Multiple sequence alignment - TraesCS3A01G536800

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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 TraesCS3A01G536800 chr3A 100.000 3512 0 0 1 3512 748338495 748342006 0.000000e+00 6486.0
1 TraesCS3A01G536800 chr3A 86.872 975 109 13 1685 2656 749876818 749875860 0.000000e+00 1074.0
2 TraesCS3A01G536800 chr3A 83.846 650 75 20 852 1488 749877561 749876929 3.020000e-165 592.0
3 TraesCS3A01G536800 chr3B 95.790 3207 100 13 333 3512 28608566 28605368 0.000000e+00 5142.0
4 TraesCS3A01G536800 chr3B 84.494 632 70 20 864 1488 825849241 825849851 1.800000e-167 599.0
5 TraesCS3A01G536800 chr3B 86.330 534 68 3 1685 2216 825849966 825850496 8.450000e-161 577.0
6 TraesCS3A01G536800 chr3B 96.333 300 11 0 37 336 28608895 28608596 8.760000e-136 494.0
7 TraesCS3A01G536800 chr3B 86.603 418 44 9 2241 2656 825850484 825850891 5.350000e-123 451.0
8 TraesCS3A01G536800 chr3B 85.061 328 32 12 2657 2970 804547968 804547644 5.660000e-83 318.0
9 TraesCS3A01G536800 chr3B 86.545 275 28 4 3180 3452 804547231 804546964 9.530000e-76 294.0
10 TraesCS3A01G536800 chr3B 84.722 144 11 6 554 686 825848186 825848329 2.200000e-27 134.0
11 TraesCS3A01G536800 chr3B 91.803 61 5 0 37 97 230046484 230046424 6.250000e-13 86.1
12 TraesCS3A01G536800 chr3D 89.568 2013 158 26 1513 3512 615456590 615458563 0.000000e+00 2507.0
13 TraesCS3A01G536800 chr3D 87.910 488 52 7 977 1462 615455469 615455951 5.090000e-158 568.0
14 TraesCS3A01G536800 chr3D 81.046 153 29 0 703 855 426160492 426160644 4.760000e-24 122.0
15 TraesCS3A01G536800 chrUn 87.402 1151 129 11 1513 2656 37114789 37113648 0.000000e+00 1308.0
16 TraesCS3A01G536800 chrUn 87.402 1151 129 11 1513 2656 247032487 247033628 0.000000e+00 1308.0
17 TraesCS3A01G536800 chrUn 87.402 1151 129 11 1513 2656 300943518 300942377 0.000000e+00 1308.0
18 TraesCS3A01G536800 chrUn 85.581 645 66 16 852 1477 247031250 247031886 0.000000e+00 651.0
19 TraesCS3A01G536800 chrUn 88.054 519 50 11 963 1477 37115900 37115390 3.880000e-169 604.0
20 TraesCS3A01G536800 chrUn 88.054 519 50 11 963 1477 300944629 300944119 3.880000e-169 604.0
21 TraesCS3A01G536800 chrUn 82.407 324 39 12 2657 2973 44702522 44702834 2.080000e-67 267.0
22 TraesCS3A01G536800 chrUn 87.817 197 21 2 2938 3131 339246732 339246928 9.810000e-56 228.0
23 TraesCS3A01G536800 chrUn 88.144 194 20 2 2941 3131 345351643 345351450 9.810000e-56 228.0
