Multiple sequence alignment - TraesCS7D01G008000

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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 TraesCS7D01G008000 chr7D 100.000 5091 0 0 667 5757 3859427 3854337 0.000000e+00 9402.0
1 TraesCS7D01G008000 chr7D 87.299 3677 384 41 1092 4717 2408088 2411732 0.000000e+00 4126.0
2 TraesCS7D01G008000 chr7D 87.540 2207 260 14 2270 4470 2651653 2653850 0.000000e+00 2538.0
3 TraesCS7D01G008000 chr7D 79.590 2631 429 62 2228 4806 3688294 3690868 0.000000e+00 1784.0
4 TraesCS7D01G008000 chr7D 89.207 593 40 12 4470 5056 2653883 2654457 0.000000e+00 719.0
5 TraesCS7D01G008000 chr7D 100.000 308 0 0 1 308 3860093 3859786 2.330000e-158 569.0
6 TraesCS7D01G008000 chr7D 77.566 945 163 29 1298 2235 2650005 2650907 5.110000e-145 525.0
7 TraesCS7D01G008000 chr7D 77.753 890 133 33 1361 2230 3685924 3686768 2.410000e-133 486.0
8 TraesCS7D01G008000 chr7D 88.974 390 28 11 5380 5757 2654672 2655058 8.730000e-128 468.0
9 TraesCS7D01G008000 chr7D 95.109 184 9 0 5125 5308 2654473 2654656 2.030000e-74 291.0
10 TraesCS7D01G008000 chr7D 95.789 95 4 0 4934 5028 2411920 2412014 2.780000e-33 154.0
11 TraesCS7D01G008000 chr7D 82.418 91 15 1 799 889 2649411 2649500 1.720000e-10 78.7
12 TraesCS7D01G008000 chr4A 86.910 4003 430 33 1355 5311 742036055 742032101 0.000000e+00 4403.0
13 TraesCS7D01G008000 chr4A 86.070 4135 450 49 1231 5311 740541277 740537215 0.000000e+00 4340.0
14 TraesCS7D01G008000 chr4A 86.188 3859 444 39 1231 5034 739630607 739626783 0.000000e+00 4102.0
15 TraesCS7D01G008000 chr4A 88.500 600 44 6 4342 4938 740161386 740161963 0.000000e+00 702.0
16 TraesCS7D01G008000 chr4A 92.936 453 24 4 5310 5757 739626526 739626077 0.000000e+00 652.0
17 TraesCS7D01G008000 chr4A 86.000 400 20 6 5383 5757 740537198 740536810 4.180000e-106 396.0
18 TraesCS7D01G008000 chr4A 87.956 274 10 2 5316 5566 742032061 742031788 9.370000e-78 302.0
19 TraesCS7D01G008000 chr4A 91.803 183 12 3 5130 5311 739626740 739626560 9.580000e-63 252.0
20 TraesCS7D01G008000 chr4A 84.685 222 27 7 672 889 740542247 740542029 1.260000e-51 215.0
21 TraesCS7D01G008000 chr4A 84.234 222 28 7 672 889 739631558 739631340 5.850000e-50 209.0
22 TraesCS7D01G008000 chr4A 89.032 155 14 1 5603 5757 742031790 742031639 7.620000e-44 189.0
23 TraesCS7D01G008000 chr4A 84.524 168 23 3 906 1071 739845046 739844880 4.620000e-36 163.0
24 TraesCS7D01G008000 chr4A 84.524 168 23 3 906 1071 740541971 740541805 4.620000e-36 163.0
25 TraesCS7D01G008000 chr4A 93.939 99 6 0 4934 5032 741177864 741177766 3.590000e-32 150.0
26 TraesCS7D01G008000 chr4A 87.121 132 13 1 5150 5277 741177372 741177241 4.650000e-31 147.0
27 TraesCS7D01G008000 chr4A 82.353 170 23 2 5588 5757 742266871 742266709 2.160000e-29 141.0
28 TraesCS7D01G008000 chr4A 85.926 135 13 4 5575 5703 739836148 739836282 7.780000e-29 139.0
29 TraesCS7D01G008000 chr4A 84.058 138 17 3 5575 5710 740864571 740864437 1.680000e-25 128.0
30 TraesCS7D01G008000 chr4A 81.481 162 17 8 5310 5459 741169189 741169029 2.820000e-23 121.0
31 TraesCS7D01G008000 chr4A 84.158 101 11 1 5310 5405 733995988 733995888 6.140000e-15 93.5
32 TraesCS7D01G008000 chr4A 85.897 78 11 0 4934 5011 742148997 742148920 3.700000e-12 84.2
33 TraesCS7D01G008000 chr7A 86.586 3489 404 22 1356 4806 2827338 2830800 0.000000e+00 3792.0
34 TraesCS7D01G008000 chr7A 85.868 3439 424 23 1355 4753 2093388 2096804 0.000000e+00 3602.0
35 TraesCS7D01G008000 chr7A 88.124 2442 263 10 2275 4693 3780565 3783002 0.000000e+00 2878.0
36 TraesCS7D01G008000 chr7A 86.982 1206 98 26 1092 2266 3779303 3780480 0.000000e+00 1303.0
37 TraesCS7D01G008000 chr7A 91.651 539 36 2 4768 5306 2096950 2097479 0.000000e+00 737.0
38 TraesCS7D01G008000 chr7A 94.066 455 16 4 4859 5311 2830818 2831263 0.000000e+00 680.0
39 TraesCS7D01G008000 chr7A 89.514 391 13 6 5312 5677 2831299 2831686 2.430000e-128 470.0
40 TraesCS7D01G008000 chr7A 93.548 248 10 3 5513 5757 2097851 2098095 1.180000e-96 364.0
41 TraesCS7D01G008000 chr7A 93.011 186 9 1 5312 5493 2097521 2097706 9.510000e-68 268.0
42 TraesCS7D01G008000 chr7A 84.838 277 29 9 1 265 2083345 2083620 3.420000e-67 267.0
43 TraesCS7D01G008000 chr7A 88.623 167 15 4 906 1071 2826348 2826511 3.520000e-47 200.0
44 TraesCS7D01G008000 chr7A 73.355 623 132 26 3669 4280 9011898 9012497 3.520000e-47 200.0
45 TraesCS7D01G008000 chr7A 79.422 277 33 12 1 265 2825447 2825711 2.130000e-39 174.0
46 TraesCS7D01G008000 chr7A 85.625 160 14 4 911 1068 2092503 2092655 5.970000e-35 159.0
47 TraesCS7D01G008000 chr7A 73.529 408 88 16 1395 1795 8780941 8780547 2.800000e-28 137.0
48 TraesCS7D01G008000 chr7A 75.899 278 46 13 1395 1660 9008267 9008535 7.830000e-24 122.0
