Multiple sequence alignment - TraesCS6B01G280400

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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 TraesCS6B01G280400 chr6B 100.000 4577 0 0 1 4577 506544784 506549360 0.000000e+00 8453.0
1 TraesCS6B01G280400 chr6B 95.781 237 10 0 1 237 302865855 302866091 2.580000e-102 383.0
2 TraesCS6B01G280400 chr6D 95.006 3524 125 28 240 3729 317855671 317852165 0.000000e+00 5485.0
3 TraesCS6B01G280400 chr6A 94.132 3374 124 31 481 3814 455317703 455314364 0.000000e+00 5066.0
4 TraesCS6B01G280400 chr6A 90.164 244 23 1 239 481 455368237 455367994 2.660000e-82 316.0
5 TraesCS6B01G280400 chr2D 88.959 788 68 7 3807 4577 484937289 484936504 0.000000e+00 955.0
6 TraesCS6B01G280400 chr2D 88.672 768 79 6 3811 4577 417187768 417188528 0.000000e+00 929.0
7 TraesCS6B01G280400 chr2D 88.067 771 75 10 3820 4577 388052806 388052040 0.000000e+00 898.0
8 TraesCS6B01G280400 chr3D 88.175 778 74 6 3809 4570 179464244 179465019 0.000000e+00 911.0
9 TraesCS6B01G280400 chr3D 88.000 775 73 9 3820 4577 305597451 305598222 0.000000e+00 898.0
10 TraesCS6B01G280400 chr3D 85.586 777 93 8 3815 4574 364739718 364740492 0.000000e+00 797.0
11 TraesCS6B01G280400 chr7D 89.043 721 63 5 3871 4577 618331898 618331180 0.000000e+00 880.0
12 TraesCS6B01G280400 chr7D 77.391 460 83 9 3874 4315 615369682 615370138 2.110000e-63 254.0
13 TraesCS6B01G280400 chr2B 85.496 786 95 5 3811 4577 24825580 24826365 0.000000e+00 802.0
14 TraesCS6B01G280400 chr2B 88.542 672 62 2 3814 4470 532551036 532551707 0.000000e+00 800.0
15 TraesCS6B01G280400 chr2B 86.827 539 55 5 3813 4336 682256205 682255668 5.100000e-164 588.0
16 TraesCS6B01G280400 chr2B 96.596 235 8 0 1 235 212381269 212381503 1.540000e-104 390.0
17 TraesCS6B01G280400 chr2B 96.203 237 9 0 1 237 553864744 553864508 5.550000e-104 388.0
18 TraesCS6B01G280400 chr1B 84.316 746 115 2 3833 4577 401468176 401468920 0.000000e+00 728.0
19 TraesCS6B01G280400 chr5B 81.218 772 113 10 3820 4575 27412160 27412915 1.100000e-165 593.0
20 TraesCS6B01G280400 chr5B 82.712 590 82 9 3833 4405 511051498 511050912 1.470000e-139 507.0
21 TraesCS6B01G280400 chr5B 95.816 239 9 1 1 238 207359472 207359710 7.180000e-103 385.0
22 TraesCS6B01G280400 chr5B 96.170 235 9 0 1 235 269926187 269926421 7.180000e-103 385.0
23 TraesCS6B01G280400 chr5B 95.781 237 10 0 1 237 570000778 570000542 2.580000e-102 383.0
24 TraesCS6B01G280400 chr4D 78.360 878 152 32 1490 2344 128168134 128167272 6.740000e-148 534.0
25 TraesCS6B01G280400 chr4D 80.083 241 48 0 2648 2888 128166986 128166746 3.640000e-41 180.0
26 TraesCS6B01G280400 chr4D 78.571 140 28 2 1813 1951 47536194 47536056 1.750000e-14 91.6
27 TraesCS6B01G280400 chr4B 78.698 845 143 33 1490 2311 192059523 192058693 3.140000e-146 529.0
28 TraesCS6B01G280400 chr4B 80.083 241 48 0 2648 2888 192058374 192058134 3.640000e-41 180.0
29 TraesCS6B01G280400 chr4B 78.723 141 28 2 1813 1952 69378373 69378512 4.880000e-15 93.5
30 TraesCS6B01G280400 chr4A 78.656 848 144 32 1487 2311 440181010 440181843 3.140000e-146 529.0
31 TraesCS6B01G280400 chr4A 73.168 928 198 39 2630 3519 440182144 440183058 2.080000e-73 287.0
32 TraesCS6B01G280400 chr4A 76.471 187 42 2 1766 1951 550482981 550482796 2.910000e-17 100.0
33 TraesCS6B01G280400 chr4A 97.222 36 1 0 3850 3885 587170200 587170235 1.370000e-05 62.1
34 TraesCS6B01G280400 chr7B 96.170 235 9 0 1 235 426204142 426203908 7.180000e-103 385.0
35 TraesCS6B01G280400 chr7B 93.676 253 12 3 1 252 565988252 565988501 4.320000e-100 375.0
36 TraesCS6B01G280400 chr3B 96.170 235 9 0 1 235 667303374 667303140 7.180000e-103 385.0


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 TraesCS6B01G280400 chr6B 506544784 506549360 4576 False 8453.0 8453 100.0000 1 4577 1 chr6B.!!$F2 4576
1 TraesCS6B01G280400 chr6D 317852165 317855671 3506 True 5485.0 5485 95.0060 240 3729 1 chr6D.!!$R1 3489
2 TraesCS6B01G280400 chr6A 455314364 455317703 3339 True 5066.0 5066 94.1320 481 3814 1 chr6A.!!$R1 3333
3 TraesCS6B01G280400 chr2D 484936504 484937289 785 True 955.0 955 88.9590 3807 4577 1 chr2D.!!$R2 770
4 TraesCS6B01G280400 chr2D 417187768 417188528 760 False 929.0 929 88.6720 3811 4577 1 chr2D.!!$F1 766
5 TraesCS6B01G280400 chr2D 388052040 388052806 766 True 898.0 898 88.0670 3820 4577 1 chr2D.!!$R1 757
6 TraesCS6B01G280400 chr3D 179464244 179465019 775 False 911.0 911 88.1750 3809 4570 1 chr3D.!!$F1 761
7 TraesCS6B01G280400 chr3D 305597451 305598222 771 False 898.0 898 88.0000 3820 4577 1 chr3D.!!$F2 757
8 TraesCS6B01G280400 chr3D 364739718 364740492 774 False 797.0 797 85.5860 3815 4574 1 chr3D.!!$F3 759
9 TraesCS6B01G280400 chr7D 618331180 618331898 718 True 880.0 880 89.0430 3871 4577 1 chr7D.!!$R1 706
10 TraesCS6B01G280400 chr2B 24825580 24826365 785 False 802.0 802 85.4960 3811 4577 1 chr2B.!!$F1 766
11 TraesCS6B01G280400 chr2B 532551036 532551707 671 False 800.0 800 88.5420 3814 4470 1 chr2B.!!$F3 656
