Multiple sequence alignment - TraesCS2D01G326600

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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 TraesCS2D01G326600 chr2D 100.000 3693 0 0 1 3693 419806100 419802408 0.000000e+00 6820.0
1 TraesCS2D01G326600 chr2D 81.579 114 17 1 3460 3569 61020623 61020736 1.410000e-14 91.6
2 TraesCS2D01G326600 chr2B 95.679 2939 83 23 539 3447 492291127 492288203 0.000000e+00 4684.0
3 TraesCS2D01G326600 chr2B 81.343 134 20 4 3466 3596 37781494 37781363 1.810000e-18 104.0
4 TraesCS2D01G326600 chr2A 94.592 2718 73 19 1021 3693 570149939 570152627 0.000000e+00 4137.0
5 TraesCS2D01G326600 chr2A 91.058 548 39 6 1 538 685662774 685662227 0.000000e+00 732.0
6 TraesCS2D01G326600 chr2A 95.510 245 4 4 787 1028 570149483 570149723 5.790000e-103 385.0
7 TraesCS2D01G326600 chr2A 90.625 192 7 6 610 796 570148516 570148701 1.020000e-60 244.0
8 TraesCS2D01G326600 chr2A 80.645 217 30 10 3448 3657 562752434 562752645 1.370000e-34 158.0
9 TraesCS2D01G326600 chr2A 78.802 217 34 10 3448 3657 562866908 562867119 6.430000e-28 135.0
10 TraesCS2D01G326600 chr1D 92.909 550 25 8 1 538 50957270 50956723 0.000000e+00 787.0
11 TraesCS2D01G326600 chr1D 92.449 543 29 6 1 538 50951750 50951215 0.000000e+00 765.0
12 TraesCS2D01G326600 chr1D 91.160 543 38 7 1 538 448435561 448435024 0.000000e+00 728.0
13 TraesCS2D01G326600 chr5D 92.096 544 34 6 1 538 407752667 407752127 0.000000e+00 758.0
14 TraesCS2D01G326600 chr5D 85.926 135 19 0 3448 3582 52392261 52392395 1.070000e-30 145.0
15 TraesCS2D01G326600 chr5D 82.258 124 21 1 3473 3596 5163931 5164053 5.040000e-19 106.0
16 TraesCS2D01G326600 chr7D 91.455 550 39 5 1 545 612624406 612623860 0.000000e+00 749.0
17 TraesCS2D01G326600 chr7D 78.995 219 33 11 3448 3658 66706284 66706497 1.790000e-28 137.0
18 TraesCS2D01G326600 chr6A 91.360 544 37 5 1 538 74903377 74903916 0.000000e+00 736.0
19 TraesCS2D01G326600 chr3D 90.975 554 36 6 1 543 581139395 581139945 0.000000e+00 734.0
20 TraesCS2D01G326600 chr3D 91.489 47 2 2 3619 3664 535670074 535670029 3.080000e-06 63.9
21 TraesCS2D01G326600 chr4D 91.075 549 35 7 1 538 49780743 49781288 0.000000e+00 730.0
22 TraesCS2D01G326600 chr7A 79.545 176 25 8 3480 3649 244468164 244468334 8.380000e-22 115.0
23 TraesCS2D01G326600 chr3B 100.000 28 0 0 3618 3645 707242879 707242852 7.000000e-03 52.8


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 TraesCS2D01G326600 chr2D 419802408 419806100 3692 True 6820.000000 6820 100.000000 1 3693 1 chr2D.!!$R1 3692
1 TraesCS2D01G326600 chr2B 492288203 492291127 2924 True 4684.000000 4684 95.679000 539 3447 1 chr2B.!!$R2 2908
