Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 169 of 322
Found at i:55223312 original size:47 final size:47
Alignment explanation
Indices: 55223224--55223318 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
55223214 GACAAAACCT
** *
55223224 TGAATGTCCCCTACAACCATGTTACGTTCACCCGTATGCCTTCAATA
1 TGAATGTCCCCTACAACCATGTTACGTTCACCCACACGCCTTCAATA
** *
55223271 TGAATGTCCCCTACAACCATGTTATTTTTACCCACACGCCTTCAATA
1 TGAATGTCCCCTACAACCATGTTACGTTCACCCACACGCCTTCAATA
55223318 T
1 T
55223319 CCTTTTTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (47 bp):
TGAATGTCCCCTACAACCATGTTACGTTCACCCACACGCCTTCAATA
Found at i:55224021 original size:18 final size:18
Alignment explanation
Indices: 55223974--55224034 Score: 70
Period size: 19 Copynumber: 3.4 Consensus size: 18
55223964 TAAAAAAACT
*
55223974 AAAAATAGAAAATCATAA
1 AAAAATAGAATATCATAA
55223992 AAAAATATGAATATCATAA
1 AAAAATA-GAATATCATAA
** *
55224011 AAATGTAGAAT-TTATAA
1 AAAAATAGAATATCATAA
55224028 AAAAATA
1 AAAAATA
55224035 TAAATTTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.28
18 11 0.31
19 15 0.42
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.25
Consensus pattern (18 bp):
AAAAATAGAATATCATAA
Found at i:55224040 original size:18 final size:18
Alignment explanation
Indices: 55223974--55224051 Score: 61
Period size: 19 Copynumber: 4.3 Consensus size: 18
55223964 TAAAAAAACT
* * *
55223974 AAAAATAGAAAATCATAA
1 AAAAATATAAATTTATAA
* *
55223992 AAAAATATGAA--TATCAT
1 AAAAATATAAATTTAT-AA
*
55224009 AAAAATGTAGAATTTATAA
1 AAAAATATA-AATTTATAA
55224028 AAAAATATAAATTTTATAA
1 AAAAATATAAA-TTTATAA
55224047 AAAAA
1 AAAAA
55224052 ATTACTAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
16 2 0.04
17 8 0.17
18 13 0.28
19 21 0.45
20 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAAATATAAATTTATAA
Found at i:55224048 original size:17 final size:17
Alignment explanation
Indices: 55223992--55224049 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
55223982 AAAATCATAA
* * *
55223992 AAAAATATGAATATCAT
1 AAAAATATAAATTTTAT
* *
55224009 AAAAATGTAGAATTTATAA
1 AAAAATATA-AATTT-TAT
55224028 AAAAATATAAATTTTAT
1 AAAAATATAAATTTTAT
55224045 AAAAA
1 AAAAA
55224050 AAATTACTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 14 0.44
18 9 0.28
19 9 0.28
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (17 bp):
AAAAATATAAATTTTAT
Found at i:55224370 original size:22 final size:22
Alignment explanation
Indices: 55224334--55224378 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
55224324 ATATATTTAA
**
55224334 TTTTTTATAGGTTTCCT-ATATT
1 TTTTTTATAAATTT-CTAATATT
55224356 TTTTTTATAAATTTCTAATATT
1 TTTTTTATAAATTTCTAATATT
55224378 T
1 T
55224379 AATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTTTTATAAATTTCTAATATT
Found at i:55236223 original size:17 final size:17
Alignment explanation
Indices: 55236201--55236250 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
55236191 ATATTTTTCC
55236201 TTTCTTTTTTCTTACTT
1 TTTCTTTTTTCTTACTT
* *
55236218 TTTCTTTTTTTCGGTCCTT
1 TTTC-TTTTTTC-TTACTT
55236237 TTTCTTTTCTTCTT
1 TTTCTTTT-TTCTT
55236251 TAATTGTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.15
18 12 0.44
19 11 0.41
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.74
Consensus pattern (17 bp):
TTTCTTTTTTCTTACTT
Found at i:55247781 original size:21 final size:21
Alignment explanation
Indices: 55247757--55247796 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55247747 AACCGTATCG
*
55247757 GAATAGGTAAGGGCGTCACTA
1 GAATAGGTAAGGGCATCACTA
55247778 GAATAGGTAAGGGCATCAC
1 GAATAGGTAAGGGCATCAC
55247797 CGGACGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.33, T:0.17
Consensus pattern (21 bp):
GAATAGGTAAGGGCATCACTA
Found at i:55251912 original size:63 final size:64
Alignment explanation
Indices: 55251810--55251952 Score: 162
Period size: 63 Copynumber: 2.2 Consensus size: 64
55251800 GACACGAGCA
* * * * *
55251810 TATGCCCAGGCCGTGTAACTCACTATCTGAGGTATAAAAACCATATGGCC-AGGGACACGGACG
1 TATGCCCAGGCCGTGTAACTCAATATCTGAGCTAAAAAAACCACACGGCCAAGGGACACGGACG
* * * * * *
55251873 TATGCCCAGGCCGTGTAACTCAATGTTTGTGCTAAAAAAATCACACGGCCAAGGTACACGGGCG
1 TATGCCCAGGCCGTGTAACTCAATATCTGAGCTAAAAAAACCACACGGCCAAGGGACACGGACG
* *
55251937 TGTGCTCAGGCCGTGT
1 TATGCCCAGGCCGTGT
55251953 GGTAGGATGT
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
63 41 0.62
64 25 0.38
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (64 bp):
TATGCCCAGGCCGTGTAACTCAATATCTGAGCTAAAAAAACCACACGGCCAAGGGACACGGACG
Found at i:55257945 original size:42 final size:42
Alignment explanation
Indices: 55257893--55257977 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
55257883 GCTCTCTTCT
*
55257893 ACTCCATACGCACAATAGATATAAAATCTGCTAGAATAGATG
1 ACTCCATACGCACAACAGATATAAAATCTGCTAGAATAGATG
* * * *
55257935 ACTCTATACGCACAGCAGATATAAGATGTGCTAGAATAGATG
1 ACTCCATACGCACAACAGATATAAAATCTGCTAGAATAGATG
55257977 A
1 A
55257978 TGACTAGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (42 bp):
ACTCCATACGCACAACAGATATAAAATCTGCTAGAATAGATG
Found at i:55257986 original size:16 final size:16
Alignment explanation
Indices: 55257965--55257996 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55257955 ATAAGATGTG
55257965 CTAGAATAGATGATGA
1 CTAGAATAGATGATGA
55257981 CTAGAATAGATGATGA
1 CTAGAATAGATGATGA
55257997 TTGATGCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (16 bp):
CTAGAATAGATGATGA
Found at i:55259205 original size:14 final size:13
Alignment explanation
Indices: 55259174--55259214 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
55259164 TTTTACTATT
*
55259174 ATATATAAATATA
1 ATATATAGATATA
55259187 A-ATATAGATATA
1 ATATATAGATATA
55259199 GATATATAGAT-TA
1 -ATATATAGATATA
55259212 ATA
1 ATA
55259215 ATAAAAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 13 0.52
13 4 0.16
14 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
ATATATAGATATA
Found at i:55259821 original size:7 final size:7
Alignment explanation
Indices: 55259783--55259819 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
55259773 ATTAAATTTT
55259783 TAAAAAA
1 TAAAAAA
55259790 TAAAAAA
1 TAAAAAA
*
55259797 TAAAAAT
1 TAAAAAA
55259804 TAAAAAA
1 TAAAAAA
*
55259811 TATAAAA
1 TAAAAAA
55259818 TA
1 TA
55259820 TATTTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAAAAA
Found at i:55262794 original size:16 final size:15
Alignment explanation
Indices: 55262775--55262804 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
55262765 TTCATTTCTT
55262775 TTGCATTTAGATTAAC
1 TTGCATTTAG-TTAAC
55262791 TTGCATTTAGTTAA
1 TTGCATTTAGTTAA
55262805 TTAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (15 bp):
TTGCATTTAGTTAAC
Found at i:55263520 original size:23 final size:23
Alignment explanation
Indices: 55263490--55263536 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
55263480 TAAGATGTTT
55263490 TCAATAGTTTTGCAAAATAAATA
1 TCAATAGTTTTGCAAAATAAATA
55263513 TCAATAGTTTTGCAAAATAAATA
1 TCAATAGTTTTGCAAAATAAATA
55263536 T
1 T
55263537 TGATTTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (23 bp):
TCAATAGTTTTGCAAAATAAATA
Found at i:55264119 original size:13 final size:13
Alignment explanation
Indices: 55264101--55264141 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
55264091 CAAAAAAATC
*
55264101 TATTTTTTATTTT
1 TATTTTTTATTAT
*
55264114 TATTTTTTAATAT
1 TATTTTTTATTAT
55264127 TATTTTCTTATTAT
1 TATTTT-TTATTAT
55264141 T
1 T
55264142 TTCTCCCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTTTATTAT
Found at i:55266019 original size:3 final size:3
Alignment explanation
Indices: 55266013--55266213 Score: 128
Period size: 3 Copynumber: 66.3 Consensus size: 3
55266003 TATCATCATC
* **
55266013 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GAAA ATGA GGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT-A ATA ATA
* ** * *
55266060 ATA ATA A-A AAA ACC ATA AT- ATAA ATA ATAA ATA A-A A-A ACA AAA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA
* *
55266103 ATA GA-A ATG GTA ATA ATA ATA ATA ATA ATA ATA ATA A-A TATA AGTA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA
* * * * * *
55266149 ATA GTA ATA GTA ATA ATA AGA GTA TTA ATA ATAA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
55266195 ATA A-A ATTA ATA ATA ATA A
1 ATA ATA A-TA ATA ATA ATA A
55266214 AAATTGATTA
Statistics
Matches: 156, Mismatches: 27, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
2 12 0.08
3 126 0.81
4 18 0.12
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:55266105 original size:26 final size:26
Alignment explanation
Indices: 55266027--55266110 Score: 71
Period size: 26 Copynumber: 3.1 Consensus size: 26
55266017 TAATAATAAT
* * *
55266027 AATAATAATAATAATAATAGAAAATGAGG
1 AATAATAATAA-AAAAACA-AAAAT-AGA
* * *
55266056 AATAATAATAAAAAAACCATAATATA
1 AATAATAATAAAAAAACAAAAATAGA
55266082 AATAATAA-ATAAAAAACAAAAATAGA
1 AATAATAATA-AAAAAACAAAAATAGA
55266108 AAT
1 AAT
55266111 GGTAATAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
25 1 0.02
26 25 0.56
27 4 0.09
28 4 0.09
29 11 0.24
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (26 bp):
