Multiple sequence alignment - TraesCS2B01G501400

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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 TraesCS2B01G501400 chr2B 100.000 6095 0 0 804 6898 696668205 696674299 0.000000e+00 11256.0
1 TraesCS2B01G501400 chr2B 100.000 302 0 0 1 302 696667402 696667703 6.040000e-155 558.0
2 TraesCS2B01G501400 chr2D 93.930 3608 169 25 3306 6898 579386973 579390545 0.000000e+00 5404.0
3 TraesCS2B01G501400 chr2D 92.749 993 62 7 2335 3322 579385970 579386957 0.000000e+00 1426.0
4 TraesCS2B01G501400 chr2D 97.333 750 14 4 1524 2269 272795780 272796527 0.000000e+00 1269.0
5 TraesCS2B01G501400 chr2D 92.132 699 43 7 816 1510 579385276 579385966 0.000000e+00 976.0
6 TraesCS2B01G501400 chr2D 89.286 280 10 6 3 282 579385014 579385273 3.990000e-87 333.0
7 TraesCS2B01G501400 chr2A 93.510 3621 177 33 3306 6898 717137781 717141371 0.000000e+00 5332.0
8 TraesCS2B01G501400 chr2A 96.662 749 21 4 1524 2269 335829011 335828264 0.000000e+00 1242.0
9 TraesCS2B01G501400 chr2A 87.037 702 44 17 816 1510 717118758 717119419 0.000000e+00 749.0
10 TraesCS2B01G501400 chr2A 92.141 369 21 5 2543 2910 717119825 717120186 1.330000e-141 514.0
11 TraesCS2B01G501400 chr2A 93.578 218 13 1 2335 2552 717119423 717119639 2.400000e-84 324.0
12 TraesCS2B01G501400 chr2A 94.608 204 10 1 3 206 717117906 717118108 1.440000e-81 315.0
13 TraesCS2B01G501400 chr2A 95.812 191 6 2 3 191 717118537 717118727 2.420000e-79 307.0
14 TraesCS2B01G501400 chr2A 87.455 279 11 7 4 282 717114356 717114610 4.040000e-77 300.0
15 TraesCS2B01G501400 chr2A 95.455 110 5 0 4 113 717115470 717115579 7.110000e-40 176.0
16 TraesCS2B01G501400 chr2A 95.455 110 5 0 4 113 717116603 717116712 7.110000e-40 176.0
17 TraesCS2B01G501400 chr2A 95.455 66 3 0 217 282 717116766 717116831 9.460000e-19 106.0
18 TraesCS2B01G501400 chr2A 92.000 75 4 2 118 191 717115558 717115631 3.400000e-18 104.0
19 TraesCS2B01G501400 chr6A 79.422 3669 600 107 2319 5922 36109540 36105962 0.000000e+00 2449.0
20 TraesCS2B01G501400 chr6A 82.532 1872 264 45 2911 4744 36252831 36250985 0.000000e+00 1587.0
21 TraesCS2B01G501400 chr6B 80.920 3087 475 72 2890 5918 66991870 66988840 0.000000e+00 2333.0
22 TraesCS2B01G501400 chr6B 80.629 3082 472 82 2888 5917 67131065 67128057 0.000000e+00 2268.0
23 TraesCS2B01G501400 chr6B 80.247 3083 485 81 2888 5917 67323590 67320579 0.000000e+00 2206.0
24 TraesCS2B01G501400 chr6B 78.536 3005 511 90 2524 5490 66971426 66968518 0.000000e+00 1853.0
25 TraesCS2B01G501400 chr6B 82.887 1642 221 44 3134 4744 67410980 67409368 0.000000e+00 1421.0
26 TraesCS2B01G501400 chr6B 78.558 1637 250 65 3930 5519 67229129 67227547 0.000000e+00 985.0
27 TraesCS2B01G501400 chr6B 81.596 902 148 14 5012 5909 67409159 67408272 0.000000e+00 730.0
28 TraesCS2B01G501400 chr6B 82.083 480 71 11 4309 4782 68781000 68780530 5.010000e-106 396.0
29 TraesCS2B01G501400 chr6B 81.760 466 68 13 4325 4782 68750713 68751169 2.350000e-99 374.0
30 TraesCS2B01G501400 chr6D 80.603 3083 482 80 2888 5917 31754425 31751406 0.000000e+00 2274.0
31 TraesCS2B01G501400 chr6D 82.904 1901 255 45 2911 4774 23440404 23438537 0.000000e+00 1646.0
32 TraesCS2B01G501400 chr6D 97.196 749 17 4 1524 2269 168249653 168248906 0.000000e+00 1264.0
33 TraesCS2B01G501400 chr6D 81.808 907 150 12 5016 5917 23438331 23437435 0.000000e+00 747.0
34 TraesCS2B01G501400 chr6D 81.588 907 152 12 5016 5917 31768452 31767556 0.000000e+00 736.0
35 TraesCS2B01G501400 chrUn 97.997 749 11 4 1524 2269 93411518 93412265 0.000000e+00 1297.0
36 TraesCS2B01G501400 chr5D 97.463 749 15 4 1524 2269 503216332 503215585 0.000000e+00 1275.0
37 TraesCS2B01G501400 chr5D 96.529 749 20 4 1524 2269 329121993 329122738 0.000000e+00 1234.0
38 TraesCS2B01G501400 chr5D 85.859 99 11 3 8 105 428386445 428386349 1.220000e-17 102.0
39 TraesCS2B01G501400 chr5D 82.418 91 14 2 19 109 508618893 508618981 2.060000e-10 78.7
40 TraesCS2B01G501400 chr3A 96.929 749 17 5 1524 2269 672911896 672912641 0.000000e+00 1251.0
41 TraesCS2B01G501400 chr4D 96.529 749 22 4 1524 2269 19926911 19926164 0.000000e+00 1236.0
42 TraesCS2B01G501400 chr3B 97.268 732 14 4 1542 2269 201525105 201524376 0.000000e+00 1236.0


