Multiple sequence alignment - TraesCS5D01G450700

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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 TraesCS5D01G450700 chr5D 100.000 3903 0 0 1 3903 499222245 499226147 0.000000e+00 7208
1 TraesCS5D01G450700 chr5D 91.551 1077 42 19 1760 2815 499108814 499109862 0.000000e+00 1439
2 TraesCS5D01G450700 chr5D 93.778 659 37 2 1103 1757 499095106 499095764 0.000000e+00 987
3 TraesCS5D01G450700 chr5D 96.129 465 16 2 1 464 499094326 499094789 0.000000e+00 758
4 TraesCS5D01G450700 chr5D 95.195 333 16 0 324 656 499054973 499055305 9.610000e-146 527
5 TraesCS5D01G450700 chr5D 95.062 324 13 2 3 325 499054102 499054423 1.250000e-139 507
6 TraesCS5D01G450700 chr5A 94.566 3644 139 30 230 3843 623489302 623492916 0.000000e+00 5578
7 TraesCS5D01G450700 chr5A 93.144 2436 132 19 400 2815 623473261 623475681 0.000000e+00 3541
8 TraesCS5D01G450700 chr5A 94.017 351 17 2 18 366 623472916 623473264 2.670000e-146 529
9 TraesCS5D01G450700 chr5A 96.000 325 11 2 1 325 623323750 623324072 9.610000e-146 527
10 TraesCS5D01G450700 chr5B 97.020 2047 54 3 1 2046 619850836 619852876 0.000000e+00 3435
11 TraesCS5D01G450700 chr5B 94.807 1868 78 10 2042 3903 619852906 619854760 0.000000e+00 2894
12 TraesCS5D01G450700 chr5B 91.581 1758 105 19 1084 2815 619592328 619594068 0.000000e+00 2386
13 TraesCS5D01G450700 chr5B 92.128 1499 109 7 449 1943 619610168 619611661 0.000000e+00 2106
14 TraesCS5D01G450700 chr5B 90.548 857 50 15 1940 2776 619762685 619763530 0.000000e+00 1105
15 TraesCS5D01G450700 chr5B 89.498 638 48 9 449 1086 619550092 619550710 0.000000e+00 789
16 TraesCS5D01G450700 chr5B 95.022 462 20 2 3 464 619549613 619550071 0.000000e+00 723
17 TraesCS5D01G450700 chr5B 93.860 456 26 1 1 456 619609688 619610141 0.000000e+00 686
18 TraesCS5D01G450700 chr5B 96.096 333 13 0 324 656 619220813 619221145 9.540000e-151 544
19 TraesCS5D01G450700 chr5B 94.362 337 18 1 320 656 619246152 619246487 2.080000e-142 516
20 TraesCS5D01G450700 chr5B 94.984 319 14 1 1 319 619039191 619039507 2.090000e-137 499
21 TraesCS5D01G450700 chr5B 89.846 325 12 11 1 325 619066068 619066371 7.860000e-107 398
22 TraesCS5D01G450700 chr7B 80.408 2797 352 113 182 2839 711456733 711453994 0.000000e+00 1949
23 TraesCS5D01G450700 chr7A 82.136 1948 248 58 182 2054 709968695 709966773 0.000000e+00 1578
24 TraesCS5D01G450700 chr7A 80.165 242 30 10 2612 2839 709966042 709965805 8.680000e-37 165
