Multiple sequence alignment - TraesCS1D01G194000

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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 TraesCS1D01G194000 chr1D 100.000 4120 0 0 1 4120 270018313 270022432 0.000000e+00 7609
1 TraesCS1D01G194000 chr1A 95.567 3316 113 20 20 3306 343615057 343618367 0.000000e+00 5278
2 TraesCS1D01G194000 chr1A 96.774 744 22 1 3305 4046 343618398 343619141 0.000000e+00 1240
3 TraesCS1D01G194000 chr1A 96.000 75 3 0 4046 4120 343620171 343620245 5.590000e-24 122
4 TraesCS1D01G194000 chr1B 94.503 1910 72 12 1 1884 343658965 343660867 0.000000e+00 2915
5 TraesCS1D01G194000 chr1B 96.564 1426 45 4 1883 3306 343660952 343662375 0.000000e+00 2359
6 TraesCS1D01G194000 chr1B 95.360 819 35 2 3305 4120 343662414 343663232 0.000000e+00 1299
7 TraesCS1D01G194000 chr5A 95.292 616 29 0 3505 4120 430642518 430641903 0.000000e+00 977
8 TraesCS1D01G194000 chr5D 95.130 616 27 3 3505 4120 325956363 325956975 0.000000e+00 968
9 TraesCS1D01G194000 chr7B 93.994 616 31 3 3505 4118 5917113 5917724 0.000000e+00 928


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 TraesCS1D01G194000 chr1D 270018313 270022432 4119 False 7609.000000 7609 100.000000 1 4120 1 chr1D.!!$F1 4119
1 TraesCS1D01G194000 chr1A 343615057 343620245 5188 False 2213.333333 5278 96.113667 20 4120 3 chr1A.!!$F1 4100
2 TraesCS1D01G194000 chr1B 343658965 343663232 4267 False 2191.000000 2915 95.475667 1 4120 3 chr1B.!!$F1 4119
3 TraesCS1D01G194000 chr5A 430641903 430642518 615 True 977.000000 977 95.292000 3505 4120 1 chr5A.!!$R1 615
4 TraesCS1D01G194000 chr5D 325956363 325956975 612 False 968.000000 968 95.130000 3505 4120 1 chr5D.!!$F1 615
5 TraesCS1D01G194000 chr7B 5917113 5917724 611 False 928.000000 928 93.994000 3505 4118 1 chr7B.!!$F1 613

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
578 602 0.173708 GGTGGTAGTTGCGAGGAGAG 59.826 60.000 0.0 0.0 0.00 3.20 F
1173 1211 1.618837 GTTGGGACAGCTCTCACACTA 59.381 52.381 0.0 0.0 42.39 2.74 F
2686 2816 1.006832 CAACCACGGCTATTTCTCGG 58.993 55.000 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 1811 1.515521 CTCCCGACCAGTTTGGCAAC 61.516 60.000 0.0 0.0 42.67 4.17 R
2748 2878 0.036022 GGCAGAGCAGTTCTTGAGGT 59.964 55.000 0.0 0.0 32.41 3.85 R
4067 5273 3.528597 AGACTCCTACGAAATTCAGGC 57.471 47.619 0.0 0.0 0.00 4.85 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
96 97 4.324991 AACCGTGACCTTCGCCCC 62.325 66.667 0.00 0.00 0.00 5.80
190 196 4.520846 GTCCAATCAAGGCGCGCG 62.521 66.667 28.44 28.44 0.00 6.86
249 255 2.395654 GTCCTCTTCACGTGAACTCAC 58.604 52.381 26.53 15.95 43.15 3.51
256 262 0.249447 CACGTGAACTCACTCAGCCA 60.249 55.000 10.90 0.00 44.34 4.75
423 437 2.203084 TGCGGCAAGGACGAACAA 60.203 55.556 0.00 0.00 35.20 2.83
472 494 0.179181 GCGTGTCCAATCTACGACGA 60.179 55.000 0.00 0.00 40.01 4.20
