Multiple sequence alignment - TraesCS2B01G522500

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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 TraesCS2B01G522500 chr2B 100.000 3116 0 0 1 3116 717326958 717330073 0.000000e+00 5755.0
1 TraesCS2B01G522500 chr2B 90.784 1671 107 15 1 1647 717344195 717345842 0.000000e+00 2189.0
2 TraesCS2B01G522500 chr2B 85.714 1148 90 36 674 1763 717131197 717132328 0.000000e+00 1144.0
3 TraesCS2B01G522500 chr2B 89.821 560 40 10 951 1495 717237209 717237766 0.000000e+00 702.0
4 TraesCS2B01G522500 chr2B 83.412 211 33 2 1 211 614246315 614246107 8.820000e-46 195.0
5 TraesCS2B01G522500 chr2B 83.871 186 27 3 2720 2902 717133606 717133791 1.150000e-39 174.0
6 TraesCS2B01G522500 chr2B 89.844 128 10 3 1821 1948 717132423 717132547 8.940000e-36 161.0
7 TraesCS2B01G522500 chr2D 90.000 1140 96 12 388 1518 591703513 591704643 0.000000e+00 1458.0
8 TraesCS2B01G522500 chr2D 90.148 609 38 4 888 1495 591602934 591603521 0.000000e+00 773.0
9 TraesCS2B01G522500 chr2D 88.754 578 41 12 925 1485 591575128 591575698 0.000000e+00 686.0
10 TraesCS2B01G522500 chr2D 81.662 698 68 33 1976 2629 591576389 591577070 2.750000e-145 525.0
11 TraesCS2B01G522500 chr2D 84.800 375 37 11 388 753 591597392 591597755 2.950000e-95 359.0
12 TraesCS2B01G522500 chr2D 85.657 251 24 8 1881 2125 591603835 591604079 1.430000e-63 254.0
13 TraesCS2B01G522500 chr2D 89.840 187 11 6 2660 2838 591577067 591577253 1.870000e-57 233.0
14 TraesCS2B01G522500 chr2D 98.148 108 2 0 742 849 591597785 591597892 4.100000e-44 189.0
15 TraesCS2B01G522500 chr2D 83.237 173 19 4 1998 2160 591438476 591438648 1.940000e-32 150.0
16 TraesCS2B01G522500 chr2D 80.556 180 18 5 1998 2160 591389333 591389512 4.220000e-24 122.0
17 TraesCS2B01G522500 chr2D 87.500 96 11 1 3021 3116 591613990 591614084 3.290000e-20 110.0
18 TraesCS2B01G522500 chr2A 88.194 1008 98 14 651 1647 726386873 726387870 0.000000e+00 1182.0
19 TraesCS2B01G522500 chr2A 89.114 542 42 8 951 1477 726322148 726322687 0.000000e+00 658.0
20 TraesCS2B01G522500 chr2A 90.449 178 11 4 2667 2838 726324074 726324251 2.420000e-56 230.0
21 TraesCS2B01G522500 chr2A 81.413 269 37 7 388 654 726386458 726386715 1.130000e-49 207.0
22 TraesCS2B01G522500 chr2A 84.762 210 20 6 1823 2028 726323015 726323216 1.900000e-47 200.0
23 TraesCS2B01G522500 chr3A 85.859 198 26 2 11 207 69662766 69662570 3.150000e-50 209.0
24 TraesCS2B01G522500 chr3B 87.027 185 22 2 24 207 97756103 97755920 1.130000e-49 207.0
25 TraesCS2B01G522500 chr3B 84.080 201 30 2 9 209 394097789 394097987 3.170000e-45 193.0
26 TraesCS2B01G522500 chr3B 98.000 50 1 0 257 306 780713229 780713278 1.540000e-13 87.9
27 TraesCS2B01G522500 chr3B 90.909 55 3 2 208 261 30081715 30081768 4.310000e-09 73.1
28 TraesCS2B01G522500 chr3D 83.981 206 30 3 4 208 298594893 298595096 8.820000e-46 195.0
29 TraesCS2B01G522500 chr3D 84.000 200 30 2 9 207 61594232 61594034 1.140000e-44 191.0
30 TraesCS2B01G522500 chr1B 83.654 208 30 3 1 206 376615212 376615007 3.170000e-45 193.0
31 TraesCS2B01G522500 chr1B 85.556 90 8 4 257 346 626090921 626091005 4.280000e-14 89.8
32 TraesCS2B01G522500 chr1B 94.000 50 2 1 2223 2272 364493853 364493805 1.200000e-09 75.0
33 TraesCS2B01G522500 chr4B 83.732 209 24 9 3 207 33067417 33067619 4.100000e-44 189.0
34 TraesCS2B01G522500 chr7B 88.000 75 5 3 200 271 15590759 15590832 5.540000e-13 86.1
35 TraesCS2B01G522500 chr7B 95.000 40 1 1 347 386 590151599 590151637 9.330000e-06 62.1
36 TraesCS2B01G522500 chr1D 95.349 43 2 0 348 390 541629 541587 5.580000e-08 69.4