12 TraesCS6B01G280400 chr2B 682255668 682256205 537 True 588.0 588 86.8270 3813 4336 1 chr2B.!!$R2 523
13 TraesCS6B01G280400 chr1B 401468176 401468920 744 False 728.0 728 84.3160 3833 4577 1 chr1B.!!$F1 744
14 TraesCS6B01G280400 chr5B 27412160 27412915 755 False 593.0 593 81.2180 3820 4575 1 chr5B.!!$F1 755
15 TraesCS6B01G280400 chr5B 511050912 511051498 586 True 507.0 507 82.7120 3833 4405 1 chr5B.!!$R1 572
16 TraesCS6B01G280400 chr4D 128166746 128168134 1388 True 357.0 534 79.2215 1490 2888 2 chr4D.!!$R2 1398
17 TraesCS6B01G280400 chr4B 192058134 192059523 1389 True 354.5 529 79.3905 1490 2888 2 chr4B.!!$R1 1398
18 TraesCS6B01G280400 chr4A 440181010 440183058 2048 False 408.0 529 75.9120 1487 3519 2 chr4A.!!$F2 2032

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
431 433 0.322975 TTCTCTCCTGAGCTTGTGCC 59.677 55.0 0.00 0.0 40.03 5.01 F
1134 1152 0.250597 GCCGGAACTACACCAAGGTT 60.251 55.0 5.05 0.0 0.00 3.50 F
1141 1159 0.511221 CTACACCAAGGTTTGCGACG 59.489 55.0 0.00 0.0 0.00 5.12 F
2317 2350 2.349886 GTGCTCATCAAGAACGATCACC 59.650 50.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2197 0.042881 AGGGTGAGGTAGAGGTTCCC 59.957 60.0 0.0 0.0 0.00 3.97 R
2250 2283 1.551908 CCAGCTCCTTGTGCTCCTCT 61.552 60.0 0.0 0.0 38.92 3.69 R
2441 2505 2.160417 GGTAACAATGCAGTCACTGAGC 59.840 50.0 9.7 0.0 32.44 4.26 R
3817 3932 0.031449 AAATGCGACCAACCAAACGG 59.969 50.0 0.0 0.0 0.00 4.44 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
26 27 8.958506 CACATATCCCTAGACTATGTTACTACC 58.041 40.741 8.30 0.00 34.66 3.18
27 28 8.902881 ACATATCCCTAGACTATGTTACTACCT 58.097 37.037 0.00 0.00 33.42 3.08
28 29 9.756571 CATATCCCTAGACTATGTTACTACCTT 57.243 37.037 0.00 0.00 0.00 3.50
29 30 9.978336 ATATCCCTAGACTATGTTACTACCTTC 57.022 37.037 0.00 0.00 0.00 3.46
30 31 7.217028 TCCCTAGACTATGTTACTACCTTCA 57.783 40.000 0.00 0.00 0.00 3.02
31 32 7.823635 TCCCTAGACTATGTTACTACCTTCAT 58.176 38.462 0.00 0.00 0.00 2.57
32 33 8.952602 TCCCTAGACTATGTTACTACCTTCATA 58.047 37.037 0.00 0.00 0.00 2.15
33 34 9.233649 CCCTAGACTATGTTACTACCTTCATAG 57.766 40.741 8.77 8.77 42.80 2.23
36 37 8.466617 AGACTATGTTACTACCTTCATAGTGG 57.533 38.462 17.43 0.00 46.89 4.00
37 38 8.280084 AGACTATGTTACTACCTTCATAGTGGA 58.720 37.037 17.43 0.00 46.89 4.02
38 39 9.080097 GACTATGTTACTACCTTCATAGTGGAT 57.920 37.037 17.43 0.00 46.89 3.41
43 44 9.925545 TGTTACTACCTTCATAGTGGATAGTAA 57.074 33.333 0.00 0.00 36.09 2.24
45 46 9.925545 TTACTACCTTCATAGTGGATAGTAACA 57.074 33.333 0.00 0.00 36.09 2.41
46 47 8.834004 ACTACCTTCATAGTGGATAGTAACAA 57.166 34.615 0.00 0.00 34.02 2.83
47 48 9.263446 ACTACCTTCATAGTGGATAGTAACAAA 57.737 33.333 0.00 0.00 34.02 2.83
50 51 8.603304 ACCTTCATAGTGGATAGTAACAAAAGT 58.397 33.333 0.00 0.00 0.00 2.66
51 52 8.883731 CCTTCATAGTGGATAGTAACAAAAGTG 58.116 37.037 0.00 0.00 0.00 3.16
52 53 9.436957 CTTCATAGTGGATAGTAACAAAAGTGT 57.563 33.333 0.00 0.00 40.75 3.55
53 54 8.771920 TCATAGTGGATAGTAACAAAAGTGTG 57.228 34.615 0.00 0.00 38.27 3.82
54 55 7.822334 TCATAGTGGATAGTAACAAAAGTGTGG 59.178 37.037 0.00 0.00 38.27 4.17
55 56 5.937111 AGTGGATAGTAACAAAAGTGTGGT 58.063 37.500 0.00 0.00 38.27 4.16
56 57 7.069877 AGTGGATAGTAACAAAAGTGTGGTA 57.930 36.000 0.00 0.00 38.27 3.25
57 58 7.511268 AGTGGATAGTAACAAAAGTGTGGTAA 58.489 34.615 0.00 0.00 38.27 2.85
58 59 7.443272 AGTGGATAGTAACAAAAGTGTGGTAAC 59.557 37.037 0.00 0.00 38.27 2.50
82 83 9.777297 AACATGCAAAGTTTCATTTATTAGGTT 57.223 25.926 0.00 0.00 0.00 3.50
102 103 9.725019 TTAGGTTATAGACTCATATTGCATTGG 57.275 33.333 0.00 0.00 0.00 3.16
103 104 7.170965 AGGTTATAGACTCATATTGCATTGGG 58.829 38.462 0.00 0.00 0.00 4.12
104 105 7.017551 AGGTTATAGACTCATATTGCATTGGGA 59.982 37.037 0.00 0.00 0.00 4.37
105 106 7.119846 GGTTATAGACTCATATTGCATTGGGAC 59.880 40.741 0.00 0.00 0.00 4.46
106 107 4.508551 AGACTCATATTGCATTGGGACA 57.491 40.909 0.00 0.00 0.00 4.02
107 108 5.057843 AGACTCATATTGCATTGGGACAT 57.942 39.130 0.00 0.00 39.30 3.06
108 109 4.825634 AGACTCATATTGCATTGGGACATG 59.174 41.667 0.00 0.00 39.30 3.21
109 110 4.539726 ACTCATATTGCATTGGGACATGT 58.460 39.130 0.00 0.00 39.30 3.21
110 111 4.340097 ACTCATATTGCATTGGGACATGTG 59.660 41.667 1.15 0.00 39.30 3.21
111 112 4.534797 TCATATTGCATTGGGACATGTGA 58.465 39.130 1.15 0.00 39.30 3.58
112 113 5.141910 TCATATTGCATTGGGACATGTGAT 58.858 37.500 1.15 0.00 39.30 3.06
113 114 3.812156 ATTGCATTGGGACATGTGATG 57.188 42.857 1.15 3.48 39.30 3.07
115 116 2.527497 TGCATTGGGACATGTGATGTT 58.473 42.857 1.15 0.00 45.03 2.71
116 117 3.694926 TGCATTGGGACATGTGATGTTA 58.305 40.909 1.15 0.00 45.03 2.41
117 118 3.443329 TGCATTGGGACATGTGATGTTAC 59.557 43.478 1.15 0.00 45.03 2.50
118 119 3.443329 GCATTGGGACATGTGATGTTACA 59.557 43.478 1.15 0.00 45.03 2.41
119 120 4.439153 GCATTGGGACATGTGATGTTACAG 60.439 45.833 1.15 0.00 45.03 2.74
120 121 4.365514 TTGGGACATGTGATGTTACAGT 57.634 40.909 1.15 0.00 45.03 3.55
121 122 5.491323 TTGGGACATGTGATGTTACAGTA 57.509 39.130 1.15 0.00 45.03 2.74
122 123 5.491323 TGGGACATGTGATGTTACAGTAA 57.509 39.130 1.15 0.00 45.03 2.24
