Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 145 of 185
Found at i:44040570 original size:15 final size:15
Alignment explanation
Indices: 44040535--44040576 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
44040525 TTAAGAATTT
*
44040535 TATTAAATTAT-ATA
1 TATTTAATTATAATA
44040549 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
44040563 TATTTAATAATAAT
1 TATTTAATTATAAT
44040577 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:44040818 original size:16 final size:16
Alignment explanation
Indices: 44040797--44040829 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44040787 AATTGATTTG
44040797 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
44040813 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
44040829 C
1 C
44040830 CAATACAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.33, G:0.06, T:0.42
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:44040927 original size:16 final size:16
Alignment explanation
Indices: 44040875--44040919 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
44040865 TTGGTTCGCT
44040875 GTAATGGAATAGAAGC
1 GTAATGGAATAGAAGC
44040891 GTAATGGAATAGAAGC
1 GTAATGGAATAGAAGC
*
44040907 GTAATGAAATAGA
1 GTAATGGAATAGA
44040920 GGCATAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.47, C:0.04, G:0.29, T:0.20
Consensus pattern (16 bp):
GTAATGGAATAGAAGC
Found at i:44041276 original size:120 final size:120
Alignment explanation
Indices: 44041139--44041381 Score: 452
Period size: 120 Copynumber: 2.0 Consensus size: 120
44041129 TTAATCATGT
44041139 TTTAACATAATTATTATTAAATATAATT-TAATAAAAATATATAATTTAATAAAATTCTTAATAA
1 TTTAACATAATTATTATTAAATAT-ATTATAATAAAAATATATAATTTAATAAAATTCTTAATAA
44041203 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
65 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
*
44041259 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATAAAAATATATAATTTAATAAAATTCTTAATAAT
*
44041324 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
44041379 TTT
1 TTT
44041382 CTATTTTATA
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
119 3 0.03
120 117 0.98
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTATAATAAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
Found at i:44041298 original size:16 final size:16
Alignment explanation
Indices: 44041254--44041300 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
44041244 TACTATAAAA
*
44041254 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
44041270 TATTATT-AAATATAT
1 TATAATTAAAATATAT
44041285 TATAATTAAAATATAT
1 TATAATTAAAATATAT
44041301 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:44041372 original size:61 final size:61
Alignment explanation
Indices: 44041187--44041374 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
44041177 ATATAATTTA
*
44041187 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
* * * * * * * * *
44041248 ATAAAA-T-ATAAT--TTAACATAATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTCA-AATCATAATATATGATACT
44041306 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
44041368 ATAAAAT
1 ATAAAAT
44041375 ATAATTTCTA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 1 0.01
58 4 0.04
59 31 0.32
60 16 0.17
61 38 0.40
62 4 0.04
63 2 0.02
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
Found at i:44042245 original size:11 final size:11
Alignment explanation
Indices: 44042229--44042254 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44042219 ATGCAAACTC
44042229 ACAAGCTCCAG
1 ACAAGCTCCAG
44042240 ACAAGCTCCAG
1 ACAAGCTCCAG
44042251 ACAA
1 ACAA
44042255 CAAGGGACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.35, G:0.15, T:0.08
Consensus pattern (11 bp):
ACAAGCTCCAG
Found at i:44043079 original size:33 final size:33
Alignment explanation
Indices: 44043037--44043103 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
44043027 TAAAACAGTG
44043037 CAACTTTAATATAACACCACAAGAAACCTAATA
1 CAACTTTAATATAACACCACAAGAAACCTAATA
44043070 CAACTTTAATATAACACCACAAGAAACCTAATA
1 CAACTTTAATATAACACCACAAGAAACCTAATA
44043103 C
1 C
44043104 TTACCAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.21
Consensus pattern (33 bp):
CAACTTTAATATAACACCACAAGAAACCTAATA
Found at i:44044274 original size:14 final size:14
Alignment explanation
Indices: 44044255--44044282 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44044245 AGCAGAAATC
44044255 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
44044269 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
44044283 AAATGTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:44044300 original size:18 final size:17
Alignment explanation
Indices: 44044258--44044301 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
44044248 AGAAATCTGG
*
44044258 AGAAAAGAAAATGGAGA
1 AGAAAAAAAAATGGAGA
44044275 A-AAGAAAAAAATGTGAGA
1 AGAA-AAAAAAATG-GAGA
44044293 AGAAAAAAA
1 AGAAAAAAA
44044302 GCGTACCGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 2 0.09
17 9 0.39
18 10 0.43
19 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAAATGGAGA
Found at i:44056942 original size:11 final size:11
Alignment explanation
Indices: 44056926--44056950 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44056916 AATTATTCAA
44056926 TTTTTTATTTT
1 TTTTTTATTTT
44056937 TTTTTTATTTT
1 TTTTTTATTTT
44056948 TTT
1 TTT
44056951 AAATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:44061543 original size:41 final size:41
Alignment explanation
Indices: 44061475--44061591 Score: 189
Period size: 41 Copynumber: 2.9 Consensus size: 41
44061465 TTAGCTTTTG
* * *
44061475 GGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGGTCA
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAATGGTCA
* *
44061516 GGGCTTTAGCGGCGTTTTTGAGGAAGCGCCGCAAATGGTCA
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAATGGTCA
44061557 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAA
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAA
44061592 AAAACATAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (41 bp):
GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAATGGTCA
Found at i:44061631 original size:155 final size:154
Alignment explanation
Indices: 44061425--44061705 Score: 429
Period size: 155 Copynumber: 1.8 Consensus size: 154
44061415 CGTTTTCCAA
* * * * *
44061425 AAAGCGCCGCAAATAACCTAAGCCCAACGACGCCGTTTTCTTAGCTTTTGGGGATTTAGCGGCGT
1 AAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTTAGCTGTTGGGGATTTAACAGCGT
* * **
44061490 TTTTAATAAAGCGCCGCTAATGGTCAGGGCTTTAGCGGCGTTTTTGAGGAAGCGCCGCAAATGGT
66 TTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCAAATGGT
44061555 CAGGGATTTAGCGGCGTTTTTGAG
131 CAGGGATTTAGCGGCGTTTTTGAG
* *
44061579 AAAGCGCCGCAAAAAAACATAAGCCCAACGATGCCGTTTT-TTGGGCTGTTGGGGATTTAACAGC
1 AAAGCGCCGC-AAAAAACATAAGCCCAACGACGCCGTTTTCTT-AGCTGTTGGGGATTTAACAGC
*
44061643 GTTTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGTGTTTTTGAAAAAGCGCCGCAAA
64 GTTTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCAAA
44061706 AAAACATAAG
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
154 12 0.11
155 101 0.89
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (154 bp):
AAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTTAGCTGTTGGGGATTTAACAGCGT
TTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCAAATGGT
CAGGGATTTAGCGGCGTTTTTGAG
Found at i:44061732 original size:114 final size:114
Alignment explanation
Indices: 44061520--44061999 Score: 719
Period size: 114 Copynumber: 4.2 Consensus size: 114
44061510 TGGTCAGGGC
* * * *
44061520 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAATGGTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGCGTTTTTGAAAAAGCG
* * *
44061585 CCGCAAAAAAACATAAGCCCAACGATGCCGTTTTTTGGGCTGTTGGGGA
66 CCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGA
* * *
44061634 TTTAACAGCGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGTGTTTTTGAAAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGCGTTTTTGAAAAAGCG
* *
44061699 CCGCAAAAAAACATAAGCCCAACGACGCTGTTTTGTGGGCTTTTGGTGA
66 CCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGA
* ** *
44061748 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATCGTCAGGGCCTTAGCGCCGTTTTTGAAAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGCGTTTTTGAAAAAGCG
44061813 CCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGA
66 CCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGA
* * * * * * * *
44061862 TTTTGCGACGTTTTTAAGAAAGCACCGCTAATGCTTAGGGCTTTAACGGCGTTTTTGAGAAAGCG
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGCGTTTTTGAAAAAGCG
* *
44061927 CTGC-AAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTCGGGGA
66 CCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGA
44061975 TTTAGCGGCGTTTTTAAGAAAGCGC
1 TTTAGCGGCGTTTTTAAGAAAGCGC
44062000 AGTAAAAAAA
Statistics
Matches: 330, Mismatches: 36, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
113 65 0.20
114 265 0.80
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGGTCAGGGATTTAGCGGCGTTTTTGAAAAAGCG
CCGCAAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTTTTGGGGA
Found at i:44062032 original size:73 final size:72
Alignment explanation
Indices: 44061903--44062056 Score: 236
Period size: 73 Copynumber: 2.1 Consensus size: 72
44061893 TGCTTAGGGC
* * * * * *
44061903 TTTAACGGCGTTTTTGAGAAAGCGCTGCAAAAAACATAAGCCCAACGACGCCGTTTTGTGGGCTT
1 TTTAGCGGCGTTTTTAAGAAAGCGCAGAAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCTT
44061968 TCGGGGA
66 TCGGGGA
*
44061975 TTTAGCGGCGTTTTTAAGAAAGCGCAGTAAAAAAACATAAGCCAAATGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCAG-AAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCT
44062040 TTCGGGGA
65 TTCGGGGA
44062048 TTTAGCGGC
1 TTTAGCGGC
44062057 CAAAAAAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 24 0.32
73 50 0.68
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (72 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCAGAAAAAAACATAAGCCAAACGACGCCGTTTTGTGAGCTT
TCGGGGA
Found at i:44062243 original size:14 final size:14
Alignment explanation
Indices: 44062209--44062257 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
44062199 TAAGGCCGGT
* *
44062209 TTAGGGAGTATGGCT
1 TTAGGGATTATGG-A
44062224 TTAGGGATTATGGA
1 TTAGGGATTATGGA
44062238 TTAGGGATTATGGA
1 TTAGGGATTATGGA
44062252 TTAGGG
1 TTAGGG
44062258 GTTGGGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.24, C:0.02, G:0.39, T:0.35
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:44062289 original size:15 final size:15
Alignment explanation
Indices: 44062223--44062291 Score: 54
Period size: 14 Copynumber: 4.8 Consensus size: 15
44062213 GGAGTATGGC
* *
44062223 TTTAGGGATTATGGA
1 TTTAGGGGTTAGGGA
* *
44062238 -TTAGGGATTATGGA
1 TTTAGGGGTTAGGGA
