Multiple sequence alignment - TraesCS7D01G411900

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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 TraesCS7D01G411900 chr7D 100.000 2773 0 0 1 2773 530431532 530428760 0.000000e+00 5121.0
1 TraesCS7D01G411900 chr7D 84.584 1492 109 63 762 2181 530361678 530360236 0.000000e+00 1369.0
2 TraesCS7D01G411900 chr7D 86.386 1021 74 30 801 1780 573969167 573970163 0.000000e+00 1055.0
3 TraesCS7D01G411900 chr7D 82.751 1316 96 58 837 2052 548324995 548326279 0.000000e+00 1051.0
4 TraesCS7D01G411900 chr7D 83.769 727 72 14 1 688 543730893 543731612 0.000000e+00 647.0
5 TraesCS7D01G411900 chr7D 81.871 684 81 17 1 649 548550431 548551106 1.130000e-148 536.0
6 TraesCS7D01G411900 chr7D 87.037 378 40 7 2399 2773 548326684 548327055 4.270000e-113 418.0
7 TraesCS7D01G411900 chr7D 84.496 387 46 8 2255 2631 573970716 573971098 1.210000e-98 370.0
8 TraesCS7D01G411900 chr7D 84.496 387 46 8 2255 2631 574248344 574248726 1.210000e-98 370.0
9 TraesCS7D01G411900 chr7D 93.793 145 9 0 531 675 573968913 573969057 4.650000e-53 219.0
10 TraesCS7D01G411900 chr7B 91.819 1589 79 23 624 2183 569439949 569438383 0.000000e+00 2167.0
11 TraesCS7D01G411900 chr7B 93.581 1075 54 7 744 1815 569481715 569480653 0.000000e+00 1589.0
12 TraesCS7D01G411900 chr7B 84.652 1277 105 42 610 1849 591565940 591567162 0.000000e+00 1188.0
13 TraesCS7D01G411900 chr7B 82.431 1440 143 63 802 2163 633001104 633002511 0.000000e+00 1157.0
14 TraesCS7D01G411900 chr7B 84.982 1132 103 37 752 1849 591684290 591685388 0.000000e+00 1086.0
15 TraesCS7D01G411900 chr7B 85.566 963 91 22 755 1692 591599776 591600715 0.000000e+00 965.0
16 TraesCS7D01G411900 chr7B 89.343 685 26 12 1 638 569440648 569439964 0.000000e+00 817.0
17 TraesCS7D01G411900 chr7B 89.309 608 33 11 2179 2773 569437184 569436596 0.000000e+00 734.0
18 TraesCS7D01G411900 chr7B 89.400 500 43 7 2276 2773 569479938 569479447 3.030000e-174 621.0
19 TraesCS7D01G411900 chr7B 88.600 500 47 7 2276 2773 591055233 591054742 1.420000e-167 599.0
20 TraesCS7D01G411900 chr7B 92.478 226 7 7 498 715 569481940 569481717 5.770000e-82 315.0
21 TraesCS7D01G411900 chr7B 76.949 590 96 30 1549 2117 591577757 591578327 1.610000e-77 300.0
22 TraesCS7D01G411900 chr7B 86.047 215 25 3 2255 2468 632799032 632798822 2.780000e-55 226.0
23 TraesCS7D01G411900 chr7B 86.047 215 25 3 2255 2468 633002648 633002858 2.780000e-55 226.0
24 TraesCS7D01G411900 chr7B 97.500 40 1 0 2029 2068 591055735 591055696 4.960000e-08 69.4
