Multiple sequence alignment - TraesCS5A01G177600

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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 TraesCS5A01G177600 chr5A 100.000 3479 0 0 1 3479 375281924 375285402 0 6425
1 TraesCS5A01G177600 chr5A 94.514 802 30 6 1 789 651536651 651535851 0 1225
2 TraesCS5A01G177600 chr5A 94.140 802 31 7 1 787 622760458 622759658 0 1206
3 TraesCS5A01G177600 chr5A 93.742 799 38 7 1 789 636989464 636990260 0 1188
4 TraesCS5A01G177600 chr5D 95.410 2680 103 13 808 3479 283004859 283007526 0 4250
5 TraesCS5A01G177600 chr5B 95.038 2640 102 15 847 3479 321209104 321211721 0 4122
6 TraesCS5A01G177600 chr7A 94.257 801 32 4 1 787 636903939 636904739 0 1212
7 TraesCS5A01G177600 chr7A 94.132 801 33 8 1 789 59015355 59014557 0 1206
8 TraesCS5A01G177600 chr4A 93.617 799 40 4 1 789 532358442 532359239 0 1182
9 TraesCS5A01G177600 chr4A 93.601 797 40 5 1 787 171213325 171214120 0 1179
10 TraesCS5A01G177600 chr6A 93.601 797 41 3 1 787 21113195 21113991 0 1181
11 TraesCS5A01G177600 chr1A 93.292 805 30 9 1 789 552157608 552156812 0 1166


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 TraesCS5A01G177600 chr5A 375281924 375285402 3478 False 6425 6425 100.000 1 3479 1 chr5A.!!$F1 3478
1 TraesCS5A01G177600 chr5A 651535851 651536651 800 True 1225 1225 94.514 1 789 1 chr5A.!!$R2 788
2 TraesCS5A01G177600 chr5A 622759658 622760458 800 True 1206 1206 94.140 1 787 1 chr5A.!!$R1 786
3 TraesCS5A01G177600 chr5A 636989464 636990260 796 False 1188 1188 93.742 1 789 1 chr5A.!!$F2 788
4 TraesCS5A01G177600 chr5D 283004859 283007526 2667 False 4250 4250 95.410 808 3479 1 chr5D.!!$F1 2671
5 TraesCS5A01G177600 chr5B 321209104 321211721 2617 False 4122 4122 95.038 847 3479 1 chr5B.!!$F1 2632
6 TraesCS5A01G177600 chr7A 636903939 636904739 800 False 1212 1212 94.257 1 787 1 chr7A.!!$F1 786
7 TraesCS5A01G177600 chr7A 59014557 59015355 798 True 1206 1206 94.132 1 789 1 chr7A.!!$R1 788
8 TraesCS5A01G177600 chr4A 532358442 532359239 797 False 1182 1182 93.617 1 789 1 chr4A.!!$F2 788
9 TraesCS5A01G177600 chr4A 171213325 171214120 795 False 1179 1179 93.601 1 787 1 chr4A.!!$F1 786
10 TraesCS5A01G177600 chr6A 21113195 21113991 796 False 1181 1181 93.601 1 787 1 chr6A.!!$F1 786
11 TraesCS5A01G177600 chr1A 552156812 552157608 796 True 1166 1166 93.292 1 789 1 chr1A.!!$R1 788

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
532 551 0.108992 GTCATGTAGAACCGCGTGGA 60.109 55.0 24.59 0.00 39.21 4.02 F
