Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 146 of 378
Found at i:41855138 original size:24 final size:26
Alignment explanation
Indices: 41855110--41855174 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
41855100 TGTGTAAGTT
41855110 GAATTAAAT-TTCAA-A-TAAATTATG
1 GAATTAAATCTT-AAGAGTAAATTATG
*
41855134 GAATTAAATCTTAATGAGTATATTATG
1 GAATTAAATCTTAA-GAGTAAATTATG
41855161 GAATTAAATCTTAA
1 GAATTAAATCTTAA
41855175 TTAGTATATG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
24 11 0.31
25 2 0.06
26 1 0.03
27 22 0.61
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (26 bp):
GAATTAAATCTTAAGAGTAAATTATG
Found at i:41855163 original size:27 final size:27
Alignment explanation
Indices: 41855128--41855183 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
41855118 TTTCAAATAA
41855128 ATTATGGAATTAAATCTTAATGAGTAT
1 ATTATGGAATTAAATCTTAATGAGTAT
*
41855155 ATTATGGAATTAAATCTTAATTAGTAT
1 ATTATGGAATTAAATCTTAATGAGTAT
41855182 AT
1 AT
41855184 GTTCATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (27 bp):
ATTATGGAATTAAATCTTAATGAGTAT
Found at i:41860298 original size:49 final size:49
Alignment explanation
Indices: 41860238--41860407 Score: 152
Period size: 49 Copynumber: 3.6 Consensus size: 49
41860228 TGTATATGTC
*
41860238 AGTGTAGGACCTGTCTGAGACATGGCATCGACACAGATAAGTGAGAGCT
1 AGTGTAAGACCTGTCTGAGACATGGCATCGACACAGATAAGTGAGAGCT
* * * * * * * *
41860287 AGTGTAAGACCTATCTGGGACATGGCATC-A-GC--TTGAG-GTGTGTT
1 AGTGTAAGACCTGTCTGAGACATGGCATCGACACAGATAAGTGAGAGCT
* * * * *
41860331 AGTGTAAGACCTGTCTGGGATATGGAATCGACATAGATAAGTGAGAGCC
1 AGTGTAAGACCTGTCTGAGACATGGCATCGACACAGATAAGTGAGAGCT
* * *
41860380 AGTATAAGACCTGTCTAAGGCATGGCAT
1 AGTGTAAGACCTGTCTGAGACATGGCAT
41860408 TAGCCTCAAT
Statistics
Matches: 90, Mismatches: 26, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
44 30 0.33
45 4 0.04
47 1 0.01
48 4 0.04
49 51 0.57
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGAGACATGGCATCGACACAGATAAGTGAGAGCT
Found at i:41860404 original size:93 final size:96
Alignment explanation
Indices: 41860238--41860486 Score: 276
Period size: 93 Copynumber: 2.6 Consensus size: 96
41860228 TGTATATGTC
* * * *
41860238 AGTGTAGGACCTGTCTGAGACATGGCATCGACACAGATAAGTGAGAGCTAGTGTAAGACCTATCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATAGATAAGTGAGAGCCAGTGTAAGACCTATCT
* **
41860303 GGGACATGGCATCAG-CT-TG-AGGTGTGTT
66 AGGACATGGCATCAGCCTATGTAGGTAAGTT
* * * *
41860331 AGTGTAAGACCTGTCTGGGATATGGAATCGACATAGATAAGTGAGAGCCAGTATAAGACCTGTCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATAGATAAGTGAGAGCCAGTGTAAGACCTATCT
* *
41860396 AAGG-CATGGCATTAGCCTCAATGTATGTAAGTT
66 -AGGACATGGCATCAGCCT--ATGTAGGTAAGTT
* * * *
41860429 AGTATAAGACCTGTTTGGAACATGGCATCGACTTAGAT--GTGAGAGCCAGTGTAAGACC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATAGATAAGTGAGAGCCAGTGTAAGACC
41860487 ATGTTTGGAA
Statistics
Matches: 130, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
93 67 0.52
94 4 0.03
96 19 0.15
97 2 0.02
98 38 0.29
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (96 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACATAGATAAGTGAGAGCCAGTGTAAGACCTATCT
AGGACATGGCATCAGCCTATGTAGGTAAGTT
Found at i:41862903 original size:28 final size:28
Alignment explanation
Indices: 41862841--41862941 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
41862831 GACAAGATTG
* * *
41862841 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTGTATA
41862871 GCACTAAGTGTGCGAGTTTGATTGTATA
1 GCACTAAGTGTGCGAGTTTGATTGTATA
**
41862899 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TGTATA
41862928 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41862942 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 25 0.39
29 18 0.28
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTGTATA
Found at i:41869190 original size:28 final size:28
Alignment explanation
Indices: 41869128--41869228 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
41869118 GACAAGATTG
* * *
41869128 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTGTATA
41869158 GCACTAAGTGTGCGAGTTTGATTGTATA
1 GCACTAAGTGTGCGAGTTTGATTGTATA
**
41869186 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TGTATA
41869215 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41869229 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 25 0.39
29 18 0.28
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTGTATA
Found at i:41878000 original size:13 final size:13
Alignment explanation
Indices: 41877982--41878006 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41877972 CTTGGTAGGG
41877982 ACACGCCCGTGTT
1 ACACGCCCGTGTT
41877995 ACACGCCCGTGT
1 ACACGCCCGTGT
41878007 GCGATTACTT
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:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
ACACGCCCGTGTT
Found at i:41887565 original size:128 final size:132
Alignment explanation
Indices: 41887333--41887571 Score: 450
Period size: 128 Copynumber: 1.8 Consensus size: 132
41887323 CTTTGACACA
41887333 ATCCACTTAGAAGCTGGAACTGTAAGTTCCTCAAGAATATCTTGCAAATTTTCAGGCTTGATTTG
1 ATCCACTTAGAAGCTGGAACTGTAAGTTCCTCAAGAATATCTTGCAAATTTTCAGGCTTGATTTG
41887398 CTCATCAAGGAAGAATAATCATTTTTTTTTTAAATTAGGTAATTCAGAATAACAAGTCCTTGCTT
66 CTCATCAAGGAAGAATAATCATTTTTTTTTTAAATTAGGTAATTCAGAATAACAAGTCCTTGCTT
41887463 TG
131 TG
41887465 ATCCACTTAGAAGCT-GAACT-T-AGTTCCTCAAGAATAT-TTGCAAATTTTCAGGCTTGATTTG
1 ATCCACTTAGAAGCTGGAACTGTAAGTTCCTCAAGAATATCTTGCAAATTTTCAGGCTTGATTTG
41887526 CTCATCAAGGAAGAATAATCATTTTTTTTTTAAATTAGGTAATTCA
66 CTCATCAAGGAAGAATAATCATTTTTTTTTTAAATTAGGTAATTCA
41887572 AAGAACTCAT
Statistics
Matches: 107, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
128 70 0.65
129 16 0.15
130 1 0.01
131 5 0.05
132 15 0.14
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (132 bp):
ATCCACTTAGAAGCTGGAACTGTAAGTTCCTCAAGAATATCTTGCAAATTTTCAGGCTTGATTTG
CTCATCAAGGAAGAATAATCATTTTTTTTTTAAATTAGGTAATTCAGAATAACAAGTCCTTGCTT
TG
Found at i:41888968 original size:29 final size:30
Alignment explanation
Indices: 41888911--41888968 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
41888901 CTTTTAAAAA
* * *
41888911 TATTTACAAAAAGAGGCATCTAATTTTTAT
1 TATTTACAAAAAGAGGCAACCAAATTTTAT
41888941 TATTTACAAAAAGA-GCAACCAAATTTTA
1 TATTTACAAAAAGAGGCAACCAAATTTTA
41888969 AAAACACTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (30 bp):
TATTTACAAAAAGAGGCAACCAAATTTTAT
Found at i:41898846 original size:33 final size:33
Alignment explanation
Indices: 41898804--41898878 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
41898794 TGAATAATAT
*
41898804 AGTATCAGTACAGTCTAGGCCAAAGCCCTATTC
1 AGTATCAGTACAGTCTAGGCCAAAGCCCTATAC
* *
41898837 AGTATCAGTACAGTCTGGGCCTAAGCCCTATAC
1 AGTATCAGTACAGTCTAGGCCAAAGCCCTATAC
*
41898870 AGTAGCAGT
1 AGTATCAGT
41898879 GTAGGCCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (33 bp):
AGTATCAGTACAGTCTAGGCCAAAGCCCTATAC
Found at i:41899098 original size:27 final size:27
Alignment explanation
Indices: 41899061--41899132 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
41899051 AGCATAGCTG
*
41899061 CCAGAAACAGTAAATGTGGCAAAGCCA
1 CCAGTAACAGTAAATGTGGCAAAGCCA
* * * *
41899088 CCTGTATCAGTAATTGTGGCATAGCCA
1 CCAGTAACAGTAAATGTGGCAAAGCCA
*
41899115 CCAGTAACAGTGAATGTG
1 CCAGTAACAGTAAATGTG
41899133 ACATACTCAC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (27 bp):
CCAGTAACAGTAAATGTGGCAAAGCCA
Found at i:41899137 original size:27 final size:26
Alignment explanation
Indices: 41899047--41899137 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 26
41899037 AGAAATAATG
* ** *
41899047 ATGTAGCATAGCTGCCAGAAACAGTAA
1 ATGTGGCATAGCCACCAGTAACAGT-A
* * *
41899074 ATGTGGCAAAGCCACCTGTATCAGTA
1 ATGTGGCATAGCCACCAGTAACAGTA
41899100 ATTGTGGCATAGCCACCAGTAACAGTGA
1 A-TGTGGCATAGCCACCAGTAACAGT-A
*
41899128 ATGTGACATA
1 ATGTGGCATA
41899138 CTCACCCGTA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
26 2 0.04
27 47 0.92
28 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
ATGTGGCATAGCCACCAGTAACAGTA
Found at i:41899310 original size:27 final size:27
Alignment explanation
Indices: 41899279--41899330 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
41899269 GGAACATAAG
* *
41899279 GGTATAATCGTCATTTTACCATACAAA
1 GGTATAAGCGTCACTTTACCATACAAA
* *
41899306 GGTATTAGCGTCACTTTACCCTACA
1 GGTATAAGCGTCACTTTACCATACA
41899331 GGAGCTTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (27 bp):
GGTATAAGCGTCACTTTACCATACAAA
Found at i:41899350 original size:27 final size:27
Alignment explanation
Indices: 41899320--41899378 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
41899310 TTAGCGTCAC
*
41899320 TTTACCCTACAGGAGCTTTACGGT-TAT
1 TTTACCCTACAGGAGCATTACGGTCT-T
*
41899347 TTTACCCTACAGGGGCATTACGGTCTT
1 TTTACCCTACAGGAGCATTACGGTCTT
41899374 TTTAC
1 TTTAC
41899379 ATTTTAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (27 bp):
TTTACCCTACAGGAGCATTACGGTCTT
Found at i:41899773 original size:27 final size:27
Alignment explanation
Indices: 41899410--41899772 Score: 293
Period size: 27 Copynumber: 13.4 Consensus size: 27
41899400 TTTCACCCTA
* * * *
41899410 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
*** * *
41899437 CAAGGGTATTTCAATAATTTTGCAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
41899464 CAATGGTATTTCT-ATAAATTTTGA-AAGT
1 CAAGGGTATTT-TGGT-AATTTT-ACAAAT
* * **
41899492 CATGGGTATTTCT-GTTATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
* *
41899519 C-AGGGATATTTTTGTAATTTTCCAAAT
1 CAAGGG-TATTTTGGTAATTTTACAAAT
*
41899546 CAAGGGTATTTTGGTAATTTTCCAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
41899573 TAGGGGTATTTTGGTAACTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** * *
41899600 TGAGGGTATTTCGGTAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
41899627 CAAGGGTATTTTGATAATTTCACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
41899654 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
41899681 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
41899708 CAAGGGTATTTTGGTAATTTTGCTAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * * ** *
41899735 CGAGGATATTTCGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
41899762 CAAGGGTATTT
1 CAAGGGTATTT
41899773 CAGTAATTCT
Statistics
Matches: 273, Mismatches: 56, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
26 4 0.01
27 245 0.90
28 24 0.09
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:41900056 original size:9 final size:9
Alignment explanation
Indices: 41900042--41900110 Score: 111
Period size: 9 Copynumber: 7.7 Consensus size: 9
41900032 TTTGGTTAAA
41900042 AATTAACCG
1 AATTAACCG
41900051 AATTAACCG
1 AATTAACCG
*
41900060 AATTAATCG
1 AATTAACCG
41900069 AATTAACCG
1 AATTAACCG
**
41900078 AATTAACTT
1 AATTAACCG
41900087 AATTAACCG
1 AATTAACCG
41900096 AATTAACCG
1 AATTAACCG
41900105 AATTAA
1 AATTAA
41900111 ATCACTACAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:41900138 original size:17 final size:17
Alignment explanation
Indices: 41900116--41900213 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
41900106 ATTAAATCAC
41900116 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
41900133 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
41900153 TACATAATAAAAAACAT
1 TACATAATTAAAAACAT
** * *
41900170 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
41900190 AACATAATTAAAAACAT
1 TACATAATTAAAAACAT
41900207 TACATAA
1 TACATAA
41900214 GTCTTGAAAT
Statistics
Matches: 55, Mismatches: 20, Indels: 12
0.63 0.23 0.14
Matches are distributed among these distances:
17 31 0.56
20 24 0.44
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:41900153 original size:37 final size:37
Alignment explanation
Indices: 41900110--41900218 Score: 200
Period size: 37 Copynumber: 2.9 Consensus size: 37
41900100 AACCGAATTA
41900110 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
41900147 AATCACTACATAATAAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
41900184 AATCACAACATAATTAAAAACATTACATAAGTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
41900219 GAAATTAACA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.30
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:41903992 original size:19 final size:19
Alignment explanation
Indices: 41903968--41904004 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
41903958 TTTATTTGTT
41903968 ATTTTTTCGGTTAACCGAA
1 ATTTTTTCGGTTAACCGAA
41903987 ATTTTTTCGGTTAACCGA
1 ATTTTTTCGGTTAACCGA
41904005 CCGGTTTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (19 bp):
ATTTTTTCGGTTAACCGAA
Found at i:41907762 original size:18 final size:18
Alignment explanation
Indices: 41907739--41907774 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41907729 GTTCAGAAGA
41907739 TAAAATCGGCTAAACTAT
1 TAAAATCGGCTAAACTAT
41907757 TAAAATCGGCTAAACTAT
1 TAAAATCGGCTAAACTAT
41907775 CATGTGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
TAAAATCGGCTAAACTAT
Found at i:41912549 original size:20 final size:21
Alignment explanation
Indices: 41912524--41912563 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41912514 GCTCTGGAAC
*
41912524 AGGGC-ACATGCCCGTGTAGA
1 AGGGCAACACGCCCGTGTAGA
*
41912544 AGGGCAACACGCTCGTGTAG
1 AGGGCAACACGCCCGTGTAG
41912564 CCATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTAGA
Found at i:41916673 original size:40 final size:40
Alignment explanation
Indices: 41916577--41916782 Score: 259
Period size: 40 Copynumber: 5.1 Consensus size: 40
41916567 CGAATGATGT
* * * * *
41916577 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAA
* * *
41916618 CCGGGTCAATTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
*
41916658 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* *
41916698 CCAGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * * *
41916738 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACTATAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
41916778 CCGGG
1 CCGGG
41916783 CTATGTCCTG
Statistics
Matches: 145, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 121 0.83
41 24 0.17
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
Found at i:41919628 original size:40 final size:40
Alignment explanation
Indices: 41919582--41919711 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
41919572 GACTAGCTCA
*
41919582 AATGCCTTCGGGAC-AAACCCCGGTTATAGTAACTCGCACG
1 AATGCCTTCGGGACTTAACCCCGGTT-TAGTAACTCGCACG
* *
41919622 AATGCCTTCGGGACTTAACCCAGGTTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAACCCCGGTTTAGTAACTCGCACG
*
41919662 AATGCCTTCGGG-CTTAA-CCCGGATTTATTAACTCGCACG
1 AATGCCTTCGGGACTTAACCCCGG-TTTAGTAACTCGCACG
*
41919701 AACGCCTTCGG
1 AATGCCTTCGG
41919712 ATCTTAGTCC
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
38 4 0.05
39 29 0.36
40 39 0.48
41 9 0.11
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCCGGTTTAGTAACTCGCACG
Found at i:41928054 original size:40 final size:40
Alignment explanation
Indices: 41927958--41928176 Score: 251
Period size: 40 Copynumber: 5.5 Consensus size: 40
41927948 CGAATGATGT
* * * *
41927958 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAA
* *
41927999 CCGGG-TCAATTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* *
41928039 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * *
41928079 CTGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * *
41928119 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* *
41928159 CTGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
41928177 ACAATCGAGC
Statistics
Matches: 154, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
40 129 0.84
41 25 0.16
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
Found at i:41928201 original size:80 final size:80
Alignment explanation
Indices: 41928025--41928202 Score: 176
Period size: 80 Copynumber: 2.2 Consensus size: 80
41928015 AGGCATTTGT
* * * * * * *
41928025 GCGAGTTACCAAAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAACTGAGTTAAGT
1 GCGAGTCACTAAATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAATTACCAAAACTGAGCTAAGT
* * * *
41928090 CCCGAAGGCATTTGT
66 CCCGAAGACAATCGA
* * * * * *
41928105 GCGAGTTACTAAATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATTACTATAACTGGGCTATGT
1 GCGAGTCACTAAATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAATTACCAAAACTGAGCTAAGT
41928170 CCCGAAGACAATCGA
66 CCCGAAGACAATCGA
* * *
41928185 GCTAGTCGCTACATCCGG
1 GCGAGTCACTAAATCCGG
41928203 TTAAATTCTG
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (80 bp):
GCGAGTCACTAAATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAATTACCAAAACTGAGCTAAGT
CCCGAAGACAATCGA
Found at i:41930863 original size:17 final size:17
Alignment explanation
Indices: 41930841--41930877 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
41930831 GAGCAATCGG
41930841 CTTTCCTTGAGTAATTC
1 CTTTCCTTGAGTAATTC
41930858 CTTTCCTTGAGTAATTC
1 CTTTCCTTGAGTAATTC
41930875 CTT
1 CTT
41930878 GCTTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.16, C:0.24, G:0.11, T:0.49
Consensus pattern (17 bp):
CTTTCCTTGAGTAATTC
Found at i:41934666 original size:9 final size:9
Alignment explanation
Indices: 41934652--41934683 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
41934642 ACACATTCCT
41934652 CATTGAACA
1 CATTGAACA
41934661 CATTGAACA
1 CATTGAACA
41934670 CATTGAACA
1 CATTGAACA
41934679 CATTG
1 CATTG
41934684 GAATATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (9 bp):
CATTGAACA
Found at i:41935985 original size:11 final size:11
Alignment explanation
Indices: 41935969--41936001 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
41935959 CATAAACCTC
41935969 AAAATAATTAT
1 AAAATAATTAT
41935980 AAAATAATTAT
1 AAAATAATTAT
*
41935991 AAATTAATTAT
1 AAAATAATTAT
41936002 TTCTATCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAATAATTAT
Found at i:41945405 original size:71 final size:71
Alignment explanation
Indices: 41945321--41945484 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41945311 CGATTTGTCT
41945321 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41945386 CTTTCA
66 CTTTCA
41945392 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41945457 CTTTCA
66 CTTTCA
41945463 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
41945485 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:41945522 original size:71 final size:70
Alignment explanation
Indices: 41945321--41945518 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
41945311 CGATTTGTCT
* * * *
41945321 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41945386 CTTTCA
65 CTTTCA
* * * *
41945392 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41945457 CTTTCA
65 CTTTCA
* *
41945463 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
41945519 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:41950466 original size:24 final size:23
Alignment explanation
Indices: 41950438--41950482 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
41950428 ATGTTGCCCT
41950438 GCTTC-AACTCAAGAAACTCTTTAC
1 GCTTCTAA-TCAAGAAA-TCTTTAC
*
41950462 GCTTCTGATCAAGAAATCTTT
1 GCTTCTAATCAAGAAATCTTT
41950483 CACTGATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 13 0.68
25 1 0.05
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.33
Consensus pattern (23 bp):
GCTTCTAATCAAGAAATCTTTAC
Found at i:41963339 original size:13 final size:13
Alignment explanation
Indices: 41963306--41963341 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
