Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 107 of 168
Found at i:31628222 original size:14 final size:17
Alignment explanation
Indices: 31628203--31628240 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
31628193 ATTTATTTCT
31628203 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
31628217 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
31628234 TAATATA
1 TAATATA
31628241 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:31628248 original size:12 final size:11
Alignment explanation
Indices: 31628220--31628263 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
31628210 ATATTTATAA
31628220 TATAATTAATT
1 TATAATTAATT
*
31628231 TAATAATATACTT
1 T-ATAAT-TAATT
31628244 TATAATTAATT
1 TATAATTAATT
31628255 TATATATTA
1 TATA-ATTA
31628264 TATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:31628267 original size:20 final size:23
Alignment explanation
Indices: 31628215--31628277 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
31628205 ATATAATATT
31628215 TATA-ATATAATTAATTTAATAA
1 TATATATATAATTAATTTAATAA
* *
31628237 TATACTTTATAATTAATTTATATAT
1 TATA-TATATAATTAATTTA-ATAA
* *
31628262 TATATAAATAAATAAT
1 TATATATATAATTAAT
31628278 ATAAATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATAATTAATTTAATAA
Found at i:31628279 original size:20 final size:20
Alignment explanation
Indices: 31628232--31628280 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
31628222 TAATTAATTT
*
31628232 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* *
31628252 ATTTATATA-TTATATAAATA
1 AATAATATACTT-TATAAATA
31628272 AATAATATA
1 AATAATATA
31628281 AATATCTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:31630106 original size:38 final size:38
Alignment explanation
Indices: 31630064--31630139 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
31630054 CTTTGTTTGT
31630064 GGCTAACCCGAGCGGTGGTTCCTGAACTTTCAGATGTC
1 GGCTAACCCGAGCGGTGGTTCCTGAACTTTCAGATGTC
31630102 GGCTAACCCGAGCGGTGGTTCCTGAACTTTCAGATGTC
1 GGCTAACCCGAGCGGTGGTTCCTGAACTTTCAGATGTC
31630140 ACACAAGGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (38 bp):
GGCTAACCCGAGCGGTGGTTCCTGAACTTTCAGATGTC
Found at i:31635550 original size:2 final size:2
Alignment explanation
Indices: 31635543--31635576 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31635533 GTTTCTGCAA
31635543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31635577 TACTGCTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31643232 original size:9 final size:9
Alignment explanation
Indices: 31643187--31643234 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
31643177 CATCCATCTT
31643187 TCAACTCTC
1 TCAACTCTC
*
31643196 GCAACTCTC
1 TCAACTCTC
* *
31643205 TCAAACCCTT
1 TC-AACTCTC
*
31643215 TCAAGTCTC
1 TCAACTCTC
31643224 TCAACTCTC
1 TCAACTCTC
31643233 TC
1 TC
31643235 GTTTTAAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.23, C:0.42, G:0.04, T:0.31
Consensus pattern (9 bp):
TCAACTCTC
Found at i:31645368 original size:38 final size:38
Alignment explanation
Indices: 31645317--31645406 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 38
31645307 CACCGGCAAT
* *
31645317 AAGCCTGAATAACACCGGCATTAAGCCAGCTAGGCACA
1 AAGCCTGAATAACACCGACACTAAGCCAGCTAGGCACA
**
31645355 AAGCCTGAATAACACCGACACTAAGCTTGCTAGGCACA
1 AAGCCTGAATAACACCGACACTAAGCCAGCTAGGCACA
31645393 AAGCCTGAATAACA
1 AAGCCTGAATAACA
31645407 GTATGATTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.39, C:0.28, G:0.19, T:0.14
Consensus pattern (38 bp):
AAGCCTGAATAACACCGACACTAAGCCAGCTAGGCACA
Found at i:31652364 original size:13 final size:13
Alignment explanation
Indices: 31652346--31652373 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31652336 TGATTATGGC
31652346 ATCAATCTTATGT
1 ATCAATCTTATGT
31652359 ATCAATCTTATGT
1 ATCAATCTTATGT
31652372 AT
1 AT
31652374 AGGGCCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (13 bp):
ATCAATCTTATGT
Found at i:31654778 original size:18 final size:17
Alignment explanation
Indices: 31654755--31654798 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
31654745 AATTGAGTAC
31654755 TCCATTTCTCATTCCATT
1 TCCATTTCTCATT-CATT
*
31654773 TCCATTTTTCATTCATT
1 TCCATTTCTCATTCATT
31654790 TGCCATTTC
1 T-CCATTTC
31654799 AACATTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.16, C:0.30, G:0.02, T:0.52
Consensus pattern (17 bp):
TCCATTTCTCATTCATT
Found at i:31655142 original size:2 final size:2
Alignment explanation
Indices: 31655135--31655162 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31655125 CATTTCATTT
31655135 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
31655163 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:31660402 original size:17 final size:18
Alignment explanation
Indices: 31660365--31660402 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31660355 ATTGCTTCTC
* *
31660365 AAAAGTGCTTTTGGGCTA
1 AAAAGTACTTTTGAGCTA
31660383 AAAAGTACTTTTGAGC-A
1 AAAAGTACTTTTGAGCTA
31660400 AAA
1 AAA
31660403 GCTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (18 bp):
AAAAGTACTTTTGAGCTA
Found at i:31669848 original size:50 final size:50
Alignment explanation
Indices: 31669773--31670036 Score: 447
Period size: 50 Copynumber: 5.3 Consensus size: 50
31669763 NNNNNNNCAC
31669773 CATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGA
1 CATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGA
31669823 CATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGA
1 CATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGA
31669873 CATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGA
1 CATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGA
* **
31669923 CATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTCTGGGA
1 CATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGA
* * **
31669973 CATGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTCTGGGA
1 CATGGCATTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTCTGGGA
*
31670024 CATGGCTTTGGCA
1 CATGGCATTGGCA
31670037 TGTTATTATC
Statistics
Matches: 201, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
50 167 0.83
51 34 0.17
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
CATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGA
Found at i:31672276 original size:18 final size:19
Alignment explanation
Indices: 31672253--31672299 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
31672243 AAAAACAAAC
31672253 TTAATTTAAT-ATATATTT
1 TTAATTTAATAATATATTT
*
31672271 TTAATTATTTATAATATATTT
1 TTAA-T-TTAATAATATATTT
*
31672292 ATAATTTA
1 TTAATTTA
31672300 TGATATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.17
19 3 0.13
20 5 0.22
21 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATTTAATAATATATTT
Found at i:31672292 original size:11 final size:11
Alignment explanation
Indices: 31672263--31672296 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31672253 TTAATTTAAT
*
31672263 ATATATTTTTA
1 ATATATTTATA
31672274 AT-TATTTATA
1 ATATATTTATA
31672284 ATATATTTATA
1 ATATATTTATA
31672295 AT
1 AT
31672297 TTATGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATATATTTATA
Found at i:31672300 original size:18 final size:19
Alignment explanation
Indices: 31672254--31672307 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
31672244 AAAACAAACT
*
31672254 TAATTTAATATATATTTTTAA
1 TAATTT-ATA-ATATATTTAA
*
31672275 TTATTTATAATATATTT-A
1 TAATTTATAATATATTTAA
*
31672293 TAATTTATGATATAT
1 TAATTTATAATATAT
31672308 AAACTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 14 0.48
19 7 0.24
20 3 0.10
21 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TAATTTATAATATATTTAA
Found at i:31677064 original size:20 final size:22
Alignment explanation
Indices: 31677039--31677081 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31677029 TAGCACATTT
31677039 TTGAC-AATTC-TAAGAAAAAA
1 TTGACAAATTCATAAGAAAAAA
*
31677059 TTGACAAATTCATAATAAAAAA
1 TTGACAAATTCATAAGAAAAAA
31677081 T
1 T
31677082 AAAATAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (22 bp):
TTGACAAATTCATAAGAAAAAA
Found at i:31685103 original size:23 final size:23
Alignment explanation
Indices: 31685068--31685120 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
31685058 AATTGAATTG
*
31685068 ATTT-TTTTCTATT-TTTTAATA
1 ATTTATTTTATATTCTTTTAATA
*
31685089 TTTTCATTTTATATTCTTTTAATA
1 ATTT-ATTTTATATTCTTTTAATA
31685113 ATTTATTT
1 ATTTATTT
31685121 GATTAAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
23 12 0.46
24 11 0.42
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTATTTTATATTCTTTTAATA
Found at i:31690792 original size:34 final size:35
Alignment explanation
Indices: 31690748--31690814 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
31690738 CAGTAAAATG
* *
31690748 TTTTCCGTAAAATGATTT-TTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
31690782 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
31690815 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:31690818 original size:14 final size:15
Alignment explanation
Indices: 31690742--31690818 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
31690732 GATTGCCAGT
* *
31690742 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
31690756 AAAATGATTTT-TGG
1 AAAATGATTTTCTGG
*
31690770 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
31690790 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
31690805 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
31690819 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:31690917 original size:20 final size:20
Alignment explanation
Indices: 31690892--31690943 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
31690882 GAAAAAGTTG
31690892 TTTTTACATATATT-AATAAA
1 TTTTTACATATATTAAAT-AA
* *
31690912 TTTTT--ATATTTTAAATTA
1 TTTTTACATATATTAAATAA
31690930 TTTTTACATATATT
1 TTTTTACATATATT
31690944 GCAATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 11 0.42
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTACATATATTAAATAA
Found at i:31697249 original size:60 final size:60
Alignment explanation
Indices: 31697148--31697276 Score: 179
Period size: 60 Copynumber: 2.1 Consensus size: 60
31697138 ACTAATATTA
* * * *
31697148 TTTGTACTTCGGTGTCTCTGTATACACTTTGGTGTCTCTATTTGCACATCTGTGCCCCTG
1 TTTGCACTTCGGTGTCTCTGTATACACTTCGGTGTCCCTATTTGCACATCTATGCCCCTG
* *
31697208 TTTGCACTTCGGTGGTCT-TGTATACACTTCGGTGTCCCTATTTGCACGTCTATGGCCCTG
1 TTTGCACTTCGGT-GTCTCTGTATACACTTCGGTGTCCCTATTTGCACATCTATGCCCCTG
*
31697268 TTCGCACTT
1 TTTGCACTT
31697277 TGGTACCCCT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 57 0.93
61 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (60 bp):
TTTGCACTTCGGTGTCTCTGTATACACTTCGGTGTCCCTATTTGCACATCTATGCCCCTG
Found at i:31700145 original size:23 final size:23
Alignment explanation
Indices: 31700115--31700162 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
31700105 ATTTAGATTG
31700115 TGAAATTCTTTTCACGATATGAA
1 TGAAATTCTTTTCACGATATGAA
31700138 TGAAATTCTTTTCACGATATGAA
1 TGAAATTCTTTTCACGATATGAA
31700161 TG
1 TG
31700163 TGTAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (23 bp):
TGAAATTCTTTTCACGATATGAA
Found at i:31705703 original size:2 final size:2
Alignment explanation
Indices: 31705696--31705727 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31705686 CAATTAGAGC
31705696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31705728 GATTCATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31707428 original size:22 final size:23
Alignment explanation
Indices: 31707403--31707460 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
31707393 AATGTTGAAG
31707403 TGTCTTGAGACGTTAAAGTC-CA
1 TGTCTTGAGACGTTAAAGTCTCA
** *
31707425 TGTCTCAAGAC--TAAAGTCTTCT
1 TGTCTTGAGACGTTAAAGTC-TCA
31707447 TGTCTTGAGACGTT
1 TGTCTTGAGACGTT
31707461 TTTTTCCTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
20 7 0.26
22 19 0.70
24 1 0.04
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (23 bp):
TGTCTTGAGACGTTAAAGTCTCA
Found at i:31711953 original size:21 final size:21
Alignment explanation
Indices: 31711928--31711977 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
31711918 GTAAATAAAC
31711928 AAATAAAACTGAAGCATAT-AA-
1 AAATAAAA-TGAA-CATATGAAT
31711949 AAATAATAATGAACATATGAAT
1 AAATAA-AATGAACATATGAAT
31711971 AAATAAA
1 AAATAAA
31711978 TAAATAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.19
21 13 0.50
22 8 0.31
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAAATGAACATATGAAT
Found at i:31712376 original size:6 final size:7
Alignment explanation
Indices: 31712348--31712375 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
31712338 ATGTGTATGT
31712348 ATGAAAA
1 ATGAAAA
31712355 ATGAAAA
1 ATGAAAA
31712362 ATGAAAA
1 ATGAAAA
31712369 ATGAAAA
1 ATGAAAA
31712376 TATATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
ATGAAAA
Found at i:31713450 original size:100 final size:99
Alignment explanation
Indices: 31713273--31713994 Score: 895
Period size: 100 Copynumber: 7.2 Consensus size: 99
31713263 ACCCCTGAGG
* * * *
31713273 TTGCAATTAAAAAGATTAAAGCCACAATGGTGAATCTTACTTCCCTGGCGGTGCAATGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGG-CAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* *
31713338 TTAAAGCTACAACGGCGAATCTTACTTCCCCGACA
