Multiple sequence alignment - TraesCS3D01G183900

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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 TraesCS3D01G183900 chr3D 100.000 5150 0 0 1 5150 169452001 169446852 0.000000e+00 9511.0
1 TraesCS3D01G183900 chr3A 95.845 4886 138 26 11 4857 197849127 197853986 0.000000e+00 7838.0
2 TraesCS3D01G183900 chr3A 82.849 344 14 12 4798 5139 197853986 197854286 3.060000e-67 267.0
3 TraesCS3D01G183900 chr3A 100.000 31 0 0 4620 4650 197853787 197853817 2.000000e-04 58.4
4 TraesCS3D01G183900 chr3B 96.060 2868 76 15 1836 4688 244385849 244383004 0.000000e+00 4636.0
5 TraesCS3D01G183900 chr3B 92.876 1544 58 23 9 1540 244387390 244385887 0.000000e+00 2194.0
6 TraesCS3D01G183900 chr3B 95.076 528 15 5 4620 5139 244383034 244382510 0.000000e+00 821.0
7 TraesCS3D01G183900 chr3B 88.636 264 29 1 1545 1808 821290091 821289829 2.310000e-83 320.0
8 TraesCS3D01G183900 chr3B 100.000 31 0 0 4620 4650 244382996 244382966 2.000000e-04 58.4
9 TraesCS3D01G183900 chr2D 89.963 269 25 2 1545 1813 120561227 120561493 3.820000e-91 346.0
10 TraesCS3D01G183900 chr2B 89.259 270 29 0 1545 1814 801215314 801215583 6.390000e-89 339.0
11 TraesCS3D01G183900 chr4B 89.179 268 28 1 1545 1812 42938154 42938420 2.970000e-87 333.0
12 TraesCS3D01G183900 chrUn 88.476 269 30 1 1545 1812 87230968 87230700 1.790000e-84 324.0
13 TraesCS3D01G183900 chrUn 88.060 268 31 1 1550 1817 224990314 224990580 2.990000e-82 316.0
14 TraesCS3D01G183900 chr7B 88.973 263 28 1 1549 1810 41043237 41043499 1.790000e-84 324.0
15 TraesCS3D01G183900 chr7D 88.390 267 30 1 1545 1811 37000918 37000653 2.310000e-83 320.0
16 TraesCS3D01G183900 chr5D 84.158 101 11 5 4809 4907 332793976 332794073 5.490000e-15 93.5
17 TraesCS3D01G183900 chr5B 84.524 84 8 4 4826 4907 388912669 388912749 1.540000e-10 78.7


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 TraesCS3D01G183900 chr3D 169446852 169452001 5149 True 9511.000000 9511 100.000 1 5150 1 chr3D.!!$R1 5149
1 TraesCS3D01G183900 chr3A 197849127 197854286 5159 False 2721.133333 7838 92.898 11 5139 3 chr3A.!!$F1 5128
2 TraesCS3D01G183900 chr3B 244382510 244387390 4880 True 1927.350000 4636 96.003 9 5139 4 chr3B.!!$R2 5130

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
462 471 1.202818 GCCCTCACAAAGACTTGACCT 60.203 52.381 0.00 0.00 36.33 3.85 F
