Multiple sequence alignment - TraesCS4B01G188500

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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 TraesCS4B01G188500 chr4B 100.000 3645 0 0 1 3645 409741022 409744666 0.000000e+00 6732.0
1 TraesCS4B01G188500 chr4D 97.356 3668 58 9 3 3645 331639906 331636253 0.000000e+00 6200.0
2 TraesCS4B01G188500 chr4D 84.400 859 98 21 1276 2123 330962096 330962929 0.000000e+00 811.0
3 TraesCS4B01G188500 chr7D 86.702 1316 116 26 1001 2289 477406729 477405446 0.000000e+00 1406.0
4 TraesCS4B01G188500 chr7D 88.396 293 28 3 2339 2626 477405447 477405156 7.490000e-92 348.0
5 TraesCS4B01G188500 chr7D 92.683 41 3 0 2369 2409 477405444 477405404 3.930000e-05 60.2
6 TraesCS4B01G188500 chr7B 88.055 946 87 14 1050 1982 501781335 501780403 0.000000e+00 1098.0
7 TraesCS4B01G188500 chr7B 84.843 508 41 11 1978 2473 501778787 501778304 2.550000e-131 479.0
8 TraesCS4B01G188500 chr7B 76.986 730 128 32 45 755 198616784 198617492 7.390000e-102 381.0
9 TraesCS4B01G188500 chr7B 73.977 611 149 8 1396 2001 424536782 424537387 4.700000e-59 239.0
10 TraesCS4B01G188500 chr7A 87.674 576 59 6 1253 1822 518665608 518666177 0.000000e+00 660.0
11 TraesCS4B01G188500 chr7A 86.842 380 39 6 1819 2195 518666379 518666750 7.280000e-112 414.0
12 TraesCS4B01G188500 chr7A 95.276 127 6 0 2381 2507 518666821 518666947 6.170000e-48 202.0
13 TraesCS4B01G188500 chr7A 87.500 64 8 0 698 761 404948018 404947955 1.400000e-09 75.0
14 TraesCS4B01G188500 chr5D 79.391 558 79 20 224 761 43330654 43330113 9.620000e-96 361.0
15 TraesCS4B01G188500 chr6D 83.038 395 55 8 225 618 227511777 227511394 7.490000e-92 348.0
16 TraesCS4B01G188500 chr6D 81.013 79 13 2 679 756 46440022 46440099 1.090000e-05 62.1
17 TraesCS4B01G188500 chr5B 82.967 364 49 7 229 590 488905248 488904896 2.110000e-82 316.0
18 TraesCS4B01G188500 chr3D 83.562 292 28 12 3321 3593 246608042 246608332 4.670000e-64 255.0
19 TraesCS4B01G188500 chr3D 79.592 245 23 13 3064 3281 246607631 246607875 2.270000e-32 150.0
20 TraesCS4B01G188500 chr3D 80.899 89 11 6 673 756 501075425 501075512 8.450000e-07 65.8
21 TraesCS4B01G188500 chr3D 81.250 80 13 2 678 756 477631913 477631835 3.040000e-06 63.9
22 TraesCS4B01G188500 chr3B 81.212 330 36 14 3289 3593 352003750 352004078 3.640000e-60 243.0
23 TraesCS4B01G188500 chr3B 78.367 245 26 12 3064 3281 352003378 352003622 2.280000e-27 134.0