65 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * *
31713373 TTGCAATTAAAAAGGTTGAAGCCACAACGGCAAGTCTTACTACCCTGGCAGTGTAGTGGAACATA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCAA-TCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* * * *
31713438 TTGAAGCAACAACGACAAATCTTGTTTCCCCGACA
65 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * *
31713473 TTGCAATTAGAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACGGTGCAGTGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGC-AATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* * **
31713538 TTGAAGCTACAACGACGAATCTTGTTTCCCTAACA
65 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * *
31713573 TTGCAATTAAAAAGATTGAAGCCACAATGGCGAGTCTTACTTCCCTTGCGGTACAGTGGGACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGC-AATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* * * *
31713638 TTGAAGCTATAACAGTGAATATTGCTTCCCCGACA
65 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * *
31713673 TTGTAATTAAAAAGATTGTAGCCGCAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGGACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGG-CAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* * * *
31713738 TTGAAGCTATAACAGTGAATATTGCTTCCCCGACA
65 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * *
31713773 TTGTAATTAAAAAGATTGTAGCCGCAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGG-CAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
*
31713838 TTGAAGCTACAACGGTGAATCTTGCTTCCCCGACA
65 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * *
31713873 TTACAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCTTGGCGGTGCAGTGGAGCAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGC-AATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* **
31713938 TTGAAGCAACAATAGCGAATCTTGCTTCCCCGACA
65 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* *
31713973 TTGCAGTTAAAAAGATTAAAGC
1 TTGCAATTAAAAAGATTGAAGC
31713995 TATAAACCAC
Statistics
Matches: 549, Mismatches: 69, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
99 2 0.00
100 545 0.99
101 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (99 bp):
TTGCAATTAAAAAGATTGAAGCCACAACGGCAATCTTACTTCCCTGGCGGTGCAGTGGAACAGAT
TGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
Found at i:31713989 original size:50 final size:50
Alignment explanation
Indices: 31713273--31713994 Score: 415
Period size: 50 Copynumber: 14.4 Consensus size: 50
31713263 ACCCCTGAGG
* * * * * *
31713273 TTGCAATTAAAAAGATTAAAGCCACAATGGTGAATCTTACTTCCCTGGCG
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* * ** * * * *
31713323 GTGCAATGGAACAGATTAAAGCTACAACGGCGAATCTTACTTCCCCGACA
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* * * *
31713373 TTGCAATTAAAAAGGTTGAAGCCACAACGGC-AAGTCTTACTACCCTGGCA
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAA-TCTTACTTCCCTGACA
* * ** * * * * * ** *
31713423 GTGTAGTGGAACATATTGAAGCAACAACGACAAATCTTGTTTCCCCGACA
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* * *
31713473 TTGCAATTAGAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACG
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* * * * * ** *
31713523 GTGCAGTGGAACAA-ATTGAAGCTACAACGACGAATCTTGTTTCCCTAACA
1 TTGCAGT-TAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* * * *
31713573 TTGCAATTAAAAAGATTGAAGCCACAATGGCGAGTCTTACTTCCCTTG-CG
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCC-TGACA
* * *** * * * * * * * *
31713623 GTACAGTGGGACAGATTGAAGCTATAACAGTGAATATTGCTTCCCCGACA
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* * * * * * *
31713673 TTGTAATTAAAAAGATTGTAGCCGCAACGGTGAATCTTACTTCCCTGGCG
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* *** * * * * * * * *
31713723 GTGCAGTGGGACAGATTGAAGCTATAACAGTGAATATTGCTTCCCCGACA
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* * * * * * *
31713773 TTGTAATTAAAAAGATTGTAGCCGCAACGGTGAATCTTACTTCCCTGGCG
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* ** * * * * *
31713823 GTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACA
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* * * * * *
31713873 TTACAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCTTGGCG
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
* ** ** * ** * *
31713923 GTGCAGTGGAGCAGATTGAAGCAACAATAGCGAATCTTGCTTCCCCGACA
1 TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
*
31713973 TTGCAGTTAAAAAGATTAAAGC
1 TTGCAGTTAAAAAGATTGAAGC
31713995 TATAAACCAC
Statistics
Matches: 475, Mismatches: 191, Indels: 12
0.70 0.28 0.02
Matches are distributed among these distances:
49 7 0.01
50 462 0.97
51 6 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
TTGCAGTTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACA
Found at i:31714200 original size:44 final size:44
Alignment explanation
Indices: 31714049--31715247 Score: 404
Period size: 44 Copynumber: 27.7 Consensus size: 44
31714039 TCGTATCCAG
* * ** *
31714049 TCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAACCACAGA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * * * * *** *
31714093 TCTTATCTCTTTGAACTTGCTGTAGAGAAGA-TCGCATC-CAG-
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * *
31714134 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * *
31714178 TCCTATCTCTTTTAAGTTGCAGTGGAGCAGA-CAAAAGAAACCA-A
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAA-ACA-CAGA
* * * * * *
31714222 TCCTATCTCTCTAAAGTTACAGTGGAACAGATAGACAAAAGAAACGAA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGAT-TA-AAAACACA-G-A
* *
31714270 TCCTATCTCCCTGAAGTTGCAGTGGAG-AGGATTAAAACCACAGA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCA-GATTAAAAACACAGA
* * * * * *
31714314 TCTTATCTCTCTGAAGTTACAGTAGAGCAGA-TCACATC-CAG-
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * * * * **
31714355 TCTTATCTCCCTGATGTTACAGTTGAGAAGAAAAAAGAAGC-CA-A
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAA-AA-CACAGA
* * * **
31714399 TCCTATCTCCCTGAAGTTACAGTGGAG-AGGATGAAAGCCACAGA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCA-GATTAAAAACACAGA
* * * * * *
31714443 TCTTATCTCTCTGAAGTTGTAGTAGAGCAGA-TCACATC-CAG-
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* ** *
31714484 TCTTATCT-TCCTGAAGTTGCAACGGAGCAGA-TAAAAGAAACTA-A
1 TCCTATCTCT-CTGAAGTTGCAGTGGAGCAGATTAAAA-ACAC-AGA
* * ** * * * *
31714528 TCCTATCTCCCTAAAGTTATAGTAGAGCGGATTAAAACCACATA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * *** *
31714572 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGA-TCGTATC-CAG-
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * *
31714613 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACCA-A
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAA-ACA-CAGA
* * *
31714657 TCCTATCTCCCTAAAGTAT-CAGTGGAGCGGATT-AAAACAACAGA
1 TCCTATCTCTCTGAAGT-TGCAGTGGAGCAGATTAAAAAC-ACAGA
* * * *** *
31714701 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGA-TCGCATC-CAG-
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * ** *
31714742 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAAAAATCA-A
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACA-CAGA
* * * *
31714786 TCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAAA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * * *** * *
31714830 TCTTATCTCTCTAAAGTTGCAGTAGAGCA-AATCGCATC-CA-T
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * **
31714871 TCTTATCTCCCCGAAGTTGCAGTGGAGCAGACAGAAGAAAC-CA-A
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGA-TTAA-AAACACAGA
* * * *
31714915 TCCTATCACTCTGAAGTTACAGTGGAGCGGATTAAAACCACAGA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * * *** *
31714959 TCTTATCTCCCTGAAGTTGCAGTGAATCAGA-TCGCATC-CAG-
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * * *
31715000 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-CAAAAGAAACCA-A
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAA-ACA-CAGA
* * * * * ** *
31715044 GCCTATCTCCCTAAAGTTGTAGTAGAGTGGATTAAAATCACAGA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * * * ***
31715088 TCTTATCTATCTGAAATTGCAGT--AG-AG-CTAATCGCATCTAG-
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACA-C-AGA
* * **
31715129 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAAAAGC-CA-A
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGA-TTAAAAA-CACAGA
* * * * * * * *
31715173 TTCTACCTCCCTGAAGTTGTAGTAGAG-TGATTAAAACCACAAA
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
* * *
31715216 ACTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TCCTATCTCTCTGAAGTTGCAGTGGAGCAGAT
31715248 CGCATCTAGT
Statistics
Matches: 849, Mismatches: 239, Indels: 134
0.69 0.20 0.11
Matches are distributed among these distances:
40 6 0.01
41 213 0.25
42 39 0.05
43 72 0.08
44 459 0.54
45 17 0.02
46 10 0.01
47 6 0.01
48 27 0.03
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (44 bp):
TCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
Found at i:31714440 original size:129 final size:129
Alignment explanation
Indices: 31714137--31715285 Score: 1405
Period size: 129 Copynumber: 8.9 Consensus size: 129
31714127 CATCCAGTCT
* * * * * *
31714137 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCCTATCTCTTTTAAGTTGCAGTG
1 TATCTCCCTGAAGTTACAGTGGAGAGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
* * * * * * * *
31714202 GAGCAGA-CAAAAGAAACCAATCCTATCTCTCTAAAGTTACAGTGGAACAGATAGACAAAAGAAA
66 GAGCAGATC----GCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG---AG-CAGACAAAAGAAA
*
31714266 CGAATCC
123 CCAATCC
* *
31714273 TATCTCCCTGAAGTTGCAGTGGAGAGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAGTGGAGAGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
* * * * * * *
31714338 GAGCAGATCACATCCAGTCTTATCTCCCTGATGTTACAGTTGAGAAGAAAAAAGAAGCCAATCC
66 GAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCC
* * *
31714402 TATCTCCCTGAAGTTACAGTGGAGAGGATGAAAGCCACAGATCTTATCTCTCTGAAGTTGTAGTA
1 TATCTCCCTGAAGTTACAGTGGAGAGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
* * ** * *
31714467 GAGCAGATCACATCCAGTCTTATCTTCCTGAAGTTGCAACGGAGCAGATAAAAGAAACTAATCC
66 GAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCC
* * * * * *
31714531 TATCTCCCTAAAGTTATAGTAGAGCGGATTAAAACCACATATCTTATCTCTCTAAAGTTGCAGTA
1 TATCTCCCTGAAGTTACAGTGGAGAGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
*
31714596 GAGCAGATCGTATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCC
66 GAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCC
* * * *
31714660 TATCTCCCTAAAG-TATCAGTGGAGCGGATTAAAACAACAGATCTTATCTCTCTAAAGTTGCAGT
1 TATCTCCCTGAAGTTA-CAGTGGAGAGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
* *
31714724 AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAAAAATCAATCC
65 AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCC
* *
31714789 TATCTCCCTGAAGTTACAGTGGAGCA-GATTAAAACCACAAATCTTATCTCTCTAAAGTTGCAGT
1 TATCTCCCTGAAGTTACAGTGGAG-AGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
* * * *
31714853 AGAGCAAATCGCATCCATTCTTATCTCCCCGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
65 AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCC
* * * *
31714918 TATCACTCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGT-
1 TATCTCCCTGAAGTTACAGTGGAGAGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
* * *
31714982 GAATCAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACAAAAGAAACCAAGCC
66 G-AGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCC
* ** * * * * *
31715047 TATCTCCCTAAAGTTGTAGTAGAGTGGATTAAAATCACAGATCTTATCTATCTGAAATTGCAGTA
1 TATCTCCCTGAAGTTACAGTGGAGAGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
* * *
31715112 GAGCTA-ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAA-AAGCCAATT
66 GAGC-AGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA-AAAGAAACCAATC
31715175 C
129 C
* ** * *
31715176 TACCTCCCTGAAGTTGTAGT--AGAGTGATTAAAACCACAAAACTTATCTCTCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTACAGTGGAGAG-GATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
* * * *
31715239 AGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGATGTAGTGGAGCA
65 AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
31715286 AACTGTTGAC
Statistics
Matches: 894, Mismatches: 108, Indels: 30
0.87 0.10 0.03
Matches are distributed among these distances:
127 4 0.00
128 78 0.09
129 712 0.80
130 9 0.01
133 24 0.03
136 66 0.07
137 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (129 bp):
TATCTCCCTGAAGTTACAGTGGAGAGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
GAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATCC
Found at i:31714491 original size:85 final size:85
Alignment explanation
Indices: 31713998--31715283 Score: 429
Period size: 85 Copynumber: 14.9 Consensus size: 85
31713988 TTAAAGCTAT
* * * ** *
31713998 AAACCACAAATCTTATCTCTTTGAAGTTGCAGTAGAACAGATCGTATCCAGTCCTATCTCCCTGA
1 AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGA
* * *
31714063 AGTTGTAGTGGAGTGGATTA
66 AGTTGCAGTGGAGAGGATGA
* * * * **
31714083 AAACCACAGATCTTATCTCTTTGAACTTGCTGTAGAGAAGATCGCATCCAGTCTTATCTCCCTGA
1 AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGA
* *
31714148 AGTTGCAGTGGAGCGGATTA
66 AGTTGCAGTGGAGAGGATGA
* * * * * * * *
