Multiple sequence alignment - TraesCS4B01G224600

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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 TraesCS4B01G224600 chr4B 100.000 3578 0 0 1 3578 470294868 470298445 0.000000e+00 6608
1 TraesCS4B01G224600 chr4B 79.231 260 45 9 1111 1367 77651299 77651552 4.750000e-39 172
2 TraesCS4B01G224600 chr4A 92.150 3274 77 54 1 3165 64955623 64958825 0.000000e+00 4457
3 TraesCS4B01G224600 chr4A 96.379 359 10 1 3207 3562 64958832 64959190 3.980000e-164 588
4 TraesCS4B01G224600 chr4A 79.231 260 45 9 1111 1367 544047783 544047530 4.750000e-39 172
5 TraesCS4B01G224600 chr4D 94.207 2313 51 25 892 3135 382737785 382740083 0.000000e+00 3452
6 TraesCS4B01G224600 chr4D 94.925 867 13 9 14 869 382736726 382737572 0.000000e+00 1328
7 TraesCS4B01G224600 chr4D 93.493 292 7 5 3124 3411 382740752 382741035 1.190000e-114 424
8 TraesCS4B01G224600 chr4D 97.521 121 3 0 3442 3562 382741903 382742023 1.300000e-49 207
9 TraesCS4B01G224600 chr4D 78.927 261 44 11 1111 1367 52763829 52764082 2.210000e-37 167
10 TraesCS4B01G224600 chr3B 75.532 282 55 11 1099 1374 74294225 74294498 3.750000e-25 126
11 TraesCS4B01G224600 chr3A 75.532 282 55 11 1099 1374 59532230 59532503 3.750000e-25 126
12 TraesCS4B01G224600 chr3D 75.177 282 56 11 1099 1374 47493580 47493853 1.740000e-23 121


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 TraesCS4B01G224600 chr4B 470294868 470298445 3577 False 6608.00 6608 100.0000 1 3578 1 chr4B.!!$F2 3577
1 TraesCS4B01G224600 chr4A 64955623 64959190 3567 False 2522.50 4457 94.2645 1 3562 2 chr4A.!!$F1 3561
2 TraesCS4B01G224600 chr4D 382736726 382742023 5297 False 1352.75 3452 95.0365 14 3562 4 chr4D.!!$F2 3548

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
237 238 1.078709 CGATCGTGCAGTGGATGTTT 58.921 50.000 7.03 0.0 0.0 2.83 F
1308 1529 1.227380 CACCATCTGCTACGAGGCC 60.227 63.158 0.00 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1840 0.110192 CAGAAAGAAGAAACGCGGCC 60.110 55.0 12.47 0.0 0.00 6.13 R
2901 3205 0.179037 TGACTACGGACCCGATCGAT 60.179 55.0 18.66 0.0 42.83 3.59 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
237 238 1.078709 CGATCGTGCAGTGGATGTTT 58.921 50.000 7.03 0.00 0.00 2.83
261 262 5.422331 TGAGACAATTAATTCGGGAGAGACT 59.578 40.000 0.00 0.00 41.75 3.24
262 263 6.070767 TGAGACAATTAATTCGGGAGAGACTT 60.071 38.462 0.00 0.00 41.75 3.01
362 367 1.531739 GGGTGCAAATTTGGGCGAGA 61.532 55.000 19.47 0.00 0.00 4.04
