Multiple sequence alignment - TraesCS1A01G068800

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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 TraesCS1A01G068800 chr1A 100.000 2549 0 0 1 2549 50510541 50513089 0.000000e+00 4708.0
1 TraesCS1A01G068800 chr1A 97.711 568 12 1 1 567 5972241 5971674 0.000000e+00 976.0
2 TraesCS1A01G068800 chr7A 97.075 1983 54 3 565 2547 49208209 49210187 0.000000e+00 3338.0
3 TraesCS1A01G068800 chr7A 96.421 1984 50 9 566 2547 689996369 689994405 0.000000e+00 3251.0
4 TraesCS1A01G068800 chr7A 96.322 1985 54 11 564 2547 150203040 150201074 0.000000e+00 3243.0
5 TraesCS1A01G068800 chr7A 96.267 1152 36 2 564 1712 18189928 18191075 0.000000e+00 1882.0
6 TraesCS1A01G068800 chr5A 96.662 2007 51 9 544 2547 563443910 563445903 0.000000e+00 3321.0
7 TraesCS1A01G068800 chr5A 96.470 1983 55 8 566 2547 14186781 14184813 0.000000e+00 3260.0
8 TraesCS1A01G068800 chr5A 95.974 1987 58 13 562 2547 90997654 90999619 0.000000e+00 3206.0
9 TraesCS1A01G068800 chr5A 93.695 571 29 4 1 567 685783511 685782944 0.000000e+00 848.0
10 TraesCS1A01G068800 chr3A 96.436 1992 51 4 560 2547 683237679 683235704 0.000000e+00 3267.0
11 TraesCS1A01G068800 chr2A 96.196 1998 62 8 553 2547 771778404 771780390 0.000000e+00 3256.0
12 TraesCS1A01G068800 chr2A 96.016 1983 53 7 565 2545 775967963 775966005 0.000000e+00 3201.0
13 TraesCS1A01G068800 chr2A 96.724 1618 40 7 931 2547 744582359 744583964 0.000000e+00 2682.0
14 TraesCS1A01G068800 chr4A 96.169 1984 51 9 565 2547 29029001 29030960 0.000000e+00 3219.0
15 TraesCS1A01G068800 chr4A 78.261 575 59 32 3 521 572502377 572502941 2.460000e-80 309.0
16 TraesCS1A01G068800 chr6A 95.689 1995 51 12 557 2547 203520923 203518960 0.000000e+00 3175.0
17 TraesCS1A01G068800 chr6A 96.473 567 12 1 1 567 39942380 39941822 0.000000e+00 929.0
18 TraesCS1A01G068800 chr6A 84.722 360 37 9 222 567 234169191 234169546 6.750000e-91 344.0
19 TraesCS1A01G068800 chr6A 92.641 231 17 0 1 231 234168533 234168763 1.460000e-87 333.0
20 TraesCS1A01G068800 chr6A 77.913 575 67 24 1 521 615069076 615068508 1.150000e-78 303.0
21 TraesCS1A01G068800 chr7D 93.695 571 29 5 1 567 113760769 113761336 0.000000e+00 848.0
22 TraesCS1A01G068800 chr7D 93.509 570 30 4 1 567 131314370 131314935 0.000000e+00 841.0
23 TraesCS1A01G068800 chr7D 86.389 360 31 9 222 567 15892284 15891929 6.660000e-101 377.0
24 TraesCS1A01G068800 chr7D 79.791 574 62 23 45 567 564304167 564304737 4.010000e-98 368.0
25 TraesCS1A01G068800 chr7D 78.671 572 65 16 1 521 29566671 29566106 6.800000e-86 327.0
