Multiple sequence alignment - TraesCS3B01G076600

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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 TraesCS3B01G076600 chr3B 100.000 4087 0 0 1 4087 47212272 47208186 0.000000e+00 7548
1 TraesCS3B01G076600 chr3B 84.471 1436 170 25 970 2372 47223147 47221732 0.000000e+00 1367
2 TraesCS3B01G076600 chr3B 87.105 760 74 14 2583 3325 47221354 47220602 0.000000e+00 839
3 TraesCS3B01G076600 chr3B 77.987 1222 212 35 1021 2202 46254332 46255536 0.000000e+00 713
4 TraesCS3B01G076600 chr3B 75.962 1456 306 27 1163 2585 47269867 47271311 0.000000e+00 710
5 TraesCS3B01G076600 chr3B 77.097 1061 183 41 2872 3911 46330041 46331062 3.570000e-155 558
6 TraesCS3B01G076600 chr3B 77.415 673 106 31 2607 3252 13970372 13969719 3.880000e-95 359
7 TraesCS3B01G076600 chr3B 79.096 354 51 15 3567 3910 46308266 46308606 5.320000e-54 222
8 TraesCS3B01G076600 chr3B 80.690 145 26 2 3739 3883 46781438 46781580 1.200000e-20 111
9 TraesCS3B01G076600 chr3B 88.298 94 5 5 2405 2494 46027816 46027907 1.550000e-19 108
10 TraesCS3B01G076600 chr3A 92.929 3465 153 38 675 4084 38137106 38133679 0.000000e+00 4957
11 TraesCS3B01G076600 chr3A 90.882 680 54 4 4 677 38138820 38138143 0.000000e+00 905
12 TraesCS3B01G076600 chr3A 77.622 1573 254 34 1041 2580 38013666 38012159 0.000000e+00 865
13 TraesCS3B01G076600 chr3A 85.622 619 88 1 1664 2281 38160010 38159392 0.000000e+00 649
14 TraesCS3B01G076600 chr3A 81.905 735 82 23 2583 3303 38142862 38142165 1.270000e-159 573
15 TraesCS3B01G076600 chr3A 84.247 584 55 13 993 1549 38160578 38160005 6.010000e-148 534
16 TraesCS3B01G076600 chr3A 88.512 383 29 5 3686 4056 38142162 38141783 2.240000e-122 449
17 TraesCS3B01G076600 chr3A 88.293 205 20 4 2388 2589 38157880 38157677 4.080000e-60 243
18 TraesCS3B01G076600 chr3A 95.238 84 4 0 2276 2359 38157961 38157878 2.560000e-27 134
19 TraesCS3B01G076600 chr1D 86.679 3153 339 44 974 4084 456280651 456277538 0.000000e+00 3421
20 TraesCS3B01G076600 chr1D 81.893 486 62 12 3557 4032 381007299 381007768 1.780000e-103 387
21 TraesCS3B01G076600 chr3D 95.217 1568 62 6 797 2359 28218315 28216756 0.000000e+00 2468
22 TraesCS3B01G076600 chr3D 84.343 1782 211 32 986 2740 27662992 27664732 0.000000e+00 1683
23 TraesCS3B01G076600 chr3D 82.939 1354 133 45 2733 4041 27665972 27667272 0.000000e+00 1131
24 TraesCS3B01G076600 chr3D 92.277 764 58 1 4 766 28219076 28218313 0.000000e+00 1083
