Multiple sequence alignment - TraesCS3A01G518000

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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 TraesCS3A01G518000 chr3A 100.000 3956 0 0 1 3956 735464353 735468308 0.000000e+00 7306
1 TraesCS3A01G518000 chr6A 95.503 2602 81 25 3 2588 615413528 615410947 0.000000e+00 4124
2 TraesCS3A01G518000 chr6A 94.917 1259 39 14 2588 3823 615410881 615409625 0.000000e+00 1947
3 TraesCS3A01G518000 chr6A 96.454 141 3 2 3818 3956 615401251 615401111 8.550000e-57 231
4 TraesCS3A01G518000 chr7D 94.836 1859 80 15 737 2588 108301731 108299882 0.000000e+00 2887
5 TraesCS3A01G518000 chr7D 94.881 1856 76 17 737 2588 21681528 21679688 0.000000e+00 2883
6 TraesCS3A01G518000 chr7D 94.632 1863 81 15 737 2588 108264808 108262954 0.000000e+00 2868
7 TraesCS3A01G518000 chr7D 90.392 1020 69 21 2588 3594 21679622 21678619 0.000000e+00 1314
8 TraesCS3A01G518000 chr7D 89.804 1020 74 21 2588 3594 108262888 108261886 0.000000e+00 1280
9 TraesCS3A01G518000 chr7D 89.706 1020 73 22 2588 3594 108299816 108298816 0.000000e+00 1273
10 TraesCS3A01G518000 chr7D 94.649 598 22 8 4 598 108302312 108301722 0.000000e+00 918
11 TraesCS3A01G518000 chr7D 94.314 598 23 8 5 598 21682109 21681519 0.000000e+00 905
12 TraesCS3A01G518000 chr7D 93.522 602 24 10 4 598 108265392 108264799 0.000000e+00 881
13 TraesCS3A01G518000 chr7D 88.976 254 12 5 3709 3951 21678432 21678184 2.310000e-77 300
14 TraesCS3A01G518000 chr7D 88.281 256 16 7 3709 3951 108261698 108261444 1.080000e-75 294
15 TraesCS3A01G518000 chr5D 94.779 1858 80 16 737 2588 30633802 30631956 0.000000e+00 2878
16 TraesCS3A01G518000 chr5D 94.370 1350 68 7 737 2083 420310003 420308659 0.000000e+00 2065
17 TraesCS3A01G518000 chr5D 89.814 1021 76 20 2588 3594 30631890 30630884 0.000000e+00 1284
18 TraesCS3A01G518000 chr5D 88.954 1023 84 19 2588 3594 420308058 420307049 0.000000e+00 1236
19 TraesCS3A01G518000 chr5D 94.343 601 21 9 4 598 420310587 420309994 0.000000e+00 909
20 TraesCS3A01G518000 chr5D 94.010 601 23 8 4 598 30634386 30633793 0.000000e+00 898
21 TraesCS3A01G518000 chr5D 88.672 256 16 6 3709 3951 420306861 420306606 2.310000e-77 300
22 TraesCS3A01G518000 chr5D 87.891 256 17 7 3709 3951 30630696 30630442 5.000000e-74 289
23 TraesCS3A01G518000 chr1D 94.528 1864 80 20 737 2588 66200035 66198182 0.000000e+00 2857
24 TraesCS3A01G518000 chr1D 93.844 601 24 9 4 598 66200619 66200026 0.000000e+00 893
25 TraesCS3A01G518000 chr1D 88.462 260 15 8 3706 3951 66196881 66196623 2.310000e-77 300
