Multiple sequence alignment - TraesCS1A01G081100

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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 TraesCS1A01G081100 chr1A 100.000 2950 0 0 1 2950 63976238 63973289 0.000000e+00 5448
1 TraesCS1A01G081100 chr1A 83.843 687 71 20 948 1605 115269459 115268784 4.180000e-173 617
2 TraesCS1A01G081100 chr1A 80.882 136 22 3 73 206 411748575 411748442 1.450000e-18 104
3 TraesCS1A01G081100 chr4A 96.635 2853 79 7 106 2950 445282176 445279333 0.000000e+00 4721
4 TraesCS1A01G081100 chr4A 93.978 2989 124 29 1 2950 110275316 110272345 0.000000e+00 4471
5 TraesCS1A01G081100 chr4A 90.159 2134 149 34 344 2440 167812423 167814532 0.000000e+00 2721
6 TraesCS1A01G081100 chr4A 90.170 529 34 12 2424 2950 167814549 167815061 0.000000e+00 673
7 TraesCS1A01G081100 chr4A 87.259 259 15 12 1 246 445282322 445282069 2.240000e-71 279
8 TraesCS1A01G081100 chr4A 80.976 205 26 11 16 218 137110716 137110523 1.830000e-32 150
9 TraesCS1A01G081100 chr5A 95.547 2717 102 9 243 2950 407306866 407309572 0.000000e+00 4329
10 TraesCS1A01G081100 chr5A 90.645 310 23 5 2644 2950 646982744 646983050 9.840000e-110 407
11 TraesCS1A01G081100 chr5A 85.829 374 48 5 1230 1602 123725064 123725433 2.760000e-105 392
12 TraesCS1A01G081100 chr5A 85.676 377 49 5 1230 1605 124665387 124665015 2.760000e-105 392
13 TraesCS1A01G081100 chr5A 93.464 153 6 3 3 152 407306397 407306548 1.060000e-54 224
14 TraesCS1A01G081100 chr7A 91.720 1244 86 12 1711 2950 53341642 53342872 0.000000e+00 1711
15 TraesCS1A01G081100 chr7A 93.642 346 16 4 1381 1725 53340693 53341033 2.030000e-141 512
16 TraesCS1A01G081100 chr6B 86.640 1265 120 26 1702 2938 267749458 267750701 0.000000e+00 1354
17 TraesCS1A01G081100 chr6B 86.184 456 44 14 1605 2050 599695748 599695302 2.660000e-130 475
18 TraesCS1A01G081100 chr2D 93.326 899 42 8 659 1539 5499817 5498919 0.000000e+00 1312
19 TraesCS1A01G081100 chr2D 90.631 523 39 8 2431 2950 5462913 5463428 0.000000e+00 686
20 TraesCS1A01G081100 chr2D 90.110 182 13 4 2 179 5499989 5499809 6.360000e-57 231
21 TraesCS1A01G081100 chr2A 92.769 484 30 5 1818 2297 461740731 461740249 0.000000e+00 695
22 TraesCS1A01G081100 chr2A 92.353 340 24 2 853 1192 331206793 331206456 1.590000e-132 483
23 TraesCS1A01G081100 chr2A 91.014 345 27 3 1391 1734 461741071 461740730 2.070000e-126 462
24 TraesCS1A01G081100 chr5B 85.928 668 71 14 948 1605 86077957 86077303 0.000000e+00 691
25 TraesCS1A01G081100 chr5B 89.474 133 9 4 2170 2299 220845246 220845116 2.350000e-36 163
26 TraesCS1A01G081100 chr4B 85.131 686 69 19 2279 2950 300019835 300020501 0.000000e+00 671
27 TraesCS1A01G081100 chr1B 92.353 340 24 2 852 1191 256539986 256539649 1.590000e-132 483
28 TraesCS1A01G081100 chr1B 92.607 257 13 5 2366 2621 163080647 163080396 6.010000e-97 364
29 TraesCS1A01G081100 chr3B 90.730 356 30 3 842 1196 419241143 419240790 3.440000e-129 472
30 TraesCS1A01G081100 chr7D 94.175 309 16 2 2644 2950 312979487 312979179 1.240000e-128 470