44062252 -TTAGGGGTT-GGGA
1 TTTAGGGGTTAGGGA
** *
44062265 TTTAAAGGTTAGGGG
1 TTTAGGGGTTAGGGA
44062280 TTTAGGGGTTAG
1 TTTAGGGGTTAG
44062292 ACGTGCTAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
13 3 0.07
14 29 0.64
15 13 0.29
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (15 bp):
TTTAGGGGTTAGGGA
Found at i:44062527 original size:14 final size:15
Alignment explanation
Indices: 44062493--44062531 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
44062483 ATTTTAAGGT
* *
44062493 TTAGGGAGTATGGAT
1 TTAGGGATTATGGAA
44062508 TTAGGGATTAT-GAA
1 TTAGGGATTATGGAA
44062522 TTAGGGATTA
1 TTAGGGATTA
44062532 CGATTTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
TTAGGGATTATGGAA
Found at i:44062607 original size:15 final size:14
Alignment explanation
Indices: 44062550--44062606 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 14
44062540 GTGTTTGGAT
44062550 TTAAGGTTTAGGGG
1 TTAAGGTTTAGGGG
44062564 TTAAGGGTTTAGGGG
1 TTAA-GGTTTAGGGG
44062579 TTAAGAG-TTAGGGAG
1 TTAAG-GTTTAGGG-G
44062594 TTAAGGTTTAGGG
1 TTAAGGTTTAGGG
44062607 ATTCAGGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
14 12 0.31
15 27 0.69
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (14 bp):
TTAAGGTTTAGGGG
Found at i:44063863 original size:72 final size:72
Alignment explanation
Indices: 44063645--44063863 Score: 154
Period size: 72 Copynumber: 3.1 Consensus size: 72
44063635 TTAGCATAGC
44063645 ATAGCAAAACGGCGTAGTTTTATTCAAAATAAAATTTTTTTGCGGCGTTAAAAACACCGCTAAAG
1 ATAGCAAAACGGCGTAGTTTTATTCAAAATAAAATTTTTTTGCGGCGTTAAAAACACCGCTAAAG
44063710 GTAAGCA
66 GTAAGCA
* ** * ** * ** *
44063717 ATAG-----CGGCGT--TTTTGTAAAAAACGCCACAAAATAATTTTAC--TTTTAAAAAATAGCC
1 ATAGCAAAACGGCGTAGTTTTAT-TCAAA----ATAAAATTTTTTTGCGGCGTT-AAAAACA-CC
* ** *
44063773 CCTTTTA-GCATAGC-
59 GC-TAAAGGTA-AGCA
44063787 ATAGCAAAACGGCGTAGTTTTATTCAAAATAAAATTTTTTTGCGGCGTTAAAAACACCGCTAAAG
1 ATAGCAAAACGGCGTAGTTTTATTCAAAATAAAATTTTTTTGCGGCGTTAAAAACACCGCTAAAG
44063852 GTAAGCA
66 GTAAGCA
44063859 ATAGC
1 ATAGC
44063864 GGCGTTTTTG
Statistics
Matches: 99, Mismatches: 28, Indels: 40
0.59 0.17 0.24
Matches are distributed among these distances:
65 5 0.05
66 3 0.03
67 6 0.06
68 2 0.02
69 6 0.06
70 20 0.20
71 10 0.10
72 25 0.25
73 6 0.06
74 2 0.02
75 6 0.06
76 3 0.03
77 5 0.05
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (72 bp):
ATAGCAAAACGGCGTAGTTTTATTCAAAATAAAATTTTTTTGCGGCGTTAAAAACACCGCTAAAG
GTAAGCA
Found at i:44064209 original size:148 final size:145
Alignment explanation
Indices: 44063502--44064474 Score: 1500
Period size: 148 Copynumber: 6.6 Consensus size: 145
44063492 AATTTTTAGA
*
44063502 ATAGCAAAACGGCGTAGTTTTATTCAAAAT-AAAATTTTTTTGCGGCG--TTAAAAACACCGCTA
1 ATAGCAAAACGGCGTAGTTTTATTCAAAATGAAAA-TTTTTTGCGGCGTTTTAAAAACGCCGCTA
44063564 AAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATAGC
65 AAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATAGC
44063629 CCCCTTTTAGCATAGC
130 CCCCTTTTAGCATAGC
*
44063645 ATAGCAAAACGGCGTAGTTTTATTCAAAAT-AAAATTTTTTTGCGGCG--TTAAAAACACCGCTA
1 ATAGCAAAACGGCGTAGTTTTATTCAAAATGAAAA-TTTTTTGCGGCGTTTTAAAAACGCCGCTA
44063707 AAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATAG-
65 AAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATAGC
44063771 CCCCTTTTAGCATAGC
130 CCCCTTTTAGCATAGC
*
44063787 ATAGCAAAACGGCGTAGTTTTATTCAAAAT-AAAATTTTTTTGCGGCG--TTAAAAACACCGCTA
1 ATAGCAAAACGGCGTAGTTTTATTCAAAATGAAAA-TTTTTTGCGGCGTTTTAAAAACGCCGCTA
44063849 AAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATAG-
65 AAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATAGC
44063913 CCCCTTTTAGCATAGC
130 CCCCTTTTAGCATAGC
44063929 ATAGCAAAACGGCGTAGTTTTATTCAAAATGAAAAATTTTTTGCGGCGTTTTTATGAAAAAATAA
1 ATAGCAAAACGGCGTAGTTTTATTCAAAATG-AAAATTTTTTGCGGCG---TT-T-------TAA
*
44063994 AAACGCCGCTAAAGGTAAGCAATAGCGACGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTT
54 AAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTT
44064059 TAAAAAATAGCCCCCTTTTAGCATAGC
119 TAAAAAATAGCCCCCTTTTAGCATAGC
*
44064086 ATAGCAAAACGGTGTAGTTTTATTCAAAATGAAAATTTTTTGCGGCGTTTGCGTAAAAACGCCGC
1 ATAGCAAAACGGCGTAGTTTTATTCAAAATGAAAATTTTTTGCGGCGTTT---TAAAAACGCCGC
44064151 TAAAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATA
63 TAAAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATA
44064216 GCCCCCTTTTAGCATAGC
128 GCCCCCTTTTAGCATAGC
*
44064234 ATAGCAAAACGGTGTAGTTTTATTCAAAATGAAAATTTTTTGCGGCGTTTGCGTAAAAACGCCGC
1 ATAGCAAAACGGCGTAGTTTTATTCAAAATGAAAATTTTTTGCGGCGTTT---TAAAAACGCCGC
44064299 TAAAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATA
63 TAAAGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATA
* *
44064364 GCCCCATTTTAACATAGC
128 GCCCCCTTTTAGCATAGC
** ** *
44064382 ATAGCAAAACGGTATAGTTTTATTCAAAATGAAAAAACTTTTACGGCGTGTTTATAAAAAACGCC
1 ATAGCAAAACGGCGTAGTTTTATTCAAAATG-AAAATTTTTTGCGGC--GTTT-T-AAAAACGCC
* *
44064447 GCTAAAAGTAAGCAATAGTGGCGTTTTT
61 GCTAAAGGTAAGCAATAGCGGCGTTTTT
44064475 AAAGAAAACG
Statistics
Matches: 794, Mismatches: 16, Indels: 33
0.94 0.02 0.04
Matches are distributed among these distances:
142 188 0.24
143 138 0.17
144 4 0.01
148 270 0.34
149 14 0.02
150 35 0.04
151 4 0.01
152 1 0.00
153 2 0.00
156 92 0.12
157 46 0.06
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (145 bp):
ATAGCAAAACGGCGTAGTTTTATTCAAAATGAAAATTTTTTGCGGCGTTTTAAAAACGCCGCTAA
AGGTAAGCAATAGCGGCGTTTTTGTAAAAAACGCCACAAAATAATTTTACTTTTAAAAAATAGCC
CCCTTTTAGCATAGC
Found at i:44064488 original size:15 final size:15
Alignment explanation
Indices: 44064468--44064499 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
44064458 GCAATAGTGG
44064468 CGTTTTTAAAGAAAA
1 CGTTTTTAAAGAAAA
44064483 CGTTTTTAAAGAAAA
1 CGTTTTTAAAGAAAA
44064498 CG
1 CG
44064500 CCACAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (15 bp):
CGTTTTTAAAGAAAA
Found at i:44065924 original size:15 final size:15
Alignment explanation
Indices: 44065904--44065933 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44065894 CTTATAGGTT
*
44065904 TAAATTATTATATAG
1 TAAATTAGTATATAG
44065919 TAAATTAGTATATAG
1 TAAATTAGTATATAG
44065934 AATCATCGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (15 bp):
TAAATTAGTATATAG
Found at i:44068174 original size:12 final size:12
Alignment explanation
Indices: 44068154--44068186 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
44068144 TTGTTTCAGG
44068154 TTGTATTATTAA
1 TTGTATTATTAA
*
44068166 TTGTGTTATTAA
1 TTGTATTATTAA
44068178 TT-TATTATT
1 TTGTATTATT
44068187 TTAAATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (12 bp):
TTGTATTATTAA
Found at i:44070987 original size:30 final size:29
Alignment explanation
Indices: 44070930--44070987 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
44070920 TGATTTGAAT
*
44070930 TTTTTAAAAATATTATATAATTTTCATAA
1 TTTTTAAAAATATTATATAATTCTCATAA
*
44070959 TTTTTAATAATGATTATAT-ATTACTCATA
1 TTTTTAAAAAT-ATTATATAATT-CTCATA
44070988 TGAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTTTAAAAATATTATATAATTCTCATAA
Found at i:44074794 original size:6 final size:6
Alignment explanation
Indices: 44074783--44074807 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44074773 ATTGATAATA
44074783 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
44074808 AAAATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:44077799 original size:16 final size:16
Alignment explanation
Indices: 44077778--44077810 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
44077768 AATTAATATC
44077778 TTAATTCTGTCTAGTA
1 TTAATTCTGTCTAGTA
*
44077794 TTAATTTTGTCTAGTA
1 TTAATTCTGTCTAGTA
44077810 T
1 T
44077811 AAAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (16 bp):
TTAATTCTGTCTAGTA
Found at i:44087622 original size:7 final size:7
Alignment explanation
Indices: 44087592--44087621 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
44087582 CACAGAAGCT
44087592 AAAGAGA
1 AAAGAGA
44087599 AAAGAGA
1 AAAGAGA
44087606 AAAGAGA
1 AAAGAGA
44087613 AAAGA-A
1 AAAGAGA
44087619 AAA
1 AAA
44087622 AAAACCCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAGAGA
Found at i:44097956 original size:25 final size:25
Alignment explanation
Indices: 44097928--44097982 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
44097918 CTTACGATCA
*
44097928 TTTTTGAACCAA-TATTCTTTCAGTT
1 TTTTTGAA-CAATTATTATTTCAGTT
* *
44097953 TTTTTGAATAATTATTATTTCATTT
1 TTTTTGAACAATTATTATTTCAGTT
44097978 TTTTT
1 TTTTT
44097983 AGATTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.24, C:0.09, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTTTGAACAATTATTATTTCAGTT
Found at i:44099369 original size:17 final size:16
Alignment explanation
Indices: 44099340--44099378 Score: 69
Period size: 17 Copynumber: 2.4 Consensus size: 16
44099330 AGGGTTTTTT
44099340 TTATATTATTTAATAA
1 TTATATTATTTAATAA
44099356 TTATATTCATTTAATAA
1 TTATATT-ATTTAATAA
44099373 TTATAT
1 TTATAT
44099379 AAATATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTATTTAATAA
Found at i:44102942 original size:17 final size:17
Alignment explanation
Indices: 44102920--44102954 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44102910 ATCACATAAA
44102920 CCCTAGCCCAAACCTAC
1 CCCTAGCCCAAACCTAC
44102937 CCCTAGCCCAAACCTAC
1 CCCTAGCCCAAACCTAC
44102954 C
1 C
44102955 AACCCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.54, G:0.06, T:0.11
Consensus pattern (17 bp):
CCCTAGCCCAAACCTAC
Found at i:44103631 original size:25 final size:25
Alignment explanation
Indices: 44103603--44103657 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
44103593 CTTACGATCA
*
44103603 TTTTTGAACCAA-TATTCTTTCAGTT
1 TTTTTGAA-CAATTATTATTTCAGTT
* *
44103628 TTTTTGAATAATTATTATTTCATTT
1 TTTTTGAACAATTATTATTTCAGTT
44103653 TTTTT
1 TTTTT
44103658 AGATTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.24, C:0.09, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTTTGAACAATTATTATTTCAGTT
Found at i:44105044 original size:17 final size:16
Alignment explanation
Indices: 44105015--44105053 Score: 69
Period size: 17 Copynumber: 2.4 Consensus size: 16
44105005 AGGGTTTTTT
44105015 TTATATTATTTAATAA
1 TTATATTATTTAATAA
44105031 TTATATTCATTTAATAA
1 TTATATT-ATTTAATAA
44105048 TTATAT
1 TTATAT
44105054 AAATATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTATTTAATAA
Found at i:44110714 original size:110 final size:109
Alignment explanation
Indices: 44110604--44110928 Score: 372
Period size: 109 Copynumber: 3.0 Consensus size: 109
44110594 AAAAAGAAAT
* * *
44110604 TTTTCTAAATAAGGCAATATTTTGCATTTGGAAGTTCGAGAAAGCGTGCCCTAATGTGCTGGGTT
1 TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAA-CGTGCCCTAATGTGCTGGGTT
* *
44110669 TCG-TTTTTCTCGTTCGACCTAATAGCCAAATATCCTTTTAAAAA
65 TCGATTTTTCTCATTCGACCAAATAGCCAAATATCCTTTTAAAAA
* * *
44110713 TTTT-AAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
