Multiple sequence alignment - TraesCS3B01G609000

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 TraesCS3B01G609000 chr3B 100.000 3591 0 0 1 3591 828294811 828291221 0.000000e+00 6632
1 TraesCS3B01G609000 chr3B 95.282 2586 79 15 1 2567 828333806 828331245 0.000000e+00 4060
2 TraesCS3B01G609000 chr3B 98.303 766 12 1 2827 3591 689149083 689148318 0.000000e+00 1341
3 TraesCS3B01G609000 chr3B 81.764 1519 216 29 1342 2827 828254290 828252800 0.000000e+00 1214
4 TraesCS3B01G609000 chr3B 88.526 889 72 17 250 1133 828256793 828255930 0.000000e+00 1050
5 TraesCS3B01G609000 chr3B 97.989 348 7 0 2832 3179 689146891 689146544 3.970000e-169 604
6 TraesCS3B01G609000 chr3B 76.138 1098 195 36 1588 2632 828111229 828112312 6.880000e-142 514
7 TraesCS3B01G609000 chr3B 96.020 201 6 1 2631 2829 828331243 828331043 3.460000e-85 326
8 TraesCS3B01G609000 chr3B 88.038 209 20 5 50 255 828257188 828256982 3.580000e-60 243
9 TraesCS3B01G609000 chr3A 84.105 1598 198 27 1269 2829 745299018 745297440 0.000000e+00 1493
10 TraesCS3B01G609000 chr3A 82.554 1519 214 20 1342 2829 745080787 745079289 0.000000e+00 1290
11 TraesCS3B01G609000 chr3A 82.434 1520 215 23 1342 2829 744941051 744939552 0.000000e+00 1280
12 TraesCS3B01G609000 chr3A 82.314 1521 215 22 1342 2829 745013978 745012479 0.000000e+00 1269
13 TraesCS3B01G609000 chr3A 84.422 873 90 26 258 1129 744942195 744941368 0.000000e+00 817
14 TraesCS3B01G609000 chr3A 84.422 873 91 26 258 1129 745015123 745014295 0.000000e+00 817
15 TraesCS3B01G609000 chr3A 84.307 873 91 27 258 1129 745081931 745081104 0.000000e+00 811
16 TraesCS3B01G609000 chr3A 84.307 873 91 27 258 1129 745195134 745194307 0.000000e+00 811
17 TraesCS3B01G609000 chr3A 87.396 603 59 8 12 611 745300876 745300288 0.000000e+00 676
18 TraesCS3B01G609000 chr3A 75.945 1085 208 30 1588 2632 744879314 744880385 3.200000e-140 508
19 TraesCS3B01G609000 chr3A 90.634 331 31 0 923 1253 745299435 745299105 1.180000e-119 440
20 TraesCS3B01G609000 chr3A 91.057 123 10 1 21 142 745082173 745082051 7.980000e-37 165
21 TraesCS3B01G609000 chr3A 90.244 123 11 1 21 142 745195376 745195254 3.710000e-35 159
22 TraesCS3B01G609000 chr3D 90.147 1157 94 11 102 1250 610686963 610685819 0.000000e+00 1487
23 TraesCS3B01G609000 chr3D 84.200 1443 174 24 1411 2829 610668078 610666666 0.000000e+00 1352
24 TraesCS3B01G609000 chr3D 97.475 713 17 1 2880 3591 21612405 21611693 0.000000e+00 1216
25 TraesCS3B01G609000 chr3D 83.576 1169 168 8 1676 2829 610628378 610627219 0.000000e+00 1074
26 TraesCS3B01G609000 chr3D 85.429 851 100 9 1993 2829 610685047 610684207 0.000000e+00 863
27 TraesCS3B01G609000 chr3D 85.567 679 86 6 1271 1939 610685728 610685052 0.000000e+00 701
