Multiple sequence alignment - TraesCS1B01G329200

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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 TraesCS1B01G329200 chr1B 100.000 2528 0 0 1 2528 555089695 555092222 0.000000e+00 4669.0
1 TraesCS1B01G329200 chr1B 98.551 2485 31 2 1 2480 555031272 555033756 0.000000e+00 4385.0
2 TraesCS1B01G329200 chr1B 90.380 2422 161 23 1 2370 555064987 555067388 0.000000e+00 3116.0
3 TraesCS1B01G329200 chr1B 90.301 2423 162 23 1 2370 555075683 555078085 0.000000e+00 3105.0
4 TraesCS1B01G329200 chr1B 90.301 2423 160 30 1 2370 555011706 555014106 0.000000e+00 3103.0
5 TraesCS1B01G329200 chr1B 90.095 2423 167 23 1 2370 555017059 555019461 0.000000e+00 3077.0
6 TraesCS1B01G329200 chr1B 90.054 2423 157 24 1 2370 555070340 555072731 0.000000e+00 3062.0
7 TraesCS1B01G329200 chr1B 91.300 1839 118 21 1 1819 555059629 555061445 0.000000e+00 2471.0
8 TraesCS1B01G329200 chr1B 90.937 1633 108 16 1 1613 555006402 555008014 0.000000e+00 2159.0
9 TraesCS1B01G329200 chr1B 87.738 734 65 6 1 720 555049643 555050365 0.000000e+00 833.0
10 TraesCS1B01G329200 chr1B 87.057 734 61 9 1 720 554997313 554998026 0.000000e+00 798.0
11 TraesCS1B01G329200 chr1B 92.021 564 41 2 1811 2370 555061466 555062029 0.000000e+00 789.0
12 TraesCS1B01G329200 chr1B 91.858 565 41 3 1811 2370 555008184 555008748 0.000000e+00 784.0
13 TraesCS1B01G329200 chr1B 100.000 46 0 0 2483 2528 555033745 555033790 4.480000e-13 86.1
14 TraesCS1B01G329200 chr1D 87.155 2429 249 29 1 2370 411743519 411745943 0.000000e+00 2699.0
15 TraesCS1B01G329200 chr1D 86.315 1878 165 41 1 1828 411700378 411702213 0.000000e+00 1960.0
16 TraesCS1B01G329200 chr1A 85.616 1884 183 29 1 1826 508213389 508215242 0.000000e+00 1897.0
17 TraesCS1B01G329200 chr1A 88.613 1168 93 18 2 1136 508182303 508183463 0.000000e+00 1384.0
18 TraesCS1B01G329200 chr1A 88.492 504 51 3 1868 2370 508215717 508216214 1.000000e-168 603.0
19 TraesCS1B01G329200 chr1A 86.061 165 9 2 2364 2528 19693726 19693576 5.590000e-37 165.0
20 TraesCS1B01G329200 chrUn 88.497 1417 133 13 424 1819 373708412 373707005 0.000000e+00 1687.0
21 TraesCS1B01G329200 chrUn 97.826 46 1 0 2483 2528 40669511 40669466 2.080000e-11 80.5
22 TraesCS1B01G329200 chr2B 95.000 120 4 2 2361 2480 737011126 737011243 1.190000e-43 187.0
23 TraesCS1B01G329200 chr2B 93.694 111 7 0 2370 2480 196207179 196207069 1.560000e-37 167.0
24 TraesCS1B01G329200 chr2B 81.513 119 8 2 2410 2528 731187248 731187144 4.480000e-13 86.1
25 TraesCS1B01G329200 chr2B 100.000 45 0 0 2483 2527 737011232 737011276 1.610000e-12 84.2
26 TraesCS1B01G329200 chr6A 95.495 111 5 0 2370 2480 175442126 175442016 7.190000e-41 178.0
27 TraesCS1B01G329200 chr6A 94.595 111 6 0 2370 2480 23315854 23315744 3.340000e-39 172.0
28 TraesCS1B01G329200 chr2A 95.495 111 5 0 2370 2480 644184626 644184516 7.190000e-41 178.0
29 TraesCS1B01G329200 chr4A 96.226 106 4 0 2371 2476 601681207 601681312 9.300000e-40 174.0
30 TraesCS1B01G329200 chr3B 95.413 109 5 0 2371 2479 809903746 809903638 9.300000e-40 174.0
31 TraesCS1B01G329200 chr3B 86.164 159 8 1 2370 2528 307839884 307840028 2.600000e-35 159.0
32 TraesCS1B01G329200 chr7B 93.860 114 6 1 2367 2480 133766350 133766238 1.200000e-38 171.0
33 TraesCS1B01G329200 chr7B 85.350 157 6 4 2372 2528 586582769 586582630 2.030000e-31 147.0
34 TraesCS1B01G329200 chr3D 91.736 121 8 2 2361 2480 557240563 557240444 1.560000e-37 167.0
35 TraesCS1B01G329200 chr4B 85.443 158 9 3 2371 2528 202303880 202303737 4.360000e-33 152.0


