Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 28 of 97
Found at i:11832580 original size:31 final size:31
Alignment explanation
Indices: 11832542--11832622 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
11832532 ACTTGATACT
*
11832542 CATGGCGTGTTACAACATTTTACGTTACATG
1 CATGGCGTGTTACCACATTTTACGTTACATG
* *
11832573 CATGGCGTATTACCACATTTTACGTTATATG
1 CATGGCGTGTTACCACATTTTACGTTACATG
*
11832604 CATGGTGTGTTACCACATT
1 CATGGCGTGTTACCACATT
11832623 ATGGGTTAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (31 bp):
CATGGCGTGTTACCACATTTTACGTTACATG
Found at i:11834281 original size:145 final size:145
Alignment explanation
Indices: 11834034--11834299 Score: 426
Period size: 145 Copynumber: 1.8 Consensus size: 145
11834024 TGGTTCTAAA
* * *
11834034 GGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGGACCAT
1 GGTTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTATGTTTGCAGTTAGACCAT
* *
11834099 GCGACGACAGCTCCATAACCACCGATAGGTCATCCTTAGACTCACAGTGCTAACGAGGAGCCAAT
66 ACGACGACAGCTCCATAACCACCGAAAGGTCATCCTTAGACTCACAGTGCTAACGAGGAGCCAAT
11834164 AAGGACGGTCATAAC
131 AAGGACGGTCATAAC
11834179 GGTTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTATGTTTGCAGTTAGACCAT
1 GGTTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTATGTTTGCAGTTAGACCAT
* * * * *
11834244 ATGACGACAGCTTC-TCAACCACTGAAAGGTCCTCCTTAGACTCATAGTGCTAACGA
66 ACGACGACAGCTCCAT-AACCACCGAAAGGTCATCCTTAGACTCACAGTGCTAACGA
11834300 CCCATTGATA
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
144 1 0.01
145 109 0.99
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (145 bp):
GGTTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTATGTTTGCAGTTAGACCAT
ACGACGACAGCTCCATAACCACCGAAAGGTCATCCTTAGACTCACAGTGCTAACGAGGAGCCAAT
AAGGACGGTCATAAC
Found at i:11834311 original size:145 final size:143
Alignment explanation
Indices: 11834034--11834364 Score: 398
Period size: 145 Copynumber: 2.3 Consensus size: 143
11834024 TGGTTCTAAA
* * *
11834034 GGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGGACCAT
1 GGTTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTATGTTTGCAGTTAGACCAT
* * *
11834099 GCGACGACAGCTCCATAACCACCGATAGGTCATCCTTAGACTCACAGTGCTAACGAGGAGCCAAT
66 ACGACGACAGCTCCATAACCACCGAAAGGTCATCCTTAGACTCACAGTGCTAAC--GGACCCAAT
**
11834164 AAGGA-CGGTCATAAC
129 AA-GATCAATCATAAC
11834179 GGTTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTATGTTTGCAGTTAGACCAT
1 GGTTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTATGTTTGCAGTTAGACCAT
* * * * *
11834244 ATGACGACAGCTTC-TCAACCACTGAAAGGTCCTCCTTAGACTCATAGTGCTAAC-GACCCATTG
66 ACGACGACAGCTCCAT-AACCACCGAAAGGTCATCCTTAGACTCACAGTGCTAACGGACCCA---
*
11834307 ATAAGATCAATTATAAC
127 ATAAGATCAATCATAAC
** * * * *
11834324 AATTTGTGTTCAACATTTCCACATATGTTTATCGAGTAACA
1 GGTTTGTGTTCAACAATTCCATATATGATTATCGAATAACA
11834365 CATTAATTTT
Statistics
Matches: 161, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
142 5 0.03
144 3 0.02
145 153 0.95
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (143 bp):
GGTTTGTGTTCAACAATTCCATATATGATTATCGAATAACATATCTATGTTTGCAGTTAGACCAT
ACGACGACAGCTCCATAACCACCGAAAGGTCATCCTTAGACTCACAGTGCTAACGGACCCAATAA
GATCAATCATAAC
Found at i:11836639 original size:118 final size:118
Alignment explanation
Indices: 11836416--11836897 Score: 590
Period size: 118 Copynumber: 4.1 Consensus size: 118
11836406 CTGGAACCAG
* * * * ** * * *
11836416 TCAGCATGTCACTCCAAGTATCTGGTTCCACTCAATGTGTCACCATAA-TTGAGGTGTGCCGTGT
1 TCAGCGTGTCACGCCAACTATCTGCTTCCACTCAGCGTGTCACCATAAGATGGGGCGTGCCGTGT
* * *
11836480 CACCCCATAATAC-AGCAAGAAGTCAGTGTGTCACCATAGAAATCTGCATGCAC
66 CACCCCACAATACTA-CAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCAC
* * * *
11836533 TCAGCGTGTCATGCCAACTATCTACTTCCACTCAGCGTGTCACCACAAGATGGGGCATGCCGTGT
1 TCAGCGTGTCACGCCAACTATCTGCTTCCACTCAGCGTGTCACCATAAGATGGGGCGTGCCGTGT
* * ** * *
11836598 CACCCCATAATATTACAAGTGGTTAGCGTGTCACCACAGAAATCTGCATGTAC
66 CACCCCACAATACTACAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCAC
* * * * * *
11836651 TCAGCATGTCACACCAACTATCTGCTTCTACTCAGTGTGTCACTATAAGATAGGGCGTGCCGTGT
1 TCAGCGTGTCACGCCAACTATCTGCTTCCACTCAGCGTGTCACCATAAGATGGGGCGTGCCGTGT
* *
11836716 CACCCCACAATACTGCAAGAAGTCAACGTGTCACCACAGAAATCTGCATGCAC
66 CACCCCACAATACTACAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCAC
* * * **
11836769 TCACCGTGTCACGCCAACTATTTGCTTCCACTCAGCGTGTCAGCATAAGATGGGATGTGCCGTGT
1 TCAGCGTGTCACGCCAACTATCTGCTTCCACTCAGCGTGTCACCATAAGATGGGGCGTGCCGTGT
* * * *
11836834 CACCCCACAATACTGCAAGAAGTTAGCATGTCACCACAGAAATCTACATGCAC
66 CACCCCACAATACTACAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCAC
11836887 TCAGCGTGTCA
1 TCAGCGTGTCA
11836898 GCTTAACATA
Statistics
Matches: 309, Mismatches: 54, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
117 39 0.13
118 269 0.87
119 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (118 bp):
TCAGCGTGTCACGCCAACTATCTGCTTCCACTCAGCGTGTCACCATAAGATGGGGCGTGCCGTGT
CACCCCACAATACTACAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCAC
Found at i:11836802 original size:236 final size:235
Alignment explanation
Indices: 11836416--11836897 Score: 660
Period size: 236 Copynumber: 2.0 Consensus size: 235
11836406 CTGGAACCAG
* * * * *
11836416 TCAGCATGTCACTCCAAGTATCTGGTTCCACTCAATGTGTCACCATAATTGAGGTGTGCCGTGTC
1 TCAGCATGTCACACCAACTATCTGCTTCCACTCAATGTGTCACCATAATAGAGGCGTGCCGTGTC
* ** * * *
11836481 ACCCCATAATACAGCAAGAAGTCAGTGTGTCACCATAGAAATCTGCATGCACTCAGCGTGTCATG
66 ACCCCACAATACAGCAAGAAGTCAACGTGTCACCACAGAAATCTGCATGCACTCACCGTGTCACG
* * *
11836546 CCAACTATCTACTTCCACTCAGCGTGTCACCACAAGATGGGGCATGCCGTGTCACCCCATAATAT
131 CCAACTATCTACTTCCACTCAGCGTGTCACCACAAGATGGGACATGCCGTGTCACCCCACAATAC
** * * *
11836611 TACAAGTGGTTAGCGTGTCACCACAGAAATCTGCATGTAC
196 TACAAGAAGTTAGCATGTCACCACAGAAATCTACATGCAC
* * *
11836651 TCAGCATGTCACACCAACTATCTGCTTCTACTCAGTGTGTCACTATAAGATAG-GGCGTGCCGTG
1 TCAGCATGTCACACCAACTATCTGCTTCCACTCAATGTGTCACCAT-A-ATAGAGGCGTGCCGTG
*
11836715 TCACCCCACAATACTGCAAGAAGTCAACGTGTCACCACAGAAATCTGCATGCACTCACCGTGTCA
64 TCACCCCACAATACAGCAAGAAGTCAACGTGTCACCACAGAAATCTGCATGCACTCACCGTGTCA
* * * * **
11836780 CGCCAACTATTTGCTTCCACTCAGCGTGTCAGCATAAGATGGGATGTGCCGTGTCACCCCACAAT
129 CGCCAACTATCTACTTCCACTCAGCGTGTCACCACAAGATGGGACATGCCGTGTCACCCCACAAT
*
11836845 ACTGCAAGAAGTTAGCATGTCACCACAGAAATCTACATGCAC
194 ACTACAAGAAGTTAGCATGTCACCACAGAAATCTACATGCAC
*
11836887 TCAGCGTGTCA
1 TCAGCATGTCA
11836898 GCTTAACATA
Statistics
Matches: 214, Mismatches: 31, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
235 40 0.19
236 171 0.80
237 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (235 bp):
TCAGCATGTCACACCAACTATCTGCTTCCACTCAATGTGTCACCATAATAGAGGCGTGCCGTGTC
ACCCCACAATACAGCAAGAAGTCAACGTGTCACCACAGAAATCTGCATGCACTCACCGTGTCACG
CCAACTATCTACTTCCACTCAGCGTGTCACCACAAGATGGGACATGCCGTGTCACCCCACAATAC
TACAAGAAGTTAGCATGTCACCACAGAAATCTACATGCAC
Found at i:11843832 original size:31 final size:31
Alignment explanation
Indices: 11843794--11843933 Score: 199
Period size: 31 Copynumber: 4.5 Consensus size: 31
11843784 TTTGTCAGTC
11843794 ATGTTGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
11843825 ATGTTGTAACACGCCATGCATATAACGTTAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
** * *
11843856 ATGTTGTAACACATCATGCAGATAACGTTAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
11843887 ATGTTGTAACATGCCATGCATATAATGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
11843918 ATATTGCAACACGCCA
1 ATGTTGTAACACGCCA
11843934 ATGATTATAA
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 96 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (31 bp):
ATGTTGTAACACGCCATGCATATAACGTAAA
Found at i:11844349 original size:63 final size:63
Alignment explanation
Indices: 11844266--11844389 Score: 212
Period size: 63 Copynumber: 2.0 Consensus size: 63
11844256 ACCATAGCCC
*
11844266 GATGACGATGGTGCTCAACAGAGAGTTGATAGAGCTCATACAGTTCAGAGAGATGAGAGAGTT
1 GATGACGATGGTGCTCAACAGAGAGTTGATAGAGCTCAGACAGTTCAGAGAGATGAGAGAGTT
* * *
11844329 GATGACGATGGTGCTCAACAGAGAGTTGATAGAGTTGAGACAGTTCAGAGAGTTGAGAGAG
1 GATGACGATGGTGCTCAACAGAGAGTTGATAGAGCTCAGACAGTTCAGAGAGATGAGAGAG
11844390 AAAGATGAGC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.33, C:0.11, G:0.34, T:0.22
Consensus pattern (63 bp):
GATGACGATGGTGCTCAACAGAGAGTTGATAGAGCTCAGACAGTTCAGAGAGATGAGAGAGTT
Found at i:11844364 original size:9 final size:9
Alignment explanation
Indices: 11844348--11844389 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
11844338 GGTGCTCAAC
11844348 AGAGAGTTG
1 AGAGAGTTG
*
11844357 ATAGAGTTG
1 AGAGAGTTG
* *
11844366 AGACAGTTC
1 AGAGAGTTG
11844375 AGAGAGTTG
1 AGAGAGTTG
11844384 AGAGAG
1 AGAGAG
11844390 AAAGATGAGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.38, T:0.21
Consensus pattern (9 bp):
AGAGAGTTG
Found at i:11865336 original size:34 final size:34
Alignment explanation
Indices: 11865260--11865343 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
11865250 CTATTAGTTT
* *
11865260 TTTCCAACAGACATGACTCTTATTTATTTTCCTA
1 TTTCCAACAAACATGACCCTTATTTATTTTCCTA
* * *
11865294 TTTTCAACACACATGACCCTTCTTT-TATTT-CTAA
1 TTTCCAACAAACATGACCCTTATTTAT-TTTCCT-A
11865328 TTTCCAACAAACATGA
1 TTTCCAACAAACATGA
11865344 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
33 3 0.07
34 39 0.93
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (34 bp):
TTTCCAACAAACATGACCCTTATTTATTTTCCTA
