Multiple sequence alignment - TraesCS3A01G457300

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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 TraesCS3A01G457300 chr3A 100.000 4364 0 0 1 4364 694960233 694955870 0.000000e+00 8059
1 TraesCS3A01G457300 chr6D 87.591 1781 141 32 1698 3441 360601536 360603273 0.000000e+00 1991
2 TraesCS3A01G457300 chr6D 80.036 1673 162 85 90 1676 360599968 360601554 0.000000e+00 1081
3 TraesCS3A01G457300 chr6D 90.698 129 8 3 4233 4360 360603672 360603797 7.510000e-38 169
4 TraesCS3A01G457300 chr6D 89.600 125 13 0 3465 3589 360603543 360603667 4.520000e-35 159
5 TraesCS3A01G457300 chr3D 87.205 1782 140 35 1698 3441 41535909 41537640 0.000000e+00 1947
6 TraesCS3A01G457300 chr3D 79.904 1672 164 83 90 1676 41534343 41535927 0.000000e+00 1068
7 TraesCS3A01G457300 chr3D 88.292 726 63 10 3641 4363 593470462 593469756 0.000000e+00 850
8 TraesCS3A01G457300 chr3D 94.574 129 6 1 4233 4360 41538040 41538168 9.570000e-47 198
9 TraesCS3A01G457300 chr3D 90.400 125 12 0 3465 3589 41537911 41538035 9.710000e-37 165
10 TraesCS3A01G457300 chr2D 87.149 1782 140 33 1698 3441 474649033 474647303 0.000000e+00 1940
11 TraesCS3A01G457300 chr2D 86.783 1778 145 36 1701 3441 603825551 603823827 0.000000e+00 1899
12 TraesCS3A01G457300 chr2D 80.048 1669 166 84 90 1676 603827119 603825536 0.000000e+00 1083
13 TraesCS3A01G457300 chr2D 79.856 1668 165 85 90 1676 474650592 474649015 0.000000e+00 1061
14 TraesCS3A01G457300 chr2D 93.182 132 8 1 4233 4363 603823427 603823296 4.450000e-45 193
15 TraesCS3A01G457300 chr2D 92.424 132 9 1 4233 4363 474646903 474646772 2.070000e-43 187
16 TraesCS3A01G457300 chr2D 90.400 125 12 0 3465 3589 474647032 474646908 9.710000e-37 165
17 TraesCS3A01G457300 chr2D 90.400 125 12 0 3465 3589 603823556 603823432 9.710000e-37 165
18 TraesCS3A01G457300 chr6A 93.049 1266 53 8 2230 3467 74575670 74576928 0.000000e+00 1818
19 TraesCS3A01G457300 chr6A 94.737 589 24 6 3500 4082 74577165 74577752 0.000000e+00 909
20 TraesCS3A01G457300 chr6A 97.209 215 6 0 4147 4361 74577750 74577964 8.920000e-97 364
21 TraesCS3A01G457300 chr6A 86.935 199 19 6 1 193 74565533 74565730 2.640000e-52 217
22 TraesCS3A01G457300 chr7A 85.245 1796 136 62 823 2580 69304893 69306597 0.000000e+00 1729
23 TraesCS3A01G457300 chr7A 77.354 446 51 28 327 746 69303404 69303825 7.350000e-53 219
24 TraesCS3A01G457300 chr5B 86.562 573 63 8 3695 4265 552147455 552146895 1.720000e-173 619
25 TraesCS3A01G457300 chr4D 80.597 737 84 26 20 726 445092352 445093059 8.370000e-142 514
26 TraesCS3A01G457300 chr7B 80.052 762 83 33 2 726 584024180 584024909 6.520000e-138 501
27 TraesCS3A01G457300 chr5D 82.558 602 69 14 12 609 286950320 286950889 8.430000e-137 497
28 TraesCS3A01G457300 chr1B 79.315 759 87 33 1 726 272404910 272404189 6.610000e-128 468
29 TraesCS3A01G457300 chr1B 86.772 189 22 3 12 199 15424646 15424832 1.590000e-49 207
30 TraesCS3A01G457300 chr4A 81.667 600 66 18 1204 1777 708367485 708368066 3.980000e-125 459
31 TraesCS3A01G457300 chr4A 84.211 228 24 8 891 1111 708367228 708367450 1.230000e-50 211
32 TraesCS3A01G457300 chrUn 85.287 401 54 5 12 408 336059 336458 4.060000e-110 409
33 TraesCS3A01G457300 chrUn 78.030 264 29 15 490 726 336465 336726 5.890000e-29 139
34 TraesCS3A01G457300 chr2B 86.857 175 21 2 12 185 767907874 767908047 1.240000e-45 195


