Multiple sequence alignment - TraesCS2B01G532200

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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 TraesCS2B01G532200 chr2B 100.000 4754 0 0 1 4754 727685056 727689809 0.000000e+00 8780.0
1 TraesCS2B01G532200 chr2B 94.059 202 8 3 4549 4750 727713462 727713659 2.150000e-78 303.0
2 TraesCS2B01G532200 chr2B 96.450 169 6 0 4385 4553 727713024 727713192 3.620000e-71 279.0
3 TraesCS2B01G532200 chr2B 100.000 40 0 0 4621 4660 753389850 753389889 1.830000e-09 75.0
4 TraesCS2B01G532200 chr2B 97.500 40 1 0 4621 4660 775266627 775266666 8.540000e-08 69.4
5 TraesCS2B01G532200 chr2D 97.009 3811 101 6 1 3798 598813087 598816897 0.000000e+00 6394.0
6 TraesCS2B01G532200 chr2D 91.487 975 51 21 3796 4750 598817032 598817994 0.000000e+00 1312.0
7 TraesCS2B01G532200 chr2A 94.621 3551 140 17 267 3797 733087083 733090602 0.000000e+00 5452.0
8 TraesCS2B01G532200 chr2A 93.596 203 12 1 1 202 733086877 733087079 7.730000e-78 302.0
9 TraesCS2B01G532200 chr2A 75.560 491 64 24 3870 4357 733091000 733091437 1.750000e-44 191.0
10 TraesCS2B01G532200 chr2A 87.143 140 9 3 4470 4601 733091645 733091783 2.960000e-32 150.0
11 TraesCS2B01G532200 chr7D 86.098 2863 383 13 909 3762 89533111 89530255 0.000000e+00 3068.0
12 TraesCS2B01G532200 chr7D 84.094 3112 453 26 672 3761 20460110 20463201 0.000000e+00 2966.0
13 TraesCS2B01G532200 chr7D 85.324 2889 400 19 905 3781 20947073 20949949 0.000000e+00 2964.0
14 TraesCS2B01G532200 chr7D 85.212 2901 410 16 896 3785 555196475 555193583 0.000000e+00 2963.0
15 TraesCS2B01G532200 chr7D 84.389 1153 177 2 909 2058 20547276 20548428 0.000000e+00 1129.0
16 TraesCS2B01G532200 chr7D 77.215 158 21 8 3957 4111 20081405 20081550 1.420000e-10 78.7
17 TraesCS2B01G532200 chr7A 85.238 2879 408 15 913 3781 20659584 20662455 0.000000e+00 2946.0
18 TraesCS2B01G532200 chr7A 84.825 2860 421 9 907 3761 20779461 20782312 0.000000e+00 2865.0
19 TraesCS2B01G532200 chr7A 80.317 3475 561 75 363 3781 20600416 20603823 0.000000e+00 2514.0
20 TraesCS2B01G532200 chr7A 74.474 380 66 20 143 508 20727207 20727569 8.300000e-28 135.0
21 TraesCS2B01G532200 chr7A 79.130 115 14 9 349 454 20977821 20977934 2.370000e-08 71.3
22 TraesCS2B01G532200 chr4A 84.965 2860 409 15 907 3757 669381996 669384843 0.000000e+00 2880.0
23 TraesCS2B01G532200 chr4A 81.070 3122 439 89 546 3605 693881036 693878005 0.000000e+00 2351.0
24 TraesCS2B01G532200 chr4A 97.500 40 1 0 4621 4660 46046648 46046687 8.540000e-08 69.4
25 TraesCS2B01G532200 chr3A 93.162 1009 47 10 1 992 308689300 308690303 0.000000e+00 1461.0