25 TraesCS7D01G411900 chr7B 95.000 40 2 0 2029 2068 569480446 569480407 2.310000e-06 63.9
26 TraesCS7D01G411900 chr7A 84.632 1848 177 61 1 1792 631653233 631651437 0.000000e+00 1740.0
27 TraesCS7D01G411900 chr7A 83.559 1916 171 70 1 1846 630670860 630672701 0.000000e+00 1661.0
28 TraesCS7D01G411900 chr7A 83.568 1777 151 69 1 1692 632187254 632188974 0.000000e+00 1533.0
29 TraesCS7D01G411900 chr7A 82.317 1657 173 69 585 2155 632265587 632267209 0.000000e+00 1327.0
30 TraesCS7D01G411900 chr7A 84.225 729 70 18 1 689 625674433 625675156 0.000000e+00 667.0
31 TraesCS7D01G411900 chr7A 83.702 724 72 16 1 688 625641660 625642373 2.330000e-180 641.0
32 TraesCS7D01G411900 chr7A 93.000 200 14 0 604 803 631878023 631877824 2.700000e-75 292.0
33 TraesCS7D01G411900 chr7A 82.759 319 45 8 2461 2773 617549669 617549355 2.720000e-70 276.0
34 TraesCS7D01G411900 chr7A 82.353 323 21 8 418 710 617552301 617551985 5.930000e-62 248.0
35 TraesCS7D01G411900 chr7A 82.906 234 35 4 1945 2175 138983443 138983674 3.620000e-49 206.0
36 TraesCS7D01G411900 chr7A 80.702 228 20 13 1864 2068 632190131 632190357 3.700000e-34 156.0
37 TraesCS7D01G411900 chr7A 78.761 226 19 15 1872 2068 630672777 630673002 1.040000e-24 124.0
38 TraesCS7D01G411900 chr7A 94.030 67 4 0 531 597 663574673 663574739 4.890000e-18 102.0
39 TraesCS7D01G411900 chr4A 83.720 1855 182 48 1 1815 141909562 141907788 0.000000e+00 1642.0
40 TraesCS7D01G411900 chr4A 80.926 540 50 29 1343 1855 141903914 141903401 7.250000e-101 377.0
41 TraesCS7D01G411900 chrUn 82.849 1481 143 58 752 2155 337590886 337589440 0.000000e+00 1225.0
42 TraesCS7D01G411900 chrUn 84.700 1268 103 42 619 1849 355335469 355334256 0.000000e+00 1182.0
43 TraesCS7D01G411900 chr1D 83.574 761 76 18 1 722 110904650 110905400 0.000000e+00 667.0
44 TraesCS7D01G411900 chr1B 83.960 692 68 20 1 653 169024434 169025121 8.430000e-175 623.0
45 TraesCS7D01G411900 chr6B 83.149 724 76 15 1 688 694680455 694681168 1.090000e-173 619.0
46 TraesCS7D01G411900 chr4B 82.495 537 62 18 6 528 527592882 527593400 2.530000e-120 442.0


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 TraesCS7D01G411900 chr7D 530428760 530431532 2772 True 5121.000000 5121 100.00000 1 2773 1 chr7D.!!$R2 2772
1 TraesCS7D01G411900 chr7D 530360236 530361678 1442 True 1369.000000 1369 84.58400 762 2181 1 chr7D.!!$R1 1419
2 TraesCS7D01G411900 chr7D 548324995 548327055 2060 False 734.500000 1051 84.89400 837 2773 2 chr7D.!!$F4 1936
