Multiple sequence alignment - TraesCS3B01G227500

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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 TraesCS3B01G227500 chr3B 100.000 2267 0 0 1 2267 324062305 324064571 0.000000e+00 4187.0
1 TraesCS3B01G227500 chr3B 93.051 2288 125 9 2 2267 321024983 321022708 0.000000e+00 3314.0
2 TraesCS3B01G227500 chr3B 93.651 1071 66 1 1199 2267 818691634 818690564 0.000000e+00 1600.0
3 TraesCS3B01G227500 chr3B 92.690 684 48 2 1199 1882 818646335 818645654 0.000000e+00 985.0
4 TraesCS3B01G227500 chr3B 94.867 526 25 1 1744 2267 818601273 818600748 0.000000e+00 821.0
5 TraesCS3B01G227500 chr3B 92.340 470 34 2 1199 1668 818601741 818601274 0.000000e+00 667.0
6 TraesCS3B01G227500 chr3B 85.668 621 69 13 1 602 727079133 727079752 8.830000e-179 636.0
7 TraesCS3B01G227500 chr3B 93.865 163 8 2 2107 2267 818645658 818645496 6.250000e-61 244.0
8 TraesCS3B01G227500 chr3B 92.208 77 6 0 1000 1076 739452690 739452614 2.380000e-20 110.0
9 TraesCS3B01G227500 chr5D 88.973 1714 131 23 1 1663 165178954 165177248 0.000000e+00 2065.0
10 TraesCS3B01G227500 chr5D 86.434 1489 140 28 210 1660 428132904 428134368 0.000000e+00 1574.0
11 TraesCS3B01G227500 chr5D 94.053 454 25 1 1648 2101 165177162 165176711 0.000000e+00 688.0
12 TraesCS3B01G227500 chr5D 90.538 465 31 6 1648 2101 25279368 25279830 8.960000e-169 603.0
13 TraesCS3B01G227500 chr5D 93.220 177 9 2 2094 2267 165176521 165176345 8.030000e-65 257.0
14 TraesCS3B01G227500 chr5D 90.476 147 14 0 2119 2265 428134431 428134577 6.390000e-46 195.0
15 TraesCS3B01G227500 chr1B 87.233 1402 131 22 5 1362 6014995 6016392 0.000000e+00 1554.0
16 TraesCS3B01G227500 chr1B 89.474 133 14 0 1000 1132 41644206 41644074 3.870000e-38 169.0
17 TraesCS3B01G227500 chr5B 95.316 491 21 1 1779 2267 37737585 37737095 0.000000e+00 778.0
18 TraesCS3B01G227500 chr5B 90.611 458 26 9 1648 2101 17982263 17981819 1.940000e-165 592.0
19 TraesCS3B01G227500 chr5B 91.143 350 31 0 1199 1548 37737942 37737593 2.040000e-130 475.0
20 TraesCS3B01G227500 chr4B 80.309 970 152 21 4 942 156186474 156185513 0.000000e+00 697.0
21 TraesCS3B01G227500 chr4B 85.390 616 73 14 1 602 637308343 637307731 6.880000e-175 623.0
22 TraesCS3B01G227500 chr4B 83.488 648 82 21 2 630 219276146 219275505 4.200000e-162 580.0
23 TraesCS3B01G227500 chr4B 83.489 642 86 16 1 624 355189182 355188543 4.200000e-162 580.0
24 TraesCS3B01G227500 chr2B 81.753 833 108 25 4 802 98119850 98119028 0.000000e+00 656.0
25 TraesCS3B01G227500 chr2B 88.783 526 53 5 1 521 159127913 159127389 6.830000e-180 640.0
26 TraesCS3B01G227500 chr6B 85.993 614 72 11 1 602 103757343 103756732 0.000000e+00 645.0
27 TraesCS3B01G227500 chr6B 84.628 618 73 19 1 602 706273229 706272618 1.500000e-166 595.0
