Multiple sequence alignment - TraesCS1A01G252100

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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 TraesCS1A01G252100 chr1A 100.000 2826 0 0 1 2826 443853180 443856005 0.000000e+00 5219.0
1 TraesCS1A01G252100 chr1A 97.082 2056 52 7 776 2826 497975697 497977749 0.000000e+00 3458.0
2 TraesCS1A01G252100 chr1A 92.590 1471 90 11 326 1780 575419163 575420630 0.000000e+00 2095.0
3 TraesCS1A01G252100 chr1A 92.488 1238 65 7 568 1780 580783461 580784695 0.000000e+00 1746.0
4 TraesCS1A01G252100 chr1A 97.740 708 15 1 1 708 497975033 497975739 0.000000e+00 1218.0
5 TraesCS1A01G252100 chr1A 98.232 396 6 1 121 516 580783060 580783454 0.000000e+00 691.0
6 TraesCS1A01G252100 chr1A 97.638 127 3 0 121 247 575419038 575419164 4.740000e-53 219.0
7 TraesCS1A01G252100 chr1A 96.386 83 2 1 27 109 580782870 580782951 4.910000e-28 135.0
8 TraesCS1A01G252100 chr1A 100.000 61 0 0 49 109 575418869 575418929 2.300000e-21 113.0
9 TraesCS1A01G252100 chr1A 97.727 44 1 0 1 44 580782815 580782858 3.020000e-10 76.8
10 TraesCS1A01G252100 chr2A 97.843 2828 57 4 1 2826 655910027 655907202 0.000000e+00 4881.0
11 TraesCS1A01G252100 chr2A 96.825 126 4 0 2252 2377 4385625 4385500 7.930000e-51 211.0
12 TraesCS1A01G252100 chr2A 96.386 83 2 1 27 109 605761624 605761705 4.910000e-28 135.0
13 TraesCS1A01G252100 chr7A 96.808 2851 62 5 1 2826 644066936 644064090 0.000000e+00 4734.0
14 TraesCS1A01G252100 chr7A 96.503 2259 52 4 121 2379 49623230 49620999 0.000000e+00 3709.0
15 TraesCS1A01G252100 chr7A 95.604 2252 65 8 1 2251 633712733 633710515 0.000000e+00 3579.0
16 TraesCS1A01G252100 chr7A 97.143 1400 37 3 982 2379 579482645 579481247 0.000000e+00 2361.0
17 TraesCS1A01G252100 chr7A 96.735 1409 44 2 972 2379 1550089 1548682 0.000000e+00 2346.0
18 TraesCS1A01G252100 chr7A 97.498 1279 31 1 972 2249 481750009 481748731 0.000000e+00 2183.0
19 TraesCS1A01G252100 chr7A 96.903 452 14 0 2375 2826 633708827 633708376 0.000000e+00 758.0
20 TraesCS1A01G252100 chr7A 96.903 452 13 1 2375 2826 633706842 633706392 0.000000e+00 756.0
21 TraesCS1A01G252100 chr7A 96.460 452 16 0 2375 2826 49620848 49620397 0.000000e+00 747.0
22 TraesCS1A01G252100 chr7A 93.976 83 4 1 27 109 153040138 153040057 1.060000e-24 124.0
23 TraesCS1A01G252100 chr7A 97.727 44 1 0 1 44 153040193 153040150 3.020000e-10 76.8
24 TraesCS1A01G252100 chr5A 96.250 2827 75 16 1 2826 168400439 168397643 0.000000e+00 4604.0
25 TraesCS1A01G252100 chr5A 94.468 1681 69 6 121 1780 133817694 133819371 0.000000e+00 2567.0
26 TraesCS1A01G252100 chr5A 96.948 1409 42 1 972 2379 572301287 572302695 0.000000e+00 2362.0
27 TraesCS1A01G252100 chr5A 96.850 127 3 1 2251 2377 291594557 291594682 7.930000e-51 211.0
28 TraesCS1A01G252100 chr5A 92.143 140 8 3 2240 2377 19220572 19220710 7.990000e-46 195.0
29 TraesCS1A01G252100 chr5A 96.809 94 2 1 25 118 345673058 345672966 3.770000e-34 156.0
30 TraesCS1A01G252100 chr3A 93.616 1676 86 16 121 1780 513294909 513296579 0.000000e+00 2483.0
31 TraesCS1A01G252100 chr3A 98.113 53 0 1 57 109 733887617 733887566 1.080000e-14 91.6
