Multiple sequence alignment - TraesCS7D01G018400

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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 TraesCS7D01G018400 chr7D 100.000 2966 0 0 1 2966 8222605 8225570 0.000000e+00 5478.0
1 TraesCS7D01G018400 chr7D 85.552 1675 190 21 473 2126 8256332 8254689 0.000000e+00 1705.0
2 TraesCS7D01G018400 chr7D 85.161 1678 194 27 473 2126 7924050 7925696 0.000000e+00 1668.0
3 TraesCS7D01G018400 chr7D 86.585 1394 166 14 751 2126 7749976 7751366 0.000000e+00 1519.0
4 TraesCS7D01G018400 chr7D 85.786 1393 182 5 748 2126 8030614 8032004 0.000000e+00 1461.0
5 TraesCS7D01G018400 chr7D 84.370 1382 192 15 761 2123 7561062 7562438 0.000000e+00 1334.0
6 TraesCS7D01G018400 chr7D 87.176 850 103 4 2123 2966 8254658 8253809 0.000000e+00 961.0
7 TraesCS7D01G018400 chr7D 85.225 846 122 2 2124 2966 7925728 7926573 0.000000e+00 867.0
8 TraesCS7D01G018400 chr7D 84.906 848 115 7 2123 2959 8086696 8087541 0.000000e+00 845.0
9 TraesCS7D01G018400 chr7D 79.385 325 52 12 100 417 7532964 7532648 6.440000e-52 215.0
10 TraesCS7D01G018400 chr7D 93.333 60 4 0 697 756 7637603 7637662 4.070000e-14 89.8
11 TraesCS7D01G018400 chr4A 96.338 1420 34 6 739 2140 731664164 731662745 0.000000e+00 2318.0
12 TraesCS7D01G018400 chr4A 84.283 1966 232 23 229 2126 731851993 731850037 0.000000e+00 1847.0
13 TraesCS7D01G018400 chr4A 85.705 1532 191 9 609 2120 732354657 732356180 0.000000e+00 1591.0
14 TraesCS7D01G018400 chr4A 98.223 844 15 0 2123 2966 731662732 731661889 0.000000e+00 1476.0
15 TraesCS7D01G018400 chr4A 85.642 1393 184 9 748 2126 732378026 732379416 0.000000e+00 1450.0
16 TraesCS7D01G018400 chr4A 84.426 1464 187 17 697 2123 731616944 731615485 0.000000e+00 1402.0
17 TraesCS7D01G018400 chr4A 81.910 1675 254 23 473 2123 732105177 732106826 0.000000e+00 1369.0
18 TraesCS7D01G018400 chr4A 97.158 739 20 1 1 738 731665053 731664315 0.000000e+00 1247.0
19 TraesCS7D01G018400 chr4A 82.082 1172 191 8 609 1765 732408771 732409938 0.000000e+00 983.0
20 TraesCS7D01G018400 chr4A 87.603 847 102 2 2123 2966 731615452 731614606 0.000000e+00 979.0
21 TraesCS7D01G018400 chr4A 83.048 1050 126 23 473 1496 731604517 731603494 0.000000e+00 905.0
22 TraesCS7D01G018400 chr4A 84.806 849 121 7 2123 2966 731501988 731501143 0.000000e+00 846.0
23 TraesCS7D01G018400 chr4A 89.850 266 24 1 11 273 732384606 732384871 3.660000e-89 339.0
24 TraesCS7D01G018400 chr7A 86.254 1957 200 27 234 2126 56204321 56206272 0.000000e+00 2060.0
25 TraesCS7D01G018400 chr7A 85.048 1672 193 27 473 2120 8695360 8693722 0.000000e+00 1650.0
26 TraesCS7D01G018400 chr7A 84.129 1424 194 20 713 2120 8634262 8635669 0.000000e+00 1349.0
27 TraesCS7D01G018400 chr7A 86.588 850 108 4 2123 2966 8693685 8692836 0.000000e+00 933.0
28 TraesCS7D01G018400 chr7A 85.998 857 106 7 2123 2966 3430722 3429867 0.000000e+00 905.0
