Multiple sequence alignment - TraesCS3B01G191200

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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 TraesCS3B01G191200 chr3B 100.000 4074 0 0 1 4074 204278285 204282358 0.000000e+00 7524
1 TraesCS3B01G191200 chr3B 76.835 695 139 18 39 723 595668492 595667810 4.970000e-99 372
2 TraesCS3B01G191200 chr3D 94.970 3340 110 21 761 4074 142473669 142476976 0.000000e+00 5184
3 TraesCS3B01G191200 chr3D 93.260 727 45 3 1 725 253616111 253616835 0.000000e+00 1068
4 TraesCS3B01G191200 chr3D 79.535 215 32 10 1044 1252 402494127 402493919 4.240000e-30 143
5 TraesCS3B01G191200 chr3A 90.893 2328 120 40 1771 4074 161444504 161446763 0.000000e+00 3040
6 TraesCS3B01G191200 chr3A 93.097 1014 35 8 747 1746 161443512 161444504 0.000000e+00 1452
7 TraesCS3B01G191200 chr3A 94.083 338 17 3 1807 2144 375017931 375018265 1.010000e-140 510
8 TraesCS3B01G191200 chr3A 92.264 349 21 6 1797 2144 487860865 487860522 1.320000e-134 490
9 TraesCS3B01G191200 chr3A 87.778 90 11 0 1044 1133 523334098 523334009 5.570000e-19 106
10 TraesCS3B01G191200 chr6B 96.974 694 20 1 1 694 199937100 199936408 0.000000e+00 1164
11 TraesCS3B01G191200 chr7A 86.749 732 81 14 1 725 156136723 156136001 0.000000e+00 800
12 TraesCS3B01G191200 chr4A 85.597 729 90 10 1 722 741081406 741080686 0.000000e+00 750
13 TraesCS3B01G191200 chr4A 95.342 322 14 1 1807 2128 115566916 115567236 1.010000e-140 510
14 TraesCS3B01G191200 chr2B 94.048 336 17 3 1810 2143 136170537 136170203 1.310000e-139 507
15 TraesCS3B01G191200 chr5B 93.787 338 17 3 1807 2142 464890573 464890238 4.700000e-139 505
16 TraesCS3B01G191200 chr5D 94.012 334 17 2 1807 2138 386862040 386861708 1.690000e-138 503
17 TraesCS3B01G191200 chr5D 76.902 723 152 14 9 725 305722905 305722192 2.950000e-106 396
18 TraesCS3B01G191200 chr5A 93.215 339 20 3 1807 2145 366235148 366234813 2.830000e-136 496
19 TraesCS3B01G191200 chrUn 78.005 732 152 9 1 726 264103927 264104655 6.210000e-123 451
20 TraesCS3B01G191200 chr2D 77.715 709 130 22 30 725 65517155 65516462 3.790000e-110 409
21 TraesCS3B01G191200 chr1D 77.166 727 143 18 1 720 39276414 39277124 6.340000e-108 401
22 TraesCS3B01G191200 chr2A 75.650 731 155 19 3 722 103347699 103348417 3.900000e-90 342


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 TraesCS3B01G191200 chr3B 204278285 204282358 4073 False 7524 7524 100.000 1 4074 1 chr3B.!!$F1 4073
1 TraesCS3B01G191200 chr3B 595667810 595668492 682 True 372 372 76.835 39 723 1 chr3B.!!$R1 684