31 TraesCS1A01G081100 chr6A 87.597 387 33 9 1670 2045 546601385 546601003 4.520000e-118 435
32 TraesCS1A01G081100 chr6A 93.966 116 3 2 2059 2170 546600939 546600824 3.910000e-39 172
33 TraesCS1A01G081100 chr6A 87.970 133 12 4 2170 2300 493535608 493535738 1.420000e-33 154
34 TraesCS1A01G081100 chr3D 83.071 508 40 11 360 845 12953898 12953415 1.260000e-113 420
35 TraesCS1A01G081100 chr3A 90.939 309 21 6 2644 2950 626731696 626731999 2.740000e-110 409
36 TraesCS1A01G081100 chr6D 83.007 459 51 18 1628 2063 400653083 400652629 9.910000e-105 390
37 TraesCS1A01G081100 chr6D 88.235 119 14 0 2059 2177 400652592 400652474 3.060000e-30 143


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 TraesCS1A01G081100 chr1A 63973289 63976238 2949 True 5448.0 5448 100.0000 1 2950 1 chr1A.!!$R1 2949
1 TraesCS1A01G081100 chr1A 115268784 115269459 675 True 617.0 617 83.8430 948 1605 1 chr1A.!!$R2 657
2 TraesCS1A01G081100 chr4A 110272345 110275316 2971 True 4471.0 4471 93.9780 1 2950 1 chr4A.!!$R1 2949
3 TraesCS1A01G081100 chr4A 445279333 445282322 2989 True 2500.0 4721 91.9470 1 2950 2 chr4A.!!$R3 2949
4 TraesCS1A01G081100 chr4A 167812423 167815061 2638 False 1697.0 2721 90.1645 344 2950 2 chr4A.!!$F1 2606
5 TraesCS1A01G081100 chr5A 407306397 407309572 3175 False 2276.5 4329 94.5055 3 2950 2 chr5A.!!$F3 2947
6 TraesCS1A01G081100 chr7A 53340693 53342872 2179 False 1111.5 1711 92.6810 1381 2950 2 chr7A.!!$F1 1569
7 TraesCS1A01G081100 chr6B 267749458 267750701 1243 False 1354.0 1354 86.6400 1702 2938 1 chr6B.!!$F1 1236
8 TraesCS1A01G081100 chr2D 5498919 5499989 1070 True 771.5 1312 91.7180 2 1539 2 chr2D.!!$R1 1537
9 TraesCS1A01G081100 chr2D 5462913 5463428 515 False 686.0 686 90.6310 2431 2950 1 chr2D.!!$F1 519
10 TraesCS1A01G081100 chr2A 461740249 461741071 822 True 578.5 695 91.8915 1391 2297 2 chr2A.!!$R2 906
11 TraesCS1A01G081100 chr5B 86077303 86077957 654 True 691.0 691 85.9280 948 1605 1 chr5B.!!$R1 657
12 TraesCS1A01G081100 chr4B 300019835 300020501 666 False 671.0 671 85.1310 2279 2950 1 chr4B.!!$F1 671
13 TraesCS1A01G081100 chr6A 546600824 546601385 561 True 303.5 435 90.7815 1670 2170 2 chr6A.!!$R1 500
14 TraesCS1A01G081100 chr6D 400652474 400653083 609 True 266.5 390 85.6210 1628 2177 2 chr6D.!!$R1 549

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
908 1198 0.389948 CCAAAGCCTAAGCGACGACT 60.390 55.000 0.0 0.0 46.67 4.18 F
1196 1486 1.004044 CAGGTCATCAAGGGACAGCTT 59.996 52.381 0.0 0.0 37.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 2694 0.319813 CCAGCGTGTCACTGTCATCA 60.320 55.0 0.65 0.0 33.09 3.07 R
2614 3673 0.322636 ACCAACCACACCGTTGAACA 60.323 50.0 3.10 0.0 44.88 3.18 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
84 89 1.795951 GCCACAACCCCTCCCCTAAA 61.796 60.000 0.00 0.00 0.00 1.85
291 559 3.933722 CCCGAGCGAGCCCATCAT 61.934 66.667 0.00 0.00 0.00 2.45
308 576 1.065199 TCATCGATTGCTTCTTGCCCT 60.065 47.619 0.00 0.00 42.00 5.19
