Multiple sequence alignment - TraesCS7A01G548900

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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 TraesCS7A01G548900 chr7A 100.000 2513 0 0 1 2513 723073814 723076326 0.000000e+00 4641.0
1 TraesCS7A01G548900 chr7A 95.474 2541 68 15 1 2513 722987088 722989609 0.000000e+00 4012.0
2 TraesCS7A01G548900 chr7A 94.637 2275 75 17 266 2513 722897844 722900098 0.000000e+00 3482.0
3 TraesCS7A01G548900 chr7A 94.684 1204 42 7 243 1428 723030178 723031377 0.000000e+00 1849.0
4 TraesCS7A01G548900 chr7A 96.069 1043 34 6 243 1282 722935881 722936919 0.000000e+00 1692.0
5 TraesCS7A01G548900 chr7A 85.580 1387 130 33 1148 2506 722793086 722794430 0.000000e+00 1389.0
6 TraesCS7A01G548900 chr7A 85.478 1391 133 32 1148 2511 722877621 722878969 0.000000e+00 1386.0
7 TraesCS7A01G548900 chr7A 95.168 683 15 8 1831 2513 722938566 722939230 0.000000e+00 1062.0
8 TraesCS7A01G548900 chr7A 93.997 683 23 8 1831 2513 723031376 723032040 0.000000e+00 1018.0
9 TraesCS7A01G548900 chr7A 93.590 234 8 1 1 234 723029893 723030119 2.390000e-90 342.0
10 TraesCS7A01G548900 chr7A 92.166 217 10 1 1 217 722935551 722935760 1.460000e-77 300.0
11 TraesCS7A01G548900 chr7A 92.222 180 13 1 987 1165 722792895 722793074 1.150000e-63 254.0
12 TraesCS7A01G548900 chr7A 88.073 218 11 6 949 1165 722877406 722877609 6.940000e-61 244.0
13 TraesCS7A01G548900 chr7A 96.000 125 5 0 1304 1428 722938443 722938567 1.180000e-48 204.0
14 TraesCS7A01G548900 chr7A 86.413 184 13 5 2330 2513 722879395 722879566 9.180000e-45 191.0
15 TraesCS7A01G548900 chr7A 81.281 203 32 5 2317 2513 722794709 722794911 2.590000e-35 159.0
16 TraesCS7A01G548900 chr7A 97.368 38 1 0 949 986 722792871 722792908 5.800000e-07 65.8
17 TraesCS7A01G548900 chr7B 86.908 1627 129 35 924 2513 728012768 728014347 0.000000e+00 1748.0
18 TraesCS7A01G548900 chr7B 84.009 1382 149 36 1148 2511 728005896 728007223 0.000000e+00 1262.0
19 TraesCS7A01G548900 chr7B 86.824 592 69 9 251 836 728012044 728012632 0.000000e+00 652.0
20 TraesCS7A01G548900 chr7B 83.022 536 80 9 265 794 728029329 728029859 2.260000e-130 475.0
21 TraesCS7A01G548900 chr7B 83.234 501 70 6 292 779 728052995 728053494 4.930000e-122 448.0
22 TraesCS7A01G548900 chr7B 90.826 218 13 2 949 1165 728005673 728005884 4.090000e-73 285.0
23 TraesCS7A01G548900 chr7B 84.021 194 28 3 2317 2509 728007498 728007689 1.540000e-42 183.0
24 TraesCS7A01G548900 chr7D 85.228 1381 130 37 1148 2511 627298537 627299860 0.000000e+00 1352.0
