Multiple sequence alignment - TraesCS3D01G318300

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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 TraesCS3D01G318300 chr3D 100.000 2450 0 0 1 2450 432075489 432077938 0.000000e+00 4525.0
1 TraesCS3D01G318300 chr1A 94.099 1610 78 10 28 1624 18497561 18495956 0.000000e+00 2431.0
2 TraesCS3D01G318300 chr1A 91.769 1628 74 19 28 1621 518797831 518796230 0.000000e+00 2209.0
3 TraesCS3D01G318300 chr6A 91.865 1635 64 21 28 1621 607377380 607378986 0.000000e+00 2218.0
4 TraesCS3D01G318300 chr6A 100.000 59 0 0 52 110 70573348 70573290 2.580000e-20 110.0
5 TraesCS3D01G318300 chr6A 96.774 31 1 0 9 39 607377340 607377370 4.000000e-03 52.8
6 TraesCS3D01G318300 chr3A 91.350 1630 78 21 28 1621 416039685 416041287 0.000000e+00 2170.0
7 TraesCS3D01G318300 chr6B 88.998 1627 99 30 28 1621 100714726 100716305 0.000000e+00 1940.0
8 TraesCS3D01G318300 chr6B 88.937 1627 100 30 28 1621 100749377 100750956 0.000000e+00 1934.0
9 TraesCS3D01G318300 chr6D 93.454 1268 72 3 364 1621 156258435 156257169 0.000000e+00 1871.0
10 TraesCS3D01G318300 chr6D 95.631 824 36 0 1622 2445 422034244 422035067 0.000000e+00 1323.0
11 TraesCS3D01G318300 chr6D 94.787 844 43 1 1603 2445 422065436 422066279 0.000000e+00 1314.0
12 TraesCS3D01G318300 chr2D 95.962 842 33 1 1609 2450 571121993 571122833 0.000000e+00 1365.0
13 TraesCS3D01G318300 chr2D 95.131 842 40 1 1603 2444 286727138 286727978 0.000000e+00 1327.0
14 TraesCS3D01G318300 chr2D 94.588 850 43 3 1603 2450 566077613 566078461 0.000000e+00 1312.0
15 TraesCS3D01G318300 chr2D 94.490 853 40 4 1603 2450 366160174 366161024 0.000000e+00 1308.0
16 TraesCS3D01G318300 chr2D 90.280 679 62 3 946 1621 642015177 642015854 0.000000e+00 885.0
17 TraesCS3D01G318300 chr2D 95.238 84 4 0 28 111 586268448 586268531 1.530000e-27 134.0
18 TraesCS3D01G318300 chr5D 95.053 849 40 2 1603 2450 65081669 65082516 0.000000e+00 1334.0
19 TraesCS3D01G318300 chr1D 95.521 826 35 1 1622 2445 276950230 276949405 0.000000e+00 1319.0
20 TraesCS3D01G318300 chr1D 95.515 825 36 1 1621 2445 276939365 276938542 0.000000e+00 1317.0
21 TraesCS3D01G318300 chr5B 90.280 679 62 3 946 1621 565832206 565832883 0.000000e+00 885.0
22 TraesCS3D01G318300 chr4D 89.123 570 36 3 100 666 304694470 304695016 0.000000e+00 686.0


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 TraesCS3D01G318300 chr3D 432075489 432077938 2449 False 4525.0 4525 100.0000 1 2450 1 chr3D.!!$F1 2449
1 TraesCS3D01G318300 chr1A 18495956 18497561 1605 True 2431.0 2431 94.0990 28 1624 1 chr1A.!!$R1 1596
