Multiple sequence alignment - TraesCS1A01G220600

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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 TraesCS1A01G220600 chr1A 100.000 3503 0 0 1 3503 389807164 389803662 0.000000e+00 6469
1 TraesCS1A01G220600 chr1A 85.430 302 35 5 2815 3115 516558036 516557743 4.390000e-79 305
2 TraesCS1A01G220600 chr3A 97.535 2596 57 3 909 3503 128578327 128580916 0.000000e+00 4433
3 TraesCS1A01G220600 chr3A 88.023 693 74 8 2815 3503 673436371 673437058 0.000000e+00 811
4 TraesCS1A01G220600 chr3A 97.333 75 2 0 824 898 128571297 128571371 1.020000e-25 128
5 TraesCS1A01G220600 chr1D 94.294 1998 89 10 824 2814 309923944 309921965 0.000000e+00 3035
6 TraesCS1A01G220600 chr1B 91.722 1208 63 4 824 2028 419953367 419952194 0.000000e+00 1642
7 TraesCS1A01G220600 chr1B 98.177 823 15 0 1 823 31862630 31863452 0.000000e+00 1437
8 TraesCS1A01G220600 chr1B 94.775 823 43 0 1 823 180402203 180403025 0.000000e+00 1282
9 TraesCS1A01G220600 chr1B 96.844 507 16 0 2009 2515 419951956 419951450 0.000000e+00 848
10 TraesCS1A01G220600 chr1B 90.591 372 33 2 3133 3503 570825388 570825758 3.140000e-135 492
11 TraesCS1A01G220600 chr4A 99.271 823 6 0 1 823 554931179 554930357 0.000000e+00 1487
12 TraesCS1A01G220600 chr4A 99.149 823 7 0 1 823 565698260 565699082 0.000000e+00 1482
13 TraesCS1A01G220600 chr4A 91.462 691 55 3 2814 3503 616606133 616606820 0.000000e+00 946
14 TraesCS1A01G220600 chr4A 90.029 692 63 5 2814 3503 38664069 38664756 0.000000e+00 891
15 TraesCS1A01G220600 chr6B 98.542 823 11 1 1 823 457178361 457179182 0.000000e+00 1452
16 TraesCS1A01G220600 chr6B 78.392 199 32 10 1999 2190 30967433 30967627 6.140000e-23 119
17 TraesCS1A01G220600 chr7D 94.881 840 37 4 4 842 532623337 532622503 0.000000e+00 1308
18 TraesCS1A01G220600 chr2D 82.136 1517 245 23 993 2493 426920295 426921801 0.000000e+00 1277
19 TraesCS1A01G220600 chr2D 93.803 823 51 0 1 823 97626124 97626946 0.000000e+00 1238
20 TraesCS1A01G220600 chr2B 94.139 819 48 0 4 822 758560712 758559894 0.000000e+00 1247
21 TraesCS1A01G220600 chr2B 91.153 373 30 3 3133 3503 795990224 795990595 1.450000e-138 503
22 TraesCS1A01G220600 chr2A 82.131 1483 240 21 1025 2493 562106200 562104729 0.000000e+00 1247
23 TraesCS1A01G220600 chr2A 86.780 295 34 4 2822 3115 715992873 715992583 1.210000e-84 324
24 TraesCS1A01G220600 chr3B 93.910 821 50 0 4 824 140859636 140858816 0.000000e+00 1240
25 TraesCS1A01G220600 chr6A 91.618 692 53 4 2814 3503 79323598 79324286 0.000000e+00 952
26 TraesCS1A01G220600 chr6A 88.704 301 32 1 2814 3114 558110423 558110721 1.990000e-97 366
27 TraesCS1A01G220600 chr3D 90.290 690 60 6 2815 3503 18792317 18791634 0.000000e+00 896
28 TraesCS1A01G220600 chr5B 91.129 372 31 2 3133 3503 526267192 526266822 1.450000e-138 503
29 TraesCS1A01G220600 chr4D 75.862 290 58 11 1933 2213 131041689 131041403 1.700000e-28 137
30 TraesCS1A01G220600 chrUn 76.444 225 45 6 1996 2213 383555359 383555136 7.950000e-22 115
