Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 72 of 135
Found at i:28433860 original size:18 final size:18
Alignment explanation
Indices: 28433803--28433868 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
28433793 GTGAACCATG
* *
28433803 TTAACTTGGTGAATTATA
1 TTAATTTGGTGAATTGTA
* *
28433821 TT-ATTATGGTGAACTGTG
1 TTAATT-TGGTGAATTGTA
*
28433839 TTAATTTGGTGATTTGTA
1 TTAATTTGGTGAATTGTA
*
28433857 TTAATATGGTGA
1 TTAATTTGGTGA
28433869 GATGTATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 2 0.05
18 33 0.87
19 3 0.08
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (18 bp):
TTAATTTGGTGAATTGTA
Found at i:28433874 original size:18 final size:17
Alignment explanation
Indices: 28433809--28433876 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 17
28433799 CATGTTAACT
* *
28433809 TGGTGAATTATATTATTA
1 TGGTGAA-TGTATTAATA
* *
28433827 TGGTGAACTGTGTTAATT
1 TGGTGAA-TGTATTAATA
*
28433845 TGGTGATTTGTATTAATA
1 TGGTGA-ATGTATTAATA
28433863 TGGTGAGATGTATT
1 TGGTGA-ATGTATT
28433877 TTGTCAAACT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.47
Consensus pattern (17 bp):
TGGTGAATGTATTAATA
Found at i:28434525 original size:17 final size:17
Alignment explanation
Indices: 28434505--28434578 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 17
28434495 TTACGATGGA
28434505 GCATGAACTGTTATTTT
1 GCATGAACTGTTATTTT
* **
28434522 GCATGAATTGTTATTCA
1 GCATGAACTGTTATTTT
* * *
28434539 GTATGAACTGATATTTC
1 GCATGAACTGTTATTTT
** * *
28434556 ATATGAACTATTGTTTT
1 GCATGAACTGTTATTTT
28434573 GCATGA
1 GCATGA
28434579 GCTGCCATTT
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (17 bp):
GCATGAACTGTTATTTT
Found at i:28435831 original size:14 final size:15
Alignment explanation
Indices: 28435797--28435838 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
28435787 TTAGGTGCCA
* *
28435797 AAAAAGTAAGTGTTG
1 AAAAATTAAGTATTG
28435812 AAAAATTAAGTATTG
1 AAAAATTAAGTATTG
*
28435827 AAAATTTAAGTA
1 AAAAATTAAGTA
28435839 CTAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (15 bp):
AAAAATTAAGTATTG
Found at i:28435835 original size:15 final size:15
Alignment explanation
Indices: 28435803--28435850 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
28435793 GCCAAAAAAG
* *
28435803 TAAGTGTTGAAAAAT
1 TAAGTATTGAAAATT
28435818 TAAGTATTGAAAATT
1 TAAGTATTGAAAATT
*
28435833 TAAGTACT--AAATT
1 TAAGTATTGAAAATT
28435846 TAAGT
1 TAAGT
28435851 TATAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 10 0.33
15 20 0.67
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.38
Consensus pattern (15 bp):
TAAGTATTGAAAATT
Found at i:28440017 original size:16 final size:15
Alignment explanation
Indices: 28439969--28440018 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
28439959 AATTATTTTT
28439969 GAGTTTTCTTTTTAA
1 GAGTTTTCTTTTTAA
* *
28439984 GA-ATTTCTCTTT--
1 GAGTTTTCTTTTTAA
28439996 GAGTTTTCTTTTATAA
1 GAGTTTTCTTTT-TAA
28440012 GAGTTTT
1 GAGTTTT
28440019 AACAATCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
12 2 0.07
13 7 0.26
14 9 0.33
15 2 0.07
16 7 0.26
ACGTcount: A:0.20, C:0.08, G:0.14, T:0.58
Consensus pattern (15 bp):
GAGTTTTCTTTTTAA
Found at i:28452137 original size:20 final size:21
Alignment explanation
Indices: 28452114--28452158 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
28452104 TTTAAAATTT
*
28452114 AAAATAGAAAATTAATATAA-
1 AAAATAAAAAATTAATATAAC
*
28452134 AAAATAAAAAATTTATATAAC
1 AAAATAAAAAATTAATATAAC
28452155 AAAA
1 AAAA
28452159 AAAGAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATAAAAAATTAATATAAC
Found at i:28454103 original size:36 final size:36
Alignment explanation
Indices: 28454034--28454119 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
28454024 CTACCTTCAT
** *
28454034 CCGATTTGCTTCCTTGTTTCTTTGCTTTTCTTTTCTG
1 CCGATTTGC-TCCCAGTTTATTTGCTTTTCTTTTCTG
*
28454071 CCGATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTG
1 CCGATTTGCTCCCAGTTTATTTGCTTTTCTTTTCTG
28454107 CCGATTTGCTCCC
1 CCGATTTGCTCCC
28454120 CCCGTTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 36 0.80
37 9 0.20
ACGTcount: A:0.06, C:0.28, G:0.13, T:0.53
Consensus pattern (36 bp):
CCGATTTGCTCCCAGTTTATTTGCTTTTCTTTTCTG
Found at i:28455523 original size:16 final size:16
Alignment explanation
Indices: 28455506--28455577 Score: 81
Period size: 16 Copynumber: 4.2 Consensus size: 16
28455496 GATTTGCTAT
* *
28455506 TACACCTCTATTCTAT
1 TACACCTCTAATCTAA
*
28455522 TACACCTCTAATCCAA
1 TACACCTCTAATCTAA
28455538 TACACCTCTAATCTAA
1 TACACCTCTAATCTAA
28455554 TACAGACACCTCTAATCTAA
1 T----ACACCTCTAATCTAA
28455574 TACA
1 TACA
28455578 GCGAACCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
16 32 0.67
20 16 0.33
ACGTcount: A:0.36, C:0.32, G:0.01, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCTAA
Found at i:28455564 original size:20 final size:20
Alignment explanation
Indices: 28455539--28455578 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28455529 CTAATCCAAT
28455539 ACACCTCTAATCTAATACAG
1 ACACCTCTAATCTAATACAG
28455559 ACACCTCTAATCTAATACAG
1 ACACCTCTAATCTAATACAG
28455579 CGAACCAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.05, T:0.25
Consensus pattern (20 bp):
ACACCTCTAATCTAATACAG
Found at i:28486782 original size:27 final size:27
Alignment explanation
Indices: 28486740--28486796 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
28486730 AAATACTTTC
*
28486740 TATTTTTT-TCTATTTTAATTTTTAAAAA
1 TATTTTTTAT-TATTTTAA-ATTTAAAAA
*
28486768 TATTTTTTATTTTTTTAAATTTAAAAA
1 TATTTTTTATTATTTTAAATTTAAAAA
28486795 TA
1 TA
28486797 CTTCATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 15 0.58
29 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTTTTTATTATTTTAAATTTAAAAA
Found at i:28492492 original size:85 final size:85
Alignment explanation
Indices: 28492349--28492520 Score: 317
Period size: 85 Copynumber: 2.0 Consensus size: 85
28492339 AGATACCTTG
*
28492349 GTGATTATTGTAGCTTCTTACAGCAATGTCAAAATATCCTACATCTTTAGCAATGGATGTCTGGC
1 GTGATTATGGTAGCTTCTTACAGCAATGTCAAAATATCCTACATCTTTAGCAATGGATGTCTGGC
28492414 AACAGCCTATACCAGAACAT
66 AACAGCCTATACCAGAACAT
* *
28492434 GTGATTATGGTAGCTTCTTACAGTAATGTCAAAATATCGTACATCTTTAGCAATGGATGTCTGGC
1 GTGATTATGGTAGCTTCTTACAGCAATGTCAAAATATCCTACATCTTTAGCAATGGATGTCTGGC
28492499 AACAGCCTATACCAGAACAT
66 AACAGCCTATACCAGAACAT
28492519 GT
1 GT
28492521 AAAATTGTCC
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (85 bp):
GTGATTATGGTAGCTTCTTACAGCAATGTCAAAATATCCTACATCTTTAGCAATGGATGTCTGGC
AACAGCCTATACCAGAACAT
Found at i:28498065 original size:43 final size:43
Alignment explanation
Indices: 28498004--28498090 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
28497994 GTTCTGTTGG
28498004 CTGTTAAAGCTTACAAACTGCAAAGTTTTCTTGACTTGCATAC
1 CTGTTAAAGCTTACAAACTGCAAAGTTTTCTTGACTTGCATAC
28498047 CTGTTAAAGCTTACAAACTGCAAAGTTTTCTTGACTTGCATAC
1 CTGTTAAAGCTTACAAACTGCAAAGTTTTCTTGACTTGCATAC
28498090 C
1 C
28498091 GTACCACCCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (43 bp):
CTGTTAAAGCTTACAAACTGCAAAGTTTTCTTGACTTGCATAC
Found at i:28501439 original size:7 final size:7
Alignment explanation
Indices: 28501427--28501451 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28501417 TATGTTATGA
28501427 AATAAAT
1 AATAAAT
28501434 AATAAAT
1 AATAAAT
28501441 AATAAAT
1 AATAAAT
28501448 AATA
1 AATA
28501452 GAAAAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:28502899 original size:17 final size:17
Alignment explanation
Indices: 28502877--28503055 Score: 91
Period size: 17 Copynumber: 10.2 Consensus size: 17
28502867 GAGATTTTTT
28502877 TTTTGAAAACACGAGAA
1 TTTTGAAAACACGAGAA
* *
28502894 TTTTG-AAACACAATAA
1 TTTTGAAAACACGAGAA
***
28502910 CTTTTTTGAAAACACGATTTT
1 ---TTTTGAAAACACGA-GAA
*
28502931 TTTTTAAAACACGA-AA
1 TTTTGAAAACACGAGAA
**
28502947 TTTT-TTAACACGAGAA
1 TTTTGAAAACACGAGAA
*
28502963 TTTTTGAAAACA-GGGTAAA
1 -TTTTGAAAACACGAG--AA
*
28502982 TTTTTTGAAAACACGAAAA
1 --TTTTGAAAACACGAGAA
* *
28503001 TTTTTAAAACACGAAAA
1 TTTTGAAAACACGAGAA
*
28503018 TTTGTG-AAACAAGAGAA
1 TTT-TGAAAACACGAGAA
*
28503035 TTATTGAAAACAAGA-AA
1 TT-TTGAAAACACGAGAA
28503052 TTTT
1 TTTT
28503056 TTTAAAACGC
Statistics
Matches: 128, Mismatches: 19, Indels: 31
0.72 0.11 0.17
Matches are distributed among these distances:
15 7 0.05
16 17 0.13
17 47 0.37
18 27 0.21
19 9 0.07
20 19 0.15
21 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTGAAAACACGAGAA
Found at i:28502950 original size:18 final size:17
Alignment explanation
Indices: 28502875--28503075 Score: 122
Period size: 18 Copynumber: 11.3 Consensus size: 17
28502865 TCGAGATTTT
28502875 TTTTTTGAAAACACGAGAA
1 TTTTTT-AAAACACGA-AA
* *
28502894 --TTTTGAAACACAATAA
1 TTTTTTAAAACACGA-AA
**
28502910 CTTTTTTGAAAACACGATTT
1 -TTTTTT-AAAACACGA-AA
28502930 TTTTTTAAAACACGAAA
1 TTTTTTAAAACACGAAA
28502947 TTTTTT--AACACGAGAA
1 TTTTTTAAAACACGA-AA
* *
28502963 TTTTTGAAAACAGGGTAAA
1 TTTTTTAAAACA-CG-AAA
28502982 TTTTTTGAAAACACGAAA
1 TTTTTT-AAAACACGAAA
*
28503000 ATTTTTAAAACACGAAA
1 TTTTTTAAAACACGAAA
* * * *
28503017 ATTTGTGAAACAAGAGAA
1 TTTTTTAAAACACGA-AA
* * *
28503035 TTATTGAAAACAAGAAA
1 TTTTTTAAAACACGAAA
*
28503052 TTTTTTTAAAACGCGACAA
1 -TTTTTTAAAACACGA-AA
28503071 TTTTT
1 TTTTT
28503076 GAAATACGAG
Statistics
Matches: 143, Mismatches: 26, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
15 7 0.05
16 16 0.11
17 35 0.24
18 49 0.34
19 21 0.15
20 15 0.10
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (17 bp):
TTTTTTAAAACACGAAA
Found at i:28502957 original size:53 final size:53
Alignment explanation
Indices: 28502872--28503007 Score: 141
Period size: 53 Copynumber: 2.5 Consensus size: 53
28502862 AACTCGAGAT
** *
28502872 TTTTTTTTTGAAAACACGAGAATTTTGAAACACAATAACTTTTTTGAAAACA-CG-A
1 TTTTTTTTT-AAAACACGA-AATTTTTTAACACAAGAA--TTTTTGAAAACAGCGTA
* *
28502927 TTTTTTTTTAAAACACGAAATTTTTTAACACGAGAATTTTTGAAAACAGGGTA
1 TTTTTTTTTAAAACACGAAATTTTTTAACACAAGAATTTTTGAAAACAGCGTA
** * *
28502980 AATTTTTTGAAAACACGAAAATTTTTAA
1 TTTTTTTTTAAAACACGAAATTTTTTAA
28503008 AACACGAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
51 12 0.17
52 1 0.01
53 39 0.56
54 9 0.13
55 9 0.13
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Consensus pattern (53 bp):
TTTTTTTTTAAAACACGAAATTTTTTAACACAAGAATTTTTGAAAACAGCGTA
Found at i:28503134 original size:21 final size:20
Alignment explanation
Indices: 28503071--28503134 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
28503061 AACGCGACAA
*
28503071 TTTTTGAAATACGAGAGATTTT
1 TTTTTGAAACACGA-AGA-TTT
* *
28503093 TTTTTAAAAACGCGAA-ATTT
1 TTTTT-GAAACACGAAGATTT
*
28503113 TTTTTGAAACACGAAGACTT
1 TTTTTGAAACACGAAGATTT
28503133 TT
1 TT
28503135 GAAAATGCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 8 0.24
20 13 0.38
21 1 0.03
22 6 0.18
23 6 0.18
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.42
Consensus pattern (20 bp):
TTTTTGAAACACGAAGATTT
Found at i:28503201 original size:15 final size:15
Alignment explanation
Indices: 28503176--28503208 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
28503166 ACGAGTAATT
28503176 TTTGAAAACACGAAAA
1 TTTGAAAACAC-AAAA
28503192 TTTG-AAACACAAAA
1 TTTGAAAACACAAAA
28503206 TTT
1 TTT
28503209 TTCTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (15 bp):
TTTGAAAACACAAAA
Found at i:28503523 original size:5 final size:5
Alignment explanation
Indices: 28503513--28503556 Score: 54
