Multiple sequence alignment - TraesCS1D01G234100

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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 TraesCS1D01G234100 chr1D 100.000 3012 0 0 1 3012 322284449 322287460 0.000000e+00 5563.0
1 TraesCS1D01G234100 chr1D 95.486 1573 43 10 1 1555 227131597 227130035 0.000000e+00 2486.0
2 TraesCS1D01G234100 chr1D 96.066 1144 36 4 1628 2768 227129637 227128500 0.000000e+00 1855.0
3 TraesCS1D01G234100 chr1D 95.169 207 9 1 2806 3012 227128505 227128300 2.900000e-85 326.0
4 TraesCS1D01G234100 chr1D 84.112 107 9 5 516 622 112443562 112443464 2.470000e-16 97.1
5 TraesCS1D01G234100 chr1D 96.078 51 1 1 1573 1623 227130041 227129992 6.920000e-12 82.4
6 TraesCS1D01G234100 chr1D 94.595 37 0 2 2757 2791 15304273 15304309 4.190000e-04 56.5
7 TraesCS1D01G234100 chr1B 94.484 2792 114 18 1 2768 327025306 327022531 0.000000e+00 4266.0
8 TraesCS1D01G234100 chr1B 95.221 1632 46 10 1 1614 435193414 435195031 0.000000e+00 2553.0
9 TraesCS1D01G234100 chr1B 96.621 1095 34 3 1650 2742 435195411 435196504 0.000000e+00 1814.0
10 TraesCS1D01G234100 chr1B 91.336 277 16 5 2739 3012 435309439 435309710 3.670000e-99 372.0
11 TraesCS1D01G234100 chr1B 95.652 207 8 1 2806 3012 327022536 327022331 6.220000e-87 331.0
12 TraesCS1D01G234100 chr1A 95.534 2508 63 9 126 2587 406188904 406191408 0.000000e+00 3965.0
13 TraesCS1D01G234100 chr1A 100.000 207 0 0 2806 3012 406203213 406203419 1.690000e-102 383.0
14 TraesCS1D01G234100 chr1A 96.094 128 4 1 2578 2704 406203055 406203182 1.090000e-49 207.0
15 TraesCS1D01G234100 chr1A 95.276 127 5 1 1 126 406187723 406187849 1.830000e-47 200.0
16 TraesCS1D01G234100 chr1A 100.000 30 0 0 2762 2791 63336185 63336156 4.190000e-04 56.5
17 TraesCS1D01G234100 chr3A 86.991 884 91 13 692 1569 739735331 739734466 0.000000e+00 974.0
18 TraesCS1D01G234100 chr3A 84.659 880 90 15 668 1536 739322282 739323127 0.000000e+00 835.0
19 TraesCS1D01G234100 chr3A 85.258 407 41 17 1613 2004 739323281 739323683 4.680000e-108 401.0
20 TraesCS1D01G234100 chr3A 84.328 134 12 4 504 637 739770403 739770279 4.080000e-24 122.0
21 TraesCS1D01G234100 chr3B 84.995 973 113 18 656 1621 816692410 816691464 0.000000e+00 957.0
22 TraesCS1D01G234100 chr3B 81.757 444 50 13 1607 2032 816691438 816691008 2.880000e-90 342.0
23 TraesCS1D01G234100 chr3B 81.733 427 47 18 1607 2015 816265220 816265633 8.050000e-86 327.0
