Multiple sequence alignment - TraesCS1B01G397600

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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 TraesCS1B01G397600 chr1B 100.000 2552 0 0 1 2552 628975759 628973208 0.000000e+00 4713.0
1 TraesCS1B01G397600 chr1B 97.914 2301 45 3 1 2300 628899541 628897243 0.000000e+00 3980.0
2 TraesCS1B01G397600 chr1B 97.567 2302 53 3 1 2300 628856688 628854388 0.000000e+00 3938.0
3 TraesCS1B01G397600 chr1B 87.586 1603 132 23 594 2159 577793171 577791599 0.000000e+00 1796.0
4 TraesCS1B01G397600 chr1B 85.542 1577 151 34 593 2159 332064946 332063437 0.000000e+00 1578.0
5 TraesCS1B01G397600 chr1B 84.965 1583 144 31 592 2159 645321435 645322938 0.000000e+00 1519.0
6 TraesCS1B01G397600 chr1B 83.656 1603 164 47 594 2159 571670835 571672376 0.000000e+00 1419.0
7 TraesCS1B01G397600 chr1B 96.459 593 21 0 1 593 628811685 628811093 0.000000e+00 979.0
8 TraesCS1B01G397600 chr1B 94.444 594 31 2 1 593 629054168 629053576 0.000000e+00 913.0
9 TraesCS1B01G397600 chr1B 93.592 593 38 0 1 593 629092432 629091840 0.000000e+00 885.0
10 TraesCS1B01G397600 chr1B 93.098 594 40 1 1 593 628994824 628994231 0.000000e+00 869.0
11 TraesCS1B01G397600 chr1B 92.256 594 45 1 1 593 628918480 628917887 0.000000e+00 841.0
12 TraesCS1B01G397600 chr1B 98.419 253 4 0 2300 2552 628897211 628896959 1.800000e-121 446.0
13 TraesCS1B01G397600 chr1B 95.257 253 12 0 2300 2552 628854356 628854104 3.950000e-108 401.0
14 TraesCS1B01G397600 chr1B 84.783 276 39 3 593 868 55228927 55228655 9.000000e-70 274.0
15 TraesCS1B01G397600 chr1B 84.502 271 39 3 593 863 55192983 55192716 5.410000e-67 265.0
16 TraesCS1B01G397600 chr1B 79.705 271 29 11 739 1003 628778633 628778383 3.380000e-39 172.0
17 TraesCS1B01G397600 chr7B 90.341 1584 129 13 593 2161 691229728 691228154 0.000000e+00 2056.0
18 TraesCS1B01G397600 chr7B 94.492 236 13 0 2306 2541 691228072 691227837 5.190000e-97 364.0
19 TraesCS1B01G397600 chr3A 89.583 1584 125 16 593 2159 47284898 47286458 0.000000e+00 1975.0
20 TraesCS1B01G397600 chr3A 88.165 1580 147 21 593 2159 634659839 634658287 0.000000e+00 1845.0
21 TraesCS1B01G397600 chr2D 89.322 1592 122 19 593 2159 12544105 12542537 0.000000e+00 1954.0
22 TraesCS1B01G397600 chr2D 92.692 260 19 0 2293 2552 551248406 551248665 2.400000e-100 375.0
23 TraesCS1B01G397600 chr2D 92.490 253 19 0 2300 2552 12542458 12542206 1.870000e-96 363.0
24 TraesCS1B01G397600 chr2D 91.538 260 22 0 2293 2552 590928169 590927910 2.410000e-95 359.0
25 TraesCS1B01G397600 chr3B 89.317 1582 131 16 594 2159 124399476 124397917 0.000000e+00 1951.0
26 TraesCS1B01G397600 chr3B 88.609 1589 139 21 588 2159 749205899 749207462 0.000000e+00 1893.0
27 TraesCS1B01G397600 chr3B 88.313 1583 144 15 594 2159 124560191 124558633 0.000000e+00 1860.0
28 TraesCS1B01G397600 chr5D 88.777 1586 139 24 592 2159 257136355 257137919 0.000000e+00 1906.0
