Multiple sequence alignment - TraesCS1B01G131200

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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 TraesCS1B01G131200 chr1B 100.000 3438 0 0 1 3438 163070630 163067193 0.000000e+00 6349.0
1 TraesCS1B01G131200 chr1B 95.119 2971 116 14 1 2954 338440177 338443135 0.000000e+00 4656.0
2 TraesCS1B01G131200 chr1B 95.684 2711 101 5 1 2695 256706736 256709446 0.000000e+00 4344.0
3 TraesCS1B01G131200 chr1B 95.152 2723 103 16 1 2701 164401153 164398438 0.000000e+00 4270.0
4 TraesCS1B01G131200 chr1B 95.099 2714 108 10 1 2691 206308150 206310861 0.000000e+00 4252.0
5 TraesCS1B01G131200 chr1B 93.274 1234 59 13 1 1212 290946664 290947895 0.000000e+00 1797.0
6 TraesCS1B01G131200 chr1B 95.868 484 19 1 2956 3438 413054859 413055342 0.000000e+00 782.0
7 TraesCS1B01G131200 chr1B 95.851 482 18 2 2959 3438 164398055 164397574 0.000000e+00 778.0
8 TraesCS1B01G131200 chr1B 95.661 484 20 1 2956 3438 575068276 575067793 0.000000e+00 776.0
9 TraesCS1B01G131200 chr1B 96.471 255 7 2 2701 2954 252929155 252929408 1.480000e-113 420.0
10 TraesCS1B01G131200 chr1B 96.457 254 9 0 2701 2954 256709481 256709734 1.480000e-113 420.0
11 TraesCS1B01G131200 chr1B 96.471 255 8 1 2701 2954 413054507 413054761 1.480000e-113 420.0
12 TraesCS1B01G131200 chr5B 94.465 2999 120 25 1 2954 299228737 299225740 0.000000e+00 4577.0
13 TraesCS1B01G131200 chr5B 94.188 2994 123 26 9 2954 197387097 197390087 0.000000e+00 4518.0
14 TraesCS1B01G131200 chr5B 95.443 2721 102 10 1 2701 104504814 104502096 0.000000e+00 4318.0
15 TraesCS1B01G131200 chr2B 94.208 3004 118 26 1 2954 506424452 506421455 0.000000e+00 4532.0
16 TraesCS1B01G131200 chr2B 95.193 2725 107 10 1 2701 300243667 300240943 0.000000e+00 4285.0
17 TraesCS1B01G131200 chr2B 96.273 483 14 4 2959 3438 506421363 506420882 0.000000e+00 789.0
18 TraesCS1B01G131200 chr2B 95.842 481 19 1 2959 3438 514553932 514553452 0.000000e+00 776.0
19 TraesCS1B01G131200 chr4B 94.206 3003 118 25 1 2954 310225967 310222972 0.000000e+00 4530.0
20 TraesCS1B01G131200 chr4B 93.577 3005 139 33 1 2954 213397320 213400321 0.000000e+00 4431.0
21 TraesCS1B01G131200 chr4B 95.721 2711 96 16 1 2695 224372251 224374957 0.000000e+00 4346.0
22 TraesCS1B01G131200 chr4B 95.187 2722 106 11 1 2701 407695566 407692849 0.000000e+00 4277.0
23 TraesCS1B01G131200 chr4B 92.333 3000 175 35 1 2954 173397518 173394528 0.000000e+00 4215.0
24 TraesCS1B01G131200 chr4B 94.518 2718 112 14 1 2695 380783980 380786683 0.000000e+00 4159.0
25 TraesCS1B01G131200 chr4B 92.141 2723 147 31 1 2691 470131103 470133790 0.000000e+00 3781.0
26 TraesCS1B01G131200 chr4B 92.295 1804 102 19 1 1782 396054325 396052537 0.000000e+00 2527.0
27 TraesCS1B01G131200 chr4B 96.881 481 14 1 2959 3438 310222871 310222391 0.000000e+00 804.0
28 TraesCS1B01G131200 chr4B 97.628 253 6 0 2702 2954 396050956 396050704 5.270000e-118 435.0
29 TraesCS1B01G131200 chr6A 93.794 2981 149 21 1 2954 158983457 158980486 0.000000e+00 4447.0
