Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_pilon, whole genome shotgun sequence
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: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 16
Found at i:2023526 original size:13 final size:13
Alignment explanation
Indices: 2023508--2023532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2023498 GATATATTTA
2023508 AAATAAAAAAAGG
1 AAATAAAAAAAGG
2023521 AAATAAAAAAAG
1 AAATAAAAAAAG
2023533 ATGAACCGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (13 bp):
AAATAAAAAAAGG
Found at i:2032673 original size:111 final size:111
Alignment explanation
Indices: 2032439--2032766 Score: 558
Period size: 111 Copynumber: 3.0 Consensus size: 111
2032429 ATTAAAAAAA
*
2032439 TTAATTCTTAATCTAATAATCATTCATTAAATAAATTAACTAATTATTACTAATAA--T---TTA
1 TTAATTCTTAATCTAATAATCATTCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
2032499 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
2032545 TTAATTCTTAATCTAATAATCATTCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATTCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
2032610 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* * *
2032656 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATTCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
2032721 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
2032767 ATGATTTCCA
Statistics
Matches: 209, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
106 55 0.26
108 1 0.00
111 153 0.73
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATTCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:2032871 original size:17 final size:18
Alignment explanation
Indices: 2032828--2032868 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2032818 GAATTATATT
2032828 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
2032845 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
2032863 ATTAAA
1 AGTAAA
2032869 TACATAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:2033127 original size:50 final size:50
Alignment explanation
Indices: 2033073--2033179 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 50
2033063 AGATACCCAG
*
2033073 GTATAGCGCGGATCA-AGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
1 GTATAGCGCGGAGCAGA-GGGCGCGCTATACCCACGTGGCGCCAAATCACC
* * * * *
2033123 GTATATCGTGGGGCAGAGGGCGCGCTATACCCACGTGGCGCCAAATTAGC
1 GTATAGCGCGGAGCAGAGGGCGCGCTATACCCACGTGGCGCCAAATCACC
2033173 GTATAGC
1 GTATAGC
2033180 ACGATTTAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
50 48 0.98
51 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGAGCAGAGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:2033194 original size:50 final size:50
Alignment explanation
Indices: 2033089--2033198 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
2033079 CGCGGATCAA
* ** *
2033089 GGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATATCGTGGGGCAG
1 GGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCACGAGGCAG
* * * ***
2033139 AGGGCGCGCTATACCCACGTGGCGCCAAATTAGCGTATAGCACGATTTAG
1 GGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCACGAGGCAG
2033189 GGGGCGCGCT
1 GGGGCGCGCT
2033199 TTACTGCTAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.21, C:0.28, G:0.34, T:0.17
Consensus pattern (50 bp):
GGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCACGAGGCAG
Found at i:2033866 original size:27 final size:26
Alignment explanation
Indices: 2033830--2033882 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
2033820 GAATTTAAAC
*
2033830 TAATTAAATAGA-TATAATATTATTTTA
1 TAATTAAATACATTAT-AT-TTATTTTA
2033857 TAATTAAATACATTATATTTATTTTA
1 TAATTAAATACATTATATTTATTTTA
2033883 AATCATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 13 0.54
28 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
TAATTAAATACATTATATTTATTTTA
Found at i:2035407 original size:16 final size:16
Alignment explanation
Indices: 2035382--2035459 Score: 70
Period size: 16 Copynumber: 4.9 Consensus size: 16
2035372 TTTCGATTTG
*
2035382 ATTTATTTTTGGTTCA
1 ATTTACTTTTGGTTCA
* *
2035398 ATTTGCTTTTGGTTTGA
1 ATTTACTTTTGG-TTCA
*
2035415 A-ATACTTTTGGTTC-
1 ATTTACTTTTGGTTCA
2035429 ATATTACTTTTGGTTCA
1 AT-TTACTTTTGGTTCA
* *
2035446 AGTTAATTTTGGTT
1 ATTTACTTTTGGTT
2035460 TGTTTTATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
14 1 0.02
15 2 0.04
16 41 0.84
17 5 0.10
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.56
Consensus pattern (16 bp):
ATTTACTTTTGGTTCA
Found at i:2037112 original size:55 final size:54
Alignment explanation
Indices: 2037003--2037158 Score: 154
Period size: 55 Copynumber: 2.9 Consensus size: 54
2036993 TATGTAAGCA
* * * * *
2037003 AAAACTATGAAATTCATAATAAGTTTATGAATTTTAGTATGGGCACTGTCTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAA-TTTCGTATTGACACTGGCTGTGC
* * *
2037058 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGATAGTGGGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTT-CGTATTGACACTGGCTGTGC
* * * *
2037113 -AACCCACGTAAATT-ATAATAAGTTTATGAATTATCGTATTGGCACT
1 AAAACTAAG-AAATTCATAATAAGTTTATGAATT-TCGTATTGACACT
2037159 ACGTGTGCAA
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
54 35 0.42
55 49 0.58
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (54 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTCGTATTGACACTGGCTGTGC
Found at i:2037165 original size:54 final size:53
Alignment explanation
Indices: 2037011--2037170 Score: 153
Period size: 54 Copynumber: 2.9 Consensus size: 53
2037001 CAAAAACTAT
* * * *
2037011 GAAATTCATAATAAGTTTATGAATTTTAGTATGGGCACTGTC-TGTGCAAAACTAA
1 GAAATTCATAATAAGTTTATGAA-TTTCGTATTGGCACT-ACGTGTGC-AAACCAA
** * ** * *
2037066 GAAATTCATAATAAGTTTATGAATTTCCGTATTGATAGTGGGTGTGCAACCCAC
1 GAAATTCATAATAAGTTTATGAATTT-CGTATTGGCACTACGTGTGCAAACCAA
2037120 GTAAATT-ATAATAAGTTTATGAATTATCGTATTGGCACTACGTGTGCAAAC
1 G-AAATTCATAATAAGTTTATGAATT-TCGTATTGGCACTACGTGTGCAAAC
2037171 TATAGAGCTT
Statistics
Matches: 85, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
54 44 0.52
55 41 0.48
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (53 bp):
GAAATTCATAATAAGTTTATGAATTTCGTATTGGCACTACGTGTGCAAACCAA
Found at i:2037399 original size:45 final size:45
Alignment explanation
Indices: 2037350--2037482 Score: 221
Period size: 45 Copynumber: 3.0 Consensus size: 45
2037340 CCTAACTGAG
* *
2037350 ATTAAAGGCCTGAAAGGATGCCATAAATAAAATGCATAACGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
* *
2037395 ATTAAAGGCATTAAAGGATGCCATAAATGAAATGCATAATGGTGC
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
*
2037440 ATTAAAGACATGAAAGGATGCCATAAATGAAATGCATAACGGT
1 ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGT
2037483 AATGAAAATA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (45 bp):
ATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGC
Found at i:2038324 original size:18 final size:20
Alignment explanation
Indices: 2038293--2038339 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
2038283 TATTAATACT
*
2038293 ATATTATAAAATTAT-TTTA
1 ATATTATAAAATTATAATTA
*
2038312 ATA-TATAACATTATAATTA
1 ATATTATAAAATTATAATTA
2038331 ATATTATAA
1 ATATTATAA
2038340 TAATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.42
19 9 0.38
20 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTATAAAATTATAATTA
Found at i:2039992 original size:90 final size:92
Alignment explanation
Indices: 2039882--2040057 Score: 293
Period size: 90 Copynumber: 1.9 Consensus size: 92
2039872 TAATCCTGAA
* * * *
2039882 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAACATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAACATAAT
2039947 TAGGGTAACTT-G-TATAAAAAAGGAT
66 TAGGGTAACTTGGCTATAAAAAAGGAT
*
2039972 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAACATAAT
2040037 TAGGGTAACTTGGCTATAAAA
66 TAGGGTAACTTGGCTATAAAA
2040058 GGGTGTGTTA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 71 0.90
91 1 0.01
92 7 0.09
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (92 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAACATAAT
TAGGGTAACTTGGCTATAAAAAAGGAT
Found at i:2046797 original size:90 final size:89
Alignment explanation
Indices: 2046692--2046866 Score: 305
Period size: 90 Copynumber: 2.0 Consensus size: 89
2046682 TCATGAATAT
* *
2046692 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAG
2046757 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
*
2046781 TTAAATTCTAATTAATTAAATATAGATTTAATTATTTTGAAATAATAAAAACCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTA
*
2046846 GGGTAACTTGGCTATAAAAGG
65 GGGTAACTTGGATATAAAAGG
2046867 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 7 0.09
90 74 0.91
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:2048657 original size:45 final size:45
Alignment explanation
Indices: 2048591--2048793 Score: 171
Period size: 45 Copynumber: 4.5 Consensus size: 45
2048581 TTAACTACTC
* * *
2048591 TTCCACTACTATTCCGTGGAGTTTGATACTTTGCTAAAAAATCCG
1 TTCCACTACTCTTTCGTGGAGTTTGATACTTTGCTGAAAAATCCG
* * * * * ** **
2048636 TTCTACTACTCTTTCATGGAG-TTCAGA-TTT-ATGATTCAATTTG
1 TTCCACTACTCTTTCGTGGAGTTTGATACTTTGCTGA-AAAATCCG
* * **
2048679 CTTCCACTACTC-TTCTGTGGCGTTTGATACTTTACTGAAAAATTTG
1 -TTCCACTACTCTTTC-GTGGAGTTTGATACTTTGCTGAAAAATCCG
*
2048725 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCCG
1 TTCCACTACTCTTTCGTGGAGTTTGATACTTTGCTGAAAAATCCG
* * *
2048770 TTCCACTGCTCTTCCGTGAAGTTT
1 TTCCACTACTCTTTCGTGGAGTTT
2048794 TATTTGACTT
Statistics
Matches: 124, Mismatches: 27, Indels: 14
0.75 0.16 0.08
Matches are distributed among these distances:
42 2 0.02
43 10 0.08
44 18 0.15
45 80 0.65
46 11 0.09
47 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (45 bp):
TTCCACTACTCTTTCGTGGAGTTTGATACTTTGCTGAAAAATCCG
Found at i:2055720 original size:20 final size:20
Alignment explanation
Indices: 2055697--2055736 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2055687 AATCGGGCTC
*
2055697 CCAAA-TTATCAATTGGGCCT
1 CCAAACTTAT-AAATGGGCCT
2055717 CCAAACTTATAAATGGGCCT
1 CCAAACTTATAAATGGGCCT
2055737 TTGGGCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (20 bp):
CCAAACTTATAAATGGGCCT
Found at i:2056203 original size:6 final size:6
Alignment explanation
Indices: 2056192--2056220 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2056182 ACCAAATAAA
2056192 AAAACC AAAACC AAAACC AAAACC AAAAC
1 AAAACC AAAACC AAAACC AAAACC AAAAC
2056221 AAGCCATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:2056958 original size:5 final size:5
Alignment explanation
Indices: 2056925--2056971 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
2056915 TGAGTTTTCT
* *
2056925 TTTAA TTT-- TTTTA TTTAA CTTTTA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA -TTTAA TTTAA TTTAA TTTAA TTTAA TTT
2056972 TTATTTGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
3 3 0.08
5 29 0.81
6 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (5 bp):
TTTAA
Found at i:2056973 original size:26 final size:24
Alignment explanation
Indices: 2056907--2056977 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 24
2056897 AGTTTAACCC
*
2056907 TTTTAATTTGAGTTTTCT-TTTAATT
1 TTTTAATTT-AATTTT-TATTTAATT
* *
2056932 TTTTTATTTAACTTTTATTTAATT
1 TTTTAATTTAATTTTTATTTAATT
2056956 TAATTTAATTTAATTTTTATTT
1 T--TTTAATTTAATTTTTATTT
2056978 GTTTTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 12 0.32
25 8 0.21
26 17 0.45
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (24 bp):
TTTTAATTTAATTTTTATTTAATT