37 TraesCS2B01G522500 chr1A 88.136 59 4 3 210 267 353635382 353635326 2.010000e-07 67.6
38 TraesCS2B01G522500 chr1A 93.182 44 2 1 347 390 464812227 464812185 2.590000e-06 63.9
39 TraesCS2B01G522500 chr1A 93.023 43 2 1 348 390 13003449 13003490 9.330000e-06 62.1
40 TraesCS2B01G522500 chr5B 93.333 45 2 1 351 394 410854766 410854722 7.210000e-07 65.8
41 TraesCS2B01G522500 chr5B 85.246 61 7 2 208 267 685082665 685082606 9.330000e-06 62.1
42 TraesCS2B01G522500 chr5B 88.000 50 4 2 350 399 141844806 141844759 1.210000e-04 58.4
43 TraesCS2B01G522500 chr7D 93.182 44 2 1 357 400 126820699 126820657 2.590000e-06 63.9
44 TraesCS2B01G522500 chr5D 93.182 44 2 1 349 392 77056580 77056622 2.590000e-06 63.9
45 TraesCS2B01G522500 chr5A 82.540 63 10 1 211 272 6983003 6983065 2.000000e-03 54.7


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 TraesCS2B01G522500 chr2B 717326958 717330073 3115 False 5755.000000 5755 100.000000 1 3116 1 chr2B.!!$F2 3115
1 TraesCS2B01G522500 chr2B 717344195 717345842 1647 False 2189.000000 2189 90.784000 1 1647 1 chr2B.!!$F3 1646
2 TraesCS2B01G522500 chr2B 717237209 717237766 557 False 702.000000 702 89.821000 951 1495 1 chr2B.!!$F1 544
3 TraesCS2B01G522500 chr2B 717131197 717133791 2594 False 493.000000 1144 86.476333 674 2902 3 chr2B.!!$F4 2228
4 TraesCS2B01G522500 chr2D 591703513 591704643 1130 False 1458.000000 1458 90.000000 388 1518 1 chr2D.!!$F4 1130
5 TraesCS2B01G522500 chr2D 591602934 591604079 1145 False 513.500000 773 87.902500 888 2125 2 chr2D.!!$F7 1237
6 TraesCS2B01G522500 chr2D 591575128 591577253 2125 False 481.333333 686 86.752000 925 2838 3 chr2D.!!$F5 1913
7 TraesCS2B01G522500 chr2D 591597392 591597892 500 False 274.000000 359 91.474000 388 849 2 chr2D.!!$F6 461
8 TraesCS2B01G522500 chr2A 726386458 726387870 1412 False 694.500000 1182 84.803500 388 1647 2 chr2A.!!$F2 1259
9 TraesCS2B01G522500 chr2A 726322148 726324251 2103 False 362.666667 658 88.108333 951 2838 3 chr2A.!!$F1 1887

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
313 314 0.257039 CCATTTAGTGGCTCCCTGCT 59.743 55.0 0.0 0.0 42.12 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2967 0.241749 ACCGATTGCATGCACAACAG 59.758 50.0 22.58 10.99 31.03 3.16 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
243 244 3.498397 CGGGCTATGTAAAATAGTGGCAG 59.502 47.826 0.00 0.00 0.00 4.85
244 245 4.461198 GGGCTATGTAAAATAGTGGCAGT 58.539 43.478 0.00 0.00 0.00 4.40
249 250 3.857052 TGTAAAATAGTGGCAGTCCTCG 58.143 45.455 0.00 0.00 0.00 4.63
263 264 4.261825 GCAGTCCTCGAAATCAGCTATAGT 60.262 45.833 0.84 0.00 0.00 2.12
265 266 4.214545 AGTCCTCGAAATCAGCTATAGTCG 59.785 45.833 0.84 1.89 0.00 4.18
289 290 6.586463 CGGCTATTAGTGGACTATTGTACATG 59.414 42.308 0.00 0.00 39.53 3.21
313 314 0.257039 CCATTTAGTGGCTCCCTGCT 59.743 55.000 0.00 0.00 42.12 4.24
378 379 7.865820 AGCCTATATGCACTACATTATGGAAT 58.134 34.615 2.72 0.00 40.38 3.01
433 434 9.196552 GAAAAGAACTGCAAATAACTTTATGCT 57.803 29.630 0.00 0.00 39.49 3.79
455 457 8.840833 TGCTAAACAAACATGTAGTTCATAGA 57.159 30.769 18.04 7.88 40.26 1.98
527 540 6.737254 ACAAGGGTTATAAGTGAACGATTG 57.263 37.500 0.00 0.00 32.99 2.67
531 544 7.373778 AGGGTTATAAGTGAACGATTGTTTC 57.626 36.000 0.00 0.00 38.78 2.78
780 1003 5.384336 TGAACCAAAAGGACAATGATCTCA 58.616 37.500 0.00 0.00 0.00 3.27
893 1122 9.258629 ACATAGGAAGAAATTTCCATCATCAAA 57.741 29.630 14.61 0.00 41.00 2.69
971 1203 3.192633 CACCCAGCAACCACCTATAAAAC 59.807 47.826 0.00 0.00 0.00 2.43
1089 1333 1.086696 CGAGAACGATGGCCAAATGT 58.913 50.000 10.96 5.66 42.66 2.71
1250 1521 2.193517 CAACCACCCCGTGTTCCA 59.806 61.111 0.00 0.00 0.00 3.53
