Multiple sequence alignment - TraesCS2A01G140500

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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 TraesCS2A01G140500 chr2A 100.000 4639 0 0 1 4639 85609731 85605093 0.000000e+00 8567.0
1 TraesCS2A01G140500 chr2A 79.151 2120 376 45 1319 3401 84607116 84609206 0.000000e+00 1406.0
2 TraesCS2A01G140500 chr2A 88.452 407 24 6 3770 4173 83992761 83993147 1.950000e-128 470.0
3 TraesCS2A01G140500 chr2A 89.744 156 15 1 469 624 85610844 85610998 1.020000e-46 198.0
4 TraesCS2A01G140500 chr2A 96.581 117 3 1 4523 4639 83988051 83988166 4.740000e-45 193.0
5 TraesCS2A01G140500 chr2B 92.489 3914 201 43 784 4639 136634492 136630614 0.000000e+00 5513.0
6 TraesCS2A01G140500 chr2B 92.844 3787 183 39 904 4639 137618784 137615035 0.000000e+00 5411.0
7 TraesCS2A01G140500 chr2B 93.096 2897 123 15 1791 4639 136811178 136808311 0.000000e+00 4170.0
8 TraesCS2A01G140500 chr2B 80.422 1752 309 23 1386 3112 167494461 167496203 0.000000e+00 1304.0
9 TraesCS2A01G140500 chr2B 87.955 797 61 13 3715 4493 137012012 137011233 0.000000e+00 907.0
10 TraesCS2A01G140500 chr2B 93.067 375 26 0 1356 1730 136811551 136811177 2.440000e-152 549.0
11 TraesCS2A01G140500 chr2B 84.569 499 66 6 3257 3749 137611778 137611285 6.980000e-133 484.0
12 TraesCS2A01G140500 chr2B 83.777 413 38 9 3853 4257 135215252 135215643 9.490000e-97 364.0
13 TraesCS2A01G140500 chr2B 90.385 156 15 0 3855 4010 182150919 182150764 6.080000e-49 206.0
14 TraesCS2A01G140500 chr2B 96.581 117 3 1 4523 4639 182150196 182150081 4.740000e-45 193.0
15 TraesCS2A01G140500 chr2B 94.828 116 5 1 4524 4639 135360745 135360859 3.690000e-41 180.0
16 TraesCS2A01G140500 chr2B 82.741 197 23 7 729 917 137618995 137618802 1.030000e-36 165.0
17 TraesCS2A01G140500 chr2D 90.871 3867 221 56 819 4639 84774473 84770693 0.000000e+00 5064.0
18 TraesCS2A01G140500 chr2D 91.885 2440 115 37 676 3071 84934835 84932435 0.000000e+00 3332.0
19 TraesCS2A01G140500 chr2D 95.196 1582 64 5 2032 3613 85403969 85402400 0.000000e+00 2490.0
20 TraesCS2A01G140500 chr2D 90.839 1288 63 16 792 2033 85405341 85404063 0.000000e+00 1674.0
21 TraesCS2A01G140500 chr2D 80.423 2033 349 34 1385 3388 85685730 85683718 0.000000e+00 1504.0
22 TraesCS2A01G140500 chr2D 80.914 1860 311 28 1917 3749 85393954 85392112 0.000000e+00 1428.0
23 TraesCS2A01G140500 chr2D 94.289 858 34 4 3073 3919 84930001 84929148 0.000000e+00 1299.0
24 TraesCS2A01G140500 chr2D 90.630 619 39 8 3844 4459 85396935 85396333 0.000000e+00 804.0
25 TraesCS2A01G140500 chr2D 85.420 679 46 17 3984 4639 84929132 84928484 0.000000e+00 656.0
26 TraesCS2A01G140500 chr2D 100.000 35 0 0 3739 3773 83190763 83190797 1.080000e-06 65.8
27 TraesCS2A01G140500 chr2D 100.000 35 0 0 3739 3773 83227572 83227606 1.080000e-06 65.8
28 TraesCS2A01G140500 chr7A 90.879 1809 112 25 904 2702 571323648 571321883 0.000000e+00 2377.0
29 TraesCS2A01G140500 chr7A 95.188 1143 43 6 2695 3826 571320489 571319348 0.000000e+00 1796.0
30 TraesCS2A01G140500 chr7A 91.984 499 37 1 3844 4342 571319138 571318643 0.000000e+00 697.0
31 TraesCS2A01G140500 chr7A 83.912 317 23 5 4338 4639 571313055 571312752 1.270000e-70 278.0
32 TraesCS2A01G140500 chr7A 87.013 77 6 3 676 750 571324109 571324035 2.970000e-12 84.2
33 TraesCS2A01G140500 chrUn 97.032 438 13 0 2984 3421 476046656 476046219 0.000000e+00 737.0
34 TraesCS2A01G140500 chrUn 91.102 236 15 3 1 230 87254294 87254529 9.690000e-82 315.0
35 TraesCS2A01G140500 chrUn 91.102 236 15 3 1 230 235070153 235070388 9.690000e-82 315.0
36 TraesCS2A01G140500 chrUn 84.270 267 26 15 366 625 87255204 87255461 3.580000e-61 246.0