26 TraesCS1A01G068800 chr7D 92.174 230 17 1 2 231 15894142 15893914 8.800000e-85 324.0
27 TraesCS1A01G068800 chr6B 93.486 568 20 2 1 567 714696986 714696435 0.000000e+00 828.0
28 TraesCS1A01G068800 chr6B 85.794 359 31 10 222 567 603887671 603888022 1.860000e-96 363.0
29 TraesCS1A01G068800 chr5D 93.978 548 29 3 1 544 480828612 480829159 0.000000e+00 826.0
30 TraesCS1A01G068800 chr2B 92.294 571 37 5 1 567 651100641 651101208 0.000000e+00 804.0
31 TraesCS1A01G068800 chr7B 93.078 549 34 3 1 545 712875279 712875827 0.000000e+00 800.0
32 TraesCS1A01G068800 chrUn 93.966 232 14 0 1 232 294333405 294333174 4.030000e-93 351.0
33 TraesCS1A01G068800 chrUn 93.966 232 14 0 1 232 303954318 303954549 4.030000e-93 351.0
34 TraesCS1A01G068800 chrUn 87.542 297 21 7 223 506 294332742 294332449 1.890000e-86 329.0
35 TraesCS1A01G068800 chrUn 87.542 297 21 7 223 506 303954981 303955274 1.890000e-86 329.0
36 TraesCS1A01G068800 chr2D 79.021 572 63 20 1 521 644822817 644823382 3.140000e-89 339.0
37 TraesCS1A01G068800 chr1B 93.043 230 15 1 2 231 566131293 566131065 4.060000e-88 335.0
38 TraesCS1A01G068800 chr1D 78.846 572 64 16 1 521 187813520 187814085 1.460000e-87 333.0
39 TraesCS1A01G068800 chr4D 77.617 554 65 23 1 521 403013998 403014525 5.370000e-72 281.0
40 TraesCS1A01G068800 chr4D 90.826 109 10 0 1 109 112583313 112583205 2.040000e-31 147.0
41 TraesCS1A01G068800 chr4B 81.090 312 39 8 2 294 313744675 313744365 5.480000e-57 231.0
42 TraesCS1A01G068800 chr4B 90.698 43 4 0 414 456 619972069 619972111 9.850000e-05 58.4
43 TraesCS1A01G068800 chr3D 78.400 375 30 22 17 340 467838794 467839168 2.000000e-46 196.0
44 TraesCS1A01G068800 chr3D 85.246 122 12 3 33 154 459446303 459446418 1.240000e-23 121.0
45 TraesCS1A01G068800 chr3D 86.364 88 9 3 372 456 421653205 421653292 2.700000e-15 93.5


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 TraesCS1A01G068800 chr1A 50510541 50513089 2548 False 4708.0 4708 100.0000 1 2549 1 chr1A.!!$F1 2548
1 TraesCS1A01G068800 chr1A 5971674 5972241 567 True 976.0 976 97.7110 1 567 1 chr1A.!!$R1 566
2 TraesCS1A01G068800 chr7A 49208209 49210187 1978 False 3338.0 3338 97.0750 565 2547 1 chr7A.!!$F2 1982
3 TraesCS1A01G068800 chr7A 689994405 689996369 1964 True 3251.0 3251 96.4210 566 2547 1 chr7A.!!$R2 1981
4 TraesCS1A01G068800 chr7A 150201074 150203040 1966 True 3243.0 3243 96.3220 564 2547 1 chr7A.!!$R1 1983
5 TraesCS1A01G068800 chr7A 18189928 18191075 1147 False 1882.0 1882 96.2670 564 1712 1 chr7A.!!$F1 1148
