Multiple sequence alignment - TraesCS7B01G450900

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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 TraesCS7B01G450900 chr7B 100.000 3051 0 0 1 3051 712762943 712759893 0.000000e+00 5635.0
1 TraesCS7B01G450900 chr7B 95.878 655 23 3 2400 3051 393381891 393381238 0.000000e+00 1057.0
2 TraesCS7B01G450900 chr7B 95.878 655 21 3 2399 3051 462899384 462898734 0.000000e+00 1055.0
3 TraesCS7B01G450900 chr7B 95.434 657 23 4 2399 3051 462934327 462933674 0.000000e+00 1040.0
4 TraesCS7B01G450900 chr7B 94.369 444 24 1 454 897 613909685 613910127 0.000000e+00 680.0
5 TraesCS7B01G450900 chr7B 93.290 462 30 1 1 461 658643590 658644051 0.000000e+00 680.0
6 TraesCS7B01G450900 chr3B 95.801 1953 75 6 457 2403 272589106 272587155 0.000000e+00 3145.0
7 TraesCS7B01G450900 chr3B 95.452 1517 64 4 890 2403 233223858 233225372 0.000000e+00 2414.0
8 TraesCS7B01G450900 chr3B 95.586 657 21 6 2400 3051 490107431 490108084 0.000000e+00 1046.0
9 TraesCS7B01G450900 chr3B 96.753 462 14 1 1 461 272589596 272589135 0.000000e+00 769.0
10 TraesCS7B01G450900 chr3B 96.437 449 16 0 449 897 233223354 233223802 0.000000e+00 741.0
11 TraesCS7B01G450900 chr5B 95.231 1950 87 5 460 2403 619684861 619682912 0.000000e+00 3081.0
12 TraesCS7B01G450900 chr5B 96.489 655 12 5 2400 3051 662776196 662776842 0.000000e+00 1072.0
13 TraesCS7B01G450900 chr5B 96.753 462 12 3 1 461 619685352 619684893 0.000000e+00 767.0
14 TraesCS7B01G450900 chr6A 94.616 1523 76 3 454 1970 567626928 567628450 0.000000e+00 2353.0
15 TraesCS7B01G450900 chr6A 94.214 1521 84 3 454 1970 580783609 580785129 0.000000e+00 2318.0
16 TraesCS7B01G450900 chr6A 95.662 461 19 1 1 461 567626443 567626902 0.000000e+00 739.0
17 TraesCS7B01G450900 chr6A 95.662 461 19 1 1 461 580783124 580783583 0.000000e+00 739.0
18 TraesCS7B01G450900 chr3A 94.661 1517 77 3 457 1970 54533431 54531916 0.000000e+00 2350.0
19 TraesCS7B01G450900 chr3A 96.095 461 17 1 1 461 54533919 54533460 0.000000e+00 750.0
20 TraesCS7B01G450900 chr2B 92.363 1519 85 14 887 2403 239997712 239996223 0.000000e+00 2134.0
21 TraesCS7B01G450900 chr2B 95.865 653 17 4 2400 3050 749981578 749980934 0.000000e+00 1048.0
22 TraesCS7B01G450900 chr2B 96.659 449 15 0 449 897 239998215 239997767 0.000000e+00 747.0
23 TraesCS7B01G450900 chr2B 91.033 513 18 9 1670 2155 216856122 216855611 0.000000e+00 667.0
24 TraesCS7B01G450900 chr6B 93.681 1361 57 10 1068 2403 664805526 664806882 0.000000e+00 2010.0
25 TraesCS7B01G450900 chr6B 95.719 654 19 4 2401 3051 648476819 648476172 0.000000e+00 1044.0
26 TraesCS7B01G450900 chr6B 95.248 463 19 3 1 461 673196480 673196019 0.000000e+00 730.0
27 TraesCS7B01G450900 chr6B 95.506 178 6 2 890 1066 673195493 673195317 1.790000e-72 283.0