30 TraesCS1B01G131200 chr7B 95.186 2721 109 10 1 2701 381026474 381023756 0.000000e+00 4279.0
31 TraesCS1B01G131200 chr7B 95.358 2456 97 6 262 2701 202726065 202723611 0.000000e+00 3888.0
32 TraesCS1B01G131200 chr7B 93.918 2121 84 20 877 2954 463801579 463803697 0.000000e+00 3160.0
33 TraesCS1B01G131200 chr7B 96.660 479 16 0 2960 3438 463803791 463804269 0.000000e+00 797.0
34 TraesCS1B01G131200 chr7B 95.661 484 20 1 2956 3438 330124838 330125321 0.000000e+00 776.0
35 TraesCS1B01G131200 chr5D 93.778 2716 125 21 1 2691 378825567 378822871 0.000000e+00 4039.0
36 TraesCS1B01G131200 chr5D 88.753 1227 104 23 1 1209 56013211 56012001 0.000000e+00 1471.0
37 TraesCS1B01G131200 chr7D 91.996 2711 178 26 1 2691 291607672 291610363 0.000000e+00 3768.0
38 TraesCS1B01G131200 chr3D 91.147 2711 180 31 1 2691 254423743 254421073 0.000000e+00 3622.0
39 TraesCS1B01G131200 chr1D 91.067 2709 180 37 1 2691 88013070 88010406 0.000000e+00 3605.0
40 TraesCS1B01G131200 chr1D 90.906 2716 187 35 1 2691 95412087 95409407 0.000000e+00 3592.0
41 TraesCS1B01G131200 chr1D 90.594 2711 189 36 1 2691 296768554 296771218 0.000000e+00 3533.0
42 TraesCS1B01G131200 chr1D 90.383 2714 202 35 1 2691 78754841 78752164 0.000000e+00 3511.0
43 TraesCS1B01G131200 chr1D 89.528 2712 189 44 1 2691 285935198 285937835 0.000000e+00 3347.0
44 TraesCS1B01G131200 chr1D 88.809 1814 158 29 139 1928 371714919 371716711 0.000000e+00 2183.0
45 TraesCS1B01G131200 chr6D 90.849 2710 195 29 1 2691 249245989 249248664 0.000000e+00 3581.0
46 TraesCS1B01G131200 chr6D 90.368 2502 190 31 1 2481 428022162 428019691 0.000000e+00 3238.0
47 TraesCS1B01G131200 chr6D 86.606 2725 265 60 5 2691 165557214 165559876 0.000000e+00 2918.0
48 TraesCS1B01G131200 chr6D 85.573 2738 298 56 5 2691 179222288 179219597 0.000000e+00 2778.0
49 TraesCS1B01G131200 chr6D 84.031 2749 306 64 5 2691 229648728 229646051 0.000000e+00 2521.0
50 TraesCS1B01G131200 chr6D 83.169 2644 337 55 5 2583 197902772 197905372 0.000000e+00 2318.0
51 TraesCS1B01G131200 chr6D 87.235 1606 141 33 1 1584 255994880 255996443 0.000000e+00 1772.0
52 TraesCS1B01G131200 chr6D 85.620 1662 162 50 5 1616 186940968 186939334 0.000000e+00 1674.0
53 TraesCS1B01G131200 chr6D 83.200 1631 197 39 5 1587 153094646 153093045 0.000000e+00 1423.0
54 TraesCS1B01G131200 chr6D 85.061 743 86 12 635 1362 249264864 249265596 0.000000e+00 734.0
55 TraesCS1B01G131200 chr6D 81.279 876 108 32 635 1491 256021339 256022177 0.000000e+00 658.0
56 TraesCS1B01G131200 chr6D 82.226 647 68 26 5 618 282833091 282833723 6.580000e-142 514.0
57 TraesCS1B01G131200 chr6D 80.469 640 79 26 5 618 202410760 202410141 6.770000e-122 448.0
58 TraesCS1B01G131200 chr6D 91.667 228 14 5 5 230 249245751 249245975 9.260000e-81 311.0
59 TraesCS1B01G131200 chr6D 89.407 236 21 4 4 239 428022398 428022167 9.330000e-76 294.0
60 TraesCS1B01G131200 chr6D 85.882 85 12 0 559 643 152993875 152993791 1.310000e-14 91.6
61 TraesCS1B01G131200 chr4D 90.775 2710 192 31 1 2689 79271472 79268800 0.000000e+00 3567.0
