Multiple sequence alignment - TraesCS3D01G376900

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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 TraesCS3D01G376900 chr3D 100.000 2527 0 0 1 2527 491433603 491431077 0 4667
1 TraesCS3D01G376900 chr3D 95.918 735 21 2 1035 1760 193372741 193373475 0 1182
2 TraesCS3D01G376900 chr3D 94.125 766 43 1 1763 2526 62752022 62752787 0 1164
3 TraesCS3D01G376900 chr3D 91.938 769 56 3 1763 2526 421158473 421159240 0 1072
4 TraesCS3D01G376900 chr3A 96.920 1039 31 1 1 1038 593302801 593303839 0 1740
5 TraesCS3D01G376900 chr3A 96.631 1039 34 1 4 1041 66036832 66035794 0 1724
6 TraesCS3D01G376900 chr3A 97.279 735 11 4 1035 1760 66035715 66034981 0 1238
7 TraesCS3D01G376900 chr7A 96.824 1039 32 1 1 1038 60300725 60301763 0 1735
8 TraesCS3D01G376900 chr7A 96.871 735 14 4 1035 1760 60301844 60302578 0 1221
9 TraesCS3D01G376900 chrUn 96.728 1039 33 1 1 1038 45094236 45095274 0 1729
10 TraesCS3D01G376900 chrUn 96.728 1039 33 1 1 1038 171044523 171045561 0 1729
11 TraesCS3D01G376900 chrUn 96.535 1039 35 1 1 1038 336782418 336783456 0 1718
12 TraesCS3D01G376900 chrUn 97.415 735 10 4 1035 1760 171045642 171046376 0 1243
13 TraesCS3D01G376900 chrUn 97.279 735 11 4 1035 1760 45095356 45096090 0 1238
14 TraesCS3D01G376900 chrUn 96.499 457 7 4 1035 1482 336783538 336783994 0 747
15 TraesCS3D01G376900 chrUn 98.504 401 6 0 1035 1435 415711345 415710945 0 708
16 TraesCS3D01G376900 chr5B 96.535 1039 35 1 4 1041 130575281 130574243 0 1718
17 TraesCS3D01G376900 chr5B 97.415 735 10 4 1035 1760 130574164 130573430 0 1243
18 TraesCS3D01G376900 chr2A 96.535 1039 35 1 4 1041 735229983 735228945 0 1718
19 TraesCS3D01G376900 chr2A 96.871 735 13 5 1035 1760 735228867 735228134 0 1221
20 TraesCS3D01G376900 chr1A 96.535 1039 35 1 1 1038 94759111 94760149 0 1718
21 TraesCS3D01G376900 chr2B 96.599 735 15 5 1035 1760 112863712 112864445 0 1210
22 TraesCS3D01G376900 chr6D 96.463 735 15 5 1035 1760 283208101 283208833 0 1203
23 TraesCS3D01G376900 chr6D 96.190 735 19 2 1035 1760 425973978 425974712 0 1194
24 TraesCS3D01G376900 chr1D 93.848 764 46 1 1763 2526 450968507 450967745 0 1149
25 TraesCS3D01G376900 chr1D 93.333 765 49 2 1763 2526 413268283 413269046 0 1129
26 TraesCS3D01G376900 chr2D 93.717 764 48 0 1763 2526 559144183 559143420 0 1146
27 TraesCS3D01G376900 chr2D 93.595 765 47 2 1763 2526 434231259 434230496 0 1140
28 TraesCS3D01G376900 chr2D 93.072 765 52 1 1763 2526 547265189 547264425 0 1118
29 TraesCS3D01G376900 chr5D 92.218 771 51 6 1763 2526 46585988 46586756 0 1083
30 TraesCS3D01G376900 chr4D 92.277 764 58 1 1763 2526 404596273 404597035 0 1083
31 TraesCS3D01G376900 chr6A 95.388 412 9 3 1358 1760 578246185 578245775 0 647


