Multiple sequence alignment - TraesCS7A01G417400

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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 TraesCS7A01G417400 chr7A 100.000 2840 0 0 1 2840 609132729 609135568 0.000000e+00 5245
1 TraesCS7A01G417400 chr7A 96.132 1060 36 2 1786 2840 114015827 114014768 0.000000e+00 1725
2 TraesCS7A01G417400 chr7A 95.369 1058 45 3 1786 2840 584024251 584025307 0.000000e+00 1679
3 TraesCS7A01G417400 chr7A 90.024 842 58 8 750 1580 609340063 609339237 0.000000e+00 1066
4 TraesCS7A01G417400 chr7A 93.906 640 34 3 1 639 731780272 731780907 0.000000e+00 961
5 TraesCS7A01G417400 chr7A 93.760 641 34 4 1 639 494626538 494625902 0.000000e+00 957
6 TraesCS7A01G417400 chr7A 93.396 212 14 0 1576 1787 609339211 609339000 5.910000e-82 315
7 TraesCS7A01G417400 chr1A 96.026 1057 39 2 1786 2840 556986187 556985132 0.000000e+00 1716
8 TraesCS7A01G417400 chr1A 94.531 640 32 2 1 639 465431117 465431754 0.000000e+00 985
9 TraesCS7A01G417400 chr4A 95.743 1057 45 0 1784 2840 45495595 45494539 0.000000e+00 1703
10 TraesCS7A01G417400 chr4A 94.219 640 33 3 1 639 467344932 467345568 0.000000e+00 974
11 TraesCS7A01G417400 chr4A 94.210 639 32 3 1 638 640204078 640204712 0.000000e+00 970
12 TraesCS7A01G417400 chrUn 95.644 1056 45 1 1786 2840 30844547 30845602 0.000000e+00 1694
13 TraesCS7A01G417400 chr5A 95.558 1058 42 2 1784 2840 680228632 680227579 0.000000e+00 1688
14 TraesCS7A01G417400 chr5A 94.860 642 23 6 1 639 20787700 20788334 0.000000e+00 994
15 TraesCS7A01G417400 chr5A 94.844 640 28 3 1 639 411880157 411880792 0.000000e+00 994
16 TraesCS7A01G417400 chr3A 95.450 1055 48 0 1786 2840 721073495 721072441 0.000000e+00 1683
17 TraesCS7A01G417400 chr3A 94.995 1059 52 1 1782 2840 705560702 705559645 0.000000e+00 1661
18 TraesCS7A01G417400 chr3A 94.099 644 33 4 1 641 538022908 538023549 0.000000e+00 974
19 TraesCS7A01G417400 chr2A 95.296 1063 38 8 1786 2840 197905919 197906977 0.000000e+00 1676
20 TraesCS7A01G417400 chr2A 93.789 644 33 5 1 642 160012490 160011852 0.000000e+00 961
21 TraesCS7A01G417400 chr7D 90.878 1162 77 10 631 1782 529680236 529681378 0.000000e+00 1531
22 TraesCS7A01G417400 chr7D 93.351 752 50 0 829 1580 529774259 529773508 0.000000e+00 1112
23 TraesCS7A01G417400 chr7D 95.673 208 9 0 1576 1783 529773482 529773275 4.530000e-88 335
24 TraesCS7A01G417400 chr7D 90.184 163 7 3 631 788 529774418 529774260 1.330000e-48 204
25 TraesCS7A01G417400 chr7B 88.740 1119 70 21 698 1783 567885005 567883910 0.000000e+00 1317
