Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008548.1 Hibiscus syriacus cultivar Beakdansim tig00111440_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1170587
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:414629 original size:22 final size:22
Alignment explanation
Indices: 414580--414628 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
414570 ATAAATTATT
* **
414580 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
414602 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
414625 TAAA
1 TAAA
414629 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:414658 original size:22 final size:22
Alignment explanation
Indices: 414632--414674 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
414622 TAATAAATTA
414632 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
414654 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
414675 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:414683 original size:22 final size:22
Alignment explanation
Indices: 414634--414682 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
414624 ATAAATTATT
**
414634 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
414656 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
414679 TAAA
1 TAAA
414683 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:414738 original size:80 final size:80
Alignment explanation
Indices: 414637--414787 Score: 266
Period size: 80 Copynumber: 1.9 Consensus size: 80
414627 AATTATTTAA
*
414637 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATACATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
414702 CTATACAACTACAAT
66 CCATACAACTACAAT
* *
414717 AATAAATCAATATATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATACATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
414782 CCATAC
66 CCATAC
414788 TAATAAATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (80 bp):
AATAAATCAATACATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:414760 original size:18 final size:18
Alignment explanation
Indices: 414739--414795 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
414729 TATATTTTAA
414739 AATAAATCAATCTATACT
1 AATAAATCAATCTATACT
* *
414757 AATAAAT-TAT-T-TA-A
1 AATAAATCAATCTATACT
*
414771 AATAAATCAATCCATACT
1 AATAAATCAATCTATACT
414789 AATAAAT
1 AATAAAT
414796 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 1 0.03
17 4 0.13
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATCTATACT
Found at i:414763 original size:22 final size:23
Alignment explanation
Indices: 414688--414762 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
414678 ATAAATTATT
414688 TAAAATAAATCAATCTATAC-AA
1 TAAAATAAATCAATCTATACTAA
* **
414710 CTACAATAATAAATCAATATATA-TTT
1 -T--AA-AATAAATCAATCTATACTAA
414736 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATACTAA
414759 TAAA
1 TAAA
414763 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAATAAATCAATCTATACTAA
Found at i:414834 original size:38 final size:37
Alignment explanation
Indices: 414752--414858 Score: 152
Period size: 38 Copynumber: 3.0 Consensus size: 37
414742 AAATCAATCT
*
414752 ATACTAATAAATTATTTAAAAT--A-AAT-CA-ATCC
1 ATACTAATAAATTATTTAAAATAAACAATCCATATTC
414784 ATACTAATAAATTATTTAAAATAAAGCAATCCATATTC
1 ATACTAATAAATTATTTAAAATAAA-CAATCCATATTC
414822 ATACTAATAAATTATTTAAAATAAATCAATCCATATT
1 ATACTAATAAATTATTTAAAATAAA-CAATCCATATT
414859 TTAAAATAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
32 22 0.33
34 1 0.01
36 3 0.04
37 2 0.03
38 39 0.58
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.36
Consensus pattern (37 bp):
ATACTAATAAATTATTTAAAATAAACAATCCATATTC
Found at i:414870 original size:204 final size:204
Alignment explanation
Indices: 414617--414990 Score: 696
Period size: 204 Copynumber: 1.8 Consensus size: 204
414607 TAAATCAATC
414617 CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAA
1 CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAA
**
414682 ATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATAT-ATATTTTAAAATAAAT
66 ATTATTTAAAATAAATCAAAATATACAACTACAATAATAAATCAA-ATCATATTTTAAAATAAAT
*
414746 CAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAGC
130 CAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAGC
414811 AATCCATATT
195 AATCCATATT
*
414821 CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAA
1 CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAA
414886 ATTATTTAAAATAAATCAAAATATACAACTACAATAATAAATCAAATCATATTTTAAAATAAATC
66 ATTATTTAAAATAAATCAAAATATACAACTACAATAATAAATCAAATCATATTTTAAAATAAATC
414951 AATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
131 AATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
414991 TTTTAAAATA
Statistics
Matches: 165, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
203 2 0.01
204 163 0.99
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (204 bp):
CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAA
ATTATTTAAAATAAATCAAAATATACAACTACAATAATAAATCAAATCATATTTTAAAATAAATC
AATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAGCA
ATCCATATT
Found at i:414887 original size:22 final size:22
Alignment explanation
Indices: 414838--414886 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
414828 ATAAATTATT
**
414838 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
414860 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
414883 TAAA
1 TAAA
414887 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:414977 original size:32 final size:31
Alignment explanation
Indices: 414938--415096 Score: 128
Period size: 31 Copynumber: 5.4 Consensus size: 31
414928 CAAATCATAT
414938 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
414970 TTTAAAATAAATCAATC---C--AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
414992 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAA-TCATACTAATAAATTA
* **
415024 TTTAAAATAAAT-TATTTTA-TAATAAATTA
1 TTTAAAATAAATCAATCATACTAATAAATTA
* **
415053 TTTTTAAAATAAAT-TATTTTA-TAATAAATTA
1 --TTTAAAATAAATCAATCATACTAATAAATTA
415084 TTTTAAAATAAAT
1 -TTTAAAATAAAT
415097 TATTTTAAAA
Statistics
Matches: 112, Mismatches: 3, Indels: 26
0.79 0.02 0.18
Matches are distributed among these distances:
22 15 0.13
23 3 0.03
24 1 0.01
26 3 0.03
28 3 0.03
29 10 0.09
30 17 0.15
31 32 0.29
32 28 0.25
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTAAAATAAATCAATCATACTAATAAATTA
Found at i:414984 original size:54 final size:54
Alignment explanation
Indices: 414921--415035 Score: 205
Period size: 54 Copynumber: 2.1 Consensus size: 54
414911 CAACTACAAT
414921 AATAAATCAAAT-CATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATC-AATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
414975 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
415029 AATAAAT
1 AATAAAT
415036 TATTTTATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
53 3 0.05
54 56 0.95
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:414996 original size:22 final size:22
Alignment explanation
Indices: 414970--415012 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
414960 TAATAAATTA
414970 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
414992 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
415013 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:415021 original size:22 final size:22
Alignment explanation
Indices: 414972--415020 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
414962 ATAAATTATT
**
414972 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
414994 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
415017 TAAA
1 TAAA
415021 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:415047 original size:15 final size:15
Alignment explanation
Indices: 415015--415111 Score: 160
Period size: 15 Copynumber: 6.5 Consensus size: 15
415005 AATTCATACT
415015 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
415029 AATAAATTATTTTAT
1 AATAAATTATTTTAA
415044 AATAAATTATTTTTAA
1 AATAAATTA-TTTTAA
*
415060 AATAAATTATTTTAT
1 AATAAATTATTTTAA
415075 AATAAATTATTTTAA
1 AATAAATTATTTTAA
415090 AATAAATTATTTTAA
1 AATAAATTATTTTAA
415105 AATAAAT
1 AATAAAT
415112 AATCTTATTA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
14 9 0.12
15 54 0.70
16 14 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:415062 original size:31 final size:30
Alignment explanation
Indices: 414989--415111 Score: 176
Period size: 31 Copynumber: 4.0 Consensus size: 30
414979 AATCAATCCA
* *
414989 TATTTTAAAATAAATCAATTCATACTAATAAAT
1 TATTTTAAAATAAAT-TATT-TTA-TAATAAAT
415022 TA-TTTAAAATAAATTATTTTATAATAAAT
1 TATTTTAAAATAAATTATTTTATAATAAAT
415051 TATTTTTAAAATAAATTATTTTATAATAAAT
1 TA-TTTTAAAATAAATTATTTTATAATAAAT
*
415082 TATTTTAAAATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAATTATTTTATAATAAAT
415112 AATCTTATTA
Statistics
Matches: 85, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
29 10 0.12
30 29 0.34
31 32 0.38
32 12 0.14
33 2 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
TATTTTAAAATAAATTATTTTATAATAAAT