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 TraesCS2B01G501400 chr2B 696667402 696674299 6897 False 5907.00 11256 100.00000 1 6898 2 chr2B.!!$F1 6897
1 TraesCS2B01G501400 chr2D 579385014 579390545 5531 False 2034.75 5404 92.02425 3 6898 4 chr2D.!!$F2 6895
2 TraesCS2B01G501400 chr2D 272795780 272796527 747 False 1269.00 1269 97.33300 1524 2269 1 chr2D.!!$F1 745
3 TraesCS2B01G501400 chr2A 717137781 717141371 3590 False 5332.00 5332 93.51000 3306 6898 1 chr2A.!!$F1 3592
4 TraesCS2B01G501400 chr2A 335828264 335829011 747 True 1242.00 1242 96.66200 1524 2269 1 chr2A.!!$R1 745
5 TraesCS2B01G501400 chr2A 717114356 717120186 5830 False 307.10 749 92.89960 3 2910 10 chr2A.!!$F2 2907
6 TraesCS2B01G501400 chr6A 36105962 36109540 3578 True 2449.00 2449 79.42200 2319 5922 1 chr6A.!!$R1 3603
7 TraesCS2B01G501400 chr6A 36250985 36252831 1846 True 1587.00 1587 82.53200 2911 4744 1 chr6A.!!$R2 1833
8 TraesCS2B01G501400 chr6B 66988840 66991870 3030 True 2333.00 2333 80.92000 2890 5918 1 chr6B.!!$R2 3028
9 TraesCS2B01G501400 chr6B 67128057 67131065 3008 True 2268.00 2268 80.62900 2888 5917 1 chr6B.!!$R3 3029
10 TraesCS2B01G501400 chr6B 67320579 67323590 3011 True 2206.00 2206 80.24700 2888 5917 1 chr6B.!!$R5 3029
11 TraesCS2B01G501400 chr6B 66968518 66971426 2908 True 1853.00 1853 78.53600 2524 5490 1 chr6B.!!$R1 2966
12 TraesCS2B01G501400 chr6B 67408272 67410980 2708 True 1075.50 1421 82.24150 3134 5909 2 chr6B.!!$R7 2775
13 TraesCS2B01G501400 chr6B 67227547 67229129 1582 True 985.00 985 78.55800 3930 5519 1 chr6B.!!$R4 1589
14 TraesCS2B01G501400 chr6D 31751406 31754425 3019 True 2274.00 2274 80.60300 2888 5917 1 chr6D.!!$R1 3029
15 TraesCS2B01G501400 chr6D 168248906 168249653 747 True 1264.00 1264 97.19600 1524 2269 1 chr6D.!!$R3 745
16 TraesCS2B01G501400 chr6D 23437435 23440404 2969 True 1196.50 1646 82.35600 2911 5917 2 chr6D.!!$R4 3006
17 TraesCS2B01G501400 chr6D 31767556 31768452 896 True 736.00 736 81.58800 5016 5917 1 chr6D.!!$R2 901
18 TraesCS2B01G501400 chrUn 93411518 93412265 747 False 1297.00 1297 97.99700 1524 2269 1 chrUn.!!$F1 745
19 TraesCS2B01G501400 chr5D 503215585 503216332 747 True 1275.00 1275 97.46300 1524 2269 1 chr5D.!!$R2 745
20 TraesCS2B01G501400 chr5D 329121993 329122738 745 False 1234.00 1234 96.52900 1524 2269 1 chr5D.!!$F1 745
21 TraesCS2B01G501400 chr3A 672911896 672912641 745 False 1251.00 1251 96.92900 1524 2269 1 chr3A.!!$F1 745
22 TraesCS2B01G501400 chr4D 19926164 19926911 747 True 1236.00 1236 96.52900 1524 2269 1 chr4D.!!$R1 745
23 TraesCS2B01G501400 chr3B 201524376 201525105 729 True 1236.00 1236 97.26800 1542 2269 1 chr3B.!!$R1 727

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
286 287 0.368227 CGATGCAGCTTCAAGTCGTC 59.632 55.000 0.00 0.00 0.00 4.20 F
1037 4663 0.176680 TTCTTCTCCATCTGCTCCGC 59.823 55.000 0.00 0.00 0.00 5.54 F
1167 4793 1.366679 CGTCTCATGAGCTGTTGCAT 58.633 50.000 18.36 0.00 42.74 3.96 F
2953 6811 0.534877 TCAGGCGTTGTTGCATCAGT 60.535 50.000 0.00 0.00 36.28 3.41 F
3208 7066 2.299326 ATTTGGGAAGCTTCAGTGCT 57.701 45.000 27.02 6.53 46.40 4.40 F
3992 7912 4.204799 GGGATTGGCTAAAGAAATACCGT 58.795 43.478 0.00 0.00 0.00 4.83 F
4928 8915 2.448926 GGGTTTGACAATTTTCCCGG 57.551 50.000 0.00 0.00 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 5136 0.726366 TGTTATACCCCCACTCCCCT 59.274 55.000 0.00 0.0 0.0 4.79 R
2937 6795 1.064060 GGATACTGATGCAACAACGCC 59.936 52.381 0.00 0.0 0.0 5.68 R
2960 6818 2.230508 GTCAACATGTCCCGTCTACTCA 59.769 50.000 0.00 0.0 0.0 3.41 R
3843 7753 1.360820 GGCCAAGAGTTCTAGCGTTC 58.639 55.000 0.00 0.0 0.0 3.95 R
4865 8852 1.671901 GAGGGAGAGGGCAGACGAAG 61.672 65.000 0.00 0.0 0.0 3.79 R
5109 9111 1.739466 CATGCATTGTAACAGGAGCGT 59.261 47.619 0.00 0.0 0.0 5.07 R
6518 10568 0.390472 CGGTCCAGGAACTCTTCAGC 60.390 60.000 2.07 0.0 34.6 4.26 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
171 172 4.884744 GGCTGGGGTGTTATTTTTGTTTTT 59.115 37.500 0.00 0.00 0.00 1.94
174 175 6.062258 TGGGGTGTTATTTTTGTTTTTGGA 57.938 33.333 0.00 0.00 0.00 3.53
178 179 7.755822 GGGGTGTTATTTTTGTTTTTGGAAAAC 59.244 33.333 8.85 8.85 0.00 2.43
179 180 8.297426 GGGTGTTATTTTTGTTTTTGGAAAACA 58.703 29.630 13.28 13.28 38.26 2.83
180 181 9.678941 GGTGTTATTTTTGTTTTTGGAAAACAA 57.321 25.926 21.27 21.27 45.21 2.83