24 TraesCS1D01G234100 chr3B 100.000 31 0 0 2761 2791 68873002 68872972 1.170000e-04 58.4
25 TraesCS1D01G234100 chr3D 86.565 856 93 13 720 1569 607310709 607309870 0.000000e+00 924.0
26 TraesCS1D01G234100 chr3D 84.906 901 96 19 655 1547 606929722 606930590 0.000000e+00 874.0
27 TraesCS1D01G234100 chr3D 82.688 439 48 13 1614 2035 606930677 606931104 6.140000e-97 364.0
28 TraesCS1D01G234100 chr3D 81.777 439 50 14 1614 2034 607309805 607309379 1.030000e-89 340.0
29 TraesCS1D01G234100 chr3D 81.020 353 55 12 271 614 606929372 606929721 1.380000e-68 270.0
30 TraesCS1D01G234100 chrUn 84.112 107 9 6 516 622 101646648 101646550 2.470000e-16 97.1
31 TraesCS1D01G234100 chr7B 94.737 38 1 1 2754 2791 63936142 63936178 1.170000e-04 58.4
32 TraesCS1D01G234100 chr7D 100.000 30 0 0 2762 2791 555660548 555660577 4.190000e-04 56.5
33 TraesCS1D01G234100 chr4B 100.000 30 0 0 2762 2791 476358116 476358145 4.190000e-04 56.5
34 TraesCS1D01G234100 chr4A 100.000 30 0 0 2762 2791 11590661 11590690 4.190000e-04 56.5
35 TraesCS1D01G234100 chr4A 100.000 30 0 0 2761 2790 93683443 93683414 4.190000e-04 56.5
36 TraesCS1D01G234100 chr6B 91.892 37 3 0 2755 2791 135505587 135505623 5.000000e-03 52.8


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 TraesCS1D01G234100 chr1D 322284449 322287460 3011 False 5563.000000 5563 100.000000 1 3012 1 chr1D.!!$F2 3011
1 TraesCS1D01G234100 chr1D 227128300 227131597 3297 True 1187.350000 2486 95.699750 1 3012 4 chr1D.!!$R2 3011
2 TraesCS1D01G234100 chr1B 327022331 327025306 2975 True 2298.500000 4266 95.068000 1 3012 2 chr1B.!!$R1 3011
3 TraesCS1D01G234100 chr1B 435193414 435196504 3090 False 2183.500000 2553 95.921000 1 2742 2 chr1B.!!$F2 2741
4 TraesCS1D01G234100 chr1A 406187723 406191408 3685 False 2082.500000 3965 95.405000 1 2587 2 chr1A.!!$F1 2586
5 TraesCS1D01G234100 chr3A 739734466 739735331 865 True 974.000000 974 86.991000 692 1569 1 chr3A.!!$R1 877
6 TraesCS1D01G234100 chr3A 739322282 739323683 1401 False 618.000000 835 84.958500 668 2004 2 chr3A.!!$F1 1336
7 TraesCS1D01G234100 chr3B 816691008 816692410 1402 True 649.500000 957 83.376000 656 2032 2 chr3B.!!$R2 1376
8 TraesCS1D01G234100 chr3D 607309379 607310709 1330 True 632.000000 924 84.171000 720 2034 2 chr3D.!!$R1 1314
9 TraesCS1D01G234100 chr3D 606929372 606931104 1732 False 502.666667 874 82.871333 271 2035 3 chr3D.!!$F1 1764