AATAATAATAAAAAAACAAAAATAGA
Found at i:55266162 original size:28 final size:27
Alignment explanation
Indices: 55266013--55266212 Score: 105
Period size: 28 Copynumber: 7.4 Consensus size: 27
55266003 TATCATCATC
*
55266013 ATAATAATAATAATAATAAT-AATAATA
1 ATAATAATAATAGTAATAATAAAT-ATA
* * *
55266040 ATAATAGAAAATGAGGAATAAT-AATAAA
1 ATAATA-ATAAT-AGTAATAATAAATATA
* **
55266068 AAAACCATAATA-TAAATAATAAATA-A
1 ATAATAATAATAGT-AATAATAAATATA
* * * * **
55266094 AAAACAAAAATAGAAATGGT--A-ATA
1 ATAATAATAATAGTAATAATAAATATA
*
55266118 ATAATAATAATAATAATAATAAATATA
1 ATAATAATAATAGTAATAATAAATATA
*
55266145 AGTAATAGTAATAGTAATAATAAGAGTAT-
1 A-TAATAATAATAGTAATAATAA-A-TATA
*
55266174 -TAATAATAAATAGTAATAAT-AATAAA
1 ATAATAAT-AATAGTAATAATAAATATA
55266200 ATTAATAATAATA
1 A-TAATAATAATA
55266213 AAAATTGATT
Statistics
Matches: 132, Mismatches: 25, Indels: 32
0.70 0.13 0.17
Matches are distributed among these distances:
23 1 0.01
24 15 0.11
25 2 0.02
26 24 0.18
27 29 0.22
28 47 0.36
29 11 0.08
30 3 0.02
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (27 bp):
ATAATAATAATAGTAATAATAAATATA
Found at i:55267988 original size:43 final size:42
Alignment explanation
Indices: 55267874--55268000 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 42
55267864 TATGAATTTG
* * * *
55267874 TAACCTTAACTTGCTCCACTGCAACTTCAGGGAGATAAGGTT
1 TAACTTTAACCTGCTCCACTGTAACTTCAGGGAGATAAGCTT
* * **
55267916 TGCTATTTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTT
1 T--AACTTT-AACCTGCTCCACTGTAACTTCAGGGAGATAAG-CTT
*
55267962 TAACTTTAACCTGCTCCACTGTAACTTCAGGAAGATAAG
1 TAACTTTAACCTGCTCCACTGTAACTTCAGGGAGATAAG
55268001 GTTCGCTGTG
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
42 1 0.01
43 29 0.43
44 7 0.10
45 28 0.41
46 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (42 bp):
TAACTTTAACCTGCTCCACTGTAACTTCAGGGAGATAAGCTT
Found at i:55267998 original size:88 final size:88
Alignment explanation
Indices: 55267885--55268403 Score: 368
Period size: 88 Copynumber: 5.8 Consensus size: 88
55267875 AACCTTAACT
* *
55267885 TGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATTTTCAGTCTGCTCCACTGTAACTTCAGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGG
*
55267950 GAGATAAGACTTTAACTTTAACC
66 GAGATAAGACTTTAACTTCAACC
* * * * * * * * * *
55267973 TGCTCCACTGTAACTTCAGGAAGATAAGGTTCGC--T-GTGA-TCTACTCTATTGCAACTTAAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGG
* * * *
55268034 TAGATAATATCTGTTTATTTATAACTTTAATC
66 GAGAT-A-A---G---ACTT-TAACTTCAACC
* * *
55268066 TGTTCCACTGCAACTTCAGGGA-A-AAGATTCGCTATCTTCAGT-TCGCTCCACTGCAACTTCAG
1 TGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTCAGTCT-GCTCCACTGCAACTTCAG
55268128 GGAGATAAGACTTTAACTTCAACC
65 GGAGATAAGACTTTAACTTCAACC
* * * ** * * *
55268152 TACTCCACTACAACTTTAGGGAGATAAGGTTTGCTA---T-A-TCTGCTCTGCTGAAACTTTAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGG
* *
55268212 GAGATGAGATCTGCTTATTTATAGCTTCAAAC
66 GAGATAAGA----C---TTTA-A-CTTCAACC
* * * * *
55268244 TGTTCCACTGCAACTTTAGGGA-A-AAGATTAGCTATCTTCGGTCTGCTCCACTGCAACTTCAGG
1 TGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGG
55268307 GAGATAAGACTTTAACTTCAACC
66 GAGATAAGACTTTAACTTCAACC
* ** * * *
55268330 TGC-CTTACTGCAACTTCAGGGAGATAAGGTTTAG-TGGCTTCAATCTGCTTCACTGCAACTTCG
1 TGCTC-CACTGCAACTTCAGGGAGATAAGGTTT-GCTATCTTCAGTCTGCTCCACTGCAACTTCA
55268393 GGGAGATAAGA
64 GGGAGATAAGA
55268404 TCCGCCATTA
Statistics
Matches: 330, Mismatches: 66, Indels: 70
0.71 0.14 0.15
Matches are distributed among these distances:
83 23 0.07
84 22 0.07
85 5 0.02
86 53 0.16
87 7 0.02
88 83 0.25
89 2 0.01
90 14 0.04
91 11 0.03
92 30 0.09
93 32 0.10
94 4 0.01
95 44 0.13
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (88 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGG
GAGATAAGACTTTAACTTCAACC
Found at i:55268148 original size:43 final size:43
Alignment explanation
Indices: 55268069--55268179 Score: 104
Period size: 43 Copynumber: 2.6 Consensus size: 43
55268059 TTTAATCTGT
* ** *
55268069 TCCACTGCAACTTCAGGGA-A-AAGATTCGCTATCTTC-AGTTCGC
1 TCCACTGCAACTTCAGGGAGATAAGATT--CTAACTTCAACCT-AC
55268112 TCCACTGCAACTTCAGGGAGATAAGACTT-TAACTTCAACCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTCTAACTTCAACCTAC
* *
55268155 TCCACTACAACTTTAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAG
55268180 GTTTGCTATA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
43 49 0.84
44 3 0.05
45 4 0.07
46 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
TCCACTGCAACTTCAGGGAGATAAGATTCTAACTTCAACCTAC
Found at i:55268294 original size:178 final size:179
Alignment explanation
Indices: 55267888--55268361 Score: 639
Period size: 178 Copynumber: 2.6 Consensus size: 179
55267878 CTTAACTTGC
* * * *
55267888 TCCACTGCAACTTCAGGGAGATAAGGTTTGCTATTTTCAGTCTGCTCCACTGTAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGA-A-AAGATTAGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* * * * *
55267953 ATAAGACTTTAACTTTAACCTGCTCCACTGTAACTTCAGGAAGATAAGGTTCGCTGTGATCTACT
64 ATAAGACTTTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATGATCTACT
* * * * * * *
55268018 CTATTGCAACTTAAGATAGATAATATCTGTTTATTTATAACTTTAATCTGT
129 CTACTGAAACTTAAGAGAGATAAGATCTGCTTATTTATAACTTCAAACTGT
*
55268069 TCCACTGCAACTTCAGGGAAAAGATTCGCTATCTTCAGT-TCGCTCCACTGCAACTTCAGGGAGA
1 TCCACTGCAACTTCAGGGAAAAGATTAGCTATCTTCAGTCT-GCTCCACTGCAACTTCAGGGAGA
* * * *
55268133 TAAGACTTTAACTTCAACCTACTCCACTACAACTTTAGGGAGATAAGGTTTGCTAT-ATCTGCTC
65 TAAGACTTTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATGATCTACTC
* * * *
55268197 TGCTGAAACTTTAGAGAGATGAGATCTGCTTATTTATAGCTTCAAACTGT
130 TACTGAAACTTAAGAGAGATAAGATCTGCTTATTTATAACTTCAAACTGT
* *
55268247 TCCACTGCAACTTTAGGGAAAAGATTAGCTATCTTCGGTCTGCTCCACTGCAACTTCAGGGAGAT
1 TCCACTGCAACTTCAGGGAAAAGATTAGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGAT
*
55268312 AAGACTTTAACTTCAACCTGC-CTTACTGCAACTTCAGGGAGATAAGGTTT
66 AAGACTTTAACTTCAACCTGCTC-CACTGCAACTTCAGGGAGATAAGGTTT
55268362 AGTGGCTTCA
Statistics
Matches: 259, Mismatches: 31, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
177 1 0.00
178 151 0.58
179 87 0.34
180 1 0.00
181 19 0.07
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (179 bp):
TCCACTGCAACTTCAGGGAAAAGATTAGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGAT
AAGACTTTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATGATCTACTCT
ACTGAAACTTAAGAGAGATAAGATCTGCTTATTTATAACTTCAAACTGT
Found at i:55268340 original size:43 final size:44
Alignment explanation
Indices: 55268286--55268403 Score: 143
Period size: 45 Copynumber: 2.7 Consensus size: 44
55268276 TATCTTCGGT
*
55268286 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTTA-ACTTCAAC
1 CTGCTTCACTGCAACTTCAGGGAGATAAGACTTTAGACTTCAAC
* * *
55268329 CTGCCTT-ACTGCAACTTCAGGGAGATAAG-GTTTAGTGGCTTCAAT
1 CTG-CTTCACTGCAACTTCAGGGAGATAAGACTTTA--GACTTCAAC
*
55268374 CTGCTTCACTGCAACTTCGGGGAGATAAGA
1 CTGCTTCACTGCAACTTCAGGGAGATAAGA
55268404 TCCGCCATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
42 4 0.06
43 25 0.39
44 5 0.08
45 30 0.47
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (44 bp):
CTGCTTCACTGCAACTTCAGGGAGATAAGACTTTAGACTTCAAC
Found at i:55272864 original size:45 final size:43
Alignment explanation
Indices: 55272704--55272880 Score: 157
Period size: 43 Copynumber: 4.0 Consensus size: 43
55272694 AGATCTGTTT
* * *
55272704 ATTTATAGCTTCAATCTGATCCACTGCAACTTTAGGGA-A-AAT
1 ATTTAT-GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* *
55272746 ATTCACTAT-CTTCGATCTGCTCCACT-CTAACTTTAGGGAGATAAG
1 ATT---TATGCTTCAATCTGCTCCACTGC-AACTTCAGGGAGATAAG
* * *
55272791 ACTTTA-ACTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAG
1 A-TTTATGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* *
55272834 GTTTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAG
1 ATTTA-T-GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
55272879 AT
1 AT
55272881 CCGCCATTAT
Statistics
Matches: 110, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
42 8 0.07
43 58 0.53
44 2 0.02
45 40 0.36
46 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (43 bp):
ATTTATGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
Found at i:55274319 original size:43 final size:44
Alignment explanation
Indices: 55274223--55274344 Score: 151
Period size: 43 Copynumber: 2.8 Consensus size: 44
55274213 TATTTATAGG
* *
55274223 TTCAATCTGCTCCACTGCAACTTCAGGGA-A-AAGATTTGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-CTAAC
***
55274266 TTTGGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-TAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTCTAAC
* *
55274309 TTCAACCTGCTCCACTGCAACTTCAGAGAGATAAGA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
55274345 TCTGCCATCA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 60 0.90
44 1 0.01
45 6 0.09
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTCTAAC
Found at i:55277210 original size:21 final size:20
Alignment explanation
Indices: 55277153--55277212 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
55277143 TTAGGTTTTA
55277153 TATATTAAATTATATATATAT
1 TATATTAAATTAT-TATATAT
* * *
