Multiple sequence alignment - TraesCS3B01G191900

Loading Multiple Alignment...

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 TraesCS3B01G191900 chr3B 100.000 4710 0 0 1 4710 205466517 205461808 0.000000e+00 8698.0
1 TraesCS3B01G191900 chr3B 95.391 1562 16 17 1 1514 205693112 205691559 0.000000e+00 2435.0
2 TraesCS3B01G191900 chr3B 97.577 1403 26 4 2163 3560 205686215 205684816 0.000000e+00 2396.0
3 TraesCS3B01G191900 chr3B 96.389 1163 25 2 3564 4710 205684738 205683577 0.000000e+00 1899.0
4 TraesCS3B01G191900 chr3B 85.294 442 55 5 4278 4709 70090736 70090295 9.300000e-122 448.0
5 TraesCS3B01G191900 chr3D 97.013 2712 63 6 857 3560 144779374 144782075 0.000000e+00 4543.0
6 TraesCS3B01G191900 chr3D 94.408 2933 96 31 1 2881 145202554 145199638 0.000000e+00 4446.0
7 TraesCS3B01G191900 chr3D 96.996 566 16 1 2879 3444 145199364 145198800 0.000000e+00 950.0
8 TraesCS3B01G191900 chr3D 91.797 512 19 9 3564 4054 145198528 145198019 0.000000e+00 691.0
9 TraesCS3B01G191900 chr3D 92.205 449 23 4 4269 4710 145192069 145191626 4.000000e-175 625.0
10 TraesCS3B01G191900 chr3D 90.244 451 35 3 4268 4710 144792886 144793335 8.790000e-162 580.0
11 TraesCS3B01G191900 chr3D 77.080 733 109 44 1 687 397540815 397541534 7.450000e-98 368.0
12 TraesCS3B01G191900 chr3D 96.347 219 7 1 3548 3765 144782134 144782352 4.480000e-95 359.0
13 TraesCS3B01G191900 chr3D 98.291 117 0 2 3444 3560 145198720 145198606 2.220000e-48 204.0
14 TraesCS3B01G191900 chr3D 94.681 94 4 1 3756 3849 144787026 144787118 1.370000e-30 145.0
15 TraesCS3B01G191900 chr3D 90.741 54 4 1 3867 3919 570533244 570533191 2.350000e-08 71.3
16 TraesCS3B01G191900 chr5D 86.161 448 52 10 4271 4710 25273689 25274134 4.260000e-130 475.0
17 TraesCS3B01G191900 chr5D 82.998 447 63 12 4270 4706 482620962 482621405 4.420000e-105 392.0
18 TraesCS3B01G191900 chr5D 74.378 402 69 24 155 537 47041584 47041970 1.770000e-29 141.0
19 TraesCS3B01G191900 chr5D 76.667 240 43 11 155 388 429033049 429032817 2.300000e-23 121.0
20 TraesCS3B01G191900 chr4B 84.272 426 57 8 4292 4710 315296754 315297176 1.580000e-109 407.0
21 TraesCS3B01G191900 chr4B 76.410 195 34 9 156 346 79735051 79735237 1.400000e-15 95.3
22 TraesCS3B01G191900 chr1D 83.683 429 56 6 4294 4710 14655086 14655512 4.420000e-105 392.0
23 TraesCS3B01G191900 chr2D 87.619 315 34 5 4401 4710 558208566 558208880 1.250000e-95 361.0
24 TraesCS3B01G191900 chr2D 80.102 196 33 6 155 347 398641686 398641494 1.770000e-29 141.0
25 TraesCS3B01G191900 chr7A 77.412 456 75 15 230 680 678594873 678594441 3.640000e-61 246.0