2 TraesCS3B01G191200 chr3D 142473669 142476976 3307 False 5184 5184 94.970 761 4074 1 chr3D.!!$F1 3313
3 TraesCS3B01G191200 chr3D 253616111 253616835 724 False 1068 1068 93.260 1 725 1 chr3D.!!$F2 724
4 TraesCS3B01G191200 chr3A 161443512 161446763 3251 False 2246 3040 91.995 747 4074 2 chr3A.!!$F2 3327
5 TraesCS3B01G191200 chr6B 199936408 199937100 692 True 1164 1164 96.974 1 694 1 chr6B.!!$R1 693
6 TraesCS3B01G191200 chr7A 156136001 156136723 722 True 800 800 86.749 1 725 1 chr7A.!!$R1 724
7 TraesCS3B01G191200 chr4A 741080686 741081406 720 True 750 750 85.597 1 722 1 chr4A.!!$R1 721
8 TraesCS3B01G191200 chr5D 305722192 305722905 713 True 396 396 76.902 9 725 1 chr5D.!!$R1 716
9 TraesCS3B01G191200 chrUn 264103927 264104655 728 False 451 451 78.005 1 726 1 chrUn.!!$F1 725
10 TraesCS3B01G191200 chr2D 65516462 65517155 693 True 409 409 77.715 30 725 1 chr2D.!!$R1 695
11 TraesCS3B01G191200 chr1D 39276414 39277124 710 False 401 401 77.166 1 720 1 chr1D.!!$F1 719
12 TraesCS3B01G191200 chr2A 103347699 103348417 718 False 342 342 75.650 3 722 1 chr2A.!!$F1 719

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
121 123 1.272769 ACTACTTCAGTCGGCTTGGTC 59.727 52.381 0.00 0.00 28.33 4.02 F
1256 1279 0.110238 CGCAACGACCAAGGTGATTG 60.110 55.000 0.00 2.17 38.74 2.67 F
1284 1307 0.257039 ACTCCTTGGCCTTGGCATAG 59.743 55.000 14.04 9.23 38.08 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1312 1335 0.109226 GACTAGCGCAAGAAGACCGT 60.109 55.000 11.47 0.0 43.02 4.83 R
2295 2334 0.249120 TCCAACTGTGTAGATGGCCG 59.751 55.000 0.00 0.0 44.24 6.13 R
3247 3318 1.672881 GCCAAGAGGAATCACAATCCG 59.327 52.381 0.00 0.0 42.03 4.18 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
121 123 1.272769 ACTACTTCAGTCGGCTTGGTC 59.727 52.381 0.00 0.00 28.33 4.02
182 184 1.841556 TTCCACGGTCCCTCTTGCT 60.842 57.895 0.00 0.00 0.00 3.91
699 717 2.107141 GATCGCCACCGGGAGAAG 59.893 66.667 6.32 0.00 46.54 2.85
805 825 4.144297 TGAAACTATGCAGCCCATTATCC 58.856 43.478 0.00 0.00 35.34 2.59
1233 1256 3.135530 AGACTGGCTCCATCATCTTTACC 59.864 47.826 0.00 0.00 0.00 2.85
1256 1279 0.110238 CGCAACGACCAAGGTGATTG 60.110 55.000 0.00 2.17 38.74 2.67
1284 1307 0.257039 ACTCCTTGGCCTTGGCATAG 59.743 55.000 14.04 9.23 38.08 2.23
1304 1327 4.170468 AGGGTGCCTTATGGTAGATTTG 57.830 45.455 0.00 0.00 35.27 2.32
1312 1335 6.069905 TGCCTTATGGTAGATTTGTTAGGACA 60.070 38.462 0.00 0.00 35.27 4.02
1322 1345 4.411256 TTTGTTAGGACACGGTCTTCTT 57.589 40.909 4.41 0.00 34.98 2.52