1603 1638 0.309922 GTTCGAGACTGACCGTGTCA 59.690 55.0 6.57 6.57 40.50 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 1815 0.674895 GGCGCCATGACAGAGAAACT 60.675 55.000 24.8 0.0 0.0 2.66 R
3416 3464 1.131126 CTCAATTACAGTTGCGGGCAG 59.869 52.381 0.0 0.0 0.0 4.85 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
189 196 3.068691 CCCTCGTCGAGCCCAAGA 61.069 66.667 17.02 0.00 0.00 3.02
252 259 1.303398 AGCTTCTCCGACGAGGACA 60.303 57.895 0.00 0.00 45.98 4.02
509 528 1.374252 CACGCGGTTCTACAGCCTT 60.374 57.895 12.47 0.00 35.89 4.35
514 533 0.526662 CGGTTCTACAGCCTTCTCGT 59.473 55.000 0.00 0.00 0.00 4.18
532 551 0.108992 GTCATGTAGAACCGCGTGGA 60.109 55.000 24.59 0.00 39.21 4.02
667 696 3.560902 TGCGCCGAATTTGAACATTTA 57.439 38.095 4.18 0.00 0.00 1.40
789 823 1.668826 ACAGGTGGAGATGCCCTTAA 58.331 50.000 0.00 0.00 34.97 1.85
790 824 2.208872 ACAGGTGGAGATGCCCTTAAT 58.791 47.619 0.00 0.00 34.97 1.40
791 825 2.173569 ACAGGTGGAGATGCCCTTAATC 59.826 50.000 0.00 0.00 34.97 1.75
792 826 1.777272 AGGTGGAGATGCCCTTAATCC 59.223 52.381 0.00 0.00 34.97 3.01
793 827 1.202940 GGTGGAGATGCCCTTAATCCC 60.203 57.143 0.00 0.00 34.97 3.85
794 828 1.777272 GTGGAGATGCCCTTAATCCCT 59.223 52.381 0.00 0.00 34.97 4.20
795 829 2.979678 GTGGAGATGCCCTTAATCCCTA 59.020 50.000 0.00 0.00 34.97 3.53
796 830 3.394606 GTGGAGATGCCCTTAATCCCTAA 59.605 47.826 0.00 0.00 34.97 2.69
797 831 4.051478 TGGAGATGCCCTTAATCCCTAAA 58.949 43.478 0.00 0.00 34.97 1.85
798 832 4.480537 TGGAGATGCCCTTAATCCCTAAAA 59.519 41.667 0.00 0.00 34.97 1.52
799 833 5.043732 TGGAGATGCCCTTAATCCCTAAAAA 60.044 40.000 0.00 0.00 34.97 1.94
903 938 0.614979 ACTGAGCTACCCACATCCGT 60.615 55.000 0.00 0.00 0.00 4.69
905 940 1.067212 CTGAGCTACCCACATCCGTAC 59.933 57.143 0.00 0.00 0.00 3.67
906 941 1.341679 TGAGCTACCCACATCCGTACT 60.342 52.381 0.00 0.00 0.00 2.73
1137 1172 2.192861 CGCCAACTCAAGCAACCCA 61.193 57.895 0.00 0.00 0.00 4.51
1168 1203 1.129917 CATCCACCTGCTCCTCAGAT 58.870 55.000 0.00 0.00 45.72 2.90
1191 1226 1.201429 GGTCTTCCCTTCTCAGCCCA 61.201 60.000 0.00 0.00 0.00 5.36
1402 1437 3.358076 GAGTCGCCGGAGTTCTGGG 62.358 68.421 5.05 0.04 42.72 4.45
1581 1616 1.375523 GTTCGTCATTGGCCGGACT 60.376 57.895 9.82 0.00 29.89 3.85
1603 1638 0.309922 GTTCGAGACTGACCGTGTCA 59.690 55.000 6.57 6.57 40.50 3.58
1780 1815 2.104967 TCGCCTTTCCTCTTCCGATTA 58.895 47.619 0.00 0.00 0.00 1.75
1989 2024 3.648067 ACTCTGACACAGATTTTGGAGGA 59.352 43.478 1.92 0.00 39.92 3.71
2115 2150 1.020861 TGTACAAGGCTGCAGATGCG 61.021 55.000 20.43 4.92 45.83 4.73
2358 2393 1.573829 GGCGCGTCTTTGGTGATCAA 61.574 55.000 8.43 0.00 0.00 2.57
