Multiple sequence alignment - TraesCS2B01G195800

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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 TraesCS2B01G195800 chr2B 100.000 4181 0 0 1 4181 173463146 173467326 0.000000e+00 7721
1 TraesCS2B01G195800 chr2D 95.004 4223 139 23 1 4181 120550051 120554243 0.000000e+00 6564
2 TraesCS2B01G195800 chr2A 94.780 3314 109 28 341 3611 124377675 124380967 0.000000e+00 5103
3 TraesCS2B01G195800 chr2A 94.177 498 18 4 3695 4181 124380965 124381462 0.000000e+00 749
4 TraesCS2B01G195800 chr2A 88.154 363 22 8 1 343 124377229 124377590 3.010000e-111 412
5 TraesCS2B01G195800 chr3A 82.658 2220 361 21 976 3180 9606851 9604641 0.000000e+00 1945
6 TraesCS2B01G195800 chr3D 83.838 1980 312 8 1205 3180 4068298 4066323 0.000000e+00 1877
7 TraesCS2B01G195800 chrUn 82.701 2029 345 6 1152 3177 242439787 242441812 0.000000e+00 1797
8 TraesCS2B01G195800 chrUn 82.701 2029 345 6 1152 3177 242452822 242454847 0.000000e+00 1797
9 TraesCS2B01G195800 chr3B 82.725 2026 344 6 1158 3180 6309545 6307523 0.000000e+00 1797
10 TraesCS2B01G195800 chr3B 82.379 2026 351 6 1158 3180 6380871 6378849 0.000000e+00 1759


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 TraesCS2B01G195800 chr2B 173463146 173467326 4180 False 7721 7721 100.000000 1 4181 1 chr2B.!!$F1 4180
1 TraesCS2B01G195800 chr2D 120550051 120554243 4192 False 6564 6564 95.004000 1 4181 1 chr2D.!!$F1 4180
2 TraesCS2B01G195800 chr2A 124377229 124381462 4233 False 2088 5103 92.370333 1 4181 3 chr2A.!!$F1 4180
3 TraesCS2B01G195800 chr3A 9604641 9606851 2210 True 1945 1945 82.658000 976 3180 1 chr3A.!!$R1 2204
4 TraesCS2B01G195800 chr3D 4066323 4068298 1975 True 1877 1877 83.838000 1205 3180 1 chr3D.!!$R1 1975
5 TraesCS2B01G195800 chrUn 242439787 242441812 2025 False 1797 1797 82.701000 1152 3177 1 chrUn.!!$F1 2025
6 TraesCS2B01G195800 chrUn 242452822 242454847 2025 False 1797 1797 82.701000 1152 3177 1 chrUn.!!$F2 2025
7 TraesCS2B01G195800 chr3B 6307523 6309545 2022 True 1797 1797 82.725000 1158 3180 1 chr3B.!!$R1 2022
8 TraesCS2B01G195800 chr3B 6378849 6380871 2022 True 1759 1759 82.379000 1158 3180 1 chr3B.!!$R2 2022

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
232 253 0.397941 AAGCTGTGCTAACTGGCTCA 59.602 50.000 0.0 0.0 38.25 4.26 F
466 579 2.178580 CCAGCTTTAATCTGGCCCAAA 58.821 47.619 0.0 0.0 43.88 3.28 F
2021 2169 0.457853 GGCTATGACGTGCTTGTCGA 60.458 55.000 0.0 0.0 41.87 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 2026 2.275318 GCTTTCTGAACCTGATCCTCG 58.725 52.381 0.0 0.0 0.00 4.63 R
