Multiple sequence alignment - TraesCS7B01G186700

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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 TraesCS7B01G186700 chr7B 100.000 4079 0 0 289 4367 312023047 312027125 0.000000e+00 7533.0
1 TraesCS7B01G186700 chr7B 98.378 2712 41 2 289 2997 311926372 311929083 0.000000e+00 4761.0
2 TraesCS7B01G186700 chr7B 92.647 1020 61 6 3354 4367 148947862 148948873 0.000000e+00 1456.0
3 TraesCS7B01G186700 chr7B 100.000 32 0 0 1 32 311926259 311926290 4.720000e-05 60.2
4 TraesCS7B01G186700 chr7B 100.000 32 0 0 1 32 312022759 312022790 4.720000e-05 60.2
5 TraesCS7B01G186700 chr2D 91.973 1657 111 8 2717 4367 253619319 253620959 0.000000e+00 2303.0
6 TraesCS7B01G186700 chr2D 86.059 581 55 16 290 866 94905561 94906119 6.250000e-168 601.0
7 TraesCS7B01G186700 chr1B 95.990 1147 43 2 1460 2605 421541287 421542431 0.000000e+00 1860.0
8 TraesCS7B01G186700 chr1B 92.841 433 22 3 3560 3987 144273047 144272619 1.730000e-173 619.0
9 TraesCS7B01G186700 chr1D 94.087 1150 62 4 1460 2605 311692045 311693192 0.000000e+00 1742.0
10 TraesCS7B01G186700 chr1D 90.909 88 8 0 3056 3143 3600820 3600733 7.670000e-23 119.0
11 TraesCS7B01G186700 chr1D 90.909 88 8 0 3056 3143 142201724 142201811 7.670000e-23 119.0
12 TraesCS7B01G186700 chr1A 93.380 1148 65 5 1460 2605 391848884 391850022 0.000000e+00 1688.0
13 TraesCS7B01G186700 chr1A 92.289 415 32 0 2676 3090 33807519 33807933 1.350000e-164 590.0
14 TraesCS7B01G186700 chr7A 91.928 1214 85 5 3160 4367 113110008 113111214 0.000000e+00 1687.0
15 TraesCS7B01G186700 chr7A 94.472 398 21 1 3970 4367 546927064 546926668 2.890000e-171 612.0
16 TraesCS7B01G186700 chr7A 92.308 416 30 2 2676 3090 718416160 718416574 1.350000e-164 590.0
17 TraesCS7B01G186700 chr7A 87.778 360 43 1 305 664 63327102 63326744 1.880000e-113 420.0
18 TraesCS7B01G186700 chr5A 91.433 1214 91 4 3160 4367 400399639 400398433 0.000000e+00 1653.0
19 TraesCS7B01G186700 chr2B 90.617 1215 100 5 3160 4367 52231794 52233001 0.000000e+00 1600.0
20 TraesCS7B01G186700 chr2B 92.530 415 31 0 2676 3090 19184953 19184539 2.910000e-166 595.0
21 TraesCS7B01G186700 chr2A 90.372 1236 83 13 3160 4367 59043867 59045094 0.000000e+00 1591.0
22 TraesCS7B01G186700 chr2A 91.667 60 4 1 667 725 349627240 349627299 1.010000e-11 82.4
23 TraesCS7B01G186700 chr3B 90.571 1209 100 5 3160 4362 799548046 799546846 0.000000e+00 1589.0
24 TraesCS7B01G186700 chr3B 91.250 480 28 9 990 1462 696327549 696327077 3.680000e-180 641.0
25 TraesCS7B01G186700 chr3B 96.094 128 5 0 865 992 696328137 696328010 4.430000e-50 209.0
26 TraesCS7B01G186700 chr5B 88.652 1031 105 6 2681 3710 651568286 651569305 0.000000e+00 1245.0
27 TraesCS7B01G186700 chr3A 92.662 477 28 6 990 1462 661472706 661472233 0.000000e+00 680.0