26 TraesCS7A01G417400 chr7B 91.684 938 55 5 648 1577 567635210 567636132 0.000000e+00 1279
27 TraesCS7A01G417400 chr7B 95.192 208 10 0 1576 1783 567636161 567636368 2.110000e-86 329


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 TraesCS7A01G417400 chr7A 609132729 609135568 2839 False 5245.000000 5245 100.000000 1 2840 1 chr7A.!!$F2 2839
1 TraesCS7A01G417400 chr7A 114014768 114015827 1059 True 1725.000000 1725 96.132000 1786 2840 1 chr7A.!!$R1 1054
2 TraesCS7A01G417400 chr7A 584024251 584025307 1056 False 1679.000000 1679 95.369000 1786 2840 1 chr7A.!!$F1 1054
3 TraesCS7A01G417400 chr7A 731780272 731780907 635 False 961.000000 961 93.906000 1 639 1 chr7A.!!$F3 638
4 TraesCS7A01G417400 chr7A 494625902 494626538 636 True 957.000000 957 93.760000 1 639 1 chr7A.!!$R2 638
5 TraesCS7A01G417400 chr7A 609339000 609340063 1063 True 690.500000 1066 91.710000 750 1787 2 chr7A.!!$R3 1037
6 TraesCS7A01G417400 chr1A 556985132 556986187 1055 True 1716.000000 1716 96.026000 1786 2840 1 chr1A.!!$R1 1054
7 TraesCS7A01G417400 chr1A 465431117 465431754 637 False 985.000000 985 94.531000 1 639 1 chr1A.!!$F1 638
8 TraesCS7A01G417400 chr4A 45494539 45495595 1056 True 1703.000000 1703 95.743000 1784 2840 1 chr4A.!!$R1 1056
9 TraesCS7A01G417400 chr4A 467344932 467345568 636 False 974.000000 974 94.219000 1 639 1 chr4A.!!$F1 638
10 TraesCS7A01G417400 chr4A 640204078 640204712 634 False 970.000000 970 94.210000 1 638 1 chr4A.!!$F2 637
11 TraesCS7A01G417400 chrUn 30844547 30845602 1055 False 1694.000000 1694 95.644000 1786 2840 1 chrUn.!!$F1 1054
12 TraesCS7A01G417400 chr5A 680227579 680228632 1053 True 1688.000000 1688 95.558000 1784 2840 1 chr5A.!!$R1 1056
13 TraesCS7A01G417400 chr5A 20787700 20788334 634 False 994.000000 994 94.860000 1 639 1 chr5A.!!$F1 638
14 TraesCS7A01G417400 chr5A 411880157 411880792 635 False 994.000000 994 94.844000 1 639 1 chr5A.!!$F2 638
15 TraesCS7A01G417400 chr3A 721072441 721073495 1054 True 1683.000000 1683 95.450000 1786 2840 1 chr3A.!!$R2 1054
16 TraesCS7A01G417400 chr3A 705559645 705560702 1057 True 1661.000000 1661 94.995000 1782 2840 1 chr3A.!!$R1 1058
17 TraesCS7A01G417400 chr3A 538022908 538023549 641 False 974.000000 974 94.099000 1 641 1 chr3A.!!$F1 640
18 TraesCS7A01G417400 chr2A 197905919 197906977 1058 False 1676.000000 1676 95.296000 1786 2840 1 chr2A.!!$F1 1054
19 TraesCS7A01G417400 chr2A 160011852 160012490 638 True 961.000000 961 93.789000 1 642 1 chr2A.!!$R1 641
