Multiple sequence alignment - TraesCS7A01G424900

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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 TraesCS7A01G424900 chr7A 100.000 2246 0 0 1 2246 617960997 617958752 0.000000e+00 4148.0
1 TraesCS7A01G424900 chr7A 96.837 664 21 0 1 664 106589782 106589119 0.000000e+00 1110.0
2 TraesCS7A01G424900 chr7A 96.687 664 20 1 1 664 647417423 647416762 0.000000e+00 1103.0
3 TraesCS7A01G424900 chr7A 93.023 387 17 5 1641 2027 647416301 647415925 7.010000e-155 556.0
4 TraesCS7A01G424900 chr3B 94.881 1172 52 4 1076 2246 782861145 782859981 0.000000e+00 1825.0
5 TraesCS7A01G424900 chr1B 94.620 1171 47 3 1076 2246 627844287 627843133 0.000000e+00 1799.0
6 TraesCS7A01G424900 chr1B 94.803 635 33 0 659 1293 40283183 40283817 0.000000e+00 990.0
7 TraesCS7A01G424900 chr1B 91.270 504 44 0 1423 1926 22074598 22075101 0.000000e+00 688.0
8 TraesCS7A01G424900 chr1B 93.558 326 14 2 1922 2246 27255596 27255277 1.560000e-131 479.0
9 TraesCS7A01G424900 chr2A 96.588 938 32 0 1 938 3341059 3341996 0.000000e+00 1555.0
10 TraesCS7A01G424900 chr2A 95.216 857 26 3 1390 2246 3342004 3342845 0.000000e+00 1341.0
11 TraesCS7A01G424900 chr2A 96.823 661 20 1 1 661 708688582 708689241 0.000000e+00 1103.0
12 TraesCS7A01G424900 chr2A 96.799 656 21 0 6 661 88835116 88835771 0.000000e+00 1096.0
13 TraesCS7A01G424900 chr4D 96.995 732 20 2 659 1389 210025892 210025162 0.000000e+00 1229.0
14 TraesCS7A01G424900 chr4D 100.000 34 0 0 1394 1427 228951342 228951309 1.860000e-06 63.9
15 TraesCS7A01G424900 chr7B 96.033 731 29 0 659 1389 365875551 365874821 0.000000e+00 1190.0
16 TraesCS7A01G424900 chr7B 94.172 326 12 2 1922 2246 670113506 670113825 7.210000e-135 490.0
17 TraesCS7A01G424900 chr7B 94.154 325 12 2 1923 2246 490139270 490138952 2.590000e-134 488.0
18 TraesCS7A01G424900 chr7B 94.081 321 13 2 1923 2243 381892744 381893058 1.210000e-132 483.0
19 TraesCS7A01G424900 chr3A 95.730 726 31 0 661 1386 575150341 575151066 0.000000e+00 1170.0
20 TraesCS7A01G424900 chr3A 97.126 661 19 0 1 661 41657214 41657874 0.000000e+00 1116.0
21 TraesCS7A01G424900 chr3A 96.974 661 20 0 1 661 433764253 433764913 0.000000e+00 1110.0
22 TraesCS7A01G424900 chr3A 96.687 664 22 0 1 664 743242764 743242101 0.000000e+00 1105.0
23 TraesCS7A01G424900 chr3A 97.050 644 19 0 659 1302 433765196 433765839 0.000000e+00 1085.0
24 TraesCS7A01G424900 chr3A 93.282 387 16 5 1641 2027 122542134 122541758 1.510000e-156 562.0
25 TraesCS7A01G424900 chr5A 96.687 664 21 1 1 664 388937590 388936928 0.000000e+00 1103.0
26 TraesCS7A01G424900 chr5A 93.973 730 36 4 659 1387 173528373 173527651 0.000000e+00 1098.0
27 TraesCS7A01G424900 chr5A 95.326 599 25 1 791 1389 683752375 683751780 0.000000e+00 948.0