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 TraesCS3D01G376900 chr3D 491431077 491433603 2526 True 4667.0 4667 100.0000 1 2527 1 chr3D.!!$R1 2526
1 TraesCS3D01G376900 chr3D 193372741 193373475 734 False 1182.0 1182 95.9180 1035 1760 1 chr3D.!!$F2 725
2 TraesCS3D01G376900 chr3D 62752022 62752787 765 False 1164.0 1164 94.1250 1763 2526 1 chr3D.!!$F1 763
3 TraesCS3D01G376900 chr3D 421158473 421159240 767 False 1072.0 1072 91.9380 1763 2526 1 chr3D.!!$F3 763
4 TraesCS3D01G376900 chr3A 593302801 593303839 1038 False 1740.0 1740 96.9200 1 1038 1 chr3A.!!$F1 1037
5 TraesCS3D01G376900 chr3A 66034981 66036832 1851 True 1481.0 1724 96.9550 4 1760 2 chr3A.!!$R1 1756
6 TraesCS3D01G376900 chr7A 60300725 60302578 1853 False 1478.0 1735 96.8475 1 1760 2 chr7A.!!$F1 1759
7 TraesCS3D01G376900 chrUn 171044523 171046376 1853 False 1486.0 1729 97.0715 1 1760 2 chrUn.!!$F2 1759
8 TraesCS3D01G376900 chrUn 45094236 45096090 1854 False 1483.5 1729 97.0035 1 1760 2 chrUn.!!$F1 1759
9 TraesCS3D01G376900 chrUn 336782418 336783994 1576 False 1232.5 1718 96.5170 1 1482 2 chrUn.!!$F3 1481
10 TraesCS3D01G376900 chr5B 130573430 130575281 1851 True 1480.5 1718 96.9750 4 1760 2 chr5B.!!$R1 1756
11 TraesCS3D01G376900 chr2A 735228134 735229983 1849 True 1469.5 1718 96.7030 4 1760 2 chr2A.!!$R1 1756
12 TraesCS3D01G376900 chr1A 94759111 94760149 1038 False 1718.0 1718 96.5350 1 1038 1 chr1A.!!$F1 1037
13 TraesCS3D01G376900 chr2B 112863712 112864445 733 False 1210.0 1210 96.5990 1035 1760 1 chr2B.!!$F1 725
14 TraesCS3D01G376900 chr6D 283208101 283208833 732 False 1203.0 1203 96.4630 1035 1760 1 chr6D.!!$F1 725
15 TraesCS3D01G376900 chr6D 425973978 425974712 734 False 1194.0 1194 96.1900 1035 1760 1 chr6D.!!$F2 725
16 TraesCS3D01G376900 chr1D 450967745 450968507 762 True 1149.0 1149 93.8480 1763 2526 1 chr1D.!!$R1 763
17 TraesCS3D01G376900 chr1D 413268283 413269046 763 False 1129.0 1129 93.3330 1763 2526 1 chr1D.!!$F1 763
18 TraesCS3D01G376900 chr2D 559143420 559144183 763 True 1146.0 1146 93.7170 1763 2526 1 chr2D.!!$R3 763
19 TraesCS3D01G376900 chr2D 434230496 434231259 763 True 1140.0 1140 93.5950 1763 2526 1 chr2D.!!$R1 763
20 TraesCS3D01G376900 chr2D 547264425 547265189 764 True 1118.0 1118 93.0720 1763 2526 1 chr2D.!!$R2 763
21 TraesCS3D01G376900 chr5D 46585988 46586756 768 False 1083.0 1083 92.2180 1763 2526 1 chr5D.!!$F1 763
22 TraesCS3D01G376900 chr4D 404596273 404597035 762 False 1083.0 1083 92.2770 1763 2526 1 chr4D.!!$F1 763

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
600 602 0.391661 GAGATCTCGTTTGCTGGCCA 60.392 55.0 4.71 4.71 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2395 2584 0.030235 TGTTCATATCCGACGAGCCG 59.97 55.0 0.0 0.0 0.0 5.52 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
