Multiple sequence alignment - TraesCS4A01G061400

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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 TraesCS4A01G061400 chr4A 100.000 3887 0 0 1 3887 58516019 58512133 0.000000e+00 7179
1 TraesCS4A01G061400 chr4D 95.145 2245 83 14 753 2984 400649618 400647387 0.000000e+00 3518
2 TraesCS4A01G061400 chr4B 95.051 2243 86 15 753 2984 495016618 495014390 0.000000e+00 3504
3 TraesCS4A01G061400 chr4B 95.257 759 24 7 1 747 68085780 68085022 0.000000e+00 1192
4 TraesCS4A01G061400 chr4B 100.000 40 0 0 2945 2984 495014350 495014311 1.500000e-09 75
5 TraesCS4A01G061400 chr1B 97.901 905 19 0 2983 3887 6401725 6400821 0.000000e+00 1567
6 TraesCS4A01G061400 chr1B 95.370 756 25 9 1 747 98433660 98432906 0.000000e+00 1194
7 TraesCS4A01G061400 chr1B 94.980 757 28 9 1 747 98413607 98412851 0.000000e+00 1179
8 TraesCS4A01G061400 chr1B 94.974 756 27 10 1 747 98386308 98385555 0.000000e+00 1175
9 TraesCS4A01G061400 chr6B 97.898 904 19 0 2984 3887 712157273 712156370 0.000000e+00 1565
10 TraesCS4A01G061400 chr6B 94.882 762 24 8 1 747 179450362 179449601 0.000000e+00 1177
11 TraesCS4A01G061400 chr7A 97.203 858 24 0 3030 3887 11046125 11046982 0.000000e+00 1452
12 TraesCS4A01G061400 chr7D 93.260 905 57 4 2985 3887 615783849 615782947 0.000000e+00 1330
13 TraesCS4A01G061400 chr5D 93.149 905 57 5 2985 3886 41796341 41795439 0.000000e+00 1323
14 TraesCS4A01G061400 chr6D 92.597 905 63 4 2985 3887 429479290 429478388 0.000000e+00 1297
15 TraesCS4A01G061400 chr3A 95.037 806 39 1 2985 3790 708974815 708974011 0.000000e+00 1266
16 TraesCS4A01G061400 chr3B 91.823 905 69 4 2985 3887 465885587 465884686 0.000000e+00 1256
17 TraesCS4A01G061400 chr3B 95.151 763 21 9 1 747 751920817 751920055 0.000000e+00 1190
18 TraesCS4A01G061400 chr5B 95.652 759 25 6 1 751 707617848 707617090 0.000000e+00 1212
19 TraesCS4A01G061400 chr5B 94.974 756 24 13 1 747 56250381 56249631 0.000000e+00 1173
20 TraesCS4A01G061400 chr2B 95.515 758 23 5 1 747 100023529 100024286 0.000000e+00 1201
21 TraesCS4A01G061400 chr6A 90.466 902 83 2 2988 3887 563397424 563396524 0.000000e+00 1186


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 TraesCS4A01G061400 chr4A 58512133 58516019 3886 True 7179.0 7179 100.0000 1 3887 1 chr4A.!!$R1 3886
1 TraesCS4A01G061400 chr4D 400647387 400649618 2231 True 3518.0 3518 95.1450 753 2984 1 chr4D.!!$R1 2231
2 TraesCS4A01G061400 chr4B 495014311 495016618 2307 True 1789.5 3504 97.5255 753 2984 2 chr4B.!!$R2 2231
3 TraesCS4A01G061400 chr4B 68085022 68085780 758 True 1192.0 1192 95.2570 1 747 1 chr4B.!!$R1 746