28 TraesCS3B01G227500 chr6B 80.000 300 43 12 519 806 706272567 706272273 2.950000e-49 206.0
29 TraesCS3B01G227500 chr6B 78.983 295 47 11 519 802 706040031 706039741 1.070000e-43 187.0
30 TraesCS3B01G227500 chr6B 92.500 120 9 0 1199 1318 693280900 693281019 2.990000e-39 172.0
31 TraesCS3B01G227500 chr6B 82.166 157 14 8 1012 1168 440454529 440454671 3.060000e-24 122.0
32 TraesCS3B01G227500 chr7D 88.847 529 47 10 1 521 67750504 67749980 6.830000e-180 640.0
33 TraesCS3B01G227500 chr5A 91.793 463 26 5 1648 2101 17838829 17838370 3.180000e-178 634.0
34 TraesCS3B01G227500 chr2A 83.101 645 90 17 1 630 664861778 664862418 9.090000e-159 569.0
35 TraesCS3B01G227500 chr7A 81.729 613 89 20 4 602 641829385 641828782 7.280000e-135 490.0
36 TraesCS3B01G227500 chr7B 80.479 292 44 8 519 799 703901378 703901667 6.340000e-51 211.0
37 TraesCS3B01G227500 chr1D 94.215 121 7 0 1134 1254 341838882 341838762 3.850000e-43 185.0
38 TraesCS3B01G227500 chr1D 87.970 133 16 0 1000 1132 25957664 25957532 8.380000e-35 158.0
39 TraesCS3B01G227500 chr1D 77.778 243 26 17 1012 1254 171906068 171906282 8.500000e-25 124.0
40 TraesCS3B01G227500 chr1D 84.058 69 5 3 2203 2265 19189387 19189319 6.760000e-06 62.1
41 TraesCS3B01G227500 chr6D 84.431 167 19 4 957 1123 425870765 425870924 8.380000e-35 158.0


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 TraesCS3B01G227500 chr3B 324062305 324064571 2266 False 4187.000000 4187 100.0000 1 2267 1 chr3B.!!$F1 2266
1 TraesCS3B01G227500 chr3B 321022708 321024983 2275 True 3314.000000 3314 93.0510 2 2267 1 chr3B.!!$R1 2265
2 TraesCS3B01G227500 chr3B 818690564 818691634 1070 True 1600.000000 1600 93.6510 1199 2267 1 chr3B.!!$R3 1068
3 TraesCS3B01G227500 chr3B 818600748 818601741 993 True 744.000000 821 93.6035 1199 2267 2 chr3B.!!$R4 1068
4 TraesCS3B01G227500 chr3B 727079133 727079752 619 False 636.000000 636 85.6680 1 602 1 chr3B.!!$F2 601
5 TraesCS3B01G227500 chr3B 818645496 818646335 839 True 614.500000 985 93.2775 1199 2267 2 chr3B.!!$R5 1068
6 TraesCS3B01G227500 chr5D 165176345 165178954 2609 True 1003.333333 2065 92.0820 1 2267 3 chr5D.!!$R1 2266
7 TraesCS3B01G227500 chr5D 428132904 428134577 1673 False 884.500000 1574 88.4550 210 2265 2 chr5D.!!$F2 2055
8 TraesCS3B01G227500 chr1B 6014995 6016392 1397 False 1554.000000 1554 87.2330 5 1362 1 chr1B.!!$F1 1357
9 TraesCS3B01G227500 chr5B 37737095 37737942 847 True 626.500000 778 93.2295 1199 2267 2 chr5B.!!$R2 1068
10 TraesCS3B01G227500 chr4B 156185513 156186474 961 True 697.000000 697 80.3090 4 942 1 chr4B.!!$R1 938
11 TraesCS3B01G227500 chr4B 637307731 637308343 612 True 623.000000 623 85.3900 1 602 1 chr4B.!!$R4 601
12 TraesCS3B01G227500 chr4B 219275505 219276146 641 True 580.000000 580 83.4880 2 630 1 chr4B.!!$R2 628
13 TraesCS3B01G227500 chr4B 355188543 355189182 639 True 580.000000 580 83.4890 1 624 1 chr4B.!!$R3 623