28 TraesCS3B01G609000 chr3D 90.949 453 31 4 775 1223 610629582 610629136 5.130000e-168 601
29 TraesCS3B01G609000 chr3D 85.934 519 69 4 262 776 610561551 610561033 5.240000e-153 551
30 TraesCS3B01G609000 chr3D 78.107 877 154 18 1790 2632 610544040 610544912 4.110000e-144 521
31 TraesCS3B01G609000 chr3D 86.280 328 42 3 25 349 610602190 610601863 1.590000e-93 353
32 TraesCS3B01G609000 chr3D 87.701 187 20 3 21 205 610561757 610561572 7.810000e-52 215
33 TraesCS3B01G609000 chr3D 78.151 357 48 10 1344 1681 610628799 610628454 2.190000e-47 200
34 TraesCS3B01G609000 chr3D 82.443 131 18 3 21 150 610698814 610698688 3.790000e-20 110
35 TraesCS3B01G609000 chr2B 98.294 762 13 0 2830 3591 15624696 15625457 0.000000e+00 1336
36 TraesCS3B01G609000 chr4D 97.375 762 19 1 2830 3591 437759637 437760397 0.000000e+00 1295
37 TraesCS3B01G609000 chr5D 97.244 762 21 0 2830 3591 449874982 449875743 0.000000e+00 1291
38 TraesCS3B01G609000 chr4A 96.986 763 23 0 2829 3591 210954701 210953939 0.000000e+00 1282
39 TraesCS3B01G609000 chr1D 96.461 763 27 0 2829 3591 64772472 64771710 0.000000e+00 1260
40 TraesCS3B01G609000 chrUn 96.101 436 16 1 2829 3263 76553260 76553695 0.000000e+00 710
41 TraesCS3B01G609000 chrUn 93.125 320 21 1 3255 3574 76562534 76562852 5.430000e-128 468


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 TraesCS3B01G609000 chr3B 828291221 828294811 3590 True 6632.000000 6632 100.000000 1 3591 1 chr3B.!!$R1 3590
1 TraesCS3B01G609000 chr3B 828331043 828333806 2763 True 2193.000000 4060 95.651000 1 2829 2 chr3B.!!$R4 2828
2 TraesCS3B01G609000 chr3B 689146544 689149083 2539 True 972.500000 1341 98.146000 2827 3591 2 chr3B.!!$R2 764
3 TraesCS3B01G609000 chr3B 828252800 828257188 4388 True 835.666667 1214 86.109333 50 2827 3 chr3B.!!$R3 2777
4 TraesCS3B01G609000 chr3B 828111229 828112312 1083 False 514.000000 514 76.138000 1588 2632 1 chr3B.!!$F1 1044
5 TraesCS3B01G609000 chr3A 744939552 744942195 2643 True 1048.500000 1280 83.428000 258 2829 2 chr3A.!!$R1 2571
6 TraesCS3B01G609000 chr3A 745012479 745015123 2644 True 1043.000000 1269 83.368000 258 2829 2 chr3A.!!$R2 2571
7 TraesCS3B01G609000 chr3A 745297440 745300876 3436 True 869.666667 1493 87.378333 12 2829 3 chr3A.!!$R5 2817
8 TraesCS3B01G609000 chr3A 745079289 745082173 2884 True 755.333333 1290 85.972667 21 2829 3 chr3A.!!$R3 2808
9 TraesCS3B01G609000 chr3A 744879314 744880385 1071 False 508.000000 508 75.945000 1588 2632 1 chr3A.!!$F1 1044
10 TraesCS3B01G609000 chr3A 745194307 745195376 1069 True 485.000000 811 87.275500 21 1129 2 chr3A.!!$R4 1108
11 TraesCS3B01G609000 chr3D 610666666 610668078 1412 True 1352.000000 1352 84.200000 1411 2829 1 chr3D.!!$R3 1418