25 TraesCS3B01G076600 chr3D 85.974 991 124 5 1370 2359 28224566 28223590 0.000000e+00 1046
26 TraesCS3B01G076600 chr3D 87.139 762 72 15 2583 3326 28223199 28222446 0.000000e+00 841
27 TraesCS3B01G076600 chr3D 77.180 1468 261 36 1148 2585 28124475 28123052 0.000000e+00 787
28 TraesCS3B01G076600 chr3D 86.819 698 65 17 2645 3326 28216319 28215633 0.000000e+00 754
29 TraesCS3B01G076600 chr3D 75.601 1414 293 32 1203 2585 28275266 28276658 0.000000e+00 652
30 TraesCS3B01G076600 chr3D 88.309 556 46 13 3543 4087 28215602 28215055 0.000000e+00 649
31 TraesCS3B01G076600 chr3D 88.889 243 23 3 3543 3783 28222416 28222176 3.090000e-76 296
32 TraesCS3B01G076600 chr3D 87.500 256 17 5 3813 4056 28222175 28221923 8.650000e-72 281
33 TraesCS3B01G076600 chr3D 89.500 200 18 3 2388 2585 28223592 28223394 2.440000e-62 250
34 TraesCS3B01G076600 chr3D 89.000 200 19 3 2388 2585 28216758 28216560 1.130000e-60 244
35 TraesCS3B01G076600 chr3D 73.438 640 113 40 2930 3545 4845578 4846184 1.940000e-43 187
36 TraesCS3B01G076600 chr3D 87.234 94 6 5 2405 2494 27533080 27533171 7.230000e-18 102
37 TraesCS3B01G076600 chr1B 80.082 1461 224 37 991 2415 510790648 510792077 0.000000e+00 1024
38 TraesCS3B01G076600 chr5A 83.546 784 121 4 1 776 435035287 435036070 0.000000e+00 726
39 TraesCS3B01G076600 chr5A 85.906 447 60 3 10 454 404219841 404219396 1.330000e-129 473
40 TraesCS3B01G076600 chr5A 77.652 792 135 19 4 768 411441738 411442514 1.040000e-120 444
41 TraesCS3B01G076600 chr5D 81.555 759 129 10 6 755 333348295 333349051 2.090000e-172 616
42 TraesCS3B01G076600 chr7B 87.196 453 55 3 4 454 399873865 399873414 2.820000e-141 512
43 TraesCS3B01G076600 chr6A 86.444 450 60 1 6 454 567347122 567346673 3.670000e-135 492
44 TraesCS3B01G076600 chr2D 85.778 450 63 1 6 454 593230240 593229791 3.700000e-130 475
45 TraesCS3B01G076600 chr2D 82.991 341 47 7 409 741 70817978 70817641 8.590000e-77 298
46 TraesCS3B01G076600 chr1A 81.687 486 63 12 3557 4032 481630356 481630825 8.290000e-102 381
47 TraesCS3B01G076600 chrUn 73.711 970 141 67 2609 3528 34705789 34706694 1.450000e-69 274


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 TraesCS3B01G076600 chr3B 47208186 47212272 4086 True 7548.0 7548 100.0000 1 4087 1 chr3B.!!$R2 4086
1 TraesCS3B01G076600 chr3B 47220602 47223147 2545 True 1103.0 1367 85.7880 970 3325 2 chr3B.!!$R3 2355
2 TraesCS3B01G076600 chr3B 46254332 46255536 1204 False 713.0 713 77.9870 1021 2202 1 chr3B.!!$F2 1181
