Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 23 of 31
Found at i:10891876 original size:2 final size:2
Alignment explanation
Indices: 10891871--10891897 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10891861 AATTATATAG
10891871 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
10891898 AGCGCACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10893343 original size:30 final size:30
Alignment explanation
Indices: 10893307--10893363 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
10893297 CTATATAGGT
* * *
10893307 ACATATTCTGAATTACGAAAATAGTTATTC
1 ACATATTCTCAAATACAAAAATAGTTATTC
*
10893337 ACATATTCTCAAATACAAAAATGGTTA
1 ACATATTCTCAAATACAAAAATAGTTA
10893364 CGATGTAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (30 bp):
ACATATTCTCAAATACAAAAATAGTTATTC
Found at i:10905233 original size:15 final size:14
Alignment explanation
Indices: 10905203--10905229 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10905193 TTTAACATAA
10905203 ATAAAATTATTTTC
1 ATAAAATTATTTTC
10905217 ATAAAATTATTTT
1 ATAAAATTATTTT
10905230 TCATGTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAAATTATTTTC
Found at i:10909941 original size:21 final size:22
Alignment explanation
Indices: 10909899--10909943 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
10909889 CCTGCAGTAT
*
10909899 AAAAATAGATGGCAATAAAGAA
1 AAAAATAGATGGCAACAAAGAA
* *
10909921 AAAAATTGATGG-AACAGAGAA
1 AAAAATAGATGGCAACAAAGAA
10909942 AA
1 AA
10909944 TTAAATATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.62, C:0.04, G:0.20, T:0.13
Consensus pattern (22 bp):
AAAAATAGATGGCAACAAAGAA
Found at i:10923070 original size:28 final size:28
Alignment explanation
Indices: 10923039--10923092 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
10923029 CAATTCAGTC
*
10923039 TTTATATTTTTATTTTGAATCAAATATT
1 TTTATATTTTTATTTTAAATCAAATATT
10923067 TTTATATTTTTATTTTAAATCAAATA
1 TTTATATTTTTATTTTAAATCAAATA
10923093 AATCTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTATATTTTTATTTTAAATCAAATATT
Found at i:10923385 original size:30 final size:30
Alignment explanation
Indices: 10923349--10923427 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
10923339 AATCATTAAT
10923349 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTTAATTTAAAATAAAAA
* * *
10923379 TATAAAAATTTAATTAA-ATATAATAAAAA
1 TATAAAAATTTATTTAATTTAAAATAAAAA
*
10923408 -ATAAATATTTATTTATATTT
1 TATAAAAATTTATTTA-ATTT
10923428 TTATAATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 13 0.32
29 11 0.27
30 17 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TATAAAAATTTATTTAATTTAAAATAAAAA
Found at i:10923425 original size:26 final size:28
Alignment explanation
Indices: 10923359--10923425 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 28
10923349 TATAAAAATT
10923359 TATTTAATTTA-A-AATAAAAATATAAA
1 TATTTAATTTATATAATAAAAATATAAA
* *
10923385 AATTTAATTAAATATAATAAAAA-ATAAA
1 TATTTAATT-TATATAATAAAAATATAAA
10923413 TATTT-ATTTATAT
1 TATTTAATTTATAT
10923426 TTTTATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 12 0.35
27 4 0.12
28 10 0.29
29 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TATTTAATTTATATAATAAAAATATAAA
Found at i:10942327 original size:21 final size:21
Alignment explanation
Indices: 10942302--10942342 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10942292 TTGAATCCTT
*
10942302 TATTTT-TTTTATCATTATTTA
1 TATTTTATTTT-TCAATATTTA
10942323 TATTTTATTTTTCAATATTT
1 TATTTTATTTTTCAATATTT
10942343 TTAATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTTATTTTTCAATATTTA
Found at i:10942366 original size:16 final size:16
Alignment explanation
Indices: 10942325--10942366 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
10942315 ATTATTTATA
10942325 TTTTATTTTTCAATAT
1 TTTTATTTTTCAATAT
* *
10942341 TTTTAATTTTC-ATGGT
1 TTTTATTTTTCAAT-AT
10942357 TTTTATTTTT
1 TTTTATTTTT
10942367 ATTTTTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTTATTTTTCAATAT
Found at i:10945900 original size:4 final size:4
Alignment explanation
Indices: 10945891--10945917 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10945881 TTAAGCATTC
10945891 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
10945918 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:10951469 original size:39 final size:39
Alignment explanation
Indices: 10951400--10951474 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
10951390 ATGAATGATA
* * * *
10951400 TGATTTATACGTATGACGGACATTGTTTTATCAATGTTT
1 TGATTTATACATATGACGAACATCGGTTTATCAATGTTT
* *
10951439 TGATTTATTCATATGACGAACATCGGTTTATGAATG
1 TGATTTATACATATGACGAACATCGGTTTATCAATG
10951475 AAATGAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.43
Consensus pattern (39 bp):
TGATTTATACATATGACGAACATCGGTTTATCAATGTTT
Found at i:10952547 original size:16 final size:14
Alignment explanation
Indices: 10952506--10952568 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 14
10952496 AATTTTACTA
10952506 TAATATAGTAATA-
1 TAATATAGTAATAT
10952519 TAAT-T--T-ATAT
1 TAATATAGTAATAT
10952529 TAATATAGTAACTTAT
1 TAATATAGTAA--TAT
*
10952545 TAATATAATAATAT
1 TAATATAGTAATAT
*
10952559 TACTATAGTA
1 TAATATAGTA
10952569 TAGTATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
9 3 0.08
10 5 0.12
11 1 0.03
12 1 0.03
13 5 0.12
14 12 0.30
16 13 0.32
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (14 bp):
TAATATAGTAATAT
Found at i:10960770 original size:14 final size:14
Alignment explanation
Indices: 10960748--10960783 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
10960738 GCATGGAGTC
*
10960748 TCAAGAATAGATAT
1 TCAAAAATAGATAT
10960762 TCAAAAATAGATAT
1 TCAAAAATAGATAT
10960776 TCAAAAAT
1 TCAAAAAT
10960784 TACAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (14 bp):
TCAAAAATAGATAT
Found at i:10964095 original size:59 final size:59
Alignment explanation
Indices: 10964003--10964123 Score: 154
Period size: 59 Copynumber: 2.1 Consensus size: 59
10963993 TTTGAACTTT
* * *
10964003 GCAGAGATAATTATTAACAGCTTAAATCTTGTGAAACAATGCAT-TAAGGACAATTTTTA
1 GCAGAGAGAATTATTAACAGCTTAAATCTTGTGAAAAAATGCATCT-AGGACAATTCTTA
* ** * *
10964062 GCAGAGAGAATTATTAACATCTTGGATTTTGTGAAAAAATGCATCTTGGACAATTCTTA
1 GCAGAGAGAATTATTAACAGCTTAAATCTTGTGAAAAAATGCATCTAGGACAATTCTTA
10964121 GCA
1 GCA
10964124 CAAAATGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 52 0.98
60 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (59 bp):
GCAGAGAGAATTATTAACAGCTTAAATCTTGTGAAAAAATGCATCTAGGACAATTCTTA
Found at i:10965380 original size:29 final size:28
Alignment explanation
Indices: 10965295--10965382 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 28
10965285 ATACGCGAAA
* *
10965295 AGGTACAAGAGAATAAGCTGTATGTGAAT
1 AGGTACAAGAGAAAAAG-TGTATATGAAT
* *
10965324 ATGTATAAGCA-AAAAAGT-TATATGTGAAT
1 AGGTACAAG-AGAAAAAGTGTATA--TGAAT
10965353 AGGTACAAGAGAAGAAAGTGTATATGAAT
1 AGGTACAAGAGAA-AAAGTGTATATGAAT
10965382 A
1 A
10965383 AATACATGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
27 3 0.06
28 2 0.04
29 32 0.68
30 6 0.13
31 4 0.09
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGTACAAGAGAAAAAGTGTATATGAAT
Found at i:10966553 original size:23 final size:23
Alignment explanation
Indices: 10966512--10966557 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
10966502 ATTAAAGTAA
10966512 TTGTAGATTTTTTTCATTTCTTAT
1 TTGTAGATTTTTTTCATTT-TTAT
10966536 TTGT-GATTTTTTGT-ATTTTTAT
1 TTGTAGATTTTTT-TCATTTTTAT
10966558 GCTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 12 0.57
24 5 0.24
ACGTcount: A:0.15, C:0.04, G:0.11, T:0.70
Consensus pattern (23 bp):
TTGTAGATTTTTTTCATTTTTAT
Found at i:10979753 original size:34 final size:35
Alignment explanation
Indices: 10979684--10979759 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
10979674 AAATTTAAAT
* *
10979684 TTAAATAATCAAAAACAAACATATCAAATATCAAC
1 TTAAATAATCAAAAACAAACATATCAAACAACAAC
* * *
10979719 TTAAATAATTAAAAATAAATAT-TCAAACAACAAC
1 TTAAATAATCAAAAACAAACATATCAAACAACAAC
10979753 TTAAATA
1 TTAAATA
10979760 CTACAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 17 0.47
