Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 44 of 332
Found at i:13246980 original size:7 final size:8
Alignment explanation
Indices: 13246963--13246987 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
13246953 CCAATTTGTG
13246963 AAAAATAA
1 AAAAATAA
13246971 AAAAATAA
1 AAAAATAA
13246979 AAAAATAA
1 AAAAATAA
13246987 A
1 A
13246988 GAACACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:13247810 original size:6 final size:6
Alignment explanation
Indices: 13247799--13247847 Score: 52
Period size: 5 Copynumber: 8.7 Consensus size: 6
13247789 TTTGCATGAA
*
13247799 TTTTCT TTTTCT TGTTTGT TTTTC- TTTTC- TTTTC- TTTTCT TTTT-T
1 TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
13247844 TTTT
1 TTTT
13247848 GTAGGTTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 20 0.51
6 14 0.36
7 5 0.13
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:13248215 original size:33 final size:33
Alignment explanation
Indices: 13248178--13248251 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
13248168 AAAATCATTA
13248178 GTGCAATAAGTTATCACATGAGTATCATACAAG
1 GTGCAATAAGTTATCACATGAGTATCATACAAG
13248211 GTGCAATAAGTTATCACATGAGTATCATACAAG
1 GTGCAATAAGTTATCACATGAGTATCATACAAG
*
13248244 TTGCAATA
1 GTGCAATA
13248252 GGAGATAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
GTGCAATAAGTTATCACATGAGTATCATACAAG
Found at i:13256616 original size:15 final size:15
Alignment explanation
Indices: 13256598--13256639 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
13256588 TCCATAACGG
*
13256598 AGAAATCCAGAATAT
1 AGAAATCCAGAATAA
13256613 AGAAATCCA-ACATAA
1 AGAAATCCAGA-ATAA
13256628 AGAAATCCAGAA
1 AGAAATCCAGAA
13256640 GAAAATATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.14
Consensus pattern (15 bp):
AGAAATCCAGAATAA
Found at i:13264022 original size:17 final size:17
Alignment explanation
Indices: 13264000--13264042 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
13263990 ATTTCATTTA
**
13264000 AAATGTCAATTTTCATC
1 AAATGTCAATTAACATC
13264017 AAATGTCAATTAACATC
1 AAATGTCAATTAACATC
13264034 AAAT-TCAAT
1 AAATGTCAAT
13264043 ATAATCATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (17 bp):
AAATGTCAATTAACATC
Found at i:13271269 original size:24 final size:24
Alignment explanation
Indices: 13271242--13271289 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
13271232 GGAAAACTTT
13271242 ACTAAAACGACCCATTCAGGTTTG
1 ACTAAAACGACCCATTCAGGTTTG
13271266 ACTAAAACGACCCATTCAGGTTTG
1 ACTAAAACGACCCATTCAGGTTTG
13271290 GAATTATCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (24 bp):
ACTAAAACGACCCATTCAGGTTTG
Found at i:13276882 original size:19 final size:19
Alignment explanation
Indices: 13276858--13276895 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
13276848 ACTCGTTTAA
13276858 AATTTGAGCTAAGATTGAG
1 AATTTGAGCTAAGATTGAG
13276877 AATTTGAGCTAAGATTGAG
1 AATTTGAGCTAAGATTGAG
13276896 TTTCAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (19 bp):
AATTTGAGCTAAGATTGAG
Found at i:13281163 original size:18 final size:18
Alignment explanation
Indices: 13281142--13281177 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13281132 TACTATGCTA
13281142 AAATTTAGATTTAAAATC
1 AAATTTAGATTTAAAATC
13281160 AAATTTAGATTTAAAATC
1 AAATTTAGATTTAAAATC
13281178 CTCCTTTAAT
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:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (18 bp):
AAATTTAGATTTAAAATC
Found at i:13281330 original size:33 final size:34
Alignment explanation
Indices: 13281274--13281340 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
13281264 TTAAAGTGAT
13281274 TGCATAAAATTATTTTTAAGCTTTAAACATTAGAC
1 TGCATAAAATTA-TTTTAAGCTTTAAACATTAGAC
13281309 TGCATAAAATTA-TTTAAGCTTTAAACATTAGA
1 TGCATAAAATTATTTTAAGCTTTAAACATTAGA
13281341 TTGACATGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 20 0.62
35 12 0.38
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (34 bp):
TGCATAAAATTATTTTAAGCTTTAAACATTAGAC
Found at i:13285161 original size:65 final size:65
Alignment explanation
Indices: 13285053--13285187 Score: 189
Period size: 65 Copynumber: 2.1 Consensus size: 65
13285043 CTATTTTTAA
* * * * * *
13285053 ATTTATACTATTTTATATTATGTTAATATCATGCTTAAGTCTAACACGACTTGACCCACAAACAC
1 ATTTATAATACTTTATATTATGTCAATATCATACTTAAATCTAACACGACTTAACCCACAAACAC
* *
13285118 ATTTATAATACTTTATATTATGTCAATATCATACTTAAATCTAACCCGACTTAACCTACAAACAC
1 ATTTATAATACTTTATATTATGTCAATATCATACTTAAATCTAACACGACTTAACCCACAAACAC
*
13285183 CTTTA
1 ATTTA
13285188 CTTTAAAATC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (65 bp):
ATTTATAATACTTTATATTATGTCAATATCATACTTAAATCTAACACGACTTAACCCACAAACAC
Found at i:13286219 original size:16 final size:16
Alignment explanation
Indices: 13286192--13286233 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
13286182 TCAAATTGAA
*
13286192 TATTTTTT-ATATTAT
1 TATTTTTTAATATAAT
13286207 T-TGTTTTTAATATAAT
1 TAT-TTTTTAATATAAT
13286223 TATTTTTTAAT
1 TATTTTTTAAT
13286234 TTGTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 6 0.26
16 15 0.65
17 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TATTTTTTAATATAAT
Found at i:13286997 original size:20 final size:20
Alignment explanation
Indices: 13286948--13286998 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
13286938 CTTTTGAAAT
* *
13286948 TTTGGTATAATCTTAAAGATA
1 TTTGGTA-AATCTTAAAAAAA
*
13286969 -TTAGTAAATCTTAAAAAAA
1 TTTGGTAAATCTTAAAAAAA
13286988 TTTGGTAAATC
1 TTTGGTAAATC
13286999 CTTGAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (20 bp):
TTTGGTAAATCTTAAAAAAA
Found at i:13287231 original size:20 final size:20
Alignment explanation
Indices: 13287191--13287245 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
13287181 TAGTATATCC
13287191 TTAAAAATTTT-A-ATAAAT
1 TTAAAAATTTTGATATAAAT
* * *
13287209 TTAGATATTTTGATATAATT
1 TTAAAAATTTTGATATAAAT
*
13287229 TTAAAAATTTTGGTATA
1 TTAAAAATTTTGATATA
13287246 TTAAAATGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 9 0.31
19 1 0.03
20 19 0.66
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
TTAAAAATTTTGATATAAAT
Found at i:13287318 original size:19 final size:19
Alignment explanation
Indices: 13287294--13287364 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
13287284 AAAGTTTAAG
13287294 AAATTTTGATATAACTTTA
1 AAATTTTGATATAACTTTA
* * *
13287313 AAATTTTTGATACATCCTTAA
1 AAA-TTTTGATATA-ACTTTA
* *
13287334 AAATTTAGCTATAACTTTA
1 AAATTTTGATATAACTTTA
13287353 AATATTTTGATA
1 AA-ATTTTGATA
13287365 AGTATTTAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
19 9 0.23
20 23 0.59
21 7 0.18
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (19 bp):
AAATTTTGATATAACTTTA
Found at i:13287378 original size:40 final size:40
Alignment explanation
Indices: 13287292--13287381 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
13287282 TAAAAGTTTA
* *
13287292 AGAAATTTTGATATAACTTTAAAATTTTTGATACATCCTT
1 AGAAATTTAGATATAACTTTAAAATTTTTGATACATACTT
* * *
13287332 AAAAATTTAGCTATAACTTT-AAATATTTTGATA-AGTATTT
1 AGAAATTTAGATATAACTTTAAAAT-TTTTGATACA-TACTT
13287372 AGAAATTTAG
1 AGAAATTTAG
13287382 GTTTAAGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 5 0.12
40 37 0.88
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (40 bp):
AGAAATTTAGATATAACTTTAAAATTTTTGATACATACTT
Found at i:13287977 original size:20 final size:19
Alignment explanation
Indices: 13287954--13288004 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
13287944 TTGTATAACG
13287954 TTAGATATTTTGATAAA-TAT
1 TTAGA-ATTTTGATAAACT-T
13287974 TTAGGAATTTTGATAAACTT
1 TTA-GAATTTTGATAAACTT
*
13287994 TTAGAAATTTG
1 TTAGAATTTTG
13288005 GTTTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 7 0.25
20 18 0.64
21 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (19 bp):
TTAGAATTTTGATAAACTT
Found at i:13295781 original size:25 final size:25
Alignment explanation
Indices: 13295729--13295779 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
13295719 TTGTATTTGA
*
13295729 TATTTTAAATAAATTTTATTTATTT
1 TATTTTAAATAAATGTTATTTATTT
* *
13295754 TATTTTATATAAATAGTTGTTTATTT
1 TATTTTAAATAAAT-GTTATTTATTT
13295780 ATATATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (25 bp):
TATTTTAAATAAATGTTATTTATTT
Found at i:13296313 original size:87 final size:88
Alignment explanation
Indices: 13296055--13296495 Score: 365
Period size: 87 Copynumber: 5.2 Consensus size: 88
13296045 TGTTTAACAA
* * * * ** *
13296055 ATTTTATTTCTAAAACGAGTATT-AAACTAAATAAAATC-AGTTTCGGGA-TTTATTTTCGCTGT
1 ATTTTATTTCCAAAACGAGTATTAAAATTAAATAAAATCTA-TTTTGAGATTTTATTCCCGCCGT
* * *
13296117 CCAATAGATATTATTCCAATTTTG
65 TCAACAGATTTTATTCCAATTTTG
* * * * * * *
13296141 ATTTGATTTCCAAAATGAGTATTAAAATTAAATAAAATTTA-ATTCAAAATTTATTCCCGCCGTT
1 ATTTTATTTCCAAAACGAGTATTAAAATTAAATAAAATCTATTTTGAGATTTTATTCCCGCCGTT
*
13296205 CAACAGATTTTATTCCAATTTTA
66 CAACAGATTTTATTCCAATTTTG
* *
13296228 ATTTTATTTCCAAAACGAGTATTAAAATTAAATAAAATCTATTTTGAGATTTTTTTCCCACCGTT
1 ATTTTATTTCCAAAACGAGTATTAAAATTAAATAAAATCTATTTTGAGATTTTATTCCCGCCGTT
* * * *
13296293 TAATATATTTTATTCCATTTTTG
66 CAACAGATTTTATTCCAATTTTG
* * * * * *
13296316 ATTTTGTTGCCAAAA-GAGAAACTAAAATGAAATAAAATCTGTTTTGAGA-TTTATTCCCGCCGT
1 ATTTTATTTCCAAAACGAG-TATTAAAATTAAATAAAATCTATTTTGAGATTTTATTCCCGCCGT
* *
13296379 TTAACATATTTTATT-CAATTTTG
65 TCAACAGATTTTATTCCAATTTTG
* ** * * * * *
13296402 ATTTTGTTTCC-AAATTAGAATT-AAATTGAAT--AATC---TTCGGGA-TTTATTCCCGCTGTT
1 ATTTTATTTCCAAAACGAGTATTAAAATTAAATAAAATCTATTTTGAGATTTTATTCCCGCCGTT
* * *
13296459 TAACAGATTTTATT-CGATCTTG
66 CAACAGATTTTATTCCAATTTTG
13296481 ATTTTATTTCCAAAA
1 ATTTTATTTCCAAAA
13296496 AAAGACTTAA
Statistics
Matches: 295, Mismatches: 53, Indels: 20
0.80 0.14 0.05