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
70 71 1.067060 TGGGAATCGTACTCATGCTCG 59.933 52.381 0.0 0.0 0.00 5.03 F
774 1865 1.588404 CGACTGTGTGTGTCAGTTGTC 59.412 52.381 0.0 0.0 44.68 3.18 F
1727 3280 0.823356 TGCAGGCAGTGGAAAAGGAC 60.823 55.000 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 2161 0.039764 AGTCGAGGAGGACCATCACA 59.960 55.0 0.00 0.0 37.66 3.58 R
1864 3426 1.392589 CATGGCCGCTGAAACCTAAT 58.607 50.0 0.00 0.0 0.00 1.73 R
2797 4386 2.040012 AGTTGACGAGTACTCCCTCTGA 59.960 50.0 17.23 3.3 0.00 3.27 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
58 59 4.839668 TTGTTTTTGTACCTGGGAATCG 57.160 40.909 0.00 0.00 0.00 3.34
70 71 1.067060 TGGGAATCGTACTCATGCTCG 59.933 52.381 0.00 0.00 0.00 5.03
315 1386 6.772716 AGGACACAACTGAAATTCTGTTATGT 59.227 34.615 23.12 23.12 44.66 2.29
514 1599 3.199946 CCTACTGGAGCTTATTTCCACCA 59.800 47.826 0.00 0.00 39.74 4.17
572 1657 6.865205 GCTCAAAAGAAGTAATCAATGCTGTT 59.135 34.615 0.00 0.00 0.00 3.16
595 1681 2.497138 TCTGAGGTTGTGTGCAATGAG 58.503 47.619 0.00 0.00 36.92 2.90
618 1704 9.589461 TGAGGGTTATGTTTCCTTAAATGTTTA 57.411 29.630 0.00 0.00 0.00 2.01
723 1809 5.305585 ACTACCAAGTTGACAACGATTCAT 58.694 37.500 12.54 1.20 36.23 2.57
774 1865 1.588404 CGACTGTGTGTGTCAGTTGTC 59.412 52.381 0.00 0.00 44.68 3.18
863 1967 9.284968 ACAAATATAGGACAAATACATAGTGGC 57.715 33.333 0.00 0.00 0.00 5.01
885 1989 3.658988 CACACGTCATGTTTCAACAATCG 59.341 43.478 0.00 5.05 40.64 3.34
1054 2161 3.721087 ATGAGGAACCACGAGGATTTT 57.279 42.857 5.68 0.00 38.69 1.82
1107 2220 1.816835 TCTATCTCACCACGTCGCTTT 59.183 47.619 0.00 0.00 0.00 3.51
1345 2458 4.200092 CTCTTTAGAACCCCATAGGCAAC 58.800 47.826 0.00 0.00 40.58 4.17
1480 2593 1.347707 GCATACCTGCCATGGTAGCTA 59.652 52.381 23.41 15.14 44.69 3.32
1563 2680 3.543680 TCTGGTTTAGTAGATGCAGCC 57.456 47.619 0.00 0.00 0.00 4.85
1727 3280 0.823356 TGCAGGCAGTGGAAAAGGAC 60.823 55.000 0.00 0.00 0.00 3.85
1787 3346 3.448934 TGAGATTGAGAAGAGAAGGCCT 58.551 45.455 0.00 0.00 0.00 5.19
1791 3350 1.566211 TGAGAAGAGAAGGCCTCCTG 58.434 55.000 5.23 0.00 42.97 3.86
1858 3420 9.477484 CTGTTGTGGTTAACCTATATCATACTC 57.523 37.037 24.78 10.04 36.82 2.59
1978 3558 2.358247 AAACGCTACGGTGCTGGG 60.358 61.111 0.00 0.00 0.00 4.45
2180 3760 1.331447 CAGCGCTGCTTATATTGCACA 59.669 47.619 26.68 0.00 36.40 4.57
2304 3884 3.008813 TCTGAAGGCAGATTGCTCTTTCT 59.991 43.478 0.67 0.00 45.88 2.52
