Multiple sequence alignment - TraesCS3B01G543800

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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 TraesCS3B01G543800 chr3B 100.000 2775 0 0 1 2775 781355289 781358063 0.000000e+00 5125.0
1 TraesCS3B01G543800 chr3B 97.978 989 17 1 1790 2775 815295941 815294953 0.000000e+00 1712.0
2 TraesCS3B01G543800 chr3B 90.467 1007 83 10 793 1789 781344441 781345444 0.000000e+00 1315.0
3 TraesCS3B01G543800 chr3B 88.489 973 74 21 816 1780 781494935 781493993 0.000000e+00 1142.0
4 TraesCS3B01G543800 chr3B 89.293 934 66 13 866 1787 781210448 781211359 0.000000e+00 1140.0
5 TraesCS3B01G543800 chr3B 91.837 98 4 3 1 95 781208490 781208586 1.730000e-27 134.0
6 TraesCS3B01G543800 chr3B 89.691 97 7 2 1 95 781341242 781341337 1.350000e-23 121.0
7 TraesCS3B01G543800 chr3B 91.667 48 2 2 44 89 781533353 781533306 6.420000e-07 65.8
8 TraesCS3B01G543800 chr7D 87.063 1832 161 36 14 1787 588418877 588420690 0.000000e+00 2001.0
9 TraesCS3B01G543800 chr7D 91.667 48 3 1 298 344 588419115 588419162 6.420000e-07 65.8
10 TraesCS3B01G543800 chr3D 93.464 1331 53 6 468 1787 584129402 584130709 0.000000e+00 1945.0
11 TraesCS3B01G543800 chr3D 88.738 1101 67 17 702 1789 584048545 584049601 0.000000e+00 1293.0
12 TraesCS3B01G543800 chr3D 87.986 1107 99 18 689 1775 584457130 584456038 0.000000e+00 1277.0
13 TraesCS3B01G543800 chr3D 91.785 353 19 3 1 344 584128911 584129262 1.490000e-132 483.0
14 TraesCS3B01G543800 chr3D 88.021 192 20 3 247 437 584129216 584129405 1.000000e-54 224.0
15 TraesCS3B01G543800 chr3D 92.784 97 4 2 1 95 584047120 584047215 1.340000e-28 137.0
16 TraesCS3B01G543800 chr3A 85.251 1790 162 43 86 1787 21361213 21359438 0.000000e+00 1749.0
17 TraesCS3B01G543800 chr3A 98.276 986 17 0 1790 2775 742957321 742958306 0.000000e+00 1727.0
18 TraesCS3B01G543800 chr3A 98.079 989 16 1 1790 2775 731001895 731000907 0.000000e+00 1718.0
19 TraesCS3B01G543800 chr3A 91.667 48 3 1 298 344 21361038 21360991 6.420000e-07 65.8
20 TraesCS3B01G543800 chr1B 98.479 986 12 1 1790 2775 552960203 552959221 0.000000e+00 1735.0
21 TraesCS3B01G543800 chr1B 98.071 985 17 1 1791 2775 310384141 310385123 0.000000e+00 1712.0
22 TraesCS3B01G543800 chr6A 98.182 990 14 2 1787 2775 555759164 555760150 0.000000e+00 1725.0
23 TraesCS3B01G543800 chr7B 98.180 989 15 1 1790 2775 734091930 734090942 0.000000e+00 1724.0
24 TraesCS3B01G543800 chr7B 98.073 986 16 1 1790 2775 507845216 507844234 0.000000e+00 1712.0
25 TraesCS3B01G543800 chr5B 97.883 992 15 1 1790 2775 21605481 21604490 0.000000e+00 1711.0
