Multiple sequence alignment - TraesCS3D01G324000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G324000 chr3D 100.000 5168 0 0 1 5168 437219290 437214123 0.000000e+00 9544.0
1 TraesCS3D01G324000 chr3D 89.320 206 18 4 4733 4936 537040678 537040881 6.640000e-64 255.0
2 TraesCS3D01G324000 chr3D 90.909 66 5 1 11 76 591552018 591552082 2.560000e-13 87.9
3 TraesCS3D01G324000 chr3D 97.778 45 1 0 86 130 537698079 537698123 1.540000e-10 78.7
4 TraesCS3D01G324000 chr3D 93.333 45 3 0 86 130 84023329 84023285 3.340000e-07 67.6
5 TraesCS3D01G324000 chr3A 96.325 4435 112 18 242 4642 575315102 575310685 0.000000e+00 7239.0
6 TraesCS3D01G324000 chr3A 89.260 419 28 12 4659 5075 575310699 575310296 4.620000e-140 508.0
7 TraesCS3D01G324000 chr3A 90.909 66 4 2 11 76 34605373 34605436 2.560000e-13 87.9
8 TraesCS3D01G324000 chr3B 96.132 4318 108 26 153 4452 572489095 572484819 0.000000e+00 6994.0
9 TraesCS3D01G324000 chr3B 92.537 201 14 1 4449 4648 572484781 572484581 2.350000e-73 287.0
10 TraesCS3D01G324000 chr3B 91.304 46 3 1 5124 5168 545430141 545430186 1.550000e-05 62.1
11 TraesCS3D01G324000 chr3B 91.304 46 3 1 5124 5168 545482871 545482916 1.550000e-05 62.1
12 TraesCS3D01G324000 chr1D 87.646 599 69 3 1072 1666 408432322 408432919 0.000000e+00 691.0
13 TraesCS3D01G324000 chr1B 87.145 599 72 3 1072 1666 549518385 549518982 0.000000e+00 675.0
14 TraesCS3D01G324000 chr1B 91.111 45 4 0 86 130 311675792 311675748 1.550000e-05 62.1
15 TraesCS3D01G324000 chr1A 86.644 599 75 3 1072 1666 504313402 504313999 0.000000e+00 658.0
16 TraesCS3D01G324000 chr1A 90.863 197 17 1 4733 4928 561333323 561333519 3.970000e-66 263.0
17 TraesCS3D01G324000 chr6B 91.837 196 16 0 4733 4928 300937499 300937694 1.830000e-69 274.0
18 TraesCS3D01G324000 chr6B 88.780 205 20 3 4733 4936 550313228 550313026 1.110000e-61 248.0
19 TraesCS3D01G324000 chrUn 90.196 204 19 1 4733 4936 21282931 21282729 1.100000e-66 265.0
20 TraesCS3D01G324000 chrUn 85.938 64 6 2 11 74 85460403 85460343 1.200000e-06 65.8
21 TraesCS3D01G324000 chr7D 89.756 205 19 2 4733 4937 124605923 124605721 1.430000e-65 261.0
22 TraesCS3D01G324000 chr7D 92.683 41 1 2 90 130 41801643 41801681 2.010000e-04 58.4
23 TraesCS3D01G324000 chr6D 88.725 204 22 1 4733 4936 193573727 193573525 1.110000e-61 248.0
24 TraesCS3D01G324000 chr6D 94.737 38 2 0 5124 5161 24034358 24034395 5.590000e-05 60.2
25 TraesCS3D01G324000 chr6D 100.000 30 0 0 101 130 143369201 143369172 7.230000e-04 56.5
26 TraesCS3D01G324000 chr2A 88.725 204 22 1 4733 4936 456704093 456704295 1.110000e-61 248.0
27 TraesCS3D01G324000 chr2A 97.959 49 0 1 85 132 683717366 683717414 3.320000e-12 84.2
28 TraesCS3D01G324000 chr2B 86.364 66 6 3 11 76 645648148 645648210 9.290000e-08 69.4
29 TraesCS3D01G324000 chr6A 94.737 38 2 0 93 130 188456951 188456914 5.590000e-05 60.2
30 TraesCS3D01G324000 chr5A 94.595 37 1 1 97 132 108576855 108576891 7.230000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G324000 chr3D 437214123 437219290 5167 True 9544.0 9544 100.0000 1 5168 1 chr3D.!!$R2 5167
1 TraesCS3D01G324000 chr3A 575310296 575315102 4806 True 3873.5 7239 92.7925 242 5075 2 chr3A.!!$R1 4833
2 TraesCS3D01G324000 chr3B 572484581 572489095 4514 True 3640.5 6994 94.3345 153 4648 2 chr3B.!!$R1 4495
3 TraesCS3D01G324000 chr1D 408432322 408432919 597 False 691.0 691 87.6460 1072 1666 1 chr1D.!!$F1 594
4 TraesCS3D01G324000 chr1B 549518385 549518982 597 False 675.0 675 87.1450 1072 1666 1 chr1B.!!$F1 594
5 TraesCS3D01G324000 chr1A 504313402 504313999 597 False 658.0 658 86.6440 1072 1666 1 chr1A.!!$F1 594

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
28 29 0.108424 AGAGAGCAGTGATTCGGTGC 60.108 55.0 0.0 2.58 37.48 5.01 F
104 105 0.109532 TCTTGACCGGGTGCAAATGA 59.890 50.0 3.3 1.34 0.00 2.57 F
106 107 0.179004 TTGACCGGGTGCAAATGAGT 60.179 50.0 3.3 0.00 0.00 3.41 F
111 112 0.321564 CGGGTGCAAATGAGTCTGGA 60.322 55.0 0.0 0.00 0.00 3.86 F
712 734 0.689745 CTCCGATCCCCCACCACTTA 60.690 60.0 0.0 0.00 0.00 2.24 F
2625 2666 0.663153 GTTTCAGAGTGGTGTGTGCC 59.337 55.0 0.0 0.00 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1786 3.439857 ACAGCAATCCACCAAGTACAT 57.560 42.857 0.00 0.0 0.00 2.29 R
1942 1977 6.012658 ACATCAATATTTTGTCAGCAACGT 57.987 33.333 0.00 0.0 33.82 3.99 R
2218 2256 4.921470 TTTTCCGATCAGTTGATTCGAC 57.079 40.909 12.36 0.0 34.37 4.20 R
2625 2666 2.290367 TGGAAACAAAGCATGACACTCG 59.710 45.455 0.00 0.0 37.44 4.18 R
2952 2993 0.785979 CGAAACATGGCAAAAGCAGC 59.214 50.000 0.00 0.0 0.00 5.25 R
4657 4745 0.035152 TAGTTGCCGACCGTCCTCTA 60.035 55.000 0.00 0.0 0.00 2.43 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.362932 TCACTTAGAGAGCAGTGATTCG 57.637 45.455 0.00 0.00 43.63 3.34
25 26 3.129462 TCACTTAGAGAGCAGTGATTCGG 59.871 47.826 0.00 0.00 43.63 4.30
26 27 3.093057 ACTTAGAGAGCAGTGATTCGGT 58.907 45.455 0.00 0.00 0.00 4.69
27 28 3.119316 ACTTAGAGAGCAGTGATTCGGTG 60.119 47.826 0.00 0.00 0.00 4.94
28 29 0.108424 AGAGAGCAGTGATTCGGTGC 60.108 55.000 0.00 2.58 37.48 5.01
