Multiple sequence alignment - TraesCS2B01G417800

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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 TraesCS2B01G417800 chr2B 100.000 2255 0 0 1 2255 598482696 598484950 0 4165
1 TraesCS2B01G417800 chr2B 93.060 1023 50 5 1233 2255 215486524 215485523 0 1476
2 TraesCS2B01G417800 chr2B 95.969 769 28 2 1 766 507426813 507427581 0 1245
3 TraesCS2B01G417800 chr2B 95.964 768 30 1 1 767 720247415 720246648 0 1245
4 TraesCS2B01G417800 chr5D 90.918 1024 51 11 1235 2255 83911416 83910432 0 1338
5 TraesCS2B01G417800 chr5D 90.049 1025 59 12 1235 2255 265678500 265679485 0 1288
6 TraesCS2B01G417800 chr5D 90.625 832 51 8 1426 2255 379414484 379413678 0 1079
7 TraesCS2B01G417800 chr5D 95.992 474 19 0 767 1240 399943010 399942537 0 771
8 TraesCS2B01G417800 chr5D 95.781 474 20 0 766 1239 13776909 13777382 0 765
9 TraesCS2B01G417800 chr4D 90.811 1023 55 9 1235 2255 297894796 297895781 0 1332
10 TraesCS2B01G417800 chr2D 90.370 1028 71 11 1235 2255 138170112 138171118 0 1325
11 TraesCS2B01G417800 chr1D 90.420 1023 55 12 1235 2253 467305097 467304114 0 1306
12 TraesCS2B01G417800 chr1D 90.184 652 37 10 1235 1883 99785829 99785202 0 824
13 TraesCS2B01G417800 chr1D 96.414 474 17 0 767 1240 79045305 79044832 0 782
14 TraesCS2B01G417800 chr1D 95.781 474 20 0 767 1240 467331343 467330870 0 765
15 TraesCS2B01G417800 chr3D 90.341 1025 56 15 1235 2255 8682102 8683087 0 1304
16 TraesCS2B01G417800 chr7B 96.871 767 24 0 1 767 116360463 116359697 0 1284
17 TraesCS2B01G417800 chr7B 95.495 777 32 1 1 774 181339060 181338284 0 1238
18 TraesCS2B01G417800 chr7B 90.178 957 42 18 1236 2162 143193253 143192319 0 1199
19 TraesCS2B01G417800 chr7B 96.211 475 16 2 767 1240 39611597 39611124 0 776
20 TraesCS2B01G417800 chr6D 89.951 1025 60 12 1235 2255 139927520 139928505 0 1282
21 TraesCS2B01G417800 chr6D 89.941 1024 61 11 1235 2255 338192266 338191282 0 1282
22 TraesCS2B01G417800 chrUn 96.475 766 27 0 1 766 36313865 36313100 0 1266
23 TraesCS2B01G417800 chr5B 96.368 771 25 2 1 768 575183050 575182280 0 1266
24 TraesCS2B01G417800 chr5B 94.728 588 28 2 1236 1823 538306579 538305995 0 911
25 TraesCS2B01G417800 chr1B 95.964 768 31 0 1 768 688136863 688136096 0 1247
26 TraesCS2B01G417800 chr1B 95.736 774 30 1 1 771 488159544 488158771 0 1243
27 TraesCS2B01G417800 chr1B 88.406 621 49 7 1236 1852 423617042 423616441 0 726
28 TraesCS2B01G417800 chr3B 95.850 771 29 2 1 768 740520749 740519979 0 1243
29 TraesCS2B01G417800 chr3B 96.414 474 17 0 767 1240 786520631 786521104 0 782
30 TraesCS2B01G417800 chr2A 88.791 1026 84 16 1235 2255 549719291 549718292 0 1229
31 TraesCS2B01G417800 chr4B 88.876 872 81 13 1394 2255 68870349 68869484 0 1059
