Multiple sequence alignment - TraesCS6B01G242000

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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 TraesCS6B01G242000 chr6B 100.000 4381 0 0 1 4381 425603074 425598694 0.000000e+00 8091
1 TraesCS6B01G242000 chr6B 93.478 414 24 1 3065 3478 275796730 275797140 2.900000e-171 612
2 TraesCS6B01G242000 chr7D 92.901 3888 174 47 181 4001 16792717 16796569 0.000000e+00 5557
3 TraesCS6B01G242000 chr7D 95.229 524 17 3 3855 4370 21071311 21071834 0.000000e+00 822
4 TraesCS6B01G242000 chr5B 94.357 3491 175 17 1 3478 35445175 35441694 0.000000e+00 5336
5 TraesCS6B01G242000 chr5B 94.048 3444 157 31 1 3435 641175931 641179335 0.000000e+00 5180
6 TraesCS6B01G242000 chr5B 96.442 534 17 2 3849 4381 35441247 35440715 0.000000e+00 880
7 TraesCS6B01G242000 chr5B 95.430 547 16 5 2932 3478 215733711 215734248 0.000000e+00 863
8 TraesCS6B01G242000 chr5B 92.063 378 26 2 3477 3851 35441654 35441278 3.000000e-146 529
9 TraesCS6B01G242000 chr2B 93.694 3489 178 20 1 3478 757697623 757694166 0.000000e+00 5186
10 TraesCS6B01G242000 chr2B 94.371 3251 143 14 154 3384 47380921 47384151 0.000000e+00 4953
11 TraesCS6B01G242000 chr2B 92.174 3463 212 25 1 3435 154578287 154581718 0.000000e+00 4839
12 TraesCS6B01G242000 chr2B 92.880 2823 153 25 646 3439 717658517 717655714 0.000000e+00 4056
13 TraesCS6B01G242000 chr2B 96.219 767 28 1 3477 4242 757694126 757693360 0.000000e+00 1254
14 TraesCS6B01G242000 chr2B 89.676 339 27 6 1 336 45601997 45601664 4.050000e-115 425
15 TraesCS6B01G242000 chr3B 93.939 3448 167 15 1 3435 16192064 16195482 0.000000e+00 5171
16 TraesCS6B01G242000 chr3B 91.432 922 58 12 3477 4381 40988375 40989292 0.000000e+00 1245
17 TraesCS6B01G242000 chr1A 92.933 3495 195 22 1 3478 480963862 480960403 0.000000e+00 5038
18 TraesCS6B01G242000 chr7A 92.675 3495 205 22 1 3478 130564256 130560796 0.000000e+00 4988
19 TraesCS6B01G242000 chr7A 93.602 2110 107 11 1375 3478 7458962 7461049 0.000000e+00 3123
20 TraesCS6B01G242000 chr7A 95.472 508 16 2 3881 4381 130560246 130559739 0.000000e+00 804
21 TraesCS6B01G242000 chr7A 85.714 497 45 16 3482 3958 509518410 509517920 6.540000e-138 501
22 TraesCS6B01G242000 chr7B 91.963 3260 175 40 646 3845 516815650 516818882 0.000000e+00 4488
23 TraesCS6B01G242000 chr7B 94.029 2847 137 14 646 3478 720228736 720231563 0.000000e+00 4285
24 TraesCS6B01G242000 chr7B 96.648 537 16 2 3846 4381 475097165 475096630 0.000000e+00 891
25 TraesCS6B01G242000 chr7B 94.382 534 23 2 3855 4381 34255315 34255848 0.000000e+00 813
26 TraesCS6B01G242000 chr7B 92.761 373 24 1 3477 3846 475097569 475097197 1.790000e-148 536
27 TraesCS6B01G242000 chr2A 90.971 2791 175 33 999 3748 677893171 677895925 0.000000e+00 3687
28 TraesCS6B01G242000 chr2A 93.825 2251 108 7 1239 3478 372748835 372746605 0.000000e+00 3358
29 TraesCS6B01G242000 chr2A 94.259 540 24 2 3849 4381 372746158 372745619 0.000000e+00 819