801 810 1.401905 CTCCTGGATTTACGCCTTTGC 59.598 52.381 0.00 0.00 0.00 3.68 F
2139 2171 0.613777 CTACTGGAAAAGACCGGGCT 59.386 55.000 2.12 2.12 40.34 5.19 F
2667 2699 1.763968 AGTGATGCTGCTACCGTAGA 58.236 50.000 9.88 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1686 2.910688 AAGAACGTGGTGAGACATGT 57.089 45.000 0.00 0.00 42.10 3.21 R
2667 2699 2.171448 GGAGTTGTGTGAGCAGGGATAT 59.829 50.000 0.00 0.00 0.00 1.63 R
3516 3550 1.556911 CTGGCATAGTCCAGTTCCACT 59.443 52.381 1.80 0.00 46.59 4.00 R
4617 4678 1.394572 TCATCGCTTCAAATGACAGCG 59.605 47.619 22.38 22.38 44.70 5.18 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
60 61 3.449227 AGTAGCAGCGCGCCACTA 61.449 61.111 30.33 25.72 44.04 2.74
61 62 2.508439 GTAGCAGCGCGCCACTAA 60.508 61.111 30.33 7.11 44.04 2.24
63 64 3.289704 TAGCAGCGCGCCACTAACA 62.290 57.895 30.33 7.69 44.04 2.41
161 163 2.427245 CCCGAGGGAGCGAATCAGT 61.427 63.158 0.84 0.00 37.50 3.41
462 471 1.202818 GCCCTCACAAAGACTTGACCT 60.203 52.381 0.00 0.00 36.33 3.85
580 589 1.608717 CTGCTGGTTACCGCTCTCCT 61.609 60.000 16.26 0.00 0.00 3.69
586 595 1.453379 TTACCGCTCTCCTCTCCGG 60.453 63.158 0.00 0.00 45.80 5.14
757 766 2.202676 CCGGCAGAGCTCTCGTTC 60.203 66.667 14.96 3.26 34.09 3.95
801 810 1.401905 CTCCTGGATTTACGCCTTTGC 59.598 52.381 0.00 0.00 0.00 3.68
896 911 4.205484 GATTCGGGGCCCCTTCCC 62.205 72.222 38.17 20.54 45.80 3.97
950 965 2.622903 TAGCGGGGATTCGAGTTGCG 62.623 60.000 0.00 0.00 42.69 4.85
995 1010 2.680913 ATTGCCGTCTCGTTGCAGC 61.681 57.895 0.00 0.00 36.21 5.25
1012 1027 2.856222 CAGCACTAATGGATCCCCTTC 58.144 52.381 9.90 0.00 0.00 3.46
1059 1074 7.075267 AGAGAGGGGGTACTGTAAGATTACTAT 59.925 40.741 4.50 0.00 37.43 2.12
1100 1120 2.788786 GCACAGTTTCAAAATCACCGTG 59.211 45.455 0.00 0.00 0.00 4.94
1144 1164 7.154656 TGTTATTCTTGCGCAGATCATATACT 58.845 34.615 11.31 0.00 0.00 2.12
1214 1234 2.561569 CCAAGGACACTGAACTCGTTT 58.438 47.619 0.00 0.00 0.00 3.60
1344 1364 3.808728 TGCTTCTATATGGTTGCCTGTC 58.191 45.455 4.39 0.00 0.00 3.51
1396 1416 9.244292 AGTATGGAGGAGAAAAAGGTTTATTTC 57.756 33.333 0.00 0.00 36.11 2.17
1402 1422 6.554982 AGGAGAAAAAGGTTTATTTCCTGCTT 59.445 34.615 0.00 0.00 36.44 3.91
1404 1424 6.759272 AGAAAAAGGTTTATTTCCTGCTTCC 58.241 36.000 0.00 0.00 36.44 3.46
1444 1464 5.363580 TCTTTTCCACAAATTGAGCCTTCTT 59.636 36.000 0.00 0.00 0.00 2.52