55277174 TATAATGATTATTATTATAGTTT
1 TAT-ATTA-AATTATTATA-TAT
55277197 TATATTAAATTATTAT
1 TATATTAAATTATTAT
55277213 GATTACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 11 0.35
22 10 0.32
23 10 0.32
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TATATTAAATTATTATATAT
Found at i:55281202 original size:9 final size:9
Alignment explanation
Indices: 55281188--55281273 Score: 120
Period size: 9 Copynumber: 9.6 Consensus size: 9
55281178 ATAAGTATAA
55281188 AATTAACCG
1 AATTAACCG
55281197 AATTAACCG
1 AATTAACCG
*
55281206 AATTAATCG
1 AATTAACCG
55281215 AATTAACCG
1 AATTAACCG
55281224 AATT-ACTCG
1 AATTAAC-CG
*
55281233 AATTACCCG
1 AATTAACCG
*
55281242 AATTAACCA
1 AATTAACCG
55281251 AATTAACCG
1 AATTAACCG
*
55281260 AATTAATCG
1 AATTAACCG
55281269 AATTA
1 AATTA
55281274 TTTGTATAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
8 2 0.03
9 65 0.96
10 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:55281308 original size:5 final size:6
Alignment explanation
Indices: 55281293--55281339 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
55281283 AATTATATGT
*
55281293 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTTTTA TTT
55281340 ATTAAGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 28 0.76
7 8 0.22
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:55281321 original size:20 final size:20
Alignment explanation
Indices: 55281298--55281336 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55281288 TATGTTTTTT
55281298 ATTTTTATTTTTAGTTTTAG
1 ATTTTTATTTTTAGTTTTAG
*
55281318 ATTTTTATTTTTATTTTTA
1 ATTTTTATTTTTAGTTTTA
55281337 TTTATTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
ATTTTTATTTTTAGTTTTAG
Found at i:55281380 original size:13 final size:13
Alignment explanation
Indices: 55281364--55281388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55281354 AATTATTATG
55281364 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
55281377 ATTGGGTTGGGT
1 ATTGGGTTGGGT
55281389 TGGGTACTTG
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:55281388 original size:18 final size:18
Alignment explanation
Indices: 55281365--55281402 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
55281355 ATTATTATGA
55281365 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
*
55281383 TTGGGTTGGGTACTTGGG
1 TTGGGTTGGGTAATTGGG
55281401 TT
1 TT
55281403 AATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.03, G:0.47, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:55291948 original size:3 final size:3
Alignment explanation
Indices: 55291940--55292115 Score: 94
Period size: 3 Copynumber: 58.3 Consensus size: 3
55291930 AACTACATAT
* **
55291940 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GAAA ATGA GGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT-A ATA
* ** *
55291987 ATA ATA ATA ATA ACA ACC ATA AT- ATAA ATA ATAA ATA A-A A-A ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA
* * * * *
55292031 AAA ATA GA-A ATG GTA GTA ATA ATA AAA ATA A-A AT- ATA AGTA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
* * * * *
55292075 GTA ATA ATA ACA GTA TTA ATA ATAA ATA GTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA A
55292116 AATTACTAAA
Statistics
Matches: 134, Mismatches: 27, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
2 11 0.08
3 108 0.81
4 15 0.11
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:55292057 original size:29 final size:29
Alignment explanation
Indices: 55291954--55292084 Score: 76
Period size: 29 Copynumber: 4.6 Consensus size: 29
55291944 TAATAATAAT
* * *
55291954 AATAATAATAATAATAATAATAGAAAATGAGG
1 AATAATAGTAATAATAA-AA-ATAAAAT-AGA
* * ** *
55291986 AATAATAATAATAACAACCAT--AATATA
1 AATAATAGTAATAATAAAAATAAAATAGA
55292013 AATAATA--AATAA-AAAACA-AAAATAGA
1 AATAATAGTAATAATAAAA-ATAAAATAGA
** *
55292039 AATGGTAGTAATAATAAAAATAAAATATA
1 AATAATAGTAATAATAAAAATAAAATAGA
*
55292068 AGTAATAGTAATAATAA
1 AATAATAGTAATAATAA
55292085 CAGTATTAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 17
0.71 0.14 0.16
Matches are distributed among these distances:
24 2 0.03
25 6 0.08
26 10 0.13
27 8 0.10
28 9 0.12
29 25 0.32
30 1 0.01
32 16 0.21
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (29 bp):
AATAATAGTAATAATAAAAATAAAATAGA
Found at i:55292083 original size:32 final size:31
Alignment explanation
Indices: 55292013--55292084 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
55292003 CCATAATATA
*
55292013 AATAATAAATAAAAAACAAAAATAGAAATGGT
1 AATAAT-AATAAAAAACAAAAATAGAAATAGT
* * *
55292045 AGTAATAATAAAAATA-AAATATAAGTAATAGT
1 AATAATAATAAAAA-ACAAAAAT-AGAAATAGT
55292077 AATAATAA
1 AATAATAA
55292085 CAGTATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.67, C:0.01, G:0.08, T:0.24
Consensus pattern (31 bp):
AATAATAATAAAAAACAAAAATAGAAATAGT
Found at i:55292120 original size:28 final size:28
Alignment explanation
Indices: 55292050--55292120 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
55292040 ATGGTAGTAA
*
55292050 TAATAAAAATAAAA-T-ATAAGTAATAG
1 TAATAATAATAAAATTAATAAGTAATAG
* **
55292076 TAATAATAACAGTATTAATAA-TAAATAG
1 TAATAATAATAAAATTAATAAGT-AATAG
55292104 TAATAATAATAAAATTA
1 TAATAATAATAAAATTA
55292121 CTAAAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
26 10 0.29
27 2 0.06
28 23 0.66
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (28 bp):
TAATAATAATAAAATTAATAAGTAATAG
Found at i:55293069 original size:14 final size:14
Alignment explanation
Indices: 55293035--55293082 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
55293025 AATACAACCC
* *
55293035 TTGTTCTCTTCGTTT
1 TTGTT-TCTTTGTTG
55293050 TTGTTT-TTGTGTTG
1 TTGTTTCTT-TGTTG
55293064 TTGTTTCTTTGTTG
1 TTGTTTCTTTGTTG
55293078 TTGTT
1 TTGTT
55293083 GTCCCGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 20 0.69
15 7 0.24
ACGTcount: A:0.00, C:0.08, G:0.21, T:0.71
Consensus pattern (14 bp):
TTGTTTCTTTGTTG
Found at i:55294583 original size:43 final size:43
Alignment explanation
Indices: 55294534--55294684 Score: 180
Period size: 43 Copynumber: 3.5 Consensus size: 43
55294524 TATCCCAAAT
* * *
55294534 ATGGTCTTACATGTTATCACATATCGATGCCATTGTCCCAGAC
1 ATGGTCTTACATGTAATCACATATCGATCCCAATGTCCCAGAC
* * * *
55294577 AGGGTCTTACACGAAATCATATAAT-GATCCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACAT-ATCGATCCCAATGTCCCAGAC
* *
55294620 ATGGTCTTACATGTAATCACA-ATACAATTCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACATAT-CGATCCCAATGTCCCAGAC
*
55294663 ATGGTCTTACATGTAGTCACAT
1 ATGGTCTTACATGTAATCACAT
55294685 CTTGATAGCC
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.02
43 86 0.96
44 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATCCCAATGTCCCAGAC
Found at i:55297851 original size:25 final size:25
Alignment explanation
Indices: 55297784--55297851 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
55297774 ATTCATGTAT
55297784 GCTCATACGAGCTGTA-AACGAGAA
1 GCTCATACGAGCTGTATAACGAGAA
* * * * *
55297808 GCTCCTTCGAGTTGAATAACGGGAA
1 GCTCATACGAGCTGTATAACGAGAA
*
55297833 GCTCATGCGAGCTGTATAA
1 GCTCATACGAGCTGTATAA
55297852 TAGGAAACTC
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
24 12 0.35
25 22 0.65
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (25 bp):
GCTCATACGAGCTGTATAACGAGAA
Found at i:55299160 original size:44 final size:44
Alignment explanation
Indices: 55299110--55299198 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
55299100 GTCATTGATA
*
55299110 AATACATAGTCATAAAATTTAACCTATTAAAAATTATTTATTTC
1 AATACATAGTCATAAAATTTAACCTAATAAAAATTATTTATTTC
55299154 AATACATAGTCATAAAATTTAACCTAATAAAAATTATTTATTTC
1 AATACATAGTCATAAAATTTAACCTAATAAAAATTATTTATTTC
55299198 A
1 A
55299199 TAATTTTTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.39
Consensus pattern (44 bp):
AATACATAGTCATAAAATTTAACCTAATAAAAATTATTTATTTC
Found at i:55299549 original size:12 final size:11
Alignment explanation
Indices: 55299501--55299560 Score: 61
Period size: 12 Copynumber: 5.5 Consensus size: 11
55299491 CAAAAAAAAT
55299501 GAAAAATATTA
1 GAAAAATATTA
*
55299512 GAAAAATATTTT
1 GAAAAATA-TTA
*
55299524 GAGAAATA-T-
1 GAAAAATATTA
55299533 GAAAAATATTA
1 GAAAAATATTA
55299544 GAAAAATTATTA
1 GAAAAA-TATTA
*
55299556 TAAAA
1 GAAAA
55299561 GGTAAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 7 0.17
10 2 0.05
11 14 0.34
12 18 0.44
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (11 bp):
GAAAAATATTA
Found at i:55299876 original size:33 final size:33
Alignment explanation
Indices: 55299830--55299902 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
55299820 CAATAGCAAT
55299830 TTTTATTTATTTATAATATTT-TATA-AATTTTA
1 TTTTATTTATTTATAATATTTCTATATAA-TTTA
* *
55299862 TTTTAGTTTTTTTATAATTTTTCTATATAATTTA
1 TTTTA-TTTATTTATAATATTTCTATATAATTTA
55299896 -TTTATTT
1 TTTTATTT
55299903 TTATAACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 8 0.22
33 18 0.50
34 8 0.22
35 2 0.06
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (33 bp):
TTTTATTTATTTATAATATTTCTATATAATTTA
Found at i:55299979 original size:21 final size:20
Alignment explanation
Indices: 55299923--55299979 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 20