24 TraesCS3A01G536800 chrUn 88.144 194 20 2 2941 3131 345354048 345353855 9.810000e-56 228.0
25 TraesCS3A01G536800 chrUn 87.817 197 21 2 2938 3131 401407487 401407683 9.810000e-56 228.0
26 TraesCS3A01G536800 chrUn 90.441 136 9 4 2666 2801 451870149 451870280 3.600000e-40 176.0
27 TraesCS3A01G536800 chr2B 85.321 327 32 11 2657 2970 671087767 671087444 1.220000e-84 324.0
28 TraesCS3A01G536800 chr2B 87.059 255 24 2 3180 3432 671087029 671086782 2.670000e-71 279.0
29 TraesCS3A01G536800 chr5D 81.739 345 63 0 2168 2512 532650884 532650540 4.440000e-74 289.0
30 TraesCS3A01G536800 chr5D 81.341 343 64 0 2168 2510 532615615 532615273 2.670000e-71 279.0
31 TraesCS3A01G536800 chr6B 95.062 162 8 0 692 853 364904387 364904226 4.500000e-64 255.0
32 TraesCS3A01G536800 chr6B 76.310 439 54 38 103 502 9055773 9055346 4.630000e-44 189.0
33 TraesCS3A01G536800 chr6B 94.340 53 3 0 40 92 676096253 676096201 8.080000e-12 82.4
34 TraesCS3A01G536800 chr4B 94.444 162 9 0 692 853 437930471 437930632 2.090000e-62 250.0
35 TraesCS3A01G536800 chr5B 85.892 241 25 5 2656 2889 410726493 410726255 7.530000e-62 248.0
36 TraesCS3A01G536800 chr5B 84.848 165 25 0 692 856 375943558 375943394 2.170000e-37 167.0
37 TraesCS3A01G536800 chr5B 91.935 62 5 0 37 98 701145647 701145708 1.740000e-13 87.9
38 TraesCS3A01G536800 chr7D 92.216 167 13 0 687 853 10809342 10809508 1.630000e-58 237.0
39 TraesCS3A01G536800 chr1D 80.592 304 59 0 1000 1303 28165396 28165699 5.860000e-58 235.0
40 TraesCS3A01G536800 chr7A 82.403 233 36 5 107 336 279187614 279187844 7.690000e-47 198.0
41 TraesCS3A01G536800 chr7A 92.727 55 4 0 43 97 81564858 81564804 2.910000e-11 80.5
42 TraesCS3A01G536800 chr4A 81.498 227 40 2 105 330 664243225 664243450 5.990000e-43 185.0
43 TraesCS3A01G536800 chr4A 78.008 241 47 2 1012 1252 639196012 639196246 2.820000e-31 147.0
44 TraesCS3A01G536800 chr4A 79.426 209 31 10 128 330 664244267 664244469 1.700000e-28 137.0
45 TraesCS3A01G536800 chr5A 83.237 173 20 7 692 856 422040599 422040428 2.180000e-32 150.0
46 TraesCS3A01G536800 chr2D 82.530 166 28 1 690 855 636546117 636546281 1.020000e-30 145.0
47 TraesCS3A01G536800 chr6D 79.042 167 30 4 690 855 459267926 459268088 3.710000e-20 110.0
48 TraesCS3A01G536800 chr6A 95.455 66 2 1 37 101 64055851 64055916 1.720000e-18 104.0
49 TraesCS3A01G536800 chr1B 95.082 61 3 0 37 97 554703317 554703377 2.890000e-16 97.1
50 TraesCS3A01G536800 chr1B 96.000 50 2 0 43 92 100987159 100987110 8.080000e-12 82.4
