Multiple sequence alignment - TraesCS6B01G371400

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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 TraesCS6B01G371400 chr6B 100.000 3358 0 0 1 3358 645378989 645375632 0.000000e+00 6202.0
1 TraesCS6B01G371400 chr7A 96.696 1604 41 3 735 2328 611969412 611967811 0.000000e+00 2658.0
2 TraesCS6B01G371400 chr7A 93.011 930 57 3 1407 2328 665946640 665945711 0.000000e+00 1351.0
3 TraesCS6B01G371400 chr7A 96.403 695 24 1 2328 3022 611966430 611965737 0.000000e+00 1144.0
4 TraesCS6B01G371400 chr7A 91.013 701 43 5 735 1416 665948949 665948250 0.000000e+00 928.0
5 TraesCS6B01G371400 chr7A 91.117 349 22 4 2682 3021 665868624 665868276 6.560000e-127 464.0
6 TraesCS6B01G371400 chr7A 94.574 258 14 0 2764 3021 665845950 665845693 1.880000e-107 399.0
7 TraesCS6B01G371400 chr7A 91.556 225 18 1 1 225 27383998 27384221 3.250000e-80 309.0
8 TraesCS6B01G371400 chr7A 82.390 159 26 2 736 893 637053816 637053973 1.620000e-28 137.0
9 TraesCS6B01G371400 chr7A 78.302 212 42 3 334 542 649192749 649192959 2.100000e-27 134.0
10 TraesCS6B01G371400 chr7A 81.013 158 27 3 738 894 79126048 79126203 4.550000e-24 122.0
11 TraesCS6B01G371400 chr3B 87.422 1606 135 31 734 2325 65276091 65277643 0.000000e+00 1784.0
12 TraesCS6B01G371400 chr3B 93.701 254 16 0 2768 3021 65329856 65330109 6.800000e-102 381.0
13 TraesCS6B01G371400 chr6A 94.065 337 19 1 3022 3358 573421432 573421097 8.310000e-141 510.0
14 TraesCS6B01G371400 chr6A 93.953 215 13 0 1 215 455989454 455989240 3.230000e-85 326.0
15 TraesCS6B01G371400 chr6A 85.366 164 9 3 570 733 573421572 573421424 4.490000e-34 156.0
16 TraesCS6B01G371400 chr3D 78.093 881 137 33 736 1585 407492196 407493051 1.080000e-139 507.0
17 TraesCS6B01G371400 chr3D 82.781 453 63 13 1880 2325 407493357 407493801 1.130000e-104 390.0
18 TraesCS6B01G371400 chr6D 93.472 337 20 2 3022 3358 428657672 428657338 1.800000e-137 499.0
19 TraesCS6B01G371400 chr6D 92.878 337 23 1 3022 3358 428759810 428759475 3.890000e-134 488.0
20 TraesCS6B01G371400 chr6D 83.488 539 61 17 213 734 428760328 428759801 8.430000e-131 477.0
21 TraesCS6B01G371400 chr6D 82.108 408 53 14 1928 2324 379330469 379330071 6.940000e-87 331.0
22 TraesCS6B01G371400 chr6D 91.018 167 13 2 569 734 428657828 428657663 1.210000e-54 224.0
23 TraesCS6B01G371400 chr4B 94.884 215 11 0 1 215 522555446 522555660 1.490000e-88 337.0
24 TraesCS6B01G371400 chr5D 92.857 224 15 1 1 224 23838126 23837904 1.160000e-84 324.0
25 TraesCS6B01G371400 chr5D 87.143 280 36 0 1925 2204 512421884 512422163 5.410000e-83 318.0
26 TraesCS6B01G371400 chr5D 89.796 245 23 2 1 245 421982372 421982614 2.520000e-81 313.0
27 TraesCS6B01G371400 chr5D 81.395 129 21 3 2071 2198 288131864 288131738 5.930000e-18 102.0
28 TraesCS6B01G371400 chr5D 100.000 28 0 0 2337 2364 482569128 482569101 6.000000e-03 52.8
29 TraesCS6B01G371400 chr7B 93.488 215 14 0 1 215 132255447 132255233 1.500000e-83 320.0
30 TraesCS6B01G371400 chr7B 81.663 409 54 14 1928 2324 612899086 612898687 1.500000e-83 320.0
31 TraesCS6B01G371400 chr7B 75.882 170 35 6 749 915 636623847 636624013 7.720000e-12 82.4
32 TraesCS6B01G371400 chr5A 93.458 214 14 0 1 214 567533896 567533683 5.410000e-83 318.0
33 TraesCS6B01G371400 chr5A 90.204 245 19 4 1 241 688361693 688361936 6.990000e-82 315.0
34 TraesCS6B01G371400 chr5A 80.296 203 36 4 736 936 592299286 592299486 2.090000e-32 150.0
35 TraesCS6B01G371400 chr5A 100.000 28 0 0 2337 2364 592299566 592299593 6.000000e-03 52.8
