Multiple sequence alignment - TraesCS1A01G137600

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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 TraesCS1A01G137600 chr1A 100.000 3608 0 0 1 3608 223829177 223825570 0.000000e+00 6663.0
1 TraesCS1A01G137600 chr1A 91.048 849 67 5 2765 3608 166662023 166662867 0.000000e+00 1138.0
2 TraesCS1A01G137600 chr1A 90.695 849 67 8 2765 3608 162701314 162700473 0.000000e+00 1120.0
3 TraesCS1A01G137600 chr1A 89.765 850 74 8 2764 3608 185846394 185847235 0.000000e+00 1075.0
4 TraesCS1A01G137600 chr1A 90.909 726 55 6 2888 3608 162650892 162650173 0.000000e+00 965.0
5 TraesCS1A01G137600 chr3A 96.830 2871 89 2 739 3608 38993871 38991002 0.000000e+00 4796.0
6 TraesCS1A01G137600 chr3A 89.583 336 33 2 1316 1649 452377035 452376700 3.330000e-115 425.0
7 TraesCS1A01G137600 chr3A 93.750 160 10 0 588 747 38995722 38995563 1.290000e-59 241.0
8 TraesCS1A01G137600 chr3A 89.744 156 12 3 621 773 685500386 685500540 2.840000e-46 196.0
9 TraesCS1A01G137600 chr3A 89.437 142 15 0 589 730 447430233 447430374 2.860000e-41 180.0
10 TraesCS1A01G137600 chr1D 94.268 3053 125 26 599 3608 50871216 50874261 0.000000e+00 4623.0
11 TraesCS1A01G137600 chr1D 93.898 508 30 1 1 508 151631632 151631126 0.000000e+00 765.0
12 TraesCS1A01G137600 chr1D 88.632 563 61 3 1 561 137555418 137555979 0.000000e+00 682.0
13 TraesCS1A01G137600 chr2D 97.059 2040 58 2 1571 3608 431523325 431521286 0.000000e+00 3434.0
14 TraesCS1A01G137600 chr2D 94.373 853 37 4 711 1552 431524166 431523314 0.000000e+00 1299.0
15 TraesCS1A01G137600 chr7D 94.718 2177 107 7 1435 3608 324505745 324503574 0.000000e+00 3376.0
16 TraesCS1A01G137600 chr7D 91.182 567 40 6 821 1383 324506306 324505746 0.000000e+00 761.0
17 TraesCS1A01G137600 chr7D 87.435 581 64 7 7 583 287568279 287567704 0.000000e+00 660.0
18 TraesCS1A01G137600 chr3D 96.673 1954 63 2 1571 3522 141488889 141490842 0.000000e+00 3247.0
19 TraesCS1A01G137600 chr3D 94.817 849 33 4 715 1552 141488052 141488900 0.000000e+00 1314.0
20 TraesCS1A01G137600 chr3D 87.977 524 61 2 10 533 280657518 280658039 5.120000e-173 617.0
21 TraesCS1A01G137600 chr3D 91.406 128 8 1 1234 1358 440054412 440054285 4.790000e-39 172.0
22 TraesCS1A01G137600 chr2B 87.277 896 58 23 1911 2761 137214352 137213468 0.000000e+00 972.0
23 TraesCS1A01G137600 chr2B 85.057 87 13 0 477 563 265614192 265614278 4.960000e-14 89.8
24 TraesCS1A01G137600 chr2A 89.880 751 71 2 2765 3515 302664303 302663558 0.000000e+00 961.0