1251 1522 2.190841 CAACCACCCCGTGTTCCAC 61.191 63.158 0.00 0.00 0.00 4.02
1638 1918 1.294659 CGCAGCCAAGAAGACTGACC 61.295 60.000 0.00 0.00 33.10 4.02
1667 1956 1.070821 CACAAGCGATGACACATCGT 58.929 50.000 26.65 15.49 42.90 3.73
1676 1965 1.511850 TGACACATCGTTGCTCCAAG 58.488 50.000 0.00 0.00 0.00 3.61
1904 2329 1.696097 ATGTGCTATCGTGGACCCCC 61.696 60.000 0.00 0.00 0.00 5.40
1905 2330 2.039787 TGCTATCGTGGACCCCCA 59.960 61.111 0.00 0.00 40.95 4.96
1907 2332 1.760875 GCTATCGTGGACCCCCAGA 60.761 63.158 0.00 0.00 44.55 3.86
1917 2342 4.675303 CCCCCAGAGGACCCACCA 62.675 72.222 0.00 0.00 42.04 4.17
1948 2374 2.357881 GAACCAACGACCCCGGAC 60.358 66.667 0.73 0.00 40.78 4.79
1963 2389 2.526120 GGACCATTAGCACGCGAGC 61.526 63.158 21.28 21.28 0.00 5.03
1994 2728 6.562270 CGCGGTGAATATATTTCAGACTTCAC 60.562 42.308 0.00 1.65 40.91 3.18
2125 2974 9.480053 AAAGATTAATTGATTGTTCCTGTTGTG 57.520 29.630 0.00 0.00 0.00 3.33
2168 3292 3.853671 GTGATTCATTCATGCGTTCAACC 59.146 43.478 0.00 0.00 36.54 3.77
2278 3429 2.143925 GAAACCACTTGTCTTCTCCGG 58.856 52.381 0.00 0.00 0.00 5.14
2300 3451 7.500892 TCCGGAAATTAATCATTAGCTTTAGCA 59.499 33.333 0.00 0.00 45.16 3.49
2318 3469 9.698309 GCTTTAGCATTGTAAGATAGAGACATA 57.302 33.333 0.00 0.00 41.59 2.29
2347 3498 3.617263 ACTAATGAAATCGGAAGTCGTGC 59.383 43.478 0.00 0.00 40.32 5.34
2351 3502 2.288825 TGAAATCGGAAGTCGTGCTCTT 60.289 45.455 0.00 0.00 40.32 2.85
2401 3558 4.232221 CAGTGCCATTCAAAAGCTTGTAG 58.768 43.478 0.00 0.00 33.94 2.74
2451 3608 9.146984 ACATGCAAATATTGAACTCAATTGAAG 57.853 29.630 9.88 6.49 43.48 3.02
2457 3614 9.722056 AAATATTGAACTCAATTGAAGATACGC 57.278 29.630 9.88 0.00 43.48 4.42
2464 3636 5.240623 ACTCAATTGAAGATACGCAAACCAA 59.759 36.000 9.88 0.00 0.00 3.67
2482 3654 7.622672 GCAAACCAAGCATAACTCAATTGATTG 60.623 37.037 8.96 8.48 36.72 2.67
2525 3727 2.712077 CGTGGACGCTTGCATTTTC 58.288 52.632 0.00 0.00 0.00 2.29
2576 3779 3.663995 TTTCATGGGAAGCACATTGTG 57.336 42.857 12.54 12.54 33.82 3.33
2582 3785 1.895131 GGGAAGCACATTGTGTCCATT 59.105 47.619 21.49 11.54 32.49 3.16
2584 3787 2.557924 GGAAGCACATTGTGTCCATTGA 59.442 45.455 17.64 0.00 35.75 2.57
2587 3790 1.067635 GCACATTGTGTCCATTGACCC 60.068 52.381 17.64 0.00 41.01 4.46
2607 3810 1.067283 CGCACAATCTCTCAGAGTGGT 60.067 52.381 0.36 0.00 43.91 4.16
2616 3819 5.016051 TCTCTCAGAGTGGTTCATATTGC 57.984 43.478 0.36 0.00 0.00 3.56
2629 3832 6.147581 GGTTCATATTGCTAGATTGTGCATG 58.852 40.000 0.00 0.00 39.07 4.06
2630 3833 5.952526 TCATATTGCTAGATTGTGCATGG 57.047 39.130 0.00 0.00 39.07 3.66
2631 3834 5.379187 TCATATTGCTAGATTGTGCATGGT 58.621 37.500 0.00 0.00 39.07 3.55
2815 4188 4.278678 ACAGTCGACTTGCTTTTTCAAG 57.721 40.909 17.26 2.24 46.57 3.02
2832 4205 2.298446 TCAAGACTCTTGACCTCAGCAG 59.702 50.000 16.22 0.00 0.00 4.24
2838 4211 0.320247 CTTGACCTCAGCAGAGCGTT 60.320 55.000 0.00 0.00 40.68 4.84
2860 4233 6.400409 CGTTGCTATGATCAATCGGTCAATAG 60.400 42.308 0.00 0.00 0.00 1.73
2870 4244 6.640518 TCAATCGGTCAATAGTTTAGCTTCT 58.359 36.000 0.00 0.00 0.00 2.85
2872 4246 8.255206 TCAATCGGTCAATAGTTTAGCTTCTAA 58.745 33.333 0.00 0.00 0.00 2.10
2874 4248 7.400599 TCGGTCAATAGTTTAGCTTCTAAGA 57.599 36.000 0.00 0.00 0.00 2.10
2898 4272 6.590234 TCACAAGTGTCACACTAGTATGAT 57.410 37.500 11.89 0.00 44.62 2.45
2902 4276 4.759782 AGTGTCACACTAGTATGATTGGC 58.240 43.478 9.30 0.00 43.46 4.52
2903 4277 4.222810 AGTGTCACACTAGTATGATTGGCA 59.777 41.667 9.30 0.00 43.46 4.92
2904 4278 4.935205 GTGTCACACTAGTATGATTGGCAA 59.065 41.667 7.20 0.68 0.00 4.52
2905 4279 4.935205 TGTCACACTAGTATGATTGGCAAC 59.065 41.667 7.20 0.00 0.00 4.17