29 30 1.078848 AGAGCAGTGATTCGGTGCC 60.079 57.895 0.00 0.47 37.98 5.01
30 31 2.045926 AGCAGTGATTCGGTGCCC 60.046 61.111 0.00 0.00 37.98 5.36
31 32 2.359850 GCAGTGATTCGGTGCCCA 60.360 61.111 0.00 0.00 0.00 5.36
32 33 2.401766 GCAGTGATTCGGTGCCCAG 61.402 63.158 0.00 0.00 0.00 4.45
33 34 1.296392 CAGTGATTCGGTGCCCAGA 59.704 57.895 0.00 0.00 0.00 3.86
34 35 1.021390 CAGTGATTCGGTGCCCAGAC 61.021 60.000 0.00 0.00 0.00 3.51
35 36 1.194781 AGTGATTCGGTGCCCAGACT 61.195 55.000 0.00 0.00 0.00 3.24
36 37 0.741221 GTGATTCGGTGCCCAGACTC 60.741 60.000 0.00 0.00 0.00 3.36
37 38 1.191489 TGATTCGGTGCCCAGACTCA 61.191 55.000 0.00 0.00 0.00 3.41
38 39 0.179000 GATTCGGTGCCCAGACTCAT 59.821 55.000 0.00 0.00 0.00 2.90
39 40 0.179000 ATTCGGTGCCCAGACTCATC 59.821 55.000 0.00 0.00 0.00 2.92
40 41 1.899437 TTCGGTGCCCAGACTCATCC 61.899 60.000 0.00 0.00 0.00 3.51
41 42 2.187946 GGTGCCCAGACTCATCCG 59.812 66.667 0.00 0.00 0.00 4.18
42 43 2.512515 GTGCCCAGACTCATCCGC 60.513 66.667 0.00 0.00 0.00 5.54
43 44 3.002583 TGCCCAGACTCATCCGCA 61.003 61.111 0.00 0.00 0.00 5.69
44 45 2.512515 GCCCAGACTCATCCGCAC 60.513 66.667 0.00 0.00 0.00 5.34
45 46 2.187946 CCCAGACTCATCCGCACC 59.812 66.667 0.00 0.00 0.00 5.01
46 47 2.187946 CCAGACTCATCCGCACCC 59.812 66.667 0.00 0.00 0.00 4.61
47 48 2.202797 CAGACTCATCCGCACCCG 60.203 66.667 0.00 0.00 0.00 5.28
48 49 2.680352 AGACTCATCCGCACCCGT 60.680 61.111 0.00 0.00 0.00 5.28
49 50 2.509336 GACTCATCCGCACCCGTG 60.509 66.667 0.00 0.00 0.00 4.94
86 87 8.873242 AAAATTCAAAACAAAACGTGATGTTC 57.127 26.923 16.68 0.00 40.84 3.18
87 88 7.826260 AATTCAAAACAAAACGTGATGTTCT 57.174 28.000 16.68 3.69 40.84 3.01
88 89 7.826260 ATTCAAAACAAAACGTGATGTTCTT 57.174 28.000 16.68 11.48 40.84 2.52
89 90 6.624710 TCAAAACAAAACGTGATGTTCTTG 57.375 33.333 16.68 18.96 40.84 3.02
90 91 6.382608 TCAAAACAAAACGTGATGTTCTTGA 58.617 32.000 22.41 22.41 40.84 3.02
91 92 6.306837 TCAAAACAAAACGTGATGTTCTTGAC 59.693 34.615 22.41 0.00 40.84 3.18
92 93 4.287238 ACAAAACGTGATGTTCTTGACC 57.713 40.909 14.70 0.00 40.84 4.02
93 94 3.242608 ACAAAACGTGATGTTCTTGACCG 60.243 43.478 14.70 0.00 40.84 4.79
94 95 1.508632 AACGTGATGTTCTTGACCGG 58.491 50.000 0.00 0.00 35.27 5.28
95 96 0.320421 ACGTGATGTTCTTGACCGGG 60.320 55.000 6.32 0.00 0.00 5.73
96 97 0.320421 CGTGATGTTCTTGACCGGGT 60.320 55.000 6.32 0.00 0.00 5.28
97 98 1.156736 GTGATGTTCTTGACCGGGTG 58.843 55.000 3.30 0.00 0.00 4.61
98 99 0.605319 TGATGTTCTTGACCGGGTGC 60.605 55.000 3.30 0.00 0.00 5.01
99 100 0.605319 GATGTTCTTGACCGGGTGCA 60.605 55.000 3.30 0.00 0.00 4.57
100 101 0.179004 ATGTTCTTGACCGGGTGCAA 60.179 50.000 3.30 8.08 0.00 4.08
101 102 0.394488 TGTTCTTGACCGGGTGCAAA 60.394 50.000 3.30 0.00 0.00 3.68
102 103 0.958822 GTTCTTGACCGGGTGCAAAT 59.041 50.000 3.30 0.00 0.00 2.32
103 104 0.958091 TTCTTGACCGGGTGCAAATG 59.042 50.000 3.30 0.00 0.00 2.32
104 105 0.109532 TCTTGACCGGGTGCAAATGA 59.890 50.000 3.30 1.34 0.00 2.57
105 106 0.523072 CTTGACCGGGTGCAAATGAG 59.477 55.000 3.30 0.00 0.00 2.90
106 107 0.179004 TTGACCGGGTGCAAATGAGT 60.179 50.000 3.30 0.00 0.00 3.41
107 108 0.605319 TGACCGGGTGCAAATGAGTC 60.605 55.000 3.30 0.00 0.00 3.36
108 109 0.321653 GACCGGGTGCAAATGAGTCT 60.322 55.000 3.30 0.00 0.00 3.24
109 110 0.606401 ACCGGGTGCAAATGAGTCTG 60.606 55.000 6.32 0.00 0.00 3.51
110 111 1.308069 CCGGGTGCAAATGAGTCTGG 61.308 60.000 0.00 0.00 0.00 3.86
111 112 0.321564 CGGGTGCAAATGAGTCTGGA 60.322 55.000 0.00 0.00 0.00 3.86
112 113 1.168714 GGGTGCAAATGAGTCTGGAC 58.831 55.000 0.00 0.00 33.52 4.02
113 114 1.271597 GGGTGCAAATGAGTCTGGACT 60.272 52.381 2.62 2.62 45.84 3.85
129 130 5.847304 TCTGGACTCAGAAATGGATATTCG 58.153 41.667 0.00 0.00 46.08 3.34
130 131 5.363868 TCTGGACTCAGAAATGGATATTCGT 59.636 40.000 0.00 0.00 46.08 3.85
131 132 6.549736 TCTGGACTCAGAAATGGATATTCGTA 59.450 38.462 0.00 0.00 46.08 3.43
132 133 7.233553 TCTGGACTCAGAAATGGATATTCGTAT 59.766 37.037 0.00 0.00 46.08 3.06
133 134 7.378966 TGGACTCAGAAATGGATATTCGTATC 58.621 38.462 0.00 0.00 32.04 2.24
134 135 7.233553 TGGACTCAGAAATGGATATTCGTATCT 59.766 37.037 0.00 0.00 32.04 1.98
135 136 7.757624 GGACTCAGAAATGGATATTCGTATCTC 59.242 40.741 0.00 0.00 32.04 2.75
136 137 8.415950 ACTCAGAAATGGATATTCGTATCTCT 57.584 34.615 0.00 0.00 32.04 3.10
137 138 8.865090 ACTCAGAAATGGATATTCGTATCTCTT 58.135 33.333 0.00 0.00 32.04 2.85
138 139 9.138062 CTCAGAAATGGATATTCGTATCTCTTG 57.862 37.037 0.00 0.00 32.04 3.02
139 140 7.600375 TCAGAAATGGATATTCGTATCTCTTGC 59.400 37.037 0.00 0.00 32.04 4.01
140 141 7.386025 CAGAAATGGATATTCGTATCTCTTGCA 59.614 37.037 0.00 0.00 32.04 4.08
141 142 8.099537 AGAAATGGATATTCGTATCTCTTGCAT 58.900 33.333 0.00 0.00 32.04 3.96
142 143 9.371136 GAAATGGATATTCGTATCTCTTGCATA 57.629 33.333 0.00 0.00 0.00 3.14
143 144 9.725019 AAATGGATATTCGTATCTCTTGCATAA 57.275 29.630 0.00 0.00 0.00 1.90
144 145 9.725019 AATGGATATTCGTATCTCTTGCATAAA 57.275 29.630 0.00 0.00 0.00 1.40
145 146 8.534333 TGGATATTCGTATCTCTTGCATAAAC 57.466 34.615 0.00 0.00 0.00 2.01
146 147 8.367911 TGGATATTCGTATCTCTTGCATAAACT 58.632 33.333 0.00 0.00 0.00 2.66