29 TraesCS1B01G397600 chr5D 89.386 1319 93 18 859 2159 353835367 353834078 0.000000e+00 1616.0
30 TraesCS1B01G397600 chr5D 92.095 253 20 0 2300 2552 353833999 353833747 8.680000e-95 357.0
31 TraesCS1B01G397600 chr6B 91.250 1360 91 9 659 2002 117771203 117769856 0.000000e+00 1827.0
32 TraesCS1B01G397600 chr6B 91.071 1120 86 3 594 1700 117801350 117800232 0.000000e+00 1502.0
33 TraesCS1B01G397600 chr7A 87.304 1591 146 18 594 2159 152034644 152036203 0.000000e+00 1768.0
34 TraesCS1B01G397600 chr7A 92.095 253 20 0 2300 2552 152036279 152036531 8.680000e-95 357.0
35 TraesCS1B01G397600 chr5A 85.474 1604 159 34 592 2159 700182691 700184256 0.000000e+00 1604.0
36 TraesCS1B01G397600 chr5A 96.622 148 4 1 2157 2303 700184159 700184306 7.050000e-61 244.0
37 TraesCS1B01G397600 chr1D 93.810 517 29 3 1 517 458230303 458229790 0.000000e+00 774.0
38 TraesCS1B01G397600 chr1D 85.445 584 57 19 3 567 458238755 458238181 1.320000e-162 582.0
39 TraesCS1B01G397600 chr1D 84.775 578 63 15 4 560 458178730 458178157 7.980000e-155 556.0
40 TraesCS1B01G397600 chr1D 80.551 581 68 24 3 562 458167143 458166587 3.060000e-109 405.0
41 TraesCS1B01G397600 chr1D 81.769 554 32 21 3 534 458273239 458272733 1.420000e-107 399.0
42 TraesCS1B01G397600 chr1D 81.841 402 40 18 195 567 458285939 458285542 8.870000e-80 307.0
43 TraesCS1B01G397600 chr1D 86.897 145 12 4 200 344 458233858 458233721 3.400000e-34 156.0
44 TraesCS1B01G397600 chr1D 83.871 124 11 6 3 123 202477642 202477525 2.680000e-20 110.0
45 TraesCS1B01G397600 chr1D 90.000 50 1 3 78 123 458286068 458286019 7.620000e-06 62.1
46 TraesCS1B01G397600 chr1A 90.526 570 35 2 1 570 550793520 550792970 0.000000e+00 736.0
47 TraesCS1B01G397600 chr1A 81.770 565 74 17 3 562 550655640 550655100 1.800000e-121 446.0
48 TraesCS1B01G397600 chr1A 80.635 630 64 28 3 590 550824759 550824146 3.900000e-118 435.0
49 TraesCS1B01G397600 chr1A 82.353 391 43 14 195 567 550835753 550835371 1.470000e-82 316.0
50 TraesCS1B01G397600 chr1A 80.593 371 46 20 210 562 550669325 550668963 1.950000e-66 263.0
51 TraesCS1B01G397600 chr5B 86.705 519 51 9 593 1099 700746044 700746556 6.170000e-156 560.0
52 TraesCS1B01G397600 chr5B 83.421 380 44 11 592 966 452113409 452113044 4.070000e-88 335.0
53 TraesCS1B01G397600 chr2B 88.578 464 41 3 594 1045 797444899 797444436 1.030000e-153 553.0
54 TraesCS1B01G397600 chr2B 96.053 152 4 2 2153 2303 19093403 19093553 1.960000e-61 246.0
55 TraesCS1B01G397600 chr2B 96.622 148 4 1 2157 2303 710553023 710552876 7.050000e-61 244.0
56 TraesCS1B01G397600 chr6D 94.071 253 14 1 2300 2552 459069633 459069884 1.430000e-102 383.0
57 TraesCS1B01G397600 chr6D 97.315 149 2 2 2157 2303 323168132 323168280 4.210000e-63 252.0
58 TraesCS1B01G397600 chr7D 97.241 145 3 1 2157 2300 439706393 439706249 7.050000e-61 244.0
59 TraesCS1B01G397600 chr4D 96.622 148 4 1 2157 2303 78731330 78731183 7.050000e-61 244.0
