Multiple sequence alignment - TraesCS3B01G016700

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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 TraesCS3B01G016700 chr3B 100.000 2495 0 0 1 2495 6950547 6953041 0.000000e+00 4608
1 TraesCS3B01G016700 chr3B 89.669 968 63 12 1545 2495 346504969 346504022 0.000000e+00 1199
2 TraesCS3B01G016700 chr3B 81.047 554 64 23 997 1539 6945395 6945918 1.070000e-108 403
3 TraesCS3B01G016700 chr7B 96.740 951 20 4 1555 2495 721397182 721398131 0.000000e+00 1574
4 TraesCS3B01G016700 chr7B 79.006 181 31 7 1 178 379209868 379209692 1.570000e-22 117
5 TraesCS3B01G016700 chr3A 86.172 1186 72 47 450 1554 13831938 13833112 0.000000e+00 1197
6 TraesCS3B01G016700 chr3A 89.880 751 56 11 1762 2495 632627671 632626924 0.000000e+00 948
7 TraesCS3B01G016700 chr3A 86.053 380 44 7 1164 1539 13818235 13818609 1.390000e-107 399
8 TraesCS3B01G016700 chr3A 85.263 380 47 7 1164 1539 13811768 13812142 1.400000e-102 383
9 TraesCS3B01G016700 chr3A 79.588 485 68 12 1 459 13831437 13831916 4.000000e-83 318
10 TraesCS3B01G016700 chr3A 92.746 193 11 2 1539 1731 632636983 632636794 2.440000e-70 276
11 TraesCS3B01G016700 chr3D 89.617 809 52 13 771 1551 6461095 6460291 0.000000e+00 1000
12 TraesCS3B01G016700 chr3D 86.082 776 72 18 1 743 6461865 6461093 0.000000e+00 802
13 TraesCS3B01G016700 chr3D 81.603 549 70 23 997 1542 6465894 6465374 2.290000e-115 425
14 TraesCS3B01G016700 chr7A 85.653 697 69 15 1778 2457 19928990 19928308 0.000000e+00 704
15 TraesCS3B01G016700 chr7A 91.525 177 14 1 1550 1725 19929485 19929309 2.480000e-60 243
16 TraesCS3B01G016700 chr5B 92.402 487 31 4 2012 2495 15282560 15282077 0.000000e+00 689
17 TraesCS3B01G016700 chr5B 87.751 449 38 4 1541 1980 15282998 15282558 2.210000e-140 508
18 TraesCS3B01G016700 chr5B 79.592 196 25 12 17 204 491995912 491996100 2.610000e-25 126
19 TraesCS3B01G016700 chr4A 92.197 487 31 5 2012 2495 731426997 731426515 0.000000e+00 682
20 TraesCS3B01G016700 chr4A 91.820 489 32 6 2012 2495 646368452 646368937 0.000000e+00 675
21 TraesCS3B01G016700 chr4A 89.538 411 26 5 1578 1980 731427396 731426995 2.860000e-139 505
22 TraesCS3B01G016700 chr4A 94.972 179 9 0 1548 1726 646368072 646368250 5.250000e-72 281
23 TraesCS3B01G016700 chr5A 84.375 192 30 0 13 204 410934936 410935127 3.280000e-44 189
24 TraesCS3B01G016700 chr5D 85.955 178 22 3 1543 1719 346039858 346040033 1.180000e-43 187
25 TraesCS3B01G016700 chr4B 81.951 205 34 3 1 203 627944092 627944295 1.190000e-38 171
26 TraesCS3B01G016700 chr4B 78.462 195 29 12 17 204 588611613 588611801 5.640000e-22 115
27 TraesCS3B01G016700 chr1B 81.553 206 29 9 1 204 623369653 623369851 7.140000e-36 161
28 TraesCS3B01G016700 chr1D 78.873 213 38 6 1 210 377372808 377372600 1.200000e-28 137