4 TraesCS4A01G061400 chr1B 6400821 6401725 904 True 1567.0 1567 97.9010 2983 3887 1 chr1B.!!$R1 904
5 TraesCS4A01G061400 chr1B 98432906 98433660 754 True 1194.0 1194 95.3700 1 747 1 chr1B.!!$R4 746
6 TraesCS4A01G061400 chr1B 98412851 98413607 756 True 1179.0 1179 94.9800 1 747 1 chr1B.!!$R3 746
7 TraesCS4A01G061400 chr1B 98385555 98386308 753 True 1175.0 1175 94.9740 1 747 1 chr1B.!!$R2 746
8 TraesCS4A01G061400 chr6B 712156370 712157273 903 True 1565.0 1565 97.8980 2984 3887 1 chr6B.!!$R2 903
9 TraesCS4A01G061400 chr6B 179449601 179450362 761 True 1177.0 1177 94.8820 1 747 1 chr6B.!!$R1 746
10 TraesCS4A01G061400 chr7A 11046125 11046982 857 False 1452.0 1452 97.2030 3030 3887 1 chr7A.!!$F1 857
11 TraesCS4A01G061400 chr7D 615782947 615783849 902 True 1330.0 1330 93.2600 2985 3887 1 chr7D.!!$R1 902
12 TraesCS4A01G061400 chr5D 41795439 41796341 902 True 1323.0 1323 93.1490 2985 3886 1 chr5D.!!$R1 901
13 TraesCS4A01G061400 chr6D 429478388 429479290 902 True 1297.0 1297 92.5970 2985 3887 1 chr6D.!!$R1 902
14 TraesCS4A01G061400 chr3A 708974011 708974815 804 True 1266.0 1266 95.0370 2985 3790 1 chr3A.!!$R1 805
15 TraesCS4A01G061400 chr3B 465884686 465885587 901 True 1256.0 1256 91.8230 2985 3887 1 chr3B.!!$R1 902
16 TraesCS4A01G061400 chr3B 751920055 751920817 762 True 1190.0 1190 95.1510 1 747 1 chr3B.!!$R2 746
17 TraesCS4A01G061400 chr5B 707617090 707617848 758 True 1212.0 1212 95.6520 1 751 1 chr5B.!!$R2 750
18 TraesCS4A01G061400 chr5B 56249631 56250381 750 True 1173.0 1173 94.9740 1 747 1 chr5B.!!$R1 746
19 TraesCS4A01G061400 chr2B 100023529 100024286 757 False 1201.0 1201 95.5150 1 747 1 chr2B.!!$F1 746
20 TraesCS4A01G061400 chr6A 563396524 563397424 900 True 1186.0 1186 90.4660 2988 3887 1 chr6A.!!$R1 899

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
759 787 1.068194 GTTCGAGTGGACACAGGAGAG 60.068 57.143 5.14 0.0 0.0 3.20 F
1449 1489 0.459934 AGCTCAATGTCTCGCAGCTC 60.460 55.000 0.00 0.0 0.0 4.09 F
2073 2113 1.144057 CTACTACCGGGCCAAGCTG 59.856 63.158 6.32 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2230 0.614134 GGAAGGTGTAGTCCCCGTCT 60.614 60.000 0.00 0.0 30.98 4.18 R
2523 2563 1.140804 GAGAAGCTCGAGGACCAGC 59.859 63.158 15.58 0.0 35.73 4.85 R
3739 3866 1.405933 GCATGGCCCAAAATCAGTTCC 60.406 52.381 0.00 0.0 0.00 3.62 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
111 113 6.377996 TGGATGGTAATCAATCTCCAAACAAG 59.622 38.462 0.00 0.00 31.23 3.16
210 212 2.030274 TGTCGAGCGTTCTTGATTCTCA 60.030 45.455 0.00 0.00 35.31 3.27