2 TraesCS3D01G318300 chr1A 518796230 518797831 1601 True 2209.0 2209 91.7690 28 1621 1 chr1A.!!$R2 1593
3 TraesCS3D01G318300 chr6A 607377340 607378986 1646 False 1135.4 2218 94.3195 9 1621 2 chr6A.!!$F1 1612
4 TraesCS3D01G318300 chr3A 416039685 416041287 1602 False 2170.0 2170 91.3500 28 1621 1 chr3A.!!$F1 1593
5 TraesCS3D01G318300 chr6B 100714726 100716305 1579 False 1940.0 1940 88.9980 28 1621 1 chr6B.!!$F1 1593
6 TraesCS3D01G318300 chr6B 100749377 100750956 1579 False 1934.0 1934 88.9370 28 1621 1 chr6B.!!$F2 1593
7 TraesCS3D01G318300 chr6D 156257169 156258435 1266 True 1871.0 1871 93.4540 364 1621 1 chr6D.!!$R1 1257
8 TraesCS3D01G318300 chr6D 422034244 422035067 823 False 1323.0 1323 95.6310 1622 2445 1 chr6D.!!$F1 823
9 TraesCS3D01G318300 chr6D 422065436 422066279 843 False 1314.0 1314 94.7870 1603 2445 1 chr6D.!!$F2 842
10 TraesCS3D01G318300 chr2D 571121993 571122833 840 False 1365.0 1365 95.9620 1609 2450 1 chr2D.!!$F4 841
11 TraesCS3D01G318300 chr2D 286727138 286727978 840 False 1327.0 1327 95.1310 1603 2444 1 chr2D.!!$F1 841
12 TraesCS3D01G318300 chr2D 566077613 566078461 848 False 1312.0 1312 94.5880 1603 2450 1 chr2D.!!$F3 847
13 TraesCS3D01G318300 chr2D 366160174 366161024 850 False 1308.0 1308 94.4900 1603 2450 1 chr2D.!!$F2 847
14 TraesCS3D01G318300 chr2D 642015177 642015854 677 False 885.0 885 90.2800 946 1621 1 chr2D.!!$F6 675
15 TraesCS3D01G318300 chr5D 65081669 65082516 847 False 1334.0 1334 95.0530 1603 2450 1 chr5D.!!$F1 847
16 TraesCS3D01G318300 chr1D 276949405 276950230 825 True 1319.0 1319 95.5210 1622 2445 1 chr1D.!!$R2 823
17 TraesCS3D01G318300 chr1D 276938542 276939365 823 True 1317.0 1317 95.5150 1621 2445 1 chr1D.!!$R1 824
18 TraesCS3D01G318300 chr5B 565832206 565832883 677 False 885.0 885 90.2800 946 1621 1 chr5B.!!$F1 675
19 TraesCS3D01G318300 chr4D 304694470 304695016 546 False 686.0 686 89.1230 100 666 1 chr4D.!!$F1 566

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
221 347 0.11319 CACCTCTCCAAAAAGGCCCT 59.887 55.0 0.0 0.0 36.01 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2283 0.10741 TGGTGAAGCTTCGTGGTGTT 60.107 50.0 21.11 0.0 0.0 3.32 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
42 64 3.330701 TGGTTGGAGGGATAGCCATATTC 59.669 47.826 0.00 0.00 33.46 1.75
137 159 0.608035 TTCGCCAAAAATCCGGCTCT 60.608 50.000 0.00 0.00 46.62 4.09
213 339 3.646715 CCCGCCCACCTCTCCAAA 61.647 66.667 0.00 0.00 0.00 3.28
214 340 2.434331 CCGCCCACCTCTCCAAAA 59.566 61.111 0.00 0.00 0.00 2.44
215 341 1.228429 CCGCCCACCTCTCCAAAAA 60.228 57.895 0.00 0.00 0.00 1.94