123 124 5.242434 TGGGACATGTGATGTTACAGTAAC 58.758 41.667 15.58 15.58 45.03 2.50
124 125 5.012664 TGGGACATGTGATGTTACAGTAACT 59.987 40.000 21.56 9.41 45.03 2.24
125 126 6.211785 TGGGACATGTGATGTTACAGTAACTA 59.788 38.462 21.56 10.50 45.03 2.24
126 127 6.757010 GGGACATGTGATGTTACAGTAACTAG 59.243 42.308 21.56 8.25 45.03 2.57
127 128 6.255887 GGACATGTGATGTTACAGTAACTAGC 59.744 42.308 21.56 12.59 45.03 3.42
128 129 6.936279 ACATGTGATGTTACAGTAACTAGCT 58.064 36.000 21.56 6.57 41.63 3.32
129 130 8.063200 ACATGTGATGTTACAGTAACTAGCTA 57.937 34.615 21.56 4.25 41.63 3.32
130 131 8.528643 ACATGTGATGTTACAGTAACTAGCTAA 58.471 33.333 21.56 3.59 41.63 3.09
131 132 9.025020 CATGTGATGTTACAGTAACTAGCTAAG 57.975 37.037 21.56 6.36 39.38 2.18
132 133 8.118976 TGTGATGTTACAGTAACTAGCTAAGT 57.881 34.615 21.56 0.00 41.49 2.24
154 155 7.868906 AGTTACTGTAACTACATCTCTCCTC 57.131 40.000 27.01 0.04 46.53 3.71
155 156 7.403671 AGTTACTGTAACTACATCTCTCCTCA 58.596 38.462 27.01 0.00 46.53 3.86
156 157 8.056400 AGTTACTGTAACTACATCTCTCCTCAT 58.944 37.037 27.01 2.44 46.53 2.90
157 158 8.688151 GTTACTGTAACTACATCTCTCCTCATT 58.312 37.037 20.50 0.00 35.36 2.57
158 159 9.916360 TTACTGTAACTACATCTCTCCTCATTA 57.084 33.333 0.00 0.00 35.36 1.90
159 160 8.824756 ACTGTAACTACATCTCTCCTCATTAA 57.175 34.615 0.00 0.00 35.36 1.40
160 161 8.688151 ACTGTAACTACATCTCTCCTCATTAAC 58.312 37.037 0.00 0.00 35.36 2.01
161 162 8.824756 TGTAACTACATCTCTCCTCATTAACT 57.175 34.615 0.00 0.00 0.00 2.24
162 163 8.904834 TGTAACTACATCTCTCCTCATTAACTC 58.095 37.037 0.00 0.00 0.00 3.01
163 164 7.962995 AACTACATCTCTCCTCATTAACTCA 57.037 36.000 0.00 0.00 0.00 3.41
164 165 7.341445 ACTACATCTCTCCTCATTAACTCAC 57.659 40.000 0.00 0.00 0.00 3.51
165 166 7.122715 ACTACATCTCTCCTCATTAACTCACT 58.877 38.462 0.00 0.00 0.00 3.41
166 167 6.219417 ACATCTCTCCTCATTAACTCACTG 57.781 41.667 0.00 0.00 0.00 3.66
167 168 4.727507 TCTCTCCTCATTAACTCACTGC 57.272 45.455 0.00 0.00 0.00 4.40
168 169 3.449018 TCTCTCCTCATTAACTCACTGCC 59.551 47.826 0.00 0.00 0.00 4.85
169 170 3.173151 TCTCCTCATTAACTCACTGCCA 58.827 45.455 0.00 0.00 0.00 4.92
170 171 3.055819 TCTCCTCATTAACTCACTGCCAC 60.056 47.826 0.00 0.00 0.00 5.01
171 172 2.637382 TCCTCATTAACTCACTGCCACA 59.363 45.455 0.00 0.00 0.00 4.17
172 173 3.264193 TCCTCATTAACTCACTGCCACAT 59.736 43.478 0.00 0.00 0.00 3.21
173 174 4.469586 TCCTCATTAACTCACTGCCACATA 59.530 41.667 0.00 0.00 0.00 2.29
174 175 5.045942 TCCTCATTAACTCACTGCCACATAA 60.046 40.000 0.00 0.00 0.00 1.90
175 176 5.295292 CCTCATTAACTCACTGCCACATAAG 59.705 44.000 0.00 0.00 0.00 1.73
176 177 4.635765 TCATTAACTCACTGCCACATAAGC 59.364 41.667 0.00 0.00 0.00 3.09
177 178 2.566833 AACTCACTGCCACATAAGCA 57.433 45.000 0.00 0.00 38.82 3.91
178 179 2.566833 ACTCACTGCCACATAAGCAA 57.433 45.000 0.00 0.00 40.35 3.91
179 180 2.862541 ACTCACTGCCACATAAGCAAA 58.137 42.857 0.00 0.00 40.35 3.68
180 181 3.424703 ACTCACTGCCACATAAGCAAAT 58.575 40.909 0.00 0.00 40.35 2.32
181 182 3.828451 ACTCACTGCCACATAAGCAAATT 59.172 39.130 0.00 0.00 40.35 1.82
182 183 4.281688 ACTCACTGCCACATAAGCAAATTT 59.718 37.500 0.00 0.00 40.35 1.82
183 184 4.558178 TCACTGCCACATAAGCAAATTTG 58.442 39.130 14.03 14.03 40.35 2.32
198 199 4.935702 CAAATTTGCTGAGTTGGACTTGA 58.064 39.130 5.01 0.00 0.00 3.02
199 200 5.535333 CAAATTTGCTGAGTTGGACTTGAT 58.465 37.500 5.01 0.00 0.00 2.57
200 201 4.778534 ATTTGCTGAGTTGGACTTGATG 57.221 40.909 0.00 0.00 0.00 3.07
201 202 2.936919 TGCTGAGTTGGACTTGATGT 57.063 45.000 0.00 0.00 0.00 3.06
202 203 3.213206 TGCTGAGTTGGACTTGATGTT 57.787 42.857 0.00 0.00 0.00 2.71
203 204 4.350368 TGCTGAGTTGGACTTGATGTTA 57.650 40.909 0.00 0.00 0.00 2.41
204 205 4.065088 TGCTGAGTTGGACTTGATGTTAC 58.935 43.478 0.00 0.00 0.00 2.50
205 206 4.202357 TGCTGAGTTGGACTTGATGTTACT 60.202 41.667 0.00 0.00 0.00 2.24
206 207 4.153117 GCTGAGTTGGACTTGATGTTACTG 59.847 45.833 0.00 0.00 0.00 2.74
207 208 4.065088 TGAGTTGGACTTGATGTTACTGC 58.935 43.478 0.00 0.00 0.00 4.40
208 209 4.202357 TGAGTTGGACTTGATGTTACTGCT 60.202 41.667 0.00 0.00 0.00 4.24
209 210 4.067896 AGTTGGACTTGATGTTACTGCTG 58.932 43.478 0.00 0.00 0.00 4.41
210 211 4.065088 GTTGGACTTGATGTTACTGCTGA 58.935 43.478 0.00 0.00 0.00 4.26
211 212 4.350368 TGGACTTGATGTTACTGCTGAA 57.650 40.909 0.00 0.00 0.00 3.02
212 213 4.318332 TGGACTTGATGTTACTGCTGAAG 58.682 43.478 0.00 0.00 0.00 3.02
213 214 4.202357 TGGACTTGATGTTACTGCTGAAGT 60.202 41.667 0.00 0.00 43.40 3.01
214 215 4.757149 GGACTTGATGTTACTGCTGAAGTT 59.243 41.667 0.00 0.00 40.56 2.66
215 216 5.932303 GGACTTGATGTTACTGCTGAAGTTA 59.068 40.000 0.00 0.00 40.56 2.24
216 217 6.128526 GGACTTGATGTTACTGCTGAAGTTAC 60.129 42.308 0.00 0.00 40.56 2.50
217 218 6.525629 ACTTGATGTTACTGCTGAAGTTACT 58.474 36.000 6.50 0.00 38.87 2.24
218 219 6.992715 ACTTGATGTTACTGCTGAAGTTACTT 59.007 34.615 6.50 0.00 38.87 2.24
219 220 7.499232 ACTTGATGTTACTGCTGAAGTTACTTT 59.501 33.333 6.50 0.00 38.87 2.66
220 221 7.421530 TGATGTTACTGCTGAAGTTACTTTC 57.578 36.000 6.50 4.60 38.87 2.62
221 222 6.989759 TGATGTTACTGCTGAAGTTACTTTCA 59.010 34.615 6.50 6.73 38.87 2.69
