Multiple sequence alignment - TraesCS4A01G184600

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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 TraesCS4A01G184600 chr4A 100.000 2892 0 0 1 2892 463542053 463544944 0.000000e+00 5341.0
1 TraesCS4A01G184600 chr4A 81.261 571 73 18 5 562 462867971 462868520 5.720000e-117 431.0
2 TraesCS4A01G184600 chr4A 83.000 100 13 3 195 294 586455710 586455805 1.430000e-13 87.9
3 TraesCS4A01G184600 chr4D 93.566 2207 93 20 705 2892 113933641 113931465 0.000000e+00 3243.0
4 TraesCS4A01G184600 chr4D 92.800 375 26 1 189 562 113936325 113935951 2.530000e-150 542.0
5 TraesCS4A01G184600 chr4D 89.600 250 10 9 446 690 113935945 113935707 1.300000e-78 303.0
6 TraesCS4A01G184600 chr4B 93.710 1256 53 13 692 1941 174696480 174695245 0.000000e+00 1858.0
7 TraesCS4A01G184600 chr4B 92.308 962 58 7 1930 2886 174695086 174694136 0.000000e+00 1352.0
8 TraesCS4A01G184600 chr4B 83.627 568 68 18 5 563 174742770 174742219 7.150000e-141 510.0
9 TraesCS4A01G184600 chr5D 83.333 150 16 8 159 303 3826518 3826373 2.340000e-26 130.0
10 TraesCS4A01G184600 chr3B 80.606 165 19 13 139 293 582755864 582755703 6.550000e-22 115.0
11 TraesCS4A01G184600 chr7B 80.124 161 21 11 146 303 583606796 583606948 3.050000e-20 110.0
12 TraesCS4A01G184600 chr2A 82.828 99 13 3 195 293 196130716 196130810 5.130000e-13 86.1
13 TraesCS4A01G184600 chr1D 86.420 81 7 4 217 297 440724396 440724472 5.130000e-13 86.1
14 TraesCS4A01G184600 chr7A 85.333 75 7 3 220 294 591631369 591631299 1.110000e-09 75.0
15 TraesCS4A01G184600 chr6B 85.333 75 4 5 218 289 637365375 637365445 1.440000e-08 71.3


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 TraesCS4A01G184600 chr4A 463542053 463544944 2891 False 5341.000000 5341 100.000000 1 2892 1 chr4A.!!$F2 2891
1 TraesCS4A01G184600 chr4A 462867971 462868520 549 False 431.000000 431 81.261000 5 562 1 chr4A.!!$F1 557
2 TraesCS4A01G184600 chr4D 113931465 113936325 4860 True 1362.666667 3243 91.988667 189 2892 3 chr4D.!!$R1 2703
3 TraesCS4A01G184600 chr4B 174694136 174696480 2344 True 1605.000000 1858 93.009000 692 2886 2 chr4B.!!$R2 2194
4 TraesCS4A01G184600 chr4B 174742219 174742770 551 True 510.000000 510 83.627000 5 563 1 chr4B.!!$R1 558

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
75 76 0.111253 GAAGGGGCTATGTGGGGATG 59.889 60.0 0.0 0.0 0.00 3.51 F
