Multiple sequence alignment - TraesCS7A01G322900

Loading Multiple Alignment...

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 TraesCS7A01G322900 chr7A 100.000 3587 0 0 1 3587 468831099 468834685 0.000000e+00 6625
1 TraesCS7A01G322900 chr7A 86.726 113 14 1 3132 3244 222578224 222578113 1.350000e-24 124
2 TraesCS7A01G322900 chr7B 94.212 3611 146 21 1 3568 423138361 423141951 0.000000e+00 5452
3 TraesCS7A01G322900 chr7D 94.682 3253 139 19 291 3511 408717649 408720899 0.000000e+00 5018
4 TraesCS7A01G322900 chr7D 97.342 301 5 2 1 301 408717332 408717629 3.200000e-140 508
5 TraesCS7A01G322900 chr7D 98.750 80 1 0 3508 3587 408721017 408721096 3.730000e-30 143
6 TraesCS7A01G322900 chr4B 85.025 601 75 8 1531 2118 671813893 671814491 6.630000e-167 597
7 TraesCS7A01G322900 chr4B 81.919 542 61 17 658 1189 671734187 671733673 1.190000e-114 424
8 TraesCS7A01G322900 chr4B 88.841 233 24 1 1897 2127 671732611 671732379 5.860000e-73 285
9 TraesCS7A01G322900 chrUn 84.095 503 63 8 1638 2127 30346827 30346329 1.510000e-128 470
10 TraesCS7A01G322900 chrUn 82.267 547 64 23 658 1189 30347546 30347018 3.290000e-120 442
11 TraesCS7A01G322900 chrUn 82.081 346 47 11 1897 2235 30340870 30340533 7.580000e-72 281
12 TraesCS7A01G322900 chrUn 77.754 463 72 16 753 1189 30342335 30341878 4.600000e-64 255
13 TraesCS7A01G322900 chrUn 87.047 193 25 0 2256 2448 30344848 30344656 6.030000e-53 219
14 TraesCS7A01G322900 chrUn 85.366 123 18 0 3119 3241 472409320 472409442 1.050000e-25 128
15 TraesCS7A01G322900 chr5A 83.968 499 62 9 1638 2118 659186291 659186789 2.520000e-126 462
16 TraesCS7A01G322900 chr5A 82.440 541 64 18 658 1188 659184788 659185307 9.140000e-121 444
17 TraesCS7A01G322900 chr5A 81.937 537 64 20 1635 2158 659185498 659186014 1.190000e-114 424
18 TraesCS7A01G322900 chr5A 82.235 349 47 11 1894 2235 659202405 659202745 1.630000e-73 287
19 TraesCS7A01G322900 chr5A 86.010 193 27 0 2256 2448 659187093 659187285 1.310000e-49 207
20 TraesCS7A01G322900 chr5A 88.356 146 17 0 1723 1868 709732256 709732111 3.680000e-40 176
21 TraesCS7A01G322900 chr5A 93.069 101 4 2 2353 2452 709723645 709723547 1.040000e-30 145
22 TraesCS7A01G322900 chr5A 85.714 105 12 2 1088 1189 659201296 659201400 1.360000e-19 108
23 TraesCS7A01G322900 chr4A 87.611 113 13 1 3132 3244 736230828 736230717 2.910000e-26 130
24 TraesCS7A01G322900 chr3B 87.611 113 13 1 3132 3244 814646920 814646809 2.910000e-26 130
25 TraesCS7A01G322900 chr5D 83.478 115 19 0 1578 1692 503148865 503148979 1.360000e-19 108