2024 2172 3.269381 AGGAGCAATCCCATTTCTTACCA 59.731 43.478 0.0 0.0 0.00 3.25 R
3319 3488 0.250467 GATACACATGGCCCTCGCAT 60.250 55.000 0.0 0.0 36.38 4.73 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
28 29 2.189521 CGGGCTGCGGTAATTCCT 59.810 61.111 0.00 0.00 0.00 3.36
39 40 1.143073 GGTAATTCCTCAATCGCCCCT 59.857 52.381 0.00 0.00 0.00 4.79
122 130 3.199551 GCGCATCAGCCATTTCCA 58.800 55.556 0.30 0.00 37.52 3.53
127 135 1.454479 ATCAGCCATTTCCAGCGGG 60.454 57.895 0.00 0.00 0.00 6.13
141 155 2.125912 CGGGGACAGAGCGACAAG 60.126 66.667 0.00 0.00 0.00 3.16
156 175 2.930562 AAGGAGAGGTTGCCGGCT 60.931 61.111 29.70 6.86 0.00 5.52
195 214 1.137872 CTGTCTCCCCTCAAATCCTCG 59.862 57.143 0.00 0.00 0.00 4.63
219 240 4.495422 CCTACACTGTTAATCGAAGCTGT 58.505 43.478 0.00 0.00 0.00 4.40
232 253 0.397941 AAGCTGTGCTAACTGGCTCA 59.602 50.000 0.00 0.00 38.25 4.26
295 316 3.243816 TGGCTCCACAGCTGCTGA 61.244 61.111 34.28 12.77 46.03 4.26
378 486 5.588648 TGGCAACGAGATTTTTCCTATAAGG 59.411 40.000 0.00 0.00 42.51 2.69
380 488 6.095021 GGCAACGAGATTTTTCCTATAAGGTT 59.905 38.462 0.00 0.00 36.53 3.50
386 494 7.385478 CGAGATTTTTCCTATAAGGTTCCTAGC 59.615 40.741 0.00 0.00 36.53 3.42
428 536 7.467267 CGACTGCATATAATTTACCTTTGCTGT 60.467 37.037 0.00 0.00 41.43 4.40
466 579 2.178580 CCAGCTTTAATCTGGCCCAAA 58.821 47.619 0.00 0.00 43.88 3.28
533 668 7.176515 ACATCTGTGTACAAATTAATTCTGCCA 59.823 33.333 0.00 1.56 36.63 4.92
610 745 8.260818 AGCTGCTCTCTTCTAACAATAAACATA 58.739 33.333 0.00 0.00 0.00 2.29
693 832 6.918022 CACTGTTGTTCCCTTCTTTAAATGTC 59.082 38.462 0.00 0.00 0.00 3.06
868 1009 7.147976 GCAGGAAATTTTCATGTAACTTGTCT 58.852 34.615 20.98 0.00 42.97 3.41
1117 1259 7.343057 TGAAGAGCTTAGATCATCAAGAACCTA 59.657 37.037 2.84 0.00 0.00 3.08
1133 1281 6.435292 AGAACCTACTGGAAGCTTCTTTTA 57.565 37.500 25.05 12.48 37.60 1.52
1386 1534 4.215109 AGTTGTTTGAGTTGGCACCTATT 58.785 39.130 0.00 0.00 0.00 1.73
1440 1588 7.878127 ACATTACTACAAGTTCATGCTACAGTT 59.122 33.333 0.00 0.00 0.00 3.16
1605 1753 9.685276 AGGAGTTTGTTTGATGATATGAATACA 57.315 29.630 0.00 0.00 0.00 2.29
1723 1871 4.952071 TGTGAAATGGAAATGAAAGGCA 57.048 36.364 0.00 0.00 0.00 4.75
1878 2026 4.614535 GCTGTGATTCATGGTTTCTGTCAC 60.615 45.833 0.00 0.00 36.09 3.67
2021 2169 0.457853 GGCTATGACGTGCTTGTCGA 60.458 55.000 0.00 0.00 41.87 4.20
2022 2170 1.346365 GCTATGACGTGCTTGTCGAA 58.654 50.000 0.00 0.00 41.87 3.71
2023 2171 1.724623 GCTATGACGTGCTTGTCGAAA 59.275 47.619 0.00 0.00 41.87 3.46
2024 2172 2.348666 GCTATGACGTGCTTGTCGAAAT 59.651 45.455 0.00 0.00 41.87 2.17
