Multiple sequence alignment - TraesCS7D01G135400

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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 TraesCS7D01G135400 chr7D 100.000 2975 0 0 1 2975 86917649 86920623 0.000000e+00 5494.0
1 TraesCS7D01G135400 chr7D 97.704 1916 38 4 811 2722 86754970 86756883 0.000000e+00 3290.0
2 TraesCS7D01G135400 chr7D 91.182 1633 97 13 1382 2975 87206912 87208536 0.000000e+00 2174.0
3 TraesCS7D01G135400 chr7D 94.718 833 18 5 1 810 86895165 86895994 0.000000e+00 1271.0
4 TraesCS7D01G135400 chr7D 92.280 842 34 9 1 813 106942251 106941412 0.000000e+00 1166.0
5 TraesCS7D01G135400 chr7D 87.037 864 64 25 3 831 492181454 492182304 0.000000e+00 931.0
6 TraesCS7D01G135400 chr7D 85.078 898 77 24 2120 2975 86293459 86294341 0.000000e+00 863.0
7 TraesCS7D01G135400 chr7D 92.476 412 22 5 2572 2975 86796658 86797068 5.530000e-162 580.0
8 TraesCS7D01G135400 chr7D 90.000 380 25 7 834 1206 87220317 87220690 2.070000e-131 479.0
9 TraesCS7D01G135400 chr7D 95.720 257 10 1 2719 2975 86760522 86760777 2.130000e-111 412.0
10 TraesCS7D01G135400 chr7D 97.382 191 4 1 1201 1390 87206698 87206888 1.030000e-84 324.0
11 TraesCS7D01G135400 chr7D 96.316 190 7 0 1201 1390 87220731 87220920 2.230000e-81 313.0
12 TraesCS7D01G135400 chr7D 90.909 220 10 5 990 1206 87206445 87206657 1.350000e-73 287.0
13 TraesCS7D01G135400 chr7D 93.651 189 11 1 2388 2575 86784481 86784669 6.280000e-72 281.0
14 TraesCS7D01G135400 chr7D 77.477 111 22 3 2198 2307 85354450 85354342 2.480000e-06 63.9
15 TraesCS7D01G135400 chr7A 89.277 2145 165 41 868 2975 87451162 87453278 0.000000e+00 2627.0
16 TraesCS7D01G135400 chr7A 91.010 1624 95 20 1382 2975 88436371 88437973 0.000000e+00 2143.0
17 TraesCS7D01G135400 chr7A 91.279 1353 87 9 1382 2713 88315962 88317304 0.000000e+00 1816.0
18 TraesCS7D01G135400 chr7A 88.889 1350 89 18 1677 2975 88122403 88123742 0.000000e+00 1605.0
19 TraesCS7D01G135400 chr7A 88.601 1351 92 19 1677 2975 88173170 88174510 0.000000e+00 1585.0
20 TraesCS7D01G135400 chr7A 88.453 1351 93 18 1677 2975 88009123 88010462 0.000000e+00 1572.0
21 TraesCS7D01G135400 chr7A 84.830 824 93 26 1 810 449617240 449618045 0.000000e+00 800.0
22 TraesCS7D01G135400 chr7A 96.725 397 13 0 1201 1597 88172773 88173169 0.000000e+00 662.0
23 TraesCS7D01G135400 chr7A 96.725 397 12 1 1201 1597 88008727 88009122 0.000000e+00 660.0
24 TraesCS7D01G135400 chr7A 90.237 379 23 9 834 1206 88435740 88436110 1.600000e-132 483.0
25 TraesCS7D01G135400 chr7A 89.646 396 16 5 811 1206 88008311 88008681 5.770000e-132 481.0
26 TraesCS7D01G135400 chr7A 89.974 379 25 8 834 1206 88500109 88500480 7.460000e-131 477.0
27 TraesCS7D01G135400 chr7A 90.175 285 19 3 2700 2975 88318624 88318908 2.180000e-96 363.0
28 TraesCS7D01G135400 chr7A 95.812 191 7 1 1201 1390 88315748 88315938 1.040000e-79 307.0
29 TraesCS7D01G135400 chr7A 95.745 188 7 1 1201 1388 88436157 88436343 4.820000e-78 302.0