190 191 7.370044 GTTTTTGGAAAACAACAACAACAAC 57.630 32.000 10.48 0.00 44.93 3.32
191 192 6.677781 TTTTGGAAAACAACAACAACAACA 57.322 29.167 0.00 0.00 39.19 3.33
192 193 6.677781 TTTGGAAAACAACAACAACAACAA 57.322 29.167 0.00 0.00 39.19 2.83
193 194 5.659048 TGGAAAACAACAACAACAACAAC 57.341 34.783 0.00 0.00 0.00 3.32
194 195 5.116180 TGGAAAACAACAACAACAACAACA 58.884 33.333 0.00 0.00 0.00 3.33
195 196 5.584649 TGGAAAACAACAACAACAACAACAA 59.415 32.000 0.00 0.00 0.00 2.83
196 197 5.904630 GGAAAACAACAACAACAACAACAAC 59.095 36.000 0.00 0.00 0.00 3.32
197 198 6.422776 AAAACAACAACAACAACAACAACA 57.577 29.167 0.00 0.00 0.00 3.33
198 199 6.422776 AAACAACAACAACAACAACAACAA 57.577 29.167 0.00 0.00 0.00 2.83
199 200 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
282 283 1.065926 TGGATCGATGCAGCTTCAAGT 60.066 47.619 16.33 0.00 0.00 3.16
284 285 1.257415 GATCGATGCAGCTTCAAGTCG 59.743 52.381 0.54 3.38 0.00 4.18
286 287 0.368227 CGATGCAGCTTCAAGTCGTC 59.632 55.000 0.00 0.00 0.00 4.20
287 288 0.723981 GATGCAGCTTCAAGTCGTCC 59.276 55.000 0.00 0.00 0.00 4.79
288 289 0.674895 ATGCAGCTTCAAGTCGTCCC 60.675 55.000 0.00 0.00 0.00 4.46
289 290 2.383527 GCAGCTTCAAGTCGTCCCG 61.384 63.158 0.00 0.00 0.00 5.14
290 291 1.006102 CAGCTTCAAGTCGTCCCGT 60.006 57.895 0.00 0.00 0.00 5.28
291 292 1.009389 CAGCTTCAAGTCGTCCCGTC 61.009 60.000 0.00 0.00 0.00 4.79
292 293 1.737008 GCTTCAAGTCGTCCCGTCC 60.737 63.158 0.00 0.00 0.00 4.79
293 294 1.080025 CTTCAAGTCGTCCCGTCCC 60.080 63.158 0.00 0.00 0.00 4.46
294 295 2.814183 CTTCAAGTCGTCCCGTCCCG 62.814 65.000 0.00 0.00 0.00 5.14
881 4503 1.344438 CCGTCCATAAGGCATAGCTGA 59.656 52.381 0.00 0.00 33.74 4.26
911 4537 3.682155 GCTCATCTCATATCATCCAGGCC 60.682 52.174 0.00 0.00 0.00 5.19
1027 4653 0.902984 TGCGCCTACCTTCTTCTCCA 60.903 55.000 4.18 0.00 0.00 3.86
1037 4663 0.176680 TTCTTCTCCATCTGCTCCGC 59.823 55.000 0.00 0.00 0.00 5.54
1167 4793 1.366679 CGTCTCATGAGCTGTTGCAT 58.633 50.000 18.36 0.00 42.74 3.96
1199 4825 5.765182 ACTTGCAGGTATAGATATTGTTGCC 59.235 40.000 0.00 0.00 0.00 4.52
1203 4829 5.347907 GCAGGTATAGATATTGTTGCCGTAC 59.652 44.000 0.00 0.00 0.00 3.67
1208 4834 8.227791 GGTATAGATATTGTTGCCGTACAATTG 58.772 37.037 3.24 3.24 44.18 2.32
1211 4837 7.618502 AGATATTGTTGCCGTACAATTGTTA 57.381 32.000 17.78 0.00 44.18 2.41
1212 4838 7.469260 AGATATTGTTGCCGTACAATTGTTAC 58.531 34.615 17.78 11.48 44.18 2.50
1213 4839 4.895224 TTGTTGCCGTACAATTGTTACA 57.105 36.364 17.78 7.36 41.27 2.41
1214 4840 5.440234 TTGTTGCCGTACAATTGTTACAT 57.560 34.783 17.78 0.00 41.27 2.29
1219 4845 5.110598 TGCCGTACAATTGTTACATATCGT 58.889 37.500 17.78 0.00 0.00 3.73
1263 4889 3.573569 CGGGTCACGTTGTACAAGA 57.426 52.632 8.98 0.00 37.93 3.02
1285 4911 2.867368 ACGTGAAATACAGTCGTTTGCA 59.133 40.909 0.00 0.00 29.25 4.08
1293 4919 8.293157 TGAAATACAGTCGTTTGCATCATTTTA 58.707 29.630 0.00 0.00 0.00 1.52
1294 4920 9.289303 GAAATACAGTCGTTTGCATCATTTTAT 57.711 29.630 0.00 0.00 0.00 1.40
1298 4924 8.006741 ACAGTCGTTTGCATCATTTTATTTTC 57.993 30.769 0.00 0.00 0.00 2.29
1308 4934 8.519526 TGCATCATTTTATTTTCGTACTTCCTT 58.480 29.630 0.00 0.00 0.00 3.36
1314 4940 9.769093 ATTTTATTTTCGTACTTCCTTCATTCG 57.231 29.630 0.00 0.00 0.00 3.34
1337 4963 6.017605 TCGGGTTTATTAGTCTCACTCGTATC 60.018 42.308 0.00 0.00 32.99 2.24
1354 4980 9.530129 CACTCGTATCTTGACTCAAATTTTAAC 57.470 33.333 0.00 0.00 0.00 2.01
1407 5033 6.183359 CGTACGTCACAAAAATAATACCACGA 60.183 38.462 7.22 0.00 0.00 4.35
1424 5050 5.302360 ACCACGAAACTTCTTGCAAGTATA 58.698 37.500 25.19 11.56 0.00 1.47
1425 5051 5.938125 ACCACGAAACTTCTTGCAAGTATAT 59.062 36.000 25.19 9.85 0.00 0.86
1519 5145 6.704056 ACCTAAAATATGATAGGGGAGTGG 57.296 41.667 15.16 0.00 42.51 4.00
1520 5146 5.551977 ACCTAAAATATGATAGGGGAGTGGG 59.448 44.000 15.16 0.00 42.51 4.61
1521 5147 5.044846 CCTAAAATATGATAGGGGAGTGGGG 60.045 48.000 6.28 0.00 35.95 4.96
1522 5148 2.668850 ATATGATAGGGGAGTGGGGG 57.331 55.000 0.00 0.00 0.00 5.40
1600 5228 9.681062 ATCTAAGATTTCGATTCCCAGTAAAAA 57.319 29.630 0.00 0.00 0.00 1.94
1803 5434 8.160106 AGGGCTCGAATAGAAAAATAGAATCAT 58.840 33.333 0.00 0.00 0.00 2.45
1987 5618 9.898152 AGAATTAGAGAAAGATCTACAAAAGGG 57.102 33.333 0.00 0.00 35.54 3.95
2184 5818 6.459670 AAAGTAAAAATTGTGGGTCGTCTT 57.540 33.333 0.00 0.00 0.00 3.01
2204 5838 4.895297 TCTTGGAGGAAAAGAAATTGCACT 59.105 37.500 0.00 0.00 30.79 4.40
