Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 132 of 204
Found at i:40305645 original size:29 final size:29
Alignment explanation
Indices: 40305609--40305678 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
40305599 CCCATTAACC
*
40305609 CCTAAACCCTTAACCCGTAACCCTTAAAT
1 CCTAAACCCTTAACCCCTAACCCTTAAAT
* *
40305638 CCTAAACCCCTAACCCCTAACCCTTATAT
1 CCTAAACCCTTAACCCCTAACCCTTAAAT
*
40305667 CCCAAA-CCTTAA
1 CCTAAACCCTTAA
40305679 ATCCATACCC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.34, C:0.41, G:0.01, T:0.23
Consensus pattern (29 bp):
CCTAAACCCTTAACCCCTAACCCTTAAAT
Found at i:40305674 original size:15 final size:14
Alignment explanation
Indices: 40305597--40305678 Score: 51
Period size: 14 Copynumber: 5.6 Consensus size: 14
40305587 CTAAATTATT
*
40305597 AACCCATTAACCCCTA
1 AACCC-TTAATCCC-A
*
40305613 AACCCTTAA-CCCGT
1 AACCCTTAATCCC-A
*
40305627 AACCCTTAAATCCTA
1 AACCCTT-AATCCCA
* * *
40305642 AACCCCTAACCCCT
1 AACCCTTAATCCCA
40305656 AACCCTTATATCCCA
1 AACCCTTA-ATCCCA
40305671 AA-CCTTAA
1 AACCCTTAA
40305679 ATCCATACCC
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
13 1 0.02
14 26 0.50
15 18 0.35
16 7 0.13
ACGTcount: A:0.35, C:0.41, G:0.01, T:0.22
Consensus pattern (14 bp):
AACCCTTAATCCCA
Found at i:40306950 original size:42 final size:41
Alignment explanation
Indices: 40306842--40306961 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 41
40306832 GCACTTTAAC
* ** * *
40306842 AAAACGCCACTAAAACCCTTAGAATTAGCGGCAG-TTACTAA
1 AAAACGCCGCTAAAACCCCAAGCATTAGCGGC-GCTTAATAA
** * * *
40306883 AAAACGCCGCTAAAAGTCTAAGCATTAGTGGTGCTTAATAA
1 AAAACGCCGCTAAAACCCCAAGCATTAGCGGCGCTTAATAA
*
40306924 AAAACGCCGCTAAAAACCCCGAGCATTAGCGGCGCTTA
1 AAAACGCCGCT-AAAACCCCAAGCATTAGCGGCGCTTA
40306962 CCTAAAACCG
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
40 1 0.02
41 42 0.67
42 20 0.32
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAACGCCGCTAAAACCCCAAGCATTAGCGGCGCTTAATAA
Found at i:40306978 original size:83 final size:82
Alignment explanation
Indices: 40306842--40306993 Score: 184
Period size: 83 Copynumber: 1.8 Consensus size: 82
40306832 GCACTTTAAC
** *
40306842 AAAACGCCACTAAAACCCTTAGAATTAGCGGCAGTTACTAAAAAACGCCGCTAAAAGTCTA-AGC
1 AAAACGCCACTAAAACCCCGAGAATTAGCGGCAGTTACTAAAAAACGCAGCTAAAAG-CTAGAGC
40306906 ATTAGTGGTGCTTAATAA
65 ATTAGTGGTGCTTAATAA
* * * *
40306924 AAAACGCCGCTAAAAACCCCGAGCATTAGCGGC-GCTTACCT-AAAACCGCAGCTAATAGCTAGA
1 AAAACGCCACT-AAAACCCCGAGAATTAGCGGCAG-TTA-CTAAAAAACGCAGCTAAAAGCTAGA
40306987 GCATTAG
63 GCATTAG
40306994 CAGCGCTACG
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
82 14 0.24
83 43 0.73
84 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (82 bp):
AAAACGCCACTAAAACCCCGAGAATTAGCGGCAGTTACTAAAAAACGCAGCTAAAAGCTAGAGCA
TTAGTGGTGCTTAATAA
Found at i:40307420 original size:15 final size:17
Alignment explanation
Indices: 40307400--40307432 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
40307390 TTGGTAGAGA
40307400 ATTGATTT-AT-TCGAG
1 ATTGATTTGATATCGAG
40307415 ATTGATTTGATATCGAG
1 ATTGATTTGATATCGAG
40307432 A
1 A
40307433 GAAAAAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (17 bp):
ATTGATTTGATATCGAG
Found at i:40310974 original size:28 final size:28
Alignment explanation
Indices: 40310938--40310991 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
40310928 TTTATCAACC
*
40310938 ATTTCTCCTTTTGACAGCTATCCAAATA
1 ATTTCTCCTTTTGACACCTATCCAAATA
*
40310966 ATTTTTCCTTTTGACACCTATCCAAA
1 ATTTCTCCTTTTGACACCTATCCAAA
40310992 AAACAAAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.41
Consensus pattern (28 bp):
ATTTCTCCTTTTGACACCTATCCAAATA
Found at i:40311015 original size:7 final size:7
Alignment explanation
Indices: 40311011--40311043 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
40311001 TATCTTTTTA
40311011 TTTTTCT
1 TTTTTCT
40311018 TTTTTCT
1 TTTTTCT
40311025 TTTTCTCT
1 TTTT-TCT
40311033 TTTTT-T
1 TTTTTCT
40311039 TTTTT
1 TTTTT
40311044 GAGATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:40311027 original size:13 final size:13
Alignment explanation
Indices: 40311003--40311041 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
40310993 AACAAAGCTA
40311003 TCTTTTTATTTTTC
1 TCTTTTT-TTTTTC
40311017 T-TTTTTCTTTTTC
1 TCTTTTT-TTTTTC
40311030 TCTTTTTTTTTT
1 TCTTTTTTTTTT
40311042 TTGAGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (13 bp):
TCTTTTTTTTTTC
Found at i:40311027 original size:19 final size:19
Alignment explanation
Indices: 40311003--40311041 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40310993 AACAAAGCTA
40311003 TCTTTTTAT-TTTTCTTTTT
1 TCTTTTTATCTTTT-TTTTT
*
40311022 TCTTTTTCTCTTTTTTTTT
1 TCTTTTTATCTTTTTTTTT
40311041 T
1 T
40311042 TTGAGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (19 bp):
TCTTTTTATCTTTTTTTTT
Found at i:40311968 original size:23 final size:22
Alignment explanation
Indices: 40311930--40311972 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
40311920 GATTGATTAT
40311930 GTTAAATTTTAATATAATTAACC
1 GTTAAATTTTAATAT-ATTAACC
**
40311953 GTTAAATTTTTTTATATTAA
1 GTTAAATTTTAATATATTAA
40311973 TAATTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
GTTAAATTTTAATATATTAACC
Found at i:40312275 original size:34 final size:36
Alignment explanation
Indices: 40312230--40312299 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
40312220 TATTAAAAAC
40312230 AAAAAACAATA-TTTTTTGTCTTTTAGTGAATTCGG
1 AAAAAACAATATTTTTTTGTCTTTTAGTGAATTCGG
40312265 AAAAAA-AATATTTTTTTGTCTTTTAGTGAATTCGG
1 AAAAAACAATATTTTTTTGTCTTTTAGTGAATTCGG
40312300 GCCACGCCCG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.44
Consensus pattern (36 bp):
AAAAAACAATATTTTTTTGTCTTTTAGTGAATTCGG
Found at i:40313948 original size:15 final size:15
Alignment explanation
Indices: 40313928--40313958 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40313918 TTCGTACTCC
*
40313928 ACCGTTTGAGGTGTT
1 ACCGTTTGAAGTGTT
40313943 ACCGTTTGAAGTGTT
1 ACCGTTTGAAGTGTT
40313958 A
1 A
40313959 TTCTGGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (15 bp):
ACCGTTTGAAGTGTT
Found at i:40320536 original size:27 final size:27
Alignment explanation
Indices: 40320463--40320574 Score: 125
Period size: 27 Copynumber: 4.0 Consensus size: 27
40320453 GACGACCATG
40320463 TGCCCCTATTTTTCAGATTTTACAATTT
1 TGCCCCTATTTTT-AGATTTTACAATTT
* ** * *
40320491 TACCTATTATTTTTAGATTTTATACTTT
1 TGCC-CCTATTTTTAGATTTTACAATTT
40320519 TGCCCCTATTTTTAGATTTTACAATTT
1 TGCCCCTATTTTTAGATTTTACAATTT
* *
40320546 TTCCCCTATTTTTTAGTTTTTTACAATTT
1 TGCCCCTA-TTTTTAG-ATTTTACAATTT
40320575 GGACCTTATT
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
27 26 0.38
28 25 0.36
29 18 0.26
ACGTcount: A:0.21, C:0.17, G:0.05, T:0.56
Consensus pattern (27 bp):
TGCCCCTATTTTTAGATTTTACAATTT
Found at i:40321985 original size:23 final size:23
Alignment explanation
Indices: 40321941--40321985 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40321931 TCATGGAATT
* *
40321941 TTCTAAAATTAGACTAATTTTTC
1 TTCTAAAATTAAACAAATTTTTC
40321964 TTCTAAAA-TAAACAAATGTTTT
1 TTCTAAAATTAAACAAAT-TTTT
40321986 AAATCGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (23 bp):
TTCTAAAATTAAACAAATTTTTC
Found at i:40326819 original size:18 final size:18
Alignment explanation
Indices: 40326791--40326831 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40326781 TGGCTCGTAC
*
40326791 GAAAT-AATAGTTTACAT
1 GAAATAAATAGTTCACAT
40326808 GAAATAAATAGTTCACAT
1 GAAATAAATAGTTCACAT
*
40326826 AAAATA
1 GAAATA
40326832 GGCAATTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (18 bp):
GAAATAAATAGTTCACAT
Found at i:40327730 original size:17 final size:17
Alignment explanation
Indices: 40327678--40327740 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
40327668 TCACAGATGA
*
40327678 TATGAGTTCGCACATGCAG
1 TATGGGTTCGCACATG--G
* *
40327697 TATGGGTTCACATATGG
1 TATGGGTTCGCACATGG
40327714 TATGGGTTCGCACATGGG
1 TATGGGTTCGCACAT-GG
*
40327732 TAGGGGTTC
1 TATGGGTTC
40327741 TTACATGTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.38
18 10 0.27
19 13 0.35
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (17 bp):
TATGGGTTCGCACATGG
Found at i:40327754 original size:19 final size:19
Alignment explanation
Indices: 40327683--40327754 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 19
40327673 GATGATATGA
** *
40327683 GTTCGCACATGCAGTATGG
1 GTTCGCACATGTGGTAGGG
* *
40327702 GTT--CACATATGGTATGG
1 GTTCGCACATGTGGTAGGG
40327719 GTTCGCACATG-GGTAGGG
1 GTTCGCACATGTGGTAGGG
**
40327737 GTTCTTACATGTGGTAGG
1 GTTCGCACATGTGGTAGG
40327755 CTCGCATACA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
17 14 0.33
18 15 0.35
19 14 0.33
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.31
Consensus pattern (19 bp):
GTTCGCACATGTGGTAGGG
Found at i:40328010 original size:24 final size:24
Alignment explanation
Indices: 40327978--40328032 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
40327968 CTCATACATG
* *
40327978 AGGGCTCACATACCTTAAGGTAAT
1 AGGGTTCACATAACTTAAGGTAAT
* *
40328002 AGGGTTCACATAACTTCAGGTGAT
1 AGGGTTCACATAACTTAAGGTAAT
40328026 AGGGTTC
1 AGGGTTC
40328033 GAATATGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (24 bp):
AGGGTTCACATAACTTAAGGTAAT
Found at i:40330114 original size:40 final size:40
Alignment explanation
Indices: 40330025--40330117 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
40330015 ACCTAAATAT
* *
40330025 CAGGCTTTGTGTCGGTGTATTTATCGGGATTTGTGCCAAC
1 CAGGCTTTGTGCCGGTGTATTTATCAGGATTTGTGCCAAC
* * * *
40330065 CAAGCTTTGTGCCGGTGTATTTATCAGGCTTTGTGCCTAG
1 CAGGCTTTGTGCCGGTGTATTTATCAGGATTTGTGCCAAC
*
40330105 CAGGGTTTGTGCC
1 CAGGCTTTGTGCC
40330118 CATGTTGTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.14, C:0.19, G:0.30, T:0.37
Consensus pattern (40 bp):
CAGGCTTTGTGCCGGTGTATTTATCAGGATTTGTGCCAAC
Found at i:40348737 original size:2 final size:2
Alignment explanation
Indices: 40348730--40348769 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40348720 TATTCTTCCA
40348730 AT AT AT 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 AT AT AT
40348770 TAGTAATAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40350210 original size:23 final size:20
Alignment explanation
Indices: 40350167--40350211 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
40350157 AAAAATTATA
*
40350167 ATATTTTTTTATGAATAAGT
1 ATATTTTTTTATAAATAAGT
40350187 ATATTATTTTTATAATATATAGT
1 ATATT-TTTTTATAA-ATA-AGT
40350210 AT
1 AT
40350212 GTACATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 3 0.14
23 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
ATATTTTTTTATAAATAAGT
Found at i:40355269 original size:20 final size:20
Alignment explanation
Indices: 40355241--40355281 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40355231 CAAGCAAAGC
