Multiple sequence alignment - TraesCS2D01G108900

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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 TraesCS2D01G108900 chr2D 100.000 2476 0 0 1 2476 60326687 60329162 0.000000e+00 4573.0
1 TraesCS2D01G108900 chr2D 100.000 115 0 0 2896 3010 60329582 60329696 2.350000e-51 213.0
2 TraesCS2D01G108900 chr2A 92.283 2462 89 34 58 2474 60807813 60805408 0.000000e+00 3400.0
3 TraesCS2D01G108900 chr2B 88.344 2548 128 58 1 2445 94660183 94662664 0.000000e+00 2904.0
4 TraesCS2D01G108900 chr2B 92.453 106 3 3 2910 3010 94663077 94663182 2.420000e-31 147.0
5 TraesCS2D01G108900 chr7B 84.925 199 26 3 151 349 683369222 683369028 6.580000e-47 198.0
6 TraesCS2D01G108900 chr1B 88.235 68 6 2 2371 2437 143448639 143448705 2.490000e-11 80.5


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 TraesCS2D01G108900 chr2D 60326687 60329696 3009 False 2393.0 4573 100.0000 1 3010 2 chr2D.!!$F1 3009
1 TraesCS2D01G108900 chr2A 60805408 60807813 2405 True 3400.0 3400 92.2830 58 2474 1 chr2A.!!$R1 2416
2 TraesCS2D01G108900 chr2B 94660183 94663182 2999 False 1525.5 2904 90.3985 1 3010 2 chr2B.!!$F1 3009

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
117 118 0.107945 AGTCATGCGAAGAGGAAGCC 60.108 55.0 0.0 0.0 0.0 4.35 F
1304 1393 0.252197 ACTCTTTCCCCACGGTATGC 59.748 55.0 0.0 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 1817 0.246635 CAGTTCAGTTCGATCGGGGT 59.753 55.0 16.41 0.0 0.00 4.95 R
2312 2434 0.385390 AACAGCTGAAAACGCAAGGG 59.615 50.0 23.35 0.0 46.39 3.95 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
20 21 0.606401 ACTTGGGCTCGGTGACATTG 60.606 55.000 0.00 0.00 0.00 2.82
40 41 6.942576 ACATTGGAATGACTATGCCCTATAAC 59.057 38.462 6.37 0.00 39.67 1.89
42 43 4.020573 TGGAATGACTATGCCCTATAACCG 60.021 45.833 0.00 0.00 29.85 4.44
46 47 3.962063 TGACTATGCCCTATAACCGAACA 59.038 43.478 0.00 0.00 0.00 3.18
54 55 4.451435 GCCCTATAACCGAACAAGATAAGC 59.549 45.833 0.00 0.00 0.00 3.09
57 58 1.734163 AACCGAACAAGATAAGCCGG 58.266 50.000 0.00 0.00 42.30 6.13
67 68 1.625818 AGATAAGCCGGGATGATGGAC 59.374 52.381 2.18 0.00 0.00 4.02
76 77 1.638529 GGATGATGGACGAGGAGGAT 58.361 55.000 0.00 0.00 0.00 3.24
77 78 1.548269 GGATGATGGACGAGGAGGATC 59.452 57.143 0.00 0.00 0.00 3.36
103 104 3.156293 CCAGGAGATCGATGAGAGTCAT 58.844 50.000 0.54 0.00 40.34 3.06
106 107 2.583739 GAGATCGATGAGAGTCATGCG 58.416 52.381 0.54 0.00 37.20 4.73
117 118 0.107945 AGTCATGCGAAGAGGAAGCC 60.108 55.000 0.00 0.00 0.00 4.35
118 119 1.153568 TCATGCGAAGAGGAAGCCG 60.154 57.895 0.00 0.00 0.00 5.52
119 120 1.153568 CATGCGAAGAGGAAGCCGA 60.154 57.895 0.00 0.00 0.00 5.54
120 121 1.153549 ATGCGAAGAGGAAGCCGAC 60.154 57.895 0.00 0.00 0.00 4.79