26 TraesCS3B01G191900 chr6D 84.571 175 14 11 551 716 454741037 454741207 1.360000e-35 161.0
27 TraesCS3B01G191900 chr4A 75.272 368 68 19 159 514 542831331 542830975 2.270000e-33 154.0
28 TraesCS3B01G191900 chr4A 76.014 296 52 15 430 716 736916686 736916971 8.220000e-28 135.0
29 TraesCS3B01G191900 chr4D 76.950 282 52 13 140 415 54060515 54060789 1.060000e-31 148.0
30 TraesCS3B01G191900 chr4D 93.103 58 4 0 4054 4111 486185982 486185925 8.400000e-13 86.1
31 TraesCS3B01G191900 chr7B 78.680 197 26 9 153 346 44116322 44116505 2.980000e-22 117.0
32 TraesCS3B01G191900 chr2A 76.836 177 31 8 444 616 227561289 227561119 1.800000e-14 91.6
33 TraesCS3B01G191900 chr2A 90.164 61 5 1 4052 4111 657518459 657518399 1.410000e-10 78.7
34 TraesCS3B01G191900 chr7D 76.471 170 25 12 233 397 104915497 104915656 1.410000e-10 78.7
35 TraesCS3B01G191900 chr6B 88.525 61 5 2 3867 3926 93341442 93341501 6.540000e-09 73.1
36 TraesCS3B01G191900 chrUn 87.931 58 5 2 3870 3926 19597674 19597618 3.040000e-07 67.6
37 TraesCS3B01G191900 chr5A 93.478 46 2 1 576 621 510184321 510184277 3.040000e-07 67.6
38 TraesCS3B01G191900 chr6A 100.000 32 0 0 4080 4111 365534656 365534625 5.090000e-05 60.2
39 TraesCS3B01G191900 chr1B 84.058 69 4 1 4050 4111 624981678 624981746 5.090000e-05 60.2
40 TraesCS3B01G191900 chr1A 92.857 42 1 2 4080 4119 61089321 61089280 5.090000e-05 60.2


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 TraesCS3B01G191900 chr3B 205461808 205466517 4709 True 8698.00 8698 100.000 1 4710 1 chr3B.!!$R2 4709
1 TraesCS3B01G191900 chr3B 205691559 205693112 1553 True 2435.00 2435 95.391 1 1514 1 chr3B.!!$R3 1513
2 TraesCS3B01G191900 chr3B 205683577 205686215 2638 True 2147.50 2396 96.983 2163 4710 2 chr3B.!!$R4 2547
3 TraesCS3B01G191900 chr3D 144779374 144782352 2978 False 2451.00 4543 96.680 857 3765 2 chr3D.!!$F4 2908
4 TraesCS3B01G191900 chr3D 145198019 145202554 4535 True 1572.75 4446 95.373 1 4054 4 chr3D.!!$R3 4053
5 TraesCS3B01G191900 chr3D 397540815 397541534 719 False 368.00 368 77.080 1 687 1 chr3D.!!$F3 686

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
399 464 6.279513 TCAAACTCAAAAAGTGTCCATTGT 57.720 33.333 0.00 0.00 38.58 2.71 F
1647 1788 0.026803 GCGACATGAATTGGAGCGTC 59.973 55.000 0.00 0.00 0.00 5.19 F
1693 1834 0.895100 TGACATCCCAAACCTGCTGC 60.895 55.000 0.00 0.00 0.00 5.25 F
1909 2050 0.964700 CTGTGTCTCTGAGTCCAGCA 59.035 55.000 4.32 4.21 40.20 4.41 F
2640 2785 1.615392 GGCTGGTCAGTTCTGCAAATT 59.385 47.619 0.00 0.00 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2282 0.476771 ACCACCATTCAACCGGAAGT 59.523 50.000 9.46 0.0 39.30 3.01 R
