Multiple sequence alignment - TraesCS2D01G358200

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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 TraesCS2D01G358200 chr2D 100.000 3365 0 0 1 3365 460363946 460367310 0.000000e+00 6215
1 TraesCS2D01G358200 chr2D 83.248 1176 156 21 1207 2363 460709511 460710664 0.000000e+00 1042
2 TraesCS2D01G358200 chr2D 71.647 850 182 46 1362 2186 621948011 621947196 2.670000e-41 180
3 TraesCS2D01G358200 chr2A 94.063 2577 91 24 1 2527 603374019 603376583 0.000000e+00 3855
4 TraesCS2D01G358200 chr2A 80.582 1375 191 41 1021 2363 603545957 603547287 0.000000e+00 990
5 TraesCS2D01G358200 chr2A 85.266 828 88 23 2516 3313 73275028 73275851 0.000000e+00 822
6 TraesCS2D01G358200 chr2A 90.950 221 18 2 2524 2742 524728193 524728413 2.540000e-76 296
7 TraesCS2D01G358200 chr2B 93.524 2347 80 37 204 2527 541631302 541633599 0.000000e+00 3426
8 TraesCS2D01G358200 chr2B 83.929 1176 148 22 1207 2363 541907061 541908214 0.000000e+00 1086
9 TraesCS2D01G358200 chr2B 89.623 212 6 3 1 208 541630966 541631165 4.310000e-64 255
10 TraesCS2D01G358200 chr1D 90.432 857 64 13 2523 3365 219710467 219711319 0.000000e+00 1112
11 TraesCS2D01G358200 chr1D 89.941 845 74 7 2528 3362 209472664 209473507 0.000000e+00 1079
12 TraesCS2D01G358200 chr5B 89.269 848 79 7 2528 3365 203570666 203569821 0.000000e+00 1051
13 TraesCS2D01G358200 chr5B 85.714 259 29 6 2519 2769 704277546 704277804 1.990000e-67 267
14 TraesCS2D01G358200 chr1A 89.059 850 74 10 2527 3358 445886782 445887630 0.000000e+00 1037
15 TraesCS2D01G358200 chr1A 86.471 850 91 14 2528 3359 374566572 374565729 0.000000e+00 911
16 TraesCS2D01G358200 chr3B 88.534 846 74 14 2529 3365 650021415 650020584 0.000000e+00 1003
17 TraesCS2D01G358200 chr3B 88.438 320 29 8 2519 2834 744516811 744516496 2.450000e-101 379
18 TraesCS2D01G358200 chr1B 87.647 850 81 16 2528 3365 342085732 342084895 0.000000e+00 966
19 TraesCS2D01G358200 chr6A 86.784 855 92 15 2529 3365 352812464 352811613 0.000000e+00 933
20 TraesCS2D01G358200 chr4B 86.449 856 94 16 2528 3365 166648007 166648858 0.000000e+00 918
21 TraesCS2D01G358200 chr3A 89.130 368 34 4 2518 2880 707170538 707170172 1.420000e-123 453
22 TraesCS2D01G358200 chr7D 89.680 281 24 4 2527 2802 430994605 430994325 1.490000e-93 353
23 TraesCS2D01G358200 chr7B 87.984 258 24 5 2520 2771 399795484 399795228 7.060000e-77 298
24 TraesCS2D01G358200 chr7A 86.245 269 30 6 2519 2781 334334311 334334044 5.500000e-73 285