49 TraesCS7D01G008000 chrUn 85.246 183 23 4 706 886 444984374 444984554 9.850000e-43 185.0


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 TraesCS7D01G008000 chr7D 3854337 3860093 5756 True 4985.500000 9402 100.000000 1 5757 2 chr7D.!!$R1 5756
1 TraesCS7D01G008000 chr7D 2408088 2412014 3926 False 2140.000000 4126 91.544000 1092 5028 2 chr7D.!!$F1 3936
2 TraesCS7D01G008000 chr7D 3685924 3690868 4944 False 1135.000000 1784 78.671500 1361 4806 2 chr7D.!!$F3 3445
3 TraesCS7D01G008000 chr7D 2649411 2655058 5647 False 769.950000 2538 86.802333 799 5757 6 chr7D.!!$F2 4958
4 TraesCS7D01G008000 chr4A 742031639 742036055 4416 True 1631.333333 4403 87.966000 1355 5757 3 chr4A.!!$R10 4402
5 TraesCS7D01G008000 chr4A 739626077 739631558 5481 True 1303.750000 4102 88.790250 672 5757 4 chr4A.!!$R7 5085
6 TraesCS7D01G008000 chr4A 740536810 740542247 5437 True 1278.500000 4340 85.319750 672 5757 4 chr4A.!!$R8 5085
7 TraesCS7D01G008000 chr4A 740161386 740161963 577 False 702.000000 702 88.500000 4342 4938 1 chr4A.!!$F2 596
8 TraesCS7D01G008000 chr7A 3779303 3783002 3699 False 2090.500000 2878 87.553000 1092 4693 2 chr7A.!!$F4 3601
9 TraesCS7D01G008000 chr7A 2825447 2831686 6239 False 1063.200000 3792 87.642200 1 5677 5 chr7A.!!$F3 5676
10 TraesCS7D01G008000 chr7A 2092503 2098095 5592 False 1026.000000 3602 89.940600 911 5757 5 chr7A.!!$F2 4846

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
816 1166 0.036765 TTGAACGGTAGCATCGCCTT 60.037 50.0 0.0 0.0 0.00 4.35 F
2147 3214 0.032815 GGAGATACTCCGGCAGCTTC 59.967 60.0 0.0 0.0 41.08 3.86 F
3947 6667 0.041833 ACTTCCTAGCTGCCCTGAGA 59.958 55.0 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2684 5388 0.037590 GATGTGTACCCAGGTTGGCA 59.962 55.0 0.00 0.0 35.79 4.92 R
4144 6865 0.510359 GACTGCTGACGTGCTGAAAG 59.490 55.0 10.97 0.0 36.10 2.62 R
5461 8575 0.179045 CCTTGGTGGTCATCCGATCC 60.179 60.0 0.00 0.0 36.30 3.36 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
54 55 4.058124 GTGTACTCTGCACAATGACTGAA 58.942 43.478 0.00 0.00 36.88 3.02
61 62 1.398960 GCACAATGACTGAACGTGAGC 60.399 52.381 0.00 0.00 0.00 4.26
124 137 2.152058 ATGCCAGCCCAGGATCGAT 61.152 57.895 0.00 0.00 0.00 3.59
133 146 2.244946 CAGGATCGATGCATGCTGG 58.755 57.895 20.33 8.03 38.29 4.85
136 149 1.134007 AGGATCGATGCATGCTGGAAA 60.134 47.619 20.33 0.00 0.00 3.13
137 150 1.002033 GGATCGATGCATGCTGGAAAC 60.002 52.381 20.33 10.95 0.00 2.78
138 151 1.945394 GATCGATGCATGCTGGAAACT 59.055 47.619 20.33 0.00 0.00 2.66
139 152 2.689553 TCGATGCATGCTGGAAACTA 57.310 45.000 20.33 0.00 0.00 2.24
141 154 1.331756 CGATGCATGCTGGAAACTACC 59.668 52.381 20.33 0.00 0.00 3.18
142 155 1.678101 GATGCATGCTGGAAACTACCC 59.322 52.381 20.33 0.00 0.00 3.69
143 156 0.403655 TGCATGCTGGAAACTACCCA 59.596 50.000 20.33 0.00 0.00 4.51
174 187 0.893270 TGACATCCAAAAGGCCCACG 60.893 55.000 0.00 0.00 0.00 4.94
176 189 0.039618 ACATCCAAAAGGCCCACGAT 59.960 50.000 0.00 0.00 0.00 3.73
178 191 1.322538 ATCCAAAAGGCCCACGATGC 61.323 55.000 0.00 0.00 0.00 3.91
187 200 2.359107 CCACGATGCAGCCACTGT 60.359 61.111 0.00 0.00 33.43 3.55
188 201 2.683859 CCACGATGCAGCCACTGTG 61.684 63.158 0.00 0.00 33.43 3.66
189 202 1.668793 CACGATGCAGCCACTGTGA 60.669 57.895 9.86 0.00 33.54 3.58
190 203 1.022982 CACGATGCAGCCACTGTGAT 61.023 55.000 9.86 0.00 33.54 3.06
191 204 1.022982 ACGATGCAGCCACTGTGATG 61.023 55.000 9.86 8.83 33.43 3.07
192 205 1.432251 GATGCAGCCACTGTGATGC 59.568 57.895 22.84 22.84 39.14 3.91
193 206 1.001269 ATGCAGCCACTGTGATGCT 60.001 52.632 26.79 18.21 39.42 3.79
194 207 0.611062 ATGCAGCCACTGTGATGCTT 60.611 50.000 26.79 21.29 39.42 3.91
195 208 0.824595 TGCAGCCACTGTGATGCTTT 60.825 50.000 26.79 3.25 39.42 3.51
196 209 0.388134 GCAGCCACTGTGATGCTTTG 60.388 55.000 22.53 10.59 35.78 2.77
197 210 0.388134 CAGCCACTGTGATGCTTTGC 60.388 55.000 9.86 2.01 31.77 3.68
205 218 0.453390 GTGATGCTTTGCTGGCTACC 59.547 55.000 0.00 0.00 0.00 3.18
211 224 1.134995 GCTTTGCTGGCTACCAAATCC 60.135 52.381 0.00 0.00 30.80 3.01
227 240 6.386654 ACCAAATCCGAACACATTTTATGTC 58.613 36.000 0.00 0.00 42.70 3.06
233 246 7.534085 TCCGAACACATTTTATGTCTACATC 57.466 36.000 0.00 0.00 42.70 3.06
236 249 6.254804 CGAACACATTTTATGTCTACATCCGA 59.745 38.462 0.00 0.00 42.70 4.55
242 255 8.665685 ACATTTTATGTCTACATCCGAGTTTTC 58.334 33.333 0.00 0.00 39.92 2.29
243 256 8.664798 CATTTTATGTCTACATCCGAGTTTTCA 58.335 33.333 0.00 0.00 37.76 2.69
244 257 7.827819 TTTATGTCTACATCCGAGTTTTCAG 57.172 36.000 0.00 0.00 37.76 3.02
253 266 3.194861 TCCGAGTTTTCAGTTGTGTCTG 58.805 45.455 0.00 0.00 36.85 3.51
254 267 2.936498 CCGAGTTTTCAGTTGTGTCTGT 59.064 45.455 0.00 0.00 36.85 3.41