Found at i:11866932 original size:18 final size:18
Alignment explanation
Indices: 11866909--11866946 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11866899 CTTTCCCTGT
11866909 TTCTTTTCTCCATTT-CTC
1 TTCTTTT-TCCATTTACTC
*
11866927 TTCTTTTTCCTTTTACTC
1 TTCTTTTTCCATTTACTC
11866945 TT
1 TT
11866947 ATGAGAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTTTTCCATTTACTC
Found at i:11873498 original size:25 final size:25
Alignment explanation
Indices: 11873470--11873518 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
11873460 AATTCCTTCA
11873470 ATATCTAATCCCTGTAATATTGTTG
1 ATATCTAATCCCTGTAATATTGTTG
*
11873495 ATATCTAATCCTTGTAATATTGTT
1 ATATCTAATCCCTGTAATATTGTT
11873519 CTATTTGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (25 bp):
ATATCTAATCCCTGTAATATTGTTG
Found at i:11874680 original size:29 final size:29
Alignment explanation
Indices: 11874646--11874711 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
11874636 TAAATACAAA
*
11874646 GTTACAC-CTCATGTAGAAAAATAAAAGTT
1 GTTACACACT-ATGTAGAAAAAAAAAAGTT
*
11874675 GTTACACACTATGTTGAAAAAAAAAAGTT
1 GTTACACACTATGTAGAAAAAAAAAAGTT
*
11874704 ATTACACA
1 GTTACACA
11874712 GCATGTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (29 bp):
GTTACACACTATGTAGAAAAAAAAAAGTT
Found at i:11874704 original size:26 final size:27
Alignment explanation
Indices: 11874637--11874704 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 27
11874627 AAACAAAGAT
*
11874637 AAATACAAAGTTACACCTCATGTAGAA
1 AAATAAAAAGTTACACCTCATGTAGAA
* *
11874664 AAATAAAAGTTGTTACACACT-ATGTTGAA
1 AAATAAAA--AGTTACAC-CTCATGTAGAA
11874693 AAA-AAAAAGTTA
1 AAATAAAAAGTTA
11874705 TTACACAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
26 4 0.12
27 7 0.21
28 4 0.12
29 17 0.50
30 2 0.06
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (27 bp):
AAATAAAAAGTTACACCTCATGTAGAA
Found at i:11874717 original size:29 final size:28
Alignment explanation
Indices: 11874655--11874718 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
11874645 AGTTACACCT
* * *
11874655 CATGTAGAAAAATAAAAGTTGTTACACA
1 CATGTTGAAAAAAAAAAGTTATTACACA
11874683 CTATGTTGAAAAAAAAAAGTTATTACACA
1 C-ATGTTGAAAAAAAAAAGTTATTACACA
11874712 GCATGTT
1 -CATGTT
11874719 TAAAGTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (28 bp):
CATGTTGAAAAAAAAAAGTTATTACACA
Found at i:11874788 original size:129 final size:131
Alignment explanation
Indices: 11874575--11874819 Score: 295
Period size: 129 Copynumber: 1.9 Consensus size: 131
11874565 AAAAATTTTG
* * ** *
11874575 TTACACGCTATGTTTAAGGTGTTTTAACTCAAAGAGTTTATTTTTTAATGAAAAACAAAGATAAA
1 TTACACGCTATGTTTAAAGTGTTTTAACTCAAAGAGTTTATGTCCTAATGAAAAACAAAAATAAA
* *
11874640 TACAAAGTTACACCTCATGTAGAAAAATA-AAAGTTGTTACACACTATGTTGAAAAAAAAAAGTT
66 TACAAAGTTACACCTCATGTAGAAAAAAATAAAGTTATTACACACTATGTTGAAAAAAAAAAGTT
11874704 A
131 A
*
11874705 TTACACAGC-ATGTTTAAAGTG-TTTAACTTC-AAGAGTTTATGTCCTAATGAAATACAAAAATA
1 TTACAC-GCTATGTTTAAAGTGTTTTAAC-TCAAAGAGTTTATGTCCTAATGAAAAACAAAAATA
* * * * *
11874767 GAA-ACCAAGTTACATGC-CATGTTGAAAAAAATAAAGTTATTATACGCTATGTT
64 -AATACAAAGTTACA-CCTCATGTAGAAAAAAATAAAGTTATTACACACTATGTT
11874820 TAAGATGTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
129 55 0.57
130 40 0.41
131 2 0.02
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (131 bp):
TTACACGCTATGTTTAAAGTGTTTTAACTCAAAGAGTTTATGTCCTAATGAAAAACAAAAATAAA
TACAAAGTTACACCTCATGTAGAAAAAAATAAAGTTATTACACACTATGTTGAAAAAAAAAAGTT
A
Found at i:11874843 original size:101 final size:100
Alignment explanation
Indices: 11874675--11874910 Score: 257
Period size: 101 Copynumber: 2.4 Consensus size: 100
11874665 AATAAAAGTT
*
11874675 GTTACAC-ACTATGTTGAAAAAAAAAAGTTATTACACAGCATGTTTAAAGTGTTTAACTTCAAGA
1 GTTACACGAC-ATGTTGAAAAAAAAAAGTTATTACACAGCATGTTTAAAGTGTTTAACTTCAACA
** * *
11874739 GTTTATGTCCTAATGAAATACAAAAATAGAA-ACCAA
65 GTTTAAATACTAATGAAAGACAAAAATA-AATACCAA
* * * *
11874775 GTTACATGCCATGTTGAAAAAAATAAAGTTATTATAC-GCTATGTTT-AAGATGTTTAAC-TCTT
1 GTTACACGACATGTTGAAAAAAA-AAAGTTATTACACAGC-ATGTTTAAAG-TGTTTAACTTC-A
* * *
11874837 ACAGTTTAAATACTAGTGAAGGACAAAGATAAATACCAA
62 ACAGTTTAAATACTAATGAAAGACAAAAATAAATACCAA
* *
11874876 GTTACACGACATATTGAAAAAAAAAAGTTGTTACA
1 GTTACACGACATGTTGAAAAAAAAAAGTTATTACA
11874911 TGTCATGTTG
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
100 38 0.34
101 75 0.66
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (100 bp):
GTTACACGACATGTTGAAAAAAAAAAGTTATTACACAGCATGTTTAAAGTGTTTAACTTCAACAG
TTTAAATACTAATGAAAGACAAAAATAAATACCAA
Found at i:11874921 original size:29 final size:29
Alignment explanation
Indices: 11874877--11874952 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 29
11874867 AAATACCAAG
* * *
11874877 TTACACGACATATTGAAAAAAAAAAGTTG
1 TTACACGTCATGTTGAAAAAAAAAAGTTA
* *
11874906 TTACATGTCATGTTG-AAAAACAAAGTTA
1 TTACACGTCATGTTGAAAAAAAAAAGTTA
* *
11874934 TTACACGTGATGTTTAAAA
1 TTACACGTCATGTTGAAAA
11874953 TGTTTAACTC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 23 0.61
29 15 0.39
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (29 bp):
TTACACGTCATGTTGAAAAAAAAAAGTTA
Found at i:11875009 original size:128 final size:129
Alignment explanation
Indices: 11874775--11875010 Score: 296
Period size: 128 Copynumber: 1.8 Consensus size: 129
11874765 TAGAAACCAA
* * * *
11874775 GTTACATGCCATGTTGAAAAAAATAAAGTTATTATACGCTATGTTTAAGATGTTTAACTCTTACA
1 GTTACATGCCATGTTG-AAAAAACAAAGTTATTACACGCTATGTTTAAAATGTTTAACTCCTACA
* * * *
11874840 GTTTAAATACTAGTGAAGGACAAAGATAAATACCAAGTTACACGACATATTGAAAAAAAAAAGTT
65 GTTTAAATACTAATGAAAGACAAAGATAAAGACCAAATTACACGACATATTGAAAAAAAAAAGTT
* *
11874905 GTTACATGTCATGTTG-AAAAACAAAGTTATTACACG-TGATGTTTAAAATGTTTAACTCCTAGA
1 GTTACATGCCATGTTGAAAAAACAAAGTTATTACACGCT-ATGTTTAAAATGTTTAACTCCTACA
** * * * *
11874968 GTTTATGTCCTAATGAAATACAAAGATAGAGATCAAATTACAC
65 GTTTAAATACTAATGAAAGACAAAGATAAAGACCAAATTACAC
11875011 ACCATGTTTA
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
127 1 0.01
128 73 0.82
130 15 0.17
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (129 bp):
GTTACATGCCATGTTGAAAAAACAAAGTTATTACACGCTATGTTTAAAATGTTTAACTCCTACAG
TTTAAATACTAATGAAAGACAAAGATAAAGACCAAATTACACGACATATTGAAAAAAAAAAGTT
Found at i:11883172 original size:16 final size:17
Alignment explanation
Indices: 11883147--11883183 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11883137 CAAGGGCTTT
* *
11883147 AGGCCCCCAATTTGGGG
1 AGGCCCCAAATTTAGGG
11883164 AGGCCCCAAATTTAGGG
1 AGGCCCCAAATTTAGGG
11883181 AGG
1 AGG
11883184 ATTTATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.16
Consensus pattern (17 bp):
AGGCCCCAAATTTAGGG
Found at i:11953277 original size:7 final size:7
Alignment explanation
Indices: 11953265--11953289 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11953255 ACTTGGATTT
11953265 TTTTTTA
1 TTTTTTA
11953272 TTTTTTA
1 TTTTTTA
11953279 TTTTTTA
1 TTTTTTA
11953286 TTTT
1 TTTT
11953290 CCATTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:11955046 original size:16 final size:15
Alignment explanation
Indices: 11955027--11955069 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
11955017 TTACTTATTT
11955027 TTAGTTATTTTTATAA
1 TTAGTTATTTTTA-AA
*
11955043 TTAGTTTATTTTTAAG
1 TTAG-TTATTTTTAAA
*
11955059 TGAGTTATTTT
1 TTAGTTATTTT
11955070 AATTTTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (15 bp):
TTAGTTATTTTTAAA
Found at i:11955089 original size:20 final size:21
Alignment explanation
Indices: 11955066--11955104 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11955056 AAGTGAGTTA
*
11955066 TTTTAATTTTA-TGTTATTCC
1 TTTTAATTTGATTGTTATTCC
11955086 TTTTAATTTGATTGTTATT
1 TTTTAATTTGATTGTTATT
11955105 TATTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTTAATTTGATTGTTATTCC
Found at i:11961568 original size:19 final size:19
Alignment explanation
Indices: 11961544--11961581 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11961534 CTGTCAAACC
*
11961544 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
*
11961563 CTCAAATCGTACTCCAATA
1 CTCAAATCATACTCCAATA
11961582 AGTGAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:11962051 original size:42 final size:42
Alignment explanation
Indices: 11962000--11962081 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
11961990 ATATAGCCGG
*
11962000 GTCAGCAACGGCTTATGTGCACTCCCACTCACACATAGCCAA
1 GTCAGCAACGACTTATGTGCACTCCCACTCACACATAGCCAA
* *
11962042 GTCAGCAACGACTTATGTGCACTCCTACTCGCACATAGCC
1 GTCAGCAACGACTTATGTGCACTCCCACTCACACATAGCC
11962082 GGATCCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (42 bp):
GTCAGCAACGACTTATGTGCACTCCCACTCACACATAGCCAA
Found at i:11969453 original size:21 final size:21
Alignment explanation
Indices: 11969429--11969468 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11969419 TACAAAATAA
*
11969429 AAAGTAAATATATTTATATTT
1 AAAGTAAATATATATATATTT
*
11969450 AAAGTACATATATATATAT
1 AAAGTAAATATATATATAT
11969469 ACACACACGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:11969758 original size:15 final size:15
Alignment explanation
Indices: 11969738--11969769 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11969728 TATATATATA
*
11969738 TTATAATTAATAATT
1 TTATAAGTAATAATT
11969753 TTATAAGTAATAATT
1 TTATAAGTAATAATT
11969768 TT
1 TT
11969770 TGNTTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATAAGTAATAATT
Found at i:11969840 original size:84 final size:85
Alignment explanation
Indices: 11969689--11969856 Score: 277
Period size: 84 Copynumber: 2.0 Consensus size: 85
11969679 TCAAAAGCTC
* *
11969689 TCTTTAAGTATATATGTTATAAGTTTATATAAATAATAGTATATATATATTATAATTAATAATTT
1 TCTTTAAGTATATATATTATAAGATTATATAAATAATAGTATATATATATTATAATTAATAATTT
11969754 TATAAGTAATAATTTTTGNTT
66 TATAAGTAATAATTTTTG-TT
*
11969775 TCTTTAAGTATATATATTATAAGATTATATAAATAAT-G-GTATATATATTATAATTAATAATTT
1 TCTTTAAGTATATATATTATAAGATTATATAAATAATAGTATATATATATTATAATTAATAATTT
*
11969838 TATAAGTCATAATTTTTGT
66 TATAAGTAATAATTTTTGT
11969857 AATGTTAACA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
83 1 0.01
84 41 0.53
85 1 0.01
86 35 0.45
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (85 bp):
TCTTTAAGTATATATATTATAAGATTATATAAATAATAGTATATATATATTATAATTAATAATTT
TATAAGTAATAATTTTTGTT
Found at i:11979387 original size:42 final size:41
Alignment explanation
Indices: 11979323--11979444 Score: 136
Period size: 42 Copynumber: 2.9 Consensus size: 41
11979313 TGACATTGAC
* *
11979323 CCGGCTATGTGTGAGTAAGAGTGCACATAAGCCGTTGCTGA
1 CCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGA
* * * *
11979364 CTCGGTTATGTGCGAGTAGGAGTGCACATAAGTCATTGCTAA
1 C-CGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGA
* * * *
11979406 CCTGACTATGTGCGAGTGGGAGTGCGCATCAGCCGTTGC
1 CC-GGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
11979445 ATATGAGATG
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.03
42 64 0.97
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.25
Consensus pattern (41 bp):
CCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGA
Found at i:11979497 original size:2 final size:2
Alignment explanation
Indices: 11979485--11979521 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11979475 ATGATGATTG
*
11979485 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11979522 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11983702 original size:37 final size:37
Alignment explanation
Indices: 11983656--11983770 Score: 212
Period size: 37 Copynumber: 3.1 Consensus size: 37
11983646 CAATATCATT
11983656 ATCATGTGTGCACTCCCTACTCTCACACTTCAACATC
1 ATCATGTGTGCACTCCCTACTCTCACACTTCAACATC
11983693 ATCATGTGTGCACTCCCTACTCTCACACTTCAACATC
1 ATCATGTGTGCACTCCCTACTCTCACACTTCAACATC
* *
11983730 ATCATGTGTGCACTCCCTCCTCGCACACTTCAACATC
1 ATCATGTGTGCACTCCCTACTCTCACACTTCAACATC
11983767 ATCA
1 ATCA
11983771 CACAACATTA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.24, C:0.38, G:0.09, T:0.29
Consensus pattern (37 bp):
ATCATGTGTGCACTCCCTACTCTCACACTTCAACATC
Found at i:11984618 original size:21 final size:21
Alignment explanation
Indices: 11984592--11984632 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11984582 GGGAGGAAAA
*
11984592 AGAAGATGCTACTAGAAAATG
1 AGAAGAAGCTACTAGAAAATG
* *
11984613 AGAAGAAGCTGCTGGAAAAT
1 AGAAGAAGCTACTAGAAAAT
11984633 AATATTTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.10, G:0.27, T:0.17
Consensus pattern (21 bp):
AGAAGAAGCTACTAGAAAATG
Found at i:11985095 original size:15 final size:15
Alignment explanation
Indices: 11985065--11985114 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
11985055 AGGATAAAAT
*
11985065 AATAAAATAAAATAA
1 AATAAAATAAATTAA
*
11985080 AATAAAATAGATTAA
1 AATAAAATAAATTAA
*
11985095 AGTAAAGATAAATGTAA
1 AATAAA-ATAAAT-TAA
11985112 AAT
1 AAT
11985115 CAGAAGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 18 0.64
16 5 0.18
17 5 0.18
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (15 bp):
AATAAAATAAATTAA
Found at i:11985952 original size:27 final size:27
Alignment explanation
Indices: 11985921--11985990 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
11985911 CACAGTTGAT
*
11985921 TGAAATTTAAAGGTTTCTTTCAATTCC
1 TGAAATTTAAAGATTTCTTTCAATTCC
11985948 TGAAATTTAAAGATTTCTTTCAATTCC
1 TGAAATTTAAAGATTTCTTTCAATTCC
11985975 TGAAATTTAAAGATTT
1 TGAAATTTAAAGATTT
11985991 AAAGATTTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (27 bp):
TGAAATTTAAAGATTTCTTTCAATTCC
Found at i:11990929 original size:2 final size:2
Alignment explanation
Indices: 11990922--11990946 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11990912 TGGATTGCTA
11990922 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11990947 AAATACTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11994723 original size:24 final size:24
Alignment explanation
Indices: 11994679--11994724 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
11994669 GAGTGTTCGG
*
11994679 TTCTTTTCTTGATTTTCTTAAAAT
1 TTCTTTTCTTAATTTTCTTAAAAT
11994703 TTCTTTTCTTAATTCTT-TTAAA
1 TTCTTTTCTTAATT-TTCTTAAA
11994725 TTTTTTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.22, C:0.13, G:0.02, T:0.63
Consensus pattern (24 bp):
TTCTTTTCTTAATTTTCTTAAAAT
Found at i:11995750 original size:2 final size:2
Alignment explanation
Indices: 11995743--11995794 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
11995733 GTATCATGTA
11995743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11995785 AT AT AT AT AT
1 AT AT AT AT AT
11995795 GTACATAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12000434 original size:40 final size:40
Alignment explanation
Indices: 12000381--12000460 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
12000371 TTCAGCACAT
*
12000381 AAAACTTAGAGTAATTGGGTCTTACCCATCATAACATACA
1 AAAACTTAGAGTAATTGGGTCCTACCCATCATAACATACA
12000421 AAAACATTA-AGTAATTGGGTCCTACCCATCATAACATACA
1 AAAAC-TTAGAGTAATTGGGTCCTACCCATCATAACATACA
12000461 TTGAACATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 35 0.92
41 3 0.08
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (40 bp):
AAAACTTAGAGTAATTGGGTCCTACCCATCATAACATACA
Found at i:12000673 original size:59 final size:61
Alignment explanation
Indices: 12000589--12000735 Score: 163
Period size: 61 Copynumber: 2.4 Consensus size: 61
12000579 TTGTATCTTC
* * * *
12000589 AGTGGTATTCCTCTACCCCACCAAGGCAATACATTT-AGGGT-ACTCCGACCCCTTTCTAT
1 AGTGGTATTACTCTGCCCCACCAAGGCAACACATTTCAAGGTAACTCCGACCCCTTTCTAT
* * * * * * *
12000648 GGTGGTTTTACTCTGCCCTACCAAGGCAACATATTTCAAGGTAACTTCGACCCTTTTCTCT
1 AGTGGTATTACTCTGCCCCACCAAGGCAACACATTTCAAGGTAACTCCGACCCCTTTCTAT
* *
12000709 AATGGTATTACTCTGCCCCACTAAGGC
1 AGTGGTATTACTCTGCCCCACCAAGGC
12000736 CATGCTATGC
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 29 0.41
60 4 0.06
61 37 0.53
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (61 bp):
AGTGGTATTACTCTGCCCCACCAAGGCAACACATTTCAAGGTAACTCCGACCCCTTTCTAT
Found at i:12002380 original size:30 final size:29
Alignment explanation
Indices: 12002344--12002518 Score: 127
Period size: 31 Copynumber: 5.7 Consensus size: 29
12002334 TTTTACTATA
*
12002344 TATTTTTTTCAATTTAGTCCTTCAAATATT
1 TATTTTTTTCAATTTAGTCCTTCAACT-TT
*
12002374 TATTTTTATTTACAATTTAGT-CATCTAACTTT
1 TA-TTTT-TTT-CAATTTAGTCCTTC-AACTTT
* * * *
12002406 TGTATATTTTCAATTTTGGTTCTTCAACTTT
1 TAT-TTTTTTCAA-TTTAGTCCTTCAACTTT
* * *
12002437 TCTTTATTTTCAATTTGGTCTTTCAACTTT
1 TATTT-TTTTCAATTTAGTCCTTCAACTTT
*
12002467 TATTTATTTTCAATTTAATCCTTCAACATTT
1 TATTT-TTTTCAATTTAGTCCTTCAAC-TTT
***
12002498 TCATGCATTTCAATTTAGTCC
1 T-ATTTTTTTCAATTTAGTCC
12002519 CTTTTCCAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
30 44 0.38
31 45 0.38
32 16 0.14
33 12 0.10
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.55
Consensus pattern (29 bp):
TATTTTTTTCAATTTAGTCCTTCAACTTT
Found at i:12002445 original size:31 final size:31
Alignment explanation
Indices: 12002400--12002482 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
12002390 TTAGTCATCT
* *
12002400 AACTTTTGTATATTTTCAATTTTGGT-TCTTC
1 AACTTTTATTTATTTTCAATTTTGGTCT-TTC
*
12002431 AACTTTTCTTTATTTTCAA-TTTGGTCTTTC
1 AACTTTTATTTATTTTCAATTTTGGTCTTTC
12002461 AACTTTTATTTATTTTCAATTT
1 AACTTTTATTTATTTTCAATTT
12002483 AATCCTTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
30 27 0.57
31 20 0.43
ACGTcount: A:0.20, C:0.13, G:0.06, T:0.60
Consensus pattern (31 bp):
AACTTTTATTTATTTTCAATTTTGGTCTTTC
Found at i:12002499 original size:61 final size:61
Alignment explanation
Indices: 12002344--12002517 Score: 167
Period size: 61 Copynumber: 2.8 Consensus size: 61
12002334 TTTTACTATA
* *
12002344 TATTT-TTTTCAATTTAGTCCTTCAAATATTTATTTTTATTTACAATTTAGTCATCTAACTTT
1 TATTTATTTTCAATTTAGTCCTTC-AACATTT-TCTTTATTTACAATTTAGTCATCTAACTTT
* * * * * * *
12002406 TGTATATTTTCAATTTTGGTTCTTCAAC-TTTTCTTTATTTTCAATTTGGTC-TTTCAACTTT
1 TATTTATTTTCAA-TTTAGTCCTTCAACATTTTCTTTATTTACAATTTAGTCATCT-AACTTT
* **
12002467 TATTTATTTTCAATTTAATCCTTCAACATTTTCATGCATTT-CAATTTAGTC
1 TATTTATTTTCAATTTAGTCCTTCAACATTTTC-TTTATTTACAATTTAGTC
12002518 CCTTTTCCAA
Statistics
Matches: 90, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
60 13 0.14
61 48 0.53
62 11 0.12
63 9 0.10
64 9 0.10
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (61 bp):
TATTTATTTTCAATTTAGTCCTTCAACATTTTCTTTATTTACAATTTAGTCATCTAACTTT
Found at i:12008019 original size:71 final size:71
Alignment explanation
Indices: 12007899--12008047 Score: 219
Period size: 71 Copynumber: 2.1 Consensus size: 71
12007889 GTTTTAACCA
* * **
12007899 TAAGTATCTGTATTTCCTCTTTAAGTATCAATACCTTTCACACAGAATGCTCCTTAAGGCACTTT
1 TAAGTATCTGTATTTCCTCTTTAAGTACCAATACCTTTCACACAAAATGCTCCCCAAGGCACTTT
12007964 ATCCTC
66 ATCCTC
* *
12007970 TAAGTATC-GATATTTCCTCTTTAAGTACCAATACTTTTCACACAAAATGCTCCCCAAGGCATTT