1651 1672 9.780413 GGCTTGTCTTCTCTTATTTAAGAAATG 57.220 33.333 1.97 0.00 41.37 2.32
1676 1697 5.784177 TCTCTTAGAACAACATGTCTCACC 58.216 41.667 0.00 0.00 0.00 4.02
1771 1792 7.392953 TGTCATTTCTAAATTACATGCAGGACA 59.607 33.333 4.84 0.00 30.08 4.02
1890 1922 7.730364 TTTTCTTTGTCAGTACTCATCCTTC 57.270 36.000 0.00 0.00 0.00 3.46
1933 1965 5.712217 TTCTGTTTTTAGTATCCGATGCG 57.288 39.130 0.00 0.00 0.00 4.73
2139 2171 0.613777 CTACTGGAAAAGACCGGGCT 59.386 55.000 2.12 2.12 40.34 5.19
2313 2345 7.560368 TGTACCAACAATTGAGGTTTCAAAAT 58.440 30.769 24.78 7.26 45.82 1.82
2347 2379 3.594134 ACAAACAGCATGAGAGAGCTAC 58.406 45.455 0.00 0.00 39.50 3.58
2352 2384 3.004210 ACAGCATGAGAGAGCTACATACG 59.996 47.826 0.00 0.00 39.50 3.06
2357 2389 4.634184 TGAGAGAGCTACATACGTTTCC 57.366 45.455 0.00 0.00 0.00 3.13
2373 2405 6.811253 ACGTTTCCTTGCATCTTTTACATA 57.189 33.333 0.00 0.00 0.00 2.29
2667 2699 1.763968 AGTGATGCTGCTACCGTAGA 58.236 50.000 9.88 0.00 0.00 2.59
2737 2769 2.349886 GCTGGAAGAACTGCTTGATACG 59.650 50.000 0.00 0.00 36.83 3.06
2829 2861 4.923281 TGCTGAATCATCGGTATGTTATCG 59.077 41.667 0.00 0.00 34.20 2.92
3237 3270 2.846193 TGTTCTGAACCTGGTGTTAGC 58.154 47.619 17.26 0.00 37.29 3.09
3265 3298 8.512138 GCTTGTCAATTCCTTAAACTAGCTTAA 58.488 33.333 0.00 0.00 36.32 1.85
3516 3550 4.954933 GGTGCTATGGCTCCGAAA 57.045 55.556 6.39 0.00 41.35 3.46
3961 3995 5.735892 CAGAAGAAACATGTGCGTGATATTG 59.264 40.000 0.00 0.00 0.00 1.90
4212 4246 3.275999 TCTGTAGCATCTACGCACTGTA 58.724 45.455 0.00 0.00 0.00 2.74
4253 4293 3.247173 GTGATTGAAGTGGATGAGCGATC 59.753 47.826 0.00 0.00 0.00 3.69
4363 4423 5.581605 CATGGTGTTTGTACATATGAAGCC 58.418 41.667 10.38 0.00 35.46 4.35
4463 4524 9.123709 GAATAATAGCTGTGATAAGTTCTCTCG 57.876 37.037 0.00 0.00 0.00 4.04
4675 4774 3.935203 ACTACTGTCATTTGAAGCGATGG 59.065 43.478 0.00 0.00 0.00 3.51
4795 4894 5.182950 TGTCTATTGATTTGCACGGTGATTT 59.817 36.000 13.29 0.00 0.00 2.17
4824 4923 3.452474 TGTTTTGACGGAAATTGCTTGG 58.548 40.909 0.00 0.00 0.00 3.61
5035 5198 8.017946 CCTTCTTTCTTAAACCGATTCTCTTTG 58.982 37.037 0.00 0.00 0.00 2.77
5038 5201 6.817765 TTCTTAAACCGATTCTCTTTGCAT 57.182 33.333 0.00 0.00 0.00 3.96
5106 5269 1.346479 TTCCGGTGTCACCTTTCCCA 61.346 55.000 19.82 0.00 35.66 4.37
5139 5302 3.748568 GCGTCATCTGACTTCTTCCTTTT 59.251 43.478 8.57 0.00 42.66 2.27
