Multiple sequence alignment - TraesCS4A01G329500

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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 TraesCS4A01G329500 chr4A 100.000 4796 0 0 1 4796 614608275 614613070 0.000000e+00 8857.0
1 TraesCS4A01G329500 chr4A 83.698 2012 198 60 1952 3921 614447801 614445878 0.000000e+00 1779.0
2 TraesCS4A01G329500 chr4A 87.745 1224 105 26 2701 3907 614417561 614416366 0.000000e+00 1387.0
3 TraesCS4A01G329500 chr4A 85.928 1272 125 22 2666 3906 614426762 614425514 0.000000e+00 1308.0
4 TraesCS4A01G329500 chr4A 87.059 935 58 25 934 1849 614448822 614447932 0.000000e+00 998.0
5 TraesCS4A01G329500 chr4A 83.642 593 73 18 1992 2568 614418149 614417565 1.960000e-148 536.0
6 TraesCS4A01G329500 chr4A 90.496 242 15 3 1609 1849 614427572 614427338 3.600000e-81 313.0
7 TraesCS4A01G329500 chr4A 86.640 247 26 6 1549 1793 614418564 614418323 2.850000e-67 267.0
8 TraesCS4A01G329500 chr4A 97.260 73 2 0 3923 3995 715845896 715845824 1.810000e-24 124.0
9 TraesCS4A01G329500 chr4A 92.857 56 4 0 546 601 614449237 614449182 1.110000e-11 82.4
10 TraesCS4A01G329500 chr5B 90.566 2332 145 43 1548 3854 696711458 696713739 0.000000e+00 3018.0
11 TraesCS4A01G329500 chr5B 87.721 1246 117 24 2701 3921 696521772 696520538 0.000000e+00 1421.0
12 TraesCS4A01G329500 chr5B 92.519 909 32 7 951 1849 696584496 696585378 0.000000e+00 1269.0
13 TraesCS4A01G329500 chr5B 79.737 1752 248 65 2059 3759 696585563 696587258 0.000000e+00 1170.0
14 TraesCS4A01G329500 chr5B 82.482 1370 149 35 2562 3906 696730336 696729033 0.000000e+00 1116.0
15 TraesCS4A01G329500 chr5B 88.115 833 56 6 1 791 696709924 696710755 0.000000e+00 950.0
16 TraesCS4A01G329500 chr5B 85.572 901 95 14 3045 3921 696576724 696575835 0.000000e+00 911.0
17 TraesCS4A01G329500 chr5B 81.234 1183 152 43 2629 3759 697025291 697026455 0.000000e+00 891.0
18 TraesCS4A01G329500 chr5B 83.446 592 75 19 1992 2568 696522359 696521776 3.290000e-146 529.0
19 TraesCS4A01G329500 chr5B 85.654 474 15 8 811 1255 696710811 696711260 2.630000e-122 449.0
20 TraesCS4A01G329500 chr5B 91.736 242 17 2 1609 1849 696577573 696577334 2.770000e-87 333.0
21 TraesCS4A01G329500 chr5B 82.656 369 47 10 1968 2329 696577199 696576841 1.300000e-80 311.0
22 TraesCS4A01G329500 chr5B 81.934 393 41 19 2019 2403 696731308 696730938 6.030000e-79 305.0
23 TraesCS4A01G329500 chr5B 87.739 261 23 6 1578 1833 696522763 696522507 3.630000e-76 296.0
24 TraesCS4A01G329500 chr5B 83.803 142 21 2 2304 2443 697024832 697024973 3.010000e-27 134.0
25 TraesCS4A01G329500 chr5B 96.104 77 2 1 3919 3995 380341815 380341740 1.810000e-24 124.0
26 TraesCS4A01G329500 chr5B 94.595 74 4 0 3922 3995 272782490 272782563 1.090000e-21 115.0
27 TraesCS4A01G329500 chr5D 95.700 1279 45 7 1913 3191 553880846 553879578 0.000000e+00 2049.0
28 TraesCS4A01G329500 chr5D 85.502 1614 154 27 2351 3918 553891679 553893258 0.000000e+00 1611.0
29 TraesCS4A01G329500 chr5D 93.935 709 18 4 3236 3921 553879577 553878871 0.000000e+00 1048.0
30 TraesCS4A01G329500 chr5D 94.655 580 21 2 934 1503 553881797 553881218 0.000000e+00 891.0
31 TraesCS4A01G329500 chr5D 93.225 369 8 1 1548 1916 553881233 553880882 1.180000e-145 527.0
32 TraesCS4A01G329500 chr5D 92.797 236 15 1 1614 1849 553889848 553890081 1.650000e-89 340.0
33 TraesCS4A01G329500 chr5D 85.866 283 34 6 1960 2237 553890218 553890499 3.630000e-76 296.0
34 TraesCS4A01G329500 chr5D 79.725 291 39 8 2446 2733 553773238 553772965 4.900000e-45 193.0