37 TraesCS2A01G140500 chrUn 84.270 267 26 15 366 625 235071063 235071320 3.580000e-61 246.0
38 TraesCS2A01G140500 chrUn 88.272 162 11 7 189 346 87254980 87255137 2.200000e-43 187.0
39 TraesCS2A01G140500 chrUn 88.272 162 11 7 189 346 235070839 235070996 2.200000e-43 187.0
40 TraesCS2A01G140500 chrUn 90.411 146 4 5 4494 4639 25416691 25416556 2.850000e-42 183.0
41 TraesCS2A01G140500 chr5B 93.388 242 10 3 1 240 606722452 606722215 2.050000e-93 353.0
42 TraesCS2A01G140500 chr5B 92.975 242 11 3 1 240 606742474 606742237 9.550000e-92 348.0
43 TraesCS2A01G140500 chr1D 93.534 232 13 2 1 230 415258829 415259060 1.240000e-90 344.0
44 TraesCS2A01G140500 chr5D 93.103 232 14 2 1 230 4113531 4113300 5.750000e-89 339.0
45 TraesCS2A01G140500 chr5D 93.103 232 14 2 1 230 444521194 444521425 5.750000e-89 339.0
46 TraesCS2A01G140500 chr3D 93.421 228 13 2 1 226 52361366 52361593 2.070000e-88 337.0
47 TraesCS2A01G140500 chr5A 90.588 255 21 3 370 624 444854216 444853965 7.440000e-88 335.0
48 TraesCS2A01G140500 chr5A 87.085 271 21 4 372 629 444855316 444855585 1.260000e-75 294.0
49 TraesCS2A01G140500 chr6D 90.476 231 20 2 1 229 46749304 46749074 2.100000e-78 303.0
50 TraesCS2A01G140500 chr3A 79.911 224 24 12 423 630 357518271 357518489 1.350000e-30 145.0
51 TraesCS2A01G140500 chr4B 87.218 133 8 6 224 350 14884747 14884876 4.840000e-30 143.0


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 TraesCS2A01G140500 chr2A 85605093 85609731 4638 True 8567.000000 8567 100.000000 1 4639 1 chr2A.!!$R1 4638
1 TraesCS2A01G140500 chr2A 84607116 84609206 2090 False 1406.000000 1406 79.151000 1319 3401 1 chr2A.!!$F3 2082
2 TraesCS2A01G140500 chr2B 136630614 136634492 3878 True 5513.000000 5513 92.489000 784 4639 1 chr2B.!!$R1 3855
3 TraesCS2A01G140500 chr2B 136808311 136811551 3240 True 2359.500000 4170 93.081500 1356 4639 2 chr2B.!!$R3 3283
4 TraesCS2A01G140500 chr2B 137611285 137618995 7710 True 2020.000000 5411 86.718000 729 4639 3 chr2B.!!$R4 3910
5 TraesCS2A01G140500 chr2B 167494461 167496203 1742 False 1304.000000 1304 80.422000 1386 3112 1 chr2B.!!$F3 1726
6 TraesCS2A01G140500 chr2B 137011233 137012012 779 True 907.000000 907 87.955000 3715 4493 1 chr2B.!!$R2 778
7 TraesCS2A01G140500 chr2D 84770693 84774473 3780 True 5064.000000 5064 90.871000 819 4639 1 chr2D.!!$R1 3820
8 TraesCS2A01G140500 chr2D 85402400 85405341 2941 True 2082.000000 2490 93.017500 792 3613 2 chr2D.!!$R5 2821
9 TraesCS2A01G140500 chr2D 84928484 84934835 6351 True 1762.333333 3332 90.531333 676 4639 3 chr2D.!!$R3 3963
10 TraesCS2A01G140500 chr2D 85683718 85685730 2012 True 1504.000000 1504 80.423000 1385 3388 1 chr2D.!!$R2 2003
11 TraesCS2A01G140500 chr2D 85392112 85396935 4823 True 1116.000000 1428 85.772000 1917 4459 2 chr2D.!!$R4 2542
12 TraesCS2A01G140500 chr7A 571318643 571324109 5466 True 1238.550000 2377 91.266000 676 4342 4 chr7A.!!$R2 3666
13 TraesCS2A01G140500 chrUn 87254294 87255461 1167 False 249.333333 315 87.881333 1 625 3 chrUn.!!$F1 624
14 TraesCS2A01G140500 chrUn 235070153 235071320 1167 False 249.333333 315 87.881333 1 625 3 chrUn.!!$F2 624

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
363 864 0.179018 AACTGAGGGGAATATGCGGC 60.179 55.0 0.00 0.00 0.00 6.53 F
1553 2480 0.389296 CGCAGTCCATGTCGTTGGTA 60.389 55.0 0.00 0.00 38.01 3.25 F
3392 8526 0.105607 GCCTGGCCTACCTAGGTAGT 60.106 60.0 36.08 11.46 44.71 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 2835 0.040646 TCTTCCACTAGGCGGAGGAA 59.959 55.000 11.46 10.52 35.85 3.36 R
3490 8624 1.140852 CAGGAAGACCACACTCCAACA 59.859 52.381 0.00 0.00 38.94 3.33 R
