Multiple sequence alignment - TraesCS3B01G597100

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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 TraesCS3B01G597100 chr3B 100.000 2906 0 0 1 2906 819703491 819706396 0.000000e+00 5367.0
1 TraesCS3B01G597100 chr3B 98.233 1811 24 4 437 2247 812489102 812487300 0.000000e+00 3160.0
2 TraesCS3B01G597100 chr3B 90.864 602 43 5 1647 2247 812486973 812486383 0.000000e+00 797.0
3 TraesCS3B01G597100 chr3B 94.118 153 7 1 84 236 812489331 812489181 6.260000e-57 231.0
4 TraesCS3B01G597100 chr3B 84.874 119 14 2 100 218 25328230 25328344 1.830000e-22 117.0
5 TraesCS3B01G597100 chr3D 91.927 1796 102 10 411 2180 604748461 604750239 0.000000e+00 2473.0
6 TraesCS3B01G597100 chr3D 88.280 1715 152 18 504 2180 604702911 604701208 0.000000e+00 2008.0
7 TraesCS3B01G597100 chr3D 92.737 358 26 0 2239 2596 345760124 345759767 4.290000e-143 518.0
8 TraesCS3B01G597100 chr3D 77.637 237 44 9 2614 2845 118421795 118422027 5.050000e-28 135.0
9 TraesCS3B01G597100 chr3D 95.652 46 1 1 2202 2247 604750241 604750285 4.020000e-09 73.1
10 TraesCS3B01G597100 chr3D 93.478 46 2 1 2202 2247 604701206 604701162 1.870000e-07 67.6
11 TraesCS3B01G597100 chr3A 90.794 1347 65 21 222 1526 735419599 735418270 0.000000e+00 1746.0
12 TraesCS3B01G597100 chr3A 92.233 412 23 3 1773 2180 735410574 735410168 2.510000e-160 575.0
13 TraesCS3B01G597100 chr3A 91.923 260 17 1 1523 1778 735412006 735411747 7.660000e-96 361.0
14 TraesCS3B01G597100 chr3A 87.375 301 29 4 972 1263 735257250 735256950 1.290000e-88 337.0
15 TraesCS3B01G597100 chr3A 88.554 166 8 3 1 156 735430011 735429847 1.060000e-44 191.0
16 TraesCS3B01G597100 chr3A 82.199 191 27 3 617 800 698032284 698032094 1.080000e-34 158.0
17 TraesCS3B01G597100 chr3A 84.337 166 19 4 624 784 698146379 698146216 3.880000e-34 156.0
18 TraesCS3B01G597100 chrUn 86.621 1450 163 18 565 2001 374475320 374476751 0.000000e+00 1574.0
19 TraesCS3B01G597100 chrUn 92.737 358 26 0 2239 2596 80157757 80158114 4.290000e-143 518.0
20 TraesCS3B01G597100 chrUn 92.437 238 17 1 2003 2240 430919059 430918823 3.590000e-89 339.0
21 TraesCS3B01G597100 chrUn 86.486 111 4 2 1 100 374475159 374475269 8.510000e-21 111.0
22 TraesCS3B01G597100 chrUn 92.537 67 3 2 2587 2653 229102108 229102172 8.570000e-16 95.3
23 TraesCS3B01G597100 chr7D 95.556 360 16 0 2237 2596 15213722 15214081 6.980000e-161 577.0
24 TraesCS3B01G597100 chr7D 91.899 358 29 0 2239 2596 52485283 52485640 4.320000e-138 501.0
25 TraesCS3B01G597100 chr7D 95.865 266 10 1 2642 2906 15215531 15215796 2.070000e-116 429.0
26 TraesCS3B01G597100 chr7D 89.179 268 25 3 2642 2906 15215442 15215708 6.000000e-87 331.0
27 TraesCS3B01G597100 chr7D 80.422 332 40 13 2595 2903 15215287 15215616 2.250000e-56 230.0
28 TraesCS3B01G597100 chr2A 95.304 362 13 1 2239 2596 708518796 708519157 3.250000e-159 571.0