611 620 7.597288 ACACATATATGTTAGTCCAGCAGTA 57.403 36.000 15.85 0.00 39.39 2.74
821 844 1.383248 CCTCCCCATTCGACCCTCT 60.383 63.158 0.00 0.00 0.00 3.69
861 891 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
862 892 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
863 893 6.857848 TCTCTCTCTCTCTCTCTCTCTCTAT 58.142 44.000 0.00 0.00 0.00 1.98
873 903 6.326161 TCTCTCTCTCTCTATCTCTCTCCAT 58.674 44.000 0.00 0.00 0.00 3.41
979 1197 1.556564 CCGATTAAAAGCTCTCGCGA 58.443 50.000 9.26 9.26 42.32 5.87
1308 1529 1.227380 CACCATCTGCTACGAGGCC 60.227 63.158 0.00 0.00 0.00 5.19
1358 1579 2.126071 CGTCGCCCACATCTTCGT 60.126 61.111 0.00 0.00 0.00 3.85
1380 1601 2.763933 CTCCAGCAGCAGGTATACATG 58.236 52.381 13.10 13.10 0.00 3.21
1407 1632 5.133153 TCCATCCATCCATCATATACCCATG 59.867 44.000 0.00 0.00 0.00 3.66
1425 1650 4.202357 CCCATGGATCGAGTTAAATCTCCA 60.202 45.833 15.22 14.10 37.21 3.86
1461 1690 3.117398 TCCTGCATGCCTCTTTGGATTAT 60.117 43.478 16.68 0.00 38.35 1.28
1469 1698 2.108952 CCTCTTTGGATTATGGGAGGGG 59.891 54.545 0.00 0.00 37.33 4.79
1473 1702 4.296313 TCTTTGGATTATGGGAGGGGAAAA 59.704 41.667 0.00 0.00 0.00 2.29
1740 1975 2.270527 GCTTCCCCAGCTGGACTC 59.729 66.667 34.91 13.78 46.27 3.36
1741 1976 2.297129 GCTTCCCCAGCTGGACTCT 61.297 63.158 34.91 0.00 46.27 3.24
1849 2084 4.735132 CCGTCACGCCACGTCCAT 62.735 66.667 0.00 0.00 38.32 3.41
2026 2280 7.065216 TCTAGTGCAAATCTTTTGATCTTCG 57.935 36.000 4.24 0.00 38.40 3.79
2038 2292 6.583427 TCTTTTGATCTTCGTTGCAAATCATG 59.417 34.615 10.68 6.00 31.20 3.07
2079 2347 6.398095 TGTGGTTCTATCTGTTCATGTGTAG 58.602 40.000 0.00 0.00 0.00 2.74
2083 2351 5.521906 TCTATCTGTTCATGTGTAGGAGC 57.478 43.478 0.00 0.00 0.00 4.70
2086 2354 5.876651 ATCTGTTCATGTGTAGGAGCATA 57.123 39.130 0.00 0.00 27.76 3.14
2087 2355 5.675684 TCTGTTCATGTGTAGGAGCATAA 57.324 39.130 0.00 0.00 27.76 1.90
2089 2357 6.051074 TCTGTTCATGTGTAGGAGCATAATG 58.949 40.000 0.00 0.00 27.76 1.90
2148 2416 2.741759 TGTATGTGTCATGTCGTGCT 57.258 45.000 0.00 0.00 0.00 4.40
2149 2417 3.859411 TGTATGTGTCATGTCGTGCTA 57.141 42.857 0.00 0.00 0.00 3.49
2156 2424 2.233676 TGTCATGTCGTGCTACCATTCT 59.766 45.455 0.00 0.00 0.00 2.40
2457 2728 2.769621 AGCATGGCGGAGGGATCA 60.770 61.111 0.00 0.00 0.00 2.92
2725 3013 4.166144 ACAACGAGAGGGATTATTGGGATT 59.834 41.667 0.00 0.00 0.00 3.01
2731 3019 4.141158 AGAGGGATTATTGGGATTGGTGAC 60.141 45.833 0.00 0.00 0.00 3.67
2828 3132 0.111639 GTTAACCAGGGGTGCAAGGA 59.888 55.000 0.00 0.00 35.34 3.36