60 TraesCS1B01G397600 chr4D 95.973 149 4 2 2157 2303 43271300 43271152 9.120000e-60 241.0


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 TraesCS1B01G397600 chr1B 628973208 628975759 2551 True 4713.0 4713 100.0000 1 2552 1 chr1B.!!$R8 2551
1 TraesCS1B01G397600 chr1B 628896959 628899541 2582 True 2213.0 3980 98.1665 1 2552 2 chr1B.!!$R13 2551
2 TraesCS1B01G397600 chr1B 628854104 628856688 2584 True 2169.5 3938 96.4120 1 2552 2 chr1B.!!$R12 2551
3 TraesCS1B01G397600 chr1B 577791599 577793171 1572 True 1796.0 1796 87.5860 594 2159 1 chr1B.!!$R4 1565
4 TraesCS1B01G397600 chr1B 332063437 332064946 1509 True 1578.0 1578 85.5420 593 2159 1 chr1B.!!$R3 1566
5 TraesCS1B01G397600 chr1B 645321435 645322938 1503 False 1519.0 1519 84.9650 592 2159 1 chr1B.!!$F2 1567
6 TraesCS1B01G397600 chr1B 571670835 571672376 1541 False 1419.0 1419 83.6560 594 2159 1 chr1B.!!$F1 1565
7 TraesCS1B01G397600 chr1B 628811093 628811685 592 True 979.0 979 96.4590 1 593 1 chr1B.!!$R6 592
8 TraesCS1B01G397600 chr1B 629053576 629054168 592 True 913.0 913 94.4440 1 593 1 chr1B.!!$R10 592
9 TraesCS1B01G397600 chr1B 629091840 629092432 592 True 885.0 885 93.5920 1 593 1 chr1B.!!$R11 592
10 TraesCS1B01G397600 chr1B 628994231 628994824 593 True 869.0 869 93.0980 1 593 1 chr1B.!!$R9 592
11 TraesCS1B01G397600 chr1B 628917887 628918480 593 True 841.0 841 92.2560 1 593 1 chr1B.!!$R7 592
12 TraesCS1B01G397600 chr7B 691227837 691229728 1891 True 1210.0 2056 92.4165 593 2541 2 chr7B.!!$R1 1948
13 TraesCS1B01G397600 chr3A 47284898 47286458 1560 False 1975.0 1975 89.5830 593 2159 1 chr3A.!!$F1 1566
14 TraesCS1B01G397600 chr3A 634658287 634659839 1552 True 1845.0 1845 88.1650 593 2159 1 chr3A.!!$R1 1566
15 TraesCS1B01G397600 chr2D 12542206 12544105 1899 True 1158.5 1954 90.9060 593 2552 2 chr2D.!!$R2 1959
16 TraesCS1B01G397600 chr3B 124397917 124399476 1559 True 1951.0 1951 89.3170 594 2159 1 chr3B.!!$R1 1565
17 TraesCS1B01G397600 chr3B 749205899 749207462 1563 False 1893.0 1893 88.6090 588 2159 1 chr3B.!!$F1 1571
18 TraesCS1B01G397600 chr3B 124558633 124560191 1558 True 1860.0 1860 88.3130 594 2159 1 chr3B.!!$R2 1565
19 TraesCS1B01G397600 chr5D 257136355 257137919 1564 False 1906.0 1906 88.7770 592 2159 1 chr5D.!!$F1 1567
20 TraesCS1B01G397600 chr5D 353833747 353835367 1620 True 986.5 1616 90.7405 859 2552 2 chr5D.!!$R1 1693
21 TraesCS1B01G397600 chr6B 117769856 117771203 1347 True 1827.0 1827 91.2500 659 2002 1 chr6B.!!$R1 1343
22 TraesCS1B01G397600 chr6B 117800232 117801350 1118 True 1502.0 1502 91.0710 594 1700 1 chr6B.!!$R2 1106
23 TraesCS1B01G397600 chr7A 152034644 152036531 1887 False 1062.5 1768 89.6995 594 2552 2 chr7A.!!$F1 1958
24 TraesCS1B01G397600 chr5A 700182691 700184306 1615 False 924.0 1604 91.0480 592 2303 2 chr5A.!!$F1 1711
25 TraesCS1B01G397600 chr1D 458238181 458238755 574 True 582.0 582 85.4450 3 567 1 chr1D.!!$R4 564
26 TraesCS1B01G397600 chr1D 458178157 458178730 573 True 556.0 556 84.7750 4 560 1 chr1D.!!$R3 556