29 TraesCS3B01G597100 chr2A 94.361 266 14 1 2642 2906 708520504 708520769 9.700000e-110 407.0
30 TraesCS3B01G597100 chr5D 92.737 358 26 0 2239 2596 444783228 444783585 4.290000e-143 518.0
31 TraesCS3B01G597100 chr5D 78.166 458 88 7 570 1021 37138816 37139267 6.130000e-72 281.0
32 TraesCS3B01G597100 chr5B 92.737 358 26 0 2239 2596 534893110 534892753 4.290000e-143 518.0
33 TraesCS3B01G597100 chr7A 92.179 358 28 0 2239 2596 90525440 90525083 9.290000e-140 507.0
34 TraesCS3B01G597100 chr7A 83.575 207 27 5 2599 2803 40531345 40531144 1.370000e-43 187.0
35 TraesCS3B01G597100 chr7A 81.215 181 25 6 97 277 330101533 330101704 1.400000e-28 137.0
36 TraesCS3B01G597100 chr4A 91.643 359 30 0 2238 2596 673284079 673284437 5.590000e-137 497.0
37 TraesCS3B01G597100 chr4A 89.130 92 4 2 390 481 738541801 738541716 3.060000e-20 110.0
38 TraesCS3B01G597100 chr4A 89.130 92 4 2 390 481 738545715 738545630 3.060000e-20 110.0
39 TraesCS3B01G597100 chr4B 83.594 256 30 10 2614 2864 658660684 658660932 2.250000e-56 230.0
40 TraesCS3B01G597100 chr4B 89.231 130 14 0 604 733 49745894 49745765 2.320000e-36 163.0
41 TraesCS3B01G597100 chr4B 81.106 217 26 15 2639 2848 667926809 667926601 3.000000e-35 159.0
42 TraesCS3B01G597100 chr6D 79.913 229 26 17 2580 2803 456949234 456949447 1.800000e-32 150.0
43 TraesCS3B01G597100 chr7B 90.698 43 4 0 100 142 745303123 745303165 1.120000e-04 58.4


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 TraesCS3B01G597100 chr3B 819703491 819706396 2905 False 5367.00 5367 100.0000 1 2906 1 chr3B.!!$F2 2905
1 TraesCS3B01G597100 chr3B 812486383 812489331 2948 True 1396.00 3160 94.4050 84 2247 3 chr3B.!!$R1 2163
2 TraesCS3B01G597100 chr3D 604748461 604750285 1824 False 1273.05 2473 93.7895 411 2247 2 chr3D.!!$F2 1836
3 TraesCS3B01G597100 chr3D 604701162 604702911 1749 True 1037.80 2008 90.8790 504 2247 2 chr3D.!!$R2 1743
4 TraesCS3B01G597100 chr3A 735418270 735419599 1329 True 1746.00 1746 90.7940 222 1526 1 chr3A.!!$R4 1304
5 TraesCS3B01G597100 chr3A 735410168 735412006 1838 True 468.00 575 92.0780 1523 2180 2 chr3A.!!$R6 657
6 TraesCS3B01G597100 chrUn 374475159 374476751 1592 False 842.50 1574 86.5535 1 2001 2 chrUn.!!$F3 2000
7 TraesCS3B01G597100 chr7D 15213722 15215796 2074 False 391.75 577 90.2555 2237 2906 4 chr7D.!!$F2 669
8 TraesCS3B01G597100 chr2A 708518796 708520769 1973 False 489.00 571 94.8325 2239 2906 2 chr2A.!!$F1 667

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
59 71 0.250295 TGAAGCCGGTTGAGTTCCAG 60.250 55.000 1.9 0.0 0.00 3.86 F
545 620 1.001633 ACGGTCTTTCCATTGCTACGT 59.998 47.619 0.0 0.0 35.57 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1278 1.030457 CGATACAACCTAGGACGGCT 58.970 55.000 17.98 0.00 0.00 5.52 R
2286 3761 5.530519 TTGCGTTTTATTGCAACAAAACA 57.469 30.435 33.33 19.66 45.45 2.83 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
18 19 4.520846 CGAAGCGGCGCCATTGAC 62.521 66.667 30.40 12.14 0.00 3.18
