Multiple sequence alignment - TraesCS7B01G429900

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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 TraesCS7B01G429900 chr7B 100.000 3560 0 0 1 3560 698681813 698685372 0.000000e+00 6575.0
1 TraesCS7B01G429900 chr7B 95.004 2682 124 6 887 3560 696238745 696241424 0.000000e+00 4202.0
2 TraesCS7B01G429900 chr7B 94.898 1862 90 5 1286 3143 693664476 693666336 0.000000e+00 2907.0
3 TraesCS7B01G429900 chr7B 92.302 1338 82 9 2233 3560 693698819 693700145 0.000000e+00 1881.0
4 TraesCS7B01G429900 chr7B 90.670 1254 80 8 2317 3560 694748766 694749992 0.000000e+00 1633.0
5 TraesCS7B01G429900 chr7B 93.377 1072 59 5 2233 3302 693684866 693685927 0.000000e+00 1576.0
6 TraesCS7B01G429900 chr7B 96.259 588 18 3 1 586 223723806 223723221 0.000000e+00 961.0
7 TraesCS7B01G429900 chr7B 96.082 587 21 2 1 587 747673924 747673340 0.000000e+00 955.0
8 TraesCS7B01G429900 chr7B 96.075 586 21 2 1 586 59876420 59877003 0.000000e+00 953.0
9 TraesCS7B01G429900 chr7B 97.068 307 9 0 587 893 693663670 693663976 5.270000e-143 518.0
10 TraesCS7B01G429900 chr7B 90.753 292 19 4 608 893 693681533 693681822 2.010000e-102 383.0
11 TraesCS7B01G429900 chr7B 76.239 686 119 23 887 1561 696297827 696298479 1.230000e-84 324.0
12 TraesCS7B01G429900 chrUn 93.995 2648 136 6 915 3560 77521338 77523964 0.000000e+00 3988.0
13 TraesCS7B01G429900 chrUn 93.186 998 56 5 2233 3228 349917742 349916755 0.000000e+00 1456.0
14 TraesCS7B01G429900 chrUn 96.416 586 19 2 1 586 23189038 23189621 0.000000e+00 965.0
15 TraesCS7B01G429900 chrUn 97.628 253 4 1 587 837 77515647 77515899 1.960000e-117 433.0
16 TraesCS7B01G429900 chrUn 90.753 292 19 4 608 893 344773459 344773170 2.010000e-102 383.0
17 TraesCS7B01G429900 chrUn 90.753 292 19 4 608 893 364810972 364810683 2.010000e-102 383.0
18 TraesCS7B01G429900 chrUn 91.045 67 6 0 827 893 77521196 77521262 1.360000e-14 91.6
19 TraesCS7B01G429900 chr7D 94.212 2419 120 14 887 3302 610421610 610419209 0.000000e+00 3674.0
20 TraesCS7B01G429900 chr7D 92.353 2210 140 14 887 3087 608272780 608274969 0.000000e+00 3118.0
21 TraesCS7B01G429900 chr7D 89.599 2221 167 24 587 2788 608222129 608224304 0.000000e+00 2763.0
22 TraesCS7B01G429900 chr7D 90.634 1655 119 16 1601 3247 514918648 514920274 0.000000e+00 2165.0
23 TraesCS7B01G429900 chr7D 94.667 300 16 0 3261 3560 608275078 608275377 1.940000e-127 466.0
24 TraesCS7B01G429900 chr7D 93.548 310 17 1 587 893 610421955 610421646 3.240000e-125 459.0
25 TraesCS7B01G429900 chr7D 92.203 295 18 3 3264 3558 514930675 514930964 2.560000e-111 412.0
26 TraesCS7B01G429900 chr7D 92.203 295 13 5 609 893 608272455 608272749 3.310000e-110 409.0
27 TraesCS7B01G429900 chr7A 94.287 2118 110 6 887 2994 700300188 700302304 0.000000e+00 3230.0