36 TraesCS6B01G371400 chrUn 93.023 215 15 0 1 215 235916631 235916845 6.990000e-82 315.0
37 TraesCS6B01G371400 chr2B 86.620 284 37 1 1925 2208 747860280 747860562 2.520000e-81 313.0
38 TraesCS6B01G371400 chr2B 82.659 173 29 1 1926 2097 511283621 511283449 5.800000e-33 152.0
39 TraesCS6B01G371400 chr2B 78.531 177 29 8 736 908 511284898 511284727 1.270000e-19 108.0
40 TraesCS6B01G371400 chr2B 95.652 46 2 0 2279 2324 747860636 747860681 1.290000e-09 75.0
41 TraesCS6B01G371400 chr5B 85.714 280 38 2 1929 2207 677708600 677708322 9.110000e-76 294.0
42 TraesCS6B01G371400 chr1D 81.875 160 26 3 736 894 417252796 417252639 7.560000e-27 132.0
43 TraesCS6B01G371400 chr4A 82.946 129 19 3 2071 2198 137066792 137066666 2.740000e-21 113.0
44 TraesCS6B01G371400 chr1B 80.892 157 19 6 334 482 174960641 174960488 2.740000e-21 113.0
45 TraesCS6B01G371400 chr7D 100.000 28 0 0 2337 2364 121514420 121514393 6.000000e-03 52.8


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 TraesCS6B01G371400 chr6B 645375632 645378989 3357 True 6202.0 6202 100.0000 1 3358 1 chr6B.!!$R1 3357
1 TraesCS6B01G371400 chr7A 611965737 611969412 3675 True 1901.0 2658 96.5495 735 3022 2 chr7A.!!$R3 2287
2 TraesCS6B01G371400 chr7A 665945711 665948949 3238 True 1139.5 1351 92.0120 735 2328 2 chr7A.!!$R4 1593
3 TraesCS6B01G371400 chr3B 65276091 65277643 1552 False 1784.0 1784 87.4220 734 2325 1 chr3B.!!$F1 1591
4 TraesCS6B01G371400 chr3D 407492196 407493801 1605 False 448.5 507 80.4370 736 2325 2 chr3D.!!$F1 1589
5 TraesCS6B01G371400 chr6D 428759475 428760328 853 True 482.5 488 88.1830 213 3358 2 chr6D.!!$R3 3145

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
199 200 0.506932 CGCACACGTCCTGTAAACTG 59.493 55.0 0.00 0.0 33.53 3.16 F
1437 3101 0.108138 CGGATTTCTTGGCGAGGACT 60.108 55.0 0.97 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 3675 0.313987 CAAGGGCACTTTTCCGGTTC 59.686 55.0 0.00 0.00 33.81 3.62 R
2504 5594 0.322648 ACTACTTTTACCGGCCGCTT 59.677 50.0 22.85 11.65 0.00 4.68 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
22 23 5.587033 CCTACGTTTCAGTTTACAAGTCC 57.413 43.478 0.00 0.00 0.00 3.85
23 24 5.295152 CCTACGTTTCAGTTTACAAGTCCT 58.705 41.667 0.00 0.00 0.00 3.85
24 25 6.449698 CCTACGTTTCAGTTTACAAGTCCTA 58.550 40.000 0.00 0.00 0.00 2.94
25 26 6.364435 CCTACGTTTCAGTTTACAAGTCCTAC 59.636 42.308 0.00 0.00 0.00 3.18
26 27 4.741676 ACGTTTCAGTTTACAAGTCCTACG 59.258 41.667 0.00 0.00 0.00 3.51
27 28 4.375706 CGTTTCAGTTTACAAGTCCTACGC 60.376 45.833 0.00 0.00 0.00 4.42
28 29 2.937591 TCAGTTTACAAGTCCTACGCG 58.062 47.619 3.53 3.53 0.00 6.01
29 30 2.294233 TCAGTTTACAAGTCCTACGCGT 59.706 45.455 19.17 19.17 0.00 6.01
30 31 3.501828 TCAGTTTACAAGTCCTACGCGTA 59.498 43.478 19.40 19.40 0.00 4.42
31 32 4.156556 TCAGTTTACAAGTCCTACGCGTAT 59.843 41.667 20.91 5.41 0.00 3.06
32 33 5.353956 TCAGTTTACAAGTCCTACGCGTATA 59.646 40.000 20.91 8.44 0.00 1.47
33 34 6.038603 TCAGTTTACAAGTCCTACGCGTATAT 59.961 38.462 20.91 3.11 0.00 0.86
34 35 6.359087 CAGTTTACAAGTCCTACGCGTATATC 59.641 42.308 20.91 12.33 0.00 1.63
35 36 6.261826 AGTTTACAAGTCCTACGCGTATATCT 59.738 38.462 20.91 14.33 0.00 1.98
36 37 7.442364 AGTTTACAAGTCCTACGCGTATATCTA 59.558 37.037 20.91 0.00 0.00 1.98
37 38 5.859521 ACAAGTCCTACGCGTATATCTAG 57.140 43.478 20.91 8.56 0.00 2.43
38 39 4.694509 ACAAGTCCTACGCGTATATCTAGG 59.305 45.833 20.91 18.03 0.00 3.02
39 40 4.550076 AGTCCTACGCGTATATCTAGGT 57.450 45.455 20.91 0.00 0.00 3.08
40 41 4.904241 AGTCCTACGCGTATATCTAGGTT 58.096 43.478 20.91 8.23 0.00 3.50
41 42 4.694509 AGTCCTACGCGTATATCTAGGTTG 59.305 45.833 20.91 3.59 0.00 3.77
