Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 160 of 235
Found at i:53925199 original size:19 final size:19
Alignment explanation
Indices: 53925175--53925213 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53925165 AAATATTTTC
53925175 AGTAAATTATTTTTCAGAA
1 AGTAAATTATTTTTCAGAA
*
53925194 AGTAAATTATTTTTTAGAA
1 AGTAAATTATTTTTCAGAA
53925213 A
1 A
53925214 TTATTTTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (19 bp):
AGTAAATTATTTTTCAGAA
Found at i:53949275 original size:50 final size:54
Alignment explanation
Indices: 53949139--53949488 Score: 364
Period size: 56 Copynumber: 6.6 Consensus size: 54
53949129 ATTTGGGTAA
* ** *
53949139 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATCACACTGGCATCC-TGAGATCA-G
* * * *
53949195 AGAGGTCTCATGTAAGACCATGTTTAGGACATCACACTGGTA-CC-GAGA-C-G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATCACACTGGCATCCTGAGATCAG
** *
53949245 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATCACACTGGCATCC-TGAGATCA-G
* * * *
53949301 AGAGGTCTCATGTAAGACCATGTTTAGGACATCACACTGGTA-CC-GAGA-C-G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATCACACTGGCATCCTGAGATCAG
** *
53949351 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATCACACTGGCATCC-TGAGATCA-G
* * * *
53949407 AGAGGTCTCATGTAAGACCATGTTTAGGACATCACACTGGTA-CC-GAGA-C-G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATCACACTGGCATCCTGAGATCAG
53949457 AGAGGTCCCATGTAAGACCATGTCTGGGACAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACAT
53949489 GGCTTTAGCA
Statistics
Matches: 243, Mismatches: 39, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
50 102 0.42
51 4 0.02
52 3 0.01
53 20 0.08
54 2 0.01
55 6 0.02
56 106 0.44
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (54 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATCACACTGGCATCCTGAGATCAG
Found at i:53949329 original size:106 final size:106
Alignment explanation
Indices: 53949139--53949491 Score: 697
Period size: 106 Copynumber: 3.3 Consensus size: 106
53949129 ATTTGGGTAA
*
53949139 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCTC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCTC
53949204 ATGTAAGACCATGTTTAGGACATCACACTGGTACCGAGACG
66 ATGTAAGACCATGTTTAGGACATCACACTGGTACCGAGACG
53949245 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCTC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCTC
53949310 ATGTAAGACCATGTTTAGGACATCACACTGGTACCGAGACG
66 ATGTAAGACCATGTTTAGGACATCACACTGGTACCGAGACG
53949351 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCTC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCTC
53949416 ATGTAAGACCATGTTTAGGACATCACACTGGTACCGAGACG
66 ATGTAAGACCATGTTTAGGACATCACACTGGTACCGAGACG
53949457 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
53949492 TTTAGCATGT
Statistics
Matches: 246, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 246 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.23
Consensus pattern (106 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCTC
ATGTAAGACCATGTTTAGGACATCACACTGGTACCGAGACG
Found at i:53949828 original size:15 final size:15
Alignment explanation
Indices: 53949808--53949838 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53949798 TATTTACTTG
53949808 TAAACTTACTAAGCA
1 TAAACTTACTAAGCA
53949823 TAAACTTACTAAGCA
1 TAAACTTACTAAGCA
53949838 T
1 T
53949839 TTTTCTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.29
Consensus pattern (15 bp):
TAAACTTACTAAGCA
Found at i:53953366 original size:50 final size:50
Alignment explanation
Indices: 53953256--53953545 Score: 314
Period size: 50 Copynumber: 5.7 Consensus size: 50
53953246 ATTTGGGTAA
* *
53953256 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
53953312 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
53953362 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
53953412 AGAGGTCCCCCGTTAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
53953462 AGAACTCCCATGTAAGGCCATATCTGGGATATGGAATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* **
53953511 AAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
53953546 TTTAGCATGT
Statistics
Matches: 200, Mismatches: 33, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
48 1 0.00
49 32 0.16
50 123 0.62
53 3 0.01
55 2 0.01
56 39 0.19
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:53953882 original size:15 final size:15
Alignment explanation
Indices: 53953862--53953892 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53953852 TATTTACTTG
*
53953862 TAAACTTACTGAGCA
1 TAAACTTACTAAGCA
53953877 TAAACTTACTAAGCA
1 TAAACTTACTAAGCA
53953892 T
1 T
53953893 TTTGCTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (15 bp):
TAAACTTACTAAGCA
Found at i:53960299 original size:28 final size:28
Alignment explanation
Indices: 53960259--53960314 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
53960249 CTTTAAGAGC
53960259 TAGGAAAACTGGCATTGCATATGTTGGT
1 TAGGAAAACTGGCATTGCATATGTTGGT
53960287 TAGGAAAACTGGCATTGCATATGTTGGT
1 TAGGAAAACTGGCATTGCATATGTTGGT
53960315 ATAGACTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (28 bp):
TAGGAAAACTGGCATTGCATATGTTGGT
Found at i:53970783 original size:17 final size:17
Alignment explanation
Indices: 53970761--53970793 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53970751 AAACAACATA
53970761 ACTCTTGACCTTTCATG
1 ACTCTTGACCTTTCATG
53970778 ACTCTTGACCTTTCAT
1 ACTCTTGACCTTTCAT
53970794 ATAACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCTTGACCTTTCATG
Found at i:53975507 original size:17 final size:17
Alignment explanation
Indices: 53975485--53975517 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53975475 AAACAACATA
53975485 ACTCTTGACATTTCATG
1 ACTCTTGACATTTCATG
*
53975502 ACTCTTGACCTTTCAT
1 ACTCTTGACATTTCAT
53975518 ATAACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.27, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCTTGACATTTCATG
Found at i:53983853 original size:17 final size:17
Alignment explanation
Indices: 53983831--53983868 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
53983821 AGTTATGTTA
53983831 TATGAAAGGTCAAGAGT
1 TATGAAAGGTCAAGAGT
53983848 TATGAAAGGTCAAGAGT
1 TATGAAAGGTCAAGAGT
53983865 TATG
1 TATG
53983869 TTGTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.26
Consensus pattern (17 bp):
TATGAAAGGTCAAGAGT
Found at i:53986160 original size:51 final size:51
Alignment explanation
Indices: 53986100--53986214 Score: 212
Period size: 51 Copynumber: 2.3 Consensus size: 51
53986090 TCCTCTCTAA
53986100 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
53986151 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
53986202 TCCCCTCAATTTC
1 TCCTCTCAATTTC
53986215 ATTTTTAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (51 bp):
TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
Found at i:53991191 original size:123 final size:123
Alignment explanation
Indices: 53990972--53991196 Score: 396
Period size: 123 Copynumber: 1.8 Consensus size: 123
53990962 CCCAAACTTG
**
53990972 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAGTATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAACATCCTGG
** *
53991037 TAGAAGCGATTTTATACTATTTGGTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGACCAGAAACATCAAAAAAATTATTTCTTACATGAC
*
53991095 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAACATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAACATCCTGG
53991160 TAGAAGCGATTTTATACTATTTGACCAGAAACATCAA
66 TAGAAGCGATTTTATACTATTTGACCAGAAACATCAA
53991197 CTCGAAATAA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 96 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (123 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAACATCCTGG
TAGAAGCGATTTTATACTATTTGACCAGAAACATCAAAAAAATTATTTCTTACATGAC
Found at i:53992880 original size:123 final size:123
Alignment explanation
Indices: 53992661--53992885 Score: 405
Period size: 123 Copynumber: 1.8 Consensus size: 123
53992651 CCCAAACTTG
**
53992661 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAGTATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAACATCCTGG
**
53992726 TAGAAGCGATTTTATACTATTTGGTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGACCAGAAACGTCAAAAAAATTATTTCTTACATGAC
*
53992784 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAACATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAACATCCTGG
53992849 TAGAAGCGATTTTATACTATTTGACCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGACCAGAAACGTCAA
53992886 CTCGAAATAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 97 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (123 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAACATCCTGG
TAGAAGCGATTTTATACTATTTGACCAGAAACGTCAAAAAAATTATTTCTTACATGAC
Found at i:54009494 original size:27 final size:26
Alignment explanation
Indices: 54009463--54009640 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
54009453 TAAATTGTAC
54009463 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
54009490 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
54009516 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
54009544 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
54009572 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
54009599 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
54009626 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54009641 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 25 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:54009579 original size:82 final size:81
Alignment explanation
Indices: 54009464--54009619 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
54009454 AAATTGTACA
* *
54009464 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
54009528 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
