Multiple sequence alignment - TraesCS2D01G257800

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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 TraesCS2D01G257800 chr2D 100.000 2579 0 0 1 2579 313812614 313810036 0.000000e+00 4763
1 TraesCS2D01G257800 chr2D 97.598 666 16 0 1 666 642831424 642830759 0.000000e+00 1142
2 TraesCS2D01G257800 chr2D 85.424 590 74 9 1000 1589 313714789 313714212 1.020000e-168 603
3 TraesCS2D01G257800 chr2A 92.291 1816 78 21 677 2441 422785213 422783409 0.000000e+00 2521
4 TraesCS2D01G257800 chr2A 84.875 562 79 4 1031 1592 423176418 423176973 1.730000e-156 562
5 TraesCS2D01G257800 chr2A 94.595 111 6 0 2469 2579 422783411 422783301 3.410000e-39 172
6 TraesCS2D01G257800 chr2B 92.178 1419 56 16 677 2059 381520699 381519300 0.000000e+00 1954
7 TraesCS2D01G257800 chr2B 91.483 681 54 3 2 679 493649017 493649696 0.000000e+00 933
8 TraesCS2D01G257800 chr2B 82.828 594 88 11 1000 1592 381317147 381316567 1.060000e-143 520
9 TraesCS2D01G257800 chr2B 95.604 273 7 2 2307 2579 381518865 381518598 1.420000e-117 433
10 TraesCS2D01G257800 chr2B 94.194 155 9 0 2147 2301 381519183 381519029 1.190000e-58 237
11 TraesCS2D01G257800 chr7D 98.198 666 12 0 1 666 20246171 20246836 0.000000e+00 1164
12 TraesCS2D01G257800 chr6D 97.504 681 13 2 1 677 230191627 230190947 0.000000e+00 1160
13 TraesCS2D01G257800 chr5B 87.040 679 82 4 2 678 435595547 435596221 0.000000e+00 761
14 TraesCS2D01G257800 chr7B 85.839 685 87 7 2 678 20575937 20575255 0.000000e+00 719
15 TraesCS2D01G257800 chr6B 85.607 667 93 3 2 667 90290770 90291434 0.000000e+00 697
16 TraesCS2D01G257800 chr3A 85.180 668 93 5 2 666 730906263 730905599 0.000000e+00 680
17 TraesCS2D01G257800 chr1A 85.030 668 94 5 2 666 567481376 567480712 0.000000e+00 675


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 TraesCS2D01G257800 chr2D 313810036 313812614 2578 True 4763.000000 4763 100.000 1 2579 1 chr2D.!!$R2 2578
1 TraesCS2D01G257800 chr2D 642830759 642831424 665 True 1142.000000 1142 97.598 1 666 1 chr2D.!!$R3 665
2 TraesCS2D01G257800 chr2D 313714212 313714789 577 True 603.000000 603 85.424 1000 1589 1 chr2D.!!$R1 589
3 TraesCS2D01G257800 chr2A 422783301 422785213 1912 True 1346.500000 2521 93.443 677 2579 2 chr2A.!!$R1 1902
4 TraesCS2D01G257800 chr2A 423176418 423176973 555 False 562.000000 562 84.875 1031 1592 1 chr2A.!!$F1 561
5 TraesCS2D01G257800 chr2B 493649017 493649696 679 False 933.000000 933 91.483 2 679 1 chr2B.!!$F1 677
6 TraesCS2D01G257800 chr2B 381518598 381520699 2101 True 874.666667 1954 93.992 677 2579 3 chr2B.!!$R2 1902
7 TraesCS2D01G257800 chr2B 381316567 381317147 580 True 520.000000 520 82.828 1000 1592 1 chr2B.!!$R1 592
8 TraesCS2D01G257800 chr7D 20246171 20246836 665 False 1164.000000 1164 98.198 1 666 1 chr7D.!!$F1 665
9 TraesCS2D01G257800 chr6D 230190947 230191627 680 True 1160.000000 1160 97.504 1 677 1 chr6D.!!$R1 676
10 TraesCS2D01G257800 chr5B 435595547 435596221 674 False 761.000000 761 87.040 2 678 1 chr5B.!!$F1 676
11 TraesCS2D01G257800 chr7B 20575255 20575937 682 True 719.000000 719 85.839 2 678 1 chr7B.!!$R1 676
12 TraesCS2D01G257800 chr6B 90290770 90291434 664 False 697.000000 697 85.607 2 667 1 chr6B.!!$F1 665
13 TraesCS2D01G257800 chr3A 730905599 730906263 664 True 680.000000 680 85.180 2 666 1 chr3A.!!$R1 664
14 TraesCS2D01G257800 chr1A 567480712 567481376 664 True 675.000000 675 85.030 2 666 1 chr1A.!!$R1 664