3 TraesCS7D01G411900 chr7D 543730893 543731612 719 False 647.000000 647 83.76900 1 688 1 chr7D.!!$F1 687
4 TraesCS7D01G411900 chr7D 573968913 573971098 2185 False 548.000000 1055 88.22500 531 2631 3 chr7D.!!$F5 2100
5 TraesCS7D01G411900 chr7D 548550431 548551106 675 False 536.000000 536 81.87100 1 649 1 chr7D.!!$F2 648
6 TraesCS7D01G411900 chr7B 569436596 569440648 4052 True 1239.333333 2167 90.15700 1 2773 3 chr7B.!!$R2 2772
7 TraesCS7D01G411900 chr7B 591565940 591567162 1222 False 1188.000000 1188 84.65200 610 1849 1 chr7B.!!$F1 1239
8 TraesCS7D01G411900 chr7B 591684290 591685388 1098 False 1086.000000 1086 84.98200 752 1849 1 chr7B.!!$F4 1097
9 TraesCS7D01G411900 chr7B 591599776 591600715 939 False 965.000000 965 85.56600 755 1692 1 chr7B.!!$F3 937
10 TraesCS7D01G411900 chr7B 633001104 633002858 1754 False 691.500000 1157 84.23900 802 2468 2 chr7B.!!$F5 1666
11 TraesCS7D01G411900 chr7B 569479447 569481940 2493 True 647.225000 1589 92.61475 498 2773 4 chr7B.!!$R3 2275
12 TraesCS7D01G411900 chr7B 591054742 591055735 993 True 334.200000 599 93.05000 2029 2773 2 chr7B.!!$R4 744
13 TraesCS7D01G411900 chr7B 591577757 591578327 570 False 300.000000 300 76.94900 1549 2117 1 chr7B.!!$F2 568
14 TraesCS7D01G411900 chr7A 631651437 631653233 1796 True 1740.000000 1740 84.63200 1 1792 1 chr7A.!!$R1 1791
15 TraesCS7D01G411900 chr7A 632265587 632267209 1622 False 1327.000000 1327 82.31700 585 2155 1 chr7A.!!$F4 1570
16 TraesCS7D01G411900 chr7A 630670860 630673002 2142 False 892.500000 1661 81.16000 1 2068 2 chr7A.!!$F6 2067
17 TraesCS7D01G411900 chr7A 632187254 632190357 3103 False 844.500000 1533 82.13500 1 2068 2 chr7A.!!$F7 2067
18 TraesCS7D01G411900 chr7A 625674433 625675156 723 False 667.000000 667 84.22500 1 689 1 chr7A.!!$F3 688
19 TraesCS7D01G411900 chr7A 625641660 625642373 713 False 641.000000 641 83.70200 1 688 1 chr7A.!!$F2 687
20 TraesCS7D01G411900 chr7A 617549355 617552301 2946 True 262.000000 276 82.55600 418 2773 2 chr7A.!!$R3 2355
21 TraesCS7D01G411900 chr4A 141903401 141909562 6161 True 1009.500000 1642 82.32300 1 1855 2 chr4A.!!$R1 1854
22 TraesCS7D01G411900 chrUn 337589440 337590886 1446 True 1225.000000 1225 82.84900 752 2155 1 chrUn.!!$R1 1403
23 TraesCS7D01G411900 chrUn 355334256 355335469 1213 True 1182.000000 1182 84.70000 619 1849 1 chrUn.!!$R2 1230
24 TraesCS7D01G411900 chr1D 110904650 110905400 750 False 667.000000 667 83.57400 1 722 1 chr1D.!!$F1 721
