Multiple sequence alignment - TraesCS2D01G048500

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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 TraesCS2D01G048500 chr2D 100.000 3312 0 0 1 3312 17776213 17772902 0.000000e+00 6117
1 TraesCS2D01G048500 chr2D 83.693 2361 305 48 98 2426 17613747 17611435 0.000000e+00 2154
2 TraesCS2D01G048500 chr2D 83.602 2360 307 48 98 2426 17641116 17638806 0.000000e+00 2141
3 TraesCS2D01G048500 chr2D 91.228 855 61 9 2460 3312 577788937 577788095 0.000000e+00 1151
4 TraesCS2D01G048500 chr2B 90.128 2431 195 18 1 2408 29262140 29264548 0.000000e+00 3118
5 TraesCS2D01G048500 chr2B 90.004 2431 198 18 1 2408 29317377 29319785 0.000000e+00 3101
6 TraesCS2D01G048500 chr2B 89.926 2432 198 20 1 2408 29348496 29350904 0.000000e+00 3090
7 TraesCS2D01G048500 chr2B 92.805 1515 78 5 746 2231 29218019 29219531 0.000000e+00 2165
8 TraesCS2D01G048500 chr2B 83.517 2354 309 45 101 2426 29548370 29550672 0.000000e+00 2124
9 TraesCS2D01G048500 chr2B 94.712 851 32 5 2464 3312 519689426 519688587 0.000000e+00 1310
10 TraesCS2D01G048500 chr2B 93.144 846 29 9 2470 3312 685817904 685818723 0.000000e+00 1214
11 TraesCS2D01G048500 chr2B 88.204 763 54 14 1 747 29217120 29217862 0.000000e+00 878
12 TraesCS2D01G048500 chr2A 92.196 1589 102 11 205 1774 19055659 19054074 0.000000e+00 2228
13 TraesCS2D01G048500 chr2A 94.714 681 35 1 1743 2422 19054071 19053391 0.000000e+00 1057
14 TraesCS2D01G048500 chr2A 93.035 603 30 5 2466 3066 10227172 10227764 0.000000e+00 870
15 TraesCS2D01G048500 chr2A 90.821 207 14 2 1 206 19056009 19055807 4.210000e-69 272
16 TraesCS2D01G048500 chr7D 93.494 830 35 6 2474 3301 625109251 625108439 0.000000e+00 1216
17 TraesCS2D01G048500 chr7D 91.088 864 49 7 2451 3312 2509732 2508895 0.000000e+00 1144
18 TraesCS2D01G048500 chr7D 96.186 603 16 4 2711 3312 52235431 52234835 0.000000e+00 979
19 TraesCS2D01G048500 chr4B 91.990 824 58 6 2491 3312 5199833 5200650 0.000000e+00 1149
20 TraesCS2D01G048500 chr3B 81.973 1348 191 36 1092 2426 765017783 765019091 0.000000e+00 1096
21 TraesCS2D01G048500 chr1B 89.756 859 65 11 2457 3312 561875141 561875979 0.000000e+00 1077
22 TraesCS2D01G048500 chr1B 93.504 508 31 2 1920 2426 651061658 651061152 0.000000e+00 754
23 TraesCS2D01G048500 chr7B 93.898 508 30 1 1920 2426 745128183 745128690 0.000000e+00 765
24 TraesCS2D01G048500 chr6B 94.397 464 18 3 2487 2948 693100810 693101267 0.000000e+00 706
25 TraesCS2D01G048500 chr6B 91.316 380 25 3 2473 2851 715203576 715203204 2.280000e-141 512
26 TraesCS2D01G048500 chr6B 90.765 379 29 1 2473 2851 57580368 57580740 4.930000e-138 501
27 TraesCS2D01G048500 chr4A 90.215 511 40 5 2459 2966 688579584 688580087 0.000000e+00 658
28 TraesCS2D01G048500 chr1A 91.864 381 28 1 2471 2851 23424331 23424708 2.260000e-146 529