5140 5303 4.214332 GCGTCATCTGACTTCTTCCTTTTT 59.786 41.667 8.57 0.00 42.66 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.359848 CTTGGCATACCGAGTGTCAC 58.640 55.000 0.00 0.00 42.03 3.67
1 2 0.249120 CCTTGGCATACCGAGTGTCA 59.751 55.000 0.00 0.00 45.17 3.58
2 3 1.090052 GCCTTGGCATACCGAGTGTC 61.090 60.000 6.79 0.00 45.17 3.67
3 4 1.078426 GCCTTGGCATACCGAGTGT 60.078 57.895 6.79 0.00 45.17 3.55
4 5 0.392998 AAGCCTTGGCATACCGAGTG 60.393 55.000 14.54 0.00 45.17 3.51
5 6 0.107654 GAAGCCTTGGCATACCGAGT 60.108 55.000 14.54 0.00 45.17 4.18
6 7 0.107703 TGAAGCCTTGGCATACCGAG 60.108 55.000 14.54 0.00 46.10 4.63
7 8 0.326595 TTGAAGCCTTGGCATACCGA 59.673 50.000 14.54 0.00 39.70 4.69
52 53 0.663269 GTGGCTTTTGTTAGTGGCGC 60.663 55.000 0.00 0.00 0.00 6.53
60 61 3.933332 GTCTAGCTATCGTGGCTTTTGTT 59.067 43.478 0.00 0.00 40.74 2.83
61 62 3.195825 AGTCTAGCTATCGTGGCTTTTGT 59.804 43.478 0.00 0.00 40.74 2.83
63 64 4.184629 CAAGTCTAGCTATCGTGGCTTTT 58.815 43.478 0.00 0.00 40.74 2.27
161 163 2.577059 GTCAAGCCGTCGGATCCA 59.423 61.111 17.49 0.00 0.00 3.41
462 471 4.373116 GAGGCGGTCGCAGGAACA 62.373 66.667 17.21 0.00 44.11 3.18
617 626 4.135153 GGAGAGCAGAAGCCGCGA 62.135 66.667 8.23 0.00 43.56 5.87
670 679 0.463833 AACGGAATGGATCGGGAAGC 60.464 55.000 0.00 0.00 32.91 3.86
757 766 1.463444 CAAAACCTCGAGCCCTAAACG 59.537 52.381 6.99 0.00 0.00 3.60
801 810 0.910088 AAACTCTCCTCCCCTTCCCG 60.910 60.000 0.00 0.00 0.00 5.14
898 913 3.053896 CAACGGGCCGAGGTTTCC 61.054 66.667 35.78 0.00 0.00 3.13
995 1010 2.780010 ACCAGAAGGGGATCCATTAGTG 59.220 50.000 15.23 8.56 42.91 2.74
1012 1027 0.246635 CCCTTACTCCACACGACCAG 59.753 60.000 0.00 0.00 0.00 4.00
1059 1074 6.999950 TGTGCAGAGTAATTAGAACCACTTA 58.000 36.000 0.00 0.00 0.00 2.24
1100 1120 9.422196 GAATAACAGAACACAAATACGATTAGC 57.578 33.333 0.00 0.00 0.00 3.09
1144 1164 4.679639 GCCATGTCACGTAGAGTTTCCATA 60.680 45.833 0.00 0.00 0.00 2.74
1270 1290 6.933514 TCATGCTTGTATATATCCACCTCA 57.066 37.500 0.00 0.00 0.00 3.86
1387 1407 7.555965 ACAAATATGGAAGCAGGAAATAAACC 58.444 34.615 0.00 0.00 0.00 3.27
1396 1416 6.515272 ACAAAGTACAAATATGGAAGCAGG 57.485 37.500 0.00 0.00 0.00 4.85
1402 1422 9.137459 TGGAAAAGAACAAAGTACAAATATGGA 57.863 29.630 0.00 0.00 0.00 3.41
1404 1424 9.743057 TGTGGAAAAGAACAAAGTACAAATATG 57.257 29.630 0.00 0.00 0.00 1.78
1651 1672 6.533367 GGTGAGACATGTTGTTCTAAGAGATC 59.467 42.308 0.00 0.00 0.00 2.75
1665 1686 2.910688 AAGAACGTGGTGAGACATGT 57.089 45.000 0.00 0.00 42.10 3.21