25 TraesCS5D01G450700 chr7D 81.925 1953 242 68 182 2044 617090881 617088950 0.000000e+00 1548
26 TraesCS5D01G450700 chr7D 89.216 306 24 5 2049 2353 617088918 617088621 1.320000e-99 374
27 TraesCS5D01G450700 chr7D 90.977 133 12 0 2707 2839 617088096 617087964 3.100000e-41 180
28 TraesCS5D01G450700 chr4B 92.115 558 37 3 2042 2599 286459663 286460213 0.000000e+00 780


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 TraesCS5D01G450700 chr5D 499222245 499226147 3902 False 7208.000000 7208 100.000000 1 3903 1 chr5D.!!$F2 3902
1 TraesCS5D01G450700 chr5D 499108814 499109862 1048 False 1439.000000 1439 91.551000 1760 2815 1 chr5D.!!$F1 1055
2 TraesCS5D01G450700 chr5D 499094326 499095764 1438 False 872.500000 987 94.953500 1 1757 2 chr5D.!!$F4 1756
3 TraesCS5D01G450700 chr5D 499054102 499055305 1203 False 517.000000 527 95.128500 3 656 2 chr5D.!!$F3 653
4 TraesCS5D01G450700 chr5A 623489302 623492916 3614 False 5578.000000 5578 94.566000 230 3843 1 chr5A.!!$F2 3613
5 TraesCS5D01G450700 chr5A 623472916 623475681 2765 False 2035.000000 3541 93.580500 18 2815 2 chr5A.!!$F3 2797
6 TraesCS5D01G450700 chr5B 619850836 619854760 3924 False 3164.500000 3435 95.913500 1 3903 2 chr5B.!!$F9 3902
7 TraesCS5D01G450700 chr5B 619592328 619594068 1740 False 2386.000000 2386 91.581000 1084 2815 1 chr5B.!!$F5 1731
8 TraesCS5D01G450700 chr5B 619609688 619611661 1973 False 1396.000000 2106 92.994000 1 1943 2 chr5B.!!$F8 1942
9 TraesCS5D01G450700 chr5B 619762685 619763530 845 False 1105.000000 1105 90.548000 1940 2776 1 chr5B.!!$F6 836
10 TraesCS5D01G450700 chr5B 619549613 619550710 1097 False 756.000000 789 92.260000 3 1086 2 chr5B.!!$F7 1083
11 TraesCS5D01G450700 chr7B 711453994 711456733 2739 True 1949.000000 1949 80.408000 182 2839 1 chr7B.!!$R1 2657
12 TraesCS5D01G450700 chr7A 709965805 709968695 2890 True 871.500000 1578 81.150500 182 2839 2 chr7A.!!$R1 2657
13 TraesCS5D01G450700 chr7D 617087964 617090881 2917 True 700.666667 1548 87.372667 182 2839 3 chr7D.!!$R1 2657
14 TraesCS5D01G450700 chr4B 286459663 286460213 550 False 780.000000 780 92.115000 2042 2599 1 chr4B.!!$F1 557

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
766 1422 0.592637 TGTGCATTTTCGCAGACAGG 59.407 50.000 0.00 0.0 44.05 4.00 F
1305 2008 1.875576 GCGAGATGATTCCGGCATTCT 60.876 52.381 0.00 0.0 0.00 2.40 F
2463 3452 0.602638 TCGGCAACTACACTTGGCTG 60.603 55.000 4.26 0.0 42.99 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 2566 0.250467 AGCGTTGACTGCCACAAGAT 60.250 50.000 0.0 0.0 0.00 2.40 R