24 TraesCS4B01G188500 chr3A 83.206 262 33 7 224 482 30559273 30559526 2.830000e-56 230.0
25 TraesCS4B01G188500 chr3A 81.849 292 27 14 3321 3593 318504875 318505159 4.740000e-54 222.0
26 TraesCS4B01G188500 chr3A 79.184 245 24 12 3064 3281 318504467 318504711 1.050000e-30 145.0
27 TraesCS4B01G188500 chr3A 86.260 131 12 4 2713 2837 2162935 2163065 1.770000e-28 137.0
28 TraesCS4B01G188500 chr3A 86.260 131 11 5 2713 2837 2629484 2629613 6.350000e-28 135.0
29 TraesCS4B01G188500 chr3A 86.260 131 11 5 2713 2837 4672278 4672407 6.350000e-28 135.0
30 TraesCS4B01G188500 chr3A 82.292 96 10 7 1442 1534 480099065 480098974 3.900000e-10 76.8
31 TraesCS4B01G188500 chr2A 77.751 409 53 20 224 618 413482663 413483047 2.200000e-52 217.0
32 TraesCS4B01G188500 chr2A 71.989 714 165 26 1312 2006 90428861 90428164 1.040000e-40 178.0
33 TraesCS4B01G188500 chr2D 72.727 715 158 28 1312 2006 90523098 90522401 4.770000e-49 206.0
34 TraesCS4B01G188500 chr2D 90.351 114 9 2 2725 2837 190429437 190429325 8.150000e-32 148.0
35 TraesCS4B01G188500 chr2D 90.351 114 9 2 2725 2837 516853417 516853305 8.150000e-32 148.0
36 TraesCS4B01G188500 chr2D 89.474 114 10 2 2725 2837 11518087 11518199 3.790000e-30 143.0
37 TraesCS4B01G188500 chr2D 82.500 80 12 2 678 756 74783966 74783888 6.530000e-08 69.4
38 TraesCS4B01G188500 chr5A 89.474 114 10 2 2725 2837 180354294 180354182 3.790000e-30 143.0
39 TraesCS4B01G188500 chr5A 86.131 137 12 5 2711 2840 375556142 375556278 1.360000e-29 141.0
40 TraesCS4B01G188500 chr2B 91.803 61 4 1 677 736 253943391 253943331 2.330000e-12 84.2
41 TraesCS4B01G188500 chr1B 88.060 67 4 3 699 763 666559224 666559288 3.900000e-10 76.8
42 TraesCS4B01G188500 chr6B 85.507 69 9 1 696 764 705112 705179 1.820000e-08 71.3


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 TraesCS4B01G188500 chr4B 409741022 409744666 3644 False 6732.000000 6732 100.000000 1 3645 1 chr4B.!!$F1 3644
1 TraesCS4B01G188500 chr4D 331636253 331639906 3653 True 6200.000000 6200 97.356000 3 3645 1 chr4D.!!$R1 3642
2 TraesCS4B01G188500 chr4D 330962096 330962929 833 False 811.000000 811 84.400000 1276 2123 1 chr4D.!!$F1 847
3 TraesCS4B01G188500 chr7D 477405156 477406729 1573 True 604.733333 1406 89.260333 1001 2626 3 chr7D.!!$R1 1625
4 TraesCS4B01G188500 chr7B 501778304 501781335 3031 True 788.500000 1098 86.449000 1050 2473 2 chr7B.!!$R1 1423
5 TraesCS4B01G188500 chr7B 198616784 198617492 708 False 381.000000 381 76.986000 45 755 1 chr7B.!!$F1 710