278 626 3.273434 TGCAGTGCATCACTCTAAATCC 58.727 45.455 15.37 0.00 43.43 3.01
279 627 3.273434 GCAGTGCATCACTCTAAATCCA 58.727 45.455 11.09 0.00 43.43 3.41
286 634 4.641989 GCATCACTCTAAATCCACATTGGT 59.358 41.667 0.00 0.00 39.03 3.67
290 638 6.957631 TCACTCTAAATCCACATTGGTATGT 58.042 36.000 0.00 0.00 45.81 2.29
292 640 6.823182 CACTCTAAATCCACATTGGTATGTCA 59.177 38.462 0.00 0.00 43.07 3.58
293 641 7.011763 CACTCTAAATCCACATTGGTATGTCAG 59.988 40.741 0.00 0.00 43.07 3.51
294 642 6.356556 TCTAAATCCACATTGGTATGTCAGG 58.643 40.000 0.00 0.00 43.07 3.86
295 643 4.591321 AATCCACATTGGTATGTCAGGT 57.409 40.909 0.00 0.00 43.07 4.00
296 644 3.348647 TCCACATTGGTATGTCAGGTG 57.651 47.619 0.00 0.00 43.07 4.00
298 646 2.290896 CCACATTGGTATGTCAGGTGGT 60.291 50.000 0.00 0.00 43.07 4.16
299 647 2.749076 CACATTGGTATGTCAGGTGGTG 59.251 50.000 0.00 0.00 43.07 4.17
300 648 2.375174 ACATTGGTATGTCAGGTGGTGT 59.625 45.455 0.00 0.00 41.07 4.16
302 650 1.723288 TGGTATGTCAGGTGGTGTCA 58.277 50.000 0.00 0.00 0.00 3.58
304 652 1.346395 GGTATGTCAGGTGGTGTCACA 59.654 52.381 5.12 0.00 45.32 3.58
306 654 0.250467 ATGTCAGGTGGTGTCACAGC 60.250 55.000 5.12 0.00 45.32 4.40
307 655 1.598130 GTCAGGTGGTGTCACAGCC 60.598 63.158 4.12 6.15 45.32 4.85
686 1034 2.507484 CTTTGTTGCTCATCCTCCACA 58.493 47.619 0.00 0.00 0.00 4.17
696 1044 4.197750 CTCATCCTCCACAAATCCTCTTG 58.802 47.826 0.00 0.00 0.00 3.02
697 1045 3.845992 TCATCCTCCACAAATCCTCTTGA 59.154 43.478 0.00 0.00 0.00 3.02
698 1046 4.476113 TCATCCTCCACAAATCCTCTTGAT 59.524 41.667 0.00 0.00 34.22 2.57
700 1048 4.592942 TCCTCCACAAATCCTCTTGATTG 58.407 43.478 0.00 0.00 42.97 2.67
703 1052 5.197224 TCCACAAATCCTCTTGATTGGAT 57.803 39.130 0.00 0.00 42.97 3.41
708 1057 0.911769 TCCTCTTGATTGGATGGCGT 59.088 50.000 0.00 0.00 0.00 5.68
730 1079 5.614760 GTGTGATTTTCATCTTGCAAATGC 58.385 37.500 0.00 0.00 42.50 3.56
731 1080 4.386350 TGTGATTTTCATCTTGCAAATGCG 59.614 37.500 0.00 0.00 45.83 4.73
741 1090 3.493877 TCTTGCAAATGCGGAAATTTGTG 59.506 39.130 0.00 0.00 45.37 3.33
747 1096 6.203530 TGCAAATGCGGAAATTTGTGAAAATA 59.796 30.769 14.25 0.00 45.37 1.40
776 1126 4.698201 TTGGTAGATGTGGTGTGAAAGA 57.302 40.909 0.00 0.00 0.00 2.52
786 1136 5.680619 TGTGGTGTGAAAGACTTATGAGTT 58.319 37.500 0.00 0.00 35.88 3.01
791 1141 7.041167 TGGTGTGAAAGACTTATGAGTTCATTG 60.041 37.037 0.00 0.00 35.88 2.82
793 1143 6.430925 TGTGAAAGACTTATGAGTTCATTGGG 59.569 38.462 0.00 0.00 35.88 4.12
797 1147 6.506538 AGACTTATGAGTTCATTGGGCTAT 57.493 37.500 0.00 0.00 35.88 2.97
816 1166 0.036765 TTGAACGGTAGCATCGCCTT 60.037 50.000 0.00 0.00 0.00 4.35
817 1167 0.036765 TGAACGGTAGCATCGCCTTT 60.037 50.000 0.00 0.00 0.00 3.11
856 1206 2.950975 TGCAAAGTTGATTCTCACTGCA 59.049 40.909 0.00 0.00 0.00 4.41
862 1212 4.582869 AGTTGATTCTCACTGCATGCTAA 58.417 39.130 20.33 0.00 0.00 3.09
867 1217 3.683365 TCTCACTGCATGCTAAACTGA 57.317 42.857 20.33 10.53 0.00 3.41
877 1227 5.163571 TGCATGCTAAACTGACAAGTTGAAA 60.164 36.000 20.33 0.00 46.15 2.69
889 1239 8.333186 ACTGACAAGTTGAAATAAACTACGAAC 58.667 33.333 10.54 0.00 39.48 3.95
890 1240 8.199176 TGACAAGTTGAAATAAACTACGAACA 57.801 30.769 10.54 0.00 39.48 3.18
894 1246 6.951643 AGTTGAAATAAACTACGAACACACC 58.048 36.000 0.00 0.00 38.62 4.16
908 1299 3.774528 CACCGCCAGCTGCTAGGA 61.775 66.667 21.84 0.00 38.05 2.94
914 1305 1.519719 CCAGCTGCTAGGACCAGAC 59.480 63.158 8.66 0.00 32.03 3.51
917 1308 1.134848 CAGCTGCTAGGACCAGACTTC 60.135 57.143 0.00 0.00 32.03 3.01
918 1309 0.179124 GCTGCTAGGACCAGACTTCG 60.179 60.000 0.00 0.00 32.03 3.79
929 1323 2.299013 ACCAGACTTCGTTAGTGCATCA 59.701 45.455 0.00 0.00 37.17 3.07
931 1325 3.369147 CCAGACTTCGTTAGTGCATCAAG 59.631 47.826 0.00 0.00 37.17 3.02
937 1331 5.932303 ACTTCGTTAGTGCATCAAGTGTAAT 59.068 36.000 0.00 0.00 35.19 1.89
938 1332 6.426937 ACTTCGTTAGTGCATCAAGTGTAATT 59.573 34.615 0.00 0.00 35.19 1.40
989 1384 0.171903 GCATCGACAGCAAGCCAAAT 59.828 50.000 6.80 0.00 0.00 2.32
1005 1400 8.620533 CAAGCCAAATTGCTATCTTAAACTAC 57.379 34.615 0.00 0.00 41.80 2.73
1009 1404 8.343366 GCCAAATTGCTATCTTAAACTACTACC 58.657 37.037 0.00 0.00 0.00 3.18
1010 1405 9.614792 CCAAATTGCTATCTTAAACTACTACCT 57.385 33.333 0.00 0.00 0.00 3.08
1075 1470 8.421002 AGTTTAAAAACCTATGAACATGCTTGT 58.579 29.630 0.00 0.00 39.71 3.16
1076 1471 9.685828 GTTTAAAAACCTATGAACATGCTTGTA 57.314 29.630 5.56 0.00 32.35 2.41
1122 1610 2.595009 GAACTCTAAGCCGCCCCCAG 62.595 65.000 0.00 0.00 0.00 4.45
1171 1676 1.142870 AGCTTTGGTTGTCTACTGGCA 59.857 47.619 0.00 0.00 0.00 4.92
1237 2099 4.313020 AGTGATTTCAATTCAGCCTCCT 57.687 40.909 0.00 0.00 0.00 3.69
1252 2114 2.580962 CCTCCTAACGGGTCTAGGTAC 58.419 57.143 0.00 0.00 37.72 3.34
1285 2150 3.835810 ATCCCTGCCATGGATGTTC 57.164 52.632 18.40 0.00 41.10 3.18