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 TraesCS7A01G322900 chr7A 468831099 468834685 3586 False 6625.000000 6625 100.000000 1 3587 1 chr7A.!!$F1 3586
1 TraesCS7A01G322900 chr7B 423138361 423141951 3590 False 5452.000000 5452 94.212000 1 3568 1 chr7B.!!$F1 3567
2 TraesCS7A01G322900 chr7D 408717332 408721096 3764 False 1889.666667 5018 96.924667 1 3587 3 chr7D.!!$F1 3586
3 TraesCS7A01G322900 chr4B 671813893 671814491 598 False 597.000000 597 85.025000 1531 2118 1 chr4B.!!$F1 587
4 TraesCS7A01G322900 chr4B 671732379 671734187 1808 True 354.500000 424 85.380000 658 2127 2 chr4B.!!$R1 1469
5 TraesCS7A01G322900 chrUn 30340533 30347546 7013 True 333.400000 470 82.648800 658 2448 5 chrUn.!!$R1 1790
6 TraesCS7A01G322900 chr5A 659184788 659187285 2497 False 384.250000 462 83.588750 658 2448 4 chr5A.!!$F1 1790

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
589 621 0.044161 GCGCGAATTACTAGCACACG 60.044 55.0 12.10 0.0 0.0 4.49 F
1047 1094 1.194781 TGGAGAGGGGCAAGTCTGAC 61.195 60.0 0.00 0.0 0.0 3.51 F
2230 4966 0.247695 GTTCACGCGGCAAATCTAGC 60.248 55.0 12.47 0.0 0.0 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 2621 0.242825 AGAATCGCCGTCAAAGTCGA 59.757 50.000 0.00 0.0 35.34 4.20 R
2236 4972 1.238439 CCAACCGATGACTGCAACTT 58.762 50.000 0.00 0.0 0.00 2.66 R
3329 7072 3.108881 AGATCGATGAACGTCAATGTCG 58.891 45.455 0.54 0.0 43.13 4.35 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
153 154 6.183347 AGATGATGACATGCATGATGATCAT 58.817 36.000 30.80 30.80 37.34 2.45
183 184 6.842437 AGCAGAACACAAGTAATCTCTCTA 57.158 37.500 0.00 0.00 0.00 2.43
301 302 4.633565 GCAGGAGAAATGAACACCTCTTAG 59.366 45.833 0.00 0.00 0.00 2.18
306 337 9.268282 AGGAGAAATGAACACCTCTTAGTAATA 57.732 33.333 0.00 0.00 0.00 0.98
349 380 6.681777 AGATACAGCTGCAAAAAGGTTTAAG 58.318 36.000 15.27 0.00 0.00 1.85
391 422 0.814457 TGCACGCACTCAAGGTTTTT 59.186 45.000 0.00 0.00 0.00 1.94
453 485 5.245301 TCGAAATGGGTTCTTTCTAGTCAGA 59.755 40.000 0.00 0.00 33.70 3.27
539 571 3.181493 GCATGCCTTGTAATGGTCTCAAG 60.181 47.826 6.36 0.00 38.45 3.02
540 572 3.788227 TGCCTTGTAATGGTCTCAAGT 57.212 42.857 0.00 0.00 37.45 3.16
542 574 5.235850 TGCCTTGTAATGGTCTCAAGTTA 57.764 39.130 0.00 0.00 37.45 2.24
571 603 8.237267 AGAACACAAGTTGCTATTTACATAAGC 58.763 33.333 1.81 0.00 38.30 3.09
584 616 5.817616 TTACATAAGCGCGAATTACTAGC 57.182 39.130 12.10 0.00 0.00 3.42
586 618 3.489785 ACATAAGCGCGAATTACTAGCAC 59.510 43.478 12.10 0.00 0.00 4.40
589 621 0.044161 GCGCGAATTACTAGCACACG 60.044 55.000 12.10 0.00 0.00 4.49
677 709 3.823873 TGGCCAATGGTTTAAGTACACTG 59.176 43.478 0.61 0.00 0.00 3.66
696 728 2.548057 CTGCAAGAAGTACAAGGCGAAA 59.452 45.455 0.00 0.00 34.07 3.46