313 581 3.790416 TTGCTTCTTGCCCTGCGGT 62.790 57.895 0.00 0.00 42.00 5.68
314 582 2.046314 GCTTCTTGCCCTGCGGTA 60.046 61.111 0.00 0.00 35.15 4.02
438 706 0.975040 GGCTCCTCTCTCCTCTTGCA 60.975 60.000 0.00 0.00 0.00 4.08
633 920 3.062466 CGGCGACCTCTCCACTCA 61.062 66.667 0.00 0.00 0.00 3.41
657 944 3.353029 CGTGTTGCGGCATGGACA 61.353 61.111 2.28 2.12 36.85 4.02
680 967 2.045885 ACACCTCCTCCCTTCTAATGGA 59.954 50.000 0.00 0.00 0.00 3.41
738 1026 2.878406 GTGGCAGCTTCAGTTCAGTTTA 59.122 45.455 0.00 0.00 0.00 2.01
774 1063 2.452600 AAGAAAGGTTGTTGGGCTCA 57.547 45.000 0.00 0.00 0.00 4.26
814 1104 7.875554 TGCATAAAAATGGGGAAAGTTAAACTC 59.124 33.333 0.00 0.00 0.00 3.01
908 1198 0.389948 CCAAAGCCTAAGCGACGACT 60.390 55.000 0.00 0.00 46.67 4.18
1182 1472 3.931190 TAGCGGGTCGAGCAGGTCA 62.931 63.158 21.95 7.26 37.01 4.02
1196 1486 1.004044 CAGGTCATCAAGGGACAGCTT 59.996 52.381 0.00 0.00 37.00 3.74
1346 1645 4.193090 TGTGTTTTGTGATTGTCGTAGGT 58.807 39.130 0.00 0.00 0.00 3.08
1488 1815 1.445582 CACTAACGACCTGCCCGAC 60.446 63.158 0.00 0.00 0.00 4.79
1668 1999 8.191446 TGTACTGCTGAAATTGATCTCTAGTAC 58.809 37.037 0.00 0.00 38.02 2.73
1681 2012 6.708502 TGATCTCTAGTACTACATCTGACAGC 59.291 42.308 0.00 0.00 0.00 4.40
1740 2694 0.966920 ACCACTCGACCGAGAAACAT 59.033 50.000 24.03 0.29 44.53 2.71
1918 2874 1.610038 CATGGACAAGTTCAAGCAGCA 59.390 47.619 0.00 0.00 0.00 4.41
1958 2915 6.238786 GCTACGATCAGAAATAAGTGAGAGGA 60.239 42.308 0.00 0.00 0.00 3.71
2051 3019 1.486726 ACCACTAGGCTTGGTATCTGC 59.513 52.381 9.13 0.00 46.01 4.26
2201 3226 5.046448 TCAACAGGGCATTTGCTTTGATATT 60.046 36.000 2.12 0.00 41.70 1.28
2353 3378 6.405278 AAACCAGGGAAACTGTATCAAAAG 57.595 37.500 0.00 0.00 46.06 2.27
2378 3404 9.574516 AGAGTATTTGAAAAAGAGTTATGTGGT 57.425 29.630 0.00 0.00 0.00 4.16
2623 3682 8.582433 AAAGTAAAACCAAATATGTTCAACGG 57.418 30.769 0.00 0.00 0.00 4.44
2624 3683 7.279750 AGTAAAACCAAATATGTTCAACGGT 57.720 32.000 0.00 0.00 0.00 4.83
2625 3684 7.142680 AGTAAAACCAAATATGTTCAACGGTG 58.857 34.615 0.00 0.00 0.00 4.94
2626 3685 5.523438 AAACCAAATATGTTCAACGGTGT 57.477 34.783 0.00 0.00 0.00 4.16
2628 3687 3.254657 ACCAAATATGTTCAACGGTGTGG 59.745 43.478 0.00 0.00 0.00 4.17
2629 3688 3.254657 CCAAATATGTTCAACGGTGTGGT 59.745 43.478 0.00 0.00 0.00 4.16
2631 3690 4.497473 AATATGTTCAACGGTGTGGTTG 57.503 40.909 0.00 0.00 46.70 3.77
2633 3692 0.322636 TGTTCAACGGTGTGGTTGGT 60.323 50.000 0.00 0.00 45.66 3.67
2635 3694 1.202817 GTTCAACGGTGTGGTTGGTTT 59.797 47.619 0.00 0.00 45.66 3.27
2636 3695 1.546961 TCAACGGTGTGGTTGGTTTT 58.453 45.000 0.00 0.00 45.66 2.43
2637 3696 1.473278 TCAACGGTGTGGTTGGTTTTC 59.527 47.619 0.00 0.00 45.66 2.29
2638 3697 1.474879 CAACGGTGTGGTTGGTTTTCT 59.525 47.619 0.00 0.00 42.73 2.52
2639 3698 1.385528 ACGGTGTGGTTGGTTTTCTC 58.614 50.000 0.00 0.00 0.00 2.87
2640 3699 0.666374 CGGTGTGGTTGGTTTTCTCC 59.334 55.000 0.00 0.00 0.00 3.71
2641 3700 1.037493 GGTGTGGTTGGTTTTCTCCC 58.963 55.000 0.00 0.00 0.00 4.30