483 505 2.658285 TCTACGACGAAAAGCAGTGAC 58.342 47.619 0.00 0.00 0.00 3.67
485 507 0.526954 ACGACGAAAAGCAGTGACGT 60.527 50.000 0.00 0.00 39.82 4.34
498 520 3.317150 CAGTGACGTTCATGCTCTGTAA 58.683 45.455 0.00 0.00 0.00 2.41
554 578 9.278978 GGAAGAAAATCTGAAGAAAACTAGAGT 57.721 33.333 0.00 0.00 0.00 3.24
557 581 8.432805 AGAAAATCTGAAGAAAACTAGAGTGGA 58.567 33.333 0.00 0.00 0.00 4.02
558 582 9.225436 GAAAATCTGAAGAAAACTAGAGTGGAT 57.775 33.333 0.00 0.00 0.00 3.41
565 589 5.091552 AGAAAACTAGAGTGGATGGTGGTA 58.908 41.667 0.00 0.00 0.00 3.25
567 591 3.759815 ACTAGAGTGGATGGTGGTAGT 57.240 47.619 0.00 0.00 0.00 2.73
570 594 1.279271 AGAGTGGATGGTGGTAGTTGC 59.721 52.381 0.00 0.00 0.00 4.17
578 602 0.173708 GGTGGTAGTTGCGAGGAGAG 59.826 60.000 0.00 0.00 0.00 3.20
591 615 3.822940 CGAGGAGAGTAGGGATAACAGT 58.177 50.000 0.00 0.00 0.00 3.55
803 829 5.643777 ACTTTTAAAGTCATGCACGATAGCT 59.356 36.000 4.30 0.00 37.02 3.32
1173 1211 1.618837 GTTGGGACAGCTCTCACACTA 59.381 52.381 0.00 0.00 42.39 2.74
1200 1238 6.368243 TCTCGCTCTTGTATATACTAGAACCG 59.632 42.308 24.44 24.44 37.55 4.44
1336 1376 5.244402 TGTGGATGTAGTTCTTCGGTTTCTA 59.756 40.000 0.00 0.00 0.00 2.10
1347 1387 5.047847 TCTTCGGTTTCTAACAAGTGAGTG 58.952 41.667 0.00 0.00 0.00 3.51
1465 1505 4.505313 AAGATCTGGAAAAGTTTTCCGC 57.495 40.909 32.25 23.48 41.43 5.54
1474 1514 3.513680 AAAGTTTTCCGCGGTTTCTTT 57.486 38.095 27.15 24.42 0.00 2.52
1535 1575 6.441924 TGTAAAATTGGAATTTAGGATGGCCA 59.558 34.615 8.56 8.56 37.62 5.36
1540 1580 7.688918 ATTGGAATTTAGGATGGCCAAATTA 57.311 32.000 10.96 0.00 38.70 1.40
1588 1628 2.031919 ACAGGATTCGCGGCAACA 59.968 55.556 6.13 0.00 0.00 3.33
1687 1727 1.743252 GGTCTCAAGCTTCCGCCAG 60.743 63.158 0.00 0.00 36.60 4.85
1768 1808 4.516652 ATGCCTCTTTATGAGCCTCTTT 57.483 40.909 0.00 0.00 41.35 2.52
1771 1811 3.376546 GCCTCTTTATGAGCCTCTTTGTG 59.623 47.826 0.00 0.00 41.35 3.33
1805 1845 3.304251 GAGAGGACCTCCACAGCC 58.696 66.667 18.32 0.00 38.89 4.85
1875 1918 7.934665 TGGGTATCACATATATGGTGTTAACAC 59.065 37.037 27.20 27.20 45.72 3.32
2004 2133 5.404968 CCGAGATCAAGAGAAGCATGATAAC 59.595 44.000 0.00 0.00 34.10 1.89
2022 2151 8.833493 CATGATAACATTCTTGATAAGCAGACA 58.167 33.333 0.00 0.00 34.15 3.41
2025 2154 5.980698 ACATTCTTGATAAGCAGACATCG 57.019 39.130 0.00 0.00 0.00 3.84
2079 2208 8.819643 AAGTACTAGACTCAAAATCAAGTGAC 57.180 34.615 0.00 0.00 37.44 3.67
2093 2222 2.233305 AGTGACGAGTCCCTGGTAAT 57.767 50.000 0.34 0.00 0.00 1.89
2101 2230 6.126883 TGACGAGTCCCTGGTAATTAAATCAT 60.127 38.462 0.34 0.00 0.00 2.45
2103 2232 6.126883 ACGAGTCCCTGGTAATTAAATCATCA 60.127 38.462 0.00 0.00 0.00 3.07
2135 2264 7.337942 TGCTTCAATCTTCTTATCCTTTTCTCC 59.662 37.037 0.00 0.00 0.00 3.71
2142 2271 4.843728 TCTTATCCTTTTCTCCGTGCAAT 58.156 39.130 0.00 0.00 0.00 3.56
