Multiple sequence alignment - TraesCS1A01G255900

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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 TraesCS1A01G255900 chr1A 100.000 3887 0 0 1 3887 448630233 448626347 0.000000e+00 7179.0
1 TraesCS1A01G255900 chr1A 80.788 203 29 6 3140 3334 251339806 251339606 2.420000e-32 150.0
2 TraesCS1A01G255900 chr1B 97.176 2550 58 6 921 3461 469161755 469159211 0.000000e+00 4298.0
3 TraesCS1A01G255900 chr1B 93.167 922 30 5 1 920 469162708 469161818 0.000000e+00 1323.0
4 TraesCS1A01G255900 chr1B 87.059 340 22 9 3551 3887 469159178 469158858 7.940000e-97 364.0
5 TraesCS1A01G255900 chr1B 83.756 197 26 3 3144 3334 242744399 242744595 8.580000e-42 182.0
6 TraesCS1A01G255900 chr1D 98.549 2274 31 1 922 3195 347786962 347784691 0.000000e+00 4015.0
7 TraesCS1A01G255900 chr1D 94.888 939 26 3 1 920 347787964 347787029 0.000000e+00 1448.0
8 TraesCS1A01G255900 chr1D 88.889 612 44 12 3280 3887 347784660 347784069 0.000000e+00 732.0
9 TraesCS1A01G255900 chr1D 97.368 38 1 0 3450 3487 86782889 86782852 9.010000e-07 65.8
10 TraesCS1A01G255900 chr6A 83.902 205 25 6 3137 3334 607089371 607089168 5.130000e-44 189.0
11 TraesCS1A01G255900 chr6A 83.902 205 25 6 3137 3334 607224557 607224354 5.130000e-44 189.0
12 TraesCS1A01G255900 chr7B 84.264 197 24 6 3144 3334 576660241 576660046 6.630000e-43 185.0
13 TraesCS1A01G255900 chr3B 83.744 203 23 10 3153 3350 12179333 12179136 2.390000e-42 183.0
14 TraesCS1A01G255900 chr3A 82.843 204 29 3 3137 3334 308203602 308203805 1.110000e-40 178.0
15 TraesCS1A01G255900 chr6D 82.075 212 31 2 3144 3349 454270591 454270801 1.440000e-39 174.0
16 TraesCS1A01G255900 chr4B 81.034 232 30 8 3111 3334 640023701 640023476 5.160000e-39 172.0
17 TraesCS1A01G255900 chr4B 82.090 201 30 3 3138 3332 22628008 22628208 2.400000e-37 167.0
18 TraesCS1A01G255900 chrUn 81.095 201 32 4 3140 3334 82426763 82426563 5.200000e-34 156.0
19 TraesCS1A01G255900 chrUn 85.915 71 7 3 3459 3527 17300712 17300781 5.390000e-09 73.1
20 TraesCS1A01G255900 chr6B 82.105 190 27 5 3151 3334 286910801 286910989 5.200000e-34 156.0
21 TraesCS1A01G255900 chr7D 87.500 104 11 2 3424 3526 230491088 230490986 6.820000e-23 119.0
22 TraesCS1A01G255900 chr7D 96.610 59 1 1 3137 3195 60368108 60368165 3.200000e-16 97.1
23 TraesCS1A01G255900 chr7D 82.105 95 14 3 3466 3559 617232581 617232489 1.160000e-10 78.7
24 TraesCS1A01G255900 chr7A 85.714 84 12 0 3443 3526 62482669 62482586 5.350000e-14 89.8