Found at i:2064190 original size:24 final size:24
Alignment explanation
Indices: 2064163--2064228 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 24
2064153 GGTATATACA
2064163 AATGATAATGATGTGGCAATATGG
1 AATGATAATGATGTGGCAATATGG
*
2064187 AATG--ACTGATGTGG-AA-ATGG
1 AATGATAATGATGTGGCAATATGG
* *
2064207 ATGATGATAATGAGGTAGCAAT
1 A--ATGATAATGATGTGGCAAT
2064229 TGATTATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
20 5 0.16
21 2 0.06
22 12 0.38
24 11 0.34
25 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (24 bp):
AATGATAATGATGTGGCAATATGG
Found at i:2064320 original size:2 final size:2
Alignment explanation
Indices: 2064313--2064357 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2064303 ACTGGATTTA
2064313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2064355 AT A
1 AT A
2064358 GGACTTTAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2071616 original size:18 final size:19
Alignment explanation
Indices: 2071582--2071631 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
2071572 AATAAATTAT
** *
2071582 TTAATATATAGAAAGTAAG
1 TTAATATATAGTTAGTAAA
2071601 TTAAT-TATAGTTAGTAAA
1 TTAATATATAGTTAGTAAA
2071619 TTAATATATAGTT
1 TTAATATATAGTT
2071632 GATTAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (19 bp):
TTAATATATAGTTAGTAAA
Found at i:2071660 original size:37 final size:36
Alignment explanation
Indices: 2071560--2071669 Score: 105
Period size: 37 Copynumber: 3.0 Consensus size: 36
2071550 AAAAAGTTCT
2071560 TTAAAATATATTAATAAATTATTTAATATATAGAAA
1 TTAAAATATATTAATAAATTATTTAATATATAGAAA
* ** * * * * **
2071596 GTAAGTTA-ATTATAGTTAGTAAATTAATATATAGTTGA
1 TTAAAATATATTA-A-TAAATTATTTAATATATAG-AAA
2071634 TTAAAATATATTAATAAATTATTTAATATATAGAAA
1 TTAAAATATATTAATAAATTATTTAATATATAGAAA
2071670 GTAAGTTATT
Statistics
Matches: 52, Mismatches: 18, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
35 4 0.08
36 7 0.13
37 30 0.58
38 7 0.13
39 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (36 bp):
TTAAAATATATTAATAAATTATTTAATATATAGAAA
Found at i:2071681 original size:23 final size:22
Alignment explanation
Indices: 2071646--2071705 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
2071636 AAAATATATT
2071646 AATAAATTATTTAATATATAGA
1 AATAAATTATTTAATATATAGA
* * **
2071668 AAGTAAGTTATTTAAAATATATT
1 AA-TAAATTATTTAATATATAGA
2071691 AATAAATTATTTAAT
1 AATAAATTATTTAAT
2071706 TATTAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
AATAAATTATTTAATATATAGA
Found at i:2071703 original size:22 final size:22
Alignment explanation
Indices: 2071634--2071704 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
2071624 ATATAGTTGA
2071634 TTAAAATATATTAATAAATTAT
1 TTAAAATATATTAATAAATTAT
* ** *
2071656 TTAATATATAGAAAGTAAGTTAT
1 TTAAAATATATTAA-TAAATTAT
2071679 TTAAAATATATTAATAAATTAT
1 TTAAAATATATTAATAAATTAT
2071701 TTAA
1 TTAA
2071705 TTATTAAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 22 0.55
23 18 0.45
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
TTAAAATATATTAATAAATTAT
Found at i:2071711 original size:74 final size:74
Alignment explanation
Indices: 2071560--2071718 Score: 214
Period size: 74 Copynumber: 2.1 Consensus size: 74
2071550 AAAAAGTTCT
* * *
2071560 TTAAAATATATTAATAAATTATTTAATATATAGAAAGTAAGTTAATTATAGTTAGTAAATTAATA
1 TTAAAATATATTAATAAATTATTTAATATATAGAAAGTAAGTTAATTAAAATTAGTAAATAAATA
*
2071625 TATAGTTGA
66 TATAATTGA
* *
2071634 TTAAAATATATTAATAAATTATTTAATATATAGAAAGTAAGTTATTTAAAATATA-TTAATAAAT
1 TTAAAATATATTAATAAATTATTTAATATATAGAAAGTAAGTTAATTAAAAT-TAGTAAATAAA-
*
2071698 TATTTAATT-A
64 TATATAATTGA
2071708 TTAAATATATA
1 TTAAA-ATATA
2071719 GTTGGTAAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
74 61 0.81
75 14 0.19
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.43
Consensus pattern (74 bp):
TTAAAATATATTAATAAATTATTTAATATATAGAAAGTAAGTTAATTAAAATTAGTAAATAAATA
TATAATTGA
Found at i:2075418 original size:2 final size:2
Alignment explanation
Indices: 2075411--2075489 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
2075401 ATTTTATTTA
2075411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2075453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2075490 GGACTTTAGC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2079524 original size:17 final size:17
Alignment explanation
Indices: 2079485--2079524 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2079475 TCTCACTAAC
2079485 TTTTTTCTTTTCATTTT
1 TTTTTTCTTTTCATTTT
*
2079502 TGTTTTCTTTT-ATTTT
1 TTTTTTCTTTTCATTTT
2079518 ATTTTTT
1 -TTTTTT
2079525 TGCATTTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTTCTTTTCATTTT
Found at i:2096261 original size:70 final size:70
Alignment explanation
Indices: 2096148--2096285 Score: 267
Period size: 70 Copynumber: 2.0 Consensus size: 70
2096138 AACATGATTG
*
2096148 TCAAAGCACAAACTAAGGATGAGCATGTCGAGAATTTGAGAAAACTCTTCCAGAGATTGAGGAAG
1 TCAAAGCACAAACTAAGGATGAGCATGTCGAGAATTTGAGAAAACTCTTCCAAAGATTGAGGAAG
2096213 TTTTT
66 TTTTT
2096218 TCAAAGCACAAACTAAGGATGAGCATGTCGAGAATTTGAGAAAACTCTTCCAAAGATTGAGGAAG
1 TCAAAGCACAAACTAAGGATGAGCATGTCGAGAATTTGAGAAAACTCTTCCAAAGATTGAGGAAG
2096283 TTT
66 TTT
2096286 CAGTTGAGGT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (70 bp):
TCAAAGCACAAACTAAGGATGAGCATGTCGAGAATTTGAGAAAACTCTTCCAAAGATTGAGGAAG
TTTTT
Found at i:2097470 original size:42 final size:42
Alignment explanation
Indices: 2097423--2097521 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
2097413 CATTCATGAG
* * *
2097423 GTATCGATACCAGTGTGGA-GGCATCGGTACCATAGTATTGTA
1 GTATCGATACCAG-GTGAAGGGCATCAGTACCATAGTATTATA
* *
2097465 GTATCGATACCAGGTTAAGGGTATCAGTACCATAGTATTATA
1 GTATCGATACCAGGTGAAGGGCATCAGTACCATAGTATTATA
*
2097507 GTATCAATACCAGGT
1 GTATCGATACCAGGT
2097522 TAAAGGTGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
41 3 0.06
42 47 0.94
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (42 bp):
GTATCGATACCAGGTGAAGGGCATCAGTACCATAGTATTATA
Found at i:2098217 original size:18 final size:18
Alignment explanation
Indices: 2098184--2098231 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
2098174 GAGAGATTTC
* * *
2098184 AAGTGGTCTTTTGGGACA
1 AAGTGGTCCTTCGGGAAA
*
2098202 TAGTGGTCCTTCGGGAAA
1 AAGTGGTCCTTCGGGAAA
2098220 AAGTGGTCCTTC
1 AAGTGGTCCTTC
2098232 TGGATAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (18 bp):
AAGTGGTCCTTCGGGAAA
Found at i:2101096 original size:57 final size:58
Alignment explanation
Indices: 2101028--2101140 Score: 133
Period size: 58 Copynumber: 2.0 Consensus size: 58
2101018 AATACTTTGC
* * * *
2101028 TTAGGATG-AAAACCCAGGAGGCTGCCCTAAATT-AAAGAA-AAAAAAGAGAAAAAACGT
1 TTAGGATGAAAAACCGA-AAGGC-GCCCTAAATTGAAAAAATAAAAAAAAGAAAAAACGT
* *
2101085 TTAGGGTGAAAAACCGAAATGCGCCCTAAATTGAAAAAATAAAAAAAAGAAAAAAC
1 TTAGGATGAAAAACCGAAAGGCGCCCTAAATTGAAAAAATAAAAAAAAGAAAAAAC
2101141 AAGAGCAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
56 10 0.21
57 15 0.32
58 22 0.47
ACGTcount: A:0.54, C:0.13, G:0.19, T:0.14
Consensus pattern (58 bp):
TTAGGATGAAAAACCGAAAGGCGCCCTAAATTGAAAAAATAAAAAAAAGAAAAAACGT
Found at i:2102155 original size:73 final size:73
Alignment explanation
Indices: 2102034--2102248 Score: 272
Period size: 73 Copynumber: 3.0 Consensus size: 73
2102024 CTATCCTCCT
* * * * *
2102034 ACGATTTCAACTTCACAATGAAGGATATCGTACCCAAAATTTTTGACTTAACTTCATGAT-TAAG
1 ACGATTTCAACTTCACAACGAAGGATATCGTACCCAAAAGTTTCGACTTAACTTCA-CATCAAAG
2102098 GAGTCACCC
65 GAGTCACCC
* *
2102107 ATGATTTCAACTTCACAACGAAGGATATCGTACCCAAAAGTTTCGACTTAACTTCACATCAAATG
1 ACGATTTCAACTTCACAACGAAGGATATCGTACCCAAAAGTTTCGACTTAACTTCACATCAAAGG
2102172 AGTCACCC
66 AGTCACCC
* * * * * * * *
2102180 ACGATTTCAACTTCACGACGAAGGATATCCTGCCCAATAG-ATCGACTTAAATTCACAACAAATG
1 ACGATTTCAACTTCACAACGAAGGATATCGTACCCAAAAGTTTCGACTTAACTTCACATCAAAGG
2102244 AGTCA
66 AGTCA
2102249 TCTGCAATAA
Statistics
Matches: 126, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
72 28 0.22
73 98 0.78
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (73 bp):
ACGATTTCAACTTCACAACGAAGGATATCGTACCCAAAAGTTTCGACTTAACTTCACATCAAAGG
AGTCACCC
Found at i:2102879 original size:23 final size:25
Alignment explanation
Indices: 2102852--2102899 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2102842 TATAATGATA
*
2102852 ATATAATATA-GT-TTTGAAAACAT
1 ATATAATATATATCTTTGAAAACAT
2102875 ATATAATATATATCTTTGAAAACAT
1 ATATAATATATATCTTTGAAAACAT
2102900 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.45
24 1 0.05
25 11 0.50
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (25 bp):
ATATAATATATATCTTTGAAAACAT
Found at i:2102950 original size:37 final size:37
Alignment explanation
Indices: 2102863--2103233 Score: 323
Period size: 37 Copynumber: 9.9 Consensus size: 37
2102853 TATAATATAG
*
2102863 TTTTGAAAACATATATAATATATA-TCTTTGAAAACATT
1 TTTTGAAAACGTATATAATATATAGT-TTTGAAAACA-T
*
2102901 TTTTAAAAACGTATATAATATATAGTTTTGAAAACAT
1 TTTTGAAAACGTATATAATATATAGTTTTGAAAACAT
* * * *
2102938 TTTTGAAAACGTATATATTATATAGTTTTAAAAATAG
1 TTTTGAAAACGTATATAATATATAGTTTTGAAAACAT
*
2102975 TTTTGAAAACGTATACAATATATAGTTTTGAAAACAT
1 TTTTGAAAACGTATATAATATATAGTTTTGAAAACAT
* *
2103012 TTTTGAAGATGTATATAATATATAGTTTTGAAAACAT
1 TTTTGAAAACGTATATAATATATAGTTTTGAAAACAT
* * * *
2103049 TGTTGAAAAC--ATGTAATATATAGTTTT-TAAATAT
1 TTTTGAAAACGTATATAATATATAGTTTTGAAAACAT
* * *
2103083 TTTTTAAAACATATAT-ATAATATAGTTTTTGAACACGTAT
1 TTTTGAAAACGTATATAAT-ATATAG-TTTTGAAAAC--AT
* * *
2103123 TTTTGAAAACATATA-ATATATATAGTTTTTTTAAAAAAATAT
1 TTTTGAAAACGTATATA-ATATATAG---TTTT--GAAAACAT
* * **
2103165 TTTTG-AAA-GCATATATTATATAGTTTAT-AAAATGTT
1 TTTTGAAAACGTATATAATATATAGTTT-TGAAAA-CAT
2103201 TTTTGAAAA--TATATAATATATAGTTTTTGAAAA
1 TTTTGAAAACGTATATAATATATAG-TTTTGAAAA
2103234 ATTGTTTTTG
Statistics
Matches: 275, Mismatches: 38, Indels: 41
0.78 0.11 0.12
Matches are distributed among these distances:
34 13 0.05
35 22 0.08
36 28 0.10
37 123 0.45
38 35 0.13
39 1 0.00
40 32 0.12
41 6 0.02
42 12 0.04
44 3 0.01
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (37 bp):
TTTTGAAAACGTATATAATATATAGTTTTGAAAACAT
Found at i:2103259 original size:32 final size:34
Alignment explanation
Indices: 2103218--2103280 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
2103208 AATATATAAT
2103218 ATATAGTTTTTGAAAA-AT-TGTTTTTGAAAAAC
1 ATATAGTTTTTGAAAACATATGTTTTTGAAAAAC
*
2103250 ATATAGTTTTTGAAAACATATTTTTTTGAAA
1 ATATAGTTTTTGAAAACATATGTTTTTGAAA
2103281 TATATTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 16 0.57
33 2 0.07
34 10 0.36
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (34 bp):
ATATAGTTTTTGAAAACATATGTTTTTGAAAAAC
Found at i:2103286 original size:15 final size:16
Alignment explanation
Indices: 2103224--2103280 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
2103214 TAATATATAG
*
2103224 TTTTTGAAAA-AT-TG
1 TTTTTGAAAACATATT
*
2103238 TTTTTGAAAAACATATAG
1 TTTTTG-AAAACATAT-T
2103256 TTTTTGAAAACATATT
1 TTTTTGAAAACATATT
2103272 TTTTTGAAA
1 TTTTTGAAA
2103281 TATATTCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
14 6 0.16
15 4 0.11
16 11 0.29
17 10 0.26
18 7 0.18
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.47
Consensus pattern (16 bp):
TTTTTGAAAACATATT
Found at i:2103332 original size:14 final size:13
Alignment explanation
Indices: 2103309--2103346 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2103299 ATTTTTTTCC
2103309 TTTTTA-TTTTAT
1 TTTTTATTTTTAT
2103321 TTATTTATTTTTTAT
1 TT-TTTA-TTTTTAT
2103336 TTTTTATTTTT
1 TTTTTATTTTT