Matches are distributed among these distances:
79 48 0.16
80 3 0.01
82 4 0.01
84 7 0.02
85 6 0.02
86 41 0.14
87 111 0.38
88 75 0.25
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (88 bp):
ATTTTATTTCCAAAACGAGTATTAAAATTAAATAAAATCTATTTTGAGATTTTATTCCCGCCGTT
CAACAGATTTTATTCCAATTTTG
Found at i:13296329 original size:88 final size:86
Alignment explanation
Indices: 13296127--13296495 Score: 369
Period size: 87 Copynumber: 4.3 Consensus size: 86
13296117 CCAATAGATA
* * ** *
13296127 TTATTCCAATTTTGA-TTTGATTTCCAAAATGAGTATTAAAATTAAATAAAATTTAATTCAAAAT
1 TTATTCCAATTTTGATTTTG-TTTCCAAAA-GAGTATTAAAATTAAATAAAATCTATTTTGAGAT
* *
13296191 TTATTCCCGCCGTTCAACAGATT
64 TTATTCCCGCCGTTTAACATATT
* *
13296214 TTATTCCAATTTTAATTTTATTTCCAAAACGAGTATTAAAATTAAATAAAATCTATTTTGAGATT
1 TTATTCCAATTTTGATTTTGTTTCCAAAA-GAGTATTAAAATTAAATAAAATCTATTTTGAGA-T
* * *
13296279 TTTTTCCCACCGTTTAATATATT
64 TTATTCCCGCCGTTTAACATATT
* * * * * *
13296302 TTATTCCATTTTTGATTTTGTTGCCAAAAGAGAAACTAAAATGAAATAAAATCTGTTTTGAGATT
1 TTATTCCAATTTTGATTTTGTTTCCAAAAGAG-TATTAAAATTAAATAAAATCTATTTTGAGATT
13296367 TATTCCCGCCGTTTAACATATT
65 TATTCCCGCCGTTTAACATATT
** * * * *
13296389 TTATT-CAATTTTGATTTTGTTTCCAAATTAGAATT-AAATTGAAT--AATC---TTCGGGATTT
1 TTATTCCAATTTTGATTTTGTTTCCAAAAGAGTATTAAAATTAAATAAAATCTATTTTGAGATTT
* *
13296447 ATTCCCGCTGTTTAACAGATT
66 ATTCCCGCCGTTTAACATATT
* * *
13296468 TTATT-CGATCTTGATTTTATTTCCAAAA
1 TTATTCCAATTTTGATTTTGTTTCCAAAA
13296496 AAAGACTTAA
Statistics
Matches: 240, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
79 51 0.21
82 4 0.02
84 7 0.03
85 3 0.01
86 22 0.09
87 80 0.33
88 73 0.30
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (86 bp):
TTATTCCAATTTTGATTTTGTTTCCAAAAGAGTATTAAAATTAAATAAAATCTATTTTGAGATTT
ATTCCCGCCGTTTAACATATT
Found at i:13296353 original size:175 final size:172
Alignment explanation
Indices: 13296054--13296415 Score: 408
Period size: 175 Copynumber: 2.1 Consensus size: 172
13296044 CTGTTTAACA
* * * *
13296054 AATTTTATTTCTAAAACGAGTATTAAACTAAATAAAATCAGTTTCGGGATTTATTTTCGCTGTCC
1 AATTTTATTTCCAAAACGAGTATTAAACTAAATAAAATCAGTTTCGAGATTTATTTTCACCGTCC
* * * * *
13296119 AATAGATATTATTCCAATTTTGATTTGATTTCCAAAATGAGTATTAAAATTAAATAAAATTTAAT
66 AATAGATATTATTCCAATTTTGATTTGATTGCCAAAATGAGAACTAAAATGAAATAAAATCTAAT
13296184 TCAAAATTTATTCCCGCCGTTCAACAGATTTTATTCCAATTTT
131 TCAAAATTTATTCCCGCCGTTCAACAGATTTTATT-CAATTTT
* *
13296227 AATTTTATTTCCAAAACGAGTATTAAAATTAAATAAAATCTA-TTTTGAGATTT-TTTTCCCACC
1 AATTTTATTTCCAAAACGAGTATT-AAACTAAATAAAATC-AGTTTCGAGATTTATTTT--CACC
** * * *
13296290 GTTTAATATATTTTATTCCATTTTTGATTTTG-TTGCCAAAA-GAGAAACTAAAATGAAATAAAA
62 GTCCAATAGATATTATTCCAATTTTGA-TTTGATTGCCAAAATGAG-AACTAAAATGAAATAAAA
** ** * * *
13296353 TCTGTTTTGAGATTTATTCCCGCCGTTTAACATATTTTATTCAATTTT
125 TCTAATTCAAAATTTATTCCCGCCGTTCAACAGATTTTATTCAATTTT
* *
13296401 GATTTTGTTTCCAAA
1 AATTTTATTTCCAAA
13296416 TTAGAATTAA
Statistics
Matches: 158, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
173 27 0.17
174 46 0.29
175 81 0.51
176 4 0.03
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (172 bp):
AATTTTATTTCCAAAACGAGTATTAAACTAAATAAAATCAGTTTCGAGATTTATTTTCACCGTCC
AATAGATATTATTCCAATTTTGATTTGATTGCCAAAATGAGAACTAAAATGAAATAAAATCTAAT
TCAAAATTTATTCCCGCCGTTCAACAGATTTTATTCAATTTT
Found at i:13296513 original size:79 final size:79
Alignment explanation
Indices: 13296363--13296514 Score: 198
Period size: 79 Copynumber: 1.9 Consensus size: 79
13296353 TCTGTTTTGA
* * * **
13296363 GATTTATTCCCGCCGTTTAACATATTTTATTCAATTTTGATTTTGTTTCCAAATTAGAATTAAAT
1 GATTTATTCCCGCCGTTTAACAGATTTTATTCAATCTTGATTTTATTTCCAAAAAAGAATTAAAT
**
13296428 TGAATAATCTTCGG
66 CAAATAATCTTCGG
* * *
13296442 GATTTATTCCCGCTGTTTAACAGATTTTATTCGATCTTGATTTTATTTCCAAAAAAAGACTT-AA
1 GATTTATTCCCGCCGTTTAACAGATTTTATTCAATCTTGATTTTATTTCC-AAAAAAGAATTAAA
13296506 TCAAATAAT
65 TCAAATAAT
13296515 TTTGTTTCGG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
79 54 0.87
80 8 0.13
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (79 bp):
GATTTATTCCCGCCGTTTAACAGATTTTATTCAATCTTGATTTTATTTCCAAAAAAGAATTAAAT
CAAATAATCTTCGG
Found at i:13302425 original size:86 final size:86
Alignment explanation
Indices: 13302280--13302450 Score: 306
Period size: 86 Copynumber: 2.0 Consensus size: 86
13302270 CTTAGATCCC
* * *
13302280 ACATTAGTTAAATACCAAGTGTGAGATGTGTATATTTATGATAACCCACTTGAAGGGTGATTGAA
1 ACATTAGTTAAATACCAAGTGTGAGATGTGTAAATATATGAGAACCCACTTGAAGGGTGATTGAA
*
13302345 TGACTAAGCTTGAAACCTTGT
66 TAACTAAGCTTGAAACCTTGT
13302366 ACATTAGTTAAATACCAAGTGTGAGATGTGTAAATATATGAGAACCCACTTGAAGGGTGATTGAA
1 ACATTAGTTAAATACCAAGTGTGAGATGTGTAAATATATGAGAACCCACTTGAAGGGTGATTGAA
13302431 TAACTAAGCTTGAAACCTTG
66 TAACTAAGCTTGAAACCTTG
13302451 CCTCGTGCGT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (86 bp):
ACATTAGTTAAATACCAAGTGTGAGATGTGTAAATATATGAGAACCCACTTGAAGGGTGATTGAA
TAACTAAGCTTGAAACCTTGT
Found at i:13303411 original size:34 final size:34
Alignment explanation
Indices: 13303371--13303436 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
13303361 TTTCCAATTG
13303371 ATGCTAAGGTGATCATGTCAACATTTCACTTTGT
1 ATGCTAAGGTGATCATGTCAACATTTCACTTTGT
*
13303405 ATGCTAAGGTGATCATGTCACCATTTCACTTT
1 ATGCTAAGGTGATCATGTCAACATTTCACTTT
13303437 CCAATTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (34 bp):
ATGCTAAGGTGATCATGTCAACATTTCACTTTGT
Found at i:13303503 original size:34 final size:34
Alignment explanation
Indices: 13303455--13303529 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
13303445 TATGATGTTT
*
13303455 TCACTTAGCCAACATTTAGTAAATTCCAAATACA
1 TCACCTAGCCAACATTTAGTAAATTCCAAATACA
13303489 TCACCTAGCCAACATTTAGTAAATTCCAAATACA
1 TCACCTAGCCAACATTTAGTAAATTCCAAATACA
13303523 TCACCTA
1 TCACCTA
13303530 ACATATTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.28
Consensus pattern (34 bp):
TCACCTAGCCAACATTTAGTAAATTCCAAATACA
Found at i:13309577 original size:19 final size:20
Alignment explanation
Indices: 13309549--13309588 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
13309539 CTATTTATAC
13309549 TTTAGATTAACTTAA-TTAA
1 TTTAGATTAACTTAACTTAA
*
13309568 TTTAGTTTAACTTAACTTAA
1 TTTAGATTAACTTAACTTAA
13309588 T
1 T
13309589 AAAGGTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTAGATTAACTTAACTTAA
Found at i:13315111 original size:34 final size:34
Alignment explanation
Indices: 13315073--13315137 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
13315063 TCAGTCAAAT
*
13315073 GTAGTTTGGGCCTAAGCCCATTTCAGTTTCAGTA
1 GTAGTTCGGGCCTAAGCCCATTTCAGTTTCAGTA
*
13315107 GTAGTTCGGGCCTTAGCCCATTTCAGTTTCA
1 GTAGTTCGGGCCTAAGCCCATTTCAGTTTCA
13315138 AGATCGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (34 bp):
GTAGTTCGGGCCTAAGCCCATTTCAGTTTCAGTA
Found at i:13320187 original size:42 final size:42
Alignment explanation
Indices: 13320079--13320188 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 42
13320069 ACCATACCAA
* * *
13320079 GCCATATCCCAGATATGGTCTTACATGAAATCTCCTATCGAT
1 GCCATATCCCAGATATGGTCTTACATCAAATCTCCAATCGAC
* * * **
13320121 GCCAATAGCCCAGCTATGGTCTTAC-TCAAAGTTTTGAATCGAC
1 GCC-ATATCCCAGATATGGTCTTACATCAAA-TCTCCAATCGAC
13320164 GCCATATCCCAGATATGGTCTTACA
1 GCCATATCCCAGATATGGTCTTACA
13320189 CGTAATCTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 26 0.47
43 29 0.53
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACATCAAATCTCCAATCGAC
Found at i:13332188 original size:18 final size:18
Alignment explanation
Indices: 13332167--13332210 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
13332157 GAAGCTGATT
*
13332167 GATCCATTTCAGAAGCCG
1 GATCCATCTCAGAAGCCG
13332185 GATCCATCTCAGAAGCCG
1 GATCCATCTCAGAAGCCG
*
13332203 GATTCATC
1 GATCCATC
13332211 ATCAAGACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (18 bp):
GATCCATCTCAGAAGCCG
Found at i:13333352 original size:18 final size:18
Alignment explanation
Indices: 13333318--13333369 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
13333308 CTGTGAACCG
*
13333318 TGTGGACCCATAC-GCCCA
1 TGTGG-CCCACACGGCCCA
13333336 TGTGGCCCACACGGCCCA
1 TGTGGCCCACACGGCCCA
13333354 TGTGGCCCACACGGCC
1 TGTGGCCCACACGGCC
13333370 AAAATTTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.17, C:0.42, G:0.27, T:0.13
Consensus pattern (18 bp):
TGTGGCCCACACGGCCCA
Found at i:13335451 original size:19 final size:21
Alignment explanation
Indices: 13335421--13335460 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
13335411 TCTAAAATAT
13335421 AAATCACACAATTTA-AAAAA
1 AAATCACACAATTTACAAAAA
13335441 AAATC-CACAATTTACAAAAA
1 AAATCACACAATTTACAAAAA
13335461 TCCACAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATCACACAATTTACAAAAA
Found at i:13336340 original size:22 final size:23
Alignment explanation
Indices: 13336306--13336349 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
13336296 CTAGTTTGTA
* *
13336306 ATCTCTTTATCTTATTTATTTTT
1 ATCTATTTATCTTATTAATTTTT
13336329 ATCTATTT-TCTTATTAATTTT
1 ATCTATTTATCTTATTAATTTT
13336350 CTCGAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.68
Consensus pattern (23 bp):
ATCTATTTATCTTATTAATTTTT
Found at i:13337226 original size:16 final size:16
Alignment explanation
Indices: 13337205--13337240 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13337195 TTTGTTCTTA
*
13337205 AAAAAAATAGAAAAAG
1 AAAAAAAGAGAAAAAG
*
13337221 AAAAAAAGAGAGAAAG
1 AAAAAAAGAGAAAAAG
13337237 AAAA
1 AAAA
13337241 CAAAAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAG
Found at i:13338676 original size:3 final size:3
Alignment explanation
Indices: 13338668--13338753 Score: 79
Period size: 3 Copynumber: 29.0 Consensus size: 3
13338658 TGCATAATAG
* * *
13338668 AAT AAT AAT AAT AAT GAA- AAT GAT AAT AAT GAT AAT AAT AAT ACT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