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
484 489 0.179238 GAAGACGCTGCTTTCTTCGC 60.179 55.0 18.98 5.09 38.69 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 2296 0.040781 TTGAACTAAAAGCGCCGTGC 60.041 50.0 2.29 0.0 46.98 5.34 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
115 116 3.071671 TGGAGAGCTGTCCATGACA 57.928 52.632 27.86 5.59 41.99 3.58
164 169 1.682854 CAAGCAAAAGTGGAAGCCTCA 59.317 47.619 0.00 0.00 0.00 3.86
484 489 0.179238 GAAGACGCTGCTTTCTTCGC 60.179 55.000 18.98 5.09 38.69 4.70
549 554 4.033990 TGTCGCTCATAGACTTGCTAAG 57.966 45.455 0.00 0.00 39.24 2.18
668 676 8.363390 TGATTAAATAAATGCGGCAATATTCCA 58.637 29.630 18.67 13.44 0.00 3.53
832 850 2.581726 CTTCTCCCTCCTCGCCTCCT 62.582 65.000 0.00 0.00 0.00 3.69
833 851 2.520741 CTCCCTCCTCGCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
834 852 4.144727 TCCCTCCTCGCCTCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
835 853 4.150454 CCCTCCTCGCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
836 854 2.769120 CCCTCCTCGCCTCCTCCTA 61.769 68.421 0.00 0.00 0.00 2.94
858 876 2.180276 CCTATATAACCAGCGCTCCCT 58.820 52.381 7.13 0.00 0.00 4.20
890 920 1.537776 CCATCGCCATCTCAGTCTCAC 60.538 57.143 0.00 0.00 0.00 3.51
931 981 1.535028 CCAGCAGCAACGACAACAATA 59.465 47.619 0.00 0.00 0.00 1.90
1377 1434 3.276846 GCCAACACCAACGCGTCT 61.277 61.111 14.44 0.00 0.00 4.18
1477 1534 2.967397 CCTACAAGACCGTGCCGA 59.033 61.111 0.00 0.00 0.00 5.54
1682 1752 1.072505 GGAACCAGCGGGAACAGAA 59.927 57.895 10.86 0.00 38.05 3.02
1698 1768 2.158608 ACAGAACAAGGAAGGTGGGAAG 60.159 50.000 0.00 0.00 0.00 3.46
1779 1849 1.115930 ATATCGGACGGAGGCTGCTT 61.116 55.000 4.02 0.00 0.00 3.91
1818 1888 3.188048 GCGGAAGATGAAGATGGCATAAG 59.812 47.826 0.00 0.00 0.00 1.73
1895 1965 5.901884 GCATGTGTATATTTCGTAGCAACAC 59.098 40.000 0.00 0.00 37.00 3.32
1957 2028 6.202188 ACGAAGTATGGAGGCAAATATAAACG 59.798 38.462 0.00 0.00 41.94 3.60
2093 2246 8.260270 ACTACTACTTACATTTTTAAAGCGGG 57.740 34.615 0.00 0.00 0.00 6.13
2134 2296 7.490962 TCAATAATTAAGGGCTTCATGTACG 57.509 36.000 0.00 0.00 0.00 3.67
2151 2313 4.434876 GCACGGCGCTTTTAGTTC 57.565 55.556 6.90 0.00 37.77 3.01
2194 2356 3.593794 GGACTACTCCGCGCCGAT 61.594 66.667 0.00 0.00 0.00 4.18
2243 2406 3.037833 CGTTGCTGCGCAGACTGA 61.038 61.111 40.21 18.80 40.61 3.41
2286 2456 1.000827 TGTAGTTTAAACCCGCGACGA 60.001 47.619 14.72 0.00 0.00 4.20
2304 2632 4.270102 GACGACTCGTGTATACTTACTGC 58.730 47.826 9.27 0.00 41.37 4.40
2305 2633 3.686241 ACGACTCGTGTATACTTACTGCA 59.314 43.478 2.53 0.00 39.18 4.41
2314 2642 1.339235 TACTTACTGCAACGCGTCGC 61.339 55.000 16.77 16.77 0.00 5.19
2482 2810 2.819595 CATTGTAGGCTGCGGCGT 60.820 61.111 18.01 18.01 39.81 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 1.073199 CTCTCGGGGGCTTGTTGTT 59.927 57.895 0.00 0.00 0.00 2.83
164 169 1.354705 GTTTAAGCCACCCCTCCTCTT 59.645 52.381 0.00 0.00 0.00 2.85
472 477 1.059835 GCTAACGAGCGAAGAAAGCAG 59.940 52.381 0.00 0.00 39.39 4.24
484 489 3.305398 AGTGACTTTGGAGCTAACGAG 57.695 47.619 0.00 0.00 0.00 4.18
549 554 5.743422 GCAAAGTTCATCTCCTACCCCTATC 60.743 48.000 0.00 0.00 0.00 2.08
832 850 4.868268 AGCGCTGGTTATATAGGATAGGA 58.132 43.478 10.39 0.00 0.00 2.94
