Multiple sequence alignment - TraesCS1A01G296800

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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 TraesCS1A01G296800 chr1A 100.000 2533 0 0 1 2533 492001377 491998845 0.000000e+00 4678.0
1 TraesCS1A01G296800 chr1A 93.237 1109 73 2 1426 2533 575003036 575004143 0.000000e+00 1631.0
2 TraesCS1A01G296800 chr1A 89.379 612 54 3 1426 2035 575076928 575077530 0.000000e+00 760.0
3 TraesCS1A01G296800 chr1A 88.871 611 58 2 1426 2035 575036359 575036960 0.000000e+00 743.0
4 TraesCS1A01G296800 chr6B 89.874 2548 227 13 1 2533 184805786 184808317 0.000000e+00 3247.0
5 TraesCS1A01G296800 chr4A 89.385 2195 221 6 350 2533 640155809 640153616 0.000000e+00 2752.0
6 TraesCS1A01G296800 chr4A 87.458 1188 124 15 1353 2532 703403632 703402462 0.000000e+00 1345.0
7 TraesCS1A01G296800 chr4A 74.796 1349 276 50 3 1334 708315836 708317137 1.320000e-152 549.0
8 TraesCS1A01G296800 chr4A 89.062 320 29 1 1 320 640174222 640174535 2.360000e-105 392.0
9 TraesCS1A01G296800 chr4A 73.261 733 147 21 812 1525 16260171 16259469 3.280000e-54 222.0
10 TraesCS1A01G296800 chr3B 91.525 1357 101 7 1187 2533 513943182 513944534 0.000000e+00 1857.0
11 TraesCS1A01G296800 chr3B 91.965 1257 87 6 1287 2533 661544680 661543428 0.000000e+00 1749.0
12 TraesCS1A01G296800 chr1B 96.105 1027 37 3 1508 2533 266115589 266114565 0.000000e+00 1672.0
13 TraesCS1A01G296800 chr1B 94.872 39 2 0 785 823 667720111 667720149 7.570000e-06 62.1
14 TraesCS1A01G296800 chr4D 88.255 1175 124 12 1369 2533 118590139 118588969 0.000000e+00 1393.0
15 TraesCS1A01G296800 chr4D 86.545 550 59 6 840 1377 118592252 118591706 2.170000e-165 592.0
16 TraesCS1A01G296800 chr3A 94.595 888 46 2 1645 2531 120813948 120814834 0.000000e+00 1373.0
17 TraesCS1A01G296800 chr3A 80.876 251 42 4 1 251 82459029 82459273 2.570000e-45 193.0
18 TraesCS1A01G296800 chr7D 94.928 828 39 3 1707 2533 37927818 37926993 0.000000e+00 1293.0
19 TraesCS1A01G296800 chr6D 87.833 526 34 14 614 1135 455718412 455718911 7.800000e-165 590.0
20 TraesCS1A01G296800 chr4B 74.500 1349 282 48 2 1334 614060623 614061925 1.730000e-146 529.0
21 TraesCS1A01G296800 chr6A 77.622 429 90 2 1 429 52704743 52704321 3.230000e-64 255.0


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 TraesCS1A01G296800 chr1A 491998845 492001377 2532 True 4678.0 4678 100.000 1 2533 1 chr1A.!!$R1 2532
1 TraesCS1A01G296800 chr1A 575003036 575004143 1107 False 1631.0 1631 93.237 1426 2533 1 chr1A.!!$F1 1107