13338713 AAT AAT AAC AAC AAT AAT AA- AA- AAT AGT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
13338754 CTAATTTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
2 6 0.09
3 58 0.84
4 5 0.07
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:13338850 original size:5 final size:5
Alignment explanation
Indices: 13338833--13338864 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
13338823 AAAGGTAAAG
*
13338833 AATAA AATGA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
13338865 ACGCACGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:13339745 original size:21 final size:21
Alignment explanation
Indices: 13339719--13339763 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13339709 TATATATATG
13339719 TTTTTTAT-TTTCGTATTTCGA
1 TTTTTTATGTTTCG-ATTTCGA
* *
13339740 TTTTTTTTGTTTCGATTTCTA
1 TTTTTTATGTTTCGATTTCGA
13339761 TTT
1 TTT
13339764 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (21 bp):
TTTTTTATGTTTCGATTTCGA
Found at i:13341283 original size:22 final size:22
Alignment explanation
Indices: 13341258--13341299 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13341248 ACTAAGTCAG
* *
13341258 CAGAACGGCTCAACGCCGTAGA
1 CAGAACAGCTAAACGCCGTAGA
*
13341280 CAGAACAGCTAAAGGCCGTA
1 CAGAACAGCTAAACGCCGTA
13341300 AATATCGCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.29, G:0.26, T:0.10
Consensus pattern (22 bp):
CAGAACAGCTAAACGCCGTAGA
Found at i:13346148 original size:11 final size:11
Alignment explanation
Indices: 13346132--13346157 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13346122 AGAATCAAGG
13346132 AAAAATAAAAT
1 AAAAATAAAAT
13346143 AAAAATAAAAT
1 AAAAATAAAAT
13346154 AAAA
1 AAAA
13346158 CCAAATAAAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:13348759 original size:3 final size:3
Alignment explanation
Indices: 13348751--13348783 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
13348741 GCTAGACAGT
*
13348751 AGA AGA AG- AGA AGA AGA AGA AGA AAA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
13348784 TTAATAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:13349395 original size:6 final size:6
Alignment explanation
Indices: 13349379--13349407 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
13349369 CAAAGGCGGT
13349379 AGGCA- AGGCAG AGGCAG AGGCAG AGGCAG
1 AGGCAG AGGCAG AGGCAG AGGCAG AGGCAG
13349408 CAGTAGTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.34, C:0.17, G:0.48, T:0.00
Consensus pattern (6 bp):
AGGCAG
Found at i:13354623 original size:17 final size:18
Alignment explanation
Indices: 13354593--13354630 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
13354583 CTCGTGTTTT
*
13354593 CCCGTGTGGGCCCACATG
1 CCCGTGTGGGCCCACACG
13354611 CCCGTGT-GGCCCACACG
1 CCCGTGTGGGCCCACACG
13354628 CCC
1 CCC
13354631 AGATTGGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.11, C:0.47, G:0.29, T:0.13
Consensus pattern (18 bp):
CCCGTGTGGGCCCACACG
Found at i:13368684 original size:38 final size:38
Alignment explanation
Indices: 13368640--13368754 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 38
13368630 TAAATTCATA
13368640 CAGTGTTATTCAGGCTTAGTGCTTAACAGGCTTAGTAC
1 CAGTGTTATTCAGGCTTAGTGCTTAACAGGCTTAGTAC
* * *
13368678 CGGTGTTATTTAGGCTTAGTGCTAGTGTTATTCAGGCTTAGTAC
1 CAGTGTTATTCAGGCTTAGTGC-----TTA-ACAGGCTTAGTAC
* *
13368722 CAATGTTATTCAGGCTTAGTGCCTAACAGGCTT
1 CAGTGTTATTCAGGCTTAGTGCTTAACAGGCTT
13368755 TGAGCCGGTG
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
38 27 0.43
39 2 0.03
43 3 0.05
44 31 0.49
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (38 bp):
CAGTGTTATTCAGGCTTAGTGCTTAACAGGCTTAGTAC
Found at i:13368695 original size:22 final size:22
Alignment explanation
Indices: 13368666--13368741 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
13368656 TAGTGCTTAA
*
13368666 CAGGCTTAGTACCGGTGTTATT
1 CAGGCTTAGTACCAGTGTTATT
* * *
13368688 TAGGCTTAGTGCTAGTGTTATT
1 CAGGCTTAGTACCAGTGTTATT
*
13368710 CAGGCTTAGTACCAATGTTATT
1 CAGGCTTAGTACCAGTGTTATT
13368732 CAGGCTTAGT
1 CAGGCTTAGT
13368742 GCCTAACAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (22 bp):
CAGGCTTAGTACCAGTGTTATT
Found at i:13373294 original size:108 final size:108
Alignment explanation
Indices: 13373105--13373310 Score: 376
Period size: 108 Copynumber: 1.9 Consensus size: 108
13373095 GAACAGTAGC
* *
13373105 AAATTGACTTCCATTAACAAAAGAGAAGAAAAGGTCTGGTCAAGAAAACCAGGGGCAACAAAACT
1 AAATTGACTTCCATTAACAAAAGAGAAGAAAAGGCCTGGTCAAGAAAACCAGGAGCAACAAAACT
*
13373170 ACATCAGTCCCAAGAAACCAAACAAACATCAAAAGACGGTATA
66 ACATCAATCCCAAGAAACCAAACAAACATCAAAAGACGGTATA
13373213 AAATTGACTTCCATTAACAAAAGAGAAGAAAAGGCCTGGTCAAGAAAACCAGGAGCAACAAAACT
1 AAATTGACTTCCATTAACAAAAGAGAAGAAAAGGCCTGGTCAAGAAAACCAGGAGCAACAAAACT
*
13373278 ACATCAATCCCGAGAAACCAAACAAACATCAAA
66 ACATCAATCCCAAGAAACCAAACAAACATCAAA
13373311 GACCCAAAAC
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 94 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (108 bp):
AAATTGACTTCCATTAACAAAAGAGAAGAAAAGGCCTGGTCAAGAAAACCAGGAGCAACAAAACT
ACATCAATCCCAAGAAACCAAACAAACATCAAAAGACGGTATA
Found at i:13382566 original size:12 final size:12
Alignment explanation
Indices: 13382549--13382576 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13382539 TCACATTGAA
13382549 TATTTAAATTTT
1 TATTTAAATTTT
13382561 TATTTAAATTTT
1 TATTTAAATTTT
13382573 TATT
1 TATT
13382577 CAACTTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTAAATTTT
Found at i:13383234 original size:5 final size:5
Alignment explanation
Indices: 13383226--13383257 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
13383216 ATACTTTAAT
13383226 TATAA TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TATAA TA
13383258 ATATTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:13383487 original size:20 final size:21
Alignment explanation
Indices: 13383440--13383490 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
13383430 TAATCCTTAT
*
13383440 ACCTAATTAACCTTAATCTAA
1 ACCTAATTAACCTTAATCAAA
* *
13383461 A-CAAATTCACC-TAATCAAA
1 ACCTAATTAACCTTAATCAAA
13383480 ACCTAATTAAC
1 ACCTAATTAAC
13383491 TACATTACTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 8 0.33
20 15 0.62
21 1 0.04
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (21 bp):
ACCTAATTAACCTTAATCAAA
Found at i:13395353 original size:8 final size:8
Alignment explanation
Indices: 13395330--13395354 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
13395320 TTTAATAATA
13395330 TATTTTAT
1 TATTTTAT
13395338 TATTTTAT
1 TATTTTAT
13395346 TATTTTAT
1 TATTTTAT
13395354 T
1 T
13395355 TAGTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:13395478 original size:38 final size:38
Alignment explanation
Indices: 13395427--13395503 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
13395417 TTCCCATGTA
13395427 AACTAACGTGAGAAGAAGAGAGAAAGAAAGAAAGTTTT
1 AACTAACGTGAGAAGAAGAGAGAAAGAAAGAAAGTTTT
13395465 AACTAACGTGAGAAGAAGAGAGAAAGAAAGAAAGTTTT
1 AACTAACGTGAGAAGAAGAGAGAAAGAAAGAAAGTTTT
13395503 A
1 A
13395504 CTTTTTTTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.53, C:0.05, G:0.26, T:0.16
Consensus pattern (38 bp):
AACTAACGTGAGAAGAAGAGAGAAAGAAAGAAAGTTTT
Found at i:13404762 original size:37 final size:35
Alignment explanation
Indices: 13404720--13404839 Score: 100
Period size: 37 Copynumber: 3.3 Consensus size: 35
13404710 TCGGTCATAG
*
13404720 TAACAATATCAATGGCATGTTTATCATGCTTTCAGCT
1 TAACAATATCAATGGCATGCTTATCATGC-TTCAG-T
* * *
13404757 TAACAAT-TCTAGTGGTATGCTTATCATGCTTCTGGTT
1 TAACAATATC-AATGGCATGCTTATCATGCTTC-AG-T
* * * *
13404794 TAGCAATCTCAATAGCGTGCTTATCATGCATTCA-T
1 TAACAATATCAATGGCATGCTTATCATGC-TTCAGT
13404829 TAACAATATCA
1 TAACAATATCA
13404840 TGTCATATAA
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
35 10 0.15
36 5 0.08
37 46 0.70
38 5 0.08
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (35 bp):
TAACAATATCAATGGCATGCTTATCATGCTTCAGT
Found at i:13407996 original size:30 final size:30
Alignment explanation
Indices: 13407962--13408022 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
13407952 TCCTTAACTC
13407962 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
13407992 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
13408022 A
1 A
13408023 GGCTCAGGAA
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:13409699 original size:31 final size:32
Alignment explanation
Indices: 13409663--13409726 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
13409653 TTCATCCAGG
**
13409663 TAAGCC-TTGTTTTTCTTCCGTTCTTCAACTT
1 TAAGCCTTTGTTTTTCTTCAATTCTTCAACTT
*
13409694 TAAGCCTTTTTTTTTCTTCAATTCTTCAACTT
1 TAAGCCTTTGTTTTTCTTCAATTCTTCAACTT
13409726 T
1 T
13409727 TTCCATCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 6 0.21
32 23 0.79
ACGTcount: A:0.16, C:0.23, G:0.06, T:0.55
Consensus pattern (32 bp):
TAAGCCTTTGTTTTTCTTCAATTCTTCAACTT
Found at i:13412712 original size:38 final size:39
Alignment explanation
Indices: 13412662--13412911 Score: 288
Period size: 46 Copynumber: 5.9 Consensus size: 39
13412652 CTGATATGAA
13412662 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
13412701 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
13412739 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG
13412782 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 --ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
13412823 ATATGAGATGTATAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 --AT--G-TG--TAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
13412869 ACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 --ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
13412912 ATGACAGAAA
Statistics
Matches: 192, Mismatches: 4, Indels: 23