4321 9697 2.670905 TGTTTCGTCACTGAACACACAG 59.329 45.455 0.00 0.00 42.78 3.66 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
39 321 6.012658 TCAAAAACTGTATGTGCAATCTCC 57.987 37.500 0.00 0.00 0.00 3.71
40 322 5.534278 TCAAAAACTGTATGTGCAATCTCCA 59.466 36.000 0.00 0.00 0.00 3.86
74 356 9.745880 ATTATGCTTATGCTTTCTCTGAAATTG 57.254 29.630 1.96 0.00 40.48 2.32
91 373 9.778741 TCTGAAATTGTACTGAGTAAAACTGAT 57.221 29.630 0.00 0.00 0.00 2.90
158 440 9.677567 GAATTTGTACTGACTGAAATTTTGCTA 57.322 29.630 0.00 0.00 30.11 3.49
205 704 3.693085 AGAACAAACTGATGCCTATGCTG 59.307 43.478 0.00 0.00 38.71 4.41
226 725 7.044181 TGCTGTTCTCTGATTTTATAGTGAGG 58.956 38.462 0.00 0.00 0.00 3.86
230 729 9.436957 TGTTCTCTGATTTTATAGTGAGGAAAC 57.563 33.333 0.00 0.00 0.00 2.78
263 764 3.452474 TGCCAAAACTGCATACACAAAC 58.548 40.909 0.00 0.00 32.85 2.93
264 765 3.118992 TGCCAAAACTGCATACACAAACA 60.119 39.130 0.00 0.00 32.85 2.83
268 769 6.420588 CCAAAACTGCATACACAAACAATTG 58.579 36.000 3.24 3.24 42.46 2.32
270 771 4.255833 ACTGCATACACAAACAATTGGG 57.744 40.909 10.83 1.44 45.82 4.12
274 775 3.616317 GCATACACAAACAATTGGGGGAC 60.616 47.826 10.83 0.00 44.59 4.46
275 776 1.036707 ACACAAACAATTGGGGGACG 58.963 50.000 10.83 0.00 44.59 4.79
278 779 0.601057 CAAACAATTGGGGGACGACC 59.399 55.000 10.83 0.00 39.11 4.79
310 811 3.503748 ACCAAAGATCTGTTAGTGCAAGC 59.496 43.478 0.00 0.00 0.00 4.01
311 812 3.119708 CCAAAGATCTGTTAGTGCAAGCC 60.120 47.826 0.00 0.00 0.00 4.35
312 813 2.409948 AGATCTGTTAGTGCAAGCCC 57.590 50.000 0.00 0.00 0.00 5.19
313 814 1.912043 AGATCTGTTAGTGCAAGCCCT 59.088 47.619 0.00 0.00 0.00 5.19
314 815 2.012673 GATCTGTTAGTGCAAGCCCTG 58.987 52.381 0.00 0.00 0.00 4.45
338 839 4.513442 GCATGTTACCAGTAGGATGTTGA 58.487 43.478 0.00 0.00 38.69 3.18
347 848 4.163078 CCAGTAGGATGTTGAGATGGAACT 59.837 45.833 0.00 0.00 36.89 3.01
348 849 5.114780 CAGTAGGATGTTGAGATGGAACTG 58.885 45.833 0.00 0.00 0.00 3.16
351 852 3.199508 AGGATGTTGAGATGGAACTGAGG 59.800 47.826 0.00 0.00 0.00 3.86
352 853 3.539604 GATGTTGAGATGGAACTGAGGG 58.460 50.000 0.00 0.00 0.00 4.30
353 854 1.630369 TGTTGAGATGGAACTGAGGGG 59.370 52.381 0.00 0.00 0.00 4.79
357 858 4.007581 TGAGATGGAACTGAGGGGAATA 57.992 45.455 0.00 0.00 0.00 1.75
358 859 4.570926 TGAGATGGAACTGAGGGGAATAT 58.429 43.478 0.00 0.00 0.00 1.28
359 860 4.349048 TGAGATGGAACTGAGGGGAATATG 59.651 45.833 0.00 0.00 0.00 1.78
361 862 1.140852 TGGAACTGAGGGGAATATGCG 59.859 52.381 0.00 0.00 0.00 4.73
362 863 1.543429 GGAACTGAGGGGAATATGCGG 60.543 57.143 0.00 0.00 0.00 5.69
363 864 0.179018 AACTGAGGGGAATATGCGGC 60.179 55.000 0.00 0.00 0.00 6.53
451 998 3.458163 CTACCCGCGCCTTCCAGA 61.458 66.667 0.00 0.00 0.00 3.86
465 1012 3.490348 CTTCCAGACATTGACAAAGGGT 58.510 45.455 0.00 0.00 0.00 4.34
490 1050 0.873743 GCCTCATCAGCGCTCAGTAC 60.874 60.000 7.13 0.00 0.00 2.73
501 1061 1.989864 CGCTCAGTACGTATGCAAACA 59.010 47.619 0.00 0.00 0.00 2.83
508 1068 5.005299 TCAGTACGTATGCAAACATGATTCG 59.995 40.000 0.00 0.00 37.04 3.34
510 1070 3.266636 ACGTATGCAAACATGATTCGGA 58.733 40.909 0.00 0.00 37.04 4.55
511 1071 3.063452 ACGTATGCAAACATGATTCGGAC 59.937 43.478 0.00 0.00 37.04 4.79
512 1072 3.546020 CGTATGCAAACATGATTCGGACC 60.546 47.826 0.00 0.00 37.04 4.46
513 1073 0.801872 TGCAAACATGATTCGGACCG 59.198 50.000 7.84 7.84 0.00 4.79
514 1074 0.802494 GCAAACATGATTCGGACCGT 59.198 50.000 14.79 0.00 0.00 4.83
515 1075 2.004017 GCAAACATGATTCGGACCGTA 58.996 47.619 14.79 4.32 0.00 4.02
517 1077 3.805422 GCAAACATGATTCGGACCGTATA 59.195 43.478 14.79 0.98 0.00 1.47
518 1078 4.451096 GCAAACATGATTCGGACCGTATAT 59.549 41.667 14.79 6.21 0.00 0.86