54009545 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
54009610 TGCGAGTTGA
65 TGCGAATTGA
54009620 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54009631 original size:82 final size:81
Alignment explanation
Indices: 54009460--54009640 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
54009450 GATTAAATTG
* *
54009460 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
54009525 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
54009541 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
54009605 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54009623 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54009641 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:54009651 original size:27 final size:27
Alignment explanation
Indices: 54009545--54009651 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
54009535 TGACCATGCG
* * * *
54009545 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
54009573 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
54009600 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
54009627 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
54009652 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:54011088 original size:24 final size:24
Alignment explanation
Indices: 54011061--54011106 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54011051 TTAAAAGGGG
*
54011061 TAAGGCATTTTGCATCAATTTTAA
1 TAAGGCATTTCGCATCAATTTTAA
* *
54011085 TAAGGTATTTCGCATGAATTTT
1 TAAGGCATTTCGCATCAATTTT
54011107 TAAAGTATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (24 bp):
TAAGGCATTTCGCATCAATTTTAA
Found at i:54011356 original size:31 final size:31
Alignment explanation
Indices: 54011320--54011411 Score: 184
Period size: 31 Copynumber: 3.0 Consensus size: 31
54011310 TGTATGAAGG
54011320 TTTAAGTCTTTAGAATTGACTTAGTAACTTT
1 TTTAAGTCTTTAGAATTGACTTAGTAACTTT
54011351 TTTAAGTCTTTAGAATTGACTTAGTAACTTT
1 TTTAAGTCTTTAGAATTGACTTAGTAACTTT
54011382 TTTAAGTCTTTAGAATTGACTTAGTAACTT
1 TTTAAGTCTTTAGAATTGACTTAGTAACTT
54011412 CTTTCGATTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (31 bp):
TTTAAGTCTTTAGAATTGACTTAGTAACTTT
Found at i:54014694 original size:38 final size:39
Alignment explanation
Indices: 54014648--54014747 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 39
54014638 GAAATCTTTG
* * * *
54014648 TTATAATTATTGAAATTATAATTTATGATT-GAATATTA
1 TTATAATTATTGTAATTATAATTTATCATTCAAACATTA
* *
54014686 TTATAATTATTGTAATTGTAATTTTTCATTCAAACATTA
1 TTATAATTATTGTAATTATAATTTATCATTCAAACATTA
* *
54014725 TTATAAATATGGTAATTATAATT
1 TTATAATTATTGTAATTATAATT
54014748 ATTACATTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
38 26 0.50
39 26 0.50
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (39 bp):
TTATAATTATTGTAATTATAATTTATCATTCAAACATTA
Found at i:54021425 original size:25 final size:24
Alignment explanation
Indices: 54021397--54021474 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 24
54021387 TGTACCTGAA
* *
54021397 TATCAGGCTTTATGTTGGTGCTATT
1 TATCGGGCTTTATGATGGTG-TATT
** *
54021422 TATCGGGCTTTATGCCGGTGTTATC
1 TATCGGGCTTTATGATGGTG-TATT
*
54021447 TATCGGGCTTTGTGATGGTGTATT
1 TATCGGGCTTTATGATGGTGTATT
54021471 TATC
1 TATC
54021475 TAGCTTTGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 7 0.16
25 37 0.84
ACGTcount: A:0.14, C:0.14, G:0.27, T:0.45
Consensus pattern (24 bp):
TATCGGGCTTTATGATGGTGTATT
Found at i:54021497 original size:40 final size:40
Alignment explanation
Indices: 54021453--54021529 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
54021443 TATCTATCGG
*
54021453 GCTTTGTGAT-GGTGTATTTATCTAGCTTTGTGCCTAGCAA
1 GCTTTGTG-TCGGTGTATTTATCGAGCTTTGTGCCTAGCAA
*
54021493 GCTTTGTGTCGGTGTGTTTATCGAGCTTTGTGCCTAG
1 GCTTTGTGTCGGTGTATTTATCGAGCTTTGTGCCTAG
54021530 AAGGCCTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.43
Consensus pattern (40 bp):
GCTTTGTGTCGGTGTATTTATCGAGCTTTGTGCCTAGCAA
Found at i:54021540 original size:40 final size:40
Alignment explanation
Indices: 54021463--54021540 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
54021453 GCTTTGTGAT
* *
54021463 GGTGTATTTATCTAGCTTTGTGCCTAGCAAGCTTTGTGTC
1 GGTGTATTTATCGAGCTTTGTGCCTAGCAAGCCTTGTGTC
*
54021503 GGTGTGTTTATCGAGCTTTGTGCCTAG-AAGGCCTTGTG
1 GGTGTATTTATCGAGCTTTGTGCCTAGCAA-GCCTTGTG
54021541 CTAGGTTGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.14, C:0.17, G:0.29, T:0.40
Consensus pattern (40 bp):
GGTGTATTTATCGAGCTTTGTGCCTAGCAAGCCTTGTGTC
Found at i:54021771 original size:110 final size:111
Alignment explanation
Indices: 54021576--54021895 Score: 387
Period size: 110 Copynumber: 2.9 Consensus size: 111
54021566 CGGTGATCAT
* *
54021576 TTAGTACGTGCTATGTACC-ATTGATACAGACAC-TAACGATGGCTTGAGATCCTGCATATGTTG
1 TTAGTAGGTACTATGTACCGA-TGATACAGAC-CGTAACGATGGCTTGAGATCCTGCATATGTTG
* * * * * *
54021639 CAGATTCTTTATAGCTTATGTGAGCAGCATCGTGAGCCG-GGGGTTAA
64 CGGATTCTCTATAGCTTGTGTGAGCAGCATCATGAGCAGAGGGATTAA
* * *
54021686 TTAGTAGGTACTATGTACCGATGATACAGGCCGTAACGTTGGCTTGAGATCCTGCATATGTTGTG
1 TTAGTAGGTACTATGTACCGATGATACAGACCGTAACGATGGCTTGAGATCCTGCATATGTTGCG
* ** * *
54021751 GCTTCTCTGCAACTTGTGTGAGCAGTATCATGAG-AGAGGGATTAA
66 GATTCTCTATAGCTTGTGTGAGCAGCATCATGAGCAGAGGGATTAA
* * * * * *
54021796 TTAGTAGGTACTATGTACTGGTGATACAGACCGTAACAATGGCTTGAGATCCTACATGTATTGCG
1 TTAGTAGGTACTATGTACCGATGATACAGACCGTAACGATGGCTTGAGATCCTGCATATGTTGCG
*
54021861 GATTCTCTATAGCTTGTGTGAGTAGCATCATGAGC
66 GATTCTCTATAGCTTGTGTGAGCAGCATCATGAGC
54021896 TGGTCAAAGT
Statistics
Matches: 175, Mismatches: 31, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
109 2 0.01
110 172 0.98
111 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (111 bp):
TTAGTAGGTACTATGTACCGATGATACAGACCGTAACGATGGCTTGAGATCCTGCATATGTTGCG
GATTCTCTATAGCTTGTGTGAGCAGCATCATGAGCAGAGGGATTAA
Found at i:54024761 original size:17 final size:18
Alignment explanation
Indices: 54024716--54024761 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
54024706 TTAAGAATCT
*
54024716 TGGGCCCACATGCCCGTA
1 TGGGCCCACACGCCCGTA
* *
54024734 TGGGCCTACACGCCCGTG
1 TGGGCCCACACGCCCGTA
54024752 T-GGCCCACAC
1 TGGGCCCACAC
54024762 ACCAAGATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.15, C:0.41, G:0.28, T:0.15
Consensus pattern (18 bp):
TGGGCCCACACGCCCGTA
Found at i:54027897 original size:22 final size:22
Alignment explanation
Indices: 54027872--54027919 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
54027862 AAAATTAGGG
*
54027872 TAAAATATACGCTTACGAG-CCT
1 TAAAATAGA-GCTTACGAGACCT
*
54027894 T-AAATCGAGCTTACGAGACCT
1 TAAAATAGAGCTTACGAGACCT
54027915 TAAAA
1 TAAAA
54027920 ATAGTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.41
21 9 0.41
22 4 0.18
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (22 bp):
TAAAATAGAGCTTACGAGACCT
Found at i:54030977 original size:26 final size:25
Alignment explanation
Indices: 54030932--54031004 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 25
54030922 TTATCACCCT
*
54030932 AATTTTATCCAAGTAAAATTTTGAC
1 AATTTTACCCAAGTAAAATTTTGAC
*
54030957 AATTTTACCCACGTTAAAATTTTGAC
1 AATTTTACCCAAG-TAAAATTTTGAC
* *
54030983 GATTTTACCCTCAGTAAAATTT
1 AATTTTACCC-AAGTAAAATTT
54031005 CGAGAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.27
26 29 0.71
27 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (25 bp):
AATTTTACCCAAGTAAAATTTTGAC
Found at i:54033071 original size:38 final size:40
Alignment explanation
Indices: 54032996--54033083 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 40
54032986 ATAAAAGTAT
*
54032996 ATTTT-TTT-ATAATTTTTATAATTTTTAATAATGTTAAA
1 ATTTTATTTAATAATTTTTATAATTTTAAATAATGTTAAA
54033034 ATTTTATTTAATAATTTTT-TAAATTTTAAAT-AT-TTAAA
1 ATTTTATTTAATAATTTTTAT-AATTTTAAATAATGTTAAA
**
54033072 AGATTATTTAAT
1 ATTTTATTTAAT
54033084 TATTGACGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 20 0.45
39 6 0.14
40 18 0.41
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (40 bp):
ATTTTATTTAATAATTTTTATAATTTTAAATAATGTTAAA
Found at i:54033183 original size:13 final size:13
Alignment explanation
Indices: 54033165--54033190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54033155 ATAATTTGAT
54033165 AAAAATATAAATA
1 AAAAATATAAATA
54033178 AAAAATATAAATA
1 AAAAATATAAATA
54033191 TAAATAAAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATATAAATA
Found at i:54036387 original size:30 final size:29
Alignment explanation
Indices: 54036339--54036395 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
54036329 TATTTTCATC
54036339 CACACGGTCAGAGACACGGACGTGTGTGA
1 CACACGGTCAGAGACACGGACGTGTGTGA
* *
54036368 CACACGGTCAGGTGACACGGCCGTGTGT
1 CACACGGTCA-GAGACACGGACGTGTGT
54036396 CCCCTGTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.23, C:0.26, G:0.35, T:0.16
Consensus pattern (29 bp):
CACACGGTCAGAGACACGGACGTGTGTGA
Found at i:54037412 original size:2 final size:2
Alignment explanation
Indices: 54037405--54037430 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54037395 GTTTGTTTTA
54037405 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
54037431 TACCTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54037905 original size:17 final size:17
Alignment explanation
Indices: 54037867--54037909 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
54037857 GATATAATAC
* * *
54037867 ATATATTTATTTTTTAA
1 ATATTTTTAATTTTAAA
54037884 A-ATTTTTAATTTTAAA
1 ATATTTTTAATTTTAAA
54037900 ATATTTTTAA
1 ATATTTTTAA
54037910 AATACTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTTTAATTTTAAA
Found at i:54037941 original size:32 final size:32
Alignment explanation
Indices: 54037902--54037977 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
54037892 ATTTTAAAAT
* * *
54037902 ATTTTTAAAATACTTTTT-TATTATTATTTTTTA
1 ATTTTTAAAATA-TTTTTAAAATACT-TTTTTTA
54037935 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATATTTTTAAAATACTTTTTTTA
54037966 ATTTTTAAAATA
1 ATTTTTAAAATA