* * *
40355241 AGAATAGAACAGAGTAGAGA
1 AGAACAGAACAAAGCAGAGA
40355261 AGAACAGAACAAAGCAGAGA
1 AGAACAGAACAAAGCAGAGA
40355281 A
1 A
40355282 TGTGTTATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.10, G:0.27, T:0.05
Consensus pattern (20 bp):
AGAACAGAACAAAGCAGAGA
Found at i:40357861 original size:11 final size:12
Alignment explanation
Indices: 40357838--40357862 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40357828 TTTAAGTATG
40357838 TTTTGGTCTTTT
1 TTTTGGTCTTTT
40357850 TTTTGGTCTTTT
1 TTTTGGTCTTTT
40357862 T
1 T
40357863 GGACTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (12 bp):
TTTTGGTCTTTT
Found at i:40358394 original size:11 final size:11
Alignment explanation
Indices: 40358367--40358435 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
40358357 CACGGATGGG
40358367 GTATAACAAAAA
1 GTATAA-AAAAA
40358379 TGTATAAAAAAA
1 -GTATAAAAAAA
**
40358391 GTATACCAAAA
1 GTATAAAAAAA
* ** *
40358402 GAATTTAAAAT
1 GTATAAAAAAA
40358413 GTATAAAAAAA
1 GTATAAAAAAA
40358424 GT-TAAAATAAA
1 GTATAAAA-AAA
40358435 G
1 G
40358436 CTTGAGTTGA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
10 5 0.11
11 28 0.64
12 5 0.11
13 6 0.14
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.23
Consensus pattern (11 bp):
GTATAAAAAAA
Found at i:40361573 original size:3 final size:3
Alignment explanation
Indices: 40361565--40361605 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
40361555 GATTCAGGAA
* *
40361565 ATG ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG GTG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
40361606 AAGGTCAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:40370158 original size:18 final size:18
Alignment explanation
Indices: 40370137--40370180 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40370127 GAATAAGAAC
40370137 AAAAAAAAAACAAAAACA
1 AAAAAAAAAACAAAAACA
* *
40370155 AAAAAAAGAACAAAAAGA
1 AAAAAAAAAACAAAAACA
40370173 AACAAAAA
1 AA-AAAAA
40370181 CCTCTACCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAACAAAAACA
Found at i:40370180 original size:29 final size:32
Alignment explanation
Indices: 40370117--40370181 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 32
40370107 AGATTCAATC
40370117 AAAACAAAAAGAATAAGAACAAAAAAAAAACA
1 AAAACAAAAAGAATAAGAACAAAAAAAAAACA
*
40370149 AAAAC-AAAA-AA-AAGAAC-AAAAAGAAACA
1 AAAACAAAAAGAATAAGAACAAAAAAAAAACA
40370177 AAAAC
1 AAAAC
40370182 CTCTACCGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 15 0.47
29 6 0.19
30 2 0.06
31 4 0.12
32 5 0.16
ACGTcount: A:0.82, C:0.11, G:0.06, T:0.02
Consensus pattern (32 bp):
AAAACAAAAAGAATAAGAACAAAAAAAAAACA
Found at i:40371481 original size:88 final size:88
Alignment explanation
Indices: 40371324--40372253 Score: 1151
Period size: 88 Copynumber: 10.6 Consensus size: 88
40371314 CCATAAGTCC
* * *
40371324 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAATTAGCAGATATTGTCTTCCTGTATTGGCAGCA
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
* * *
40371389 AAGTAGATTGAAGACCTCAACCT
66 AAGTAGATCGAAGAACTCAGCCT
* * * * * * *
40371412 TATCTCCCTGAACAGTAGTGGAGTAGGTTGAAAATAGTAGATATTATTTTCCTGTATTGGTAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
40371477 AAGTAGATCGAAGATACT-AGCCT
66 AAGTAGATCGAAGA-ACTCAGCCT
* *
40371500 TGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
*
40371565 AAGTAGATCGAAGATA-TCAGCCC
66 AAGTAGATCGAAGA-ACTCAGCCT
* ** *
40371588 TGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAATAGATCTTGTCTTCCTGTATTGGCAACG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
* *
40371653 AAGAAGATCGAAGACCTCAGCCT
66 AAGTAGATCGAAGAACTCAGCCT
*
40371676 TATCTCCCTGAGCAGCAGTGGAGTAGCTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
*
40371741 AAGTATATCGAAGATAC-CAGCCT
66 AAGTAGATCGAAGA-ACTCAGCCT
* * * * *
40371764 TGTCTCCCTGAGCAGTAGTGGAGTAGGTTAAAAATAGTAGATCTTGTCTTCTTGTATTGGCAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
* *
40371829 AAGTAGATTGAAG-ATTCTAGCCT
66 AAGTAGATCGAAGAACTC-AGCCT
** * * *
40371852 TATCTCCCTGAGCAAAAGTGGAGTAGGTTGAAAATAGTAGATCTTGTCTTCTTGTATTGACAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
40371917 AAGTAGATCGAAGATAC-CAGCCT
66 AAGTAGATCGAAGA-ACTCAGCCT
* * * * *
40371940 TGTCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAACAGATCTTGTCTTCCTGTATTGGCAGGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
* * *
40372005 AAGTAGATC-AAAAACACCAGTCT
66 AAGTAGATCGAAGAAC-TCAGCCT
*
40372028 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTTCTGTATTGGCAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
40372093 AAGTAGATCGAAGATAC-CAGCCT
66 AAGTAGATCGAAGA-ACTCAGCCT
* * * ** *
40372116 TGTCTCCCTGAGTAGCAGTGGAGTAGGTT-AAAGATAGCAGATATTACCTTCCTGTATTGACAGC
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAA-ATAGCAGATCTTGTCTTCCTGTATTGGCAGC
*
40372180 GAAGCAGATCGACA-ACAC-CAGCCT
65 GAAGTAGATCGA-AGA-ACTCAGCCT
** * ** * * *
40372204 TGCCTCTCTGAGTTTGCAGTGGACTAGGTTGAAAATTGTAGATCTTGTCT
1 TATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCT
40372254 CCCTAAGCAG
Statistics
Matches: 738, Mismatches: 88, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
86 3 0.00
87 8 0.01
88 687 0.93
89 34 0.05
90 6 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (88 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
AAGTAGATCGAAGAACTCAGCCT
Found at i:40373727 original size:17 final size:20
Alignment explanation
Indices: 40373692--40373733 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
40373682 AAATATTGTA
40373692 ATTTTAATTCAATCATTATT
1 ATTTTAATTCAATCATTATT
*
40373712 -TTTTAATT-ATTC-TTATT
1 ATTTTAATTCAATCATTATT
40373729 ATTTT
1 ATTTT
40373734 TGAGTATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.25
18 7 0.35
19 8 0.40
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTAATTCAATCATTATT
Found at i:40383956 original size:29 final size:29
Alignment explanation
Indices: 40383903--40383972 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
40383893 CTTTCACAAA
* *
40383903 TTTAAAATTTAGTCTTTGTACTTTT-G-T
1 TTTAAAATTTAGTCATTGTAATTTTAGAT
40383930 TTTCAAAAATTTAGTCCATT-TAATTTTAGAT
1 TTT--AAAATTTAGT-CATTGTAATTTTAGAT
40383961 TTTAAAATTTAG
1 TTTAAAATTTAG
40383973 ACCCAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
27 3 0.08
29 25 0.69
30 4 0.11
31 4 0.11
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (29 bp):
TTTAAAATTTAGTCATTGTAATTTTAGAT
Found at i:40384428 original size:24 final size:24
Alignment explanation
Indices: 40384401--40384464 Score: 58
Period size: 27 Copynumber: 2.5 Consensus size: 24
40384391 ATCACACCAA
40384401 TAATTTTTTTTTAAA-AATAAATAT
1 TAATTTTTTTTTAAATAA-AAATAT
*
40384425 TAATATTTTATATTTAAATAAAATTAT
1 TAAT-TTTT-T-TTTAAATAAAAATAT
* *
40384452 TAATATTTATTTA
1 TAATTTTTTTTTA
40384465 GTTCTTCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
24 8 0.24
25 4 0.12
26 4 0.12
27 15 0.45
28 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAATTTTTTTTTAAATAAAAATAT
Found at i:40384429 original size:27 final size:28
Alignment explanation
Indices: 40384399--40384456 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
40384389 ATATCACACC
*
40384399 AATAATTTT-TTTTTAAA-AATAAATATT
1 AATAATTTTATATTTAAATAA-AAATATT
*
40384426 AAT-ATTTTATATTTAAATAAAATTATT
1 AATAATTTTATATTTAAATAAAAATATT
40384453 AATA
1 AATA
40384457 TTTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 5 0.19
27 19 0.73
28 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
AATAATTTTATATTTAAATAAAAATATT
Found at i:40386999 original size:17 final size:17
Alignment explanation
Indices: 40386979--40387042 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
40386969 TTCCTGATTA
*
40386979 GTTTATTAATTTTTATC
1 GTTTATTTATTTTTATC
* *
40386996 GTTTGTTTATTTTTATT
1 GTTTATTTATTTTTATC
*
40387013 ATTTATTTA--TTT-TC
1 GTTTATTTATTTTTATC
40387027 G-TTATTTATTTTTATC
1 GTTTATTTATTTTTATC
40387043 TCAATTATCT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
13 7 0.19
14 1 0.03
15 6 0.16
16 2 0.05
17 21 0.57
ACGTcount: A:0.19, C:0.05, G:0.06, T:0.70
Consensus pattern (17 bp):
GTTTATTTATTTTTATC
Found at i:40388260 original size:20 final size:19
Alignment explanation
Indices: 40388235--40388281 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
40388225 TCCCATTCTT
40388235 TTCTTTTGTTTTGATTTTCA
1 TTCTTTTGTTTT-ATTTTCA
* *
40388255 TTCTTTTTGTTTTTTTTTCT
1 TTC-TTTTGTTTTATTTTCA
40388275 TTCTTTT
1 TTCTTTT
40388282 CCATTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.04, C:0.11, G:0.06, T:0.79
Consensus pattern (19 bp):
TTCTTTTGTTTTATTTTCA
Found at i:40389590 original size:41 final size:41
Alignment explanation
Indices: 40389526--40389696 Score: 288
Period size: 41 Copynumber: 4.2 Consensus size: 41
40389516 AGCACTTCAT
* * * * *
40389526 CTGCTAGGTTTAAAGTCTAATTCAGTTCACTGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
*
40389567 CTGCTAAGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
40389608 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
40389649 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
40389690 CTGCTAG
1 CTGCTAG
40389697 ACATATAGTC
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (41 bp):
CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
Found at i:40389719 original size:82 final size:82
Alignment explanation
Indices: 40389549--40389719 Score: 270
Period size: 82 Copynumber: 2.1 Consensus size: 82
40389539 AGTCTAATTC
*
40389549 AGTTCACTGGCACTTAGCCTGCTAAGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
1 AGTTCACCGGCACTTAGCCTGCTAAGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
* * * *
40389614 GGCTTATAGCCTGATTC
66 GACATATAGCCTGAATA
*
40389631 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
1 AGTTCACCGGCACTTAGCCTGCTAAGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
*
40389696 GACATATAGTCTGAATA
66 GACATATAGCCTGAATA
*
40389713 ATTTCAC
1 AGTTCAC
40389720 TGGTAATAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (82 bp):
AGTTCACCGGCACTTAGCCTGCTAAGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
GACATATAGCCTGAATA
Found at i:40391369 original size:23 final size:23
Alignment explanation
Indices: 40391342--40391387 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
40391332 TAATTTGTTA
40391342 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
40391365 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
40391388 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:40397530 original size:41 final size:41
Alignment explanation
Indices: 40397337--40397507 Score: 288
Period size: 41 Copynumber: 4.2 Consensus size: 41
40397327 AGCACTTCAT
* * * * *
40397337 CTGCTAGGTTTAAAGTCTAATTCAGTTCACTGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
40397378 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
