Multiple sequence alignment - TraesCS1B01G439500

Loading Multiple Alignment...

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 TraesCS1B01G439500 chr1B 100.000 3729 0 0 1 3729 661137040 661133312 0.000000e+00 6887.0
1 TraesCS1B01G439500 chr1B 85.590 229 27 6 40 266 286758824 286758600 6.230000e-58 235.0
2 TraesCS1B01G439500 chr1B 82.969 229 30 8 40 266 38111104 38110883 8.170000e-47 198.0
3 TraesCS1B01G439500 chr1D 97.789 2849 50 7 446 3289 475238458 475235618 0.000000e+00 4900.0
4 TraesCS1B01G439500 chr1D 94.222 1696 75 9 1086 2758 475280542 475278847 0.000000e+00 2567.0
5 TraesCS1B01G439500 chr1D 96.206 1397 27 15 2339 3729 475232033 475230657 0.000000e+00 2263.0
6 TraesCS1B01G439500 chr1D 97.614 1006 17 5 2339 3339 475233047 475232044 0.000000e+00 1718.0
7 TraesCS1B01G439500 chr1D 95.686 904 24 8 2760 3656 475272530 475271635 0.000000e+00 1439.0
8 TraesCS1B01G439500 chr1D 80.910 1341 210 25 1094 2429 474235533 474234234 0.000000e+00 1016.0
9 TraesCS1B01G439500 chr1D 95.572 271 11 1 150 419 475238806 475238536 2.060000e-117 433.0
10 TraesCS1B01G439500 chr1D 95.455 154 7 0 1 154 475239227 475239074 2.880000e-61 246.0
11 TraesCS1B01G439500 chr1D 86.636 217 12 4 446 662 475281060 475280861 1.350000e-54 224.0
12 TraesCS1B01G439500 chr1D 97.959 49 1 0 3291 3339 475233106 475233058 6.640000e-13 86.1
13 TraesCS1B01G439500 chr1A 92.901 1479 81 13 954 2421 570924266 570922801 0.000000e+00 2128.0
14 TraesCS1B01G439500 chr1A 98.596 926 11 1 2416 3339 570922547 570921622 0.000000e+00 1637.0
15 TraesCS1B01G439500 chr1A 96.703 364 11 1 3350 3713 570918797 570918435 4.120000e-169 604.0
16 TraesCS1B01G439500 chr1A 89.706 136 9 3 528 662 570924724 570924593 6.410000e-38 169.0
17 TraesCS1B01G439500 chrUn 80.824 1335 210 24 1094 2423 150139521 150140814 0.000000e+00 1005.0
18 TraesCS1B01G439500 chrUn 80.761 1341 212 25 1094 2429 172388597 172387298 0.000000e+00 1005.0
19 TraesCS1B01G439500 chrUn 80.824 1335 210 24 1094 2423 321412219 321413512 0.000000e+00 1005.0
20 TraesCS1B01G439500 chrUn 80.537 1341 215 25 1094 2429 172395704 172394405 0.000000e+00 989.0
21 TraesCS1B01G439500 chrUn 83.633 611 89 7 1094 1703 366677305 366676705 6.990000e-157 564.0
22 TraesCS1B01G439500 chr7A 96.053 76 3 0 3654 3729 715238943 715238868 1.410000e-24 124.0
23 TraesCS1B01G439500 chr4B 78.281 221 29 14 47 266 120511968 120511766 1.410000e-24 124.0
24 TraesCS1B01G439500 chr3A 94.737 76 4 0 3654 3729 715980979 715980904 6.540000e-23 119.0
25 TraesCS1B01G439500 chr3B 90.789 76 7 0 3654 3729 787966852 787966777 6.590000e-18 102.0
26 TraesCS1B01G439500 chr6B 94.118 51 3 0 3399 3449 326967437 326967487 1.110000e-10 78.7