222 223 6.598753 TGTTACTGCTGAAGTTACTTTCAC 57.401 37.500 6.50 0.00 38.87 3.18
223 224 6.346096 TGTTACTGCTGAAGTTACTTTCACT 58.654 36.000 6.50 0.00 38.87 3.41
224 225 7.494211 TGTTACTGCTGAAGTTACTTTCACTA 58.506 34.615 6.50 0.00 38.87 2.74
225 226 8.148351 TGTTACTGCTGAAGTTACTTTCACTAT 58.852 33.333 6.50 0.00 38.87 2.12
226 227 8.436200 GTTACTGCTGAAGTTACTTTCACTATG 58.564 37.037 0.00 0.00 40.56 2.23
227 228 5.934625 ACTGCTGAAGTTACTTTCACTATGG 59.065 40.000 0.00 0.00 34.57 2.74
228 229 4.695455 TGCTGAAGTTACTTTCACTATGGC 59.305 41.667 0.00 0.26 33.71 4.40
229 230 4.938226 GCTGAAGTTACTTTCACTATGGCT 59.062 41.667 0.00 0.00 33.71 4.75
230 231 6.106673 GCTGAAGTTACTTTCACTATGGCTA 58.893 40.000 0.00 0.00 33.71 3.93
231 232 6.256757 GCTGAAGTTACTTTCACTATGGCTAG 59.743 42.308 0.00 0.00 33.71 3.42
232 233 7.241042 TGAAGTTACTTTCACTATGGCTAGT 57.759 36.000 0.00 0.00 38.79 2.57
233 234 7.321153 TGAAGTTACTTTCACTATGGCTAGTC 58.679 38.462 0.00 0.00 35.99 2.59
234 235 7.178628 TGAAGTTACTTTCACTATGGCTAGTCT 59.821 37.037 0.00 0.00 35.99 3.24
235 236 7.483580 AGTTACTTTCACTATGGCTAGTCTT 57.516 36.000 0.00 0.00 35.99 3.01
236 237 8.591114 AGTTACTTTCACTATGGCTAGTCTTA 57.409 34.615 0.00 0.00 35.99 2.10
237 238 8.468399 AGTTACTTTCACTATGGCTAGTCTTAC 58.532 37.037 0.00 0.00 35.99 2.34
238 239 6.223351 ACTTTCACTATGGCTAGTCTTACC 57.777 41.667 0.00 0.00 35.99 2.85
291 292 5.124776 TGCAGTAAGTAATTGGGTATTGTGC 59.875 40.000 0.00 0.00 0.00 4.57
296 297 2.869233 AATTGGGTATTGTGCGCATC 57.131 45.000 15.91 8.33 0.00 3.91
313 314 2.693069 CATCAATCGATGTAGAGGGCC 58.307 52.381 0.00 0.00 43.52 5.80
342 343 9.772973 GATTTTAACCCTGTTTTTAACCTTGAT 57.227 29.630 0.00 0.00 0.00 2.57
345 346 8.999905 TTAACCCTGTTTTTAACCTTGATAGT 57.000 30.769 0.00 0.00 0.00 2.12
357 358 4.973168 ACCTTGATAGTTGACAAGCTGAA 58.027 39.130 0.00 0.00 41.15 3.02
387 388 4.261614 CCTCTGTTTCTTTTGTTGTAGGCC 60.262 45.833 0.00 0.00 0.00 5.19
406 408 2.413634 GCCAACGTATTACAAGTGTGCC 60.414 50.000 0.00 0.00 0.00 5.01
431 433 0.322975 TTCTCTCCTGAGCTTGTGCC 59.677 55.000 0.00 0.00 40.03 5.01
437 439 2.432146 CTCCTGAGCTTGTGCCTGTATA 59.568 50.000 0.00 0.00 40.80 1.47
440 442 3.397482 CTGAGCTTGTGCCTGTATATCC 58.603 50.000 0.00 0.00 40.80 2.59
447 449 0.389817 TGCCTGTATATCCGCGATGC 60.390 55.000 8.23 0.00 0.00 3.91
449 451 1.350193 CCTGTATATCCGCGATGCAC 58.650 55.000 8.23 0.00 0.00 4.57
461 463 3.487376 CCGCGATGCACAATCAATTAACT 60.487 43.478 8.23 0.00 34.68 2.24
466 468 6.432936 CGATGCACAATCAATTAACTGCTAT 58.567 36.000 0.00 0.00 34.68 2.97
483 485 7.725818 ACTGCTATAATGATGATCTGTTGTG 57.274 36.000 0.00 0.00 0.00 3.33
490 492 1.131883 GATGATCTGTTGTGCTGGTGC 59.868 52.381 0.00 0.00 40.20 5.01
492 494 0.801251 GATCTGTTGTGCTGGTGCTC 59.199 55.000 0.00 0.00 40.48 4.26
510 512 3.128589 TGCTCGGGATCAAAATTTAGTGC 59.871 43.478 0.00 0.00 0.00 4.40
535 537 7.587037 TCATTTCAGTGAGAACCAAGAAAAT 57.413 32.000 0.00 0.00 35.83 1.82
544 546 6.589907 GTGAGAACCAAGAAAATTGTTTGTGT 59.410 34.615 0.00 0.00 0.00 3.72
549 551 8.608844 AACCAAGAAAATTGTTTGTGTACAAA 57.391 26.923 6.11 6.11 41.02 2.83
550 552 8.785329 ACCAAGAAAATTGTTTGTGTACAAAT 57.215 26.923 12.72 0.00 46.12 2.32
551 553 8.663911 ACCAAGAAAATTGTTTGTGTACAAATG 58.336 29.630 12.72 4.71 46.12 2.32
552 554 8.663911 CCAAGAAAATTGTTTGTGTACAAATGT 58.336 29.630 12.72 1.14 46.12 2.71
575 577 4.797471 ACAGTGCAACGAACGTATTAGTA 58.203 39.130 0.00 0.00 45.86 1.82
576 578 4.855388 ACAGTGCAACGAACGTATTAGTAG 59.145 41.667 0.00 0.00 45.86 2.57
577 579 3.855950 AGTGCAACGAACGTATTAGTAGC 59.144 43.478 0.00 0.00 45.86 3.58
578 580 3.855950 GTGCAACGAACGTATTAGTAGCT 59.144 43.478 0.00 0.00 0.00 3.32
579 581 3.855379 TGCAACGAACGTATTAGTAGCTG 59.145 43.478 0.00 0.00 0.00 4.24
634 636 1.905215 CACAGGAGAGATGGGTTGTCT 59.095 52.381 0.00 0.00 0.00 3.41
643 645 0.921896 ATGGGTTGTCTCTGGATGGG 59.078 55.000 0.00 0.00 0.00 4.00
649 651 0.835276 TGTCTCTGGATGGGAGCATG 59.165 55.000 0.00 0.00 0.00 4.06
713 715 1.593196 GCGCATTCAGCCATACCTTA 58.407 50.000 0.30 0.00 41.38 2.69
717 719 3.434641 CGCATTCAGCCATACCTTATCAG 59.565 47.826 0.00 0.00 41.38 2.90
721 730 2.972713 TCAGCCATACCTTATCAGGGAC 59.027 50.000 0.00 0.00 46.01 4.46
795 804 5.136020 CAGATCTCATCTTTAAATTCGCGC 58.864 41.667 0.00 0.00 37.58 6.86
908 920 2.031870 GTTCAAAGGACCCATATGGCC 58.968 52.381 16.97 12.97 37.83 5.36
1037 1055 0.962356 CATTGCGTCCTCTTGGCCTT 60.962 55.000 3.32 0.00 0.00 4.35
1134 1152 0.250597 GCCGGAACTACACCAAGGTT 60.251 55.000 5.05 0.00 0.00 3.50
1141 1159 0.511221 CTACACCAAGGTTTGCGACG 59.489 55.000 0.00 0.00 0.00 5.12
2317 2350 2.349886 GTGCTCATCAAGAACGATCACC 59.650 50.000 0.00 0.00 0.00 4.02
2514 2587 2.346766 AACCATGCAGAGTTGTGACA 57.653 45.000 3.49 0.00 0.00 3.58
2517 2590 1.596603 CATGCAGAGTTGTGACACCA 58.403 50.000 2.45 0.00 0.00 4.17
2613 2686 2.241880 CGTGAAAACCGTGGACGCT 61.242 57.895 0.00 0.00 38.18 5.07
2888 2961 4.931661 TCGGAAGATACAATCCAGGTAC 57.068 45.455 0.00 0.00 35.34 3.34