42 43 4.453819 GTCCTACGCGTATATCTAGGTTGT 59.546 45.833 20.91 0.00 0.00 3.32
43 44 4.692625 TCCTACGCGTATATCTAGGTTGTC 59.307 45.833 20.91 0.00 0.00 3.18
44 45 4.453478 CCTACGCGTATATCTAGGTTGTCA 59.547 45.833 20.91 0.00 0.00 3.58
45 46 4.906065 ACGCGTATATCTAGGTTGTCAA 57.094 40.909 11.67 0.00 0.00 3.18
46 47 5.449107 ACGCGTATATCTAGGTTGTCAAT 57.551 39.130 11.67 0.00 0.00 2.57
47 48 5.839621 ACGCGTATATCTAGGTTGTCAATT 58.160 37.500 11.67 0.00 0.00 2.32
48 49 6.278363 ACGCGTATATCTAGGTTGTCAATTT 58.722 36.000 11.67 0.00 0.00 1.82
49 50 6.759827 ACGCGTATATCTAGGTTGTCAATTTT 59.240 34.615 11.67 0.00 0.00 1.82
50 51 7.922278 ACGCGTATATCTAGGTTGTCAATTTTA 59.078 33.333 11.67 0.00 0.00 1.52
51 52 8.922676 CGCGTATATCTAGGTTGTCAATTTTAT 58.077 33.333 0.00 0.00 0.00 1.40
166 167 7.759489 ACTTGTATTAGCTTGGTCAAATTGA 57.241 32.000 0.00 0.00 0.00 2.57
167 168 8.353423 ACTTGTATTAGCTTGGTCAAATTGAT 57.647 30.769 0.00 0.00 0.00 2.57
168 169 8.246180 ACTTGTATTAGCTTGGTCAAATTGATG 58.754 33.333 0.00 0.00 0.00 3.07
169 170 7.936496 TGTATTAGCTTGGTCAAATTGATGA 57.064 32.000 0.00 0.00 0.00 2.92
181 182 7.178712 GTCAAATTGATGACCTAGGAATACG 57.821 40.000 17.98 0.00 43.11 3.06
182 183 5.758296 TCAAATTGATGACCTAGGAATACGC 59.242 40.000 17.98 0.00 0.00 4.42
183 184 4.955811 ATTGATGACCTAGGAATACGCA 57.044 40.909 17.98 2.77 0.00 5.24
184 185 3.728076 TGATGACCTAGGAATACGCAC 57.272 47.619 17.98 0.00 0.00 5.34
185 186 3.028130 TGATGACCTAGGAATACGCACA 58.972 45.455 17.98 1.79 0.00 4.57
186 187 2.953466 TGACCTAGGAATACGCACAC 57.047 50.000 17.98 0.00 0.00 3.82
198 199 2.895039 CGCACACGTCCTGTAAACT 58.105 52.632 0.00 0.00 33.53 2.66
199 200 0.506932 CGCACACGTCCTGTAAACTG 59.493 55.000 0.00 0.00 33.53 3.16
200 201 1.860676 GCACACGTCCTGTAAACTGA 58.139 50.000 0.00 0.00 0.00 3.41
201 202 1.792949 GCACACGTCCTGTAAACTGAG 59.207 52.381 0.00 0.00 0.00 3.35
202 203 2.545113 GCACACGTCCTGTAAACTGAGA 60.545 50.000 0.00 0.00 0.00 3.27
203 204 3.309388 CACACGTCCTGTAAACTGAGAG 58.691 50.000 0.00 0.00 0.00 3.20
204 205 3.004419 CACACGTCCTGTAAACTGAGAGA 59.996 47.826 0.00 0.00 0.00 3.10
205 206 3.253677 ACACGTCCTGTAAACTGAGAGAG 59.746 47.826 0.00 0.00 0.00 3.20
206 207 3.502595 CACGTCCTGTAAACTGAGAGAGA 59.497 47.826 0.00 0.00 0.00 3.10
207 208 3.754323 ACGTCCTGTAAACTGAGAGAGAG 59.246 47.826 0.00 0.00 0.00 3.20
208 209 3.127895 CGTCCTGTAAACTGAGAGAGAGG 59.872 52.174 0.00 0.00 0.00 3.69
209 210 4.083565 GTCCTGTAAACTGAGAGAGAGGT 58.916 47.826 0.00 0.00 0.00 3.85
210 211 5.254901 GTCCTGTAAACTGAGAGAGAGGTA 58.745 45.833 0.00 0.00 0.00 3.08
211 212 5.355910 GTCCTGTAAACTGAGAGAGAGGTAG 59.644 48.000 0.00 0.00 0.00 3.18
231 232 1.819288 GTAGCTAGCTCACCTGTGTCA 59.181 52.381 23.26 0.00 0.00 3.58
236 237 3.118956 GCTAGCTCACCTGTGTCATTAGT 60.119 47.826 7.70 0.00 0.00 2.24
316 318 5.339990 GTTAAGCGATTATGTTGCATGGTT 58.660 37.500 0.00 0.00 39.90 3.67
317 319 3.425577 AGCGATTATGTTGCATGGTTG 57.574 42.857 0.00 0.00 39.90 3.77
332 334 5.705609 CATGGTTGCAGGTACTAAAGTTT 57.294 39.130 0.00 0.00 36.02 2.66
355 357 2.414058 TTTTAACGGTCGCTCGTACA 57.586 45.000 3.53 0.00 43.07 2.90
369 371 4.025979 CGCTCGTACAAAGTTTCAAGAGTT 60.026 41.667 9.78 0.00 0.00 3.01
370 372 5.198274 GCTCGTACAAAGTTTCAAGAGTTG 58.802 41.667 9.78 0.00 0.00 3.16
442 447 6.659361 ATTTGAAAGTCATCATCACGAGAG 57.341 37.500 0.00 0.00 0.00 3.20
445 450 4.218417 TGAAAGTCATCATCACGAGAGACA 59.782 41.667 0.00 0.00 35.89 3.41
446 451 4.790765 AAGTCATCATCACGAGAGACAA 57.209 40.909 0.00 0.00 35.89 3.18
457 462 6.280855 TCACGAGAGACAAGGATATGAAAA 57.719 37.500 0.00 0.00 0.00 2.29
