Multiple sequence alignment - TraesCS1A01G305000

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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 TraesCS1A01G305000 chr1A 100.000 3149 0 0 1 3149 497783006 497779858 0.000000e+00 5816.0
1 TraesCS1A01G305000 chr6A 97.317 2460 64 2 4 2463 169895750 169893293 0.000000e+00 4176.0
2 TraesCS1A01G305000 chr6A 86.777 363 25 6 2486 2826 482087722 482088083 1.770000e-102 383.0
3 TraesCS1A01G305000 chr2B 95.422 1376 55 2 951 2318 678556940 678555565 0.000000e+00 2185.0
4 TraesCS1A01G305000 chr2B 94.883 1329 62 3 1140 2463 749290101 749288774 0.000000e+00 2073.0
5 TraesCS1A01G305000 chr2B 84.190 1518 208 22 960 2465 83565119 83563622 0.000000e+00 1445.0
6 TraesCS1A01G305000 chr2B 87.812 640 55 3 2487 3103 786906640 786906001 0.000000e+00 728.0
7 TraesCS1A01G305000 chr2B 87.676 641 55 4 2486 3103 786886574 786885935 0.000000e+00 725.0
8 TraesCS1A01G305000 chr2B 87.656 640 55 4 2487 3103 786893315 786892677 0.000000e+00 723.0
9 TraesCS1A01G305000 chr2B 87.344 640 57 4 2487 3103 786937166 786936528 0.000000e+00 712.0
10 TraesCS1A01G305000 chr2B 87.344 640 58 3 2487 3103 786950794 786950155 0.000000e+00 712.0
11 TraesCS1A01G305000 chr2B 81.388 677 104 7 12 681 110824385 110823724 1.660000e-147 532.0
12 TraesCS1A01G305000 chr6B 88.642 1708 161 16 772 2462 192737185 192735494 0.000000e+00 2049.0
13 TraesCS1A01G305000 chr6B 95.388 954 41 1 1144 2094 634998393 634997440 0.000000e+00 1515.0
14 TraesCS1A01G305000 chr6B 87.578 644 56 9 2483 3103 718936797 718936155 0.000000e+00 725.0
15 TraesCS1A01G305000 chr6B 81.872 673 103 8 12 681 68800299 68799643 1.650000e-152 549.0
16 TraesCS1A01G305000 chr6B 91.837 49 4 0 3101 3149 718936136 718936088 5.640000e-08 69.4
17 TraesCS1A01G305000 chr2D 92.523 1324 77 8 1150 2463 636591876 636590565 0.000000e+00 1877.0
18 TraesCS1A01G305000 chr7B 89.127 1306 134 5 995 2293 517117874 517116570 0.000000e+00 1618.0
19 TraesCS1A01G305000 chr7B 84.834 422 33 8 2487 2886 743525485 743525073 2.280000e-106 396.0
20 TraesCS1A01G305000 chr2A 84.279 1533 216 16 940 2463 52100019 52101535 0.000000e+00 1472.0
21 TraesCS1A01G305000 chr3B 83.544 1580 208 30 910 2463 571749220 571747667 0.000000e+00 1430.0
22 TraesCS1A01G305000 chr5A 92.742 868 55 3 1604 2463 622995615 622994748 0.000000e+00 1247.0
23 TraesCS1A01G305000 chr5A 89.441 161 15 2 2487 2646 632294771 632294930 5.330000e-48 202.0
24 TraesCS1A01G305000 chr6D 94.944 712 28 3 1760 2463 472923857 472924568 0.000000e+00 1109.0
25 TraesCS1A01G305000 chr6D 90.288 278 13 2 490 763 472923238 472923505 5.000000e-93 351.0
26 TraesCS1A01G305000 chr6D 86.972 284 8 3 769 1048 472923559 472923817 3.070000e-75 292.0
27 TraesCS1A01G305000 chr1D 88.383 637 52 2 2489 3103 334468919 334468283 0.000000e+00 747.0