40397419 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
*
40397460 TTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
40397501 CTGCTAG
1 CTGCTAG
40397508 ACATATAGTC
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (41 bp):
CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
Found at i:40397530 original size:82 final size:82
Alignment explanation
Indices: 40397360--40397535 Score: 280
Period size: 82 Copynumber: 2.1 Consensus size: 82
40397350 AGTCTAATTC
40397360 AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
1 AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
* * * *
40397425 GGCTTATAGCCTGATTC
66 GACATATAGCCTGAATA
* *
40397442 AGTTCACCGGCACTTAGCTTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
1 AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
*
40397507 GACATATAGTCTGAATA
66 GACATATAGCCTGAATA
*
40397524 ATTTCACTGGCA
1 AGTTCACTGGCA
40397536 ATAAATCCGA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (82 bp):
AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
GACATATAGCCTGAATA
Found at i:40399102 original size:23 final size:23
Alignment explanation
Indices: 40399075--40399120 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
40399065 TAATTTGTTA
40399075 TATTAA-ACATATATTAACCTTAT
1 TATTAATA-ATATATTAACCTTAT
40399098 TATTAATTTAATATATTAACCTT
1 TATTAA--TAATATATTAACCTT
40399121 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 13 0.65
26 1 0.05
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATAATATATTAACCTTAT
Found at i:40403190 original size:25 final size:27
Alignment explanation
Indices: 40403162--40403215 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
40403152 TTTAATCATC
40403162 TATGCATAT-ATATA-AATTAT-AAATA
1 TATG-ATATGATATAGAATTATAAAATA
*
40403187 TATGATATGATATAGCATTATAAAATA
1 TATGATATGATATAGAATTATAAAATA
40403214 TA
1 TA
40403216 GTAGGAGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 4 0.16
25 9 0.36
26 5 0.20
27 7 0.28
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (27 bp):
TATGATATGATATAGAATTATAAAATA
Found at i:40403314 original size:18 final size:18
Alignment explanation
Indices: 40403277--40403318 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
40403267 TTTTAACTAG
40403277 TATAATAATAAACAATAA
1 TATAATAATAAACAATAA
*
40403295 TATATATAATAAGCAA-AA
1 TATA-ATAATAAACAATAA
40403313 TATAAT
1 TATAAT
40403319 GTACTACTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 10 0.45
19 10 0.45
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (18 bp):
TATAATAATAAACAATAA
Found at i:40403362 original size:239 final size:241
Alignment explanation
Indices: 40403091--40403663 Score: 764
Period size: 239 Copynumber: 2.3 Consensus size: 241
40403081 ATATTAATGC
* *
40403091 ATATATAATTATTATAATATAGATTATAATAAAAGATTTAATATTACATGATATTATAATGTTTA
1 ATATATAA-TATTATTATATAGATTATAATAAAAGATATAATATTACATGATATTATAATGTTTA
*
40403156 ATCATCTATGCATATATATAAATTATAAATATATGATATGATATAGCATTATAAAATATAGTAGG
65 ATCAT-TATGCATATATATAAACTATAAATATATGATATGATATAGCATTATAAAATATAGTAGG
* * * * *
40403221 AGGGCTAACTTTTAAATGTACGAAGAGTAT-AGAGA-TTCAAAGCATATTTTAACTAGTATAATA
129 AGGGCTAACTTTCAAATGCACAAAGAGTATAAG-GACTT-AAAACATATTTCAACTAGTATAATA
*
40403284 ATAAACAAT-AAT-ATATATAAT-AA-GCAAAATATAATGTACTACTGTT
192 ATAAACAATAAATAATATATAATAAATGCAAAATATAATGTACTACTATT
* * * * * *
40403330 ATATATAACTATTATTATATAGATTGTAATAAAGGATATAGTTTTACATGATATTATTATGATTA
1 ATATATAA-TATTATTATATAGATTATAATAAAAGATATAATATTACATGATATTATAATGTTTA
*
40403395 ATCATTTATGCATATATATAAACTATTAATATATGATATGATATAGCATTATAAAATATAGTAGG
65 ATCA-TTATGCATATATATAAACTATAAATATATGATATGATATAGCATTATAAAATATAGTAGG
*
40403460 AGGGCTAACTTTCAAATGCACAAAGAGTATAAGGACTTAAAACATATTTCAATTAGTATAATAAT
129 AGGGCTAACTTTCAAATGCACAAAGAGTATAAGGACTTAAAACATATTTCAACTAGTATAATAAT
* * *
40403525 AAACAATAAACAATAATATATAATAAAATGTAATATATAATGTATTACTATT
194 AAACAAT--A-AATAATATATAAT-AAATGCAAAATATAATGTACTACTATT
* *
40403577 ATATATCAATATTATTTTATTATATATTATAATAAAAGATATAATATTACATAATATTATAATGT
1 ATATAT-AATATTA--TTA-TATAGATTATAATAAAAGATATAATATTACATGATATTATAATGT
40403642 TTAA-CATTGATGCATATATATA
62 TTAATCATT-ATGCATATATATA
40403664 TATATATATA
Statistics
Matches: 289, Mismatches: 29, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
239 177 0.61
240 5 0.02
243 3 0.01
244 9 0.03
246 2 0.01
247 30 0.10
248 4 0.01
249 18 0.06
250 41 0.14
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.38
Consensus pattern (241 bp):
ATATATAATATTATTATATAGATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAA
TCATTATGCATATATATAAACTATAAATATATGATATGATATAGCATTATAAAATATAGTAGGAG
GGCTAACTTTCAAATGCACAAAGAGTATAAGGACTTAAAACATATTTCAACTAGTATAATAATAA
ACAATAAATAATATATAATAAATGCAAAATATAATGTACTACTATT
Found at i:40404363 original size:113 final size:114
Alignment explanation
Indices: 40404206--40404935 Score: 765
Period size: 114 Copynumber: 6.3 Consensus size: 114
40404196 AAAATAAGCA
* ** *
40404206 TTAGCGGCATTTTCCAGAAAGCACCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
* * *
40404270 TCAGGGATTTAGCGGCGTTTTTGAGGAAGCGTCGCTAATGCTTAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGTCGCTAATGCTCAGGGCT
* * * *
40404319 TTAGCTGCATTTCTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCCATTTTCTGAGCA
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACG-CCGTTTTCTGAGCA
* *
40404383 TTCGAGGATTTAGCGGCG-TTTTGAGGAAGCG-CTGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGTC-GCTAATGCTCAGGGCT
* * **
40404432 TTAGCGGCGATTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGTTGTTTTCTGAGCAT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
* * * * *
40404497 TTGGGGATTTAGCGGCGTTTTTCAGGAAGTGACGCTAATGCTCAGGGAT
66 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGTCGCTAATGCTCAGGGCT
*
40404546 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAGCAAAAAAACCTAAACCCAACGACGCC
1 TTAGCGGCGTTTTTGAGAAA--G-CG--------CC--GCAAAAAAACCTAAGCCCAACGACGCC
* * * * * *
40404611 GTTTTC-GATCTTTTTGGGGATTTAGCGGTGTTTTTAAGAAAGTGTCGCTAATGCTCAGGGCT
53 GTTTTCTGAGC-ATTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGTCGCTAATGCTCAGGGCT
* * * * *
40404673 TTAGCGGTGTTTTTGACAAAGTGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGACCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
* *
40404738 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGTCGCTAATGCTCAGGGCT
* * *
40404787 TTAGCGGCGTTTTTG-GTAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGACCT
1 TTAGCGGCGTTTTTGAG-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCA
* * * * * * *
40404851 TTCGGGGGCTTTAACGGCATTTTTAA-TACAGCGCCGCTAATTCTCTA-GGAT
65 TTC-GGGGATTTAGCGGCGTTTTTAAGGA-AGCGTCGCTAATGCTC-AGGGCT
* * * * *
40404902 TTAACGGCATTTTTGGGAAAGCTCAGCAAAAAAA
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAA
40404936 TTATTTGTCT
Statistics
Matches: 535, Mismatches: 57, Indels: 48
0.84 0.09 0.08
Matches are distributed among these distances:
112 1 0.00
113 122 0.23
114 237 0.44
115 69 0.13
116 5 0.01
117 2 0.00
124 1 0.00
125 3 0.01
126 3 0.01
127 92 0.17
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGTCGCTAATGCTCAGGGCT
Found at i:40404589 original size:13 final size:13
Alignment explanation
Indices: 40404571--40404596 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40404561 AGAAAGCGCC
40404571 GCAAAAAAACCTA
1 GCAAAAAAACCTA
40404584 GCAAAAAAACCTA
1 GCAAAAAAACCTA
40404597 AACCCAACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.23, G:0.08, T:0.08
Consensus pattern (13 bp):
GCAAAAAAACCTA
Found at i:40404776 original size:241 final size:241
Alignment explanation
Indices: 40404346--40404821 Score: 665
Period size: 241 Copynumber: 2.0 Consensus size: 241
40404336 AAAGCGCCGC
* * *
40404346 AAAAAACCTAAGCCCAACGACGCCCATTTTCTGAGCATTCGAGGATTTAGCGGCGTTTTGAGGAA
1 AAAAAACCTAAACCCAACGACGCCCATTTTCTGAGCATTCGAGGATTTAGCGGCGTTTTAAGAAA
*
40404411 GCGCTGCTAATGCTCAGGGCTTTAGCGGCGATTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCA
66 GCGCTGCTAATGCTCAGGGCTTTAGCGGCGATTTTGACAAAGCGCCGCAAAAAAACCTAAGCCCA
* ** * * *
40404476 ACGATGTTGTTTTCTGAGCATTTGGGGATTTAGCGGCGTTTTTCAGGAAGTGACGCTAATGCTCA
131 ACGACGCCGTTTTCTGAGCATTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGACGCTAATGCTCA
40404541 GGGATTTAGCGGCGTTTTTGAG-AAAGCGCCGCAAAAAAACCTAGCA
196 GGGATTTAGCGGCGTTTTTG-GTAAAGCGCCGCAAAAAAACCTAGCA
* * * * * *
40404587 AAAAAACCTAAACCCAACGACG-CCGTTTTC-GATCTTTTTGGGGATTTAGCGGTGTTTTTAAGA
1 AAAAAACCTAAACCCAACGACGCCCATTTTCTGAGC-ATTCGAGGATTTAGCGGCG-TTTTAAGA
* * * *
40404650 AAGTG-TCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTGACAAAGTGCCGCAAAAAAACCTAAGC
64 AAGCGCT-GCTAATGCTCAGGGCTTTAGCGGCGATTTTGACAAAGCGCCGCAAAAAAACCTAAGC
* *
40404714 CCAACGACGCCGTTTTCTGA-CCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATG
128 CCAACGACGCCGTTTTCTGAGCATTT-GGGGATTTAGCGGCGTTTTTAAGAAAGCGACGCTAATG
*
40404778 CTCAGGGCTTTAGCGGCGTTTTTGGTAAAGCGCCGCAAAAAAAC
192 CTCAGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCAAAAAAAC
40404822 ATAAGCCCAA
Statistics
Matches: 207, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
239 3 0.01
240 28 0.14
241 176 0.85
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (241 bp):
AAAAAACCTAAACCCAACGACGCCCATTTTCTGAGCATTCGAGGATTTAGCGGCGTTTTAAGAAA
GCGCTGCTAATGCTCAGGGCTTTAGCGGCGATTTTGACAAAGCGCCGCAAAAAAACCTAAGCCCA
ACGACGCCGTTTTCTGAGCATTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGACGCTAATGCTCA
GGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCAAAAAAACCTAGCA
Found at i:40408473 original size:17 final size:17
Alignment explanation
Indices: 40408421--40408476 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
40408411 TAAAGTTATA
*
40408421 TTTTAAATATTTTATTT
1 TTTTAAATATTTAATTT
* *
40408438 TATTTTAATCA-TGAATTT
1 T-TTTAAAT-ATTTAATTT
40408456 TTTTAAATATTTAATTT
1 TTTTAAATATTTAATTT
40408473 TTTT
1 TTTT
40408477 TAAAGTCCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 1 0.03
17 17 0.55
18 12 0.39
19 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTAAATATTTAATTT
Found at i:40408474 original size:18 final size:18
Alignment explanation
Indices: 40408421--40408480 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
40408411 TAAAGTTATA
*
40408421 TTTTAAATATTTTATTTT
1 TTTTAAATATTTAATTTT
*
40408439 ATTTT-AATCA-TGAA-TTT
1 -TTTTAAAT-ATTTAATTTT
40408456 TTTTAAATATTTAATTTT
1 TTTTAAATATTTAATTTT
40408474 TTTTAAA
1 TTTTAAA
40408481 GTCCAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
16 5 0.15
17 9 0.26
18 15 0.44
19 5 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTAAATATTTAATTTT
Found at i:40408518 original size:9 final size:9
Alignment explanation
Indices: 40408491--40408571 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
40408481 GTCCAAATTT
40408491 CATAACTTA
1 CATAACTTA
* *
40408500 CGTAAGTTA