147 148 8.865001 GGATATTCGTATCTCTTGCATAAACTC 58.135 37.037 0.00 0.00 0.00 3.01
148 149 9.632807 GATATTCGTATCTCTTGCATAAACTCT 57.367 33.333 0.00 0.00 0.00 3.24
149 150 9.988815 ATATTCGTATCTCTTGCATAAACTCTT 57.011 29.630 0.00 0.00 0.00 2.85
150 151 7.757097 TTCGTATCTCTTGCATAAACTCTTC 57.243 36.000 0.00 0.00 0.00 2.87
151 152 7.101652 TCGTATCTCTTGCATAAACTCTTCT 57.898 36.000 0.00 0.00 0.00 2.85
170 171 5.656416 TCTTCTTGAACCCTTTGAAACACAT 59.344 36.000 0.00 0.00 0.00 3.21
201 202 6.395426 TGTTCTGAATTTGACATGCTCTTT 57.605 33.333 0.00 0.00 0.00 2.52
368 374 8.253113 ACATACAATCAAGATTTGCCCTAAAAG 58.747 33.333 0.00 0.00 0.00 2.27
369 375 6.916360 ACAATCAAGATTTGCCCTAAAAGA 57.084 33.333 0.00 0.00 0.00 2.52
547 563 1.176527 CATCACCAACCCACCATCAC 58.823 55.000 0.00 0.00 0.00 3.06
548 564 0.776810 ATCACCAACCCACCATCACA 59.223 50.000 0.00 0.00 0.00 3.58
595 617 2.364579 AATCCGTCCCGCCTACCA 60.365 61.111 0.00 0.00 0.00 3.25
710 732 2.365635 CTCCGATCCCCCACCACT 60.366 66.667 0.00 0.00 0.00 4.00
712 734 0.689745 CTCCGATCCCCCACCACTTA 60.690 60.000 0.00 0.00 0.00 2.24
723 745 1.336517 CCACCACTTAGCTTTCGACGA 60.337 52.381 0.00 0.00 0.00 4.20
1736 1761 6.875726 CACTGAAGAATTGATGTTGTCCTCTA 59.124 38.462 0.00 0.00 0.00 2.43
1761 1786 4.227073 TGATGGTGGATTGATGTTGTCCTA 59.773 41.667 0.00 0.00 33.15 2.94
1942 1977 7.776107 TGATAAATTTTGGATGCAACCGATTA 58.224 30.769 8.65 3.18 0.00 1.75
2194 2232 7.940137 TCTTAGTCCCTAACTTTGTGCAAATAA 59.060 33.333 0.00 0.00 39.55 1.40
2235 2273 3.150848 TCAGTCGAATCAACTGATCGG 57.849 47.619 0.00 0.00 46.15 4.18
2238 2276 3.926527 CAGTCGAATCAACTGATCGGAAA 59.073 43.478 9.00 0.00 45.64 3.13
2252 2290 8.594881 ACTGATCGGAAAATTATGAGACATAC 57.405 34.615 9.00 0.00 0.00 2.39
2400 2440 7.889469 TCTATGTAACCTTCTGTAAGTTTCGT 58.111 34.615 0.00 0.00 33.76 3.85
2401 2441 9.013229 TCTATGTAACCTTCTGTAAGTTTCGTA 57.987 33.333 0.00 0.00 33.76 3.43
2625 2666 0.663153 GTTTCAGAGTGGTGTGTGCC 59.337 55.000 0.00 0.00 0.00 5.01
2659 2700 5.277490 GCTTTGTTTCCAGCATTTTCCTTTC 60.277 40.000 0.00 0.00 35.95 2.62
2949 2990 6.091713 GTGCTGGTAAGTTATGTTCGTATGTT 59.908 38.462 0.00 0.00 0.00 2.71
2952 2993 5.806502 TGGTAAGTTATGTTCGTATGTTCCG 59.193 40.000 0.00 0.00 0.00 4.30
2966 3007 1.010419 GTTCCGCTGCTTTTGCCATG 61.010 55.000 0.00 0.00 46.87 3.66
3088 3132 6.701841 AGGTAGTAACTTGCATCATGTTATCG 59.298 38.462 8.03 0.00 36.73 2.92
3393 3437 1.318576 CCGAAAAACTTGCTGGACCT 58.681 50.000 0.00 0.00 0.00 3.85
3604 3648 5.537188 TGTGTTAACAATTCATTTCAGGGC 58.463 37.500 10.51 0.00 31.82 5.19
4246 4290 0.396435 TGTGCTCTTGTCCATTCGGT 59.604 50.000 0.00 0.00 0.00 4.69
4466 4553 8.633561 CATGCTTCGAATGATATACCCTCTATA 58.366 37.037 0.00 0.00 0.00 1.31
4500 4588 5.592104 TTGATTACCTGCTCGAACAGATA 57.408 39.130 17.30 0.95 40.25 1.98
4505 4593 2.760650 ACCTGCTCGAACAGATATGACA 59.239 45.455 17.30 0.00 40.25 3.58
4568 4656 3.600388 ACTGCAATAACCAGTGACTAGC 58.400 45.455 0.00 0.00 41.68 3.42
4581 4669 4.220821 CAGTGACTAGCCTTCCTACAAAGA 59.779 45.833 0.00 0.00 0.00 2.52
4619 4707 5.912892 TGTCATCAGGCGAATAGATGTAAA 58.087 37.500 0.00 0.00 39.96 2.01
4648 4736 2.290641 AGAGAACGTGTGCAATGAAACC 59.709 45.455 0.00 0.00 0.00 3.27
4649 4737 2.020720 AGAACGTGTGCAATGAAACCA 58.979 42.857 0.00 0.00 0.00 3.67
4650 4738 2.622942 AGAACGTGTGCAATGAAACCAT 59.377 40.909 0.00 0.00 0.00 3.55
4651 4739 2.420628 ACGTGTGCAATGAAACCATG 57.579 45.000 0.00 0.00 0.00 3.66
4652 4740 1.952990 ACGTGTGCAATGAAACCATGA 59.047 42.857 0.00 0.00 0.00 3.07
4653 4741 2.360483 ACGTGTGCAATGAAACCATGAA 59.640 40.909 0.00 0.00 0.00 2.57
4654 4742 3.005684 ACGTGTGCAATGAAACCATGAAT 59.994 39.130 0.00 0.00 0.00 2.57
4655 4743 4.217334 ACGTGTGCAATGAAACCATGAATA 59.783 37.500 0.00 0.00 0.00 1.75
4656 4744 5.159925 CGTGTGCAATGAAACCATGAATAA 58.840 37.500 0.00 0.00 0.00 1.40
4657 4745 5.806502 CGTGTGCAATGAAACCATGAATAAT 59.193 36.000 0.00 0.00 0.00 1.28
4658 4746 6.971756 CGTGTGCAATGAAACCATGAATAATA 59.028 34.615 0.00 0.00 0.00 0.98
4659 4747 7.166307 CGTGTGCAATGAAACCATGAATAATAG 59.834 37.037 0.00 0.00 0.00 1.73
4660 4748 8.190122 GTGTGCAATGAAACCATGAATAATAGA 58.810 33.333 0.00 0.00 0.00 1.98
4661 4749 8.407832 TGTGCAATGAAACCATGAATAATAGAG 58.592 33.333 0.00 0.00 0.00 2.43
4662 4750 7.864379 GTGCAATGAAACCATGAATAATAGAGG 59.136 37.037 0.00 0.00 0.00 3.69
4663 4751 7.779326 TGCAATGAAACCATGAATAATAGAGGA 59.221 33.333 0.00 0.00 0.00 3.71
4664 4752 8.078596 GCAATGAAACCATGAATAATAGAGGAC 58.921 37.037 0.00 0.00 0.00 3.85
4665 4753 7.969536 ATGAAACCATGAATAATAGAGGACG 57.030 36.000 0.00 0.00 0.00 4.79
4666 4754 6.288294 TGAAACCATGAATAATAGAGGACGG 58.712 40.000 0.00 0.00 0.00 4.79
4667 4755 5.888982 AACCATGAATAATAGAGGACGGT 57.111 39.130 0.00 0.00 0.00 4.83
4668 4756 5.470047 ACCATGAATAATAGAGGACGGTC 57.530 43.478 0.00 0.00 0.00 4.79
4669 4757 4.022242 ACCATGAATAATAGAGGACGGTCG 60.022 45.833 1.43 0.00 0.00 4.79
4670 4758 4.486090 CATGAATAATAGAGGACGGTCGG 58.514 47.826 1.43 0.00 0.00 4.79
4671 4759 2.295349 TGAATAATAGAGGACGGTCGGC 59.705 50.000 1.43 0.00 0.00 5.54
4672 4760 1.991121 ATAATAGAGGACGGTCGGCA 58.009 50.000 1.43 0.00 0.00 5.69