26 TraesCS2B01G532200 chr7B 81.000 100 17 2 367 464 601113087 601113186 1.420000e-10 78.7
27 TraesCS2B01G532200 chr7B 97.500 40 1 0 4621 4660 532454853 532454814 8.540000e-08 69.4
28 TraesCS2B01G532200 chr7B 97.500 40 1 0 4621 4660 604279421 604279460 8.540000e-08 69.4
29 TraesCS2B01G532200 chr3B 95.349 43 2 0 4620 4662 500544770 500544812 8.540000e-08 69.4
30 TraesCS2B01G532200 chr3B 97.436 39 1 0 4622 4660 828472102 828472140 3.070000e-07 67.6


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 TraesCS2B01G532200 chr2B 727685056 727689809 4753 False 8780.00 8780 100.0000 1 4754 1 chr2B.!!$F1 4753
1 TraesCS2B01G532200 chr2B 727713024 727713659 635 False 291.00 303 95.2545 4385 4750 2 chr2B.!!$F4 365
2 TraesCS2B01G532200 chr2D 598813087 598817994 4907 False 3853.00 6394 94.2480 1 4750 2 chr2D.!!$F1 4749
3 TraesCS2B01G532200 chr2A 733086877 733091783 4906 False 1523.75 5452 87.7300 1 4601 4 chr2A.!!$F1 4600
4 TraesCS2B01G532200 chr7D 89530255 89533111 2856 True 3068.00 3068 86.0980 909 3762 1 chr7D.!!$R1 2853
5 TraesCS2B01G532200 chr7D 20460110 20463201 3091 False 2966.00 2966 84.0940 672 3761 1 chr7D.!!$F2 3089
6 TraesCS2B01G532200 chr7D 20947073 20949949 2876 False 2964.00 2964 85.3240 905 3781 1 chr7D.!!$F4 2876
7 TraesCS2B01G532200 chr7D 555193583 555196475 2892 True 2963.00 2963 85.2120 896 3785 1 chr7D.!!$R2 2889
8 TraesCS2B01G532200 chr7D 20547276 20548428 1152 False 1129.00 1129 84.3890 909 2058 1 chr7D.!!$F3 1149
9 TraesCS2B01G532200 chr7A 20659584 20662455 2871 False 2946.00 2946 85.2380 913 3781 1 chr7A.!!$F2 2868
10 TraesCS2B01G532200 chr7A 20779461 20782312 2851 False 2865.00 2865 84.8250 907 3761 1 chr7A.!!$F4 2854
11 TraesCS2B01G532200 chr7A 20600416 20603823 3407 False 2514.00 2514 80.3170 363 3781 1 chr7A.!!$F1 3418
12 TraesCS2B01G532200 chr4A 669381996 669384843 2847 False 2880.00 2880 84.9650 907 3757 1 chr4A.!!$F2 2850
13 TraesCS2B01G532200 chr4A 693878005 693881036 3031 True 2351.00 2351 81.0700 546 3605 1 chr4A.!!$R1 3059
14 TraesCS2B01G532200 chr3A 308689300 308690303 1003 False 1461.00 1461 93.1620 1 992 1 chr3A.!!$F1 991

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
420 427 2.550606 TGTGATACGTTTTCTTGTGGCC 59.449 45.455 0.00 0.0 0.00 5.36 F
1093 1206 0.027455 CAGCACGTTGTTTGCGAAGA 59.973 50.000 0.00 0.0 45.15 2.87 F
2089 2212 0.396435 TGAATGTCCTGCGGAGTTGT 59.604 50.000 2.36 0.0 29.39 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1695 1.390463 GAGCGTTCCAAATCGTCACTC 59.610 52.381 0.0 0.0 0.0 3.51 R
3022 3146 0.037590 TTAGGGACATGCACACCACC 59.962 55.000 0.0 0.0 0.0 4.61 R