26 TraesCS3A01G518000 chr2D 94.352 1859 87 15 737 2588 343142964 343141117 0.000000e+00 2835
27 TraesCS3A01G518000 chr2D 89.062 1024 77 25 2588 3594 343141051 343140046 0.000000e+00 1238
28 TraesCS3A01G518000 chr2D 94.176 601 22 10 4 598 343143548 343142955 0.000000e+00 904
29 TraesCS3A01G518000 chr2D 89.453 256 13 7 3709 3951 343139858 343139604 1.070000e-80 311
30 TraesCS3A01G518000 chr3B 85.673 1389 157 27 1219 2577 18007521 18006145 0.000000e+00 1424
31 TraesCS3A01G518000 chr7B 85.438 1394 165 28 1219 2588 712608234 712609613 0.000000e+00 1415
32 TraesCS3A01G518000 chr7B 85.590 1381 160 27 1224 2577 733217522 733216154 0.000000e+00 1411
33 TraesCS3A01G518000 chr7B 88.184 1041 89 24 2574 3593 712609678 712610705 0.000000e+00 1210
34 TraesCS3A01G518000 chr7B 81.771 576 76 17 529 1100 712607616 712608166 4.660000e-124 455
35 TraesCS3A01G518000 chr7B 81.404 527 54 29 8 525 712607088 712607579 1.330000e-104 390
36 TraesCS3A01G518000 chr7B 85.922 206 25 3 3749 3951 733214883 733214679 2.390000e-52 217
37 TraesCS3A01G518000 chr4B 87.273 1045 89 30 2572 3593 638491726 638490703 0.000000e+00 1153
38 TraesCS3A01G518000 chr1B 87.317 205 23 3 3749 3951 621583603 621583400 8.550000e-57 231


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 TraesCS3A01G518000 chr3A 735464353 735468308 3955 False 7306.000000 7306 100.000000 1 3956 1 chr3A.!!$F1 3955
1 TraesCS3A01G518000 chr6A 615409625 615413528 3903 True 3035.500000 4124 95.210000 3 3823 2 chr6A.!!$R2 3820
2 TraesCS3A01G518000 chr7D 108298816 108302312 3496 True 1692.666667 2887 93.063667 4 3594 3 chr7D.!!$R3 3590
3 TraesCS3A01G518000 chr7D 21678184 21682109 3925 True 1350.500000 2883 92.140750 5 3951 4 chr7D.!!$R1 3946
4 TraesCS3A01G518000 chr7D 108261444 108265392 3948 True 1330.750000 2868 91.559750 4 3951 4 chr7D.!!$R2 3947
5 TraesCS3A01G518000 chr5D 30630442 30634386 3944 True 1337.250000 2878 91.623500 4 3951 4 chr5D.!!$R1 3947
6 TraesCS3A01G518000 chr5D 420306606 420310587 3981 True 1127.500000 2065 91.584750 4 3951 4 chr5D.!!$R2 3947
7 TraesCS3A01G518000 chr1D 66196623 66200619 3996 True 1350.000000 2857 92.278000 4 3951 3 chr1D.!!$R1 3947
8 TraesCS3A01G518000 chr2D 343139604 343143548 3944 True 1322.000000 2835 91.760750 4 3951 4 chr2D.!!$R1 3947
9 TraesCS3A01G518000 chr3B 18006145 18007521 1376 True 1424.000000 1424 85.673000 1219 2577 1 chr3B.!!$R1 1358
10 TraesCS3A01G518000 chr7B 712607088 712610705 3617 False 867.500000 1415 84.199250 8 3593 4 chr7B.!!$F1 3585