3141 3561 0.179004 ATCAGTGGGCGGTCAAAACA 60.179 50.000 0.00 0.0 0.00 2.83 R
3325 3745 3.525537 GCTCTAGAGTGCAGCATTAACA 58.474 45.455 20.75 0.0 34.92 2.41 R
3573 4151 4.151798 GCAGCTCGTTACAGAAACAAATC 58.848 43.478 0.00 0.0 38.03 2.17 R
4574 5199 2.590291 TCGCGTGCATGTGTGGTT 60.590 55.556 18.54 0.0 0.00 3.67 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
399 464 6.279513 TCAAACTCAAAAAGTGTCCATTGT 57.720 33.333 0.00 0.00 38.58 2.71
417 482 9.187455 GTCCATTGTATTAAAAATGTGTTCGTT 57.813 29.630 7.64 0.00 32.90 3.85
1031 1171 2.125512 GCGTCTTCATCCGCCACT 60.126 61.111 0.00 0.00 43.96 4.00
1607 1748 2.048222 GCTCTGCGTGCTACACCA 60.048 61.111 0.00 0.00 0.00 4.17
1624 1765 0.183731 CCATAAACCTGGGGAGGAGC 59.816 60.000 0.00 0.00 32.28 4.70
1647 1788 0.026803 GCGACATGAATTGGAGCGTC 59.973 55.000 0.00 0.00 0.00 5.19
1693 1834 0.895100 TGACATCCCAAACCTGCTGC 60.895 55.000 0.00 0.00 0.00 5.25
1733 1874 1.755395 CCGTCGTCCCCTATGGTGA 60.755 63.158 0.00 0.00 34.77 4.02
1906 2047 1.957177 GTGTCTGTGTCTCTGAGTCCA 59.043 52.381 4.32 0.36 0.00 4.02
1909 2050 0.964700 CTGTGTCTCTGAGTCCAGCA 59.035 55.000 4.32 4.21 40.20 4.41
1937 2078 4.842531 ACCTCATATGTGTTGGTGATCA 57.157 40.909 1.90 0.00 34.10 2.92
1998 2139 7.413438 GCTTTCACTATCACAGTATGGACTTTG 60.413 40.741 0.00 0.00 43.62 2.77
2057 2198 2.746362 CCATGGAAGACAGCAAGTTCTC 59.254 50.000 5.56 0.00 0.00 2.87
2141 2282 6.325919 CTTGGTTAAGCCTGATGTTGTTTA 57.674 37.500 1.51 0.00 38.35 2.01
2292 2436 2.240667 CCACTGGAGATCATTTCCTGGT 59.759 50.000 6.13 0.00 37.82 4.00
2500 2645 9.883142 ATTTTGAAATTCAACAAAGTAAGGTGA 57.117 25.926 8.06 0.00 35.89 4.02
2640 2785 1.615392 GGCTGGTCAGTTCTGCAAATT 59.385 47.619 0.00 0.00 0.00 1.82
3252 3672 2.352561 TCCAAATGAGTACCAGGGGA 57.647 50.000 0.00 0.00 0.00 4.81
3262 3682 3.506808 CCAGGGGATGGGTCAACA 58.493 61.111 0.00 0.00 46.36 3.33
3325 3745 2.890945 GCCCCTACAAATTGACAACACT 59.109 45.455 0.00 0.00 0.00 3.55
3562 4140 9.806448 ATGGTTATAATTATTGATGTGGCTACA 57.194 29.630 4.99 4.99 41.89 2.74
3573 4151 3.558931 TGTGGCTACATACCTGAATGG 57.441 47.619 0.00 0.00 42.93 3.16
3934 4543 7.878644 AGAGGAAGTAGTTACAAAAAGGTGATC 59.121 37.037 0.00 0.00 0.00 2.92
4058 4667 7.172342 TCTCTATCTCTCTTGCCTAATACTCC 58.828 42.308 0.00 0.00 0.00 3.85
4062 4671 4.079154 TCTCTCTTGCCTAATACTCCCTCA 60.079 45.833 0.00 0.00 0.00 3.86
4063 4672 3.961408 TCTCTTGCCTAATACTCCCTCAC 59.039 47.826 0.00 0.00 0.00 3.51
4193 4818 3.359523 CGGTCGTCGTCCTGGTCA 61.360 66.667 6.94 0.00 0.00 4.02
4222 4847 7.537306 CGTCACATAATTTTGTAGAAAACCCTG 59.463 37.037 0.00 1.39 33.86 4.45
4224 4849 8.356657 TCACATAATTTTGTAGAAAACCCTGTG 58.643 33.333 19.25 19.25 37.69 3.66
