Multiple sequence alignment - TraesCS3B01G016400

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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 TraesCS3B01G016400 chr3B 100.000 4546 0 0 1 4546 6673931 6669386 0.000000e+00 8395.0
1 TraesCS3B01G016400 chr3B 75.573 917 164 42 2385 3280 3602626 3603503 9.160000e-107 398.0
2 TraesCS3B01G016400 chr3B 75.727 894 161 38 2406 3280 5233555 5232699 9.160000e-107 398.0
3 TraesCS3B01G016400 chr3B 85.660 265 35 3 1014 1275 13745008 13745272 4.480000e-70 276.0
4 TraesCS3B01G016400 chr3B 83.755 277 37 5 1001 1272 3601468 3601741 5.840000e-64 255.0
5 TraesCS3B01G016400 chr3B 83.755 277 37 5 1001 1272 5234743 5234470 5.840000e-64 255.0
6 TraesCS3B01G016400 chr3B 73.798 603 131 19 1396 1992 545205991 545205410 3.560000e-51 213.0
7 TraesCS3B01G016400 chr3A 95.461 2181 84 11 2373 4546 9844860 9842688 0.000000e+00 3465.0
8 TraesCS3B01G016400 chr3A 91.757 2026 116 23 216 2222 9847291 9845298 0.000000e+00 2769.0
9 TraesCS3B01G016400 chr3A 80.186 969 151 30 2397 3337 9812553 9811598 0.000000e+00 688.0
10 TraesCS3B01G016400 chr3A 83.058 726 109 7 1354 2072 9814127 9813409 0.000000e+00 647.0
11 TraesCS3B01G016400 chr3A 79.754 568 102 10 1430 1992 11065425 11064866 2.550000e-107 399.0
12 TraesCS3B01G016400 chr3A 86.434 258 32 1 1021 1275 11028152 11027895 3.460000e-71 279.0
13 TraesCS3B01G016400 chr3A 84.532 278 40 1 1001 1275 11066657 11066380 5.800000e-69 272.0
14 TraesCS3B01G016400 chr3A 84.532 278 40 1 1001 1275 11072866 11072589 5.800000e-69 272.0
15 TraesCS3B01G016400 chr3A 94.531 128 5 2 2247 2373 9845159 9845033 3.590000e-46 196.0
16 TraesCS3B01G016400 chr3A 87.931 116 13 1 709 823 9847029 9846914 7.930000e-28 135.0
17 TraesCS3B01G016400 chr3A 92.683 41 3 0 1277 1317 699803341 699803381 4.910000e-05 60.2
18 TraesCS3B01G016400 chr3D 90.500 2000 117 24 214 2189 4183731 4181781 0.000000e+00 2573.0
19 TraesCS3B01G016400 chr3D 92.913 1524 87 13 2373 3882 4181317 4179801 0.000000e+00 2196.0
20 TraesCS3B01G016400 chr3D 84.972 539 64 12 3893 4429 4179250 4178727 8.660000e-147 531.0
21 TraesCS3B01G016400 chr3D 95.312 128 6 0 2 129 4183860 4183733 2.140000e-48 204.0
22 TraesCS3B01G016400 chr3D 92.969 128 4 4 2247 2373 4181613 4181490 1.000000e-41 182.0
23 TraesCS3B01G016400 chrUn 85.877 878 105 15 2406 3275 35628603 35629469 0.000000e+00 917.0
24 TraesCS3B01G016400 chrUn 83.921 709 102 7 1365 2068 327485193 327484492 0.000000e+00 667.0
25 TraesCS3B01G016400 chrUn 98.864 88 1 0 126 213 62690467 62690554 1.690000e-34 158.0
26 TraesCS3B01G016400 chr7D 98.876 89 1 0 127 215 252265192 252265280 4.710000e-35 159.0
27 TraesCS3B01G016400 chr2D 79.116 249 39 8 1001 1248 1922943 1922707 4.710000e-35 159.0
28 TraesCS3B01G016400 chr2D 97.872 47 1 0 1275 1321 520521673 520521627 1.050000e-11 82.4
29 TraesCS3B01G016400 chr2D 91.837 49 4 0 1275 1323 277679612 277679660 8.160000e-08 69.4
30 TraesCS3B01G016400 chr2B 97.826 92 1 1 128 218 478114461 478114370 1.690000e-34 158.0
31 TraesCS3B01G016400 chr2B 96.774 93 2 1 127 218 546976380 546976472 2.190000e-33 154.0
32 TraesCS3B01G016400 chr5B 96.703 91 3 0 123 213 253207071 253207161 7.880000e-33 152.0
