Multiple sequence alignment - TraesCS1B01G256700

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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 TraesCS1B01G256700 chr1B 100.000 7462 0 0 1 7462 452310581 452318042 0.000000e+00 13780.0
1 TraesCS1B01G256700 chr1D 95.836 7084 216 31 402 7462 336546756 336553783 0.000000e+00 11374.0
2 TraesCS1B01G256700 chr1D 94.355 124 3 2 204 323 336546295 336546418 3.550000e-43 187.0
3 TraesCS1B01G256700 chr1D 93.443 122 8 0 2 123 336546176 336546297 1.650000e-41 182.0
4 TraesCS1B01G256700 chr1D 92.157 102 6 2 107 206 447863821 447863720 7.800000e-30 143.0
5 TraesCS1B01G256700 chr1D 83.846 130 15 5 210 335 473785040 473784913 1.320000e-22 119.0
6 TraesCS1B01G256700 chr1D 77.895 190 35 7 3880 4067 480625475 480625659 2.200000e-20 111.0
7 TraesCS1B01G256700 chr1D 90.278 72 6 1 330 400 336546658 336546729 7.970000e-15 93.5
8 TraesCS1B01G256700 chr1D 89.231 65 6 1 337 400 336546584 336546648 6.210000e-11 80.5
9 TraesCS1B01G256700 chr1A 97.016 3418 71 12 4068 7462 435060028 435063437 0.000000e+00 5718.0
10 TraesCS1B01G256700 chr1A 94.857 3247 124 25 644 3876 435056806 435060023 0.000000e+00 5031.0
11 TraesCS1B01G256700 chr1A 85.393 356 18 8 206 530 435056455 435056807 9.270000e-89 339.0
12 TraesCS1B01G256700 chr1A 92.683 123 9 0 1 123 435054723 435054845 2.140000e-40 178.0
13 TraesCS1B01G256700 chr1A 88.235 85 6 2 204 284 435054843 435054927 1.710000e-16 99.0
14 TraesCS1B01G256700 chr3B 83.569 353 36 12 6195 6538 16225863 16225524 2.020000e-80 311.0
15 TraesCS1B01G256700 chr7A 93.583 187 12 0 3880 4066 468931711 468931897 5.700000e-71 279.0
16 TraesCS1B01G256700 chr7A 98.851 87 1 0 121 207 556151915 556152001 1.000000e-33 156.0
17 TraesCS1B01G256700 chr7A 93.000 100 5 2 107 206 80994069 80994166 2.170000e-30 145.0
18 TraesCS1B01G256700 chr7A 80.000 115 18 5 122 235 20512267 20512377 6.210000e-11 80.5
19 TraesCS1B01G256700 chr6D 88.889 189 16 4 3881 4066 414777691 414777877 2.090000e-55 228.0
20 TraesCS1B01G256700 chr6A 88.827 179 18 1 3889 4065 559849163 559849341 1.260000e-52 219.0
21 TraesCS1B01G256700 chr4B 96.774 93 3 0 114 206 29271930 29271838 1.000000e-33 156.0
22 TraesCS1B01G256700 chr4A 94.118 102 4 2 106 206 589084957 589084857 3.610000e-33 154.0
23 TraesCS1B01G256700 chr4A 82.796 93 12 4 214 304 721370084 721370174 6.210000e-11 80.5
24 TraesCS1B01G256700 chr5B 95.699 93 4 0 115 207 655839912 655840004 4.660000e-32 150.0
25 TraesCS1B01G256700 chr3D 94.845 97 4 1 122 218 37369011 37369106 4.660000e-32 150.0
26 TraesCS1B01G256700 chr3D 94.118 85 5 0 122 206 224304667 224304751 6.080000e-26 130.0
27 TraesCS1B01G256700 chr3D 78.689 122 21 5 3948 4066 563658261 563658380 8.030000e-10 76.8
28 TraesCS1B01G256700 chr3D 95.238 42 2 0 3881 3922 600094665 600094706 4.830000e-07 67.6
29 TraesCS1B01G256700 chr2A 94.792 96 4 1 121 216 628780925 628781019 1.680000e-31 148.0
30 TraesCS1B01G256700 chr5A 91.589 107 7 2 112 218 643736504 643736400 6.030000e-31 147.0
31 TraesCS1B01G256700 chr6B 88.793 116 13 0 3949 4064 625323324 625323439 7.800000e-30 143.0
32 TraesCS1B01G256700 chr5D 78.534 191 32 7 3880 4066 369379711 369379896 4.730000e-22 117.0