6 TraesCS1A01G068800 chr5A 563443910 563445903 1993 False 3321.0 3321 96.6620 544 2547 1 chr5A.!!$F2 2003
7 TraesCS1A01G068800 chr5A 14184813 14186781 1968 True 3260.0 3260 96.4700 566 2547 1 chr5A.!!$R1 1981
8 TraesCS1A01G068800 chr5A 90997654 90999619 1965 False 3206.0 3206 95.9740 562 2547 1 chr5A.!!$F1 1985
9 TraesCS1A01G068800 chr5A 685782944 685783511 567 True 848.0 848 93.6950 1 567 1 chr5A.!!$R2 566
10 TraesCS1A01G068800 chr3A 683235704 683237679 1975 True 3267.0 3267 96.4360 560 2547 1 chr3A.!!$R1 1987
11 TraesCS1A01G068800 chr2A 771778404 771780390 1986 False 3256.0 3256 96.1960 553 2547 1 chr2A.!!$F2 1994
12 TraesCS1A01G068800 chr2A 775966005 775967963 1958 True 3201.0 3201 96.0160 565 2545 1 chr2A.!!$R1 1980
13 TraesCS1A01G068800 chr2A 744582359 744583964 1605 False 2682.0 2682 96.7240 931 2547 1 chr2A.!!$F1 1616
14 TraesCS1A01G068800 chr4A 29029001 29030960 1959 False 3219.0 3219 96.1690 565 2547 1 chr4A.!!$F1 1982
15 TraesCS1A01G068800 chr4A 572502377 572502941 564 False 309.0 309 78.2610 3 521 1 chr4A.!!$F2 518
16 TraesCS1A01G068800 chr6A 203518960 203520923 1963 True 3175.0 3175 95.6890 557 2547 1 chr6A.!!$R2 1990
17 TraesCS1A01G068800 chr6A 39941822 39942380 558 True 929.0 929 96.4730 1 567 1 chr6A.!!$R1 566
18 TraesCS1A01G068800 chr6A 234168533 234169546 1013 False 338.5 344 88.6815 1 567 2 chr6A.!!$F1 566
19 TraesCS1A01G068800 chr6A 615068508 615069076 568 True 303.0 303 77.9130 1 521 1 chr6A.!!$R3 520
20 TraesCS1A01G068800 chr7D 113760769 113761336 567 False 848.0 848 93.6950 1 567 1 chr7D.!!$F1 566
21 TraesCS1A01G068800 chr7D 131314370 131314935 565 False 841.0 841 93.5090 1 567 1 chr7D.!!$F2 566
22 TraesCS1A01G068800 chr7D 564304167 564304737 570 False 368.0 368 79.7910 45 567 1 chr7D.!!$F3 522
23 TraesCS1A01G068800 chr7D 15891929 15894142 2213 True 350.5 377 89.2815 2 567 2 chr7D.!!$R2 565
24 TraesCS1A01G068800 chr7D 29566106 29566671 565 True 327.0 327 78.6710 1 521 1 chr7D.!!$R1 520
25 TraesCS1A01G068800 chr6B 714696435 714696986 551 True 828.0 828 93.4860 1 567 1 chr6B.!!$R1 566
26 TraesCS1A01G068800 chr5D 480828612 480829159 547 False 826.0 826 93.9780 1 544 1 chr5D.!!$F1 543
27 TraesCS1A01G068800 chr2B 651100641 651101208 567 False 804.0 804 92.2940 1 567 1 chr2B.!!$F1 566
28 TraesCS1A01G068800 chr7B 712875279 712875827 548 False 800.0 800 93.0780 1 545 1 chr7B.!!$F1 544
29 TraesCS1A01G068800 chrUn 294332449 294333405 956 True 340.0 351 90.7540 1 506 2 chrUn.!!$R1 505
30 TraesCS1A01G068800 chrUn 303954318 303955274 956 False 340.0 351 90.7540 1 506 2 chrUn.!!$F1 505
