Multiple sequence alignment - TraesCS2D01G478800

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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 TraesCS2D01G478800 chr2D 100.000 3723 0 0 1 3723 579997470 579993748 0.000000e+00 6876.0
1 TraesCS2D01G478800 chr2D 80.000 290 49 3 1311 1599 580007174 580006893 4.870000e-49 206.0
2 TraesCS2D01G478800 chr2B 94.970 2465 96 11 1233 3687 698296461 698294015 0.000000e+00 3840.0
3 TraesCS2D01G478800 chr2B 92.834 935 47 15 1 933 698297923 698297007 0.000000e+00 1338.0
4 TraesCS2D01G478800 chr2B 92.628 312 13 3 925 1235 698296814 698296512 1.230000e-119 440.0
5 TraesCS2D01G478800 chr2B 83.898 236 38 0 1364 1599 698306266 698306031 3.740000e-55 226.0
6 TraesCS2D01G478800 chr2B 82.627 236 39 2 1365 1599 698954509 698954275 1.360000e-49 207.0
7 TraesCS2D01G478800 chr2A 93.313 1645 78 9 1255 2867 717858173 717856529 0.000000e+00 2399.0
8 TraesCS2D01G478800 chr2A 92.428 1215 64 13 29 1235 717859445 717858251 0.000000e+00 1709.0
9 TraesCS2D01G478800 chr2A 93.728 574 32 2 2865 3436 717845128 717844557 0.000000e+00 857.0
10 TraesCS2D01G478800 chr2A 94.922 256 13 0 3432 3687 717838173 717837918 5.790000e-108 401.0
11 TraesCS2D01G478800 chr2A 80.277 289 50 3 1311 1599 717882224 717881943 1.050000e-50 211.0
12 TraesCS2D01G478800 chr5B 83.158 95 14 2 67 160 425871827 425871734 6.630000e-13 86.1
13 TraesCS2D01G478800 chr5B 100.000 28 0 0 134 161 636700185 636700158 7.000000e-03 52.8
14 TraesCS2D01G478800 chr1B 81.720 93 15 2 67 158 396367911 396367820 3.990000e-10 76.8
15 TraesCS2D01G478800 chr7B 100.000 28 0 0 134 161 409503067 409503040 7.000000e-03 52.8
16 TraesCS2D01G478800 chr5D 100.000 28 0 0 134 161 484948058 484948085 7.000000e-03 52.8


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 TraesCS2D01G478800 chr2D 579993748 579997470 3722 True 6876.000000 6876 100.000000 1 3723 1 chr2D.!!$R1 3722
1 TraesCS2D01G478800 chr2B 698294015 698297923 3908 True 1872.666667 3840 93.477333 1 3687 3 chr2B.!!$R3 3686
2 TraesCS2D01G478800 chr2A 717856529 717859445 2916 True 2054.000000 2399 92.870500 29 2867 2 chr2A.!!$R4 2838
3 TraesCS2D01G478800 chr2A 717844557 717845128 571 True 857.000000 857 93.728000 2865 3436 1 chr2A.!!$R2 571

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
979 1181 1.862806 GCAGACAGCCACGAAGAAC 59.137 57.895 0.0 0.0 37.23 3.01 F