0.88 0.02 0.11
Matches are distributed among these distances:
38 74 0.39
41 5 0.03
43 3 0.02
44 3 0.02
46 107 0.56
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (39 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:13412806 original size:46 final size:46
Alignment explanation
Indices: 13412739--13412955 Score: 310
Period size: 46 Copynumber: 4.7 Consensus size: 46
13412729 TGGCAACCTG
*
13412739 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* *
13412785 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
*
13412831 TGTATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* ** *
13412877 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAA
* * * *
13412923 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
13412956 TCACGTCAAA
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 157 0.99
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.21
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
Found at i:13413261 original size:23 final size:25
Alignment explanation
Indices: 13413216--13413262 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
13413206 AATAAATATA
*
13413216 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
13413241 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
13413263 ATGAATGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:13419244 original size:11 final size:11
Alignment explanation
Indices: 13419230--13419254 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13419220 AGAAGATTAA
13419230 AAGAGAGCTTT
1 AAGAGAGCTTT
13419241 AAGAGAGCTTT
1 AAGAGAGCTTT
13419252 AAG
1 AAG
13419255 GGATTTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (11 bp):
AAGAGAGCTTT
Found at i:13419559 original size:9 final size:9
Alignment explanation
Indices: 13419521--13419562 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
13419511 AGGTTTATAG
13419521 TAAAACTTTT
1 TAAAA-TTTT
13419531 T-AAATTTT
1 TAAAATTTT
13419539 TAATAATTTT
1 TAA-AATTTT
*
13419549 TAAAATCTT
1 TAAAATTTT
13419558 TAAAA
1 TAAAA
13419563 AAAATCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 5 0.17
9 14 0.48
10 10 0.34
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (9 bp):
TAAAATTTT
Found at i:13419675 original size:19 final size:19
Alignment explanation
Indices: 13419651--13419695 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
13419641 TAACTGAAAA
13419651 TGTCATGTCATTATTGACT
1 TGTCATGTCATTATTGACT
13419670 TGTCATGTCATTATTGACT
1 TGTCATGTCATTATTGACT
13419689 TGTCATG
1 TGTCATG
13419696 GCACATTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.47
Consensus pattern (19 bp):
TGTCATGTCATTATTGACT
Found at i:13421801 original size:27 final size:26
Alignment explanation
Indices: 13421753--13421812 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
13421743 GCGAGGCTGC
*
13421753 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* *
13421780 CAGATATTGTGGCTAAGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
13421806 CAAATAT
1 CAGATAT
13421813 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:13422175 original size:8 final size:8
Alignment explanation
Indices: 13422162--13422208 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
13422152 AAGTGGGCCG
13422162 TTGGCCCA
1 TTGGCCCA
**
13422170 TTGGCCTG
1 TTGGCCCA
13422178 TTGGCCCA
1 TTGGCCCA
**
13422186 TTGGCCTG
1 TTGGCCCA
13422194 TTGGCCCA
1 TTGGCCCA
13422202 TTGGCCC
1 TTGGCCC
13422209 GTTTTCGGCC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.06, C:0.34, G:0.30, T:0.30
Consensus pattern (8 bp):
TTGGCCCA
Found at i:13422182 original size:16 final size:16
Alignment explanation
Indices: 13422157--13422207 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
13422147 TACCAAAGTG
13422157 GGCC-GTTGGCCCATT
1 GGCCTGTTGGCCCATT
13422172 GGCCTGTTGGCCCATT
1 GGCCTGTTGGCCCATT
13422188 GGCCTGTTGGCCCATT
1 GGCCTGTTGGCCCATT
13422204 GGCC
1 GGCC
13422208 CGTTTTCGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 4 0.11
16 31 0.89
ACGTcount: A:0.06, C:0.33, G:0.33, T:0.27
Consensus pattern (16 bp):
GGCCTGTTGGCCCATT
Found at i:13422560 original size:26 final size:27
Alignment explanation
Indices: 13422531--13422584 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
13422521 TCACACAAGT
*
13422531 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
13422557 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
13422584 T
1 T
13422585 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:13422615 original size:27 final size:27
Alignment explanation
Indices: 13422585--13422730 Score: 175
Period size: 27 Copynumber: 5.4 Consensus size: 27
13422575 GGGGCAAAAT
* * *
13422585 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
13422612 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
13422639 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
13422666 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
13422693 GATAATTCTACCATACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
13422720 AGTAATTCTAC
1 GGTAATTCTAC
13422731 AACTAATCCA
Statistics
Matches: 102, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 102 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:13428934 original size:54 final size:54
Alignment explanation
Indices: 13428876--13428987 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
13428866 TTAACACCCT
*
13428876 AGGGGCAAAATGGTAATTT-TACCCCACAAGTGTATCTCAGTAATTCTACCCTAC
1 AGGGGCAAAATGGT-ATTTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
* *** * * *
13428930 AGGGGTATTTTGGTATTTCTACCCTACAAGGGTATTTCAGTAATTCTATCCTAC
1 AGGGGCAAAATGGTATTTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
13428984 AGGG
1 AGGG
13428988 TATTTCGGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 4 0.08
54 45 0.92
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (54 bp):
AGGGGCAAAATGGTATTTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
Found at i:13428937 original size:27 final size:27
Alignment explanation
Indices: 13428888--13429031 Score: 166
Period size: 27 Copynumber: 5.4 Consensus size: 27
13428878 GGGCAAAATG
* * * *
13428888 GTAATTTTACCCCACAAGTGTATCTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* **
13428915 GTAATTCTACCCTACAGGGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
13428942 GTATTTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
13428969 GTAATTCTATCCTAC-AGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
13428995 GTAATTCTACCCTAC-AGGGATATTTTA
1 GTAATTCTACCCTACAAGGG-TATTTCA
13429022 GTAATTCTAC
1 GTAATTCTAC
13429032 AACTTATCCA
Statistics
Matches: 99, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
26 28 0.28
27 71 0.72
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:13429019 original size:53 final size:54
Alignment explanation
Indices: 13428887--13429031 Score: 195
Period size: 53 Copynumber: 2.7 Consensus size: 54
13428877 GGGGCAAAAT
* * * * *
13428887 GGTAATTTTACCCCACAAGTGTATCTCAGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* *
13428941 GGTATTTCTACCCTACAAGGGTATTTCAGTAATTCTATCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
*
13428994 GGTAATTCTACCCTAC-AGGGATATTTTAGTAATTCTAC
1 GGTAATTCTACCCTACAAGGG-TATTTCAGTAATTCTAC
13429032 AACTTATCCA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
52 4 0.05
53 38 0.47
54 38 0.47
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
Found at i:13431004 original size:25 final size:27
Alignment explanation
Indices: 13430967--13431019 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
13430957 TCAAACATGC
13430967 ATTTAGGTCAATTTAACT-CTAGGGGT
1 ATTTAGGTCAATTTAACTACTAGGGGT
* *
13430993 ATTTCGGT-AATTTATCTACTAGGGGT
1 ATTTAGGTCAATTTAACTACTAGGGGT
13431019 A
1 A
13431020 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTACTAGGGGT
Found at i:13432537 original size:26 final size:26
Alignment explanation
Indices: 13432506--13432613 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
13432496 TGAAATGCCC
*
13432506 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
13432532 ATCATGGAACATTTATCTAACCCTTT
1 ATCATGGAACATTTACCTAACCCATT
* *
13432558 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
13432584 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
13432610 ATCA
1 ATCA
13432614 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:13434033 original size:27 final size:30
Alignment explanation
Indices: 13434003--13434062 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 30
13433993 TAAAACATAA
*
13434003 AAAATAAATTATGT-AC-ATAAA-TATATT
1 AAAATAAATTATGTAACAATAAATTAAATT
13434030 --AA-AAATTATGTAACAATAAATTAAATT
1 AAAATAAATTATGTAACAATAAATTAAATT
13434057 AAAATA
1 AAAATA
13434063 GATAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
24 9 0.35
25 4 0.15
26 5 0.19
27 5 0.19
29 2 0.08
30 1 0.04
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAATAAATTATGTAACAATAAATTAAATT
Found at i:13434039 original size:24 final size:27
Alignment explanation
Indices: 13434008--13434060 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 27
13433998 CATAAAAAAT
*
13434008 AAATTATGT-AC-ATAAA-TATATTAA
1 AAATTATGTAACAATAAATTAAATTAA
13434032 AAATTATGTAACAATAAATTAAATTAA
1 AAATTATGTAACAATAAATTAAATTAA
13434059 AA
1 AA
13434061 TAGATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 2 0.08
26 5 0.20
27 9 0.36
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (27 bp):
AAATTATGTAACAATAAATTAAATTAA
Found at i:13434189 original size:18 final size:18
Alignment explanation
Indices: 13434166--13434204 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
13434156 TAAAACTCTA
13434166 AAAAATTTCTATGAAAAG
1 AAAAATTTCTATGAAAAG
13434184 AAAAATTTCTATGAAAAG
