Multiple sequence alignment - TraesCS2D01G206600

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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 TraesCS2D01G206600 chr2D 100.000 4082 0 0 1 4082 159851498 159855579 0.000000e+00 7539.0
1 TraesCS2D01G206600 chr2D 93.333 75 4 1 216 289 159851630 159851704 4.310000e-20 110.0
2 TraesCS2D01G206600 chr2D 93.333 75 4 1 133 207 159851713 159851786 4.310000e-20 110.0
3 TraesCS2D01G206600 chr2B 95.681 3774 116 21 1 3739 216941150 216944911 0.000000e+00 6023.0
4 TraesCS2D01G206600 chr2B 92.090 354 25 3 3730 4082 216946117 216946468 2.830000e-136 496.0
5 TraesCS2D01G206600 chr2A 95.090 3849 135 18 133 3943 171079089 171082921 0.000000e+00 6011.0
6 TraesCS2D01G206600 chr2A 90.661 257 14 4 53 303 171078921 171079173 2.350000e-87 333.0
7 TraesCS2D01G206600 chr2A 95.455 154 5 2 3930 4082 171083907 171084059 1.130000e-60 244.0
8 TraesCS2D01G206600 chr2A 94.318 88 5 0 216 303 171079001 171079088 7.120000e-28 135.0
9 TraesCS2D01G206600 chr2A 90.789 76 4 3 133 207 171079174 171079247 9.340000e-17 99.0
10 TraesCS2D01G206600 chrUn 100.000 391 0 0 1698 2088 479827048 479827438 0.000000e+00 723.0
11 TraesCS2D01G206600 chr3D 100.000 29 0 0 2066 2094 61698138 61698166 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 TraesCS2D01G206600 chr2D 159851498 159855579 4081 False 2586.333333 7539 95.555333 1 4082 3 chr2D.!!$F1 4081
1 TraesCS2D01G206600 chr2B 216941150 216946468 5318 False 3259.500000 6023 93.885500 1 4082 2 chr2B.!!$F1 4081
2 TraesCS2D01G206600 chr2A 171078921 171082921 4000 False 1644.500000 6011 92.714500 53 3943 4 chr2A.!!$F2 3890

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
834 938 1.359848 GCAGTATGACAACCCGAGTG 58.640 55.0 0.0 0.0 39.69 3.51 F
1338 1445 0.249405 ACTTAACCGCAACCGACGAA 60.249 50.0 0.0 0.0 36.29 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2793 2900 1.065491 GGATGTGCACACCATAGTCCA 60.065 52.381 24.37 0.0 0.0 4.02 R
3126 3233 1.754226 ACAGTCGGCACCAAACAAAAT 59.246 42.857 0.00 0.0 0.0 1.82 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
131 132 4.447290 TGATTTTTGTCCTGTGAACTCGA 58.553 39.130 0.00 0.00 0.00 4.04
132 133 4.878971 TGATTTTTGTCCTGTGAACTCGAA 59.121 37.500 0.00 0.00 0.00 3.71
254 347 7.500691 CGTGTGATAATTTTGTTTGTTCATGG 58.499 34.615 0.00 0.00 0.00 3.66
313 406 2.009774 CTGAGCATTCGGGTTTACTGG 58.990 52.381 0.00 0.00 0.00 4.00
491 592 4.615901 CGAAGCCTGCCACATACA 57.384 55.556 0.00 0.00 0.00 2.29
492 593 2.089854 CGAAGCCTGCCACATACAC 58.910 57.895 0.00 0.00 0.00 2.90
495 596 2.483714 CGAAGCCTGCCACATACACTAT 60.484 50.000 0.00 0.00 0.00 2.12
496 597 3.243737 CGAAGCCTGCCACATACACTATA 60.244 47.826 0.00 0.00 0.00 1.31