900 3101 0.181587 TCAGACCCAACTGCGGAAAA 59.818 50.0 0.0 0.0 37.75 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 3703 0.248498 CGGTAAGAATCGCGCTCTCA 60.248 55.0 5.56 0.0 0.0 3.27 R
2568 4946 0.537188 CCCGACCTAGTGCAATGAGT 59.463 55.0 0.00 0.0 0.0 3.41 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
32 33 9.971744 GATGCAAAAATAAATACATCAAACACC 57.028 29.630 0.00 0.00 35.21 4.16
42 43 1.739466 CATCAAACACCGGGATGAGTG 59.261 52.381 6.32 0.00 40.61 3.51
45 46 0.324943 AAACACCGGGATGAGTGAGG 59.675 55.000 6.32 0.00 37.43 3.86
73 74 1.696314 GGAAGGGGCTATGTGGGGA 60.696 63.158 0.00 0.00 0.00 4.81
74 75 1.068352 GGAAGGGGCTATGTGGGGAT 61.068 60.000 0.00 0.00 0.00 3.85
75 76 0.111253 GAAGGGGCTATGTGGGGATG 59.889 60.000 0.00 0.00 0.00 3.51
76 77 1.363530 AAGGGGCTATGTGGGGATGG 61.364 60.000 0.00 0.00 0.00 3.51
77 78 2.845345 GGGGCTATGTGGGGATGGG 61.845 68.421 0.00 0.00 0.00 4.00
97 98 1.522569 GGATGAGGGTGGGAAGTCG 59.477 63.158 0.00 0.00 0.00 4.18
110 111 3.628646 AAGTCGCCATGGGTGAGGC 62.629 63.158 15.13 0.00 43.30 4.70
142 143 6.343703 GCCCAATAGAATGCTTTTGATTTCT 58.656 36.000 5.50 0.00 35.78 2.52
144 145 7.632245 GCCCAATAGAATGCTTTTGATTTCTCT 60.632 37.037 5.50 0.00 35.78 3.10
327 330 6.268158 TCACCTACACTTACCTGAAACATGTA 59.732 38.462 0.00 0.00 0.00 2.29
646 785 1.140252 TCTCGCATAAAGGCTTACCCC 59.860 52.381 0.00 0.00 36.11 4.95
690 829 3.060339 GCAAACAGTGCGAAAATTCCAAG 60.060 43.478 0.00 0.00 45.10 3.61
703 842 2.649531 TTCCAAGAGAGGCGGAAAAA 57.350 45.000 0.00 0.00 35.89 1.94
900 3101 0.181587 TCAGACCCAACTGCGGAAAA 59.818 50.000 0.00 0.00 37.75 2.29
901 3102 0.593128 CAGACCCAACTGCGGAAAAG 59.407 55.000 0.00 0.00 0.00 2.27
902 3103 0.182775 AGACCCAACTGCGGAAAAGT 59.817 50.000 0.00 0.00 0.00 2.66
903 3104 0.310854 GACCCAACTGCGGAAAAGTG 59.689 55.000 0.00 0.00 0.00 3.16
905 3106 0.744281 CCCAACTGCGGAAAAGTGTT 59.256 50.000 0.00 0.00 0.00 3.32
906 3107 1.950909 CCCAACTGCGGAAAAGTGTTA 59.049 47.619 0.00 0.00 0.00 2.41
907 3108 2.359531 CCCAACTGCGGAAAAGTGTTAA 59.640 45.455 0.00 0.00 0.00 2.01
908 3109 3.550030 CCCAACTGCGGAAAAGTGTTAAG 60.550 47.826 0.00 0.00 0.00 1.85
909 3110 3.042887 CAACTGCGGAAAAGTGTTAAGC 58.957 45.455 0.00 0.00 0.00 3.09
910 3111 1.263217 ACTGCGGAAAAGTGTTAAGCG 59.737 47.619 0.00 0.00 0.00 4.68
911 3112 0.589223 TGCGGAAAAGTGTTAAGCGG 59.411 50.000 0.00 0.00 0.00 5.52