2894 2970 7.308469 CGGAAGATACAATCCAGGTACTACTAC 60.308 44.444 0.00 0.00 36.02 2.73
2933 3011 7.562454 TCGATTCCTTGGTGTATTTTTATCC 57.438 36.000 0.00 0.00 0.00 2.59
3176 3271 2.032071 GGTCACAGTCCCGGTTGG 59.968 66.667 0.00 0.00 0.00 3.77
3447 3548 3.253955 GTGCCGTTCACGCTCAAT 58.746 55.556 0.00 0.00 35.76 2.57
3669 3778 0.174845 GATACTGTGGGCAGCACGTA 59.825 55.000 0.00 0.00 46.30 3.57
3684 3793 6.159988 GCAGCACGTATAATATCTTCTCCTT 58.840 40.000 0.00 0.00 0.00 3.36
3686 3795 7.171678 GCAGCACGTATAATATCTTCTCCTTTT 59.828 37.037 0.00 0.00 0.00 2.27
3751 3866 2.227388 CACAGTTTTCACATCCCAGCTC 59.773 50.000 0.00 0.00 0.00 4.09
3765 3880 5.659440 TCCCAGCTCCAAAAATATCAAAC 57.341 39.130 0.00 0.00 0.00 2.93
3776 3891 8.573035 TCCAAAAATATCAAACGAAAACTAGCT 58.427 29.630 0.00 0.00 0.00 3.32
3799 3914 8.915654 AGCTCTAAAAATCGTTTTTGCTATTTG 58.084 29.630 10.72 0.00 42.41 2.32
3836 3951 0.031449 CCGTTTGGTTGGTCGCATTT 59.969 50.000 0.00 0.00 0.00 2.32
3930 4045 1.831580 GAACATCAAAGCAGGCCTCT 58.168 50.000 0.00 0.00 0.00 3.69
4037 4171 2.766313 TGACGCAACTGCTCATAACTT 58.234 42.857 0.00 0.00 39.32 2.66
4046 4180 0.107654 GCTCATAACTTCCCACGCCT 60.108 55.000 0.00 0.00 0.00 5.52
4051 4185 1.640917 TAACTTCCCACGCCTTCTCT 58.359 50.000 0.00 0.00 0.00 3.10
4129 4263 1.003839 TTTCTTCGATGGCCACGCT 60.004 52.632 8.16 0.00 0.00 5.07
4462 4603 3.264845 GGTGCAAGGGGAGGGGAA 61.265 66.667 0.00 0.00 0.00 3.97
4475 4616 3.379445 GGGAACTCGAGGACGCCA 61.379 66.667 18.41 0.00 39.58 5.69
4546 4687 1.987807 ATGGCCGGGACCTCTTCATG 61.988 60.000 2.18 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.958506 GGTAGTAACATAGTCTAGGGATATGTG 58.041 40.741 12.94 0.00 39.46 3.21
2 3 9.756571 AAGGTAGTAACATAGTCTAGGGATATG 57.243 37.037 0.00 7.70 33.93 1.78
3 4 9.978336 GAAGGTAGTAACATAGTCTAGGGATAT 57.022 37.037 0.00 0.00 0.00 1.63
6 7 7.217028 TGAAGGTAGTAACATAGTCTAGGGA 57.783 40.000 0.00 0.00 0.00 4.20
7 8 9.233649 CTATGAAGGTAGTAACATAGTCTAGGG 57.766 40.741 0.00 0.00 38.06 3.53
8 9 9.796180 ACTATGAAGGTAGTAACATAGTCTAGG 57.204 37.037 0.00 0.00 46.61 3.02
11 12 8.280084 TCCACTATGAAGGTAGTAACATAGTCT 58.720 37.037 13.37 0.00 46.61 3.24
12 13 8.461249 TCCACTATGAAGGTAGTAACATAGTC 57.539 38.462 13.37 0.00 46.61 2.59
17 18 9.925545 TTACTATCCACTATGAAGGTAGTAACA 57.074 33.333 0.00 0.00 33.78 2.41
19 20 9.925545 TGTTACTATCCACTATGAAGGTAGTAA 57.074 33.333 0.00 0.00 34.88 2.24
20 21 9.925545 TTGTTACTATCCACTATGAAGGTAGTA 57.074 33.333 0.00 0.00 33.29 1.82
21 22 8.834004 TTGTTACTATCCACTATGAAGGTAGT 57.166 34.615 0.00 0.00 35.34 2.73
24 25 8.603304 ACTTTTGTTACTATCCACTATGAAGGT 58.397 33.333 0.00 0.00 0.00 3.50
25 26 8.883731 CACTTTTGTTACTATCCACTATGAAGG 58.116 37.037 0.00 0.00 0.00 3.46
26 27 9.436957 ACACTTTTGTTACTATCCACTATGAAG 57.563 33.333 0.00 0.00 28.43 3.02
27 28 9.214957 CACACTTTTGTTACTATCCACTATGAA 57.785 33.333 0.00 0.00 31.66 2.57
28 29 7.822334 CCACACTTTTGTTACTATCCACTATGA 59.178 37.037 0.00 0.00 31.66 2.15
29 30 7.606456 ACCACACTTTTGTTACTATCCACTATG 59.394 37.037 0.00 0.00 31.66 2.23
30 31 7.686434 ACCACACTTTTGTTACTATCCACTAT 58.314 34.615 0.00 0.00 31.66 2.12
31 32 7.069877 ACCACACTTTTGTTACTATCCACTA 57.930 36.000 0.00 0.00 31.66 2.74
32 33 5.937111 ACCACACTTTTGTTACTATCCACT 58.063 37.500 0.00 0.00 31.66 4.00
33 34 7.227116 TGTTACCACACTTTTGTTACTATCCAC 59.773 37.037 0.00 0.00 31.66 4.02
34 35 7.281098 TGTTACCACACTTTTGTTACTATCCA 58.719 34.615 0.00 0.00 31.66 3.41
35 36 7.733402 TGTTACCACACTTTTGTTACTATCC 57.267 36.000 0.00 0.00 31.66 2.59
36 37 7.749126 GCATGTTACCACACTTTTGTTACTATC 59.251 37.037 0.00 0.00 35.03 2.08
37 38 7.229707 TGCATGTTACCACACTTTTGTTACTAT 59.770 33.333 0.00 0.00 35.03 2.12
38 39 6.542735 TGCATGTTACCACACTTTTGTTACTA 59.457 34.615 0.00 0.00 35.03 1.82
39 40 5.358442 TGCATGTTACCACACTTTTGTTACT 59.642 36.000 0.00 0.00 35.03 2.24
40 41 5.583495 TGCATGTTACCACACTTTTGTTAC 58.417 37.500 0.00 0.00 35.03 2.50
41 42 5.836821 TGCATGTTACCACACTTTTGTTA 57.163 34.783 0.00 0.00 35.03 2.41
42 43 4.727507 TGCATGTTACCACACTTTTGTT 57.272 36.364 0.00 0.00 35.03 2.83
43 44 4.727507 TTGCATGTTACCACACTTTTGT 57.272 36.364 0.00 0.00 35.03 2.83
44 45 5.108517 ACTTTGCATGTTACCACACTTTTG 58.891 37.500 0.00 0.00 35.03 2.44
45 46 5.337578 ACTTTGCATGTTACCACACTTTT 57.662 34.783 0.00 0.00 35.03 2.27
46 47 5.337578 AACTTTGCATGTTACCACACTTT 57.662 34.783 4.11 0.00 35.03 2.66
47 48 5.105554 TGAAACTTTGCATGTTACCACACTT 60.106 36.000 6.11 0.00 35.03 3.16
48 49 4.400884 TGAAACTTTGCATGTTACCACACT 59.599 37.500 6.11 0.00 35.03 3.55
49 50 4.677584 TGAAACTTTGCATGTTACCACAC 58.322 39.130 6.11 0.00 35.03 3.82
50 51 4.991153 TGAAACTTTGCATGTTACCACA 57.009 36.364 6.11 3.43 37.31 4.17
51 52 6.843069 AAATGAAACTTTGCATGTTACCAC 57.157 33.333 6.11 1.45 0.00 4.16
56 57 9.777297 AACCTAATAAATGAAACTTTGCATGTT 57.223 25.926 0.00 0.00 0.00 2.71
76 77 9.725019 CCAATGCAATATGAGTCTATAACCTAA 57.275 33.333 0.00 0.00 0.00 2.69
77 78 8.321353 CCCAATGCAATATGAGTCTATAACCTA 58.679 37.037 0.00 0.00 0.00 3.08
78 79 7.017551 TCCCAATGCAATATGAGTCTATAACCT 59.982 37.037 0.00 0.00 0.00 3.50