2269 5903 3.965594 TCGCGCTAAAATTGATTATTGCG 59.034 39.130 5.56 0.00 44.10 4.85
2270 5904 3.117832 CGCGCTAAAATTGATTATTGCGG 59.882 43.478 5.56 0.00 41.99 5.69
2271 5905 3.425193 GCGCTAAAATTGATTATTGCGGG 59.575 43.478 0.00 0.00 41.99 6.13
2272 5906 3.980775 CGCTAAAATTGATTATTGCGGGG 59.019 43.478 0.00 0.00 38.74 5.73
2273 5907 4.306600 GCTAAAATTGATTATTGCGGGGG 58.693 43.478 0.00 0.00 0.00 5.40
2298 5932 3.229697 GGGGGATAAACCAGGATGAAG 57.770 52.381 0.00 0.00 39.69 3.02
2299 5933 2.158460 GGGGGATAAACCAGGATGAAGG 60.158 54.545 0.00 0.00 39.69 3.46
2300 5934 2.783510 GGGGATAAACCAGGATGAAGGA 59.216 50.000 0.00 0.00 39.69 3.36
2301 5935 3.204382 GGGGATAAACCAGGATGAAGGAA 59.796 47.826 0.00 0.00 39.69 3.36
2302 5936 4.464947 GGGATAAACCAGGATGAAGGAAG 58.535 47.826 0.00 0.00 39.69 3.46
2303 5937 4.079730 GGGATAAACCAGGATGAAGGAAGT 60.080 45.833 0.00 0.00 39.69 3.01
2304 5938 4.884164 GGATAAACCAGGATGAAGGAAGTG 59.116 45.833 0.00 0.00 39.69 3.16
2305 5939 3.884037 AAACCAGGATGAAGGAAGTGT 57.116 42.857 0.00 0.00 39.69 3.55
2306 5940 3.884037 AACCAGGATGAAGGAAGTGTT 57.116 42.857 0.00 0.00 39.69 3.32
2307 5941 3.146104 ACCAGGATGAAGGAAGTGTTG 57.854 47.619 0.00 0.00 39.69 3.33
2308 5942 2.443255 ACCAGGATGAAGGAAGTGTTGT 59.557 45.455 0.00 0.00 39.69 3.32
2309 5943 3.117512 ACCAGGATGAAGGAAGTGTTGTT 60.118 43.478 0.00 0.00 39.69 2.83
2310 5944 3.891366 CCAGGATGAAGGAAGTGTTGTTT 59.109 43.478 0.00 0.00 39.69 2.83
2311 5945 4.261741 CCAGGATGAAGGAAGTGTTGTTTG 60.262 45.833 0.00 0.00 39.69 2.93
2312 5946 4.339247 CAGGATGAAGGAAGTGTTGTTTGT 59.661 41.667 0.00 0.00 39.69 2.83
2313 5947 4.580580 AGGATGAAGGAAGTGTTGTTTGTC 59.419 41.667 0.00 0.00 0.00 3.18
2314 5948 4.338118 GGATGAAGGAAGTGTTGTTTGTCA 59.662 41.667 0.00 0.00 0.00 3.58
2315 5949 5.010012 GGATGAAGGAAGTGTTGTTTGTCAT 59.990 40.000 0.00 0.00 0.00 3.06
2316 5950 5.247507 TGAAGGAAGTGTTGTTTGTCATG 57.752 39.130 0.00 0.00 0.00 3.07
2317 5951 4.097741 TGAAGGAAGTGTTGTTTGTCATGG 59.902 41.667 0.00 0.00 0.00 3.66
2318 5952 3.897239 AGGAAGTGTTGTTTGTCATGGA 58.103 40.909 0.00 0.00 0.00 3.41
2319 5953 4.277476 AGGAAGTGTTGTTTGTCATGGAA 58.723 39.130 0.00 0.00 0.00 3.53
2320 5954 4.709397 AGGAAGTGTTGTTTGTCATGGAAA 59.291 37.500 0.00 0.00 0.00 3.13
2321 5955 5.043248 GGAAGTGTTGTTTGTCATGGAAAG 58.957 41.667 0.00 0.00 0.00 2.62
2322 5956 5.394115 GGAAGTGTTGTTTGTCATGGAAAGT 60.394 40.000 0.00 0.00 0.00 2.66
2323 5957 5.659440 AGTGTTGTTTGTCATGGAAAGTT 57.341 34.783 0.00 0.00 0.00 2.66
2324 5958 6.767524 AGTGTTGTTTGTCATGGAAAGTTA 57.232 33.333 0.00 0.00 0.00 2.24
2325 5959 7.346751 AGTGTTGTTTGTCATGGAAAGTTAT 57.653 32.000 0.00 0.00 0.00 1.89
2333 5967 7.887996 TTGTCATGGAAAGTTATTTGAATGC 57.112 32.000 0.00 0.00 0.00 3.56
2357 5991 2.512692 AGCATGCATGTTTACCTCCA 57.487 45.000 26.79 0.00 0.00 3.86
2373 6007 9.948964 GTTTACCTCCATTTTCTAGTTACCTTA 57.051 33.333 0.00 0.00 0.00 2.69
2377 6011 6.386050 CCTCCATTTTCTAGTTACCTTAGGGA 59.614 42.308 2.32 0.00 36.25 4.20
2477 6115 5.843019 TCCACCAAAAGAATCTCCTAACT 57.157 39.130 0.00 0.00 0.00 2.24
2501 6139 7.544566 ACTTCAAGCTAGCAATTCATGATTTTG 59.455 33.333 18.83 7.97 0.00 2.44
2586 6435 6.870439 TGATGAGAAACAGAAGATGTGTACTG 59.130 38.462 0.00 0.00 43.00 2.74
2626 6475 7.440198 TGACATATTTTTGGAATGAGCACAAA 58.560 30.769 0.00 0.00 32.77 2.83
2937 6795 2.352960 GGAAAGCCTAGCGAATGTTCAG 59.647 50.000 0.00 0.00 0.00 3.02
2952 6810 0.592637 TTCAGGCGTTGTTGCATCAG 59.407 50.000 0.00 0.00 36.28 2.90
2953 6811 0.534877 TCAGGCGTTGTTGCATCAGT 60.535 50.000 0.00 0.00 36.28 3.41
2960 6818 3.181497 GCGTTGTTGCATCAGTATCCAAT 60.181 43.478 0.00 0.00 34.15 3.16
2970 6828 5.465051 CATCAGTATCCAATGAGTAGACGG 58.535 45.833 0.00 0.00 0.00 4.79
2972 6830 3.889538 CAGTATCCAATGAGTAGACGGGA 59.110 47.826 0.00 0.00 0.00 5.14
3041 6899 2.921634 TTCCAAGACGAGATCGACAG 57.078 50.000 9.58 0.22 43.02 3.51
3082 6940 6.183360 TGTGGATCTCGTTCATAGTGATGATT 60.183 38.462 0.00 0.00 41.77 2.57
3165 7023 8.666573 GCAGGTAAGTAAAGGAAAATCTTAGTC 58.333 37.037 0.00 0.00 0.00 2.59
3171 7029 8.834749 AGTAAAGGAAAATCTTAGTCTGTCAC 57.165 34.615 0.00 0.00 0.00 3.67
3208 7066 2.299326 ATTTGGGAAGCTTCAGTGCT 57.701 45.000 27.02 6.53 46.40 4.40
3525 7425 5.106555 ACTGTACAAGGCAAATGAATTCTCG 60.107 40.000 7.05 0.00 0.00 4.04
