Multiple sequence alignment - TraesCS4A01G433700

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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 TraesCS4A01G433700 chr4A 100.000 3082 0 0 1 3082 704480974 704477893 0.000000e+00 5692.0
1 TraesCS4A01G433700 chr4A 100.000 291 0 0 3437 3727 704477538 704477248 4.240000e-149 538.0
2 TraesCS4A01G433700 chr4A 84.387 269 21 1 3 271 473522501 473522254 1.030000e-60 244.0
3 TraesCS4A01G433700 chr4A 92.857 42 3 0 391 432 733464737 733464696 1.120000e-05 62.1
4 TraesCS4A01G433700 chr5A 95.906 2711 104 7 379 3082 32103308 32106018 0.000000e+00 4385.0
5 TraesCS4A01G433700 chr5A 94.910 2711 100 18 379 3082 30784422 30781743 0.000000e+00 4207.0
6 TraesCS4A01G433700 chr5A 98.282 291 5 0 3437 3727 30780952 30780662 9.230000e-141 510.0
7 TraesCS4A01G433700 chr5A 96.319 163 5 1 2921 3082 30781222 30781060 2.210000e-67 267.0
8 TraesCS4A01G433700 chr5A 91.061 179 9 2 93 271 680691424 680691253 6.220000e-58 235.0
9 TraesCS4A01G433700 chr2B 96.183 2279 84 3 1 2276 16908713 16906435 0.000000e+00 3723.0
10 TraesCS4A01G433700 chr2B 96.147 2102 78 3 368 2466 16931633 16929532 0.000000e+00 3430.0
11 TraesCS4A01G433700 chr2B 95.882 1870 74 3 1 1867 16933512 16931643 0.000000e+00 3024.0
12 TraesCS4A01G433700 chr2B 96.539 809 21 3 2274 3082 16906200 16905399 0.000000e+00 1332.0
13 TraesCS4A01G433700 chr2B 84.175 594 73 12 1072 1659 38257472 38256894 1.170000e-154 556.0
14 TraesCS4A01G433700 chr2B 96.907 291 9 0 3437 3727 16905371 16905081 4.330000e-134 488.0
15 TraesCS4A01G433700 chr2B 92.308 182 10 1 3546 3727 734783404 734783581 4.780000e-64 255.0
16 TraesCS4A01G433700 chr2B 94.737 57 3 0 1662 1718 38256503 38256447 5.130000e-14 89.8
17 TraesCS4A01G433700 chr7B 88.825 2076 210 19 412 2476 606589022 606591086 0.000000e+00 2529.0
18 TraesCS4A01G433700 chr7B 92.388 381 24 5 2706 3082 606640454 606640833 4.240000e-149 538.0
19 TraesCS4A01G433700 chr7B 91.228 228 12 5 2466 2686 606591265 606591491 1.680000e-78 303.0
20 TraesCS4A01G433700 chr7B 82.069 145 20 4 2705 2845 706073453 706073311 6.540000e-23 119.0
21 TraesCS4A01G433700 chr7B 80.137 146 26 2 289 432 720709648 720709792 5.090000e-19 106.0
22 TraesCS4A01G433700 chr7A 89.008 1301 129 10 1458 2748 143879807 143881103 0.000000e+00 1598.0
23 TraesCS4A01G433700 chr7A 86.951 820 98 6 1 813 143804753 143805570 0.000000e+00 913.0
24 TraesCS4A01G433700 chr7A 80.470 553 74 25 1120 1659 576090806 576091337 3.490000e-105 392.0
25 TraesCS4A01G433700 chr3B 90.665 782 49 13 2310 3082 817858009 817858775 0.000000e+00 1018.0
26 TraesCS4A01G433700 chr3B 89.145 433 45 1 1760 2192 397300444 397300874 4.240000e-149 538.0
27 TraesCS4A01G433700 chr3B 81.651 545 72 16 1120 1659 491822160 491821639 9.570000e-116 427.0
28 TraesCS4A01G433700 chr3B 97.826 46 1 0 3440 3485 817858800 817858845 3.090000e-11 80.5
29 TraesCS4A01G433700 chr6D 83.824 952 113 15 1760 2694 122234233 122233306 0.000000e+00 867.0