912 3113 0.869730 GCGGAAAAGTGTTAAGCGGA 59.130 50.000 0.00 0.00 0.00 5.54
913 3114 1.399343 GCGGAAAAGTGTTAAGCGGAC 60.399 52.381 0.00 0.00 0.00 4.79
914 3115 1.136446 CGGAAAAGTGTTAAGCGGACG 60.136 52.381 0.00 0.00 0.00 4.79
915 3116 1.399343 GGAAAAGTGTTAAGCGGACGC 60.399 52.381 8.91 8.91 42.33 5.19
1461 3662 4.220382 TCCCATCGTTTCATCTTTGCATTT 59.780 37.500 0.00 0.00 0.00 2.32
1502 3703 3.947834 CCTCATCCATTTCGGCTTTAACT 59.052 43.478 0.00 0.00 33.14 2.24
1531 3732 3.181178 GCGATTCTTACCGATTACCGTTC 59.819 47.826 0.00 0.00 36.31 3.95
1536 3737 3.131046 TCTTACCGATTACCGTTCCCTTC 59.869 47.826 0.00 0.00 36.31 3.46
1620 3821 3.264947 CCTTGTTTCAGCTCATCATCGA 58.735 45.455 0.00 0.00 0.00 3.59
1625 3826 5.872635 TGTTTCAGCTCATCATCGATTTTC 58.127 37.500 0.00 0.00 0.00 2.29
1709 3912 5.862924 AATATGGCTATAACGCACATGTC 57.137 39.130 0.00 0.00 0.00 3.06
1717 3920 1.237533 AACGCACATGTCTTGATGCA 58.762 45.000 0.00 0.00 37.97 3.96
1915 4118 2.959516 TCATGCTGTGAGGTTAGTTCG 58.040 47.619 0.00 0.00 31.80 3.95
1964 4337 9.522804 GTACTGTGAAAACAATCAACCATTTAA 57.477 29.630 0.00 0.00 0.00 1.52
2012 4385 8.534496 GGTATCAAAACACTACCTAAGTTCCTA 58.466 37.037 0.00 0.00 35.76 2.94
2081 4454 9.586435 AAAGTTTAAGGATTTTCTGACTGTTTG 57.414 29.630 0.00 0.00 0.00 2.93
2120 4495 8.538701 TGATTTTGGTCCTATTGCAACAATAAT 58.461 29.630 0.00 3.85 0.00 1.28
2154 4529 6.020971 ACGATGTATCTATTCCACGCATTA 57.979 37.500 0.00 0.00 0.00 1.90
2180 4555 7.175104 AGATCAGTGAAAAATTAGGCCTACAA 58.825 34.615 13.46 0.00 0.00 2.41
2185 4560 7.606456 CAGTGAAAAATTAGGCCTACAACTAGA 59.394 37.037 13.46 0.00 0.00 2.43
2205 4580 2.202703 CGGTAAGCGCGCCTAAGT 60.203 61.111 30.33 5.49 0.00 2.24
2242 4617 1.739067 GTCTCGCTTTGGCCATAAGT 58.261 50.000 21.25 0.00 34.44 2.24
2258 4633 0.107165 AAGTGGAGAATTAGGCGGCC 60.107 55.000 12.11 12.11 0.00 6.13
2343 4718 2.498726 GAGAAGGAGGAGCCGCAG 59.501 66.667 0.00 0.00 43.43 5.18
2363 4738 2.033194 GCCGTTGCTTTCGCTAGGT 61.033 57.895 0.00 0.00 36.97 3.08
2383 4758 4.154347 GAGTGAGAGGCCCAGCGG 62.154 72.222 0.00 0.00 0.00 5.52
2473 4848 0.314935 ATTGGGCTGCGTTGTCAAAG 59.685 50.000 0.00 0.00 0.00 2.77
2476 4851 1.576421 GGCTGCGTTGTCAAAGAGG 59.424 57.895 2.40 0.00 0.00 3.69
2477 4852 1.081840 GCTGCGTTGTCAAAGAGGC 60.082 57.895 2.40 2.16 0.00 4.70
2478 4853 1.785041 GCTGCGTTGTCAAAGAGGCA 61.785 55.000 2.40 2.76 35.61 4.75