33 TraesCS1B01G256700 chr5D 85.106 94 13 1 3975 4068 336042753 336042845 2.220000e-15 95.3
34 TraesCS1B01G256700 chr2B 81.000 100 18 1 214 312 223715923 223715824 2.230000e-10 78.7
35 TraesCS1B01G256700 chrUn 83.544 79 13 0 212 290 1588868 1588946 2.890000e-09 75.0


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 TraesCS1B01G256700 chr1B 452310581 452318042 7461 False 13780.0 13780 100.0000 1 7462 1 chr1B.!!$F1 7461
1 TraesCS1B01G256700 chr1D 336546176 336553783 7607 False 2383.4 11374 92.6286 2 7462 5 chr1D.!!$F2 7460
2 TraesCS1B01G256700 chr1A 435054723 435063437 8714 False 2273.0 5718 91.6368 1 7462 5 chr1A.!!$F1 7461

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
592 2464 0.035915 GAAAGGCTGAGTGAGGGGAC 60.036 60.0 0.00 0.0 0.00 4.46 F
976 2849 0.108567 GGAAACAGACTCGCTCTCCC 60.109 60.0 0.00 0.0 0.00 4.30 F
1842 3720 0.316522 CGATGATGGATGACGAGGCT 59.683 55.0 0.00 0.0 0.00 4.58 F
2723 4604 0.746659 AGGTGCAACAACTCAAAGCC 59.253 50.0 3.64 0.0 39.98 4.35 F
3000 4881 0.389948 AGCGACATTTGGACTCGGAC 60.390 55.0 0.00 0.0 0.00 4.79 F
3180 5061 2.890808 TGGATAAGATGAGTGGCGAC 57.109 50.0 0.00 0.0 0.00 5.19 F
4293 6200 0.250467 TTGCAGCACCAAGGAGAGAC 60.250 55.0 0.00 0.0 0.00 3.36 F
5173 7080 5.278022 GCACTGAAGGGAACAAAGTAAGAAG 60.278 44.0 0.00 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 3855 0.253044 CCTCGGCTTCCTCCAAATCA 59.747 55.000 0.0 0.00 0.00 2.57 R
2442 4323 0.388659 CCTCCTCTTCTGGCTCATCG 59.611 60.000 0.0 0.00 0.00 3.84 R
3000 4881 0.390860 CCGAACTGGATGGGCTAGAG 59.609 60.000 0.0 0.00 42.00 2.43 R
3705 5592 2.205074 CGATGGTCAGCCTCACATTAC 58.795 52.381 0.0 0.00 35.27 1.89 R
4028 5916 3.330701 ACAGAGATTGTTGAAGGGGCTAA 59.669 43.478 0.0 0.00 36.31 3.09 R
5173 7080 3.447944 ACCAGGGTTCTCGAGAAGAATAC 59.552 47.826 27.7 16.15 45.57 1.89 R
5705 7612 0.729116 CGGACATGTTGATGGCAGTC 59.271 55.000 0.0 0.00 39.74 3.51 R
7072 8998 1.202256 CGCGTTCTGCATAGAGGTACA 60.202 52.381 0.0 0.00 46.97 2.90 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
21 22 0.402504 ACCGTCTTAATTGCCCCACA 59.597 50.000 0.00 0.00 0.00 4.17
31 32 7.821846 GTCTTAATTGCCCCACATTTTATTGAA 59.178 33.333 0.00 0.00 0.00 2.69
106 107 4.899352 AGATCCTAGAATTCATTCGGGG 57.101 45.455 8.44 9.59 41.56 5.73
120 121 5.815581 TCATTCGGGGAGATAAATAATGGG 58.184 41.667 0.00 0.00 0.00 4.00
121 122 5.312178 TCATTCGGGGAGATAAATAATGGGT 59.688 40.000 0.00 0.00 0.00 4.51
122 123 6.502510 TCATTCGGGGAGATAAATAATGGGTA 59.497 38.462 0.00 0.00 0.00 3.69
123 124 5.750352 TCGGGGAGATAAATAATGGGTAC 57.250 43.478 0.00 0.00 0.00 3.34
124 125 5.408824 TCGGGGAGATAAATAATGGGTACT 58.591 41.667 0.00 0.00 0.00 2.73
125 126 5.482878 TCGGGGAGATAAATAATGGGTACTC 59.517 44.000 0.00 0.00 0.00 2.59
126 127 5.338137 CGGGGAGATAAATAATGGGTACTCC 60.338 48.000 0.00 0.00 41.01 3.85
148 149 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
149 150 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
150 151 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
151 152 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
152 153 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
202 203 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