2 TraesCS2D01G326600 chr2A 570148516 570152627 4111 False 1588.666667 4137 93.575667 610 3693 3 chr2A.!!$F3 3083
3 TraesCS2D01G326600 chr2A 685662227 685662774 547 True 732.000000 732 91.058000 1 538 1 chr2A.!!$R1 537
4 TraesCS2D01G326600 chr1D 50956723 50957270 547 True 787.000000 787 92.909000 1 538 1 chr1D.!!$R2 537
5 TraesCS2D01G326600 chr1D 50951215 50951750 535 True 765.000000 765 92.449000 1 538 1 chr1D.!!$R1 537
6 TraesCS2D01G326600 chr1D 448435024 448435561 537 True 728.000000 728 91.160000 1 538 1 chr1D.!!$R3 537
7 TraesCS2D01G326600 chr5D 407752127 407752667 540 True 758.000000 758 92.096000 1 538 1 chr5D.!!$R1 537
8 TraesCS2D01G326600 chr7D 612623860 612624406 546 True 749.000000 749 91.455000 1 545 1 chr7D.!!$R1 544
9 TraesCS2D01G326600 chr6A 74903377 74903916 539 False 736.000000 736 91.360000 1 538 1 chr6A.!!$F1 537
10 TraesCS2D01G326600 chr3D 581139395 581139945 550 False 734.000000 734 90.975000 1 543 1 chr3D.!!$F1 542
11 TraesCS2D01G326600 chr4D 49780743 49781288 545 False 730.000000 730 91.075000 1 538 1 chr4D.!!$F1 537

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
349 365 0.100682 GCGCGTGGATGTCTCTCTTA 59.899 55.0 8.43 0.0 0.0 2.10 F
916 1748 0.266753 AATAACCTCCGCCCTCCCTA 59.733 55.0 0.00 0.0 0.0 3.53 F
1789 2853 1.434513 ATGCAAGGTCAAGGGGTGGA 61.435 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
1443 2505 1.078426 AACTTCCGGGATTGGCGAG 60.078 57.895 0.00 0.00 0.00 5.03 R
2188 3252 1.271656 GTCCAAGCTCTTGCATTGCTT 59.728 47.619 10.49 13.29 46.38 3.91 R
2922 3996 1.136828 TGTCCACTTGCCTTGGTAGT 58.863 50.000 0.00 0.00 35.42 2.73 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
42 43 2.281208 TCGGGAACTTTGTGGCGG 60.281 61.111 0.00 0.00 0.00 6.13
209 211 5.803461 CGTTCGTATTCAATCTCCACTACAA 59.197 40.000 0.00 0.00 0.00 2.41
294 299 2.892425 CTCGGCTCATTCCCGCAC 60.892 66.667 0.00 0.00 45.19 5.34
349 365 0.100682 GCGCGTGGATGTCTCTCTTA 59.899 55.000 8.43 0.00 0.00 2.10
363 379 7.287512 TGTCTCTCTTATTCTCATCCTCATG 57.712 40.000 0.00 0.00 0.00 3.07
379 395 3.607741 CTCATGCATGTGGAGAAAGAGT 58.392 45.455 25.43 0.00 0.00 3.24
416 436 5.962031 TCCAACTCCCTCTAAACTAGCAATA 59.038 40.000 0.00 0.00 0.00 1.90
419 439 7.419057 CCAACTCCCTCTAAACTAGCAATATGA 60.419 40.741 0.00 0.00 0.00 2.15
439 459 8.928270 ATATGAGACTAAACTTTAGTTCCACG 57.072 34.615 14.17 0.00 37.25 4.94
446 466 3.470645 ACTTTAGTTCCACGTCTTGCT 57.529 42.857 0.00 0.00 0.00 3.91
492 513 7.950684 GGGCCTCTAGGATTTATTAGGAATTTT 59.049 37.037 0.84 0.00 37.39 1.82
514 535 2.576191 TGAAACTGCTATTGGGCTAGGT 59.424 45.455 0.00 0.00 0.00 3.08
555 577 4.631813 CCAGCAGTATTCACTCTTAACACC 59.368 45.833 0.00 0.00 30.46 4.16
579 601 8.902806 ACCTTTCTATCAATGAAATAATTCGCA 58.097 29.630 0.00 0.00 38.46 5.10