28 TraesCS1A01G305000 chr1D 86.677 653 51 21 2463 3084 402301687 402301040 0.000000e+00 691.0
29 TraesCS1A01G305000 chr1D 88.020 601 47 8 2485 3064 86109808 86109212 0.000000e+00 688.0
30 TraesCS1A01G305000 chr1B 87.578 644 57 3 2463 3084 540160659 540160017 0.000000e+00 725.0
31 TraesCS1A01G305000 chr1B 74.428 743 165 20 962 1687 11631575 11632309 2.370000e-76 296.0
32 TraesCS1A01G305000 chr1B 93.750 48 2 1 3102 3149 540159812 540159766 1.570000e-08 71.3
33 TraesCS1A01G305000 chr5B 88.552 594 46 2 2532 3103 259560424 259559831 0.000000e+00 701.0
34 TraesCS1A01G305000 chr5B 82.887 672 98 12 12 681 429779024 429779680 3.500000e-164 588.0
35 TraesCS1A01G305000 chr7A 79.570 186 23 3 329 502 706698223 706698405 5.520000e-23 119.0


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 TraesCS1A01G305000 chr1A 497779858 497783006 3148 True 5816.00 5816 100.000000 1 3149 1 chr1A.!!$R1 3148
1 TraesCS1A01G305000 chr6A 169893293 169895750 2457 True 4176.00 4176 97.317000 4 2463 1 chr6A.!!$R1 2459
2 TraesCS1A01G305000 chr2B 678555565 678556940 1375 True 2185.00 2185 95.422000 951 2318 1 chr2B.!!$R3 1367
3 TraesCS1A01G305000 chr2B 749288774 749290101 1327 True 2073.00 2073 94.883000 1140 2463 1 chr2B.!!$R4 1323
4 TraesCS1A01G305000 chr2B 83563622 83565119 1497 True 1445.00 1445 84.190000 960 2465 1 chr2B.!!$R1 1505
5 TraesCS1A01G305000 chr2B 786906001 786906640 639 True 728.00 728 87.812000 2487 3103 1 chr2B.!!$R7 616
6 TraesCS1A01G305000 chr2B 786885935 786886574 639 True 725.00 725 87.676000 2486 3103 1 chr2B.!!$R5 617
7 TraesCS1A01G305000 chr2B 786892677 786893315 638 True 723.00 723 87.656000 2487 3103 1 chr2B.!!$R6 616
8 TraesCS1A01G305000 chr2B 786936528 786937166 638 True 712.00 712 87.344000 2487 3103 1 chr2B.!!$R8 616
9 TraesCS1A01G305000 chr2B 786950155 786950794 639 True 712.00 712 87.344000 2487 3103 1 chr2B.!!$R9 616
10 TraesCS1A01G305000 chr2B 110823724 110824385 661 True 532.00 532 81.388000 12 681 1 chr2B.!!$R2 669
11 TraesCS1A01G305000 chr6B 192735494 192737185 1691 True 2049.00 2049 88.642000 772 2462 1 chr6B.!!$R2 1690
12 TraesCS1A01G305000 chr6B 634997440 634998393 953 True 1515.00 1515 95.388000 1144 2094 1 chr6B.!!$R3 950
13 TraesCS1A01G305000 chr6B 68799643 68800299 656 True 549.00 549 81.872000 12 681 1 chr6B.!!$R1 669
14 TraesCS1A01G305000 chr6B 718936088 718936797 709 True 397.20 725 89.707500 2483 3149 2 chr6B.!!$R4 666
15 TraesCS1A01G305000 chr2D 636590565 636591876 1311 True 1877.00 1877 92.523000 1150 2463 1 chr2D.!!$R1 1313
16 TraesCS1A01G305000 chr7B 517116570 517117874 1304 True 1618.00 1618 89.127000 995 2293 1 chr7B.!!$R1 1298
17 TraesCS1A01G305000 chr2A 52100019 52101535 1516 False 1472.00 1472 84.279000 940 2463 1 chr2A.!!$F1 1523
18 TraesCS1A01G305000 chr3B 571747667 571749220 1553 True 1430.00 1430 83.544000 910 2463 1 chr3B.!!$R1 1553