35 19 0.53
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (35 bp):
TTAAATAATCAAAAACAAACATATCAAACAACAAC
Found at i:10980074 original size:18 final size:17
Alignment explanation
Indices: 10980053--10980108 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
10980043 TCAAAGATAT
10980053 TATAAGTTAATTAATAA
1 TATAAGTTAATTAATAA
10980070 T-TATAGTT--TT-ATGAA
1 TATA-AGTTAATTAAT-AA
*
10980085 T-TAATTTAATTAATAA
1 TATAAGTTAATTAATAA
10980101 TATAAGTT
1 TATAAGTT
10980109 TATCTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 7 0.23
17 12 0.39
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (17 bp):
TATAAGTTAATTAATAA
Found at i:10984825 original size:6 final size:6
Alignment explanation
Indices: 10984816--10984853 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
10984806 TTATGGAGGA
*
10984816 AGGGGC AGGGGC AGGGGC AGGGGC AGGGGC AGAGGC AG
1 AGGGGC AGGGGC AGGGGC AGGGGC AGGGGC AGGGGC AG
10984854 TCGTACAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.63, T:0.00
Consensus pattern (6 bp):
AGGGGC
Found at i:10984839 original size:18 final size:18
Alignment explanation
Indices: 10984811--10984853 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
10984801 TCCTTTTATG
*
10984811 GAGGAAGGGGCAGGGGCA
1 GAGGCAGGGGCAGGGGCA
*
10984829 GGGGCAGGGGCAGGGGCA
1 GAGGCAGGGGCAGGGGCA
10984847 GAGGCAG
1 GAGGCAG
10984854 TCGTACAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.63, T:0.00
Consensus pattern (18 bp):
GAGGCAGGGGCAGGGGCA
Found at i:11018707 original size:42 final size:42
Alignment explanation
Indices: 11018660--11018742 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
11018650 TACTCGTAAG
* * *
11018660 AGGAAGAGATTAGTCTTGAAGTAGGAGTTTGAGTTTGGGTGA
1 AGGAAGAGATCAGTCTTGAAGTAAGAATTTGAGTTTGGGTGA
* *
11018702 AGGAAGAGATCAGTTTTGAGGTAAGAATTTGAGTTTGGGTG
1 AGGAAGAGATCAGTCTTGAAGTAAGAATTTGAGTTTGGGTG
11018743 GGATGGACCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.31
Consensus pattern (42 bp):
AGGAAGAGATCAGTCTTGAAGTAAGAATTTGAGTTTGGGTGA
Found at i:11019272 original size:15 final size:15
Alignment explanation
Indices: 11019229--11019272 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
11019219 GATGAGAATA
*
11019229 TGATTATTGAAAATG
1 TGATTGTTGAAAATG
11019244 TGATTGTT-AGAAATG
1 TGATTGTTGA-AAATG
11019259 TGATTGTTGAAAAT
1 TGATTGTTGAAAAT
11019273 ATAACCTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (15 bp):
TGATTGTTGAAAATG
Found at i:11019506 original size:21 final size:21
Alignment explanation
Indices: 11019481--11019522 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11019471 ACTATAAGCA
11019481 ATTAAAATAATAA-ATAATAAT
1 ATTAAAA-AATAACATAATAAT
*
11019502 ATTAAAAAATAACATTATAAT
1 ATTAAAAAATAACATAATAAT
11019523 TTTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAAAAAATAACATAATAAT
Found at i:11020093 original size:24 final size:24
Alignment explanation
Indices: 11020066--11020121 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
11020056 AGGCAATGTG
*
11020066 AGAAGAAAAAGAAAAAGGCAAAAA
1 AGAAGAAAAAGAAAAAAGCAAAAA
* * * *
11020090 AGAATACAGAGAAAAAAGCAAGAA
1 AGAAGAAAAAGAAAAAAGCAAAAA
*
11020114 GGAAGAAA
1 AGAAGAAA
11020122 GAAAGTGAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.70, C:0.05, G:0.23, T:0.02
Consensus pattern (24 bp):
AGAAGAAAAAGAAAAAAGCAAAAA
Found at i:11020142 original size:28 final size:28
Alignment explanation
Indices: 11020100--11020154 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
11020090 AGAATACAGA
11020100 GAAAAAAGCAAGAAGGAAGAA-AGAAAGT
1 GAAAAAAGCAAGAAGG-AGAAGAGAAAGT
* *
11020128 GAAAAAGGCAGGAAGGAGAAGAGAAAG
1 GAAAAAAGCAAGAAGGAGAAGAGAAAG
11020155 GTCAAAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.60, C:0.04, G:0.35, T:0.02
Consensus pattern (28 bp):
GAAAAAAGCAAGAAGGAGAAGAGAAAGT
Found at i:11020979 original size:31 final size:31
Alignment explanation
Indices: 11020937--11021010 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
11020927 AATACAGAGC
*
11020937 TTTGTTCAATTTAGTTTTTATACTATAAAGT
1 TTTGTTCAATTTAGTCTTTATACTATAAAGT
* * *
11020968 TTTGTTTAATTTAGTCTTTGTACTATAGAGT
1 TTTGTTCAATTTAGTCTTTATACTATAAAGT
*
11020999 TGTGTTCAATTT
1 TTTGTTCAATTT
11021011 GGTACTGTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (31 bp):
TTTGTTCAATTTAGTCTTTATACTATAAAGT
Found at i:11035309 original size:2 final size:2
Alignment explanation
Indices: 11035266--11035291 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11035256 TTACATATGC
11035266 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
11035292 GTATGGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11037099 original size:42 final size:42
Alignment explanation
Indices: 11037040--11037131 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
11037030 GATGGACAAC
* *
11037040 GGAAAGAATCCAATCAAAGAGGAAGAA-AAGGTTTTATCATTG
1 GGAAAGAAGCCAATCAAAGAGGAA-AAGAAGGTTTTATCATGG
* * * *
11037082 GGAAAGAAGGCAATCAAAGAGGAAAAGAATGTTTTTTCCTGG
1 GGAAAGAAGCCAATCAAAGAGGAAAAGAAGGTTTTATCATGG
11037124 GGAAAGAA
1 GGAAAGAA
11037132 TTATGAGCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.45, C:0.09, G:0.27, T:0.20
Consensus pattern (42 bp):
GGAAAGAAGCCAATCAAAGAGGAAAAGAAGGTTTTATCATGG
Found at i:11046457 original size:33 final size:31
Alignment explanation
Indices: 11046404--11046468 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
11046394 CTTGTTATTT
**
11046404 TATATTATATAATGTTGATGTGAT-ATATTAA
1 TATATTATATAATGGCGATGT-ATCATATTAA
11046435 TATATTATAATTAATGGCGATGTATCATATTAA
1 TATATTAT-A-TAATGGCGATGTATCATATTAA
11046468 T
1 T
11046469 TCGGCATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 8 0.28
32 3 0.10
33 18 0.62
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.46
Consensus pattern (31 bp):
TATATTATATAATGGCGATGTATCATATTAA
Found at i:11047573 original size:13 final size:13
Alignment explanation
Indices: 11047555--11047595 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
11047545 TTTTGTTAGC
11047555 TTAGGGTTTGAAT
1 TTAGGGTTTGAAT
*
11047568 TTAGGGTTTGTAT
1 TTAGGGTTTGAAT
11047581 ATT-GGGTTT-AAT
1 -TTAGGGTTTGAAT
11047593 TTA
1 TTA
11047596 TTGTTGGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 18 0.75
14 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (13 bp):
TTAGGGTTTGAAT
Found at i:11048331 original size:20 final size:21
Alignment explanation
Indices: 11048308--11048349 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
11048298 AAACATTTAC
11048308 ATTAATTAAAT-TTTTATTAA
1 ATTAATTAAATATTTTATTAA
11048328 ATTAATTAAATACTTTTATTAA
1 ATTAATTAAATA-TTTTATTAA
11048350 TCAATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAATTAAATATTTTATTAA
Found at i:11048666 original size:401 final size:406
Alignment explanation
Indices: 11048073--11048950 Score: 1118
Period size: 401 Copynumber: 2.2 Consensus size: 406
11048063 ATATAATGTA
* * * *
11048073 TTATAAGTAAAT-AAGCATTAAATTAAATGAGTAATATTATATAATATTACTTTTTTATTTAAAT
1 TTATAAGTAATTAAAGAATT-AATTAAATTAGTAATATCATATAATATTA-TTTTTTATTTAAAT
*
11048137 TAATTAAGTGTTTAGGGTTATATTTACAAAATTTAACTAATTATGAAGAATCATTTATTAGTTAT
64 TAATTAAGAGTTTAGGGTTATATTTACAAAATTTAACTAATTATGAAGAATC---TATTAGTTAT
* * *
11048202 TAATAAATTAATCAATTAATTAAATTAGTGATTGAACAAATCAAATGATAGTAATTAATCAATTC
126 TAATAAATTAATCAATTAATTAAATTAGTAATTGAACAAATCAAATGATAATAAATAATCAATTC
*
11048267 AAAATGTATCAGTAAATTTAGTAAAATTTATAAA-CATTTACATTAATTAAATTTTTATTAAATT
191 AAAATGTATCAGTAAATTTAGTAAAATTTA-AAAGCATTTACATTAATTAAAGTTTTATTAAATT
* ** * * * * *
11048331 AATTAAATACTTTTATTAATCAATTG-AAAAAAGTTTTAATAGTTAAGCTATCAACTAAATTAGT
255 AATTAAATAATTAAACTAATCAAATGAAAAAAAGTTTTAACAGTTAAGCAATAAACTAAATTAGT
** * ***
11048395 AATATTATTTAAT-TTTA-AAGATATTTTAATAAATTAACATTTTTAGTGGGGTAATTAAATAAT
320 AATATTATTTAATCACTATAA-ATATTTTAATAAATTAACATCTTTAGTGCCATAATTAAATAAT
*
11048458 TTAGTTAGTTAAGTGTTAGAG-TG
384 TTAGTTAATTAAGTGTTAG-GTTG
** *
11048481 TTATAAGTGCTTAAAGAATTAATTAAATTAGTAATATCATAAAATATTATTTTCTTATTTAAATT
1 TTATAAGTAATTAAAGAATTAATTAAATTAGTAATATCATATAATATTATTTT-TTATTTAAATT
* * *
11048546 AATTAAGGAGTTTAGGGAATTA-A-TTACAACATTTAACTAATTTTGGAGAATC-A-T-G-TATT