1 TTTTCAAAATAAGGCAATATTTTGCGTTT-GGAAATTCGAG-AAACGTGCCCTAATGTGCTGGGT
* * * *
44110777 GTCGATTTTTCTCATTCAACCAAAT-GACTAAATATCATTTTAAAAA
64 TTCGATTTTTCTCATTCGACCAAATAG-CCAAATATCCTTTTAAAAA
* * ** ** *
44110823 -TTTCGAAGTAAGATAATATTTTGCGTTTGGAAATTTAAGGAAACGTGCCCTAATGCGCTGGGTT
1 TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGA-GAAACGTGCCCTAATGTGCTGGGTT
* * *
44110887 TCGATTTTTC-CATTTGACCAAATAGCCAAATATTCTCTTAAA
65 TCGATTTTTCTCATTCGACCAAATAGCCAAATATCCTTTTAAA
44110929 TCTTAATCCA
Statistics
Matches: 180, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
108 45 0.25
109 78 0.43
110 57 0.32
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (109 bp):
TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCATTCGACCAAATAGCCAAATATCCTTTTAAAAA
Found at i:44126146 original size:22 final size:20
Alignment explanation
Indices: 44126121--44126160 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
44126111 TTTGTTTCAA
44126121 ATCTTAAATTTGATTTATATTT
1 ATCTTAAATTT--TTTATATTT
44126143 ATCTTAAATTTTTTATAT
1 ATCTTAAATTTTTTATAT
44126161 GAAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (20 bp):
ATCTTAAATTTTTTATATTT
Found at i:44137045 original size:38 final size:38
Alignment explanation
Indices: 44137001--44137076 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
44136991 AATCTATGTT
44137001 AGTTCCAGATTTTCAGTTTAATTGAATAAGTTGTTAGC
1 AGTTCCAGATTTTCAGTTTAATTGAATAAGTTGTTAGC
44137039 AGTTCCAGATTTTCAGTTTAATTGAATAAGTTGTTAGC
1 AGTTCCAGATTTTCAGTTTAATTGAATAAGTTGTTAGC
44137077 TATTTTTGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (38 bp):
AGTTCCAGATTTTCAGTTTAATTGAATAAGTTGTTAGC
Found at i:44141911 original size:15 final size:14
Alignment explanation
Indices: 44141885--44141927 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
44141875 AGTTTTAAAA
*
44141885 ATAAAGAATTAAATT
1 ATAAA-AATTAAATG
*
44141900 ATGATAAATTAAATG
1 AT-AAAAATTAAATG
44141915 ATAAAAATTAAAT
1 ATAAAAATTAAAT
44141928 CTTAAATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 10 0.42
15 12 0.50
16 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
ATAAAAATTAAATG
Found at i:44146252 original size:17 final size:17
Alignment explanation
Indices: 44146213--44146255 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
44146203 TTTTGCATAT
*
44146213 ATTAAATTTTAATTTTA
1 ATTAATTTTTAATTTTA
44146230 ATTTAATTTTTACA-TTTA
1 A-TTAATTTTTA-ATTTTA
44146248 ATTAATTT
1 ATTAATTT
44146256 CTTTTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 14 0.61
19 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTAATTTTTAATTTTA
Found at i:44166750 original size:140 final size:138
Alignment explanation
Indices: 44166498--44166910 Score: 465
Period size: 140 Copynumber: 2.9 Consensus size: 138
44166488 GTCGGCACAA
* * * * *
44166498 TGTTGGACAAAACTGACTTTTATTTAAGTGTTGCCTTAGGCATGCATATCTCAGCCTTTACACAA
1 TGTTGGACAAAATTGACTTTTATTTAAGCGTTGTCTTAGGCATGCATATCTCAACC-TTATACAA
* * * ** *** * * *
44166563 AGATTTGGTCAAAGCGTACACCGACAAGTCTATCCCAACACTTAGGAAAGTGTTGGCCCAAAAGT
65 AGAGTT-GACCAAGAATATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAGT
44166628 GTC-GACATAG
129 GTCGGA-ATAG
*
44166638 TGTTGGACAAAATTGACTTTTATTTAAGCGTTGTCTTAGGTATGCATATCTCAACCATTATACAA
1 TGTTGGACAAAATTGACTTTTATTTAAGCGTTGTCTTAGGCATGCATATCTCAACC-TTATACAA
* *
44166703 AGAGTTGACCAAGGAATATGTCGGTAAGTCTATCCGAACACTTAGGAAAGTGTCGACCCAAAAGT
65 AGAGTTGACCAA-GAATATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAGT
44166768 GTCGGAATAG
129 GTCGGAATAG
* * * * *
44166778 TATTGGACAAAGTCGA-TTCTTATTTAAGCATT-TCCTTAGGCATGCATATCCCAAGCCTTATAC
1 TGTTGGACAAAATTGACTT-TTATTTAAGCGTTGT-CTTAGGCATGCATATCTCAA-CCTTATAC
** *
44166841 AAAGAGTTGACCAA-AACGTATGTTAGCAAGTCTATCCCAACACTTAGAAAAGTGTCGACCCAAA
63 AAAGAGTTGACCAAGAA--TATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAA
44166905 AGTGTC
126 AGTGTC
44166911 ACCTTAAGAC
Statistics
Matches: 235, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
138 2 0.01
139 7 0.03
140 222 0.94
141 4 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (138 bp):
TGTTGGACAAAATTGACTTTTATTTAAGCGTTGTCTTAGGCATGCATATCTCAACCTTATACAAA
GAGTTGACCAAGAATATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAGTGT
CGGAATAG
Found at i:44167230 original size:8 final size:8
Alignment explanation
Indices: 44167217--44167248 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
44167207 GACAAAATAT
44167217 ATATTATA
1 ATATTATA
44167225 ATATTATA
1 ATATTATA
44167233 ATATTATA
1 ATATTATA
44167241 ATATTATA
1 ATATTATA
44167249 TGTTAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTATA
Found at i:44167282 original size:16 final size:16
Alignment explanation
Indices: 44167213--44167291 Score: 65
Period size: 16 Copynumber: 4.8 Consensus size: 16
44167203 AGGCGACAAA
44167213 ATATATATTATAATAT
1 ATATATATTATAATAT
44167229 -TATAATATTATAATATT
1 ATAT-ATATTATAATA-T
* *
44167246 ATATGTTAATTATTAA-GT
1 ATAT-AT-ATTA-TAATAT
*
44167264 ATATATATTATATTAT
1 ATATATATTATAATAT
44167280 ATAT-TATTATAA
1 ATATATATTATAA
44167292 GTAAATATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
15 12 0.24
16 20 0.40
17 2 0.04
18 9 0.18
19 4 0.08
20 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATATATATTATAATAT
Found at i:44167300 original size:30 final size:32
Alignment explanation
Indices: 44167232--44167300 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
44167222 ATAATATTAT
*
44167232 AATATTATAATATTATATGTTAATTATTAAGTA
1 AATA-TATAATATTATATATTAATTATTAAGTA
* *
44167265 TATATATTATATTATATATT-ATTA-TAAGTA
1 AATATATAATATTATATATTAATTATTAAGTA
44167295 AATATA
1 AATATA
44167301 ATAAATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 11 0.34
31 4 0.12
32 14 0.44
33 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (32 bp):
AATATATAATATTATATATTAATTATTAAGTA
Found at i:44167555 original size:41 final size:42
Alignment explanation
Indices: 44167502--44167587 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 42
44167492 TTTAAAAATT
44167502 AAAAAAGTATTTTAAAAATATTTTAAAA-TAAAAAAATAAAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAAA
*
44167543 AAAAAAGTATTTTAAAAGTATTTTAAAATTAAAAAAATAAAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAAA
44167585 AAA
1 AAA
44167588 TAAAAAAAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 27 0.63
42 16 0.37
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (42 bp):
AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAAA
Found at i:44167559 original size:11 final size:11
Alignment explanation
Indices: 44167545--44167570 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44167535 AAATAAAAAA
44167545 AAAAGTATTTT
1 AAAAGTATTTT
44167556 AAAAGTATTTT
1 AAAAGTATTTT
44167567 AAAA
1 AAAA
44167571 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:44168486 original size:11 final size:11
Alignment explanation
Indices: 44168470--44168551 Score: 50
Period size: 11 Copynumber: 7.9 Consensus size: 11
44168460 GTGATGAATT
44168470 TATTGAATTTA
1 TATTGAATTTA
*
44168481 TATTG-ATTGA
1 TATTGAATTTA
* *
44168491 -ATTGGTATATA
1 TATT-GAATTTA
*
44168502 TATTGAATATA
1 TATTGAATTTA
44168513 TATTG-A-TTA
1 TATTGAATTTA
*
44168522 T-TTGAATTGA
1 TATTGAATTTA
*
44168532 -ATTGAATATA
1 TATTGAATTTA
*
44168542 TATTGTATTT
1 TATTGAATTT
44168552 GAAAAGTGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
8 3 0.06
9 7 0.13
10 15 0.28
11 26 0.48
12 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.51
Consensus pattern (11 bp):
TATTGAATTTA
Found at i:44168506 original size:17 final size:14
Alignment explanation
Indices: 44168469--44168516 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
44168459 TGTGATGAAT
44168469 TTATTGAATTTATA
1 TTATTGAATTTATA
44168483 TTGATTGAATTGGTATA
1 TT-ATTGAATT--TATA
*
44168500 TATATTGAATATATA
1 T-TATTGAATTTATA
44168515 TT
1 TT
44168517 GATTATTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 3 0.10
15 13 0.45
17 12 0.41
18 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (14 bp):
TTATTGAATTTATA
Found at i:44168561 original size:29 final size:28
Alignment explanation
Indices: 44168503--44168566 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
44168493 TGGTATATAT
*
44168503 ATTGAATATATATTGATTATTTGAATTGA
1 ATTGAATATATATTGA-TATTTGAAGTGA
44168532 ATTGAATATATATTG-TATTTGAAAAGTGA
1 ATTGAATATATATTGATATTTG--AAGTGA
44168561 ATTGAA
1 ATTGAA
44168567 ACCCTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 6 0.19
29 26 0.81
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (28 bp):
ATTGAATATATATTGATATTTGAAGTGA
Found at i:44168664 original size:41 final size:40
Alignment explanation
Indices: 44168601--44168723 Score: 119
Period size: 37 Copynumber: 3.1 Consensus size: 40
44168591 GTCGGATGTA
* *
44168601 GATGAGACACTAGGTGTTAATTTACTACTTCGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAATTC
* * * *
44168642 GATTAGGCACTGGGTGTCAATTTAT--TTCGGTTTAA-CC
1 GATGAGACACTGGGTGTCAATTTATACTTCGGATTAATTC
* * *
44168679 GATGAGACACTGAGTGTCTATTTATTACTTCGAATT-ATTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAATTC
44168719 GATGA
1 GATGA
44168724 TGCACTAGGT
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
37 21 0.32
38 10 0.15
39 1 0.02
40 13 0.20
41 20 0.31
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATACTTCGGATTAATTC
Found at i:44171654 original size:96 final size:96
Alignment explanation
Indices: 44171490--44171683 Score: 291
Period size: 96 Copynumber: 2.0 Consensus size: 96
44171480 TATTATCAAT
* * * *
44171490 ATATATGTAATGAGTAACTAAGCTTTACTCGTATAGTATTCAATATGTTATCCAGTCTTTTGCAA
1 ATATATATAATGAGTAACTAAGCTTTACTCGTATAATATTCAATATGTTATCCAGTCTATTACAA
*
44171555 CAAAATGGGGGCATCGCCTCACATTTCGATC
66 CAAAATGGGGACATCGCCTCACATTTCGATC
* *
44171586 ATATATATAATGAGTAACTAAGCTTTACTCTTATAATATTCAATATTTTATCCAGAT-TATTACA
1 ATATATATAATGAGTAACTAAGCTTTACTCGTATAATATTCAATATGTTATCCAG-TCTATTACA
* *
44171650 ACAAAATGGGGATATCGCCTTACATTTCGATC
65 ACAAAATGGGGACATCGCCTCACATTTCGATC
44171682 AT
1 AT
44171684 CGCTTCATAC
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 87 0.99
97 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (96 bp):
ATATATATAATGAGTAACTAAGCTTTACTCGTATAATATTCAATATGTTATCCAGTCTATTACAA
CAAAATGGGGACATCGCCTCACATTTCGATC
Found at i:44176394 original size:42 final size:42
Alignment explanation
Indices: 44176346--44176537 Score: 233
Period size: 42 Copynumber: 4.5 Consensus size: 42
44176336 AACAGAAACC
* * ** *
44176346 CATAAGGGTTGAACGGAAGCTCGTAAGAGCTGAA-TGAAAAT
1 CATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGGAAAAT
* *
44176387 CGATAAGGGTTAAACTGAAGCTTAAAAGAGCTGAACGGAAACT
1 C-ATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGGAAAAT
**
44176430 CATAAGGGTTAAACTGAAGCTCAAAAAGAGCTGAACGGAAACC
1 CATAAGGGTTAAACTGAAGCTC-AAAAGAGCTGAACGGAAAAT