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 TraesCS3A01G457300 chr3A 694955870 694960233 4363 True 8059.000000 8059 100.000000 1 4364 1 chr3A.!!$R1 4363
1 TraesCS3A01G457300 chr6D 360599968 360603797 3829 False 850.000000 1991 86.981250 90 4360 4 chr6D.!!$F1 4270
2 TraesCS3A01G457300 chr3D 593469756 593470462 706 True 850.000000 850 88.292000 3641 4363 1 chr3D.!!$R1 722
3 TraesCS3A01G457300 chr3D 41534343 41538168 3825 False 844.500000 1947 88.020750 90 4360 4 chr3D.!!$F1 4270
4 TraesCS3A01G457300 chr2D 474646772 474650592 3820 True 838.250000 1940 87.457250 90 4363 4 chr2D.!!$R1 4273
5 TraesCS3A01G457300 chr2D 603823296 603827119 3823 True 835.000000 1899 87.603250 90 4363 4 chr2D.!!$R2 4273
6 TraesCS3A01G457300 chr6A 74575670 74577964 2294 False 1030.333333 1818 94.998333 2230 4361 3 chr6A.!!$F2 2131
7 TraesCS3A01G457300 chr7A 69303404 69306597 3193 False 974.000000 1729 81.299500 327 2580 2 chr7A.!!$F1 2253
8 TraesCS3A01G457300 chr5B 552146895 552147455 560 True 619.000000 619 86.562000 3695 4265 1 chr5B.!!$R1 570
9 TraesCS3A01G457300 chr4D 445092352 445093059 707 False 514.000000 514 80.597000 20 726 1 chr4D.!!$F1 706
10 TraesCS3A01G457300 chr7B 584024180 584024909 729 False 501.000000 501 80.052000 2 726 1 chr7B.!!$F1 724
11 TraesCS3A01G457300 chr5D 286950320 286950889 569 False 497.000000 497 82.558000 12 609 1 chr5D.!!$F1 597
12 TraesCS3A01G457300 chr1B 272404189 272404910 721 True 468.000000 468 79.315000 1 726 1 chr1B.!!$R1 725
13 TraesCS3A01G457300 chr4A 708367228 708368066 838 False 335.000000 459 82.939000 891 1777 2 chr4A.!!$F1 886
14 TraesCS3A01G457300 chrUn 336059 336726 667 False 274.000000 409 81.658500 12 726 2 chrUn.!!$F1 714

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
729 796 0.034896 TGTTTCTCTCTTCGGGTGGC 59.965 55.000 0.00 0.0 0.00 5.01 F
877 1969 0.340208 GAGAAGGGAAGGGGAGGAGA 59.660 60.000 0.00 0.0 0.00 3.71 F
878 1970 0.341609 AGAAGGGAAGGGGAGGAGAG 59.658 60.000 0.00 0.0 0.00 3.20 F
879 1971 0.692756 GAAGGGAAGGGGAGGAGAGG 60.693 65.000 0.00 0.0 0.00 3.69 F
1345 2455 0.933047 CGCTCGATTTCGCGGATACA 60.933 55.000 6.13 0.0 45.17 2.29 F
1502 2638 1.081774 GCGGTTTTGTGCGCATGTA 60.082 52.632 15.91 0.0 0.00 2.29 F
3072 4256 1.063806 CTCGGTTCAGCTTGACGAAG 58.936 55.000 0.00 0.0 32.80 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 3402 0.034186 GGGTTCATGGCATCCACTCA 60.034 55.000 0.0 0.0 35.80 3.41 R
2266 3413 1.278127 AGGGTCGTAGTTGGGTTCATG 59.722 52.381 0.0 0.0 0.00 3.07 R
2300 3447 3.059884 TCATCGCAACTCTCAGTGTTTC 58.940 45.455 0.0 0.0 0.00 2.78 R
2821 4005 3.889538 TCGAACCCGTATTCTGAGATCAT 59.110 43.478 0.0 0.0 37.05 2.45 R
2881 4065 2.359900 GACAATCCAGCGGACAAATCT 58.640 47.619 0.0 0.0 32.98 2.40 R
3192 4376 2.969628 ACTCCGTGTGAATCTGATCC 57.030 50.000 0.0 0.0 0.00 3.36 R
4122 5557 2.027745 ACATCTGAATGTCCTTGCGAGT 60.028 45.455 0.0 0.0 42.59 4.18 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
52 57 3.239587 TCGGATCTGCACAAATCGTAA 57.760 42.857 0.00 0.00 0.00 3.18
57 62 1.459209 TCTGCACAAATCGTAACGCTG 59.541 47.619 0.00 0.00 0.00 5.18
61 66 3.040099 GCACAAATCGTAACGCTGTTTT 58.960 40.909 0.00 0.00 0.00 2.43
121 126 3.492337 AGAGCCCGTTTGAATTAAACCA 58.508 40.909 0.00 0.00 44.62 3.67
126 131 4.991687 GCCCGTTTGAATTAAACCATGAAA 59.008 37.500 0.00 0.00 44.62 2.69
129 134 7.623297 GCCCGTTTGAATTAAACCATGAAATTC 60.623 37.037 0.00 5.23 44.62 2.17
167 172 2.882761 CACTCCGTACTTATCGATCCCA 59.117 50.000 0.00 0.00 0.00 4.37
187 192 2.761208 CAGTCAATCCCGACCTTCTACT 59.239 50.000 0.00 0.00 36.52 2.57
