Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 18 of 141
Found at i:5374497 original size:27 final size:27
Alignment explanation
Indices: 5374440--5374642 Score: 178
Period size: 27 Copynumber: 7.5 Consensus size: 27
5374430 CTTTAGGGGC
* **
5374440 ATTTCGGTTATTTTA-CCTTATAGGGGT
1 ATTTCGGTAATTTTACCCTTCGA-GGGT
* * *
5374467 ATTTTGGTCATTTTACCCTTCGAGGGC
1 ATTTCGGTAATTTTACCCTTCGAGGGT
*
5374494 ATTTCGATAATTTTA-CCTATCGAGGGT
1 ATTTCGGTAATTTTACCCT-TCGAGGGT
* * *
5374521 ATTTCAGTAACTTTACCCATC-AGGGGT
1 ATTTCGGTAATTTTACCCTTCGA-GGGT
* * * *
5374548 ATTTCGGTGATTTTACCTTTTGAGGGC
1 ATTTCGGTAATTTTACCCTTCGAGGGT
* *
5374575 ATTTCAGTAATTTTACCCTTTGAGGGT
1 ATTTCGGTAATTTTACCCTTCGAGGGT
* * *
5374602 ATTTCGATAATTTTACCCATCAAGGGT
1 ATTTCGGTAATTTTACCCTTCGAGGGT
*
5374629 ATTTAGGTAATTTT
1 ATTTCGGTAATTTT
5374643 TGGCCCAAGC
Statistics
Matches: 140, Mismatches: 31, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
26 4 0.03
27 128 0.91
28 8 0.06
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (27 bp):
ATTTCGGTAATTTTACCCTTCGAGGGT
Found at i:5374521 original size:54 final size:54
Alignment explanation
Indices: 5374436--5374642 Score: 204
Period size: 54 Copynumber: 3.8 Consensus size: 54
5374426 TACTCTTTAG
* * * ** *
5374436 GGGCATTTCGGTTATTTTACCTTATAG-GGGTATTTTGGTCATTTTACCCTTCGA
1 GGGCATTTCGATAATTTTACC-TATCGAGGGTATTTCAGTAATTTTACCCTTCGA
* *
5374490 GGGCATTTCGATAATTTTACCTATCGAGGGTATTTCAGTAACTTTACCCATC-A
1 GGGCATTTCGATAATTTTACCTATCGAGGGTATTTCAGTAATTTTACCCTTCGA
* * * * * * *
5374543 GGGGTATTTCGGTGATTTTACCTTTTGAGGGCATTTCAGTAATTTTACCCTTTGA
1 -GGGCATTTCGATAATTTTACCTATCGAGGGTATTTCAGTAATTTTACCCTTCGA
* * *
5374598 GGGTATTTCGATAATTTTACCCATCAAGGGTATTT-AGGTAATTTT
1 GGGCATTTCGATAATTTTACCTATCGAGGGTATTTCA-GTAATTTT
5374643 TGGCCCAAGC
Statistics
Matches: 125, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
53 6 0.05
54 118 0.94
55 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.42
Consensus pattern (54 bp):
GGGCATTTCGATAATTTTACCTATCGAGGGTATTTCAGTAATTTTACCCTTCGA
Found at i:5374575 original size:81 final size:81
Alignment explanation
Indices: 5374461--5374642 Score: 235
Period size: 81 Copynumber: 2.2 Consensus size: 81
5374451 TTTACCTTAT
* *
5374461 AGGGGTATTTTGGTCATTTTACCCTTCGAGGGCATTTC-GATAATTTTA-CCTATCGAGGGTATT
1 AGGGGTATTTAGGTAATTTTACCCTTCGAGGGCATTTCAG-TAATTTTACCCT-TCGAGGGTATT
5374524 TC-AGTAACTTTACCCATC
64 TCGA-TAACTTTACCCATC
* * * * *
5374542 AGGGGTATTTCGGTGATTTTACCTTTTGAGGGCATTTCAGTAATTTTACCCTTTGAGGGTATTTC
1 AGGGGTATTTAGGTAATTTTACCCTTCGAGGGCATTTCAGTAATTTTACCCTTCGAGGGTATTTC
*
5374607 GATAATTTTACCCATC
66 GATAACTTTACCCATC
*
5374623 AAGGGTATTTAGGTAATTTT
1 AGGGGTATTTAGGTAATTTT
5374643 TGGCCCAAGC
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
81 84 0.94
82 5 0.06
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.41
Consensus pattern (81 bp):
AGGGGTATTTAGGTAATTTTACCCTTCGAGGGCATTTCAGTAATTTTACCCTTCGAGGGTATTTC
GATAACTTTACCCATC
Found at i:5376563 original size:20 final size:20
Alignment explanation
Indices: 5376521--5376585 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
5376511 CCCCTGAATA
* *
5376521 CACTTCGGTGT-CCTTGTTTG
1 CACTTCGGT-TCCCTTATTCG
5376541 CACTTCGGTTCTCC-TATTCG
1 CACTTCGGTTC-CCTTATTCG
* * *
5376561 CACATCTGTTCCCTTATTTG
1 CACTTCGGTTCCCTTATTCG
5376581 CACTT
1 CACTT
5376586 TGATGTCCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 3 0.08
20 31 0.86
21 2 0.06
ACGTcount: A:0.11, C:0.31, G:0.15, T:0.43
Consensus pattern (20 bp):
CACTTCGGTTCCCTTATTCG
Found at i:5390841 original size:13 final size:13
Alignment explanation
Indices: 5390823--5390858 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
5390813 ACGAGATTGT
5390823 AAAAAAAATTTGA
1 AAAAAAAATTTGA
5390836 AAAAAAAATTTGA
1 AAAAAAAATTTGA
5390849 AAAAAAAATT
1 AAAAAAAATT
5390859 AATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:5391871 original size:15 final size:16
Alignment explanation
Indices: 5391851--5391882 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5391841 AGAAAATGAA
5391851 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
5391866 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
5391882 A
1 A
5391883 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:5399219 original size:29 final size:29
Alignment explanation
Indices: 5399186--5399258 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
5399176 ATGTATTAGT
*
5399186 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
5399215 TTAGGACATATTTAAAACACTTAAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
5399244 TTAGGACATATTTAA
1 TTAGGACATATTTAA
5399259 TAATATCTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACTTAAACTAA
Found at i:5403966 original size:28 final size:29
Alignment explanation
Indices: 5403908--5403979 Score: 119
Period size: 28 Copynumber: 2.5 Consensus size: 29
5403898 ATGTATTAGT
*
5403908 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
*
5403937 TTAGGAAATATTTAAAA-ACTTAAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
5403965 TTAGGACATATTTAA
1 TTAGGACATATTTAA
5403980 TAATATCTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 24 0.60
29 16 0.40
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACTTAAACTAA
Found at i:5405088 original size:39 final size:40
Alignment explanation
Indices: 5405034--5405147 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 40
5405024 ATGTGTTTTT
** *
5405034 AGGGGTACTAAAGTATAAACAGGGGCATATATGTG-ATTA
1 AGGGGTACCGAAGTATAAACAGGGGCACATATGTGCATTA
* * *
5405073 AGGGGTACCGCAGTATAAACAGGGGCACGTATGTGCATTC
1 AGGGGTACCGAAGTATAAACAGGGGCACATATGTGCATTA
* *
5405113 TGGGGTACCGAAGTACAAACAGGGGCACATATGTG
1 AGGGGTACCGAAGTATAAACAGGGGCACATATGTG
5405148 TATTCATTCA
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
39 30 0.47
40 34 0.53
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.21
Consensus pattern (40 bp):
AGGGGTACCGAAGTATAAACAGGGGCACATATGTGCATTA
Found at i:5419865 original size:3 final size:3
Alignment explanation
Indices: 5419857--5419896 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
5419847 TAACATTTAC
* * *
5419857 AGA AGA AGA AGA AGA ATA AGA AGA ATA AGA TGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5419897 CCTTTTTCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (3 bp):
AGA
Found at i:5443441 original size:41 final size:41
Alignment explanation
Indices: 5443364--5443547 Score: 174
Period size: 41 Copynumber: 4.5 Consensus size: 41
5443354 CTTACCTTTC
* * ** *
5443364 GGGGTTTTGGCGGTGTTTTCAAAAAAGCGTCGCTAATGCTT
1 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTT
* * * *
5443405 GGGGCTTTAGCGGTGTTTTTGAAAATGCGCCTCTAATGCTT
1 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTT
** * *
5443446 GGGGTTTTAATGGCATTTTTG-AAAAGCGTCGCTAATG-TT
1 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTT
* * * * *
5443485 CGGTGTTTTAGCAGCATTTTTTAAAAAGCGCCGCTAATGCTA
1 -GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTT
*
5443527 GGGGTTTTAGAGGCGTTTTTG
1 GGGGTTTTAGCGGCGTTTTTG
5443548 TGCTGGGGGC
Statistics
Matches: 113, Mismatches: 27, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.02
40 29 0.26
41 81 0.72
42 1 0.01
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.36
Consensus pattern (41 bp):
GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTT
Found at i:5443481 original size:81 final size:81
Alignment explanation
Indices: 5443386--5443535 Score: 203
Period size: 81 Copynumber: 1.9 Consensus size: 81
5443376 GTGTTTTCAA
* ** * * *
5443386 AAAAGCGTCGCTAATGCTT-GGGGCTTTAGCGGTGTTTTTGAAAATGCGCCTCTAATGCTTGGGG
1 AAAAGCGTCGCTAATG-TTCGGGGCTTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTAGGGG
5443450 TTTTAATGGCATTTTTG
65 TTTTAATGGCATTTTTG
* * *
5443467 AAAAGCGTCGCTAATGTTCGGTGTTTTAGCAGCATTTTTTAAAAAGCGCCGCTAATGCTAGGGGT
1 AAAAGCGTCGCTAATGTTCGGGGCTTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTAGGGGT
5443532 TTTA
66 TTTA
5443536 GAGGCGTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.03
81 57 0.97
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (81 bp):
AAAAGCGTCGCTAATGTTCGGGGCTTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTAGGGGT
TTTAATGGCATTTTTG
Found at i:5443556 original size:26 final size:26
Alignment explanation
Indices: 5443522--5443572 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
5443512 GCGCCGCTAA
*
5443522 TGCTAGGGGTTTTAGAGGCGTTTTTG
1 TGCTAGGGGCTTTAGAGGCGTTTTTG
* * *
5443548 TGCTGGGGGCTTTAGCGGTGTTTTT
1 TGCTAGGGGCTTTAGAGGCGTTTTT
5443573 AAAAAAGCGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.08, C:0.10, G:0.39, T:0.43
Consensus pattern (26 bp):
TGCTAGGGGCTTTAGAGGCGTTTTTG
Found at i:5443579 original size:189 final size:190
Alignment explanation
Indices: 5443364--5443737 Score: 471
Period size: 189 Copynumber: 2.0 Consensus size: 190
5443354 CTTACCTTTC
* * * * **
5443364 GGGGTTTTGGCGGTGTTTTCAAAAAAGCGTCGCTAATGCTTGGGGCTTTAGCGGTGTTTTTGAAA
1 GGGGCTTTAGCGGTGTTTTCAAAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCATTTTTGAAA
* * * * ** * * *
5443429 ATGCGCCTCTAATGCTTGGGGTTTTAATGGCATTTTTGA-AAAGCGTCGCTAATGTTCGGTGTTT
66 AAGCGCCGCTAATGCTCGGGGTTTTAACGGCATTTTTGAGAAAGCACCACTAATGCTCGGGGTTT
* * *
5443493 TAGCAGCATTTTTTAAAAAGCGCCGCTAATGCTAGGGGTTTTAGAGGCGTTTTTGTGCTG
131 TAGCAGCATTTTTTAAAAAGCGCCACTAATGCTAGGGGCTTTAGAGGCATTTTTGTGCTG
* * * *
5443553 GGGGCTTTAGCGGTGTTTTTAAAAAAGCGCCGCTAATGCTCGGTGTTTTAGCGGCATTTTTTAAA
1 GGGGCTTTAGCGGTGTTTTCAAAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCATTTTTGAAA
* * *
5443618 AAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTTAGAAAGCACCACTAATGCTCGGGGTTT
66 AAGCGCCGCTAATGCTCGGGGTTTTAACGGCATTTTTGAGAAAGCACCACTAATGCTCGGGGTTT
* * * * *
5443683 TAGCGGCATTTTTTAGAAAGCTCCACTAATGCTCGGGGCTTTAGCGGCATTTTTG
131 TAGCAGCATTTTTTAAAAAGCGCCACTAATGCTAGGGGCTTTAGAGGCATTTTTG
5443738 GAAAAGCGCC
Statistics
Matches: 154, Mismatches: 30, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
189 87 0.56
190 67 0.44
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.35
Consensus pattern (190 bp):
GGGGCTTTAGCGGTGTTTTCAAAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCATTTTTGAAA
AAGCGCCGCTAATGCTCGGGGTTTTAACGGCATTTTTGAGAAAGCACCACTAATGCTCGGGGTTT
TAGCAGCATTTTTTAAAAAGCGCCACTAATGCTAGGGGCTTTAGAGGCATTTTTGTGCTG
Found at i:5443603 original size:41 final size:41
Alignment explanation
Indices: 5443548--5443793 Score: 303
Period size: 41 Copynumber: 6.0 Consensus size: 41
5443538 GGCGTTTTTG
* * ** *
5443548 TGCTGGGGGCTTTAGCGGTGTTTTTAAAAAAGCGCCGCTAA
1 TGCTCGGGGTTTTAGCGGCATTTTTTAAAAAGCGCCGCTAA
*
5443589 TGCTCGGTGTTTTAGCGGCATTTTTTAAAAAGCGCCGCTAA
1 TGCTCGGGGTTTTAGCGGCATTTTTTAAAAAGCGCCGCTAA
* * * *
5443630 TGCTCGGGGTTTTAGCGGCGTTTTTTAGAAAGCACCACTAA
1 TGCTCGGGGTTTTAGCGGCATTTTTTAAAAAGCGCCGCTAA
* * *
5443671 TGCTCGGGGTTTTAGCGGCATTTTTTAGAAAGCTCCACTAA
1 TGCTCGGGGTTTTAGCGGCATTTTTTAAAAAGCGCCGCTAA
* **
5443712 TGCTCGGGGCTTTAGCGGCATTTTTGGAAAAGCGCCGCTAA
1 TGCTCGGGGTTTTAGCGGCATTTTTTAAAAAGCGCCGCTAA
* * * * *
5443753 TGCTAGGGGCTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAA
1 TGCTCGGGGTTTTAGCGGCATTTTTTAAAAAGCGCCGCTAA
5443794 AAACATTTTA
Statistics
Matches: 182, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 182 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (41 bp):
TGCTCGGGGTTTTAGCGGCATTTTTTAAAAAGCGCCGCTAA
Found at i:5443680 original size:149 final size:148
Alignment explanation
Indices: 5443400--5443695 Score: 403
Period size: 149 Copynumber: 2.0 Consensus size: 148
5443390 GCGTCGCTAA
* * * * * *