32 TraesCS2B01G417800 chr4B 95.207 605 25 4 1233 1837 346143427 346144027 0 953
33 TraesCS2B01G417800 chr4B 96.203 474 18 0 767 1240 68874629 68874156 0 776
34 TraesCS2B01G417800 chr4B 95.789 475 18 2 767 1240 474331809 474331336 0 765
35 TraesCS2B01G417800 chr6B 92.517 588 23 9 1236 1823 170975273 170974707 0 822
36 TraesCS2B01G417800 chr6B 96.414 474 17 0 767 1240 410213873 410214346 0 782


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 TraesCS2B01G417800 chr2B 598482696 598484950 2254 False 4165.0 4165 100.0000 1 2255 1 chr2B.!!$F2 2254
1 TraesCS2B01G417800 chr2B 215485523 215486524 1001 True 1476.0 1476 93.0600 1233 2255 1 chr2B.!!$R1 1022
2 TraesCS2B01G417800 chr2B 507426813 507427581 768 False 1245.0 1245 95.9690 1 766 1 chr2B.!!$F1 765
3 TraesCS2B01G417800 chr2B 720246648 720247415 767 True 1245.0 1245 95.9640 1 767 1 chr2B.!!$R2 766
4 TraesCS2B01G417800 chr5D 83910432 83911416 984 True 1338.0 1338 90.9180 1235 2255 1 chr5D.!!$R1 1020
5 TraesCS2B01G417800 chr5D 265678500 265679485 985 False 1288.0 1288 90.0490 1235 2255 1 chr5D.!!$F2 1020
6 TraesCS2B01G417800 chr5D 379413678 379414484 806 True 1079.0 1079 90.6250 1426 2255 1 chr5D.!!$R2 829
7 TraesCS2B01G417800 chr4D 297894796 297895781 985 False 1332.0 1332 90.8110 1235 2255 1 chr4D.!!$F1 1020
8 TraesCS2B01G417800 chr2D 138170112 138171118 1006 False 1325.0 1325 90.3700 1235 2255 1 chr2D.!!$F1 1020
9 TraesCS2B01G417800 chr1D 467304114 467305097 983 True 1306.0 1306 90.4200 1235 2253 1 chr1D.!!$R3 1018
10 TraesCS2B01G417800 chr1D 99785202 99785829 627 True 824.0 824 90.1840 1235 1883 1 chr1D.!!$R2 648
11 TraesCS2B01G417800 chr3D 8682102 8683087 985 False 1304.0 1304 90.3410 1235 2255 1 chr3D.!!$F1 1020
12 TraesCS2B01G417800 chr7B 116359697 116360463 766 True 1284.0 1284 96.8710 1 767 1 chr7B.!!$R2 766
13 TraesCS2B01G417800 chr7B 181338284 181339060 776 True 1238.0 1238 95.4950 1 774 1 chr7B.!!$R4 773
14 TraesCS2B01G417800 chr7B 143192319 143193253 934 True 1199.0 1199 90.1780 1236 2162 1 chr7B.!!$R3 926
15 TraesCS2B01G417800 chr6D 139927520 139928505 985 False 1282.0 1282 89.9510 1235 2255 1 chr6D.!!$F1 1020
16 TraesCS2B01G417800 chr6D 338191282 338192266 984 True 1282.0 1282 89.9410 1235 2255 1 chr6D.!!$R1 1020
17 TraesCS2B01G417800 chrUn 36313100 36313865 765 True 1266.0 1266 96.4750 1 766 1 chrUn.!!$R1 765
18 TraesCS2B01G417800 chr5B 575182280 575183050 770 True 1266.0 1266 96.3680 1 768 1 chr5B.!!$R2 767
19 TraesCS2B01G417800 chr5B 538305995 538306579 584 True 911.0 911 94.7280 1236 1823 1 chr5B.!!$R1 587
20 TraesCS2B01G417800 chr1B 688136096 688136863 767 True 1247.0 1247 95.9640 1 768 1 chr1B.!!$R3 767