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 TraesCS1B01G329200 chr1B 555089695 555092222 2527 False 4669.00 4669 100.00000 1 2528 1 chr1B.!!$F3 2527
1 TraesCS1B01G329200 chr1B 555059629 555078085 18456 False 2508.60 3116 90.81120 1 2370 5 chr1B.!!$F6 2369
2 TraesCS1B01G329200 chr1B 555006402 555019461 13059 False 2280.75 3103 90.79775 1 2370 4 chr1B.!!$F4 2369
3 TraesCS1B01G329200 chr1B 555031272 555033790 2518 False 2235.55 4385 99.27550 1 2528 2 chr1B.!!$F5 2527
4 TraesCS1B01G329200 chr1B 555049643 555050365 722 False 833.00 833 87.73800 1 720 1 chr1B.!!$F2 719
5 TraesCS1B01G329200 chr1B 554997313 554998026 713 False 798.00 798 87.05700 1 720 1 chr1B.!!$F1 719
6 TraesCS1B01G329200 chr1D 411743519 411745943 2424 False 2699.00 2699 87.15500 1 2370 1 chr1D.!!$F2 2369
7 TraesCS1B01G329200 chr1D 411700378 411702213 1835 False 1960.00 1960 86.31500 1 1828 1 chr1D.!!$F1 1827
8 TraesCS1B01G329200 chr1A 508182303 508183463 1160 False 1384.00 1384 88.61300 2 1136 1 chr1A.!!$F1 1134
9 TraesCS1B01G329200 chr1A 508213389 508216214 2825 False 1250.00 1897 87.05400 1 2370 2 chr1A.!!$F2 2369
10 TraesCS1B01G329200 chrUn 373707005 373708412 1407 True 1687.00 1687 88.49700 424 1819 1 chrUn.!!$R2 1395