519 1079 5.614668 GCAAACATGATTCGGACCGTATATG 60.615 44.000 14.79 15.56 0.00 1.78
520 1080 3.585862 ACATGATTCGGACCGTATATGC 58.414 45.455 14.79 0.00 0.00 3.14
522 1082 3.021269 TGATTCGGACCGTATATGCAC 57.979 47.619 14.79 0.00 0.00 4.57
539 1099 1.876416 GCACCACGAAGCCAAGTTCTA 60.876 52.381 0.00 0.00 0.00 2.10
573 1133 2.680841 TGTACACCACAAGTTTCAGCAC 59.319 45.455 0.00 0.00 32.95 4.40
578 1138 2.564947 ACCACAAGTTTCAGCACCAAAA 59.435 40.909 0.00 0.00 0.00 2.44
580 1140 3.368323 CCACAAGTTTCAGCACCAAAAGT 60.368 43.478 0.00 0.00 0.00 2.66
626 1186 7.716998 AGACACTTGTGATGTAATTGACTCTTT 59.283 33.333 7.83 0.00 0.00 2.52
627 1187 8.225603 ACACTTGTGATGTAATTGACTCTTTT 57.774 30.769 7.83 0.00 0.00 2.27
628 1188 8.686334 ACACTTGTGATGTAATTGACTCTTTTT 58.314 29.630 7.83 0.00 0.00 1.94
650 1210 5.867903 TTTTCCAGAGAAATTGGCAGAAA 57.132 34.783 0.00 0.00 41.55 2.52
652 1212 5.395682 TTCCAGAGAAATTGGCAGAAATG 57.604 39.130 0.00 0.00 35.62 2.32
653 1213 3.194116 TCCAGAGAAATTGGCAGAAATGC 59.806 43.478 0.00 0.00 35.62 3.56
654 1214 3.194968 CCAGAGAAATTGGCAGAAATGCT 59.805 43.478 0.00 0.00 34.73 3.79
655 1215 9.822332 TTTCCAGAGAAATTGGCAGAAATGCTG 62.822 40.741 0.00 0.00 41.09 4.41
670 1230 8.557869 CAGAAATGCTGCTAATTCATTAGAAC 57.442 34.615 10.26 0.43 41.07 3.01
671 1231 7.646922 CAGAAATGCTGCTAATTCATTAGAACC 59.353 37.037 10.26 0.00 41.07 3.62
672 1232 7.340232 AGAAATGCTGCTAATTCATTAGAACCA 59.660 33.333 10.26 0.00 41.72 3.67
673 1233 6.630444 ATGCTGCTAATTCATTAGAACCAG 57.370 37.500 10.26 8.77 41.72 4.00
674 1234 4.883585 TGCTGCTAATTCATTAGAACCAGG 59.116 41.667 10.26 0.00 41.72 4.45
679 1239 9.778741 CTGCTAATTCATTAGAACCAGGTAATA 57.221 33.333 10.26 0.00 41.72 0.98
729 1289 3.237628 GCGTTGAAGCTTCTCCATTTTC 58.762 45.455 26.09 0.00 0.00 2.29
730 1290 3.057946 GCGTTGAAGCTTCTCCATTTTCT 60.058 43.478 26.09 0.00 0.00 2.52
732 1292 4.023707 CGTTGAAGCTTCTCCATTTTCTGT 60.024 41.667 26.09 0.00 0.00 3.41
734 1294 6.374578 GTTGAAGCTTCTCCATTTTCTGTAC 58.625 40.000 26.09 0.00 0.00 2.90
738 1298 4.932200 AGCTTCTCCATTTTCTGTACTTCG 59.068 41.667 0.00 0.00 0.00 3.79
745 1305 5.239963 TCCATTTTCTGTACTTCGTTTTCCC 59.760 40.000 0.00 0.00 0.00 3.97
846 1415 1.969862 CCCAGAGCCCAAGCAAAAG 59.030 57.895 0.00 0.00 43.56 2.27
850 1419 2.288640 CCAGAGCCCAAGCAAAAGAAAG 60.289 50.000 0.00 0.00 43.56 2.62
906 1770 0.519077 CTTGCTCTCCGCCAGAAAAC 59.481 55.000 0.00 0.00 38.05 2.43
1022 1922 2.757099 GACGGCGGAGGAACCCTA 60.757 66.667 13.24 0.00 31.76 3.53
1023 1923 3.073101 ACGGCGGAGGAACCCTAC 61.073 66.667 13.24 0.00 31.76 3.18
1052 1952 3.068691 CGACTCTTCCGCCTCCCA 61.069 66.667 0.00 0.00 0.00 4.37
1055 1955 0.389757 GACTCTTCCGCCTCCCATAC 59.610 60.000 0.00 0.00 0.00 2.39
1168 2081 5.697473 TTGTTGAAGTTTGTGTGTTCTGA 57.303 34.783 0.00 0.00 0.00 3.27
1169 2082 5.041951 TGTTGAAGTTTGTGTGTTCTGAC 57.958 39.130 0.00 0.00 0.00 3.51
1553 2480 0.389296 CGCAGTCCATGTCGTTGGTA 60.389 55.000 0.00 0.00 38.01 3.25
1745 2672 2.165030 CTGGAGTGCCTTTGCCAATAAG 59.835 50.000 0.00 0.00 36.33 1.73
1769 2696 0.605319 AGCGGAAAAGGAATGCGACA 60.605 50.000 0.00 0.00 33.04 4.35
1854 2781 2.537625 GTGCACGATGATTACTCTCAGC 59.462 50.000 0.00 0.00 0.00 4.26
1900 2827 4.385825 ACGAAATGCCTGACAACTTCTAA 58.614 39.130 0.00 0.00 0.00 2.10
1901 2828 4.213482 ACGAAATGCCTGACAACTTCTAAC 59.787 41.667 0.00 0.00 0.00 2.34
1902 2829 4.452455 CGAAATGCCTGACAACTTCTAACT 59.548 41.667 0.00 0.00 0.00 2.24
1903 2830 5.049405 CGAAATGCCTGACAACTTCTAACTT 60.049 40.000 0.00 0.00 0.00 2.66
1904 2831 5.948992 AATGCCTGACAACTTCTAACTTC 57.051 39.130 0.00 0.00 0.00 3.01
1905 2832 3.740115 TGCCTGACAACTTCTAACTTCC 58.260 45.455 0.00 0.00 0.00 3.46