25 TraesCS2D01G358200 chr6B 84.646 254 31 6 2518 2764 659507904 659508156 2.590000e-61 246


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 TraesCS2D01G358200 chr2D 460363946 460367310 3364 False 6215.0 6215 100.0000 1 3365 1 chr2D.!!$F1 3364
1 TraesCS2D01G358200 chr2D 460709511 460710664 1153 False 1042.0 1042 83.2480 1207 2363 1 chr2D.!!$F2 1156
2 TraesCS2D01G358200 chr2A 603374019 603376583 2564 False 3855.0 3855 94.0630 1 2527 1 chr2A.!!$F3 2526
3 TraesCS2D01G358200 chr2A 603545957 603547287 1330 False 990.0 990 80.5820 1021 2363 1 chr2A.!!$F4 1342
4 TraesCS2D01G358200 chr2A 73275028 73275851 823 False 822.0 822 85.2660 2516 3313 1 chr2A.!!$F1 797
5 TraesCS2D01G358200 chr2B 541630966 541633599 2633 False 1840.5 3426 91.5735 1 2527 2 chr2B.!!$F2 2526
6 TraesCS2D01G358200 chr2B 541907061 541908214 1153 False 1086.0 1086 83.9290 1207 2363 1 chr2B.!!$F1 1156
7 TraesCS2D01G358200 chr1D 219710467 219711319 852 False 1112.0 1112 90.4320 2523 3365 1 chr1D.!!$F2 842
8 TraesCS2D01G358200 chr1D 209472664 209473507 843 False 1079.0 1079 89.9410 2528 3362 1 chr1D.!!$F1 834
9 TraesCS2D01G358200 chr5B 203569821 203570666 845 True 1051.0 1051 89.2690 2528 3365 1 chr5B.!!$R1 837
10 TraesCS2D01G358200 chr1A 445886782 445887630 848 False 1037.0 1037 89.0590 2527 3358 1 chr1A.!!$F1 831
11 TraesCS2D01G358200 chr1A 374565729 374566572 843 True 911.0 911 86.4710 2528 3359 1 chr1A.!!$R1 831
12 TraesCS2D01G358200 chr3B 650020584 650021415 831 True 1003.0 1003 88.5340 2529 3365 1 chr3B.!!$R1 836
13 TraesCS2D01G358200 chr1B 342084895 342085732 837 True 966.0 966 87.6470 2528 3365 1 chr1B.!!$R1 837
14 TraesCS2D01G358200 chr6A 352811613 352812464 851 True 933.0 933 86.7840 2529 3365 1 chr6A.!!$R1 836
15 TraesCS2D01G358200 chr4B 166648007 166648858 851 False 918.0 918 86.4490 2528 3365 1 chr4B.!!$F1 837

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
293 468 0.239347 CTTTCAAAGGAGGCACGCAG 59.761 55.000 0.00 0.0 0.00 5.18 F
377 563 1.212935 ACGAGCTTAGGGCCATGATTT 59.787 47.619 6.18 0.0 43.05 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2330 1.058404 GCGACGTGAAGTAGTTGTCC 58.942 55.000 0.00 0.0 0.00 4.02 R
2372 2617 2.746359 GTGCTGACTGCTGGGAGT 59.254 61.111 5.87 0.0 43.37 3.85 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
68 83 5.774102 ACCAAAGTATACTATATGGGGGC 57.226 43.478 24.80 0.00 32.10 5.80
286 461 2.604614 CGCCGTTTTCTTTCAAAGGAGG 60.605 50.000 0.00 0.00 0.00 4.30
290 465 3.372060 GTTTTCTTTCAAAGGAGGCACG 58.628 45.455 0.00 0.00 0.00 5.34