1 AAAAATTTCTATGAAAAG
13434202 AAA
1 AAA
13434205 GATATGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (18 bp):
AAAAATTTCTATGAAAAG
Found at i:13434638 original size:18 final size:18
Alignment explanation
Indices: 13434615--13434652 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
13434605 GTACATAGAA
13434615 GTAACTACAAAGTACATT
1 GTAACTACAAAGTACATT
*
13434633 GTAACTACGAAGTACATT
1 GTAACTACAAAGTACATT
13434651 GT
1 GT
13434653 TCTTTTGTTT
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:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (18 bp):
GTAACTACAAAGTACATT
Found at i:13435805 original size:23 final size:22
Alignment explanation
Indices: 13435779--13435821 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
13435769 ATCCTTCTGT
13435779 ATTT-TTTAATATTTATAATTTCA
1 ATTTATTT-ATATTT-TAATTTCA
*
13435802 ATTTATTTTTATTTTAATTT
1 ATTTATTTATATTTTAATTT
13435822 GGGCCCGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 9 0.50
24 3 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTATTTATATTTTAATTTCA
Found at i:13436045 original size:22 final size:25
Alignment explanation
Indices: 13436014--13436064 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
13436004 TTTAATCCTT
*
13436014 TTTTATATATA-TA-AT-TTATTTA
1 TTTTAAATATATTATATATTATTTA
13436036 TTTTAAATATATTATATATTATTTA
1 TTTTAAATATATTATATATTATTTA
13436061 TTTT
1 TTTT
13436065 TACTAACAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 2 0.08
24 2 0.08
25 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTAAATATATTATATATTATTTA
Found at i:13436156 original size:12 final size:12
Alignment explanation
Indices: 13436141--13436183 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
13436131 TTATATTGTT
13436141 TATATTTTATTA
1 TATATTTTATTA
13436153 TATATTTTATTTA
1 TATATTTTA-TTA
*
13436166 CATATTTTATTA
1 TATATTTTATTA
13436178 TATATT
1 TATATT
13436184 ATATCATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTTTATTA
Found at i:13436172 original size:13 final size:13
Alignment explanation
Indices: 13436142--13436176 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
13436132 TATATTGTTT
*
13436142 ATATTTTA-TTAT
1 ATATTTTATTTAC
13436154 ATATTTTATTTAC
1 ATATTTTATTTAC
13436167 ATATTTTATT
1 ATATTTTATT
13436177 ATATATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (13 bp):
ATATTTTATTTAC
Found at i:13436186 original size:5 final size:5
Alignment explanation
Indices: 13436129--13436244 Score: 55
Period size: 5 Copynumber: 23.2 Consensus size: 5
13436119 ATGCATTGTT
* * * * *
13436129 TATTA TATTG T-TTA TATTT TATTA TA-TA TTTTA T-TTA CA-TA TTTTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* * *
13436175 T-TATA TATTA TATCA TCTTGA TATATA TATTA TCAATTA TATTA T-TTT
1 TAT-TA TATTA TATTA TATT-A TAT-TA TATTA T--ATTA TATTA TATTA
*
13436223 TATTTT TATTA TATTA TATTA T
1 TA-TTA TATTA TATTA TATTA T
13436245 TATTGTAAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
4 15 0.18
5 51 0.60
6 13 0.15
7 6 0.07
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:13448339 original size:90 final size:90
Alignment explanation
Indices: 13448196--13448812 Score: 1000
Period size: 90 Copynumber: 6.9 Consensus size: 90
13448186 AGATCACCGG
* * * * *
13448196 TGACAGATTTGGCGTCTCTATATTAGACAGGGAGCAGATCGAAGATAGCAGATCTGGCATTCATG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
* *
13448261 TATTTACATCGGAGCAGATCGAAGA
66 TGTTTACATCGAAGCAGATCGAAGA
* * **
13448286 CGATAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAATAGATCTGACATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
*
13448351 TGTTTACATCAAAGCAGATCGAAGA
66 TGTTTACATCGAAGCAGATCGAAGA
* *
13448376 TGACAGATTTGGCATCTCTGTATTAGATGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
*
13448441 TGTTTACATCAAAGCAGATCGAAGA
66 TGTTTACATCGAAGCAGATCGAAGA
* * *
13448466 TGATAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGATAGCAGATCTAACATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
*
13448531 TGTTTACATCGAAGTAGATCGAAGA
66 TGTTTACATCGAAGCAGATCGAAGA
* *
13448556 CGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
*
13448621 TGTTTACATCGAAGCAAATCGAAGA
66 TGTTTACATCGAAGCAGATCGAAGA
* *
13448646 TGATAGATTTGGCATCTCTGTATTAGATGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
13448711 TGTTTACATCGAAGCAGATCGAAGA
66 TGTTTACATCGAAGCAGATCGAAGA
* *
13448736 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGGTAGCAGATCTGATATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
13448801 TGTTTACATCGA
66 TGTTTACATCGA
13448813 GGTACAGATT
Statistics
Matches: 486, Mismatches: 41, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 486 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (90 bp):
TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
TGTTTACATCGAAGCAGATCGAAGA
Found at i:13448502 original size:180 final size:180
Alignment explanation
Indices: 13448196--13448949 Score: 1113
Period size: 180 Copynumber: 4.3 Consensus size: 180
13448186 AGATCACCGG
* * * * * *
13448196 TGACAGATTTGGCGTCTCTATATTAGACAGGGAGCAGATCGAAGATAGCAGATCTGGCATTCATG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTG
* * *
13448261 TATTTACATCGGAGCAGATCGAAGACGATAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
66 TGTTTACATCGAAGCAGATCGAAGATGATAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
** *
13448326 GAAGATAATAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGA
131 GAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGA
*
13448376 TGACAGATTTGGCATCTCTGTATTAGATGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTG
* *
13448441 TGTTTACATCAAAGCAGATCGAAGATGATAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATC
66 TGTTTACATCGAAGCAGATCGAAGATGATAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
* *
13448506 GAAGATAGCAGATCTAACATTCGTGTGTTTACATCGAAGTAGATCGAAGA
131 GAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGA
*
13448556 CGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTG
* *
13448621 TGTTTACATCGAAGCAAATCGAAGATGATAGATTTGGCATCTCTGTATTAGATGGGGAGCAGATC
66 TGTTTACATCGAAGCAGATCGAAGATGATAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
13448686 GAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGA
131 GAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGA
* * *
13448736 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGGTAGCAGATCTGATATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTG
* *
13448801 TGTTTACAT-----C-GA--G--G-T-ACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATC
66 TGTTTACATCGAAGCAGATCGAAGATGATAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
* * *
13448854 GAAGATAGCAGATCTGACATTCGTAT-ATTACATCGAAGCAGATCAAAGA
131 GAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGA
* * * *
13448903 T-AGCAGATTTGGCGTCTCTGTATTTGACGAGGAGCAGATCAAGGATA
1 TGA-CAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATA
13448950 TTAACATGGC
Statistics
Matches: 531, Mismatches: 42, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
166 1 0.00
167 60 0.11
168 60 0.11
169 1 0.00
170 1 0.00
172 1 0.00
174 1 0.00
175 1 0.00
180 405 0.76
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (180 bp):
TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTG
TGTTTACATCGAAGCAGATCGAAGATGATAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
GAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGA
Found at i:13448681 original size:270 final size:268
Alignment explanation
Indices: 13448196--13448949 Score: 1111
Period size: 270 Copynumber: 2.8 Consensus size: 268
13448186 AGATCACCGG
* * * *
13448196 TGACAGATTTGGCGTCTCTATATTAGAC-AGGGAGCAGATCGAAGATAGCAGATCTGGCATTCAT
1 TGACAGATTTGGCATCTCTGTATTAGACGA-GGAGCAGATCGAAGATAGCAGATCTGACATTCGT
* *
13448260 GTATTTACATCGGAGCAGATCGAAGACGATAGATTTGGCATCTCTGTATTAGACGGGGAGCAGAT
65 GTGTTTACATC-GAG-AGATCGAAGACGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGAT
** *
13448325 CGAAGATAATAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCA
128 CGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGATTTGGCA
13448390 TCTCTGTATTAGATGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTGTGTTTACATCAAAG
193 TCTCTGTATTAGATGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTGTGTTTACATCAAAG
13448455 CAGATCGAAGA
258 CAGATCGAAGA
* *
13448466 TGATAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGATAGCAGATCTAACATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
13448531 TGTTTACATCGAAGTAGATCGAAGACGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
66 TGTTTACATCG-AG-AGATCGAAGACGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
* * *
13448596 AAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAAATCGAAGATGATAGATTTGGCAT
129 GAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGATTTGGCAT
* *
13448661 CTCTGTATTAGATGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
194 CTCTGTATTAGATGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTGTGTTTACATCAAAGC
13448726 AGATCGAAGA
259 AGATCGAAGA
* * *
13448736 TGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGGTAGCAGATCTGATATTCGTG
1 TGACAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
*
13448801 TGTTTACATCGAG-G-T--------ACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGA
66 TGTTTACATCGAGAGATCGAAGACGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGA
* * * *
13448856 AGATAGCAGATCTGACATTCGTAT-ATTACATCGAAGCAGATCAAAGAT-AGCAGATTTGGCGTC
131 AGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGA-CAGATTTGGCATC
* * * *
13448919 TCTGTATTTGACGAGGAGCAGATCAAGGATA
195 TCTGTATTAGATGGGGAGCAGATCAAAGATA
13448950 TTAACATGGC
Statistics
Matches: 446, Mismatches: 35, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
256 1 0.00