1 TAAGTATCTG-TATTTCCTCTTTAAGTACCAATACCTTTCACACAAAATGCTCCCCAAGGCACTT
*
12008034 TGTCCTC
65 TATCCTC
12008041 TAAGTAT
1 TAAGTAT
12008048 TGATGCTTGT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
70 1 0.01
71 69 0.99
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (71 bp):
TAAGTATCTGTATTTCCTCTTTAAGTACCAATACCTTTCACACAAAATGCTCCCCAAGGCACTTT
ATCCTC
Found at i:12014708 original size:22 final size:22
Alignment explanation
Indices: 12014683--12014737 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
12014673 CCTTGTAATC
*
12014683 CTTGCAAAGGTTATACCTTACT
1 CTTGAAAAGGTTATACCTTACT
12014705 CTTGAAAAGGTTATACCTTACT
1 CTTGAAAAGGTTATACCTTACT
12014727 CTTGAAAAGGT
1 CTTGAAAAGGT
12014738 AAAGTGCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (22 bp):
CTTGAAAAGGTTATACCTTACT
Found at i:12016276 original size:3 final size:3
Alignment explanation
Indices: 12016270--12016329 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
12016260 ACAGAAGAAT
* *
12016270 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AT TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
12016317 TAGA AAA TAA TAA
1 TA-A TAA TAA TAA
12016330 AAATGCTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 1 0.02
3 47 0.96
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12017020 original size:12 final size:11
Alignment explanation
Indices: 12016996--12017038 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
12016986 GAAACAATGA
12016996 AATAATGAAAAT
1 AATAAT-AAAAT
12017008 AATGAATAAAAT
1 AAT-AATAAAAT
* *
12017020 AATAATATAGT
1 AATAATAAAAT
12017031 AATAATAA
1 AATAATAA
12017039 TAAATACAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 13 0.48
12 11 0.41
13 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:12025027 original size:22 final size:23
Alignment explanation
Indices: 12024996--12025042 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
12024986 ATATAGAGTT
12024996 ATTTAAGCTTAATT-TTGATAGTA
1 ATTTAAGCTTAATTCTTG-TAGTA
*
12025019 ATTT-AGCTTAGTTCTTGTAGTA
1 ATTTAAGCTTAATTCTTGTAGTA
12025041 AT
1 AT
12025043 GCAAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (23 bp):
ATTTAAGCTTAATTCTTGTAGTA
Found at i:12029137 original size:19 final size:18
Alignment explanation
Indices: 12029080--12029140 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
12029070 ATTAGGTACT
* *
12029080 TTTTAGTGAGTTATTTTAA
1 TTTTAGTTA-TTATTTTTA
**
12029099 TTTTATGTTATTCCTTTTA
1 TTTTA-GTTATTATTTTTA
12029118 TTTTAGTTATTATTTATTA
1 TTTTAGTTATTATTT-TTA
12029137 TTTT
1 TTTT
12029141 TTATATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.24
19 23 0.68
20 3 0.09
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.67
Consensus pattern (18 bp):
TTTTAGTTATTATTTTTA
Found at i:12029141 original size:25 final size:25
Alignment explanation
Indices: 12029090--12029141 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
12029080 TTTTAGTGAG
*
12029090 TTATTTTAATTTTATGTTATTCCTT
1 TTATTTTAATTTTATGTTATTACTT
* *
12029115 TTATTTTAGTTATTAT-TTATTATTT
1 TTATTTTAATT-TTATGTTATTACTT
12029140 TT
1 TT
12029142 TATATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (25 bp):
TTATTTTAATTTTATGTTATTACTT
Found at i:12030541 original size:20 final size:20
Alignment explanation
Indices: 12030496--12030533 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12030486 TTTTGGCCCC
12030496 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
12030516 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
12030534 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:12032879 original size:14 final size:15
Alignment explanation
Indices: 12032860--12032896 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
12032850 CAGATATTTT
12032860 GATTTTAAG-CTTTG
1 GATTTTAAGCCTTTG
12032874 GATTTTAAAGCCTTTG
1 GATTTT-AAGCCTTTG
12032890 G-TTTTAA
1 GATTTTAA
12032897 ATTTGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.38
15 7 0.33
16 6 0.29
ACGTcount: A:0.24, C:0.08, G:0.19, T:0.49
Consensus pattern (15 bp):
GATTTTAAGCCTTTG
Found at i:12032890 original size:16 final size:15
Alignment explanation
Indices: 12032860--12032897 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
12032850 CAGATATTTT
12032860 GATTTT-AAGCTTTG
1 GATTTTAAAGCTTTG
12032874 GATTTTAAAGCCTTTG
1 GATTTTAAAG-CTTTG
12032890 G-TTTTAAA
1 GATTTTAAA
12032898 TTTGTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 10 0.45
16 6 0.27
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.47
Consensus pattern (15 bp):
GATTTTAAAGCTTTG
Found at i:12046001 original size:9 final size:8
Alignment explanation
Indices: 12045984--12046063 Score: 79
Period size: 8 Copynumber: 9.2 Consensus size: 8
12045974 ACCTTACTCG
12045984 TTTTTATT
1 TTTTTATT
12045992 TTTTTCATT
1 TTTTT-ATT
12046001 TTTTTATT
1 TTTTTATT
12046009 ATCTTTTATT
1 -T-TTTTATT
12046019 TTATTTATT
1 TT-TTTATT
*
12046028 TTATTATT
1 TTTTTATT
12046036 TATTATTATT
1 T-TT-TTATT
*
12046046 ATTTTATT
1 TTTTTATT
*
12046054 TATTTATT
1 TTTTTATT
12046062 TT
1 TT
12046064 AATCTATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
8 27 0.45
9 21 0.35
10 12 0.20
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTATT
Found at i:12046028 original size:27 final size:29
Alignment explanation
Indices: 12045985--12046064 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 29
12045975 CCTTACTCGT
*
12045985 TTTTATTTT-TTTCATTTTTTTA-TTA-TC
1 TTTTATTTTATTT-ATTTTTTTATTTATTA
*
12046012 TTTTATTTTATTTATTTTATTATTTATTA
1 TTTTATTTTATTTATTTTTTTATTTATTA
12046041 TTATTATTTTATTTATTTATTTTA
1 TT-TTATTTTATTTATTT-TTTTA
12046065 ATCTATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 17 0.38
28 6 0.13
29 3 0.07
30 15 0.33
31 4 0.09
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTTATTTTATTTATTTTTTTATTTATTA
Found at i:12046031 original size:21 final size:21
Alignment explanation
Indices: 12045987--12046073 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 21
12045977 TTACTCGTTT
12045987 TTATTT-TTTTCATTT-TTTTA
1 TTATTTATTTT-ATTTATTTTA
12046007 TTATCTTTTATTTTATTTATTTTA
1 TTA---TTTATTTTATTTATTTTA
12046031 TTATTTATTATTA-TTATTTTA
1 TTATTTATT-TTATTTATTTTA
*
12046052 TTTATTTATTTTAATCTATTTT
1 -TTATTTATTTT-ATTTATTTT
12046074 TTTTTCTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 15
0.78 0.01 0.21
Matches are distributed among these distances:
20 3 0.05
21 16 0.28
22 13 0.23
23 13 0.23
24 12 0.21
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTATTTTATTTATTTTA
Found at i:12046056 original size:34 final size:32
Alignment explanation
Indices: 12045985--12046064 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 32
12045975 CCTTACTCGT
*
12045985 TTTTATTT-TTTTCATTTTTTTATTATCTTTTA
1 TTTTATTTATTTT-ATTTTTTTATTATATTTTA
12046017 TTTTATTTATTTTATTATTTATTATTATTATTTTA
1 TTTTATTTATTTTATT-TTT-TTATTA-TATTTTA
12046052 -TTTATTTATTTTA
1 TTTTATTTATTTTA
12046065 ATCTATTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 11 0.26
33 7 0.16
34 19 0.44
35 6 0.14
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTATTTATTTTATTTTTTTATTATATTTTA
Found at i:12046064 original size:9 final size:9
Alignment explanation
Indices: 12045986--12046064 Score: 64
Period size: 9 Copynumber: 9.0 Consensus size: 9
12045976 CTTACTCGTT
12045986 TTTATTTT-
1 TTTATTTTA
12045994 TTTCATTTT-
1 TTT-ATTTTA
12046003 TTTATTATCT-
1 TTTATT-T-TA
12046013 TTTATTTTA
1 TTTATTTTA
12046022 TTTATTTTA
1 TTTATTTTA
12046031 -TTA-TTTA
1 TTTATTTTA
12046038 -TTATTATTA
1 TTTATT-TTA
12046047 TTT-TATTTA
1 TTTAT-TTTA
12046056 TTTATTTTA
1 TTTATTTTA
12046065 ATCTATTTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 17
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.11
8 11 0.18
9 33 0.53
10 11 0.18
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:12046071 original size:18 final size:17
Alignment explanation
Indices: 12046018--12046072 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
12046008 TATCTTTTAT
12046018 TTTATTTATTTT-ATTA
1 TTTATTTATTTTAATTA
*
12046034 TTTA-TTATTATTATTTTA
1 TTTATTTATT-TTA-ATTA
12046052 TTTATTTATTTTAATCTA
1 TTTATTTATTTTAAT-TA
12046070 TTT
1 TTT
12046073 TTTTTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 5 0.16
16 6 0.19
17 1 0.03
18 15 0.47
19 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTATTTTAATTA
Found at i:12061552 original size:15 final size:14
Alignment explanation
Indices: 12061504--12061562 Score: 100
Period size: 14 Copynumber: 4.1 Consensus size: 14
12061494 TTCTTAAAAC
12061504 AACTTTAAAACCAA
1 AACTTTAAAACCAA
12061518 AACTTTAAAACCAA
1 AACTTTAAAACCAA
12061532 AACTTTAAAATCCAA
1 AACTTTAAAA-CCAA
*
12061547 AGCTTTAAAACCAA
1 AACTTTAAAACCAA
12061561 AA
1 AA
12061563 TCTCTTATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
14 29 0.69
15 13 0.31
ACGTcount: A:0.56, C:0.20, G:0.02, T:0.22
Consensus pattern (14 bp):
AACTTTAAAACCAA
Found at i:12061553 original size:29 final size:28
Alignment explanation
Indices: 12061504--12061562 Score: 100
Period size: 29 Copynumber: 2.1 Consensus size: 28
12061494 TTCTTAAAAC
12061504 AACTTTAAAACCAAAACTTTAAAACCAA
1 AACTTTAAAACCAAAACTTTAAAACCAA
*
12061532 AACTTTAAAATCCAAAGCTTTAAAACCAA
1 AACTTTAAAA-CCAAAACTTTAAAACCAA
12061561 AA
1 AA
12061563 TCTCTTATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.56, C:0.20, G:0.02, T:0.22
Consensus pattern (28 bp):
AACTTTAAAACCAAAACTTTAAAACCAA