190 195 2.758979 TCAATCCCGACCTTCTACTGAC 59.241 50.000 0.00 0.00 0.00 3.51
191 196 1.390565 ATCCCGACCTTCTACTGACG 58.609 55.000 0.00 0.00 0.00 4.35
251 261 7.158021 CCTAATGGATCATAACTTCTCTCACC 58.842 42.308 0.00 0.00 34.57 4.02
289 301 1.347707 TGTCACACACATCTTCTCCCC 59.652 52.381 0.00 0.00 0.00 4.81
298 310 2.307098 ACATCTTCTCCCCACTTGAAGG 59.693 50.000 0.00 0.00 38.10 3.46
301 313 1.789576 TTCTCCCCACTTGAAGGGCC 61.790 60.000 0.00 0.00 45.39 5.80
314 326 1.248101 AAGGGCCCAAACATGTACGC 61.248 55.000 27.56 0.00 0.00 4.42
351 363 4.256920 ACGTCAAGCATGCTAATCTCTTT 58.743 39.130 23.00 0.00 0.00 2.52
352 364 4.697352 ACGTCAAGCATGCTAATCTCTTTT 59.303 37.500 23.00 0.00 0.00 2.27
410 424 9.680315 AAGTAACATAGTTATTATCTGCGAGTC 57.320 33.333 0.00 0.00 0.00 3.36
411 425 9.069082 AGTAACATAGTTATTATCTGCGAGTCT 57.931 33.333 0.00 0.00 0.00 3.24
469 491 3.190849 CACGGGCATGCGAGTGAG 61.191 66.667 28.95 12.80 36.79 3.51
470 492 3.381983 ACGGGCATGCGAGTGAGA 61.382 61.111 12.44 0.00 0.00 3.27
471 493 2.584418 CGGGCATGCGAGTGAGAG 60.584 66.667 12.44 0.00 0.00 3.20
472 494 2.895680 GGGCATGCGAGTGAGAGA 59.104 61.111 12.44 0.00 0.00 3.10
473 495 1.227205 GGGCATGCGAGTGAGAGAG 60.227 63.158 12.44 0.00 0.00 3.20
474 496 1.670949 GGGCATGCGAGTGAGAGAGA 61.671 60.000 12.44 0.00 0.00 3.10
475 497 0.248990 GGCATGCGAGTGAGAGAGAG 60.249 60.000 12.44 0.00 0.00 3.20
476 498 0.737804 GCATGCGAGTGAGAGAGAGA 59.262 55.000 0.00 0.00 0.00 3.10
477 499 1.268692 GCATGCGAGTGAGAGAGAGAG 60.269 57.143 0.00 0.00 0.00 3.20
478 500 2.287769 CATGCGAGTGAGAGAGAGAGA 58.712 52.381 0.00 0.00 0.00 3.10
481 503 2.205074 GCGAGTGAGAGAGAGAGAGAG 58.795 57.143 0.00 0.00 0.00 3.20
484 506 3.131223 CGAGTGAGAGAGAGAGAGAGAGT 59.869 52.174 0.00 0.00 0.00 3.24
493 515 4.532126 AGAGAGAGAGAGAGTGAGAGTGAA 59.468 45.833 0.00 0.00 0.00 3.18
554 577 1.780309 TGACCCTTTTCCTGGTGTGAT 59.220 47.619 0.00 0.00 34.20 3.06
624 659 9.597170 GGTCCTAATTTAGAATTAAGAGTTCGT 57.403 33.333 4.96 0.00 0.00 3.85
630 665 7.900782 TTTAGAATTAAGAGTTCGTGAAGGG 57.099 36.000 0.00 0.00 0.00 3.95
632 667 5.866207 AGAATTAAGAGTTCGTGAAGGGTT 58.134 37.500 0.00 0.00 0.00 4.11
635 688 5.744666 TTAAGAGTTCGTGAAGGGTTTTG 57.255 39.130 0.00 0.00 0.00 2.44
671 725 3.921677 TCTCTTTGGTTTATTCGCTCGT 58.078 40.909 0.00 0.00 0.00 4.18
680 734 3.513680 TTATTCGCTCGTTGCCTTCTA 57.486 42.857 0.00 0.00 38.78 2.10
715 782 2.034001 CGTGTCGGTTCTCAGTTGTTTC 60.034 50.000 0.00 0.00 0.00 2.78
719 786 3.736759 GTCGGTTCTCAGTTGTTTCTCTC 59.263 47.826 0.00 0.00 0.00 3.20
729 796 0.034896 TGTTTCTCTCTTCGGGTGGC 59.965 55.000 0.00 0.00 0.00 5.01
744 817 0.868406 GTGGCTATATTGCTCCGCAC 59.132 55.000 9.02 5.06 38.71 5.34
757 830 4.715523 CGCACCCACACCCGGATT 62.716 66.667 0.73 0.00 0.00 3.01
763 836 0.891904 CCCACACCCGGATTCGTTTT 60.892 55.000 0.73 0.00 33.95 2.43
806 880 5.357314 TCTGTTTTCACCCACACGATTTTTA 59.643 36.000 0.00 0.00 0.00 1.52
807 881 5.962433 TGTTTTCACCCACACGATTTTTAA 58.038 33.333 0.00 0.00 0.00 1.52
809 883 7.042335 TGTTTTCACCCACACGATTTTTAATT 58.958 30.769 0.00 0.00 0.00 1.40
810 884 8.195436 TGTTTTCACCCACACGATTTTTAATTA 58.805 29.630 0.00 0.00 0.00 1.40
874 1966 0.341609 AGAGAGAAGGGAAGGGGAGG 59.658 60.000 0.00 0.00 0.00 4.30
876 1968 0.341609 AGAGAAGGGAAGGGGAGGAG 59.658 60.000 0.00 0.00 0.00 3.69
877 1969 0.340208 GAGAAGGGAAGGGGAGGAGA 59.660 60.000 0.00 0.00 0.00 3.71
878 1970 0.341609 AGAAGGGAAGGGGAGGAGAG 59.658 60.000 0.00 0.00 0.00 3.20