216 342 1.244019 CCGCCCACCTCTCCAAAAAG 61.244 60.000 0.00 0.00 0.00 2.27
217 343 1.244019 CGCCCACCTCTCCAAAAAGG 61.244 60.000 0.00 0.00 38.70 3.11
218 344 1.536073 GCCCACCTCTCCAAAAAGGC 61.536 60.000 0.00 0.00 36.01 4.35
219 345 0.900182 CCCACCTCTCCAAAAAGGCC 60.900 60.000 0.00 0.00 36.01 5.19
220 346 0.900182 CCACCTCTCCAAAAAGGCCC 60.900 60.000 0.00 0.00 36.01 5.80
221 347 0.113190 CACCTCTCCAAAAAGGCCCT 59.887 55.000 0.00 0.00 36.01 5.19
222 348 0.113190 ACCTCTCCAAAAAGGCCCTG 59.887 55.000 0.00 0.00 36.01 4.45
223 349 1.253593 CCTCTCCAAAAAGGCCCTGC 61.254 60.000 0.00 0.00 37.29 4.85
235 361 2.935481 CCCTGCCCACCTCTCCAA 60.935 66.667 0.00 0.00 0.00 3.53
250 376 3.783082 CTCTCCAACCCTATCTTTTCCCT 59.217 47.826 0.00 0.00 0.00 4.20
262 388 2.644798 TCTTTTCCCTCTTCCTTCCCTG 59.355 50.000 0.00 0.00 0.00 4.45
277 403 3.087370 TCCCTGAAATCTCTCGTCTCA 57.913 47.619 0.00 0.00 0.00 3.27
320 446 1.847818 CAAATCGAATAGACGGCCGA 58.152 50.000 35.90 10.61 35.43 5.54
385 511 4.381718 CCTTAGTCCTCCGTTCGAGATTTT 60.382 45.833 0.00 0.00 41.63 1.82
391 517 0.719465 CCGTTCGAGATTTTCACGGG 59.281 55.000 13.46 0.00 35.86 5.28
519 672 2.823758 GGAGGTAGATGCAGGGGCC 61.824 68.421 0.00 0.00 40.13 5.80
520 673 2.042762 AGGTAGATGCAGGGGCCA 59.957 61.111 4.39 0.00 40.13 5.36
569 748 3.437795 GCAGATGTGCCTTGCGCT 61.438 61.111 9.73 0.00 44.72 5.92
600 779 2.230660 GTGTAGGAAGCTGGCAAACTT 58.769 47.619 2.31 2.31 0.00 2.66
602 781 2.158682 TGTAGGAAGCTGGCAAACTTCA 60.159 45.455 23.59 8.39 43.32 3.02
745 938 0.317269 GTGTGTGTGTGTGCTGATGC 60.317 55.000 0.00 0.00 40.20 3.91
769 962 6.587608 GCTTGATTTGTTTTTCATACAGGAGG 59.412 38.462 0.00 0.00 0.00 4.30
819 1012 3.046374 GGGGCTACATCTCCCTTTTCTA 58.954 50.000 0.00 0.00 42.25 2.10
824 1017 5.532779 GGCTACATCTCCCTTTTCTATTTGG 59.467 44.000 0.00 0.00 0.00 3.28
825 1018 6.122964 GCTACATCTCCCTTTTCTATTTGGT 58.877 40.000 0.00 0.00 0.00 3.67
826 1019 6.603599 GCTACATCTCCCTTTTCTATTTGGTT 59.396 38.462 0.00 0.00 0.00 3.67
829 1022 7.896811 ACATCTCCCTTTTCTATTTGGTTTTC 58.103 34.615 0.00 0.00 0.00 2.29
839 1034 8.760980 TTTCTATTTGGTTTTCTCTCCAAGAA 57.239 30.769 0.00 0.00 43.28 2.52
903 1098 3.264947 TGTACTGCTTGACTGATGATGC 58.735 45.455 0.00 0.00 0.00 3.91
987 1182 3.966979 ACCATTGCATTGTAGATGGACA 58.033 40.909 17.69 0.00 41.20 4.02
1099 1295 4.153117 GGAGAGAAGCAATTACATATGCCG 59.847 45.833 1.58 0.00 43.57 5.69
1331 1527 4.025979 CGTTCGGAATAGAGTAATTGGTGC 60.026 45.833 0.00 0.00 0.00 5.01
1512 1709 4.879545 ACCGAGTGACAACTACATTTTGTT 59.120 37.500 0.00 0.00 37.31 2.83
1684 1888 9.601217 TTGGCAACTAACAATTTTTAGCTTTTA 57.399 25.926 10.61 0.00 33.02 1.52