28 TraesCS7B01G450900 chr4B 95.738 657 17 6 2400 3051 18151149 18151799 0.000000e+00 1048.0
29 TraesCS7B01G450900 chr1B 95.434 657 25 3 2400 3051 670440213 670439557 0.000000e+00 1042.0
30 TraesCS7B01G450900 chr1B 94.432 449 25 0 449 897 512227851 512227403 0.000000e+00 691.0
31 TraesCS7B01G450900 chr1B 93.723 462 24 4 4 461 512228332 512227872 0.000000e+00 688.0
32 TraesCS7B01G450900 chr1B 95.506 178 6 2 890 1066 512227346 512227170 1.790000e-72 283.0
33 TraesCS7B01G450900 chrUn 93.074 462 31 1 1 461 328035483 328035944 0.000000e+00 675.0
34 TraesCS7B01G450900 chr7D 99.020 306 3 0 2098 2403 613748545 613748850 1.600000e-152 549.0
35 TraesCS7B01G450900 chr3D 98.693 306 4 0 2098 2403 501321931 501321626 7.440000e-151 544.0
36 TraesCS7B01G450900 chr3D 98.693 306 4 0 2098 2403 580207993 580208298 7.440000e-151 544.0
37 TraesCS7B01G450900 chr3D 98.693 306 4 0 2098 2403 583552387 583552082 7.440000e-151 544.0
38 TraesCS7B01G450900 chr1A 84.860 535 39 18 1068 1582 560951754 560951242 4.540000e-138 501.0
39 TraesCS7B01G450900 chr1D 88.718 390 32 8 1184 1566 467928400 467928016 1.660000e-127 466.0
40 TraesCS7B01G450900 chr2D 86.986 292 27 8 1855 2136 159689414 159689124 4.910000e-83 318.0
41 TraesCS7B01G450900 chr2D 92.593 54 4 0 1756 1809 159689557 159689504 9.070000e-11 78.7
42 TraesCS7B01G450900 chr2D 100.000 30 0 0 1827 1856 159689458 159689429 4.250000e-04 56.5
43 TraesCS7B01G450900 chr2A 86.007 293 28 7 1855 2136 170934811 170934521 4.940000e-78 302.0
44 TraesCS7B01G450900 chr2A 91.549 71 6 0 1756 1826 170934968 170934898 6.960000e-17 99.0


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 TraesCS7B01G450900 chr7B 712759893 712762943 3050 True 5635.0 5635 100.000000 1 3051 1 chr7B.!!$R4 3050
1 TraesCS7B01G450900 chr7B 393381238 393381891 653 True 1057.0 1057 95.878000 2400 3051 1 chr7B.!!$R1 651
2 TraesCS7B01G450900 chr7B 462898734 462899384 650 True 1055.0 1055 95.878000 2399 3051 1 chr7B.!!$R2 652
3 TraesCS7B01G450900 chr7B 462933674 462934327 653 True 1040.0 1040 95.434000 2399 3051 1 chr7B.!!$R3 652
4 TraesCS7B01G450900 chr3B 272587155 272589596 2441 True 1957.0 3145 96.277000 1 2403 2 chr3B.!!$R1 2402
5 TraesCS7B01G450900 chr3B 233223354 233225372 2018 False 1577.5 2414 95.944500 449 2403 2 chr3B.!!$F2 1954
6 TraesCS7B01G450900 chr3B 490107431 490108084 653 False 1046.0 1046 95.586000 2400 3051 1 chr3B.!!$F1 651
7 TraesCS7B01G450900 chr5B 619682912 619685352 2440 True 1924.0 3081 95.992000 1 2403 2 chr5B.!!$R1 2402
8 TraesCS7B01G450900 chr5B 662776196 662776842 646 False 1072.0 1072 96.489000 2400 3051 1 chr5B.!!$F1 651
9 TraesCS7B01G450900 chr6A 567626443 567628450 2007 False 1546.0 2353 95.139000 1 1970 2 chr6A.!!$F1 1969