3761 7667 9.549078 GGAAATTCAAGAGGTTAAGAGGTATAG 57.451 37.037 0.00 0.00 0.00 1.31
3879 7796 9.487442 ACTCTTGGCCCAATTTTATTAATTAGA 57.513 29.630 0.00 0.00 0.00 2.10
3992 7912 4.204799 GGGATTGGCTAAAGAAATACCGT 58.795 43.478 0.00 0.00 0.00 4.83
3993 7913 4.643334 GGGATTGGCTAAAGAAATACCGTT 59.357 41.667 0.00 0.00 0.00 4.44
4020 7940 5.594199 AGGGACCAAGTACTTAAATGGTT 57.406 39.130 16.31 0.81 45.85 3.67
4202 8122 5.220700 GCATTGCATTGTTGTTCCCATAATG 60.221 40.000 10.11 0.00 32.73 1.90
4295 8229 5.316167 TGTCCAACAGCATATTCAGACTTT 58.684 37.500 0.00 0.00 0.00 2.66
4296 8230 6.472016 TGTCCAACAGCATATTCAGACTTTA 58.528 36.000 0.00 0.00 0.00 1.85
4297 8231 6.939730 TGTCCAACAGCATATTCAGACTTTAA 59.060 34.615 0.00 0.00 0.00 1.52
4298 8232 7.446931 TGTCCAACAGCATATTCAGACTTTAAA 59.553 33.333 0.00 0.00 0.00 1.52
4299 8233 8.462016 GTCCAACAGCATATTCAGACTTTAAAT 58.538 33.333 0.00 0.00 0.00 1.40
4300 8234 9.023962 TCCAACAGCATATTCAGACTTTAAATT 57.976 29.630 0.00 0.00 0.00 1.82
4301 8235 9.079833 CCAACAGCATATTCAGACTTTAAATTG 57.920 33.333 0.00 0.00 0.00 2.32
4302 8236 9.079833 CAACAGCATATTCAGACTTTAAATTGG 57.920 33.333 0.00 0.00 0.00 3.16
4303 8237 7.260603 ACAGCATATTCAGACTTTAAATTGGC 58.739 34.615 0.00 0.00 0.00 4.52
4304 8238 7.093814 ACAGCATATTCAGACTTTAAATTGGCA 60.094 33.333 0.00 0.00 0.00 4.92
4451 8421 8.773033 ATTAGAGATTGTTTATGCCCAAGATT 57.227 30.769 0.00 0.00 0.00 2.40
4865 8852 9.575783 TCAAGTTTTTGTGTTATGTTCCTTTAC 57.424 29.630 0.00 0.00 35.73 2.01
4928 8915 2.448926 GGGTTTGACAATTTTCCCGG 57.551 50.000 0.00 0.00 0.00 5.73
4958 8946 4.792068 TCCTTGAAAACCATCTCAACTGT 58.208 39.130 0.00 0.00 0.00 3.55
4972 8960 7.148018 CCATCTCAACTGTACATGCCTTATTTT 60.148 37.037 0.00 0.00 0.00 1.82
5109 9111 7.978414 TCACATTGATTGCACAGAAAGTTTTTA 59.022 29.630 0.00 0.00 0.00 1.52
5113 9115 4.364415 TTGCACAGAAAGTTTTTACGCT 57.636 36.364 0.00 0.00 0.00 5.07
5229 9235 4.585879 TCATTTTACTCTTACAGTGGGCC 58.414 43.478 0.00 0.00 36.43 5.80
5266 9272 4.741321 TTCATGATTGAGGGAAAATGGC 57.259 40.909 0.00 0.00 32.27 4.40
5286 9292 3.391626 GGCTATATACTAATCAGGCCCCC 59.608 52.174 0.00 0.00 33.07 5.40
5341 9363 2.826725 ACTTCAGGAGCACCACTAGTAC 59.173 50.000 2.07 0.00 38.94 2.73
5604 9654 9.685276 ACCAAATTAGACATGATCTGACATTTA 57.315 29.630 0.00 0.00 38.49 1.40
6022 10072 8.918202 AGGTAACATCTAGTCAAACATGAAAA 57.082 30.769 0.00 0.00 41.41 2.29
6056 10106 3.768215 ACTGTGGAACTAGGCTACTAACC 59.232 47.826 0.00 0.00 38.04 2.85
6057 10107 3.102204 TGTGGAACTAGGCTACTAACCC 58.898 50.000 0.00 0.00 38.04 4.11
6110 10160 1.328680 GTTGCATCACGCTACTGGATG 59.671 52.381 0.00 0.00 42.30 3.51
6286 10336 2.106074 CAGACGCCGGCATTGCTAA 61.106 57.895 28.98 0.00 0.00 3.09
6411 10461 5.426504 CAAGGTAGTCATCAAGCTCTGAAT 58.573 41.667 0.00 0.00 37.67 2.57
6419 10469 6.047870 GTCATCAAGCTCTGAATACATCTGT 58.952 40.000 0.00 0.00 37.67 3.41
6503 10553 4.823276 CCACTCGGCTGACTCATC 57.177 61.111 0.00 0.00 0.00 2.92
6518 10568 5.337554 TGACTCATCGGTTTGTAGTATTCG 58.662 41.667 0.00 0.00 0.00 3.34
6533 10583 2.393271 ATTCGCTGAAGAGTTCCTGG 57.607 50.000 0.00 0.00 0.00 4.45
6538 10588 0.969894 CTGAAGAGTTCCTGGACCGT 59.030 55.000 0.00 0.00 0.00 4.83
6539 10589 0.679505 TGAAGAGTTCCTGGACCGTG 59.320 55.000 0.00 0.00 0.00 4.94
6540 10590 0.680061 GAAGAGTTCCTGGACCGTGT 59.320 55.000 0.00 0.00 0.00 4.49
6569 10619 2.294979 TCGGATAAGTAGCTCGCTGAA 58.705 47.619 0.85 0.00 0.00 3.02
6584 10634 2.434359 GAACCTGCGCCGTAAGCT 60.434 61.111 4.18 0.00 40.39 3.74
6585 10635 2.434359 AACCTGCGCCGTAAGCTC 60.434 61.111 4.18 0.00 40.39 4.09
6685 10735 0.885879 TGCCAGTACTCGTCGAATGT 59.114 50.000 0.00 0.00 0.00 2.71
6716 10766 3.947196 TCACCATGACCAATGTAGCAATC 59.053 43.478 0.00 0.00 34.11 2.67
6774 10824 2.496470 GTCCTCACTTTCCATACCTCGT 59.504 50.000 0.00 0.00 0.00 4.18
6792 10842 6.174760 ACCTCGTTAAAGTATATGTTTGCCA 58.825 36.000 0.00 0.00 0.00 4.92
6862 10912 5.787953 TCTCAAAATCTTGCAAATGGACA 57.212 34.783 0.00 0.00 32.14 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.831715 ACACCAAATTAGTTTCATGAAATTCC 57.168 30.769 23.05 11.14 32.36 3.01
116 117 9.837525 GATTGATCAATAATTGGAGTTATGAGC 57.162 33.333 20.75 0.00 0.00 4.26
171 172 5.116180 TGTTGTTGTTGTTGTTGTTTTCCA 58.884 33.333 0.00 0.00 0.00 3.53
174 175 6.422776 TGTTGTTGTTGTTGTTGTTGTTTT 57.577 29.167 0.00 0.00 0.00 2.43