257 58 0.13
258 61 0.14
266 1 0.00
267 1 0.00
269 3 0.01
270 320 0.72
271 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (268 bp):
TGACAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGATAGCAGATCTGACATTCGTG
TGTTTACATCGAGAGATCGAAGACGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGA
AGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGATTTGGCATCT
CTGTATTAGATGGGGAGCAGATCAAAGATAGCAGATCTGACATTCGTGTGTTTACATCAAAGCAG
ATCGAAGA
Found at i:13448866 original size:45 final size:44
Alignment explanation
Indices: 13448817--13448949 Score: 117
Period size: 45 Copynumber: 3.0 Consensus size: 44
13448807 CATCGAGGTA
*
13448817 CAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTAGAC-GGGAGCAAATCAAAGATAG
* * * * * *
13448862 CAGATCTGACAT-TCGTATATTACATC-GAAGCAGATCAAAGATAG
1 CAGATTTGGCATCTC-TGTATTAGA-CGGGAGCAAATCAAAGATAG
* * * *
13448906 CAGATTTGGCGTCTCTGTATTTGACGAGGAGCAGATCAAGGATA
1 CAGATTTGGCATCTCTGTATTAGACG-GGAGCAAATCAAAGATA
13448950 TTAACATGGC
Statistics
Matches: 68, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
43 1 0.01
44 32 0.47
45 34 0.50
46 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (44 bp):
CAGATTTGGCATCTCTGTATTAGACGGGAGCAAATCAAAGATAG
Found at i:13450447 original size:22 final size:24
Alignment explanation
Indices: 13450422--13450474 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
13450412 ATTTTAATCC
13450422 TTTTTTATATA-TA-AT-TTATTTA
1 TTTTTTATATATTATATATTA-TTA
**
13450444 TTTTAAATATATTATATATTATTA
1 TTTTTTATATATTATATATTATTA
13450468 TTTTTTA
1 TTTTTTA
13450475 CTAACAACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 9 0.38
23 2 0.08
24 10 0.42
25 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTTTATATATTATATATTATTA
Found at i:13450574 original size:10 final size:10
Alignment explanation
Indices: 13450539--13450593 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
13450529 GCATTGTTTC
*
13450539 TTATATTGT-
1 TTATATTTTA
13450548 TTATATTTTA
1 TTATATTTTA
13450558 TGATATATTTTA
1 T--TATATTTTA
*
13450570 TTATATATTA
1 TTATATTTTA
13450580 -TATTATTTTA
1 TTA-TATTTTA
13450590 TTAT
1 TTAT
13450594 TGTAAATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 10 0.26
10 16 0.42
11 2 0.05
12 10 0.26
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (10 bp):
TTATATTTTA
Found at i:13450583 original size:12 final size:12
Alignment explanation
Indices: 13450549--13450585 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
13450539 TTATATTGTT
*
13450549 TATATTTTATGA
1 TATATTTTATTA
13450561 TATATTTTATTA
1 TATATTTTATTA
*
13450573 TATATTATATTA
1 TATATTTTATTA
13450585 T
1 T
13450586 TTTATTATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
TATATTTTATTA
Found at i:13452121 original size:63 final size:63
Alignment explanation
Indices: 13452054--13452248 Score: 205
Period size: 63 Copynumber: 3.1 Consensus size: 63
13452044 AAAAATATTT
13452054 AAAATGTTATATTTTTCAATATTATTAAACATACATATTTATTATTTATATTTAGTCATATAA
1 AAAATGTTATATTTTTCAATATTATTAAACATACATATTTATTATTTATATTTAGTCATATAA
* ** * * *** * * ***
13452117 AAAATATTAATATAATAAATAAATTTTATTATTTATAAAT-TTTATT-TTTATTTTTAAAAATAT
1 AAAATGTT-ATAT--T-TTTCAATATTATTAAACATACATATTTATTATTTATATTTAGTCATAT
**
13452180 TT
62 AA
13452182 AAAATGTTATATTTTTCAATATTATTAAACATACATATTTATTATTTATATTTAGTCATATAA
1 AAAATGTTATATTTTTCAATATTATTAAACATACATATTTATTATTTATATTTAGTCATATAA
13452245 AAAA
1 AAAA
13452249 ATATTAATAT
Statistics
Matches: 96, Mismatches: 30, Indels: 12
0.70 0.22 0.09
Matches are distributed among these distances:
61 15 0.16
62 7 0.07
63 24 0.25
64 8 0.08
65 20 0.21
66 7 0.07
67 15 0.16
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (63 bp):
AAAATGTTATATTTTTCAATATTATTAAACATACATATTTATTATTTATATTTAGTCATATAA
Found at i:13452156 original size:16 final size:15
Alignment explanation
Indices: 13452135--13452167 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
13452125 AATATAATAA
13452135 ATAAATTTTATTATTT
1 ATAAATTTTATT-TTT
13452151 ATAAATTTTATTTTT
1 ATAAATTTTATTTTT
13452166 AT
1 AT
13452168 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATAAATTTTATTTTT
Found at i:13452171 original size:128 final size:131
Alignment explanation
Indices: 13452021--13452288 Score: 506
Period size: 128 Copynumber: 2.1 Consensus size: 131
13452011 ATTATATTGA
13452021 TAATAAATTTTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACAT
1 TAATAAATTTTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACAT
*
13452086 ACATATTTATTATTTATATTTAGTCATAT-AAAAAATATTAATATAATAAATAAATTTTATTA-T
66 ACATATTTATTATTTATATTTAGTCATATAAAAAAATATTAATATAATAAATAAAATTTATTATT
13452149 T
131 T
13452150 T-ATAAATTTTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACAT
1 TAATAAATTTTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACAT
13452214 ACATATTTATTATTTATATTTAGTCATATAAAAAAATATTAATATAATAAATAAAATTTATTATT
66 ACATATTTATTATTTATATTTAGTCATATAAAAAAATATTAATATAATAAATAAAATTTATTATT
13452279 T
131 T
13452280 TAATAAATT
1 TAATAAATT
13452289 ATTTAATATT
Statistics
Matches: 135, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
128 92 0.68
129 33 0.24
130 3 0.02
131 7 0.05
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (131 bp):
TAATAAATTTTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACAT
ACATATTTATTATTTATATTTAGTCATATAAAAAAATATTAATATAATAAATAAAATTTATTATT
T
Found at i:13452172 original size:21 final size:23
Alignment explanation
Indices: 13452140--13452182 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
13452130 AATAAATAAA
*
13452140 TTTTATTATTTATAAAT-TTTAT
1 TTTTATTATTTAAAAATATTTAT
13452162 TTTTATT-TTTAAAAATATTTA
1 TTTTATTATTTAAAAATATTTA
13452183 AAATGTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTATTATTTAAAAATATTTAT
Found at i:13452227 original size:65 final size:65
Alignment explanation
Indices: 13452030--13452234 Score: 197
Period size: 65 Copynumber: 3.2 Consensus size: 65
13452020 ATAATAAATT
13452030 TTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACATACATATTTA
1 TTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACATACATATTTA
* *** ** * ** * * ***
13452095 TTA--TTTATATTTAGTCATATAAAAAATATTAATATAATAAATAAATTTTATTATTTATA-A-A
1 TTATTTTTATTTTTAAAAATATTTAAAATGTT-ATAT--T-TTTCAATATTATTAAACATACATA
13452156 -TT-
62 TTTA
13452158 TTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACATACATATTTA
1 TTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACATACATATTTA
*
13452223 TTATTTATATTT
1 TTATTTTTATTT
13452235 AGTCATATAA
Statistics
Matches: 101, Mismatches: 29, Indels: 20
0.67 0.19 0.13
Matches are distributed among these distances:
61 13 0.13
62 2 0.02
63 24 0.24
64 12 0.12
65 35 0.35
66 2 0.02
67 13 0.13
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (65 bp):
TTATTTTTATTTTTAAAAATATTTAAAATGTTATATTTTTCAATATTATTAAACATACATATTTA
Found at i:13452402 original size:15 final size:15
Alignment explanation
Indices: 13452382--13452438 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
13452372 ATTCAATATT
13452382 AATATTTTAATAATA
1 AATATTTTAATAATA
*
13452397 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
13452416 AATATATTAATAATA
1 AATATTTTAATAATA
*
13452431 AATGTTTT
1 AATATTTT
13452439 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:13452927 original size:13 final size:14
Alignment explanation
Indices: 13452899--13452927 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13452889 CAAAAAAGTA
13452899 AATCATTTTCCAAT
1 AATCATTTTCCAAT
13452913 AATCATTTT-CAAT
1 AATCATTTTCCAAT
13452926 AA
1 AA
13452928 AACAAACGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (14 bp):
AATCATTTTCCAAT
Found at i:13466849 original size:33 final size:33
Alignment explanation
Indices: 13466802--13466865 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
13466792 ATGCTACTGT
* *
13466802 ATAGGGCTAAGGCCCAGACTGTACTGTTACTAA
1 ATAGGGCTAAGGCCCAAACTGTACTGATACTAA
**
13466835 ATAGGGCTTTGGCCCAAACTGTACTGATACT
1 ATAGGGCTAAGGCCCAAACTGTACTGATACT
13466866 GTGTTGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (33 bp):
ATAGGGCTAAGGCCCAAACTGTACTGATACTAA
Found at i:13474654 original size:33 final size:33
Alignment explanation
Indices: 13474611--13474675 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
13474601 CCCACAATGC
*
13474611 TACTGTATAGGGCTAAGGCCCAGACTGTACTGT
1 TACTGAATAGGGCTAAGGCCCAGACTGTACTGT
** *
13474644 TACTGAATAGGGCTTTGGTCCAGACTGTACTG
1 TACTGAATAGGGCTAAGGCCCAGACTGTACTG
13474676 AAACTGTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (33 bp):
TACTGAATAGGGCTAAGGCCCAGACTGTACTGT
Found at i:13476628 original size:13 final size:13
Alignment explanation
Indices: 13476610--13476634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13476600 AAGTAATCGC
13476610 ACACGGGCGTGTT
1 ACACGGGCGTGTT
13476623 ACACGGGCGTGT
1 ACACGGGCGTGT
13476635 CCCGCCGAGC
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:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:13480101 original size:24 final size:24
Alignment explanation
Indices: 13480074--13480137 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
13480064 GTAATTTTTC
* *
13480074 GTCAATTCCTCCTTTGTATTTACT
1 GTCAATTCATCCTTTGCATTTACT
*
13480098 GTCAATTCATCATTTGCATTTACT
1 GTCAATTCATCCTTTGCATTTACT
* *
13480122 ATCGATTCATCCTTTG
1 GTCAATTCATCCTTTG
13480138 ACATAGAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.47
Consensus pattern (24 bp):
GTCAATTCATCCTTTGCATTTACT
Found at i:13489581 original size:25 final size:24
Alignment explanation
Indices: 13489549--13489607 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
13489539 GCGACCCATT
13489549 TTTTAATAATATATATAATA-TATA
1 TTTTAATAATAT-TATAATATTATA
* **
13489573 TTTTAAATATTATTATTTTATTATA
1 TTTT-AATAATATTATAATATTATA