Found at i:415088 original size:46 final size:44
Alignment explanation
Indices: 415015--415111 Score: 158
Period size: 46 Copynumber: 2.2 Consensus size: 44
415005 AATTCATACT
*
415015 AATAAATTATTTAAAATAAATTATTTTATAATAAATTATTTTTAA
1 AATAAATTATTTAAAATAAATTATTTTAAAATAAATTA-TTTTAA
*
415060 AATAAATTATTTTATAATAAATTATTTTAAAATAAATTATTTTAA
1 AATAAATTA-TTTAAAATAAATTATTTTAAAATAAATTATTTTAA
415105 AATAAAT
1 AATAAAT
415112 AATCTTATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 22 0.45
46 27 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (44 bp):
AATAAATTATTTAAAATAAATTATTTTAAAATAAATTATTTTAA
Found at i:415113 original size:134 final size:133
Alignment explanation
Indices: 414429--415035 Score: 582
Period size: 140 Copynumber: 4.6 Consensus size: 133
414419 CAACTACAAT
* *
414429 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTGATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATT
* * ** *
414494 TAAAATAAATCAATCCATATTTTA-AAATA-AATCAATCCATACAAATAAATTATTTAAAATAAA
66 TAAAATAAATCAA---A-A-TATACAACTACAAT-AATAAAT-CAAATATA-T-TTTAAAATAAA
*
414557 TCAATCCATACT
122 TCAATCCATACA
* *
414569 AATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATT
* * ** * *
414634 TAAAATAAATCAATCCATATTTTA-AAATA-AATCAATCCATACTAATAAATTATTTAAAATAAA
66 TAAAATAAATCAA---A-A-TATACAACTACAAT-AATAAAT-CAAATATA-T-TTTAAAATAAA
*
414697 TCAATCTATACA
122 TCAATCCATACA
* * **
414709 ACTACA--A--T--AATAAATCAATATATATTTTAAAATAAATCAATCTATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATT
* *
414768 TAAAATAAATC---A-AT----C--C-ATACT-AAT-AAAT-TA-TTTAAAATAAAGCAATCCAT
66 TAAAATAAATCAAAATATACAACTACAATAATAAATCAAATATATTTTAAAATAAATCAATCCAT
414818 ATTCATA
131 A--C--A
414825 CTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
1 --AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
414890 TTTAAAATAAATCAAAATATACAACTACAATAATAAATCAAATCATATTTTAAAATAAATCAATC
64 TTTAAAATAAATCAAAATATACAACTACAATAATAAATCAAAT-ATATTTTAAAATAAATCAATC
*
414955 CATACT
128 CATACA
414961 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACTAATAAATTAT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTAT
415025 TTAAAATAAAT
65 TTAAAATAAAT
415036 TATTTTATAA
Statistics
Matches: 413, Mismatches: 24, Indels: 66
0.82 0.05 0.13
Matches are distributed among these distances:
112 19 0.05
114 1 0.00
115 1 0.00
116 4 0.01
118 6 0.01
119 2 0.00
120 3 0.01
122 1 0.00
124 60 0.15
125 1 0.00
127 2 0.00
128 2 0.00
132 1 0.00
133 1 0.00
134 134 0.32
135 4 0.01
136 4 0.01
137 4 0.01
138 2 0.00
139 2 0.00
140 159 0.38
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (133 bp):
AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATT
TAAAATAAATCAAAATATACAACTACAATAATAAATCAAATATATTTTAAAATAAATCAATCCAT
ACA
Found at i:416968 original size:68 final size:68
Alignment explanation
Indices: 416859--416995 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
416849 TCTATCCCAA
* *
416859 AATAAAACTCTCGAATATATAGGATCATGAGTGTTAATGAATGGAGATGTATGTTGATTGACATT
1 AATAAAACTCCCGAATATATAGGATCATGAGTGTTAATGAATGAAGATGTATGTTGATTGACATT
416924 AAC
66 AAC
416927 AATAAAACTCCCGAATATATAGGATCATGAGTGTTAATGAATGAAGATGTATGTTGATTGACATT
1 AATAAAACTCCCGAATATATAGGATCATGAGTGTTAATGAATGAAGATGTATGTTGATTGACATT
416992 AAC
66 AAC
416995 A
1 A
416996 TGGGCTTATT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.31
Consensus pattern (68 bp):
AATAAAACTCCCGAATATATAGGATCATGAGTGTTAATGAATGAAGATGTATGTTGATTGACATT
AAC
Found at i:421869 original size:21 final size:21
Alignment explanation
Indices: 421827--421879 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
421817 ATTCCACGAA
* *
421827 GAGTTCAACGACTATGACTGT
1 GAGTTCAACGGCGATGACTGT
**
421848 GAGTTCAACGGCGATGGTTGT
1 GAGTTCAACGGCGATGACTGT
*
421869 GAGCTCAACGG
1 GAGTTCAACGG
421880 ATGGACAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (21 bp):
GAGTTCAACGGCGATGACTGT
Found at i:425408 original size:18 final size:19
Alignment explanation
Indices: 425367--425415 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
425357 ATATACATTT
*
425367 TATGAACGGTAAAATACGG
1 TATGAACAGTAAAATACGG
*
425386 TATGAACAGTAAAATA-TG
1 TATGAACAGTAAAATACGG
425404 TATGAACAGTAA
1 TATGAACAGTAA
425416 TGAACAGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.24
Consensus pattern (19 bp):
TATGAACAGTAAAATACGG
Found at i:425420 original size:10 final size:11
Alignment explanation
Indices: 425405--425437 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
425395 TAAAATATGT
425405 ATGAACAGTA-
1 ATGAACAGTAC
425415 ATGAACAGTACC
1 ATGAACAGTA-C
425427 ATGAACAGTAC
1 ATGAACAGTAC
425438 CTGCTATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 1 0.05
12 10 0.48
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (11 bp):
ATGAACAGTAC
Found at i:425432 original size:12 final size:12
Alignment explanation
Indices: 425405--425438 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
425395 TAAAATATGT
425405 ATGAACAGTA--
1 ATGAACAGTACC
425415 ATGAACAGTACC
1 ATGAACAGTACC
425427 ATGAACAGTACC
1 ATGAACAGTACC
425439 TGCTATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:426111 original size:40 final size:40
Alignment explanation
Indices: 426060--426140 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
426050 ACTGAATATT
* *
426060 TGTCCCGAAGGACCACTATATCTCGAAAGACCACTGTATA
1 TGTCCCAAAGGACCACTATATCCCGAAAGACCACTGTATA
* *
426100 TGTCCCAAAGGACCACTATGTCCCGAAGGACCACTGTATA
1 TGTCCCAAAGGACCACTATATCCCGAAAGACCACTGTATA
426140 T
1 T
426141 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (40 bp):
TGTCCCAAAGGACCACTATATCCCGAAAGACCACTGTATA
Found at i:426121 original size:18 final size:18
Alignment explanation
Indices: 426098--426134 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
426088 GACCACTGTA
426098 TATGTCCCAAAGGACCAC
1 TATGTCCCAAAGGACCAC
*
426116 TATGTCCCGAAGGACCAC
1 TATGTCCCAAAGGACCAC
426134 T
1 T
426135 GTATATCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (18 bp):
TATGTCCCAAAGGACCAC
Found at i:440352 original size:19 final size:19
Alignment explanation
Indices: 440328--440371 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
440318 AATTTAAACA
440328 TTATTTTTATATTAGGCAT
1 TTATTTTTATATTAGGCAT
440347 TTATTTTTATATTAGGCAT
1 TTATTTTTATATTAGGCAT
440366 TTATTT
1 TTATTT
440372 ATAGACTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (19 bp):
TTATTTTTATATTAGGCAT
Found at i:443604 original size:29 final size:29
Alignment explanation
Indices: 443515--443605 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
443505 TTGGTCTTCA
* * *
443515 AAATTTCTATTTTTACTATTCTAGTTTTT
1 AAATTTCTATTTTTGCTATTTTAGTATTT
* *
443544 AAATTTCTGTTTGTGCTATTTTAGTCATTT
1 AAATTTCTATTTTTGCTATTTTAGT-ATTT
* * *
443574 AATTTTCTATTTTTGCTATTTTAATACTT
1 AAATTTCTATTTTTGCTATTTTAGTATTT
443603 AAA
1 AAA
443606 ATTTTTGTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
29 26 0.52
30 24 0.48
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.58
Consensus pattern (29 bp):
AAATTTCTATTTTTGCTATTTTAGTATTT
Found at i:446354 original size:22 final size:23
Alignment explanation
Indices: 446311--446355 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
446301 GAGCGAGGGA
*
446311 GGAATCAGTACCCCCTCGTGGGG
1 GGAATCAGTACCCCCTCATGGGG
446334 GGAATCAGTA-CCCCTCATGGGG
1 GGAATCAGTACCCCCTCATGGGG
446356 AATCGGTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.20, C:0.29, G:0.33, T:0.18
Consensus pattern (23 bp):
GGAATCAGTACCCCCTCATGGGG
Found at i:448550 original size:23 final size:23
Alignment explanation
Indices: 448520--448608 Score: 135
Period size: 23 Copynumber: 3.9 Consensus size: 23
448510 TTCCCTACAT
448520 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
448543 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
*
448566 GGGGGAATCAGTTCCCCTTC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
448588 GGGGGTATCGATTCCCTCTTC
1 GGGGGAATCGGTTCCC-CTTC
448609 TTTATAATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
22 15 0.25
23 46 0.75
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:464684 original size:20 final size:20
Alignment explanation
Indices: 464655--464727 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
464645 AAATGACCAA
*
464655 CAAATTCGCAACGCAAACTC
1 CAAATTCGCAACACAAACTC
* **
464675 CAATTTCGCAACACAATTTC
1 CAAATTCGCAACACAAACTC
* * *
464695 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-AAACTC
464716 CAAATTCGCAAC
1 CAAATTCGCAAC
464728 TCGATTTCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACACAAACTC
Found at i:464735 original size:41 final size:40
Alignment explanation
Indices: 464656--464788 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 40
464646 AATGACCAAC
* * * * * *
464656 AAATTCGCAACGCAAACTCCAATTTCGCAACACAATTTCC
1 AAATTCGCAACACGAATTTCAAATTCGCAACACAATTTCA
* *
464696 AAATTCGCAACACTGAATTTCAAATTCGCAACTCGATTTCA
1 AAATTCGCAACAC-GAATTTCAAATTCGCAACACAATTTCA
* * * * *
464737 AAATTCGTAACTCGATTTTCGAATTCGCAACACAAATTT-T
1 AAATTCGCAACACGAATTTCAAATTCGCAACAC-AATTTCA
*
464777 AATTTCGCAACA
1 AAATTCGCAACA
464789 TGTTTTATCT