19 TraesCS1A01G305000 chr5A 622994748 622995615 867 True 1247.00 1247 92.742000 1604 2463 1 chr5A.!!$R1 859
20 TraesCS1A01G305000 chr6D 472923238 472924568 1330 False 584.00 1109 90.734667 490 2463 3 chr6D.!!$F1 1973
21 TraesCS1A01G305000 chr1D 334468283 334468919 636 True 747.00 747 88.383000 2489 3103 1 chr1D.!!$R2 614
22 TraesCS1A01G305000 chr1D 402301040 402301687 647 True 691.00 691 86.677000 2463 3084 1 chr1D.!!$R3 621
23 TraesCS1A01G305000 chr1D 86109212 86109808 596 True 688.00 688 88.020000 2485 3064 1 chr1D.!!$R1 579
24 TraesCS1A01G305000 chr1B 540159766 540160659 893 True 398.15 725 90.664000 2463 3149 2 chr1B.!!$R1 686
25 TraesCS1A01G305000 chr1B 11631575 11632309 734 False 296.00 296 74.428000 962 1687 1 chr1B.!!$F1 725
26 TraesCS1A01G305000 chr5B 259559831 259560424 593 True 701.00 701 88.552000 2532 3103 1 chr5B.!!$R1 571
27 TraesCS1A01G305000 chr5B 429779024 429779680 656 False 588.00 588 82.887000 12 681 1 chr5B.!!$F1 669

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
218 219 1.123861 TCCTCAACACCAGCAGCTCT 61.124 55.000 0.0 0.0 0.0 4.09 F
746 756 2.029073 CTGCTTGGTCGTCACGGT 59.971 61.111 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1172 1252 2.037251 AGGCAAGACAACGAGCTTAGAA 59.963 45.455 0.00 0.0 0.0 2.10 R
2695 2837 0.038892 GTGGGATGCTGCAACAACAG 60.039 55.000 6.36 0.0 40.8 3.16 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
218 219 1.123861 TCCTCAACACCAGCAGCTCT 61.124 55.000 0.00 0.00 0.00 4.09
227 228 3.317571 AGCAGCTCTGTCGGCCTT 61.318 61.111 0.00 0.00 0.00 4.35
746 756 2.029073 CTGCTTGGTCGTCACGGT 59.971 61.111 0.00 0.00 0.00 4.83
816 880 3.228188 ACTGCCAATGACAAAGAGGAA 57.772 42.857 0.00 0.00 0.00 3.36
1172 1252 1.815421 GCCGCAATCCATGTCGTCT 60.815 57.895 0.00 0.00 0.00 4.18
1371 1462 2.400158 GCAAGCTGCTCTGGCTGAG 61.400 63.158 16.23 16.23 45.33 3.35
1408 1499 2.270850 GTTGGATGGCACGGGCTA 59.729 61.111 10.74 2.50 40.87 3.93
2557 2678 6.636705 TGTTTACATCATCGGCTAGTTTACT 58.363 36.000 0.00 0.00 0.00 2.24
2565 2686 2.692041 TCGGCTAGTTTACTAAGGAGGC 59.308 50.000 0.00 0.00 0.00 4.70
2583 2704 2.633488 GGCAACTAGAAGGATCACCAC 58.367 52.381 0.00 0.00 38.94 4.16
2657 2799 8.637986 TGAGCAACACTATTAAAATTGACCTTT 58.362 29.630 0.00 0.00 0.00 3.11
2660 2802 7.330946 GCAACACTATTAAAATTGACCTTTCCC 59.669 37.037 0.00 0.00 0.00 3.97
2687 2829 3.600388 CGTAGCCAAGTCCAAGATTTCT 58.400 45.455 0.00 0.00 0.00 2.52
2695 2837 6.514048 GCCAAGTCCAAGATTTCTGCATATAC 60.514 42.308 0.00 0.00 0.00 1.47
2892 3041 4.269183 TGACGCATCAATGAAATTACCCT 58.731 39.130 0.00 0.00 32.46 4.34
2936 3085 1.273886 GAAGCTCCAACTCCTTCGTCT 59.726 52.381 0.00 0.00 0.00 4.18
2946 3095 2.760650 ACTCCTTCGTCTGCATGATACA 59.239 45.455 0.00 0.00 0.00 2.29
2949 3098 2.604914 CCTTCGTCTGCATGATACACAC 59.395 50.000 0.00 0.00 0.00 3.82