31 TraesCS1A01G220600 chrUn 76.744 215 42 6 1996 2203 362328973 362329186 2.860000e-21 113


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 TraesCS1A01G220600 chr1A 389803662 389807164 3502 True 6469 6469 100.000 1 3503 1 chr1A.!!$R1 3502
1 TraesCS1A01G220600 chr3A 128578327 128580916 2589 False 4433 4433 97.535 909 3503 1 chr3A.!!$F2 2594
2 TraesCS1A01G220600 chr3A 673436371 673437058 687 False 811 811 88.023 2815 3503 1 chr3A.!!$F3 688
3 TraesCS1A01G220600 chr1D 309921965 309923944 1979 True 3035 3035 94.294 824 2814 1 chr1D.!!$R1 1990
4 TraesCS1A01G220600 chr1B 31862630 31863452 822 False 1437 1437 98.177 1 823 1 chr1B.!!$F1 822
5 TraesCS1A01G220600 chr1B 180402203 180403025 822 False 1282 1282 94.775 1 823 1 chr1B.!!$F2 822
6 TraesCS1A01G220600 chr1B 419951450 419953367 1917 True 1245 1642 94.283 824 2515 2 chr1B.!!$R1 1691
7 TraesCS1A01G220600 chr4A 554930357 554931179 822 True 1487 1487 99.271 1 823 1 chr4A.!!$R1 822
8 TraesCS1A01G220600 chr4A 565698260 565699082 822 False 1482 1482 99.149 1 823 1 chr4A.!!$F2 822
9 TraesCS1A01G220600 chr4A 616606133 616606820 687 False 946 946 91.462 2814 3503 1 chr4A.!!$F3 689
10 TraesCS1A01G220600 chr4A 38664069 38664756 687 False 891 891 90.029 2814 3503 1 chr4A.!!$F1 689
11 TraesCS1A01G220600 chr6B 457178361 457179182 821 False 1452 1452 98.542 1 823 1 chr6B.!!$F2 822
12 TraesCS1A01G220600 chr7D 532622503 532623337 834 True 1308 1308 94.881 4 842 1 chr7D.!!$R1 838
13 TraesCS1A01G220600 chr2D 426920295 426921801 1506 False 1277 1277 82.136 993 2493 1 chr2D.!!$F2 1500
14 TraesCS1A01G220600 chr2D 97626124 97626946 822 False 1238 1238 93.803 1 823 1 chr2D.!!$F1 822
15 TraesCS1A01G220600 chr2B 758559894 758560712 818 True 1247 1247 94.139 4 822 1 chr2B.!!$R1 818
16 TraesCS1A01G220600 chr2A 562104729 562106200 1471 True 1247 1247 82.131 1025 2493 1 chr2A.!!$R1 1468
17 TraesCS1A01G220600 chr3B 140858816 140859636 820 True 1240 1240 93.910 4 824 1 chr3B.!!$R1 820
18 TraesCS1A01G220600 chr6A 79323598 79324286 688 False 952 952 91.618 2814 3503 1 chr6A.!!$F1 689
19 TraesCS1A01G220600 chr3D 18791634 18792317 683 True 896 896 90.290 2815 3503 1 chr3D.!!$R1 688

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
872 878 0.887933 AGGAATTTCGTTTGGCGCAT 59.112 45.000 10.83 0.0 41.07 4.73 F
1704 1723 1.202855 CCGAAGCCCATGATCTTCCAT 60.203 52.381 16.21 0.0 36.29 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 1819 0.178970 GCGGGAGGAGGGTGTAGATA 60.179 60.000 0.0 0.0 0.0 1.98 R
3194 3479 1.740025 GCGAGCTATGCCAGAGTTTTT 59.260 47.619 0.0 0.0 0.0 1.94 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
477 478 3.456644 TGAGGTTGTTACTCTGTTGGGAA 59.543 43.478 0.00 0.00 35.98 3.97
872 878 0.887933 AGGAATTTCGTTTGGCGCAT 59.112 45.000 10.83 0.00 41.07 4.73
873 879 2.088423 AGGAATTTCGTTTGGCGCATA 58.912 42.857 10.83 0.00 41.07 3.14
874 880 2.159435 AGGAATTTCGTTTGGCGCATAC 60.159 45.455 10.83 2.35 41.07 2.39
1037 1046 2.741985 CGTCCACCGCATGCTCAA 60.742 61.111 17.13 0.00 0.00 3.02
