Multiple sequence alignment - TraesCS2A01G365800

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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 TraesCS2A01G365800 chr2A 100.000 2863 0 0 1 2863 610659600 610662462 0.000000e+00 5288
1 TraesCS2A01G365800 chr2A 89.087 1347 76 27 739 2056 587735787 587737091 0.000000e+00 1607
2 TraesCS2A01G365800 chr2A 85.541 740 86 11 1 734 34163003 34163727 0.000000e+00 754
3 TraesCS2A01G365800 chr2A 92.549 510 35 3 2054 2560 11552387 11552896 0.000000e+00 728
4 TraesCS2A01G365800 chr2A 92.157 510 39 1 2054 2562 627918587 627918078 0.000000e+00 719
5 TraesCS2A01G365800 chr2A 91.813 513 40 2 2054 2564 766222302 766221790 0.000000e+00 713
6 TraesCS2A01G365800 chr2A 97.231 325 9 0 424 748 610646416 610646740 4.170000e-153 551
7 TraesCS2A01G365800 chr2A 89.744 312 17 9 2559 2863 587737090 587737393 4.470000e-103 385
8 TraesCS2A01G365800 chr2A 77.717 552 81 30 148 679 513837779 513838308 1.670000e-77 300
9 TraesCS2A01G365800 chr2D 93.816 1326 54 13 747 2056 445387595 445388908 0.000000e+00 1969
10 TraesCS2A01G365800 chr2D 96.405 306 9 2 2559 2863 445388907 445389211 1.180000e-138 503
11 TraesCS2A01G365800 chr2D 89.524 315 24 7 426 734 13858729 13859040 9.620000e-105 390
12 TraesCS2A01G365800 chr2B 91.134 1331 62 22 740 2056 523525391 523526679 0.000000e+00 1753
13 TraesCS2A01G365800 chr2B 82.781 755 92 21 1 734 705682193 705682930 8.650000e-180 640
14 TraesCS2A01G365800 chr2B 92.157 306 18 5 2559 2863 523526678 523526978 7.330000e-116 427
15 TraesCS2A01G365800 chr2B 84.142 309 40 8 148 452 232934640 232934943 1.000000e-74 291
16 TraesCS2A01G365800 chr6B 90.250 759 47 14 1 748 210551552 210550810 0.000000e+00 966
17 TraesCS2A01G365800 chr6B 89.458 332 23 9 426 748 210556192 210555864 2.660000e-110 409
18 TraesCS2A01G365800 chr6B 84.181 354 32 13 1604 1950 145901039 145900703 3.560000e-84 322
19 TraesCS2A01G365800 chr6B 84.589 292 29 5 5 293 292803814 292803536 2.810000e-70 276
20 TraesCS2A01G365800 chr4A 89.592 759 54 12 1 748 669077196 669077940 0.000000e+00 941
21 TraesCS2A01G365800 chr4A 91.829 514 40 2 2054 2565 617503604 617504117 0.000000e+00 715
22 TraesCS2A01G365800 chr4A 88.024 334 27 11 425 748 669054931 669055261 1.610000e-102 383
23 TraesCS2A01G365800 chr4A 75.979 562 89 33 142 677 698663607 698663066 6.130000e-62 248
24 TraesCS2A01G365800 chr3A 87.584 741 70 16 1 734 293069888 293069163 0.000000e+00 839
25 TraesCS2A01G365800 chr3A 92.308 507 39 0 2054 2560 336886272 336885766 0.000000e+00 721
26 TraesCS2A01G365800 chr3A 84.642 293 36 6 163 450 81466328 81466040 1.680000e-72 283
27 TraesCS2A01G365800 chr7A 93.110 508 34 1 2054 2560 674010190 674009683 0.000000e+00 743
28 TraesCS2A01G365800 chr1A 92.534 509 36 2 2054 2560 532809605 532810113 0.000000e+00 728
29 TraesCS2A01G365800 chr1A 92.338 509 38 1 2054 2561 532864885 532865393 0.000000e+00 723