33 TraesCS3B01G016400 chr5B 74.336 339 79 3 1422 1753 662856301 662855964 2.210000e-28 137.0
34 TraesCS3B01G016400 chr4B 96.703 91 3 0 123 213 282239784 282239874 7.880000e-33 152.0
35 TraesCS3B01G016400 chr4B 94.737 95 5 0 126 220 453246245 453246339 1.020000e-31 148.0
36 TraesCS3B01G016400 chr5A 95.699 93 4 0 126 218 207681827 207681919 2.830000e-32 150.0
37 TraesCS3B01G016400 chr6D 93.750 96 6 0 128 223 361523780 361523875 1.320000e-30 145.0
38 TraesCS3B01G016400 chr7B 93.333 45 3 0 1277 1321 696896020 696896064 2.940000e-07 67.6
39 TraesCS3B01G016400 chr7B 95.122 41 2 0 1277 1317 693245720 693245760 1.060000e-06 65.8
40 TraesCS3B01G016400 chr7A 93.333 45 3 0 1277 1321 699839055 699839099 2.940000e-07 67.6
41 TraesCS3B01G016400 chr6A 89.796 49 3 2 1275 1321 117424597 117424645 1.370000e-05 62.1


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 TraesCS3B01G016400 chr3B 6669386 6673931 4545 True 8395.00 8395 100.0000 1 4546 1 chr3B.!!$R1 4545
1 TraesCS3B01G016400 chr3B 3601468 3603503 2035 False 326.50 398 79.6640 1001 3280 2 chr3B.!!$F2 2279
2 TraesCS3B01G016400 chr3B 5232699 5234743 2044 True 326.50 398 79.7410 1001 3280 2 chr3B.!!$R3 2279
3 TraesCS3B01G016400 chr3B 545205410 545205991 581 True 213.00 213 73.7980 1396 1992 1 chr3B.!!$R2 596
4 TraesCS3B01G016400 chr3A 9842688 9847291 4603 True 1641.25 3465 92.4200 216 4546 4 chr3A.!!$R4 4330
5 TraesCS3B01G016400 chr3A 9811598 9814127 2529 True 667.50 688 81.6220 1354 3337 2 chr3A.!!$R3 1983
6 TraesCS3B01G016400 chr3A 11064866 11066657 1791 True 335.50 399 82.1430 1001 1992 2 chr3A.!!$R5 991
7 TraesCS3B01G016400 chr3D 4178727 4183860 5133 True 1137.20 2573 91.3332 2 4429 5 chr3D.!!$R1 4427
8 TraesCS3B01G016400 chrUn 35628603 35629469 866 False 917.00 917 85.8770 2406 3275 1 chrUn.!!$F1 869
9 TraesCS3B01G016400 chrUn 327484492 327485193 701 True 667.00 667 83.9210 1365 2068 1 chrUn.!!$R1 703

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
639 656 0.178903 TACCTGTTGGCCTGACCTCT 60.179 55.000 3.32 0.0 40.22 3.69 F
648 665 0.529555 GCCTGACCTCTCAGCGAATC 60.530 60.000 0.00 0.0 42.55 2.52 F
833 850 0.682292 TCCACACACGCCATCTAACA 59.318 50.000 0.00 0.0 0.00 2.41 F
868 885 0.742990 CCGACGGCTTTGCTAATCCA 60.743 55.000 0.00 0.0 0.00 3.41 F
1490 2417 1.598685 GGCGTCCGACCCAGAAAAA 60.599 57.895 0.00 0.0 0.00 1.94 F
2639 4196 2.100631 CACCCGGCAAGTAAGAGCG 61.101 63.158 0.00 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2876 1.568504 AGCTAAGGGTCCGATGAACA 58.431 50.000 0.00 0.0 0.00 3.18 R
2082 3032 1.755959 AGTGCCAACAAAACATGCAGA 59.244 42.857 0.00 0.0 31.69 4.26 R
2199 3153 1.933853 ACTTCACGTTCACAGTTCTGC 59.066 47.619 0.00 0.0 0.00 4.26 R
2403 3944 4.919754 ACGTCGTTAATAGTCTGTGAAACC 59.080 41.667 0.00 0.0 34.36 3.27 R
3174 4742 0.480690 AACTGGGTGCCCACATAACA 59.519 50.000 5.73 0.0 41.89 2.41 R
4471 6587 0.105142 ATCGGGTATAGGTGTGGGCT 60.105 55.000 0.00 0.0 0.00 5.19 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
44 45 4.778415 CGGTGGCACGACCTCTCG 62.778 72.222 12.17 3.58 46.06 4.04
49 50 2.357034 GCACGACCTCTCGGCAAA 60.357 61.111 0.00 0.00 44.80 3.68
74 75 4.287552 GGATACTAGGTGACCCTCTGAAA 58.712 47.826 0.00 0.00 41.45 2.69