62 TraesCS1B01G131200 chr4D 88.872 1950 171 34 5 1930 144583620 144581693 0.000000e+00 2357.0
63 TraesCS1B01G131200 chr4D 87.757 972 83 21 1 964 201239265 201240208 0.000000e+00 1103.0
64 TraesCS1B01G131200 chr4A 87.371 1449 145 21 1 1441 52168602 52170020 0.000000e+00 1628.0
65 TraesCS1B01G131200 chr3B 95.679 486 18 2 2956 3438 477785227 477785712 0.000000e+00 778.0
66 TraesCS1B01G131200 chr5A 96.457 254 9 0 2701 2954 465656841 465657094 1.480000e-113 420.0
67 TraesCS1B01G131200 chr2A 96.457 254 9 0 2701 2954 572967195 572966942 1.480000e-113 420.0


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 TraesCS1B01G131200 chr1B 163067193 163070630 3437 True 6349.0 6349 100.0000 1 3438 1 chr1B.!!$R1 3437
1 TraesCS1B01G131200 chr1B 338440177 338443135 2958 False 4656.0 4656 95.1190 1 2954 1 chr1B.!!$F4 2953
2 TraesCS1B01G131200 chr1B 206308150 206310861 2711 False 4252.0 4252 95.0990 1 2691 1 chr1B.!!$F1 2690
3 TraesCS1B01G131200 chr1B 164397574 164401153 3579 True 2524.0 4270 95.5015 1 3438 2 chr1B.!!$R3 3437
4 TraesCS1B01G131200 chr1B 256706736 256709734 2998 False 2382.0 4344 96.0705 1 2954 2 chr1B.!!$F5 2953
5 TraesCS1B01G131200 chr1B 290946664 290947895 1231 False 1797.0 1797 93.2740 1 1212 1 chr1B.!!$F3 1211
6 TraesCS1B01G131200 chr1B 413054507 413055342 835 False 601.0 782 96.1695 2701 3438 2 chr1B.!!$F6 737
7 TraesCS1B01G131200 chr5B 299225740 299228737 2997 True 4577.0 4577 94.4650 1 2954 1 chr5B.!!$R2 2953
8 TraesCS1B01G131200 chr5B 197387097 197390087 2990 False 4518.0 4518 94.1880 9 2954 1 chr5B.!!$F1 2945
9 TraesCS1B01G131200 chr5B 104502096 104504814 2718 True 4318.0 4318 95.4430 1 2701 1 chr5B.!!$R1 2700
10 TraesCS1B01G131200 chr2B 300240943 300243667 2724 True 4285.0 4285 95.1930 1 2701 1 chr2B.!!$R1 2700
11 TraesCS1B01G131200 chr2B 506420882 506424452 3570 True 2660.5 4532 95.2405 1 3438 2 chr2B.!!$R3 3437
12 TraesCS1B01G131200 chr4B 213397320 213400321 3001 False 4431.0 4431 93.5770 1 2954 1 chr4B.!!$F1 2953
13 TraesCS1B01G131200 chr4B 224372251 224374957 2706 False 4346.0 4346 95.7210 1 2695 1 chr4B.!!$F2 2694
14 TraesCS1B01G131200 chr4B 407692849 407695566 2717 True 4277.0 4277 95.1870 1 2701 1 chr4B.!!$R2 2700
15 TraesCS1B01G131200 chr4B 173394528 173397518 2990 True 4215.0 4215 92.3330 1 2954 1 chr4B.!!$R1 2953
16 TraesCS1B01G131200 chr4B 380783980 380786683 2703 False 4159.0 4159 94.5180 1 2695 1 chr4B.!!$F3 2694
17 TraesCS1B01G131200 chr4B 470131103 470133790 2687 False 3781.0 3781 92.1410 1 2691 1 chr4B.!!$F4 2690
18 TraesCS1B01G131200 chr4B 310222391 310225967 3576 True 2667.0 4530 95.5435 1 3438 2 chr4B.!!$R3 3437
19 TraesCS1B01G131200 chr4B 396050704 396054325 3621 True 1481.0 2527 94.9615 1 2954 2 chr4B.!!$R4 2953
20 TraesCS1B01G131200 chr6A 158980486 158983457 2971 True 4447.0 4447 93.7940 1 2954 1 chr6A.!!$R1 2953
21 TraesCS1B01G131200 chr7B 381023756 381026474 2718 True 4279.0 4279 95.1860 1 2701 1 chr7B.!!$R2 2700
22 TraesCS1B01G131200 chr7B 202723611 202726065 2454 True 3888.0 3888 95.3580 262 2701 1 chr7B.!!$R1 2439