13489598 TTTTAATAAT
1 TTTTAATAAT
13489608 TTTTAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTAATAATATTATAATATTATA
Found at i:13489859 original size:15 final size:15
Alignment explanation
Indices: 13489841--13489869 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13489831 AGCAAAGAGA
13489841 GAGAAGAAGAAGAAG
1 GAGAAGAAGAAGAAG
13489856 GAGAAGAAGAAGAA
1 GAGAAGAAGAAGAA
13489870 AAATGTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
GAGAAGAAGAAGAAG
Found at i:13490961 original size:11 final size:11
Alignment explanation
Indices: 13490926--13490953 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
13490916 GAGAGTAAGA
13490926 AATTTTAATGT
1 AATTTTAATGT
13490937 AATTTTAATGT
1 AATTTTAATGT
13490948 AATTTT
1 AATTTT
13490954 GATATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
AATTTTAATGT
Found at i:13492793 original size:33 final size:33
Alignment explanation
Indices: 13492736--13492813 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
13492726 TGCCACATCT
* * * * *
13492736 GTACTCTATTCCTTCCGGCTCATATCCATCACC
1 GTACTCTACTCCTCCCAGCCCATATCCAGCACC
*
13492769 GTACTCTACTCCTCCCAGCCCATATCCAGCGCC
1 GTACTCTACTCCTCCCAGCCCATATCCAGCACC
*
13492802 GTTCTCTACTCC
1 GTACTCTACTCC
13492814 ACCCGGCTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.17, C:0.44, G:0.10, T:0.29
Consensus pattern (33 bp):
GTACTCTACTCCTCCCAGCCCATATCCAGCACC
Found at i:13493330 original size:25 final size:25
Alignment explanation
Indices: 13493302--13493396 Score: 101
Period size: 25 Copynumber: 4.0 Consensus size: 25
13493292 TTAAGTATAA
*
13493302 AAAATAATAA-ATTAATAACATTATT
1 AAAATAATAATATTAA-AAAATTATT
13493327 AAAATAATAATATTAAAAAATTATT
1 AAAATAATAATATTAAAAAATTATT
* * *
13493352 -AAA-CATAAT-TT-CAGAATTATT
1 AAAATAATAATATTAAAAAATTATT
*
13493373 CAAATAATAATATTAAAAAATTAT
1 AAAATAATAATATTAAAAAATTAT
13493397 GAAACTTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
21 8 0.14
22 5 0.09
23 10 0.17
24 5 0.09
25 25 0.43
26 5 0.09
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (25 bp):
AAAATAATAATATTAAAAAATTATT
Found at i:13493330 original size:87 final size:86
Alignment explanation
Indices: 13493148--13493372 Score: 294
Period size: 87 Copynumber: 2.6 Consensus size: 86
13493138 TCCAATAAAA
* * * * * *
13493148 AATTATTAAATTAATAATACTAAAAA-AATTAGACTTAATTTTAAAAATATTAAAAAATCTAAGC
1 AATTATTAAAATAATAATATTAAAAATTATTAAACTTAATTTCAAAATTATTAAAAAATCTAAGC
13493212 ATAAAAATAATAAATTATCAG
66 ATAAAAATAATAAATTATCAG
* * *
13493233 AATTATTAAAATAATAATATTAAAAATTATTAAACTTAATTTCAAAATTATTAAAAATTTTAAGT
1 AATTATTAAAATAATAATATTAAAAATTATTAAACTTAATTTCAAAATTATTAAAAAATCTAAGC
13493298 ATAAAAAATAATAAATTAAT-A-
66 AT-AAAAATAATAAATT-ATCAG
* *
13493319 ACATTATTAAAATAATAATATTAAAAAATTATTAAACATAATTTCAGAATTATT
1 A-ATTATTAAAATAATAATATT-AAAAATTATTAAACTTAATTTCAAAATTATT
13493373 CAAATAATAA
Statistics
Matches: 124, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
85 24 0.19
86 34 0.27
87 35 0.28
88 31 0.25
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (86 bp):
AATTATTAAAATAATAATATTAAAAATTATTAAACTTAATTTCAAAATTATTAAAAAATCTAAGC
ATAAAAATAATAAATTATCAG
Found at i:13493417 original size:134 final size:134
Alignment explanation
Indices: 13493224--13493494 Score: 481
Period size: 134 Copynumber: 2.0 Consensus size: 134
13493214 AAAAATAATA
*
13493224 AATTATCAGAATTATTAAAATAATAATATTAAAAATTATTAAACTTAATTTCAAAATTATTAAAA
1 AATTATCAGAATTATTAAAATAATAATATTAAAAATTATGAAACTTAATTTCAAAATTATTAAAA
*
13493289 ATTTTAAGTATAAAAAATAATAAATTAATAACATTATTAAAATAATAATATTAAAAAATTATTAA
66 AATTTAAGTATAAAAAATAATAAATTAATAACATTATTAAAATAATAATATTAAAAAATTATTAA
13493354 ACAT
131 ACAT
*
13493358 AATT-TCAGAATTATTCAAATAATAATATTAAAAAATTATGAAACTTAATTTCAAAATTATTAAA
1 AATTATCAGAATTATTAAAATAATAATATT-AAAAATTATGAAACTTAATTTCAAAATTATTAAA
*
13493422 AAATTTAAGTATAAAAAATAATAAATTAATAACATTATTAAAATAATAATATTAAATAATTATTA
65 AAATTTAAGTATAAAAAATAATAAATTAATAACATTATTAAAATAATAATATTAAAAAATTATTA
*
13493487 AACTT
130 AACAT
13493492 AAT
1 AAT
13493495 AATTTTTCTT
Statistics
Matches: 131, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
133 24 0.18
134 107 0.82
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (134 bp):
AATTATCAGAATTATTAAAATAATAATATTAAAAATTATGAAACTTAATTTCAAAATTATTAAAA
AATTTAAGTATAAAAAATAATAAATTAATAACATTATTAAAATAATAATATTAAAAAATTATTAA
ACAT
Found at i:13493464 original size:25 final size:25
Alignment explanation
Indices: 13493436--13493497 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
13493426 TTAAGTATAA
13493436 AAAATAATAA-ATT-AATAACATTATT
1 AAAATAATAATATTAAAT-A-ATTATT
13493461 AAAATAATAATATTAAATAATTATT
1 AAAATAATAATATTAAATAATTATT
*
13493486 AAACTTAATAAT
1 AAA-ATAATAAT
13493498 TTTTCTTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 19 0.58
26 11 0.33
27 3 0.09
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAATAATAATATTAAATAATTATT
Found at i:13495980 original size:5 final size:5
Alignment explanation
Indices: 13495959--13496000 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
13495949 AATAATTAAG
*
13495959 TATA- TATAT TATA- TATAT TATAT TATGT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
13496001 AAACAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
4 8 0.24
5 26 0.76
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:13502171 original size:13 final size:13
Alignment explanation
Indices: 13502153--13502179 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13502143 TTCGATGCCA
13502153 ATGTAATCTTTCG
1 ATGTAATCTTTCG
13502166 ATGTAATCTTTCG
1 ATGTAATCTTTCG
13502179 A
1 A
13502180 ATTCGATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (13 bp):
ATGTAATCTTTCG
Found at i:13502681 original size:171 final size:171
Alignment explanation
Indices: 13502390--13503079 Score: 861
Period size: 171 Copynumber: 4.1 Consensus size: 171
13502380 TTTTGCCCCT
* * * * *
13502390 TTTTTTAGGGTTATGGTTTTTGATTATTTTAGGGTTATGGTTTAGTGGTTTAGG-GTTTA-AG--
1 TTTTTTAAGGTTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTTAGTGGTTTAGGTTTTTAGAGTT
* * *
13502451 -A---TTTTAGTGTTTTTTAAGGG-AAAATTAATTTAATTTGAGTTGAGGGTTAATTAATTAAAT
66 TAGGGTTTTAATG-TTTTTAAGGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATCAAAT
13502511 TAACTATGAAATT-AAAAAATCAATTAAATTAGGGTTTAAGG
130 TAACTATGAAATTAAAAAAATCAATTAAATTAGGGTTTAAGG
* *
13502552 TTTTTTATGGTTAGGGTTTTTGATTGTTTTAGGGCTAGGGTTTAGTGGTTTATGGTTTTTAGAGT
1 TTTTTTAAGGTTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTTAGTGGTTTA-GGTTTTTAGAGT
* * * *
13502617 TTAGGGTTTCAATGTTTTTAAGGGCAAAATTAATTTAATTAGAGTTTAGGGTTAATTAATTAAAT
65 TTAGGGTTTTAATGTTTTTAAGGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATCAAAT
*
13502682 TAACTATGAAATTTAAAAAAAAATCAATTAAATTAGGGCTT-AGG
130 TAACTATGAAA-TT--AAAAAAATCAATTAAATTAGGGTTTAAGG
* * * * *
13502726 GTTTTTAAGGTTAAGGTTTTT-ATTGTTTTAGGGTTAAGG-TTAATGGTTTAGGGTTTTTAGGGT
1 TTTTTTAAGGTTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTTAGTGGTTTA-GGTTTTTAGAGT
* *
13502789 TTAGGATTTTAATAATTTTTAAGGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATCAAA
65 TTAGGGTTTTAAT-GTTTTTAAGGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATCAAA
* *
13502854 TTAACTATGAAATTAAAAAAATTAATTAAATTAGGGTTTAAAG
129 TTAACTATGAAATTAAAAAAATCAATTAAATTAGGGTTTAAGG
* * * * *
13502897 TTTTTTAAGGTTAGGATTTTTTATTTTTTTAGGGTTAGTGTTTAGTGGTTTAAGGTTTTTA-ATA
1 TTTTTTAAGGTTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTTAGTGGTTT-AGGTTTTTAGA-G
* * * *
13502961 TTTATGGTTTTAGTGTTTTTAAGGGAAAAATTAA-TTAATTAGATTTGAGGATTAATTAATCAAA
64 TTTAGGGTTTTAATGTTTTTAAGGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATCAAA
* * *
13503025 TTAACTATGAAATTAAAAAAATTAATTAAATTAAGGTTTAGGG
129 TTAACTATGAAATTAAAAAAATCAATTAAATTAGGGTTTAAGG
*
13503068 TTTTTTAGGGTT
1 TTTTTTAAGGTT
13503080 TATTAATTAA
Statistics
Matches: 461, Mismatches: 47, Indels: 31
0.86 0.09 0.06
Matches are distributed among these distances:
162 47 0.10
163 2 0.00
164 4 0.01
165 2 0.00
168 1 0.00
170 33 0.07
171 154 0.33
172 70 0.15
173 103 0.22
174 22 0.05
175 23 0.05
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.45
Consensus pattern (171 bp):
TTTTTTAAGGTTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTTAGTGGTTTAGGTTTTTAGAGTT
TAGGGTTTTAATGTTTTTAAGGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATCAAATT
AACTATGAAATTAAAAAAATCAATTAAATTAGGGTTTAAGG
Found at i:13502972 original size:24 final size:24
Alignment explanation
Indices: 13502937--13502982 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
13502927 AGGGTTAGTG
13502937 TTTAGTGGTTTAAG-GTTTTTAATA
1 TTTAGTGGTTT-AGTGTTTTTAATA
13502961 TTTA-TGGTTTTAGTGTTTTTAA
1 TTTAGTGG-TTTAGTGTTTTTAA
13502983 GGGAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.59
Consensus pattern (24 bp):
TTTAGTGGTTTAGTGTTTTTAATA
Found at i:13503323 original size:125 final size:125
Alignment explanation
Indices: 13503100--13503407 Score: 458
Period size: 125 Copynumber: 2.5 Consensus size: 125
13503090 ATTAACTATT
* *
13503100 AATTACGGAAAAAAGCTCCCATGTGGACGCTCTTTTGCTATAATAGTATCTGAAAAAATAATTTT
1 AATTACGGAAAAAAGCTCCCATGTGGACACTCTTTTGCTATAGTAGTATCTG-AAAAATAATTTT
* * *
13503165 GAAAAGATGTTTCTGAATAAATAGTATCAAAAACGCTTCAAGAAGGATGCACTGTTAGCAA
65 GAAAAGATATTTCTGAACAAATAGTATCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAA
* * * *
13503226 AATTACGGAAAAAAATCTCCCACGTGGAC-CTTTTTTTGCTACAGTAGTATCTGAAAAA-AATTT
1 AATTACGG-AAAAAAGCTCCCATGTGGACAC-TCTTTTGCTATAGTAGTATCTGAAAAATAATTT
* *
13503289 TGAGAAGATATTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAA
64 TGAAAAGATATTTCTGAACAAATAGTATCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAA
* *
13503351 AATTACAGAAAAAAGCTCCCATATGGACACTCTTTTGCTATAGTAGTATCTGAAAAA