2103347 CGGTCTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 9 0.39
14 4 0.17
15 8 0.35
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:2103336 original size:7 final size:7
Alignment explanation
Indices: 2103315--2103346 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2103305 TTCCTTTTTA
2103315 TTTTATT
1 TTTTATT
2103322 TATTTATT
1 T-TTTATT
2103330 TTTTATT
1 TTTTATT
2103337 TTTTATT
1 TTTTATT
2103344 TTT
1 TTT
2103347 CGGTCTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:2110065 original size:32 final size:32
Alignment explanation
Indices: 2110029--2110143 Score: 122
Period size: 32 Copynumber: 3.6 Consensus size: 32
2110019 GTTTGTTGGA
*
2110029 TAAAATTATTATGCTTTATGGTTATTGAATAT
1 TAAAATTATTATGTTTTATGGTTATTGAATAT
* * * *
2110061 TAAAATTATTATGTTTTTAAGTTTGTTGTATAT
1 TAAAATTATTATG-TTTTATGGTTATTGAATAT
* * * *
2110094 TAAAATTATTATGTTTTATGTTTACTGGACAT
1 TAAAATTATTATGTTTTATGGTTATTGAATAT
* *
2110126 TGAAATAATTATGTTTTA
1 TAAAATTATTATGTTTTA
2110144 AGTGTGTTGG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
32 43 0.61
33 27 0.39
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (32 bp):
TAAAATTATTATGTTTTATGGTTATTGAATAT
Found at i:2110113 original size:65 final size:63
Alignment explanation
Indices: 2110010--2110158 Score: 176
Period size: 65 Copynumber: 2.3 Consensus size: 63
2110000 TGAACTTGTA
* * * *
2110010 ATGTTTTAAGTTTGTTG-GA-TAAAATTATTATGCTTTATGGTTATTGAATATTAAAATTATT
1 ATGTTTTAAGTTTGTTGATATTAAAATTATTATGCTTTATGGTTACTGAACATTAAAATAATT
* * * *
2110071 ATGTTTTTAAGTTTGTTGTATATTAAAATTATTATGTTTTATGTTTACTGGACATTGAAATAATT
1 ATG-TTTTAAGTTTGTTG-ATATTAAAATTATTATGCTTTATGGTTACTGAACATTAAAATAATT
*
2110136 ATGTTTTAAGTGTGTTGGATATT
1 ATGTTTTAAGTTTGTT-GATATT
2110159 GGAATTGTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
61 3 0.04
62 14 0.19
64 18 0.24
65 39 0.53
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (63 bp):
ATGTTTTAAGTTTGTTGATATTAAAATTATTATGCTTTATGGTTACTGAACATTAAAATAATT
Found at i:2110211 original size:32 final size:32
Alignment explanation
Indices: 2110069--2110213 Score: 105
Period size: 32 Copynumber: 4.5 Consensus size: 32
2110059 ATTAAAATTA
* ** * *
2110069 TTATGTTTTTAAGTTTGTTGTATATTAAAATTA
1 TTATG-TTTTAAGTTTGTTGGATATTGGAAGTG
* ** * * *
2110102 TTATGTTTTATGTTTACTGGACATT-GAAATAA
1 TTATGTTTTAAGTTTGTTGGATATTGGAAGT-G
* *
2110134 TTATGTTTTAAGTGTGTTGGATATTGGAATTG
1 TTATGTTTTAAGTTTGTTGGATATTGGAAGTG
* *
2110166 TTATATTTTAAGTTTGTT-GAGTTTTGGAAGTG
1 TTATGTTTTAAGTTTGTTGGA-TATTGGAAGTG
*
2110198 TTATGTTCTAAGTTTG
1 TTATGTTTTAAGTTTG
2110214 ATGGTTATAA
Statistics
Matches: 89, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
31 5 0.06
32 75 0.84
33 9 0.10
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.52
Consensus pattern (32 bp):
TTATGTTTTAAGTTTGTTGGATATTGGAAGTG
Found at i:2145095 original size:17 final size:17
Alignment explanation
Indices: 2145049--2145095 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2145039 CAATCAGTGA
*
2145049 TTAACAAATTAATTATC
1 TTAACAAATTAATCATC
* *
2145066 TTTAGAAATTAATCA-C
1 TTAACAAATTAATCATC
2145082 TTAACAAATATAAT
1 TTAACAAAT-TAAT
2145096 TTACTCTCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (17 bp):
TTAACAAATTAATCATC
Found at i:2148454 original size:54 final size:54
Alignment explanation
Indices: 2148380--2148678 Score: 440
Period size: 54 Copynumber: 5.5 Consensus size: 54
2148370 ATGAGCGGCA
*
2148380 AATTATGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATG
1 AATTCTGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATG
* * * * * *
2148434 AATTCCGTGGGTTGCACACTTAGTGCCTATACAGTCATTCATAAACACATTATG
1 AATTCTGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATG
*
2148488 AATTCTGTGGGTTGCACACTTAGTGCATATACGGTCGTTCATCAACATATGATG
1 AATTCTGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATG
* * ** *
2148542 AATTTTTTGGGTTGCACACTTAGTGCCTATATAGTCGTTCATCAATATATGATG
1 AATTCTGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATG
*
2148596 AATTATGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATAAT-ATG
1 AATTCTGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACAT-ATGATG
2148650 AATT-TCGTGGGTTGCACACTTAGTGCCTA
1 AATTCT-GTGGGTTGCACACTTAGTGCCTA
2148679 CAGTACACAT
Statistics
Matches: 218, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.00
54 215 0.99
55 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (54 bp):
AATTCTGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATG
Found at i:2155172 original size:54 final size:54
Alignment explanation
Indices: 2155090--2155847 Score: 910
Period size: 54 Copynumber: 14.1 Consensus size: 54
2155080 CATAGTTCCG
* * * * * * * *
2155090 ATACGGTCGTTTATAAAAATATTATGAATTCCGTGAGCTGCACACTTAGTACTT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* **
2155144 ATACGATCGTTCATCAACATATGATGAATTTAGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
*
2155198 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGTACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* * **
2155252 ATATGGTCGTTCATCAACATATGATAAATTATGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
*
2155306 ATACGGTCGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* * * * * ** * * * *
2155360 ATACGGTCATTCATAAACACATTATGAAATCTATGGGTTGCGCCCTTACTACCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* **
2155414 ATACGATCGTTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* * **
2155468 ATA-GAGTTGTTCATCAACATATGATAAATTATGTGGGTTGCACACTTAGTGCCT
1 ATACG-GTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* * * * *
2155522 ATACGGTTGTTCATCAACATATGATGAATTCCATGGGTTGCATAATTAGTACCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* * * *
2155576 ATACGGTCGTTAATCAACATATGATAAATTACGTGGGTTGAACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* * * * * * *
2155630 ATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCGCAGTTAGTGCCA
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* ** *
2155684 AT-CAGTCGTTCATCAACATATGATGAATTATGTGGGTTGCGCACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* * * *
2155737 ATACGGTCATTCATCAACATATGATGTATTCTGTGGGTTGCACACTTAGTGTCT
1 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
* * * *
2155791 ATATGGTCGTTCAT-AAGCACATTATGAATTTCGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATCAA-CATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
2155845 ATA
1 ATA
2155848 GTACACATAG
Statistics
Matches: 601, Mismatches: 99, Indels: 8
0.85 0.14 0.01
Matches are distributed among these distances:
53 48 0.08
54 552 0.92
55 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCT
Found at i:2158276 original size:36 final size:36
Alignment explanation
Indices: 2158229--2158297 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
2158219 AATATTTTCC
2158229 TTGACTTGTTGATAGAGCCTTTTAACAAATTATGCT
1 TTGACTTGTTGATAGAGCCTTTTAACAAATTATGCT
2158265 TTGACTTGTTGATAGAGCCTTTTAACAAATTAT
1 TTGACTTGTTGATAGAGCCTTTTAACAAATTAT
2158298 AATTTGTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (36 bp):
TTGACTTGTTGATAGAGCCTTTTAACAAATTATGCT
Found at i:2169875 original size:54 final size:54
Alignment explanation
Indices: 2169810--2170138 Score: 435
Period size: 54 Copynumber: 6.1 Consensus size: 54
2169800 CTAAGTATAT
* * * ** *
2169810 TATCGGCACTAAGTGTGCAACCCACAGAATTCATCATAAGTTTATGAATGACCA
1 TATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAACCG
* * *
2169864 TATCGACACTAAGTATGCAACCCACATAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAACCG
* * * *
2169918 TATCGGCACTAAGTGTGCAACCCACATAATTTATAATAAGTTTATGAA-ATATCG
1 TATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACA-ACCG
* * * *
2169972 TATCGGCACTAAGTGTGTAACCCTCAAAATTCATAATAAGTTTATGAACAACCA
1 TATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAACCG
**
2170026 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACAACCG
1 TATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAACCG
* * * *
2170080 TATCGACACTAAGTGTGCAACCTACAAAATTCATAATAAGTTTATTAACGATCG
1 TATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAACCG
2170134 TATCG
1 TATCG
2170139 GCATTACGTT
Statistics
Matches: 244, Mismatches: 29, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
54 243 1.00
55 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAACCG
Found at i:2170082 original size:162 final size:162
Alignment explanation
Indices: 2169810--2170141 Score: 511
Period size: 162 Copynumber: 2.0 Consensus size: 162
2169800 CTAAGTATAT
* * **
2169810 TATCGGCACTAAGTGTGCAACCCACAGAATTCATCATAAGTTTATGAATGACCATATCGACACTA
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAACCATATCGACACTA
* * *
2169875 AGTATGCAACCCACATAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACC
66 AGTATGCAACCCACAGAATTCATAATAAGTTTATGAACAACCGTATCGACACTAAGTGTGCAACC
* * *
2169940 CACATAATTTATAATAAGTTTATGAAATATCG
131 CACAAAATTCATAATAAGTTTATGAAAGATCG
* *
2169972 TATCGGCACTAAGTGTGTAACCCTCAAAATTCATAATAAGTTTATGAACAACCATATCGACACTA
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAACCATATCGACACTA
* *
2170037 AGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACAACCGTATCGACACTAAGTGTGCAACC
66 AGTATGCAACCCACAGAATTCATAATAAGTTTATGAACAACCGTATCGACACTAAGTGTGCAACC
* * *
2170102 TACAAAATTCATAATAAGTTTATTAACGATCG
131 CACAAAATTCATAATAAGTTTATGAAAGATCG
2170134 TATCGGCA
1 TATCGGCA
2170142 TTACGTTTGC
Statistics
Matches: 153, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
162 153 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (162 bp):
TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAACCATATCGACACTA
AGTATGCAACCCACAGAATTCATAATAAGTTTATGAACAACCGTATCGACACTAAGTGTGCAACC
CACAAAATTCATAATAAGTTTATGAAAGATCG
Found at i:2176744 original size:27 final size:27
Alignment explanation
Indices: 2176714--2176799 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
2176704 AAATTCATAA
2176714 TAAGTTTATGAACGACCGTATTGACAC
1 TAAGTTTATGAACGACCGTATTGACAC
* * * * * *
2176741 TAAG--TATGAAACCCACAGAATTCATAA
1 TAAGTTTATG-AA-CGACCGTATTGACAC
* *
2176768 TAAGTTTATGAATGACCGTTTTGACAC
1 TAAGTTTATGAACGACCGTATTGACAC
2176795 TAAGT
1 TAAGT
2176800 GTGCAACCCA
Statistics
Matches: 41, Mismatches: 14, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
25 4 0.10
26 2 0.05
27 29 0.71
28 2 0.05
29 4 0.10
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (27 bp):
TAAGTTTATGAACGACCGTATTGACAC
Found at i:2176763 original size:54 final size:54
Alignment explanation
Indices: 2176677--2176964 Score: 384
Period size: 54 Copynumber: 5.3 Consensus size: 54
2176667 TTAAGTGTAT
2176677 TATTGAACACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGACCG
1 TATTG-ACACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCG
* * *
2176732 TATTGACACTAAGTATGAAACCCACAGAATTCATAATAAGTTTATGAATGACCG
1 TATTGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
* * *
2176786 TTTTGACACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAATGACTG
1 TATTGACACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCG
* *
2176840 TATCGACACTATGTGTGCAACCCACA-ACATTCATAATAAGTTTATGAACGACCG
1 TATTGACACTAAGTGTGCAACCCACAGA-ATTCATAATAAGTTTATGAACGACCG
* * * *
2176894 TATCGACACTAACTGTGCAACCCACAAAATTCATAATAAGATTATGAACGACCG
1 TATTGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
* **
2176948 TATCGGTACTAAGTGTG
1 TATTGACACTAAGTGTG
2176965 AATCCCAAAA
Statistics
Matches: 210, Mismatches: 18, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
53 2 0.01
54 201 0.96
55 7 0.03
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (54 bp):
TATTGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
Found at i:2205321 original size:772 final size:773
Alignment explanation
Indices: 2203892--2205443 Score: 2703
Period size: 772 Copynumber: 2.0 Consensus size: 773
2203882 CTAATCAAGT
2203892 TACTTTCTTAGGCTTCATTGTAAGTTCACAGGGATTATCAGTGGATCCAGAAAAGATTAAGGCAA
1 TACTTTCTTAGGCTTCATTGTAAGTTCACAGGGATTATCAGTGGATCCAGAAAAGATTAAGGCAA
* *
2203957 TACAAGAATGGCCAAAGCCGGTCAATGTCAGCCAAGTTCGTAGTTTCTATGGATTAGCCAGCTTT
66 TACAAGAATGGCCAAAGCCGGTCAATGTCAGCCAAGTCCGTAGTTTCGATGGATTAGCCAGCTTT
*
2204022 TATAGAAGGTTTGTACCAAATTTCAATTCTATTATCGCCCTCTTAACAGGGATCATTAAGAAGAA
131 TATAGAAGGTTTGTACCAAATTTCAATTCTATTACCGCCCTCTTAACAGGGATCATTAAGAAGAA
* * *
2204087 TTCGAACTTCTCTTGGGGTAAAGAACAAAATGAAGCATTCAACGAACTCAAGGGTTGTTTAAAAA
196 TTCAAACTTCTCTTAGGGAAAAGAACAAAATGAAGCATTCAACGAACTCAAGGGTTGTTTAAAAA
* *
2204152 AGGTTCCACTATTAGTATTGCCAAACTTTGAGAAAACATTTGAAGTTGAATGTGATGCCTCAGGA
261 AGGCTCCACTATTAGCATTGCCAAACTTTGAGAAAACATTTGAAGTTGAATGTGATGCCTCAGGA
* **
2204217 ATTGGGAGCGGGGCTGTTTTAAGTCAATAAGGAAACCCCATTGCCTACTTTAGTGAAAAACTGAA
326 ATTGGGAGCGGGGCTGTTTTAAGTCAAGAAGGAAACCCCATAACCTACTTTAGTGAAAAACTGAA
* *
2204282 TGGTGCAACTTTGAACTATCCAACATATGAAAAAGAAATGTACACACTTATTCGGACCTTGGAGA
391 TGGTGCAACTTTGAACTATCCAACATATGAAAAAGAAATGTACACACTCATTCAGACCTTGGAGA
2204347 CTTGGCAGCACTACTTATTGCCAAAAGAATTTGTGATACACACTGATCATGAGGCATTAAAGCAT
456 CTTGGCAGCACTACTTATTGCCAAAAGAATTTGTGATACACACTGATCATGAGGCATTAAAGCAT
* * *
2204412 ATCAAAGGACAACACAAACTCAACAGGAGACATGCCAAATGGGTTGAATTCCTTGAGTATTTTTC
521 ATCAAAGGACAACACAAACTCAACAGGAGACATGCCAAATGAGTTGAACTCCTTGAGTATTTTCC
* *
2204477 TTATGTCATACACTATAAGAAAGAAAATGACCCACTAGTTATAAGACCTAGGAACCAGAAGTATC
586 TTATGTCATACACTATAAGAAAGAAAAGGACCCACTAGTTATAAGAACTAGGAACCAGAAGTATC
* *
2204542 AAGGTGAAAAGGGGTTGATGCCACAAGTATAAAATACTTGATAAGTCGATAAAAGTCACTAGGAC
651 AAGGTGAAAAGGGGTTGATGCCACAAGTATAAAATACTTGATAAGTCGATAAAAGTAACCAGGAC
*
2204607 TTAAAGAAGAGAATAATCTCACTTATATTGATCAAAAGGTCTGATTACAAATGATATA
716 CTAAAGAAGAGAATAATCTCACTTATATTGATCAAAAGGTCTGATTACAAATGATATA
2204665 TACTTTCTTAGGCTTCATTGTAAGTTCACAGGGATTATCAGTGGATCCAGAAAAGATTAAGGCAA
1 TACTTTCTTAGGCTTCATTGTAAGTTCACAGGGATTATCAGTGGATCCAGAAAAGATTAAGGCAA
*
2204730 TACAAGAATGGCCAAAGCCGGTCAATGTCAGCCAAGTCCGTGGTTTCGATGGATTAGCCAGCTTT
66 TACAAGAATGGCCAAAGCCGGTCAATGTCAGCCAAGTCCGTAGTTTCGATGGATTAGCCAGCTTT
* *
2204795 TATAGAAGGTTTGTACCAAATTTCAGTTCTATTGCCGCCC-CTTAACAGGGATCATTAAGAAGAA
131 TATAGAAGGTTTGTACCAAATTTCAATTCTATTACCGCCCTCTTAACAGGGATCATTAAGAAGAA
**
2204859 TTCAAACTTCTCTTAGGGAAAAGAACAAAATGAAGCATTCAACGAACTCAAGGGTTGTTTAACTA
196 TTCAAACTTCTCTTAGGGAAAAGAACAAAATGAAGCATTCAACGAACTCAAGGGTTGTTTAAAAA
* * *
2204924 AGGCTCCACTATTAGCATTGTCGAACTTTGAGAAAACATTTGAAGTTGAATGTGATGCCTCTGGA
261 AGGCTCCACTATTAGCATTGCCAAACTTTGAGAAAACATTTGAAGTTGAATGTGATGCCTCAGGA
* * * *
2204989 ATTGGGATCGGTGTTGTTTTAAGTCAAGAAGGAAAGCCCATAACCTACTTTAGTGAAAAACTGAA
326 ATTGGGAGCGGGGCTGTTTTAAGTCAAGAAGGAAACCCCATAACCTACTTTAGTGAAAAACTGAA
* *
2205054 TGGTGCAACTTTGAACTATCCAACATATGATAAAGAAATGTACGCACTCATTCAGACCTTGGAGA
391 TGGTGCAACTTTGAACTATCCAACATATGAAAAAGAAATGTACACACTCATTCAGACCTTGGAGA
*
2205119 CTTGGCAGCGCTACTTATTGCCAAAAGAATTTGTGATACACACTGATCATGAGGCATTAAAGCAT
456 CTTGGCAGCACTACTTATTGCCAAAAGAATTTGTGATACACACTGATCATGAGGCATTAAAGCAT
*
2205184 ATCAAAGGACAACACAAACTCAACAGGAGACATGCCAAATGAGTTGAACTCCTTGAGTCTTTTCC
521 ATCAAAGGACAACACAAACTCAACAGGAGACATGCCAAATGAGTTGAACTCCTTGAGTATTTTCC
*
2205249 TTATGTTATACACTATAAGAAA-AGAAAGGACCCACTAGTTATAAGAACTAGGAACCAGAAGTAT
586 TTATGTCATACACTATAAGAAAGA-AAAGGACCCACTAGTTATAAGAACTAGGAACCAGAAGTAT
2205313 CAAGGTGAAAAGGGGTTGATGCCACAAGTATAAAATACTTGATAAGTCGATAAAAGTAACCAGGA
650 CAAGGTGAAAAGGGGTTGATGCCACAAGTATAAAATACTTGATAAGTCGATAAAAGTAACCAGGA
* * *
2205378 CCTAAGGAAGAGAATAATCTCATTTATATTTATCAAAAGGTCTGATTACAAATGATATA
715 CCTAAAGAAGAGAATAATCTCACTTATATTGATCAAAAGGTCTGATTACAAATGATATA
*
2205437 TGCTTTC
1 TACTTTC
2205444 CTATTTATAG
Statistics
Matches: 736, Mismatches: 42, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
771 1 0.00
772 571 0.78
773 164 0.22
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (773 bp):
TACTTTCTTAGGCTTCATTGTAAGTTCACAGGGATTATCAGTGGATCCAGAAAAGATTAAGGCAA
TACAAGAATGGCCAAAGCCGGTCAATGTCAGCCAAGTCCGTAGTTTCGATGGATTAGCCAGCTTT
TATAGAAGGTTTGTACCAAATTTCAATTCTATTACCGCCCTCTTAACAGGGATCATTAAGAAGAA
TTCAAACTTCTCTTAGGGAAAAGAACAAAATGAAGCATTCAACGAACTCAAGGGTTGTTTAAAAA
AGGCTCCACTATTAGCATTGCCAAACTTTGAGAAAACATTTGAAGTTGAATGTGATGCCTCAGGA
ATTGGGAGCGGGGCTGTTTTAAGTCAAGAAGGAAACCCCATAACCTACTTTAGTGAAAAACTGAA
TGGTGCAACTTTGAACTATCCAACATATGAAAAAGAAATGTACACACTCATTCAGACCTTGGAGA
CTTGGCAGCACTACTTATTGCCAAAAGAATTTGTGATACACACTGATCATGAGGCATTAAAGCAT
ATCAAAGGACAACACAAACTCAACAGGAGACATGCCAAATGAGTTGAACTCCTTGAGTATTTTCC
TTATGTCATACACTATAAGAAAGAAAAGGACCCACTAGTTATAAGAACTAGGAACCAGAAGTATC
AAGGTGAAAAGGGGTTGATGCCACAAGTATAAAATACTTGATAAGTCGATAAAAGTAACCAGGAC
CTAAAGAAGAGAATAATCTCACTTATATTGATCAAAAGGTCTGATTACAAATGATATA
Found at i:2210235 original size:13 final size:14
Alignment explanation
Indices: 2210215--2210252 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2210205 TAAATTACTG
2210215 AAAAATAAAGGGC-
1 AAAAATAAAGGGCA
*
2210228 AGAAATAAAAGGGCA
1 AAAAAT-AAAGGGCA
2210243 AAAAATAAAG
1 AAAAATAAAG
2210253 TAAATGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 5 0.24
14 11 0.52
15 5 0.24
ACGTcount: A:0.66, C:0.05, G:0.21, T:0.08
Consensus pattern (14 bp):
AAAAATAAAGGGCA
Found at i:2210280 original size:5 final size:5
Alignment explanation
Indices: 2210272--2210300 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2210262 TGTTAGGGAC
2210272 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
2210301 GGGTACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:2211826 original size:54 final size:54
Alignment explanation
Indices: 2211751--2212135 Score: 515
Period size: 54 Copynumber: 7.1 Consensus size: 54
2211741 GTTACCCATA
* *
2211751 TAGTGCCTAAACGGTTGTTCATCGACATATGATGAATTCTGTGAATTGCACACT
1 TAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGCACACT
* * * **
2211805 TAGT-CCTGAAATGTTTTTTCATCAACATATGATGAATTCCATGAATTGCACACT
1 TAGTGCC-GAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGCACACT
* * * *
2211859 TAGTGACGAACCGGTTGTTCATCAACCTATGATGAATTCCGTGAATTGCACACT
1 TAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGCACACT
* * * *
2211913 TAGTGCCAAAATGGTTGTTCATCAACATATGATGAATTTTGTGAACTGCACACT
1 TAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGCACACT
* *
2211967 TAGTGCCGAAAAGGTTGTTCATCAACATATGATGAATTTTGT-AAGTTGCACACT
1 TAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAA-TTGCACACT
* *
2212021 TAGTGCCTAAACGGTTGTTCATCAACATATGATGAATT-TCGTGAATTGGACACT
1 TAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCT-GTGAATTGCACACT
* * * *
2212075 TAGTGTCGAAACGGTTTTTCATCAACATATGATGAATTCCGTGAATTACACACT
1 TAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGCACACT
2212129 TAGTGCC
1 TAGTGCC
2212136 TATTTGGTAA
Statistics
Matches: 290, Mismatches: 35, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
53 5 0.02
54 282 0.97
55 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (54 bp):
TAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTGCACACT
Found at i:2211878 original size:108 final size:108
Alignment explanation
Indices: 2211689--2212137 Score: 546
Period size: 108 Copynumber: 4.2 Consensus size: 108
2211679 TTCGTTACGA
* * * ** * * * * *
2211689 TGCACACTTAGGGCCTATACGGTCATTCATAAACATATTATGAATTTCGT-AGGTTACCCA-TAT
1 TGCACACTTAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTTCGTGA-ATTGCACACT-T
* * * *
2211752 AGTGCCTAAACGGTTGTTCATCGACATATGATGAATTCTGTGAAT
64 AGTGACGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* * * *
2211797 TGCACACTTAGT-CCTGAAATGTTTTTTCATCAACATATGATGAATTCCATGAATTGCACACTTA
1 TGCACACTTAGTGCCT-AAATGGTTGTTCATCAACATATGATGAATTTCGTGAATTGCACACTTA
* *
2211861 GTGACGAACCGGTTGTTCATCAACCTATGATGAATTCCGTGAAT
65 GTGACGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* * *
2211905 TGCACACTTAGTGCCAAAATGGTTGTTCATCAACATATGATGAATTTTGTGAACTGCACACTTAG
1 TGCACACTTAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTTCGTGAATTGCACACTTAG
* * **
2211970 TGCCGAAAAGGTTGTTCATCAACATATGATGAATTTTGT-AAGT
66 TGACGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAA-T
* *
2212013 TGCACACTTAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTTCGTGAATTGGACACTTAG
1 TGCACACTTAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTTCGTGAATTGCACACTTAG
* *
2212078 TGTCGAAACGGTTTTTCATCAACATATGATGAATTCCGTGAAT
66 TGACGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
*
2212121 TACACACTTAGTGCCTA
1 TGCACACTTAGTGCCTA
2212138 TTTGGTAATC
Statistics
Matches: 292, Mismatches: 43, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
107 5 0.02
108 281 0.96
109 6 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (108 bp):
TGCACACTTAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTTCGTGAATTGCACACTTAG
TGACGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
Found at i:2213981 original size:13 final size:13
Alignment explanation
Indices: 2213960--2213992 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2213950 AAATACTCAT
*
2213960 ATTCTAACATATC
1 ATTCAAACATATC
2213973 ATTCAAACATATC
1 ATTCAAACATATC
2213986 ATTCAAA
1 ATTCAAA
2213993 AACCCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTCAAACATATC
Found at i:2229085 original size:8 final size:8
Alignment explanation
Indices: 2229068--2229098 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2229058 TGGATGGTGA
2229068 TTTCGCTT
1 TTTCGCTT
*
2229076 TTTCGTTT
1 TTTCGCTT
2229084 TTTCGCTT
1 TTTCGCTT
2229092 TTTCGCT
1 TTTCGCT
2229099 AATCACTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.13, T:0.65
Consensus pattern (8 bp):
TTTCGCTT
Found at i:2231421 original size:54 final size:54
Alignment explanation
Indices: 2231363--2231782 Score: 296
Period size: 54 Copynumber: 7.8 Consensus size: 54
2231353 TATACGGTCA
* * * * *
2231363 TTCATAAACATATTATGAATTTCGT-AGGTTACCCACATAGTGTCT-AAACGATTG
1 TTCATCAACATATGATGAATTTCGTGA-ATTACACACATAGTGT-TAAAACGATGG
* * *
2231417 TTCATCAACATATGATGAATTTCGTGAATTACACACTTAGTGTTAAAATGGTGG
1 TTCATCAACATATGATGAATTTCGTGAATTACACACATAGTGTTAAAACGATGG
* * * *** *
2231471 TTCATCAACATATGATGAATTTCTTGAATTGCACACTTAGTGCCGAAAC-AGTTG
1 TTCATCAACATATGATGAATTTCGTGAATTACACACATAGTGTTAAAACGA-TGG
* * * * * ** * **
2231525 TTCGTCAACATATGGTGAA-TTCTGTGAATTGCAGACTTAGTGTCGAAACGGTTT
1 TTCATCAACATATGATGAATTTC-GTGAATTACACACATAGTGTTAAAACGATGG
* * * * ** *
2231579 TTCATCAACATATGATGAATTCCATGAATTTCACACTTAGTGTCGAAAC-AGTTG
1 TTCATCAACATATGATGAATTTCGTGAATTACACACATAGTGTTAAAACGA-TGG
* * ** * **
2231633 TTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCAAAACGGTTA
1 TTCATCAACATATGATGAATTTCGTGAATTACACACATAGTGTTAAAACGATGG
* * *** *
2231687 TTCATCAACATATGATGAA-TTCTGTGAATTGCACACTTAGTGCCGAAAC-AGTTG
1 TTCATCAACATATGATGAATTTC-GTGAATTACACACATAGTGTTAAAACGA-TGG
* * *
2231741 TTCATAAACATATGATGAATTCCGTGAATTACACACTTAGTG
1 TTCATCAACATATGATGAATTTCGTGAATTACACACATAGTG
2231783 CCTATTTGGT
Statistics
Matches: 310, Mismatches: 45, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
53 6 0.02
54 299 0.96
55 5 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTTCGTGAATTACACACATAGTGTTAAAACGATGG
Found at i:2231533 original size:108 final size:108
Alignment explanation
Indices: 2231414--2231782 Score: 560
Period size: 108 Copynumber: 3.4 Consensus size: 108
2231404 GTCTAAACGA
* * * **
2231414 TTGTTCATCAACATATGATGAATTTCGTGAATTACACACTTAGTGTTAAAATGGTGGTTCATCAA