879 1971 0.692756 GAAGGGAAGGGGAGGAGAGG 60.693 65.000 0.00 0.00 0.00 3.69
880 1972 2.770475 GGGAAGGGGAGGAGAGGC 60.770 72.222 0.00 0.00 0.00 4.70
881 1973 3.157949 GGAAGGGGAGGAGAGGCG 61.158 72.222 0.00 0.00 0.00 5.52
1000 2105 3.706373 GAAGGGGAGCCGCTGTCA 61.706 66.667 6.88 0.00 39.23 3.58
1099 2206 3.115892 TTTCGCCGGTGATGTCGC 61.116 61.111 20.33 0.00 0.00 5.19
1162 2269 3.508952 ATCCCTTTCCCCTCTCTACAA 57.491 47.619 0.00 0.00 0.00 2.41
1197 2305 1.748329 TTCCAGTCGTGCAGCTCTGT 61.748 55.000 9.88 0.00 0.00 3.41
1317 2427 4.989168 CCGGGTTATTAGTTCAGCAGATAC 59.011 45.833 0.00 0.00 0.00 2.24
1345 2455 0.933047 CGCTCGATTTCGCGGATACA 60.933 55.000 6.13 0.00 45.17 2.29
1408 2523 8.795786 TTTTTCTTCAGATTATGGACGTTTTG 57.204 30.769 0.00 0.00 0.00 2.44
1416 2531 5.943416 AGATTATGGACGTTTTGGTGATGAA 59.057 36.000 0.00 0.00 0.00 2.57
1472 2587 1.441311 CACACAAAGTGGGTTGGGC 59.559 57.895 1.93 0.00 44.69 5.36
1502 2638 1.081774 GCGGTTTTGTGCGCATGTA 60.082 52.632 15.91 0.00 0.00 2.29
1538 2674 6.714810 AGATGTGCCATTCAGTTTTGTTAGTA 59.285 34.615 0.00 0.00 0.00 1.82
1546 2682 9.659830 CCATTCAGTTTTGTTAGTACTTTGTAC 57.340 33.333 0.00 0.05 0.00 2.90
1559 2695 6.211515 AGTACTTTGTACGTAGTTGTTCAGG 58.788 40.000 0.00 0.00 37.78 3.86
1560 2696 5.266733 ACTTTGTACGTAGTTGTTCAGGA 57.733 39.130 0.00 0.00 37.78 3.86
1576 2712 5.929992 TGTTCAGGATTTTGGTAGTAGTTCG 59.070 40.000 0.00 0.00 0.00 3.95
1585 2721 5.772825 TTGGTAGTAGTTCGTAGTGTTGT 57.227 39.130 0.00 0.00 0.00 3.32
1695 2832 4.153475 CAGTTATGGTTGTAGTTTCCGTGG 59.847 45.833 0.00 0.00 0.00 4.94
1696 2833 4.040706 AGTTATGGTTGTAGTTTCCGTGGA 59.959 41.667 0.00 0.00 0.00 4.02
1719 2856 7.558444 TGGAAGGTGTAAGTTTATTCAGTGTTT 59.442 33.333 0.00 0.00 0.00 2.83
1783 2923 3.818210 ACACGCAACATTTTAGTGATGGA 59.182 39.130 6.44 0.00 36.71 3.41
1852 2992 5.189736 AGCATGTAGGGAACATCTTCAGTAA 59.810 40.000 0.00 0.00 46.15 2.24
1853 2993 5.525378 GCATGTAGGGAACATCTTCAGTAAG 59.475 44.000 0.00 0.00 46.15 2.34
1879 3019 2.561478 TTTCAGGTTCCAGTAGGTGC 57.439 50.000 0.00 0.00 35.89 5.01
1897 3037 1.529438 TGCCGCTTTCTTCAGTTAACG 59.471 47.619 0.00 0.00 0.00 3.18
1967 3107 2.436469 AATGATCAGCGCGCACCA 60.436 55.556 35.10 23.48 0.00 4.17
2006 3147 6.647334 TCTGATTTTGTAAAGCAATGTCCA 57.353 33.333 0.00 0.00 36.89 4.02
2042 3183 6.038936 TCCTCATACATACTCGATGAAAACGA 59.961 38.462 0.00 0.00 39.40 3.85
2059 3200 4.330944 AACGACACTGTCCATCTAACAA 57.669 40.909 3.50 0.00 0.00 2.83
2060 3201 4.330944 ACGACACTGTCCATCTAACAAA 57.669 40.909 3.50 0.00 0.00 2.83
2061 3202 4.894784 ACGACACTGTCCATCTAACAAAT 58.105 39.130 3.50 0.00 0.00 2.32
2158 3301 8.964420 TTTCAACATATTTTACAGCTTGTAGC 57.036 30.769 0.00 0.00 42.84 3.58
2172 3315 3.189495 GCTTGTAGCCTTTTCTCTTGTCC 59.811 47.826 0.00 0.00 34.48 4.02
2199 3343 4.743493 TGTGGAGTTTTTCAGTTTGCTTC 58.257 39.130 0.00 0.00 0.00 3.86
2202 3346 4.405358 TGGAGTTTTTCAGTTTGCTTCCAT 59.595 37.500 0.00 0.00 0.00 3.41
2266 3413 3.139850 CAGAGATCAATGAGTGGATGCC 58.860 50.000 0.00 0.00 0.00 4.40
2300 3447 2.885644 CCCTGATGACGGTTCGCG 60.886 66.667 0.00 0.00 0.00 5.87
2598 3758 2.370281 TCTGCAAGAATGTCGACCTC 57.630 50.000 14.12 9.82 42.31 3.85
2798 3981 4.226427 ACTTTGCAGATATCTTGAGGCA 57.774 40.909 10.53 10.53 0.00 4.75
2841 4025 6.153680 AGGATATGATCTCAGAATACGGGTTC 59.846 42.308 0.00 0.00 0.00 3.62
2915 4099 5.084818 TGGATTGTCGAATGTGTAGACAT 57.915 39.130 0.00 0.00 45.24 3.06
3069 4253 2.383527 GCCTCGGTTCAGCTTGACG 61.384 63.158 0.00 0.00 0.00 4.35