28 TraesCS7B01G429900 chr7A 94.051 2118 115 6 887 2994 700338006 700340122 0.000000e+00 3203.0
29 TraesCS7B01G429900 chr7A 89.072 668 29 13 2922 3560 700340098 700340750 0.000000e+00 789.0
30 TraesCS7B01G429900 chr7A 88.922 668 30 13 2922 3560 700302280 700302932 0.000000e+00 784.0
31 TraesCS7B01G429900 chr3B 96.593 587 18 2 1 587 3671813 3671229 0.000000e+00 972.0
32 TraesCS7B01G429900 chr3B 96.252 587 19 3 1 586 777858222 777858806 0.000000e+00 959.0
33 TraesCS7B01G429900 chr2B 96.422 587 18 3 1 586 242942389 242942973 0.000000e+00 965.0
34 TraesCS7B01G429900 chr6B 96.252 587 20 2 1 587 48120853 48121437 0.000000e+00 961.0
35 TraesCS7B01G429900 chr4B 96.259 588 18 4 1 586 34771443 34772028 0.000000e+00 961.0
36 TraesCS7B01G429900 chr4A 87.346 648 51 12 2915 3560 735216342 735215724 0.000000e+00 713.0
37 TraesCS7B01G429900 chr4A 85.014 694 88 9 2535 3218 662021098 662020411 0.000000e+00 691.0
38 TraesCS7B01G429900 chr4A 89.873 316 21 5 584 893 662053221 662052911 2.580000e-106 396.0


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 TraesCS7B01G429900 chr7B 698681813 698685372 3559 False 6575.0 6575 100.000000 1 3560 1 chr7B.!!$F6 3559
1 TraesCS7B01G429900 chr7B 696238745 696241424 2679 False 4202.0 4202 95.004000 887 3560 1 chr7B.!!$F4 2673
2 TraesCS7B01G429900 chr7B 693698819 693700145 1326 False 1881.0 1881 92.302000 2233 3560 1 chr7B.!!$F2 1327
3 TraesCS7B01G429900 chr7B 693663670 693666336 2666 False 1712.5 2907 95.983000 587 3143 2 chr7B.!!$F7 2556
4 TraesCS7B01G429900 chr7B 694748766 694749992 1226 False 1633.0 1633 90.670000 2317 3560 1 chr7B.!!$F3 1243
5 TraesCS7B01G429900 chr7B 693681533 693685927 4394 False 979.5 1576 92.065000 608 3302 2 chr7B.!!$F8 2694
6 TraesCS7B01G429900 chr7B 223723221 223723806 585 True 961.0 961 96.259000 1 586 1 chr7B.!!$R1 585
7 TraesCS7B01G429900 chr7B 747673340 747673924 584 True 955.0 955 96.082000 1 587 1 chr7B.!!$R2 586
8 TraesCS7B01G429900 chr7B 59876420 59877003 583 False 953.0 953 96.075000 1 586 1 chr7B.!!$F1 585
9 TraesCS7B01G429900 chr7B 696297827 696298479 652 False 324.0 324 76.239000 887 1561 1 chr7B.!!$F5 674
10 TraesCS7B01G429900 chrUn 77521196 77523964 2768 False 2039.8 3988 92.520000 827 3560 2 chrUn.!!$F3 2733
11 TraesCS7B01G429900 chrUn 349916755 349917742 987 True 1456.0 1456 93.186000 2233 3228 1 chrUn.!!$R2 995
12 TraesCS7B01G429900 chrUn 23189038 23189621 583 False 965.0 965 96.416000 1 586 1 chrUn.!!$F1 585
13 TraesCS7B01G429900 chr7D 608222129 608224304 2175 False 2763.0 2763 89.599000 587 2788 1 chr7D.!!$F3 2201
14 TraesCS7B01G429900 chr7D 514918648 514920274 1626 False 2165.0 2165 90.634000 1601 3247 1 chr7D.!!$F1 1646