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
40 38 0.52
41 35 0.48
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.29
Consensus pattern (40 bp):
AAATTCGCAACACGAATTTCAAATTCGCAACACAATTTCA
Found at i:464742 original size:20 final size:19
Alignment explanation
Indices: 464679--464788 Score: 94
Period size: 20 Copynumber: 5.5 Consensus size: 19
464669 AAACTCCAAT
*
464679 TTCGCAACACAATTTCCAAA
1 TTCGCAACACGATTT-CAAA
464699 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-G-ATTTCAAA
*
464720 TTCGCAACTCGATTTCAAAA
1 TTCGCAACACGATTTC-AAA
* * *
464740 TTCGTAACTCGATTTTCGAA
1 TTCGCAACACGA-TTTCAAA
* * *
464760 TTCGCAACACAAATTTTAAT
1 TTCGCAACAC-GATTTCAAA
464780 TTCGCAACA
1 TTCGCAACA
464789 TGTTTTATCT
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.07
20 48 0.64
21 18 0.24
22 4 0.05
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (19 bp):
TTCGCAACACGATTTCAAA
Found at i:466220 original size:3 final size:3
Alignment explanation
Indices: 466214--466305 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
466204 TTTTTATCCA
*
466214 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
466262 TAT TAA TAT TAT TAT TAA TAT TAT TAT TAT TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
466306 AATATATTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:466775 original size:24 final size:24
Alignment explanation
Indices: 466687--466775 Score: 67
Period size: 24 Copynumber: 3.7 Consensus size: 24
466677 CCACCCACCT
** *
466687 GAAAAAAA-AAAAAGA-AGGGACA
1 GAAAAAAAGAAAAAGAGATAGAAA
* * *
466709 GAGAAAAAAGAAACTAGACAAAGAAA
1 GA-AAAAAAGAAA-AAGAGATAGAAA
*
466735 GAAAAAAAGAAGAAGAGATAGAAA
1 GAAAAAAAGAAAAAGAGATAGAAA
466759 GAAAAAAA-AAAACAGAG
1 GAAAAAAAGAAAA-AGAG
466776 CAAATATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.04
23 9 0.17
24 24 0.45
25 12 0.23
26 6 0.11
ACGTcount: A:0.72, C:0.04, G:0.21, T:0.02
Consensus pattern (24 bp):
GAAAAAAAGAAAAAGAGATAGAAA
Found at i:467590 original size:20 final size:18
Alignment explanation
Indices: 467551--467591 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
467541 CAATTAATTA
*
467551 ATAATTAGTTTTATTTTT
1 ATAATTAGTTTTAATTTT
467569 ATAATTTAGTTATTAATTTT
1 ATAA-TTAGTT-TTAATTTT
467589 ATA
1 ATA
467592 TGTCTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
20 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
ATAATTAGTTTTAATTTT
Found at i:467682 original size:22 final size:20
Alignment explanation
Indices: 467641--467685 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
467631 ATAGAATTAT
**
467641 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
467661 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
467683 TAT
1 TAT
467686 ATGTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Found at i:468415 original size:3 final size:3
Alignment explanation
Indices: 468383--468469 Score: 56
Period size: 3 Copynumber: 28.3 Consensus size: 3
468373 TTCAAATTTT
* * *
468383 TTA TTA CTTA TTA TTT TTT TTA -TA TATA TTA TTA TTA CTTA TTA TTT
1 TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA
*
468430 TTT TTA TATA TTA TTA TT- TT- TTA TT- TTA TTTA TTTA TTA T
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA T
468470 ATTCAAGAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
2 8 0.11
3 45 0.62
4 19 0.26
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:468419 original size:31 final size:32
Alignment explanation
Indices: 468383--468447 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 32
468373 TTCAAATTTT
468383 TTATTACTTATTATTTTTTTTATATA-TATTA
1 TTATTACTTATTATTTTTTTTATATATTATTA
468414 TTATTACTTATTATTTTTTTTATATATTATTA
1 TTATTACTTATTATTTTTTTTATATATTATTA
468446 TT
1 TT
468448 TTTTATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (32 bp):
TTATTACTTATTATTTTTTTTATATATTATTA
Found at i:468440 original size:29 final size:29
Alignment explanation
Indices: 468383--468469 Score: 117
Period size: 26 Copynumber: 3.0 Consensus size: 29
468373 TTCAAATTTT
468383 TTATTACTTATTATTTTTTTTATATATATTA
1 TTATTACTTATTA-TTTTTTT-TATATATTA
468414 TTATTACTTATTATTTTTTTTATATATTA
1 TTATTACTTATTATTTTTTTTATATATTA
* *
468443 TTATT--TT-TTATTTTATTTATTTATTA
1 TTATTACTTATTATTTTTTTTATATATTA
468469 T
1 T
468470 ATTCAAGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
26 18 0.33
27 2 0.04
29 14 0.26
30 7 0.13
31 13 0.24
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (29 bp):
TTATTACTTATTATTTTTTTTATATATTA
Found at i:468441 original size:16 final size:15
Alignment explanation
Indices: 468378--468469 Score: 82
Period size: 16 Copynumber: 5.9 Consensus size: 15
468368 TTCCTTTCAA
468378 ATTTTTTATTACTTATT
1 ATTTTTT-TTA-TTATT
468395 ATTTTTTTTA-TATAT
1 ATTTTTTTTATTAT-T
* *
468410 ATTATTATTACTTATT
1 ATTTTTTTTA-TTATT
468426 ATTTTTTTTATATATT
1 ATTTTTTTTAT-TATT
468442 ATTATTTTTTATT-TT
1 ATT-TTTTTTATTATT
*
468457 A-TTTATTTATTAT
1 ATTTTTTTTATTAT
468470 ATTCAAGAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
13 8 0.12
14 5 0.08
15 13 0.20
16 20 0.31
17 18 0.28
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTTTTTTATTATT
Found at i:470085 original size:14 final size:14
Alignment explanation
Indices: 470047--470100 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
470037 ATTTTAAATA
*
470047 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
470061 TTTTACATTTGCAT
1 ATTTACATTTGCAT
470075 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
470090 CTTTGCATTTG
1 ATTTACATTTG
470101 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:472807 original size:180 final size:179
Alignment explanation
Indices: 472505--472863 Score: 709
Period size: 180 Copynumber: 2.0 Consensus size: 179
472495 ACACTACATT
472505 TATCTGAGATTCTGAAGAAATGTCTCTACCTGTTTTGAGACACAAACTCTAGATGTTTACCTTTT
1 TATCTGAGATTCTGAAGAAATGTCTCTACCTGTTTTGAGACACAAACTCTAGATGTTTACCTTTT
472570 CGGGTATAGTTGATCGATGATACTACATTCCACCATATACATGACTTCAAAAGTCACACATTTGT
66 CGGGTATAGTTGATCGATGATACTACATTCCACCATATACATGACTTCAAAAGTCACACATTTGT
472635 CTTTTCGAACACAAAACCATCATAAACCAAAAGACCTCAAAAGAACCAAA
131 CTTTTCGAACACAAAACCATCATAAACC-AAAGACCTCAAAAGAACCAAA
472685 TATCTGAGATTCTGAAGAAATGTCTCTACCTGTTTTGAGACACAAACTCTAGATGTTTACCTTTT
1 TATCTGAGATTCTGAAGAAATGTCTCTACCTGTTTTGAGACACAAACTCTAGATGTTTACCTTTT
472750 CGGGTATAGTTGATCGATGATACTACATTCCACCATATACATGACTTCAAAAGTCACACATTTGT
66 CGGGTATAGTTGATCGATGATACTACATTCCACCATATACATGACTTCAAAAGTCACACATTTGT
472815 CTTTTCGAACACAAAACCATCATAAACCAAAGACCTCAAAAGAACCAAA
131 CTTTTCGAACACAAAACCATCATAAACCAAAGACCTCAAAAGAACCAAA
472864 CTTTCAATTA
Statistics
Matches: 179, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
179 21 0.12
180 158 0.88
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (179 bp):
TATCTGAGATTCTGAAGAAATGTCTCTACCTGTTTTGAGACACAAACTCTAGATGTTTACCTTTT
CGGGTATAGTTGATCGATGATACTACATTCCACCATATACATGACTTCAAAAGTCACACATTTGT
CTTTTCGAACACAAAACCATCATAAACCAAAGACCTCAAAAGAACCAAA
Found at i:475845 original size:83 final size:83
Alignment explanation
Indices: 475697--475926 Score: 408
Period size: 83 Copynumber: 2.8 Consensus size: 83
475687 AATGGAACAA
* * *
475697 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
1 ATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAC
475761 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
475780 ATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
475845 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
*
475863 ATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
475927 ATAGCATCTT
Statistics
Matches: 142, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
82 4 0.03
83 138 0.97
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
ATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
AATCATTGAATTTGGAAG
Found at i:475937 original size:52 final size:52
Alignment explanation
Indices: 475875--476635 Score: 1403
Period size: 52 Copynumber: 14.8 Consensus size: 52
475865 GAATTTGCTA
475875 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
475927 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
475978 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AG-A-
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476027 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476079 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
476131 ATAGCATCTTCTGGAAGTGTTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTG-TTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476184 ATAG-ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476235 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476286 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476338 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
476390 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476442 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476494 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* * *
476545 ATAGCATCTTCTGGAAGTTTTCTGTGAGTTATCTGATCTGGTTAGA-AGAAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
476596 ATAGCATCTTCTGGAAGTTTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