3070 4254 1.289066 CCTCGGTTCAGCTTGACGA 59.711 57.895 0.00 0.00 0.00 4.20
3072 4256 1.063806 CTCGGTTCAGCTTGACGAAG 58.936 55.000 0.00 0.00 32.80 3.79
3192 4376 3.194329 GCTTCCTTTTTCCATCTTCCAGG 59.806 47.826 0.00 0.00 0.00 4.45
3207 4391 1.482182 TCCAGGGATCAGATTCACACG 59.518 52.381 0.00 0.00 0.00 4.49
3279 4463 4.441792 TCTATGCGCTTGTGTATGATTGT 58.558 39.130 9.73 0.00 0.00 2.71
3287 4471 7.655732 TGCGCTTGTGTATGATTGTATACTTAT 59.344 33.333 9.73 0.00 35.16 1.73
3487 4919 6.269315 CACTACTGCAATCGACTCTTTAGAT 58.731 40.000 0.00 0.00 0.00 1.98
3501 4933 9.959775 CGACTCTTTAGATTTCAGATTTTGTAC 57.040 33.333 0.00 0.00 0.00 2.90
3591 5023 7.661847 CCAAGGTCAGAAGAGTAATAAGTTTGT 59.338 37.037 0.00 0.00 0.00 2.83
3607 5039 5.113502 AGTTTGTGAAGCATAAGCAGAAC 57.886 39.130 0.00 0.00 45.49 3.01
3894 5329 9.638239 GTGGCTTTCAATGTGAAATCTATTTAA 57.362 29.630 4.01 0.00 44.37 1.52
3943 5378 6.377327 TGAAAAGTTACTTTTGCCTCTCTG 57.623 37.500 25.23 0.00 42.72 3.35
3983 5418 7.981142 AGCTTGAATTTTGCCAATAATGATTG 58.019 30.769 0.00 0.00 41.94 2.67
4036 5471 9.490663 GACACAAGCATTTTCATATTAGTGTAC 57.509 33.333 0.00 0.00 36.71 2.90
4037 5472 8.175069 ACACAAGCATTTTCATATTAGTGTACG 58.825 33.333 0.00 0.00 35.04 3.67
4038 5473 8.175069 CACAAGCATTTTCATATTAGTGTACGT 58.825 33.333 0.00 0.00 0.00 3.57
4091 5526 4.504916 CCGGACTCTGCAGGCTCG 62.505 72.222 15.13 12.49 0.00 5.03
4122 5557 2.668212 CCGCGGTGCCTTCTTTCA 60.668 61.111 19.50 0.00 0.00 2.69
4123 5558 2.556287 CGCGGTGCCTTCTTTCAC 59.444 61.111 0.00 0.00 0.00 3.18
4133 5568 1.801178 CCTTCTTTCACTCGCAAGGAC 59.199 52.381 0.00 0.00 36.48 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 35 3.452755 ACGATTTGTGCAGATCCGATA 57.547 42.857 6.96 0.00 0.00 2.92
31 36 2.315925 ACGATTTGTGCAGATCCGAT 57.684 45.000 6.96 0.00 0.00 4.18
52 57 7.480810 AGATTTTTCTCTAAACAAAACAGCGT 58.519 30.769 0.00 0.00 0.00 5.07
80 85 6.870439 GGCTCTACGAGTTTAAGGTCTTTTTA 59.130 38.462 0.00 0.00 31.39 1.52
81 86 5.699915 GGCTCTACGAGTTTAAGGTCTTTTT 59.300 40.000 0.00 0.00 31.39 1.94
82 87 5.236282 GGCTCTACGAGTTTAAGGTCTTTT 58.764 41.667 0.00 0.00 31.39 2.27
83 88 4.322574 GGGCTCTACGAGTTTAAGGTCTTT 60.323 45.833 0.00 0.00 31.39 2.52
86 91 2.479219 CGGGCTCTACGAGTTTAAGGTC 60.479 54.545 0.00 0.00 31.39 3.85
121 126 7.126115 TGCTAATTTCAGGGATTGGAATTTCAT 59.874 33.333 0.00 0.00 41.31 2.57
126 131 5.522641 AGTGCTAATTTCAGGGATTGGAAT 58.477 37.500 0.00 0.00 36.51 3.01
129 134 3.633986 GGAGTGCTAATTTCAGGGATTGG 59.366 47.826 0.00 0.00 0.00 3.16
167 172 2.761208 CAGTAGAAGGTCGGGATTGACT 59.239 50.000 0.00 0.00 38.91 3.41
187 192 0.682852 CCCCAAACTGGTCTACGTCA 59.317 55.000 0.00 0.00 35.17 4.35
190 195 1.740296 CGCCCCAAACTGGTCTACG 60.740 63.158 0.00 0.00 35.17 3.51
191 196 2.038837 GCGCCCCAAACTGGTCTAC 61.039 63.158 0.00 0.00 35.17 2.59
230 236 4.895889 TCGGTGAGAGAAGTTATGATCCAT 59.104 41.667 0.00 0.00 0.00 3.41
251 261 3.310860 AAGTGGCCCCGCTTAGTCG 62.311 63.158 11.21 0.00 43.90 4.18
261 271 0.823356 ATGTGTGTGACAAGTGGCCC 60.823 55.000 0.00 0.00 38.36 5.80
263 273 1.597742 AGATGTGTGTGACAAGTGGC 58.402 50.000 0.00 0.00 38.36 5.01
289 301 1.001181 CATGTTTGGGCCCTTCAAGTG 59.999 52.381 25.70 11.11 0.00 3.16
298 310 1.319614 ATGGCGTACATGTTTGGGCC 61.320 55.000 17.27 17.27 38.70 5.80
314 326 5.030295 GCTTGACGTTGTGAATATTCATGG 58.970 41.667 20.65 12.39 39.73 3.66
324 336 2.162319 TAGCATGCTTGACGTTGTGA 57.838 45.000 28.02 0.00 0.00 3.58
409 423 5.294356 ACAACATTACTAACTTGTCGCAGA 58.706 37.500 0.00 0.00 0.00 4.26