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGTCAAAACGGTTATTCATCAA
2231479 CATATGATGAATTTCTTGAATTGCACACTTAGTGCCGAAACAG
66 CATATGATGAATTTCTTGAATTGCACACTTAGTGCCGAAACAG
* * * * * * *
2231522 TTGTTCGTCAACATATGGTGAATTCTGTGAATTGCAGACTTAGTGTCGAAACGGTTTTTCATCAA
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGTCAAAACGGTTATTCATCAA
* * * *
2231587 CATATGATGAATTCCATGAATTTCACACTTAGTGTCGAAACAG
66 CATATGATGAATTTCTTGAATTGCACACTTAGTGCCGAAACAG
*
2231630 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCAAAACGGTTATTCATCAA
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGTCAAAACGGTTATTCATCAA
2231695 CATATGATGAA-TTCTGTGAATTGCACACTTAGTGCCGAAACAG
66 CATATGATGAATTTCT-TGAATTGCACACTTAGTGCCGAAACAG
*
2231738 TTGTTCATAAACATATGATGAATTCCGTGAATTACACACTTAGTG
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTG
2231783 CCTATTTGGT
Statistics
Matches: 232, Mismatches: 28, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
107 2 0.01
108 230 0.99
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (108 bp):
TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGTCAAAACGGTTATTCATCAA
CATATGATGAATTTCTTGAATTGCACACTTAGTGCCGAAACAG
Found at i:2231616 original size:162 final size:162
Alignment explanation
Indices: 2231400--2231782 Score: 559
Period size: 162 Copynumber: 2.4 Consensus size: 162
2231390 GTTACCCACA
* * * *
2231400 TAGTGTCTAAACGATTGTTCATCAACATATGATGAATTTCGTGAATTACACACTTAGTGTTAAAA
1 TAGTGTCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGTCAAAA
** * * * * * *
2231465 TGGTGGTTCATCAACATATGATGAATTTCTTGAATTGCACACTTAGTGCCGAAACAGTTGTTCGT
66 CAGTGGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCAAAACAGTTATTCAT
* *
2231530 CAACATATGGTGAATTCTGTGAATTGCAGACT
131 CAACATATGATGAATTCTGTGAATTGCACACT
* * * *
2231562 TAGTGTCGAAACGGTTTTTCATCAACATATGATGAATTCCATGAATTTCACACTTAGTGTCGAAA
1 TAGTGTCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGTCAAAA
* *
2231627 CAGTTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCAAAACGGTTATTCAT
66 CAGTGGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCAAAACAGTTATTCAT
2231692 CAACATATGATGAATTCTGTGAATTGCACACT
131 CAACATATGATGAATTCTGTGAATTGCACACT
* * *
2231724 TAGTGCCGAAACAGTTGTTCATAAACATATGATGAATTCCGTGAATTACACACTTAGTG
1 TAGTGTCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTG
2231783 CCTATTTGGT
Statistics
Matches: 195, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
162 195 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (162 bp):
TAGTGTCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGTCAAAA
CAGTGGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCAAAACAGTTATTCAT
CAACATATGATGAATTCTGTGAATTGCACACT
Found at i:2231783 original size:54 final size:54
Alignment explanation
Indices: 2231414--2231784 Score: 499
Period size: 54 Copynumber: 6.9 Consensus size: 54
2231404 GTCTAAACGA
* *** **
2231414 TTGTTCATCAACATATGATGAATTTCGTGAATTACACACTTAGTGTTAAAATGG
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCGAAACAG
* * * *
2231468 TGGTTCATCAACATATGATGAATTTCTTGAATTGCACACTTAGTGCCGAAACAG
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCGAAACAG
* * * * * * *
2231522 TTGTTCGTCAACATATGGTGAATTCTGTGAATTGCAGACTTAGTGTCGAAACGG
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCGAAACAG
* * * *
2231576 TTTTTCATCAACATATGATGAATTCCATGAATTTCACACTTAGTGTCGAAACAG
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCGAAACAG
* *
2231630 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCAAAACGG
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCGAAACAG
* * *
2231684 TTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAG
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCGAAACAG
*
2231738 TTGTTCATAAACATATGATGAATTCCGTGAATTACACACTTAGTGCC
1 TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCC
2231785 TATTTGGTAA
Statistics
Matches: 277, Mismatches: 40, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 277 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (54 bp):
TTGTTCATCAACATATGATGAATTCCGTGAATTACACACTTAGTGCCGAAACAG
Found at i:2233816 original size:15 final size:14
Alignment explanation
Indices: 2233794--2233833 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
2233784 TTATATTTTT
*
2233794 AAATAATAATAGTA
1 AAATAATAATAATA
2233808 AATATAATAATAATA
1 AA-ATAATAATAATA
*
2233823 AAATGATAATA
1 AAATAATAATA
2233834 TTTAATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:2233967 original size:3 final size:3
Alignment explanation
Indices: 2233950--2234118 Score: 77
Period size: 3 Copynumber: 58.0 Consensus size: 3
2233940 TGACAATATT
* * * * *
2233950 TAA T-A TAA CAA TAA TAA TAA GT-A TAA TAA CAA TAC CAA -CA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
2233993 T-A TAA TAA TAA TAG TAA TAG TAG T-A TAG TAA TAA TAA TACT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * * * *
2234037 TAA CAT TAA TAG TAA TAA TAA T-A TAA TAA TAC TAG T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
2234083 TGC TAA T-A TAA T-A TCAA TAA TAA TAG TAA GTAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA -TAA TAA
2234119 CATTATTTAA
Statistics
Matches: 121, Mismatches: 32, Indels: 26
0.68 0.18 0.15
Matches are distributed among these distances:
2 14 0.12
3 99 0.82
4 8 0.07
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2234047 original size:36 final size:36
Alignment explanation
Indices: 2233998--2234069 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
2233988 CATAATATAA
* * *
2233998 TAATAATAGTAATAGTAGT-ATAGTAATAATAATACT
1 TAATAACAGTAATAGTAATAATAAT-ATAATAATACT
*
2234034 TAATAACATTAATAGTAATAATAATATAATAATACT
1 TAATAACAGTAATAGTAATAATAATATAATAATACT
2234070 AGTATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (36 bp):
TAATAACAGTAATAGTAATAATAATATAATAATACT
Found at i:2234055 original size:28 final size:26
Alignment explanation
Indices: 2233986--2234083 Score: 87
Period size: 26 Copynumber: 3.8 Consensus size: 26
2233976 TAACAATACC
2233986 AACA-TAATA-TAATAATAATAGTAAT
1 AACACTAATAGTAATAATAATA-TAAT
** *
2234011 AGTAGT-ATAGTAATAATAATACTTAAT
1 AACACTAATAGTAATAATAATA--TAAT
*
2234038 AACATTAATAGTAATAATAATATAAT
1 AACACTAATAGTAATAATAATATAAT
* *
2234064 AATACTAGTA-TAATAATAAT
1 AACACTAATAGTAATAATAAT
2234084 GCTAATATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
25 15 0.25
26 23 0.38
27 7 0.12
28 15 0.25
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (26 bp):
AACACTAATAGTAATAATAATATAAT
Found at i:2237176 original size:40 final size:40
Alignment explanation
Indices: 2237132--2237221 Score: 162
Period size: 40 Copynumber: 2.2 Consensus size: 40
2237122 ATGCTTATTT
2237132 GGTGCTGCTGTGGGAGATGAGTTAGAGAGGGGGACCACTC
1 GGTGCTGCTGTGGGAGATGAGTTAGAGAGGGGGACCACTC
*
2237172 GGTGCTGCTGTGGGAGATGAGTTAGAGGGGGGGACCACTC
1 GGTGCTGCTGTGGGAGATGAGTTAGAGAGGGGGACCACTC
*
2237212 GGTGCAGCTG
1 GGTGCTGCTG
2237222 ATGCGTGGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.18, C:0.16, G:0.47, T:0.20
Consensus pattern (40 bp):
GGTGCTGCTGTGGGAGATGAGTTAGAGAGGGGGACCACTC
Found at i:2238026 original size:9 final size:9
Alignment explanation
Indices: 2238014--2238073 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
2238004 TTTTCTCTCT
2238014 TTTTTTTCA
1 TTTTTTTCA
*
2238023 TTTTCATTCA
1 TTTT-TTTCA
*
2238033 TTTTTCTC-
1 TTTTTTTCA
*
2238041 TCTTTTTC-
1 TTTTTTTCA
2238049 -TTTTTTCA
1 TTTTTTTCA
2238057 TTTTTTTCA
1 TTTTTTTCA
2238066 TTTCTTTT
1 TTT-TTTT
2238074 TCATATCAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.15
8 6 0.15
9 17 0.41
10 12 0.29
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:2238054 original size:28 final size:27
Alignment explanation
Indices: 2237993--2238075 Score: 98
Period size: 30 Copynumber: 3.0 Consensus size: 27
2237983 TGTAATTTAT
*
2237993 TTATTTTC-TTTTTTTCTCTCTTTTTT
1 TTATTTTCATTTTTTTCTCTCTTTTTC
2238019 TTCATTTTCATTCATTTTTCTCTCTTTTTC
1 TT-ATTTTCATT--TTTTTCTCTCTTTTTC
*
2238049 TT-TTTTCATTTTTTTCATTTCTTTTTC
1 TTATTTTCATTTTTTTC-TCTCTTTTTC
2238076 ATATCAACTA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
26 8 0.16
27 15 0.30
28 10 0.20
30 17 0.34
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (27 bp):
TTATTTTCATTTTTTTCTCTCTTTTTC
Found at i:2238707 original size:118 final size:118
Alignment explanation
Indices: 2238504--2238730 Score: 339
Period size: 118 Copynumber: 1.9 Consensus size: 118
2238494 AGCAAAAGAG
* * * *
2238504 TGAACAAGTTATTCTCATTATGAACTTATTCTCTCTCTTATGATGAGTTCTTCTCATTATGAACT
1 TGAACAAGTTATTCTCATTAAGAACTTATTCTCCCTCTTAGGATAAGTTCTTCTCATTATGAACT
* * *
2238569 ATTCATTAGAAATGTCGATCCTCCTCCTTCTGTGATGGATTTGAGCTGAATGT
66 ATTCATTAGAAATGTCGATCCACCTCCTTCAGCGATGGATTTGAGCTGAATGT
*
2238622 TGAACAAGTTCTTCTCATTAAGAACTTATTCTCCCTCTTAGGATAAGTTCTTCTCATTATGAACT
1 TGAACAAGTTATTCTCATTAAGAACTTATTCTCCCTCTTAGGATAAGTTCTTCTCATTATGAACT
* * *
2238687 CTTCATTAGAAATGAT-GATCCACCTCTTTCAGCGATGTATTTGA
66 ATTCATTAGAAATG-TCGATCCACCTCCTTCAGCGATGGATTTGA
2238731 ATCTTTAAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
118 96 0.99
119 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (118 bp):
TGAACAAGTTATTCTCATTAAGAACTTATTCTCCCTCTTAGGATAAGTTCTTCTCATTATGAACT
ATTCATTAGAAATGTCGATCCACCTCCTTCAGCGATGGATTTGAGCTGAATGT
Found at i:2239132 original size:29 final size:28
Alignment explanation
Indices: 2239083--2239138 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
2239073 CAAGTGAGAC
* * *
2239083 AAAATTTTGTTTCGAGTGAAACGATCTT
1 AAAATTTTGTTTCAAGGGAAACAATCTT
2239111 AAAATTTATGTTTCAAGGGAAACAATCT
1 AAAATTT-TGTTTCAAGGGAAACAATCT
2239139 CAAGTGAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (28 bp):
AAAATTTTGTTTCAAGGGAAACAATCTT
Found at i:2243267 original size:14 final size:16
Alignment explanation
Indices: 2243233--2243275 Score: 63
Period size: 14 Copynumber: 2.8 Consensus size: 16
2243223 TTTAATATAC
2243233 ATTTAATATTTTTAGTA
1 ATTTAAT-TTTTTAGTA
2243250 ATTTAATTTTTTA-T-
1 ATTTAATTTTTTAGTA
2243264 ATTTAATTTTTT
1 ATTTAATTTTTT
2243276 TTGAATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.46
15 1 0.04
16 6 0.23
17 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
ATTTAATTTTTTAGTA
Found at i:2243736 original size:38 final size:37
Alignment explanation
Indices: 2243692--2243982 Score: 241
Period size: 38 Copynumber: 7.8 Consensus size: 37
2243682 TATATATAAC
* *
2243692 ATATATAGTATATAGTTTTGAAACATTTTCTCGAAAAT
1 ATATATAATATATAGTTTTGAAACATTTT-TTGAAAAT
2243730 ATATATAATATATAGTTTTGAAACATTTTTTG-AAA-
1 ATATATAATATATAGTTTTGAAACATTTTTTGAAAAT
2243765 ATATATAATATATAGTTTTGAAAACATTTTTTTTGAAAAT
1 ATATATAATATATAGTTTTG-AAACA--TTTTTTGAAAAT
*
2243805 ATATATAATATATAGTTTTG-----------GAAAAC
1 ATATATAATATATAGTTTTGAAACATTTTTTGAAAAT
* *
2243831 ATATATAATATATAGTTTTGGAAAATATTTTTTAAAAAT
1 ATATATAATATATAGTTTT-G-AAACATTTTTTGAAAAT
* *
2243870 GTATATAATATATAGTCTTAGAAACA-TTTTTGAAAAT
1 ATATATAATATATAGT-TTTGAAACATTTTTTGAAAAT
* * * *
2243907 ACATACAATATATATAGTTTTAAAAACTTTTTTTTTTGAAAAT
1 ATATA-TA-ATATATAGTTTT-GAAAC---ATTTTTTGAAAAT
*
2243950 ATATATAATATATAATTTTGAAAACATTGTTTT
1 ATATATAATATATAGTTTTG-AAACATT-TTTT
2243983 TTAAAACATT
Statistics
Matches: 205, Mismatches: 20, Indels: 55
0.73 0.07 0.20
Matches are distributed among these distances:
26 24 0.12
27 1 0.00
35 20 0.10
36 8 0.04
37 15 0.07
38 44 0.21
39 40 0.20
40 22 0.11
41 15 0.07
42 1 0.00
43 15 0.07
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAACATTTTTTGAAAAT
Found at i:2243748 original size:73 final size:75
Alignment explanation