26 TraesCS3B01G543800 chrUn 87.612 1001 90 22 819 1787 45483377 45482379 0.000000e+00 1131.0
27 TraesCS3B01G543800 chrUn 97.059 34 1 0 43 76 419501568 419501601 1.070000e-04 58.4
28 TraesCS3B01G543800 chr2D 82.456 171 26 3 130 297 641009409 641009240 2.230000e-31 147.0
29 TraesCS3B01G543800 chr2B 84.783 92 14 0 130 221 800214969 800215060 2.940000e-15 93.5


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 TraesCS3B01G543800 chr3B 781355289 781358063 2774 False 5125.0 5125 100.000 1 2775 1 chr3B.!!$F1 2774
1 TraesCS3B01G543800 chr3B 815294953 815295941 988 True 1712.0 1712 97.978 1790 2775 1 chr3B.!!$R3 985
2 TraesCS3B01G543800 chr3B 781493993 781494935 942 True 1142.0 1142 88.489 816 1780 1 chr3B.!!$R1 964
3 TraesCS3B01G543800 chr3B 781341242 781345444 4202 False 718.0 1315 90.079 1 1789 2 chr3B.!!$F3 1788
4 TraesCS3B01G543800 chr3B 781208490 781211359 2869 False 637.0 1140 90.565 1 1787 2 chr3B.!!$F2 1786
5 TraesCS3B01G543800 chr7D 588418877 588420690 1813 False 1033.4 2001 89.365 14 1787 2 chr7D.!!$F1 1773
6 TraesCS3B01G543800 chr3D 584456038 584457130 1092 True 1277.0 1277 87.986 689 1775 1 chr3D.!!$R1 1086
7 TraesCS3B01G543800 chr3D 584128911 584130709 1798 False 884.0 1945 91.090 1 1787 3 chr3D.!!$F2 1786
8 TraesCS3B01G543800 chr3D 584047120 584049601 2481 False 715.0 1293 90.761 1 1789 2 chr3D.!!$F1 1788
9 TraesCS3B01G543800 chr3A 742957321 742958306 985 False 1727.0 1727 98.276 1790 2775 1 chr3A.!!$F1 985
10 TraesCS3B01G543800 chr3A 731000907 731001895 988 True 1718.0 1718 98.079 1790 2775 1 chr3A.!!$R1 985
11 TraesCS3B01G543800 chr3A 21359438 21361213 1775 True 907.4 1749 88.459 86 1787 2 chr3A.!!$R2 1701
12 TraesCS3B01G543800 chr1B 552959221 552960203 982 True 1735.0 1735 98.479 1790 2775 1 chr1B.!!$R1 985
13 TraesCS3B01G543800 chr1B 310384141 310385123 982 False 1712.0 1712 98.071 1791 2775 1 chr1B.!!$F1 984
14 TraesCS3B01G543800 chr6A 555759164 555760150 986 False 1725.0 1725 98.182 1787 2775 1 chr6A.!!$F1 988
15 TraesCS3B01G543800 chr7B 734090942 734091930 988 True 1724.0 1724 98.180 1790 2775 1 chr7B.!!$R2 985
16 TraesCS3B01G543800 chr7B 507844234 507845216 982 True 1712.0 1712 98.073 1790 2775 1 chr7B.!!$R1 985
17 TraesCS3B01G543800 chr5B 21604490 21605481 991 True 1711.0 1711 97.883 1790 2775 1 chr5B.!!$R1 985
18 TraesCS3B01G543800 chrUn 45482379 45483377 998 True 1131.0 1131 87.612 819 1787 1 chrUn.!!$R1 968

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