29 TraesCS3B01G016700 chr6B 79.487 195 27 11 17 204 206666669 206666857 2.610000e-25 126
30 TraesCS3B01G016700 chr6B 79.058 191 28 9 30 214 687017233 687017049 1.210000e-23 121


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 TraesCS3B01G016700 chr3B 6950547 6953041 2494 False 4608.000000 4608 100.000000 1 2495 1 chr3B.!!$F2 2494
1 TraesCS3B01G016700 chr3B 346504022 346504969 947 True 1199.000000 1199 89.669000 1545 2495 1 chr3B.!!$R1 950
2 TraesCS3B01G016700 chr3B 6945395 6945918 523 False 403.000000 403 81.047000 997 1539 1 chr3B.!!$F1 542
3 TraesCS3B01G016700 chr7B 721397182 721398131 949 False 1574.000000 1574 96.740000 1555 2495 1 chr7B.!!$F1 940
4 TraesCS3B01G016700 chr3A 632626924 632627671 747 True 948.000000 948 89.880000 1762 2495 1 chr3A.!!$R1 733
5 TraesCS3B01G016700 chr3A 13831437 13833112 1675 False 757.500000 1197 82.880000 1 1554 2 chr3A.!!$F3 1553
6 TraesCS3B01G016700 chr3D 6460291 6465894 5603 True 742.333333 1000 85.767333 1 1551 3 chr3D.!!$R1 1550
7 TraesCS3B01G016700 chr7A 19928308 19929485 1177 True 473.500000 704 88.589000 1550 2457 2 chr7A.!!$R1 907
8 TraesCS3B01G016700 chr5B 15282077 15282998 921 True 598.500000 689 90.076500 1541 2495 2 chr5B.!!$R1 954
9 TraesCS3B01G016700 chr4A 731426515 731427396 881 True 593.500000 682 90.867500 1578 2495 2 chr4A.!!$R1 917
10 TraesCS3B01G016700 chr4A 646368072 646368937 865 False 478.000000 675 93.396000 1548 2495 2 chr4A.!!$F1 947

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
851 4997 0.319641 AAACCGCGTGAACTCTCTCC 60.32 55.0 4.92 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 6255 1.482182 CACACAGGCCATGTAGCTCTA 59.518 52.381 11.99 0.0 41.41 2.43 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
28 4058 4.957327 AGTCTCACTCCTATTTAGGGTCAC 59.043 45.833 3.84 0.00 43.79 3.67
149 4179 9.906660 TTTTCCTGTGACATGTATTAACATTTC 57.093 29.630 0.00 0.00 44.07 2.17
207 4237 6.585695 AGACGAAGAGACCAATAAACTACA 57.414 37.500 0.00 0.00 0.00 2.74
210 4240 6.518493 ACGAAGAGACCAATAAACTACAACA 58.482 36.000 0.00 0.00 0.00 3.33
231 4261 7.225538 ACAACAGAGAAAATGACAGAGTAGTTG 59.774 37.037 0.00 0.00 36.94 3.16
242 4272 1.348036 AGAGTAGTTGGACCCAAGTGC 59.652 52.381 17.07 15.68 39.61 4.40
244 4274 2.565834 GAGTAGTTGGACCCAAGTGCTA 59.434 50.000 21.66 9.47 46.83 3.49
323 4374 2.969443 AGAATTCGGTTCGTTGCAAG 57.031 45.000 0.00 0.00 41.84 4.01
331 4387 4.039032 TCGGTTCGTTGCAAGAAAAATTC 58.961 39.130 0.00 0.00 0.00 2.17
339 4395 6.693545 TCGTTGCAAGAAAAATTCGTGTATTT 59.306 30.769 0.00 0.00 40.58 1.40
347 4403 6.751888 AGAAAAATTCGTGTATTTAGCATGCC 59.248 34.615 15.66 0.00 34.02 4.40
352 4408 1.338020 GTGTATTTAGCATGCCCTGGC 59.662 52.381 15.66 0.00 42.35 4.85
370 4426 1.377725 CCAGCTGCGTTCCTTCCAT 60.378 57.895 8.66 0.00 0.00 3.41
378 4434 2.038426 TGCGTTCCTTCCATCAGAAAGA 59.962 45.455 0.00 0.00 32.88 2.52