54037978 AATTTTTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 13 0.34
32 24 0.63
33 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (32 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:54037983 original size:21 final size:21
Alignment explanation
Indices: 54037945--54037984 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54037935 ATTTTAAAAT
**
54037945 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
54037966 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
54037985 GGTATTTATT
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:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:54037991 original size:22 final size:20
Alignment explanation
Indices: 54037944--54037998 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
54037934 AATTTTAAAA
* *
54037944 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
54037964 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
54037987 TATTTATTAAAA
1 TATTT-TTAAAA
54037999 AATGGGCCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:54038400 original size:22 final size:22
Alignment explanation
Indices: 54038352--54038402 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
54038342 TTTCGTAATT
* *
54038352 TTATTG-TT-AATATTTTATTA
1 TTATTGTTTAAATATTGTATAA
54038372 TTATTGTTTAAATATTGTATAA
1 TTATTGTTTAAATATTGTATAA
*
54038394 TTCTTGTTT
1 TTATTGTTT
54038403 TATTGTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.23
21 2 0.08
22 18 0.69
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (22 bp):
TTATTGTTTAAATATTGTATAA
Found at i:54038408 original size:19 final size:17
Alignment explanation
Indices: 54038384--54038418 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
54038374 ATTGTTTAAA
54038384 TATTGTATAATTCTTGTTT
1 TATTGT-TAATT-TTGTTT
54038403 TATTGTTAATTTTGTT
1 TATTGTTAATTTTGTT
54038419 ACCATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTGTTT
Found at i:54047798 original size:36 final size:39
Alignment explanation
Indices: 54047758--54047829 Score: 105
Period size: 36 Copynumber: 1.9 Consensus size: 39
54047748 ATGATTAAAC
*
54047758 AATTCAATAAAATAAATA-T-TACA-AAATGTGAAATTT
1 AATTCAATAAAATAAATAGTAGACATAAATGTGAAATTT
*
54047794 AATTCAATAATATAAATAGTAGACATAAATGTGAAA
1 AATTCAATAAAATAAATAGTAGACATAAATGTGAAA
54047830 AAAAAGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 17 0.55
37 1 0.03
38 3 0.10
39 10 0.32
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (39 bp):
AATTCAATAAAATAAATAGTAGACATAAATGTGAAATTT
Found at i:54047924 original size:19 final size:19
Alignment explanation
Indices: 54047900--54047945 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
54047890 TTTTTGGAAG
54047900 TTTAGGGGAAGTAAAACTT
1 TTTAGGGGAAGTAAAACTT
*
54047919 TTTAGGGGAAGTAAAAGTT
1 TTTAGGGGAAGTAAAACTT
*
54047938 TTGAGGGG
1 TTTAGGGG
54047946 GAAAAAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (19 bp):
TTTAGGGGAAGTAAAACTT
Found at i:54049640 original size:6 final size:6
Alignment explanation
Indices: 54049631--54049670 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
54049621 GAAAAAGAAG
54049631 AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAA
1 AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAA
54049671 TTTCTTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:54056007 original size:38 final size:39
Alignment explanation
Indices: 54055956--54056041 Score: 129
Period size: 38 Copynumber: 2.2 Consensus size: 39
54055946 AAACTTAATA
* *
54055956 AAAGACACATATTAATGATGTTCAGATTATGACATAAAT
1 AAAGACTCATATTAATGATGTTCAAATTATGACATAAAT
* *
54055995 AAA-ACTCATATTAATGTTGTTCAAATTATGACATAATT
1 AAAGACTCATATTAATGATGTTCAAATTATGACATAAAT
54056033 AAAGACTCA
1 AAAGACTCA
54056042 AACTATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 34 0.81
39 8 0.19
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (39 bp):
AAAGACTCATATTAATGATGTTCAAATTATGACATAAAT
Found at i:54064109 original size:38 final size:39
Alignment explanation
Indices: 54064067--54064142 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
54064057 AAAAGGTACA
54064067 TATTAATGATGTTCAAATTATGAAATAATTAAA-ACTCT
1 TATTAATGATGTTCAAATTATGAAATAATTAAAGACTCT
* *
54064105 TATTAATGTTGTTCAAATTATGACATAATTAAAGACTC
1 TATTAATGATGTTCAAATTATGAAATAATTAAAGACTC
54064143 AAACTATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 31 0.89
39 4 0.11
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (39 bp):
TATTAATGATGTTCAAATTATGAAATAATTAAAGACTCT
Found at i:54064643 original size:16 final size:17
Alignment explanation
Indices: 54064617--54064650 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54064607 TTATAATTGT
*
54064617 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTAATTA
54064634 ATTG-GAAAATTAATTA
1 ATTGAGAAAATTAATTA
54064650 A
1 A
54064651 GTAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
ATTGAGAAAATTAATTA
Found at i:54067997 original size:56 final size:56
Alignment explanation
Indices: 54067911--54068030 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
54067901 ACAAGGGATG
54067911 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
54067967 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
54068023 ATGGGCAA
1 ATGGGCAA
54068031 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:54069300 original size:39 final size:40
Alignment explanation
Indices: 54069201--54069344 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
54069191 CGAATGATGT
* * *
54069201 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAA
* * *
54069241 CCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-A
*
54069281 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
*
54069320 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54069345 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
39 34 0.39
40 43 0.49
41 10 0.11
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
Found at i:54069358 original size:40 final size:39
Alignment explanation
Indices: 54069253--54069351 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
54069243 AGACTAAGAT
** * *
54069253 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGC
1 CCGAAGGCATTTGAACGAGTTACTATA-ACCGGGCTAAGC
** *
54069292 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAG-C
54069332 CCGAAGGCATTTGAACGAGT
1 CCGAAGGCATTTGAACGAGT
54069352 AGCTATATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 33 0.62
40 20 0.38
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAGC
Found at i:54069363 original size:79 final size:80
Alignment explanation
Indices: 54069200--54069350 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 80
54069190 TCGAATGATG
*
54069200 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
**
54069265 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * * *
54069280 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCAGACTAAGAT-CCGAAGGCAT
54069342 TTGAACGAG
64 TTGAACGAG
54069351 TAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 41 0.68
80 18 0.30
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:54080857 original size:47 final size:47
Alignment explanation
Indices: 54080803--54080896 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
54080793 TATAGCTTCA
*
54080803 AAATACTATATTTGTAACAAATAGGGCTTCTAAGATCCAATACATAC
1 AAATACTATATTTGTAACAAATAGGGCTTCTAAGACCCAATACATAC
54080850 AAATACTATATTTGTAACAAATAGGGCTTCTAAGACCCAATACATAC
1 AAATACTATATTTGTAACAAATAGGGCTTCTAAGACCCAATACATAC
54080897 TCATGCAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (47 bp):
AAATACTATATTTGTAACAAATAGGGCTTCTAAGACCCAATACATAC
Found at i:54082453 original size:23 final size:22
Alignment explanation
Indices: 54082410--54082453 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
54082400 TTCTAAGTCG
54082410 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
54082433 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
54082454 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:54082563 original size:45 final size:45
Alignment explanation
Indices: 54082499--54082591 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
54082489 ACAGATACTT
* *
54082499 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
* * *
54082544 GGTGGAATCAGCACATAGCAAGCACTTTACTAATCAATGATGTTC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
54082589 GGT
1 GGT
54082592 TCACATAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
Found at i:54082719 original size:50 final size:51
Alignment explanation
Indices: 54082588--54082723 Score: 179
Period size: 50 Copynumber: 2.7 Consensus size: 51
54082578 CAATGATGTT
* * * *
54082588 CGGTTCACATAGTAGCCTGCACATAGTACTACAGATGTGACTATTACGATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACTATTACGATC
*
54082639 CGATACACGTAGTAGCCTGCACATAGTACTACACATGCGACCTA-T-C-ATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGA-CTATTACGA-TC
*
54082689 CGGTACACGTAGTAGCCTGCACATAATACTACACA
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACA
54082724 CGTGACCATC
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
49 1 0.01
50 36 0.47
51 36 0.47
52 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (51 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACTATTACGATC
Found at i:54083912 original size:21 final size:21
Alignment explanation
Indices: 54083874--54083915 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54083864 AGAAAGGCAG
*
54083874 CCACAACGAGACCGTTCACCT
1 CCACAACGAGACCATTCACCT
* *
54083895 CCACAACGAGGCTATTCACCT
1 CCACAACGAGACCATTCACCT
54083916 TGTGTTCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.40, G:0.14, T:0.17
Consensus pattern (21 bp):
CCACAACGAGACCATTCACCT
Found at i:54084687 original size:21 final size:22
Alignment explanation
Indices: 54084649--54084693 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
54084639 ATTATGAATA
*
54084649 TTAATTTATAATATAATTAATT
1 TTAATTTATAATACAATTAATT