30 TraesCS2A01G365800 chr7B 92.520 508 37 1 2054 2560 635921307 635920800 0.000000e+00 726
31 TraesCS2A01G365800 chr5D 88.627 510 34 12 229 734 565752596 565752107 1.470000e-167 599
32 TraesCS2A01G365800 chr5D 89.809 314 24 6 426 734 565757454 565757144 2.070000e-106 396
33 TraesCS2A01G365800 chr5D 89.320 206 10 2 3 207 565752783 565752589 6.130000e-62 248
34 TraesCS2A01G365800 chr4D 89.524 315 25 6 426 734 20109402 20109714 2.670000e-105 392


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 TraesCS2A01G365800 chr2A 610659600 610662462 2862 False 5288.0 5288 100.0000 1 2863 1 chr2A.!!$F5 2862
1 TraesCS2A01G365800 chr2A 587735787 587737393 1606 False 996.0 1607 89.4155 739 2863 2 chr2A.!!$F6 2124
2 TraesCS2A01G365800 chr2A 34163003 34163727 724 False 754.0 754 85.5410 1 734 1 chr2A.!!$F2 733
3 TraesCS2A01G365800 chr2A 11552387 11552896 509 False 728.0 728 92.5490 2054 2560 1 chr2A.!!$F1 506
4 TraesCS2A01G365800 chr2A 627918078 627918587 509 True 719.0 719 92.1570 2054 2562 1 chr2A.!!$R1 508
5 TraesCS2A01G365800 chr2A 766221790 766222302 512 True 713.0 713 91.8130 2054 2564 1 chr2A.!!$R2 510
6 TraesCS2A01G365800 chr2A 513837779 513838308 529 False 300.0 300 77.7170 148 679 1 chr2A.!!$F3 531
7 TraesCS2A01G365800 chr2D 445387595 445389211 1616 False 1236.0 1969 95.1105 747 2863 2 chr2D.!!$F2 2116
8 TraesCS2A01G365800 chr2B 523525391 523526978 1587 False 1090.0 1753 91.6455 740 2863 2 chr2B.!!$F3 2123
9 TraesCS2A01G365800 chr2B 705682193 705682930 737 False 640.0 640 82.7810 1 734 1 chr2B.!!$F2 733
10 TraesCS2A01G365800 chr6B 210550810 210551552 742 True 966.0 966 90.2500 1 748 1 chr6B.!!$R2 747
11 TraesCS2A01G365800 chr4A 669077196 669077940 744 False 941.0 941 89.5920 1 748 1 chr4A.!!$F3 747
12 TraesCS2A01G365800 chr4A 617503604 617504117 513 False 715.0 715 91.8290 2054 2565 1 chr4A.!!$F1 511
13 TraesCS2A01G365800 chr4A 698663066 698663607 541 True 248.0 248 75.9790 142 677 1 chr4A.!!$R1 535
14 TraesCS2A01G365800 chr3A 293069163 293069888 725 True 839.0 839 87.5840 1 734 1 chr3A.!!$R2 733
15 TraesCS2A01G365800 chr3A 336885766 336886272 506 True 721.0 721 92.3080 2054 2560 1 chr3A.!!$R3 506
16 TraesCS2A01G365800 chr7A 674009683 674010190 507 True 743.0 743 93.1100 2054 2560 1 chr7A.!!$R1 506
17 TraesCS2A01G365800 chr1A 532809605 532810113 508 False 728.0 728 92.5340 2054 2560 1 chr1A.!!$F1 506
18 TraesCS2A01G365800 chr1A 532864885 532865393 508 False 723.0 723 92.3380 2054 2561 1 chr1A.!!$F2 507
19 TraesCS2A01G365800 chr7B 635920800 635921307 507 True 726.0 726 92.5200 2054 2560 1 chr7B.!!$R1 506
20 TraesCS2A01G365800 chr5D 565752107 565752783 676 True 423.5 599 88.9735 3 734 2 chr5D.!!$R2 731

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
914 1014 0.257905 TTGAGACGGAGGGCTAGCTA 59.742 55.0 15.72 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2453 2600 1.141881 CGCCAAGTATCGAGGTGCT 59.858 57.895 0.0 0.0 0.0 4.4 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