1 CATAACTTA
40408509 CATAACTTA
1 CATAACTTA
40408518 CATAA-TT-
1 CATAACTTA
40408525 CATAACTTA
1 CATAACTTA
*
40408534 CATAATTTA
1 CATAACTTA
* *
40408543 AATTTATA-ATA
1 CA--TA-ACTTA
40408554 CATAACTTA
1 CATAACTTA
40408563 CATAACTTA
1 CATAACTTA
40408572 TTAATATTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.09
8 5 0.09
9 41 0.72
11 5 0.09
12 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.37
Consensus pattern (9 bp):
CATAACTTA
Found at i:40408530 original size:16 final size:16
Alignment explanation
Indices: 40408489--40408567 Score: 83
Period size: 16 Copynumber: 5.0 Consensus size: 16
40408479 AAGTCCAAAT
*
40408489 TTCATAACTTACGTAA
1 TTCATAACTTACATAA
40408505 GTTACATAACTTACATAA
1 -TT-CATAACTTACATAA
40408523 TTCATAACTTACATAA
1 TTCATAACTTACATAA
* *
40408539 TT--TAAATT-TATAA
1 TTCATAACTTACATAA
*
40408552 TACATAACTTACATAA
1 TTCATAACTTACATAA
40408568 CTTATTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 20 0.38
17 4 0.08
18 13 0.25
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (16 bp):
TTCATAACTTACATAA
Found at i:40408596 original size:19 final size:18
Alignment explanation
Indices: 40408572--40408625 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
40408562 ACATAACTTA
40408572 TTAATATTTATATATAGTT
1 TTAATATTTATATATA-TT
40408591 TTAATA--TATATAT-TT
1 TTAATATTTATATATATT
*
40408606 TTAAAATTTATATATATT
1 TTAATATTTATATATATT
40408624 TT
1 TT
40408626 TAAAAATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 7 0.23
17 14 0.45
18 4 0.13
19 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTAATATTTATATATATT
Found at i:40408600 original size:15 final size:15
Alignment explanation
Indices: 40408580--40408609 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40408570 TATTAATATT
40408580 TATATATAGTTTTAA
1 TATATATAGTTTTAA
*
40408595 TATATATATTTTTAA
1 TATATATAGTTTTAA
40408610 AATTTATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TATATATAGTTTTAA
Found at i:40408618 original size:21 final size:20
Alignment explanation
Indices: 40408595--40408633 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
40408585 ATAGTTTTAA
40408595 TATATATATTTTT-AAAATT
1 TATATATATTTTTAAAAATT
40408614 TATATATATTTTTAAAAATT
1 TATATATATTTTTAAAAATT
40408634 GATACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATATATTTTTAAAAATT
Found at i:40408685 original size:23 final size:20
Alignment explanation
Indices: 40408635--40408697 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 20
40408625 TTAAAAATTG
40408635 ATACATTACATAACTTACATA
1 ATACA-TACATAACTTACATA
*
40408656 ACCTACATACATAAACTTACA-C
1 A--TACATACAT-AACTTACATA
*
40408678 ATA-ATACATAACTTATATA
1 ATACATACATAACTTACATA
40408697 A
1 A
40408698 CTTAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
18 7 0.20
19 7 0.20
20 2 0.06
21 1 0.03
22 6 0.17
23 12 0.34
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ATACATACATAACTTACATA
Found at i:40408748 original size:31 final size:31
Alignment explanation
Indices: 40408652--40408761 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 31
40408642 ACATAACTTA
* *
40408652 CATAACCTACATACATAAA-CTTACA-CATAAT
1 CATAACTTACATACATAAATATTA-ATCAT-AT
* * *
40408683 ACATAACTTATATAACTTAAATTTATCAATCATAT
1 -CATAACTTACAT-ACATAAA--TATTAATCATAT
40408718 CATAACTTACATACATAAATATTAATCATAT
1 CATAACTTACATACATAAATATTAATCATAT
*
40408749 CACAACTTACATA
1 CATAACTTACATA
40408762 ACCAACATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
31 23 0.36
32 10 0.16
33 12 0.19
34 11 0.17
35 3 0.05
36 5 0.08
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (31 bp):
CATAACTTACATACATAAATATTAATCATAT
Found at i:40408796 original size:12 final size:12
Alignment explanation
Indices: 40408759--40408810 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
40408749 CACAACTTAC
*
40408759 ATAACCAACATA
1 ATAACCTACATA
* * *
40408771 ATGACTTACTTA
1 ATAACCTACATA
40408783 ATAACCTACATA
1 ATAACCTACATA
*
40408795 ATAACTTACATA
1 ATAACCTACATA
40408807 ATAA
1 ATAA
40408811 TACATAACCT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (12 bp):
ATAACCTACATA
Found at i:40408809 original size:24 final size:24
Alignment explanation
Indices: 40408759--40408817 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
40408749 CACAACTTAC
* * *
40408759 ATAACCAACATAATGACTTACTTA
1 ATAACCTACATAATAACTTACATA
40408783 ATAACCTACATAATAACTTACATA
1 ATAACCTACATAATAACTTACATA
40408807 ATAA--TACATAA
1 ATAACCTACATAA
40408818 CCTACATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 7 0.22
24 25 0.78
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.29
Consensus pattern (24 bp):
ATAACCTACATAATAACTTACATA
Found at i:40408952 original size:34 final size:34
Alignment explanation
Indices: 40408858--40408954 Score: 103
Period size: 34 Copynumber: 2.9 Consensus size: 34
40408848 ACAAAAAAAC
*
40408858 AAAA-AAAAACTTACATAACTTACAT--TACATA
1 AAAACAAAAACTTACATAACTTACATAATACACA
** * * *
40408889 ACCTACATAAA-TTAAATAAGTTACATAATACACA
1 A-AAACAAAAACTTACATAACTTACATAATACACA
40408923 AAAACAAAAACTTACATAACTTACATAATACA
1 AAAACAAAAACTTACATAACTTACATAATACA
40408955 TAACTTACAT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
31 1 0.02
32 14 0.28
33 10 0.20
34 25 0.50
ACGTcount: A:0.57, C:0.18, G:0.01, T:0.25
Consensus pattern (34 bp):
AAAACAAAAACTTACATAACTTACATAATACACA
Found at i:40408980 original size:41 final size:41
Alignment explanation
Indices: 40408935--40409263 Score: 284
Period size: 41 Copynumber: 7.4 Consensus size: 41
40408925 AACAAAAACT
*
40408935 TACATAACTTACATAATACATAACTTACATAACCTACTTAA
1 TACATAACTTACATAATACATAACTTACATAACTTACTTAA
* *
40408976 TACATAACTTACATAATACACAACTTACATAACTTACATAA
1 TACATAACTTACATAATACATAACTTACATAACTTACTTAA
* *
40409017 TACATAACTTACATAACTTATATAAGACAACTTACATAATTTACTTAA
1 TACATAACTTACATAA--TACAT-----AACTTACATAACTTACTTAA
*
40409065 TACATAACTTACATAATACATAACTTACATAACATACATAAGACATAA
1 TACATAACTTACATAATACATAACTTACATAAC-T---T---ACTTAA
* * *
40409113 CTTACATAAGTTTCATAATACATAACTTACATAACTTACATAA
1 --TACATAACTTACATAATACATAACTTACATAACTTACTTAA
*
40409156 TACATAACTTACATAATTTACTTAA--TACATAACTTACATAATACA
1 TACATAACTTACATAA--TACATAACTTACATAACTTAC-T--TA-A
* * *
40409201 TAACTTGCATAATTTACTTAATACATAACTTACATAATTTACTTAA
1 T-A----CATAACTTACATAATACATAACTTACATAACTTACTTAA
40409247 TACATAACTTACATAAT
1 TACATAACTTACATAAT
40409264 TTAATTAATA
Statistics
Matches: 237, Mismatches: 22, Indels: 58
0.75 0.07 0.18
Matches are distributed among these distances:
41 104 0.44
42 1 0.00
43 15 0.06
44 2 0.01
45 4 0.02
46 8 0.03
47 2 0.01
48 45 0.19
49 2 0.01
50 54 0.23
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.34
Consensus pattern (41 bp):
TACATAACTTACATAATACATAACTTACATAACTTACTTAA
Found at i:40408980 original size:66 final size:65
Alignment explanation
Indices: 40408856--40409255 Score: 343
Period size: 66 Copynumber: 6.0 Consensus size: 65
40408846 ACACAAAAAA
* * **
40408856 ACAAAAAA-A-AACTTACATAACTTACAT--TACATAACCTACATAAATTAAATAAGTTACATAA
1 ACAAAAAACATAACTTACATAACTTACATAATACATAACTTACATAACTTACTTAA--TACATAA
40408917 -T
64 CT
* *
40408918 ACACAAAAACAAAAACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAA
1 ACA-AAAAAC-ATAACTTACATAACTTACATAATACATAACTTACATAACTTACTTAATACATAA
40408983 CTT
64 C-T
* * * *
40408986 ACATAATACACAACTTACATAACTTACATAATACATAACTTACATAACTTA-TATAAGAC--AAC
1 ACAAAAAACATAACTTACATAACTTACATAATACATAACTTACATAACTTACT-TAATACATAAC
40409048 TT
65 -T
** * * * *
40409050 ACATAATTTACTTAA--TACATAACTTACATAATACATAACTTACATAACATACATAAGACATAA
1 ACA-AA-AAACATAACTTACATAACTTACATAATACATAACTTACATAACTTACTTAATACATAA
40409113 CTT
64 C-T
*
40409116 ACATAAGTTTCATAATACATAACTTACATAACTTACATAATACATAACTTACATAATTTACTTAA
1 AC--AA-----A-AA-ACATAACTTACATAACTTACATAATACATAACTTACATAACTTACTTAA
40409181 TACATAACTT
57 TACATAAC-T
* * * * * *
40409191 ACATAATACATAACTTGCATAATTTACTTAATACATAACTTACATAATTTACTTAATACATAACT
1 ACAAAAAACATAACTTACATAACTTACATAATACATAACTTACATAACTTACTTAATACATAACT
40409256 TACATAATTT
Statistics
Matches: 286, Mismatches: 28, Indels: 45
0.80 0.08 0.13
Matches are distributed among these distances:
62 3 0.01
63 5 0.02
64 49 0.17
65 4 0.01
66 136 0.48
67 6 0.02
68 26 0.09
72 2 0.01
73 6 0.02
75 49 0.17
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (65 bp):
ACAAAAAACATAACTTACATAACTTACATAATACATAACTTACATAACTTACTTAATACATAACT
Found at i:40409212 original size:25 final size:25
Alignment explanation
Indices: 40408931--40409203 Score: 292
Period size: 25 Copynumber: 10.8 Consensus size: 25
40408921 CAAAAACAAA
40408931 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
40408956 AACTTACATAACCTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
*
40408981 AACTTACATAA--TACACAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
40409006 AACTTACATAA--TACATAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
* *
40409031 AACTTATATAAGACAACTTACATAATTTACTT
1 AACTTACAT-----AACTTACATAA--TACAT
40409063 AA--TACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
40409086 AACTTACATAACATACATAAGACAT
1 AACTTACATAACTTACATAATACAT
* *
40409111 AACTTACATAAGTTTCATAATACAT
1 AACTTACATAACTTACATAATACAT
40409136 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
40409161 AACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
40409186 AACTTACATAA--TACATAA
1 AACTTACATAACTTACATAA
40409204 CTTGCATAAT
Statistics
Matches: 216, Mismatches: 21, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
23 17 0.08
25 179 0.83
30 6 0.03
32 14 0.06
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:40409217 original size:25 final size:25
Alignment explanation
Indices: 40408931--40409296 Score: 241
Period size: 25 Copynumber: 14.8 Consensus size: 25
40408921 CAAAAACAAA
*
40408931 AACTTACATAACTTACATAATACAT
1 AACTTACATAATTTACATAATACAT
** *
40408956 AACTTACATAACCTACTTAATACAT
1 AACTTACATAATTTACATAATACAT
*
40408981 AACTTACATAA--TACACAACTTACAT
1 AACTTACATAATTTACATAA--TACAT
40409006 AACTTACATAA--TACATAACTTACAT
1 AACTTACATAATTTACATAA--TACAT
* * *
40409031 AACTTATATAA--GACA-ACTTACAT
1 AACTTACATAATTTACATA-ATACAT
* *
40409054 AATTTACTTAA--TACATAACTTACAT
1 AACTTACATAATTTACATAA--TACAT
*
40409079 AA--TACATAACTTACATAACATACAT
1 AACTTACATAATTTACAT-A-ATACAT
* * *
40409104 AA--GACATAACTTACATAAGTTTCAT
1 AACTTACATAATTTACATAA--TACAT
*
40409129 AA--TACATAACTTACATAACTTACAT
1 AACTTACATAATTTACATAA--TACAT
* *
40409154 AA--TACATAACTTACATAATTTACTT
1 AACTTACATAATTTACATAA--TACAT
*
40409179 AA--TACATAACTTACATAATACAT
1 AACTTACATAATTTACATAATACAT
* *
40409202 AACTTGCATAATTTACTTAATACAT
1 AACTTACATAATTTACATAATACAT
*
40409227 AACTTACATAATTTACTTAATACAT
1 AACTTACATAATTTACATAATACAT
*
40409252 AACTTACATAATTTA-ATTAATATAT
1 AACTTACATAATTTACA-TAATACAT
*
40409277 AACTTACATAACTTACATAA
1 AACTTACATAATTTACATAA
40409297 ATATATGATG
Statistics