15 TraesCS7B01G429900 chr7D 610419209 610421955 2746 True 2066.5 3674 93.880000 587 3302 2 chr7D.!!$R1 2715
16 TraesCS7B01G429900 chr7D 608272455 608275377 2922 False 1331.0 3118 93.074333 609 3560 3 chr7D.!!$F4 2951
17 TraesCS7B01G429900 chr7A 700300188 700302932 2744 False 2007.0 3230 91.604500 887 3560 2 chr7A.!!$F1 2673
18 TraesCS7B01G429900 chr7A 700338006 700340750 2744 False 1996.0 3203 91.561500 887 3560 2 chr7A.!!$F2 2673
19 TraesCS7B01G429900 chr3B 3671229 3671813 584 True 972.0 972 96.593000 1 587 1 chr3B.!!$R1 586
20 TraesCS7B01G429900 chr3B 777858222 777858806 584 False 959.0 959 96.252000 1 586 1 chr3B.!!$F1 585
21 TraesCS7B01G429900 chr2B 242942389 242942973 584 False 965.0 965 96.422000 1 586 1 chr2B.!!$F1 585
22 TraesCS7B01G429900 chr6B 48120853 48121437 584 False 961.0 961 96.252000 1 587 1 chr6B.!!$F1 586
23 TraesCS7B01G429900 chr4B 34771443 34772028 585 False 961.0 961 96.259000 1 586 1 chr4B.!!$F1 585
24 TraesCS7B01G429900 chr4A 735215724 735216342 618 True 713.0 713 87.346000 2915 3560 1 chr4A.!!$R3 645
25 TraesCS7B01G429900 chr4A 662020411 662021098 687 True 691.0 691 85.014000 2535 3218 1 chr4A.!!$R1 683

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
402 408 0.912487 TCCCGGTTGGAGCCACTAAT 60.912 55.0 0.0 0.0 38.61 1.73 F
1125 1545 0.178903 TCTACCTCACCACTTGGGCT 60.179 55.0 0.0 0.0 42.05 5.19 F
1900 2334 0.327924 AACGGGCAAGTCCATCATCA 59.672 50.0 0.0 0.0 36.21 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 4483 1.661463 TCCTCCTTGGTCTGCTTGAT 58.339 50.000 0.00 0.0 37.07 2.57 R
2435 4535 2.247790 GCTTTCTTCGCTTGAGCCA 58.752 52.632 0.00 0.0 37.91 4.75 R
3262 5492 4.647611 TCATCATAACGTTGGAGGTGTTT 58.352 39.130 11.99 0.0 0.00 2.83 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
73 74 5.883685 ACCTGATACTGATGATCATGTGT 57.116 39.130 14.30 13.37 32.85 3.72
110 111 3.649843 AGGGTTGGGTTCGATGACTATA 58.350 45.455 0.00 0.00 0.00 1.31
283 286 1.135402 GCAGCGTTGATAAACCAAGGG 60.135 52.381 2.38 0.00 33.83 3.95
297 300 5.367945 AACCAAGGGCGAAGATATAAGAA 57.632 39.130 0.00 0.00 0.00 2.52
321 324 8.596781 AAAGGACACTTCTCTCTATTAGCTAA 57.403 34.615 8.99 8.99 35.41 3.09
322 325 7.817418 AGGACACTTCTCTCTATTAGCTAAG 57.183 40.000 12.54 0.00 0.00 2.18
399 405 3.637273 GTCCCGGTTGGAGCCACT 61.637 66.667 0.00 0.00 46.38 4.00
402 408 0.912487 TCCCGGTTGGAGCCACTAAT 60.912 55.000 0.00 0.00 38.61 1.73
414 420 1.065709 GCCACTAATCGGGACCAAAGA 60.066 52.381 0.00 0.00 0.00 2.52
492 498 3.934068 GGTTTGAACCGAGACTAATGGA 58.066 45.455 0.00 0.00 39.66 3.41
495 501 5.175859 GTTTGAACCGAGACTAATGGATGA 58.824 41.667 0.00 0.00 0.00 2.92
566 572 1.135721 CCCTTACGAACCGGGACTAAG 59.864 57.143 6.32 5.01 40.55 2.18
624 630 1.146041 GCACCATGCCGACCTCATA 59.854 57.895 0.00 0.00 37.42 2.15