25 TraesCS7D01G411900 chr1B 169024434 169025121 687 False 623.000000 623 83.96000 1 653 1 chr1B.!!$F1 652
26 TraesCS7D01G411900 chr6B 694680455 694681168 713 False 619.000000 619 83.14900 1 688 1 chr6B.!!$F1 687
27 TraesCS7D01G411900 chr4B 527592882 527593400 518 False 442.000000 442 82.49500 6 528 1 chr4B.!!$F1 522

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
742 937 0.811616 CAAGCGAGGGGAGTACATGC 60.812 60.0 0.0 0.0 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2703 9396 0.238025 TTTGCGCTGCATGTACACAG 59.762 50.0 9.73 3.11 38.76 3.66 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
148 155 1.278302 TGGAAATGGCCATCCCGAGA 61.278 55.000 21.08 5.18 34.68 4.04
168 180 3.887716 AGACCGTATATCTTTACCACGCT 59.112 43.478 0.00 0.00 0.00 5.07
199 211 1.682451 CGAGGATGTTCCCGGGCTTA 61.682 60.000 18.49 3.87 37.19 3.09
715 870 4.320456 CCCTCTGCTGGTGCGTGT 62.320 66.667 0.00 0.00 43.34 4.49
719 874 4.662961 CTGCTGGTGCGTGTCGGA 62.663 66.667 0.00 0.00 43.34 4.55
742 937 0.811616 CAAGCGAGGGGAGTACATGC 60.812 60.000 0.00 0.00 0.00 4.06
939 1181 3.285484 CCAATTTCTCCATCCAGTCCTG 58.715 50.000 0.00 0.00 0.00 3.86
1027 1282 3.461773 AGATGCTCCGTCGGTGGG 61.462 66.667 11.88 4.35 0.00 4.61
1197 1452 1.209275 GCGGGATTCTCGACGACATG 61.209 60.000 10.80 0.00 0.00 3.21
1237 1495 0.106819 GCTGAGGCTGGTTCCATCAT 60.107 55.000 0.00 0.00 35.22 2.45
1238 1496 1.964552 CTGAGGCTGGTTCCATCATC 58.035 55.000 0.00 1.20 0.00 2.92
1239 1497 1.211212 CTGAGGCTGGTTCCATCATCA 59.789 52.381 9.15 9.15 0.00 3.07
1412 1700 2.409870 CCACGCCCATGAAGAAGCC 61.410 63.158 0.00 0.00 0.00 4.35
1759 2118 1.362717 ACGCAGCTTCACGTGTAGT 59.637 52.632 21.25 7.56 41.76 2.73
1768 2127 3.108521 CACGTGTAGTGTGGCTCTC 57.891 57.895 7.58 0.00 45.51 3.20
1796 2182 7.766278 TCAAGAAAATAGCTGATCCAGAACTAC 59.234 37.037 0.00 0.00 32.44 2.73
1804 2190 4.642885 GCTGATCCAGAACTACTAGTGTCT 59.357 45.833 5.39 2.70 32.44 3.41
1815 2217 6.086785 ACTACTAGTGTCTTGGTCACTTTC 57.913 41.667 5.39 0.00 42.50 2.62
1834 2245 8.424918 TCACTTTCATGTATATCCTTCTTCTCC 58.575 37.037 0.00 0.00 0.00 3.71
1846 2260 3.257127 CCTTCTTCTCCAAGACTCGAACT 59.743 47.826 0.00 0.00 38.44 3.01
1847 2261 3.924918 TCTTCTCCAAGACTCGAACTG 57.075 47.619 0.00 0.00 33.38 3.16
1848 2262 2.029828 TCTTCTCCAAGACTCGAACTGC 60.030 50.000 0.00 0.00 33.38 4.40
1849 2263 1.621992 TCTCCAAGACTCGAACTGCT 58.378 50.000 0.00 0.00 0.00 4.24
1870 3285 4.618460 GCTAGTTGCTTGTACAGTAGCTCA 60.618 45.833 18.00 4.92 38.22 4.26