291 466 0.951558 TTCTTTCAAAGGAGGCACGC 59.048 50.000 0.00 0.00 0.00 5.34
293 468 0.239347 CTTTCAAAGGAGGCACGCAG 59.761 55.000 0.00 0.00 0.00 5.18
360 546 5.405873 CGATCACTACAGCTCTATTCTACGA 59.594 44.000 0.00 0.00 0.00 3.43
377 563 1.212935 ACGAGCTTAGGGCCATGATTT 59.787 47.619 6.18 0.00 43.05 2.17
389 575 4.566488 GGGCCATGATTTGATCTACCCTAG 60.566 50.000 4.39 0.00 31.84 3.02
390 576 4.042187 GGCCATGATTTGATCTACCCTAGT 59.958 45.833 0.00 0.00 0.00 2.57
391 577 5.248477 GGCCATGATTTGATCTACCCTAGTA 59.752 44.000 0.00 0.00 0.00 1.82
409 595 2.107178 GTATGAGCGAACTTACGTCCG 58.893 52.381 0.00 0.00 35.59 4.79
458 647 1.213013 CGTGGACTCAAGAGGTCGG 59.787 63.158 1.73 0.00 34.82 4.79
627 820 2.203209 GGGGCCACGGAATAGCAG 60.203 66.667 4.39 0.00 0.00 4.24
637 830 4.142138 CCACGGAATAGCAGGGATATACTC 60.142 50.000 0.00 0.00 0.00 2.59
717 911 5.803470 GCACTAGTCACCCCAAGAGTAAATT 60.803 44.000 0.00 0.00 0.00 1.82
750 944 3.955650 TGTAGGAGTACAGGTTTCAGC 57.044 47.619 0.00 0.00 34.02 4.26
751 945 3.236047 TGTAGGAGTACAGGTTTCAGCA 58.764 45.455 0.00 0.00 34.02 4.41
752 946 3.644265 TGTAGGAGTACAGGTTTCAGCAA 59.356 43.478 0.00 0.00 34.02 3.91
753 947 3.127425 AGGAGTACAGGTTTCAGCAAC 57.873 47.619 0.00 0.00 34.18 4.17
754 948 2.438021 AGGAGTACAGGTTTCAGCAACA 59.562 45.455 0.00 0.00 37.07 3.33
755 949 3.118038 AGGAGTACAGGTTTCAGCAACAA 60.118 43.478 0.00 0.00 37.07 2.83
776 978 3.674997 ACAGCAACAATACCAGTACCAG 58.325 45.455 0.00 0.00 0.00 4.00
777 979 2.420022 CAGCAACAATACCAGTACCAGC 59.580 50.000 0.00 0.00 0.00 4.85
778 980 1.396996 GCAACAATACCAGTACCAGCG 59.603 52.381 0.00 0.00 0.00 5.18
779 981 2.006888 CAACAATACCAGTACCAGCGG 58.993 52.381 0.00 0.00 0.00 5.52
801 1003 1.380650 ATGCATGCACATGGCCAGA 60.381 52.632 25.37 0.00 43.89 3.86
917 1132 2.383527 GCGCTCCGTCTTCACTTGG 61.384 63.158 0.00 0.00 0.00 3.61
918 1133 2.383527 CGCTCCGTCTTCACTTGGC 61.384 63.158 0.00 0.00 0.00 4.52
1431 1658 1.800315 CGCGTCCGTCGACTTCAAT 60.800 57.895 14.70 0.00 42.86 2.57
2103 2330 2.811317 GCCAACCTCACGCTCTCG 60.811 66.667 0.00 0.00 42.43 4.04
2250 2477 2.642171 TCCACAGGACCAAGACCTAT 57.358 50.000 0.00 0.00 35.84 2.57
2313 2555 3.777910 GGCGCCGGTAAGGAGGAA 61.778 66.667 12.58 0.00 45.00 3.36
2372 2617 3.986006 GCACCCGTGAGTCCGTGA 61.986 66.667 0.00 0.00 0.00 4.35
2427 2672 2.413837 GTACACGTGCTGGAAGACAAT 58.586 47.619 17.22 0.00 34.07 2.71
2491 2736 1.334960 CGATGGCTGGTTTGTGTTGAC 60.335 52.381 0.00 0.00 0.00 3.18
2515 2760 5.736486 TTGTTTGCAAATCGTGTGTACTA 57.264 34.783 16.21 0.00 0.00 1.82