51 TraesCS3A01G536800 chr2A 91.803 61 5 0 37 97 774467539 774467479 6.250000e-13 86.1
52 TraesCS3A01G536800 chr7B 77.778 126 26 2 128 252 423564817 423564941 3.760000e-10 76.8


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 TraesCS3A01G536800 chr3A 748338495 748342006 3511 False 6486.00 6486 100.00000 1 3512 1 chr3A.!!$F1 3511
1 TraesCS3A01G536800 chr3A 749875860 749877561 1701 True 833.00 1074 85.35900 852 2656 2 chr3A.!!$R1 1804
2 TraesCS3A01G536800 chr3B 28605368 28608895 3527 True 2818.00 5142 96.06150 37 3512 2 chr3B.!!$R2 3475
3 TraesCS3A01G536800 chr3B 825848186 825850891 2705 False 440.25 599 85.53725 554 2656 4 chr3B.!!$F1 2102
4 TraesCS3A01G536800 chr3B 804546964 804547968 1004 True 306.00 318 85.80300 2657 3452 2 chr3B.!!$R3 795
5 TraesCS3A01G536800 chr3D 615455469 615458563 3094 False 1537.50 2507 88.73900 977 3512 2 chr3D.!!$F2 2535
6 TraesCS3A01G536800 chrUn 247031250 247033628 2378 False 979.50 1308 86.49150 852 2656 2 chrUn.!!$F5 1804
7 TraesCS3A01G536800 chrUn 37113648 37115900 2252 True 956.00 1308 87.72800 963 2656 2 chrUn.!!$R1 1693
8 TraesCS3A01G536800 chrUn 300942377 300944629 2252 True 956.00 1308 87.72800 963 2656 2 chrUn.!!$R2 1693
9 TraesCS3A01G536800 chrUn 345351450 345354048 2598 True 228.00 228 88.14400 2941 3131 2 chrUn.!!$R3 190
10 TraesCS3A01G536800 chr2B 671086782 671087767 985 True 301.50 324 86.19000 2657 3432 2 chr2B.!!$R1 775

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
360 394 0.657312 TTGCTGCAGTGAGTTGTTCG 59.343 50.0 16.64 0.0 0.0 3.95 F
1022 1996 0.108615 GAGGGTGTGGTGATCAGACG 60.109 60.0 0.00 0.0 40.2 4.18 F
1613 3199 0.364180 CAATGCAGATTTGTTGCGCG 59.636 50.0 0.00 0.0 44.4 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 2346 1.329292 GCGTGTGTTGTATGTGTGTGT 59.671 47.619 0.00 0.00 0.00 3.72 R
2036 3631 1.347817 GAACTGCTTCTCCGCGACTG 61.348 60.000 8.23 0.00 0.00 3.51 R
3170 5026 1.202290 GCAATCTACAATGCGGTTGGG 60.202 52.381 6.60 0.31 42.28 4.12 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
50 51 5.517904 TGTATTTACCAAACCGAAAAACCG 58.482 37.500 0.00 0.00 0.00 4.44
51 52 2.488639 TTACCAAACCGAAAAACCGC 57.511 45.000 0.00 0.00 0.00 5.68
57 58 3.802685 CCAAACCGAAAAACCGCATAAAA 59.197 39.130 0.00 0.00 0.00 1.52
73 74 5.462405 GCATAAAACGAACCATGTAAACCA 58.538 37.500 0.00 0.00 0.00 3.67
111 112 1.398390 GAGTGAATGACGGTGAATGCC 59.602 52.381 0.00 0.00 0.00 4.40
229 230 4.159879 TGGAAATACTCGGTCCTTCTCTTC 59.840 45.833 0.00 0.00 32.28 2.87