6 TraesCS4B01G188500 chr7B 424536782 424537387 605 False 239.000000 239 73.977000 1396 2001 1 chr7B.!!$F2 605
7 TraesCS4B01G188500 chr7A 518665608 518666947 1339 False 425.333333 660 89.930667 1253 2507 3 chr7A.!!$F1 1254
8 TraesCS4B01G188500 chr5D 43330113 43330654 541 True 361.000000 361 79.391000 224 761 1 chr5D.!!$R1 537
9 TraesCS4B01G188500 chr3D 246607631 246608332 701 False 202.500000 255 81.577000 3064 3593 2 chr3D.!!$F2 529
10 TraesCS4B01G188500 chr2D 90522401 90523098 697 True 206.000000 206 72.727000 1312 2006 1 chr2D.!!$R2 694

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
815 880 0.179121 GAAAATAAAAGGGCCGGGCG 60.179 55.0 23.19 0.0 0.0 6.13 F
2323 4291 0.119155 AAGAGGGAGATGTGGGTGGA 59.881 55.0 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 4511 2.421424 GCAAAATGCGACAGGATCTTCT 59.579 45.455 0.0 0.0 31.71 2.85 R
3495 5662 0.735978 CGCACATACAAGAGACGCCA 60.736 55.000 0.0 0.0 0.00 5.69 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
37 38 6.131544 ACTTATCAAAACAGACACAACCAC 57.868 37.500 0.00 0.00 0.00 4.16
43 44 5.124138 TCAAAACAGACACAACCACGTAAAT 59.876 36.000 0.00 0.00 0.00 1.40
222 223 1.993369 GCGCAAACTAGATGGCACCC 61.993 60.000 0.30 0.00 0.00 4.61
356 357 4.442073 GCATAAACAACAGCAACACAAGAG 59.558 41.667 0.00 0.00 0.00 2.85
424 425 5.816258 GGAATTAGGGTTAGAAGAAGAACGG 59.184 44.000 0.00 0.00 0.00 4.44
482 486 4.138487 ACGAAACACAGGAGAAGAAGTT 57.862 40.909 0.00 0.00 0.00 2.66
525 529 1.407437 GGTTCATCGATGCACTCCCTT 60.407 52.381 24.05 0.00 0.00 3.95
526 530 1.667724 GTTCATCGATGCACTCCCTTG 59.332 52.381 20.81 0.00 0.00 3.61
614 629 3.436243 GAGAAGGAGGAGAGGAAACAGA 58.564 50.000 0.00 0.00 0.00 3.41
618 633 2.112691 AGGAGGAGAGGAAACAGAGGAA 59.887 50.000 0.00 0.00 0.00 3.36
619 634 2.907042 GGAGGAGAGGAAACAGAGGAAA 59.093 50.000 0.00 0.00 0.00 3.13
620 635 3.307129 GGAGGAGAGGAAACAGAGGAAAC 60.307 52.174 0.00 0.00 0.00 2.78
621 636 3.318313 AGGAGAGGAAACAGAGGAAACA 58.682 45.455 0.00 0.00 0.00 2.83
623 638 4.068599 GGAGAGGAAACAGAGGAAACAAG 58.931 47.826 0.00 0.00 0.00 3.16
624 639 4.068599 GAGAGGAAACAGAGGAAACAAGG 58.931 47.826 0.00 0.00 0.00 3.61
654 669 5.357032 GGGAGAAAAAGACTCAGAAAACACA 59.643 40.000 0.00 0.00 36.26 3.72
731 795 4.028026 CAGTTTGCGGAAACAACTAAAACG 60.028 41.667 30.29 6.86 43.51 3.60
779 844 2.781174 TCCCATACCCGCCTCTAAAAAT 59.219 45.455 0.00 0.00 0.00 1.82
786 851 4.850680 ACCCGCCTCTAAAAATAATCACA 58.149 39.130 0.00 0.00 0.00 3.58