31714168 AAACCACAGATCCTATCTCTTTTAAGTTGCAGTGGAGCAGA-CAAAAGAAACCAATCCTATCTCT
1 AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC---A-AATCCAGTCTTATCTCC
* * *
31714232 CTAAAGTTACAGTGGA-ACAGATAGA
62 CTGAAGTTGCAGTGGAGA-GGAT-GA
** * * * * * *
31714257 CAAAAGAAACGAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGATTAAAACCACAGATCTTATC
1 -AAACCACA-G-ATCTTATCTCTCTGAAGTTGCAGTAGAGCA-GA-TCAAATC-CAG-TCTTATC
* * * *
31714321 TCTCTGAAGTTACAGTAGAGCA-GAT-C
59 TCCCTGAAGTTGCAGTGGAG-AGGATGA
* * * * * * * ** * * *
31714347 ACATC-CAG-TCTTATCTCCCTGATGTTACAGTTGAGAAGAAAAAAGAAGCCAATCCTATCTCCC
1 AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG--ATCA-AATCCAGTCTTATCTCCC
*
31714410 TGAAGTTACAGTGGAGAGGATGA
63 TGAAGTTGCAGTGGAGAGGATGA
* * * *
31714433 AAGCCACAGATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCACATCCAGTCTTATCTTCCTGA
1 AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGA
**
31714498 AGTTGCAACGGAGCA-GAT-A
66 AGTTGCAGTGGAG-AGGATGA
** * * * ** * * * *
31714517 AAAGAAACTA-ATCCTATCTCCCTAAAGTTATAGTAGAGCGGATTAAAACCACATATCTTATCTC
1 AAA-CCAC-AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCAAATC-CA-GTCTTATCTC
* * *
31714581 TCTAAAGTTGCAGTAGAGCA-GATCG-
61 CCTGAAGTTGCAGTGGAG-AGGAT-GA
* * * * * * *
31714606 -TATC-CAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACCAATCCTATCTCC
1 AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC---A-AATCCAGTCTTATCTCC
* * *
31714667 CTAAAGTAT-CAGTGGAGCGGATTA
62 CTGAAGT-TGCAGTGGAGAGGATGA
* * **
31714691 AAACAACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGA
1 AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGA
**
31714756 AGTTGCAGTGGAGCA-GACAA
66 AGTTGCAGTGGAG-AGGATGA
** * * * * * * * *
31714776 AAAAAATCA-ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAAATCTTATCTCT
1 AAACCA-CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCAAATC-C-AGTCTTATCTCC
* *
31714840 CTAAAGTTGCAGT--AGA-G--CA
62 CTGAAGTTGCAGTGGAGAGGATGA
* * * * * * * *
31714859 AATCGCATCCA-TTCTTATCTCCCCGAAGTTGCAGTGGAGCAGA-CAGAAGAAACCAATCCTATC
1 AAAC-CA--CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC---A-AATCCAGTCTTATC
* * * * *
31714922 ACTCTGAAGTTACAGTGGAGCGGATTA
59 TCCCTGAAGTTGCAGTGGAGAGGATGA
* * ** *
31714949 AAACCACAGATCTTATCTCCCTGAAGTTGCAGT-GAATCAGATCGCATCCAGTCTTATCTCCCTA
1 AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAG-AGCAGATCAAATCCAGTCTTATCTCCCTG
* **
31715013 AAGTTGCAGTGGAGCAGACAAAA
65 AAGTTGCAGTGGAG-AG-GATGA
* * * * ** * **
31715036 GAAACCA-AG--CCTATCTCCCTAAAGTTGTAGTAGAGTGGATTAAAATCACAGATCTTATCTAT
1 -AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCAAATC-CAG-TCTTATCTCC
* *
31715098 CTGAAATTGCAGT--AGA-GCT--
62 CTGAAGTTGCAGTGGAGAGGATGA
* * * * * *
31715117 AATCGCATCTAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AAAAGCCAAT-TCTAC
1 AAAC-CA-C-AGATCTTATCTCTCTGAAGTTGCAGT--AG-AG-CAGATCAAATCCAGTCT-TAT
* *
31715179 CTCCCTGAAGTTGTAGT--AGAGTGATTA
58 CTCCCTGAAGTTGCAGTGGAGAG-GATGA
* * ** * *
31715206 AAACCACAAAACTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCCCTAA
1 AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGA
* *
31715271 AGATGTAGTGGAG
66 AGTTGCAGTGGAG
31715284 CAAACTGTTG
Statistics
Matches: 899, Mismatches: 212, Indels: 179
0.70 0.16 0.14
Matches are distributed among these distances:
80 3 0.00
81 2 0.00
83 7 0.01
84 33 0.04
85 477 0.53
86 43 0.05
87 63 0.07
88 188 0.21
89 12 0.01
90 12 0.01
91 5 0.01
92 53 0.06
94 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (85 bp):
AAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGA
AGTTGCAGTGGAGAGGATGA
Found at i:31716716 original size:12 final size:11
Alignment explanation
Indices: 31716683--31716715 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
31716673 AAAATAAAAA
*
31716683 AAAAATATTTT
1 AAAAGTATTTT
31716694 AAAAGTATTTT
1 AAAAGTATTTT
31716705 AAAAGTATTTT
1 AAAAGTATTTT
31716716 TTGTCCAAGC
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:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:31717291 original size:16 final size:15
Alignment explanation
Indices: 31717262--31717299 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
31717252 AACTATTATT
31717262 TTTTA-TTT-TTTTG
1 TTTTATTTTGTTTTG
31717275 TTTATATTTTGTTTTG
1 TTT-TATTTTGTTTTG
31717291 TTTTATTTT
1 TTTTATTTT
31717300 TATATTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.14
14 2 0.09
15 9 0.41
16 8 0.36
ACGTcount: A:0.11, C:0.00, G:0.08, T:0.82
Consensus pattern (15 bp):
TTTTATTTTGTTTTG
Found at i:31717300 original size:16 final size:16
Alignment explanation
Indices: 31717270--31717299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31717260 TTTTTTATTT
31717270 TTTTGTTTATATTTTG
1 TTTTGTTTATATTTTG
31717286 TTTTGTTT-TATTTT
1 TTTTGTTTATATTTT
31717300 TATATTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (16 bp):
TTTTGTTTATATTTTG
Found at i:31724433 original size:50 final size:50
Alignment explanation
Indices: 31724373--31724860 Score: 363
Period size: 50 Copynumber: 9.8 Consensus size: 50
31724363 CATTGCAATT
* **
31724373 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCGGTATAGTG
1 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCAGTGCAGTG
* * * * * * * * *
31724423 AAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATT
1 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCAGTGCAGTG
* *
31724473 AAAAAGATTGAAGCCACAA-AGGTGAATCTTACTTCCCTGGCGGTGCAGTGG
1 AAAAAGATTGAAGCCACAACA-GCGAATCTTACTTCCCTGGCAGTGCAGT-G
* * ** ** * * * *
31724524 AACAA-ATTGAAGCTACAACAGCGAATCTTGTTTCCCTAACATTACAATT
1 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCAGTGCAGTG
* * **
31724573 AAAAAGATTGAAGCCACAACGGC-AAGTCTTACTTCCCTGGCAATATAGTG
1 AAAAAGATTGAAGCCACAACAGCGAA-TCTTACTTCCCTGGCAGTGCAGTG
* * * * ** * * * *
31724623 GAATAGATTGAAGCTACAACGGCGAATCTTGTTTCCCTGACATTGCAATT
1 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCAGTGCAGTG
* * * * * *
31724673 AAAAATATTGAAGCCACAACGGCGAGTTTTAATTCCCTGG-AGGTGTAGTG
1 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCA-GTGCAGTG
* * * * * * * * * *
31724723 GAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATT
1 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCAGTGCAGTG
* * * *
31724773 AAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCTCTGGCAGTGTAGTG
1 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCAGTGCAGTG
* * *
31724823 GAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCT
1 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCT
31724861 AACATTACAG
Statistics
Matches: 330, Mismatches: 100, Indels: 16
0.74 0.22 0.04
Matches are distributed among these distances:
49 8 0.02
50 314 0.95
51 8 0.02
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (50 bp):
AAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCAGTGCAGTG
Found at i:31724866 original size:100 final size:100
Alignment explanation
Indices: 31724363--31724866 Score: 722
Period size: 100 Copynumber: 5.0 Consensus size: 100
31724353 ATCTCTTTGG
* * * * *
31724363 CATTGCAATTAAAAAGATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCGGTATAGTGAAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTGTAGTGGAACA
* *
31724428 GATTGAAGCTACAACAGTGAATCTTGCTTCCCCGA
66 GATTGAAGCTACAACAGCGAATCTTGCTTCCCTGA
* * * * *
31724463 CATTGCAATTAAAAAGATTGAAGCCACAAAGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTGTAGTGGAACA
* * *
31724528 AATTGAAGCTACAACAGCGAATCTTGTTTCCCTAA
66 GATTGAAGCTACAACAGCGAATCTTGCTTCCCTGA
* * * * *
31724563 CATTACAATTAAAAAGATTGAAGCCACAACGGCAAGTCTTACTTCCCTGGCAATATAGTGGAATA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTGTAGTGGAACA
* *
31724628 GATTGAAGCTACAACGGCGAATCTTGTTTCCCTGA
66 GATTGAAGCTACAACAGCGAATCTTGCTTCCCTGA
* * *
31724663 CATTGCAATTAAAAATATTGAAGCCACAACGGCGAGTTTTAATTCCCTGG-AGGTGTAGTGGAAC
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCA-GTGTAGTGGAAC
* *
31724727 AGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGA
65 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCTGA
*
31724763 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCTCTGGCAGTGTAGTGGAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTGTAGTGGAACA
* *
31724828 GATTGAAGCTACAACAGCGAATCTTACTTCCCTAA
66 GATTGAAGCTACAACAGCGAATCTTGCTTCCCTGA
31724863 CATT
1 CATT
31724867 ACAGTCAATT
Statistics
Matches: 360, Mismatches: 42, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
99 1 0.00
100 358 0.99
101 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (100 bp):
CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCAGTGTAGTGGAACA
GATTGAAGCTACAACAGCGAATCTTGCTTCCCTGA
Found at i:31725046 original size:45 final size:44
Alignment explanation
Indices: 31724994--31725097 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 44
31724984 GTCTTATCCT
* * * *
31724994 CCTGAAGTTGCAGTGGGGCAAACTGAAGATAGCGAGTCTTGTCTC
1 CCTGAAGTTGCAGTGGAGCAAACTGAAGATA-CGAATCCTATCTC
* * **
31725039 CCTGAAGTTGCAGTGGAGCAGACTGAAGCTATTAATCCTATCTC
1 CCTGAAGTTGCAGTGGAGCAAACTGAAGATACGAATCCTATCTC
31725083 CCTGAAGTTGCAGTG
1 CCTGAAGTTGCAGTG
31725098 AAGTGGATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 23 0.45
45 28 0.55
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (44 bp):
CCTGAAGTTGCAGTGGAGCAAACTGAAGATACGAATCCTATCTC
Found at i:31725211 original size:44 final size:44
Alignment explanation
Indices: 31725155--31725269 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 44
31725145 CAGATCATAT
* *
31725155 CAAACCTTATCTCTCTGAAGTTGCAGTAAAGTAGGTTGAAG-TA
1 CAAACCTTATCTCCCTGAAGTTGCAGTAAAGCAGGTTGAAGATA
* * * *
31725198 -ATTAACCTTATCTCCCTAAAGTCGCAGTGAAGCGGGTTGAAGATA
1 CA--AACCTTATCTCCCTGAAGTTGCAGTAAAGCAGGTTGAAGATA
**
31725243 CAAGTCTTATCTCCCTGAAGTTGCAGT
1 CAAACCTTATCTCCCTGAAGTTGCAGT
31725270 GGAGCAGACT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
42 1 0.02
44 54 0.93
45 2 0.03
46 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
CAAACCTTATCTCCCTGAAGTTGCAGTAAAGCAGGTTGAAGATA
Found at i:31725270 original size:44 final size:43
Alignment explanation
Indices: 31725157--31725320 Score: 125
Period size: 44 Copynumber: 3.7 Consensus size: 43
31725147 GATCATATCA
* * *
31725157 AACCTTATCTCTCTGAAGTTGCAGTAAAGTAGGTTGAAGTAATT
1 AACCTTATCTCCCTGAAGTTGCAGTGAAGCAGGTTGAAGTAA-T
* * *
31725201 AACCTTATCTCCCTAAAGTCGCAGTGAAGCGGGTTGAAGATACA-
1 AACCTTATCTCCCTGAAGTTGCAGTGAAGCAGGTTGAAG-TA-AT
** * ** * *
31725245 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCTACT
1 AACCTTATCTCCCTGAAGTTGCAGTGAAGCAGGTTGAAG-TAAT
* * *
31725289 AATCC-TACCTCCTTGAAGTTGCAGTGGAGCAG
1 AA-CCTTATCTCCCTGAAGTTGCAGTGAAGCAG
31725321 ATTAACACAA
Statistics
Matches: 95, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
44 91 0.96
45 3 0.03
46 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
AACCTTATCTCCCTGAAGTTGCAGTGAAGCAGGTTGAAGTAAT
Found at i:31727077 original size:7 final size:7
Alignment explanation
Indices: 31727065--31727092 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
31727055 TATAAATATA
31727065 TTTTCAT
1 TTTTCAT
31727072 TTTTCAT
1 TTTTCAT
31727079 TTTTCAT
1 TTTTCAT
31727086 TTTTCAT
1 TTTTCAT
31727093 ACATACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:31727510 original size:21 final size:21
Alignment explanation
Indices: 31727463--31727512 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
31727453 CATTTATTTA
31727463 TTTATTTATTCATATGTTCAT
1 TTTATTTATTCATATGTTCAT
31727484 TATTATTT-TT-ATATGCTTCAGT
1 T-TTATTTATTCATATG-TTCA-T
31727506 TTTATTT
1 TTTATTT
31727513 GTTTATTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.19
21 13 0.50
22 8 0.31
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (21 bp):
TTTATTTATTCATATGTTCAT
Found at i:31732755 original size:50 final size:50
Alignment explanation
Indices: 31732696--31733619 Score: 481
Period size: 50 Copynumber: 18.7 Consensus size: 50
31732686 GCAATTAAAA
* * * *
31732696 AGATTGAAGCCACAACAGCGAGTCTTACTTCTCTGGCAGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * ** * * * * * ** *
31732746 AGATTGAAGCTATAACGGCAAATTTTGTTTCCCCGACATTGTAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * *
31732796 AGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCGGTACAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* ** * * * * ** *
31732846 AGATTGAAGCTACAACGACGAATCTTGTTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * ** *
31732896 AGATTGAAGCCACAATGGCGAGTCTTACTTCCCTAGTGGTGTAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * *
31732946 AAATTGAAGCTACAACGACG-A----A--T-CCTGGC-GATGCAGTGGAAT
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAG-TGCAGTGGAAC
* * * * * * * ** *
31732988 AGATTAAAGCTACAACGGCAAATCTTA-TTTCCTCGACATTGTAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCT-GGCAGTGCAGTGGAAC
** ** *
31733038 AGATTGAA-C-ACATAACGATGAATCTTACTTCCCTGGTGGTGCACTGGAAC
1 AGATTGAAGCTAC--AACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * ** * * * * * ** *
31733088 AGATTGAAGCTACAACTGTGAATCTTGTTTCCCCGACATTGTAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * * *
31733138 AGATTGATGCCACAACAGCGAGTCTTACTTCCCCGGCAGTACAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * * * ** *
31733188 AGATTGAAGCTACAACGGTGAATCTT-GTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * *
31733237 AGATTGAAGCCACAACGGTGAGTCTTACTTCCCTGGCAGTGCAGTGGGAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * * * * ** *
31733287 AGATTGAAGCTACAACGACAAATTTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * *
31733337 AGATTGAAGCCACAATGGGGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * ** * * ** *
31733387 AGATTGAAGCTACAACGGCGTATCTT-GTTTCCTCGATATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCT-GGCAGTGCAGTGGAAC
* * * * *
31733437 ATATTGAAGCCACAACGGCAAATCTTACTTCCCTGGCAGTGTAGTGGAGC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * *** * ** *
31733487 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCAACATTGCAGTTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* ** * * * **
31733537 AGATTGAAGCTACAACAGTAAATCTGACTTCCCTGGCGGTGTAGAAGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
* * * *
31733587 TGATTGAAGCTACAACAGTGAATCTTGCTTCCC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCC
31733620 CGACATTGCA
Statistics
Matches: 617, Mismatches: 239, Indels: 36
0.69 0.27 0.04
Matches are distributed among these distances:
41 1 0.00
42 29 0.05
43 2 0.00
45 1 0.00
47 1 0.00
48 3 0.00
49 48 0.08
50 519 0.84
51 11 0.02
52 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGAAC
Found at i:31733111 original size:142 final size:142
Alignment explanation
Indices: 31732827--31733103 Score: 376
Period size: 142 Copynumber: 2.0 Consensus size: 142
31732817 GTCTTACTTC
* * * *
31732827 CCTGGCGGTACAGTGGAACAGATTGAAGCTACAACGACGAATCTTGTTTCCCCGACATTGCAATT
1 CCTGGCGATACAGTGGAACAGATTAAAGCTACAACGACAAATCTTATTTCCCCGACATTGCAATT
* * * * *
31732892 AAAAAGATTGAAGCCACAATGGCGAGTCTTACTTCCCTAGTGGTGTAGTGGAACAAATTGAAGCT
66 AAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGTGGTGCACTGGAACAAATTGAAGCT
31732957 ACAACGACGAAT
131 ACAACGACGAAT
* * * * *
31732969 CCTGGCGATGCAGTGGAATAGATTAAAGCTACAACGGCAAATCTTATTTCCTCGACATTGTAATT
1 CCTGGCGATACAGTGGAACAGATTAAAGCTACAACGACAAATCTTATTTCCCCGACATTGCAATT
* * * *
31733034 AAAAAGATTGAA-CACATAACGATGAATCTTACTTCCCTGGTGGTGCACTGGAACAGATTGAAGC
66 AAAAAGATTGAAGC-CACAACGACGAATCTTACTTCCCTAGTGGTGCACTGGAACAAATTGAAGC
31733098 TACAAC
130 TACAAC
31733104 TGTGAATCTT
Statistics
Matches: 116, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
141 1 0.01
142 115 0.99
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (142 bp):
CCTGGCGATACAGTGGAACAGATTAAAGCTACAACGACAAATCTTATTTCCCCGACATTGCAATT
AAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGTGGTGCACTGGAACAAATTGAAGCT
ACAACGACGAAT
Found at i:31733161 original size:242 final size:242
Alignment explanation
Indices: 31732735--31733204 Score: 683
Period size: 242 Copynumber: 1.9 Consensus size: 242
31732725 TCTCTGGCAG
* * * *
31732735 TGCAGTGGAACAGATTGAAGCTATAACGGCAAATTTTGTTTCCCCGACATTGTAATTAAAAAGAT
1 TGCAGTGGAACAGATTAAAGCTACAACGGCAAATCTTATTTCCCCGACATTGTAATTAAAAAGAT
* * *
31732800 TGAAGCCACAACGGCGAGTCTTACTTCCCTGGCGGTACAGTGGAACAGATTGAAGCTACAACGAC
66 TGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTACACTGGAACAGATTGAAGCTACAACGAC
** *
31732865 GAATCTTGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAATGGCGAGTCTTACTTCCCT
131 GAATCTTGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACAGCGAGTCTTACTTCCCC
** **
31732930 AGTGGTGTAGTGGAACAAATTGAAGCTACAACGACGAATCCTGGCGA
196 AGCAGTACAGTGGAACAAATTGAAGCTACAACGACGAATCCTGGCGA
* *
31732977 TGCAGTGGAATAGATTAAAGCTACAACGGCAAATCTTATTTCCTCGACATTGTAATTAAAAAGAT
1 TGCAGTGGAACAGATTAAAGCTACAACGGCAAATCTTATTTCCCCGACATTGTAATTAAAAAGAT
* * * *
31733042 TGAA-CACATAACGATGAATCTTACTTCCCTGGTGGTGCACTGGAACAGATTGAAGCTACAACTG
66 TGAAGC-CACAACGACGAATCTTACTTCCCTGGCGGTACACTGGAACAGATTGAAGCTACAAC-G
* * *
31733106 -TGAATCTTGTTTCCCCGACATTGTAATTAAAAAGATTGATGCCACAACAGCGAGTCTTACTTCC
129 ACGAATCTTGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACAGCGAGTCTTACTTCC
* *
31733170 CCGGCAGTACAGTGGAACAGATTGAAGCTACAACG
194 CCAGCAGTACAGTGGAACAAATTGAAGCTACAACG
31733205 GTGAATCTTG
Statistics
Matches: 201, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
241 1 0.00
242 199 0.99
243 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (242 bp):
TGCAGTGGAACAGATTAAAGCTACAACGGCAAATCTTATTTCCCCGACATTGTAATTAAAAAGAT
TGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTACACTGGAACAGATTGAAGCTACAACGAC
GAATCTTGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACAGCGAGTCTTACTTCCCC
AGCAGTACAGTGGAACAAATTGAAGCTACAACGACGAATCCTGGCGA
Found at i:31733648 original size:100 final size:100
Alignment explanation
Indices: 31732969--31733646 Score: 779
Period size: 100 Copynumber: 6.8 Consensus size: 100
31732959 AACGACGAAT
* * * * ** * *
31732969 CCTGGC-GATGCAGTGGAATAGATTAAAGCTACAACGGCAAATCTTATTTCCTCGACATTGTAAT
1 CCTGGCAG-TGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAAT
* **
31733033 TAAAAAGATTGAA-CACATAACGATGAATCTTACTTC
65 TAAAAAGATTGAAGC-CACAACGGCGAATCTTACTTC
** * * * * *
31733069 CCTGGTGGTGCACTGGAACAGATTGAAGCTACAACTGTGAATCTTGTTTCCCCGACATTGTAATT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
* * *
31733134 AAAAAGATTGATGCCACAACAGCGAGTCTTACTTC
66 AAAAAGATTGAAGCCACAACGGCGAATCTTACTTC
* * * *
31733169 CCCGGCAGTACAGTGGAACAGATTGAAGCTACAACGGTGAATCTTG-TTCCCCGACATTGCAATT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
* *
31733233 AAAAAGATTGAAGCCACAACGGTGAGTCTTACTTC
66 AAAAAGATTGAAGCCACAACGGCGAATCTTACTTC
* * * * *
31733268 CCTGGCAGTGCAGTGGGACAGATTGAAGCTACAAC-GACAAATTTTACTTCCCTGACATTGCAAT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAG-CGAATCTTGCTTCCCCGACATTGCAAT
* *
31733332 TAAAAAGATTGAAGCCACAATGGGGAATCTTACTTC
65 TAAAAAGATTGAAGCCACAACGGCGAATCTTACTTC
* * * * * *
31733368 CCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGTATCTTGTTTCCTCGATATTGCAATT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
* *
31733433 AAAAATATTGAAGCCACAACGGCAAATCTTACTTC
66 AAAAAGATTGAAGCCACAACGGCGAATCTTACTTC
* * * *
31733468 CCTGGCAGTGTAGTGGAGCAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCAACATTGCAGTT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
* * ** *
31733533 AAAAAGATTGAAGCTACAACAGTAAATCTGACTTC
66 AAAAAGATTGAAGCCACAACGGCGAATCTTACTTC
* * ** * *
31733568 CCTGGCGGTGTAGAAGAACTGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATT
1 CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
*
31733633 AAAAAGATTAAAGC
66 AAAAAGATTGAAGC
31733647 TATAAACCAC
Statistics
Matches: 499, Mismatches: 74, Indels: 10
0.86 0.13 0.02
Matches are distributed among these distances:
98 1 0.00
99 86 0.17
100 409 0.82
101 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (100 bp):
CCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAATT
AAAAAGATTGAAGCCACAACGGCGAATCTTACTTC
Found at i:31733961 original size:85 final size:84
Alignment explanation
Indices: 31733871--31734285 Score: 291
Period size: 85 Copynumber: 4.8 Consensus size: 84
31733861 CTACAGATCT
* * * *
31733871 TATCTCTCTGAAATTGCAGTAGAGCAGATCACATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
*
31733936 CAGACAAAAGAAACCAATCC
66 CAGAC-AAAGAATCCAATCC
*** * * * ** **
31733956 TATCTCCCTGAAGTCATAGTAGAGCGGATTAAAACCACAGATCTTATCTCTTTGAAGTTGCAGCA
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TCAAATC-CAG-TCTTATCTCCCTGAAGTTGCAGTG
* * *
31734021 GAGCAGATC---GCATCCAGTCT
63 GAGCAGA-CAAAGAATCCAATCC
* * * * *
31734041 TATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACCAATCCTATCTCCCTAAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATC---A-AATCCAGTCTTATCTCCCTGAAGTTGCAGT
** ** *
31734105 GGAGTGGATTAA-AATCACATATCT
62 GGAGCAGACAAAGAATC-CA-ATCC
* * * * *
31734129 TATCTCTCTGAAGTTACAGTAGAGCAGATCACATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
*
31734194 CAGACAGAAGAAGCCAATCC
66 CAGACA-AAGAATCCAATCC
* * * * * * *
31734214 TACCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TCAAATC-CAG-TCTTATCTCCCTGAAGTTGCAGTG
31734279 GAGCAGA
63 GAGCAGA
31734286 TCGTATCTAG
Statistics
Matches: 246, Mismatches: 65, Indels: 35
0.71 0.19 0.10
Matches are distributed among these distances:
85 131 0.53
86 19 0.08
87 13 0.05
88 81 0.33
89 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
CAGACAAAGAATCCAATCC
Found at i:31733969 original size:44 final size:43
Alignment explanation
Indices: 31733867--31734285 Score: 241
Period size: 44 Copynumber: 9.7 Consensus size: 43
31733857 AAAACTACAG
* * * *
31733867 ATCTTATCTCTCTGAAATTGCAGTAGAGCAGATC--A-CATCCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAGAATCCA
* * *
31733908 GTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-AAAGAATCCA
* *** * * ** *
31733952 ATCCTATCTCCCTGAAGTCATAGTAGAGCGGATTAA-AACCACA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAGAATC-CA
** ** *
31733995 GATCTTATCTCTTTGAAGTTGCAGCAGAGCAGATC---GCATCCA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAGAATCCA
* *
31734037 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-AAAGAATCCA
* * ** **
31734081 ATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAA-AATCACA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAGAATC-CA
* * * * *
31734124 TATCTTATCTCTCTGAAGTTACAGTAGAGCAGATC--A-CATCTA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAGAATCCA
* * *
31734166 GTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACAGAAGAAGCCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA-AAGAATCCA
* * ** *
31734210 ATCCTACCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AACCACA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAGAATC-CA
* * *
31734253 GATCTTATCTCTCTAAAGTTGCAGTAGAGCAGA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
31734286 TCGTATCTAG
Statistics
Matches: 283, Mismatches: 74, Indels: 39
0.71 0.19 0.10
Matches are distributed among these distances:
40 3 0.01
41 81 0.29
42 12 0.04
43 20 0.07
44 167 0.59
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAGAATCCA
Found at i:31734036 original size:129 final size:129
Alignment explanation
Indices: 31733701--31734327 Score: 816
Period size: 129 Copynumber: 4.9 Consensus size: 129
31733691 TCGCATCTAG
* * * * * *
31733701 TCCTATCTTCCTGAAATTACAGTAGAGCGGGTTAAAACCACAGATCTTATCTCTTTGAAGTTACA
1 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* * * * * * *
31733766 GTATAGCATATCGCATTCAGTTTTATCTCTCTAAAGTTGCAGTGGAGCAGACAAAAGAAACAAA
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * *
31733830 TTCTATCTCCCT---G---CAGTGGAGCGGATTAAAACTACAGATCTTATCTCTCTGAAATTGCA
1 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* *
31733889 GTAGAGCAGATCACATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * * *
31733953 TCCTATCTCCCTGAAGTCATAGTAGAGCGGATTAAAACCACAGATCTTATCTCTTTGAAGTTGCA
1 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
*
31734018 GCAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * * * * *
31734082 TCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCACATATCTTATCTCTCTGAAGTTACA
1 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* * * * *
31734147 GTAGAGCAGATCACATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACAGAAGAAGCCAA
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * * *
31734211 TCCTACCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCA
1 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* * * * * *
31734276 GTAGAGCAGATCGTATCTAGTCTTATCTCCCTAAAGATGTAGTGGAACAGAC
66 GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
31734328 TATTGATAGC
Statistics
Matches: 436, Mismatches: 56, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
123 108 0.25
126 1 0.00
129 327 0.75
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (129 bp):
TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
GTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
Found at i:31748533 original size:41 final size:40
Alignment explanation
Indices: 31748488--31748572 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
31748478 AAATAGGCTT
31748488 TTAGCGGC-ATTTGGATAAAAAATGCCACTAAAAATCAAGCA
1 TTAGCGGCGATTT-GAT-AAAAATGCCACTAAAAATCAAGCA
* ** * *
31748529 TTAGCGGCGCTTTTCTAAAAATGCCACTAAAGATCGAGCA
1 TTAGCGGCGATTTGATAAAAATGCCACTAAAAATCAAGCA
31748569 TTAG
1 TTAG
31748573 TTGGAAAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
40 26 0.68
41 9 0.24
42 3 0.08
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (40 bp):
TTAGCGGCGATTTGATAAAAATGCCACTAAAAATCAAGCA
Found at i:31752036 original size:19 final size:20
Alignment explanation
Indices: 31752012--31752055 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
31752002 CGGATACATG
31752012 TTTATTTTT-GATCTCATAA
1 TTTATTTTTGGATCTCATAA
31752031 TTTATTTTTGGATCTCATAA
1 TTTATTTTTGGATCTCATAA
31752051 TTTAT
1 TTTAT
31752056 CCTTTCACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTATTTTTGGATCTCATAA
Found at i:31752518 original size:25 final size:25
Alignment explanation
Indices: 31752445--31752518 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
31752435 TTCCTGAAAC
31752445 TTGTTCTCCTTGTTGATGTCAAAAA
1 TTGTTCTCCTTGTTGATGTCAAAAA
* * * *
31752470 TTGTCCTCCTTG-CG-T-T--TAAC
1 TTGTTCTCCTTGTTGATGTCAAAAA
*
31752490 TTGTTCTCCTTGTTGATGTCAAAAT
1 TTGTTCTCCTTGTTGATGTCAAAAA
31752515 TTGT
1 TTGT
31752519 CTTCATGAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 13 0.36
21 1 0.03
22 2 0.06
23 2 0.06
24 1 0.03
25 17 0.47
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (25 bp):
TTGTTCTCCTTGTTGATGTCAAAAA