2025 2173 2.880822 ATGACGTGCTTGTCGAAATG 57.119 45.000 0.00 0.00 41.87 2.32
2026 2174 0.865111 TGACGTGCTTGTCGAAATGG 59.135 50.000 0.00 0.00 41.87 3.16
2027 2175 0.865769 GACGTGCTTGTCGAAATGGT 59.134 50.000 0.00 0.00 0.00 3.55
2028 2176 2.063266 GACGTGCTTGTCGAAATGGTA 58.937 47.619 0.00 0.00 0.00 3.25
2029 2177 2.477375 GACGTGCTTGTCGAAATGGTAA 59.523 45.455 0.00 0.00 0.00 2.85
2030 2178 2.478894 ACGTGCTTGTCGAAATGGTAAG 59.521 45.455 0.00 0.00 0.00 2.34
2071 2229 6.926313 ACTCTGGTCAGTTATACTTCACTTC 58.074 40.000 0.00 0.00 0.00 3.01
2586 2749 7.067494 GGCTGTGTTCCTGATACTTTCATTTAT 59.933 37.037 0.00 0.00 32.72 1.40
2587 2750 9.109393 GCTGTGTTCCTGATACTTTCATTTATA 57.891 33.333 0.00 0.00 32.72 0.98
2621 2784 0.590195 GGCTGTGTGAAAGCACTGAG 59.410 55.000 7.16 0.00 45.36 3.35
2836 2999 4.793216 GCTATTGTAAGCGTTCAAACATGG 59.207 41.667 0.00 0.00 31.76 3.66
2877 3040 0.472044 GAGAGATGGAGAAAGGGGGC 59.528 60.000 0.00 0.00 0.00 5.80
2990 3153 8.282256 AGAAATGATAAATAAGGGGCTTACACT 58.718 33.333 0.00 0.00 0.00 3.55
3228 3396 7.352739 GTGAACGACTACTTTCAACAATTCAT 58.647 34.615 0.00 0.00 36.36 2.57
3306 3475 1.656095 GCTTGTAGCGAGCTTGTACAG 59.344 52.381 1.86 6.03 37.84 2.74
3319 3488 6.404403 CGAGCTTGTACAGGTGATACTAGAAA 60.404 42.308 6.86 0.00 31.44 2.52
3330 3499 1.491668 TACTAGAAATGCGAGGGCCA 58.508 50.000 6.18 0.00 38.85 5.36
3339 3508 1.956170 GCGAGGGCCATGTGTATCG 60.956 63.158 6.18 5.39 0.00 2.92
3363 3532 2.351726 GTGGCCTAAAGACATAAGCACG 59.648 50.000 3.32 0.00 0.00 5.34
3364 3533 1.330829 GGCCTAAAGACATAAGCACGC 59.669 52.381 0.00 0.00 0.00 5.34
3372 3546 2.634940 AGACATAAGCACGCCTATCCAT 59.365 45.455 0.00 0.00 0.00 3.41
3454 3628 1.202510 AGAGAGCAGCCGTGATTGATC 60.203 52.381 0.00 0.00 0.00 2.92
3519 3693 2.533266 GACTGGTGTCTGTGTGTCAT 57.467 50.000 0.00 0.00 39.94 3.06
3524 3698 2.138320 GGTGTCTGTGTGTCATGTGAG 58.862 52.381 0.00 0.00 0.00 3.51
3530 3704 1.134431 TGTGTGTCATGTGAGCAGTGT 60.134 47.619 0.00 0.00 0.00 3.55
3572 3746 9.814899 CAATCTCAGAGATGTATATGATAACCC 57.185 37.037 14.02 0.00 34.65 4.11
3608 3782 6.868339 AGGTTTGCAGCTGTTATATTGTTTTC 59.132 34.615 16.64 0.00 0.00 2.29
3636 3810 3.500448 TTTCAGTCCTTATGCACACCA 57.500 42.857 0.00 0.00 0.00 4.17
3653 3827 4.274950 CACACCAAAATTCTACTGTCGGTT 59.725 41.667 0.00 0.00 0.00 4.44
3749 3923 0.523072 CAGGGAAATGTTCTGCACCG 59.477 55.000 0.00 0.00 0.00 4.94
3792 3966 3.673809 GTCGTTGTATGAGTTGGTGAGTC 59.326 47.826 0.00 0.00 0.00 3.36
3846 4020 0.961753 CACCTTTGGACCCTCTTTGC 59.038 55.000 0.00 0.00 0.00 3.68
3877 4051 6.068010 ACTGATTTGTACATCTGTTTTCCCA 58.932 36.000 0.00 0.00 32.93 4.37