815 880 0.179121 GAAAATAAAAGGGCCGGGCG 60.179 55.000 23.19 0.00 0.00 6.13
889 955 2.434774 GTCACCCACCAGGAACCC 59.565 66.667 0.00 0.00 39.89 4.11
890 956 2.856988 TCACCCACCAGGAACCCC 60.857 66.667 0.00 0.00 39.89 4.95
916 982 5.758784 CCTAGGTTTCCTTCCTTTATAAGCG 59.241 44.000 0.00 0.00 36.60 4.68
1953 2262 3.019564 GTCACTTTGATCCCCTCAATGG 58.980 50.000 0.00 0.00 43.30 3.16
2131 4061 0.827507 ACGTGGGCCAGAGCAAATTT 60.828 50.000 6.40 0.00 42.56 1.82
2319 4287 1.211457 CAAGGAAGAGGGAGATGTGGG 59.789 57.143 0.00 0.00 0.00 4.61
2323 4291 0.119155 AAGAGGGAGATGTGGGTGGA 59.881 55.000 0.00 0.00 0.00 4.02
2543 4511 5.817988 CGATCACTTCGTCATTCCTAGTTA 58.182 41.667 0.00 0.00 43.01 2.24
2580 4548 6.183360 CGCATTTTGCATGTAATAAAGTGCTT 60.183 34.615 20.22 0.00 45.36 3.91
2626 4599 1.398692 TTTCACTTGGTTGTGGCTCC 58.601 50.000 0.00 0.00 38.40 4.70
2689 4662 4.080975 TGTGTATGAGCTCCATGAATGTCA 60.081 41.667 12.15 0.00 36.71 3.58
2690 4663 5.061853 GTGTATGAGCTCCATGAATGTCAT 58.938 41.667 12.15 0.12 37.65 3.06
2691 4664 5.530171 GTGTATGAGCTCCATGAATGTCATT 59.470 40.000 12.15 0.00 34.28 2.57
2692 4665 6.039047 GTGTATGAGCTCCATGAATGTCATTT 59.961 38.462 12.15 0.00 34.28 2.32
2703 4676 8.814931 TCCATGAATGTCATTTTTCTTTGGTAT 58.185 29.630 0.00 0.00 34.28 2.73
2733 4706 4.411540 AGACTAGATGACCTGCCAAATGAT 59.588 41.667 0.00 0.00 0.00 2.45
2761 4734 2.611722 GCCCATTTAAAACCATGTGCGT 60.612 45.455 0.00 0.00 0.00 5.24
2888 4861 8.757164 ATTAAGTTTTAGCAACCACTTAATGC 57.243 30.769 16.90 0.00 44.86 3.56
3043 5016 2.608752 GGTATCCGACGAAATACGCCAT 60.609 50.000 0.00 0.00 46.94 4.40
3204 5223 9.512435 CATTAGAAAGGTATTTGAAGATTGCAG 57.488 33.333 0.00 0.00 0.00 4.41
3426 5593 7.491372 TGAAGTCCATGTAATACGAACAGATTC 59.509 37.037 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.007626 TGTGTCTGTTTTGATAAGTCAGTGC 59.992 40.000 0.00 0.00 35.39 4.40
37 38 8.800231 TGCATTTGAATTCATATCCATTTACG 57.200 30.769 9.40 0.00 0.00 3.18
43 44 8.139350 GTCTTGATGCATTTGAATTCATATCCA 58.861 33.333 9.40 6.97 0.00 3.41
205 206 0.392461 TCGGGTGCCATCTAGTTTGC 60.392 55.000 0.00 0.00 0.00 3.68
264 265 4.083164 GGGTTTGGGGTAATATATTTCGCG 60.083 45.833 0.00 0.00 0.00 5.87
356 357 2.292103 TGTGTTTTCTTGGTGCTTGC 57.708 45.000 0.00 0.00 0.00 4.01
394 395 7.685486 TCTTCTTCTAACCCTAATTCCCCTTAA 59.315 37.037 0.00 0.00 0.00 1.85
424 425 0.736325 CGTGGTGGATTCGTCTGGTC 60.736 60.000 0.00 0.00 0.00 4.02
482 486 4.794439 CCGACGTCTGGCGCATCA 62.794 66.667 14.70 0.00 46.11 3.07