2901 3205 2.845550 CGATCGCTCCGTCCATGGA 61.846 63.158 11.44 11.44 36.37 3.41
2926 3230 1.278985 TCGGGTCCGTAGTCAGTAGAA 59.721 52.381 9.36 0.00 40.74 2.10
2931 3235 3.370953 GGTCCGTAGTCAGTAGAAGGGTA 60.371 52.174 0.00 0.00 0.00 3.69
2946 3250 3.629142 AGGGTAGTAGTTTGACATGGC 57.371 47.619 0.00 0.00 0.00 4.40
3127 3440 5.301551 TCTCTAAATTGGTTTTGCAGCTTCA 59.698 36.000 0.00 0.00 0.00 3.02
3179 4179 7.703298 TTTTTATTTTCGAACGAGTGAGAGA 57.297 32.000 0.00 0.00 0.00 3.10
3180 4180 6.686130 TTTATTTTCGAACGAGTGAGAGAC 57.314 37.500 0.00 0.00 0.00 3.36
3181 4181 3.703286 TTTTCGAACGAGTGAGAGACA 57.297 42.857 0.00 0.00 0.00 3.41
3182 4182 3.703286 TTTCGAACGAGTGAGAGACAA 57.297 42.857 0.00 0.00 0.00 3.18
3184 4184 2.219458 TCGAACGAGTGAGAGACAAGT 58.781 47.619 0.00 0.00 0.00 3.16
3185 4185 2.223611 TCGAACGAGTGAGAGACAAGTC 59.776 50.000 0.00 0.00 0.00 3.01
3186 4186 2.576406 GAACGAGTGAGAGACAAGTCG 58.424 52.381 0.00 0.00 40.68 4.18
3187 4187 0.875728 ACGAGTGAGAGACAAGTCGG 59.124 55.000 5.07 0.00 39.81 4.79
3188 4188 0.169230 CGAGTGAGAGACAAGTCGGG 59.831 60.000 0.00 0.00 35.15 5.14
3189 4189 0.109039 GAGTGAGAGACAAGTCGGGC 60.109 60.000 0.00 0.00 34.09 6.13
3190 4190 0.827925 AGTGAGAGACAAGTCGGGCA 60.828 55.000 0.00 0.00 34.09 5.36
3191 4191 0.667792 GTGAGAGACAAGTCGGGCAC 60.668 60.000 0.00 1.46 34.09 5.01
3192 4192 0.827925 TGAGAGACAAGTCGGGCACT 60.828 55.000 0.00 0.00 36.64 4.40
3205 4205 0.664767 GGGCACTCACTATCGATCGC 60.665 60.000 11.09 0.00 0.00 4.58
3277 4280 2.831333 CAACAGTGCTCTGAAGTCACT 58.169 47.619 21.96 0.00 43.76 3.41
3281 4284 1.346068 AGTGCTCTGAAGTCACTTCCC 59.654 52.381 15.20 1.87 39.51 3.97
3472 5312 1.450312 GCCGCTGTTGCATCTAGGT 60.450 57.895 0.00 0.00 39.64 3.08
3563 5403 8.585471 AAACATGGATCATGATTCTTAACTGT 57.415 30.769 15.17 7.88 43.81 3.55
3564 5404 8.585471 AACATGGATCATGATTCTTAACTGTT 57.415 30.769 15.17 12.46 43.81 3.16
3565 5405 7.993101 ACATGGATCATGATTCTTAACTGTTG 58.007 34.615 15.17 3.33 43.81 3.33
3566 5406 7.830697 ACATGGATCATGATTCTTAACTGTTGA 59.169 33.333 15.17 0.00 43.81 3.18
3567 5407 8.680001 CATGGATCATGATTCTTAACTGTTGAA 58.320 33.333 15.17 0.00 43.81 2.69
3568 5408 8.634335 TGGATCATGATTCTTAACTGTTGAAA 57.366 30.769 15.17 0.00 0.00 2.69
3569 5409 8.514594 TGGATCATGATTCTTAACTGTTGAAAC 58.485 33.333 15.17 0.00 0.00 2.78
3570 5410 7.693951 GGATCATGATTCTTAACTGTTGAAACG 59.306 37.037 10.14 0.00 0.00 3.60
3571 5411 7.490962 TCATGATTCTTAACTGTTGAAACGT 57.509 32.000 2.69 0.00 0.00 3.99