2550 4139 3.068590 CCAGCCATCCCAATTTACATGTC 59.931 47.826 0.00 0.00 0.00 3.06
2551 4140 3.700539 CAGCCATCCCAATTTACATGTCA 59.299 43.478 0.00 0.00 0.00 3.58
2552 4141 4.342951 CAGCCATCCCAATTTACATGTCAT 59.657 41.667 0.00 0.00 0.00 3.06
2553 4142 4.964262 AGCCATCCCAATTTACATGTCATT 59.036 37.500 0.00 0.00 0.00 2.57
2554 4143 5.426185 AGCCATCCCAATTTACATGTCATTT 59.574 36.000 0.00 0.00 0.00 2.32
2771 4360 8.919777 AACATAAAAGCAGTTAAGTACTTCCT 57.080 30.769 12.39 6.65 33.85 3.36
2772 4361 8.549338 ACATAAAAGCAGTTAAGTACTTCCTC 57.451 34.615 12.39 4.09 33.85 3.71
2773 4362 7.606839 ACATAAAAGCAGTTAAGTACTTCCTCC 59.393 37.037 12.39 0.00 33.85 4.30
2774 4363 3.870633 AGCAGTTAAGTACTTCCTCCG 57.129 47.619 12.39 0.00 33.85 4.63
2775 4364 3.163467 AGCAGTTAAGTACTTCCTCCGT 58.837 45.455 12.39 0.00 33.85 4.69
2776 4365 4.338879 AGCAGTTAAGTACTTCCTCCGTA 58.661 43.478 12.39 0.00 33.85 4.02
2777 4366 4.768968 AGCAGTTAAGTACTTCCTCCGTAA 59.231 41.667 12.39 0.00 33.85 3.18
2778 4367 5.244626 AGCAGTTAAGTACTTCCTCCGTAAA 59.755 40.000 12.39 0.00 33.85 2.01
2779 4368 5.575995 GCAGTTAAGTACTTCCTCCGTAAAG 59.424 44.000 12.39 0.00 33.85 1.85
2780 4369 6.571150 GCAGTTAAGTACTTCCTCCGTAAAGA 60.571 42.308 12.39 0.00 33.85 2.52
2781 4370 7.373493 CAGTTAAGTACTTCCTCCGTAAAGAA 58.627 38.462 12.39 0.00 33.85 2.52
2782 4371 7.869429 CAGTTAAGTACTTCCTCCGTAAAGAAA 59.131 37.037 12.39 0.00 33.85 2.52
2783 4372 8.591940 AGTTAAGTACTTCCTCCGTAAAGAAAT 58.408 33.333 12.39 0.00 31.29 2.17
2784 4373 9.860898 GTTAAGTACTTCCTCCGTAAAGAAATA 57.139 33.333 12.39 0.00 0.00 1.40
2791 4380 9.198475 ACTTCCTCCGTAAAGAAATATAAGAGA 57.802 33.333 0.00 0.00 0.00 3.10
2794 4383 9.198475 TCCTCCGTAAAGAAATATAAGAGAAGT 57.802 33.333 0.00 0.00 0.00 3.01
2795 4384 9.250624 CCTCCGTAAAGAAATATAAGAGAAGTG 57.749 37.037 0.00 0.00 0.00 3.16
2804 4393 8.869109 AGAAATATAAGAGAAGTGATCAGAGGG 58.131 37.037 0.00 0.00 0.00 4.30
2832 4421 0.038251 TCAACTAGTCAGCCTGTGCG 60.038 55.000 0.00 0.00 44.33 5.34
2843 4432 0.099436 GCCTGTGCGGATCAACATTC 59.901 55.000 0.00 0.00 33.16 2.67
2855 4444 6.257849 GCGGATCAACATTCTGTTCTAACATA 59.742 38.462 0.00 0.00 38.77 2.29
2938 4527 4.597507 TGTGTTCCCTAAAAGAGTGGAGAT 59.402 41.667 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
281 1352 7.581213 ATTTCAGTTGTGTCCTATTTTGACA 57.419 32.000 0.00 0.00 40.28 3.58
326 1399 7.954788 ATTTAACCGCAGAAGCAAAATAAAA 57.045 28.000 0.00 0.00 42.27 1.52
327 1400 9.646427 ATTATTTAACCGCAGAAGCAAAATAAA 57.354 25.926 0.00 0.00 42.27 1.40
