Multiple sequence alignment - TraesCS3A01G234100

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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 TraesCS3A01G234100 chr3A 100.000 3473 0 0 985 4457 437661245 437657773 0.000000e+00 6414.0
1 TraesCS3A01G234100 chr3A 97.774 2516 36 7 985 3498 437876336 437873839 0.000000e+00 4318.0
2 TraesCS3A01G234100 chr3A 96.170 966 21 2 3507 4457 437873695 437872731 0.000000e+00 1565.0
3 TraesCS3A01G234100 chr3A 90.961 1051 89 3 987 2034 437892607 437891560 0.000000e+00 1410.0
4 TraesCS3A01G234100 chr3A 100.000 740 0 0 1 740 437662229 437661490 0.000000e+00 1367.0
5 TraesCS3A01G234100 chr3A 98.870 708 7 1 1 708 437877368 437876662 0.000000e+00 1262.0
6 TraesCS3A01G234100 chr3A 88.042 1037 101 12 999 2025 437870826 437869803 0.000000e+00 1206.0
7 TraesCS3A01G234100 chr3A 87.657 1037 105 12 999 2025 437649496 437648473 0.000000e+00 1184.0
8 TraesCS3A01G234100 chr3A 89.017 783 59 10 2736 3498 437669940 437669165 0.000000e+00 944.0
9 TraesCS3A01G234100 chr3A 89.586 701 40 10 2736 3412 437882629 437881938 0.000000e+00 859.0
10 TraesCS3A01G234100 chr3A 83.544 553 47 18 2961 3496 437645933 437645408 1.120000e-130 477.0
11 TraesCS3A01G234100 chr3A 82.523 555 58 16 2961 3496 437867344 437866810 6.800000e-123 451.0
12 TraesCS3A01G234100 chr3A 90.282 319 22 5 2090 2406 437868128 437867817 4.150000e-110 409.0
13 TraesCS3A01G234100 chr3A 88.166 338 26 7 2080 2406 437883244 437882910 1.500000e-104 390.0
14 TraesCS3A01G234100 chr3A 89.338 272 28 1 2135 2406 437670491 437670221 1.540000e-89 340.0
15 TraesCS3A01G234100 chr3A 87.795 254 20 8 2399 2647 437867789 437867542 2.030000e-73 287.0
16 TraesCS3A01G234100 chr3A 86.585 246 25 4 2403 2645 437646375 437646135 9.510000e-67 265.0
17 TraesCS3A01G234100 chr3A 87.500 168 10 8 503 659 437871179 437871012 2.740000e-42 183.0
18 TraesCS3A01G234100 chr3A 85.799 169 13 8 502 659 437649849 437649681 7.670000e-38 169.0
19 TraesCS3A01G234100 chr3A 87.778 90 10 1 2641 2730 8658483 8658395 2.190000e-18 104.0
20 TraesCS3A01G234100 chr3D 95.930 2531 67 6 985 3498 324397892 324395381 0.000000e+00 4071.0
21 TraesCS3A01G234100 chr3D 92.388 1051 75 2 987 2034 324422195 324421147 0.000000e+00 1493.0
22 TraesCS3A01G234100 chr3D 97.035 742 18 2 1 740 324398883 324398144 0.000000e+00 1245.0
23 TraesCS3A01G234100 chr3D 87.343 1035 94 19 999 2024 324393568 324392562 0.000000e+00 1151.0
24 TraesCS3A01G234100 chr3D 89.813 697 42 9 2736 3412 324411757 324411070 0.000000e+00 867.0
25 TraesCS3A01G234100 chr3D 91.718 326 22 4 2083 2406 324390835 324390513 8.790000e-122 448.0
26 TraesCS3A01G234100 chr3D 80.882 544 50 25 2970 3498 324390044 324389540 3.250000e-101 379.0
27 TraesCS3A01G234100 chr3D 91.544 272 23 0 2135 2406 324412311 324412040 4.210000e-100 375.0