55299913 TATAGAAAAA
* * *
55299923 TAAAAATTATTAAAAGTT-T
1 TAAAAACTATAAAAATTTAT
* *
55299942 TAAAAACTATTAGAATTTAT
1 TAAAAACTATAAAAATTTAT
55299962 TAAAATACTATAAAAATT
1 TAAAA-ACTATAAAAATT
55299980 ATGAACCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 15 0.48
20 6 0.19
21 10 0.32
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (20 bp):
TAAAAACTATAAAAATTTAT
Found at i:55299980 original size:66 final size:66
Alignment explanation
Indices: 55299904--55300028 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
55299894 TATTTATTTT
*
55299904 TATAACAATTATAGAA-AAATA-AAAATTATTAAAAGTTTTAAAAACTATTAG-AATTTATTAAA
1 TATAAAAATTAT-GAACAAATAGAAAATT-TTAAAA-TTTTAAAAACTATTAGAAATTTATTAAA
55299966 ATAC
63 ATAC
** *
55299970 TATAAAAATTATGAACCTTATAGAAAATTTTAAAATTTTAAAAATTATTAGAAATTTAT
1 TATAAAAATTATGAA-CAAATAGAAAATTTTAAAATTTTAAAAACTATTAGAAATTTAT
55300029 AATATATAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
65 3 0.06
66 26 0.51
67 16 0.31
68 6 0.12
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.38
Consensus pattern (66 bp):
TATAAAAATTATGAACAAATAGAAAATTTTAAAATTTTAAAAACTATTAGAAATTTATTAAAATA
C
Found at i:55300111 original size:24 final size:24
Alignment explanation
Indices: 55300074--55300121 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
55300064 ATTACTTATC
*
55300074 ATTTTATAAAATTTTAATAATTTT
1 ATTTTATAAAATTTCAATAATTTT
* *
55300098 ATTTTGTAACATTTCAATAATTTT
1 ATTTTATAAAATTTCAATAATTTT
55300122 TATTAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTTATAAAATTTCAATAATTTT
Found at i:55310755 original size:30 final size:30
Alignment explanation
Indices: 55310719--55310777 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
55310709 AGTTTCAGAT
55310719 TGAAGAAAAAGTTTTCTCGAAAGTATCACC
1 TGAAGAAAAAGTTTTCTCGAAAGTATCACC
*
55310749 TGAAGAAAAAGTTTTCTTGAAAGTATCAC
1 TGAAGAAAAAGTTTTCTCGAAAGTATCAC
55310778 TGTGGAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (30 bp):
TGAAGAAAAAGTTTTCTCGAAAGTATCACC
Found at i:55317351 original size:20 final size:19
Alignment explanation
Indices: 55317311--55317352 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
55317301 TTTTCCAAAT
*
55317311 TTTCTTACTTTCATTTGCA
1 TTTCTTACTTTCATTTACA
55317330 TTTCATTACTTTCCA-TTACA
1 TTTC-TTACTTT-CATTTACA
55317350 TTT
1 TTT
55317353 ACTTTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 14 0.70
21 2 0.10
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCATTTACA
Found at i:55325302 original size:20 final size:20
Alignment explanation
Indices: 55325277--55325323 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
55325267 AGTCATGGAC
55325277 ATGGTTTAAATGAAATTTTA
1 ATGGTTTAAATGAAATTTTA
55325297 ATGGTTTAAATGAAATTTTA
1 ATGGTTTAAATGAAATTTTA
55325317 ATGGTTT
1 ATGGTTT
55325324 TAAAAGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (20 bp):
ATGGTTTAAATGAAATTTTA
Found at i:55332079 original size:65 final size:65
Alignment explanation
Indices: 55331968--55332101 Score: 232
Period size: 65 Copynumber: 2.1 Consensus size: 65
55331958 GAGAATACCC
*
55331968 TCAAATTGTGAGCTTTTGGTATGCTTCGCGGAAAAGATTCCGAGGATAAGGACTTTGTGGTCCGG
1 TCAAATTGTGAGCTTTTGGTATGCTTCGCGGAAAAGATTACGAGGATAAGGACTTTGTGGTCCGG
** *
55332033 TCAAATTGTGAGCTTTTGGTATGCTTCGCGGAAAAGATTATTAGGATAAGGATTTTGTGGTCCGG
1 TCAAATTGTGAGCTTTTGGTATGCTTCGCGGAAAAGATTACGAGGATAAGGACTTTGTGGTCCGG
55332098 TCAA
1 TCAA
55332102 GTGATGCGGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (65 bp):
TCAAATTGTGAGCTTTTGGTATGCTTCGCGGAAAAGATTACGAGGATAAGGACTTTGTGGTCCGG
Found at i:55333084 original size:10 final size:10
Alignment explanation
Indices: 55333065--55333124 Score: 70
Period size: 10 Copynumber: 6.1 Consensus size: 10
55333055 TGAAATTCTA
55333065 AAAGATAAAT
1 AAAGATAAAT
55333075 ACAA-ATAAAT
1 A-AAGATAAAT
*
55333085 AAAGATAATT
1 AAAGATAAAT
*
55333095 AAATATAAAT
1 AAAGATAAAT
55333105 AAAGATAAAT
1 AAAGATAAAT
*
55333115 GAA-ATAAAT
1 AAAGATAAAT
55333124 A
1 A
55333125 CTAGAATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
9 8 0.19
10 32 0.76
11 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:55333088 original size:20 final size:19
Alignment explanation
Indices: 55333065--55333124 Score: 84
Period size: 20 Copynumber: 3.1 Consensus size: 19
55333055 TGAAATTCTA
55333065 AAAGATAAATACAAATAAAT
1 AAAGATAAATA-AAATAAAT
*
55333085 AAAGATAATTAAATATAAAT
1 AAAGATAAATAAA-ATAAAT
*
55333105 AAAGATAAATGAAATAAAT
1 AAAGATAAATAAAATAAAT
55333124 A
1 A
55333125 CTAGAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.25
20 27 0.75
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (19 bp):
AAAGATAAATAAAATAAAT
Found at i:55333144 original size:23 final size:23
Alignment explanation
Indices: 55333116--55333168 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
55333106 AAGATAAATG
55333116 AAATAAATACTAGAATTAAATCA
1 AAATAAATACTAGAATTAAATCA
* *
55333139 AAATAAATCCTAGAATTAAATCT
1 AAATAAATACTAGAATTAAATCA
55333162 AAATAAA
1 AAATAAA
55333169 AATCCTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.26
Consensus pattern (23 bp):
AAATAAATACTAGAATTAAATCA
Found at i:55333964 original size:96 final size:98
Alignment explanation
Indices: 55333785--55333975 Score: 287
Period size: 96 Copynumber: 2.0 Consensus size: 98
55333775 TTTTAATTTA
* * * * *
55333785 AATTATTTATTTTTACTTAAGAATATATTGAACCTTTTGATGCGAAGAGAGATGACAGCCAAGCA
1 AATTATTTATTATTACTTAAGAACATATCGAACCTTTTGACGAGAAGAGAGATGACAGCCAAGCA
55333850 CCCCACCCCGGTTACTCAGCCCAACACATTCCT
66 CCCCACCCCGGTTACTCAGCCCAACACATTCCT
55333883 AATT-TTTATTATT-CTTAAGAACATATCGAACCTTTTGACGAGAAGAGAGATGACAGCCAAGCA
1 AATTATTTATTATTACTTAAGAACATATCGAACCTTTTGACGAGAAGAGAGATGACAGCCAAGCA
*** *
55333946 CTTTACCTCGGTTACTCAGCCCAACACATT
66 CCCCACCCCGGTTACTCAGCCCAACACATT
55333976 TTTAAAAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
96 72 0.86
97 8 0.10
98 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (98 bp):
AATTATTTATTATTACTTAAGAACATATCGAACCTTTTGACGAGAAGAGAGATGACAGCCAAGCA
CCCCACCCCGGTTACTCAGCCCAACACATTCCT
Found at i:55334497 original size:15 final size:15
Alignment explanation
Indices: 55334477--55334506 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55334467 AAAATTATAT
55334477 GGGCAGCAACAACCA
1 GGGCAGCAACAACCA
55334492 GGGCAGCAACAACCA
1 GGGCAGCAACAACCA
55334507 AATCAGCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.33, G:0.27, T:0.00
Consensus pattern (15 bp):
GGGCAGCAACAACCA
Found at i:55334772 original size:13 final size:11
Alignment explanation
Indices: 55334746--55334788 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 11
55334736 ATCTAAAAAT
55334746 AATAAATAATAA
1 AATAAA-AATAA
55334758 AATAATAAGATAA
1 AATAA-AA-ATAA
55334771 AATAAAAATAAA
1 AATAAAAAT-AA
55334783 AATAAA
1 AATAAA
55334789 GATTGGGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.07
12 16 0.57
13 10 0.36
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:55334774 original size:18 final size:15
Alignment explanation
Indices: 55334741--55334788 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
55334731 TTAATATCTA
55334741 AAAATAATAAATAAT
1 AAAATAATAAATAAT
55334756 AAAATAATAAGATAA-
1 AAAATAATAA-ATAAT
*
55334771 AATAAAAATAAA-AAT
1 AA-AATAATAAATAAT
55334786 AAA
1 AAA
55334789 GATTGGGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 3 0.10
15 15 0.52
16 11 0.38
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAATAAATAAT
Found at i:55342228 original size:46 final size:46
Alignment explanation
Indices: 55342175--55342396 Score: 288
Period size: 46 Copynumber: 4.8 Consensus size: 46
55342165 TATTTGGGCA
55342175 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** * *
55342221 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
* *
55342268 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
55342314 CCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
55342360 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55342397 GCGGGTTACA
Statistics
Matches: 152, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
43 1 0.01
44 2 0.01
45 1 0.01
46 111 0.73
47 32 0.21
48 1 0.01
49 3 0.02
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:55342330 original size:93 final size:94
Alignment explanation
Indices: 55342171--55342396 Score: 325
Period size: 93 Copynumber: 2.4 Consensus size: 94
55342161 AGGATATTTG
* * *
55342171 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
* * *
55342236 TTGAGTCCGAGTTCGAGAGATGTA-AC-TA
66 TTGAGTCCGAGTTC-ACAGATGGATACGAA
55342264 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
** *
55342329 TTGAGTCCGAGTTCACTTATGGATGCGAA
66 TTGAGTCCGAGTTCACAGATGGATACGAA
*
55342358 CGC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55342397 GCGGGTTACA
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
92 41 0.34
93 77 0.64
94 3 0.02
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (94 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCACAGATGGATACGAA
Found at i:55343993 original size:10 final size:10
Alignment explanation
Indices: 55343978--55344023 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
55343968 ATTCTAAAAG