35 TraesCS4A01G329500 chr1A 95.916 808 30 3 3991 4796 504584797 504583991 0.000000e+00 1306.0
36 TraesCS4A01G329500 chr7A 96.975 628 17 2 4171 4796 461802993 461802366 0.000000e+00 1053.0
37 TraesCS4A01G329500 chr7A 81.149 801 110 21 3995 4779 526631888 526632663 5.310000e-169 604.0
38 TraesCS4A01G329500 chr7A 97.917 144 3 0 3995 4138 461803406 461803263 2.870000e-62 250.0
39 TraesCS4A01G329500 chr7A 95.833 72 3 0 3923 3994 650618027 650618098 3.030000e-22 117.0
40 TraesCS4A01G329500 chr3B 91.248 537 47 0 4260 4796 677745622 677745086 0.000000e+00 732.0
41 TraesCS4A01G329500 chr3B 97.260 73 2 0 3923 3995 389035536 389035608 1.810000e-24 124.0
42 TraesCS4A01G329500 chr6D 82.657 813 104 25 3995 4796 100196845 100196059 0.000000e+00 686.0
43 TraesCS4A01G329500 chr6B 82.099 810 105 23 4002 4796 515193401 515194185 0.000000e+00 656.0
44 TraesCS4A01G329500 chr7B 89.549 488 51 0 4309 4796 339687580 339687093 1.900000e-173 619.0
45 TraesCS4A01G329500 chr2A 92.857 378 24 1 1913 2290 507020029 507019655 3.260000e-151 545.0
46 TraesCS4A01G329500 chr2A 91.914 371 19 4 1548 1916 507020424 507020063 4.280000e-140 508.0
47 TraesCS4A01G329500 chr2A 90.289 381 34 1 1910 2290 347014690 347015067 3.330000e-136 496.0
48 TraesCS4A01G329500 chr2A 81.381 333 56 6 4467 4796 711549910 711550239 2.850000e-67 267.0
49 TraesCS4A01G329500 chr6A 92.408 382 25 2 1909 2290 158667439 158667816 4.220000e-150 542.0
50 TraesCS4A01G329500 chr6A 92.722 371 18 3 1548 1916 158667044 158667407 1.180000e-145 527.0
51 TraesCS4A01G329500 chr4D 95.890 73 3 0 3923 3995 9068718 9068646 8.430000e-23 119.0
52 TraesCS4A01G329500 chr3D 95.890 73 3 0 3923 3995 245862546 245862618 8.430000e-23 119.0
53 TraesCS4A01G329500 chr2D 95.890 73 3 0 3923 3995 588560645 588560573 8.430000e-23 119.0
54 TraesCS4A01G329500 chr5A 93.151 73 5 0 3923 3995 368103358 368103286 1.830000e-19 108.0


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 TraesCS4A01G329500 chr4A 614608275 614613070 4795 False 8857.000000 8857 100.000000 1 4796 1 chr4A.!!$F1 4795
1 TraesCS4A01G329500 chr4A 614445878 614449237 3359 True 953.133333 1779 87.871333 546 3921 3 chr4A.!!$R4 3375
2 TraesCS4A01G329500 chr4A 614425514 614427572 2058 True 810.500000 1308 88.212000 1609 3906 2 chr4A.!!$R3 2297
3 TraesCS4A01G329500 chr4A 614416366 614418564 2198 True 730.000000 1387 86.009000 1549 3907 3 chr4A.!!$R2 2358
4 TraesCS4A01G329500 chr5B 696709924 696713739 3815 False 1472.333333 3018 88.111667 1 3854 3 chr5B.!!$F3 3853
5 TraesCS4A01G329500 chr5B 696584496 696587258 2762 False 1219.500000 1269 86.128000 951 3759 2 chr5B.!!$F2 2808
6 TraesCS4A01G329500 chr5B 696520538 696522763 2225 True 748.666667 1421 86.302000 1578 3921 3 chr5B.!!$R2 2343
7 TraesCS4A01G329500 chr5B 696729033 696731308 2275 True 710.500000 1116 82.208000 2019 3906 2 chr5B.!!$R4 1887
8 TraesCS4A01G329500 chr5B 696575835 696577573 1738 True 518.333333 911 86.654667 1609 3921 3 chr5B.!!$R3 2312
9 TraesCS4A01G329500 chr5B 697024832 697026455 1623 False 512.500000 891 82.518500 2304 3759 2 chr5B.!!$F4 1455
10 TraesCS4A01G329500 chr5D 553878871 553881797 2926 True 1128.750000 2049 94.378750 934 3921 4 chr5D.!!$R2 2987
11 TraesCS4A01G329500 chr5D 553889848 553893258 3410 False 749.000000 1611 88.055000 1614 3918 3 chr5D.!!$F1 2304
12 TraesCS4A01G329500 chr1A 504583991 504584797 806 True 1306.000000 1306 95.916000 3991 4796 1 chr1A.!!$R1 805