28 TraesCS7A01G424900 chr5A 93.558 326 14 2 1922 2246 422094863 422094544 1.560000e-131 479.0
29 TraesCS7A01G424900 chr4B 95.958 569 23 0 659 1227 239621137 239621705 0.000000e+00 924.0
30 TraesCS7A01G424900 chr4B 93.865 326 13 2 1922 2246 501694427 501694108 3.350000e-133 484.0
31 TraesCS7A01G424900 chr4B 100.000 34 0 0 1394 1427 225960854 225960821 1.860000e-06 63.9
32 TraesCS7A01G424900 chr1D 91.340 485 40 2 1442 1926 15314236 15313754 0.000000e+00 662.0
33 TraesCS7A01G424900 chr1D 100.000 34 0 0 1394 1427 950366 950333 1.860000e-06 63.9
34 TraesCS7A01G424900 chr1A 90.079 504 48 2 1423 1926 16409266 16408765 0.000000e+00 652.0
35 TraesCS7A01G424900 chr1A 93.282 387 16 5 1641 2027 287040376 287040752 1.510000e-156 562.0
36 TraesCS7A01G424900 chr2B 93.789 322 14 1 1922 2243 8262131 8261816 1.560000e-131 479.0
37 TraesCS7A01G424900 chr5B 100.000 45 0 0 1386 1430 415394881 415394837 1.430000e-12 84.2
38 TraesCS7A01G424900 chr6D 100.000 34 0 0 1394 1427 79068125 79068092 1.860000e-06 63.9
39 TraesCS7A01G424900 chr6D 100.000 34 0 0 1394 1427 244272272 244272239 1.860000e-06 63.9


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 TraesCS7A01G424900 chr7A 617958752 617960997 2245 True 4148.0 4148 100.000 1 2246 1 chr7A.!!$R2 2245
1 TraesCS7A01G424900 chr7A 106589119 106589782 663 True 1110.0 1110 96.837 1 664 1 chr7A.!!$R1 663
2 TraesCS7A01G424900 chr7A 647415925 647417423 1498 True 829.5 1103 94.855 1 2027 2 chr7A.!!$R3 2026
3 TraesCS7A01G424900 chr3B 782859981 782861145 1164 True 1825.0 1825 94.881 1076 2246 1 chr3B.!!$R1 1170
4 TraesCS7A01G424900 chr1B 627843133 627844287 1154 True 1799.0 1799 94.620 1076 2246 1 chr1B.!!$R2 1170
5 TraesCS7A01G424900 chr1B 40283183 40283817 634 False 990.0 990 94.803 659 1293 1 chr1B.!!$F2 634
6 TraesCS7A01G424900 chr1B 22074598 22075101 503 False 688.0 688 91.270 1423 1926 1 chr1B.!!$F1 503
7 TraesCS7A01G424900 chr2A 3341059 3342845 1786 False 1448.0 1555 95.902 1 2246 2 chr2A.!!$F3 2245
8 TraesCS7A01G424900 chr2A 708688582 708689241 659 False 1103.0 1103 96.823 1 661 1 chr2A.!!$F2 660
9 TraesCS7A01G424900 chr2A 88835116 88835771 655 False 1096.0 1096 96.799 6 661 1 chr2A.!!$F1 655
10 TraesCS7A01G424900 chr4D 210025162 210025892 730 True 1229.0 1229 96.995 659 1389 1 chr4D.!!$R1 730
11 TraesCS7A01G424900 chr7B 365874821 365875551 730 True 1190.0 1190 96.033 659 1389 1 chr7B.!!$R1 730
12 TraesCS7A01G424900 chr3A 575150341 575151066 725 False 1170.0 1170 95.730 661 1386 1 chr3A.!!$F2 725
13 TraesCS7A01G424900 chr3A 41657214 41657874 660 False 1116.0 1116 97.126 1 661 1 chr3A.!!$F1 660
14 TraesCS7A01G424900 chr3A 743242101 743242764 663 True 1105.0 1105 96.687 1 664 1 chr3A.!!$R2 663