96 97 2.068837 TTAAGGTCGGCACAGTTACG 57.931 50.000 0.00 0.00 0.00 3.18
113 114 1.076533 ACGTGATTGCACCGTCGATC 61.077 55.000 0.00 0.00 42.09 3.69
123 124 1.298413 CCGTCGATCACCTAGCACG 60.298 63.158 0.00 0.00 0.00 5.34
129 130 4.328169 CGTCGATCACCTAGCACGTATATA 59.672 45.833 0.00 0.00 0.00 0.86
130 131 5.558307 GTCGATCACCTAGCACGTATATAC 58.442 45.833 2.53 2.53 0.00 1.47
131 132 5.350914 GTCGATCACCTAGCACGTATATACT 59.649 44.000 11.05 0.00 0.00 2.12
132 133 5.579904 TCGATCACCTAGCACGTATATACTC 59.420 44.000 11.05 0.80 0.00 2.59
133 134 5.220624 CGATCACCTAGCACGTATATACTCC 60.221 48.000 11.05 0.00 0.00 3.85
134 135 4.330250 TCACCTAGCACGTATATACTCCC 58.670 47.826 11.05 0.00 0.00 4.30
135 136 4.042560 TCACCTAGCACGTATATACTCCCT 59.957 45.833 11.05 6.36 0.00 4.20
136 137 4.395542 CACCTAGCACGTATATACTCCCTC 59.604 50.000 11.05 0.00 0.00 4.30
137 138 4.289148 ACCTAGCACGTATATACTCCCTCT 59.711 45.833 11.05 3.98 0.00 3.69
138 139 4.636648 CCTAGCACGTATATACTCCCTCTG 59.363 50.000 11.05 0.00 0.00 3.35
139 140 4.101645 AGCACGTATATACTCCCTCTGT 57.898 45.455 11.05 0.00 0.00 3.41
140 141 4.073549 AGCACGTATATACTCCCTCTGTC 58.926 47.826 11.05 0.00 0.00 3.51
141 142 3.190953 GCACGTATATACTCCCTCTGTCC 59.809 52.174 11.05 0.00 0.00 4.02
142 143 3.757493 CACGTATATACTCCCTCTGTCCC 59.243 52.174 11.05 0.00 0.00 4.46
143 144 3.396946 ACGTATATACTCCCTCTGTCCCA 59.603 47.826 11.05 0.00 0.00 4.37
144 145 4.044317 ACGTATATACTCCCTCTGTCCCAT 59.956 45.833 11.05 0.00 0.00 4.00
145 146 5.252397 ACGTATATACTCCCTCTGTCCCATA 59.748 44.000 11.05 0.00 0.00 2.74
146 147 6.185511 CGTATATACTCCCTCTGTCCCATAA 58.814 44.000 11.05 0.00 0.00 1.90
147 148 6.834451 CGTATATACTCCCTCTGTCCCATAAT 59.166 42.308 11.05 0.00 0.00 1.28
148 149 7.997223 CGTATATACTCCCTCTGTCCCATAATA 59.003 40.741 11.05 0.00 0.00 0.98
149 150 9.884814 GTATATACTCCCTCTGTCCCATAATAT 57.115 37.037 5.58 0.00 0.00 1.28
152 153 5.594777 ACTCCCTCTGTCCCATAATATAGG 58.405 45.833 0.00 0.00 0.00 2.57
153 154 5.318889 ACTCCCTCTGTCCCATAATATAGGA 59.681 44.000 0.00 0.00 0.00 2.94
205 206 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
206 207 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
207 208 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
208 209 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
209 210 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
210 211 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
211 212 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
212 213 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
222 223 4.322801 GGACGGAGGGAGTATTAATCATGG 60.323 50.000 0.00 0.00 0.00 3.66
552 557 4.724279 AAAGGGGAGCAGAAGTAGAAAA 57.276 40.909 0.00 0.00 0.00 2.29
559 564 6.484977 GGGGAGCAGAAGTAGAAAATTCATAG 59.515 42.308 0.00 0.00 0.00 2.23
563 568 7.756558 AGCAGAAGTAGAAAATTCATAGCAAC 58.243 34.615 0.00 0.00 0.00 4.17
565 570 7.362056 GCAGAAGTAGAAAATTCATAGCAACCA 60.362 37.037 0.00 0.00 0.00 3.67
567 572 9.247861 AGAAGTAGAAAATTCATAGCAACCAAT 57.752 29.630 0.00 0.00 0.00 3.16
569 574 9.643693 AAGTAGAAAATTCATAGCAACCAATTG 57.356 29.630 0.00 0.00 38.99 2.32
570 575 9.023962 AGTAGAAAATTCATAGCAACCAATTGA 57.976 29.630 7.12 0.00 38.15 2.57