30 TraesCS4A01G433700 chr6D 86.842 266 32 2 1308 1570 122235219 122235484 1.010000e-75 294.0
31 TraesCS4A01G433700 chr6D 94.340 53 3 0 1662 1714 122234472 122234420 8.580000e-12 82.4
32 TraesCS4A01G433700 chr4B 82.418 546 72 17 1120 1659 475798156 475797629 4.390000e-124 455.0
33 TraesCS4A01G433700 chr4B 92.818 181 9 1 3546 3726 649484685 649484509 3.690000e-65 259.0
34 TraesCS4A01G433700 chr5D 92.531 241 14 2 3487 3727 433882193 433881957 3.560000e-90 342.0
35 TraesCS4A01G433700 chr5B 87.313 268 13 2 1 268 203359973 203360219 1.690000e-73 287.0
36 TraesCS4A01G433700 chr5B 91.758 182 11 1 3546 3727 704998154 704998331 2.220000e-62 250.0
37 TraesCS4A01G433700 chr2D 91.758 182 11 1 3546 3727 548455894 548455717 2.220000e-62 250.0
38 TraesCS4A01G433700 chr2D 93.478 46 2 1 2907 2951 72604972 72605017 2.400000e-07 67.6
39 TraesCS4A01G433700 chr1A 91.803 183 10 2 3546 3727 560362268 560362090 2.220000e-62 250.0
40 TraesCS4A01G433700 chr1D 90.659 182 13 1 3546 3727 371669876 371670053 4.810000e-59 239.0
41 TraesCS4A01G433700 chr6B 82.192 146 23 2 289 432 546655126 546655270 5.050000e-24 122.0
42 TraesCS4A01G433700 chr6B 95.349 43 2 0 2796 2838 584051504 584051546 6.680000e-08 69.4


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 TraesCS4A01G433700 chr4A 704477248 704480974 3726 True 3115.000000 5692 100.000000 1 3727 2 chr4A.!!$R3 3726
1 TraesCS4A01G433700 chr5A 32103308 32106018 2710 False 4385.000000 4385 95.906000 379 3082 1 chr5A.!!$F1 2703
2 TraesCS4A01G433700 chr5A 30780662 30784422 3760 True 1661.333333 4207 96.503667 379 3727 3 chr5A.!!$R2 3348
3 TraesCS4A01G433700 chr2B 16929532 16933512 3980 True 3227.000000 3430 96.014500 1 2466 2 chr2B.!!$R2 2465
4 TraesCS4A01G433700 chr2B 16905081 16908713 3632 True 1847.666667 3723 96.543000 1 3727 3 chr2B.!!$R1 3726
5 TraesCS4A01G433700 chr2B 38256447 38257472 1025 True 322.900000 556 89.456000 1072 1718 2 chr2B.!!$R3 646
6 TraesCS4A01G433700 chr7B 606589022 606591491 2469 False 1416.000000 2529 90.026500 412 2686 2 chr7B.!!$F3 2274
7 TraesCS4A01G433700 chr7A 143879807 143881103 1296 False 1598.000000 1598 89.008000 1458 2748 1 chr7A.!!$F2 1290
8 TraesCS4A01G433700 chr7A 143804753 143805570 817 False 913.000000 913 86.951000 1 813 1 chr7A.!!$F1 812
9 TraesCS4A01G433700 chr7A 576090806 576091337 531 False 392.000000 392 80.470000 1120 1659 1 chr7A.!!$F3 539
10 TraesCS4A01G433700 chr3B 817858009 817858845 836 False 549.250000 1018 94.245500 2310 3485 2 chr3B.!!$F2 1175
11 TraesCS4A01G433700 chr3B 491821639 491822160 521 True 427.000000 427 81.651000 1120 1659 1 chr3B.!!$R1 539
12 TraesCS4A01G433700 chr6D 122233306 122234472 1166 True 474.700000 867 89.082000 1662 2694 2 chr6D.!!$R1 1032
13 TraesCS4A01G433700 chr4B 475797629 475798156 527 True 455.000000 455 82.418000 1120 1659 1 chr4B.!!$R1 539

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
103 104 0.824109 CTATTCCACTGCCGGACTCA 59.176 55.000 5.05 0.00 33.75 3.41 F
452 460 1.149174 CACGGGGCAATAGCTGGAT 59.851 57.895 0.00 0.00 41.70 3.41 F