263 264 8.267620 TCTCATTAATATGGGCATGTAAATCG 57.732 34.615 0.00 0.00 31.92 3.34
270 271 1.539496 GGGCATGTAAATCGCGGACTA 60.539 52.381 6.13 0.00 0.00 2.59
316 1927 6.637657 TGTTGCAATGCATGGACAATTATTA 58.362 32.000 9.39 0.00 38.76 0.98
352 2196 5.528043 AAATGTGCAGTGGTTATTGTCAA 57.472 34.783 0.00 0.00 0.00 3.18
365 2209 9.414295 GTGGTTATTGTCAATTTTAACCTAACC 57.586 33.333 21.38 17.17 42.57 2.85
424 2296 6.034591 CCGTCGTCAGTCAGTAGATTTAATT 58.965 40.000 0.00 0.00 0.00 1.40
460 2332 1.279846 TCGGGAAAGCCGGTAAAAGAT 59.720 47.619 1.90 0.00 36.04 2.40
461 2333 2.089201 CGGGAAAGCCGGTAAAAGATT 58.911 47.619 1.90 0.00 33.83 2.40
496 2368 3.610911 CCAGCTCGAAAGGGAGTAAATT 58.389 45.455 0.00 0.00 36.41 1.82
589 2461 4.606071 CGAAAGGCTGAGTGAGGG 57.394 61.111 0.00 0.00 0.00 4.30
590 2462 1.078848 CGAAAGGCTGAGTGAGGGG 60.079 63.158 0.00 0.00 0.00 4.79
591 2463 1.544825 CGAAAGGCTGAGTGAGGGGA 61.545 60.000 0.00 0.00 0.00 4.81
592 2464 0.035915 GAAAGGCTGAGTGAGGGGAC 60.036 60.000 0.00 0.00 0.00 4.46
593 2465 1.831652 AAAGGCTGAGTGAGGGGACG 61.832 60.000 0.00 0.00 0.00 4.79
636 2508 3.526430 CGGGATTCGCTCCAGAGA 58.474 61.111 0.00 0.00 46.98 3.10
653 2525 3.056832 AGAGAGGAAACCCCAGAAAAGT 58.943 45.455 0.00 0.00 37.41 2.66
664 2536 0.232303 CAGAAAAGTGGCGACGACAC 59.768 55.000 26.43 26.43 42.83 3.67
715 2587 4.924187 CCGATCCGGCCTCCTCCT 62.924 72.222 0.00 0.00 41.17 3.69
717 2589 3.299190 GATCCGGCCTCCTCCTCG 61.299 72.222 0.00 0.00 0.00 4.63
718 2590 4.924187 ATCCGGCCTCCTCCTCGG 62.924 72.222 0.00 0.00 43.42 4.63
723 2595 2.835895 GCCTCCTCCTCGGACTCC 60.836 72.222 0.00 0.00 36.69 3.85
794 2666 3.637273 GACCACAGAACCCCCGCT 61.637 66.667 0.00 0.00 0.00 5.52
880 2753 0.394625 GAGCGTCAGGGAGTAGGAGT 60.395 60.000 0.00 0.00 0.00 3.85
883 2756 1.970092 CGTCAGGGAGTAGGAGTAGG 58.030 60.000 0.00 0.00 0.00 3.18
886 2759 2.510800 GTCAGGGAGTAGGAGTAGGAGT 59.489 54.545 0.00 0.00 0.00 3.85
891 2764 4.907269 AGGGAGTAGGAGTAGGAGTAGTAC 59.093 50.000 0.00 0.00 0.00 2.73
975 2848 0.456995 CGGAAACAGACTCGCTCTCC 60.457 60.000 0.00 0.00 0.00 3.71
976 2849 0.108567 GGAAACAGACTCGCTCTCCC 60.109 60.000 0.00 0.00 0.00 4.30
980 2853 2.124693 CAGACTCGCTCTCCCCTCC 61.125 68.421 0.00 0.00 0.00 4.30
1168 3046 3.780173 GCAGGCGCTCTTCCTCCT 61.780 66.667 7.64 0.00 34.30 3.69
1169 3047 2.498726 CAGGCGCTCTTCCTCCTC 59.501 66.667 7.64 0.00 0.00 3.71
1170 3048 2.762043 AGGCGCTCTTCCTCCTCC 60.762 66.667 7.64 0.00 0.00 4.30
1245 3123 2.203167 CGGACCCGATCGAGGAGA 60.203 66.667 23.89 0.00 42.83 3.71
1493 3371 2.357517 GGGCGATGGCTATGACGG 60.358 66.667 0.00 0.00 39.81 4.79
1495 3373 3.406361 GCGATGGCTATGACGGCG 61.406 66.667 4.80 4.80 35.83 6.46
1497 3375 2.421739 GATGGCTATGACGGCGGT 59.578 61.111 13.24 0.00 0.00 5.68
1499 3377 3.460672 ATGGCTATGACGGCGGTGG 62.461 63.158 13.24 0.00 0.00 4.61
1664 3542 2.761559 TGGTTCGAATTCGTGTCATGT 58.238 42.857 25.93 0.00 40.80 3.21
1674 3552 5.729974 ATTCGTGTCATGTGATGAATGAG 57.270 39.130 11.16 0.00 41.69 2.90
1675 3553 3.524541 TCGTGTCATGTGATGAATGAGG 58.475 45.455 0.00 0.00 41.69 3.86
1676 3554 3.055891 TCGTGTCATGTGATGAATGAGGT 60.056 43.478 0.00 0.00 41.69 3.85
1719 3597 3.157680 CTGAAAGGTCGTGGGGGT 58.842 61.111 0.00 0.00 0.00 4.95