Matches: 296, Mismatches: 29, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
23 34 0.11
24 3 0.01
25 256 0.86
26 2 0.01
27 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (25 bp):
AACTTACATAATTTACATAATACAT
Found at i:40409256 original size:66 final size:65
Alignment explanation
Indices: 40408936--40409263 Score: 367
Period size: 66 Copynumber: 4.9 Consensus size: 65
40408926 ACAAAAACTT
** *
40408936 ACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAACTTACATAATACACAACT
1 ACATAA-TTACATAATACATAACTTACATAATTTACTTAATACATAACTTACATAATACATAACT
40409001 T
65 T
* * *
40409002 ACATAACTTACATAATACATAACTTACATAACTTATA-TAAGACAACTTACATAATTTACTTAAT
1 ACATAA-TTACATAATACATAACTTACATAA-TT-TACT----TAA--TACATAACTTACATAAT
40409066 ACATAACTT
57 ACATAACTT
* * * * *
40409075 ACATAA-TACATAACTTACATAACATACATAA--GACATAACTTACATAAGTTTCATAATACATA
1 ACATAATTACATAA--TACATAACTTACATAATTTACTTAA--TACATAACTTACATAATACATA
40409137 ACTT
62 ACTT
40409141 ACATAACTTACATAATACATAACTTACATAATTTACTTAATACATAACTTACATAATACATAACT
1 ACATAA-TTACATAATACATAACTTACATAATTTACTTAATACATAACTTACATAATACATAACT
40409206 T
65 T
* *
40409207 GCATAATTTACTTAATACATAACTTACATAATTTACTTAATACATAACTTACATAAT
1 ACATAA-TTACATAATACATAACTTACATAATTTACTTAATACATAACTTACATAAT
40409264 TTAATTAATA
Statistics
Matches: 226, Mismatches: 21, Indels: 30
0.82 0.08 0.11
Matches are distributed among these distances:
66 157 0.69
67 1 0.00
68 14 0.06
69 1 0.00
71 9 0.04
73 44 0.19
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.34
Consensus pattern (65 bp):
ACATAATTACATAATACATAACTTACATAATTTACTTAATACATAACTTACATAATACATAACTT
Found at i:40414835 original size:21 final size:21
Alignment explanation
Indices: 40414809--40414857 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
40414799 CTACAACTTA
* *
40414809 AAGCAGATGCGGCATCGAGAG
1 AAGCAGACGCGGCAGCGAGAG
* *
40414830 AAGCAGACGCTGCAGCGAGGG
1 AAGCAGACGCGGCAGCGAGAG
40414851 AAGCAGA
1 AAGCAGA
40414858 GTAGAGCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.39, T:0.06
Consensus pattern (21 bp):
AAGCAGACGCGGCAGCGAGAG
Found at i:40415282 original size:43 final size:43
Alignment explanation
Indices: 40415207--40415432 Score: 319
Period size: 43 Copynumber: 5.3 Consensus size: 43
40415197 ACCAAACAAA
* * *
40415207 TAGCGACGTTTGTGTAAAAA-CGCCGCTAAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCT-AAAGAACATGATCTT
* * * *
40415250 TAGTGGCGTTTGCGGAAGAAGTGCCGCTAAAGAACATGATCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
40415293 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
*
40415336 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAGGAACATGATCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
* * * * *
40415379 TAGCGGCGTTTGTTGAAAAAGCTCCGTTAAAGAACAGGACCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
40415422 TAGCGGCGTTT
1 TAGCGGCGTTT
40415433 ATAAAAATAT
Statistics
Matches: 164, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
43 158 0.96
44 6 0.04
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
Found at i:40416276 original size:34 final size:34
Alignment explanation
Indices: 40416158--40416342 Score: 226
Period size: 34 Copynumber: 5.4 Consensus size: 34
40416148 TTTATGGCAA
40416158 GTACATGCGAACTGTATATGTGTGTGAACCCTAG
1 GTACATGCGAACTGTATATGTGTGTGAACCCTAG
* * *
40416192 GTGACATGTGACCTGTATATGTGTATGAACCCTAG
1 GT-ACATGCGAACTGTATATGTGTGTGAACCCTAG
* * *
40416227 GTAACATGTGGACTGTATATGTGTGCGAACCCTAG
1 GT-ACATGCGAACTGTATATGTGTGTGAACCCTAG
*
40416262 GTACATGCGAACTGTATATGTGTGCGAACCCTAG
1 GTACATGCGAACTGTATATGTGTGTGAACCCTAG
* * * * * *
40416296 GTAGATGCAAATTGTATATATATGTGAACCCTAT
1 GTACATGCGAACTGTATATGTGTGTGAACCCTAG
*
40416330 GTACATGTGAACT
1 GTACATGCGAACT
40416343 CTGCGAAGCC
Statistics
Matches: 129, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
34 68 0.53
35 61 0.47
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (34 bp):
GTACATGCGAACTGTATATGTGTGTGAACCCTAG
Found at i:40432561 original size:39 final size:39
Alignment explanation
Indices: 40432515--40432590 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
40432505 TGTATAAATT
40432515 ATAGAAATATACAAAAAGAGAAAAATTAGTAAATTATTC
1 ATAGAAATATACAAAAAGAGAAAAATTAGTAAATTATTC
*
40432554 ATAGAAATATATAAAAAGAGAAAAATTAGTAAATTAT
1 ATAGAAATATACAAAAAGAGAAAAATTAGTAAATTAT
40432591 GTAATGAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (39 bp):
ATAGAAATATACAAAAAGAGAAAAATTAGTAAATTATTC
Found at i:40434068 original size:20 final size:20
Alignment explanation
Indices: 40434043--40434085 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
40434033 AAGTAACTAA
40434043 TAGTACTTTTGATTTTTATC
1 TAGTACTTTTGATTTTTATC
40434063 TAGTACTTTTGATTTTTATC
1 TAGTACTTTTGATTTTTATC
40434083 TAG
1 TAG
40434086 ATAATGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (20 bp):
TAGTACTTTTGATTTTTATC
Found at i:40435929 original size:13 final size:13
Alignment explanation
Indices: 40435911--40435936 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40435901 ATGTCTTTTA
40435911 CTTCCATTTTTCT
1 CTTCCATTTTTCT
40435924 CTTCCATTTTTCT
1 CTTCCATTTTTCT
40435937 GTAGTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTCCATTTTTCT
Found at i:40439992 original size:11 final size:11
Alignment explanation
Indices: 40439970--40440021 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
40439960 AACTAATCCT
40439970 CTCTCAAATTTC
1 CTCTC-AATTTC
40439982 CTCTCAATTTC
1 CTCTCAATTTC
*
40439993 CTCTAAATTTC
1 CTCTCAATTTC
* *
40440004 CTCTCAATCTG
1 CTCTCAATTTC
40440015 CTCTCAA
1 CTCTCAA
40440022 ACTCCTTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
11 31 0.86
12 5 0.14
ACGTcount: A:0.23, C:0.35, G:0.02, T:0.40
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:40440027 original size:22 final size:23
Alignment explanation
Indices: 40439970--40440022 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
40439960 AACTAATCCT
*
40439970 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATCTC
*
40439993 CTCT-AAATTTCCTCTCAATCTG
1 CTCTCAAATTTCCTCTCAATCTC
40440015 CTCTCAAA
1 CTCTCAAA
40440023 CTCCTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.25, C:0.34, G:0.02, T:0.40
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATCTC
Found at i:40440044 original size:11 final size:11
Alignment explanation
Indices: 40439969--40440045 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
40439959 AAACTAATCC
40439969 TCTCTCAAATT
1 TCTCTCAAATT
40439980 TCCTCTC-AATT
1 T-CTCTCAAATT
40439991 TC-CTCTAAATT
1 TCTCTC-AAATT
40440002 TCCTCTC-AATCT
1 T-CTCTCAAAT-T
* *
40440014 GCTCTCAAACT
1 TCTCTCAAATT
*
40440025 CCT-TCCAAATT
1 TCTCT-CAAATT
40440036 TCTCTCAAAT
1 TCTCTCAAAT
40440046 CCATATTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
9 3 0.06
10 2 0.04
11 34 0.65
12 10 0.19
13 3 0.06
ACGTcount: A:0.25, C:0.34, G:0.01, T:0.40
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:40440137 original size:20 final size:21
Alignment explanation
Indices: 40440100--40440138 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40440090 CTTAACTTCC
*
40440100 TTTTTTTAAATAATTTTAATT
1 TTTTTTTAAATAAATTTAATT
40440121 TTTTTTTAAA-AAATTTAA
1 TTTTTTTAAATAAATTTAA
40440139 CCGTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTTTAAATAAATTTAATT
Found at i:40441249 original size:7 final size:7
Alignment explanation
Indices: 40441237--40441262 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40441227 TAGTCGATTG
40441237 GTATTTA
1 GTATTTA
40441244 GTATTTA
1 GTATTTA
40441251 GTATTTA
1 GTATTTA
40441258 GTATT
1 GTATT
40441263 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:40441928 original size:18 final size:18
Alignment explanation
Indices: 40441901--40441940 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40441891 CAGGTGCATT
* *
40441901 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
40441919 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
40441937 TCCT
1 TCCT
40441941 TTTCCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:40442444 original size:23 final size:22
Alignment explanation
Indices: 40442410--40443074 Score: 393
Period size: 22 Copynumber: 30.4 Consensus size: 22
40442400 GAGTTATTAC
40442410 TTAAAAACCCTAAACCCTTAAAA
1 TTAAAAACCCTAAACCCTT-AAA
* * *
40442433 TTAAAAATCCTAAACCTTTAAC
1 TTAAAAACCCTAAACCCTTAAA
** *
40442455 TTAAAAACCCTAAACTAATTTAA
1 TTAAAAACCCTAAAC-CCTTAAA
* *
40442478 TTAAAAACCCTAAGCCTTTAAAA
1 TTAAAAACCCTAAACCCTT-AAA
*
40442501 TTAAAAACCCTAAACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAA
* *
40442523 TTAAAAA-CCTTAACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAA
*
40442544 GTAAAAACCCT-AACCCTTAAA
1 TTAAAAACCCTAAACCCTTAAA
40442565 TTAAAAACCCTAAACCCTTAAAA
1 TTAAAAACCCTAAACCCTT-AAA
*
40442588 TTAAAAACCCTAAACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAA
** *
40442610 TTAAAAACCCTAAACAAATTTAA
1 TTAAAAACCCTAAAC-CCTTAAA
* *
40442633 TTAAAAACCTTAAACCCTAAAA
1 TTAAAAACCCTAAACCCTTAAA
*** *
40442655 TCCTAAATCCTAAACCC-TAAA
1 TTAAAAACCCTAAACCCTTAAA
**** *
40442676 -CCCTAACCCTTAA--CTT-AA
1 TTAAAAACCCTAAACCCTTAAA
40442694 --AA--ACCCTAAA--C-T-AA
1 TTAAAAACCCTAAACCCTTAAA
* * *
40442708 TT-TAAA-CCTAAAACCATAAA
1 TTAAAAACCCTAAACCCTTAAA
** ** *
40442728 CTCTTAAACTTAAAAACCCTAACCCTTAAC
1 ---TT-AA---AAACCCTA-AACCCTTAAA
* *
40442758 TT-AAAACCTTAAACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAA
* ** *
40442779 TTAAAAACTCTAAACTAATTTAA
1 TTAAAAACCCTAAAC-CCTTAAA
*
40442802 TTAAAAACCCTAAACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAA
* *
40442824 TTAAAAACCCTAACCCCTTAAC
1 TTAAAAACCCTAAACCCTTAAA
** *
40442846 TTAAAAACCCTAAACTAATTTAA
1 TTAAAAACCCTAAAC-CCTTAAA
40442869 TTAAAAACCCTAAACCCTTAAA
1 TTAAAAACCCTAAACCCTTAAA
* *
40442891 TTTAAAAACCCTAACCCCTTAAC
1 -TTAAAAACCCTAAACCCTTAAA
* ** *
40442914 TTAAAAACTCTAAACTAATTTAA
1 TTAAAAACCCTAAAC-CCTTAAA
*
40442937 -TAAAAACCTTAAACCCTTAAA
1 TTAAAAACCCTAAACCCTTAAA
** *
40442958 CTTAAAAACCCT-AACTAATTTAA
1 -TTAAAAACCCTAAAC-CCTTAAA
* * *
40442981 TTGAAAACCCTAACCCCTTAAC
1 TTAAAAACCCTAAACCCTTAAA
* * *
40443003 TTAAAAACGCT-AACCCTCAAC
1 TTAAAAACCCTAAACCCTTAAA
* *
40443024 TTAAAAA-CCTTAACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAA
* *
40443045 TTAAAAACCCTTAACCCTTAAC
1 TTAAAAACCCTAAACCCTTAAA
*
40443067 TTTAAAAC
1 TTAAAAAC
40443075 TTTAAACTAG
Statistics
Matches: 501, Mismatches: 105, Indels: 73
0.74 0.15 0.11
Matches are distributed among these distances:
14 3 0.01
15 8 0.02
16 6 0.01
17 1 0.00
18 4 0.01
19 2 0.00
20 13 0.03
21 88 0.18
22 195 0.39
23 167 0.33
25 1 0.00
27 2 0.00
28 3 0.01
29 1 0.00
30 7 0.01
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.26
Consensus pattern (22 bp):
TTAAAAACCCTAAACCCTTAAA
Found at i:40442458 original size:45 final size:44
Alignment explanation
Indices: 40442408--40443113 Score: 548