65 AATTAA-GAGTTTAGGG--TTATATTTACAAAATTTAACTAATTATGAAGAATCTATTAGTTATT
* *
11048605 AGT-AATTAATCAATTAATTAAATTAGTAATTTAACAAATCAAATGATAATAAATAATCAATTCA
127 AATAAATTAATCAATTAATTAAATTAGTAATTGAACAAATCAAATGATAATAAATAATCAATTCA
* * ** *
11048669 AAATGTATTAGTAAATTTAGTACAATTTAAAAGTGTTTACATTAATTAAGGTTTTATTAAATTAA
192 AAATGTATCAGTAAATTTAGTAAAATTTAAAAGCATTTACATTAATTAAAGTTTTATTAAATTAA
* * * *
11048734 TTAAATAATTAAACTAATGAAATGAAAAAAAGTTTTAGCAGTTATGCAATAAAGTAAATTAGTAA
257 TTAAATAATTAAACTAATCAAATGAAAAAAAGTTTTAACAGTTAAGCAATAAACTAAATTAGTAA
**
11048799 TATTATTTAATCACTATAAATATTTTAATAAATTAAGGTCTTTAGTGCCATAATTAAATAATTTA
322 TATTATTTAATCACTATAAATATTTTAATAAATTAACATCTTTAGTGCCATAATTAAATAATTTA
11048864 GTTAATTAAGTGTTAGGTTG
387 GTTAATTAAGTGTTAGGTTG
* *
11048884 TTATAAGTAATTAAGGAATTAATTAAATTAGTAATTAATTC-TATAATATTAGTTTTTATTTAAA
1 TTATAAGTAATTAAAGAATTAATTAAATTAGTAA-T-A-TCATATAATATTATTTTTTATTTAAA
11048948 TTA
63 TTA
11048951 TTCTAGTGTT
Statistics
Matches: 409, Mismatches: 48, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
400 3 0.01
401 130 0.32
402 52 0.13
403 91 0.22
404 16 0.04
405 14 0.03
406 2 0.00
407 4 0.01
408 52 0.13
409 41 0.10
410 1 0.00
411 3 0.01
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (406 bp):
TTATAAGTAATTAAAGAATTAATTAAATTAGTAATATCATATAATATTATTTTTTATTTAAATTA
ATTAAGAGTTTAGGGTTATATTTACAAAATTTAACTAATTATGAAGAATCTATTAGTTATTAATA
AATTAATCAATTAATTAAATTAGTAATTGAACAAATCAAATGATAATAAATAATCAATTCAAAAT
GTATCAGTAAATTTAGTAAAATTTAAAAGCATTTACATTAATTAAAGTTTTATTAAATTAATTAA
ATAATTAAACTAATCAAATGAAAAAAAGTTTTAACAGTTAAGCAATAAACTAAATTAGTAATATT
ATTTAATCACTATAAATATTTTAATAAATTAACATCTTTAGTGCCATAATTAAATAATTTAGTTA
ATTAAGTGTTAGGTTG
Found at i:11050654 original size:20 final size:19
Alignment explanation
Indices: 11050610--11050665 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
11050600 ATATATATAT
11050610 ATGTATTGATACATTTCAA
1 ATGTATTGATACATTTCAA
* *
11050629 AGTGTATTGGTACATTTTAGA
1 A-TGTATTGATACATTTCA-A
11050650 ATGTATCT-ATACATTT
1 ATGTAT-TGATACATTT
11050666 TGGGGCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 27 0.87
21 3 0.10
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (19 bp):
ATGTATTGATACATTTCAA
Found at i:11050961 original size:21 final size:22
Alignment explanation
Indices: 11050931--11050985 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
11050921 TAGGTACTTC
* *
11050931 AAAATTTATTTAAAAAAATTTA
1 AAAACTTATTTAAAAAAATTCA
* *
11050953 AAAAC-TATTCAAAAAAGTTCA
1 AAAACTTATTTAAAAAAATTCA
11050974 AAAACTTATTTA
1 AAAACTTATTTA
11050986 CAATTTCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAACTTATTTAAAAAAATTCA
Found at i:11051009 original size:21 final size:21
Alignment explanation
Indices: 11050985--11051047 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
11050975 AAACTTATTT
* *
11050985 ACAATTTCAAAAATCATTCAA
1 ACAAGTTCAAAGATCATTCAA
*
11051006 ACAAGTTCAAGGATCACTT-AA
1 ACAAGTTCAAAGATCA-TTCAA
11051027 ACAAGTTCAAAGATCATTCAA
1 ACAAGTTCAAAGATCATTCAA
11051048 GCAATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (21 bp):
ACAAGTTCAAAGATCATTCAA
Found at i:11056829 original size:28 final size:28
Alignment explanation
Indices: 11056798--11056852 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
11056788 ATTATTGAGG
*
11056798 ATGTTT-TCATTCTTCGATATTATTATGA
1 ATGTTTGT-ATTCTTAGATATTATTATGA
*
11056826 ATGTTTGTGTTCTTAGATATTATTATG
1 ATGTTTGTATTCTTAGATATTATTATG
11056853 GATATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.55
Consensus pattern (28 bp):
ATGTTTGTATTCTTAGATATTATTATGA
Found at i:11083663 original size:98 final size:97
Alignment explanation
Indices: 11083536--11083726 Score: 337
Period size: 98 Copynumber: 2.0 Consensus size: 97
11083526 GATATATAAA
11083536 TATTAATTGTAGACAAATAAAATGTAATAAATTAAAAAATATGAAAGAATATTTGACCTTTCAAC
1 TATTAATTGTAGACAAATAAAATGTAATAAATTAAAAAATATGAAAGAATATTTGACCTTTCAAC
* *
11083601 TATTAAAATCATGTTTAATATCAAGATATGAT
66 TAATAAAATCATATTTAATATCAAGATATGAT
*
11083633 TATTAATTGTAGACATAATAAAATGTAATAAATTAAAAAATATGAAAGAATATTTGACCTTTTAA
1 TATTAATTGTAGACA-AATAAAATGTAATAAATTAAAAAATATGAAAGAATATTTGACCTTTCAA
*
11083698 TTAATAAAATCATATTTAATATCAAGATA
65 CTAATAAAATCATATTTAATATCAAGATA
11083727 ATATCAAGGT
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
97 15 0.17
98 74 0.83
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (97 bp):
TATTAATTGTAGACAAATAAAATGTAATAAATTAAAAAATATGAAAGAATATTTGACCTTTCAAC
TAATAAAATCATATTTAATATCAAGATATGAT
Found at i:11084855 original size:2 final size:2
Alignment explanation
Indices: 11084848--11084874 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11084838 ATTACGAAAG
11084848 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11084875 AATTATAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11084909 original size:9 final size:9
Alignment explanation
Indices: 11084885--11084922 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
11084875 AATTATAGAC
11084885 ATAATAAAAT
1 ATAA-AAAAT
11084895 ATAAAAAAT
1 ATAAAAAAT
11084904 -TAAAAAAT
1 ATAAAAAAT
11084912 ATAAAAAAT
1 ATAAAAAAT
11084921 AT
1 AT
11084923 TTGACTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.30
9 15 0.56
10 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:11086364 original size:2 final size:2
Alignment explanation
Indices: 11086315--11086346 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11086305 AAACAGACTA
11086315 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
11086347 TATTTAATTA
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:11087115 original size:98 final size:98
Alignment explanation
Indices: 11086940--11087138 Score: 335
Period size: 98 Copynumber: 2.0 Consensus size: 98
11086930 AAAGACAAAT
*
11086940 ATATGAATATTAATTGTAGACATAATAAAATGTATTAAATAAAAAAATATGAAAGGATATTTGAC
1 ATATGAATATTAATTGTAGACATAATAAAATGTAATAAATAAAAAAATATGAAAGGATATTTGAC
11087005 CTCTCAACTATTAAAATCATAATTAATATCGAG
66 CTCTCAACTATTAAAATCATAATTAATATCGAG
* * *
11087038 ATATGATTATTAATTGTAGACATAATAAAATGTAATAAATTAAAAAATATGAAAGGATGTTTGAC
1 ATATGAATATTAATTGTAGACATAATAAAATGTAATAAATAAAAAAATATGAAAGGATATTTGAC
* * *
11087103 CTTTCAATTATTAAAATCATATTTAATATCGAG
66 CTCTCAACTATTAAAATCATAATTAATATCGAG
11087136 ATA
1 ATA
11087139 ATATCAAGAT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (98 bp):
ATATGAATATTAATTGTAGACATAATAAAATGTAATAAATAAAAAAATATGAAAGGATATTTGAC
CTCTCAACTATTAAAATCATAATTAATATCGAG
Found at i:11091327 original size:16 final size:16
Alignment explanation
Indices: 11091301--11091338 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11091291 ACATATTTTA
*
11091301 TATATATATAATAATAT
1 TATATAGATAAT-ATAT
11091318 T-TATAGATAATATAT
1 TATATAGATAATATAT
11091333 TATATA
1 TATATA
11091339 TTAATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 13 0.68
17 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TATATAGATAATATAT
Found at i:11096611 original size:15 final size:15
Alignment explanation
Indices: 11096591--11096623 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11096581 ATGGGAACTC
11096591 TGGAATGTACGGTGG
1 TGGAATGTACGGTGG
*
11096606 TGGAATGTATGGTGG
1 TGGAATGTACGGTGG
11096621 TGG
1 TGG
11096624 TCTTGGTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.48, T:0.30
Consensus pattern (15 bp):
TGGAATGTACGGTGG
Found at i:11136459 original size:5 final size:5
Alignment explanation
Indices: 11136445--11136479 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
11136435 CCCTCACAAG
* *
11136445 AGAAT AGAAA GGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
11136480 CAATTAGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (5 bp):
AGAAA
Found at i:11138332 original size:207 final size:207
Alignment explanation
Indices: 11137976--11138392 Score: 717
Period size: 207 Copynumber: 2.0 Consensus size: 207
11137966 TTGTTCAACT
* * *
11137976 TCTACTTCACCTGATAGAAACGTGGTAAACAATCTGAGTGAATTCCCGGGAATGGTGAATGATAT
1 TCTACTTCACCTGATAGAAACATGGTAAACAATCGGAGTGAATTCCCGAGAATGGTGAATGATAT
11138041 GGGTCGAAATGTAGTACGGTCTCCTTTACTGTCCTCAGCCTCTACATCCCCAGACAGAGCTTTGA
66 GGGTCGAAATGTAGTACGGTCTCCTTTACTGTCCTCAGCCTCTACATCCCCAGACAGAGCTTTGA