65 66 4.394712 CACTGGTCCCGTGGAGGC 62.395 72.222 5.55 0.00 39.21 4.70
66 67 4.640690 ACTGGTCCCGTGGAGGCT 62.641 66.667 0.00 0.00 39.21 4.58
67 68 3.775654 CTGGTCCCGTGGAGGCTC 61.776 72.222 5.78 5.78 39.21 4.70
68 69 4.316823 TGGTCCCGTGGAGGCTCT 62.317 66.667 15.23 0.00 39.21 4.09
69 70 3.462678 GGTCCCGTGGAGGCTCTC 61.463 72.222 15.23 5.26 39.21 3.20
140 141 2.561885 CGCTCCACTCGACGAGTT 59.438 61.111 27.28 10.65 41.37 3.01
159 160 4.643387 GGTGTGGCCGCTTGGAGT 62.643 66.667 18.96 0.00 33.02 3.85
243 272 2.633488 TCATCGATCTGAGACGTCTGT 58.367 47.619 25.58 5.90 0.00 3.41
274 303 2.635229 CTTGAGGACGATGGCGGAGG 62.635 65.000 0.00 0.00 43.17 4.30
391 421 2.163454 TCCAGGGTGGATTTGCAGT 58.837 52.632 0.00 0.00 42.67 4.40
441 476 3.104512 CAGGATGTTAGGTACCAGGTCA 58.895 50.000 15.94 8.03 0.00 4.02
472 528 6.414408 ACAGATACAAGCTTGAATTCGAAG 57.586 37.500 32.50 19.13 0.00 3.79
473 529 6.166279 ACAGATACAAGCTTGAATTCGAAGA 58.834 36.000 32.50 6.38 0.00 2.87
577 666 0.670546 CTGGATGCGTCGTTCCTTGT 60.671 55.000 14.73 0.00 32.95 3.16
603 694 2.505167 GGGATAAGTAGGCGCCGGT 61.505 63.158 23.20 7.21 0.00 5.28
642 737 1.724582 CCCATTTCGGCCCGATGAAC 61.725 60.000 6.69 0.00 35.23 3.18
643 738 0.748005 CCATTTCGGCCCGATGAACT 60.748 55.000 6.69 0.00 35.23 3.01
811 909 2.630580 GTCTGAGACTGAAACCAGACCT 59.369 50.000 5.12 0.00 45.77 3.85
914 1014 0.257905 TTGAGACGGAGGGCTAGCTA 59.742 55.000 15.72 0.00 0.00 3.32
917 1019 1.271102 GAGACGGAGGGCTAGCTAATG 59.729 57.143 15.72 3.93 0.00 1.90
1149 1263 1.374758 CAAGAAGCCGAGGAACGCT 60.375 57.895 0.00 0.00 41.07 5.07
1205 1322 2.116366 GGTGCGTGCACTGTTAAAAAG 58.884 47.619 22.82 0.00 45.52 2.27
1206 1323 1.516864 GTGCGTGCACTGTTAAAAAGC 59.483 47.619 17.32 7.93 43.12 3.51
1207 1324 1.128513 GCGTGCACTGTTAAAAAGCC 58.871 50.000 16.19 0.00 0.00 4.35
1243 1362 1.464608 CGCCTGTGAATTCGATGTTGT 59.535 47.619 0.04 0.00 0.00 3.32
1257 1376 4.216042 TCGATGTTGTTTTGCTGATGTGAT 59.784 37.500 0.00 0.00 0.00 3.06
1266 1385 5.406767 TTTGCTGATGTGATTTTTGTTGC 57.593 34.783 0.00 0.00 0.00 4.17
1355 1474 1.555967 TGGGAAGGTATTTGCTTGCC 58.444 50.000 0.00 0.00 38.75 4.52
1419 1539 3.061563 CGCTTGCAATGAATGATTGTTGG 59.938 43.478 0.00 0.00 43.17 3.77
1627 1764 4.016444 TGCACACTATTCTGAAATTCCCC 58.984 43.478 0.00 0.00 0.00 4.81
1679 1816 6.040247 CAGAAGTATAAACCGCAGTGTATGA 58.960 40.000 0.00 0.00 28.88 2.15
1732 1872 3.915437 AATGGTTTTGTCATGGTCGAC 57.085 42.857 7.13 7.13 36.40 4.20
1977 2117 3.084039 GCTGACCCAATTCAGTCAATCA 58.916 45.455 8.11 0.00 44.34 2.57
1995 2135 5.760743 TCAATCACCTAACACAATCGTTTCA 59.239 36.000 0.00 0.00 0.00 2.69
2027 2173 0.037326 TCCGTGAACATCCTCAGCAC 60.037 55.000 0.00 0.00 0.00 4.40
2056 2202 0.822811 TGGCGCCGGTAGTATGTAAA 59.177 50.000 23.90 0.00 0.00 2.01