1924 3355 4.711721 TGACGAATTGAAAGCGAGATTTG 58.288 39.130 0.00 0.00 0.00 2.32
2008 3485 7.228507 TGAATTATAATTCTGCACGCACCTAAT 59.771 33.333 29.37 0.00 43.97 1.73
2068 3587 1.511850 TGTCCATGTTCAGACTTGCG 58.488 50.000 0.00 0.00 34.02 4.85
2134 3720 9.842775 TCTCATCTTGCTGTTTTCTTGATATAT 57.157 29.630 0.00 0.00 0.00 0.86
2269 8359 2.127251 GCTTTTGCCTTCTTCGGTTTG 58.873 47.619 0.00 0.00 40.15 2.93
2386 8978 7.148018 ACAGGTGTACATGATTTCCATTTCATC 60.148 37.037 0.00 0.00 31.94 2.92
2388 8980 6.201517 GTGTACATGATTTCCATTTCATCCG 58.798 40.000 0.00 0.00 31.94 4.18
2456 9085 1.072173 CACTCCATGGTCACCACTGAA 59.928 52.381 12.58 0.00 35.80 3.02
2490 9178 1.754226 GAGACCCTCAAGCACCTCTAG 59.246 57.143 0.00 0.00 0.00 2.43
2515 9205 3.564225 CCTTTCTATCGCCAAATGGTACC 59.436 47.826 4.43 4.43 37.57 3.34
2609 9302 2.714250 ACCAAACAGTTACTGGGATGGA 59.286 45.455 27.62 0.00 36.65 3.41
2617 9310 3.000727 GTTACTGGGATGGACTTTCACG 58.999 50.000 0.00 0.00 0.00 4.35
2619 9312 0.321564 CTGGGATGGACTTTCACGCA 60.322 55.000 0.00 0.00 0.00 5.24
2682 9375 5.779529 AAATTGCTGAGTTGATGTGTCTT 57.220 34.783 0.00 0.00 0.00 3.01
2729 9423 1.202065 ACATGCAGCGCAAATTACTCG 60.202 47.619 11.47 0.00 43.62 4.18
2761 9457 3.746940 TGTAGCGGACCTTTAAAGCTTT 58.253 40.909 17.30 17.30 39.14 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.043116 TGGTACATGGCTCCCGAGAG 61.043 60.000 0.00 0.00 43.57 3.20
126 133 0.756442 CGGGATGGCCATTTCCATGT 60.756 55.000 27.82 5.49 46.29 3.21
141 148 4.074970 GGTAAAGATATACGGTCTCGGGA 58.925 47.826 0.00 0.00 41.39 5.14
148 155 3.887716 AGAGCGTGGTAAAGATATACGGT 59.112 43.478 0.00 0.00 46.32 4.83
217 234 4.760047 GGGATGCACGAGCGTGGT 62.760 66.667 22.50 0.00 45.49 4.16
715 870 3.452786 CCCTCGCTTGCTCTCCGA 61.453 66.667 0.00 0.00 0.00 4.55
719 874 1.000486 TACTCCCCTCGCTTGCTCT 60.000 57.895 0.00 0.00 0.00 4.09
939 1181 0.179006 GATTGGATGGAGAGGTGGGC 60.179 60.000 0.00 0.00 0.00 5.36
1020 1275 1.030488 CGTAGAAGCTCTCCCACCGA 61.030 60.000 0.00 0.00 0.00 4.69
1027 1282 2.278923 GGCGCCGTAGAAGCTCTC 60.279 66.667 12.58 0.00 0.00 3.20
1197 1452 1.674359 TCTCGAGAGACTCTGCCATC 58.326 55.000 12.08 0.00 35.39 3.51
1466 1763 1.154836 CGCTTCGTCTTTGCGTCAC 60.155 57.895 0.00 0.00 44.00 3.67
1759 2118 2.613026 TTTTCTTGACGAGAGCCACA 57.387 45.000 0.00 0.00 35.37 4.17
1760 2119 3.062774 GCTATTTTCTTGACGAGAGCCAC 59.937 47.826 0.00 0.00 35.37 5.01
1761 2120 3.055819 AGCTATTTTCTTGACGAGAGCCA 60.056 43.478 0.00 0.00 35.37 4.75
1762 2121 3.308323 CAGCTATTTTCTTGACGAGAGCC 59.692 47.826 0.00 0.00 35.37 4.70
