACGGTGAATCTTATCTCCCTGGAGTTAAGGCTTGGATTAACTGAAG
1 GGAGCAGATTAAAGCCACGACGGTGAATCTTATCTCCCTGGAGTTAAGACTTGAATTAACTGAAG
** * * * * *
24879411 TGGAGTGGATTGAAGCTGTGGGTAGCGAATCGTATCAGTTTGGCATTACAGTAGAACGGATTAAA
66 TGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCACTCTGGCATTACAGTAGAACGGATTAAA
*
24879476 GCCGCAACGGTGAGTTTTACTTCTCTGGCTTTGCAAC
131 GCCACAACGGTGAGTTTTACTTCTCTGGCTTTGCAAC
* * * **
24879513 GGAGCAGATTGAAGCCACGACGGTGAATCTTATCTCTCTGGCGTTAAGACTTGAATTGGCTGAAG
1 GGAGCAGATTAAAGCCACGACGGTGAATCTTATCTCCCTGGAGTTAAGACTTGAATTAACTGAAG
* * *
24879578 TGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTCTGGCATTACAGTGGAACGGATTGAA
66 TGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCACTCTGGCATTACAGTAGAACGGATTAAA
24879643 GCCACAACGGTGA
131 GCCACAACGGTGA
24879656 ATCTTGTTTT
Statistics
Matches: 125, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
167 125 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (167 bp):
GGAGCAGATTAAAGCCACGACGGTGAATCTTATCTCCCTGGAGTTAAGACTTGAATTAACTGAAG
TGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCACTCTGGCATTACAGTAGAACGGATTAAA
GCCACAACGGTGAGTTTTACTTCTCTGGCTTTGCAAC
Found at i:24879671 original size:50 final size:50
Alignment explanation
Indices: 24879617--24880510 Score: 354
Period size: 50 Copynumber: 18.0 Consensus size: 50
24879607 TCCTATCTCT
* * ** *
24879617 CTGGCATTACAGTGGAACGGATTGAAGCCACAACGGTGAATCTTGTTTTC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* ** * *
24879667 CTGGCAGTGCTTTGGAATAGATTGAAGCTACAACGGTGGATCTTGTTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* * ** * **
24879717 CCGACATTGCAATTAAATAGATTGAAGCCACAATGGTGAATCTTACTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* * ** * * * * * *
24879767 TTAGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTGGATCTGGTTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* * * * * * * *
24879817 CCGACATTGCAAT-TAAAAGATTGAAGCCACAACGGCGAGTTTTATTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* *** * * * * *
24879866 CTTGTGGTGTAGTGGAATAGATTGAAGCCACGACGGTGGATCTGGTTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* ** * * * *
24879916 TTAACATTGCAAT-TAAAAGATTGAAGCCACAACGGCGAGTCTTGTTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
*** * * * * * *
24879965 CTGGTGGTGTAGTGGAACAGATTGAAGCCACGACGGTGGATCTGGTTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* ** * * * *
24880015 TTAACATTGCAAT-TAAAAGATTGAAGCCACAATGGCGAATCTTGTTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
*** * * * * * * *
24880064 CTGGTGGTGTAGTGGAACAGATTGAAGCCACGACGGTGGATCTGGGTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* ** * * *
24880114 TTAACATTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTTGTTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* * * * * * * * *
24880163 CTGG--TGGTATAGTGGAACAAATTGAAGCTACGACGGCGGATCTGGTTTCC
1 CTGGCATTGCA-A-TGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* * ** * * ** ***
24880213 CCGACATTGCAATTAAAAAGATTGAAGCCACAACAGCAAATCTTACCT-C
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
** * * * * * *
24880262 CT-TAATGATGCAGTGGAACAGATTGAAGCTACGACGGTGGATCTGGTTTCC
1 CTGGCAT--TGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* * ** * * ***
24880313 CCGACATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACCTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* * * * * * *
24880363 TTAGG---TGCAGTGGAATAGATTGAAGCTACAACGGCGGATCTAGATTCC
1 CT-GGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* * ** * * * * * * **
24880411 CCGACATTGCAATTTAAAATATTGAAGCTACGACGGCGGATCTTACTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
* * * * *
24880461 CTGGCAGTGCAGTGGAACAGATTGGAGTCACAACGGTGAAT-TTGGTTTCC
1 CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTT-GTTTCC
24880511 TCGACATTGC
Statistics
Matches: 577, Mismatches: 250, Indels: 34
0.67 0.29 0.04
Matches are distributed among these distances:
47 4 0.01
48 36 0.06
49 134 0.23
50 394 0.68
51 4 0.01
52 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (50 bp):
CTGGCATTGCAATGGAATAGATTGAAGCCACAACGGTGAATCTTGTTTCC
Found at i:24879691 original size:167 final size:167
Alignment explanation
Indices: 24879350--24879710 Score: 420
Period size: 167 Copynumber: 2.2 Consensus size: 167
24879340 TATAGTGGAG
* * *
24879350 CAGATTAAAGCCACGACGGTGAATCTTATCTCCCTGGAGTTAAGGCTTGGATTAACTGAAGTGGA
1 CAGATTGAAGCCACGACGGTGAATCTTATCTCCCTGGAGTTAAGACTTGAATTAACTGAAGTGGA
** * * * * * *
24879415 GTGGATTGAAGCTGTGGGTAGCGAATCGTATCAGTTTGGCATTACAGTAGAACGGATTAAAGCCG
66 GCAGATTAAAGCTGTGGGCAGCGAATCCTATCACTCTGGCATTACAGTAGAACGGATTAAAGCCA
* ** *
24879480 CAACGGTGAGTTTTACTTCTCTGGCTTTGCAACGGAG
131 CAACGGTGAATTTTACTTCTCTGGCAGTGCAACGGAA
* * **
24879517 CAGATTGAAGCCACGACGGTGAATCTTATCTCTCTGGCGTTAAGACTTGAATTGGCTGAAGTGGA
1 CAGATTGAAGCCACGACGGTGAATCTTATCTCCCTGGAGTTAAGACTTGAATTAACTGAAGTGGA
* * *
24879582 GCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTCTGGCATTACAGTGGAACGGATTGAAGCCA
66 GCAGATTAAAGCTGTGGGCAGCGAATCCTATCACTCTGGCATTACAGTAGAACGGATTAAAGCCA
* ***
24879647 CAACGGTGAATCTTGT-TTTC-CTGGCAGTGCTTTGGAA
131 CAACGGTGAAT-TT-TACTTCTCTGGCAGTGCAACGGAA
* * * *
24879684 TAGATTGAAGCTACAACGGTGGATCTT
1 CAGATTGAAGCCACGACGGTGAATCTT
24879711 GTTTCCCCGA
Statistics
Matches: 162, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
167 156 0.96
168 5 0.03
169 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (167 bp):
CAGATTGAAGCCACGACGGTGAATCTTATCTCCCTGGAGTTAAGACTTGAATTAACTGAAGTGGA
GCAGATTAAAGCTGTGGGCAGCGAATCCTATCACTCTGGCATTACAGTAGAACGGATTAAAGCCA
CAACGGTGAATTTTACTTCTCTGGCAGTGCAACGGAA