2079 2225 4.963318 TTAATCAGCCCACCTCTATCAG 57.037 45.455 0.00 0.00 0.00 2.90
2128 2274 4.574013 GGAGTTGATTCTGATACTGCAAGG 59.426 45.833 0.00 0.00 39.30 3.61
2135 2281 3.689347 TCTGATACTGCAAGGCACATTT 58.311 40.909 0.00 0.00 39.30 2.32
2140 2286 1.202440 ACTGCAAGGCACATTTGTGTG 60.202 47.619 11.99 4.27 42.43 3.82
2160 2306 2.950309 TGGGCGTTTGTGCTTTACTTTA 59.050 40.909 0.00 0.00 34.52 1.85
2163 2309 3.004002 GGCGTTTGTGCTTTACTTTAGGT 59.996 43.478 0.00 0.00 34.52 3.08
2230 2377 7.552330 ACAAACATTCACTTTTTGCAGGTTATT 59.448 29.630 0.00 0.00 34.22 1.40
2232 2379 7.713764 ACATTCACTTTTTGCAGGTTATTTC 57.286 32.000 0.00 0.00 0.00 2.17
2237 2384 4.898861 ACTTTTTGCAGGTTATTTCCAGGA 59.101 37.500 0.00 0.00 0.00 3.86
2324 2471 2.495084 CGTCTACCCGATGAGAGATGA 58.505 52.381 0.00 0.00 0.00 2.92
2354 2501 4.381185 GGGATATTTTCAACCGGTTTGGAC 60.381 45.833 19.55 4.02 42.00 4.02
2376 2523 3.442625 CGGCGGTCATGTAATAGGATAGA 59.557 47.826 0.00 0.00 0.00 1.98
2519 2666 8.648557 TTAATAATATGAGCCGTATGCATCTC 57.351 34.615 0.19 4.12 44.83 2.75
2522 2669 0.676184 TGAGCCGTATGCATCTCTCC 59.324 55.000 0.19 0.00 44.83 3.71
2542 2689 0.179034 GATGCAGAGGCTGGGGTAAG 60.179 60.000 0.00 0.00 41.91 2.34
2608 2755 2.023771 CACCGCCGATCGATGGATG 61.024 63.158 25.92 17.60 41.67 3.51
2620 2767 1.073783 ATGGATGGATCGGTCCCCA 60.074 57.895 13.41 13.91 44.41 4.96
2719 2872 1.173043 GTTTCATTCATGCCCGTCCA 58.827 50.000 0.00 0.00 0.00 4.02
2738 2891 2.684881 CCATGCTCATCAACCCTTGTAC 59.315 50.000 0.00 0.00 0.00 2.90
2741 2894 4.471904 TGCTCATCAACCCTTGTACTAG 57.528 45.455 0.00 0.00 0.00 2.57
2742 2895 4.093743 TGCTCATCAACCCTTGTACTAGA 58.906 43.478 5.85 0.00 0.00 2.43
2743 2896 4.160439 TGCTCATCAACCCTTGTACTAGAG 59.840 45.833 5.85 0.00 0.00 2.43
2744 2897 4.402793 GCTCATCAACCCTTGTACTAGAGA 59.597 45.833 5.85 0.00 0.00 3.10
2745 2898 5.451242 GCTCATCAACCCTTGTACTAGAGAG 60.451 48.000 5.85 3.33 0.00 3.20
2746 2899 5.580998 TCATCAACCCTTGTACTAGAGAGT 58.419 41.667 5.85 0.00 39.92 3.24
2777 2930 2.095847 CGGTGCATGCATTTGTGCC 61.096 57.895 25.64 17.68 40.56 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 4.214327 GAGGAAGCCGGCGGAGAG 62.214 72.222 33.44 2.59 0.00 3.20
225 254 1.064803 GCACAGACGTCTCAGATCGAT 59.935 52.381 16.96 0.00 0.00 3.59
234 263 2.936912 GCTCCAGGCACAGACGTCT 61.937 63.158 13.58 13.58 41.35 4.18
243 272 2.350134 CTCAAGCAGCTCCAGGCA 59.650 61.111 0.00 0.00 44.79 4.75
391 421 1.059584 ACCACACACCACCAGATCCA 61.060 55.000 0.00 0.00 0.00 3.41
472 528 3.839293 ACAACGAGAAGCTGAGTGTATC 58.161 45.455 0.00 0.00 0.00 2.24
473 529 3.944055 ACAACGAGAAGCTGAGTGTAT 57.056 42.857 0.00 0.00 0.00 2.29
566 654 1.557443 CCTCACGCACAAGGAACGAC 61.557 60.000 0.00 0.00 34.35 4.34
569 657 1.966451 CCCCTCACGCACAAGGAAC 60.966 63.158 0.00 0.00 34.35 3.62
577 666 1.410004 CCTACTTATCCCCTCACGCA 58.590 55.000 0.00 0.00 0.00 5.24
720 815 4.662961 CGACCTGCCACGACAGCA 62.663 66.667 0.00 0.00 36.29 4.41