13 TraesCS4A01G329500 chr7A 461802366 461803406 1040 True 651.500000 1053 97.446000 3995 4796 2 chr7A.!!$R1 801
14 TraesCS4A01G329500 chr7A 526631888 526632663 775 False 604.000000 604 81.149000 3995 4779 1 chr7A.!!$F1 784
15 TraesCS4A01G329500 chr3B 677745086 677745622 536 True 732.000000 732 91.248000 4260 4796 1 chr3B.!!$R1 536
16 TraesCS4A01G329500 chr6D 100196059 100196845 786 True 686.000000 686 82.657000 3995 4796 1 chr6D.!!$R1 801
17 TraesCS4A01G329500 chr6B 515193401 515194185 784 False 656.000000 656 82.099000 4002 4796 1 chr6B.!!$F1 794
18 TraesCS4A01G329500 chr2A 507019655 507020424 769 True 526.500000 545 92.385500 1548 2290 2 chr2A.!!$R1 742
19 TraesCS4A01G329500 chr6A 158667044 158667816 772 False 534.500000 542 92.565000 1548 2290 2 chr6A.!!$F1 742

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
468 479 0.465642 GAGGGGTTAAAGGGGATGCG 60.466 60.0 0.0 0.0 0.0 4.73 F
834 913 0.727398 GCTTTGTGGCGTGATACTCC 59.273 55.0 0.0 0.0 0.0 3.85 F
2444 4307 0.399075 AACACAACCCCTCCCGTTAG 59.601 55.0 0.0 0.0 0.0 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 1972 0.318107 CTTGGTGTTGCTTTGGCTCG 60.318 55.000 0.00 0.0 39.59 5.03 R
2458 4356 1.517361 CCCGTCACAGATGCAGCTA 59.483 57.895 3.06 0.0 0.00 3.32 R
3934 6136 0.165944 CGCACGCCCTTTAAACTGAG 59.834 55.000 0.00 0.0 0.00 3.35 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.372206 GCTATGACGTTCAACTCTTGCAT 59.628 43.478 0.00 0.00 0.00 3.96
61 62 2.460330 GGACACGCCTGACTCATTG 58.540 57.895 0.00 0.00 0.00 2.82
71 72 4.336433 CGCCTGACTCATTGGTGAAAATAT 59.664 41.667 0.00 0.00 33.05 1.28
98 99 9.031360 GCAAGACTCGAGATATAAAATGTTGTA 57.969 33.333 21.68 0.00 0.00 2.41
235 236 6.975471 TGTGGGATGAAGGATATATTGGAT 57.025 37.500 0.00 0.00 0.00 3.41
240 241 6.069440 GGGATGAAGGATATATTGGATCACCA 60.069 42.308 0.00 0.00 45.34 4.17
253 254 4.717877 TGGATCACCAATCATATTTCGCT 58.282 39.130 0.00 0.00 43.91 4.93
272 273 7.489574 TTCGCTTGGCTTTTAAATTTGAATT 57.510 28.000 0.00 0.00 0.00 2.17
299 300 1.095807 GCCCTTATCGAACCTGGTGC 61.096 60.000 0.00 0.00 0.00 5.01
318 319 1.137282 GCTAGAAGCTCCCACACCTAC 59.863 57.143 0.00 0.00 38.45 3.18
330 331 1.971357 CACACCTACAGAGTCCCTTGT 59.029 52.381 0.00 0.00 0.00 3.16
347 348 3.562973 CCTTGTATAGTGCAATGCAGAGG 59.437 47.826 8.73 4.02 40.08 3.69
380 381 5.659079 TGAACCCAAAACCTCTTAACACAAT 59.341 36.000 0.00 0.00 0.00 2.71
427 428 9.391006 GATAAGAGGTCATAAACAACCACAATA 57.609 33.333 0.00 0.00 0.00 1.90
453 454 5.422331 ACTCATAATCGTATGTATGGGAGGG 59.578 44.000 0.00 0.00 38.63 4.30
455 456 2.715763 ATCGTATGTATGGGAGGGGT 57.284 50.000 0.00 0.00 0.00 4.95
468 479 0.465642 GAGGGGTTAAAGGGGATGCG 60.466 60.000 0.00 0.00 0.00 4.73
524 560 1.999071 TTTGTGATAATGGCGCCCGC 61.999 55.000 26.77 15.26 41.06 6.13
543 579 3.985279 CCGCGCATAACTTTAGCTATGTA 59.015 43.478 8.75 0.00 0.00 2.29
544 580 4.446385 CCGCGCATAACTTTAGCTATGTAA 59.554 41.667 8.75 0.00 0.00 2.41
598 634 2.091885 TCCATCTATCCAACTTTGCCCC 60.092 50.000 0.00 0.00 0.00 5.80
599 635 2.091665 CCATCTATCCAACTTTGCCCCT 60.092 50.000 0.00 0.00 0.00 4.79
605 641 0.758685 CCAACTTTGCCCCTTGACCA 60.759 55.000 0.00 0.00 0.00 4.02
617 653 3.578282 CCCCTTGACCATAGTTTTGCTTT 59.422 43.478 0.00 0.00 0.00 3.51
626 662 6.290605 ACCATAGTTTTGCTTTGATTTTGCT 58.709 32.000 0.00 0.00 0.00 3.91
691 727 2.229792 TGGCTCCTTCACATTTCACAC 58.770 47.619 0.00 0.00 0.00 3.82
692 728 1.541588 GGCTCCTTCACATTTCACACC 59.458 52.381 0.00 0.00 0.00 4.16
701 737 7.013274 TCCTTCACATTTCACACCTAGAAAAAG 59.987 37.037 0.00 0.00 38.36 2.27