499 600 5.407407 AGCCTGCCACATACACTATATAC 57.593 43.478 0.00 0.00 0.00 1.47
500 601 5.087323 AGCCTGCCACATACACTATATACT 58.913 41.667 0.00 0.00 0.00 2.12
537 638 2.429971 TGTTGCAATCTGCTGAACCAAA 59.570 40.909 0.59 0.00 45.31 3.28
762 865 2.420022 CCAATGTTAGAGCTCCAAACCG 59.580 50.000 20.88 12.41 0.00 4.44
834 938 1.359848 GCAGTATGACAACCCGAGTG 58.640 55.000 0.00 0.00 39.69 3.51
1013 1120 0.317799 CCAGCCATGAGATCGAGAGG 59.682 60.000 0.00 0.00 0.00 3.69
1026 1133 1.371558 GAGAGGCACGGGAACTTGT 59.628 57.895 0.00 0.00 31.02 3.16
1189 1296 1.680249 GGATCAAGCTGACCAAGGACC 60.680 57.143 0.00 0.00 0.00 4.46
1333 1440 1.598430 CCACAAACTTAACCGCAACCG 60.598 52.381 0.00 0.00 0.00 4.44
1338 1445 0.249405 ACTTAACCGCAACCGACGAA 60.249 50.000 0.00 0.00 36.29 3.85
1401 1508 2.115427 TCGGTGATTCCCAATAGCTCA 58.885 47.619 0.00 0.00 0.00 4.26
1445 1552 2.169978 TCAGCAATGGGAGTGATCAGAG 59.830 50.000 0.00 0.00 0.00 3.35
1489 1596 0.874175 TGTTGAGTTCGACAGCCACG 60.874 55.000 0.00 0.00 35.44 4.94
1554 1661 6.931281 ACATCCATTCAATTGTATCCGTAGAG 59.069 38.462 5.13 0.00 0.00 2.43
2088 2195 1.834263 CTTGGAGAAGGAGGATTCGGT 59.166 52.381 0.00 0.00 34.27 4.69
2329 2436 9.599866 CACACCTCTATGATAACAGTAATTTGA 57.400 33.333 0.00 0.00 0.00 2.69
2493 2600 3.496131 GATTTTGGGCTCGCGCGA 61.496 61.111 32.60 32.60 36.88 5.87
2505 2612 2.167219 CGCGCGACTCATTGACCAT 61.167 57.895 28.94 0.00 0.00 3.55
2760 2867 1.727511 GCAGGCTTGATGGCGCATTA 61.728 55.000 10.83 0.00 46.88 1.90
2793 2900 2.736144 CAGCATGCTTGATGGTTGTT 57.264 45.000 19.98 0.00 40.98 2.83
2799 2906 3.500448 TGCTTGATGGTTGTTGGACTA 57.500 42.857 0.00 0.00 0.00 2.59
3006 3113 2.158608 GGAGAGGTCCAATGGTTATGGG 60.159 54.545 0.00 0.00 43.31 4.00
3018 3125 2.817258 TGGTTATGGGAAAACAAGCTCG 59.183 45.455 0.00 0.00 0.00 5.03
3020 3127 4.004982 GGTTATGGGAAAACAAGCTCGTA 58.995 43.478 0.00 0.00 0.00 3.43
3114 3221 9.778993 CAGTTCCTTTCTATATGTTCAACATTG 57.221 33.333 8.69 0.15 39.88 2.82
3208 3315 2.133359 AACTCTGGCTGGATGCTGCA 62.133 55.000 17.41 4.13 42.39 4.41
3252 3362 7.125204 ACTTGTGTATAGATTGGCTACCTGTAA 59.875 37.037 0.00 0.00 0.00 2.41
3300 3411 3.056749 GTGAGTACCTAGAGTGGTGTTGG 60.057 52.174 0.00 0.00 41.05 3.77
3309 3433 0.817013 AGTGGTGTTGGCAGTTGTTG 59.183 50.000 0.00 0.00 0.00 3.33
3329 3453 5.221204 TGTTGTATTCAGCAAGACAATTGCA 60.221 36.000 14.38 0.00 43.72 4.08
3476 3600 5.767168 GCATATGTCCTTCCTGCTTATCTTT 59.233 40.000 4.29 0.00 0.00 2.52
3507 3631 6.923508 CCTTTTTGTTGAACTATGTTCCCTTC 59.076 38.462 7.81 0.00 0.00 3.46
3522 3646 1.059913 CCTTCCACTCCCTCAACTGT 58.940 55.000 0.00 0.00 0.00 3.55
3549 3673 7.518052 GCATTGAGAAACTAGATGTAGATGTGC 60.518 40.741 3.49 0.00 0.00 4.57
3554 3678 5.793030 AACTAGATGTAGATGTGCCCTAC 57.207 43.478 3.49 0.00 37.57 3.18