3 TraesCS3B01G076600 chr3B 47269867 47271311 1444 False 710.0 710 75.9620 1163 2585 1 chr3B.!!$F6 1422
4 TraesCS3B01G076600 chr3B 46330041 46331062 1021 False 558.0 558 77.0970 2872 3911 1 chr3B.!!$F4 1039
5 TraesCS3B01G076600 chr3B 13969719 13970372 653 True 359.0 359 77.4150 2607 3252 1 chr3B.!!$R1 645
6 TraesCS3B01G076600 chr3A 38133679 38142862 9183 True 1721.0 4957 88.5570 4 4084 4 chr3A.!!$R2 4080
7 TraesCS3B01G076600 chr3A 38012159 38013666 1507 True 865.0 865 77.6220 1041 2580 1 chr3A.!!$R1 1539
8 TraesCS3B01G076600 chr3A 38157677 38160578 2901 True 390.0 649 88.3500 993 2589 4 chr3A.!!$R3 1596
9 TraesCS3B01G076600 chr1D 456277538 456280651 3113 True 3421.0 3421 86.6790 974 4084 1 chr1D.!!$R1 3110
10 TraesCS3B01G076600 chr3D 27662992 27667272 4280 False 1407.0 1683 83.6410 986 4041 2 chr3D.!!$F4 3055
11 TraesCS3B01G076600 chr3D 28215055 28224566 9511 True 791.2 2468 89.0624 4 4087 10 chr3D.!!$R2 4083
12 TraesCS3B01G076600 chr3D 28123052 28124475 1423 True 787.0 787 77.1800 1148 2585 1 chr3D.!!$R1 1437
13 TraesCS3B01G076600 chr3D 28275266 28276658 1392 False 652.0 652 75.6010 1203 2585 1 chr3D.!!$F3 1382
14 TraesCS3B01G076600 chr1B 510790648 510792077 1429 False 1024.0 1024 80.0820 991 2415 1 chr1B.!!$F1 1424
15 TraesCS3B01G076600 chr5A 435035287 435036070 783 False 726.0 726 83.5460 1 776 1 chr5A.!!$F2 775
16 TraesCS3B01G076600 chr5A 411441738 411442514 776 False 444.0 444 77.6520 4 768 1 chr5A.!!$F1 764
17 TraesCS3B01G076600 chr5D 333348295 333349051 756 False 616.0 616 81.5550 6 755 1 chr5D.!!$F1 749
18 TraesCS3B01G076600 chrUn 34705789 34706694 905 False 274.0 274 73.7110 2609 3528 1 chrUn.!!$F1 919

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
127 5791 0.390078 TCCGGTGAAAATCGCGCTTA 60.390 50.000 5.56 0.0 0.00 3.09 F
439 6110 1.070758 GGATGGATACGTGCAGGATGT 59.929 52.381 14.38 0.0 44.54 3.06 F
1710 8566 1.188863 GCCACTTGAGCCCATTCAAT 58.811 50.000 0.00 0.0 36.55 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 8338 1.153958 GCGGCAATCAAGCAGTTCC 60.154 57.895 0.0 0.0 35.83 3.62 R
2394 10699 2.146342 ACACTTGAGAATCGCAACAGG 58.854 47.619 0.0 0.0 38.61 4.00 R
3578 13469 0.039798 CATGGTCAGCACTGCAACAC 60.040 55.000 3.3 0.0 0.00 3.32 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
22 5685 1.762522 CGGTGAGGGGATGGAGGATG 61.763 65.000 0.00 0.00 0.00 3.51
23 5686 1.453669 GTGAGGGGATGGAGGATGC 59.546 63.158 0.00 0.00 0.00 3.91