32 TraesCS1A01G252100 chr4A 93.437 1676 90 14 121 1780 490340905 490342576 0.000000e+00 2468.0
33 TraesCS1A01G252100 chr4A 93.309 1674 91 16 121 1780 429488081 429489747 0.000000e+00 2451.0
34 TraesCS1A01G252100 chr4A 96.739 92 2 1 27 118 490340744 490340834 4.880000e-33 152.0
35 TraesCS1A01G252100 chr4A 98.387 62 1 0 48 109 429487911 429487972 2.980000e-20 110.0
36 TraesCS1A01G252100 chr4A 97.727 44 1 0 1 44 429487827 429487870 3.020000e-10 76.8
37 TraesCS1A01G252100 chr6A 93.138 1676 94 15 121 1780 401364388 401366058 0.000000e+00 2438.0
38 TraesCS1A01G252100 chr6A 98.649 74 1 0 36 109 401364206 401364279 6.350000e-27 132.0
39 TraesCS1A01G252100 chr6A 95.455 44 2 0 1 44 603915421 603915464 1.400000e-08 71.3
40 TraesCS1A01G252100 chr4B 96.267 1259 40 3 994 2251 113838290 113839542 0.000000e+00 2058.0
41 TraesCS1A01G252100 chr4B 96.970 165 5 0 660 824 343640117 343640281 7.710000e-71 278.0
42 TraesCS1A01G252100 chr4B 93.333 165 11 0 660 824 343787486 343787650 7.820000e-61 244.0
43 TraesCS1A01G252100 chr4B 93.548 155 8 2 171 323 608980300 608980146 2.190000e-56 230.0
44 TraesCS1A01G252100 chr4D 88.155 1469 115 40 323 1776 261239527 261238103 0.000000e+00 1694.0
45 TraesCS1A01G252100 chr4D 97.203 143 4 0 682 824 261239222 261239080 2.810000e-60 243.0
46 TraesCS1A01G252100 chr4D 87.097 93 4 2 861 953 225340944 225340860 6.440000e-17 99.0
47 TraesCS1A01G252100 chr4D 87.097 93 5 3 861 953 410839334 410839419 6.440000e-17 99.0
48 TraesCS1A01G252100 chr4D 96.970 33 1 0 77 109 480890066 480890034 3.930000e-04 56.5
49 TraesCS1A01G252100 chr5B 85.685 992 108 21 801 1776 291688775 291687802 0.000000e+00 1014.0
50 TraesCS1A01G252100 chr5B 92.857 42 2 1 27 68 61788239 61788279 3.040000e-05 60.2
51 TraesCS1A01G252100 chr6D 85.458 1004 97 27 801 1776 202663328 202664310 0.000000e+00 1000.0
52 TraesCS1A01G252100 chr6D 97.030 505 15 0 320 824 297179389 297178885 0.000000e+00 850.0
53 TraesCS1A01G252100 chr6D 88.811 143 12 4 684 824 202663173 202663313 3.740000e-39 172.0
54 TraesCS1A01G252100 chr6D 88.043 92 5 5 648 737 202663103 202663190 1.380000e-18 104.0
55 TraesCS1A01G252100 chr6D 84.000 75 6 5 665 737 202663192 202663262 1.820000e-07 67.6
56 TraesCS1A01G252100 chr6D 95.000 40 1 1 616 655 202662919 202662957 8.450000e-06 62.1
57 TraesCS1A01G252100 chr5D 97.030 505 15 0 320 824 140961168 140960664 0.000000e+00 850.0
58 TraesCS1A01G252100 chr6B 96.681 452 15 0 2375 2826 180277292 180276841 0.000000e+00 752.0
59 TraesCS1A01G252100 chr3B 96.460 452 16 0 2375 2826 62765236 62764785 0.000000e+00 747.0
60 TraesCS1A01G252100 chr3B 96.460 452 16 0 2375 2826 62766562 62766111 0.000000e+00 747.0
61 TraesCS1A01G252100 chr1D 88.488 582 49 14 801 1376 428055664 428055095 0.000000e+00 688.0
62 TraesCS1A01G252100 chr1D 96.498 257 8 1 568 824 428055934 428055679 9.360000e-115 424.0
63 TraesCS1A01G252100 chr7D 100.000 33 0 0 1 33 103531570 103531602 8.450000e-06 62.1


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 TraesCS1A01G252100 chr1A 443853180 443856005 2825 False 5219.000000 5219 100.000000 1 2826 1 chr1A.!!$F1 2825