10 TraesCS7B01G450900 chr6A 580783124 580785129 2005 False 1528.5 2318 94.938000 1 1970 2 chr6A.!!$F2 1969
11 TraesCS7B01G450900 chr3A 54531916 54533919 2003 True 1550.0 2350 95.378000 1 1970 2 chr3A.!!$R1 1969
12 TraesCS7B01G450900 chr2B 239996223 239998215 1992 True 1440.5 2134 94.511000 449 2403 2 chr2B.!!$R3 1954
13 TraesCS7B01G450900 chr2B 749980934 749981578 644 True 1048.0 1048 95.865000 2400 3050 1 chr2B.!!$R2 650
14 TraesCS7B01G450900 chr2B 216855611 216856122 511 True 667.0 667 91.033000 1670 2155 1 chr2B.!!$R1 485
15 TraesCS7B01G450900 chr6B 664805526 664806882 1356 False 2010.0 2010 93.681000 1068 2403 1 chr6B.!!$F1 1335
16 TraesCS7B01G450900 chr6B 648476172 648476819 647 True 1044.0 1044 95.719000 2401 3051 1 chr6B.!!$R1 650
17 TraesCS7B01G450900 chr6B 673195317 673196480 1163 True 506.5 730 95.377000 1 1066 2 chr6B.!!$R2 1065
18 TraesCS7B01G450900 chr4B 18151149 18151799 650 False 1048.0 1048 95.738000 2400 3051 1 chr4B.!!$F1 651
19 TraesCS7B01G450900 chr1B 670439557 670440213 656 True 1042.0 1042 95.434000 2400 3051 1 chr1B.!!$R1 651
20 TraesCS7B01G450900 chr1B 512227170 512228332 1162 True 554.0 691 94.553667 4 1066 3 chr1B.!!$R2 1062
21 TraesCS7B01G450900 chr1A 560951242 560951754 512 True 501.0 501 84.860000 1068 1582 1 chr1A.!!$R1 514

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
455 493 0.179100 ACCGTCGAGAGATGCAATGG 60.179 55.0 0.0 0.0 45.72 3.16 F
695 733 0.388520 CAAGCATCACAGACCGTCGA 60.389 55.0 0.0 0.0 0.00 4.20 F
1437 1560 0.633921 TCCTCCTCCTCCTCCTCTTG 59.366 60.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 1443 0.622136 TGGTCCTCGTAGCAGTAGGA 59.378 55.000 0.00 0.00 37.07 2.94 R
1792 1954 2.360801 GAGCACAACAAGTAAAGCCCAA 59.639 45.455 0.00 0.00 0.00 4.12 R
2845 3015 1.175262 AGATCCCATCTCTAGGGCCT 58.825 55.000 12.58 12.58 46.36 5.19 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
99 100 1.161843 TCGGCGGGAATTTGTCTTTC 58.838 50.000 7.21 0.00 0.00 2.62
365 370 2.590575 CCGGTTGTCGTGGTGCTT 60.591 61.111 0.00 0.00 37.11 3.91
366 371 2.184167 CCGGTTGTCGTGGTGCTTT 61.184 57.895 0.00 0.00 37.11 3.51
452 490 1.446099 GCACCGTCGAGAGATGCAA 60.446 57.895 2.50 0.00 45.72 4.08
455 493 0.179100 ACCGTCGAGAGATGCAATGG 60.179 55.000 0.00 0.00 45.72 3.16
547 585 3.072944 GGCTAGCTAGGCAGATGATTTG 58.927 50.000 35.27 3.09 46.94 2.32
695 733 0.388520 CAAGCATCACAGACCGTCGA 60.389 55.000 0.00 0.00 0.00 4.20
708 746 1.955080 ACCGTCGAATACTCCCAGATC 59.045 52.381 0.00 0.00 0.00 2.75
713 752 3.132289 GTCGAATACTCCCAGATCCAACA 59.868 47.826 0.00 0.00 0.00 3.33
832 871 1.138568 CTCCCAGATCCAATCCTGCT 58.861 55.000 0.00 0.00 0.00 4.24
966 1070 2.066592 TCTCTCCCTACCCAGATCGAT 58.933 52.381 0.00 0.00 0.00 3.59
1002 1106 1.153489 CACGCTCCCATCCACTGAG 60.153 63.158 0.00 0.00 0.00 3.35