2854 4062 1.073763 CCCACTTGGACCATGTCTTCA 59.926 52.381 10.0 0.0 37.39 3.02 R
3446 4661 0.036875 AGGTAAGGTGCAGAGTTGGC 59.963 55.000 0.0 0.0 0.00 4.52 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
88 89 4.806892 ACAGGCCCAATGATATTTCATCA 58.193 39.130 0.00 0.00 41.83 3.07
153 154 7.375053 TCTGCCTTATGTTTACCACATTTTTC 58.625 34.615 0.00 0.00 44.40 2.29
348 907 5.423290 AGGATGACCTTCCAAATTCAAATCC 59.577 40.000 4.99 0.00 45.36 3.01
400 959 7.805163 ACTGTGAACATTTATATGATCCTGGA 58.195 34.615 0.00 0.00 33.83 3.86
456 1088 9.680315 ATTGCCAAATTTAATTTTGTGTTCATG 57.320 25.926 17.23 0.00 35.30 3.07
717 1373 4.635765 TGCAGCTATCTGGTAATGTGTTTC 59.364 41.667 0.00 0.00 40.65 2.78
723 1379 6.770785 GCTATCTGGTAATGTGTTTCCCATTA 59.229 38.462 0.00 0.00 34.51 1.90
727 1383 5.852282 GGTAATGTGTTTCCCATTAGCAT 57.148 39.130 14.17 0.00 45.66 3.79
766 1422 0.592637 TGTGCATTTTCGCAGACAGG 59.407 50.000 0.00 0.00 44.05 4.00
936 1611 4.846779 TTCTGAAGTATGCAAAACCCAC 57.153 40.909 0.00 0.00 0.00 4.61
1305 2008 1.875576 GCGAGATGATTCCGGCATTCT 60.876 52.381 0.00 0.00 0.00 2.40
1663 2396 4.082125 CCCTGAGCTGAAAATAAACCTGT 58.918 43.478 0.00 0.00 0.00 4.00
1809 2566 7.551262 ACAATAAAGGTGCGTACAATCTGAATA 59.449 33.333 5.86 0.00 0.00 1.75
1817 2574 5.523552 TGCGTACAATCTGAATATCTTGTGG 59.476 40.000 4.33 0.00 34.02 4.17
2463 3452 0.602638 TCGGCAACTACACTTGGCTG 60.603 55.000 4.26 0.00 42.99 4.85
2477 3483 3.129988 ACTTGGCTGAAATGAAGCATAGC 59.870 43.478 0.00 0.00 42.69 2.97
2653 3849 1.942657 CGTTGCCATGAATCGGATCTT 59.057 47.619 0.00 0.00 0.00 2.40
2667 3863 8.668353 TGAATCGGATCTTCTGTTATCTTTTTG 58.332 33.333 0.00 0.00 0.00 2.44
2668 3864 8.792830 AATCGGATCTTCTGTTATCTTTTTGA 57.207 30.769 0.00 0.00 0.00 2.69
2854 4062 3.689649 CCAAGCCGCTTAAGTTAACTGAT 59.310 43.478 9.34 0.00 0.00 2.90
2855 4063 4.437390 CCAAGCCGCTTAAGTTAACTGATG 60.437 45.833 9.34 5.16 0.00 3.07
2856 4064 4.202245 AGCCGCTTAAGTTAACTGATGA 57.798 40.909 9.34 0.00 0.00 2.92
2985 4193 7.615365 TGCATCTGTTGTAAGGAGGATTAAAAT 59.385 33.333 0.00 0.00 0.00 1.82
3020 4228 2.237392 GTGGAGGGAACATGCTCTTAGT 59.763 50.000 0.00 0.00 0.00 2.24
3069 4277 5.587844 CAGAGGGAACATACTCTTGGAATTG 59.412 44.000 0.00 0.00 41.90 2.32
3081 4290 3.207321 TCTTGGAATTGGGGGCATAATCT 59.793 43.478 0.00 0.00 0.00 2.40
3213 4424 6.293004 TGTTTCCCAAAGTTGTGAAGAAAT 57.707 33.333 0.00 0.00 0.00 2.17
3320 4534 5.683876 TCCACTTCCTTAAGAATCTCCTG 57.316 43.478 3.36 0.00 36.50 3.86