256 257 3.572682 TCGAAACCCATGATCTAGCGTAT 59.427 43.478 0.00 0.00 0.00 3.06
271 272 1.064060 GCGTATGTGGTTCAATCCAGC 59.936 52.381 0.00 0.00 38.23 4.85
301 302 4.322198 GGTGTTCATGCATCATTTCCTTGT 60.322 41.667 0.00 0.00 0.00 3.16
352 386 2.426381 TGTTGATGTTTTGCTGCAGTGA 59.574 40.909 16.64 0.81 0.00 3.41
360 394 0.657312 TTGCTGCAGTGAGTTGTTCG 59.343 50.000 16.64 0.00 0.00 3.95
364 398 0.880278 TGCAGTGAGTTGTTCGCCTC 60.880 55.000 0.00 0.00 36.99 4.70
365 399 1.891060 GCAGTGAGTTGTTCGCCTCG 61.891 60.000 0.00 0.00 36.99 4.63
421 458 2.093890 TGGCTGTGTGCATCCTAATTG 58.906 47.619 0.00 0.00 45.15 2.32
423 460 2.493278 GGCTGTGTGCATCCTAATTGTT 59.507 45.455 0.00 0.00 45.15 2.83
432 469 3.557595 GCATCCTAATTGTTCAGAGACCG 59.442 47.826 0.00 0.00 0.00 4.79
454 491 7.168219 ACCGGGTATATACTCTTATGTTCGTA 58.832 38.462 6.32 0.00 0.00 3.43
502 539 5.064198 TCAAGTAAAGAACGCCCATTTATCG 59.936 40.000 0.00 0.00 0.00 2.92
599 636 1.618837 GAGCAGGACTAGTGTGGACAA 59.381 52.381 0.00 0.00 0.00 3.18
645 693 3.497297 TGAGTGATTGCATTCATGTGC 57.503 42.857 13.96 1.45 45.25 4.57
748 796 6.246420 ACACGTGTAATATATACGGACCTC 57.754 41.667 21.98 0.00 45.75 3.85
780 828 5.236047 CGTTTTCATTTCCAGGCAAAAATCA 59.764 36.000 0.00 0.00 0.00 2.57
783 831 2.837532 TTTCCAGGCAAAAATCAGGC 57.162 45.000 0.00 0.00 0.00 4.85
799 847 1.227734 GGCGTGGCCGGTGTTATAT 60.228 57.895 1.90 0.00 39.62 0.86
845 893 9.807386 GTGTATAAAAATACATCGATACCAAGC 57.193 33.333 0.00 0.00 39.01 4.01
1022 1996 0.108615 GAGGGTGTGGTGATCAGACG 60.109 60.000 0.00 0.00 40.20 4.18
1243 2217 0.537188 CGATGTGGCCTCTTACACCT 59.463 55.000 3.32 0.00 36.80 4.00
1372 2346 1.609841 CCAGAGAAGCACATGAGCACA 60.610 52.381 17.61 0.00 36.85 4.57
1537 3120 5.046910 TCGCTTTTCCAAGTGAATTCATC 57.953 39.130 12.12 5.72 44.85 2.92
1610 3196 7.492020 TGGTTAATATCAATGCAGATTTGTTGC 59.508 33.333 0.00 0.00 41.86 4.17
1613 3199 0.364180 CAATGCAGATTTGTTGCGCG 59.636 50.000 0.00 0.00 44.40 6.86
1754 3343 1.015868 CATCGCATGGTACATGTGCA 58.984 50.000 16.11 2.63 43.78 4.57
1822 3411 1.682740 TCATGCGCCACATCATGATT 58.317 45.000 5.16 0.00 42.72 2.57
1895 3484 2.093447 GGCTCCAACTACTACATGTGCT 60.093 50.000 9.11 0.00 0.00 4.40
2036 3631 1.443802 GTTCACTTACAGGAGCCAGC 58.556 55.000 0.00 0.00 0.00 4.85
2056 3651 2.095252 GTCGCGGAGAAGCAGTTCC 61.095 63.158 6.13 0.00 36.85 3.62
2163 3758 1.348064 ACAAGTTCCCGACATCTCCA 58.652 50.000 0.00 0.00 0.00 3.86