733 765 2.119801 AGTCCATGACAACTGCATCC 57.880 50.000 0.00 0.00 34.60 3.51
962 1009 7.234782 TGTGTGTATATAACTAGGGGATTGAGG 59.765 40.741 0.00 0.00 0.00 3.86
1047 1094 1.194781 TGGAGAGGGGCAAGTCTGAC 61.195 60.000 0.00 0.00 0.00 3.51
1575 2413 2.763448 ACTAGTCCTCAGGCAAGACATC 59.237 50.000 0.00 0.00 32.82 3.06
1696 2539 4.824289 AGCATGCCAAATCCTTGTTTTAG 58.176 39.130 15.66 0.00 0.00 1.85
1699 2542 6.014669 AGCATGCCAAATCCTTGTTTTAGTTA 60.015 34.615 15.66 0.00 0.00 2.24
1768 2621 6.259608 CCATGCAAGAGACTCTTCGAAATATT 59.740 38.462 14.99 0.00 33.78 1.28
1786 2639 1.065358 TTCGACTTTGACGGCGATTC 58.935 50.000 16.62 1.19 32.38 2.52
2199 4935 9.078990 ACATGACTATACAAGCTACTAGCAATA 57.921 33.333 10.73 0.43 45.56 1.90
2230 4966 0.247695 GTTCACGCGGCAAATCTAGC 60.248 55.000 12.47 0.00 0.00 3.42
2236 4972 1.586422 GCGGCAAATCTAGCTCATCA 58.414 50.000 0.00 0.00 0.00 3.07
2250 5011 2.222976 GCTCATCAAGTTGCAGTCATCG 60.223 50.000 0.00 0.00 0.00 3.84
2271 5092 3.733684 CGGTTGGTTTGAGTTGTTTCCAG 60.734 47.826 0.00 0.00 0.00 3.86
2375 5196 0.920763 ATGGGGAACTGCCAGGATCA 60.921 55.000 0.00 0.00 38.95 2.92
2509 5331 2.951457 TCAGTCATTGCATTGCATGG 57.049 45.000 12.95 7.89 38.76 3.66
2510 5332 2.448453 TCAGTCATTGCATTGCATGGA 58.552 42.857 12.95 10.18 38.76 3.41
2537 5359 2.290367 TGTGTTTTCTGATGCCGTTCAG 59.710 45.455 2.81 2.81 43.70 3.02
2545 5367 3.452990 TCTGATGCCGTTCAGGGTTAATA 59.547 43.478 8.13 0.00 42.78 0.98
2658 5480 4.630069 ACTGCACAAGCTAATTAACCTACG 59.370 41.667 0.00 0.00 42.74 3.51
2703 5526 2.361119 GGACTTCTTTGTTGGTGGGTTC 59.639 50.000 0.00 0.00 0.00 3.62
2813 5638 8.148437 TGTAGTTTTAGTGGGTTGGATGTATA 57.852 34.615 0.00 0.00 0.00 1.47
2814 5639 8.042515 TGTAGTTTTAGTGGGTTGGATGTATAC 58.957 37.037 0.00 0.00 0.00 1.47
3044 6737 9.956720 GTTTCATCCCAGTTTGATTTATCATAG 57.043 33.333 0.00 0.00 36.56 2.23
3329 7072 7.081349 CGTACCTGATATCTTGAGATGAAGAC 58.919 42.308 3.98 0.00 34.79 3.01
3351 7094 3.547868 CGACATTGACGTTCATCGATCTT 59.452 43.478 0.00 0.00 42.86 2.40
3437 7192 4.539870 CTGTTTGCTTCATCGTTTCACAT 58.460 39.130 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.948309 CCACCTATTAGCAGGGCTTAATTAAT 59.052 38.462 0.00 0.00 40.44 1.40
232 233 2.265904 TCACCCCTCGTGAGTGACG 61.266 63.158 0.00 0.00 46.80 4.35
349 380 1.581934 TCTTATGCATACGCCAGTGC 58.418 50.000 5.74 0.00 41.61 4.40
453 485 1.133853 GGCTGCTCCCTGAGAAATCAT 60.134 52.381 0.00 0.00 0.00 2.45
571 603 1.541475 TCGTGTGCTAGTAATTCGCG 58.459 50.000 0.00 0.00 0.00 5.87
584 616 7.555639 TTTTATTTTAGCGGAAATTCGTGTG 57.444 32.000 5.80 0.00 31.96 3.82
586 618 8.442605 TCTTTTTATTTTAGCGGAAATTCGTG 57.557 30.769 5.80 0.00 31.96 4.35
