Multiple sequence alignment - TraesCS3D01G504700

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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 TraesCS3D01G504700 chr3D 100.000 3572 0 0 1 3572 592243510 592239939 0.000000e+00 6597
1 TraesCS3D01G504700 chr3D 96.621 3581 107 10 1 3572 592323803 592320228 0.000000e+00 5930
2 TraesCS3D01G504700 chr3D 96.590 3578 103 9 1 3572 592275155 592271591 0.000000e+00 5914
3 TraesCS3D01G504700 chr3D 96.478 3578 105 10 1 3572 592295303 592291741 0.000000e+00 5890
4 TraesCS3D01G504700 chr3D 95.827 2660 98 5 1 2659 592356910 592354263 0.000000e+00 4285
5 TraesCS3D01G504700 chr3D 94.785 767 26 2 2820 3572 592172477 592171711 0.000000e+00 1182
6 TraesCS3D01G504700 chr3B 95.102 2450 103 7 213 2659 793532969 793530534 0.000000e+00 3843
7 TraesCS3D01G504700 chr3B 94.949 2455 102 9 213 2659 793614170 793611730 0.000000e+00 3827
8 TraesCS3D01G504700 chr3B 94.898 2450 108 7 213 2659 793560189 793557754 0.000000e+00 3816
9 TraesCS3D01G504700 chr3B 94.900 2451 106 9 213 2659 793670698 793668263 0.000000e+00 3816
10 TraesCS3D01G504700 chr3B 94.778 2451 110 8 213 2659 793588453 793586017 0.000000e+00 3801
11 TraesCS3D01G504700 chr3B 83.594 768 65 20 2820 3563 792570651 792571381 0.000000e+00 664
12 TraesCS3D01G504700 chr3B 86.217 653 39 14 2934 3570 792504582 792505199 0.000000e+00 660
13 TraesCS3D01G504700 chr3B 86.070 603 34 11 2982 3570 793478041 793477475 1.420000e-168 603
14 TraesCS3D01G504700 chr3B 85.904 603 35 11 2982 3570 792473623 792474189 6.600000e-167 597
15 TraesCS3D01G504700 chr3B 85.738 603 36 11 2982 3570 792480986 792481552 3.070000e-165 592
16 TraesCS3D01G504700 chr3B 85.240 603 38 21 2982 3570 792491905 792492470 1.110000e-159 573
17 TraesCS3D01G504700 chr3B 92.045 176 11 3 2658 2832 63001508 63001335 9.910000e-61 244
18 TraesCS3D01G504700 chr3B 90.303 165 13 2 2820 2982 793557755 793557592 2.790000e-51 213
19 TraesCS3D01G504700 chr3B 89.697 165 14 2 2820 2982 792452645 792452808 1.300000e-49 207
20 TraesCS3D01G504700 chr3B 89.697 165 14 2 2820 2982 793485808 793485645 1.300000e-49 207
21 TraesCS3D01G504700 chr3A 90.868 219 20 0 1 219 99619756 99619974 9.700000e-76 294
22 TraesCS3D01G504700 chr3A 88.293 205 18 5 2656 2855 477708332 477708129 1.280000e-59 241
23 TraesCS3D01G504700 chr2D 90.583 223 17 1 1 219 170439528 170439306 3.490000e-75 292
24 TraesCS3D01G504700 chr1D 90.952 210 19 0 1 210 58544135 58544344 2.100000e-72 283
25 TraesCS3D01G504700 chr4D 93.103 174 11 1 2656 2828 455021255 455021082 1.650000e-63 254
26 TraesCS3D01G504700 chr4D 92.614 176 12 1 2654 2828 93336852 93336677 5.920000e-63 252
27 TraesCS3D01G504700 chrUn 92.045 176 11 3 2658 2832 407971347 407971174 9.910000e-61 244