476636 ATTGGACATA
Statistics
Matches: 695, Mismatches: 8, Indels: 13
0.97 0.01 0.02
Matches are distributed among these distances:
49 46 0.07
50 3 0.00
51 233 0.34
52 377 0.54
53 36 0.05
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
Found at i:476376 original size:259 final size:259
Alignment explanation
Indices: 475875--476635 Score: 1433
Period size: 259 Copynumber: 3.0 Consensus size: 259
475865 GAATTTGCTA
*
475875 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
475940 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTGGAAGTGTTCTTTG
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
476004 AGTTATCTGATCTGGTTAGAAG-A-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
131 AGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
476067 GTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
196 GTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476131 ATAGCATCTTCTGGAAGTGTTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG-ATCTTCT
1 ATAGCATCTTCTGGAAGTG-TTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCT
476195 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
65 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
476260 GAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
130 GAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
476325 GGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
195 GGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
476390 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
476455 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
* *
476520 AGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTTTTCTGTGAGTTATCTGATCTG
131 AGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* *
476585 GTTAGA-AGAAAATAGCATCTTCTGGAAGTTTTCTTTGAGTTATCTGATCTG
196 GTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
476636 ATTGGACATA
Statistics
Matches: 495, Mismatches: 5, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
256 60 0.12
257 89 0.18
258 81 0.16
259 265 0.54
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (259 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
AGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
Found at i:477253 original size:113 final size:113
Alignment explanation
Indices: 477100--477644 Score: 761
Period size: 113 Copynumber: 4.7 Consensus size: 113
477090 AAATCCACTA
* * *
477100 GATGGATCATTCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAA
1 GATGGATCA-ACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* *
477165 GTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTT
65 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTT
*
477214 GATGGATCAACAGTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 GATGGATCAACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * * * *
477279 TTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTT
66 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTT
* * * *
477327 GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
1 GATGGATCAACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
477392 TTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTT
66 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTT
477440 GATGGATCAACATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 GATGGATCAACATTTCCAGA-GAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGA
* * *
477505 AGAAGTTCATAATGAGAAGAACGTGTTCAACCTTTTGCTTGAATTCATCACTT
61 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTT
* *
477558 GATGGATCATTCTTTTCCAGAGGAAGAGTTCATAAT--GAAGAACTCGTCATCTGAAGAAGGAAG
1 GATGGATCA-ACATTTCCAGA-GAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAG
*
477621 AAAAAGTTCATAATGAGAAGAACT
60 AAGAAGTTCATAATGAGAAGAACT
477645 CATCAAAAGC
Statistics
Matches: 389, Mismatches: 36, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
113 212 0.54
114 12 0.03
115 17 0.04
117 50 0.13
118 74 0.19
119 24 0.06
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (113 bp):
GATGGATCAACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTT
Found at i:477901 original size:3 final size:3
Alignment explanation
Indices: 477895--477980 Score: 129
Period size: 3 Copynumber: 29.0 Consensus size: 3
477885 TTATCCATAT
*
477895 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
477942 ATA TTA TTA TTA ATA TTA TTA TTA TTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
477981 AATATATTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
2 2 0.03
3 72 0.97
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:478443 original size:24 final size:24
Alignment explanation
Indices: 478354--478443 Score: 69
Period size: 24 Copynumber: 3.7 Consensus size: 24
478344 CCACCCACCT
* *
478354 GAAAAAAAAAAA-A-AGAAGGGACA
1 GAAAAAAAAAAACAGAGAA-AGAAA
* *
478377 GAGAAAAAAGAAACTAGACAAAGAAA
1 GA-AAAAAAAAAAC-AGAGAAAGAAA
* *
478403 GAAAAAAAGAAGA-AGAGATAGAAA
1 GAAAAAAA-AAAACAGAGAAAGAAA
478427 GAAAAAAAAAAACAGAG
1 GAAAAAAAAAAACAGAG
478444 CAAATATAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
23 5 0.10
24 30 0.58
25 6 0.12
26 8 0.15
27 3 0.06
ACGTcount: A:0.72, C:0.04, G:0.21, T:0.02
Consensus pattern (24 bp):
GAAAAAAAAAAACAGAGAAAGAAA
Found at i:479260 original size:20 final size:18
Alignment explanation
Indices: 479221--479261 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
479211 CAATTAATTA
*
479221 ATAATTAGTTTTATTTTT
1 ATAATTAGTTTTAATTTT
479239 ATAATTTAGTTATTAATTTT
1 ATAA-TTAGTT-TTAATTTT
479259 ATA
1 ATA
479262 TGTCTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
20 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
ATAATTAGTTTTAATTTT
Found at i:479352 original size:22 final size:20
Alignment explanation
Indices: 479311--479355 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
479301 ATAGAATTAT
**
479311 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
479331 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
479353 TAT
1 TAT
479356 ATGTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Found at i:484765 original size:16 final size:16
Alignment explanation
Indices: 484744--484776 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
484734 TAAAAAATAA
484744 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
484760 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
484776 A
1 A
484777 ATTTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:484855 original size:10 final size:10
Alignment explanation
Indices: 484840--484903 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
484830 CATTTAATAA
484840 ATAAACGAAC
1 ATAAACGAAC
484850 ATAAACGAAC
1 ATAAACGAAC
*
484860 ACGAACACGAAC
1 A-TAA-ACGAAC
*
484872 ATAAATGAAC
1 ATAAACGAAC
484882 AT----GAAC
1 ATAAACGAAC
484888 ATAAACGAAC
1 ATAAACGAAC
484898 ATAAAC
1 ATAAAC
484904 ATTAGAGACC
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
6 6 0.13
10 28 0.62
11 4 0.09
12 7 0.16
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:484872 original size:22 final size:22
Alignment explanation
Indices: 484844--484888 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
484834 TAATAAATAA
484844 ACGAACATAAACGAACACGAAC
1 ACGAACATAAACGAACACGAAC
* *
484866 ACGAACATAAATGAACATGAAC
1 ACGAACATAAACGAACACGAAC
484888 A
1 A
484889 TAAACGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (22 bp):
ACGAACATAAACGAACACGAAC
Found at i:484899 original size:16 final size:16
Alignment explanation
Indices: 484840--484905 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
484830 CATTTAATAA
484840 ATAAACGAACATAAAC
1 ATAAACGAACATAAAC
* **
484856 GA-ACACGAACACGAAC
1 -ATAAACGAACATAAAC
* *
484872 ATAAATGAACATGAAC
1 ATAAACGAACATAAAC
484888 ATAAACGAACATAAAC
1 ATAAACGAACATAAAC
484904 AT
1 AT
484906 TAGAGACCCT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
15 1 0.03
16 38 0.95
17 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.12
Consensus pattern (16 bp):
ATAAACGAACATAAAC
Found at i:486660 original size:64 final size:64
Alignment explanation
Indices: 486592--486821 Score: 204
Period size: 64 Copynumber: 3.6 Consensus size: 64
486582 TTGTTTGAAG
* * *
486592 GTGTATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATT
1 GTGTATCGATGCATAGGTAGTGCATCGATGCATC-CCTTTAATAAGAAA-ACATCGAATGCAATT
*
486655 C
64 A
* *
486656 GTGTATCGATGCATAAGTAGTGCATCGATGCATCCCTTTAATAAGGAAACATCGAATGCAATTA
1 GTGTATCGATGCATAGGTAGTGCATCGATGCATCCCTTTAATAAGAAAACATCGAATGCAATTA
* * * * * *
486720 TTGCATCGATGCATAAGGCA-TGCATCGATGCAT-CCTAGTAATAA-ACAAACATCGAATACATT
1 GTGTATCGATGCAT-AGGTAGTGCATCGATGCATCCCT-TTAATAAGA-AAACATCGAATGCA-A
486782 TTA
62 TTA
* * * *
486785 -TGCACCGATGCATCA-ATAGTGCATCGATGCATACCTT
1 GTGTATCGATGCAT-AGGTAGTGCATCGATGCATCCCTT
486822 CATTAAAAGA
Statistics
Matches: 139, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
63 4 0.03
64 121 0.87
65 14 0.10
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (64 bp):
GTGTATCGATGCATAGGTAGTGCATCGATGCATCCCTTTAATAAGAAAACATCGAATGCAATTA
Found at i:487864 original size:103 final size:103
Alignment explanation