28 TraesCS3A01G234100 chr3D 87.698 252 22 5 2399 2647 324390485 324390240 7.300000e-73 285.0
29 TraesCS3A01G234100 chr3D 85.714 259 25 7 2399 2647 324412012 324411756 3.420000e-66 263.0
30 TraesCS3A01G234100 chr3B 95.751 2518 89 7 985 3498 424738829 424741332 0.000000e+00 4041.0
31 TraesCS3A01G234100 chr3B 93.008 1044 59 7 987 2024 424575332 424576367 0.000000e+00 1511.0
32 TraesCS3A01G234100 chr3B 87.140 1042 100 17 999 2029 424784203 424785221 0.000000e+00 1151.0
33 TraesCS3A01G234100 chr3B 96.291 701 22 3 43 740 424738067 424738766 0.000000e+00 1147.0
34 TraesCS3A01G234100 chr3B 88.352 704 36 18 2737 3412 424600735 424601420 0.000000e+00 804.0
35 TraesCS3A01G234100 chr3B 89.881 336 24 7 2073 2406 424787696 424788023 1.480000e-114 424.0
36 TraesCS3A01G234100 chr3B 83.226 465 59 12 3035 3496 424788667 424789115 4.150000e-110 409.0
37 TraesCS3A01G234100 chr3B 87.891 256 17 7 2399 2647 424788051 424788299 5.640000e-74 289.0
38 TraesCS3A01G234100 chr3B 86.290 248 19 8 2399 2645 424600500 424600733 5.720000e-64 255.0
39 TraesCS3A01G234100 chr3B 83.858 254 25 4 4049 4286 424780140 424780393 1.250000e-55 228.0
40 TraesCS3A01G234100 chr3B 90.000 110 7 4 182 288 729951571 729951679 6.010000e-29 139.0
41 TraesCS3A01G234100 chr3B 94.203 69 4 0 3903 3971 424779722 424779790 6.100000e-19 106.0
42 TraesCS3A01G234100 chr3B 93.878 49 1 1 460 506 513664731 513664779 6.180000e-09 73.1
43 TraesCS3A01G234100 chr5B 93.254 252 10 4 2135 2386 57698314 57698558 9.110000e-97 364.0
44 TraesCS3A01G234100 chr5B 91.351 185 11 2 1841 2025 57685095 57685274 9.570000e-62 248.0
45 TraesCS3A01G234100 chr5B 85.417 96 10 4 2643 2737 509175651 509175559 3.670000e-16 97.1
46 TraesCS3A01G234100 chr5B 92.453 53 3 1 3507 3559 124294165 124294114 1.720000e-09 75.0
47 TraesCS3A01G234100 chrUn 96.610 118 4 0 3381 3498 326169703 326169586 3.520000e-46 196.0
48 TraesCS3A01G234100 chr6A 87.736 106 9 4 182 284 555925693 555925589 2.180000e-23 121.0
49 TraesCS3A01G234100 chr4D 87.879 99 6 2 2645 2737 358476837 358476935 1.310000e-20 111.0
50 TraesCS3A01G234100 chr4B 86.869 99 7 2 2645 2737 441677196 441677294 6.100000e-19 106.0
51 TraesCS3A01G234100 chr1D 86.747 83 10 1 2646 2728 114067097 114067178 1.710000e-14 91.6
52 TraesCS3A01G234100 chr6D 82.353 102 13 5 2642 2741 96747798 96747896 2.860000e-12 84.2
53 TraesCS3A01G234100 chr5D 91.489 47 3 1 3507 3553 113657438 113657393 3.720000e-06 63.9
54 TraesCS3A01G234100 chr5A 88.679 53 5 1 3507 3559 118768532 118768481 3.720000e-06 63.9


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 TraesCS3A01G234100 chr3A 437657773 437662229 4456 True 3890.500000 6414 100.000000 1 4457 2 chr3A.!!$R4 4456