5443400 TGCTTGGGGCTTTAGCGGTGTTTTTGAAAATGCGCCTCTAATGCTTGGGGTTTTAATGGCATTTT
1 TGCTGGGGGCTTTAGCGGTGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGTTTTAACGGCATTTT
* * * * * *
5443465 TGAAAAGCGTCGCTAATGTTCGGTGTTTTAGCAGCATTTTTTAAAAAGCGCCGCTAATGCTAGGG
66 TAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCAGCATTTTTTAAAAAGCACCACTAATGCTAGGG
*
5443530 GTTTTAGAGGCGTTTTTG
131 GTTTTAGAGGCATTTTTG
* *
5443548 TGCTGGGGGCTTTAGCGGTGTTTTTAAAAAAGCGCCGCTAATGCTCGGTGTTTTAGCGGCATTTT
1 TGCTGGGGGCTTTAGCGGTGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGTTTTAACGGCA-TTT
* * * *
5443613 TTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTTAGAAAGCACCACTAATGCTCGG
65 TTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCAGCATTTTTTAAAAAGCACCACTAATGCTAGG
*
5443678 GGTTTTAGCGGCATTTTT
130 GGTTTTAGAGGCATTTTT
5443696 TAGAAAGCTC
Statistics
Matches: 127, Mismatches: 20, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
148 53 0.42
149 74 0.58
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (148 bp):
TGCTGGGGGCTTTAGCGGTGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGTTTTAACGGCATTTT
TAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCAGCATTTTTTAAAAAGCACCACTAATGCTAGGG
GTTTTAGAGGCATTTTTG
Found at i:5444179 original size:15 final size:14
Alignment explanation
Indices: 5444141--5444175 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
5444131 ACTATTTTAA
5444141 GGTTTAGGGAGTAT
1 GGTTTAGGGAGTAT
*
5444155 GGATTTAGGGATTAT
1 GG-TTTAGGGAGTAT
5444170 GGTTTA
1 GGTTTA
5444176 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGAGTAT
Found at i:5444198 original size:7 final size:7
Alignment explanation
Indices: 5444186--5444222 Score: 56
Period size: 8 Copynumber: 5.0 Consensus size: 7
5444176 AGGGTTGGGA
5444186 TTTAAGG
1 TTTAAGG
5444193 TTTAAGG
1 TTTAAGG
5444200 TTTAGAGG
1 TTTA-AGG
5444208 TTTAGAGG
1 TTTA-AGG
5444216 TTTAAGG
1 TTTAAGG
5444223 GTTAGACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 14 0.48
8 15 0.52
ACGTcount: A:0.27, C:0.00, G:0.32, T:0.41
Consensus pattern (7 bp):
TTTAAGG
Found at i:5444209 original size:28 final size:27
Alignment explanation
Indices: 5444136--5444209 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 27
5444126 GAGTTACTAT
* *
5444136 TTTAAGGTTTAGGGAGTATGGATTTAGGG
1 TTTAAGGTTTAGAG-GT-TGGATTTAAGG
* *
5444165 ATTATGGTTTA-AGGGTTGGGATTTAAGG
1 TTTAAGGTTTAGA-GGTT-GGATTTAAGG
5444193 TTTAAGGTTTAGAGGTT
1 TTTAAGGTTTAGAGGTT
5444210 TAGAGGTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
27 1 0.03
28 24 0.67
29 11 0.31
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (27 bp):
TTTAAGGTTTAGAGGTTGGATTTAAGG
Found at i:5444227 original size:23 final size:23
Alignment explanation
Indices: 5444170--5444262 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 23
5444160 TAGGGATTAT
5444170 GGTTTAAGGGTT-G-GGATTTAA
1 GGTTTAAGGGTTAGAGGATTTAA
*
5444191 GGTTTAAGGTTTAGAGG-TTTAGA
1 GGTTTAAGGGTTAGAGGATTTA-A
* *
5444214 GGTTTAAGGGTTAGA-CA-TTAG
1 GGTTTAAGGGTTAGAGGATTTAA
* * *
5444235 GGGTTAAGAGTTA-AGGATTTAG
1 GGTTTAAGGGTTAGAGGATTTAA
5444257 GGTTTA
1 GGTTTA
5444263 GGTATTCAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
20 1 0.02
21 23 0.40
22 17 0.29
23 17 0.29
ACGTcount: A:0.27, C:0.01, G:0.35, T:0.37
Consensus pattern (23 bp):
GGTTTAAGGGTTAGAGGATTTAA
Found at i:5444473 original size:14 final size:15
Alignment explanation
Indices: 5444438--5444484 Score: 71
Period size: 14 Copynumber: 3.3 Consensus size: 15
5444428 TATTTTAAGG
*
5444438 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
5444453 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
5444468 -TTAGGGATTATGG-
1 TTTAGGGATTATGGA
5444481 TTTA
1 TTTA
5444485 AGTGTTAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 16 0.53
15 14 0.47
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:5444512 original size:21 final size:22
Alignment explanation
Indices: 5444431--5444512 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 22
5444421 GAGTTCATAT
*
5444431 TTTAAGGTTTAGGGAG-TATGGA
1 TTTAAGGTTTAGGG-GTTAGGGA
* * * *
5444453 TTTAGGGATTATGGATTAGGGA
1 TTTAAGGTTTAGGGGTTAGGGA
* * *
5444475 -TTATGGTTTAAGTGTTA-GGA
1 TTTAAGGTTTAGGGGTTAGGGA
5444495 TTTAAGGTTTAGGGGTTA
1 TTTAAGGTTTAGGGGTTA
5444513 AGAGTTAGGG
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
20 3 0.07
21 26 0.58
22 16 0.36
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (22 bp):
TTTAAGGTTTAGGGGTTAGGGA
Found at i:5444527 original size:21 final size:21
Alignment explanation
Indices: 5444503--5444543 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5444493 GATTTAAGGT
* *
5444503 TTAGGGGTTAAGAGTTAGGGG
1 TTAGAGGTTAAGAGCTAGGGG
5444524 TTAGAGGTTAAGAGCTAGGG
1 TTAGAGGTTAAGAGCTAGGG
5444544 ATTTAGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.02, G:0.44, T:0.27
Consensus pattern (21 bp):
TTAGAGGTTAAGAGCTAGGGG
Found at i:5444606 original size:295 final size:295
Alignment explanation
Indices: 5444076--5444659 Score: 851
Period size: 295 Copynumber: 2.0 Consensus size: 295
5444066 TATAGTTTAG
** ** *
5444076 GGTTTTTGGTTTAAGGTATATGATTTATTTAAGATTTAAGGCCGATTTAAGAGTTACTATTTTAA
1 GGTTTTTAATTTAAGGTATATGATAAATTTAAGATTTAAGACCGATTTAAGAGTTACTATTTTAA
*
5444141 GGTTTAGGGAGTATGGATTTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTAAGGTTTAGA
66 GGTTTAGGGAGTATGGATTTAGGGATTATGGATTAAGGGTTGGGATTTAAGGTTTAAGGTTTAGA
* * * * *
5444206 GGTTTAGAGGTTTAAGGGTTAGACATTAGGGGTTAAGAGTTAAGGATTTAGGGTTTAGGTATTCA
131 GGTTTAGAGGGTTAAGAGTTAGACATTAGAGGTTAAGAGCTAAGGATTTAGGGTTTAGGGATTCA
5444271 GGGTCAAGTTAGGGTTTTGGGTTTAGATTAATTATTTTTTAACTTATATTTTAAATATGTTATTA
196 GGGTCAAGTTAGGGTTTTGGGTTTAGATTAATTATTTTTTAACTTATATTTTAAATATGTTATTA
5444336 TATAATTGTAAAAGAGATAATAATAAATTTTTTTT
261 TATAATTGTAAAAGAGATAATAATAAATTTTTTTT
* *
5444371 GGTTTTTAATTTAGGGTATATGATAAATTTAAGATTTAAGACC-AGTTTAGGAGTT-CATATTTT
1 GGTTTTTAATTTAAGGTATATGATAAATTTAAGATTTAAGACCGA-TTTAAGAGTTAC-TATTTT
*
5444434 AAGGTTTAGGGAGTATGGATTTAGGGATTATGGATT-AGGGATTATGG-TTTAA-GTGTT-AGGA
64 AAGGTTTAGGGAGTATGGATTTAGGGATTATGGATTAAGGG-TT-GGGATTTAAGGT-TTAAGG-
*** * *
5444495 TTTA-AGGTTTAG-GGGTTAAGAGTTAGGGGTTAGAGGTTAAGAGCTAGGGATTTAGTGTTTAGG
125 TTTAGAGGTTTAGAGGGTTAAGAGTTAGACATTAGAGGTTAAGAGCTAAGGATTTAGGGTTTAGG
*
5444558 GATTCAAGGGTCAAGTTAGGGTTTTGGGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATA
190 GATTC-AGGGTCAAGTTAGGGTTTTGGGTTTAGATTAATTA-TTTTTTAACTTATATTTTAAATA
*
5444623 TGTTCTTATATAATTGTAAAAGAGATAATAATAAATT
253 TGTTATTATATAATTGTAAAAGAGATAATAATAAATT
5444660 AAATATATTG
Statistics
Matches: 260, Mismatches: 21, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
293 46 0.18
294 54 0.21
295 158 0.61
296 2 0.01
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.42
Consensus pattern (295 bp):
GGTTTTTAATTTAAGGTATATGATAAATTTAAGATTTAAGACCGATTTAAGAGTTACTATTTTAA
GGTTTAGGGAGTATGGATTTAGGGATTATGGATTAAGGGTTGGGATTTAAGGTTTAAGGTTTAGA
GGTTTAGAGGGTTAAGAGTTAGACATTAGAGGTTAAGAGCTAAGGATTTAGGGTTTAGGGATTCA
GGGTCAAGTTAGGGTTTTGGGTTTAGATTAATTATTTTTTAACTTATATTTTAAATATGTTATTA
TATAATTGTAAAAGAGATAATAATAAATTTTTTTT
Found at i:5444884 original size:21 final size:21
Alignment explanation
Indices: 5444860--5444899 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5444850 TAGGGATTAT
*
5444860 GGTTTATGATTTAAGGGTTGG
1 GGTTTAAGATTTAAGGGTTGG
*
5444881 GGTTTAAGGTTTAAGGGTT
1 GGTTTAAGATTTAAGGGTT
5444900 AGAGATTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTTAAGATTTAAGGGTTGG
Found at i:5444964 original size:7 final size:7
Alignment explanation
Indices: 5444848--5445008 Score: 53
Period size: 7 Copynumber: 22.7 Consensus size: 7
5444838 GGATTATAGT
5444848 TTTAGGG
1 TTTAGGG
* *
5444855 ATTATGG
1 TTTAGGG
* *
5444862 TTTATGA
1 TTTAGGG
5444869 TTTAAGGG
1 TTT-AGGG
*
5444877 -TTGGGG
1 TTTAGGG
*
5444883 TTTAAGG
1 TTTAGGG
5444890 TTTAAGGG
1 TTT-AGGG
*
5444898 -TTAGAG
1 TTTAGGG
* *
5444904 ATTAGAG
1 TTTAGGG
*
5444911 ATTAGGG
1 TTTAGGG
* *
5444918 GTCATGGG
1 TTTA-GGG
5444926 TTTAGGAG
1 TTTAGG-G
5444934 -TTAGGG
1 TTTAGGG
* *
5444940 TTTATGT
1 TTTAGGG
* *
5444947 TTTATGA
1 TTTAGGG
5444954 TTTAGGG
1 TTTAGGG
5444961 TTTAGGAG
1 TTTAGG-G
*
5444969 -ATAGGAG
1 TTTAGG-G
*
5444976 TTAAGGG
1 TTTAGGG
*
5444983 -GTAGGGG
1 TTTA-GGG
5444990 TTTAGGG
1 TTTAGGG
5444997 TTTAGGG
1 TTTAGGG
5445004 TTTAG
1 TTTAG
5445009 ATTAATTGGT
Statistics
Matches: 116, Mismatches: 27, Indels: 22
0.70 0.16 0.13
Matches are distributed among these distances:
6 8 0.07
7 91 0.78
8 17 0.15
ACGTcount: A:0.23, C:0.01, G:0.38, T:0.39
Consensus pattern (7 bp):
TTTAGGG
Found at i:5453772 original size:15 final size:15
Alignment explanation
Indices: 5453752--5453802 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
5453742 ACTTTCATCA
5453752 TTCTTTTCATTCTTT
1 TTCTTTTCATTCTTT
*
5453767 TTCTTTTCACTCTTT
1 TTCTTTTCATTCTTT
*
5453782 TT-GTTTC-TCTCTTT
1 TTCTTTTCAT-TCTTT
5453796 TTCTTTT
1 TTCTTTT
5453803 TCTCGCTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.73
Consensus pattern (15 bp):
TTCTTTTCATTCTTT
Found at i:5453788 original size:14 final size:15
Alignment explanation
Indices: 5453756--5453798 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
5453746 TCATCATTCT
* *
5453756 TTTCATTCTTTTTCT
1 TTTCACTCTTTTTCG
5453771 TTTCACTCTTTTT-G
1 TTTCACTCTTTTTCG
*
5453785 TTTCTCTCTTTTTC
1 TTTCACTCTTTTTC
5453799 TTTTTCTCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTCACTCTTTTTCG
Found at i:5453806 original size:14 final size:14
Alignment explanation
Indices: 5453762--5453806 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5453752 TTCTTTTCAT
*
5453762 TCTTTTTCTTTTCAC
1 TCTTTTTCTTTT-TC
* *
5453777 TCTTTTTGTTTCTC
1 TCTTTTTCTTTTTC
5453791 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
5453805 TC
1 TC
5453807 GCTCGATAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (14 bp):
TCTTTTTCTTTTTC
Found at i:5455906 original size:13 final size:12
Alignment explanation
Indices: 5455888--5455919 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
5455878 ACACAAAAAT
5455888 TTTTTTTTTCGAA
1 TTTTTTTTTC-AA
5455901 TTTTTTTTTCAA
1 TTTTTTTTTCAA
5455913 TTTTTTT
1 TTTTTTT
5455920 ACAATCTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:5463018 original size:50 final size:50
Alignment explanation
Indices: 5462900--5463010 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
5462890 AGAGGTCCCA
* * * ** *
5462900 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGATGTCCCC
1 TGTAAGACCATGTCTGGGACATAGCATGGGCACCGAGATGAGAACTCCAC
* * * *
5462950 CGTAAGACGATGTCTGGGACATAGCATGGGCACCGATATGAGAACTCCAG
1 TGTAAGACCATGTCTGGGACATAGCATGGGCACCGAGATGAGAACTCCAC
5463000 TGTAAGACCAT
1 TGTAAGACCAT
5463011 ATTTGGGATA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATAGCATGGGCACCGAGATGAGAACTCCAC
Found at i:5467182 original size:40 final size:40
Alignment explanation
Indices: 5467082--5467346 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
5467072 GCTCCTCGTT
* * * *
5467082 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
5467122 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
5467161 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
5467201 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
5467241 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
5467281 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
5467322 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
5467347 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:5467306 original size:80 final size:80
Alignment explanation