1385 1408 5.161358 GGTTAGGTGCTTCTAAATTTGTGC 58.839 41.667 0.00 0.72 31.85 4.57
1405 1428 1.593006 CAGCTTTAATAGTGGCGACGG 59.407 52.381 0.00 0.00 0.00 4.79
1513 1536 5.699458 GGTTATCTGGATGGTTGGTATTACG 59.301 44.000 0.00 0.00 0.00 3.18
1603 1628 1.527433 AAGGGAAAGCGCCTTTCTGC 61.527 55.000 22.65 12.66 46.20 4.26
1640 1678 5.480422 ACAATTTCCCAGATTACAAGTTCCC 59.520 40.000 0.00 0.00 0.00 3.97
1681 1719 4.021925 GAGACAACCGCCAGGCCT 62.022 66.667 5.63 0.00 42.76 5.19
1684 1722 4.643387 ACAACCGCCAGGCCTGTC 62.643 66.667 30.63 18.82 42.76 3.51
1696 1734 2.113139 CCTGTCGCCACAAAGGGT 59.887 61.111 0.00 0.00 38.09 4.34
1853 1891 1.361668 CGTCTGAGATGGTTTGGGCG 61.362 60.000 0.00 0.00 0.00 6.13
1938 1976 0.790993 AGAGAGGTTGGGGTAGACCA 59.209 55.000 0.21 0.00 42.91 4.02
1956 1994 2.162681 CCAAACTTGACATGGGAGGAC 58.837 52.381 0.00 0.00 0.00 3.85
2151 2189 3.791973 TGTTTGTTTGTTGGCCTGTAG 57.208 42.857 3.32 0.00 0.00 2.74
2180 2218 5.705609 TTGATTAGGTTTTGTCCTGAAGC 57.294 39.130 0.00 0.00 38.41 3.86
2363 2402 1.686355 TTTCCGAAACAGCACACCAT 58.314 45.000 0.00 0.00 0.00 3.55
2384 2423 7.063780 CACCATTCTTTTCCAATCTTGTATTGC 59.936 37.037 0.00 0.00 0.00 3.56
2407 2446 7.093354 TGCGCTATTGTTTATTTGAATCCAAA 58.907 30.769 9.73 0.00 45.28 3.28
2488 2528 7.041167 TGAGCTATTATTTCACCATACATGCAC 60.041 37.037 0.00 0.00 0.00 4.57
2503 2543 2.363788 TGCACGAAGTACATCTGACC 57.636 50.000 0.00 0.00 41.61 4.02
2506 2546 2.604914 GCACGAAGTACATCTGACCATG 59.395 50.000 0.00 0.00 41.61 3.66
2612 2652 7.381766 TCTTTGTCCTTTGATGTCATACATG 57.618 36.000 0.00 0.00 39.27 3.21
2660 2700 5.069251 GCACTACTACCTTCTGACATACCAT 59.931 44.000 0.00 0.00 0.00 3.55
2754 2804 4.221262 AGCACCTTTTGATGTTATGCATGT 59.779 37.500 10.16 0.00 38.06 3.21
2774 2824 6.586344 CATGTTAGGAATCCTGTACTCATGT 58.414 40.000 12.96 0.00 34.61 3.21
2790 2840 8.724229 TGTACTCATGTCATTTTTCAGATCTTG 58.276 33.333 0.00 0.00 0.00 3.02
2873 2943 6.295292 GCATGTACTATGGACTGATGGTATGA 60.295 42.308 0.00 0.00 0.00 2.15
2899 2970 4.460263 ACTATGCAGTTGACCTGTTGAAA 58.540 39.130 0.00 0.00 43.55 2.69
3031 3102 7.446625 AGCTTTACTGTGAATGAAGAGAACAAT 59.553 33.333 0.00 0.00 0.00 2.71
3247 3318 3.282021 TGAGCTTTCCATGCATCTTACC 58.718 45.455 0.00 0.00 0.00 2.85
3308 3379 1.891919 TGGAACAAGGTCAGCGTGC 60.892 57.895 0.00 0.00 31.92 5.34
3378 3449 7.254185 CCATTACATATTGTGTTGAATTGCTGC 60.254 37.037 0.00 0.00 42.29 5.25
3402 3474 9.171877 TGCTACATTGTGTTGATGTTATATTGA 57.828 29.630 0.00 0.00 38.58 2.57
3442 3514 2.963432 TCGTTGAGATCCGGTAAAACC 58.037 47.619 0.00 0.00 34.05 3.27