23 TraesCS1B01G131200 chr7B 463801579 463804269 2690 False 1978.5 3160 95.2890 877 3438 2 chr7B.!!$F2 2561
24 TraesCS1B01G131200 chr5D 378822871 378825567 2696 True 4039.0 4039 93.7780 1 2691 1 chr5D.!!$R2 2690
25 TraesCS1B01G131200 chr5D 56012001 56013211 1210 True 1471.0 1471 88.7530 1 1209 1 chr5D.!!$R1 1208
26 TraesCS1B01G131200 chr7D 291607672 291610363 2691 False 3768.0 3768 91.9960 1 2691 1 chr7D.!!$F1 2690
27 TraesCS1B01G131200 chr3D 254421073 254423743 2670 True 3622.0 3622 91.1470 1 2691 1 chr3D.!!$R1 2690
28 TraesCS1B01G131200 chr1D 88010406 88013070 2664 True 3605.0 3605 91.0670 1 2691 1 chr1D.!!$R2 2690
29 TraesCS1B01G131200 chr1D 95409407 95412087 2680 True 3592.0 3592 90.9060 1 2691 1 chr1D.!!$R3 2690
30 TraesCS1B01G131200 chr1D 296768554 296771218 2664 False 3533.0 3533 90.5940 1 2691 1 chr1D.!!$F2 2690
31 TraesCS1B01G131200 chr1D 78752164 78754841 2677 True 3511.0 3511 90.3830 1 2691 1 chr1D.!!$R1 2690
32 TraesCS1B01G131200 chr1D 285935198 285937835 2637 False 3347.0 3347 89.5280 1 2691 1 chr1D.!!$F1 2690
33 TraesCS1B01G131200 chr1D 371714919 371716711 1792 False 2183.0 2183 88.8090 139 1928 1 chr1D.!!$F3 1789
34 TraesCS1B01G131200 chr6D 165557214 165559876 2662 False 2918.0 2918 86.6060 5 2691 1 chr6D.!!$F1 2686
35 TraesCS1B01G131200 chr6D 179219597 179222288 2691 True 2778.0 2778 85.5730 5 2691 1 chr6D.!!$R3 2686
36 TraesCS1B01G131200 chr6D 229646051 229648728 2677 True 2521.0 2521 84.0310 5 2691 1 chr6D.!!$R6 2686
37 TraesCS1B01G131200 chr6D 197902772 197905372 2600 False 2318.0 2318 83.1690 5 2583 1 chr6D.!!$F2 2578
38 TraesCS1B01G131200 chr6D 249245751 249248664 2913 False 1946.0 3581 91.2580 1 2691 2 chr6D.!!$F7 2690
39 TraesCS1B01G131200 chr6D 255994880 255996443 1563 False 1772.0 1772 87.2350 1 1584 1 chr6D.!!$F4 1583
40 TraesCS1B01G131200 chr6D 428019691 428022398 2707 True 1766.0 3238 89.8875 1 2481 2 chr6D.!!$R7 2480
41 TraesCS1B01G131200 chr6D 186939334 186940968 1634 True 1674.0 1674 85.6200 5 1616 1 chr6D.!!$R4 1611
42 TraesCS1B01G131200 chr6D 153093045 153094646 1601 True 1423.0 1423 83.2000 5 1587 1 chr6D.!!$R2 1582
43 TraesCS1B01G131200 chr6D 249264864 249265596 732 False 734.0 734 85.0610 635 1362 1 chr6D.!!$F3 727
44 TraesCS1B01G131200 chr6D 256021339 256022177 838 False 658.0 658 81.2790 635 1491 1 chr6D.!!$F5 856
45 TraesCS1B01G131200 chr6D 282833091 282833723 632 False 514.0 514 82.2260 5 618 1 chr6D.!!$F6 613
46 TraesCS1B01G131200 chr6D 202410141 202410760 619 True 448.0 448 80.4690 5 618 1 chr6D.!!$R5 613
47 TraesCS1B01G131200 chr4D 79268800 79271472 2672 True 3567.0 3567 90.7750 1 2689 1 chr4D.!!$R1 2688
48 TraesCS1B01G131200 chr4D 144581693 144583620 1927 True 2357.0 2357 88.8720 5 1930 1 chr4D.!!$R2 1925
49 TraesCS1B01G131200 chr4D 201239265 201240208 943 False 1103.0 1103 87.7570 1 964 1 chr4D.!!$F1 963
50 TraesCS1B01G131200 chr4A 52168602 52170020 1418 False 1628.0 1628 87.3710 1 1441 1 chr4A.!!$F1 1440