29 TraesCS2D01G048500 chr3A 90.746 389 28 5 2465 2851 113324849 113324467 2.280000e-141 512
30 TraesCS2D01G048500 chr3A 90.862 383 29 1 2469 2851 750712931 750713307 2.950000e-140 508


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 TraesCS2D01G048500 chr2D 17772902 17776213 3311 True 6117.000000 6117 100.0000 1 3312 1 chr2D.!!$R3 3311
1 TraesCS2D01G048500 chr2D 17611435 17613747 2312 True 2154.000000 2154 83.6930 98 2426 1 chr2D.!!$R1 2328
2 TraesCS2D01G048500 chr2D 17638806 17641116 2310 True 2141.000000 2141 83.6020 98 2426 1 chr2D.!!$R2 2328
3 TraesCS2D01G048500 chr2D 577788095 577788937 842 True 1151.000000 1151 91.2280 2460 3312 1 chr2D.!!$R4 852
4 TraesCS2D01G048500 chr2B 29262140 29264548 2408 False 3118.000000 3118 90.1280 1 2408 1 chr2B.!!$F1 2407
5 TraesCS2D01G048500 chr2B 29317377 29319785 2408 False 3101.000000 3101 90.0040 1 2408 1 chr2B.!!$F2 2407
6 TraesCS2D01G048500 chr2B 29348496 29350904 2408 False 3090.000000 3090 89.9260 1 2408 1 chr2B.!!$F3 2407
7 TraesCS2D01G048500 chr2B 29548370 29550672 2302 False 2124.000000 2124 83.5170 101 2426 1 chr2B.!!$F4 2325
8 TraesCS2D01G048500 chr2B 29217120 29219531 2411 False 1521.500000 2165 90.5045 1 2231 2 chr2B.!!$F6 2230
9 TraesCS2D01G048500 chr2B 519688587 519689426 839 True 1310.000000 1310 94.7120 2464 3312 1 chr2B.!!$R1 848
10 TraesCS2D01G048500 chr2B 685817904 685818723 819 False 1214.000000 1214 93.1440 2470 3312 1 chr2B.!!$F5 842
11 TraesCS2D01G048500 chr2A 19053391 19056009 2618 True 1185.666667 2228 92.5770 1 2422 3 chr2A.!!$R1 2421
12 TraesCS2D01G048500 chr2A 10227172 10227764 592 False 870.000000 870 93.0350 2466 3066 1 chr2A.!!$F1 600
13 TraesCS2D01G048500 chr7D 625108439 625109251 812 True 1216.000000 1216 93.4940 2474 3301 1 chr7D.!!$R3 827
14 TraesCS2D01G048500 chr7D 2508895 2509732 837 True 1144.000000 1144 91.0880 2451 3312 1 chr7D.!!$R1 861
15 TraesCS2D01G048500 chr7D 52234835 52235431 596 True 979.000000 979 96.1860 2711 3312 1 chr7D.!!$R2 601
16 TraesCS2D01G048500 chr4B 5199833 5200650 817 False 1149.000000 1149 91.9900 2491 3312 1 chr4B.!!$F1 821
17 TraesCS2D01G048500 chr3B 765017783 765019091 1308 False 1096.000000 1096 81.9730 1092 2426 1 chr3B.!!$F1 1334
18 TraesCS2D01G048500 chr1B 561875141 561875979 838 False 1077.000000 1077 89.7560 2457 3312 1 chr1B.!!$F1 855
19 TraesCS2D01G048500 chr1B 651061152 651061658 506 True 754.000000 754 93.5040 1920 2426 1 chr1B.!!$R1 506
20 TraesCS2D01G048500 chr7B 745128183 745128690 507 False 765.000000 765 93.8980 1920 2426 1 chr7B.!!$F1 506
21 TraesCS2D01G048500 chr4A 688579584 688580087 503 False 658.000000 658 90.2150 2459 2966 1 chr4A.!!$F1 507

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