178 179 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
179 180 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
180 181 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
181 182 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
182 183 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
183 184 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
184 185 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
185 186 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
186 187 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
187 188 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
188 189 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
189 190 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
190 191 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
191 192 5.500931 CGTTGTTGTTGTTGTTGTTGTTGTT 60.501 36.000 0.00 0.00 0.00 2.83
192 193 4.026475 CGTTGTTGTTGTTGTTGTTGTTGT 60.026 37.500 0.00 0.00 0.00 3.32
193 194 4.207224 TCGTTGTTGTTGTTGTTGTTGTTG 59.793 37.500 0.00 0.00 0.00 3.33
194 195 4.360563 TCGTTGTTGTTGTTGTTGTTGTT 58.639 34.783 0.00 0.00 0.00 2.83
195 196 3.966154 TCGTTGTTGTTGTTGTTGTTGT 58.034 36.364 0.00 0.00 0.00 3.32
196 197 4.201570 CCATCGTTGTTGTTGTTGTTGTTG 60.202 41.667 0.00 0.00 0.00 3.33
197 198 3.923461 CCATCGTTGTTGTTGTTGTTGTT 59.077 39.130 0.00 0.00 0.00 2.83
198 199 3.191581 TCCATCGTTGTTGTTGTTGTTGT 59.808 39.130 0.00 0.00 0.00 3.32
199 200 3.763902 TCCATCGTTGTTGTTGTTGTTG 58.236 40.909 0.00 0.00 0.00 3.33
803 804 8.673711 CAGGTTTATATAAGGAGAGAGAGATCG 58.326 40.741 0.00 0.00 0.00 3.69
805 806 8.683445 TCCAGGTTTATATAAGGAGAGAGAGAT 58.317 37.037 0.00 0.00 0.00 2.75
807 808 7.396055 CCTCCAGGTTTATATAAGGAGAGAGAG 59.604 44.444 21.70 11.96 44.12 3.20
808 809 7.242359 CCTCCAGGTTTATATAAGGAGAGAGA 58.758 42.308 21.70 5.37 44.12 3.10
809 810 6.071051 GCCTCCAGGTTTATATAAGGAGAGAG 60.071 46.154 21.70 14.20 44.12 3.20
811 812 5.544176 TGCCTCCAGGTTTATATAAGGAGAG 59.456 44.000 21.70 15.35 44.12 3.20
812 813 5.473273 TGCCTCCAGGTTTATATAAGGAGA 58.527 41.667 21.70 7.51 44.12 3.71
813 814 5.825593 TGCCTCCAGGTTTATATAAGGAG 57.174 43.478 16.41 16.41 41.72 3.69
815 816 4.702131 GCATGCCTCCAGGTTTATATAAGG 59.298 45.833 6.36 0.00 37.57 2.69
817 818 5.317600 TGCATGCCTCCAGGTTTATATAA 57.682 39.130 16.68 0.00 37.57 0.98
881 4503 4.906618 TGATATGAGATGAGCATGTGCAT 58.093 39.130 7.83 0.00 45.16 3.96
1072 4698 3.131478 GGTCCGGCCAACATTCCG 61.131 66.667 2.24 0.00 44.89 4.30
1167 4793 9.851686 AATATCTATACCTGCAAGTCAAAATCA 57.148 29.630 0.00 0.00 0.00 2.57
1224 4850 8.877808 ACCCGTTAAGCAATACTAATACTAAC 57.122 34.615 0.00 0.00 0.00 2.34
1246 4872 1.523934 CGTTCTTGTACAACGTGACCC 59.476 52.381 3.59 0.00 41.39 4.46
1263 4889 3.310227 TGCAAACGACTGTATTTCACGTT 59.690 39.130 0.00 0.00 46.35 3.99
1270 4896 9.638239 AAATAAAATGATGCAAACGACTGTATT 57.362 25.926 0.00 0.00 0.00 1.89
1293 4919 4.634443 CCCGAATGAAGGAAGTACGAAAAT 59.366 41.667 0.00 0.00 0.00 1.82
1294 4920 3.998341 CCCGAATGAAGGAAGTACGAAAA 59.002 43.478 0.00 0.00 0.00 2.29
1298 4924 2.667473 ACCCGAATGAAGGAAGTACG 57.333 50.000 0.00 0.00 0.00 3.67
1308 4934 6.540438 AGTGAGACTAATAAACCCGAATGA 57.460 37.500 0.00 0.00 0.00 2.57
1310 4936 5.126707 ACGAGTGAGACTAATAAACCCGAAT 59.873 40.000 0.00 0.00 0.00 3.34
1314 4940 7.274603 AGATACGAGTGAGACTAATAAACCC 57.725 40.000 0.00 0.00 0.00 4.11
1370 4996 8.908172 TTTTGTGACGTACGACATATATGTTA 57.092 30.769 24.41 6.50 41.95 2.41
1386 5012 7.073265 AGTTTCGTGGTATTATTTTTGTGACG 58.927 34.615 0.00 0.00 0.00 4.35
1494 5120 7.422562 CCCACTCCCCTATCATATTTTAGGTTT 60.423 40.741 6.88 0.00 34.35 3.27
1510 5136 0.726366 TGTTATACCCCCACTCCCCT 59.274 55.000 0.00 0.00 0.00 4.79
1511 5137 1.598869 TTGTTATACCCCCACTCCCC 58.401 55.000 0.00 0.00 0.00 4.81
1512 5138 3.053170 ACAATTGTTATACCCCCACTCCC 60.053 47.826 4.92 0.00 0.00 4.30
1513 5139 4.245251 ACAATTGTTATACCCCCACTCC 57.755 45.455 4.92 0.00 0.00 3.85
1514 5140 5.997843 AGTACAATTGTTATACCCCCACTC 58.002 41.667 17.78 0.00 0.00 3.51
1515 5141 7.513560 TTAGTACAATTGTTATACCCCCACT 57.486 36.000 17.78 12.59 0.00 4.00
1516 5142 8.756486 ATTTAGTACAATTGTTATACCCCCAC 57.244 34.615 17.78 5.33 0.00 4.61
1642 5271 3.102052 TGTACCAAGTCTGAAACCGAC 57.898 47.619 0.00 0.00 0.00 4.79