386 4442 6.352516 TCCTTCCATCAGAAAGAGATAAAGC 58.647 40.000 0.00 0.00 32.88 3.51
392 4448 8.517878 TCCATCAGAAAGAGATAAAGCAAAAAG 58.482 33.333 0.00 0.00 0.00 2.27
440 4502 2.711009 AGGAACTCATTGTGGAAGACCA 59.289 45.455 0.00 0.00 44.76 4.02
448 4542 4.856789 TGGAAGACCAGCGTCCTA 57.143 55.556 0.00 0.00 44.45 2.94
460 4554 4.161565 ACCAGCGTCCTAGATCATACAAAA 59.838 41.667 0.00 0.00 0.00 2.44
630 4761 1.073284 GGCCCTACCAGTTCAACTCAA 59.927 52.381 0.00 0.00 38.86 3.02
644 4775 6.427853 AGTTCAACTCAACGATGATTGATCAA 59.572 34.615 11.26 11.26 40.69 2.57
722 4867 2.116366 GTTGCCGTGTTGTTGCTTAAG 58.884 47.619 0.00 0.00 0.00 1.85
765 4910 0.531532 CCATCCATCGTCAGCTGGAC 60.532 60.000 15.13 9.86 44.44 4.02
768 4913 2.362369 CCATCGTCAGCTGGACCCT 61.362 63.158 15.13 0.00 43.95 4.34
851 4997 0.319641 AAACCGCGTGAACTCTCTCC 60.320 55.000 4.92 0.00 0.00 3.71
868 5014 5.942961 TCTCTCCACCACTACCTATAAGAG 58.057 45.833 0.00 0.00 0.00 2.85
890 5036 0.388649 AACACACACTCGATCGAGCC 60.389 55.000 38.12 0.00 45.54 4.70
898 5044 2.429907 CGATCGAGCCGCATCTCC 60.430 66.667 10.26 0.00 0.00 3.71
1017 5194 1.064946 GATGTCGTCTGCCCTCTCG 59.935 63.158 0.00 0.00 0.00 4.04
1422 5608 3.147595 ATGCTGCTCGCCGGAGTA 61.148 61.111 5.05 0.00 42.53 2.59
1437 5623 1.270732 GGAGTACCGATCTCCGCTCTA 60.271 57.143 5.14 0.00 41.36 2.43
1458 5644 4.459089 GTCCTGCACCTCCTCGGC 62.459 72.222 0.00 0.00 35.61 5.54
1488 5674 1.679680 GGATCCATTCTGCACCATGTG 59.320 52.381 6.95 0.00 36.51 3.21
1798 6255 1.112113 CTACCTATGCTGACACCCGT 58.888 55.000 0.00 0.00 0.00 5.28
1867 6339 8.084590 AGGTGAAAAAGTAGACGAGTAAAATG 57.915 34.615 0.00 0.00 0.00 2.32
1975 6456 7.273457 TCTGGGTGGAAGGTTGTAATAAATA 57.727 36.000 0.00 0.00 0.00 1.40
2011 6529 3.327439 AGCAATAGGTAGGGTAGGCATT 58.673 45.455 0.00 0.00 0.00 3.56
2013 6531 4.286291 AGCAATAGGTAGGGTAGGCATTAC 59.714 45.833 0.00 0.00 0.00 1.89
2053 6571 5.769484 TGTGTACCCGCTTTTTCAAAATA 57.231 34.783 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.288158 GTGACCCTAAATAGGAGTGAGACTAAT 59.712 40.741 8.09 0.00 46.63 1.73
112 4142 9.631257 ACATGTCACAGGAAAATATATCATTGA 57.369 29.630 0.00 0.00 0.00 2.57
127 4157 7.072177 ACGAAATGTTAATACATGTCACAGG 57.928 36.000 0.00 0.00 45.58 4.00
128 4158 9.689075 CTAACGAAATGTTAATACATGTCACAG 57.311 33.333 0.00 0.00 45.58 3.66
129 4159 9.210329 ACTAACGAAATGTTAATACATGTCACA 57.790 29.630 0.00 1.86 45.58 3.58
185 4215 6.643770 TGTTGTAGTTTATTGGTCTCTTCGTC 59.356 38.462 0.00 0.00 0.00 4.20
207 4237 6.708054 CCAACTACTCTGTCATTTTCTCTGTT 59.292 38.462 0.00 0.00 0.00 3.16
210 4240 6.459923 GTCCAACTACTCTGTCATTTTCTCT 58.540 40.000 0.00 0.00 0.00 3.10
242 4272 3.638484 TCATCGCATACGTCACCAATAG 58.362 45.455 0.00 0.00 41.18 1.73
244 4274 2.595124 TCATCGCATACGTCACCAAT 57.405 45.000 0.00 0.00 41.18 3.16
