Multiple sequence alignment - TraesCS5A01G530500

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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 TraesCS5A01G530500 chr5A 100.000 4426 0 0 1 4426 689247343 689242918 0.000000e+00 8174.0
1 TraesCS5A01G530500 chr5A 93.338 4473 233 46 8 4426 296996862 297001323 0.000000e+00 6549.0
2 TraesCS5A01G530500 chr5A 94.118 2567 118 9 1870 4415 98737302 98734748 0.000000e+00 3873.0
3 TraesCS5A01G530500 chr5A 92.935 184 9 3 1307 1488 10119562 10119743 9.440000e-67 265.0
4 TraesCS5A01G530500 chr3A 94.043 4465 205 28 1 4423 148256876 148261321 0.000000e+00 6715.0
5 TraesCS5A01G530500 chr3A 93.841 3848 179 18 605 4423 148180891 148184709 0.000000e+00 5740.0
6 TraesCS5A01G530500 chr3A 93.989 183 8 2 1307 1488 652730597 652730777 1.570000e-69 274.0
7 TraesCS5A01G530500 chr7D 95.654 2715 97 9 1726 4426 600611324 600614031 0.000000e+00 4340.0
8 TraesCS5A01G530500 chr7D 94.851 2719 93 12 1726 4426 600557727 600560416 0.000000e+00 4202.0
9 TraesCS5A01G530500 chr7D 95.146 2575 82 14 1871 4426 183565778 183568328 0.000000e+00 4023.0
10 TraesCS5A01G530500 chr7D 94.786 2570 89 19 1871 4424 563086560 563084020 0.000000e+00 3962.0
11 TraesCS5A01G530500 chr7D 90.719 668 42 16 9 663 600556191 600556851 0.000000e+00 872.0
12 TraesCS5A01G530500 chr7D 91.052 637 40 6 9 632 600609564 600610196 0.000000e+00 845.0
13 TraesCS5A01G530500 chr7D 92.599 581 28 7 844 1410 600610752 600611331 0.000000e+00 821.0
14 TraesCS5A01G530500 chr7D 91.419 571 34 7 854 1410 600557165 600557734 0.000000e+00 769.0
15 TraesCS5A01G530500 chr1D 95.918 2572 81 12 1871 4426 285763026 285760463 0.000000e+00 4146.0
16 TraesCS5A01G530500 chr1D 88.376 671 59 15 12 674 66928276 66928935 0.000000e+00 789.0
17 TraesCS5A01G530500 chr3D 95.294 2571 88 14 1871 4423 111193025 111195580 0.000000e+00 4047.0
18 TraesCS5A01G530500 chr5B 93.767 2567 129 8 1871 4415 121407759 121410316 0.000000e+00 3825.0
19 TraesCS5A01G530500 chr5B 88.095 672 62 15 12 674 636916495 636915833 0.000000e+00 782.0
20 TraesCS5A01G530500 chr5B 84.893 609 59 21 720 1305 710236477 710237075 6.380000e-163 584.0
21 TraesCS5A01G530500 chr5B 86.607 112 13 2 1484 1594 710237157 710237267 6.010000e-24 122.0
22 TraesCS5A01G530500 chr2D 95.031 2415 80 13 2031 4415 48749203 48746799 0.000000e+00 3759.0
23 TraesCS5A01G530500 chr2D 88.490 669 60 12 12 674 472764705 472764048 0.000000e+00 793.0
24 TraesCS5A01G530500 chr2B 94.133 1943 100 8 2479 4415 177031210 177033144 0.000000e+00 2944.0
25 TraesCS5A01G530500 chr2B 87.892 669 63 14 12 674 90147308 90147964 0.000000e+00 771.0
26 TraesCS5A01G530500 chr3B 93.866 1940 103 10 2479 4412 33635362 33637291 0.000000e+00 2909.0
27 TraesCS5A01G530500 chr3B 89.412 680 58 8 2 674 34653905 34653233 0.000000e+00 845.0