28 TraesCS7B01G186700 chr3A 86.923 520 43 14 3161 3658 114241266 114240750 1.060000e-155 560.0
29 TraesCS7B01G186700 chr3A 82.828 495 60 16 376 866 30941252 30941725 1.880000e-113 420.0
30 TraesCS7B01G186700 chr3A 96.094 128 5 0 865 992 661473291 661473164 4.430000e-50 209.0
31 TraesCS7B01G186700 chr3D 91.875 480 27 5 990 1462 526973944 526973470 0.000000e+00 660.0
32 TraesCS7B01G186700 chr3D 89.522 439 37 5 3166 3598 96127178 96126743 8.260000e-152 547.0
33 TraesCS7B01G186700 chr3D 91.899 358 29 0 307 664 402477253 402476896 6.520000e-138 501.0
34 TraesCS7B01G186700 chr3D 90.000 360 36 0 305 664 494416233 494416592 2.380000e-127 466.0
35 TraesCS7B01G186700 chr3D 91.406 128 5 1 865 992 526974516 526974395 2.090000e-38 171.0
36 TraesCS7B01G186700 chr3D 100.000 35 0 0 2626 2660 526973463 526973429 1.010000e-06 65.8
37 TraesCS7B01G186700 chr6B 93.970 398 23 1 3970 4367 506171158 506171554 6.250000e-168 601.0
38 TraesCS7B01G186700 chr6B 91.724 435 27 3 3558 3987 708553227 708553657 2.910000e-166 595.0
39 TraesCS7B01G186700 chr6B 92.048 415 33 0 2676 3090 506170746 506171160 6.290000e-163 584.0
40 TraesCS7B01G186700 chr6B 83.333 570 71 14 289 853 607915576 607916126 5.040000e-139 505.0
41 TraesCS7B01G186700 chr6B 80.203 394 48 21 470 858 558488448 558488816 7.200000e-68 268.0
42 TraesCS7B01G186700 chr4A 92.289 415 32 0 2676 3090 735512638 735513052 1.350000e-164 590.0
43 TraesCS7B01G186700 chr6D 87.398 492 59 3 2676 3167 456464398 456464886 2.950000e-156 562.0
44 TraesCS7B01G186700 chr5D 88.859 377 41 1 289 664 55337838 55337462 3.080000e-126 462.0
45 TraesCS7B01G186700 chr5D 90.164 183 15 3 652 831 55337513 55337331 7.300000e-58 235.0
46 TraesCS7B01G186700 chr6A 88.169 355 41 1 305 659 128941021 128940668 5.220000e-114 422.0
47 TraesCS7B01G186700 chr6A 80.508 236 20 13 655 866 198697 198464 1.630000e-34 158.0
48 TraesCS7B01G186700 chr6A 91.304 92 8 0 3052 3143 92816009 92815918 4.580000e-25 126.0
49 TraesCS7B01G186700 chr4D 91.919 297 24 0 368 664 200998602 200998306 2.430000e-112 416.0
50 TraesCS7B01G186700 chr4B 80.684 497 61 21 375 866 597431421 597430955 1.930000e-93 353.0
51 TraesCS7B01G186700 chr7D 91.257 183 13 1 652 831 476879762 476879580 3.370000e-61 246.0
52 TraesCS7B01G186700 chr7D 88.079 151 13 3 719 866 743066 743214 1.610000e-39 174.0


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 TraesCS7B01G186700 chr7B 312022759 312027125 4366 False 3796.600000 7533 100.0000 1 4367 2 chr7B.!!$F3 4366
1 TraesCS7B01G186700 chr7B 311926259 311929083 2824 False 2410.600000 4761 99.1890 1 2997 2 chr7B.!!$F2 2996
2 TraesCS7B01G186700 chr7B 148947862 148948873 1011 False 1456.000000 1456 92.6470 3354 4367 1 chr7B.!!$F1 1013