2906 4280 9.574876 AGTGTCACACTAGTATGATTGGCAACA 62.575 40.741 9.30 3.35 44.77 3.33
2989 4363 6.930667 TTCAGAAACAAAGGGTACACTAAC 57.069 37.500 0.00 0.00 0.00 2.34
2990 4364 6.243216 TCAGAAACAAAGGGTACACTAACT 57.757 37.500 0.00 0.00 0.00 2.24
2991 4365 7.364149 TCAGAAACAAAGGGTACACTAACTA 57.636 36.000 0.00 0.00 0.00 2.24
2992 4366 7.794041 TCAGAAACAAAGGGTACACTAACTAA 58.206 34.615 0.00 0.00 0.00 2.24
2993 4367 8.434392 TCAGAAACAAAGGGTACACTAACTAAT 58.566 33.333 0.00 0.00 0.00 1.73
2994 4368 9.715121 CAGAAACAAAGGGTACACTAACTAATA 57.285 33.333 0.00 0.00 0.00 0.98
2998 4372 9.828039 AACAAAGGGTACACTAACTAATATAGC 57.172 33.333 0.00 0.00 0.00 2.97
2999 4373 8.139989 ACAAAGGGTACACTAACTAATATAGCG 58.860 37.037 0.00 0.00 0.00 4.26
3000 4374 7.830099 AAGGGTACACTAACTAATATAGCGT 57.170 36.000 0.00 0.00 0.00 5.07
3001 4375 7.830099 AGGGTACACTAACTAATATAGCGTT 57.170 36.000 0.00 0.00 0.00 4.84
3002 4376 8.242729 AGGGTACACTAACTAATATAGCGTTT 57.757 34.615 0.00 0.00 0.00 3.60
3003 4377 8.355913 AGGGTACACTAACTAATATAGCGTTTC 58.644 37.037 0.00 0.00 0.00 2.78
3004 4378 8.137437 GGGTACACTAACTAATATAGCGTTTCA 58.863 37.037 0.00 0.00 0.00 2.69
3005 4379 9.688592 GGTACACTAACTAATATAGCGTTTCAT 57.311 33.333 0.00 0.00 0.00 2.57
3007 4381 8.073355 ACACTAACTAATATAGCGTTTCATGC 57.927 34.615 0.00 0.00 0.00 4.06
3008 4382 7.170998 ACACTAACTAATATAGCGTTTCATGCC 59.829 37.037 0.00 0.00 0.00 4.40
3009 4383 7.385205 CACTAACTAATATAGCGTTTCATGCCT 59.615 37.037 0.00 0.00 0.00 4.75
3010 4384 8.582437 ACTAACTAATATAGCGTTTCATGCCTA 58.418 33.333 0.00 0.00 0.00 3.93
3011 4385 9.587772 CTAACTAATATAGCGTTTCATGCCTAT 57.412 33.333 0.00 0.00 0.00 2.57
3013 4387 9.587772 AACTAATATAGCGTTTCATGCCTATAG 57.412 33.333 0.00 0.00 0.00 1.31
3014 4388 8.967918 ACTAATATAGCGTTTCATGCCTATAGA 58.032 33.333 0.00 0.00 0.00 1.98
3015 4389 9.457110 CTAATATAGCGTTTCATGCCTATAGAG 57.543 37.037 0.00 0.00 0.00 2.43
3016 4390 5.730296 ATAGCGTTTCATGCCTATAGAGT 57.270 39.130 0.00 0.00 0.00 3.24
3017 4391 4.408182 AGCGTTTCATGCCTATAGAGTT 57.592 40.909 0.00 0.00 0.00 3.01
3018 4392 4.770795 AGCGTTTCATGCCTATAGAGTTT 58.229 39.130 0.00 0.00 0.00 2.66
3019 4393 5.186198 AGCGTTTCATGCCTATAGAGTTTT 58.814 37.500 0.00 0.00 0.00 2.43
3020 4394 5.294552 AGCGTTTCATGCCTATAGAGTTTTC 59.705 40.000 0.00 0.00 0.00 2.29
3021 4395 5.294552 GCGTTTCATGCCTATAGAGTTTTCT 59.705 40.000 0.00 0.00 37.46 2.52
3022 4396 6.183360 GCGTTTCATGCCTATAGAGTTTTCTT 60.183 38.462 0.00 0.00 34.79 2.52
3023 4397 7.626452 GCGTTTCATGCCTATAGAGTTTTCTTT 60.626 37.037 0.00 0.00 34.79 2.52
3024 4398 8.237267 CGTTTCATGCCTATAGAGTTTTCTTTT 58.763 33.333 0.00 0.00 34.79 2.27
3074 4448 8.558973 AAATATAGGATCAAGCAGATACAAGC 57.441 34.615 4.45 0.00 40.31 4.01
3075 4449 3.920231 AGGATCAAGCAGATACAAGCA 57.080 42.857 4.45 0.00 40.31 3.91
3076 4450 4.434545 AGGATCAAGCAGATACAAGCAT 57.565 40.909 4.45 0.00 40.31 3.79
3077 4451 5.557576 AGGATCAAGCAGATACAAGCATA 57.442 39.130 4.45 0.00 40.31 3.14
3078 4452 5.933617 AGGATCAAGCAGATACAAGCATAA 58.066 37.500 4.45 0.00 40.31 1.90
3079 4453 6.540995 AGGATCAAGCAGATACAAGCATAAT 58.459 36.000 4.45 0.00 40.31 1.28
3080 4454 6.430308 AGGATCAAGCAGATACAAGCATAATG 59.570 38.462 4.45 0.00 40.31 1.90
3081 4455 6.429078 GGATCAAGCAGATACAAGCATAATGA 59.571 38.462 0.00 0.00 37.53 2.57
3082 4456 6.856135 TCAAGCAGATACAAGCATAATGAG 57.144 37.500 0.00 0.00 0.00 2.90
3083 4457 6.351711 TCAAGCAGATACAAGCATAATGAGT 58.648 36.000 0.00 0.00 0.00 3.41
3084 4458 6.825213 TCAAGCAGATACAAGCATAATGAGTT 59.175 34.615 0.00 0.00 0.00 3.01
3085 4459 7.986889 TCAAGCAGATACAAGCATAATGAGTTA 59.013 33.333 0.00 0.00 0.00 2.24