913 1744 1.148498 CCAATAACCTCCGCCCTCC 59.852 63.158 0.00 0.00 0.00 4.30
916 1748 0.266753 AATAACCTCCGCCCTCCCTA 59.733 55.000 0.00 0.00 0.00 3.53
1207 2269 3.775866 AGAAGAAGAGGGTAAGTAAGGGC 59.224 47.826 0.00 0.00 0.00 5.19
1312 2374 1.815132 GATCTGCCGATTTTTCGTGC 58.185 50.000 0.00 0.00 0.00 5.34
1443 2505 7.712204 TTTATGTATTCTTGGTCTTTTCCCC 57.288 36.000 0.00 0.00 0.00 4.81
1445 2507 4.918588 TGTATTCTTGGTCTTTTCCCCTC 58.081 43.478 0.00 0.00 0.00 4.30
1624 2688 9.525409 GATATTTTGGGTTCAAATTCTGATCTG 57.475 33.333 0.00 0.00 41.84 2.90
1789 2853 1.434513 ATGCAAGGTCAAGGGGTGGA 61.435 55.000 0.00 0.00 0.00 4.02
2188 3252 5.547465 TCAAAAAGAACAGAGCCTATTCGA 58.453 37.500 0.00 0.00 0.00 3.71
2239 3303 0.242825 CGTTCCGTCCACAGAGCTTA 59.757 55.000 0.00 0.00 0.00 3.09
2446 3510 0.324738 ACAAGAGGATCCTCGAGGCA 60.325 55.000 31.51 15.79 46.90 4.75
2452 3516 1.744639 GATCCTCGAGGCAGATGCA 59.255 57.895 27.39 8.01 44.36 3.96
2563 3630 1.066787 GGTCCAAGACACTAGGCTGTC 60.067 57.143 0.00 5.54 40.91 3.51
2795 3862 5.163794 CCTTTTGTTGTTACAGTTCGTGAGT 60.164 40.000 0.00 0.00 35.28 3.41
2891 3965 7.442666 CACCTAAGTCTAGTTCTTGCTCTTTTT 59.557 37.037 11.21 0.00 0.00 1.94
2927 4001 7.918562 GTGATGATCTTGAGACTTTCTACTACC 59.081 40.741 0.00 0.00 0.00 3.18
2960 4034 6.592607 GTGGACATTCTCCTGTATTAAAACGA 59.407 38.462 0.00 0.00 40.26 3.85
3190 4272 9.595823 AATATTTCGCTATTGTAGTACAACTGT 57.404 29.630 17.79 5.44 41.40 3.55
3206 4288 1.003118 ACTGTGTGTGGTGTGTTGTCT 59.997 47.619 0.00 0.00 0.00 3.41
3207 4289 2.083774 CTGTGTGTGGTGTGTTGTCTT 58.916 47.619 0.00 0.00 0.00 3.01
3267 4350 0.595095 GTTTTGACTCAGCCTGGCAG 59.405 55.000 22.65 13.84 0.00 4.85
3326 4409 7.513371 AGAAACTCCTTGGACTATCTATACG 57.487 40.000 0.00 0.00 0.00 3.06
3441 4525 8.585881 TCTTATTATACTCCCTCCATTTCTTCG 58.414 37.037 0.00 0.00 0.00 3.79
3654 4770 6.481313 GTGAAGTAAAAAGAAACGTAGGGAGT 59.519 38.462 0.00 0.00 0.00 3.85
3661 4777 5.635417 AAGAAACGTAGGGAGTACTACAC 57.365 43.478 7.57 0.00 42.68 2.90
3662 4778 4.655963 AGAAACGTAGGGAGTACTACACA 58.344 43.478 7.57 0.00 42.68 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.971695 CTCCCGCCACAAAGTTCCC 60.972 63.158 0.00 0.00 0.00 3.97
88 90 4.161565 TCCTTCTCTTGCGCCTATAAAAGA 59.838 41.667 4.18 5.08 0.00 2.52
209 211 2.468532 CGGAAGCTGAAACGTTTTGT 57.531 45.000 15.89 0.00 0.00 2.83
349 365 3.137728 TCCACATGCATGAGGATGAGAAT 59.862 43.478 33.82 7.46 45.45 2.40
379 395 2.292323 GGAGTTGGACCTCTAAGGGAGA 60.292 54.545 0.00 0.00 44.45 3.71
416 436 6.756221 ACGTGGAACTAAAGTTTAGTCTCAT 58.244 36.000 24.84 12.09 38.56 2.90
419 439 6.402456 AGACGTGGAACTAAAGTTTAGTCT 57.598 37.500 24.84 16.18 38.56 3.24
439 459 1.666888 CCCATTCGTGCAAAGCAAGAC 60.667 52.381 7.11 0.00 45.42 3.01