25 TraesCS1A01G255900 chr5D 91.935 62 4 1 3465 3526 552700134 552700194 6.920000e-13 86.1
26 TraesCS1A01G255900 chr5D 90.698 43 4 0 3459 3501 542630448 542630490 1.510000e-04 58.4
27 TraesCS1A01G255900 chr4A 87.037 54 6 1 3449 3502 29156611 29156663 4.190000e-05 60.2
28 TraesCS1A01G255900 chr5A 96.875 32 1 0 3594 3625 1813313 1813344 2.000000e-03 54.7
29 TraesCS1A01G255900 chr4D 100.000 29 0 0 3449 3477 405765269 405765241 2.000000e-03 54.7
30 TraesCS1A01G255900 chr2D 96.875 32 1 0 3594 3625 634064354 634064385 2.000000e-03 54.7


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 TraesCS1A01G255900 chr1A 448626347 448630233 3886 True 7179 7179 100.000000 1 3887 1 chr1A.!!$R2 3886
1 TraesCS1A01G255900 chr1B 469158858 469162708 3850 True 1995 4298 92.467333 1 3887 3 chr1B.!!$R1 3886
2 TraesCS1A01G255900 chr1D 347784069 347787964 3895 True 2065 4015 94.108667 1 3887 3 chr1D.!!$R2 3886

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
122 123 0.384309 TCGCTAGTGGCTTATCGTGG 59.616 55.000 2.90 0.00 39.13 4.94 F
773 794 1.288932 ACTGGGCCAAATGCTAGGATT 59.711 47.619 8.04 3.24 40.92 3.01 F
2559 2649 0.041238 ATGGGACGTTCAGAGGAGGA 59.959 55.000 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1992 0.991146 TCATTTGCTGAGGCCCTACA 59.009 50.0 0.00 0.0 37.74 2.74 R
2694 2784 0.250467 ACCATGTGTCAGACAGCCAC 60.250 55.0 2.53 0.0 38.23 5.01 R
3530 3629 0.179113 AGGCAAACAAGCAAACCACG 60.179 50.0 0.00 0.0 35.83 4.94 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
110 111 4.567159 GCAACTTAGTATGCTTTCGCTAGT 59.433 41.667 10.62 0.00 39.46 2.57
120 121 2.810650 CTTTCGCTAGTGGCTTATCGT 58.189 47.619 2.90 0.00 39.13 3.73
122 123 0.384309 TCGCTAGTGGCTTATCGTGG 59.616 55.000 2.90 0.00 39.13 4.94
169 170 8.361139 AGCTGTAATATAGACGCTAGTGAATTT 58.639 33.333 10.99 0.00 0.00 1.82
204 205 1.600916 GACGCTTGGGTCAGCCTTT 60.601 57.895 12.02 0.00 36.31 3.11
378 379 8.885722 CATGCCTAATGAAAAATAAGCAACAAT 58.114 29.630 0.00 0.00 38.72 2.71
408 410 8.225603 AGGAAGTAATGCAACTGTAAATATGG 57.774 34.615 0.00 0.00 0.00 2.74
486 506 5.416639 TGATGAGCTGCATTAGTTTTCATGT 59.583 36.000 1.02 0.00 37.34 3.21
773 794 1.288932 ACTGGGCCAAATGCTAGGATT 59.711 47.619 8.04 3.24 40.92 3.01
780 801 5.316987 GGCCAAATGCTAGGATTGTAGTAT 58.683 41.667 10.53 0.00 40.92 2.12
827 848 9.350357 CAACTTATGTTCCATTGAAAATCTCAG 57.650 33.333 0.00 0.00 32.55 3.35
843 864 3.772387 TCTCAGACTCCACTCATTGTCT 58.228 45.455 0.00 0.00 39.98 3.41
858 879 4.840680 TCATTGTCTACCAGGCATATAGCT 59.159 41.667 0.00 0.00 44.79 3.32