811 909 7.234371 CACTCTCCCATTATCTATTCAGAAGGA 59.766 40.741 0.00 0.00 33.50 3.36
914 1014 3.055094 AGGAGCGTTTCTGTATGACCATT 60.055 43.478 0.00 0.00 0.00 3.16
917 1019 2.271800 CAGGAGCGTTTCTGTATGACC 58.728 52.381 0.00 0.00 0.00 4.02
1230 1349 5.630680 ACATCAGCAAAACAACATCGAATTC 59.369 36.000 0.00 0.00 0.00 2.17
1243 1362 5.502058 CGCAACAAAAATCACATCAGCAAAA 60.502 36.000 0.00 0.00 0.00 2.44
1257 1376 1.069296 CCTGCTCGATCGCAACAAAAA 60.069 47.619 11.09 0.00 39.80 1.94
1266 1385 1.268999 CCTTCTTCTCCTGCTCGATCG 60.269 57.143 9.36 9.36 0.00 3.69
1355 1474 1.579932 CAAGCAAGGCACTGCAGAG 59.420 57.895 23.35 14.77 40.86 3.35
1419 1539 7.512297 CATTTTCACAACCAAATATGCTCAAC 58.488 34.615 0.00 0.00 0.00 3.18
1627 1764 7.901889 CAGAGTTTATCATGTTCAGAATGTTCG 59.098 37.037 0.00 0.00 37.40 3.95
1722 1862 2.571757 GTCCTGCGTCGACCATGA 59.428 61.111 10.58 8.69 0.00 3.07
1969 2109 4.894784 ACGATTGTGTTAGGTGATTGACT 58.105 39.130 0.00 0.00 0.00 3.41
1977 2117 5.237779 ACGAAATGAAACGATTGTGTTAGGT 59.762 36.000 0.00 0.00 0.00 3.08
2056 2202 5.747248 GCTGATAGAGGTGGGCTGATTAATT 60.747 44.000 0.00 0.00 0.00 1.40
2099 2245 5.869344 CAGTATCAGAATCAACTCCGTCAAA 59.131 40.000 0.00 0.00 0.00 2.69
2116 2262 3.057386 CACAAATGTGCCTTGCAGTATCA 60.057 43.478 0.00 0.00 40.08 2.15
2135 2281 1.599606 AAAGCACAAACGCCCACACA 61.600 50.000 0.00 0.00 0.00 3.72
2140 2286 2.502213 AAAGTAAAGCACAAACGCCC 57.498 45.000 0.00 0.00 0.00 6.13
2160 2306 6.711277 TCATTTCTGCAGTTTCATACTACCT 58.289 36.000 14.67 0.00 34.56 3.08
2230 2377 3.524648 GAACGCCGTGGTCCTGGAA 62.525 63.158 0.00 0.00 0.00 3.53
2232 2379 3.605749 ATGAACGCCGTGGTCCTGG 62.606 63.158 0.00 0.00 0.00 4.45
2324 2471 2.812011 GGTTGAAAATATCCCGCGCTAT 59.188 45.455 5.56 0.00 0.00 2.97
2354 2501 2.743636 ATCCTATTACATGACCGCCG 57.256 50.000 0.00 0.00 0.00 6.46
2376 2523 4.826274 ACACAATAGGAGCACTACATGT 57.174 40.909 2.69 2.69 36.19 3.21
2453 2600 1.141881 CGCCAAGTATCGAGGTGCT 59.858 57.895 0.00 0.00 0.00 4.40
2519 2666 2.108566 CCAGCCTCTGCATCGGAG 59.891 66.667 5.65 0.20 41.13 4.63
2522 2669 1.971505 TTACCCCAGCCTCTGCATCG 61.972 60.000 0.00 0.00 41.13 3.84
2620 2767 2.668212 CACCCACGCAACGACCAT 60.668 61.111 0.00 0.00 0.00 3.55
2719 2872 4.716784 TCTAGTACAAGGGTTGATGAGCAT 59.283 41.667 0.00 0.00 0.00 3.79
2738 2891 5.239744 ACCGCATGTTGATACTACTCTCTAG 59.760 44.000 0.00 0.00 0.00 2.43
2741 2894 4.045104 CACCGCATGTTGATACTACTCTC 58.955 47.826 0.00 0.00 0.00 3.20
2742 2895 3.738281 GCACCGCATGTTGATACTACTCT 60.738 47.826 0.00 0.00 0.00 3.24
2743 2896 2.540101 GCACCGCATGTTGATACTACTC 59.460 50.000 0.00 0.00 0.00 2.59
2744 2897 2.093711 TGCACCGCATGTTGATACTACT 60.094 45.455 0.00 0.00 31.71 2.57
2745 2898 2.276201 TGCACCGCATGTTGATACTAC 58.724 47.619 0.00 0.00 31.71 2.73
2746 2899 2.682155 TGCACCGCATGTTGATACTA 57.318 45.000 0.00 0.00 31.71 1.82


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

AutoCloner maintained by Alex Coulton.