Period size: 5 Copynumber: 8.4 Consensus size: 5
28503503 GAATTTAACG
28503513 AATAA AATAA AATAA AATTAA AA-AA ACATAA ATATAA AATAA AA
1 AATAA AATAA AATAA AA-TAA AATAA A-ATAA A-ATAA AATAA AA
28503557 AATACTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
4 3 0.09
5 19 0.54
6 13 0.37
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:28503550 original size:16 final size:15
Alignment explanation
Indices: 28503513--28503556 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
28503503 GAATTTAACG
28503513 AATAAAATAAAATAA
1 AATAAAATAAAATAA
28503528 AATTAAAA-AAACATAA
1 AA-TAAAATAAA-ATAA
28503544 ATATAAAATAAAA
1 A-ATAAAATAAAA
28503557 AATACTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAATAAAATAA
Found at i:28503566 original size:22 final size:21
Alignment explanation
Indices: 28503519--28503567 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
28503509 AACGAATAAA
28503519 ATAAAATAAAATTAAAAAAAC
1 ATAAAATAAAATTAAAAAAAC
28503540 ATAAATATAAAA-TAAAAAATAC
1 ATAAA-ATAAAATTAAAAAA-AC
*
28503562 TTAAAA
1 ATAAAA
28503568 ATATGCAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (21 bp):
ATAAAATAAAATTAAAAAAAC
Found at i:28504015 original size:26 final size:27
Alignment explanation
Indices: 28503977--28504117 Score: 96
Period size: 26 Copynumber: 5.1 Consensus size: 27
28503967 TATAAAATAT
*
28503977 TTTTTTCCTTTTTCCTTTTTTCTCTTTC
1 TTTTTT-CTTCTTCCTTTTTTCTCTTTC
* *
28504005 TTTTTTCTT-TTTCTTTCTTCT-TCTTC
1 TTTTTTCTTCTTCCTTTTTTCTCT-TTC
*
28504031 TTCTTCTTCTTCTTCC-TTCTT-TCTTTC
1 TT-TT-TTCTTCTTCCTTTTTTCTCTTTC
*
28504058 TCTTTTTCTTTCTTCTTCTTCTTTTTTCTTTC
1 T-TTTTTC-TTCTTC--CTT-TTTTCTCTTTC
*
28504090 TTTTTT-TTCTTCTTCTTTTTC-CTTTC
1 TTTTTTCTTCTTCCT-TTTTTCTCTTTC
28504116 TT
1 TT
28504118 CTTCGTTCAG
Statistics
Matches: 94, Mismatches: 6, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
25 1 0.01
26 25 0.27
27 23 0.24
28 19 0.20
29 10 0.11
30 1 0.01
31 8 0.09
32 7 0.07
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTTTTCTTCTTCCTTTTTTCTCTTTC
Found at i:28504018 original size:6 final size:6
Alignment explanation
Indices: 28503978--28504120 Score: 92
Period size: 6 Copynumber: 22.3 Consensus size: 6
28503968 ATAAAATATT
* *
28503978 TTTTTCC TTTTTCC TTTTTTC TCTTTC TTTTTTC TTTTTC --TTTC TTCTTC
1 TTTTT-C TTTTT-C -TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC
* * * * *
28504028 TTCTTC TTCTTC TTCTTCC TTCTTTC TTTCTC TTTTTC TTTCTTC TTCTTC
1 TTTTTC TTTTTC TT-TTTC TT-TTTC TTTTTC TTTTTC TTT-TTC TTTTTC
* *
28504079 TTTTTTC TTTCTTT TTTTTC TTCTTC TTTTTCC TTTCTTC TT
1 -TTTTTC TTT-TTC TTTTTC TTTTTC TTTTT-C TTT-TTC TT
28504121 CGTTCAGCCC
Statistics
Matches: 112, Mismatches: 14, Indels: 20
0.77 0.10 0.14
Matches are distributed among these distances:
4 4 0.04
6 56 0.50
7 45 0.40
8 7 0.06
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:28504027 original size:3 final size:3
Alignment explanation
Indices: 28504009--28504121 Score: 90
Period size: 3 Copynumber: 37.0 Consensus size: 3
28503999 TCTTTCTTTT
*
28504009 TTC TTT TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTCC TTC TTTC TT-
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC -TTC TTC
* * *
28504056 TCTC TTT TTC TTTC TTC TTC TTC TT- TT- TTC TTTC TTT TTT TTC TTC
1 T-TC TTC TTC -TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC
* *
28504102 TTC TTT TTC CT- TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC
28504122 GTTCAGCCCC
Statistics
Matches: 91, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
2 6 0.07
3 69 0.76
4 16 0.18
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:28504689 original size:29 final size:29
Alignment explanation
Indices: 28504621--28504689 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
28504611 GAAAATTTTG
* * * *
28504621 GGGTCAAAATGTAATTTTAAAAAGTTGAG
1 GGGTCAAAGTGAAATTTCAAAAAGTTGAA
* *
28504650 GGGTTAAAGTGAAATTTCAAAAAGTTTAA
1 GGGTCAAAGTGAAATTTCAAAAAGTTGAA
*
28504679 GGGTCATAGTG
1 GGGTCAAAGTG
28504690 CAATGATAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.30
Consensus pattern (29 bp):
GGGTCAAAGTGAAATTTCAAAAAGTTGAA
Found at i:28512303 original size:49 final size:49
Alignment explanation
Indices: 28512248--28512393 Score: 211
Period size: 49 Copynumber: 3.0 Consensus size: 49
28512238 TTCGTTTTCT
* * *
28512248 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACAAATCACATAC
* *
28512297 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACAAATCACATAC
* * *
28512346 CGATGCCATAGCCCAGCTATGGTCTTATACGGAATCGCATAATCACAT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACA-AATCACAT
28512394 GTTCACATGT
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
49 80 0.93
50 6 0.07
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.25
Consensus pattern (49 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACAAATCACATAC
Found at i:28513851 original size:3 final size:3
Alignment explanation
Indices: 28513843--28513889 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
28513833 AACAAAATTG
* * *
28513843 ATA ATA ATA ATA ATAA ATA GTA ATA ATA ATA ATA TTA TTA A-A ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28513888 AT
1 AT
28513890 TAATTAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:28514637 original size:5 final size:5
Alignment explanation
Indices: 28514622--28514650 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
28514612 TATGTAAAAG
28514622 ATAAA AT-AA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
28514651 CAAGCAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:28518434 original size:22 final size:22
Alignment explanation
Indices: 28518399--28518462 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
28518389 TATAATCTAA
*
28518399 ATTAAAAACAAAAAATATATTTG
1 ATTAAAAA-TAAAAATATATTTG
28518422 ATTAAAAATAAAAATATATTTG
1 ATTAAAAATAAAAATATATTTG
28518444 ATTAAAAATAAAAATATAT
1 ATTAAAAATAAAAATATAT
28518463 ATATTTAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
22 32 0.80
23 8 0.20
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (22 bp):
ATTAAAAATAAAAATATATTTG
Found at i:28518470 original size:22 final size:22
Alignment explanation
Indices: 28518400--28518470 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
28518390 ATAATCTAAA
* *
28518400 TTAAAAACAAAAA-ATATATTT
1 TTAAAAATAAAAATATATATAT
*
28518421 GATTAAAAATAAAAATATATTTGA-
1 --TTAAAAATAAAAATATATAT-AT
28518445 TTAAAAATAAAAATATATATAT
1 TTAAAAATAAAAATATATATAT
28518467 TTAA
1 TTAA
28518471 TATATAATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.02
22 23 0.56
23 12 0.29
24 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (22 bp):
TTAAAAATAAAAATATATATAT
Found at i:28521780 original size:11 final size:11
Alignment explanation
Indices: 28521764--28521788 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28521754 GGCGTGGAAA
28521764 ATTTCTCTGGC
1 ATTTCTCTGGC
28521775 ATTTCTCTGGC
1 ATTTCTCTGGC
28521786 ATT
1 ATT
28521789 CATAAAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.48
Consensus pattern (11 bp):
ATTTCTCTGGC
Found at i:28530918 original size:20 final size:20
Alignment explanation
Indices: 28530893--28530932 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28530883 TAAGTGCCTA
* *
28530893 AAATGAATTTTTATATAATT
1 AAATGAATATCTATATAATT
*
28530913 AAATGACTATCTATATAATT
1 AAATGAATATCTATATAATT
28530933 TACCCATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATGAATATCTATATAATT
Found at i:28540571 original size:41 final size:41
Alignment explanation
Indices: 28540514--28540619 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
28540504 AATGAGATAA
* *
28540514 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
28540555 TTCAGACTATACGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
28540596 TTCGGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
28540620 AATTGCCAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
Found at i:28541635 original size:41 final size:41
Alignment explanation
Indices: 28541573--28541674 Score: 168
Period size: 41 Copynumber: 2.5 Consensus size: 41
28541563 AGATAATTCA
* * *
28541573 GACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGTTTCT
1 GACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATATTTCG
*
28541614 GACTATACGTCTAGCAGGCTTGACGCCGGTGAAATATTTCG
1 GACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATATTTCG
28541655 GACTTTACGTCTAGCAGGCT
1 GACTTTACGTCTAGCAGGCT
28541675 AATTGCCAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (41 bp):
GACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATATTTCG
Found at i:28547492 original size:22 final size:22
Alignment explanation
Indices: 28547467--28547508 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28547457 ATATATACAT
*
28547467 ATCAATTAAATAAATACATGTC
1 ATCAATCAAATAAATACATGTC
28547489 ATCAATCAAATAAATACATG
1 ATCAATCAAATAAATACATG
28547509 GTTTAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (22 bp):
ATCAATCAAATAAATACATGTC
Found at i:28547766 original size:31 final size:31
Alignment explanation
Indices: 28547708--28547766 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
28547698 AAGTATATGA
*
28547708 TTAAATCAAAATTAAAATTTTAAATATACAT
1 TTAAATCAAAATTAAAATTTCAAATATACAT
* *
28547739 TTAAATCACAATTAAAATTTCACATATA
1 TTAAATCAAAATTAAAATTTCAAATATA
28547767 TACTTACACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (31 bp):
TTAAATCAAAATTAAAATTTCAAATATACAT
Found at i:28553655 original size:20 final size:21
Alignment explanation
Indices: 28553632--28553671 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
28553622 GTTATGTCAC
*
28553632 ATTAACAAAA-ATTTTAAAAA
1 ATTAACAAAATATTCTAAAAA
*
28553652 ATTAATAAAATATTCTAAAA
1 ATTAACAAAATATTCTAAAA
28553672 TTTTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAACAAAATATTCTAAAAA
Found at i:28553812 original size:20 final size:20
Alignment explanation
Indices: 28553789--28553840 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
28553779 ATTATTAGCA
*
28553789 ATTATTTAAAAATATTAAAT
1 ATTATATAAAAATATTAAAT
* * *
28553809 ATTAAATAATATTATTAAAT
1 ATTATATAAAAATATTAAAT
*
28553829 ATT-TCTAAAAAT
1 ATTATATAAAAAT
28553841 CATAAAATTA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTATATAAAAATATTAAAT
Found at i:28561355 original size:50 final size:52
Alignment explanation
Indices: 28561298--28561417 Score: 128
Period size: 50 Copynumber: 2.4 Consensus size: 52
28561288 TATCCCAAAT
* * *
28561298 ATGGTCTTACATAGGAG-T-TCTCATATCGGTGCCCATGCCATGTCGC-AGAC
1 ATGGTCTTACATAGGAGATCTCTCATATCGGTGCCAACGCCATATC-CTAGAC
* * *
28561348 ATGGTCTT--ATGGGGGATCTCTCATCTCGGTGCCAACGCCATATCCTAGAC
1 ATGGTCTTACATAGGAGATCTCTCATATCGGTGCCAACGCCATATCCTAGAC
28561398 ATGGTCTTACAT-GG-GATCTC
1 ATGGTCTTACATAGGAGATCTC
28561418 ATCCCCTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
48 5 0.08
49 2 0.03
50 48 0.81
51 2 0.03
52 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (52 bp):
ATGGTCTTACATAGGAGATCTCTCATATCGGTGCCAACGCCATATCCTAGAC
Found at i:28564808 original size:21 final size:20
Alignment explanation
Indices: 28564784--28564835 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
28564774 GATTTCTCCA
*
28564784 TTTTTTTTTCCTTTTTACTGT
1 TTTTTTTTTCATTTTT-CTGT
28564805 TTTTTGTTTTCATTTTTCTGT
1 TTTTT-TTTTCATTTTTCTGT
28564826 TGTTTTTTTT
1 T-TTTTTTTT