Found at i:31756568 original size:42 final size:42
Alignment explanation
Indices: 31756522--31756652 Score: 110
Period size: 42 Copynumber: 3.1 Consensus size: 42
31756512 AAGAACGGAA
* *
31756522 CTTTTAGTAGCGTTTT-CGATAAAAGCGTCGCTAAAGGTCATG-
1 CTTTTAGCAGC-TTTTGCGATAAAAGCG-CGCTAAAGATCATGT
* *
31756564 CTTTTAGCGGCTTTTGTGATAAAAGCGCGCTAAAGATCATGT
1 CTTTTAGCAGCTTTTGCGATAAAAGCGCGCTAAAGATCATGT
* * *
31756606 C-TTTAGCGGCATTTTTG-GGT-AAAGCGCCGCTAAAGGTCATGTT
1 CTTTTAGCAGC--TTTTGCGATAAAAGCG-CGCTAAAGATCATG-T
31756649 CTTT
1 CTTT
31756653 AGCGACGTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
41 32 0.42
42 35 0.46
43 7 0.09
44 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (42 bp):
CTTTTAGCAGCTTTTGCGATAAAAGCGCGCTAAAGATCATGT
Found at i:31756611 original size:41 final size:43
Alignment explanation
Indices: 31756534--31756656 Score: 148
Period size: 41 Copynumber: 2.9 Consensus size: 43
31756524 TTTAGTAGCG
* *
31756534 TTTTCGATAAAAGCGTCGCTAAAGGTCATG-CTTTTAGCGGC--
1 TTTTGGATAAAAGCGCCGCTAAAGGTCATGTC-TTTAGCGGCAT
*
31756575 TTTTGTGATAAAAGCG-CGCTAAAGATCATGTCTTTAGCGGCAT
1 TTTTG-GATAAAAGCGCCGCTAAAGGTCATGTCTTTAGCGGCAT
*
31756618 TTTTGGGT-AAAGCGCCGCTAAAGGTCATGTTCTTTAGCG
1 TTTTGGATAAAAGCGCCGCTAAAGGTCATG-TCTTTAGCG
31756657 ACGTTTTTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
41 32 0.44
42 26 0.36
43 14 0.19
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (43 bp):
TTTTGGATAAAAGCGCCGCTAAAGGTCATGTCTTTAGCGGCAT
Found at i:31756948 original size:11 final size:11
Alignment explanation
Indices: 31756932--31756956 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31756922 ATTTGGGAGT
31756932 AAAATGAGTGA
1 AAAATGAGTGA
31756943 AAAATGAGTGA
1 AAAATGAGTGA
31756954 AAA
1 AAA
31756957 TCGGAAAATC
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:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (11 bp):
AAAATGAGTGA
Found at i:31758068 original size:7 final size:7
Alignment explanation
Indices: 31758056--31758114 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
31758046 TAATTTAGCC
31758056 ATTTTTA
1 ATTTTTA
31758063 ATTTTTA
1 ATTTTTA
31758070 A--TTTA
1 ATTTTTA
*
31758075 ATATTTTT
1 AT-TTTTA
31758083 ATTTTTA
1 ATTTTTA
31758090 A--TTTA
1 ATTTTTA
31758095 ATTTTT-
1 ATTTTTA
31758101 ATATTTTA
1 AT-TTTTA
31758109 ATTTTT
1 ATTTTT
31758115 TGTTTGTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
5 10 0.23
6 2 0.05
7 24 0.56
8 7 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTA
Found at i:31758086 original size:20 final size:18
Alignment explanation
Indices: 31758056--31758112 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 18
31758046 TAATTTAGCC
31758056 ATTTTTAATTTTTAATTTAA
1 ATTTTT-ATTTTTAATTT-A
31758076 TATTTTTATTTTTAATTTA
1 -ATTTTTATTTTTAATTTA
31758095 ATTTTTATATTTTAATTT
1 ATTTTTAT-TTTTAATTT
31758113 TTTGTTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.23
19 10 0.29
20 11 0.31
21 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTATTTTTAATTTA
Found at i:31760964 original size:16 final size:16
Alignment explanation
Indices: 31760943--31760973 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31760933 TCCCAACCCC
*
31760943 ATGCAGTATGTCATGT
1 ATGCAGTATGCCATGT
31760959 ATGCAGTATGCCATG
1 ATGCAGTATGCCATG
31760974 CTCAGAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (16 bp):
ATGCAGTATGCCATGT
Found at i:31762792 original size:171 final size:171
Alignment explanation
Indices: 31762507--31762818 Score: 615
Period size: 171 Copynumber: 1.8 Consensus size: 171
31762497 CCTAGATTTC
*
31762507 CTCCTCCTAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
1 CTCCTCCAAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
31762572 TTATCCAGTAGAGTTTTAGCCAAACTCCACCTCTCTCACCACAAAGAAATAAAATAAATATCCTT
66 TTATCCAGTAGAGTTTTAGCCAAACTCCACCTCTCTCACCACAAAGAAATAAAATAAATATCCTT
31762637 TTGCATTCCATTTTGAATTCCTAGATTTCCTCCTCCTAATT
131 TTGCATTCCATTTTGAATTCCTAGATTTCCTCCTCCTAATT
31762678 CTCCTCCAAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
1 CTCCTCCAAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
31762743 TTATCCAGTAGAGTTTTAGCCAAACTCCACCTCTCTCACCACAAAGAAATAAAATAAATATCCTT
66 TTATCCAGTAGAGTTTTAGCCAAACTCCACCTCTCTCACCACAAAGAAATAAAATAAATATCCTT
31762808 TTGCATTCCAT
131 TTGCATTCCAT
31762819 GAGATTCGAA
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 140 1.00
ACGTcount: A:0.30, C:0.34, G:0.06, T:0.29
Consensus pattern (171 bp):
CTCCTCCAAATCACCCAACTACCAACCACATCCCCTGGTTCTCTCCTCATTGACCAATTCAAACC
TTATCCAGTAGAGTTTTAGCCAAACTCCACCTCTCTCACCACAAAGAAATAAAATAAATATCCTT
TTGCATTCCATTTTGAATTCCTAGATTTCCTCCTCCTAATT
Found at i:31764617 original size:12 final size:12
Alignment explanation
Indices: 31764602--31764640 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
31764592 TTATATTTTA
*
31764602 TTTGTTTTTGTT
1 TTTGTTTTTATT
31764614 TTTGTTTTTATT
1 TTTGTTTTTATT
*
31764626 TTTATTTTTTATT
1 TTT-GTTTTTATT
31764639 TT
1 TT
31764641 ATTATGCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTGTTTTTATT
Found at i:31764633 original size:18 final size:18
Alignment explanation
Indices: 31764585--31764643 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
31764575 AGTGATCTCA
* *
31764585 TTTAGTTTTATATTTTA-
1 TTTATTTTTATTTTTTAT
* *
31764602 TTTGTTTTTGTTTTTGT-T
1 TTTATTTTTATTTTT-TAT
31764620 TTTATTTTTATTTTTTAT
1 TTTATTTTTATTTTTTAT
31764638 TTTATT
1 TTTATT
31764644 ATGCACTGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTATTTTTATTTTTTAT
Found at i:31766339 original size:21 final size:21
Alignment explanation
Indices: 31766313--31766365 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
31766303 CAATTTTCAT
* *
31766313 ACGGGCATGTGCCTTGGCCAC
1 ACGGGCATGTGCCCTAGCCAC
* *
31766334 ACGGGCGTGTCCCCTAGCCAC
1 ACGGGCATGTGCCCTAGCCAC
*
31766355 ATGGGCATGTG
1 ACGGGCATGTG
31766366 AGATTTCTAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.32, G:0.34, T:0.19
Consensus pattern (21 bp):
ACGGGCATGTGCCCTAGCCAC
Found at i:31774760 original size:43 final size:45
Alignment explanation
Indices: 31774713--31774815 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 45
31774703 AAAGTATGTG
31774713 TATATATATATTTACAA-AAGTT-T-AAAATATGTACGT--ATATA
1 TATATATATATTTA-AATAAGTTATAAAAATATGTACGTACATATA
* * * *
31774754 TATATATATATATAAATGAGTTATAAAAATATGTACGTGCATATG
1 TATATATATATTTAAATAAGTTATAAAAATATGTACGTACATATA
31774799 TATATATATATTATAAA
1 TATATATATATT-TAAA
31774816 AATGTATGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 2 0.04
41 17 0.33
42 1 0.02
43 13 0.25
45 15 0.29
46 4 0.08
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.41
Consensus pattern (45 bp):
TATATATATATTTAAATAAGTTATAAAAATATGTACGTACATATA
Found at i:31774816 original size:35 final size:34
Alignment explanation
Indices: 31774774--31774850 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 34
31774764 TATAAATGAG
*
31774774 TTATAAAAA-TATGTACGTGCATATGTATATATATA
1 TTATAAAAAGTATGTACGTACATATGTATATA-A-A
* *
31774809 TTATAAAAATGTATGTATGTATATATGTATATAAA
1 TTATAAAAA-GTATGTACGTACATATGTATATAAA
31774844 TTATAAA
1 TTATAAA
31774851 GTATAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 17 0.46
36 1 0.03
37 19 0.51
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (34 bp):
TTATAAAAAGTATGTACGTACATATGTATATAAA
Found at i:31774854 original size:16 final size:17
Alignment explanation
Indices: 31774828--31774871 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
31774818 TGTATGTATG
* * *
31774828 TATATATGTATATAAAT
1 TATATAAGTATAAAAAA
31774845 TATA-AAGTATAAAAAA
1 TATATAAGTATAAAAAA
31774861 TATATAAGTAT
1 TATATAAGTAT
31774872 GTATATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (17 bp):
TATATAAGTATAAAAAA
Found at i:31774927 original size:29 final size:27
Alignment explanation
Indices: 31774868--31774927 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
31774858 AAATATATAA
* *
31774868 GTATGTATATATATAAATCAAAGATAT
1 GTATGTATATATATAAATCAAAGAAAG
31774895 GTATGTATATATAATTAAATCTAAA-AAAG
1 GTATGTATATAT-A-TAAATC-AAAGAAAG
31774924 GTAT
1 GTAT
31774928 AAATGAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.43
28 1 0.04
29 12 0.43
30 3 0.11
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.37
Consensus pattern (27 bp):
GTATGTATATATATAAATCAAAGAAAG
Found at i:31776604 original size:45 final size:44
Alignment explanation
Indices: 31776546--31776926 Score: 178
Period size: 44 Copynumber: 8.6 Consensus size: 44
31776536 GTTTTAATCC
* * **
31776546 GCTCCACTGCAACTTTAGGGAGATAGGA-TTAGTTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTT-GTTA-CTTCAAACT
31776591 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAAACT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAAACT
* * * *
31776635 GCCCCACTGCAACTTCAAGGG-GATAAG-GTTCGTCACTTCAACCT
1 GCTCCACTGCAACTTC-AGGGAGATAAGACTT-GTTACTTCAAACT
* * * * * ** ** *
31776679 ACTCTA-TGCAACTTTAGAGAAATAAGGTTTGTGGCTTTAATA-T
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAA-ACT
* * * * *
31776722 ACTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTA--CTTCAAACT
* * * * *
31776768 GAC-CTACAGCAACTTCAGAGG-TATAGGATTCATTGTT--TT-AATCT
1 G-CTCCACTGCAACTTCAG-GGAGATAAGA--C-TTGTTACTTCAAACT
* ** **
31776812 GCTCCACTGCAACTTCAAGGAGA-AAGGA-TTAATAGCTTCAATTT
1 GCTCCACTGCAACTTCAGGGAGATAA-GACTTGTTA-CTTCAAACT
* ** *
31776856 GCTCCACTGCTACTTCAGGGAGATAAGA-TTGACATCTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTA-CTTCAAACT
*
31776900 GCTTCACTGCAACTTCA-GGACGATAAG
1 GCTCCACTGCAACTTCAGGGA-GATAAG
31776927 GTTTGTGGTT
Statistics
Matches: 259, Mismatches: 53, Indels: 49
0.72 0.15 0.14
Matches are distributed among these distances:
40 3 0.01
42 3 0.01
43 37 0.14
44 144 0.56
45 38 0.15
46 25 0.10
47 3 0.01
48 1 0.00
49 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAAACT
Found at i:31777294 original size:45 final size:45
Alignment explanation
Indices: 31777238--31777684 Score: 413
Period size: 45 Copynumber: 10.0 Consensus size: 45
31777228 GTTTCTTCGA
*
31777238 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
* * *
31777283 TTTGCTCCGCTGTCAGTACAGGAAGGCAAGATCTGTTACCTTCAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
* * * * *
31777328 TCTACTTCACTGTCAGTACAGGAAGGCAAG-GCTGGTGTCTTC-G
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
* * * * *
31777371 ATCTACTTCACTGTTAGTATAGGAAGACAAGATCTGTTATCTTCAG
1 -TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
* ** * * *
31777417 TCTGCTTCACTGTCAGTGTAGGAAGGCAAG-GCTGATGTCTTC-G
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
* ** * *
31777460 ATCTGCTTCGCTATCAGTACAGGAATACAAGATTTGTTATCTTTAG
1 -TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
* * * * * *
31777506 TCTACTTTGTTGTCAGTACAGGAAGGCAAG-GCTGGTGTCTTC-G
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
* *
31777549 ATCTGCTTTGCTGTCAGTATAGGAAGGCAAGATCTGTTATCTTCAG
1 -TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
* * ** * * * *
31777595 GCTGCTTCGCTGTCAGTGCAAAAAGGCAAG-GCTGATGTCTTCAA
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
* * * *
31777639 TCTACTTCACTGTCAGTACAGGAATGTAAGATCTGTTATCTTCAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
31777684 T
1 T
31777685 GATCTGTTCT
Statistics
Matches: 317, Mismatches: 75, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
43 3 0.01
44 134 0.42
45 177 0.56
46 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (45 bp):
TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG
Found at i:31777407 original size:89 final size:89
Alignment explanation
Indices: 31777242--31777684 Score: 521
Period size: 89 Copynumber: 5.0 Consensus size: 89
31777232 CTTCGATCTG
* * * * *
31777242 CTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTC-AGTTTGCTCCGCTGTCAGTACAGGA
1 CTTCGCTGTCAGTACAGGAAGGCAAG-GCTGATGTCTTCGA-TCTGCTTCGCTGTCAGTACAGGA
* *
31777306 AGGCAAGATCTGTTACCTTCAGTCTA
64 AGACAAGATCTGTTATCTTCAGTCTA
* * * * * *
31777332 CTTCACTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGTTAGTATAGGAAG
1 CTTCGCTGTCAGTACAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAG
*
31777397 ACAAGATCTGTTATCTTCAGTCTG
66 ACAAGATCTGTTATCTTCAGTCTA
* ** * *
31777421 CTTCACTGTCAGTGTAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTATCAGTACAGGAAT
1 CTTCGCTGTCAGTACAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAG
* *
31777486 ACAAGATTTGTTATCTTTAGTCTA
66 ACAAGATCTGTTATCTTCAGTCTA
* * * * *
31777510 CTTTGTTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTTGCTGTCAGTATAGGAAG
1 CTTCGCTGTCAGTACAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAG
* * *
31777575 GCAAGATCTGTTATCTTCAGGCTG
66 ACAAGATCTGTTATCTTCAGTCTA
* ** * * *
31777599 CTTCGCTGTCAGTGCAAAAAGGCAAGGCTGATGTCTTCAATCTACTTCACTGTCAGTACAGGAAT
1 CTTCGCTGTCAGTACAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCAGTACAGGAA-
*
31777664 G-TAAGATCTGTTATCTTCAGT
65 GACAAGATCTGTTATCTTCAGT
31777685 GATCTGTTCT
Statistics
Matches: 298, Mismatches: 53, Indels: 5
0.84 0.15 0.01
Matches are distributed among these distances:
89 271 0.91
90 27 0.09
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (89 bp):
CTTCGCTGTCAGTACAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAG
ACAAGATCTGTTATCTTCAGTCTA
Found at i:31777538 original size:178 final size:177
Alignment explanation
Indices: 31777238--31777684 Score: 606