25 TraesCS7A01G548900 chr7D 91.127 417 18 8 1632 2048 627305466 627305863 4.730000e-152 547.0
26 TraesCS7A01G548900 chr7D 95.266 338 9 1 924 1261 627305109 627305439 1.710000e-146 529.0
27 TraesCS7A01G548900 chr7D 89.103 312 33 1 528 838 627304664 627304975 1.090000e-103 387.0
28 TraesCS7A01G548900 chr7D 94.444 180 9 1 987 1165 627298346 627298525 2.460000e-70 276.0
29 TraesCS7A01G548900 chr7D 96.364 165 6 0 1 165 154734319 154734483 3.190000e-69 272.0
30 TraesCS7A01G548900 chr5D 96.364 165 6 0 1 165 416449191 416449027 3.190000e-69 272.0
31 TraesCS7A01G548900 chr2D 96.364 165 6 0 1 165 70372363 70372527 3.190000e-69 272.0
32 TraesCS7A01G548900 chr2A 96.364 165 6 0 1 165 585866424 585866260 3.190000e-69 272.0
33 TraesCS7A01G548900 chr6D 95.294 170 8 0 1 170 141408105 141407936 1.150000e-68 270.0
34 TraesCS7A01G548900 chr4D 95.758 165 7 0 1 165 166793321 166793485 1.480000e-67 267.0


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 TraesCS7A01G548900 chr7A 723073814 723076326 2512 False 4641.000000 4641 100.000000 1 2513 1 chr7A.!!$F3 2512
1 TraesCS7A01G548900 chr7A 722987088 722989609 2521 False 4012.000000 4012 95.474000 1 2513 1 chr7A.!!$F2 2512
2 TraesCS7A01G548900 chr7A 722897844 722900098 2254 False 3482.000000 3482 94.637000 266 2513 1 chr7A.!!$F1 2247
3 TraesCS7A01G548900 chr7A 723029893 723032040 2147 False 1069.666667 1849 94.090333 1 2513 3 chr7A.!!$F7 2512
4 TraesCS7A01G548900 chr7A 722935551 722939230 3679 False 814.500000 1692 94.850750 1 2513 4 chr7A.!!$F6 2512
5 TraesCS7A01G548900 chr7A 722877406 722879566 2160 False 607.000000 1386 86.654667 949 2513 3 chr7A.!!$F5 1564
6 TraesCS7A01G548900 chr7A 722792871 722794911 2040 False 466.950000 1389 89.112750 949 2513 4 chr7A.!!$F4 1564
7 TraesCS7A01G548900 chr7B 728012044 728014347 2303 False 1200.000000 1748 86.866000 251 2513 2 chr7B.!!$F4 2262
8 TraesCS7A01G548900 chr7B 728005673 728007689 2016 False 576.666667 1262 86.285333 949 2511 3 chr7B.!!$F3 1562
9 TraesCS7A01G548900 chr7B 728029329 728029859 530 False 475.000000 475 83.022000 265 794 1 chr7B.!!$F1 529
10 TraesCS7A01G548900 chr7D 627298346 627299860 1514 False 814.000000 1352 89.836000 987 2511 2 chr7D.!!$F2 1524
11 TraesCS7A01G548900 chr7D 627304664 627305863 1199 False 487.666667 547 91.832000 528 2048 3 chr7D.!!$F3 1520

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
994 1155 1.272203 ACAACACACAACCCAGAACCA 60.272 47.619 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 4011 0.042448 GCGACACACTTCACGTTTCC 60.042 55.0 0.0 0.0 0.0 3.13 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