20 TraesCS7A01G417400 chr7D 529680236 529681378 1142 False 1531.000000 1531 90.878000 631 1782 1 chr7D.!!$F1 1151
21 TraesCS7A01G417400 chr7D 529773275 529774418 1143 True 550.333333 1112 93.069333 631 1783 3 chr7D.!!$R1 1152
22 TraesCS7A01G417400 chr7B 567883910 567885005 1095 True 1317.000000 1317 88.740000 698 1783 1 chr7B.!!$R1 1085
23 TraesCS7A01G417400 chr7B 567635210 567636368 1158 False 804.000000 1279 93.438000 648 1783 2 chr7B.!!$F1 1135

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
677 686 0.178992 TCACAGCAACCCCTCCTTTG 60.179 55.0 0.0 0.0 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 2395 0.876399 TTTGGATCGTGACGACTCGA 59.124 50.0 10.91 13.7 44.0 4.04 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
166 168 2.261671 GACATCCCGTGCGAGTGT 59.738 61.111 0.00 0.0 0.00 3.55
178 180 1.676678 GCGAGTGTGATGGAGGGCTA 61.677 60.000 0.00 0.0 0.00 3.93
276 278 1.133181 TTGAGGAGTGGTGGGCATGA 61.133 55.000 0.00 0.0 0.00 3.07
462 467 6.676237 TGCTTCTGTTTTCGAATGCATATA 57.324 33.333 0.00 0.0 0.00 0.86
538 545 2.485122 GCTGCATTTTAGCGCGGT 59.515 55.556 17.70 17.7 36.85 5.68
598 605 2.931386 GCGCGTGGCATATCTGTC 59.069 61.111 8.43 0.0 42.87 3.51
660 669 7.277405 TCTTATGATCTAGAGATAGGCCTCA 57.723 40.000 9.68 0.0 35.68 3.86
677 686 0.178992 TCACAGCAACCCCTCCTTTG 60.179 55.000 0.00 0.0 0.00 2.77
690 699 2.489073 CCTCCTTTGTGCCCACTACTTT 60.489 50.000 0.00 0.0 0.00 2.66
691 700 2.554032 CTCCTTTGTGCCCACTACTTTG 59.446 50.000 0.00 0.0 0.00 2.77
692 701 1.000274 CCTTTGTGCCCACTACTTTGC 60.000 52.381 0.00 0.0 0.00 3.68
734 746 4.288645 GCTCTCAGCTACGTACGC 57.711 61.111 16.72 0.0 38.45 4.42
776 793 1.697432 TCCAAACCCAACTGATCGAGT 59.303 47.619 0.00 0.0 35.94 4.18
788 805 6.923508 CCAACTGATCGAGTAAGCACAATATA 59.076 38.462 0.00 0.0 33.09 0.86
789 806 7.438160 CCAACTGATCGAGTAAGCACAATATAA 59.562 37.037 0.00 0.0 33.09 0.98
790 807 8.483218 CAACTGATCGAGTAAGCACAATATAAG 58.517 37.037 0.00 0.0 33.09 1.73
791 808 7.717568 ACTGATCGAGTAAGCACAATATAAGT 58.282 34.615 0.00 0.0 30.86 2.24
792 809 8.198109 ACTGATCGAGTAAGCACAATATAAGTT 58.802 33.333 0.00 0.0 30.86 2.66
793 810 9.678941 CTGATCGAGTAAGCACAATATAAGTTA 57.321 33.333 0.00 0.0 0.00 2.24
806 823 8.188139 CACAATATAAGTTATCAACACAACCCC 58.812 37.037 0.00 0.0 0.00 4.95
807 824 7.340999 ACAATATAAGTTATCAACACAACCCCC 59.659 37.037 0.00 0.0 0.00 5.40
808 825 2.194201 AGTTATCAACACAACCCCCG 57.806 50.000 0.00 0.0 0.00 5.73