2403 2438 0.329596 AGGCAAGGGAAGACATGGTC 59.670 55.000 0.00 0.00 0.00 4.02
2489 2524 4.155099 CAGTACTCAGTAGATGGATAGCCG 59.845 50.000 0.00 0.00 36.79 5.52
2496 2531 5.047731 TCAGTAGATGGATAGCCGAAATCTG 60.048 44.000 8.26 6.76 36.79 2.90
2499 2534 5.495926 AGATGGATAGCCGAAATCTGATT 57.504 39.130 0.00 0.00 36.79 2.57
2593 2628 5.880054 TGCTGCTTTGTAGGAGTTATTTC 57.120 39.130 0.00 0.00 41.52 2.17
2617 2652 0.542702 AGTTTCTGCAATGGTGGGGG 60.543 55.000 0.00 0.00 0.00 5.40
2673 2708 4.652421 CCATCATGATTTGAATGGTTCCCT 59.348 41.667 5.16 0.00 38.03 4.20
2707 2744 8.668510 ATGGACTTATTGCTTCATACTGTTAG 57.331 34.615 0.00 0.00 0.00 2.34
2808 2845 7.442666 GGTATTTGCACCTTCCATTTTTGTTAA 59.557 33.333 0.00 0.00 35.55 2.01
2815 2852 8.442384 GCACCTTCCATTTTTGTTAATACATTG 58.558 33.333 0.00 0.00 33.44 2.82
2963 3000 1.989706 TCTTACCTGGGCCAACAAAC 58.010 50.000 8.04 0.00 0.00 2.93
2971 3008 0.966179 GGGCCAACAAACGGAAGATT 59.034 50.000 4.39 0.00 0.00 2.40
2972 3009 1.067846 GGGCCAACAAACGGAAGATTC 60.068 52.381 4.39 0.00 0.00 2.52
2984 3021 3.859061 GGAAGATTCCGATACCCCTTT 57.141 47.619 0.00 0.00 37.65 3.11
3021 3058 7.033791 GCAGTGACAATGATTCATCAGAAATT 58.966 34.615 7.16 0.00 40.64 1.82
3032 3069 9.676861 TGATTCATCAGAAATTATCAACAGACT 57.323 29.630 0.00 0.00 37.29 3.24
3051 3088 5.526846 CAGACTAGGAATTCATGGAAGAAGC 59.473 44.000 10.62 0.00 0.00 3.86
3052 3089 5.190528 AGACTAGGAATTCATGGAAGAAGCA 59.809 40.000 10.62 0.00 0.00 3.91
3059 3096 2.362736 TCATGGAAGAAGCAGATGCAC 58.637 47.619 7.68 0.95 45.16 4.57
3118 3157 3.970610 CGTTGTTGCATCAGTCAAAGAAG 59.029 43.478 0.00 0.00 0.00 2.85
3121 3160 3.004002 TGTTGCATCAGTCAAAGAAGCAG 59.996 43.478 0.00 0.00 40.27 4.24
3162 3202 2.673043 GCACTTGATCAACCTTGCATGG 60.673 50.000 16.76 16.76 0.00 3.66
3191 3231 6.378710 AGTGCCTTGTTTCTTTCTTTCTAC 57.621 37.500 0.00 0.00 0.00 2.59
3192 3232 6.122964 AGTGCCTTGTTTCTTTCTTTCTACT 58.877 36.000 0.00 0.00 0.00 2.57
3193 3233 6.038714 AGTGCCTTGTTTCTTTCTTTCTACTG 59.961 38.462 0.00 0.00 0.00 2.74
3194 3234 5.885912 TGCCTTGTTTCTTTCTTTCTACTGT 59.114 36.000 0.00 0.00 0.00 3.55
3195 3235 7.012044 GTGCCTTGTTTCTTTCTTTCTACTGTA 59.988 37.037 0.00 0.00 0.00 2.74
3201 3241 8.342634 TGTTTCTTTCTTTCTACTGTATGTTGC 58.657 33.333 0.00 0.00 0.00 4.17
3264 3311 6.374333 TGTTGTTGAAACTTGAGCTTAGAGTT 59.626 34.615 4.03 4.52 35.27 3.01
3416 3464 1.398692 TTGGGTTGCCAAGTCTGAAC 58.601 50.000 0.00 0.00 0.00 3.18
3464 3514 8.324163 ACTGTGATACAAAAAGGAATAGTCAC 57.676 34.615 0.00 0.00 35.32 3.67
3470 3520 2.403252 AAAGGAATAGTCACCTGCGG 57.597 50.000 0.00 0.00 36.56 5.69
