Multiple sequence alignment - TraesCS6A01G003600

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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 TraesCS6A01G003600 chr6A 100.000 2570 0 0 1 2570 1649398 1651967 0.000000e+00 4747.0
1 TraesCS6A01G003600 chr6A 90.512 664 39 8 544 1203 66391700 66392343 0.000000e+00 856.0
2 TraesCS6A01G003600 chr6A 83.187 571 96 0 1252 1822 215010398 215010968 8.150000e-145 523.0
3 TraesCS6A01G003600 chr6A 81.056 549 104 0 2022 2570 215011177 215011725 3.040000e-119 438.0
4 TraesCS6A01G003600 chr6A 88.218 331 18 11 233 543 570436660 570436331 2.410000e-100 375.0
5 TraesCS6A01G003600 chr6A 89.177 231 21 4 544 771 1654546 1654317 4.190000e-73 285.0
6 TraesCS6A01G003600 chr2D 95.037 2035 79 6 543 2570 119022683 119020664 0.000000e+00 3179.0
7 TraesCS6A01G003600 chr2D 89.587 557 27 8 9 543 534525041 534525588 0.000000e+00 678.0
8 TraesCS6A01G003600 chr3D 90.177 1639 94 22 819 2438 526149389 526150979 0.000000e+00 2073.0
9 TraesCS6A01G003600 chr5A 92.497 893 44 10 691 1580 73832986 73832114 0.000000e+00 1256.0
10 TraesCS6A01G003600 chr5A 89.771 567 32 11 1 543 265553882 265554446 0.000000e+00 702.0
11 TraesCS6A01G003600 chr5A 89.767 557 34 11 9 543 601636450 601635895 0.000000e+00 691.0
12 TraesCS6A01G003600 chr5A 85.833 240 21 6 544 771 73831870 73832108 2.550000e-60 243.0
13 TraesCS6A01G003600 chr5A 97.143 35 1 0 732 766 73833020 73832986 2.760000e-05 60.2
14 TraesCS6A01G003600 chr7B 85.779 886 84 11 578 1462 736879330 736880174 0.000000e+00 900.0
15 TraesCS6A01G003600 chr7B 83.392 572 92 2 1276 1847 474547706 474547138 6.300000e-146 527.0
16 TraesCS6A01G003600 chr7B 88.636 396 20 5 172 543 693801351 693800957 2.330000e-125 459.0
17 TraesCS6A01G003600 chr5B 89.574 681 45 11 794 1452 571860989 571860313 0.000000e+00 841.0
18 TraesCS6A01G003600 chr5B 89.929 566 32 12 1 543 697373337 697372774 0.000000e+00 706.0
19 TraesCS6A01G003600 chr5B 89.771 567 33 10 1 543 707617498 707618063 0.000000e+00 702.0
20 TraesCS6A01G003600 chr5B 89.928 556 34 12 9 543 603889957 603890511 0.000000e+00 697.0
21 TraesCS6A01G003600 chr5B 95.362 345 16 0 1108 1452 571551427 571551083 1.340000e-152 549.0
22 TraesCS6A01G003600 chr5B 81.056 549 104 0 2022 2570 708969579 708969031 3.040000e-119 438.0
23 TraesCS6A01G003600 chr5B 91.111 180 15 1 544 723 571550161 571550339 2.550000e-60 243.0
24 TraesCS6A01G003600 chr5B 89.503 181 16 2 544 723 571861164 571860986 2.570000e-55 226.0
25 TraesCS6A01G003600 chr5B 90.588 85 6 2 794 877 571550336 571550419 7.520000e-21 111.0
26 TraesCS6A01G003600 chr2A 90.528 549 41 7 1 543 768473510 768472967 0.000000e+00 715.0