30 TraesCS6B01G242000 chr1B 94.757 534 27 1 3849 4381 629311195 629310662 0.000000e+00 830
31 TraesCS6B01G242000 chr3A 94.828 522 20 2 3855 4369 145555699 145556220 0.000000e+00 808
32 TraesCS6B01G242000 chr3A 85.915 497 44 16 3482 3958 44770938 44771428 1.410000e-139 507
33 TraesCS6B01G242000 chr4A 92.021 376 25 2 3477 3847 514358881 514359256 1.400000e-144 523
34 TraesCS6B01G242000 chr6A 88.679 424 34 7 3482 3897 74988375 74988792 5.060000e-139 505
35 TraesCS6B01G242000 chr6A 85.714 497 43 17 3482 3958 387219544 387219056 2.350000e-137 499


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 TraesCS6B01G242000 chr6B 425598694 425603074 4380 True 8091.000000 8091 100.000000 1 4381 1 chr6B.!!$R1 4380
1 TraesCS6B01G242000 chr7D 16792717 16796569 3852 False 5557.000000 5557 92.901000 181 4001 1 chr7D.!!$F1 3820
2 TraesCS6B01G242000 chr7D 21071311 21071834 523 False 822.000000 822 95.229000 3855 4370 1 chr7D.!!$F2 515
3 TraesCS6B01G242000 chr5B 641175931 641179335 3404 False 5180.000000 5180 94.048000 1 3435 1 chr5B.!!$F2 3434
4 TraesCS6B01G242000 chr5B 35440715 35445175 4460 True 2248.333333 5336 94.287333 1 4381 3 chr5B.!!$R1 4380
5 TraesCS6B01G242000 chr5B 215733711 215734248 537 False 863.000000 863 95.430000 2932 3478 1 chr5B.!!$F1 546
6 TraesCS6B01G242000 chr2B 47380921 47384151 3230 False 4953.000000 4953 94.371000 154 3384 1 chr2B.!!$F1 3230
7 TraesCS6B01G242000 chr2B 154578287 154581718 3431 False 4839.000000 4839 92.174000 1 3435 1 chr2B.!!$F2 3434
8 TraesCS6B01G242000 chr2B 717655714 717658517 2803 True 4056.000000 4056 92.880000 646 3439 1 chr2B.!!$R2 2793
9 TraesCS6B01G242000 chr2B 757693360 757697623 4263 True 3220.000000 5186 94.956500 1 4242 2 chr2B.!!$R3 4241
10 TraesCS6B01G242000 chr3B 16192064 16195482 3418 False 5171.000000 5171 93.939000 1 3435 1 chr3B.!!$F1 3434
11 TraesCS6B01G242000 chr3B 40988375 40989292 917 False 1245.000000 1245 91.432000 3477 4381 1 chr3B.!!$F2 904
12 TraesCS6B01G242000 chr1A 480960403 480963862 3459 True 5038.000000 5038 92.933000 1 3478 1 chr1A.!!$R1 3477
13 TraesCS6B01G242000 chr7A 7458962 7461049 2087 False 3123.000000 3123 93.602000 1375 3478 1 chr7A.!!$F1 2103
14 TraesCS6B01G242000 chr7A 130559739 130564256 4517 True 2896.000000 4988 94.073500 1 4381 2 chr7A.!!$R2 4380
15 TraesCS6B01G242000 chr7B 516815650 516818882 3232 False 4488.000000 4488 91.963000 646 3845 1 chr7B.!!$F2 3199
16 TraesCS6B01G242000 chr7B 720228736 720231563 2827 False 4285.000000 4285 94.029000 646 3478 1 chr7B.!!$F3 2832
17 TraesCS6B01G242000 chr7B 34255315 34255848 533 False 813.000000 813 94.382000 3855 4381 1 chr7B.!!$F1 526
18 TraesCS6B01G242000 chr7B 475096630 475097569 939 True 713.500000 891 94.704500 3477 4381 2 chr7B.!!$R1 904
19 TraesCS6B01G242000 chr2A 677893171 677895925 2754 False 3687.000000 3687 90.971000 999 3748 1 chr2A.!!$F1 2749
20 TraesCS6B01G242000 chr2A 372745619 372748835 3216 True 2088.500000 3358 94.042000 1239 4381 2 chr2A.!!$R1 3142