1776 3654 3.603532 TGAGGAGCACATGAATGAAGAC 58.396 45.455 0.00 0.00 0.00 3.01
1780 3658 4.100035 AGGAGCACATGAATGAAGACGATA 59.900 41.667 0.00 0.00 0.00 2.92
1781 3659 4.210120 GGAGCACATGAATGAAGACGATAC 59.790 45.833 0.00 0.00 0.00 2.24
1782 3660 4.758688 AGCACATGAATGAAGACGATACA 58.241 39.130 0.00 0.00 0.00 2.29
1815 3693 3.883744 AAACAGGGAGCTGCCGACG 62.884 63.158 19.62 13.80 37.63 5.12
1832 3710 2.031012 GGCGGATGCGATGATGGA 59.969 61.111 12.10 0.00 44.10 3.41
1842 3720 0.316522 CGATGATGGATGACGAGGCT 59.683 55.000 0.00 0.00 0.00 4.58
1926 3804 2.366590 TGCAGATCTGATCCGTGCTTAT 59.633 45.455 27.04 0.93 33.20 1.73
1977 3855 3.996614 GCTTACGGCAATGGTGGT 58.003 55.556 0.00 0.00 41.35 4.16
1981 3859 2.091541 CTTACGGCAATGGTGGTGATT 58.908 47.619 0.00 0.00 0.00 2.57
2036 3914 5.370679 TGATGATGGTGATGATGACGATTT 58.629 37.500 0.00 0.00 0.00 2.17
2099 3977 1.153168 ACGATGCTAAGGCGCCAAT 60.153 52.632 31.54 19.88 42.25 3.16
2199 4080 5.368230 GGAGGAGGAGGAAGAAGATGTTATT 59.632 44.000 0.00 0.00 0.00 1.40
2277 4158 9.716531 AGATCGCATATAGAAATTCTTGATTCA 57.283 29.630 0.00 0.00 0.00 2.57
2442 4323 3.071479 TGCGTATTTTGAGGAGTTGTCC 58.929 45.455 0.00 0.00 44.33 4.02
2559 4440 3.046968 GTGGAACTGGAAGAAGAGGAC 57.953 52.381 0.00 0.00 37.43 3.85
2646 4527 3.926058 TCTTCGGCTAAAATAAGGGCT 57.074 42.857 0.00 0.00 0.00 5.19
2687 4568 7.834881 ATACGAATACAGGGAAGAGAATACA 57.165 36.000 0.00 0.00 0.00 2.29
2701 4582 4.280929 AGAGAATACAAAAAGCAACCCCAC 59.719 41.667 0.00 0.00 0.00 4.61
2706 4587 0.829990 AAAAAGCAACCCCACACAGG 59.170 50.000 0.00 0.00 37.03 4.00
2723 4604 0.746659 AGGTGCAACAACTCAAAGCC 59.253 50.000 3.64 0.00 39.98 4.35
2748 4629 2.509964 GAGGAGGATACAAACCCACCAT 59.490 50.000 0.00 0.00 41.41 3.55
2811 4692 2.158475 AGCAGATGGTTTCAAGTGGGAA 60.158 45.455 0.00 0.00 0.00 3.97
2814 4695 3.503748 CAGATGGTTTCAAGTGGGAAGTC 59.496 47.826 0.00 0.00 0.00 3.01
2815 4696 1.961793 TGGTTTCAAGTGGGAAGTCG 58.038 50.000 0.00 0.00 0.00 4.18
2985 4866 2.032377 GGAACGTCAATTGTTTGAGCGA 60.032 45.455 5.13 0.00 42.41 4.93
3000 4881 0.389948 AGCGACATTTGGACTCGGAC 60.390 55.000 0.00 0.00 0.00 4.79
3056 4937 2.984562 TGGCGATGATAGCAAAACTGA 58.015 42.857 0.00 0.00 36.08 3.41
3059 4940 3.247173 GGCGATGATAGCAAAACTGAGAG 59.753 47.826 0.00 0.00 36.08 3.20
3076 4957 3.828451 TGAGAGGGAAAAGAAGCATTTGG 59.172 43.478 0.00 0.00 0.00 3.28
3180 5061 2.890808 TGGATAAGATGAGTGGCGAC 57.109 50.000 0.00 0.00 0.00 5.19
3449 5330 6.018098 GCAGATCCATGACTGTTATTCTTCTG 60.018 42.308 13.11 9.31 36.62 3.02
3491 5372 7.410174 TGATTTGATTATGTTAACCAGTCCCT 58.590 34.615 2.48 0.00 0.00 4.20
3492 5373 7.893302 TGATTTGATTATGTTAACCAGTCCCTT 59.107 33.333 2.48 0.00 0.00 3.95
3493 5374 9.403583 GATTTGATTATGTTAACCAGTCCCTTA 57.596 33.333 2.48 0.00 0.00 2.69
3639 5525 7.102346 ACATGATTAACTTCAGAAGACTCAGG 58.898 38.462 17.56 15.10 0.00 3.86
3705 5592 7.862372 TGATCAAGAAAGAAAAAGGATTTCACG 59.138 33.333 0.00 0.00 37.28 4.35
3941 5829 5.625150 CCCCCTACTCTAGAAAATCCATTG 58.375 45.833 0.00 0.00 0.00 2.82
3950 5838 9.601217 ACTCTAGAAAATCCATTGTGTGTATAC 57.399 33.333 0.00 0.00 0.00 1.47
3951 5839 8.958119 TCTAGAAAATCCATTGTGTGTATACC 57.042 34.615 0.00 0.00 0.00 2.73
3952 5840 7.990886 TCTAGAAAATCCATTGTGTGTATACCC 59.009 37.037 0.00 0.00 0.00 3.69