1 TraesCS3A01G234100 chr3A 437891560 437892607 1047 True 1410.000000 1410 90.961000 987 2034 1 chr3A.!!$R2 1047
2 TraesCS3A01G234100 chr3A 437866810 437877368 10558 True 1210.125000 4318 91.119500 1 4457 8 chr3A.!!$R6 4456
3 TraesCS3A01G234100 chr3A 437669165 437670491 1326 True 642.000000 944 89.177500 2135 3498 2 chr3A.!!$R5 1363
4 TraesCS3A01G234100 chr3A 437881938 437883244 1306 True 624.500000 859 88.876000 2080 3412 2 chr3A.!!$R7 1332
5 TraesCS3A01G234100 chr3A 437645408 437649849 4441 True 523.750000 1184 85.896250 502 3496 4 chr3A.!!$R3 2994
6 TraesCS3A01G234100 chr3D 324421147 324422195 1048 True 1493.000000 1493 92.388000 987 2034 1 chr3D.!!$R1 1047
7 TraesCS3A01G234100 chr3D 324389540 324398883 9343 True 1263.166667 4071 90.101000 1 3498 6 chr3D.!!$R2 3497
8 TraesCS3A01G234100 chr3D 324411070 324412311 1241 True 501.666667 867 89.023667 2135 3412 3 chr3D.!!$R3 1277
9 TraesCS3A01G234100 chr3B 424738067 424741332 3265 False 2594.000000 4041 96.021000 43 3498 2 chr3B.!!$F5 3455
10 TraesCS3A01G234100 chr3B 424575332 424576367 1035 False 1511.000000 1511 93.008000 987 2024 1 chr3B.!!$F1 1037
11 TraesCS3A01G234100 chr3B 424600500 424601420 920 False 529.500000 804 87.321000 2399 3412 2 chr3B.!!$F4 1013
12 TraesCS3A01G234100 chr3B 424779722 424789115 9393 False 434.500000 1151 87.699833 999 4286 6 chr3B.!!$F6 3287

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
45 46 1.800586 GATTGTTGCTTGCTCTCACGA 59.199 47.619 0.00 0.0 0.00 4.35 F
323 324 3.589951 ATCTATTGGCAGCCATGTCTT 57.410 42.857 17.09 0.0 31.53 3.01 F
1499 4986 2.358898 ACAAAGCGGCCATCATTATGAC 59.641 45.455 2.24 0.0 34.84 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 4986 0.034059 GATCCACCCGCCTATGTCTG 59.966 60.0 0.0 0.0 0.00 3.51 R
1897 5411 0.529378 CTCCCAGAAAGGCATTGTGC 59.471 55.0 0.0 0.0 44.08 4.57 R
3498 9683 1.145803 GGAAGAACACGAAACCGAGG 58.854 55.0 0.0 0.0 0.00 4.63 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
45 46 1.800586 GATTGTTGCTTGCTCTCACGA 59.199 47.619 0.00 0.00 0.00 4.35
323 324 3.589951 ATCTATTGGCAGCCATGTCTT 57.410 42.857 17.09 0.00 31.53 3.01
1499 4986 2.358898 ACAAAGCGGCCATCATTATGAC 59.641 45.455 2.24 0.00 34.84 3.06
1810 5323 7.624549 TGATGATATAATAAGAAGTCCAGGGC 58.375 38.462 0.00 0.00 0.00 5.19
1897 5411 9.519191 TCATATTGGAATTGGTAGTGATATTGG 57.481 33.333 0.00 0.00 0.00 3.16
2186 8189 8.208903 TGCTGAGAGATGATGAGAATTTCATTA 58.791 33.333 0.00 2.59 46.51 1.90
2332 8338 7.826252 ACTTGAGAATAAAGAGCTTCATTGCTA 59.174 33.333 0.00 0.00 44.17 3.49
2373 8379 1.187567 GGCTTTGCAACCACATCCCT 61.188 55.000 0.00 0.00 0.00 4.20
2639 8691 4.785376 ACTGATGGAAAGGAATCTACCACT 59.215 41.667 0.00 0.00 34.32 4.00
2673 8725 1.659098 CCGATCCAAAGTAAGTGTCGC 59.341 52.381 0.00 0.00 0.00 5.19
3015 9090 8.621532 TTTGAAAGAGTATAAATGCTGACACT 57.378 30.769 0.00 0.00 0.00 3.55