809 826 1.700739 AGTTATCAACACAACCCCCGA 59.299 47.619 0.00 0.0 0.00 5.14
876 896 2.103042 GTGCAAGCTCGGCTTCGAT 61.103 57.895 11.13 0.0 46.77 3.59
916 936 3.969250 TTCCGCCAGGTTCCATCGC 62.969 63.158 0.00 0.0 39.05 4.58
920 940 4.096003 CCAGGTTCCATCGCCCGT 62.096 66.667 0.00 0.0 0.00 5.28
938 958 0.541863 GTCCACGATGGGGAACTGAT 59.458 55.000 0.00 0.0 38.32 2.90
940 960 0.530650 CCACGATGGGGAACTGATCG 60.531 60.000 0.00 0.0 43.65 3.69
1027 1047 2.202797 CGCAGACCATCCTCACGG 60.203 66.667 0.00 0.0 0.00 4.94
1264 1292 3.385384 CGCTGCTGAGGGAGGTCA 61.385 66.667 0.00 0.0 33.95 4.02
1270 1298 2.038813 TGAGGGAGGTCATGCCGA 59.961 61.111 0.00 0.0 46.07 5.54
1338 1366 2.125673 GTGGACGTGCTGGCGTAT 60.126 61.111 8.99 0.0 45.79 3.06
1474 1502 0.744057 CATGCAGGCGTACATGGTCA 60.744 55.000 11.09 0.0 39.98 4.02
1565 1593 0.969894 CTCCAGAAGACCCACTCGTT 59.030 55.000 0.00 0.0 0.00 3.85
1582 1645 3.545124 TTGTTCGATGCGGTGGGCT 62.545 57.895 0.00 0.0 44.05 5.19
1791 1854 2.877691 GTGCTCGGGATTGTTGGC 59.122 61.111 0.00 0.0 0.00 4.52
1959 2024 1.473278 ACGATCTCGAACAGGAAGGAC 59.527 52.381 6.60 0.0 43.02 3.85
2080 2145 2.733218 CGAAGTCGTCGCTGCCAA 60.733 61.111 0.00 0.0 44.14 4.52
2115 2180 1.886222 CGCTCCCCAAAAACCTGATCA 60.886 52.381 0.00 0.0 0.00 2.92
2147 2212 2.121538 CAGGATCACGAGAGGCGGA 61.122 63.158 0.00 0.0 46.49 5.54
2174 2239 0.413832 AGGCCTACTGTCCCTTCTCA 59.586 55.000 1.29 0.0 0.00 3.27
2285 2350 0.395311 TAGGGTAGACGTCTGCCTGG 60.395 60.000 39.82 0.0 46.34 4.45
2423 2489 5.716228 TGACTCATTAATTTTCCCATGCAGT 59.284 36.000 0.00 0.0 0.00 4.40
2475 2541 4.537433 GCTCGGCTCAATCCCGCT 62.537 66.667 0.00 0.0 45.19 5.52
2671 2753 2.754552 TGAATGGGCCAAGAGAATTTCG 59.245 45.455 11.89 0.0 0.00 3.46
2735 2817 2.447429 TCCAACAATCCCCCACAAAGTA 59.553 45.455 0.00 0.0 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 168 1.284785 CACCCTTTTAGCCCTCCATCA 59.715 52.381 0.00 0.00 0.00 3.07
178 180 0.978667 ACAAAACGGGCCACCCTTTT 60.979 50.000 4.39 1.48 45.27 2.27
276 278 3.411446 TGATGCTCTTTGTCGTCCATTT 58.589 40.909 0.00 0.00 0.00 2.32
487 492 1.007038 CAGCAGTGCGCCAAAATGT 60.007 52.632 10.00 0.00 44.04 2.71
499 504 4.996434 GTGCACCGCTCCAGCAGT 62.996 66.667 5.22 0.00 42.21 4.40
586 593 1.401552 GCGCAAAAGACAGATATGCCA 59.598 47.619 0.30 0.00 33.55 4.92
660 669 0.468029 CACAAAGGAGGGGTTGCTGT 60.468 55.000 0.00 0.00 0.00 4.40
677 686 2.076863 CAGTAGCAAAGTAGTGGGCAC 58.923 52.381 0.00 0.00 0.00 5.01
734 746 0.035036 TTTGGGTGCAATGCATGGTG 59.965 50.000 12.38 0.00 41.91 4.17