3953 5841 6.731467 AGAAAATCCATTGTGTGTATACCCT 58.269 36.000 0.00 0.00 0.00 4.34
3954 5842 7.182060 AGAAAATCCATTGTGTGTATACCCTT 58.818 34.615 0.00 0.00 0.00 3.95
3955 5843 8.333235 AGAAAATCCATTGTGTGTATACCCTTA 58.667 33.333 0.00 0.00 0.00 2.69
3956 5844 8.887264 AAAATCCATTGTGTGTATACCCTTAA 57.113 30.769 0.00 0.00 0.00 1.85
3957 5845 9.487442 AAAATCCATTGTGTGTATACCCTTAAT 57.513 29.630 0.00 0.00 0.00 1.40
3958 5846 8.463930 AATCCATTGTGTGTATACCCTTAATG 57.536 34.615 0.00 6.70 0.00 1.90
3959 5847 6.964464 TCCATTGTGTGTATACCCTTAATGT 58.036 36.000 0.00 0.00 0.00 2.71
3960 5848 7.406916 TCCATTGTGTGTATACCCTTAATGTT 58.593 34.615 0.00 0.00 0.00 2.71
3961 5849 7.338196 TCCATTGTGTGTATACCCTTAATGTTG 59.662 37.037 0.00 0.00 0.00 3.33
4028 5916 2.296945 TTTGCCCCCTCAACACTGCT 62.297 55.000 0.00 0.00 0.00 4.24
4162 6050 8.650143 ATTTTACACTGGAAATGTTACATCCT 57.350 30.769 0.00 0.00 34.24 3.24
4293 6200 0.250467 TTGCAGCACCAAGGAGAGAC 60.250 55.000 0.00 0.00 0.00 3.36
4511 6418 7.387643 AGGTAAGTTTCATCAGTTAACTCCTC 58.612 38.462 4.77 0.00 31.26 3.71
4533 6440 6.881065 CCTCTCATTTCAGGTCTCAAATTACA 59.119 38.462 0.00 0.00 0.00 2.41
5173 7080 5.278022 GCACTGAAGGGAACAAAGTAAGAAG 60.278 44.000 0.00 0.00 0.00 2.85
5381 7288 6.035975 GGTTTGGTGAAATGTTTTTGACTGAG 59.964 38.462 0.00 0.00 30.67 3.35
5504 7411 7.551035 AACTGATGATAATGCAGAGAAAGTC 57.449 36.000 0.00 0.00 33.94 3.01
5505 7412 6.647229 ACTGATGATAATGCAGAGAAAGTCA 58.353 36.000 0.00 0.00 33.94 3.41
5705 7612 3.303881 TCGACACATCCTTCTCTTGTG 57.696 47.619 1.02 1.02 44.85 3.33
5877 7784 8.677300 TGATCTTTAGTCAATTTATTCAGCCAC 58.323 33.333 0.00 0.00 0.00 5.01
5972 7879 2.440539 AGATCCAACCACGATATCGC 57.559 50.000 24.59 5.32 44.43 4.58
6218 8125 5.958380 AGGTGAAGGTGACAAGTATGATAGA 59.042 40.000 0.00 0.00 0.00 1.98
6326 8233 7.334421 GCTGAAATGGATCACTGTTCTAAGTTA 59.666 37.037 0.00 0.00 0.00 2.24
6449 8356 1.272480 ACTTACAACCAGATTGCCCCC 60.272 52.381 0.00 0.00 42.62 5.40
6753 8660 9.884465 GACTTGGAAACTGTATTATGATAATGC 57.116 33.333 7.91 7.10 0.00 3.56
6841 8763 4.943705 GCATCTTACAAGAGGAAATGGACA 59.056 41.667 7.76 0.00 39.04 4.02
6845 8767 9.347240 CATCTTACAAGAGGAAATGGACATATT 57.653 33.333 0.00 0.00 39.04 1.28
7062 8988 2.783135 TGTTTTCATGGTCAGAGGCTC 58.217 47.619 6.34 6.34 0.00 4.70
7072 8998 3.238597 GGTCAGAGGCTCCTAGATCATT 58.761 50.000 11.71 0.00 0.00 2.57
7139 9065 8.194104 TCATATTGCTTTGTGTTAACACTTGTT 58.806 29.630 32.58 16.65 46.55 2.83
7205 9131 2.124507 TTAGTGGCTGGCCTTCGCTT 62.125 55.000 13.05 0.00 36.94 4.68
7276 9202 6.183360 CGTAAGTACCCCTTCAGCTACTATTT 60.183 42.308 0.00 0.00 34.46 1.40
7350 9276 7.827819 TTTACTTCGTCCAATGTCTTCTATG 57.172 36.000 0.00 0.00 0.00 2.23
7371 9297 0.818040 ACCGAGCTTTGTTGGTCCAC 60.818 55.000 0.00 0.00 0.00 4.02
7441 9367 4.273724 GCTAATAAACCTGCTTCACTAGGC 59.726 45.833 0.00 0.00 37.61 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.487822 TCAATAAAATGTGGGGCAATTAAGA 57.512 32.000 0.00 0.00 0.00 2.10
12 13 6.112058 GCTAATTCAATAAAATGTGGGGCAA 58.888 36.000 0.00 0.00 0.00 4.52
59 60 6.952773 TTTGGTAAGCATTTAGTGTCTTGT 57.047 33.333 0.00 0.00 0.00 3.16
102 103 5.338137 GGAGTACCCATTATTTATCTCCCCG 60.338 48.000 0.00 0.00 35.56 5.73