* *
54084671 TTAATTT-TAATCCAATTTATT
1 TTAATTTATAATACAATTAATT
54084692 TT
1 TT
54084694 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTTATAATACAATTAATT
Found at i:54091330 original size:43 final size:43
Alignment explanation
Indices: 54091243--54091405 Score: 161
Period size: 43 Copynumber: 3.8 Consensus size: 43
54091233 GATTCGTACA
* * ***
54091243 ATGCCAACGTCCCAGACGTGGTCCTACA-TGTAATCACAAATCG
1 ATGCCATCGTCCCAGACGTGGTCTTACACAAAAAT-ACAAATCG
* *
54091286 ATGCCA-CTGTCCCAGACAG-GGTCTTACCCAAAAATACAAGTCG
1 ATGCCATC-GTCCCAGAC-GTGGTCTTACACAAAAATACAAATCG
* * * *
54091329 ATGTCATCATCCCAGACGTGGTCTTACACAGAAATACAACTCG
1 ATGCCATCGTCCCAGACGTGGTCTTACACAAAAATACAAATCG
* *
54091372 ATGCCATCGTTCCAGACGTGGTCTTACACGAAAA
1 ATGCCATCGTCCCAGACGTGGTCTTACACAAAAA
54091406 CACTTATCAG
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 2 0.02
43 92 0.93
44 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (43 bp):
ATGCCATCGTCCCAGACGTGGTCTTACACAAAAATACAAATCG
Found at i:54096467 original size:54 final size:54
Alignment explanation
Indices: 54096409--54096524 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
54096399 GTGCAACTTA
*** * *
54096409 CTAACTTGGGTCACACGGCCGTGTTGTAGGCCGTGTGCTAGACAGTGTAACTCT
1 CTAACTTGGGTCACACGGCCGTGACATAGGCCGTGTACTAAACAGTGTAACTCT
* * * *
54096463 CTAACTTGTGTTACACGGTCGTGACATAGGCCGTGTACTAAACCGTGTAACTCT
1 CTAACTTGGGTCACACGGCCGTGACATAGGCCGTGTACTAAACAGTGTAACTCT
*
54096517 CTGACTTG
1 CTAACTTG
54096525 ATACACACAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (54 bp):
CTAACTTGGGTCACACGGCCGTGACATAGGCCGTGTACTAAACAGTGTAACTCT
Found at i:54115234 original size:23 final size:23
Alignment explanation
Indices: 54115190--54115234 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54115180 AATATTCAAA
* *
54115190 TGATGATTGAAATCTGATTAAAC
1 TGATAATTGAAATCTAATTAAAC
54115213 TGATAATTGAAAT-TAATGTAAA
1 TGATAATTGAAATCTAAT-TAAA
54115235 GAAGATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
TGATAATTGAAATCTAATTAAAC
Found at i:54116074 original size:58 final size:58
Alignment explanation
Indices: 54115994--54116119 Score: 191
Period size: 58 Copynumber: 2.2 Consensus size: 58
54115984 TTTTAATAAG
* *
54115994 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAATAAAATTCTTAACATA
* * *
54116052 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAATAAAATTCTTAACATA
54116110 ATTATTATTA
1 ATTATTATTA
54116120 TATGAATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 23 0.37
58 39 0.63
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAATAAAATTCTTAACATA
Found at i:54116147 original size:58 final size:56
Alignment explanation
Indices: 54115994--54116134 Score: 171
Period size: 58 Copynumber: 2.5 Consensus size: 56
54115984 TTTTAATAAG
* * * *
54115994 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATCATATTTTAACATA
1 ATTATTATT-AATATAATTTAAT-AAAATAATATATAATTTAATAAAATTTTAACATA
*
54116052 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATT-AATATAATTTAATAAAATAATATATAATTTAATAAAATT-TTAACATA
54116110 ATTATTATT-ATATGAA-TTAA-AAAAT
1 ATTATTATTAATAT-AATTTAATAAAAT
54116135 CGTAATATAT
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
55 5 0.07
56 8 0.11
57 25 0.33
58 38 0.50
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (56 bp):
ATTATTATTAATATAATTTAATAAAATAATATATAATTTAATAAAATTTTAACATA
Found at i:54117857 original size:38 final size:38
Alignment explanation
Indices: 54117806--54117881 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
54117796 TGAATGGTCT
54117806 CATTTAGTTTGGAACGCATTTGTCGGGCCTTTGATCTC
1 CATTTAGTTTGGAACGCATTTGTCGGGCCTTTGATCTC
*
54117844 CATTTAGTTTGGAATGCATTTGTCGGGCCTTTGATCTC
1 CATTTAGTTTGGAACGCATTTGTCGGGCCTTTGATCTC
54117882 GTATCATTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (38 bp):
CATTTAGTTTGGAACGCATTTGTCGGGCCTTTGATCTC
Found at i:54125998 original size:18 final size:18
Alignment explanation
Indices: 54125975--54126014 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
54125965 CTGACATGGT
54125975 TAATTTCCCAAAAAAGTA
1 TAATTTCCCAAAAAAGTA
54125993 TAATTTCCCAAAAAAGTA
1 TAATTTCCCAAAAAAGTA
54126011 TAAT
1 TAAT
54126015 CTTAAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (18 bp):
TAATTTCCCAAAAAAGTA
Found at i:54127237 original size:11 final size:11
Alignment explanation
Indices: 54127221--54127246 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54127211 TCAATCACCC
54127221 AAAAAAGAAAT
1 AAAAAAGAAAT
54127232 AAAAAAGAAAT
1 AAAAAAGAAAT
54127243 AAAA
1 AAAA
54127247 GAAAAGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAGAAAT
Found at i:54134960 original size:42 final size:42
Alignment explanation
Indices: 54134789--54134951 Score: 193
Period size: 42 Copynumber: 3.9 Consensus size: 42
54134779 GTTTACAAAC
* *
54134789 AAAAACGCCGCTAAATACCATGTTCTTTAGCGGCGCTTAGA-
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAT
* * *
54134830 AAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAT
* ** ***
54134872 AAAAACGCCGCTAAAGAACATGTTCTTTAGTGGCATTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAT
* * *
54134914 ACAAACGCCGCGAAAGAACATGTTCTTTAGTGGCGCTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
54134952 TTATACAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 39 0.37
42 67 0.63
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAT
Found at i:54135042 original size:14 final size:14
Alignment explanation
Indices: 54135019--54135052 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
54135009 GCCCTCCTGT
*
54135019 AGCAAAAATTCAAA
1 AGCAACAATTCAAA
54135033 AGCAACAATTCAAA
1 AGCAACAATTCAAA
54135047 AGCAAC
1 AGCAAC
54135053 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.12
Consensus pattern (14 bp):
AGCAACAATTCAAA
Found at i:54135344 original size:21 final size:21
Alignment explanation
Indices: 54135276--54135346 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
54135266 TTTTGCTCTG
*
54135276 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
54135297 CTCCGCTTCCCTCGCTGCAG-
1 CTCTGCTTCCCTCGCTGCAGC
* *
54135317 CTGCTGCTTCCCTCGCTTCCGC
1 CT-CTGCTTCCCTCGCTGCAGC
54135339 CTCTGCTT
1 CTCTGCTT
54135347 TAAGTTGTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 39 0.91
22 2 0.05
ACGTcount: A:0.03, C:0.46, G:0.18, T:0.32
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:54141416 original size:25 final size:25
Alignment explanation
Indices: 54141385--54141489 Score: 133
Period size: 25 Copynumber: 4.2 Consensus size: 25
54141375 TGATATATAT
*
54141385 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
54141410 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
*
54141436 TTATGTATTAAGTAAGCTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
54141461 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
54141486 TTAT
1 TTAT
54141490 CAAAGTAATG
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.03
25 44 0.64
26 19 0.28
27 2 0.03
28 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:54141472 original size:16 final size:16
Alignment explanation
Indices: 54141400--54141617 Score: 56
Period size: 18 Copynumber: 13.8 Consensus size: 16
54141390 TATTAAGTAA
54141400 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
* * *
54141416 ACGTGTATAAGTTATGT
1 A-TTATGTAAGTTATGT
*
54141433 AAGTTATGT-A-TTAAGT
1 -A-TTATGTAAGTTATGT
* *
54141449 AAGCTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGT
54141467 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
** *
54141483 AAGTTATCAAAGTAATGT
1 -A-TTATGTAAGTTATGT
54141501 ATGTTATGTAAG-T-TGT
1 A--TTATGTAAGTTATGT
*
54141517 A--A-GTTA-TTATGT
1 ATTATGTAAGTTATGT
*
54141529 ATTATGTAAGTTGTAAGTT
1 ATTATGTAAG-T-TATG-T
*
54141548 ATTATGT-A-TTGTGT
1 ATTATGTAAGTTATGT
*
54141562 AAGT-TGTAAGTTAAATGT
1 -ATTATGTAAGTT--ATGT
54141580 ATTATGTAAG-T-TGT
1 ATTATGTAAGTTATGT
*
54141594 A--A-GTTA-TTATGT
1 ATTATGTAAGTTATGT
54141606 ATTATGTAAGTT
1 ATTATGTAAGTT
54141618 GTAAGTTATT
Statistics
Matches: 145, Mismatches: 29, Indels: 56
0.63 0.13 0.24
Matches are distributed among these distances:
11 8 0.06
12 10 0.07
14 10 0.07
15 11 0.08
16 36 0.25
17 21 0.14
18 41 0.28
19 8 0.06
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:54141540 original size:26 final size:26
Alignment explanation
Indices: 54141453--54141783 Score: 399
Period size: 26 Copynumber: 13.1 Consensus size: 26
54141443 TTAAGTAAGC
54141453 TATGTAAGTTGT--G-TATTATGTAAGT
1 TATGTAAGTTGTAAGTTATTATGT-A-T
* *
54141478 TATGTAAGTTATCAAAGTAATGTATG--T
1 TATGTAAGTTGT--AAGTTAT-TATGTAT
54141505 TATGTAAGTTGTAAGTTATTATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
54141531 TATGTAAGTTGTAAGTTATTATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
* *
54141557 TGTGTAAGTTGTAAGTTA-AATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
54141582 TATGTAAGTTGTAAGTTATTATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
54141608 TATGTAAGTTGTAAGTTATTATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
*
54141634 TGTGTAAGTTGTAAGTTA-TATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
* *
54141659 TATGTCA---GTCA---A--ATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
*
54141677 TATGTAAGTTGTAAGTTA-AATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
54141702 TATGTAAGTTGTAAGTTATTATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
*
54141728 TATGTAAGTAATGTAAGTTA-AATGTAT
1 TATGTAAGT--TGTAAGTTATTATGTAT
54141755 TATGTAAGTTGTAAGTTATTATGTAT
1 TATGTAAGTTGTAAGTTATTATGTAT
54141781 TAT
1 TAT
54141784 TTAATAAAAT
Statistics
Matches: 269, Mismatches: 17, Indels: 39
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.04
19 1 0.00
21 3 0.01
22 3 0.01
24 5 0.02
25 85 0.32
26 117 0.43
27 27 0.10
28 9 0.03
29 1 0.00
30 2 0.01
31 4 0.01
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
TATGTAAGTTGTAAGTTATTATGTAT
Found at i:54141585 original size:77 final size:76