21 TraesCS6B01G242000 chr1B 629310662 629311195 533 True 830.000000 830 94.757000 3849 4381 1 chr1B.!!$R1 532
22 TraesCS6B01G242000 chr3A 145555699 145556220 521 False 808.000000 808 94.828000 3855 4369 1 chr3A.!!$F2 514

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
247 262 1.027357 CCCCTCTCATTTTGGATGCG 58.973 55.0 0.0 0.0 0.00 4.73 F
1688 1729 0.537143 ACTTGGCATGTCGCAGGAAA 60.537 50.0 0.0 0.0 45.17 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1917 0.458543 ATGCGAGCTTCCTGTGTACG 60.459 55.0 0.00 0.0 0.0 3.67 R
3671 3864 0.324923 TGGCGTCTGGTACCCTGTAT 60.325 55.0 10.07 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
247 262 1.027357 CCCCTCTCATTTTGGATGCG 58.973 55.000 0.00 0.00 0.00 4.73
370 385 7.175104 AGATGTTTGTAGTTGTCCACCAATAT 58.825 34.615 0.00 0.00 35.02 1.28
385 401 8.952278 GTCCACCAATATACATAGTTTGTGAAA 58.048 33.333 0.00 0.00 39.48 2.69
386 402 9.521841 TCCACCAATATACATAGTTTGTGAAAA 57.478 29.630 0.00 0.00 39.48 2.29
474 492 9.187996 TGGCATAATATTTGTTTGAATCTGAGA 57.812 29.630 0.00 0.00 0.00 3.27
673 701 9.665719 ATTTATTTGATGGTGAAATTTGGTACC 57.334 29.630 4.43 4.43 0.00 3.34
676 704 4.085733 TGATGGTGAAATTTGGTACCCTG 58.914 43.478 10.07 0.00 32.20 4.45
886 922 2.891580 GAGTGGGATAAGGAGCATCGTA 59.108 50.000 0.00 0.00 34.37 3.43
894 931 1.589196 GGAGCATCGTACTCGTGCC 60.589 63.158 9.47 3.49 41.31 5.01
936 974 6.705863 AGAAGCAAGACTTGTCAAATTTCT 57.294 33.333 16.39 12.05 39.29 2.52
1072 1113 4.281182 ACGAGCCTTATATTCGGAGATTGT 59.719 41.667 0.00 0.00 38.58 2.71
1296 1337 2.070783 GTTAATTGGCGAGAACGGACA 58.929 47.619 0.00 0.00 40.15 4.02
1636 1677 2.629137 TCTTGCATTTGTCATGTGCCTT 59.371 40.909 3.10 0.00 38.06 4.35
1688 1729 0.537143 ACTTGGCATGTCGCAGGAAA 60.537 50.000 0.00 0.00 45.17 3.13
2052 2103 3.010027 TGGTTGCCTTATGTGGAAGATCA 59.990 43.478 0.00 0.00 0.00 2.92
2613 2664 0.713883 CACGTTGACTATGCACCGAC 59.286 55.000 0.00 0.00 0.00 4.79
3093 3164 2.158623 ACACATCAAGAGGAGCCAACAA 60.159 45.455 0.00 0.00 0.00 2.83
3096 3167 3.760684 ACATCAAGAGGAGCCAACAAATC 59.239 43.478 0.00 0.00 0.00 2.17
3272 3367 4.331968 GGAACACACAATTCCATAGTCCA 58.668 43.478 0.00 0.00 44.42 4.02
3330 3426 6.238184 GCAAAAATATAAGGCCAACATTGAGC 60.238 38.462 5.01 1.10 0.00 4.26
3378 3483 0.968393 GGAGGAGTCCAGCGAAGAGT 60.968 60.000 12.86 0.00 43.31 3.24
3400 3505 0.875059 GAGCCTACACTTGCAACCAC 59.125 55.000 0.00 0.00 0.00 4.16
3470 3576 2.080693 CTAGGTGGCGTTTGTATGCAA 58.919 47.619 0.00 0.00 38.06 4.08
3474 3580 2.094752 GGTGGCGTTTGTATGCAAGAAT 60.095 45.455 0.00 0.00 38.06 2.40
3615 3806 6.379988 TGTGCTATCTTCTGTGTATGAACCTA 59.620 38.462 0.00 0.00 0.00 3.08
3671 3864 9.243637 GTGTCAAACAGCAAGTTGAAAATAATA 57.756 29.630 7.16 0.00 41.19 0.98
3748 3992 2.632544 CCACGGTCACTGGCGTCTA 61.633 63.158 0.00 0.00 0.00 2.59
3780 4024 2.620585 GGAAGCAAAAGCAGAGTCTTGT 59.379 45.455 0.00 0.00 0.00 3.16
3782 4026 4.275936 GGAAGCAAAAGCAGAGTCTTGTAA 59.724 41.667 0.00 0.00 0.00 2.41
