Multiple sequence alignment - TraesCS2A01G243500

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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 TraesCS2A01G243500 chr2A 100.000 2489 0 0 1 2489 342650632 342648144 0.000000e+00 4597.0
1 TraesCS2A01G243500 chr2A 100.000 61 0 0 2738 2798 342647895 342647835 2.280000e-21 113.0
2 TraesCS2A01G243500 chr2B 96.539 1907 47 8 596 2488 368415901 368414000 0.000000e+00 3138.0
3 TraesCS2A01G243500 chr2B 94.979 478 23 1 99 576 368416364 368415888 0.000000e+00 749.0
4 TraesCS2A01G243500 chr2B 96.721 61 2 0 2738 2798 368413904 368413844 4.930000e-18 102.0
5 TraesCS2A01G243500 chr2D 96.184 1782 45 3 708 2488 291994241 291992482 0.000000e+00 2892.0
6 TraesCS2A01G243500 chr2D 94.983 578 25 4 1 576 291996671 291996096 0.000000e+00 904.0
7 TraesCS2A01G243500 chr2D 98.361 61 1 0 2738 2798 291992385 291992325 1.060000e-19 108.0
8 TraesCS2A01G243500 chr2D 100.000 30 0 0 597 626 291996108 291996079 3.890000e-04 56.5
9 TraesCS2A01G243500 chr5D 84.477 554 69 13 36 574 42567272 42566721 5.310000e-147 531.0
10 TraesCS2A01G243500 chr5D 90.000 60 4 1 2378 2435 256849738 256849679 2.990000e-10 76.8
11 TraesCS2A01G243500 chr7D 82.793 401 55 7 181 574 42059597 42059990 2.060000e-91 346.0
12 TraesCS2A01G243500 chr7D 95.122 41 1 1 2757 2796 242289353 242289313 2.330000e-06 63.9
13 TraesCS2A01G243500 chr7B 80.087 462 75 16 1 453 481692209 481692662 7.470000e-86 327.0
14 TraesCS2A01G243500 chr7B 83.846 130 12 8 2366 2488 203741574 203741701 6.330000e-22 115.0
15 TraesCS2A01G243500 chr6B 77.281 581 77 27 1 573 647281 646748 9.800000e-75 291.0
16 TraesCS2A01G243500 chr6D 83.036 224 33 4 332 550 97657571 97657794 6.110000e-47 198.0
17 TraesCS2A01G243500 chr6D 79.897 194 32 5 1 193 464485049 464484862 4.860000e-28 135.0
18 TraesCS2A01G243500 chr6D 78.070 114 17 2 9 122 473490350 473490455 6.470000e-07 65.8
19 TraesCS2A01G243500 chr6D 94.737 38 2 0 2269 2306 3123562 3123525 3.010000e-05 60.2
20 TraesCS2A01G243500 chrUn 81.046 153 26 2 392 541 108598933 108599085 4.900000e-23 119.0
21 TraesCS2A01G243500 chr4A 78.344 157 22 10 2335 2481 457822177 457822331 1.070000e-14 91.6
22 TraesCS2A01G243500 chr4D 78.344 157 20 10 2338 2487 117658485 117658336 3.840000e-14 89.8
23 TraesCS2A01G243500 chr6A 79.200 125 18 2 1 125 616399313 616399197 2.310000e-11 80.5
24 TraesCS2A01G243500 chr6A 92.857 42 3 0 2265 2306 99990337 99990296 8.370000e-06 62.1
25 TraesCS2A01G243500 chr5A 90.164 61 4 1 482 540 705399425 705399365 8.310000e-11 78.7