446 466 2.650196 GCAGCCCATTCGTGCAAA 59.350 55.556 0.00 0.00 37.16 3.68
492 513 3.010138 ACCTAGCCCAATAGCAGTTTCAA 59.990 43.478 0.00 0.00 34.23 2.69
514 535 6.267471 ACTGCTGGAATTTTGTCTATTTTGGA 59.733 34.615 0.00 0.00 0.00 3.53
637 671 2.419667 GCCTCTTGTAAACGGCACTAA 58.580 47.619 0.00 0.00 37.29 2.24
642 676 2.396157 CGGGCCTCTTGTAAACGGC 61.396 63.158 0.84 0.00 36.78 5.68
699 734 3.507377 AAGGACGGTTTGGGGGCTG 62.507 63.158 0.00 0.00 0.00 4.85
700 735 3.182996 AAGGACGGTTTGGGGGCT 61.183 61.111 0.00 0.00 0.00 5.19
701 736 2.675423 GAAGGACGGTTTGGGGGC 60.675 66.667 0.00 0.00 0.00 5.80
1207 2269 2.674563 ATCACACCACACACACGGGG 62.675 60.000 0.00 0.00 0.00 5.73
1443 2505 1.078426 AACTTCCGGGATTGGCGAG 60.078 57.895 0.00 0.00 0.00 5.03
1445 2507 2.406616 CCAACTTCCGGGATTGGCG 61.407 63.158 14.74 0.00 36.72 5.69
1624 2688 3.092334 AGACCAATCCAAAACGCAAAC 57.908 42.857 0.00 0.00 0.00 2.93
1765 2829 2.753966 CCTTGACCTTGCATCGGCG 61.754 63.158 0.00 0.00 45.35 6.46
1789 2853 2.836981 CTCCTTGTCATCCTCCAGAACT 59.163 50.000 0.00 0.00 0.00 3.01
2188 3252 1.271656 GTCCAAGCTCTTGCATTGCTT 59.728 47.619 10.49 13.29 46.38 3.91
2239 3303 1.834263 GACTGCTTGGAGATACTGGGT 59.166 52.381 0.00 0.00 0.00 4.51
2452 3516 4.954970 CTGCACCCTGGGCAACGT 62.955 66.667 14.08 0.00 41.39 3.99
2856 3925 8.140112 AGAACTAGACTTAGGTGAACATGATT 57.860 34.615 0.00 0.00 0.00 2.57
2857 3926 7.726033 AGAACTAGACTTAGGTGAACATGAT 57.274 36.000 0.00 0.00 0.00 2.45
2913 3987 4.593634 ACTTGCCTTGGTAGTAGAAAGTCT 59.406 41.667 0.00 0.00 0.00 3.24
2922 3996 1.136828 TGTCCACTTGCCTTGGTAGT 58.863 50.000 0.00 0.00 35.42 2.73
2927 4001 1.815003 GGAGAATGTCCACTTGCCTTG 59.185 52.381 0.00 0.00 46.10 3.61
3189 4271 2.747446 AGAAAGACAACACACCACACAC 59.253 45.455 0.00 0.00 0.00 3.82
3190 4272 3.006940 GAGAAAGACAACACACCACACA 58.993 45.455 0.00 0.00 0.00 3.72
3236 4319 5.570589 GCTGAGTCAAAACACATTATGAAGC 59.429 40.000 0.00 0.00 0.00 3.86
3267 4350 5.922544 ACAGTTCACATTTGCATCTTAAAGC 59.077 36.000 0.00 0.00 0.00 3.51
3349 4432 8.133627 GGTATCATACGAAGAAACACTAGCTTA 58.866 37.037 0.00 0.00 0.00 3.09
3357 4440 7.572353 GCAAAACAGGTATCATACGAAGAAACA 60.572 37.037 0.00 0.00 0.00 2.83
3365 4448 5.991328 AGATGCAAAACAGGTATCATACG 57.009 39.130 0.00 0.00 30.84 3.06
3398 4482 3.795561 AAGATCGAACGCAAGAAACTG 57.204 42.857 0.00 0.00 43.62 3.16
3654 4770 8.474831 ACATGAGTAATAGCACAATGTGTAGTA 58.525 33.333 15.36 7.06 35.75 1.82
3661 4777 7.485913 GGTCAAAACATGAGTAATAGCACAATG 59.514 37.037 0.00 0.00 39.19 2.82
3662 4778 7.394359 AGGTCAAAACATGAGTAATAGCACAAT 59.606 33.333 0.00 0.00 39.19 2.71


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

AutoCloner maintained by Alex Coulton.