Found at i:24879899 original size:99 final size:99
Alignment explanation
Indices: 24879636--24880538 Score: 1040
Period size: 99 Copynumber: 9.1 Consensus size: 99
24879626 CAGTGGAACG
* ** * ** ** * *
24879636 GATTGAAGCCACAACGGTGAATCTTGTTTTCCTGGCAGTGCTTTGGAATAGATTGAAGCTACAAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCTACGAC
*
24879701 GGTGGATCTTGTTTCCCCGACATTGCAATTAAATA
66 GGTGGATCTGGTTTCCCCGACATTGCAATTAAA-A
* * * * *
24879736 GATTGAAGCCACAATGGTGAATCTTACTTCCTTAGCGGTGCAGTGGAACAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCTACGAC
24879801 GGTGGATCTGGTTTCCCCGACATTGCAATTAAAA
66 GGTGGATCTGGTTTCCCCGACATTGCAATTAAAA
* * * * * * *
24879835 GATTGAAGCCACAACGGCGAGTTTTATTTCCCTTGTGGTGTAGTGGAATAGATTGAAGCCACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCTACGAC
***
24879900 GGTGGATCTGGTTTCCTTAACATTGCAATTAAAA
66 GGTGGATCTGGTTTCCCCGACATTGCAATTAAAA
* ** * *
24879934 GATTGAAGCCACAACGGCGAGTCTTGTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCTACGAC
***
24879999 GGTGGATCTGGTTTCCTTAACATTGCAATTAAAA
66 GGTGGATCTGGTTTCCCCGACATTGCAATTAAAA
* ** * *
24880033 GATTGAAGCCACAATGGCGAATCTTGTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCTACGAC
* ***
24880098 GGTGGATCTGGGTTCCTTAACATTGCAATTAAAA
66 GGTGGATCTGGTTTCCCCGACATTGCAATTAAAA
** ** *
24880132 GATTGAAGCCACAACGGCGAATCTTGTTTCCCTGGTGGTATAGTGGAACAAATTGAAGCTACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCTACGAC
*
24880197 GGCGGATCTGGTTTCCCCGACATTGCAATTAAAAA
66 GGTGGATCTGGTTTCCCCGACATTGCAATT-AAAA
* * * * ** *
24880232 GATTGAAGCCACAACAGCAAATCTTACCTCCTTAATGATGCAGTGGAACAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCTACGAC
24880297 GGTGGATCTGGTTTCCCCGACATTGCAATTAAAAA
66 GGTGGATCTGGTTTCCCCGACATTGCAATT-AAAA
* * *
24880332 GATTGAAGCCACAACGGCGAATCTTACCT-CCT--TAGGTGCAGTGGAATAGATTGAAGCTACAA
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGT-GGTGCAGTGGAACAGATTGAAGCTACGA
* * *
24880394 CGGCGGATCTAGATTCCCCGACATTGCAATTTAAAA
65 CGGTGGATCTGGTTTCCCCGACATTGCAA-TTAAAA
* * * * ** * *
24880430 TATTGAAGCTACGACGGCGGATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGGAG-TCACAA
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCT-ACGA
* * *
24880494 CGGTGAATTTGGTTTCCTCGACATTGCAGATTAAACA
65 CGGTGGATCTGGTTTCCCCGACATTGCA-ATTAAA-A
*
24880531 AATTGAAG
1 GATTGAAG
24880539 AAAATAATCC
Statistics
Matches: 714, Mismatches: 80, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
97 1 0.00
98 79 0.11
99 371 0.52
100 254 0.36
101 9 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (99 bp):
GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCTACGAC
GGTGGATCTGGTTTCCCCGACATTGCAATTAAAA
Found at i:24889513 original size:24 final size:25
Alignment explanation
Indices: 24889454--24889516 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
24889444 TTGAGCCAGT
*
24889454 ATTCTTTTATTCTTTTTTCGAGTAATT
1 ATTCTTTTATTCTTTTTTC--GTAATC
24889481 ATTCTTTTATTC-TTTTTC-TACATC
1 ATTCTTTTATTCTTTTTTCGTA-ATC
24889505 ATTCTTTTATTC
1 ATTCTTTTATTC
24889517 ATTTCATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
23 2 0.06
24 14 0.41
26 6 0.18
27 12 0.35
ACGTcount: A:0.17, C:0.16, G:0.03, T:0.63
Consensus pattern (25 bp):
ATTCTTTTATTCTTTTTTCGTAATC
Found at i:24889528 original size:23 final size:23
Alignment explanation
Indices: 24889476--24889529 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
24889466 TTTTTTCGAG
* *
24889476 TAATTATTCTTTTATTCTTTTTC
1 TAATCATTCTTTTATTCTATTTC
24889499 TACATCATTCTTTTATTC-ATTTC
1 TA-ATCATTCTTTTATTCTATTTC
24889522 ATAATCAT
1 -TAATCAT
24889530 ATTTTGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATCATTCTTTTATTCTATTTC
Found at i:24894799 original size:167 final size:166
Alignment explanation
Indices: 24894410--24894810 Score: 484
Period size: 167 Copynumber: 2.4 Consensus size: 166
24894400 GTAGTGTAAT
* ** * *
24894410 GGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGC-GTTATAGTGGAGCAGATTAAAGCCACG
1 GGATTGAAGCCACAACGGCGAATCTTA-TTTCCTGGCAG-TGCAGTGGAACAGATTGAAGCCACG
* * * **
24894474 ACGGTGAATCTTATCTCCCTGGTGTTAAGGCTTGGATTAACTAAAGTGGAGTGGATTGAAACTGT
64 ACGATGAATCTTATCTCCCTGGTGTTAAGACTTGAATTAACTAAAGTGGAGCAGATTGAAACTGT
24894539 GGGCAGCGAATCCTATCACTTTGGCATTACAGTAGAAC
129 GGGCAGCGAATCCTATCACTTTGGCATTACAGTAGAAC
* *** * * * *
24894577 GGATTAAAGCTGTAACGGCGAATTTTACTTCTCTGGCATTGCAG-CGAAGCAGATTGAAGCCACG
1 GGATTGAAGCCACAACGGCGAATCTTATTTC-CTGGCAGTGCAGTGGAA-CAGATTGAAGCCACG
* ** *
24894641 ACGATGAATCTTATCTCTCTGGTGTTAAGACTTGAATTGGCTGAAGTGGAGCAGATT-AAAGCTG
64 ACGATGAATCTTATCTCCCTGGTGTTAAGACTTGAATTAACTAAAGTGGAGCAGATTGAAA-CTG
* *
24894705 TGGGCAGCGAATCCTATCTCTTTGGCATTACAGTGGAAC
128 TGGGCAGCGAATCCTATCACTTTGGCATTACAGTAGAAC
* * *
24894744 GGATTGAAGCCACAACAGTGAATCTTATTTTCCTGGCAGTGCAGTGGAACAGATTGAAGCTACGA
1 GGATTGAAGCCACAACGGCGAATCTTA-TTTCCTGGCAGTGCAGTGGAACAGATTGAAGCCACGA
24894809 CG
65 CG
24894811 GCAGATCTTG
Statistics
Matches: 193, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
166 7 0.04
167 180 0.93
168 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (166 bp):
GGATTGAAGCCACAACGGCGAATCTTATTTCCTGGCAGTGCAGTGGAACAGATTGAAGCCACGAC
GATGAATCTTATCTCCCTGGTGTTAAGACTTGAATTAACTAAAGTGGAGCAGATTGAAACTGTGG
GCAGCGAATCCTATCACTTTGGCATTACAGTAGAAC
Found at i:24894819 original size:50 final size:50
Alignment explanation
Indices: 24894735--24895005 Score: 151
Period size: 50 Copynumber: 5.4 Consensus size: 50
24894725 TTTGGCATTA
*
24894735 CAGTGGAACGGATTGAAGCCACAACAGTG-A-ATCTTATTTTCCTGGCAGTG
1 CAGTGGAACAGATTGAAGCCACAAC-G-GCAGATCTTATTTTCCTGGCAGTG
* * * * * * *
24894785 CAGTGGAACAGATTGAAGCTACGACGGCAGATCTTGTTTCCCCGACATTG