27 TraesCS6A01G003600 chr2A 90.143 558 31 11 9 543 384554747 384555303 0.000000e+00 704.0
28 TraesCS6A01G003600 chr2A 83.012 571 97 0 1252 1822 689607367 689607937 3.790000e-143 518.0
29 TraesCS6A01G003600 chr2A 81.455 550 100 2 2022 2570 689608173 689608721 1.400000e-122 449.0
30 TraesCS6A01G003600 chr2B 90.123 567 31 10 1 543 100023879 100023314 0.000000e+00 713.0
31 TraesCS6A01G003600 chr2B 89.046 566 38 8 1 543 53239794 53240358 0.000000e+00 680.0
32 TraesCS6A01G003600 chr7A 90.323 558 29 12 9 543 8738165 8737610 0.000000e+00 708.0
33 TraesCS6A01G003600 chr7A 83.453 556 92 0 1276 1831 151358059 151357504 3.790000e-143 518.0
34 TraesCS6A01G003600 chr4A 90.143 558 31 5 9 543 24612692 24612136 0.000000e+00 704.0
35 TraesCS6A01G003600 chr3B 89.771 567 33 10 1 543 2119156 2118591 0.000000e+00 702.0
36 TraesCS6A01G003600 chr5D 88.948 561 33 11 1 542 347477433 347477983 0.000000e+00 665.0
37 TraesCS6A01G003600 chr5D 88.193 559 34 8 9 543 8038608 8039158 2.790000e-179 638.0
38 TraesCS6A01G003600 chr5D 83.012 571 96 1 1252 1822 475818598 475819167 1.360000e-142 516.0
39 TraesCS6A01G003600 chr5D 80.874 549 105 0 2022 2570 408252340 408252888 1.410000e-117 433.0
40 TraesCS6A01G003600 chr6D 83.633 556 91 0 1276 1831 289734429 289733874 8.150000e-145 523.0
41 TraesCS6A01G003600 chr6D 81.056 549 104 0 2022 2570 289733674 289733126 3.040000e-119 438.0
42 TraesCS6A01G003600 chr4B 81.172 478 90 0 2022 2499 442428316 442427839 4.010000e-103 385.0
43 TraesCS6A01G003600 chr7D 87.826 115 6 2 663 769 611230720 611230834 7.460000e-26 128.0
44 TraesCS6A01G003600 chr1D 97.619 42 0 1 804 844 208818652 208818693 1.280000e-08 71.3


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 TraesCS6A01G003600 chr6A 1649398 1651967 2569 False 4747.0 4747 100.0000 1 2570 1 chr6A.!!$F1 2569
1 TraesCS6A01G003600 chr6A 66391700 66392343 643 False 856.0 856 90.5120 544 1203 1 chr6A.!!$F2 659
2 TraesCS6A01G003600 chr6A 215010398 215011725 1327 False 480.5 523 82.1215 1252 2570 2 chr6A.!!$F3 1318
3 TraesCS6A01G003600 chr2D 119020664 119022683 2019 True 3179.0 3179 95.0370 543 2570 1 chr2D.!!$R1 2027
4 TraesCS6A01G003600 chr2D 534525041 534525588 547 False 678.0 678 89.5870 9 543 1 chr2D.!!$F1 534
5 TraesCS6A01G003600 chr3D 526149389 526150979 1590 False 2073.0 2073 90.1770 819 2438 1 chr3D.!!$F1 1619
6 TraesCS6A01G003600 chr5A 265553882 265554446 564 False 702.0 702 89.7710 1 543 1 chr5A.!!$F2 542
7 TraesCS6A01G003600 chr5A 601635895 601636450 555 True 691.0 691 89.7670 9 543 1 chr5A.!!$R1 534
8 TraesCS6A01G003600 chr5A 73832114 73833020 906 True 658.1 1256 94.8200 691 1580 2 chr5A.!!$R2 889