3086 4460 7.721286 AGCAGATACAAGCATAATGAGTTAC 57.279 36.000 0.00 0.00 0.00 2.50
3087 4461 7.275183 AGCAGATACAAGCATAATGAGTTACA 58.725 34.615 0.00 0.00 0.00 2.41
3088 4462 7.225538 AGCAGATACAAGCATAATGAGTTACAC 59.774 37.037 0.00 0.00 0.00 2.90
3089 4463 7.519008 GCAGATACAAGCATAATGAGTTACACC 60.519 40.741 0.00 0.00 0.00 4.16
3090 4464 6.992715 AGATACAAGCATAATGAGTTACACCC 59.007 38.462 0.00 0.00 0.00 4.61
3091 4465 3.938963 ACAAGCATAATGAGTTACACCCG 59.061 43.478 0.00 0.00 0.00 5.28
3092 4466 4.188462 CAAGCATAATGAGTTACACCCGA 58.812 43.478 0.00 0.00 0.00 5.14
3093 4467 4.689612 AGCATAATGAGTTACACCCGAT 57.310 40.909 0.00 0.00 0.00 4.18
3094 4468 4.632153 AGCATAATGAGTTACACCCGATC 58.368 43.478 0.00 0.00 0.00 3.69
3095 4469 4.345257 AGCATAATGAGTTACACCCGATCT 59.655 41.667 0.00 0.00 0.00 2.75
3096 4470 4.686554 GCATAATGAGTTACACCCGATCTC 59.313 45.833 0.00 0.00 0.00 2.75
3097 4471 5.509840 GCATAATGAGTTACACCCGATCTCT 60.510 44.000 0.00 0.00 0.00 3.10
3098 4472 4.392921 AATGAGTTACACCCGATCTCTG 57.607 45.455 0.00 0.00 0.00 3.35
3099 4473 3.081710 TGAGTTACACCCGATCTCTGA 57.918 47.619 0.00 0.00 0.00 3.27
3100 4474 3.427573 TGAGTTACACCCGATCTCTGAA 58.572 45.455 0.00 0.00 0.00 3.02
3101 4475 4.023980 TGAGTTACACCCGATCTCTGAAT 58.976 43.478 0.00 0.00 0.00 2.57
3102 4476 5.198207 TGAGTTACACCCGATCTCTGAATA 58.802 41.667 0.00 0.00 0.00 1.75
3103 4477 5.655090 TGAGTTACACCCGATCTCTGAATAA 59.345 40.000 0.00 0.00 0.00 1.40
3104 4478 5.903810 AGTTACACCCGATCTCTGAATAAC 58.096 41.667 0.00 0.00 0.00 1.89
3105 4479 5.657302 AGTTACACCCGATCTCTGAATAACT 59.343 40.000 0.00 0.00 0.00 2.24
3106 4480 6.832384 AGTTACACCCGATCTCTGAATAACTA 59.168 38.462 0.00 0.00 30.60 2.24
3107 4481 7.341256 AGTTACACCCGATCTCTGAATAACTAA 59.659 37.037 0.00 0.00 30.60 2.24
3108 4482 6.540438 ACACCCGATCTCTGAATAACTAAA 57.460 37.500 0.00 0.00 0.00 1.85
3109 4483 6.942976 ACACCCGATCTCTGAATAACTAAAA 58.057 36.000 0.00 0.00 0.00 1.52
3110 4484 7.565680 ACACCCGATCTCTGAATAACTAAAAT 58.434 34.615 0.00 0.00 0.00 1.82
3111 4485 7.495934 ACACCCGATCTCTGAATAACTAAAATG 59.504 37.037 0.00 0.00 0.00 2.32
3112 4486 6.483640 ACCCGATCTCTGAATAACTAAAATGC 59.516 38.462 0.00 0.00 0.00 3.56
3113 4487 6.483307 CCCGATCTCTGAATAACTAAAATGCA 59.517 38.462 0.00 0.00 0.00 3.96
3114 4488 7.348201 CCGATCTCTGAATAACTAAAATGCAC 58.652 38.462 0.00 0.00 0.00 4.57
3115 4489 7.011389 CCGATCTCTGAATAACTAAAATGCACA 59.989 37.037 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 209 7.811117 TTACATAGCCCGCTATTTAAAACAT 57.189 32.000 11.19 0.00 37.16 2.71
243 244 4.468643 CGACTATAGCTGATTTCGAGGAC 58.531 47.826 0.00 0.00 0.00 3.85
244 245 3.502595 CCGACTATAGCTGATTTCGAGGA 59.497 47.826 9.13 0.00 0.00 3.71
249 250 7.486551 CACTAATAGCCGACTATAGCTGATTTC 59.513 40.741 0.00 0.00 38.18 2.17
263 264 5.829391 TGTACAATAGTCCACTAATAGCCGA 59.171 40.000 0.00 0.00 31.39 5.54
265 266 7.667557 TCATGTACAATAGTCCACTAATAGCC 58.332 38.462 0.00 0.00 31.39 3.93
352 353 7.257790 TCCATAATGTAGTGCATATAGGCTT 57.742 36.000 11.14 1.79 36.67 4.35
353 354 6.874278 TCCATAATGTAGTGCATATAGGCT 57.126 37.500 11.14 0.00 36.67 4.58
354 355 7.012704 CCATTCCATAATGTAGTGCATATAGGC 59.987 40.741 1.55 1.55 40.84 3.93
355 356 8.267183 TCCATTCCATAATGTAGTGCATATAGG 58.733 37.037 0.00 0.00 40.84 2.57
356 357 9.322773 CTCCATTCCATAATGTAGTGCATATAG 57.677 37.037 0.00 0.00 40.84 1.31
362 363 4.074970 CCCTCCATTCCATAATGTAGTGC 58.925 47.826 0.00 0.00 40.84 4.40
378 379 6.664816 GGATGCAAATAATCATAATCCCTCCA 59.335 38.462 0.00 0.00 0.00 3.86
455 457 7.283329 AGATAAAGGAGGCACGAGATAAATTT 58.717 34.615 0.00 0.00 0.00 1.82