Period size: 178 Copynumber: 2.5 Consensus size: 177
31777228 GTTTCTTCGA
* * * * * *
31777238 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTTTGCTCCGCTGTCAGTACA
1 TCTGCTTCGCTGTCAGTGCAGGAAGGCAAG-GCTGATGTCTTCA-TCTGCTTCGCTGTCAGTACA
* *
31777303 GGAAGGCAAGATCTGTTACCTTCAGTCTACTTCACTGTCAGTACAGGAAGGCAAGGCTGGTGTCT
64 GGAATGCAAGATCTGTTATCTTCAGTCTACTTCACTGTCAGTACAGGAAGGCAAGGCTGGTGTCT
*
31777368 TCGATCTACTTCACTGTTAGTATAGGAAGACAAGATCTGTTATCTTCAG
129 TCGATCTACTTCACTGTCAGTATAGGAAGACAAGATCTGTTATCTTCAG
* * *
31777417 TCTGCTTCACTGTCAGTGTAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTATCAGTACAG
1 TCTGCTTCGCTGTCAGTGCAGGAAGGCAAGGCTGATGTCTTC-ATCTGCTTCGCTGTCAGTACAG
* * * ***
31777482 GAATACAAGATTTGTTATCTTTAGTCTACTTTGTTGTCAGTACAGGAAGGCAAGGCTGGTGTCTT
65 GAATGCAAGATCTGTTATCTTCAGTCTACTTCACTGTCAGTACAGGAAGGCAAGGCTGGTGTCTT
* ** *
31777547 CGATCTGCTTTGCTGTCAGTATAGGAAGGCAAGATCTGTTATCTTCAG
130 CGATCTACTTCACTGTCAGTATAGGAAGACAAGATCTGTTATCTTCAG
* ** * *
31777595 GCTGCTTCGCTGTCAGTGCAAAAAGGCAAGGCTGATGTCTTCAATCTACTTCACTGTCAGTACAG
1 TCTGCTTCGCTGTCAGTGCAGGAAGGCAAGGCTGATGTCTTC-ATCTGCTTCGCTGTCAGTACAG
*
31777660 GAATGTAAGATCTGTTATCTTCAGT
65 GAATGCAAGATCTGTTATCTTCAGT
31777685 GATCTGTTCT
Statistics
Matches: 232, Mismatches: 35, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
178 204 0.88
179 28 0.12
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (177 bp):
TCTGCTTCGCTGTCAGTGCAGGAAGGCAAGGCTGATGTCTTCATCTGCTTCGCTGTCAGTACAGG
AATGCAAGATCTGTTATCTTCAGTCTACTTCACTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTC
GATCTACTTCACTGTCAGTATAGGAAGACAAGATCTGTTATCTTCAG
Found at i:31784236 original size:16 final size:17
Alignment explanation
Indices: 31784210--31784253 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
31784200 TGTATGTATG
* * *
31784210 TATATATGTATATAAAT
1 TATATAAGTATAAAAAA
31784227 TATA-AAGTATAAAAAA
1 TATATAAGTATAAAAAA
31784243 TATATAAGTAT
1 TATATAAGTAT
31784254 GTATATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (17 bp):
TATATAAGTATAAAAAA
Found at i:31784264 original size:27 final size:26
Alignment explanation
Indices: 31784234--31784289 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
31784224 AATTATAAAG
31784234 TATAAA-AAATATATAAGTATGTATATA
1 TATAAACAAATATAT--GTATGTATATA
31784261 TATAAATCAAATATATGTATGTATATA
1 TATAAA-CAAATATATGTATGTATATA
31784288 TA
1 TA
31784290 ATTAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 19 0.70
29 8 0.30
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (26 bp):
TATAAACAAATATATGTATGTATATA
Found at i:31784309 original size:29 final size:27
Alignment explanation
Indices: 31784250--31784309 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
31784240 AAATATATAA
* *
31784250 GTATGTATATATATAAATCAAATATAT
1 GTATGTATATATATAAATCAAATAAAG
31784277 GTATGTATATATAATTAAATCTAAA-AAAG
1 GTATGTATATAT-A-TAAATC-AAATAAAG
31784306 GTAT
1 GTAT
31784310 AAATGAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.43
28 1 0.04
29 12 0.43
30 3 0.11
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (27 bp):
GTATGTATATATATAAATCAAATAAAG
Found at i:31784329 original size:3 final size:3
Alignment explanation
Indices: 31784321--31784398 Score: 61
Period size: 3 Copynumber: 26.0 Consensus size: 3
31784311 AATGAGTAAC
* * *
31784321 TAA TAA TAA -ACA TGA TAA TAG TAA TAA CAA T-A TAAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
* * * *
31784366 TAA TAA TAA TAA TAG TAG TAA AAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31784399 ATTTATTAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
2 3 0.05
3 54 0.92
4 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:31788544 original size:16 final size:16
Alignment explanation
Indices: 31788523--31788559 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
31788513 AAATAATAAT
31788523 AAAAAATCAAAATCAA
1 AAAAAATCAAAATCAA
*
31788539 AAAAAATCAAAGTCAA
1 AAAAAATCAAAATCAA
31788555 AAAAA
1 AAAAA
31788560 GGAGAACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.76, C:0.11, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAAAATCAAAATCAA
Found at i:31789411 original size:13 final size:14
Alignment explanation
Indices: 31789393--31789426 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
31789383 AGTCAAACAA
31789393 AAAAATGAAAAA-T
1 AAAAATGAAAAAGT
31789406 AAAAATGAAAAAGT
1 AAAAATGAAAAAGT
31789420 AAAAATG
1 AAAAATG
31789427 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (14 bp):
AAAAATGAAAAAGT
Found at i:31790726 original size:50 final size:50
Alignment explanation
Indices: 31790648--31791489 Score: 516
Period size: 50 Copynumber: 16.9 Consensus size: 50
31790638 ATTGCAATTC
* ** * *
31790648 AAAAGATTGAAGCTACAACAGTAAATCTCACCTCCCTGGCGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
* * * ****
31790698 AATAGATTGAAGCTACGACGGCGAATCTCACTTCCCCGAC-ATTGCAATTC
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGA-TGCAGCGG
* * **
31790748 AAAAGATTGAAGCTACAACAGCGAATCTCACCTCCTTGGCGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
* * * * ****
31790798 AACAGATTGAAGCTACAATGGTGAATCTCACTTCCCCGAC-ATTGCAATTT
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGA-TGCAGCGG
* * * * *
31790848 AAAAGATTGAAGCTACAACAGCAAATCTCACCTCCCTGGTGATGCAGC-G
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
* * * ***
31790897 AAACAGATCGAAGCTACAACGGCGAATCTCACTTCCCTGAC-ATTGCA-ATT
1 AAA-AGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGA-TGCAGCGG
* * * * **
31790947 CAAAGATTGAAGCCACAACGGTGAATCTTAC-TCCTAGGCGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
** * * * ****
31790996 AGCAGATTGAAGCTATAACGGCAAATCTCACTTCCCCGAC-ATTGCAATTC
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGA-TGCAGCGG
* * * * * * *
31791046 AAAAGATTTAAGCCACAACGGTGAATCTTACTTTCCAGGCGATGTAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
** * * * * ****
31791096 AGTAGATTGAAGATGCAACGGTGAATCTCACTTCCCCGAC-ATTGCAATTC
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGA-TGCAGCGG
* * * * *
31791146 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGTGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
** * * * ** ****
31791196 AGCAGACTGAAGCTACAACGGTGAATTTCACTTCCCCAAC-ATTGCAATTC
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGA-TGCAGCGG
* * *
31791246 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
** * * ****
31791296 AGCAGATTGAAGCTACAACGGCGAATCTCACTTCCTCGAC-ATTGCAATTC
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGA-TGCAGCGG
* * * * * *
31791346 AAAAGATTTAAGCCACAACGGTGAATCTTACTTCCCAGGTGATGCAGCGG
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
** * * * * * ****
31791396 AGCAGATTGAAACTACAACGGTGAATCTCACTTCCTCGACAATGCAATTC
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
* * *
31791446 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATG
1 AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATG
31791490 TAGTGGAATA
Statistics
Matches: 571, Mismatches: 203, Indels: 36
0.70 0.25 0.04
Matches are distributed among these distances:
48 9 0.02
49 58 0.10
50 498 0.87
51 6 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGGCGATGCAGCGG
Found at i:31791535 original size:100 final size:100
Alignment explanation
Indices: 31790638--31791489 Score: 1186
Period size: 100 Copynumber: 8.5 Consensus size: 100
31790628 AAAACCATAG
* * * * * * **
31790638 ATTGCAATTCAAAAGATTGAAGCTACAACAGTAAATCTCACCTCCCTGGCGATGCAGCGGAATAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
*
31790703 ATTGAAGCTACGACGGCGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * * * * ** *
31790738 ATTGCAATTCAAAAGATTGAAGCTACAACAGCGAATCTCACCTCCTTGGCGATGCAGCGGAACAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
* *
31790803 ATTGAAGCTACAATGGTGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * * ** * * * * * *
31790838 ATTGCAATTTAAAAGATTGAAGCTACAACAGCAAATCTCACCTCCCTGGTGATGCAGCGAAACAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
* *
31790903 ATCGAAGCTACAACGGCGAATCTCACTTCCCTGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
*
31790938 ATTGCAATTC-AAAGATTGAAGCCACAACGGTGAATCTTAC-TCCTAGGCGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
* *
31791001 ATTGAAGCTATAACGGCAAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* * * *
31791036 ATTGCAATTCAAAAGATTTAAGCCACAACGGTGAATCTTACTTTCCAGGCGATGTAGCGGAGTAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
* * *
31791101 ATTGAAGATGCAACGGTGAATCTCACTTCCCCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
*
31791136 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGTGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
* * * *
31791201 ACTGAAGCTACAACGGTGAATTTCACTTCCCCAAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
*
31791236 ATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
*
31791301 ATTGAAGCTACAACGGCGAATCTCACTTCCTCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* *
31791336 ATTGCAATTCAAAAGATTTAAGCCACAACGGTGAATCTTACTTCCCAGGTGATGCAGCGGAGCAG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
* * *
31791401 ATTGAAACTACAACGGTGAATCTCACTTCCTCGAC
66 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
* *
31791436 AATGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATG
1 ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATG
31791490 TAGTGGAATA
Statistics
Matches: 683, Mismatches: 67, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
98 59 0.09
99 54 0.08
100 570 0.83
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (100 bp):
ATTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGCAG
ATTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
Found at i:31791965 original size:13 final size:13
Alignment explanation
Indices: 31791947--31791971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31791937 TCTAGCCCGA
31791947 CGCCGCCTCCATG
1 CGCCGCCTCCATG
31791960 CGCCGCCTCCAT
1 CGCCGCCTCCAT
31791972 CAGTGCAAGT
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:0.08, C:0.56, G:0.20, T:0.16
Consensus pattern (13 bp):
CGCCGCCTCCATG
Found at i:31792029 original size:6 final size:6
Alignment explanation
Indices: 31792018--31792044 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31792008 CCCACTTGCT
31792018 CCATCA CCATCA CCATCA CCATCA CCA
1 CCATCA CCATCA CCATCA CCATCA CCA
31792045 CTTGCCTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
CCATCA
Found at i:31793313 original size:24 final size:25
Alignment explanation
Indices: 31793285--31793335 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
31793275 ATATATTTTG
31793285 TAATTTACGTATACATACATAT-TA
1 TAATTTACGTATACATACATATATA
* * *
31793309 TAATTTATGTCTATATACATATATA
1 TAATTTACGTATACATACATATATA
31793334 TA
1 TA
31793336 TCCCTCTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (25 bp):
TAATTTACGTATACATACATATATA
Found at i:31797062 original size:46 final size:46
Alignment explanation
Indices: 31796995--31797494 Score: 804
Period size: 46 Copynumber: 10.8 Consensus size: 46
31796985 GACTAGAAGC
31796995 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
*
31797041 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATTGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
*
31797087 AGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
*
31797133 AGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
* * *
31797179 AGCAGATCTTGCCTTCCTGTATTTGGCAGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
* * * *
31797225 GGCAGATCTTATCTTCCTGTATTTGGCAGTGGACTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
* * *
31797271 AGCAGATCTTGTCTTCCTGTATTTGGCAACAGAGTAGATCTAAGAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATC-GA-AGAT
31797319 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
31797365 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
*
31797411 AGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
* * * * *
31797457 AGCAGATCTTATCTTCTTGTA-CTGGCAGTGGAGCAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGAT
31797495 TGAAAGCACC
Statistics
Matches: 421, Mismatches: 31, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
45 13 0.03
46 364 0.86
47 2 0.00
48 42 0.10
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (46 bp):
AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
Found at i:31797772 original size:19 final size:19
Alignment explanation
Indices: 31797748--31797787 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
31797738 GGCAGCAGTG
31797748 GAATAGATTGAAGATTACA
1 GAATAGATTGAAGATTACA
31797767 GAATAGATTGAAGATTACA
1 GAATAGATTGAAGATTACA
31797786 GA
1 GA
31797788 TCTTATCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.25
Consensus pattern (19 bp):
GAATAGATTGAAGATTACA
Found at i:31797991 original size:43 final size:44
Alignment explanation
Indices: 31797941--31798048 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
31797931 CTAAGATTAC
* *
31797941 AGTGGAGTACATTGAAGCCGGTAG-TCCTATCTCCCTAAGTAGT
1 AGTGGAGTACATTGAAGACGGTAGATCCTATCTCCCTAAGCAGT
** ** *
31797984 AGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTACATTGAAGACGGTAGATCCTATCTCCCTAAGCAGT
* * *
31798028 AGTGGAGCAGATCGAAGACGG
1 AGTGGAGTACATTGAAGACGG
31798049 CGAATCTTAT
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
43 19 0.37
44 33 0.63