Indices: 5467049--5467346 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
5467039 AAATCACGTA
* ** * * *
5467049 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
5467111 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
5467127 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
5467190 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
5467207 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
5467271 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
5467287 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
5467347 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:5467355 original size:41 final size:41
Alignment explanation
Indices: 5467278--5467355 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
5467268 TTTGTATCTC
* * *
5467278 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
5467319 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
5467356 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:5473724 original size:50 final size:50
Alignment explanation
Indices: 5473614--5473799 Score: 171
Period size: 50 Copynumber: 3.7 Consensus size: 50
5473604 GGTAAAGAGG
* * * * **
5473614 TCCCATGTAAAACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGATG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAAC
** * * *
5473664 TCCCCCGTAAGACCATGTCTGGGACATAGCATGGGCACTGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAAC
* * * * * *
5473714 TCCAATGTAAGACCATATTTGGGATATGGCATTGGCAGT-ACA-GAAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAAC
*
5473762 ATCCCATGTAAGACCATGTCAT-GGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTC-TGGGACATGGCATTGGCA
5473800 TGTTATTATT
Statistics
Matches: 108, Mismatches: 26, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
48 5 0.05
49 32 0.30
50 71 0.66
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAAC
Found at i:5477382 original size:22 final size:22
Alignment explanation
Indices: 5477357--5477399 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5477347 AAGACCAATT
*
5477357 TTTCTCCTAAATTTTTATTTAG
1 TTTCTCCTAAATTTTAATTTAG
*
5477379 TTTCTCGTAAATTTTAATTTA
1 TTTCTCCTAAATTTTAATTTA
5477400 ACTATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTCTCCTAAATTTTAATTTAG
Found at i:5477452 original size:25 final size:24
Alignment explanation
Indices: 5477405--5477452 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
5477395 ATTTAACTAT
* *
5477405 TTAATTTTTAAATTTATTGAATTA
1 TTAATTTTTAAATTAATTAAATTA
*
5477429 TTAATATTTTATATTAATTAAATT
1 TTAAT-TTTTAAATTAATTAAATT
5477453 TTTGAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTAATTTTTAAATTAATTAAATTA
Found at i:5480817 original size:18 final size:19
Alignment explanation
Indices: 5480789--5480825 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5480779 GCATTCACAT
*
5480789 CTTTCCTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTATCCA
5480808 CTTT-CTCTCTTCTATCCA
1 CTTTCCTCTCTTCTATCCA
5480826 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.08, C:0.41, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTATCCA
Found at i:5483228 original size:21 final size:21
Alignment explanation
Indices: 5483203--5483251 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
5483193 CAGTTGAAAC
5483203 CACACGAAAAGAATTATCCGA
1 CACACGAAAAGAATTATCCGA
5483224 CACACGAAAAGAATTATCCGA
1 CACACGAAAAGAATTATCCGA
5483245 CACACGA
1 CACACGA
5483252 TTTAGAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.27, G:0.14, T:0.12
Consensus pattern (21 bp):
CACACGAAAAGAATTATCCGA
Found at i:5485487 original size:36 final size:36
Alignment explanation
Indices: 5485447--5485519 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
5485437 TTGAGAAAGG
5485447 AAGAATTCTCCATTTTTGCACATTGAGCATTCGGTT
1 AAGAATTCTCCATTTTTGCACATTGAGCATTCGGTT
5485483 AAGAATTCTCCATTTTTGCACATTGAGCATTCGGTT
1 AAGAATTCTCCATTTTTGCACATTGAGCATTCGGTT
5485519 A
1 A
5485520 TATCTCCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (36 bp):
AAGAATTCTCCATTTTTGCACATTGAGCATTCGGTT
Found at i:5487730 original size:33 final size:33
Alignment explanation
Indices: 5487662--5487731 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
5487652 CATAAAGATC
* *
5487662 TAAAATAAAATATTTGCAATATTTCAGTAATAA
1 TAAAATAAAATATTTGCAATATGTCAGAAATAA
*
5487695 TAAAATAAAATA-TTGTATATATGT-AGAAATAAA
1 TAAAATAAAATATTTGCA-ATATGTCAGAAAT-AA
5487728 TAAA
1 TAAA
5487732 CATGTAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (33 bp):
TAAAATAAAATATTTGCAATATGTCAGAAATAA
Found at i:5488954 original size:26 final size:26
Alignment explanation
Indices: 5488925--5488974 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
5488915 CCACATTAGC
* *
5488925 TGGGCTAGGTTAATTGGGTTTTTGTT
1 TGGGCTAGGTTAAGTGGGTATTTGTT
5488951 TGGGCTAGGTTAAGTGGGTATTTG
1 TGGGCTAGGTTAAGTGGGTATTTG
5488975 GGATCTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.14, C:0.04, G:0.38, T:0.44
Consensus pattern (26 bp):
TGGGCTAGGTTAAGTGGGTATTTGTT
Found at i:5489575 original size:44 final size:43
Alignment explanation
Indices: 5489488--5490334 Score: 281
Period size: 44 Copynumber: 19.6 Consensus size: 43
5489478 GATGCGATTT
* *
5489488 ACTGCAACTTC-AGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATTGCTTCAATCCGCTCC
* * *
5489532 ACTACAACTTCAAGGAGATAGGATTATTGGCTTCAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGATTATT-GCTTCAATCCGCTCC
* * * * *
5489576 ACTGCAACCTCAGGGAGATAAGA-T-TTGCTTTTTCAGTCTGCCCC
1 ACTGCAACTTCAAGGAGATAAGATTATTGC---TTCAATCCGCTCC
** * * ** *
5489620 ACTGTGACTTCAGAGG-GATAAGACTTGTT-TTCTCTGTCTGCTCC
1 ACTGCAACTTCA-AGGAGATAAGA-TTATTGCT-TCAATCCGCTCC
* ** * * * * *
5489664 ACTGCAACCTCAAGGAGATAAGA--CCTGATGCGATCCACTCT
1 ACTGCAACTTCAAGGAGATAAGATTATTGCTTCAATCCGCTCC
* * *
5489705 ACTACAACTTC-AGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATTGCTTCAATCCGCTCC
* * *
5489749 ACTACAACTTCAAGGAGA-AAGGATTATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAA-GATTAT-TGCTTCAATCCGCTCC
* * ** * * * * *
5489793 ACTGCAACCTCAGGGAGATAAGA--CCTGATGCGATCCACTCT
1 ACTGCAACTTCAAGGAGATAAGATTATTGCTTCAATCCGCTCC
* * *
5489834 ACTGCAACTTC-AGAGTGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATTGCTTCAATCCGCTCC
* * * * *
5489878 A---CAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGATTAT-TGCTTCAATCCGCTCC
* * * * *
5489919 ACTGCAACCTCAGGGAGATAAGATT-TGCTTCTTCGATCTG-TCCC
1 ACTGCAACTTCAAGGAGATAAGATTAT--TGCTTCAATCCGCT-CC
* * ** * * * * *
5489963 ACTGCAACTTCAGGGGGATAAGA--CCTGATGCGATCCACTCT
1 ACTGCAACTTCAAGGAGATAAGATTATTGCTTCAATCCGCTCC
* * *
5490004 ACTGCAACTTC-AGAGAGATAAGATCTATTACTTTAACCCGCTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATTGCTTCAATCCGCTCC
* * * * * *
5490048 ACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGATTAT-TGCTTCAATCCGCTCC
* * * * * *
5490092 ACTACAACCTCAAGGAGATAAGATTTTTCATCTTCGATCTG-TCCC
1 ACTGCAACTTCAAGGAGATAAGATTATT--GCTTCAATCCGCT-CC
* * * ** * * *
5490137 ACTGCAACTTCAGGGGGATAAAACCTGCTTAC-TCAGTCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGA--TTATTGCTTCAATCCGCTCC
* * * * * * *
5490181 GCTGCAACCTCAGGGAGATAAGACCTAATG---CGATCCACTCC
1 ACTGCAACTTCAAGGAGATAAGA-TTATTGCTTCAATCCGCTCC
* * * *
5490222 ACTTCAACTTC-AGAGAGATAAGATCTATTACTTTAACCCGCTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATTGCTTCAATCCGCTCC
* * * * * *
5490266 ACTACAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGATTAT-TGCTTCAATCCGCTCC
* *
5490310 ACTACAACCTC-AGAGAGATAAGATT
1 ACTGCAACTTCAAG-GAGATAAGATT
5490335 TACTATCTTC
Statistics
Matches: 585, Mismatches: 165, Indels: 106
0.68 0.19 0.12
Matches are distributed among these distances:
40 8 0.01
41 135 0.23
42 5 0.01
43 25 0.04
44 366 0.63
45 40 0.07
46 1 0.00
47 5 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
ACTGCAACTTCAAGGAGATAAGATTATTGCTTCAATCCGCTCC
Found at i:5489789 original size:217 final size:213
Alignment explanation
Indices: 5489348--5489815 Score: 733
Period size: 217 Copynumber: 2.2 Consensus size: 213
5489338 TGCTGTTGTA
* * * * *
5489348 GCTTCAATCTGTTCCACTAC-ACCGCCAGGAAAATAAGATTTGCTATTCTCAGTCTGCCCCACTG
1 GCTTCAATCTGCTCCACTGCAACC-TCAGGGAGATAAGATTTGCTATTCTCAGTCTGCCCCACTG
* * *
5489412 TAACTTCAGGGGGATAAGAGTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAGGGAGACAAGACC
65 TAACTTCAGAGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAAGGAGACAAGACC
*
5489477 TGATGCGATTTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTT
130 TGATGCGATTTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTT
* *
5489542 CAAGGAGATAGGATTATTG
195 CAAGGAGAAAGGATTATCG
*
5489561 GCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCT-TTTTCAGTCTGCCCCACTGT
1 GCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTATTCTCAGTCTGCCCCACTGT
* * *
5489625 GACTTCAGAGGGATAAGACTTGTTTTCTCTGTCTGCTCCACTGCAACCTCAAGGAGATAAGACCT
66 AACTTCAGAGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAAGGAGACAAGACCT
5489690 GATGCGATCCACTCTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACA
131 GATGCGAT----T-TACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACA
5489755 ACTTCAAGGAGAAAGGATTATCG
191 ACTTCAAGGAGAAAGGATTATCG
5489778 GCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGA
1 GCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGA
5489816 CCTGATGCGA
Statistics
Matches: 234, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
212 86 0.37
213 35 0.15
214 3 0.01
216 1 0.00
217 109 0.47
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (213 bp):
GCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTATTCTCAGTCTGCCCCACTGT
AACTTCAGAGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAAGGAGACAAGACCT
GATGCGATTTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTC
AAGGAGAAAGGATTATCG
Found at i:5489791 original size:129 final size:129
Alignment explanation
Indices: 5489656--5490332 Score: 548
Period size: 129 Copynumber: 5.2 Consensus size: 129
5489646 GTTTTCTCTG
*
5489656 TCTGCTCCACTGCAACCTCAAGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
*
5489721 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAAGGAGAAAGGATTATCGGCTTCAA
66 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAAAGGATTATCGGCTTCAA
* *
5489785 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGT
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
* *
5489850 GATAAGATCTATTACTTTAATCCGCT-C-C-ACAACTTTAGGGAGATAGGATTATCGGCTTCAA
66 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAAAGGATTATCGGCTTCAA
* ** * ** * *
5489911 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTTCTTCGAT-CTGTCCCACTGCAACTTCA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGA---CCTGATGCGATCCACT-CTACTACAACTTCA
* * * * * * * * * **
5489975 GGGGGATAAGACCTGA-TGC---GATCCACTCTACTGCAACTTCAGAGAGATAA-GATCTAT-TA
62 GAGAGATAAGATCT-ATTACTTTAATCCGCTCCACTACAACTTCAGGGAGA-AAGGAT-TATCGG
*
5490034 CTTTAA
124 CTTCAA
* * * * * * * * *
5490040 CCCGCTCCACTACAACTTCAGGGAGATAGGA--TTAT-CGGCCTCAATCTGCTCCACTACAACCT
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGC-G-ATCCA-CT-CT--ACTACAACTT
* ** * * *
5490102 CA-AGGAGATAAGAT-TTTTCATCTTCGATCTG-TCCCACTGCAACTTCAGGGGGATAA--A--A
60 CAGA-GAGATAAGATCTATT-A-CTTTAATCCGCT-CCACTACAACTTCAGGGAGA-AAGGATTA
* * *
5490160 CCTGCTTACTCAG
120 TCGGC-T--TCAA
* * * *
5490173 TCTGCTCCGCTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTTCAACTTCAGAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
* * *
5490238 GATAAGATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTTAA
66 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAAAGGATTATCGGCTTCAA
* *