52 53 1.279271 AGGCTCCGTAATCAAGTGCTT 59.721 47.619 0.00 0.00 0.00 3.91
56 57 3.521560 CTCCGTAATCAAGTGCTTGCTA 58.478 45.455 7.03 0.00 40.24 3.49
108 109 6.591448 CCATTTCTCCCTGCAAAATAAGTTTC 59.409 38.462 0.00 0.00 0.00 2.78
129 130 1.035932 ACCCGAGTGAGTATGGACCG 61.036 60.000 0.00 0.00 0.00 4.79
258 259 1.487976 GGGACAGAGGCTGATGATTCA 59.512 52.381 0.00 0.00 35.18 2.57
338 339 9.101655 CAACAAAAAGATGAATGGAAAGTCTTT 57.898 29.630 0.00 0.00 39.92 2.52
404 405 3.365220 CGATCGTGACTTCTTTCTTGGAC 59.635 47.826 7.03 0.00 0.00 4.02
405 406 3.812156 TCGTGACTTCTTTCTTGGACA 57.188 42.857 0.00 0.00 0.00 4.02
421 422 3.426615 TGGACACCTGAAGTTTGTGTTT 58.573 40.909 7.82 0.00 42.89 2.83
434 435 6.348621 AGTTTGTGTTTGCATTTCATCAAC 57.651 33.333 0.00 0.00 0.00 3.18
497 499 7.435488 GCTCGTGTAAAGCAAGATCTTCTATTA 59.565 37.037 4.57 2.44 39.61 0.98
541 543 1.589196 GCACATACTCGGCTCGGTC 60.589 63.158 0.00 0.00 0.00 4.79
600 602 0.391661 GAGATCTCGTTTGCTGGCCA 60.392 55.000 4.71 4.71 0.00 5.36
755 757 7.868922 GCATGAACATTTAGATATTGGAATGCA 59.131 33.333 0.00 0.00 35.45 3.96
854 856 6.741992 ATGCTGATTGACGACTGAATAAAA 57.258 33.333 0.00 0.00 0.00 1.52
856 858 7.144722 TGCTGATTGACGACTGAATAAAAAT 57.855 32.000 0.00 0.00 0.00 1.82
897 899 1.754226 AGAGAGAAAGAGCGGATCCAC 59.246 52.381 13.41 0.99 0.00 4.02
926 928 1.324383 TGCAGTACCTGTTCTGTCGA 58.676 50.000 5.92 0.00 33.43 4.20
1144 1315 5.794894 AGAATCTGGTACACTCGAATTGTT 58.205 37.500 4.75 0.00 0.00 2.83
1146 1317 6.369065 AGAATCTGGTACACTCGAATTGTTTC 59.631 38.462 4.75 2.68 0.00 2.78
1259 1430 4.258543 CCATGTTACAACTTCCGTACCAT 58.741 43.478 0.00 0.00 0.00 3.55
1338 1509 6.773638 ACTCTTCTGTGTGGTATTCATTCTT 58.226 36.000 0.00 0.00 0.00 2.52
1409 1580 3.815809 TCCAACCACTTCACCTACTTTG 58.184 45.455 0.00 0.00 0.00 2.77
1417 1588 0.250553 TCACCTACTTTGTTGCCCCG 60.251 55.000 0.00 0.00 0.00 5.73
1435 1606 0.319813 CGAACCGTTTCCCGTACCTT 60.320 55.000 0.00 0.00 33.66 3.50
1442 1622 4.686348 CCGTTTCCCGTACCTTAGAAGGA 61.686 52.174 15.33 0.00 41.13 3.36
1560 1740 5.818336 TCATGGAAAAGCCGTTATTCGATTA 59.182 36.000 0.00 0.00 42.86 1.75
1624 1804 6.021596 CAGCGATGTACAAACAAGGATTTAC 58.978 40.000 0.00 0.00 39.58 2.01
1760 1940 2.478894 CGGTTGTTCTTAACAGCGATGT 59.521 45.455 0.00 0.00 42.68 3.06
1761 1941 3.664276 CGGTTGTTCTTAACAGCGATGTG 60.664 47.826 7.27 0.00 42.68 3.21
2087 2268 3.474570 GAGGCGCACTCCTCCCAT 61.475 66.667 10.83 0.00 45.40 4.00
2096 2277 1.134965 CACTCCTCCCATGAAGACGAC 60.135 57.143 0.00 0.00 0.00 4.34
2246 2435 2.677914 TCACTGAAGAGGAGTGGTTGA 58.322 47.619 0.00 0.00 41.11 3.18
2392 2581 3.235195 CGTATCTTCGTCGGATGATTCC 58.765 50.000 0.00 0.00 37.93 3.01