1 CAGTGGAACAGATTGAAGCCACAACGGCAGATCTTATTTTCCTGGCAGTG
* ** * * * * *
24894835 CAATTAAATAGATTGAAGCCACAATGGC-GAATCTTA-CTTCCTTAGCGGTG
1 CAGTGGAACAGATTGAAGCCACAACGGCAG-ATCTTATTTTCC-TGGCAGTG
* * ** * * *
24894885 CAGTGGAACAGATTGAAGCTACGACGGCAGATC-TGGTTTCCACGACATTG
1 CAGTGGAACAGATTGAAGCCACAACGGCAGATCTTATTTTCC-TGGCAGTG
* * * * * * **
24894935 CAAT-TAAAAGATTGAAGCCTCAACGGC-GAGTCTTGTTTCCCTGGTGGTG
1 CAGTGGAACAGATTGAAGCCACAACGGCAGA-TCTTATTTTCCTGGCAGTG
*
24894984 TAGTGGAACAGATTGAAGCCAC
1 CAGTGGAACAGATTGAAGCCAC
24895006 GATGGTGGAT
Statistics
Matches: 156, Mismatches: 56, Indels: 18
0.68 0.24 0.08
Matches are distributed among these distances:
48 3 0.02
49 32 0.21
50 120 0.77
51 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (50 bp):
CAGTGGAACAGATTGAAGCCACAACGGCAGATCTTATTTTCCTGGCAGTG
Found at i:24895017 original size:99 final size:99
Alignment explanation
Indices: 24894745--24895645 Score: 988
Period size: 99 Copynumber: 9.1 Consensus size: 99
24894735 CAGTGGAACG
* * * * *
24894745 GATTGAAGCCACAACAGTGAATCTTATTTTCCTGGCAGTGCAGTGGAACAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGAC
* *
24894810 GGCAGATCTTGTTTCCCCGACATTGCAATTAAATA
66 GGCGGATCTGGTTTCCCCGACATTGCAATTAAA-A
* * *
24894845 GATTGAAGCCACAATGGCGAATCTTACTTCCTTAGCGGTGCAGTGGAACAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGAC
* *
24894910 GGCAGATCTGGTTTCCACGACATTGCAATTAAAA
66 GGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
* * ** * * * *
24894944 GATTGAAGCCTCAACGGCGAGTCTTGTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGAT
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGAC
* ****
24895009 GGTGGATCTGG-TTCGTTAACATTGCAATTAAAA
66 GGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
** * * * *
24895042 GATTGAAGCCACAACGGCGAATCTTGTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGGC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGAC
* * ***
24895107 GGTGGATTTGGTTTCCTTAACATTGCAATTAAAA
66 GGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
* ** * **
24895141 GATTGAAGCCACAACAGCGAATCTTGTTTCCCTGGTGGTATAGTGGAACAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGAC
* *
24895206 GGCGGATCTAGTTTCCTCGACATT-CAATTAAAAA
66 GGCGGATCTGGTTTCCCCGACATTGCAATT-AAAA
* * * *
24895240 GATTGAAGCCAAAACGGCGAATCTTACCTCCTTAGCGGTGCAGTGGAACAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGAC
**
24895305 GGCGGATCTGGTTT-CCCGACATTAAAATTAAAAA
66 GGCGGATCTGGTTTCCCCGACATTGCAATT-AAAA
* * * * * * *
24895339 GATTGAAGCCGCAACAGCAAATCTTACCTCCTTAGCGATGCAGTGGAACAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGAC
* * *
24895404 GGTGGATCTGGTTTCCCAGACATTGGAATTAAAAA
66 GGCGGATCTGGTTTCCCCGACATTGCAATT-AAAA
* * ** *
24895439 GATTGAAACCACAACGGCGAATCTTACCT-CCT-TAGGTACAGTGGAACAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGAC
*
24895502 GGCGGATTTGGTTTCCCCGACATTGCAATTTAAAA
66 GGCGGATCTGGTTTCCCCGACATTGCAA-TTAAAA
* * * * * * *
24895537 TATTGAAGCTACGACAGC-AGATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGGAG-TCACA
1 GATTGAAGCCACAACGGCGA-ATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCT-ACG
* *
24895600 ACGGCGAATTTGGTTTCCCCGACATTGCAGATTAAACA
64 ACGGCGGATCTGGTTTCCCCGACATTGCA-ATTAAA-A
*
24895638 AATTGAAG
1 GATTGAAG
24895646 AAAATAATCC
Statistics
Matches: 699, Mismatches: 91, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
97 1 0.00
98 178 0.25
99 327 0.47
100 184 0.26
101 9 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (99 bp):
GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACGAC
GGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
Found at i:24895121 original size:50 final size:50
Alignment explanation
Indices: 24894969--24895221 Score: 129
Period size: 50 Copynumber: 5.1 Consensus size: 50
24894959 GGCGAGTCTT
* *
24894969 GTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGATGGTGGATCTG
1 GTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGACGGTGGATTTG
** ***** * * * * * * *
24895019 G-TTCGTTAACATTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTT-
1 GTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGACGGTGGAT-TTG
*
24895067 GTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGGCGGTGGATTTG
1 GTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGACGGTGGATTTG
* ***** * * * * * * * *
24895117 GTTTCCTTAACATTGCAAT-TAAAAGATTGAAGCCACAACAGCGAATCTT-
1 GTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGACGGTGGAT-TTG
* * * * *
24895166 GTTTCCCTGGTGGTATAGTGGAACAGATTGAAGCTACGACGGCGGATCTA
1 GTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGACGGTGGATTTG
24895216 GTTTCC
1 GTTTCC
24895222 TCGACATTCA
Statistics
Matches: 134, Mismatches: 62, Indels: 14
0.64 0.30 0.07
Matches are distributed among these distances:
48 22 0.16
49 50 0.37
50 62 0.46
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (50 bp):
GTTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCCACGACGGTGGATTTG
Found at i:24896815 original size:13 final size:14
Alignment explanation
Indices: 24896797--24896827 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
24896787 TTTATTTTTG
24896797 TATA-TTTACATTT
1 TATATTTTACATTT
24896810 TATATTTTACATTT
1 TATATTTTACATTT
24896824 TATA
1 TATA
24896828 CGTTTGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTTTACATTT
Found at i:24896825 original size:21 final size:21
Alignment explanation
Indices: 24896783--24896825 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
24896773 ATTTTACTGC
**
24896783 ACATTTTATTTTTGTATATTT
1 ACATTTTATTTTTACATATTT
24896804 ACATTTTATATTTTACAT-TTT
1 ACATTTTAT-TTTTACATATTT
24896825 A
1 A