11 TraesCS3A01G518000 chr7B 733214679 733217522 2843 True 814.000000 1411 85.756000 1224 3951 2 chr7B.!!$R1 2727
12 TraesCS3A01G518000 chr4B 638490703 638491726 1023 True 1153.000000 1153 87.273000 2572 3593 1 chr4B.!!$R1 1021

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
635 716 0.698238 AGGTACAAGCAAGGATGGCA 59.302 50.000 0.00 0.00 37.68 4.92 F
636 717 1.285962 AGGTACAAGCAAGGATGGCAT 59.714 47.619 0.00 0.00 37.68 4.40 F
637 718 1.678101 GGTACAAGCAAGGATGGCATC 59.322 52.381 19.23 19.23 37.68 3.91 F
2434 2742 1.808411 TCTTTCCGTCAGTTCATGCC 58.192 50.000 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 2742 0.508641 CGAACAAGAACCAGTGCTCG 59.491 55.000 0.0 0.0 0.00 5.03 R
2494 2803 6.605594 GGAATGGTGTGTTCCCTTCATAATAA 59.394 38.462 0.0 0.0 39.36 1.40 R
2649 3042 4.710324 TGGGTACTCTACACCAAACTTTG 58.290 43.478 0.0 0.0 37.84 2.77 R
3596 4099 4.751767 TTTTGAAATCCTGCACCAAAGT 57.248 36.364 0.0 0.0 0.00 2.66 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
204 244 2.018542 GCATGTTTGCTGGCATCAAT 57.981 45.000 4.40 0.00 45.77 2.57
369 412 2.294512 CAGATGATGCGACACCTAGCTA 59.705 50.000 0.00 0.00 0.00 3.32
494 541 4.478686 AGGTAATTGTTTCTCCATAGCCCT 59.521 41.667 0.00 0.00 0.00 5.19
630 711 4.693532 CGCAGGTACAAGCAAGGA 57.306 55.556 9.10 0.00 0.00 3.36
631 712 3.159298 CGCAGGTACAAGCAAGGAT 57.841 52.632 9.10 0.00 0.00 3.24
632 713 0.729116 CGCAGGTACAAGCAAGGATG 59.271 55.000 9.10 0.00 0.00 3.51
633 714 1.098050 GCAGGTACAAGCAAGGATGG 58.902 55.000 4.13 0.00 0.00 3.51
634 715 1.098050 CAGGTACAAGCAAGGATGGC 58.902 55.000 0.00 0.00 32.57 4.40
635 716 0.698238 AGGTACAAGCAAGGATGGCA 59.302 50.000 0.00 0.00 37.68 4.92
636 717 1.285962 AGGTACAAGCAAGGATGGCAT 59.714 47.619 0.00 0.00 37.68 4.40
637 718 1.678101 GGTACAAGCAAGGATGGCATC 59.322 52.381 19.23 19.23 37.68 3.91
638 719 2.648059 GTACAAGCAAGGATGGCATCT 58.352 47.619 25.48 10.14 37.68 2.90
639 720 2.226962 ACAAGCAAGGATGGCATCTT 57.773 45.000 25.48 16.89 37.68 2.40
687 768 8.027189 GTGATTCACCTAAAATTTCCTACAACC 58.973 37.037 5.44 0.00 0.00 3.77
751 960 5.587844 TCTTTTCATAGGATGAGCAAGAAGC 59.412 40.000 9.24 0.00 40.94 3.86
1075 1291 3.430218 GGACAGTGAGAACGATGAAAGTG 59.570 47.826 0.00 0.00 0.00 3.16
1100 1316 6.090898 GCTACACACAAGTACAAGAAGGTATG 59.909 42.308 0.00 0.00 0.00 2.39
1458 1699 3.708121 TCCTTCTCTGCAGCATCATCTTA 59.292 43.478 9.47 0.00 0.00 2.10
1459 1700 4.347292 TCCTTCTCTGCAGCATCATCTTAT 59.653 41.667 9.47 0.00 0.00 1.73
1546 1787 4.285775 GGATGTTCAAATTTTGGGGGAGAA 59.714 41.667 9.18 0.00 0.00 2.87
1584 1825 5.358725 TCATGCTCTAGTATGGTAAACACGA 59.641 40.000 8.00 0.00 38.44 4.35