Indices: 487537--487857 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
487527 GTCGAGGGTC
487537 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
487602 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
487640 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
487705 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
487743 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
487808 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
487846 TATGTGGTCCTT
1 TATGTGGTCCTT
487858 ATGGACAGTA
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:487923 original size:23 final size:23
Alignment explanation
Indices: 487873--487941 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
487863 CAGTATTATA
* *
487873 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATATG
* * *
487896 CGGCACTCCGATGCAATTATATG
1 TGGCACTACGGTGCAATTATATG
**
487919 TGGCACTTTGGTGCAATTATATG
1 TGGCACTACGGTGCAATTATATG
487942 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATATG
Found at i:492057 original size:64 final size:64
Alignment explanation
Indices: 491989--492209 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 64
491979 TTGAAGGTGT
* * * *
491989 ATCGATGCATTAGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATCTC-ATTAATAAGAAA-ACATCGAATGCAATTAGTG
492052 C
64 C
* *
492053 ATCGATGCATAAGTAGTGCATCGATGTATCTCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCTCATTAATAAGAAAACATCGAATGCAATTAGTGC
* * * * *
492117 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAA-ACAAACATCGAATACATTTTA-T
1 ATCGATGCATAA-GTAGTGCATCGATGCATCTCATTAATAAGA-AAACATCGAATGCA-ATTAGT
492179 GC
63 GC
* *
492181 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
492210 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
63 2 0.01
64 121 0.90
65 12 0.09
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCTCATTAATAAGAAAACATCGAATGCAATTAGTGC
Found at i:493252 original size:103 final size:103
Alignment explanation
Indices: 492925--493245 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
492915 GTCGAGGGTC
*
492925 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGATGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
492990 TTGATCCTTGGCATATGTATATGATTCTTAATGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
493028 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
493093 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
493131 TATGTGGTCCTTCGGGACATATATCTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * * * *
493196 TTGATCCCTAGTATATTTATATAATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
493234 TATGTGGTCCTT
1 TATGTGGTCCTT
493246 ATGGACAGTA
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:493298 original size:23 final size:23
Alignment explanation
Indices: 493272--493327 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
493262 GGAACTCCGA
*
493272 TGCAATTCTACGCGGCACTCTGG
1 TGCAATTATACGCGGCACTCTGG
* * *
493295 TGCAATTATATGTGGCACTTTGG
1 TGCAATTATACGCGGCACTCTGG
493318 TGCAATTATA
1 TGCAATTATA
493328 TGAGCTGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (23 bp):
TGCAATTATACGCGGCACTCTGG
Found at i:493328 original size:23 final size:23
Alignment explanation
Indices: 493285--493329 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
493275 AATTCTACGC
493285 GGCACTCTGGTGCAATTATATGT
1 GGCACTCTGGTGCAATTATATGT
*
493308 GGCACTTTGGTGCAATTATATG
1 GGCACTCTGGTGCAATTATATG
493330 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTATATGT
Found at i:494427 original size:10 final size:10
Alignment explanation
Indices: 494412--494482 Score: 52
Period size: 10 Copynumber: 6.3 Consensus size: 10
494402 TAAATGAGTT
494412 AACATAAACG
1 AACATAAACG
494422 AACATAACCGAACG
1 AACAT-A---AACG
494436 AACATAAACG
1 AACATAAACG
*
494446 AACAAAACCGAACG
1 AAC-ATA---AACG
494460 AACATAAACG
1 AACATAAACG
*
494470 AACATAACCG
1 AACATAAACG
494480 AAC
1 AAC
494483 GTTCACGAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
10 28 0.56
11 3 0.06
13 3 0.06
14 16 0.32
ACGTcount: A:0.56, C:0.25, G:0.11, T:0.07
Consensus pattern (10 bp):
AACATAAACG
Found at i:494435 original size:14 final size:14
Alignment explanation
Indices: 494418--494483 Score: 67
Period size: 14 Copynumber: 5.3 Consensus size: 14
494408 AGTTAACATA
494418 AACGAACATAACCG
1 AACGAACATAACCG
494432 AACGAACAT-A---
1 AACGAACATAACCG
*
494442 AACGAACAAAACCG
1 AACGAACATAACCG
494456 AACGAACAT-A---
1 AACGAACATAACCG
494466 AACGAACATAACCG
1 AACGAACATAACCG
494480 AACG
1 AACG
494484 TTCACGAACG
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
10 17 0.40
11 2 0.05
13 2 0.05
14 21 0.50
ACGTcount: A:0.55, C:0.26, G:0.14, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:494493 original size:24 final size:24
Alignment explanation
Indices: 494412--494483 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
494402 TAAATGAGTT
494412 AACATAAACGAACATAACCGAACG
1 AACATAAACGAACATAACCGAACG
*
494436 AACATAAACGAACAAAACCGAACG
1 AACATAAACGAACATAACCGAACG
494460 AACATAAACGAACATAACCGAACG
1 AACATAAACGAACATAACCGAACG
494484 TTCACGAACG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.07
Consensus pattern (24 bp):
AACATAAACGAACATAACCGAACG
Found at i:494541 original size:43 final size:40
Alignment explanation
Indices: 494494--494585 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 40
494484 TTCACGAACG
* *
494494 TAAATGAACGAACGAGACCTATGTTCATGTTCGTTCATTTAA
1 TAAATGAACG-ACAAAACCT-TGTTCATGTTCGTTCATTTAA
*
494536 TTAAATGAAC-ACAAAATCTTGTTCATGTTCGTTCATTTAA
1 -TAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
*
494576 TAAATAAACG
1 TAAATGAACG
494586 CACATACACG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
39 8 0.18
40 21 0.48
41 6 0.14
43 9 0.20
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (40 bp):
TAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
Found at i:497107 original size:2 final size:2
Alignment explanation
Indices: 497100--497136 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
497090 TTACTCCATT
497100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
497137 TACTATTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:501013 original size:64 final size:63
Alignment explanation
Indices: 500964--501118 Score: 242
Period size: 64 Copynumber: 2.4 Consensus size: 63
500954 TGCACTAAGG
*
500964 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGGTC
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCATCGATGCATGG-C
*
501027 TGTGCATTGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGC
1 -GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGC
501091 AGTGCATCGATGCATAAAATGCATTCGA
1 -GTGCATCGATGCATAAAATGCATTCGA
501119 AATGGTGTGT
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
64 55 0.65
65 28 0.33
66 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGC
Found at i:501657 original size:193 final size:194
Alignment explanation
Indices: 501324--501709 Score: 670
Period size: 193 Copynumber: 2.0 Consensus size: 194
501314 TAATTATATC
*
501324 GAATATACTTAGAAAATCTTTTATAAAATCTTAAAATTCATTTATCTTAATTTGTTTTATTGAAA
1 GAATATACTTAGAAAATATTTTATAAAATCTTAAAATTCATTTATCTTAATTTGTTTTATTGAAA
501389 CATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATCTGAGTAATTTTAAGAT
66 CATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATCTGAGTAATTTTAAGAT
* * *
501454 TTTTAAGAAAATCATTTTTGAAATCAAATTTGAAAATTACT-C-CCTTTCTATGATACATCTTT
131 TTTTAAGAAAATCATTTTGGAAACCAAATTTGAAAATTACTCCTCCTTACTATGATACATCTTT
* *
501516 GAATTTACTTAGAAAATATTTTATAAAATCTTAAAATTCATTTATCTT-ATTTTTTTTATATCGA
1 GAATATACTTAGAAAATATTTTATAAAATCTTAAAATTCATTTATCTTAATTTGTTTTAT-T-GA
*
501580 AACATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTGAGTAATTTTAAG
64 AACATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATCTGAGTAATTTTAAG
501645 ATTTTTAAGAAAATCATTTTGGAAACCAAATTTGAAAATTACTCCTCCTTACTATGATACATCTT
129 ATTTTTAAGAAAATCATTTTGGAAACCAAATTTGAAAATTACTCCTCCTTACTATGATACATCTT
501710 CCCCCCTTTT
Statistics
Matches: 183, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
191 10 0.05
192 47 0.26
193 107 0.58
194 1 0.01
195 18 0.10
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (194 bp):
GAATATACTTAGAAAATATTTTATAAAATCTTAAAATTCATTTATCTTAATTTGTTTTATTGAAA
CATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATCTGAGTAATTTTAAGAT
TTTTAAGAAAATCATTTTGGAAACCAAATTTGAAAATTACTCCTCCTTACTATGATACATCTTT
Found at i:502575 original size:10 final size:11
Alignment explanation
Indices: 502551--502578 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
502541 TTTTTATTTC
502551 AAAATTCTTGA
1 AAAATTCTTGA
502562 AAAATTCTTGA
1 AAAATTCTTGA
502573 AAAATT
1 AAAATT
502579 TAGTGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (11 bp):
AAAATTCTTGA
Found at i:506656 original size:22 final size:21
Alignment explanation
Indices: 506614--506653 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
506604 AAGACTGTTT
506614 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
506635 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