3471 3521 1.568504 AAGGAATAGTCACCTGCGGA 58.431 50.000 0.00 0.00 36.56 5.54
3472 3522 1.794714 AGGAATAGTCACCTGCGGAT 58.205 50.000 0.00 0.00 34.99 4.18
3473 3523 1.414181 AGGAATAGTCACCTGCGGATG 59.586 52.381 0.00 0.00 34.99 3.51
3474 3524 1.221414 GAATAGTCACCTGCGGATGC 58.779 55.000 0.00 0.00 43.20 3.91
3478 3528 0.250901 AGTCACCTGCGGATGCTTTT 60.251 50.000 0.00 0.00 43.34 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 241 1.303398 TGTCCTCGTCGGAGAAGCT 60.303 57.895 0.00 0.00 44.20 3.74
428 438 3.790437 CCGTCCCTGCTGCATCCT 61.790 66.667 1.31 0.00 0.00 3.24
509 528 0.098200 CGCGGTTCTACATGACGAGA 59.902 55.000 0.00 0.00 0.00 4.04
514 533 0.108992 GTCCACGCGGTTCTACATGA 60.109 55.000 12.47 0.00 0.00 3.07
760 793 4.722700 CCACCTGTTGGCCTCCCG 62.723 72.222 3.32 0.00 39.07 5.14
772 806 1.777272 GGATTAAGGGCATCTCCACCT 59.223 52.381 0.00 0.00 36.21 4.00
774 808 1.777272 AGGGATTAAGGGCATCTCCAC 59.223 52.381 0.00 0.00 36.21 4.02
797 831 3.785364 TGAGGGGAATTTCCGGATTTTT 58.215 40.909 4.15 0.00 37.43 1.94
798 832 3.466395 TGAGGGGAATTTCCGGATTTT 57.534 42.857 4.15 1.19 37.43 1.82
799 833 3.466395 TTGAGGGGAATTTCCGGATTT 57.534 42.857 4.15 1.64 37.43 2.17
800 834 3.466395 TTTGAGGGGAATTTCCGGATT 57.534 42.857 4.15 0.00 37.43 3.01
801 835 3.688049 ATTTGAGGGGAATTTCCGGAT 57.312 42.857 4.15 0.00 37.43 4.18
802 836 4.017867 AGTTATTTGAGGGGAATTTCCGGA 60.018 41.667 0.00 0.00 37.43 5.14
803 837 4.278310 AGTTATTTGAGGGGAATTTCCGG 58.722 43.478 9.31 0.00 37.43 5.14
804 838 5.914898 AAGTTATTTGAGGGGAATTTCCG 57.085 39.130 9.31 0.00 37.43 4.30
808 842 9.387397 TCCTTAAAAAGTTATTTGAGGGGAATT 57.613 29.630 15.10 0.00 42.99 2.17
809 843 8.966155 TCCTTAAAAAGTTATTTGAGGGGAAT 57.034 30.769 15.10 0.00 42.99 3.01
810 844 8.785184 TTCCTTAAAAAGTTATTTGAGGGGAA 57.215 30.769 15.10 0.00 42.99 3.97
811 845 8.785184 TTTCCTTAAAAAGTTATTTGAGGGGA 57.215 30.769 15.10 0.00 42.99 4.81
841 875 8.550710 TTCCCTCGAATTTTTATTTAACTCGA 57.449 30.769 0.00 0.00 33.29 4.04
842 876 7.908601 CCTTCCCTCGAATTTTTATTTAACTCG 59.091 37.037 0.00 0.00 0.00 4.18
895 930 1.144057 GGCAGGGAGTACGGATGTG 59.856 63.158 0.00 0.00 0.00 3.21
903 938 2.041922 ATCGGCAGGCAGGGAGTA 60.042 61.111 0.00 0.00 0.00 2.59
905 940 3.160047 AGATCGGCAGGCAGGGAG 61.160 66.667 0.00 0.00 0.00 4.30
906 941 3.473647 CAGATCGGCAGGCAGGGA 61.474 66.667 0.00 0.00 0.00 4.20
1124 1159 1.529244 GGCAGTGGGTTGCTTGAGT 60.529 57.895 0.00 0.00 43.57 3.41
1137 1172 3.321648 TGGATGAGGCGTGGCAGT 61.322 61.111 0.00 0.00 0.00 4.40