24896826 TACGTTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
ACATTTTATTTTTACATATTT
Found at i:24896858 original size:11 final size:11
Alignment explanation
Indices: 24896842--24896909 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
24896832 TGTATATATA
24896842 TATATATATTT
1 TATATATATTT
24896853 TATATACTATTCT
1 TATATA-TATT-T
24896866 T-T-TATATTT
1 TATATATATTT
*
24896875 TATTTATTTTATTT
1 TA--TA-TATATTT
**
24896889 TATATATATAA
1 TATATATATTT
24896900 TATATATATT
1 TATATATATT
24896910 CATACACCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
9 2 0.04
10 4 0.09
11 21 0.47
12 8 0.18
13 2 0.04
14 8 0.18
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATATATTT
Found at i:24897915 original size:12 final size:12
Alignment explanation
Indices: 24897898--24897955 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
24897888 ACTATCTAGA
24897898 TAAATATTAAAT
1 TAAATATTAAAT
24897910 TAAATATCTAATAT
1 TAAATAT-TAA-AT
*
24897924 T-AATATCTATA-
1 TAAATAT-TAAAT
*
24897935 TAGATATTAAAT
1 TAAATATTAAAT
24897947 TAAAT-TTAA
1 TAAATATTAA
24897956 TATTCAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 8 0.21
12 16 0.42
13 11 0.29
14 3 0.08
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:24897942 original size:37 final size:35
Alignment explanation
Indices: 24897890--24897959 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 35
24897880 AACAAAATAC
24897890 TATCTAGATAAATATTAAATTAAATATCTAATATTAA
1 TATCTAGATAAATATTAAATTAAAT-T-TAATATTAA
* *
24897927 TATCTATATAGATATTAAATTAAATTTAATATT
1 TATCTAGATAAATATTAAATTAAATTTAATATT
24897960 CAATTCAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 7 0.23
36 1 0.03
37 23 0.74
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (35 bp):
TATCTAGATAAATATTAAATTAAATTTAATATTAA
Found at i:24900027 original size:51 final size:49
Alignment explanation
Indices: 24899965--24900287 Score: 218
Period size: 51 Copynumber: 6.4 Consensus size: 49
24899955 TTTGGGGTTT
* * * *
24899965 TTCACACAGTACTACCCATGTTACTTTTATCATTCGATACACGTAGTAGCC
1 TTCACATAGTACTACACATGTGAC-TTAATCA-TCGATACACGTAGTAGCC
* * ** * *
24900016 TTCACATAGTACTACACACGTGA-TCAAGTTTTACGGTTCACGTAGTAGCC
1 TTCACATAGTACTACACATGTGACTTAA-TCAT-CGATACACGTAGTAGCC
** ** * *
24900066 TTCACATAGTACTACACATGTGACCAAAGCTTTTCGGTACACATAGTAGCC
1 TTCACATAGTACTACACATGTGACTTAA--TCATCGATACACGTAGTAGCC
* * * *
24900117 TTCACTTAGTACTACACATGTGACCATCAATTATCGATTCACGTAGTAGCC
1 TTCACATAGTACTACACATGTGA-C-TTAATCATCGATACACGTAGTAGCC
* ** ** * * *
24900168 TTCACACAGTACTACACACATGACCAAAGCTTC-TCGGTACACATTGTAGCC
1 TTCACATAGTACTACACATGTGACTTAA---TCATCGATACACGTAGTAGCC
* * * *
24900219 TTCACTTAGTACTACACATGTGACCATTATTTATCAATACACGTAGTAGCC
1 TTCACATAGTACTACACATGTGA-C-TTAATCATCGATACACGTAGTAGCC
*
24900270 TTCACACAGTACTACACA
1 TTCACATAGTACTACACA
24900288 CTTGTTCATC
Statistics
Matches: 212, Mismatches: 48, Indels: 24
0.75 0.17 0.08
Matches are distributed among these distances:
49 5 0.02
50 40 0.19
51 157 0.74
52 7 0.03
53 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (49 bp):
TTCACATAGTACTACACATGTGACTTAATCATCGATACACGTAGTAGCC
Found at i:24900192 original size:102 final size:102
Alignment explanation
Indices: 24899997--24900288 Score: 410
Period size: 102 Copynumber: 2.9 Consensus size: 102
24899987 ACTTTTATCA
* * * * * *
24899997 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG---ATCAAGTTTTACGGTTCACGT
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCAA-TTAT-CGATTCACGT
* **
24900059 AGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
64 AGTAGCCTTCACACAGTACTACACACATGACCAAAGCTT
24900098 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCAATTATCGATTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCAATTATCGATTCACGTAG
24900163 TAGCCTTCACACAGTACTACACACATGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACATGACCAAAGCTT
* * * * * *
24900200 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCAATACACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCAATTATCGATTCACGTAG
24900265 TAGCCTTCACACAGTACTACACAC
66 TAGCCTTCACACAGTACTACACAC
24900289 TTGTTCATCG
Statistics
Matches: 173, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
101 37 0.21
102 128 0.74
103 3 0.02
104 5 0.03
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.28
Consensus pattern (102 bp):
TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCAATTATCGATTCACGTAG
TAGCCTTCACACAGTACTACACACATGACCAAAGCTT
Found at i:24900273 original size:153 final size:151
Alignment explanation
Indices: 24899998--24900287 Score: 386
Period size: 153 Copynumber: 1.9 Consensus size: 151
24899988 CTTTTATCAT
* * * * * *
24899998 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTA
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACATGACCAAGTTCTACGGTACACATAGTA
** **
24900063 GCCTTCACATAGTACTACACATGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTA
66 GCCTTCACATAGTACTACACATGTGACCAAA-CTTTTCAATACACATAGTAGCCTTCACACAGTA
24900128 CTACACATGTGACCATCAATTA
130 CTACACATGTGACCATCAATTA
* *
24900150 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACATGACCAAAGCTTCT-CGGTACACATTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACATGACC-AAG-TTCTACGGTACACATAG
* * *
24900214 TAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCAATACACGTAGTAGCCTTCACACA
64 TAGCCTTCACATAGTACTACACATGTGACCA-AACTTT-TCAATACACATAGTAGCCTTCACACA
24900278 GTACTACACA
127 GTACTACACA
24900288 CTTGTTCATC
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
152 42 0.35
153 73 0.61
154 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (151 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTACACACATGACCAAGTTCTACGGTACACATAGTA