31 TraesCS1A01G068800 chr2D 644822817 644823382 565 False 339.0 339 79.0210 1 521 1 chr2D.!!$F1 520
32 TraesCS1A01G068800 chr1D 187813520 187814085 565 False 333.0 333 78.8460 1 521 1 chr1D.!!$F1 520
33 TraesCS1A01G068800 chr4D 403013998 403014525 527 False 281.0 281 77.6170 1 521 1 chr4D.!!$F1 520

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
902 2714 0.10412 CGGCGAGAGAGAGAGAGAGA 59.896 60.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 3991 0.670239 CCCAGCCGCACCAATTTTTC 60.67 55.0 0.0 0.0 0.0 2.29 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
790 2560 2.036256 GCTTGTGGGACCCAGCAT 59.964 61.111 15.52 0.00 32.34 3.79
834 2634 2.043992 TGGCGGGTGTGCTATATAAGT 58.956 47.619 0.00 0.00 34.52 2.24
900 2712 0.461163 CACGGCGAGAGAGAGAGAGA 60.461 60.000 16.62 0.00 0.00 3.10
901 2713 0.179084 ACGGCGAGAGAGAGAGAGAG 60.179 60.000 16.62 0.00 0.00 3.20
902 2714 0.104120 CGGCGAGAGAGAGAGAGAGA 59.896 60.000 0.00 0.00 0.00 3.10
905 2717 2.546795 GGCGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
906 2718 2.748605 CGAGAGAGAGAGAGAGAGAGC 58.251 57.143 0.00 0.00 0.00 4.09
907 2719 2.101415 CGAGAGAGAGAGAGAGAGAGCA 59.899 54.545 0.00 0.00 0.00 4.26
909 2721 2.840038 AGAGAGAGAGAGAGAGAGCACA 59.160 50.000 0.00 0.00 0.00 4.57
911 2723 2.573462 AGAGAGAGAGAGAGAGCACAGT 59.427 50.000 0.00 0.00 0.00 3.55
912 2724 2.679837 GAGAGAGAGAGAGAGCACAGTG 59.320 54.545 0.00 0.00 0.00 3.66
913 2725 1.745087 GAGAGAGAGAGAGCACAGTGG 59.255 57.143 1.84 0.00 0.00 4.00
914 2726 0.173255 GAGAGAGAGAGCACAGTGGC 59.827 60.000 1.84 0.00 0.00 5.01
915 2727 1.153862 GAGAGAGAGCACAGTGGCG 60.154 63.158 1.84 0.00 39.27 5.69
916 2728 2.125753 GAGAGAGCACAGTGGCGG 60.126 66.667 1.84 0.00 39.27 6.13
917 2729 3.655810 GAGAGAGCACAGTGGCGGG 62.656 68.421 1.84 0.00 39.27 6.13
918 2730 3.695606 GAGAGCACAGTGGCGGGA 61.696 66.667 1.84 0.00 39.27 5.14
920 2732 2.743928 GAGCACAGTGGCGGGAAG 60.744 66.667 1.84 0.00 39.27 3.46
930 2742 3.890674 GCGGGAAGCTAGTTGTGG 58.109 61.111 0.00 0.00 44.04 4.17
931 2743 1.295423 GCGGGAAGCTAGTTGTGGA 59.705 57.895 0.00 0.00 44.04 4.02
932 2744 0.741221 GCGGGAAGCTAGTTGTGGAG 60.741 60.000 0.00 0.00 44.04 3.86
933 2745 0.108138 CGGGAAGCTAGTTGTGGAGG 60.108 60.000 0.00 0.00 0.00 4.30
934 2746 0.253327 GGGAAGCTAGTTGTGGAGGG 59.747 60.000 0.00 0.00 0.00 4.30
1023 2835 2.177594 CTTCCTCAAGCTCCCACGCT 62.178 60.000 0.00 0.00 43.31 5.07
1028 2840 1.192146 TCAAGCTCCCACGCTACCTT 61.192 55.000 0.00 0.00 39.86 3.50
1476 3289 4.316025 AGCACTACCAATACCCATTTGT 57.684 40.909 0.00 0.00 0.00 2.83
1835 3665 0.614812 GGGCCAACTGCATCCAATTT 59.385 50.000 4.39 0.00 43.89 1.82