3825 4069 2.203788 AGGGTCCTTGGCGTCTGA 60.204 61.111 0.00 0.00 0.00 3.27
4082 4390 6.604396 TCACATATAACTCGGTTTCCTGTAGA 59.396 38.462 0.00 0.00 0.00 2.59
4119 4427 6.126507 ACAACCCTTTTCCATTTCCATTCTTT 60.127 34.615 0.00 0.00 0.00 2.52
4192 4501 1.606531 GGGCCATCTGACTGCTTCT 59.393 57.895 4.39 0.00 0.00 2.85
4295 4605 4.095782 GTCCACTTCACTAACTTGCACAAA 59.904 41.667 0.00 0.00 0.00 2.83
4374 4690 7.554118 CCCATCTACAACACACAAATCTCTTAT 59.446 37.037 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
327 342 8.475639 CAAACATCTACCAACTACACTACCTAT 58.524 37.037 0.00 0.00 0.00 2.57
474 492 5.535753 ATTTGCTTGCCAAAGTAGTCTTT 57.464 34.783 0.00 0.00 45.87 2.52
673 701 5.493809 TCATATGCACACATATCATCCAGG 58.506 41.667 0.00 0.00 44.55 4.45
676 704 7.605309 TCTTCTTCATATGCACACATATCATCC 59.395 37.037 0.00 0.00 44.55 3.51
814 849 3.072915 TCATCATCCGCCATCCTACAAAT 59.927 43.478 0.00 0.00 0.00 2.32
894 931 7.541162 TGCTTCTTACATTTCCATTCTCAATG 58.459 34.615 0.00 0.00 38.63 2.82
963 1001 9.979578 AGTTGCAAATAAAGTGATGTTTTGATA 57.020 25.926 0.00 0.00 30.69 2.15
1072 1113 2.766313 CAACACGAATGGGAGAAGACA 58.234 47.619 0.00 0.00 0.00 3.41
1116 1157 4.903010 AACGCCGCGTGGTTCACT 62.903 61.111 20.97 0.00 39.99 3.41
1296 1337 4.563374 GGCTGAACACCAATTAAAATGCCT 60.563 41.667 0.00 0.00 33.45 4.75
1636 1677 9.571810 GCAATCAAACAAACATGTTAGATATGA 57.428 29.630 12.39 12.84 0.00 2.15
1708 1749 2.990740 TAGGCTCCAAACAAACCCAT 57.009 45.000 0.00 0.00 0.00 4.00
1876 1917 0.458543 ATGCGAGCTTCCTGTGTACG 60.459 55.000 0.00 0.00 0.00 3.67
2052 2103 6.238953 GCACATCTCATTAAGATCAAAGCCAT 60.239 38.462 0.00 0.00 43.13 4.40
2613 2664 2.282555 CAGACTACCATTTCGTCATGCG 59.717 50.000 3.55 3.55 43.01 4.73
3223 3318 4.104102 TCTTCTTTCTACCTTTCTTGCCCA 59.896 41.667 0.00 0.00 0.00 5.36
3330 3426 1.048724 TTGTATGCCTCCTCCTCCGG 61.049 60.000 0.00 0.00 0.00 5.14
3378 3483 1.278127 GGTTGCAAGTGTAGGCTCCTA 59.722 52.381 0.00 0.00 0.00 2.94
3400 3505 4.283212 ACTTCTTCCTTCCTCTCTTCACAG 59.717 45.833 0.00 0.00 0.00 3.66
3470 3576 7.394359 ACCAAGTGCATACATAAGACAAATTCT 59.606 33.333 0.00 0.00 35.32 2.40
3474 3580 5.767665 ACACCAAGTGCATACATAAGACAAA 59.232 36.000 0.00 0.00 36.98 2.83
3671 3864 0.324923 TGGCGTCTGGTACCCTGTAT 60.325 55.000 10.07 0.00 0.00 2.29
3748 3992 0.468226 TTTGCTTCCAGTCGACCACT 59.532 50.000 13.01 0.00 34.67 4.00
3780 4024 1.616159 GGTGCCCTGTTTCTGCTTTA 58.384 50.000 0.00 0.00 0.00 1.85
3782 4026 1.531602 GGGTGCCCTGTTTCTGCTT 60.532 57.895 0.00 0.00 0.00 3.91
3815 4059 2.847234 ACCAGGGTCAGACGCCAA 60.847 61.111 13.84 0.00 0.00 4.52
3860 4136 5.606348 ATGGGTGTTTGCTAGAACAAAAA 57.394 34.783 0.00 0.00 40.99 1.94
4082 4390 4.486125 AAAGGGTTGTTGACTTGCATTT 57.514 36.364 0.00 0.00 0.00 2.32
4119 4427 3.827876 TGGCAAGATTCAAGAAATGCTGA 59.172 39.130 14.12 4.13 32.60 4.26
4192 4501 4.449743 GGATTTTGTGTACTACGTCAGCAA 59.550 41.667 0.00 0.00 0.00 3.91
4295 4605 1.425066 TCCAAGGCTTGTCTCCATGTT 59.575 47.619 24.57 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.