Multiple sequence alignment - TraesCS7A01G067700

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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 TraesCS7A01G067700 chr7A 100.000 3245 0 0 1 3245 33973380 33970136 0.000000e+00 5993.0
1 TraesCS7A01G067700 chr7A 97.416 2245 26 3 1 2245 33986787 33984575 0.000000e+00 3795.0
2 TraesCS7A01G067700 chr7A 89.566 738 64 6 1511 2245 33736957 33736230 0.000000e+00 924.0
3 TraesCS7A01G067700 chr7A 93.592 593 34 4 1517 2108 33666624 33666035 0.000000e+00 881.0
4 TraesCS7A01G067700 chr7A 88.428 579 48 5 853 1412 33679141 33678563 0.000000e+00 680.0
5 TraesCS7A01G067700 chr7A 86.929 482 29 12 1052 1508 33738574 33738102 8.030000e-141 510.0
6 TraesCS7A01G067700 chr7A 90.041 241 22 2 102 341 33720528 33720289 8.740000e-81 311.0
7 TraesCS7A01G067700 chr7A 85.845 219 19 3 853 1059 33740886 33740668 4.210000e-54 222.0
8 TraesCS7A01G067700 chr7A 98.276 58 1 0 408 465 33720047 33719990 5.730000e-18 102.0
9 TraesCS7A01G067700 chr7A 100.000 28 0 0 1482 1509 33678542 33678515 6.000000e-03 52.8
10 TraesCS7A01G067700 chr7D 96.277 2256 55 13 1 2245 33466654 33464417 0.000000e+00 3674.0
11 TraesCS7A01G067700 chr2A 94.240 1007 58 0 2239 3245 772936112 772937118 0.000000e+00 1539.0
12 TraesCS7A01G067700 chr2A 90.675 1008 93 1 2239 3245 610749758 610750765 0.000000e+00 1339.0
13 TraesCS7A01G067700 chr2A 89.760 957 91 5 2239 3190 780701007 780701961 0.000000e+00 1218.0
14 TraesCS7A01G067700 chr2A 85.545 1010 141 4 2239 3245 688111050 688112057 0.000000e+00 1051.0
15 TraesCS7A01G067700 chr2A 93.103 58 4 0 598 655 776499494 776499437 5.770000e-13 86.1
16 TraesCS7A01G067700 chr6A 91.658 1007 84 0 2239 3245 8462762 8461756 0.000000e+00 1395.0
17 TraesCS7A01G067700 chr1A 91.360 1007 86 1 2239 3245 426038888 426037883 0.000000e+00 1376.0
18 TraesCS7A01G067700 chr1A 90.656 1006 93 1 2239 3243 435451384 435452389 0.000000e+00 1336.0
19 TraesCS7A01G067700 chr5A 90.972 1008 90 1 2239 3245 34410667 34409660 0.000000e+00 1356.0
20 TraesCS7A01G067700 chr3A 90.945 1005 88 3 2242 3245 679066321 679065319 0.000000e+00 1349.0
21 TraesCS7A01G067700 chr3A 94.545 55 2 1 598 652 61877569 61877516 2.070000e-12 84.2
22 TraesCS7A01G067700 chr4A 90.748 735 51 6 1511 2242 692261100 692261820 0.000000e+00 965.0
23 TraesCS7A01G067700 chr4A 90.612 735 52 6 1511 2242 692165446 692166166 0.000000e+00 959.0
24 TraesCS7A01G067700 chr4A 90.476 735 53 7 1511 2242 692088286 692089006 0.000000e+00 953.0
25 TraesCS7A01G067700 chr4A 86.047 688 46 20 858 1508 692260115 692260789 0.000000e+00 693.0
26 TraesCS7A01G067700 chr4A 85.901 688 47 19 858 1508 692164461 692165135 0.000000e+00 688.0
27 TraesCS7A01G067700 chr4A 85.591 694 47 21 852 1508 692087298 692087975 0.000000e+00 678.0