21 TraesCS2B01G417800 chr1B 488158771 488159544 773 True 1243.0 1243 95.7360 1 771 1 chr1B.!!$R2 770
22 TraesCS2B01G417800 chr1B 423616441 423617042 601 True 726.0 726 88.4060 1236 1852 1 chr1B.!!$R1 616
23 TraesCS2B01G417800 chr3B 740519979 740520749 770 True 1243.0 1243 95.8500 1 768 1 chr3B.!!$R1 767
24 TraesCS2B01G417800 chr2A 549718292 549719291 999 True 1229.0 1229 88.7910 1235 2255 1 chr2A.!!$R1 1020
25 TraesCS2B01G417800 chr4B 346143427 346144027 600 False 953.0 953 95.2070 1233 1837 1 chr4B.!!$F1 604
26 TraesCS2B01G417800 chr4B 68869484 68874629 5145 True 917.5 1059 92.5395 767 2255 2 chr4B.!!$R2 1488
27 TraesCS2B01G417800 chr6B 170974707 170975273 566 True 822.0 822 92.5170 1236 1823 1 chr6B.!!$R1 587

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
850 858 0.038067 TGCAGAACTTACCGCGCTTA 60.038 50.0 5.56 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 5475 0.323629 TAGGCAACAAAGAGGTCGGG 59.676 55.0 0.0 0.0 41.41 5.14 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
77 78 8.850452 CAGTAAAACAATTCGAATAAAGGCTTC 58.150 33.333 11.83 0.00 0.00 3.86
88 92 1.826385 AAAGGCTTCGCTGTAGCATT 58.174 45.000 0.00 5.68 43.65 3.56
778 786 3.511477 ACACTGACAGTAAGGGAGACAT 58.489 45.455 8.02 0.00 0.00 3.06
785 793 3.515901 ACAGTAAGGGAGACATGACTTCC 59.484 47.826 14.09 14.09 35.86 3.46
790 798 0.833949 GGAGACATGACTTCCCCCTC 59.166 60.000 0.00 0.00 0.00 4.30
836 844 1.180456 CCACCCAACAATGCTGCAGA 61.180 55.000 20.43 2.70 0.00 4.26
840 848 1.342174 CCCAACAATGCTGCAGAACTT 59.658 47.619 20.43 3.81 0.00 2.66
850 858 0.038067 TGCAGAACTTACCGCGCTTA 60.038 50.000 5.56 0.00 0.00 3.09
865 873 2.880890 GCGCTTATTGATCATTGGAGGT 59.119 45.455 0.00 0.00 0.00 3.85
867 875 3.499918 CGCTTATTGATCATTGGAGGTCC 59.500 47.826 0.00 0.00 0.00 4.46
906 914 3.537874 CGGACCGGGGAGATGACC 61.538 72.222 6.32 0.00 0.00 4.02
916 924 1.658686 GGAGATGACCGTGACGCTCT 61.659 60.000 0.00 0.00 0.00 4.09
943 951 1.837439 TGGCTATGATCACCGGTCTTT 59.163 47.619 2.59 0.00 0.00 2.52
1102 1110 2.614481 GGTGCTCCTTTCACGTGGATTA 60.614 50.000 17.00 0.00 35.39 1.75
1103 1111 2.415512 GTGCTCCTTTCACGTGGATTAC 59.584 50.000 17.00 3.52 0.00 1.89
1111 1119 3.861276 TCACGTGGATTACATCGAACT 57.139 42.857 17.00 0.00 0.00 3.01
1285 4914 1.689233 CCTTCTCCCACCATCCCGA 60.689 63.158 0.00 0.00 0.00 5.14
1621 5308 2.224159 AAGACCATCACCACGGCCT 61.224 57.895 0.00 0.00 0.00 5.19
1623 5310 1.153429 GACCATCACCACGGCCTAC 60.153 63.158 0.00 0.00 0.00 3.18
1624 5311 1.895020 GACCATCACCACGGCCTACA 61.895 60.000 0.00 0.00 0.00 2.74
1625 5312 1.449601 CCATCACCACGGCCTACAC 60.450 63.158 0.00 0.00 0.00 2.90
1700 5462 2.358737 CACCACCACGGCCTCTTC 60.359 66.667 0.00 0.00 39.03 2.87
1713 5475 3.067040 CGGCCTCTTCTAAGTCCTAGTTC 59.933 52.174 0.00 0.00 0.00 3.01