Found at i:12066479 original size:16 final size:16
Alignment explanation
Indices: 12066458--12066490 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12066448 TCAATGAAAT
*
12066458 AAAAAAAGAA-AGATG
1 AAAAAAAAAATAGATG
12066473 AAAAAAAAAATAGATG
1 AAAAAAAAAATAGATG
12066489 AA
1 AA
12066491 GCTTTTAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (16 bp):
AAAAAAAAAATAGATG
Found at i:12067771 original size:21 final size:21
Alignment explanation
Indices: 12067727--12067774 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
12067717 AAACCTCGAC
* * **
12067727 TACATCTCCAAAACTTTCGGG
1 TACATTTCCAAAACCTTCAAG
12067748 TACATTTCCAAAACCTTCAAG
1 TACATTTCCAAAACCTTCAAG
12067769 TACATT
1 TACATT
12067775 CTTGCCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.31
Consensus pattern (21 bp):
TACATTTCCAAAACCTTCAAG
Found at i:12067883 original size:21 final size:21
Alignment explanation
Indices: 12067857--12067896 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12067847 CAACCTTTTC
* *
12067857 CTAAAATCTTCAAGTACATCA
1 CTAAAACCTCCAAGTACATCA
12067878 CTAAAACCTCCAAGTACAT
1 CTAAAACCTCCAAGTACAT
12067897 TTCCAAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.28, G:0.05, T:0.25
Consensus pattern (21 bp):
CTAAAACCTCCAAGTACATCA
Found at i:12067904 original size:21 final size:21
Alignment explanation
Indices: 12067853--12067918 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
12067843 GGAGCAACCT
* *
12067853 TTTCCTAAAATCTTCAAGTACA
1 TTTCC-AAAACCTCCAAGTACA
** *
12067875 TCACTAAAACCTCCAAGTACA
1 TTTCCAAAACCTCCAAGTACA
* *
12067896 TTTCCAAAACCTCTAGGTACA
1 TTTCCAAAACCTCCAAGTACA
12067917 TT
1 TT
12067919 CTTACGAAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.30
Consensus pattern (21 bp):
TTTCCAAAACCTCCAAGTACA
Found at i:12067916 original size:144 final size:144
Alignment explanation
Indices: 12067683--12067972 Score: 368
Period size: 144 Copynumber: 2.0 Consensus size: 144
12067673 GTTATGCACA
* * * * * **
12067683 CTCATTTTGAGATGAGGAGCAACATTTTCCTATAAAACCTCGACTACATCTCCAAAACTTTCGGG
1 CTCATTTTCAGATGAGGAGCAACATTTTCCTATAAAACCTCAACTACATCACCAAAACCTCCAAG
* *
12067748 TACATTTCCAAAACCTTCAAGTACATTCTTGCCAAACCTCTTGGGTAATTAGCATTAATATTTCT
66 TACATTTCCAAAACCTTCAAGTACATTCTTACCAAACCT-TTGAGTAATTAGCATTAATATTTCT
12067813 TTAAAGTTACATAAC
130 TTAAAGTTACATAAC
* * * * *
12067828 CTCATTTTCAGATGAGGAGCAACCTTTTCCTA-AAATCTTCAAGTACATCACTAAAACCTCCAAG
1 CTCATTTTCAGATGAGGAGCAACATTTTCCTATAAAACCTCAACTACATCACCAAAACCTCCAAG
* * * *
12067892 TACATTTCCAAAACC-TCTAGGTACATTCTTACGAAACCTTTGAGTAATTATCATTAATATTTTT
66 TACATTTCCAAAACCTTC-AAGTACATTCTTACCAAACCTTTGAGTAATTAGCATTAATATTTCT
* *
12067956 TTATAGTTACGTAAC
130 TTAAAGTTACATAAC
12067971 CT
1 CT
12067973 TAATTTGAGA
Statistics
Matches: 124, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
143 39 0.31
144 55 0.44
145 30 0.24
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (144 bp):
CTCATTTTCAGATGAGGAGCAACATTTTCCTATAAAACCTCAACTACATCACCAAAACCTCCAAG
TACATTTCCAAAACCTTCAAGTACATTCTTACCAAACCTTTGAGTAATTAGCATTAATATTTCTT
TAAAGTTACATAAC
Found at i:12068088 original size:21 final size:21
Alignment explanation
Indices: 12068062--12068135 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
12068052 ACCTCTAAGC
* * *
12068062 TCAAAACCTTTGGGTCCATTT
1 TCAAAACCTCTAGGTACATTT
*
12068083 TCAAAACCTCTAGGTAAATTT
1 TCAAAACCTCTAGGTACATTT
*
12068104 TCAAAACCTCTAGGTACATTC
1 TCAAAACCTCTAGGTACATTT
12068125 TCAAAACCTCT
1 TCAAAACCTCT
12068136 GAGTACCTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (21 bp):
TCAAAACCTCTAGGTACATTT
Found at i:12068504 original size:10 final size:10
Alignment explanation
Indices: 12068491--12068527 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
12068481 CCCTTTTACA
12068491 TTATTTTATC
1 TTATTTTATC
12068501 TTATTTTAT-
1 TTATTTTATC
*
12068510 TT-TCTTATC
1 TTATTTTATC
12068519 TTATTTTAT
1 TTATTTTAT
12068528 TTTTAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
8 5 0.22
9 4 0.17
10 14 0.61
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (10 bp):
TTATTTTATC
Found at i:12068519 original size:18 final size:18
Alignment explanation
Indices: 12068496--12068530 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12068486 TTACATTATT
12068496 TTATCTTATTTTATTTTC
1 TTATCTTATTTTATTTTC
12068514 TTATCTTATTTTATTTT
1 TTATCTTATTTTATTTT
12068531 TAGTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATCTTATTTTATTTTC
Found at i:12073675 original size:18 final size:17
Alignment explanation
Indices: 12073650--12073692 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
12073640 AAAATGAAAC
12073650 AATGAAATAATGAA-AAT
1 AATGAAATAAT-AATAAT
12073667 AATGAAAATAATAATAAT
1 AATG-AAATAATAATAAT
12073685 AAT-AAATA
1 AATGAAATA
12073693 CAAGAGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 6 0.25
18 13 0.54
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (17 bp):
AATGAAATAATAATAAT
Found at i:12073689 original size:9 final size:9
Alignment explanation
Indices: 12073650--12073687 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
12073640 AAAATGAAAC
12073650 AATG-AAAT
1 AATGAAAAT
12073658 AATGAAAAT
1 AATGAAAAT
12073667 AATGAAAAT
1 AATGAAAAT
12073676 AAT-AATAAT
1 AATGAA-AAT
12073685 AAT
1 AAT
12073688 AAATACAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (9 bp):
AATGAAAAT
Found at i:12088936 original size:29 final size:31
Alignment explanation
Indices: 12088880--12088953 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 31
12088870 TGCTAGTTAT
12088880 TATGGATATTGATGATATCTAGCTTAGCTAC
1 TATGGATATTGATGATATCTAGCTTAGCTAC
* *
12088911 TATGGATATTG-T-ATATCTTGTTTAGCTAC
1 TATGGATATTGATGATATCTAGCTTAGCTAC
*
12088940 TGTGGATATT-ATGA
1 TATGGATATTGATGA
12088954 ATATTTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 25 0.66
30 2 0.05
31 11 0.29
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.43
Consensus pattern (31 bp):
TATGGATATTGATGATATCTAGCTTAGCTAC
Found at i:12095853 original size:42 final size:42
Alignment explanation
Indices: 12095801--12095887 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
12095791 ACATGGTTGG
* * *
12095801 GTCATCATCGGCTTATGTGCACTCCCACTTGCACTTAGCCAA
1 GTCATCATCGGCTTATGTACACTCCCACTCGCACATAGCCAA
* *
12095843 GTCATCATCGGCTTATGTACACTCCTACTCGCACATAGCCGA
1 GTCATCATCGGCTTATGTACACTCCCACTCGCACATAGCCAA
12095885 GTC
1 GTC
12095888 CACATCAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (42 bp):
GTCATCATCGGCTTATGTACACTCCCACTCGCACATAGCCAA
Found at i:12103252 original size:38 final size:39
Alignment explanation
Indices: 12103210--12103312 Score: 147
Period size: 38 Copynumber: 2.6 Consensus size: 39
12103200 ATAGTGCCCG
*
12103210 TGTGCATGATGTGGGGGGATGTACACGAT-TGCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGTGC-CTGATA
* *
12103248 TGTGCACGATGTGGGGGGATGCACACGATGGTGCCTGCTA
1 TGTGCACGATGTGGGGGGATGTACACGAT-GTGCCTGATA
12103288 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
12103313 TGAGCCGGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 27 0.47
39 4 0.07
40 27 0.47
ACGTcount: A:0.19, C:0.16, G:0.40, T:0.25
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGTACACGATGTGCCTGATA
Found at i:12106022 original size:20 final size:19
Alignment explanation
Indices: 12105999--12106052 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
12105989 CAGATGTAAA
12105999 TAACATAAAACT-AACATTAT
1 TAACATAAAA-TAAACATT-T
*
12106019 TAACTTAAAATAAACATTT
1 TAACATAAAATAAACATTT
* *
12106038 AAACATAAATTAAAC
1 TAACATAAAATAAAC
12106053 TAAACTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (19 bp):
TAACATAAAATAAACATTT
Found at i:12107246 original size:18 final size:18
Alignment explanation
Indices: 12107223--12107257 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12107213 ACAAAAGAAT
12107223 ATCCCAATCACTCAATTC
1 ATCCCAATCACTCAATTC
12107241 ATCCCAATCACTCAATT
1 ATCCCAATCACTCAATT
12107258 TAATTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (18 bp):
ATCCCAATCACTCAATTC
Found at i:12125607 original size:17 final size:17
Alignment explanation
Indices: 12125585--12125633 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
12125575 TGGTATAGTT
12125585 ATGTTGACGTGGCACAA
1 ATGTTGACGTGGCACAA
*
12125602 ATGTTGACATGGCAC-A
1 ATGTTGACGTGGCACAA
*
12125618 ATGTTGACGTGTCACA
1 ATGTTGACGTGGCACA
12125634 TGAATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (17 bp):
ATGTTGACGTGGCACAA
Found at i:12125622 original size:16 final size:17
Alignment explanation
Indices: 12125585--12125625 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
12125575 TGGTATAGTT
*
12125585 ATGTTGACGTGGCACAA
1 ATGTTGACATGGCACAA
12125602 ATGTTGACATGGCAC-A
1 ATGTTGACATGGCACAA
12125618 ATGTTGAC
1 ATGTTGAC
12125626 GTGTCACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (17 bp):
ATGTTGACATGGCACAA
Found at i:12132897 original size:27 final size:29
Alignment explanation
Indices: 12132867--12132930 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
12132857 GACATTAAAA
* * *
12132867 TATAACAA-AAT-GTTTTTGAATATGGCG
1 TATAACAATAATAGTTTTTCAACATGACG
*
12132894 TATAACAATAATATTTTTTCAACATGACG
1 TATAACAATAATAGTTTTTCAACATGACG
12132923 TATAACAA
1 TATAACAA
12132931 CTGTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 8 0.26
28 3 0.10
29 20 0.65
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (29 bp):
