Multiple sequence alignment - TraesCS2B01G333200

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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 TraesCS2B01G333200 chr2B 100.000 2723 0 0 1568 4290 476460657 476457935 0.000000e+00 5029.0
1 TraesCS2B01G333200 chr2B 100.000 1399 0 0 1 1399 476462224 476460826 0.000000e+00 2584.0
2 TraesCS2B01G333200 chr2A 97.449 1764 27 6 2533 4290 539012195 539013946 0.000000e+00 2992.0
3 TraesCS2B01G333200 chr2A 97.514 1408 17 5 1 1399 539009508 539010906 0.000000e+00 2390.0
4 TraesCS2B01G333200 chr2A 95.921 956 12 4 1568 2496 539011240 539012195 0.000000e+00 1524.0
5 TraesCS2B01G333200 chr2D 96.005 1627 53 5 2666 4290 402239456 402241072 0.000000e+00 2634.0
6 TraesCS2B01G333200 chr2D 96.869 1022 22 6 331 1348 402236237 402237252 0.000000e+00 1701.0
7 TraesCS2B01G333200 chr2D 95.553 787 15 6 1568 2350 402237710 402238480 0.000000e+00 1242.0
8 TraesCS2B01G333200 chr2D 93.731 335 5 3 1 332 402235590 402235911 4.990000e-134 488.0
9 TraesCS2B01G333200 chr2D 96.983 232 7 0 2395 2626 402238850 402239081 1.450000e-104 390.0
10 TraesCS2B01G333200 chr2D 94.444 36 1 1 2614 2648 402239439 402239474 2.000000e-03 54.7
11 TraesCS2B01G333200 chr6A 90.805 87 5 2 340 425 66388081 66388165 3.510000e-21 113.0
12 TraesCS2B01G333200 chr5D 90.698 86 6 2 339 422 516792225 516792140 3.510000e-21 113.0
13 TraesCS2B01G333200 chr5D 88.764 89 9 1 335 422 297499914 297499826 1.630000e-19 108.0
14 TraesCS2B01G333200 chr5B 88.172 93 8 3 339 429 711236732 711236641 1.630000e-19 108.0
15 TraesCS2B01G333200 chr5B 87.640 89 9 2 335 422 337831165 337831078 7.590000e-18 102.0
16 TraesCS2B01G333200 chr1A 87.356 87 9 1 339 423 490312117 490312203 9.820000e-17 99.0
17 TraesCS2B01G333200 chr1D 87.059 85 11 0 339 423 476230677 476230761 3.530000e-16 97.1
18 TraesCS2B01G333200 chr4D 91.379 58 5 0 2293 2350 190466160 190466217 3.560000e-11 80.5


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 TraesCS2B01G333200 chr2B 476457935 476462224 4289 True 3806.50 5029 100.000000 1 4290 2 chr2B.!!$R1 4289
1 TraesCS2B01G333200 chr2A 539009508 539013946 4438 False 2302.00 2992 96.961333 1 4290 3 chr2A.!!$F1 4289
2 TraesCS2B01G333200 chr2D 402235590 402241072 5482 False 1084.95 2634 95.597500 1 4290 6 chr2D.!!$F1 4289

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
981 1323 0.035915 GGCCACCTCTCTTTGGTCTC 60.036 60.000 0.0 0.0 34.41 3.36 F
2382 2992 2.165167 CAAAGCTTGAGATGGGCTTGA 58.835 47.619 0.0 0.0 44.17 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 2992 0.690762 ACAGTTGAACCGGTATGGCT 59.309 50.000 8.00 1.06 43.94 4.75 R
3857 5153 2.399611 GCATGTTGAGGCGCGTAC 59.600 61.111 8.43 0.00 0.00 3.67 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