26 TraesCS2A01G243500 chr5A 89.474 57 4 2 2742 2798 275289613 275289559 1.390000e-08 71.3
27 TraesCS2A01G243500 chr7A 87.719 57 5 2 2742 2798 163434403 163434349 6.470000e-07 65.8
28 TraesCS2A01G243500 chr7A 94.444 36 2 0 2265 2300 110927131 110927096 3.890000e-04 56.5
29 TraesCS2A01G243500 chr7A 94.444 36 2 0 2265 2300 177697389 177697354 3.890000e-04 56.5
30 TraesCS2A01G243500 chr3D 88.679 53 5 1 2742 2793 176132576 176132628 2.330000e-06 63.9
31 TraesCS2A01G243500 chr1B 100.000 33 0 0 2265 2297 164949810 164949842 8.370000e-06 62.1
32 TraesCS2A01G243500 chr1B 97.222 36 1 0 2265 2300 487040978 487040943 8.370000e-06 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 TraesCS2A01G243500 chr2A 342647835 342650632 2797 True 2355.000000 4597 100.000000 1 2798 2 chr2A.!!$R1 2797
1 TraesCS2A01G243500 chr2B 368413844 368416364 2520 True 1329.666667 3138 96.079667 99 2798 3 chr2B.!!$R1 2699
2 TraesCS2A01G243500 chr2D 291992325 291996671 4346 True 990.125000 2892 97.382000 1 2798 4 chr2D.!!$R1 2797
3 TraesCS2A01G243500 chr5D 42566721 42567272 551 True 531.000000 531 84.477000 36 574 1 chr5D.!!$R1 538
4 TraesCS2A01G243500 chr6B 646748 647281 533 True 291.000000 291 77.281000 1 573 1 chr6B.!!$R1 572

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
863 2638 1.019673 GCGACACCGTCTATCCTACA 58.980 55.000 0.0 0.0 38.24 2.74 F
1152 2927 1.374758 CGAGGAGTTCCGCAAGCTT 60.375 57.895 0.0 0.0 42.08 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 3490 1.040339 GGGTGGTTGTCCAAACTGCA 61.040 55.000 0.0 0.0 46.15 4.41 R
1972 3747 4.050553 CAAGCCACCACAACACTAATTTG 58.949 43.478 0.0 0.0 0.00 2.32 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
29 30 6.808321 AGTTATGTGCCTTAGAGTATCCAA 57.192 37.500 0.00 0.00 33.66 3.53
149 152 6.203647 GGTTATGGGACGCAACAAATATTAC 58.796 40.000 0.00 0.00 0.00 1.89
193 196 2.355444 TCATCAATGCACTGTAATGCCG 59.645 45.455 0.00 0.00 45.50 5.69
259 263 8.316640 TGCTGTTTTGTGAACTAAAATTTGTT 57.683 26.923 0.00 0.00 30.62 2.83
506 520 1.807142 CCTTTGGTTCGAAGGAAGCTC 59.193 52.381 0.00 0.00 45.40 4.09
566 585 9.889128 TTGAACTTGACTATCATGATATGAACA 57.111 29.630 15.71 10.44 43.50 3.18
567 586 9.889128 TGAACTTGACTATCATGATATGAACAA 57.111 29.630 15.71 15.84 43.50 2.83
569 588 9.896645 AACTTGACTATCATGATATGAACAACT 57.103 29.630 15.71 6.72 43.50 3.16
570 589 9.896645 ACTTGACTATCATGATATGAACAACTT 57.103 29.630 15.71 5.75 43.50 2.66
573 592 9.112725 TGACTATCATGATATGAACAACTTTGG 57.887 33.333 15.71 2.56 43.50 3.28
574 593 7.934457 ACTATCATGATATGAACAACTTTGGC 58.066 34.615 15.71 0.00 43.50 4.52