3 TraesCS7B01G186700 chr2D 253619319 253620959 1640 False 2303.000000 2303 91.9730 2717 4367 1 chr2D.!!$F2 1650
4 TraesCS7B01G186700 chr2D 94905561 94906119 558 False 601.000000 601 86.0590 290 866 1 chr2D.!!$F1 576
5 TraesCS7B01G186700 chr1B 421541287 421542431 1144 False 1860.000000 1860 95.9900 1460 2605 1 chr1B.!!$F1 1145
6 TraesCS7B01G186700 chr1D 311692045 311693192 1147 False 1742.000000 1742 94.0870 1460 2605 1 chr1D.!!$F2 1145
7 TraesCS7B01G186700 chr1A 391848884 391850022 1138 False 1688.000000 1688 93.3800 1460 2605 1 chr1A.!!$F2 1145
8 TraesCS7B01G186700 chr7A 113110008 113111214 1206 False 1687.000000 1687 91.9280 3160 4367 1 chr7A.!!$F1 1207
9 TraesCS7B01G186700 chr5A 400398433 400399639 1206 True 1653.000000 1653 91.4330 3160 4367 1 chr5A.!!$R1 1207
10 TraesCS7B01G186700 chr2B 52231794 52233001 1207 False 1600.000000 1600 90.6170 3160 4367 1 chr2B.!!$F1 1207
11 TraesCS7B01G186700 chr2A 59043867 59045094 1227 False 1591.000000 1591 90.3720 3160 4367 1 chr2A.!!$F1 1207
12 TraesCS7B01G186700 chr3B 799546846 799548046 1200 True 1589.000000 1589 90.5710 3160 4362 1 chr3B.!!$R1 1202
13 TraesCS7B01G186700 chr3B 696327077 696328137 1060 True 425.000000 641 93.6720 865 1462 2 chr3B.!!$R2 597
14 TraesCS7B01G186700 chr5B 651568286 651569305 1019 False 1245.000000 1245 88.6520 2681 3710 1 chr5B.!!$F1 1029
15 TraesCS7B01G186700 chr3A 114240750 114241266 516 True 560.000000 560 86.9230 3161 3658 1 chr3A.!!$R1 497
16 TraesCS7B01G186700 chr3A 661472233 661473291 1058 True 444.500000 680 94.3780 865 1462 2 chr3A.!!$R2 597
17 TraesCS7B01G186700 chr3D 526973429 526974516 1087 True 298.933333 660 94.4270 865 2660 3 chr3D.!!$R3 1795
18 TraesCS7B01G186700 chr6B 506170746 506171554 808 False 592.500000 601 93.0090 2676 4367 2 chr6B.!!$F4 1691
19 TraesCS7B01G186700 chr6B 607915576 607916126 550 False 505.000000 505 83.3330 289 853 1 chr6B.!!$F2 564
20 TraesCS7B01G186700 chr5D 55337331 55337838 507 True 348.500000 462 89.5115 289 831 2 chr5D.!!$R1 542

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
565 566 0.539669 TCTGCTCCACTTCGACTGGA 60.540 55.0 10.06 10.06 36.34 3.86 F
682 683 1.712977 CTCCGAACCCTCGTAGTCCG 61.713 65.0 0.00 0.00 43.87 4.79 F
2873 3400 0.550914 TAATCAAGGGGCGCCTGAAT 59.449 50.0 28.56 17.66 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2420 2947 4.682589 GCGTCTTTTACTTGGCCCTACTAT 60.683 45.833 0.0 0.0 0.00 2.12 R
3114 3641 8.207545 TCCAAAAATTAAACAGTGGCAACTAAT 58.792 29.630 0.0 0.0 33.79 1.73 R
3755 4303 0.457035 GGCAGGCATACAACACATGG 59.543 55.000 0.0 0.0 0.00 3.66 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
320 321 2.133201 TCCTCTCCCCTCTCCCCT 59.867 66.667 0.00 0.00 0.00 4.79
349 350 2.045242 CCCTCGTCCTCCTCGTCA 60.045 66.667 0.00 0.00 0.00 4.35
524 525 0.673437 CCTCCTCCGATGCTTCTCTC 59.327 60.000 0.00 0.00 0.00 3.20