460 465 8.474831 TCACGAGAGACAAGGATATGAAAATAA 58.525 33.333 0.00 0.00 0.00 1.40
462 467 9.667107 ACGAGAGACAAGGATATGAAAATAAAA 57.333 29.630 0.00 0.00 0.00 1.52
519 524 4.991687 AGTTTGAAAAACGAAAGCCAAACA 59.008 33.333 20.14 0.00 43.16 2.83
537 542 4.841441 AAAAAGCATGCCCGAGGA 57.159 50.000 15.66 0.00 0.00 3.71
552 557 3.053896 GGAACTCGTTTGCCCCCG 61.054 66.667 0.00 0.00 0.00 5.73
603 618 5.048713 CACTGGAAATGTGGGACTAAACTTC 60.049 44.000 0.00 0.00 0.00 3.01
604 619 5.055265 TGGAAATGTGGGACTAAACTTCA 57.945 39.130 0.00 0.00 0.00 3.02
605 620 5.070001 TGGAAATGTGGGACTAAACTTCAG 58.930 41.667 0.00 0.00 0.00 3.02
606 621 4.082733 GGAAATGTGGGACTAAACTTCAGC 60.083 45.833 0.00 0.00 0.00 4.26
607 622 2.561478 TGTGGGACTAAACTTCAGCC 57.439 50.000 0.00 0.00 0.00 4.85
640 655 2.325583 TCCAACAGACCAACACACTC 57.674 50.000 0.00 0.00 0.00 3.51
641 656 1.134220 TCCAACAGACCAACACACTCC 60.134 52.381 0.00 0.00 0.00 3.85
642 657 1.408127 CCAACAGACCAACACACTCCA 60.408 52.381 0.00 0.00 0.00 3.86
643 658 2.364632 CAACAGACCAACACACTCCAA 58.635 47.619 0.00 0.00 0.00 3.53
645 660 1.308998 CAGACCAACACACTCCAACC 58.691 55.000 0.00 0.00 0.00 3.77
649 664 0.746563 CCAACACACTCCAACCGTGT 60.747 55.000 0.00 0.00 45.80 4.49
652 667 4.848685 ACACTCCAACCGTGTGAC 57.151 55.556 0.00 0.00 43.44 3.67
809 824 1.595093 CGTTCCTGGGGATTGGCAAC 61.595 60.000 0.00 0.00 0.00 4.17
819 834 2.170166 GGATTGGCAACCATCACTTCA 58.830 47.619 0.00 0.00 31.53 3.02
1173 1198 1.146263 GGAGGGCGATTCCGAACAT 59.854 57.895 0.00 0.00 38.22 2.71
1214 1239 5.639931 ACTTAGCAGAGCTACTAGTTTTTGC 59.360 40.000 0.00 5.02 41.12 3.68
1351 1396 0.112606 CGGCCTATAGAGTCCCAGGA 59.887 60.000 0.00 0.00 0.00 3.86
1437 3101 0.108138 CGGATTTCTTGGCGAGGACT 60.108 55.000 0.97 0.00 0.00 3.85
1732 3419 3.898529 ACTAAAAAGTCGAGAGGTGTCG 58.101 45.455 0.00 0.00 41.51 4.35
1766 3453 7.951530 ACTAGGAAAAGATTTTGTTTGCATG 57.048 32.000 0.00 0.00 0.00 4.06
1801 3502 1.071471 CAGTCCTGCTTTGTCGGGT 59.929 57.895 0.00 0.00 34.12 5.28
2235 3939 0.883833 GTGCATCACTGTTTGGGGAG 59.116 55.000 0.00 0.00 0.00 4.30
2337 5427 2.097825 GATCAACATGGAAAGGCAGCT 58.902 47.619 0.00 0.00 0.00 4.24
2384 5474 3.947841 TGCCGCACGCTGTTGTTC 61.948 61.111 0.00 0.00 38.78 3.18
2499 5589 2.484264 GGCAGAACCGTATGGATAATGC 59.516 50.000 8.33 9.87 39.21 3.56
2504 5594 6.017440 GCAGAACCGTATGGATAATGCTTAAA 60.017 38.462 8.33 0.00 39.21 1.52
2510 5600 8.952992 CCGTATGGATAATGCTTAAAAGCGGC 62.953 46.154 9.96 0.00 46.89 6.53
2584 5674 0.457851 TTTTGGCTGTGAAACACGGG 59.542 50.000 11.76 0.00 45.67 5.28
2606 5696 5.336690 GGGCGATTATATTACGTGGTAGGAA 60.337 44.000 0.00 0.00 0.00 3.36
2608 5698 6.815142 GGCGATTATATTACGTGGTAGGAATT 59.185 38.462 0.00 0.00 0.00 2.17
2672 5762 0.715551 GGGCGAGGTTAAAACGTACG 59.284 55.000 15.01 15.01 0.00 3.67
2679 5769 4.149747 CGAGGTTAAAACGTACGGCTAAAA 59.850 41.667 21.06 4.31 0.00 1.52
2680 5770 5.332959 CGAGGTTAAAACGTACGGCTAAAAA 60.333 40.000 21.06 3.22 0.00 1.94
2714 5804 3.909776 TTATAGCGTGAGGATGTACCG 57.090 47.619 0.00 0.00 44.74 4.02
2725 5815 0.602060 GATGTACCGGGGCTAGCTAC 59.398 60.000 15.72 9.29 0.00 3.58
2786 5876 3.440522 CACGTGAGAGGAAGAGACATGTA 59.559 47.826 10.90 0.00 0.00 2.29
2798 5888 2.124151 CATGTACCCAGGCTGCCC 60.124 66.667 16.57 0.00 0.00 5.36
2827 5917 0.395586 TTGGCACAGCAACAGACCTT 60.396 50.000 0.00 0.00 42.39 3.50
2919 6009 4.832608 GGGGGCAAGCGTCTACGG 62.833 72.222 4.49 0.00 40.23 4.02
2943 6033 1.153168 CAGGCCCCGTGAATACAGG 60.153 63.158 0.00 0.00 0.00 4.00
2984 6074 1.416243 AAACGGACGGCCTGGATATA 58.584 50.000 5.33 0.00 0.00 0.86