79 80 7.119846 GTCCCAATGCAATATGAGTCTATAACC 59.880 40.741 0.00 0.00 0.00 2.85
80 81 7.661437 TGTCCCAATGCAATATGAGTCTATAAC 59.339 37.037 0.00 0.00 0.00 1.89
81 82 7.744733 TGTCCCAATGCAATATGAGTCTATAA 58.255 34.615 0.00 0.00 0.00 0.98
82 83 7.315066 TGTCCCAATGCAATATGAGTCTATA 57.685 36.000 0.00 0.00 0.00 1.31
83 84 6.191657 TGTCCCAATGCAATATGAGTCTAT 57.808 37.500 0.00 0.00 0.00 1.98
84 85 5.628797 TGTCCCAATGCAATATGAGTCTA 57.371 39.130 0.00 0.00 0.00 2.59
85 86 4.508551 TGTCCCAATGCAATATGAGTCT 57.491 40.909 0.00 0.00 0.00 3.24
86 87 4.581824 ACATGTCCCAATGCAATATGAGTC 59.418 41.667 0.00 0.00 0.00 3.36
87 88 4.340097 CACATGTCCCAATGCAATATGAGT 59.660 41.667 0.00 0.00 0.00 3.41
88 89 4.581409 TCACATGTCCCAATGCAATATGAG 59.419 41.667 0.00 0.00 0.00 2.90
89 90 4.534797 TCACATGTCCCAATGCAATATGA 58.465 39.130 0.00 0.00 0.00 2.15
90 91 4.922471 TCACATGTCCCAATGCAATATG 57.078 40.909 0.00 0.00 0.00 1.78
91 92 4.897076 ACATCACATGTCCCAATGCAATAT 59.103 37.500 0.00 0.00 39.92 1.28
92 93 4.279982 ACATCACATGTCCCAATGCAATA 58.720 39.130 0.00 0.00 39.92 1.90
93 94 3.101437 ACATCACATGTCCCAATGCAAT 58.899 40.909 0.00 0.00 39.92 3.56
94 95 2.527497 ACATCACATGTCCCAATGCAA 58.473 42.857 0.00 0.00 39.92 4.08
95 96 2.219080 ACATCACATGTCCCAATGCA 57.781 45.000 0.00 0.00 39.92 3.96
96 97 3.443329 TGTAACATCACATGTCCCAATGC 59.557 43.478 0.00 0.00 44.07 3.56
97 98 4.701651 ACTGTAACATCACATGTCCCAATG 59.298 41.667 0.00 0.45 44.07 2.82
98 99 4.922206 ACTGTAACATCACATGTCCCAAT 58.078 39.130 0.00 0.00 44.07 3.16
99 100 4.365514 ACTGTAACATCACATGTCCCAA 57.634 40.909 0.00 0.00 44.07 4.12
100 101 5.012664 AGTTACTGTAACATCACATGTCCCA 59.987 40.000 27.12 0.00 44.07 4.37
101 102 5.488341 AGTTACTGTAACATCACATGTCCC 58.512 41.667 27.12 1.55 44.07 4.46
102 103 6.255887 GCTAGTTACTGTAACATCACATGTCC 59.744 42.308 27.12 1.73 44.07 4.02
103 104 7.036220 AGCTAGTTACTGTAACATCACATGTC 58.964 38.462 27.12 9.51 44.07 3.06
105 106 8.926715 TTAGCTAGTTACTGTAACATCACATG 57.073 34.615 27.12 12.57 41.07 3.21
106 107 8.750298 ACTTAGCTAGTTACTGTAACATCACAT 58.250 33.333 27.12 11.85 41.07 3.21
107 108 8.118976 ACTTAGCTAGTTACTGTAACATCACA 57.881 34.615 27.12 10.61 41.07 3.58
108 109 8.983307 AACTTAGCTAGTTACTGTAACATCAC 57.017 34.615 27.12 15.70 45.22 3.06
122 123 9.683870 AGATGTAGTTACAGTAACTTAGCTAGT 57.316 33.333 27.29 9.99 46.27 2.57
124 125 9.902684 AGAGATGTAGTTACAGTAACTTAGCTA 57.097 33.333 27.29 9.61 46.27 3.32
125 126 8.810990 AGAGATGTAGTTACAGTAACTTAGCT 57.189 34.615 27.29 23.02 46.27 3.32
126 127 8.130469 GGAGAGATGTAGTTACAGTAACTTAGC 58.870 40.741 27.29 19.58 46.27 3.09
127 128 9.398538 AGGAGAGATGTAGTTACAGTAACTTAG 57.601 37.037 27.29 0.00 46.27 2.18
128 129 9.393512 GAGGAGAGATGTAGTTACAGTAACTTA 57.606 37.037 27.29 18.24 46.27 2.24
129 130 7.889073 TGAGGAGAGATGTAGTTACAGTAACTT 59.111 37.037 27.29 12.68 46.27 2.66
131 132 7.627298 TGAGGAGAGATGTAGTTACAGTAAC 57.373 40.000 14.76 14.76 39.92 2.50
132 133 8.824756 AATGAGGAGAGATGTAGTTACAGTAA 57.175 34.615 0.00 0.00 39.92 2.24
133 134 9.916360 TTAATGAGGAGAGATGTAGTTACAGTA 57.084 33.333 0.00 0.00 39.92 2.74
134 135 8.688151 GTTAATGAGGAGAGATGTAGTTACAGT 58.312 37.037 0.00 0.00 39.92 3.55
135 136 8.908903 AGTTAATGAGGAGAGATGTAGTTACAG 58.091 37.037 0.00 0.00 39.92 2.74
136 137 8.824756 AGTTAATGAGGAGAGATGTAGTTACA 57.175 34.615 0.00 0.00 40.98 2.41
137 138 8.904834 TGAGTTAATGAGGAGAGATGTAGTTAC 58.095 37.037 0.00 0.00 0.00 2.50
138 139 8.904834 GTGAGTTAATGAGGAGAGATGTAGTTA 58.095 37.037 0.00 0.00 0.00 2.24
139 140 7.617723 AGTGAGTTAATGAGGAGAGATGTAGTT 59.382 37.037 0.00 0.00 0.00 2.24
140 141 7.068103 CAGTGAGTTAATGAGGAGAGATGTAGT 59.932 40.741 0.00 0.00 0.00 2.73
141 142 7.424803 CAGTGAGTTAATGAGGAGAGATGTAG 58.575 42.308 0.00 0.00 0.00 2.74
142 143 6.183360 GCAGTGAGTTAATGAGGAGAGATGTA 60.183 42.308 0.00 0.00 0.00 2.29
143 144 5.395103 GCAGTGAGTTAATGAGGAGAGATGT 60.395 44.000 0.00 0.00 0.00 3.06
144 145 5.049167 GCAGTGAGTTAATGAGGAGAGATG 58.951 45.833 0.00 0.00 0.00 2.90
145 146 4.100808 GGCAGTGAGTTAATGAGGAGAGAT 59.899 45.833 0.00 0.00 0.00 2.75
146 147 3.449018 GGCAGTGAGTTAATGAGGAGAGA 59.551 47.826 0.00 0.00 0.00 3.10
147 148 3.196469 TGGCAGTGAGTTAATGAGGAGAG 59.804 47.826 0.00 0.00 0.00 3.20
148 149 3.055819 GTGGCAGTGAGTTAATGAGGAGA 60.056 47.826 0.00 0.00 0.00 3.71
149 150 3.265791 GTGGCAGTGAGTTAATGAGGAG 58.734 50.000 0.00 0.00 0.00 3.69
150 151 2.637382 TGTGGCAGTGAGTTAATGAGGA 59.363 45.455 0.00 0.00 0.00 3.71
151 152 3.057969 TGTGGCAGTGAGTTAATGAGG 57.942 47.619 0.00 0.00 0.00 3.86
152 153 5.220739 GCTTATGTGGCAGTGAGTTAATGAG 60.221 44.000 0.00 0.00 0.00 2.90
153 154 4.635765 GCTTATGTGGCAGTGAGTTAATGA 59.364 41.667 0.00 0.00 0.00 2.57
154 155 4.395854 TGCTTATGTGGCAGTGAGTTAATG 59.604 41.667 0.00 0.00 34.56 1.90
155 156 4.588899 TGCTTATGTGGCAGTGAGTTAAT 58.411 39.130 0.00 0.00 34.56 1.40
156 157 4.014569 TGCTTATGTGGCAGTGAGTTAA 57.985 40.909 0.00 0.00 34.56 2.01
157 158 3.694043 TGCTTATGTGGCAGTGAGTTA 57.306 42.857 0.00 0.00 34.56 2.24
158 159 2.566833 TGCTTATGTGGCAGTGAGTT 57.433 45.000 0.00 0.00 34.56 3.01