2479 4854 0.236711 CTGCGTTGTCAAAGAGGCAG 59.763 55.000 12.08 12.08 44.84 4.85
2482 4857 1.299541 CGTTGTCAAAGAGGCAGTGT 58.700 50.000 0.00 0.00 30.49 3.55
2483 4858 1.261619 CGTTGTCAAAGAGGCAGTGTC 59.738 52.381 0.00 0.00 30.49 3.67
2484 4859 2.288666 GTTGTCAAAGAGGCAGTGTCA 58.711 47.619 0.00 0.00 30.49 3.58
2485 4860 2.245159 TGTCAAAGAGGCAGTGTCAG 57.755 50.000 0.00 0.00 0.00 3.51
2489 4864 2.700371 TCAAAGAGGCAGTGTCAGAGAA 59.300 45.455 0.00 0.00 0.00 2.87
2490 4865 2.805099 CAAAGAGGCAGTGTCAGAGAAC 59.195 50.000 0.00 0.00 0.00 3.01
2491 4866 2.008242 AGAGGCAGTGTCAGAGAACT 57.992 50.000 0.00 0.00 0.00 3.01
2492 4867 1.892474 AGAGGCAGTGTCAGAGAACTC 59.108 52.381 0.00 0.00 0.00 3.01
2496 4871 2.036475 GGCAGTGTCAGAGAACTCTTCA 59.964 50.000 1.24 2.67 37.98 3.02
2507 4885 4.090819 GAGAACTCTTCACCTTACCCTCT 58.909 47.826 0.00 0.00 0.00 3.69
2568 4946 2.683968 CGCCTGAGTGCTGTTTAAGTA 58.316 47.619 0.00 0.00 0.00 2.24
2584 4962 6.872020 TGTTTAAGTACTCATTGCACTAGGTC 59.128 38.462 0.00 0.00 0.00 3.85
2595 4973 1.254026 CACTAGGTCGGGACAGAACA 58.746 55.000 0.75 0.00 0.00 3.18
2599 4977 1.080705 GGTCGGGACAGAACACTCG 60.081 63.158 0.75 0.00 0.00 4.18
2728 5107 6.490241 TTCTAGCAATGAGGAATGAGATCA 57.510 37.500 0.00 0.00 0.00 2.92
2800 5179 9.661563 ATTATTACCATAGATTAAAATCGCGGA 57.338 29.630 6.13 0.00 40.35 5.54
2843 5233 0.029433 GAAATCTGCCCCGCGATTTC 59.971 55.000 8.23 10.34 43.31 2.17
2883 5273 0.598680 GAGATCACGCCGCAATAGCT 60.599 55.000 0.00 0.00 39.10 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.361433 TCATCCCGGTGTTTGATGTATTTAT 58.639 36.000 14.77 0.00 37.67 1.40
18 19 4.199310 CTCATCCCGGTGTTTGATGTATT 58.801 43.478 14.77 0.00 37.67 1.89
22 23 1.739466 CACTCATCCCGGTGTTTGATG 59.261 52.381 10.43 10.43 37.75 3.07
27 28 1.983224 CCTCACTCATCCCGGTGTT 59.017 57.895 0.00 0.00 35.26 3.32
30 31 1.690633 ATGCCTCACTCATCCCGGT 60.691 57.895 0.00 0.00 0.00 5.28
32 33 1.227764 CCATGCCTCACTCATCCCG 60.228 63.158 0.00 0.00 0.00 5.14
45 46 2.841044 CCCCTTCCATGGCCATGC 60.841 66.667 36.08 0.00 37.49 4.06
57 58 1.363530 CCATCCCCACATAGCCCCTT 61.364 60.000 0.00 0.00 0.00 3.95
76 77 2.286885 TTCCCACCCTCATCCCCC 60.287 66.667 0.00 0.00 0.00 5.40
77 78 1.619669 ACTTCCCACCCTCATCCCC 60.620 63.158 0.00 0.00 0.00 4.81
82 83 3.319198 GGCGACTTCCCACCCTCA 61.319 66.667 0.00 0.00 0.00 3.86