Indices: 2243684--2243977 Score: 240
Period size: 75 Copynumber: 4.0 Consensus size: 75
2243674 TTATTCAATA
* *
2243684 TATAT-AACATATATAGTATATAGTTTTG-AAACA-TTTTCTCGAAAATATATATAATATATAGT
1 TATATGAAAATATATAATATATAGTTTTGAAAACATTTTTCTCGAAAATATATATAATATATAGT
2243746 TTTGAAACAT
66 TTTGAAACAT
* * * *
2243756 TTTTTGAAAATATATAATATATAGTTTTGAAAACATTTTTTTTGAAAATATATATAATATATAGT
1 TATATGAAAATATATAATATATAGTTTTGAAAACATTTTTCTCGAAAATATATATAATATATAGT
2243821 TTTG------
66 TTTGAAACAT
* * * * *
2243825 GA-A--AACATATATAATATATAGTTTTGGAAAATATTTTT-T-AAAAATGTATATAATATATAG
1 TATATGAAAATATATAATATATAGTTTT-GAAAACATTTTTCTCGAAAATATATATAATATATAG
*
2243885 TCTTAGAAACAT
65 T-TTTGAAACAT
* * * * * *
2243897 T-TTTGAAAATACATACAATATATATAGTTTTAAAAACTTTTTTTTTTGAAAATATATATAATAT
1 TATATGAAAAT--ATA-TA-ATATATAGTTTTGAAAAC-ATTTTTCTCGAAAATATATATAATAT
*
2243961 ATAATTTTGAAAACAT
61 ATAGTTTTG-AAACAT
2243977 T
1 T
2243978 GTTTTTTAAA
Statistics
Matches: 175, Mismatches: 25, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
65 20 0.11
66 25 0.14
67 11 0.06
72 3 0.02
73 21 0.12
74 9 0.05
75 31 0.18
76 3 0.02
77 5 0.03
78 17 0.10
79 4 0.02
80 26 0.15
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (75 bp):
TATATGAAAATATATAATATATAGTTTTGAAAACATTTTTCTCGAAAATATATATAATATATAGT
TTTGAAACAT
Found at i:2243829 original size:26 final size:26
Alignment explanation
Indices: 2243794--2243858 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
2243784 GAAAACATTT
*
2243794 TTTTTGAAAATATATATAATATATAG
1 TTTTGGAAAATATATATAATATATAG
*
2243820 TTTTGGAAAACATATATAATATATAG
1 TTTTGGAAAATATATATAATATATAG
2243846 TTTTGGAAAATAT
1 TTTTGGAAAATAT
2243859 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (26 bp):
TTTTGGAAAATATATATAATATATAG
Found at i:2243960 original size:43 final size:41
Alignment explanation
Indices: 2243896--2243988 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 41
2243886 CTTAGAAACA
* *
2243896 TTTTTGAAAATACATACAATATATATAGTTTTAAAAACTTTTT
1 TTTTTGAAAATACATACAATATATA-A-TTTTAAAAACATTGT
* * *
2243939 TTTTTGAAAATATATATAATATATAATTTTGAAAACATTGT
1 TTTTTGAAAATACATACAATATATAATTTTAAAAACATTGT
2243980 TTTTT-AAAA
1 TTTTTGAAAA
2243989 CATTTTTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 4 0.09
41 17 0.38
42 1 0.02
43 23 0.51
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.47
Consensus pattern (41 bp):
TTTTTGAAAATACATACAATATATAATTTTAAAAACATTGT
Found at i:2244006 original size:52 final size:53
Alignment explanation
Indices: 2243939--2244044 Score: 142
Period size: 52 Copynumber: 2.0 Consensus size: 53
2243929 AAAACTTTTT
* * ** *
2243939 TTTTTGAAAATATATATAATATATA-ATTTTGAAAACATTGTTTTTTAAAACA
1 TTTTTGAAAACATATATAATATATAGATTTTGAAAAAATAATTTTTAAAAACA
* *
2243991 TTTTTGAAAGCATATATAATATATAGATTTTTAAAAAATAATTTTTAAAAACA
1 TTTTTGAAAACATATATAATATATAGATTTTGAAAAAATAATTTTTAAAAACA
2244044 T
1 T
2244045 ATAATATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 23 0.50
53 23 0.50
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (53 bp):
TTTTTGAAAACATATATAATATATAGATTTTGAAAAAATAATTTTTAAAAACA
Found at i:2244012 original size:95 final size:91
Alignment explanation
Indices: 2243891--2244065 Score: 224
Period size: 95 Copynumber: 1.9 Consensus size: 91
2243881 ATAGTCTTAG
* * * ** *
2243891 AAACATTTTTGAAAATACATACAATATATATAGTTTTAAAAACTTTTTTTTTTGAAAATATATAT
1 AAACATTTTTGAAAACACATACAATATATAGAGTTTTAAAAA--ATAATTTTT-AAAA-ACATAT
2243956 AATATATAATTTTGAAAACATTGTTTTTTA
62 AATATATAATTTTGAAAACATTGTTTTTTA
* * * *
2243986 AAACATTTTTGAAAGCATATATAATATATAGATTTTTAAAAAATAATTTTTAAAAACATATAATA
1 AAACATTTTTGAAAACACATACAATATATAGAGTTTTAAAAAATAATTTTTAAAAACATATAATA
2244051 TATAATTTTGAAAAC
66 TATAATTTTGAAAAC
2244066 GTTTTTGAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
91 24 0.34
92 4 0.06
93 6 0.09
95 36 0.51
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (91 bp):
AAACATTTTTGAAAACACATACAATATATAGAGTTTTAAAAAATAATTTTTAAAAACATATAATA
TATAATTTTGAAAACATTGTTTTTTA
Found at i:2244099 original size:23 final size:26
Alignment explanation
Indices: 2244066--2244120 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
2244056 TTTTGAAAAC
2244066 GTTTTTGAAAACAAATA-TA-ATATA
1 GTTTTTGAAAACAAATAGTATATATA
* *
2244090 GTTTTT-AAAACATATAGTATATATT
1 GTTTTTGAAAACAAATAGTATATATA
2244115 GTTTTT
1 GTTTTT
2244121 CTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 9 0.33
24 8 0.30
25 10 0.37
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (26 bp):
GTTTTTGAAAACAAATAGTATATATA
Found at i:2252402 original size:22 final size:22
Alignment explanation
Indices: 2252334--2252402 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
2252324 CCTACTTCAG
*
2252334 TTCATTCCCTTTTTGAATTTAATT
1 TTCATTTCC-TTTTGAATTTAA-T
** * * *
2252358 TTC-TTTTATTTTGTACTTCAT
1 TTCATTTCCTTTTGAATTTAAT
2252379 TTCATTTCCTTTTGAATTTAAT
1 TTCATTTCCTTTTGAATTTAAT
2252401 TT
1 TT
2252403 TTTTTTCATT
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
21 4 0.12
22 24 0.73
23 2 0.06
24 3 0.09
ACGTcount: A:0.19, C:0.14, G:0.04, T:0.62
Consensus pattern (22 bp):
TTCATTTCCTTTTGAATTTAAT
Found at i:2254567 original size:21 final size:22
Alignment explanation
Indices: 2254541--2254581 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2254531 AATGTTGAAG
2254541 AATTCAAGA-TCAAGAATCAGA
1 AATTCAAGATTCAAGAATCAGA
*
2254562 AATTCAAGATTCCAGAATCA
1 AATTCAAGATTCAAGAATCA
2254582 AGAGTCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (22 bp):
AATTCAAGATTCAAGAATCAGA
Found at i:2255532 original size:39 final size:38
Alignment explanation
Indices: 2255484--2255779 Score: 310
Period size: 39 Copynumber: 7.8 Consensus size: 38
2255474 TATATATAAC
2255484 ATATATAATATATAGTTTTGAAACATTTTTTTCGAAAAT
1 ATATATAATATATAGTTTTGAAACATTTTTTT-GAAAAT
***
2255523 ATATATAATATATAGTTTTTGAAACATTTTTGAAAAAAT
1 ATATATAATATATAG-TTTTGAAACATTTTTTTGAAAAT
*
2255562 ATATATAATATATAGTTTTGAAAACA-TTTTTTGAAAAC
1 ATATATAATATATAGTTTTG-AAACATTTTTTTGAAAAT
* *
2255600 ATATATAATATAGAGTTTTGGAAA-ATATTTTTTGAAAAC
1 ATATATAATATATAGTTTT-GAAACAT-TTTTTTGAAAAT
* *
2255639 GTATATAATATATAGTTTTGGAA-ATATTTTTTG---A-
1 ATATATAATATATAGTTTTGAAACAT-TTTTTTGAAAAT
* *
2255673 A-A-AT-ATATATAGTTTTGGAAACA--ATTTCGAAAAT
1 ATATATAATATATAGTTTT-GAAACATTTTTTTGAAAAT
* *
2255707 ATATACAATATATAGTTTTGAAAACATTTTTTTTAAAAT
1 ATATATAATATATAGTTTTG-AAACATTTTTTTGAAAAT
2255746 ATATATAATATATAGTTTTGAAAACATTGTTTTT
1 ATATATAATATATAGTTTTG-AAACATT-TTTTT
2255780 TTAAAACATT
Statistics
Matches: 219, Mismatches: 20, Indels: 35
0.80 0.07 0.13
Matches are distributed among these distances:
30 4 0.02
31 12 0.05
32 5 0.02
33 3 0.01
34 1 0.00
35 2 0.01
36 2 0.01
37 18 0.08
38 47 0.21
39 105 0.48
40 20 0.09
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (38 bp):
ATATATAATATATAGTTTTGAAACATTTTTTTGAAAAT
Found at i:2255595 original size:13 final size:13
Alignment explanation
Indices: 2255577--2255601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2255567 TAATATATAG
2255577 TTTTGAAAACATT
1 TTTTGAAAACATT
2255590 TTTTGAAAACAT
1 TTTTGAAAACAT
2255602 ATATAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACATT
Found at i:2255707 original size:30 final size:31
Alignment explanation
Indices: 2255646--2255711 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2255636 AACGTATATA
* * *
2255646 ATATATAGTTTTGGAAATATTTTTTGAAAAT
1 ATATATAGTTTTGGAAACATATTTCGAAAAT
2255677 ATATATAGTTTTGGAAACA-ATTTCGAAAAT
1 ATATATAGTTTTGGAAACATATTTCGAAAAT
2255707 ATATA
1 ATATA
2255712 CAATATATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (31 bp):
ATATATAGTTTTGGAAACATATTTCGAAAAT
Found at i:2255724 original size:107 final size:108
Alignment explanation
Indices: 2255569--2255765 Score: 281
Period size: 107 Copynumber: 1.8 Consensus size: 108
2255559 AATATATATA
* * * *
2255569 ATATATAGTTTTGAAAACATTTTTTGAAAACATATATAATATAGAGTTTTGGAAA-ATATTTTTT
1 ATATATAGTTTTGAAAACATATTTCGAAAACATATACAATATAGAGTTTTGAAAACAT-TTTTTT
*
2255633 GAAAACGTATATAATATATAGTTTTGGAAATATTTTTTGAAAAT
65 GAAAACATATATAATATATAGTTTTGGAAATATTTTTTGAAAAT
* * * *
2255677 ATATATAGTTTTGGAAACA-ATTTCGAAAATATATACAATATATAGTTTTGAAAACATTTTTTTT
1 ATATATAGTTTTGAAAACATATTTCGAAAACATATACAATATAGAGTTTTGAAAACATTTTTTTG
*
2255741 AAAATATATATAATATATAGTTTTG
66 AAAACATATATAATATATAGTTTTG
2255766 AAAACATTGT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
107 58 0.74
108 20 0.26
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (108 bp):
ATATATAGTTTTGAAAACATATTTCGAAAACATATACAATATAGAGTTTTGAAAACATTTTTTTG
AAAACATATATAATATATAGTTTTGGAAATATTTTTTGAAAAT
Found at i:2259081 original size:31 final size:31
Alignment explanation
Indices: 2259046--2259104 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2259036 TAAGTTAACC
*
2259046 TTAAAATTTAAATAAAATATTAATTTAATCA
1 TTAAAATTTAAATAAAATATCAATTTAATCA
* *
2259077 TTAAACTTTATATAAAATATCAATTTAA
1 TTAAAATTTAAATAAAATATCAATTTAA
2259105 CCCCTGACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (31 bp):
TTAAAATTTAAATAAAATATCAATTTAATCA
Found at i:2261239 original size:46 final size:45
Alignment explanation
Indices: 2261186--2261286 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
2261176 TACCATGTAC
* * *
2261186 CGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGAAT
1 CGATGCACTCAGGATATTT-TG-AAACATCGAAAGCACTTGATGAAT
* * *
2261232 CGATGCACTCTGGCTATTTTGAAACATCGAAAGCACTTGATGCAT
1 CGATGCACTCAGGATATTTTGAAACATCGAAAGCACTTGATGAAT
2261277 CGATGCACTC
1 CGATGCACTC
2261287 TTAGTGCACC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 31 0.65
46 14 0.29
47 3 0.06
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (45 bp):
CGATGCACTCAGGATATTTTGAAACATCGAAAGCACTTGATGAAT
Found at i:2266132 original size:45 final size:45
Alignment explanation
Indices: 2266077--2266183 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
2266067 GCACCAATCC
* *
2266077 ATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCATTTG
1 ATGCATCGATGCACTC-TG-ACTAAATTGAAACATCGAATGCACTTG
* **
2266122 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCTGACTAAATTGAAACATCGAATGCACTTG
2266167 ATGCATCGATGCACTCT
1 ATGCATCGATGCACTCT
2266184 TAGTGCACCG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 5 0.09
45 49 0.89
46 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCTGACTAAATTGAAACATCGAATGCACTTG
Found at i:2271316 original size:65 final size:65
Alignment explanation
Indices: 2271163--2271372 Score: 191
Period size: 65 Copynumber: 3.2 Consensus size: 65
2271153 TTTTTCAGAG
* * * *
2271163 TGATGCACCGATGCACCA-ATCCATGCATCGATGCAC-CATGA-ATTAAATT-GAACATCGAATG
1 TGATGCATCGATGCACCATA-CCATGCACCGATGCACTCAGGATATT---TTAAAACATCGAATG
2271224 CATT
62 CATT
* *
2271228 TGATGTATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATAAAAACATCGAATGCA
1 TGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATATTT-T-AAAACATCGAATGCA
2271291 TT
64 TT
* ** * * * * *
2271293 TGATGCATCGATGCACCA-GCCATGCATTGATGCACTCTGGCTATTTTGAAACATCGAATGTACT
1 TGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATATTTTAAAACATCGAATGCATT
2271357 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
2271373 TCTTAGAGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 47 0.39
65 67 0.55
66 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATATTTTAAAACATCGAATGCATT
Found at i:2284246 original size:2 final size:2
Alignment explanation
Indices: 2284234--2284268 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2284224 AATTGATTAA
* *