*
11138106 ACGAGAATGAACAGTCTCCTTTACTATCATCGGCTTCGTCATCACCAGACAGAGCTTTGGAGAAA
131 ACGAGAATGAACAGTCTCCTTTACTATCATCGGCTTCGTCATCACCAGACAGAGCTTTCGAGAAA
11138171 AGCCCAGAGATG
196 AGCCCAGAGATG
*
11138183 TCTACTTCACCTGATAGAAACATGGTAAACAATCGGAGTGAATTCCCGAGAATGGTTAATGATAT
1 TCTACTTCACCTGATAGAAACATGGTAAACAATCGGAGTGAATTCCCGAGAATGGTGAATGATAT
* * * * *
11138248 GGGTCGAAATGTTGTACGGTCTCCTTTACTGTCGTCAGCTTCTACATCTCCAGGCAGAGCTTTGA
66 GGGTCGAAATGTAGTACGGTCTCCTTTACTGTCCTCAGCCTCTACATCCCCAGACAGAGCTTTGA
* * *
11138313 ACGAGAATGAGCGGTCTCCTTTGCTATCATCGGCTTCGTCATCACCAGACAGAGCTTTCGAGAAA
131 ACGAGAATGAACAGTCTCCTTTACTATCATCGGCTTCGTCATCACCAGACAGAGCTTTCGAGAAA
11138378 AGCCCAGAGATG
196 AGCCCAGAGATG
11138390 TCT
1 TCT
11138393 CCCTTGATGG
Statistics
Matches: 197, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
207 197 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (207 bp):
TCTACTTCACCTGATAGAAACATGGTAAACAATCGGAGTGAATTCCCGAGAATGGTGAATGATAT
GGGTCGAAATGTAGTACGGTCTCCTTTACTGTCCTCAGCCTCTACATCCCCAGACAGAGCTTTGA
ACGAGAATGAACAGTCTCCTTTACTATCATCGGCTTCGTCATCACCAGACAGAGCTTTCGAGAAA
AGCCCAGAGATG
Found at i:11141469 original size:36 final size:36
Alignment explanation
Indices: 11141396--11141469 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
11141386 CCATAAATTC
* **
11141396 CCAGTTCCAGTGAATCCAATGATGCCACAAGTTTTT
1 CCAGTTCCAGTGAATCCAATGATGCAACAAGCATTT
* * *
11141432 CCAGTTCCCGTGAATCCGATGCTGCAACAAGCATTT
1 CCAGTTCCAGTGAATCCAATGATGCAACAAGCATTT
11141468 CC
1 CC
11141470 CGGATTACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (36 bp):
CCAGTTCCAGTGAATCCAATGATGCAACAAGCATTT
Found at i:11150693 original size:18 final size:18
Alignment explanation
Indices: 11150670--11150704 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11150660 AATTAGGATT
11150670 CAGGTACCTCAAAATTAA
1 CAGGTACCTCAAAATTAA
*
11150688 CAGGTATCTCAAAATTA
1 CAGGTACCTCAAAATTA
11150705 TCGAGTACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (18 bp):
CAGGTACCTCAAAATTAA
Found at i:11157942 original size:17 final size:17
Alignment explanation
Indices: 11157888--11157951 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
11157878 ACAATGTAAA
*
11157888 TAATTTTTAACTTTATT
1 TAATTTTTAAATTTATT
* *
11157905 TAGTTTATTTAAAAGTTATT
1 TA-ATT-TTT-AAATTTATT
*
11157925 TAATTTTTAATTTTATT
1 TAATTTTTAAATTTATT
*
11157942 TTATTTTTAA
1 TAATTTTTAA
11157952 CTTTCAACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
17 18 0.49
18 5 0.14
19 5 0.14
20 9 0.24
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (17 bp):
TAATTTTTAAATTTATT
Found at i:11159852 original size:14 final size:14
Alignment explanation
Indices: 11159829--11159864 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11159819 GCCCTTATCT
*
11159829 AGATAGAGTTTACA
1 AGATAAAGTTTACA
11159843 AGATAAAGTTTACA
1 AGATAAAGTTTACA
11159857 AGATAAAG
1 AGATAAAG
11159865 ATAATGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (14 bp):
AGATAAAGTTTACA
Found at i:11162839 original size:27 final size:27
Alignment explanation
Indices: 11162798--11162850 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
11162788 TTGTGGAATG
* *
11162798 AAATAGAATAAAATAATTATTTTATAA
1 AAATAAAATAAAATAATTATTATATAA
*
11162825 AAATAAAATAGAATAATTATTATATA
1 AAATAAAATAAAATAATTATTATATA
11162851 GTTTGGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (27 bp):
AAATAAAATAAAATAATTATTATATAA
Found at i:11164351 original size:45 final size:45
Alignment explanation
Indices: 11164298--11164428 Score: 172
Period size: 45 Copynumber: 2.9 Consensus size: 45
11164288 TTTGTTTAAA
* *
11164298 ATGACGTGTAACAATCTAACCATGACATGTAACATGTTTTTGCAC
1 ATGACGTGTAACAACCTAATCATGACATGTAACATGTTTTTGCAC
* * * * *
11164343 ATGACGTGTAACAACCTAATCATAACGTGTCACACGTTTTTGTAC
1 ATGACGTGTAACAACCTAATCATGACATGTAACATGTTTTTGCAC
* * *
11164388 ATGACATGTAACAACCTAATCATGACATGTAATATTTTTTT
1 ATGACGTGTAACAACCTAATCATGACATGTAACATGTTTTT
11164429 ATACATAGTT
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (45 bp):
ATGACGTGTAACAACCTAATCATGACATGTAACATGTTTTTGCAC
Found at i:11168322 original size:51 final size:50
Alignment explanation
Indices: 11168219--11168341 Score: 144
Period size: 51 Copynumber: 2.4 Consensus size: 50
11168209 AAATTTTTTA
* *
11168219 ATTAAAACTTTAATTTAA-TTTTAAATTTAAATGTTAATTATTATAGTTTAT
1 ATTAAAA-TTTAATTTAATTTTTAAATTTAAATATTAATTATTATAG-ATAT
11168270 ATTAAAATTTTAATTTAATTTTTAAATTTAAAATATTAATT-TTCATA-ATAT
1 ATTAAAA-TTTAATTTAATTTTTAAATTT-AAATATTAATTATT-ATAGATAT
*
11168321 ATTAAAACTTAAGTTTAATTT
1 ATTAAAATTTAA-TTTAATTT
11168342 AGAGAGAGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
50 4 0.06
51 35 0.55
52 12 0.19
53 13 0.20
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (50 bp):
ATTAAAATTTAATTTAATTTTTAAATTTAAATATTAATTATTATAGATAT
Found at i:11168753 original size:35 final size:35
Alignment explanation
Indices: 11168685--11168753 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
11168675 TGAAATTAAC
** *
11168685 TAGAAGAAATAAAATACTACTTCATCTAGAACAAT
1 TAGAAGAAATAAAATACTACTTCATAAAAAACAAT
* * *
11168720 TAGAATAAGTAAAATACTATTTCATAAAAAACAA
1 TAGAAGAAATAAAATACTACTTCATAAAAAACAA
11168754 CTAAAACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (35 bp):
TAGAAGAAATAAAATACTACTTCATAAAAAACAAT
Found at i:11168786 original size:34 final size:35
Alignment explanation
Indices: 11168748--11168819 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
11168738 ATTTCATAAA
* * *
11168748 AAACAACTAAAACAAAT-AAGCATTACTTCATGCG
1 AAACAACTAAAACAAATGAAACACTACTCCATGCG
* *
11168782 AAACAATTAAAATAAATGAAACACTACTCCATGCG
1 AAACAACTAAAACAAATGAAACACTACTCCATGCG
11168817 AAA
1 AAA
11168820 TAATTAATAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 15 0.47
35 17 0.53
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.19
Consensus pattern (35 bp):
AAACAACTAAAACAAATGAAACACTACTCCATGCG
Found at i:11169124 original size:28 final size:29
Alignment explanation
Indices: 11169062--11169125 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
11169052 ATTTAAGTAT
*
11169062 AGCTTATTCTCTTATACTTGTTTGCATAC
1 AGCTTTTTCTCTTATACTTGTTTGCATAC
* * *
11169091 ATCTTTTTCTCTTA-ATTTGTTCT-CATAG
1 AGCTTTTTCTCTTATACTTGTT-TGCATAC
11169119 AGCTTTT
1 AGCTTTT
11169126 CTTGTATATC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (29 bp):
AGCTTTTTCTCTTATACTTGTTTGCATAC
Found at i:11186672 original size:27 final size:27
Alignment explanation
Indices: 11186642--11186694 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
11186632 TTGTGCTTTT
*
11186642 CTTTCTTTTATTTATCTTTTCTATTAA
1 CTTTCTTTTATTCATCTTTTCTATTAA
11186669 CTTTCTTTTATTCATCTTTTCTATTA
1 CTTTCTTTTATTCATCTTTTCTATTA
11186695 TTTATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (27 bp):
CTTTCTTTTATTCATCTTTTCTATTAA
Found at i:11198582 original size:48 final size:49
Alignment explanation
Indices: 11198468--11198618 Score: 259
Period size: 49 Copynumber: 3.1 Consensus size: 49
11198458 CCAGCCCGAC
*
11198468 GGGCCGCAGGGGGGAATCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCA
11198517 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCA
* *
11198566 GGGCCGCA-GGGGGAACCGGGACTCGTGGGAGCCAGAGGAGGGGGGGGCA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGG-GGGGCGGGCA
11198615 GGGC
1 GGGC
11198619 TAGCCCGGCC
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
48 29 0.30
49 69 0.70
ACGTcount: A:0.15, C:0.21, G:0.59, T:0.05
Consensus pattern (49 bp):
GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCA
Found at i:11211377 original size:21 final size:22
Alignment explanation
Indices: 11211348--11211390 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
11211338 AATACCCTTC
*
11211348 ATTATAATATTTAAT-TTTTAA
1 ATTAAAATATTTAATATTTTAA
*
11211369 ATTAAAATATTTATTATTTTAA
1 ATTAAAATATTTAATATTTTAA
11211391 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTAAAATATTTAATATTTTAA
Found at i:11211614 original size:23 final size:23
Alignment explanation
Indices: 11211588--11211634 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
11211578 TTTAATTTAA