410 424 5.389516 GGACAACATTACTAACTTGTCGCAG 60.390 44.000 11.61 0.00 42.25 5.18
411 425 4.449743 GGACAACATTACTAACTTGTCGCA 59.550 41.667 11.61 0.00 42.25 5.10
463 485 4.160439 TCACTCTCTCTCTCTCTCTCACTC 59.840 50.000 0.00 0.00 0.00 3.51
464 486 4.096681 TCACTCTCTCTCTCTCTCTCACT 58.903 47.826 0.00 0.00 0.00 3.41
465 487 4.160439 TCTCACTCTCTCTCTCTCTCTCAC 59.840 50.000 0.00 0.00 0.00 3.51
466 488 4.352893 TCTCACTCTCTCTCTCTCTCTCA 58.647 47.826 0.00 0.00 0.00 3.27
467 489 4.404073 ACTCTCACTCTCTCTCTCTCTCTC 59.596 50.000 0.00 0.00 0.00 3.20
468 490 4.161189 CACTCTCACTCTCTCTCTCTCTCT 59.839 50.000 0.00 0.00 0.00 3.10
469 491 4.160439 TCACTCTCACTCTCTCTCTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
470 492 4.096681 TCACTCTCACTCTCTCTCTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
471 493 4.471904 TCACTCTCACTCTCTCTCTCTC 57.528 50.000 0.00 0.00 0.00 3.20
472 494 4.532126 TCTTCACTCTCACTCTCTCTCTCT 59.468 45.833 0.00 0.00 0.00 3.10
473 495 4.832248 TCTTCACTCTCACTCTCTCTCTC 58.168 47.826 0.00 0.00 0.00 3.20
474 496 4.908601 TCTTCACTCTCACTCTCTCTCT 57.091 45.455 0.00 0.00 0.00 3.10
475 497 5.245531 TCTTCTTCACTCTCACTCTCTCTC 58.754 45.833 0.00 0.00 0.00 3.20
476 498 5.241403 TCTTCTTCACTCTCACTCTCTCT 57.759 43.478 0.00 0.00 0.00 3.10
477 499 5.705441 TCTTCTTCTTCACTCTCACTCTCTC 59.295 44.000 0.00 0.00 0.00 3.20
478 500 5.630121 TCTTCTTCTTCACTCTCACTCTCT 58.370 41.667 0.00 0.00 0.00 3.10
481 503 6.024552 ACATCTTCTTCTTCACTCTCACTC 57.975 41.667 0.00 0.00 0.00 3.51
484 506 7.613411 TCATCTACATCTTCTTCTTCACTCTCA 59.387 37.037 0.00 0.00 0.00 3.27
493 515 7.415592 TCACATGTCATCTACATCTTCTTCT 57.584 36.000 0.00 0.00 46.15 2.85
539 562 4.827284 ACCTGTTTATCACACCAGGAAAAG 59.173 41.667 11.26 0.00 45.97 2.27
554 577 5.246656 TCAATCCCGTCTTTAGACCTGTTTA 59.753 40.000 4.40 0.00 41.86 2.01
615 650 3.617284 ACAAAACCCTTCACGAACTCTT 58.383 40.909 0.00 0.00 0.00 2.85
624 659 4.775253 AGTCTGGAAAAACAAAACCCTTCA 59.225 37.500 0.00 0.00 0.00 3.02
625 660 5.339008 AGTCTGGAAAAACAAAACCCTTC 57.661 39.130 0.00 0.00 0.00 3.46
626 661 5.755409 AAGTCTGGAAAAACAAAACCCTT 57.245 34.783 0.00 0.00 0.00 3.95
627 662 5.755409 AAAGTCTGGAAAAACAAAACCCT 57.245 34.783 0.00 0.00 0.00 4.34
628 663 6.170506 AGAAAAGTCTGGAAAAACAAAACCC 58.829 36.000 0.00 0.00 30.83 4.11
630 665 8.534333 AAGAGAAAAGTCTGGAAAAACAAAAC 57.466 30.769 0.00 0.00 32.80 2.43
632 667 7.602265 CCAAAGAGAAAAGTCTGGAAAAACAAA 59.398 33.333 0.00 0.00 32.80 2.83
635 688 6.631016 ACCAAAGAGAAAAGTCTGGAAAAAC 58.369 36.000 0.00 0.00 32.80 2.43
671 725 1.281867 CCACACAGGGATAGAAGGCAA 59.718 52.381 0.00 0.00 0.00 4.52
702 769 4.501571 CCCGAAGAGAGAAACAACTGAGAA 60.502 45.833 0.00 0.00 0.00 2.87
715 782 3.862642 GCAATATAGCCACCCGAAGAGAG 60.863 52.174 0.00 0.00 0.00 3.20
719 786 2.417719 GAGCAATATAGCCACCCGAAG 58.582 52.381 0.00 0.00 34.23 3.79
744 817 0.891904 AAAACGAATCCGGGTGTGGG 60.892 55.000 0.00 0.00 40.78 4.61
766 839 9.736023 GTGAAAACAGATTGTAAGATTGTTCTT 57.264 29.630 0.00 0.00 44.44 2.52
767 840 8.352942 GGTGAAAACAGATTGTAAGATTGTTCT 58.647 33.333 0.00 0.00 31.30 3.01
768 841 7.595130 GGGTGAAAACAGATTGTAAGATTGTTC 59.405 37.037 0.00 0.00 31.30 3.18
769 842 7.069331 TGGGTGAAAACAGATTGTAAGATTGTT 59.931 33.333 0.00 0.00 33.73 2.83
770 843 6.549364 TGGGTGAAAACAGATTGTAAGATTGT 59.451 34.615 0.00 0.00 0.00 2.71
771 844 6.863126 GTGGGTGAAAACAGATTGTAAGATTG 59.137 38.462 0.00 0.00 0.00 2.67
772 845 6.549364 TGTGGGTGAAAACAGATTGTAAGATT 59.451 34.615 0.00 0.00 0.00 2.40