28 TraesCS3D01G504700 chrUn 90.303 165 13 2 2820 2982 261906602 261906765 2.790000e-51 213
29 TraesCS3D01G504700 chr7D 86.758 219 29 0 1 219 559109258 559109476 9.910000e-61 244
30 TraesCS3D01G504700 chr7A 92.442 172 12 1 2654 2824 40550422 40550251 9.910000e-61 244


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 TraesCS3D01G504700 chr3D 592239939 592243510 3571 True 6597.0 6597 100.0000 1 3572 1 chr3D.!!$R2 3571
1 TraesCS3D01G504700 chr3D 592320228 592323803 3575 True 5930.0 5930 96.6210 1 3572 1 chr3D.!!$R5 3571
2 TraesCS3D01G504700 chr3D 592271591 592275155 3564 True 5914.0 5914 96.5900 1 3572 1 chr3D.!!$R3 3571
3 TraesCS3D01G504700 chr3D 592291741 592295303 3562 True 5890.0 5890 96.4780 1 3572 1 chr3D.!!$R4 3571
4 TraesCS3D01G504700 chr3D 592354263 592356910 2647 True 4285.0 4285 95.8270 1 2659 1 chr3D.!!$R6 2658
5 TraesCS3D01G504700 chr3D 592171711 592172477 766 True 1182.0 1182 94.7850 2820 3572 1 chr3D.!!$R1 752
6 TraesCS3D01G504700 chr3B 793530534 793532969 2435 True 3843.0 3843 95.1020 213 2659 1 chr3B.!!$R4 2446
7 TraesCS3D01G504700 chr3B 793611730 793614170 2440 True 3827.0 3827 94.9490 213 2659 1 chr3B.!!$R6 2446
8 TraesCS3D01G504700 chr3B 793668263 793670698 2435 True 3816.0 3816 94.9000 213 2659 1 chr3B.!!$R7 2446
9 TraesCS3D01G504700 chr3B 793586017 793588453 2436 True 3801.0 3801 94.7780 213 2659 1 chr3B.!!$R5 2446
10 TraesCS3D01G504700 chr3B 793557592 793560189 2597 True 2014.5 3816 92.6005 213 2982 2 chr3B.!!$R8 2769
11 TraesCS3D01G504700 chr3B 792570651 792571381 730 False 664.0 664 83.5940 2820 3563 1 chr3B.!!$F6 743
12 TraesCS3D01G504700 chr3B 792504582 792505199 617 False 660.0 660 86.2170 2934 3570 1 chr3B.!!$F5 636
13 TraesCS3D01G504700 chr3B 793477475 793478041 566 True 603.0 603 86.0700 2982 3570 1 chr3B.!!$R2 588
14 TraesCS3D01G504700 chr3B 792473623 792474189 566 False 597.0 597 85.9040 2982 3570 1 chr3B.!!$F2 588
15 TraesCS3D01G504700 chr3B 792480986 792481552 566 False 592.0 592 85.7380 2982 3570 1 chr3B.!!$F3 588
16 TraesCS3D01G504700 chr3B 792491905 792492470 565 False 573.0 573 85.2400 2982 3570 1 chr3B.!!$F4 588

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
493 495 0.531090 GTAGGTTGTCCGTGTGTGCA 60.531 55.0 0.0 0.0 39.05 4.57 F
1098 1103 0.106419 TCCACAACCCACCTGAAACC 60.106 55.0 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1602 0.674581 CGCTTGTCTGATCAGCCCAA 60.675 55.0 18.36 19.33 0.0 4.12 R
2920 2935 0.036732 TCTCCCGCCCATATGATTGC 59.963 55.0 3.65 3.12 0.0 3.56 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
104 105 9.859427 CAACTGCATCTTTCCTTTCATAATTTA 57.141 29.630 0.00 0.00 0.00 1.40
154 155 5.104776 TGCAAAGAAGACATATAGCTCTGGT 60.105 40.000 0.00 0.00 0.00 4.00