11211588 TTTTTA-AATTTAAAA-TAATAAC
1 TTTTTATAATTTAAAATTAA-AAC
11211610 TTTTTATAATTTAAAATTAAAAC
1 TTTTTATAATTTAAAATTAAAAC
11211633 TT
1 TT
11211635 AAACCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.26
23 14 0.61
24 3 0.13
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTTATAATTTAAAATTAAAAC
Found at i:11212753 original size:33 final size:32
Alignment explanation
Indices: 11212693--11212788 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 32
11212683 GAAAAAGTTA
* *
11212693 AAATAAAATATATAATATAAAAAATTATATTAAG
1 AAATAAAATA-A-AATATATAAAATTATAATAAG
*
11212727 AAATGAAAATAAAATATATAAGATTATAATAAG
1 AAAT-AAAATAAAATATATAAAATTATAATAAG
* *
11212760 AAATAAAAATAAAATATATGACATTATAA
1 AAAT-AAAATAAAATATATAAAATTATAA
11212789 ATATATTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 44 0.80
34 5 0.09
35 6 0.11
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (32 bp):
AAATAAAATAAAATATATAAAATTATAATAAG
Found at i:11213025 original size:15 final size:15
Alignment explanation
Indices: 11212969--11213024 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
11212959 ATTTTCCCTA
11212969 TAATTATATTACTTG
1 TAATTATATTACTTG
* *
11212984 CAATTACATTACTTG
1 TAATTATATTACTTG
11212999 TAATTATATTA-TCTG
1 TAATTATATTACT-TG
11213014 TAATTATATTA
1 TAATTATATTA
11213025 TATTGTAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
14 1 0.03
15 35 0.97
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (15 bp):
TAATTATATTACTTG
Found at i:11218412 original size:20 final size:21
Alignment explanation
Indices: 11218377--11218419 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
11218367 CAGTTGTTAT
*
11218377 TTCTATAGAAGATGTTCTTAC
1 TTCTATAGAAGATGTTCTCAC
*
11218398 TTCTATAG-GGATGTTCTCAC
1 TTCTATAGAAGATGTTCTCAC
11218418 TT
1 TT
11218420 TCTAATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.44
Consensus pattern (21 bp):
TTCTATAGAAGATGTTCTCAC
Found at i:11218422 original size:21 final size:22
Alignment explanation
Indices: 11218376--11218423 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
11218366 CCAGTTGTTA
*
11218376 TTTCTATAGAAGATGTTCTTAC
1 TTTCTATAGAAGATGTTCTCAC
*
11218398 -TTCTATAG-GGATGTTCTCAC
1 TTTCTATAGAAGATGTTCTCAC
11218418 TTTCTA
1 TTTCTA
11218424 ATCTTTCCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.46
Consensus pattern (22 bp):
TTTCTATAGAAGATGTTCTCAC
Found at i:11221350 original size:30 final size:32
Alignment explanation
Indices: 11221314--11221374 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
11221304 CATAGCGTGT
*
11221314 AATATA-TTTTTAT-ATATGACGTGTAACAAC
1 AATATATTTTTTATAACATGACGTGTAACAAC
*
11221344 AATATATTTTTTTTAACATGACGTGTAACAA
1 AATATATTTTTTATAACATGACGTGTAACAA
11221375 TAGTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 6 0.22
31 6 0.22
32 15 0.56
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (32 bp):
AATATATTTTTTATAACATGACGTGTAACAAC
Found at i:11222155 original size:27 final size:29
Alignment explanation
Indices: 11222124--11222178 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
11222114 AAACACTATA
*
11222124 AACATGACATGTAATAA-TTTTT-TTTTC
1 AACATAACATGTAATAACTTTTTCTTTTC
* *
11222151 AACATAACGTGTGATAACTTTTTCTTTT
1 AACATAACATGTAATAACTTTTTCTTTT
11222179 TCATATGACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 14 0.61
28 5 0.22
29 4 0.17
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (29 bp):
AACATAACATGTAATAACTTTTTCTTTTC
Found at i:11227361 original size:31 final size:31
Alignment explanation
Indices: 11227323--11227382 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
11227313 TTGGATTGCT
* *
11227323 TTGAATTCGAATGGCGTATATAGGCCCTCCA
1 TTGAATTCAAATGGCATATATAGGCCCTCCA
11227354 TTGAATTCAAATGGCATATATAGGCCCTC
1 TTGAATTCAAATGGCATATATAGGCCCTC
11227383 AATGGAAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (31 bp):
TTGAATTCAAATGGCATATATAGGCCCTCCA
Found at i:11233526 original size:17 final size:17
Alignment explanation
Indices: 11233504--11233541 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
11233494 TTGAATAGCA
*
11233504 CCAAACATGTAGTCTTT
1 CCAAACATGCAGTCTTT
11233521 CCAAACATGCAGTCTTT
1 CCAAACATGCAGTCTTT
11233538 CCAA
1 CCAA
11233542 CACAAGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (17 bp):
CCAAACATGCAGTCTTT
Found at i:11234172 original size:30 final size:30
Alignment explanation
Indices: 11234136--11234197 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
11234126 AAACAAAAGC
11234136 TTCAGAATTGAACAAAAAGAGGAGACTGAT
1 TTCAGAATTGAACAAAAAGAGGAGACTGAT
11234166 TTCAGAATTGAACAAAAAGAGGAGACTGAT
1 TTCAGAATTGAACAAAAAGAGGAGACTGAT
11234196 TT
1 TT
11234198 TCGGGGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.23
Consensus pattern (30 bp):
TTCAGAATTGAACAAAAAGAGGAGACTGAT
Found at i:11243310 original size:18 final size:19
Alignment explanation
Indices: 11243289--11243331 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
11243279 CGCCAAACAC
11243289 TTTATTCTTTT-TTATTTT
1 TTTATTCTTTTCTTATTTT
* *
11243307 TTTATCCTTTTCTTTTTTT
1 TTTATTCTTTTCTTATTTT
11243326 TTTATT
1 TTTATT
11243332 TATTCACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTATTCTTTTCTTATTTT
Found at i:11243323 original size:17 final size:18
Alignment explanation
Indices: 11243289--11243326 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
11243279 CGCCAAACAC
* *
11243289 TTTATTCTTTTTTATTTT
1 TTTATCCTTTTCTATTTT
11243307 TTTATCCTTTTCT-TTTT
1 TTTATCCTTTTCTATTTT
11243324 TTT
1 TTT
11243327 TTATTTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTATCCTTTTCTATTTT
Found at i:11250690 original size:2 final size:2
Alignment explanation
Indices: 11250683--11250718 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
11250673 CATCTAAAGG
*
11250683 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11250719 CATTCTCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11253958 original size:2 final size:2
Alignment explanation
Indices: 11253951--11253977 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11253941 TTGATCACCG
11253951 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11253978 GTTTTGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11275454 original size:128 final size:129
Alignment explanation
Indices: 11275210--11275467 Score: 419
Period size: 128 Copynumber: 2.0 Consensus size: 129
11275200 ATAAAGCAAA
* * * *
11275210 ACTACTGGCTGTGAAGGAAGCTTTTGCCTTTTATGCAACATCTTGGTGGGTAAATACACATAAAA
1 ACTACTGGCTGTGAAGGAAGCTTTTACCTTTTATGCAACATCTCGATGGGCAAATACACATAAAA
* *
11275275 TTGATTGTTGAAAGTGACTCATGTAATGAGGTTAAATGGGTGCATGATTCTAGTAGTGTTCCTT
66 TTGATTGTTGAAAGTGACTCATGTAATGAGATTAAATGGGTGCATGATTCTAGTAATGTTCCTT
* * *
11275339 ACTACTGGTTGTGAAGGACGCTTTTATCTTTTATGCAACATCTCGATGGGCAAATACACAT-AAA
1 ACTACTGGCTGTGAAGGAAGCTTTTACCTTTTATGCAACATCTCGATGGGCAAATACACATAAAA
*
11275403 TTGATTGTTGAAAGTGACTCATGTAATGTGATTAAATGGGTGCATGATTCTAGTAATGTTCCTT
66 TTGATTGTTGAAAGTGACTCATGTAATGAGATTAAATGGGTGCATGATTCTAGTAATGTTCCTT
11275467 A
1 A
11275468 GAGAATGAGG
Statistics
Matches: 119, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
128 65 0.55
129 54 0.45
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (129 bp):
ACTACTGGCTGTGAAGGAAGCTTTTACCTTTTATGCAACATCTCGATGGGCAAATACACATAAAA
TTGATTGTTGAAAGTGACTCATGTAATGAGATTAAATGGGTGCATGATTCTAGTAATGTTCCTT
Found at i:11284451 original size:22 final size:22
Alignment explanation
Indices: 11284423--11284467 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
11284413 CCTTAGAGAA
*
11284423 GGATTTTTAGGTTCTTTGGGGT
1 GGATTTTCAGGTTCTTTGGGGT
11284445 GGATTTTCAGGTTCTTTGGGGT
1 GGATTTTCAGGTTCTTTGGGGT
11284467 G
1 G
11284468 AATCATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.07, G:0.38, T:0.47
Consensus pattern (22 bp):
GGATTTTCAGGTTCTTTGGGGT
Found at i:11290469 original size:4 final size:4
Alignment explanation
Indices: 11290460--11290499 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
11290450 CATCCCTGGT
11290460 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
11290500 CTGATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:11293107 original size:79 final size:83