1574 1849 0.396435 TCAACCGCACCAGAGACAAT 59.604 50.000 0.0 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2573 1.448540 CAGCGAACTCCTTGGCGAT 60.449 57.895 0.0 0.0 36.29 4.58 R
3186 3492 0.780637 TCCCTATCCTCTCTCGCCAT 59.219 55.000 0.0 0.0 0.00 4.40 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
43 44 9.088512 CATGTAGTTTGTTACAGAGAGGATTAC 57.911 37.037 0.00 0.00 37.01 1.89
108 109 5.542251 AGCTTAATTTTTGGGCCTAAGTGAA 59.458 36.000 4.53 0.00 0.00 3.18
115 117 6.793505 TTTTGGGCCTAAGTGAAGTAAAAA 57.206 33.333 4.53 0.00 0.00 1.94
164 166 3.030291 ACTGGAGATGCTCTTAGACCTG 58.970 50.000 0.00 0.00 0.00 4.00
290 293 9.508642 CTCCAGTTCTTCTACCTATTTTCTTTT 57.491 33.333 0.00 0.00 0.00 2.27
643 648 9.918630 ACATGATTTTTGTCCTTTTCTCTAATG 57.081 29.630 0.00 0.00 0.00 1.90
853 860 7.795734 CGTTTGCTCATTATTCAGTGCTTATAG 59.204 37.037 0.00 0.00 0.00 1.31
979 1181 1.862806 GCAGACAGCCACGAAGAAC 59.137 57.895 0.00 0.00 37.23 3.01
1241 1500 2.932614 CAAGTAAGCAAGATCTCCACCG 59.067 50.000 0.00 0.00 0.00 4.94
1265 1532 2.135933 CCGTCAGCCGATTCCTATTTC 58.864 52.381 0.00 0.00 39.56 2.17
1271 1538 5.049818 GTCAGCCGATTCCTATTTCTCATTG 60.050 44.000 0.00 0.00 0.00 2.82
1274 1541 5.529060 AGCCGATTCCTATTTCTCATTGTTC 59.471 40.000 0.00 0.00 0.00 3.18
1302 1569 1.143277 TCCAAACAGGGCGAGGTTTTA 59.857 47.619 0.00 0.00 35.17 1.52
1309 1581 1.544246 AGGGCGAGGTTTTAATGCAAC 59.456 47.619 0.00 0.00 0.00 4.17
1311 1583 1.198178 GGCGAGGTTTTAATGCAACGA 59.802 47.619 0.00 0.00 0.00 3.85
1357 1629 7.884877 TGGATCACTAAACTGAATCTTGATTGT 59.115 33.333 0.09 0.00 0.00 2.71
1358 1630 8.180267 GGATCACTAAACTGAATCTTGATTGTG 58.820 37.037 0.09 1.92 0.00 3.33
1359 1631 6.902341 TCACTAAACTGAATCTTGATTGTGC 58.098 36.000 0.09 0.00 0.00 4.57
1511 1786 2.165301 GCTGGATGTGTACGGCGTC 61.165 63.158 19.21 9.31 29.03 5.19
1541 1816 1.305930 GGGATTCAGCGGACCACAAC 61.306 60.000 0.00 0.00 0.00 3.32
1574 1849 0.396435 TCAACCGCACCAGAGACAAT 59.604 50.000 0.00 0.00 0.00 2.71
1646 1942 3.259902 CTGATCCATGGCGTATCATCAG 58.740 50.000 19.05 19.05 31.58 2.90
1685 1985 1.533711 GCATGGGATACTGGCAGGT 59.466 57.895 20.34 6.93 0.00 4.00
1733 2033 6.851222 ATTCATAGGTTAATTCGACTGCAG 57.149 37.500 13.48 13.48 0.00 4.41
1752 2052 6.261826 ACTGCAGTTATCCAAATTCTATGAGC 59.738 38.462 15.25 0.00 0.00 4.26
1753 2053 5.532406 TGCAGTTATCCAAATTCTATGAGCC 59.468 40.000 0.00 0.00 0.00 4.70