565 566 0.539669 TCTGCTCCACTTCGACTGGA 60.540 55.000 10.06 10.06 36.34 3.86
682 683 1.712977 CTCCGAACCCTCGTAGTCCG 61.713 65.000 0.00 0.00 43.87 4.79
1067 1570 2.126463 CTTCGCGCTCAAGGACGA 60.126 61.111 5.56 0.00 0.00 4.20
1356 1871 9.658799 CAGTAAATGATTCTCTGAAAGTTCCTA 57.341 33.333 4.35 0.00 33.76 2.94
1480 1996 7.495934 GTGTATTATGTACTGATTTCTGCACCT 59.504 37.037 0.00 0.00 0.00 4.00
1703 2220 6.079424 AGCAATACGTTACCAATTTTGTGT 57.921 33.333 0.00 0.00 0.00 3.72
2420 2947 7.394016 CACCCACTATAATTGCATCATACCTA 58.606 38.462 0.00 0.00 0.00 3.08
2873 3400 0.550914 TAATCAAGGGGCGCCTGAAT 59.449 50.000 28.56 17.66 0.00 2.57
3001 3528 2.308570 AGCCATGTCACCATAAGGACAA 59.691 45.455 0.00 0.00 46.10 3.18
3029 3556 5.222079 TCATGTACTTTGAAGGTACTGCA 57.778 39.130 16.81 0.00 46.31 4.41
3071 3598 5.944007 TCAGTCATTCTGCACTAGTGTACTA 59.056 40.000 23.44 8.50 43.32 1.82
3114 3641 7.801716 AGTGAGTTTGATGTTTGTTAAGCTA 57.198 32.000 0.00 0.00 0.00 3.32
3254 3784 6.044404 TCTCCAAGGGTGAGTTTCTTAAATCT 59.956 38.462 0.00 0.00 29.99 2.40
3264 3794 7.442666 GTGAGTTTCTTAAATCTGACTTGGTCT 59.557 37.037 0.00 0.00 33.15 3.85
3269 3799 7.311092 TCTTAAATCTGACTTGGTCTTGGTA 57.689 36.000 0.00 0.00 33.15 3.25
3349 3879 1.067142 GCGAGGTACATTGTCAGGTCA 60.067 52.381 0.00 0.00 0.00 4.02
3400 3930 0.032267 GCTACGTGACTATCAGGGGC 59.968 60.000 0.00 3.98 36.65 5.80
3426 3956 1.227586 CGATGCAGCTGCTGGAGAT 60.228 57.895 36.61 22.84 42.66 2.75
3445 3975 0.110486 TTGGCCTGAAGGTGAAGGAC 59.890 55.000 3.32 0.00 42.53 3.85
3463 3993 2.305928 GACTATGAGCTGCTCAGGAGA 58.694 52.381 33.66 21.20 44.08 3.71
3479 4009 1.270358 GGAGAAACTTCAGCGACACCT 60.270 52.381 0.00 0.00 0.00 4.00
3659 4207 5.678107 GCAGAAAGATATTTGGCTGAAGTGG 60.678 44.000 5.87 0.00 0.00 4.00
3672 4220 4.154918 GGCTGAAGTGGTCTTTCATTGTAG 59.845 45.833 0.00 0.00 33.64 2.74
3673 4221 4.757149 GCTGAAGTGGTCTTTCATTGTAGT 59.243 41.667 0.00 0.00 33.64 2.73
3743 4291 8.141268 CCTTCAGGTTTAGCTTGTTATGAAAAA 58.859 33.333 0.00 0.00 0.00 1.94
3814 4362 2.114616 TCACATTTTGTTTGGCAGGGT 58.885 42.857 0.00 0.00 0.00 4.34
3885 4435 3.243501 TGCATCTTGCTGAAACTTTGACC 60.244 43.478 0.75 0.00 45.31 4.02
3886 4436 3.858503 GCATCTTGCTGAAACTTTGACCC 60.859 47.826 0.00 0.00 40.96 4.46
3915 4465 8.816894 TCTAGTTGGATCTTCAGTTTCTTGTAT 58.183 33.333 0.00 0.00 0.00 2.29
3916 4466 7.913674 AGTTGGATCTTCAGTTTCTTGTATC 57.086 36.000 0.00 0.00 0.00 2.24
3917 4467 7.684529 AGTTGGATCTTCAGTTTCTTGTATCT 58.315 34.615 0.00 0.00 0.00 1.98
3981 4538 6.073711 CGAACTCAAGAGTCCTTTCTAAAACC 60.074 42.308 2.78 0.00 41.58 3.27
4013 4570 1.481363 GTACCTCCTGCTACTGGAACC 59.519 57.143 0.00 0.00 31.33 3.62
4136 4693 1.066143 GCTGCTAGTAAACCAGGCTGA 60.066 52.381 17.94 0.00 0.00 4.26
4140 4697 3.003480 GCTAGTAAACCAGGCTGAACTG 58.997 50.000 17.94 0.84 38.21 3.16