2 TraesCS1A01G296800 chr1A 575076928 575077530 602 False 760.0 760 89.379 1426 2035 1 chr1A.!!$F3 609
3 TraesCS1A01G296800 chr1A 575036359 575036960 601 False 743.0 743 88.871 1426 2035 1 chr1A.!!$F2 609
4 TraesCS1A01G296800 chr6B 184805786 184808317 2531 False 3247.0 3247 89.874 1 2533 1 chr6B.!!$F1 2532
5 TraesCS1A01G296800 chr4A 640153616 640155809 2193 True 2752.0 2752 89.385 350 2533 1 chr4A.!!$R2 2183
6 TraesCS1A01G296800 chr4A 703402462 703403632 1170 True 1345.0 1345 87.458 1353 2532 1 chr4A.!!$R3 1179
7 TraesCS1A01G296800 chr4A 708315836 708317137 1301 False 549.0 549 74.796 3 1334 1 chr4A.!!$F2 1331
8 TraesCS1A01G296800 chr4A 16259469 16260171 702 True 222.0 222 73.261 812 1525 1 chr4A.!!$R1 713
9 TraesCS1A01G296800 chr3B 513943182 513944534 1352 False 1857.0 1857 91.525 1187 2533 1 chr3B.!!$F1 1346
10 TraesCS1A01G296800 chr3B 661543428 661544680 1252 True 1749.0 1749 91.965 1287 2533 1 chr3B.!!$R1 1246
11 TraesCS1A01G296800 chr1B 266114565 266115589 1024 True 1672.0 1672 96.105 1508 2533 1 chr1B.!!$R1 1025
12 TraesCS1A01G296800 chr4D 118588969 118592252 3283 True 992.5 1393 87.400 840 2533 2 chr4D.!!$R1 1693
13 TraesCS1A01G296800 chr3A 120813948 120814834 886 False 1373.0 1373 94.595 1645 2531 1 chr3A.!!$F2 886
14 TraesCS1A01G296800 chr7D 37926993 37927818 825 True 1293.0 1293 94.928 1707 2533 1 chr7D.!!$R1 826
15 TraesCS1A01G296800 chr4B 614060623 614061925 1302 False 529.0 529 74.500 2 1334 1 chr4B.!!$F1 1332


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
657 658 0.036164 TGTCGCCCACAACTATGCTT 59.964 50.0 0.0 0.0 29.3 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 3814 1.110442 CTTGCACAAGGTTGGGTTCA 58.89 50.0 2.32 0.0 34.87 3.18 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
55 56 2.448542 GGAGGGGGCAGCCTATCA 60.449 66.667 12.43 0.00 0.00 2.15
117 118 0.625316 CCATCCATGAAGACCCCACA 59.375 55.000 0.00 0.00 0.00 4.17
120 121 0.692476 TCCATGAAGACCCCACACAG 59.308 55.000 0.00 0.00 0.00 3.66
146 147 1.279271 CAAGATCGTCTCCAAGGGGTT 59.721 52.381 0.00 0.00 34.93 4.11
244 245 2.200370 ACAGGAGGGACCGTGACA 59.800 61.111 0.00 0.00 44.74 3.58
257 258 3.299050 GTGACAACGACCATGACCA 57.701 52.632 0.00 0.00 0.00 4.02
332 333 4.408821 GGGTGACCGCATCAGGCA 62.409 66.667 0.00 0.00 45.17 4.75
346 347 4.292178 GGCATAGCCTCTCGCGCT 62.292 66.667 5.56 0.00 46.69 5.92
432 433 2.126850 CGTCGTCGCTCTGCTGAA 60.127 61.111 0.00 0.00 0.00 3.02
436 437 2.258591 GTCGCTCTGCTGAACCGA 59.741 61.111 10.55 10.55 0.00 4.69
443 444 2.046023 TGCTGAACCGAGCATGGG 60.046 61.111 0.00 0.00 44.16 4.00