14 TraesCS3B01G227500 chr2B 98119028 98119850 822 True 656.000000 656 81.7530 4 802 1 chr2B.!!$R1 798
15 TraesCS3B01G227500 chr2B 159127389 159127913 524 True 640.000000 640 88.7830 1 521 1 chr2B.!!$R2 520
16 TraesCS3B01G227500 chr6B 103756732 103757343 611 True 645.000000 645 85.9930 1 602 1 chr6B.!!$R1 601
17 TraesCS3B01G227500 chr6B 706272273 706273229 956 True 400.500000 595 82.3140 1 806 2 chr6B.!!$R3 805
18 TraesCS3B01G227500 chr7D 67749980 67750504 524 True 640.000000 640 88.8470 1 521 1 chr7D.!!$R1 520
19 TraesCS3B01G227500 chr2A 664861778 664862418 640 False 569.000000 569 83.1010 1 630 1 chr2A.!!$F1 629
20 TraesCS3B01G227500 chr7A 641828782 641829385 603 True 490.000000 490 81.7290 4 602 1 chr7A.!!$R1 598

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
799 1027 0.762418 TTCGCCCCTCACTTTCTCAA 59.238 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2652 1.246649 CAATGCCTGTGTTGCCACTA 58.753 50.0 0.0 0.0 42.34 2.74 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
164 167 7.785033 TCTTCACACATGATAGCTCATTTCTA 58.215 34.615 0.00 0.00 40.20 2.10
200 204 8.527567 TTTAAAAGAATTGCCGAATTACAAGG 57.472 30.769 0.00 0.00 31.58 3.61
349 384 4.127171 GCTAGCGGTTGAATCTTGGATTA 58.873 43.478 0.00 0.00 0.00 1.75
701 927 6.096141 TCACAAGGTCTTCAAATTGTTTGCTA 59.904 34.615 0.00 0.00 40.43 3.49
706 932 5.746721 GGTCTTCAAATTGTTTGCTACGTTT 59.253 36.000 0.00 0.00 40.43 3.60
755 981 1.302511 GTGCATCAACCACCGTCCT 60.303 57.895 0.00 0.00 0.00 3.85
799 1027 0.762418 TTCGCCCCTCACTTTCTCAA 59.238 50.000 0.00 0.00 0.00 3.02
1103 1359 2.852495 CTACCCATGCTTGGCGTCGT 62.852 60.000 13.15 8.09 42.15 4.34
1113 1369 2.149803 TTGGCGTCGTCTTCATCGGT 62.150 55.000 0.00 0.00 0.00 4.69
1258 1514 1.134367 GTCCTCATCGTCCACATCGAA 59.866 52.381 0.00 0.00 40.61 3.71
1298 1554 0.759346 AGGTGCGTCTGTTCTCCTTT 59.241 50.000 0.00 0.00 0.00 3.11
1314 1570 1.152922 TTTTTCCTCGCCCCGTTGT 60.153 52.632 0.00 0.00 0.00 3.32
1362 1618 1.899814 AGGGCTCACGTTATTGACTGA 59.100 47.619 0.00 0.00 0.00 3.41
1385 1641 2.009774 GCTATTGTGGTTCTGCGTCAT 58.990 47.619 0.00 0.00 0.00 3.06
1447 1703 2.195567 GGTGTGCCTGCTTGCTTCA 61.196 57.895 0.00 0.00 0.00 3.02
1460 1716 3.250521 GCTTGCTTCATCTCCTCTATTGC 59.749 47.826 0.00 0.00 0.00 3.56
1461 1717 4.449131 CTTGCTTCATCTCCTCTATTGCA 58.551 43.478 0.00 0.00 0.00 4.08
1540 1798 1.134521 TGATTTCGCTAGCGGAATGGT 60.135 47.619 40.76 23.62 46.36 3.55
1704 2075 9.639563 TTGCATAGTATTATTCATTTTCTCCCA 57.360 29.630 0.00 0.00 0.00 4.37
1720 2091 0.981183 CCCACACCTGCACCTAGTTA 59.019 55.000 0.00 0.00 0.00 2.24
1789 2160 4.004196 ACACCTTACACCTGAACTAAGC 57.996 45.455 0.00 0.00 0.00 3.09
1801 2172 9.424319 ACACCTGAACTAAGCATATTATAATCG 57.576 33.333 0.00 0.00 0.00 3.34