28 TraesCS7A01G067700 chr4A 85.958 527 47 12 1 505 692085708 692086229 3.680000e-149 538.0
29 TraesCS7A01G067700 chr4A 85.687 524 40 13 5 504 692163695 692164207 1.330000e-143 520.0
30 TraesCS7A01G067700 chr4A 85.496 524 41 13 5 504 692259351 692259863 6.210000e-142 514.0
31 TraesCS7A01G067700 chr4A 89.277 401 40 2 1 401 692083064 692083461 1.740000e-137 499.0
32 TraesCS7A01G067700 chr4A 91.489 141 8 2 676 815 692164317 692164454 1.190000e-44 191.0
33 TraesCS7A01G067700 chr4A 91.489 141 7 3 676 815 692259972 692260108 4.270000e-44 189.0
34 TraesCS7A01G067700 chr6B 94.643 56 3 0 598 653 9150744 9150799 1.600000e-13 87.9
35 TraesCS7A01G067700 chr6B 95.455 44 2 0 610 653 8821954 8821911 1.620000e-08 71.3
36 TraesCS7A01G067700 chr2D 93.220 59 4 0 598 656 633777821 633777879 1.600000e-13 87.9
37 TraesCS7A01G067700 chr3B 90.769 65 5 1 598 662 41313791 41313728 5.770000e-13 86.1
38 TraesCS7A01G067700 chr3B 91.803 61 3 2 598 658 580114697 580114639 2.070000e-12 84.2
39 TraesCS7A01G067700 chr4D 92.982 57 4 0 598 654 505305711 505305655 2.070000e-12 84.2
40 TraesCS7A01G067700 chr3D 92.857 56 3 1 598 653 485072619 485072565 2.680000e-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 TraesCS7A01G067700 chr7A 33970136 33973380 3244 True 5993.00 5993 100.000000 1 3245 1 chr7A.!!$R2 3244
1 TraesCS7A01G067700 chr7A 33984575 33986787 2212 True 3795.00 3795 97.416000 1 2245 1 chr7A.!!$R3 2244
2 TraesCS7A01G067700 chr7A 33666035 33666624 589 True 881.00 881 93.592000 1517 2108 1 chr7A.!!$R1 591
3 TraesCS7A01G067700 chr7A 33736230 33740886 4656 True 552.00 924 87.446667 853 2245 3 chr7A.!!$R6 1392
4 TraesCS7A01G067700 chr7A 33678515 33679141 626 True 366.40 680 94.214000 853 1509 2 chr7A.!!$R4 656
5 TraesCS7A01G067700 chr7A 33719990 33720528 538 True 206.50 311 94.158500 102 465 2 chr7A.!!$R5 363
6 TraesCS7A01G067700 chr7D 33464417 33466654 2237 True 3674.00 3674 96.277000 1 2245 1 chr7D.!!$R1 2244
7 TraesCS7A01G067700 chr2A 772936112 772937118 1006 False 1539.00 1539 94.240000 2239 3245 1 chr2A.!!$F3 1006
8 TraesCS7A01G067700 chr2A 610749758 610750765 1007 False 1339.00 1339 90.675000 2239 3245 1 chr2A.!!$F1 1006
9 TraesCS7A01G067700 chr2A 780701007 780701961 954 False 1218.00 1218 89.760000 2239 3190 1 chr2A.!!$F4 951
10 TraesCS7A01G067700 chr2A 688111050 688112057 1007 False 1051.00 1051 85.545000 2239 3245 1 chr2A.!!$F2 1006
11 TraesCS7A01G067700 chr6A 8461756 8462762 1006 True 1395.00 1395 91.658000 2239 3245 1 chr6A.!!$R1 1006
12 TraesCS7A01G067700 chr1A 426037883 426038888 1005 True 1376.00 1376 91.360000 2239 3245 1 chr1A.!!$R1 1006
13 TraesCS7A01G067700 chr1A 435451384 435452389 1005 False 1336.00 1336 90.656000 2239 3243 1 chr1A.!!$F1 1004