304 2748 0.821711 TGCAGGTTCACCGGAAAAGG 60.822 55.0 9.46 0.0 42.08 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 5834 0.035739 GAACCGGCACAACCCTCTAA 59.964 55.0 0.0 0.0 33.26 2.1 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
147 2525 9.844790 CACAAATTCACAATAGCTAAAGATCAA 57.155 29.630 0.00 0.00 0.00 2.57
168 2546 8.647143 ATCAATCGACTGAATTTTGTTTTTGT 57.353 26.923 0.00 0.00 0.00 2.83
212 2597 2.508586 GAAGAAGGAAGCGCCGAGGT 62.509 60.000 2.29 0.00 43.43 3.85
233 2627 1.132689 AGAGGAAGGAGACACCAAGGT 60.133 52.381 0.00 0.00 42.04 3.50
266 2660 2.508300 GGGAAGAAGCAACCCCACTATA 59.492 50.000 0.00 0.00 38.69 1.31
281 2675 5.266788 CCCACTATATATCGTTAGGGTGGA 58.733 45.833 12.69 0.00 43.72 4.02
304 2748 0.821711 TGCAGGTTCACCGGAAAAGG 60.822 55.000 9.46 0.00 42.08 3.11
310 2754 0.848053 TTCACCGGAAAAGGAACCCT 59.152 50.000 9.46 0.00 33.87 4.34
347 2791 4.947147 GTGGGTGCAGGTTCGCCA 62.947 66.667 0.00 0.00 40.60 5.69
349 2793 4.329545 GGGTGCAGGTTCGCCAGA 62.330 66.667 0.00 0.00 40.60 3.86
355 2799 1.168714 GCAGGTTCGCCAGAGATTTT 58.831 50.000 0.00 0.00 40.60 1.82
365 2809 2.875296 CCAGAGATTTTTGGGTGGTCA 58.125 47.619 0.00 0.00 0.00 4.02
367 2811 3.490348 CAGAGATTTTTGGGTGGTCACT 58.510 45.455 0.93 0.00 0.00 3.41
380 2824 1.627297 GGTCACTGGGCTTAGAGGGG 61.627 65.000 0.00 0.00 0.00 4.79
385 2829 2.692741 GGGCTTAGAGGGGTGGCT 60.693 66.667 0.00 0.00 0.00 4.75
424 2869 2.531942 GGTGGGGGAGGTTGAGGT 60.532 66.667 0.00 0.00 0.00 3.85
575 3023 2.934364 GCTAATCCAGCCATCCATCTCG 60.934 54.545 0.00 0.00 45.23 4.04
635 3083 1.807755 GCAGGCGATTGTCATCTAGCA 60.808 52.381 0.00 0.00 0.00 3.49
640 3088 3.126858 GGCGATTGTCATCTAGCAAAACA 59.873 43.478 0.00 0.00 0.00 2.83
658 3109 9.512435 AGCAAAACACTAACTATATACAGTACG 57.488 33.333 0.00 0.00 0.00 3.67
669 3120 8.392372 ACTATATACAGTACGAGCTTTGATCA 57.608 34.615 0.00 0.00 0.00 2.92
685 3136 2.089753 TGATCATTCCTCCCTCCTCCAT 60.090 50.000 0.00 0.00 0.00 3.41
752 3232 5.363562 TGGTGCTTGACAATATGAGATCT 57.636 39.130 0.00 0.00 0.00 2.75
872 4785 1.080501 CGATCGATCACATCCCCCG 60.081 63.158 24.40 4.65 0.00 5.73
879 4792 1.335132 ATCACATCCCCCGTACGCTT 61.335 55.000 10.49 0.00 0.00 4.68
903 4816 3.184379 ACTGCACTATAAATACATGCGCG 59.816 43.478 0.00 0.00 39.18 6.86
1216 5186 6.071952 CCAACAAAGAGGTAATGCATAAGTGT 60.072 38.462 0.00 0.00 0.00 3.55
1217 5187 7.120579 CCAACAAAGAGGTAATGCATAAGTGTA 59.879 37.037 0.00 0.00 0.00 2.90
1218 5188 8.677300 CAACAAAGAGGTAATGCATAAGTGTAT 58.323 33.333 0.00 0.00 31.52 2.29
1219 5189 8.213518 ACAAAGAGGTAATGCATAAGTGTATG 57.786 34.615 0.00 0.00 40.23 2.39