3457 9642 4.305989 GCGGATTTTCTGCCATGAATTA 57.694 40.909 0.00 0.00 42.80 1.40
3498 9683 5.049474 TGTGGCAATGCAATCGAAGTATATC 60.049 40.000 7.79 0.00 0.00 1.63
3499 9684 4.455533 TGGCAATGCAATCGAAGTATATCC 59.544 41.667 7.79 0.00 0.00 2.59
3500 9685 4.697352 GGCAATGCAATCGAAGTATATCCT 59.303 41.667 7.79 0.00 0.00 3.24
3501 9686 5.163814 GGCAATGCAATCGAAGTATATCCTC 60.164 44.000 7.79 0.00 0.00 3.71
3502 9687 5.445142 GCAATGCAATCGAAGTATATCCTCG 60.445 44.000 0.00 0.00 0.00 4.63
3503 9688 4.174411 TGCAATCGAAGTATATCCTCGG 57.826 45.455 0.00 0.00 0.00 4.63
3504 9689 3.572682 TGCAATCGAAGTATATCCTCGGT 59.427 43.478 0.00 0.00 0.00 4.69
3505 9690 4.038763 TGCAATCGAAGTATATCCTCGGTT 59.961 41.667 0.00 0.00 0.00 4.44
3506 9691 4.989168 GCAATCGAAGTATATCCTCGGTTT 59.011 41.667 0.00 0.00 0.00 3.27
3507 9692 5.118817 GCAATCGAAGTATATCCTCGGTTTC 59.881 44.000 0.00 0.00 0.00 2.78
3509 9694 3.879295 TCGAAGTATATCCTCGGTTTCGT 59.121 43.478 4.04 0.00 37.69 3.85
3608 10230 3.198872 CCCTCGAAGCTGAAAGTATTCC 58.801 50.000 0.00 0.00 35.30 3.01
3799 10421 3.237522 GCACCTAGCTAAGACGACG 57.762 57.895 0.00 0.00 41.15 5.12
3811 10433 4.175489 ACGACGGAGCCATCGACG 62.175 66.667 12.24 12.15 46.86 5.12
3850 10472 4.460263 CCCTCATGGATCCGATTAAACAA 58.540 43.478 7.39 0.00 35.39 2.83
3851 10473 4.516698 CCCTCATGGATCCGATTAAACAAG 59.483 45.833 7.39 0.00 35.39 3.16
3868 10490 4.336889 ACAAGAGGAATTCAAGACGACA 57.663 40.909 7.93 0.00 0.00 4.35
3880 10502 5.196341 TCAAGACGACAGTAGTGACAAAT 57.804 39.130 4.09 0.00 0.00 2.32
3959 10581 2.016318 TCTCCGCACATGCTTTTATGG 58.984 47.619 1.82 0.00 39.32 2.74
3986 10608 4.329462 TTTTTGTTGAATGTGGGGCTAC 57.671 40.909 0.00 0.00 0.00 3.58
4006 10628 5.005107 GCTACCTAAGAAACGTACAAATCGG 59.995 44.000 0.00 0.00 0.00 4.18
4104 10726 2.292267 CAAGCACTCAAACTCACCAGT 58.708 47.619 0.00 0.00 0.00 4.00
4175 10797 3.379372 CGTTCATGAAGGGATTGCTCATT 59.621 43.478 18.34 0.00 0.00 2.57
4332 10969 4.573900 AGATCAAGCAAATGACGAGAAGT 58.426 39.130 0.00 0.00 30.82 3.01
4384 11021 6.483307 AGAAAGAAGATCAAATGTTGACGTCA 59.517 34.615 15.76 15.76 43.48 4.35
4433 11070 3.431626 GGCATGTATAGTACACAGTGGCA 60.432 47.826 5.31 0.00 42.23 4.92
4437 11074 5.515797 TGTATAGTACACAGTGGCAGATC 57.484 43.478 5.31 0.00 32.89 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.613129 TGGATCGAGGATGACATGGAT 58.387 47.619 0.00 0.0 0.00 3.41
653 695 4.499183 AGCGTCAGATTTACTTCCTCAAG 58.501 43.478 0.00 0.0 35.50 3.02
1499 4986 0.034059 GATCCACCCGCCTATGTCTG 59.966 60.000 0.00 0.0 0.00 3.51
1897 5411 0.529378 CTCCCAGAAAGGCATTGTGC 59.471 55.000 0.00 0.0 44.08 4.57
2208 8211 7.413166 GTCCCAGTGACTATGGTTGAAAACTT 61.413 42.308 0.00 0.0 43.10 2.66
2257 8261 6.603940 AGTATATTTGGGAGCTCTCTGATC 57.396 41.667 16.21 0.0 0.00 2.92