25 TraesCS1A01G137600 chr2A 89.388 245 17 7 585 822 559613532 559613774 2.110000e-77 300.0
26 TraesCS1A01G137600 chr2A 90.226 133 12 1 589 720 409195005 409195137 4.790000e-39 172.0
27 TraesCS1A01G137600 chr2A 91.736 121 6 3 589 707 433548150 433548268 8.010000e-37 165.0
28 TraesCS1A01G137600 chr6A 92.178 473 37 0 2765 3237 167191373 167191845 0.000000e+00 669.0
29 TraesCS1A01G137600 chr5D 88.390 534 59 2 1 533 476146874 476147405 1.090000e-179 640.0
30 TraesCS1A01G137600 chr4D 87.523 553 65 4 7 557 254720736 254720186 1.410000e-178 636.0
31 TraesCS1A01G137600 chr4D 82.540 189 26 6 525 710 417875033 417874849 3.730000e-35 159.0
32 TraesCS1A01G137600 chr4A 87.755 539 58 7 2 537 340173143 340172610 1.100000e-174 623.0
33 TraesCS1A01G137600 chr4A 87.382 531 64 3 7 536 451363818 451363290 1.110000e-169 606.0
34 TraesCS1A01G137600 chr1B 87.791 516 61 2 1 515 217358040 217358554 1.430000e-168 603.0
35 TraesCS1A01G137600 chr1B 88.496 339 34 3 1316 1649 635830911 635831249 4.340000e-109 405.0
36 TraesCS1A01G137600 chr1B 86.826 334 38 5 823 1153 635829039 635829369 5.690000e-98 368.0
37 TraesCS1A01G137600 chr1B 86.186 333 42 4 823 1153 382701235 382700905 1.230000e-94 357.0
38 TraesCS1A01G137600 chr1B 83.478 115 19 0 533 647 551403879 551403765 1.370000e-19 108.0
39 TraesCS1A01G137600 chrUn 88.496 339 34 3 1316 1649 349787385 349787047 4.340000e-109 405.0
40 TraesCS1A01G137600 chrUn 86.826 334 38 5 823 1153 377928474 377928804 5.690000e-98 368.0
41 TraesCS1A01G137600 chrUn 88.806 134 13 2 590 722 335670830 335670698 2.880000e-36 163.0
42 TraesCS1A01G137600 chr7B 88.529 340 32 5 1316 1649 600922463 600922125 4.340000e-109 405.0
43 TraesCS1A01G137600 chr7B 88.201 339 35 3 1316 1649 608180869 608180531 2.020000e-107 399.0
44 TraesCS1A01G137600 chr7B 86.228 334 40 5 823 1153 608182742 608182412 1.230000e-94 357.0


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 TraesCS1A01G137600 chr1A 223825570 223829177 3607 True 6663.0 6663 100.0000 1 3608 1 chr1A.!!$R3 3607
1 TraesCS1A01G137600 chr1A 166662023 166662867 844 False 1138.0 1138 91.0480 2765 3608 1 chr1A.!!$F1 843
2 TraesCS1A01G137600 chr1A 162700473 162701314 841 True 1120.0 1120 90.6950 2765 3608 1 chr1A.!!$R2 843
3 TraesCS1A01G137600 chr1A 185846394 185847235 841 False 1075.0 1075 89.7650 2764 3608 1 chr1A.!!$F2 844
4 TraesCS1A01G137600 chr1A 162650173 162650892 719 True 965.0 965 90.9090 2888 3608 1 chr1A.!!$R1 720
5 TraesCS1A01G137600 chr3A 38991002 38995722 4720 True 2518.5 4796 95.2900 588 3608 2 chr3A.!!$R2 3020