3022 6112 2.014128 CCACCGTTAGGCATTTTCGAT 58.986 47.619 0.00 0.00 42.76 3.59
3023 6113 2.422127 CCACCGTTAGGCATTTTCGATT 59.578 45.455 0.00 0.00 42.76 3.34
3024 6114 3.119637 CCACCGTTAGGCATTTTCGATTT 60.120 43.478 0.00 0.00 42.76 2.17
3025 6115 3.851403 CACCGTTAGGCATTTTCGATTTG 59.149 43.478 0.00 0.00 42.76 2.32
3026 6116 3.754323 ACCGTTAGGCATTTTCGATTTGA 59.246 39.130 0.00 0.00 42.76 2.69
3027 6117 4.095610 CCGTTAGGCATTTTCGATTTGAC 58.904 43.478 0.00 0.00 0.00 3.18
3028 6118 4.142687 CCGTTAGGCATTTTCGATTTGACT 60.143 41.667 3.90 3.90 32.32 3.41
3029 6119 5.022021 CGTTAGGCATTTTCGATTTGACTC 58.978 41.667 1.76 0.00 29.70 3.36
3030 6120 5.163854 CGTTAGGCATTTTCGATTTGACTCT 60.164 40.000 1.76 0.00 29.70 3.24
3037 6127 7.012421 GGCATTTTCGATTTGACTCTACCTTAT 59.988 37.037 0.00 0.00 0.00 1.73
3073 6163 5.654650 CCACTATCTAGACCTCTTGTGTCTT 59.345 44.000 0.00 0.00 42.78 3.01
3074 6164 6.405286 CCACTATCTAGACCTCTTGTGTCTTG 60.405 46.154 0.00 0.00 42.78 3.02
3080 6170 5.559148 AGACCTCTTGTGTCTTGAGAAAT 57.441 39.130 0.00 0.00 40.06 2.17
3098 6188 8.902540 TGAGAAATATGTACTGAAGTTTGTGT 57.097 30.769 0.00 0.00 0.00 3.72
3110 6200 7.155328 ACTGAAGTTTGTGTTCTCTAATCGAT 58.845 34.615 0.00 0.00 0.00 3.59
3146 6236 1.395954 TGTCGACGATCTGAGTTACCG 59.604 52.381 11.62 0.00 0.00 4.02
3248 6338 5.193099 AGTACTCCCATGTAAATGCCTTT 57.807 39.130 0.00 0.00 0.00 3.11
3249 6339 6.321821 AGTACTCCCATGTAAATGCCTTTA 57.678 37.500 0.00 0.00 0.00 1.85
3291 6381 7.939039 TGATCTTCAGGTTGTTCACTCTATTTT 59.061 33.333 0.00 0.00 0.00 1.82
3296 6386 8.603242 TCAGGTTGTTCACTCTATTTTACTTC 57.397 34.615 0.00 0.00 0.00 3.01
3307 6397 8.009974 CACTCTATTTTACTTCGGTTTGTCTTG 58.990 37.037 0.00 0.00 0.00 3.02
3327 6417 8.447833 TGTCTTGTTACTTTAGTTGTGTCTTTG 58.552 33.333 0.00 0.00 0.00 2.77
3350 6440 9.485206 TTTGTCAACTGAGTTACTAGAATTACC 57.515 33.333 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.295152 AGGACTTGTAAACTGAAACGTAGG 58.705 41.667 0.00 0.00 0.00 3.18
1 2 6.087291 CGTAGGACTTGTAAACTGAAACGTAG 59.913 42.308 0.00 0.00 0.00 3.51
2 3 5.914635 CGTAGGACTTGTAAACTGAAACGTA 59.085 40.000 0.00 0.00 0.00 3.57
3 4 4.741676 CGTAGGACTTGTAAACTGAAACGT 59.258 41.667 0.00 0.00 0.00 3.99
4 5 4.375706 GCGTAGGACTTGTAAACTGAAACG 60.376 45.833 0.00 0.00 0.00 3.60
5 6 4.375706 CGCGTAGGACTTGTAAACTGAAAC 60.376 45.833 0.00 0.00 0.00 2.78
6 7 3.737266 CGCGTAGGACTTGTAAACTGAAA 59.263 43.478 0.00 0.00 0.00 2.69
7 8 3.243501 ACGCGTAGGACTTGTAAACTGAA 60.244 43.478 11.67 0.00 0.00 3.02
8 9 2.294233 ACGCGTAGGACTTGTAAACTGA 59.706 45.455 11.67 0.00 0.00 3.41
9 10 2.669364 ACGCGTAGGACTTGTAAACTG 58.331 47.619 11.67 0.00 0.00 3.16
10 11 4.708726 ATACGCGTAGGACTTGTAAACT 57.291 40.909 24.78 0.00 0.00 2.66
11 12 6.433766 AGATATACGCGTAGGACTTGTAAAC 58.566 40.000 24.78 8.64 0.00 2.01
12 13 6.624352 AGATATACGCGTAGGACTTGTAAA 57.376 37.500 24.78 0.00 0.00 2.01
13 14 6.369890 CCTAGATATACGCGTAGGACTTGTAA 59.630 42.308 24.78 0.00 34.99 2.41
14 15 5.871524 CCTAGATATACGCGTAGGACTTGTA 59.128 44.000 24.78 10.35 34.99 2.41
15 16 4.694509 CCTAGATATACGCGTAGGACTTGT 59.305 45.833 24.78 8.30 34.99 3.16
16 17 4.694509 ACCTAGATATACGCGTAGGACTTG 59.305 45.833 25.95 20.57 36.34 3.16
17 18 4.904241 ACCTAGATATACGCGTAGGACTT 58.096 43.478 25.95 11.92 36.34 3.01
18 19 4.550076 ACCTAGATATACGCGTAGGACT 57.450 45.455 25.95 22.48 36.34 3.85
19 20 4.453819 ACAACCTAGATATACGCGTAGGAC 59.546 45.833 25.95 17.64 36.34 3.85
20 21 4.645535 ACAACCTAGATATACGCGTAGGA 58.354 43.478 25.95 16.64 36.34 2.94
21 22 4.453478 TGACAACCTAGATATACGCGTAGG 59.547 45.833 24.78 21.85 38.45 3.18