451 452 4.776322 CGAGCATGGGTTCGGGCA 62.776 66.667 0.00 0.00 43.05 5.36
455 456 2.350458 GCATGGGTTCGGGCAATGT 61.350 57.895 0.00 0.00 0.00 2.71
456 457 1.887344 GCATGGGTTCGGGCAATGTT 61.887 55.000 0.00 0.00 0.00 2.71
480 481 2.588989 CTCCAAGGCTCTGGCTCC 59.411 66.667 9.90 0.00 37.50 4.70
489 490 4.704833 TCTGGCTCCGCAAGTGGC 62.705 66.667 0.00 0.00 39.90 5.01
532 533 2.203523 TGCCTGTGCATGCCACTT 60.204 55.556 16.68 0.00 44.23 3.16
544 545 2.034687 CCACTTCCCTGGCTGTGG 59.965 66.667 13.68 13.68 42.98 4.17
615 616 4.767255 CGCTCCCAGGAAGCGCTT 62.767 66.667 25.35 25.35 44.91 4.68
652 653 0.470766 ACCTTTGTCGCCCACAACTA 59.529 50.000 0.00 0.00 45.12 2.24
657 658 0.036164 TGTCGCCCACAACTATGCTT 59.964 50.000 0.00 0.00 29.30 3.91
668 669 3.521126 ACAACTATGCTTCCACCATCTCT 59.479 43.478 0.00 0.00 0.00 3.10
711 712 2.583441 CCCCTCACCGCTCTCACAA 61.583 63.158 0.00 0.00 0.00 3.33
766 767 2.044252 CAGCCAGGCTCCAAGCAT 60.044 61.111 12.53 0.00 44.75 3.79
826 827 1.617018 CCCAACGCCTCCTCTGATCA 61.617 60.000 0.00 0.00 0.00 2.92
891 892 1.656441 GGGTGCTGTTGCTGTTGAG 59.344 57.895 0.00 0.00 40.48 3.02
900 901 4.660938 GCTGTTGAGGGGGCGGTT 62.661 66.667 0.00 0.00 0.00 4.44
937 938 0.942252 GCCACTTTTCGAAGACCGTT 59.058 50.000 0.00 0.00 39.75 4.44
962 966 3.095163 CATCCTGCCCCCTGCTCT 61.095 66.667 0.00 0.00 42.00 4.09
1059 1063 0.448990 CCATCACCAAGTCATGTGCG 59.551 55.000 0.00 0.00 32.51 5.34
1176 1180 2.821378 CAAAGATGGGCAAGATGTCACA 59.179 45.455 0.00 0.00 0.00 3.58
1197 1201 2.985847 GCTGCCCTGGACGCTTTT 60.986 61.111 0.00 0.00 0.00 2.27
1200 1204 4.056125 GCCCTGGACGCTTTTGCC 62.056 66.667 0.00 0.00 43.93 4.52
1237 1241 1.153309 CTGCCGCCAGATGTGATCA 60.153 57.895 0.00 0.00 41.77 2.92
1239 1243 0.107066 TGCCGCCAGATGTGATCATT 60.107 50.000 0.00 0.00 34.06 2.57
1246 1250 3.219281 CCAGATGTGATCATTGCCATGA 58.781 45.455 2.51 2.51 43.85 3.07
1265 1269 1.882623 GAGAGGGTTGTTCAAGCTTGG 59.117 52.381 25.73 8.01 0.00 3.61
1274 1278 1.042229 TTCAAGCTTGGCTGCAACAT 58.958 45.000 25.73 0.00 39.62 2.71
1384 2973 1.264020 CTTGAGCGCTTGTTGTTGCTA 59.736 47.619 13.26 0.00 37.91 3.49
1395 2984 2.238646 TGTTGTTGCTATCTACCTGGGG 59.761 50.000 0.00 0.00 0.00 4.96
1434 3025 5.747675 TGTTAGCACAAAAACATGTCATGTG 59.252 36.000 23.69 23.69 44.07 3.21
1467 3060 2.517402 GTGTGGGGTGCCAAACGA 60.517 61.111 0.00 0.00 0.00 3.85
1477 3070 0.531974 TGCCAAACGAGTTTCGAGCT 60.532 50.000 5.38 0.00 43.74 4.09
1526 3119 1.208535 CCGTGCTGGGTTATGTTCCTA 59.791 52.381 0.00 0.00 0.00 2.94
1544 3137 7.062322 TGTTCCTATGACCATTAGAATGCAAT 58.938 34.615 0.00 0.00 35.08 3.56