28 TraesCS5A01G530500 chr4B 88.376 671 60 13 12 674 355188046 355187386 0.000000e+00 791.0
29 TraesCS5A01G530500 chr5D 85.784 612 57 15 720 1305 556547758 556547151 4.860000e-174 621.0
30 TraesCS5A01G530500 chrUn 85.019 514 46 20 713 1205 244922576 244922073 1.110000e-135 494.0
31 TraesCS5A01G530500 chrUn 85.019 514 46 20 713 1205 285318593 285318090 1.110000e-135 494.0
32 TraesCS5A01G530500 chr6D 92.655 177 12 1 1313 1489 57117485 57117310 2.040000e-63 254.0
33 TraesCS5A01G530500 chr4A 84.699 183 9 4 1307 1488 623979285 623979121 9.850000e-37 165.0
34 TraesCS5A01G530500 chr2A 96.154 52 2 0 673 724 750035717 750035768 7.890000e-13 86.1
35 TraesCS5A01G530500 chr1A 92.727 55 4 0 673 727 34428195 34428141 3.670000e-11 80.5


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 TraesCS5A01G530500 chr5A 689242918 689247343 4425 True 8174.000000 8174 100.000000 1 4426 1 chr5A.!!$R2 4425
1 TraesCS5A01G530500 chr5A 296996862 297001323 4461 False 6549.000000 6549 93.338000 8 4426 1 chr5A.!!$F2 4418
2 TraesCS5A01G530500 chr5A 98734748 98737302 2554 True 3873.000000 3873 94.118000 1870 4415 1 chr5A.!!$R1 2545
3 TraesCS5A01G530500 chr3A 148256876 148261321 4445 False 6715.000000 6715 94.043000 1 4423 1 chr3A.!!$F2 4422
4 TraesCS5A01G530500 chr3A 148180891 148184709 3818 False 5740.000000 5740 93.841000 605 4423 1 chr3A.!!$F1 3818
5 TraesCS5A01G530500 chr7D 183565778 183568328 2550 False 4023.000000 4023 95.146000 1871 4426 1 chr7D.!!$F1 2555
6 TraesCS5A01G530500 chr7D 563084020 563086560 2540 True 3962.000000 3962 94.786000 1871 4424 1 chr7D.!!$R1 2553
7 TraesCS5A01G530500 chr7D 600609564 600614031 4467 False 2002.000000 4340 93.101667 9 4426 3 chr7D.!!$F3 4417
8 TraesCS5A01G530500 chr7D 600556191 600560416 4225 False 1947.666667 4202 92.329667 9 4426 3 chr7D.!!$F2 4417
9 TraesCS5A01G530500 chr1D 285760463 285763026 2563 True 4146.000000 4146 95.918000 1871 4426 1 chr1D.!!$R1 2555
10 TraesCS5A01G530500 chr1D 66928276 66928935 659 False 789.000000 789 88.376000 12 674 1 chr1D.!!$F1 662
11 TraesCS5A01G530500 chr3D 111193025 111195580 2555 False 4047.000000 4047 95.294000 1871 4423 1 chr3D.!!$F1 2552
12 TraesCS5A01G530500 chr5B 121407759 121410316 2557 False 3825.000000 3825 93.767000 1871 4415 1 chr5B.!!$F1 2544
13 TraesCS5A01G530500 chr5B 636915833 636916495 662 True 782.000000 782 88.095000 12 674 1 chr5B.!!$R1 662
14 TraesCS5A01G530500 chr5B 710236477 710237267 790 False 353.000000 584 85.750000 720 1594 2 chr5B.!!$F2 874
15 TraesCS5A01G530500 chr2D 48746799 48749203 2404 True 3759.000000 3759 95.031000 2031 4415 1 chr2D.!!$R1 2384
16 TraesCS5A01G530500 chr2D 472764048 472764705 657 True 793.000000 793 88.490000 12 674 1 chr2D.!!$R2 662
17 TraesCS5A01G530500 chr2B 177031210 177033144 1934 False 2944.000000 2944 94.133000 2479 4415 1 chr2B.!!$F2 1936