3444 3516 3.055675 TCGTTGAGATCCGGTAAAACCAT 60.056 43.478 0.00 0.00 38.47 3.55
3468 3540 1.400846 CATCTGCTGTTCCAGACATGC 59.599 52.381 0.00 0.00 44.00 4.06
3644 3719 1.045911 GTCGGAGGAGGAGGCAGAAT 61.046 60.000 0.00 0.00 0.00 2.40
3766 3841 3.991051 CGGTCGGTGGCTGTGAGT 61.991 66.667 0.00 0.00 0.00 3.41
3959 4034 3.062466 TCGTCCTCCAGACCTGCG 61.062 66.667 0.00 0.00 43.08 5.18
4047 4122 2.035626 CGGCCATTTCCACCAGGT 59.964 61.111 2.24 0.00 35.89 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 6.014669 GCTGGATAGTCTAGACATCTGGATTT 60.015 42.308 24.44 3.32 35.90 2.17
121 123 2.549064 TCACGCCCTATGATGGAATG 57.451 50.000 0.00 0.00 0.00 2.67
182 184 0.605319 GGTGATTGGGAGCGTGTGAA 60.605 55.000 0.00 0.00 0.00 3.18
699 717 2.333688 CCTCTAGCTAGGGTTTTGCC 57.666 55.000 19.37 0.00 32.55 4.52
734 753 9.819267 ATAATTTTGAACGTTTCCCTACAAAAA 57.181 25.926 20.27 10.49 39.44 1.94
735 754 9.819267 AATAATTTTGAACGTTTCCCTACAAAA 57.181 25.926 19.28 19.28 39.98 2.44
736 755 9.250624 CAATAATTTTGAACGTTTCCCTACAAA 57.749 29.630 0.46 4.32 0.00 2.83
737 756 7.868415 CCAATAATTTTGAACGTTTCCCTACAA 59.132 33.333 0.46 0.00 0.00 2.41
738 757 7.230913 TCCAATAATTTTGAACGTTTCCCTACA 59.769 33.333 0.46 0.00 0.00 2.74
739 758 7.595604 TCCAATAATTTTGAACGTTTCCCTAC 58.404 34.615 0.46 0.00 0.00 3.18
740 759 7.762588 TCCAATAATTTTGAACGTTTCCCTA 57.237 32.000 0.46 0.00 0.00 3.53
741 760 6.658188 TCCAATAATTTTGAACGTTTCCCT 57.342 33.333 0.46 0.00 0.00 4.20
742 761 7.093992 TGATCCAATAATTTTGAACGTTTCCC 58.906 34.615 0.46 0.00 0.00 3.97
743 762 8.702163 ATGATCCAATAATTTTGAACGTTTCC 57.298 30.769 0.46 0.00 0.00 3.13
805 825 2.289569 GGCTGAGCCTGATCCATTAGAG 60.290 54.545 17.96 0.00 46.69 2.43
1256 1279 2.283173 CCAAGGAGTGGCAACCCC 60.283 66.667 8.11 0.00 41.72 4.95
1284 1307 3.898482 ACAAATCTACCATAAGGCACCC 58.102 45.455 0.00 0.00 39.06 4.61
1293 1316 4.224370 ACCGTGTCCTAACAAATCTACCAT 59.776 41.667 0.00 0.00 37.08 3.55
1304 1327 2.067013 GCAAGAAGACCGTGTCCTAAC 58.933 52.381 1.06 0.00 32.18 2.34
1312 1335 0.109226 GACTAGCGCAAGAAGACCGT 60.109 55.000 11.47 0.00 43.02 4.83
1322 1345 2.346803 GAATCCAAACAGACTAGCGCA 58.653 47.619 11.47 0.00 0.00 6.09
1385 1408 1.593006 CCGTCGCCACTATTAAAGCTG 59.407 52.381 0.00 0.00 0.00 4.24
1405 1428 7.711339 CCACAAGATTTACACCTCTTATCCTAC 59.289 40.741 0.00 0.00 30.70 3.18
1550 1574 3.539604 GCATCTGAAATGTACTGCCTCT 58.460 45.455 0.00 0.00 0.00 3.69
1603 1628 3.365969 GGGAAATTGTAGTGCCTTGAACG 60.366 47.826 0.00 0.00 0.00 3.95
1606 1631 3.073798 TCTGGGAAATTGTAGTGCCTTGA 59.926 43.478 0.00 0.00 0.00 3.02