22 23 5.602458 TGACAACCTAGATATACGCGTAG 57.398 43.478 24.78 11.28 0.00 3.51
23 24 6.564709 ATTGACAACCTAGATATACGCGTA 57.435 37.500 22.94 22.94 0.00 4.42
24 25 4.906065 TTGACAACCTAGATATACGCGT 57.094 40.909 19.17 19.17 0.00 6.01
25 26 6.764877 AAATTGACAACCTAGATATACGCG 57.235 37.500 3.53 3.53 0.00 6.01
140 141 9.290988 TCAATTTGACCAAGCTAATACAAGTTA 57.709 29.630 0.00 0.00 0.00 2.24
141 142 8.177119 TCAATTTGACCAAGCTAATACAAGTT 57.823 30.769 0.00 0.00 0.00 2.66
142 143 7.759489 TCAATTTGACCAAGCTAATACAAGT 57.241 32.000 0.00 0.00 0.00 3.16
143 144 8.461222 TCATCAATTTGACCAAGCTAATACAAG 58.539 33.333 0.15 0.00 0.00 3.16
144 145 8.243426 GTCATCAATTTGACCAAGCTAATACAA 58.757 33.333 0.15 0.00 40.11 2.41
145 146 7.761409 GTCATCAATTTGACCAAGCTAATACA 58.239 34.615 0.15 0.00 40.11 2.29
157 158 6.292919 GCGTATTCCTAGGTCATCAATTTGAC 60.293 42.308 9.08 2.20 44.27 3.18
158 159 5.758296 GCGTATTCCTAGGTCATCAATTTGA 59.242 40.000 9.08 0.75 0.00 2.69
159 160 5.527214 TGCGTATTCCTAGGTCATCAATTTG 59.473 40.000 9.08 0.00 0.00 2.32
160 161 5.527582 GTGCGTATTCCTAGGTCATCAATTT 59.472 40.000 9.08 0.00 0.00 1.82
161 162 5.057149 GTGCGTATTCCTAGGTCATCAATT 58.943 41.667 9.08 0.00 0.00 2.32
162 163 4.100963 TGTGCGTATTCCTAGGTCATCAAT 59.899 41.667 9.08 3.24 0.00 2.57
163 164 3.449377 TGTGCGTATTCCTAGGTCATCAA 59.551 43.478 9.08 0.00 0.00 2.57
164 165 3.028130 TGTGCGTATTCCTAGGTCATCA 58.972 45.455 9.08 0.00 0.00 3.07
165 166 3.381949 GTGTGCGTATTCCTAGGTCATC 58.618 50.000 9.08 0.00 0.00 2.92
166 167 2.223735 CGTGTGCGTATTCCTAGGTCAT 60.224 50.000 9.08 5.09 0.00 3.06
167 168 1.133598 CGTGTGCGTATTCCTAGGTCA 59.866 52.381 9.08 0.00 0.00 4.02
168 169 1.836383 CGTGTGCGTATTCCTAGGTC 58.164 55.000 9.08 0.00 0.00 3.85
180 181 0.506932 CAGTTTACAGGACGTGTGCG 59.493 55.000 10.99 0.00 40.69 5.34
181 182 1.792949 CTCAGTTTACAGGACGTGTGC 59.207 52.381 10.99 1.88 40.69 4.57
182 183 3.004419 TCTCTCAGTTTACAGGACGTGTG 59.996 47.826 10.99 0.00 40.69 3.82
183 184 3.220110 TCTCTCAGTTTACAGGACGTGT 58.780 45.455 6.01 6.01 43.86 4.49
184 185 3.502595 TCTCTCTCAGTTTACAGGACGTG 59.497 47.826 0.00 0.00 0.00 4.49
185 186 3.752665 TCTCTCTCAGTTTACAGGACGT 58.247 45.455 0.00 0.00 0.00 4.34
186 187 3.127895 CCTCTCTCTCAGTTTACAGGACG 59.872 52.174 0.00 0.00 0.00 4.79
187 188 4.083565 ACCTCTCTCTCAGTTTACAGGAC 58.916 47.826 0.00 0.00 0.00 3.85
188 189 4.390129 ACCTCTCTCTCAGTTTACAGGA 57.610 45.455 0.00 0.00 0.00 3.86
189 190 5.258051 ACTACCTCTCTCTCAGTTTACAGG 58.742 45.833 0.00 0.00 0.00 4.00
190 191 6.037830 GCTACTACCTCTCTCTCAGTTTACAG 59.962 46.154 0.00 0.00 0.00 2.74
191 192 5.881443 GCTACTACCTCTCTCTCAGTTTACA 59.119 44.000 0.00 0.00 0.00 2.41
192 193 6.117488 AGCTACTACCTCTCTCTCAGTTTAC 58.883 44.000 0.00 0.00 0.00 2.01
193 194 6.316280 AGCTACTACCTCTCTCTCAGTTTA 57.684 41.667 0.00 0.00 0.00 2.01
194 195 5.187621 AGCTACTACCTCTCTCTCAGTTT 57.812 43.478 0.00 0.00 0.00 2.66
195 196 4.855298 AGCTACTACCTCTCTCTCAGTT 57.145 45.455 0.00 0.00 0.00 3.16
196 197 4.202326 GCTAGCTACTACCTCTCTCTCAGT 60.202 50.000 7.70 0.00 0.00 3.41
197 198 4.040461 AGCTAGCTACTACCTCTCTCTCAG 59.960 50.000 17.69 0.00 0.00 3.35
198 199 3.971305 AGCTAGCTACTACCTCTCTCTCA 59.029 47.826 17.69 0.00 0.00 3.27
199 200 4.039973 TGAGCTAGCTACTACCTCTCTCTC 59.960 50.000 19.38 0.18 0.00 3.20
200 201 3.971305 TGAGCTAGCTACTACCTCTCTCT 59.029 47.826 19.38 0.00 0.00 3.10
201 202 4.062991 GTGAGCTAGCTACTACCTCTCTC 58.937 52.174 19.38 0.88 0.00 3.20
202 203 3.181448 GGTGAGCTAGCTACTACCTCTCT 60.181 52.174 26.30 1.90 0.00 3.10
203 204 3.143728 GGTGAGCTAGCTACTACCTCTC 58.856 54.545 26.30 11.43 0.00 3.20