4058 4534 0.445829 TCACAACAAGCACACACACG 59.554 50.000 0.0 0.0 0.0 4.49 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
39 40 6.263392 TGACGCTAATGCTTAATAGACTCTCT 59.737 38.462 0.00 0.00 36.97 3.10
239 241 8.333235 TGTGGAAATTTCTAGCCTCCTAAAATA 58.667 33.333 17.42 0.00 0.00 1.40
275 277 3.324846 TGTGAGTGTCTCCTAAAGTGCAT 59.675 43.478 0.00 0.00 0.00 3.96
420 427 2.550606 TGTGATACGTTTTCTTGTGGCC 59.449 45.455 0.00 0.00 0.00 5.36
479 495 9.775854 AAATCTGGAGAAGATACATATGTTGAG 57.224 33.333 14.77 0.00 45.37 3.02
483 501 9.605275 CTGGAGAAGATACATATGTTGAGAAAA 57.395 33.333 14.77 0.00 0.00 2.29
962 1071 5.104527 ACTGAGGCAAATATACAACTAGGCA 60.105 40.000 0.00 0.00 0.00 4.75
1093 1206 0.027455 CAGCACGTTGTTTGCGAAGA 59.973 50.000 0.00 0.00 45.15 2.87
1112 1225 3.532542 AGAACGGGAAGCAAATACTAGC 58.467 45.455 0.00 0.00 0.00 3.42
1335 1448 6.622833 TTTTACCTGAAGAAAGGGTTTACG 57.377 37.500 0.00 0.00 42.11 3.18
1527 1644 1.205655 TCACGCTCCCTTGATGAAGAG 59.794 52.381 0.00 0.00 0.00 2.85
1575 1692 6.166279 CAGAGATAAACTTGAGCAGTGGTTA 58.834 40.000 0.00 0.00 35.12 2.85
1578 1695 7.335422 AGAGATAAACTTGAGCAGTGGTTATTG 59.665 37.037 0.00 0.00 35.12 1.90
1818 1938 3.084039 GGACATCACATGCCTTGAAGAA 58.916 45.455 0.00 0.00 0.00 2.52
2089 2212 0.396435 TGAATGTCCTGCGGAGTTGT 59.604 50.000 2.36 0.00 29.39 3.32
2468 2591 7.383102 AGTTAATTGACAGAAACATGCTAGG 57.617 36.000 2.93 0.00 0.00 3.02
2588 2711 6.493189 TGGTGTTACATATGAGGATAAGCA 57.507 37.500 10.38 3.09 0.00 3.91
3022 3146 7.912250 CAGATTTGAGAGGGATTAAATGTTTCG 59.088 37.037 0.00 0.00 0.00 3.46
3263 3392 2.688507 TGAGGTTCTCTCGTTGAATGC 58.311 47.619 0.00 0.00 45.32 3.56
3444 3579 2.785681 GCTGTCGAATTTGACGCATCTG 60.786 50.000 24.98 12.52 41.87 2.90
3464 3599 3.877559 TGGAATTCACCAGAGCATACAG 58.122 45.455 7.93 0.00 34.77 2.74
3821 4157 2.031069 GTCCGGGTTTCTCTGCTTTTTC 60.031 50.000 0.00 0.00 0.00 2.29
3829 4282 6.430000 GGGTTTCTCTGCTTTTTCACATACTA 59.570 38.462 0.00 0.00 0.00 1.82
3966 4441 1.478510 CTACTGACTGATTCCGGCTGT 59.521 52.381 0.00 0.00 0.00 4.40
4046 4522 8.179615 GCTTAACTTGTTTAAACTGTGTACTGT 58.820 33.333 18.72 5.31 0.00 3.55
4058 4534 2.156117 TGTGTACTGTTATTTCACGCGC 59.844 45.455 5.73 0.00 32.55 6.86
4126 4603 9.696917 AAATAATAAGAAAACTTGGCTTGTGAG 57.303 29.630 0.00 0.00 0.00 3.51
4140 4617 4.035675 GGCTTGTGAGTCATAAGTAATGCC 59.964 45.833 25.04 18.54 35.51 4.40
4159 4636 4.724399 TGCCCAGACACTCATTTTTCTTA 58.276 39.130 0.00 0.00 0.00 2.10
4186 4663 1.133945 TGGTTGCTGCCTGTCTGTTTA 60.134 47.619 0.00 0.00 0.00 2.01
4209 4686 0.746204 GCTAGCCTTGCTCTGTTCCC 60.746 60.000 2.29 0.00 40.44 3.97