30 TraesCS7D01G135400 chr7A 95.745 188 7 1 1201 1388 88500527 88500713 4.820000e-78 302.0
31 TraesCS7D01G135400 chr7A 86.111 288 13 12 919 1206 88172467 88172727 4.850000e-73 285.0
32 TraesCS7D01G135400 chr7A 88.936 235 15 6 976 1206 88315480 88315707 2.260000e-71 279.0
33 TraesCS7D01G135400 chr7A 91.667 180 13 2 811 990 88121330 88121507 6.370000e-62 248.0
34 TraesCS7D01G135400 chr7B 89.808 1825 116 27 1201 2975 35507525 35509329 0.000000e+00 2276.0
35 TraesCS7D01G135400 chr7B 87.888 1643 106 38 1382 2975 35308069 35309667 0.000000e+00 1845.0
36 TraesCS7D01G135400 chr7B 93.925 428 24 2 1382 1808 35637813 35638239 0.000000e+00 645.0
37 TraesCS7D01G135400 chr7B 88.281 384 26 9 834 1206 35507103 35507478 2.720000e-120 442.0
38 TraesCS7D01G135400 chr7B 86.329 395 30 13 834 1206 35637161 35637553 2.760000e-110 409.0
39 TraesCS7D01G135400 chr7B 95.789 190 8 0 1201 1390 35637600 35637789 1.040000e-79 307.0
40 TraesCS7D01G135400 chr7B 87.662 154 15 4 854 1006 35301965 35302115 3.050000e-40 176.0
41 TraesCS7D01G135400 chr5D 92.721 838 32 9 1 811 309634385 309635220 0.000000e+00 1182.0
42 TraesCS7D01G135400 chr4D 92.253 839 33 10 1 810 299302569 299301734 0.000000e+00 1160.0
43 TraesCS7D01G135400 chr4D 92.089 809 46 16 1 798 180141724 180142525 0.000000e+00 1123.0
44 TraesCS7D01G135400 chr1D 90.676 858 46 12 3 829 423471263 423470409 0.000000e+00 1110.0
45 TraesCS7D01G135400 chr1D 88.594 868 59 17 3 836 342100373 342101234 0.000000e+00 1018.0
46 TraesCS7D01G135400 chr6D 89.273 867 54 17 3 835 113393919 113394780 0.000000e+00 1050.0
47 TraesCS7D01G135400 chr6D 88.700 823 67 20 1 810 239672589 239671780 0.000000e+00 981.0
48 TraesCS7D01G135400 chr4A 83.859 824 110 16 1 810 390369373 390370187 0.000000e+00 763.0
49 TraesCS7D01G135400 chr6A 82.473 833 95 41 1 810 523484632 523483828 0.000000e+00 682.0


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 TraesCS7D01G135400 chr7D 86917649 86920623 2974 False 5494.000000 5494 100.000000 1 2975 1 chr7D.!!$F5 2974
1 TraesCS7D01G135400 chr7D 86754970 86760777 5807 False 1851.000000 3290 96.712000 811 2975 2 chr7D.!!$F7 2164
2 TraesCS7D01G135400 chr7D 86895165 86895994 829 False 1271.000000 1271 94.718000 1 810 1 chr7D.!!$F4 809
3 TraesCS7D01G135400 chr7D 106941412 106942251 839 True 1166.000000 1166 92.280000 1 813 1 chr7D.!!$R2 812
4 TraesCS7D01G135400 chr7D 492181454 492182304 850 False 931.000000 931 87.037000 3 831 1 chr7D.!!$F6 828
5 TraesCS7D01G135400 chr7D 87206445 87208536 2091 False 928.333333 2174 93.157667 990 2975 3 chr7D.!!$F8 1985
6 TraesCS7D01G135400 chr7D 86293459 86294341 882 False 863.000000 863 85.078000 2120 2975 1 chr7D.!!$F1 855
7 TraesCS7D01G135400 chr7D 87220317 87220920 603 False 396.000000 479 93.158000 834 1390 2 chr7D.!!$F9 556
8 TraesCS7D01G135400 chr7A 87451162 87453278 2116 False 2627.000000 2627 89.277000 868 2975 1 chr7A.!!$F1 2107