1470 1494 1.883084 GGTTGATACGGCTGCCTCG 60.883 63.158 17.92 6.95 0.00 4.63 F
1978 4047 1.546589 TACGGGGTTGCCAATCTCGT 61.547 55.000 20.68 20.68 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 1478 0.249447 CATCGAGGCAGCCGTATCAA 60.249 55.000 5.55 0.0 0.00 2.57 R
1955 4024 1.092348 GATTGGCAACCCCGTAGTTC 58.908 55.000 0.00 0.0 35.87 3.01 R
2365 4677 1.434696 GGCATTGAAGTGATGGCCG 59.565 57.895 0.00 0.0 42.38 6.13 R
3690 6897 5.826208 AGTACAACCGAGGTTTCAGAAAAAT 59.174 36.000 4.52 0.0 36.00 1.82 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 23 2.912542 CGATCCGGGCTGCTAGGA 60.913 66.667 16.26 16.26 38.56 2.94
103 104 0.824109 CTATTCCACTGCCGGACTCA 59.176 55.000 5.05 0.00 33.75 3.41
194 198 1.407979 GGGAACCGTCGTCACTATCAT 59.592 52.381 0.00 0.00 40.86 2.45
218 222 2.342279 CACCCATGGACACGTCGT 59.658 61.111 15.22 0.00 0.00 4.34
351 358 3.081409 CGAGGGATCGGTTGGGGT 61.081 66.667 0.00 0.00 0.00 4.95
452 460 1.149174 CACGGGGCAATAGCTGGAT 59.851 57.895 0.00 0.00 41.70 3.41
584 592 5.619132 TGATGGCAATCAGAATCAGTCTA 57.381 39.130 0.00 0.00 37.91 2.59
692 702 4.523943 CCTTCCATGTCTTTTCACCAATGA 59.476 41.667 0.00 0.00 0.00 2.57
799 810 7.361542 GGTCAGCGCATATGATCTTAATTTGAT 60.362 37.037 11.47 0.00 0.00 2.57
1044 1056 3.099905 TGAGTTCCGGAATGACAGAGAT 58.900 45.455 22.04 0.00 0.00 2.75
1155 1170 3.181467 CCAATGGCAACCTTCAAGAAACA 60.181 43.478 0.00 0.00 0.00 2.83
1207 1223 6.835488 ACGTTCCTCCTACCTATGTACAATAA 59.165 38.462 0.00 0.00 0.00 1.40
1306 1330 9.120538 TCTCTGTTAGATTAAAAACTGCAACTT 57.879 29.630 0.00 0.00 0.00 2.66
1389 1413 4.576463 ACAGAATCATAAACGATGCCTTCC 59.424 41.667 0.00 0.00 35.29 3.46
1454 1478 4.019681 TGAAGTCTCATAAAATGGTCCGGT 60.020 41.667 0.00 0.00 0.00 5.28
1470 1494 1.883084 GGTTGATACGGCTGCCTCG 60.883 63.158 17.92 6.95 0.00 4.63
1515 1539 8.554011 TGTAAGAGGCCAAGGTACTATATTTTT 58.446 33.333 5.01 0.00 38.49 1.94
1537 1563 4.142609 TCTCTGTGCATAATCTGGGTTC 57.857 45.455 0.00 0.00 0.00 3.62
1583 1611 5.848406 AGGCAACGATCAAAATGGTTTTTA 58.152 33.333 0.00 0.00 46.39 1.52
1646 3186 8.192774 CAGATACCAAATAGATTTGTGTGCATT 58.807 33.333 12.71 1.25 44.21 3.56
1819 3888 2.607282 CGCGTCACTAGAAAGAAGGTGT 60.607 50.000 0.00 0.00 0.00 4.16
1955 4024 3.863424 GCATTTCAGATTGATGCACTTGG 59.137 43.478 0.00 0.00 44.18 3.61
1978 4047 1.546589 TACGGGGTTGCCAATCTCGT 61.547 55.000 20.68 20.68 0.00 4.18
2092 4161 8.922237 AGAGAGATAAGAGCAAGATCATTGTTA 58.078 33.333 0.00 0.00 0.00 2.41
2107 4176 4.286032 TCATTGTTACTTGTAGTGGCTCCT 59.714 41.667 0.00 0.00 0.00 3.69
2196 4265 2.772691 GGAGGCTACGGTGTCTCGG 61.773 68.421 5.66 0.00 0.00 4.63
2254 4323 3.477530 CTCTGTTTTCTTCTTTCGGGGT 58.522 45.455 0.00 0.00 0.00 4.95
2281 4588 3.829948 CTGCAAATTCAACTACAGGCTG 58.170 45.455 14.16 14.16 0.00 4.85
2379 4691 1.349688 ACTAACCGGCCATCACTTCAA 59.650 47.619 0.00 0.00 0.00 2.69
2391 4703 5.585390 CCATCACTTCAATGCCTGATTTAC 58.415 41.667 0.00 0.00 32.78 2.01
2416 4731 7.492669 ACTGACATCATAACTTTTCATCTACGG 59.507 37.037 0.00 0.00 0.00 4.02