1906 2833 2.737252 GCCTGACAACTTCTAACTTCCG 59.263 50.000 0.00 0.00 0.00 4.30
1907 2834 3.802675 GCCTGACAACTTCTAACTTCCGT 60.803 47.826 0.00 0.00 0.00 4.69
1908 2835 4.377897 CCTGACAACTTCTAACTTCCGTT 58.622 43.478 0.00 0.00 37.15 4.44
1909 2836 4.814771 CCTGACAACTTCTAACTTCCGTTT 59.185 41.667 0.00 0.00 34.59 3.60
1910 2837 5.050295 CCTGACAACTTCTAACTTCCGTTTC 60.050 44.000 0.00 0.00 34.59 2.78
1912 2839 5.032327 ACAACTTCTAACTTCCGTTTCCT 57.968 39.130 0.00 0.00 34.59 3.36
1913 2840 5.055144 ACAACTTCTAACTTCCGTTTCCTC 58.945 41.667 0.00 0.00 34.59 3.71
1915 2842 3.251571 CTTCTAACTTCCGTTTCCTCCG 58.748 50.000 0.00 0.00 34.59 4.63
1916 2843 1.067354 TCTAACTTCCGTTTCCTCCGC 60.067 52.381 0.00 0.00 34.59 5.54
1919 2846 0.901580 ACTTCCGTTTCCTCCGCCTA 60.902 55.000 0.00 0.00 0.00 3.93
1920 2847 0.179108 CTTCCGTTTCCTCCGCCTAG 60.179 60.000 0.00 0.00 0.00 3.02
1967 3159 8.035394 CCTAAGGAAATTATAGCTTATCTCGCA 58.965 37.037 0.00 0.00 0.00 5.10
2132 3419 4.437390 GGTTTTGTAGACATCAAGGATGCG 60.437 45.833 6.15 0.00 43.15 4.73
2261 3548 2.612212 CACACCACTATGCGGGAAATAC 59.388 50.000 0.00 0.00 0.00 1.89
2652 3944 7.329962 TCGACGAGTTGACAACAAAATATACAT 59.670 33.333 20.08 0.00 37.77 2.29
3056 5749 2.971330 TGGCAACCCATCAATGAACTTT 59.029 40.909 0.00 0.00 35.79 2.66
3093 8218 6.537301 CCAGGATGACATGAATTCAAAAATGG 59.463 38.462 13.09 8.92 39.69 3.16
3182 8307 7.090953 ACAGTTTCGGAATTTTACAGTTCAA 57.909 32.000 0.00 0.00 0.00 2.69
3247 8381 5.221048 GCATAAGTAAGTTTGGCGAATCCAT 60.221 40.000 0.00 0.00 46.04 3.41
3320 8454 0.461516 CCTGCACTCATGTCATCGCT 60.462 55.000 0.00 0.00 0.00 4.93
3392 8526 0.105607 GCCTGGCCTACCTAGGTAGT 60.106 60.000 36.08 11.46 44.71 2.73
3490 8624 4.482990 ACAACTTGGATCCCAGACAAAAT 58.517 39.130 19.41 0.00 33.81 1.82
3524 8658 5.888724 TGGTCTTCCTGTTTTTGTAACATCA 59.111 36.000 0.00 0.00 34.23 3.07
3564 8698 1.728971 CGGATGAGTCAGAGCAACAAC 59.271 52.381 0.00 0.00 0.00 3.32
3565 8699 2.771089 GGATGAGTCAGAGCAACAACA 58.229 47.619 0.00 0.00 0.00 3.33
3603 8737 5.707298 GGATCAACTGAAGACAATCAAGGAA 59.293 40.000 0.00 0.00 0.00 3.36
3791 8941 0.910566 TGGTTACTACGCCCATGGGT 60.911 55.000 31.58 15.92 41.13 4.51
3813 9159 3.266772 TGACTGCAAATCAACCCCTCTAT 59.733 43.478 0.00 0.00 0.00 1.98
3814 9160 4.263905 TGACTGCAAATCAACCCCTCTATT 60.264 41.667 0.00 0.00 0.00 1.73
3815 9161 5.045213 TGACTGCAAATCAACCCCTCTATTA 60.045 40.000 0.00 0.00 0.00 0.98
3816 9162 6.018433 ACTGCAAATCAACCCCTCTATTAT 57.982 37.500 0.00 0.00 0.00 1.28
3817 9163 6.435164 ACTGCAAATCAACCCCTCTATTATT 58.565 36.000 0.00 0.00 0.00 1.40
3818 9164 7.582719 ACTGCAAATCAACCCCTCTATTATTA 58.417 34.615 0.00 0.00 0.00 0.98
3819 9165 8.227507 ACTGCAAATCAACCCCTCTATTATTAT 58.772 33.333 0.00 0.00 0.00 1.28
3820 9166 9.082313 CTGCAAATCAACCCCTCTATTATTATT 57.918 33.333 0.00 0.00 0.00 1.40
3979 9333 6.518493 AGATCTGTGCATTGTGAACAATTTT 58.482 32.000 5.94 0.00 43.48 1.82
4067 9431 3.087031 AGATTTGCCATCAGGTGTTGAG 58.913 45.455 0.00 0.00 39.68 3.02
4087 9451 2.030185 AGATGCTGCTTTCAGTTTGCTG 60.030 45.455 0.00 0.00 42.29 4.41
4277 9653 8.582437 ACTGTTCTTCATCATTCATCATGTTTT 58.418 29.630 0.00 0.00 34.06 2.43
4278 9654 9.419297 CTGTTCTTCATCATTCATCATGTTTTT 57.581 29.630 0.00 0.00 34.06 1.94
4346 9722 3.124466 TGTGTTCAGTGACGAAACAACAG 59.876 43.478 7.26 0.00 0.00 3.16
4349 9725 2.546778 TCAGTGACGAAACAACAGACC 58.453 47.619 0.00 0.00 0.00 3.85
4445 9841 8.746052 TTTCCAAGATCTTTCTGAACTTTACA 57.254 30.769 4.86 0.00 35.93 2.41
4474 9870 3.919216 ACAGAGAACCATTCTGAACTCG 58.081 45.455 9.06 0.00 43.75 4.18
4516 9928 6.895607 ACGTTTTTCTTTTGGTGTTTATGG 57.104 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 321 9.362539 AGAAAGCATAAGCATAATTTTGTTCTG 57.637 29.630 0.00 0.00 45.49 3.02