1915 2217 7.663081 CCTAGTAACTGATTTATCCATGCACAT 59.337 37.037 0.00 0.00 0.00 3.21
1964 2266 7.201812 GCAAGGGTTTGAGGATTTGAAAATTTT 60.202 33.333 2.28 2.28 36.36 1.82
2007 2309 4.082523 AGACCGGCACACATCCCG 62.083 66.667 0.00 0.00 43.97 5.14
2073 2375 6.560253 TCCAAGCTTTGTTCTCTTATTGAC 57.440 37.500 0.00 0.00 0.00 3.18
2077 2379 7.365741 CAAGCTTTGTTCTCTTATTGACATGT 58.634 34.615 0.00 0.00 0.00 3.21
2082 2384 3.281727 TCTCTTATTGACATGTGGCCC 57.718 47.619 1.15 0.00 0.00 5.80
2169 2471 1.674817 CGCCATCGTGAAAGTTAGGGT 60.675 52.381 0.00 0.00 0.00 4.34
2173 2475 3.818773 CCATCGTGAAAGTTAGGGTTGTT 59.181 43.478 0.00 0.00 0.00 2.83
2324 2626 3.550431 AGCTGAGCACGGTGGTGT 61.550 61.111 18.66 0.00 46.13 4.16
2413 2715 1.068588 CCCACACGATATCATGGACGT 59.931 52.381 15.91 0.00 39.53 4.34
2421 2723 2.665649 TATCATGGACGTTTCGCTGT 57.334 45.000 0.00 0.00 0.00 4.40
2551 2853 2.028385 GGTGGAAGAAAACGGAGAGCTA 60.028 50.000 0.00 0.00 0.00 3.32
2750 3052 0.558712 AGTGGGTTTGTTTGGGCCTA 59.441 50.000 4.53 0.00 0.00 3.93
2941 3245 3.671008 ATATAATGGCGGCTCGTAACA 57.329 42.857 11.43 0.00 0.00 2.41
3118 3424 4.195334 CCATCCCCGGAAGCCCTG 62.195 72.222 0.73 0.00 0.00 4.45
3185 3491 0.320247 CACCTCTGTCTGCCACACTC 60.320 60.000 0.00 0.00 0.00 3.51
3186 3492 0.760567 ACCTCTGTCTGCCACACTCA 60.761 55.000 0.00 0.00 0.00 3.41
3253 3559 5.244178 AGAGTTTCATTCCTCGACAGTAGTT 59.756 40.000 0.00 0.00 32.88 2.24
3258 3564 3.678056 TTCCTCGACAGTAGTTGCATT 57.322 42.857 0.00 0.00 0.00 3.56
3304 3612 0.038159 CGACTCTTGGTCCACCTCAC 60.038 60.000 0.00 0.00 41.64 3.51
3462 3770 1.950973 GACTCCTTCTCCGACCAGCC 61.951 65.000 0.00 0.00 0.00 4.85
3464 3772 1.671901 CTCCTTCTCCGACCAGCCTC 61.672 65.000 0.00 0.00 0.00 4.70
3496 3804 4.678309 CGAGGAGTTTGAGGTTATGTCTCC 60.678 50.000 0.00 0.00 39.88 3.71
3547 3855 2.756760 GTCCAACCCACTACATCGTCTA 59.243 50.000 0.00 0.00 0.00 2.59
3548 3856 2.756760 TCCAACCCACTACATCGTCTAC 59.243 50.000 0.00 0.00 0.00 2.59
3579 3887 4.602995 GACGACAGTCTGTCTTCCATATC 58.397 47.826 26.46 11.25 44.85 1.63
3588 3896 5.852229 GTCTGTCTTCCATATCGTTATCGTC 59.148 44.000 0.00 0.00 38.33 4.20
3609 3917 2.292016 CGACATCTTCTAGCTCCGACAT 59.708 50.000 0.00 0.00 0.00 3.06
3616 3924 2.447443 TCTAGCTCCGACATGTGACTT 58.553 47.619 1.15 0.00 0.00 3.01
3671 3979 3.444034 TCGATGGTGTTTCAGAGGTCTAG 59.556 47.826 0.00 0.00 0.00 2.43
3687 3995 3.182967 GTCTAGAGACGGCATCAAGTTG 58.817 50.000 0.00 0.00 35.12 3.16
