Multiple sequence alignment - TraesCS6B01G441800

Loading Multiple Alignment...

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 TraesCS6B01G441800 chr6B 100.000 3894 0 0 1 3894 705785733 705781840 0.000000e+00 7191
1 TraesCS6B01G441800 chr6B 94.746 3921 153 25 2 3893 706410769 706406873 0.000000e+00 6050
2 TraesCS6B01G441800 chr6B 94.623 3924 155 27 1 3893 706353785 706349887 0.000000e+00 6026
3 TraesCS6B01G441800 chr6B 96.674 3007 57 13 904 3894 705758761 705755782 0.000000e+00 4959
4 TraesCS6B01G441800 chr6B 88.277 1689 157 23 1418 3085 706528980 706527312 0.000000e+00 1984
5 TraesCS6B01G441800 chr6B 87.723 1735 153 28 1363 3078 706443982 706442289 0.000000e+00 1969
6 TraesCS6B01G441800 chr6B 90.973 853 50 12 1 846 706524572 706523740 0.000000e+00 1123
7 TraesCS6B01G441800 chr6B 91.128 789 56 10 24 803 705760917 705760134 0.000000e+00 1057
8 TraesCS6B01G441800 chr6B 88.393 672 59 6 3227 3893 706521777 706521120 0.000000e+00 791
9 TraesCS6B01G441800 chr6B 95.129 349 17 0 839 1187 706523715 706523367 5.690000e-153 551
10 TraesCS6B01G441800 chr6B 88.248 451 40 9 382 827 706113260 706112818 9.580000e-146 527
11 TraesCS6B01G441800 chr6B 89.027 401 20 9 1 384 706113827 706113434 3.520000e-130 475
12 TraesCS6B01G441800 chr6B 88.837 215 18 2 955 1168 706444716 706444507 3.860000e-65 259
13 TraesCS6B01G441800 chr6B 88.182 220 20 2 955 1173 706529796 706529582 1.390000e-64 257
14 TraesCS6B01G441800 chr6B 92.683 123 9 0 1250 1372 706529366 706529244 1.110000e-40 178
15 TraesCS6B01G441800 chr6B 91.870 123 10 0 1250 1372 706444288 706444166 5.170000e-39 172
16 TraesCS6B01G441800 chr6D 94.618 3735 153 23 1 3700 463075133 463071412 0.000000e+00 5740
17 TraesCS6B01G441800 chr6D 92.219 1555 101 13 2156 3700 463069054 463067510 0.000000e+00 2183
18 TraesCS6B01G441800 chr6D 88.768 1745 148 25 1363 3085 463079999 463078281 0.000000e+00 2093
19 TraesCS6B01G441800 chr6D 84.750 400 43 14 454 846 470466492 470466104 6.100000e-103 385
20 TraesCS6B01G441800 chr6D 83.838 396 48 13 459 846 289521405 289521018 2.860000e-96 363
21 TraesCS6B01G441800 chr6D 95.000 120 6 0 1250 1369 463091028 463090909 5.140000e-44 189
22 TraesCS6B01G441800 chr6D 89.209 139 12 3 3080 3218 446736199 446736334 1.860000e-38 171
23 TraesCS6B01G441800 chr6A 90.037 2148 152 19 1313 3450 609815278 609813183 0.000000e+00 2724
24 TraesCS6B01G441800 chr6A 87.787 1744 167 19 1363 3088 609821474 609819759 0.000000e+00 1999
25 TraesCS6B01G441800 chr6A 84.853 713 77 10 142 846 609817055 609816366 0.000000e+00 689
26 TraesCS6B01G441800 chr6A 85.405 370 15 14 957 1316 609816247 609815907 8.010000e-92 348
27 TraesCS6B01G441800 chr6A 86.900 229 21 3 955 1182 609821821 609821601 8.350000e-62 248
28 TraesCS6B01G441800 chr3B 83.881 670 98 8 3227 3889 640670921 640670255 7.100000e-177 630
29 TraesCS6B01G441800 chr2B 84.006 669 93 12 3231 3893 247365754 247365094 7.100000e-177 630
30 TraesCS6B01G441800 chr5A 82.589 672 106 10 3227 3894 144390591 144391255 2.020000e-162 582
31 TraesCS6B01G441800 chrUn 79.333 300 34 13 143 424 12497960 12498249 6.640000e-43 185
32 TraesCS6B01G441800 chr4A 89.130 138 13 2 3084 3220 661487096 661486960 1.860000e-38 171