1291 2166 0.107703 TGCCATGGATGTTCTCGTCC 60.108 55.000 18.40 0.00 46.78 4.79
1347 2222 2.780924 ACCCACACACCCACCCAT 60.781 61.111 0.00 0.00 0.00 4.00
1358 2384 0.984230 CCCACCCATACACACAGAGT 59.016 55.000 0.00 0.00 0.00 3.24
1374 2402 4.213059 CACAGAGTGAAAGAGAAAAGGAGC 59.787 45.833 0.00 0.00 35.23 4.70
1389 2417 3.005539 AGCGATGGAGGCTGTGGT 61.006 61.111 0.00 0.00 39.77 4.16
1504 2532 8.489990 AGATTGACATCAACTACATCAAGAAG 57.510 34.615 0.00 0.00 38.86 2.85
1685 2722 3.778955 CAGACACTGGGAGACGGT 58.221 61.111 0.00 0.00 40.00 4.83
1712 2749 2.522436 TCCACCGGGTGAAGACGT 60.522 61.111 28.36 0.00 35.23 4.34
1758 2795 1.202557 GGAGATCCAGCTGCTCAAGAG 60.203 57.143 18.01 0.55 35.64 2.85
1778 2815 6.933514 AGAGGAGATCAGAGGATTTATTCC 57.066 41.667 0.00 0.00 45.85 3.01
1846 2883 1.691976 AGGTGGTCATTGTCGTCTGAA 59.308 47.619 0.00 0.00 0.00 3.02
1894 2931 2.668632 GACGAGGATGGCACCCAA 59.331 61.111 0.00 0.00 36.95 4.12
1896 2933 0.394352 GACGAGGATGGCACCCAATT 60.394 55.000 0.00 0.00 36.95 2.32
1913 2950 1.151760 ATTAGCAGCATCCATCCCCA 58.848 50.000 0.00 0.00 0.00 4.96
1938 2975 2.365901 GGGTATGGACGGTCCCCA 60.366 66.667 23.81 7.89 35.03 4.96
1942 2979 0.544697 GTATGGACGGTCCCCACAAT 59.455 55.000 23.81 12.68 35.03 2.71
1948 2985 1.450312 CGGTCCCCACAATGAGCTC 60.450 63.158 6.82 6.82 0.00 4.09
1957 2994 2.092538 CCACAATGAGCTCCTGGATCTT 60.093 50.000 12.15 0.00 0.00 2.40
2047 3096 2.095314 TGCAAATCATGTGTACAAGGCG 60.095 45.455 0.00 0.00 0.00 5.52
2069 3124 2.760634 TGAGAGCCAATACGAAGCAA 57.239 45.000 0.00 0.00 0.00 3.91
2087 3154 3.264845 GGGCTTGGGTCCCTCCAA 61.265 66.667 10.00 0.00 43.82 3.53
2103 3170 2.647802 CTCCAAGGAAACTAGGGGGAAA 59.352 50.000 0.00 0.00 42.68 3.13
2105 3172 2.378886 CCAAGGAAACTAGGGGGAAACT 59.621 50.000 0.00 0.00 42.68 2.66
2147 3214 0.032815 GGAGATACTCCGGCAGCTTC 59.967 60.000 0.00 0.00 41.08 3.86
2180 3253 4.742201 CCACCAGTGGCGGTCTCG 62.742 72.222 9.78 0.00 44.73 4.04
2218 3291 2.655090 TCAAAGAGTGCATTGGGACA 57.345 45.000 0.00 0.00 37.91 4.02
2236 4937 6.310941 TGGGACAAAGAGGTAATTCATTCAA 58.689 36.000 0.00 0.00 31.92 2.69
2247 4948 8.511604 AGGTAATTCATTCAATCAGTTACCTG 57.488 34.615 7.34 0.00 44.79 4.00
2251 4952 8.641498 AATTCATTCAATCAGTTACCTGTCTT 57.359 30.769 0.00 0.00 39.82 3.01
2261 4964 6.588204 TCAGTTACCTGTCTTTTTCTTGCTA 58.412 36.000 0.00 0.00 39.82 3.49
2263 4966 8.372459 TCAGTTACCTGTCTTTTTCTTGCTATA 58.628 33.333 0.00 0.00 39.82 1.31
2288 4991 8.574251 ACTAGCTTCATCTATCGATGTAATCT 57.426 34.615 8.54 4.78 45.76 2.40
2312 5015 9.950680 TCTTTGTCTGATTAGTTTTTCATGTTC 57.049 29.630 0.00 0.00 0.00 3.18
2340 5044 7.406031 TCTGTACCTAGGTTCTTCATTGTAG 57.594 40.000 22.11 5.86 0.00 2.74
2359 5063 6.691754 TGTAGTTGATGACTTGCAGAAAAA 57.308 33.333 0.00 0.00 39.86 1.94
2417 5121 5.007682 GGTTTAAGTGGCAGATTTCTGGTA 58.992 41.667 9.49 0.00 43.94 3.25
2435 5139 2.550606 GGTAACAACGTCCATTCAGCAA 59.449 45.455 0.00 0.00 0.00 3.91
2472 5176 4.377897 CAGCAGCTCATCTGTTCATGATA 58.622 43.478 0.00 0.00 44.66 2.15
2477 5181 6.238676 GCAGCTCATCTGTTCATGATAATGTT 60.239 38.462 0.00 0.00 44.66 2.71
2519 5223 4.619863 GCCGACCAACACTCAAGACTATTA 60.620 45.833 0.00 0.00 0.00 0.98
2531 5235 9.311916 CACTCAAGACTATTATTCTTCAAGGAG 57.688 37.037 7.04 7.04 30.56 3.69
2603 5307 3.015327 AGCTCTCAAGAAATGTGATGGC 58.985 45.455 0.00 0.00 31.56 4.40
2622 5326 1.251251 CCTTCCCCTTGCTCTTGTTG 58.749 55.000 0.00 0.00 0.00 3.33
2646 5350 1.042003 TGCCAGGTTCTTGCAAAGCA 61.042 50.000 0.00 0.00 45.70 3.91
2665 5369 2.436417 CACAGGTAATCCAACACCCAG 58.564 52.381 0.00 0.00 35.25 4.45
2667 5371 0.999712 AGGTAATCCAACACCCAGGG 59.000 55.000 2.85 2.85 35.25 4.45
2669 5373 1.064685 GGTAATCCAACACCCAGGGAG 60.065 57.143 14.54 7.02 33.47 4.30
2684 5388 0.331616 GGGAGTGGGCAAGGTTATGT 59.668 55.000 0.00 0.00 0.00 2.29
2710 5414 1.482593 CCTGGGTACACATCTGGAGAC 59.517 57.143 0.00 0.00 0.00 3.36
2956 5676 1.442526 CGGAGCATCATCCAGCCAAC 61.443 60.000 0.00 0.00 39.53 3.77
3137 5857 0.183014 ATCATGCAAGGCCCAGAGAG 59.817 55.000 0.00 0.00 0.00 3.20
3481 6201 2.030451 GGAAGTTCAAGCTCAAGCAAGG 60.030 50.000 5.01 0.00 45.16 3.61
3492 6212 2.300152 CTCAAGCAAGGTGTAGGAGACA 59.700 50.000 0.00 0.00 34.94 3.41
3496 6216 1.623811 GCAAGGTGTAGGAGACAGGAA 59.376 52.381 0.00 0.00 39.29 3.36
3554 6274 1.341080 AATTGGAAACACTGGCAGGG 58.659 50.000 16.86 16.86 42.67 4.45
3740 6460 0.683504 GGACCCCTTCGCTCTCACTA 60.684 60.000 0.00 0.00 0.00 2.74
3749 6469 4.266502 CCTTCGCTCTCACTAAATTTCGAG 59.733 45.833 0.00 0.00 0.00 4.04
3800 6520 5.296151 TCTCTCTGGAGAAAAGAAAGCAA 57.704 39.130 1.86 0.00 44.62 3.91
3833 6553 1.456296 TTGAATCGCTCAAGCTGCAT 58.544 45.000 1.02 0.00 39.20 3.96
3891 6611 1.938585 TCTGGGTGGTCTCACTAAGG 58.061 55.000 0.00 0.00 43.17 2.69