121 122 2.881352 GCGAAGAGGAAGCCGACG 60.881 66.667 0.00 0.00 0.00 5.12
122 123 2.875485 CGAAGAGGAAGCCGACGA 59.125 61.111 0.00 0.00 0.00 4.20
123 124 1.514443 CGAAGAGGAAGCCGACGAC 60.514 63.158 0.00 0.00 0.00 4.34
124 125 1.514443 GAAGAGGAAGCCGACGACG 60.514 63.158 0.00 0.00 39.43 5.12
149 150 8.573885 CGGGTAACTACATGATCTCTATGTTTA 58.426 37.037 0.00 0.00 39.36 2.01
174 175 5.744819 TGATGTGATGCATTTAAAATCGCTG 59.255 36.000 0.00 0.00 38.06 5.18
192 193 6.546972 TCGCTGTGTTTGTGTTGAAATATA 57.453 33.333 0.00 0.00 0.00 0.86
193 194 7.139896 TCGCTGTGTTTGTGTTGAAATATAT 57.860 32.000 0.00 0.00 0.00 0.86
221 222 8.939201 TCAATTTGTTTGAATAGTTTGAGCAA 57.061 26.923 0.00 0.00 41.38 3.91
222 223 8.816144 TCAATTTGTTTGAATAGTTTGAGCAAC 58.184 29.630 0.00 0.00 41.38 4.17
223 224 8.602328 CAATTTGTTTGAATAGTTTGAGCAACA 58.398 29.630 0.00 0.00 36.22 3.33
224 225 7.754069 TTTGTTTGAATAGTTTGAGCAACAG 57.246 32.000 0.00 0.00 37.93 3.16
236 240 7.771183 AGTTTGAGCAACAGATTTCAAAGTTA 58.229 30.769 0.00 0.00 39.09 2.24
286 290 0.530650 TGCTAGCTGCGGAATAGTGC 60.531 55.000 17.23 0.00 46.63 4.40
331 355 6.374417 AAGTAGGATAGGAAGCTGTTTTGA 57.626 37.500 0.00 0.00 0.00 2.69
334 358 8.090788 AGTAGGATAGGAAGCTGTTTTGATAA 57.909 34.615 0.00 0.00 0.00 1.75
369 402 3.564225 GGATCGGCCCTTAAACAGTATTG 59.436 47.826 0.00 0.00 0.00 1.90
429 462 6.665248 AGGGAATGAATTAACTTTCCTCCAAG 59.335 38.462 0.00 0.00 41.10 3.61
508 541 0.914417 TAGCTGAGGGTGGAAAGGGG 60.914 60.000 0.00 0.00 0.00 4.79
511 544 2.142292 CTGAGGGTGGAAAGGGGGTG 62.142 65.000 0.00 0.00 0.00 4.61
512 545 2.037677 AGGGTGGAAAGGGGGTGT 60.038 61.111 0.00 0.00 0.00 4.16
513 546 2.138453 GAGGGTGGAAAGGGGGTGTC 62.138 65.000 0.00 0.00 0.00 3.67
514 547 2.439245 GGTGGAAAGGGGGTGTCC 59.561 66.667 0.00 0.00 0.00 4.02
556 589 9.713684 ACCCTGGAATTTTCAGAAATGATATTA 57.286 29.630 6.25 0.00 35.69 0.98
603 637 4.137116 ACTGTTGTATACATGCATCCGT 57.863 40.909 6.36 0.00 35.85 4.69
631 667 4.240881 CACACACAGTGGGCACTT 57.759 55.556 1.44 0.00 44.69 3.16
720 756 1.375326 GGAGGAAGAGCCAAACCGT 59.625 57.895 0.00 0.00 40.02 4.83
879 915 1.371467 TCCTCATCCCCTTGAAGCAA 58.629 50.000 0.00 0.00 0.00 3.91
884 920 2.376518 TCATCCCCTTGAAGCAACTCTT 59.623 45.455 0.00 0.00 37.83 2.85
993 1073 3.193267 ACTGCAGAGACAATCAGAGAGAC 59.807 47.826 23.35 0.00 0.00 3.36
1137 1226 0.742505 TGCTGCCATTAGCTTGATGC 59.257 50.000 0.00 0.00 44.01 3.91
1150 1239 8.938906 CATTAGCTTGATGCCTGTTTTTAAATT 58.061 29.630 0.00 0.00 44.23 1.82
1160 1249 8.371770 TGCCTGTTTTTAAATTTAAAATCGCT 57.628 26.923 28.00 0.00 40.92 4.93
1199 1288 3.641031 CATAGTCATGGACGCGTCA 57.359 52.632 37.26 24.47 37.67 4.35
1250 1339 1.615883 GCGAGGCTCAATCAGGAGATA 59.384 52.381 15.95 0.00 37.05 1.98