2516 2761 5.085636 TGTTTGCAAATCGTGTGTACTAC 57.914 39.130 16.21 0.00 0.00 2.73
2518 2763 5.294799 TGTTTGCAAATCGTGTGTACTACTT 59.705 36.000 16.21 0.00 0.00 2.24
2520 2765 5.994887 TGCAAATCGTGTGTACTACTTTT 57.005 34.783 0.00 0.00 0.00 2.27
2521 2766 5.981174 TGCAAATCGTGTGTACTACTTTTC 58.019 37.500 0.00 0.00 0.00 2.29
2523 2768 6.924612 TGCAAATCGTGTGTACTACTTTTCTA 59.075 34.615 0.00 0.00 0.00 2.10
2524 2769 7.601130 TGCAAATCGTGTGTACTACTTTTCTAT 59.399 33.333 0.00 0.00 0.00 1.98
2525 2770 8.440833 GCAAATCGTGTGTACTACTTTTCTATT 58.559 33.333 0.00 0.00 0.00 1.73
2553 2799 8.622948 AGAAAAATTCCTGTACCTCACTAAAG 57.377 34.615 0.00 0.00 0.00 1.85
2565 2811 2.232941 CTCACTAAAGTTGAGCCGGGTA 59.767 50.000 5.91 0.00 0.00 3.69
2572 2819 2.159382 AGTTGAGCCGGGTAACATTTG 58.841 47.619 5.91 0.00 39.74 2.32
2588 2835 8.331730 GTAACATTTGGTACCACTACTTCAAT 57.668 34.615 16.04 7.01 32.21 2.57
2595 2842 6.446451 TGGTACCACTACTTCAATATACCCT 58.554 40.000 11.60 0.00 31.63 4.34
2706 2954 2.048222 CCAGCTCGCTTTGACCGA 60.048 61.111 0.00 0.00 0.00 4.69
2775 3031 5.407084 GCAAAAACGCCATAACCATTAAACT 59.593 36.000 0.00 0.00 0.00 2.66
3070 3346 0.955178 CTCCGGTGCTCGATCTGTAT 59.045 55.000 0.00 0.00 42.43 2.29
3154 3431 4.272748 GCTTTTGTTCTACTTTCTGACGGT 59.727 41.667 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 83 2.029666 GCATCGATCGACCCCCTG 59.970 66.667 22.06 15.41 0.00 4.45
133 148 2.826702 ACTTCCACCGGCGAAGTT 59.173 55.556 24.76 13.44 46.01 2.66
152 171 2.861935 CGATTTCATTACTAACCGGCGT 59.138 45.455 6.01 0.00 0.00 5.68
202 231 0.460109 CGGCATCATCAACTCCGACA 60.460 55.000 0.00 0.00 42.43 4.35
269 439 3.372060 CGTGCCTCCTTTGAAAGAAAAC 58.628 45.455 6.49 0.00 0.00 2.43
286 461 0.592247 CTGTCAAACCAACTGCGTGC 60.592 55.000 0.00 0.00 0.00 5.34
290 465 1.668751 TCGAACTGTCAAACCAACTGC 59.331 47.619 0.00 0.00 0.00 4.40
291 466 3.194861 TCTCGAACTGTCAAACCAACTG 58.805 45.455 0.00 0.00 0.00 3.16
293 468 4.527564 CATTCTCGAACTGTCAAACCAAC 58.472 43.478 0.00 0.00 0.00 3.77
360 546 3.139770 AGATCAAATCATGGCCCTAAGCT 59.860 43.478 0.00 0.00 43.05 3.74
377 563 4.635699 TCGCTCATACTAGGGTAGATCA 57.364 45.455 0.00 0.00 0.00 2.92
426 615 2.227626 AGTCCACGCTCATCGATCATAG 59.772 50.000 0.00 0.00 41.67 2.23
627 820 3.678056 TGTTGGATGCGAGTATATCCC 57.322 47.619 0.00 0.00 41.75 3.85
637 830 1.001487 TCTTGTTGCTTGTTGGATGCG 60.001 47.619 0.00 0.00 0.00 4.73
717 911 4.931027 ACTCCTACAGTTCTACCTGAGA 57.069 45.455 0.00 0.00 36.30 3.27