619 651 5.633601 GCCACTCCAGCTTGTAAAAATAAAC 59.366 40.000 0.00 0.00 0.00 2.01
621 653 4.083003 CGCCACTCCAGCTTGTAAAAATAA 60.083 41.667 0.00 0.00 0.00 1.40
637 669 1.933853 CCATTAAGCTACACGCCACTC 59.066 52.381 0.00 0.00 40.39 3.51
677 709 3.492313 CATTTCGCCTTGTACTTCTTGC 58.508 45.455 0.00 0.00 0.00 4.01
696 728 7.504238 TCATGGACTTGTTTAACAGTTAACCAT 59.496 33.333 13.97 13.97 34.26 3.55
882 924 3.828451 ACAAATGATGGGGTCAACTTCTG 59.172 43.478 0.00 0.00 40.97 3.02
962 1009 2.092914 ACTACCTTAGGTTGGCATCTGC 60.093 50.000 10.01 0.00 37.09 4.26
973 1020 8.204903 TCTCCTAGATAGTGTACTACCTTAGG 57.795 42.308 0.00 0.00 34.16 2.69
1018 1065 1.118356 CCCCTCTCCATCTTCTCCCG 61.118 65.000 0.00 0.00 0.00 5.14
1047 1094 3.016971 TCCATGGCCACCCTCAGG 61.017 66.667 8.16 3.47 40.04 3.86
1095 1142 0.321475 GCTGCTGCTCCTGTTCTTCT 60.321 55.000 8.53 0.00 36.03 2.85
1233 1283 9.273016 CTTCCATTCTTACTGAACAAAAGAGTA 57.727 33.333 0.00 0.00 37.52 2.59
1575 2413 4.389687 GCAATTACCTGAACATTTTGCTGG 59.610 41.667 0.00 0.00 36.10 4.85
1768 2621 0.242825 AGAATCGCCGTCAAAGTCGA 59.757 50.000 0.00 0.00 35.34 4.20
1786 2639 3.640967 CCTTCCTCCACTTCCTCTATCAG 59.359 52.174 0.00 0.00 0.00 2.90
1940 3398 5.363517 CGTTTTGCGACACTTAAGAACTAG 58.636 41.667 10.09 0.00 44.77 2.57
2199 4935 3.564511 CCGCGTGAACAATCTTCAAATT 58.435 40.909 4.92 0.00 0.00 1.82
2230 4966 2.350804 CCGATGACTGCAACTTGATGAG 59.649 50.000 0.00 0.00 0.00 2.90
2236 4972 1.238439 CCAACCGATGACTGCAACTT 58.762 50.000 0.00 0.00 0.00 2.66
2250 5011 3.194755 ACTGGAAACAACTCAAACCAACC 59.805 43.478 0.00 0.00 42.06 3.77
2271 5092 5.665459 ACTATGCTCAACAGATTAGGTCAC 58.335 41.667 0.00 0.00 0.00 3.67
2375 5196 4.476113 TGACATCTCCTCCAAAATCCTCAT 59.524 41.667 0.00 0.00 0.00 2.90
2509 5331 5.065218 ACGGCATCAGAAAACACATATCTTC 59.935 40.000 0.00 0.00 0.00 2.87
2510 5332 4.943705 ACGGCATCAGAAAACACATATCTT 59.056 37.500 0.00 0.00 0.00 2.40
2537 5359 6.181908 TGGTGTTTGACCTGTATATTAACCC 58.818 40.000 0.00 0.00 46.32 4.11
2545 5367 2.553028 CCAGCTGGTGTTTGACCTGTAT 60.553 50.000 25.53 0.00 46.32 2.29
2658 5480 7.806014 TCCTTAATCTTCATTTTACAACGCAAC 59.194 33.333 0.00 0.00 0.00 4.17
3044 6737 8.215926 ACTATGTGAGAGAGTAAGTGTATGAC 57.784 38.462 0.00 0.00 0.00 3.06
3298 7041 5.079689 TCAAGATATCAGGTACGTGCAAA 57.920 39.130 10.71 0.00 0.00 3.68
3329 7072 3.108881 AGATCGATGAACGTCAATGTCG 58.891 45.455 0.54 0.00 43.13 4.35
3351 7094 3.617143 ATCGCAAGCAGCTGAGCCA 62.617 57.895 20.43 6.96 42.61 4.75
3425 7180 8.955061 AAAAATAACTCTGATGTGAAACGATG 57.045 30.769 0.00 0.00 42.39 3.84


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

AutoCloner maintained by Alex Coulton.