5490302 TCTGCTCCACTACAACCTCAGAGAGATAAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGA
5490333 TTTACTATCT
Statistics
Matches: 428, Mismatches: 82, Indels: 76
0.73 0.14 0.13
Matches are distributed among these distances:
123 1 0.00
124 4 0.01
125 1 0.00
126 67 0.16
127 3 0.01
128 7 0.02
129 240 0.56
130 31 0.07
131 6 0.01
132 7 0.02
133 53 0.12
134 3 0.01
135 4 0.01
136 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (129 bp):
TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAAAGGATTATCGGCTTCAA
Found at i:5489925 original size:85 final size:86
Alignment explanation
Indices: 5489834--5490115 Score: 245
Period size: 85 Copynumber: 3.3 Consensus size: 86
5489824 GATCCACTCT
* *
5489834 ACTGCAACTTCAGAGTGATAAGATCTATTACTTTAATCCGCT-CCACAACTTTAGGGAGATAGGA
1 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCCACAACTTCAGGGAGATAGGA
5489898 TTATCGGCTTCAATCTGCTCC
66 TTATCGGCTTCAATCTGCTCC
* * * * ** * *
5489919 ACTGCAACCTCAGGGAGATAAGATTTGCTT-CTTCGATCTG-TCCCACTGCAACTTCAGGGGGAT
1 ACTGCAACTTCAGAGAGATAAGATCT-ATTACTTTAATCCGCTCCCA---CAACTTCAGGGAGAT
* * * * * * ** *
5489982 A--A-GACCTGATGCGATCCACTCT
62 AGGATTATCGGCTTCAATCTGCTCC
*
5490004 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC-C-ACAACTTCAGGGAGATAG
*
5490069 GATTATCGGCCTCAATCTGCTCC
64 GATTATCGGCTTCAATCTGCTCC
* *
5490092 ACTACAACCTCA-AGGAGATAAGAT
1 ACTGCAACTTCAGA-GAGATAAGAT
5490116 TTTTCATCTT
Statistics
Matches: 144, Mismatches: 40, Indels: 23
0.70 0.19 0.11
Matches are distributed among these distances:
84 3 0.02
85 87 0.60
86 6 0.04
87 3 0.02
88 45 0.31
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (86 bp):
ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCCACAACTTCAGGGAGATAGGA
TTATCGGCTTCAATCTGCTCC
Found at i:5490203 original size:218 final size:218
Alignment explanation
Indices: 5489964--5490382 Score: 716
Period size: 218 Copynumber: 1.9 Consensus size: 218
5489954 ATCTGTCCCA
* * * *
5489964 CTGCAACTTCAGGGGGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATC
1 CTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTGCAACTTCAGAGAGATAAGATC
5490029 TATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCCAC
66 TATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCCAC
*
5490094 TACAACCTCA-AGGAGATAAGATTT-TTCATCTTCGATCTGTCCCACTGCAACTTCAGGGGGATA
131 TACAACCTCAGA-GAGATAAGATTTACT-ATCTTCGATCTGTCCCACTGCAACTTCAGGGGGATA
5490157 AAACCTGCTTACTCAGTCTGCTCCG
194 AAACCTGCTTACTCAGTCTGCTCCG
*
5490182 CTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTTCAACTTCAGAGAGATAAGATC
1 CTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTGCAACTTCAGAGAGATAAGATC
* *
5490247 TATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCAC
66 TATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCCAC
* *
5490312 TACAACCTCAGAGAGATAAGATTTACTATCTTCGATCTGTCCCACTGTAACTTCAGGGGGATAAG
131 TACAACCTCAGAGAGATAAGATTTACTATCTTCGATCTGTCCCACTGCAACTTCAGGGGGATAAA
5490377 ACCTGC
196 ACCTGC
5490383 AATTTCCCAA
Statistics
Matches: 189, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
218 187 0.99
219 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (218 bp):
CTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTGCAACTTCAGAGAGATAAGATC
TATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCCAC
TACAACCTCAGAGAGATAAGATTTACTATCTTCGATCTGTCCCACTGCAACTTCAGGGGGATAAA
ACCTGCTTACTCAGTCTGCTCCG
Found at i:5490541 original size:129 final size:129
Alignment explanation
Indices: 5490374--5490815 Score: 706
Period size: 129 Copynumber: 3.4 Consensus size: 129
5490364 TCAGGGGGAT
* * *
5490374 AAGACCTGCAATTTCCCAACCTATTCCACTGCTAACCAGGGATATAGGACTTGTGGCTTAAATCT
1 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCT
* *
5490439 GCTTCCTTACACTTGAAGATAAGATTCGCCATCTTCAATCTGCTTCGCTACTGCTTAGGGAGAC
66 GCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTTCGCTACTGCTTAGGGAGAC
*
5490503 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTTGCTTAAATCT
1 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCT
* * * *
5490568 GCTTCCTTACACTTGAAGATAAGATTCACCGTCTTCGACCTGCTCCGCTACTGCTTAGAGAGAC
66 GCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTTCGCTACTGCTTAGGGAGAC
* * *
5490632 AAGATCTGTAATTTCCCAACATGTTCCACTGCTGACCAGGGATGTAGGACTTGTGGCTTAAATCT
1 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCT
* ** *
5490697 GCTTCCTTACACTTGAAGATAAGATTTGTTGTCTTCGATTTGC-TCTGCTACTGCTTAGGGAGAC
66 GCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTTC-GCTACTGCTTAGGGAGAC
*
5490761 AAGATCTGTAATTTCCCAACCTATTCCACTACTGACCAGGGATATAGGACTTGTG
1 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTG
5490816 ATTTCACCGA
Statistics
Matches: 286, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
128 1 0.00
129 285 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (129 bp):
AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCT
GCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTTCGCTACTGCTTAGGGAGAC
Found at i:5492083 original size:22 final size:22
Alignment explanation
Indices: 5492058--5492117 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
5492048 CCTTAGCCTC
*
5492058 TTCATTTTTACTTTTTCA-TATT
1 TTCATTTTT-CATTTTCATTATT
*
5492080 TTCATATTTTCATTTTCATTTTT
1 TTCAT-TTTTCATTTTCATTATT
5492103 TTCATTTTTCATTTT
1 TTCATTTTTCATTTT
5492118 TTTTACTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 22 0.65
23 12 0.35
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (22 bp):
TTCATTTTTCATTTTCATTATT
Found at i:5492089 original size:16 final size:15
Alignment explanation
Indices: 5492058--5492118 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 15
5492048 CCTTAGCCTC
5492058 TTCATTTTT-ACT-TT
1 TTCATTTTTCA-TATT
5492072 TTCATATTTTCATATT
1 TTCAT-TTTTCATATT
*
5492088 TTCA-TTTTCATTTTT
1 TTCATTTTTCA-TATT
5492103 TTCATTTTTCAT-TT
1 TTCATTTTTCATATT
5492117 TT
1 TT
5492119 TTTACTCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
14 15 0.37
15 13 0.32
16 13 0.32
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.70
Consensus pattern (15 bp):
TTCATTTTTCATATT
Found at i:5492092 original size:30 final size:30
Alignment explanation
Indices: 5492058--5492119 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
5492048 CCTTAGCCTC
*
5492058 TTCATTTTTA-CTTTTTCATATTTTCATATT
1 TTCATTTTCATCTTTTTCAT-TTTTCATATT
* *
5492088 TTCATTTTCATTTTTTTCATTTTTCATTTT
1 TTCATTTTCATCTTTTTCATTTTTCATATT
5492118 TT
1 TT
5492120 TTACTCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (30 bp):
TTCATTTTCATCTTTTTCATTTTTCATATT
Found at i:5492094 original size:14 final size:15
Alignment explanation
Indices: 5492077--5492119 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5492067 ACTTTTTCAT
5492077 ATTTTCA-TATTTTC
1 ATTTTCATTATTTTC
*
5492091 ATTTTCATTTTTTTC
1 ATTTTCATTATTTTC
5492106 ATTTTTCATT-TTTT
1 A-TTTTCATTATTTT
5492120 TTACTCAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.27
15 11 0.42
16 8 0.31
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTTCATTATTTTC
Found at i:5492119 original size:8 final size:8
Alignment explanation
Indices: 5492069--5492119 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
5492059 TCATTTTTAC
5492069 TTTTTCAT
1 TTTTTCAT
*
5492077 ATTTTCAT
1 TTTTTCAT
*
5492085 ATTTTCA-
1 TTTTTCAT
5492092 -TTTTCATT
1 TTTTTCA-T
5492100 TTTTTCA-
1 TTTTTCAT
5492107 TTTTTCAT
1 TTTTTCAT
5492115 TTTTT
1 TTTTT
5492120 TTACTCAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
6 6 0.16
7 7 0.18
8 19 0.50
9 6 0.16
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCAT
Found at i:5492119 original size:16 final size:16
Alignment explanation
Indices: 5492069--5492120 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
5492059 TCATTTTTAC
5492069 TTTTTCATATTTTCA-T
1 TTTTTCAT-TTTTCATT
*
5492085 ATTTTCA-TTTTCATT
1 TTTTTCATTTTTCATT
5492100 TTTTTCATTTTTCATT
1 TTTTTCATTTTTCATT
5492116 TTTTT
1 TTTTT
5492121 TACTCAAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 19 0.59
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTCATTTTTCATT
Found at i:5492991 original size:15 final size:14
Alignment explanation
Indices: 5492967--5493005 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
5492957 TGGCCTCTCC
5492967 TTTTCTTTTTCCTT
1 TTTTCTTTTTCCTT
5492981 TTTTCCTTTTTCCTT
1 TTTT-CTTTTTCCTT
* *
5492996 CTCTCTTTTT
1 TTTTCTTTTT
5493006 TCATTTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTTCCTT
Found at i:5497667 original size:33 final size:33
Alignment explanation
Indices: 5497599--5497668 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
5497589 CATAAAGATC
* *
5497599 TAAAATAAAATATTTGCAATATTTCAGTAATAA
1 TAAAATAAAATATTTGCAATATGTCAGAAATAA
*
5497632 TAAAATAAAATA-TTGTATATATGT-AGAAATAAA
1 TAAAATAAAATATTTGCA-ATATGTCAGAAAT-AA
5497665 TAAA
1 TAAA
5497669 CATGTAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (33 bp):
TAAAATAAAATATTTGCAATATGTCAGAAATAA
Found at i:5508945 original size:50 final size:49
Alignment explanation
Indices: 5508720--5508949 Score: 263
Period size: 50 Copynumber: 4.7 Consensus size: 49
5508710 TAGGACGCTA
* * * *
5508720 ATGCCATATCCCAGATATGGTCTTACA-TGGGA-TCACATC-TCT-AGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTC-C-TCGTCTGTGCCG
** * * * *
5508767 ATGCC-TGTCCCAGACATGGTCTTACACTTACTCTTCTTTGTCCGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCAC-TCCTCGTCTGTGCCG
* *
5508816 ATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCCCGGTCTGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTC-GTCTGTGCCG
5508866 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGATCTGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCG-TCTGTGCCG
*
5508916 ATGCCATGTCCTAGACATGGTCTTACACTGGCAC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCAC
5508950 ACTTACTGTC
Statistics
Matches: 155, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
46 19 0.12
47 7 0.05
48 2 0.01
49 14 0.09
50 113 0.73
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.28
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGTCTGTGCCG
Found at i:5509033 original size:44 final size:44
Alignment explanation
Indices: 5508970--5509064 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
5508960 ATGGTCCAAC
* *
5508970 CATGGTCTTTTCCGTCAATTCTTTCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
*
5509014 CATGGACTTTTTCGTCAATTCTTCCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
5509058 CATGGAC
1 CATGGAC
5509065 CTTGAGATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (44 bp):
CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
Found at i:5517000 original size:22 final size:21
Alignment explanation
Indices: 5516961--5517006 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
5516951 CAAACGAGGA
*
5516961 TATTTGGAAACTTCTTGAAAGT
1 TATTTGGAAAATTCTTGAAA-T
* *
5516983 TATTTGTAAAATTTTTGAAAT
1 TATTTGGAAAATTCTTGAAAT
5517004 TAT
1 TAT
5517007 AGGAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (21 bp):
TATTTGGAAAATTCTTGAAAT
Found at i:5517351 original size:259 final size:259
Alignment explanation
Indices: 5516911--5517428 Score: 826
Period size: 259 Copynumber: 2.0 Consensus size: 259
5516901 AAGTTCTTGA
* *
5516911 AAGTTCTTCAATGTAGAATTGAACCCAAAAATATATAATTCAAACGAGGATATTTGGAAACTTCT
1 AAGTTCTTCAATGTAGAACTGAACCCAAAAATATATAATTCAAACGAGGAAATTTGGAAA--TCT
* * * *
5516976 TGAAAGTTATTTGTAAAATTTTTGAAATTATAGGAATTATAGTGAAATCTACCATCTTCATCGAT
64 TGAAAGTTATTTGTAAAAATTTTGAAATTATAGGAATTATAGTGAAATCTACAATCTTCATCAAC
* *
5517041 GAATAAAGGTCAAACACTGTTTTCGATTATGCTTTGTTAATAGTATTTATAATTTTTTTTACTTA