28564836 GTAAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.04, C:0.10, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTCATTTTTCTGT
Found at i:28564809 original size:22 final size:21
Alignment explanation
Indices: 28564784--28564835 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
28564774 GATTTCTCCA
*
28564784 TTTTTTTTTCCTTTTTACTGTT
1 TTTTTTTTTCATTTTT-CTGTT
*
28564806 TTTTGTTTTCATTTTTCTGTT
1 TTTTTTTTTCATTTTTCTGTT
*
28564827 GTTTTTTTT
1 TTTTTTTTT
28564836 GTAAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.04, C:0.10, G:0.08, T:0.79
Consensus pattern (21 bp):
TTTTTTTTTCATTTTTCTGTT
Found at i:28565390 original size:3 final size:3
Alignment explanation
Indices: 28565373--28565457 Score: 75
Period size: 3 Copynumber: 27.3 Consensus size: 3
28565363 ATCATTAAGT
*
28565373 TTA TTA -TA TTAA TTA TTA TTA TTG TTA TTA TTA CTGTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA
* * *
28565420 GTA TTA TTTA TTA TTA -TA TTA CATA TTA ATA TTA TTA T
1 TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
28565458 ACTTATATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
2 4 0.06
3 51 0.76
4 10 0.15
5 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:28565432 original size:16 final size:15
Alignment explanation
Indices: 28565373--28565440 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 15
28565363 ATCATTAAGT
*
28565373 TTATTATATTAATTA
1 TTATTATATTATTTA
*
28565388 TTA-T-TATT-GTTA
1 TTATTATATTATTTA
*
28565400 TTATTACT-GTA-TTA
1 TTATTA-TATTATTTA
28565414 TTATTAGTATTATTTA
1 TTATTA-TATTATTTA
28565430 TTATTATATTA
1 TTATTATATTA
28565441 CATATTAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.14
13 5 0.12
14 12 0.28
15 11 0.26
16 9 0.21
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (15 bp):
TTATTATATTATTTA
Found at i:28570456 original size:15 final size:14
Alignment explanation
Indices: 28570414--28570458 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
28570404 AAAGATGTGA
*
28570414 AAAAATAAAAATAG
1 AAAAATAAAAATGG
28570428 AAAAATGAAAAATGG
1 AAAAAT-AAAAATGG
28570443 AAAAAGTAAAAATGG
1 AAAAA-TAAAAATGG
28570458 A
1 A
28570459 GAGGCTAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 6 0.21
15 21 0.75
16 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (14 bp):
AAAAATAAAAATGG
Found at i:28571955 original size:100 final size:100
Alignment explanation
Indices: 28571755--28572896 Score: 1631
Period size: 100 Copynumber: 11.4 Consensus size: 100
28571745 GTTATAGCGA
*
28571755 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAATT-AAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
*
28571819 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGCGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
* * * *
28571854 AGCAAATTGAAGTCACAACGACAGATCTGGTTTCCCTGACAGCGCAATTAAAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
* * * * *
28571919 CAACGGCGGATCATGCTTCCCTGGTGGTGCAGCGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
*
28571954 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
* *
28572019 CAACGACGGATCTTACTTCCCTGGCGGTGCAGTGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
*
28572054 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
* * *
28572119 CAACGGCGGATTTTACTTCCCTGGCGGTGTAGTGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
* * * *
28572154 AGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCTCGACAGCACAATTTAAAAGGATTGAAGCC
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAA-TTAAAAAGATTGAAGCC
*
28572219 ACAACGGCAGATCTTACTTCCGTGGCGGTGCAGTGG
65 ACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
* * *
28572255 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCAACAGCGTAATTTAAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
* *
28572320 CAACGGCAGATCTTACTTCTCTGGCGGTGTAGTGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
** * * *
28572355 AGCAGATTGAAGTCACAACAACGGATCTGGTTTCCCCGATAGCGTAATTTAAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
* * *
28572420 CAACGGTAGATCTTACTTCTCTGGCGGTGTAGTGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
* ** * * *
28572455 AGCAGATTGAAGTCACGACAACGGATCTAGTTTCCCCGACAGCGTAATTAAAAGGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
28572520 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
* *
28572555 AGCAGATTGAAGTCACAACGGCGGATCTAGTTTCCCCGACAGCGCAATTAAAAAGATTAAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
* * * *
28572620 CAACGGCGGATCTTACTTTCCTAGCGGTGCAGCGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
* * *
28572655 AGCAGATTGAATTCACAACGACGGATCTGGTTTCCCCAACAGCGCAATTAAAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
* * *
28572720 CAATGGCATATCTTACTTCCCTGGCGATGCAGTGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
* * *
28572755 AGCATGATTGAAGTCACAACGACGGATCTGATTTCCCCGACAGCACAATTAAAAAGATTGAAGCC
1 AGCA-GATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCC
* * * * *
28572820 ACAACGGCGGATCTTATTTCCTTAGCGGTGCAGTTG
65 ACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
* * * * * *
28572856 AACAGGTTGAAG-CTACGATGGCGGATCTTGTTTCCTCGACA
1 AGCAGATTGAAGTC-ACAACGGCGGATCTGGTTTCCCCGACA
28572897 TTGTAATTGG
Statistics
Matches: 943, Mismatches: 96, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
99 45 0.05
100 721 0.76
101 177 0.19
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (100 bp):
AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCA
CAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGG
Found at i:28572766 original size:501 final size:501
Alignment explanation
Indices: 28571755--28572852 Score: 1669
Period size: 501 Copynumber: 2.2 Consensus size: 501
28571745 GTTATAGCGA
28571755 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAA-TTAAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAATTTAAAAGATTGAAGCCA
*
28571819 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGCGGAGCAAATTGAAGTCACAACGACAGATCTGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGCGGAGCAAATTGAAGTCACAACAACAGATCTGG
* * * *
28571884 TTTCCCTGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCGGATCATGCTTCCCTGGTGGTGC
131 TTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCATACTTCCCTGGCGGTGC
** * *
28571949 AGCGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAAGATTGA
196 AGCGGAGCAGATTGAAGTCACAACAACGGATCTAGTTTCCCCGACAGCGCAATTAAAAAGATTGA
*
28572014 AGCCACAACGACGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGTCACAACGGCGGA
261 AGCCACAACGACAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGTCACAACGGCGGA
* * * * *
28572079 TCTGGTTTCTCCGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCGGATTTTACTTCCCTGGC
326 TCTAGTTTCCCCGACAGCGCAATTAAAAAGATTAAAGCCACAACGGCGGATCTTACTTCCCTAGC
* * * * * *
28572144 GGTGTAGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCTCGACAGCACAATTTAAAAG
391 GGTGCAGCGGAGCAGATTGAAGTCACAACGACAGATCTGGTTTCCCCAACAGCACAATTTAAAAA
* *
28572209 GATTGAAGCCACAACGGCAGATCTTACTTCCGTGGCGGTGCAGTGG
456 GATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGATGCAGTGG
* **
28572255 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCAACAGCGTAATTTAAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAATTTAAAAGATTGAAGCCA
* * * * *
28572320 CAACGGCAGATCTTACTTCTCTGGCGGTGTAGTGGAGCAGATTGAAGTCACAACAACGGATCTGG
66 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGCGGAGCAAATTGAAGTCACAACAACAGATCTGG
* * * * * * *
28572385 TTTCCCCGATAGCGTAATTTAAAAGATTGAAGCCACAACGGTAGATCTTACTTCTCTGGCGGTGT
131 TTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCATACTTCCCTGGCGGTGC
* * * *
28572450 AGTGGAGCAGATTGAAGTCACGACAACGGATCTAGTTTCCCCGACAGCGTAATTAAAAGGATTGA
196 AGCGGAGCAGATTGAAGTCACAACAACGGATCTAGTTTCCCCGACAGCGCAATTAAAAAGATTGA
*
28572515 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGTCACAACGGCGGA
261 AGCCACAACGACAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGTCACAACGGCGGA
*
28572580 TCTAGTTTCCCCGACAGCGCAATTAAAAAGATTAAAGCCACAACGGCGGATCTTACTTTCCTAGC
326 TCTAGTTTCCCCGACAGCGCAATTAAAAAGATTAAAGCCACAACGGCGGATCTTACTTCCCTAGC
* * *
28572645 GGTGCAGCGGAGCAGATTGAATTCACAACGACGGATCTGGTTTCCCCAACAGCGCAA-TTAAAAA
391 GGTGCAGCGGAGCAGATTGAAGTCACAACGACAGATCTGGTTTCCCCAACAGCACAATTTAAAAA
* *
28572709 GATTGAAGCCACAATGGCATATCTTACTTCCCTGGCGATGCAGTGG
456 GATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGATGCAGTGG
* * *
28572755 AGCATGATTGAAGTCACAACGACGGATCTGATTTCCCCGACAGCACAATTAAAAAGATTGAAGCC
1 AGCA-GATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAATTTAAAAGATTGAAGCC
* * * *
28572820 ACAACGGCGGATCTTATTTCCTTAGCGGTGCAG
65 ACAACGGCAGATCTTACTTCCCTGGCGGTGCAG
28572853 TTGAACAGGT
Statistics
Matches: 535, Mismatches: 61, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
500 96 0.18
501 439 0.82
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (501 bp):
AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAATTTAAAAGATTGAAGCCA
CAACGGCAGATCTTACTTCCCTGGCGGTGCAGCGGAGCAAATTGAAGTCACAACAACAGATCTGG
TTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCATACTTCCCTGGCGGTGC
AGCGGAGCAGATTGAAGTCACAACAACGGATCTAGTTTCCCCGACAGCGCAATTAAAAAGATTGA
AGCCACAACGACAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGTCACAACGGCGGA
TCTAGTTTCCCCGACAGCGCAATTAAAAAGATTAAAGCCACAACGGCGGATCTTACTTCCCTAGC
GGTGCAGCGGAGCAGATTGAAGTCACAACGACAGATCTGGTTTCCCCAACAGCACAATTTAAAAA
GATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGATGCAGTGG
Found at i:28572866 original size:50 final size:49
Alignment explanation
Indices: 28571807--28572891 Score: 329
Period size: 50 Copynumber: 21.7 Consensus size: 49
28571797 CACAATTAAA
* * * ** *
28571807 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTA-TTTCCTAGCGGTGCAGTTGAAC
* * * * ** * * * * *
28571857 AAATTGAAGTCACAACGACAGATCTGGTTTCCCT-GACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTATTT-CCTAG-CGGTGCAGTTGAAC
** * * * ** *
28571907 AGATTGAAGCCACAACGGCGGATCATGCTTCCCTGGTGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATC-TTATTTCCTAGCGGTGCAGTTGAAC
* * * * * * *
28571957 AGATTGAAGTCACAACGGCGGATCTGGT-TTCTCCGA-CAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCT--TATT-TCCTAGCGGTGCAGTTGAAC
* * * * *
28572007 AGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTA-TTTCCTAGCGGTGCAGTTGAAC
* * * * * * *
28572057 AGATTGAAGTCACAACGGCGGATCTGGT-TTCTCCGA-CAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCT--TATT-TCCTAGCGGTGCAGTTGAAC
* * * * * *
28572107 AGATTGAAGCCACAACGGCGGATTTTACTTCCCTGGCGGTGTAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTA-TTTCCTAGCGGTGCAGTTGAAC
* * ** * * ** * * *
28572157 AGATTGAAGTCACAACGGCAGATCTGGTTTCCTCGACAGCACAATTTAAA
1 AGATTGAAGCCACAACGGCGGATCTTATTTCCTAG-CGGTGCAGTTGAAC
* * * * *
28572207 AGGATTGAAGCCACAACGGCAGATCTTACTTCCGTGGCGGTGCAGTGGAGC
1 A-GATTGAAGCCACAACGGCGGATCTTATTTCC-TAGCGGTGCAGTTGAAC
* ** * * * * * * * *
28572258 AGATTGAAGTCACAACGGCGGATCTGGTTTCCCCAACAGCGTAATTTAAA
1 AGATTGAAGCCACAACGGCGGATCTTATTT-CCTAGCGGTGCAGTTGAAC
* * * * * *
28572308 AGATTGAAGCCACAACGGCAGATCTTACTTCTCTGGCGGTGTAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTATTTC-CTAGCGGTGCAGTTGAAC
* ** ** * * *
28572358 AGATTGAAGTCACAACAACGGATCTGGTTTCCCCGATAGC-GT--AATTTAAA
1 AGATTGAAGCCACAACGGCGGATCTTATTT--CC--TAGCGGTGCAGTTGAAC
** * * * * *
28572408 AGATTGAAGCCACAACGGTAGATCTTACTTCTCTGGCGGTGTAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTATTTC-CTAGCGGTGCAGTTGAAC
* * ** ** * * * * *
28572458 AGATTGAAGTCACGACAACGGATC-TAGTTTCCCCGACAGCGTAATT-AAA