159 160 2.566833 TTGCTTATGTGGCAGTGAGT 57.433 45.000 0.00 0.00 40.90 3.41
160 161 4.445452 AATTTGCTTATGTGGCAGTGAG 57.555 40.909 0.00 0.00 40.90 3.51
161 162 4.558178 CAAATTTGCTTATGTGGCAGTGA 58.442 39.130 5.01 0.00 40.90 3.41
162 163 4.914312 CAAATTTGCTTATGTGGCAGTG 57.086 40.909 5.01 0.00 40.90 3.66
176 177 4.935702 TCAAGTCCAACTCAGCAAATTTG 58.064 39.130 14.03 14.03 0.00 2.32
177 178 5.069516 ACATCAAGTCCAACTCAGCAAATTT 59.930 36.000 0.00 0.00 0.00 1.82
178 179 4.586001 ACATCAAGTCCAACTCAGCAAATT 59.414 37.500 0.00 0.00 0.00 1.82
179 180 4.147321 ACATCAAGTCCAACTCAGCAAAT 58.853 39.130 0.00 0.00 0.00 2.32
180 181 3.554934 ACATCAAGTCCAACTCAGCAAA 58.445 40.909 0.00 0.00 0.00 3.68
181 182 3.213206 ACATCAAGTCCAACTCAGCAA 57.787 42.857 0.00 0.00 0.00 3.91
182 183 2.936919 ACATCAAGTCCAACTCAGCA 57.063 45.000 0.00 0.00 0.00 4.41
183 184 4.153117 CAGTAACATCAAGTCCAACTCAGC 59.847 45.833 0.00 0.00 0.00 4.26
184 185 4.153117 GCAGTAACATCAAGTCCAACTCAG 59.847 45.833 0.00 0.00 0.00 3.35
185 186 4.065088 GCAGTAACATCAAGTCCAACTCA 58.935 43.478 0.00 0.00 0.00 3.41
186 187 4.153117 CAGCAGTAACATCAAGTCCAACTC 59.847 45.833 0.00 0.00 0.00 3.01
187 188 4.067896 CAGCAGTAACATCAAGTCCAACT 58.932 43.478 0.00 0.00 0.00 3.16
188 189 4.065088 TCAGCAGTAACATCAAGTCCAAC 58.935 43.478 0.00 0.00 0.00 3.77
189 190 4.350368 TCAGCAGTAACATCAAGTCCAA 57.650 40.909 0.00 0.00 0.00 3.53
190 191 4.202357 ACTTCAGCAGTAACATCAAGTCCA 60.202 41.667 0.00 0.00 31.97 4.02
191 192 4.319177 ACTTCAGCAGTAACATCAAGTCC 58.681 43.478 0.00 0.00 31.97 3.85
192 193 5.931441 AACTTCAGCAGTAACATCAAGTC 57.069 39.130 0.00 0.00 32.94 3.01
193 194 6.525629 AGTAACTTCAGCAGTAACATCAAGT 58.474 36.000 0.00 0.00 32.94 3.16
194 195 7.426929 AAGTAACTTCAGCAGTAACATCAAG 57.573 36.000 0.00 0.00 32.94 3.02
195 196 7.497579 TGAAAGTAACTTCAGCAGTAACATCAA 59.502 33.333 0.00 0.00 32.94 2.57
196 197 6.989759 TGAAAGTAACTTCAGCAGTAACATCA 59.010 34.615 0.00 0.00 32.94 3.07
197 198 7.171678 AGTGAAAGTAACTTCAGCAGTAACATC 59.828 37.037 0.00 0.00 36.01 3.06
198 199 6.992715 AGTGAAAGTAACTTCAGCAGTAACAT 59.007 34.615 0.00 0.00 36.01 2.71
199 200 6.346096 AGTGAAAGTAACTTCAGCAGTAACA 58.654 36.000 0.00 0.00 36.01 2.41
200 201 6.846325 AGTGAAAGTAACTTCAGCAGTAAC 57.154 37.500 0.00 0.00 36.01 2.50
201 202 7.602644 CCATAGTGAAAGTAACTTCAGCAGTAA 59.397 37.037 0.00 0.00 36.01 2.24
202 203 7.097192 CCATAGTGAAAGTAACTTCAGCAGTA 58.903 38.462 0.00 0.00 36.01 2.74
203 204 5.934625 CCATAGTGAAAGTAACTTCAGCAGT 59.065 40.000 0.00 0.00 36.01 4.40
204 205 5.163814 GCCATAGTGAAAGTAACTTCAGCAG 60.164 44.000 0.00 0.00 36.01 4.24
205 206 4.695455 GCCATAGTGAAAGTAACTTCAGCA 59.305 41.667 0.00 0.00 36.01 4.41
206 207 4.938226 AGCCATAGTGAAAGTAACTTCAGC 59.062 41.667 0.00 0.00 36.01 4.26
207 208 7.324178 ACTAGCCATAGTGAAAGTAACTTCAG 58.676 38.462 0.00 0.00 40.84 3.02
208 209 7.178628 AGACTAGCCATAGTGAAAGTAACTTCA 59.821 37.037 0.00 0.00 42.46 3.02
209 210 7.548967 AGACTAGCCATAGTGAAAGTAACTTC 58.451 38.462 0.00 0.00 42.46 3.01
210 211 7.483580 AGACTAGCCATAGTGAAAGTAACTT 57.516 36.000 0.00 0.00 42.46 2.66
211 212 7.483580 AAGACTAGCCATAGTGAAAGTAACT 57.516 36.000 0.00 0.00 42.46 2.24
212 213 7.705752 GGTAAGACTAGCCATAGTGAAAGTAAC 59.294 40.741 0.00 0.00 42.46 2.50
213 214 7.618512 AGGTAAGACTAGCCATAGTGAAAGTAA 59.381 37.037 0.00 0.00 42.46 2.24
214 215 7.124052 AGGTAAGACTAGCCATAGTGAAAGTA 58.876 38.462 0.00 0.00 42.46 2.24
215 216 5.958987 AGGTAAGACTAGCCATAGTGAAAGT 59.041 40.000 0.00 0.00 42.46 2.66
216 217 6.472686 AGGTAAGACTAGCCATAGTGAAAG 57.527 41.667 0.00 0.00 42.46 2.62
217 218 6.869206 AAGGTAAGACTAGCCATAGTGAAA 57.131 37.500 0.00 0.00 42.46 2.69
218 219 6.869206 AAAGGTAAGACTAGCCATAGTGAA 57.131 37.500 0.00 0.00 42.46 3.18
219 220 6.869206 AAAAGGTAAGACTAGCCATAGTGA 57.131 37.500 0.00 0.00 42.46 3.41
220 221 7.921745 GTCTAAAAGGTAAGACTAGCCATAGTG 59.078 40.741 0.00 0.00 42.46 2.74
221 222 8.009622 GTCTAAAAGGTAAGACTAGCCATAGT 57.990 38.462 0.00 0.00 45.16 2.12
260 261 5.009610 ACCCAATTACTTACTGCAGTGTTTG 59.990 40.000 29.57 18.83 0.00 2.93
296 297 0.319900 CCGGCCCTCTACATCGATTG 60.320 60.000 0.00 0.00 0.00 2.67
342 343 4.574828 GGAACTGTTTCAGCTTGTCAACTA 59.425 41.667 0.00 0.00 34.37 2.24
345 346 3.620488 AGGAACTGTTTCAGCTTGTCAA 58.380 40.909 0.98 0.00 37.18 3.18
387 388 2.477375 ACGGCACACTTGTAATACGTTG 59.523 45.455 0.00 0.00 0.00 4.10
398 399 3.008049 AGGAGAGAATTAACGGCACACTT 59.992 43.478 0.00 0.00 0.00 3.16
406 408 4.328440 CACAAGCTCAGGAGAGAATTAACG 59.672 45.833 0.00 0.00 44.98 3.18
431 433 2.064573 TGTGCATCGCGGATATACAG 57.935 50.000 6.13 0.00 0.00 2.74
437 439 1.311859 ATTGATTGTGCATCGCGGAT 58.688 45.000 6.13 0.00 34.08 4.18
440 442 3.479590 CAGTTAATTGATTGTGCATCGCG 59.520 43.478 0.00 0.00 34.08 5.87
461 463 6.204108 CAGCACAACAGATCATCATTATAGCA 59.796 38.462 0.00 0.00 0.00 3.49
466 468 4.637091 CACCAGCACAACAGATCATCATTA 59.363 41.667 0.00 0.00 0.00 1.90
483 485 0.960364 TTTTGATCCCGAGCACCAGC 60.960 55.000 0.00 0.00 42.56 4.85