571 576 9.638239 GTAGAAAATTCATAGCAACCAATTGAA 57.362 29.630 7.12 0.00 38.15 2.69
573 578 9.729281 AGAAAATTCATAGCAACCAATTGAATT 57.271 25.926 7.12 0.00 44.57 2.17
574 579 9.763465 GAAAATTCATAGCAACCAATTGAATTG 57.237 29.630 10.84 10.84 42.89 2.32
575 580 8.851541 AAATTCATAGCAACCAATTGAATTGT 57.148 26.923 15.93 2.73 42.89 2.71
576 581 8.851541 AATTCATAGCAACCAATTGAATTGTT 57.148 26.923 15.93 15.82 42.40 2.83
577 582 7.887996 TTCATAGCAACCAATTGAATTGTTC 57.112 32.000 15.93 3.25 38.15 3.18
578 583 6.990798 TCATAGCAACCAATTGAATTGTTCA 58.009 32.000 15.93 8.59 38.15 3.18
626 643 2.900546 CCAACTTCTGACCTCTACCTGT 59.099 50.000 0.00 0.00 0.00 4.00
631 648 0.250513 CTGACCTCTACCTGTTGGCC 59.749 60.000 0.00 0.00 36.63 5.36
639 656 0.178903 TACCTGTTGGCCTGACCTCT 60.179 55.000 3.32 0.00 40.22 3.69
643 660 1.376553 GTTGGCCTGACCTCTCAGC 60.377 63.158 3.32 0.00 42.55 4.26
648 665 0.529555 GCCTGACCTCTCAGCGAATC 60.530 60.000 0.00 0.00 42.55 2.52
649 666 1.110442 CCTGACCTCTCAGCGAATCT 58.890 55.000 0.00 0.00 42.55 2.40
672 689 1.686355 ACTAGATGACCCTGAGAGCG 58.314 55.000 0.00 0.00 0.00 5.03
716 733 1.403814 TTGGAGCCTCGATCACCTAG 58.596 55.000 0.00 0.00 0.00 3.02
717 734 1.109920 TGGAGCCTCGATCACCTAGC 61.110 60.000 0.00 0.00 0.00 3.42
722 739 0.817654 CCTCGATCACCTAGCACACA 59.182 55.000 0.00 0.00 0.00 3.72
723 740 1.410517 CCTCGATCACCTAGCACACAT 59.589 52.381 0.00 0.00 0.00 3.21
724 741 2.623416 CCTCGATCACCTAGCACACATA 59.377 50.000 0.00 0.00 0.00 2.29
832 849 1.803334 TTCCACACACGCCATCTAAC 58.197 50.000 0.00 0.00 0.00 2.34
833 850 0.682292 TCCACACACGCCATCTAACA 59.318 50.000 0.00 0.00 0.00 2.41
834 851 1.078709 CCACACACGCCATCTAACAG 58.921 55.000 0.00 0.00 0.00 3.16
843 860 2.677902 CGCCATCTAACAGCAAGGAAGA 60.678 50.000 0.00 0.00 0.00 2.87
863 880 1.214589 GAGTCCGACGGCTTTGCTA 59.785 57.895 9.66 0.00 0.00 3.49
868 885 0.742990 CCGACGGCTTTGCTAATCCA 60.743 55.000 0.00 0.00 0.00 3.41
968 990 6.072508 CCCAACACAATATATATCACACCTGC 60.073 42.308 0.00 0.00 0.00 4.85
969 991 6.486320 CCAACACAATATATATCACACCTGCA 59.514 38.462 0.00 0.00 0.00 4.41
974 996 6.168389 CAATATATATCACACCTGCAGAGCA 58.832 40.000 17.39 0.00 36.92 4.26
1227 1262 1.725164 GAACTGCTTACTCGTTTCCCG 59.275 52.381 0.00 0.00 38.13 5.14
1297 1436 3.418047 CCTCCGTCCCAAAATAAGTGTT 58.582 45.455 0.00 0.00 0.00 3.32
1316 1455 6.639563 AGTGTTGTGGCTTTAGTTCAAATTT 58.360 32.000 0.00 0.00 0.00 1.82
1337 1476 3.149196 TCAACAACTTGGGCAATCTCTC 58.851 45.455 0.00 0.00 0.00 3.20
1382 1679 3.581024 TGTGTACAGGTAATGGACGAC 57.419 47.619 0.00 0.00 46.91 4.34
1428 2346 1.652563 GTGCAAACTCCGGTGAACC 59.347 57.895 11.17 0.00 0.00 3.62
1469 2396 2.371864 AGGCTGGATCCTGAGGCT 59.628 61.111 21.91 20.48 40.12 4.58
1490 2417 1.598685 GGCGTCCGACCCAGAAAAA 60.599 57.895 0.00 0.00 0.00 1.94
1955 2900 2.771943 TCATCGGACCCTTAGCTTTGAT 59.228 45.455 0.00 0.00 0.00 2.57
2090 3040 3.574284 TTTTGCGCTAAATCTGCATGT 57.426 38.095 12.99 0.00 38.60 3.21
2091 3041 3.574284 TTTGCGCTAAATCTGCATGTT 57.426 38.095 9.73 0.00 38.60 2.71
2092 3042 3.574284 TTGCGCTAAATCTGCATGTTT 57.426 38.095 9.73 0.00 38.60 2.83
2108 3058 5.868258 TGCATGTTTTGTTGGCACTTATATG 59.132 36.000 0.00 0.00 0.00 1.78