41963296 CCTGCCAAAT
* *
41963306 TGACACGACCGTG
1 TGACACGCCCATG
41963319 TGACACGCCCATG
1 TGACACGCCCATG
41963332 TGACACGCCC
1 TGACACGCCC
41963342 GCGTAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.22, C:0.39, G:0.25, T:0.14
Consensus pattern (13 bp):
TGACACGCCCATG
Found at i:41967920 original size:21 final size:20
Alignment explanation
Indices: 41967883--41967922 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
41967873 GCTCTAGAAC
*
41967883 AGGGCACACGCCCGTGTAGA
1 AGGGCACACGCACGTGTAGA
*
41967903 AGGGCAACACGCATGTGTAG
1 AGGGC-ACACGCACGTGTAG
41967923 CCATTAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.25, G:0.35, T:0.12
Consensus pattern (20 bp):
AGGGCACACGCACGTGTAGA
Found at i:41969145 original size:46 final size:46
Alignment explanation
Indices: 41969094--41969206 Score: 181
Period size: 46 Copynumber: 2.5 Consensus size: 46
41969084 GTAGCAGATG
* *
41969094 CATGTCCTAAATATGTCTTACACTGGCTTACGTCTCGAGGCTGATA
1 CATGTCCTAAACATGTCTTACACTGGCTTACGTCTCGAGCCTGATA
* *
41969140 CATGTCCTAGACATGTCTTACACTGGCTTACGTCTCGAGCCTGATG
1 CATGTCCTAAACATGTCTTACACTGGCTTACGTCTCGAGCCTGATA
*
41969186 CATGTCCCAAACATGTCTTAC
1 CATGTCCTAAACATGTCTTAC
41969207 TCTAGCACTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (46 bp):
CATGTCCTAAACATGTCTTACACTGGCTTACGTCTCGAGCCTGATA
Found at i:41973836 original size:27 final size:27
Alignment explanation
Indices: 41973806--41973870 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
41973796 ACTACCAAAG
* *
41973806 TACCCTCGATTTATAGGATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
*
41973833 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
*
41973860 TACCTTCGATT
1 TACCCTCGATT
41973871 GTGAAATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTATTT
Found at i:41973960 original size:27 final size:27
Alignment explanation
Indices: 41973902--41974108 Score: 134
Period size: 27 Copynumber: 7.7 Consensus size: 27
41973892 TATAGGGTAG
*
41973902 AATTACCAAAATACCCCTAG-TTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
* * *
41973928 AATTACCAAAATACCATTGGTTTGTCA
1 AATTACCAAAATACCCTTAGTTTGTAA
* * *
41973955 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
* * **
41973982 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAATACCCTTAGTTTGTAA
* *
41974009 AATTA-CAGAAATACCCTTGACTTTCTAAA
1 AATTACCA-AAATACCCTT-AGTTTGT-AA
* * **
41974038 AATTA-TAGAAATACCATT-GTTTACAA
1 AATTACCA-AAATACCCTTAGTTTGTAA
*** * *
41974064 AATTATTGAAATACCCTTGGTTTGTAG
1 AATTACCAAAATACCCTTAGTTTGTAA
* *
41974091 ATTTACCAAAACACCCTT
1 AATTACCAAAATACCCTT
41974109 GTAGGATGAA
Statistics
Matches: 141, Mismatches: 34, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
26 35 0.25
27 84 0.60
28 4 0.03
29 18 0.13
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTAGTTTGTAA
Found at i:41974047 original size:29 final size:26
Alignment explanation
Indices: 41974002--41974082 Score: 92
Period size: 26 Copynumber: 3.0 Consensus size: 26
41973992 ATACCCCTAA
*
41974002 TTTACAAAATTACAGAAATACCCTTG
1 TTTACAAAATTATAGAAATACCCTTG
*
41974028 ACTTT-CTAAAAATTATAGAAATACCATTG
1 --TTTAC--AAAATTATAGAAATACCCTTG
*
41974057 TTTACAAAATTATTGAAATACCCTTG
1 TTTACAAAATTATAGAAATACCCTTG
41974083 GTTTGTAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 19 0.41
27 4 0.09
28 4 0.09
29 19 0.41
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (26 bp):
TTTACAAAATTATAGAAATACCCTTG
Found at i:41975035 original size:24 final size:25
Alignment explanation
Indices: 41974964--41975033 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
41974954 AGGAAGTGCT
* * *
41974964 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
41974989 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
41975014 AAAAGGGCTTTACCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
41975034 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:41975046 original size:24 final size:25
Alignment explanation
Indices: 41974976--41975046 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
41974966 AAGGGCTATG
* *
41974976 CCCCAGTTTACCGAAAAG-GGCTTTG
1 CCCCAGTTTATC-AAAAGAGGCTTTA
41975001 CCCCAGTTTATCAAAA-AGGGCTTTA
1 CCCCAGTTTATCAAAAGA-GGCTTTA
*
41975026 CCCCAG-TTATTAAAAGAGGCT
1 CCCCAGTTTATCAAAAGAGGCT
41975047 AGGCCTCCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 16 0.40
25 24 0.60
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (25 bp):
CCCCAGTTTATCAAAAGAGGCTTTA
Found at i:41975289 original size:30 final size:30
Alignment explanation
Indices: 41975253--41975322 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
41975243 CGCTTACAGT
*
41975253 AAAGGCTTCGACCAGTTATATGATTTATGA
1 AAAGGCTTCGACCAGTGATATGATTTATGA
* *
41975283 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGC-TTCGACCAGTGATATGATTTATGA
41975314 AAA-GCTTCG
1 AAAGGCTTCG
41975323 GCCCAGTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.09
30 8 0.23
31 24 0.69
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (30 bp):
AAAGGCTTCGACCAGTGATATGATTTATGA
Found at i:41975305 original size:31 final size:29
Alignment explanation
Indices: 41975264--41975334 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 29
41975254 AAGGCTTCGA
*
41975264 CCAGTTATATGATTTATGAAAAGGCTTTGGC
1 CCAG-TATATGATTTATGAAAA-GCTTCGGC
41975295 CCAGTGATATGATTTATGAAAAGCTTCGGC
1 CCAGT-ATATGATTTATGAAAAGCTTCGGC
41975325 CCAGTATATG
1 CCAGTATATG
41975335 TCGAGACTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
29 5 0.13
30 13 0.34
31 20 0.53
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (29 bp):
CCAGTATATGATTTATGAAAAGCTTCGGC
Found at i:41975328 original size:30 final size:30
Alignment explanation
Indices: 41975253--41975334 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 30
41975243 CGCTTACAGT
*
41975253 AAAGGCTTC-GACCAGTTATATGATTTATGA
1 AAAGGCTTCGGCCCAG-TATATGATTTATGA
*
41975283 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGT-ATATGATTTATGA
41975314 AAA-GCTTCGGCCCAGTATATG
1 AAAGGCTTCGGCCCAGTATATG
41975335 TCGAGACTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
29 5 0.11
30 21 0.45
31 21 0.45
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTATATGATTTATGA
Found at i:41978574 original size:66 final size:68
Alignment explanation
Indices: 41978498--41978684 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
41978488 TAGTACCACT
*
41978498 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
41978560 CACG
65 CACG
41978564 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
41978629 ATCACG
63 ATCACG
41978635 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
41978685 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:41978609 original size:71 final size:71
Alignment explanation
Indices: 41978521--41978684 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41978511 CGATTTGTCT
41978521 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41978586 CTTTCA
66 CTTTCA
41978592 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41978657 CTTTCA
66 CTTTCA
41978663 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
41978685 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:41978722 original size:71 final size:70
Alignment explanation
Indices: 41978521--41978718 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
41978511 CGATTTGTCT
* * *
41978521 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
41978586 CTTTCA
65 CTTTCA
* * *
41978592 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
41978657 CTTTCA
65 CTTTCA
* *
41978663 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
41978719 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:41987257 original size:40 final size:40
Alignment explanation
Indices: 41987184--41987363 Score: 258
Period size: 40 Copynumber: 4.5 Consensus size: 40
41987174 GATACCCGGC
* * * *
41987184 TAAGCCCCGAAGGCATTTATGCTAG-TGATTATATCCGGGT
1 TAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCCGGGT
41987224 TAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGT
1 TAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGT
* *
41987264 TAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT--GGGC
1 TAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGT
*
41987302 TAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGT
1 TAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGT
*
41987342 TAAGACCCGAAGGCAATTGTGC
1 TAAGACCCGAAGGCATTTGTGC
41987364 TTGTGGTTAT
Statistics
Matches: 127, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
38 35 0.28
40 90 0.71
41 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
TAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGT
Found at i:41987320 original size:78 final size:79
Alignment explanation
Indices: 41987175--41987383 Score: 280
Period size: 78 Copynumber: 2.7 Consensus size: 79
41987165 GCATTGAATG
* * * * *
41987175 ATACCC-GGCTAAGCCCCGAAGGCATTTATGCTAGTGATTATATCCGGGTTAAGACCCGAAGGCA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTGATTATAT-CGGGCTAAGACCCGAAGGCA
41987239 TTTGTGCGAGTTGCT
65 TTTGTGCGAGTTGCT
*
41987254 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT-GGGCTAAGACCCGAAGGCA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCGAG-TGATTATATCGGGCTAAGACCCGAAGGCA
41987317 TTTGTGCGAGTTGCT
65 TTTGTGCGAGTTGCT
* ** * *
41987332 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCCGGCTAA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCGGGCTAA
41987384 ATTCCGAAGA
Statistics
Matches: 115, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
77 2 0.02
78 70 0.61
79 11 0.10
80 30 0.26
81 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
ATACCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCGGGCTAAGACCCGAAGGCAT
TTGTGCGAGTTGCT