GCCTTCACATAGTACTACACATGTGACCAAACTTTTCAATACACATAGTAGCCTTCACACAGTAC
TACACATGTGACCATCAATTA
Found at i:24906330 original size:24 final size:24
Alignment explanation
Indices: 24906261--24906388 Score: 107
Period size: 25 Copynumber: 5.2 Consensus size: 24
24906251 TAGGGATTAT
* * **
24906261 CGATTGCAGCTTGTGAGAGCTTGT
1 CGATTTCAGCTCGTGAGAGCTTAC
* *
24906285 CAATTCTCAGCTTGT-ATGAGCTTAC
1 CGATT-TCAGCTCGTGA-GAGCTTAC
*
24906310 CGATTTCAGCTCGTGAAAGCTTAC
1 CGATTTCAGCTCGTGAGAGCTTAC
24906334 CGATTCTCAGCTCGT-ATGAGCTTAC
1 CGATT-TCAGCTCGTGA-GAGCTTAC
* * *
24906359 CAATTTATAGCTCGTGAGAGCATAC
1 CGATTT-CAGCTCGTGAGAGCTTAC
24906384 CGATT
1 CGATT
24906389 CATAGCTCAT
Statistics
Matches: 85, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
24 27 0.32
25 57 0.67
26 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (24 bp):
CGATTTCAGCTCGTGAGAGCTTAC
Found at i:24906340 original size:49 final size:50
Alignment explanation
Indices: 24906287--24906404 Score: 159
Period size: 50 Copynumber: 2.4 Consensus size: 50
24906277 GAGCTTGTCA
* * *
24906287 ATTCTCAGCTTGTATGAGCTTACCGATTT-CAGCTCGTGAAAGCTTACCG
1 ATTCTCAGCTCGTATGAGCTTACCAATTTACAGCTCGTGAAAGCATACCG
* *
24906336 ATTCTCAGCTCGTATGAGCTTACCAATTTATAGCTCGTGAGAGCATACCG
1 ATTCTCAGCTCGTATGAGCTTACCAATTTACAGCTCGTGAAAGCATACCG
*
24906386 ATTCAT-AGCTCATATGAGC
1 ATTC-TCAGCTCGTATGAGC
24906405 ATAGATGTAC
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
49 27 0.44
50 33 0.54
51 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (50 bp):
ATTCTCAGCTCGTATGAGCTTACCAATTTACAGCTCGTGAAAGCATACCG
Found at i:24906355 original size:25 final size:25
Alignment explanation
Indices: 24906287--24906404 Score: 111
Period size: 25 Copynumber: 4.8 Consensus size: 25
24906277 GAGCTTGTCA
*
24906287 ATTCTCAGCTTGTATGAGCTTACCG
1 ATTCTCAGCTCGTATGAGCTTACCG
*
24906312 ATT-TCAGCTCGTGA-AAGCTTACCG
1 ATTCTCAGCTCGT-ATGAGCTTACCG
*
24906336 ATTCTCAGCTCGTATGAGCTTACCA
1 ATTCTCAGCTCGTATGAGCTTACCG
* *
24906361 ATT-TATAGCTCGTGA-GAGCATACCG
1 ATTCT-CAGCTCGT-ATGAGCTTACCG
*
24906386 ATTCAT-AGCTCATATGAGC
1 ATTC-TCAGCTCGTATGAGC
24906405 ATAGATGTAC
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
24 23 0.30
25 52 0.68
26 1 0.01
27 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (25 bp):
ATTCTCAGCTCGTATGAGCTTACCG
Found at i:24907522 original size:20 final size:20
Alignment explanation
Indices: 24907489--24907527 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
24907479 GCCACATGGT
24907489 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATGGTATC
24907509 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
24907528 TTTGAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATC
Found at i:24909908 original size:14 final size:14
Alignment explanation
Indices: 24909885--24909918 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
24909875 CGCTGATCCT
*
24909885 GAAA-AATTTGGTA
1 GAAATAATTTGGCA
24909898 GAAATAATTTGGCA
1 GAAATAATTTGGCA
24909912 GAAATAA
1 GAAATAA
24909919 CATAAATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (14 bp):
GAAATAATTTGGCA
Found at i:24916294 original size:27 final size:27
Alignment explanation
Indices: 24916265--24916504 Score: 297
Period size: 27 Copynumber: 8.9 Consensus size: 27
24916255 TTTATTACGA
*
24916265 AAATACCCCCATAGGGTAAAATGATCA
1 AAATACCCCCATAGGGTAAAATGATCG
* * * *
24916292 AAATACTCACATAGGGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGATCG
* *
24916319 AAATACCTCTATAGGGTAAAATGA-CTG
1 AAATACCCCCATAGGGTAAAATGATC-G
* * * * *
24916346 GAATACCCCAATAAGGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGATCG
24916373 AAATACCCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
24916400 AAATACCCCCATAGGGTAAAATGA-CTG
1 AAATACCCCCATAGGGTAAAATGATC-G
* *
24916427 AAATACCCCTATAGGGTAGAATGAAT-G
1 AAATACCCCCATAGGGTAAAATG-ATCG
*
24916454 AAATAGCCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
24916481 AAATACCCCCATAGGGTAAAATGA
1 AAATACCCCCATAGGGTAAAATGA
24916505 CTATTATACC
Statistics
Matches: 183, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.02
27 177 0.97
28 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGATCG
Found at i:24916404 original size:81 final size:81
Alignment explanation
Indices: 24916265--24916506 Score: 340
Period size: 81 Copynumber: 3.0 Consensus size: 81
24916255 TTTATTACGA
* * * * * * * *
24916265 AAATACCCCCATAGGGTAAAATGATCAAAATACTCACATAGGGTAAAATGACCAAAATACCTCTA
1 AAATACCCCAATAGGGTAAAATGAACAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCA
24916330 TAGGGTAAAATGACTG
66 TAGGGTAAAATGACTG
* * *
24916346 GAATACCCCAATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCA
1 AAATACCCCAATAGGGTAAAATGAACAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCA
24916411 TAGGGTAAAATGACTG
66 TAGGGTAAAATGACTG
* * ** *
24916427 AAATACCCCTATAGGGTAGAATGAATGAAATAGCCCCATAGGGTAAAATGATCGAAATACCCCCA
1 AAATACCCCAATAGGGTAAAATGAACAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCA
24916492 TAGGGTAAAATGACT
66 TAGGGTAAAATGACT
24916507 ATTATACCCC
Statistics
Matches: 143, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 143 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (81 bp):
AAATACCCCAATAGGGTAAAATGAACAAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCA
TAGGGTAAAATGACTG
Found at i:24922420 original size:29 final size:28
Alignment explanation
Indices: 24922370--24922427 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
24922360 TTCTTTCTCC
* **
24922370 AAATTCAGCATATATTGATAAATTTCAAA
1 AAATTCACCATATATACATAAATTT-AAA
*
24922399 AAATTCACCATATATACTTAAATTTAAA