1302 1391 2.236395 CAGAACTCTTTCCCCACGGTAT 59.764 50.000 0.00 0.00 31.28 2.73
1303 1392 2.236395 AGAACTCTTTCCCCACGGTATG 59.764 50.000 0.00 0.00 31.28 2.39
1304 1393 0.252197 ACTCTTTCCCCACGGTATGC 59.748 55.000 0.00 0.00 0.00 3.14
1305 1394 0.810031 CTCTTTCCCCACGGTATGCG 60.810 60.000 0.00 0.00 0.00 4.73
1358 1447 5.386060 TGTATACTGTATGGAGGACCTGAG 58.614 45.833 10.51 0.00 37.04 3.35
1430 1519 4.034410 TGGCACATAGTAATACAGTGGGA 58.966 43.478 10.86 0.00 0.00 4.37
1548 1640 3.664240 TGTCCTCCGACAAGAGCTA 57.336 52.632 0.00 0.00 46.09 3.32
1669 1764 0.904649 TCGGAGGAGAGGTACGTACA 59.095 55.000 26.02 0.00 0.00 2.90
1672 1767 3.326006 TCGGAGGAGAGGTACGTACATAT 59.674 47.826 26.02 17.65 0.00 1.78
1678 1779 7.992033 GGAGGAGAGGTACGTACATATACATAT 59.008 40.741 26.02 2.61 0.00 1.78
1698 1799 1.883084 CCTACGCGACAATGCCTCC 60.883 63.158 15.93 0.00 0.00 4.30
1699 1800 1.141881 CTACGCGACAATGCCTCCT 59.858 57.895 15.93 0.00 0.00 3.69
1716 1817 5.045651 TGCCTCCTCTCAATCATTAACTGAA 60.046 40.000 0.00 0.00 37.44 3.02
1889 1997 4.746611 TCGTAATTATCTGTGCTGATGCTG 59.253 41.667 2.46 0.00 40.48 4.41
1894 2002 0.607217 TCTGTGCTGATGCTGGGTTG 60.607 55.000 0.00 0.00 40.48 3.77
1898 2006 0.961019 TGCTGATGCTGGGTTGTTTC 59.039 50.000 0.00 0.00 40.48 2.78
2394 2521 5.812652 TGTAAGACGTTTTGGCAGTTTAAG 58.187 37.500 0.83 0.00 0.00 1.85
2430 2557 9.520515 AAAAATGTCTTACAATAGTGGACAGAT 57.479 29.630 6.83 0.00 41.44 2.90
2437 2564 5.957771 ACAATAGTGGACAGATGGTGTAT 57.042 39.130 0.00 0.00 40.56 2.29
2448 2577 3.750130 CAGATGGTGTATTATCCTGCTGC 59.250 47.826 0.00 0.00 0.00 5.25
2467 2596 2.680841 TGCTATGCGGCTTAACGAAAAT 59.319 40.909 0.00 0.00 35.47 1.82
2474 2603 5.279384 TGCGGCTTAACGAAAATTTGTTAA 58.721 33.333 14.79 14.79 42.03 2.01
2475 2604 5.747197 TGCGGCTTAACGAAAATTTGTTAAA 59.253 32.000 15.85 3.11 43.02 1.52
2914 3043 1.597742 CGGCCCCTCAAAGACATATG 58.402 55.000 0.00 0.00 0.00 1.78
2915 3044 1.140852 CGGCCCCTCAAAGACATATGA 59.859 52.381 10.38 0.00 0.00 2.15
2916 3045 2.808202 CGGCCCCTCAAAGACATATGAG 60.808 54.545 10.38 0.00 42.15 2.90
2921 3050 5.749462 CCCCTCAAAGACATATGAGAAACT 58.251 41.667 10.38 0.00 44.64 2.66
2969 3101 1.062587 GTGGCATGTTGCTCATACGAC 59.937 52.381 0.00 0.00 44.28 4.34
2982 3115 7.290857 TGCTCATACGACATAGTTCTTTTTC 57.709 36.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.002656 GCATAGTCATTCCAATGTCACCG 59.997 47.826 0.00 0.00 37.65 4.94
12 13 3.316308 GGGCATAGTCATTCCAATGTCAC 59.684 47.826 0.00 0.00 37.65 3.67
20 21 4.222145 TCGGTTATAGGGCATAGTCATTCC 59.778 45.833 0.00 0.00 0.00 3.01
40 41 0.177141 TCCCGGCTTATCTTGTTCGG 59.823 55.000 0.00 0.00 37.50 4.30
42 43 3.194005 TCATCCCGGCTTATCTTGTTC 57.806 47.619 0.00 0.00 0.00 3.18