40 322 9.578439 GAGAAAGCATAAGCATAATTTTGTTCT 57.422 29.630 0.00 0.00 45.49 3.01
171 453 7.280876 GCATCAGTTTGTTCTGGAGATGTTATA 59.719 37.037 0.00 0.00 36.25 0.98
174 456 4.217118 GCATCAGTTTGTTCTGGAGATGTT 59.783 41.667 0.00 0.00 36.25 2.71
175 457 3.755378 GCATCAGTTTGTTCTGGAGATGT 59.245 43.478 0.00 0.00 36.25 3.06
177 459 3.009916 AGGCATCAGTTTGTTCTGGAGAT 59.990 43.478 0.00 0.00 36.25 2.75
178 460 2.373169 AGGCATCAGTTTGTTCTGGAGA 59.627 45.455 0.00 0.00 36.25 3.71
181 463 3.181493 GCATAGGCATCAGTTTGTTCTGG 60.181 47.826 0.00 0.00 40.72 3.86
182 464 3.693085 AGCATAGGCATCAGTTTGTTCTG 59.307 43.478 0.67 0.00 44.61 3.02
184 466 3.441572 ACAGCATAGGCATCAGTTTGTTC 59.558 43.478 0.67 0.00 44.61 3.18
185 467 3.424703 ACAGCATAGGCATCAGTTTGTT 58.575 40.909 0.67 0.00 44.61 2.83
186 468 3.077484 ACAGCATAGGCATCAGTTTGT 57.923 42.857 0.67 0.00 44.61 2.83
205 704 9.660180 AGTTTCCTCACTATAAAATCAGAGAAC 57.340 33.333 0.00 0.00 0.00 3.01
240 741 4.333913 TTGTGTATGCAGTTTTGGCAAT 57.666 36.364 0.00 0.00 45.60 3.56
263 764 2.437716 CCGGTCGTCCCCCAATTG 60.438 66.667 0.00 0.00 0.00 2.32
264 765 3.723922 CCCGGTCGTCCCCCAATT 61.724 66.667 0.00 0.00 0.00 2.32
268 769 3.858225 GAATCCCGGTCGTCCCCC 61.858 72.222 0.00 0.00 0.00 5.40
270 771 2.713967 TTCGAATCCCGGTCGTCCC 61.714 63.158 12.10 0.00 39.52 4.46
274 775 0.671163 TTTGGTTCGAATCCCGGTCG 60.671 55.000 5.84 6.61 39.88 4.79
275 776 1.084289 CTTTGGTTCGAATCCCGGTC 58.916 55.000 5.84 0.00 39.14 4.79
278 779 2.609459 CAGATCTTTGGTTCGAATCCCG 59.391 50.000 5.84 0.00 40.25 5.14
338 839 3.073650 GCATATTCCCCTCAGTTCCATCT 59.926 47.826 0.00 0.00 0.00 2.90
347 848 2.836154 GGCCGCATATTCCCCTCA 59.164 61.111 0.00 0.00 0.00 3.86
348 849 2.358737 CGGCCGCATATTCCCCTC 60.359 66.667 14.67 0.00 0.00 4.30
359 860 1.344226 GAAAAAGAACATGCGGCCGC 61.344 55.000 42.35 42.35 42.35 6.53
361 862 0.039527 ACGAAAAAGAACATGCGGCC 60.040 50.000 0.00 0.00 0.00 6.13
362 863 1.052287 CACGAAAAAGAACATGCGGC 58.948 50.000 0.00 0.00 0.00 6.53
363 864 2.286713 TGACACGAAAAAGAACATGCGG 60.287 45.455 0.00 0.00 0.00 5.69
451 998 0.893727 GCGGGACCCTTTGTCAATGT 60.894 55.000 9.41 0.00 46.38 2.71
476 1023 1.600663 GCATACGTACTGAGCGCTGAT 60.601 52.381 18.48 1.37 0.00 2.90
483 1043 5.973651 ATCATGTTTGCATACGTACTGAG 57.026 39.130 0.00 0.00 33.30 3.35
490 1050 3.546020 GGTCCGAATCATGTTTGCATACG 60.546 47.826 2.77 0.00 33.30 3.06
501 1061 3.585862 GTGCATATACGGTCCGAATCAT 58.414 45.455 20.51 7.87 0.00 2.45
508 1068 0.386476 TCGTGGTGCATATACGGTCC 59.614 55.000 16.59 0.33 38.29 4.46
510 1070 1.805120 GCTTCGTGGTGCATATACGGT 60.805 52.381 16.59 0.00 38.29 4.83
511 1071 0.859232 GCTTCGTGGTGCATATACGG 59.141 55.000 16.59 6.44 38.29 4.02
512 1072 0.859232 GGCTTCGTGGTGCATATACG 59.141 55.000 12.31 12.31 39.04 3.06
513 1073 1.948104 TGGCTTCGTGGTGCATATAC 58.052 50.000 0.00 0.00 0.00 1.47
514 1074 2.093181 ACTTGGCTTCGTGGTGCATATA 60.093 45.455 0.00 0.00 0.00 0.86
515 1075 1.340017 ACTTGGCTTCGTGGTGCATAT 60.340 47.619 0.00 0.00 0.00 1.78
517 1077 0.823356 AACTTGGCTTCGTGGTGCAT 60.823 50.000 0.00 0.00 0.00 3.96
518 1078 1.444119 GAACTTGGCTTCGTGGTGCA 61.444 55.000 0.00 0.00 0.00 4.57
519 1079 1.166531 AGAACTTGGCTTCGTGGTGC 61.167 55.000 0.00 0.00 0.00 5.01
520 1080 2.163818 TAGAACTTGGCTTCGTGGTG 57.836 50.000 0.00 0.00 0.00 4.17
522 1082 2.673368 GTGATAGAACTTGGCTTCGTGG 59.327 50.000 0.00 0.00 0.00 4.94
539 1099 4.469586 TGTGGTGTACAGATATGTGGTGAT 59.530 41.667 2.50 0.00 33.42 3.06
573 1133 7.832503 ACTTGACAAGAAATTTCACTTTTGG 57.167 32.000 21.95 7.76 0.00 3.28
578 1138 8.956426 TGTCTAAACTTGACAAGAAATTTCACT 58.044 29.630 21.95 4.08 40.89 3.41
