Multiple sequence alignment - TraesCS1B01G172000

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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 TraesCS1B01G172000 chr1B 100.000 5214 0 0 1 5214 306213733 306218946 0 9629
1 TraesCS1B01G172000 chr1B 94.596 3516 177 13 1703 5214 333476326 333479832 0 5428
2 TraesCS1B01G172000 chr1B 92.430 2391 140 15 3 2384 171621797 171624155 0 3374
3 TraesCS1B01G172000 chr5B 94.790 5221 228 17 3 5214 194205563 194200378 0 8094
4 TraesCS1B01G172000 chr5B 94.073 3661 180 22 1561 5214 181621491 181617861 0 5524
5 TraesCS1B01G172000 chr5B 92.579 3436 225 26 1784 5208 273096688 273100104 0 4905
6 TraesCS1B01G172000 chr5B 91.903 2396 145 23 3 2384 180047436 180049796 0 3304
7 TraesCS1B01G172000 chr6B 93.990 5225 263 23 3 5214 149528476 149533662 0 7862
8 TraesCS1B01G172000 chr6B 94.487 3791 166 20 1433 5214 227584863 227581107 0 5803
9 TraesCS1B01G172000 chr6B 95.036 3626 164 14 1602 5214 341936448 341940070 0 5685
10 TraesCS1B01G172000 chr6B 94.663 3504 171 14 1716 5214 388445396 388448888 0 5421
11 TraesCS1B01G172000 chr6B 92.923 3476 191 21 2 3459 133990929 133987491 0 5005
12 TraesCS1B01G172000 chr6B 86.959 2032 221 36 599 2609 105921242 105919234 0 2244
13 TraesCS1B01G172000 chr2B 90.604 4821 357 70 223 5003 504831935 504836699 0 6305
14 TraesCS1B01G172000 chr2B 92.710 3443 223 25 1779 5209 769025285 769021859 0 4942
15 TraesCS1B01G172000 chr2B 92.500 2400 138 19 3 2394 107112293 107109928 0 3397
16 TraesCS1B01G172000 chr3B 92.768 3443 221 25 1779 5209 543863820 543860394 0 4953
17 TraesCS1B01G172000 chr3B 92.256 2402 140 19 3 2394 361612009 361609644 0 3363
18 TraesCS1B01G172000 chr4A 93.497 2245 118 15 2 2235 744462346 744460119 0 3312


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 TraesCS1B01G172000 chr1B 306213733 306218946 5213 False 9629 9629 100.000 1 5214 1 chr1B.!!$F2 5213
1 TraesCS1B01G172000 chr1B 333476326 333479832 3506 False 5428 5428 94.596 1703 5214 1 chr1B.!!$F3 3511
2 TraesCS1B01G172000 chr1B 171621797 171624155 2358 False 3374 3374 92.430 3 2384 1 chr1B.!!$F1 2381
3 TraesCS1B01G172000 chr5B 194200378 194205563 5185 True 8094 8094 94.790 3 5214 1 chr5B.!!$R2 5211
4 TraesCS1B01G172000 chr5B 181617861 181621491 3630 True 5524 5524 94.073 1561 5214 1 chr5B.!!$R1 3653
5 TraesCS1B01G172000 chr5B 273096688 273100104 3416 False 4905 4905 92.579 1784 5208 1 chr5B.!!$F2 3424
6 TraesCS1B01G172000 chr5B 180047436 180049796 2360 False 3304 3304 91.903 3 2384 1 chr5B.!!$F1 2381