122 123 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
123 124 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
124 125 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
125 126 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
126 127 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
176 177 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
178 179 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
184 185 9.900112 AATCCTACTCCCTCTGTAAACTAATAT 57.100 33.333 0.00 0.00 0.00 1.28
185 186 9.725206 AAATCCTACTCCCTCTGTAAACTAATA 57.275 33.333 0.00 0.00 0.00 0.98
186 187 8.625467 AAATCCTACTCCCTCTGTAAACTAAT 57.375 34.615 0.00 0.00 0.00 1.73
187 188 8.445361 AAAATCCTACTCCCTCTGTAAACTAA 57.555 34.615 0.00 0.00 0.00 2.24
188 189 9.725206 ATAAAATCCTACTCCCTCTGTAAACTA 57.275 33.333 0.00 0.00 0.00 2.24
189 190 6.954352 AAAATCCTACTCCCTCTGTAAACT 57.046 37.500 0.00 0.00 0.00 2.66
190 191 9.682465 AAATAAAATCCTACTCCCTCTGTAAAC 57.318 33.333 0.00 0.00 0.00 2.01
191 192 9.681062 CAAATAAAATCCTACTCCCTCTGTAAA 57.319 33.333 0.00 0.00 0.00 2.01
192 193 8.272173 CCAAATAAAATCCTACTCCCTCTGTAA 58.728 37.037 0.00 0.00 0.00 2.41
193 194 7.404980 ACCAAATAAAATCCTACTCCCTCTGTA 59.595 37.037 0.00 0.00 0.00 2.74
194 195 6.217693 ACCAAATAAAATCCTACTCCCTCTGT 59.782 38.462 0.00 0.00 0.00 3.41
195 196 6.663734 ACCAAATAAAATCCTACTCCCTCTG 58.336 40.000 0.00 0.00 0.00 3.35
196 197 6.910259 ACCAAATAAAATCCTACTCCCTCT 57.090 37.500 0.00 0.00 0.00 3.69
197 198 8.900781 GTTTACCAAATAAAATCCTACTCCCTC 58.099 37.037 0.00 0.00 34.50 4.30
198 199 8.395605 TGTTTACCAAATAAAATCCTACTCCCT 58.604 33.333 0.00 0.00 34.50 4.20
199 200 8.464404 GTGTTTACCAAATAAAATCCTACTCCC 58.536 37.037 0.00 0.00 34.50 4.30
200 201 9.239551 AGTGTTTACCAAATAAAATCCTACTCC 57.760 33.333 0.00 0.00 34.50 3.85
241 242 5.738693 CGCGATTTACATGCCCATATTAATG 59.261 40.000 0.00 0.00 0.00 1.90
328 1939 5.911752 TGACAATAACCACTGCACATTTTT 58.088 33.333 0.00 0.00 0.00 1.94
347 2191 5.475564 GGAGCAGGTTAGGTTAAAATTGACA 59.524 40.000 0.00 0.00 0.00 3.58
349 2193 5.636123 TGGAGCAGGTTAGGTTAAAATTGA 58.364 37.500 0.00 0.00 0.00 2.57
352 2196 5.201243 GGATGGAGCAGGTTAGGTTAAAAT 58.799 41.667 0.00 0.00 0.00 1.82
365 2209 3.664025 TTCGCCGTGGATGGAGCAG 62.664 63.158 0.00 0.00 0.00 4.24
400 2245 3.489180 AAATCTACTGACTGACGACGG 57.511 47.619 0.00 0.00 0.00 4.79
401 2246 8.610855 TTAATTAAATCTACTGACTGACGACG 57.389 34.615 0.00 0.00 0.00 5.12
403 2248 9.031360 GCATTAATTAAATCTACTGACTGACGA 57.969 33.333 1.21 0.00 0.00 4.20
409 2281 5.560378 GCGCGCATTAATTAAATCTACTGAC 59.440 40.000 29.10 0.00 0.00 3.51
460 2332 3.415212 GAGCTGGCTATATTCATGGCAA 58.585 45.455 0.00 0.00 40.26 4.52
461 2333 2.613725 CGAGCTGGCTATATTCATGGCA 60.614 50.000 0.00 0.00 40.26 4.92
496 2368 1.125093 TTCCTTCGTTCTGGCCCTGA 61.125 55.000 0.00 0.00 0.00 3.86
582 2454 1.972223 CGTCACTCGTCCCCTCACT 60.972 63.158 0.00 0.00 34.52 3.41
583 2455 2.567049 CGTCACTCGTCCCCTCAC 59.433 66.667 0.00 0.00 34.52 3.51
584 2456 2.675423 CCGTCACTCGTCCCCTCA 60.675 66.667 0.00 0.00 37.94 3.86
585 2457 2.675772 ACCGTCACTCGTCCCCTC 60.676 66.667 0.00 0.00 37.94 4.30
586 2458 2.989824 CACCGTCACTCGTCCCCT 60.990 66.667 0.00 0.00 37.94 4.79