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
313 825 0.776810 TCCTGCCAGTCCCAATTCAA 59.223 50.0 0.00 0.0 0.0 2.69 F
609 1167 5.011533 AGTGGGATAAGCAGCTGATAAGTAG 59.988 44.0 20.43 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 3331 5.284079 GCAAATGTGAACAACTTCTCATGT 58.716 37.500 0.0 0.0 38.90 3.21 R
2674 3994 6.594159 AGATAAACTACAACGTTCCATTGAGG 59.406 38.462 0.0 0.0 39.47 3.86 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
232 705 2.943033 GTCGGCAGTACAAAAGGCATAT 59.057 45.455 0.00 0.0 0.00 1.78
313 825 0.776810 TCCTGCCAGTCCCAATTCAA 59.223 50.000 0.00 0.0 0.00 2.69
609 1167 5.011533 AGTGGGATAAGCAGCTGATAAGTAG 59.988 44.000 20.43 0.0 0.00 2.57
1768 2418 7.776030 TCCCATTTCAACAAAAGTAGACTAACA 59.224 33.333 0.00 0.0 0.00 2.41
1905 3190 7.496529 ACATTCATCCATTGTTTATCCTACG 57.503 36.000 0.00 0.0 0.00 3.51
2035 3331 0.175760 GCCTGACCGAGATGCTACAA 59.824 55.000 0.00 0.0 0.00 2.41
2589 3888 8.635765 ACAAGTTTGGTTATGTCATCAAGTAT 57.364 30.769 0.00 0.0 0.00 2.12
2691 4011 2.301870 AGCTCCTCAATGGAACGTTGTA 59.698 45.455 5.00 0.0 45.63 2.41
2695 4015 4.710324 TCCTCAATGGAACGTTGTAGTTT 58.290 39.130 5.00 0.0 42.94 2.66
2696 4016 5.856156 TCCTCAATGGAACGTTGTAGTTTA 58.144 37.500 5.00 0.0 42.94 2.01
2744 4093 4.707448 ACAACTCAGTACTCTTGATCGGAT 59.293 41.667 10.19 0.0 0.00 4.18
2886 4236 6.314896 CCAGAAGACACTTGAGAATAATCACC 59.685 42.308 0.00 0.0 0.00 4.02
2899 4249 7.920151 TGAGAATAATCACCAAAACAAACACAG 59.080 33.333 0.00 0.0 0.00 3.66
2954 4305 6.751514 TTACACTCACACAAAACTGACAAT 57.248 33.333 0.00 0.0 0.00 2.71
2957 4412 3.443329 ACTCACACAAAACTGACAATGCA 59.557 39.130 0.00 0.0 0.00 3.96
3100 4556 1.070134 AGCGCTCAGGTAAGTGTTCAA 59.930 47.619 2.64 0.0 0.00 2.69
3123 4579 1.070758 GAGTTCAACTGGTGAGCCTCA 59.929 52.381 15.49 0.0 38.18 3.86
3271 4727 3.250040 GCCTACATCGTCAACAAAACACT 59.750 43.478 0.00 0.0 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 705 4.454847 TCGTTCACTGGTGTGTTTGTTTAA 59.545 37.500 0.53 0.00 44.14 1.52
609 1167 3.975670 CACCGATTCGTATAGTCAAGCTC 59.024 47.826 5.20 0.00 0.00 4.09
907 1530 1.443828 GGAACGAGGGAGAGATGGC 59.556 63.158 0.00 0.00 0.00 4.40
1406 2049 8.978539 GGGAAACAACTCTGATTAAATTTTCAC 58.021 33.333 0.00 0.00 0.00 3.18
1768 2418 7.109501 TGTTGTATGTTCTGCATTGGTACTAT 58.890 34.615 0.00 0.00 38.94 2.12
1905 3190 8.116753 CGATGAATCCATGAAGTAGTTGTTTAC 58.883 37.037 0.00 0.00 32.09 2.01
2035 3331 5.284079 GCAAATGTGAACAACTTCTCATGT 58.716 37.500 0.00 0.00 38.90 3.21
2674 3994 6.594159 AGATAAACTACAACGTTCCATTGAGG 59.406 38.462 0.00 0.00 39.47 3.86
2886 4236 5.407995 TGCCTTCTTTTCTGTGTTTGTTTTG 59.592 36.000 0.00 0.00 0.00 2.44
2954 4305 1.604308 CATTGTCAGGGCCTGTGCA 60.604 57.895 31.60 26.48 40.13 4.57
2957 4412 0.254178 CTAGCATTGTCAGGGCCTGT 59.746 55.000 31.60 14.23 32.61 4.00
3100 4556 1.202818 GGCTCACCAGTTGAACTCCTT 60.203 52.381 0.00 0.00 32.21 3.36
3271 4727 1.974028 TACCTGGGCTTATTGGTGGA 58.026 50.000 0.00 0.00 34.33 4.02


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

AutoCloner maintained by Alex Coulton.