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
352 398 1.383456 ATTACAATGGCGCGCATGGT 61.383 50.0 34.42 26.6 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 29174 0.391661 TCAGAGCGGCAGAAACCATC 60.392 55.0 1.45 0.0 0.0 3.51 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
96 102 1.569479 GAGGGTGTCTTCTTGCACGC 61.569 60.000 0.00 0.00 45.17 5.34
238 280 4.771577 TGCCATGTATCAGGTCATTTTGTT 59.228 37.500 0.00 0.00 0.00 2.83
352 398 1.383456 ATTACAATGGCGCGCATGGT 61.383 50.000 34.42 26.60 0.00 3.55
353 399 2.263771 TTACAATGGCGCGCATGGTG 62.264 55.000 34.42 24.87 0.00 4.17
842 6241 4.263905 TGAACCTAGCTTGACCAATCCATT 60.264 41.667 0.00 0.00 0.00 3.16
1491 28314 4.517934 AGGGCGCGGCTAGGTCTA 62.518 66.667 32.30 0.00 0.00 2.59
1873 29140 3.129502 TCCTGTCGCGTAGGTCCG 61.130 66.667 24.16 6.47 36.67 4.79
1902 29169 1.145598 CCACGCTGGAGAGATGCAT 59.854 57.895 0.00 0.00 40.96 3.96
1907 29174 1.991264 CGCTGGAGAGATGCATTATCG 59.009 52.381 0.00 0.00 40.86 2.92
2017 29285 0.739813 GTAACATCTCGCCGGCAAGT 60.740 55.000 28.98 13.69 0.00 3.16
2101 29369 1.674359 TCCAGCAAAAAGACTTCGCA 58.326 45.000 6.89 0.00 0.00 5.10
2109 29377 0.250901 AAAGACTTCGCATGTGGCCT 60.251 50.000 3.32 0.00 40.31 5.19
2308 29577 0.241213 GGTTTCGCAGCTTTTCTCCC 59.759 55.000 0.00 0.00 0.00 4.30
2340 29609 2.039480 AGCATCCACACATGTCAACTCT 59.961 45.455 0.00 0.00 0.00 3.24
2474 29743 1.259244 GCTAAAGCTTAGCAGTAGCGC 59.741 52.381 18.59 0.00 43.37 5.92
2475 29744 3.932626 GCTAAAGCTTAGCAGTAGCGCC 61.933 54.545 18.59 0.00 43.37 6.53
2482 29751 2.580867 GCAGTAGCGCCGACTCTG 60.581 66.667 2.29 7.15 0.00 3.35
2483 29752 2.878429 CAGTAGCGCCGACTCTGT 59.122 61.111 2.29 0.00 0.00 3.41
2484 29753 1.989966 GCAGTAGCGCCGACTCTGTA 61.990 60.000 2.29 0.00 0.00 2.74
2485 29754 0.028242 CAGTAGCGCCGACTCTGTAG 59.972 60.000 2.29 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 102 1.270550 GAAGCACATGAAACCCACCAG 59.729 52.381 0.00 0.00 0.00 4.00
238 280 2.959707 AGGCATAAACAACCAAACCGAA 59.040 40.909 0.00 0.00 0.00 4.30
352 398 4.002982 CTGAATTTGGTCAAGATCGGTCA 58.997 43.478 0.00 0.00 0.00 4.02
353 399 4.003648 ACTGAATTTGGTCAAGATCGGTC 58.996 43.478 0.00 0.00 0.00 4.79
842 6241 7.457561 TGCCACTATGTCAAAATATATAGGCA 58.542 34.615 0.00 0.00 36.67 4.75
1168 11941 1.080025 GCACGGTGGTGGAGTACTC 60.080 63.158 14.87 14.87 44.54 2.59
1491 28314 2.164624 GAGACTAGTCACGACAATGGCT 59.835 50.000 24.44 0.00 38.37 4.75
1630 28461 9.638239 GGTTTTGCAAGAAGATATGTTAAATCA 57.362 29.630 0.00 0.00 0.00 2.57
1902 29169 1.134521 AGCGGCAGAAACCATCGATAA 60.135 47.619 1.45 0.00 0.00 1.75
1907 29174 0.391661 TCAGAGCGGCAGAAACCATC 60.392 55.000 1.45 0.00 0.00 3.51
2049 29317 4.678044 CGCATTTGCTGGAACTAGAGACTA 60.678 45.833 0.00 0.00 39.32 2.59
2101 29369 0.540365 CTGGAACCAACAGGCCACAT 60.540 55.000 5.01 0.00 32.38 3.21
2109 29377 2.559440 GCATTTTTGCTGGAACCAACA 58.441 42.857 0.00 0.00 0.00 3.33
2308 29577 1.227350 TGGATGCTCGAATGAGGCG 60.227 57.895 0.00 0.00 42.79 5.52
2391 29660 1.161843 GCCAAAAACCAGCGCTACTA 58.838 50.000 10.99 0.00 0.00 1.82
2474 29743 3.506096 TCGGCGCTACAGAGTCGG 61.506 66.667 7.64 0.00 42.96 4.79
2475 29744 2.277373 GTCGGCGCTACAGAGTCG 60.277 66.667 7.64 0.25 44.06 4.18
2476 29745 1.226435 CAGTCGGCGCTACAGAGTC 60.226 63.158 7.64 0.00 0.00 3.36
2477 29746 2.701780 CCAGTCGGCGCTACAGAGT 61.702 63.158 7.64 2.22 0.00 3.24
2478 29747 2.103143 CCAGTCGGCGCTACAGAG 59.897 66.667 7.64 0.90 0.00 3.35


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

AutoCloner maintained by Alex Coulton.