Alignment explanation
Indices: 54141504--54141781 Score: 401
Period size: 77 Copynumber: 3.7 Consensus size: 76
54141494 GTAATGTATG
54141504 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGT
1 TTATGTAAGTTGTAAGTTA-TATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGT
*
54141569 AAGTTAAATGTA
65 AAGTTATATGTA
54141581 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGT
1 TTATGTAAGTTGTAAGTTA-TATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGT
54141646 AAGTTATATGTA
65 AAGTTATATGTA
* * * *
54141658 TTATGTCA---GTCA---A-ATGTATTATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTA
1 TTATGTAAGTTGTAAGTTATATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGTA
54141715 AGTTATTATGTA
66 AGTTA-TATGTA
*
54141727 TTATGTAAGTAATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 TTATGTAAGT--TGTAAGTTATATGTATTATGTAAGTTGTAAGTTATTATGTATT
54141782 ATTTAATAAA
Statistics
Matches: 182, Mismatches: 8, Indels: 20
0.87 0.04 0.10
Matches are distributed among these distances:
68 23 0.13
69 37 0.20
71 1 0.01
74 6 0.03
77 84 0.46
78 24 0.13
79 7 0.04
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (76 bp):
TTATGTAAGTTGTAAGTTATATGTATTATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGTA
AGTTATATGTA
Found at i:54141707 original size:18 final size:18
Alignment explanation
Indices: 54141686--54141764 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 18
54141676 TTATGTAAGT
54141686 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
*
54141704 TGTAAGTTGTAA-GTTATTA
1 TGTAAGTT-AAATG-TATTA
*
54141723 TGT-A-TT--ATGTAAGTAA
1 TGTAAGTTAAATGT-A-TTA
54141739 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
54141757 TGTAAGTT
1 TGTAAGTT
54141765 GTAAGTTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
14 2 0.04
15 2 0.04
16 5 0.10
17 3 0.06
18 22 0.45
19 11 0.22
20 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (18 bp):
TGTAAGTTAAATGTATTA
Found at i:54141753 original size:53 final size:51
Alignment explanation
Indices: 54141453--54141783 Score: 393
Period size: 51 Copynumber: 6.6 Consensus size: 51
54141443 TTAAGTAAGC
*
54141453 TATGTAAGTTGT--G-TATTATGTAAGTTATGTAAGTTATCAAAG-T-AATGTATGT
1 TATGTAAGTTGTAAGTTATTATGT-A-TTATGTAAGTTGT--AAGTTAAATGTA--T
*
54141505 TATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTAT
1 TATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTA-AATGTAT
* * *
54141557 TGTGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTAT
1 TATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTA-AATGTAT
* *
54141608 TATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGTAAGTTATATGTAT
1 TATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTAT
* *
54141659 TATGTCA---GTCA---A--ATGTATTATGTAAGTTGTAAGTTAAATGTAT
1 TATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTAT
54141702 TATGTAAGTTGTAAGTTATTATGTATTATGTAAGTAATGTAAGTTAAATGTAT
1 TATGTAAGTTGTAAGTTATTATGTATTATGTAAGT--TGTAAGTTAAATGTAT
54141755 TATGTAAGTTGTAAGTTATTATGTATTAT
1 TATGTAAGTTGTAAGTTATTATGTATTAT
54141784 TTAATAAAAT
Statistics
Matches: 249, Mismatches: 13, Indels: 33
0.84 0.04 0.11
Matches are distributed among these distances:
43 35 0.14
45 1 0.00
46 3 0.01
48 3 0.01
49 1 0.00
51 80 0.32
52 54 0.22
53 57 0.23
54 7 0.03
55 8 0.03
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (51 bp):
TATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTAT
Found at i:54142061 original size:13 final size:13
Alignment explanation
Indices: 54142043--54142113 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
54142033 ATTTATAATT
54142043 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
54142056 ATTTAAGTAACAT
1 ATTTAAGTAATAA
54142069 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
54142082 ATTTAAGTAACAT
1 ATTTAAGTAATAA
54142095 ATTTAAGTAATAA
1 ATTTAAGTAATAA
54142108 ATTTAA
1 ATTTAA
54142114 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:54142072 original size:26 final size:26
Alignment explanation
Indices: 54142042--54142113 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
54142032 TATTTATAAT
54142042 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
54142068 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
54142094 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
54142114 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:54142140 original size:17 final size:17
Alignment explanation
Indices: 54142118--54142634 Score: 259
Period size: 17 Copynumber: 27.6 Consensus size: 17
54142108 ATTTAAACAA
54142118 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
54142135 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
** *
54142152 ATTTTAGTAACAAATTT
1 ATTTTAGTAAGTAATGT
*
54142169 AAACAAATTTTAGTAAATAATGT
1 ------ATTTTAGTAAGTAATGT
54142192 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
** *
54142209 ATTTTAGTAACAAATTT
1 ATTTTAGTAAGTAATGT
*
54142226 AAACAAATTTTAGTAAATAATGT
1 ------ATTTTAGTAAGTAATGT
54142249 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
** *
54142266 ATTTTAGTAACAAATTT
1 ATTTTAGTAAGTAATGT
*
54142283 AAACAAATTTTAGTAAATAATGT
1 ------ATTTTAGTAAGTAATGT
54142306 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
** *
54142323 ATTTTAGTAACAAATTT
1 ATTTTAGTAAGTAATGT
*
54142340 AAACAAATTTTAGTAAATAATGT
1 ------ATTTTAGTAAGTAATGT
54142363 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
54142380 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
** ***
54142397 ATTTTAGT-TTTAAACAA
1 ATTTTAGTAAGT-AATGT
*
54142414 ATTTTAGTAAGTAATTT
1 ATTTTAGTAAGTAATGT
54142431 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
54142448 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
* *
54142465 AAACAAATTTTAATAAGTAATTT
1 ------ATTTTAGTAAGTAATGT
** *
54142488 ATTTTAGTAACAAATTT
1 ATTTTAGTAAGTAATGT
54142505 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
*
54142528 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
*
54142545 AATCAAATTGTAGTAAGTAATTT
1 -AT----TT-TAGTAAGTAATGT
54142568 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
54142585 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
54142602 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
54142625 ATTTTAGTAA
1 ATTTTAGTAA
54142635 TAAAATTAAC
Statistics
Matches: 393, Mismatches: 51, Indels: 112
0.71 0.09 0.20
Matches are distributed among these distances:
16 4 0.01
17 268 0.68
18 5 0.01
22 4 0.01
23 109 0.28
24 3 0.01
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:54142167 original size:57 final size:57
Alignment explanation
Indices: 54142085--54142497 Score: 619
Period size: 57 Copynumber: 7.1 Consensus size: 57
54142075 GTAATAAATT
** * * *
54142085 TAAGTAACATATTTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
54142142 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
54142199 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
54142256 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
54142313 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
* * *
54142370 TAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTTTTAAACAAATTTTAGTAAGTAATTTATTT
1 TAAGTAATGTATTTTAGTAA--CA---A----A--TTTAAACAAATTTTAGTAAATAATGTATTT
54142435 TAG
55 TAG
* * * *
54142438 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAATAAGTAATTTATTTTAG
1 TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
54142495 TAA
1 TAA
54142498 CAAATTTAAA
Statistics
Matches: 335, Mismatches: 10, Indels: 22
0.91 0.03 0.06
Matches are distributed among these distances:
57 278 0.83
59 2 0.01
62 1 0.00
63 1 0.00
66 2 0.01
68 51 0.15
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (57 bp):
TAAGTAATGTATTTTAGTAACAAATTTAAACAAATTTTAGTAAATAATGTATTTTAG
Found at i:54142518 original size:23 final size:23
Alignment explanation
Indices: 54142448--54142520 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
54142438 TAAGTAATGT
*
54142448 ATTTTAGTAATAAATTTAAACAA
1 ATTTTAGTAACAAATTTAAACAA
* **
54142471 ATTTTAATAAGTAATTT------
1 ATTTTAGTAACAAATTTAAACAA
54142488 ATTTTAGTAACAAATTTAAACAA
1 ATTTTAGTAACAAATTTAAACAA
54142511 ATTTTAGTAA
1 ATTTTAGTAA
54142521 GTAATGTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
17 14 0.37
23 24 0.63
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (23 bp):
ATTTTAGTAACAAATTTAAACAA
Found at i:54142603 original size:57 final size:57
Alignment explanation
Indices: 54142511--54142634 Score: 221
Period size: 57 Copynumber: 2.2 Consensus size: 57
54142501 ATTTAAACAA
* *
54142511 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAATCAAATTGTAGTAAGTAATTT
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTGTAGTAAGTAATGT
*
54142568 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTGTAGTAAGTAATGT
54142625 ATTTTAGTAA
1 ATTTTAGTAA
54142635 TAAAATTAAC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (57 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAAATTGTAGTAAGTAATGT
Found at i:54142612 original size:40 final size:40
Alignment explanation
Indices: 54142568--54142643 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
54142558 TAAGTAATTT
*
54142568 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAAATTAAACAA
54142608 ATTTTAGTAAGTAATGTATTTTAGTAATAAAATTAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAAATTAA
54142644 CATTCAATCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.43
Consensus pattern (40 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAAATTAAACAA
Found at i:54144788 original size:84 final size:86
Alignment explanation
Indices: 54144681--54144874 Score: 320
Period size: 84 Copynumber: 2.2 Consensus size: 86
54144671 CCACATTTCC
* *
54144681 GGCGTTTTCCTAAAAAACACCACTAAATATTACAGCTGTGAACAGAAATGACACCGTTTT-CGTG
1 GGCGTTTTCCT-AAAAACGCCACTAAATATTACAGCTGTGAACAGAAAAGACACCGTTTTGCGTG
54144745 GTCTGG-AATTGCATTATTTGT
65 GTCTGGAAATTGCATTATTTGT