473 475 9.463443 GCTAGCCGATTTACATGAAATTAATTT 57.537 29.630 13.24 13.24 37.90 1.82
620 641 4.284746 GGAGAGAGAGTGAGGAAAAGGAAA 59.715 45.833 0.00 0.00 0.00 3.13
638 663 2.401583 AAGCAGAGTGTGTGTGTGAA 57.598 45.000 0.00 0.00 0.00 3.18
748 776 3.411351 CGGGCGTTGTTCGAGTGG 61.411 66.667 0.00 0.00 42.86 4.00
749 777 2.029964 GGGCGTTGTTCGAGTGGA 59.970 61.111 0.00 0.00 42.86 4.02
750 778 2.315386 GGGCGTTGTTCGAGTGGAC 61.315 63.158 0.00 0.00 42.86 4.02
751 779 1.593209 GGCGTTGTTCGAGTGGACA 60.593 57.895 0.00 0.00 42.86 4.02
759 787 1.068194 GTTCGAGTGGACACAGGAGAG 60.068 57.143 5.14 0.00 0.00 3.20
842 870 2.428085 AAAAGCCCACCGCGGTTTT 61.428 52.632 32.11 23.65 44.76 2.43
902 933 3.635331 CCGCTAGCTACGCATACTAAAA 58.365 45.455 13.93 0.00 0.00 1.52
914 945 2.460757 TACTAAAACCGAGCCCACAC 57.539 50.000 0.00 0.00 0.00 3.82
946 977 3.061848 CCACCACCGCATTCCCAC 61.062 66.667 0.00 0.00 0.00 4.61
971 1002 2.028484 GGCTCACGACACGAACCA 59.972 61.111 0.00 0.00 0.00 3.67
1030 1061 2.124778 GCTTCCTCTGCTGCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
1449 1489 0.459934 AGCTCAATGTCTCGCAGCTC 60.460 55.000 0.00 0.00 0.00 4.09
1533 1573 3.486263 GTCACCTACATGTGGCGC 58.514 61.111 9.11 0.00 36.87 6.53
1549 1589 3.127533 GCCCTGTCGACACCATGC 61.128 66.667 15.76 10.84 0.00 4.06
1563 1603 2.045926 ATGCCCGAGGTGAGCAAC 60.046 61.111 0.00 0.00 40.46 4.17
1571 1611 4.326255 GGTGAGCAACCTGATGGG 57.674 61.111 1.45 0.00 46.55 4.00
1576 1616 2.825836 GCAACCTGATGGGCTCCG 60.826 66.667 0.00 0.00 39.10 4.63
1577 1617 2.989639 CAACCTGATGGGCTCCGA 59.010 61.111 0.00 0.00 39.10 4.55
1580 1620 3.461773 CCTGATGGGCTCCGACGT 61.462 66.667 0.00 0.00 0.00 4.34
1581 1621 2.105128 CTGATGGGCTCCGACGTC 59.895 66.667 5.18 5.18 0.00 4.34
1582 1622 3.758088 CTGATGGGCTCCGACGTCG 62.758 68.421 30.33 30.33 39.44 5.12
1648 1688 3.646976 CGATGCTGCCGATGCTGG 61.647 66.667 0.00 0.00 38.71 4.85
1893 1933 1.388547 TTTGCTTCAACCAGAACGCT 58.611 45.000 0.00 0.00 33.97 5.07
1907 1947 2.232941 AGAACGCTTACGGGATTCAGAA 59.767 45.455 0.00 0.00 46.04 3.02
1995 2035 3.197766 TCAACAAGCCTATCATCTTCGGT 59.802 43.478 0.00 0.00 0.00 4.69
2000 2040 3.833732 AGCCTATCATCTTCGGTACAGA 58.166 45.455 0.00 0.00 0.00 3.41
2073 2113 1.144057 CTACTACCGGGCCAAGCTG 59.856 63.158 6.32 0.00 0.00 4.24
2190 2230 2.358615 GGCATATCCATCGGCGCA 60.359 61.111 10.83 0.00 34.01 6.09
2193 2233 1.630244 GCATATCCATCGGCGCAGAC 61.630 60.000 13.72 0.00 0.00 3.51
2441 2481 4.003788 CACCGCGGACTTCAGGGT 62.004 66.667 35.90 1.64 0.00 4.34
2451 2491 3.582164 GGACTTCAGGGTCAGGATATCT 58.418 50.000 2.05 0.00 37.91 1.98
2781 2821 1.660575 CGACGTCGTGTTCAGCCTT 60.661 57.895 29.08 0.00 34.11 4.35