2139 3093 5.134661 ACCCTATTGACGAAAGGTGAAAAA 58.865 37.500 0.00 0.00 0.00 1.94
2222 3299 4.143305 GCAGAACTGTGAACGTGAAGTATC 60.143 45.833 0.00 0.00 0.00 2.24
2285 3647 7.040686 GGCAGTTTTCTAGATAACCTTTTGACA 60.041 37.037 18.85 0.00 0.00 3.58
2532 4089 4.480541 TGTAGGCATGCAAATTTTACACG 58.519 39.130 21.36 0.00 0.00 4.49
2536 4093 3.492756 GGCATGCAAATTTTACACGTTGT 59.507 39.130 21.36 0.00 0.00 3.32
2545 4102 9.352163 GCAAATTTTACACGTTGTTTTCTTATG 57.648 29.630 0.00 0.00 0.00 1.90
2639 4196 2.100631 CACCCGGCAAGTAAGAGCG 61.101 63.158 0.00 0.00 0.00 5.03
2659 4218 9.871238 AAGAGCGTCATTTTTCTCTTACTATAA 57.129 29.630 1.93 0.00 42.23 0.98
3005 4571 8.887393 TCCTTTTGTACTTTATTACCTCTTCCT 58.113 33.333 0.00 0.00 0.00 3.36
3329 4901 7.769044 TGTGTCTAAGAGAAAACTAGCTTTTGT 59.231 33.333 0.00 4.53 31.81 2.83
3527 5099 2.666190 GCGGCAGCACTCAAGACA 60.666 61.111 3.18 0.00 44.35 3.41
3566 5138 2.496899 AGGGCAACACTGAGTAATGG 57.503 50.000 0.00 0.00 39.74 3.16
3595 5167 4.724074 ATTTGTGCTCACATACCCAATG 57.276 40.909 3.31 0.00 41.52 2.82
3598 5170 3.081061 TGTGCTCACATACCCAATGAAC 58.919 45.455 0.00 0.00 39.07 3.18
3599 5171 2.095853 GTGCTCACATACCCAATGAACG 59.904 50.000 0.00 0.00 39.07 3.95
3899 5475 6.534793 TCTTTTTCTTTCCTTTTGCACATCAC 59.465 34.615 0.00 0.00 0.00 3.06
3924 6039 6.316390 CCTTTAGAGATTCCACCACAACATAC 59.684 42.308 0.00 0.00 0.00 2.39
3948 6063 7.889469 ACAATCAAACATCAATCTTTACTGCT 58.111 30.769 0.00 0.00 0.00 4.24
4064 6179 9.639601 GTGTCGATATGAATATGAGGAACAATA 57.360 33.333 0.00 0.00 0.00 1.90
4138 6253 6.098982 ACAACATTTGAAATTGGGAAGTGGTA 59.901 34.615 0.00 0.00 0.00 3.25
4180 6295 5.713389 CCCATTGCTCATATATGGTGATGTT 59.287 40.000 12.78 0.00 37.67 2.71
4268 6383 4.559502 CCTTGGGGCTGAATACGG 57.440 61.111 0.00 0.00 0.00 4.02
4292 6407 0.035439 GGCTTCGAATTCCCCAGACA 60.035 55.000 0.00 0.00 0.00 3.41
4348 6464 2.234168 GAGGTGTAGGGTTCTCTGTTCC 59.766 54.545 0.00 0.00 0.00 3.62
4354 6470 1.076677 AGGGTTCTCTGTTCCGTCCTA 59.923 52.381 0.00 0.00 0.00 2.94
4355 6471 1.897802 GGGTTCTCTGTTCCGTCCTAA 59.102 52.381 0.00 0.00 0.00 2.69
4397 6513 5.184892 ACAATTCTCTGAGGGTTATTGCT 57.815 39.130 4.59 0.62 0.00 3.91
4408 6524 1.340697 GGTTATTGCTCCGGGGAAGTT 60.341 52.381 4.80 0.00 0.00 2.66
4445 6561 5.733226 TGTGGATGTAACGATTATTGCTG 57.267 39.130 0.00 0.00 0.00 4.41
4471 6587 6.988580 CCAGCTATATTGTTCTTGAGTGATCA 59.011 38.462 0.00 0.00 0.00 2.92
4472 6588 7.171167 CCAGCTATATTGTTCTTGAGTGATCAG 59.829 40.741 0.00 0.00 0.00 2.90
4488 6604 1.046472 TCAGCCCACACCTATACCCG 61.046 60.000 0.00 0.00 0.00 5.28
4500 6616 9.374838 CCACACCTATACCCGATAAATAAATAC 57.625 37.037 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.092538 AGGAAGTGGAGGATGATTGCAG 60.093 50.000 0.00 0.00 0.00 4.41
44 45 3.391049 GTCACCTAGTATCCGATTTGCC 58.609 50.000 0.00 0.00 0.00 4.52
74 75 3.434299 CGTAACTGTGCCGACCTTAATTT 59.566 43.478 0.00 0.00 0.00 1.82
96 97 0.370273 GTGATCGACGGTGCAATCAC 59.630 55.000 10.33 10.33 40.68 3.06
113 114 4.333690 AGGGAGTATATACGTGCTAGGTG 58.666 47.826 7.23 0.00 0.00 4.00
180 181 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
181 182 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
182 183 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