4673 4761 1.766494 TAATAGAGGACGGTCGGCAA 58.234 50.000 1.43 0.00 0.00 4.52
4683 4771 3.488090 GTCGGCAACTACAGCGGC 61.488 66.667 0.00 0.00 33.00 6.53
4688 4776 3.047280 CAACTACAGCGGCGGCAA 61.047 61.111 19.21 2.54 43.41 4.52
4689 4777 3.047877 AACTACAGCGGCGGCAAC 61.048 61.111 19.21 0.00 43.41 4.17
4760 4850 7.489574 TTTTGGCTTGTGATTTTTCCATTAC 57.510 32.000 0.00 0.00 0.00 1.89
4782 4872 6.320494 ACTAGATTCGAGCACTGTAATAGG 57.680 41.667 0.00 0.00 0.00 2.57
4849 4939 9.943163 GATTTTCTATAGCTTTGATCTGGTTTC 57.057 33.333 0.00 0.00 0.00 2.78
4884 4974 3.196254 GTGAAATTGTACCCCTCCTCGTA 59.804 47.826 0.00 0.00 0.00 3.43
4886 4976 4.286549 TGAAATTGTACCCCTCCTCGTAAA 59.713 41.667 0.00 0.00 0.00 2.01
5038 5128 5.665916 ACTGCATTTATCAAGGAAAAGGG 57.334 39.130 0.00 0.00 0.00 3.95
5042 5132 6.930731 TGCATTTATCAAGGAAAAGGGTTAC 58.069 36.000 0.00 0.00 0.00 2.50
5046 5136 9.586435 CATTTATCAAGGAAAAGGGTTACATTC 57.414 33.333 0.00 0.00 0.00 2.67
5061 5151 2.450476 ACATTCAACCAGCTGATTCCC 58.550 47.619 17.39 0.00 0.00 3.97
5063 5153 2.205022 TTCAACCAGCTGATTCCCAG 57.795 50.000 17.39 0.00 45.67 4.45
5071 5161 2.177950 CTGATTCCCAGCTGTGTGC 58.822 57.895 13.81 0.00 43.29 4.57
5081 5171 2.012237 GCTGTGTGCGAGATCATGG 58.988 57.895 0.00 0.00 0.00 3.66
5082 5172 0.742281 GCTGTGTGCGAGATCATGGT 60.742 55.000 0.00 0.00 0.00 3.55
5083 5173 1.730501 CTGTGTGCGAGATCATGGTT 58.269 50.000 0.00 0.00 0.00 3.67
5084 5174 2.079158 CTGTGTGCGAGATCATGGTTT 58.921 47.619 0.00 0.00 0.00 3.27
5085 5175 3.261580 CTGTGTGCGAGATCATGGTTTA 58.738 45.455 0.00 0.00 0.00 2.01
5086 5176 3.669536 TGTGTGCGAGATCATGGTTTAA 58.330 40.909 0.00 0.00 0.00 1.52
5087 5177 4.068599 TGTGTGCGAGATCATGGTTTAAA 58.931 39.130 0.00 0.00 0.00 1.52
5088 5178 4.154015 TGTGTGCGAGATCATGGTTTAAAG 59.846 41.667 0.00 0.00 0.00 1.85
5089 5179 4.391830 GTGTGCGAGATCATGGTTTAAAGA 59.608 41.667 0.00 0.00 0.00 2.52
5090 5180 4.391830 TGTGCGAGATCATGGTTTAAAGAC 59.608 41.667 0.00 0.00 0.00 3.01
5091 5181 4.631813 GTGCGAGATCATGGTTTAAAGACT 59.368 41.667 0.00 0.00 0.00 3.24
5092 5182 5.810587 GTGCGAGATCATGGTTTAAAGACTA 59.189 40.000 0.00 0.00 0.00 2.59
5093 5183 6.019479 GTGCGAGATCATGGTTTAAAGACTAG 60.019 42.308 0.00 0.00 0.00 2.57
5094 5184 5.463724 GCGAGATCATGGTTTAAAGACTAGG 59.536 44.000 0.00 0.00 0.00 3.02
5095 5185 5.986135 CGAGATCATGGTTTAAAGACTAGGG 59.014 44.000 0.00 0.00 0.00 3.53
5096 5186 6.253946 AGATCATGGTTTAAAGACTAGGGG 57.746 41.667 0.00 0.00 0.00 4.79
5097 5187 5.731678 AGATCATGGTTTAAAGACTAGGGGT 59.268 40.000 0.00 0.00 0.00 4.95
5098 5188 6.906901 AGATCATGGTTTAAAGACTAGGGGTA 59.093 38.462 0.00 0.00 0.00 3.69
5099 5189 6.555463 TCATGGTTTAAAGACTAGGGGTAG 57.445 41.667 0.00 0.00 0.00 3.18
5100 5190 5.427481 TCATGGTTTAAAGACTAGGGGTAGG 59.573 44.000 0.00 0.00 0.00 3.18
5101 5191 4.106324 TGGTTTAAAGACTAGGGGTAGGG 58.894 47.826 0.00 0.00 0.00 3.53
5102 5192 3.457380 GGTTTAAAGACTAGGGGTAGGGG 59.543 52.174 0.00 0.00 0.00 4.79
5103 5193 3.426393 TTAAAGACTAGGGGTAGGGGG 57.574 52.381 0.00 0.00 0.00 5.40
5104 5194 1.411741 AAAGACTAGGGGTAGGGGGA 58.588 55.000 0.00 0.00 0.00 4.81
5105 5195 1.646442 AAGACTAGGGGTAGGGGGAT 58.354 55.000 0.00 0.00 0.00 3.85
5106 5196 2.564689 AGACTAGGGGTAGGGGGATA 57.435 55.000 0.00 0.00 0.00 2.59
5107 5197 2.080231 AGACTAGGGGTAGGGGGATAC 58.920 57.143 0.00 0.00 0.00 2.24
5122 5212 2.490991 GGATACCTGTCCCATTTACGC 58.509 52.381 0.00 0.00 31.82 4.42
5123 5213 2.104281 GGATACCTGTCCCATTTACGCT 59.896 50.000 0.00 0.00 31.82 5.07
5124 5214 3.433173 GGATACCTGTCCCATTTACGCTT 60.433 47.826 0.00 0.00 31.82 4.68
5125 5215 4.202284 GGATACCTGTCCCATTTACGCTTA 60.202 45.833 0.00 0.00 31.82 3.09
5126 5216 2.981898 ACCTGTCCCATTTACGCTTAC 58.018 47.619 0.00 0.00 0.00 2.34
5127 5217 2.285977 CCTGTCCCATTTACGCTTACC 58.714 52.381 0.00 0.00 0.00 2.85
5128 5218 2.285977 CTGTCCCATTTACGCTTACCC 58.714 52.381 0.00 0.00 0.00 3.69
5129 5219 1.629353 TGTCCCATTTACGCTTACCCA 59.371 47.619 0.00 0.00 0.00 4.51
5130 5220 2.240160 TGTCCCATTTACGCTTACCCAT 59.760 45.455 0.00 0.00 0.00 4.00
5131 5221 2.616842 GTCCCATTTACGCTTACCCATG 59.383 50.000 0.00 0.00 0.00 3.66
5132 5222 1.336755 CCCATTTACGCTTACCCATGC 59.663 52.381 0.00 0.00 0.00 4.06
5133 5223 1.336755 CCATTTACGCTTACCCATGCC 59.663 52.381 0.00 0.00 0.00 4.40
5134 5224 1.336755 CATTTACGCTTACCCATGCCC 59.663 52.381 0.00 0.00 0.00 5.36
5135 5225 0.745128 TTTACGCTTACCCATGCCCG 60.745 55.000 0.00 0.00 0.00 6.13
5136 5226 1.901654 TTACGCTTACCCATGCCCGT 61.902 55.000 0.00 0.00 0.00 5.28
5137 5227 2.300850 TACGCTTACCCATGCCCGTC 62.301 60.000 0.00 0.00 0.00 4.79
5138 5228 2.270850 GCTTACCCATGCCCGTCA 59.729 61.111 0.00 0.00 0.00 4.35
5139 5229 2.112815 GCTTACCCATGCCCGTCAC 61.113 63.158 0.00 0.00 0.00 3.67
5140 5230 1.451387 CTTACCCATGCCCGTCACC 60.451 63.158 0.00 0.00 0.00 4.02
5141 5231 1.910580 CTTACCCATGCCCGTCACCT 61.911 60.000 0.00 0.00 0.00 4.00
5142 5232 2.191786 TTACCCATGCCCGTCACCTG 62.192 60.000 0.00 0.00 0.00 4.00
5143 5233 3.716195 CCCATGCCCGTCACCTGA 61.716 66.667 0.00 0.00 0.00 3.86