328 1401 9.081997 CATTATTTAACCGCAGAAGCAAAATAA 57.918 29.630 0.00 0.00 42.27 1.40
329 1402 7.704472 CCATTATTTAACCGCAGAAGCAAAATA 59.296 33.333 0.00 0.00 42.27 1.40
330 1403 6.534793 CCATTATTTAACCGCAGAAGCAAAAT 59.465 34.615 0.00 0.00 42.27 1.82
380 1460 6.126863 TGTCCCTGAACTTTAATCACATCT 57.873 37.500 0.00 0.00 0.00 2.90
514 1599 4.019174 CCAGAAACAGGCTTATGGATTGT 58.981 43.478 0.00 0.00 39.58 2.71
572 1657 2.708216 TTGCACACAACCTCAGAAGA 57.292 45.000 0.00 0.00 0.00 2.87
618 1704 6.301486 TGCCTATGAAGAATGCATCATTAGT 58.699 36.000 0.00 0.00 34.81 2.24
723 1809 3.188460 GCGCCTGTCTCAGTTTCAAATTA 59.812 43.478 0.00 0.00 0.00 1.40
774 1865 3.173599 CAAGTGCGTTGCCATAAATGAG 58.826 45.455 0.00 0.00 0.00 2.90
863 1967 3.658988 CGATTGTTGAAACATGACGTGTG 59.341 43.478 0.00 0.00 41.14 3.82
885 1989 4.035091 GGTTTCCTCATTGTTTTGTTTGGC 59.965 41.667 0.00 0.00 0.00 4.52
1054 2161 0.039764 AGTCGAGGAGGACCATCACA 59.960 55.000 0.00 0.00 37.66 3.58
1107 2220 3.199290 GCTAGACAGCTCTCCCTCA 57.801 57.895 0.00 0.00 44.93 3.86
1345 2458 0.585357 GATCGTAGCTGCAAGGCATG 59.415 55.000 1.02 0.00 38.13 4.06
1539 2656 4.938226 GCTGCATCTACTAAACCAGAAACT 59.062 41.667 0.00 0.00 0.00 2.66
1727 3280 3.452627 ACTCCTGAGCCATAGTTACAAGG 59.547 47.826 0.00 0.00 0.00 3.61
1787 3346 3.460340 TGAGGAAACAAAACCTACCAGGA 59.540 43.478 0.00 0.00 37.67 3.86
1791 3350 4.499188 GCAAGTGAGGAAACAAAACCTACC 60.499 45.833 0.00 0.00 36.57 3.18
1858 3420 4.759693 TGGCCGCTGAAACCTAATATTATG 59.240 41.667 0.00 0.00 0.00 1.90
1864 3426 1.392589 CATGGCCGCTGAAACCTAAT 58.607 50.000 0.00 0.00 0.00 1.73
2180 3760 8.576442 ACAACGGTTATGATTTTCTGAAGAATT 58.424 29.630 0.00 0.00 33.54 2.17
2304 3884 3.661911 CCGCATCAAACCGGTCAA 58.338 55.556 8.04 0.00 39.67 3.18
2518 4102 2.516702 TGGGATGGCTGGAGTACTACTA 59.483 50.000 6.66 0.00 0.00 1.82
2522 4106 1.898863 ATTGGGATGGCTGGAGTACT 58.101 50.000 0.00 0.00 0.00 2.73
2554 4143 9.332301 GGTCAATTAAAAATCACGAAATACGAA 57.668 29.630 0.00 0.00 45.77 3.85
2765 4354 9.198475 TCTCTTATATTTCTTTACGGAGGAAGT 57.802 33.333 0.00 0.00 0.00 3.01
2768 4357 9.198475 ACTTCTCTTATATTTCTTTACGGAGGA 57.802 33.333 0.00 0.00 0.00 3.71
2769 4358 9.250624 CACTTCTCTTATATTTCTTTACGGAGG 57.749 37.037 0.00 0.00 0.00 4.30
2778 4367 8.869109 CCCTCTGATCACTTCTCTTATATTTCT 58.131 37.037 0.00 0.00 0.00 2.52
2779 4368 8.865090 TCCCTCTGATCACTTCTCTTATATTTC 58.135 37.037 0.00 0.00 0.00 2.17