129 GAATAAAGGTCAAACACTGTTTTCGATTATCCTTTGTGAATAGTATTTATAA-TTTTTTTACTTA
5517106 AGTTCTTGAATGTATAACTAATATTAAACTAATGTTTAG-AAGTGAAGTTTTAGTGCTGAAACAT
193 AGTTCTTGAATGTATAACTAATATTAAACTAATGTTT-GCAAGTGAAGTTTTAGTGCTGAAACAT
5517170 CTC
257 CTC
* * *
5517173 AAGTTCTTCAATGTAGAACTGAACCCAGATATATATAATTCAAACGAGGAAATTTGGAAA-GTTG
1 AAGTTCTTCAATGTAGAACTGAACCCAAAAATATATAATTCAAACGAGGAAATTTGGAAATCTTG
5517237 AAAGTTATTTGTAAAAATTTTGAAATTATAGGAATTATAGTGAAATCTACAATCTTCATCAACGA
66 AAAGTTATTTGTAAAAATTTTGAAATTATAGGAATTATAGTGAAATCTACAATCTTCATCAACGA
* * * *
5517302 ATAAAGGTCGAACACCT-TTTTTGGTTATCCTTTGTGAGTAGTATTTATAATTTTTTTACTTAAG
131 ATAAAGGTCAAACA-CTGTTTTCGATTATCCTTTGTGAATAGTATTTATAATTTTTTTACTTAAG
*
5517366 TTCTTGGATGTATAACTAATATTAAACTAATGTTTGCAAGTGAAGTTTTAGTGCTGAAACATC
195 TTCTTGAATGTATAACTAATATTAAACTAATGTTTGCAAGTGAAGTTTTAGTGCTGAAACATC
5517429 ATAAATGGCA
Statistics
Matches: 238, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
257 1 0.00
258 74 0.31
259 105 0.44
260 2 0.01
262 56 0.24
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (259 bp):
AAGTTCTTCAATGTAGAACTGAACCCAAAAATATATAATTCAAACGAGGAAATTTGGAAATCTTG
AAAGTTATTTGTAAAAATTTTGAAATTATAGGAATTATAGTGAAATCTACAATCTTCATCAACGA
ATAAAGGTCAAACACTGTTTTCGATTATCCTTTGTGAATAGTATTTATAATTTTTTTACTTAAGT
TCTTGAATGTATAACTAATATTAAACTAATGTTTGCAAGTGAAGTTTTAGTGCTGAAACATCTC
Found at i:5520370 original size:11 final size:11
Alignment explanation
Indices: 5520354--5520401 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
5520344 AATAAAGAAT
*
5520354 GATGCTTGATG
1 GATGCTTGAAG
5520365 GATGCTTGAAG
1 GATGCTTGAAG
5520376 GATGCTTGAAG
1 GATGCTTGAAG
*
5520387 GATGCTTGAGG
1 GATGCTTGAAG
5520398 GATG
1 GATG
5520402 ATGAATGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.23, C:0.08, G:0.40, T:0.29
Consensus pattern (11 bp):
GATGCTTGAAG
Found at i:5521948 original size:50 final size:50
Alignment explanation
Indices: 5521887--5522023 Score: 170
Period size: 50 Copynumber: 2.7 Consensus size: 50
5521877 TTATCATTCA
* *
5521887 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCCA-A-CTTTCCG
1 ATACACGTAGTAGCCTACACATAGTACTACACACGTGA-CCATATCTAT-CG
* * *
5521937 GTACACATAGTAGCCTACACATAGTACTACACATGTGACCATTATCTATCG
1 ATACACGTAGTAGCCTACACATAGTACTACACACGTGACCA-TATCTATCG
* *
5521988 ATACACGTAGTAGCCTGCACTTAGTACTACACACGT
1 ATACACGTAGTAGCCTACACATAGTACTACACACGT
5522024 ATTTATAGGC
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
49 3 0.04
50 34 0.46
51 34 0.46
52 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (50 bp):
ATACACGTAGTAGCCTACACATAGTACTACACACGTGACCATATCTATCG
Found at i:5521968 original size:12 final size:13
Alignment explanation
Indices: 5521938--5521970 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5521928 AACTTTCCGG
5521938 TACACATAGTAGCC
1 TACACATAGTA-CC
5521952 TACACATAGTA-C
1 TACACATAGTACC
5521964 TACACAT
1 TACACAT
5521971 GTGACCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Found at i:5527629 original size:23 final size:23
Alignment explanation
Indices: 5527600--5527675 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
5527590 ATAAGTGCCA
5527600 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
5527623 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
5527646 CACTGAAATGTAGCCGGAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
5527669 CACTGAT
1 CACTGAT
5527676 CAATAACACT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:5528034 original size:23 final size:23
Alignment explanation
Indices: 5528005--5528080 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
5527995 ATAAGTGCCA
5528005 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
5528028 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
5528051 CACTGAAATGTAGCCGGAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
5528074 CACTGAT
1 CACTGAT
5528081 CAATAACACT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:5528266 original size:405 final size:405
Alignment explanation
Indices: 5527515--5528324 Score: 1620
Period size: 405 Copynumber: 2.0 Consensus size: 405
5527505 ATCGTTACAT
5527515 TATCTCATGTATTTTCACTTAGCCAATTTCCCGTTGAACACTCGGAATATACACGGATACGTAGA
1 TATCTCATGTATTTTCACTTAGCCAATTTCCCGTTGAACACTCGGAATATACACGGATACGTAGA
5527580 GAATTAGTACATAAGTGCCACACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTA
66 GAATTAGTACATAAGTGCCACACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTA
5527645 CCACTGAAATGTAGCCGGAGCTACCACTGATCAATAACACTGGAAATGTCCACGGGCCTGCTCAC
131 CCACTGAAATGTAGCCGGAGCTACCACTGATCAATAACACTGGAAATGTCCACGGGCCTGCTCAC
5527710 ACAAGCTATCAGGTGTCTGCAACACATGCTAGATCACCCAGCACCCGGGACTCACTGTAACACTG
196 ACAAGCTATCAGGTGTCTGCAACACATGCTAGATCACCCAGCACCCGGGACTCACTGTAACACTG
5527775 TAACACTGGTCTCTAGTGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACTGGGAATTT
261 TAACACTGGTCTCTAGTGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACTGGGAATTT
5527840 ACACTTAACACTTTATTTTGAACATTTTATCACTTGAATAATTCATGAATAATTTTCCTTTCACA
326 ACACTTAACACTTTATTTTGAACATTTTATCACTTGAATAATTCATGAATAATTTTCCTTTCACA
5527905 TTCAATATTAATTCA
391 TTCAATATTAATTCA
5527920 TATCTCATGTATTTTCACTTAGCCAATTTCCCGTTGAACACTCGGAATATACACGGATACGTAGA
1 TATCTCATGTATTTTCACTTAGCCAATTTCCCGTTGAACACTCGGAATATACACGGATACGTAGA
5527985 GAATTAGTACATAAGTGCCACACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTA
66 GAATTAGTACATAAGTGCCACACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTA
5528050 CCACTGAAATGTAGCCGGAGCTACCACTGATCAATAACACTGGAAATGTCCACGGGCCTGCTCAC
131 CCACTGAAATGTAGCCGGAGCTACCACTGATCAATAACACTGGAAATGTCCACGGGCCTGCTCAC
5528115 ACAAGCTATCAGGTGTCTGCAACACATGCTAGATCACCCAGCACCCGGGACTCACTGTAACACTG
196 ACAAGCTATCAGGTGTCTGCAACACATGCTAGATCACCCAGCACCCGGGACTCACTGTAACACTG
5528180 TAACACTGGTCTCTAGTGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACTGGGAATTT
261 TAACACTGGTCTCTAGTGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACTGGGAATTT
5528245 ACACTTAACACTTTATTTTGAACATTTTATCACTTGAATAATTCATGAATAATTTTCCTTTCACA
326 ACACTTAACACTTTATTTTGAACATTTTATCACTTGAATAATTCATGAATAATTTTCCTTTCACA
5528310 TTCAATATTAATTCA
391 TTCAATATTAATTCA
5528325 CATATCAAAT
Statistics
Matches: 405, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
405 405 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (405 bp):
TATCTCATGTATTTTCACTTAGCCAATTTCCCGTTGAACACTCGGAATATACACGGATACGTAGA
GAATTAGTACATAAGTGCCACACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTA
CCACTGAAATGTAGCCGGAGCTACCACTGATCAATAACACTGGAAATGTCCACGGGCCTGCTCAC
ACAAGCTATCAGGTGTCTGCAACACATGCTAGATCACCCAGCACCCGGGACTCACTGTAACACTG
TAACACTGGTCTCTAGTGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACTGGGAATTT
ACACTTAACACTTTATTTTGAACATTTTATCACTTGAATAATTCATGAATAATTTTCCTTTCACA
TTCAATATTAATTCA
Found at i:5528326 original size:17 final size:18
Alignment explanation
Indices: 5528304--5528344 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5528294 TAATTTTCCT
5528304 TTCACAT-TC-AATATTAA
1 TTCACATATCAAATA-TAA
5528321 TTCACATATCAAATATAA
1 TTCACATATCAAATATAA
5528339 TTCACA
1 TTCACA
5528345 ATTTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 4 0.18
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (18 bp):
TTCACATATCAAATATAA
Found at i:5539202 original size:21 final size:21
Alignment explanation
Indices: 5539168--5539222 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
5539158 TGAAGTGTGT
* *
5539168 TGTGGTTGCGTCT-GATTCTGG
1 TGTGGATGCATCTGGATT-TGG
*
5539189 TGTGGATGCATCTGGATTTGT
1 TGTGGATGCATCTGGATTTGG
5539210 TGTGGATGCATCT
1 TGTGGATGCATCT
5539223 AAGTATGCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.11, C:0.13, G:0.35, T:0.42
Consensus pattern (21 bp):
TGTGGATGCATCTGGATTTGG
Found at i:5547499 original size:41 final size:41
Alignment explanation
Indices: 5547436--5547714 Score: 290
Period size: 41 Copynumber: 6.7 Consensus size: 41
5547426 CTTTGAATGT
* * * *
5547436 AAGGGGTTACTAAGTGCAGATTCCCCGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATGAAA
* * *
5547477 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATGAAA
* * **
5547518 AAGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGA
1 AAGGGGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-TGAAA
* * *
5547561 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATGAAA
* * **
5547602 AAGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGA
1 AAGGGGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-TGAAA
* * * *
5547645 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTTAT-TAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATGAAA
*
5547685 AAGGTGGTTGCTAAGTGGTGATTCCACCGT
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGT
5547715 GTAACGGTTA
Statistics
Matches: 200, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
40 5 0.03
41 100 0.50
42 47 0.23
43 48 0.24
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATGAAA
Found at i:5547584 original size:84 final size:84
Alignment explanation
Indices: 5547476--5547714 Score: 451
Period size: 84 Copynumber: 2.8 Consensus size: 84
5547466 CATTGATCAA
5547476 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAAGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAAGTGGTTGCTAAGTGCTGATTC
5547541 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
5547560 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAAGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAAGTGGTTGCTAAGTGCTGATTC
5547625 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
* * *
5547644 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTTATTATAAGGTGGTTGCTAAGTGGTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAAGTGGTTGCTAAGTGCTGATTC
5547709 CACCGT
66 CACCGT
5547715 GTAACGGTTA
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 152 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAAGTGGTTGCTAAGTGCTGATTC
CACCGTATCCTTGATTGTG
Found at i:5551682 original size:41 final size:40
Alignment explanation
Indices: 5551619--5551724 Score: 140
Period size: 41 Copynumber: 2.6 Consensus size: 40
5551609 CTTTGAATGT
* *
5551619 AAGGGGTTGCTAAGTGCAGATTCCCTGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGAT-AAA
* * * *
5551660 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATAAA
5551700 AAGGTGGTTGCTAAGTGCTGATTCC
1 AAGG-GGTTGCTAAGTGCTGATTCC
5551725 AACGTATCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 5 0.09
41 52 0.91
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (40 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATAAA
Found at i:5552051 original size:84 final size:84
Alignment explanation
Indices: 5551659--5552319 Score: 814
Period size: 84 Copynumber: 7.8 Consensus size: 84
5551649 CATTGATCAA
*
5551659 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
* * *
5551724 CAACGTATCATTGAATGTG
66 CACCGTATCCTTGATTGTG
* * * * * ** * ** *
5551743 AAAGGGGTTACTAAGTGTTGAATCCACCG-ATAACGGATAACATTCCGAGT-GTT-C-AACGGGA
1 AAAGGGGTTGCTATGTGCTGATTCC-CCGTATCATTGAT--TA-TAAG-GTGGTTGCTAA-GTG-
** ***
5551804 AATT--TTGAAAAATTATCCTTGATTGTG
59 --TTGATT-CCACCGTATCCTTGATTGTG
* * * *
5551831 AAAGGGATTGCTACGTGGTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
*
5551896 CACTGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
* **
5551915 -AAGGGGTTGCTATGTGCTAATTCCTTGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
* *
5551979 CACCGTATCCTTGACTGTA
66 CACCGTATCCTTGATTGTG
5551998 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
*
5552063 CATCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
*
5552082 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