773 846 6.016276 GTGTGGGTGAAAACAGATTGTAAGAT 60.016 38.462 0.00 0.00 0.00 2.40
776 849 4.035792 CGTGTGGGTGAAAACAGATTGTAA 59.964 41.667 0.00 0.00 0.00 2.41
777 850 3.562141 CGTGTGGGTGAAAACAGATTGTA 59.438 43.478 0.00 0.00 0.00 2.41
780 854 2.925724 TCGTGTGGGTGAAAACAGATT 58.074 42.857 0.00 0.00 0.00 2.40
784 858 4.457834 AAAAATCGTGTGGGTGAAAACA 57.542 36.364 0.00 0.00 0.00 2.83
910 2009 4.208686 CTGCTACTCCCGGACGGC 62.209 72.222 0.73 0.00 0.00 5.68
916 2015 2.187946 CCCTTGCTGCTACTCCCG 59.812 66.667 0.00 0.00 0.00 5.14
918 2017 0.909623 TAACCCCTTGCTGCTACTCC 59.090 55.000 0.00 0.00 0.00 3.85
922 2021 0.253044 CAGCTAACCCCTTGCTGCTA 59.747 55.000 0.00 0.00 45.76 3.49
982 2081 3.706373 GACAGCGGCTCCCCTTCA 61.706 66.667 0.00 0.00 0.00 3.02
1000 2105 1.695597 CTTCCCCCTGCTCCTCCAT 60.696 63.158 0.00 0.00 0.00 3.41
1162 2269 7.545965 CACGACTGGAATAACTAAAATCAGAGT 59.454 37.037 0.00 0.00 0.00 3.24
1180 2288 2.025969 CACAGAGCTGCACGACTGG 61.026 63.158 1.02 0.00 35.08 4.00
1215 2323 2.671370 ATCAAGGGATCTGCGCGCAT 62.671 55.000 36.48 22.32 34.07 4.73
1221 2329 1.442526 CCGCACATCAAGGGATCTGC 61.443 60.000 0.00 0.00 40.70 4.26
1258 2367 9.506018 TGATTCTCATCAAATTAGTCTGAAACA 57.494 29.630 0.00 0.00 36.41 2.83
1317 2427 2.629022 CGAAATCGAGCGGCATAAAAG 58.371 47.619 1.45 0.00 43.02 2.27
1386 2501 6.001460 ACCAAAACGTCCATAATCTGAAGAA 58.999 36.000 0.00 0.00 0.00 2.52
1387 2502 5.411361 CACCAAAACGTCCATAATCTGAAGA 59.589 40.000 0.00 0.00 0.00 2.87
1401 2516 8.303156 TCATATCAATTTTCATCACCAAAACGT 58.697 29.630 0.00 0.00 0.00 3.99
1472 2587 0.463116 AAAACCGCCCATACGCTAGG 60.463 55.000 0.00 0.00 0.00 3.02
1485 2600 1.258427 CATACATGCGCACAAAACCG 58.742 50.000 14.90 0.00 0.00 4.44
1487 2602 2.660490 ACACATACATGCGCACAAAAC 58.340 42.857 14.90 0.00 0.00 2.43
1502 2638 2.269978 GCACATCTGCCCAACACAT 58.730 52.632 0.00 0.00 37.45 3.21
1538 2674 5.266733 TCCTGAACAACTACGTACAAAGT 57.733 39.130 0.00 0.00 0.00 2.66
1546 2682 5.699458 ACTACCAAAATCCTGAACAACTACG 59.301 40.000 0.00 0.00 0.00 3.51
1559 2695 7.383300 ACAACACTACGAACTACTACCAAAATC 59.617 37.037 0.00 0.00 0.00 2.17
1560 2696 7.212274 ACAACACTACGAACTACTACCAAAAT 58.788 34.615 0.00 0.00 0.00 1.82
1576 2712 7.570161 ACGCTAAGAACAAAATACAACACTAC 58.430 34.615 0.00 0.00 0.00 2.73
1695 2832 8.837389 AGAAACACTGAATAAACTTACACCTTC 58.163 33.333 0.00 0.00 0.00 3.46
1696 2833 8.747538 AGAAACACTGAATAAACTTACACCTT 57.252 30.769 0.00 0.00 0.00 3.50
1765 2904 4.380867 CCACCTCCATCACTAAAATGTTGC 60.381 45.833 0.00 0.00 0.00 4.17
1802 2942 0.326618 TCTCTCTTCCCATCCCCACC 60.327 60.000 0.00 0.00 0.00 4.61
1803 2943 1.127343 CTCTCTCTTCCCATCCCCAC 58.873 60.000 0.00 0.00 0.00 4.61
1804 2944 1.018840 TCTCTCTCTTCCCATCCCCA 58.981 55.000 0.00 0.00 0.00 4.96
1805 2945 2.182516 TTCTCTCTCTTCCCATCCCC 57.817 55.000 0.00 0.00 0.00 4.81
1806 2946 2.637382 GGATTCTCTCTCTTCCCATCCC 59.363 54.545 0.00 0.00 0.00 3.85
1807 2947 3.312890 TGGATTCTCTCTCTTCCCATCC 58.687 50.000 0.00 0.00 0.00 3.51
1808 2948 3.244181 GCTGGATTCTCTCTCTTCCCATC 60.244 52.174 0.00 0.00 0.00 3.51
1809 2949 2.705127 GCTGGATTCTCTCTCTTCCCAT 59.295 50.000 0.00 0.00 0.00 4.00
1810 2950 2.114616 GCTGGATTCTCTCTCTTCCCA 58.885 52.381 0.00 0.00 0.00 4.37
1811 2951 2.114616 TGCTGGATTCTCTCTCTTCCC 58.885 52.381 0.00 0.00 0.00 3.97
1812 2952 3.134442 ACATGCTGGATTCTCTCTCTTCC 59.866 47.826 0.00 0.00 0.00 3.46
1813 2953 4.405116 ACATGCTGGATTCTCTCTCTTC 57.595 45.455 0.00 0.00 0.00 2.87