TATAACAATAATAGTTTTTCAACATGACG
Found at i:12133078 original size:45 final size:43
Alignment explanation
Indices: 12133029--12133167 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 43
12133019 TTTTTTAATT
* * *
12133029 TGGCGTGTAATATCCTGACTATGACGTGTCACATGTTTTTGTACA
1 TGGCGTGTAATAT-CTAAC-ATGGCGTGTCACATGTTTCTGTACA
*
12133074 TGGCGTGTCACATGTTTCTATACATGGCGTGTCACATGTTTCTGTACA
1 TGGCGTGT-A-A--TATCTA-ACATGGCGTGTCACATGTTTCTGTACA
* * *
12133122 TAGTGTGTAACAATCTAACCATGGCGTGTCACATGTTTCTGTACA
1 TGGCGTGTAA-TATCTAA-CATGGCGTGTCACATGTTTCTGTACA
12133167 T
1 T
12133168 AACGTGTCAC
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
44 1 0.01
45 39 0.49
46 2 0.03
47 2 0.03
48 31 0.39
49 4 0.05
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TGGCGTGTAATATCTAACATGGCGTGTCACATGTTTCTGTACA
Found at i:12133085 original size:24 final size:24
Alignment explanation
Indices: 12133053--12133198 Score: 156
Period size: 24 Copynumber: 6.2 Consensus size: 24
12133043 CTGACTATGA
*
12133053 CGTGTCACATGTTTTTGTACATGG
1 CGTGTCACATGTTTCTGTACATGG
*
12133077 CGTGTCACATGTTTCTATACATGG
1 CGTGTCACATGTTTCTGTACATGG
*
12133101 CGTGTCACATGTTTCTGTACATAG
1 CGTGTCACATGTTTCTGTACATGG
* * * *
12133125 TGTGTAACA---ATCT-AACCATGG
1 CGTGTCACATGTTTCTGTA-CATGG
**
12133146 CGTGTCACATGTTTCTGTACATAA
1 CGTGTCACATGTTTCTGTACATGG
*
12133170 CGTGTCACATGTTTCTATACATGG
1 CGTGTCACATGTTTCTGTACATGG
*
12133194 TGTGT
1 CGTGT
12133199 AACAACCTAA
Statistics
Matches: 98, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.01
21 14 0.14
24 82 0.84
25 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (24 bp):
CGTGTCACATGTTTCTGTACATGG
Found at i:12133260 original size:69 final size:69
Alignment explanation
Indices: 12133072--12133271 Score: 274
Period size: 69 Copynumber: 2.9 Consensus size: 69
12133062 TGTTTTTGTA
** * *
12133072 CATGGCGTGTCACATGTTTCTATACATGGCGTGTCACATGTTTCTGTACATAGTGTGTAACAATC
1 CATGGCGTGTCACATGTTTCTATACATAACGTGTCACATGTTTCTGTACATGGTGTGTAACAACC
12133137 TAAC
66 TAAC
* *
12133141 CATGGCGTGTCACATGTTTCTGTACATAACGTGTCACATGTTTCTATACATGGTGTGTAACAACC
1 CATGGCGTGTCACATGTTTCTATACATAACGTGTCACATGTTTCTGTACATGGTGTGTAACAACC
12133206 TAAC
66 TAAC
* * * * * * **
12133210 CATGGCGTGTCACATGTTTTTACACATAACGTGTAATATATTTTTGTACATGACGTGTAACA
1 CATGGCGTGTCACATGTTTCTATACATAACGTGTCACATGTTTCTGTACATGGTGTGTAACA
12133272 TCATAACGTG
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 115 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (69 bp):
CATGGCGTGTCACATGTTTCTATACATAACGTGTCACATGTTTCTGTACATGGTGTGTAACAACC
TAAC
Found at i:12140536 original size:73 final size:73
Alignment explanation
Indices: 12140416--12140576 Score: 184
Period size: 73 Copynumber: 2.2 Consensus size: 73
12140406 TAACAATGCA
* *
12140416 CTTAGTCGACTAAGTTGTCTCTGTCTTCTGAACCTAATTTTTGGCAGT-GAGCTCTTAGTCAACT
1 CTTAGTCGACTAAGTTGTCTCTGTCTTCTGAACCTAATTTCTAGCAGTAG-GCTCTTAGTCAACT
12140480 AACTTCCTT
65 AACTTCCTT
* * * * *
12140489 CTTAGTCGATTAAGTTGTTTCTGTC-T-TGAAGTCTAGATTTCTAGCAGTAGGCTTTTAGTCGAC
1 CTTAGTCGACTAAGTTGTCTCTGTCTTCTGAA-CCTA-ATTTCTAGCAGTAGGCTCTTAGTCAAC
*
12140552 TAACTTTCTT
64 TAACTTCCTT
* *
12140562 CTTGGTTGACTAAGT
1 CTTAGTCGACTAAGT
12140577 CTTCTATGTC
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
71 4 0.05
72 4 0.05
73 65 0.88
74 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (73 bp):
CTTAGTCGACTAAGTTGTCTCTGTCTTCTGAACCTAATTTCTAGCAGTAGGCTCTTAGTCAACTA
ACTTCCTT
Found at i:12150409 original size:43 final size:42
Alignment explanation
Indices: 12150361--12150484 Score: 140
Period size: 43 Copynumber: 2.9 Consensus size: 42
12150351 CTGATCATCA
* * **
12150361 TCATCATCAGCTCATGCGCACTCCCTACTCACACATAGCTGGG
1 TCATCATC-GCTTATGCGCACTCCCTACTCGCACATAGCCAGG
* * *
12150404 TCATCACCGGGTTATGCGCACTCCCTACTCGCACATAACCAGG
1 TCATCATC-GCTTATGCGCACTCCCTACTCGCACATAGCCAGG
* *
12150447 TCATCCTCGACTTATGCGCACTCTCTACTCGCACATAG
1 TCATCATCG-CTTATGCGCACTCCCTACTCGCACATAG
12150485 TCGAGTCAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 1 0.01
43 66 0.99
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.24
Consensus pattern (42 bp):
TCATCATCGCTTATGCGCACTCCCTACTCGCACATAGCCAGG
Found at i:12152736 original size:30 final size:30
Alignment explanation
Indices: 12152702--12152797 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 30
12152692 GGAGTTAACA
*
12152702 AGGTTATGTCTGATCTTTGAAAAGGCAGAG
1 AGGTTATGTCTGATCCTTGAAAAGGCAGAG
* * * *
12152732 AGGTTATGTCTAATCCTTGAAAAGACAAAA
1 AGGTTATGTCTGATCCTTGAAAAGGCAGAG
12152762 AGGTTATG-CTTGATCCTTGAAAAGGCAG-G
1 AGGTTATGTC-TGATCCTTGAAAAGGCAGAG
12152791 -GGTTATG
1 AGGTTATG
12152798 CTTAATCCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 7 0.12
29 1 0.02
30 48 0.86
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.29
Consensus pattern (30 bp):
AGGTTATGTCTGATCCTTGAAAAGGCAGAG
Found at i:12152776 original size:60 final size:58
Alignment explanation
Indices: 12152701--12152812 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 58
12152691 TGGAGTTAAC
* *
12152701 AAGGTTATGTCTGATCTTTGAAAAGGCAGAGAGGTTATG-TCTAATCCTTGAAAAGACAAA
1 AAGGTTATGTCTGATCCTTGAAAAGGCAG-G-GGTTATGCT-TAATCCATGAAAAGACAAA
12152761 AAGGTTATG-CTTGATCCTTGAAAAGGCAGGGGTTATGCTTAATCCATGAAAA
1 AAGGTTATGTC-TGATCCTTGAAAAGGCAGGGGTTATGCTTAATCCATGAAAA
12152813 ATAATGATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
58 19 0.40
59 3 0.06
60 26 0.54
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (58 bp):
AAGGTTATGTCTGATCCTTGAAAAGGCAGGGGTTATGCTTAATCCATGAAAAGACAAA
Found at i:12152805 original size:28 final size:28
Alignment explanation
Indices: 12152718--12152812 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 28
12152708 TGTCTGATCT
12152718 TTGAAAAGGCAGAGAGGTTATG-TCTAATCC
1 TTGAAAAGGCAG-G-GGTTATGCT-TAATCC
* ** *
12152748 TTGAAAAGACAAAAAGGTTATGCTTGATCC
1 TTGAAAAGGC--AGGGGTTATGCTTAATCC
12152778 TTGAAAAGGCAGGGGTTATGCTTAATCC
1 TTGAAAAGGCAGGGGTTATGCTTAATCC
*
12152806 ATGAAAA
1 TTGAAAA
12152813 ATAATGATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
28 21 0.40
30 30 0.57
31 1 0.02
32 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (28 bp):
TTGAAAAGGCAGGGGTTATGCTTAATCC
Found at i:12157162 original size:100 final size:99
Alignment explanation
Indices: 12156986--12157184 Score: 353
Period size: 100 Copynumber: 2.0 Consensus size: 99
12156976 AACAAAAAAC
* *
12156986 CGGTGAGTGAACTGCATTCAAAACTTGTTTTGGGGATATAATGTATTTGTCAAACATTTGAACGG
1 CGGTGAGTGAACTGCATTCAAAACTTGTTTTGGGGATATAATGTATTTGCCAAACATTTGAACGA
*
12157051 ATTATCCAGCTTTTCATAAAAACAAGTGCCTTGG
66 ATTATCAAGCTTTTCATAAAAACAAGTGCCTTGG
*
12157085 NCGGTGAGTGAACTGCATTCAAAACTTGTTTTGGGGATATAATGTATTTGCCAAACATTTGAATG
1 -CGGTGAGTGAACTGCATTCAAAACTTGTTTTGGGGATATAATGTATTTGCCAAACATTTGAACG
12157150 AATTATCAAGCTTTTCATAAAAACAAGTGCCTTGG
65 AATTATCAAGCTTTTCATAAAAACAAGTGCCTTGG
12157185 GAACAAGCTT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 95 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (99 bp):
CGGTGAGTGAACTGCATTCAAAACTTGTTTTGGGGATATAATGTATTTGCCAAACATTTGAACGA
ATTATCAAGCTTTTCATAAAAACAAGTGCCTTGG
Found at i:12158929 original size:84 final size:84
Alignment explanation
Indices: 12158788--12158957 Score: 331
Period size: 84 Copynumber: 2.0 Consensus size: 84
12158778 GACTAACGTC
12158788 TTATCACTTTGAAGAAACATGTTTATGACATGGGTGTTTAAGAGCCTTTTGATGCACTTGGTTAA
1 TTATCACTTTGAAGAAACATGTTTATGACATGGGTGTTTAAGAGCCTTTTGATGCACTTGGTTAA
*
12158853 TGGTAGGATTTGACATTGT
66 TGGGAGGATTTGACATTGT
12158872 TTATCACTTTGAAGAAACATGTTTATGACATGGGTGTTTAAGAGCCTTTTGATGCACTTGGTTAA
1 TTATCACTTTGAAGAAACATGTTTATGACATGGGTGTTTAAGAGCCTTTTGATGCACTTGGTTAA
12158937 TGGGAGGATTTGACATTGT
66 TGGGAGGATTTGACATTGT
12158956 TT
1 TT
12158958 TATGCTTGAT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (84 bp):
TTATCACTTTGAAGAAACATGTTTATGACATGGGTGTTTAAGAGCCTTTTGATGCACTTGGTTAA
TGGGAGGATTTGACATTGT
Found at i:12166610 original size:20 final size:21
Alignment explanation
Indices: 12166579--12166618 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12166569 TACGAAACCT
*
12166579 TAAATATTTATTTTTTATTTA
1 TAAATATTTATTATTTATTTA
12166600 TAAAT-TTTATTATTTATTT
1 TAAATATTTATTATTTATTT
12166619 CTCATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TAAATATTTATTATTTATTTA
Found at i:12172855 original size:20 final size:20
Alignment explanation
Indices: 12172830--12172875 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
12172820 CTTCTAAACC
12172830 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
12172850 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
12172870 TCAAAT
1 TCAAAT
12172876 GGGGTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:12173271 original size:36 final size:32
Alignment explanation
Indices: 12173224--12173330 Score: 90
Period size: 36 Copynumber: 3.2 Consensus size: 32
12173214 GTTTAAACAT
* *
12173224 AACCTTGACAATGCCTTTCAAGGATCAAGTAC
1 AACCTTCACAATGCCTTTCAAGGATCAAGCAC
* * * *
12173256 AACCTCTCAATACAATACATTTTATGGATCAAGCAC
1 AACCT-TC---ACAATGCCTTTCAAGGATCAAGCAC
*
12173292 AACCTTCACAATGCCTTTCAAAGGCT-AAGGCAC
1 AACCTTCACAATGCCTTTC-AAGGATCAA-GCAC
12173325 AACCTT
1 AACCTT
12173331 TTCTCTTTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
32 16 0.28
33 15 0.26
35 2 0.03
36 25 0.43
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (32 bp):
AACCTTCACAATGCCTTTCAAGGATCAAGCAC
Found at i:12173945 original size:21 final size:21