27 TraesCS1B01G439500 chr2B 100.000 28 0 0 1060 1087 712074092 712074065 7.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G439500 chr1B 661133312 661137040 3728 True 6887.000000 6887 100.000000 1 3729 1 chr1B.!!$R3 3728
1 TraesCS1B01G439500 chr1D 475230657 475239227 8570 True 1607.683333 4900 96.765833 1 3729 6 chr1D.!!$R3 3728
2 TraesCS1B01G439500 chr1D 475271635 475272530 895 True 1439.000000 1439 95.686000 2760 3656 1 chr1D.!!$R2 896
3 TraesCS1B01G439500 chr1D 475278847 475281060 2213 True 1395.500000 2567 90.429000 446 2758 2 chr1D.!!$R4 2312
4 TraesCS1B01G439500 chr1D 474234234 474235533 1299 True 1016.000000 1016 80.910000 1094 2429 1 chr1D.!!$R1 1335
5 TraesCS1B01G439500 chr1A 570918435 570924724 6289 True 1134.500000 2128 94.476500 528 3713 4 chr1A.!!$R1 3185
6 TraesCS1B01G439500 chrUn 150139521 150140814 1293 False 1005.000000 1005 80.824000 1094 2423 1 chrUn.!!$F1 1329
7 TraesCS1B01G439500 chrUn 172387298 172388597 1299 True 1005.000000 1005 80.761000 1094 2429 1 chrUn.!!$R1 1335
8 TraesCS1B01G439500 chrUn 321412219 321413512 1293 False 1005.000000 1005 80.824000 1094 2423 1 chrUn.!!$F2 1329
9 TraesCS1B01G439500 chrUn 172394405 172395704 1299 True 989.000000 989 80.537000 1094 2429 1 chrUn.!!$R2 1335
10 TraesCS1B01G439500 chrUn 366676705 366677305 600 True 564.000000 564 83.633000 1094 1703 1 chrUn.!!$R3 609

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
794 1142 0.759436 GCCCAACCCTCGATCTAGGA 60.759 60.000 14.78 0.0 39.15 2.94 F
803 1151 1.205568 CGATCTAGGACTCGAGCGC 59.794 63.158 13.61 0.0 37.05 5.92 F
1677 2135 2.041115 GGAGAGGCCCTTTGTTCGC 61.041 63.158 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2580 0.105964 TCTGGACCTTTCACGGTGTG 59.894 55.000 8.17 0.3 37.42 3.82 R
2250 2735 0.460311 ATCCTTGTCGTGATCCGTCC 59.540 55.000 3.97 0.0 37.94 4.79 R
2777 8066 2.816087 CAAGTTCAAGCAGCCAGTACAT 59.184 45.455 0.00 0.0 0.00 2.29 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
24 25 3.473625 TCAGACCATCATCATGTGCATC 58.526 45.455 0.00 0.00 0.00 3.91
41 42 4.899239 CCATGCCTCGTCCTCCGC 62.899 72.222 0.00 0.00 36.19 5.54
59 60 3.097137 CTGCAGCAGCTGATGACGC 62.097 63.158 34.79 20.25 41.71 5.19
94 95 3.234353 ACCAATATCCTCGCTGATCTCA 58.766 45.455 0.00 0.00 0.00 3.27
134 135 4.363990 CGTCCTGCGTCTGTGGCT 62.364 66.667 0.00 0.00 35.54 4.75
159 432 1.075226 AGCGAGGATAAGGGGCAGA 60.075 57.895 0.00 0.00 0.00 4.26
175 448 2.574212 GAGTGCGGCGCGATTTTG 60.574 61.111 28.09 0.00 0.00 2.44
187 461 1.332816 GCGATTTTGCGTGCGATGATA 60.333 47.619 0.00 0.00 0.00 2.15
243 517 5.221126 GGGGAGATGTTTGTTTCATATCTGC 60.221 44.000 0.00 0.00 34.97 4.26
300 574 2.238521 GTGGGAATGGCAGAGTTTTCA 58.761 47.619 0.00 0.00 0.00 2.69
381 655 4.929808 ACAACGGTTAGATCAAGCTTAGTG 59.070 41.667 0.00 0.00 32.23 2.74
405 679 5.620738 TCTCATAGCAAGGCTGTAATTCT 57.379 39.130 0.07 0.00 40.10 2.40