463 465 3.526931 TCAAGATAAAGGAGGCACGAG 57.473 47.619 0.00 0.00 0.00 4.18
527 540 4.918588 TGGGAGGACAATTAGAAGGAAAC 58.081 43.478 0.00 0.00 0.00 2.78
531 544 3.181439 GGGATGGGAGGACAATTAGAAGG 60.181 52.174 0.00 0.00 0.00 3.46
655 831 2.564947 CCCCTAGATGTATGTCCTGCTC 59.435 54.545 0.00 0.00 0.00 4.26
780 1003 3.307480 CCAGGTAACATTTCCTCCTCGTT 60.307 47.826 0.00 0.00 41.41 3.85
898 1127 1.892209 ATTCCTCGGCTTCACGTTTT 58.108 45.000 0.00 0.00 34.94 2.43
961 1192 1.134610 CGGCGTGGAGGTTTTATAGGT 60.135 52.381 0.00 0.00 0.00 3.08
1089 1333 0.179065 CGATGCTCTGGATCTTGCCA 60.179 55.000 0.00 0.00 36.30 4.92
1200 1471 2.030562 ACCAAGAACCGCCGTGAG 59.969 61.111 0.00 0.00 0.00 3.51
1227 1498 2.446994 ACGGGGTGGTTGAGGTGA 60.447 61.111 0.00 0.00 0.00 4.02
1408 1688 4.796231 GACGTCGCGGCTGGTGAT 62.796 66.667 9.90 0.00 37.52 3.06
1626 1906 1.878656 CTCGGCCGGTCAGTCTTCTT 61.879 60.000 27.83 0.00 0.00 2.52
1882 2307 0.461870 GGTCCACGATAGCACATGCA 60.462 55.000 6.64 0.00 45.16 3.96
1883 2308 1.160329 GGGTCCACGATAGCACATGC 61.160 60.000 0.00 0.00 42.67 4.06
1904 2329 2.941415 GCAAATAGTGGTGGGTCCTCTG 60.941 54.545 0.00 0.00 39.91 3.35
1905 2330 1.282157 GCAAATAGTGGTGGGTCCTCT 59.718 52.381 0.00 0.00 42.01 3.69
1907 2332 1.372501 AGCAAATAGTGGTGGGTCCT 58.627 50.000 0.00 0.00 36.32 3.85
1948 2374 0.316442 CATTGCTCGCGTGCTAATGG 60.316 55.000 29.49 17.93 32.85 3.16
1963 2389 3.829886 AATATATTCACCGCGCCATTG 57.170 42.857 0.00 0.00 0.00 2.82
1970 2704 6.480320 AGTGAAGTCTGAAATATATTCACCGC 59.520 38.462 11.15 0.00 44.70 5.68
1994 2728 5.627367 CGCCTTCTTCGATCAATTAGTAGAG 59.373 44.000 0.00 0.00 0.00 2.43
2106 2955 4.669206 TGCACAACAGGAACAATCAATT 57.331 36.364 0.00 0.00 0.00 2.32
2118 2967 0.241749 ACCGATTGCATGCACAACAG 59.758 50.000 22.58 10.99 31.03 3.16
2125 2974 0.447801 AACGAAGACCGATTGCATGC 59.552 50.000 11.82 11.82 41.76 4.06
2168 3292 0.606401 ATGGTGAACGGCCAAGACAG 60.606 55.000 2.24 0.00 39.72 3.51
2319 3470 8.427216 ACGACTTCCGATTTCATTAGTGAAACA 61.427 37.037 14.80 0.00 46.98 2.83
2325 3476 3.617263 GCACGACTTCCGATTTCATTAGT 59.383 43.478 0.00 0.00 41.76 2.24
2326 3477 3.865745 AGCACGACTTCCGATTTCATTAG 59.134 43.478 0.00 0.00 41.76 1.73
2401 3558 3.194861 TGCTCACCTTACACAATATCGC 58.805 45.455 0.00 0.00 0.00 4.58
2436 3593 6.552859 TTGCGTATCTTCAATTGAGTTCAA 57.447 33.333 8.41 5.09 40.51 2.69
2441 3598 5.295431 TGGTTTGCGTATCTTCAATTGAG 57.705 39.130 8.41 3.62 0.00 3.02
2445 3602 3.505680 TGCTTGGTTTGCGTATCTTCAAT 59.494 39.130 0.00 0.00 0.00 2.57
2447 3604 2.499197 TGCTTGGTTTGCGTATCTTCA 58.501 42.857 0.00 0.00 0.00 3.02
2448 3605 3.764885 ATGCTTGGTTTGCGTATCTTC 57.235 42.857 0.00 0.00 0.00 2.87
2450 3607 4.261801 AGTTATGCTTGGTTTGCGTATCT 58.738 39.130 0.00 0.00 32.77 1.98
2451 3608 4.094294 TGAGTTATGCTTGGTTTGCGTATC 59.906 41.667 0.00 0.00 32.77 2.24
2454 3611 2.226330 TGAGTTATGCTTGGTTTGCGT 58.774 42.857 0.00 0.00 0.00 5.24
2455 3612 2.987413 TGAGTTATGCTTGGTTTGCG 57.013 45.000 0.00 0.00 0.00 4.85
2456 3613 5.229423 TCAATTGAGTTATGCTTGGTTTGC 58.771 37.500 3.38 0.00 0.00 3.68
2457 3614 7.385752 ACAATCAATTGAGTTATGCTTGGTTTG 59.614 33.333 14.54 10.45 40.14 2.93
2464 3636 6.435277 AGGAACACAATCAATTGAGTTATGCT 59.565 34.615 14.54 3.65 46.45 3.79
2482 3654 4.338379 AGTCTAGGACAACAAGGAACAC 57.662 45.455 0.52 0.00 34.60 3.32
2549 3751 7.178274 ACAATGTGCTTCCCATGAAAAATAGTA 59.822 33.333 0.00 0.00 0.00 1.82
2576 3779 0.451783 GATTGTGCGGGTCAATGGAC 59.548 55.000 0.00 0.00 43.55 4.02
2582 3785 0.247460 CTGAGAGATTGTGCGGGTCA 59.753 55.000 0.00 0.00 0.00 4.02
2584 3787 0.534412 CTCTGAGAGATTGTGCGGGT 59.466 55.000 2.60 0.00 0.00 5.28