Period size: 45 Copynumber: 16.2 Consensus size: 44
40442398 TTGAGTTATT
* *
40442408 ACTTAAAAACCCTAAACCCTTAAAATTAAAAATCCTAAACCTTTA
1 ACTTAAAAACCCTAAACCCTT-AACTTAAAAACCCTAAACCTTTA
** *
40442453 ACTTAAAAACCCTAAACTAATTTAA-TTAAAAACCCTAAGCCTTTAA
1 ACTTAAAAACCCTAAAC--CCTTAACTTAAAAACCCTAAACCTTT-A
* * *
40442499 AATTAAAAACCCTAAACCCTTAACTTAAAAA-CCTTAACCCTTA
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCTTTA
* * *
40442542 ACGTAAAAACCCT-AACCCTTAAATTAAAAACCCTAAACCCTTAA
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAA-CCTTTA
* *
40442586 AATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACAAATTTA
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAAC--CTTTA
* * * *** *
40442632 A-TTAAAAACCTTAAACCCTAAAATCCTAAATCCTAAACC----
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCTTTA
*
40442671 -C-T--AAACCCT-AACCCTTAACTTAAAAACCCTAAACTAATTTAA
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAAC--CTTT-A
* * * *
40442713 ACCT-AAAACCATAAACTCTTAAACTTAAAAACCCT-AACCCTTA
1 ACTTAAAAACCCTAAACCCTT-AACTTAAAAACCCTAAACCTTTA
* * *
40442756 ACTT-AAAACCTTAAACCCTTAACTTAAAAACTCTAAACTAATTTA
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAAC--CTTTA
* *
40442801 A-TTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCCTTA
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCTTTA
** *
40442844 ACTTAAAAACCCTAAACTAATTTAA-TTAAAAACCCTAAACCCTTAA
1 ACTTAAAAACCCTAAAC--CCTTAACTTAAAAACCCTAAA-CCTTTA
* * * *
40442890 ATTTAAAAACCCTAACCCCTTAACTTAAAAACTCTAAACTAATTTA
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAAC--CTTTA
* *
40442936 A--TAAAAACCTTAAACCCTTAAACTTAAAAACCCT-AACTAATTTA
1 ACTTAAAAACCCTAAACCCTT-AACTTAAAAACCCTAAAC--CTTTA
* * * * *
40442980 A-TTGAAAACCCTAACCCCTTAACTTAAAAACGCT-AACCCTCA
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCTTTA
* * *
40443022 ACTTAAAAA-CCTTAACCCTTAACTTAAAAACCCTTAACCCTTA
1 ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCTTTA
* ** * * *
40443065 ACTTTAAAACTTTAAA--CTAGAACTTAAAAACCGT-AACCCTTA
1 ACTTAAAAACCCTAAACCCT-TAACTTAAAAACCCTAAACCTTTA
40443107 ACTTAAA
1 ACTTAAA
40443114 TTTATTTGAT
Statistics
Matches: 536, Mismatches: 86, Indels: 81
0.76 0.12 0.12
Matches are distributed among these distances:
35 19 0.04
36 6 0.01
38 1 0.00
42 70 0.13
43 77 0.14
44 99 0.18
45 189 0.35
46 59 0.11
47 16 0.03
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.26
Consensus pattern (44 bp):
ACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCTTTA
Found at i:40442704 original size:7 final size:7
Alignment explanation
Indices: 40442637--40442685 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
40442627 ATTTAATTAA
*
40442637 AAACCTT
1 AAACCCT
40442644 AAACCCT
1 AAACCCT
*
40442651 AAAATCCT
1 -AAACCCT
*
40442659 AAATCCT
1 AAACCCT
40442666 AAACCCT
1 AAACCCT
40442673 AAACCCT
1 AAACCCT
40442680 -AACCCT
1 AAACCCT
40442686 TAACTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.16
7 26 0.68
8 6 0.16
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:40442851 original size:67 final size:66
Alignment explanation
Indices: 40442410--40443113 Score: 229
Period size: 67 Copynumber: 10.4 Consensus size: 66
40442400 GAGTTATTAC
* * * *
40442410 TTAAAAACCCTAAACCCTTAAAATTAAAAATCCTAAACCTTTAACTTAAAAACCCTAAACTAATT
1 TTAAAAACCCT-AACCCTT-AACTTAAAAACCCTAACCCCTTAACTTAAAAACCCTAAACTAATT
40442475 TAA
64 TAA
* * * * **
40442478 TTAAAAACCCTAAGCCTTTAAAATTAAAAACCCTAAACCCTTAACTTAAAAA-CCTTAAC--CCT
1 TTAAAAACCCTAA-CCCTT-AACTTAAAAACCCTAACCCCTTAACTTAAAAACCCTAAACTAATT
40442540 TAA
64 TAA
* * * * **
40442543 CGTAAAAACCCTAACCCTTAAATTAAAAACCCTAAACCCTTAAAATTAAAAACCCTAAAC--CCT
1 -TTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCCTT-AACTTAAAAACCCTAAACTAATT
40442606 TAA
64 TAA
** * * * *
40442609 CTTAAAAACCCTAAACAAATTTAA-TTAAAAACCTTAAACCCTAAAATCCTAAATCCTAAACCCT
1 -TTAAAAACCCT-AAC--CCTTAACTTAAAAACCCTAACCCCT-TAA--CTTAA----AAACCCT
*
40442673 AAACCCTAACCCTTAA
55 AAA--CTAA--TTTAA
** * * * *
40442689 CTTAAAAACCCTAAACTAATTTAAACCT-AAAACCATAAACTCTTAAACTTAAAAACCCT-AAC-
1 -TTAAAAACCCT-AAC--CCTT-AACTTAAAAACCCTAACCCCTT-AACTTAAAAACCCTAAACT
**
40442751 -CCTTAA
60 AATTTAA
* * *** *
40442757 CTT-AAAACCTTAAACCCTTAACTTAAAAACTCTAAACTAATTTAA-TTAAAAACCCTAAAC--C
1 -TTAAAAACCCT-AACCCTTAACTTAAAAACCCT-AAC-CCCTTAACTTAAAAACCCTAAACTAA
*
40442818 CTTAA
62 TTTAA
*** **
40442823 CTTAAAAACCCTAACCCCTTAACTTAAAAACCCTAAACTAATTTAA-TTAAAAACCCTAAAC-CC
1 -TTAAAAACCCTAA-CCCTTAACTTAAAAACCCT-AAC-CCCTTAACTTAAAAACCCTAAACTAA
*
40442886 TTAAA
62 TTTAA
* *** * **
40442891 TTTAAAAACCCTAACCCCTTAACTTAAAAACTCTAAACTAATTTAA--TAAAAACCTTAAAC-CC
1 -TTAAAAACCCTAA-CCCTTAACTTAAAAACCCT-AAC-CCCTTAACTTAAAAACCCTAAACTAA
*
40442953 TTAAA
62 TTTAA
** * * * *
40442958 CTTAAAAACCCTAACTAATTTAA-TTGAAAACCCTAACCCCTTAACTTAAAAACGCTAACCCTCA
1 -TTAAAAACCCTAAC--CCTTAACTTAAAAACCCTAACCCCTTAACTTAAAAACCCTAA-ACTAA
*
40443022 ---AC
62 TTTAA
* * **
40443024 TTAAAAACCTTAACCCTTAACTTAAAAACCCTTAA-CCCTTAACTTTAAAACTTTAAACTAGA--
1 TTAAAAACCCTAACCCTTAACTTAAAAACCC-TAACCCCTTAACTTAAAAACCCTAAACTA-ATT
*
40443086 -AC
64 TAA
*
40443088 TTAAAAACCGTAACCCTTAACTTAAA
1 TTAAAAACCCTAACCCTTAACTTAAA
40443114 TTTATTTGAT
Statistics
Matches: 532, Mismatches: 65, Indels: 82
0.78 0.10 0.12
Matches are distributed among these distances:
63 6 0.01
64 81 0.15
65 56 0.11
66 58 0.11
67 128 0.24
68 126 0.24
69 5 0.01
70 3 0.01
72 1 0.00
74 12 0.02
75 7 0.01
76 1 0.00
79 4 0.01
80 26 0.05
81 17 0.03
82 1 0.00
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.26
Consensus pattern (66 bp):
TTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCCTTAACTTAAAAACCCTAAACTAATTTA
A
Found at i:40446550 original size:124 final size:125
Alignment explanation
Indices: 40446293--40446659 Score: 601
Period size: 124 Copynumber: 2.9 Consensus size: 125
40446283 ATGCTACTAG
* *
40446293 AGCAAAAGCGCGTCCATGAGGGCGCGCTTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGC
1 AGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGC
* *
40446358 GATTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTCTTCCATGACCTACTGT
66 GATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCTACTGT
40446418 AGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGC
1 AGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGC
* *
40446483 -AATTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTCTTCCAGGACCTACTGT
66 GATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCTACTGT
* * * * *
40446542 AGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAAATCTTATCAAACAGCATTCTGCTAGAAGC
1 AGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGC
* * *
40446607 GATTTTGTACTATTTGATCAGAAACGTCAACTCAAAATTATTTCTTCCAGGAC
66 GATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
40446660 ATAAAAACCC
Statistics
Matches: 225, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
124 115 0.51
125 110 0.49
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (125 bp):
AGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAGC
GATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCTACTGT
Found at i:40449155 original size:2 final size:2
Alignment explanation
Indices: 40449148--40449176 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
40449138 TATCCCATCA
40449148 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40449177 TGAGATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40452344 original size:44 final size:46
Alignment explanation
Indices: 40452278--40452365 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
40452268 AATCGATAAA
40452278 TTTACATATAAA-TTTATCTTTTTCA-TTTTTTACCAAATAAAATT
1 TTTACATATAAATTTTATCTTTTTCATTTTTTTACCAAATAAAATT
*
40452322 TTTACATATAAACTCTTT-T-TTTTTCATTTTTTTATCAAATAAAA
1 TTTACATATAAA-T-TTTATCTTTTTCATTTTTTTACCAAATAAAA
40452366 ATTCATTAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
44 12 0.31
45 7 0.18
46 17 0.44
47 3 0.08
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.53
Consensus pattern (46 bp):
TTTACATATAAATTTTATCTTTTTCATTTTTTTACCAAATAAAATT
Found at i:40452392 original size:12 final size:12
Alignment explanation
Indices: 40452375--40452401 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40452365 AATTCATTAG
40452375 ATACATATATTT
1 ATACATATATTT
40452387 ATACATATATTT
1 ATACATATATTT
40452399 ATA
1 ATA
40452402 TTATTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (12 bp):
ATACATATATTT
Found at i:40452457 original size:16 final size:17
Alignment explanation
Indices: 40452431--40452465 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40452421 TCTTTAAGAA
40452431 ATTATAATTATATAATT
1 ATTATAATTATATAATT
*
40452448 ATTA-AATTATATATTT
1 ATTATAATTATATAATT
40452464 AT
1 AT
40452466 ACTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATAATTATATAATT
Found at i:40452457 original size:22 final size:21
Alignment explanation
Indices: 40452395--40452466 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
40452385 TTATACATAT
40452395 ATTTATATTATTATTAAATTATA
1 ATTTATA--ATTATTAAATTATA
* **
40452418 ATTTCT--TTAAGAAATTATA
1 ATTTATAATTATTAAATTATA
40452437 ATTATATAATTATTAAATTATA
1 ATT-TATAATTATTAAATTATA
40452459 TATTTATA
1 -ATTTATA
40452467 CTATTTATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 14 0.36
20 2 0.05
22 15 0.38
23 8 0.21
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (21 bp):
ATTTATAATTATTAAATTATA
Found at i:40454214 original size:23 final size:22
Alignment explanation
Indices: 40454164--40454225 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
40454154 AAAAGCATAA
40454164 ATAT-AAATTAATATAATAAGT
1 ATATAAAATTAATATAATAAGT
*
40454185 AGCATAAAATTAATATAAATTAA-T
1 A-TATAAAATTAATAT-AA-TAAGT
40454209 ATATAAATATTTAATAT
1 ATATAAA-A-TTAATAT
40454226 TACTATTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 1 0.03
22 2 0.06
23 15 0.45
24 5 0.15
25 10 0.30
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (22 bp):
ATATAAAATTAATATAATAAGT
Found at i:40459158 original size:22 final size:20
Alignment explanation
Indices: 40459107--40459158 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 20
40459097 TTTTACAATA
40459107 TTTATTTAAAACTTGTTTAT
1 TTTATTTAAAACTTGTTTAT
40459127 TATTATTTTAAAA-TTGTTCTACAT
1 T-TTA-TTTAAAACTTGTT-T--AT
40459151 TTTATTTA
1 TTTATTTA
40459159 TTTTAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 1 0.04
21 8 0.30
22 12 0.44
23 3 0.11
24 3 0.11
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATTTAAAACTTGTTTAT
Found at i:40461316 original size:18 final size:19
Alignment explanation
Indices: 40461293--40461328 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40461283 GATCCTTCTG
40461293 ATTTG-TTTCGTTATTTTA
1 ATTTGTTTTCGTTATTTTA
*
40461311 ATTTGTTTTCTTTATTTT
1 ATTTGTTTTCGTTATTTT
40461329 CTGAATTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (19 bp):