3688 3996 2.166459 TCTAGAGACGGCATCAAGTTGG 59.834 50.000 2.34 0.00 0.00 3.77
3689 3997 0.687354 AGAGACGGCATCAAGTTGGT 59.313 50.000 2.34 0.00 0.00 3.67
3690 3998 1.079503 GAGACGGCATCAAGTTGGTC 58.920 55.000 2.34 2.20 0.00 4.02
3691 3999 0.670546 AGACGGCATCAAGTTGGTCG 60.671 55.000 2.34 3.77 0.00 4.79
3692 4000 0.669318 GACGGCATCAAGTTGGTCGA 60.669 55.000 12.17 0.00 0.00 4.20
3693 4001 0.949105 ACGGCATCAAGTTGGTCGAC 60.949 55.000 7.13 7.13 0.00 4.20
3694 4002 0.670546 CGGCATCAAGTTGGTCGACT 60.671 55.000 16.46 0.00 0.00 4.18
3695 4003 1.523758 GGCATCAAGTTGGTCGACTT 58.476 50.000 16.46 0.00 40.37 3.01
3696 4004 1.880027 GGCATCAAGTTGGTCGACTTT 59.120 47.619 16.46 2.61 37.76 2.66
3697 4005 2.293399 GGCATCAAGTTGGTCGACTTTT 59.707 45.455 16.46 2.25 37.76 2.27
3698 4006 3.243401 GGCATCAAGTTGGTCGACTTTTT 60.243 43.478 16.46 2.61 37.76 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.247567 ACTACATGCAAGGTGCCAAC 58.752 50.000 4.76 0.00 44.23 3.77
21 22 6.155737 GGGGTAATCCTCTCTGTAACAAACTA 59.844 42.308 0.00 0.00 35.33 2.24
23 24 5.045797 AGGGGTAATCCTCTCTGTAACAAAC 60.046 44.000 0.00 0.00 41.44 2.93
79 80 5.503634 AGGCCCAAAAATTAAGCTTCAAT 57.496 34.783 0.00 0.00 0.00 2.57
164 166 8.561212 CACACTACTACTCATGATCTAACCTAC 58.439 40.741 0.00 0.00 0.00 3.18
538 543 7.591057 TGACGCAATTTAAAGAAATTCTCACAG 59.409 33.333 0.00 0.00 42.22 3.66
577 582 6.814146 TGTTCACCAATTTTTAAAAACGCTCT 59.186 30.769 15.35 0.00 0.00 4.09
718 724 2.813474 GCCGTGCGCTGTACATGA 60.813 61.111 9.73 0.00 0.00 3.07
741 747 5.413523 GCGACCCCTCAAAAATAAAAGAGTA 59.586 40.000 0.00 0.00 0.00 2.59
750 756 3.009143 AGAGTAAGCGACCCCTCAAAAAT 59.991 43.478 0.00 0.00 0.00 1.82
853 860 0.456628 GAGTCCTCCTACTCAACGCC 59.543 60.000 0.00 0.00 44.41 5.68
996 1198 1.766143 GCTCCGTGCGGTTCATCATC 61.766 60.000 10.60 0.00 36.47 2.92
997 1199 1.815421 GCTCCGTGCGGTTCATCAT 60.815 57.895 10.60 0.00 36.47 2.45
998 1200 2.434185 GCTCCGTGCGGTTCATCA 60.434 61.111 10.60 0.00 36.47 3.07
1023 1225 3.068691 CCTCGGTTCTCCCTCGCA 61.069 66.667 0.00 0.00 0.00 5.10
1241 1500 1.814169 GGAATCGGCTGACGGGAAC 60.814 63.158 1.72 0.00 44.45 3.62
1265 1532 3.266510 TGGAATCGGAGGAACAATGAG 57.733 47.619 0.00 0.00 0.00 2.90
1271 1538 2.084546 CCTGTTTGGAATCGGAGGAAC 58.915 52.381 0.00 0.00 38.35 3.62
1274 1541 1.032114 GCCCTGTTTGGAATCGGAGG 61.032 60.000 0.00 0.00 38.35 4.30
1541 1816 0.955919 GGTTGAAGAGGAGGTTGCGG 60.956 60.000 0.00 0.00 0.00 5.69