*
54144766 GGCGTTTTCCTAAAAATGCCACTAAATATTACAGCTGTGAACAGAAAAGACACCGTTTTGCGTGG
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAAAGACACCGTTTTGCGTGG
54144831 TCTGGAATAATTGCATTATTTGT
66 TCTGG-A-AATTGCATTATTTGT
54144854 GGCGTTTTCCTAAAAACGCCA
1 GGCGTTTTCCTAAAAACGCCA
54144875 GGACTGCTTC
Statistics
Matches: 101, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
84 45 0.45
85 21 0.21
88 35 0.35
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (86 bp):
GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAAAGACACCGTTTTGCGTGG
TCTGGAAATTGCATTATTTGT
Found at i:54146966 original size:112 final size:112
Alignment explanation
Indices: 54146793--54147607 Score: 1443
Period size: 112 Copynumber: 7.3 Consensus size: 112
54146783 AACACCTAGA
54146793 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
54146858 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACTCT
66 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACTCT
* *
54146905 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGACAAAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
**
54146970 GTGTATTATTTGCGGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
66 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACTCT
54147017 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
*
54147082 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACGCT
66 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACTCT
54147129 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
*
54147194 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACGCT
66 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACTCT
54147241 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
*
54147306 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACGCT
66 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACTCT
**
54147353 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCATTGTCTGG
1 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
** *
54147418 GTGTATTATTTGCGGCGTTTTTTACAAACGCTGCTAATGTTCACTCT
66 GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACTCT
* *
54147465 TTACCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTATGG
1 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
*
54147530 GTGTATTATTTGCGGCT-TTTTTTATAAACGCTGCTAATGTTCACTCT
66 GTGTATTATTTGC-GATGTTTTTTATAAACGCTGCTAATGTTCACTCT
* ***
54147577 TTAGCGGCGCTTTTCCTTAAACGCCACTAAT
1 TTAGCGGCGCTTTACAAAAAACGCCACTAAT
54147608 GCTCACTCTT
Statistics
Matches: 675, Mismatches: 27, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
112 674 1.00
113 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (112 bp):
TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
GTGTATTATTTGCGATGTTTTTTATAAACGCTGCTAATGTTCACTCT
Found at i:54147600 original size:40 final size:40
Alignment explanation
Indices: 54147554--54147710 Score: 251
Period size: 40 Copynumber: 3.9 Consensus size: 40
54147544 GCTTTTTTTA
** *
54147554 TAAACGCTGCTAATGTTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
54147594 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
*
54147634 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTACT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
* * *
54147674 TAAACGCCGCTAATGCTCACTCTTTAGCAGCGTTTTT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTT
54147711 GCTCCAAACG
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 110 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.34
Consensus pattern (40 bp):
TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
Found at i:54149237 original size:12 final size:12
Alignment explanation
Indices: 54149220--54149244 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54149210 ATGTTTTAAA
54149220 ATTTTATTTTAT
1 ATTTTATTTTAT
54149232 ATTTTATTTTAT
1 ATTTTATTTTAT
54149244 A
1 A
54149245 AATATTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTATTTTAT
Found at i:54158318 original size:44 final size:44
Alignment explanation
Indices: 54158242--54158666 Score: 320
Period size: 44 Copynumber: 9.6 Consensus size: 44
54158232 TGCCTCACTA
* * *
54158242 CCAATATAAGAAGACATA-ATCTGCTATTTTCGATCTACTTCACG
1 CCAATATATGAAGACA-AGATCTTCTATCTTCGATCTACTTCACG
* * * * *
54158286 CTAATACATGAAGACAAGATCTTTTTTCTTCGATCTACTTCACCA
1 CCAATATATGAAGACAAGATCTTCTATCTTCGATCTACTTCA-CG
* * * *
54158331 CCAGTATGA-GAAGACAATATCTGC-ATCTTCGATCTACTTCATG
1 CCAATAT-ATGAAGACAAGATCTTCTATCTTCGATCTACTTCACG
* * * * *
54158374 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
1 CCAATATATGAAGACAAGATCTTCTATCTTCGATCTACTTC-ACG
** * * * * *
54158419 CCAGA-ATGGGAAAACAAGATCTGC-ATCTTCGATCCACTTCGCTA
1 CCA-ATATATGAAGACAAGATCTTCTATCTTCGATCTACTTCAC-G
* * * *
54158463 CCAATATAGGAAGACAAGATCTACTGTCTTTGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTTCTATCTTCGATCTACTTCACG
* * * * * *
54158507 CCAATACATGAAGACAAGATCTGCTTTATTCGATCTACTTCGCCA
1 CCAATATATGAAGACAAGATCTTCTATCTTCGATCTACTTC-ACG
* ** ** * * *
54158552 CCAGTATGGGAAGACAAGATCTGTAAATCTTCGATCCACTTCGCTA
1 CCAATATATGAAGACAAGATCT-TCTATCTTCGATCTACTTCAC-G
* *
54158598 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTTCTATCTTCGATCTACTTCACG
* *
54158642 CCAATTTATGAAGACAATATCTTCT
1 CCAATATATGAAGACAAGATCTTCT
54158667 GCTTTTTAAC
Statistics
Matches: 298, Mismatches: 70, Indels: 26
0.76 0.18 0.07
Matches are distributed among these distances:
42 1 0.00
43 22 0.07
44 154 0.52
45 85 0.29
46 36 0.12
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (44 bp):
CCAATATATGAAGACAAGATCTTCTATCTTCGATCTACTTCACG
Found at i:54158385 original size:88 final size:89
Alignment explanation
Indices: 54158236--54158666 Score: 408
Period size: 88 Copynumber: 4.8 Consensus size: 89
54158226 TCAGTCTGCC
* * * * *
54158236 TCACTACCAATATAAGAAGACATA-ATCTGCTATTTTCGATCTACTTCACGCTAATACATGAAGA
1 TCACCACCAATATGAGAAGACA-AGATCTGCTATCTTCGATCTACTTCACGCCAATATATGAAGA
*
54158300 CAAGATCTTTTTTCTTCGATCTACT
65 CAAGATCTTCTTTCTTCGATCTACT
* * * *
54158325 TCACCACCAGTATGAGAAGACAATATCTGC-ATCTTCGATCTACTTCATGCCAATACATGAAGAC
1 TCACCACCAATATGAGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATATGAAGAC
*
54158389 AAGATCTGCTTTCTTCGATCTACT
66 AAGATCTTCTTTCTTCGATCTACT
* * * * * * *
54158413 TCGCCACCAGA-ATGGGAAAACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAG
1 TCACCACCA-ATATGAGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATATGAAG
* * *
54158476 ACAAGATCTACTGTCTTTGATCTACT
64 ACAAGATCTTCTTTCTTCGATCTACT
* * * * * * * **
54158502 TCA-CGCCAATA-CATGAAGACAAGATCTGCTTTATTCGATCTACTTCGCCACCAGTATGGGAAG
1 TCACCACCAATATGA-GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATATATGAAG
*** *
54158565 ACAAGATCTGTAAATCTTCGATCCACT
64 ACAAGATCT-TCTTTCTTCGATCTACT
* * *
54158592 TCGCTACCAATAT-AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATTTATGAAGA
1 TCACCACCAATATGA-GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATATGAAGA
*
54158656 CAATATCTTCT
65 CAAGATCTTCT
54158667 GCTTTTTAAC
Statistics
Matches: 278, Mismatches: 54, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
87 1 0.00
88 112 0.40
89 96 0.35
90 32 0.12
91 37 0.13
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (89 bp):
TCACCACCAATATGAGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATATGAAGAC
AAGATCTTCTTTCTTCGATCTACT
Found at i:54158654 original size:135 final size:134
Alignment explanation
Indices: 54158295--54158663 Score: 528
Period size: 133 Copynumber: 2.8 Consensus size: 134
54158285 GCTAATACAT
* ** * * * * *
54158295 GAAGACAAGATCTTTTTTCTTCGATCTACTTCACCACCAGTAT-GAGAAGACAATATCTGC-ATC
1 GAAGACAAGATCTGTAATCTTCGATCCACTTCGCTACCAATATAG-GAAGACAAGATCTGCTATC
* *
54158358 TTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAG
65 TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTATTCGATCTACTTCGCCACCAG
54158423 AATGG
130 AATGG
* * * *
54158428 GAAAACAAGATCTG-CATCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTACTGTCT
1 GAAGACAAGATCTGTAATCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCT
* *
54158492 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTATTCGATCTACTTCGCCACCAGT
66 TCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTATTCGATCTACTTCGCCACCAGA
54158557 ATGG
131 ATGG
54158561 GAAGACAAGATCTGTAAATCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATC
1 GAAGACAAGATCTGT-AATCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATC
** *
54158626 TTCGATCTACTTCACGCCAATTTATGAAGACAATATCT
65 TTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
54158664 TCTGCTTTTT
Statistics
Matches: 209, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
132 35 0.17
133 94 0.45
135 80 0.38
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (134 bp):
GAAGACAAGATCTGTAATCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCT
TCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTATTCGATCTACTTCGCCACCAGA
ATGG
Found at i:54159570 original size:25 final size:26
Alignment explanation
Indices: 54159532--54159580 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
54159522 GTGTCCTGAA
54159532 AAGAAAAAGATATT-CAAGAACAATG
1 AAGAAAAAGATATTACAAGAACAATG
54159557 AAGAATAAAG-TATTACAAGAACAA
1 AAGAA-AAAGATATTACAAGAACAA
54159581 ACAAATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.16
Consensus pattern (26 bp):
AAGAAAAAGATATTACAAGAACAATG
Found at i:54164288 original size:16 final size:15
Alignment explanation
Indices: 54164267--54164296 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54164257 AATTAAATAC
54164267 AACAACATTTATTAAT
1 AACAACATTT-TTAAT
54164283 AACAACATTTTTAA
1 AACAACATTTTTAA
54164297 GTTGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
AACAACATTTTTAAT
Found at i:54164811 original size:21 final size:20
Alignment explanation
Indices: 54164787--54164840 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
54164777 AATAAAAAGG
54164787 ATAAATTTTAAAACAATGTTA
1 ATAAATTTTAAAAC-ATGTTA