Alignment explanation
Indices: 12173919--12173964 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
12173909 ACAAGTTTAA
* * *
12173919 AAAAATTATTGAAACAAGTTC
1 AAAAATCATTAAAAAAAGTTC
*
12173940 AAAAATCATTAAAAAAATTTC
1 AAAAATCATTAAAAAAAGTTC
12173961 AAAA
1 AAAA
12173965 TTCAAGCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (21 bp):
AAAAATCATTAAAAAAAGTTC
Found at i:12174045 original size:21 final size:22
Alignment explanation
Indices: 12174015--12174101 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 22
12174005 TAGGTACTTC
*
12174015 AAAACTTATTTAAAAAAGTT-TA
1 AAAAC-TATTTAAAAAAGTTCAA
* *
12174037 AAAACTATTCAAACAAGTTCAA
1 AAAACTATTTAAAAAAGTTCAA
* * *
12174059 AAAATTATTTAAACAACTTCAA
1 AAAACTATTTAAAAAAGTTCAA
* * *
12174081 AAATC-ATTCAAACAAGTTCAA
1 AAAACTATTTAAAAAAGTTCAA
12174102 GGATCACTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
21 26 0.48
22 28 0.52
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (22 bp):
AAAACTATTTAAAAAAGTTCAA
Found at i:12174083 original size:43 final size:43
Alignment explanation
Indices: 12174015--12174101 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
12174005 TAGGTACTTC
* * *
12174015 AAAACTTATTTAAAAAAGTTTAAAAA-CTATTCAAACAAGTTCA
1 AAAAATTATTTAAAAAACTTCAAAAATC-ATTCAAACAAGTTCA
*
12174058 AAAAATTATTTAAACAACTTCAAAAATCATTCAAACAAGTTCA
1 AAAAATTATTTAAAAAACTTCAAAAATCATTCAAACAAGTTCA
12174101 A
1 A
12174102 GGATCACTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (43 bp):
AAAAATTATTTAAAAAACTTCAAAAATCATTCAAACAAGTTCA
Found at i:12174107 original size:21 final size:21
Alignment explanation
Indices: 12174012--12174130 Score: 105
Period size: 21 Copynumber: 5.6 Consensus size: 21
12174002 ACTTAGGTAC
* * * *
12174012 TTCAAAACTTATTTAAAAAAG
1 TTCAAAAATCATTCAAACAAG
*
12174033 TTTAAAAA-CTATTCAAACAAG
1 TTCAAAAATC-ATTCAAACAAG
* * *
12174054 TTCAAAAAATTATTTAAACAAC
1 TTC-AAAAATCATTCAAACAAG
12174076 TTCAAAAATCATTCAAACAAG
1 TTCAAAAATCATTCAAACAAG
** *
12174097 TTCAAGGATCACTCAAACAAG
1 TTCAAAAATCATTCAAACAAG
*
12174118 TTCAAAGATCATT
1 TTCAAAAATCATT
12174131 AATTTTGATC
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
21 61 0.78
22 17 0.22
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.29
Consensus pattern (21 bp):
TTCAAAAATCATTCAAACAAG
Found at i:12184168 original size:20 final size:20
Alignment explanation
Indices: 12184143--12184182 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12184133 CTATAAATAT
12184143 CTCATTTCTCCAGCAACTTC
1 CTCATTTCTCCAGCAACTTC
* *
12184163 CTCATTTTTCCAGCAGCTTC
1 CTCATTTCTCCAGCAACTTC
12184183 TTTTTCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.38, G:0.07, T:0.38
Consensus pattern (20 bp):
CTCATTTCTCCAGCAACTTC
Found at i:12192179 original size:21 final size:21
Alignment explanation
Indices: 12192153--12192204 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12192143 ACAAGTTTAA
*
12192153 AAAAATTATTCAAA-CAAGTTC
1 AAAAATCATT-AAAGCAAGTTC
*
12192174 AAAAATCATTAAAGCAATTTC
1 AAAAATCATTAAAGCAAGTTC
*
12192195 AAAACTCATT
1 AAAAATCATT
12192205 CAGATGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAAATCATTAAAGCAAGTTC
Found at i:12192284 original size:21 final size:22
Alignment explanation
Indices: 12192249--12192312 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
12192239 TAGGTACTTC
*
12192249 AAAACTTATTTAAAAAAGTTTT
1 AAAACTTATTCAAAAAAGTTTT
**
12192271 AAAAC-TATTCAAAAAAGTTCAA
1 AAAACTTATTCAAAAAAGTT-TT
* *
12192293 AAAACTTATTTAAACAAGTT
1 AAAACTTATTCAAAAAAGTT
12192313 CAAAAATCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 13 0.37
22 10 0.29
23 12 0.34
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAACTTATTCAAAAAAGTTTT
Found at i:12192312 original size:44 final size:44
Alignment explanation
Indices: 12192249--12192335 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
12192239 TAGGTACTTC
**
12192249 AAAACTTATTTAAAAAAGTTTTAAAA-CTATTCAAAAAAGTTCAA
1 AAAACTTATTTAAAAAAGTTCAAAAATC-ATTCAAAAAAGTTCAA
* *
12192293 AAAACTTATTTAAACAAGTTCAAAAATCATTCAAACAAGTTCA
1 AAAACTTATTTAAAAAAGTTCAAAAATCATTCAAAAAAGTTCA
12192336 CAGATCACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.30
Consensus pattern (44 bp):
AAAACTTATTTAAAAAAGTTCAAAAATCATTCAAAAAAGTTCAA
Found at i:12192328 original size:21 final size:21
Alignment explanation
Indices: 12192277--12192372 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
12192267 TTTTAAAACT
* *
12192277 ATTCAAAAAAGTTCAAAAAACTT
1 ATTCAAACAAGTTC-AAAAA-TC
*
12192300 ATTTAAACAAGTTCAAAAATC
1 ATTCAAACAAGTTCAAAAATC
* *
12192321 ATTCAAACAAGTTCACAGATC
1 ATTCAAACAAGTTCAAAAATC
* *
12192342 ACTCAAACAAGTTCAAAGATC
1 ATTCAAACAAGTTCAAAAATC
*
12192363 ATTGAAACAA
1 ATTCAAACAA
12192373 TTTTGAACAC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 46 0.73
22 5 0.08
23 12 0.19
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (21 bp):
ATTCAAACAAGTTCAAAAATC
Found at i:12193821 original size:26 final size:26
Alignment explanation
Indices: 12193785--12193845 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
12193775 ACCATATACC
* *
12193785 CATCATCATCATGCACACTATCCCAT
1 CATCATCATCATACACACCATCCCAT
12193811 CATCATCATCATACACACCATCCCAT
1 CATCATCATCATACACACCATCCCAT
12193837 CATCATCAT
1 CATCATCAT
12193846 TCCCAGCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.33, C:0.39, G:0.02, T:0.26
Consensus pattern (26 bp):
CATCATCATCATACACACCATCCCAT
Found at i:12193992 original size:86 final size:86
Alignment explanation
Indices: 12193855--12194016 Score: 236
Period size: 86 Copynumber: 1.9 Consensus size: 86
12193845 TTCCCAGCTC
* * * * *
12193855 ATGCGCACTCCCTACTCGCACATGTCTAGGTCATCACCGGGTTATGTGCACTCCCTACTCGCACA
1 ATGCACACTCCCTACTCGCACATATCGAGGTCATCACCGGCTTATGCGCACTCCCTACTCGCACA
*
12193920 TAACCGGGTCATCACCAGGCT
66 TAACCGAGTCATCACCAGGCT
*
12193941 ATGCACACTCCCTACTCGCACATAATCGA-GTCATCATCGGCTTATGCGCACTCCCTACTCGCAC
1 ATGCACACTCCCTACTCGCACAT-ATCGAGGTCATCACCGGCTTATGCGCACTCCCTACTCGCAC
*
12194005 ATAGCCGAGTCA
65 ATAACCGAGTCA
12194017 ATATCATTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
86 64 0.96
87 3 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (86 bp):
ATGCACACTCCCTACTCGCACATATCGAGGTCATCACCGGCTTATGCGCACTCCCTACTCGCACA
TAACCGAGTCATCACCAGGCT
Found at i:12194014 original size:43 final size:43
Alignment explanation
Indices: 12193855--12194016 Score: 202
Period size: 43 Copynumber: 3.8 Consensus size: 43
12193845 TTCCCAGCTC
** * *
12193855 ATGCGCACTCCCTACTCGCACAT-GTCTAGGTCATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGA-GTCATCACCGGCTT
* *
12193898 ATGTGCACTCCCTACTCGCACATAACCGGGTCATCACCAGGC-T
1 ATGCGCACTCCCTACTCGCACATAACCGAGTCATCACC-GGCTT
* * *
12193941 ATGCACACTCCCTACTCGCACATAATCGAGTCATCATCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGAGTCATCACCGGCTT
*
12193984 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGAGTCA
12194017 ATATCATTAC
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
42 3 0.03
43 96 0.94
44 3 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGAGTCATCACCGGCTT
Found at i:12197172 original size:21 final size:21
Alignment explanation
Indices: 12197146--12197198 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
12197136 GATAGAAAGT
*
12197146 TTCTCGCTGCAGCGAACTTTA
1 TTCTCGCTGCAGCGAACTTCA
12197167 TTCTCGCTGCAGCGAACTTCA
1 TTCTCGCTGCAGCGAACTTCA
*
12197188 TTCTCACTGCA
1 TTCTCGCTGCA
12197199 ATGAGAACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.32
Consensus pattern (21 bp):
TTCTCGCTGCAGCGAACTTCA
Found at i:12197447 original size:26 final size:26
Alignment explanation
Indices: 12197418--12197478 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
12197408 ACCATATACC
*
12197418 CATCATCATCATGCACACCATCCCAT
1 CATCATCATCATACACACCATCCCAT
12197444 CATCATCATCATACACACCATCCCAT
1 CATCATCATCATACACACCATCCCAT
12197470 CATCATCAT
1 CATCATCAT
12197479 TCCTAGCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.33, C:0.41, G:0.02, T:0.25
Consensus pattern (26 bp):
CATCATCATCATACACACCATCCCAT
Found at i:12197546 original size:43 final size:42
Alignment explanation
Indices: 12197488--12197640 Score: 180
Period size: 43 Copynumber: 3.6 Consensus size: 42
12197478 TTCCTAGCTC
* * * * *
12197488 ATGCGCACTTCCTACTCGCACATGGCTAGTTCATCACCGAGTT
1 ATGCACACTCCCTACTCGCACAT-ACTGGGTCATCACCGAGTT
* * *
12197531 ATGCACATTCCCTACTCGCACATAATCGGGTCATCACCGGGTT
1 ATGCACACTCCCTACTCGCACATACT-GGGTCATCACCGAGTT
* * *
12197574 ATGCGCACTCCCTACTCGCACATAACTGGGTCATCATCGACTT
1 ATGCACACTCCCTACTCGCACAT-ACTGGGTCATCACCGAGTT
12197617 ATGCACACTCCCTACTCGCACATA
1 ATGCACACTCCCTACTCGCACATA
12197641 GCCGAGTCAA
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
42 2 0.02
43 89 0.96
44 2 0.02
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.25
Consensus pattern (42 bp):
ATGCACACTCCCTACTCGCACATACTGGGTCATCACCGAGTT
Found at i:12201868 original size:19 final size:19
Alignment explanation
Indices: 12201845--12201894 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
12201835 TGAAAGAAAA
12201845 AGAAAGAGAAGAAGCTGCG
1 AGAAAGAGAAGAAGCTGCG
* *
12201864 GGAAA-ATGAAGAAGCTGCT
1 AGAAAGA-GAAGAAGCTGCG
12201883 AGAAAGAGAAGA
1 AGAAAGAGAAGA
12201895 TATTTATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.50, C:0.08, G:0.34, T:0.08
Consensus pattern (19 bp):
AGAAAGAGAAGAAGCTGCG
Found at i:12212965 original size:55 final size:55