1852 2992 4.236527 ACTGGAACCTGAAAAAGACACT 57.763 40.909 4.82 0.00 0.00 3.55
1853 2993 4.515567 CCTACTGGAACCTGAAAAAGACAC 59.484 45.833 4.82 0.00 34.57 3.67
1879 3019 3.872560 AACGTTAACTGAAGAAAGCGG 57.127 42.857 0.00 0.00 0.00 5.52
1897 3037 8.476064 AACTAGCTAACTATCCTACCCTAAAC 57.524 38.462 0.00 0.00 0.00 2.01
1967 3107 4.942761 ATCAGAAAATAAATGCCGGCAT 57.057 36.364 36.10 36.10 38.46 4.40
2018 3159 6.142480 GTCGTTTTCATCGAGTATGTATGAGG 59.858 42.308 0.00 0.00 37.99 3.86
2135 3278 6.884295 AGGCTACAAGCTGTAAAATATGTTGA 59.116 34.615 0.00 0.00 41.99 3.18
2148 3291 3.817647 ACAAGAGAAAAGGCTACAAGCTG 59.182 43.478 0.00 0.00 41.99 4.24
2152 3295 3.399330 CGGACAAGAGAAAAGGCTACAA 58.601 45.455 0.00 0.00 0.00 2.41
2158 3301 3.372206 CACATAGCGGACAAGAGAAAAGG 59.628 47.826 0.00 0.00 0.00 3.11
2172 3315 4.749245 AACTGAAAAACTCCACATAGCG 57.251 40.909 0.00 0.00 0.00 4.26
2244 3389 2.548904 GCATCCACTCATTGATCTCTGC 59.451 50.000 0.00 0.00 0.00 4.26
2254 3401 1.410648 GGGTTCATGGCATCCACTCAT 60.411 52.381 0.00 0.00 35.80 2.90
2255 3402 0.034186 GGGTTCATGGCATCCACTCA 60.034 55.000 0.00 0.00 35.80 3.41
2266 3413 1.278127 AGGGTCGTAGTTGGGTTCATG 59.722 52.381 0.00 0.00 0.00 3.07
2300 3447 3.059884 TCATCGCAACTCTCAGTGTTTC 58.940 45.455 0.00 0.00 0.00 2.78
2533 3691 8.701908 ATTTGATTGCCTGTTAGATGACATAT 57.298 30.769 0.00 0.00 0.00 1.78
2534 3692 7.774625 TGATTTGATTGCCTGTTAGATGACATA 59.225 33.333 0.00 0.00 0.00 2.29
2679 3862 4.581309 AATCATGAGTGGAATGTCAGGT 57.419 40.909 0.09 0.00 0.00 4.00
2821 4005 3.889538 TCGAACCCGTATTCTGAGATCAT 59.110 43.478 0.00 0.00 37.05 2.45
2841 4025 6.727824 TTCTTAAATTTCAGAAGAGGCTCG 57.272 37.500 9.22 0.00 31.16 5.03
2881 4065 2.359900 GACAATCCAGCGGACAAATCT 58.640 47.619 0.00 0.00 32.98 2.40
2915 4099 8.058667 AGCAACAATGATTTGAGATGACATTA 57.941 30.769 0.00 0.00 36.64 1.90
3013 4197 3.572682 ACACTATCCTTGTCTTGTGTCGA 59.427 43.478 0.00 0.00 34.10 4.20
3069 4253 8.011067 CAAAGAAAGTATTGTTTGGCATCTTC 57.989 34.615 0.00 0.00 42.82 2.87
3070 4254 7.951530 CAAAGAAAGTATTGTTTGGCATCTT 57.048 32.000 0.00 0.00 42.82 2.40
3192 4376 2.969628 ACTCCGTGTGAATCTGATCC 57.030 50.000 0.00 0.00 0.00 3.36
3207 4391 3.801114 ACAAGCAAGGTCAAAAACTCC 57.199 42.857 0.00 0.00 0.00 3.85
3287 4471 6.604396 AGAAATCACATACTTGATGATGCCAA 59.396 34.615 0.00 0.00 39.06 4.52
3475 4907 9.959775 GTACAAAATCTGAAATCTAAAGAGTCG 57.040 33.333 0.00 0.00 0.00 4.18
3530 4962 3.391049 GCGACAACCTATCCTGGATTAC 58.609 50.000 15.55 0.00 0.00 1.89
3591 5023 8.752005 AATTATTAGGTTCTGCTTATGCTTCA 57.248 30.769 1.96 0.00 40.48 3.02
3623 5055 5.757808 CAGGCCTTTCTCTTCTATCTAAAGC 59.242 44.000 0.00 0.00 0.00 3.51
3943 5378 4.207891 TCAAGCTAGGAAGGAACATGAC 57.792 45.455 0.00 0.00 0.00 3.06
4036 5471 2.595124 TGTGCATATGTACCAGGACG 57.405 50.000 19.58 0.00 0.00 4.79
4037 5472 5.215252 ACTATGTGCATATGTACCAGGAC 57.785 43.478 19.58 0.00 0.00 3.85
4038 5473 4.022329 CGACTATGTGCATATGTACCAGGA 60.022 45.833 19.58 3.09 0.00 3.86
4122 5557 2.027745 ACATCTGAATGTCCTTGCGAGT 60.028 45.455 0.00 0.00 42.59 4.18
4123 5558 2.625737 ACATCTGAATGTCCTTGCGAG 58.374 47.619 0.00 0.00 42.59 5.03
4133 5568 5.027293 TCATGTGGAGGTACATCTGAATG 57.973 43.478 7.56 8.58 39.17 2.67
4186 5621 5.278022 GCTCACGAGAGGAACAAAGAAAAAT 60.278 40.000 11.94 0.00 42.33 1.82
4199 5634 2.447244 AAACTGAAGCTCACGAGAGG 57.553 50.000 11.94 0.00 42.33 3.69


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

AutoCloner maintained by Alex Coulton.