506654 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:508657 original size:64 final size:64
Alignment explanation
Indices: 508589--508743 Score: 224
Period size: 64 Copynumber: 2.4 Consensus size: 64
508579 TGCACTAAGG
* * * * *
508589 GTGCATCGATGCATAAAATGTATTTGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGGTC
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCATAGATGCATGG-A
*
508652 T
64 A
508653 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATAGATGCATGGAA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATAGATGCATGGAA
508717 GTGCATCGATGCATAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
508744 AATGGTGTGT
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
64 54 0.65
65 27 0.33
66 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATAGATGCATGGAA
Found at i:508777 original size:20 final size:20
Alignment explanation
Indices: 508752--508806 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
508742 GAAATGGTGT
508752 GTGCATCGATGCATCAATGA
1 GTGCATCGATGCATCAATGA
*
508772 GTGCATCAATGCATCAATGA
1 GTGCATCGATGCATCAATGA
508792 GTGCATCGATGCATC
1 GTGCATCGATGCATC
508807 CCTTCACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (20 bp):
GTGCATCGATGCATCAATGA
Found at i:520647 original size:54 final size:54
Alignment explanation
Indices: 520579--521327 Score: 1041
Period size: 54 Copynumber: 13.9 Consensus size: 54
520569 GTGAAGCAAA
*** *
520579 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGACAAAGCAAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * * *
520633 AAAAGATTGTTCGAGTTCCTACTCCCTAAATAAAGAGAGAGCGAACCTGTAGGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * *
520687 AGAAGATTTTTTGAATTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
*
520741 AGAAGATTGTTTGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* *
520795 AGTAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* *
520849 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCAAACCCGTATGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * *
520903 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAATAGGGAGCGAACCAGTTGGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * * **
520957 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAAAGGTAGTGAACCTATAGGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * * *
521011 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAAAGGGAGCGAACCCATTGAC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * * *
521065 AGAAGATTGTTCGAGTTCTTACTGCCTAAAGAAAGAAGGAGGGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * *
521119 AGAAAATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAACGAATCCGTAGGC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * *
521173 AGAAGATTGTTCAAGTTCAC-ACTCCCTAAAGAAAGAGAGAGCGAACCCGTTGGC
1 AGAAGATTGTTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * * * *
521227 AGAAGATTGTTCAAGTTCCTACTCCCTAAAGAAATAGGGAGCGAGCCCGTTGAC
1 AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
* * * * *
521281 AAAAGATTGTTCGAGCTCTATACTCCATAAAGAAATAGGGAGCGAAC
1 AGAAGATTGTTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAAC
521328 GCGTTTTTCG
Statistics
Matches: 623, Mismatches: 69, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
53 1 0.00
54 596 0.96
55 26 0.04
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (54 bp):
AGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGC
Found at i:521532 original size:2 final size:2
Alignment explanation
Indices: 521525--521571 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
521515 TTTACTCCAT
521525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
521567 TA TA T
1 TA TA T
521572 TACTATTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:521715 original size:8 final size:8
Alignment explanation
Indices: 521702--521742 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
521692 TATGTATGTA
521702 TATATATG
1 TATATATG
521710 TATATATG
1 TATATATG
*
521718 TATGTATG
1 TATATATG
*
521726 TATATATA
1 TATATATG
521734 TATATATG
1 TATATATG
521742 T
1 T
521743 GTATGTGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:521719 original size:22 final size:22
Alignment explanation
Indices: 521691--521738 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
521681 TTGTGATCAC
*
521691 ATATGTATGTATATATATGTAT
1 ATATGTATGTATATATATATAT
*
521713 ATATGTATGTATGTATATATAT
1 ATATGTATGTATATATATATAT
521735 ATAT
1 ATAT
521739 ATGTGTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
ATATGTATGTATATATATATAT
Found at i:521721 original size:26 final size:26
Alignment explanation
Indices: 521692--521748 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
521682 TGTGATCACA
*
521692 TATGTATGTATATATATGTATATATG
1 TATGTATGTATATATATATATATATG
*
521718 TATGTATGTATATATATATATATGTG
1 TATGTATGTATATATATATATATATG
521744 TATGT
1 TATGT
521749 GTGTGTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (26 bp):
TATGTATGTATATATATATATATATG
Found at i:525215 original size:65 final size:64
Alignment explanation
Indices: 525143--525296 Score: 184
Period size: 65 Copynumber: 2.4 Consensus size: 64
525133 TACACTATGG
* ** *
525143 GTGCATCGGTACATTATTTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTC
1 GTGCATCGGTACATAAAATACATTCGATGTTTCAATAA-AGCCAAGAGTGCATCGATGCATGGT-
525207 T
64 T
* * **
525208 GTGCATCGGTACATAAAATATATTCGATGTTTTAATAAATTCAAGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACATAAAATACATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGTT
* * *
525272 GTGCATCAGTACACAAAATGCATTC
1 GTGCATCGGTACATAAAATACATTC
525297 AAAATAGGGT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 22 0.29
65 52 0.68
66 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATACATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGTT
Found at i:527938 original size:20 final size:20
Alignment explanation
Indices: 527913--527966 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
527903 AAACCCGACA
527913 AGTGTATCGATGCATTGCAT
1 AGTGTATCGATGCATTGCAT
527933 AGTGTATCGATGCATTGCAT
1 AGTGTATCGATGCATTGCAT
527953 AGTGTATCGATGCA
1 AGTGTATCGATGCA
527967 CATTCAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (20 bp):
AGTGTATCGATGCATTGCAT
Found at i:540197 original size:23 final size:23
Alignment explanation
Indices: 540182--540238 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
540172 TGATTGAAAC
540182 TCAAACTCAAGTTTGATTCAACT
1 TCAAACTCAAGTTTGATTCAACT
540205 TCAAACTCAAGTTTGATTCAACT
1 TCAAACTCAAGTTTGATTCAACT
540228 TCAAACTCAAG
1 TCAAACTCAAG
540239 CTCGAACCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.32
Consensus pattern (23 bp):
TCAAACTCAAGTTTGATTCAACT
Found at i:540305 original size:30 final size:31
Alignment explanation
Indices: 540266--540327 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
540256 AATAACATAT
* * *
540266 AAATGTTAATGTTATCAATAAT-TTAATTTAA
1 AAATGTTAAT-TAATCAAAAATAATAATTTAA
540297 AAAT-TTAATTAATCAAAAATAATAATTTAA
1 AAATGTTAATTAATCAAAAATAATAATTTAA
540327 A
1 A
540328 TTTTTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.33
30 14 0.52
31 4 0.15
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (31 bp):
AAATGTTAATTAATCAAAAATAATAATTTAA
Found at i:540857 original size:2 final size:2
Alignment explanation
Indices: 540850--540886 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
540840 TGAAAATTTC
540850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
540887 AAAGGAGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:551001 original size:19 final size:20
Alignment explanation
Indices: 550975--551022 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
550965 TATTTTATGA
* *
550975 AAATATATTAATTATGATAT
1 AAATATATAAAATATGATAT
*
550995 AAA-ATATAAAATATTATAT
1 AAATATATAAAATATGATAT
551014 AAATATATA
1 AAATATATA
551023 TAGCATCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATATATAAAATATGATAT
Found at i:551110 original size:3 final size:3
Alignment explanation
Indices: 551104--551176 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
551094 ATGAATAATA
551104 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
551151 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
551177 CTACTACTAC
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:563275 original size:19 final size:18
Alignment explanation
Indices: 563251--563298 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
563241 TAACTTTTTG
*
563251 GTCAAAGTCAACGTTCAAA
1 GTCAAAGTCAACGGTC-AA
* *
563270 GTCAAAGTCCATGGTCAA
1 GTCAAAGTCAACGGTCAA
563288 GTCAAAGTCAA
1 GTCAAAGTCAA
563299 TGATTCAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (18 bp):
GTCAAAGTCAACGGTCAA
Found at i:564594 original size:50 final size:50
Alignment explanation
Indices: 564494--564596 Score: 120
Period size: 50 Copynumber: 2.1 Consensus size: 50
564484 TTTTTTATTG
* * * *
564494 ATTCATATATTATGAATTCAAATATTTATGTATATCCGATTCTTTCTTTT
1 ATTCATATATTATCAATCCAAATATTTATGTATATCCGATCCATTCTTTT
**
564544 ATTCATATATTA-CATATCCAAATATTTATGTATATTTGATCCAATT-TTTT
1 ATTCATATATTATCA-ATCCAAATATTTATGTATATCCGATCC-ATTCTTTT