Alignment explanation
Indices: 11292965--11293121 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 83
11292955 CTGTTCATCC
* * *
11292965 GGAATTTCAATTTTGCTGCAAAATTTTTTAATGAAATATATATAGATAATAAGATGGTTGTTATT
1 GGAATTTCAATTTTGCTGC-AAATTTTTTAATG-AAGACATATAGATAATAAGATAGTTGTTATT
11293030 ATCATGTTATACAGTTGGCA
64 ATCATGTTATACAGTTGGCA
11293050 GGAATTTCAATTTTGCTGC-AATTTTTTAATG-AGACATA-A-ATAATAAG-TCAGTTGTTATTA
1 GGAATTTCAATTTTGCTGCAAATTTTTTAATGAAGACATATAGATAATAAGAT-AGTTGTTATTA
11293110 TCATGTTATACA
65 TCATGTTATACA
11293122 TGTGTGTGTT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
78 1 0.01
79 30 0.44
80 1 0.01
81 5 0.07
83 12 0.18
85 19 0.28
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.41
Consensus pattern (83 bp):
GGAATTTCAATTTTGCTGCAAATTTTTTAATGAAGACATATAGATAATAAGATAGTTGTTATTAT
CATGTTATACAGTTGGCA
Found at i:11303271 original size:2 final size:2
Alignment explanation
Indices: 11303264--11303295 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11303254 ACGAAACTAC
11303264 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
11303296 GACAAAGATT
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:11317692 original size:28 final size:29
Alignment explanation
Indices: 11317623--11317692 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
11317613 TGAGGCATAA
11317623 CGTGTAACAATAATGATATTATATGTATGGT
1 CGTGTAACAA-AATGATATTATA-GTATGGT
*
11317654 -GTGTAACAAAATAGTTATTATA-TA-GGT
1 CGTGTAACAAAAT-GATATTATAGTATGGT
11317681 CGTGTAACAAAA
1 CGTGTAACAAAA
11317693 GAAATATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 13 0.36
29 3 0.08
30 17 0.47
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (29 bp):
CGTGTAACAAAATGATATTATAGTATGGT
Found at i:11318850 original size:28 final size:28
Alignment explanation
Indices: 11318783--11318843 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
11318773 TTACATAAGG
* *
11318783 CATGTAGCAATTTAGTGATGATGCATGA
1 CATGTAGCAACTTAGTGATGACGCATGA
11318811 CATGTAGCAACTTAGTGATGACGCATGA
1 CATGTAGCAACTTAGTGATGACGCATGA
11318839 CATGT
1 CATGT
11318844 TTTAACTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (28 bp):
CATGTAGCAACTTAGTGATGACGCATGA
Found at i:11320450 original size:2 final size:2
Alignment explanation
Indices: 11320445--11320475 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11320435 TTAAAAATAC
11320445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11320476 GGCATGGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11325308 original size:31 final size:31
Alignment explanation
Indices: 11325248--11325308 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
11325238 TGGAAAAACG
* *
11325248 TTACTTCAACCTTTCAACTTCTTATATGAAC
1 TTACTTCAACCTATCAACTTCTCATATGAAC
11325279 TTACTTCAACCCTATCAACTTCTCA-ATGAA
1 TTACTTCAA-CCTATCAACTTCTCATATGAA
11325309 ACCCTTGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (31 bp):
TTACTTCAACCTATCAACTTCTCATATGAAC
Found at i:11339473 original size:24 final size:24
Alignment explanation
Indices: 11339428--11339475 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
11339418 AGATAGAGAA
*
11339428 AATAAATAAAATATGTTTTAATTG
1 AATAAATAAAATAAGTTTTAATTG
*
11339452 AATAAAT-AATTAAGTTTATAATTG
1 AATAAATAAAATAAGTTT-TAATTG
11339476 TACTGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (24 bp):
AATAAATAAAATAAGTTTTAATTG
Found at i:11342434 original size:14 final size:13
Alignment explanation
Indices: 11342408--11342445 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
11342398 GAGTGAGTGA
*
11342408 GAAGGGAAAGGGG
1 GAAGGGGAAGGGG
11342421 GAAGGAGGAAGGGG
1 GAAGG-GGAAGGGG
11342435 GAAGGGGAAGG
1 GAAGGGGAAGG
11342446 TGCAGCCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (13 bp):
GAAGGGGAAGGGG
Found at i:11342607 original size:25 final size:26
Alignment explanation
Indices: 11342572--11342631 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
11342562 AACTTTTTTC
* *
11342572 TTTTTTAATTTTCTTTGGTAAA-CTT
1 TTTTTTTATTTTCTTTGCTAAATCTT
* *
11342597 TTTTTTTATTTTGTTTTCTAAATTCTT
1 TTTTTTTATTTTCTTTGCTAAA-TCTT
11342624 TTTTTTTA
1 TTTTTTTA
11342632 ATTCCTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 18 0.62
27 11 0.38
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTTTTTATTTTCTTTGCTAAATCTT
Found at i:11344309 original size:7 final size:7
Alignment explanation
Indices: 11344299--11344327 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
11344289 GTTAAAAGTA
11344299 GTCACTG
1 GTCACTG
11344306 GTCACTG
1 GTCACTG
11344313 GTCACTG
1 GTCACTG
11344320 GTCACTG
1 GTCACTG
11344327 G
1 G
11344328 ATTAAGCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (7 bp):
GTCACTG
Found at i:11351485 original size:18 final size:20
Alignment explanation
Indices: 11351450--11351486 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
11351440 TATGAAATAA
*
11351450 TACTTGAAAAAAGCTTTAAT
1 TACTTGAAAAAAGATTTAAT
11351470 TACTT-AAAAAA-ATTTAA
1 TACTTGAAAAAAGATTTAA
11351487 ATAAATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (20 bp):
TACTTGAAAAAAGATTTAAT
Found at i:11359632 original size:30 final size:30
Alignment explanation
Indices: 11359592--11359657 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
11359582 TTAAAAATAT
*
11359592 TTTTTAT-TTTTTA-TTT-AGTTAAATTAAA
1 TTTTTATATTTTTATTTTAAATTAAA-TAAA
11359620 TTTTTATATTTTTATTTTAAATTAAATAAA
1 TTTTTATATTTTTATTTTAAATTAAATAAA
11359650 TTTTTATA
1 TTTTTATA
11359658 ACTACCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.21
29 6 0.18
30 15 0.44
31 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (30 bp):
TTTTTATATTTTTATTTTAAATTAAATAAA
Found at i:11376159 original size:42 final size:42
Alignment explanation
Indices: 11376113--11376291 Score: 268
Period size: 42 Copynumber: 4.3 Consensus size: 42
11376103 CAAAGAAAAC
* *
11376113 CGAGAATGTGGCAGAGAGAGATGAGGGTGTGGCAGAAATAGA
1 CGAGAATGTGGCAGAGAGAGACGAGGGTGTGGCAGAAACAGA
*
11376155 CGAGAATGTGGCAGAGAGACACGAGGGTGTGGCAGAAACAGA
1 CGAGAATGTGGCAGAGAGAGACGAGGGTGTGGCAGAAACAGA
* ***
11376197 CCAGAATGTGGCAGATTTAGACGAGGGTGTGGCAGAAACAGA
1 CGAGAATGTGGCAGAGAGAGACGAGGGTGTGGCAGAAACAGA
* *
11376239 CGAGAACGTGGTAGAGAGAGACGAGGGTGTGGCAGAAACAGA
1 CGAGAATGTGGCAGAGAGAGACGAGGGTGTGGCAGAAACAGA
*
11376281 CCAGAATGTGG
1 CGAGAATGTGG
11376292 TAGAATTGGA
Statistics
Matches: 121, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 121 1.00
ACGTcount: A:0.35, C:0.12, G:0.40, T:0.13
Consensus pattern (42 bp):
CGAGAATGTGGCAGAGAGAGACGAGGGTGTGGCAGAAACAGA
Found at i:11376290 original size:21 final size:21
Alignment explanation
Indices: 11376113--11376296 Score: 143
Period size: 21 Copynumber: 8.8 Consensus size: 21
11376103 CAAAGAAAAC
* *
11376113 CGAGAATGTGGCAGAGAGAGA
1 CGAGAATGTGGCAGAAACAGA
* ** *
11376134 TGAGGGTGTGGCAGAAATAGA
1 CGAGAATGTGGCAGAAACAGA
* * *
11376155 CGAGAATGTGGCAGAGAGACA
1 CGAGAATGTGGCAGAAACAGA
**
11376176 CGAGGGTGTGGCAGAAACAGA
1 CGAGAATGTGGCAGAAACAGA
* ***
11376197 CCAGAATGTGGCAGATTTAGA
1 CGAGAATGTGGCAGAAACAGA
**
11376218 CGAGGGTGTGGCAGAAACAGA
1 CGAGAATGTGGCAGAAACAGA
* * * *
11376239 CGAGAACGTGGTAGAGAGAGA
1 CGAGAATGTGGCAGAAACAGA
**
11376260 CGAGGGTGTGGCAGAAACAGA
1 CGAGAATGTGGCAGAAACAGA
* *
11376281 CCAGAATGTGGTAGAA
1 CGAGAATGTGGCAGAA
11376297 TTGGACGAGA
Statistics
Matches: 119, Mismatches: 44, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 119 1.00
ACGTcount: A:0.35, C:0.12, G:0.40, T:0.13
Consensus pattern (21 bp):
CGAGAATGTGGCAGAAACAGA
Found at i:11376944 original size:81 final size:81
Alignment explanation
Indices: 11376801--11376950 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 81
11376791 AATGGACCTT
* * *
11376801 CTCTCACGCCATACATCTGATGAGGAATTCTTGGGCCAAAGGCCACCGGACAACATGTGGAAAGA
1 CTCTCACGCCATACATCTGATGAGGAATGCTTGGACCAAAGGCCACCGGACAACATGAGGAAAGA
11376866 GAATAAACATGACTAC
66 GAATAAACATGACTAC
* *** * *
11376882 CTCTCACGCCGTACATCTGATGATTCATGCTTGGACCAAAGGCCACCGGACCAGATGAGGAAAGA
1 CTCTCACGCCATACATCTGATGAGGAATGCTTGGACCAAAGGCCACCGGACAACATGAGGAAAGA
11376947 GAAT
66 GAAT