5552147 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
** * * *
5552166 AAAGGGGTTGCTACATGTTGATTCCCCGTATCATTGATTATATGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
*
5552231 CACTGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
* * *
5552250 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCATTGATTATAAGGTGGTAGCTAAGTGGTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
5552315 CACCG
66 CACCG
5552320 GGATCCTTTG
Statistics
Matches: 493, Mismatches: 67, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
83 74 0.15
84 344 0.70
85 12 0.02
86 8 0.02
87 12 0.02
88 42 0.09
89 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
CACCGTATCCTTGATTGTG
Found at i:5560624 original size:30 final size:32
Alignment explanation
Indices: 5560583--5560642 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
5560573 GTCACTGTAC
*
5560583 TGGGCTTAGGCCCACTTG-TTCTGTATTGGTT
1 TGGGCTTAGGCCCAATTGATTCTGTATTGGTT
*
5560614 TGGGC-TAGGCCCAATTGATTCTGTTTTGG
1 TGGGCTTAGGCCCAATTGATTCTGTATTGG
5560643 ATGCGACCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.12, C:0.18, G:0.30, T:0.40
Consensus pattern (32 bp):
TGGGCTTAGGCCCAATTGATTCTGTATTGGTT
Found at i:5564352 original size:13 final size:13
Alignment explanation
Indices: 5564334--5564369 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
5564324 GGCTTATCGG
5564334 TAATGTTTTTTAC
1 TAATGTTTTTTAC
5564347 TAATGTTTTTTAC
1 TAATGTTTTTTAC
*
5564360 TAAGGTTTTT
1 TAATGTTTTT
5564370 AGAAAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61
Consensus pattern (13 bp):
TAATGTTTTTTAC
Found at i:5568341 original size:33 final size:33
Alignment explanation
Indices: 5568203--5568352 Score: 111
Period size: 33 Copynumber: 4.5 Consensus size: 33
5568193 TGACTTACCT
* * *
5568203 CGTGTTTACTGTCCCGATGTACTTTCTTTGTTC
1 CGTGTTTACTGTCCCGATGTACTATCTCTATTC
** * * * *
5568236 CGTGTTTACCCTCTCGGTGGACTATCTCTATTT
1 CGTGTTTACTGTCCCGATGTACTATCTCTATTC
* * ** * * * * *
5568269 TGTGTTTATTGTCCAAATGAAATTTTTCTGTTC
1 CGTGTTTACTGTCCCGATGTACTATCTCTATTC
*
5568302 CATGTTTACTGTCCCGATGTACTATCTCTATTC
1 CGTGTTTACTGTCCCGATGTACTATCTCTATTC
* *
5568335 TGTGTTTACTGTTCCGAT
1 CGTGTTTACTGTCCCGAT
5568353 AGACTTTCTC
Statistics
Matches: 81, Mismatches: 36, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
33 81 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (33 bp):
CGTGTTTACTGTCCCGATGTACTATCTCTATTC
Found at i:5571139 original size:79 final size:79
Alignment explanation
Indices: 5571009--5571437 Score: 585
Period size: 79 Copynumber: 5.4 Consensus size: 79
5570999 GCCTCTATTA
* * *
5571009 TACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTGCACAT
1 TACTTCGGTACCCCTGATTGCACTTACGTGCCCCTG-TTGTACTTCGATACCCCTGATTGCACAT
5571074 ACGTGCCCCTGTTTG
65 ACGTGCCCCTGTTTG
*
5571089 TACTTCGGTACCCCTGATTGCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTGATTGCACATA
1 TACTTCGGTACCCCTGATTGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATA
5571154 CGTGCCCCTGTTTG
66 CGTGCCCCTGTTTG
* * * *
5571168 TACTTCGGTACCCCTAAATACACTTACATG-CCCTAGTTGTACTTCGATACCCCTGATTGCACAT
1 TACTTCGGTACCCCTGATTGCACTTACGTGCCCCT-GTTGTACTTCGATACCCCTGATTGCACAT
* *
5571232 ACATGCCCTTGTTTG
65 ACGTGCCCCTGTTTG
* * *
5571247 TAGTTTGGTACCCCTGAATT-CACTTACGTGCCCCTGTTGTACTTTGATACCCCTGATTGCACAT
1 TACTTCGGTACCCCTG-ATTGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACAT
* * *
5571311 ACGTACCTCTGTTGG
65 ACGTGCCCCTGTTTG
* *
5571326 TACTTCAGTACCCCTGGA-TGCACTTACGTGCCCCTATTTGTACTTCGATACCCCTGATTGCACA
1 TACTTCGGTACCCCT-GATTGCACTTACGTGCCCCT-GTTGTACTTCGATACCCCTGATTGCACA
** * *
5571390 TTTGTTCCCTTGTTTG
64 TACGTGCCCCTGTTTG
*
5571406 TACTTCGGTACCCCTGAATGCACTTACGTGCC
1 TACTTCGGTACCCCTGATTGCACTTACGTGCC
5571438 ACTATTTATA
Statistics
Matches: 310, Mismatches: 32, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
78 5 0.02
79 200 0.65
80 105 0.34
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.34
Consensus pattern (79 bp):
TACTTCGGTACCCCTGATTGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATA
CGTGCCCCTGTTTG
Found at i:5571181 original size:20 final size:20
Alignment explanation
Indices: 5571009--5571422 Score: 153
Period size: 20 Copynumber: 20.9 Consensus size: 20
5570999 GCCTCTATTA
*
5571009 TACTTCGATACCCCTGATTG
1 TACTTCGGTACCCCTGATTG
* * * *
5571029 CACATAC-GTGCCCCTGTTTG
1 TAC-TTCGGTACCCCTGATTG
5571049 TACTTCGGTACCCCTGATTG
1 TACTTCGGTACCCCTGATTG
* * * *
5571069 CACATAC-GTGCCCCTGTTTG
1 TAC-TTCGGTACCCCTGATTG
5571089 TACTTCGGTACCCCTGATTG
1 TACTTCGGTACCCCTGATTG
* *
5571109 CACTTAC-GTGCCCCTG-TTG
1 TACTT-CGGTACCCCTGATTG
5571128 TACTTCGGTACCCCTGATTG
1 TACTTCGGTACCCCTGATTG
* * * *
5571148 CACATAC-GTGCCCCTGTTTG
1 TAC-TTCGGTACCCCTGATTG
* * *
5571168 TACTTCGGTACCCCTAAATA
1 TACTTCGGTACCCCTGATTG
* * *
5571188 CACTTAC-AT-GCCCT-AGTTG
1 TACTT-CGGTACCCCTGA-TTG
*
5571207 TACTTCGATACCCCTGATTG
1 TACTTCGGTACCCCTGATTG
* * * * * *
5571227 CACATAC-ATGCCCTTGTTTG
1 TAC-TTCGGTACCCCTGATTG
* *
5571247 TAGTTTGGTACCCCTGAATT-
1 TACTTCGGTACCCCTG-ATTG
* *
5571267 CACTTAC-GTGCCCCTG-TTG
1 TACTT-CGGTACCCCTGATTG
* *
5571286 TACTTTGATACCCCTGATTG
1 TACTTCGGTACCCCTGATTG
* * *
5571306 CACATAC-GTACCTCTG-TTGG
1 TAC-TTCGGTACCCCTGATT-G
*
5571326 TACTTCAGTACCCCTGGA-TG
1 TACTTCGGTACCCCT-GATTG
* *
5571346 CACTTAC-GTGCCCCT-ATTTG
1 TACTT-CGGTACCCCTGA-TTG
*
5571366 TACTTCGATACCCCTGATTG
1 TACTTCGGTACCCCTGATTG
* * * * *
5571386 CACATT-TGTTCCCTTGTTTG
1 TAC-TTCGGTACCCCTGATTG
5571406 TACTTCGGTACCCCTGA
1 TACTTCGGTACCCCTGA
5571423 ATGCACTTAC
Statistics
Matches: 277, Mismatches: 84, Indels: 66
0.65 0.20 0.15
Matches are distributed among these distances:
18 6 0.02
19 51 0.18
20 200 0.72
21 20 0.07
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.34
Consensus pattern (20 bp):
TACTTCGGTACCCCTGATTG
Found at i:5571200 original size:119 final size:119
Alignment explanation
Indices: 5570988--5571437 Score: 550
Period size: 119 Copynumber: 3.8 Consensus size: 119
5570978 ATTGTATGAA
* * *
5570988 TGCACTTACGTGCCTCTATTATACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTGTACT
1 TGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTGTACT
*
5571053 TCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
66 TCGGTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
*
5571107 TGCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTACT
1 TGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTGTACT
* * * * *
5571172 TCGGTACCCCTAAATACACTTACATG-CCCTAG-TTGTACTTCGATACCCCTGAT
66 TCGGTACCCCTGAATGCACATACGTGCCCCT-GTTTGTACTTCGGTACCCCTGAT
* * * * * * *
5571225 TGCACATACATGCCCTTGTTTGTAGTTTGGTACCCCTGAATT-CACTTACGTGCCCCTG-TTGTA
1 TGCACTTACGTGCCCCTG-TTGTACTTCGATACCCCTG-ATTGCACATACGTGCCCCTGTTTGTA
* * * * * * *
5571288 CTTTGATACCCCTGATTGCACATACGTACCTCTGTTGGTACTTCAGTACCCCTGGA-
64 CTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCT-GAT
* ** * *
5571344 TGCACTTACGTGCCCCTATTTGTACTTCGATACCCCTGATTGCACATTTGTTCCCTTGTTTGTAC
1 TGCACTTACGTGCCCCT-GTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTGTAC
*
5571409 TTCGGTACCCCTGAATGCACTTACGTGCC
65 TTCGGTACCCCTGAATGCACATACGTGCC
5571438 ACTATTTATA
Statistics
Matches: 277, Mismatches: 45, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
118 68 0.25
119 174 0.63
120 35 0.13
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.34
Consensus pattern (119 bp):
TGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTGTACT
TCGGTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
Found at i:5571464 original size:40 final size:40
Alignment explanation
Indices: 5570988--5571437 Score: 538
Period size: 40 Copynumber: 11.3 Consensus size: 40
5570978 ATTGTATGAA
* * * *
5570988 TGCACTTACGTGCCTCT-ATTATACTTCGATACCCCTGAT
1 TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
*
5571027 TGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
1 TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
*
5571067 TGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
1 TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
5571107 TGCACTTACGTGCCCCTG-TTGTACTTCGGTACCCCTGAT
1 TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
* * *
5571146 TGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTAAA
1 TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
* * *
5571186 TACACTTACATG-CCCTAG-TTGTACTTCGATACCCCTGAT
1 TGCACTTACGTGCCCCT-GTTTGTACTTCGGTACCCCTGAT
* * * * *
5571225 TGCACATACATGCCCTTGTTTGTAGTTTGGTACCCCTGAAT
1 TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG-AT
* *
5571266 T-CACTTACGTGCCCCTG-TTGTACTTTGATACCCCTGAT
1 TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
* * * * *
5571304 TGCACATACGTACCTCTGTTGGTACTTCAGTACCCCTGGA-
1 TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCT-GAT
* *
5571344 TGCACTTACGTGCCCCTATTTGTACTTCGATACCCCTGAT
1 TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
* * * *
5571384 TGCACATT-TGTTCCCTTGTTTGTACTTCGGTACCCCTGAA
1 TGCAC-TTACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
5571424 TGCACTTACGTGCC
1 TGCACTTACGTGCC
5571438 ACTATTTATA
Statistics
Matches: 351, Mismatches: 48, Indels: 23
0.83 0.11 0.05
Matches are distributed among these distances:
38 3 0.01
39 120 0.34
40 221 0.63
41 7 0.02
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.34
Consensus pattern (40 bp):
TGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGAT
Found at i:5576366 original size:50 final size:50
Alignment explanation
Indices: 5576301--5576433 Score: 149
Period size: 50 Copynumber: 2.7 Consensus size: 50
5576291 CAATACCACA
* ** * *
5576301 TCCCAGATATGGTCTTACAAGAGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACAAGAGACCTCTCATATCGGTGCCAACGCCATG
* ** *
5576351 TCCCAGACATAGTCTTACGGGAGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACAAGAGACCTCTCATATCGGTGCCAACGCCATG
* * * *
5576401 TTCCAGGCATGGTCTTACATGGGACCTCTCATA
1 TCCCAGACATGGTCTTACAAGAGACCTCTCATA
5576434 ACCTCAGTAA
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACAAGAGACCTCTCATATCGGTGCCAACGCCATG
Found at i:5581975 original size:50 final size:50
Alignment explanation
Indices: 5581800--5581985 Score: 176
Period size: 50 Copynumber: 3.6 Consensus size: 50
5581790 GAGTGAGATT
* * **
5581800 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGTC
1 CCATGTAAGACCATGTCTGGAACATGGCATGGGC---ACCGA---TATGAGAGGTC
* * * *
5581856 CCATGTAAGACCATGCCTGGAACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CCATGTAAGACCATGTCTGGAACATGGCATGGGCACCGATATGAGAGGT-C
* **
5581907 CCCT-TAAGACCATGTCTGGAACATGGCATGGGCACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGAACATGGCATGGGCACCGATATGAGAGGTC
* * *
5581956 CCATGTAAGACCATATCTGGGATATGGCAT
1 CCATGTAAGACCATGTCTGGAACATGGCAT
5581986 TGGTAGTACA
Statistics
Matches: 111, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
49 4 0.04
50 69 0.62
51 4 0.04
53 3 0.03
56 31 0.28
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGAACATGGCATGGGCACCGATATGAGAGGTC
Found at i:5583736 original size:22 final size:21
Alignment explanation
Indices: 5583707--5583749 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
5583697 CCGCAGATAT
5583707 AGTTATAAGAGAAAGACCACA
1 AGTTATAAGAGAAAGACCACA
5583728 AGTTGATAAGAGAAAGACCACA
1 AGTT-ATAAGAGAAAGACCACA
5583750 CGATCAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (21 bp):
AGTTATAAGAGAAAGACCACA
Found at i:5593198 original size:15 final size:15
Alignment explanation
Indices: 5593178--5593232 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
5593168 ACTCTCGACA
*
5593178 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