125 5789 1.635663 CTTCCGGTGAAAATCGCGCT 61.636 55.000 5.56 0.00 0.00 5.92
127 5791 0.390078 TCCGGTGAAAATCGCGCTTA 60.390 50.000 5.56 0.00 0.00 3.09
181 5845 2.032550 TGACGTCGTTTCTTTCTCGAGT 59.967 45.455 13.13 0.00 34.33 4.18
193 5857 3.364889 TTCTCGAGTCATTGTCGTTGT 57.635 42.857 13.13 0.00 38.60 3.32
294 5958 1.573108 GTGATGTTCTCCCTCCTGGA 58.427 55.000 0.00 0.00 42.41 3.86
413 6082 1.569493 CAAGTTTCAGTGACGGGCG 59.431 57.895 0.00 0.00 0.00 6.13
439 6110 1.070758 GGATGGATACGTGCAGGATGT 59.929 52.381 14.38 0.00 44.54 3.06
463 6134 3.049674 CGTCTGGCATTGCGGTGT 61.050 61.111 1.91 0.00 0.00 4.16
489 6160 3.807622 CGACAACAATATGGCCTAACGAT 59.192 43.478 3.32 0.00 0.00 3.73
535 6206 1.271127 TGGGACGATGGAAGATGGCA 61.271 55.000 0.00 0.00 0.00 4.92
692 7428 4.288366 TCAAGATTGTAGATGTGGGGACAA 59.712 41.667 0.00 0.00 46.06 3.18
700 7436 4.657814 AGATGTGGGGACAATAGTTGTT 57.342 40.909 0.00 0.00 45.52 2.83
710 7446 6.352737 GGGGACAATAGTTGTTAGGAAGATGA 60.353 42.308 0.00 0.00 45.52 2.92
828 7567 5.806286 TGTTTGACGAAGCTGTAGAAAAAG 58.194 37.500 0.00 0.00 0.00 2.27
838 7577 5.532557 AGCTGTAGAAAAAGATTTGTTGCC 58.467 37.500 0.00 0.00 0.00 4.52
896 7635 1.687563 GCCCAACACAACCACTAAGT 58.312 50.000 0.00 0.00 0.00 2.24
949 7688 3.072468 CCACTCCGCTCCCCGTTA 61.072 66.667 0.00 0.00 34.38 3.18
954 7693 3.846430 CCGCTCCCCGTTACTCCC 61.846 72.222 0.00 0.00 34.38 4.30
1113 7882 4.421479 CACGCGAGCGAGGAGGTT 62.421 66.667 24.72 0.00 42.83 3.50
1710 8566 1.188863 GCCACTTGAGCCCATTCAAT 58.811 50.000 0.00 0.00 36.55 2.57
1727 8583 2.038426 TCAATGTGGTGTTGATCTCCGT 59.962 45.455 0.00 0.00 31.07 4.69
2103 8968 4.776837 TGGGTGCTATGGAAAACAATTGAT 59.223 37.500 13.59 0.00 0.00 2.57
2248 9113 4.691216 AGGTTCAACTTAAGTCGATGAAGC 59.309 41.667 27.70 27.70 44.53 3.86
2345 10647 5.769484 TCATCCTTAGTCCTCGTATTGTC 57.231 43.478 0.00 0.00 0.00 3.18
2394 10699 4.808895 TGTACATGCATGTTCGAATACCTC 59.191 41.667 35.45 13.87 41.97 3.85
2395 10700 3.206150 ACATGCATGTTCGAATACCTCC 58.794 45.455 26.61 0.00 37.90 4.30
2418 10729 3.183574 TGTTGCGATTCTCAAGTGTAACG 59.816 43.478 0.00 0.00 45.86 3.18
2683 11227 3.371595 CCCAAGATCACTTTTCCCGGTAT 60.372 47.826 0.00 0.00 33.70 2.73
2769 12559 3.906218 AGATCAATGCTAGGCCATGTCTA 59.094 43.478 5.01 0.00 0.00 2.59
3073 12921 3.281158 TGATGCATGATACACAAGGTGG 58.719 45.455 2.46 0.00 37.94 4.61
3239 13095 5.243954 TGTCCATTCGACTATAGGGATTCAG 59.756 44.000 4.43 0.00 42.49 3.02
3253 13109 5.300752 AGGGATTCAGACATGCTAATAACG 58.699 41.667 0.00 0.00 0.00 3.18