788 805 2.106857 TCGGGGGTTGTGTTGATAACTT 59.893 45.455 0.00 0.00 0.00 2.66
789 806 1.700739 TCGGGGGTTGTGTTGATAACT 59.299 47.619 0.00 0.00 0.00 2.24
790 807 2.081462 CTCGGGGGTTGTGTTGATAAC 58.919 52.381 0.00 0.00 0.00 1.89
791 808 1.979308 TCTCGGGGGTTGTGTTGATAA 59.021 47.619 0.00 0.00 0.00 1.75
792 809 1.646912 TCTCGGGGGTTGTGTTGATA 58.353 50.000 0.00 0.00 0.00 2.15
793 810 0.991920 ATCTCGGGGGTTGTGTTGAT 59.008 50.000 0.00 0.00 0.00 2.57
794 811 0.323629 GATCTCGGGGGTTGTGTTGA 59.676 55.000 0.00 0.00 0.00 3.18
806 823 2.854777 GTGTCAGTCAAATCGATCTCGG 59.145 50.000 0.00 0.00 40.29 4.63
807 824 2.854777 GGTGTCAGTCAAATCGATCTCG 59.145 50.000 0.00 0.00 41.45 4.04
808 825 3.849911 TGGTGTCAGTCAAATCGATCTC 58.150 45.455 0.00 0.00 0.00 2.75
809 826 3.961480 TGGTGTCAGTCAAATCGATCT 57.039 42.857 0.00 0.00 0.00 2.75
916 936 3.395702 TTCCCCATCGTGGACGGG 61.396 66.667 5.71 0.00 40.96 5.28
920 940 0.830648 GATCAGTTCCCCATCGTGGA 59.169 55.000 5.71 0.00 40.96 4.02
984 1004 4.666253 ATGCCCACGTTGCCAGCT 62.666 61.111 4.50 0.00 0.00 4.24
1005 1025 1.663074 GAGGATGGTCTGCGCGATC 60.663 63.158 12.10 1.75 0.00 3.69
1113 1133 4.143333 CGGACGCGTGGGAGGAAT 62.143 66.667 20.70 0.00 0.00 3.01
1168 1188 3.474570 GATGGCCAGGTCGGAGCT 61.475 66.667 13.05 3.41 36.56 4.09
1299 1327 1.227556 GTTCGACACCACCAGCAGT 60.228 57.895 0.00 0.00 0.00 4.40
1338 1366 2.747460 GACAGCTTCCATGCCGCA 60.747 61.111 0.00 0.00 0.00 5.69
1344 1372 1.299976 GAACCCCGACAGCTTCCAT 59.700 57.895 0.00 0.00 0.00 3.41
1456 1484 0.462581 CTGACCATGTACGCCTGCAT 60.463 55.000 0.00 0.00 0.00 3.96
1474 1502 4.521062 GCCGTCTCCATGCTCGCT 62.521 66.667 0.00 0.00 0.00 4.93
1565 1593 4.015406 AGCCCACCGCATCGAACA 62.015 61.111 0.00 0.00 41.38 3.18
2115 2180 1.591280 ATCCTGTACGGGAGAGGGGT 61.591 60.000 27.05 7.97 39.21 4.95
2147 2212 0.971447 GACAGTAGGCCTCCGGAACT 60.971 60.000 9.68 3.17 0.00 3.01
2285 2350 1.153628 CCGGCCCGCACTATATAGC 60.154 63.158 9.78 0.00 0.00 2.97
2330 2395 0.876399 TTTGGATCGTGACGACTCGA 59.124 50.000 10.91 13.70 44.00 4.04
2423 2489 8.657074 AGCTATGCACGTTGTCTATATTTTTA 57.343 30.769 0.00 0.00 0.00 1.52
2497 2579 1.896694 CTCCTCCTCTTTGCTCGCT 59.103 57.895 0.00 0.00 0.00 4.93
2671 2753 3.868369 GCCCAAAGCCCAACTAAAATTCC 60.868 47.826 0.00 0.00 34.35 3.01
2708 2790 3.718956 TGTGGGGGATTGTTGGAATTTTT 59.281 39.130 0.00 0.00 0.00 1.94
2735 2817 6.776116 ACTAAATGATGAGATGTGCCAATGAT 59.224 34.615 0.00 0.00 0.00 2.45
2781 2863 0.889306 AGTCTCCACTAAGCACCGAC 59.111 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.