7 TraesCS1B01G172000 chr6B 149528476 149533662 5186 False 7862 7862 93.990 3 5214 1 chr6B.!!$F1 5211
8 TraesCS1B01G172000 chr6B 227581107 227584863 3756 True 5803 5803 94.487 1433 5214 1 chr6B.!!$R3 3781
9 TraesCS1B01G172000 chr6B 341936448 341940070 3622 False 5685 5685 95.036 1602 5214 1 chr6B.!!$F2 3612
10 TraesCS1B01G172000 chr6B 388445396 388448888 3492 False 5421 5421 94.663 1716 5214 1 chr6B.!!$F3 3498
11 TraesCS1B01G172000 chr6B 133987491 133990929 3438 True 5005 5005 92.923 2 3459 1 chr6B.!!$R2 3457
12 TraesCS1B01G172000 chr6B 105919234 105921242 2008 True 2244 2244 86.959 599 2609 1 chr6B.!!$R1 2010
13 TraesCS1B01G172000 chr2B 504831935 504836699 4764 False 6305 6305 90.604 223 5003 1 chr2B.!!$F1 4780
14 TraesCS1B01G172000 chr2B 769021859 769025285 3426 True 4942 4942 92.710 1779 5209 1 chr2B.!!$R2 3430
15 TraesCS1B01G172000 chr2B 107109928 107112293 2365 True 3397 3397 92.500 3 2394 1 chr2B.!!$R1 2391
16 TraesCS1B01G172000 chr3B 543860394 543863820 3426 True 4953 4953 92.768 1779 5209 1 chr3B.!!$R2 3430
17 TraesCS1B01G172000 chr3B 361609644 361612009 2365 True 3363 3363 92.256 3 2394 1 chr3B.!!$R1 2391
18 TraesCS1B01G172000 chr4A 744460119 744462346 2227 True 3312 3312 93.497 2 2235 1 chr4A.!!$R1 2233

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
369 376 1.717032 TAGGACAAGGTGTGAGCTGT 58.283 50.000 0.00 0.0 0.00 4.40 F
1244 1297 1.202639 CCTTTTGTTTCCTGGGTTGGC 60.203 52.381 0.00 0.0 0.00 4.52 F
2077 2290 0.036164 CCACCGTGGATTTCACTGGA 59.964 55.000 12.68 0.0 41.57 3.86 F
2838 3080 0.321671 CCCAGAACAGACACATCGGT 59.678 55.000 0.00 0.0 34.38 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1404 0.736325 CGAAGAGAAATGGTCGGCGT 60.736 55.000 6.85 0.0 0.0 5.68 R
2124 2337 2.093500 ACAGCCTTGACAGCATCGATAA 60.093 45.455 0.00 0.0 0.0 1.75 R
3251 3494 1.092921 AAACTCGTTGCCACGCTTGA 61.093 50.000 5.28 0.0 46.7 3.02 R
4325 4585 1.508632 GTCCACTTCAACGCTTGCTA 58.491 50.000 0.00 0.0 0.0 3.49 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
78 81 5.831525 ACATCAATTGTGTCAGATGCCATAT 59.168 36.000 5.13 0.00 41.08 1.78
115 120 4.218417 GTGGCAAGTATTTTGTCTGACCAT 59.782 41.667 5.17 0.00 0.00 3.55
169 174 5.384063 AATGTGGCAAATTCATTGTACGA 57.616 34.783 0.00 0.00 41.32 3.43
214 220 4.083431 GCCATGATGACTTGTGATATCTGC 60.083 45.833 3.98 0.00 0.00 4.26
328 334 1.788308 CACATTTTTGCCGCTGAACAG 59.212 47.619 0.00 0.00 0.00 3.16
357 364 7.319646 GCAATTCATTGGTGTATTTAGGACAA 58.680 34.615 1.77 0.00 38.21 3.18