2269 3864 5.536260 ACTACCGAAACTTAGACAAGAACC 58.464 41.667 0.00 0.00 35.60 3.62
2426 4021 0.247460 CTGCTTGATGAGGTGGTCGA 59.753 55.000 0.00 0.00 0.00 4.20
2696 4296 3.724732 AAATTAAGGTGGGGCGAACTA 57.275 42.857 0.00 0.00 0.00 2.24
2909 4529 3.502237 GCAGTGCCATGTCCTTTTG 57.498 52.632 2.85 0.00 0.00 2.44
2910 4530 0.961019 GCAGTGCCATGTCCTTTTGA 59.039 50.000 2.85 0.00 0.00 2.69
2911 4531 1.340889 GCAGTGCCATGTCCTTTTGAA 59.659 47.619 2.85 0.00 0.00 2.69
2915 4541 5.058490 CAGTGCCATGTCCTTTTGAATTTT 58.942 37.500 0.00 0.00 0.00 1.82
3009 4802 1.974265 TTGCATTCTCCGTTTCCACA 58.026 45.000 0.00 0.00 0.00 4.17
3194 5077 4.036734 CCAACCGCATTGTAGATTGCTATT 59.963 41.667 5.37 0.00 36.47 1.73
3244 5127 3.056107 CAGAAACATACCTCTCCCGTTCA 60.056 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.298854 GGTTTTTCGGTTTGGTAAATACAGTAT 58.701 33.333 0.00 0.00 0.00 2.12
24 25 7.519649 CGGTTTTTCGGTTTGGTAAATACAGTA 60.520 37.037 0.00 0.00 0.00 2.74
25 26 6.506147 GGTTTTTCGGTTTGGTAAATACAGT 58.494 36.000 0.00 0.00 0.00 3.55
26 27 5.626132 CGGTTTTTCGGTTTGGTAAATACAG 59.374 40.000 0.00 0.00 0.00 2.74
27 28 5.517904 CGGTTTTTCGGTTTGGTAAATACA 58.482 37.500 0.00 0.00 0.00 2.29
28 29 4.382457 GCGGTTTTTCGGTTTGGTAAATAC 59.618 41.667 0.00 0.00 0.00 1.89
29 30 4.037208 TGCGGTTTTTCGGTTTGGTAAATA 59.963 37.500 0.00 0.00 0.00 1.40
30 31 3.181478 TGCGGTTTTTCGGTTTGGTAAAT 60.181 39.130 0.00 0.00 0.00 1.40
31 32 2.165030 TGCGGTTTTTCGGTTTGGTAAA 59.835 40.909 0.00 0.00 0.00 2.01
32 33 1.747355 TGCGGTTTTTCGGTTTGGTAA 59.253 42.857 0.00 0.00 0.00 2.85
33 34 1.386533 TGCGGTTTTTCGGTTTGGTA 58.613 45.000 0.00 0.00 0.00 3.25
34 35 0.747852 ATGCGGTTTTTCGGTTTGGT 59.252 45.000 0.00 0.00 0.00 3.67
35 36 2.708386 TATGCGGTTTTTCGGTTTGG 57.292 45.000 0.00 0.00 0.00 3.28
50 51 5.462405 TGGTTTACATGGTTCGTTTTATGC 58.538 37.500 0.00 0.00 0.00 3.14
51 52 7.932120 TTTGGTTTACATGGTTCGTTTTATG 57.068 32.000 0.00 0.00 0.00 1.90
57 58 6.448852 GGTTTATTTGGTTTACATGGTTCGT 58.551 36.000 0.00 0.00 0.00 3.85
73 74 3.059188 CACTCTGTGCGTTCGGTTTATTT 60.059 43.478 0.00 0.00 0.00 1.40
111 112 2.045926 CCCCGAACTTGAGGCCTG 60.046 66.667 12.00 0.00 0.00 4.85
153 154 2.203728 TGGCCAGGTACGACCAGT 60.204 61.111 0.00 0.00 41.95 4.00
229 230 1.137086 AGATCATGGGTTTCGACTCGG 59.863 52.381 0.00 0.00 0.00 4.63
256 257 1.003003 TCATCGCTGGATTGAACCACA 59.997 47.619 0.00 0.00 35.91 4.17
271 272 1.004610 GATGCATGAACACCGTCATCG 60.005 52.381 2.46 0.00 36.04 3.84
301 302 0.817634 CCCAACAGCGACACCTTCAA 60.818 55.000 0.00 0.00 0.00 2.69