Found at i:41995379 original size:40 final size:40
Alignment explanation
Indices: 41995263--41995462 Score: 257
Period size: 39 Copynumber: 5.1 Consensus size: 40
41995253 TGAATGATAC
* * *
41995263 CCGGGCTAAG-CCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
41995302 CC-GGTTAAGACCCGAAGGC-TTTGTGCGAGTTGCTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
41995340 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
41995380 CC-GGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* ** *
41995419 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
41995459 CCGG
1 CCGG
41995463 CTAAATTCCG
Statistics
Matches: 141, Mismatches: 15, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
38 21 0.15
39 66 0.47
40 54 0.38
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (40 bp):
CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:41995475 original size:79 final size:78
Alignment explanation
Indices: 41995259--41995466 Score: 319
Period size: 79 Copynumber: 2.7 Consensus size: 78
41995249 CAATTGAATG
* * * *
41995259 ATACCCGGGCTAAG-CCCGAAGGCATTTATGCTAGTGATTATATCCGGTTAAGACCCGAAGGCTT
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGCTAAGACCCGAAGGCTT
41995323 TGTGCGAGTTGCT
66 TGTGCGAGTTGCT
* * *
41995336 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGCTAAGACCCGAAGGCAT
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGCTAAGACCCGAAGGC-T
41995401 TTGTGCGAGTTGCT
65 TTGTGCGAGTTGCT
* *
41995415 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCCGGCTAA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGCTAA
41995467 ATTCCGAAGA
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
77 12 0.10
78 43 0.37
79 62 0.53
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (78 bp):
ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGCTAAGACCCGAAGGCTT
TGTGCGAGTTGCT
Found at i:41996882 original size:19 final size:19
Alignment explanation
Indices: 41996860--41996898 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41996850 TTTAATTATT
* *
41996860 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
41996879 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
41996898 T
1 T
41996899 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:42012725 original size:17 final size:17
Alignment explanation
Indices: 42012700--42012736 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
42012690 ATGCAATAAT
42012700 ATGAAAATGTAATGACA
1 ATGAAAATGTAATGACA
*
42012717 ATGACAATGTAATGACA
1 ATGAAAATGTAATGACA
42012734 ATG
1 ATG
42012737 TATACTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (17 bp):
ATGAAAATGTAATGACA
Found at i:42013233 original size:21 final size:21
Alignment explanation
Indices: 42013188--42013241 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
42013178 TTATTTTTAC
*
42013188 CAACTTCTTCTTCTTCAGTAA
1 CAACTTCTTCTTCTTCAGCAA
*
42013209 CAACTTCTTCTTCTAT-AGCAT
1 CAACTTCTTCTTCT-TCAGCAA
42013230 CAACTTCCTTCT
1 CAACTT-CTTCT
42013242 CAACAATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.22, C:0.31, G:0.04, T:0.43
Consensus pattern (21 bp):
CAACTTCTTCTTCTTCAGCAA
Found at i:42015376 original size:22 final size:22
Alignment explanation
Indices: 42015344--42015430 Score: 84
Period size: 22 Copynumber: 4.0 Consensus size: 22
42015334 CACTAAGTCA
*
42015344 ACAGGACGGCTCAACGCCTTAG
1 ACAGGACGGCTCAACGCCATAG
* * * *
42015366 ATAGGATGGCTCAACGGCATGG
1 ACAGGACGGCTCAACGCCATAG
* * *
42015388 ACAGGATGACTCAACGCCGTAG
1 ACAGGACGGCTCAACGCCATAG
* *
42015410 ACAGGACGGCTAAAGGCCATA
1 ACAGGACGGCTCAACGCCATA
42015431 AATATTGCAG
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.31, C:0.25, G:0.30, T:0.14
Consensus pattern (22 bp):
ACAGGACGGCTCAACGCCATAG
Found at i:42017505 original size:5 final size:5
Alignment explanation
Indices: 42017495--42017522 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
42017485 AATAAACTTC
42017495 AATAA AATAA AATAA AATAA AATAA AAT
1 AATAA AATAA AATAA AATAA AATAA AAT
42017523 CACAGAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:42025523 original size:30 final size:30
Alignment explanation
Indices: 42025489--42025549 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
42025479 TACTTAACTC
42025489 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
42025519 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
42025549 A
1 A
42025550 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:42033415 original size:18 final size:18
Alignment explanation
Indices: 42033388--42033425 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
42033378 AGAGCGAAAG
42033388 AAACGAG-AAATGGGCCA
1 AAACGAGAAAATGGGCCA
42033405 AAACAGAGAAAATGGGCCA
1 AAAC-GAGAAAATGGGCCA
42033424 AA
1 AA
42033426 GTACGAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 3 0.16
19 12 0.63
ACGTcount: A:0.53, C:0.16, G:0.26, T:0.05
Consensus pattern (18 bp):
AAACGAGAAAATGGGCCA
Found at i:42034604 original size:17 final size:17
Alignment explanation
Indices: 42034582--42034616 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42034572 GGCGCCGTTG
42034582 TCGGGGAACTAAGATAT
1 TCGGGGAACTAAGATAT
42034599 TCGGGGAACTAAGATAT
1 TCGGGGAACTAAGATAT
42034616 T
1 T
42034617 AGGAACGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (17 bp):
TCGGGGAACTAAGATAT
Found at i:42036266 original size:13 final size:15
Alignment explanation
Indices: 42036235--42036266 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
42036225 TTGGGTGTCG
42036235 TCTTTATCAATTGCT
1 TCTTTATCAATTGCT
42036250 TCTTT-TCAATT-CT
1 TCTTTATCAATTGCT
42036263 TCTT
1 TCTT
42036267 CCAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 6 0.35
15 5 0.29
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.59
Consensus pattern (15 bp):
TCTTTATCAATTGCT
Found at i:42042436 original size:27 final size:27
Alignment explanation
Indices: 42042119--42042435 Score: 390
Period size: 27 Copynumber: 11.8 Consensus size: 27
42042109 ATTACTGAAA
** *
42042119 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
42042146 TACCCTCAATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
42042173 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
42042200 TACCCT-TAGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
42042227 TACCC-CGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
42042253 TACCC-CGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
42042279 TA-CCTCTGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
*
42042306 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
42042333 TACCCTTGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
42042360 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
42042387 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
42042414 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
42042436 TAAAATACCC
Statistics
Matches: 258, Mismatches: 27, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
25 2 0.01
26 45 0.17
27 207 0.80
28 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:42042444 original size:27 final size:27
Alignment explanation
Indices: 42042360--42042636 Score: 125
Period size: 27 Copynumber: 10.2 Consensus size: 27
42042350 ATTACCGTTT
* * ***
42042360 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ****
42042387 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
42042414 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
42042441 TACCCT-TAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACTAAAA
* ** *
42042468 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACTAAAA
* * *** **
42042495 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
42042522 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
*
42042549 TACCCT-GATTTACAAAGTTAC-AGAAA
1 TACCCTCGATTTACAAAATTACTA-AAA
*
42042575 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTCGA-TTTAC--AAAATTACTA-AAA
* * * *
42042604 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
42042631 TACCCT
1 TACCCT
42042637 TAGTTTGTAG
Statistics
Matches: 207, Mismatches: 32, Indels: 22
0.79 0.12 0.08
Matches are distributed among these distances:
25 1 0.00
26 21 0.10
27 159 0.77
28 7 0.03
29 19 0.09
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:42042593 original size:54 final size:53
Alignment explanation
Indices: 42042428--42042663 Score: 197
Period size: 54 Copynumber: 4.4 Consensus size: 53
42042418 CTCGATTTAC
* * ** *
42042428 AAAATTACTAAAATACCCTTAGTTTGTAAAATTACCA-AAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTGA-TTTACAAAATTA-CAGAAATACCCTTAGTTTGT
* *** * * *
42042482 AAAATTACCAAAATACCCTTGGTTTGTGAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCC-TGATTTACAAAATTACAGAAATACCCTTAGTTTGT
* * *
42042536 AAAATTACCAAAATACCCTGATTTACAAAGTTACAGAAATACCCTTGACTTTCT
1 AAAATTACCAAAATACCCTGATTTACAAAATTACAGAAATACCCTT-AGTTTGT
* * * *
42042590 AAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTAGTTTGT
1 -AAAATTACCA-AAATACC-CTGATTTACAAAATTACAGAAATACCCTTAGTTTGT
* * *
42042645 AGATTTACCAAAACACCCT
1 AAAATTACCAAAATACCCT
42042664 TGTAGGATGA
Statistics
Matches: 146, Mismatches: 29, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
53 23 0.16
54 77 0.53
55 21 0.14
56 25 0.17
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (53 bp):
AAAATTACCAAAATACCCTGATTTACAAAATTACAGAAATACCCTTAGTTTGT
Found at i:42042642 original size:27 final size:27
Alignment explanation
Indices: 42042427--42042664 Score: 178
Period size: 27 Copynumber: 8.8 Consensus size: 27
42042417 CCTCGATTTA
*
42042427 CAAAATTACTAAAATACCCTTAGTTTG
1 CAAAATTACCAAAATACCCTTAGTTTG
* *
42042454 TAAAATTACCAAAATACCCCTAGTTTG
1 CAAAATTACCAAAATACCCTTAGTTTG
* *
42042481 TAAAATTACCAAAATACCCTTGGTTTG
1 CAAAATTACCAAAATACCCTTAGTTTG