369 376 1.717032 TAGGACAAGGTGTGAGCTGT 58.283 50.000 0.00 0.00 0.00 4.40
388 395 5.125417 AGCTGTCACATGTTAGTTTTTGTGT 59.875 36.000 0.00 0.00 40.22 3.72
436 444 6.203808 TCGTACTATCTTGTGCTAACATGT 57.796 37.500 0.00 0.00 35.83 3.21
518 526 8.772705 CAAAATGTAACCAATGTGCTTAATTGT 58.227 29.630 0.00 0.00 33.93 2.71
540 548 8.864069 TTGTCACATTTATGTTTTCGACAATT 57.136 26.923 16.27 0.00 41.20 2.32
572 585 2.737252 TGCGTGCGTGTTTATGTGATAA 59.263 40.909 0.00 0.00 0.00 1.75
662 708 4.378770 CCGTGACAATTTGATCTGTTCCTG 60.379 45.833 2.79 0.00 0.00 3.86
690 736 1.766143 GAATGGCTCGCGGTGATCAC 61.766 60.000 17.91 17.91 0.00 3.06
735 781 2.615493 GGATCCACCACAACAGAATCGT 60.615 50.000 6.95 0.00 38.79 3.73
876 927 3.573538 TGATAGTGCAAAACATGGCAACT 59.426 39.130 0.00 0.00 42.45 3.16
889 940 5.072741 ACATGGCAACTACTGATCACTTTT 58.927 37.500 0.00 0.00 37.61 2.27
966 1018 4.021981 TGACTGACTACATTGACTGACAGG 60.022 45.833 7.51 0.00 0.00 4.00
989 1041 2.166907 ACCGATGATCAGAAGGGAGT 57.833 50.000 15.49 0.00 0.00 3.85
990 1042 1.759445 ACCGATGATCAGAAGGGAGTG 59.241 52.381 15.49 0.00 0.00 3.51
1017 1070 1.419387 GAGATGGGTATGCAGGCTCTT 59.581 52.381 0.00 0.00 0.00 2.85
1158 1211 1.654220 CGTGTTCTGCACTTTGGGG 59.346 57.895 0.00 0.00 45.57 4.96
1226 1279 2.125766 GAGGAAGCGTTGTTCCCCCT 62.126 60.000 9.04 0.00 46.49 4.79
1244 1297 1.202639 CCTTTTGTTTCCTGGGTTGGC 60.203 52.381 0.00 0.00 0.00 4.52
1351 1404 6.544928 TGTACCTCATCTCAGCTATTTTCA 57.455 37.500 0.00 0.00 0.00 2.69
1361 1414 1.014352 GCTATTTTCACGCCGACCAT 58.986 50.000 0.00 0.00 0.00 3.55
1398 1451 2.568509 CAACAAATGCTTCCCCATCCTT 59.431 45.455 0.00 0.00 0.00 3.36
1668 1725 8.731605 TGTCGACTGCATTTAATGGTATTTTTA 58.268 29.630 17.92 0.00 0.00 1.52
2077 2290 0.036164 CCACCGTGGATTTCACTGGA 59.964 55.000 12.68 0.00 41.57 3.86
2124 2337 1.001378 GTTTGCTGTTTCTGCGTGGAT 60.001 47.619 0.00 0.00 0.00 3.41
2359 2578 2.234661 CTCACTCCACATGGCAACTCTA 59.765 50.000 0.00 0.00 34.44 2.43
2611 2851 7.618019 AAAGATCTACATCTATGGTTGCCTA 57.382 36.000 0.00 0.00 38.55 3.93
2775 3017 1.304713 GGGTGGACGTCCCTCAGTA 60.305 63.158 31.19 9.20 41.58 2.74
2838 3080 0.321671 CCCAGAACAGACACATCGGT 59.678 55.000 0.00 0.00 34.38 4.69
2937 3179 1.277273 CTGGTCTCAGCAAGGATGACA 59.723 52.381 0.00 0.00 33.86 3.58
3251 3494 4.646572 TCCCTTTTTGCACTTGTTTTTGT 58.353 34.783 0.00 0.00 0.00 2.83
3449 3697 2.222886 CAGGTCATCTCCTCGTACGAT 58.777 52.381 19.87 0.00 35.37 3.73
3858 4111 2.696707 ACTATTGCTGGATTTGCATGGG 59.303 45.455 0.00 0.00 40.34 4.00