2395 2584 3.438297 TCTTCGTCGGATGATTCCTTC 57.562 47.619 0.00 0.00 40.17 3.46
2495 2684 0.701310 AAGGGAACTGAACCAGGGGT 60.701 55.000 0.00 0.00 42.68 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.010516 GCCTGTAGATCTTCTTCTCATAGCA 59.989 44.000 0.00 0.00 0.00 3.49
56 57 5.366186 ACATGCCTGTAGATCTTCTTCTCAT 59.634 40.000 0.00 0.00 32.49 2.90
108 109 1.134788 GGTCCATACTCACTCGGGTTG 60.135 57.143 0.00 0.00 0.00 3.77
129 130 6.039616 AGATTGAGAAGAAAGATGAGCGTAC 58.960 40.000 0.00 0.00 0.00 3.67
258 259 9.793259 TCATCTTGTAGTTAGAAATCACCTTTT 57.207 29.630 0.00 0.00 0.00 2.27
338 339 7.053498 TGGGTTGAAGATCAATTCATATCGAA 58.947 34.615 0.00 0.00 38.79 3.71
387 388 3.561725 CAGGTGTCCAAGAAAGAAGTCAC 59.438 47.826 0.00 0.00 0.00 3.67
404 405 3.229276 TGCAAACACAAACTTCAGGTG 57.771 42.857 0.00 0.00 38.47 4.00
405 406 4.470334 AATGCAAACACAAACTTCAGGT 57.530 36.364 0.00 0.00 0.00 4.00
421 422 4.297510 CACTTTTCCGTTGATGAAATGCA 58.702 39.130 0.00 0.00 32.87 3.96
497 499 6.998802 AGACAAGACACAGCTAAATAAGTCT 58.001 36.000 0.00 0.00 37.90 3.24
505 507 2.872245 GTGCAAGACAAGACACAGCTAA 59.128 45.455 0.00 0.00 33.23 3.09
541 543 3.129113 TGCCAATCGAAGATGAACCATTG 59.871 43.478 0.00 0.00 45.12 2.82
600 602 2.492025 TCTAAACTCATGGATGGGCCT 58.508 47.619 4.53 0.00 37.63 5.19
752 754 4.380843 TTCCTAATTCAGGGAGTTTGCA 57.619 40.909 0.00 0.00 45.58 4.08
755 757 9.413734 CTATGAAATTCCTAATTCAGGGAGTTT 57.586 33.333 12.09 12.09 40.45 2.66
926 928 3.003068 CGCTAGCTTTGCATGATTAGCTT 59.997 43.478 13.93 6.11 40.91 3.74
955 957 1.710013 TTCATTCACTTCGACGGCTC 58.290 50.000 0.00 0.00 0.00 4.70
1259 1430 1.684450 TCCATTCCGGATCGATCGAAA 59.316 47.619 23.50 11.84 39.64 3.46
1338 1509 1.071542 TGTGATTCCAAGAGCCGAACA 59.928 47.619 0.00 0.00 0.00 3.18
1409 1580 2.640989 GAAACGGTTCGGGGCAAC 59.359 61.111 0.00 0.00 0.00 4.17
1435 1606 8.040727 TCGATGAAAGAACATGAAATCCTTCTA 58.959 33.333 0.00 0.00 32.33 2.10
1442 1622 6.153340 ACCCAATCGATGAAAGAACATGAAAT 59.847 34.615 0.00 0.00 0.00 2.17
1560 1740 5.478407 CCCGGCTCAACATTCTTTTAAAAT 58.522 37.500 0.09 0.00 0.00 1.82
1624 1804 4.003648 CCAACCTAGGTGCAGAAGTAAAG 58.996 47.826 17.14 0.00 0.00 1.85
2087 2268 1.166129 CTTCCTCCTCGTCGTCTTCA 58.834 55.000 0.00 0.00 0.00 3.02
2096 2277 2.829120 AGAACTTTCCTCTTCCTCCTCG 59.171 50.000 0.00 0.00 0.00 4.63
2229 2418 1.694150 TGGTCAACCACTCCTCTTCAG 59.306 52.381 0.00 0.00 42.01 3.02
2230 2419 1.694150 CTGGTCAACCACTCCTCTTCA 59.306 52.381 0.00 0.00 42.01 3.02
2392 2581 0.591659 TCATATCCGACGAGCCGAAG 59.408 55.000 0.00 0.00 0.00 3.79
2395 2584 0.030235 TGTTCATATCCGACGAGCCG 59.970 55.000 0.00 0.00 0.00 5.52
2495 2684 2.707849 GCGCCTCCGGAACTGTCTA 61.708 63.158 5.23 0.00 34.32 2.59


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

AutoCloner maintained by Alex Coulton.