** **
44176473 CATAAGGCCTAAACTGAAGCTCAAAAGAGCTGAACGGAAACC
1 CATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGGAAAAT
*
44176515 CATAAGGGTTAAACTGAAACTCA
1 CATAAGGGTTAAACTGAAGCTCA
44176538 TATGAGTTAA
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 88 0.66
43 45 0.34
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (42 bp):
CATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGGAAAAT
Found at i:44176491 original size:85 final size:85
Alignment explanation
Indices: 44176340--44176537 Score: 272
Period size: 85 Copynumber: 2.3 Consensus size: 85
44176330 GTGCTAAACA
* * ** * * * **
44176340 GAAACCCATAAGGGTTGAACGGAAGCTC-GTAAGAGCTGAATGAAAATCGATAAGGGTTAAACTG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAAGAGCTGAACGAAAACCCATAAGGCCTAAACTG
*
44176404 AAGCTTAAAAGAGCTGAACG
66 AAGCTCAAAAGAGCTGAACG
* *
44176424 GAAACTCATAAGGGTTAAACTGAAGCTCAAAAAGAGCTGAACGGAAACCCATAAGGCCTAAACTG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAAGAGCTGAACGAAAACCCATAAGGCCTAAACTG
44176489 AAGCTCAAAAGAGCTGAACG
66 AAGCTCAAAAGAGCTGAACG
*
44176509 GAAACCCATAAGGGTTAAACTGAAACTCA
1 GAAACCCATAAGGGTTAAACTGAAGCTCA
44176538 TATGAGTTAA
Statistics
Matches: 99, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 25 0.25
85 74 0.75
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (85 bp):
GAAACCCATAAGGGTTAAACTGAAGCTCAAAAAGAGCTGAACGAAAACCCATAAGGCCTAAACTG
AAGCTCAAAAGAGCTGAACG
Found at i:44176539 original size:21 final size:21
Alignment explanation
Indices: 44176332--44176539 Score: 103
Period size: 21 Copynumber: 9.9 Consensus size: 21
44176322 GCACACAAGT
* *
44176332 GCTAAACAGAAACCCATAAGG
1 GCTAAACTGAAACTCATAAGG
* * * * * *
44176353 GTTGAACGGAAGCTCGTAAGA
1 GCTAAACTGAAACTCATAAGG
* *
44176374 GCTGAA-TGAAAATCGATAAGG
1 GCTAAACTGAAACTC-ATAAGG
* * * * *
44176395 GTTAAACTGAAGCTTAAAAGA
1 GCTAAACTGAAACTCATAAGG
* *
44176416 GCTGAACGGAAACTCATAAGG
1 GCTAAACTGAAACTCATAAGG
* * * *
44176437 GTTAAACTGAAGCTCAAAAAGA
1 GCTAAACTGAAACTC-ATAAGG
* * *
44176459 GCTGAACGGAAACCCATAAGG
1 GCTAAACTGAAACTCATAAGG
* * * *
44176480 CCTAAACTGAAGCTCAAAAGA
1 GCTAAACTGAAACTCATAAGG
* * *
44176501 GCTGAACGGAAACCCATAAGG
1 GCTAAACTGAAACTCATAAGG
*
44176522 GTTAAACTGAAACTCATA
1 GCTAAACTGAAACTCATA
44176540 TGAGTTAACA
Statistics
Matches: 126, Mismatches: 58, Indels: 6
0.66 0.31 0.03
Matches are distributed among these distances:
20 5 0.04
21 102 0.81
22 19 0.15
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
GCTAAACTGAAACTCATAAGG
Found at i:44176848 original size:45 final size:46
Alignment explanation
Indices: 44176763--44176849 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
44176753 ATTTCAATTT
* * *
44176763 ATAATTTAACAATATTTCATTTTTTTAACAATATGCTAAATATATA
1 ATAATTTAACAATATTTCATTTTTTCAAAAATATACTAAATATATA
*
44176809 ATAATTTAACAATATTTCA-TTTTTCAAAAATATATTAAATA
1 ATAATTTAACAATATTTCATTTTTTCAAAAATATACTAAATA
44176850 CGTAACATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 18 0.49
46 19 0.51
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (46 bp):
ATAATTTAACAATATTTCATTTTTTCAAAAATATACTAAATATATA
Found at i:44208146 original size:44 final size:42
Alignment explanation
Indices: 44208061--44208148 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 42
44208051 TTTGAAATAA
44208061 AATAAAAGTTGTGATAATTACATTTAAAAATAATTACAATTT
1 AATAAAAGTTGTGATAATTACATTTAAAAATAATTACAATTT
* *
44208103 AATAGAAA-TTGTGATAATTACACATTTAAAAATATTTAGAATTT
1 AATA-AAAGTTGTGATAATT--ACATTTAAAAATAATTACAATTT
44208147 AA
1 AA
44208149 ATTACAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 15 0.37
43 3 0.07
44 23 0.56
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.38
Consensus pattern (42 bp):
AATAAAAGTTGTGATAATTACATTTAAAAATAATTACAATTT
Found at i:44221469 original size:18 final size:18
Alignment explanation
Indices: 44221433--44221471 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
44221423 ATATAAAAAT
* **
44221433 ATTTTAAATAATTTTTTA
1 ATTTTAAAAAATTAATTA
44221451 ATTTTAAAAAATTAATTA
1 ATTTTAAAAAATTAATTA
44221469 ATT
1 ATT
44221472 GTTGACGTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAAAAAATTAATTA
Found at i:44226865 original size:22 final size:21
Alignment explanation
Indices: 44226840--44226889 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
44226830 TGTTTTCAGA
* *
44226840 TTTATTTCGAATTTAGCTTTTT
1 TTTATTTC-AATTTAACCTTTT
*
44226862 TTTAGTTCAATTTAACCTTTT
1 TTTATTTCAATTTAACCTTTT
44226883 TTTATTT
1 TTTATTT
44226890 TTATTCATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.64
Consensus pattern (21 bp):
TTTATTTCAATTTAACCTTTT
Found at i:44228228 original size:12 final size:11
Alignment explanation
Indices: 44228206--44228231 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44228196 AAAATGCAGT
44228206 AAAACAAAAAA
1 AAAACAAAAAA
44228217 AAAACAAAAAA
1 AAAACAAAAAA
44228228 AAAA
1 AAAA
44228232 TATGGTAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:44235278 original size:98 final size:98
Alignment explanation
Indices: 44235109--44235310 Score: 404
Period size: 98 Copynumber: 2.1 Consensus size: 98
44235099 CTTAGGTGAT
44235109 CTACATGCTTGGAGAATCTCTACAACCATATGATGTTAAGGATCCCAATATCATTTAATTCCAAA
1 CTACATGCTTGGAGAATCTCTACAACCATATGATGTTAAGGATCCCAATATCATTTAATTCCAAA
44235174 TTGAACAGACTCAATGGTACCTTTAAAGCTTCC
66 TTGAACAGACTCAATGGTACCTTTAAAGCTTCC
44235207 CTACATGCTTGGAGAATCTCTACAACCATATGATGTTAAGGATCCCAATATCATTTAATTCCAAA
1 CTACATGCTTGGAGAATCTCTACAACCATATGATGTTAAGGATCCCAATATCATTTAATTCCAAA
44235272 TTGAACAGACTCAATGGTACCTTTAAAGCTTCC
66 TTGAACAGACTCAATGGTACCTTTAAAGCTTCC
44235305 CTACAT
1 CTACAT
44235311 ATATAAGCTA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 104 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.31
Consensus pattern (98 bp):
CTACATGCTTGGAGAATCTCTACAACCATATGATGTTAAGGATCCCAATATCATTTAATTCCAAA
TTGAACAGACTCAATGGTACCTTTAAAGCTTCC
Found at i:44239857 original size:24 final size:23
Alignment explanation
Indices: 44239826--44239871 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
44239816 GGTTAATGAC
44239826 TTTAGTTT-CAACTATATATTTGA
1 TTTAGTTTGC-ACTATATATTTGA
*
44239849 TTTATGTTTGCATTATATATTTG
1 TTTA-GTTTGCACTATATATTTG
44239872 GCTTAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 15 0.75
25 1 0.05
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.57
Consensus pattern (23 bp):
TTTAGTTTGCACTATATATTTGA
Found at i:44243649 original size:21 final size:21
Alignment explanation
Indices: 44243607--44243689 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
44243597 ATCAGTATAT
*
44243607 GACACAT-AAGTGCCTGAAAC
1 GACACATGAAGTGCCTGATAC
* *
44243627 GACACATGAGGTGTCTGATAC
1 GACACATGAAGTGCCTGATAC
* *
44243648 GACACACGAGGTGCCTGATATAC
1 GACACATGAAGTGCCTG--ATAC
* *
44243671 GACACATAAAGTGTCTGAT
1 GACACATGAAGTGCCTGAT
44243690 CGGCAAAGCC
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.14
21 27 0.53
23 17 0.33
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (21 bp):
GACACATGAAGTGCCTGATAC
Found at i:44243670 original size:23 final size:22
Alignment explanation
Indices: 44243616--44243676 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
44243606 TGACACATAA
*
44243616 GTGCCTGAA-ACGACACATGAG
1 GTGCCTGAATACGACACACGAG
*
44243637 GTGTCTG-ATACGACACACGAG
1 GTGCCTGAATACGACACACGAG
44243658 GTGCCTGATATACGACACA
1 GTGCCTGA-ATACGACACA
44243677 TAAAGTGTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.03
21 23 0.68
23 10 0.29
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (22 bp):
GTGCCTGAATACGACACACGAG
Found at i:44244860 original size:3 final size:3
Alignment explanation
Indices: 44244852--44244880 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
44244842 TATTCCTAGT
44244852 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
44244881 TATTTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:44245030 original size:14 final size:14
Alignment explanation
Indices: 44245011--44245056 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
44245001 TATTTAAAAT
44245011 ATAATAATAATTTA
1 ATAATAATAATTTA
*
44245025 ATAATACTAATTTA
1 ATAATAATAATTTA
*
44245039 ATAATATTAATTTA
1 ATAATAATAATTTA
44245053 ATAA
1 ATAA
44245057 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:44248472 original size:27 final size:29
Alignment explanation
Indices: 44248420--44248482 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
44248410 AAAGCCGGAG
* *
44248420 TTTTTGAAAAAAAGGGGTTTATTG-AAT-T
1 TTTTTTAAAAAAAGGGG-TCATTGAAATGT
44248448 TTTTTTAAAAAAAGGGG-CATCTGAAATGT
1 TTTTTTAAAAAAAGGGGTCAT-TGAAATGT
44248477 TTTTTT
1 TTTTTT
44248483 GGAGAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 2 0.07
27 2 0.07
28 19 0.63
29 7 0.23
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.44
Consensus pattern (29 bp):
TTTTTTAAAAAAAGGGGTCATTGAAATGT
Found at i:44248883 original size:3 final size:3
Alignment explanation
Indices: 44248875--44248954 Score: 81
Period size: 3 Copynumber: 26.7 Consensus size: 3
44248865 CATTATGTTC
* *
44248875 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATCT -TT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
* * * * *
44248920 ATT ATT AGT ATT AAT GTT ATT GTT ATT ACT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
44248955 ATTTCCATTT
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
2 1 0.02
3 59 0.97
4 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:44249607 original size:108 final size:108
Alignment explanation
Indices: 44249418--44249736 Score: 550
Period size: 108 Copynumber: 3.0 Consensus size: 108
44249408 TTTCTAAATG
* *
44249418 AGGCAATTTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTAGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
44249483 CGTTCAACCAAATGGCTTAATATCCTTTTAAAATTTTAAAGTA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAATTTTAAAGTA
*
44249526 AGGCAATGTTTTGCGTTTAGAAATTTGAGAAAACATGCCCTAAGGCGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTAGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
44249591 CGTTCAACCAAATGGCTTAATATCCTTTTAAAATTTTAAAGTA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAATTTTAAAGTA
44249634 AGGCAATGTTTTGCGTTTAGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTAGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * ** *
44249699 CATTTAACCAAATTGCCAAATATCCTTTT-GAATTTTAA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAATTTTAA
44249737 TCCATGCCAT
Statistics
Matches: 201, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
107 8 0.04
108 193 0.96
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (108 bp):
AGGCAATGTTTTGCGTTTAGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATGGCTTAATATCCTTTTAAAATTTTAAAGTA
Found at i:44250022 original size:6 final size:6
Alignment explanation
Indices: 44250011--44250036 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
