Multiple sequence alignment - TraesCS3B01G500300

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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 TraesCS3B01G500300 chr3B 100.000 3172 0 0 1 3172 744590760 744593931 0.000000e+00 5858.0
1 TraesCS3B01G500300 chr3B 95.973 3203 60 18 1 3172 746856198 746853034 0.000000e+00 5136.0
2 TraesCS3B01G500300 chr3B 84.378 1197 138 28 1 1163 745203223 745202042 0.000000e+00 1129.0
3 TraesCS3B01G500300 chr3B 84.629 1158 128 31 1 1136 745540301 745541430 0.000000e+00 1107.0
4 TraesCS3B01G500300 chr3B 89.227 854 82 3 254 1098 746793772 746792920 0.000000e+00 1059.0
5 TraesCS3B01G500300 chr3B 88.631 862 90 4 1 856 745474688 745473829 0.000000e+00 1042.0
6 TraesCS3B01G500300 chr3B 88.235 833 92 4 1 830 744419687 744418858 0.000000e+00 990.0
7 TraesCS3B01G500300 chr3B 87.427 859 102 4 1 856 747493213 747494068 0.000000e+00 983.0
8 TraesCS3B01G500300 chr3B 89.446 578 51 5 1620 2191 746792905 746792332 0.000000e+00 721.0
9 TraesCS3B01G500300 chr3B 85.398 452 61 4 1736 2183 744339123 744338673 6.200000e-127 464.0
10 TraesCS3B01G500300 chr3B 83.463 514 69 8 1682 2180 746286471 746286983 6.200000e-127 464.0
11 TraesCS3B01G500300 chr3B 84.211 247 32 6 924 1163 745473740 745473494 1.900000e-57 233.0
12 TraesCS3B01G500300 chr3B 78.995 219 21 16 2824 3031 746853712 746853508 3.320000e-25 126.0
13 TraesCS3B01G500300 chr3B 77.778 207 28 13 2371 2565 746849093 746849293 9.300000e-21 111.0
14 TraesCS3B01G500300 chr3B 77.295 207 29 14 2371 2565 744597055 744596855 4.330000e-19 106.0
15 TraesCS3B01G500300 chr3B 89.655 58 6 0 2196 2253 744852436 744852379 1.220000e-09 75.0
16 TraesCS3B01G500300 chr3B 89.091 55 6 0 2199 2253 746295396 746295342 5.680000e-08 69.4
17 TraesCS3B01G500300 chr3D 92.072 1337 67 8 1 1316 560331311 560332629 0.000000e+00 1845.0
18 TraesCS3B01G500300 chr3D 93.970 879 27 4 1318 2191 560332722 560333579 0.000000e+00 1306.0
19 TraesCS3B01G500300 chr3D 87.805 1107 104 13 1 1098 560477972 560479056 0.000000e+00 1267.0
20 TraesCS3B01G500300 chr3D 84.027 1177 137 28 3 1133 560234937 560233766 0.000000e+00 1085.0
21 TraesCS3B01G500300 chr3D 87.239 862 104 3 1 856 560785697 560784836 0.000000e+00 977.0
22 TraesCS3B01G500300 chr3D 88.095 588 51 9 1617 2195 560479168 560479745 0.000000e+00 680.0
23 TraesCS3B01G500300 chr3D 94.545 330 17 1 2439 2768 560333839 560334167 2.820000e-140 508.0
24 TraesCS3B01G500300 chr3D 83.463 514 69 8 1682 2180 560553062 560553574 6.200000e-127 464.0
25 TraesCS3B01G500300 chr3D 90.521 211 19 1 2193 2403 560333629 560333838 8.670000e-71 278.0
26 TraesCS3B01G500300 chr3D 84.644 267 33 7 914 1173 560784653 560784388 3.140000e-65 259.0
27 TraesCS3B01G500300 chr3D 89.017 173 14 1 2374 2546 560334178 560334345 3.210000e-50 209.0
28 TraesCS3B01G500300 chr3D 82.745 255 23 10 2379 2628 560754904 560755142 1.150000e-49 207.0
29 TraesCS3B01G500300 chr3D 80.916 131 15 5 2824 2950 560333892 560334016 9.370000e-16 95.3
30 TraesCS3B01G500300 chr3D 79.389 131 19 5 2824 2947 560480046 560480175 5.640000e-13 86.1
31 TraesCS3B01G500300 chr3D 89.091 55 6 0 2199 2253 560556237 560556183 5.680000e-08 69.4
32 TraesCS3B01G500300 chr3A 87.311 859 103 4 1 856 696332784 696331929 0.000000e+00 977.0
33 TraesCS3B01G500300 chr3A 87.194 859 104 4 1 856 629087181 629088036 0.000000e+00 972.0
34 TraesCS3B01G500300 chr3A 80.668 838 120 22 341 1138 629019536 629018701 2.090000e-171 612.0
35 TraesCS3B01G500300 chr3A 80.024 841 121 24 341 1138 696270292 696269456 2.120000e-161 579.0
36 TraesCS3B01G500300 chr3A 86.192 449 57 4 1736 2180 696288811 696288364 6.150000e-132 481.0
37 TraesCS3B01G500300 chr3A 84.289 471 64 9 1707 2170 629057938 629058405 4.820000e-123 451.0
38 TraesCS3B01G500300 chr3A 87.054 224 28 1 940 1163 696476928 696476706 5.250000e-63 252.0
39 TraesCS3B01G500300 chr1A 94.545 55 3 0 1292 1346 547376775 547376829 5.640000e-13 86.1
40 TraesCS3B01G500300 chr1B 97.297 37 1 0 3068 3104 638893351 638893315 2.640000e-06 63.9
41 TraesCS3B01G500300 chr6D 100.000 31 0 0 1232 1262 467193792 467193762 1.230000e-04 58.4