33 TraesCS6B01G441800 chr2A 88.194 144 13 3 3079 3220 158180049 158180190 6.690000e-38 169


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 TraesCS6B01G441800 chr6B 705781840 705785733 3893 True 7191.000000 7191 100.000000 1 3894 1 chr6B.!!$R1 3893
1 TraesCS6B01G441800 chr6B 706406873 706410769 3896 True 6050.000000 6050 94.746000 2 3893 1 chr6B.!!$R3 3891
2 TraesCS6B01G441800 chr6B 706349887 706353785 3898 True 6026.000000 6026 94.623000 1 3893 1 chr6B.!!$R2 3892
3 TraesCS6B01G441800 chr6B 705755782 705760917 5135 True 3008.000000 4959 93.901000 24 3894 2 chr6B.!!$R4 3870
4 TraesCS6B01G441800 chr6B 706521120 706529796 8676 True 814.000000 1984 90.606167 1 3893 6 chr6B.!!$R7 3892
5 TraesCS6B01G441800 chr6B 706442289 706444716 2427 True 800.000000 1969 89.476667 955 3078 3 chr6B.!!$R6 2123
6 TraesCS6B01G441800 chr6B 706112818 706113827 1009 True 501.000000 527 88.637500 1 827 2 chr6B.!!$R5 826
7 TraesCS6B01G441800 chr6D 463067510 463079999 12489 True 3338.666667 5740 91.868333 1 3700 3 chr6D.!!$R4 3699
8 TraesCS6B01G441800 chr6A 609813183 609821821 8638 True 1201.600000 2724 86.996400 142 3450 5 chr6A.!!$R1 3308
9 TraesCS6B01G441800 chr3B 640670255 640670921 666 True 630.000000 630 83.881000 3227 3889 1 chr3B.!!$R1 662
10 TraesCS6B01G441800 chr2B 247365094 247365754 660 True 630.000000 630 84.006000 3231 3893 1 chr2B.!!$R1 662
11 TraesCS6B01G441800 chr5A 144390591 144391255 664 False 582.000000 582 82.589000 3227 3894 1 chr5A.!!$F1 667

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
941 8573 1.554042 GCAGGTGTGTGGACGTAACG 61.554 60.0 0.00 0.0 0.00 3.18 F
1010 8643 1.148310 CGTCCATTTGAGCGTTCAGT 58.852 50.0 1.23 0.0 34.15 3.41 F
1845 10477 0.974383 ACGTTCCTTAGGACACTGGG 59.026 55.0 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 10477 1.344114 TGAAGCCATTTTTGGACAGGC 59.656 47.619 0.0 0.0 45.54 4.85 R
1928 10560 1.450312 GAATGGTCCCTCGCAGTGG 60.450 63.158 0.0 0.0 41.51 4.00 R
3819 13248 2.961062 GGGAGGGTAGTAAGCGATGTTA 59.039 50.000 0.0 0.0 0.00 2.41 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
159 6252 6.748333 TTGATCTACTCCAGAAAAGCATTG 57.252 37.500 0.00 0.00 36.67 2.82
173 6266 5.444663 AAAGCATTGAGAAACTTCCACTC 57.555 39.130 0.00 0.00 0.00 3.51
233 6329 7.335422 ACCAGAAAATCTGCTAGACATGTAAAG 59.665 37.037 0.00 0.00 42.98 1.85
744 7037 7.072202 AGAGATTGAGAGAATATGATGGGTGTT 59.928 37.037 0.00 0.00 0.00 3.32
790 7084 2.079925 CAGAGTACAAGGCTTGAAGGC 58.920 52.381 32.50 17.91 41.73 4.35
908 8540 1.882989 GAGAAGGACTGAGCCGTGCT 61.883 60.000 0.00 0.00 43.88 4.40
941 8573 1.554042 GCAGGTGTGTGGACGTAACG 61.554 60.000 0.00 0.00 0.00 3.18
1010 8643 1.148310 CGTCCATTTGAGCGTTCAGT 58.852 50.000 1.23 0.00 34.15 3.41
1130 8764 2.748058 ATTCGGCCGAGCAAAGGTGT 62.748 55.000 29.20 4.26 0.00 4.16
1189 8824 5.130145 CCTCCTGAATCCTGATTACTCAGTT 59.870 44.000 9.05 0.00 46.33 3.16
1190 8825 6.325028 CCTCCTGAATCCTGATTACTCAGTTA 59.675 42.308 9.05 0.00 46.33 2.24
1191 8826 7.353414 TCCTGAATCCTGATTACTCAGTTAG 57.647 40.000 9.05 0.00 46.33 2.34
1192 8827 6.897966 TCCTGAATCCTGATTACTCAGTTAGT 59.102 38.462 9.05 0.00 46.33 2.24
1193 8828 8.059461 TCCTGAATCCTGATTACTCAGTTAGTA 58.941 37.037 9.05 0.00 46.33 1.82