1603 1844 5.640357 ACACGACGGACAATTTATACAACAT 59.360 36.000 0.00 0.00 0.00 2.71
1837 2083 5.810080 TTTCCCCGTGATTAAATGGTTTT 57.190 34.783 0.00 0.00 0.00 2.43
1957 2208 3.006940 GGTGATTCATTTGGTGCGACTA 58.993 45.455 0.00 0.00 0.00 2.59
2114 2399 6.824305 ACTCAACATATTTTCAACAGAGGG 57.176 37.500 0.00 0.00 0.00 4.30
2168 2454 9.713684 TTCTTGGGTGGAAGATCAATAATTAAT 57.286 29.630 0.00 0.00 31.98 1.40
2259 2545 8.352942 GGAAATGAAGAGAAAAGCACTTAGAAA 58.647 33.333 0.00 0.00 0.00 2.52
2315 2601 3.859961 CGAAAGTGATCGTGTATGCTTCT 59.140 43.478 0.00 0.00 38.01 2.85
2434 2742 1.808411 TCTTTCCGTCAGTTCATGCC 58.192 50.000 0.00 0.00 0.00 4.40
2494 2803 7.174080 GCAAGAAAGTTTGTCTTCCTAGATTCT 59.826 37.037 0.00 0.00 32.96 2.40
2550 2859 7.148086 CGGGATCAGAGATTTGATGGTTAAAAA 60.148 37.037 0.00 0.00 37.90 1.94
2551 2860 7.976175 GGGATCAGAGATTTGATGGTTAAAAAC 59.024 37.037 0.00 0.00 37.90 2.43
2552 2861 8.522830 GGATCAGAGATTTGATGGTTAAAAACA 58.477 33.333 0.00 0.00 37.90 2.83
2649 3042 3.703001 TCTGAGAGGAATGGGTTTCAC 57.297 47.619 0.00 0.00 35.94 3.18
2701 3094 5.637810 GCCAAAGCAAATAGGAAGGTAAAAC 59.362 40.000 0.00 0.00 39.53 2.43
2900 3302 2.578495 GTTCACGATGAACGACGTAGT 58.422 47.619 0.00 0.00 45.88 2.73
2953 3355 9.066892 ACATTCTGTTTAGTATTCACAACACAT 57.933 29.630 0.00 0.00 0.00 3.21
2997 3401 8.408043 TCATCAAGAACTTCATGGTAAATTGT 57.592 30.769 0.00 0.00 0.00 2.71
3114 3527 9.528018 TGTCTTTCCAATTTTTCTGTGTATTTC 57.472 29.630 0.00 0.00 0.00 2.17
3359 3847 9.495754 GAGGAACGATATGATTTTCTTTTTCTG 57.504 33.333 0.00 0.00 0.00 3.02
3594 4097 2.053627 CATTTTGTTGCGCCTGTTCTC 58.946 47.619 4.18 0.00 0.00 2.87
3596 4099 2.248280 TTTGTTGCGCCTGTTCTCTA 57.752 45.000 4.18 0.00 0.00 2.43
3776 4369 6.017605 CAGTACCAAAAGTGCTATCATCCATC 60.018 42.308 0.00 0.00 39.74 3.51
3831 4424 3.251004 GTGCCACAACAAACAACCAAAAA 59.749 39.130 0.00 0.00 0.00 1.94
3875 4473 8.746922 TTTTCAGTCATCACTTGCATATTTTC 57.253 30.769 0.00 0.00 0.00 2.29
3894 4492 1.416401 TCGCCTTCTTGAACTTCCAGT 59.584 47.619 0.00 0.00 0.00 4.00
3897 4495 3.740115 GCCTTCTTGAACTTCCAGTACA 58.260 45.455 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 44 9.249457 GACATTATTCATAGTGTTTCGATCTGA 57.751 33.333 0.00 0.00 34.01 3.27
204 244 5.055812 GGCACAAAACAAATGAGAAATGGA 58.944 37.500 0.00 0.00 0.00 3.41
578 659 3.067180 CGATGCCATCCTTGCTTGTATTT 59.933 43.478 0.00 0.00 0.00 1.40
622 703 3.604875 CAAAAGATGCCATCCTTGCTT 57.395 42.857 0.00 0.00 0.00 3.91
656 737 7.010160 AGGAAATTTTAGGTGAATCACAGGAA 58.990 34.615 15.86 2.95 35.86 3.36