1779 1983 2.735663 CAACAACAAGCACACAAGCAAA 59.264 40.909 0.00 0.00 36.85 3.68
1786 1990 1.406539 AGCACACAAGCAAACAAGGAG 59.593 47.619 0.00 0.00 36.85 3.69
1792 1996 6.734137 CACACAAGCAAACAAGGAGTATAAA 58.266 36.000 0.00 0.00 0.00 1.40
1795 1999 6.359617 CACAAGCAAACAAGGAGTATAAAACG 59.640 38.462 0.00 0.00 0.00 3.60
1857 2062 0.395311 AGCCGGTGAAGACGAGGATA 60.395 55.000 1.90 0.00 0.00 2.59
1898 2103 4.262506 CCTTTTGAAGGGAAGTACGTCTCT 60.263 45.833 5.24 5.24 45.27 3.10
2146 2352 1.053424 ACCGTCTAGGGTGCTCAAAA 58.947 50.000 0.00 0.00 46.96 2.44
2221 2429 1.409427 GGTGGAAGTGTAGATCGGAGG 59.591 57.143 0.00 0.00 0.00 4.30
2245 2453 5.476945 GCTTCTCAACCAATCCCTAGAAAAA 59.523 40.000 0.00 0.00 0.00 1.94
2399 2607 3.329520 ACTGTTATCCACTAAACCAGCCA 59.670 43.478 0.00 0.00 0.00 4.75
2428 2636 0.822164 GGTACTACCGCACCAGACAT 59.178 55.000 0.00 0.00 34.77 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.327386 ACCAAACACATCCATAGATTAGGT 57.673 37.500 0.00 0.00 0.00 3.08
1 2 6.039717 CCAACCAAACACATCCATAGATTAGG 59.960 42.308 0.00 0.00 0.00 2.69
2 3 6.828273 TCCAACCAAACACATCCATAGATTAG 59.172 38.462 0.00 0.00 0.00 1.73
3 4 6.726379 TCCAACCAAACACATCCATAGATTA 58.274 36.000 0.00 0.00 0.00 1.75
4 5 5.579047 TCCAACCAAACACATCCATAGATT 58.421 37.500 0.00 0.00 0.00 2.40
5 6 5.191727 TCCAACCAAACACATCCATAGAT 57.808 39.130 0.00 0.00 0.00 1.98
6 7 4.567537 CCTCCAACCAAACACATCCATAGA 60.568 45.833 0.00 0.00 0.00 1.98
7 8 3.696051 CCTCCAACCAAACACATCCATAG 59.304 47.826 0.00 0.00 0.00 2.23
10 11 1.480312 CCCTCCAACCAAACACATCCA 60.480 52.381 0.00 0.00 0.00 3.41
218 344 2.935481 TTGGAGAGGTGGGCAGGG 60.935 66.667 0.00 0.00 0.00 4.45
219 345 2.352805 GTTGGAGAGGTGGGCAGG 59.647 66.667 0.00 0.00 0.00 4.85
220 346 2.352805 GGTTGGAGAGGTGGGCAG 59.647 66.667 0.00 0.00 0.00 4.85
221 347 2.409984 TAGGGTTGGAGAGGTGGGCA 62.410 60.000 0.00 0.00 0.00 5.36
222 348 0.988678 ATAGGGTTGGAGAGGTGGGC 60.989 60.000 0.00 0.00 0.00 5.36
223 349 1.132500 GATAGGGTTGGAGAGGTGGG 58.868 60.000 0.00 0.00 0.00 4.61
224 350 2.182516 AGATAGGGTTGGAGAGGTGG 57.817 55.000 0.00 0.00 0.00 4.61
225 351 4.518249 GAAAAGATAGGGTTGGAGAGGTG 58.482 47.826 0.00 0.00 0.00 4.00
226 352 3.523972 GGAAAAGATAGGGTTGGAGAGGT 59.476 47.826 0.00 0.00 0.00 3.85
227 353 3.117851 GGGAAAAGATAGGGTTGGAGAGG 60.118 52.174 0.00 0.00 0.00 3.69
228 354 3.783082 AGGGAAAAGATAGGGTTGGAGAG 59.217 47.826 0.00 0.00 0.00 3.20
229 355 3.780850 GAGGGAAAAGATAGGGTTGGAGA 59.219 47.826 0.00 0.00 0.00 3.71
230 356 3.783082 AGAGGGAAAAGATAGGGTTGGAG 59.217 47.826 0.00 0.00 0.00 3.86
231 357 3.815507 AGAGGGAAAAGATAGGGTTGGA 58.184 45.455 0.00 0.00 0.00 3.53