5593193 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
5593208 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
5593222 TTCTTTT-TCTC
1 TTCTTTTCTCTC
5593233 GCTCGATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:5604727 original size:20 final size:20
Alignment explanation
Indices: 5604699--5604744 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
5604689 GCTGATAGAA
* *
5604699 AGCTAAATTGAGCTCGAATG
1 AGCTGAATTGAGCTCAAATG
5604719 AGCTGAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
5604739 AGCTGA
1 AGCTGA
5604745 TCGAAGCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (20 bp):
AGCTGAATTGAGCTCAAATG
Found at i:5604752 original size:20 final size:20
Alignment explanation
Indices: 5604708--5604762 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
5604698 AAGCTAAATT
* *
5604708 GAGCTCGAATGAGCTGAATT
1 GAGCTCAAATGAGCTGAATC
5604728 GAGCTCAAATGAGCTG-ATC
1 GAGCTCAAATGAGCTGAATC
* *
5604747 GAAGCTAAAACGAGCT
1 G-AGCTCAAATGAGCT
5604763 AAAGGAGCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (20 bp):
GAGCTCAAATGAGCTGAATC
Found at i:5606438 original size:24 final size:24
Alignment explanation
Indices: 5606402--5606448 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5606392 CATTTCATAC
*
5606402 CAAATCCCGTACCATTTCGTACCG
1 CAAATCCCATACCATTTCGTACCG
*
5606426 CAAATCTCATACCATTTCGTACC
1 CAAATCCCATACCATTTCGTACC
5606449 AATACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.36, G:0.09, T:0.28
Consensus pattern (24 bp):
CAAATCCCATACCATTTCGTACCG
Found at i:5614821 original size:18 final size:18
Alignment explanation
Indices: 5614800--5614838 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5614790 AAAGGAAGAT
5614800 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
5614818 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
5614836 AGA
1 AGA
5614839 GCAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:5616644 original size:33 final size:34
Alignment explanation
Indices: 5616607--5616678 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
5616597 GAGTTAGTTT
5616607 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
* * *
5616640 ATTAATTTTATTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
5616674 ATTAA
1 ATTAA
5616679 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:5623020 original size:15 final size:15
Alignment explanation
Indices: 5623000--5623039 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
5622990 CTTAGCTGTA
5623000 GGTTTTCATTTGTTT
1 GGTTTTCATTTGTTT
5623015 GGTTTTCATTTGTTT
1 GGTTTTCATTTGTTT
*
5623030 GCTTTTCATT
1 GGTTTTCATT
5623040 CTTCCTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.07, C:0.10, G:0.17, T:0.65
Consensus pattern (15 bp):
GGTTTTCATTTGTTT
Found at i:5623773 original size:19 final size:21
Alignment explanation
Indices: 5623740--5623787 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5623730 AAATAAAGAA
5623740 AAAAAGA-AATCAAAAA-A-C
1 AAAAAGAGAATCAAAAAGAGC
*
5623758 AAAAAGAGAATGAAAAAGAGC
1 AAAAAGAGAATCAAAAAGAGC
5623779 AAAAAGAGA
1 AAAAAGAGA
5623788 TTGAGAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 8 0.31
20 1 0.04
21 10 0.38
ACGTcount: A:0.73, C:0.06, G:0.17, T:0.04
Consensus pattern (21 bp):
AAAAAGAGAATCAAAAAGAGC
Found at i:5632364 original size:30 final size:28
Alignment explanation
Indices: 5632330--5632385 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
5632320 GTGATTAAAT
5632330 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
5632360 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
5632386 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:5638196 original size:25 final size:25
Alignment explanation
Indices: 5638167--5638214 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
5638157 CAACTTCTAA
5638167 AGAAAA-CTCAAGAGAGAATTCTTGG
1 AGAAAAGCTCAAG-GAGAATTCTTGG
5638192 AGAAAAGCTCAAGGAGAATTCTT
1 AGAAAAGCTCAAGGAGAATTCTT
5638215 CACTTAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (25 bp):
AGAAAAGCTCAAGGAGAATTCTTGG
Found at i:5644975 original size:6 final size:6
Alignment explanation
Indices: 5644964--5645012 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
5644954 CTTTATTTTA
* *
5644964 TTTTCT TTTTCT TTTTCACT CTTT-T TTTTCT TATTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTT--CT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
5645013 ACAGTCTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
8 5 0.14
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:5645225 original size:18 final size:16
Alignment explanation
Indices: 5645187--5645225 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
5645177 ATGCATATTA
*
5645187 CTTGTACAGATTGTAG
1 CTTGTACAGATTGGAG
5645203 CTTGTACAGATTCGGATG
1 CTTGTACAGATT-GGA-G
5645221 CTTGT
1 CTTGT
5645226 TCGTGGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (16 bp):
CTTGTACAGATTGGAG
Found at i:5646694 original size:20 final size:20
Alignment explanation
Indices: 5646646--5646694 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5646636 TTTAACTTAG
5646646 TTCAGCTCACTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
* * *
5646666 GTCAACTCATTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
5646686 TTCAGCTCA
1 TTCAGCTCA
5646695 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.27
Consensus pattern (20 bp):
TTCAGCTCACTCGAGCTCAA
Found at i:5650186 original size:233 final size:233
Alignment explanation
Indices: 5649773--5650238 Score: 869
Period size: 233 Copynumber: 2.0 Consensus size: 233
5649763 AAGATTTCAC
*
5649773 AACTCCCTTCAAACGGCTCTAATCTCCCCTCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
1 AACTCCCTTCAAACGGCTCTAATCTCCCATCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
*
5649838 TGGCTTCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAAAAAATTCTTGA
66 TGGCTCCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAAAAAATTCTTGA
**
5649903 AGAACTCAAAGAGAATTTTCACTCAAAGTAAATCTGAAATTTTCAATGTAATTATAATGTGTTCA
131 AGAACTCAAAGAGAATTTTCACTCAAAACAAATCTGAAATTTTCAATGTAATTATAATGTGTTCA
5649968 ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
196 ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
*
5650006 AACTCCCTTCAAACGGGTCTAATCTCCCATCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
1 AACTCCCTTCAAACGGCTCTAATCTCCCATCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
*
5650071 TGGCTCCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAGAAAATTCTTGA
66 TGGCTCCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAAAAAATTCTTGA
*
5650136 AGAACTCAAAGAGAATTTTCACTCAAAACAAATCTGAAATTTTTAATGTAATTATAATGTGTTCA
131 AGAACTCAAAGAGAATTTTCACTCAAAACAAATCTGAAATTTTCAATGTAATTATAATGTGTTCA
5650201 ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
196 ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
5650239 CTATTTTCTA
Statistics
Matches: 226, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
233 226 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (233 bp):
AACTCCCTTCAAACGGCTCTAATCTCCCATCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
TGGCTCCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAAAAAATTCTTGA
AGAACTCAAAGAGAATTTTCACTCAAAACAAATCTGAAATTTTCAATGTAATTATAATGTGTTCA
ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
Found at i:5652285 original size:22 final size:24
Alignment explanation
Indices: 5652251--5652294 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
5652241 CTTGGACCAA
5652251 GATTTCCAAGA-T-TTGAAATCTT
1 GATTTCCAAGATTCTTGAAATCTT
* *
5652273 GATTTTCATGATTCTTGAAATC
1 GATTTCCAAGATTCTTGAAATC
5652295 GCTGCAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 1 0.06
24 8 0.44
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (24 bp):
GATTTCCAAGATTCTTGAAATCTT
Found at i:5657964 original size:160 final size:160
Alignment explanation
Indices: 5657700--5658019 Score: 604
Period size: 160 Copynumber: 2.0 Consensus size: 160
5657690 AAATATTGGT
5657700 CCAAGAAACCAAATCTTGCAGCCAAATCGCATTGGATCTCCGTTACGAGCCTCAACGACCCAATT
1 CCAAGAAACCAAATCTTGCAGCCAAATCGCATTGGATCTCCGTTACGAGCCTCAACGACCCAATT
***
5657765 TTGGTAAGAGATGGAATACAAGCCCAAGTTCTTGAAGGCAAGGTCCAATAAGATGATTCCAAGCC
66 TCAATAAGAGATGGAATACAAGCCCAAGTTCTTGAAGGCAAGGTCCAATAAGATGATTCCAAGCC
5657830 CAAACAAGAAGTCCACCCATACTTAGTTGA
131 CAAACAAGAAGTCCACCCATACTTAGTTGA
5657860 CCAAGAAACCAAATCTTGCAGCCAAATCGCATTGGATCTCCGTTACGAGCCTCAACGACCCAATT
1 CCAAGAAACCAAATCTTGCAGCCAAATCGCATTGGATCTCCGTTACGAGCCTCAACGACCCAATT
5657925 TCAATAAGAGATGGAATACAAGCCCAAGTTCTTGAAGGCAAGGTCCAATAAGATGATTCCAAGCC
66 TCAATAAGAGATGGAATACAAGCCCAAGTTCTTGAAGGCAAGGTCCAATAAGATGATTCCAAGCC
*
5657990 CAATCAAGAAGTCCACCCATACTTAGTTGA
131 CAAACAAGAAGTCCACCCATACTTAGTTGA
5658020 AAATTAGGCC
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
160 156 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (160 bp):
CCAAGAAACCAAATCTTGCAGCCAAATCGCATTGGATCTCCGTTACGAGCCTCAACGACCCAATT
TCAATAAGAGATGGAATACAAGCCCAAGTTCTTGAAGGCAAGGTCCAATAAGATGATTCCAAGCC
CAAACAAGAAGTCCACCCATACTTAGTTGA
Found at i:5658687 original size:248 final size:248
Alignment explanation
Indices: 5658249--5658743 Score: 974
Period size: 248 Copynumber: 2.0 Consensus size: 248
5658239 GCCGGCCACC
5658249 CTTGTAACTCACTTCTCAATTATATTAAAAATTTTAGATTTGTTTAAGTGCAGAATTCTCTTTGA
1 CTTGTAACTCACTTCTCAATTATATTAAAAATTTTAGATTTGTTTAAGTGCAGAATTCTCTTTGA
5658314 GTTTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATTGTG
66 GTTTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATTGTG
5658379 GGAGCCATCTTCAACCTTCTTCTTGCCATTGAAATTCTTTGGAGGGGAGATTAGAGCCGTTTGAA
131 GGAGCCATCTTCAACCTTCTTCTTGCCATTGAAATTCTTTGGAGGGGAGATTAGAGCCGTTTGAA
5658444 GGGAGTTGTGGAATCTTTCGGGATTTCAAGGCTTCTTAGGACTTATCTTTTAA
196 GGGAGTTGTGGAATCTTTCGGGATTTCAAGGCTTCTTAGGACTTATCTTTTAA
5658497 CTTGTAACTCACTTCTCAATTATATTAAAAATTTTAGATTTGTTTAAGTGCAGAATTCTCTTTGA
1 CTTGTAACTCACTTCTCAATTATATTAAAAATTTTAGATTTGTTTAAGTGCAGAATTCTCTTTGA
5658562 GTTTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAA-ATATCTTTTGATTGT
66 GTTTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACA-ATCTTTTGATTGT
5658626 GGGAGCCATCTTCAACCTTCTTCTTGCCATTGAAATTCTTTGGAGGGGAGATTAGAGCCGTTTGA
130 GGGAGCCATCTTCAACCTTCTTCTTGCCATTGAAATTCTTTGGAGGGGAGATTAGAGCCGTTTGA
5658691 AGGGAGTTGTGGAATCTTTCGGGATTTCAAGGCTTCTTAGGACTTATCTTTTA
195 AGGGAGTTGTGGAATCTTTCGGGATTTCAAGGCTTCTTAGGACTTATCTTTTA
5658744 TTTGCTTGCT
Statistics
Matches: 246, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
247 1 0.00
248 245 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (248 bp):
CTTGTAACTCACTTCTCAATTATATTAAAAATTTTAGATTTGTTTAAGTGCAGAATTCTCTTTGA
GTTTTTCTCTAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATTGTG
GGAGCCATCTTCAACCTTCTTCTTGCCATTGAAATTCTTTGGAGGGGAGATTAGAGCCGTTTGAA
GGGAGTTGTGGAATCTTTCGGGATTTCAAGGCTTCTTAGGACTTATCTTTTAA
Found at i:5666281 original size:23 final size:24
Alignment explanation
Indices: 5666248--5666293 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
5666238 AAACACTTGT
5666248 TTTTTCATTTTCACACTCTTTTTC
1 TTTTTCATTTTCACACTCTTTTTC
**
5666272 TTTTTC-TTTTGTCACTCTTTTT
1 TTTTTCATTTTCACACTCTTTTT
5666294 TTTATCACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.09, C:0.22, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTTCATTTTCACACTCTTTTTC
Found at i:5670377 original size:36 final size:37
Alignment explanation
Indices: 5670337--5670409 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
5670327 TCAAAAACCT
5670337 GCAAAACAAACAC-TCAA-CACTCAAAAAGAAAAATTA
1 GCAAAACAAAC-CGTCAATCACTCAAAAAGAAAAATTA
* ** *