24 25 1.063006 CGGCGCCATTGACATTCAG 59.937 57.895 28.98 0.37 0.00 3.02
37 38 3.507233 TGACATTCAGGCCTTCAATCAAC 59.493 43.478 0.00 0.00 0.00 3.18
38 39 3.760684 GACATTCAGGCCTTCAATCAACT 59.239 43.478 0.00 0.00 0.00 3.16
39 40 3.760684 ACATTCAGGCCTTCAATCAACTC 59.239 43.478 0.00 0.00 0.00 3.01
41 42 3.063510 TCAGGCCTTCAATCAACTCTG 57.936 47.619 0.00 0.00 0.00 3.35
53 65 1.151668 CAACTCTGAAGCCGGTTGAG 58.848 55.000 1.90 2.60 40.74 3.02
59 71 0.250295 TGAAGCCGGTTGAGTTCCAG 60.250 55.000 1.90 0.00 0.00 3.86
187 199 3.556775 ACTAGCTAGCTCGAGTACTTTCG 59.443 47.826 23.26 0.00 41.79 3.46
239 251 2.838386 CGTACACTAGGTGCACGTAT 57.162 50.000 18.82 7.90 44.93 3.06
240 252 3.950087 CGTACACTAGGTGCACGTATA 57.050 47.619 18.82 6.95 44.93 1.47
241 253 3.611517 CGTACACTAGGTGCACGTATAC 58.388 50.000 18.82 16.29 44.93 1.47
242 254 3.063861 CGTACACTAGGTGCACGTATACA 59.936 47.826 18.82 0.00 44.93 2.29
243 255 4.260907 CGTACACTAGGTGCACGTATACAT 60.261 45.833 18.82 8.41 44.93 2.29
244 256 4.041740 ACACTAGGTGCACGTATACATG 57.958 45.455 18.82 15.88 36.98 3.21
302 353 2.514824 GGGTCGCTGGCCTCATTC 60.515 66.667 3.32 0.00 0.00 2.67
320 371 7.545489 CCTCATTCATGATCGATCTAATCAGA 58.455 38.462 25.02 14.98 36.63 3.27
371 422 2.028165 GCACGCGACTTAATCTGAGTTC 59.972 50.000 15.93 0.00 0.00 3.01
375 426 4.142359 ACGCGACTTAATCTGAGTTCATCT 60.142 41.667 15.93 0.00 0.00 2.90
384 435 9.311916 CTTAATCTGAGTTCATCTTACAAGAGG 57.688 37.037 0.00 0.00 38.66 3.69
385 436 7.487822 AATCTGAGTTCATCTTACAAGAGGA 57.512 36.000 2.36 2.36 43.30 3.71
386 437 7.673641 ATCTGAGTTCATCTTACAAGAGGAT 57.326 36.000 7.12 0.00 44.24 3.24
387 438 8.774546 ATCTGAGTTCATCTTACAAGAGGATA 57.225 34.615 7.12 0.00 44.24 2.59
388 439 8.774546 TCTGAGTTCATCTTACAAGAGGATAT 57.225 34.615 7.12 0.09 44.24 1.63
397 448 9.636879 CATCTTACAAGAGGATATGATACACAG 57.363 37.037 0.00 0.00 39.04 3.66
497 572 3.632145 GCCGGATAATTCCAACAACATCT 59.368 43.478 5.05 0.00 42.74 2.90
498 573 4.819630 GCCGGATAATTCCAACAACATCTA 59.180 41.667 5.05 0.00 42.74 1.98
499 574 5.277828 GCCGGATAATTCCAACAACATCTAC 60.278 44.000 5.05 0.00 42.74 2.59
500 575 6.055588 CCGGATAATTCCAACAACATCTACT 58.944 40.000 0.00 0.00 42.74 2.57
501 576 6.542370 CCGGATAATTCCAACAACATCTACTT 59.458 38.462 0.00 0.00 42.74 2.24
502 577 7.713507 CCGGATAATTCCAACAACATCTACTTA 59.286 37.037 0.00 0.00 42.74 2.24
545 620 1.001633 ACGGTCTTTCCATTGCTACGT 59.998 47.619 0.00 0.00 35.57 3.57
1094 1191 1.162698 CAGCCGGATGGATATTGCAG 58.837 55.000 13.14 0.00 37.49 4.41
1173 1278 0.389391 GTTATCTCCTGCAGCGGCTA 59.611 55.000 8.66 0.00 41.91 3.93
1924 3228 0.471211 AGTCCACGAACCTTCCCAGA 60.471 55.000 0.00 0.00 0.00 3.86
2020 3324 6.969828 ACATTTCGAATTTGGAGTCTAGTC 57.030 37.500 0.00 0.00 0.00 2.59
2273 3748 5.226396 TCCGGTCTATTGCAACAAAATTTG 58.774 37.500 0.00 3.89 0.00 2.32
2402 3877 8.997621 AAATACTAACTTCGTTGCAATAGAGA 57.002 30.769 0.59 0.00 0.00 3.10