* *
54164808 ATAAACTCT-AAACATGTTA
1 ATAAATTTTAAAACATGTTA
54164827 ATAATAATTTTAAA
1 AT-A-AATTTTAAA
54164841 TAACGATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 8 0.31
20 5 0.19
21 11 0.42
22 2 0.08
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (20 bp):
ATAAATTTTAAAACATGTTA
Found at i:54173460 original size:15 final size:15
Alignment explanation
Indices: 54173440--54173470 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54173430 TATGAATGTC
54173440 ACAATAACAAATACA
1 ACAATAACAAATACA
*
54173455 ACAATAATAAATACA
1 ACAATAACAAATACA
54173470 A
1 A
54173471 TAATGGCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (15 bp):
ACAATAACAAATACA
Found at i:54173620 original size:15 final size:14
Alignment explanation
Indices: 54173593--54173638 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
54173583 ATATAAATGA
*
54173593 AAACACAAAAAAAT
1 AAACAAAAAAAAAT
54173607 AAACAAATAAAAAAT
1 AAACAAA-AAAAAAT
*
54173622 AAACAAAAAAATAT
1 AAACAAAAAAAAAT
54173636 AAA
1 AAA
54173639 GAATAAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 15 0.52
15 14 0.48
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (14 bp):
AAACAAAAAAAAAT
Found at i:54173621 original size:7 final size:7
Alignment explanation
Indices: 54173600--54173646 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
54173590 TGAAAACACA
54173600 AAAAAAT
1 AAAAAAT
54173607 AAACAAAT
1 AAA-AAAT
54173615 AAAAAAT
1 AAAAAAT
54173622 AAACAAA-
1 AAA-AAAT
*
54173629 AAAATAT
1 AAAAAAT
*
54173636 AAAGAAT
1 AAAAAAT
54173643 AAAA
1 AAAA
54173647 GGTACATGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 2 0.06
7 21 0.64
8 10 0.30
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:54173646 original size:14 final size:14
Alignment explanation
Indices: 54173600--54173646 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
54173590 TGAAAACACA
54173600 AAAAAATAAACAAAT
1 AAAAAATAAAC-AAT
54173615 AAAAAATAAACAA-
1 AAAAAATAAACAAT
*
54173628 AAAAATATAAAGAAT
1 AAAAA-ATAAACAAT
54173643 AAAA
1 AAAA
54173647 GGTACATGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 5 0.17
14 9 0.31
15 15 0.52
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (14 bp):
AAAAAATAAACAAT
Found at i:54174862 original size:18 final size:18
Alignment explanation
Indices: 54174839--54174890 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
54174829 ATTTGCATGT
54174839 AGAATAAAAAAAATAAAA
1 AGAATAAAAAAAATAAAA
* * *
54174857 AGAATAATAAATAT-AAC
1 AGAATAAAAAAAATAAAA
*
54174874 A-AATAGAAAAAATAAAA
1 AGAATAAAAAAAATAAAA
54174891 TTGCAAATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
16 9 0.35
17 5 0.19
18 12 0.46
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (18 bp):
AGAATAAAAAAAATAAAA
Found at i:54193032 original size:1 final size:1
Alignment explanation
Indices: 54193026--54193130 Score: 210
Period size: 1 Copynumber: 105.0 Consensus size: 1
54193016 CTCTGACGAA
54193026 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54193091 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54193131 CCCAAATTTC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 104 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:54220649 original size:48 final size:48
Alignment explanation
Indices: 54220545--54220821 Score: 448
Period size: 48 Copynumber: 5.7 Consensus size: 48
54220535 TGCATGTGTC
*
54220545 TGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTATATG
1 TGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATGAGATATGTATATG
* *
54220595 TGGTAAAGCCGAATGGCTAGTTTGAAATATGTATGAGATATGTATATG
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
54220643 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
*
54220691 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGCATATG
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
*
54220739 TGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGTATATG
1 TGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATGTATATG
*
54220789 TGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTA
54220822 GGCGATGTGC
Statistics
Matches: 213, Mismatches: 10, Indels: 10
0.91 0.04 0.04
Matches are distributed among these distances:
47 1 0.00
48 142 0.67
49 6 0.03
50 63 0.30
51 1 0.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (48 bp):
TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATG
Found at i:54220847 original size:96 final size:97
Alignment explanation
Indices: 54220550--54220840 Score: 421
Period size: 98 Copynumber: 3.0 Consensus size: 97
54220540 GTGTCTGGTA
54220550 AAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
1 AAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
*
54220615 TTTGAAATATGTATGAGATAT--GTATATGTGGT
66 TGTGAAATATGTATGAGATATGCGTATAT-T-GT
*
54220647 AAAGCCGAATGGCTAATGTG-AA-ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 -AAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* * * *
54220710 ATGTGAAATATGTATGAGATATGCATATGTGGT
65 GTGTGAAATATGTATGAGATATGCGTATATTGT
54220743 AAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCT
1 -AAGCCGAATGGCT-AATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCT
* * *
54220807 AGTGTGAAATATGTAGGCGATGTGCGTATATTGT
64 AGTGTGAAATATGTATGAGATATGCGTATATTGT
54220841 GGCCGAACGA
Statistics
Matches: 174, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
95 1 0.01
96 80 0.46
97 4 0.02
98 89 0.51
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (97 bp):
AAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG
TGTGAAATATGTATGAGATATGCGTATATTGT
Found at i:54221012 original size:37 final size:37
Alignment explanation
Indices: 54220957--54221058 Score: 143
Period size: 37 Copynumber: 2.8 Consensus size: 37
54220947 ACATGAAACT
54220957 TGGAAATATATTCCGGGTAAGACCCGATGACTACGTA
1 TGGAAATATATTCCGGGTAAGACCCGATGACTACGTA
* *
54220994 TGGAAATATATTCTGGGTAAGACCCGATGACTACGTG
1 TGGAAATATATTCCGGGTAAGACCCGATGACTACGTA
* * *
54221031 TGGAGAT-TTTGTCCGTGTAAGACCCGAT
1 TGGAAATATAT-TCCGGGTAAGACCCGAT
54221059 AACTTCGTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 2 0.03
37 56 0.97
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (37 bp):
TGGAAATATATTCCGGGTAAGACCCGATGACTACGTA
Found at i:54226002 original size:19 final size:19
Alignment explanation
Indices: 54225978--54226015 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54225968 TTTTGAGCTT
54225978 GGTTTTTTAATGATTTCTA
1 GGTTTTTTAATGATTTCTA
54225997 GGTTTTTTAATGATTTCTA
1 GGTTTTTTAATGATTTCTA
54226016 TATTTTTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.58
Consensus pattern (19 bp):
GGTTTTTTAATGATTTCTA
Found at i:54226021 original size:19 final size:19
Alignment explanation
Indices: 54225980--54226022 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
54225970 TTGAGCTTGG
*
54225980 TTTTTTAATGATTTCTAGG
1 TTTTTTAATGATTTCTAGA
*
54225999 TTTTTTAATGATTTCTATA
1 TTTTTTAATGATTTCTAGA
54226018 TTTTT
1 TTTTT
54226023 GTGATTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.65
Consensus pattern (19 bp):
TTTTTTAATGATTTCTAGA
Found at i:54242107 original size:43 final size:43
Alignment explanation
Indices: 54242052--54242163 Score: 215
Period size: 43 Copynumber: 2.6 Consensus size: 43
54242042 GCTGGTATTA
*
54242052 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCTGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
54242095 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
54242138 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
54242164 GTAATGCCGG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.10, C:0.26, G:0.34, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:54242172 original size:43 final size:43
Alignment explanation
Indices: 54242031--54242176 Score: 197
Period size: 43 Copynumber: 3.4 Consensus size: 43
54242021 GATAAATCCC
* * *
54242031 GCAGGCCTAATGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
** *
54242072 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
**
54242115 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
54242158 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAATGCCGGTGA
54242177 AATGATATGT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 14 0.15
42 2 0.02
43 79 0.83
ACGTcount: A:0.13, C:0.24, G:0.34, T:0.29
Consensus pattern (43 bp):
GCAGGCTTAATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:54245850 original size:3 final size:3
Alignment explanation
Indices: 54245844--54245875 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
54245834 CTATATTTGA
54245844 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54245876 ACCTATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54256817 original size:25 final size:25
Alignment explanation
Indices: 54256783--54256835 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
54256773 ATCGGTGTAC
54256783 AAGCTATATTTAGTGTTAACAAAGT
1 AAGCTATATTTAGTGTTAACAAAGT
54256808 AAGCTATATTTAGTGTTAACAAAGT
1 AAGCTATATTTAGTGTTAACAAAGT
54256833 AAG
1 AAG
54256836 TCAATGTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (25 bp):
AAGCTATATTTAGTGTTAACAAAGT
Found at i:54272201 original size:23 final size:23
Alignment explanation
Indices: 54272174--54272219 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
54272164 ATGCAATATT
54272174 AGATAAGA-TATGTAAATCTTAGA
1 AGATAAGATTATGT-AATCTTAGA
* *
54272197 AGATATGATTTTGTAATCTTAGA
1 AGATAAGATTATGTAATCTTAGA
54272220 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (23 bp):
AGATAAGATTATGTAATCTTAGA
Found at i:54272232 original size:21 final size:23
Alignment explanation
Indices: 54272188--54272233 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
54272178 AAGATATGTA
*
54272188 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATATGAATTTGT
*
54272211 AATCTTAG-AGAT-TTAATTTGT
1 AATCTTAGAAGATATGAATTTGT
54272232 AA
1 AA