9 TraesCS6A01G003600 chr7B 736879330 736880174 844 False 900.0 900 85.7790 578 1462 1 chr7B.!!$F1 884
10 TraesCS6A01G003600 chr7B 474547138 474547706 568 True 527.0 527 83.3920 1276 1847 1 chr7B.!!$R1 571
11 TraesCS6A01G003600 chr5B 697372774 697373337 563 True 706.0 706 89.9290 1 543 1 chr5B.!!$R2 542
12 TraesCS6A01G003600 chr5B 707617498 707618063 565 False 702.0 702 89.7710 1 543 1 chr5B.!!$F2 542
13 TraesCS6A01G003600 chr5B 603889957 603890511 554 False 697.0 697 89.9280 9 543 1 chr5B.!!$F1 534
14 TraesCS6A01G003600 chr5B 571860313 571861164 851 True 533.5 841 89.5385 544 1452 2 chr5B.!!$R4 908
15 TraesCS6A01G003600 chr5B 708969031 708969579 548 True 438.0 438 81.0560 2022 2570 1 chr5B.!!$R3 548
16 TraesCS6A01G003600 chr2A 768472967 768473510 543 True 715.0 715 90.5280 1 543 1 chr2A.!!$R1 542
17 TraesCS6A01G003600 chr2A 384554747 384555303 556 False 704.0 704 90.1430 9 543 1 chr2A.!!$F1 534
18 TraesCS6A01G003600 chr2A 689607367 689608721 1354 False 483.5 518 82.2335 1252 2570 2 chr2A.!!$F2 1318
19 TraesCS6A01G003600 chr2B 100023314 100023879 565 True 713.0 713 90.1230 1 543 1 chr2B.!!$R1 542
20 TraesCS6A01G003600 chr2B 53239794 53240358 564 False 680.0 680 89.0460 1 543 1 chr2B.!!$F1 542
21 TraesCS6A01G003600 chr7A 8737610 8738165 555 True 708.0 708 90.3230 9 543 1 chr7A.!!$R1 534
22 TraesCS6A01G003600 chr7A 151357504 151358059 555 True 518.0 518 83.4530 1276 1831 1 chr7A.!!$R2 555
23 TraesCS6A01G003600 chr4A 24612136 24612692 556 True 704.0 704 90.1430 9 543 1 chr4A.!!$R1 534
24 TraesCS6A01G003600 chr3B 2118591 2119156 565 True 702.0 702 89.7710 1 543 1 chr3B.!!$R1 542
25 TraesCS6A01G003600 chr5D 347477433 347477983 550 False 665.0 665 88.9480 1 542 1 chr5D.!!$F2 541
26 TraesCS6A01G003600 chr5D 8038608 8039158 550 False 638.0 638 88.1930 9 543 1 chr5D.!!$F1 534
27 TraesCS6A01G003600 chr5D 475818598 475819167 569 False 516.0 516 83.0120 1252 1822 1 chr5D.!!$F4 570
28 TraesCS6A01G003600 chr5D 408252340 408252888 548 False 433.0 433 80.8740 2022 2570 1 chr5D.!!$F3 548
29 TraesCS6A01G003600 chr6D 289733126 289734429 1303 True 480.5 523 82.3445 1276 2570 2 chr6D.!!$R1 1294

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
120 121 0.250234 CACCATCGTGACCCAGTGAT 59.750 55.0 0.0 0.0 43.14 3.06 F
494 532 0.402566 ATGAAGGAGGGGAGGGGATG 60.403 60.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1090 1238 0.699577 TCAAACAGAAGGGTGGGGGA 60.700 55.000 0.00 0.0 0.00 4.81 R
2288 2538 1.272147 ACTGGAAGACTTGCCCAATCC 60.272 52.381 4.07 0.0 37.43 3.01 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
23 24 2.121506 TTCCAGGGCCAGGGAAGT 60.122 61.111 21.62 0.00 38.23 3.01
109 110 2.982130 GTCCTCCAGCACCATCGT 59.018 61.111 0.00 0.00 0.00 3.73