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (44 bp):
AGTGGAGTACATTGAAGACGGTAGATCCTATCTCCCTAAGCAGT
Found at i:31798124 original size:43 final size:43
Alignment explanation
Indices: 31798096--31798504 Score: 229
Period size: 43 Copynumber: 9.6 Consensus size: 43
31798086 AAGCCACTAG
31798096 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
* * * * **
31798139 TCTTATCTCCCTAAGCAGTAGTGGAGCGGATC-ACATCAA--G-
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACTGA
* * * *
31798179 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGA
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
* * * * * **
31798222 TCTTATTTCCCTAAGCAGTAGTGGAGCGGATC-ACATCAA--G-
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACTGA
* *
31798262 TCTTATCTCCCTAAGCACTAAGCAATAGTGGAGCAGACAAAAGAAACCGA
1 CCTTATCTCCCTAAG---T-AG---TAGTGGAGCAGACAAAAGAAACTGA
* * * **
31798312 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA--G-
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACTGA
* * * *
31798352 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGA
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
* * * * * **
31798395 TCTTATCTCCCTAAGCAGTAGTGAAGCGGATC-ACATCAA--G-
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACTGA
* * * *
31798435 TCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGA
1 CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
** *
31798478 TTTTATCTCCCTAAGCAGTAGTGGAGC
1 CCTTATCTCCCTAAGTAGTAGTGGAGC
31798505 GGATCACATC
Statistics
Matches: 294, Mismatches: 45, Indels: 54
0.75 0.11 0.14
Matches are distributed among these distances:
39 3 0.01
40 110 0.37
41 4 0.01
42 3 0.01
43 134 0.46
44 6 0.02
46 3 0.01
47 15 0.05
49 1 0.00
50 15 0.05
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (43 bp):
CCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGA
Found at i:31798316 original size:173 final size:166
Alignment explanation
Indices: 31798097--31798556 Score: 785
Period size: 173 Copynumber: 2.7 Consensus size: 166
31798087 AGCCACTAGC
* * *
31798097 CTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGATCTTATCTCCCTAAGCAGTAGTG
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
31798162 GAGCGGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTA
66 GAGCGGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTA
* *
31798227 TTTCCCTAAGCAGTAGTGGAGCGGATCACATCAAGT
131 TCTCCCTAAGCAGTAGTGAAGCGGATCACATCAAGT
31798263 CTTATCTCCCTAAGCACTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGC
1 CTTATCT--C----C-CTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGC
*
31798328 AGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACC
59 AGTAGTGGAGCGGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACC
31798393 GATCTTATCTCCCTAAGCAGTAGTGAAGCGGATCACATCAAGT
124 GATCTTATCTCCCTAAGCAGTAGTGAAGCGGATCACATCAAGT
*
31798436 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATTTTATCTCCCTAAGCAGTAGTG
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
*
31798501 GAGCGGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGAAA
66 GAGCGGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAA
31798557 ATGATGAATC
Statistics
Matches: 278, Mismatches: 9, Indels: 14
0.92 0.03 0.05
Matches are distributed among these distances:
166 116 0.42
167 1 0.00
168 1 0.00
171 1 0.00
172 1 0.00
173 158 0.57
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (166 bp):
CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
GAGCGGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTA
TCTCCCTAAGCAGTAGTGAAGCGGATCACATCAAGT
Found at i:31798344 original size:90 final size:83
Alignment explanation
Indices: 31798097--31798556 Score: 785
Period size: 83 Copynumber: 5.5 Consensus size: 83
31798087 AGCCACTAGC
* * *
31798097 CTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACTGATCTTATCTCCCTAAGCAGTAGTG
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
31798162 GAGCGGATCACATCAAGT
66 GAGCGGATCACATCAAGT
*
31798180 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATTTCCCTAAGCAGTAGTG
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
31798245 GAGCGGATCACATCAAGT
66 GAGCGGATCACATCAAGT
31798263 CTTATCTCCCTAAGCACTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGC
1 CTTATCT--C----C-CTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGC
*
31798328 AGTAGTGGAGCAGATCACATCAAGT
59 AGTAGTGGAGCGGATCACATCAAGT
31798353 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
*
31798418 AAGCGGATCACATCAAGT
66 GAGCGGATCACATCAAGT
*
31798436 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATTTTATCTCCCTAAGCAGTAGTG
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
31798501 GAGCGGATCACATCAAGT
66 GAGCGGATCACATCAAGT
*
31798519 CTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGAAA
1 CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAA
31798557 ATGATGAATC
Statistics
Matches: 359, Mismatches: 11, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
83 276 0.77
84 1 0.00
85 1 0.00
88 1 0.00
89 1 0.00
90 79 0.22
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (83 bp):
CTTATCTCCCTAAGCAATAGTGGAGCAGACAAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTG
GAGCGGATCACATCAAGT
Found at i:31800210 original size:17 final size:19
Alignment explanation
Indices: 31800190--31800244 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
31800180 TTTCCAGCTT
*
31800190 TATTTTTA-A-TATATGTA
1 TATTTTTATATTATATATA
31800207 TATTTTTATATTATATATA
1 TATTTTTATATTATATATA
* *
31800226 TATATATATA-TATATATA
1 TATTTTTATATTATATATA
31800244 T
1 T
31800245 TACTATACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.24
18 10 0.30
19 15 0.45
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATTTTTATATTATATATA
Found at i:31800225 original size:2 final size:2
Alignment explanation
Indices: 31800198--31800244 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
31800188 TTTATTTTTA
* * *
31800198 AT AT AT GT AT AT TT TT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31800239 AT AT AT
1 AT AT AT
31800245 TACTATACTC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
AT
Found at i:31800251 original size:8 final size:7
Alignment explanation
Indices: 31800198--31800251 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 7
31800188 TTTATTTTTA
31800198 ATATATGT
1 ATATAT-T
31800206 ATAT-TT
1 ATATATT
*
31800212 TTATATT
1 ATATATT
31800219 ATATA-T
1 ATATATT
31800225 ATATA-T
1 ATATATT
31800231 ATATATAT
1 ATATAT-T
31800239 ATATATT
1 ATATATT
31800246 ACTATA
1 A-TATA
31800252 CTCTACCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 16 0.40
7 9 0.22
8 15 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (7 bp):
ATATATT
Found at i:31800918 original size:16 final size:16
Alignment explanation
Indices: 31800880--31800923 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
31800870 TTACATACTT
* *
31800880 ATACATATATGTATAT
1 ATACATATATATATAC
* *
31800896 TTTCATATATATATAC
1 ATACATATATATATAC
31800912 ATACATATATAT
1 ATACATATATAT
31800924 TTACTTACTC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (16 bp):
ATACATATATATATAC
Found at i:31802884 original size:45 final size:44
Alignment explanation
Indices: 31802814--31803154 Score: 230
Period size: 45 Copynumber: 7.6 Consensus size: 44
31802804 TAAAATCTGT
* * *
31802814 CACTGGGCTGTGGATACACAACAAAAATTCTCAGATTAAACTTGC
1 CACTAGGCTGTGGATACACAGCAAAAATTCT-AGATGAAACTTGC
* * *
31802859 CACT-GGACTGTGGGTACATAGC-AAAATATCATAGATAAAAGC-TGC
1 CACTAGG-CTGTGGATACACAGCAAAAAT-TC-TAGATGAAA-CTTGC
* * *
31802904 CACTAGGCTATAGATACACAGCAAAAATTCATAGATGAAACCTGC
1 CACTAGGCTGTGGATACACAGCAAAAATTC-TAGATGAAACTTGC
* * * * *
31802949 CACT-GGACTGTGGATGCACAACAAAATATTGCT-GATAAAATTTGT
1 CACTAGG-CTGTGGATACACAGCAAAA-ATT-CTAGATGAAACTTGC
* * * *
31802994 CACTAGGCTATGGATACATAGTAAAAATTCGTAGATGATACTTGC
1 CACTAGGCTGTGGATACACAGCAAAAATTC-TAGATGAAACTTGC
* * * * *
31803039 CACTAGACTATTGG-TACACAAC-AAAATATCACAGAT-AAAATATGC
1 CACTAGGCT-GTGGATACACAGCAAAAAT-TC-TAGATGAAACT-TGC
* * * *
31803084 CATTAGGTTGTGGATACACAGCAAAAATTCGCAGATGAAACTTGT
1 CACTAGGCTGTGGATACACAGCAAAAATTC-TAGATGAAACTTGC
* *
31803129 CACTAGGCTGTGGGTACACAACAAAA
1 CACTAGGCTGTGGATACACAGCAAAA
31803155 TATCGAAGAT
Statistics
Matches: 230, Mismatches: 47, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
43 1 0.00
44 25 0.11
45 176 0.77
46 27 0.12
47 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (44 bp):
CACTAGGCTGTGGATACACAGCAAAAATTCTAGATGAAACTTGC
Found at i:31803085 original size:135 final size:133
Alignment explanation
Indices: 31802801--31803168 Score: 345
Period size: 135 Copynumber: 2.7 Consensus size: 133
31802791 CTAATTTTAT
* * *
31802801 AGATAAAATCTGTCACTGGGCTGTGGATACACAACAAAAATT-CTCAGATTAAACTTGCCACT-G
1 AGATAAAATCTGCCACT-GGCTGTGGATACACAACAAAAATTGCT--GATAAAACTTGTCACTAG
* * *
31802864 GACTGTGGGTACATAGCAAAATATCATAGATAAAAGCTGCCACTAGGCTATAGATACACAGCAAA
63 G-CTGTGGGTACATAGAAAAATATCATAGATAAAAGCTGCCACTAGACTATAGATACACAACAAA
*
31802929 AATTCAT
127 AATTCAC
* * * *
31802936 AGATGAAACCTGCCACTGGACTGTGGATGCACAACAAAATATTGCTGATAAAATTTGTCACTAGG
1 AGATAAAATCTGCCACTGG-CTGTGGATACACAACAAAA-ATTGCTGATAAAACTTGTCACTAGG
* * * * * * *
31803001 CTATGGATACATAGTAAAAAT-TCGTAGATGATA-CTTGCCACTAGACTATTGGTACACAAC-AA
64 CTGTGGGTACATAG-AAAAATATCATAGATAAAAGC-TGCCACTAGACTATAGATACACAACAAA
31803063 AATATCAC
127 AAT-TCAC
* * * * * *
31803071 AGATAAAATATGCCATTAGGTTGTGGATACACAGCAAAAATTCGCAGATGAAACTTGTCACTAGG
1 AGATAAAATCTGCCACT-GGCTGTGGATACACAACAAAAATT-GCTGATAAAACTTGTCACTAGG
*
31803136 CTGTGGGTACACA-ACAAAATATCGA-AGATAAAA
64 CTGTGGGTACATAGA-AAAATATC-ATAGATAAAA
31803169 TCTGTCATTG
Statistics
Matches: 187, Mismatches: 34, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
133 1 0.01
134 16 0.09
135 156 0.83
136 12 0.06
137 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (133 bp):
AGATAAAATCTGCCACTGGCTGTGGATACACAACAAAAATTGCTGATAAAACTTGTCACTAGGCT
GTGGGTACATAGAAAAATATCATAGATAAAAGCTGCCACTAGACTATAGATACACAACAAAAATT
CAC
Found at i:31803184 original size:90 final size:90
Alignment explanation
Indices: 31802801--31803175 Score: 421
Period size: 90 Copynumber: 4.2 Consensus size: 90
31802791 CTAATTTTAT
* * * *
31802801 AGATAAAATCTGTCACTGGGCTGTGGATACACAACAAAAATTCTCAGATTAAACTTGCCACTGGA
1 AGATAAAATCTGTCACTAGGCTGTGGATACACAGCAAAAATTCGCAGATGAAACTTGCCACTGGA
* * *
31802866 CTGTGGGTACATAGCAAAATATCAT
66 CTGTGGGTACACAACAAAATATCAC
* * * * ** *
31802891 AGATAAAAGCTGCCACTAGGCTATAGATACACAGCAAAAATTCATAGATGAAACCTGCCACTGGA
1 AGATAAAATCTGTCACTAGGCTGTGGATACACAGCAAAAATTCGCAGATGAAACTTGCCACTGGA
* * **
31802956 CTGTGGATGCACAACAAAATATTGC
66 CTGTGGGTACACAACAAAATATCAC
* * * * * * * *
31802981 TGATAAAATTTGTCACTAGGCTATGGATACATAGTAAAAATTCGTAGATGATACTTGCCACTAGA
1 AGATAAAATCTGTCACTAGGCTGTGGATACACAGCAAAAATTCGCAGATGAAACTTGCCACTGGA
* *
31803046 CTATTGGTACACAACAAAATATCAC
66 CTGTGGGTACACAACAAAATATCAC
* * * * *
31803071 AGATAAAATATGCCATTAGGTTGTGGATACACAGCAAAAATTCGCAGATGAAACTTGTCACTAGG
1 AGATAAAATCTGTCACTAGGCTGTGGATACACAGCAAAAATTCGCAGATGAAACTTGCCACT-GG
31803136 -CTGTGGGTACACAACAAAATATCGA-
65 ACTGTGGGTACACAACAAAATATC-AC
31803161 AGATAAAATCTGTCA
1 AGATAAAATCTGTCA
31803176 TTGGGTTGTA
Statistics
Matches: 233, Mismatches: 50, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
90 231 0.99
91 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (90 bp):
AGATAAAATCTGTCACTAGGCTGTGGATACACAGCAAAAATTCGCAGATGAAACTTGCCACTGGA
CTGTGGGTACACAACAAAATATCAC
Found at i:31803194 original size:45 final size:45
Alignment explanation
Indices: 31803053--31803196 Score: 141
Period size: 45 Copynumber: 3.2 Consensus size: 45
31803043 AGACTATTGG
* *
31803053 TACACAACAAAATATC-ACAGATAAAATATGCCATTAGGTTGTGGA
1 TACACAACAAAATATCGA-AGATAAAATCTGTCATTAGGTTGTGGA
* * * * * *
31803098 TACACAGCAAAA-ATTCGCAGATGAAA-CTTGTCACTAGGCTGTGGG
1 TACACAACAAAATA-TCGAAGATAAAATC-TGTCATTAGGTTGTGGA
* *
31803143 TACACAACAAAATATCGAAGATAAAATCTGTCATTGGGTTGTAGA
1 TACACAACAAAATATCGAAGATAAAATCTGTCATTAGGTTGTGGA
*
31803188 TGCACAACA
1 TACACAACA
31803197 TATTTGTAGG
Statistics
Matches: 77, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
44 1 0.01
45 74 0.96
46 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (45 bp):
TACACAACAAAATATCGAAGATAAAATCTGTCATTAGGTTGTGGA
Found at i:31803791 original size:28 final size:28
Alignment explanation
Indices: 31803743--31803959 Score: 226
Period size: 28 Copynumber: 7.8 Consensus size: 28
31803733 AATTTTGAGC
31803743 AAAACTATAAAATCTAAAAAAATAGGGGA
1 AAAACTATAAAATCT-AAAAAATAGGGGA
*
31803772 AAAACTATAAAATCTAAAAAATAGGGGC
1 AAAACTATAAAATCTAAAAAATAGGGGA
* *
31803800 AAAATTATAAAATCTAAAAAA-ATGGGA
1 AAAACTATAAAATCTAAAAAATAGGGGA
* ** * *
31803827 AAAATTATAAAATCTAAAAGTTAAGGGT
1 AAAACTATAAAATCTAAAAAATAGGGGA
* *
31803855 AAAACTATAAAATCTAGAAAATATGGGA
1 AAAACTATAAAATCTAAAAAATAGGGGA
* * * *
31803883 AAAATTGTAAAAT-TAAAAAAAAGGAG-
1 AAAACTATAAAATCTAAAAAATAGGGGA
* *
31803909 AAAACTGTAAAATTTAAAAAATA-GGGA
1 AAAACTATAAAATCTAAAAAATAGGGGA
* *
31803936 CAAAATTATAAAATCTGAAAAATA
1 -AAAACTATAAAATCTAAAAAATA
31803960 AGAAACATAC
Statistics
Matches: 157, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
26 14 0.09
27 40 0.25
28 88 0.56
29 15 0.10
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.22
Consensus pattern (28 bp):
AAAACTATAAAATCTAAAAAATAGGGGA