2508 8549 8.158132 TGAGTAACAAGGTATACATCCACAAAA 58.842 33.333 5.01 0.0 0.00 2.44
2520 8561 7.554835 TCAAAACACAAGTGAGTAACAAGGTAT 59.445 33.333 7.28 0.0 0.00 2.73
2606 8655 4.215399 TCCTTTCCATCAGTGCGTAAAAAG 59.785 41.667 0.00 0.0 0.00 2.27
2639 8691 6.781014 ACTTTGGATCGGATGGAGTAGTATTA 59.219 38.462 0.00 0.0 0.00 0.98
2862 8931 8.753133 ACAAAAGAAGGAGAACAAAGAAATCTT 58.247 29.630 0.00 0.0 37.91 2.40
3431 9616 1.976474 GGCAGAAAATCCGCCCACA 60.976 57.895 0.00 0.0 40.07 4.17
3457 9642 3.491447 GCCACAAATCTTTTGAGCAGTGT 60.491 43.478 6.96 0.0 0.00 3.55
3498 9683 1.145803 GGAAGAACACGAAACCGAGG 58.854 55.000 0.00 0.0 0.00 4.63
3499 9684 0.782384 CGGAAGAACACGAAACCGAG 59.218 55.000 0.00 0.0 42.40 4.63
3500 9685 1.216941 GCGGAAGAACACGAAACCGA 61.217 55.000 0.00 0.0 42.40 4.69
3501 9686 1.203313 GCGGAAGAACACGAAACCG 59.797 57.895 0.00 0.0 42.63 4.44
3502 9687 0.041576 GTGCGGAAGAACACGAAACC 60.042 55.000 0.00 0.0 40.32 3.27
3503 9688 0.935196 AGTGCGGAAGAACACGAAAC 59.065 50.000 0.00 0.0 44.30 2.78
3504 9689 1.329292 CAAGTGCGGAAGAACACGAAA 59.671 47.619 0.00 0.0 44.30 3.46
3505 9690 0.934496 CAAGTGCGGAAGAACACGAA 59.066 50.000 0.00 0.0 44.30 3.85
3506 9691 0.103390 TCAAGTGCGGAAGAACACGA 59.897 50.000 0.00 0.0 44.30 4.35
3507 9692 0.934496 TTCAAGTGCGGAAGAACACG 59.066 50.000 0.00 0.0 44.30 4.49
3509 9694 2.807967 CAGATTCAAGTGCGGAAGAACA 59.192 45.455 0.00 0.0 44.30 3.18
3608 10230 0.888736 TGTTGTGCCAACCTCCATCG 60.889 55.000 13.35 0.0 0.00 3.84
3799 10421 0.173708 ACTTTCTCGTCGATGGCTCC 59.826 55.000 4.48 0.0 0.00 4.70
3811 10433 0.591659 GGGCGAACAACCACTTTCTC 59.408 55.000 0.00 0.0 0.00 2.87
3850 10472 4.767928 ACTACTGTCGTCTTGAATTCCTCT 59.232 41.667 2.27 0.0 0.00 3.69
3851 10473 4.859798 CACTACTGTCGTCTTGAATTCCTC 59.140 45.833 2.27 0.0 0.00 3.71
3868 10490 5.806654 AAATTGCCCAATTTGTCACTACT 57.193 34.783 15.87 0.0 45.99 2.57
3880 10502 2.166050 CCGATCATGTCAAATTGCCCAA 59.834 45.455 0.00 0.0 0.00 4.12
3986 10608 8.807667 ATATACCGATTTGTACGTTTCTTAGG 57.192 34.615 0.00 0.0 0.00 2.69
4006 10628 4.096682 GTCCATCTCGCTACCAGGATATAC 59.903 50.000 0.00 0.0 0.00 1.47
4104 10726 1.327303 GCCATCCCGAATTATTGCCA 58.673 50.000 0.00 0.0 0.00 4.92
4141 10763 3.057969 TCATGAACGACCATTGAAGCT 57.942 42.857 0.00 0.0 0.00 3.74
4175 10797 1.826921 GGGCCTCGAGTATCACCGA 60.827 63.158 12.31 0.0 33.17 4.69
4332 10969 7.606073 TCATACTGAAAAATCACGGATCTGAAA 59.394 33.333 9.00 0.0 0.00 2.69
4360 10997 6.658831 TGACGTCAACATTTGATCTTCTTTC 58.341 36.000 17.62 0.0 42.47 2.62
4405 11042 2.538449 GTGTACTATACATGCCGCACAC 59.462 50.000 0.00 0.0 41.34 3.82
4411 11048 3.131396 GCCACTGTGTACTATACATGCC 58.869 50.000 7.08 0.0 41.34 4.40
4433 11070 2.367512 GGCCTGGGTCCTGGATCT 60.368 66.667 15.84 0.0 37.23 2.75


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

AutoCloner maintained by Alex Coulton.