3330 4544 3.107402 AGAATCTCCTGTGCTGACCTA 57.893 47.619 0.00 0.00 0.00 3.08
3336 4550 3.954904 TCTCCTGTGCTGACCTATTACTC 59.045 47.826 0.00 0.00 0.00 2.59
3347 4561 7.560262 TGCTGACCTATTACTCTGTTAGTGTAT 59.440 37.037 0.00 0.00 39.39 2.29
3385 4600 9.712305 AGAATTTATAAGTGAGGATTACCATCG 57.288 33.333 0.00 0.00 38.94 3.84
3396 4611 6.093495 TGAGGATTACCATCGTCAAAATCAAC 59.907 38.462 5.37 0.00 46.53 3.18
3399 4614 3.559238 ACCATCGTCAAAATCAACTGC 57.441 42.857 0.00 0.00 0.00 4.40
3421 4636 4.096382 GCTGTTCTCCAAAGTTGTGAAGAA 59.904 41.667 0.00 0.00 0.00 2.52
3429 4644 8.531146 TCTCCAAAGTTGTGAAGAAAAGAAAAT 58.469 29.630 0.00 0.00 0.00 1.82
3651 4869 5.221244 ACCTTGGAGCAACATCTTACAAAAC 60.221 40.000 0.00 0.00 0.00 2.43
3721 4940 1.949525 CTTGAACACCAAGTGGACTGG 59.050 52.381 3.83 0.00 45.52 4.00
3777 4996 6.422776 AAAGCAAACAAGATCCTATACACG 57.577 37.500 0.00 0.00 0.00 4.49
3866 5086 0.868406 CCACACTCAGGAAGAAACGC 59.132 55.000 0.00 0.00 0.00 4.84
3886 5106 2.224314 GCCTTGGATCGAATCGAATTCC 59.776 50.000 16.06 16.06 39.99 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 9.783256 CAATATGATGGTAATGATGCACATAAG 57.217 33.333 0.00 0.00 38.38 1.73
348 907 2.732597 GCGTGCTCAACTACTACTGGAG 60.733 54.545 0.00 0.00 0.00 3.86
554 1209 5.178797 CCTTTATTCTTTCTCGAAGCAGGA 58.821 41.667 0.00 0.00 35.24 3.86
717 1373 8.853077 TCTTATGAAGAACATATGCTAATGGG 57.147 34.615 1.58 0.00 40.56 4.00
723 1379 5.994054 ACGCATCTTATGAAGAACATATGCT 59.006 36.000 1.58 0.00 42.01 3.79
726 1382 6.293081 GCACACGCATCTTATGAAGAACATAT 60.293 38.462 0.00 0.00 41.63 1.78
727 1383 5.006649 GCACACGCATCTTATGAAGAACATA 59.993 40.000 0.00 0.00 41.63 2.29
759 1415 2.674380 GCCAAGGTGCCCTGTCTG 60.674 66.667 0.00 0.00 32.13 3.51
936 1611 4.855298 TTAGTACATCCAAAGGGGGAAG 57.145 45.455 0.00 0.00 41.12 3.46
993 1692 3.403038 GCCACACTTATCCATTATCGCT 58.597 45.455 0.00 0.00 0.00 4.93
1305 2008 3.596214 GGAAATACTCTGCGAAGGACAA 58.404 45.455 0.00 0.00 0.00 3.18
1663 2396 4.901849 AGCAGCATAGTATTTACCTCCTGA 59.098 41.667 0.00 0.00 0.00 3.86
1809 2566 0.250467 AGCGTTGACTGCCACAAGAT 60.250 50.000 0.00 0.00 0.00 2.40
1817 2574 1.392853 CTGATCAAGAGCGTTGACTGC 59.607 52.381 6.69 1.84 0.00 4.40
2087 2886 8.146479 TGATGAAAATTAGCTGCTAGTACATG 57.854 34.615 9.62 0.00 0.00 3.21
2463 3452 6.045318 TCTACTGTCAGCTATGCTTCATTTC 58.955 40.000 0.00 0.00 36.40 2.17
2477 3483 4.455877 GGTGGGAACAAAATCTACTGTCAG 59.544 45.833 0.00 0.00 46.06 3.51