29 TraesCS7D01G018400 chr7A 84.545 660 87 11 2124 2776 8591598 8592249 8.960000e-180 640.0
30 TraesCS7D01G018400 chr7A 78.571 252 45 7 473 717 8589464 8589713 1.100000e-34 158.0
31 TraesCS7D01G018400 chr3B 85.694 1391 175 17 748 2120 741463142 741464526 0.000000e+00 1445.0
32 TraesCS7D01G018400 chr3B 85.294 850 119 4 2123 2966 741464563 741465412 0.000000e+00 872.0


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 TraesCS7D01G018400 chr7D 8222605 8225570 2965 False 5478.000000 5478 100.000000 1 2966 1 chr7D.!!$F6 2965
1 TraesCS7D01G018400 chr7D 7749976 7751366 1390 False 1519.000000 1519 86.585000 751 2126 1 chr7D.!!$F3 1375
2 TraesCS7D01G018400 chr7D 8030614 8032004 1390 False 1461.000000 1461 85.786000 748 2126 1 chr7D.!!$F4 1378
3 TraesCS7D01G018400 chr7D 7561062 7562438 1376 False 1334.000000 1334 84.370000 761 2123 1 chr7D.!!$F1 1362
4 TraesCS7D01G018400 chr7D 8253809 8256332 2523 True 1333.000000 1705 86.364000 473 2966 2 chr7D.!!$R2 2493
5 TraesCS7D01G018400 chr7D 7924050 7926573 2523 False 1267.500000 1668 85.193000 473 2966 2 chr7D.!!$F7 2493
6 TraesCS7D01G018400 chr7D 8086696 8087541 845 False 845.000000 845 84.906000 2123 2959 1 chr7D.!!$F5 836
7 TraesCS7D01G018400 chr4A 731850037 731851993 1956 True 1847.000000 1847 84.283000 229 2126 1 chr4A.!!$R3 1897
8 TraesCS7D01G018400 chr4A 731661889 731665053 3164 True 1680.333333 2318 97.239667 1 2966 3 chr4A.!!$R5 2965
9 TraesCS7D01G018400 chr4A 732354657 732356180 1523 False 1591.000000 1591 85.705000 609 2120 1 chr4A.!!$F2 1511
10 TraesCS7D01G018400 chr4A 732378026 732379416 1390 False 1450.000000 1450 85.642000 748 2126 1 chr4A.!!$F3 1378
11 TraesCS7D01G018400 chr4A 732105177 732106826 1649 False 1369.000000 1369 81.910000 473 2123 1 chr4A.!!$F1 1650
12 TraesCS7D01G018400 chr4A 731614606 731616944 2338 True 1190.500000 1402 86.014500 697 2966 2 chr4A.!!$R4 2269
13 TraesCS7D01G018400 chr4A 732408771 732409938 1167 False 983.000000 983 82.082000 609 1765 1 chr4A.!!$F5 1156
14 TraesCS7D01G018400 chr4A 731603494 731604517 1023 True 905.000000 905 83.048000 473 1496 1 chr4A.!!$R2 1023
15 TraesCS7D01G018400 chr4A 731501143 731501988 845 True 846.000000 846 84.806000 2123 2966 1 chr4A.!!$R1 843
16 TraesCS7D01G018400 chr7A 56204321 56206272 1951 False 2060.000000 2060 86.254000 234 2126 1 chr7A.!!$F2 1892
17 TraesCS7D01G018400 chr7A 8634262 8635669 1407 False 1349.000000 1349 84.129000 713 2120 1 chr7A.!!$F1 1407
18 TraesCS7D01G018400 chr7A 8692836 8695360 2524 True 1291.500000 1650 85.818000 473 2966 2 chr7A.!!$R2 2493
19 TraesCS7D01G018400 chr7A 3429867 3430722 855 True 905.000000 905 85.998000 2123 2966 1 chr7A.!!$R1 843
20 TraesCS7D01G018400 chr7A 8589464 8592249 2785 False 399.000000 640 81.558000 473 2776 2 chr7A.!!$F3 2303