1565 3178 0.179187 TGTTGTTGTGTCCGTTTGCG 60.179 50.000 0.00 0.00 37.95 4.85
1583 3196 1.229428 CGCTGCTTCTTGGAAGACAA 58.771 50.000 10.94 0.00 34.13 3.18
1603 3216 2.125350 CTCAAGGCGCTCCCTGTC 60.125 66.667 7.64 0.00 45.62 3.51
1888 3512 0.640768 GCATCAGCTTCACGACGTAC 59.359 55.000 0.00 0.00 37.91 3.67
2040 3664 4.329545 GACCTGGCTTGCCACCGA 62.330 66.667 10.65 0.00 0.00 4.69
2190 3814 2.842496 TCACTTGGAGCAATGAGAGGAT 59.158 45.455 0.00 0.00 0.00 3.24
2216 3840 2.221169 CAACCTTGTGCAAGCTAGACA 58.779 47.619 6.42 0.00 37.11 3.41
2243 3867 2.746277 GCAACGCCGATTGGGACT 60.746 61.111 0.00 0.00 38.47 3.85
2266 3890 2.863809 ACCTTCAACACCCATGTTCTC 58.136 47.619 0.00 0.00 46.46 2.87
2304 3928 1.102154 CTCTCTGATCACTGTCCGCT 58.898 55.000 0.00 0.00 0.00 5.52
2452 4076 2.017113 GCCATACCAAGCGCTTTACCT 61.017 52.381 22.51 5.38 0.00 3.08
2475 4099 6.024552 TCAAACTCAAAAAGACTGCACTTT 57.975 33.333 0.00 0.00 41.09 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.682257 GATGATAGGCTGCCCCCTC 59.318 63.158 16.57 10.27 36.41 4.30
40 41 2.219875 CGATGATAGGCTGCCCCCT 61.220 63.158 16.57 0.00 39.05 4.79
41 42 2.348998 CGATGATAGGCTGCCCCC 59.651 66.667 16.57 5.31 0.00 5.40
42 43 2.348998 CCGATGATAGGCTGCCCC 59.651 66.667 16.57 5.70 0.00 5.80
43 44 2.348998 CCCGATGATAGGCTGCCC 59.651 66.667 16.57 0.00 0.00 5.36
44 45 2.359230 GCCCGATGATAGGCTGCC 60.359 66.667 11.65 11.65 46.14 4.85
55 56 2.514592 CAAGCCACGATGCCCGAT 60.515 61.111 2.54 0.00 41.76 4.18
117 118 0.252284 AGACGATCTTGGGACCCTGT 60.252 55.000 13.00 0.47 0.00 4.00
120 121 0.976073 TGGAGACGATCTTGGGACCC 60.976 60.000 2.45 2.45 0.00 4.46
178 179 2.202932 GGGATCACGCGCATGTCT 60.203 61.111 5.73 0.00 0.00 3.41
203 204 1.378646 TCGACAGGGCGAGAGATGT 60.379 57.895 0.00 0.00 35.01 3.06
251 252 0.456221 GTCATCTCGACCGTGGTCAT 59.544 55.000 18.54 2.46 44.77 3.06
312 313 2.436646 CTGATGCGGTCACCCCAC 60.437 66.667 0.00 0.00 32.22 4.61
332 333 2.631580 GGCTAGCGCGAGAGGCTAT 61.632 63.158 22.43 0.00 41.76 2.97
375 376 4.689549 TCCCGCCCCTCTTCACGA 62.690 66.667 0.00 0.00 0.00 4.35
395 396 2.592993 CCACCACCATCCCGACAGT 61.593 63.158 0.00 0.00 0.00 3.55
397 398 4.028490 GCCACCACCATCCCGACA 62.028 66.667 0.00 0.00 0.00 4.35
436 437 2.053865 CATTGCCCGAACCCATGCT 61.054 57.895 0.00 0.00 0.00 3.79
451 452 1.526575 CCTTGGAGCACCGCAACATT 61.527 55.000 0.00 0.00 39.42 2.71
455 456 4.269523 AGCCTTGGAGCACCGCAA 62.270 61.111 0.00 0.00 39.42 4.85
456 457 4.704833 GAGCCTTGGAGCACCGCA 62.705 66.667 0.00 0.00 39.42 5.69
498 499 3.923864 ACCAACTCCAGCACGCGA 61.924 61.111 15.93 0.00 0.00 5.87