407 681 7.124573 TCTCATAGCAAGGCTGTAATTCTTA 57.875 36.000 0.07 0.00 40.10 2.10
419 693 7.064253 AGGCTGTAATTCTTACGTGTTGTTATC 59.936 37.037 0.00 0.00 38.98 1.75
420 694 7.148540 GGCTGTAATTCTTACGTGTTGTTATCA 60.149 37.037 0.00 0.00 38.98 2.15
421 695 8.225107 GCTGTAATTCTTACGTGTTGTTATCAA 58.775 33.333 0.00 0.00 38.98 2.57
422 696 9.741168 CTGTAATTCTTACGTGTTGTTATCAAG 57.259 33.333 0.00 0.00 38.98 3.02
423 697 9.263538 TGTAATTCTTACGTGTTGTTATCAAGT 57.736 29.630 0.00 0.00 38.98 3.16
794 1142 0.759436 GCCCAACCCTCGATCTAGGA 60.759 60.000 14.78 0.00 39.15 2.94
803 1151 1.205568 CGATCTAGGACTCGAGCGC 59.794 63.158 13.61 0.00 37.05 5.92
1061 1519 3.120854 GCAGATTGATCGGTTTATCGCTC 60.121 47.826 0.00 0.00 0.00 5.03
1391 1849 5.727434 CAATGGCCTTCTCTTGCTTAAATT 58.273 37.500 3.32 0.00 0.00 1.82
1519 1977 5.582665 GTCAGGTATCTTGTGTTTGATCCTC 59.417 44.000 0.00 0.00 0.00 3.71
1520 1978 5.485353 TCAGGTATCTTGTGTTTGATCCTCT 59.515 40.000 0.00 0.00 0.00 3.69
1564 2022 4.017222 TCTTCTTGATTCCCCATGTTCCAT 60.017 41.667 0.00 0.00 0.00 3.41
1602 2060 3.305608 GCCTTTTGTCACAGGAATTGGAG 60.306 47.826 1.84 0.00 30.81 3.86
1677 2135 2.041115 GGAGAGGCCCTTTGTTCGC 61.041 63.158 0.00 0.00 0.00 4.70
1838 2299 8.803397 GGTCAATACCAAGTAATTAAACCTCT 57.197 34.615 0.00 0.00 45.98 3.69
2098 2580 8.543862 TTATGATGATGATGATGTTAGCACTC 57.456 34.615 0.00 0.00 0.00 3.51
2291 2779 5.876651 TTTGCCTATCATCTGAAGAGCTA 57.123 39.130 0.00 0.00 0.00 3.32
2347 2835 2.285083 CCGAACCTGTCTTTCACAACA 58.715 47.619 0.00 0.00 33.31 3.33
2364 2852 6.336566 TCACAACACACAAGCATTTGTAAAT 58.663 32.000 0.00 0.00 45.53 1.40
3086 8376 3.073209 TGGGTACAGTCTGGTTGCAAATA 59.927 43.478 0.00 0.00 0.00 1.40
3116 8406 6.601613 TGTTGACTTGTTCTGTCCTACATTTT 59.398 34.615 0.00 0.00 33.83 1.82
3339 8631 7.731882 TTGGTTGTATTGAAATCTCACGTTA 57.268 32.000 0.00 0.00 0.00 3.18
3341 8633 8.330466 TGGTTGTATTGAAATCTCACGTTAAT 57.670 30.769 0.00 0.00 0.00 1.40
3342 8634 8.788806 TGGTTGTATTGAAATCTCACGTTAATT 58.211 29.630 0.00 0.00 0.00 1.40
3343 8635 9.620660 GGTTGTATTGAAATCTCACGTTAATTT 57.379 29.630 0.00 0.00 0.00 1.82
3436 11550 9.745323 GCTAGTAATTTTGCATGTTCAATTTTC 57.255 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.552743 GGATGCACATGATGATGGTCTG 59.447 50.000 0.00 0.00 33.39 3.51
41 42 3.090656 CGTCATCAGCTGCTGCAG 58.909 61.111 24.80 24.80 42.74 4.41
59 60 4.680237 TGGTCGTGGCCGCTTCAG 62.680 66.667 15.69 0.00 0.00 3.02
94 95 3.081409 AGCTACCAATCCGCCCGT 61.081 61.111 0.00 0.00 0.00 5.28
134 135 1.319541 CCTTATCCTCGCTCGGAGAA 58.680 55.000 9.69 0.00 46.23 2.87
159 432 4.759096 GCAAAATCGCGCCGCACT 62.759 61.111 10.75 0.00 0.00 4.40
175 448 3.044305 GGCCCTATCATCGCACGC 61.044 66.667 0.00 0.00 0.00 5.34
180 453 0.880278 CACAACCGGCCCTATCATCG 60.880 60.000 0.00 0.00 0.00 3.84