2892 2932 1.072806 GTGGCAGCCAGATGATATGGA 59.927 52.381 16.83 0.00 40.51 3.41
2940 2980 7.676893 TGATCTAGGAAGTTCTTAGTTTGGGTA 59.323 37.037 18.50 1.86 29.33 3.69
2953 2993 0.250510 TTGGGTATTGCGTGCAGTGA 60.251 50.000 0.00 0.00 0.00 3.41
2954 2994 0.035534 TGGGTATTGCGTGCAGTGAT 60.036 50.000 0.00 0.00 0.00 3.06
2955 2995 1.094785 GGGTATTGCGTGCAGTGATT 58.905 50.000 0.00 0.00 0.00 2.57
2956 2996 1.472480 GGGTATTGCGTGCAGTGATTT 59.528 47.619 0.00 0.00 0.00 2.17
3032 3155 2.568546 TTGAGCTAGGGATTGGAGGA 57.431 50.000 0.00 0.00 0.00 3.71
3051 3174 3.149196 GGAAGTGTGAAGAGCATTTGGA 58.851 45.455 0.00 0.00 0.00 3.53
3151 3276 8.653036 ACCCTATAGACTCACCTAATTACATC 57.347 38.462 0.00 0.00 0.00 3.06
3202 3328 4.907809 TGGGGTGAATATGTCGTACAAAA 58.092 39.130 0.00 0.00 0.00 2.44
3344 3470 7.829725 TCCTTGATGAAATGACGATCAATTTT 58.170 30.769 0.00 0.00 35.95 1.82
3665 3791 1.972872 CACTCAACTTGCAAGTCCCT 58.027 50.000 31.20 14.41 38.57 4.20
3739 3866 7.251321 AGGATCCTATTTACAGCTTCCATAG 57.749 40.000 14.27 0.00 0.00 2.23
3754 3881 3.631250 TCCATAGGAACTGATTTTGGGC 58.369 45.455 0.00 0.00 41.52 5.36
3800 3927 3.943381 CTCACAGCAAAGGCAATATCTGA 59.057 43.478 0.00 0.00 44.61 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 113 3.467803 CTCCCTCGATGTATTGTTTCCC 58.532 50.000 0.00 0.00 0.00 3.97
291 293 4.680237 TCACTGACCGCGGCCAAG 62.680 66.667 28.58 22.18 0.00 3.61
304 306 1.679898 CTTCTTCGCCCCCTTCACT 59.320 57.895 0.00 0.00 0.00 3.41
415 417 0.178068 AATACGCGAAGGATGTGGCT 59.822 50.000 15.93 0.00 0.00 4.75
473 475 0.257328 TTTGCCACCACAACTGAGGA 59.743 50.000 0.00 0.00 0.00 3.71
620 641 1.482182 TCTTCACACACACACTCTGCT 59.518 47.619 0.00 0.00 0.00 4.24
739 767 0.959553 TCTCCTGTGTCCACTCGAAC 59.040 55.000 0.00 0.00 0.00 3.95
743 771 1.261238 CCCCTCTCCTGTGTCCACTC 61.261 65.000 0.00 0.00 0.00 3.51
748 776 2.352032 CCGTCCCCTCTCCTGTGTC 61.352 68.421 0.00 0.00 0.00 3.67
749 777 2.283966 CCGTCCCCTCTCCTGTGT 60.284 66.667 0.00 0.00 0.00 3.72
750 778 3.775654 GCCGTCCCCTCTCCTGTG 61.776 72.222 0.00 0.00 0.00 3.66
751 779 3.625632 ATGCCGTCCCCTCTCCTGT 62.626 63.158 0.00 0.00 0.00 4.00
759 787 2.501610 GACTCAGATGCCGTCCCC 59.498 66.667 0.00 0.00 0.00 4.81
842 870 0.533308 CTCGGGTTGTTCGGGTCAAA 60.533 55.000 0.00 0.00 0.00 2.69
914 945 3.589542 TGGAAGTGGCCAAGGGGG 61.590 66.667 7.24 0.00 34.31 5.40
953 984 3.103911 GGTTCGTGTCGTGAGCCG 61.104 66.667 0.00 0.00 38.13 5.52
954 985 1.593209 TTGGTTCGTGTCGTGAGCC 60.593 57.895 0.00 0.00 37.25 4.70
957 988 1.227321 GGGTTGGTTCGTGTCGTGA 60.227 57.895 0.00 0.00 0.00 4.35