750 944 4.305989 ACTGGTATTGTTGCTGTTGTTG 57.694 40.909 0.00 0.00 0.00 3.33
751 945 4.277423 GGTACTGGTATTGTTGCTGTTGTT 59.723 41.667 0.00 0.00 0.00 2.83
752 946 3.818773 GGTACTGGTATTGTTGCTGTTGT 59.181 43.478 0.00 0.00 0.00 3.32
753 947 3.818210 TGGTACTGGTATTGTTGCTGTTG 59.182 43.478 0.00 0.00 0.00 3.33
754 948 4.072131 CTGGTACTGGTATTGTTGCTGTT 58.928 43.478 0.00 0.00 0.00 3.16
755 949 3.674997 CTGGTACTGGTATTGTTGCTGT 58.325 45.455 0.00 0.00 0.00 4.40
949 1164 2.425592 TGGGAACAGTGTGGCTCG 59.574 61.111 0.00 0.00 35.01 5.03
1431 1658 2.034687 GCCTCCAGCTTGAAGCCA 59.965 61.111 14.45 0.00 43.77 4.75
1695 1922 2.202892 GCCTCCACGATCGGGAAC 60.203 66.667 21.38 13.04 33.11 3.62
2103 2330 1.058404 GCGACGTGAAGTAGTTGTCC 58.942 55.000 0.00 0.00 0.00 4.02
2250 2477 2.925706 TAGGTGCTGACGGGGCAA 60.926 61.111 1.13 0.00 41.54 4.52
2372 2617 2.746359 GTGCTGACTGCTGGGAGT 59.254 61.111 5.87 0.00 43.37 3.85
2427 2672 2.672651 CGCACAGCACATTCCCCA 60.673 61.111 0.00 0.00 0.00 4.96
2491 2736 4.975502 AGTACACACGATTTGCAAACAATG 59.024 37.500 15.41 14.47 35.21 2.82
2520 2765 9.449719 GAGGTACAGGAATTTTTCTCAAATAGA 57.550 33.333 0.00 0.00 0.00 1.98
2521 2766 9.231297 TGAGGTACAGGAATTTTTCTCAAATAG 57.769 33.333 0.00 0.00 0.00 1.73
2523 2768 7.725844 AGTGAGGTACAGGAATTTTTCTCAAAT 59.274 33.333 0.00 0.00 32.77 2.32
2524 2769 7.060421 AGTGAGGTACAGGAATTTTTCTCAAA 58.940 34.615 0.00 0.00 32.77 2.69
2525 2770 6.601332 AGTGAGGTACAGGAATTTTTCTCAA 58.399 36.000 0.00 0.00 32.77 3.02
2544 2790 1.002087 ACCCGGCTCAACTTTAGTGAG 59.998 52.381 0.00 0.00 0.00 3.51
2553 2799 1.201414 CCAAATGTTACCCGGCTCAAC 59.799 52.381 0.00 0.00 0.00 3.18
2572 2819 6.990908 AGGGTATATTGAAGTAGTGGTACC 57.009 41.667 4.43 4.43 0.00 3.34
2588 2835 7.297614 AGTATTTGGACCGTAGTTAGGGTATA 58.702 38.462 3.68 0.00 43.84 1.47
2595 2842 4.175516 CGCAAGTATTTGGACCGTAGTTA 58.824 43.478 0.00 0.00 34.79 2.24
2706 2954 0.397254 CCCTAGGATCGACCAGGTGT 60.397 60.000 11.48 0.00 42.04 4.16
2775 3031 2.682494 GTCCGACCAGGTGGGCTA 60.682 66.667 15.96 0.00 42.58 3.93
2802 3058 2.043450 AGGAGAGGGAGACAGCGG 60.043 66.667 0.00 0.00 0.00 5.52
3070 3346 6.155737 AGGAACTCTTTACCGGAGCTAAATTA 59.844 38.462 9.46 0.00 34.46 1.40
3154 3431 0.927767 AAAACCCTACCACCCACACA 59.072 50.000 0.00 0.00 0.00 3.72
3237 3519 5.163814 GCAAACATTACAACAACTGCCAAAA 60.164 36.000 0.00 0.00 0.00 2.44
3238 3520 4.331168 GCAAACATTACAACAACTGCCAAA 59.669 37.500 0.00 0.00 0.00 3.28
3241 3523 3.452474 TGCAAACATTACAACAACTGCC 58.548 40.909 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.