15 TraesCS7A01G424900 chr3A 433764253 433765839 1586 False 1097.5 1110 97.012 1 1302 2 chr3A.!!$F3 1301
16 TraesCS7A01G424900 chr5A 388936928 388937590 662 True 1103.0 1103 96.687 1 664 1 chr5A.!!$R2 663
17 TraesCS7A01G424900 chr5A 173527651 173528373 722 True 1098.0 1098 93.973 659 1387 1 chr5A.!!$R1 728
18 TraesCS7A01G424900 chr5A 683751780 683752375 595 True 948.0 948 95.326 791 1389 1 chr5A.!!$R4 598
19 TraesCS7A01G424900 chr4B 239621137 239621705 568 False 924.0 924 95.958 659 1227 1 chr4B.!!$F1 568
20 TraesCS7A01G424900 chr1A 16408765 16409266 501 True 652.0 652 90.079 1423 1926 1 chr1A.!!$R1 503

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
997 1285 0.033109 GGGAGCCAAAGCCCTAACAT 60.033 55.0 0.0 0.0 41.31 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2490 0.029267 AGGAAGGAGGCCATGGAGAT 60.029 55.0 18.4 0.0 0.0 2.75 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
91 92 5.806654 ATTTGGCACCTTACAATCAAACT 57.193 34.783 0.00 0.0 0.00 2.66
107 108 9.005777 ACAATCAAACTTACACCACGTTTATAT 57.994 29.630 0.00 0.0 30.41 0.86
315 316 9.166173 GGAGCAAAATAAAGGCAAATCTAAAAT 57.834 29.630 0.00 0.0 0.00 1.82
358 359 9.329913 CAGTCTGTGTGCATAAATAAAGTAAAC 57.670 33.333 0.00 0.0 0.00 2.01
410 411 6.742109 GGATACAAGTAGTTACTATCCGCAA 58.258 40.000 0.00 0.0 32.40 4.85
956 1243 5.255397 ACCACCAAAATCTCTCAATACCA 57.745 39.130 0.00 0.0 0.00 3.25
997 1285 0.033109 GGGAGCCAAAGCCCTAACAT 60.033 55.000 0.00 0.0 41.31 2.71
1217 1505 2.356535 GCCAACATGAAGAGGATGAGGT 60.357 50.000 0.00 0.0 0.00 3.85
1328 1682 6.274674 TCCCTCCCAATCATATCATAGACAT 58.725 40.000 0.00 0.0 0.00 3.06
1427 1785 8.842280 TCGGTGAACTTAACTCAAACAATAATT 58.158 29.630 0.00 0.0 0.00 1.40
1665 2023 5.545335 TCAGAGCATCATTACCCAGTCATAT 59.455 40.000 0.00 0.0 37.82 1.78
1672 2030 7.400439 CATCATTACCCAGTCATATTCTCCAT 58.600 38.462 0.00 0.0 0.00 3.41
1682 2040 5.911178 AGTCATATTCTCCATGGACCCTTTA 59.089 40.000 11.44 0.0 0.00 1.85
1720 2078 3.868369 GCCTACATACACTCCAGCAACAA 60.868 47.826 0.00 0.0 0.00 2.83
1776 2134 5.177511 TGTGTCAGCGAACATAAGAAGAAAG 59.822 40.000 0.00 0.0 0.00 2.62
1938 2297 6.345096 ACACTGTAGATTTTTGAATTGGGG 57.655 37.500 0.00 0.0 0.00 4.96
1970 2329 4.286297 TGAATGGAGAAGACGGAAACAT 57.714 40.909 0.00 0.0 0.00 2.71
1979 2338 4.039245 AGAAGACGGAAACATGACTCAAGA 59.961 41.667 0.00 0.0 0.00 3.02
2048 2407 4.081030 GCATCGGCATCGGCATCG 62.081 66.667 0.00 0.0 43.71 3.84
2049 2408 3.417224 CATCGGCATCGGCATCGG 61.417 66.667 0.00 0.0 43.71 4.18
2053 2412 3.730761 GGCATCGGCATCGGCATC 61.731 66.667 0.00 0.0 43.71 3.91
2094 2453 3.068881 CCTCCTTCCTTCACCGCA 58.931 61.111 0.00 0.0 0.00 5.69
2131 2490 4.039092 GGAGGGCAGCAGCTTCCA 62.039 66.667 13.62 0.0 41.23 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 7.830940 ATGTTCGAATATAAACGTGGTGTAA 57.169 32.000 5.50 0.00 0.00 2.41