3894 6614 3.170717 CTGGGTGGTCTCACTAAGGTAA 58.829 50.000 0.00 0.00 43.17 2.85
3935 6655 0.905357 GCCTGAGCCAAGACTTCCTA 59.095 55.000 0.00 0.00 0.00 2.94
3947 6667 0.041833 ACTTCCTAGCTGCCCTGAGA 59.958 55.000 0.00 0.00 0.00 3.27
3963 6683 1.228862 AGAAAAATGCCCGGCCTGT 60.229 52.632 7.03 0.00 0.00 4.00
3964 6684 0.831711 AGAAAAATGCCCGGCCTGTT 60.832 50.000 7.03 0.00 0.00 3.16
3980 6700 0.740149 TGTTGCACTTGAAGCTGGTG 59.260 50.000 0.00 0.00 0.00 4.17
3999 6719 3.633361 GCAACTAGCCTGGACAAGT 57.367 52.632 0.00 0.00 37.23 3.16
4040 6761 2.125753 GAGAGCCTGACACGCCTG 60.126 66.667 0.00 0.00 0.00 4.85
4041 6762 2.601666 AGAGCCTGACACGCCTGA 60.602 61.111 0.00 0.00 0.00 3.86
4062 6783 1.758280 CCATTGTGGTGGAATCCATGG 59.242 52.381 4.81 4.97 42.02 3.66
4065 6786 2.692709 TGTGGTGGAATCCATGGTTT 57.307 45.000 12.58 10.04 39.81 3.27
4076 6797 1.355381 TCCATGGTTTGTCAGCTGGAT 59.645 47.619 15.13 0.00 30.04 3.41
4082 6803 3.202818 TGGTTTGTCAGCTGGATATCCAT 59.797 43.478 24.73 8.54 46.46 3.41
4084 6805 4.202441 GTTTGTCAGCTGGATATCCATGT 58.798 43.478 24.73 12.15 46.46 3.21
4097 6818 0.339859 TCCATGTGGGAGCTCTACCT 59.660 55.000 14.64 3.82 42.15 3.08
4144 6865 6.874288 ATGCAAAAATCTAGATGGCTCTAC 57.126 37.500 5.86 0.00 32.66 2.59
4147 6868 6.886459 TGCAAAAATCTAGATGGCTCTACTTT 59.114 34.615 5.86 0.00 32.66 2.66
4149 6870 7.066284 GCAAAAATCTAGATGGCTCTACTTTCA 59.934 37.037 5.86 0.00 32.66 2.69
4160 6881 1.339929 TCTACTTTCAGCACGTCAGCA 59.660 47.619 0.36 0.00 36.85 4.41
4166 6887 2.029666 AGCACGTCAGCAGTCCAC 59.970 61.111 0.36 0.00 36.85 4.02
4173 6894 1.802069 GTCAGCAGTCCACTCCTTTC 58.198 55.000 0.00 0.00 0.00 2.62
4191 6912 5.046304 TCCTTTCGACATCTTGAGGAGATTT 60.046 40.000 0.00 0.00 42.55 2.17
4196 6917 5.042593 CGACATCTTGAGGAGATTTCTCTG 58.957 45.833 7.47 0.00 42.55 3.35
4202 6923 2.134346 GAGGAGATTTCTCTGCATCGC 58.866 52.381 7.47 0.00 41.99 4.58
4211 6932 3.869272 CTGCATCGCGAAGTGGGC 61.869 66.667 15.24 12.77 39.32 5.36
4250 6971 3.893813 AGTGGAAAGAAGCAGCAAAGAAT 59.106 39.130 0.00 0.00 0.00 2.40
4258 6979 1.615392 AGCAGCAAAGAATCACCCAAC 59.385 47.619 0.00 0.00 0.00 3.77
4262 6983 1.880027 GCAAAGAATCACCCAACTCGT 59.120 47.619 0.00 0.00 0.00 4.18
4280 7001 1.993370 CGTCGTCCCAAGATCTTGTTC 59.007 52.381 29.03 18.64 38.85 3.18
4300 7021 2.492088 TCCTCTAGACACCATCAACACG 59.508 50.000 0.00 0.00 0.00 4.49
4348 7070 1.101331 CTTGCAATGAGCTTCCTCCC 58.899 55.000 0.00 0.00 45.94 4.30
4388 7119 7.227873 TCACATCCTGGTAATGACACTTTTTA 58.772 34.615 2.65 0.00 0.00 1.52
4562 7346 8.448615 GTTGTGTCACCACTAGGATTTATTTAC 58.551 37.037 0.00 0.00 42.34 2.01
4589 7378 8.654485 TGTAACAGACCTAAGTTAATGACCTA 57.346 34.615 0.00 0.00 32.55 3.08
4610 7404 6.183360 ACCTATTAAGCTGAGCAAACGATTTC 60.183 38.462 7.39 0.00 0.00 2.17
4682 7477 7.551585 TCTGTTTGTTGTTGGACATGTATTTT 58.448 30.769 0.00 0.00 0.00 1.82
4823 7852 1.008079 GTTGTGCACTGCTTCCTGC 60.008 57.895 19.41 0.00 43.25 4.85
4857 7886 2.770164 AGCGAGGTTAAGTTCTGCAT 57.230 45.000 0.00 0.00 0.00 3.96
4870 7902 3.136077 AGTTCTGCATGCTGATGGTCTAT 59.864 43.478 25.45 6.50 0.00 1.98
4892 7926 6.662865 ATATATGTAGCTGAGCTGTGAAGT 57.337 37.500 18.79 1.34 40.10 3.01
4946 7980 4.686972 TGCCGATAATTCTGAAGTCTGAG 58.313 43.478 0.00 0.00 0.00 3.35
5017 8051 6.109156 TCTGAACATTTGGCTGTAGTTAGA 57.891 37.500 0.00 0.00 0.00 2.10
5060 8095 3.929610 GACAATCTTTCTCCTTCAGACCG 59.070 47.826 0.00 0.00 0.00 4.79
5084 8152 3.403038 CCATTAATGGTGGACGGAGATC 58.597 50.000 24.12 0.00 43.05 2.75
5104 8172 4.537433 GCCTGCCCCTCACGCTAG 62.537 72.222 0.00 0.00 0.00 3.42
5105 8173 4.537433 CCTGCCCCTCACGCTAGC 62.537 72.222 4.06 4.06 0.00 3.42
5106 8174 3.465403 CTGCCCCTCACGCTAGCT 61.465 66.667 13.93 0.00 0.00 3.32
5107 8175 3.729965 CTGCCCCTCACGCTAGCTG 62.730 68.421 13.93 10.24 0.00 4.24
5148 8216 1.346068 ACCCTCTCTTTCTGTGCTGAC 59.654 52.381 0.00 0.00 0.00 3.51
5172 8240 3.317711 GGTTGACAATCACACACCAATCA 59.682 43.478 0.00 0.00 0.00 2.57
5174 8242 4.834357 TGACAATCACACACCAATCAAG 57.166 40.909 0.00 0.00 0.00 3.02
5369 8475 0.249238 ATCTTCATCGAGCGACTGCC 60.249 55.000 0.00 0.00 44.31 4.85
5520 8759 9.515226 TGGTTTAGTTTTATCTCATATATGCCC 57.485 33.333 7.92 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.450818 AGATAGTGGTTGCAATTCCCTAA 57.549 39.130 0.59 0.00 0.00 2.69
16 17 4.968259 AGTACACAAGATAGTGGTTGCAA 58.032 39.130 0.00 0.00 43.72 4.08
17 18 4.283467 AGAGTACACAAGATAGTGGTTGCA 59.717 41.667 0.00 0.00 43.72 4.08
46 47 0.969149 TGGAGCTCACGTTCAGTCAT 59.031 50.000 17.19 0.00 0.00 3.06
81 82 0.471022 GCCTTGGGAGGGGACAAAAA 60.471 55.000 0.00 0.00 43.75 1.94
82 83 1.155155 GCCTTGGGAGGGGACAAAA 59.845 57.895 0.00 0.00 43.75 2.44
86 87 2.356667 CAAGCCTTGGGAGGGGAC 59.643 66.667 0.00 0.00 43.75 4.46