575 594 7.776969 ACTATCATGATATGAACAACTTTGGCT 59.223 33.333 15.71 0.00 43.50 4.75
576 595 6.441093 TCATGATATGAACAACTTTGGCTC 57.559 37.500 0.00 0.00 36.11 4.70
577 596 5.945191 TCATGATATGAACAACTTTGGCTCA 59.055 36.000 0.00 0.00 36.11 4.26
578 597 6.604396 TCATGATATGAACAACTTTGGCTCAT 59.396 34.615 11.41 11.41 38.02 2.90
579 598 6.839124 TGATATGAACAACTTTGGCTCATT 57.161 33.333 11.76 3.95 36.69 2.57
580 599 7.230849 TGATATGAACAACTTTGGCTCATTT 57.769 32.000 11.76 6.57 36.69 2.32
581 600 7.092079 TGATATGAACAACTTTGGCTCATTTG 58.908 34.615 11.76 0.00 36.69 2.32
582 601 3.456280 TGAACAACTTTGGCTCATTTGC 58.544 40.909 0.00 0.00 0.00 3.68
583 602 3.118847 TGAACAACTTTGGCTCATTTGCA 60.119 39.130 0.00 0.00 34.04 4.08
584 603 3.540314 ACAACTTTGGCTCATTTGCAA 57.460 38.095 0.00 0.00 34.04 4.08
585 604 3.871485 ACAACTTTGGCTCATTTGCAAA 58.129 36.364 15.44 15.44 34.04 3.68
586 605 4.260170 ACAACTTTGGCTCATTTGCAAAA 58.740 34.783 17.19 0.00 34.96 2.44
587 606 4.699257 ACAACTTTGGCTCATTTGCAAAAA 59.301 33.333 17.19 6.71 35.69 1.94
645 1533 8.193438 AGTTATATAGACAAGTGTTCGTAACCC 58.807 37.037 0.00 0.00 0.00 4.11
686 1574 4.260784 CGTACCTGTCGGTATGTACCTAAC 60.261 50.000 7.56 6.24 46.93 2.34
746 2521 5.627040 GCCTCCGCCTGCTAGTTTTATATAT 60.627 44.000 0.00 0.00 0.00 0.86
747 2522 6.406624 GCCTCCGCCTGCTAGTTTTATATATA 60.407 42.308 0.00 0.00 0.00 0.86
755 2530 7.488471 CCTGCTAGTTTTATATATAGTCGTGGC 59.512 40.741 0.00 0.00 0.00 5.01
783 2558 3.449377 TGTTTTTGGGAAGGTTGAACTCC 59.551 43.478 0.00 0.00 0.00 3.85
863 2638 1.019673 GCGACACCGTCTATCCTACA 58.980 55.000 0.00 0.00 38.24 2.74
910 2685 2.825532 CCATACAAACTCAAACCCCCAG 59.174 50.000 0.00 0.00 0.00 4.45
945 2720 3.080121 CTCCGCTTCTCCCTGGCT 61.080 66.667 0.00 0.00 0.00 4.75
1152 2927 1.374758 CGAGGAGTTCCGCAAGCTT 60.375 57.895 0.00 0.00 42.08 3.74
1176 2951 3.157087 GCCCTCAAAATCTTCCAAGACA 58.843 45.455 0.00 0.00 37.98 3.41
1251 3026 1.590147 GGTCGTCTCCATGACCGTT 59.410 57.895 0.00 0.00 46.67 4.44
1476 3251 4.069232 CCGAACCTCTCAGCGCCA 62.069 66.667 2.29 0.00 0.00 5.69
2364 4139 1.103398 AGTGTCCTTGCACTGCAACC 61.103 55.000 12.59 4.65 46.72 3.77
2374 4149 1.666888 GCACTGCAACCGATCCAAAAG 60.667 52.381 0.00 0.00 0.00 2.27
2478 4254 9.061435 GTCTATTCCTCTTATCTTTTTGGATGG 57.939 37.037 0.00 0.00 0.00 3.51
2488 4264 0.796255 TTTTGGATGGGTTGGGGGAT 59.204 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.272978 TGGATACTCTAAGGCACATAACTTTC 58.727 38.462 0.00 0.0 37.61 2.62
7 8 6.583562 ACTTGGATACTCTAAGGCACATAAC 58.416 40.000 5.42 0.0 39.01 1.89