3913 4166 2.291282 CCCCTTACATGGCAACTACCAA 60.291 50.000 0.00 0.00 44.65 3.67
3933 4189 9.244799 CTACCAACTTTTCCACTTATTTTTCAC 57.755 33.333 0.00 0.00 0.00 3.18
4325 4585 2.042639 GAGCCATGCCACCCCATT 60.043 61.111 0.00 0.00 0.00 3.16
4365 4625 1.903183 GCTCCTGAGACCAACCTAAGT 59.097 52.381 0.00 0.00 0.00 2.24
4612 4872 0.107897 CATACCCAACGCACCAGCTA 60.108 55.000 0.00 0.00 39.10 3.32
4653 4913 2.353704 CGAGTCTGGTTATGTTCCTGCA 60.354 50.000 0.00 0.00 0.00 4.41
4829 5089 4.400961 GCGCACTTCCAGGCTCCT 62.401 66.667 0.30 0.00 0.00 3.69
4916 5176 2.272146 CAACACGCCCTGCCCTAT 59.728 61.111 0.00 0.00 0.00 2.57
4947 5207 2.474816 GATCATTCTGTAGTGGCCGAC 58.525 52.381 0.00 0.00 0.00 4.79
4986 5246 2.376518 TCTTTCACCCTTGGATTCTGCT 59.623 45.455 0.00 0.00 0.00 4.24
4990 5250 1.201429 ACCCTTGGATTCTGCTCCGT 61.201 55.000 0.00 0.00 38.21 4.69
5083 5343 2.421424 GGCATCAGTCAAGATCAACCAC 59.579 50.000 0.00 0.00 0.00 4.16
5175 5435 2.759795 GAGGGCAGGAAGGCTGTT 59.240 61.111 0.00 0.00 43.56 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.233431 GCCAATTTGCCACATTGTCCTA 59.767 45.455 3.13 0.00 30.73 2.94
169 174 3.414549 AAACACGAAAATTGCGTCTGT 57.585 38.095 0.00 0.00 40.44 3.41
328 334 6.925165 CCTAAATACACCAATGAATTGCCATC 59.075 38.462 0.00 0.00 36.48 3.51
369 376 6.824196 TCCACTACACAAAAACTAACATGTGA 59.176 34.615 11.30 0.00 44.52 3.58
375 382 7.506328 AATCCTCCACTACACAAAAACTAAC 57.494 36.000 0.00 0.00 0.00 2.34
388 395 6.187727 AGAAAGTCACAAAATCCTCCACTA 57.812 37.500 0.00 0.00 0.00 2.74
436 444 8.494347 CACTTGAAAACAAAATGTTGAAGTTGA 58.506 29.630 1.62 0.00 40.14 3.18
490 498 9.553064 AATTAAGCACATTGGTTACATTTTGAA 57.447 25.926 0.00 0.00 39.68 2.69
491 499 8.986847 CAATTAAGCACATTGGTTACATTTTGA 58.013 29.630 0.00 0.00 39.68 2.69
572 585 8.362639 AGAAAATGTCAACTAGTGAATGCAAAT 58.637 29.630 0.00 0.00 38.23 2.32
690 736 6.419710 CCATGAAATCATCATCATCGTTTTGG 59.580 38.462 0.00 0.00 45.91 3.28
735 781 1.140052 TCTTTTCTCCGTCCAGTTGCA 59.860 47.619 0.00 0.00 0.00 4.08
857 908 4.023279 CAGTAGTTGCCATGTTTTGCACTA 60.023 41.667 0.00 0.00 37.18 2.74
966 1018 4.141914 ACTCCCTTCTGATCATCGGTAAAC 60.142 45.833 0.00 0.00 0.00 2.01
989 1041 0.471191 CATACCCATCTCAGCAGCCA 59.529 55.000 0.00 0.00 0.00 4.75
990 1042 0.888285 GCATACCCATCTCAGCAGCC 60.888 60.000 0.00 0.00 0.00 4.85
1017 1070 3.326836 TTCGTGCACCAGACATTCATA 57.673 42.857 12.15 0.00 0.00 2.15
1158 1211 1.153549 GATCTGTCCACGAGGCACC 60.154 63.158 0.00 0.00 33.74 5.01
1226 1279 1.573108 TGCCAACCCAGGAAACAAAA 58.427 45.000 0.00 0.00 0.00 2.44