1 AATTACGGAAAAAAGCTCCCATGTGGACACTCTTTTGCTATAGTAGTATCTGAAAAA
13503408 GCCTTAGACT
Statistics
Matches: 163, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
124 42 0.26
125 70 0.43
126 14 0.09
127 37 0.23
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (125 bp):
AATTACGGAAAAAAGCTCCCATGTGGACACTCTTTTGCTATAGTAGTATCTGAAAAATAATTTTG
AAAAGATATTTCTGAACAAATAGTATCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAA
Found at i:13506674 original size:130 final size:129
Alignment explanation
Indices: 13506485--13506858 Score: 648
Period size: 130 Copynumber: 2.9 Consensus size: 129
13506475 GCATTTATCT
* * *
13506485 TAATAAAAATTATTGGCTAATTTAAAAGAACATTTATTGTATTAAAATTAAAAAAAGTAAAGTAC
1 TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
13506550 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAATAAATATAAAAA
66 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAATAAATAT-AAAA
13506615 TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
1 TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
*
13506680 AATTAAAATATTAAAAATAACTTTTATTTTATTAATTAAAACTATAT-AAAAATAAATATAAAA
66 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAATAAATATAAAA
13506743 -AAT-AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
1 TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
* *
13506806 AATTAAAATATTAAAAACAACTTTTATTTCATT-ATATGAAACTATATAAAAAA
66 AATTAAAATATTAAAAACAACTTTTATTTTATTAAT-TAAAACTATATAAAAAA
13506859 GTTTCTCCAA
Statistics
Matches: 235, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
125 2 0.01
126 101 0.43
127 8 0.03
128 4 0.02
129 12 0.05
130 108 0.46
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (129 bp):
TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAATAAATATAAAA
Found at i:13506694 original size:54 final size:54
Alignment explanation
Indices: 13506636--13506821 Score: 140
Period size: 55 Copynumber: 3.1 Consensus size: 54
13506626 ATTGGCTAAT
13506636 TTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATA
1 TTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATA
* * * * * *
13506690 TTAAAAATAACTTTTATTTTATTAATTAAAACTATATAAAAA-TAAATATAAAAAATAAAAATAT
1 TT-AAAAGAACATTTA--TT-TTAA-TAAAA-T-TAAAAAAAGTAAA-GT--ACAAT-TAAA-A-
13506754 TGGCTAA
53 ----T-A
13506761 TTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATA
1 -TTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATA
13506816 TTAAAA
1 TTAAAA
13506822 ACAACTTTTA
Statistics
Matches: 100, Mismatches: 12, Indels: 40
0.66 0.08 0.26
Matches are distributed among these distances:
54 8 0.08
55 12 0.12
56 1 0.01
57 2 0.02
58 4 0.04
59 5 0.05
60 5 0.05
61 9 0.09
62 3 0.03
63 8 0.08
64 3 0.03
65 9 0.09
66 5 0.05
67 5 0.05
68 4 0.04
69 2 0.02
70 1 0.01
71 12 0.12
72 2 0.02
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (54 bp):
TTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATA
Found at i:13506809 original size:126 final size:128
Alignment explanation
Indices: 13506485--13506857 Score: 644
Period size: 126 Copynumber: 2.9 Consensus size: 128
13506475 GCATTTATCT
* *
13506485 TAATAAAAATTATTGGCTAATTTAAAAGAACATTTATTGTATTAAAATTAAAAAAAGTAAAGTAC
1 TAATAAAAA-TATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
13506550 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAAATAAATATAAAAA
65 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATAT-AAAAATAAATATAAAAA
13506615 TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
1 TAAT-AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
*
13506680 AATTAAAATATTAAAAATAACTTTTATTTTATTAATTAAAACTATATAAAAATAAATAT-AAAA
65 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAATAAATATAAAAA
13506743 -AATAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACA
1 TAATAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACA
* *
13506807 ATTAAAATATTAAAAACAACTTTTATTTCATT-ATATGAAACTATATAAAAA
66 ATTAAAATATTAAAAACAACTTTTATTTTATTAAT-TAAAACTATATAAAAA
13506858 AGTTTCTCCA
Statistics
Matches: 235, Mismatches: 6, Indels: 8
0.94 0.02 0.03
Matches are distributed among these distances:
125 2 0.01
126 106 0.45
127 3 0.01
128 4 0.02
129 12 0.05
130 103 0.44
131 5 0.02
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (128 bp):
TAATAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACA
ATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAATAAATATAAAAA
Found at i:13510862 original size:22 final size:22
Alignment explanation
Indices: 13510834--13510881 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
13510824 TGTTATATTG
*
13510834 TTTGTCAATAATTGTAATTTTC
1 TTTGTCAATAATTGTAATTCTC
13510856 TTTGTCAATAATTGTAATTCTC
1 TTTGTCAATAATTGTAATTCTC
13510878 TTTG
1 TTTG
13510882 AACCTCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.54
Consensus pattern (22 bp):
TTTGTCAATAATTGTAATTCTC
Found at i:13511142 original size:14 final size:14
Alignment explanation
Indices: 13511119--13511152 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13511109 TGAATTAAAT
13511119 TAATAAATAATTTA
1 TAATAAATAATTTA
*
13511133 TAATATATAATTTA
1 TAATAAATAATTTA
13511147 -AATAAA
1 TAATAAA
13511153 AATGATTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATAAATAATTTA
Found at i:13512108 original size:25 final size:25
Alignment explanation
Indices: 13512080--13512127 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
13512070 CGAGTAAATT
13512080 TGAAAAAGATATAGGCTATCCTATC
1 TGAAAAAGATATAGGCTATCCTATC
13512105 TGAAAAAGATATAGGCTATCCTA
1 TGAAAAAGATATAGGCTATCCTA
13512128 GAATGGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (25 bp):
TGAAAAAGATATAGGCTATCCTATC
Found at i:13512460 original size:22 final size:22
Alignment explanation
Indices: 13512435--13512476 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13512425 CTTAAGCACT
13512435 TCGTATAACATTAA-AACATAGC
1 TCGTAT-ACATTAACAACATAGC
*
13512457 TCGTATACCTTAACAACATA
1 TCGTATACATTAACAACATA
13512477 AGGGGTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (22 bp):
TCGTATACATTAACAACATAGC
Found at i:13513656 original size:41 final size:41
Alignment explanation
Indices: 13513610--13513687 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
13513600 TATCACAAAT
* * *
13513610 CTCACAAAAGCCCATGCTCTCAATGAGCACGCAGAGTAAGG
1 CTCACAAAAGCCCACGCTCTCAAAGAACACGCAGAGTAAGG
*
13513651 CTCACAAAAGCTCACGCTCTCAAAGAACACGCAGAGT
1 CTCACAAAAGCCCACGCTCTCAAAGAACACGCAGAGT
13513688 GAGACTTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (41 bp):
CTCACAAAAGCCCACGCTCTCAAAGAACACGCAGAGTAAGG
Found at i:13513821 original size:28 final size:28
Alignment explanation
Indices: 13513789--13513888 Score: 94
Period size: 28 Copynumber: 3.6 Consensus size: 28
13513779 AAAGCTAAAT
13513789 AGAGAGCTCACACAAAGTAGAGCCAAAC
1 AGAGAGCTCACACAAAGTAGAGCCAAAC
* * * ** **
13513817 AGAGAGCTCGCACAAAAT-GAACTTAGT
1 AGAGAGCTCACACAAAGTAGAGCCAAAC
** *
13513844 AGAGAGCTTGCATAAAGTAGAGCCAAAC
1 AGAGAGCTCACACAAAGTAGAGCCAAAC
*
13513872 AAAGAGCTCACACAAAG
1 AGAGAGCTCACACAAAG
13513889 CGAACTTAAC
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
27 19 0.37
28 33 0.63
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (28 bp):
AGAGAGCTCACACAAAGTAGAGCCAAAC
Found at i:13513861 original size:55 final size:55
Alignment explanation
Indices: 13513786--13513913 Score: 168
Period size: 55 Copynumber: 2.3 Consensus size: 55
13513776 GGCAAAGCTA
** * * * *
13513786 AATAGAGAGCTCACACAAAGTAGAGCCAAACAGAGAGCTCGCACAAAATGAACTT
1 AATAGAGAGCTTGCATAAAGTAGAGCCAAACAAAGAGCTCACACAAAACGAACTT
* *
13513841 AGTAGAGAGCTTGCATAAAGTAGAGCCAAACAAAGAGCTCACACAAAGCGAACTT
1 AATAGAGAGCTTGCATAAAGTAGAGCCAAACAAAGAGCTCACACAAAACGAACTT
*
13513896 AACAGA-AGCTTGCATAAA
1 AATAGAGAGCTTGCATAAA
13513914 TTTGTGCTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 12 0.19
55 51 0.81
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (55 bp):
AATAGAGAGCTTGCATAAAGTAGAGCCAAACAAAGAGCTCACACAAAACGAACTT
Found at i:13516783 original size:34 final size:34
Alignment explanation
Indices: 13516745--13516842 Score: 115
Period size: 34 Copynumber: 2.9 Consensus size: 34
13516735 TTACTGTTGA
* *
13516745 ATTGATTTATGATAAGCATATTAATTGCTACCAT
1 ATTGATCTATTATAAGCATATTAATTGCTACCAT
* * * * *
13516779 ATTGAACTATTATAAACATATTAATTGTTATCTT
1 ATTGATCTATTATAAGCATATTAATTGCTACCAT
* *
13516813 ATTGATCTGTTATAAGCATATTAAATGCTA
1 ATTGATCTATTATAAGCATATTAATTGCTA
13516843 TCGAATTGAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (34 bp):
ATTGATCTATTATAAGCATATTAATTGCTACCAT
Found at i:13516851 original size:34 final size:34
Alignment explanation
Indices: 13516756--13516875 Score: 116
Period size: 34 Copynumber: 3.5 Consensus size: 34
13516746 TTGATTTATG
* *
13516756 ATAAGCATATTAATTGCTA-CCATATTGAACTATT
1 ATAAGCATATTAATTGCTATCCA-ATTGATCTGTT
* * **
13516790 ATAAACATATTAATTGTTATCTTATTGATCTGTT
1 ATAAGCATATTAATTGCTATCCAATTGATCTGTT
* * * *
13516824 ATAAGCATATTAAATGCTATCGAATTGATATGCT
1 ATAAGCATATTAATTGCTATCCAATTGATCTGTT
*
13516858 ATAAGCATGTTACATTGC
1 ATAAGCATATTA-ATTGC
13516876 ATTGCATGAG
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
34 64 0.93
35 5 0.07
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (34 bp):
ATAAGCATATTAATTGCTATCCAATTGATCTGTT
Found at i:13519477 original size:17 final size:17
Alignment explanation
Indices: 13519425--13519484 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 17
13519415 AAAAATTTAA
13519425 TATTT-AAAATAAT-TT
1 TATTTAAAAATAATATT
* ** *
13519440 TAATTAATTACAATA-T
1 TATTTAAAAATAATATT
13519456 TATTTAAAAATAATATT
1 TATTTAAAAATAATATT
13519473 TATTTAAAAATA
1 TATTTAAAAATA
13519485 TTTTAATATT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
15 4 0.12
16 17 0.50
17 13 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTAAAAATAATATT
Done.