702 738 7.013274 CCTTCACATTTCACACCTAGAAAAAGA 59.987 37.037 0.00 0.00 38.36 2.52
712 748 5.715753 ACACCTAGAAAAAGAGGTCGATACT 59.284 40.000 0.00 0.00 44.54 2.12
834 913 0.727398 GCTTTGTGGCGTGATACTCC 59.273 55.000 0.00 0.00 0.00 3.85
847 926 6.099341 GCGTGATACTCCAAAAATCCAAAAT 58.901 36.000 0.00 0.00 0.00 1.82
860 940 9.958180 CAAAAATCCAAAATAAAGAAGGGGTAT 57.042 29.630 0.00 0.00 0.00 2.73
894 974 1.880941 ATTAAACCCTCTCCTCGGCT 58.119 50.000 0.00 0.00 0.00 5.52
1429 1693 7.573968 ACACATTCTTAGGGCTGAAATTATC 57.426 36.000 0.00 0.00 0.00 1.75
1486 1750 7.930325 TGAATTTGCTGAAATTGGAAATGTGTA 59.070 29.630 0.00 0.00 41.06 2.90
1506 1770 8.902540 TGTGTATGAGAACAAATTCTTACAGT 57.097 30.769 3.09 0.00 45.60 3.55
1534 1798 9.042008 TCTAAAACTTTGCTGAAACTAGTACTG 57.958 33.333 5.39 0.00 0.00 2.74
1702 1972 1.452833 GCATGCCTTCCCAGAGGAC 60.453 63.158 6.36 0.00 43.90 3.85
1886 2165 3.330701 AGCTCAAATACTCTGGTTCCCAA 59.669 43.478 0.00 0.00 30.80 4.12
2192 2558 0.687354 AGGAGACGAAGCAACACCAT 59.313 50.000 0.00 0.00 0.00 3.55
2193 2559 0.798776 GGAGACGAAGCAACACCATG 59.201 55.000 0.00 0.00 0.00 3.66
2217 2583 2.747460 TTGCTGTCTCATGCGCCC 60.747 61.111 4.18 0.00 0.00 6.13
2268 2874 8.605325 AACACTCCTAGCCTCTTACTTATTTA 57.395 34.615 0.00 0.00 0.00 1.40
2269 2875 8.785184 ACACTCCTAGCCTCTTACTTATTTAT 57.215 34.615 0.00 0.00 0.00 1.40
2270 2876 9.214962 ACACTCCTAGCCTCTTACTTATTTATT 57.785 33.333 0.00 0.00 0.00 1.40
2444 4307 0.399075 AACACAACCCCTCCCGTTAG 59.601 55.000 0.00 0.00 0.00 2.34
2785 4877 9.574458 TCAACGAGTTTTTAATCATGTTTTGAA 57.426 25.926 0.00 0.00 38.03 2.69
3018 5122 2.285368 TCTGCCCCGACCCAAGAT 60.285 61.111 0.00 0.00 0.00 2.40
3136 5246 0.039617 CCAAACAAAAGGATGCGCGA 60.040 50.000 12.10 0.00 0.00 5.87
3137 5247 1.052287 CAAACAAAAGGATGCGCGAC 58.948 50.000 12.10 0.88 0.00 5.19
3183 5293 5.689383 AAATACAACAGAGCGAACAACAT 57.311 34.783 0.00 0.00 0.00 2.71
3187 5297 5.689383 ACAACAGAGCGAACAACATTAAT 57.311 34.783 0.00 0.00 0.00 1.40
3210 5322 4.162320 TGTCTTCCTCTCTCTCTCTCTCTC 59.838 50.000 0.00 0.00 0.00 3.20
3212 5324 4.651503 TCTTCCTCTCTCTCTCTCTCTCTC 59.348 50.000 0.00 0.00 0.00 3.20
3213 5325 4.271807 TCCTCTCTCTCTCTCTCTCTCT 57.728 50.000 0.00 0.00 0.00 3.10
3214 5326 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
3215 5327 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
3220 5333 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3226 5339 3.963374 CTCTCTCTCTCTCTCTCTCTCCA 59.037 52.174 0.00 0.00 0.00 3.86
3473 5605 4.399618 TGACCTCTATTTTCGGAGTGAGAG 59.600 45.833 0.00 0.00 0.00 3.20
3501 5633 5.527214 TGTGATTATGTGCTGTATAGTTGGC 59.473 40.000 0.00 0.00 0.00 4.52
3843 6043 2.186160 CGCTGGCTTGTGTGACCAA 61.186 57.895 0.00 0.00 31.81 3.67
3910 6112 4.725790 CATCGCATGGAGTAGATATGGA 57.274 45.455 0.00 0.00 0.00 3.41
3911 6113 5.273674 CATCGCATGGAGTAGATATGGAT 57.726 43.478 0.00 0.00 0.00 3.41
3912 6114 5.668471 CATCGCATGGAGTAGATATGGATT 58.332 41.667 0.00 0.00 0.00 3.01
3913 6115 6.809869 CATCGCATGGAGTAGATATGGATTA 58.190 40.000 0.00 0.00 0.00 1.75
3914 6116 6.850752 TCGCATGGAGTAGATATGGATTAA 57.149 37.500 0.00 0.00 0.00 1.40
3915 6117 6.631016 TCGCATGGAGTAGATATGGATTAAC 58.369 40.000 0.00 0.00 0.00 2.01
3916 6118 6.437477 TCGCATGGAGTAGATATGGATTAACT 59.563 38.462 0.00 0.00 0.00 2.24
3917 6119 7.039011 TCGCATGGAGTAGATATGGATTAACTT 60.039 37.037 0.00 0.00 0.00 2.66
3918 6120 8.251026 CGCATGGAGTAGATATGGATTAACTTA 58.749 37.037 0.00 0.00 0.00 2.24
3919 6121 9.944376 GCATGGAGTAGATATGGATTAACTTAA 57.056 33.333 0.00 0.00 0.00 1.85