3572 5412 7.351981 TCATGATTCTTAACTGTTGAAACGTG 58.648 34.615 2.69 9.34 33.64 4.49
3573 5413 6.912203 TGATTCTTAACTGTTGAAACGTGA 57.088 33.333 2.69 0.00 0.00 4.35
3574 5414 7.490962 TGATTCTTAACTGTTGAAACGTGAT 57.509 32.000 2.69 0.00 0.00 3.06
3575 5415 8.596271 TGATTCTTAACTGTTGAAACGTGATA 57.404 30.769 2.69 0.00 0.00 2.15
3576 5416 9.214957 TGATTCTTAACTGTTGAAACGTGATAT 57.785 29.630 2.69 0.00 0.00 1.63
3577 5417 9.690434 GATTCTTAACTGTTGAAACGTGATATC 57.310 33.333 2.69 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.199558 GTAGGTGATCGATCGGGCTAC 59.800 57.143 20.03 11.93 0.00 3.58
237 238 5.422331 AGTCTCTCCCGAATTAATTGTCTCA 59.578 40.000 5.17 0.00 0.00 3.27
589 598 7.010771 TCCTACTGCTGGACTAACATATATGT 58.989 38.462 12.75 12.75 44.20 2.29
611 620 1.893801 CACACTTTCCCTACTCGTCCT 59.106 52.381 0.00 0.00 0.00 3.85
772 795 2.228103 TGCCAATATAGTAGACGCGGAG 59.772 50.000 12.47 0.00 0.00 4.63
821 844 0.106918 GAGAGAGGGCGAGAGGAGAA 60.107 60.000 0.00 0.00 0.00 2.87
861 891 6.550108 GGTGTTGGTAAGTATGGAGAGAGATA 59.450 42.308 0.00 0.00 0.00 1.98
862 892 5.364157 GGTGTTGGTAAGTATGGAGAGAGAT 59.636 44.000 0.00 0.00 0.00 2.75
863 893 4.710375 GGTGTTGGTAAGTATGGAGAGAGA 59.290 45.833 0.00 0.00 0.00 3.10
873 903 0.244450 CTCGCCGGTGTTGGTAAGTA 59.756 55.000 16.01 0.00 0.00 2.24
979 1197 0.312416 GCTGTGCTAGATCGATCGGT 59.688 55.000 19.33 8.34 0.00 4.69
1076 1294 2.372688 CAAGGCCCCCTCCTCCTA 59.627 66.667 0.00 0.00 34.82 2.94
1380 1601 5.068636 GGTATATGATGGATGGATGGATGC 58.931 45.833 0.00 0.00 0.00 3.91
1407 1632 6.049149 TCAACATGGAGATTTAACTCGATCC 58.951 40.000 0.00 0.00 37.74 3.36
1425 1650 3.480505 TGCAGGATGATCGATCAACAT 57.519 42.857 30.41 23.01 40.69 2.71
1469 1698 0.679960 ATGGCGCCTACTGGGTTTTC 60.680 55.000 29.70 0.00 37.43 2.29
1473 1702 4.489771 GCATGGCGCCTACTGGGT 62.490 66.667 29.70 1.59 37.43 4.51
1605 1840 0.110192 CAGAAAGAAGAAACGCGGCC 60.110 55.000 12.47 0.00 0.00 6.13
1740 1975 1.526384 CGCGCATATCATTCATCGCAG 60.526 52.381 8.75 0.00 42.28 5.18
1741 1976 0.439600 CGCGCATATCATTCATCGCA 59.560 50.000 8.75 0.00 42.28 5.10
2079 2347 2.292267 CCAGTCACACCATTATGCTCC 58.708 52.381 0.00 0.00 0.00 4.70
2083 2351 5.702865 CTTCAAACCAGTCACACCATTATG 58.297 41.667 0.00 0.00 0.00 1.90
2086 2354 2.362077 GCTTCAAACCAGTCACACCATT 59.638 45.455 0.00 0.00 0.00 3.16
2087 2355 1.956477 GCTTCAAACCAGTCACACCAT 59.044 47.619 0.00 0.00 0.00 3.55
2089 2357 1.680338 AGCTTCAAACCAGTCACACC 58.320 50.000 0.00 0.00 0.00 4.16