311 4362 3.794564 ACGAATTTTTCTTGCAACGAACC 59.205 39.130 8.55 0.00 0.00 3.62
317 4368 7.649705 TGCTAAATACACGAATTTTTCTTGCAA 59.350 29.630 0.00 0.00 32.67 4.08
323 4374 6.019881 GGGCATGCTAAATACACGAATTTTTC 60.020 38.462 18.92 0.00 31.63 2.29
331 4387 1.603802 CCAGGGCATGCTAAATACACG 59.396 52.381 18.92 0.00 0.00 4.49
339 4395 4.511246 GCTGGCCAGGGCATGCTA 62.511 66.667 33.46 0.00 44.11 3.49
352 4408 1.372087 GATGGAAGGAACGCAGCTGG 61.372 60.000 17.12 8.27 0.00 4.85
421 4483 2.485814 GCTGGTCTTCCACAATGAGTTC 59.514 50.000 0.00 0.00 39.03 3.01
424 4486 1.081892 CGCTGGTCTTCCACAATGAG 58.918 55.000 0.00 0.00 39.03 2.90
440 4502 9.561069 AATTAATTTTGTATGATCTAGGACGCT 57.439 29.630 0.00 0.00 0.00 5.07
541 4640 4.175337 GCCTCGGTAGCATGGGCA 62.175 66.667 12.77 0.00 44.61 5.36
542 4641 4.175337 TGCCTCGGTAGCATGGGC 62.175 66.667 11.32 11.32 42.73 5.36
543 4642 1.399744 TAGTGCCTCGGTAGCATGGG 61.400 60.000 0.00 0.00 43.29 4.00
544 4643 0.249489 GTAGTGCCTCGGTAGCATGG 60.249 60.000 0.00 0.00 43.29 3.66
545 4644 0.249489 GGTAGTGCCTCGGTAGCATG 60.249 60.000 0.00 0.00 43.29 4.06
546 4645 0.686441 TGGTAGTGCCTCGGTAGCAT 60.686 55.000 0.00 0.00 43.29 3.79
547 4646 1.304630 TGGTAGTGCCTCGGTAGCA 60.305 57.895 0.00 0.00 38.35 3.49
600 4722 3.046374 ACTGGTAGGGCCTCGATAATTT 58.954 45.455 10.74 0.00 38.35 1.82
630 4761 8.538409 TCATCGATTAATTGATCAATCATCGT 57.462 30.769 34.55 26.73 40.75 3.73
644 4775 4.747108 CGCCTCTCAGTTTCATCGATTAAT 59.253 41.667 0.00 0.00 0.00 1.40
722 4867 2.229302 CGGTAATCACCTAGCTAGCTCC 59.771 54.545 23.26 11.83 43.33 4.70
765 4910 4.998672 TCTCGTTGTTAATTGTGGTTAGGG 59.001 41.667 0.00 0.00 0.00 3.53
768 4913 6.711194 TGGAATCTCGTTGTTAATTGTGGTTA 59.289 34.615 0.00 0.00 0.00 2.85
868 5014 0.666274 TCGATCGAGTGTGTGTTGCC 60.666 55.000 15.15 0.00 0.00 4.52
876 5022 2.669808 GATGCGGCTCGATCGAGTGT 62.670 60.000 37.59 22.64 43.70 3.55
890 5036 0.798776 GAATAATGGCGGGAGATGCG 59.201 55.000 0.00 0.00 0.00 4.73
898 5044 2.287788 GGTGAATGCTGAATAATGGCGG 60.288 50.000 0.00 0.00 0.00 6.13
1175 5358 4.143333 CGTAGTGGTCCTGCCCGG 62.143 72.222 0.00 0.00 36.04 5.73
1350 5536 4.361971 ATGGCCAGCAGCTGCAGT 62.362 61.111 38.24 18.36 45.16 4.40
1474 5660 3.144657 TCAAGACACATGGTGCAGAAT 57.855 42.857 0.00 0.00 36.98 2.40
1488 5674 8.127327 ACGAATGAATGATGAATCAATCAAGAC 58.873 33.333 13.53 8.20 46.31 3.01
1571 5762 7.989416 ATGCCTGAATTCAAACATTCAAAAT 57.011 28.000 9.88 0.00 41.59 1.82
1798 6255 1.482182 CACACAGGCCATGTAGCTCTA 59.518 52.381 11.99 0.00 41.41 2.43
1867 6339 5.176774 GCTGCACCTGGTTTTATTTGTTTAC 59.823 40.000 0.00 0.00 0.00 2.01
1975 6456 5.894393 ACCTATTGCTATGTCTCACTGTAGT 59.106 40.000 0.00 0.00 0.00 2.73
2013 6531 8.693625 GGGTACACATATATAGCTAGGTTTAGG 58.306 40.741 0.00 0.00 0.00 2.69
2165 6685 5.904362 AATTGATCTTTTGTACAGAGGCC 57.096 39.130 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.