4300 4885 1.536418 ACCTGTCCCTAGCTGTGCA 60.536 57.895 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
320 321 1.383109 ACGAGGGGGATCTGCATCA 60.383 57.895 0.00 0.00 0.00 3.07
565 566 1.806461 TTCTCTTCTGTCTGCGCCGT 61.806 55.000 4.18 0.00 0.00 5.68
1356 1871 7.824779 GTCTTAAATGTTCCTCAAGAGTACCAT 59.175 37.037 0.00 0.00 0.00 3.55
1497 2013 9.931210 ATTACTTAGCACTAATTATCAAAACGC 57.069 29.630 0.00 0.00 0.00 4.84
2420 2947 4.682589 GCGTCTTTTACTTGGCCCTACTAT 60.683 45.833 0.00 0.00 0.00 2.12
3114 3641 8.207545 TCCAAAAATTAAACAGTGGCAACTAAT 58.792 29.630 0.00 0.00 33.79 1.73
3138 3665 5.841810 TCATTTGTTCATCAAGTGGTTTCC 58.158 37.500 0.00 0.00 41.84 3.13
3225 3755 3.202151 AGAAACTCACCCTTGGAGAACAA 59.798 43.478 0.00 0.00 36.26 2.83
3264 3794 9.693739 ATTAACCATAATTGACATGTCTACCAA 57.306 29.630 25.55 13.16 0.00 3.67
3269 3799 9.219603 CCGATATTAACCATAATTGACATGTCT 57.780 33.333 25.55 9.24 33.75 3.41
3282 3812 6.697641 ATTAGGACCACCGATATTAACCAT 57.302 37.500 0.00 0.00 41.83 3.55
3293 3823 2.026641 TCGTTCCTATTAGGACCACCG 58.973 52.381 12.12 11.63 45.78 4.94
3349 3879 3.572682 TCTCATTACGCCTGATACCGAAT 59.427 43.478 0.00 0.00 0.00 3.34
3400 3930 2.202851 AGCTGCATCGCCTTCTCG 60.203 61.111 1.02 0.00 0.00 4.04
3426 3956 0.110486 GTCCTTCACCTTCAGGCCAA 59.890 55.000 5.01 0.00 39.32 4.52
3445 3975 3.132646 AGTTTCTCCTGAGCAGCTCATAG 59.867 47.826 25.59 23.07 39.92 2.23
3463 3993 2.146342 CATCAGGTGTCGCTGAAGTTT 58.854 47.619 0.00 0.00 32.98 2.66
3479 4009 2.760092 GGATACCAAAGCCAAAGCATCA 59.240 45.455 0.00 0.00 43.56 3.07
3659 4207 9.431887 TCAGTATTTGGTACTACAATGAAAGAC 57.568 33.333 0.00 0.00 41.73 3.01
3743 4291 7.706179 GCATACAACACATGGCAAGTAAATAAT 59.294 33.333 0.00 0.00 0.00 1.28
3755 4303 0.457035 GGCAGGCATACAACACATGG 59.543 55.000 0.00 0.00 0.00 3.66
3867 4417 3.011566 TGGGTCAAAGTTTCAGCAAGA 57.988 42.857 0.00 0.00 0.00 3.02
3886 4436 8.449397 CAAGAAACTGAAGATCCAACTAGATTG 58.551 37.037 0.00 0.00 38.12 2.67
3915 4465 8.969260 AGTGATGCATATTTGTTCATAGAAGA 57.031 30.769 0.00 0.00 0.00 2.87
3953 4510 3.070302 AGAAAGGACTCTTGAGTTCGCTT 59.930 43.478 4.67 2.54 32.75 4.68
3957 4514 6.073711 CGGTTTTAGAAAGGACTCTTGAGTTC 60.074 42.308 4.67 2.77 32.75 3.01
3981 4538 1.549170 AGGAGGTACAACTTGGCTACG 59.451 52.381 0.00 0.00 0.00 3.51
4040 4597 4.280677 CAGACAGAGAGGAAAGAGTTGAGT 59.719 45.833 0.00 0.00 0.00 3.41
4084 4641 1.151450 CAGGTTCTGGGCTTGGTGT 59.849 57.895 0.00 0.00 0.00 4.16
4136 4693 3.368323 CCAACTTGCACTTGGAAACAGTT 60.368 43.478 14.84 3.01 44.54 3.16
4285 4870 0.764890 AAAGTGCACAGCTAGGGACA 59.235 50.000 21.04 0.00 0.00 4.02
4300 4885 2.922740 TTAGCAGGAACGACCAAAGT 57.077 45.000 0.00 0.00 42.04 2.66


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

AutoCloner maintained by Alex Coulton.