1168 1208 2.490685 GCCGAAGAGGTCCGAGAC 59.509 66.667 0.00 0.00 43.70 3.36
1297 1337 3.119096 GTTGACGAAGGAGCGGCC 61.119 66.667 0.00 0.00 38.91 6.13
1298 1338 3.479269 CGTTGACGAAGGAGCGGC 61.479 66.667 0.00 0.00 43.02 6.53
1533 1573 2.436646 GGCATGGTGTCGACAGGG 60.437 66.667 20.73 9.77 0.00 4.45
1563 1603 3.432051 GACGTCGGAGCCCATCAGG 62.432 68.421 0.00 0.00 39.47 3.86
1789 1829 2.792290 CGAAGATCGCCGTGCACAG 61.792 63.158 18.64 6.69 31.14 3.66
1893 1933 2.301870 ACTGCTGTTCTGAATCCCGTAA 59.698 45.455 0.00 0.00 0.00 3.18
1907 1947 1.446792 CGAGCGATGGAACTGCTGT 60.447 57.895 0.00 0.00 39.49 4.40
1995 2035 2.603021 GCCTCCATGATCTCCTCTGTA 58.397 52.381 0.00 0.00 0.00 2.74
2000 2040 1.459455 CGTCGCCTCCATGATCTCCT 61.459 60.000 0.00 0.00 0.00 3.69
2190 2230 0.614134 GGAAGGTGTAGTCCCCGTCT 60.614 60.000 0.00 0.00 30.98 4.18
2193 2233 1.664321 CGAGGAAGGTGTAGTCCCCG 61.664 65.000 0.00 0.00 34.13 5.73
2441 2481 4.827835 CCACGGAGAAGTTAGATATCCTGA 59.172 45.833 0.00 0.00 0.00 3.86
2523 2563 1.140804 GAGAAGCTCGAGGACCAGC 59.859 63.158 15.58 0.00 35.73 4.85
2724 2764 4.803426 GCGTCCTCCTCCGTGCAG 62.803 72.222 0.00 0.00 0.00 4.41
2892 2932 9.213799 GATCAGTCTCTAAATTCTGTTCTGTTT 57.786 33.333 0.00 0.00 0.00 2.83
2897 2937 8.908903 TCCTAGATCAGTCTCTAAATTCTGTTC 58.091 37.037 0.00 0.00 35.87 3.18
2901 2941 9.487442 AACTTCCTAGATCAGTCTCTAAATTCT 57.513 33.333 0.00 0.00 35.87 2.40
2910 2950 8.527810 CAAACTAAGAACTTCCTAGATCAGTCT 58.472 37.037 0.00 0.00 38.52 3.24
2940 2980 4.175516 CCAAATAAATCACTGCACGCAAT 58.824 39.130 0.00 0.00 0.00 3.56
2953 2993 8.547069 CACATTCACAAAACGAACCAAATAAAT 58.453 29.630 0.00 0.00 0.00 1.40
2954 2994 7.545965 ACACATTCACAAAACGAACCAAATAAA 59.454 29.630 0.00 0.00 0.00 1.40
2955 2995 7.009631 CACACATTCACAAAACGAACCAAATAA 59.990 33.333 0.00 0.00 0.00 1.40
2956 2996 6.473778 CACACATTCACAAAACGAACCAAATA 59.526 34.615 0.00 0.00 0.00 1.40
3032 3155 4.090761 TCTCCAAATGCTCTTCACACTT 57.909 40.909 0.00 0.00 0.00 3.16
3073 3196 2.382882 TCAGCAGAGAGAATGGATCGT 58.617 47.619 0.00 0.00 0.00 3.73
3151 3276 2.615493 GGGGAGTGTTGGTGTGTAGATG 60.615 54.545 0.00 0.00 0.00 2.90
3202 3328 4.406456 TCCATGTTTTGTAGCAAGATGGT 58.594 39.130 9.00 0.00 42.88 3.55
3344 3470 3.266636 CATGACCGTACCAAGCACATAA 58.733 45.455 0.00 0.00 0.00 1.90
3665 3791 8.658840 AAAAGGCCTCTTATATACCAAACAAA 57.341 30.769 5.23 0.00 32.01 2.83
3739 3866 1.405933 GCATGGCCCAAAATCAGTTCC 60.406 52.381 0.00 0.00 0.00 3.62
3754 3881 4.821260 TGTAGTTAGCCAATACATGCATGG 59.179 41.667 29.41 15.07 37.29 3.66


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

AutoCloner maintained by Alex Coulton.