18 TraesCS5A01G530500 chr2B 90147308 90147964 656 False 771.000000 771 87.892000 12 674 1 chr2B.!!$F1 662
19 TraesCS5A01G530500 chr3B 33635362 33637291 1929 False 2909.000000 2909 93.866000 2479 4412 1 chr3B.!!$F1 1933
20 TraesCS5A01G530500 chr3B 34653233 34653905 672 True 845.000000 845 89.412000 2 674 1 chr3B.!!$R1 672
21 TraesCS5A01G530500 chr4B 355187386 355188046 660 True 791.000000 791 88.376000 12 674 1 chr4B.!!$R1 662
22 TraesCS5A01G530500 chr5D 556547151 556547758 607 True 621.000000 621 85.784000 720 1305 1 chr5D.!!$R1 585
23 TraesCS5A01G530500 chrUn 244922073 244922576 503 True 494.000000 494 85.019000 713 1205 1 chrUn.!!$R1 492
24 TraesCS5A01G530500 chrUn 285318090 285318593 503 True 494.000000 494 85.019000 713 1205 1 chrUn.!!$R2 492

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
781 846 0.631753 CACCACCCTCTCCTCTCCTA 59.368 60.000 0.0 0.0 0.00 2.94 F
1125 1518 0.249398 CCTTGCTAGTTACCGCCACT 59.751 55.000 0.0 0.0 0.00 4.00 F
1503 1921 0.881118 GGCTTTGCGAGAATCCACAA 59.119 50.000 0.0 0.0 0.00 3.33 F
1582 2000 1.004277 GGCTAGTTTCACATCCCACCA 59.996 52.381 0.0 0.0 0.00 4.17 F
3049 3591 1.021968 GCACAGGACAACTCCGTTTT 58.978 50.000 0.0 0.0 42.22 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 2000 2.153645 TGATCAGCAGCGTTTTGACAT 58.846 42.857 0.00 0.0 0.00 3.06 R
2968 3510 2.159599 GCATCACTAGCTCTGTTGTTGC 60.160 50.000 0.00 0.0 0.00 4.17 R
3247 3790 0.984230 CCACTCCTCCTTGCTACCAA 59.016 55.000 0.00 0.0 0.00 3.67 R
3361 3907 3.438781 GTCGATTGTGGCCTGAACAAATA 59.561 43.478 10.83 0.0 40.69 1.40 R
4338 4909 0.178967 TGGCACAAGAATCAGCCCAA 60.179 50.000 0.00 0.0 46.45 4.12 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
57 58 2.676748 TCAAGGCTTTTGACACCCAAT 58.323 42.857 0.00 0.00 34.23 3.16
60 61 2.242043 AGGCTTTTGACACCCAATCAG 58.758 47.619 0.00 0.00 34.23 2.90
125 126 4.533919 TGATTCGGTCCAATTTTGCAAT 57.466 36.364 0.00 0.00 0.00 3.56
437 455 2.109480 CCATCCAACATCCATCCATCCT 59.891 50.000 0.00 0.00 0.00 3.24
493 522 1.378646 GGCAGCCCAAACCCTAGAC 60.379 63.158 0.00 0.00 0.00 2.59
563 594 2.288025 GCCACCTCCTTCCCGTACA 61.288 63.158 0.00 0.00 0.00 2.90
632 691 4.316823 TCCTCCTCACCCACCGCT 62.317 66.667 0.00 0.00 0.00 5.52
705 764 1.693640 CCCTGATGCCAAGTCCCTT 59.306 57.895 0.00 0.00 0.00 3.95
744 803 1.000396 GCTGCTCCAATCCAACCCT 60.000 57.895 0.00 0.00 0.00 4.34
747 806 0.776810 TGCTCCAATCCAACCCTGAA 59.223 50.000 0.00 0.00 0.00 3.02
763 827 4.169696 AATCGATTCCGGCCGCCA 62.170 61.111 22.85 8.58 36.24 5.69
781 846 0.631753 CACCACCCTCTCCTCTCCTA 59.368 60.000 0.00 0.00 0.00 2.94
859 1234 3.400054 GGCTACGGAACCCCTGCT 61.400 66.667 0.00 0.00 0.00 4.24
862 1237 1.078426 CTACGGAACCCCTGCTTGG 60.078 63.158 0.00 0.00 0.00 3.61
871 1246 4.170062 CCTGCTTGGCGATGCACG 62.170 66.667 5.15 0.00 45.66 5.34
1036 1411 0.952280 GGAGATCTACGCCATCGACA 59.048 55.000 0.00 0.00 38.35 4.35