1212 1224 1.300620 CAAGTCTTCACCGCCGTCA 60.301 57.895 0.00 0.00 0.00 4.35
1568 1581 1.717791 TTCGACGCGGTGATCGGTAT 61.718 55.000 12.47 0.00 38.86 2.73
1672 1691 2.243810 AGAGAGCCGAAGAGAACACTT 58.756 47.619 0.00 0.00 0.00 3.16
1704 1723 1.202855 CCGAAGCCCATGATCTTCCAT 60.203 52.381 16.21 0.00 36.29 3.41
1758 1777 3.913573 GCGCTCGCCATGTACGTG 61.914 66.667 8.18 8.18 34.56 4.49
2172 2447 1.448013 GTACCTGCTCCGGTTCAGC 60.448 63.158 16.62 12.37 38.49 4.26
2444 2720 1.337260 CCTGACGAGGAAGGACAAGTG 60.337 57.143 0.00 0.00 42.93 3.16
2503 2779 4.380973 CCAAGACGAGCAAAGTCATCTAGA 60.381 45.833 0.00 0.00 40.84 2.43
2516 2792 7.682787 AAGTCATCTAGAATTGTAGGGATGT 57.317 36.000 9.57 0.00 32.48 3.06
2568 2844 4.024725 TGTTGTTTTGCGGTACTGTACATC 60.025 41.667 18.79 10.24 0.00 3.06
2794 3077 2.238701 CCTTGCTACCCCCACCCTT 61.239 63.158 0.00 0.00 0.00 3.95
2820 3103 1.755179 CTGCCATCTCCACGGAAAAT 58.245 50.000 0.00 0.00 0.00 1.82
2874 3158 8.880750 CGTGTATCTCCATCGTCTAAATCTATA 58.119 37.037 0.00 0.00 0.00 1.31
3162 3447 9.945904 AACCAAACTTTATTAAACTGGTTTTCA 57.054 25.926 14.30 0.00 41.69 2.69
3194 3479 7.446931 TGCCATGACAAATAGAAGTACTTTTGA 59.553 33.333 19.68 6.23 34.27 2.69
3379 3666 6.927294 AGTCCGATAAAGCCTTCATAAAAG 57.073 37.500 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.341383 GGACTGCCACCAGGATGAATT 60.341 52.381 0.00 0.00 43.53 2.17
90 91 3.469863 AAAGCCAGTTCCGCCACGA 62.470 57.895 0.00 0.00 0.00 4.35
477 478 0.036952 CGAGTCTCCCAGCACAATGT 60.037 55.000 0.00 0.00 0.00 2.71
865 871 3.418047 TCTGCTATACTAGTATGCGCCA 58.582 45.455 23.09 13.49 0.00 5.69
1037 1046 1.524863 CTTGACGACTCGGTGGAGGT 61.525 60.000 2.98 0.00 44.93 3.85
1585 1598 1.876714 CACCGGCGAAGTATCCGTG 60.877 63.158 9.30 0.60 43.87 4.94
1672 1691 1.315257 GGCTTCGGGTAGTGGTACGA 61.315 60.000 0.00 0.00 0.00 3.43
1758 1777 1.153686 GACGGCGAAGGGGAAGTAC 60.154 63.158 16.62 0.00 0.00 2.73
1800 1819 0.178970 GCGGGAGGAGGGTGTAGATA 60.179 60.000 0.00 0.00 0.00 1.98
2424 2700 0.969894 ACTTGTCCTTCCTCGTCAGG 59.030 55.000 0.00 0.00 42.01 3.86
2528 2804 9.909644 CAAAACAACACTCTACTATGTACTACT 57.090 33.333 0.00 0.00 0.00 2.57
2529 2805 8.645487 GCAAAACAACACTCTACTATGTACTAC 58.355 37.037 0.00 0.00 0.00 2.73
2530 2806 7.539710 CGCAAAACAACACTCTACTATGTACTA 59.460 37.037 0.00 0.00 0.00 1.82
2531 2807 6.365247 CGCAAAACAACACTCTACTATGTACT 59.635 38.462 0.00 0.00 0.00 2.73
2532 2808 6.400727 CCGCAAAACAACACTCTACTATGTAC 60.401 42.308 0.00 0.00 0.00 2.90
2568 2844 2.634982 AAATGTGGTTATGCAGTGCG 57.365 45.000 11.20 0.00 0.00 5.34
2794 3077 1.924939 TGGAGATGGCAGCTTGGGA 60.925 57.895 6.75 0.00 0.00 4.37
3160 3445 6.647334 TCTATTTGTCATGGCAAAGTTTGA 57.353 33.333 27.65 19.10 41.00 2.69
3161 3446 6.925165 ACTTCTATTTGTCATGGCAAAGTTTG 59.075 34.615 27.65 18.42 41.00 2.93
3162 3447 7.054491 ACTTCTATTTGTCATGGCAAAGTTT 57.946 32.000 27.65 15.57 41.00 2.66
3194 3479 1.740025 GCGAGCTATGCCAGAGTTTTT 59.260 47.619 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.