12 TraesCS3B01G609000 chr3D 21611693 21612405 712 True 1216.000000 1216 97.475000 2880 3591 1 chr3D.!!$R1 711
13 TraesCS3B01G609000 chr3D 610684207 610686963 2756 True 1017.000000 1487 87.047667 102 2829 3 chr3D.!!$R7 2727
14 TraesCS3B01G609000 chr3D 610627219 610629582 2363 True 625.000000 1074 84.225333 775 2829 3 chr3D.!!$R6 2054
15 TraesCS3B01G609000 chr3D 610544040 610544912 872 False 521.000000 521 78.107000 1790 2632 1 chr3D.!!$F1 842
16 TraesCS3B01G609000 chr3D 610561033 610561757 724 True 383.000000 551 86.817500 21 776 2 chr3D.!!$R5 755
17 TraesCS3B01G609000 chr2B 15624696 15625457 761 False 1336.000000 1336 98.294000 2830 3591 1 chr2B.!!$F1 761
18 TraesCS3B01G609000 chr4D 437759637 437760397 760 False 1295.000000 1295 97.375000 2830 3591 1 chr4D.!!$F1 761
19 TraesCS3B01G609000 chr5D 449874982 449875743 761 False 1291.000000 1291 97.244000 2830 3591 1 chr5D.!!$F1 761
20 TraesCS3B01G609000 chr4A 210953939 210954701 762 True 1282.000000 1282 96.986000 2829 3591 1 chr4A.!!$R1 762
21 TraesCS3B01G609000 chr1D 64771710 64772472 762 True 1260.000000 1260 96.461000 2829 3591 1 chr1D.!!$R1 762

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
912 1676 5.486419 AGCATCCATTCCATTCCTTTCTTTT 59.514 36.000 0.0 0.0 0.00 2.27 F
1674 3937 1.340308 TGGTGATGGAGGATGCAACAG 60.340 52.381 0.0 0.0 40.35 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 4555 1.294780 CTGAGTCGAAGGCTTGCCT 59.705 57.895 3.46 8.56 45.33 4.75 R
3363 5760 0.757512 AGTCCATCATGATCGCAGCT 59.242 50.000 4.86 0.00 0.00 4.24 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
165 167 7.728532 CCAGCCTTTAATTTTATGGTATAGGGT 59.271 37.037 0.00 0.00 30.01 4.34
726 1237 6.215845 AGTGTGCAAATGAAGGAAATAACAC 58.784 36.000 0.00 0.00 35.57 3.32
912 1676 5.486419 AGCATCCATTCCATTCCTTTCTTTT 59.514 36.000 0.00 0.00 0.00 2.27
942 1706 6.926313 ACAGTAGTACTCTTCCACTTGATTC 58.074 40.000 0.00 0.00 0.00 2.52
996 1762 6.376864 CACTTTCTCTTCTCTCTAGATCACCA 59.623 42.308 0.00 0.00 0.00 4.17
1051 1817 2.093394 TCAAACTTCTGGAACACCGACA 60.093 45.455 0.00 0.00 0.00 4.35
1096 1862 4.116238 CCTTGTGCTTCTAGCTAGCTAAC 58.884 47.826 24.20 18.68 42.97 2.34
1359 3572 5.780793 GGTATGTATACTCCCAAGAGGTCAT 59.219 44.000 4.17 0.00 45.11 3.06
1646 3891 4.062490 AGTACTACCACTCCTTCACCAT 57.938 45.455 0.00 0.00 0.00 3.55
1674 3937 1.340308 TGGTGATGGAGGATGCAACAG 60.340 52.381 0.00 0.00 40.35 3.16
1824 4174 2.659610 GGAGCGAGCTCAGTTGGT 59.340 61.111 24.21 2.27 44.40 3.67
1858 4208 2.426023 GTGTCGGGGCTCAACTGT 59.574 61.111 0.00 0.00 0.00 3.55
1933 4283 2.131067 CCAACCCCGCCACTTTTGT 61.131 57.895 0.00 0.00 0.00 2.83
1990 4340 3.049674 CGCAATGTGCCTGTCGGT 61.050 61.111 0.00 0.00 41.12 4.69