1086 1461 2.685380 CCCGTCTCCTGCCTCCTT 60.685 66.667 0.00 0.00 0.00 3.36
1123 1516 0.978151 TTCCTTGCTAGTTACCGCCA 59.022 50.000 0.00 0.00 0.00 5.69
1125 1518 0.249398 CCTTGCTAGTTACCGCCACT 59.751 55.000 0.00 0.00 0.00 4.00
1264 1680 1.277580 CCTCTCCTGTCCATGGCCTT 61.278 60.000 6.96 0.00 0.00 4.35
1273 1689 4.467769 CTGTCCATGGCCTTGATTTCTAT 58.532 43.478 19.85 0.00 0.00 1.98
1503 1921 0.881118 GGCTTTGCGAGAATCCACAA 59.119 50.000 0.00 0.00 0.00 3.33
1582 2000 1.004277 GGCTAGTTTCACATCCCACCA 59.996 52.381 0.00 0.00 0.00 4.17
1652 2070 2.957680 TGATGCCTGCTGTTTTTCTTCA 59.042 40.909 0.00 0.00 0.00 3.02
1845 2263 5.016831 TCCTATCTACAACACTTGCTCTGA 58.983 41.667 0.00 0.00 0.00 3.27
2083 2501 1.146041 AGCACACTTTCCAGCGTCA 59.854 52.632 0.00 0.00 0.00 4.35
2259 2695 4.265073 GTTTGGAGTAGTTGATCATGGCT 58.735 43.478 0.00 0.00 0.00 4.75
2454 2984 6.865726 TGATCAAGCGCTTCTTTCTATCTATC 59.134 38.462 22.21 10.25 31.27 2.08
2455 2985 6.398234 TCAAGCGCTTCTTTCTATCTATCT 57.602 37.500 22.21 0.00 31.27 1.98
2456 2986 7.511959 TCAAGCGCTTCTTTCTATCTATCTA 57.488 36.000 22.21 0.00 31.27 1.98
2457 2987 8.116651 TCAAGCGCTTCTTTCTATCTATCTAT 57.883 34.615 22.21 0.00 31.27 1.98
2458 2988 9.232473 TCAAGCGCTTCTTTCTATCTATCTATA 57.768 33.333 22.21 0.00 31.27 1.31
2527 3063 6.382859 TGAGGCAGGACTATACAAGTGAATTA 59.617 38.462 0.00 0.00 39.07 1.40
2770 3310 4.920749 ACTACTAGGAGATATGGGTGAGGA 59.079 45.833 9.61 0.00 0.00 3.71
2781 3321 3.782656 TGGGTGAGGAACTAAAAGGAC 57.217 47.619 0.00 0.00 41.55 3.85
2968 3510 9.624697 ACAACAACTTATGTAATATGCAAACAG 57.375 29.630 0.00 0.00 42.99 3.16
3049 3591 1.021968 GCACAGGACAACTCCGTTTT 58.978 50.000 0.00 0.00 42.22 2.43
3052 3594 1.235724 CAGGACAACTCCGTTTTCCC 58.764 55.000 7.98 0.00 41.68 3.97
3357 3903 4.189188 CAGACCCCGGCGACTACG 62.189 72.222 9.30 0.00 42.93 3.51
3405 3951 4.019321 ACCACTACAGCCAATGTAAGTCAT 60.019 41.667 0.00 0.00 43.78 3.06
3725 4271 8.324306 TGATTCTTCTCTTCTGGTTCATGTAAT 58.676 33.333 0.00 0.00 0.00 1.89
3730 4276 5.366768 TCTCTTCTGGTTCATGTAATAGGGG 59.633 44.000 0.00 0.00 0.00 4.79
3783 4329 9.809096 ATATTGTCATTCTGTTAGTCTAGTGTG 57.191 33.333 0.00 0.00 0.00 3.82
3870 4416 4.621087 GGGGCCCAGTTTGTGCCT 62.621 66.667 26.86 0.00 44.71 4.75
3964 4521 0.033228 GATGACTGGAGCAGGATCCG 59.967 60.000 5.98 2.47 42.77 4.18
4393 4964 1.245376 TGGATGCGTACGTGGTCTGA 61.245 55.000 17.90 1.91 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 8.603181 GCCATATTTAATTCACAATTGACCAAC 58.397 33.333 13.59 0.00 32.38 3.77
613 644 2.603473 CGGTGGGTGAGGAGGACA 60.603 66.667 0.00 0.00 0.00 4.02
724 783 1.377202 GGTTGGATTGGAGCAGCGA 60.377 57.895 0.00 0.00 0.00 4.93
744 803 2.587753 GCGGCCGGAATCGATTCA 60.588 61.111 32.92 0.00 38.53 2.57
747 806 4.910585 GTGGCGGCCGGAATCGAT 62.911 66.667 29.38 0.00 39.00 3.59
763 827 1.501604 GATAGGAGAGGAGAGGGTGGT 59.498 57.143 0.00 0.00 0.00 4.16