55343978 ATAAATACAA-
1 ATAAATA-AAT
55343988 ATAAATAAAT
1 ATAAATAAAT
*
55343998 ATAATTAAAT
1 ATAAATAAAT
*
55344008 ATAAATAAAG
1 ATAAATAAAT
55344018 ATAAAT
1 ATAAAT
55344024 GAAAACAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
9 2 0.06
10 30 0.94
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:55344033 original size:20 final size:19
Alignment explanation
Indices: 55343974--55344033 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
55343964 TAAAATTCTA
55343974 AAAGATAAATACAAATAAAT
1 AAAGATAAATA-AAATAAAT
* *
55343994 AAATATAATTAAATATAAAT
1 AAAGATAAATAAA-ATAAAT
*
55344014 AAAGATAAATGAAAACAAAT
1 AAAGATAAAT-AAAATAAAT
55344034 CCTAGAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 2 0.06
20 28 0.85
21 3 0.09
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAGATAAATAAAATAAAT
Found at i:55347043 original size:68 final size:67
Alignment explanation
Indices: 55346971--55347120 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
55346961 CATCATGTGT
* * * *
55346971 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
55347033 ATGTAG
62 ATGTAG
** * *
55347039 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
55347104 AG
66 AG
55347106 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
55347121 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:55347076 original size:64 final size:64
Alignment explanation
Indices: 55346995--55347178 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
55346985 AGACATTATG
* *
55346995 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
55347059 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
55347124 AA
63 AA
* * * *
55347126 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
55347179 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:55351490 original size:68 final size:67
Alignment explanation
Indices: 55351418--55351567 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
55351408 CATCATGTGT
* * * *
55351418 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
55351480 ATGTAG
62 ATGTAG
** * *
55351486 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
55351551 AG
66 AG
55351553 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
55351568 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:55351523 original size:64 final size:64
Alignment explanation
Indices: 55351442--55351625 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
55351432 AGACATTATG
* *
55351442 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
55351506 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
55351571 AA
63 AA
* * * *
55351573 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
55351626 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:55356720 original size:19 final size:20
Alignment explanation
Indices: 55356697--55356739 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
55356687 TTAATAGACA
55356697 TAAAAAT-AGAAA-TAAAAC
1 TAAAAATAAGAAATTAAAAC
*
55356715 TAAAAATAAGAAATTAAAAT
1 TAAAAATAAGAAATTAAAAC
55356735 TAAAA
1 TAAAA
55356740 TTAAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 5 0.23
20 10 0.45
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (20 bp):
TAAAAATAAGAAATTAAAAC
Found at i:55358499 original size:25 final size:24
Alignment explanation
Indices: 55358470--55358525 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
55358460 GTAGTAAATC
* *
55358470 AATAAACTAAGATAAAATGAAAGAA
1 AATAAAATAAAATAAAAT-AAAGAA
55358495 AATAATAATAAAATAAAATAAAGAA
1 AATAA-AATAAAATAAAATAAAGAA
55358520 AATAAA
1 AATAAA
55358526 GAACAGGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 16 0.57
26 11 0.39
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (24 bp):
AATAAAATAAAATAAAATAAAGAA
Found at i:55358511 original size:5 final size:5
Alignment explanation
Indices: 55358470--55358525 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
55358460 GTAGTAAATC
* * * * *
55358470 AATAA ACTAA GATAA AATGA AAGAA AATAA TAATAA AATAA AAT-A AAGAA
1 AATAA AATAA AATAA AATAA AATAA AATAA -AATAA AATAA AATAA AATAA
55358520 AATAA A
1 AATAA A
55358526 GAACAGGGGA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
4 3 0.08
5 31 0.79
6 5 0.13
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:55365685 original size:18 final size:17
Alignment explanation
Indices: 55365662--55365711 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
55365652 TAAATAAAGG
55365662 AAAATAAAATTAAAAAT
1 AAAATAAAATTAAAAAT
*
55365679 AAAAATATAATTGAAAAAT
1 -AAAATAAAATT-AAAAAT
*
55365698 ATAATAAAA-TAAAA
1 AAAATAAAATTAAAA
55365712 GGGACTTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 4 0.14
17 1 0.04
18 17 0.61
19 6 0.21
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAATAAAATTAAAAAT
Found at i:55375330 original size:17 final size:17
Alignment explanation
Indices: 55375276--55375335 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
55375266 TGCCAGAAGC
*
55375276 AAATAAAAGAAAAATTAA
1 AAATAAAACAAAAA-TAA
55375294 AAATTAAAACAAAAAT-A
1 AAA-TAAAACAAAAATAA
* *
55375311 AAATACAATAAAAATAA
1 AAATAAAACAAAAATAA
55375328 AAATAAAA
1 AAATAAAA
55375336 ATGGCTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.28
17 12 0.33
18 4 0.11
19 10 0.28
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (17 bp):
AAATAAAACAAAAATAA
Found at i:55375336 original size:12 final size:12
Alignment explanation
Indices: 55375276--55375337 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
55375266 TGCCAGAAGC
55375276 AAATAAAAGA-AA
1 AAATAAAA-ATAA
* *
55375288 AATTAAAAATTA
1 AAATAAAAATAA
*
55375300 AAACAAAAAT-A
1 AAATAAAAATAA
*
55375311 AAAT-ACAATAA
1 AAATAAAAATAA
55375322 AAATAAAAATAA
1 AAATAAAAATAA
55375334 AAAT
1 AAAT
55375338 GGCTAAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
10 4 0.10
11 10 0.25
12 26 0.65
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (12 bp):
AAATAAAAATAA
Found at i:55378276 original size:24 final size:24
Alignment explanation
Indices: 55378246--55378302 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
55378236 GAACGATTCA
55378246 TTTAGTGTTTTAGGAACATGT-TTG
1 TTTAGTGTTTTAGGAACAT-TCTTG
55378270 TTTAGTGTTTTAGGAACATTCTTG
1 TTTAGTGTTTTAGGAACATTCTTG
*
55378294 TTGAGTGTT
1 TTTAGTGTT
55378303 CACAAACGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.19, C:0.05, G:0.25, T:0.51
Consensus pattern (24 bp):
TTTAGTGTTTTAGGAACATTCTTG
Found at i:55379318 original size:30 final size:30
Alignment explanation
Indices: 55379261--55379318 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
55379251 CTTTCGAGCA
* **
55379261 TAGGGGTAAAATGGTCATTTTGTCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
55379291 TAGGGGCAAAATGGTCATTTTACCAAAG
1 TAGGGGCAAAATGGTCATTTTACCAAAG
55379319 ATGTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:55379959 original size:50 final size:50
Alignment explanation
Indices: 55379898--55380170 Score: 337
Period size: 50 Copynumber: 5.5 Consensus size: 50
55379888 CATGTCAGTT
*
55379898 TAAGACCATGTCTGGGACATGGCATCGACATG-GA-TACGCAAGAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGACATGTAAGTACG--AGAGCTAGTG
* *
55379948 TAAGACAATGTCTAGGACATGGCATCGACATGTAAGTACGAGAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGACATGTAAGTACGAGAGCTAGTG
*
55379998 TAAGACCATGTCTGGGACATGGCATCGACATG-GA-TACGCAAGAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGACATGTAAGTACG--AGAGCTAGTG
* *
55380048 TAAGACAATGTCTAGGACATGGCATCGACATGTAAGTACGAGAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGACATGTAAGTACGAGAGCTAGTG
* * * *
55380098 TAAGACCATGTCTGGGACATGGCATC-AGCCTCG-ATGGA-GATAGCCT-GTG
1 TAAGACCATGTCTGGGACATGGCATCGA-CAT-GTAAGTACGAGAG-CTAGTG
55380147 TAAGACCATGTCTGGGACATGGCA
1 TAAGACCATGTCTGGGACATGGCA
55380171 GCGAAAACTT
Statistics
Matches: 199, Mismatches: 15, Indels: 19
0.85 0.06 0.08
Matches are distributed among these distances:
48 4 0.02
49 33 0.17
50 151 0.76
51 3 0.02
52 8 0.04
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.21
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATCGACATGTAAGTACGAGAGCTAGTG
Found at i:55380016 original size:100 final size:100
Alignment explanation
Indices: 55379898--55380123 Score: 452
Period size: 100 Copynumber: 2.3 Consensus size: 100
55379888 CATGTCAGTT
55379898 TAAGACCATGTCTGGGACATGGCATCGACATGGATACGCAAGAGCTAGTGTAAGACAATGTCTAG
1 TAAGACCATGTCTGGGACATGGCATCGACATGGATACGCAAGAGCTAGTGTAAGACAATGTCTAG
55379963 GACATGGCATCGACATGTAAGTACGAGAGCTAGTG
66 GACATGGCATCGACATGTAAGTACGAGAGCTAGTG
55379998 TAAGACCATGTCTGGGACATGGCATCGACATGGATACGCAAGAGCTAGTGTAAGACAATGTCTAG
1 TAAGACCATGTCTGGGACATGGCATCGACATGGATACGCAAGAGCTAGTGTAAGACAATGTCTAG
55380063 GACATGGCATCGACATGTAAGTACGAGAGCTAGTG
66 GACATGGCATCGACATGTAAGTACGAGAGCTAGTG
55380098 TAAGACCATGTCTGGGACATGGCATC
1 TAAGACCATGTCTGGGACATGGCATC
55380124 AGCCTCGATG
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 126 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (100 bp):
TAAGACCATGTCTGGGACATGGCATCGACATGGATACGCAAGAGCTAGTGTAAGACAATGTCTAG
GACATGGCATCGACATGTAAGTACGAGAGCTAGTG
Found at i:55380073 original size:150 final size:149
Alignment explanation