1138 1256 3.763757 CGGTACCCTCCCTCCCCT 61.764 72.222 6.25 0.00 0.00 4.79
1283 1406 0.977627 TGGACGAGCTGGACATGGAT 60.978 55.000 1.44 0.00 0.00 3.41
1320 1443 2.919328 GGCCCAACTTTGCCTGCT 60.919 61.111 0.00 0.00 44.46 4.24
1435 1558 0.998945 CCTCCTCCTCCTCCTCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
1437 1560 0.633921 TCCTCCTCCTCCTCCTCTTG 59.366 60.000 0.00 0.00 0.00 3.02
1443 1569 1.206849 CTCCTCCTCCTCTTGCTTGTC 59.793 57.143 0.00 0.00 0.00 3.18
1815 1977 3.181449 TGGGCTTTACTTGTTGTGCTCTA 60.181 43.478 0.00 0.00 0.00 2.43
2084 2249 4.836125 AGTCTGTTGTGCTTGGTTAATG 57.164 40.909 0.00 0.00 0.00 1.90
2157 2322 0.748450 GCCATTGCCATGCACTACAT 59.252 50.000 0.00 0.00 38.71 2.29
2476 2643 7.043961 TCTATGAGTTCATCTAAGCAACGAT 57.956 36.000 0.00 0.00 37.76 3.73
2694 2861 0.538584 TGAAGATCCAGCAGCACGAT 59.461 50.000 0.00 0.00 0.00 3.73
2788 2955 1.077429 GAGAGGGAGGCGCCAAAAT 60.077 57.895 31.54 12.06 38.95 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
365 370 1.594833 CGTCGGGGAGATCCAACAA 59.405 57.895 0.47 0.00 37.91 2.83
366 371 3.014085 GCGTCGGGGAGATCCAACA 62.014 63.158 0.47 0.00 37.91 3.33
523 561 1.834378 ATCTGCCTAGCTAGCCGCA 60.834 57.895 19.55 19.55 42.61 5.69
547 585 5.065731 CAGTCAGCCAGATGATTTTTCCTAC 59.934 44.000 0.00 0.00 0.00 3.18
695 733 2.173569 GGCTGTTGGATCTGGGAGTATT 59.826 50.000 0.00 0.00 0.00 1.89
708 746 2.118076 ATGGGTGTGGGCTGTTGG 59.882 61.111 0.00 0.00 0.00 3.77
713 752 4.684134 GGTGCATGGGTGTGGGCT 62.684 66.667 0.00 0.00 0.00 5.19
966 1070 3.615811 AGGGGGAGGTGGAGCTGA 61.616 66.667 0.00 0.00 0.00 4.26
1002 1106 0.394899 CCTTCCCAGGATGAACAGGC 60.395 60.000 1.25 0.00 44.19 4.85
1094 1198 2.125912 AGCTGCGTGGCGTAGAAG 60.126 61.111 10.53 0.00 41.80 2.85
1320 1443 0.622136 TGGTCCTCGTAGCAGTAGGA 59.378 55.000 0.00 0.00 37.07 2.94
1401 1524 2.966516 GAGGAGGTTAATCGGGACTGAT 59.033 50.000 0.00 0.00 0.00 2.90
1435 1558 5.359860 TGGATCTCTAGATAACGACAAGCAA 59.640 40.000 0.00 0.00 34.37 3.91
1437 1560 5.440234 TGGATCTCTAGATAACGACAAGC 57.560 43.478 0.00 0.00 34.37 4.01
1443 1569 6.183360 CGTACTCCATGGATCTCTAGATAACG 60.183 46.154 16.63 11.02 34.37 3.18
1792 1954 2.360801 GAGCACAACAAGTAAAGCCCAA 59.639 45.455 0.00 0.00 0.00 4.12
1815 1977 2.656947 TTTGGTTTCAGTAGGCTGCT 57.343 45.000 0.00 0.00 42.29 4.24
2084 2249 6.828785 AGTCCAGAAATATGTGTCCATAAACC 59.171 38.462 0.00 0.00 37.12 3.27
2476 2643 6.077993 AGGTATGTAGATGCACTCCTATCAA 58.922 40.000 0.00 0.00 0.00 2.57
2845 3015 1.175262 AGATCCCATCTCTAGGGCCT 58.825 55.000 12.58 12.58 46.36 5.19
2889 3061 4.431131 CCTTGGCGGGCACTCCAT 62.431 66.667 0.00 0.00 32.04 3.41
2900 3072 3.376918 GCCTCCACTTGCCTTGGC 61.377 66.667 4.43 4.43 33.71 4.52


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

AutoCloner maintained by Alex Coulton.