490 492 4.635765 TGAGCACTAAATTTTGATCCCGAG 59.364 41.667 6.63 0.00 0.00 4.63
492 494 4.963276 TGAGCACTAAATTTTGATCCCG 57.037 40.909 6.63 0.00 0.00 5.14
510 512 6.624352 TTTCTTGGTTCTCACTGAAATGAG 57.376 37.500 0.00 0.00 46.40 2.90
544 546 4.318192 CGTTCGTTGCACTGTACATTTGTA 60.318 41.667 0.00 0.00 0.00 2.41
549 551 1.860676 ACGTTCGTTGCACTGTACAT 58.139 45.000 0.00 0.00 0.00 2.29
550 552 2.488639 TACGTTCGTTGCACTGTACA 57.511 45.000 2.62 0.00 0.00 2.90
551 553 4.618489 ACTAATACGTTCGTTGCACTGTAC 59.382 41.667 2.62 0.00 0.00 2.90
552 554 4.797471 ACTAATACGTTCGTTGCACTGTA 58.203 39.130 2.62 0.00 0.00 2.74
553 555 3.645884 ACTAATACGTTCGTTGCACTGT 58.354 40.909 2.62 0.00 0.00 3.55
554 556 4.259292 GCTACTAATACGTTCGTTGCACTG 60.259 45.833 2.62 0.00 33.94 3.66
555 557 3.855950 GCTACTAATACGTTCGTTGCACT 59.144 43.478 2.62 0.00 33.94 4.40
556 558 3.855950 AGCTACTAATACGTTCGTTGCAC 59.144 43.478 2.62 0.00 35.37 4.57
558 560 4.100529 TCAGCTACTAATACGTTCGTTGC 58.899 43.478 2.62 0.00 33.95 4.17
562 564 3.969352 CAGCTCAGCTACTAATACGTTCG 59.031 47.826 0.00 0.00 36.40 3.95
575 577 0.037877 AATGTTCCTGCAGCTCAGCT 59.962 50.000 8.66 0.00 41.50 4.24
576 578 0.450983 GAATGTTCCTGCAGCTCAGC 59.549 55.000 8.66 0.00 41.50 4.26
577 579 1.738350 CTGAATGTTCCTGCAGCTCAG 59.262 52.381 8.66 8.66 42.49 3.35
578 580 1.817357 CTGAATGTTCCTGCAGCTCA 58.183 50.000 8.66 7.17 0.00 4.26
634 636 1.211212 CAAGTCATGCTCCCATCCAGA 59.789 52.381 0.00 0.00 0.00 3.86
649 651 0.868406 CCTTCCACGTTCTGCAAGTC 59.132 55.000 0.00 0.00 33.76 3.01
696 698 3.755378 CCTGATAAGGTATGGCTGAATGC 59.245 47.826 0.00 0.00 41.94 3.56
713 715 1.759445 CGTCCATCTTCTGTCCCTGAT 59.241 52.381 0.00 0.00 0.00 2.90
717 719 0.895530 TGTCGTCCATCTTCTGTCCC 59.104 55.000 0.00 0.00 0.00 4.46
721 730 1.673033 GGTGGTGTCGTCCATCTTCTG 60.673 57.143 0.00 0.00 39.81 3.02
795 804 1.949525 CTGGAGAACTGGTTGTTGGTG 59.050 52.381 0.00 0.00 39.30 4.17
869 879 0.593128 CCAGACCAAAAAGGACAGCG 59.407 55.000 0.00 0.00 41.22 5.18
870 880 1.692411 ACCAGACCAAAAAGGACAGC 58.308 50.000 0.00 0.00 41.22 4.40
871 881 3.287222 TGAACCAGACCAAAAAGGACAG 58.713 45.455 0.00 0.00 41.22 3.51
914 926 3.428532 ACAGTGTATATAGTAGGGCGGG 58.571 50.000 0.00 0.00 0.00 6.13
915 927 5.010314 TGAAACAGTGTATATAGTAGGGCGG 59.990 44.000 0.00 0.00 0.00 6.13
916 928 5.919141 GTGAAACAGTGTATATAGTAGGGCG 59.081 44.000 0.00 0.00 36.32 6.13
918 930 8.008513 ACAGTGAAACAGTGTATATAGTAGGG 57.991 38.462 9.97 0.00 44.89 3.53
985 1000 1.880340 CCATTGCGACGAGAGAGGC 60.880 63.158 0.00 0.00 0.00 4.70
1026 1044 1.378250 CAGGAGCAAGGCCAAGAGG 60.378 63.158 5.01 0.00 38.23 3.69
1037 1055 1.891919 GAAACGGCACACAGGAGCA 60.892 57.895 0.00 0.00 31.64 4.26
2164 2197 0.042881 AGGGTGAGGTAGAGGTTCCC 59.957 60.000 0.00 0.00 0.00 3.97
2250 2283 1.551908 CCAGCTCCTTGTGCTCCTCT 61.552 60.000 0.00 0.00 38.92 3.69
2441 2505 2.160417 GGTAACAATGCAGTCACTGAGC 59.840 50.000 9.70 0.00 32.44 4.26
2514 2587 2.812358 TGCTTATCGCATCGTATGGT 57.188 45.000 0.00 0.00 45.47 3.55
2613 2686 2.725641 CCGGCGATGACGATGGTA 59.274 61.111 9.30 0.00 42.66 3.25
2857 2930 2.230508 TGTATCTTCCGAAGAGCACGTT 59.769 45.455 15.85 1.52 41.61 3.99
2888 2961 6.442112 TCGATCTGCATTTCATCTGTAGTAG 58.558 40.000 0.00 0.00 0.00 2.57
2894 2970 4.755629 AGGAATCGATCTGCATTTCATCTG 59.244 41.667 0.00 0.00 0.00 2.90
2933 3011 5.168526 TGACAATCCAAGAAACGTTTGAG 57.831 39.130 20.10 7.58 0.00 3.02
3176 3271 4.783621 TGCAGGACTCCCATGCGC 62.784 66.667 0.00 0.00 38.55 6.09
3447 3548 3.947841 GCGAACGCCTTGCACACA 61.948 61.111 8.03 0.00 34.56 3.72
3619 3728 5.395682 TGGCCTTCAATCTTTCATCTTTG 57.604 39.130 3.32 0.00 0.00 2.77
3669 3778 8.964476 TCGCAAAGAAAAGGAGAAGATATTAT 57.036 30.769 0.00 0.00 0.00 1.28
3684 3793 8.547967 AAGATATTACACTTCTCGCAAAGAAA 57.452 30.769 3.96 0.00 43.39 2.52
3686 3795 7.548097 AGAAGATATTACACTTCTCGCAAAGA 58.452 34.615 0.00 0.00 46.28 2.52
3739 3854 4.646040 TGATATTTTTGGAGCTGGGATGTG 59.354 41.667 0.00 0.00 0.00 3.21
3751 3866 8.742554 AGCTAGTTTTCGTTTGATATTTTTGG 57.257 30.769 0.00 0.00 0.00 3.28
3765 3880 8.709496 AAAACGATTTTTAGAGCTAGTTTTCG 57.291 30.769 0.00 0.00 36.27 3.46
3776 3891 9.737427 TGACAAATAGCAAAAACGATTTTTAGA 57.263 25.926 0.02 0.00 40.65 2.10
3799 3914 6.809689 CCAAACGGGTCCTTAATATTTTTGAC 59.190 38.462 0.00 0.00 0.00 3.18
3817 3932 0.031449 AAATGCGACCAACCAAACGG 59.969 50.000 0.00 0.00 0.00 4.44
4037 4171 2.282958 ACGAGAGAAGGCGTGGGA 60.283 61.111 0.00 0.00 39.56 4.37
4046 4180 0.677098 CGAGGGAGGTGACGAGAGAA 60.677 60.000 0.00 0.00 0.00 2.87
4051 4185 4.671590 TGGCGAGGGAGGTGACGA 62.672 66.667 0.00 0.00 0.00 4.20
4211 4348 2.490148 CGCCAGATCTACTCCGGCA 61.490 63.158 18.24 0.00 37.49 5.69
4248 4385 1.607467 GCATGGTGCAGAAAGGGGT 60.607 57.895 0.00 0.00 44.26 4.95
4324 4461 1.685765 CCGATGGAGAGGACCACCA 60.686 63.158 7.37 7.37 43.03 4.17
4475 4616 1.429825 CCGACTCGAAGATGACGCT 59.570 57.895 0.00 0.00 33.89 5.07
4536 4677 2.671070 CGCCACCCATGAAGAGGT 59.329 61.111 0.00 0.00 36.58 3.85


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

AutoCloner maintained by Alex Coulton.