2148 2416 2.335681 TCACCACCTGGAGAATGGTA 57.664 50.000 6.41 0.00 45.11 3.25
2156 2424 1.279496 CTGGAGATTCACCACCTGGA 58.721 55.000 0.00 0.00 38.94 3.86
2368 2636 2.404995 GCTGGTGATGCTGCTGGAC 61.405 63.158 0.00 0.00 0.00 4.02
2725 3013 1.337384 CCATCATCCCTCCGTCACCA 61.337 60.000 0.00 0.00 0.00 4.17
2731 3019 2.341543 CTCGCCATCATCCCTCCG 59.658 66.667 0.00 0.00 0.00 4.63
2828 3132 1.635817 ATATGGAGCAAGTGGGGCGT 61.636 55.000 0.00 0.00 36.08 5.68
2901 3205 0.179037 TGACTACGGACCCGATCGAT 60.179 55.000 18.66 0.00 42.83 3.59
2926 3230 3.182152 AGCCATGTCAAACTACTACCCT 58.818 45.455 0.00 0.00 0.00 4.34
2931 3235 3.261897 ACTGCTAGCCATGTCAAACTACT 59.738 43.478 13.29 0.00 0.00 2.57
2946 3250 2.084546 GGCCCAAAGTAACACTGCTAG 58.915 52.381 0.00 0.00 0.00 3.42
3127 3440 2.102070 ACTCACAGTCGAGTCGATCT 57.898 50.000 19.75 14.32 42.70 2.75
3164 4164 2.219458 ACTTGTCTCTCACTCGTTCGA 58.781 47.619 0.00 0.00 0.00 3.71
3173 4173 0.827925 AGTGCCCGACTTGTCTCTCA 60.828 55.000 0.00 0.00 0.00 3.27
3178 4178 0.601558 TAGTGAGTGCCCGACTTGTC 59.398 55.000 0.00 0.00 33.83 3.18
3179 4179 1.204941 GATAGTGAGTGCCCGACTTGT 59.795 52.381 0.00 0.00 33.83 3.16
3180 4180 1.799181 CGATAGTGAGTGCCCGACTTG 60.799 57.143 0.00 0.00 33.83 3.16
3181 4181 0.456221 CGATAGTGAGTGCCCGACTT 59.544 55.000 0.00 0.00 33.83 3.01
3182 4182 0.393944 TCGATAGTGAGTGCCCGACT 60.394 55.000 0.00 0.00 35.53 4.18
3184 4184 0.952280 GATCGATAGTGAGTGCCCGA 59.048 55.000 0.00 0.00 37.40 5.14
3185 4185 0.386100 CGATCGATAGTGAGTGCCCG 60.386 60.000 10.26 0.00 37.40 6.13
3186 4186 0.664767 GCGATCGATAGTGAGTGCCC 60.665 60.000 21.57 0.00 37.40 5.36
3187 4187 0.312416 AGCGATCGATAGTGAGTGCC 59.688 55.000 21.57 0.00 37.40 5.01
3188 4188 1.680668 GAGCGATCGATAGTGAGTGC 58.319 55.000 21.57 0.00 37.40 4.40
3189 4189 1.261885 ACGAGCGATCGATAGTGAGTG 59.738 52.381 31.66 0.00 36.85 3.51
3190 4190 1.261885 CACGAGCGATCGATAGTGAGT 59.738 52.381 33.55 14.58 38.96 3.41
3191 4191 1.261885 ACACGAGCGATCGATAGTGAG 59.738 52.381 39.88 22.94 38.96 3.51
3192 4192 1.296727 ACACGAGCGATCGATAGTGA 58.703 50.000 39.88 0.00 38.96 3.41
3205 4205 7.995998 GCAACAACAAATAAACAAATACACGAG 59.004 33.333 0.00 0.00 0.00 4.18
3281 4284 0.370273 GCTGTTCATAACTCCACGCG 59.630 55.000 3.53 3.53 0.00 6.01
3465 5305 4.099573 GGCATGGCATACGTATACCTAGAT 59.900 45.833 22.51 8.06 0.00 1.98
3472 5312 0.616371 GGGGGCATGGCATACGTATA 59.384 55.000 22.06 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.