580 1140 8.956426 AGTGTCTAAACTTGACAAGAAATTTCA 58.044 29.630 21.95 10.48 44.63 2.69
581 1141 9.788960 AAGTGTCTAAACTTGACAAGAAATTTC 57.211 29.630 21.95 10.33 44.63 2.17
627 1187 5.867903 TTCTGCCAATTTCTCTGGAAAAA 57.132 34.783 0.00 0.00 43.51 1.94
628 1188 5.867903 TTTCTGCCAATTTCTCTGGAAAA 57.132 34.783 0.00 0.00 43.51 2.29
630 1190 4.322198 GCATTTCTGCCAATTTCTCTGGAA 60.322 41.667 0.00 0.00 42.88 3.53
632 1192 3.518590 GCATTTCTGCCAATTTCTCTGG 58.481 45.455 0.00 0.00 42.88 3.86
645 1205 7.646922 GGTTCTAATGAATTAGCAGCATTTCTG 59.353 37.037 5.36 0.00 39.60 3.02
646 1206 7.340232 TGGTTCTAATGAATTAGCAGCATTTCT 59.660 33.333 9.53 0.00 38.44 2.52
647 1207 7.483307 TGGTTCTAATGAATTAGCAGCATTTC 58.517 34.615 9.53 0.00 38.44 2.17
650 1210 5.533903 CCTGGTTCTAATGAATTAGCAGCAT 59.466 40.000 12.70 0.00 40.94 3.79
652 1212 4.884164 ACCTGGTTCTAATGAATTAGCAGC 59.116 41.667 0.00 5.35 39.60 5.25
653 1213 8.682936 ATTACCTGGTTCTAATGAATTAGCAG 57.317 34.615 3.84 7.04 39.60 4.24
660 1220 9.754382 GACGTAATATTACCTGGTTCTAATGAA 57.246 33.333 17.91 0.00 0.00 2.57
661 1221 8.916062 TGACGTAATATTACCTGGTTCTAATGA 58.084 33.333 17.91 0.00 0.00 2.57
662 1222 9.706691 ATGACGTAATATTACCTGGTTCTAATG 57.293 33.333 17.91 4.19 0.00 1.90
664 1224 9.754382 GAATGACGTAATATTACCTGGTTCTAA 57.246 33.333 17.91 0.00 0.00 2.10
666 1226 7.070821 AGGAATGACGTAATATTACCTGGTTCT 59.929 37.037 17.91 6.95 0.00 3.01
667 1227 7.170998 CAGGAATGACGTAATATTACCTGGTTC 59.829 40.741 17.91 15.66 38.74 3.62
668 1228 6.990349 CAGGAATGACGTAATATTACCTGGTT 59.010 38.462 17.91 9.47 38.74 3.67
669 1229 6.522054 CAGGAATGACGTAATATTACCTGGT 58.478 40.000 17.91 4.05 38.74 4.00
670 1230 5.408604 GCAGGAATGACGTAATATTACCTGG 59.591 44.000 17.91 8.35 41.49 4.45
671 1231 5.118664 CGCAGGAATGACGTAATATTACCTG 59.881 44.000 17.91 17.01 43.26 4.00
672 1232 5.221382 ACGCAGGAATGACGTAATATTACCT 60.221 40.000 17.91 8.21 38.45 3.08
673 1233 4.986659 ACGCAGGAATGACGTAATATTACC 59.013 41.667 17.91 7.33 38.45 2.85
674 1234 5.107607 CCACGCAGGAATGACGTAATATTAC 60.108 44.000 14.55 14.55 41.22 1.89
679 1239 1.651987 CCACGCAGGAATGACGTAAT 58.348 50.000 0.00 0.00 41.22 1.89
689 1249 0.180171 CATACATTCCCCACGCAGGA 59.820 55.000 0.00 0.00 41.22 3.86
738 1298 2.882137 TGGTGTTCAGATTCGGGAAAAC 59.118 45.455 6.10 6.10 31.77 2.43
745 1305 2.084610 TGAGCTGGTGTTCAGATTCG 57.915 50.000 0.00 0.00 42.92 3.34
846 1415 2.176926 GCCGCTGGCTCTAGCTTTC 61.177 63.158 11.61 0.00 46.69 2.62
906 1770 1.153549 CGGAAGAGCTTTCCCTCCG 60.154 63.158 16.96 10.61 35.17 4.63
1025 1925 1.726533 GGAAGAGTCGGAGGCGTAGG 61.727 65.000 0.00 0.00 36.95 3.18
1026 1926 1.728672 GGAAGAGTCGGAGGCGTAG 59.271 63.158 0.00 0.00 36.95 3.51
1027 1927 2.110967 CGGAAGAGTCGGAGGCGTA 61.111 63.158 0.00 0.00 36.95 4.42
1168 2081 1.910772 ACCCTGCGAGCTCAGAAGT 60.911 57.895 15.40 3.66 36.19 3.01
1169 2082 1.447489 CACCCTGCGAGCTCAGAAG 60.447 63.158 15.40 10.28 36.19 2.85
1198 2111 4.459089 GCCTTCCGCTTCCTCGCT 62.459 66.667 0.00 0.00 0.00 4.93
1553 2480 4.840716 AAAGATCCAGAGTTGCAGATCT 57.159 40.909 7.81 7.81 45.68 2.75
1745 2672 2.914838 CGCATTCCTTTTCCGCTTTAAC 59.085 45.455 0.00 0.00 0.00 2.01
1769 2696 6.389830 TCTGCATACAACATGAACTTTTGT 57.610 33.333 0.00 1.38 37.27 2.83
1854 2781 0.389025 GGAAACACAACCCTTGCCAG 59.611 55.000 0.00 0.00 0.00 4.85
1901 2828 0.179108 CTAGGCGGAGGAAACGGAAG 60.179 60.000 0.00 0.00 0.00 3.46
1902 2829 0.901580 ACTAGGCGGAGGAAACGGAA 60.902 55.000 0.00 0.00 0.00 4.30
1903 2830 1.304713 ACTAGGCGGAGGAAACGGA 60.305 57.895 0.00 0.00 0.00 4.69
1904 2831 1.153628 CACTAGGCGGAGGAAACGG 60.154 63.158 0.00 0.00 0.00 4.44