2293 2423 4.418392 CATGGCAAAAGTATGTGAAGCTC 58.582 43.478 0.00 0.00 0.00 4.09
2347 2477 1.471119 CTGCACTTCATGGATGCCTT 58.529 50.000 12.32 0.00 38.63 4.35
2613 2743 1.600636 CGTTGTGCCCCTGATGTGT 60.601 57.895 0.00 0.00 0.00 3.72
2686 2816 1.006832 CAACCACGGCTATTTCTCGG 58.993 55.000 0.00 0.00 0.00 4.63
2909 3039 3.306364 GCCTTGAGTTCTCTGAAGCACTA 60.306 47.826 1.53 0.00 34.41 2.74
2961 3091 4.342359 AGAAATGGTAGTACGACTGGAGT 58.658 43.478 6.07 0.00 0.00 3.85
3089 3219 2.260844 ATGATGGTGTGCGATTAGGG 57.739 50.000 0.00 0.00 0.00 3.53
3314 3485 2.613977 CCAGCGATCAGACCTGTTTTCT 60.614 50.000 0.00 0.00 0.00 2.52
3369 3542 2.289694 CCTTCTCTGACCCGTGTTTCAT 60.290 50.000 0.00 0.00 0.00 2.57
3477 3650 3.723260 TGAGTAATTTGACAGCGACACA 58.277 40.909 0.00 0.00 0.00 3.72
3493 3666 4.386049 GCGACACATTTATTCCTATCCTCG 59.614 45.833 0.00 0.00 0.00 4.63
3550 3724 6.204882 GCAAGTGTGTAAACTGGATTTCTACT 59.795 38.462 0.00 0.00 0.00 2.57
3736 3910 9.485591 GAATTCGATGCTCTTAAAAATCGTTAA 57.514 29.630 4.10 0.00 41.92 2.01
3996 4172 3.004839 TGCGCAATCTCATACTCCTCTAC 59.995 47.826 8.16 0.00 0.00 2.59
4042 5248 6.417258 TGAAATAGAGGTGCATGAATCAGAA 58.583 36.000 0.00 0.00 0.00 3.02
4074 5280 8.757982 ATATAATGACAAGTGAAAGCCTGAAT 57.242 30.769 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.874019 CGGTGATTCTCTGCCGTCG 60.874 63.158 0.00 0.00 39.41 5.12
54 55 1.508632 CGGGTTCAGATTTGTCGTGT 58.491 50.000 0.00 0.00 0.00 4.49
113 119 2.887568 GAGCGACATGTGCGGAGG 60.888 66.667 1.15 0.00 37.44 4.30
114 120 1.875813 GAGAGCGACATGTGCGGAG 60.876 63.158 1.15 0.00 37.44 4.63
190 196 4.395583 GGCAAGCTGCTCGTGTGC 62.396 66.667 14.09 14.09 44.28 4.57
191 197 4.081030 CGGCAAGCTGCTCGTGTG 62.081 66.667 1.00 0.00 44.28 3.82
229 235 2.395654 GTGAGTTCACGTGAAGAGGAC 58.604 52.381 30.38 19.11 37.10 3.85
249 255 1.310933 GCACTGGACCATTGGCTGAG 61.311 60.000 13.27 0.00 0.00 3.35
256 262 2.363306 TGACTTTGCACTGGACCATT 57.637 45.000 0.00 0.00 0.00 3.16
423 437 8.762645 TCCACTGATATCTGACTAAACATCTTT 58.237 33.333 15.75 0.00 0.00 2.52
438 452 3.248602 GGACACGCAATTCCACTGATATC 59.751 47.826 0.00 0.00 0.00 1.63
472 494 1.949525 AGCATGAACGTCACTGCTTTT 59.050 42.857 11.56 0.00 37.70 2.27
483 505 1.321743 GCGACTTACAGAGCATGAACG 59.678 52.381 0.00 0.00 0.00 3.95
485 507 2.741759 TGCGACTTACAGAGCATGAA 57.258 45.000 0.00 0.00 34.39 2.57
554 578 0.249120 CTCGCAACTACCACCATCCA 59.751 55.000 0.00 0.00 0.00 3.41
557 581 0.537188 CTCCTCGCAACTACCACCAT 59.463 55.000 0.00 0.00 0.00 3.55
558 582 0.541063 TCTCCTCGCAACTACCACCA 60.541 55.000 0.00 0.00 0.00 4.17
565 589 0.331954 TCCCTACTCTCCTCGCAACT 59.668 55.000 0.00 0.00 0.00 3.16
567 591 2.957006 GTTATCCCTACTCTCCTCGCAA 59.043 50.000 0.00 0.00 0.00 4.85
570 594 3.822940 ACTGTTATCCCTACTCTCCTCG 58.177 50.000 0.00 0.00 0.00 4.63
578 602 8.693625 ACTTGTAGACAATACTGTTATCCCTAC 58.306 37.037 0.00 0.00 35.30 3.18