4216 4695 3.486383 CCTTGCTCTGTTCCCTTTTGTA 58.514 45.455 0.00 0.00 0.00 2.41
4334 4813 5.172687 TGGAAGGCTACATCATGTTTACA 57.827 39.130 0.00 0.00 0.00 2.41
4367 4846 4.035017 AGTTTTCAAAATTCGCTGACACG 58.965 39.130 0.00 0.00 0.00 4.49
4420 4940 8.837099 AACCATCCATGACCAAAATATTTCTA 57.163 30.769 0.10 0.00 0.00 2.10
4457 4985 3.909776 TGCAGCAGAAGATGAAACAAG 57.090 42.857 0.00 0.00 31.30 3.16
4526 5105 0.453390 GGTAAGCTGAAGTGGCATGC 59.547 55.000 9.90 9.90 0.00 4.06
4618 5478 5.654650 ACAACTACTCCCATTGTTCACAAAA 59.345 36.000 0.00 0.00 39.55 2.44
4645 5505 8.050316 ACTCCCTCCATTCATAAATAAGTGAT 57.950 34.615 0.00 0.00 0.00 3.06
4682 5542 8.089625 TCAAAGATAATATCCCTGACTTGTGA 57.910 34.615 0.00 0.00 0.00 3.58
4694 5554 1.003866 GACTTGTGACCAAACAGCGTC 60.004 52.381 0.00 0.00 0.00 5.19
4750 5610 6.350110 GCACTCTAAATGCAGGAAATAACCAA 60.350 38.462 0.00 0.00 42.88 3.67
4751 5611 7.029563 CACTCTAAATGCAGGAAATAACCAAC 58.970 38.462 0.00 0.00 0.00 3.77
4752 5612 6.948309 ACTCTAAATGCAGGAAATAACCAACT 59.052 34.615 0.00 0.00 0.00 3.16
4753 5613 7.121315 ACTCTAAATGCAGGAAATAACCAACTC 59.879 37.037 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.666253 GCTGCCTGGGCTCAACCA 62.666 66.667 13.05 0.00 42.05 3.67
68 69 2.581354 GATGGAGCAGCTCACGGT 59.419 61.111 24.09 6.28 31.08 4.83
111 113 4.439289 CGCTGCAGATCGATTCCAGATATA 60.439 45.833 20.43 0.00 0.00 0.86
202 204 6.811253 AGAAATTTCCACATTAGCGTAACA 57.189 33.333 14.61 0.00 0.00 2.41
204 206 6.037830 GGCTAGAAATTTCCACATTAGCGTAA 59.962 38.462 20.99 0.00 34.40 3.18
239 241 5.824624 AGACACTCACACATCAAGAATGTTT 59.175 36.000 0.00 0.00 46.73 2.83
259 261 5.664457 CTGTCATATGCACTTTAGGAGACA 58.336 41.667 0.00 0.00 33.11 3.41
396 399 5.106475 GGCCACAAGAAAACGTATCACAATA 60.106 40.000 0.00 0.00 0.00 1.90
407 410 5.195001 TGTTGATTAGGCCACAAGAAAAC 57.805 39.130 5.01 5.61 0.00 2.43
479 495 6.512297 TCCAAGCAACTTAGTTCCATTTTTC 58.488 36.000 0.00 0.00 0.00 2.29
483 501 3.507622 GCTCCAAGCAACTTAGTTCCATT 59.492 43.478 0.00 0.00 41.89 3.16
497 515 3.406595 ATACCGGCCAGCTCCAAGC 62.407 63.158 0.00 0.00 42.84 4.01
809 871 5.362430 TGTGGTGAAATAAGCAGAACCTTTT 59.638 36.000 0.00 0.00 0.00 2.27
988 1099 1.734465 CTCCGCCATCACTTTCTGAAC 59.266 52.381 0.00 0.00 30.60 3.18
1093 1206 2.277084 CGCTAGTATTTGCTTCCCGTT 58.723 47.619 0.00 0.00 0.00 4.44
1112 1225 2.898840 CCATGCTGCCCTGTAGCG 60.899 66.667 0.00 0.00 43.95 4.26
1335 1448 7.820648 TCAAAGAAAGCAGATATCTTGGTTTC 58.179 34.615 28.95 28.95 45.07 2.78
1527 1644 1.471119 TGTCCACACCGACTAGATCC 58.529 55.000 0.00 0.00 33.70 3.36