1848 5479 6.762187 TGTGTAATTACTTCGGAACTTGAACA 59.238 34.615 16.33 5.07 0.00 3.18
2184 5818 3.253188 CGAGTGCAATTTCTTTTCCTCCA 59.747 43.478 0.00 0.00 0.00 3.86
2204 5838 2.685897 CCCTTTTTAATGGATTCGGCGA 59.314 45.455 4.99 4.99 0.00 5.54
2278 5912 2.158460 CCTTCATCCTGGTTTATCCCCC 60.158 54.545 0.00 0.00 34.77 5.40
2279 5913 2.783510 TCCTTCATCCTGGTTTATCCCC 59.216 50.000 0.00 0.00 34.77 4.81
2280 5914 4.079730 ACTTCCTTCATCCTGGTTTATCCC 60.080 45.833 0.00 0.00 34.77 3.85
2281 5915 4.884164 CACTTCCTTCATCCTGGTTTATCC 59.116 45.833 0.00 0.00 0.00 2.59
2282 5916 5.501156 ACACTTCCTTCATCCTGGTTTATC 58.499 41.667 0.00 0.00 0.00 1.75
2283 5917 5.520748 ACACTTCCTTCATCCTGGTTTAT 57.479 39.130 0.00 0.00 0.00 1.40
2284 5918 4.993705 ACACTTCCTTCATCCTGGTTTA 57.006 40.909 0.00 0.00 0.00 2.01
2285 5919 3.884037 ACACTTCCTTCATCCTGGTTT 57.116 42.857 0.00 0.00 0.00 3.27
2286 5920 3.117512 ACAACACTTCCTTCATCCTGGTT 60.118 43.478 0.00 0.00 0.00 3.67
2287 5921 2.443255 ACAACACTTCCTTCATCCTGGT 59.557 45.455 0.00 0.00 0.00 4.00
2288 5922 3.146104 ACAACACTTCCTTCATCCTGG 57.854 47.619 0.00 0.00 0.00 4.45
2289 5923 4.339247 ACAAACAACACTTCCTTCATCCTG 59.661 41.667 0.00 0.00 0.00 3.86
2290 5924 4.536765 ACAAACAACACTTCCTTCATCCT 58.463 39.130 0.00 0.00 0.00 3.24
2291 5925 4.338118 TGACAAACAACACTTCCTTCATCC 59.662 41.667 0.00 0.00 0.00 3.51
2292 5926 5.499139 TGACAAACAACACTTCCTTCATC 57.501 39.130 0.00 0.00 0.00 2.92
2293 5927 5.221303 CCATGACAAACAACACTTCCTTCAT 60.221 40.000 0.00 0.00 0.00 2.57
2294 5928 4.097741 CCATGACAAACAACACTTCCTTCA 59.902 41.667 0.00 0.00 0.00 3.02
2295 5929 4.338118 TCCATGACAAACAACACTTCCTTC 59.662 41.667 0.00 0.00 0.00 3.46
2296 5930 4.277476 TCCATGACAAACAACACTTCCTT 58.723 39.130 0.00 0.00 0.00 3.36
2297 5931 3.897239 TCCATGACAAACAACACTTCCT 58.103 40.909 0.00 0.00 0.00 3.36
2298 5932 4.647424 TTCCATGACAAACAACACTTCC 57.353 40.909 0.00 0.00 0.00 3.46
2299 5933 5.650543 ACTTTCCATGACAAACAACACTTC 58.349 37.500 0.00 0.00 0.00 3.01
2300 5934 5.659440 ACTTTCCATGACAAACAACACTT 57.341 34.783 0.00 0.00 0.00 3.16
2301 5935 5.659440 AACTTTCCATGACAAACAACACT 57.341 34.783 0.00 0.00 0.00 3.55
2302 5936 8.327429 CAAATAACTTTCCATGACAAACAACAC 58.673 33.333 0.00 0.00 0.00 3.32
2303 5937 8.253810 TCAAATAACTTTCCATGACAAACAACA 58.746 29.630 0.00 0.00 0.00 3.33
2304 5938 8.641499 TCAAATAACTTTCCATGACAAACAAC 57.359 30.769 0.00 0.00 0.00 3.32
2305 5939 9.829507 ATTCAAATAACTTTCCATGACAAACAA 57.170 25.926 0.00 0.00 0.00 2.83
2306 5940 9.258826 CATTCAAATAACTTTCCATGACAAACA 57.741 29.630 0.00 0.00 0.00 2.83
2307 5941 8.223100 GCATTCAAATAACTTTCCATGACAAAC 58.777 33.333 0.00 0.00 0.00 2.93
2308 5942 7.930325 TGCATTCAAATAACTTTCCATGACAAA 59.070 29.630 0.00 0.00 0.00 2.83
2309 5943 7.440198 TGCATTCAAATAACTTTCCATGACAA 58.560 30.769 0.00 0.00 0.00 3.18
2310 5944 6.990798 TGCATTCAAATAACTTTCCATGACA 58.009 32.000 0.00 0.00 0.00 3.58
2311 5945 7.887996 TTGCATTCAAATAACTTTCCATGAC 57.112 32.000 0.00 0.00 0.00 3.06
2314 5948 9.101655 GCTAATTGCATTCAAATAACTTTCCAT 57.898 29.630 0.00 0.00 42.31 3.41
2315 5949 8.477984 GCTAATTGCATTCAAATAACTTTCCA 57.522 30.769 0.00 0.00 42.31 3.53
2333 5967 5.163530 TGGAGGTAAACATGCATGCTAATTG 60.164 40.000 26.53 13.19 0.00 2.32
2373 6007 4.262249 GCACTAGCTTCGAAATCTATCCCT 60.262 45.833 0.00 0.00 37.91 4.20
2397 6031 2.757868 GAGACTGAAAGAGCTAGCCTCA 59.242 50.000 12.13 8.53 43.31 3.86
2477 6115 7.380536 ACAAAATCATGAATTGCTAGCTTGAA 58.619 30.769 17.23 1.91 0.00 2.69
2736 6586 1.077787 CAGGTTGGCCAGGCGATAA 60.078 57.895 5.11 0.00 37.19 1.75
2777 6630 6.183360 TGCATCAAAACTTCTCCAACTTTGAT 60.183 34.615 3.19 3.19 43.85 2.57
2886 6740 6.366061 GTCACACAAAGAGCAAACTTCTTTTT 59.634 34.615 0.00 0.00 32.10 1.94
2937 6795 1.064060 GGATACTGATGCAACAACGCC 59.936 52.381 0.00 0.00 0.00 5.68
2952 6810 3.635373 TGTCCCGTCTACTCATTGGATAC 59.365 47.826 0.00 0.00 0.00 2.24
2953 6811 3.905968 TGTCCCGTCTACTCATTGGATA 58.094 45.455 0.00 0.00 0.00 2.59
2960 6818 2.230508 GTCAACATGTCCCGTCTACTCA 59.769 50.000 0.00 0.00 0.00 3.41
2970 6828 2.571212 TCAACAGTGGTCAACATGTCC 58.429 47.619 0.00 0.00 0.00 4.02
2972 6830 3.565482 GTGATCAACAGTGGTCAACATGT 59.435 43.478 0.00 0.00 46.49 3.21
3082 6940 4.278170 CAGTGAAAGGGTTGCATCAAGTAA 59.722 41.667 0.00 0.00 0.00 2.24
3165 7023 7.402811 TTCTTGTGTTTATCTTACGTGACAG 57.597 36.000 0.00 0.00 0.00 3.51