Indices: 55379898--55380170 Score: 376
Period size: 150 Copynumber: 1.8 Consensus size: 149
55379888 CATGTCAGTT
* * *
55379898 TAAGACCATGTCTGGGACATGGCATCGACATG-GA-TACGCAAGAGCTAGTGTAAGACAATGTCT
1 TAAGACAATGTCTAGGACATGGCATCGACATGTAAGTACG--AGAGCTAGTGTAAGACAATGTCT
*
55379961 AGGACATGGCATC-GACAT-GTAAGTACGAGAG-CTAGTGTAAGACCATGTCTGGGACATGGCAT
64 AGGACATGGCATCAG-CATCG-AAGGA-GAGAGCCT-GTGTAAGACCATGTCTGGGACATGGCAT
55380023 CGACATGGATACGCAAGAGCTAGTG
125 CGACATGGATACGCAAGAGCTAGTG
* *
55380048 TAAGACAATGTCTAGGACATGGCATCGACATGTAAGTACGAGAGCTAGTGTAAGACCATGTCTGG
1 TAAGACAATGTCTAGGACATGGCATCGACATGTAAGTACGAGAGCTAGTGTAAGACAATGTCTAG
* * *
55380113 GACATGGCATCAGCCTCGATGGAGATAGCCTGTGTAAGACCATGTCTGGGACATGGCA
66 GACATGGCATCAGCATCGAAGGAGAGAGCCTGTGTAAGACCATGTCTGGGACATGGCA
55380171 GCGAAAACTT
Statistics
Matches: 109, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
149 31 0.28
150 71 0.65
151 3 0.03
152 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.21
Consensus pattern (149 bp):
TAAGACAATGTCTAGGACATGGCATCGACATGTAAGTACGAGAGCTAGTGTAAGACAATGTCTAG
GACATGGCATCAGCATCGAAGGAGAGAGCCTGTGTAAGACCATGTCTGGGACATGGCATCGACAT
GGATACGCAAGAGCTAGTG
Found at i:55387091 original size:13 final size:13
Alignment explanation
Indices: 55387065--55387104 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
55387055 GCTTGGTATG
* *
55387065 GACACACCCGTGT
1 GACACGCCCATGT
55387078 GACACGCCCATGT
1 GACACGCCCATGT
*
55387091 GACGCGCCCATGT
1 GACACGCCCATGT
55387104 G
1 G
55387105 CGATTAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.15
Consensus pattern (13 bp):
GACACGCCCATGT
Found at i:55387123 original size:20 final size:20
Alignment explanation
Indices: 55387098--55387143 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
55387088 TGTGACGCGC
55387098 CCATGTGCGATTAATTCAGG
1 CCATGTGCGATTAATTCAGG
55387118 CCATGTGCGATTAATTCAGG
1 CCATGTGCGATTAATTCAGG
55387138 CCATGT
1 CCATGT
55387144 TCGAGCCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (20 bp):
CCATGTGCGATTAATTCAGG
Found at i:55387461 original size:17 final size:18
Alignment explanation
Indices: 55387439--55387472 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55387429 ATAATTTACA
55387439 GTTTATC-AATACCCCCG
1 GTTTATCAAATACCCCCG
55387456 GTTTATCAAATACCCCC
1 GTTTATCAAATACCCCC
55387473 ACACTTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.35, G:0.09, T:0.29
Consensus pattern (18 bp):
GTTTATCAAATACCCCCG
Found at i:55396083 original size:94 final size:94
Alignment explanation
Indices: 55395874--55396284 Score: 243
Period size: 94 Copynumber: 4.3 Consensus size: 94
55395864 ATGTGAGAGT
* * * * *
55395874 CAGTATAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACGTGTTT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGACGAGGGCCAGTGTAAGACATGTCT
*
55395939 GGGACATGCATCAGCCGCATCATGATAGC
66 AGGACATGCATCAGCCGCATCATGATAGC
* * * ** *
55395968 CCGTGTAAGACCACGTTTGGGACATGGCATCGG-AGTAGAGGTGAGTGCCAGTGTAAGACATGTC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-TAGAGACGAGGGCCAGTGTAAGACATGTC
* * * *
55396032 TAGGATATGCATCGGACTCG-ATGATGTTAGC
65 TAGGACATGCATCAG-C-CGCATCATGATAGC
* * * * * *
55396063 CAGTGTAAGA-CATATCTGGGACAT-GCATCGGC-TACGAGAC-A-TGTCAATATAAAACCATGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATA-GAGACGAGGGCCAGTGTAAGA-CATGT
* * * * * *
55396123 TTGGGACATGGCATC-GACATGGAT-ACGCAAGAGC
64 CTAGGACAT-GCATCAG-C-CGCATCATG--ATAGC
* * * * *
55396157 TAGTGTAAGACCATGTCTAGGACATGAG-ATCAGCAT-GTAAGTACGAGAGCTAGTGTAAGACCA
1 CAGTGTAAGACCATGTCTGGGACATG-GCATCGGCATAG--AG-ACGAGGGCCAGTGTAAGA-CA
* * * *
55396220 TGTCTGGGACATGACATCGGCCTCGAT-AGAGATAGC
61 TGTCTAGGACATG-CATCAGCCGC-ATCA-TGATAGC
55396256 CAGTGTAAGACCATGTCTGGGACATGGCA
1 CAGTGTAAGACCATGTCTGGGACATGGCA
55396285 ACGGTAACTT
Statistics
Matches: 241, Mismatches: 52, Indels: 43
0.72 0.15 0.13
Matches are distributed among these distances:
91 9 0.04
92 20 0.08
93 18 0.07
94 86 0.36
95 32 0.13
96 7 0.03
97 4 0.02
98 3 0.01
99 31 0.13
100 29 0.12
101 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.22
Consensus pattern (94 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGACGAGGGCCAGTGTAAGACATGTCT
AGGACATGCATCAGCCGCATCATGATAGC
Found at i:55396180 original size:50 final size:49
Alignment explanation
Indices: 55396116--55396284 Score: 175
Period size: 50 Copynumber: 3.4 Consensus size: 49
55396106 TCAATATAAA
*
55396116 ACCATGTTTGGGACATGGCATCGACATGGATACGCAAGAGCTAGTGTAAG
1 ACCATGTCTGGGACATGGCATCGACATGGATACG-AAGAGCTAGTGTAAG
* *
55396166 ACCATGTCTAGGACATGAG-ATC-AGCATGTAAGTACG-AGAGCTAGTGTAAG
1 ACCATGTCTGGGACATG-GCATCGA-CATG-GA-TACGAAGAGCTAGTGTAAG
* * * * * *
55396216 ACCATGTCTGGGACATGACATCGGCCTCGATA-GAGATAGCCAGTGTAAG
1 ACCATGTCTGGGACATGGCATCGACATGGATACGA-AGAGCTAGTGTAAG
55396265 ACCATGTCTGGGACATGGCA
1 ACCATGTCTGGGACATGGCA
55396285 ACGGTAACTT
Statistics
Matches: 99, Mismatches: 12, Indels: 17
0.77 0.09 0.13
Matches are distributed among these distances:
47 1 0.01
48 2 0.02
49 33 0.33
50 57 0.58
51 2 0.02
52 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (49 bp):
ACCATGTCTGGGACATGGCATCGACATGGATACGAAGAGCTAGTGTAAG
Found at i:55397125 original size:55 final size:55
Alignment explanation
Indices: 55397031--55397161 Score: 140
Period size: 55 Copynumber: 2.4 Consensus size: 55
55397021 CTCAAACTTT
* * * * * *
55397031 TAAA-TCAGTATTGTCCACAGTTAGGCCACACGGGTGTGTGCCATAGCCGTG-TC
1 TAAAGTCAGTATTGCCCACGGGTAGGCCACAAGGGCGTGTGCCATAGCCGTGCCC
* * *
55397084 TATAAGTCAGTATTGCCCACGGGTAGGCTACAAGGGCGTGTGTCATGGCCGTGCCC
1 TA-AAGTCAGTATTGCCCACGGGTAGGCCACAAGGGCGTGTGCCATAGCCGTGCCC
* *
55397140 TAAAGTCAGTGTTGCACACGGG
1 TAAAGTCAGTATTGCCCACGGG
55397162 CTGAGGACGT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
53 2 0.03
54 2 0.03
55 57 0.89
56 3 0.05
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (55 bp):
TAAAGTCAGTATTGCCCACGGGTAGGCCACAAGGGCGTGTGCCATAGCCGTGCCC
Found at i:55397697 original size:3 final size:3
Alignment explanation
Indices: 55397689--55397732 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
55397679 TATTAAAATG
55397689 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
55397733 GATTAAGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:55400495 original size:19 final size:19
Alignment explanation
Indices: 55400450--55400510 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
55400440 ATCTAATTAC
55400450 AAATATTTAATTATTATATTT
1 AAATATTTAATTA-TA-ATTT
*
55400471 AAATATTTAAATATAATTT
1 AAATATTTAATTATAATTT
*
55400490 ATATATTCTAATTA-AATTT
1 AAATATT-TAATTATAATTT
55400509 AA
1 AA
55400511 TAAATAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 7 0.20
21 12 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAATTATAATTT
Found at i:55400801 original size:13 final size:13
Alignment explanation
Indices: 55400738--55400801 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
55400728 ACACTTAAAT
*
55400738 TTTTCCAAAGCAC
1 TTTTCAAAAGCAC
* *
55400751 TTCTCAAAAGTA-
1 TTTTCAAAAGCAC
*
55400763 TTTCTCAAAAACAC
1 TTT-TCAAAAGCAC
* *
55400777 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
55400790 TTTTCAAAAGCA
1 TTTTCAAAAGCA
55400802 ATAAAAAACT
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
12 2 0.05
13 33 0.87
14 3 0.08
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:55412418 original size:16 final size:17
Alignment explanation
Indices: 55412391--55412435 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
55412381 GAAAAAAGAC
55412391 AATAAA-ATAATA-GAA
1 AATAAATATAATATGAA
55412406 AATAAATATAATATGAA
1 AATAAATATAATATGAA
*
55412423 AAT-GATATAATAT
1 AATAAATATAATAT
55412436 ATATATGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (17 bp):
AATAAATATAATATGAA
Found at i:55413071 original size:19 final size:18
Alignment explanation
Indices: 55413021--55413071 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
55413011 TTTTTTAACC
*
55413021 ATTTATGAACT-TTTTTT
1 ATTTTTGAACTATTTTTT
* *
55413038 ATTTTTAAATATATTTTTT
1 ATTTTTGAA-CTATTTTTT
55413057 ATTTTTTGAACTATT
1 A-TTTTTGAACTATT
55413072 ATGAAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 7 0.27
18 1 0.04
19 11 0.42
20 7 0.27
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (18 bp):
ATTTTTGAACTATTTTTT
Found at i:55422375 original size:44 final size:44
Alignment explanation
Indices: 55422312--55422407 Score: 156
Period size: 44 Copynumber: 2.2 Consensus size: 44
55422302 TCACAGCTCC
* * *
55422312 TGTGAGCAGCATCGTGTAATGGTTAATGTCTGATTTATAGCTTG
1 TGTGAGCAGCATCGTGTAATGGTTAATGTCTAATTCATAGCTGG
*
55422356 TGTGAGTAGCATCGTGTAATGGTTAATGTCTAATTCATAGCTGG
1 TGTGAGCAGCATCGTGTAATGGTTAATGTCTAATTCATAGCTGG
55422400 TGTGAGCA
1 TGTGAGCA
55422408 TTATTATCCC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.36
Consensus pattern (44 bp):
TGTGAGCAGCATCGTGTAATGGTTAATGTCTAATTCATAGCTGG
Found at i:55425137 original size:11 final size:12
Alignment explanation
Indices: 55425112--55425141 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
55425102 CTAGCTTGGT
55425112 TAGTTTAATTTA
1 TAGTTTAATTTA
55425124 TAGTTTAA-TTA
1 TAGTTTAATTTA
55425135 TAGTTTA
1 TAGTTTA