3933 6135 9.765295 TGGATTAACTTAAGTTACTACCTCTCT 57.235 33.333 24.39 0.83 39.92 3.10
3938 6140 8.570068 AACTTAAGTTACTACCTCTCTCTCAG 57.430 38.462 19.26 0.00 36.32 3.35
3939 6141 7.692172 ACTTAAGTTACTACCTCTCTCTCAGT 58.308 38.462 1.12 0.00 0.00 3.41
3940 6142 8.165397 ACTTAAGTTACTACCTCTCTCTCAGTT 58.835 37.037 1.12 0.00 0.00 3.16
3941 6143 8.937207 TTAAGTTACTACCTCTCTCTCAGTTT 57.063 34.615 0.00 0.00 0.00 2.66
3943 6145 8.937207 AAGTTACTACCTCTCTCTCAGTTTAA 57.063 34.615 0.00 0.00 0.00 1.52
3944 6146 8.937207 AGTTACTACCTCTCTCTCAGTTTAAA 57.063 34.615 0.00 0.00 0.00 1.52
3945 6147 9.016438 AGTTACTACCTCTCTCTCAGTTTAAAG 57.984 37.037 0.00 0.00 0.00 1.85
3946 6148 6.844097 ACTACCTCTCTCTCAGTTTAAAGG 57.156 41.667 0.00 0.00 0.00 3.11
3947 6149 5.717654 ACTACCTCTCTCTCAGTTTAAAGGG 59.282 44.000 0.00 0.00 0.00 3.95
3948 6150 3.262151 ACCTCTCTCTCAGTTTAAAGGGC 59.738 47.826 0.00 0.00 0.00 5.19
3949 6151 3.516615 CTCTCTCTCAGTTTAAAGGGCG 58.483 50.000 0.00 0.00 0.00 6.13
3950 6152 2.897969 TCTCTCTCAGTTTAAAGGGCGT 59.102 45.455 0.00 0.00 0.00 5.68
3951 6153 2.996621 CTCTCTCAGTTTAAAGGGCGTG 59.003 50.000 0.00 0.00 0.00 5.34
3952 6154 1.464997 CTCTCAGTTTAAAGGGCGTGC 59.535 52.381 0.00 0.00 0.00 5.34
3953 6155 0.165944 CTCAGTTTAAAGGGCGTGCG 59.834 55.000 0.00 0.00 0.00 5.34
3954 6156 1.442017 CAGTTTAAAGGGCGTGCGC 60.442 57.895 8.17 8.17 41.06 6.09
3955 6157 2.501008 GTTTAAAGGGCGTGCGCG 60.501 61.111 16.86 16.86 43.06 6.86
3956 6158 2.973600 TTTAAAGGGCGTGCGCGT 60.974 55.556 22.18 2.94 43.06 6.01
3957 6159 1.667191 TTTAAAGGGCGTGCGCGTA 60.667 52.632 22.18 0.00 43.06 4.42
3958 6160 1.899521 TTTAAAGGGCGTGCGCGTAC 61.900 55.000 22.18 17.94 43.06 3.67
3965 6167 3.511595 CGTGCGCGTACCCCTAGA 61.512 66.667 21.71 0.00 0.00 2.43
3966 6168 2.842256 CGTGCGCGTACCCCTAGAT 61.842 63.158 21.71 0.00 0.00 1.98
3967 6169 1.007618 GTGCGCGTACCCCTAGATC 60.008 63.158 17.10 0.00 0.00 2.75
3968 6170 2.254651 GCGCGTACCCCTAGATCG 59.745 66.667 8.43 0.00 0.00 3.69
3969 6171 2.550101 GCGCGTACCCCTAGATCGT 61.550 63.158 8.43 0.00 0.00 3.73
3970 6172 1.573436 CGCGTACCCCTAGATCGTC 59.427 63.158 0.00 0.00 0.00 4.20
3971 6173 1.162181 CGCGTACCCCTAGATCGTCA 61.162 60.000 0.00 0.00 0.00 4.35
3972 6174 1.245732 GCGTACCCCTAGATCGTCAT 58.754 55.000 0.00 0.00 0.00 3.06
3973 6175 1.612463 GCGTACCCCTAGATCGTCATT 59.388 52.381 0.00 0.00 0.00 2.57
3974 6176 2.035576 GCGTACCCCTAGATCGTCATTT 59.964 50.000 0.00 0.00 0.00 2.32
3975 6177 3.492137 GCGTACCCCTAGATCGTCATTTT 60.492 47.826 0.00 0.00 0.00 1.82
3976 6178 4.049186 CGTACCCCTAGATCGTCATTTTG 58.951 47.826 0.00 0.00 0.00 2.44
3977 6179 4.202080 CGTACCCCTAGATCGTCATTTTGA 60.202 45.833 0.00 0.00 0.00 2.69
3978 6180 4.138487 ACCCCTAGATCGTCATTTTGAC 57.862 45.455 0.00 0.00 43.65 3.18
3979 6181 3.118371 ACCCCTAGATCGTCATTTTGACC 60.118 47.826 2.26 0.00 44.20 4.02
3980 6182 3.118408 CCCCTAGATCGTCATTTTGACCA 60.118 47.826 2.26 0.00 44.20 4.02
3981 6183 4.513442 CCCTAGATCGTCATTTTGACCAA 58.487 43.478 2.26 0.00 44.20 3.67
3982 6184 4.332819 CCCTAGATCGTCATTTTGACCAAC 59.667 45.833 2.26 0.00 44.20 3.77
3983 6185 4.332819 CCTAGATCGTCATTTTGACCAACC 59.667 45.833 2.26 0.00 44.20 3.77
3984 6186 4.021102 AGATCGTCATTTTGACCAACCT 57.979 40.909 2.26 0.00 44.20 3.50
3985 6187 5.160607 AGATCGTCATTTTGACCAACCTA 57.839 39.130 2.26 0.00 44.20 3.08
3986 6188 5.556915 AGATCGTCATTTTGACCAACCTAA 58.443 37.500 2.26 0.00 44.20 2.69
3987 6189 6.180472 AGATCGTCATTTTGACCAACCTAAT 58.820 36.000 2.26 0.00 44.20 1.73