** * * *
42042508 TGAAATTACCGAAATACCCTCAATTTG
1 CAAAATTACCAAAATACCCTTAGTTTG
* * *
42042535 TAAAATTACCAAAATACCCTGA-TTTA
1 CAAAATTACCAAAATACCCTTAGTTTG
* *
42042561 CAAAGTTA-CAGAAATACCCTTGACTTT-
1 CAAAATTACCA-AAATACCCTT-AGTTTG
* * * *
42042588 CTAAAAATTA-TAGAAATACCATTGGTTTA
1 C--AAAATTACCA-AAATACCCTTAGTTTG
**
42042617 CAAAATTACTGAAATACCCTTAGTTTG
1 CAAAATTACCAAAATACCCTTAGTTTG
* * * *
42042644 TAGATTTACCAAAACACCCTT
1 CAAAATTACCAAAATACCCTT
42042665 GTAGGATGAA
Statistics
Matches: 172, Mismatches: 32, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
25 2 0.01
26 18 0.10
27 127 0.74
28 7 0.04
29 18 0.10
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
CAAAATTACCAAAATACCCTTAGTTTG
Found at i:42042760 original size:27 final size:27
Alignment explanation
Indices: 42042683--42042760 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
42042673 AAATGTCTAA
*
42042683 AATACCCCTAT-TAGGTAAAAAGACCGT
1 AATACCCCTATAT-GGTAAAATGACCGT
* *
42042710 AA-AGCCCCTATAGGGTAAAGTGACCGT
1 AATA-CCCCTATATGGTAAAATGACCGT
42042737 AATACCCCTATATGGTAAAATGAC
1 AATACCCCTATATGGTAAAATGAC
42042761 GAATATGCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.02
27 41 0.95
28 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (27 bp):
AATACCCCTATATGGTAAAATGACCGT
Found at i:42043953 original size:25 final size:24
Alignment explanation
Indices: 42043920--42043967 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
42043910 TTATAACATG
* * *
42043920 AAAATGACCGTTTTGCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
42043944 AAAAGTGACCATTATACCCCTAGG
1 AAAA-TGACCATTATACCCCTAGG
42043968 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:42044018 original size:9 final size:9
Alignment explanation
Indices: 42044006--42044062 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
42043996 TTTGATAAAC
42044006 ATGATATGT
1 ATGATATGT
*
42044015 ATGATATGCAC
1 ATGATATG--T
*
42044026 ATGACATGT
1 ATGATATGT
*
42044035 ATGATATGCAC
1 ATGATATG--T
42044046 ATGATATGT
1 ATGATATGT
42044055 ATGATATG
1 ATGATATG
42044063 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:42044029 original size:20 final size:20
Alignment explanation
Indices: 42044004--42044074 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
42043994 ATTTTGATAA
42044004 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
42044024 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
42044044 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
42044064 ACATGAGATGT
1 ACATGATATGT
42044075 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:42044051 original size:11 final size:11
Alignment explanation
Indices: 42044015--42044069 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
42044005 CATGATATGT
42044015 ATGATATGCAC
1 ATGATATGCAC
* *
42044026 ATGACATG--T
1 ATGATATGCAC
42044035 ATGATATGCAC
1 ATGATATGCAC
*
42044046 ATGATATG--T
1 ATGATATGCAC
42044055 ATGATATGCAC
1 ATGATATGCAC
42044066 ATGA
1 ATGA
42044070 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:42044172 original size:24 final size:24
Alignment explanation
Indices: 42044120--42044330 Score: 319
Period size: 23 Copynumber: 9.0 Consensus size: 24
42044110 GAGGAAGTGC
42044120 AAAAGGGGCTTATGCCCCAGTTATT
1 AAAA-GGGCTTATGCCCCAGTTATT
42044145 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42044168 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42044192 -AAAGGGCTTATGTCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42044215 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42044239 -AAAGGGCTTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42044261 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42044284 AAAAGGGCTT-TGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42044307 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42044331 ATGATAAAGC
Statistics
Matches: 174, Mismatches: 5, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
22 12 0.07
23 101 0.58
24 54 0.31
25 7 0.04
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:42044190 original size:47 final size:47
Alignment explanation
Indices: 42044120--42044330 Score: 331
Period size: 47 Copynumber: 4.5 Consensus size: 47
42044110 GAGGAAGTGC
42044120 AAAAGGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAA-GGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
*
42044168 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGTCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
42044215 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
*
42044261 AAAAGGGCTT-TGCCCCAGTTATTAAAAGGGCTT-TGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATT
*
42044307 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42044331 ATGATAAAGC
Statistics
Matches: 155, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
45 15 0.10
46 44 0.28
47 84 0.54
48 12 0.08
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
Found at i:42045707 original size:18 final size:16
Alignment explanation
Indices: 42045683--42045774 Score: 76
Period size: 18 Copynumber: 5.2 Consensus size: 16
42045673 AATCCTCCTA
42045683 TTTATTTTTTTATTTAT
1 TTTATTTTTTT-TTTAT
42045700 TCTTATTTTTATTTTTATT
1 T-TTATTTTT-TTTTTA-T
*
42045719 TTTATTTTATTTTTAT
1 TTTATTTTTTTTTTAT
*
42045735 TTTGTTTTTTATTTTCAT
1 TTTATTTTTT-TTTT-AT
*
42045753 TTCAATTTTATTATTTTAT
1 TT-TATTTT-TT-TTTTAT
42045772 TTT
1 TTT
42045775 GAAAGACATA
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
16 9 0.15
17 11 0.18
18 23 0.37
19 12 0.19
20 7 0.11
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTATTTTTTTTTTAT
Found at i:42045711 original size:6 final size:6
Alignment explanation
Indices: 42045683--42045754 Score: 87
Period size: 6 Copynumber: 12.2 Consensus size: 6
42045673 AATCCTCCTA
*
42045683 TTTATT TTT-TT ATTTATT CTTATT TTTATT TTTATT TTTA-T TTTATT
1 TTTATT TTTATT -TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
42045730 TTTATT TTGT-TT TTTATT TTCATT T
1 TTTATT TT-TATT TTTATT TTTATT T
42045755 CAATTTTATT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
5 8 0.14
6 47 0.81
7 3 0.05
ACGTcount: A:0.15, C:0.03, G:0.01, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:42045734 original size:29 final size:29
Alignment explanation
Indices: 42045683--42045774 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
42045673 AATCCTCCTA
* *
42045683 TTTATTTTTTTATTTATTCTTATTTTTATT
1 TTTATTTTTAT-TTTATTTTTATTTTTATT
42045713 TTTATTTTTATTTTATTTTTATTTTGT-TT
1 TTTATTTTTATTTTATTTTTATTTT-TATT
* * *
42045742 TTTATTTTCATTTCAATTTTATTATTTTATT
1 TTTATTTTTATTTTATTTTTA-T-TTTTATT
42045773 TT
1 TT
42045775 GAAAGACATA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
29 33 0.62
30 13 0.25
31 7 0.13
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.78
Consensus pattern (29 bp):
TTTATTTTTATTTTATTTTTATTTTTATT
Found at i:42056113 original size:16 final size:16
Alignment explanation
Indices: 42056069--42056119 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
42056059 TTATTTATTA
*
42056069 TTTTATGTTC-TTAAT
1 TTTTATTTTCATTAAT
***
42056084 TTTTATTAAAATTAAT
1 TTTTATTTTCATTAAT
42056100 TTTTATTTTCATTAGAT
1 TTTTATTTTCATTA-AT
42056117 TTT
1 TTT
42056120 AGAATTTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTTATTTTCATTAAT
Found at i:42062135 original size:20 final size:20
Alignment explanation
Indices: 42062110--42062172 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
42062100 GATGAATACC
42062110 AAGTAAGTTCGAATAACTCA
1 AAGTAAGTTCGAATAACTCA
**
42062130 AAGTAAACTCGAAT-AC-C-
1 AAGTAAGTTCGAATAACTCA
*
42062147 AGGTAAGTTCGAATAACTCA
1 AAGTAAGTTCGAATAACTCA
42062167 AAGTAA
1 AAGTAA
42062173 ACTCATTGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 11 0.32
18 3 0.09
19 3 0.09
20 17 0.50
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (20 bp):
AAGTAAGTTCGAATAACTCA
Found at i:42062153 original size:37 final size:37
Alignment explanation
Indices: 42062103--42062176 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
42062093 ATATCGAGAT
42062103 GAATACCAAGTAAGTTCGAATAACTCAAAGTAAACTC
1 GAATACCAAGTAAGTTCGAATAACTCAAAGTAAACTC
*
42062140 GAATACCAGGTAAGTTCGAATAACTCAAAGTAAACTC
1 GAATACCAAGTAAGTTCGAATAACTCAAAGTAAACTC
42062177 ATTGTATGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.22
Consensus pattern (37 bp):
GAATACCAAGTAAGTTCGAATAACTCAAAGTAAACTC
Found at i:42062158 original size:17 final size:17
Alignment explanation
Indices: 42062103--42062161 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
42062093 ATATCGAGAT
42062103 GAATACCAAGTAAGTTC
1 GAATACCAAGTAAGTTC
**
42062120 GAATAACTCAAAGTAAACTC
1 GAAT-AC-C-AAGTAAGTTC
*
42062140 GAATACCAGGTAAGTTC
1 GAATACCAAGTAAGTTC
42062157 GAATA
1 GAATA
42062162 ACTCAAAGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 16 0.47
18 3 0.09
19 3 0.09
20 12 0.35
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (17 bp):
GAATACCAAGTAAGTTC
Found at i:42064731 original size:45 final size:45
Alignment explanation
Indices: 42064667--42064884 Score: 284
Period size: 45 Copynumber: 4.9 Consensus size: 45
42064657 TATTGTACGG
* * *
42064667 TACTATTCGGGTCTTTGAGCCTAGCAGGCTATGATGCCAGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
42064712 TACTATTCGAGCCTTTGAGCCTAGCAGGCTATGATACCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
42064757 TACTATTCGGGCCTTTGAGCCTAGCAGGATATAATGCC-GTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
42064801 TACTATTTGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
42064846 TGA-TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGCCGGTG
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTG
42064885 GAGGAATTTG
Statistics
Matches: 157, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