204 205 2.781174 AGGTGAGCTAGCTACTACCTCT 59.219 50.000 28.80 16.51 34.81 3.69
205 206 2.882137 CAGGTGAGCTAGCTACTACCTC 59.118 54.545 30.43 15.18 34.73 3.85
206 207 2.242708 ACAGGTGAGCTAGCTACTACCT 59.757 50.000 28.80 28.80 36.23 3.08
207 208 2.359531 CACAGGTGAGCTAGCTACTACC 59.640 54.545 26.29 26.29 34.81 3.18
208 209 3.018149 ACACAGGTGAGCTAGCTACTAC 58.982 50.000 19.38 16.40 34.81 2.73
209 210 3.280295 GACACAGGTGAGCTAGCTACTA 58.720 50.000 19.38 4.32 34.81 1.82
210 211 2.096248 GACACAGGTGAGCTAGCTACT 58.904 52.381 19.38 13.52 34.81 2.57
211 212 1.819288 TGACACAGGTGAGCTAGCTAC 59.181 52.381 19.38 15.35 34.81 3.58
293 295 4.920376 ACCATGCAACATAATCGCTTAAC 58.080 39.130 0.00 0.00 0.00 2.01
310 312 5.705609 AAACTTTAGTACCTGCAACCATG 57.294 39.130 0.00 0.00 0.00 3.66
311 313 5.830991 TCAAAACTTTAGTACCTGCAACCAT 59.169 36.000 0.00 0.00 0.00 3.55
312 314 5.194432 TCAAAACTTTAGTACCTGCAACCA 58.806 37.500 0.00 0.00 0.00 3.67
316 318 9.738832 GTTAAAATCAAAACTTTAGTACCTGCA 57.261 29.630 0.00 0.00 0.00 4.41
317 319 8.898792 CGTTAAAATCAAAACTTTAGTACCTGC 58.101 33.333 0.00 0.00 0.00 4.85
318 320 9.389570 CCGTTAAAATCAAAACTTTAGTACCTG 57.610 33.333 0.00 0.00 0.00 4.00
319 321 9.123902 ACCGTTAAAATCAAAACTTTAGTACCT 57.876 29.630 0.00 0.00 0.00 3.08
320 322 9.385902 GACCGTTAAAATCAAAACTTTAGTACC 57.614 33.333 0.00 0.00 0.00 3.34
328 330 4.609783 CGAGCGACCGTTAAAATCAAAACT 60.610 41.667 0.00 0.00 0.00 2.66
329 331 3.596562 CGAGCGACCGTTAAAATCAAAAC 59.403 43.478 0.00 0.00 0.00 2.43
332 334 2.406130 ACGAGCGACCGTTAAAATCAA 58.594 42.857 0.00 0.00 40.17 2.57
341 343 0.031178 AACTTTGTACGAGCGACCGT 59.969 50.000 7.61 7.61 45.54 4.83
412 417 9.778993 CGTGATGATGACTTTCAAATAAGATTT 57.221 29.630 0.00 0.00 0.00 2.17
417 422 8.034804 TCTCTCGTGATGATGACTTTCAAATAA 58.965 33.333 0.00 0.00 0.00 1.40
430 435 5.772169 TCATATCCTTGTCTCTCGTGATGAT 59.228 40.000 0.00 0.00 0.00 2.45
537 542 4.572571 TGCGGGGGCAAACGAGTT 62.573 61.111 0.00 0.00 0.00 3.01
561 566 3.782443 GTGGTAGACCCGGGGCAG 61.782 72.222 32.91 0.07 35.15 4.85
565 570 2.284405 AGTGGTGGTAGACCCGGG 60.284 66.667 22.25 22.25 45.45 5.73
581 596 5.070001 TGAAGTTTAGTCCCACATTTCCAG 58.930 41.667 0.00 0.00 0.00 3.86
582 597 5.055265 TGAAGTTTAGTCCCACATTTCCA 57.945 39.130 0.00 0.00 0.00 3.53
584 599 4.082733 GGCTGAAGTTTAGTCCCACATTTC 60.083 45.833 0.00 0.00 0.00 2.17
605 620 3.758554 TGTTGGAATCTTTGAGCTTAGGC 59.241 43.478 0.00 0.00 39.06 3.93
606 621 5.123027 GTCTGTTGGAATCTTTGAGCTTAGG 59.877 44.000 0.00 0.00 0.00 2.69
607 622 5.123027 GGTCTGTTGGAATCTTTGAGCTTAG 59.877 44.000 0.00 0.00 0.00 2.18
613 628 4.338118 GTGTTGGTCTGTTGGAATCTTTGA 59.662 41.667 0.00 0.00 0.00 2.69
640 655 3.073086 TGAGTTGTCACACGGTTGG 57.927 52.632 0.00 0.00 0.00 3.77
649 664 1.024271 GCAAGCCAAGTGAGTTGTCA 58.976 50.000 0.00 0.00 33.87 3.58
650 665 0.312102 GGCAAGCCAAGTGAGTTGTC 59.688 55.000 6.14 0.00 33.87 3.18
651 666 1.447317 CGGCAAGCCAAGTGAGTTGT 61.447 55.000 12.19 0.00 33.87 3.32
652 667 1.283793 CGGCAAGCCAAGTGAGTTG 59.716 57.895 12.19 0.00 35.37 3.16
692 707 1.075542 TTTGACTTGCACTATCGCCG 58.924 50.000 0.00 0.00 0.00 6.46
693 708 3.126858 TGATTTTGACTTGCACTATCGCC 59.873 43.478 0.00 0.00 0.00 5.54
695 710 5.281693 TGTGATTTTGACTTGCACTATCG 57.718 39.130 0.00 0.00 0.00 2.92
699 714 5.464168 GCTAATGTGATTTTGACTTGCACT 58.536 37.500 0.00 0.00 0.00 4.40
809 824 1.065854 GGGGAGACAGTGAAGTGATGG 60.066 57.143 0.00 0.00 0.00 3.51
1173 1198 5.130311 TGCTAAGTGGCATCTGAATTACCTA 59.870 40.000 0.00 0.00 37.29 3.08
1214 1239 3.904136 AACTTCATCTTTTGCGTGAGG 57.096 42.857 0.00 0.00 0.00 3.86