5144 5234 2.436646 CCATGCCCGTCACCTGAC 60.437 66.667 0.00 0.00 41.47 3.51
5145 5235 2.347114 CATGCCCGTCACCTGACA 59.653 61.111 6.27 0.00 44.99 3.58
5146 5236 1.742880 CATGCCCGTCACCTGACAG 60.743 63.158 6.27 0.00 44.99 3.51
5147 5237 2.959484 ATGCCCGTCACCTGACAGG 61.959 63.158 20.45 20.45 44.99 4.00
5149 5239 2.923035 CCCGTCACCTGACAGGGT 60.923 66.667 25.34 8.49 45.33 4.34
5150 5240 1.608336 CCCGTCACCTGACAGGGTA 60.608 63.158 25.34 10.07 45.33 3.69
5151 5241 1.189524 CCCGTCACCTGACAGGGTAA 61.190 60.000 25.34 7.49 45.33 2.85
5152 5242 0.682852 CCGTCACCTGACAGGGTAAA 59.317 55.000 25.34 4.96 44.99 2.01
5153 5243 1.278127 CCGTCACCTGACAGGGTAAAT 59.722 52.381 25.34 0.66 44.99 1.40
5154 5244 2.346803 CGTCACCTGACAGGGTAAATG 58.653 52.381 25.34 13.83 44.99 2.32
5155 5245 2.711542 GTCACCTGACAGGGTAAATGG 58.288 52.381 25.34 6.02 44.18 3.16
5156 5246 1.633432 TCACCTGACAGGGTAAATGGG 59.367 52.381 25.34 4.72 40.58 4.00
5157 5247 1.354368 CACCTGACAGGGTAAATGGGT 59.646 52.381 25.34 0.00 40.58 4.51
5158 5248 2.574369 CACCTGACAGGGTAAATGGGTA 59.426 50.000 25.34 0.00 40.58 3.69
5159 5249 2.574824 ACCTGACAGGGTAAATGGGTAC 59.425 50.000 25.34 0.00 40.58 3.34
5160 5250 4.654078 ACCTGACAGGGTAAATGGGTACC 61.654 52.174 25.34 2.17 46.17 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.119316 ACCGAATCACTGCTCTCTAAGTG 60.119 47.826 0.00 0.00 44.23 3.16
5 6 3.093057 ACCGAATCACTGCTCTCTAAGT 58.907 45.455 0.00 0.00 0.00 2.24
6 7 3.443037 CACCGAATCACTGCTCTCTAAG 58.557 50.000 0.00 0.00 0.00 2.18
7 8 2.417379 GCACCGAATCACTGCTCTCTAA 60.417 50.000 0.00 0.00 0.00 2.10
8 9 1.135139 GCACCGAATCACTGCTCTCTA 59.865 52.381 0.00 0.00 0.00 2.43
9 10 0.108424 GCACCGAATCACTGCTCTCT 60.108 55.000 0.00 0.00 0.00 3.10
10 11 1.086634 GGCACCGAATCACTGCTCTC 61.087 60.000 0.06 0.00 0.00 3.20
11 12 1.078848 GGCACCGAATCACTGCTCT 60.079 57.895 0.06 0.00 0.00 4.09
12 13 2.109126 GGGCACCGAATCACTGCTC 61.109 63.158 0.06 0.00 40.86 4.26
13 14 2.045926 GGGCACCGAATCACTGCT 60.046 61.111 0.06 0.00 40.86 4.24
25 26 2.512515 GCGGATGAGTCTGGGCAC 60.513 66.667 0.00 0.00 0.00 5.01
26 27 3.002583 TGCGGATGAGTCTGGGCA 61.003 61.111 0.00 0.00 0.00 5.36
27 28 2.512515 GTGCGGATGAGTCTGGGC 60.513 66.667 0.00 0.00 0.00 5.36
28 29 2.187946 GGTGCGGATGAGTCTGGG 59.812 66.667 0.00 0.00 0.00 4.45
29 30 2.187946 GGGTGCGGATGAGTCTGG 59.812 66.667 0.00 0.00 0.00 3.86
30 31 2.202797 CGGGTGCGGATGAGTCTG 60.203 66.667 0.00 0.00 0.00 3.51
31 32 2.680352 ACGGGTGCGGATGAGTCT 60.680 61.111 0.00 0.00 0.00 3.24
32 33 2.509336 CACGGGTGCGGATGAGTC 60.509 66.667 0.00 0.00 0.00 3.36
60 61 9.323963 GAACATCACGTTTTGTTTTGAATTTTT 57.676 25.926 12.67 0.00 38.19 1.94
61 62 8.716909 AGAACATCACGTTTTGTTTTGAATTTT 58.283 25.926 12.67 0.00 38.19 1.82
62 63 8.250538 AGAACATCACGTTTTGTTTTGAATTT 57.749 26.923 12.67 0.00 38.19 1.82
63 64 7.826260 AGAACATCACGTTTTGTTTTGAATT 57.174 28.000 12.67 0.00 38.19 2.17
64 65 7.543868 TCAAGAACATCACGTTTTGTTTTGAAT 59.456 29.630 20.46 3.12 38.19 2.57
65 66 6.863645 TCAAGAACATCACGTTTTGTTTTGAA 59.136 30.769 20.46 12.60 38.19 2.69
66 67 6.306837 GTCAAGAACATCACGTTTTGTTTTGA 59.693 34.615 19.74 19.74 38.19 2.69
67 68 6.453659 GGTCAAGAACATCACGTTTTGTTTTG 60.454 38.462 12.67 15.70 38.19 2.44
68 69 5.575218 GGTCAAGAACATCACGTTTTGTTTT 59.425 36.000 12.67 6.09 38.19 2.43
69 70 5.099575 GGTCAAGAACATCACGTTTTGTTT 58.900 37.500 12.67 3.11 38.19 2.83
70 71 4.668289 GGTCAAGAACATCACGTTTTGTT 58.332 39.130 11.57 11.57 38.19 2.83
71 72 3.242608 CGGTCAAGAACATCACGTTTTGT 60.243 43.478 0.00 0.00 38.19 2.83
72 73 3.288242 CGGTCAAGAACATCACGTTTTG 58.712 45.455 0.00 0.00 38.19 2.44
73 74 2.289547 CCGGTCAAGAACATCACGTTTT 59.710 45.455 0.00 0.00 38.19 2.43
74 75 1.871039 CCGGTCAAGAACATCACGTTT 59.129 47.619 0.00 0.00 38.19 3.60
75 76 1.508632 CCGGTCAAGAACATCACGTT 58.491 50.000 0.00 0.00 41.86 3.99
76 77 0.320421 CCCGGTCAAGAACATCACGT 60.320 55.000 0.00 0.00 0.00 4.49
77 78 0.320421 ACCCGGTCAAGAACATCACG 60.320 55.000 0.00 0.00 0.00 4.35
78 79 1.156736 CACCCGGTCAAGAACATCAC 58.843 55.000 0.00 0.00 0.00 3.06
79 80 0.605319 GCACCCGGTCAAGAACATCA 60.605 55.000 0.00 0.00 0.00 3.07
80 81 0.605319 TGCACCCGGTCAAGAACATC 60.605 55.000 0.00 0.00 0.00 3.06
81 82 0.179004 TTGCACCCGGTCAAGAACAT 60.179 50.000 0.00 0.00 0.00 2.71
82 83 0.394488 TTTGCACCCGGTCAAGAACA 60.394 50.000 0.00 0.00 0.00 3.18
83 84 0.958822 ATTTGCACCCGGTCAAGAAC 59.041 50.000 0.00 0.00 0.00 3.01
84 85 0.958091 CATTTGCACCCGGTCAAGAA 59.042 50.000 0.00 0.00 0.00 2.52
85 86 0.109532 TCATTTGCACCCGGTCAAGA 59.890 50.000 0.00 0.00 0.00 3.02
86 87 0.523072 CTCATTTGCACCCGGTCAAG 59.477 55.000 0.00 0.00 0.00 3.02
87 88 0.179004 ACTCATTTGCACCCGGTCAA 60.179 50.000 0.00 0.00 0.00 3.18
88 89 0.605319 GACTCATTTGCACCCGGTCA 60.605 55.000 0.00 0.00 0.00 4.02
89 90 0.321653 AGACTCATTTGCACCCGGTC 60.322 55.000 0.00 0.00 0.00 4.79
90 91 0.606401 CAGACTCATTTGCACCCGGT 60.606 55.000 0.00 0.00 0.00 5.28
91 92 1.308069 CCAGACTCATTTGCACCCGG 61.308 60.000 0.00 0.00 0.00 5.73
92 93 0.321564 TCCAGACTCATTTGCACCCG 60.322 55.000 0.00 0.00 0.00 5.28
93 94 1.168714 GTCCAGACTCATTTGCACCC 58.831 55.000 0.00 0.00 0.00 4.61