112 125 2.623915 GCATGCATCGATCCTGGGC 61.624 63.158 14.21 0.00 0.00 5.36
113 126 1.072678 AGCATGCATCGATCCTGGG 59.927 57.895 21.98 0.00 0.00 4.45
117 130 1.002033 GTTTCCAGCATGCATCGATCC 60.002 52.381 21.98 0.00 31.97 3.36
124 137 0.403655 TGGGTAGTTTCCAGCATGCA 59.596 50.000 21.98 0.00 31.97 3.96
133 146 3.626028 CAGTTTGTGCTGGGTAGTTTC 57.374 47.619 0.00 0.00 33.11 2.78
145 158 3.713858 TTTGGATGTCAGCAGTTTGTG 57.286 42.857 0.00 0.00 0.00 3.33
160 173 1.976474 GCATCGTGGGCCTTTTGGA 60.976 57.895 4.53 0.00 44.07 3.53
174 187 1.030488 AGCATCACAGTGGCTGCATC 61.030 55.000 23.03 0.00 36.34 3.91
176 189 0.824595 AAAGCATCACAGTGGCTGCA 60.825 50.000 23.03 0.00 38.04 4.41
178 191 0.388134 GCAAAGCATCACAGTGGCTG 60.388 55.000 5.19 2.92 38.04 4.85
187 200 0.038021 TGGTAGCCAGCAAAGCATCA 59.962 50.000 0.00 0.00 0.00 3.07
188 201 1.176527 TTGGTAGCCAGCAAAGCATC 58.823 50.000 0.00 0.00 39.14 3.91
189 202 1.631405 TTTGGTAGCCAGCAAAGCAT 58.369 45.000 5.37 0.00 44.86 3.79
190 203 3.123943 TTTGGTAGCCAGCAAAGCA 57.876 47.368 5.37 0.00 44.86 3.91
194 207 0.326595 TCGGATTTGGTAGCCAGCAA 59.673 50.000 0.00 0.00 40.29 3.91
195 208 0.326595 TTCGGATTTGGTAGCCAGCA 59.673 50.000 0.00 0.00 33.81 4.41
196 209 0.733150 GTTCGGATTTGGTAGCCAGC 59.267 55.000 0.00 0.00 33.81 4.85
197 210 1.737793 GTGTTCGGATTTGGTAGCCAG 59.262 52.381 0.00 0.00 33.81 4.85
205 218 8.233868 TGTAGACATAAAATGTGTTCGGATTTG 58.766 33.333 0.00 0.00 45.03 2.32
211 224 6.254804 TCGGATGTAGACATAAAATGTGTTCG 59.745 38.462 0.00 0.00 45.03 3.95
227 240 4.750098 ACACAACTGAAAACTCGGATGTAG 59.250 41.667 0.00 0.00 32.01 2.74
233 246 2.936498 ACAGACACAACTGAAAACTCGG 59.064 45.455 0.00 0.00 40.63 4.63
236 249 5.356751 TGCAATACAGACACAACTGAAAACT 59.643 36.000 0.00 0.00 40.63 2.66
253 266 5.801350 TTTAGAGTGATGCACTGCAATAC 57.199 39.130 8.03 10.00 45.44 1.89
254 267 5.528690 GGATTTAGAGTGATGCACTGCAATA 59.471 40.000 8.03 0.00 45.44 1.90
278 626 2.749076 CACCACCTGACATACCAATGTG 59.251 50.000 0.00 0.00 46.49 3.21
279 627 7.999457 GTGACACCACCTGACATACCAATGT 62.999 48.000 0.00 0.00 41.93 2.71
286 634 1.001974 GCTGTGACACCACCTGACATA 59.998 52.381 2.45 0.00 42.53 2.29
290 638 2.828868 GGCTGTGACACCACCTGA 59.171 61.111 2.45 0.00 42.53 3.86
666 1014 2.507484 TGTGGAGGATGAGCAACAAAG 58.493 47.619 0.00 0.00 0.00 2.77
667 1015 2.655090 TGTGGAGGATGAGCAACAAA 57.345 45.000 0.00 0.00 0.00 2.83
668 1016 2.655090 TTGTGGAGGATGAGCAACAA 57.345 45.000 0.00 0.00 0.00 2.83
669 1017 2.655090 TTTGTGGAGGATGAGCAACA 57.345 45.000 0.00 0.00 0.00 3.33
670 1018 2.424956 GGATTTGTGGAGGATGAGCAAC 59.575 50.000 0.00 0.00 0.00 4.17
686 1034 2.954318 CGCCATCCAATCAAGAGGATTT 59.046 45.455 0.00 0.00 43.76 2.17
696 1044 3.119531 TGAAAATCACACGCCATCCAATC 60.120 43.478 0.00 0.00 0.00 2.67
697 1045 2.824936 TGAAAATCACACGCCATCCAAT 59.175 40.909 0.00 0.00 0.00 3.16
698 1046 2.234143 TGAAAATCACACGCCATCCAA 58.766 42.857 0.00 0.00 0.00 3.53
700 1048 2.684881 AGATGAAAATCACACGCCATCC 59.315 45.455 0.00 0.00 33.00 3.51
703 1052 2.351641 GCAAGATGAAAATCACACGCCA 60.352 45.455 0.00 0.00 0.00 5.69
708 1057 4.386350 CGCATTTGCAAGATGAAAATCACA 59.614 37.500 19.34 0.00 33.43 3.58
750 1100 8.713971 TCTTTCACACCACATCTACCAATATAT 58.286 33.333 0.00 0.00 0.00 0.86
754 1104 5.003804 GTCTTTCACACCACATCTACCAAT 58.996 41.667 0.00 0.00 0.00 3.16
764 1114 5.758296 TGAACTCATAAGTCTTTCACACCAC 59.242 40.000 0.00 0.00 33.48 4.16
771 1121 5.649831 AGCCCAATGAACTCATAAGTCTTTC 59.350 40.000 0.00 0.00 35.10 2.62
776 1126 6.662755 TCAATAGCCCAATGAACTCATAAGT 58.337 36.000 0.00 0.00 35.10 2.24
786 1136 2.799126 ACCGTTCAATAGCCCAATGA 57.201 45.000 0.00 0.00 0.00 2.57
791 1141 2.143925 GATGCTACCGTTCAATAGCCC 58.856 52.381 1.07 0.00 42.67 5.19
793 1143 1.192534 GCGATGCTACCGTTCAATAGC 59.807 52.381 0.00 0.00 43.46 2.97
797 1147 0.036765 AAGGCGATGCTACCGTTCAA 60.037 50.000 0.00 0.00 0.00 2.69
816 1166 4.970472 GCATTTGCATTGACTCGAAAAA 57.030 36.364 0.00 0.00 41.59 1.94
847 1197 3.244181 TGTCAGTTTAGCATGCAGTGAGA 60.244 43.478 21.98 13.23 0.00 3.27
856 1206 9.463443 GTTTATTTCAACTTGTCAGTTTAGCAT 57.537 29.630 0.00 0.00 40.66 3.79
862 1212 8.428186 TCGTAGTTTATTTCAACTTGTCAGTT 57.572 30.769 0.00 0.00 44.72 3.16
867 1217 7.906527 GTGTGTTCGTAGTTTATTTCAACTTGT 59.093 33.333 0.00 0.00 38.07 3.16
877 1227 2.288948 TGGCGGTGTGTTCGTAGTTTAT 60.289 45.455 0.00 0.00 0.00 1.40
908 1299 2.299013 TGATGCACTAACGAAGTCTGGT 59.701 45.455 0.00 0.00 45.00 4.00
914 1305 5.839262 TTACACTTGATGCACTAACGAAG 57.161 39.130 0.00 0.00 0.00 3.79
917 1308 7.851822 AAAAATTACACTTGATGCACTAACG 57.148 32.000 0.00 0.00 0.00 3.18
944 1339 2.061028 GCGTTCCTGCCAATTTGAAAG 58.939 47.619 0.00 0.00 0.00 2.62
989 1384 9.471702 AGTACAGGTAGTAGTTTAAGATAGCAA 57.528 33.333 0.00 0.00 32.36 3.91