183 184 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
184 185 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
186 187 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
187 188 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
188 189 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
189 190 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
190 191 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
191 192 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
192 193 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
193 194 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
194 195 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
195 196 4.474303 TTAATACTCCCTCCGTCCCATA 57.526 45.455 0.00 0.00 0.00 2.74
196 197 3.339713 TTAATACTCCCTCCGTCCCAT 57.660 47.619 0.00 0.00 0.00 4.00
197 198 2.852714 TTAATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
198 199 3.236896 TGATTAATACTCCCTCCGTCCC 58.763 50.000 0.00 0.00 0.00 4.46
199 200 4.322801 CCATGATTAATACTCCCTCCGTCC 60.323 50.000 0.00 0.00 0.00 4.79
200 201 4.283722 ACCATGATTAATACTCCCTCCGTC 59.716 45.833 0.00 0.00 0.00 4.79
201 202 4.232091 ACCATGATTAATACTCCCTCCGT 58.768 43.478 0.00 0.00 0.00 4.69
202 203 4.891992 ACCATGATTAATACTCCCTCCG 57.108 45.455 0.00 0.00 0.00 4.63
203 204 8.652290 GGATATACCATGATTAATACTCCCTCC 58.348 40.741 0.00 0.00 38.79 4.30
204 205 9.213777 TGGATATACCATGATTAATACTCCCTC 57.786 37.037 0.00 0.00 44.64 4.30
222 223 8.108551 ACCAACTAGACGTTCTATGGATATAC 57.891 38.462 15.57 0.00 34.36 1.47
241 242 3.031013 CAACTCCCCTTTTTGACCAACT 58.969 45.455 0.00 0.00 0.00 3.16
417 422 8.692710 TGAGTTGTATGTAGTAAAGTCCTATGG 58.307 37.037 0.00 0.00 0.00 2.74
552 557 8.095792 TGAACAATTCAATTGGTTGCTATGAAT 58.904 29.630 14.70 0.00 41.00 2.57
570 575 8.575589 TGTAGCTGTATGTTGAATTGAACAATT 58.424 29.630 14.51 11.76 43.14 2.32
571 576 8.109705 TGTAGCTGTATGTTGAATTGAACAAT 57.890 30.769 14.51 6.32 39.25 2.71
572 577 7.503521 TGTAGCTGTATGTTGAATTGAACAA 57.496 32.000 14.51 2.11 39.25 2.83
573 578 7.503521 TTGTAGCTGTATGTTGAATTGAACA 57.496 32.000 12.95 12.95 40.08 3.18
574 579 8.853345 CAATTGTAGCTGTATGTTGAATTGAAC 58.147 33.333 0.27 0.27 33.38 3.18
575 580 8.575589 ACAATTGTAGCTGTATGTTGAATTGAA 58.424 29.630 9.97 0.00 34.89 2.69
576 581 8.109705 ACAATTGTAGCTGTATGTTGAATTGA 57.890 30.769 9.97 0.00 34.89 2.57
577 582 7.485913 GGACAATTGTAGCTGTATGTTGAATTG 59.514 37.037 11.95 0.00 36.23 2.32
578 583 7.176515 TGGACAATTGTAGCTGTATGTTGAATT 59.823 33.333 11.95 0.00 0.00 2.17
579 584 6.658816 TGGACAATTGTAGCTGTATGTTGAAT 59.341 34.615 11.95 0.00 0.00 2.57
591 608 3.821033 AGAAGTTGGTGGACAATTGTAGC 59.179 43.478 11.95 7.34 41.95 3.58
643 660 5.707764 TCAGGGTCATCTAGTATCAGATTCG 59.292 44.000 0.00 0.00 32.83 3.34
648 665 4.458989 GCTCTCAGGGTCATCTAGTATCAG 59.541 50.000 0.00 0.00 0.00 2.90
649 666 4.402829 GCTCTCAGGGTCATCTAGTATCA 58.597 47.826 0.00 0.00 0.00 2.15
672 689 4.119442 TGTAACTCTGCCGACCTTAATC 57.881 45.455 0.00 0.00 0.00 1.75
832 849 1.273606 TCGGACTCTTCTTCCTTGCTG 59.726 52.381 0.00 0.00 0.00 4.41
833 850 1.273886 GTCGGACTCTTCTTCCTTGCT 59.726 52.381 0.00 0.00 0.00 3.91