94 95 2.191128 AGTCCAGACTCATTTGCACC 57.809 50.000 0.00 0.00 36.92 5.01
106 107 5.363868 ACGAATATCCATTTCTGAGTCCAGA 59.636 40.000 0.00 0.00 46.95 3.86
107 108 5.605534 ACGAATATCCATTTCTGAGTCCAG 58.394 41.667 0.00 0.00 41.74 3.86
108 109 5.614324 ACGAATATCCATTTCTGAGTCCA 57.386 39.130 0.00 0.00 0.00 4.02
109 110 7.607250 AGATACGAATATCCATTTCTGAGTCC 58.393 38.462 0.00 0.00 38.43 3.85
110 111 8.519526 AGAGATACGAATATCCATTTCTGAGTC 58.480 37.037 0.00 0.00 38.43 3.36
111 112 8.415950 AGAGATACGAATATCCATTTCTGAGT 57.584 34.615 0.00 0.00 38.43 3.41
112 113 9.138062 CAAGAGATACGAATATCCATTTCTGAG 57.862 37.037 0.00 0.00 38.43 3.35
113 114 7.600375 GCAAGAGATACGAATATCCATTTCTGA 59.400 37.037 0.00 0.00 38.43 3.27
114 115 7.386025 TGCAAGAGATACGAATATCCATTTCTG 59.614 37.037 0.00 0.00 38.43 3.02
115 116 7.445121 TGCAAGAGATACGAATATCCATTTCT 58.555 34.615 0.00 0.00 38.43 2.52
116 117 7.658179 TGCAAGAGATACGAATATCCATTTC 57.342 36.000 0.00 0.00 38.43 2.17
117 118 9.725019 TTATGCAAGAGATACGAATATCCATTT 57.275 29.630 0.00 0.00 38.43 2.32
118 119 9.725019 TTTATGCAAGAGATACGAATATCCATT 57.275 29.630 0.00 0.00 38.43 3.16
119 120 9.155975 GTTTATGCAAGAGATACGAATATCCAT 57.844 33.333 0.00 0.00 38.43 3.41
120 121 8.367911 AGTTTATGCAAGAGATACGAATATCCA 58.632 33.333 0.00 0.00 38.43 3.41
121 122 8.764524 AGTTTATGCAAGAGATACGAATATCC 57.235 34.615 0.00 0.00 38.43 2.59
122 123 9.632807 AGAGTTTATGCAAGAGATACGAATATC 57.367 33.333 0.00 0.00 38.00 1.63
123 124 9.988815 AAGAGTTTATGCAAGAGATACGAATAT 57.011 29.630 0.00 0.00 0.00 1.28
124 125 9.464714 GAAGAGTTTATGCAAGAGATACGAATA 57.535 33.333 0.00 0.00 0.00 1.75
125 126 8.200792 AGAAGAGTTTATGCAAGAGATACGAAT 58.799 33.333 0.00 0.00 0.00 3.34
126 127 7.548097 AGAAGAGTTTATGCAAGAGATACGAA 58.452 34.615 0.00 0.00 0.00 3.85
127 128 7.101652 AGAAGAGTTTATGCAAGAGATACGA 57.898 36.000 0.00 0.00 0.00 3.43
128 129 7.489435 TCAAGAAGAGTTTATGCAAGAGATACG 59.511 37.037 0.00 0.00 0.00 3.06
129 130 8.709386 TCAAGAAGAGTTTATGCAAGAGATAC 57.291 34.615 0.00 0.00 0.00 2.24
130 131 9.155975 GTTCAAGAAGAGTTTATGCAAGAGATA 57.844 33.333 0.00 0.00 0.00 1.98
131 132 7.120432 GGTTCAAGAAGAGTTTATGCAAGAGAT 59.880 37.037 0.00 0.00 0.00 2.75
132 133 6.428159 GGTTCAAGAAGAGTTTATGCAAGAGA 59.572 38.462 0.00 0.00 0.00 3.10
133 134 6.348868 GGGTTCAAGAAGAGTTTATGCAAGAG 60.349 42.308 0.00 0.00 0.00 2.85
134 135 5.473504 GGGTTCAAGAAGAGTTTATGCAAGA 59.526 40.000 0.00 0.00 0.00 3.02
135 136 5.474876 AGGGTTCAAGAAGAGTTTATGCAAG 59.525 40.000 0.00 0.00 0.00 4.01
136 137 5.385198 AGGGTTCAAGAAGAGTTTATGCAA 58.615 37.500 0.00 0.00 0.00 4.08
137 138 4.985538 AGGGTTCAAGAAGAGTTTATGCA 58.014 39.130 0.00 0.00 0.00 3.96
138 139 5.966742 AAGGGTTCAAGAAGAGTTTATGC 57.033 39.130 0.00 0.00 0.00 3.14
139 140 7.510549 TCAAAGGGTTCAAGAAGAGTTTATG 57.489 36.000 0.00 0.00 0.00 1.90
140 141 8.414003 GTTTCAAAGGGTTCAAGAAGAGTTTAT 58.586 33.333 0.00 0.00 0.00 1.40
141 142 7.394923 TGTTTCAAAGGGTTCAAGAAGAGTTTA 59.605 33.333 0.00 0.00 0.00 2.01
142 143 6.210584 TGTTTCAAAGGGTTCAAGAAGAGTTT 59.789 34.615 0.00 0.00 0.00 2.66
143 144 5.714806 TGTTTCAAAGGGTTCAAGAAGAGTT 59.285 36.000 0.00 0.00 0.00 3.01
144 145 5.125578 GTGTTTCAAAGGGTTCAAGAAGAGT 59.874 40.000 0.00 0.00 0.00 3.24
145 146 5.125417 TGTGTTTCAAAGGGTTCAAGAAGAG 59.875 40.000 0.00 0.00 0.00 2.85
146 147 5.013547 TGTGTTTCAAAGGGTTCAAGAAGA 58.986 37.500 0.00 0.00 0.00 2.87
147 148 5.323371 TGTGTTTCAAAGGGTTCAAGAAG 57.677 39.130 0.00 0.00 0.00 2.85
148 149 5.930837 ATGTGTTTCAAAGGGTTCAAGAA 57.069 34.783 0.00 0.00 0.00 2.52
149 150 6.459024 CGTTATGTGTTTCAAAGGGTTCAAGA 60.459 38.462 0.00 0.00 0.00 3.02
150 151 5.685511 CGTTATGTGTTTCAAAGGGTTCAAG 59.314 40.000 0.00 0.00 0.00 3.02
151 152 5.125739 ACGTTATGTGTTTCAAAGGGTTCAA 59.874 36.000 0.00 0.00 0.00 2.69
170 171 6.852858 TGTCAAATTCAGAACATCACGTTA 57.147 33.333 0.00 0.00 38.19 3.18
354 360 9.087424 GATTGTATGTTTCTTTTAGGGCAAATC 57.913 33.333 0.00 0.00 0.00 2.17
359 365 8.825667 TTTTGATTGTATGTTTCTTTTAGGGC 57.174 30.769 0.00 0.00 0.00 5.19
368 374 7.540745 AGCACGGTAATTTTGATTGTATGTTTC 59.459 33.333 0.00 0.00 0.00 2.78
369 375 7.328249 CAGCACGGTAATTTTGATTGTATGTTT 59.672 33.333 0.00 0.00 0.00 2.83
547 563 2.509336 GTCGCAGGGACGGTGATG 60.509 66.667 1.18 0.00 45.65 3.07
548 564 3.771160 GGTCGCAGGGACGGTGAT 61.771 66.667 11.28 0.00 45.65 3.06
595 617 1.627329 GGTAAGAAAAGGACGGGAGGT 59.373 52.381 0.00 0.00 0.00 3.85
710 732 2.031807 CGATCCTCTCGTCGAAAGCTAA 59.968 50.000 0.00 0.00 42.56 3.09
712 734 0.378962 CGATCCTCTCGTCGAAAGCT 59.621 55.000 0.00 0.00 42.56 3.74
723 745 2.516460 CCGGTCGGTCGATCCTCT 60.516 66.667 0.55 0.00 0.00 3.69
936 958 4.162320 CCACCACTACATAACCTGTCTGAT 59.838 45.833 0.00 0.00 39.39 2.90
1736 1761 4.403432 GGACAACATCAATCCACCATCAAT 59.597 41.667 0.00 0.00 32.35 2.57
1761 1786 3.439857 ACAGCAATCCACCAAGTACAT 57.560 42.857 0.00 0.00 0.00 2.29
1942 1977 6.012658 ACATCAATATTTTGTCAGCAACGT 57.987 33.333 0.00 0.00 33.82 3.99
2218 2256 4.921470 TTTTCCGATCAGTTGATTCGAC 57.079 40.909 12.36 0.00 34.37 4.20