3503 6710 5.291128 CACTTTGATATCGCTTCTACCGTTT 59.709 40.000 0.00 0.00 0.00 3.60
3690 6897 4.279145 CCTAGGAAGGTGCTTCTGTACTA 58.721 47.826 1.05 0.00 40.07 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.163622 CGCCATGATCAGTTCTTGGTTAAAT 60.164 40.000 12.70 0.00 46.56 1.40
103 104 3.157252 AGTGATGGCGAGGCGGAT 61.157 61.111 0.00 0.00 0.00 4.18
107 108 0.250209 ATCATCAGTGATGGCGAGGC 60.250 55.000 28.54 0.00 43.35 4.70
182 185 2.359214 GTGGAGAGCATGATAGTGACGA 59.641 50.000 0.00 0.00 0.00 4.20
351 358 0.171679 CAGCTCAATTCGCATGCCAA 59.828 50.000 13.15 6.06 0.00 4.52
545 553 7.506328 TGCCATCAATTATGATTCTTCTCTG 57.494 36.000 0.00 0.00 43.89 3.35
584 592 2.111384 ACGTGCATGGTCTATTCCTCT 58.889 47.619 11.36 0.00 0.00 3.69
692 702 2.893424 AGGATGAAAGGGCACACAAAT 58.107 42.857 0.00 0.00 0.00 2.32
799 810 9.409312 CAGTGCAATTGAGTTCAAAATACATAA 57.591 29.630 10.34 0.00 39.55 1.90
916 928 4.850680 ACTCAAACCCTGTGACTTTTGTA 58.149 39.130 0.00 0.00 32.02 2.41
1070 1084 4.732672 AGAAGCCTACTAAACCTAACCG 57.267 45.455 0.00 0.00 0.00 4.44
1155 1170 7.180322 AGATCATATGATGCTTACCTTCGAT 57.820 36.000 22.86 0.00 34.37 3.59
1241 1264 4.998671 TTCAAACCTGCAACATCTGAAA 57.001 36.364 0.00 0.00 0.00 2.69
1306 1330 0.330941 TCAGTTGCATGGGCCACATA 59.669 50.000 9.28 0.00 38.10 2.29
1389 1413 2.805353 CCACACGAAGAGCGGACG 60.805 66.667 0.00 0.00 46.49 4.79
1454 1478 0.249447 CATCGAGGCAGCCGTATCAA 60.249 55.000 5.55 0.00 0.00 2.57
1515 1539 4.225942 AGAACCCAGATTATGCACAGAGAA 59.774 41.667 0.00 0.00 0.00 2.87
1819 3888 2.775384 AGTAAAACCTGTCACCTGTCCA 59.225 45.455 0.00 0.00 0.00 4.02
1955 4024 1.092348 GATTGGCAACCCCGTAGTTC 58.908 55.000 0.00 0.00 35.87 3.01
1978 4047 2.151202 GCATCAAGAAAGGAACACGGA 58.849 47.619 0.00 0.00 0.00 4.69
2092 4161 2.031495 AAGGAGGAGCCACTACAAGT 57.969 50.000 0.00 0.00 40.02 3.16
2107 4176 8.703743 ACAAATAATTTAGCCAATGCATAAGGA 58.296 29.630 19.34 1.82 41.13 3.36
2196 4265 2.286772 CCTGTAAACCACGCTTGTCAAC 60.287 50.000 0.00 0.00 0.00 3.18
2254 4323 4.071423 TGTAGTTGAATTTGCAGCAGCTA 58.929 39.130 1.76 0.00 42.74 3.32
2299 4606 2.158871 ACAGTCTAAGTGGCGGACAAAA 60.159 45.455 0.00 0.00 32.98 2.44
2365 4677 1.434696 GGCATTGAAGTGATGGCCG 59.565 57.895 0.00 0.00 42.38 6.13
2379 4691 7.285566 AGTTATGATGTCAGTAAATCAGGCAT 58.714 34.615 0.00 0.00 36.31 4.40
2391 4703 7.492669 ACCGTAGATGAAAAGTTATGATGTCAG 59.507 37.037 0.00 0.00 0.00 3.51
2416 4731 5.690857 GGCGACCTGATATTCAAGTACTAAC 59.309 44.000 0.00 0.00 0.00 2.34
2484 4988 8.421784 ACTCAATTAACTCTAAGACTGACAACA 58.578 33.333 0.00 0.00 0.00 3.33
2757 5276 7.201574 CCACAATATTCAACCATGCATTGAAAG 60.202 37.037 20.67 15.01 46.26 2.62
2876 5397 7.175467 TGTGACATTTCTCTCATAGCAAACAAT 59.825 33.333 0.00 0.00 0.00 2.71
3503 6710 8.744568 AGAAGCGATATGACATCAGATATCTA 57.255 34.615 4.54 0.00 31.79 1.98
3690 6897 5.826208 AGTACAACCGAGGTTTCAGAAAAAT 59.174 36.000 4.52 0.00 36.00 1.82


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

AutoCloner maintained by Alex Coulton.