587 2459 4.065281 CCACCGTCACTCGTCCCC 62.065 72.222 0.00 0.00 37.94 4.81
588 2460 4.736896 GCCACCGTCACTCGTCCC 62.737 72.222 0.00 0.00 37.94 4.46
589 2461 3.986006 TGCCACCGTCACTCGTCC 61.986 66.667 0.00 0.00 37.94 4.79
590 2462 2.733593 GTGCCACCGTCACTCGTC 60.734 66.667 0.00 0.00 37.94 4.20
591 2463 3.499929 CTGTGCCACCGTCACTCGT 62.500 63.158 0.00 0.00 37.94 4.18
592 2464 2.693250 TTCTGTGCCACCGTCACTCG 62.693 60.000 0.00 0.00 35.58 4.18
593 2465 1.069090 TTCTGTGCCACCGTCACTC 59.931 57.895 0.00 0.00 35.58 3.51
636 2508 1.757764 GCCACTTTTCTGGGGTTTCCT 60.758 52.381 0.00 0.00 36.20 3.36
642 2514 2.325082 CGTCGCCACTTTTCTGGGG 61.325 63.158 0.00 0.00 44.00 4.96
880 2753 7.955185 AGCAGAGGTATAGTAGTACTACTCCTA 59.045 40.741 33.47 23.62 44.58 2.94
883 2756 7.599998 GTCAGCAGAGGTATAGTAGTACTACTC 59.400 44.444 33.47 21.30 44.58 2.59
886 2759 7.256261 GGAGTCAGCAGAGGTATAGTAGTACTA 60.256 44.444 12.38 12.38 34.82 1.82
891 2764 4.980573 AGGAGTCAGCAGAGGTATAGTAG 58.019 47.826 0.00 0.00 0.00 2.57
895 2768 2.786445 AGGAGGAGTCAGCAGAGGTATA 59.214 50.000 0.00 0.00 0.00 1.47
1164 3042 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1165 3043 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1166 3044 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1167 3045 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
1168 3046 2.387772 CCGAGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 45.00 3.71
1169 3047 2.197324 CCGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 45.00 4.30
1170 3048 2.520741 GCCGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 45.00 3.69
1499 3377 2.969238 CATCATCACCTCGCCGCC 60.969 66.667 0.00 0.00 0.00 6.13
1579 3457 1.719709 CGGCACTGTGATGCTCATG 59.280 57.895 12.86 0.00 45.38 3.07
1664 3542 3.779738 TGATACCACCACCTCATTCATCA 59.220 43.478 0.00 0.00 0.00 3.07
1674 3552 0.532862 CATCGCCTGATACCACCACC 60.533 60.000 0.00 0.00 32.18 4.61
1675 3553 1.160329 GCATCGCCTGATACCACCAC 61.160 60.000 0.00 0.00 32.18 4.16
1676 3554 1.146041 GCATCGCCTGATACCACCA 59.854 57.895 0.00 0.00 32.18 4.17
1719 3597 2.368594 CCTAGCCCACCTCCCTCA 59.631 66.667 0.00 0.00 0.00 3.86
1815 3693 1.376424 ATCCATCATCGCATCCGCC 60.376 57.895 0.00 0.00 33.11 6.13
1832 3710 4.074526 ACGCTGCAGCCTCGTCAT 62.075 61.111 32.07 6.85 37.91 3.06
1842 3720 0.605083 AGTCATCTTCAGACGCTGCA 59.395 50.000 0.00 0.00 40.84 4.41
1926 3804 5.044772 TGCCTCCAAATTACCACCATTACTA 60.045 40.000 0.00 0.00 0.00 1.82
1969 3847 3.434309 CTTCCTCCAAATCACCACCATT 58.566 45.455 0.00 0.00 0.00 3.16
1977 3855 0.253044 CCTCGGCTTCCTCCAAATCA 59.747 55.000 0.00 0.00 0.00 2.57
1981 3859 0.617535 TCATCCTCGGCTTCCTCCAA 60.618 55.000 0.00 0.00 0.00 3.53
2099 3977 1.570813 CGCCTTAGCATCATCGTTGA 58.429 50.000 0.00 0.00 39.83 3.18
2199 4080 3.961408 GCTTAGTCTCCACCTCATCCTTA 59.039 47.826 0.00 0.00 0.00 2.69
2277 4158 3.321111 TGAGCACTTTTACTTCCTCGTCT 59.679 43.478 0.00 0.00 0.00 4.18
2442 4323 0.388659 CCTCCTCTTCTGGCTCATCG 59.611 60.000 0.00 0.00 0.00 3.84
2667 4548 8.184848 GCTTTTTGTATTCTCTTCCCTGTATTC 58.815 37.037 0.00 0.00 0.00 1.75
2687 4568 0.829990 CCTGTGTGGGGTTGCTTTTT 59.170 50.000 0.00 0.00 0.00 1.94
2701 4582 2.801063 CTTTGAGTTGTTGCACCTGTG 58.199 47.619 0.00 0.00 0.00 3.66