1471 5441 2.586079 CGCGCCACCGAGATCATT 60.586 61.111 0.00 0.00 36.29 2.57
1478 5448 2.888594 CCACCGAGATCATTTACGTGT 58.111 47.619 0.00 0.00 0.00 4.49
2510 6492 0.382515 GCTATGTCGACGGCTCTCTT 59.617 55.000 11.62 0.00 0.00 2.85
2698 6680 1.512926 ATTCTTGAGCGCTCGTTTGT 58.487 45.000 30.75 14.89 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 2525 7.537306 CCGATACAAAAACAAAATTCAGTCGAT 59.463 33.333 0.00 0.00 0.00 3.59
168 2546 6.128391 CCTTCTCAAAACAAATTCGACCGATA 60.128 38.462 0.00 0.00 0.00 2.92
212 2597 2.111972 ACCTTGGTGTCTCCTTCCTCTA 59.888 50.000 0.00 0.00 37.07 2.43
266 2660 2.326428 CACCCTCCACCCTAACGATAT 58.674 52.381 0.00 0.00 0.00 1.63
304 2748 6.756299 CCCTAACGATAGATAGTAGGGTTC 57.244 45.833 0.56 0.00 41.14 3.62
310 2754 5.319453 CCACCACCCTAACGATAGATAGTA 58.681 45.833 0.56 0.00 39.58 1.82
347 2791 3.490348 CAGTGACCACCCAAAAATCTCT 58.510 45.455 0.00 0.00 0.00 3.10
349 2793 2.597455 CCAGTGACCACCCAAAAATCT 58.403 47.619 0.00 0.00 0.00 2.40
355 2799 1.063070 TAAGCCCAGTGACCACCCAA 61.063 55.000 0.00 0.00 0.00 4.12
365 2809 1.616628 CCACCCCTCTAAGCCCAGT 60.617 63.158 0.00 0.00 0.00 4.00
367 2811 3.015145 GCCACCCCTCTAAGCCCA 61.015 66.667 0.00 0.00 0.00 5.36
385 2829 4.011517 GTCTTTCCGCCGTCCCCA 62.012 66.667 0.00 0.00 0.00 4.96
406 2850 2.531685 CCTCAACCTCCCCCACCA 60.532 66.667 0.00 0.00 0.00 4.17
575 3023 2.715737 TGTTTTAAGCCGTTGGATGC 57.284 45.000 0.00 0.00 0.00 3.91
615 3063 0.864455 GCTAGATGACAATCGCCTGC 59.136 55.000 0.00 0.00 37.92 4.85
635 3083 9.727627 GCTCGTACTGTATATAGTTAGTGTTTT 57.272 33.333 7.50 0.00 32.19 2.43
640 3088 9.334947 TCAAAGCTCGTACTGTATATAGTTAGT 57.665 33.333 7.50 0.00 32.19 2.24
658 3109 3.475575 GAGGGAGGAATGATCAAAGCTC 58.524 50.000 0.00 0.00 0.00 4.09
669 3120 2.906169 AAGATGGAGGAGGGAGGAAT 57.094 50.000 0.00 0.00 0.00 3.01
685 3136 3.850774 TGTAGTCAGAGAGGGGTCTAAGA 59.149 47.826 0.00 0.00 0.00 2.10
752 3232 4.721776 AGCTTGAAGGTATGGTTGGATAGA 59.278 41.667 0.00 0.00 0.00 1.98
804 4688 1.345410 AATTGCACGCGGTTTTATGC 58.655 45.000 12.47 10.95 38.59 3.14
872 4785 5.968387 ATTTATAGTGCAGTGAAGCGTAC 57.032 39.130 3.69 0.00 37.31 3.67
879 4792 4.211164 GCGCATGTATTTATAGTGCAGTGA 59.789 41.667 0.30 0.00 35.63 3.41
1864 5834 0.035739 GAACCGGCACAACCCTCTAA 59.964 55.000 0.00 0.00 33.26 2.10
2099 6081 4.207281 CCGATCGGCGCCTGAAGA 62.207 66.667 26.68 15.03 39.11 2.87
2390 6372 2.787473 TGAGATGGCCGAAGTGAAAT 57.213 45.000 0.00 0.00 0.00 2.17
2698 6680 4.687215 GAGCCTGCGACTGTGCCA 62.687 66.667 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.