2587 3790 1.067283 ACCACTCTGAGAGATTGTGCG 60.067 52.381 17.71 2.10 33.32 5.34
2607 3810 5.829391 ACCATGCACAATCTAGCAATATGAA 59.171 36.000 0.00 0.00 44.88 2.57
2629 3832 4.269363 ACACTTATCGCTATAAACGCAACC 59.731 41.667 0.00 0.00 0.00 3.77
2630 3833 5.385396 ACACTTATCGCTATAAACGCAAC 57.615 39.130 0.00 0.00 0.00 4.17
2631 3834 8.975410 ATATACACTTATCGCTATAAACGCAA 57.025 30.769 0.00 0.00 0.00 4.85
2779 4151 1.730064 GACTGTAATGCGCGAAAAGGA 59.270 47.619 12.10 0.00 0.00 3.36
2815 4188 1.404047 GCTCTGCTGAGGTCAAGAGTC 60.404 57.143 20.66 0.00 40.53 3.36
2832 4205 2.156504 CCGATTGATCATAGCAACGCTC 59.843 50.000 0.00 0.00 40.44 5.03
2838 4211 6.101650 ACTATTGACCGATTGATCATAGCA 57.898 37.500 0.00 0.00 0.00 3.49
2845 4218 7.275920 AGAAGCTAAACTATTGACCGATTGAT 58.724 34.615 0.00 0.00 0.00 2.57
2860 4233 7.385205 TGACACTTGTGATCTTAGAAGCTAAAC 59.615 37.037 7.83 0.00 0.00 2.01
2870 4244 6.650427 ACTAGTGTGACACTTGTGATCTTA 57.350 37.500 27.07 5.56 45.36 2.10
2872 4246 6.434340 TCATACTAGTGTGACACTTGTGATCT 59.566 38.462 32.45 17.13 46.18 2.75
2874 4248 6.590234 TCATACTAGTGTGACACTTGTGAT 57.410 37.500 32.45 21.57 46.18 3.06
2963 4337 9.227777 GTTAGTGTACCCTTTGTTTCTGAATAT 57.772 33.333 0.00 0.00 0.00 1.28
2964 4338 8.434392 AGTTAGTGTACCCTTTGTTTCTGAATA 58.566 33.333 0.00 0.00 0.00 1.75
2965 4339 7.287810 AGTTAGTGTACCCTTTGTTTCTGAAT 58.712 34.615 0.00 0.00 0.00 2.57
2966 4340 6.655930 AGTTAGTGTACCCTTTGTTTCTGAA 58.344 36.000 0.00 0.00 0.00 3.02
2967 4341 6.243216 AGTTAGTGTACCCTTTGTTTCTGA 57.757 37.500 0.00 0.00 0.00 3.27
2968 4342 8.617290 ATTAGTTAGTGTACCCTTTGTTTCTG 57.383 34.615 0.00 0.00 0.00 3.02
2972 4346 9.828039 GCTATATTAGTTAGTGTACCCTTTGTT 57.172 33.333 0.00 0.00 0.00 2.83
2973 4347 8.139989 CGCTATATTAGTTAGTGTACCCTTTGT 58.860 37.037 0.00 0.00 0.00 2.83
2974 4348 8.139989 ACGCTATATTAGTTAGTGTACCCTTTG 58.860 37.037 0.00 0.00 38.33 2.77
2975 4349 8.242729 ACGCTATATTAGTTAGTGTACCCTTT 57.757 34.615 0.00 0.00 38.33 3.11
2976 4350 7.830099 ACGCTATATTAGTTAGTGTACCCTT 57.170 36.000 0.00 0.00 38.33 3.95
2977 4351 7.830099 AACGCTATATTAGTTAGTGTACCCT 57.170 36.000 0.00 0.00 38.98 4.34
2978 4352 8.137437 TGAAACGCTATATTAGTTAGTGTACCC 58.863 37.037 0.00 0.00 38.98 3.69
2979 4353 9.688592 ATGAAACGCTATATTAGTTAGTGTACC 57.311 33.333 0.00 0.00 38.98 3.34
2981 4355 9.188588 GCATGAAACGCTATATTAGTTAGTGTA 57.811 33.333 0.00 0.00 38.98 2.90
2982 4356 7.170998 GGCATGAAACGCTATATTAGTTAGTGT 59.829 37.037 0.00 0.00 41.02 3.55
2983 4357 7.385205 AGGCATGAAACGCTATATTAGTTAGTG 59.615 37.037 0.00 0.00 34.19 2.74
2984 4358 7.442656 AGGCATGAAACGCTATATTAGTTAGT 58.557 34.615 0.00 0.00 0.00 2.24
2985 4359 7.891183 AGGCATGAAACGCTATATTAGTTAG 57.109 36.000 0.00 0.00 0.00 2.34
2987 4361 9.587772 CTATAGGCATGAAACGCTATATTAGTT 57.412 33.333 0.00 0.00 0.00 2.24
2988 4362 8.967918 TCTATAGGCATGAAACGCTATATTAGT 58.032 33.333 0.00 0.00 0.00 2.24
2989 4363 9.457110 CTCTATAGGCATGAAACGCTATATTAG 57.543 37.037 0.00 0.00 0.00 1.73
2990 4364 8.967918 ACTCTATAGGCATGAAACGCTATATTA 58.032 33.333 0.00 0.00 0.00 0.98
2991 4365 7.841956 ACTCTATAGGCATGAAACGCTATATT 58.158 34.615 0.00 0.00 0.00 1.28
2992 4366 7.411486 ACTCTATAGGCATGAAACGCTATAT 57.589 36.000 0.00 0.00 0.00 0.86
2993 4367 6.835819 ACTCTATAGGCATGAAACGCTATA 57.164 37.500 0.00 0.00 0.00 1.31
2994 4368 5.730296 ACTCTATAGGCATGAAACGCTAT 57.270 39.130 0.00 0.00 0.00 2.97
2995 4369 5.531122 AACTCTATAGGCATGAAACGCTA 57.469 39.130 0.00 0.00 0.00 4.26
2996 4370 4.408182 AACTCTATAGGCATGAAACGCT 57.592 40.909 0.00 0.00 0.00 5.07
2997 4371 5.294552 AGAAAACTCTATAGGCATGAAACGC 59.705 40.000 0.00 0.00 0.00 4.84