1 AGATTGAAGCCACAACGGCGGATCTTA-TTTCCTAG-CGGTGCAGTTGAAC
* * * * *
28572507 AGGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 A-GATTGAAGCCACAACGGCGGATCTTA-TTTCCTAGCGGTGCAGTTGAAC
* ** * * * * *
28572558 AGATTGAAGTCACAACGGCGGATC-TAGTTTCCCCGACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTA-TTTCCTAG-CGGTGCAGTTGAAC
* ** *
28572608 AGATTAAAGCCACAACGGCGGATCTTACTTTCCTAGCGGTGCAGCGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTA-TTTCCTAGCGGTGCAGTTGAAC
** * ** * * * * * * *
28572658 AGATTGAATTCACAACGACGGATCTGGTTTCCCCAACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTATTT-CCTAGCGGTGCAGTTGAAC
* ** * * * * *
28572708 AGATTGAAGCCACAATGGCATATCTTACTTCCCTGGCGATGCAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTTA-TTTCCTAGCGGTGCAGTTGAAC
* * * ** * ** * * *
28572758 ATGATTGAAGTCACAACGACGGATCTGATTTCCCCGACAGCACAATTAAAA
1 A-GATTGAAGCCACAACGGCGGATCTTATTTCCTAG-CGGTGCAGTTGAAC
28572809 AGATTGAAGCCACAACGGCGGATCTTATTTCCTTAGCGGTGCAGTTGAAC
1 AGATTGAAGCCACAACGGCGGATCTTATTTCC-TAGCGGTGCAGTTGAAC
* * * * *
28572859 AGGTTGAAGCTACGATGGCGGATCTTGTTTCCT
1 AGATTGAAGCCACAACGGCGGATCTTATTTCCT
28572892 CGACATTGTA
Statistics
Matches: 700, Mismatches: 294, Indels: 83
0.65 0.27 0.08
Matches are distributed among these distances:
47 3 0.00
48 5 0.01
49 33 0.05
50 558 0.80
51 92 0.13
52 6 0.01
53 3 0.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (49 bp):
AGATTGAAGCCACAACGGCGGATCTTATTTCCTAGCGGTGCAGTTGAAC
Found at i:28572883 original size:401 final size:400
Alignment explanation
Indices: 28571755--28572896 Score: 1680
Period size: 401 Copynumber: 2.9 Consensus size: 400
28571745 GTTATAGCGA
28571755 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAATT-AAAAGATTGAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAATTAAAAAGATTGAAGCCA
* * *
28571819 CAACGGCAGATCTTACTTCCCTGGCGGTGCAGCGGAGCAAATTGAAGTCACAACGACAGATCTGG
66 CAACGGCAGATCTTACTTTCCTGGCGGTGCAGCGGAGCAGATTGAAGTCACAACGACGGATCTGG
** * * * *
28571884 TTTCCCTGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCGGATCATGCTTCCCTGGTGGTGC
131 TTTCCCCAACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
28571949 AGCGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAAGATTGA
196 AGTGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
* * *
28572014 AGCCACAACGACGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGTCACAACGGCGGA
261 AGCCACAACGGCGGATCTTACTTCCTTGGCGGTGCAGTGGAGCAGATTGAAGTCACGACGGCGGA
* * * *
28572079 TCTGGTTTCTCCGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCGGATTTTACTTCCCTGGC
326 TCTAGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGC
*
28572144 GGTGTAGTGG
391 GGTGCAGTGG
* * *
28572154 AGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCTCGACAGCACAATTTAAAAGGATTGAAGCC
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAA-TTAAAAAGATTGAAGCC
* *
28572219 ACAACGGCAGATCTTAC-TTCCGTGGCGGTGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCT
65 ACAACGGCAGATCTTACTTTCC-TGGCGGTGCAGCGGAGCAGATTGAAGTCACAACGACGGATCT
* * *
28572283 GGTTTCCCCAACAGCGTAATTTAAAAGATTGAAGCCACAACGGCAGATCTTACTTCTCTGGCGGT
129 GGTTTCCCCAACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGT
* * * * *
28572348 GTAGTGGAGCAGATTGAAGTCACAACAACGGATCTGGTTTCCCCGATAGCGTAATTTAAAAGATT
194 GCAGTGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATT
** * **
28572413 GAAGCCACAACGGTAGATCTTACTT-CTCTGGCGGTGTAGTGGAGCAGATTGAAGTCACGACAAC
259 GAAGCCACAACGGCGGATCTTACTTCCT-TGGCGGTGCAGTGGAGCAGATTGAAGTCACGACGGC
* *
28572477 GGATCTAGTTTCCCCGACAGCGTAATTAAAAGGATTGAAGCCACAACGGCAGATCTTACTTCCCT
323 GGATCTAGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCT
28572542 GGCGGTGCAGTGG
388 GGCGGTGCAGTGG
* * *
28572555 AGCAGATTGAAGTCACAACGGCGGATCTAGTTTCCCCGACAGCGCAATTAAAAAGATTAAAGCCA
1 AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAATTAAAAAGATTGAAGCCA
* * *
28572620 CAACGGCGGATCTTACTTTCCTAGCGGTGCAGCGGAGCAGATTGAATTCACAACGACGGATCTGG
66 CAACGGCAGATCTTACTTTCCTGGCGGTGCAGCGGAGCAGATTGAAGTCACAACGACGGATCTGG
* * *
28572685 TTTCCCCAACAGCGCAATTAAAAAGATTGAAGCCACAATGGCATATCTTACTTCCCTGGCGATGC
131 TTTCCCCAACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* *
28572750 AGTGGAGCATGATTGAAGTCACAACGACGGATCTGATTTCCCCGACAGCACAATTAAAAAGATTG
196 AGTGGAGCA-GATTGAAGTCACAACGACGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTG
* * * * * *
28572815 AAGCCACAACGGCGGATCTTATTTCCTTAGCGGTGCAGTTGAACAGGTTGAAG-CTACGATGGCG
260 AAGCCACAACGGCGGATCTTACTTCCTTGGCGGTGCAGTGGAGCAGATTGAAGTC-ACGACGGCG
* *
28572879 GATCTTGTTTCCTCGACA
324 GATCTAGTTTCCCCGACA
28572897 TTGTAATTGG
Statistics
Matches: 658, Mismatches: 77, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
399 45 0.07
400 145 0.22
401 466 0.71
402 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (400 bp):
AGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCACAATTAAAAAGATTGAAGCCA
CAACGGCAGATCTTACTTTCCTGGCGGTGCAGCGGAGCAGATTGAAGTCACAACGACGGATCTGG
TTTCCCCAACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
AGTGGAGCAGATTGAAGTCACAACGACGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
AGCCACAACGGCGGATCTTACTTCCTTGGCGGTGCAGTGGAGCAGATTGAAGTCACGACGGCGGA
TCTAGTTTCCCCGACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGC
GGTGCAGTGG
Found at i:28573848 original size:22 final size:22
Alignment explanation
Indices: 28573797--28573848 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
28573787 GATTTCTCCA
*
28573797 TTTTTTTTCCTTTTTACTGTTT
1 TTTTTTTTCATTTTTACTGTTT
*
28573819 TTTGTTTTCATTTTT-CTGTTGT
1 TTTTTTTTCATTTTTACTGTT-T
28573841 TTTTTTTT
1 TTTTTTTT
28573849 GTAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.04, C:0.10, G:0.08, T:0.79
Consensus pattern (22 bp):
TTTTTTTTCATTTTTACTGTTT
Found at i:28574402 original size:3 final size:3
Alignment explanation
Indices: 28574385--28574469 Score: 75
Period size: 3 Copynumber: 27.3 Consensus size: 3
28574375 ATCATTAAGT
*
28574385 TTA TTA -TA TTAA TTA TTA TTA TTG TTA TTA TTA CTGTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA
* * *
28574432 GTA TTA TTTA TTA TTA -TA TTA CATA TTA ATA TTA TTA T
1 TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
28574470 ACTTATATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
2 4 0.06
3 51 0.76
4 10 0.15
5 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:28574444 original size:16 final size:15
Alignment explanation
Indices: 28574385--28574452 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 15
28574375 ATCATTAAGT
*
28574385 TTATTATATTAATTA
1 TTATTATATTATTTA
*
28574400 TTA-T-TATT-GTTA
1 TTATTATATTATTTA
*
28574412 TTATTACT-GTA-TTA
1 TTATTA-TATTATTTA
28574426 TTATTAGTATTATTTA
1 TTATTA-TATTATTTA
28574442 TTATTATATTA
1 TTATTATATTA
28574453 CATATTAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.14
13 5 0.12
14 12 0.28
15 11 0.26
16 9 0.21
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (15 bp):
TTATTATATTATTTA
Found at i:28576043 original size:42 final size:42
Alignment explanation
Indices: 28575974--28576057 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
28575964 TATGCTTTAA
* * * *
28575974 AACCATACGTGCAAGGACATAGACATGTG-CCTAGGCCGTGTG
1 AACCACACGTACAAGGACACAGACATGTGTCC-AAGCCGTGTG
* *
28576016 AACCACACGTACAAGGACACGGGCATGTGTCCAAGCCGTGTG
1 AACCACACGTACAAGGACACAGACATGTGTCCAAGCCGTGTG
28576058 GTGTATATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.17
Consensus pattern (42 bp):
AACCACACGTACAAGGACACAGACATGTGTCCAAGCCGTGTG
Found at i:28577697 original size:4 final size:4
Alignment explanation
Indices: 28577688--28577729 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
28577678 TTTACAAAAT
* *
28577688 TTTA TTTA TTTA TTTA TTTA TTCA TTTA -TTA CTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
28577730 TTATTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:28577738 original size:23 final size:26
Alignment explanation
Indices: 28577693--28577740 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
28577683 AAAATTTTAT
28577693 TTATTTATTTATTTATTCATTTATTAC
1 TTATTTATTTATTTATT-ATTTATTAC
28577720 TTATTTA-TT-TTTATT-TTTATT
1 TTATTTATTTATTTATTATTTATT
28577741 TTTACATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
25 6 0.29
26 2 0.10
27 7 0.33
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (26 bp):
TTATTTATTTATTTATTATTTATTAC
Found at i:28577740 original size:12 final size:13
Alignment explanation
Indices: 28577687--28577744 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 13
28577677 TTTTACAAAA
28577687 TTTTATTTATT-T
1 TTTTATTTATTAT
*
28577699 ATTTATTTATTCAT
1 TTTTATTTATT-AT
*
28577713 TTATTACTTATTTAT
1 TT-TTATTTA-TTAT
28577728 TTTTATTT-TTAT
1 TTTTATTTATTAT
28577740 TTTTA
1 TTTTA
28577745 CATGTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 19 0.50
14 7 0.18
15 10 0.26
16 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTATTTATTAT
Found at i:28577984 original size:14 final size:14
Alignment explanation
Indices: 28577955--28577997 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
28577945 CTATGACGTG
*
28577955 ATTATTAATCTTATT
1 ATTATT-ATATTATT
28577970 ATTATTATATTATT
1 ATTATTATATTATT
* *
28577984 AGTATTATAGTATT
1 ATTATTATATTATT
28577998 CCTTTATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (14 bp):
ATTATTATATTATT
Found at i:28585572 original size:16 final size:17
Alignment explanation
Indices: 28585532--28585576 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
28585522 TTTTAAAAAT
*
28585532 AAATTAAAATACATAAA
1 AAATTAAAATACACAAA
28585549 AAATTAAAATACACAAA
1 AAATTAAAATACACAAA
*
28585566 AAATAAAAATA
1 AAATTAAAATA
28585577 ATTATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATTAAAATACACAAA
Found at i:28591061 original size:5 final size:5
Alignment explanation
Indices: 28591053--28591079 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28591043 TAGCTTTTGT
28591053 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
28591080 CATCAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:28594634 original size:26 final size:26
Alignment explanation
Indices: 28594605--28594698 Score: 109
Period size: 26 Copynumber: 3.6 Consensus size: 26
28594595 ACCTTTCGGA
*
28594605 GGTATTTCGATAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATTGAG
* *
28594631 GGTATTTTGGTAATTTACCCATTGAG
1 GGTATTTCGATAATTTACCCATTGAG
* *
28594657 GGTATTTTTG-TAATTTAACCATTGAG
1 GGTA-TTTCGATAATTTACCCATTGAG
* *
28594683 AGTATTTCAATAATTT
1 GGTATTTCGATAATTT
28594699 TGGCCCATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
25 3 0.05
26 51 0.86
27 5 0.08
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.43
Consensus pattern (26 bp):
GGTATTTCGATAATTTACCCATTGAG
Found at i:28601311 original size:46 final size:46
Alignment explanation
Indices: 28601236--28601371 Score: 227
Period size: 46 Copynumber: 3.0 Consensus size: 46
28601226 TTGCTATAAT
*
28601236 TCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCACAAC
1 TCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAAC
* * *
28601282 TCAGTATGGCTTTCTTTACTGAAACACCATACCTACTTTTCACAAC
1 TCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAAC
*
28601328 TCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCACA
1 TCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACA
28601372 CTTTGTCATG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 82 1.00
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.35