1774 5566 0.175531 GTTGGCTTGGCACTTGTTGT 59.824 50.000 0.00 0.00 0.00 3.32
1845 5667 2.571212 CACTTGTTGGCTACCACTTGA 58.429 47.619 0.00 0.00 30.78 3.02
1889 5756 2.224769 CCACTTGGTTGGCTTCCTTCTA 60.225 50.000 0.00 0.00 0.00 2.10
1970 5837 3.938334 ACATTTTCTTTTGTTGTGGCCAC 59.062 39.130 29.67 29.67 0.00 5.01
2021 5888 0.678048 ACGAGGCTCTTGGAATTGGC 60.678 55.000 13.50 0.00 0.00 4.52
2127 5994 1.645710 ACCTTCAACTCTGGATCCGT 58.354 50.000 7.39 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.215196 GTTTCCTTGGCACGTCTTGTA 58.785 47.619 0.00 0.0 0.00 2.41
778 786 2.191400 CTGAATGAGAGGGGGAAGTCA 58.809 52.381 0.00 0.0 0.00 3.41
785 793 1.630369 TGACCAACTGAATGAGAGGGG 59.370 52.381 0.00 0.0 0.00 4.79
790 798 1.081892 CGGCTGACCAACTGAATGAG 58.918 55.000 0.00 0.0 34.57 2.90
836 844 3.527533 TGATCAATAAGCGCGGTAAGTT 58.472 40.909 12.91 3.9 0.00 2.66
840 848 2.805671 CCAATGATCAATAAGCGCGGTA 59.194 45.455 12.91 0.0 0.00 4.02
850 858 3.041211 TCTCGGACCTCCAATGATCAAT 58.959 45.455 0.00 0.0 35.14 2.57
865 873 1.116308 TGGAAAGTGTGTGTCTCGGA 58.884 50.000 0.00 0.0 0.00 4.55
867 875 3.032017 AGATGGAAAGTGTGTGTCTCG 57.968 47.619 0.00 0.0 0.00 4.04
906 914 1.401670 GCCATATCCTAGAGCGTCACG 60.402 57.143 0.00 0.0 0.00 4.35
907 915 1.889829 AGCCATATCCTAGAGCGTCAC 59.110 52.381 0.00 0.0 0.00 3.67
916 924 3.960755 CCGGTGATCATAGCCATATCCTA 59.039 47.826 0.00 0.0 0.00 2.94
963 971 5.059161 CCATCAGAATCGGTGTTCATACAT 58.941 41.667 0.00 0.0 36.50 2.29
1030 1038 1.679898 CTTCTGGTTCCCGAGGCTT 59.320 57.895 0.00 0.0 0.00 4.35
1038 1046 2.550830 TGTCTTCTGCTTCTGGTTCC 57.449 50.000 0.00 0.0 0.00 3.62
1102 1110 2.812011 GGCAAGTACCAAAGTTCGATGT 59.188 45.455 0.00 0.0 0.00 3.06
1103 1111 2.161609 GGGCAAGTACCAAAGTTCGATG 59.838 50.000 0.00 0.0 0.00 3.84
1111 1119 1.440618 TCCTCAGGGCAAGTACCAAA 58.559 50.000 0.00 0.0 0.00 3.28
1285 4914 2.036992 GAGGATGGCGAAGATGAGATGT 59.963 50.000 0.00 0.0 0.00 3.06
1621 5308 1.750341 CTCGTGGTGGTGGTGGTGTA 61.750 60.000 0.00 0.0 0.00 2.90
1623 5310 2.280797 CTCGTGGTGGTGGTGGTG 60.281 66.667 0.00 0.0 0.00 4.17
1624 5311 4.250305 GCTCGTGGTGGTGGTGGT 62.250 66.667 0.00 0.0 0.00 4.16
1625 5312 3.883744 GAGCTCGTGGTGGTGGTGG 62.884 68.421 0.00 0.0 0.00 4.61
1700 5462 2.950975 GAGGTCGGGAACTAGGACTTAG 59.049 54.545 0.00 0.0 35.39 2.18
1713 5475 0.323629 TAGGCAACAAAGAGGTCGGG 59.676 55.000 0.00 0.0 41.41 5.14
1788 5580 0.476338 TAGCCAACAAGTGCCAAGGA 59.524 50.000 0.00 0.0 0.00 3.36
1845 5667 0.393820 CCAACAAGTGCCAAGCCAAT 59.606 50.000 0.00 0.0 0.00 3.16
1889 5756 2.440409 CACAAGCCAACAAGGAGCTAT 58.560 47.619 0.00 0.0 41.22 2.97
1970 5837 1.966451 GTGGGGAGTGCAAAGGTCG 60.966 63.158 0.00 0.0 0.00 4.79


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

AutoCloner maintained by Alex Coulton.