1905 2832 1.153628 CCACTAGGCGGAGGAAACG 60.154 63.158 0.00 0.00 0.00 3.60
1906 2833 0.611714 TTCCACTAGGCGGAGGAAAC 59.388 55.000 9.10 0.00 37.22 2.78
1907 2834 0.902531 CTTCCACTAGGCGGAGGAAA 59.097 55.000 6.72 0.00 39.47 3.13
1908 2835 0.040646 TCTTCCACTAGGCGGAGGAA 59.959 55.000 11.46 10.52 35.85 3.36
1909 2836 0.683504 GTCTTCCACTAGGCGGAGGA 60.684 60.000 10.21 10.21 36.38 3.71
1910 2837 1.677637 GGTCTTCCACTAGGCGGAGG 61.678 65.000 6.32 6.32 33.01 4.30
1912 2839 0.970937 CAGGTCTTCCACTAGGCGGA 60.971 60.000 0.00 0.00 35.89 5.54
1913 2840 1.258445 ACAGGTCTTCCACTAGGCGG 61.258 60.000 0.00 0.00 35.89 6.13
1915 2842 1.267121 TGACAGGTCTTCCACTAGGC 58.733 55.000 0.65 0.00 35.89 3.93
1916 2843 3.515502 TCATTGACAGGTCTTCCACTAGG 59.484 47.826 0.65 0.00 35.89 3.02
1919 2846 2.705658 TGTCATTGACAGGTCTTCCACT 59.294 45.455 15.41 0.00 37.67 4.00
1920 2847 2.808543 GTGTCATTGACAGGTCTTCCAC 59.191 50.000 19.53 1.46 43.57 4.02
1967 3159 1.186200 TCTGCTCGCCATAGTGTTCT 58.814 50.000 0.00 0.00 0.00 3.01
2132 3419 0.253044 TGCTACATCCTGCAACCTCC 59.747 55.000 0.00 0.00 36.15 4.30
2261 3548 1.233019 CAGTCAGCAACACCTCTTGG 58.767 55.000 0.00 0.00 39.83 3.61
2415 3707 9.424319 GATCAACTCTCTTTTGTAGTCATGTAA 57.576 33.333 0.00 0.00 0.00 2.41
2652 3944 4.536888 ACTAGTACCACCTTCTCTCTCTGA 59.463 45.833 0.00 0.00 0.00 3.27
3093 8218 2.349249 CGCGATGCATCTTGGATTTCTC 60.349 50.000 23.73 0.00 0.00 2.87
3182 8307 2.114616 ACCTCATTCTTCTGCCTCGAT 58.885 47.619 0.00 0.00 0.00 3.59
3247 8381 4.980573 ACAGGTGGCACTTTCTTGTATTA 58.019 39.130 18.45 0.00 0.00 0.98
3392 8526 8.827832 ATTCATCAAAATTTCCACTCCAGATA 57.172 30.769 0.00 0.00 0.00 1.98
3430 8564 3.199071 TGGCGTGATATTTCTGTAACCCT 59.801 43.478 0.00 0.00 0.00 4.34
3431 8565 3.537580 TGGCGTGATATTTCTGTAACCC 58.462 45.455 0.00 0.00 0.00 4.11
3490 8624 1.140852 CAGGAAGACCACACTCCAACA 59.859 52.381 0.00 0.00 38.94 3.33
3524 8658 2.772287 GCAACAGTTTCTAGGCAGTCT 58.228 47.619 0.00 0.00 0.00 3.24
3564 8698 4.279169 AGTTGATCCATTTCCAGTGTTGTG 59.721 41.667 0.00 0.00 0.00 3.33
3565 8699 4.279169 CAGTTGATCCATTTCCAGTGTTGT 59.721 41.667 0.00 0.00 0.00 3.32
3603 8737 0.179121 TCTTCAGTGCGTGTTGTCGT 60.179 50.000 0.00 0.00 0.00 4.34
3791 8941 1.425066 AGAGGGGTTGATTTGCAGTCA 59.575 47.619 0.22 0.22 0.00 3.41
3833 9179 9.975218 AATTATCAAACTGTAACCTACTGGAAT 57.025 29.630 0.00 0.00 37.04 3.01
3926 9280 6.529463 ACATTATTGCTTGCAGTGAAAAAC 57.471 33.333 0.00 0.00 0.00 2.43
3933 9287 2.299582 TGGCAACATTATTGCTTGCAGT 59.700 40.909 11.12 0.00 46.17 4.40
3979 9333 4.261698 CCGCATTTGCATATGGATTCAGAA 60.262 41.667 17.33 0.00 42.21 3.02
4067 9431 2.719426 AGCAAACTGAAAGCAGCATC 57.281 45.000 0.00 0.00 46.26 3.91
4148 9512 0.110192 CAGTTTCTCGCGGGAAAAGC 60.110 55.000 33.95 22.73 37.02 3.51
4149 9513 1.508632 TCAGTTTCTCGCGGGAAAAG 58.491 50.000 33.95 27.37 37.02 2.27
4213 9581 4.696899 ACAATGCAACATCATCTCTGTG 57.303 40.909 0.00 0.00 0.00 3.66
4279 9655 6.771267 GGAAGTTACTTTCCTCCTGAGAAAAA 59.229 38.462 0.00 0.00 42.73 1.94
4280 9656 6.296803 GGAAGTTACTTTCCTCCTGAGAAAA 58.703 40.000 0.00 0.00 42.73 2.29
4281 9657 5.866207 GGAAGTTACTTTCCTCCTGAGAAA 58.134 41.667 0.00 0.00 42.73 2.52
4321 9697 2.670905 TGTTTCGTCACTGAACACACAG 59.329 45.455 0.00 0.00 42.78 3.66
4394 9787 6.124340 TGTTTCATCATCCAATACTCAGCAT 58.876 36.000 0.00 0.00 0.00 3.79
4403 9796 7.909518 TCTTGGAAATTGTTTCATCATCCAAT 58.090 30.769 4.94 0.00 42.65 3.16
4445 9841 7.009179 TCAGAATGGTTCTCTGTTTGTAGAT 57.991 36.000 0.16 0.00 41.00 1.98
4474 9870 7.417496 AAACGTACACATAAGAAGAAGAACC 57.583 36.000 0.00 0.00 0.00 3.62
4516 9928 3.321111 TCGATGAGGTTAGGAATAGGTGC 59.679 47.826 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.