3027 3176 3.020984 TCCGGCAACAAAGAAACTTTCT 58.979 40.909 0.00 0.00 43.15 2.52
3081 3230 2.113139 CACACTTCCCCGCTGGTT 59.887 61.111 0.00 0.00 34.77 3.67
3094 3408 1.267121 GCTGGTTGTACCCTCTCTCA 58.733 55.000 0.00 0.00 37.50 3.27
3095 3409 1.834263 GCTGGTTGTACCCTCTCTCAT 59.166 52.381 0.00 0.00 37.50 2.90
3097 3411 3.451178 GCTGGTTGTACCCTCTCTCATTA 59.549 47.826 0.00 0.00 37.50 1.90
3099 3413 5.396884 GCTGGTTGTACCCTCTCTCATTAAT 60.397 44.000 0.00 0.00 37.50 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.179161 CGGACGCGAGATTCACTTCT 60.179 55.000 15.93 0.00 0.00 2.85
125 126 1.308326 CGGGAGGGAGAGGAAGAGT 59.692 63.158 0.00 0.00 0.00 3.24
156 157 1.001641 GGGCCTCATCTTGCACACT 60.002 57.895 0.84 0.00 0.00 3.55
392 398 1.540367 CCCCCACCAACCTGGACTA 60.540 63.158 0.00 0.00 40.96 2.59
393 399 2.858974 CCCCCACCAACCTGGACT 60.859 66.667 0.00 0.00 40.96 3.85
746 756 1.915228 GGCTCCTGGGCATCAAGTA 59.085 57.895 8.98 0.00 40.53 2.24
816 880 2.297597 CACCAGTTCTTCTTCGTCCTCT 59.702 50.000 0.00 0.00 0.00 3.69
1172 1252 2.037251 AGGCAAGACAACGAGCTTAGAA 59.963 45.455 0.00 0.00 0.00 2.10
1408 1499 3.072184 TCTGCTCTCTCCAAAAAGCTCTT 59.928 43.478 0.00 0.00 35.76 2.85
2245 2359 2.031870 AGCTACATCGCATAGACACCA 58.968 47.619 0.00 0.00 0.00 4.17
2528 2649 7.391148 ACTAGCCGATGATGTAAACATTTTT 57.609 32.000 0.00 0.00 36.57 1.94
2557 2678 4.406003 GTGATCCTTCTAGTTGCCTCCTTA 59.594 45.833 0.00 0.00 0.00 2.69
2565 2686 2.092914 GGGGTGGTGATCCTTCTAGTTG 60.093 54.545 0.00 0.00 34.23 3.16
2573 2694 2.573463 AGTATTTGGGGTGGTGATCCT 58.427 47.619 0.00 0.00 34.23 3.24
2657 2799 1.968493 GACTTGGCTACGGATATGGGA 59.032 52.381 0.00 0.00 0.00 4.37
2660 2802 3.069586 TCTTGGACTTGGCTACGGATATG 59.930 47.826 0.00 0.00 0.00 1.78
2687 2829 3.080319 TGCTGCAACAACAGTATATGCA 58.920 40.909 0.00 0.00 44.07 3.96
2695 2837 0.038892 GTGGGATGCTGCAACAACAG 60.039 55.000 6.36 0.00 40.80 3.16
2746 2895 3.198635 AGCGGAATCAGATTCTTTGGAGA 59.801 43.478 20.41 0.00 39.24 3.71
2877 3026 5.163663 GCGACATCAAGGGTAATTTCATTGA 60.164 40.000 9.75 9.75 34.64 2.57
2892 3041 3.985279 GTGGCTATATTACGCGACATCAA 59.015 43.478 15.93 0.00 35.36 2.57
2936 3085 4.751767 TGTAGATGGTGTGTATCATGCA 57.248 40.909 0.00 0.00 0.00 3.96
2946 3095 3.525537 CGAAGCTGAATGTAGATGGTGT 58.474 45.455 0.00 0.00 0.00 4.16
3027 3176 0.393448 ATTGCTGCAAATGCCACACA 59.607 45.000 20.06 0.00 41.18 3.72
3081 3230 7.015292 GGTACATCATTAATGAGAGAGGGTACA 59.985 40.741 21.97 0.00 40.64 2.90
3094 3408 5.509498 ACTGCAGGTTGGTACATCATTAAT 58.491 37.500 19.93 0.00 39.30 1.40
3095 3409 4.917385 ACTGCAGGTTGGTACATCATTAA 58.083 39.130 19.93 0.00 39.30 1.40
3097 3411 3.439857 ACTGCAGGTTGGTACATCATT 57.560 42.857 19.93 0.00 39.30 2.57
3099 3413 2.354704 GCTACTGCAGGTTGGTACATCA 60.355 50.000 19.93 0.00 37.39 3.07


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

AutoCloner maintained by Alex Coulton.