Alignment explanation
Indices: 12212888--12213103 Score: 306
Period size: 55 Copynumber: 3.9 Consensus size: 55
12212878 TGATGATGGG
*
12212888 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATAAGCTGATGACCGGTGGGTGA
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGGTGA
* * *
12212943 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTAATGACTGATGGGTGA
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGGTGA
* * ** ****
12212998 TGATTCTAGCTATGTGCGGTGTGGGAGTGCATATGAGCTGATGATTGGAAAATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGGTGA
* *
12213053 TGATTCCAGTTATGTGCAGTGTGGGAGTGCACATGAGCTGATGACCGGTGG
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGG
12213104 TTGTATACAT
Statistics
Matches: 139, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 139 1.00
ACGTcount: A:0.22, C:0.14, G:0.37, T:0.28
Consensus pattern (55 bp):
TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGGTGA
Found at i:12212981 original size:28 final size:28
Alignment explanation
Indices: 12212895--12212982 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
12212885 GGGTGATTCC
12212895 AGCTATGTGCGGTGTGGGAGTGCACATA
1 AGCTATGTGCGGTGTGGGAGTGCACATA
** * *
12212923 AGCTGATGACCGGTG-GGTGA-TG-A-TTCC
1 AGCT-ATGTGCGGTGTGG-GAGTGCACAT-A
*
12212950 AGCTATGTGCGGTGTGGGAGTGCACATG
1 AGCTATGTGCGGTGTGGGAGTGCACATA
12212978 AGCTA
1 AGCTA
12212983 ATGACTGATG
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
26 11 0.24
27 9 0.20
28 14 0.31
29 11 0.24
ACGTcount: A:0.20, C:0.16, G:0.39, T:0.25
Consensus pattern (28 bp):
AGCTATGTGCGGTGTGGGAGTGCACATA
Found at i:12213037 original size:110 final size:107
Alignment explanation
Indices: 12212850--12213097 Score: 322
Period size: 110 Copynumber: 2.3 Consensus size: 107
12212840 ATAACTGCGC
* *
12212850 ATGTGCGGTGTAGGAGTGCACAT--GCTAGTGA-TGATGGGTGATTCCAGCTATGTGCGGTGTGG
1 ATGTGCGGTGTGGGAGTGCACATGAGCTAATGACTGATGGGTGATTCCAGCTATGTGCGGTGTGG
****
12212912 GAGTGCACATAAGCTGATGACCGGTGGGTGATGATTCCAGCT
66 GAGTGCACATAAGCTGATGACCGGAAAATGATGATTCCAGCT
*
12212954 ATGTGCGGTGTGGGAGTGCACATGAGCTAATGACTGATGGGTGATGATTCTAGCTATGTGCGGTG
1 ATGTGCGGTGTGGGAGTGCACATGAGCTAATGACTGAT-GG-G-TGATTCCAGCTATGTGCGGTG
* * ** *
12213019 TGGGAGTGCATATGAGCTGATGATTGGAAAATGATGATTCCAGTT
63 TGGGAGTGCACATAAGCTGATGACCGGAAAATGATGATTCCAGCT
* *
12213064 ATGTGCAGTGTGGGAGTGCACATGAGCTGATGAC
1 ATGTGCGGTGTGGGAGTGCACATGAGCTAATGAC
12213098 CGGTGGTTGT
Statistics
Matches: 124, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
104 22 0.18
106 7 0.06
107 4 0.03
108 2 0.02
109 1 0.01
110 88 0.71
ACGTcount: A:0.22, C:0.13, G:0.37, T:0.28
Consensus pattern (107 bp):
ATGTGCGGTGTGGGAGTGCACATGAGCTAATGACTGATGGGTGATTCCAGCTATGTGCGGTGTGG
GAGTGCACATAAGCTGATGACCGGAAAATGATGATTCCAGCT
Found at i:12218913 original size:32 final size:32
Alignment explanation
Indices: 12218854--12218926 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
12218844 ATTTGCTAAC
* * *
12218854 GTGGCAATGCCACGTGGTATAGACATGATGAT
1 GTGGCAATGCCACGTGGCATAGACATGATAAG
* *
12218886 GTGGCAATGCCATGTGGCATTTG-CATGATAAG
1 GTGGCAATGCCACGTGGCA-TAGACATGATAAG
12218918 GTGGCAATG
1 GTGGCAATG
12218927 TTGCTATGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (32 bp):
GTGGCAATGCCACGTGGCATAGACATGATAAG
Found at i:12226345 original size:14 final size:15
Alignment explanation
Indices: 12226305--12226347 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
12226295 AAAAAATTTC
12226305 AATATTTAAATAATAA
1 AATATTTAAA-AATAA
*
12226321 AATAATTAAAAAT-A
1 AATATTTAAAAATAA
*
12226335 TATATTTAAAAAT
1 AATATTTAAAAAT
12226348 TATTTGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 3 0.12
16 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATTTAAAAATAA
Found at i:12226892 original size:2 final size:2
Alignment explanation
Indices: 12226876--12226925 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
12226866 ACTCCCTAAT
* * * *
12226876 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TG TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12226918 TA TGA TA T
1 TA T-A TA T
12226926 TGTTATATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:12228678 original size:181 final size:181
Alignment explanation
Indices: 12228374--12228734 Score: 584
Period size: 181 Copynumber: 2.0 Consensus size: 181
12228364 AATTGTTTGA
*
12228374 ACAAACATAACACTTGAAAAATCATAATTATTTAAAGGACTTTCTTCCTTTCATTCTTCCATCAT
1 ACAAACATAACACTTGAAAAATCATAATTATTTAAAGAACTTTCTTCCTTTCATTCTTCCATCAT
12228439 TATTGTTGAAAATGTCCAACAATCCTCTATCATTTTTAAAGTAATCTAAATTTTTTATAATTTAG
66 TATTGTTGAAAATGTCCAACAATCCTCTATCATTTTTAAAGTAATCTAAATTTTTTATAATTTAG
* *
12228504 -AATTCGATTGCATAAATGAAAGTGTCTTT-CAATTGAACTTTCACTTAGTGG
131 AAATT-GATTGCATAAATGAAAGTAT-TTTCCAATTGAAATTTCACTTAGTGG
* * * * * *
12228555 ACAAACATAACTCTTGAATAATCATAATTGTTTAACGAACTTTCTTCCTTTCATTCTTCTATTAT
1 ACAAACATAACACTTGAAAAATCATAATTATTTAAAGAACTTTCTTCCTTTCATTCTTCCATCAT
*
12228620 TATTGTTGAAAATGTCCAACAATCC-CTCATCATTTTTAAAGTAATCTAGATTTTTTATAATTTA
66 TATTGTTGAAAATGTCCAACAATCCTCT-ATCATTTTTAAAGTAATCTAAATTTTTTATAATTTA
12228684 GAAATTGATTGCATAAATGAAAGTATTTTCCAATTGAAATTTCACTTAGTG
130 GAAATTGATTGCATAAATGAAAGTATTTTCCAATTGAAATTTCACTTAGTG
12228735 AAAATATGTA
Statistics
Matches: 167, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
180 5 0.03
181 158 0.95
182 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (181 bp):
ACAAACATAACACTTGAAAAATCATAATTATTTAAAGAACTTTCTTCCTTTCATTCTTCCATCAT
TATTGTTGAAAATGTCCAACAATCCTCTATCATTTTTAAAGTAATCTAAATTTTTTATAATTTAG
AAATTGATTGCATAAATGAAAGTATTTTCCAATTGAAATTTCACTTAGTGG
Found at i:12230502 original size:26 final size:27
Alignment explanation
Indices: 12230456--12230515 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
12230446 AAATAATAAC
*
12230456 AATAAAAACAACAAAATAAAGTAAGTA
1 AATAAAAACAACAAAATAAAGTAAATA
*
12230483 AATAAAAA-AA-AACATAAAAGTAAATA
1 AATAAAAACAACAAAAT-AAAGTAAATA
12230509 AATAAAA
1 AATAAAA
12230516 GTTCCCCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 4 0.13
26 18 0.60
27 8 0.27
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (27 bp):
AATAAAAACAACAAAATAAAGTAAATA
Found at i:12233304 original size:26 final size:26
Alignment explanation
Indices: 12233243--12233304 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
12233233 ACCATATACC
*
12233243 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
* *
12233269 CATCAGCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
12233295 CATCATCATC
1 CATCATCATC
12233305 TCATATGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.40, G:0.05, T:0.23
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:12233617 original size:42 final size:42
Alignment explanation
Indices: 12233495--12233617 Score: 174
Period size: 42 Copynumber: 2.9 Consensus size: 42
12233485 ACGGAGGCAA
* * **
12233495 CAACGGCTTATGTGCACTCCCACTCACACATAGCTAGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
12233537 CAACGGCTTATGTGCACTCTTACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
12233579 CAATGGTTTATGTGCACTCCTACTCGCACATAGCCGGGT
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
12233618 TCAAATCAAC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:12246104 original size:53 final size:53
Alignment explanation
Indices: 12246021--12246167 Score: 161
Period size: 53 Copynumber: 2.8 Consensus size: 53
12246011 AAAAACCTAT
* ** * *
12246021 TGTAAGGGTTATTGCTTGATCTCGCGAAAAAGAAAAAATCCATTTATGGGTTG
1 TGTAAGGGTTATTGCTTGATCCCGTTAAAAAGAAAGAATCCATTTATGGATTG
* * * * *
12246074 TGTAAAGGTTATTGCGTGATCCCGTTAAAAAGTAAGAATCCCTTTGTGGATTG
1 TGTAAGGGTTATTGCTTGATCCCGTTAAAAAGAAAGAATCCATTTATGGATTG
** *
12246127 TGTGTGGGTTATTGCTTTG-TCCCGTTAAAAAGCAAGAATCC
1 TGTAAGGGTTATTGC-TTGATCCCGTTAAAAAGAAAGAATCC
12246168 TTGATAGTGG
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 76 0.97
54 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (53 bp):
TGTAAGGGTTATTGCTTGATCCCGTTAAAAAGAAAGAATCCATTTATGGATTG
Found at i:12253572 original size:19 final size:20
Alignment explanation
Indices: 12253548--12253585 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12253538 CTATAAATAC
12253548 CTTGAA-TTTCCAGCAGCTT
1 CTTGAATTTTCCAGCAGCTT
12253567 CTTGAATTTTCCAGCAGCT
1 CTTGAATTTTCCAGCAGCT
12253586 GGTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (20 bp):
CTTGAATTTTCCAGCAGCTT
Found at i:12259226 original size:42 final size:42
Alignment explanation
Indices: 12259166--12259275 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
12259156 TGTGGATCCG
* * * *
12259166 GCTATGTGTGAGTAGGAGTGTACATAAGCCGGTAATGACCCA
1 GCTATGTGCGAGTGGGAGTGCACATAAGCCGATAATGACCCA
* *
12259208 GCTATGTGGGAGTGGGAGTGCACATAAGCCTATAATGACCCA
1 GCTATGTGCGAGTGGGAGTGCACATAAGCCGATAATGACCCA
* *
12259250 GCCATGTGCTAGTGGGGAGTGCACAT
1 GCTATGTGCGAGT-GGGAGTGCACAT
12259276 GAGCTGATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 47 0.80
43 12 0.20
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (42 bp):
GCTATGTGCGAGTGGGAGTGCACATAAGCCGATAATGACCCA
Found at i:12259826 original size:19 final size:19
Alignment explanation
Indices: 12259790--12259826 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12259780 AGGTTTGGTG
*
12259790 AGAAACCCTTGGCCAGTTA
1 AGAAACCCTCGGCCAGTTA
*
12259809 AGAAACCCTCGGCTAGTT
1 AGAAACCCTCGGCCAGTT
12259827 GATAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (19 bp):
AGAAACCCTCGGCCAGTTA
Done.