1150 1185 1.422531 GATCTGAGGAGCAGGTGGAT 58.577 55.000 0.00 0.00 44.98 3.41
1371 1406 3.429141 GACTCGAGGTCGCCGTGA 61.429 66.667 18.41 0.00 39.60 4.35
1454 1489 2.888863 CCCGAGAGAGCTCACACC 59.111 66.667 17.77 5.06 41.36 4.16
1581 1616 2.156917 ACACGGTCAGTCTCGAACATA 58.843 47.619 0.00 0.00 0.00 2.29
1603 1638 3.381983 TCTGACATGCTCCGGCGT 61.382 61.111 6.01 0.00 42.25 5.68
1780 1815 0.674895 GGCGCCATGACAGAGAAACT 60.675 55.000 24.80 0.00 0.00 2.66
2115 2150 0.872388 CACGGGAAGGTAGCACAAAC 59.128 55.000 0.00 0.00 0.00 2.93
2292 2327 1.381928 ATGGCTCAGCGCAGAAATGG 61.382 55.000 11.47 0.00 41.67 3.16
2358 2393 1.632920 CCTTTTCTCCTTGCCTCCTCT 59.367 52.381 0.00 0.00 0.00 3.69
2403 2438 0.737715 CCTCTGGCGAAAACCTCTCG 60.738 60.000 0.00 0.00 39.33 4.04
2489 2524 7.985476 TCCTCGGAAATTTGTAATCAGATTTC 58.015 34.615 0.00 12.58 45.86 2.17
2496 2531 8.488651 TCTACTTTCCTCGGAAATTTGTAATC 57.511 34.615 11.26 0.00 42.34 1.75
2499 2534 9.760077 GATATCTACTTTCCTCGGAAATTTGTA 57.240 33.333 11.26 9.37 42.34 2.41
2593 2628 3.941483 CCCACCATTGCAGAAACTACTAG 59.059 47.826 0.00 0.00 0.00 2.57
2617 2652 4.236935 CATGAACAACAGCCACCAATTAC 58.763 43.478 0.00 0.00 0.00 1.89
2673 2708 7.053498 TGAAGCAATAAGTCCATAACATGCTA 58.947 34.615 0.00 0.00 41.64 3.49
2808 2845 9.423061 GACCAATTTAAGCAAACTTCAATGTAT 57.577 29.630 0.00 0.00 37.33 2.29
2815 2852 7.871853 TGTAGAGACCAATTTAAGCAAACTTC 58.128 34.615 0.00 0.00 37.33 3.01
2929 2966 5.123979 CCAGGTAAGATGGCTGAACTTTAAC 59.876 44.000 0.00 0.00 0.00 2.01
3021 3058 7.675161 TCCATGAATTCCTAGTCTGTTGATA 57.325 36.000 2.27 0.00 0.00 2.15
3032 3069 5.698741 TCTGCTTCTTCCATGAATTCCTA 57.301 39.130 2.27 0.00 0.00 2.94
3034 3071 4.499357 GCATCTGCTTCTTCCATGAATTCC 60.499 45.833 2.27 0.00 38.21 3.01
3051 3088 1.901591 AACCACTCCTTGTGCATCTG 58.098 50.000 0.00 0.00 44.92 2.90
3052 3089 2.664402 AAACCACTCCTTGTGCATCT 57.336 45.000 0.00 0.00 44.92 2.90
3059 3096 2.755103 GGCTGGATTAAACCACTCCTTG 59.245 50.000 0.00 0.00 35.91 3.61
3118 3157 4.440802 CCATACTGACACCTCTTCTACTGC 60.441 50.000 0.00 0.00 0.00 4.40
3121 3160 3.447586 TGCCATACTGACACCTCTTCTAC 59.552 47.826 0.00 0.00 0.00 2.59
3201 3241 4.644103 AGCTACAATAAAAGGCATGCTG 57.356 40.909 18.92 8.51 0.00 4.41
3209 3256 6.984740 TTCACGCAAAAGCTACAATAAAAG 57.015 33.333 0.00 0.00 0.00 2.27
3220 3267 4.257536 ACACAATTTTTCACGCAAAAGC 57.742 36.364 0.00 0.00 35.34 3.51
3232 3279 6.650390 AGCTCAAGTTTCAACAACACAATTTT 59.350 30.769 0.00 0.00 0.00 1.82
3416 3464 1.131126 CTCAATTACAGTTGCGGGCAG 59.869 52.381 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.