Consensus pattern (46 bp):
TCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAAC
Found at i:28602351 original size:5 final size:5
Alignment explanation
Indices: 28602341--28602366 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28602331 TGAGCATTCG
28602341 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
28602367 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:28603642 original size:16 final size:17
Alignment explanation
Indices: 28603596--28603643 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
28603586 AAATTCTTTT
*
28603596 TAAATCGCAAAATTCAC
1 TAAATCACAAAATTCAC
28603613 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
*
28603630 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
28603644 TTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:28608262 original size:21 final size:21
Alignment explanation
Indices: 28608216--28608284 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
28608206 TTTACTTTCC
* *
28608216 GTTTAACTC-TCACGAGCTTCT
1 GTTTAACTCAT-ATGAGCTTTT
*
28608237 ATTTAACTCATATGAG-TTTT
1 GTTTAACTCATATGAGCTTTT
* * *
28608257 CGTTTAGCTCTTTTGAGCTTTT
1 -GTTTAACTCATATGAGCTTTT
28608279 GTTTAA
1 GTTTAA
28608285 TCCTTATGGG
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
20 3 0.08
21 29 0.78
22 5 0.14
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.48
Consensus pattern (21 bp):
GTTTAACTCATATGAGCTTTT
Found at i:28608312 original size:21 final size:21
Alignment explanation
Indices: 28608286--28608361 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
28608276 TTTGTTTAAT
*
28608286 CCTTATGGGTTTCCGTTCAAC
1 CCTTATGGATTTCCGTTCAAC
* * *
28608307 CCTTATGGATTTTCGTTTAGC
1 CCTTATGGATTTCCGTTCAAC
*
28608328 TCTTA-GGATCTTCCGTTCAAC
1 CCTTATGGAT-TTCCGTTCAAC
* *
28608349 CTTTATGGGTTTC
1 CCTTATGGATTTC
28608362 TGTTTAGCAC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 4 0.10
21 35 0.83
22 3 0.07
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (21 bp):
CCTTATGGATTTCCGTTCAAC
Found at i:28608375 original size:63 final size:63
Alignment explanation
Indices: 28608253--28608376 Score: 142
Period size: 63 Copynumber: 2.0 Consensus size: 63
28608243 CTCATATGAG
** ** * *
28608253 TTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGTTTCCGTTCAACCCTTATGGA
1 TTTTCGTTTAGCTCTTAGGAGCTTCCGTTCAATCCTTATGGGTTTCCGTTCAACACTTATGGA
* * * *
28608316 TTTTCGTTTAGCTCTTAGGATCTTCCGTTCAA-CCTTTATGGGTTTCTGTTTAGCACTTATG
1 TTTTCGTTTAGCTCTTAGGAGCTTCCGTTCAATCC-TTATGGGTTTCCGTTCAACACTTATG
28608377 TGCTTCCATT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.48
Consensus pattern (63 bp):
TTTTCGTTTAGCTCTTAGGAGCTTCCGTTCAATCCTTATGGGTTTCCGTTCAACACTTATGGA
Found at i:28608383 original size:42 final size:42
Alignment explanation
Indices: 28608287--28608388 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
28608277 TTGTTTAATC
* * *
28608287 CTTATGGGTTTCCGTTCAACCCTTATGGATTTTCGTTTAGCT
1 CTTATGTGCTTCCGTTCAACCCTTATGGATTTTCGTTTAGCA
* * *
28608329 CTTAGGAT-CTTCCGTTCAACCTTTATGG-GTTTCTGTTTAGCA
1 CTTATG-TGCTTCCGTTCAACCCTTATGGATTTTC-GTTTAGCA
*
28608371 CTTATGTGCTTCCATTCA
1 CTTATGTGCTTCCGTTCA
28608389 GGCTTCGGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
41 5 0.10
42 44 0.90
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (42 bp):
CTTATGTGCTTCCGTTCAACCCTTATGGATTTTCGTTTAGCA
Found at i:28608779 original size:21 final size:21
Alignment explanation
Indices: 28608733--28608801 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
28608723 TTTACTTTCC
* *
28608733 GTTTAACTC-TCACGAGCTTCT
1 GTTTAACTCAT-ATGAGCTTTT
*
28608754 ATTTAACTCATATGAG-TTTT
1 GTTTAACTCATATGAGCTTTT
* * *
28608774 CGTTTAGCTCTTTTGAGCTTTT
1 -GTTTAACTCATATGAGCTTTT
28608796 GTTTAA
1 GTTTAA
28608802 TCCTTATGGG
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
20 3 0.08
21 29 0.78
22 5 0.14
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.48
Consensus pattern (21 bp):
GTTTAACTCATATGAGCTTTT
Found at i:28608829 original size:21 final size:21
Alignment explanation
Indices: 28608803--28608878 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
28608793 TTTGTTTAAT
*
28608803 CCTTATGGGTTTCCGTTCAAC
1 CCTTATGGATTTCCGTTCAAC
* * *
28608824 CCTTATGGATTTTCGTTTAGC
1 CCTTATGGATTTCCGTTCAAC
*
28608845 TCTTA-GGATCTTCCGTTCAAC
1 CCTTATGGAT-TTCCGTTCAAC
* *
28608866 CTTTATGGGTTTC
1 CCTTATGGATTTC
28608879 TGTTTAGCAC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 4 0.10
21 35 0.83
22 3 0.07
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (21 bp):
CCTTATGGATTTCCGTTCAAC
Found at i:28608892 original size:63 final size:63
Alignment explanation
Indices: 28608770--28608893 Score: 142
Period size: 63 Copynumber: 2.0 Consensus size: 63
28608760 CTCATATGAG
** ** * *
28608770 TTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGTTTCCGTTCAACCCTTATGGA
1 TTTTCGTTTAGCTCTTAGGAGCTTCCGTTCAATCCTTATGGGTTTCCGTTCAACACTTATGGA
* * * *
28608833 TTTTCGTTTAGCTCTTAGGATCTTCCGTTCAA-CCTTTATGGGTTTCTGTTTAGCACTTATG
1 TTTTCGTTTAGCTCTTAGGAGCTTCCGTTCAATCC-TTATGGGTTTCCGTTCAACACTTATG
28608894 TGCTTCCATT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.48
Consensus pattern (63 bp):
TTTTCGTTTAGCTCTTAGGAGCTTCCGTTCAATCCTTATGGGTTTCCGTTCAACACTTATGGA
Found at i:28608900 original size:42 final size:42
Alignment explanation
Indices: 28608804--28608905 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
28608794 TTGTTTAATC
* * *
28608804 CTTATGGGTTTCCGTTCAACCCTTATGGATTTTCGTTTAGCT
1 CTTATGTGCTTCCGTTCAACCCTTATGGATTTTCGTTTAGCA
* * *
28608846 CTTAGGAT-CTTCCGTTCAACCTTTATGG-GTTTCTGTTTAGCA
1 CTTATG-TGCTTCCGTTCAACCCTTATGGATTTTC-GTTTAGCA
*
28608888 CTTATGTGCTTCCATTCA
1 CTTATGTGCTTCCGTTCA
28608906 GGCTTCGGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
41 5 0.10
42 44 0.90
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (42 bp):
CTTATGTGCTTCCGTTCAACCCTTATGGATTTTCGTTTAGCA
Found at i:28609009 original size:517 final size:517
Alignment explanation
Indices: 28608036--28609588 Score: 3079
Period size: 517 Copynumber: 3.0 Consensus size: 517
28608026 ATTTATTCTA
*
28608036 TTGTTGAAAACGAAATATTGTTAAAGTTATAAAATTAAATTGAATATTCGGACTAAATAGAACGC
1 TTGTTGAAAACGAAATATTGTTAAAGTTATAAAATTAAATTGAATATTCGAACTAAATAGAACGC
28608101 AGGATATGAGTACATTCAGCAATTGATGAATTGACGGCATTGAAGGAAAGTGACAGCAAATTACC
66 AGGATATGAGTACATTCAGCAATTGATGAATTGACGGCATTGAAGGAAAGTGACAGCAAATTACC
28608166 CAAGTAAATCGAGGTTCAGCATTTGTTGCGAACTTACGTGTTTACTTTCCGTTTAACTCTCACGA
131 CAAGTAAATCGAGGTTCAGCATTTGTTGCGAACTTACGTGTTTACTTTCCGTTTAACTCTCACGA
28608231 GCTTCTATTTAACTCATATGAGTTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGT
196 GCTTCTATTTAACTCATATGAGTTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGT
28608296 TTCCGTTCAACCCTTATGGATTTTCGTTTAGCTCTTAGGATCTTCCGTTCAACCTTTATGGGTTT
261 TTCCGTTCAACCCTTATGGATTTTCGTTTAGCTCTTAGGATCTTCCGTTCAACCTTTATGGGTTT
28608361 CTGTTTAGCACTTATGTGCTTCCATTCAGGCTTCGGGCTTTTGAAAATGATGTATTTTTATCTGT
326 CTGTTTAGCACTTATGTGCTTCCATTCAGGCTTCGGGCTTTTGAAAATGATGTATTTTTATCTGT
28608426 AAGCCGTTCTCTGATTTTGTAACAGCCCGTTTTCAGTGATTTTGGGACCACAAATCTGAGTAAGA
391 AAGCCGTTCTCTGATTTTGTAACAGCCCGTTTTCAGTGATTTTGGGACCACAAATCTGAGTAAGA
28608491 AAGAAAAATTATTTTAATATTATTGCATGGTTTGCATTATGATAGGAATGACGTATGAAATT
456 AAGAAAAATTATTTTAATATTATTGCATGGTTTGCATTATGATAGGAATGACGTATGAAATT
28608553 TTGTTGAAAACGAAATATTGTTAAAGTTATAAAATTAAATTGAATATTCGAACTAAATAGAACGC
1 TTGTTGAAAACGAAATATTGTTAAAGTTATAAAATTAAATTGAATATTCGAACTAAATAGAACGC
28608618 AGGATATGAGTACATTCAGCAATTGATGAATTGACGGCATTGAAGGAAAGTGACAGCAAATTACC
66 AGGATATGAGTACATTCAGCAATTGATGAATTGACGGCATTGAAGGAAAGTGACAGCAAATTACC
28608683 CAAGTAAATCGAGGTTCAGCATTTGTTGCGAACTTACGTGTTTACTTTCCGTTTAACTCTCACGA
131 CAAGTAAATCGAGGTTCAGCATTTGTTGCGAACTTACGTGTTTACTTTCCGTTTAACTCTCACGA
28608748 GCTTCTATTTAACTCATATGAGTTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGT
196 GCTTCTATTTAACTCATATGAGTTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGT
28608813 TTCCGTTCAACCCTTATGGATTTTCGTTTAGCTCTTAGGATCTTCCGTTCAACCTTTATGGGTTT
261 TTCCGTTCAACCCTTATGGATTTTCGTTTAGCTCTTAGGATCTTCCGTTCAACCTTTATGGGTTT
28608878 CTGTTTAGCACTTATGTGCTTCCATTCAGGCTTCGGGCTTTTGAAAATGATGTATTTTTATCTGT
326 CTGTTTAGCACTTATGTGCTTCCATTCAGGCTTCGGGCTTTTGAAAATGATGTATTTTTATCTGT
28608943 AAGCCGTTCTCTGATTTTGTAACAGCCCGTTTTCAGTGATTTTGGGACCACAAATCTGAGTAAGA
391 AAGCCGTTCTCTGATTTTGTAACAGCCCGTTTTCAGTGATTTTGGGACCACAAATCTGAGTAAGA
28609008 AAGAAAAATTATTTTAATATTATTGCATGGTTTGCATTATGATAGGAATGACGTATGAAATT
456 AAGAAAAATTATTTTAATATTATTGCATGGTTTGCATTATGATAGGAATGACGTATGAAATT
28609070 TTGTTGAAAACGAAATATTGTTAAAGTTATAAAATTAAATTGAATATTCGAACTAAATAGAACGC
1 TTGTTGAAAACGAAATATTGTTAAAGTTATAAAATTAAATTGAATATTCGAACTAAATAGAACGC
28609135 AGGATATGAGTACATTCAGCAATTGATGAATTGACGGCATTGAAGGAAAGTGACAGCAAATTACC
66 AGGATATGAGTACATTCAGCAATTGATGAATTGACGGCATTGAAGGAAAGTGACAGCAAATTACC
28609200 CAAGTAAATCGAGGTTCAGCATTTGTTGCGAACTTACGTGTTTACTTTCCGTTTAACTCTCACGA
131 CAAGTAAATCGAGGTTCAGCATTTGTTGCGAACTTACGTGTTTACTTTCCGTTTAACTCTCACGA
28609265 GCTTCTATTTAACTCATATGAGTTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGT
196 GCTTCTATTTAACTCATATGAGTTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGT
28609330 TTCCGTTCAACCCTTATGGATTTTCGTTTAGCTCTTAGGATCTTCCGTTCAACCTTTATGGGTTT
261 TTCCGTTCAACCCTTATGGATTTTCGTTTAGCTCTTAGGATCTTCCGTTCAACCTTTATGGGTTT
28609395 CTGTTTAGCACTTATGTGCTTCCATTCAGGCTTCGGGCTTTTGAAAATGATGTATTTTTATCTGT
326 CTGTTTAGCACTTATGTGCTTCCATTCAGGCTTCGGGCTTTTGAAAATGATGTATTTTTATCTGT
*
28609460 AAGCCGTTCTCTGATTTTGTAACAGCCCGTTTTCAGTGATTTTGGGACCACAAATTTGAGTAAGA
391 AAGCCGTTCTCTGATTTTGTAACAGCCCGTTTTCAGTGATTTTGGGACCACAAATCTGAGTAAGA
*
28609525 AAGAAAAATTATTTTAATATTATTGCATGGTCTGCATTATGATAGGAATGACGTATGAAATT
456 AAGAAAAATTATTTTAATATTATTGCATGGTTTGCATTATGATAGGAATGACGTATGAAATT
28609587 TT
1 TT
28609589 CGATAAGAAA
Statistics
Matches: 1033, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
517 1033 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (517 bp):
TTGTTGAAAACGAAATATTGTTAAAGTTATAAAATTAAATTGAATATTCGAACTAAATAGAACGC
AGGATATGAGTACATTCAGCAATTGATGAATTGACGGCATTGAAGGAAAGTGACAGCAAATTACC
CAAGTAAATCGAGGTTCAGCATTTGTTGCGAACTTACGTGTTTACTTTCCGTTTAACTCTCACGA
GCTTCTATTTAACTCATATGAGTTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGT
TTCCGTTCAACCCTTATGGATTTTCGTTTAGCTCTTAGGATCTTCCGTTCAACCTTTATGGGTTT
CTGTTTAGCACTTATGTGCTTCCATTCAGGCTTCGGGCTTTTGAAAATGATGTATTTTTATCTGT
AAGCCGTTCTCTGATTTTGTAACAGCCCGTTTTCAGTGATTTTGGGACCACAAATCTGAGTAAGA
AAGAAAAATTATTTTAATATTATTGCATGGTTTGCATTATGATAGGAATGACGTATGAAATT
Found at i:28609296 original size:21 final size:21
Alignment explanation
Indices: 28609250--28609318 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
28609240 TTTACTTTCC
* *
28609250 GTTTAACTC-TCACGAGCTTCT
1 GTTTAACTCAT-ATGAGCTTTT
*
28609271 ATTTAACTCATATGAG-TTTT
1 GTTTAACTCATATGAGCTTTT
* * *
28609291 CGTTTAGCTCTTTTGAGCTTTT
1 -GTTTAACTCATATGAGCTTTT
28609313 GTTTAA
1 GTTTAA
28609319 TCCTTATGGG
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
20 3 0.08
21 29 0.78
22 5 0.14
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.48
Consensus pattern (21 bp):
GTTTAACTCATATGAGCTTTT
Found at i:28609346 original size:21 final size:21
Alignment explanation
Indices: 28609320--28609395 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
28609310 TTTGTTTAAT
*
28609320 CCTTATGGGTTTCCGTTCAAC
1 CCTTATGGATTTCCGTTCAAC
* * *
28609341 CCTTATGGATTTTCGTTTAGC
1 CCTTATGGATTTCCGTTCAAC