9 TraesCS7D01G135400 chr7A 88435740 88437973 2233 False 976.000000 2143 92.330667 834 2975 3 chr7A.!!$F7 2141
10 TraesCS7D01G135400 chr7A 88121330 88123742 2412 False 926.500000 1605 90.278000 811 2975 2 chr7A.!!$F4 2164
11 TraesCS7D01G135400 chr7A 88008311 88010462 2151 False 904.333333 1572 91.608000 811 2975 3 chr7A.!!$F3 2164
12 TraesCS7D01G135400 chr7A 88172467 88174510 2043 False 844.000000 1585 90.479000 919 2975 3 chr7A.!!$F5 2056
13 TraesCS7D01G135400 chr7A 449617240 449618045 805 False 800.000000 800 84.830000 1 810 1 chr7A.!!$F2 809
14 TraesCS7D01G135400 chr7A 88315480 88318908 3428 False 691.250000 1816 91.550500 976 2975 4 chr7A.!!$F6 1999
15 TraesCS7D01G135400 chr7A 88500109 88500713 604 False 389.500000 477 92.859500 834 1388 2 chr7A.!!$F8 554
16 TraesCS7D01G135400 chr7B 35308069 35309667 1598 False 1845.000000 1845 87.888000 1382 2975 1 chr7B.!!$F2 1593
17 TraesCS7D01G135400 chr7B 35507103 35509329 2226 False 1359.000000 2276 89.044500 834 2975 2 chr7B.!!$F3 2141
18 TraesCS7D01G135400 chr7B 35637161 35638239 1078 False 453.666667 645 92.014333 834 1808 3 chr7B.!!$F4 974
19 TraesCS7D01G135400 chr5D 309634385 309635220 835 False 1182.000000 1182 92.721000 1 811 1 chr5D.!!$F1 810
20 TraesCS7D01G135400 chr4D 299301734 299302569 835 True 1160.000000 1160 92.253000 1 810 1 chr4D.!!$R1 809
21 TraesCS7D01G135400 chr4D 180141724 180142525 801 False 1123.000000 1123 92.089000 1 798 1 chr4D.!!$F1 797
22 TraesCS7D01G135400 chr1D 423470409 423471263 854 True 1110.000000 1110 90.676000 3 829 1 chr1D.!!$R1 826
23 TraesCS7D01G135400 chr1D 342100373 342101234 861 False 1018.000000 1018 88.594000 3 836 1 chr1D.!!$F1 833
24 TraesCS7D01G135400 chr6D 113393919 113394780 861 False 1050.000000 1050 89.273000 3 835 1 chr6D.!!$F1 832
25 TraesCS7D01G135400 chr6D 239671780 239672589 809 True 981.000000 981 88.700000 1 810 1 chr6D.!!$R1 809
26 TraesCS7D01G135400 chr4A 390369373 390370187 814 False 763.000000 763 83.859000 1 810 1 chr4A.!!$F1 809
27 TraesCS7D01G135400 chr6A 523483828 523484632 804 True 682.000000 682 82.473000 1 810 1 chr6A.!!$R1 809

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
922 982 0.107897 CAGTGTGCGGGCCACTATAA 60.108 55.0 4.39 0.0 44.92 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 3076 0.878961 GTTCACCAGTCACACGGGAC 60.879 60.0 0.0 0.0 36.9 4.46 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
262 271 7.684529 AGTAGTTTCAGGATCACTTCTTGATT 58.315 34.615 0.00 0.00 45.67 2.57
404 418 5.116377 GCTTAAATAGTCTTGATCTCGCGAG 59.884 44.000 30.03 30.03 0.00 5.03
493 511 4.701663 CAGGTGATGCAACCGAGT 57.298 55.556 1.88 0.00 45.53 4.18
552 570 4.578516 TGTGTTTCGTTTCCTGTTGATCAT 59.421 37.500 0.00 0.00 0.00 2.45
728 781 4.082125 GGATTGTGTGAAGATGACCCTTT 58.918 43.478 0.00 0.00 0.00 3.11
793 847 2.240279 GACACGTGGGAGATATAGCCT 58.760 52.381 21.57 0.00 0.00 4.58
913 973 3.027170 GCGATGAACAGTGTGCGGG 62.027 63.158 0.00 0.00 0.00 6.13