564594 ATT
1 ATT
564597 GATACAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 1 0.02
50 42 0.93
51 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (50 bp):
ATTCATATATTATCAATCCAAATATTTATGTATATCCGATCCATTCTTTT
Found at i:564627 original size:10 final size:10
Alignment explanation
Indices: 564612--564650 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
564602 AATTTAAAAT
564612 TTTATGAATA
1 TTTATGAATA
564622 TTTATG-A-A
1 TTTATGAATA
564630 TTTA--AATA
1 TTTATGAATA
564638 TTTATGAATA
1 TTTATGAATA
564648 TTT
1 TTT
564651 GATACAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
7 1 0.04
8 10 0.40
9 1 0.04
10 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (10 bp):
TTTATGAATA
Found at i:566047 original size:2 final size:2
Alignment explanation
Indices: 566040--566081 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
566030 ATCTAAAGAT
566040 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
566082 CTATTTTCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:571102 original size:2 final size:2
Alignment explanation
Indices: 571095--571137 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
571085 ATAGTTTCGT
571095 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
571137 G
1 G
571138 CTCATCAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:571731 original size:2 final size:2
Alignment explanation
Indices: 571724--571753 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
571714 AATCATAGCC
571724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
571754 GATTATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:574310 original size:21 final size:23
Alignment explanation
Indices: 574267--574310 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
574257 ATACGATTTG
**
574267 AATTTTAATAGGATAAATTTATA
1 AATTTTAATAGGATAAAAATATA
574290 AATTTT-A-AGGATAAAAATATA
1 AATTTTAATAGGATAAAAATATA
574311 TTATCAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
AATTTTAATAGGATAAAAATATA
Found at i:574418 original size:11 final size:11
Alignment explanation
Indices: 574402--574482 Score: 87
Period size: 11 Copynumber: 7.6 Consensus size: 11
574392 GAATTATCAC
574402 TTTTATTTTAG
1 TTTTATTTTAG
* *
574413 TTTTA-TTCAC
1 TTTTATTTTAG
574423 TTTTATTTTAG
1 TTTTATTTTAG
* *
574434 TTTTA-TTCAC
1 TTTTATTTTAG
574444 TTTTATTTTAG
1 TTTTATTTTAG
* *
574455 TTTTA-TTCAC
1 TTTTATTTTAG
574465 TTTTATTTTAG
1 TTTTATTTTAG
574476 TTTTATT
1 TTTTATT
574483 CACTTTTGCT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
10 24 0.44
11 31 0.56
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (11 bp):
TTTTATTTTAG
Found at i:574422 original size:21 final size:21
Alignment explanation
Indices: 574398--574511 Score: 192
Period size: 21 Copynumber: 5.4 Consensus size: 21
574388 ACAAGAATTA
574398 TCACTTTTATTTTAGTTTTAT
1 TCACTTTTATTTTAGTTTTAT
574419 TCACTTTTATTTTAGTTTTAT
1 TCACTTTTATTTTAGTTTTAT
574440 TCACTTTTATTTTAGTTTTAT
1 TCACTTTTATTTTAGTTTTAT
574461 TCACTTTTATTTTAGTTTTAT
1 TCACTTTTATTTTAGTTTTAT
** *
574482 TCACTTTTGCTTTAGTTTTGT
1 TCACTTTTATTTTAGTTTTAT
*
574503 TCAATTTTA
1 TCACTTTTA
574512 CTCATTGATT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 88 1.00
ACGTcount: A:0.18, C:0.11, G:0.06, T:0.65
Consensus pattern (21 bp):
TCACTTTTATTTTAGTTTTAT
Found at i:574671 original size:31 final size:31
Alignment explanation
Indices: 574636--574763 Score: 100
Period size: 31 Copynumber: 4.2 Consensus size: 31
574626 ATTAATTTTT
* *
574636 AATTTGATTATTAAACTTTAGACAAAATATC
1 AATTTGATCATTAAACTTTAGATAAAATATC
* * * * * *
574667 AATTTAACCACTAAACTTCAGATGAAGTATC
1 AATTTGATCATTAAACTTTAGATAAAATATC
* * *
574698 AATTAGAACCTTAAACTTTAGATAAAATA-C
1 AATTTGATCATTAAACTTTAGATAAAATATC
* *
574728 TAATTTGATC-TCTTAA-TTTAGATAAAATATA
1 -AATTTGATCAT-TAAACTTTAGATAAAATATC
574759 AATTT
1 AATTT
574764 ATCTCCTCGA
Statistics
Matches: 74, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
30 20 0.27
31 54 0.73
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.37
Consensus pattern (31 bp):
AATTTGATCATTAAACTTTAGATAAAATATC
Found at i:574748 original size:30 final size:31
Alignment explanation
Indices: 574714--574788 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
574704 AACCTTAAAC
*
574714 TTTAGATAAAATACT-AATTTGATCT-CT-TAA
1 TTTAGATAAAATA-TAAATTT-ATCTCCTCGAA
*
574744 TTTAGATAAAATATAAATTTATCTCCTCGAT
1 TTTAGATAAAATATAAATTTATCTCCTCGAA
574775 TTTAGATAAAATAT
1 TTTAGATAAAATAT
574789 CAACTTGACC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 5 0.12
30 20 0.50
31 15 0.38
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (31 bp):
TTTAGATAAAATATAAATTTATCTCCTCGAA
Found at i:574971 original size:2 final size:2
Alignment explanation
Indices: 574964--575001 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
574954 CCTCAAACTA
574964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
575002 GGCTAGGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:577949 original size:3 final size:3
Alignment explanation
Indices: 577936--577969 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
577926 ATTTAATGTC
*
577936 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
577970 TATTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:577974 original size:3 final size:3
Alignment explanation
Indices: 577968--578006 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
577958 AATAATAATA
577968 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
578007 TCCATTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:578619 original size:180 final size:181
Alignment explanation
Indices: 578317--578678 Score: 717
Period size: 180 Copynumber: 2.0 Consensus size: 181
578307 AAAAAGGAAA
578317 ATCAAGATATTTTCTAAAGTGTGAGGCCTTTAGATTTTAGGGTCATGTGACATATCACATGTTAT
1 ATCAAGATATTTTCTAAAGTGTGAGGCCTTTAGATTTTAGGGTCATGTGACATATCACATGTTAT
578382 TGACGGACGTGATGAAAATAAAATGTGGATTTATAAGGAGACAATTCATATATTTAGCCAC-ACA
66 TGACGGACGTGATGAAAATAAAATGTGGATTTATAAGGAGACAATTCATATATTTAGCCACGACA
578446 GCTAGCTAATCCCTCTAAAGAACAAAATCAAATGAAATACAGACAAGATCG
131 GCTAGCTAATCCCTCTAAAGAACAAAATCAAATGAAATACAGACAAGATCG
578497 ATCAAGATATTTTCTAAAGTGTGAGGCCTTTAGATTTTAGGGTCATGTGACATATCACATGTTAT
1 ATCAAGATATTTTCTAAAGTGTGAGGCCTTTAGATTTTAGGGTCATGTGACATATCACATGTTAT
578562 TGACGGACGTGATGAAAATAAAATGTGGATTTATAAGGAGACAATTCATATATTTAGCCACGACA
66 TGACGGACGTGATGAAAATAAAATGTGGATTTATAAGGAGACAATTCATATATTTAGCCACGACA
578627 GCTAGCTAATCCCTCTAAAGAACAAAATCAAATGAAATACAGACAAGATCG
131 GCTAGCTAATCCCTCTAAAGAACAAAATCAAATGAAATACAGACAAGATCG
578678 A
1 A
578679 AGGCACACTG
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 126 0.70
181 55 0.30
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (181 bp):
ATCAAGATATTTTCTAAAGTGTGAGGCCTTTAGATTTTAGGGTCATGTGACATATCACATGTTAT
TGACGGACGTGATGAAAATAAAATGTGGATTTATAAGGAGACAATTCATATATTTAGCCACGACA
GCTAGCTAATCCCTCTAAAGAACAAAATCAAATGAAATACAGACAAGATCG
Found at i:580259 original size:21 final size:21
Alignment explanation
Indices: 580235--580276 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
580225 CCCAGAATGG
*
580235 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
580256 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
580277 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:580462 original size:19 final size:20
Alignment explanation
Indices: 580438--580492 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
580428 ATATGTTCCC
580438 GGGGAATC-GATACCCCT-GG
1 GGGGAATCTG-TACCCCTGGG
*
580457 GGGGAATCTGTTCCCCTGGG
1 GGGGAATCTGTACCCCTGGG
580477 GGGGAATCTGTACCCC
1 GGGGAATCTGTACCCC
580493 CTGGACAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.16, C:0.27, G:0.36, T:0.20
Consensus pattern (20 bp):
GGGGAATCTGTACCCCTGGG
Found at i:580469 original size:34 final size:33
Alignment explanation
Indices: 580389--580471 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
580379 AAACCATGCA
* *
580389 GGGGGAATCTGTACCCGGAGAATCGATACTTGG
1 GGGGGAATCTGTTCCCGGAGAATCGATACCTGG
* *
580422 GGGGGAATATGTTCCCGGGGAATCGATACCCCT-G
1 GGGGGAATCTGTTCCCGGAGAATCGATA--CCTGG
580456 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
580472 CTGGGGGGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.58
34 16 0.37
35 2 0.05
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (33 bp):
GGGGGAATCTGTTCCCGGAGAATCGATACCTGG
Found at i:581295 original size:36 final size:36
Alignment explanation
Indices: 581224--581294 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
581214 ATTTAAACCA
581224 CATGCATTAAACATTAAATTTAGGTCAATTTTTTTT
1 CATGCATTAAACATTAAATTTAGGTCAATTTTTTTT
581260 CATGCA-TAAACATTAAATTTAGGTCAATTTTTTTT
1 CATGCATTAAACATTAAATTTAGGTCAATTTTTTTT
581295 TAAAGATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.83
36 6 0.17
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.46
Consensus pattern (36 bp):
CATGCATTAAACATTAAATTTAGGTCAATTTTTTTT
Found at i:583874 original size:21 final size:21
Alignment explanation
Indices: 583848--583889 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
583838 CCAGAATGGG
*