1 AAATTCACCATATATACATAAATTTAAA
24922427 A
1 A
24922428 CGTTTTCAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.34
Consensus pattern (28 bp):
AAATTCACCATATATACATAAATTTAAA
Found at i:24922628 original size:19 final size:19
Alignment explanation
Indices: 24922593--24922630 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
24922583 TAGAATTTTT
*
24922593 TTATTTTTATAACTTTTAA
1 TTATTTTTATAAATTTTAA
24922612 TTATTTTTA-AAGATTTTAA
1 TTATTTTTATAA-ATTTTAA
24922631 ATTCAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (19 bp):
TTATTTTTATAAATTTTAA
Found at i:24938610 original size:20 final size:20
Alignment explanation
Indices: 24938573--24938611 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
24938563 TTTATCCTAT
*
24938573 TTTTTAAAACTATAAATTTA
1 TTTTTAAAACTAAAAATTTA
24938593 TTTTT-AAACTAAATAATTT
1 TTTTTAAAACTAAA-AATTT
24938612 TTTCAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTTAAAACTAAAAATTTA
Found at i:24942080 original size:16 final size:16
Alignment explanation
Indices: 24942059--24942101 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
24942049 ATGAAAAGGT
24942059 TGAAAAGGATATCAAA
1 TGAAAAGGATATCAAA
*
24942075 TGAAAAGGATATCAAT
1 TGAAAAGGATATCAAA
24942091 TGAAAAGGATA
1 TGAAAAGGATA
24942102 CTAGTGGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (16 bp):
TGAAAAGGATATCAAA
Found at i:24946007 original size:110 final size:110
Alignment explanation
Indices: 24945814--24946025 Score: 311
Period size: 110 Copynumber: 1.9 Consensus size: 110
24945804 AAGAAGTAGA
* *
24945814 ACCCTTGTTGAATTATAGAAATTTATTTCAACTAGAAAAACAAACTCCTAGTCTAACTAGTAGTA
1 ACCCTTATTGAATTATAGAAATTTATTTCAACTAGAAAAACAAACTCCTAGTCTAACTAGAAGTA
* *
24945879 TAGGGGGCAGCAACCCTAGTTAATAATATTAGGGTTTGTTGTCCC
66 TAGGGGCCAGCAACCCTAGTTAATAATACTAGGGTTTGTTGTCCC
* * **
24945924 ACCCTTATTGAATTGTAGAATTTTATTTCAACTA-AGAAAATGAACTCCTAGTCTAACTAGAAGT
1 ACCCTTATTGAATTATAGAAATTTATTTCAACTAGA-AAAACAAACTCCTAGTCTAACTAGAAGT
*
24945988 ATAGGGGCCCA-CAACCCTAGTTAGTAATACTAGGGTTT
65 ATAGGGG-CCAGCAACCCTAGTTAATAATACTAGGGTTT
24946026 TCCGTCCCTC
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
109 1 0.01
110 88 0.97
111 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (110 bp):
ACCCTTATTGAATTATAGAAATTTATTTCAACTAGAAAAACAAACTCCTAGTCTAACTAGAAGTA
TAGGGGCCAGCAACCCTAGTTAATAATACTAGGGTTTGTTGTCCC
Found at i:24946431 original size:62 final size:64
Alignment explanation
Indices: 24946360--24946486 Score: 195
Period size: 63 Copynumber: 2.0 Consensus size: 64
24946350 TATTTCCAGG
* *
24946360 TCATTTTCATTTAAATTTTGGAG-AAACCACATTCATTTCCAAATGATTCC-ATTTCTCCATTT
1 TCATTTTCATTTAAATGTTGGAGAAAACCACAATCATTTCCAAATGATTCCTATTTCTCCATTT
* * *
24946422 TCATTTTCATTTTAATGTTGGAGAAAACCATAATCATTTCCAAATGTTTCCTATTTCTCCATTT
1 TCATTTTCATTTAAATGTTGGAGAAAACCACAATCATTTCCAAATGATTCCTATTTCTCCATTT
24946486 T
1 T
24946487 TATAATTTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 21 0.36
63 24 0.41
64 13 0.22
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (64 bp):
TCATTTTCATTTAAATGTTGGAGAAAACCACAATCATTTCCAAATGATTCCTATTTCTCCATTT
Found at i:24952643 original size:10 final size:10
Alignment explanation
Indices: 24952587--24952643 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
24952577 ACATAGTCAT
*
24952587 ATAATATAAG
1 ATAAAATAAG
24952597 ATAAGAA-AAG
1 ATAA-AATAAG
*
24952607 ATAAAACAAG
1 ATAAAATAAG
24952617 ATAAAATGAA-
1 ATAAAAT-AAG
24952627 ATAAAATAAG
1 ATAAAATAAG
24952637 ATAAAAT
1 ATAAAAT
24952644 GGAACTTGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.10
10 34 0.83
11 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (10 bp):
ATAAAATAAG
Found at i:24958154 original size:12 final size:14
Alignment explanation
Indices: 24958137--24958169 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
24958127 TAATGGTCAC
24958137 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
24958149 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
24958163 ATGTGTA
1 ATGTGTA
24958170 CCGGAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 1 0.05
14 11 0.58
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.39
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:24958163 original size:51 final size:50
Alignment explanation
Indices: 24958083--24958282 Score: 197
Period size: 51 Copynumber: 3.9 Consensus size: 50
24958073 TGCCTATAAA
**
24958083 CACGTGTGTAGTACTAACTGCAGGCTACTATGTGTATCGATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGA-AGATAATGGT
* * * * **
24958134 CACATGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGAAGGTTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATC-GAAGATAATGGT
* * * * *
24958185 CACGTGTATAGTACTATGTGCAGGCTACTATGTGAACTGGAA-AGT-TTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGTA-TCGAAGA-TAATGGT
* * *
24958235 CACGTGTGTAGTACTATGTGAAGGTTACTACGTGTATCGAATGATAAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGAA-GATAAT
24958283 AATTACACGG
Statistics
Matches: 120, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
49 4 0.03
50 36 0.30
51 78 0.65
52 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGAAGATAATGGT
Found at i:24960843 original size:2 final size:2
Alignment explanation
Indices: 24960836--24960868 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24960826 CATACATACT
24960836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24960869 GAAACTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24962102 original size:19 final size:21
Alignment explanation
Indices: 24962078--24962125 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
24962068 TTGTTTCATA