3631 3755 9.634021 TGCAAACATATTTATACTCCCATAACA 57.366 29.630 0.00 0.00 0.00 2.41
3833 5172 5.482908 AGATCTTACATGCCCATATTCGTC 58.517 41.667 0.00 0.00 0.00 4.20
3886 5226 4.696479 ATTCACTGGAGGTCCATCATAC 57.304 45.455 0.00 0.00 46.46 2.39
3971 5314 5.988561 TCAAACTACAAAATTTGCCATGTCC 59.011 36.000 5.52 0.00 36.06 4.02
3972 5315 4.173036 ACTACAAAATTTGCCATGTCCG 57.827 40.909 5.52 0.00 0.00 4.79
3974 5317 3.467374 ACAAAATTTGCCATGTCCGTT 57.533 38.095 5.52 0.00 0.00 4.44
3977 5320 0.968405 AATTTGCCATGTCCGTTGCT 59.032 45.000 0.00 0.00 0.00 3.91
3980 5323 2.126346 GCCATGTCCGTTGCTTGC 60.126 61.111 0.00 0.00 0.00 4.01
4002 5345 4.843147 CGAAGCAACTGTGTAAAATGTCA 58.157 39.130 0.00 0.00 0.00 3.58
4043 5386 7.502226 TCAGGCAATGTATTATTTTAGGTGAGG 59.498 37.037 0.00 0.00 0.00 3.86
4056 5399 7.610580 TTTTAGGTGAGGGTTCATGAAATTT 57.389 32.000 10.35 0.00 35.39 1.82
4064 5407 6.434028 TGAGGGTTCATGAAATTTGGAACTAG 59.566 38.462 10.35 0.00 39.55 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.685276 ATATCCACAAATGAGTAACTCAAATCA 57.315 29.630 0.00 0.00 44.04 2.57
48 49 8.832521 TGTACGCGGATTATTCTATTCATTTTT 58.167 29.630 12.47 0.00 0.00 1.94
67 68 1.333881 CCCTACGAGAGAATGTACGCG 60.334 57.143 3.53 3.53 35.67 6.01
137 139 9.647797 AACAAAACTATCACACGTTCTGATATA 57.352 29.630 11.43 0.00 31.61 0.86
156 158 7.008859 CACTGTCAAACATGAACAAACAAAAC 58.991 34.615 0.00 0.00 0.00 2.43
228 321 6.503616 TGAACAAACAAAATTATCACACGC 57.496 33.333 0.00 0.00 0.00 5.34
313 406 4.901197 AAAGGGAAGAGAGAAGGAAGTC 57.099 45.455 0.00 0.00 0.00 3.01
381 474 9.161629 TCATGACGTGTTGTTTTCTTCATATAT 57.838 29.630 0.00 0.00 0.00 0.86
382 475 8.541133 TCATGACGTGTTGTTTTCTTCATATA 57.459 30.769 0.00 0.00 0.00 0.86
537 638 0.104304 CAGGAAGCTATTACGGCCGT 59.896 55.000 36.01 36.01 0.00 5.68
598 701 2.231380 ATGGAAAGAGGCCACGGGT 61.231 57.895 5.01 0.00 38.44 5.28
834 938 2.124983 TCTCGATGGCCTTGCAGC 60.125 61.111 3.32 0.00 0.00 5.25
980 1087 2.573869 CTGGAGAAAGAGCGGCGA 59.426 61.111 12.98 0.00 0.00 5.54
1189 1296 3.229276 AGTGATCTCGTCTTTGAGCTG 57.771 47.619 0.00 0.00 35.90 4.24
1387 1494 3.624777 CACCAGTTGAGCTATTGGGAAT 58.375 45.455 3.36 0.00 34.99 3.01
1401 1508 1.119684 GGCCAAGAAAACCACCAGTT 58.880 50.000 0.00 0.00 41.81 3.16
1445 1552 1.673168 GAGCTCATTGGATGGGTCAC 58.327 55.000 9.40 0.00 31.83 3.67
1489 1596 3.382546 CCTTTTGGATCCCATGTGTCATC 59.617 47.826 9.90 0.00 44.07 2.92
1554 1661 4.575885 TGCTACTATTCCACAACACCTTC 58.424 43.478 0.00 0.00 0.00 3.46
1696 1803 6.410540 GGAGGTATTTTCTGAGATCAACTGT 58.589 40.000 0.00 0.00 0.00 3.55
2088 2195 1.133809 AAAGGCCCTGGTAGACTGCA 61.134 55.000 0.00 0.00 0.00 4.41
2329 2436 3.979911 TGAACCTCAATGGCCATGTTAT 58.020 40.909 21.63 0.00 40.22 1.89