2706 4587 1.559831 GTGGCTTTGAGTTGTTGCAC 58.440 50.000 0.00 0.00 0.00 4.57
2723 4604 1.134491 GGGTTTGTATCCTCCTCCGTG 60.134 57.143 0.00 0.00 0.00 4.94
2985 4866 2.166664 GCTAGAGTCCGAGTCCAAATGT 59.833 50.000 0.00 0.00 0.00 2.71
3000 4881 0.390860 CCGAACTGGATGGGCTAGAG 59.609 60.000 0.00 0.00 42.00 2.43
3056 4937 2.564504 GCCAAATGCTTCTTTTCCCTCT 59.435 45.455 0.00 0.00 36.87 3.69
3059 4940 2.837532 TGCCAAATGCTTCTTTTCCC 57.162 45.000 0.00 0.00 42.00 3.97
3076 4957 4.569564 GGCAGATTTTCCAGATTTTGATGC 59.430 41.667 0.00 0.00 0.00 3.91
3449 5330 6.801575 TCAAATCAACACCACTAAGGAAAAC 58.198 36.000 0.00 0.00 41.22 2.43
3639 5525 2.297701 TGTTCCTCAAACTGGTCAAGC 58.702 47.619 0.00 0.00 38.76 4.01
3705 5592 2.205074 CGATGGTCAGCCTCACATTAC 58.795 52.381 0.00 0.00 35.27 1.89
4028 5916 3.330701 ACAGAGATTGTTGAAGGGGCTAA 59.669 43.478 0.00 0.00 36.31 3.09
4147 6035 6.261826 CAGATTCTCCAGGATGTAACATTTCC 59.738 42.308 0.00 0.00 0.00 3.13
4162 6050 6.187727 AGTTAAAGTTGACCAGATTCTCCA 57.812 37.500 0.00 0.00 0.00 3.86
4203 6091 6.474102 CGACAAGTAGAAATTCTAGGAGAAGC 59.526 42.308 2.48 0.00 37.69 3.86
4293 6200 4.148128 AGTCCAAGATCTAGCACATTGG 57.852 45.455 0.00 0.00 41.45 3.16
4511 6418 7.388776 TCTGTGTAATTTGAGACCTGAAATGAG 59.611 37.037 0.00 0.00 0.00 2.90
5173 7080 3.447944 ACCAGGGTTCTCGAGAAGAATAC 59.552 47.826 27.70 16.15 45.57 1.89
5504 7411 6.446781 ACAAATGGCTTCAGTATTGATCTG 57.553 37.500 0.00 0.00 32.27 2.90
5505 7412 6.660521 TGAACAAATGGCTTCAGTATTGATCT 59.339 34.615 0.00 0.00 32.27 2.75
5660 7567 9.617975 GAAGCTAAGGAAATAACATATTCATGC 57.382 33.333 0.00 0.00 35.39 4.06
5705 7612 0.729116 CGGACATGTTGATGGCAGTC 59.271 55.000 0.00 0.00 39.74 3.51
6218 8125 3.706086 ACAAATGGTCCTTTTCTGCTTGT 59.294 39.130 0.00 0.00 0.00 3.16
6326 8233 9.676129 TCCTCCAGAACTTTATCCTTAGATATT 57.324 33.333 0.00 0.00 34.91 1.28
6333 8240 5.966935 TCATCTCCTCCAGAACTTTATCCTT 59.033 40.000 0.00 0.00 33.62 3.36
6341 8248 2.745968 GAGGTCATCTCCTCCAGAACT 58.254 52.381 1.70 0.00 45.84 3.01
6449 8356 6.542852 CCAATGTTACCATTAACTCAACTCG 58.457 40.000 0.00 0.00 39.28 4.18
6744 8651 7.246311 GCTCTTTTATATGCACGCATTATCAT 58.754 34.615 10.23 0.11 37.82 2.45
6753 8660 4.882671 AGTTGGCTCTTTTATATGCACG 57.117 40.909 0.00 0.00 0.00 5.34
6794 8713 6.628844 GCAGAGCCAAACTAAAATTCCATGAT 60.629 38.462 0.00 0.00 0.00 2.45
6804 8723 5.312895 TGTAAGATGCAGAGCCAAACTAAA 58.687 37.500 0.00 0.00 0.00 1.85
6853 8775 5.657826 TTTTCAGGCTTATAGCATTGCAA 57.342 34.783 11.91 0.00 44.75 4.08
6980 8906 3.883830 AAATGACTCGATGAGCAGACT 57.116 42.857 0.00 0.00 32.04 3.24
7062 8988 6.435591 TCTGCATAGAGGTACAATGATCTAGG 59.564 42.308 0.00 0.00 0.00 3.02
7072 8998 1.202256 CGCGTTCTGCATAGAGGTACA 60.202 52.381 0.00 0.00 46.97 2.90
7139 9065 5.086621 TGCTGCAGATATCTCCCTATGTAA 58.913 41.667 20.43 0.00 0.00 2.41
7205 9131 3.244735 TGCCACCATACTTGAGTTAGCAA 60.245 43.478 0.00 0.00 0.00 3.91
7338 9264 3.034635 AGCTCGGTCCATAGAAGACATT 58.965 45.455 0.00 0.00 35.89 2.71
7350 9276 2.244946 GACCAACAAAGCTCGGTCC 58.755 57.895 7.60 0.00 41.77 4.46
7371 9297 3.516981 AGTCAGTCATCACCATTCTCG 57.483 47.619 0.00 0.00 0.00 4.04
7383 9309 9.574516 TGTTGAGCTTATATATCTAGTCAGTCA 57.425 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.