55425142 TAAACCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (12 bp):
TAGTTTAATTTA
Found at i:55427252 original size:25 final size:25
Alignment explanation
Indices: 55427218--55427269 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
55427208 GTAACACGCT
55427218 CATAGTTTTCATTTTCTATGAAAAG
1 CATAGTTTTCATTTTCTATGAAAAG
55427243 CATAGTTTTCATTTTCTATGAAAAG
1 CATAGTTTTCATTTTCTATGAAAAG
55427268 CA
1 CA
55427270 ATCATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (25 bp):
CATAGTTTTCATTTTCTATGAAAAG
Found at i:55428626 original size:3 final size:3
Alignment explanation
Indices: 55428620--55428644 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55428610 TCCTCTTCTA
55428620 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
55428645 TTCTTCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:55430336 original size:18 final size:18
Alignment explanation
Indices: 55430300--55430343 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
55430290 ATCTACCTCT
* *
55430300 TCCTCCTCTTCATCCTCA
1 TCCTCCTCCTCATCATCA
55430318 TCCTCCTCCTCATCATCA
1 TCCTCCTCCTCATCATCA
*
55430336 TCATCCTC
1 TCCTCCTC
55430344 TACCCCATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.50, G:0.00, T:0.36
Consensus pattern (18 bp):
TCCTCCTCCTCATCATCA
Found at i:55430352 original size:21 final size:21
Alignment explanation
Indices: 55430300--55430361 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
55430290 ATCTACCTCT
* *
55430300 TCCTCCTCTTCATCCTCATCC
1 TCCTCCCCATCATCCTCATCC
* *
55430321 TCCTCCTCATCATCATCATCC
1 TCCTCCCCATCATCCTCATCC
*
55430342 T-CTACCCCATCTTCCTCATC
1 TCCT-CCCCATCATCCTCATC
55430362 ATCATCACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (21 bp):
TCCTCCCCATCATCCTCATCC
Found at i:55430688 original size:15 final size:15
Alignment explanation
Indices: 55430668--55430712 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
55430658 CACTCCCAGG
55430668 ATCATCTTCATCTTC
1 ATCATCTTCATCTTC
* *
55430683 ATCATCCTCATCCTC
1 ATCATCTTCATCTTC
*
55430698 ATCCTCTTCATCTTC
1 ATCATCTTCATCTTC
55430713 CTCTTCCTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.18, C:0.40, G:0.00, T:0.42
Consensus pattern (15 bp):
ATCATCTTCATCTTC
Found at i:55435950 original size:34 final size:35
Alignment explanation
Indices: 55435912--55435978 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
55435902 TTAATTTTGA
**
55435912 AAAGTAATAA-TTATTATTCAATAGATACATTTAG
1 AAAGTAATAATTTACCATTCAATAGATACATTTAG
* *
55435946 AAAGTGATAATTTACCATTCAATGGATACATTT
1 AAAGTAATAATTTACCATTCAATAGATACATTT
55435979 TCATAAGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 9 0.32
35 19 0.68
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (35 bp):
AAAGTAATAATTTACCATTCAATAGATACATTTAG
Found at i:55445338 original size:34 final size:36
Alignment explanation
Indices: 55445289--55445363 Score: 127
Period size: 35 Copynumber: 2.1 Consensus size: 36
55445279 CACTTACTCA
55445289 ATTTTGAAAAGTGATAA-TTATCATTCAATAGATAC
1 ATTTTGAAAAGTGATAATTTATCATTCAATAGATAC
*
55445324 ATTTTG-AAAGTGATAATTTATCATTCAATGGATAC
1 ATTTTGAAAAGTGATAATTTATCATTCAATAGATAC
55445359 ATTTT
1 ATTTT
55445364 CATTGGACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 10 0.26
35 28 0.74
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (36 bp):
ATTTTGAAAAGTGATAATTTATCATTCAATAGATAC
Found at i:55450000 original size:42 final size:42
Alignment explanation
Indices: 55449922--55450001 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
55449912 GTGCAGGTTT
* * * *
55449922 CACACGGCTGAGACATACGCCCGTGTTCTAGGCCGTGTAGCA
1 CACACGGCTAAGACACACACCCGTGTTCTAGCCCGTGTAGCA
55449964 CACACGGCTAAGACACACACCCGTG-TCTATGCCCGTGT
1 CACACGGCTAAGACACACACCCGTGTTCTA-GCCCGTGT
55450002 GCTCAATTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.12
42 29 0.88
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.19
Consensus pattern (42 bp):
CACACGGCTAAGACACACACCCGTGTTCTAGCCCGTGTAGCA
Found at i:55450588 original size:16 final size:18
Alignment explanation
Indices: 55450556--55450594 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
55450546 ATTTTGGAAT
*
55450556 TAAAAATTATATTAAATG
1 TAAAAATTATATTAAATA
55450574 TAAAAA-TAT-TTAAATA
1 TAAAAATTATATTAAATA
55450590 TAAAA
1 TAAAA
55450595 TGTGAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 3 0.15
18 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAAATTATATTAAATA
Found at i:55456569 original size:34 final size:35
Alignment explanation
Indices: 55456531--55456597 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
55456521 TGAATTTTGG
*
55456531 AAAGTGATAA-TTATCATTCAATAGATACATTTAT
1 AAAGTGATAATTTACCATTCAATAGATACATTTAT
*
55456565 AAAGTGATAATTTACCATTCAATGGATACATTT
1 AAAGTGATAATTTACCATTCAATAGATACATTT
55456598 CCATGGGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 10 0.33
35 20 0.67
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (35 bp):
AAAGTGATAATTTACCATTCAATAGATACATTTAT
Found at i:55466949 original size:5 final size:5
Alignment explanation
Indices: 55466939--55466967 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
55466929 TTGTGTGATC
55466939 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
55466968 GTTTCACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:55467198 original size:5 final size:5
Alignment explanation
Indices: 55467188--55467216 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
55467178 TTGTGTGATC
55467188 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
55467217 GTTTCACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:55467296 original size:249 final size:249
Alignment explanation
Indices: 55466858--55467354 Score: 994
Period size: 249 Copynumber: 2.0 Consensus size: 249
55466848 ATTTGAGTCA
55466858 AATTTTTCGACATAGTGAATTTTCTTCTCCTCTGCCCGTGGTTTTTTCCCGAAAGGGTTTCTACG
1 AATTTTTCGACATAGTGAATTTTCTTCTCCTCTGCCCGTGGTTTTTTCCCGAAAGGGTTTCTACG
55466923 TAAAATTTGTGTGATCTTTATTTTATTTATTTTATTTTATTTTATGTTTCACAAATTGGTATCCG
66 TAAAATTTGTGTGATCTTTATTTTATTTATTTTATTTTATTTTATGTTTCACAAATTGGTATCCG
55466988 AGCTTCTGGGTTATTCATCTCGATCGCGGTAATGGCATCTTTGAAGTATGAAATTCCGCTGTTGG
131 AGCTTCTGGGTTATTCATCTCGATCGCGGTAATGGCATCTTTGAAGTATGAAATTCCGCTGTTGG
55467053 ATCGCAACACCAGATTTGTGTTGCGGCAAATTAAGATGCAAGCAGTTCTTGCAT
196 ATCGCAACACCAGATTTGTGTTGCGGCAAATTAAGATGCAAGCAGTTCTTGCAT
55467107 AATTTTTCGACATAGTGAATTTTCTTCTCCTCTGCCCGTGGTTTTTTCCCGAAAGGGTTTCTACG
1 AATTTTTCGACATAGTGAATTTTCTTCTCCTCTGCCCGTGGTTTTTTCCCGAAAGGGTTTCTACG
55467172 TAAAATTTGTGTGATCTTTATTTTATTTATTTTATTTTATTTTATGTTTCACAAATTGGTATCCG
66 TAAAATTTGTGTGATCTTTATTTTATTTATTTTATTTTATTTTATGTTTCACAAATTGGTATCCG
55467237 AGCTTCTGGGTTATTCATCTCGATCGCGGTAATGGCATCTTTGAAGTATGAAATTCCGCTGTTGG
131 AGCTTCTGGGTTATTCATCTCGATCGCGGTAATGGCATCTTTGAAGTATGAAATTCCGCTGTTGG
55467302 ATCGCAACACCAGATTTGTGTTGCGGCAAATTAAGATGCAAGCAGTTCTTGCA
196 ATCGCAACACCAGATTTGTGTTGCGGCAAATTAAGATGCAAGCAGTTCTTGCA
55467355 CAGATGGATC
Statistics
Matches: 248, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
249 248 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (249 bp):
AATTTTTCGACATAGTGAATTTTCTTCTCCTCTGCCCGTGGTTTTTTCCCGAAAGGGTTTCTACG
TAAAATTTGTGTGATCTTTATTTTATTTATTTTATTTTATTTTATGTTTCACAAATTGGTATCCG
AGCTTCTGGGTTATTCATCTCGATCGCGGTAATGGCATCTTTGAAGTATGAAATTCCGCTGTTGG
ATCGCAACACCAGATTTGTGTTGCGGCAAATTAAGATGCAAGCAGTTCTTGCAT
Found at i:55470948 original size:5 final size:5
Alignment explanation
Indices: 55470938--55470969 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
55470928 TTGTGTGTTC
55470938 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
55470970 TCACAGGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:55470952 original size:9 final size:9
Alignment explanation
Indices: 55470938--55470968 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
55470928 TTGTGTGTTC
55470938 TTTATTTTA
1 TTTATTTTA
55470947 TTTATTTTA
1 TTTATTTTA
55470956 TTTTATTTTA
1 -TTTATTTTA
55470966 TTT
1 TTT
55470969 TTCACAGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:55475269 original size:5 final size:5
Alignment explanation
Indices: 55475259--55475291 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
55475249 GGAAGCTGTG
55475259 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA- AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
55475292 GAACACACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:55480407 original size:16 final size:16
Alignment explanation
Indices: 55480386--55480453 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
55480376 TTTGGTTCGC
55480386 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
55480402 TGTATTGGATTAGAGC
1 TGTATTGGATTAGAGG
55480418 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
55480434 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
55480450 TGTA
1 TGTA
55480454 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.25, C:0.01, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:55480716 original size:18 final size:17
Alignment explanation
Indices: 55480689--55480723 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55480679 TTATTTTTAA
*