42 10 0.06
43 18 0.11
44 45 0.29
45 83 0.53
46 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:42064830 original size:89 final size:89
Alignment explanation
Indices: 42064667--42064871 Score: 281
Period size: 89 Copynumber: 2.3 Consensus size: 89
42064657 TATTGTACGG
* * *
42064667 TACTATTCGGGTCTTTGAGCCTAGCAGGCTATGATGCCAGTGAGATACTATTCGAGCCTTTGAGC
1 TACTATTCGGG-CTTTGAGCCTAGCAGGATATAATGCCAGTGAGATACTATTCGAGCCTTCGAGC
* *
42064732 CTAGCAGGCTATGATACCGGTGAGA
65 CTAGCAGGCTATAATACCGGTGAAA
* *
42064757 TACTATTCGGGCCTTTGAGCCTAGCAGGATATAATGCC-GTGAGATACTATTTGGGCCTTCGAGC
1 TACTATTCGGG-CTTTGAGCCTAGCAGGATATAATGCCAGTGAGATACTATTCGAGCCTTCGAGC
*
42064821 CTAGCAGGCTATAATGCCGGTGAAA
65 CTAGCAGGCTATAATACCGGTGAAA
*
42064846 TGA-TA-TCGGGCTTCGAGCCTAGCAGG
1 T-ACTATTCGGGCTTTGAGCCTAGCAGG
42064872 CGAAATGCCG
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
87 15 0.14
88 5 0.05
89 48 0.46
90 36 0.35
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (89 bp):
TACTATTCGGGCTTTGAGCCTAGCAGGATATAATGCCAGTGAGATACTATTCGAGCCTTCGAGCC
TAGCAGGCTATAATACCGGTGAAA
Found at i:42072310 original size:39 final size:39
Alignment explanation
Indices: 42072267--42072469 Score: 318
Period size: 39 Copynumber: 5.2 Consensus size: 39
42072257 GTGTGAGATA
* * *
42072267 TATATCCGGGCTAATTCCCAAAGGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
*
42072306 TATATCTGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
42072345 TATATCCGGGATAAGTCTCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
42072384 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* * *
42072423 TATATCTGGGCTAAGTCCCGAAGGC-TTTGTGCTGGTAT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
42072461 TATATCCGG
1 TATATCCGG
42072470 CCTTAAAGTC
Statistics
Matches: 151, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
38 19 0.13
39 132 0.87
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.32
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
Found at i:42072490 original size:40 final size:38
Alignment explanation
Indices: 42072267--42072499 Score: 286
Period size: 39 Copynumber: 6.0 Consensus size: 38
42072257 GTGTGAGATA
* *
42072267 TATATCCGGGCTAATTCCCAAAGGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTGGTGT
* *
42072306 TATATCTGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTGGTGT
* * *
42072345 TATATCCGGGATAAGTCTCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTGGTGT
*
42072384 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTGGTGT
* *
42072423 TATATCTGGGCTAAGTCCCGAAGGCTTTGTGCTGGTAT
1 TATATCCGGGCTAAGTCCCGAAGGCTTTGTGCTGGTGT
* * * *
42072461 TATATCCGGCCTTAAAGTCCCGCATGCTTTGTGGTGGTG
1 TATATCCGGGC-T-AAGTCCCGAAGGCTTTGTGCTGGTG
42072500 ATTGAATTTG
Statistics
Matches: 174, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
38 20 0.11
39 133 0.76
40 21 0.12
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (38 bp):
TATATCCGGGCTAAGTCCCGAAGGCTTTGTGCTGGTGT
Found at i:42086320 original size:81 final size:81
Alignment explanation
Indices: 42086205--42086402 Score: 308
Period size: 81 Copynumber: 2.4 Consensus size: 81
42086195 TACTAAAATG
* *
42086205 CCCTCGATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTA
*
42086270 CAAAATTACCGTTTTA
66 CAAAATTACCATTTTA
* *
42086286 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTA
42086351 CAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* * *
42086367 CCATC-ATTTTACAAAATTACCATTTTACCCTCGATT
1 CCCTCGA-TTTATAGAATTACCATTTTACCCTCGATT
42086403 GTCAAATTAC
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
80 1 0.01
81 107 0.99
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.39
Consensus pattern (81 bp):
CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTA
CAAAATTACCATTTTA
Found at i:42086392 original size:16 final size:16
Alignment explanation
Indices: 42086347--42086394 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
42086337 TTACCCTCGA
42086347 TTTACAAAATTACCAT
1 TTTACAAAATTACCAT
*
42086363 TTTAC--CA-T--CAT
1 TTTACAAAATTACCAT
42086374 TTTACAAAATTACCAT
1 TTTACAAAATTACCAT
42086390 TTTAC
1 TTTAC
42086395 CCTCGATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
11 8 0.32
13 2 0.08
14 2 0.08
16 13 0.52
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTACAAAATTACCAT
Found at i:42086408 original size:27 final size:27
Alignment explanation
Indices: 42086205--42086402 Score: 254
Period size: 27 Copynumber: 7.3 Consensus size: 27
42086195 TACTAAAATG
** *
42086205 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* * * *
42086232 CCCTCGATTTATAGAATTACCGTTTCA
1 CCCTCGATTTACAAAATTACCATTTTA
*
42086259 CCCTCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* *
42086286 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* * *
42086313 CCCTCGATTTACAGAATTATCGTTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
42086340 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
*
42086367 CCATC-ATTTTACAAAATTACCATTTTA
1 CCCTCGA-TTTACAAAATTACCATTTTA
42086394 CCCTCGATT
1 CCCTCGATT
42086403 GTCAAATTAC
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 150 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.39
Consensus pattern (27 bp):
CCCTCGATTTACAAAATTACCATTTTA
Found at i:42086424 original size:27 final size:27
Alignment explanation
Indices: 42086401--42086583 Score: 167
Period size: 27 Copynumber: 6.8 Consensus size: 27
42086391 TTACCCTCGA
* *
42086401 TTGTCAAATTACTGAAATACCCCTA--
1 TTGTAAAATTACCGAAATACCCCTAGT
* * *
42086426 TGGATAGAATTACCAAAATACCCCTAGT
1 TTG-TAAAATTACCGAAATACCCCTAGT
*
42086454 TTGTAAAATTACCAAAATACCCCTAGT
1 TTGTAAAATTACCGAAATACCCCTAGT
* *
42086481 TTGTAAAATTACCGAAATACCACTGGT
1 TTGTAAAATTACCGAAATACCCCTAGT
* *
42086508 TTGTGAAATTACCGAAATA-CCCTCAAT
1 TTGTAAAATTACCGAAATACCCCT-AGT
* * *
42086535 TTGTAAAAATACCAAAATA-CCCTTGAT
1 TTGTAAAATTACCGAAATACCCCTAG-T
** *
42086562 TTACAAAATTACAGAAATACCC
1 TTGTAAAATTACCGAAATACCC
42086584 TTGACTTTCT
Statistics
Matches: 128, Mismatches: 24, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
25 2 0.02
26 21 0.16
27 101 0.79
28 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.28
Consensus pattern (27 bp):
TTGTAAAATTACCGAAATACCCCTAGT
Found at i:42086529 original size:81 final size:81
Alignment explanation
Indices: 42086433--42086582 Score: 205
Period size: 81 Copynumber: 1.9 Consensus size: 81
42086423 CTATGGATAG
* * ** *
42086433 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCGA
1 AATTACCAAAATACCCTC-AATTTGTAAAAATACCAAAATA-CCCTAGATTTACAAAATTACAGA
42086496 AATACCACTGGTTTGTGA
64 AATACCACTGGTTTGTGA
* *
42086514 AATTACCGAAATACCCTCAATTTGTAAAAATACCAAAATACCCTTGATTTACAAAATTACAGAAA
1 AATTACCAAAATACCCTCAATTTGTAAAAATACCAAAATACCCTAGATTTACAAAATTACAGAAA
42086579 TACC
66 TACC
42086583 CTTGACTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
80 5 0.08
81 54 0.90
82 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (81 bp):
AATTACCAAAATACCCTCAATTTGTAAAAATACCAAAATACCCTAGATTTACAAAATTACAGAAA
TACCACTGGTTTGTGA
Found at i:42086571 original size:54 final size:54
Alignment explanation
Indices: 42086436--42086636 Score: 149
Period size: 54 Copynumber: 3.7 Consensus size: 54
42086426 TGGATAGAAT
* ** * * *
42086436 TACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCC-CTAGTTTGTAAAAT
1 TACCAAAATACCCTTGA-TTTACAAAATTACCGAAATACCCTC-AATTTGTAAAAA
* * ***
42086490 TACCGAAATACCAC-TGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAAA
1 TACCAAAATACC-CTTGATTTACAAAATTACCGAAATACCCTCAATTTGTAAAAA
* * * *
42086544 TACCAAAATACCCTTGATTTACAAAATTACAGAAATACCCTTGACTTTCTAAAAA
1 TACCAAAATACCCTTGATTTACAAAATTACCGAAATACCC-TCAATTTGTAAAAA
* * * *
42086599 TTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATA
1 -TACCA-AAATACCCTTGATTTACAAAATTACCGAAATA
42086637 GCCTTGGTTT
Statistics
Matches: 121, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
53 1 0.01
54 75 0.62
55 14 0.12
56 31 0.26
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (54 bp):
TACCAAAATACCCTTGATTTACAAAATTACCGAAATACCCTCAATTTGTAAAAA
Found at i:42086607 original size:29 final size:27
Alignment explanation
Indices: 42086513--42086642 Score: 111
Period size: 27 Copynumber: 4.7 Consensus size: 27
42086503 CTGGTTTGTG
* ** **
42086513 AAATTACCGAAATACCCTCAATTTGTA
1 AAATTACAGAAATACCCTTGATTTACA
*
42086540 AAAATACCA-AAATACCCTTGATTTACA
1 AAATTA-CAGAAATACCCTTGATTTACA
42086567 AAATTACAGAAATACCCTTGACTTT-CTAA
1 AAATTACAGAAATACCCTTGA-TTTAC--A
* * *
42086596 AAATTATAGAAATACCATTGGTTTACA
1 AAATTACAGAAATACCCTTGATTTACA
* *
42086623 AAATTACTGAAATAGCCTTG
1 AAATTACAGAAATACCCTTG
42086643 GTTTGTAGAT
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
26 2 0.02
27 54 0.65
28 7 0.08
29 20 0.24
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTACAGAAATACCCTTGATTTACA
Found at i:42087516 original size:17 final size:17
Alignment explanation
Indices: 42087494--42087534 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
42087484 GACCGAAGTG
42087494 GGGCCCAATGGGCTTTC
1 GGGCCCAATGGGCTTTC
42087511 GGGCCCAATGGGCTTTC
1 GGGCCCAATGGGCTTTC
42087528 GGGCCCA
1 GGGCCCA
42087535 TTTGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.12, C:0.32, G:0.37, T:0.20
Consensus pattern (17 bp):
GGGCCCAATGGGCTTTC
Found at i:42087925 original size:11 final size:11
Alignment explanation
Indices: 42087889--42087944 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
42087879 CATGGTATGT
42087889 ATGATATGCAC
1 ATGATATGCAC
* *
42087900 ATGACATG--T
1 ATGATATGCAC
42087909 ATGATATGCAC
1 ATGATATGCAC
*
42087920 ATGATATG--T
1 ATGATATGCAC
42087929 ATGATATGCAC
1 ATGATATGCAC
42087940 ATGAT
1 ATGAT
42087945 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:42087944 original size:20 final size:20