525 529 1.521457 GGAATCAGGCGCATCGACA 60.521 57.895 10.83 0.00 37.34 4.35
526 530 2.589492 CGGAATCAGGCGCATCGAC 61.589 63.158 10.83 0.00 33.59 4.20
614 629 2.032071 CCGACGCCCTTGTTTCCT 59.968 61.111 0.00 0.00 0.00 3.36
618 633 2.047213 TTTCTCCCGACGCCCTTGTT 62.047 55.000 0.00 0.00 0.00 2.83
619 634 2.047213 TTTTCTCCCGACGCCCTTGT 62.047 55.000 0.00 0.00 0.00 3.16
620 635 0.887387 TTTTTCTCCCGACGCCCTTG 60.887 55.000 0.00 0.00 0.00 3.61
621 636 0.605589 CTTTTTCTCCCGACGCCCTT 60.606 55.000 0.00 0.00 0.00 3.95
623 638 1.004200 TCTTTTTCTCCCGACGCCC 60.004 57.895 0.00 0.00 0.00 6.13
624 639 0.320508 AGTCTTTTTCTCCCGACGCC 60.321 55.000 0.00 0.00 0.00 5.68
654 669 0.830866 AAGGTCTCCGTTTCGTCCCT 60.831 55.000 0.00 0.00 0.00 4.20
709 773 4.099824 CGTTTTAGTTGTTTCCGCAAACT 58.900 39.130 3.22 0.00 42.29 2.66
786 851 6.426633 CGGCCCTTTTATTTTCAGTTTTCATT 59.573 34.615 0.00 0.00 0.00 2.57
815 880 0.681175 ATGGTGTTTTCTTGGGCTGC 59.319 50.000 0.00 0.00 0.00 5.25
889 955 5.977821 ATAAAGGAAGGAAACCTAGGAGG 57.022 43.478 17.98 0.00 42.49 4.30
890 956 6.993308 GCTTATAAAGGAAGGAAACCTAGGAG 59.007 42.308 17.98 0.00 36.67 3.69
901 967 3.802685 CGAAGGTCGCTTATAAAGGAAGG 59.197 47.826 0.00 0.00 31.14 3.46
916 982 0.522180 TGAGAGACGAAGCGAAGGTC 59.478 55.000 0.00 0.00 37.06 3.85
1189 1257 4.662468 TCTGATTCCTTCGATTCCTCTG 57.338 45.455 0.00 0.00 0.00 3.35
1191 1259 5.467035 AGATCTGATTCCTTCGATTCCTC 57.533 43.478 0.00 0.00 0.00 3.71
1953 2262 4.500265 TGGAGAGCCCAACAAAGC 57.500 55.556 0.00 0.00 43.29 3.51
2319 4287 2.762327 TCAATAGAGTAACCGGGTCCAC 59.238 50.000 6.32 1.58 0.00 4.02
2323 4291 3.029570 GTCCTCAATAGAGTAACCGGGT 58.970 50.000 6.32 0.00 40.40 5.28
2539 4507 4.744795 AATGCGACAGGATCTTCTAACT 57.255 40.909 0.00 0.00 0.00 2.24
2543 4511 2.421424 GCAAAATGCGACAGGATCTTCT 59.579 45.455 0.00 0.00 31.71 2.85
2580 4548 8.380099 AGTAAACATAGGAACTGAATACCACAA 58.620 33.333 0.00 0.00 41.52 3.33
2670 4643 7.558807 AGAAAAATGACATTCATGGAGCTCATA 59.441 33.333 17.19 3.99 37.15 2.15
2703 4676 6.314917 TGGCAGGTCATCTAGTCTTCATATA 58.685 40.000 0.00 0.00 0.00 0.86
2733 4706 3.445008 TGGTTTTAAATGGGCCTATGCA 58.555 40.909 0.67 0.00 40.13 3.96
2809 4782 2.531771 TCGGGTTTGACATGGTCTCTA 58.468 47.619 0.00 0.00 33.15 2.43
3426 5593 5.587844 AGCAGCAGGTGTAATCTTCAATTAG 59.412 40.000 0.66 0.00 0.00 1.73
3495 5662 0.735978 CGCACATACAAGAGACGCCA 60.736 55.000 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.