300 574 0.107848 CGCAAAGTTCCCGGGTAGAT 60.108 55.000 22.86 2.73 0.00 1.98
381 655 6.229733 AGAATTACAGCCTTGCTATGAGATC 58.770 40.000 0.00 0.00 36.40 2.75
407 681 8.399425 TGTTCATTAAACTTGATAACAACACGT 58.601 29.630 0.00 0.00 38.76 4.49
419 693 7.908230 ACAAGCAAACATGTTCATTAAACTTG 58.092 30.769 12.39 17.21 44.52 3.16
420 694 8.491331 AACAAGCAAACATGTTCATTAAACTT 57.509 26.923 12.39 5.39 32.46 2.66
421 695 8.491331 AAACAAGCAAACATGTTCATTAAACT 57.509 26.923 12.39 0.00 36.74 2.66
422 696 9.209297 GAAAACAAGCAAACATGTTCATTAAAC 57.791 29.630 12.39 0.00 36.74 2.01
423 697 9.160496 AGAAAACAAGCAAACATGTTCATTAAA 57.840 25.926 12.39 0.00 36.74 1.52
424 698 8.715191 AGAAAACAAGCAAACATGTTCATTAA 57.285 26.923 12.39 0.00 36.74 1.40
426 700 7.042523 GCTAGAAAACAAGCAAACATGTTCATT 60.043 33.333 12.39 4.39 36.74 2.57
803 1151 0.034337 TTTTTCCCCACCTCTCGTCG 59.966 55.000 0.00 0.00 0.00 5.12
996 1433 3.070018 CTGCCTCGGCTTATAAAGGATG 58.930 50.000 9.65 0.00 42.51 3.51
1061 1519 5.855045 ACTCCCTCCGTAAGCAAATATAAG 58.145 41.667 0.00 0.00 0.00 1.73
1391 1849 4.502171 TTAACCACATAGACGTCAACGA 57.498 40.909 19.50 0.00 43.02 3.85
1519 1977 4.873129 ATAGTGCGGCGCGACCAG 62.873 66.667 28.09 8.53 39.03 4.00
1564 2022 2.068821 GGCCCAGCTCATCTCTCCA 61.069 63.158 0.00 0.00 0.00 3.86
1677 2135 0.618393 ACCCCATTGCATCCCCTTTG 60.618 55.000 0.00 0.00 0.00 2.77
1774 2235 6.761731 TTTGTAAAAGTGATGATTTTGGCG 57.238 33.333 0.00 0.00 32.38 5.69
2087 2569 1.343142 TCACGGTGTGAGTGCTAACAT 59.657 47.619 8.17 0.00 37.67 2.71
2090 2572 2.479837 CTTTCACGGTGTGAGTGCTAA 58.520 47.619 8.17 0.00 43.69 3.09
2091 2573 1.270094 CCTTTCACGGTGTGAGTGCTA 60.270 52.381 8.17 0.00 43.69 3.49
2092 2574 0.532862 CCTTTCACGGTGTGAGTGCT 60.533 55.000 8.17 0.00 43.69 4.40
2098 2580 0.105964 TCTGGACCTTTCACGGTGTG 59.894 55.000 8.17 0.30 37.42 3.82
2250 2735 0.460311 ATCCTTGTCGTGATCCGTCC 59.540 55.000 3.97 0.00 37.94 4.79
2251 2736 2.295253 AATCCTTGTCGTGATCCGTC 57.705 50.000 3.97 0.08 37.94 4.79
2252 2737 2.346803 CAAATCCTTGTCGTGATCCGT 58.653 47.619 3.97 0.00 37.94 4.69
2291 2779 6.859112 TCTTTTCTAGGTGCTCAACTCTAT 57.141 37.500 0.00 0.00 0.00 1.98
2347 2835 6.639632 AGACTCATTTACAAATGCTTGTGT 57.360 33.333 9.37 0.54 45.53 3.72
2364 2852 2.158813 AGGCGTGAAAGGAAAAGACTCA 60.159 45.455 0.00 0.00 0.00 3.41
2777 8066 2.816087 CAAGTTCAAGCAGCCAGTACAT 59.184 45.455 0.00 0.00 0.00 2.29
3086 8376 5.930135 AGGACAGAACAAGTCAACAACTAT 58.070 37.500 0.00 0.00 37.17 2.12
3383 11497 3.617263 CGCCAAGAGTATGGTAAACAGAC 59.383 47.826 0.00 0.00 42.75 3.51
3436 11550 6.144854 GCATATGCCACACATGTTAATACAG 58.855 40.000 17.26 0.00 40.06 2.74
3495 11609 9.669353 CATATATGATAAACAAAGGAAGCACAC 57.331 33.333 6.92 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.