834 851 1.715993 GTCGGACTCTTCTTCCTTGC 58.284 55.000 0.00 0.00 0.00 4.01
843 860 1.668151 GCAAAGCCGTCGGACTCTT 60.668 57.895 17.49 6.10 0.00 2.85
863 880 5.983333 AAGACATCACTAGGGATTGGATT 57.017 39.130 4.21 0.00 0.00 3.01
893 910 9.566432 AATAATTGTTGAGTTGAAAGAGAGAGT 57.434 29.630 0.00 0.00 0.00 3.24
895 912 9.784531 AGAATAATTGTTGAGTTGAAAGAGAGA 57.215 29.630 0.00 0.00 0.00 3.10
920 942 6.768381 GGGAAGAAAGGTTCCTGTTATGATAG 59.232 42.308 2.79 0.00 44.89 2.08
923 945 4.352595 TGGGAAGAAAGGTTCCTGTTATGA 59.647 41.667 2.79 0.00 44.89 2.15
939 961 7.936847 GGTGTGATATATATTGTGTTGGGAAGA 59.063 37.037 0.00 0.00 0.00 2.87
968 990 6.700960 CCTAATTACAATGTCTCTCTGCTCTG 59.299 42.308 0.00 0.00 0.00 3.35
969 991 6.609212 TCCTAATTACAATGTCTCTCTGCTCT 59.391 38.462 0.00 0.00 0.00 4.09
974 996 7.726033 ACTGTCCTAATTACAATGTCTCTCT 57.274 36.000 0.00 0.00 0.00 3.10
980 1002 8.574251 TTGCATTACTGTCCTAATTACAATGT 57.426 30.769 0.00 0.00 0.00 2.71
1297 1436 6.634805 TGTTGAAATTTGAACTAAAGCCACA 58.365 32.000 19.16 0.00 0.00 4.17
1316 1455 3.149196 GAGAGATTGCCCAAGTTGTTGA 58.851 45.455 1.45 0.00 35.46 3.18
1337 1476 7.420184 TGCATGTGTATATGTTAAATCCTCG 57.580 36.000 0.00 0.00 0.00 4.63
1382 1679 1.888018 CTTGCCATTGCTGGTGGAG 59.112 57.895 6.75 0.00 45.10 3.86
1390 1687 4.197498 ATCGCGGCTTGCCATTGC 62.197 61.111 6.13 6.23 42.08 3.56
1490 2417 2.035312 ACGTAGTCCTCCACGGCT 59.965 61.111 0.00 0.00 42.35 5.52
1559 2486 2.233922 GGATGGAAAGTCGAGGAAGTGA 59.766 50.000 0.00 0.00 0.00 3.41
1687 2614 2.440247 GCATAGCCGGCACCCTTT 60.440 61.111 31.54 9.39 0.00 3.11
1931 2876 1.568504 AGCTAAGGGTCCGATGAACA 58.431 50.000 0.00 0.00 0.00 3.18
1934 2879 2.184533 TCAAAGCTAAGGGTCCGATGA 58.815 47.619 0.00 0.00 0.00 2.92
2072 3022 3.574284 AAACATGCAGATTTAGCGCAA 57.426 38.095 11.47 0.00 39.48 4.85
2073 3023 3.244156 CAAAACATGCAGATTTAGCGCA 58.756 40.909 11.47 0.00 40.50 6.09
2074 3024 3.244976 ACAAAACATGCAGATTTAGCGC 58.755 40.909 0.00 0.00 33.85 5.92
2075 3025 4.090354 CCAACAAAACATGCAGATTTAGCG 59.910 41.667 0.00 0.00 33.85 4.26
2076 3026 4.143052 GCCAACAAAACATGCAGATTTAGC 60.143 41.667 0.00 0.00 0.00 3.09
2077 3027 4.989797 TGCCAACAAAACATGCAGATTTAG 59.010 37.500 0.00 0.00 0.00 1.85
2078 3028 4.749099 GTGCCAACAAAACATGCAGATTTA 59.251 37.500 0.00 0.00 31.69 1.40
2079 3029 3.560896 GTGCCAACAAAACATGCAGATTT 59.439 39.130 0.00 0.00 31.69 2.17
2080 3030 3.132925 GTGCCAACAAAACATGCAGATT 58.867 40.909 0.00 0.00 31.69 2.40
2081 3031 2.366266 AGTGCCAACAAAACATGCAGAT 59.634 40.909 0.00 0.00 31.69 2.90
2082 3032 1.755959 AGTGCCAACAAAACATGCAGA 59.244 42.857 0.00 0.00 31.69 4.26
2083 3033 2.228138 AGTGCCAACAAAACATGCAG 57.772 45.000 0.00 0.00 31.69 4.41
2084 3034 2.687700 AAGTGCCAACAAAACATGCA 57.312 40.000 0.00 0.00 0.00 3.96
2085 3035 5.868801 ACATATAAGTGCCAACAAAACATGC 59.131 36.000 0.00 0.00 0.00 4.06
2086 3036 7.274033 CAGACATATAAGTGCCAACAAAACATG 59.726 37.037 0.00 0.00 0.00 3.21
2087 3037 7.315142 CAGACATATAAGTGCCAACAAAACAT 58.685 34.615 0.00 0.00 0.00 2.71
2088 3038 6.294453 CCAGACATATAAGTGCCAACAAAACA 60.294 38.462 0.00 0.00 0.00 2.83
2089 3039 6.072175 TCCAGACATATAAGTGCCAACAAAAC 60.072 38.462 0.00 0.00 0.00 2.43
2090 3040 6.007076 TCCAGACATATAAGTGCCAACAAAA 58.993 36.000 0.00 0.00 0.00 2.44