2578 4095 0.724549 TCGGCGTGATGTTGCATTAC 59.275 50.000 6.85 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.015084 AGAGTTGATTGAAGGCCTGAATG 58.985 43.478 5.69 0.00 0.00 2.67
24 25 2.163211 GCTTCAGAGTTGATTGAAGGCC 59.837 50.000 14.04 0.00 46.51 5.19
37 38 1.433534 GAACTCAACCGGCTTCAGAG 58.566 55.000 0.00 4.42 0.00 3.35
38 39 0.034896 GGAACTCAACCGGCTTCAGA 59.965 55.000 0.00 0.00 0.00 3.27
39 40 0.250295 TGGAACTCAACCGGCTTCAG 60.250 55.000 0.00 0.00 0.00 3.02
41 42 0.955919 CCTGGAACTCAACCGGCTTC 60.956 60.000 0.00 0.00 32.89 3.86
112 124 2.486636 TACAGCAGCGTTGAGGTCGG 62.487 60.000 2.38 0.00 0.00 4.79
113 125 1.073216 CTACAGCAGCGTTGAGGTCG 61.073 60.000 2.38 0.00 0.00 4.79
115 127 1.374758 GCTACAGCAGCGTTGAGGT 60.375 57.895 2.38 2.31 41.37 3.85
116 128 3.479370 GCTACAGCAGCGTTGAGG 58.521 61.111 2.38 0.00 41.37 3.86
157 169 3.403968 TCGAGCTAGCTAGTCTGGTATG 58.596 50.000 19.38 4.49 0.00 2.39
244 256 1.297664 CCTGCTAGTCTGCTTGATGC 58.702 55.000 0.00 0.00 43.25 3.91
302 353 9.430838 GTTTGTTTTCTGATTAGATCGATCATG 57.569 33.333 26.47 9.86 33.39 3.07
320 371 4.116961 TGTGATCTCGTCGAGTTTGTTTT 58.883 39.130 21.15 0.28 0.00 2.43
371 422 9.636879 CTGTGTATCATATCCTCTTGTAAGATG 57.363 37.037 0.00 0.00 33.93 2.90
375 426 7.914427 ACCTGTGTATCATATCCTCTTGTAA 57.086 36.000 0.00 0.00 0.00 2.41
388 439 9.063615 CGTATGCCTATATATACCTGTGTATCA 57.936 37.037 0.00 0.00 38.60 2.15
441 496 5.067936 AGTCAGACACCGTATAGGATTCTTG 59.932 44.000 2.66 0.00 45.00 3.02
497 572 7.723172 GGTAGGTGAAGAGGCTAAGTATAAGTA 59.277 40.741 0.00 0.00 0.00 2.24
498 573 6.550481 GGTAGGTGAAGAGGCTAAGTATAAGT 59.450 42.308 0.00 0.00 0.00 2.24
499 574 6.015265 GGGTAGGTGAAGAGGCTAAGTATAAG 60.015 46.154 0.00 0.00 0.00 1.73
500 575 5.837438 GGGTAGGTGAAGAGGCTAAGTATAA 59.163 44.000 0.00 0.00 0.00 0.98
501 576 5.103387 TGGGTAGGTGAAGAGGCTAAGTATA 60.103 44.000 0.00 0.00 0.00 1.47
502 577 4.224762 GGGTAGGTGAAGAGGCTAAGTAT 58.775 47.826 0.00 0.00 0.00 2.12
509 584 1.218316 CGTGGGTAGGTGAAGAGGC 59.782 63.158 0.00 0.00 0.00 4.70
545 620 3.636300 CTGGATTTCTGTTGTTTCCACCA 59.364 43.478 0.00 0.00 33.12 4.17
1094 1191 1.066303 CGGGATCAGCAGTGTAGAGAC 59.934 57.143 0.00 0.00 0.00 3.36
1122 1227 5.305585 TCTTCTTCATACACTGTGAAACCC 58.694 41.667 15.86 0.00 35.36 4.11
1173 1278 1.030457 CGATACAACCTAGGACGGCT 58.970 55.000 17.98 0.00 0.00 5.52
1218 1338 2.594592 GCCACAGCAACCGGAAGT 60.595 61.111 9.46 0.00 39.53 3.01
2273 3748 5.746245 TGCAACAAAACATAGTTGTAGCAAC 59.254 36.000 4.02 4.02 45.16 4.17
2286 3761 5.530519 TTGCGTTTTATTGCAACAAAACA 57.469 30.435 33.33 19.66 45.45 2.83
2402 3877 7.195646 CGATACAATTTGTTGCAATATGAGGT 58.804 34.615 7.45 0.65 0.00 3.85
2516 4029 9.549078 TGAATATTGCCACGAATAGTTATGTTA 57.451 29.630 0.00 0.00 0.00 2.41
2809 6066 8.303876 ACATGTATTTAAGGAAATGTTGACCAC 58.696 33.333 0.00 0.00 35.96 4.16


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

AutoCloner maintained by Alex Coulton.