3549 13425 2.041216 GCTCTTCCTTTTTAGGGGGTGA 59.959 50.000 0.00 0.00 0.00 4.02
3578 13469 5.998363 GGGGGTATTGTATAGCTCTTCTTTG 59.002 44.000 0.00 0.00 0.00 2.77
3585 13476 5.304778 TGTATAGCTCTTCTTTGTGTTGCA 58.695 37.500 0.00 0.00 0.00 4.08
3593 13487 1.401552 TCTTTGTGTTGCAGTGCTGAC 59.598 47.619 17.60 15.01 0.00 3.51
3631 13525 7.661437 ACACATGTCTTGTTCATACACTGTTAT 59.339 33.333 0.00 0.00 36.00 1.89
3967 13884 3.691118 TGTTGAGCCATGATAGTTTCAGC 59.309 43.478 0.00 0.00 37.89 4.26
3969 13886 2.093500 TGAGCCATGATAGTTTCAGCGT 60.093 45.455 0.00 0.00 37.89 5.07
4046 13965 6.793492 AAGCATGTCTACTTTCTTGTCTTC 57.207 37.500 0.00 0.00 0.00 2.87
4077 13996 1.105167 TGCTTTGCTGCTGCTTGTCT 61.105 50.000 17.00 0.00 40.48 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.961381 ATCCTCCATCCCCTCACCGA 61.961 60.000 0.00 0.00 0.00 4.69
125 5789 1.669760 CCGCCAAGACCGCAGTTAA 60.670 57.895 0.00 0.00 0.00 2.01
127 5791 3.936203 TCCGCCAAGACCGCAGTT 61.936 61.111 0.00 0.00 0.00 3.16
181 5845 2.034939 ACGTGACCTACAACGACAATGA 59.965 45.455 1.80 0.00 0.00 2.57
193 5857 2.094906 CCGATCAAGTTGACGTGACCTA 60.095 50.000 7.96 0.00 37.20 3.08
294 5958 2.232941 CACTTGCTCCAAAATGATGCCT 59.767 45.455 0.00 0.00 0.00 4.75
413 6082 1.762222 GCACGTATCCATCCACACGC 61.762 60.000 0.00 0.00 37.92 5.34
439 6110 1.514678 GCAATGCCAGACGACACCAA 61.515 55.000 0.00 0.00 0.00 3.67
463 6134 3.558931 AGGCCATATTGTTGTCGATGA 57.441 42.857 5.01 0.00 0.00 2.92
489 6160 3.448660 CAGGAGTGATCAGTGTATCCACA 59.551 47.826 8.05 0.00 44.39 4.17
498 6169 1.905215 CCACCTTCAGGAGTGATCAGT 59.095 52.381 1.67 1.67 38.94 3.41
535 6206 1.135373 CACACTCTACGATCGGTTGCT 60.135 52.381 20.98 0.00 0.00 3.91
616 6291 2.130821 TATTCCGGTGGCCACAAGCA 62.131 55.000 35.78 17.96 46.50 3.91
657 6354 2.086869 CAATCTTGATGACGTGCCCTT 58.913 47.619 0.00 0.00 0.00 3.95
692 7428 8.367660 TCTGAAGTCATCTTCCTAACAACTAT 57.632 34.615 5.68 0.00 46.66 2.12
700 7436 6.665248 TGAGTCAATCTGAAGTCATCTTCCTA 59.335 38.462 0.00 0.00 46.66 2.94
710 7446 5.824624 ACAAACACATGAGTCAATCTGAAGT 59.175 36.000 0.00 0.00 0.00 3.01
828 7567 3.401182 TCTGCAAAATGGGCAACAAATC 58.599 40.909 0.00 0.00 41.39 2.17
855 7594 1.355971 CCGTTGTGTTCACCCGATAG 58.644 55.000 11.62 0.00 0.00 2.08
856 7595 0.037139 CCCGTTGTGTTCACCCGATA 60.037 55.000 11.62 0.00 0.00 2.92
857 7596 1.302192 CCCGTTGTGTTCACCCGAT 60.302 57.895 11.62 0.00 0.00 4.18
948 7687 0.399376 ACCACACCACACAGGGAGTA 60.399 55.000 0.00 0.00 43.89 2.59