1302 1389 5.186021 TGGAGAGTCAGAAGATACAAAGGAC 59.814 44.000 0.00 0.00 0.00 3.85
1416 1503 2.811542 AAAGGCAGAAGGAGAGGCGC 62.812 60.000 0.00 0.00 0.00 6.53
1801 1888 2.309613 AGCAAGAATCAGCAACAACCA 58.690 42.857 0.92 0.00 0.00 3.67
1905 1992 4.829492 CCTCAAACAAATGGGTTCTCTTCT 59.171 41.667 0.00 0.00 0.00 2.85
2214 2301 1.324736 CATAACGGAAGCTTGCGAGAC 59.675 52.381 41.04 9.73 45.24 3.36
2558 2648 0.176680 CATGGGACGTTCAGAGGAGG 59.823 60.000 0.00 0.00 0.00 4.30
2559 2649 0.041238 ATGGGACGTTCAGAGGAGGA 59.959 55.000 0.00 0.00 0.00 3.71
2560 2650 0.612174 TGGGACGTTCAGAGGAGGAG 60.612 60.000 0.00 0.00 0.00 3.69
3091 3181 4.452795 CCATGTGCATGCAAATGAAGAAAA 59.547 37.500 40.45 6.81 42.66 2.29
3120 3210 2.945668 AGCTATCTTTGCCGAAATGGAC 59.054 45.455 0.00 0.00 42.00 4.02
3149 3239 4.408182 TTCTCTCTTAGTAATGGCCAGC 57.592 45.455 13.05 3.86 0.00 4.85
3203 3301 5.010282 TCTCCCCAGCTTAAAGTCATTTTC 58.990 41.667 0.00 0.00 0.00 2.29
3208 3306 7.039993 TCCCCAGCTTAAAGTCATTTTCTAAAC 60.040 37.037 0.00 0.00 0.00 2.01
3258 3356 5.338381 CCCATAACTAGTTCAGAAGCCTCAA 60.338 44.000 12.39 0.00 0.00 3.02
3272 3370 5.192522 AGAAGCCTCAATGAATAAAGGAGGA 59.807 40.000 10.02 0.00 46.38 3.71
3286 3384 3.508952 AGGAGGAGACTTATGGGGAAA 57.491 47.619 0.00 0.00 44.43 3.13
3287 3385 3.388913 AGGAGGAGACTTATGGGGAAAG 58.611 50.000 0.00 0.00 44.43 2.62
3289 3387 3.523972 GGAGGAGACTTATGGGGAAAGTT 59.476 47.826 0.00 0.00 44.43 2.66
3291 3389 4.175962 AGGAGACTTATGGGGAAAGTTGA 58.824 43.478 0.00 0.00 37.44 3.18
3292 3390 4.226168 AGGAGACTTATGGGGAAAGTTGAG 59.774 45.833 0.00 0.00 37.44 3.02
3303 3401 1.128188 AAAGTTGAGGAGGAGGCGGT 61.128 55.000 0.00 0.00 0.00 5.68
3374 3472 5.842339 AGGTTTCCAGTCCAATCCATTATT 58.158 37.500 0.00 0.00 0.00 1.40
3375 3473 6.263754 AGGTTTCCAGTCCAATCCATTATTT 58.736 36.000 0.00 0.00 0.00 1.40
3439 3537 4.906618 TCCTGGTAAGTCCTGAATGTTTC 58.093 43.478 0.00 0.00 37.33 2.78
3442 3541 5.711976 CCTGGTAAGTCCTGAATGTTTCATT 59.288 40.000 0.00 0.00 39.30 2.57
3510 3609 3.309954 GCGAGAATGGCAAGTTTAGTAGG 59.690 47.826 0.00 0.00 40.68 3.18
3517 3616 5.174037 TGGCAAGTTTAGTAGGTAAGCAT 57.826 39.130 0.00 0.00 0.00 3.79
3523 3622 5.755849 AGTTTAGTAGGTAAGCATGGCAAT 58.244 37.500 0.00 0.00 0.00 3.56
3525 3624 6.663523 AGTTTAGTAGGTAAGCATGGCAATTT 59.336 34.615 0.00 0.00 0.00 1.82
3526 3625 4.989279 AGTAGGTAAGCATGGCAATTTG 57.011 40.909 0.00 0.00 0.00 2.32
3530 3629 2.418609 GGTAAGCATGGCAATTTGGTCC 60.419 50.000 0.00 0.00 0.00 4.46