803 829 3.755112 TCGTGTGGTTTCTGGAATGTA 57.245 42.857 0.00 0.00 0.00 2.29
1173 1211 7.388500 GGTTCTAGTATATACAAGAGCGAGACT 59.612 40.741 15.18 0.00 0.00 3.24
1200 1238 3.951680 TCTTTCCCACTCCTTTGAACAAC 59.048 43.478 0.00 0.00 0.00 3.32
1307 1345 5.873164 ACCGAAGAACTACATCCACAAATAC 59.127 40.000 0.00 0.00 0.00 1.89
1336 1376 3.544684 TGTTGATCAGCACTCACTTGTT 58.455 40.909 8.32 0.00 0.00 2.83
1347 1387 0.242017 GGTTGCACCTGTTGATCAGC 59.758 55.000 2.05 2.05 42.38 4.26
1465 1505 2.293122 TGAAGATGCCACAAAGAAACCG 59.707 45.455 0.00 0.00 0.00 4.44
1535 1575 9.938280 TGCTACGGCATAAGATACTATTAATTT 57.062 29.630 0.00 0.00 44.28 1.82
1771 1811 1.515521 CTCCCGACCAGTTTGGCAAC 61.516 60.000 0.00 0.00 42.67 4.17
1812 1852 2.412770 GCCAATCCTTCAAATTTGTGCG 59.587 45.455 17.47 7.44 0.00 5.34
1815 1855 5.549742 TCTTGCCAATCCTTCAAATTTGT 57.450 34.783 17.47 0.00 0.00 2.83
2004 2133 5.981915 TCTCGATGTCTGCTTATCAAGAATG 59.018 40.000 0.00 0.00 0.00 2.67
2022 2151 4.262377 CCAGTATGAATGGAAGCTCTCGAT 60.262 45.833 0.00 0.00 40.51 3.59
2025 2154 3.135530 ACCCAGTATGAATGGAAGCTCTC 59.864 47.826 0.00 0.00 40.51 3.20
2079 2208 6.288294 TGATGATTTAATTACCAGGGACTCG 58.712 40.000 0.00 0.00 34.60 4.18
2135 2264 7.565450 TCAATCTGATAAAAACAATTGCACG 57.435 32.000 5.05 0.00 0.00 5.34
2142 2271 9.022884 TCCATGACATCAATCTGATAAAAACAA 57.977 29.630 0.00 0.00 34.28 2.83
2200 2330 4.469227 TGTGCCTGGCCAATTGTTATTATT 59.531 37.500 17.53 0.00 0.00 1.40
2293 2423 2.949451 AGTGTCTAAGCACAGATCCG 57.051 50.000 0.00 0.00 41.52 4.18
2347 2477 5.559770 TGCAGTACCTGAATTTCTGATTCA 58.440 37.500 4.98 1.95 36.67 2.57
2613 2743 3.064408 GCTTCATGAAGATGATCGCACAA 59.936 43.478 34.43 0.00 40.79 3.33
2686 2816 1.820519 TGGCAGATCCATGTTTTGAGC 59.179 47.619 0.00 0.00 40.72 4.26
2748 2878 0.036022 GGCAGAGCAGTTCTTGAGGT 59.964 55.000 0.00 0.00 32.41 3.85
2909 3039 0.675633 AAGCAAAAGCAGCGAATGGT 59.324 45.000 0.00 0.00 42.89 3.55
2961 3091 7.447238 CAGTTCCTTTACTTCCTCAATAACCAA 59.553 37.037 0.00 0.00 0.00 3.67
3089 3219 1.517242 CAGGAGAAACTGTGTGGCTC 58.483 55.000 0.00 0.00 33.81 4.70
3314 3485 9.817809 GATACAAATCATTACTTACTGAGTCCA 57.182 33.333 0.00 0.00 34.59 4.02
3369 3542 6.881065 GGAAGTAGCTGCATAATCATCCAATA 59.119 38.462 4.12 0.00 0.00 1.90
3477 3650 9.277783 CTGAAACAATCGAGGATAGGAATAAAT 57.722 33.333 0.00 0.00 0.00 1.40
3493 3666 5.633830 TCAGGATTTCTGCTGAAACAATC 57.366 39.130 19.47 13.51 45.62 2.67
3625 3799 4.811557 GTGCAGGATTTTATCGTTAGAGCT 59.188 41.667 0.00 0.00 0.00 4.09
3996 4172 4.340381 CAGGAGCAATTAAGGATTCCTTGG 59.660 45.833 25.26 13.86 44.44 3.61
4067 5273 3.528597 AGACTCCTACGAAATTCAGGC 57.471 47.619 0.00 0.00 0.00 4.85
4074 5280 4.828939 TGACAGGTAAAGACTCCTACGAAA 59.171 41.667 0.00 0.00 32.26 3.46


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

AutoCloner maintained by Alex Coulton.