2091 3041 5.565509 TCCAGACATATAAGTGCCAACAAA 58.434 37.500 0.00 0.00 0.00 2.83
2092 3042 5.172687 TCCAGACATATAAGTGCCAACAA 57.827 39.130 0.00 0.00 0.00 2.83
2108 3058 3.604875 TCGTCAATAGGGTTTCCAGAC 57.395 47.619 0.00 0.00 34.83 3.51
2192 3146 3.802685 ACGTTCACAGTTCTGCTAGTTTC 59.197 43.478 0.00 0.00 0.00 2.78
2195 3149 2.361119 TCACGTTCACAGTTCTGCTAGT 59.639 45.455 0.00 0.00 0.00 2.57
2196 3150 3.013276 TCACGTTCACAGTTCTGCTAG 57.987 47.619 0.00 0.00 0.00 3.42
2197 3151 3.181479 ACTTCACGTTCACAGTTCTGCTA 60.181 43.478 0.00 0.00 0.00 3.49
2199 3153 1.933853 ACTTCACGTTCACAGTTCTGC 59.066 47.619 0.00 0.00 0.00 4.26
2200 3154 5.223382 AGATACTTCACGTTCACAGTTCTG 58.777 41.667 0.00 0.00 0.00 3.02
2201 3155 5.455056 AGATACTTCACGTTCACAGTTCT 57.545 39.130 0.00 0.00 0.00 3.01
2358 3723 7.818997 TGTCCGATATAACTGTTATGAGACT 57.181 36.000 20.42 0.00 0.00 3.24
2403 3944 4.919754 ACGTCGTTAATAGTCTGTGAAACC 59.080 41.667 0.00 0.00 34.36 3.27
2545 4102 8.773404 AGTGTTAGTGTCACCTAATATTGAAC 57.227 34.615 0.00 0.00 36.58 3.18
2627 4184 5.035784 AGAAAAATGACGCTCTTACTTGC 57.964 39.130 0.00 0.00 0.00 4.01
2663 4222 7.780008 TGTGCACGTAATTAGCATTATTACT 57.220 32.000 13.13 0.00 40.78 2.24
2667 4226 8.616942 TGTTTATGTGCACGTAATTAGCATTAT 58.383 29.630 27.56 7.41 40.78 1.28
2880 4446 8.530804 AGAGCTCTTTTTCCTATGCATAAATT 57.469 30.769 11.45 0.00 0.00 1.82
3005 4571 6.459670 TCGAGTTTGTGCAATCCTATACTA 57.540 37.500 0.00 0.00 0.00 1.82
3013 4579 2.686558 TGCTTCGAGTTTGTGCAATC 57.313 45.000 0.00 0.00 0.00 2.67
3174 4742 0.480690 AACTGGGTGCCCACATAACA 59.519 50.000 5.73 0.00 41.89 2.41
3354 4926 7.734942 TGCATAGACATCCACACAATTAGATA 58.265 34.615 0.00 0.00 0.00 1.98
3416 4988 3.340814 ACTGCCAGAACTACCTTGATG 57.659 47.619 0.00 0.00 0.00 3.07
3566 5138 3.624326 TGTGAGCACAAATACAACTGC 57.376 42.857 0.00 0.00 38.56 4.40
3794 5367 7.164122 ACTCATCACAATCAAGCTTCTCTTAA 58.836 34.615 0.00 0.00 32.74 1.85
3875 5451 6.238184 GGTGATGTGCAAAAGGAAAGAAAAAG 60.238 38.462 0.00 0.00 0.00 2.27
3899 5475 4.651778 TGTTGTGGTGGAATCTCTAAAGG 58.348 43.478 0.00 0.00 0.00 3.11
3924 6039 9.844790 TTAGCAGTAAAGATTGATGTTTGATTG 57.155 29.630 0.00 0.00 0.00 2.67
4124 6239 5.697067 TGTTACTGTTACCACTTCCCAATT 58.303 37.500 0.00 0.00 0.00 2.32
4138 6253 2.829720 TGGGCGTAGATCTGTTACTGTT 59.170 45.455 5.18 0.00 0.00 3.16
4180 6295 1.891933 TGCCAACCCCATCTCTATCA 58.108 50.000 0.00 0.00 0.00 2.15
4259 6374 4.891727 AGCCGCCGCCGTATTCAG 62.892 66.667 0.00 0.00 34.57 3.02
4268 6383 4.237809 GGAATTCGAAGCCGCCGC 62.238 66.667 3.35 0.00 35.37 6.53
4272 6387 1.090052 GTCTGGGGAATTCGAAGCCG 61.090 60.000 3.35 0.00 37.07 5.52
4348 6464 7.303634 ACATATACTTTTTGCTGTTAGGACG 57.696 36.000 0.00 0.00 0.00 4.79
4380 6496 1.757118 CGGAGCAATAACCCTCAGAGA 59.243 52.381 0.00 0.00 0.00 3.10
4397 6513 1.420430 CCTATGCTAACTTCCCCGGA 58.580 55.000 0.73 0.00 0.00 5.14
4408 6524 0.550914 CCACAAAGCCCCCTATGCTA 59.449 55.000 0.00 0.00 38.34 3.49
4445 6561 5.118990 TCACTCAAGAACAATATAGCTGGC 58.881 41.667 0.00 0.00 0.00 4.85
4471 6587 0.105142 ATCGGGTATAGGTGTGGGCT 60.105 55.000 0.00 0.00 0.00 5.19
4472 6588 1.636148 TATCGGGTATAGGTGTGGGC 58.364 55.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.