Multiple sequence alignment - TraesCS2B01G365300

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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 TraesCS2B01G365300 chr2B 100.000 3964 0 0 1 3964 519187836 519183873 0.000000e+00 7321
1 TraesCS2B01G365300 chr2A 96.357 3980 112 18 1 3964 585215307 585211345 0.000000e+00 6516
2 TraesCS2B01G365300 chr2D 92.373 3527 195 33 467 3964 441576675 441573194 0.000000e+00 4955
3 TraesCS2B01G365300 chr2D 95.522 469 17 3 1 469 441577252 441576788 0.000000e+00 747
4 TraesCS2B01G365300 chr5B 87.973 873 90 7 2136 3000 19791268 19790403 0.000000e+00 1016
5 TraesCS2B01G365300 chr5B 81.832 655 72 24 1455 2093 19792018 19791395 1.270000e-139 507
6 TraesCS2B01G365300 chr5B 85.271 516 38 7 762 1262 19792789 19792297 7.650000e-137 497
7 TraesCS2B01G365300 chr5B 85.161 310 31 8 2 306 19793186 19792887 1.790000e-78 303
8 TraesCS2B01G365300 chr6B 84.549 233 32 4 2732 2962 435832622 435832392 1.110000e-55 228
9 TraesCS2B01G365300 chr6A 84.549 233 32 4 2732 2962 392193952 392193722 1.110000e-55 228


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 TraesCS2B01G365300 chr2B 519183873 519187836 3963 True 7321.00 7321 100.00000 1 3964 1 chr2B.!!$R1 3963
1 TraesCS2B01G365300 chr2A 585211345 585215307 3962 True 6516.00 6516 96.35700 1 3964 1 chr2A.!!$R1 3963
2 TraesCS2B01G365300 chr2D 441573194 441577252 4058 True 2851.00 4955 93.94750 1 3964 2 chr2D.!!$R1 3963
3 TraesCS2B01G365300 chr5B 19790403 19793186 2783 True 580.75 1016 85.05925 2 3000 4 chr5B.!!$R1 2998