46 47 2.039084 GTCCATCATCCCGGCTTATCTT 59.961 50.000 0.00 0.00 0.00 2.40
54 55 1.810606 CTCCTCGTCCATCATCCCGG 61.811 65.000 0.00 0.00 0.00 5.73
57 58 1.548269 GATCCTCCTCGTCCATCATCC 59.452 57.143 0.00 0.00 0.00 3.51
76 77 1.215423 TCATCGATCTCCTGGACCTGA 59.785 52.381 0.00 0.00 0.00 3.86
77 78 1.612950 CTCATCGATCTCCTGGACCTG 59.387 57.143 0.00 0.00 0.00 4.00
83 84 3.612241 GCATGACTCTCATCGATCTCCTG 60.612 52.174 0.00 0.00 34.28 3.86
103 104 2.261671 GTCGGCTTCCTCTTCGCA 59.738 61.111 0.00 0.00 0.00 5.10
106 107 1.514443 CGTCGTCGGCTTCCTCTTC 60.514 63.158 0.00 0.00 0.00 2.87
117 118 1.398041 TCATGTAGTTACCCGTCGTCG 59.602 52.381 0.00 0.00 0.00 5.12
118 119 3.314635 AGATCATGTAGTTACCCGTCGTC 59.685 47.826 0.00 0.00 0.00 4.20
119 120 3.285484 AGATCATGTAGTTACCCGTCGT 58.715 45.455 0.00 0.00 0.00 4.34
120 121 3.564644 AGAGATCATGTAGTTACCCGTCG 59.435 47.826 0.00 0.00 0.00 5.12
121 122 6.207025 ACATAGAGATCATGTAGTTACCCGTC 59.793 42.308 0.00 0.00 34.88 4.79
122 123 6.069331 ACATAGAGATCATGTAGTTACCCGT 58.931 40.000 0.00 0.00 34.88 5.28
123 124 6.576662 ACATAGAGATCATGTAGTTACCCG 57.423 41.667 0.00 0.00 34.88 5.28
149 150 6.419710 CAGCGATTTTAAATGCATCACATCAT 59.580 34.615 0.00 0.00 38.34 2.45
168 169 3.773860 TTTCAACACAAACACAGCGAT 57.226 38.095 0.00 0.00 0.00 4.58
171 172 8.915871 ATCATATATTTCAACACAAACACAGC 57.084 30.769 0.00 0.00 0.00 4.40
206 207 7.509141 TGAAATCTGTTGCTCAAACTATTCA 57.491 32.000 0.00 0.00 39.70 2.57
215 216 6.542005 TCACTAACTTTGAAATCTGTTGCTCA 59.458 34.615 0.00 0.00 0.00 4.26
216 217 6.959361 TCACTAACTTTGAAATCTGTTGCTC 58.041 36.000 0.00 0.00 0.00 4.26
217 218 6.942532 TCACTAACTTTGAAATCTGTTGCT 57.057 33.333 0.00 0.00 0.00 3.91
218 219 7.043391 GGTTTCACTAACTTTGAAATCTGTTGC 60.043 37.037 1.17 0.00 43.16 4.17
219 220 7.973388 TGGTTTCACTAACTTTGAAATCTGTTG 59.027 33.333 8.97 0.00 42.33 3.33
221 222 7.639113 TGGTTTCACTAACTTTGAAATCTGT 57.361 32.000 8.97 0.00 42.33 3.41
222 223 8.925161 TTTGGTTTCACTAACTTTGAAATCTG 57.075 30.769 8.97 0.00 42.33 2.90
236 240 9.421399 CCCTATCCTATAAATTTTGGTTTCACT 57.579 33.333 0.00 0.00 0.00 3.41
284 288 9.974980 CTTTACTATTTGTTTTTAGGGAAAGCA 57.025 29.630 0.00 0.00 36.78 3.91
331 355 7.624077 AGGGCCGATCCTCTATACTAAAATTAT 59.376 37.037 0.00 0.00 29.56 1.28
334 358 5.342866 AGGGCCGATCCTCTATACTAAAAT 58.657 41.667 0.00 0.00 29.56 1.82
369 402 1.066605 GTCATGCATGTGCCTTCATCC 59.933 52.381 25.43 0.01 41.18 3.51
429 462 2.502510 CGCGCAACAAGGCATGTC 60.503 61.111 8.75 0.00 42.99 3.06
473 506 1.134491 AGCTACGCCCCTGTAAATCAC 60.134 52.381 0.00 0.00 0.00 3.06
556 589 8.655651 TTTTTGAGAAGCACCGATTTAAAAAT 57.344 26.923 0.00 0.00 0.00 1.82
603 637 3.314913 CCACTGTGTGTGTTTCTTGCATA 59.685 43.478 7.08 0.00 44.81 3.14