922 982 0.107897 CAGTGTGCGGGCCACTATAA 60.108 55.000 4.39 0.00 44.92 0.98
1061 1450 2.490217 CGAATGGCGTCGACCTCT 59.510 61.111 10.58 0.00 43.86 3.69
1599 2167 2.559231 GAGTGACTCGGAGAAGAAAGGT 59.441 50.000 12.86 0.00 34.09 3.50
1904 2559 3.733337 GTGATCTCCACACAGTTGTCTT 58.267 45.455 0.00 0.00 45.03 3.01
1977 2633 7.762159 TGAGTATGCGTGTCAATATTCAAGTTA 59.238 33.333 0.00 0.00 0.00 2.24
2193 2859 7.276438 GGCTTTATTATTTCAACAGAGGCTTTG 59.724 37.037 3.08 3.08 0.00 2.77
2195 2861 9.346725 CTTTATTATTTCAACAGAGGCTTTGTC 57.653 33.333 11.46 0.00 0.00 3.18
2276 2944 0.252103 TCGAAGTAGAAGGTGCCCCT 60.252 55.000 0.00 0.00 45.63 4.79
2408 3076 3.125573 TCGACGTCTCGGCCTCTG 61.126 66.667 14.70 0.00 40.58 3.35
2505 3195 6.297418 CCCCCTTTTAGAGGTAACATTAAGGT 60.297 42.308 0.00 0.00 44.71 3.50
2506 3196 6.827251 CCCCTTTTAGAGGTAACATTAAGGTC 59.173 42.308 0.00 0.00 44.71 3.85
2511 3202 8.431910 TTTAGAGGTAACATTAAGGTCTGAGT 57.568 34.615 0.00 0.00 41.41 3.41
2533 3224 2.674380 CTGAACAGGGCCTGGCAC 60.674 66.667 35.34 24.64 35.51 5.01
2660 3381 0.615331 GCTCCCATCACTCAACCTCA 59.385 55.000 0.00 0.00 0.00 3.86
2819 8526 5.446473 GCACTATACATGACAGAAGCAACAC 60.446 44.000 0.00 0.00 0.00 3.32
2823 8530 1.198408 CATGACAGAAGCAACACGCAT 59.802 47.619 0.00 0.00 46.13 4.73
2850 8559 7.909641 GCATAAAAACAGTGCAAAGACAAAAAT 59.090 29.630 0.00 0.00 38.68 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
404 418 3.733337 AGGACTCAACAATCTCACACAC 58.267 45.455 0.00 0.00 0.00 3.82
493 511 1.000607 CTCGTCGAACTCCCACTTGAA 60.001 52.381 0.00 0.00 0.00 2.69
728 781 1.929836 GCATTGTGGTTTTGTCGCAAA 59.070 42.857 1.63 1.63 38.00 3.68
793 847 1.447140 GCTGTAACGCCCACGATGA 60.447 57.895 0.00 0.00 43.93 2.92
913 973 5.151389 CAGTTCCAAAACGTTTATAGTGGC 58.849 41.667 20.02 10.40 40.48 5.01
922 982 1.470805 GCCTTGCAGTTCCAAAACGTT 60.471 47.619 0.00 0.00 40.48 3.99
1061 1450 5.185635 CACAATCTTTCCCAAATCCAAGCTA 59.814 40.000 0.00 0.00 0.00 3.32
1599 2167 1.500474 GGATCTCCATCACCACAGGA 58.500 55.000 0.00 0.00 35.64 3.86
1904 2559 1.272490 CACAAACGTCCTCAGAGGCTA 59.728 52.381 12.26 0.00 34.61 3.93
2276 2944 1.890041 CGTGTGCCGGAACCAGAAA 60.890 57.895 11.01 0.00 0.00 2.52
2329 2997 3.870559 ACTAGGAGACCAGGAAAGGAAA 58.129 45.455 0.00 0.00 0.00 3.13
2408 3076 0.878961 GTTCACCAGTCACACGGGAC 60.879 60.000 0.00 0.00 36.90 4.46
2505 3195 2.242926 CCCTGTTCAGAGTCACTCAGA 58.757 52.381 7.77 0.71 32.06 3.27
2506 3196 1.337635 GCCCTGTTCAGAGTCACTCAG 60.338 57.143 7.77 0.00 32.06 3.35
2511 3202 1.483595 CCAGGCCCTGTTCAGAGTCA 61.484 60.000 10.47 0.00 0.00 3.41
2533 3224 3.135225 TGAAATTACCCATACCGCATCG 58.865 45.455 0.00 0.00 0.00 3.84
2660 3381 5.048846 TCTTTCAAAAAGTGCCTCCTAGT 57.951 39.130 0.00 0.00 0.00 2.57
2819 8526 2.326664 TGCACTGTTTTTATGCATGCG 58.673 42.857 14.09 0.00 44.17 4.73
2850 8559 5.474189 CCTTGTCGTTTTCCCCAATTAGTTA 59.526 40.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.