50 51 7.606839 TGCTGATATAGTCAATAGTAGTAGCGT 59.393 37.037 0.00 0.00 36.14 5.07
262 299 2.452937 GGGGAGGGGCACTGGATAC 61.453 68.421 0.00 0.00 0.00 2.24
409 506 2.975489 ACTGACATCCTGTTGACCTCTT 59.025 45.455 0.00 0.00 0.00 2.85
637 737 2.432444 CAAGATTACAAAGTCCGGCCA 58.568 47.619 2.24 0.00 0.00 5.36
922 1075 2.842394 CTAGTGCAGCAGTCCCACGG 62.842 65.000 5.84 0.00 34.79 4.94
994 1155 1.272203 ACAACACACAACCCAGAACCA 60.272 47.619 0.00 0.00 0.00 3.67
1037 1198 0.904649 TCCCGAGTGTTCATCATGCT 59.095 50.000 0.00 0.00 0.00 3.79
1385 3078 2.672651 CCACGCCAGCCACAATGA 60.673 61.111 0.00 0.00 0.00 2.57
1485 3178 1.961180 ATCTGAACCTTCCGGCTCCG 61.961 60.000 0.00 0.48 39.44 4.63
1539 3241 4.384940 AGAGATGAACAGATCGATCGAGA 58.615 43.478 23.84 0.68 0.00 4.04
1606 3311 5.181433 TGCGTGTGCTATATTTGGTGTTTAA 59.819 36.000 0.00 0.00 43.34 1.52
1653 3364 4.570772 TCTCTCTTTGACTTTGTGTTTCCG 59.429 41.667 0.00 0.00 0.00 4.30
1678 3391 1.009829 GGTGTGCAAATAGCTCTCGG 58.990 55.000 0.00 0.00 45.94 4.63
1904 3621 8.317679 AGATCTATAGGTCATTTGACATTAGCC 58.682 37.037 15.41 5.86 46.47 3.93
1905 3622 6.455647 TCTATAGGTCATTTGACATTAGCCG 58.544 40.000 12.43 0.00 46.47 5.52
1906 3623 3.627395 AGGTCATTTGACATTAGCCGA 57.373 42.857 12.43 0.00 46.47 5.54
1907 3624 4.156455 AGGTCATTTGACATTAGCCGAT 57.844 40.909 12.43 0.00 46.47 4.18
1908 3625 4.130118 AGGTCATTTGACATTAGCCGATC 58.870 43.478 12.43 0.00 46.47 3.69
1911 3628 5.009010 GGTCATTTGACATTAGCCGATCAAT 59.991 40.000 12.43 0.00 46.47 2.57
1914 3631 7.800380 GTCATTTGACATTAGCCGATCAATTAG 59.200 37.037 5.84 0.00 44.18 1.73
1931 3648 4.844349 ATTAGTACCATGTGTCCAGCTT 57.156 40.909 0.00 0.00 0.00 3.74
2127 3861 9.379791 AGTGTCATAATGTATATGCATCAGATG 57.620 33.333 0.19 5.98 0.00 2.90
2296 4034 0.529773 ACGTGAAGTGTGTCGCATGT 60.530 50.000 0.00 0.00 0.00 3.21
2297 4036 0.161658 CGTGAAGTGTGTCGCATGTC 59.838 55.000 0.00 0.00 0.00 3.06
2384 4603 5.880332 TCATTGGAGTAATTAAAGCGCTCTT 59.120 36.000 12.06 10.24 0.00 2.85
2396 4737 2.869897 AGCGCTCTTTTTCGACTCTAG 58.130 47.619 2.64 0.00 0.00 2.43
2403 4744 5.556355 TCTTTTTCGACTCTAGATACGCA 57.444 39.130 11.98 1.58 0.00 5.24
2473 4817 7.105588 GGGCCAAGAAATATTTCTGAAACAAT 58.894 34.615 27.25 10.33 46.22 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 253 2.044806 GATGCGTATCCAGTGCCCCT 62.045 60.000 1.49 0.00 0.00 4.79
637 737 2.665185 GACCAGCACGCTTTCGGT 60.665 61.111 0.00 0.00 40.69 4.69
922 1075 2.971915 CGAAGACGACAACACACTCTAC 59.028 50.000 0.00 0.00 42.66 2.59
994 1155 2.093711 TCGATCCGGTCATCATGTTGTT 60.094 45.455 0.00 0.00 0.00 2.83