3988 6190 7.335627 AGATCGTCATTTTGACCAACCTAATA 58.664 34.615 2.26 0.00 44.20 0.98
3989 6191 6.730960 TCGTCATTTTGACCAACCTAATAC 57.269 37.500 2.26 0.00 44.20 1.89
3990 6192 6.231951 TCGTCATTTTGACCAACCTAATACA 58.768 36.000 2.26 0.00 44.20 2.29
3991 6193 6.711194 TCGTCATTTTGACCAACCTAATACAA 59.289 34.615 2.26 0.00 44.20 2.41
3992 6194 7.021196 CGTCATTTTGACCAACCTAATACAAG 58.979 38.462 2.26 0.00 44.20 3.16
3993 6195 7.308348 CGTCATTTTGACCAACCTAATACAAGT 60.308 37.037 2.26 0.00 44.20 3.16
4067 6279 2.774351 CTCCCCCATCCCCTCCAC 60.774 72.222 0.00 0.00 0.00 4.02
4254 6707 4.147449 CTGGCTGCGTGGATCCGA 62.147 66.667 7.39 0.00 0.00 4.55
4750 7212 1.614241 GCGTAGGAGGTGTGTGGGAT 61.614 60.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.043059 GCGTGTCCTTCATGAATTAAACAAAAA 60.043 33.333 8.96 0.00 35.23 1.94
52 53 6.433716 TCTTGCATATTTTCACCAATGAGTCA 59.566 34.615 0.00 0.00 35.83 3.41
61 62 4.870426 TCTCGAGTCTTGCATATTTTCACC 59.130 41.667 13.13 0.00 0.00 4.02
71 72 7.549134 ACAACATTTTATATCTCGAGTCTTGCA 59.451 33.333 13.13 0.00 0.00 4.08
132 133 7.664552 TGGGACGGAAGAAGTATCTTATAAA 57.335 36.000 0.00 0.00 45.91 1.40
133 134 7.850935 ATGGGACGGAAGAAGTATCTTATAA 57.149 36.000 0.00 0.00 45.91 0.98
181 182 9.778741 AAGACGTCATTAATCCAATATACATGT 57.221 29.630 19.50 2.69 0.00 3.21
200 201 3.857052 TCATCCCACAACATAAGACGTC 58.143 45.455 7.70 7.70 0.00 4.34
210 211 6.542821 TCCAATATATCCTTCATCCCACAAC 58.457 40.000 0.00 0.00 0.00 3.32
235 236 4.898829 CCAAGCGAAATATGATTGGTGA 57.101 40.909 2.02 0.00 45.45 4.02
240 241 8.947055 ATTTAAAAGCCAAGCGAAATATGATT 57.053 26.923 0.00 0.00 0.00 2.57
251 252 7.746034 GCAGTAATTCAAATTTAAAAGCCAAGC 59.254 33.333 0.00 0.00 0.00 4.01
252 253 7.951565 CGCAGTAATTCAAATTTAAAAGCCAAG 59.048 33.333 0.00 0.00 0.00 3.61
253 254 7.439655 ACGCAGTAATTCAAATTTAAAAGCCAA 59.560 29.630 0.00 0.00 41.94 4.52
272 273 0.818938 TTCGATAAGGGCACGCAGTA 59.181 50.000 0.00 0.00 41.61 2.74
299 300 2.428890 CTGTAGGTGTGGGAGCTTCTAG 59.571 54.545 0.00 0.00 33.31 2.43
318 319 4.471904 TTGCACTATACAAGGGACTCTG 57.528 45.455 0.00 0.00 38.49 3.35
330 331 3.647590 TGATCCCTCTGCATTGCACTATA 59.352 43.478 7.38 0.00 33.79 1.31
347 348 2.287970 GGTTTTGGGTTCAACGTGATCC 60.288 50.000 0.00 0.00 35.90 3.36
427 428 7.287927 CCCTCCCATACATACGATTATGAGTAT 59.712 40.741 0.00 0.00 37.86 2.12
437 438 2.482414 AACCCCTCCCATACATACGA 57.518 50.000 0.00 0.00 0.00 3.43
450 451 1.613061 CGCATCCCCTTTAACCCCT 59.387 57.895 0.00 0.00 0.00 4.79
453 454 0.465642 CCTCCGCATCCCCTTTAACC 60.466 60.000 0.00 0.00 0.00 2.85
455 456 0.837272 CTCCTCCGCATCCCCTTTAA 59.163 55.000 0.00 0.00 0.00 1.52
468 479 5.959583 TCTAATCTTCCTTTTCCTCCTCC 57.040 43.478 0.00 0.00 0.00 4.30
524 560 9.769093 AAAAAGTTACATAGCTAAAGTTATGCG 57.231 29.630 12.20 0.00 41.17 4.73
543 579 3.057526 GCCGAGGAGTGCAATAAAAAGTT 60.058 43.478 0.00 0.00 0.00 2.66
544 580 2.488153 GCCGAGGAGTGCAATAAAAAGT 59.512 45.455 0.00 0.00 0.00 2.66
598 634 7.951530 AAATCAAAGCAAAACTATGGTCAAG 57.048 32.000 0.00 0.00 0.00 3.02
599 635 7.254727 GCAAAATCAAAGCAAAACTATGGTCAA 60.255 33.333 0.00 0.00 0.00 3.18
605 641 5.107375 CGCAGCAAAATCAAAGCAAAACTAT 60.107 36.000 0.00 0.00 0.00 2.12
636 672 1.296392 CAGAAGTGGCGTGATGGGA 59.704 57.895 0.00 0.00 0.00 4.37
691 727 6.702716 AGAGTATCGACCTCTTTTTCTAGG 57.297 41.667 9.98 0.00 42.67 3.02
816 895 2.093306 TGGAGTATCACGCCACAAAG 57.907 50.000 0.00 0.00 43.20 2.77
834 913 9.958180 ATACCCCTTCTTTATTTTGGATTTTTG 57.042 29.630 0.00 0.00 0.00 2.44
847 926 7.072708 TGGGAATCGATTTATACCCCTTCTTTA 59.927 37.037 24.58 7.86 36.82 1.85