107 108 5.147330 ACCTGATGTGAAGTATGTTCGAA 57.853 39.130 0.00 0.00 0.00 3.71
193 194 5.350504 AGCATTGAGTACTAGCTCATTGT 57.649 39.130 16.73 7.31 43.99 2.71
205 206 5.702670 CCAAGAAGTGAAGAAGCATTGAGTA 59.297 40.000 0.00 0.00 0.00 2.59
284 285 6.664428 TTTGCCTTTATTTTGCTCCTTACT 57.336 33.333 0.00 0.00 0.00 2.24
315 316 5.221641 ACAGACTGCCTACAAGTTAATGTGA 60.222 40.000 1.25 0.00 34.75 3.58
358 359 4.724074 TTCTATGCCTCATTTTGCTTGG 57.276 40.909 0.00 0.00 0.00 3.61
406 407 6.715344 TTGGAGTAGTATTTACTTGTTGCG 57.285 37.500 0.00 0.00 37.73 4.85
410 411 9.601217 GATGTGATTGGAGTAGTATTTACTTGT 57.399 33.333 0.00 0.00 37.73 3.16
672 958 6.974048 GCATGATGTTGAATTATGTGCTACAA 59.026 34.615 0.00 0.00 0.00 2.41
956 1243 5.793030 CGGGAGGTCTCTAGTTAATGATT 57.207 43.478 0.00 0.00 0.00 2.57
997 1285 3.643320 ACTCTTCTATTCGATGCCATGGA 59.357 43.478 18.40 0.31 0.00 3.41
1217 1505 0.469494 TCTTGTCCACAGCAGAGCAA 59.531 50.000 0.00 0.00 0.00 3.91
1328 1682 2.244510 AGGTGGCATCCCAAATCATACA 59.755 45.455 0.00 0.00 44.33 2.29
1427 1785 2.506231 TGTCTCCACACCCTGTTGTAAA 59.494 45.455 0.00 0.00 0.00 2.01
1665 2023 3.256704 AGTGTAAAGGGTCCATGGAGAA 58.743 45.455 16.81 0.00 0.00 2.87
1672 2030 3.773119 GAGTATGGAGTGTAAAGGGTCCA 59.227 47.826 0.00 0.00 43.23 4.02
1682 2040 1.885049 AGGCATGGAGTATGGAGTGT 58.115 50.000 0.00 0.00 37.26 3.55
1720 2078 4.623932 TCTTCTGTTAATCTGCAGGTGT 57.376 40.909 15.13 1.72 33.81 4.16
1776 2134 0.605319 TGGCGTCAAACACTCATCCC 60.605 55.000 0.00 0.00 0.00 3.85
1928 2287 4.898265 TCAAACATGTTCTCCCCAATTCAA 59.102 37.500 12.39 0.00 0.00 2.69
1934 2293 3.164268 CCATTCAAACATGTTCTCCCCA 58.836 45.455 12.39 0.00 0.00 4.96
1938 2297 6.606768 GTCTTCTCCATTCAAACATGTTCTC 58.393 40.000 12.39 0.00 0.00 2.87
1970 2329 6.249192 TCCTCTATCTTGTTCTCTTGAGTCA 58.751 40.000 0.00 0.00 0.00 3.41
1979 2338 5.660864 CCTCTCCTTTCCTCTATCTTGTTCT 59.339 44.000 0.00 0.00 0.00 3.01
2048 2407 2.832201 GAAGCTGCTGGGGATGCC 60.832 66.667 1.35 0.00 0.00 4.40
2049 2408 1.823041 GAGAAGCTGCTGGGGATGC 60.823 63.158 0.00 0.00 0.00 3.91
2050 2409 0.179051 GAGAGAAGCTGCTGGGGATG 60.179 60.000 0.00 0.00 0.00 3.51
2051 2410 0.326427 AGAGAGAAGCTGCTGGGGAT 60.326 55.000 0.00 0.00 0.00 3.85
2052 2411 0.975040 GAGAGAGAAGCTGCTGGGGA 60.975 60.000 0.00 0.00 0.00 4.81
2053 2412 1.521616 GAGAGAGAAGCTGCTGGGG 59.478 63.158 0.00 0.00 0.00 4.96
2094 2453 2.406559 CCATCTCATCTCCCTCCTTGT 58.593 52.381 0.00 0.00 0.00 3.16
2131 2490 0.029267 AGGAAGGAGGCCATGGAGAT 60.029 55.000 18.40 0.00 0.00 2.75
2193 2552 2.053465 CGTGTGTGCGTTTGGTCG 60.053 61.111 0.00 0.00 0.00 4.79
2198 2557 0.882927 ATGTAGGCGTGTGTGCGTTT 60.883 50.000 0.00 0.00 34.38 3.60


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

AutoCloner maintained by Alex Coulton.