40 41 5.413833 CCACATGTTAGCTTCTTCTCATTGT 59.586 40.000 0.00 0.00 0.00 2.71
41 42 6.595326 CCACATGTTAGCTTCTTCTCATTGTA 59.405 38.462 0.00 0.00 0.00 2.41
42 43 7.281774 CCACATGTTAGCTTCTTCTCATTGTAT 59.718 37.037 0.00 0.00 0.00 2.29
43 44 9.317936 CACATGTTAGCTTCTTCTCATTGTATA 57.682 33.333 0.00 0.00 0.00 1.47
44 45 9.890629 ACATGTTAGCTTCTTCTCATTGTATAA 57.109 29.630 0.00 0.00 0.00 0.98
495 835 2.705658 TCACACTCACAGGAAAGACCAT 59.294 45.455 0.00 0.00 42.04 3.55
767 1109 4.442192 GGAATCGCTTTATGTGGAGAGAGT 60.442 45.833 0.00 0.00 0.00 3.24
794 1136 5.863935 GCAGTGATTCCATTGTAAAGAAACC 59.136 40.000 0.00 0.00 33.17 3.27
981 1323 0.035915 GGCCACCTCTCTTTGGTCTC 60.036 60.000 0.00 0.00 34.41 3.36
2382 2992 2.165167 CAAAGCTTGAGATGGGCTTGA 58.835 47.619 0.00 0.00 44.17 3.02
2462 3381 3.536956 AAGAATTTCCATGCATGCCAG 57.463 42.857 21.69 8.13 0.00 4.85
2731 4021 2.501723 TCTAGAGCCAAGGTTGCTTAGG 59.498 50.000 0.00 0.00 39.69 2.69
2790 4080 4.566759 CAGACACACGGATTACCACATAAG 59.433 45.833 0.00 0.00 35.59 1.73
2846 4138 2.239654 TGATCCATCCAAGGACTGAACC 59.760 50.000 0.00 0.00 41.30 3.62
2959 4251 8.681486 CATGACATCAGGGAAGAACAAATATA 57.319 34.615 0.00 0.00 0.00 0.86
2960 4252 9.293404 CATGACATCAGGGAAGAACAAATATAT 57.707 33.333 0.00 0.00 0.00 0.86
3096 4388 5.809464 TGTATAAGAATTTCAGTGCATGCG 58.191 37.500 14.09 0.00 0.00 4.73
3333 4626 5.221561 TGCTCACTTACAGCACCTACTTTAA 60.222 40.000 0.00 0.00 42.09 1.52
3335 4628 6.371825 GCTCACTTACAGCACCTACTTTAATT 59.628 38.462 0.00 0.00 36.82 1.40
3371 4664 3.973206 AACGAATGTATGTCCACTGGA 57.027 42.857 0.00 0.00 0.00 3.86
3407 4700 3.305950 CCACTGTATCAGGCTATCAGCTC 60.306 52.174 0.00 0.00 41.99 4.09
3408 4701 3.320256 CACTGTATCAGGCTATCAGCTCA 59.680 47.826 0.00 0.00 41.99 4.26
3409 4702 3.573538 ACTGTATCAGGCTATCAGCTCAG 59.426 47.826 0.00 0.00 41.99 3.35
3410 4703 2.298446 TGTATCAGGCTATCAGCTCAGC 59.702 50.000 0.00 0.00 41.99 4.26
3411 4704 1.719529 ATCAGGCTATCAGCTCAGCT 58.280 50.000 0.00 0.00 41.99 4.24
3451 4744 2.808543 AGCCAGTTTTCAGAAGTTAGCG 59.191 45.455 0.00 0.00 0.00 4.26
3481 4777 8.978874 ATTAATTGATGATGTAGTAGTGCCAA 57.021 30.769 0.00 0.00 0.00 4.52
3482 4778 6.932356 AATTGATGATGTAGTAGTGCCAAG 57.068 37.500 0.00 0.00 0.00 3.61
3483 4779 5.675684 TTGATGATGTAGTAGTGCCAAGA 57.324 39.130 0.00 0.00 0.00 3.02
3651 4947 8.958119 TCTATGTATTGAAATAACAGGTCACC 57.042 34.615 0.00 0.00 0.00 4.02
3857 5153 0.908198 AGACTTCTAAGCCAGGCTGG 59.092 55.000 29.44 29.44 39.62 4.85
4252 5551 1.541233 CGAAGCAGGTTCTTGACAGGT 60.541 52.381 10.58 0.00 32.33 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.286800 GGTGAAAGCATTGCGTATACATTTATA 58.713 33.333 2.38 0.00 0.00 0.98
41 42 7.138736 GGTGAAAGCATTGCGTATACATTTAT 58.861 34.615 2.38 0.00 0.00 1.40
42 43 6.094186 TGGTGAAAGCATTGCGTATACATTTA 59.906 34.615 2.38 0.00 40.88 1.40