44250001 GTGGCGACTC
44250011 TCGTTT TCGTTT TCGTTT TCGTTT TC
1 TCGTTT TCGTTT TCGTTT TCGTTT TC
44250037 AAAACATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.15, T:0.65
Consensus pattern (6 bp):
TCGTTT
Found at i:44256353 original size:21 final size:19
Alignment explanation
Indices: 44256298--44256355 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
44256288 TATTTTTTTC
44256298 TATTTTTTAAAATAATTTTAA
1 TATTTTTTAAAAT--TTTTAA
* **
44256319 TACTTTTTGTAATTTTTAAAA
1 TATTTTTTAAAATTTTT--AA
44256340 TATTTTTTAAAATTTT
1 TATTTTTTAAAATTTT
44256356 ACATTTTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 4 0.14
21 25 0.86
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTTTTTAAAATTTTTAA
Found at i:44256800 original size:26 final size:27
Alignment explanation
Indices: 44256764--44256817 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
44256754 GATCTAGGAA
44256764 TGTGTCGAA-TTTTATCTTCCAATCCC
1 TGTGTCGAATTTTTATCTTCCAATCCC
44256790 TGTGTCGAATTTTTATCTTCCAATCCC
1 TGTGTCGAATTTTTATCTTCCAATCCC
44256817 T
1 T
44256818 ATTAGGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.44
Consensus pattern (27 bp):
TGTGTCGAATTTTTATCTTCCAATCCC
Found at i:44265734 original size:9 final size:9
Alignment explanation
Indices: 44265720--44265750 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44265710 GTTAAACGAA
44265720 TCGAGTTAT
1 TCGAGTTAT
*
44265729 TCGAGTTAA
1 TCGAGTTAT
44265738 TCGAGTTAT
1 TCGAGTTAT
44265747 TCGA
1 TCGA
44265751 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:44265829 original size:9 final size:9
Alignment explanation
Indices: 44265805--44265841 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
44265795 TGAGTTTTCG
*
44265805 AATTCAAAT
1 AATTCGAAT
*
44265814 AACTCGAAT
1 AATTCGAAT
44265823 AATTCGAAT
1 AATTCGAAT
44265832 AATTCGAAT
1 AATTCGAAT
44265841 A
1 A
44265842 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:44266089 original size:30 final size:31
Alignment explanation
Indices: 44266055--44266114 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
44266045 AAACCTTTTA
*
44266055 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
44266085 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
44266115 TCATTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:44276597 original size:34 final size:35
Alignment explanation
Indices: 44276553--44276619 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
44276543 CTGTAAAATG
44276553 TTTTCCGTAAAATGAATT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
* *
44276587 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTT
44276620 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
Found at i:44277967 original size:35 final size:35
Alignment explanation
Indices: 44277921--44277990 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
44277911 TTTCATTGTC
*
44277921 AATCATTTCAATATCCAACAA-GCTTAAAACATAAT
1 AATCAATTCAATATCCAACAATG-TTAAAACATAAT
44277956 AATCAATTCAATATCCAACAATGTTAAAACATAAT
1 AATCAATTCAATATCCAACAATGTTAAAACATAAT
44277991 CAATATCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.29
Consensus pattern (35 bp):
AATCAATTCAATATCCAACAATGTTAAAACATAAT
Found at i:44277993 original size:27 final size:27
Alignment explanation
Indices: 44277963--44278032 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
44277953 AATAATCAAT
*
44277963 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
44277990 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
44278018 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
44278033 CTAAAATCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:44284868 original size:46 final size:46
Alignment explanation
Indices: 44284801--44285013 Score: 335
Period size: 46 Copynumber: 4.7 Consensus size: 46
44284791 ATACTTATAN
* *
44284801 ACTTATCTGATCAAGTGAGAAAGTGATAAGTGTTAGCCTGAGCTAC
1 ACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTAC
44284847 ACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTAC
1 ACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTAC
* * *
44284893 TCTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTAC
1 ACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTAC
*
44284939 ACTTATCTGATCATGTGAGAAAGTGATAAGTGGTAGCC-TAGCTAC
1 ACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTAC
44284984 ACTTATCTGATC-AG-G-GACAAGTGATAAGTG
1 ACTTATCTGATCAAGTGAGA-AAGTGATAAGTG
44285014 ATCATACGTA
Statistics
Matches: 156, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
42 2 0.01
43 13 0.08
44 1 0.01
45 19 0.12
46 121 0.78
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
ACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTAC
Found at i:44295937 original size:31 final size:28
Alignment explanation
Indices: 44295902--44295978 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 28
44295892 AATTTTTAAA
*
44295902 ATTTTAAAATTTAAATATATATATAAGAATT
1 ATTTTAAAATTTAAAAAT-TAT-TAA-AATT
*
44295933 ATTTTAAAAATTAAAAATTATTAAAATT
1 ATTTTAAAATTTAAAAATTATTAAAATT
*
44295961 ATTTAAAAATTATAAAAA
1 ATTTTAAAATT-TAAAAA
44295979 AATATTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 13 0.32
29 9 0.22
30 3 0.07
31 16 0.39
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
ATTTTAAAATTTAAAAATTATTAAAATT
Found at i:44295957 original size:10 final size:10
Alignment explanation
Indices: 44295942--44296007 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
44295932 TATTTTAAAA
44295942 ATTAAAAATT
1 ATTAAAAATT
44295952 ATT-AAAATT
1 ATTAAAAATT
44295961 ATTTAAAAATT
1 A-TTAAAAATT
* *
44295972 ATAAAAAAAT
1 ATTAAAAATT
**
44295982 ATTTTTAAATT
1 A-TTAAAAATT
*
44295993 -TTAAAAATA
1 ATTAAAAATT
44296002 ATTAAA
1 ATTAAA
44296008 TATTGACATA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
9 13 0.30
10 18 0.42
11 12 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:44295972 original size:39 final size:39
Alignment explanation
Indices: 44295895--44295973 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 39
44295885 TTTAATTAAT
* * *
44295895 TTTTAAAATTTTAAAATTTAAATATATATATAAGAATTA
1 TTTTAAAAATTAAAAATTTAAATATATATATAAAAATTA
*
44295934 TTTTAAAAATTAAAAATTATTAAA-AT-TATTTAAAAATTA
1 TTTTAAAAATTAAAAA-T-TTAAATATATATATAAAAATTA
44295973 T
1 T
44295974 AAAAAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
39 26 0.76
40 3 0.09
41 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (39 bp):
TTTTAAAAATTAAAAATTTAAATATATATATAAAAATTA
Found at i:44295979 original size:21 final size:21
Alignment explanation
Indices: 44295943--44295999 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
44295933 ATTTTAAAAA
* *
44295943 TTAAAAATTAT-TAAAATTAT
1 TTAAAAATTATAAAAAAATAT
44295963 TTAAAAATTATAAAAAAATAT
1 TTAAAAATTATAAAAAAATAT
** *
44295984 TTTTAAATTTTAAAAA
1 TTAAAAATTATAAAAA
44296000 TAATTAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAATTATAAAAAAATAT
Found at i:44297054 original size:16 final size:16
Alignment explanation
Indices: 44297029--44297062 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44297019 TAATAAATCT
* *
44297029 AAAATTTAAAATTTAA
1 AAAATATAAAAATTAA
44297045 AAAATATAAAAATTAA
1 AAAATATAAAAATTAA
44297061 AA
1 AA
44297063 TTAACTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAAAAATTAA
Found at i:44297076 original size:31 final size:32
Alignment explanation
Indices: 44297017--44297081 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
44297007 TTATTATTTT
44297017 TATAATAAATCTAAAATTTAAAATTTAAAAAA
1 TATAATAAATCTAAAATTTAAAATTTAAAAAA
44297049 TATAA-AAAT-TAAAA-TTAACTAATTTAAAAAA
1 TATAATAAATCTAAAATTTAA--AATTTAAAAAA
44297080 TA
1 TA
44297082 CATATACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 4 0.13
30 5 0.16
31 17 0.55
32 5 0.16
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (32 bp):
TATAATAAATCTAAAATTTAAAATTTAAAAAA
Found at i:44297138 original size:6 final size:6
Alignment explanation
Indices: 44297127--44297152 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
44297117 AAAGAATATC
44297127 CTGCCT CTGCCT CTGCCT CTGCCT CT
1 CTGCCT CTGCCT CTGCCT CTGCCT CT
44297153 ACTGTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.15, T:0.35
Consensus pattern (6 bp):
CTGCCT
Found at i:44298415 original size:21 final size:21
Alignment explanation
Indices: 44298391--44298434 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
44298381 GCAAAGTCTA
44298391 AGAAGAA-TG-GAAGCCAAGAGG
1 AGAAGAAGTGAGAAG-CAA-AGG
44298412 AGAAGAAGTGAGAAGCAAAGG
1 AGAAGAAGTGAGAAGCAAAGG
44298433 AG
1 AG
44298435 TTCGAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 12 0.57
22 5 0.24
23 4 0.19
ACGTcount: A:0.50, C:0.07, G:0.39, T:0.05
Consensus pattern (21 bp):
AGAAGAAGTGAGAAGCAAAGG
Found at i:44304491 original size:31 final size:32
Alignment explanation
Indices: 44304448--44304531 Score: 113
Period size: 31 Copynumber: 2.7 Consensus size: 32
44304438 TAGGATAAAC
*
44304448 TACATTTTTAATCATTTAATTATTAACAAATT-
1 TACA-TTTTAATCATTTAATTATTAAAAAATTA
*
44304480 TACATTTTAATCATATAATTA-TAAAAAATTA
1 TACATTTTAATCATTTAATTATTAAAAAATTA
44304511 TA-A-TTTAATCATTTAATTATT
1 TACATTTTAATCATTTAATTATT
44304532 CGAAATTGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 15 0.32
30 10 0.21
31 18 0.38
32 4 0.09
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (32 bp):
TACATTTTAATCATTTAATTATTAAAAAATTA
Found at i:44304537 original size:29 final size:29
Alignment explanation
Indices: 44304448--44304538 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
44304438 TAGGATAAAC
44304448 TACATTTTTAATCATTTAATTATTAACAAATT
1 TACA-TTTTAATCATTTAATTATT--CAAATT
* ** *
44304480 TACATTTTAATCATATAATTATAAAAAAT
1 TACATTTTAATCATTTAATTATTCAAATT
* *
44304509 TATAATTTAATCATTTAATTATTCGAAATT
1 TACATTTTAATCATTTAATTATTC-AAATT
44304539 GGTTATTTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
29 23 0.48
30 4 0.08
31 17 0.35
32 4 0.08
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.47
Consensus pattern (29 bp):
TACATTTTAATCATTTAATTATTCAAATT
Found at i:44307914 original size:38 final size:38
Alignment explanation
Indices: 44307863--44307936 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
44307853 ACACTGTCCG
44307863 CGGTGAATTGTATTTTGTCATCTCTACTCTAAACTTCC
1 CGGTGAATTGTATTTTGTCATCTCTACTCTAAACTTCC
*
44307901 CGGTGAATTGTATTTTGTCATCTCTACTTTAAACTT
1 CGGTGAATTGTATTTTGTCATCTCTACTCTAAACTT
44307937 GGGAAGGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (38 bp):
CGGTGAATTGTATTTTGTCATCTCTACTCTAAACTTCC
Found at i:44308118 original size:16 final size:16
Alignment explanation
Indices: 44308079--44308127 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
44308069 AGTACATTTG
* *
44308079 TGTGTGTCTATGTATG
1 TGTGTGTATATGTATA
* *
44308095 TATATGTATATGTATA
1 TGTGTGTATATGTATA
*
44308111 TGTGTGTATATATATA