11376951 GAAGAGGTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 60 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (81 bp):
CTCTCACGCCATACATCTGATGAGGAATGCTTGGACCAAAGGCCACCGGACAACATGAGGAAAGA
GAATAAACATGACTAC
Found at i:11380459 original size:3 final size:3
Alignment explanation
Indices: 11380453--11380492 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
11380443 AAAAGAAATG
11380453 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11380493 GTTGTTGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11386787 original size:27 final size:27
Alignment explanation
Indices: 11386660--11386791 Score: 176
Period size: 27 Copynumber: 4.9 Consensus size: 27
11386650 TCTTTGGGTT
* **
11386660 CTTCTGCGCTTGGAACGTCCC-AAGGCG
1 CTTCTGCGCTTGGAAC-ACCCTTGGGCG
*
11386687 CTTCTGCGCTTGGAACACCTTTGGGCG
1 CTTCTGCGCTTGGAACACCCTTGGGCG
*
11386714 CTTCTGCGCTTGGAACACCTTTGGGCG
1 CTTCTGCGCTTGGAACACCCTTGGGCG
* *
11386741 CTTCTGTGCGTGGAACACCCTTGGGCG
1 CTTCTGCGCTTGGAACACCCTTGGGCG
*
11386768 CTTCTGTGCTTGGAACACCCTTGG
1 CTTCTGCGCTTGGAACACCCTTGG
11386792 TGCTTCCATG
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
26 2 0.02
27 94 0.98
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (27 bp):
CTTCTGCGCTTGGAACACCCTTGGGCG
Found at i:11386975 original size:27 final size:27
Alignment explanation
Indices: 11386933--11387011 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
11386923 GGTATTTCTG
11386933 CACTTGGAAC-GCCCCTGGGCGCTTCCA
1 CACTTGGAACAG-CCCTGGGCGCTTCCA
* * * *
11386960 TACTTGGAATAGCCCTGAGTGCTTCCA
1 CACTTGGAACAGCCCTGGGCGCTTCCA
* * *
11386987 CGCTTGGAACATCCCTGGACGCTTC
1 CACTTGGAACAGCCCTGGGCGCTTC
11387012 TGCGTTTAGA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.24
Consensus pattern (27 bp):
CACTTGGAACAGCCCTGGGCGCTTCCA
Found at i:11387079 original size:27 final size:26
Alignment explanation
Indices: 11387020--11387079 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
11387010 TCTGCGTTTA
*
11387020 GAACA-CCTTAGGCGCTTCCAACTTG
1 GAACACCCTTAGGCACTTCCAACTTG
* *
11387045 AAATACCCTTAGGCACTTCCATACTTG
1 GAACACCCTTAGGCACTTCCA-ACTTG
11387072 GAACACCC
1 GAACACCC
11387080 AGGTGGGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 3 0.11
26 14 0.50
27 11 0.39
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.23
Consensus pattern (26 bp):
GAACACCCTTAGGCACTTCCAACTTG
Found at i:11394030 original size:200 final size:199
Alignment explanation
Indices: 11393673--11394075 Score: 626
Period size: 200 Copynumber: 2.0 Consensus size: 199
11393663 AGGACACAGC
* *
11393673 AATACACATGGATTTAGAATTTCATAATATTAACATAAATATTTAATATAACAATGTAACAGTCA
1 AATACACATGGATTTAGAATTCCATAATATTAACATAAATATTTAAAATAACAATGTAACAGTCA
* *
11393738 TCTGCTTCGAAATAAATCTCAGACAGCAAGTTATGAAAAGAAAGGTTTCTTCACCAAAATACAAA
66 TCTGCTTCGAAATAAATCTCAGACAGCAAGTTATGAAAAGAAAAGTTCCTTCACCAAAATACAAA
* * ** *
11393803 GAGCCTTCTCATTTTACAAGGTATCTAATTATATTAAGTTTAATCTGATTCATGTCTATCCAAGC
131 GAGCCCTCTCATTTTACAAGGTATCTAATTATATTAAGCTTAATCCCATTCATGTCTATACAAGC
11393868 ATCA
196 ATCA
* * * *
11393872 AATACATATGGATTTAGAATTCCATAATATTAACATAAATATTTAAAAATAACAATTTAGCATTC
1 AATACACATGGATTTAGAATTCCATAATATTAACATAAATATTT-AAAATAACAATGTAACAGTC
* *
11393937 ATCTGCTTTGAAATAAATCTCAGACAGCAAGTTATGGAAAGAAAAGTTCCTTCACCAAAATACAA
65 ATCTGCTTCGAAATAAATCTCAGACAGCAAGTTATGAAAAGAAAAGTTCCTTCACCAAAATACAA
* * * *
11394002 AGAGCCCTCTCATTTTGCTAGTTATCTAATTATATTAAGCTTAATCCCATTCATGTCTATACATG
130 AGAGCCCTCTCATTTTACAAGGTATCTAATTATATTAAGCTTAATCCCATTCATGTCTATACAAG
11394067 CATCA
195 CATCA
11394072 AATA
1 AATA
11394076 AGCATAGACA
Statistics
Matches: 184, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
199 42 0.23
200 142 0.77
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (199 bp):
AATACACATGGATTTAGAATTCCATAATATTAACATAAATATTTAAAATAACAATGTAACAGTCA
TCTGCTTCGAAATAAATCTCAGACAGCAAGTTATGAAAAGAAAAGTTCCTTCACCAAAATACAAA
GAGCCCTCTCATTTTACAAGGTATCTAATTATATTAAGCTTAATCCCATTCATGTCTATACAAGC
ATCA
Found at i:11398461 original size:25 final size:26
Alignment explanation
Indices: 11398408--11398463 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
11398398 TATCATCATC
11398408 TATTATCACTTATCAACATGTCACAA
1 TATTATCACTTATCAACATGTCACAA
11398434 TATTATCTA-TTAT-AACATGTCA-ATA
1 TATTATC-ACTTATCAACATGTCACA-A
11398459 TATTA
1 TATTA
11398464 CGTAGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 1 0.04
25 15 0.54
26 11 0.39
27 1 0.04
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (26 bp):
TATTATCACTTATCAACATGTCACAA
Found at i:11398472 original size:25 final size:25
Alignment explanation
Indices: 11398422--11398473 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
11398412 ATCACTTATC
*
11398422 AACATGTCACAATATTATCTATTAT
1 AACATGTCACAATATTATCTAGTAT
11398447 AACATGTCA-ATATATTA-CGTAGTAT
1 AACATGTCACA-ATATTATC-TAGTAT
11398472 AA
1 AA
11398474 AATGATAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (25 bp):
AACATGTCACAATATTATCTAGTAT
Found at i:11399994 original size:16 final size:16
Alignment explanation
Indices: 11399975--11400012 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
11399965 ATGGATGGAG
11399975 AAATTAAAAATTAAAA
1 AAATTAAAAATTAAAA
* *
11399991 AAATT-AAAATTGAAT
1 AAATTAAAAATTAAAA
11400006 AAATTAA
1 AAATTAA
11400013 TGATATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATTAAAAATTAAAA
Found at i:11405825 original size:28 final size:29
Alignment explanation
Indices: 11405770--11405835 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
11405760 ATTATTTAAG
*
11405770 TAAATTTTTATTTTTTTATTACGTTCAAT
1 TAAATTTTTATTTTTTTATTACGATCAAT
* *
11405799 TCAATTTTTATTTTTATT-TT-TGATCAAT
1 TAAATTTTTATTTTT-TTATTACGATCAAT
11405827 TAAATTTTT
1 TAAATTTTT
11405836 GTTACTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 14 0.44
29 16 0.50
30 2 0.06
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (29 bp):
TAAATTTTTATTTTTTTATTACGATCAAT
Found at i:11407936 original size:29 final size:28
Alignment explanation
Indices: 11407902--11407976 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 28
11407892 ATGGTCAATC
*
11407902 ATAAAAATTTATTTAATTTAA-AATAAAA
1 ATAAAAATTTATTTAATATAATAA-AAAA
*
11407930 ATAAAAAACTTTCATTAAATATAATAAAAAA
1 AT-AAAAA-TTT-ATTTAATATAATAAAAAA
11407961 ATAAAAATTTATTTAA
1 ATAAAAATTTATTTAA
11407977 ATTCTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 7 0.17
29 8 0.20
30 8 0.20
31 15 0.38
32 2 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
ATAAAAATTTATTTAATATAATAAAAAA
Found at i:11407977 original size:29 final size:29
Alignment explanation
Indices: 11407902--11407978 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 29
11407892 ATGGTCAATC
*
11407902 ATAAAAATTTATTT-AATTTAAAATAAAA
1 ATAAAAATTTATTTAAATATAAAATAAAA
11407930 ATAAAAAACTTTCA-TTAAATATAATAA-AAAA
1 AT-AAAAA-TTT-ATTTAAATATAA-AATAAAA
11407961 ATAAAAATTTATTTAAAT
1 ATAAAAATTTATTTAAAT
11407979 TCTTTTAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
28 3 0.07
29 14 0.33
30 10 0.24
31 13 0.31
32 2 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (29 bp):
ATAAAAATTTATTTAAATATAAAATAAAA
Found at i:11417072 original size:134 final size:134
Alignment explanation
Indices: 11416832--11417101 Score: 540
Period size: 134 Copynumber: 2.0 Consensus size: 134
11416822 GAGACTCATG
11416832 ATCTAATTGGGAAGGATCATGGAAGTTAATTAGGCTAAAAAAAGTCTCCTGCCAATGGAAATGGC
1 ATCTAATTGGGAAGGATCATGGAAGTTAATTAGGCTAAAAAAAGTCTCCTGCCAATGGAAATGGC
11416897 TAAAGACTTGTGTTCGTTTTATACTCCATGATGTCTTATTAATATATGAAATACTTGCTTTTCAT
66 TAAAGACTTGTGTTCGTTTTATACTCCATGATGTCTTATTAATATATGAAATACTTGCTTTTCAT
11416962 ATAT
131 ATAT
11416966 ATCTAATTGGGAAGGATCATGGAAGTTAATTAGGCTAAAAAAAGTCTCCTGCCAATGGAAATGGC
1 ATCTAATTGGGAAGGATCATGGAAGTTAATTAGGCTAAAAAAAGTCTCCTGCCAATGGAAATGGC
11417031 TAAAGACTTGTGTTCGTTTTATACTCCATGATGTCTTATTAATATATGAAATACTTGCTTTTCAT
66 TAAAGACTTGTGTTCGTTTTATACTCCATGATGTCTTATTAATATATGAAATACTTGCTTTTCAT
11417096 ATAT
131 ATAT
11417100 AT
1 AT
11417102 ATATATATAT
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 136 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (134 bp):
ATCTAATTGGGAAGGATCATGGAAGTTAATTAGGCTAAAAAAAGTCTCCTGCCAATGGAAATGGC