2653 3849 9.784531 AGAGTCTTCAATCAAAAAGATAACAGA 57.215 29.630 0.00 0.00 35.39 3.41
2667 3863 5.070180 TGGGATCAGATCAGAGTCTTCAATC 59.930 44.000 12.66 0.00 0.00 2.67
2668 3864 4.967442 TGGGATCAGATCAGAGTCTTCAAT 59.033 41.667 12.66 0.00 0.00 2.57
2854 4062 1.073763 CCCACTTGGACCATGTCTTCA 59.926 52.381 10.00 0.00 37.39 3.02
2855 4063 1.351017 TCCCACTTGGACCATGTCTTC 59.649 52.381 10.00 0.00 38.61 2.87
2856 4064 1.444933 TCCCACTTGGACCATGTCTT 58.555 50.000 10.00 0.00 38.61 3.01
2887 4095 4.273318 CCAGAATTTATATAGGGCCCAGC 58.727 47.826 27.56 0.00 0.00 4.85
2985 4193 1.561076 CCTCCACCAACATCCTGATGA 59.439 52.381 13.81 0.00 41.20 2.92
3020 4228 7.092354 TGTTTACTAAAGATTATGCCCCCACTA 60.092 37.037 0.00 0.00 0.00 2.74
3069 4277 4.519350 GCTGTTTACTAAGATTATGCCCCC 59.481 45.833 0.00 0.00 0.00 5.40
3182 4393 5.752955 CACAACTTTGGGAAACAACAATAGG 59.247 40.000 0.00 0.00 39.19 2.57
3213 4424 9.515226 AAAAGGTAGAATGCTACTGTATTTTCA 57.485 29.630 10.81 0.00 45.10 2.69
3320 4534 6.037098 CACTAACAGAGTAATAGGTCAGCAC 58.963 44.000 0.00 0.00 35.64 4.40
3368 4582 4.819105 TTGACGATGGTAATCCTCACTT 57.181 40.909 0.00 0.00 30.50 3.16
3370 4584 5.584649 TGATTTTGACGATGGTAATCCTCAC 59.415 40.000 0.00 0.00 30.50 3.51
3379 4593 3.058016 CAGCAGTTGATTTTGACGATGGT 60.058 43.478 0.00 0.00 0.00 3.55
3380 4594 3.058016 ACAGCAGTTGATTTTGACGATGG 60.058 43.478 0.00 0.00 0.00 3.51
3385 4600 4.036734 TGGAGAACAGCAGTTGATTTTGAC 59.963 41.667 0.00 0.00 38.30 3.18
3388 4603 5.127682 ACTTTGGAGAACAGCAGTTGATTTT 59.872 36.000 0.00 0.00 38.30 1.82
3392 4607 3.281727 ACTTTGGAGAACAGCAGTTGA 57.718 42.857 0.00 0.00 38.30 3.18
3396 4611 2.945008 TCACAACTTTGGAGAACAGCAG 59.055 45.455 0.00 0.00 0.00 4.24
3399 4614 5.818136 TTCTTCACAACTTTGGAGAACAG 57.182 39.130 0.00 0.00 0.00 3.16
3429 4644 9.440773 CAGAGTTGGCTTCATATTGCTAATATA 57.559 33.333 0.00 0.00 32.91 0.86
3433 4648 4.336433 GCAGAGTTGGCTTCATATTGCTAA 59.664 41.667 0.00 0.00 0.00 3.09
3446 4661 0.036875 AGGTAAGGTGCAGAGTTGGC 59.963 55.000 0.00 0.00 0.00 4.52
3565 4783 7.138692 AGCTTGTGAAATTCAGTGTATCTTC 57.861 36.000 0.00 0.00 0.00 2.87
3651 4869 6.639632 TCTGAATCTGTTTTTCAAGGGAAG 57.360 37.500 0.00 0.00 32.98 3.46
3721 4940 4.988540 GGGGAGTTTTGATTTGTTTGTAGC 59.011 41.667 0.00 0.00 0.00 3.58
3777 4996 3.696898 CAGTCTTCGTAGTCTGTATGCC 58.303 50.000 7.87 0.00 34.23 4.40
3866 5086 3.733337 AGGAATTCGATTCGATCCAAGG 58.267 45.455 23.69 0.00 37.46 3.61


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

AutoCloner maintained by Alex Coulton.