55480689 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55480707 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55480724 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55480789 original size:157 final size:157
Alignment explanation
Indices: 55480576--55480892 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
55480566 TAGAATACCC
*
55480576 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
* * *
55480641 TTATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTTTTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
55480706 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
55480733 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
* *
55480798 ATATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
55480863 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
55480890 TTA
1 TTA
55480893 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:55480863 original size:16 final size:16
Alignment explanation
Indices: 55480826--55480867 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
55480816 TTAATCATAT
*
55480826 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
55480842 TT-AAATATATTATAA
1 TTAAAATATATTATAA
55480857 TTAAAATATAT
1 TTAAAATATAT
55480868 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:55480874 original size:14 final size:15
Alignment explanation
Indices: 55480835--55480876 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55480825 TTTAAACATA
*
55480835 ATTATTATTAAATAT
1 ATTATAATTAAATAT
55480850 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
55480864 A-TATAATTTAATA
1 ATTATAATTAAATA
55480877 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:55483897 original size:11 final size:11
Alignment explanation
Indices: 55483881--55483906 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55483871 TCGGGAGGCA
55483881 AAGGTAGAACG
1 AAGGTAGAACG
55483892 AAGGTAGAACG
1 AAGGTAGAACG
55483903 AAGG
1 AAGG
55483907 AAGAGGCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.08, G:0.38, T:0.08
Consensus pattern (11 bp):
AAGGTAGAACG
Found at i:55486756 original size:30 final size:30
Alignment explanation
Indices: 55486720--55486780 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
55486710 ACAAAGCGTG
55486720 AGTTTTCTTTTAAAACTCAGTATGTAACCC
1 AGTTTTCTTTTAAAACTCAGTATGTAACCC
55486750 AGTTTTCTTTTAAAACTCAGTATGTAACCC
1 AGTTTTCTTTTAAAACTCAGTATGTAACCC
55486780 A
1 A
55486781 TACGTTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (30 bp):
AGTTTTCTTTTAAAACTCAGTATGTAACCC
Found at i:55488386 original size:50 final size:50
Alignment explanation
Indices: 55488311--55488550 Score: 339
Period size: 50 Copynumber: 4.9 Consensus size: 50
55488301 TGATGCTAGG
*
55488311 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGGATCGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
* *
55488361 GAGATATGAGAGCTAGTGTAAGACCATATTTGGGACATGGCATCGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
55488411 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CT-
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
* * *
55488459 -TGATATGTG-TC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
* * * *
55488506 GATATACGAGAG-TCAGTGTAAGACCATGTCTGGAACATGGTATCG
1 GAGATATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCG
55488551 ACTTTGATGG
Statistics
Matches: 169, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
45 32 0.19
46 3 0.02
47 7 0.04
48 5 0.03
49 2 0.01
50 120 0.71
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (50 bp):
GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
Found at i:55488525 original size:95 final size:94
Alignment explanation
Indices: 55488311--55488600 Score: 330
Period size: 95 Copynumber: 3.0 Consensus size: 94
55488301 TGATGCTAGG
* * * *
55488311 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGGATCGGCCTCGAGATATGAGAGCTA
1 GAGATACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CT--TGATAT--GAGCCA
*
55488376 GTGTAAGACCATATTTGGGACATGGCATCGGCCTC
61 GTGTAAGACCAT-GTTGGGACATGGCATCGGCCTC
* * *
55488411 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATGTGTCAGTGTA
1 GAGATACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATGAGCCAGTGTA
55488476 AGACCATGTCTGGGACATGGCATCGGCCTC
66 AGACCATGT-TGGGACATGGCATCGGCCTC
* * * * *
55488506 GATATACGAGAG-TCAGTGTAAGACCATGTCTGGAACATGGTATCGACTTTGATGGGTGAGCCAG
1 GAGATACGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAT--ATGAGCCAG
* *
55488570 TGTAAGACCATGTTCGGTACATGGCGTCGGC
62 TGTAAGACCATGTT-GGGACATGGCATCGGC
55488601 ACTTTACCCT
Statistics
Matches: 168, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
94 2 0.01
95 75 0.45
96 5 0.03
97 6 0.04
98 33 0.20
99 2 0.01
100 45 0.27
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (94 bp):
GAGATACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATGAGCCAGTGTA
AGACCATGTTGGGACATGGCATCGGCCTC
Found at i:55489943 original size:4 final size:4
Alignment explanation
Indices: 55489934--55489958 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55489924 GTCTAGGGAC
55489934 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
55489959 GATATGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:55493019 original size:27 final size:28
Alignment explanation
Indices: 55492990--55493092 Score: 126
Period size: 27 Copynumber: 3.8 Consensus size: 28
55492980 AGACCCCGAT
55492990 TTGTAAAATTACCGAAATACCCTTGAT-
1 TTGTAAAATTACCGAAATACCCTTGATA
*
55493017 TTGTAAAATTA-TGAAAATACCCTTG-TGA
1 TTGTAAAATTACCG-AAATACCCTTGAT-A
55493045 -TGTAAAATTACCGAAATACCCTT-ATA
1 TTGTAAAATTACCGAAATACCCTTGATA
* *
55493071 GTGTAAAATTACCAAAATACCC
1 TTGTAAAATTACCGAAATACCC
55493093 CCATAAGGTA
Statistics
Matches: 67, Mismatches: 3, Indels: 12
0.82 0.04 0.15
Matches are distributed among these distances:
26 3 0.04
27 63 0.94
28 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (28 bp):
TTGTAAAATTACCGAAATACCCTTGATA
Found at i:55493103 original size:27 final size:27
Alignment explanation
Indices: 55493045--55493106 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
55493035 ACCCTTGTGA
* **
55493045 TGTAAAATTACCGAAATACCCTTATAG
1 TGTAAAATTACCAAAATACCCCCATAG
55493072 TGTAAAATTACCAAAATACCCCCATAAG
1 TGTAAAATTACCAAAATACCCCCAT-AG
55493100 -GTAAAAT
1 TGTAAAAT
55493107 GTCTGTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 29 0.94
28 2 0.06
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (27 bp):
TGTAAAATTACCAAAATACCCCCATAG
Found at i:55493104 original size:54 final size:54
Alignment explanation
Indices: 55492992--55493106 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
55492982 ACCCCGATTT
* ** *** * *
55492992 GTAAAATTACCGAAATACCCTTGATTTGTAAAATTATGAAAATACCCTTGTGAT
1 GTAAAATTACCGAAATACCCTTGATGTGTAAAATTACCAAAATACCCCCATAAG
55493046 GTAAAATTACCGAAATACCCTT-ATAGTGTAAAATTACCAAAATACCCCCATAAG
1 GTAAAATTACCGAAATACCCTTGAT-GTGTAAAATTACCAAAATACCCCCATAAG
55493100 GTAAAAT
1 GTAAAAT
55493107 GTCTGTTTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 2 0.04
54 50 0.96
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (54 bp):
GTAAAATTACCGAAATACCCTTGATGTGTAAAATTACCAAAATACCCCCATAAG
Found at i:55493612 original size:27 final size:27
Alignment explanation
Indices: 55493511--55493613 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 27
55493501 TATGTTGATT
* ** *
55493511 ATGGCTTTGTGCAAATCTTATTTAC-C
1 ATGGCTATGTGCTGATCATATTTACTC
* *
55493537 AGTGGCTATGTGTCT-ATCATATTTATTG
1 A-TGGCTATGTG-CTGATCATATTTACTC
*
55493565 ATGGCTCTGTG-TCGATCATATTTACTC
1 ATGGCTATGTGCT-GATCATATTTACTC
* *
55493592 ATGGCTGTGTGCTGATTATATT
1 ATGGCTATGTGCTGATCATATT
55493614 ACTGTCGCTA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 56 0.92
28 3 0.05
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (27 bp):
ATGGCTATGTGCTGATCATATTTACTC
Found at i:55493914 original size:32 final size:32
Alignment explanation
Indices: 55493878--55493946 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
55493868 ATTTATGAGA
*
55493878 TCTGTCACT-GTATTGGGCTTAGGCCCACTTG-T
1 TCTGTCACTGGT-TTGGGC-TAGGCCCAATTGAT
* *
55493910 TCTGTTATTGGTTTGGGCTAGGCCCAATTGAT
1 TCTGTCACTGGTTTGGGCTAGGCCCAATTGAT
55493942 TCTGT
1 TCTGT
55493947 TATGGGCTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 11 0.34
32 19 0.59
33 2 0.06
ACGTcount: A:0.13, C:0.20, G:0.26, T:0.41
Consensus pattern (32 bp):
TCTGTCACTGGTTTGGGCTAGGCCCAATTGAT
Found at i:55495068 original size:15 final size:15
Alignment explanation
Indices: 55495048--55495077 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55495038 CTATGCATGC
*
55495048 AAAACATGAAAGACA
1 AAAACATAAAAGACA
55495063 AAAACATAAAAGACA
1 AAAACATAAAAGACA
55495078 TAGTAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAACATAAAAGACA
Found at i:55496688 original size:32 final size:32
Alignment explanation
Indices: 55496652--55496712 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
55496642 TTTGTATGTG
55496652 TATTTAAAATATTTCACATATAAAAATAATGA
1 TATTTAAAATATTTCACATATAAAAATAATGA
*
55496684 TATTTAAAATATTTCACATATAAATATAA
1 TATTTAAAATATTTCACATATAAAAATAA
55496713 AAATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (32 bp):
TATTTAAAATATTTCACATATAAAAATAATGA
Done.