1763 2122 4.177026 TCAGCTATTTTCTTGACGAGAGC 58.823 43.478 0.00 0.00 35.37 4.09
1768 2127 5.111989 TCTGGATCAGCTATTTTCTTGACG 58.888 41.667 0.00 0.00 0.00 4.35
1796 2182 5.300752 ACATGAAAGTGACCAAGACACTAG 58.699 41.667 0.00 0.00 46.01 2.57
1804 2190 7.861629 AGAAGGATATACATGAAAGTGACCAA 58.138 34.615 0.00 0.00 0.00 3.67
1815 2217 7.961351 AGTCTTGGAGAAGAAGGATATACATG 58.039 38.462 0.00 0.00 40.00 3.21
1834 2245 2.410053 GCAACTAGCAGTTCGAGTCTTG 59.590 50.000 0.00 0.00 44.79 3.02
1847 2261 3.851098 AGCTACTGTACAAGCAACTAGC 58.149 45.455 19.15 11.38 41.32 3.42
1848 2262 5.060662 TGAGCTACTGTACAAGCAACTAG 57.939 43.478 19.15 0.00 41.32 2.57
1849 2263 5.661056 ATGAGCTACTGTACAAGCAACTA 57.339 39.130 19.15 5.31 41.32 2.24
1870 3285 6.515832 TCGATCAAGTACAGAACATGCATAT 58.484 36.000 0.00 0.00 0.00 1.78
1924 3355 4.503741 TTCTTTGCAGATTTGTAGCACC 57.496 40.909 0.00 0.00 38.11 5.01
2008 3485 8.855110 TGTAAAAAGGATAGCTTTGTTGATTGA 58.145 29.630 0.00 0.00 0.00 2.57
2068 3587 5.055812 TGAATTCAAATTGCAACTTGGACC 58.944 37.500 19.53 8.22 0.00 4.46
2098 3680 6.010294 ACAGCAAGATGAGATTTTGTCAAG 57.990 37.500 0.00 0.00 0.00 3.02
2107 3690 8.749026 ATATCAAGAAAACAGCAAGATGAGAT 57.251 30.769 0.00 0.00 0.00 2.75
2134 3720 2.517650 TTGTCGCACACATGTAGTCA 57.482 45.000 0.00 0.00 33.90 3.41
2203 7512 0.596577 GGTGGGCGAACCTTCTTTTC 59.403 55.000 0.97 0.00 41.11 2.29
2269 8359 2.352960 CTCCTTTGAAATACCTCGCTGC 59.647 50.000 0.00 0.00 0.00 5.25
2386 8978 1.298667 AACCGAATCAGGGTTCCGG 59.701 57.895 0.00 0.00 44.25 5.14
2456 9085 2.173569 AGGGTCTCTGTGCTCTTGTTTT 59.826 45.455 0.00 0.00 0.00 2.43
2490 9178 4.137543 ACCATTTGGCGATAGAAAGGATC 58.862 43.478 0.00 0.00 39.32 3.36
2515 9205 7.332182 GTCTCTAGTTTGAAGTTCAGGTATTGG 59.668 40.741 5.56 0.00 0.00 3.16
2609 9302 1.944024 TCAAACCGATTGCGTGAAAGT 59.056 42.857 0.00 0.00 38.98 2.66
2617 9310 4.219033 CACAAACTAGTCAAACCGATTGC 58.781 43.478 0.00 0.00 38.98 3.56
2619 9312 4.514066 GTCCACAAACTAGTCAAACCGATT 59.486 41.667 0.00 0.00 0.00 3.34
2657 9350 5.413833 AGACACATCAACTCAGCAATTTAGG 59.586 40.000 0.00 0.00 0.00 2.69
2660 9353 5.779529 AAGACACATCAACTCAGCAATTT 57.220 34.783 0.00 0.00 0.00 1.82
2703 9396 0.238025 TTTGCGCTGCATGTACACAG 59.762 50.000 9.73 3.11 38.76 3.66
2729 9423 5.813080 AGGTCCGCTACATTTTGAAATAC 57.187 39.130 0.00 0.00 0.00 1.89
2745 9439 8.508875 TGTTTCTATTAAAGCTTTAAAGGTCCG 58.491 33.333 29.92 16.49 36.35 4.79


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

AutoCloner maintained by Alex Coulton.