27 TraesCS1B01G397600 chr1D 458229790 458233858 4068 True 465.0 774 90.3535 1 517 2 chr1D.!!$R6 516
28 TraesCS1B01G397600 chr1D 458166587 458167143 556 True 405.0 405 80.5510 3 562 1 chr1D.!!$R2 559
29 TraesCS1B01G397600 chr1D 458272733 458273239 506 True 399.0 399 81.7690 3 534 1 chr1D.!!$R5 531
30 TraesCS1B01G397600 chr1A 550792970 550793520 550 True 736.0 736 90.5260 1 570 1 chr1A.!!$R3 569
31 TraesCS1B01G397600 chr1A 550655100 550655640 540 True 446.0 446 81.7700 3 562 1 chr1A.!!$R1 559
32 TraesCS1B01G397600 chr1A 550824146 550824759 613 True 435.0 435 80.6350 3 590 1 chr1A.!!$R4 587
33 TraesCS1B01G397600 chr5B 700746044 700746556 512 False 560.0 560 86.7050 593 1099 1 chr5B.!!$F1 506

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
562 4170 0.378257 CACAAGTGTTCGTGCTTGCT 59.622 50.0 4.45 0.0 44.12 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 5419 4.261238 GGAGAGAGCTGCATTTCATTGATG 60.261 45.833 1.02 0.0 31.98 3.07 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
124 3680 1.407437 GCCATCGGTCCTTGATGAGTT 60.407 52.381 8.02 0.0 44.76 3.01
139 3695 4.873827 TGATGAGTTATTAAACACGGCTCC 59.126 41.667 0.00 0.0 38.12 4.70
163 3721 4.034975 GCGCTGCTCTTCTTTCTTGATAAT 59.965 41.667 0.00 0.0 0.00 1.28
562 4170 0.378257 CACAAGTGTTCGTGCTTGCT 59.622 50.000 4.45 0.0 44.12 3.91
664 4282 5.799936 GCTTTTAGTTGCGAATTATGCTCAA 59.200 36.000 4.05 0.0 0.00 3.02
1128 4798 0.105964 CTCACACACCGAGGAACCAA 59.894 55.000 0.00 0.0 0.00 3.67
1165 4835 1.280710 TGTGCAACGAGAATGGGGTAT 59.719 47.619 0.00 0.0 42.39 2.73
1389 5063 1.137086 GAGATAGAGGGCAAAGCACGA 59.863 52.381 0.00 0.0 36.86 4.35
1726 5441 4.575236 TCATCAATGAAATGCAGCTCTCTC 59.425 41.667 0.00 0.0 33.08 3.20
1942 5662 6.074142 GCTCAAACTTTTTGTGGAAGCTAATG 60.074 38.462 0.00 0.0 0.00 1.90
2358 6125 4.520492 AGTGGAAAGACTTTAACATGGCTG 59.480 41.667 0.00 0.0 0.00 4.85
2400 6167 4.525487 AGTGAGACCGTGACTTGGTTTATA 59.475 41.667 0.00 0.0 40.63 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 3695 0.179230 CAAGAAAGAAGAGCAGCGCG 60.179 55.000 0.00 0.00 0.00 6.86
163 3721 2.169978 CCATCTCAGATCAGGAGCAACA 59.830 50.000 9.00 0.00 32.38 3.33
432 4018 1.217942 GTTATCCTCCCTTTGGGCCAT 59.782 52.381 7.26 0.00 43.94 4.40
664 4282 0.614697 GGGCACACTAGGGGCAAAAT 60.615 55.000 0.00 0.00 0.00 1.82
1165 4835 0.539986 GGAGCAACTACCCCGATTCA 59.460 55.000 0.00 0.00 0.00 2.57
1389 5063 5.596845 GCAATAGCTAGCTCTCTGTTAGTT 58.403 41.667 23.26 0.00 37.91 2.24
1704 5419 4.261238 GGAGAGAGCTGCATTTCATTGATG 60.261 45.833 1.02 0.00 31.98 3.07
1942 5662 9.736023 CTTAATTGTTGGCTCTGTAATAATTCC 57.264 33.333 0.00 0.00 32.39 3.01
2358 6125 4.838986 TCACTATGTATAGCTTCCTTCCCC 59.161 45.833 0.00 0.00 33.68 4.81
2400 6167 9.915629 TTCAGTACAAACATGTGTTTTTAAACT 57.084 25.926 8.32 7.09 45.07 2.66


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

AutoCloner maintained by Alex Coulton.