5670373 GCAAACCTCACCGTTAATCACTCAAAAAGAAAAATTA
1 GCAAAACAAACCGTCAATCACTCAAAAAGAAAAATTA
5670410 AATTCTCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 1 0.03
36 11 0.35
37 19 0.61
ACGTcount: A:0.55, C:0.23, G:0.07, T:0.15
Consensus pattern (37 bp):
GCAAAACAAACCGTCAATCACTCAAAAAGAAAAATTA
Found at i:5673755 original size:101 final size:100
Alignment explanation
Indices: 5673595--5673778 Score: 253
Period size: 101 Copynumber: 1.8 Consensus size: 100
5673585 ACCCGGTTCA
* * * * *
5673595 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCACCGATGCACGTACTAGCCTGCAC
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATATT-ACCGATACACATACTAGCCTGCAC
5673660 ATAGTACTACACACATGATCAAAGCTATTCGGTACG
65 ATAGTACTACACACATGATCAAAGCTATTCGGTACG
* * * *
5673696 CATAGTAGCCTACACATAGTACTACACATGCGACCTATCATT-CTGGTACACATAGTAGCCTGGA
1 CATAGTAGCCTACACATAGTACTACACATGCGACC-AT-ATTACCGATACACATACTAGCCTGCA
5673760 CATAGTACTACACACATGA
64 CATAGTACTACACACATGA
5673779 CCTAGCAACT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
101 68 0.94
102 2 0.03
103 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (100 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATATTACCGATACACATACTAGCCTGCACA
TAGTACTACACACATGATCAAAGCTATTCGGTACG
Found at i:5673781 original size:50 final size:49
Alignment explanation
Indices: 5673588--5673782 Score: 176
Period size: 50 Copynumber: 3.9 Consensus size: 49
5673578 AAATGATACC
* ** * *
5673588 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCA-C
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACATGACC--TATCATT
* * * * ** *
5673638 CGATGCACGTACTAGCCTGCACATAGTACTACACACATGATCAAAGCTATT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACATGA-CCTATC-ATT
* * ***
5673689 CGGTACGCATAGTAGCCTACACATAGTACTACACATGCGACCTATCATT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACACATGACCTATCATT
*
5673738 CTGGTACACATAGTAGCCTGGACATAGTACTACACACATGACCTA
1 C-GGTACACATAGTAGCCTGCACATAGTACTACACACATGACCTA
5673783 GCAACTTCAC
Statistics
Matches: 112, Mismatches: 29, Indels: 8
0.75 0.19 0.05
Matches are distributed among these distances:
49 5 0.04
50 75 0.67
51 32 0.29
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (49 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACACATGACCTATCATT
Found at i:5674992 original size:60 final size:60
Alignment explanation
Indices: 5674928--5675041 Score: 210
Period size: 60 Copynumber: 1.9 Consensus size: 60
5674918 TTTTATTAAG
*
5674928 ATTTTTAATATTATTTTATTATTAAATGATTAATATAAAAGGGAGGAAAGATGAAGAGAA
1 ATTTTTAATATTATTTTATTATTAAATGAATAATATAAAAGGGAGGAAAGATGAAGAGAA
*
5674988 ATTTTTAGTATTATTTTATTATTAAATGAATAATATAAAAGGGAGGAAAGATGA
1 ATTTTTAATATTATTTTATTATTAAATGAATAATATAAAAGGGAGGAAAGATGA
5675042 TGAAAAATCG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.38
Consensus pattern (60 bp):
ATTTTTAATATTATTTTATTATTAAATGAATAATATAAAAGGGAGGAAAGATGAAGAGAA
Found at i:5679553 original size:6 final size:6
Alignment explanation
Indices: 5679544--5679590 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
5679534 TTTCTTTTCC
* *
5679544 TTTCTT TTTCTT TTTCTCT CTT-TT TTTCTT GTTCTT TTTCTT TTTCT
1 TTTCTT TTTCTT TTTCT-T TTTCTT TTTCTT TTTCTT TTTCTT TTTCT
5679591 ACAGTCTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 3 0.09
6 29 0.83
7 3 0.09
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:5679554 original size:16 final size:17
Alignment explanation
Indices: 5679533--5679590 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
5679523 CTTTTTTCGA
5679533 TTTTCTTTTC-CTTTCT
1 TTTTCTTTTCTCTTTCT
5679549 TTTTCTTTTTCTCTCTT-T
1 TTTTC-TTTTCTCT-TTCT
*
5679567 TTTTCTTGTTCTTTTTCT
1 TTTTCTT-TTCTCTTTCT
5679585 TTTTCT
1 TTTTCT
5679591 ACAGTCTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 5 0.14
17 9 0.25
18 20 0.56
19 2 0.06
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTCTCTTTCT
Found at i:5682366 original size:79 final size:82
Alignment explanation
Indices: 5682235--5682419 Score: 211
Period size: 79 Copynumber: 2.3 Consensus size: 82
5682225 GCTACTCGTT
* * * *
5682235 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCGTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* * *
5682298 GGATTTAGTAAC-TCGCG
65 GGATATAGTAACTTAGCA
* **
5682315 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
5682378 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
5682395 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5682420 CATCATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.60
80 33 0.37
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:5682419 original size:40 final size:40
Alignment explanation
Indices: 5682216--5682419 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
5682206 TGGAATTGAA
** *
5682216 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
5682256 CCGGTTATAGTAACTCGCACAATTGCGTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5682296 CCGGATTTAGTAACTCGCGCAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5682335 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
5682375 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5682415 CCGGA
1 CCGGA
5682420 CATCATTCAA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.24
40 89 0.66
41 12 0.09
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:5682949 original size:118 final size:118
Alignment explanation
Indices: 5682741--5682975 Score: 434
Period size: 118 Copynumber: 2.0 Consensus size: 118
5682731 ATTTGAGCAT
*
5682741 CGAAAAGGGGAACACAAGGCACTTAGCCCATATTTATACATTAGACATTAAAGTCACATATGTAC
1 CGAAAAGAGGAACACAAGGCACTTAGCCCATATTTATACATTAGACATTAAAGTCACATATGTAC
* *
5682806 GGAATCATGAATTAAACTCAACATTTTAGCTAATTTTTCCCCCTTGGCCGAAC
66 GGAATCATGAATCAAACTCAACATTTTAGCTAATTTTTACCCCTTGGCCGAAC
*
5682859 CGAAAAGAGGAACACAAGGCACTTAGCCCATATTTATACATTAGACATTAAAGTCACATATGTAT
1 CGAAAAGAGGAACACAAGGCACTTAGCCCATATTTATACATTAGACATTAAAGTCACATATGTAC
5682924 GGAATCATGAATCAAACTCAACATTTTAGCTAATTTTTACCCCTTGGCCGAA
66 GGAATCATGAATCAAACTCAACATTTTAGCTAATTTTTACCCCTTGGCCGAA
5682976 TTTTCTAAGC
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (118 bp):
CGAAAAGAGGAACACAAGGCACTTAGCCCATATTTATACATTAGACATTAAAGTCACATATGTAC
GGAATCATGAATCAAACTCAACATTTTAGCTAATTTTTACCCCTTGGCCGAAC
Found at i:5703859 original size:23 final size:24
Alignment explanation
Indices: 5703832--5703876 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5703822 AAAATATATT
*
5703832 AAATAT-ATATTTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
5703855 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
5703877 AATACTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:5705820 original size:9 final size:9
Alignment explanation
Indices: 5705806--5705849 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
5705796 TTTTGTTACA
5705806 ACAATTAAT
1 ACAATTAAT
5705815 ACAATTAAT
1 ACAATTAAT
5705824 ACAATT-A-
1 ACAATTAAT
5705831 ACAATTAAT
1 ACAATTAAT
5705840 ACAATTAAT
1 ACAATTAAT
5705849 A
1 A
5705850 ATTTGATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.18
8 2 0.06
9 25 0.76
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:5705836 original size:16 final size:16
Alignment explanation
Indices: 5705815--5705852 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5705805 AACAATTAAT
5705815 ACAATTAATACAATTA
1 ACAATTAATACAATTA
5705831 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
5705847 ATAATT
1 ACAATT
5705853 TGATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:5705973 original size:22 final size:23
Alignment explanation
Indices: 5705945--5705999 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5705935 AAGTAACAAC
* *
5705945 TAATTTTAAT-AACAATTAGTTT
1 TAATTTTAATAAAAAAATAGTTT
* *
5705967 TAATTTTATTAAAAAAATATTTT
1 TAATTTTAATAAAAAAATAGTTT
5705990 TAATTTTAAT
1 TAATTTTAAT
5706000 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TAATTTTAATAAAAAAATAGTTT
Found at i:5711201 original size:20 final size:19
Alignment explanation
Indices: 5711176--5711224 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
5711166 ATGTAATAAT
*
5711176 CTAAGACAAATTTAATTGAA
1 CTAAGACAAA-TTAATTCAA
*
5711196 CTAAGACACAATTAATTCAG
1 CTAAGACA-AATTAATTCAA
5711216 CTAAGACAA
1 CTAAGACAA
5711225 GGCATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 23 0.88
21 2 0.08
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.24
Consensus pattern (19 bp):
CTAAGACAAATTAATTCAA
Found at i:5726563 original size:23 final size:23
Alignment explanation
Indices: 5726532--5726582 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
5726522 ACTTACTTTC
* *
5726532 TTACTGTAGTAATTTTCAGGGTA
1 TTACAGTAGTAATTTTCAGGATA
5726555 TTACAGTAGTAATTTTCAGGATA
1 TTACAGTAGTAATTTTCAGGATA
5726578 TTACA
1 TTACA
5726583 CTTATAGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCAGGATA
Found at i:5728451 original size:20 final size:19
Alignment explanation
Indices: 5728426--5728474 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
5728416 ATGTAATAAT
*
5728426 CTAAGACAAATTTAATTGAA
1 CTAAGACAAA-TTAATTCAA
*
5728446 CTAAGACAGAATTAATTCAG
1 CTAAGACA-AATTAATTCAA
5728466 CTAAGACAA
1 CTAAGACAA
5728475 GGCGTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 23 0.88
21 2 0.08
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.24
Consensus pattern (19 bp):
CTAAGACAAATTAATTCAA
Found at i:5732346 original size:38 final size:38
Alignment explanation
Indices: 5732126--5732334 Score: 278
Period size: 38 Copynumber: 5.5 Consensus size: 38
5732116 ACACCGGTAA
* * * *
5732126 TAAGCCTACTAGGCACTAAGCTTGAATAACACCGGCAT
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACTGGCAC
* *
5732164 TAAGCTTGCTAGGCACAAAGCCTGAATAACA-TCGAG-AC
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACT-G-GCAC
* * *
5732202 TAAGCCTGTTAGGCACAAAGCCTGAATAACACAGGCAC
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACTGGCAC
* * *
5732240 AAAGCCTGCTAGGCACAAAACTTGAATAACACTGGTAC
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACTGGCAC
5732278 TAAGCCTGCTAGGCACAAAGCTTGAATAACACTGGCAC
1 TAAGCCTGCTAGGCACAAAGCTTGAATAACACTGGCAC
5732316 TAAGCCTGCTAGGCACAAA
1 TAAGCCTGCTAGGCACAAA
5732335 ACGTTAATAA
Statistics
Matches: 149, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.01
38 147 0.99
39 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (38 bp):
TAAGCCTGCTAGGCACAAAGCTTGAATAACACTGGCAC
Found at i:5733322 original size:16 final size:16
Alignment explanation
Indices: 5733301--5733340 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5733291 AAAATAATTA
*
5733301 TTTATTTTTCTTAATG
1 TTTATTTTTATTAATG
* *
5733317 TTTATTTTTATTTATT
1 TTTATTTTTATTAATG
5733333 TTTATTTT
1 TTTATTTT
5733341 CTTTTTCACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTATTTTTATTAATG
Found at i:5739635 original size:22 final size:21
Alignment explanation
Indices: 5739600--5739642 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5739590 CATCACATAT
5739600 TATCTTAAAGTTTACGTTTTTC
1 TATCTTAAAGTTTAC-TTTTTC
* *
5739622 TATCTTGAATTTTACTTTTTC
1 TATCTTAAAGTTTACTTTTTC
5739643 AAATGATCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (21 bp):
TATCTTAAAGTTTACTTTTTC
Found at i:5741117 original size:22 final size:22
Alignment explanation
Indices: 5741092--5741137 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5741082 AGTGATATAC
5741092 TAAGTGATTCAATTGATTAAGT
1 TAAGTGATTCAATTGATTAAGT
5741114 TAAGTGATTCAATTGATTAAGT
1 TAAGTGATTCAATTGATTAAGT
5741136 TA
1 TA
5741138 TTAAGCATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (22 bp):
TAAGTGATTCAATTGATTAAGT
Done.