TAAAGACTTGTGTTCGTTTTATACTCCATGATGTCTTATTAATATATGAAATACTTGCTTTTCAT
ATAT
Found at i:11417101 original size:2 final size:2
Alignment explanation
Indices: 11417094--11417134 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11417084 CTTGCTTTTC
11417094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11417135 ATGATCTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11417639 original size:3 final size:3
Alignment explanation
Indices: 11417627--11417655 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
11417617 ATACTTCATC
11417627 AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
11417656 GTTGTTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:11419290 original size:2 final size:2
Alignment explanation
Indices: 11419283--11419314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11419273 TAAGAATAAC
11419283 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
11419315 CAATTACTCA
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:11420971 original size:5 final size:5
Alignment explanation
Indices: 11420961--11421012 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
11420951 CAGACTGTAC
11420961 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG
1 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG
11421011 GG
1 GG
11421013 TGTCATCATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (5 bp):
GGAAG
Found at i:11427937 original size:155 final size:155
Alignment explanation
Indices: 11427655--11427963 Score: 467
Period size: 155 Copynumber: 2.0 Consensus size: 155
11427645 GAAGCTATGG
* * *
11427655 ATGCTGAAATCAAAATGATTAAGAAGGATGGTACTTGGATTATTACAGATAGGCTTGAAAATCAA
1 ATGCTAAAATCAAAATGATTAAGAAGAATGGTACTTGGATCATTACAGATAGGCTTGAAAATCAA
*
11427720 AAGGTGATAGGCGTCAAGTGCATATTCAAAACAAAATTAAATCTTGATGGTTCAGAGAACAAATA
66 AAGGTGATAGGCGTCAAGTGCATATTCAAAACAAAATTAAATCTTAATGGTTCAGAGAACAAATA
* *
11427785 TAAAG-CAGATTAATGATGAAAAGGA
131 CAAAGCCAGATTAATAAT-AAAAGGA
* * *
11427810 ATGCTAAAATCAATATGATTAAGAATAATGGTACTTGGATCATTACTGATAGGCTTGAAAATCAA
1 ATGCTAAAATCAAAATGATTAAGAAGAATGGTACTTGGATCATTACAGATAGGCTTGAAAATCAA
* * * * * *
11427875 AATGTGATAGGTGTTAAGTGGATATTCGAAACAAAATTAAATCTTAATGGTTCAGTGAACAAATA
66 AAGGTGATAGGCGTCAAGTGCATATTCAAAACAAAATTAAATCTTAATGGTTCAGAGAACAAATA
11427940 CAAAGCCAGATTAATAATAAAAGG
131 CAAAGCCAGATTAATAATAAAAGG
11427964 GTATGCTTAA
Statistics
Matches: 138, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
155 127 0.92
156 11 0.08
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.27
Consensus pattern (155 bp):
ATGCTAAAATCAAAATGATTAAGAAGAATGGTACTTGGATCATTACAGATAGGCTTGAAAATCAA
AAGGTGATAGGCGTCAAGTGCATATTCAAAACAAAATTAAATCTTAATGGTTCAGAGAACAAATA
CAAAGCCAGATTAATAATAAAAGGA
Found at i:11445750 original size:3 final size:3
Alignment explanation
Indices: 11445744--11445768 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11445734 TAACAATAGA
11445744 AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT A
11445769 AGAAAAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:11455469 original size:2 final size:2
Alignment explanation
Indices: 11455462--11455488 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11455452 CCAAATTTCA
11455462 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11455489 ATTTACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11459562 original size:2 final size:2
Alignment explanation
Indices: 11459555--11459586 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11459545 CCTGTTACTC
11459555 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11459587 GACTTTAACC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11470773 original size:2 final size:2
Alignment explanation
Indices: 11470768--11470792 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11470758 GTATGTGTAT
11470768 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
11470793 TGGATAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11479137 original size:2 final size:2
Alignment explanation
Indices: 11479132--11479158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11479122 AAAAGATATG
11479132 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
11479159 GGAGGGAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11486196 original size:17 final size:17
Alignment explanation
Indices: 11486174--11486206 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11486164 ATGACGAGGG
11486174 AGAAAAATGGAGAGCAT
1 AGAAAAATGGAGAGCAT
*
11486191 AGAAAAATGGGGAGCA
1 AGAAAAATGGAGAGCA
11486207 AAGCAGACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.33, T:0.09
Consensus pattern (17 bp):
AGAAAAATGGAGAGCAT
Found at i:11487513 original size:15 final size:15
Alignment explanation
Indices: 11487478--11487521 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11487468 ACTTTACAAT
* *
11487478 GCAATGTGATTACAG
1 GCAATGTGATTGCAA
*
11487493 GTAATGTGATTGCAA
1 GCAATGTGATTGCAA
*
11487508 GCAATGTTATTGCA
1 GCAATGTGATTGCA
11487522 TGGAAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (15 bp):
GCAATGTGATTGCAA
Found at i:11487809 original size:34 final size:33
Alignment explanation
Indices: 11487737--11487819 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 33
11487727 TTTTAATGTC
* *
11487737 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATATTTTATTTTCATTTATTAATATAATCTT
* *
11487770 ATATATTTTATTTTCATTTCTTTAATATAATTTT
1 ATATATTTTATTTTCATTT-ATTAATATAATCTT
*
11487804 TTATATTATATATTTT
1 ATATATT-T-TATTTT
11487820 AGTTTAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 18 0.43
34 17 0.40
35 1 0.02
36 6 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTATTAATATAATCTT
Found at i:11487846 original size:74 final size:73
Alignment explanation
Indices: 11487710--11487848 Score: 165
Period size: 74 Copynumber: 1.9 Consensus size: 73
11487700 TTATATAATA
* * * *
11487710 TCATCTCTTAAATATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATCTTATATA
1 TCATCTCTTAAATATATTTTTAATATCATATATTTTAGTTTAATTTATTATTATAATATTATATA
11487775 TTTTATTT
66 TTTTATTT
* * * *
11487783 TCATTTCTTTAATATAATTTTTTATATTATATATTTTAGTTTAATTTATT-TTACCT-ATATTAT
1 TCATCTCTTAAATAT-ATTTTTAATATCATATATTTTAGTTTAATTTATTATTA--TAATATTAT
11487846 ATA
63 ATA
11487849 AATTTTAGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
73 16 0.29
74 38 0.69
75 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.61
Consensus pattern (73 bp):
TCATCTCTTAAATATATTTTTAATATCATATATTTTAGTTTAATTTATTATTATAATATTATATA
TTTTATTT
Found at i:11488707 original size:21 final size:21
Alignment explanation
Indices: 11488673--11488725 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
11488663 AAAATATATA
* *
11488673 AAAATATAAATATTAATTTAT-
1 AAAATTTAATTATT-ATTTATC
*
11488694 AAAATTTAATTATTTTTTATC
1 AAAATTTAATTATTATTTATC
11488715 AAAATTTAATT
1 AAAATTTAATT
11488726 TTTTAATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTTAATTATTATTTATC
Found at i:11488729 original size:20 final size:20
Alignment explanation
Indices: 11488689--11488729 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
11488679 TAAATATTAA
11488689 TTTATAAAATTTAATTATTT
1 TTTATAAAATTTAATTATTT
11488709 TTTATCAAAATTTAATT-TTT
1 TTTAT-AAAATTTAATTATTT
11488729 T
1 T
11488730 AATTGTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATAAAATTTAATTATTT
Found at i:11489306 original size:15 final size:16
Alignment explanation
Indices: 11489278--11489307 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11489268 CGTGCATGTA
11489278 TTTATTTATTTTTATT
1 TTTATTTATTTTTATT
11489294 TTTATTT-TTTTTAT
1 TTTATTTATTTTTAT
11489308 ATTTGGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTATTTTTATT
Found at i:11491799 original size:28 final size:28
Alignment explanation
Indices: 11491761--11491815 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
11491751 TTAATGTAAA
11491761 GGGGTTCTTGTGAAAGAGGAACCATTAG
1 GGGGTTCTTGTGAAAGAGGAACCATTAG
* * *
11491789 GGGGTTCTTGTGGAAGAGTAAGCATTA
1 GGGGTTCTTGTGAAAGAGGAACCATTA
11491816 AGGTTGCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (28 bp):
GGGGTTCTTGTGAAAGAGGAACCATTAG
Done.