868 1198 0.600255 CGTTCCACTTCAGCTTCCGT 60.6 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2864 0.044397 GGGGGAAAGGAGGAGTAGGT 59.956 60.0 0.0 0.0 0.0 3.08 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
33 34 5.789521 TCATCATTCTCCGTAAACTGAACA 58.210 37.500 0.00 0.00 0.00 3.18
75 76 8.744008 AAAGACGGATTCTCAATGTATATACG 57.256 34.615 8.33 0.00 31.02 3.06
76 77 7.450124 AGACGGATTCTCAATGTATATACGT 57.550 36.000 8.33 5.07 0.00 3.57
77 78 8.557592 AGACGGATTCTCAATGTATATACGTA 57.442 34.615 8.02 0.00 0.00 3.57
154 156 4.493547 CATGCGGTTGTAAATGAACCATT 58.506 39.130 0.00 0.00 42.75 3.16
264 416 2.775911 TCATCACTGCAAGCTAGCTT 57.224 45.000 24.42 24.42 37.60 3.74
288 440 7.193377 TCACTTTTATTCTTTGTTACCGGAC 57.807 36.000 9.46 0.00 0.00 4.79
324 476 6.468543 TGTGCATGTGTAGAAGGTTGTATTA 58.531 36.000 0.00 0.00 0.00 0.98
392 551 3.088532 TCCATGTAACTTTGGATGCACC 58.911 45.455 0.00 0.00 37.10 5.01
483 642 7.733773 ACGACCTATGATGATATATTCCCAA 57.266 36.000 0.00 0.00 0.00 4.12
560 719 6.859112 TGAGGCTACTTATCTTCTCAAAGT 57.141 37.500 0.00 0.00 37.27 2.66
747 1077 8.050778 ACGTGCAGGAAAATGAAAAGATATAA 57.949 30.769 14.38 0.00 0.00 0.98
868 1198 0.600255 CGTTCCACTTCAGCTTCCGT 60.600 55.000 0.00 0.00 0.00 4.69
958 1289 6.831353 CCGACATCCACTATCCTATAGAAGAT 59.169 42.308 0.00 0.00 0.00 2.40
1033 1366 1.202557 TGTTAACCGCTCCGAGTGTTT 60.203 47.619 8.14 2.72 0.00 2.83
1125 1460 4.201940 TGCATGTGCTCTATATTGTTGTGC 60.202 41.667 6.55 0.00 42.66 4.57
1194 1530 8.991783 AGATCTCATGATTATCAAAACCATGT 57.008 30.769 16.42 0.00 36.79 3.21
1322 1687 9.822185 AATGGCCAGAATAATATCTTTGAAAAC 57.178 29.630 13.05 0.00 0.00 2.43
1438 1804 8.492748 CAATATTTGTCATTCTATGCAAATGCC 58.507 33.333 20.00 0.00 41.92 4.40
1671 2040 5.783111 ACCAACAACTAAGCAATTCATTCC 58.217 37.500 0.00 0.00 0.00 3.01
1786 2193 5.576447 TCAACCCTTCTTTGTTTGACTTC 57.424 39.130 0.00 0.00 0.00 3.01
2019 2438 1.324736 GCCAAGTTGTATTCTCTCGCG 59.675 52.381 0.00 0.00 0.00 5.87
2027 2446 2.486592 TGTATTCTCTCGCGAAGTGACA 59.513 45.455 11.33 7.18 44.70 3.58
2031 2450 2.596452 TCTCTCGCGAAGTGACAAATC 58.404 47.619 11.33 0.00 44.70 2.17
2091 2510 1.071814 GGTGGGCGTGTTTCTGGTA 59.928 57.895 0.00 0.00 0.00 3.25
2204 2623 6.765989 TGGGAGATTTTCGTGGTATTAATCAG 59.234 38.462 0.00 0.00 0.00 2.90
2246 2665 5.704515 CAGGCCATAATGATGAACCTAAGAG 59.295 44.000 5.01 0.00 37.34 2.85
2396 2816 4.275689 TGTGTTGGAGTGTCAAGCTATTTG 59.724 41.667 0.00 0.00 38.17 2.32
2428 2848 9.604626 GTACTACTACTAATATTGTACAAGCGG 57.395 37.037 14.65 5.12 31.94 5.52
2429 2849 8.455903 ACTACTACTAATATTGTACAAGCGGA 57.544 34.615 14.65 0.00 0.00 5.54
2430 2850 8.566260 ACTACTACTAATATTGTACAAGCGGAG 58.434 37.037 14.65 10.82 0.00 4.63
2431 2851 6.746120 ACTACTAATATTGTACAAGCGGAGG 58.254 40.000 14.65 5.30 0.00 4.30
2432 2852 4.957296 ACTAATATTGTACAAGCGGAGGG 58.043 43.478 14.65 3.82 0.00 4.30