1852 2223 6.489022 CACACCTTCCATGAATCATGATATGT 59.511 38.462 23.55 15.81 43.81 2.29
1939 2539 9.981114 ATAAGTTGTTTTATAGCAAGCACTTTT 57.019 25.926 0.00 0.00 0.00 2.27
2041 2641 1.518903 GGGTTTCCAGAGTGTGCTGC 61.519 60.000 0.00 0.00 34.56 5.25
2052 2652 0.740737 GTGTGCTGCTTGAACCAACT 59.259 50.000 0.00 0.00 0.00 3.16
2171 2970 9.736414 AGCAGAGTCTTATATATTAACGGTCTA 57.264 33.333 0.00 0.00 0.00 2.59
2183 2982 2.871096 ACGGTCTATGCCAAGGAAAA 57.129 45.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 204 9.850628 GACCAAGTTACCAGGAAAAATAATAAC 57.149 33.333 0.00 0.00 0.00 1.89
269 300 4.897140 TGAAATGGGCAGGAAAAATTCAG 58.103 39.130 0.00 0.00 0.00 3.02
280 312 1.068434 ACCGTGTTTTGAAATGGGCAG 59.932 47.619 0.00 0.00 0.00 4.85
603 674 7.177832 TCCTATTTTCCGAGTGTCAAAGATA 57.822 36.000 0.00 0.00 0.00 1.98
701 927 2.288763 GCCCATGAACCAATCAAAACGT 60.289 45.455 0.00 0.00 42.54 3.99
706 932 2.496871 GACATGCCCATGAACCAATCAA 59.503 45.455 14.69 0.00 42.54 2.57
755 981 0.466543 CCGTTGGATCCGGGACAATA 59.533 55.000 7.39 0.00 41.78 1.90
799 1027 2.224695 GGCTGTGTTAGGGTTAAGTGGT 60.225 50.000 0.00 0.00 0.00 4.16
937 1180 0.840722 GAGGTTGGAAGGGGAGGTCA 60.841 60.000 0.00 0.00 0.00 4.02
998 1254 1.207791 GGTCAGATCCACCACCATCT 58.792 55.000 6.57 0.00 33.63 2.90
1095 1351 2.180769 CCGATGAAGACGACGCCA 59.819 61.111 0.00 0.00 0.00 5.69
1103 1359 3.247056 TTGGCGGCACCGATGAAGA 62.247 57.895 12.92 0.00 43.94 2.87
1113 1369 2.688666 AGGGAGATCTTGGCGGCA 60.689 61.111 7.97 7.97 0.00 5.69
1206 1462 0.242825 GAAGTCGTGGTGGATGACGA 59.757 55.000 0.00 0.00 44.34 4.20
1258 1514 3.580458 CTGGGATGGATCTTCTACGGAAT 59.420 47.826 0.00 0.00 0.00 3.01
1298 1554 2.031465 GACAACGGGGCGAGGAAA 59.969 61.111 0.00 0.00 0.00 3.13
1349 1605 5.232202 CACAATAGCGATCAGTCAATAACGT 59.768 40.000 0.00 0.00 0.00 3.99
1385 1641 1.063327 CACAACCGCAAACGCAAGA 59.937 52.632 0.00 0.00 43.62 3.02
1441 1697 3.739209 CGTGCAATAGAGGAGATGAAGCA 60.739 47.826 0.00 0.00 0.00 3.91
1447 1703 1.414181 CCACCGTGCAATAGAGGAGAT 59.586 52.381 0.00 0.00 0.00 2.75
1502 1759 2.978010 CCCAAAAGAGGCACGCGT 60.978 61.111 5.58 5.58 0.00 6.01
1507 1764 1.885887 CGAAATCACCCAAAAGAGGCA 59.114 47.619 0.00 0.00 0.00 4.75
1540 1798 4.162320 AGTTCCTCGGCTAGATTCATTCAA 59.838 41.667 0.00 0.00 0.00 2.69
1703 2074 4.154195 GTCAAATAACTAGGTGCAGGTGTG 59.846 45.833 0.00 0.00 0.00 3.82
1704 2075 4.041691 AGTCAAATAACTAGGTGCAGGTGT 59.958 41.667 0.00 0.00 0.00 4.16
1720 2091 2.157738 GAGCAGCTGGACAAGTCAAAT 58.842 47.619 17.12 0.00 0.00 2.32
1801 2172 9.917129 GGTAAGTATTTAAATAGAGAGGCTCTC 57.083 37.037 32.45 32.45 43.70 3.20
2052 2652 1.246649 CAATGCCTGTGTTGCCACTA 58.753 50.000 0.00 0.00 42.34 2.74
2183 2982 4.439253 AGAAAGGCTAGTGACTTGGTTT 57.561 40.909 0.00 0.00 41.48 3.27


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

AutoCloner maintained by Alex Coulton.