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 TraesCS3B01G500300 chr3B 744590760 744593931 3171 False 5858.000000 5858 100.000000 1 3172 1 chr3B.!!$F1 3171
1 TraesCS3B01G500300 chr3B 746853034 746856198 3164 True 2631.000000 5136 87.484000 1 3172 2 chr3B.!!$R9 3171
2 TraesCS3B01G500300 chr3B 745202042 745203223 1181 True 1129.000000 1129 84.378000 1 1163 1 chr3B.!!$R5 1162
3 TraesCS3B01G500300 chr3B 745540301 745541430 1129 False 1107.000000 1107 84.629000 1 1136 1 chr3B.!!$F2 1135
4 TraesCS3B01G500300 chr3B 744418858 744419687 829 True 990.000000 990 88.235000 1 830 1 chr3B.!!$R2 829
5 TraesCS3B01G500300 chr3B 747493213 747494068 855 False 983.000000 983 87.427000 1 856 1 chr3B.!!$F5 855
6 TraesCS3B01G500300 chr3B 746792332 746793772 1440 True 890.000000 1059 89.336500 254 2191 2 chr3B.!!$R8 1937
7 TraesCS3B01G500300 chr3B 745473494 745474688 1194 True 637.500000 1042 86.421000 1 1163 2 chr3B.!!$R7 1162
8 TraesCS3B01G500300 chr3B 746286471 746286983 512 False 464.000000 464 83.463000 1682 2180 1 chr3B.!!$F3 498
9 TraesCS3B01G500300 chr3D 560233766 560234937 1171 True 1085.000000 1085 84.027000 3 1133 1 chr3D.!!$R1 1130
10 TraesCS3B01G500300 chr3D 560331311 560334345 3034 False 706.883333 1845 90.173500 1 2950 6 chr3D.!!$F3 2949
11 TraesCS3B01G500300 chr3D 560477972 560480175 2203 False 677.700000 1267 85.096333 1 2947 3 chr3D.!!$F4 2946
12 TraesCS3B01G500300 chr3D 560784388 560785697 1309 True 618.000000 977 85.941500 1 1173 2 chr3D.!!$R3 1172
13 TraesCS3B01G500300 chr3D 560553062 560553574 512 False 464.000000 464 83.463000 1682 2180 1 chr3D.!!$F1 498
14 TraesCS3B01G500300 chr3A 696331929 696332784 855 True 977.000000 977 87.311000 1 856 1 chr3A.!!$R4 855
15 TraesCS3B01G500300 chr3A 629087181 629088036 855 False 972.000000 972 87.194000 1 856 1 chr3A.!!$F2 855
16 TraesCS3B01G500300 chr3A 629018701 629019536 835 True 612.000000 612 80.668000 341 1138 1 chr3A.!!$R1 797
17 TraesCS3B01G500300 chr3A 696269456 696270292 836 True 579.000000 579 80.024000 341 1138 1 chr3A.!!$R2 797