2625 2666 2.290367 TGGAAACAAAGCATGACACTCG 59.710 45.455 0.00 0.00 37.44 4.18
2659 2700 3.871006 TCACATGCAGAGTTAAATAGGCG 59.129 43.478 0.00 0.00 0.00 5.52
2949 2990 1.462731 AACATGGCAAAAGCAGCGGA 61.463 50.000 0.00 0.00 0.00 5.54
2952 2993 0.785979 CGAAACATGGCAAAAGCAGC 59.214 50.000 0.00 0.00 0.00 5.25
2966 3007 8.225777 CCTTTACAAACTTATAGTGGTCGAAAC 58.774 37.037 0.00 0.00 0.00 2.78
3088 3132 4.651994 CTGATTCGTTGGAATTAGTGCAC 58.348 43.478 9.40 9.40 42.86 4.57
3604 3648 2.943680 ATGCATCGACCGCAGAGACG 62.944 60.000 15.68 0.00 43.88 4.18
4213 4257 1.936547 GAGCACATAGGGCTTCGAAAG 59.063 52.381 0.00 0.00 42.78 2.62
4246 4290 2.671963 CAGCAGAAGCAGCAGCCA 60.672 61.111 0.00 0.00 45.49 4.75
4466 4553 7.054491 AGCAGGTAATCAAACTGTTGAAAAT 57.946 32.000 0.00 0.00 46.66 1.82
4500 4588 4.942761 AAAACCTGCAACTTCATGTCAT 57.057 36.364 0.00 0.00 0.00 3.06
4505 4593 6.808212 CGAAATGATAAAACCTGCAACTTCAT 59.192 34.615 0.00 0.00 0.00 2.57
4568 4656 2.420129 CGGGTCCATCTTTGTAGGAAGG 60.420 54.545 0.00 0.00 32.30 3.46
4619 4707 1.337260 GCACACGTTCTCTCTGTCCAT 60.337 52.381 0.00 0.00 0.00 3.41
4648 4736 4.486090 CCGACCGTCCTCTATTATTCATG 58.514 47.826 0.00 0.00 0.00 3.07
4649 4737 3.056749 GCCGACCGTCCTCTATTATTCAT 60.057 47.826 0.00 0.00 0.00 2.57
4650 4738 2.295349 GCCGACCGTCCTCTATTATTCA 59.705 50.000 0.00 0.00 0.00 2.57
4651 4739 2.295349 TGCCGACCGTCCTCTATTATTC 59.705 50.000 0.00 0.00 0.00 1.75
4652 4740 2.313317 TGCCGACCGTCCTCTATTATT 58.687 47.619 0.00 0.00 0.00 1.40
4653 4741 1.991121 TGCCGACCGTCCTCTATTAT 58.009 50.000 0.00 0.00 0.00 1.28
4654 4742 1.406539 GTTGCCGACCGTCCTCTATTA 59.593 52.381 0.00 0.00 0.00 0.98
4655 4743 0.175073 GTTGCCGACCGTCCTCTATT 59.825 55.000 0.00 0.00 0.00 1.73
4656 4744 0.683504 AGTTGCCGACCGTCCTCTAT 60.684 55.000 0.00 0.00 0.00 1.98
4657 4745 0.035152 TAGTTGCCGACCGTCCTCTA 60.035 55.000 0.00 0.00 0.00 2.43
4658 4746 1.303888 TAGTTGCCGACCGTCCTCT 60.304 57.895 0.00 0.00 0.00 3.69
4659 4747 1.153881 GTAGTTGCCGACCGTCCTC 60.154 63.158 0.00 0.00 0.00 3.71
4660 4748 1.874345 CTGTAGTTGCCGACCGTCCT 61.874 60.000 0.00 0.00 0.00 3.85
4661 4749 1.445582 CTGTAGTTGCCGACCGTCC 60.446 63.158 0.00 0.00 0.00 4.79
4662 4750 2.092882 GCTGTAGTTGCCGACCGTC 61.093 63.158 0.00 0.00 0.00 4.79
4663 4751 2.048503 GCTGTAGTTGCCGACCGT 60.049 61.111 0.00 0.00 0.00 4.83
4664 4752 3.179265 CGCTGTAGTTGCCGACCG 61.179 66.667 0.00 0.00 0.00 4.79
4665 4753 2.813908 CCGCTGTAGTTGCCGACC 60.814 66.667 0.00 0.00 0.00 4.79
4666 4754 3.488090 GCCGCTGTAGTTGCCGAC 61.488 66.667 0.00 0.00 0.00 4.79
4671 4759 3.047280 TTGCCGCCGCTGTAGTTG 61.047 61.111 0.00 0.00 35.36 3.16
4672 4760 3.047877 GTTGCCGCCGCTGTAGTT 61.048 61.111 0.00 0.00 35.36 2.24
4683 4771 0.041663 ACAATCGTCAAACGTTGCCG 60.042 50.000 0.00 4.80 43.14 5.69
4749 4839 7.064609 CAGTGCTCGAATCTAGTAATGGAAAAA 59.935 37.037 0.00 0.00 0.00 1.94
4760 4850 5.473846 TCCCTATTACAGTGCTCGAATCTAG 59.526 44.000 0.00 0.00 0.00 2.43
4823 4913 9.943163 GAAACCAGATCAAAGCTATAGAAAATC 57.057 33.333 3.21 0.00 0.00 2.17
4827 4917 7.851228 TCTGAAACCAGATCAAAGCTATAGAA 58.149 34.615 3.21 0.00 35.88 2.10
4828 4918 7.423844 TCTGAAACCAGATCAAAGCTATAGA 57.576 36.000 3.21 0.00 35.88 1.98
4829 4919 7.254727 GCTTCTGAAACCAGATCAAAGCTATAG 60.255 40.741 0.00 0.00 40.10 1.31
4830 4920 6.540189 GCTTCTGAAACCAGATCAAAGCTATA 59.460 38.462 0.00 0.00 40.10 1.31
4831 4921 5.356470 GCTTCTGAAACCAGATCAAAGCTAT 59.644 40.000 0.00 0.00 40.10 2.97
4832 4922 4.697352 GCTTCTGAAACCAGATCAAAGCTA 59.303 41.667 0.00 0.00 40.10 3.32
4841 4931 3.117888 ACTCAAAGGCTTCTGAAACCAGA 60.118 43.478 12.07 6.16 38.80 3.86
4844 4934 3.214328 TCACTCAAAGGCTTCTGAAACC 58.786 45.455 0.00 1.52 0.00 3.27
4849 4939 5.192327 ACAATTTCACTCAAAGGCTTCTG 57.808 39.130 0.00 1.59 0.00 3.02
4852 4942 4.280929 GGGTACAATTTCACTCAAAGGCTT 59.719 41.667 0.00 0.00 0.00 4.35
4856 4946 4.459337 GGAGGGGTACAATTTCACTCAAAG 59.541 45.833 0.00 0.00 0.00 2.77
4884 4974 9.926158 TCATTTGCAATAACAAGTACATCATTT 57.074 25.926 0.00 0.00 0.00 2.32
4927 5017 3.610786 TCATTGCACGCGTTTTAGAAA 57.389 38.095 10.22 0.00 0.00 2.52
4928 5018 3.610786 TTCATTGCACGCGTTTTAGAA 57.389 38.095 10.22 7.94 0.00 2.10
4929 5019 3.242772 TGTTTCATTGCACGCGTTTTAGA 60.243 39.130 10.22 0.87 0.00 2.10
4931 5021 3.066369 TGTTTCATTGCACGCGTTTTA 57.934 38.095 10.22 0.00 0.00 1.52
4932 5022 1.914634 TGTTTCATTGCACGCGTTTT 58.085 40.000 10.22 0.00 0.00 2.43
4933 5023 1.914634 TTGTTTCATTGCACGCGTTT 58.085 40.000 10.22 0.00 0.00 3.60
4934 5024 1.851666 CTTTGTTTCATTGCACGCGTT 59.148 42.857 10.22 0.00 0.00 4.84
4935 5025 1.476074 CTTTGTTTCATTGCACGCGT 58.524 45.000 5.58 5.58 0.00 6.01
4936 5026 0.159345 GCTTTGTTTCATTGCACGCG 59.841 50.000 3.53 3.53 0.00 6.01
4937 5027 1.190763 CTGCTTTGTTTCATTGCACGC 59.809 47.619 0.00 0.00 0.00 5.34
4938 5028 2.722629 CTCTGCTTTGTTTCATTGCACG 59.277 45.455 0.00 0.00 0.00 5.34
4939 5029 3.709987 ACTCTGCTTTGTTTCATTGCAC 58.290 40.909 0.00 0.00 0.00 4.57
4940 5030 4.821260 TCTACTCTGCTTTGTTTCATTGCA 59.179 37.500 0.00 0.00 0.00 4.08
4941 5031 5.362556 TCTACTCTGCTTTGTTTCATTGC 57.637 39.130 0.00 0.00 0.00 3.56