232 358 4.527944 GAAGAGGGAAAAGATAGGGTTGG 58.472 47.826 0.00 0.00 0.00 3.77
233 359 4.228438 AGGAAGAGGGAAAAGATAGGGTTG 59.772 45.833 0.00 0.00 0.00 3.77
234 360 4.449389 AGGAAGAGGGAAAAGATAGGGTT 58.551 43.478 0.00 0.00 0.00 4.11
235 361 4.095616 AGGAAGAGGGAAAAGATAGGGT 57.904 45.455 0.00 0.00 0.00 4.34
250 376 3.449018 CGAGAGATTTCAGGGAAGGAAGA 59.551 47.826 0.00 0.00 0.00 2.87
262 388 3.304391 CGGGAGATGAGACGAGAGATTTC 60.304 52.174 0.00 0.00 0.00 2.17
320 446 0.247736 GCACTGACCTTGAGATCCGT 59.752 55.000 0.00 0.00 0.00 4.69
519 672 2.016393 TTGCCTCTATCTCCCGCGTG 62.016 60.000 4.92 0.00 0.00 5.34
520 673 1.739338 CTTGCCTCTATCTCCCGCGT 61.739 60.000 4.92 0.00 0.00 6.01
569 748 3.390521 CCTACACCTGCTGCCCGA 61.391 66.667 0.00 0.00 0.00 5.14
580 759 1.897560 AGTTTGCCAGCTTCCTACAC 58.102 50.000 0.00 0.00 0.00 2.90
745 938 7.596248 CACCTCCTGTATGAAAAACAAATCAAG 59.404 37.037 0.00 0.00 0.00 3.02
769 962 1.235724 CCTTGTCGTTCCCCTTTCAC 58.764 55.000 0.00 0.00 0.00 3.18
814 1007 8.630037 GTTCTTGGAGAGAAAACCAAATAGAAA 58.370 33.333 0.00 0.00 45.59 2.52
819 1012 6.129179 TCTGTTCTTGGAGAGAAAACCAAAT 58.871 36.000 0.00 0.00 45.59 2.32
824 1017 4.709250 ACCTCTGTTCTTGGAGAGAAAAC 58.291 43.478 0.00 0.00 45.59 2.43
825 1018 6.099845 AGTTACCTCTGTTCTTGGAGAGAAAA 59.900 38.462 0.00 0.00 45.59 2.29
826 1019 5.602978 AGTTACCTCTGTTCTTGGAGAGAAA 59.397 40.000 0.00 0.00 45.59 2.52
829 1022 5.011125 TCAAGTTACCTCTGTTCTTGGAGAG 59.989 44.000 0.00 0.00 36.63 3.20
903 1098 2.462889 ACAAAAACAACTCAGCATGCG 58.537 42.857 13.01 7.64 34.76 4.73
1021 1217 9.797642 AGCTATCATATTGATAAACCATTGTGA 57.202 29.630 0.00 0.00 38.72 3.58
1099 1295 6.699366 TCATCCTATCTCTCTCATCAATTGC 58.301 40.000 0.00 0.00 0.00 3.56
1331 1527 5.178797 ACTTCACCAGATCTACCGAAATTG 58.821 41.667 0.00 0.00 0.00 2.32
1659 1863 9.771534 ATAAAAGCTAAAAATTGTTAGTTGCCA 57.228 25.926 15.37 1.25 34.20 4.92
1779 1983 8.665685 CAAGCTTATTCGTTTTATACTCCTTGT 58.334 33.333 0.00 0.00 0.00 3.16
1786 1990 7.749126 ACTTGTGCAAGCTTATTCGTTTTATAC 59.251 33.333 11.43 0.00 41.99 1.47
1792 1996 5.682943 TTACTTGTGCAAGCTTATTCGTT 57.317 34.783 11.43 0.00 41.99 3.85
1795 1999 4.859245 GCCTTTACTTGTGCAAGCTTATTC 59.141 41.667 11.43 0.00 41.99 1.75
1898 2103 2.425592 CTCCACACCGCTCCAACA 59.574 61.111 0.00 0.00 0.00 3.33
2078 2283 0.107410 TGGTGAAGCTTCGTGGTGTT 60.107 50.000 21.11 0.00 0.00 3.32
2146 2352 3.868754 GCGGATCTTGTTACTCTTGGGTT 60.869 47.826 0.00 0.00 0.00 4.11
2221 2429 3.914426 TCTAGGGATTGGTTGAGAAGC 57.086 47.619 0.00 0.00 0.00 3.86
2245 2453 3.573967 CCCTAGCCAATCAAACTTGTTGT 59.426 43.478 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.