2642 3701 1.686741 GGTGTGGTTGGTTTTCTCCCA 60.687 52.381 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 89 1.460305 CAGATGGGATCGGGGGAGT 60.460 63.158 0.00 0.00 0.00 3.85
546 833 2.203337 ATGTGCACCAAGGCGTGT 60.203 55.556 15.69 0.00 36.08 4.49
633 920 3.726517 GCCGCAACACGCAGACAT 61.727 61.111 0.00 0.00 42.60 3.06
657 944 3.267031 CCATTAGAAGGGAGGAGGTGTTT 59.733 47.826 0.00 0.00 29.54 2.83
687 975 3.778954 ACTGAAGCTGCTCCTTTACTT 57.221 42.857 1.00 0.00 0.00 2.24
688 976 3.778954 AACTGAAGCTGCTCCTTTACT 57.221 42.857 1.00 0.00 0.00 2.24
690 978 6.952773 TTTTAAACTGAAGCTGCTCCTTTA 57.047 33.333 1.00 0.22 0.00 1.85
718 1006 2.057137 AAACTGAACTGAAGCTGCCA 57.943 45.000 0.00 0.00 0.00 4.92
766 1055 2.284754 TAGTGCACAAATGAGCCCAA 57.715 45.000 21.04 0.00 0.00 4.12
814 1104 4.828939 TGGAGGAGCAAGCAATAATAATGG 59.171 41.667 0.00 0.00 0.00 3.16
908 1198 0.107703 CATGCTTAGGCCTCGGACAA 60.108 55.000 9.68 0.00 37.74 3.18
1114 1404 1.826921 GCTGGCCTGCATGCATACT 60.827 57.895 27.96 0.00 0.00 2.12
1182 1472 3.370840 TGCATTAAGCTGTCCCTTGAT 57.629 42.857 0.00 0.00 45.94 2.57
1346 1645 0.596600 GACGTCGTCTTGGCTGTCAA 60.597 55.000 18.09 0.00 0.00 3.18
1668 1999 4.684242 TGTAAAACACGCTGTCAGATGTAG 59.316 41.667 3.32 0.00 0.00 2.74
1681 2012 5.675444 CGAAAAGAGAAGGTTGTAAAACACG 59.325 40.000 0.00 0.00 34.45 4.49
1740 2694 0.319813 CCAGCGTGTCACTGTCATCA 60.320 55.000 0.65 0.00 33.09 3.07
1768 2722 1.181786 CTCGTCCTTGCCTTCTCTCT 58.818 55.000 0.00 0.00 0.00 3.10
1918 2874 2.997584 TAGCTCCCCTGCTCGACCT 61.998 63.158 0.00 0.00 42.97 3.85
2051 3019 8.893219 ATAGTACCAAGATCACATTACACATG 57.107 34.615 0.00 0.00 0.00 3.21
2364 3389 5.804639 TCTGCACATACCACATAACTCTTT 58.195 37.500 0.00 0.00 0.00 2.52
2611 3670 2.817258 CCAACCACACCGTTGAACATAT 59.183 45.455 3.10 0.00 44.88 1.78
2612 3671 2.222886 CCAACCACACCGTTGAACATA 58.777 47.619 3.10 0.00 44.88 2.29
2614 3673 0.322636 ACCAACCACACCGTTGAACA 60.323 50.000 3.10 0.00 44.88 3.18
2618 3677 1.474879 AGAAAACCAACCACACCGTTG 59.525 47.619 0.00 0.00 42.31 4.10
2621 3680 0.666374 GGAGAAAACCAACCACACCG 59.334 55.000 0.00 0.00 0.00 4.94
2622 3681 1.037493 GGGAGAAAACCAACCACACC 58.963 55.000 0.00 0.00 0.00 4.16
2623 3682 1.770294 TGGGAGAAAACCAACCACAC 58.230 50.000 0.00 0.00 34.44 3.82
2624 3683 2.291930 ACTTGGGAGAAAACCAACCACA 60.292 45.455 0.00 0.00 42.75 4.17
2625 3684 2.384828 ACTTGGGAGAAAACCAACCAC 58.615 47.619 0.00 0.00 42.75 4.16
2626 3685 2.838637 ACTTGGGAGAAAACCAACCA 57.161 45.000 0.00 0.00 42.75 3.67
2628 3687 4.729227 TCAAACTTGGGAGAAAACCAAC 57.271 40.909 0.00 0.00 42.75 3.77
2629 3688 4.442753 GCATCAAACTTGGGAGAAAACCAA 60.443 41.667 0.00 0.00 45.25 3.67
2631 3690 3.321968 AGCATCAAACTTGGGAGAAAACC 59.678 43.478 0.00 0.00 0.00 3.27
2633 3692 4.214310 TGAGCATCAAACTTGGGAGAAAA 58.786 39.130 0.00 0.00 45.97 2.29
2635 3694 3.507162 TGAGCATCAAACTTGGGAGAA 57.493 42.857 0.00 0.00 45.97 2.87


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

AutoCloner maintained by Alex Coulton.