24962078 GAAAATAG-CTT-GGTCAACG
1 GAAAATAGACTTAGGTCAACG
24962097 GAAAAT-GACTTACAGGTCAACG
1 GAAAATAGACTT--AGGTCAACG
24962119 GAAAATA
1 GAAAATA
24962126 AGTCTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.04
19 9 0.38
22 14 0.58
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (21 bp):
GAAAATAGACTTAGGTCAACG
Found at i:24962425 original size:31 final size:30
Alignment explanation
Indices: 24962363--24962428 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
24962353 TTTAGTCATA
*
24962363 TAATAAATTATTAATATAATTTATTATTTT
1 TAATAAATTATTAATATAAATTATTATTTT
24962393 TAATAAATTATTTAATATTTAAATT-TTA-TTT
1 TAATAAATTA-TTAATA--TAAATTATTATTTT
24962424 TAATA
1 TAATA
24962429 GTAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 10 0.31
31 14 0.44
32 3 0.09
33 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TAATAAATTATTAATATAAATTATTATTTT
Found at i:24967338 original size:9 final size:9
Alignment explanation
Indices: 24967321--24967357 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
24967311 TTTTTCCTTC
24967321 AAAACCCTA
1 AAAACCCTA
*
24967330 AAAATCCTA
1 AAAACCCTA
24967339 AAAACCCT-
1 AAAACCCTA
24967347 AAAACCCTA
1 AAAACCCTA
24967356 AA
1 AA
24967358 CCTTAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAACCCTA
Found at i:24968172 original size:15 final size:15
Alignment explanation
Indices: 24968152--24968180 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24968142 GTCAGTACCA
24968152 TTTCCTTTTCTTTTC
1 TTTCCTTTTCTTTTC
24968167 TTTCCTTTTCTTTT
1 TTTCCTTTTCTTTT
24968181 TTTTATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCCTTTTCTTTTC
Found at i:24968233 original size:13 final size:14
Alignment explanation
Indices: 24968211--24968243 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
24968201 GTTTCGTAAA
*
24968211 ATAAATATAA-AAG
1 ATAAAAATAATAAG
24968224 ATAAAAATAATAAG
1 ATAAAAATAATAAG
24968238 ATAAAA
1 ATAAAA
24968244 GAAACATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (14 bp):
ATAAAAATAATAAG
Found at i:24971217 original size:32 final size:31
Alignment explanation
Indices: 24971172--24971267 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
24971162 CTTAGATAAT
24971172 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
24971203 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
24971235 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
24971266 TT
1 TT
24971268 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:24971619 original size:29 final size:27
Alignment explanation
Indices: 24971570--24971628 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
24971560 AATCTATCCT
*
24971570 TTTTATTTATTTATTTATTATTTAACTAA
1 TTTTATTTATTTAGTTATTATTT--CTAA
*
24971599 TTTTATTTATTCTCGTT-TTATTTCTAA
1 TTTTATTTATT-TAGTTATTATTTCTAA
24971626 TTT
1 TTT
24971629 GTGTTTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.26
29 17 0.63
30 3 0.11
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTATTTATTTAGTTATTATTTCTAA
Found at i:24971836 original size:20 final size:19
Alignment explanation
Indices: 24971811--24971874 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 19
24971801 TATTCTTAAA
*
24971811 AAAAAAAAGTAAAAAAGCGC
1 AAAAAAAAG-AAAAAAGCAC
24971831 AAAAAAAAGAGTAAAAAGCAC
1 AAAAAAAAGA--AAAAAGCAC
*
24971852 AAAAAAAAGCAAAAAGCA-
1 AAAAAAAAGAAAAAAGCAC
24971870 AAAAA
1 AAAAA
24971875 GCAAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 5 0.12
19 9 0.22
20 9 0.22
21 17 0.43
ACGTcount: A:0.75, C:0.09, G:0.12, T:0.03
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAGCAC
Found at i:24971836 original size:21 final size:21
Alignment explanation
Indices: 24971809--24971860 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
24971799 CTTATTCTTA
* *
24971809 AAAAAAAAAAGTAAAAAAGCGC
1 AAAAAAAAGAGT-AAAAAGCAC
24971831 AAAAAAAAGAGTAAAAAGCAC
1 AAAAAAAAGAGTAAAAAGCAC
24971852 AAAAAAAAG
1 AAAAAAAAG
24971861 CAAAAAGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.75, C:0.08, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAAAAAGAGTAAAAAGCAC
Found at i:24971837 original size:22 final size:21
Alignment explanation
Indices: 24971809--24971874 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 21
24971799 CTTATTCTTA
*
24971809 AAAAAAAAAAGTAAAAAAGCGC
1 AAAAAAAAAAGT-AAAAAGCAC
*
24971831 AAAAAAAAGAGTAAAAAGCAC
1 AAAAAAAAAAGTAAAAAGCAC
*
24971852 --AAAAAAAAGCAAAAAGCA-
1 AAAAAAAAAAGTAAAAAGCAC
24971870 AAAAA
1 AAAAA
24971875 GCAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 16 0.42
20 3 0.08
21 8 0.21
22 11 0.29
ACGTcount: A:0.76, C:0.09, G:0.12, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAGTAAAAAGCAC
Found at i:24971882 original size:8 final size:8
Alignment explanation
Indices: 24971854--24971882 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
24971844 AAAAGCACAA
24971854 AAAAAAGC
1 AAAAAAGC
24971862 -AAAAAGC
1 AAAAAAGC
24971869 AAAAAAGC
1 AAAAAAGC
24971877 AAAAAA
1 AAAAAA
24971883 AAAAAGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGC
Found at i:24971887 original size:15 final size:15
Alignment explanation
Indices: 24971852--24971887 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
24971842 TAAAAAGCAC
24971852 AAAAAAAAGCAAAAA
1 AAAAAAAAGCAAAAA
**
24971867 GCAAAAAAGCAAAAA
1 AAAAAAAAGCAAAAA
24971882 AAAAAA
1 AAAAAA
24971888 GTTGCCTACC
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGCAAAAA
Found at i:24977480 original size:32 final size:31
Alignment explanation
Indices: 24977437--24977528 Score: 166
Period size: 32 Copynumber: 2.9 Consensus size: 31
24977427 CCCCCTTCCC
*