84 85 2.610859 ATGGCGACTTCCCACCCT 60.611 61.111 0.00 0.00 34.68 4.34
87 88 2.438434 CCCATGGCGACTTCCCAC 60.438 66.667 6.09 0.00 34.68 4.61
88 89 2.933287 ACCCATGGCGACTTCCCA 60.933 61.111 6.09 0.00 36.66 4.37
91 92 1.450312 CCTCACCCATGGCGACTTC 60.450 63.158 6.09 0.00 0.00 3.01
92 93 2.671070 CCTCACCCATGGCGACTT 59.329 61.111 6.09 0.00 0.00 3.01
110 111 2.887152 GCATTCTATTGGGCCCAAGTAG 59.113 50.000 38.82 33.30 39.47 2.57
300 303 5.547465 TGTTTCAGGTAAGTGTAGGTGATG 58.453 41.667 0.00 0.00 0.00 3.07
563 700 5.695851 CACATACTCCTTCTGTGCTTTTT 57.304 39.130 0.00 0.00 34.47 1.94
569 706 1.002366 GCGCACATACTCCTTCTGTG 58.998 55.000 0.30 0.00 42.44 3.66
570 707 0.108138 GGCGCACATACTCCTTCTGT 60.108 55.000 10.83 0.00 0.00 3.41
571 708 0.108186 TGGCGCACATACTCCTTCTG 60.108 55.000 10.83 0.00 0.00 3.02
572 709 0.176680 CTGGCGCACATACTCCTTCT 59.823 55.000 10.83 0.00 0.00 2.85
573 710 1.432270 GCTGGCGCACATACTCCTTC 61.432 60.000 10.83 0.00 35.78 3.46
574 711 1.450312 GCTGGCGCACATACTCCTT 60.450 57.895 10.83 0.00 35.78 3.36
575 712 2.187946 GCTGGCGCACATACTCCT 59.812 61.111 10.83 0.00 35.78 3.69
576 713 2.897350 GGCTGGCGCACATACTCC 60.897 66.667 10.83 0.00 38.10 3.85
577 714 2.897350 GGGCTGGCGCACATACTC 60.897 66.667 10.83 0.00 40.09 2.59
578 715 3.716195 TGGGCTGGCGCACATACT 61.716 61.111 10.83 0.00 46.59 2.12
690 829 4.150627 GCTTTTGAAATTTTTCCGCCTCTC 59.849 41.667 0.00 0.00 36.36 3.20
932 3133 1.798813 GGAACGAATGAGTGAGCGTTT 59.201 47.619 0.00 0.00 45.61 3.60
1461 3662 3.395639 AGGCAATTCGTCGAACAAGTAA 58.604 40.909 10.39 0.00 0.00 2.24
1502 3703 0.248498 CGGTAAGAATCGCGCTCTCA 60.248 55.000 5.56 0.00 0.00 3.27
1531 3732 2.689983 GGTTCATATGGCAAGTGAAGGG 59.310 50.000 15.45 0.00 32.98 3.95
1536 3737 6.757897 TTTAAGAGGTTCATATGGCAAGTG 57.242 37.500 2.13 0.00 0.00 3.16
1625 3826 1.134610 GGGATGCATTTTCTTGGGCAG 60.135 52.381 0.00 0.00 39.95 4.85
1676 3879 9.186323 GCGTTATAGCCATATTATAGATCACAG 57.814 37.037 0.00 0.00 0.00 3.66
1691 3894 2.935849 CAAGACATGTGCGTTATAGCCA 59.064 45.455 1.15 0.00 36.02 4.75
1693 3896 4.766007 CATCAAGACATGTGCGTTATAGC 58.234 43.478 1.15 0.00 37.71 2.97
1709 3912 6.250344 TCTTTCTTTCATCTGTGCATCAAG 57.750 37.500 0.00 0.00 0.00 3.02
1717 3920 5.480642 TCTGAGCTCTTTCTTTCATCTGT 57.519 39.130 16.19 0.00 0.00 3.41
1928 4131 8.677148 ATTGTTTTCACAGTACACTGATTACT 57.323 30.769 16.05 0.00 46.59 2.24