4942 5032 8.807667 AAAATCTACTCTGCTTTGTTTCATTG 57.192 30.769 0.00 0.00 0.00 2.82
5038 5128 4.142381 GGGAATCAGCTGGTTGAATGTAAC 60.142 45.833 19.03 0.00 0.00 2.50
5042 5132 2.426024 CTGGGAATCAGCTGGTTGAATG 59.574 50.000 19.03 0.91 36.60 2.67
5061 5151 0.651031 CATGATCTCGCACACAGCTG 59.349 55.000 13.48 13.48 42.61 4.24
5063 5153 0.742281 ACCATGATCTCGCACACAGC 60.742 55.000 0.00 0.00 40.87 4.40
5068 5158 4.631813 AGTCTTTAAACCATGATCTCGCAC 59.368 41.667 0.00 0.00 0.00 5.34
5069 5159 4.832248 AGTCTTTAAACCATGATCTCGCA 58.168 39.130 0.00 0.00 0.00 5.10
5070 5160 5.463724 CCTAGTCTTTAAACCATGATCTCGC 59.536 44.000 0.00 0.00 0.00 5.03
5071 5161 5.986135 CCCTAGTCTTTAAACCATGATCTCG 59.014 44.000 0.00 0.00 0.00 4.04
5072 5162 6.126739 ACCCCTAGTCTTTAAACCATGATCTC 60.127 42.308 0.00 0.00 0.00 2.75
5073 5163 5.731678 ACCCCTAGTCTTTAAACCATGATCT 59.268 40.000 0.00 0.00 0.00 2.75
5074 5164 6.002653 ACCCCTAGTCTTTAAACCATGATC 57.997 41.667 0.00 0.00 0.00 2.92
5075 5165 6.101296 CCTACCCCTAGTCTTTAAACCATGAT 59.899 42.308 0.00 0.00 0.00 2.45
5076 5166 5.427481 CCTACCCCTAGTCTTTAAACCATGA 59.573 44.000 0.00 0.00 0.00 3.07
5077 5167 5.397559 CCCTACCCCTAGTCTTTAAACCATG 60.398 48.000 0.00 0.00 0.00 3.66
5078 5168 4.725304 CCCTACCCCTAGTCTTTAAACCAT 59.275 45.833 0.00 0.00 0.00 3.55
5079 5169 4.106324 CCCTACCCCTAGTCTTTAAACCA 58.894 47.826 0.00 0.00 0.00 3.67
5080 5170 3.457380 CCCCTACCCCTAGTCTTTAAACC 59.543 52.174 0.00 0.00 0.00 3.27
5081 5171 3.457380 CCCCCTACCCCTAGTCTTTAAAC 59.543 52.174 0.00 0.00 0.00 2.01
5082 5172 3.343760 TCCCCCTACCCCTAGTCTTTAAA 59.656 47.826 0.00 0.00 0.00 1.52
5083 5173 2.942118 TCCCCCTACCCCTAGTCTTTAA 59.058 50.000 0.00 0.00 0.00 1.52
5084 5174 2.599697 TCCCCCTACCCCTAGTCTTTA 58.400 52.381 0.00 0.00 0.00 1.85
5085 5175 1.411741 TCCCCCTACCCCTAGTCTTT 58.588 55.000 0.00 0.00 0.00 2.52
5086 5176 1.646442 ATCCCCCTACCCCTAGTCTT 58.354 55.000 0.00 0.00 0.00 3.01
5087 5177 2.080231 GTATCCCCCTACCCCTAGTCT 58.920 57.143 0.00 0.00 0.00 3.24
5088 5178 1.078490 GGTATCCCCCTACCCCTAGTC 59.922 61.905 0.00 0.00 36.00 2.59
5089 5179 1.174343 GGTATCCCCCTACCCCTAGT 58.826 60.000 0.00 0.00 36.00 2.57
5090 5180 1.078989 CAGGTATCCCCCTACCCCTAG 59.921 61.905 0.00 0.00 41.87 3.02
5091 5181 1.173425 CAGGTATCCCCCTACCCCTA 58.827 60.000 0.00 0.00 41.87 3.53
5092 5182 0.939961 ACAGGTATCCCCCTACCCCT 60.940 60.000 0.00 0.00 41.87 4.79
5093 5183 0.473309 GACAGGTATCCCCCTACCCC 60.473 65.000 0.00 0.00 41.87 4.95
5094 5184 0.473309 GGACAGGTATCCCCCTACCC 60.473 65.000 0.00 0.00 41.87 3.69
5095 5185 3.160767 GGACAGGTATCCCCCTACC 57.839 63.158 0.00 0.00 41.34 3.18
5110 5200 2.406596 TGGGTAAGCGTAAATGGGAC 57.593 50.000 0.00 0.00 0.00 4.46
5111 5201 2.925724 CATGGGTAAGCGTAAATGGGA 58.074 47.619 0.00 0.00 0.00 4.37
5112 5202 1.336755 GCATGGGTAAGCGTAAATGGG 59.663 52.381 0.00 0.00 0.00 4.00
5113 5203 1.336755 GGCATGGGTAAGCGTAAATGG 59.663 52.381 0.00 0.00 0.00 3.16
5114 5204 1.336755 GGGCATGGGTAAGCGTAAATG 59.663 52.381 0.00 0.00 0.00 2.32
5115 5205 1.687563 GGGCATGGGTAAGCGTAAAT 58.312 50.000 0.00 0.00 0.00 1.40
5116 5206 0.745128 CGGGCATGGGTAAGCGTAAA 60.745 55.000 0.00 0.00 0.00 2.01
5117 5207 1.153329 CGGGCATGGGTAAGCGTAA 60.153 57.895 0.00 0.00 0.00 3.18
5118 5208 2.300850 GACGGGCATGGGTAAGCGTA 62.301 60.000 0.00 0.00 0.00 4.42
5119 5209 3.675619 GACGGGCATGGGTAAGCGT 62.676 63.158 0.00 0.00 0.00 5.07
5120 5210 2.895372 GACGGGCATGGGTAAGCG 60.895 66.667 0.00 0.00 0.00 4.68
5121 5211 2.112815 GTGACGGGCATGGGTAAGC 61.113 63.158 0.00 0.00 0.00 3.09
5122 5212 1.451387 GGTGACGGGCATGGGTAAG 60.451 63.158 0.00 0.00 0.00 2.34
5123 5213 1.921346 AGGTGACGGGCATGGGTAA 60.921 57.895 0.00 0.00 0.00 2.85
5124 5214 2.285069 AGGTGACGGGCATGGGTA 60.285 61.111 0.00 0.00 0.00 3.69
5125 5215 4.033776 CAGGTGACGGGCATGGGT 62.034 66.667 0.00 0.00 0.00 4.51
5126 5216 3.716195 TCAGGTGACGGGCATGGG 61.716 66.667 0.00 0.00 0.00 4.00
5127 5217 2.436646 GTCAGGTGACGGGCATGG 60.437 66.667 0.00 0.00 35.12 3.66
5135 5225 2.618045 CCCATTTACCCTGTCAGGTGAC 60.618 54.545 17.85 2.99 41.42 3.67
5136 5226 1.633432 CCCATTTACCCTGTCAGGTGA 59.367 52.381 17.85 1.96 41.42 4.02
5137 5227 1.354368 ACCCATTTACCCTGTCAGGTG 59.646 52.381 17.85 11.36 41.42 4.00
5138 5228 1.755200 ACCCATTTACCCTGTCAGGT 58.245 50.000 17.85 8.44 44.37 4.00
5139 5229 2.092592 GGTACCCATTTACCCTGTCAGG 60.093 54.545 12.40 12.40 36.26 3.86
5140 5230 2.574369 TGGTACCCATTTACCCTGTCAG 59.426 50.000 10.07 0.00 40.96 3.51
5141 5231 2.306512 GTGGTACCCATTTACCCTGTCA 59.693 50.000 10.07 0.00 40.96 3.58
5142 5232 2.678769 CGTGGTACCCATTTACCCTGTC 60.679 54.545 10.07 0.00 40.96 3.51
5143 5233 1.279846 CGTGGTACCCATTTACCCTGT 59.720 52.381 10.07 0.00 40.96 4.00
5144 5234 1.407712 CCGTGGTACCCATTTACCCTG 60.408 57.143 10.07 0.00 40.96 4.45
5145 5235 0.913924 CCGTGGTACCCATTTACCCT 59.086 55.000 10.07 0.00 40.96 4.34
5146 5236 0.107066 CCCGTGGTACCCATTTACCC 60.107 60.000 10.07 0.00 40.96 3.69
5147 5237 0.620030 ACCCGTGGTACCCATTTACC 59.380 55.000 10.07 0.00 41.89 2.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.