3543 3642 0.681564 TTGGTCCGTGGTTTGCTTGT 60.682 50.000 0.00 0.00 0.00 3.16
3549 3648 0.179113 CGTGGTTTGCTTGTTTGCCT 60.179 50.000 0.00 0.00 0.00 4.75
3571 3670 6.257630 GCCTGAAAATTGCTTGTCAACTAAAA 59.742 34.615 0.00 0.00 37.53 1.52
3584 3683 6.872920 TGTCAACTAAAATTGCCTCTTTTGT 58.127 32.000 0.00 0.00 0.00 2.83
3587 3686 6.756074 TCAACTAAAATTGCCTCTTTTGTGTG 59.244 34.615 0.00 0.00 0.00 3.82
3591 3690 7.986889 ACTAAAATTGCCTCTTTTGTGTGAATT 59.013 29.630 0.00 0.00 0.00 2.17
3625 3724 7.444487 TCATGAAAAATGTTTGATTTGCCATGA 59.556 29.630 14.32 14.32 37.76 3.07
3628 3727 5.945466 AAATGTTTGATTTGCCATGAACC 57.055 34.783 0.00 0.00 0.00 3.62
3639 3738 1.204704 GCCATGAACCAAAGCCTAACC 59.795 52.381 0.00 0.00 0.00 2.85
3663 3762 7.122204 ACCTTTGGGATTTTATCTTTTCCGTAG 59.878 37.037 0.00 0.00 36.25 3.51
3742 3843 4.640789 ACTAGTCTAGAACAATCGCTGG 57.359 45.455 14.02 0.00 0.00 4.85
3863 3965 0.745468 GTCCTTACTCGGGATCGCTT 59.255 55.000 8.28 0.00 35.15 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 3.627577 CGAAAGCATACTAAGTTGCCCAT 59.372 43.478 0.00 0.00 39.72 4.00
110 111 3.838244 ATTAAGAGCCACGATAAGCCA 57.162 42.857 0.00 0.00 0.00 4.75
120 121 2.076100 CGTCACAGCAATTAAGAGCCA 58.924 47.619 0.00 0.00 0.00 4.75
122 123 2.736721 TGACGTCACAGCAATTAAGAGC 59.263 45.455 15.76 0.00 0.00 4.09
169 170 6.402334 CCAAGCGTCCGTTACATACAAAAATA 60.402 38.462 0.00 0.00 0.00 1.40
204 205 4.444306 CCCAGTCTACAAGTTCCAAACAGA 60.444 45.833 0.00 0.00 0.00 3.41
344 345 6.855763 TTTTTCATTAGGCATGTCCAAGAT 57.144 33.333 8.58 0.00 37.29 2.40
345 346 6.855763 ATTTTTCATTAGGCATGTCCAAGA 57.144 33.333 8.58 0.00 37.29 3.02
352 353 7.830940 TGTTGCTTATTTTTCATTAGGCATG 57.169 32.000 0.00 0.00 31.57 4.06
773 794 7.725844 TCATAGAGATCCAAGAAGCATACTACA 59.274 37.037 0.00 0.00 0.00 2.74
827 848 3.118956 CCTGGTAGACAATGAGTGGAGTC 60.119 52.174 0.00 0.00 0.00 3.36
843 864 8.838649 TCTGAATAATAGCTATATGCCTGGTA 57.161 34.615 6.68 0.00 44.23 3.25
1302 1389 1.005294 GCGCAGTGCTGGTTGATTTG 61.005 55.000 14.33 0.00 41.73 2.32
1416 1503 2.745884 TCGTGCAATTCCTGGGCG 60.746 61.111 0.00 0.00 0.00 6.13
1801 1888 3.055530 CCAGACACTTCAGGCTTAGATGT 60.056 47.826 0.67 0.00 0.00 3.06
1905 1992 0.991146 TCATTTGCTGAGGCCCTACA 59.009 50.000 0.00 0.00 37.74 2.74
2169 2256 2.095110 TGCACTTTTCATCTCATTGCCG 60.095 45.455 0.00 0.00 0.00 5.69
2214 2301 1.014352 GCTGCATTACAACTACCGGG 58.986 55.000 6.32 0.00 0.00 5.73
2531 2618 3.894547 AACGTCCCATGTGCCGACC 62.895 63.158 0.00 0.00 0.00 4.79
2628 2718 5.005779 CCAATCTATTGAAGTGTAGTCGCAC 59.994 44.000 4.25 0.00 40.14 5.34