2780 4369 8.789767 TCCCTCTGATCACTTCTCTTATATTT 57.210 34.615 0.00 0.00 0.00 1.40
2781 4370 8.010105 ACTCCCTCTGATCACTTCTCTTATATT 58.990 37.037 0.00 0.00 0.00 1.28
2782 4371 7.534852 ACTCCCTCTGATCACTTCTCTTATAT 58.465 38.462 0.00 0.00 0.00 0.86
2783 4372 6.916909 ACTCCCTCTGATCACTTCTCTTATA 58.083 40.000 0.00 0.00 0.00 0.98
2784 4373 5.776358 ACTCCCTCTGATCACTTCTCTTAT 58.224 41.667 0.00 0.00 0.00 1.73
2785 4374 5.199982 ACTCCCTCTGATCACTTCTCTTA 57.800 43.478 0.00 0.00 0.00 2.10
2786 4375 4.059773 ACTCCCTCTGATCACTTCTCTT 57.940 45.455 0.00 0.00 0.00 2.85
2787 4376 3.756082 ACTCCCTCTGATCACTTCTCT 57.244 47.619 0.00 0.00 0.00 3.10
2788 4377 4.532834 AGTACTCCCTCTGATCACTTCTC 58.467 47.826 0.00 0.00 0.00 2.87
2789 4378 4.532834 GAGTACTCCCTCTGATCACTTCT 58.467 47.826 12.13 0.00 0.00 2.85
2790 4379 3.314080 CGAGTACTCCCTCTGATCACTTC 59.686 52.174 17.23 0.00 0.00 3.01
2791 4380 3.283751 CGAGTACTCCCTCTGATCACTT 58.716 50.000 17.23 0.00 0.00 3.16
2792 4381 2.240160 ACGAGTACTCCCTCTGATCACT 59.760 50.000 17.23 0.00 0.00 3.41
2793 4382 2.614983 GACGAGTACTCCCTCTGATCAC 59.385 54.545 17.23 0.00 0.00 3.06
2794 4383 2.238898 TGACGAGTACTCCCTCTGATCA 59.761 50.000 17.23 6.93 0.00 2.92
2795 4384 2.920524 TGACGAGTACTCCCTCTGATC 58.079 52.381 17.23 4.64 0.00 2.92
2796 4385 3.018149 GTTGACGAGTACTCCCTCTGAT 58.982 50.000 17.23 0.00 0.00 2.90
2797 4386 2.040012 AGTTGACGAGTACTCCCTCTGA 59.960 50.000 17.23 3.30 0.00 3.27
2798 4387 2.438411 AGTTGACGAGTACTCCCTCTG 58.562 52.381 17.23 5.29 0.00 3.35
2799 4388 2.883122 AGTTGACGAGTACTCCCTCT 57.117 50.000 17.23 6.17 0.00 3.69
2800 4389 3.608796 ACTAGTTGACGAGTACTCCCTC 58.391 50.000 17.23 11.96 29.97 4.30
2801 4390 3.008813 TGACTAGTTGACGAGTACTCCCT 59.991 47.826 17.23 2.26 31.94 4.20
2802 4391 3.341823 TGACTAGTTGACGAGTACTCCC 58.658 50.000 17.23 9.78 31.94 4.30
2803 4392 3.181508 GCTGACTAGTTGACGAGTACTCC 60.182 52.174 17.23 4.79 31.94 3.85
2804 4393 3.181508 GGCTGACTAGTTGACGAGTACTC 60.182 52.174 13.18 13.18 31.94 2.59
2905 4494 4.268720 GGAACACACCCAGGCAAA 57.731 55.556 0.00 0.00 0.00 3.68
2920 4509 3.115390 CCCATCTCCACTCTTTTAGGGA 58.885 50.000 0.00 0.00 35.81 4.20
2923 4512 5.604650 AGTATCCCCATCTCCACTCTTTTAG 59.395 44.000 0.00 0.00 0.00 1.85
2928 4517 2.248686 ACAGTATCCCCATCTCCACTCT 59.751 50.000 0.00 0.00 0.00 3.24
2938 4527 2.790433 GTCAAAAGCACAGTATCCCCA 58.210 47.619 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.