2284234 AT AT CT AT AT AT AT CT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2284269 GCTTAAGCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2284249 original size:10 final size:10
Alignment explanation
Indices: 2284234--2284267 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2284224 AATTGATTAA
2284234 ATATCTATAT
1 ATATCTATAT
2284244 ATATCTATAT
1 ATATCTATAT
*
2284254 ATATATATAT
1 ATATCTATAT
2284264 ATAT
1 ATAT
2284268 AGCTTAAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATCTATAT
Found at i:2284834 original size:21 final size:21
Alignment explanation
Indices: 2284810--2284853 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2284800 GAGCTGGAGG
* *
2284810 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
2284831 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
2284852 AG
1 AG
2284854 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:2285964 original size:2 final size:2
Alignment explanation
Indices: 2285957--2285986 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2285947 TTTCGAAATC
2285957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2285987 TAAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2291759 original size:64 final size:62
Alignment explanation
Indices: 2291690--2291868 Score: 148
Period size: 64 Copynumber: 2.8 Consensus size: 62
2291680 TTGGACCCTT
*
2291690 AGTGCATCGGTGCA-CTAAGAGCGCATCGATGCATCAAGTGCTTTCGATG-TTTCA-AAATAGCC
1 AGTGCATCGGTGCAGCT--G-GCGCATCGATGCATCAA-TGCATTCGATGTTTTCATAAA-AGCC
*
2291752 AG
61 AC
* * * *
2291754 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGGTGCA--GCTGGCGCATCGATGCATCAATGCATTCGATGTTTTCATAAAAGCCAC
* * * * *
2291818 AGTGCATCGGTGCATCGTATGTGCATCGATGCATGAAATACATTCGATGTT
1 AGTGCATCGGTGCAGC-T-GGCGCATCGATGCAT-CAATGCATTCGATGTT
2291869 CAATTTAATT
Statistics
Matches: 96, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 11 0.11
64 64 0.67
65 18 0.19
67 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (62 bp):
AGTGCATCGGTGCAGCTGGCGCATCGATGCATCAATGCATTCGATGTTTTCATAAAAGCCAC
Found at i:2297503 original size:29 final size:29
Alignment explanation
Indices: 2297461--2297516 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2297451 CAACCTCCAT
2297461 TGGACAACAAGTATCACCTAACTCATCTA
1 TGGACAACAAGTATCACCTAACTCATCTA
* *
2297490 TGGACAGCAAGTATCACCTTACTCATC
1 TGGACAACAAGTATCACCTAACTCATC
2297517 ACACATTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.25
Consensus pattern (29 bp):
TGGACAACAAGTATCACCTAACTCATCTA
Found at i:2300924 original size:2 final size:2
Alignment explanation
Indices: 2300917--2300941 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2300907 TCACGAAGGC
2300917 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2300942 ATTATTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2303227 original size:346 final size:346
Alignment explanation
Indices: 2302583--2303274 Score: 1251
Period size: 346 Copynumber: 2.0 Consensus size: 346
2302573 ATCAGTATTA
*
2302583 TGAAATAAAACATATTTTCAGACTCGTATATATAATAAAATACAACCTACATGCCCCCTAATTAC
1 TGAAATAAAACATATTTTCAGACTCGTATATATAATAAAATACAACCTACATGCCCCCTAATCAC
* *
2302648 ATGCACCGTACTCCGCAAGCAATACCGGTGGAACTCCCTTACTGAAGTAGATAGTTGTACTAGTA
66 ATGCAACGTACTCCGCAAGCAATACCGGTGGAACTCCCTTACTGAAGTAGATAGTTGCACTAGTA
*
2302713 CTATTCTTTTAACCTGAAATGGTGAGTAACAGAGTGAGCTTTGGAAAGCTCAGTAATACAATACT
131 CGATTCTTTTAACCTGAAATGGTGAGTAACAGAGTGAGCTTTGGAAAGCTCAGTAATACAATACT
2302778 ACCAACTGATGCTACAGGACATGTAGATAAATGTAGAACAATAAAATTTCCTTATTGAATCAAAC
196 ACCAACTGATGCTACAGGACATGTAGATAAATGTAGAACAATAAAATTTCCTTATTGAATCAAAC
* *
2302843 GTATACATATTTTTGGAATAAGTTGGGGTTCCACTGGTAGTTCATCGAGTAGAA-TCCATGAAGA
261 GTATACAGATTTTTGGAATAAGTTAGGGTTCCACTGGTAGTTCATCGAGTAGAAGT-CATGAAGA
2302907 TCTCAGTTTATAGGGAACATTC
325 TCTCAGTTTATAGGGAACATTC
* *
2302929 TGAAATAAAACATATTTTTAGACTCTTATATATAATAAAATACAACCTACATGCCCCCTAATCAC
1 TGAAATAAAACATATTTTCAGACTCGTATATATAATAAAATACAACCTACATGCCCCCTAATCAC
2302994 ATGCAACGTACTCCGCAAGCAATACCGGTGGAACTCCCTTACTGAAGTAGATAGTTGCACTAGTA
66 ATGCAACGTACTCCGCAAGCAATACCGGTGGAACTCCCTTACTGAAGTAGATAGTTGCACTAGTA
2303059 CGATTCTTTTAACCTGAAATGGTGAGTAACAGAGTGAGCTTTGGAAAGCTCAGTAATACAATACT
131 CGATTCTTTTAACCTGAAATGGTGAGTAACAGAGTGAGCTTTGGAAAGCTCAGTAATACAATACT
* *
2303124 ACCAGCTGATGCTACAGGACATGTAGATAAATGTAGAATAATAAAATTTCCTTATTGAATCAAAC
196 ACCAACTGATGCTACAGGACATGTAGATAAATGTAGAACAATAAAATTTCCTTATTGAATCAAAC
* * *
2303189 GTATATAGGTTTTTGGAATAAGTTAGGGTTCTACTGGTAGTTCATCGAGTAGAAGTCATGAAGAT
261 GTATACAGATTTTTGGAATAAGTTAGGGTTCCACTGGTAGTTCATCGAGTAGAAGTCATGAAGAT
2303254 CTCAGTTTATAGGGAACATTC
326 CTCAGTTTATAGGGAACATTC
2303275 ATAGTATCAA
Statistics
Matches: 332, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
346 331 1.00
347 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (346 bp):
TGAAATAAAACATATTTTCAGACTCGTATATATAATAAAATACAACCTACATGCCCCCTAATCAC
ATGCAACGTACTCCGCAAGCAATACCGGTGGAACTCCCTTACTGAAGTAGATAGTTGCACTAGTA
CGATTCTTTTAACCTGAAATGGTGAGTAACAGAGTGAGCTTTGGAAAGCTCAGTAATACAATACT
ACCAACTGATGCTACAGGACATGTAGATAAATGTAGAACAATAAAATTTCCTTATTGAATCAAAC
GTATACAGATTTTTGGAATAAGTTAGGGTTCCACTGGTAGTTCATCGAGTAGAAGTCATGAAGAT
CTCAGTTTATAGGGAACATTC
Found at i:2305725 original size:2 final size:2
Alignment explanation
Indices: 2305718--2305788 Score: 119
Period size: 2 Copynumber: 36.0 Consensus size: 2
2305708 ATATGTACCC
2305718 AT AT AT AT A- AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2305760 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2305789 TTGTTGCATT
Statistics
Matches: 66, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.03
2 63 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2309868 original size:21 final size:21
Alignment explanation
Indices: 2309827--2309880 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2309817 ATTCTGACTA
2309827 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
2309848 TCGCGTTGCGATTTTCTAAAT
1 TCGCATTGCGATTTCCCAAAT
*
2309869 T-GCAATGCGATT
1 TCGCATTGCGATT
2309881 ACGTAAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2309983 original size:79 final size:79
Alignment explanation
Indices: 2309874--2310133 Score: 380
Period size: 79 Copynumber: 3.3 Consensus size: 79
2309864 TAAATTGCAA
2309874 TGCGA-TTACGTAAAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGC
1 TGCGATTTACGT--AATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGC
2309938 GAATACGTAATCGCAT
64 GAATACGTAATCGCAT
2309954 TGCGATTTACGTAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGA
1 TGCGATTTACGTAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGA
2310019 ATACGTAATCGCAT
66 ATACGTAATCGCAT
* * * * * *
2310033 TGCGATTTACGTAATCGCATTGCGATTTACGT-AATCGCATTGCGATTTTCCTAATTCGCATTGC
1 TGCGATTTACGTAATCGCAATGCGA-TTACGTAAATCGCAATGCGA-TTACGTAAATCGCAATGC
* * *
2310097 TATTTACGTAATCGTAT
64 GA-ATACGTAATCGCAT
2310114 TGCGATTTACGTAATCGCAA
1 TGCGATTTACGTAATCGCAA
2310134 CGAGATTCTG
Statistics
Matches: 166, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
79 103 0.62
80 26 0.16
81 37 0.22
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (79 bp):
TGCGATTTACGTAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGA
ATACGTAATCGCAT
Found at i:2310140 original size:20 final size:20
Alignment explanation
Indices: 2309870--2310133 Score: 308
Period size: 20 Copynumber: 13.2 Consensus size: 20
2309860 TTTCTAAATT
2309870 GCAATGCGA-TTACGTAAAATC
1 GCAATGCGATTTACGT--AATC
2309891 GCAATGCGA-TTACGTAAATC
1 GCAATGCGATTTACGT-AATC
2309911 GCAATGCGA-TTACGTAAATC
1 GCAATGCGATTTACGT-AATC
*
2309931 GCAATGCGA-ATACGTAATC
1 GCAATGCGATTTACGTAATC
*
2309950 GCATTGCGATTTACGTAATC
1 GCAATGCGATTTACGTAATC
2309970 GCAATGCGA-TTACGTAAATC
1 GCAATGCGATTTACGT-AATC
2309990 GCAATGCGA-TTACGTAAATC
1 GCAATGCGATTTACGT-AATC
*
2310010 GCAATGCGA-ATACGTAATC
1 GCAATGCGATTTACGTAATC
*
2310029 GCATTGCGATTTACGTAATC
1 GCAATGCGATTTACGTAATC
*
2310049 GCATTGCGATTTACGTAATC
1 GCAATGCGATTTACGTAATC
* * *
2310069 GCATTGCGATTTTCCTAATTC
1 GCAATGCGATTTACGTAA-TC
* *
2310090 GCATTGCTATTTACGTAATC
1 GCAATGCGATTTACGTAATC
* *
2310110 GTATTGCGATTTACGTAATC
1 GCAATGCGATTTACGTAATC
2310130 GCAA
1 GCAA
2310134 CGAGATTCTG
Statistics
Matches: 223, Mismatches: 16, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
19 30 0.13
20 161 0.72
21 32 0.14
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (20 bp):
GCAATGCGATTTACGTAATC
Found at i:2310170 original size:81 final size:81
Alignment explanation
Indices: 2309941--2310173 Score: 228
Period size: 81 Copynumber: 2.9 Consensus size: 81
2309931 GCAATGCGAA
* * * *
2309941 TACGTAATCGCATTGCGATTTACGTAATCGCAATGCGA-TTACGTAAATCGCAATGCG-ATTACG
1 TACGTAATCGCATTGCGATTTACGTAATCGCAACGAGATTTACGT-AATCGCAATACGAATTTC-
* * * *
2310004 TAAA-TCGCAATGCGA-A
64 CAAATTCGCATTGCTATT
** * * * * *
2310020 TACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCT
1 TACGTAATCGCATTGCGATTTACGTAATCGCAACGAGATTTACGTAATCGCAATACGAATTTCCA
2310085 AATTCGCATTGCTATT
66 AATTCGCATTGCTATT
*
2310101 TACGTAATCGTATTGCGATTTACGTAATCGCAACGAGATTCTGAC-T-ATCGCAATACTGAATTT
1 TACGTAATCGCATTGCGATTTACGTAATCGCAACGAGATT-T-ACGTAATCGCAATAC-GAATTT
2310164 -CAAATTCGCA
63 CCAAATTCGCA
2310174 ACTCGATTTC
Statistics
Matches: 130, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
79 50 0.38
80 18 0.14
81 53 0.41
82 7 0.05
83 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (81 bp):
TACGTAATCGCATTGCGATTTACGTAATCGCAACGAGATTTACGTAATCGCAATACGAATTTCCA
AATTCGCATTGCTATT
Found at i:2311046 original size:24 final size:24
Alignment explanation
Indices: 2310995--2311048 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2310985 GTATTCAAAA
*
2310995 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
2311019 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
2311043 TTTGAT
1 TTTGAT
2311049 GATTTTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:2313616 original size:33 final size:33
Alignment explanation
Indices: 2313574--2313663 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
2313564 ATGACTATCA
2313574 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
*
2313607 CAATGCGAAATGAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
*
2313640 CAAAGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
2313664 CGAATTTAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:2313626 original size:19 final size:18
Alignment explanation
Indices: 2313550--2313667 Score: 72
Period size: 19 Copynumber: 6.7 Consensus size: 18
2313540 CTTAATGTGT
**
2313550 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
*
2313570 ATCACAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
2313589 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
2313603 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
2313622 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
2313636 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
2313655 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
2313668 TTTAGTTTCG
Statistics
Matches: 76, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
14 17 0.22
15 4 0.05
16 4 0.05
17 4 0.05
18 4 0.05
19 35 0.46
20 8 0.11
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:2313685 original size:19 final size:19
Alignment explanation
Indices: 2313663--2313737 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
2313653 AAATCGCAAC
2313663 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCGTT
*
2313682 GCG-ATTT--TGTCG--TT
1 GCGAATTTCATTTCGCGTT
*
2313696 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
2313715 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