1 TraesCS1A01G252100 chr1A 497975033 497977749 2716 False 2338.000000 3458 97.411000 1 2826 2 chr1A.!!$F2 2825
2 TraesCS1A01G252100 chr1A 575418869 575420630 1761 False 809.000000 2095 96.742667 49 1780 3 chr1A.!!$F3 1731
3 TraesCS1A01G252100 chr1A 580782815 580784695 1880 False 662.200000 1746 96.208250 1 1780 4 chr1A.!!$F4 1779
4 TraesCS1A01G252100 chr2A 655907202 655910027 2825 True 4881.000000 4881 97.843000 1 2826 1 chr2A.!!$R2 2825
5 TraesCS1A01G252100 chr7A 644064090 644066936 2846 True 4734.000000 4734 96.808000 1 2826 1 chr7A.!!$R4 2825
6 TraesCS1A01G252100 chr7A 579481247 579482645 1398 True 2361.000000 2361 97.143000 982 2379 1 chr7A.!!$R3 1397
7 TraesCS1A01G252100 chr7A 1548682 1550089 1407 True 2346.000000 2346 96.735000 972 2379 1 chr7A.!!$R1 1407
8 TraesCS1A01G252100 chr7A 49620397 49623230 2833 True 2228.000000 3709 96.481500 121 2826 2 chr7A.!!$R5 2705
9 TraesCS1A01G252100 chr7A 481748731 481750009 1278 True 2183.000000 2183 97.498000 972 2249 1 chr7A.!!$R2 1277
10 TraesCS1A01G252100 chr7A 633706392 633712733 6341 True 1697.666667 3579 96.470000 1 2826 3 chr7A.!!$R7 2825
11 TraesCS1A01G252100 chr5A 168397643 168400439 2796 True 4604.000000 4604 96.250000 1 2826 1 chr5A.!!$R1 2825
12 TraesCS1A01G252100 chr5A 133817694 133819371 1677 False 2567.000000 2567 94.468000 121 1780 1 chr5A.!!$F2 1659
13 TraesCS1A01G252100 chr5A 572301287 572302695 1408 False 2362.000000 2362 96.948000 972 2379 1 chr5A.!!$F4 1407
14 TraesCS1A01G252100 chr3A 513294909 513296579 1670 False 2483.000000 2483 93.616000 121 1780 1 chr3A.!!$F1 1659
15 TraesCS1A01G252100 chr4A 490340744 490342576 1832 False 1310.000000 2468 95.088000 27 1780 2 chr4A.!!$F2 1753
16 TraesCS1A01G252100 chr4A 429487827 429489747 1920 False 879.266667 2451 96.474333 1 1780 3 chr4A.!!$F1 1779
17 TraesCS1A01G252100 chr6A 401364206 401366058 1852 False 1285.000000 2438 95.893500 36 1780 2 chr6A.!!$F2 1744
18 TraesCS1A01G252100 chr4B 113838290 113839542 1252 False 2058.000000 2058 96.267000 994 2251 1 chr4B.!!$F1 1257
19 TraesCS1A01G252100 chr4D 261238103 261239527 1424 True 968.500000 1694 92.679000 323 1776 2 chr4D.!!$R3 1453
20 TraesCS1A01G252100 chr5B 291687802 291688775 973 True 1014.000000 1014 85.685000 801 1776 1 chr5B.!!$R1 975
21 TraesCS1A01G252100 chr6D 297178885 297179389 504 True 850.000000 850 97.030000 320 824 1 chr6D.!!$R1 504
22 TraesCS1A01G252100 chr6D 202662919 202664310 1391 False 281.140000 1000 88.262400 616 1776 5 chr6D.!!$F1 1160
23 TraesCS1A01G252100 chr5D 140960664 140961168 504 True 850.000000 850 97.030000 320 824 1 chr5D.!!$R1 504
24 TraesCS1A01G252100 chr3B 62764785 62766562 1777 True 747.000000 747 96.460000 2375 2826 2 chr3B.!!$R1 451
25 TraesCS1A01G252100 chr1D 428055095 428055934 839 True 556.000000 688 92.493000 568 1376 2 chr1D.!!$R1 808

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
231 394 0.687354 TCCCTGTGCTTCTCTTCACC 59.313 55.000 0.0 0.0 32.51 4.02 F