ATTTGTTTTCGTTATTTTA
Found at i:40464623 original size:15 final size:15
Alignment explanation
Indices: 40464603--40464635 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40464593 TCGAGAAGAA
*
40464603 AGAAACAAGTCAGGC
1 AGAAACAAGTCAGAC
40464618 AGAAACAAGTCAGAC
1 AGAAACAAGTCAGAC
40464633 AGA
1 AGA
40464636 TAGGAAAGAA
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:0.52, C:0.18, G:0.24, T:0.06
Consensus pattern (15 bp):
AGAAACAAGTCAGAC
Found at i:40473983 original size:169 final size:170
Alignment explanation
Indices: 40473777--40474599 Score: 1147
Period size: 169 Copynumber: 4.9 Consensus size: 170
40473767 AGTAGATTAA
* * *
40473777 AGCTGAAGTGGAACGGATTAAAGCTGTGGGTAGCGAATCCTATCTCTTTGGCATTACCCTGGAAC
1 AGCTGAAGTGGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACCGTGGAAC
* * * *
40473842 AGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCC-GGATGCTGCAGTGGACCAGATTAAAGCTGA
66 AGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCAGGACGTTGCAGCGGAGCAGATTAAAGCTGA
* *
40473906 GGGTAGCGAATCTTATCTCCCTGGCGTTAAGACTTGTAAT
131 GGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGGAAT
* * * *
40473946 AGTTGAAGTGGAGCGGATTAAAGCTGTCGGCAGCGAATCCTATCTCTTTGGCATTATCGTGGAAT
1 AGCTGAAGTGGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACCGTGGAAC
* *
40474011 AGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCAGG-CATTGCAGCGGAGCAGATTAAAGCTAA
66 AGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCAGGACGTTGCAGCGGAGCAGATTAAAGCTGA
*
40474075 GGGTAGCGAATCTTATCTCCCTGGCGTTAAGACTTGGAAT
131 GGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGGAAT
* * *
40474115 AGCTGAAGTAGAGTGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACCGTGAAAC
1 AGCTGAAGTGGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACCGTGGAAC
* * * *
40474180 AAATTAAAGCTAAAGATAGCGAATCTTGTTTCCC-GGGCGTTGCAGTGGAGCAGATTCAAA-CTG
66 AGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCAGGACGTTGCAGCGGAGCAGATT-AAAGCTG
* *
40474243 AGGGCAGTGAATCTTATCTCTCTGGCGTTAAGACTTGGAAT
130 AGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGGAAT
* * * *
40474284 AGCTGAAGCGGAGTGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACTGTGAAAC
1 AGCTGAAGTGGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACCGTGGAAC
* * * * *
40474349 ATATTAAAGCTAAAGGTGGCGAGTCTTGTTTCCCTGG-CGTTGCAGCAGAGCAGATTAAAGCTGA
66 AGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCAGGACGTTGCAGCGGAGCAGATTAAAGCTGA
*
40474413 GGGCAGCGAATCTTATCTCCCTCGCGTTAAGACTTGGAAT
131 GGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGGAAT
* * * *
40474453 AGCTGACGTGGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCGTTACAGTAGAAC
1 AGCTGAAGTGGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACCGTGGAAC
* * * * * * *
40474518 AGATTAAGGCTAAAGGTAGCGAATCTGGTTTCCCTGG-CGTAGTAGC-GAGTAGATTAAAGCTAA
66 AGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCAGGACGTTGCAGCGGAGCAGATTAAAGCTGA
* * *
40474581 AGGCAGCAAATCTCATCTC
131 GGGCAGCGAATCTTATCTC
40474600 TCCAGCATTA
Statistics
Matches: 589, Mismatches: 60, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
168 36 0.06
169 546 0.93
170 7 0.01
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (170 bp):
AGCTGAAGTGGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACCGTGGAAC
AGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCAGGACGTTGCAGCGGAGCAGATTAAAGCTGA
GGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGGAAT
Found at i:40474727 original size:41 final size:41
Alignment explanation
Indices: 40474670--40474760 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
40474660 AAACCACAGA
* ** *
40474670 TCTTATCTCTCAGAAGTTGCAGTAGAGCATATCGTGTCCAG
1 TCTTATCTCTCAGAAGTTGCAGTAGAGCAGATCGCATCAAG
* *
40474711 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAG
1 TCTTATCTCTCAGAAGTTGCAGTAGAGCAGATCGCATCAAG
40474752 TCTTATCTC
1 TCTTATCTC
40474761 CCTAAAATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (41 bp):
TCTTATCTCTCAGAAGTTGCAGTAGAGCAGATCGCATCAAG
Found at i:40476113 original size:3 final size:3
Alignment explanation
Indices: 40476107--40476213 Score: 123
Period size: 3 Copynumber: 36.0 Consensus size: 3
40476097 AATAGCTTGC
40476107 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
40476155 TAT TACT CTAT TGT TAT TAT T-T TCAT TA- TAT TA- TAT T-T TAC TAT
1 TAT TA-T -TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
* *
40476199 TAT TCT TAG TAT TAT
1 TAT TAT TAT TAT TAT
40476214 AGATTTGTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
2 8 0.09
3 75 0.84
4 4 0.04
5 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:40476482 original size:22 final size:22
Alignment explanation
Indices: 40476439--40476482 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40476429 ACTGCAACTT
* * *
40476439 TATGTATATGTTAATATGTTAA
1 TATGCATATATTAATATATTAA
*
40476461 TATGCATATATTATTATATTAA
1 TATGCATATATTAATATATTAA
40476483 GTTCTCCATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (22 bp):
TATGCATATATTAATATATTAA
Found at i:40476525 original size:2 final size:2
Alignment explanation
Indices: 40476518--40476563 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
40476508 CTCTAGACTC
40476518 AT AT AT AT 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 AT AT AT AT
40476560 AT AT
1 AT AT
40476564 TTACGTCACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40482404 original size:82 final size:81
Alignment explanation
Indices: 40482265--40482420 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
40482255 TTAGATTTGA
** * * *
40482265 TGAATTCATCAAGTCTGTCTCAATAGGACCACCCAAACTTTGGGCTATGAACTCATTAAGAGTAA
1 TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAAATCTAGGCTATGAACTCATTAAGAGTAA
40482330 TAAACTCAACAAGTCAG
66 T-AACTCAACAAGTCAG
40482347 TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAAATCTAGGCTATGAA-TCCATTAAGAGTA
1 TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAAATCTAGGCTATGAACT-CATTAAGAGTA
40482411 ATAACTCAAC
65 ATAACTCAAC
40482421 CTTATGCATG
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 9 0.13
82 59 0.87
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (81 bp):
TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAAATCTAGGCTATGAACTCATTAAGAGTAA
TAACTCAACAAGTCAG
Found at i:40492066 original size:2 final size:2
Alignment explanation
Indices: 40492059--40492088 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40492049 ATGGGCAATA
40492059 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
40492089 TTAAATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40498374 original size:18 final size:17
Alignment explanation
Indices: 40498347--40498407 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
40498337 AAATTTATTT
40498347 AAAATTAAAA-AACATTA
1 AAAATTAAAAGAA-ATTA
*
40498364 AAAATTCAAAAGAAATTT
1 AAAATT-AAAAGAAATTA
* *
40498382 AAAATTATAA-AAACTA
1 AAAATTAAAAGAAATTA
*
40498398 AAAAATAAAA
1 AAAATTAAAA
40498408 ATATGTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
16 12 0.33
17 9 0.25
18 13 0.36
19 2 0.06
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (17 bp):
AAAATTAAAAGAAATTA
Found at i:40498557 original size:21 final size:19
Alignment explanation
Indices: 40498517--40498562 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
40498507 GAATTTAGGT
40498517 TTTTA-GAAAATTTTAGAA
1 TTTTATGAAAATTTTAGAA
40498535 TTTTATGAAAATTTTAAAGAA
1 TTTTATGAAAATTTT--AGAA
40498556 TTTTATG
1 TTTTATG
40498563 GTTTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.20
19 9 0.36
21 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (19 bp):
TTTTATGAAAATTTTAGAA
Found at i:40498822 original size:21 final size:21
Alignment explanation
Indices: 40498798--40498838 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40498788 AAATAATAGA
* *
40498798 TTAAGAATTTTTTTAGTTTTT
1 TTAAGAATTTTATGAGTTTTT
*
40498819 TTAATAATTTTATGAGTTTT
1 TTAAGAATTTTATGAGTTTT
40498839 AAAATATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (21 bp):
TTAAGAATTTTATGAGTTTTT
Found at i:40502089 original size:52 final size:54
Alignment explanation
Indices: 40502025--40502131 Score: 137
Period size: 58 Copynumber: 1.9 Consensus size: 54
40502015 TATTATTTTA
*
40502025 AAAAAAATT-A-AAAATATATTTATATTCATTTTAATTTAATATTGAATAAATT
1 AAAAAAATTAATAAAATATATTTACATTCATTTTAATTTAATATTGAATAAATT
* *
40502077 AAAAACATTAAAAATTAAAATATATTTACATTTATTTTAATTTAATATTGAATAA
1 AAAAAAATT---AA-TAAAATATATTTACATTCATTTTAATTTAATATTGAATAA
40502132 TTTTATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
52 8 0.17
56 1 0.02
58 37 0.80
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (54 bp):
AAAAAAATTAATAAAATATATTTACATTCATTTTAATTTAATATTGAATAAATT
Found at i:40509167 original size:68 final size:69
Alignment explanation
Indices: 40509035--40509179 Score: 229
Period size: 69 Copynumber: 2.1 Consensus size: 69
40509025 TCTTTCAACA
* *
40509035 AATCATTTTAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATAGCAGTAAAATGTT
1 AATCATTTTAAAAAACAAACAAAATATGCTATACTAACAAAATGATCCTATAGCAATAAAATGTT
40509100 AACC
66 AACC
* *
40509104 AATCATTTTAAAAAACAAACAAAATATGCTATGCTAAC-AAATGATCCTATAGCAATAAGATGTT
1 AATCATTTTAAAAAACAAACAAAATATGCTATACTAACAAAATGATCCTATAGCAATAAAATGTT
*
40509168 GACC
66 AACC
*
40509172 AACCATTT
1 AATCATTT
40509180 CAACTAATCA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
68 34 0.49
69 36 0.51
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (69 bp):
AATCATTTTAAAAAACAAACAAAATATGCTATACTAACAAAATGATCCTATAGCAATAAAATGTT
AACC
Found at i:40509616 original size:161 final size:159
Alignment explanation
Indices: 40509292--40509726 Score: 470
Period size: 162 Copynumber: 2.7 Consensus size: 159
40509282 TATGCCATCC
* * * * * * *
40509292 TTTTTT-GGCTTCTAGTTCTCATGCTCATACCAGACT--GAGAACAAAAATCAGAACCCCAAATT
1 TTTTTTGGGCTTCTAGTTTTCGTACTCGTACAAGACTAAGAAAAAAAAAATCAGAA-CCCAAATT
* * *
40509354 AGATTTAAATAATTTGGAATTGACATTAAAAAAGTATTTACGATATACTTGTGATCCAATTGTGT
65 AGATTTAAATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACTTGTGATCCAATTGTAT
*
40509419 TAGGCAGAATGCATAGTGTCATGTTGTTC-
130 TAGACAGAATGCATAGTGTCATGTTGTTCA
* * *
40509448 TTTTTTTGGCTTCTAGTTTGT-GTACTCGTACCAGGCTAAGATTAAAAAAAAATCAGAACCTCAA
1 TTTTTTGGGCTTCTAGTTT-TCGTACTCGTACAAGACTAAGA--AAAAAAAAATCAGAACC-CAA
* ** * * * *
40509512 ATTAGATTAAAATATTTTTAAATTGACATTAAAAATAGTGTATACGATATACCTGTGATCTAGTT
62 ATTAGATTTAAATATTTTGGAATTGACATTAAAAA-AGTGTTTACGATATACTTGTGATCCAATT
* * * *
40509577 GTATTAGACTGAATGCTTGGTGTTATGTTGTT-A
126 GTATTAGACAGAATGCATAGTGTCATGTTGTTCA
* ** * *
40509610 TTTTTTGGGCTTCTTGTTTTCGTACTCGTACAAGACTAAGACCAAAAAACTTAGAACCCAAATTA
1 TTTTTTGGGCTTCTAGTTTTCGTACTCGTACAAGACTAAGAAAAAAAAAATCAGAACCCAAATTA
* *
40509675 GATTTTAATATTTTGGAATTGACAATGAAAAAA-TGTTTACGATATACTTGTG