1693 1731 1.890979 CAGATGCAGATCGCCACCC 60.891 63.158 0.00 0.00 41.33 4.61
1694 1732 2.541120 GCAGATGCAGATCGCCACC 61.541 63.158 0.00 0.00 41.33 4.61
1696 1734 2.203112 GGCAGATGCAGATCGCCA 60.203 61.111 12.81 0.00 42.77 5.69
1762 1800 2.195741 TTTCAGCAGAGATGCTTGCT 57.804 45.000 0.00 0.00 43.52 3.91
1853 1891 1.889573 GGAGGCCTGCGCTGAATAC 60.890 63.158 12.00 4.64 34.44 1.89
1938 1976 2.040412 GGAGTCCTCCCATGTCAAGTTT 59.960 50.000 0.41 0.00 43.94 2.66
1956 1994 5.967088 TCCTTCAAATCTCTCTTTACGGAG 58.033 41.667 0.00 0.00 34.88 4.63
2151 2189 8.576442 TCAGGACAAAACCTAATCAATTTTCTC 58.424 33.333 0.00 0.00 38.32 2.87
2256 2295 2.706190 AGGATGGCAGGTAATGGTAGTC 59.294 50.000 0.00 0.00 0.00 2.59
2295 2334 0.249120 TCCAACTGTGTAGATGGCCG 59.751 55.000 0.00 0.00 44.24 6.13
2304 2343 3.214328 GTCCAAGTCAATCCAACTGTGT 58.786 45.455 0.00 0.00 0.00 3.72
2363 2402 5.048083 AGCGCAATACAAGATTGGAAAAGAA 60.048 36.000 11.47 0.00 0.00 2.52
2488 2528 5.862924 AAAACATGGTCAGATGTACTTCG 57.137 39.130 0.00 0.00 35.43 3.79
2503 2543 9.829507 AGAGGAAGATCTAGTATCAAAAACATG 57.170 33.333 0.00 0.00 0.00 3.21
2506 2546 9.744468 GAGAGAGGAAGATCTAGTATCAAAAAC 57.256 37.037 0.00 0.00 0.00 2.43
2530 2570 3.969287 TCCAGTTGAAGACATGGAGAG 57.031 47.619 0.00 0.00 36.92 3.20
2612 2652 7.875041 TGCTATATTAGGATGCTTTTCTCTGTC 59.125 37.037 0.00 0.00 0.00 3.51
2754 2804 7.437713 AATGACATGAGTACAGGATTCCTAA 57.562 36.000 4.51 0.00 29.64 2.69
2790 2840 7.094805 TGACCATGAGCAACTAAAAAGATGTAC 60.095 37.037 0.00 0.00 0.00 2.90
3031 3102 3.818387 CTCGTACTCTACTTGCGACAAA 58.182 45.455 0.00 0.00 0.00 2.83
3247 3318 1.672881 GCCAAGAGGAATCACAATCCG 59.327 52.381 0.00 0.00 42.03 4.18
3378 3449 9.636965 CGTCAATATAACATCAACACAATGTAG 57.363 33.333 0.00 0.00 36.35 2.74
3402 3474 3.247648 CGAAAATTCTGTTCTGGACACGT 59.752 43.478 0.00 0.00 33.82 4.49
3468 3540 3.308866 AGCGTTGCTTTTTATAGCCGTAG 59.691 43.478 0.00 0.00 40.49 3.51
3628 3703 2.021208 GCAAATTCTGCCTCCTCCTCC 61.021 57.143 2.35 0.00 46.13 4.30
3629 3704 1.387539 GCAAATTCTGCCTCCTCCTC 58.612 55.000 2.35 0.00 46.13 3.71
3630 3705 3.584947 GCAAATTCTGCCTCCTCCT 57.415 52.632 2.35 0.00 46.13 3.69
3760 3835 4.624364 CCCAGCACCGCACTCACA 62.624 66.667 0.00 0.00 0.00 3.58
3959 4034 0.980231 AGGGTGGAGCAGGAGATGAC 60.980 60.000 0.00 0.00 0.00 3.06
4023 4098 3.361977 GGAAATGGCCGTGTGCGT 61.362 61.111 0.00 0.00 42.61 5.24
4025 4100 2.258286 GTGGAAATGGCCGTGTGC 59.742 61.111 0.00 0.00 40.16 4.57
4027 4102 1.603455 CTGGTGGAAATGGCCGTGT 60.603 57.895 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.