*
28609362 TCTTA-GGATCTTCCGTTCAAC
1 CCTTATGGAT-TTCCGTTCAAC
* *
28609383 CTTTATGGGTTTC
1 CCTTATGGATTTC
28609396 TGTTTAGCAC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 4 0.10
21 35 0.83
22 3 0.07
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (21 bp):
CCTTATGGATTTCCGTTCAAC
Found at i:28609409 original size:63 final size:63
Alignment explanation
Indices: 28609287--28609410 Score: 142
Period size: 63 Copynumber: 2.0 Consensus size: 63
28609277 CTCATATGAG
** ** * *
28609287 TTTTCGTTTAGCTCTTTTGAGCTTTTGTTTAATCCTTATGGGTTTCCGTTCAACCCTTATGGA
1 TTTTCGTTTAGCTCTTAGGAGCTTCCGTTCAATCCTTATGGGTTTCCGTTCAACACTTATGGA
* * * *
28609350 TTTTCGTTTAGCTCTTAGGATCTTCCGTTCAA-CCTTTATGGGTTTCTGTTTAGCACTTATG
1 TTTTCGTTTAGCTCTTAGGAGCTTCCGTTCAATCC-TTATGGGTTTCCGTTCAACACTTATG
28609411 TGCTTCCATT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.48
Consensus pattern (63 bp):
TTTTCGTTTAGCTCTTAGGAGCTTCCGTTCAATCCTTATGGGTTTCCGTTCAACACTTATGGA
Found at i:28609417 original size:42 final size:42
Alignment explanation
Indices: 28609321--28609422 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
28609311 TTGTTTAATC
* * *
28609321 CTTATGGGTTTCCGTTCAACCCTTATGGATTTTCGTTTAGCT
1 CTTATGTGCTTCCGTTCAACCCTTATGGATTTTCGTTTAGCA
* * *
28609363 CTTAGGAT-CTTCCGTTCAACCTTTATGG-GTTTCTGTTTAGCA
1 CTTATG-TGCTTCCGTTCAACCCTTATGGATTTTC-GTTTAGCA
*
28609405 CTTATGTGCTTCCATTCA
1 CTTATGTGCTTCCGTTCA
28609423 GGCTTCGGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
41 5 0.10
42 44 0.90
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (42 bp):
CTTATGTGCTTCCGTTCAACCCTTATGGATTTTCGTTTAGCA
Found at i:28614048 original size:18 final size:18
Alignment explanation
Indices: 28614015--28614067 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
28614005 ATTCACCTAA
*
28614015 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
28614034 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
28614052 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
28614068 TTATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:28617054 original size:17 final size:17
Alignment explanation
Indices: 28617034--28617389 Score: 227
Period size: 17 Copynumber: 20.3 Consensus size: 17
28617024 AATACGATTT
28617034 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *****
28617051 TTTTTGAAACAATTTTTA
1 TTTTTAAAAC-ACGAAAA
*
28617069 TTTTTGAGAACACGAAAA
1 TTTTT-AAAACACGAAAA
*
28617087 TTTTTTTAAAACACGAGAA
1 --TTTTTAAAACACGAAAA
* *
28617106 -TTTTAGAGACAAGAAAA
1 TTTTTA-AAACACGAAAA
*
28617123 TTCTTAAAAACACGAAAA
1 TT-TTTAAAACACGAAAA
*
28617141 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
*
28617159 TTTTTAAAACACGGAAA
1 TTTTTAAAACACGAAAA
28617176 -TTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
*
28617193 TTTTTAAAACACGAAAT
1 TTTTTAAAACACGAAAA
* *
28617210 TTTTTGAAACACGAAATT
1 TTTTTAAAACACGAAA-A
28617228 TTTTTAAAACAC-AGAAA
1 TTTTTAAAACACGA-AAA
28617245 -TTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
*
28617262 TTTTTAAAACACG-ACA
1 TTTTTAAAACACGAAAA
*
28617278 TTTTTGAAACACGAGAAGA
1 TTTTTAAAACACGA-AA-A
****** *
28617297 TTTTTTCTTTTTCTAAAA
1 -TTTTTAAAACACGAAAA
** *
28617315 AATTTAAAATACGAAAA
1 TTTTTAAAACACGAAAA
* * * *
28617332 TTTGTGAAACGCGAGAA
1 TTTTTAAAACACGAAAA
*
28617349 TTGTTGAAAACACGAAAA
1 TT-TTTAAAACACGAAAA
*
28617367 TTTTTAAAAACACGATAA
1 TTTTT-AAAACACGAAAA
28617385 TTTTT
1 TTTTT
28617390 TTTAAAATGC
Statistics
Matches: 256, Mismatches: 62, Indels: 41
0.71 0.17 0.11
Matches are distributed among these distances:
16 29 0.11
17 104 0.41
18 92 0.36
19 19 0.07
20 12 0.05
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:28617135 original size:35 final size:34
Alignment explanation
Indices: 28617068--28617301 Score: 242
Period size: 35 Copynumber: 6.7 Consensus size: 34
28617058 AACAATTTTT
*
28617068 ATTTTTGAGAACACGAAAATTTTTTTAAAACACGAGA
1 ATTTTAGA-AACACGAAAA--TTTTTAAAACACGAGA
* * * *
28617105 ATTTTAGAGACAAGAAAATTCTTAAAAACACGAAA
1 ATTTTAGAAACACGAAAATT-TTTAAAACACGAGA
* *
28617140 ATTTTTGAAAACACGAGAATTTTTAAAACACG-GAA
1 ATTTTAG-AAACACGAAAATTTTTAAAACACGAG-A
28617175 ATTTTAGAAACACGAAAATTTTTAAAACACGA-A
1 ATTTTAGAAACACGAAAATTTTTAAAACACGAGA
* *
28617208 ATTTTTTGAAACACGAAATTTTTTTAAAACAC-AGAA
1 A-TTTTAGAAACACGAAA-ATTTTTAAAACACGAG-A
*
28617244 ATTTTAGAAACACGAAAATTTTTAAAACACGA-C
1 ATTTTAGAAACACGAAAATTTTTAAAACACGAGA
*
28617277 ATTTTTGAAACACGAGAAGATTTTT
1 ATTTTAGAAACACGA-AA-ATTTTT
28617302 TCTTTTTCTA
Statistics
Matches: 167, Mismatches: 19, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
33 16 0.10
34 55 0.33
35 69 0.41
36 20 0.12
37 7 0.04
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (34 bp):
ATTTTAGAAACACGAAAATTTTTAAAACACGAGA
Found at i:28617245 original size:69 final size:67
Alignment explanation
Indices: 28617068--28617291 Score: 308
Period size: 69 Copynumber: 3.2 Consensus size: 67
28617058 AACAATTTTT
* * *
28617068 ATTTTTGAGAACACGAAAATTTTTTTAAAACACGAGAATTTTAGAGACAAGAAAATTCTTAAAAA
1 ATTTTTGA-AACACG-AAATTTTTTTAAAACACGA-AATTTTAGAAACACGAAAATT-TTTAAAA
28617133 CACGAAA
62 CACG-AA
28617140 ATTTTTGAAAACACGAGAA--TTTTTAAAACACGGAAATTTTAGAAACACGAAAATTTTTAAAAC
1 ATTTTTG-AAACACGA-AATTTTTTTAAAACAC-GAAATTTTAGAAACACGAAAATTTTTAAAAC
28617203 ACGAA
63 ACGAA
28617208 ATTTTTTGAAACACGAAATTTTTTTAAAACACAGAAATTTTAGAAACACGAAAATTTTTAAAACA
1 A-TTTTTGAAACACGAAATTTTTTTAAAACAC-GAAATTTTAGAAACACGAAAATTTTTAAAACA
*
28617273 CGAC
64 CGAA
28617277 ATTTTTGAAACACGA
1 ATTTTTGAAACACGA
28617292 GAAGATTTTT
Statistics
Matches: 141, Mismatches: 5, Indels: 16
0.87 0.03 0.10
Matches are distributed among these distances:
67 2 0.01
68 25 0.18
69 64 0.45
70 31 0.22
71 3 0.02
72 15 0.11
73 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (67 bp):
ATTTTTGAAACACGAAATTTTTTTAAAACACGAAATTTTAGAAACACGAAAATTTTTAAAACACG
AA
Found at i:28617368 original size:18 final size:17
Alignment explanation
Indices: 28617320--28617388 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
28617310 TAAAAAATTT
*
28617320 AAAATACGAAAATTTGTG
1 AAAACACGAAAATTT-TG
* *
28617338 -AAACGCGAGAATTGTTG
1 AAAACACGAAAATT-TTG
*
28617355 AAAACACGAAAATTTTTA
1 AAAACACGAAAA-TTTTG
*
28617373 AAAACACGATAATTTT
1 AAAACACGAAAATTTT
28617389 TTTTAAAATG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
17 16 0.39
18 23 0.56
19 2 0.05
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (17 bp):
AAAACACGAAAATTTTG
Found at i:28617389 original size:18 final size:18
Alignment explanation
Indices: 28617355--28617389 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28617345 AGAATTGTTG
28617355 AAAACACGAAAATTTTTA
1 AAAACACGAAAATTTTTA
*
28617373 AAAACACGATAATTTTT
1 AAAACACGAAAATTTTT
28617390 TTTAAAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (18 bp):
AAAACACGAAAATTTTTA
Found at i:28617539 original size:17 final size:17
Alignment explanation
Indices: 28617519--28617665 Score: 70
Period size: 17 Copynumber: 8.5 Consensus size: 17
28617509 TTAAATACGA
28617519 GAAATTTTTGAAAACAC
1 GAAATTTTTGAAAACAC
*
28617536 GAAA-ATTTG-AAACAC
1 GAAATTTTTGAAAACAC
** *
28617551 GGGATTTTTGAAAATAC
1 GAAATTTTTGAAAACAC
* * *
28617568 GAAAAAATTTTAAAAACAT
1 G--AAATTTTTGAAAACAC
28617587 GAAAATTTTTG-AAACAC
1 G-AAATTTTTGAAAACAC
** **
28617604 G-GTTTTTTTTAAACAC
1 GAAATTTTTGAAAACAC
*
28617620 GAAAAGTTTTTGAAAACAT
1 G-AAA-TTTTTGAAAACAC
* *
28617639 GAAGATTTGTG-AAACGC
1 GAA-ATTTTTGAAAACAC
28617656 GAGAATTTTT
1 GA-AATTTTT
28617666 TTTTGAAAAC
Statistics
Matches: 94, Mismatches: 26, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
15 13 0.14
16 15 0.16
17 27 0.29
18 16 0.17
19 23 0.24
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.32
Consensus pattern (17 bp):
GAAATTTTTGAAAACAC
Found at i:28617610 original size:51 final size:53
Alignment explanation
Indices: 28617511--28617653 Score: 166
Period size: 52 Copynumber: 2.8 Consensus size: 53
28617501 AAAAAATTTT
* *
28617511 AAATACGAGAAATTTTTGAAAACACGAAAA--TTTGAAACACGGGATTTTTGA
1 AAATACGAAAAATTTTTGAAAACATGAAAATTTTTGAAACACGGGATTTTTGA
* * * **
28617562 AAATACGAAAAAATTTTAAAAACATGAAAATTTTTGAAACAC-GGTTTTTTTT
1 AAATACGAAAAATTTTTGAAAACATGAAAATTTTTGAAACACGGGATTTTTGA
* * * *
28617614 AAACACGAAAAGTTTTTGAAAACATGAAGATTTGTGAAAC
1 AAATACGAAAAATTTTTGAAAACATGAAAATTTTTGAAAC
28617654 GCGAGAATTT
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
51 26 0.34
52 41 0.53
53 10 0.13
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (53 bp):
AAATACGAAAAATTTTTGAAAACATGAAAATTTTTGAAACACGGGATTTTTGA
Found at i:28617652 original size:52 final size:50
Alignment explanation
Indices: 28617507--28617667 Score: 153
Period size: 52 Copynumber: 3.1 Consensus size: 50
28617497 GTGAAAAAAA
* *
28617507 TTTTAAATACGAGAAATTTTTGAAAACACGAAAATTTGAAACACGGGATTT
1 TTTTAAATACGA-AAATTTTTGAAAACATGAAATTTTGAAACACGGGATTT
** * * *
28617558 TTGAAAATACGAAAAAATTTTAAAAACATGAAAATTTTTGAAACAC-GGTTTT
1 TTTTAAATACG-AAAATTTTTGAAAACATG-AAA-TTTTGAAACACGGGATTT
* * *
28617610 TTTTAAACACGAAAAGTTTTTGAAAACATGAAGATTTGTGAAACGCGAGAATTT
1 TTTTAAATACGAAAA-TTTTTGAAAACATGAA-ATTT-TGAAACACG-GGATTT
28617664 TTTT
1 TTTT
28617668 TTGAAAACTA
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
51 32 0.37
52 37 0.43
53 10 0.11
54 8 0.09
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (50 bp):
TTTTAAATACGAAAATTTTTGAAAACATGAAATTTTGAAACACGGGATTT
Found at i:28617686 original size:18 final size:19
Alignment explanation
Indices: 28617663--28617704 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
28617653 CGCGAGAATT
28617663 TTTTTTTGAAAACT-AAAA
1 TTTTTTTGAAAACTCAAAA
* *
28617681 TTTTTTTTAAAACTCGAAA
1 TTTTTTTGAAAACTCAAAA
28617700 TTTTT
1 TTTTT
28617705 GAAACACGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (19 bp):
TTTTTTTGAAAACTCAAAA
Found at i:28617686 original size:19 final size:19
Alignment explanation
Indices: 28617662--28617704 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28617652 ACGCGAGAAT
28617662 TTTTTTTTGAAAACT-AAAA
1 TTTTTTTT-AAAACTCAAAA
*
28617681 TTTTTTTTAAAACTCGAAA
1 TTTTTTTTAAAACTCAAAA
28617700 TTTTT
1 TTTTT
28617705 GAAACACGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTTTTTTAAAACTCAAAA
Found at i:28618317 original size:1 final size:1
Alignment explanation
Indices: 28618311--28618349 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
28618301 TGGCTTGCTG
* * *
28618311 TTTTTTTTTTTTTTTTTTTTTCTTTTTTTCTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28618350 CTTCTTCCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:28618338 original size:21 final size:21
Alignment explanation
Indices: 28618312--28618401 Score: 76
Period size: 21 Copynumber: 4.1 Consensus size: 21
28618302 GGCTTGCTGT
* * *
28618312 TTTTTTTTTTTTTTTTTTTTC
1 TTTTTTTCTTTCTTTTTCTTC
28618333 TTTTTTTCTTTCTTTTTCTTC
1 TTTTTTTCTTTCTTTTTCTTC
*
28618354 TTCCTTCTTCTTTCTTTCTTC-TC
1 TT--TTTTTCTTTCTTT-TTCTTC
*
28618377 TTTTCTTTCTCT-TTTTTCTTTC
1 TTTT-TTTCTTTCTTTTTC-TTC
28618399 TTT
1 TTT
28618402 CCCGATCAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.05
21 25 0.44
22 10 0.18
23 16 0.28
24 3 0.05
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTCTTTCTTTTTCTTC
Found at i:28618354 original size:13 final size:12
Alignment explanation
Indices: 28618311--28618401 Score: 96
Period size: 14 Copynumber: 7.2 Consensus size: 12
28618301 TGGCTTGCTG
28618311 TTTTTTT-TTT-
1 TTTTTTTCTTTC
*
28618321 TTTTTTTTTTTC
1 TTTTTTTCTTTC
28618333 TTTTTTTCTTTC