1148 1557 1.591703 CACTGCTTGACCCTCGCTA 59.408 57.895 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 2242 0.378257 CACCACCATAGCATGTTCGC 59.622 55.0 0.00 0.0 0.00 4.70 R
2601 5613 0.834687 TCCGTGGCTAGGGTTTGAGT 60.835 55.0 8.77 0.0 33.55 3.41 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
155 318 7.475840 CAGACTGAATTAGGCATTTAGGTTTC 58.524 38.462 0.00 0.00 36.64 2.78
231 394 0.687354 TCCCTGTGCTTCTCTTCACC 59.313 55.000 0.00 0.00 32.51 4.02
529 694 8.255206 TCAGTTTTGTACATGACTATATCGGTT 58.745 33.333 0.00 0.00 0.00 4.44
674 991 4.519540 AACAAAATGTAGCACATGGGAC 57.480 40.909 0.00 0.00 37.97 4.46
774 1127 7.282224 GTGTTTGCCATTTATAGTAGACATGGA 59.718 37.037 13.07 0.00 37.20 3.41
1148 1557 1.591703 CACTGCTTGACCCTCGCTA 59.408 57.895 0.00 0.00 0.00 4.26
1515 1924 5.184096 ACAACACCATGTTCACACTTTGTTA 59.816 36.000 0.00 0.00 38.77 2.41
1910 2692 3.833070 GAGGAGTGAAGGTGTTAAGAGGA 59.167 47.826 0.00 0.00 0.00 3.71
2077 2859 8.149631 AGTTTGGTAATTGATGGGAATTGAAT 57.850 30.769 0.00 0.00 0.00 2.57
2318 4353 7.710044 ACATCTAAGTGAGTGAATCAAGCATAG 59.290 37.037 0.00 0.00 40.43 2.23
2322 4357 6.291648 AGTGAGTGAATCAAGCATAGAGAA 57.708 37.500 0.00 0.00 40.43 2.87
2412 4761 1.134729 GCCCTATTTTACGGACGGTCA 60.135 52.381 10.76 0.00 0.00 4.02
2452 4801 1.328430 ACCCTTGTAGCTACTCCCGC 61.328 60.000 23.84 0.00 0.00 6.13
2506 4855 1.247567 CCGGCTGGAATTTGAACTGT 58.752 50.000 5.28 0.00 37.49 3.55
2601 5613 1.859383 TCGACAACAGATTTGCACGA 58.141 45.000 0.00 0.00 32.52 4.35
2660 6334 6.797748 AAATCGGAAGGTTTTTGAAAACACCA 60.798 34.615 18.01 10.41 42.97 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
231 394 6.575083 ATTTCTGATGAATTCTACGTCACG 57.425 37.500 7.05 0.00 31.56 4.35
774 1127 0.968405 GACCATGTTTGCCCATGTGT 59.032 50.000 7.17 5.25 40.50 3.72
785 1138 6.814954 ACTCTATCTACAATGGACCATGTT 57.185 37.500 8.02 0.20 0.00 2.71
787 1140 7.531857 ACTACTCTATCTACAATGGACCATG 57.468 40.000 8.02 5.11 0.00 3.66
857 1251 9.797642 AATGCACTTGTGGATATTTATGATAGA 57.202 29.630 8.12 0.00 0.00 1.98
1088 1497 4.609947 CACTAGACAGCAGAGTGATGATC 58.390 47.826 0.00 0.00 42.65 2.92
1148 1557 1.374190 CTTGTCAGGCAGCCTCTGT 59.626 57.895 12.53 0.00 33.43 3.41
1223 1632 1.264749 ACATCCTGTGAAGCCCGCTA 61.265 55.000 0.00 0.00 0.00 4.26
1515 1924 1.555477 CCCATTGCCTGGCCAAATGT 61.555 55.000 22.70 0.53 44.46 2.71
1623 2242 0.378257 CACCACCATAGCATGTTCGC 59.622 55.000 0.00 0.00 0.00 4.70
1733 2433 2.047274 CACCACCATCGCGAGGTT 60.047 61.111 22.35 6.24 37.23 3.50
1910 2692 5.711976 AGCTTAAACCTAACATGCTGAACAT 59.288 36.000 0.00 0.00 40.66 2.71
1984 2766 1.008881 GCATCCATGAGCATGCACG 60.009 57.895 21.98 4.54 44.18 5.34
2051 2833 8.657387 TTCAATTCCCATCAATTACCAAACTA 57.343 30.769 0.00 0.00 0.00 2.24
2084 2867 3.358118 TCTTTCATCCATGAGCATGCAA 58.642 40.909 21.98 8.14 38.19 4.08
2335 4370 7.762382 AGATTCGTGTGGATATTTTCCTTTTC 58.238 34.615 0.00 0.00 45.68 2.29
2452 4801 2.466867 CGAAGGTGGTCCGAATTGG 58.533 57.895 0.00 0.00 39.05 3.16
2601 5613 0.834687 TCCGTGGCTAGGGTTTGAGT 60.835 55.000 8.77 0.00 33.55 3.41
2720 7716 9.006839 GTTTAGTATTTTTGCTAGTTGGTAGGT 57.993 33.333 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.