54272234 ATATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (23 bp):
AATCTTAGAAGATATGAATTTGT
Found at i:54284485 original size:28 final size:27
Alignment explanation
Indices: 54284447--54284599 Score: 132
Period size: 28 Copynumber: 5.6 Consensus size: 27
54284437 AAACGAACGG
* *
54284447 CACTTAGTGTGCGAAGTATTGAGGATGG
1 CACTTAGTGTGCGAAGTATCGA-GATGA
* *
54284475 CACTTAGTGTGC-AAGACATCCGAAATGA
1 CACTTAGTGTGCGAAG-TAT-CGAGATGA
** *
54284503 CAC--AGTGTATGAAGTATTGATGATGA
1 CACTTAGTGTGCGAAGTATCGA-GATGA
** *
54284529 CACTTAGTGTGCGAAACATCCGAAATGA
1 CACTTAGTGTGCGAAGTAT-CGAGATGA
*
54284557 CACTTAGTGTGCGAAGTATCGAGGATGG
1 CACTTAGTGTGCGAAGTATCGA-GATGA
54284585 CACTTAGTGTGCGAA
1 CACTTAGTGTGCGAA
54284600 ACATCCGGTA
Statistics
Matches: 98, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
25 2 0.02
26 14 0.14
27 9 0.09
28 69 0.70
29 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (27 bp):
CACTTAGTGTGCGAAGTATCGAGATGA
Found at i:54284615 original size:28 final size:27
Alignment explanation
Indices: 54284529--54284632 Score: 95
Period size: 28 Copynumber: 3.7 Consensus size: 27
54284519 TTGATGATGA
*
54284529 CACTTAGTGTGCGAAACATCCGAAATG
1 CACTTAGTGTGCGAAACATCCGGAATG
** *
54284556 ACACTTAGTGTGCGAAGTAT-CGAGGATGG
1 -CACTTAGTGTGCGAAACATCCG-GAAT-G
*
54284585 CACTTAGTGTGCGAAACATCCGGTATAG
1 CACTTAGTGTGCGAAACATCCGGAAT-G
*
54284613 CACTTAGCGTGC-AAGACATC
1 CACTTAGTGTGCGAA-ACATC
54284633 GATTGTGCAG
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
27 4 0.06
28 56 0.89
29 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (27 bp):
CACTTAGTGTGCGAAACATCCGGAATG
Found at i:54284619 original size:56 final size:56
Alignment explanation
Indices: 54284447--54284606 Score: 245
Period size: 54 Copynumber: 2.9 Consensus size: 56
54284437 AAACGAACGG
54284447 CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGC-AAGACATCCGAAATGA
1 CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGCGAA-ACATCCGAAATGA
** * *
54284503 CAC--AGTGTATGAAGTATTGATGATGACACTTAGTGTGCGAAACATCCGAAATGA
1 CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGCGAAACATCCGAAATGA
*
54284557 CACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGAAACATCCG
1 CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGCGAAACATCCG
54284607 GTATAGCACT
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
54 47 0.51
55 2 0.02
56 43 0.47
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (56 bp):
CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGCGAAACATCCGAAATGA
Found at i:54284634 original size:56 final size:56
Alignment explanation
Indices: 54284447--54284634 Score: 179
Period size: 56 Copynumber: 3.4 Consensus size: 56
54284437 AAACGAACGG
* * * *
54284447 CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGC-AAGACATCCGAAATGA
1 CACTTAGCGTGCGAAGCATCGAGGATGACACTTAGTGTGCGAA-ACATCCGAAATGA
* ** * * *
54284503 CAC--AGTGTATGAAGTATTGATGATGACACTTAGTGTGCGAAACATCCGAAATGA
1 CACTTAGCGTGCGAAGCATCGAGGATGACACTTAGTGTGCGAAACATCCGAAATGA
* * * **
54284557 CACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGAAACATCCGGTAT-A
1 CACTTAGCGTGCGAAGCATCGAGGATGACACTTAGTGTGCGAAACATCCGAAATGA
54284612 GCACTTAGCGTGC-AAGACATCGA
1 -CACTTAGCGTGCGAAG-CATCGA
54284635 TTGTGCAGCG
Statistics
Matches: 114, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
54 47 0.41
55 6 0.05
56 61 0.54
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (56 bp):
CACTTAGCGTGCGAAGCATCGAGGATGACACTTAGTGTGCGAAACATCCGAAATGA
Found at i:54288255 original size:96 final size:96
Alignment explanation
Indices: 54288119--54288295 Score: 291
Period size: 96 Copynumber: 1.8 Consensus size: 96
54288109 CGGCGGTGTC
* *
54288119 TCTACCCGTGTGTTTATTACCATGCATACTGACTTGAAATTTTTATGTGCAGAGGACACACGGTC
1 TCTACCCGTGTGTTTACTACCATGCATACTGACTTGAAATTTTTACGTGCAGAGGACACACGGTC
* *
54288184 GGACAACATGCCCATGACACATGCCCTTGTG
66 AGACAACACGCCCATGACACATGCCCTTGTG
* * *
54288215 TCTACCCGTGTGTTTACTACCATGCATACTGACTTTAAATTTTTACGTGTAGGGGACACACGGTC
1 TCTACCCGTGTGTTTACTACCATGCATACTGACTTGAAATTTTTACGTGCAGAGGACACACGGTC
54288280 AGACAACACGCCCATG
66 AGACAACACGCCCATG
54288296 GGGCTAGTCA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (96 bp):
TCTACCCGTGTGTTTACTACCATGCATACTGACTTGAAATTTTTACGTGCAGAGGACACACGGTC
AGACAACACGCCCATGACACATGCCCTTGTG
Found at i:54320305 original size:16 final size:16
Alignment explanation
Indices: 54320284--54320315 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54320274 TTGTAAAAAT
54320284 GAGTCTAGTCCTCGTA
1 GAGTCTAGTCCTCGTA
54320300 GAGTCTAGTCCTCGTA
1 GAGTCTAGTCCTCGTA
54320316 CACCTTGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (16 bp):
GAGTCTAGTCCTCGTA
Found at i:54320465 original size:30 final size:31
Alignment explanation
Indices: 54320426--54320483 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
54320416 ATAGACCACA
*
54320426 TTTTGGCAAAATGACCATTTTTCCCCTAGGC
1 TTTTGGCAAAATGACCATTTTACCCCTAGGC
* *
54320457 TTTT-GCAAAATTACGATTTTACCCCTA
1 TTTTGGCAAAATGACCATTTTACCCCTA
54320484 TGTTCGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (31 bp):
TTTTGGCAAAATGACCATTTTACCCCTAGGC
Found at i:54328623 original size:39 final size:40
Alignment explanation
Indices: 54328524--54328667 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
54328514 CGAATGATGT
* * *
54328524 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAA
* * *
54328564 CCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-A
*
54328604 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
*
54328643 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54328668 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
39 34 0.39
40 43 0.49
41 10 0.11
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
Found at i:54328681 original size:40 final size:39
Alignment explanation
Indices: 54328576--54328674 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
54328566 AGACTAAGAT
** * *
54328576 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGC
1 CCGAAGGCATTTGAACGAGTTACTATA-ACCGGGCTAAGC
** *
54328615 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAG-C
54328655 CCGAAGGCATTTGAACGAGT
1 CCGAAGGCATTTGAACGAGT
54328675 AGCTATATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 33 0.62
40 20 0.38
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAGC
Found at i:54328686 original size:79 final size:80
Alignment explanation
Indices: 54328523--54328673 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 80
54328513 TCGAATGATG
*
54328523 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
**
54328588 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * * *
54328603 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCAGACTAAGAT-CCGAAGGCAT
54328665 TTGAACGAG
64 TTGAACGAG
54328674 TAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 41 0.68
80 18 0.30
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:54335215 original size:56 final size:56
Alignment explanation
Indices: 54335129--54335248 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
54335119 ACAAGGGATG
54335129 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
54335185 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
54335241 ATGGGCAA
1 ATGGGCAA
54335249 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:54336477 original size:40 final size:41
Alignment explanation
Indices: 54336418--54336569 Score: 211
Period size: 40 Copynumber: 3.8 Consensus size: 41
54336408 CATTTGAATG
* * *
54336418 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
54336458 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
*
54336498 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
* * *
54336538 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
54336570 TTGTGGTTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 99 0.97
41 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATT
Found at i:54336581 original size:80 final size:80
Alignment explanation
Indices: 54336418--54336589 Score: 213
Period size: 80 Copynumber: 2.2 Consensus size: 80
54336408 CATTTGAATG
* * * * *
54336418 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
54336483 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* *
54336498 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGC
** *
54336562 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
54336578 ATATCC-GGCTAA
1 ATATCCGGGCTAA
54336590 ATTCCGAAGA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 6 0.08
80 71 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:54340396 original size:16 final size:17
Alignment explanation
Indices: 54340377--54340408 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54340367 TTTAATTTTA
54340377 TTCAATTATTT-AATTC
1 TTCAATTATTTGAATTC
54340393 TTCAATTATTTGAATT
1 TTCAATTATTTGAATT
54340409 ATTAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.56
Consensus pattern (17 bp):
TTCAATTATTTGAATTC
Found at i:54353632 original size:15 final size:16
Alignment explanation
Indices: 54353611--54353653 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
54353601 TTCTATAGTC
54353611 TTCTATAGTTTCACAA
1 TTCTATAGTTTCACAA
*
54353627 -TCTATAGTTTTTACAA
1 TTCTATAG-TTTCACAA
54353643 TTCTATAGTTT
1 TTCTATAGTTT
54353654 TCAAAGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 10 0.42
17 7 0.29
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (16 bp):
TTCTATAGTTTCACAA
Found at i:54353649 original size:17 final size:17
Alignment explanation
Indices: 54353611--54353656 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
54353601 TTCTATAGTC
54353611 TTCTATAG-TTTCACAA
1 TTCTATAGTTTTCACAA
*
54353627 -TCTATAGTTTTTACAA
1 TTCTATAGTTTTCACAA
54353643 TTCTATAGTTTTCA
1 TTCTATAGTTTTCA
54353657 AAGTCTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 7 0.27
16 7 0.27
17 12 0.46
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (17 bp):
TTCTATAGTTTTCACAA
Done.