2205 4555 4.680237 CGCCCACAGCTTCGACCA 62.680 66.667 0.00 0.00 40.39 4.02
2216 4566 1.301677 CTTCGACCAGGCAAGCCTTC 61.302 60.000 11.67 6.80 45.70 3.46
2226 4576 1.357991 GCAAGCCTTCGACTCAGCTC 61.358 60.000 0.00 0.00 33.56 4.09
2448 4825 1.335142 CCTAGGATTACAGAGCGTCGC 60.335 57.143 9.80 9.80 0.00 5.19
2550 4942 1.152902 GCAGCAGGGGCATGTATGA 60.153 57.895 0.00 0.00 44.61 2.15
2905 5301 3.469008 AGAACAGATCACACACGGAAA 57.531 42.857 0.00 0.00 0.00 3.13
2949 5345 2.544267 CGTCTTTTCTGGCGTCTTTCTT 59.456 45.455 0.00 0.00 0.00 2.52
2958 5354 6.877611 TCTGGCGTCTTTCTTTTATTCTTT 57.122 33.333 0.00 0.00 0.00 2.52
3101 5497 2.660224 AACGCGTCATGCACACGA 60.660 55.556 21.17 1.29 46.97 4.35
3168 5565 8.952278 ACAAACAGACTAAAACAAGATTACACA 58.048 29.630 0.00 0.00 0.00 3.72
3363 5760 5.705609 TGATAGCGAACATCTATGTGCTA 57.294 39.130 14.09 14.09 42.58 3.49
3412 5809 3.911868 ACAAAGCGCAATTGCAGATTTA 58.088 36.364 28.77 0.00 42.21 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
620 1130 9.210426 CAGTTTGCAATAAATTAGTTAGCGTAG 57.790 33.333 0.00 0.00 0.00 3.51
726 1237 6.127897 GGAATAGAGAAGTGGACAAACATTGG 60.128 42.308 0.00 0.00 34.12 3.16
996 1762 2.371510 GGCAGGAAGGAAGATCATAGCT 59.628 50.000 0.00 0.00 0.00 3.32
1051 1817 2.162681 GCATACCTGAAGCTGGTTGTT 58.837 47.619 0.00 0.00 36.99 2.83
1238 2781 2.992543 CCGTTTAAACCGGTCGATTACA 59.007 45.455 8.04 0.00 40.59 2.41
1309 2930 9.639601 CCTATTTGATTCACTTTTTCCCTTTAC 57.360 33.333 0.00 0.00 0.00 2.01
1646 3891 0.618680 CCTCCATCACCAGGACCAGA 60.619 60.000 0.00 0.00 30.32 3.86
1674 3937 5.594926 CCATGAACCCTTCTTCATTATTGC 58.405 41.667 0.00 0.00 38.57 3.56
1710 4054 2.415608 CCTCCAGCGACTAAGCCGA 61.416 63.158 0.00 0.00 38.01 5.54
1776 4125 2.972625 TCGACTTGCTATTCCTGTTGG 58.027 47.619 0.00 0.00 0.00 3.77
1933 4283 3.436924 TAGCGGCGACAAGAGCGA 61.437 61.111 12.98 0.00 35.00 4.93
2205 4555 1.294780 CTGAGTCGAAGGCTTGCCT 59.705 57.895 3.46 8.56 45.33 4.75
2216 4566 3.827898 GTCGGGGGAGCTGAGTCG 61.828 72.222 0.00 0.00 0.00 4.18
2448 4825 3.009033 TCTGTTGTCATCTTTACCCCCAG 59.991 47.826 0.00 0.00 0.00 4.45
2550 4942 2.104967 CATTGCCATTGACCATGTCCT 58.895 47.619 0.00 0.00 0.00 3.85
2659 5052 3.508840 GGCCCATTTCACGAGGCG 61.509 66.667 0.00 0.00 46.75 5.52
2949 5345 9.314321 CCGTTTAGCTCATCTCTAAAGAATAAA 57.686 33.333 0.00 0.00 36.88 1.40
2958 5354 5.714047 CATATGCCGTTTAGCTCATCTCTA 58.286 41.667 0.00 0.00 0.00 2.43
3168 5565 4.375313 AGATTAAGGGGGTGAATCTCAGT 58.625 43.478 0.00 0.00 35.48 3.41
3363 5760 0.757512 AGTCCATCATGATCGCAGCT 59.242 50.000 4.86 0.00 0.00 4.24
3412 5809 6.324770 AGAAGGTTTTGATCAAAGTGGACAAT 59.675 34.615 19.64 8.58 0.00 2.71


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

AutoCloner maintained by Alex Coulton.