4010 4184 0.453390 CCTTTTCCGCATCCTTCTGC 59.547 55.000 0.00 0.00 38.81 4.26
4089 4263 8.431910 TCTATCTCTACTGGGTTAGTTTTTGT 57.568 34.615 0.00 0.00 40.89 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.305219 CGAAGCAAAGGGGCGATTGA 61.305 55.000 0.00 0.00 39.27 2.57
106 108 1.065273 GCTGGAAATGGCTGATGCG 59.935 57.895 0.00 0.00 40.82 4.73
127 135 0.172352 CTCTCCTTGTCGCTCTGTCC 59.828 60.000 0.00 0.00 0.00 4.02
131 145 0.605589 CAACCTCTCCTTGTCGCTCT 59.394 55.000 0.00 0.00 0.00 4.09
139 153 2.930562 AGCCGGCAACCTCTCCTT 60.931 61.111 31.54 0.00 0.00 3.36
184 203 1.482593 AGTGTAGGCCGAGGATTTGAG 59.517 52.381 0.00 0.00 0.00 3.02
195 214 2.608090 GCTTCGATTAACAGTGTAGGCC 59.392 50.000 0.00 0.00 0.00 5.19
219 240 1.055849 TCAACCTGAGCCAGTTAGCA 58.944 50.000 2.18 0.00 34.23 3.49
232 253 7.151976 CGAACCTTTTATTGGAAAATCAACCT 58.848 34.615 0.00 0.00 0.00 3.50
295 316 7.701539 TTGCATAATAATGAACACTTGAGGT 57.298 32.000 0.00 0.00 34.84 3.85
393 501 6.808008 AATTATATGCAGTCGGATGGAAAG 57.192 37.500 0.00 0.00 0.00 2.62
394 502 7.174253 GGTAAATTATATGCAGTCGGATGGAAA 59.826 37.037 0.00 0.00 0.00 3.13
428 536 3.822735 GCTGGGAGCATAAATATTGCAGA 59.177 43.478 0.96 0.00 41.89 4.26
533 668 7.385267 TGCAAACATAGCAAGGATGTTATTTT 58.615 30.769 1.70 0.00 44.75 1.82
630 766 5.674933 AAAGAAAGGACTCGAACATGAAC 57.325 39.130 0.00 0.00 0.00 3.18
693 832 1.341080 AAGCACCCAACCAAGGAATG 58.659 50.000 0.00 0.00 0.00 2.67
868 1009 4.791334 TGAGGACCACCCAGGAAATAATAA 59.209 41.667 0.00 0.00 41.22 1.40
1117 1259 5.036117 TCACTGTAAAAGAAGCTTCCAGT 57.964 39.130 22.81 22.44 32.25 4.00
1133 1281 6.827727 AGACACTGGTTTTTATACTCACTGT 58.172 36.000 0.00 0.00 0.00 3.55
1386 1534 3.235200 CCCACCCAAATTACTGACCAAA 58.765 45.455 0.00 0.00 0.00 3.28
1440 1588 6.289834 TGACAACTCTACAAAAACCCGAATA 58.710 36.000 0.00 0.00 0.00 1.75
1689 1837 7.707624 TTCCATTTCACATAGAAGCTCAAAT 57.292 32.000 0.00 0.00 37.57 2.32
1878 2026 2.275318 GCTTTCTGAACCTGATCCTCG 58.725 52.381 0.00 0.00 0.00 4.63
2021 2169 5.129320 GGAGCAATCCCATTTCTTACCATTT 59.871 40.000 0.00 0.00 0.00 2.32
2022 2170 4.651045 GGAGCAATCCCATTTCTTACCATT 59.349 41.667 0.00 0.00 0.00 3.16
2023 2171 4.078980 AGGAGCAATCCCATTTCTTACCAT 60.079 41.667 0.00 0.00 0.00 3.55
2024 2172 3.269381 AGGAGCAATCCCATTTCTTACCA 59.731 43.478 0.00 0.00 0.00 3.25
2025 2173 3.903467 AGGAGCAATCCCATTTCTTACC 58.097 45.455 0.00 0.00 0.00 2.85
2026 2174 5.685728 AGTAGGAGCAATCCCATTTCTTAC 58.314 41.667 0.00 0.00 0.00 2.34
2027 2175 5.667626 AGAGTAGGAGCAATCCCATTTCTTA 59.332 40.000 0.00 0.00 0.00 2.10