120 121 0.250234 CACCATCGTGACCCAGTGAT 59.750 55.000 0.00 0.00 43.14 3.06
257 259 6.985645 TGTTTCCTTTGTTTGGAGATTGATTG 59.014 34.615 0.00 0.00 34.76 2.67
481 505 3.181514 ACGCGAAAATAAACCGATGAAGG 60.182 43.478 15.93 0.00 37.30 3.46
482 506 3.062909 CGCGAAAATAAACCGATGAAGGA 59.937 43.478 0.00 0.00 34.73 3.36
494 532 0.402566 ATGAAGGAGGGGAGGGGATG 60.403 60.000 0.00 0.00 0.00 3.51
611 666 5.365403 TTGGTCATTGTATTCACGAAACC 57.635 39.130 0.00 0.00 32.32 3.27
628 683 4.746611 CGAAACCTAAAGTTACGGTCACTT 59.253 41.667 1.95 1.95 37.88 3.16
641 696 2.415491 CGGTCACTTGACTCGCTGAATA 60.415 50.000 9.20 0.00 44.20 1.75
665 720 2.030946 GTCAGCGTACGGTAACTCGTAT 59.969 50.000 20.88 0.00 45.51 3.06
689 744 3.932545 TTTGGCTCGTATTTTGCACAT 57.067 38.095 0.00 0.00 0.00 3.21
728 783 1.187087 AAAACTGTTTGACCCGCCAA 58.813 45.000 6.53 0.00 0.00 4.52
760 818 6.481954 GACACGTCCATTTCATAAAGAAGT 57.518 37.500 0.00 0.00 37.57 3.01
778 866 1.009389 GTGAGCGACCACTTTCCTCG 61.009 60.000 0.00 0.00 34.38 4.63
854 946 4.847444 GCTCGGCTTCTCCCCAGC 62.847 72.222 0.00 0.00 36.45 4.85
897 997 2.309162 GCTAAGGAAAGAAAGGGGAGGT 59.691 50.000 0.00 0.00 0.00 3.85
948 1048 2.029073 CCGCCGACGAAGCCATAT 59.971 61.111 0.00 0.00 43.93 1.78
1073 1221 3.771577 TCTCTGAAACTCTGAAACCCC 57.228 47.619 0.00 0.00 0.00 4.95
1083 1231 0.774908 CTGAAACCCCCTGTAACCCA 59.225 55.000 0.00 0.00 0.00 4.51
1090 1238 1.308746 CCCTGTAACCCATCCCCCT 60.309 63.158 0.00 0.00 0.00 4.79
1104 1258 3.017581 CCCTCCCCCACCCTTCTG 61.018 72.222 0.00 0.00 0.00 3.02
1392 1546 2.184020 TTGAGGGGGATGCACTCACG 62.184 60.000 9.77 0.00 40.63 4.35
1565 1721 3.252458 GTGACATTTGGACACAAGTACCC 59.748 47.826 0.00 0.00 37.97 3.69
1598 1754 9.322773 GTATCTTGATCATGATGAGAGTTTCAA 57.677 33.333 26.38 8.34 39.77 2.69
1656 1812 1.162698 CAGATCTGCCCACTGTTGTG 58.837 55.000 10.38 0.00 43.45 3.33
1674 1830 5.473162 TGTTGTGAGTCCTATGAAACCAATG 59.527 40.000 0.00 0.00 0.00 2.82
1743 1900 2.822707 AGGAAGCATTGGAGAAGCAT 57.177 45.000 0.00 0.00 0.00 3.79
1756 1913 6.575244 TGGAGAAGCATATTAAGGAGGAAA 57.425 37.500 0.00 0.00 0.00 3.13
1796 1953 7.416817 CAATGTCAGTTTGTAACTCATGACAA 58.583 34.615 9.58 0.00 42.73 3.18
2012 2262 6.618811 CAGATGAGTTTGAAGAGGAAAATGG 58.381 40.000 0.00 0.00 0.00 3.16
2288 2538 6.446781 AGATTTGCATGATCCACAGTTTAG 57.553 37.500 0.00 0.00 0.00 1.85
2366 2616 5.931146 ACAGTTGCAAAAACAGATTTGACAA 59.069 32.000 0.00 5.18 41.73 3.18
2448 2698 2.225068 ACATATGGTGCAGCTACGAC 57.775 50.000 18.08 0.00 0.00 4.34
2545 2795 5.876460 GCATTTACCTCCAAATTTCTTGCAT 59.124 36.000 0.00 0.00 0.00 3.96
2547 2797 7.223387 GCATTTACCTCCAAATTTCTTGCATAG 59.777 37.037 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.610859 GACTTCCCTGGCCCTGGA 60.611 66.667 8.48 9.71 0.00 3.86