2694 2784 0.250467 ACCATGTGTCAGACAGCCAC 60.250 55.000 2.53 0.00 38.23 5.01
3091 3181 5.643379 TCGGCAAAGATAGCTTCAATTTT 57.357 34.783 0.00 0.00 31.82 1.82
3111 3201 0.094730 GAAAGCGTCCGTCCATTTCG 59.905 55.000 0.00 0.00 0.00 3.46
3120 3210 2.923605 ACTAAGAGAGAAAGCGTCCG 57.076 50.000 0.00 0.00 0.00 4.79
3149 3239 3.378911 TTTTTAAGCCGCCCAAAAGAG 57.621 42.857 0.00 0.00 0.00 2.85
3258 3356 6.044871 CCCCATAAGTCTCCTCCTTTATTCAT 59.955 42.308 0.00 0.00 0.00 2.57
3272 3370 4.175962 TCCTCAACTTTCCCCATAAGTCT 58.824 43.478 0.00 0.00 34.88 3.24
3286 3384 1.128188 AAACCGCCTCCTCCTCAACT 61.128 55.000 0.00 0.00 0.00 3.16
3287 3385 0.611714 TAAACCGCCTCCTCCTCAAC 59.388 55.000 0.00 0.00 0.00 3.18
3289 3387 1.580059 AATAAACCGCCTCCTCCTCA 58.420 50.000 0.00 0.00 0.00 3.86
3291 3389 3.451402 AAAAATAAACCGCCTCCTCCT 57.549 42.857 0.00 0.00 0.00 3.69
3321 3419 3.623510 GCTACATACTGGCCAGTTCTTTC 59.376 47.826 41.69 22.42 42.54 2.62
3374 3472 5.278266 CCGCTTTCTCAACCTTCATAAACAA 60.278 40.000 0.00 0.00 0.00 2.83
3375 3473 4.215399 CCGCTTTCTCAACCTTCATAAACA 59.785 41.667 0.00 0.00 0.00 2.83
3420 3518 7.432869 CAAAATGAAACATTCAGGACTTACCA 58.567 34.615 0.00 0.00 43.98 3.25
3487 3586 2.778299 ACTAAACTTGCCATTCTCGCA 58.222 42.857 0.00 0.00 0.00 5.10
3493 3592 5.566469 TGCTTACCTACTAAACTTGCCATT 58.434 37.500 0.00 0.00 0.00 3.16
3510 3609 2.735126 CGGACCAAATTGCCATGCTTAC 60.735 50.000 0.00 0.00 0.00 2.34
3517 3616 0.757188 AACCACGGACCAAATTGCCA 60.757 50.000 0.00 0.00 0.00 4.92
3523 3622 0.457851 CAAGCAAACCACGGACCAAA 59.542 50.000 0.00 0.00 0.00 3.28
3525 3624 0.681564 AACAAGCAAACCACGGACCA 60.682 50.000 0.00 0.00 0.00 4.02
3526 3625 0.458260 AAACAAGCAAACCACGGACC 59.542 50.000 0.00 0.00 0.00 4.46
3530 3629 0.179113 AGGCAAACAAGCAAACCACG 60.179 50.000 0.00 0.00 35.83 4.94
3543 3642 4.134379 TGACAAGCAATTTTCAGGCAAA 57.866 36.364 0.00 0.00 0.00 3.68
3549 3648 8.121708 GCAATTTTAGTTGACAAGCAATTTTCA 58.878 29.630 0.00 0.00 39.03 2.69
3571 3670 8.907222 ATTTTAATTCACACAAAAGAGGCAAT 57.093 26.923 0.00 0.00 0.00 3.56
3603 3702 6.857451 GGTTCATGGCAAATCAAACATTTTTC 59.143 34.615 0.00 0.00 0.00 2.29
3628 3727 4.890158 AAATCCCAAAGGTTAGGCTTTG 57.110 40.909 0.00 0.00 39.49 2.77
3639 3738 8.051901 ACTACGGAAAAGATAAAATCCCAAAG 57.948 34.615 0.00 0.00 0.00 2.77
3663 3762 6.920210 GCTTTATCTCCAGCAATCCAAAATAC 59.080 38.462 0.00 0.00 35.95 1.89
3863 3965 4.437682 CCTGTAGGCCCATTTATTCTCA 57.562 45.455 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.