777 793 2.352715 GCATCTGGTTGGCTACAAAACC 60.353 50.000 0.80 0.00 45.11 3.27
828 844 8.801882 TTGGATCCATTAAGTAATCTCGTTTT 57.198 30.769 17.06 0.00 0.00 2.43
905 1031 2.258013 ACCACACGAACCATTGGCG 61.258 57.895 1.54 1.64 31.76 5.69
913 1301 5.006844 CACACGAACCATTGGCGTTATATAA 59.993 40.000 1.54 0.00 35.90 0.98
940 1338 1.153842 TACACGCATGCTCAGTCCG 60.154 57.895 17.13 0.00 0.00 4.79
946 1344 1.296392 CATGCTCAGTCCGGTCCAA 59.704 57.895 0.00 0.00 0.00 3.53
952 1350 1.004918 CAGTCCGGTCCAAGTCACC 60.005 63.158 0.00 0.00 0.00 4.02
979 1379 5.163663 GGCTTTCCATCGACACAATATCAAA 60.164 40.000 0.00 0.00 0.00 2.69
990 1397 4.133078 CACAATATCAAAGAGGAGCTCCC 58.867 47.826 29.54 19.90 36.42 4.30
991 1398 3.782523 ACAATATCAAAGAGGAGCTCCCA 59.217 43.478 29.54 6.85 37.41 4.37
1003 1410 3.083349 CTCCCAGTCCGGCCATGA 61.083 66.667 2.24 0.00 0.00 3.07
1125 1545 0.178903 TCTACCTCACCACTTGGGCT 60.179 55.000 0.00 0.00 42.05 5.19
1413 1847 4.028131 ACGTCATCAGTTTATACCCTGGA 58.972 43.478 0.00 0.00 0.00 3.86
1438 1872 1.064458 GAGAGGCGCTTCTACCGAC 59.936 63.158 23.14 5.68 0.00 4.79
1470 1904 2.860293 CGGCATCGCGAACTTGTT 59.140 55.556 15.24 0.00 0.00 2.83
1900 2334 0.327924 AACGGGCAAGTCCATCATCA 59.672 50.000 0.00 0.00 36.21 3.07
2121 2555 4.467769 GGATCATCATCTTCACCACCAAT 58.532 43.478 0.00 0.00 0.00 3.16
2195 2629 1.683385 CATCGAGATGTCCTACTGCCA 59.317 52.381 4.99 0.00 34.23 4.92
2352 4452 3.496160 CGAAGAAGAAAAAGAGGGACCCA 60.496 47.826 14.60 0.00 0.00 4.51
2392 4492 0.461548 AATCGAGGCGATCAAGCAGA 59.538 50.000 2.56 0.00 46.30 4.26
2435 4535 0.474660 AAGGTGAAGGAGGCAGAGGT 60.475 55.000 0.00 0.00 0.00 3.85
2509 4621 2.545810 AGGAGGAAGACCAAGAGAAGG 58.454 52.381 0.00 0.00 38.94 3.46
2551 4663 2.675658 TGGGGATATTAAGCAAGGCC 57.324 50.000 0.00 0.00 0.00 5.19
3021 5200 2.417243 GCCCTGACCAAATGTAACATGC 60.417 50.000 0.00 0.00 0.00 4.06
3262 5492 1.275856 GTGCCAAAATGATTCAGCCCA 59.724 47.619 0.00 0.00 0.00 5.36
3424 5668 7.265673 TGATTAGACGGATTGAGGAAACTAAG 58.734 38.462 0.00 0.00 44.43 2.18
3547 5791 6.766467 AGGAATAAAGACAAACAAGTCGAACT 59.234 34.615 0.00 0.00 43.24 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 7.471890 ACCCAACCCTACATAATTGTTCTTAA 58.528 34.615 0.00 0.00 37.28 1.85
283 286 6.981559 AGAAGTGTCCTTTCTTATATCTTCGC 59.018 38.462 0.00 0.00 35.45 4.70
297 300 7.837187 ACTTAGCTAATAGAGAGAAGTGTCCTT 59.163 37.037 6.64 0.00 32.95 3.36
399 405 0.913924 GGGGTCTTTGGTCCCGATTA 59.086 55.000 0.00 0.00 44.27 1.75
402 408 2.931649 GGGGGTCTTTGGTCCCGA 60.932 66.667 0.00 0.00 44.27 5.14
492 498 6.742559 ATGGGTCGTTACTAATACCTTCAT 57.257 37.500 0.00 0.00 32.38 2.57
495 501 7.201947 GGACTAATGGGTCGTTACTAATACCTT 60.202 40.741 0.00 0.00 37.12 3.50
566 572 4.202388 TGAACACTAGTAGAAAACCACCCC 60.202 45.833 3.59 0.00 0.00 4.95