2313734 GCGA
1 GCGA
2313738 TGGTCATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
14 5 0.11
15 3 0.06
16 4 0.09
17 4 0.09
18 4 0.09
19 27 0.57
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:2313738 original size:19 final size:19
Alignment explanation
Indices: 2313694--2313738 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
2313684 GATTTTGTCG
*
2313694 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2313713 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2313732 TTGCGAT
1 TTGCGAT
2313739 GGTCATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2313744 original size:19 final size:19
Alignment explanation
Indices: 2313703--2313746 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2313693 GTTGCGATTT
* **
2313703 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATGG
2313722 TCATTTCGCATTGCGATGG
1 TCATTTCGCATTGCGATGG
2313741 TCATTT
1 TCATTT
2313747 TTTCATTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATGG
Found at i:2313864 original size:14 final size:14
Alignment explanation
Indices: 2313845--2313881 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2313835 CATCAATTAA
2313845 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2313859 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2313873 ACAAATCAA
1 ACAAATCAA
2313882 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2315295 original size:21 final size:21
Alignment explanation
Indices: 2315229--2315295 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2315219 GTGAATCGGG
*
2315229 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2315249 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2315271 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2315292 CTCT
1 CTCT
2315296 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2315809 original size:20 final size:19
Alignment explanation
Indices: 2315772--2315841 Score: 122
Period size: 19 Copynumber: 3.6 Consensus size: 19
2315762 AAAAATGACT
2315772 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2315791 ATCGCAACGAGAGAATGAAA
1 ATCGCAACGCGA-AATGAAA
2315811 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2315830 ATCGCAACGCGA
1 ATCGCAACGCGA
2315842 TTATAGTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 30 0.62
20 18 0.38
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2315872 original size:20 final size:19
Alignment explanation
Indices: 2315847--2315948 Score: 114
Period size: 19 Copynumber: 5.3 Consensus size: 19
2315837 CGCGATTATA
* *
2315847 GTTTCGAGTTGCGATTTTTG
1 GTTTCGCGTTGCGA-TTTTC
2315867 GTTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
* *
2315886 ATTTCGTGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
2315905 GTTTCGCGTTGCGATTTTA
1 GTTTCGCGTTGCGATTTTC
* *
2315924 TTTCTCTCGTTGCGATTTTC
1 GTT-TCGCGTTGCGATTTTC
*
2315944 ATTTC
1 GTTTC
2315949 AACCAAAAGA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
19 41 0.59
20 29 0.41
ACGTcount: A:0.09, C:0.18, G:0.23, T:0.51
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTC
Found at i:2315935 original size:58 final size:57
Alignment explanation
Indices: 2315838--2315948 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 57
2315828 AAATCGCAAC
2315838 GCGATTATAGTTTCGAGTTGCGATTTTTGGTTTCGCGTTGCGATTTTCATTTCGTGTT
1 GCGATTATAGTTTCGAGTTGCGATTTTT-GTTTCGCGTTGCGATTTTCATTTCGTGTT
* * * *
2315896 GCGATTTTCGTTTCGCGTTGCGATTTTAT-TTCTCTCGTTGCGATTTTCATTTC
1 GCGATTATAGTTTCGAGTTGCGATTTT-TGTT-TCGCGTTGCGATTTTCATTTC
2315949 AACCAAAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
57 2 0.04
58 44 0.94
59 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.50
Consensus pattern (57 bp):
GCGATTATAGTTTCGAGTTGCGATTTTTGTTTCGCGTTGCGATTTTCATTTCGTGTT
Found at i:2316152 original size:94 final size:94
Alignment explanation
Indices: 2316039--2316602 Score: 899
Period size: 94 Copynumber: 6.1 Consensus size: 94
2316029 ATGGATTGCA
* * * *
2316039 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACATACT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2316103 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2316132 TTACTTTCAACTAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
2316197 TTATCAGAATTGACACCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2316226 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
2316291 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
2316320 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
2316384 TTTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
2316414 TTACTTTCATCCAAAAGATAAAACAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
2316479 TTAGCAGAATTGGGAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2316508 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
2316568 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
2316598 TTACT
1 TTACT
2316603 AAGCAATCTA
Statistics
Matches: 440, Mismatches: 26, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
90 40 0.09
93 40 0.09
94 343 0.78
95 17 0.04
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2318370 original size:19 final size:19
Alignment explanation
Indices: 2318295--2318399 Score: 103
Period size: 20 Copynumber: 5.7 Consensus size: 19
2318285 TCTTTTGGTT
*
2318295 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
2318314 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
2318334 GGAAATGACTATCACAACGC
1 -GAAATGAAAATCGCAACGC
2318354 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
2318371 G--A-GAGAATCGCATCGC
1 GAAATGAAAATCGCAACGC
2318387 GAAATGAAAATCG
1 GAAATGAAAATCG
2318400 TAATGCGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 22 0.32
20 30 0.43
21 2 0.03
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2318425 original size:19 final size:19
Alignment explanation
Indices: 2318403--2318447 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2318393 AAAATCGTAA
** *
2318403 TGCGATTTTGGTTTCTCGT
1 TGCGATTTTCATTTCGCGT
2318422 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
2318441 TGCGATT
1 TGCGATT
2318448 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:2318455 original size:33 final size:34
Alignment explanation
Indices: 2318416--2318481 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
2318406 GATTTTGGTT
**
2318416 TCTCGTTGCGATTTTCATTT-CGCGTTGCGATTC
1 TCTCGTTGCGATAGTCATTTCCGCGTTGCGATTC
*
2318449 TCTCGTTGCGATAGTCATTTCCGTGTTGCGATT
1 TCTCGTTGCGATAGTCATTTCCGCGTTGCGATT
2318482 TTCATTGTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.62
34 11 0.38
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (34 bp):
TCTCGTTGCGATAGTCATTTCCGCGTTGCGATTC
Found at i:2319078 original size:20 final size:20
Alignment explanation
Indices: 2319055--2319229 Score: 206
Period size: 20 Copynumber: 8.7 Consensus size: 20
2319045 CGATAGTCAG
2319055 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
2319075 ATTCGCGTTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
2319095 AATTTGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
2319116 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * * *
2319136 AATCGCGTTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
2319156 AATTCGTATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* * *
2319177 AATCGCGTTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
2319197 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2319217 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2319230 ATTAGGAAAA
Statistics
Matches: 129, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
20 98 0.76
21 31 0.24
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2319106 original size:41 final size:40
Alignment explanation
Indices: 2319057--2319229 Score: 211
Period size: 41 Copynumber: 4.3 Consensus size: 40
2319047 ATAGTCAGAT
* * *
2319057 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCCTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
* * *
2319097 TTTGCATTGCGATTTACGTAATCGCGTTGCGATTTACGTAA
1 -TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
* * * *
2319138 TCGCGTTGCGATTTTCCTAATTCGTATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGT-ATTCGCATTGCGATTTACGTAA
* * *
2319179 TCGCGTTGTGATTTACGTATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
2319219 TCGCATTGCGA
1 TCGCATTGCGA
2319230 ATTAGGAAAA
Statistics
Matches: 113, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
40 43 0.38
41 70 0.62
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
Found at i:2319243 original size:61 final size:61
Alignment explanation
Indices: 2319057--2319229 Score: 267
Period size: 61 Copynumber: 2.9 Consensus size: 61
2319047 ATAGTCAGAT
* *
2319057 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCCTAATTTGCATTGCGATTTACGTAA
1 TCGCGTTGCGATTTACGTATTCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGTAA
* *
2319118 TCGCGTTGCGATTTACGTAATCGCGTTGCGATTTTCCTAATTCGTATTGCGATTTACGTAA
1 TCGCGTTGCGATTTACGTATTCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGTAA
* * * *
2319179 TCGCGTTGTGATTTACGTATTCGCATTGCGATTTACGT-ATTCGCATTGCGA
1 TCGCGTTGCGATTTACGTATTCGCGTTGCGATTTTCCTAATTCGCATTGCGA
2319230 ATTAGGAAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 12 0.12
61 90 0.88
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (61 bp):
TCGCGTTGCGATTTACGTATTCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGTAA
Found at i:2319996 original size:21 final size:21
Alignment explanation
Indices: 2319930--2320010 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 21
2319920 AGAGAGATAC
*
2319930 AAAATAGAAAAA-AAAAACAA
1 AAAATAGAAAAATAAAAAGAA
* * *
2319950 AAAA-ACAAAAAATAATATGAA
1 AAAATA-GAAAAATAAAAAGAA
* *
2319971 GAAATAGAAAAATAAGAAGAA
1 AAAATAGAAAAATAAAAAGAA
* *
2319992 AAAATTGAAGAA-AAAAAGA
1 AAAATAGAAAAATAAAAAGA
2320011 GCGAGAAATG
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
19 1 0.02
20 15 0.33
21 29 0.63
22 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.10
Consensus pattern (21 bp):
AAAATAGAAAAATAAAAAGAA
Found at i:2327267 original size:45 final size:45
Alignment explanation
Indices: 2327153--2327483 Score: 236
Period size: 45 Copynumber: 7.4 Consensus size: 45
2327143 AAATTCATTT
* * *
2327153 TTGTCATTCTTGACGTTCTCGTGAAGAAGAGTCAA-CTTTTTAGTG
1 TTGTCATTCTTAACTTTCTCGTGAAGAGGAGTCAATC-TTTTAGTG
* * * * *
2327198 TTTTCATTCTTAACTTTATTGTGAATATGAGTCAATCTTTTAGTG
1 TTGTCATTCTTAACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * *
2327243 TTGTCATTCTTTATTTTCTCGTGAAGAGGTA-TCAATCTTTCACTG
1 TTGTCATTCTTAACTTTCTCGTGAAGAGG-AGTCAATCTTTTAGTG
* * * * * *
2327288 TAGTTATTCTTAACTTTCTCATAAAGAGGCGTTAATCTTTTTAGTG
1 TTGTCATTCTTAACTTTCTCGTGAAGAGGAGTCAATC-TTTTAGTG
* * * * *
2327334 ATGTTATTCTTGACTTTCTCGTAAAGAGGAGTCGATCTTTTAGTG
1 TTGTCATTCTTAACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * ** ** *
2327379 TTTTCCTTATTATCTTTCTCACGAAGAAAAGTCAAT-TTTTAGCG
1 TTGTCATTCTTAACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * * * * *
2327423 ATATGATTCTTAACTTTCTCGGGAAGAGGATTCAACCTTGTAGAG
1 TTGTCATTCTTAACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* *
2327468 ATGTCATTCTCAACTT
1 TTGTCATTCTTAACTT
2327484 GACTTTCTAG
Statistics
Matches: 217, Mismatches: 64, Indels: 10
0.75 0.22 0.03
Matches are distributed among these distances:
44 31 0.14
45 148 0.68
46 38 0.18
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.43
Consensus pattern (45 bp):
TTGTCATTCTTAACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
Done.