2028 2176 4.476479 AGAGTAGGAGCAATCCCATTTCTT 59.524 41.667 0.00 0.00 0.00 2.52
2029 2177 4.043596 AGAGTAGGAGCAATCCCATTTCT 58.956 43.478 0.00 0.00 0.00 2.52
2030 2178 4.133078 CAGAGTAGGAGCAATCCCATTTC 58.867 47.826 0.00 0.00 0.00 2.17
2590 2753 8.694540 TGCTTTCACACAGCCATTAATAATAAT 58.305 29.630 0.00 0.00 36.33 1.28
2599 2762 1.338973 CAGTGCTTTCACACAGCCATT 59.661 47.619 0.00 0.00 45.49 3.16
2621 2784 3.625649 ATCTGAAAGCCTCCTGAAGTC 57.374 47.619 0.00 0.00 0.00 3.01
2836 2999 5.783111 TCTAAAAATTTCCAAAGCTGCCTC 58.217 37.500 0.00 0.00 0.00 4.70
3015 3178 8.041323 TCTCCAGTTTTGAAGTATCCAACTATC 58.959 37.037 0.00 0.00 37.50 2.08
3228 3396 0.545309 CTCTCCCTCTCCACCACCAA 60.545 60.000 0.00 0.00 0.00 3.67
3289 3458 1.067846 CACCTGTACAAGCTCGCTACA 60.068 52.381 0.00 0.00 0.00 2.74
3306 3475 3.654414 CCCTCGCATTTCTAGTATCACC 58.346 50.000 0.00 0.00 0.00 4.02
3319 3488 0.250467 GATACACATGGCCCTCGCAT 60.250 55.000 0.00 0.00 36.38 4.73
3330 3499 4.161565 TCTTTAGGCCACTTCGATACACAT 59.838 41.667 5.01 0.00 0.00 3.21
3339 3508 4.095036 GTGCTTATGTCTTTAGGCCACTTC 59.905 45.833 5.01 0.00 0.00 3.01
3363 3532 8.465273 AAAACTTAAGGAATACATGGATAGGC 57.535 34.615 7.53 0.00 0.00 3.93
3364 3533 9.853177 AGAAAACTTAAGGAATACATGGATAGG 57.147 33.333 7.53 0.00 0.00 2.57
3405 3579 4.986034 CAGCTCAATGAAAATGCTTGTCAA 59.014 37.500 0.00 0.00 0.00 3.18
3454 3628 2.806818 GACATGCTGTATGCCAGATCTG 59.193 50.000 16.24 16.24 44.49 2.90
3519 3693 0.603707 GCTGCCTAACACTGCTCACA 60.604 55.000 0.00 0.00 0.00 3.58
3524 3698 2.208431 CTAGATGCTGCCTAACACTGC 58.792 52.381 0.00 0.00 0.00 4.40
3530 3704 2.707791 AGATTGCCTAGATGCTGCCTAA 59.292 45.455 0.00 0.00 0.00 2.69
3572 3746 1.066002 CTGCAAACCTGGTGAACTGTG 59.934 52.381 0.00 0.00 0.00 3.66
3629 3803 3.364964 CCGACAGTAGAATTTTGGTGTGC 60.365 47.826 0.00 0.00 0.00 4.57
3630 3804 3.813166 ACCGACAGTAGAATTTTGGTGTG 59.187 43.478 0.00 0.00 0.00 3.82
3636 3810 7.041576 GGTGTAGAAAACCGACAGTAGAATTTT 60.042 37.037 0.00 0.00 31.00 1.82
3720 3894 1.005805 ACATTTCCCTGCAGCATGGTA 59.994 47.619 15.70 4.30 35.86 3.25
3817 3991 2.893489 GGTCCAAAGGTGCTCTGATTTT 59.107 45.455 0.00 0.00 0.00 1.82
3846 4020 5.291858 ACAGATGTACAAATCAGTATGCGTG 59.708 40.000 0.00 0.00 34.76 5.34
3909 4083 8.856153 TTGGACTATAGTTTGCTCAATTTACA 57.144 30.769 6.88 0.00 0.00 2.41
4010 4184 7.383102 AGAAGTAAACTTGGAATACATGCAG 57.617 36.000 0.00 0.00 36.11 4.41
4089 4263 9.681692 GAAATATTGCTGCAAATGATGTACATA 57.318 29.630 20.06 3.40 38.38 2.29


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

AutoCloner maintained by Alex Coulton.