624 630 5.221263 ACGTAGCTTTGATAATCGGAGATGT 60.221 40.000 0.00 0.00 45.12 3.06
777 793 0.179089 ATGCAGACTTGGCTAGCTCG 60.179 55.000 15.72 5.82 0.00 5.03
828 844 5.219343 AGCATTGATCGAATAGTCCATGA 57.781 39.130 0.00 0.00 0.00 3.07
837 853 1.224069 CCGGCGAGCATTGATCGAAT 61.224 55.000 26.79 0.00 44.55 3.34
905 1031 6.939627 TGCGTGTACATGTTGCTTATATAAC 58.060 36.000 16.28 0.00 0.00 1.89
932 1330 0.038159 GTGACTTGGACCGGACTGAG 60.038 60.000 9.46 7.01 0.00 3.35
933 1331 1.469335 GGTGACTTGGACCGGACTGA 61.469 60.000 9.46 0.00 0.00 3.41
940 1338 2.668550 GCCGTGGTGACTTGGACC 60.669 66.667 0.00 0.00 0.00 4.46
946 1344 0.321653 GATGGAAAGCCGTGGTGACT 60.322 55.000 0.00 0.00 36.79 3.41
952 1350 0.948623 TGTGTCGATGGAAAGCCGTG 60.949 55.000 0.00 0.00 36.79 4.94
979 1379 2.043450 CGGACTGGGAGCTCCTCT 60.043 66.667 31.36 14.39 36.20 3.69
990 1397 2.821366 GCTGTCATGGCCGGACTG 60.821 66.667 23.14 22.62 36.26 3.51
991 1398 4.457496 CGCTGTCATGGCCGGACT 62.457 66.667 23.14 0.00 36.26 3.85
1051 1459 1.127343 GACCAGAGGAAGATGAGGGG 58.873 60.000 0.00 0.00 0.00 4.79
1054 1462 1.135915 CACGGACCAGAGGAAGATGAG 59.864 57.143 0.00 0.00 0.00 2.90
1142 1562 1.404391 TCTCGAGGTACGGATTGAAGC 59.596 52.381 13.56 0.00 42.82 3.86
1197 1631 1.080434 GAGGAAGAAGTCGCTGCGT 60.080 57.895 22.48 1.98 0.00 5.24
1438 1872 2.278857 CCGCCGATGGAAGACGAG 60.279 66.667 0.00 0.00 0.00 4.18
1464 1898 4.444449 GGAAGGTAGGAGTCAACAACAAGT 60.444 45.833 0.00 0.00 0.00 3.16
1470 1904 3.006537 CGAAAGGAAGGTAGGAGTCAACA 59.993 47.826 0.00 0.00 0.00 3.33
1519 1953 2.556287 GCGTTGGCGGTTCTTCAG 59.444 61.111 0.00 0.00 38.78 3.02
1900 2334 3.495331 AGCAGTCGATGTCCTCTATGAT 58.505 45.455 0.00 0.00 0.00 2.45
2121 2555 2.180276 GGGTCTAGCTTCTCCTTGTGA 58.820 52.381 0.00 0.00 0.00 3.58
2195 2629 1.986882 CACCTTGAAGCCCTCAAAGT 58.013 50.000 0.95 0.00 43.54 2.66
2352 4452 1.842562 AGGCCTATCAAGCACACATCT 59.157 47.619 1.29 0.00 0.00 2.90
2383 4483 1.661463 TCCTCCTTGGTCTGCTTGAT 58.339 50.000 0.00 0.00 37.07 2.57
2392 4492 4.394712 CGCCGCTTCCTCCTTGGT 62.395 66.667 0.00 0.00 37.07 3.67
2435 4535 2.247790 GCTTTCTTCGCTTGAGCCA 58.752 52.632 0.00 0.00 37.91 4.75
2509 4621 2.281484 TGCCTCGGGTGCTTTGTC 60.281 61.111 0.00 0.00 0.00 3.18
2551 4663 3.661678 CGCGTGATGTCACTTTACTTGTG 60.662 47.826 11.03 0.00 44.34 3.33
2573 4685 4.524328 TCATTCTTTTTCCTTGGCTTCCTC 59.476 41.667 0.00 0.00 0.00 3.71
2869 4996 5.967674 GCTAATTGCATATTGTCACTGTCAC 59.032 40.000 0.00 0.00 42.31 3.67
3021 5200 9.781834 TGTTTTGTTCTGTTCTTACAACAATAG 57.218 29.630 0.00 0.00 35.83 1.73
3262 5492 4.647611 TCATCATAACGTTGGAGGTGTTT 58.352 39.130 11.99 0.00 0.00 2.83
3403 5647 6.845758 TTCTTAGTTTCCTCAATCCGTCTA 57.154 37.500 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.