24977437 AGAGTTTTATTAGGATTCAATTACTCTTTAA
1 AGAGTTTTATTAGGATTCAATTACTCTTGAA
24977468 AGAGTTTTTATTAGGATTCAATTACTCTTGAA
1 AGAG-TTTTATTAGGATTCAATTACTCTTGAA
24977500 AGAGTTTTATTAGGATTCAATTACTCTTG
1 AGAGTTTTATTAGGATTCAATTACTCTTG
24977529 TAATTTGCCT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 29 0.49
32 30 0.51
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (31 bp):
AGAGTTTTATTAGGATTCAATTACTCTTGAA
Found at i:24977879 original size:29 final size:27
Alignment explanation
Indices: 24977830--24977888 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
24977820 AATCTATCCT
*
24977830 TTTTATTTATTTATTTATTATTTAACTAA
1 TTTTATTTATTTAGTTATTATTT--CTAA
*
24977859 TTTTATTTATTCTCGTT-TTATTTCTAA
1 TTTTATTTATT-TAGTTATTATTTCTAA
24977886 TTT
1 TTT
24977889 GTGTTTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.26
29 17 0.63
30 3 0.11
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTATTTATTTAGTTATTATTTCTAA
Found at i:24979403 original size:21 final size:21
Alignment explanation
Indices: 24979377--24979423 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
24979367 TATAAGAGTT
24979377 AAAAAATAAATATAT-TATATA
1 AAAAAATAAATATATAT-TATA
**
24979398 AAAAAATGCATATATATTATA
1 AAAAAATAAATATATATTATA
24979419 AAAAA
1 AAAAA
24979424 TGCGTGTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAAATAAATATATATTATA
Found at i:24979439 original size:21 final size:20
Alignment explanation
Indices: 24979376--24979440 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
24979366 TTATAAGAGT
** *
24979376 TAAAAAATAAATATATTATA
1 TAAAAAATGCATATATAATA
*
24979396 TAAAAAAATGCATATATATTA
1 T-AAAAAATGCATATATAATA
* *
24979417 TAAAAAATGCGTGTATAAATA
1 TAAAAAATGCATATAT-AATA
24979438 TAA
1 TAA
24979441 TAATAATAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (20 bp):
TAAAAAATGCATATATAATA
Found at i:24990726 original size:13 final size:13
Alignment explanation
Indices: 24990708--24990774 Score: 82
Period size: 13 Copynumber: 5.1 Consensus size: 13
24990698 AGTTTAGTAT
24990708 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
24990721 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
24990734 TGCTTTTGAGAAA-
1 TGCTTTTGA-AAAG
* *
24990747 TGCTGTGGAAAAAG
1 TGCTTTTG-AAAAG
*
24990761 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
24990774 T
1 T
24990775 TTTGTTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
13 36 0.78
14 10 0.22
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:24990750 original size:26 final size:28
Alignment explanation
Indices: 24990708--24990772 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
24990698 AGTTTAGTAT
* *
24990708 TGCTTTTGA-AAAGTGCTTTTG-AAAAG
1 TGCTTTTGAGAAAGTGCTGTGGAAAAAG
24990734 TGCTTTTGAGAAA-TGCTGTGGAAAAAG
1 TGCTTTTGAGAAAGTGCTGTGGAAAAAG
24990761 TGCTTTTGAGAA
1 TGCTTTTGAGAA
24990773 GTTTTGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 15 0.43
27 20 0.57
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (28 bp):
TGCTTTTGAGAAAGTGCTGTGGAAAAAG
Found at i:24991085 original size:21 final size:19
Alignment explanation
Indices: 24991011--24991086 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 19
24991001 TAATTATTTA
*
24991011 TTAAATTTA-ATTAGAATAT
1 TTAAATATATATTA-AATAT
*
24991030 ATAAACTATAT-TTAAATAT
1 TTAAA-TATATATTAAATAT
24991049 TTAAATATAATCATTAAATATT
1 TTAAATAT-AT-ATTAAATA-T
*
24991071 TGTAATTATATATTAA
1 T-TAAATATATATTAA
24991087 CACAGTTGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
18 3 0.07
19 15 0.33
20 6 0.13
21 12 0.26
22 4 0.09
23 6 0.13
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
TTAAATATATATTAAATAT
Found at i:24993143 original size:72 final size:72
Alignment explanation
Indices: 24992836--24993117 Score: 440
Period size: 72 Copynumber: 3.9 Consensus size: 72
24992826 CTAATTTTGT
* * **
24992836 ATAAATAAGTAGAATATAAATTCAATATCCAAAAACTAAACATAAACAATTATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACCATTGATAAAACTAG
*
24992901 CCTTA-AGC
66 -ATTACA-C
* * *
24992909 ATAAATAAGTAGACCATAAATTCAACATCCAAAAACCAAACATAGACAACCATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACCATTGATAAAACTAG
24992974 ATTACAC
66 ATTACAC
* *
24992981 ATAAATAAGTAGAACATAAATTTAATATCCAAAAACCAAATATAAACAACCATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACCATTGATAAAACTAG
24993046 ATTACAC
66 ATTACAC
*
24993053 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACCATTGATAAAACTAG
24993118 TTTAGCATTG
Statistics
Matches: 192, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
72 133 0.69
73 59 0.31
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.23
Consensus pattern (72 bp):
ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACCATTGATAAAACTAG
ATTACAC
Found at i:24999524 original size:43 final size:43
Alignment explanation
Indices: 24999456--24999646 Score: 222
Period size: 43 Copynumber: 4.4 Consensus size: 43
24999446 CTATCACCTC
* * * * * *
24999456 AGTGCATCATTGGATAAACCGAAGGAAATATACTGGAACATGT
1 AGTGCATCATCGAATAAACCAAAGGAAATATACTAGCACATAT
* *
24999499 AGTGCATCATCGAATAAATCAAAGGAAATATACTAGCACACAT
1 AGTGCATCATCGAATAAACCAAAGGAAATATACTAGCACATAT
* *
24999542 AGTGCATCATC-AGATAAATCAAAGGAAATATACTAGCACATGT
1 AGTGCATCATCGA-ATAAACCAAAGGAAATATACTAGCACATAT
* * * * *
24999585 AGTGCATCATCGAATAAACCGAAGCAATTATACTGGCACCTAT
1 AGTGCATCATCGAATAAACCAAAGGAAATATACTAGCACATAT
*
24999628 AGTGCATCATCAAATAAAC
1 AGTGCATCATCGAATAAAC
24999647 TGAAGTATAA
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.01
43 126 0.98
44 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (43 bp):
AGTGCATCATCGAATAAACCAAAGGAAATATACTAGCACATAT
Done.