3171 7029 7.812648 TCCCAAATTCTTGTGTTTATCTTACG 58.187 34.615 0.00 0.00 0.00 3.18
3266 7127 6.260271 ACGCTAGAATTATTTTAGACTTGGCC 59.740 38.462 6.69 0.00 0.00 5.36
3525 7425 1.168714 CAAGTCTAAGGTGCTTGCCC 58.831 55.000 0.00 0.00 34.16 5.36
3843 7753 1.360820 GGCCAAGAGTTCTAGCGTTC 58.639 55.000 0.00 0.00 0.00 3.95
3963 7883 4.608170 TCTTTAGCCAATCCCAAATCCT 57.392 40.909 0.00 0.00 0.00 3.24
3992 7912 3.306472 AAGTACTTGGTCCCTTGCAAA 57.694 42.857 7.48 0.00 0.00 3.68
3993 7913 4.440826 TTAAGTACTTGGTCCCTTGCAA 57.559 40.909 18.56 0.00 0.00 4.08
4280 8214 7.408756 TGCCAATTTAAAGTCTGAATATGCT 57.591 32.000 0.00 0.00 0.00 3.79
4295 8229 7.936496 TCTTAACACATCTGATGCCAATTTA 57.064 32.000 17.24 5.50 0.00 1.40
4296 8230 6.839124 TCTTAACACATCTGATGCCAATTT 57.161 33.333 17.24 6.35 0.00 1.82
4297 8231 7.414222 AATCTTAACACATCTGATGCCAATT 57.586 32.000 17.24 8.99 0.00 2.32
4298 8232 8.523915 TTAATCTTAACACATCTGATGCCAAT 57.476 30.769 17.24 4.60 0.00 3.16
4299 8233 7.936496 TTAATCTTAACACATCTGATGCCAA 57.064 32.000 17.24 5.77 0.00 4.52
4300 8234 8.523915 AATTAATCTTAACACATCTGATGCCA 57.476 30.769 17.24 0.00 0.00 4.92
4301 8235 7.800380 CGAATTAATCTTAACACATCTGATGCC 59.200 37.037 17.24 0.00 0.00 4.40
4302 8236 8.551205 TCGAATTAATCTTAACACATCTGATGC 58.449 33.333 17.24 0.00 0.00 3.91
4451 8421 4.502105 TTCCATTAGCAAGGTAGATGCA 57.498 40.909 0.00 0.00 46.22 3.96
4522 8498 8.764524 ATCTGTGTGTGAAACTTCTATAAGAC 57.235 34.615 0.00 0.00 38.04 3.01
4616 8598 2.543777 TGTGACAGTGTAAAGAGCCC 57.456 50.000 0.00 0.00 0.00 5.19
4734 8716 6.351033 GCTCCTTGGGGAAGTTAAATTAAAGG 60.351 42.308 10.39 10.39 41.69 3.11
4746 8729 9.232473 GTTAATATATTTAGCTCCTTGGGGAAG 57.768 37.037 2.68 0.00 41.69 3.46
4865 8852 1.671901 GAGGGAGAGGGCAGACGAAG 61.672 65.000 0.00 0.00 0.00 3.79
4979 8970 6.183360 GGCTTGACAAAGAAAACGTGATTTTT 60.183 34.615 0.00 0.00 40.73 1.94
5109 9111 1.739466 CATGCATTGTAACAGGAGCGT 59.261 47.619 0.00 0.00 0.00 5.07
5113 9115 3.070476 TGCTCATGCATTGTAACAGGA 57.930 42.857 0.00 0.00 45.31 3.86
5229 9235 4.735985 TCATGAATCCATCAAACAAAGCG 58.264 39.130 0.00 0.00 42.54 4.68
5266 9272 5.030147 TGTGGGGGCCTGATTAGTATATAG 58.970 45.833 0.84 0.00 0.00 1.31
5286 9292 6.334202 GTTTCTTAGGTAGTCCTCTGATGTG 58.666 44.000 0.00 0.00 43.94 3.21
5341 9363 3.757493 AGCAAGAAGAAAAGATGCAGGAG 59.243 43.478 0.00 0.00 39.42 3.69
5535 9585 5.300752 CACCCTCATGGATATGTACTGAAC 58.699 45.833 0.00 0.00 38.00 3.18
5553 9603 2.124570 GATGTGGATGCGCACCCT 60.125 61.111 24.38 0.00 0.00 4.34
5604 9654 2.568509 CCTGCATGGGGTGAAGAAAAAT 59.431 45.455 0.00 0.00 35.21 1.82
5946 9996 2.224818 ACAAAACCCCATTGCAATGCAT 60.225 40.909 30.15 16.27 38.76 3.96
5995 10045 8.547967 TTCATGTTTGACTAGATGTTACCTTC 57.452 34.615 0.00 0.00 0.00 3.46
6056 10106 3.389925 ACTTTTGCATGTTCATGTGGG 57.610 42.857 13.24 4.20 0.00 4.61
6057 10107 4.624015 AGAACTTTTGCATGTTCATGTGG 58.376 39.130 21.48 3.92 43.38 4.17
6110 10160 3.043586 CCACTCGACGCAACTATCATAC 58.956 50.000 0.00 0.00 0.00 2.39
6210 10260 2.325583 GTGATCCCGAAGCACCATAA 57.674 50.000 0.00 0.00 0.00 1.90
6240 10290 2.104267 CTGAAGCGGCATTCAGCAT 58.896 52.632 20.89 0.00 46.95 3.79
6387 10437 2.935201 CAGAGCTTGATGACTACCTTGC 59.065 50.000 0.00 0.00 0.00 4.01
6411 10461 5.440610 TGAGCATCTCAGTAGACAGATGTA 58.559 41.667 9.95 0.00 45.43 2.29
6419 10469 3.319031 TGGGATGAGCATCTCAGTAGA 57.681 47.619 8.90 0.00 42.97 2.59
6498 10548 4.207224 CAGCGAATACTACAAACCGATGAG 59.793 45.833 0.00 0.00 35.78 2.90
6503 10553 4.171005 TCTTCAGCGAATACTACAAACCG 58.829 43.478 0.00 0.00 0.00 4.44
6518 10568 0.390472 CGGTCCAGGAACTCTTCAGC 60.390 60.000 2.07 0.00 34.60 4.26
6538 10588 3.425577 ACTTATCCGAAATACGCGACA 57.574 42.857 15.93 0.00 41.07 4.35
6539 10589 3.360168 GCTACTTATCCGAAATACGCGAC 59.640 47.826 15.93 0.00 41.07 5.19
6540 10590 3.251729 AGCTACTTATCCGAAATACGCGA 59.748 43.478 15.93 0.00 41.07 5.87
6685 10735 0.961857 GGTCATGGTGATGCAGCACA 60.962 55.000 33.62 20.96 44.62 4.57
6716 10766 5.293814 AGAAGCATCAAATGAGAATGTCGAG 59.706 40.000 0.00 0.00 0.00 4.04
6774 10824 6.408035 TCCGACTGGCAAACATATACTTTAA 58.592 36.000 0.00 0.00 34.14 1.52
6862 10912 6.846505 TCTCCAGAAGATATGGGAGTTATTGT 59.153 38.462 6.45 0.00 45.65 2.71


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

AutoCloner maintained by Alex Coulton.