1 TTTTTTTCTTTC
*
28618345 TTTTTCTTCTTCC
1 TTTTT-TTCTTTC
28618358 TTCTTCTTTCTTTC
1 TT-TT-TTTCTTTC
28618372 TTCTCTTTTCTTTC
1 TT-T-TTTTCTTTC
28618386 TCTTTTTTCTTTC
1 T-TTTTTTCTTTC
28618399 TTT
1 TTT
28618402 CCCGATCAGC
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
10 7 0.10
11 3 0.04
12 18 0.25
13 18 0.25
14 22 0.31
15 3 0.04
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:28618367 original size:27 final size:26
Alignment explanation
Indices: 28618337--28618402 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
28618327 TTTTTCTTTT
28618337 TTTCTTTCTTT-TTCTTCTTCCTTCTTC
1 TTTCTTTCTTTCTT-TTCTTCC-TCTTC
* *
28618364 TTTCTTTCTTCTCTTTTCTTTCTCTTT
1 TTTCTTTCTT-TCTTTTCTTCCTCTTC
28618391 TTTCTTTCTTTC
1 TTTCTTTCTTTC
28618403 CCGATCAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.06
27 24 0.69
28 7 0.20
29 2 0.06
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTCTTTCTTTCTTTTCTTCCTCTTC
Found at i:28618368 original size:4 final size:4
Alignment explanation
Indices: 28618329--28618402 Score: 62
Period size: 4 Copynumber: 18.0 Consensus size: 4
28618319 TTTTTTTTTT
* * *
28618329 TTTC TTTT TTTC TTTC TTTT TCTTC -TTC CTTC -TTC TTTC TTTC TTCTC
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TT-TC
*
28618377 TTTTC TTTC TCTTT TTTC TTTC TTTC
1 -TTTC TTTC T-TTC TTTC TTTC TTTC
28618403 CCGATCAGCC
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
3 6 0.10
4 41 0.71
5 9 0.16
6 2 0.03
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:28618374 original size:18 final size:19
Alignment explanation
Indices: 28618329--28618386 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 19
28618319 TTTTTTTTTT
*
28618329 TTTCTTT-TTTTCTTTCTT-
1 TTTCTTTCTTCTC-TTCTTC
28618347 TTTC-TTCTTC-CTTCTTC
1 TTTCTTTCTTCTCTTCTTC
28618364 TTTCTTTCTTCTCTT-TTC
1 TTTCTTTCTTCTCTTCTTC
28618382 TTTCT
1 TTTCT
28618387 CTTTTTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 5 0.14
17 7 0.20
18 20 0.57
19 3 0.09
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTCTTTCTTCTCTTCTTC
Found at i:28618381 original size:31 final size:31
Alignment explanation
Indices: 28618330--28618402 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
28618320 TTTTTTTTTT
*
28618330 TTCTTTTTTTCTTTCTTTTTC-TTCTTCCTTC
1 TTCTTTCTTTCTTTCTTTTTCTTTC-TCCTTC
* *
28618361 TTCTTTCTTTC-TTCTCTTTTCTTTCTCTTTT
1 TTCTTTCTTTCTTTCT-TTTTCTTTCTCCTTC
28618392 TTCTTTCTTTC
1 TTCTTTCTTTC
28618403 CCGATCAGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 4 0.11
31 30 0.81
32 3 0.08
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (31 bp):
TTCTTTCTTTCTTTCTTTTTCTTTCTCCTTC
Found at i:28618518 original size:10 final size:11
Alignment explanation
Indices: 28618503--28618561 Score: 61
Period size: 10 Copynumber: 5.5 Consensus size: 11
28618493 CTTTCACCCA
28618503 TTTTTCTTCT-
1 TTTTTCTTCTC
28618513 TTTTTCTTTCTC
1 TTTTTC-TTCTC
28618525 TTTTT-TTCTC
1 TTTTTCTTCTC
*
28618535 TTTTGCTTCT-
1 TTTTTCTTCTC
*
28618545 TGTTTCTTTCTC
1 TTTTTC-TTCTC
28618557 TTTTT
1 TTTTT
28618562 TTTTTGCTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 19 0.47
11 12 0.30
12 9 0.22
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTTTCTTCTC
Found at i:28618531 original size:16 final size:16
Alignment explanation
Indices: 28618507--28618564 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
28618497 CACCCATTTT
28618507 TCTTCTTTTTTCTTTC
1 TCTTCTTTTTTCTTTC
28618523 TCTT-TTTTTCTCTTT-
1 TCTTCTTTTT-TCTTTC
*
28618538 TGCTTCTTGTTTCTTTC
1 T-CTTCTTTTTTCTTTC
28618555 TCTT-TTTTTT
1 TCTTCTTTTTT
28618565 TTGCTTTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 11 0.31
16 20 0.56
17 5 0.14
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (16 bp):
TCTTCTTTTTTCTTTC
Found at i:28618538 original size:22 final size:20
Alignment explanation
Indices: 28618503--28618561 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
28618493 CTTTCACCCA
*
28618503 TTTTTCTTCT-TTTTTCTTTC
1 TTTTTTTTCTCTTTTTC-TTC
*
28618523 TCTTTTTTTCTCTTTTGCTTC
1 T-TTTTTTTCTCTTTTTCTTC
28618544 TTGTTTCTTTCTCTTTTT
1 TT-TTT-TTTCTCTTTTT
28618562 TTTTTGCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 2 0.06
21 15 0.47
22 15 0.47
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTTTTTCTCTTTTTCTTC
Found at i:28618545 original size:32 final size:32
Alignment explanation
Indices: 28618503--28618563 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
28618493 CTTTCACCCA
* *
28618503 TTTTTCTTCTTTTTTCTTTCTCTTTTTTTCTC
1 TTTTGCTTCTTGTTTCTTTCTCTTTTTTTCTC
28618535 TTTTGCTTCTTGTTTCTTTCTCTTTTTTT
1 TTTTGCTTCTTGTTTCTTTCTCTTTTTTT
28618564 TTTGCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (32 bp):
TTTTGCTTCTTGTTTCTTTCTCTTTTTTTCTC
Found at i:28619097 original size:30 final size:30
Alignment explanation
Indices: 28619063--28619210 Score: 187
Period size: 30 Copynumber: 5.0 Consensus size: 30
28619053 GGCAAAAGTA
*
28619063 TAATTTTGAGAAAGTTTAGGAGTTAAAATG
1 TAATTTTGAGAAAGTTTAGGAGTCAAAATG
* *
28619093 TAATTTTGAGAAAGTTTAGGGGTCAAAATA
1 TAATTTTGAGAAAGTTTAGGAGTCAAAATG
* * **
28619123 TAA-TTT-AAAAAGTTTAGGGGTTGAAATG
1 TAATTTTGAGAAAGTTTAGGAGTCAAAATG
28619151 TAATTTTGAGAAAGTTTA-GAGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGA-GTCAAAATG
28619181 TAATTTT-AGAAAAGTTTAGGAGTCAAAATG
1 TAATTTTGAG-AAAGTTTAGGAGTCAAAATG
28619211 CAAAAAAATT
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
28 21 0.21
29 9 0.09
30 70 0.69
31 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (30 bp):
TAATTTTGAGAAAGTTTAGGAGTCAAAATG
Found at i:28619138 original size:58 final size:59
Alignment explanation
Indices: 28619051--28619210 Score: 225
Period size: 58 Copynumber: 2.7 Consensus size: 59
28619041 AAAAATTTTT
*
28619051 GGGG-CAAAAGTATAATTTTGAGAAAGTTTAGGAGTTAAAATGTAATTTTGAGAAAGTTTA
1 GGGGTCAAAA-TATAATTTT-AAAAAGTTTAGGAGTTAAAATGTAATTTTGAGAAAGTTTA
* *
28619111 GGGGTCAAAATATAA-TTTAAAAAGTTTAGGGGTTGAAATGTAATTTTGAGAAAGTTTA
1 GGGGTCAAAATATAATTTTAAAAAGTTTAGGAGTTAAAATGTAATTTTGAGAAAGTTTA
* * *
28619169 GAGGTCAAAATGTAATTTTAGAAAAGTTTAGGAGTCAAAATG
1 GGGGTCAAAATATAATTTTA-AAAAGTTTAGGAGTTAAAATG
28619211 CAAAAAAATT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
58 50 0.56
59 7 0.08
60 27 0.30
61 5 0.06
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.33
Consensus pattern (59 bp):
GGGGTCAAAATATAATTTTAAAAAGTTTAGGAGTTAAAATGTAATTTTGAGAAAGTTTA
Found at i:28619597 original size:30 final size:31
Alignment explanation
Indices: 28619561--28619625 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
28619551 ATTTTATGTA
*
28619561 TTATTATACTAAATTATTTAAATA-TATTTT
1 TTATTATACTAAATTATTTAAATACCATTTT
*
28619591 TTATTATATTAAATTATTTAAATACCATTTT
1 TTATTATACTAAATTATTTAAATACCATTTT
28619622 TTAT
1 TTAT
28619626 ATTTAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (31 bp):
TTATTATACTAAATTATTTAAATACCATTTT
Found at i:28619638 original size:28 final size:30
Alignment explanation
Indices: 28619561--28619640 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
28619551 ATTTTATGTA
* *
28619561 TTATTATACTAAATTATTTAAATATATTTT
1 TTATTATATTAAATTATTTAAATACATTTT
28619591 TTATTATATTAAATTATTTAAATACCATTTT
1 TTATTATATTAAATTATTTAAATA-CATTTT
*
28619622 TTA-TAT-TTAAGTT-TTTAAA
1 TTATTATATTAAATTATTTAAA
28619641 GTATTTTATG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 6 0.13
29 6 0.13
30 26 0.57
31 8 0.17
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (30 bp):
TTATTATATTAAATTATTTAAATACATTTT
Found at i:28620109 original size:6 final size:6
Alignment explanation
Indices: 28620092--28620132 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
28620082 AAGATGAGTT
*
28620092 ATTT-G ATTT-G ATTTTG ATTTGG ATTTGG ATTTGG ATTTGG A
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG A
28620133 AACATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 9 0.26
6 25 0.74
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.54
Consensus pattern (6 bp):
ATTTGG
Found at i:28621750 original size:17 final size:17
Alignment explanation
Indices: 28621728--28621764 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28621718 GAGGACTACA
28621728 ATAATAATAAT-ATAATC
1 ATAATAATAATCAT-ATC
28621745 ATAATAATAATCATATC
1 ATAATAATAATCATATC
28621762 ATA
1 ATA
28621765 GGAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAATAATCATATC
Found at i:28623706 original size:834 final size:828
Alignment explanation
Indices: 28622124--28623778 Score: 2529
Period size: 834 Copynumber: 2.0 Consensus size: 828
28622114 TCTAGGAAGG
* *
28622124 GTCGAAACTATATAATAAGGACTAAATTGAAACTTAAATAGAATTTTAGGGGAGAAATCGAGATA
1 GTCGAAACTATATAAAAAGGACTAAATTGAAACTTAAATAAAATTTTAGGGGAGAAATCGAGATA
* * *
28622189 AAAACAAAATATGGGAATAAATTGCAACACATGAATGAAAGAGAAGGACGAAATAGGAAAATATT
66 AAAACAAAATATGAGAATAAATTGCAACACACGAATGAAAGAGAAGGACGAAACAGGAAAATATT
*
28622254 CCCTGTCCTTATGCGCACCGTTCCTCATGGGGACCAAAATAAAACAAAGATAAAATTGTATGGTA
131 CCCTGTCCTTATGCGCACCATTCCTCATGGGGACCAAAATAAAACAAAGATAAAATTGTATGGTA
*
28622319 AAATTTTAAATACAAAAAAAATAGATAGGATTAGATTAAAAAATAAGTAAAAGGTGGAAGGATTG
196 AAATTTTAAATACAAAAAAAATAGATAGGATTAGATTAAAAAATAAATAAAAGGTGGAAGGATTG
* * *
28622384 AAAACGCAAATAAACCATATAAAAGAAAACACGCGGATCTACCGGGTTAGGTCGGGTAGGATCGG
261 AAAACGCAAATAAACCATATAAAAGAAAACACGCAGATCTACCGGGTCAGGTCGAGTAGGATCGG
* *
28622449 GTTCGCGTCAAAACGATGCCGTTTTGGCGTCTATGAGCACTAGCCCAACACGCTGTCGTTTCATA
326 GTTCGCATCAAAACGATGCCGTTTTGGCGTCTATGAGCACTAGCCCAAAACGCTGTCGTTTCATA
* **
28622514 CGCTTATTTAATCTAACTTTTTTTTTAAAAAAAAACTCATTTTTGCCTTTTTTTTTTAAAACTGA
391 CGCTTATTTAATCTAACTTTTTTTTT-AAAAAAAACTCATTTCTGCCTTTTTTTTAAAAAACTGA
* ** * *
28622579 AAGTCCCTCTTGTTTTTCTCTGAAACAACACCCCTACTCCGGCTGTCGGGCCACCGTGACGGCGG
455 AAGTCCCCCTTGTTTTTCTCTGAAACAACACAACTACTCCGGCTGTCAGGCCACCGTGACGGCCG
* *
28622644 TCAATCACCGGCAACGGCACCGCCATCCACAGTGGCCGAAAAGACCCAAAAATTCTCATTTTATT
520 CCAATCACCGGCAACGGCACCGCCATCCACAGTGGCCGAAAAGACCCAAAAATTCCCATTTTATT
* * * *
28622709 CCTTTTTAACGCGGAACCCCGATTTTAGAGTCAAAAATGCCAAAGCCAAAACCTGACCTTCTAGA
585 CCTTTTTAACACGGAACCCCAATTTTAGAGTAAAAAATGCCAAAGCCAAAACCCGACCTTCTAGA
* * ** *
28622774 AATAGAGAAAACATTTCGGTTATCTTTCCCTTTTGGTAACATAAGCTTCATTTCCTGCGACTGTG
650 AATAGAGAAAACATTTCGATTATCTTTCCCTTTTGGTAACAGAAGCTTCACCTCCCGCGACTGTG
28622839 GAAGGCCAAGCGCCAGGTCAGTTTTTCCTTTTTCTTTTCTTTTTATTTCTGTTTTTTATAAGT-A
715 GAAGGCCAAGCGCCAGGTCAGTTTTTCC----T-TTTTC----T-TTT-TGTTTTTTATAAGTAA
28622903 AAAAAAAA-AGATTCAAAGAATAAAAAAATAAAAATCATAAAAGAATCACCTTATTATATA
769 AAAAAAAACAGATTCAAAGAAT-AAAAAATAAAAATCATAAAAGAATCACCTTATTATATA
*
28622963 GTCGAAACTATATAAAAAGGACTAAATTGAAACTTAAATAAAATTTTAGGGGAGAAATCGGGATA
1 GTCGAAACTATATAAAAAGGACTAAATTGAAACTTAAATAAAATTTTAGGGGAGAAATCGAGATA
* *
28623028 AAAACAGAATATGAGACTAAATTGCAACACACGAATGAAAGAGAAGGACGAAACAGGAAAATATT
66 AAAACAAAATATGAGAATAAATTGCAACACACGAATGAAAGAGAAGGACGAAACAGGAAAATATT
* *
28623093 CCTTGTCCTTATGCGCACCATTTCTCATGGGGA-CAAAATAAAACAAAGATAAAATTGTATGGTA
131 CCCTGTCCTTATGCGCACCATTCCTCATGGGGACCAAAATAAAACAAAGATAAAATTGTATGGTA
28623157 AAATTTTAAATACAAAAAAAA-AGATAGGATTAGATTAAAAAATAAATAAAAGGTGGAAGGATTG
196 AAATTTTAAATACAAAAAAAATAGATAGGATTAGATTAAAAAATAAATAAAAGGTGGAAGGATTG
* *
28623221 AAAACGCAAATAAACCATCTAAAAGAAAACACGTAGATCTACCGGGTCAGGTCGAGTCA-GATCG
261 AAAACGCAAATAAACCATATAAAAGAAAACACGCAGATCTACCGGGTCAGGTCGAGT-AGGATCG
* * * * *
28623285 GGTTTGCATCAAAATGATGTCGTTTTGGCGTCTATGAGCACTGGCCCAAAACGTTGTCGTTTCAT