659 740 8.335532 TGTAGGAAATTTTAGGTGAATCACAG 57.664 34.615 15.86 0.00 35.86 3.66
771 980 1.080501 GCTGTCTCTGCGCACACTA 60.081 57.895 5.66 0.00 0.00 2.74
1075 1291 4.377897 ACCTTCTTGTACTTGTGTGTAGC 58.622 43.478 0.00 0.00 0.00 3.58
1188 1414 3.070018 CACACTTTTAGAGGGCAGACTG 58.930 50.000 0.00 0.00 29.07 3.51
1546 1787 6.832384 ACTAGAGCATGAACCATTGAATGATT 59.168 34.615 6.76 0.00 0.00 2.57
1584 1825 6.374333 AGCTTCATGTTGTATAAATTGTCCGT 59.626 34.615 0.00 0.00 0.00 4.69
1603 1844 5.357742 TGAAGTGCCTAATGATAGCTTCA 57.642 39.130 0.00 0.00 35.35 3.02
1802 2044 3.807071 CACGGGGAAAAAGTGGAAAAATG 59.193 43.478 0.00 0.00 32.68 2.32
1804 2046 3.097614 TCACGGGGAAAAAGTGGAAAAA 58.902 40.909 0.00 0.00 36.60 1.94
1957 2208 2.941453 ACATATGCTTCGACGTGACT 57.059 45.000 1.58 0.00 0.00 3.41
2134 2419 1.814429 TCCACCCAAGAAGTCCAGAA 58.186 50.000 0.00 0.00 0.00 3.02
2168 2454 7.316640 TCCTGATTTGTGAAAAAGAACGAAAA 58.683 30.769 0.00 0.00 0.00 2.29
2259 2545 2.800250 CTTTCCCAGCTCCATTGAAGT 58.200 47.619 0.00 0.00 0.00 3.01
2378 2686 4.118410 TGGACACACAATTTGATTGCAAC 58.882 39.130 0.00 0.00 43.98 4.17
2434 2742 0.508641 CGAACAAGAACCAGTGCTCG 59.491 55.000 0.00 0.00 0.00 5.03
2494 2803 6.605594 GGAATGGTGTGTTCCCTTCATAATAA 59.394 38.462 0.00 0.00 39.36 1.40
2649 3042 4.710324 TGGGTACTCTACACCAAACTTTG 58.290 43.478 0.00 0.00 37.84 2.77
2900 3302 2.935238 GCAAATCTGACCCTTGCGTCTA 60.935 50.000 5.52 0.00 36.44 2.59
3114 3527 1.639280 ACAGTGGCAAACGCAAAAAG 58.361 45.000 0.00 0.00 0.00 2.27
3153 3571 6.931838 AGTAACCTCAAAATGACAGACGATA 58.068 36.000 0.00 0.00 0.00 2.92
3156 3574 6.645415 AGTTAGTAACCTCAAAATGACAGACG 59.355 38.462 9.46 0.00 0.00 4.18
3211 3633 0.467106 TGTGCTTGGTTGGCTGCTTA 60.467 50.000 0.00 0.00 0.00 3.09
3359 3847 4.937201 ACAACTTGGATTCCCTTTCAAC 57.063 40.909 0.00 0.00 0.00 3.18
3367 3855 5.186198 ACACTGCTATACAACTTGGATTCC 58.814 41.667 0.00 0.00 0.00 3.01
3594 4097 5.452078 TTTGAAATCCTGCACCAAAGTAG 57.548 39.130 0.00 0.00 0.00 2.57
3596 4099 4.751767 TTTTGAAATCCTGCACCAAAGT 57.248 36.364 0.00 0.00 0.00 2.66
3632 4164 5.445939 CGATTGCGCTGTAGAAAGTACATTT 60.446 40.000 9.73 0.00 0.00 2.32
3690 4223 5.228945 AGTAGCAACACTGACCTTAACAT 57.771 39.130 0.00 0.00 0.00 2.71
3756 4349 5.125900 TGTTGATGGATGATAGCACTTTTGG 59.874 40.000 0.00 0.00 0.00 3.28
3776 4369 9.480053 AAAAACATGAAGGAACTATGATTGTTG 57.520 29.630 0.00 0.00 38.49 3.33
3812 4405 5.237344 TCAAGTTTTTGGTTGTTTGTTGTGG 59.763 36.000 0.00 0.00 34.97 4.17


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

AutoCloner maintained by Alex Coulton.