1370 3063 1.065491 TCTTATCATTGTGGCTGGCGT 60.065 47.619 0.00 0.00 0.00 5.68
1485 3178 0.179936 CCTCATGTTCCTCTGCCTCC 59.820 60.000 0.00 0.00 0.00 4.30
1539 3241 3.760580 ACTGAGAACACTAGCAAGCTT 57.239 42.857 0.00 0.00 0.00 3.74
1653 3364 2.162408 GAGCTATTTGCACACCAAGTCC 59.838 50.000 0.00 0.00 45.94 3.85
1678 3391 2.255856 GAGCGGGGATCGATCGAC 59.744 66.667 22.06 14.00 44.44 4.20
1891 3608 7.807977 ACTAATTGATCGGCTAATGTCAAAT 57.192 32.000 0.00 0.00 34.62 2.32
1892 3609 7.225931 GGTACTAATTGATCGGCTAATGTCAAA 59.774 37.037 0.00 0.00 34.62 2.69
1893 3610 6.704493 GGTACTAATTGATCGGCTAATGTCAA 59.296 38.462 0.00 0.00 35.33 3.18
1894 3611 6.183360 TGGTACTAATTGATCGGCTAATGTCA 60.183 38.462 0.00 0.00 0.00 3.58
1895 3612 6.220930 TGGTACTAATTGATCGGCTAATGTC 58.779 40.000 0.00 0.00 0.00 3.06
1896 3613 6.169557 TGGTACTAATTGATCGGCTAATGT 57.830 37.500 0.00 0.00 0.00 2.71
1897 3614 6.650807 ACATGGTACTAATTGATCGGCTAATG 59.349 38.462 0.00 0.00 0.00 1.90
1898 3615 6.650807 CACATGGTACTAATTGATCGGCTAAT 59.349 38.462 0.00 0.00 0.00 1.73
1899 3616 5.989168 CACATGGTACTAATTGATCGGCTAA 59.011 40.000 0.00 0.00 0.00 3.09
1900 3617 5.069914 ACACATGGTACTAATTGATCGGCTA 59.930 40.000 0.00 0.00 0.00 3.93
1901 3618 4.141711 ACACATGGTACTAATTGATCGGCT 60.142 41.667 0.00 0.00 0.00 5.52
1902 3619 4.127171 ACACATGGTACTAATTGATCGGC 58.873 43.478 0.00 0.00 0.00 5.54
1903 3620 4.750098 GGACACATGGTACTAATTGATCGG 59.250 45.833 0.00 0.00 0.00 4.18
1904 3621 5.356426 TGGACACATGGTACTAATTGATCG 58.644 41.667 0.00 0.00 0.00 3.69
1905 3622 5.237344 GCTGGACACATGGTACTAATTGATC 59.763 44.000 0.00 0.00 0.00 2.92
1906 3623 5.104360 AGCTGGACACATGGTACTAATTGAT 60.104 40.000 0.00 0.00 0.00 2.57
1907 3624 4.225042 AGCTGGACACATGGTACTAATTGA 59.775 41.667 0.00 0.00 0.00 2.57
1908 3625 4.517285 AGCTGGACACATGGTACTAATTG 58.483 43.478 0.00 0.00 0.00 2.32
1911 3628 4.634012 AAAGCTGGACACATGGTACTAA 57.366 40.909 0.00 0.00 0.00 2.24
1914 3631 2.678336 GCTAAAGCTGGACACATGGTAC 59.322 50.000 0.00 0.00 38.21 3.34
2127 3861 7.736447 AGATCGACCTTTTTATCATCCATTC 57.264 36.000 0.00 0.00 0.00 2.67
2273 4011 0.042448 GCGACACACTTCACGTTTCC 60.042 55.000 0.00 0.00 0.00 3.13
2296 4034 8.553153 TCATTAACTTGGGAAATGGTATGTAGA 58.447 33.333 0.00 0.00 32.63 2.59
2297 4036 8.746052 TCATTAACTTGGGAAATGGTATGTAG 57.254 34.615 0.00 0.00 32.63 2.74
2384 4603 5.886992 TCATTGCGTATCTAGAGTCGAAAA 58.113 37.500 18.97 13.43 0.00 2.29
2396 4737 5.149054 CAAGGAAACTCTCATTGCGTATC 57.851 43.478 0.00 0.00 42.68 2.24


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

AutoCloner maintained by Alex Coulton.