6 TraesCS1A01G137600 chr1D 50871216 50874261 3045 False 4623.0 4623 94.2680 599 3608 1 chr1D.!!$F1 3009
7 TraesCS1A01G137600 chr1D 151631126 151631632 506 True 765.0 765 93.8980 1 508 1 chr1D.!!$R1 507
8 TraesCS1A01G137600 chr1D 137555418 137555979 561 False 682.0 682 88.6320 1 561 1 chr1D.!!$F2 560
9 TraesCS1A01G137600 chr2D 431521286 431524166 2880 True 2366.5 3434 95.7160 711 3608 2 chr2D.!!$R1 2897
10 TraesCS1A01G137600 chr7D 324503574 324506306 2732 True 2068.5 3376 92.9500 821 3608 2 chr7D.!!$R2 2787
11 TraesCS1A01G137600 chr7D 287567704 287568279 575 True 660.0 660 87.4350 7 583 1 chr7D.!!$R1 576
12 TraesCS1A01G137600 chr3D 141488052 141490842 2790 False 2280.5 3247 95.7450 715 3522 2 chr3D.!!$F2 2807
13 TraesCS1A01G137600 chr3D 280657518 280658039 521 False 617.0 617 87.9770 10 533 1 chr3D.!!$F1 523
14 TraesCS1A01G137600 chr2B 137213468 137214352 884 True 972.0 972 87.2770 1911 2761 1 chr2B.!!$R1 850
15 TraesCS1A01G137600 chr2A 302663558 302664303 745 True 961.0 961 89.8800 2765 3515 1 chr2A.!!$R1 750
16 TraesCS1A01G137600 chr5D 476146874 476147405 531 False 640.0 640 88.3900 1 533 1 chr5D.!!$F1 532
17 TraesCS1A01G137600 chr4D 254720186 254720736 550 True 636.0 636 87.5230 7 557 1 chr4D.!!$R1 550
18 TraesCS1A01G137600 chr4A 340172610 340173143 533 True 623.0 623 87.7550 2 537 1 chr4A.!!$R1 535
19 TraesCS1A01G137600 chr4A 451363290 451363818 528 True 606.0 606 87.3820 7 536 1 chr4A.!!$R2 529
20 TraesCS1A01G137600 chr1B 217358040 217358554 514 False 603.0 603 87.7910 1 515 1 chr1B.!!$F1 514
21 TraesCS1A01G137600 chr1B 635829039 635831249 2210 False 386.5 405 87.6610 823 1649 2 chr1B.!!$F2 826
22 TraesCS1A01G137600 chr7B 608180531 608182742 2211 True 378.0 399 87.2145 823 1649 2 chr7B.!!$R2 826

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
34 35 0.670546 CAACGATGGAGAAGTGGCGT 60.671 55.000 0.0 0.0 0.00 5.68 F
1038 2755 1.078143 GCTCCTGGCTGACGGATTT 60.078 57.895 0.0 0.0 38.06 2.17 F
1446 4544 0.036010 GCAGGAGCACCAGAAGCTTA 60.036 55.000 0.0 0.0 43.58 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 4428 0.036732 AGGCAACCAATTCAGCGAGA 59.963 50.0 0.0 0.0 37.17 4.04 R
1979 5118 1.382522 CAGCGTTCCCATGCATACTT 58.617 50.0 0.0 0.0 37.39 2.24 R
3345 6530 0.968901 TGGGCGTCGAGATTGTAGGT 60.969 55.0 0.0 0.0 0.00 3.08 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
34 35 0.670546 CAACGATGGAGAAGTGGCGT 60.671 55.000 0.00 0.0 0.00 5.68