160 161 6.435904 AGAAGACATATAGCTCTGGTGATACC 59.564 42.308 0.00 0.00 39.22 2.73
176 177 0.902984 TACCCCGCTGTCACATCAGT 60.903 55.000 0.00 0.00 37.70 3.41
242 243 7.498570 AGAACGTGTTTTGGTACCATTAACTTA 59.501 33.333 27.37 14.62 0.00 2.24
401 403 0.959372 AGATGTTCCCGTCGACGACT 60.959 55.000 37.65 19.85 43.02 4.18
424 426 2.879462 CGCCTACGGTGACTTCGC 60.879 66.667 0.00 0.00 34.74 4.70
493 495 0.531090 GTAGGTTGTCCGTGTGTGCA 60.531 55.000 0.00 0.00 39.05 4.57
1084 1089 2.169769 GGAAATACCTCGTCCATCCACA 59.830 50.000 0.00 0.00 35.41 4.17
1098 1103 0.106419 TCCACAACCCACCTGAAACC 60.106 55.000 0.00 0.00 0.00 3.27
1597 1602 4.207165 ACCTGCTAAACAATTGTGTGAGT 58.793 39.130 12.82 1.21 38.27 3.41
1760 1765 6.997239 ATGGATCCATCATATCAACAATCG 57.003 37.500 22.15 0.00 29.42 3.34
1789 1794 4.076394 TGTACAAGGAAGGTAACCAATGC 58.924 43.478 0.00 0.00 37.17 3.56
1856 1861 3.960102 CCCAAATTTTGAGCTAGCCCATA 59.040 43.478 12.13 0.00 0.00 2.74
1942 1951 2.902423 TAATGGCATGCCGGTGGTCC 62.902 60.000 30.87 5.79 39.42 4.46
1997 2006 0.175760 GTCAGAAGCATCGGTAGCCA 59.824 55.000 0.00 0.00 0.00 4.75
1998 2007 1.123077 TCAGAAGCATCGGTAGCCAT 58.877 50.000 0.00 0.00 0.00 4.40
2355 2364 6.183360 CGGGTATCATACAAGTGAGAAGAGAA 60.183 42.308 0.00 0.00 0.00 2.87
2356 2365 7.206687 GGGTATCATACAAGTGAGAAGAGAAG 58.793 42.308 0.00 0.00 0.00 2.85
2357 2366 7.068839 GGGTATCATACAAGTGAGAAGAGAAGA 59.931 40.741 0.00 0.00 0.00 2.87
2358 2367 8.637986 GGTATCATACAAGTGAGAAGAGAAGAT 58.362 37.037 0.00 0.00 0.00 2.40
2359 2368 9.677567 GTATCATACAAGTGAGAAGAGAAGATC 57.322 37.037 0.00 0.00 0.00 2.75
2360 2369 7.953005 TCATACAAGTGAGAAGAGAAGATCT 57.047 36.000 0.00 0.00 41.27 2.75
2414 2429 3.055602 ACTCAGAACTGCATGCATCTACA 60.056 43.478 22.97 10.77 0.00 2.74
2482 2497 6.547283 GTGGAATTACTTTCTCTAGCTTTGC 58.453 40.000 0.00 0.00 34.56 3.68
2622 2637 3.827008 AGTGGACGCATGACTATTCAT 57.173 42.857 0.00 0.00 43.80 2.57
2774 2789 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2900 2915 9.940974 TTACTTATACTTCAATGGTAGGGAGTA 57.059 33.333 0.00 0.00 0.00 2.59
2918 2933 6.046168 AGGGAGTAAGCTAGATCTGAGGAATA 59.954 42.308 5.18 0.00 0.00 1.75
2920 2935 7.093945 GGGAGTAAGCTAGATCTGAGGAATAAG 60.094 44.444 5.18 0.00 0.00 1.73
3093 3110 2.108250 ACTCCAACAACATAGGGCTTGT 59.892 45.455 0.00 0.00 31.76 3.16
3312 3335 5.897824 TCTGGTCGGTAGATATTTTCTTCCT 59.102 40.000 0.00 0.00 39.22 3.36
3346 3369 3.769844 TCCCGCATTCTCTAGAAAACTCT 59.230 43.478 0.00 0.00 37.61 3.24
3354 3377 8.510505 GCATTCTCTAGAAAACTCTCAATTGTT 58.489 33.333 5.13 0.00 37.61 2.83
3359 3382 7.279615 TCTAGAAAACTCTCAATTGTTGGTCA 58.720 34.615 5.13 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 6.681729 TGTCTAGGAAGTTTACCACTGAAT 57.318 37.500 0.00 0.00 35.12 2.57