325 GGTTCGCATCAAAACGATGCCGTTTTGGCGTCTATGAGCACTAGCCCAAAACGCTGTCGTTTCAT
*
28623350 ACGCTTATTTAATCT-A-TTTTTTTTT-AAAAAAGCTCATTTCTGCCTTTTTTTTAAAAAAACTG
390 ACGCTTATTTAATCTAACTTTTTTTTTAAAAAAAACTCATTTCTGCCTTTTTTTT-AAAAAACTG
28623412 AAAGTCCCCCTTGTTTTTCTCTGAAACAACACAACTACTCCGG-TCGTCAGGCCACCGTGACGGC
454 AAAGTCCCCCTTGTTTTTCTCTGAAACAACACAACTACTCCGGCT-GTCAGGCCACCGTGACGGC
** * * * * * * *
28623476 CGCCGGTCACCGGCAATGGCGCCGCCGTCCACGGTGGCTGGAAAGACTCAAAAATTCCCATTTTA
518 CGCCAATCACCGGCAACGGCACCGCCATCCACAGTGGCCGAAAAGACCCAAAAATTCCCATTTTA
* *
28623541 TTCCTTTTTAACACGGAACCCCAATTTTGGAGTAAAAAATGCCAAAGCCAAAACCCGGCCTTCTA
583 TTCCTTTTTAACACGGAACCCCAATTTTAGAGTAAAAAATGCCAAAGCCAAAACCCGACCTTCTA
* * * * *
28623606 GAAATAGAGAAAACCTTTCGATTTTCTTTCCTTTTTGGTGACGGAAGCTTCACCTCCCGCGA-TC
648 GAAATAGAGAAAACATTTCGATTATCTTTCCCTTTTGGTAACAGAAGCTTCACCTCCCGCGACT-
* *
28623670 GTGGAAGGCCAAGTGCCAGGTCAGTTTTTTCTTTTTCTTTTTGTTTTTTATAAGTAAAAAAAAAA
712 GTGGAAGGCCAAGCGCCAGGTCAGTTTTTCCTTTTTCTTTTTGTTTTTTATAAGTAAAAAAAAAA
28623735 CAGATTCAAAGAATAAAAAATAAAAATCATAAAAGAATCACCTT
777 CAGATTCAAAGAATAAAAAATAAAAATCATAAAAGAATCACCTT
28623779 TCGATTTTTC
Statistics
Matches: 748, Mismatches: 62, Indels: 27
0.89 0.07 0.03
Matches are distributed among these distances:
823 14 0.02
824 42 0.06
825 14 0.02
829 5 0.01
830 1 0.00
833 27 0.04
834 258 0.34
835 9 0.01
836 1 0.00
837 172 0.23
838 53 0.07
839 152 0.20
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (828 bp):
GTCGAAACTATATAAAAAGGACTAAATTGAAACTTAAATAAAATTTTAGGGGAGAAATCGAGATA
AAAACAAAATATGAGAATAAATTGCAACACACGAATGAAAGAGAAGGACGAAACAGGAAAATATT
CCCTGTCCTTATGCGCACCATTCCTCATGGGGACCAAAATAAAACAAAGATAAAATTGTATGGTA
AAATTTTAAATACAAAAAAAATAGATAGGATTAGATTAAAAAATAAATAAAAGGTGGAAGGATTG
AAAACGCAAATAAACCATATAAAAGAAAACACGCAGATCTACCGGGTCAGGTCGAGTAGGATCGG
GTTCGCATCAAAACGATGCCGTTTTGGCGTCTATGAGCACTAGCCCAAAACGCTGTCGTTTCATA
CGCTTATTTAATCTAACTTTTTTTTTAAAAAAAACTCATTTCTGCCTTTTTTTTAAAAAACTGAA
AGTCCCCCTTGTTTTTCTCTGAAACAACACAACTACTCCGGCTGTCAGGCCACCGTGACGGCCGC
CAATCACCGGCAACGGCACCGCCATCCACAGTGGCCGAAAAGACCCAAAAATTCCCATTTTATTC
CTTTTTAACACGGAACCCCAATTTTAGAGTAAAAAATGCCAAAGCCAAAACCCGACCTTCTAGAA
ATAGAGAAAACATTTCGATTATCTTTCCCTTTTGGTAACAGAAGCTTCACCTCCCGCGACTGTGG
AAGGCCAAGCGCCAGGTCAGTTTTTCCTTTTTCTTTTTGTTTTTTATAAGTAAAAAAAAAACAGA
TTCAAAGAATAAAAAATAAAAATCATAAAAGAATCACCTTATTATATA
Found at i:28625855 original size:43 final size:43
Alignment explanation
Indices: 28625794--28625882 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
28625784 AAAAGAAAAG
28625794 AAATTTTTAAATGCTACTCCCACAGTTCATATATAATGCCATC
1 AAATTTTTAAATGCTACTCCCACAGTTCATATATAATGCCATC
*
28625837 AAATTTTTAAATGCTACTCCCATAGTTCATATATAATGCCATC
1 AAATTTTTAAATGCTACTCCCACAGTTCATATATAATGCCATC
28625880 AAA
1 AAA
28625883 ATAAGAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (43 bp):
AAATTTTTAAATGCTACTCCCACAGTTCATATATAATGCCATC
Found at i:28628598 original size:2 final size:2
Alignment explanation
Indices: 28628591--28628631 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28628581 CCGCACTGTA
28628591 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28628632 ATCACTGACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28634424 original size:11 final size:11
Alignment explanation
Indices: 28634406--28634446 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
28634396 ATGATAACCA
28634406 TAAAATAATAG
1 TAAAATAATAG
*
28634417 TAATATAATAG
1 TAAAATAATAG
*
28634428 CAAAATAATAG
1 TAAAATAATAG
28634439 TAAAATAA
1 TAAAATAA
28634447 CATCAAAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (11 bp):
TAAAATAATAG
Found at i:28634453 original size:22 final size:22
Alignment explanation
Indices: 28634399--28634454 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
28634389 TATCCAAATG
*
28634399 ATAACCAT-AAAATAATAGTAAT
1 ATAA-CATCAAAATAATAGTAAA
* *
28634421 ATAATAGCAAAATAATAGTAAA
1 ATAACATCAAAATAATAGTAAA
28634443 ATAACATCAAAA
1 ATAACATCAAAA
28634455 CGGCAACAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.23
Consensus pattern (22 bp):
ATAACATCAAAATAATAGTAAA
Found at i:28636689 original size:5 final size:5
Alignment explanation
Indices: 28636679--28636704 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28636669 CCAAGATGAG
28636679 CCGAC CCGAC CCGAC CCGAC CCGAC C
1 CCGAC CCGAC CCGAC CCGAC CCGAC C
28636705 GATCTCTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.62, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:28657116 original size:6 final size:6
Alignment explanation
Indices: 28657105--28657138 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
28657095 TTTTACTTCT
28657105 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA GTTT
1 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA GTTT
28657139 ACTTTTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.53
Consensus pattern (6 bp):
GTTTGA
Found at i:28663605 original size:18 final size:18
Alignment explanation
Indices: 28663582--28663620 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28663572 ACCTAATCCA
*
28663582 AACCCAAATATCCAACCC
1 AACCCAAATACCCAACCC
* *
28663600 AACCCAATTACCCAACTC
1 AACCCAAATACCCAACCC
28663618 AAC
1 AAC
28663621 ACAATCACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.13
Consensus pattern (18 bp):
AACCCAAATACCCAACCC
Found at i:28663776 original size:9 final size:9
Alignment explanation
Indices: 28663762--28663803 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
28663752 ATGTAGTGAT
28663762 TTAATTCGG
1 TTAATTCGG
28663771 TTAATTCAGG
1 TTAATTC-GG
28663781 -TAATTCGG
1 TTAATTCGG
*
28663789 TTAATTCGT
1 TTAATTCGG
28663798 TTAATT
1 TTAATT
28663804 TGATTAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 2 0.07
9 26 0.87
10 2 0.07
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.48
Consensus pattern (9 bp):
TTAATTCGG
Found at i:28666524 original size:98 final size:97
Alignment explanation
Indices: 28666416--28666608 Score: 260
Period size: 98 Copynumber: 2.0 Consensus size: 97
28666406 AATTTATTGA
* * * * *
28666416 TTTCTTAAATCACGTGCCCATGTCCATTGACGCGTTTATTTATTTTAATTTAATTAATTATATAT
1 TTTCTCAAATCACGTGCCCACGTACATTGACGCGTTTATTTATCTTAATTTAA-TAACTATATAT
* *
28666481 GTATTTTACTTAATTAATTTAAAAAATTATTAG
65 GTATTTTACTCAATTAATGTAAAAAATTATTAG
* * * * *
28666514 TTTCTCAAATCACGTGCGCACGTATATTGATGTGTTTATTTATCTTAATTTAATAACTATATATT
1 TTTCTCAAATCACGTGCCCACGTACATTGACGCGTTTATTTATCTTAATTTAATAACTATATATG
*
28666579 TATTTTACTCAATTAATGTAAATAATTATT
66 TATTTTACTCAATTAATGTAAAAAATTATT
28666609 TTTTAAAAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
97 37 0.45
98 45 0.55
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (97 bp):
TTTCTCAAATCACGTGCCCACGTACATTGACGCGTTTATTTATCTTAATTTAATAACTATATATG
TATTTTACTCAATTAATGTAAAAAATTATTAG
Found at i:28666740 original size:111 final size:110
Alignment explanation
Indices: 28666491--28666749 Score: 360
Period size: 111 Copynumber: 2.3 Consensus size: 110
28666481 GTATTTTACT
* * * *
28666491 TAATTAATTTAAAAAATTATTAGTTTCTCAAATCACGTGCGCACGTATATTGATGTGTTTATTTA
1 TAATTATTTTTAAAAATTATTAGTTTCTTAAATCACGTGCGCACGTATATTGATGTGTCTATTTA
* *
28666556 TCTTAATTTAATAACTATATATTTATTTTACTCAATTAATGTAAA
66 TCTTAATTTAACAACTATATATTTATTTTACTCAATTAAAGTAAA
* *
28666601 TAATTATTTTTTAAAAATTATTAATTTCTTAAATCACGTGCGCACTTATATT-ATCGTGTCTATT
1 TAATTA-TTTTTAAAAATTATTAGTTTCTTAAATCACGTGCGCACGTATATTGAT-GTGTCTATT
* *
28666665 TATTTTAATTTAACAATTATATATTTATTTTACTCAATTAAAGTAAA
64 TATCTTAATTTAACAACTATATATTTATTTTACTCAATTAAAGTAAA
* *
28666712 TAATTA-TTTTAAAATTTCCATTAGTTTCTTAATTCACG
1 TAATTATTTTTAAAAATT--ATTAGTTTCTTAAATCACG
28666750 CACGTATTTT
Statistics
Matches: 132, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
109 10 0.08
110 8 0.06
111 114 0.86
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (110 bp):
TAATTATTTTTAAAAATTATTAGTTTCTTAAATCACGTGCGCACGTATATTGATGTGTCTATTTA
TCTTAATTTAACAACTATATATTTATTTTACTCAATTAAAGTAAA
Found at i:28666776 original size:111 final size:110
Alignment explanation
Indices: 28666491--28666784 Score: 330
Period size: 111 Copynumber: 2.7 Consensus size: 110
28666481 GTATTTTACT
* * * * ** *
28666491 TAATTAATTTAAAAAATTATTAGTTTCTCAAATCACGTGCGCACGTATATTGAT-GTGTTTATTT
1 TAATTATTTTTAAAAATTATTAATTTCTTAAATCACGCACGCACTTATATT-ATCGTGTTTATTT
* * *
28666555 ATCTTAATTTAATAACTATATATTTATTTTACTCAATTAATGTAAA
65 ATTTTAATTTAACAACTATATATTTATTTTACTCAATTAAAGTAAA
** *
28666601 TAATTATTTTTTAAAAATTATTAATTTCTTAAATCACGTGCGCACTTATATTATCGTGTCTATTT
1 TAATTA-TTTTTAAAAATTATTAATTTCTTAAATCACGCACGCACTTATATTATCGTGTTTATTT
*
28666666 ATTTTAATTTAACAATTATATATTTATTTTACTCAATTAAAGTAAA
65 ATTTTAATTTAACAACTATATATTTATTTTACTCAATTAAAGTAAA
* * * * * *
28666712 TAATTA-TTTTAAAATTTCCATTAGTTTCTTAATTCACGCACGTA-TT-T-TTA-CGAGTTTAAT
1 TAATTATTTTTAAAAATT--ATTAATTTCTTAAATCACGCACGCACTTATATTATCGTGTTTATT
28666772 TATTTTAATTTAA
64 TATTTTAATTTAA
28666785 TTATTTATAT
Statistics
Matches: 161, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
107 20 0.12
108 3 0.02
109 11 0.07
110 10 0.06
111 117 0.73
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (110 bp):
TAATTATTTTTAAAAATTATTAATTTCTTAAATCACGCACGCACTTATATTATCGTGTTTATTTA
TTTTAATTTAACAACTATATATTTATTTTACTCAATTAAAGTAAA
Found at i:28666800 original size:15 final size:14
Alignment explanation
Indices: 28666766--28666817 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
28666756 TTTTTACGAG
28666766 TTTAATTATTTTAA
1 TTTAATTATTTTAA
*
28666780 TTTAATTATTTATAT
1 TTTAATTATTT-TAA
28666795 TTTAATTTATTTTAA
1 TTTAA-TTATTTTAA
28666810 TTTAATTA
1 TTTAATTA
28666818 ATATAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 14 0.41
15 14 0.41
16 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAATTATTTTAA
Found at i:28666807 original size:10 final size:10
Alignment explanation
Indices: 28666766--28666813 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
28666756 TTTTTACGAG
28666766 TTTAA-TTAT
1 TTTAATTTAT
28666775 TTTAATTTA-
1 TTTAATTTAT
* *
28666784 ATTATTTATAT
1 TTTAATT-TAT
28666795 TTTAATTTAT
1 TTTAATTTAT
28666805 TTTAATTTA
1 TTTAATTTA
28666814 ATTAATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 10 0.31
10 17 0.53
11 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATTTAT
Found at i:28667292 original size:22 final size:22
Alignment explanation
Indices: 28667264--28667336 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
28667254 AAAGGCTAGA
28667264 AAAATACCACAAAGGCCAAATC
1 AAAATACCACAAAGGCCAAATC
* *
28667286 AAAATACGCCACAAATG-CTAA-C
1 AAAATA--CCACAAAGGCCAAATC
* *
28667308 AGAATGCCACAAAGGCCAAATC
1 AAAATACCACAAAGGCCAAATC
*
28667330 AGAATAC
1 AAAATAC
28667337 GCCATAAATG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
20 8 0.20
21 3 0.08
22 18 0.45
23 3 0.08
24 8 0.20
ACGTcount: A:0.51, C:0.26, G:0.12, T:0.11
Consensus pattern (22 bp):
AAAATACCACAAAGGCCAAATC
Found at i:28667300 original size:24 final size:24
Alignment explanation
Indices: 28667270--28667340 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
28667260 TAGAAAAATA
*
28667270 CCACAAAGGCCAAATCAAAATACG
1 CCACAAAGGCCAAATCAGAATACG
* *
28667294 CCACAAATG-CTAA-CAGAAT--G
1 CCACAAAGGCCAAATCAGAATACG
28667314 CCACAAAGGCCAAATCAGAATACG
1 CCACAAAGGCCAAATCAGAATACG
28667338 CCA
1 CCA
28667341 TAAATGCTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
20 9 0.24
21 3 0.08
22 11 0.29
23 3 0.08
24 12 0.32
ACGTcount: A:0.46, C:0.30, G:0.14, T:0.10
Consensus pattern (24 bp):
CCACAAAGGCCAAATCAGAATACG
Done.