1291 1336 4.235762 GCCCGCGGCTAATCCTGA 62.236 66.667 22.85 0.00 46.69 3.86
1437 3101 1.003972 CGAACAAACTTGCAAGAGCGA 60.004 47.619 32.50 0.00 46.23 4.93
1732 3419 4.650754 TCTTTTCCTAGTATCGCACTCC 57.349 45.455 0.00 0.00 38.80 3.85
1799 3500 7.971183 TTCCAATTTTATACAAAGGCAAACC 57.029 32.000 0.00 0.00 0.00 3.27
1801 3502 9.784531 TGATTTCCAATTTTATACAAAGGCAAA 57.215 25.926 0.00 0.00 0.00 3.68
1973 3675 0.313987 CAAGGGCACTTTTCCGGTTC 59.686 55.000 0.00 0.00 33.81 3.62
2099 3801 3.864789 AATCCAAGCTCCCACGAATAT 57.135 42.857 0.00 0.00 0.00 1.28
2384 5474 1.597742 CCTCGTAATGGGCAAGATGG 58.402 55.000 0.00 0.00 0.00 3.51
2499 5589 2.227149 ACTTTTACCGGCCGCTTTTAAG 59.773 45.455 22.85 19.53 0.00 1.85
2504 5594 0.322648 ACTACTTTTACCGGCCGCTT 59.677 50.000 22.85 11.65 0.00 4.68
2579 5669 2.664568 CCACGTAATATAATCGCCCGTG 59.335 50.000 0.00 0.00 42.60 4.94
2582 5672 4.158394 TCCTACCACGTAATATAATCGCCC 59.842 45.833 0.00 0.00 0.00 6.13
2584 5674 7.543172 TCAATTCCTACCACGTAATATAATCGC 59.457 37.037 0.00 0.00 0.00 4.58
2606 5696 6.603237 TCTTGACGCGAAAATGATATCAAT 57.397 33.333 15.93 0.00 0.00 2.57
2608 5698 6.415798 TTTCTTGACGCGAAAATGATATCA 57.584 33.333 15.93 8.10 0.00 2.15
2644 5734 1.823169 TAACCTCGCCCACCAGACAC 61.823 60.000 0.00 0.00 0.00 3.67
2705 5795 0.541296 TAGCTAGCCCCGGTACATCC 60.541 60.000 12.13 0.00 0.00 3.51
2714 5804 0.744771 GCACAGTTGTAGCTAGCCCC 60.745 60.000 12.13 2.30 0.00 5.80
2725 5815 3.333414 CCACTCACGGCACAGTTG 58.667 61.111 0.00 0.00 0.00 3.16
2786 5876 1.004230 TATACAGGGCAGCCTGGGT 59.996 57.895 12.43 9.76 41.67 4.51
2798 5888 4.023279 TGTTGCTGTGCCAAAAGTATACAG 60.023 41.667 5.50 0.00 41.15 2.74
2827 5917 2.938086 ATGTACCGCGGCACACTCA 61.938 57.895 32.54 18.20 0.00 3.41
2943 6033 1.021390 CACACTGACCAGATTCGCCC 61.021 60.000 3.76 0.00 0.00 6.13
3023 6113 9.796180 GATAGAACTCCTATAAGGTAGAGTCAA 57.204 37.037 0.00 0.00 38.61 3.18
3024 6114 8.384718 GGATAGAACTCCTATAAGGTAGAGTCA 58.615 40.741 0.00 0.00 38.61 3.41
3025 6115 8.384718 TGGATAGAACTCCTATAAGGTAGAGTC 58.615 40.741 0.00 0.00 38.61 3.36
3026 6116 8.165397 GTGGATAGAACTCCTATAAGGTAGAGT 58.835 40.741 0.00 0.00 41.25 3.24
3027 6117 8.387813 AGTGGATAGAACTCCTATAAGGTAGAG 58.612 40.741 0.00 0.00 38.17 2.43
3028 6118 8.290463 AGTGGATAGAACTCCTATAAGGTAGA 57.710 38.462 0.00 0.00 38.17 2.59
3037 6127 7.740365 AGGTCTAGATAGTGGATAGAACTCCTA 59.260 40.741 0.00 0.00 38.89 2.94
3060 6150 6.773638 ACATATTTCTCAAGACACAAGAGGT 58.226 36.000 0.00 0.00 0.00 3.85
3061 6151 8.037758 AGTACATATTTCTCAAGACACAAGAGG 58.962 37.037 0.00 0.00 0.00 3.69
3073 6163 8.902540 ACACAAACTTCAGTACATATTTCTCA 57.097 30.769 0.00 0.00 0.00 3.27
3074 6164 9.813080 GAACACAAACTTCAGTACATATTTCTC 57.187 33.333 0.00 0.00 0.00 2.87
3129 6219 0.731417 ACCGGTAACTCAGATCGTCG 59.269 55.000 4.49 0.00 0.00 5.12
3146 6236 2.401351 GAATCGTAAGCCGGTGATACC 58.599 52.381 1.90 0.00 37.11 2.73
3162 6252 7.088905 AGGGTCGAAACATACATATACGAATC 58.911 38.462 0.00 0.00 0.00 2.52
3229 6319 5.450818 TCTAAAGGCATTTACATGGGAGT 57.549 39.130 0.00 0.00 0.00 3.85
3240 6330 9.965824 CATAATCCGTTTAATTCTAAAGGCATT 57.034 29.630 0.00 0.00 33.46 3.56
3249 6339 9.277783 CCTGAAGATCATAATCCGTTTAATTCT 57.722 33.333 0.00 0.00 31.78 2.40
3291 6381 7.981225 ACTAAAGTAACAAGACAAACCGAAGTA 59.019 33.333 0.00 0.00 0.00 2.24
3296 6386 6.685403 CACAACTAAAGTAACAAGACAAACCG 59.315 38.462 0.00 0.00 0.00 4.44
3307 6397 8.597144 GTTGACAAAGACACAACTAAAGTAAC 57.403 34.615 0.00 0.00 40.13 2.50
3327 6417 9.303537 GATGGTAATTCTAGTAACTCAGTTGAC 57.696 37.037 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.