14 TraesCS7A01G067700 chr5A 34409660 34410667 1007 True 1356.00 1356 90.972000 2239 3245 1 chr5A.!!$R1 1006
15 TraesCS7A01G067700 chr3A 679065319 679066321 1002 True 1349.00 1349 90.945000 2242 3245 1 chr3A.!!$R2 1003
16 TraesCS7A01G067700 chr4A 692083064 692089006 5942 False 667.00 953 87.825500 1 2242 4 chr4A.!!$F1 2241
17 TraesCS7A01G067700 chr4A 692259351 692261820 2469 False 590.25 965 88.445000 5 2242 4 chr4A.!!$F3 2237
18 TraesCS7A01G067700 chr4A 692163695 692166166 2471 False 589.50 959 88.422250 5 2242 4 chr4A.!!$F2 2237

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
148 149 4.156455 TCCACCCAATCTAGAATCAAGC 57.844 45.455 0.0 0.0 0.00 4.01 F
1271 7043 0.178767 TGGGAGAATCAGATGCGGTG 59.821 55.000 0.0 0.0 36.25 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 9034 9.288576 CATATATCCTGCAGGTTTCTTCAATAA 57.711 33.333 31.58 8.78 36.34 1.40 R
3206 10138 0.398318 AGAGGAGCCCACAGTTGAAC 59.602 55.000 0.00 0.00 0.00 3.18 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
148 149 4.156455 TCCACCCAATCTAGAATCAAGC 57.844 45.455 0.00 0.00 0.00 4.01
1271 7043 0.178767 TGGGAGAATCAGATGCGGTG 59.821 55.000 0.00 0.00 36.25 4.94
1917 8841 2.741211 GAACCTTGTCGACGGGCC 60.741 66.667 22.04 13.25 0.00 5.80
2182 9108 6.827727 TCTTGTAAGCTTCAACCTCTACTTT 58.172 36.000 0.00 0.00 0.00 2.66
2229 9155 4.981806 TGGGCTTGTGCTAATTGAATAC 57.018 40.909 0.00 0.00 39.59 1.89
2260 9186 2.068834 TTAACTTTCCGGTTTGCCCA 57.931 45.000 0.00 0.00 0.00 5.36
2282 9208 4.766404 ACGGATTTTTAGTGAAGGCAAG 57.234 40.909 0.00 0.00 0.00 4.01
2432 9358 1.222661 GTCCGGGTTACCCACATCC 59.777 63.158 21.58 0.00 45.83 3.51
2458 9384 0.105593 GCTGCCGGATCAGAAGATGA 59.894 55.000 5.05 0.00 43.70 2.92
2468 9394 5.874810 CGGATCAGAAGATGAAGTGGTTTTA 59.125 40.000 0.00 0.00 42.53 1.52
2549 9475 0.955919 CCGGTTTCTCTTGTGGAGGC 60.956 60.000 0.00 0.00 42.10 4.70
2599 9526 7.086376 CCCTGTTTGAAAGATGTTGATGTTAG 58.914 38.462 0.00 0.00 0.00 2.34
2601 9529 6.142139 TGTTTGAAAGATGTTGATGTTAGCG 58.858 36.000 0.00 0.00 0.00 4.26
2626 9557 7.099120 GGTTGATAATTTGAACAGGCAGATTT 58.901 34.615 0.00 0.00 0.00 2.17
2627 9558 7.063780 GGTTGATAATTTGAACAGGCAGATTTG 59.936 37.037 0.00 0.00 0.00 2.32
2637 9569 7.147312 TGAACAGGCAGATTTGATAAAAAGTG 58.853 34.615 0.00 0.00 0.00 3.16
2638 9570 5.473039 ACAGGCAGATTTGATAAAAAGTGC 58.527 37.500 4.52 4.52 0.00 4.40
2672 9604 0.666374 ACAGCTGGCGGTTTGTTAAC 59.334 50.000 19.93 0.00 0.00 2.01
2692 9624 1.228552 GCACAAAAGGGAGCCAGGA 60.229 57.895 0.00 0.00 0.00 3.86
2754 9686 5.751243 TTTTCACAGCTTCTGTAACTTCC 57.249 39.130 0.00 0.00 43.43 3.46
2825 9757 3.059884 CTGTGTACTCGCACATCAAACT 58.940 45.455 0.00 0.00 46.65 2.66
2891 9823 1.293498 CAAGGTCGACCCCTGTCAG 59.707 63.158 30.82 9.28 41.85 3.51
2998 9930 0.606096 TGTGTTGCTTAGCCGCTCTA 59.394 50.000 0.29 0.00 0.00 2.43