1574 1849 2.280797 GCGGTGAGTGTCTGGCAA 60.281 61.111 0.00 0.00 0.00 4.52
1685 1985 2.560542 ACAGCGAAACCATGCCATAAAA 59.439 40.909 0.00 0.00 0.00 1.52
1733 2033 6.767902 TGACAGGCTCATAGAATTTGGATAAC 59.232 38.462 0.00 0.00 0.00 1.89
1826 2126 3.557577 TCCATTCTTCATGTTTGCACG 57.442 42.857 0.00 0.00 0.00 5.34
1915 2217 3.006003 TGGTTGTGCGTGTAGTCTAATGA 59.994 43.478 0.00 0.00 0.00 2.57
2007 2309 4.758561 CAAAGTTGTGCTACAGTACGAAC 58.241 43.478 0.00 0.00 33.15 3.95
2073 2375 7.393841 AAAATTGATTAAATTGGGCCACATG 57.606 32.000 5.23 0.00 38.52 3.21
2077 2379 6.131972 TGGAAAATTGATTAAATTGGGCCA 57.868 33.333 0.00 0.00 38.52 5.36
2173 2475 9.554395 TTCACTTTTAGTTCAACATCATAGTCA 57.446 29.630 0.00 0.00 0.00 3.41
2271 2573 1.448540 CAGCGAACTCCTTGGCGAT 60.449 57.895 0.00 0.00 36.29 4.58
2291 2593 2.827921 TCAGCTGAGAAGAGCATGTGTA 59.172 45.455 13.74 0.00 41.83 2.90
2398 2700 2.124903 GCGAAACGTCCATGATATCGT 58.875 47.619 0.00 0.00 38.15 3.73
2421 2723 2.499693 TCATCAAGGTTGGAGATACGCA 59.500 45.455 0.00 0.00 0.00 5.24
2551 2853 1.545582 CATGCGTCCACCAAAATCCTT 59.454 47.619 0.00 0.00 0.00 3.36
2798 3100 9.764363 GTTATGAGTGACACATAAGATAATCCA 57.236 33.333 14.28 0.00 39.71 3.41
2810 3112 9.136323 ACTATGATATGAGTTATGAGTGACACA 57.864 33.333 8.59 0.00 0.00 3.72
2915 3219 5.847111 ACGAGCCGCCATTATATAATCTA 57.153 39.130 4.93 0.00 0.00 1.98
2930 3234 2.961522 AAAATGTGTGTTACGAGCCG 57.038 45.000 0.00 0.00 0.00 5.52
3144 3450 1.003839 GGACACATGGCCTTGTCGA 60.004 57.895 20.81 0.00 42.67 4.20
3185 3491 0.894141 CCCTATCCTCTCTCGCCATG 59.106 60.000 0.00 0.00 0.00 3.66
3186 3492 0.780637 TCCCTATCCTCTCTCGCCAT 59.219 55.000 0.00 0.00 0.00 4.40
3304 3612 1.152963 CCTTCCCCTACAATGCCGG 60.153 63.158 0.00 0.00 0.00 6.13
3547 3855 1.202952 AGACTGTCGTCCCAGAGAAGT 60.203 52.381 1.52 0.00 41.16 3.01
3548 3856 1.201181 CAGACTGTCGTCCCAGAGAAG 59.799 57.143 1.52 0.00 41.16 2.85
3576 3884 5.919272 AGAAGATGTCGACGATAACGATA 57.081 39.130 11.62 0.00 41.62 2.92
3579 3887 3.901290 GCTAGAAGATGTCGACGATAACG 59.099 47.826 11.62 0.00 45.75 3.18
3588 3896 1.671328 TGTCGGAGCTAGAAGATGTCG 59.329 52.381 0.00 0.00 0.00 4.35
3609 3917 2.425592 CAGCGGTGGGAAGTCACA 59.574 61.111 6.74 0.00 39.27 3.58
3616 3924 4.980805 GTTGACGCAGCGGTGGGA 62.981 66.667 34.24 13.44 39.89 4.37
3671 3979 1.079503 GACCAACTTGATGCCGTCTC 58.920 55.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.