1721 1742 7.039082 ACAATAAAAGCATGTCTACAATGGGTT 60.039 33.333 0.00 0.00 0.00 4.11
1764 1785 6.155475 AGACAGTCTTATCTTATGTCCTGC 57.845 41.667 0.00 0.00 40.88 4.85
1852 1884 5.949735 ACAAAGAAAATACACCATTAGCGG 58.050 37.500 0.00 0.00 0.00 5.52
1890 1922 7.657761 ACAGAAAGTAAATCCTCTATAATGCCG 59.342 37.037 0.00 0.00 0.00 5.69
1933 1965 6.535508 AGAACACGGCAGATAAAATCTAGAAC 59.464 38.462 0.00 0.00 37.58 3.01
2139 2171 3.968649 TGGTCCGCTTATCCACCTTAATA 59.031 43.478 0.00 0.00 0.00 0.98
2327 2359 3.593096 TGTAGCTCTCTCATGCTGTTTG 58.407 45.455 0.00 0.00 40.08 2.93
2347 2379 6.607689 TGTAAAAGATGCAAGGAAACGTATG 58.392 36.000 0.00 0.00 0.00 2.39
2667 2699 2.171448 GGAGTTGTGTGAGCAGGGATAT 59.829 50.000 0.00 0.00 0.00 1.63
2737 2769 4.393371 GTGTTAGCAGAAGGATCAAAGGAC 59.607 45.833 0.00 0.00 0.00 3.85
2829 2861 2.370281 TACTAAGCACTGCTGTGAGC 57.630 50.000 25.94 12.41 46.55 4.26
3237 3270 6.150140 AGCTAGTTTAAGGAATTGACAAGCTG 59.850 38.462 0.00 0.00 34.36 4.24
3265 3298 4.508662 GACAAAGGAGTAGCACTAGCAAT 58.491 43.478 0.00 0.00 45.49 3.56
3266 3299 3.306780 GGACAAAGGAGTAGCACTAGCAA 60.307 47.826 0.00 0.00 45.49 3.91
3516 3550 1.556911 CTGGCATAGTCCAGTTCCACT 59.443 52.381 1.80 0.00 46.59 4.00
4253 4293 2.110967 CCAGAAGGCCACATGCTCG 61.111 63.158 5.01 0.00 40.92 5.03
4363 4423 3.613432 GCCAGACTGATCAAAAAGCAAGG 60.613 47.826 3.32 0.00 0.00 3.61
4463 4524 7.278868 AGAGTTACAAATCTAGCATGCAGTAAC 59.721 37.037 21.98 21.47 39.95 2.50
4560 4621 8.240682 AGTGAGATGATGATTATTACTCGCTAC 58.759 37.037 0.00 0.00 40.35 3.58
4617 4678 1.394572 TCATCGCTTCAAATGACAGCG 59.605 47.619 22.38 22.38 44.70 5.18
4675 4774 0.316204 ATGTCAGCAAGCAAACAGGC 59.684 50.000 0.00 0.00 0.00 4.85
4795 4894 0.394488 TCCGTCAAAACAAGTGCCCA 60.394 50.000 0.00 0.00 0.00 5.36
4887 5048 2.415090 CGAGAACGGTTGGACGAAGTAT 60.415 50.000 0.00 0.00 36.92 2.12
4888 5049 1.069022 CGAGAACGGTTGGACGAAGTA 60.069 52.381 0.00 0.00 36.92 2.24
4889 5050 0.318445 CGAGAACGGTTGGACGAAGT 60.318 55.000 0.00 0.00 38.95 3.01
5035 5198 5.707242 ATCAATGGATGAGACATGAATGC 57.293 39.130 0.00 0.00 42.53 3.56
5038 5201 8.756486 AACAATATCAATGGATGAGACATGAA 57.244 30.769 0.00 0.00 42.53 2.57
5106 5269 3.184581 GTCAGATGACGCGAAAAAGAGTT 59.815 43.478 15.93 0.00 35.12 3.01


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

AutoCloner maintained by Alex Coulton.