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
51 52 1.910772 CCCCTGGGCTAGATCTCGG 60.911 68.421 7.39 0.0 0.0 4.63 F
1074 1204 4.082625 CCATTTGTCAAAGCAGCATCACTA 60.083 41.667 4.03 0.0 0.0 2.74 F
1447 1594 0.888619 AGAATCTCAGCGTTCCGTCA 59.111 50.000 0.00 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1411 0.109132 AGCCTGTGCAATTTAAGCGC 60.109 50.000 0.0 0.0 42.56 5.92 R
2359 2745 2.030958 GAACCCACCGTAACTGGCG 61.031 63.158 0.0 0.0 0.00 5.69 R
3349 3748 2.147150 GGTGAAGTGTTCTGAAGGAGC 58.853 52.381 0.0 0.0 0.00 4.70 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
51 52 1.910772 CCCCTGGGCTAGATCTCGG 60.911 68.421 7.39 0.00 0.00 4.63
258 264 7.972832 TTCAAAAGCCTCTACTCGATAAAAA 57.027 32.000 0.00 0.00 0.00 1.94
439 445 6.975772 TGGCTGCAATACCGATAAAATAAAAC 59.024 34.615 0.50 0.00 0.00 2.43
750 871 6.895756 TCCTTCAATTAGTGTAGGCTTAGAGA 59.104 38.462 0.45 0.00 42.98 3.10
751 872 7.068839 TCCTTCAATTAGTGTAGGCTTAGAGAG 59.931 40.741 0.45 0.00 42.98 3.20
852 982 7.172868 AGCTCATAACTCCTGATATCATGAG 57.827 40.000 27.07 27.07 42.10 2.90
1074 1204 4.082625 CCATTTGTCAAAGCAGCATCACTA 60.083 41.667 4.03 0.00 0.00 2.74
1276 1412 6.652900 TGGGTTCTAGCCAAAAATAAATTTGC 59.347 34.615 0.00 0.00 43.74 3.68
1445 1592 2.069273 CAAAGAATCTCAGCGTTCCGT 58.931 47.619 0.00 0.00 0.00 4.69
1446 1593 1.997669 AAGAATCTCAGCGTTCCGTC 58.002 50.000 0.00 0.00 0.00 4.79
1447 1594 0.888619 AGAATCTCAGCGTTCCGTCA 59.111 50.000 0.00 0.00 0.00 4.35
1467 1614 6.410845 CGTCATAATTTGTACAACCTCATCG 58.589 40.000 8.07 4.99 0.00 3.84
1612 1888 5.479724 TGACTGGGAATCAAAATTATGCACA 59.520 36.000 0.00 0.00 0.00 4.57
1873 2155 1.079503 CTGTTCTAGAAGGCAACCGC 58.920 55.000 5.12 0.00 37.44 5.68
2002 2298 2.092968 TCCAGTATCTTGATGGGCACAC 60.093 50.000 0.00 0.00 34.71 3.82
2049 2345 6.111768 ACATTTCAGAAAGTGCATATCGAC 57.888 37.500 1.28 0.00 0.00 4.20
2144 2526 8.442374 TCCCTAAACTAACAACCTAACTTGATT 58.558 33.333 0.00 0.00 0.00 2.57
2359 2745 3.372206 CAGACATCCCAGAATCAACGAAC 59.628 47.826 0.00 0.00 0.00 3.95
2382 2768 2.140717 CAGTTACGGTGGGTTCTTCAC 58.859 52.381 0.00 0.00 34.61 3.18
2473 2862 2.157738 ACATTGAGCTGGTTCAGAAGC 58.842 47.619 5.33 5.33 39.82 3.86
2478 2867 0.471617 AGCTGGTTCAGAAGCACAGT 59.528 50.000 11.11 0.00 42.06 3.55
2682 3076 8.469200 TCATGGCAGAAATTTCTTCGAATTTAT 58.531 29.630 18.16 2.62 38.85 1.40
3059 3454 6.029607 CACATCGCAAAGCAATAGTAAATGT 58.970 36.000 0.00 0.00 0.00 2.71
3124 3523 2.762535 TGCAAGTACTAGGGTGCTTC 57.237 50.000 16.15 0.00 44.36 3.86
3145 3544 6.969473 GCTTCCAGAATGAATTTAACTACAGC 59.031 38.462 0.00 0.00 39.69 4.40
3163 3562 3.502211 ACAGCCATGCAAGTACTAAACAC 59.498 43.478 0.00 0.00 0.00 3.32
3203 3602 8.792633 TGAATTTAACTTACAATCTCACCTTGG 58.207 33.333 0.00 0.00 0.00 3.61
3322 3721 8.608844 AACTAACAAGTTGAGTGAAAGATAGG 57.391 34.615 10.54 0.00 0.00 2.57
3349 3748 8.944029 AGAACAAAGAACTAATGATGTCTCATG 58.056 33.333 0.00 0.00 41.34 3.07
3535 3948 7.962441 ACTTTTTGCCTCACCTTGTATAAAAT 58.038 30.769 0.00 0.00 0.00 1.82
3596 4009 1.909302 GGTCAGAGTCCATTCCTCCAA 59.091 52.381 0.00 0.00 0.00 3.53
3621 4034 4.461781 CCAGGAGTTCTGATGCTGAAATTT 59.538 41.667 0.00 0.00 46.18 1.82
3651 4064 6.994496 TCAATCATGTTCAAGAACTGAAGAGT 59.006 34.615 13.49 3.89 44.83 3.24
3656 4069 3.558931 TCAAGAACTGAAGAGTGGCAA 57.441 42.857 0.00 0.00 30.61 4.52
3657 4070 3.470709 TCAAGAACTGAAGAGTGGCAAG 58.529 45.455 0.00 0.00 30.61 4.01