946 1321 3.474570 GGCGTGGATCCAGAGGCT 61.475 66.667 26.73 0.00 0.00 4.58
1036 1411 0.836400 AAGTCGATGTGGTGGACCCT 60.836 55.000 0.00 0.00 36.32 4.34
1086 1461 2.632996 GGAAGATGATGGATACGGACCA 59.367 50.000 0.00 0.00 41.83 4.02
1123 1516 2.540265 CTGAGAGGAACAACAGCAGT 57.460 50.000 0.00 0.00 0.00 4.40
1162 1556 1.258982 CGACGCATCCTGAGCAATAAC 59.741 52.381 0.00 0.00 0.00 1.89
1196 1594 1.915266 CCTCCCAGCAGACCTGACA 60.915 63.158 0.47 0.00 44.64 3.58
1264 1680 7.041576 GCATGACATGACAAGCTATAGAAATCA 60.042 37.037 19.76 1.62 32.77 2.57
1582 2000 2.153645 TGATCAGCAGCGTTTTGACAT 58.846 42.857 0.00 0.00 0.00 3.06
1652 2070 9.739276 TCAATCAGGAACTAAATGACAACTTAT 57.261 29.630 0.00 0.00 36.02 1.73
2083 2501 3.011818 TGCATCATCGTTTGCTCAGATT 58.988 40.909 0.00 0.00 39.60 2.40
2770 3310 4.179298 GGAAGCGTATCGTCCTTTTAGTT 58.821 43.478 0.00 0.00 39.80 2.24
2781 3321 7.132213 ACAAATAAATTCATGGAAGCGTATCG 58.868 34.615 0.00 0.00 0.00 2.92
2823 3363 4.771577 TCATTTGGGCTGATTTGTACACAT 59.228 37.500 0.00 0.00 0.00 3.21
2968 3510 2.159599 GCATCACTAGCTCTGTTGTTGC 60.160 50.000 0.00 0.00 0.00 4.17
3049 3591 5.779241 ATTCTGATTCTGTAACAAGGGGA 57.221 39.130 0.00 0.00 0.00 4.81
3052 3594 7.108847 AGAGGAATTCTGATTCTGTAACAAGG 58.891 38.462 5.23 0.00 41.18 3.61
3247 3790 0.984230 CCACTCCTCCTTGCTACCAA 59.016 55.000 0.00 0.00 0.00 3.67
3349 3895 4.026804 CCTGAACAAATATGTCGTAGTCGC 60.027 45.833 0.00 0.00 39.40 5.19
3357 3903 4.782019 TTGTGGCCTGAACAAATATGTC 57.218 40.909 3.32 0.00 39.40 3.06
3361 3907 3.438781 GTCGATTGTGGCCTGAACAAATA 59.561 43.478 10.83 0.00 40.69 1.40
3405 3951 3.836562 GGTTAGTTGTAACAGAGAGGGGA 59.163 47.826 0.00 0.00 40.46 4.81
3725 4271 2.039951 CCTTCCACGGTCCCCCTA 59.960 66.667 0.00 0.00 0.00 3.53
3730 4276 1.097547 CATCATGCCTTCCACGGTCC 61.098 60.000 0.00 0.00 0.00 4.46
3777 4323 2.092968 GGCCATGACCTTCATCACACTA 60.093 50.000 0.00 0.00 34.28 2.74
3783 4329 2.435805 TGACTAGGCCATGACCTTCATC 59.564 50.000 5.66 2.51 41.50 2.92
3870 4416 8.560355 ACTGTTAAACATATGCAGTGACAATA 57.440 30.769 10.88 0.00 38.74 1.90
3939 4485 0.671472 CTGCTCCAGTCATCGCACAA 60.671 55.000 0.00 0.00 0.00 3.33
3989 4546 9.322773 AGAATCAATCTGTATACAGTGACAATG 57.677 33.333 27.83 18.58 44.12 2.82
4084 4645 8.482429 CCTTTTTCTTCTGATTTTGATTTGACG 58.518 33.333 0.00 0.00 0.00 4.35
4222 4785 6.936335 CCCAACAATTAAGCCTTCTCATTTTT 59.064 34.615 0.00 0.00 0.00 1.94
4289 4859 4.609301 AGCCCAACAATTCAGCCTATTTA 58.391 39.130 0.00 0.00 0.00 1.40
4338 4909 0.178967 TGGCACAAGAATCAGCCCAA 60.179 50.000 0.00 0.00 46.45 4.12
4339 4910 0.895100 GTGGCACAAGAATCAGCCCA 60.895 55.000 13.86 0.00 46.45 5.36
4381 4952 2.673833 CAACCTTCTCAGACCACGTAC 58.326 52.381 0.00 0.00 0.00 3.67
4393 4964 3.857157 TTTGGTCACTAGCAACCTTCT 57.143 42.857 13.64 0.00 42.54 2.85


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

AutoCloner maintained by Alex Coulton.