1575 1692 2.159627 GCGTTCCAAATCGTCACTCAAT 59.840 45.455 0.00 0.00 0.00 2.57
1578 1695 1.390463 GAGCGTTCCAAATCGTCACTC 59.610 52.381 0.00 0.00 0.00 3.51
1818 1938 3.935828 GCTCTAGAAATTTCCTCAGCGTT 59.064 43.478 14.61 0.00 0.00 4.84
2089 2212 5.353394 ACTATTTGCTCGGACAAAGGATA 57.647 39.130 9.15 0.00 42.45 2.59
2468 2591 6.038714 ACCAAATGAGTTTCTCTTGACAAGTC 59.961 38.462 14.75 4.89 0.00 3.01
2588 2711 2.921221 TCCTCTCAAAAGACCTCCCAT 58.079 47.619 0.00 0.00 0.00 4.00
3022 3146 0.037590 TTAGGGACATGCACACCACC 59.962 55.000 0.00 0.00 0.00 4.61
3094 3218 6.923508 TGCCGTAAATGTCTAATAGACTCATG 59.076 38.462 19.76 8.50 45.27 3.07
3326 3461 1.135141 CAGCTTGGAAGAGAGGAGACG 60.135 57.143 0.00 0.00 0.00 4.18
3444 3579 2.615912 GCTGTATGCTCTGGTGAATTCC 59.384 50.000 2.27 0.00 38.95 3.01
3464 3599 1.797635 GAAATGATAGCTGCTCTCCGC 59.202 52.381 4.91 0.00 39.77 5.54
3478 3613 3.343617 GAAACCATCCCGTGAGAAATGA 58.656 45.455 0.00 0.00 0.00 2.57
3798 3942 0.693049 AAGCAGAGAAACCCGGACAT 59.307 50.000 0.73 0.00 0.00 3.06
3821 4157 5.065602 AGCAGCAAATGATGTGTAGTATGTG 59.934 40.000 0.00 0.00 33.30 3.21
3829 4282 3.553508 GGAACAAGCAGCAAATGATGTGT 60.554 43.478 0.00 0.00 32.67 3.72
3966 4441 4.511454 CGCTTGCAGTCTTATAATAAGCCA 59.489 41.667 0.00 0.00 36.59 4.75
4033 4509 5.557514 CGCGTGAAATAACAGTACACAGTTT 60.558 40.000 0.00 0.00 0.00 2.66
4058 4534 0.445829 TCACAACAAGCACACACACG 59.554 50.000 0.00 0.00 0.00 4.49
4065 4541 5.181690 TGAAATAGGTTCACAACAAGCAC 57.818 39.130 0.00 0.00 41.47 4.40
4066 4542 4.261572 GCTGAAATAGGTTCACAACAAGCA 60.262 41.667 0.00 0.00 41.47 3.91
4109 4585 4.574599 ATGACTCACAAGCCAAGTTTTC 57.425 40.909 0.00 0.00 0.00 2.29
4126 4603 4.770795 AGTGTCTGGGCATTACTTATGAC 58.229 43.478 0.00 0.00 41.97 3.06
4159 4636 4.581824 CAGACAGGCAGCAACCATAATTAT 59.418 41.667 0.00 0.00 0.00 1.28
4186 4663 2.503895 ACAGAGCAAGGCTAGCAATT 57.496 45.000 18.24 7.87 39.88 2.32
4334 4813 9.353999 GCGAATTTTGAAAACTTAAGGACATAT 57.646 29.630 7.53 0.00 0.00 1.78
4367 4846 1.599576 GTTGCCTCCTCACTCCTCC 59.400 63.158 0.00 0.00 0.00 4.30
4420 4940 5.434408 TGCTGCAACTCTTCATATCATCTT 58.566 37.500 0.00 0.00 0.00 2.40
4457 4985 6.454795 TGCATATTTCTTTTGGGAAAGTGTC 58.545 36.000 0.00 0.00 42.32 3.67
4526 5105 2.070305 TTGGGATACACATGCATGGG 57.930 50.000 27.38 27.38 37.19 4.00
4618 5478 9.170890 TCACTTATTTATGAATGGAGGGAGTAT 57.829 33.333 0.00 0.00 0.00 2.12
4682 5542 0.732571 CAGTTGTGACGCTGTTTGGT 59.267 50.000 0.00 0.00 0.00 3.67
4694 5554 3.781079 TGAAAACTTGAGGCAGTTGTG 57.219 42.857 0.00 0.00 37.07 3.33


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

AutoCloner maintained by Alex Coulton.