583848 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
583869 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
583890 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:584068 original size:35 final size:34
Alignment explanation
Indices: 584001--584085 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
583991 AAACCATGCA
* *
584001 GGGGAAATCTGTACCCGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
584035 GGGGGAATCTGTTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCTG
584070 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
584086 CCCGTACAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 26 0.54
35 22 0.46
ACGTcount: A:0.19, C:0.27, G:0.34, T:0.20
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:584086 original size:20 final size:20
Alignment explanation
Indices: 584029--584087 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
584019 GGAATCGATA
584029 CCCCTGGGGGGAATCTGTT-
1 CCCCTGGGGGGAATCTGTTC
*
584048 -CCC---GGGGAATC-GATAC
1 CCCCTGGGGGGAATCTG-TTC
584064 CCCCTGGGGGGAATCTGTTC
1 CCCCTGGGGGGAATCTGTTC
584084 CCCC
1 CCCC
584088 CGTACAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 13
0.67 0.04 0.28
Matches are distributed among these distances:
14 1 0.03
15 9 0.29
17 3 0.10
18 3 0.10
20 14 0.45
21 1 0.03
ACGTcount: A:0.14, C:0.34, G:0.32, T:0.20
Consensus pattern (20 bp):
CCCCTGGGGGGAATCTGTTC
Found at i:589841 original size:26 final size:25
Alignment explanation
Indices: 589779--589841 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
589769 AAAATGTACA
*
589779 AAATTATT--AAAATATTTAAAAAT
1 AAATTATTAAAAAATACTTAAAAAT
* *
589802 AAATAAATATAAAAATACTTAAAAATT
1 AAATTATTA-AAAAATACTTAAAAA-T
589829 AAATTATTAAAAA
1 AAATTATTAAAAA
589842 CTTTTATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.19
26 17 0.55
27 8 0.26
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATTATTAAAAAATACTTAAAAAT
Found at i:591450 original size:22 final size:21
Alignment explanation
Indices: 591425--591473 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
591415 TGTTTGACAA
591425 AATGTTCACGAATCATTAATAT
1 AATGTTCACG-ATCATTAATAT
* *
591447 AATGTT--CGTTTATTAATAT
1 AATGTTCACGATCATTAATAT
591466 AATGTTCA
1 AATGTTCA
591474 TTAAATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 15 0.65
20 2 0.09
22 6 0.26
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTTCACGATCATTAATAT
Found at i:592259 original size:20 final size:20
Alignment explanation
Indices: 592226--592276 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
592216 ATAGTGTAGT
* * *
592226 ATTTTAATAATTTAATTTTA
1 ATTTTTATATTTTTATTTTA
*
592246 ATTTTT-TATTTTTATTTTT
1 ATTTTTATATTTTTATTTTA
592265 ATTTTTATATTT
1 ATTTTTATATTT
592277 GTTTGTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTTTTATATTTTTATTTTA
Found at i:592262 original size:13 final size:13
Alignment explanation
Indices: 592240--592272 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
592230 TAATAATTTA
*
592240 ATTTTAATTTTTT
1 ATTTTTATTTTTT
592253 ATTTTTA-TTTTT
1 ATTTTTATTTTTT
592265 ATTTTTAT
1 ATTTTTAT
592273 ATTTGTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:592270 original size:6 final size:6
Alignment explanation
Indices: 592248--592272 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
592238 TAATTTTAAT
592248 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
592273 ATTTGTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:592275 original size:14 final size:14
Alignment explanation
Indices: 592225--592276 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
592215 AATAGTGTAG
*
592225 TATTTTAATAATTT
1 TATTTTAATATTTT
*
592239 AATTTTAAT-TTTT
1 TATTTTAATATTTT
592252 TATTTT--TATTTT
1 TATTTTAATATTTT
*
592264 TATTTTTATATTT
1 TATTTTAATATTT
592277 GTTTGTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 1 0.03
12 10 0.31
13 8 0.25
14 13 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTAATATTTT
Found at i:592718 original size:33 final size:33
Alignment explanation
Indices: 592680--592787 Score: 87
Period size: 33 Copynumber: 3.2 Consensus size: 33
592670 TATACTTTAA
592680 ATAAAAGAATTTAAATTCAATTTTTTATGTATT
1 ATAAAAGAATTTAAATTCAATTTTTTATGTATT
* * * *
592713 ATAAAACACA-TTAAA-TCTAATGATATTGTACTTTA-A
1 ATAAAAGA-ATTTAAATTC-AAT--T-TTTTA-TGTATT
* *
592749 ATAAAAGAATTTAAATTCGATTTTTTATGAATT
1 ATAAAAGAATTTAAATTCAATTTTTTATGTATT
592782 ATAAAA
1 ATAAAA
592788 CAGATATAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
32 4 0.07
33 25 0.45
34 2 0.04
35 2 0.04
36 18 0.32
37 5 0.09
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (33 bp):
ATAAAAGAATTTAAATTCAATTTTTTATGTATT
Found at i:592739 original size:69 final size:69
Alignment explanation
Indices: 592652--592789 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
592642 TTTCATGTAC
*
592652 CATTAAATCTAAAGATATTATACTTTAAATAAAAGAATTTAAATTCAATTTTTTATGTATTATAA
1 CATTAAATCTAAAGATATTATACTTTAAATAAAAGAATTTAAATTCAATTTTTTATGAATTATAA
592717 AACA
66 AACA
* * *
592721 CATTAAATCTAATGATATTGTACTTTAAATAAAAGAATTTAAATTCGATTTTTTATGAATTATAA
1 CATTAAATCTAAAGATATTATACTTTAAATAAAAGAATTTAAATTCAATTTTTTATGAATTATAA
592786 AACA
66 AACA
592790 GATATAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (69 bp):
CATTAAATCTAAAGATATTATACTTTAAATAAAAGAATTTAAATTCAATTTTTTATGAATTATAA
AACA
Found at i:593456 original size:2 final size:2
Alignment explanation
Indices: 593449--593498 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
593439 AATGGTTGTA
593449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
593491 AT AT AT AT
1 AT AT AT AT
593499 CTTTTTTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:594068 original size:3 final size:3
Alignment explanation
Indices: 594060--594086 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
594050 ACAAGTTTAA
594060 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
594087 TGAAAAGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:596783 original size:2 final size:2
Alignment explanation
Indices: 596776--596811 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
596766 TAATCATTAA
596776 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
596812 CATGTAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:597020 original size:26 final size:26
Alignment explanation
Indices: 596990--597055 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
596980 AAAGGCAATA
596990 AATTTTTAAAAATATATAAA-ATTTAT
1 AATTTTTAAAAATATA-AAATATTTAT
* *
597016 AATTTTTTAAATTATAAAATATTTAT
1 AATTTTTAAAAATATAAAATATTTAT
* * *
597042 TATTATAAAAAATA
1 AATTTTTAAAAATA
597056 AACTTCTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
25 3 0.09
26 29 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTTTTAAAAATATAAAATATTTAT
Found at i:607829 original size:228 final size:226
Alignment explanation
Indices: 607427--607873 Score: 770
Period size: 228 Copynumber: 2.0 Consensus size: 226
607417 GTAAATTATC
* * *
607427 TATCCTTTTTATAAAAGTATCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTATCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
607492 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
607557 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG-AACACTATTAAAAAAATTG
607622 AAACATAAATTACATAACTTTCAAAAAAGTATA
195 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
607655 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTG-AAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTATCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
607719 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
607784 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAACACTATTAAATAAATTG
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAACACTATTAAAAAAATTG
607849 AAACATAAATTACATAACTTTAAAA
195 AAACATAAATTACATAACTTTAAAA
607874 GCAGTTTTAA
Statistics
Matches: 208, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
226 4 0.02
227 39 0.19
228 163 0.78
229 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTATCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:607968 original size:20 final size:20
Alignment explanation
Indices: 607936--607980 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
607926 AAATATACCA
607936 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
607956 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGATAAAACC
607976 -GTAAA
1 GGTAAA
607981 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.04
19 4 0.17
20 16 0.67
21 3 0.12
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.18
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:608127 original size:17 final size:17
Alignment explanation
Indices: 608107--608152 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
608097 TAACAGGTAA
608107 AATATGATAAAACCGGT
1 AATATGATAAAACCGGT
608124 AATAAAATGATAAAACCGGT
1 AAT---ATGATAAAACCGGT
*
608144 AAAATGATA
1 AATATGATA
608153 CCGGATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 9 0.36
20 16 0.64
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (17 bp):
AATATGATAAAACCGGT
Done.