2433 2853 2.256117 ATATTGTACAAGCGGAGGGC 57.744 50.000 14.65 0.00 44.05 5.19
2444 2864 4.373116 GGAGGGCGCTTGTGACGA 62.373 66.667 7.64 0.00 0.00 4.20
2445 2865 3.112709 GAGGGCGCTTGTGACGAC 61.113 66.667 7.64 0.00 38.01 4.34
2448 2868 2.260434 GGCGCTTGTGACGACCTA 59.740 61.111 7.64 0.00 30.32 3.08
2449 2869 2.092882 GGCGCTTGTGACGACCTAC 61.093 63.158 7.64 0.00 30.32 3.18
2647 3073 0.106469 CTCTCCTGGTCGGGATCTCA 60.106 60.000 0.00 0.00 34.56 3.27
2651 3077 2.044352 TGGTCGGGATCTCAGCGA 60.044 61.111 0.00 0.00 0.00 4.93
2870 3299 3.388841 GGCGTCTCCCCTTCTCAA 58.611 61.111 0.00 0.00 0.00 3.02
2871 3300 1.079057 GGCGTCTCCCCTTCTCAAC 60.079 63.158 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.849510 TCTTGTTCAGTTTACGGAGAATGA 58.150 37.500 0.00 0.00 0.00 2.57
16 17 5.607477 ACATCTTGTTCAGTTTACGGAGAA 58.393 37.500 0.00 0.00 0.00 2.87
95 96 3.141398 TGCCTCAGACAGTTCAAACATC 58.859 45.455 0.00 0.00 0.00 3.06
98 99 5.886960 ATAATGCCTCAGACAGTTCAAAC 57.113 39.130 0.00 0.00 0.00 2.93
264 416 6.073657 CGTCCGGTAACAAAGAATAAAAGTGA 60.074 38.462 0.00 0.00 0.00 3.41
324 476 9.367160 TCAACCTTCTAATCTTTGAAAGGAAAT 57.633 29.630 4.94 0.00 0.00 2.17
360 516 7.504238 TCCAAAGTTACATGGACACTAATTGTT 59.496 33.333 5.91 0.00 40.74 2.83
392 551 7.513505 CGCCATGATCGCTAAATTTAACTTTTG 60.514 37.037 0.00 0.00 0.00 2.44
483 642 9.113838 CATGATTTGCTAACATAGTCTAGGTTT 57.886 33.333 14.60 0.00 34.24 3.27
591 759 7.822822 ACACCAAGATATACTTATTATTCGCCC 59.177 37.037 0.00 0.00 37.03 6.13
764 1094 4.160065 TCGGTTTGTCGGGATTATCTAACA 59.840 41.667 0.00 0.00 0.00 2.41
765 1095 4.685924 TCGGTTTGTCGGGATTATCTAAC 58.314 43.478 0.00 0.00 0.00 2.34
976 1309 8.896722 AGGAGAAAGACTCAAGGTATAAGTTA 57.103 34.615 0.00 0.00 46.54 2.24
1020 1353 2.279582 AGTATGAAACACTCGGAGCG 57.720 50.000 4.58 0.00 0.00 5.03
1033 1366 0.543277 CTCCCTGCTGGCAAGTATGA 59.457 55.000 3.63 0.00 0.00 2.15
1101 1435 5.676837 GCACAACAATATAGAGCACATGCAA 60.677 40.000 6.64 0.00 45.16 4.08
1194 1530 9.739276 ATTGGACAACATAATCTTTTCTCACTA 57.261 29.630 0.00 0.00 0.00 2.74
1237 1601 6.892658 ACCTAGTTTTTGTGAACATGCATA 57.107 33.333 0.00 0.00 31.94 3.14
1255 1619 6.202954 CACAAAAACCTCTCACAACTACCTAG 59.797 42.308 0.00 0.00 0.00 3.02
1322 1687 7.378461 ACACAATTAAGTAAAACGCATTGTGAG 59.622 33.333 23.01 4.79 45.96 3.51
1327 1692 7.166804 GTGACACACAATTAAGTAAAACGCATT 59.833 33.333 0.00 0.00 34.08 3.56
1331 1696 6.487960 TGGTGACACACAATTAAGTAAAACG 58.512 36.000 8.08 0.00 35.86 3.60
1549 1916 4.141158 CCCCATTCTGGAACCTAGCTAATT 60.141 45.833 0.00 0.00 40.96 1.40
1582 1951 8.810041 AGTGGCTTTCAAAATTATCTCTTGAAT 58.190 29.630 3.70 0.00 38.49 2.57
1616 1985 7.554211 TGCATTAATTTGGAGATTGCATAACA 58.446 30.769 0.00 0.00 0.00 2.41
1622 1991 5.362263 ACCATGCATTAATTTGGAGATTGC 58.638 37.500 8.74 1.37 33.36 3.56