1 TGTGTGTATATGTATA
44308127 T
1 T
44308128 CACTTCAACG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (16 bp):
TGTGTGTATATGTATA
Found at i:44308481 original size:48 final size:48
Alignment explanation
Indices: 44308407--44308502 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
44308397 AGAGGCCAAG
* * * *
44308407 GGCTTTTCTTGTTGTTTCTGCTGCACTTCTTCTTTCTTTGAAACATTA
1 GGCTTTTCTTGTAGTTTCTGCCGCACTTCTTCTTCCTCTGAAACATTA
*
44308455 GGCTTTTCTTGTAGTTTCTGCCGCACTTTTTCTTCCTCTGAAACATTA
1 GGCTTTTCTTGTAGTTTCTGCCGCACTTCTTCTTCCTCTGAAACATTA
44308503 CTTTCATCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.14, C:0.23, G:0.15, T:0.49
Consensus pattern (48 bp):
GGCTTTTCTTGTAGTTTCTGCCGCACTTCTTCTTCCTCTGAAACATTA
Found at i:44309264 original size:48 final size:48
Alignment explanation
Indices: 44309190--44309285 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
44309180 AGAGGCCAAG
* * * *
44309190 GGCTTTTCTTGTTGTTTCTGCTGCACTTCTTCTTTCTTTGAAACATTA
1 GGCTTTTCTTGTAGTTTCTGCCGCACTTCTTCTTCCTCTGAAACATTA
*
44309238 GGCTTTTCTTGTAGTTTCTGCCGCACTTTTTCTTCCTCTGAAACATTA
1 GGCTTTTCTTGTAGTTTCTGCCGCACTTCTTCTTCCTCTGAAACATTA
44309286 CTTTCATCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.14, C:0.23, G:0.15, T:0.49
Consensus pattern (48 bp):
GGCTTTTCTTGTAGTTTCTGCCGCACTTCTTCTTCCTCTGAAACATTA
Found at i:44309867 original size:776 final size:777
Alignment explanation
Indices: 44308362--44309926 Score: 2943
Period size: 776 Copynumber: 2.0 Consensus size: 777
44308352 GAACCAAGAG
*
44308362 CAACAGTTGCTGCAAGCTGATTTCGATTTCAATGCAGAGGCCAAGGGCTTTTCTTGTTGTTTCTG
1 CAACAGCTGCTGCAAGCTGATTTCGATTTCAATGCAGAGGCCAAGGGCTTTTCTTGTTGTTTCTG
44308427 CTGCACTTCTTCTTTCTTTGAAACATTAGGCTTTTCTTGTAGTTTCTGCCGCACTTTTTCTTCCT
66 CTGCACTTCTTCTTTCTTTGAAACATTAGGCTTTTCTTGTAGTTTCTGCCGCACTTTTTCTTCCT
*
44308492 CTGAAACATTACTTTCATCTTCCGAACTGCAATGATACCAATATAACTTAAGCTGAAAAGTTCCC
131 CTGAAACATTACTTTCATCTTCAGAACTGCAATGATACCAATATAACTTAAGCTGAAAAGTTCCC
*
44308557 ACAAGATCTCGAATTTCTTGTAGATTGTATATGAAATCCCAAATATAAGCATCGTAAGCATAATA
196 ACAAGATCTCGAATTTCTTGTAGATTGTATATGAAACCCCAAATATAAGCATCGTAAGCATAATA
*
44308622 TGCAGCCCATGTTACTTGGATGTGAGTATTGGATACGGACATGTGATTGAGTATGCTTGATTTCT
261 T------CATGTTACTTGGATGTGAGTATTGGATACAGACATGTGATTGAGTATGCTTGATTTCT
*
44308687 TCTCAGTTTTATCATATATTTAGAGCATTAGTGGAAACAAATACCGGATATCAAACTTTTAAAAG
320 TCTCAGTTTTATCATATATTTAGAGCATTAGTGGAAACAAATACCAGATATCAAACTTTTAAAAG
44308752 AAAGTTTTTCTTTCCCAAAGATATGCTATATGTAATATTTGATAGAGGAGGGGGAAAAGAGAAGT
385 AAAGTTTTTCTTTCCCAAAGATATGCTATATGTAATATTTGATAGAGGAGGGGGAAAAGAGAAGT
44308817 CTACACTGAAGAAAACTGCATACAACAACCCAAATATATGCATCATAAGTGCAGCCTATGTTAAT
450 CTACACTGAAGAAAACTGCATACAACAACCCAAATATATGCATCATAAGTGCAGCCTATGTTAAT
*
44308882 TGGACATGAGTGAGTGTCAGATATGGAGATGCGATTGAGTATGCTCGATTCTTCTTAGTTTTTTC
515 TGGACATGAGTGAGTGTCAGATATGGAGATGCGATTGAGTATGCTCAATTCTTCTTAGTTTTTTC
*
44308947 ATTTACTTGGAGCATCATATTCATACCTCTATACTCTCTATACTCATTTCCGAATATTGACATCA
580 ATTTACTTGGAGCATCATATTCATACCTCTATACTCTCTATACTCATTTCCAAATATTGACATCA
*
44309012 ATCTTTTAAAAGAAAGTCTTTCTTGCCCAAAGATCTACTTATATCTAATTTTTGATACAGTAGCA
645 ATCCTTTAAAAGAAAGTCTTTCTTGCCCAAAGATCTACTTATATCTAATTTTTGATACAGTAGCA
*
44309077 TAAATGTAGGGAGAAAAAGAGAAACATACTCTGAACAACAACAGCAGAATCTTTTCAAGCTGCAG
710 TAAATGTAGGGAGAAAAAGAGAAACATACTCTGAACAACAACAGAAGAATCTTTTCAAGCTGCAG
44309142 TTC
775 TTC
44309145 CAACAGCTGCTGCAAGCTGATTTCGATTTCAATGCAGAGGCCAAGGGCTTTTCTTGTTGTTTCTG
1 CAACAGCTGCTGCAAGCTGATTTCGATTTCAATGCAGAGGCCAAGGGCTTTTCTTGTTGTTTCTG
44309210 CTGCACTTCTTCTTTCTTTGAAACATTAGGCTTTTCTTGTAGTTTCTGCCGCACTTTTTCTTCCT
66 CTGCACTTCTTCTTTCTTTGAAACATTAGGCTTTTCTTGTAGTTTCTGCCGCACTTTTTCTTCCT
44309275 CTGAAACATTACTTTCATCTTCAGAACTGCAATGATACCAATATAACTTAAGCTGAAAAGTTCCC
131 CTGAAACATTACTTTCATCTTCAGAACTGCAATGATACCAATATAACTTAAGCTGAAAAGTTCCC
44309340 ACAAGATCTCGAATTTCTTGTAGATTGTATATGAAACCCCAAATATAAGCATCGTAAGCATAATA
196 ACAAGATCTCGAATTTCTTGTAGATTGTATATGAAACCCCAAATATAAGCATCGTAAGCATAATA
44309405 T-ATGTTACTTGGATGTGAGTATTGGATACAGACATGTGATTGAGTATGCTTGATTTCTTCTCAG
261 TCATGTTACTTGGATGTGAGTATTGGATACAGACATGTGATTGAGTATGCTTGATTTCTTCTCAG
*
44309469 TTTTATCATATATTTAGAGCATTATTGGAAACAAATACCAGATATCAAACTTTTAAAAGAAAGTT
326 TTTTATCATATATTTAGAGCATTAGTGGAAACAAATACCAGATATCAAACTTTTAAAAGAAAGTT
*
44309534 TTTCTTTCCCAAAGATATGCTATATGTAATATTTGATAGAGGTGGGGGAAAAGAGAAGTCTACAC
391 TTTCTTTCCCAAAGATATGCTATATGTAATATTTGATAGAGGAGGGGGAAAAGAGAAGTCTACAC
*
44309599 TGAAGAAAACTGCATACAACAACCCAAATATATGCATCATAAGTGCAGCCTGTGTTAATTGGACA
456 TGAAGAAAACTGCATACAACAACCCAAATATATGCATCATAAGTGCAGCCTATGTTAATTGGACA
44309664 TGAGTGAGTGTCAGATATGGAGATGCGATTGAGTATGCTCAATTCTTCTTAGTTTTTTCATTTAC
521 TGAGTGAGTGTCAGATATGGAGATGCGATTGAGTATGCTCAATTCTTCTTAGTTTTTTCATTTAC
*
44309729 TTGGAGCATCATATTCATACCTCTATACTCTCTATACTCATTTCCAAATATTGAGATCAATCCTT
586 TTGGAGCATCATATTCATACCTCTATACTCTCTATACTCATTTCCAAATATTGACATCAATCCTT
*
44309794 TAAAAGAAAGTCTTTCTTGCCCAAAGATCTACTTATATCTAATTTTTGATACAGTAGCATAGATG
651 TAAAAGAAAGTCTTTCTTGCCCAAAGATCTACTTATATCTAATTTTTGATACAGTAGCATAAATG
44309859 TAGGGAGAAAAAGAGAAACATACTCTGAACAACAACAGAAGAATCTTTTCAAGCTGCAGTTC
716 TAGGGAGAAAAAGAGAAACATACTCTGAACAACAACAGAAGAATCTTTTCAAGCTGCAGTTC
44309921 CAACAG
1 CAACAG
44309927 TAGCACAACG
Statistics
Matches: 768, Mismatches: 14, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
776 510 0.66
783 258 0.34
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (777 bp):
CAACAGCTGCTGCAAGCTGATTTCGATTTCAATGCAGAGGCCAAGGGCTTTTCTTGTTGTTTCTG
CTGCACTTCTTCTTTCTTTGAAACATTAGGCTTTTCTTGTAGTTTCTGCCGCACTTTTTCTTCCT
CTGAAACATTACTTTCATCTTCAGAACTGCAATGATACCAATATAACTTAAGCTGAAAAGTTCCC
ACAAGATCTCGAATTTCTTGTAGATTGTATATGAAACCCCAAATATAAGCATCGTAAGCATAATA
TCATGTTACTTGGATGTGAGTATTGGATACAGACATGTGATTGAGTATGCTTGATTTCTTCTCAG
TTTTATCATATATTTAGAGCATTAGTGGAAACAAATACCAGATATCAAACTTTTAAAAGAAAGTT
TTTCTTTCCCAAAGATATGCTATATGTAATATTTGATAGAGGAGGGGGAAAAGAGAAGTCTACAC
TGAAGAAAACTGCATACAACAACCCAAATATATGCATCATAAGTGCAGCCTATGTTAATTGGACA
TGAGTGAGTGTCAGATATGGAGATGCGATTGAGTATGCTCAATTCTTCTTAGTTTTTTCATTTAC
TTGGAGCATCATATTCATACCTCTATACTCTCTATACTCATTTCCAAATATTGACATCAATCCTT
TAAAAGAAAGTCTTTCTTGCCCAAAGATCTACTTATATCTAATTTTTGATACAGTAGCATAAATG
TAGGGAGAAAAAGAGAAACATACTCTGAACAACAACAGAAGAATCTTTTCAAGCTGCAGTTC
Found at i:44309984 original size:30 final size:30
Alignment explanation
Indices: 44309922--44309991 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
44309912 CTGCAGTTCC
* * * **
44309922 AACAGTAGCACAACGCGCAGCTATAATTAG
1 AACAGTAGCACAAAGCCCAGCTACAACCAG
*
44309952 AACAGTAGCAGAAAGCCCAGCTACAACCAG
1 AACAGTAGCACAAAGCCCAGCTACAACCAG
*
44309982 AACAGGAGCA
1 AACAGTAGCA
44309992 TGATGGCCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.43, C:0.26, G:0.21, T:0.10
Consensus pattern (30 bp):
AACAGTAGCACAAAGCCCAGCTACAACCAG
Found at i:44319304 original size:126 final size:126
Alignment explanation
Indices: 44318977--44319330 Score: 577
Period size: 125 Copynumber: 2.8 Consensus size: 126
44318967 ATTATTTCGC
44318977 GTTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTG
1 GTTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTG
* *
44319041 TGAAATCGCGCCCTTGTGGACGCGATTTTGCTACAATAGGTCATGTAAGAAACAATTTTTTT
65 TGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAACAATTTTTTT
* * * * * * *
44319103 -CTGATGCTTCTAAGCAAATAGTATAAAATCGTTTCTACGAGAATGCTATTTGAGAAGAAATTGT
1 GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
* *
44319167 GAAATCGCGCCCTCGTGGACGTGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTT
66 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAACAATTTTTTT
*
44319228 GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGATATTTGAGAAGAAATTGT
1 GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
44319293 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
44319331 CAAGTTTGGG
Statistics
Matches: 206, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
125 112 0.54
126 94 0.46
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (126 bp):
GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAACAATTTTTTT
Found at i:44322460 original size:10 final size:10
Alignment explanation
Indices: 44322445--44322469 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44322435 CAAATCTAAC
44322445 ATTATGTAAA
1 ATTATGTAAA
44322455 ATTATGTAAA
1 ATTATGTAAA
44322465 ATTAT
1 ATTAT
44322470 TAAGCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:44322616 original size:110 final size:110
Alignment explanation
Indices: 44322452--44323340 Score: 1661
Period size: 110 Copynumber: 8.0 Consensus size: 110
44322442 AACATTATGT
* *
44322452 AAAATTATGTAAAATTATTAAGCCAAAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAATAAA
1 AAAA-TATGTAAAATTATTAAGCC--AAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAA
44322517 CTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
63 CTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
44322565 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
1 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
*
44322630 AAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAATTATC
66 AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
44322675 AAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAATAAAATTTATGAAATAAACT
1 -AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACT
44322740 AAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
65 AAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
44322786 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
1 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
44322851 AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
66 AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
44322896 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAATAAAATTTATGAAATAAACTA
1 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
44322961 AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
66 AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
44323006 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
1 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
*
44323071 AAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAATTATC
66 AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
44323116 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAAATTTATGAAATAAACT
1 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGT-AAAATTTATGAAATAAACT
*
44323181 AAAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAATTATC
65 AAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
44323227 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
1 AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
44323292 AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
66 AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAA-TTATC
44323338 AAA
1 AAA
44323341 TTAAGTTAGG
Statistics