114 118 3.451178 GCAAGACATGAGGGGAGTAAGTA 59.549 47.826 0.00 0.0 0.00 2.24
120 124 8.568617 AGACATGAGGGGAGTAAGTATTAATT 57.431 34.615 0.00 0.0 28.70 1.40
156 161 3.399983 GGGTATTTATAAGGAAGGGGGCA 59.600 47.826 0.00 0.0 0.00 5.36
518 523 8.474025 GCTATAAGTGAATGCTATAGAGGACAT 58.526 37.037 3.21 0.0 0.00 3.06
648 654 4.320935 GGTTCACCATCACAATACGCTTTT 60.321 41.667 0.00 0.0 35.64 2.27
709 717 9.640952 AACATATATGCAAGGTGGTACTAATTT 57.359 29.630 12.79 0.0 0.00 1.82
733 742 2.853731 ACCACGTCGCAAAATTTTCA 57.146 40.000 0.00 0.0 0.00 2.69
873 2583 5.817816 ACGAGAGAAAAGAAGAAGAAAAGCA 59.182 36.000 0.00 0.0 0.00 3.91
924 2641 4.430441 GATCCCATATACACCTCCTTCCT 58.570 47.826 0.00 0.0 0.00 3.36
970 2687 4.096003 CCCCACACCGCCTCGATT 62.096 66.667 0.00 0.0 0.00 3.34
978 2695 4.143333 CGCCTCGATTGGGACCGT 62.143 66.667 0.00 0.0 0.00 4.83
1038 2755 1.078143 GCTCCTGGCTGACGGATTT 60.078 57.895 0.00 0.0 38.06 2.17
1256 3102 1.253593 GGAAGGTAAGGACGGACGGT 61.254 60.000 0.00 0.0 0.00 4.83
1331 4428 1.830847 GTTTTTCTGGGTGGGCGGT 60.831 57.895 0.00 0.0 0.00 5.68
1390 4488 1.153449 GTCGTCGGATTGGATGGCA 60.153 57.895 0.00 0.0 0.00 4.92
1446 4544 0.036010 GCAGGAGCACCAGAAGCTTA 60.036 55.000 0.00 0.0 43.58 3.09
1484 4583 4.635765 GTGCTACCAATCTGCATCAAACTA 59.364 41.667 0.00 0.0 39.00 2.24
1495 4594 3.287222 GCATCAAACTATTGGGCCACTA 58.713 45.455 5.23 4.1 37.15 2.74
1557 4659 3.636764 CCATTATTGGCCTAGGTTGGAAC 59.363 47.826 11.31 0.0 35.85 3.62
1800 4939 4.037923 ACAAAAACATGGTGAAGTAGCTGG 59.962 41.667 0.00 0.0 0.00 4.85
1806 4945 2.187958 TGGTGAAGTAGCTGGCTGTAT 58.812 47.619 5.25 0.0 0.00 2.29
1942 5081 3.258123 TGGGTAAAGAAATTTGCAGCTCC 59.742 43.478 0.00 0.0 0.00 4.70
1961 5100 6.090898 CAGCTCCGAATACTTTATATTTCCCG 59.909 42.308 0.00 0.0 0.00 5.14
1979 5118 3.075884 CCCGGTTGTTCTTAATTTCGGA 58.924 45.455 0.00 0.0 38.64 4.55
2388 5552 8.700973 TCTTAAGGTCTTTGTTTGCCTTTTTAT 58.299 29.630 1.85 0.0 41.16 1.40
2420 5584 0.456482 TTTGCTTGGATTGATGCGCG 60.456 50.000 0.00 0.0 0.00 6.86
2552 5716 4.105697 AGAAAAAGGTTCCATGAGGGTGTA 59.894 41.667 0.00 0.0 38.11 2.90
2629 5794 4.715523 TGCTACGCCAAGTGCCCC 62.716 66.667 0.00 0.0 36.24 5.80
3035 6218 6.384015 AGTTGGTGTGATATCATGTCCTTAGA 59.616 38.462 9.02 0.0 0.00 2.10
3330 6514 1.265095 GTGCAACACTGTGATGTGAGG 59.735 52.381 15.86 0.0 40.12 3.86
3345 6530 2.221169 GTGAGGTGAACACAAGCATGA 58.779 47.619 0.00 0.0 38.05 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.733041 CCATCGTTGTCGTCACGCT 60.733 57.895 0.00 0.0 38.33 5.07
34 35 2.803133 CGGAGACAAAGCACTTCACTGA 60.803 50.000 0.00 0.0 0.00 3.41