1194 8829 8.356657 CCTGAATCCTGATTACTCAGTTAGTAG 58.643 40.741 9.05 2.79 46.33 2.57
1195 8830 8.824756 TGAATCCTGATTACTCAGTTAGTAGT 57.175 34.615 9.05 0.00 46.33 2.73
1196 8831 9.256228 TGAATCCTGATTACTCAGTTAGTAGTT 57.744 33.333 9.05 0.00 46.33 2.24
1845 10477 0.974383 ACGTTCCTTAGGACACTGGG 59.026 55.000 0.00 0.00 0.00 4.45
1928 10560 2.945456 ACCTTGACTTGGGAAAGAACC 58.055 47.619 0.00 0.00 0.00 3.62
2034 10666 3.965565 AATTCCCCTAGGTATAGGCCT 57.034 47.619 11.78 11.78 46.50 5.19
2035 10667 5.162693 TGAAATTCCCCTAGGTATAGGCCTA 60.163 44.000 16.60 16.60 46.50 3.93
2559 11196 0.955428 CGGCTTAAAGCAGCTCACCA 60.955 55.000 0.00 0.00 44.75 4.17
2694 11336 0.818445 CACTGGATCTGCTCCCATGC 60.818 60.000 0.00 0.00 44.23 4.06
3742 13171 8.282256 TGGAGAGCTGACATTATAGGCTATATA 58.718 37.037 14.70 6.91 33.13 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 6163 1.360393 TATTGTCCAGGCCATCCCCC 61.360 60.000 5.01 0.00 0.00 5.40
159 6252 5.771602 GAAAGATCGAGTGGAAGTTTCTC 57.228 43.478 0.00 0.00 32.02 2.87
233 6329 1.817209 CCGGCCACTAGAGAACCTC 59.183 63.158 2.24 0.00 0.00 3.85
520 6808 7.941238 AGAGTCTTTTTCTCAATCCTTTGATCA 59.059 33.333 0.00 0.00 40.95 2.92
568 6857 4.467769 CATACCTAGGGTTCTTCTACCGA 58.532 47.826 14.81 0.00 39.18 4.69
652 6943 3.710722 CCGCCTCCCACTGCTTCT 61.711 66.667 0.00 0.00 0.00 2.85
908 8540 4.202357 ACACACCTGCAAGAATACTCTCAA 60.202 41.667 0.00 0.00 34.07 3.02
941 8573 1.594331 AGAAAGAAACCACGCTCACC 58.406 50.000 0.00 0.00 0.00 4.02
1010 8643 2.241176 AGTTGAGTTGGAGGTTGGAACA 59.759 45.455 0.00 0.00 0.00 3.18
1130 8764 1.342474 CCCAAGAGAGAGTGGCTAGGA 60.342 57.143 0.00 0.00 33.21 2.94
1187 8822 8.049655 AGCAGTACTAAGTGGTAACTACTAAC 57.950 38.462 0.00 0.00 35.01 2.34
1189 8824 8.105829 AGAAGCAGTACTAAGTGGTAACTACTA 58.894 37.037 0.00 0.00 35.73 1.82
1190 8825 6.947158 AGAAGCAGTACTAAGTGGTAACTACT 59.053 38.462 0.00 0.00 35.73 2.57
1191 8826 7.155655 AGAAGCAGTACTAAGTGGTAACTAC 57.844 40.000 0.00 0.00 35.73 2.73
1192 8827 7.771927 AAGAAGCAGTACTAAGTGGTAACTA 57.228 36.000 0.00 0.00 35.73 2.24
1193 8828 6.667558 AAGAAGCAGTACTAAGTGGTAACT 57.332 37.500 0.00 0.00 35.73 2.24
1194 8829 7.373493 TGTAAGAAGCAGTACTAAGTGGTAAC 58.627 38.462 0.00 0.00 35.73 2.50
1195 8830 7.528996 TGTAAGAAGCAGTACTAAGTGGTAA 57.471 36.000 0.00 0.00 35.73 2.85
1196 8831 7.614583 AGATGTAAGAAGCAGTACTAAGTGGTA 59.385 37.037 0.00 0.00 35.73 3.25
1197 8832 6.437793 AGATGTAAGAAGCAGTACTAAGTGGT 59.562 38.462 0.00 0.00 38.41 4.16
1198 8833 6.868622 AGATGTAAGAAGCAGTACTAAGTGG 58.131 40.000 0.00 0.00 0.00 4.00
1543 10175 1.876156 GGCAGTAGCATAAGCATGGTC 59.124 52.381 0.00 0.00 41.88 4.02
1845 10477 1.344114 TGAAGCCATTTTTGGACAGGC 59.656 47.619 0.00 0.00 45.54 4.85
1928 10560 1.450312 GAATGGTCCCTCGCAGTGG 60.450 63.158 0.00 0.00 41.51 4.00
2034 10666 8.594550 GCCATACTTTCCTTAGATTGGATAGTA 58.405 37.037 12.79 12.79 45.28 1.82
2035 10667 7.293535 AGCCATACTTTCCTTAGATTGGATAGT 59.706 37.037 9.91 9.91 44.21 2.12
2694 11336 3.326889 TCTCTCCGAGAGATAGCGGGG 62.327 61.905 22.00 0.00 45.77 5.73
3742 13171 5.474825 CCAAACTTTTATGGCATACGGTTT 58.525 37.500 6.72 14.25 0.00 3.27
3819 13248 2.961062 GGGAGGGTAGTAAGCGATGTTA 59.039 50.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.