949 7688 1.692749 ACCACACCACACAGGGAGT 60.693 57.895 0.00 0.00 43.89 3.85
954 7693 2.534019 GCGACACCACACCACACAG 61.534 63.158 0.00 0.00 0.00 3.66
1506 8338 1.153958 GCGGCAATCAAGCAGTTCC 60.154 57.895 0.00 0.00 35.83 3.62
1635 8488 4.643387 AGCACAGCCCCGGTGAAC 62.643 66.667 0.00 0.00 38.54 3.18
1710 8566 2.631160 AAACGGAGATCAACACCACA 57.369 45.000 0.00 0.00 0.00 4.17
1727 8583 5.187621 AGGTTGATTATTCCCTCCGAAAA 57.812 39.130 0.00 0.00 33.08 2.29
2103 8968 4.513442 GGAGCCCAATAATCATACGCATA 58.487 43.478 0.00 0.00 0.00 3.14
2297 10599 3.107601 TCACCTGGAGGATAGAAACTGG 58.892 50.000 0.00 0.00 38.94 4.00
2345 10647 4.103357 CACACCGAGATTAAGTTACTCCG 58.897 47.826 0.00 1.74 0.00 4.63
2394 10699 2.146342 ACACTTGAGAATCGCAACAGG 58.854 47.619 0.00 0.00 38.61 4.00
2395 10700 4.664139 CGTTACACTTGAGAATCGCAACAG 60.664 45.833 0.00 0.00 38.61 3.16
2418 10729 4.568956 TGGACGGTAACTAAGTTTAAGCC 58.431 43.478 0.00 0.00 0.00 4.35
2683 11227 7.199766 AGAAACATGCGAAAACTCATAAACAA 58.800 30.769 0.00 0.00 0.00 2.83
3073 12921 7.750903 GCACATTAGAAGATCAAACCAAACTAC 59.249 37.037 0.00 0.00 0.00 2.73
3138 12989 8.749499 GTGAAAATCAAACAGTTCAATTCTCAG 58.251 33.333 0.00 0.00 32.12 3.35
3144 12995 8.040132 TCCAAAGTGAAAATCAAACAGTTCAAT 58.960 29.630 0.00 0.00 32.12 2.57
3429 13303 3.686726 GTGAGGTGATGGAGTTGAATGAC 59.313 47.826 0.00 0.00 0.00 3.06
3549 13425 2.089581 AGCTATACAATACCCCCACCCT 60.090 50.000 0.00 0.00 0.00 4.34
3578 13469 0.039798 CATGGTCAGCACTGCAACAC 60.040 55.000 3.30 0.00 0.00 3.32
3585 13476 2.645838 ACAAACTCATGGTCAGCACT 57.354 45.000 0.00 0.00 0.00 4.40
3662 13556 5.584253 ACTAACTTGATACAGACGCAGAT 57.416 39.130 0.00 0.00 0.00 2.90
3664 13558 6.090783 TGTTACTAACTTGATACAGACGCAG 58.909 40.000 0.71 0.00 0.00 5.18
3666 13560 6.320171 TCTGTTACTAACTTGATACAGACGC 58.680 40.000 0.00 0.00 37.62 5.19
3667 13561 8.912787 AATCTGTTACTAACTTGATACAGACG 57.087 34.615 0.00 0.00 43.11 4.18
3707 13603 1.151810 AGCCCTTCTTCACCTGGGA 60.152 57.895 0.00 0.00 42.11 4.37
3771 13667 2.546778 ACATATAAACACTGCCGACGG 58.453 47.619 10.29 10.29 0.00 4.79
3879 13781 6.096423 TCCGACTTGATACAATGCTAGTAAGT 59.904 38.462 0.00 0.00 0.00 2.24
3944 13861 4.437930 GCTGAAACTATCATGGCTCAACAC 60.438 45.833 0.00 0.00 37.44 3.32
3967 13884 2.027569 CACGTTTCGGTGATACATGACG 59.972 50.000 0.00 0.00 40.38 4.35
3969 13886 3.306917 ACACGTTTCGGTGATACATGA 57.693 42.857 0.00 0.00 40.38 3.07


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

AutoCloner maintained by Alex Coulton.