860 940 7.837187 AGAGGGTTTAATTTGGGAATCGATTTA 59.163 33.333 12.81 0.00 0.00 1.40
1429 1693 7.484641 CACAAGAATTTGTTCCGGTATACATTG 59.515 37.037 0.00 8.25 45.01 2.82
1534 1798 7.913674 AATTTGTTCTCACCTTCTCAGATAC 57.086 36.000 0.00 0.00 0.00 2.24
1702 1972 0.318107 CTTGGTGTTGCTTTGGCTCG 60.318 55.000 0.00 0.00 39.59 5.03
2192 2558 2.745821 GCATGAGACAGCAACTTGATCA 59.254 45.455 0.00 0.00 0.00 2.92
2193 2559 2.222976 CGCATGAGACAGCAACTTGATC 60.223 50.000 0.00 0.00 0.00 2.92
2268 2874 9.995003 TTGTACAAAGAGCAATCCAAAATAAAT 57.005 25.926 5.64 0.00 0.00 1.40
2269 2875 9.255304 GTTGTACAAAGAGCAATCCAAAATAAA 57.745 29.630 10.51 0.00 0.00 1.40
2270 2876 8.417106 TGTTGTACAAAGAGCAATCCAAAATAA 58.583 29.630 10.51 0.00 0.00 1.40
2271 2877 7.865385 GTGTTGTACAAAGAGCAATCCAAAATA 59.135 33.333 10.51 0.00 0.00 1.40
2444 4307 1.596727 GCAGCTAGCAGTGTAGAATGC 59.403 52.381 18.83 10.72 44.79 3.56
2458 4356 1.517361 CCCGTCACAGATGCAGCTA 59.483 57.895 3.06 0.00 0.00 3.32
2535 4435 5.163530 TGACACAACACAATGAGAGCAAAAT 60.164 36.000 0.00 0.00 0.00 1.82
2785 4877 1.985473 TGAAGGTGCATGCAGAGTTT 58.015 45.000 23.41 12.83 0.00 2.66
2884 4983 3.378427 GTGAACTGATTGTTATGCCCCTC 59.622 47.826 0.00 0.00 39.30 4.30
3079 5189 0.968393 GGAGAGCGTTCCTCACCTCT 60.968 60.000 0.00 0.00 44.95 3.69
3183 5293 6.969043 AGAGAGAGAGAGAGGAAGACATTAA 58.031 40.000 0.00 0.00 0.00 1.40
3187 5297 4.104086 AGAGAGAGAGAGAGAGGAAGACA 58.896 47.826 0.00 0.00 0.00 3.41
3210 5322 5.471116 CACATACATGGAGAGAGAGAGAGAG 59.529 48.000 0.00 0.00 0.00 3.20
3212 5324 5.375773 TCACATACATGGAGAGAGAGAGAG 58.624 45.833 0.00 0.00 0.00 3.20
3213 5325 5.375773 CTCACATACATGGAGAGAGAGAGA 58.624 45.833 0.00 0.00 36.67 3.10
3214 5326 4.022935 GCTCACATACATGGAGAGAGAGAG 60.023 50.000 14.42 3.28 36.67 3.20
3215 5327 3.888323 GCTCACATACATGGAGAGAGAGA 59.112 47.826 14.42 0.00 36.67 3.10
3220 5333 3.869832 CACAAGCTCACATACATGGAGAG 59.130 47.826 0.00 9.44 37.22 3.20
3226 5339 4.248859 GACTGTCACAAGCTCACATACAT 58.751 43.478 2.24 0.00 0.00 2.29
3473 5605 7.953158 ACTATACAGCACATAATCACATCAC 57.047 36.000 0.00 0.00 0.00 3.06
3501 5633 1.722011 AGGTACCTGCGTCATTTTCG 58.278 50.000 15.42 0.00 0.00 3.46
3795 5995 1.842562 AGGCTCCAAGTGCTACATCAT 59.157 47.619 0.00 0.00 0.00 2.45
3843 6043 6.989169 GCAAGTGAATATACACCAGAGAAGAT 59.011 38.462 0.00 0.00 41.12 2.40
3907 6109 9.765295 AGAGAGGTAGTAACTTAAGTTAATCCA 57.235 33.333 26.56 11.79 41.58 3.41
3912 6114 9.669887 CTGAGAGAGAGGTAGTAACTTAAGTTA 57.330 37.037 21.52 21.52 39.31 2.24
3913 6115 8.165397 ACTGAGAGAGAGGTAGTAACTTAAGTT 58.835 37.037 23.58 23.58 41.73 2.66
3914 6116 7.692172 ACTGAGAGAGAGGTAGTAACTTAAGT 58.308 38.462 1.12 1.12 0.00 2.24
3915 6117 8.570068 AACTGAGAGAGAGGTAGTAACTTAAG 57.430 38.462 0.00 0.00 0.00 1.85
3916 6118 8.937207 AAACTGAGAGAGAGGTAGTAACTTAA 57.063 34.615 0.00 0.00 0.00 1.85
3918 6120 8.937207 TTAAACTGAGAGAGAGGTAGTAACTT 57.063 34.615 0.00 0.00 0.00 2.66
3919 6121 8.937207 TTTAAACTGAGAGAGAGGTAGTAACT 57.063 34.615 0.00 0.00 0.00 2.24
3920 6122 8.245491 CCTTTAAACTGAGAGAGAGGTAGTAAC 58.755 40.741 0.00 0.00 0.00 2.50
3921 6123 7.396623 CCCTTTAAACTGAGAGAGAGGTAGTAA 59.603 40.741 0.00 0.00 0.00 2.24
3922 6124 6.890814 CCCTTTAAACTGAGAGAGAGGTAGTA 59.109 42.308 0.00 0.00 0.00 1.82
3923 6125 5.717654 CCCTTTAAACTGAGAGAGAGGTAGT 59.282 44.000 0.00 0.00 0.00 2.73
3924 6126 5.394773 GCCCTTTAAACTGAGAGAGAGGTAG 60.395 48.000 0.00 0.00 0.00 3.18
3925 6127 4.466726 GCCCTTTAAACTGAGAGAGAGGTA 59.533 45.833 0.00 0.00 0.00 3.08