66 GATTTAAATATTTTGGAATTGAC-ATTAAAAAAGTGTTTACGATATACTTGTG
40509727 TTCCCGTTGT
Statistics
Matches: 231, Mismatches: 37, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
156 6 0.03
157 23 0.10
158 18 0.08
159 29 0.13
160 22 0.10
161 48 0.21
162 85 0.37
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (159 bp):
TTTTTTGGGCTTCTAGTTTTCGTACTCGTACAAGACTAAGAAAAAAAAAATCAGAACCCAAATTA
GATTTAAATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACTTGTGATCCAATTGTATT
AGACAGAATGCATAGTGTCATGTTGTTCA
Found at i:40514514 original size:9 final size:9
Alignment explanation
Indices: 40514484--40514516 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
40514474 TAGTTAGTGG
40514484 TTAACTTGTT
1 TTAA-TTGTT
40514494 TTAATT-TT
1 TTAATTGTT
40514502 TTAATTGTT
1 TTAATTGTT
40514511 TTAATT
1 TTAATT
40514517 ACGGGTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 10 0.45
10 4 0.18
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (9 bp):
TTAATTGTT
Found at i:40514580 original size:18 final size:17
Alignment explanation
Indices: 40514547--40514581 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
40514537 TTCTAAATGT
*
40514547 TTTTTTAATTTTAATTA
1 TTTTTTAATTTAAATTA
40514564 TTTTTTAAGTTTAAATTA
1 TTTTTTAA-TTTAAATTA
40514582 ATTTGTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTTTAATTTAAATTA
Found at i:40523669 original size:20 final size:20
Alignment explanation
Indices: 40523633--40523670 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40523623 CATTCCACCA
*
40523633 AAATCAAATTTAGAATTCAC
1 AAATCAAATTTAAAATTCAC
40523653 AAAT-AAATTTGAAAATTC
1 AAATCAAATTT-AAAATTC
40523671 TCGAAACCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATCAAATTTAAAATTCAC
Found at i:40529781 original size:26 final size:26
Alignment explanation
Indices: 40529751--40529809 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
40529741 TATTTTCTTG
* *
40529751 AAATTTTAC-CAGTGGCAAAATCTTCA
1 AAATTTTACTAAG-GGCAAAATCGTCA
*
40529777 AAATTTTACTAAGGGTAAAATCGTCA
1 AAATTTTACTAAGGGCAAAATCGTCA
40529803 AAATTTT
1 AAATTTT
40529810 GTTGGGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (26 bp):
AAATTTTACTAAGGGCAAAATCGTCA
Found at i:40533205 original size:16 final size:17
Alignment explanation
Indices: 40533184--40533221 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
40533174 TATCTTTGAT
40533184 TTATATATA-TTCATAC
1 TTATATATATTTCATAC
*
40533200 TTATATATATTTTATAC
1 TTATATATATTTCATAC
40533217 TTATA
1 TTATA
40533222 ATTTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATATATTTCATAC
Found at i:40533455 original size:39 final size:42
Alignment explanation
Indices: 40533401--40533503 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 42
40533391 ATATGTATTT
*
40533401 TATATATCTTCTTTATATTTTATGAT-TTACAT-ATATCTATG
1 TATATA-CTTCTTTATATTTTATGATATTACATAATATATATG
40533442 TATATACTT-TTTATATTTTATGATAGTTACATACATATATATG
1 TATATACTTCTTTATATTTTATGATA-TTACATA-ATATATATG
*
40533485 TGTATACTTACTTATATAT
1 TATATACTT-CTT-TATAT
40533504 ATATTTTTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
39 15 0.28
40 3 0.06
41 12 0.23
43 16 0.30
45 2 0.04
46 5 0.09
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (42 bp):
TATATACTTCTTTATATTTTATGATATTACATAATATATATG
Found at i:40534212 original size:109 final size:109
Alignment explanation
Indices: 40534021--40534436 Score: 568
Period size: 109 Copynumber: 3.8 Consensus size: 109
40534011 AAAAAATAAG
* ** * *
40534021 TAAGGCAATGTTTTGCGTTTGGAAATTGGAGAAAACAAGCCCTAATGTGTTGGGATTCGATTTTT
1 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGATTCAATTTTT
* *
40534086 CTTGTTCAACCAAATAGCCAAATACCCTTTCAAAAATTTCAAAA
66 CTTGTTCAACCAAATAGCCAAATATCTTTTCAAAAATTTCAAAA
*
40534130 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGATTCAATTTTT
1 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGATTCAATTTTT
* *
40534195 CTTGTTCAACCAAATAGCGAAATATCTTTTCAAAAATTTCAATA
66 CTTGTTCAACCAAATAGCCAAATATCTTTTCAAAAATTTCAAAA
* * * * * *
40534239 TAAGGCAATGTTTTGCGTTTGAAAATTTGAGAAAGCGTGCCCTAATGTGTTGGGTTTCGATTTTT
1 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGATTCAATTTTT
** * *
40534304 CTCATTCATCCAAATAGCCAAATATCTTTTCAAAAATTTTAAAA
66 CTTGTTCAACCAAATAGCCAAATATCTTTTCAAAAATTTCAAAA
* * * * *
40534348 TAAGGCAATGTTTTGCGTTTGGAAACTCGAGAAAACGTGCCCTAATGCGCAGGGTTTCAATTCTT
1 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGATTCAATTTTT
*
40534413 C--G-TCGGACCAAATAGCCAAATATC
66 CTTGTTC-AACCAAATAGCCAAATATC
40534437 CTCTTATATC
Statistics
Matches: 271, Mismatches: 35, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
106 2 0.01
107 17 0.06
109 252 0.93
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (109 bp):
TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGATTCAATTTTT
CTTGTTCAACCAAATAGCCAAATATCTTTTCAAAAATTTCAAAA
Found at i:40536952 original size:27 final size:27
Alignment explanation
Indices: 40536893--40536958 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
40536883 CCCAAACTGA
*
40536893 TATAAAATGACTGTTATGCCCCCACAT
1 TATAAAATGACTGTCATGCCCCCACAT
** * **
40536920 GGTAAAATGACTGTCATGCCCCTATGT
1 TATAAAATGACTGTCATGCCCCCACAT
40536947 TATAAAATGACT
1 TATAAAATGACT
40536959 ATATGCTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (27 bp):
TATAAAATGACTGTCATGCCCCCACAT
Found at i:40548334 original size:20 final size:20
Alignment explanation
Indices: 40548306--40548356 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
40548296 GATACCATTT
* *
40548306 TATCAATACTTTTTGAAA-AA
1 TATCGATACTATTT-AAAGAA
*
40548326 TATCGATACCTATTTAAAGAG
1 TATCGATA-CTATTTAAAGAA
40548347 TATCGATACT
1 TATCGATACT
40548357 GATGGGACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (20 bp):
TATCGATACTATTTAAAGAA
Found at i:40550471 original size:28 final size:28
Alignment explanation
Indices: 40550440--40550498 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
40550430 TTTGAACAAA
*
40550440 AAAAAATTCAAAGCATGAATAATATTTC
1 AAAAAATTCAAAGCATGAATAATATGTC
**
40550468 AAAACTTTCAAAGCATGAATAATATGTC
1 AAAAAATTCAAAGCATGAATAATATGTC
40550496 AAA
1 AAA
40550499 TATTTTTGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (28 bp):
AAAAAATTCAAAGCATGAATAATATGTC
Found at i:40551759 original size:49 final size:50
Alignment explanation
Indices: 40551691--40551892 Score: 182
Period size: 49 Copynumber: 4.0 Consensus size: 50
40551681 CTCGTAAGTC
* * * *
40551691 CCTCTCATGCATTTGGGAGCAGGGTCA-TCTTATTACTTTTC-GTAAGCCT
1 CCTCCCATGCGTTTAGGAGCAGGGTCACT-TTATTACTTTTCTATAAGCCT
* *
40551740 CCTTCCATGCGTTTAGGAGCAGGGTCACTTTATTATAATTTTCTATAAGCCTT
1 CCTCCCATGCGTTTAGGAGCAGGGTCACTTTA-T-TACTTTTCTATAAGCC-T
* * * * *
40551793 CC-CCCATACGTTCAGGAACAGGG-C-CTTTATTACTACATTCTATAAGCCC
1 CCTCCCATGCGTTTAGGAGCAGGGTCACTTTATTACT--TTTCTATAAGCCT
* * *
40551842 CCTCCCATACGTTTAGGAGCAGGGTCACTTTATTAC-CTTCTGTAAGCCT
1 CCTCCCATGCGTTTAGGAGCAGGGTCACTTTATTACTTTTCTATAAGCCT
40551891 CC
1 CC
40551893 CTTCATGCAT
Statistics
Matches: 125, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
48 3 0.02
49 41 0.33
50 37 0.30
51 9 0.07
52 32 0.26
53 3 0.02
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (50 bp):
CCTCCCATGCGTTTAGGAGCAGGGTCACTTTATTACTTTTCTATAAGCCT
Found at i:40551815 original size:52 final size:52
Alignment explanation
Indices: 40551733--40551877 Score: 174
Period size: 50 Copynumber: 2.8 Consensus size: 52
40551723 TTACTTTTCG
* * *
40551733 TAAGCCTCCTTCCATGCGTTTAGGAGCAGGGTCACTTTATTA-TA-ATTTTCTA
1 TAAGCCCCCTCCCATACGTTTAGGAGCAGGGTCACTTTATTACTACA--TTCTA
* * *
40551785 TAAGCCTTCC-CCCATACGTTCAGGAACAGGG-C-CTTTATTACTACATTCTA
1 TAAGCC-CCCTCCCATACGTTTAGGAGCAGGGTCACTTTATTACTACATTCTA
40551835 TAAGCCCCCTCCCATACGTTTAGGAGCAGGGTCACTTTATTAC
1 TAAGCCCCCTCCCATACGTTTAGGAGCAGGGTCACTTTATTAC
40551878 CTTCTGTAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
49 2 0.03
50 38 0.47
51 4 0.05
52 33 0.41
53 3 0.04
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (52 bp):
TAAGCCCCCTCCCATACGTTTAGGAGCAGGGTCACTTTATTACTACATTCTA
Found at i:40552209 original size:22 final size:22
Alignment explanation
Indices: 40552147--40552219 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
40552137 ATTGTTCAAA
* **
40552147 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
40552169 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
40552191 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
40552213 CATGAGA
1 CATGAGA
40552220 ACTTGGCCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:40552449 original size:20 final size:19
Alignment explanation
Indices: 40552400--40552449 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
40552390 TGAAAGTCTT
*
40552400 AAAAACCGTTATATTTTGG
1 AAAAACCTTTATATTTTGG
**
40552419 AAATTCACTTTATATTTTCGG
1 AAAAAC-CTTTATATTTT-GG
40552440 AAAAACCTTT
1 AAAAACCTTT
40552450 GTTTTCATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAAAACCTTTATATTTTGG
Found at i:40559546 original size:21 final size:21
Alignment explanation
Indices: 40559522--40559570 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
40559512 CACATCACAG
*
40559522 ATAATATGCAGTCAAGCTGCC
1 ATAATATGCAGTCAAGCTACC
40559543 ATAATATGCAGTCAAGCTACC
1 ATAATATGCAGTCAAGCTACC
*
40559564 AGAATAT
1 ATAATAT
40559571 AGGCAAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (21 bp):
ATAATATGCAGTCAAGCTACC
Found at i:40562712 original size:16 final size:16
Alignment explanation
Indices: 40562691--40562734 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
40562681 GTATAAAAAA
40562691 TATTTTTAATATTAAT
1 TATTTTTAATATTAAT
40562707 TATTTTTAATATTAAT
1 TATTTTTAATATTAAT
* *
40562723 TAATTTTCATAT
1 TATTTTTAATAT
40562735 GGATGCTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAATATTAAT
Found at i:40566964 original size:28 final size:28
Alignment explanation
Indices: 40566920--40566989 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
40566910 ACATTTAATT
* *
40566920 AATTTTTTAAAATTTAAAAAT-TTA-AA
1 AATTTTTAAAAAATTAAAAATATTATAA
*
40566946 AACTATTTTAAAAAATTAAAATTATTATAA
1 AA-T-TTTTAAAAAATTAAAAATATTATAA
40566976 AATTTTTAAAAAAT
1 AATTTTTAAAAAAT
40566990 ATTTTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 26 0.70
29 4 0.11
30 4 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTTTTAAAAAATTAAAAATATTATAA
Found at i:40567010 original size:21 final size:19
Alignment explanation
Indices: 40566932--40567002 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
40566922 TTTTTTAAAA
40566932 TTTAAAAATTTAAAAACTAT
1 TTTAAAAATTTAAAAA-TAT
* *
40566952 TTTAAAAAATTAAAATTAT
1 TTTAAAAATTTAAAAATAT
* *
40566971 TATAAAATTTTTAAAAAATAT
1 TTTAAAA-ATTT-AAAAATAT
*
40566992 TTTTAAAATTT
1 TTTAAAAATTT
40567003 TTAAAAATTA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 9 0.22
20 19 0.47
21 12 0.30
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAAAAATTTAAAAATAT
Done.