Matches: 763, Mismatches: 10, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
110 514 0.67
111 226 0.30
112 19 0.02
113 4 0.01
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (110 bp):
AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTA
AAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:44322842 original size:221 final size:221
Alignment explanation
Indices: 44322452--44323340 Score: 1656
Period size: 221 Copynumber: 4.0 Consensus size: 221
44322442 AACATTATGT
* * * *
44322452 AAAATTATGTAAAATTATTAAGCCAAAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAATAAA
1 AAAAATATGTAAAATTATTAAGCC--AAAAATTGTATTAATGGTTAATAAAATTTATGAAATAAA
44322517 CTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTAT
64 CTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTAT
*
44322582 TAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAGA
129 TAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAA
44322647 AATTGTGTTAATGGTTAGTAAAATTATC
194 AATTGTGTTAATGGTTAGTAAAATTATC
44322675 AAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAATAAAATTTATGAAATAAACT
1 AAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAATAAAATTTATGAAATAAACT
44322740 AAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATTA
66 AAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATTA
44322805 AGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAAA
131 AGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAAA
44322870 TTGTGTTAATGGTTAGTAAAATTATC
196 TTGTGTTAATGGTTAGTAAAATTATC
44322896 -AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAATAAAATTTATGAAATAAACT
1 AAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAATAAAATTTATGAAATAAACT
44322960 AAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATTA
66 AAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATTA
*
44323025 AGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAGAAA
131 AGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAAA
44323090 TTGTGTTAATGGTTAGTAAAATTATC
196 TTGTGTTAATGGTTAGTAAAATTATC
*
44323116 -AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAAATTTATGAAATAAAC
1 AAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAAT-AAAATTTATGAAATAAAC
*
44323180 TAAAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATT
65 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATT
44323245 AAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAA
130 AAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAA
44323310 ATTGTGTTAATGGTTAGTAAAATTTATC
195 ATTGTGTTAATGGTTAGTAAAA-TTATC
44323338 AAA
1 AAA
44323341 TTAAGTTAGG
Statistics
Matches: 654, Mismatches: 9, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
220 263 0.40
221 361 0.55
222 5 0.01
223 25 0.04
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (221 bp):
AAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAATAAAATTTATGAAATAAACT
AAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATTA
AGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAAA
TTGTGTTAATGGTTAGTAAAATTATC
Found at i:44323300 original size:441 final size:444
Alignment explanation
Indices: 44322452--44323340 Score: 1687
Period size: 441 Copynumber: 2.0 Consensus size: 444
44322442 AACATTATGT
* *
44322452 AAAATTATGTAAAATTATTAAGCCAAAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAATAAA
1 AAAATTATGTAAAATTATTAAGCC-AAAAAATTGTATTAATGGTTAATAAAATTTATCAAATAAA
44322517 CTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTAT
65 CTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTAT
44322582 TAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAGA
130 TAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAGA
44322647 AATTGTGTTAATGGTTAGTAAAATTATCAAAAATATGTAAAATTATTAAGCCAAAAATTGTATTA
195 AATTGTGTTAATGGTTAGTAAAATTATCAAAAATATGTAAAATTATTAAGCCAAAAATTGTATTA
44322712 ATGGTTAATAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGT
260 ATGGTTAATAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGT
44322777 AAAATTATCAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGA
325 AAAATTATCAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGA
44322842 AATAAACTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAA-TTATC
390 AATAAACTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
*
44322896 AAAA-TATGTAAAATTATTAAGCC-AAAAATTGTATTAATGGTTAATAAAATTTATGAAATAAAC
1 AAAATTATGTAAAATTATTAAGCCAAAAAATTGTATTAATGGTTAATAAAATTTATCAAATAAAC
44322959 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATT
66 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATT
44323024 AAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAGAA
131 AAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAGAA
44323089 ATTGTGTTAATGGTTAGTAAAATTATC-AAAATATGTAAAATTATTAAGCCAAAAATTGTATTAA
196 ATTGTGTTAATGGTTAGTAAAATTATCAAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAA
* *
44323153 TGGTTAGTAAAAATTTATGAAATAAACTAAAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGT
261 TGGTTAAT-AAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGT
44323218 AAAATTATCAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGA
325 AAAATTATCAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGA
44323283 AATAAACTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
390 AATAAACTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
44323338 AAA
1 AAA
44323341 TTAAGTTAGG
Statistics
Matches: 438, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
440 44 0.10
441 363 0.83
442 8 0.02
443 19 0.04
444 4 0.01
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (444 bp):
AAAATTATGTAAAATTATTAAGCCAAAAAATTGTATTAATGGTTAATAAAATTTATCAAATAAAC
TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAATATGTAAAATTATT
AAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTATTAAGTCCAGAA
ATTGTGTTAATGGTTAGTAAAATTATCAAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAA
TGGTTAATAAAATTTATGAAATAAACTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTA
AAATTATCAAAATATGTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAA
ATAAACTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
Found at i:44323597 original size:6 final size:6
Alignment explanation
Indices: 44323586--44323613 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
44323576 AATTAAATTA
44323586 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
44323614 TTTAATTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (6 bp):
GGTTAG
Found at i:44323631 original size:35 final size:34
Alignment explanation
Indices: 44323406--44323636 Score: 239
Period size: 29 Copynumber: 7.1 Consensus size: 34
44323396 AGTTAATTTA
* *
44323406 GGTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAG
1 GGTTAGGGTTAGGGTTTTTAATT-AGTTAGGTTAG
44323441 GGTTAGGGTTAGGGTTTTTAATTA---A-GTTA-
1 GGTTAGGGTTAGGGTTTTTAATTAGTTAGGTTAG
44323470 GGTTAGGGTTAGGG--TTT--TTAGTTAGGTTA-
1 GGTTAGGGTTAGGGTTTTTAATTAGTTAGGTTAG
44323499 GGTTAGGGTTAGGGTTTTTAATTA---A-GTTA-
1 GGTTAGGGTTAGGGTTTTTAATTAGTTAGGTTAG
44323528 GGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAG
1 GGTTAGGGTTAGGGTTTTTAATT-AGTTAGGTTAG
44323563 GGTTAGGGTT----TTTAATTAAATTAGGTTAGGGTTAG
1 GGTTAGGGTTAGGGTTT--TT-AATTA-GTTA-GGTTAG
44323598 GGTTAGGGTTAGGGTTTTTAATTGAGTTAGGTTAG
1 GGTTAGGGTTAGGGTTTTTAATT-AGTTAGGTTAG
44323633 GGTT
1 GGTT
44323637 TTCAATTAAA
Statistics
Matches: 171, Mismatches: 1, Indels: 48
0.78 0.00 0.22
Matches are distributed among these distances:
25 3 0.02
27 3 0.02
28 1 0.01
29 59 0.35
30 6 0.04
31 7 0.04
33 7 0.04
34 13 0.08
35 58 0.34
36 8 0.05
37 3 0.02
39 3 0.02
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (34 bp):
GGTTAGGGTTAGGGTTTTTAATTAGTTAGGTTAG
Found at i:44323631 original size:64 final size:67
Alignment explanation
Indices: 44323524--44323651 Score: 192
Period size: 64 Copynumber: 1.9 Consensus size: 67
44323514 TTTTAATTAA
*
44323524 GTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGT
1 GTTAGGTTAGGGTTAGGGTTTTTAATT-AG-TAGGTTAGGGTTAGGGTTTTCAATTAAATTAGGT
44323589 TAGG
64 TAGG
44323593 GTTAGGGTTAGGGTTAGGGTTTTTAATT-G-A-GTTA-GGTTAGGGTTTTCAATTAAATTAGG
1 GTTA-GGTTAGGGTTAGGGTTTTTAATTAGTAGGTTAGGGTTAGGGTTTTCAATTAAATTAGG
44323652 GTTTTTATTT
Statistics
Matches: 57, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
64 24 0.42
65 4 0.07
66 1 0.02
68 1 0.02
69 4 0.07
70 23 0.40
ACGTcount: A:0.24, C:0.01, G:0.32, T:0.43
Consensus pattern (67 bp):
GTTAGGTTAGGGTTAGGGTTTTTAATTAGTAGGTTAGGGTTAGGGTTTTCAATTAAATTAGGTTA
GG
Found at i:44323636 original size:29 final size:29
Alignment explanation
Indices: 44323339--44323601 Score: 348
Period size: 29 Copynumber: 8.9 Consensus size: 29
44323329 AAATTTATCA
***
44323339 AATTAAGTTAGGTTAGGGTTAGGGTTAGG
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
** * *
44323368 GTTTAAGTTAGGTTAAGGTT-GAGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
* *
44323396 AGTTAATTTAGGTTAGGGTTAGGGTTTTTAGTT
1 AATTAAGTTAGGTTAGGGTTAGGG--TTT--TT
*
44323429 AATTTAGGTTAGGGTTAGGGTTAGGGTTTTT
1 AA-TTAAGTTA-GGTTAGGGTTAGGGTTTTT
44323460 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
* *
44323489 AGTTAGGTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
44323518 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
44323547 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
*
44323576 AATTAAATTAGGTTAGGGTTAGGGTT
1 AATTAAGTTAGGTTAGGGTTAGGGTT
44323602 AGGGTTAGGG
Statistics
Matches: 206, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
28 20 0.10
29 146 0.71
30 7 0.03
31 7 0.03
33 6 0.03
34 6 0.03
35 14 0.07
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (29 bp):
AATTAAGTTAGGTTAGGGTTAGGGTTTTT
Found at i:44323730 original size:26 final size:25
Alignment explanation
Indices: 44323700--44323748 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
44323690 CTTCAAAAAT
44323700 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
**
44323726 TTCTATTTTATTACATCAAATAA
1 TTCTATCGTATTACATCAAATAA
44323749 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Found at i:44324174 original size:18 final size:18
Alignment explanation
Indices: 44324147--44324181 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44324137 CGAAAAAAGA
* *
44324147 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
44324165 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
44324182 AAACATACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:44325370 original size:29 final size:29
Alignment explanation
Indices: 44325328--44325644 Score: 340
Period size: 29 Copynumber: 11.1 Consensus size: 29
44325318 NNNNNNNNNN
* *
44325328 GTTTTTAGTTAATTTAGGTTAGGGTTAGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
*
44325357 GTTTTTAATTAATTTAGGTTAGGGTTAGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
44325386 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