2120 4495 3.142174 AGATACATCGTCGATGCAGAGA 58.858 45.455 30.31 14.03 43.15 3.10
2154 4529 7.175104 TGTAGGCCTAATTTTTCACTGATCTT 58.825 34.615 15.83 0.00 0.00 2.40
2205 4580 4.373116 GGTCGGTTCCGCTCAGCA 62.373 66.667 6.35 0.00 0.00 4.41
2224 4599 1.678728 CCACTTATGGCCAAAGCGAGA 60.679 52.381 10.96 0.00 39.82 4.04
2242 4617 2.504032 CGGCCGCCTAATTCTCCA 59.496 61.111 14.67 0.00 0.00 3.86
2269 4644 3.827898 CCTCGCCGGACTCCAGAC 61.828 72.222 5.05 0.00 33.16 3.51
2363 4738 1.381872 GCTGGGCCTCTCACTCCTA 60.382 63.158 4.53 0.00 0.00 2.94
2383 4758 0.683504 TAAGTCCACGCCCTCTCTCC 60.684 60.000 0.00 0.00 0.00 3.71
2473 4848 1.892474 AGAGTTCTCTGACACTGCCTC 59.108 52.381 1.23 0.00 0.00 4.70
2476 4851 3.056304 GTGAAGAGTTCTCTGACACTGC 58.944 50.000 21.11 6.78 0.00 4.40
2477 4852 3.320541 AGGTGAAGAGTTCTCTGACACTG 59.679 47.826 24.16 0.00 32.56 3.66
2478 4853 3.571590 AGGTGAAGAGTTCTCTGACACT 58.428 45.455 24.16 15.34 32.56 3.55
2479 4854 4.329462 AAGGTGAAGAGTTCTCTGACAC 57.671 45.455 20.67 20.67 0.00 3.67
2482 4857 3.833070 GGGTAAGGTGAAGAGTTCTCTGA 59.167 47.826 2.96 0.00 0.00 3.27
2483 4858 3.835395 AGGGTAAGGTGAAGAGTTCTCTG 59.165 47.826 2.96 0.00 0.00 3.35
2484 4859 4.090819 GAGGGTAAGGTGAAGAGTTCTCT 58.909 47.826 0.00 0.00 0.00 3.10
2485 4860 4.090819 AGAGGGTAAGGTGAAGAGTTCTC 58.909 47.826 0.00 0.00 0.00 2.87
2489 4864 3.436243 CTGAGAGGGTAAGGTGAAGAGT 58.564 50.000 0.00 0.00 0.00 3.24
2490 4865 2.763448 CCTGAGAGGGTAAGGTGAAGAG 59.237 54.545 0.00 0.00 0.00 2.85
2491 4866 2.821437 CCTGAGAGGGTAAGGTGAAGA 58.179 52.381 0.00 0.00 0.00 2.87
2492 4867 1.208293 GCCTGAGAGGGTAAGGTGAAG 59.792 57.143 0.00 0.00 35.37 3.02
2496 4871 1.307084 GGGCCTGAGAGGGTAAGGT 60.307 63.158 0.84 0.00 35.37 3.50
2507 4885 3.009115 GGCAGTAGGTGGGCCTGA 61.009 66.667 4.53 0.00 46.47 3.86
2568 4946 0.537188 CCCGACCTAGTGCAATGAGT 59.463 55.000 0.00 0.00 0.00 3.41
2584 4962 1.444553 GAGCGAGTGTTCTGTCCCG 60.445 63.158 0.00 0.00 0.00 5.14
2599 4977 1.927895 TTAAGCGCTAAGAGCTGAGC 58.072 50.000 12.05 0.00 45.31 4.26
2661 5040 5.189180 GTCTGGGATCAATACTGAGCTTTT 58.811 41.667 0.00 0.00 38.10 2.27
2670 5049 4.202050 GCCAAACATGTCTGGGATCAATAC 60.202 45.833 19.79 0.00 32.95 1.89
2800 5179 4.104143 CGATAGCGGCCTTTTCGT 57.896 55.556 0.00 0.00 0.00 3.85
2843 5233 1.009829 CGCGATTCTGGGAAGGAAAG 58.990 55.000 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.