109 110 0.546507 TGGGCTACATCACTGGGTCA 60.547 55.000 0.00 0.00 0.00 4.02
120 121 2.124736 GCCGATGCTTGGGCTACA 60.125 61.111 16.99 0.00 43.01 2.74
257 259 2.973694 TACCTTAACTCACGGATGGC 57.026 50.000 0.00 0.00 0.00 4.40
481 505 1.007607 TTTTTCCATCCCCTCCCCTC 58.992 55.000 0.00 0.00 0.00 4.30
482 506 3.231133 TTTTTCCATCCCCTCCCCT 57.769 52.632 0.00 0.00 0.00 4.79
555 610 6.334102 AGAGACAAGTTCAGTTACTGTAGG 57.666 41.667 12.41 2.16 32.61 3.18
611 666 4.615961 CGAGTCAAGTGACCGTAACTTTAG 59.384 45.833 7.82 0.00 45.85 1.85
628 683 1.751351 CTGACCCTATTCAGCGAGTCA 59.249 52.381 0.00 0.00 36.83 3.41
641 696 0.610232 AGTTACCGTACGCTGACCCT 60.610 55.000 10.49 0.00 0.00 4.34
665 720 4.233789 GTGCAAAATACGAGCCAAAATGA 58.766 39.130 0.00 0.00 0.00 2.57
689 744 2.932855 TTGGGTCAAATACGTCCACA 57.067 45.000 0.00 0.00 0.00 4.17
760 818 1.176619 TCGAGGAAAGTGGTCGCTCA 61.177 55.000 0.00 0.00 33.66 4.26
802 893 3.515104 CAGGGGGAAATATGCAAAACTGT 59.485 43.478 0.00 0.00 0.00 3.55
854 946 2.438868 TGGAGACGGCGATATGAATG 57.561 50.000 16.62 0.00 0.00 2.67
897 997 1.391933 CCGATCACCTCCCACGATCA 61.392 60.000 0.00 0.00 36.20 2.92
993 1093 0.605319 GACGAGGCACCATGGTTCAA 60.605 55.000 16.84 0.00 0.00 2.69
1073 1221 1.353394 GGAGGGGGATGGGTTACAGG 61.353 65.000 0.00 0.00 0.00 4.00
1090 1238 0.699577 TCAAACAGAAGGGTGGGGGA 60.700 55.000 0.00 0.00 0.00 4.81
1104 1258 6.206600 TCGTGAGATTAACGACTTTCAAAC 57.793 37.500 0.00 0.00 44.58 2.93
1392 1546 8.483758 TCTACTAAATCTTCCAACTTATCCACC 58.516 37.037 0.00 0.00 0.00 4.61
1565 1721 8.457261 TCTCATCATGATCAAGATACATCTACG 58.543 37.037 12.81 0.00 35.76 3.51
1598 1754 3.705051 ACATCATCCCAGTCAAATTGCT 58.295 40.909 0.00 0.00 0.00 3.91
1656 1812 4.333926 GTCTGCATTGGTTTCATAGGACTC 59.666 45.833 0.00 0.00 0.00 3.36
1674 1830 1.742268 GCTTTCTCCTTGATGGTCTGC 59.258 52.381 0.00 0.00 37.07 4.26
1796 1953 4.226427 TGCTCTGCTTCATATCCAAAGT 57.774 40.909 0.00 0.00 0.00 2.66
1854 2035 2.666508 CTGCTCATCTGCATTTGTTTGC 59.333 45.455 0.00 0.00 42.48 3.68
1951 2201 2.836981 CCTCAGGAACATCCTCTTCAGT 59.163 50.000 0.00 0.00 45.66 3.41
2012 2262 5.049129 CCTTCAACATCAGAAAGTTCTCCAC 60.049 44.000 0.00 0.00 34.74 4.02
2258 2508 6.160684 TGTGGATCATGCAAATCTTCTTTTG 58.839 36.000 11.07 0.00 39.16 2.44
2288 2538 1.272147 ACTGGAAGACTTGCCCAATCC 60.272 52.381 4.07 0.00 37.43 3.01
2366 2616 5.263599 TCCTGTCATTGACTGGCATTTTAT 58.736 37.500 28.59 0.00 46.58 1.40
2448 2698 3.441222 TGACCATGCAATTAGTTCTGCTG 59.559 43.478 0.00 0.00 39.38 4.41
2545 2795 7.374975 CCCTGAAGTACTCCAAATATTCCTA 57.625 40.000 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.