**
44325415 G---TT-A--GGGTTAGGGTTAGGGTT---
1 GTTTTTAATTAAGTTA-GGTTAGGGTTAGG
*
44325436 -TTTAATTAATTTAGGTTA-G----GGTTAGG
1 GTTT--TTAA-TTAAGTTAGGTTAGGGTTAGG
* *
44325462 GTTTTTAGTTAATTTAGGTTAGGGTTAGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
* *
44325491 GTTTTTAGTTAATTTAGGTTAGGGTTAGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
44325520 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGG
1 GTTTTTAATT--A--A-GTTA-GGTTAGGGTTAGG
44325555 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
44325584 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
*
44325613 GTTTTTAATTAAATTAGGTTAGGGTTAGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGG
44325642 GTT
1 GTT
44325645 AGGGTTAGGG
Statistics
Matches: 252, Mismatches: 11, Indels: 50
0.81 0.04 0.16
Matches are distributed among these distances:
23 8 0.03
24 16 0.06
25 7 0.03
26 3 0.01
27 4 0.02
29 180 0.71
30 4 0.02
31 2 0.01
33 2 0.01
34 3 0.01
35 23 0.09
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (29 bp):
GTTTTTAATTAAGTTAGGTTAGGGTTAGG
Found at i:44325413 original size:6 final size:6
Alignment explanation
Indices: 44325398--44325435 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
44325388 TTTTAATTAA
44325398 GTTA-G GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTT
1 GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTT
44325436 TTTAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.37
Consensus pattern (6 bp):
GTTAGG
Found at i:44325573 original size:93 final size:93
Alignment explanation
Indices: 44325328--44325650 Score: 431
Period size: 93 Copynumber: 3.7 Consensus size: 93
44325318 NNNNNNNNNN
* *
44325328 GTTTTTAGTTAATTTAGGTTAGGGTTAGGGTTTTTAATT-AA-T---TTA-GGTTAGGGTTAGGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGG
44325387 TTTTTAATTAAGTTAGGTTAGGGTTAGG
66 TTTTTAATTAAGTTAGGTTAGGGTTAGG
44325415 G-------TT-AG---GGTTAGGGTTAGGGTTTTTAATT-AA-T---TTA-GGTTAGGGTTAGGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGG
* *
44325463 TTTTTAGTTAATTTAGGTTAGGGTTAGG
66 TTTTTAATTAAGTTAGGTTAGGGTTAGG
* *
44325491 GTTTTTAGTTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGG
44325556 TTTTTAATTAAGTTAGGTTAGGGTTAGG
66 TTTTTAATTAAGTTAGGTTAGGGTTAGG
44325584 GTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGG
1 GTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGG
44325649 TT
66 TT
44325651 AGGGTTTTTA
Statistics
Matches: 211, Mismatches: 8, Indels: 28
0.85 0.03 0.11
Matches are distributed among these distances:
76 70 0.33
79 1 0.00
80 2 0.01
83 2 0.01
84 1 0.00
87 24 0.11
88 2 0.01
89 1 0.00
92 3 0.01
93 105 0.50
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.46
Consensus pattern (93 bp):
GTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGG
TTTTTAATTAAGTTAGGTTAGGGTTAGG
Found at i:44325640 original size:6 final size:6
Alignment explanation
Indices: 44325629--44325656 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
44325619 AATTAAATTA
44325629 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
44325657 TTTAATTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (6 bp):
GGTTAG
Found at i:44325674 original size:64 final size:67
Alignment explanation
Indices: 44325504--44325694 Score: 193
Period size: 64 Copynumber: 2.9 Consensus size: 67
44325494 TTTAGTTAAT
* **** * *
44325504 TTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG-TTAGGGTT--TTTA-ATT
1 TTAGGTTAGGGTTAGGGTTTTTAATT--AGTAGGTTAGGGTTAGGGTTTTCAATTAAATTAGGTT
*
44325565 A-AG
64 AGGG
*
44325568 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT
1 TTAGGTTAGGGTTAGGGTTTTTAATT-AG-TAGGTTAGGGTTAGGGTTTTCAATTAAATTAGGTT
44325633 AGGG
64 AGGG
44325637 TTAGGGTTAGGGTTAGGGTTTTTAATT-G-A-GTTA-GGTTAGGGTTTTCAATTAAATTAGG
1 TTA-GGTTAGGGTTAGGGTTTTTAATTAGTAGGTTAGGGTTAGGGTTTTCAATTAAATTAGG
44325695 GTTTTTATTT
Statistics
Matches: 111, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
63 2 0.02
64 66 0.59
65 8 0.07
66 1 0.01
67 3 0.03
68 4 0.04
69 4 0.04
70 23 0.21
ACGTcount: A:0.25, C:0.01, G:0.31, T:0.43
Consensus pattern (67 bp):
TTAGGTTAGGGTTAGGGTTTTTAATTAGTAGGTTAGGGTTAGGGTTTTCAATTAAATTAGGTTAG
GG
Found at i:44325674 original size:93 final size:95
Alignment explanation
Indices: 44325449--44325694 Score: 344
Period size: 93 Copynumber: 2.6 Consensus size: 95
44325439 AATTAATTTA
* *
44325449 GGTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGG
1 GGTTAGGGTTAGGG--TTTA-TTAA-TTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
44325514 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
62 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
*
44325548 GGTTAGGGTT----TTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGT
1 GGTTAGGGTTAGGGTTT-ATTAA-TTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
44325609 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
64 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
*
44325641 GGTTAGGGTTAGGGTTT-TTAATT-GAGTTA-GGTTAGGGTTTTCAATTAAATTAGG
1 GGTTAGGGTTAGGGTTTATTAATTAG-GTTAGGGTTAGGGTTTTTAATTAAATTAGG
44325695 GTTTTTATTT
Statistics
Matches: 136, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
93 112 0.82
94 7 0.05
95 4 0.03
97 3 0.02
99 10 0.07
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (95 bp):
GGTTAGGGTTAGGGTTTATTAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
GGGTTTTTAATTAAATTAGGTTAGGGTTAG
Found at i:44325679 original size:29 final size:29
Alignment explanation
Indices: 44325415--44325644 Score: 343
Period size: 29 Copynumber: 7.7 Consensus size: 29
44325405 TAGGGTTAGG
44325415 GTTAGGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTA-GGTTAGGGTTAGGGTTTTTAATTAA
* *
44325445 TTTAGGTTAGGGTTAGGGTTTTTAGTTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
* *
44325474 TTTAGGTTAGGGTTAGGGTTTTTAGTTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
*
44325503 TTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GTTAGGTTAGGGTTAGGGTTTTTAATT--A--A
44325536 GGTTAGGGTTAGGGTTAGGGTTTTTAATTAA
1 -GTTA-GGTTAGGGTTAGGGTTTTTAATTAA
44325567 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
44325596 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAA
*
44325625 ATTAGGTTAGGGTTAGGGTT
1 GTTAGGTTAGGGTTAGGGTT
44325645 AGGGTTAGGG
Statistics
Matches: 189, Mismatches: 5, Indels: 13
0.91 0.02 0.06
Matches are distributed among these distances:
29 152 0.80
30 7 0.04
31 2 0.01
33 2 0.01
34 3 0.02
35 23 0.12
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (29 bp):
GTTAGGTTAGGGTTAGGGTTTTTAATTAA
Found at i:44325773 original size:26 final size:25
Alignment explanation
Indices: 44325743--44325791 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
44325733 CTTCAAAAAT
44325743 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
**
44325769 TTCTATTTTATTACATCAAATAA
1 TTCTATCGTATTACATCAAATAA
44325792 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Found at i:44326230 original size:18 final size:18
Alignment explanation
Indices: 44326186--44326231 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
44326176 TATTCGGAAA
* *
44326186 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
*
44326204 AGGGTACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
44326222 AGGAAACATA
1 AGGATACATA
44326232 CCTGGCATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:44326879 original size:7 final size:7
Alignment explanation
Indices: 44326869--44326893 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44326859 TTATATACAT
44326869 AATACTA
1 AATACTA
44326876 AATACTA
1 AATACTA
44326883 AATACTA
1 AATACTA
44326890 AATA
1 AATA
44326894 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:44327542 original size:17 final size:16
Alignment explanation
Indices: 44327520--44327551 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
44327510 ATAATTATCT
44327520 AAAAATACTTAAATAAA
1 AAAAAT-CTTAAATAAA
44327537 AAAAATCTTAAATAA
1 AAAAATCTTAAATAA
44327552 TAATTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAATCTTAAATAAA
Found at i:44327686 original size:31 final size:31
Alignment explanation
Indices: 44327648--44327708 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
44327638 GTGATGAAAG
44327648 TATAAAAAAATTTAAAATTATTTTAAAAAAA
1 TATAAAAAAATTTAAAATTATTTTAAAAAAA
*
44327679 TATAAAAAAATTTATAATTATTTTAAAAAA
1 TATAAAAAAATTTAAAATTATTTTAAAAAA
44327709 TAGATTTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
TATAAAAAAATTTAAAATTATTTTAAAAAAA
Found at i:44327691 original size:21 final size:21
Alignment explanation
Indices: 44327650--44327691 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44327640 GATGAAAGTA
* **
44327650 TAAAAAAATTTAAAATTATTT
1 TAAAAAAATATAAAAAAATTT
44327671 TAAAAAAATATAAAAAAATTT
1 TAAAAAAATATAAAAAAATTT
44327692 ATAATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAAAATATAAAAAAATTT
Found at i:44328064 original size:29 final size:28
Alignment explanation
Indices: 44328022--44328083 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
44328012 CGATTTTCCG
* *
44328022 AAAAATGGACCATTCCGGTAAATAATTA
1 AAAAATCGACCATTCCGATAAATAATTA
* **
44328050 AAAAATCGACCCATTTCGATAAATTTTTA
1 AAAAATCGA-CCATTCCGATAAATAATTA
44328079 AAAAA
1 AAAAA
44328084 ATAGCTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (28 bp):
AAAAATCGACCATTCCGATAAATAATTA
Found at i:44332125 original size:52 final size:52
Alignment explanation
Indices: 44332058--44332158 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
44332048 TCCAATAAAC
44332058 CCAAATGTGTCTTTGTGATAATACAAGTTCTGGTCTTATAGAAAAAAGGAGG
1 CCAAATGTGTCTTTGTGATAATACAAGTTCTGGTCTTATAGAAAAAAGGAGG
* * ***
44332110 CCAAGTGTGTCTTTGTGATACTATTTGTTCTGGTCTTATAGAAAAAAGG
1 CCAAATGTGTCTTTGTGATAATACAAGTTCTGGTCTTATAGAAAAAAGG
44332159 TTAGGGTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (52 bp):
CCAAATGTGTCTTTGTGATAATACAAGTTCTGGTCTTATAGAAAAAAGGAGG
Found at i:44339375 original size:14 final size:15
Alignment explanation
Indices: 44339353--44339429 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
44339343 CAATCAAACA
44339353 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
44339367 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
44339382 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
44339402 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
44339416 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
44339430 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:44339394 original size:20 final size:20
Alignment explanation
Indices: 44339369--44339408 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44339359 AATATTTTCC
*
44339369 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
44339389 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
44339409 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Done.