Found at i:31803842 original size:55 final size:56
Alignment explanation
Indices: 31803741--31803959 Score: 259
Period size: 55 Copynumber: 3.9 Consensus size: 56
31803731 AAAATTTTGA
*
31803741 GCAAAACTATAAAATCTAAAAAAATAGGGGAAAAACTATAAAATCTAAAAAATAGGG
1 GCAAAACTATAAAATCTAAAAAAATA-GGGAAAAATTATAAAATCTAAAAAATAGGG
* ** *
31803798 GCAAAATTATAAAATCTAAAAAAAT-GGGAAAAATTATAAAATCTAAAAGTTAAGG
1 GCAAAACTATAAAATCTAAAAAAATAGGGAAAAATTATAAAATCTAAAAAATAGGG
* * * * *
31803853 GTAAAACTATAAAATCT-AGAAAATATGGGAAAAATTGTAAAAT-TAAAAAAAAGGA
1 GCAAAACTATAAAATCTAAAAAAATA-GGGAAAAATTATAAAATCTAAAAAATAGGG
* * *
31803908 G-AAAACTGTAAAAT-TTAAAAAATAGGGACAAAATTATAAAATCTGAAAAATA
1 GCAAAACTATAAAATCTAAAAAAATAGGGA-AAAATTATAAAATCTAAAAAATA
31803960 AGAAACATAC
Statistics
Matches: 138, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
53 5 0.04
54 37 0.27
55 56 0.41
56 16 0.12
57 24 0.17
ACGTcount: A:0.59, C:0.06, G:0.13, T:0.21
Consensus pattern (56 bp):
GCAAAACTATAAAATCTAAAAAAATAGGGAAAAATTATAAAATCTAAAAAATAGGG
Found at i:31803876 original size:83 final size:84
Alignment explanation
Indices: 31803743--31803959 Score: 255
Period size: 83 Copynumber: 2.6 Consensus size: 84
31803733 AATTTTGAGC
* *
31803743 AAAACTATAAAATCTAAAAAAATAGGGGAAAAACTATAAAATCTAAAAAATAGGGGCAAAATTAT
1 AAAACTATAAAATCTAAAAAAATAAGGGAAAAACTATAAAATCTAAAAAATAGGGGAAAAATTAT
*
31803808 AAAATCTAAAAAAATGG-GA
66 AAAAT-TAAAAAAAAGGAGA
* ** * * * *
31803827 AAAATTATAAAATCT-AAAAGTTAAGGGTAAAACTATAAAATCTAGAAAATATGGGAAAAATTGT
1 AAAACTATAAAATCTAAAAAAATAAGGGAAAAACTATAAAATCTAAAAAATAGGGGAAAAATTAT
31803891 AAAATTAAAAAAAAGGAG-
66 AAAATTAAAAAAAAGGAGA
* * * *
31803909 AAAACTGTAAAAT-TTAAAAAAT-AGGGACAAAATTATAAAATCTGAAAAATA
1 AAAACTATAAAATCTAAAAAAATAAGGGA-AAAACTATAAAATCTAAAAAATA
31803960 AGAAACATAC
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
81 5 0.04
82 46 0.41
83 47 0.42
84 14 0.12
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.22
Consensus pattern (84 bp):
AAAACTATAAAATCTAAAAAAATAAGGGAAAAACTATAAAATCTAAAAAATAGGGGAAAAATTAT
AAAATTAAAAAAAAGGAGA
Found at i:31809834 original size:12 final size:12
Alignment explanation
Indices: 31809811--31809845 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
31809801 ACTTTAATCT
31809811 TTTTTATTATTG
1 TTTTTATTATTG
31809823 TTATTT-TTATTG
1 TT-TTTATTATTG
31809835 TTTTTATTATT
1 TTTTTATTATT
31809846 ACTTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (12 bp):
TTTTTATTATTG
Found at i:31809853 original size:11 final size:10
Alignment explanation
Indices: 31809823--31809873 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
31809813 TTTATTATTG
31809823 TTATT-TTTA
1 TTATTCTTTA
*
31809832 TTGTT-TTTA
1 TTATTCTTTA
31809841 TTATTACTTTA
1 TTATT-CTTTA
31809852 TTATTC-TTA
1 TTATTCTTTA
31809861 TTATTCTTGTA
1 TTATTCTT-TA
31809872 TT
1 TT
31809874 TCTTACTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 21 0.58
10 2 0.06
11 13 0.36
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.71
Consensus pattern (10 bp):
TTATTCTTTA
Found at i:31809853 original size:20 final size:20
Alignment explanation
Indices: 31809828--31809865 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31809818 TATTGTTATT
* *
31809828 TTTATTGTTTTTATTATTAC
1 TTTATTATTCTTATTATTAC
31809848 TTTATTATTCTTATTATT
1 TTTATTATTCTTATTATT
31809866 CTTGTATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTATTATTCTTATTATTAC
Found at i:31809918 original size:3 final size:3
Alignment explanation
Indices: 31809910--31809939 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31809900 ATTAGGTTTC
31809910 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31809940 CGTATTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:31811457 original size:12 final size:12
Alignment explanation
Indices: 31811437--31811478 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
31811427 TATTTCATGT
*
31811437 TTATGTTTATTG
1 TTATTTTTATTG
31811449 TTATTTTTA--G
1 TTATTTTTATTG
*
31811459 TTCTTTTTATTG
1 TTATTTTTATTG
31811471 TTATTTTT
1 TTATTTTT
31811479 TTAGACTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.14, C:0.02, G:0.10, T:0.74
Consensus pattern (12 bp):
TTATTTTTATTG
Found at i:31816974 original size:21 final size:20
Alignment explanation
Indices: 31816949--31817019 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
31816939 AGTTTATTTC
31816949 ATTAAGCTTATTTATATTTTA
1 ATTAAGCTTATTT-TATTTTA
* * *
31816970 ATTAATCATGTTTTAGTTTTA
1 ATTAAGCTTATTTTA-TTTTA
* * *
31816991 ATTAATCTTAATTTA-CTTA
1 ATTAAGCTTATTTTATTTTA
31817010 ATTAAGCTTA
1 ATTAAGCTTA
31817020 ATTGTTAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 12 0.29
20 2 0.05
21 27 0.66
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.54
Consensus pattern (20 bp):
ATTAAGCTTATTTTATTTTA
Found at i:31817433 original size:57 final size:57
Alignment explanation
Indices: 31817364--31817475 Score: 179
Period size: 57 Copynumber: 2.0 Consensus size: 57
31817354 TTACGTTATT
**
31817364 TGAGAATTTACAATTCTGAAAGTTAGAATATGAAAGTTTAACTATTCAAAAATCATA
1 TGAGAATTTACAATTCTGAAAAATAGAATATGAAAGTTTAACTATTCAAAAATCATA
* * *
31817421 TGAGAATTTACAATTTTGAAAAATAGAATATGAAAGTTTTACTGTTCAAAAATCA
1 TGAGAATTTACAATTCTGAAAAATAGAATATGAAAGTTTAACTATTCAAAAATCA
31817476 AGGACTAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (57 bp):
TGAGAATTTACAATTCTGAAAAATAGAATATGAAAGTTTAACTATTCAAAAATCATA
Found at i:31817473 original size:29 final size:29
Alignment explanation
Indices: 31817387--31817473 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
31817377 TTCTGAAAGT
*
31817387 TAGAATATGAAAGTTTAACTATTCAAAAA
1 TAGAATATGAAAGTTTTACTATTCAAAAA
* * *
31817416 T--CATATGAGAA--TTTACAATTTTGAAAAA
1 TAGAATATGA-AAGTTTTAC--TATTCAAAAA
*
31817444 TAGAATATGAAAGTTTTACTGTTCAAAAA
1 TAGAATATGAAAGTTTTACTATTCAAAAA
31817473 T
1 T
31817474 CAAGGACTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
26 4 0.09
27 6 0.14
28 11 0.25
29 12 0.27
30 6 0.14
31 5 0.11
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.34
Consensus pattern (29 bp):
TAGAATATGAAAGTTTTACTATTCAAAAA
Found at i:31817903 original size:37 final size:37
Alignment explanation
Indices: 31817860--31817930 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
31817850 TTGGATAATG
* *
31817860 ATTTTCTTTAGTAATTTATTTTCCACCAAACAAAATA
1 ATTTTCTTTAATAATTCATTTTCCACCAAACAAAATA
31817897 ATTTTCTTTAATAATTCATTTTCCACCAAACAAA
1 ATTTTCTTTAATAATTCATTTTCCACCAAACAAA
31817931 CATACCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.42
Consensus pattern (37 bp):
ATTTTCTTTAATAATTCATTTTCCACCAAACAAAATA
Found at i:31818417 original size:25 final size:26
Alignment explanation
Indices: 31818363--31818417 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
31818353 CGGCCCGTTT
* *
31818363 TTAATTAAAATTAAAATTAAATTTTT
1 TTAATTAAAATTAAAACTAAATTTTA
31818389 TTAA-TAAAATTAAAACT-AATTGTTA
1 TTAATTAAAATTAAAACTAAATT-TTA
31818414 TTAA
1 TTAA
31818418 AATTAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
TTAATTAAAATTAAAACTAAATTTTA
Found at i:31818436 original size:16 final size:16
Alignment explanation
Indices: 31818399--31818438 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
31818389 TTAATAAAAT
* *
31818399 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
31818415 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
31818431 TAAAATTA
1 TAAAATTA
31818439 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:31818511 original size:66 final size:67
Alignment explanation
Indices: 31818427--31818569 Score: 252
Period size: 68 Copynumber: 2.1 Consensus size: 67
31818417 AAATTAATTG
*
31818427 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
31818491 GA
66 GA
*
31818493 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
31818558 TGA
65 TGA
31818561 TTAGTAAAA
1 TTAGTAAAA
31818570 CAAACTTGAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
66 26 0.36
68 46 0.64
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:31818523 original size:9 final size:9
Alignment explanation
Indices: 31818511--31818538 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
31818501 TTTATCAAAT
31818511 TATTAATTG
1 TATTAATTG
31818520 TATTAATTG
1 TATTAATTG
31818529 TATTAATTG
1 TATTAATTG
31818538 T
1 T
31818539 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:31818685 original size:23 final size:24
Alignment explanation
Indices: 31818638--31818683 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
31818628 AAATAAACTT
31818638 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
31818662 AAAATAAAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
31818684 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:31822721 original size:18 final size:18
Alignment explanation
Indices: 31822688--31822723 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31822678 TTACTTGACT
*
31822688 TGCCCGTGTGATCACACA
1 TGCCCGTGTGACCACACA
*
31822706 TGCCCGTGTGCCCACACA
1 TGCCCGTGTGACCACACA
31822724 AACTACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.39, G:0.22, T:0.19
Consensus pattern (18 bp):
TGCCCGTGTGACCACACA
Found at i:31825164 original size:49 final size:50
Alignment explanation
Indices: 31825105--31825209 Score: 151
Period size: 49 Copynumber: 2.1 Consensus size: 50
31825095 CGTGGCCGTA
* * *
31825105 TGGGCCACACGGGCTAGGCCAGAT-TGGGCGTGTAGG-GCACACAGGCATG
1 TGGGCCACACGGGCAAGGCCA-ATCTGGGCGTGTAGGCCCACACAAGCATG
*
31825154 TGGGCTACACGGGCAAGGCCAATCTGGGCGTGTAGGCCCACACAAGCATG
1 TGGGCCACACGGGCAAGGCCAATCTGGGCGTGTAGGCCCACACAAGCATG
31825204 TGGGCC
1 TGGGCC
31825210 CAAAATTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
48 2 0.04
49 31 0.63
50 16 0.33
ACGTcount: A:0.21, C:0.27, G:0.38, T:0.14
Consensus pattern (50 bp):
TGGGCCACACGGGCAAGGCCAATCTGGGCGTGTAGGCCCACACAAGCATG
Found at i:31832288 original size:32 final size:32
Alignment explanation
Indices: 31832234--31832316 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
31832224 TGAGTGTGGC
* * *
31832234 CGTGT-GGCCACACAGGCTAGGCCAGAT-TTAG
1 CGTGTGGGCCACACGGGCAAGGCCA-ATCTCAG
* *
31832265 CGTGTGGGCCACATGGGCAAGGCCAATCTCGG
1 CGTGTGGGCCACACGGGCAAGGCCAATCTCAG
31832297 CGTGTGGGCACACACGGGCA
1 CGTGTGGGC-CACACGGGCA
31832317 TGTTGGCCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
31 7 0.16
32 27 0.63
33 9 0.21
ACGTcount: A:0.20, C:0.28, G:0.36, T:0.16
Consensus pattern (32 bp):
CGTGTGGGCCACACGGGCAAGGCCAATCTCAG
Found at i:31833710 original size:40 final size:40
Alignment explanation
Indices: 31833655--31833778 Score: 203
Period size: 40 Copynumber: 3.1 Consensus size: 40
31833645 TGTTATACTC
31833655 TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCT
1 TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCT
* * *
31833695 TCTGTCTAGTGTGTTTCAGTTGGATTAGCTCCTATGAGCT
1 TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCT
* *
31833735 TCTGTCTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCT
31833775 TCTG
1 TCTG
31833779 GTGTGTTTTG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.43
Consensus pattern (40 bp):
TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCT
Found at i:31833786 original size:36 final size:36
Alignment explanation
Indices: 31833659--31833792 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 36
31833649 ATACTCTCTG
*
31833659 TCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCT
1 TCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCA
* * *
31833695 TCTGTCTAGTGTGTTTCAGTTGGATTAGCTCCTATGAGCTTCTG
1 TCTG----GTGTGTTTCGGTTGGATTAGCTCTTATGAG---C-A
*
31833739 TCTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCA
*
31833775 TCTGGTGTGTTTTGGTTG
1 TCTGGTGTGTTTCGGTTG
31833793 ATCTGACGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
36 21 0.26
37 1 0.01
40 55 0.67
43 1 0.01
44 4 0.05
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.44
Consensus pattern (36 bp):
TCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCA
Found at i:31834598 original size:32 final size:32
Alignment explanation
Indices: 31834562--31834624 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
31834552 GTGTGGGTCG
*
31834562 CACGGGCT-AGGCCAGAT-TGGGTGGGTGGGCCA
1 CACGGG-TAAGGCCA-ATCTGGGTAGGTGGGCCA
*
31834594 CACGGGTAAGGCCAATCTGGGTATGTGGGCC
1 CACGGGTAAGGCCAATCTGGGTAGGTGGGCC
31834625 CGTAATTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.17, C:0.22, G:0.43, T:0.17
Consensus pattern (32 bp):
CACGGGTAAGGCCAATCTGGGTAGGTGGGCCA
Found at i:31845214 original size:15 final size:16
Alignment explanation
Indices: 31845194--31845227 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
31845184 GGTAATTGAC
31845194 AAAAAAAGA-AAAAAG
1 AAAAAAAGAGAAAAAG
*
31845209 AAAAAAAGAGAGAAAG
1 AAAAAAAGAGAAAAAG
31845225 AAA
1 AAA
31845228 TAAATGGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAG
Found at i:31845224 original size:16 final size:16
Alignment explanation
Indices: 31845194--31845245 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
31845184 GGTAATTGAC
*
31845194 AAAAAAAGA-AAAAAG
1 AAAAAAAGAGAGAAAG
31845209 AAAAAAAGAGAGAAAG
1 AAAAAAAGAGAGAAAG
* *
31845225 AAATAAATG-GAGACAG
1 AAA-AAAAGAGAGAAAG
31845241 AAAAA
1 AAAAA
31845246 TAAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 11 0.34
16 17 0.53
17 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAGAGAAAG
Done.