Alignment explanation
Indices: 42087878--42087944 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
42087868 ATTTTGATAA
*
42087878 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
42087898 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
42087918 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
42087938 ACATGAT
1 ACATGAT
42087945 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:42088020 original size:24 final size:24
Alignment explanation
Indices: 42087994--42088187 Score: 291
Period size: 24 Copynumber: 8.0 Consensus size: 24
42087984 GAGGAAGTGC
*
42087994 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
42088018 AAAAGTGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42088042 AAAAATGGGCTTATGCCCCAGTTATC
1 -AAAA-GGGCTTATGCCCCAGTTATT
*
42088068 GAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42088092 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42088116 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42088140 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42088164 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42088188 ATGATAAAGC
Statistics
Matches: 156, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
24 120 0.77
25 18 0.12
26 18 0.12
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:42089727 original size:27 final size:27
Alignment explanation
Indices: 42089670--42089774 Score: 69
Period size: 27 Copynumber: 4.1 Consensus size: 27
42089660 CAGCCATGGG
* * *
42089670 TAAATATGATCGGCACAGAGTCATTAA
1 TAAATATGATAGGCACAGAGCCATCAA
*
42089697 TAAATATGATAGGCACATAGCCA-CAA
1 TAAATATGATAGGCACAGAGCCATCAA
** * *
42089723 CTAAATACAATTGGCACAAAGCCAT-AA
1 -TAAATATGATAGGCACAGAGCCATCAA
* *
42089750 T-CA-A-GATA-GCACAGAGCCATAAA
1 TAAATATGATAGGCACAGAGCCATCAA
42089773 TA
1 TA
42089775 GATTAAGCGA
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
22 11 0.18
23 5 0.08
24 1 0.02
25 1 0.02
26 3 0.05
27 41 0.66
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (27 bp):
TAAATATGATAGGCACAGAGCCATCAA
Found at i:42090124 original size:27 final size:26
Alignment explanation
Indices: 42090075--42090138 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 26
42090065 CAAAACAATC
*
42090075 ATTTTAC-CATACAGGGTATTTCGGTA
1 ATTTTACAC-TACAGGGTATTTCGATA
42090101 ATTTTACACTACAAGGGTATTTCGATA
1 ATTTTACACTAC-AGGGTATTTCGATA
42090128 ATTTTACACTA
1 ATTTTACACTA
42090139 GGGGTCTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 10 0.29
27 25 0.71
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (26 bp):
ATTTTACACTACAGGGTATTTCGATA
Found at i:42092348 original size:28 final size:28
Alignment explanation
Indices: 42092285--42092349 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
42092275 ATTTACTAGA
*
42092285 ATACCCCTATGTATGCAAAATTACCATC
1 ATACCCCTATGTATGCAAAATGACCATC
* * *
42092313 ATATCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATC
42092341 ATACCCCTA
1 ATACCCCTA
42092350 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATC
Found at i:42092496 original size:28 final size:28
Alignment explanation
Indices: 42092455--42092545 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
42092445 AGGAAGCGTC
* *
42092455 CTGGTGGCTA-TGCCATAAATTATCTGCT
1 CTGGTGGC-ACTGCCACAAATTATCTGAT
* *
42092483 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCACTGCCACAAATTATCTGAT
*
42092511 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTG-AT
42092540 CTGGTG
1 CTGGTG
42092546 ACTCAGTCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 48 0.87
29 7 0.13
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGAT
Found at i:42092556 original size:29 final size:28
Alignment explanation
Indices: 42092466--42092556 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
42092456 TGGTGGCTAT
* * * * * *
42092466 GCCATAAATTATCTGCTCTGGTGGCCCT
1 GCCACAAAATATCTGTTCTGGTGACACA
* * *
42092494 GCCACAAATTATCTGTTCTGGTGGCACT
1 GCCACAAAATATCTGTTCTGGTGACACA
*
42092522 GCCACAAAATATCTGTATCTGGTGACTCA
1 GCCACAAAATATCTGT-TCTGGTGACACA
*
42092551 GTCACA
1 GCCACA
42092557 TTTTCTGTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
28 40 0.74
29 14 0.26
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (28 bp):
GCCACAAAATATCTGTTCTGGTGACACA
Found at i:42093032 original size:19 final size:19
Alignment explanation
Indices: 42093008--42093046 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42092998 TTTTAATTAT
* *
42093008 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
42093027 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
42093046 T
1 T
42093047 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:42100292 original size:56 final size:56
Alignment explanation
Indices: 42100231--42100367 Score: 256
Period size: 56 Copynumber: 2.4 Consensus size: 56
42100221 GACCATGGCA
42100231 TCGATATATGTGTGCGAGTAAGACCACGTTTAATATGTTGGCATCGATATGTGACT
1 TCGATATATGTGTGCGAGTAAGACCACGTTTAATATGTTGGCATCGATATGTGACT
42100287 TCGATATATGTGTGCGAGTAAGACCACGTTTAATATGTTGGCATCGATATGTGACT
1 TCGATATATGTGTGCGAGTAAGACCACGTTTAATATGTTGGCATCGATATGTGACT
* *
42100343 CCGATATATGTGTGTGAGTAAGACC
1 TCGATATATGTGTGCGAGTAAGACC
42100368 CTGTCTAGGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 79 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.33
Consensus pattern (56 bp):
TCGATATATGTGTGCGAGTAAGACCACGTTTAATATGTTGGCATCGATATGTGACT
Found at i:42102976 original size:48 final size:47
Alignment explanation
Indices: 42102921--42103016 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 47
42102911 CCAAGCAAGG
*
42102921 CTAAAAACCTAAAAGGGATTGTGAGAGGAATGACTAGTGATATTCGGC
1 CTAAAAACCGAAAAGGGATTGTGAGAGGAA-GACTAGTGATATTCGGC
42102969 CTAAAAACCGAAAAGGGATTGTGAGAGGAAGACTAGTGATATTCGGC
1 CTAAAAACCGAAAAGGGATTGTGAGAGGAAGACTAGTGATATTCGGC
42103016 C
1 C
42103017 AAAGAGAAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 18 0.38
48 29 0.62
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (47 bp):
CTAAAAACCGAAAAGGGATTGTGAGAGGAAGACTAGTGATATTCGGC
Found at i:42105902 original size:53 final size:53
Alignment explanation
Indices: 42105822--42105926 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
42105812 TTCCTTTTTA
* * * *
42105822 AACTTACCATTGCAATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
1 AACTCACCATTGCAATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * *
42105875 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTAT
1 AACTCACCATTGCAATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTAT
42105927 AGTAGTTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (53 bp):
AACTCACCATTGCAATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:42105961 original size:55 final size:54
Alignment explanation
Indices: 42105840--42106025 Score: 176
Period size: 55 Copynumber: 3.4 Consensus size: 54
42105830 ATTGCAATGT
* * * * * *
42105840 CTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCATTGCCATGC
1 CTTGACATAGTCTTACATGGTATCCTTGCCTTATAGAAATTAACAATGCCATGC
* * * * ** * *
42105893 CTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTATCAATGCCATGT
1 CTTGACATAGTCTTACATGGTATCCTTGCCTTATAG-AAATTAACAATGCCATGC
* * * * *
42105948 CTTGACATAGTCTTACATGATTTCCTTGCCTTGTAAAAATTAACAATGTCATGC
1 CTTGACATAGTCTTACATGGTATCCTTGCCTTATAGAAATTAACAATGCCATGC
*
42106002 CTTGACATAGTCTTACTTGGTATC
1 CTTGACATAGTCTTACATGGTATC
42106026 TTTAAACCCT
Statistics
Matches: 105, Mismatches: 26, Indels: 3
0.78 0.19 0.02
Matches are distributed among these distances:
53 30 0.29
54 35 0.33
55 40 0.38
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (54 bp):
CTTGACATAGTCTTACATGGTATCCTTGCCTTATAGAAATTAACAATGCCATGC
Found at i:42115618 original size:34 final size:34
Alignment explanation
Indices: 42115575--42115641 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
42115565 GAAGTGTTTT
** *
42115575 TCCAAAACACAAATTGTGTGAAAATTCGTTCTAA
1 TCCAAAACACAAATTGCATGAAAATTCATTCTAA
42115609 TCCAAAACACAAATTGCATGAAAATTCATTCTA
1 TCCAAAACACAAATTGCATGAAAATTCATTCTA
42115642 CATAAAACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.28
Consensus pattern (34 bp):
TCCAAAACACAAATTGCATGAAAATTCATTCTAA
Found at i:42127812 original size:5 final size:5
Alignment explanation
Indices: 42127802--42127826 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42127792 TATTGGGGTT
42127802 GACAG GACAG GACAG GACAG GACAG
1 GACAG GACAG GACAG GACAG GACAG
42127827 AAATGAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
GACAG
Found at i:42131798 original size:37 final size:37
Alignment explanation
Indices: 42131747--42131822 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
42131737 ATGATCGATG
*
42131747 TTGTTGTGATTAGCCAAATG-TAT-TGGCTTATAATGAT
1 TTGTTGTGATTAGCC--ATGAGATGTGGCTTATAATGAT
42131784 TTGTTGT-ATATAGCCATGAGATGTGGCTTATAATGAT
1 TTGTTGTGAT-TAGCCATGAGATGTGGCTTATAATGAT
42131821 TT
1 TT
42131823 TGGCTTGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
35 3 0.09
36 4 0.11
37 28 0.80
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (37 bp):
TTGTTGTGATTAGCCATGAGATGTGGCTTATAATGAT
Found at i:42132829 original size:43 final size:43
Alignment explanation
Indices: 42132708--42132829 Score: 106
Period size: 43 Copynumber: 2.8 Consensus size: 43
42132698 CAATGGCAAC
* * * *
42132708 GTCCCAGACGTGGTCTT--ACATGTAATCACAAATTGATGTCACT
1 GTCCCAGACGTGGTCTTACACAAG-AA-CACAAATCGATGCCAAT
* * * * *
42132751 GTCCTAGACAG-GGTCTGACACGAGAACATACATCGATGCCAAT
1 GTCCCAGAC-GTGGTCTTACACAAGAACACAAATCGATGCCAAT
*
42132794 GTCCCAGACGTGGTCTTACACAAGAACACATATCGA
1 GTCCCAGACGTGGTCTTACACAAGAACACAAATCGA
42132830 AAATCCTATG
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
42 1 0.02
43 54 0.89
44 3 0.05
45 3 0.05
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (43 bp):