996 1391 6.812160 CCAAGCAGTACAGGTAGTAGTTTAAG 59.188 42.308 0.00 0.00 34.09 1.85
1005 1400 4.471904 TTGATCCAAGCAGTACAGGTAG 57.528 45.455 0.00 0.00 0.00 3.18
1009 1404 3.875727 CCTCATTGATCCAAGCAGTACAG 59.124 47.826 0.00 0.00 0.00 2.74
1010 1405 3.264193 ACCTCATTGATCCAAGCAGTACA 59.736 43.478 0.00 0.00 0.00 2.90
1071 1466 9.098355 TCTATTACTAAAGCACTGCAATACAAG 57.902 33.333 3.30 0.00 0.00 3.16
1072 1467 9.613428 ATCTATTACTAAAGCACTGCAATACAA 57.387 29.630 3.30 0.00 0.00 2.41
1073 1468 9.613428 AATCTATTACTAAAGCACTGCAATACA 57.387 29.630 3.30 0.00 0.00 2.29
1076 1471 9.838339 ACTAATCTATTACTAAAGCACTGCAAT 57.162 29.630 3.30 0.00 0.00 3.56
1122 1610 4.988540 GCAACCTTGGGAAACATAAAGAAC 59.011 41.667 0.00 0.00 0.00 3.01
1171 1676 1.139058 CCCTTGATACGGCAGTAAGCT 59.861 52.381 0.00 0.00 44.79 3.74
1181 1689 3.119531 TGCTTTTCATTGCCCTTGATACG 60.120 43.478 0.00 0.00 0.00 3.06
1237 2099 3.203040 AGCTAAGGTACCTAGACCCGTTA 59.797 47.826 16.67 0.00 40.74 3.18
1252 2114 3.539604 CAGGGATGAAGTTGAGCTAAGG 58.460 50.000 0.00 0.00 0.00 2.69
1285 2150 1.726791 CATGGAGTTTTCACGGACGAG 59.273 52.381 0.00 0.00 0.00 4.18
1291 2166 4.633126 AGATCACATCATGGAGTTTTCACG 59.367 41.667 0.00 0.00 0.00 4.35
1347 2222 6.049149 CCTTTTCTCTTTCACTCTGTGTGTA 58.951 40.000 9.41 0.00 46.27 2.90
1358 2384 3.007940 TCCATCGCTCCTTTTCTCTTTCA 59.992 43.478 0.00 0.00 0.00 2.69
1361 2387 2.093235 CCTCCATCGCTCCTTTTCTCTT 60.093 50.000 0.00 0.00 0.00 2.85
1367 2393 1.222936 CAGCCTCCATCGCTCCTTT 59.777 57.895 0.00 0.00 33.17 3.11
1369 2395 2.364842 ACAGCCTCCATCGCTCCT 60.365 61.111 0.00 0.00 33.17 3.69
1370 2396 2.202987 CACAGCCTCCATCGCTCC 60.203 66.667 0.00 0.00 33.17 4.70
1374 2402 1.448540 GTCACCACAGCCTCCATCG 60.449 63.158 0.00 0.00 0.00 3.84
1409 2437 1.741770 GCACCATCCACTCCACGAC 60.742 63.158 0.00 0.00 0.00 4.34
1504 2532 2.033424 GGCCGAAATCATAGCAAACTCC 59.967 50.000 0.00 0.00 0.00 3.85
1712 2749 0.106419 AACTTGTTCCGGGCCTTCAA 60.106 50.000 0.84 0.84 0.00 2.69
1749 2786 2.024560 TCCTCTGATCTCCTCTTGAGCA 60.025 50.000 0.00 0.00 41.18 4.26
1772 2809 5.422012 TGTATGTGTCTCTCAGCTGGAATAA 59.578 40.000 15.13 0.00 0.00 1.40
1778 2815 2.538437 GCTGTATGTGTCTCTCAGCTG 58.462 52.381 7.63 7.63 45.14 4.24
1846 2883 2.335369 GTCGGCGTGTCTGTCTGT 59.665 61.111 6.85 0.00 0.00 3.41
1894 2931 1.151760 TGGGGATGGATGCTGCTAAT 58.848 50.000 0.00 0.00 0.00 1.73
1896 2933 0.402887 CATGGGGATGGATGCTGCTA 59.597 55.000 0.00 0.00 0.00 3.49
1913 2950 2.915869 GTCCATACCCACGGGCAT 59.084 61.111 0.69 0.00 39.32 4.40
1938 2975 5.226194 GATAAGATCCAGGAGCTCATTGT 57.774 43.478 17.19 0.00 0.00 2.71
1957 2994 1.828081 CTGCTGCTCCTGCTGGATA 59.172 57.895 13.33 4.80 42.29 2.59
2047 3096 3.198068 TGCTTCGTATTGGCTCTCAATC 58.802 45.455 0.00 0.00 44.32 2.67
2087 3154 1.993301 CCAGTTTCCCCCTAGTTTCCT 59.007 52.381 0.00 0.00 0.00 3.36
2089 3156 1.616187 GCCCAGTTTCCCCCTAGTTTC 60.616 57.143 0.00 0.00 0.00 2.78
2304 5007 7.016153 ACCTAGGTACAGAATTGAACATGAA 57.984 36.000 14.41 0.00 0.00 2.57
2312 5015 7.607991 ACAATGAAGAACCTAGGTACAGAATTG 59.392 37.037 24.24 24.24 0.00 2.32
2317 5021 7.171630 ACTACAATGAAGAACCTAGGTACAG 57.828 40.000 16.67 5.63 0.00 2.74
2318 5022 7.233962 TCAACTACAATGAAGAACCTAGGTACA 59.766 37.037 16.67 13.38 0.00 2.90
2417 5121 2.297701 ACTTGCTGAATGGACGTTGTT 58.702 42.857 0.00 0.00 0.00 2.83
2420 5124 2.076863 GCTACTTGCTGAATGGACGTT 58.923 47.619 0.00 0.00 38.95 3.99
2424 5128 3.253188 GTGTTTGCTACTTGCTGAATGGA 59.747 43.478 0.00 0.00 43.37 3.41
2435 5139 1.538512 CTGCTGCATGTGTTTGCTACT 59.461 47.619 1.31 0.00 43.18 2.57
2444 5148 0.378610 CAGATGAGCTGCTGCATGTG 59.621 55.000 18.42 14.52 42.74 3.21
2472 5176 5.789643 AGAGTTGCCATTGTGTAAACATT 57.210 34.783 0.00 0.00 0.00 2.71
2519 5223 3.814504 TGGAAAGCCTCCTTGAAGAAT 57.185 42.857 0.00 0.00 45.64 2.40
2531 5235 4.759183 GGTAGATCATCATCTTGGAAAGCC 59.241 45.833 0.00 0.00 45.70 4.35
2585 5289 3.726557 AGGCCATCACATTTCTTGAGA 57.273 42.857 5.01 0.00 0.00 3.27
2603 5307 1.251251 CAACAAGAGCAAGGGGAAGG 58.749 55.000 0.00 0.00 0.00 3.46
2622 5326 2.924105 GCAAGAACCTGGCAGTGGC 61.924 63.158 14.43 10.30 40.13 5.01
2646 5350 1.354368 CCTGGGTGTTGGATTACCTGT 59.646 52.381 0.00 0.00 37.15 4.00
2665 5369 0.331616 ACATAACCTTGCCCACTCCC 59.668 55.000 0.00 0.00 0.00 4.30
2667 5371 0.811281 GCACATAACCTTGCCCACTC 59.189 55.000 0.00 0.00 32.21 3.51
2677 5381 0.251608 ACCCAGGTTGGCACATAACC 60.252 55.000 0.00 0.00 46.26 2.85
2684 5388 0.037590 GATGTGTACCCAGGTTGGCA 59.962 55.000 0.00 0.00 35.79 4.92
2710 5414 6.373186 TCATTCTTGCAAATAGCTCATCAG 57.627 37.500 0.00 0.00 45.94 2.90
2878 5598 9.533253 CATCAACATCACTACATGTATTGTCTA 57.467 33.333 19.26 4.74 39.87 2.59
2956 5676 2.125310 TGTTACCGCTGGCATCCG 60.125 61.111 0.00 0.00 0.00 4.18