1845 3675 1.209990 GCATCCAATTTGGCCCATTCA 59.790 47.619 10.76 0.00 37.47 2.57
2159 3991 0.958091 TGAAGGGTGGAAAATGCACG 59.042 50.000 0.00 0.00 39.79 5.34
2226 4058 1.078708 GGTGTTTAGGGCTGCGCTA 60.079 57.895 20.82 20.82 0.00 4.26
2366 4202 6.811170 GTGAGAGTGTTTTTCCATTGTTTTGA 59.189 34.615 0.00 0.00 0.00 2.69
2502 4338 9.791801 AAAGGGAATAAATTTGCATGTTAGTTT 57.208 25.926 0.00 0.00 0.00 2.66
2547 4383 2.610859 GGCTTCTCACCCCCTCCA 60.611 66.667 0.00 0.00 0.00 3.86
2548 4384 2.231380 GGCTTCTCACCCCCTCCAA 61.231 63.158 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 58 7.494298 ACACAAAATATTTCAACACTTTCCCAC 59.506 33.333 0.10 0.0 0.00 4.61
790 2560 1.098869 CTCTCTGCTCAACGGCTCTA 58.901 55.000 0.00 0.0 0.00 2.43
860 2660 1.301244 CACTGCCGTGCTCTCTGTT 60.301 57.895 0.00 0.0 33.82 3.16
900 2712 3.699894 CCCGCCACTGTGCTCTCT 61.700 66.667 1.29 0.0 0.00 3.10
901 2713 3.240134 TTCCCGCCACTGTGCTCTC 62.240 63.158 1.29 0.0 0.00 3.20
902 2714 3.241530 TTCCCGCCACTGTGCTCT 61.242 61.111 1.29 0.0 0.00 4.09
905 2717 3.605749 TAGCTTCCCGCCACTGTGC 62.606 63.158 1.29 0.0 40.39 4.57
906 2718 1.448540 CTAGCTTCCCGCCACTGTG 60.449 63.158 0.00 0.0 40.39 3.66
907 2719 1.481056 AACTAGCTTCCCGCCACTGT 61.481 55.000 0.00 0.0 40.39 3.55
909 2721 1.296715 CAACTAGCTTCCCGCCACT 59.703 57.895 0.00 0.0 40.39 4.00
911 2723 1.003839 CACAACTAGCTTCCCGCCA 60.004 57.895 0.00 0.0 40.39 5.69
912 2724 1.745489 CCACAACTAGCTTCCCGCC 60.745 63.158 0.00 0.0 40.39 6.13
913 2725 0.741221 CTCCACAACTAGCTTCCCGC 60.741 60.000 0.00 0.0 39.57 6.13
914 2726 0.108138 CCTCCACAACTAGCTTCCCG 60.108 60.000 0.00 0.0 0.00 5.14
915 2727 0.253327 CCCTCCACAACTAGCTTCCC 59.747 60.000 0.00 0.0 0.00 3.97
916 2728 0.393132 GCCCTCCACAACTAGCTTCC 60.393 60.000 0.00 0.0 0.00 3.46
917 2729 0.741221 CGCCCTCCACAACTAGCTTC 60.741 60.000 0.00 0.0 0.00 3.86
918 2730 1.296715 CGCCCTCCACAACTAGCTT 59.703 57.895 0.00 0.0 0.00 3.74
920 2732 2.820037 GCGCCCTCCACAACTAGC 60.820 66.667 0.00 0.0 0.00 3.42
921 2733 2.509336 CGCGCCCTCCACAACTAG 60.509 66.667 0.00 0.0 0.00 2.57
1476 3289 7.784470 ACCTACAAATGCCCAAAAGTATTTA 57.216 32.000 0.00 0.0 37.28 1.40
1845 3675 3.434940 AAAATACGCAAGAGAACCCCT 57.565 42.857 0.00 0.0 43.62 4.79
2159 3991 0.670239 CCCAGCCGCACCAATTTTTC 60.670 55.000 0.00 0.0 0.00 2.29
2226 4058 2.032620 CCATCTGTCCTAGCGGTTACT 58.967 52.381 0.00 0.0 0.00 2.24
2366 4202 6.183361 CCTTCCAACCCTCCAAAATTTAAGTT 60.183 38.462 0.00 0.0 0.00 2.66


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

AutoCloner maintained by Alex Coulton.