331 332 2.426381 TCACTGCAGCAAAACATCAACA 59.574 40.909 15.27 0.00 0.00 3.33
336 370 2.428171 ACAACTCACTGCAGCAAAACAT 59.572 40.909 15.27 0.00 0.00 2.71
352 386 1.961277 CAAGGCGAGGCGAACAACT 60.961 57.895 0.00 0.00 0.00 3.16
360 394 0.815615 CATAAGGGTCAAGGCGAGGC 60.816 60.000 0.00 0.00 0.00 4.70
404 441 4.696877 TCTGAACAATTAGGATGCACACAG 59.303 41.667 0.00 0.00 0.00 3.66
414 451 2.236395 ACCCGGTCTCTGAACAATTAGG 59.764 50.000 0.00 0.00 0.00 2.69
421 458 5.315348 AGAGTATATACCCGGTCTCTGAAC 58.685 45.833 9.32 0.00 32.19 3.18
423 460 5.579753 AAGAGTATATACCCGGTCTCTGA 57.420 43.478 9.32 0.00 33.44 3.27
454 491 4.383173 TCATAATGTCGCATCAAGCAGAT 58.617 39.130 0.00 0.00 46.13 2.90
520 557 5.154222 CAGTTGGGAAGAAAGAAATAACGC 58.846 41.667 0.00 0.00 0.00 4.84
645 693 1.008538 GGCTGCGTTGTGGTTTGAG 60.009 57.895 0.00 0.00 0.00 3.02
729 777 6.803642 GGATGGAGGTCCGTATATATTACAC 58.196 44.000 0.00 0.00 39.43 2.90
748 796 2.486203 TGGAAATGAAAACGACGGATGG 59.514 45.455 0.00 0.00 0.00 3.51
783 831 1.000506 AGCTATATAACACCGGCCACG 59.999 52.381 0.00 0.00 40.55 4.94
845 893 3.074412 ACTGTTTTCATGTTAGGCTCCG 58.926 45.455 0.00 0.00 0.00 4.63
1022 1996 0.603975 GTTCACCTCCACTGTCTGGC 60.604 60.000 0.00 0.00 40.39 4.85
1243 2217 2.955660 GGTCACCAACAATGTGAAAGGA 59.044 45.455 0.00 0.00 43.82 3.36
1372 2346 1.329292 GCGTGTGTTGTATGTGTGTGT 59.671 47.619 0.00 0.00 0.00 3.72
1510 2516 6.429692 TGAATTCACTTGGAAAAGCGAGAATA 59.570 34.615 3.38 0.00 39.39 1.75
1537 3120 4.024133 GCCCAACAATAAAACAAAAGGCTG 60.024 41.667 0.00 0.00 33.86 4.85
1610 3196 3.444916 ACGGCTTATGGATTATATCGCG 58.555 45.455 0.00 0.00 0.00 5.87
1613 3199 5.975410 GCAGACGGCTTATGGATTATATC 57.025 43.478 0.00 0.00 40.25 1.63
1754 3343 3.379445 ACGCTCCGGACGGAACAT 61.379 61.111 23.77 0.00 44.66 2.71
2036 3631 1.347817 GAACTGCTTCTCCGCGACTG 61.348 60.000 8.23 0.00 0.00 3.51
2333 3928 4.419522 AAGTTGTATGTGATGTTTCCGC 57.580 40.909 0.00 0.00 0.00 5.54
2337 3932 5.243730 CCCCTCAAAGTTGTATGTGATGTTT 59.756 40.000 0.00 0.00 0.00 2.83
2338 3933 4.766891 CCCCTCAAAGTTGTATGTGATGTT 59.233 41.667 0.00 0.00 0.00 2.71
2696 4296 8.780846 TTGCATCAAAAGAAATTATGCTTCAT 57.219 26.923 8.20 0.00 42.63 2.57
3170 5026 1.202290 GCAATCTACAATGCGGTTGGG 60.202 52.381 6.60 0.31 42.28 4.12
3173 5029 5.356751 TGAAATAGCAATCTACAATGCGGTT 59.643 36.000 0.00 0.00 46.98 4.44
3471 5374 1.281899 GAGCGTCAGTGTTAGCATCC 58.718 55.000 9.16 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.