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
165 166 2.067197 CCCCTTTCCCTTGTCGACT 58.933 57.895 17.92 0.0 0.0 4.18 F
1448 1772 1.006571 ACGTCTGCACCACTTACCG 60.007 57.895 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 2081 2.149973 GGGGGACTGCAGATGAAATT 57.850 50.0 23.35 0.00 0.00 1.82 R
2703 3111 0.320771 GCGTGAATGACCTGGTCACT 60.321 55.0 30.50 21.67 45.65 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
165 166 2.067197 CCCCTTTCCCTTGTCGACT 58.933 57.895 17.92 0.00 0.00 4.18
802 857 4.019174 TCTTTCAGAATCAAGATTGGGCC 58.981 43.478 0.00 0.00 0.00 5.80
840 895 3.395607 TGTGCTGGGATATCTTAAGCCAT 59.604 43.478 16.79 0.00 32.83 4.40
1197 1427 1.315690 CTGCTATCATGGGTTGGCTG 58.684 55.000 0.00 0.00 0.00 4.85
1249 1479 7.055667 AGTGATAGAAACAGAGTTTGACTGA 57.944 36.000 0.00 0.00 38.55 3.41
1448 1772 1.006571 ACGTCTGCACCACTTACCG 60.007 57.895 0.00 0.00 0.00 4.02
1469 1793 2.723746 CAGCCACGCAGCAAAACT 59.276 55.556 0.00 0.00 34.23 2.66
1550 1874 3.983741 ACCGTCTTAGCAGAATCATAGC 58.016 45.455 0.00 0.00 0.00 2.97
1705 2034 3.118149 ACTGCTGCATGATATGTCCTCAA 60.118 43.478 1.31 0.00 0.00 3.02
1741 2081 6.036577 TGAACTAATATATGCGGCTGATCA 57.963 37.500 0.00 0.00 0.00 2.92
2193 2543 6.333416 TGATTAGCAGCTCTTGTACAAGTAG 58.667 40.000 29.83 24.94 39.38 2.57
2291 2691 7.658179 ACGCATCGAATTATATTGTCTTCAT 57.342 32.000 0.00 0.00 0.00 2.57
2292 2692 8.087982 ACGCATCGAATTATATTGTCTTCATT 57.912 30.769 0.00 0.00 0.00 2.57
2470 2870 3.492102 TCTGCTATCCATTAGGTTGGC 57.508 47.619 0.00 0.00 40.43 4.52
2490 2890 3.195825 GGCCTCAGCTCAAAAGAGTACTA 59.804 47.826 0.00 0.00 39.73 1.82
2495 2895 7.199766 CCTCAGCTCAAAAGAGTACTATACTG 58.800 42.308 0.00 0.00 39.59 2.74
2703 3111 4.281435 TGTTGAGTACCGAACCAGATGTAA 59.719 41.667 0.00 0.00 0.00 2.41
2738 3146 1.135315 CGCTGGAAATGTCAAGCCG 59.865 57.895 6.69 0.00 46.83 5.52
2887 3363 8.472683 TTTCACAAACTTTTACATGGTTCTTG 57.527 30.769 0.00 0.00 0.00 3.02
2935 3412 3.201290 CAATTTCACGGAGATCAGGGAG 58.799 50.000 0.00 0.00 0.00 4.30
2937 3414 2.461300 TTCACGGAGATCAGGGAGAT 57.539 50.000 0.00 0.00 40.48 2.75
2961 3438 9.567848 GATCTTCACAAAACAAGAAAAGTTGTA 57.432 29.630 0.00 0.00 39.82 2.41
3164 3641 2.271800 GTATGAAGGAAGTGGCGTCAG 58.728 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
802 857 1.301716 ACACGCAGGTTAGGTGCAG 60.302 57.895 0.00 0.00 41.26 4.41
840 895 1.000163 GACGACCAACTCTTGCTCTCA 60.000 52.381 0.00 0.00 0.00 3.27
1115 1327 2.335752 TGCAAAATTACCAATGCAGCG 58.664 42.857 0.00 0.00 43.32 5.18
1249 1479 5.594317 ACTAAGGAAATCACAACTGCAGTTT 59.406 36.000 29.23 17.28 35.83 2.66
1255 1485 6.618287 TGAACACTAAGGAAATCACAACTG 57.382 37.500 0.00 0.00 0.00 3.16
1469 1793 2.746279 ATCCAAGTGTGACAAACCCA 57.254 45.000 0.00 0.00 0.00 4.51
1550 1874 4.096003 AACCCTCCACCGGATGCG 62.096 66.667 9.46 0.00 0.00 4.73
1741 2081 2.149973 GGGGGACTGCAGATGAAATT 57.850 50.000 23.35 0.00 0.00 1.82
2193 2543 2.423538 CCACAGCTTGCCAAATAGGTAC 59.576 50.000 0.00 0.00 40.61 3.34
2243 2643 1.074775 GTCCAGCCACATCCCACAA 59.925 57.895 0.00 0.00 0.00 3.33
2356 2756 2.969628 AGCACTAGATAGCCACATCCT 58.030 47.619 0.00 0.00 0.00 3.24
2703 3111 0.320771 GCGTGAATGACCTGGTCACT 60.321 55.000 30.50 21.67 45.65 3.41
2738 3146 1.729149 GCAATTCGTAGTGCACTTGCC 60.729 52.381 27.06 12.42 44.41 4.52
2935 3412 8.466086 ACAACTTTTCTTGTTTTGTGAAGATC 57.534 30.769 0.00 0.00 29.66 2.75
2937 3414 8.573035 AGTACAACTTTTCTTGTTTTGTGAAGA 58.427 29.630 0.00 0.00 35.87 2.87
2961 3438 4.343526 CCATGCTCAACCTCTGATACTAGT 59.656 45.833 0.00 0.00 32.14 2.57
3103 3580 1.215647 CTAGCACCACCACCGAGTC 59.784 63.158 0.00 0.00 0.00 3.36
3115 3592 0.801067 CAACGACGCCTACCTAGCAC 60.801 60.000 0.00 0.00 0.00 4.40



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

AutoCloner maintained by Alex Coulton.