4315 4940 4.712122 TTCCTAAATTCAACCCGCAATC 57.288 40.909 0.00 0.00 0.00 2.67
4508 5133 3.848272 TCCGTCTTTATTTCGTACCGT 57.152 42.857 0.00 0.00 0.00 4.83
4553 5178 6.756074 TGAACAACTCAGCAAAACCAAATTAG 59.244 34.615 0.00 0.00 0.00 1.73
4557 5182 6.319141 ACTCAGCAAAACCAAATTAGAGAC 57.681 37.500 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1607 1748 1.216990 CTGCTCCTCCCCAGGTTTAT 58.783 55.000 0.00 0.00 41.28 1.40
1624 1765 1.019673 CTCCAATTCATGTCGCCCTG 58.980 55.000 0.00 0.00 0.00 4.45
1647 1788 3.247648 CGTCAGGTAAGGGCATATTTTCG 59.752 47.826 0.00 0.00 0.00 3.46
1733 1874 0.960364 CGCCCAGCACAGGTAACAAT 60.960 55.000 0.00 0.00 41.41 2.71
1906 2047 6.263842 CCAACACATATGAGGTTAATCATGCT 59.736 38.462 10.38 0.00 40.16 3.79
1909 2050 7.345691 TCACCAACACATATGAGGTTAATCAT 58.654 34.615 10.38 0.00 42.52 2.45
1998 2139 6.266786 TCCATTTCTTTTCCCTTAAGTTGGTC 59.733 38.462 0.97 0.00 0.00 4.02
2057 2198 1.536766 TGTCAAAATCAAGAGCAGCCG 59.463 47.619 0.00 0.00 0.00 5.52
2141 2282 0.476771 ACCACCATTCAACCGGAAGT 59.523 50.000 9.46 0.00 39.30 3.01
2292 2436 1.074889 GGGCTGGGAACAAAGGAGTAA 59.925 52.381 0.00 0.00 42.06 2.24
2454 2598 9.299963 TCAAAATCACAAGAACACAAATAACAG 57.700 29.630 0.00 0.00 0.00 3.16
2500 2645 3.244491 TGCTAATTTGCCAAGCCACAAAT 60.244 39.130 9.41 0.00 45.84 2.32
3141 3561 0.179004 ATCAGTGGGCGGTCAAAACA 60.179 50.000 0.00 0.00 0.00 2.83
3325 3745 3.525537 GCTCTAGAGTGCAGCATTAACA 58.474 45.455 20.75 0.00 34.92 2.41
3562 4140 8.739972 GTTACAGAAACAAATCCATTCAGGTAT 58.260 33.333 0.00 0.00 38.05 2.73
3573 4151 4.151798 GCAGCTCGTTACAGAAACAAATC 58.848 43.478 0.00 0.00 38.03 2.17
3934 4543 6.414987 GCAAACGAATTAGCCAAAATAGCTAG 59.585 38.462 0.00 0.00 43.39 3.42
4058 4667 5.991606 TGAGACACTTATTTTGTGAGTGAGG 59.008 40.000 9.45 0.00 44.80 3.86
4062 4671 7.484035 GTCTTGAGACACTTATTTTGTGAGT 57.516 36.000 6.28 0.00 44.18 3.41
4193 4818 8.241367 GGTTTTCTACAAAATTATGTGACGGAT 58.759 33.333 0.00 0.00 33.98 4.18
4292 4917 4.939052 TTGCGGGTTGAATTTAGGAAAA 57.061 36.364 0.00 0.00 0.00 2.29
4452 5077 9.737844 ATTTATTAAGGTTGCATCCAAAACAAT 57.262 25.926 16.12 9.23 31.68 2.71
4508 5133 6.885918 TGTTCATTTTCTATCTGGATCTGCAA 59.114 34.615 0.00 0.00 0.00 4.08
4553 5178 7.010275 GTGGTTATAGATGGTTTCTTTCGTCTC 59.990 40.741 0.00 0.00 35.79 3.36
4557 5182 6.370442 TGTGTGGTTATAGATGGTTTCTTTCG 59.630 38.462 0.00 0.00 35.79 3.46
4574 5199 2.590291 TCGCGTGCATGTGTGGTT 60.590 55.556 18.54 0.00 0.00 3.67
4615 5240 7.833786 TCAGCATAAGATCAGAAATTTGCTTT 58.166 30.769 0.00 0.00 37.10 3.51


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

AutoCloner maintained by Alex Coulton.