532 533 4.980592 TCCAGCCACAGCCAGGGA 62.981 66.667 0.00 0.00 41.25 4.20
543 544 4.821589 CTTCGGCCTCGTCCAGCC 62.822 72.222 0.00 0.00 46.17 4.85
637 638 0.036164 AGCATAGTTGTGGGCGACAA 59.964 50.000 11.22 11.22 42.55 3.18
657 658 2.725312 GGAGCGCAGAGATGGTGGA 61.725 63.158 11.47 0.00 0.00 4.02
668 669 1.260538 ATCACTTCTCCTGGAGCGCA 61.261 55.000 19.08 4.52 0.00 6.09
750 751 2.274760 GATGCTTGGAGCCTGGCT 59.725 61.111 23.64 23.64 41.51 4.75
766 767 2.049156 CGCAGGTGAGAGCAACGA 60.049 61.111 0.00 0.00 36.63 3.85
826 827 2.555547 GCTGCAAAGGACCGCTTGT 61.556 57.895 10.09 0.00 0.00 3.16
1200 1204 2.433145 TGCTCCTTGAAGCGCTCG 60.433 61.111 12.06 0.00 45.54 5.03
1237 1241 2.225091 TGAACAACCCTCTCATGGCAAT 60.225 45.455 0.00 0.00 0.00 3.56
1239 1243 0.770499 TGAACAACCCTCTCATGGCA 59.230 50.000 0.00 0.00 0.00 4.92
1246 1250 1.986882 CCAAGCTTGAACAACCCTCT 58.013 50.000 28.05 0.00 0.00 3.69
1265 1269 2.703409 CCGTAGCGATGTTGCAGC 59.297 61.111 0.00 0.00 37.31 5.25
1384 2973 2.514726 AACTATGGCCCCAGGTAGAT 57.485 50.000 0.00 0.00 0.00 1.98
1395 2984 7.083875 TGTGCTAACATTAAGAAACTATGGC 57.916 36.000 0.00 0.00 0.00 4.40
1423 3014 2.361757 CCAAACACACCACATGACATGT 59.638 45.455 15.48 15.48 46.22 3.21
1434 3025 2.831284 ACACGGGCCAAACACACC 60.831 61.111 4.39 0.00 0.00 4.16
1461 3054 3.566523 ACTCTAGCTCGAAACTCGTTTG 58.433 45.455 0.00 0.00 41.35 2.93
1462 3055 3.919223 ACTCTAGCTCGAAACTCGTTT 57.081 42.857 0.00 0.00 41.35 3.60
1467 3060 4.051922 CAACACAACTCTAGCTCGAAACT 58.948 43.478 0.00 0.00 0.00 2.66
1477 3070 2.582052 CCAAAGGCCAACACAACTCTA 58.418 47.619 5.01 0.00 0.00 2.43
1526 3119 6.071221 ACAACACATTGCATTCTAATGGTCAT 60.071 34.615 4.93 0.00 39.66 3.06
1544 3137 1.401670 GCAAACGGACACAACAACACA 60.402 47.619 0.00 0.00 0.00 3.72
1565 3178 2.163211 GGATTGTCTTCCAAGAAGCAGC 59.837 50.000 0.00 0.00 36.68 5.25
1583 3196 2.366167 AGGGAGCGCCTTGAGGAT 60.366 61.111 2.29 0.00 37.39 3.24
1603 3216 9.314321 AGTTAATCGGTTGTTCTATCATGTAAG 57.686 33.333 0.00 0.00 0.00 2.34
1797 3420 2.335712 CCCGAAGCAGGTCTTTGCC 61.336 63.158 0.00 0.00 45.18 4.52
2190 3814 1.110442 CTTGCACAAGGTTGGGTTCA 58.890 50.000 2.32 0.00 34.87 3.18
2243 3867 2.746279 ACATGGGTGTTGAAGGTTGA 57.254 45.000 0.00 0.00 34.01 3.18
2266 3890 2.751806 GAGGGAGGAAGAAAGTGCATTG 59.248 50.000 0.00 0.00 0.00 2.82
2304 3928 1.536766 CTTGTCATCGGCAAGCAGAAA 59.463 47.619 0.00 0.00 37.18 2.52
2452 4076 5.643379 AAGTGCAGTCTTTTTGAGTTTGA 57.357 34.783 0.00 0.00 0.00 2.69



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

AutoCloner maintained by Alex Coulton.