114 118 3.432262 GCCCCCTGCGGTAATTAAT 57.568 52.632 0.00 0.0 0.00 1.40
156 161 6.239345 GGGTAGCTGAGTAATTACACTATGCT 60.239 42.308 17.65 19.9 39.21 3.79
571 576 7.728532 AGGGATAGATGTGTGTGTATGTATGTA 59.271 37.037 0.00 0.0 0.00 2.29
583 588 9.725019 TGCTTTATTATTAGGGATAGATGTGTG 57.275 33.333 0.00 0.0 0.00 3.82
610 615 1.418264 TGAACCCACGGAGTCAATTCA 59.582 47.619 0.00 0.0 41.61 2.57
612 617 1.544759 GGTGAACCCACGGAGTCAATT 60.545 52.381 0.00 0.0 41.61 2.32
648 654 7.090953 AGTGAAAACGTAAATTGACAGGAAA 57.909 32.000 0.00 0.0 0.00 3.13
694 702 4.106663 TGGTTCCCAAATTAGTACCACCTT 59.893 41.667 0.00 0.0 31.14 3.50
709 717 0.820074 ATTTTGCGACGTGGTTCCCA 60.820 50.000 0.00 0.0 0.00 4.37
733 742 2.030185 GCGGGACAGATCATGTACGTAT 60.030 50.000 0.00 0.0 44.60 3.06
978 2695 2.874664 CGTCGTTTGGGGAGGGACA 61.875 63.158 0.00 0.0 0.00 4.02
1029 2746 1.377202 GGAGCCAGCAAATCCGTCA 60.377 57.895 0.00 0.0 0.00 4.35
1239 3085 1.538687 CCACCGTCCGTCCTTACCTT 61.539 60.000 0.00 0.0 0.00 3.50
1331 4428 0.036732 AGGCAACCAATTCAGCGAGA 59.963 50.000 0.00 0.0 37.17 4.04
1484 4583 0.475906 GGCTCTCATAGTGGCCCAAT 59.524 55.000 0.00 0.0 38.77 3.16
1557 4659 0.449388 GGCGAATCTGCAAGGACAAG 59.551 55.000 0.00 0.0 36.28 3.16
1568 4670 0.257039 AATCAGGCCAAGGCGAATCT 59.743 50.000 5.01 0.0 43.06 2.40
1800 4939 6.624352 TCATCTCCAAGCAAAATATACAGC 57.376 37.500 0.00 0.0 0.00 4.40
1806 4945 7.828717 TGAACAGTATCATCTCCAAGCAAAATA 59.171 33.333 0.00 0.0 0.00 1.40
1904 5043 9.920946 TTCTTTACCCAGCAAAAATCTAGATAT 57.079 29.630 5.46 0.0 0.00 1.63
1942 5081 7.486802 ACAACCGGGAAATATAAAGTATTCG 57.513 36.000 6.32 0.0 0.00 3.34
1961 5100 6.745907 GCATACTTCCGAAATTAAGAACAACC 59.254 38.462 0.00 0.0 0.00 3.77
1979 5118 1.382522 CAGCGTTCCCATGCATACTT 58.617 50.000 0.00 0.0 37.39 2.24
2388 5552 2.031120 CAAGCAAACAAAGACCTCCCA 58.969 47.619 0.00 0.0 0.00 4.37
2420 5584 4.203950 TGTTGTAAATTGTGTCAGTCGC 57.796 40.909 0.00 0.0 0.00 5.19
2449 5613 5.422012 TGAAACTATGGTCTATGCTGTCAGA 59.578 40.000 3.32 0.0 0.00 3.27
2455 5619 8.100791 TGTAAAACTGAAACTATGGTCTATGCT 58.899 33.333 0.00 0.0 0.00 3.79
2552 5716 7.430760 AGCTCTTTCTCCACTTCTGTAATAT 57.569 36.000 0.00 0.0 0.00 1.28
3035 6218 1.752694 CATTCCATCGGGGGCGTTT 60.753 57.895 0.00 0.0 37.22 3.60
3330 6514 3.138304 TGTAGGTCATGCTTGTGTTCAC 58.862 45.455 0.00 0.0 0.00 3.18
3345 6530 0.968901 TGGGCGTCGAGATTGTAGGT 60.969 55.000 0.00 0.0 0.00 3.08


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

AutoCloner maintained by Alex Coulton.