3137 5857 4.607955 GAACAAGAGTTAAACCTTGCACC 58.392 43.478 14.51 4.64 42.46 5.01
3249 5969 1.215423 GCCATCCTCCAAGGGTACAAT 59.785 52.381 0.00 0.00 35.59 2.71
3397 6117 3.570125 TGGCAGAATCTCTATCGGTGTAG 59.430 47.826 0.00 0.00 0.00 2.74
3481 6201 5.153950 ACTCATTTTCCTGTCTCCTACAC 57.846 43.478 0.00 0.00 33.45 2.90
3492 6212 6.613153 AGTCTGTAGCTTACTCATTTTCCT 57.387 37.500 0.00 0.00 0.00 3.36
3496 6216 6.115448 ACCAAGTCTGTAGCTTACTCATTT 57.885 37.500 0.00 0.00 0.00 2.32
3731 6451 2.609916 GCCCTCGAAATTTAGTGAGAGC 59.390 50.000 13.38 9.57 0.00 4.09
3740 6460 1.804748 GACAACTCGCCCTCGAAATTT 59.195 47.619 0.00 0.00 44.98 1.82
3800 6520 3.497640 GCGATTCAAGATAGCAGCAAGAT 59.502 43.478 0.00 0.00 0.00 2.40
3935 6655 0.893447 GCATTTTTCTCAGGGCAGCT 59.107 50.000 0.00 0.00 0.00 4.24
3947 6667 1.370810 CAACAGGCCGGGCATTTTT 59.629 52.632 31.59 13.85 0.00 1.94
3963 6683 1.737355 GCCACCAGCTTCAAGTGCAA 61.737 55.000 0.00 0.00 38.99 4.08
3964 6684 2.195567 GCCACCAGCTTCAAGTGCA 61.196 57.895 0.00 0.00 38.99 4.57
3969 6689 1.896220 CTAGTTGCCACCAGCTTCAA 58.104 50.000 0.00 0.00 44.23 2.69
4023 6744 2.125753 CAGGCGTGTCAGGCTCTC 60.126 66.667 16.51 1.21 45.76 3.20
4032 6753 1.600636 CCACAATGGTCAGGCGTGT 60.601 57.895 6.26 0.00 31.35 4.49
4076 6797 2.180086 AGGTAGAGCTCCCACATGGATA 59.820 50.000 10.93 0.00 44.07 2.59
4082 6803 2.052690 GCGAGGTAGAGCTCCCACA 61.053 63.158 10.93 0.00 0.00 4.17
4084 6805 2.442272 GGCGAGGTAGAGCTCCCA 60.442 66.667 10.93 0.00 0.00 4.37
4097 6818 3.921767 CTGCAGCGACTTGAGGCGA 62.922 63.158 11.00 0.00 0.00 5.54
4144 6865 0.510359 GACTGCTGACGTGCTGAAAG 59.490 55.000 10.97 0.00 36.10 2.62
4147 6868 2.340078 GGACTGCTGACGTGCTGA 59.660 61.111 10.97 0.00 36.10 4.26
4149 6870 2.029666 GTGGACTGCTGACGTGCT 59.970 61.111 0.00 0.00 0.00 4.40
4160 6881 2.530701 AGATGTCGAAAGGAGTGGACT 58.469 47.619 0.00 0.00 0.00 3.85
4166 6887 3.779759 CTCCTCAAGATGTCGAAAGGAG 58.220 50.000 2.10 2.10 42.73 3.69
4191 6912 1.153765 CCACTTCGCGATGCAGAGA 60.154 57.895 20.65 0.00 0.00 3.10
4202 6923 0.871722 TTGTTTCATCGCCCACTTCG 59.128 50.000 0.00 0.00 0.00 3.79
4250 6971 2.567497 GGGACGACGAGTTGGGTGA 61.567 63.158 0.00 0.00 0.00 4.02
4258 6979 1.202582 ACAAGATCTTGGGACGACGAG 59.797 52.381 33.11 9.94 44.45 4.18
4262 6983 2.233922 GAGGAACAAGATCTTGGGACGA 59.766 50.000 33.11 0.00 44.45 4.20
4280 7001 2.231478 ACGTGTTGATGGTGTCTAGAGG 59.769 50.000 0.00 0.00 0.00 3.69
4300 7021 4.265073 AGAGCACAATTCATTACCTGGAC 58.735 43.478 0.00 0.00 0.00 4.02
4348 7070 0.758734 TGTGAACTGTGGAGAGGTGG 59.241 55.000 0.00 0.00 0.00 4.61
4388 7119 3.282021 CCTGTACTGCCTGCACAATAAT 58.718 45.455 0.00 0.00 0.00 1.28
4562 7346 8.095169 AGGTCATTAACTTAGGTCTGTTACAAG 58.905 37.037 0.00 0.00 0.00 3.16
4573 7362 9.482627 CTCAGCTTAATAGGTCATTAACTTAGG 57.517 37.037 0.00 0.00 34.77 2.69
4575 7364 8.482943 TGCTCAGCTTAATAGGTCATTAACTTA 58.517 33.333 0.00 0.00 34.77 2.24
4589 7378 4.702131 AGGAAATCGTTTGCTCAGCTTAAT 59.298 37.500 0.00 0.00 36.54 1.40
4610 7404 5.649782 AGTCACCATATTTCTTGCAAAGG 57.350 39.130 0.00 0.00 46.24 3.11
4682 7477 5.733620 AGTTGACTAGGACCGAAATAACA 57.266 39.130 0.00 0.00 0.00 2.41
4763 7563 9.968870 CCAGAATCTATCCTAAACAAGTAGTAC 57.031 37.037 0.00 0.00 0.00 2.73
4857 7886 6.891908 TCAGCTACATATATAGACCATCAGCA 59.108 38.462 0.00 0.00 0.00 4.41
4870 7902 6.471233 AACTTCACAGCTCAGCTACATATA 57.529 37.500 0.00 0.00 36.40 0.86
4892 7926 3.601537 AGGGGTCTCCTCTTCTAGGTAAA 59.398 47.826 0.00 0.00 44.06 2.01
4946 7980 3.417185 GAAGCTAACTACACGCAAATGC 58.583 45.455 0.00 0.00 37.78 3.56
5017 8051 1.425066 TGTCAGGCCTCAAACCTCAAT 59.575 47.619 0.00 0.00 34.42 2.57
5104 8172 2.876368 AAGTACCAGCCGGCATCAGC 62.876 60.000 31.54 15.54 41.10 4.26
5105 8173 0.464036 TAAGTACCAGCCGGCATCAG 59.536 55.000 31.54 16.26 34.57 2.90
5106 8174 1.070134 GATAAGTACCAGCCGGCATCA 59.930 52.381 31.54 7.68 34.57 3.07
5107 8175 1.344763 AGATAAGTACCAGCCGGCATC 59.655 52.381 31.54 19.47 34.57 3.91
5148 8216 2.296792 TGGTGTGTGATTGTCAACCAG 58.703 47.619 0.00 0.00 0.00 4.00
5172 8240 6.062258 TCCCTTAAAAGATTGATCGGACTT 57.938 37.500 0.00 0.00 0.00 3.01
5174 8242 5.220605 CGTTCCCTTAAAAGATTGATCGGAC 60.221 44.000 0.00 0.00 0.00 4.79
5308 8378 4.265320 CGTTTTTCTTCAGAAACCAACAGC 59.735 41.667 13.51 0.00 43.01 4.40
5348 8454 1.764851 CAGTCGCTCGATGAAGATCC 58.235 55.000 0.00 0.00 0.00 3.36
5369 8475 3.271729 TCGTCTCCTGAGCAGTAAGTAG 58.728 50.000 0.00 0.00 0.00 2.57
5461 8575 0.179045 CCTTGGTGGTCATCCGATCC 60.179 60.000 0.00 0.00 36.30 3.36
5520 8759 7.121463 ACCGAGTTACTGGATAAGCTAGATATG 59.879 40.741 7.62 0.00 0.00 1.78
5566 8806 1.402968 CGAGCCAATGGAACCAGAATG 59.597 52.381 2.05 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.