833 851 4.038162 GGAGCGCTGGTTATATAGGATAGG 59.962 50.000 18.48 0.00 0.00 2.57
834 852 4.038162 GGGAGCGCTGGTTATATAGGATAG 59.962 50.000 18.48 0.00 0.00 2.08
835 853 3.958798 GGGAGCGCTGGTTATATAGGATA 59.041 47.826 18.48 0.00 0.00 2.59
836 854 2.766828 GGGAGCGCTGGTTATATAGGAT 59.233 50.000 18.48 0.00 0.00 3.24
858 876 2.367202 GCGATGGAGTTGGGGGAGA 61.367 63.158 0.00 0.00 0.00 3.71
890 920 2.370189 GAGTATGTGAGGGGAGGAATGG 59.630 54.545 0.00 0.00 0.00 3.16
931 981 7.328493 CGTTGTGAACCGTATGTATGATATGAT 59.672 37.037 0.00 0.00 0.00 2.45
972 1029 5.172591 CGCGACGTGTTAGTGTATATTTGAT 59.827 40.000 0.00 0.00 0.00 2.57
1199 1256 1.993391 GGACCCTCGAACCCCATCA 60.993 63.158 0.00 0.00 0.00 3.07
1257 1314 1.751924 GGGAGCACGAAGTAGATCTGT 59.248 52.381 5.18 0.00 41.61 3.41
1477 1534 1.592223 GCCTCTTCACTACCAGCGT 59.408 57.895 0.00 0.00 0.00 5.07
1682 1752 1.518367 TCACTTCCCACCTTCCTTGT 58.482 50.000 0.00 0.00 0.00 3.16
1698 1768 2.821366 CCAGGCTGGCGACATCAC 60.821 66.667 22.68 0.00 41.51 3.06
1779 1849 2.979676 CGCCAAGCCACTGAAGCA 60.980 61.111 0.00 0.00 0.00 3.91
1818 1888 3.340789 AAAAACTCTGCGCCGACC 58.659 55.556 4.18 0.00 0.00 4.79
1895 1965 5.801444 TGCTCAACTAATGCGATCAAAATTG 59.199 36.000 0.00 0.00 0.00 2.32
1957 2028 9.654663 AATTCAGTAGTCTAGTTTATGTTCACC 57.345 33.333 0.00 0.00 0.00 4.02
1974 2045 5.313623 CACGTTTAGGCGAAAATTCAGTAG 58.686 41.667 0.00 0.00 35.59 2.57
2073 2144 7.684937 TTAGCCCGCTTTAAAAATGTAAGTA 57.315 32.000 0.00 0.00 0.00 2.24
2074 2145 6.578163 TTAGCCCGCTTTAAAAATGTAAGT 57.422 33.333 0.00 0.00 0.00 2.24
2075 2146 6.864165 TGTTTAGCCCGCTTTAAAAATGTAAG 59.136 34.615 0.00 0.00 0.00 2.34
2076 2147 6.746120 TGTTTAGCCCGCTTTAAAAATGTAA 58.254 32.000 0.00 0.00 0.00 2.41
2112 2274 5.825679 TGCGTACATGAAGCCCTTAATTATT 59.174 36.000 0.00 0.00 0.00 1.40
2115 2277 3.377172 GTGCGTACATGAAGCCCTTAATT 59.623 43.478 0.00 0.00 0.00 1.40
2134 2296 0.040781 TTGAACTAAAAGCGCCGTGC 60.041 50.000 2.29 0.00 46.98 5.34
2151 2313 4.488126 TGTCTTTTTCGAGCCTCATTTG 57.512 40.909 0.00 0.00 0.00 2.32
2194 2356 3.130633 CAGATCGAACACAGAAACACCA 58.869 45.455 0.00 0.00 0.00 4.17
2286 2456 4.409570 CGTTGCAGTAAGTATACACGAGT 58.590 43.478 5.50 0.00 32.50 4.18
2314 2642 3.591196 TTGCCCTCATTTCAAATTCCG 57.409 42.857 0.00 0.00 0.00 4.30
2349 2677 3.551454 CCACAAACTTTGCTCTCCATGTG 60.551 47.826 1.14 0.00 37.31 3.21
2358 2686 1.226945 GCGCACCACAAACTTTGCT 60.227 52.632 0.30 0.00 32.56 3.91
2443 2771 8.822855 CAATGCCAGTACAAGAAAATACGTATA 58.177 33.333 8.83 0.00 0.00 1.47
2444 2772 7.335924 ACAATGCCAGTACAAGAAAATACGTAT 59.664 33.333 1.14 1.14 0.00 3.06
2445 2773 6.651643 ACAATGCCAGTACAAGAAAATACGTA 59.348 34.615 0.00 0.00 0.00 3.57
2446 2774 5.472137 ACAATGCCAGTACAAGAAAATACGT 59.528 36.000 0.00 0.00 0.00 3.57
2447 2775 5.938322 ACAATGCCAGTACAAGAAAATACG 58.062 37.500 0.00 0.00 0.00 3.06
2448 2776 7.472543 CCTACAATGCCAGTACAAGAAAATAC 58.527 38.462 0.00 0.00 0.00 1.89
2457 2785 1.678728 GCAGCCTACAATGCCAGTACA 60.679 52.381 0.00 0.00 36.41 2.90
2482 2810 3.133464 GCAAGCGCATGGCCTGTA 61.133 61.111 15.22 0.00 45.17 2.74


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

AutoCloner maintained by Alex Coulton.