2998 4372 6.910536 AGAAAACTCTATAGGCATGAAACG 57.089 37.500 0.00 0.00 0.00 3.60
3048 4422 9.007901 GCTTGTATCTGCTTGATCCTATATTTT 57.992 33.333 0.00 0.00 36.65 1.82
3049 4423 8.159447 TGCTTGTATCTGCTTGATCCTATATTT 58.841 33.333 0.00 0.00 36.65 1.40
3050 4424 7.683578 TGCTTGTATCTGCTTGATCCTATATT 58.316 34.615 0.00 0.00 36.65 1.28
3051 4425 7.250032 TGCTTGTATCTGCTTGATCCTATAT 57.750 36.000 0.00 0.00 36.65 0.86
3052 4426 6.670695 TGCTTGTATCTGCTTGATCCTATA 57.329 37.500 0.00 0.00 36.65 1.31
3053 4427 5.557576 TGCTTGTATCTGCTTGATCCTAT 57.442 39.130 0.00 0.00 36.65 2.57
3054 4428 5.557576 ATGCTTGTATCTGCTTGATCCTA 57.442 39.130 0.00 0.00 36.65 2.94
3055 4429 3.920231 TGCTTGTATCTGCTTGATCCT 57.080 42.857 0.00 0.00 36.65 3.24
3056 4430 6.429078 TCATTATGCTTGTATCTGCTTGATCC 59.571 38.462 0.00 0.00 36.65 3.36
3057 4431 7.172875 ACTCATTATGCTTGTATCTGCTTGATC 59.827 37.037 0.00 0.00 36.65 2.92
3058 4432 6.996879 ACTCATTATGCTTGTATCTGCTTGAT 59.003 34.615 0.00 0.00 39.11 2.57
3059 4433 6.351711 ACTCATTATGCTTGTATCTGCTTGA 58.648 36.000 0.00 0.00 0.00 3.02
3060 4434 6.615264 ACTCATTATGCTTGTATCTGCTTG 57.385 37.500 0.00 0.00 0.00 4.01
3061 4435 7.770433 TGTAACTCATTATGCTTGTATCTGCTT 59.230 33.333 0.00 0.00 0.00 3.91
3062 4436 7.225538 GTGTAACTCATTATGCTTGTATCTGCT 59.774 37.037 0.00 0.00 0.00 4.24
3063 4437 7.348201 GTGTAACTCATTATGCTTGTATCTGC 58.652 38.462 0.00 0.00 0.00 4.26
3064 4438 7.041780 GGGTGTAACTCATTATGCTTGTATCTG 60.042 40.741 0.00 0.00 37.19 2.90
3065 4439 6.992715 GGGTGTAACTCATTATGCTTGTATCT 59.007 38.462 0.00 0.00 37.19 1.98
3066 4440 6.073765 CGGGTGTAACTCATTATGCTTGTATC 60.074 42.308 0.00 0.00 36.87 2.24
3067 4441 5.758296 CGGGTGTAACTCATTATGCTTGTAT 59.242 40.000 0.00 0.00 36.87 2.29
3068 4442 5.105269 TCGGGTGTAACTCATTATGCTTGTA 60.105 40.000 0.00 0.00 36.87 2.41
3069 4443 3.938963 CGGGTGTAACTCATTATGCTTGT 59.061 43.478 0.00 0.00 36.87 3.16
3070 4444 4.188462 TCGGGTGTAACTCATTATGCTTG 58.812 43.478 0.00 0.00 36.87 4.01
3071 4445 4.481368 TCGGGTGTAACTCATTATGCTT 57.519 40.909 0.00 0.00 36.87 3.91
3072 4446 4.345257 AGATCGGGTGTAACTCATTATGCT 59.655 41.667 0.00 0.00 36.87 3.79
3073 4447 4.632153 AGATCGGGTGTAACTCATTATGC 58.368 43.478 0.00 0.00 36.87 3.14
3074 4448 5.923114 CAGAGATCGGGTGTAACTCATTATG 59.077 44.000 0.00 0.00 36.87 1.90
3075 4449 5.833667 TCAGAGATCGGGTGTAACTCATTAT 59.166 40.000 0.00 0.00 36.87 1.28
3076 4450 5.198207 TCAGAGATCGGGTGTAACTCATTA 58.802 41.667 0.00 0.00 36.87 1.90
3077 4451 4.023980 TCAGAGATCGGGTGTAACTCATT 58.976 43.478 0.00 0.00 36.87 2.57
3078 4452 3.632333 TCAGAGATCGGGTGTAACTCAT 58.368 45.455 0.00 0.00 36.87 2.90
3079 4453 3.081710 TCAGAGATCGGGTGTAACTCA 57.918 47.619 0.00 0.00 36.87 3.41
3080 4454 4.657436 ATTCAGAGATCGGGTGTAACTC 57.343 45.455 0.00 0.00 36.74 3.01
3081 4455 5.657302 AGTTATTCAGAGATCGGGTGTAACT 59.343 40.000 6.63 6.63 36.74 2.24
3082 4456 5.903810 AGTTATTCAGAGATCGGGTGTAAC 58.096 41.667 0.00 0.00 0.00 2.50
3083 4457 7.649533 TTAGTTATTCAGAGATCGGGTGTAA 57.350 36.000 0.00 0.00 0.00 2.41
3084 4458 7.649533 TTTAGTTATTCAGAGATCGGGTGTA 57.350 36.000 0.00 0.00 0.00 2.90
3085 4459 6.540438 TTTAGTTATTCAGAGATCGGGTGT 57.460 37.500 0.00 0.00 0.00 4.16
3086 4460 7.519008 GCATTTTAGTTATTCAGAGATCGGGTG 60.519 40.741 0.00 0.00 0.00 4.61
3087 4461 6.483640 GCATTTTAGTTATTCAGAGATCGGGT 59.516 38.462 0.00 0.00 0.00 5.28
3088 4462 6.483307 TGCATTTTAGTTATTCAGAGATCGGG 59.517 38.462 0.00 0.00 0.00 5.14
3089 4463 7.011389 TGTGCATTTTAGTTATTCAGAGATCGG 59.989 37.037 0.00 0.00 0.00 4.18
3090 4464 7.909267 TGTGCATTTTAGTTATTCAGAGATCG 58.091 34.615 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.