1671 2040 9.530633 AACAAAGAGTTTACTAAGAGTGTACAG 57.469 33.333 0.00 0.00 37.03 2.74
2019 2438 3.141398 TGTGCTCTGGATTTGTCACTTC 58.859 45.455 0.00 0.00 0.00 3.01
2027 2446 2.494870 GGATGCTTTGTGCTCTGGATTT 59.505 45.455 0.00 0.00 43.37 2.17
2031 2450 1.542492 AAGGATGCTTTGTGCTCTGG 58.458 50.000 0.00 0.00 43.37 3.86
2091 2510 1.003355 CACCTCCTGCATTGGTCGT 60.003 57.895 2.90 0.00 30.72 4.34
2204 2623 4.082408 GGCCTGTTATAAGTTGGTGGTTTC 60.082 45.833 0.00 0.00 0.00 2.78
2246 2665 0.541764 TTGGTGCCCATGGTCCTTTC 60.542 55.000 11.73 0.00 31.53 2.62
2427 2847 4.373116 TCGTCACAAGCGCCCTCC 62.373 66.667 2.29 0.00 0.00 4.30
2428 2848 3.112709 GTCGTCACAAGCGCCCTC 61.113 66.667 2.29 0.00 0.00 4.30
2429 2849 4.681978 GGTCGTCACAAGCGCCCT 62.682 66.667 2.29 0.00 0.00 5.19
2430 2850 3.291101 TAGGTCGTCACAAGCGCCC 62.291 63.158 2.29 0.00 0.00 6.13
2431 2851 2.092882 GTAGGTCGTCACAAGCGCC 61.093 63.158 2.29 0.00 0.00 6.53
2432 2852 1.071567 GAGTAGGTCGTCACAAGCGC 61.072 60.000 0.00 0.00 0.00 5.92
2433 2853 0.456312 GGAGTAGGTCGTCACAAGCG 60.456 60.000 0.00 0.00 0.00 4.68
2434 2854 0.889306 AGGAGTAGGTCGTCACAAGC 59.111 55.000 0.00 0.00 0.00 4.01
2435 2855 1.473278 GGAGGAGTAGGTCGTCACAAG 59.527 57.143 0.00 0.00 41.16 3.16
2436 2856 1.075050 AGGAGGAGTAGGTCGTCACAA 59.925 52.381 0.00 0.00 41.16 3.33
2437 2857 0.697079 AGGAGGAGTAGGTCGTCACA 59.303 55.000 0.00 0.00 41.16 3.58
2438 2858 1.836802 AAGGAGGAGTAGGTCGTCAC 58.163 55.000 0.00 0.00 41.16 3.67
2439 2859 2.444421 GAAAGGAGGAGTAGGTCGTCA 58.556 52.381 0.00 0.00 41.16 4.35
2440 2860 1.750206 GGAAAGGAGGAGTAGGTCGTC 59.250 57.143 0.00 0.00 39.05 4.20
2441 2861 1.619160 GGGAAAGGAGGAGTAGGTCGT 60.619 57.143 0.00 0.00 0.00 4.34
2442 2862 1.112950 GGGAAAGGAGGAGTAGGTCG 58.887 60.000 0.00 0.00 0.00 4.79
2443 2863 1.498264 GGGGAAAGGAGGAGTAGGTC 58.502 60.000 0.00 0.00 0.00 3.85
2444 2864 0.044397 GGGGGAAAGGAGGAGTAGGT 59.956 60.000 0.00 0.00 0.00 3.08
2445 2865 0.343726 AGGGGGAAAGGAGGAGTAGG 59.656 60.000 0.00 0.00 0.00 3.18
2446 2866 1.693083 GGAGGGGGAAAGGAGGAGTAG 60.693 61.905 0.00 0.00 0.00 2.57
2447 2867 0.342313 GGAGGGGGAAAGGAGGAGTA 59.658 60.000 0.00 0.00 0.00 2.59
2448 2868 1.083141 GGAGGGGGAAAGGAGGAGT 59.917 63.158 0.00 0.00 0.00 3.85
2449 2869 1.694525 GGGAGGGGGAAAGGAGGAG 60.695 68.421 0.00 0.00 0.00 3.69
2539 2961 1.077357 GGAGGAGGAGTGAGCGAGA 60.077 63.158 0.00 0.00 0.00 4.04
2621 3047 0.614979 CCGACCAGGAGAGGAAGGAA 60.615 60.000 0.00 0.00 45.00 3.36
2864 3293 2.548295 GCGCCAAACCCGTTGAGAA 61.548 57.895 0.00 0.00 39.87 2.87
2865 3294 2.975799 GCGCCAAACCCGTTGAGA 60.976 61.111 0.00 0.00 39.87 3.27
2866 3295 4.038080 GGCGCCAAACCCGTTGAG 62.038 66.667 24.80 0.00 39.87 3.02


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

AutoCloner maintained by Alex Coulton.