43 44 5.105957 TGGTGAAAGCATTGCGTATACATTT 60.106 36.000 2.38 0.00 40.88 2.32
44 45 4.397730 TGGTGAAAGCATTGCGTATACATT 59.602 37.500 2.38 0.00 40.88 2.71
45 46 3.944650 TGGTGAAAGCATTGCGTATACAT 59.055 39.130 2.38 0.00 40.88 2.29
46 47 3.339141 TGGTGAAAGCATTGCGTATACA 58.661 40.909 2.38 0.00 40.88 2.29
203 204 5.312079 AGAGTAGCAATCATAATCCCAAGC 58.688 41.667 0.00 0.00 0.00 4.01
495 835 2.630580 GGGCCAGTGTACCATTTTTCAA 59.369 45.455 4.39 0.00 0.00 2.69
767 1109 5.559770 TCTTTACAATGGAATCACTGCAGA 58.440 37.500 23.35 0.00 0.00 4.26
794 1136 1.420138 AGTAGGTGTGGTGGTTCAAGG 59.580 52.381 0.00 0.00 0.00 3.61
882 1224 3.492829 GGCCAGCAGGTGAGTACTTATAC 60.493 52.174 0.00 0.00 37.19 1.47
953 1295 2.683768 AGAGAGGTGGCCCTATTACTG 58.316 52.381 0.00 0.00 42.86 2.74
981 1323 3.486375 CCATTTCGCTTGATACTGCACAG 60.486 47.826 0.00 0.00 0.00 3.66
2382 2992 0.690762 ACAGTTGAACCGGTATGGCT 59.309 50.000 8.00 1.06 43.94 4.75
2499 3418 8.752187 ACTATTTTGCTGGTACAATCAATCATT 58.248 29.630 0.00 0.00 38.70 2.57
2502 3421 8.893727 ACTACTATTTTGCTGGTACAATCAATC 58.106 33.333 0.00 0.00 38.70 2.67
2664 3954 6.968131 TGTGCATCTAGTAACTTTGTGATC 57.032 37.500 0.00 0.00 0.00 2.92
2731 4021 7.331791 AGGTAGAGGATGAACTGTGAATTTAC 58.668 38.462 0.00 0.00 0.00 2.01
2774 4064 4.811969 TGTGTCTTATGTGGTAATCCGT 57.188 40.909 0.00 0.00 36.30 4.69
2823 4115 3.634397 TCAGTCCTTGGATGGATCAAC 57.366 47.619 0.00 0.00 38.52 3.18
2959 4251 9.632638 ACCAACATTTCACTTTAGATAGCATAT 57.367 29.630 0.00 0.00 0.00 1.78
2960 4252 9.461312 AACCAACATTTCACTTTAGATAGCATA 57.539 29.630 0.00 0.00 0.00 3.14
2961 4253 7.944729 ACCAACATTTCACTTTAGATAGCAT 57.055 32.000 0.00 0.00 0.00 3.79
2962 4254 7.759489 AACCAACATTTCACTTTAGATAGCA 57.241 32.000 0.00 0.00 0.00 3.49
2977 4269 9.582648 ACATTCCTTTACTAAGTAACCAACATT 57.417 29.630 0.00 0.00 0.00 2.71
3333 4626 7.228706 ACATTCGTTTGACCTCTACTTCAAAAT 59.771 33.333 0.00 0.00 42.02 1.82
3335 4628 6.053005 ACATTCGTTTGACCTCTACTTCAAA 58.947 36.000 0.00 0.00 38.98 2.69
3371 4664 3.297134 ACAGTGGGATGTTGTCACTTT 57.703 42.857 0.00 0.00 39.43 2.66
3408 4701 9.090103 TGGCTAAATCTAATATACAGTGTAGCT 57.910 33.333 9.25 0.00 32.70 3.32
3409 4702 9.360093 CTGGCTAAATCTAATATACAGTGTAGC 57.640 37.037 9.25 3.59 0.00 3.58
3483 4779 9.595823 ACACACGTTAAGCTCATATAATAAACT 57.404 29.630 0.00 0.00 0.00 2.66
3504 4800 5.051891 AGAAATAATTGAGCAGCACACAC 57.948 39.130 0.00 0.00 0.00 3.82
3651 4947 7.143340 TCAATGGGTAGATACTTCGTTATTCG 58.857 38.462 0.00 0.00 41.41 3.34
3857 5153 2.399611 GCATGTTGAGGCGCGTAC 59.600 61.111 8.43 0.00 0.00 3.67
3982 5278 6.967199 CAGTTTTGACAGTTACACCTTCTTTC 59.033 38.462 0.00 0.00 0.00 2.62
4109 5405 5.049405 CCTTGTTCATTGTTCACTCCAGTAC 60.049 44.000 0.00 0.00 0.00 2.73
4252 5551 5.026121 AGATCATCCAGTCACTTGAACCTA 58.974 41.667 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.