GTCCCAGACGTGGTCTTACACAAGAACACAAATCGATGCCAAT
Found at i:42136881 original size:29 final size:29
Alignment explanation
Indices: 42136839--42136897 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42136829 ATTTTGTACG
42136839 AAGCTATCGATATCGAAGTCATCCCCAGC
1 AAGCTATCGATATCGAAGTCATCCCCAGC
42136868 AAGCTATCGATATCGAAGTCATCCCCAGC
1 AAGCTATCGATATCGAAGTCATCCCCAGC
42136897 A
1 A
42136898 CTAACTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (29 bp):
AAGCTATCGATATCGAAGTCATCCCCAGC
Found at i:42139309 original size:29 final size:29
Alignment explanation
Indices: 42139276--42139340 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
42139266 GTGACGAGAT
42139276 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42139305 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
42139334 CGGCACT
1 TGGCACT
42139341 GGGTGTGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:42139446 original size:2 final size:2
Alignment explanation
Indices: 42139441--42139467 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42139431 GTGCGTACTC
42139441 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
42139468 CTCCGATCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42143918 original size:43 final size:42
Alignment explanation
Indices: 42143862--42143992 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 42
42143852 ACATATCGTA
* *
42143862 CAATGCCAATGTCCCAGATATGGTCTTACATGTA-AGCACATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACACG-AGA-CACATAT
* * *
42143905 CGATGCCACTGTCCCAGACAGGGTCTTACACGAGCACACATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGAG-ACACATAT
* *
42143948 CAATGCCAATGTCCCAAACGTGGTCTTACACGAGAACACATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGAG-ACACATAT
42143991 CA
1 CA
42143993 GAAATCCTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
42 1 0.01
43 73 0.97
44 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (42 bp):
CAATGCCAATGTCCCAGACATGGTCTTACACGAGACACATAT
Found at i:42145567 original size:29 final size:29
Alignment explanation
Indices: 42145535--42145664 Score: 165
Period size: 29 Copynumber: 4.5 Consensus size: 29
42145525 ATAGTGAATC
*
42145535 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
*
42145564 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
* *
42145593 CGCACACTTAGTGCTATAGA--ATCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AACT
* * *
42145621 CGCACACTTAGTGCTATACAATTTTAAACC
1 CGCACACTTAGTGCTATA-TATTTTCAACT
42145651 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42145665 CAATCTTGTC
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.02
28 21 0.23
29 49 0.54
30 17 0.19
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAACT
Found at i:42147768 original size:26 final size:26
Alignment explanation
Indices: 42147736--42147785 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
42147726 TTAGCCCCTA
*
42147736 AATTTATTATTGTTATAATTTATCTC
1 AATTTATTATTGTTACAATTTATCTC
42147762 AATTTATTATTGTTACAATTTATC
1 AATTTATTATTGTTACAATTTATC
42147786 CCTAATTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (26 bp):
AATTTATTATTGTTACAATTTATCTC
Found at i:42150882 original size:7 final size:7
Alignment explanation
Indices: 42150861--42150922 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
42150851 CAACTTACCT
42150861 AATTGTGC
1 AATT-TGC
*
42150869 AAGTTGC
1 AATTTGC
42150876 AATTTGC
1 AATTTGC
*
42150883 AATTTTC
1 AATTTGC
*
42150890 AAGTTGC
1 AATTTGC
*
42150897 AATGTGC
1 AATTTGC
42150904 AAGTTGTGC
1 AA-TT-TGC
*
42150913 AAGTTGC
1 AATTTGC
42150920 AAT
1 AAT
42150923 GAAGCCTAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
7 32 0.76
8 5 0.12
9 5 0.12
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (7 bp):
AATTTGC
Found at i:42150892 original size:21 final size:23
Alignment explanation
Indices: 42150863--42150923 Score: 90
Period size: 21 Copynumber: 2.7 Consensus size: 23
42150853 ACTTACCTAA
*
42150863 TTGTGCAAGTTGCAATTTGCAA-
1 TTGTGCAAGTTGCAATGTGCAAG
*
42150885 TT-TTCAAGTTGCAATGTGCAAG
1 TTGTGCAAGTTGCAATGTGCAAG
42150907 TTGTGCAAGTTGCAATG
1 TTGTGCAAGTTGCAATG
42150924 AAGCCTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.50
22 4 0.12
23 13 0.38
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (23 bp):
TTGTGCAAGTTGCAATGTGCAAG
Found at i:42156193 original size:28 final size:29
Alignment explanation
Indices: 42156161--42156259 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
42156151 ATAATAAGCC
*
42156161 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
42156189 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
42156217 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
42156246 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42156260 CAATTCATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:42159028 original size:40 final size:40
Alignment explanation
Indices: 42158954--42159107 Score: 157
Period size: 40 Copynumber: 3.9 Consensus size: 40
42158944 CCGCACCAAG
* * * * * *
42158954 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
42158994 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
** * *
42159034 GCCTTCGGGTCTTAGCCCGGATATAATTACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * *
42159074 GTCC-TCGGGACTTAGCCCGGATATCACAATTTGC
1 G-CCTTCGGGTCTTAGCCCGGATATAACAACTTGC
42159108 TCATGCACAC
Statistics
Matches: 93, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 91 0.98
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:42160022 original size:13 final size:13
Alignment explanation
Indices: 42160004--42160028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42159994 CACTAAATTT
42160004 TCATGGATTCAAA
1 TCATGGATTCAAA
42160017 TCATGGATTCAA
1 TCATGGATTCAA
42160029 TATACCATTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:42167209 original size:28 final size:29
Alignment explanation
Indices: 42167177--42167275 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
42167167 ATAATAAGCC
*
42167177 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
42167205 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
42167233 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
42167262 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42167276 CAATTCATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:42170296 original size:46 final size:46
Alignment explanation
Indices: 42170190--42170455 Score: 189
Period size: 46 Copynumber: 5.6 Consensus size: 46
42170180 TATGAGACTT
* * * * * * * *
42170190 AGTGTAAGACCATGTCTAGGACATGGCATTAACATTGATACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAACCTCGAGATGAAAGCC
* *
42170238 AGTGTAAGACATGTCTGAGACATGCATCAACCTCGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATGAAAGCC
* * *
42170284 AGTGTAAGACATGTCTGGGACATGCATCGA-CTACGAGATG--TGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAACCT-CGAGATGAAAGCC
* *** *
42170328 AGTGTAAGACCATGTCTGGGACATGGCATTGAAACCAATAGATGAAAACC
1 AGTGTAAGA-CATGTCTGGGACAT-GCA-T-CAACCTCGAGATGAAAGCC
* *** *
42170378 AGTGTAAGACCTGTCTGGGACATGACATTGGCCTCGATATATGAAAGCC
1 AGTGTAAGACATGTCTGGGACATG-CATCAACCTCG--AGATGAAAGCC
42170427 AGTGTAAGATC-TGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
42170456 GACTTGATGG
Statistics
Matches: 173, Mismatches: 32, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
44 11 0.06
45 16 0.09
46 53 0.31
47 15 0.09
48 17 0.10
49 49 0.28
50 12 0.07
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATGAAAGCC
Found at i:42170400 original size:49 final size:49
Alignment explanation
Indices: 42170327--42170454 Score: 168
Period size: 49 Copynumber: 2.6 Consensus size: 49
42170317 CGAGATGTGT
42170327 CAGTGTAAGACCATGTCTGGGACATGGCATTGAAAC-CAATAGATGAAAAC
1 CAGTGTAAGACC-TGTCTGGGACATGGCATTG-AACTCAATAGATGAAAAC
* ** * * *
42170377 CAGTGTAAGACCTGTCTGGGACATGACATTGGCCTCGATATATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATTGAACTCAATAGATGAAAAC
*
42170426 CAGTGTAAGATCTGTCTGGGACATGGCAT
1 CAGTGTAAGACCTGTCTGGGACATGGCAT
42170455 CGACTTGATG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
48 1 0.01
49 56 0.81
50 12 0.17
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATTGAACTCAATAGATGAAAAC
Found at i:42170400 original size:140 final size:140
Alignment explanation
Indices: 42170144--42170500 Score: 368
Period size: 140 Copynumber: 2.5 Consensus size: 140
42170134 TTTGTGTGCT
* * * * *
42170144 AGTGTAAGACATGTCTGTGACATGCATCGGCCAC-ATTATGAGACTTAGTGTAAGACCATGTCTA
1 AGTGTAAGACATGTCTGGGACATGCATCGACTACGATGATGAG--TCAGTGTAAGACCATGTCTA
* * * *
42170208 GGACATGGCATTAACATTGATACGAGAGCTAGTGTAAGACATGTCTGAGACATG-CATCAACCTC
64 GGACATGGCATTAACATAGATA-GAAAACCAGTGTAAGACATGTCTGAGACATGACATCAACCTC
*
42170272 G-AGATGTAAGCC
128 GAAGATGAAAGCC
* *
42170284 AGTGTAAGACATGTCTGGGACATGCATCGACTACGA-GATGTGTCAGTGTAAGACCATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCGACTACGATGATGAGTCAGTGTAAGACCATGTCTAGG
* * ***
42170348 ACATGGCATTGAAACCAATAGAT-GAAAACCAGTGTAAGACCTGTCTGGGACATGACATTGGCCT
66 ACATGGCATT--AA-C-ATAGATAGAAAACCAGTGTAAGACATGTCTGAGACATGACATCAACCT
*
42170412 CGATATATGAAAGCC
127 CGA-AGATGAAAGCC
* * *
42170427 AGTGTAAGATC-TGTCTGGGACATGGCATCGACT-TGATGGATGAGCCAATGTAAAGACCATGTC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACTACGAT-GATGAGTCAGTGT-AAGACCATGTC
42170490 TAGGACATGGC
62 TAGGACATGGC
42170501 GTCGGCATTA
Statistics
Matches: 181, Mismatches: 23, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
138 30 0.17
140 63 0.35
141 10 0.06
142 5 0.03
143 32 0.18
144 10 0.06
145 10 0.06
146 21 0.12
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACTACGATGATGAGTCAGTGTAAGACCATGTCTAGG
ACATGGCATTAACATAGATAGAAAACCAGTGTAAGACATGTCTGAGACATGACATCAACCTCGAA
GATGAAAGCC
Done.