21 TraesCS7D01G018400 chr3B 741463142 741465412 2270 False 1158.500000 1445 85.494000 748 2966 2 chr3B.!!$F1 2218

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
613 669 1.270305 TGCTCCTCTTCGGTTGTTCTG 60.270 52.381 0.00 0.0 0.00 3.02 F
911 1568 1.739196 GCTGCAGACGCACTCATCA 60.739 57.895 20.43 0.0 45.36 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1442 2141 5.939764 ATACACCATCTTAGCAAGAGTCA 57.060 39.130 0.0 0.0 41.61 3.41 R
2336 3089 7.281774 CAGTTCTCCTATACTTGCACATTCATT 59.718 37.037 0.0 0.0 0.00 2.57 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
132 133 2.223971 ACCGTTAGTGACACAAGTGAGG 60.224 50.000 8.59 5.91 0.00 3.86
153 154 7.963532 TGAGGAAAGTCTTCACAGTAACTATT 58.036 34.615 0.00 0.00 32.75 1.73
186 187 8.049117 TGTGCTATCTAGAAGTTGGAAAATGAT 58.951 33.333 0.00 0.00 0.00 2.45
200 201 4.279420 GGAAAATGATCCATTCTACCCAGC 59.721 45.833 0.00 0.00 39.42 4.85
231 232 8.991026 CAACATTATTTGGTTGACATTTGTGAT 58.009 29.630 0.00 0.00 45.50 3.06
527 552 3.127425 AGTACTGTTGCTCTTTCACCC 57.873 47.619 0.00 0.00 0.00 4.61
551 576 6.425721 CCATTTGCACAAGATCAAATTTGAGT 59.574 34.615 24.17 14.50 39.92 3.41
588 616 6.696441 ATTCTCTGCTCAATCCTTGATTTC 57.304 37.500 0.00 0.00 39.30 2.17
613 669 1.270305 TGCTCCTCTTCGGTTGTTCTG 60.270 52.381 0.00 0.00 0.00 3.02
911 1568 1.739196 GCTGCAGACGCACTCATCA 60.739 57.895 20.43 0.00 45.36 3.07
1131 1801 2.352805 GGCAGGTCCACTTCCCAG 59.647 66.667 0.00 0.00 34.01 4.45
1280 1979 2.764128 TGTCCATCGGGAGGAGCC 60.764 66.667 0.00 0.00 46.12 4.70
1442 2141 1.213926 GATGGGAGGTCTTGGCAAGAT 59.786 52.381 30.70 17.53 40.18 2.40
2099 2808 6.150318 CCTATCATCTGAAATGAAGCAATGC 58.850 40.000 0.00 0.00 0.00 3.56
2177 2920 7.763613 AGAAGAGGGAGCAATGGATTTAATAT 58.236 34.615 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 5.773575 TCGATCTGTCACTTATTCTATGGC 58.226 41.667 0.00 0.00 0.00 4.40
132 133 7.659652 AGCAATAGTTACTGTGAAGACTTTC 57.340 36.000 0.00 0.00 0.00 2.62
153 154 6.763135 CCAACTTCTAGATAGCACAATAAGCA 59.237 38.462 0.00 0.00 0.00 3.91
231 232 7.936847 ACATAGAAAAAGTTGTCTGTACCATCA 59.063 33.333 0.00 0.00 0.00 3.07
314 316 3.302480 CGACAACACTTCCTTTTCACTCG 60.302 47.826 0.00 0.00 0.00 4.18
527 552 7.042321 ACACTCAAATTTGATCTTGTGCAAATG 60.042 33.333 26.12 13.09 42.17 2.32
551 576 3.565482 GCAGAGAATTCACCTCAACAACA 59.435 43.478 8.44 0.00 33.25 3.33
588 616 1.069906 CAACCGAAGAGGAGCAAAACG 60.070 52.381 0.00 0.00 45.00 3.60
911 1568 1.968493 ACACATACGGGTCACTGTCTT 59.032 47.619 0.00 0.00 37.41 3.01
1131 1801 3.927142 GCGTGATATAGCCATGTACCTTC 59.073 47.826 0.00 0.00 0.00 3.46
1280 1979 2.203972 CTGCCGCCAAGGATGTTGTG 62.204 60.000 0.00 0.00 45.00 3.33
1442 2141 5.939764 ATACACCATCTTAGCAAGAGTCA 57.060 39.130 0.00 0.00 41.61 3.41
2336 3089 7.281774 CAGTTCTCCTATACTTGCACATTCATT 59.718 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.