3684 4098 0.188342 AAGAGGCACCCAACAATGGT 59.812 50.000 0.00 0.00 46.01 3.55
3749 4163 6.272318 CACTTGGCTGTTCAGATTTTTAACA 58.728 36.000 3.84 0.00 0.00 2.41
3860 4275 3.270877 CCACAGAAATAGGTGTAGCCAC 58.729 50.000 0.00 0.00 40.61 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.330701 AGGGGACTAAATGCTCAAACAGA 59.669 43.478 0.00 0.00 40.61 3.41
51 52 9.294030 GATATGATTGTTCATTGGTCTTTCAAC 57.706 33.333 0.00 0.00 42.61 3.18
152 158 5.250774 AGAACCAAGCCTAGTTCATCCTTAA 59.749 40.000 11.54 0.00 43.89 1.85
284 290 4.442893 CCTGTTCATTGCCGTCTCCTAATA 60.443 45.833 0.00 0.00 0.00 0.98
339 345 6.323739 GGTTGGGAATATTATCACACCACAAT 59.676 38.462 0.00 0.00 30.98 2.71
347 353 7.605449 CCATGATTGGTTGGGAATATTATCAC 58.395 38.462 0.00 0.00 38.30 3.06
439 445 7.649973 AGTTAGAGCATACATACTAGAAACGG 58.350 38.462 0.00 0.00 0.00 4.44
750 871 4.229582 TGGAAATATTTAGGCCTGTCCACT 59.770 41.667 17.99 0.00 37.29 4.00
751 872 4.532834 TGGAAATATTTAGGCCTGTCCAC 58.467 43.478 17.99 0.00 37.29 4.02
1074 1204 5.747342 TCCTTGCCGTTGTATATAACCTTT 58.253 37.500 6.76 0.00 0.00 3.11
1275 1411 0.109132 AGCCTGTGCAATTTAAGCGC 60.109 50.000 0.00 0.00 42.56 5.92
1276 1412 2.253603 GAAGCCTGTGCAATTTAAGCG 58.746 47.619 0.00 0.00 41.13 4.68
1445 1592 9.256477 GTATCGATGAGGTTGTACAAATTATGA 57.744 33.333 10.51 3.54 0.00 2.15
1446 1593 8.214472 CGTATCGATGAGGTTGTACAAATTATG 58.786 37.037 10.51 0.00 0.00 1.90
1447 1594 7.384115 CCGTATCGATGAGGTTGTACAAATTAT 59.616 37.037 10.51 4.54 0.00 1.28
1467 1614 5.163893 TGCAAAGTTCTTTTCGATCCGTATC 60.164 40.000 0.00 0.00 0.00 2.24
1873 2155 1.689273 CTAGTGCTTAGGTGGGCTAGG 59.311 57.143 0.00 0.00 0.00 3.02
2002 2298 8.573035 TGTACTTTTGCCTTGTAATTAAGAAGG 58.427 33.333 15.78 15.78 39.51 3.46
2049 2345 7.594015 GCAAAATATGATATTTCTGCAGACAGG 59.406 37.037 18.03 0.00 44.59 4.00
2144 2526 3.199946 GTCAGGATCCACCATCACCTAAA 59.800 47.826 15.82 0.00 42.04 1.85
2359 2745 2.030958 GAACCCACCGTAACTGGCG 61.031 63.158 0.00 0.00 0.00 5.69
2416 2805 4.689612 TCTTAGGCAAGTGTTCAACTCT 57.310 40.909 0.00 0.00 38.56 3.24
3059 3454 6.045072 ACTAAGATACATGAAACGGTCCAA 57.955 37.500 0.00 0.00 0.00 3.53
3124 3523 6.757897 TGGCTGTAGTTAAATTCATTCTGG 57.242 37.500 0.00 0.00 0.00 3.86
3145 3544 3.071479 ACCGTGTTTAGTACTTGCATGG 58.929 45.455 20.99 20.99 40.85 3.66
3163 3562 3.369546 AAATTCACTCCAAAAGCACCG 57.630 42.857 0.00 0.00 0.00 4.94
3322 3721 8.539770 TGAGACATCATTAGTTCTTTGTTCTC 57.460 34.615 0.00 0.00 0.00 2.87
3349 3748 2.147150 GGTGAAGTGTTCTGAAGGAGC 58.853 52.381 0.00 0.00 0.00 4.70
3447 3859 4.286032 AGTTTCTACCCTGCACATAACTGA 59.714 41.667 0.00 0.00 0.00 3.41
3535 3948 6.005198 ACAAACCCGGACTAATTTGTAATCA 58.995 36.000 0.73 0.00 42.06 2.57
3551 3964 3.977244 GGCACTGGCACAAACCCG 61.977 66.667 0.00 0.00 43.71 5.28
3596 4009 2.475155 TCAGCATCAGAACTCCTGGAT 58.525 47.619 0.00 0.00 43.12 3.41
3621 4034 7.167535 TCAGTTCTTGAACATGATTGATGGTA 58.832 34.615 14.80 0.00 36.23 3.25
3651 4064 1.210478 GCCTCTTGGAGTATCTTGCCA 59.790 52.381 0.00 0.00 34.57 4.92
3656 4069 1.273838 TGGGTGCCTCTTGGAGTATCT 60.274 52.381 0.00 0.00 34.57 1.98
3657 4070 1.204146 TGGGTGCCTCTTGGAGTATC 58.796 55.000 0.00 0.00 34.57 2.24
3860 4275 5.231357 GTCATTGCACATTGTTAGCATCATG 59.769 40.000 2.99 5.42 38.19 3.07


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

AutoCloner maintained by Alex Coulton.