3033 9965 4.380550 GGCAAAGGATTTTCGTTAGAAGGG 60.381 45.833 0.00 0.00 35.03 3.95
3051 9983 3.041946 AGGGGAGGTATCTTTGCAGTAG 58.958 50.000 0.00 0.00 0.00 2.57
3062 9994 7.335924 GGTATCTTTGCAGTAGAACCATGTTTA 59.664 37.037 17.43 1.44 0.00 2.01
3165 10097 0.880278 CTGTGTTGGGACCGTCAGTG 60.880 60.000 0.00 0.00 0.00 3.66
3170 10102 2.227194 GTTGGGACCGTCAGTGAATTT 58.773 47.619 0.00 0.00 0.00 1.82
3185 10117 2.812591 TGAATTTAGTGCGGCGGTTTAA 59.187 40.909 9.78 0.00 0.00 1.52
3206 10138 9.727627 GTTTAAATGGAAGCAATCTCTGAATAG 57.272 33.333 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 4.085924 CGAAACGGATTCTATAACGAACGG 60.086 45.833 0.00 0.00 35.79 4.44
148 149 5.222631 GGCCATTAGATTGCTAAATTTCGG 58.777 41.667 0.00 0.00 39.85 4.30
2108 9034 9.288576 CATATATCCTGCAGGTTTCTTCAATAA 57.711 33.333 31.58 8.78 36.34 1.40
2157 9083 6.031751 AGTAGAGGTTGAAGCTTACAAGAG 57.968 41.667 0.00 0.00 0.00 2.85
2182 9108 4.356405 CATAGATGCCTTGATGTGGGTA 57.644 45.455 0.00 0.00 0.00 3.69
2229 9155 4.854839 CCGGAAAGTTAAATTAGCAAACGG 59.145 41.667 0.00 0.00 0.00 4.44
2260 9186 4.022329 CCTTGCCTTCACTAAAAATCCGTT 60.022 41.667 0.00 0.00 0.00 4.44
2282 9208 1.346068 CTCTCCTCCGATTCAATCCCC 59.654 57.143 0.00 0.00 0.00 4.81
2458 9384 5.826208 CCCGCTAATAGGAATAAAACCACTT 59.174 40.000 0.00 0.00 0.00 3.16
2468 9394 2.031495 AGAGGCCCGCTAATAGGAAT 57.969 50.000 0.00 0.00 0.00 3.01
2599 9526 3.179048 GCCTGTTCAAATTATCAACCGC 58.821 45.455 0.00 0.00 0.00 5.68
2601 9529 5.643379 TCTGCCTGTTCAAATTATCAACC 57.357 39.130 0.00 0.00 0.00 3.77
2626 9557 7.168219 AGACTCATACCTTGCACTTTTTATCA 58.832 34.615 0.00 0.00 0.00 2.15
2627 9558 7.617041 AGACTCATACCTTGCACTTTTTATC 57.383 36.000 0.00 0.00 0.00 1.75
2637 9569 3.868077 CAGCTGTAAGACTCATACCTTGC 59.132 47.826 5.25 0.00 34.07 4.01
2638 9570 4.437239 CCAGCTGTAAGACTCATACCTTG 58.563 47.826 13.81 0.00 34.07 3.61
2692 9624 1.014352 GTTGTCTGTGCTCAAACCGT 58.986 50.000 0.00 0.00 0.00 4.83
2769 9701 7.546250 AGACCCTCTTCGACATAATGATATT 57.454 36.000 0.00 0.00 0.00 1.28
2776 9708 5.699458 GTGAAAAAGACCCTCTTCGACATAA 59.301 40.000 0.00 0.00 35.27 1.90
2778 9710 4.065789 GTGAAAAAGACCCTCTTCGACAT 58.934 43.478 0.00 0.00 35.27 3.06
2977 9909 2.173382 GCGGCTAAGCAACACACG 59.827 61.111 0.00 0.00 37.05 4.49
3033 9965 4.081087 TGGTTCTACTGCAAAGATACCTCC 60.081 45.833 19.36 10.91 31.22 4.30
3051 9983 7.873739 CAAAGAGTGGAATTAAACATGGTTC 57.126 36.000 0.00 0.00 0.00 3.62
3165 10097 3.474693 TTAAACCGCCGCACTAAATTC 57.525 42.857 0.00 0.00 0.00 2.17
3170 10102 1.088306 CCATTTAAACCGCCGCACTA 58.912 50.000 0.00 0.00 0.00 2.74
3185 10117 7.114754 TGAACTATTCAGAGATTGCTTCCATT 58.885 34.615 0.00 0.00 34.08 3.16
3206 10138 0.398318 AGAGGAGCCCACAGTTGAAC 59.602 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.