3926 6128 3.262151 GCCCTTTAAACTGAGAGAGAGGT 59.738 47.826 0.00 0.00 0.00 3.85
3927 6129 3.677424 CGCCCTTTAAACTGAGAGAGAGG 60.677 52.174 0.00 0.00 0.00 3.69
3928 6130 3.056465 ACGCCCTTTAAACTGAGAGAGAG 60.056 47.826 0.00 0.00 0.00 3.20
3929 6131 2.897969 ACGCCCTTTAAACTGAGAGAGA 59.102 45.455 0.00 0.00 0.00 3.10
3930 6132 2.996621 CACGCCCTTTAAACTGAGAGAG 59.003 50.000 0.00 0.00 0.00 3.20
3931 6133 2.870435 GCACGCCCTTTAAACTGAGAGA 60.870 50.000 0.00 0.00 0.00 3.10
3932 6134 1.464997 GCACGCCCTTTAAACTGAGAG 59.535 52.381 0.00 0.00 0.00 3.20
3933 6135 1.519408 GCACGCCCTTTAAACTGAGA 58.481 50.000 0.00 0.00 0.00 3.27
3934 6136 0.165944 CGCACGCCCTTTAAACTGAG 59.834 55.000 0.00 0.00 0.00 3.35
3935 6137 1.847890 GCGCACGCCCTTTAAACTGA 61.848 55.000 0.30 0.00 34.56 3.41
3936 6138 1.442017 GCGCACGCCCTTTAAACTG 60.442 57.895 0.30 0.00 34.56 3.16
3937 6139 2.951458 GCGCACGCCCTTTAAACT 59.049 55.556 0.30 0.00 34.56 2.66
3938 6140 1.899521 TACGCGCACGCCCTTTAAAC 61.900 55.000 5.73 0.00 45.53 2.01
3939 6141 1.667191 TACGCGCACGCCCTTTAAA 60.667 52.632 5.73 0.00 45.53 1.52
3940 6142 2.048409 TACGCGCACGCCCTTTAA 60.048 55.556 5.73 0.00 45.53 1.52
3941 6143 2.810458 GTACGCGCACGCCCTTTA 60.810 61.111 5.73 0.00 45.53 1.85
3953 6155 1.245732 ATGACGATCTAGGGGTACGC 58.754 55.000 0.29 0.29 43.76 4.42
3954 6156 4.049186 CAAAATGACGATCTAGGGGTACG 58.951 47.826 0.00 0.00 0.00 3.67
3955 6157 5.048507 GTCAAAATGACGATCTAGGGGTAC 58.951 45.833 0.00 0.00 37.67 3.34
3956 6158 5.272283 GTCAAAATGACGATCTAGGGGTA 57.728 43.478 0.00 0.00 37.67 3.69
3957 6159 4.138487 GTCAAAATGACGATCTAGGGGT 57.862 45.455 0.00 0.00 37.67 4.95
3968 6170 7.882179 ACTTGTATTAGGTTGGTCAAAATGAC 58.118 34.615 1.88 1.88 46.23 3.06
3969 6171 7.175990 GGACTTGTATTAGGTTGGTCAAAATGA 59.824 37.037 0.00 0.00 0.00 2.57
3970 6172 7.312899 GGACTTGTATTAGGTTGGTCAAAATG 58.687 38.462 0.00 0.00 0.00 2.32
3971 6173 6.436218 GGGACTTGTATTAGGTTGGTCAAAAT 59.564 38.462 0.00 0.00 0.00 1.82
3972 6174 5.771165 GGGACTTGTATTAGGTTGGTCAAAA 59.229 40.000 0.00 0.00 0.00 2.44
3973 6175 5.318630 GGGACTTGTATTAGGTTGGTCAAA 58.681 41.667 0.00 0.00 0.00 2.69
3974 6176 4.263594 GGGGACTTGTATTAGGTTGGTCAA 60.264 45.833 0.00 0.00 0.00 3.18
3975 6177 3.264964 GGGGACTTGTATTAGGTTGGTCA 59.735 47.826 0.00 0.00 0.00 4.02
3976 6178 3.371273 GGGGGACTTGTATTAGGTTGGTC 60.371 52.174 0.00 0.00 0.00 4.02
3977 6179 2.579400 GGGGGACTTGTATTAGGTTGGT 59.421 50.000 0.00 0.00 0.00 3.67
3978 6180 2.420967 CGGGGGACTTGTATTAGGTTGG 60.421 54.545 0.00 0.00 0.00 3.77
3979 6181 2.914059 CGGGGGACTTGTATTAGGTTG 58.086 52.381 0.00 0.00 0.00 3.77
3980 6182 1.211212 GCGGGGGACTTGTATTAGGTT 59.789 52.381 0.00 0.00 0.00 3.50
3981 6183 0.835276 GCGGGGGACTTGTATTAGGT 59.165 55.000 0.00 0.00 0.00 3.08
3982 6184 0.249741 CGCGGGGGACTTGTATTAGG 60.250 60.000 0.00 0.00 0.00 2.69
3983 6185 0.462789 ACGCGGGGGACTTGTATTAG 59.537 55.000 12.47 0.00 0.00 1.73
3984 6186 0.461135 GACGCGGGGGACTTGTATTA 59.539 55.000 12.47 0.00 0.00 0.98
3985 6187 1.219935 GACGCGGGGGACTTGTATT 59.780 57.895 12.47 0.00 0.00 1.89
3986 6188 2.897972 GACGCGGGGGACTTGTAT 59.102 61.111 12.47 0.00 0.00 2.29
3987 6189 3.751246 CGACGCGGGGGACTTGTA 61.751 66.667 12.47 0.00 0.00 2.41
4254 6707 2.045926 GCCTGCACCTCCATTCGT 60.046 61.111 0.00 0.00 0.00 3.85
4343 6799 4.087892 CCCACCGAGCAGGACAGG 62.088 72.222 5.19 4.21 45.00 4.00
4711 7173 2.125147 CGACGGCACCACCATCAT 60.125 61.111 0.00 0.00 39.03 2.45


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

AutoCloner maintained by Alex Coulton.