631 667 2.203337 GTCAGTTGCTGCCCACCA 60.203 61.111 0.00 0.00 0.00 4.17
720 756 7.177216 TCGATTCTAGGTAGTAGGTTCAAAACA 59.823 37.037 0.00 0.00 0.00 2.83
879 915 5.723887 AGAGAGAGAGAGAGAGAGAAAGAGT 59.276 44.000 0.00 0.00 0.00 3.24
884 920 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
993 1073 0.946221 GCTCCCTCGACATTATGCCG 60.946 60.000 0.00 0.00 0.00 5.69
1029 1110 4.344679 AGAATCTGCATCTTCTCCTGTAGG 59.655 45.833 5.35 0.00 0.00 3.18
1137 1226 9.579610 CACAGCGATTTTAAATTTAAAAACAGG 57.420 29.630 29.99 22.12 43.43 4.00
1160 1249 0.251033 AAGGATTGCTCAGCTGCACA 60.251 50.000 9.47 6.62 43.20 4.57
1199 1288 2.254152 TCAGCCCCTTGATGTACTCT 57.746 50.000 0.00 0.00 0.00 3.24
1250 1339 2.049063 GTGTCTTCCTCGCGTGCT 60.049 61.111 5.77 0.00 0.00 4.40
1304 1393 3.913573 GATAGGTGTGTGCGCGCG 61.914 66.667 28.44 28.44 0.00 6.86
1305 1394 2.813474 TGATAGGTGTGTGCGCGC 60.813 61.111 27.26 27.26 0.00 6.86
1358 1447 4.120589 CCTAAGCTTCAGAACCGGATAAC 58.879 47.826 9.46 0.00 0.00 1.89
1698 1799 4.572389 CGGGGTTCAGTTAATGATTGAGAG 59.428 45.833 0.00 0.00 37.89 3.20
1699 1800 4.224147 TCGGGGTTCAGTTAATGATTGAGA 59.776 41.667 0.00 0.00 37.89 3.27
1716 1817 0.246635 CAGTTCAGTTCGATCGGGGT 59.753 55.000 16.41 0.00 0.00 4.95
1889 1997 8.225603 ACATCATATTGATACAGAAACAACCC 57.774 34.615 0.00 0.00 34.28 4.11
1894 2002 8.615211 TCTGCAACATCATATTGATACAGAAAC 58.385 33.333 0.00 0.00 34.28 2.78
1898 2006 7.012610 TGGTTCTGCAACATCATATTGATACAG 59.987 37.037 0.00 0.00 34.28 2.74
2312 2434 0.385390 AACAGCTGAAAACGCAAGGG 59.615 50.000 23.35 0.00 46.39 3.95
2316 2438 2.618241 AGAATGAACAGCTGAAAACGCA 59.382 40.909 23.35 8.86 0.00 5.24
2369 2496 4.483476 AACTGCCAAAACGTCTTACATC 57.517 40.909 0.00 0.00 0.00 3.06
2394 2521 7.518731 TTGTAAGACATTTTTGCAGTTCAAC 57.481 32.000 0.00 0.00 33.73 3.18
2430 2557 4.803924 GCATAGCAGCAGGATAATACACCA 60.804 45.833 0.00 0.00 0.00 4.17
2437 2564 0.603707 GCCGCATAGCAGCAGGATAA 60.604 55.000 0.00 0.00 31.58 1.75
2448 2577 5.092781 ACAAATTTTCGTTAAGCCGCATAG 58.907 37.500 0.00 0.00 0.00 2.23
2895 3024 1.140852 TCATATGTCTTTGAGGGGCCG 59.859 52.381 1.90 0.00 0.00 6.13
2896 3025 2.439507 TCTCATATGTCTTTGAGGGGCC 59.560 50.000 1.90 0.00 39.84 5.80
2897 3026 3.845781 TCTCATATGTCTTTGAGGGGC 57.154 47.619 1.90 0.00 39.84 5.80
2898 3027 5.749462 AGTTTCTCATATGTCTTTGAGGGG 58.251 41.667 1.90 0.00 39.84 4.79
2899 3028 7.497249 CCTTAGTTTCTCATATGTCTTTGAGGG 59.503 40.741 1.90 0.00 39.84 4.30
2900 3029 8.260818 TCCTTAGTTTCTCATATGTCTTTGAGG 58.739 37.037 1.90 3.17 39.84 3.86
2901 3030 9.658799 TTCCTTAGTTTCTCATATGTCTTTGAG 57.341 33.333 1.90 0.00 40.58 3.02
2969 3101 4.201950 CCGCCCATGAGAAAAAGAACTATG 60.202 45.833 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.