1244 1297 1.332686 CAGATGTGTTCGGCATGGATG 59.667 52.381 0.00 0.00 0.00 3.51
1351 1404 0.736325 CGAAGAGAAATGGTCGGCGT 60.736 55.000 6.85 0.00 0.00 5.68
1361 1414 0.951558 GTTGCTTGGGCGAAGAGAAA 59.048 50.000 13.81 1.28 42.25 2.52
1668 1725 3.054361 AGTGTTCACAGAAAAGGACTGGT 60.054 43.478 5.74 0.00 39.38 4.00
1674 1734 8.026607 TGTTAAAAAGAGTGTTCACAGAAAAGG 58.973 33.333 5.74 0.00 0.00 3.11
1891 2073 3.930634 AAAGAAGAAGTTGCCATCTGC 57.069 42.857 0.00 0.00 41.77 4.26
2124 2337 2.093500 ACAGCCTTGACAGCATCGATAA 60.093 45.455 0.00 0.00 0.00 1.75
2277 2495 3.032017 AGTCATCTCTTGTGAACCACG 57.968 47.619 0.00 0.00 37.14 4.94
2531 2768 2.819608 CACGTCCATCCACTTTCCAAAT 59.180 45.455 0.00 0.00 0.00 2.32
2611 2851 3.376859 TGCGCGACATCAAAAATAATCCT 59.623 39.130 12.10 0.00 0.00 3.24
2775 3017 4.767841 CGCGTCGCTGTCAGAGCT 62.768 66.667 16.36 0.00 46.64 4.09
2838 3080 2.904866 GCCACGGCAACCAGTTGA 60.905 61.111 14.56 0.00 42.93 3.18
2937 3179 2.679837 GCACGTTCTCCATGTCATCATT 59.320 45.455 0.00 0.00 31.15 2.57
3251 3494 1.092921 AAACTCGTTGCCACGCTTGA 61.093 50.000 5.28 0.00 46.70 3.02
3374 3621 1.939934 TGTTCAACCGAGCAGAAACAG 59.060 47.619 0.00 0.00 0.00 3.16
3449 3697 3.931247 CCCCGGTGTTGGACGTCA 61.931 66.667 18.91 0.27 0.00 4.35
3858 4111 3.313526 CCATGTGGCATAGTTAGCAGTTC 59.686 47.826 0.00 0.00 0.00 3.01
3947 4204 9.762933 ATGAACAAAATATATTTGCCATGGTAC 57.237 29.630 14.67 0.00 32.93 3.34
4211 4471 3.055747 TGATGTACGGATGCCTGTTGTTA 60.056 43.478 0.00 0.00 33.18 2.41
4325 4585 1.508632 GTCCACTTCAACGCTTGCTA 58.491 50.000 0.00 0.00 0.00 3.49
4365 4625 6.158520 TGTCAGATGAATGGGAATCTTCCTTA 59.841 38.462 8.78 0.00 46.72 2.69
4380 4640 4.005650 GCTTGGAATCAGTGTCAGATGAA 58.994 43.478 0.00 0.00 0.00 2.57
4612 4872 5.306160 ACTCGTCTCTACTTCTCCTAGCTAT 59.694 44.000 0.00 0.00 0.00 2.97
4623 4883 5.254901 ACATAACCAGACTCGTCTCTACTT 58.745 41.667 0.00 0.00 37.98 2.24
4626 4886 4.639310 GGAACATAACCAGACTCGTCTCTA 59.361 45.833 0.00 0.00 37.98 2.43
4653 4913 2.351276 GGCGGGAACAGTGTGGAT 59.649 61.111 0.00 0.00 0.00 3.41
4916 5176 6.929049 CACTACAGAATGATCGGGCTTATTTA 59.071 38.462 0.00 0.00 39.69 1.40
4947 5207 8.180267 GGTGAAAGATCAACAAACATATCTGAG 58.820 37.037 0.00 0.00 43.12 3.35
4986 5246 1.269726 GGACCACGAACAACTTACGGA 60.270 52.381 0.00 0.00 0.00 4.69
5083 5343 0.250640 GGCATAGGATCTGGCACCAG 60.251 60.000 10.60 10.60 44.86 4.00
5175 5435 3.066900 GGACTATCAGCTCTGCGAACTTA 59.933 47.826 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.