44 45 8.390354 TCAAAATCGAGCATAATTCTTACACTG 58.610 33.333 0.00 0.0 0.00 3.66
46 47 9.722056 AATCAAAATCGAGCATAATTCTTACAC 57.278 29.630 0.00 0.0 0.00 2.90
91 93 1.705337 ATGGTACGCATGAGCAACGC 61.705 55.000 0.00 0.0 42.27 4.84
164 167 8.592155 CATTACAGTGCATTGATGATTTCTTTG 58.408 33.333 16.98 0.0 0.00 2.77
466 479 8.076178 CCAAAGGAAAATTGTTCTAGTGTACAG 58.924 37.037 0.00 0.0 0.00 2.74
561 580 3.118847 TGCAAATGAGCCAAAGTTGTTCA 60.119 39.130 0.00 0.0 0.00 3.18
562 581 3.456280 TGCAAATGAGCCAAAGTTGTTC 58.544 40.909 0.00 0.0 0.00 3.18
563 582 3.540314 TGCAAATGAGCCAAAGTTGTT 57.460 38.095 0.00 0.0 0.00 2.83
564 583 3.540314 TTGCAAATGAGCCAAAGTTGT 57.460 38.095 0.00 0.0 0.00 3.32
565 584 4.879104 TTTTGCAAATGAGCCAAAGTTG 57.121 36.364 13.65 0.0 0.00 3.16
590 609 5.994668 TGTTTCAGCCAAAGTTGTTCTTTTT 59.005 32.000 0.00 0.0 42.95 1.94
591 610 5.546526 TGTTTCAGCCAAAGTTGTTCTTTT 58.453 33.333 0.00 0.0 42.95 2.27
592 611 5.146010 TGTTTCAGCCAAAGTTGTTCTTT 57.854 34.783 0.00 0.0 45.96 2.52
593 612 4.799564 TGTTTCAGCCAAAGTTGTTCTT 57.200 36.364 0.00 0.0 38.10 2.52
594 613 5.343307 AATGTTTCAGCCAAAGTTGTTCT 57.657 34.783 0.00 0.0 0.00 3.01
630 1518 1.202722 ACCCAGGGTTACGAACACTTG 60.203 52.381 4.76 0.0 44.36 3.16
638 1526 3.622166 AATAGTTCACCCAGGGTTACG 57.378 47.619 9.12 0.0 31.02 3.18
678 1566 7.698506 AGAAAGGCCAATTTAAGTTAGGTAC 57.301 36.000 5.01 0.0 0.00 3.34
686 1574 8.079809 TCGTTTAGAAAGAAAGGCCAATTTAAG 58.920 33.333 5.01 0.0 0.00 1.85
746 2521 4.416620 CAAAAACAACTTTGCCACGACTA 58.583 39.130 0.00 0.0 30.03 2.59
747 2522 3.249917 CAAAAACAACTTTGCCACGACT 58.750 40.909 0.00 0.0 30.03 4.18
755 2530 5.241662 TCAACCTTCCCAAAAACAACTTTG 58.758 37.500 0.00 0.0 36.28 2.77
863 2638 3.703127 GAAGGGAGCGAACGGGGT 61.703 66.667 0.00 0.0 0.00 4.95
910 2685 1.834896 GAGAGGAGAGAGGGGTTTTCC 59.165 57.143 0.00 0.0 39.75 3.13
945 2720 0.251073 GCTAGGTTAGGGTTTCGGCA 59.749 55.000 0.00 0.0 0.00 5.69
1152 2927 0.695924 TGGAAGATTTTGAGGGCGGA 59.304 50.000 0.00 0.0 0.00 5.54
1715 3490 1.040339 GGGTGGTTGTCCAAACTGCA 61.040 55.000 0.00 0.0 46.15 4.41
1972 3747 4.050553 CAAGCCACCACAACACTAATTTG 58.949 43.478 0.00 0.0 0.00 2.32
2202 3977 4.145052 TCTCTGAGCAGCTATTAATCGGA 58.855 43.478 0.00 0.0 0.00 4.55
2364 4139 6.313658 TGTGAACATGTATCTCTTTTGGATCG 59.686 38.462 0.00 0.0 0.00 3.69
2374 4149 6.486253 TTCAAGCTTGTGAACATGTATCTC 57.514 37.500 25.19 0.0 32.56 2.75
2749 4525 4.383173 CATCATTTCTGACCATCCGATCA 58.617 43.478 0.00 0.0 33.22 2.92


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

AutoCloner maintained by Alex Coulton.