2493 2600 1.406069 GCTCGGTCATGGTCAATGAGT 60.406 52.381 0.00 0.00 46.09 3.41
2505 2612 1.529152 TAGTTTGCGAGGCTCGGTCA 61.529 55.000 35.03 23.59 40.84 4.02
2637 2744 1.227823 CACAACTGGTCGCCTTCCA 60.228 57.895 0.00 0.00 0.00 3.53
2760 2867 2.037511 GCATGCTGCCTCTCTATCTTCT 59.962 50.000 11.37 0.00 37.42 2.85
2793 2900 1.065491 GGATGTGCACACCATAGTCCA 60.065 52.381 24.37 0.00 0.00 4.02
2799 2906 2.519771 AATCTGGATGTGCACACCAT 57.480 45.000 29.24 18.95 33.08 3.55
3006 3113 2.286833 TGCAGTGTACGAGCTTGTTTTC 59.713 45.455 12.97 4.45 0.00 2.29
3114 3221 6.843779 GCACCAAACAAAATCGAAAATGTTAC 59.156 34.615 11.80 0.00 35.09 2.50
3120 3227 2.860735 CGGCACCAAACAAAATCGAAAA 59.139 40.909 0.00 0.00 0.00 2.29
3126 3233 1.754226 ACAGTCGGCACCAAACAAAAT 59.246 42.857 0.00 0.00 0.00 1.82
3252 3362 8.523915 TCAGGATACATTCATTGCTTATGTTT 57.476 30.769 0.00 0.00 41.41 2.83
3300 3411 4.222114 GTCTTGCTGAATACAACAACTGC 58.778 43.478 0.00 0.00 30.48 4.40
3309 3433 4.797471 TGTGCAATTGTCTTGCTGAATAC 58.203 39.130 7.40 1.90 45.13 1.89
3476 3600 7.648039 ACATAGTTCAACAAAAAGGTAACCA 57.352 32.000 0.00 0.00 37.17 3.67
3507 3631 0.037303 ATGCACAGTTGAGGGAGTGG 59.963 55.000 0.00 0.00 32.80 4.00
3522 3646 7.493645 CACATCTACATCTAGTTTCTCAATGCA 59.506 37.037 0.00 0.00 0.00 3.96
3532 3656 5.459505 AGTAGGGCACATCTACATCTAGTT 58.540 41.667 0.00 0.00 39.48 2.24
3549 3673 4.430908 GTGTAAGGTCGATTCAAGTAGGG 58.569 47.826 0.00 0.00 0.00 3.53
3554 3678 3.226346 TCGGTGTAAGGTCGATTCAAG 57.774 47.619 0.00 0.00 0.00 3.02
3622 3746 9.816787 AGTTTATTACTTCCTTTTGTTATGGGA 57.183 29.630 0.00 0.00 31.29 4.37
3886 5226 6.647895 ACCGTGGTTTAATACTGTTACTTCAG 59.352 38.462 0.00 0.00 40.80 3.02
3977 5320 3.766676 TTTTACACAGTTGCTTCGCAA 57.233 38.095 0.00 0.00 46.80 4.85
3980 5323 4.843147 TGACATTTTACACAGTTGCTTCG 58.157 39.130 0.00 0.00 0.00 3.79
3987 5330 6.274157 TGGTTGTTTGACATTTTACACAGT 57.726 33.333 0.00 0.00 0.00 3.55
3988 5331 8.349245 TCTATGGTTGTTTGACATTTTACACAG 58.651 33.333 0.00 0.00 0.00 3.66
3992 5335 9.394477 GAACTCTATGGTTGTTTGACATTTTAC 57.606 33.333 0.00 0.00 0.00 2.01
3998 5341 5.063204 CCTGAACTCTATGGTTGTTTGACA 58.937 41.667 0.00 0.00 0.00 3.58
3999 5342 4.083271 GCCTGAACTCTATGGTTGTTTGAC 60.083 45.833 0.00 0.00 0.00 3.18
4000 5343 4.072131 GCCTGAACTCTATGGTTGTTTGA 58.928 43.478 0.00 0.00 0.00 2.69
4001 5344 3.820467 TGCCTGAACTCTATGGTTGTTTG 59.180 43.478 0.00 0.00 0.00 2.93
4002 5345 4.098914 TGCCTGAACTCTATGGTTGTTT 57.901 40.909 0.00 0.00 0.00 2.83
4043 5386 7.976175 GGATTCTAGTTCCAAATTTCATGAACC 59.024 37.037 7.89 0.00 38.24 3.62
4056 5399 5.935945 TCAAAGTGTTGGATTCTAGTTCCA 58.064 37.500 11.59 11.59 41.50 3.53


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

AutoCloner maintained by Alex Coulton.