154 155 0.464036 GATGTGACAGCGGGGTATCA 59.536 55.000 0.00 0.00 0.00 2.15
160 161 1.742880 CCACTGATGTGACAGCGGG 60.743 63.158 14.70 3.14 46.55 6.13
176 177 1.243342 CGGCAAGGCTGTTTCATCCA 61.243 55.000 0.00 0.00 0.00 3.41
242 243 3.443976 GTTTGTTCGCAAAGTGGATGTT 58.556 40.909 0.00 0.00 46.45 2.71
367 369 1.980765 ACATCTGCTCCCACTGAAAGA 59.019 47.619 0.00 0.00 37.43 2.52
424 426 5.048504 AGCCGGCATATCATCTTTACATTTG 60.049 40.000 31.54 0.00 0.00 2.32
493 495 3.928992 CGCATACGCTCATCCTTATGAAT 59.071 43.478 0.00 0.00 41.57 2.57
550 552 2.427095 AGTGGCTGTCAAGTTTGGTTTC 59.573 45.455 0.00 0.00 0.00 2.78
1084 1089 0.923358 TGACTGGTTTCAGGTGGGTT 59.077 50.000 0.00 0.00 44.99 4.11
1098 1103 2.124983 CCAGGTCCGCCATGACTG 60.125 66.667 0.00 0.00 37.19 3.51
1232 1237 2.842462 TGCGGTGGAGTCTGTGGT 60.842 61.111 0.00 0.00 0.00 4.16
1406 1411 3.986006 TCCGCCTTTCGTGACGCT 61.986 61.111 0.00 0.00 36.19 5.07
1597 1602 0.674581 CGCTTGTCTGATCAGCCCAA 60.675 55.000 18.36 19.33 0.00 4.12
1760 1765 1.270147 ACCTTCCTTGTACACGTCAGC 60.270 52.381 0.00 0.00 0.00 4.26
1856 1861 5.594725 TCCACGAGATAGAAGTTATTGCTCT 59.405 40.000 0.00 0.00 0.00 4.09
2355 2364 9.573716 GCAAGGTGGTGCATTAGATCTAGATCT 62.574 44.444 32.38 32.38 45.49 2.75
2356 2365 5.736951 AGGTGGTGCATTAGATCTAGATC 57.263 43.478 22.92 22.92 38.09 2.75
2357 2366 5.744300 GCAAGGTGGTGCATTAGATCTAGAT 60.744 44.000 4.47 4.47 44.29 1.98
2358 2367 4.443457 GCAAGGTGGTGCATTAGATCTAGA 60.443 45.833 2.02 0.00 44.29 2.43
2359 2368 3.812053 GCAAGGTGGTGCATTAGATCTAG 59.188 47.826 2.02 0.00 44.29 2.43
2360 2369 3.808728 GCAAGGTGGTGCATTAGATCTA 58.191 45.455 0.00 0.00 44.29 1.98
2414 2429 4.072131 AGCAACACCATCGAACATAAACT 58.928 39.130 0.00 0.00 0.00 2.66
2482 2497 7.096558 GCGATTACAAAGTTATAGAACTCCTCG 60.097 40.741 2.67 7.27 45.50 4.63
2622 2637 3.134081 GTGGAACTGGTAGCAATAGCCTA 59.866 47.826 0.00 0.00 43.56 3.93
2810 2825 8.232412 AGTGGACTATATTAACTACTCCATCCA 58.768 37.037 0.00 0.00 0.00 3.41
2848 2863 3.244630 TGGTCTACGGTAAAGGCACATTT 60.245 43.478 0.00 0.00 0.00 2.32
2895 2910 7.576856 GCTTATTCCTCAGATCTAGCTTACTCC 60.577 44.444 0.00 0.00 0.00 3.85
2900 2915 6.491714 TTGCTTATTCCTCAGATCTAGCTT 57.508 37.500 10.36 0.00 0.00 3.74
2918 2933 0.478072 TCCCGCCCATATGATTGCTT 59.522 50.000 3.65 0.00 0.00 3.91
2920 2935 0.036732 TCTCCCGCCCATATGATTGC 59.963 55.000 3.65 3.12 0.00 3.56
3093 3110 8.765488 TCTCATATTCTGCCATCCAAATTAAA 57.235 30.769 0.00 0.00 0.00 1.52
3203 3226 1.600916 GCTTGAAGGGAGCAACGGT 60.601 57.895 0.00 0.00 39.89 4.83
3312 3335 2.203451 GCGGGATAGGTCGGGAGA 60.203 66.667 0.00 0.00 0.00 3.71
3359 3382 0.621862 GGAAGGGAGAGGATGTGGGT 60.622 60.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.