Multiple sequence alignment - TraesCS1D01G314800

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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 TraesCS1D01G314800 chr1D 100.000 2711 0 0 1 2711 410073158 410070448 0.000000e+00 5007
1 TraesCS1D01G314800 chr1A 90.999 2633 140 52 6 2571 505926974 505924372 0.000000e+00 3459
2 TraesCS1D01G314800 chr1B 91.203 2535 97 48 1 2461 552475374 552472892 0.000000e+00 3330
3 TraesCS1D01G314800 chr1B 93.151 146 9 1 2567 2711 552472102 552471957 2.110000e-51 213
4 TraesCS1D01G314800 chr3A 78.452 478 72 18 1050 1505 573112486 573112954 1.590000e-72 283
5 TraesCS1D01G314800 chr3D 75.501 649 105 29 1050 1654 434210918 434211556 4.450000e-68 268
6 TraesCS1D01G314800 chr2A 87.166 187 22 2 1114 1299 680357721 680357536 7.600000e-51 211
7 TraesCS1D01G314800 chr6D 88.824 170 17 2 1114 1282 139916327 139916495 9.840000e-50 207
8 TraesCS1D01G314800 chr6A 88.824 170 17 2 1114 1282 183188190 183188358 9.840000e-50 207
9 TraesCS1D01G314800 chr2D 86.559 186 25 0 1114 1299 538055269 538055084 3.540000e-49 206
10 TraesCS1D01G314800 chr2B 86.631 187 23 2 1114 1299 640765309 640765124 3.540000e-49 206


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 TraesCS1D01G314800 chr1D 410070448 410073158 2710 True 5007.0 5007 100.000 1 2711 1 chr1D.!!$R1 2710
1 TraesCS1D01G314800 chr1A 505924372 505926974 2602 True 3459.0 3459 90.999 6 2571 1 chr1A.!!$R1 2565
2 TraesCS1D01G314800 chr1B 552471957 552475374 3417 True 1771.5 3330 92.177 1 2711 2 chr1B.!!$R1 2710
3 TraesCS1D01G314800 chr3D 434210918 434211556 638 False 268.0 268 75.501 1050 1654 1 chr3D.!!$F1 604

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
492 500 0.036448 TCTAGCCGCCGCTACTATCT 59.964 55.0 2.4 0.0 46.08 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 2518 0.17904 TTTTTCCAAGGAGCCGTCGT 60.179 50.0 0.0 0.0 0.0 4.34 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
17 18 4.240049 GGAACTCGACACCGTGAC 57.760 61.111 5.28 0.00 37.05 3.67
87 89 7.287696 GTGTTCCATTCCATAATAGGGACAAAT 59.712 37.037 0.00 0.00 35.41 2.32
129 131 2.033662 GCCGATCACATTTTAGACGAGC 60.034 50.000 0.00 0.00 0.00 5.03
145 148 0.693049 GAGCAACCTCTTGAGGGGAA 59.307 55.000 19.51 0.00 35.16 3.97
194 197 9.962783 TCTAGTGAGTAGTTAGTTTTGTTTCTC 57.037 33.333 0.00 0.00 0.00 2.87
205 208 9.285770 GTTAGTTTTGTTTCTCTTTTAGTGTGG 57.714 33.333 0.00 0.00 0.00 4.17
208 211 5.828299 TTGTTTCTCTTTTAGTGTGGGTG 57.172 39.130 0.00 0.00 0.00 4.61
209 212 4.850680 TGTTTCTCTTTTAGTGTGGGTGT 58.149 39.130 0.00 0.00 0.00 4.16
280 284 4.683781 CGCTCTCTTCTATAAACTCATGGC 59.316 45.833 0.00 0.00 0.00 4.40
284 288 4.119862 TCTTCTATAAACTCATGGCACGC 58.880 43.478 0.00 0.00 0.00 5.34
345 353 3.710326 TGACCTTCGTCATCTAATCCG 57.290 47.619 0.00 0.00 44.20 4.18
390 398 1.076332 GGTCCTTTCGGATCAACGTG 58.924 55.000 0.00 0.00 42.43 4.49
492 500 0.036448 TCTAGCCGCCGCTACTATCT 59.964 55.000 2.40 0.00 46.08 1.98
494 502 2.093075 TCTAGCCGCCGCTACTATCTAT 60.093 50.000 2.40 0.00 46.08 1.98
498 506 1.540267 CCGCCGCTACTATCTATGTGT 59.460 52.381 0.00 0.00 0.00 3.72
503 511 4.859798 GCCGCTACTATCTATGTGTCATTC 59.140 45.833 0.00 0.00 0.00 2.67
512 520 5.004922 TCTATGTGTCATTCGTATGTGCA 57.995 39.130 1.75 0.76 33.34 4.57
527 535 0.039437 GTGCAAGTCGGAGAAGACGA 60.039 55.000 0.00 0.00 45.26 4.20
553 561 2.975732 TGCCAAAATTCAGTTGTGCA 57.024 40.000 0.00 0.00 33.00 4.57
559 567 5.638657 GCCAAAATTCAGTTGTGCAATATGA 59.361 36.000 0.00 0.00 0.00 2.15
563 571 5.847111 ATTCAGTTGTGCAATATGATGCT 57.153 34.783 0.00 0.00 46.54 3.79
669 692 4.397832 TTCGTAACCGCCCCAGGC 62.398 66.667 0.00 0.00 46.75 4.85
703 726 1.382695 GGATCCTGAGGGTCCGGAA 60.383 63.158 16.37 0.00 0.00 4.30
739 762 1.615883 ACAAATTGTAATGCCGCCACA 59.384 42.857 0.00 0.00 0.00 4.17
788 811 3.721706 AAAGCGCTCCCTCCCTGG 61.722 66.667 12.06 0.00 0.00 4.45
873 901 1.140134 TTTAACCAGCTGCTCCCCCT 61.140 55.000 8.66 0.00 0.00 4.79
901 929 4.202901 CCTATAATAAGTCCCTCCTCCCCA 60.203 50.000 0.00 0.00 0.00 4.96
913 941 1.768077 CTCCCCATCCCTCTCCCAC 60.768 68.421 0.00 0.00 0.00 4.61
992 1030 4.862018 CGTCAACAAGAAAAAGAAAGCCAA 59.138 37.500 0.00 0.00 0.00 4.52
993 1031 5.004726 CGTCAACAAGAAAAAGAAAGCCAAG 59.995 40.000 0.00 0.00 0.00 3.61
994 1032 4.869861 TCAACAAGAAAAAGAAAGCCAAGC 59.130 37.500 0.00 0.00 0.00 4.01
995 1033 3.797039 ACAAGAAAAAGAAAGCCAAGCC 58.203 40.909 0.00 0.00 0.00 4.35
996 1034 3.197549 ACAAGAAAAAGAAAGCCAAGCCA 59.802 39.130 0.00 0.00 0.00 4.75
1288 1335 2.406002 GACCAACTTCCCCTTCGCCA 62.406 60.000 0.00 0.00 0.00 5.69
1362 1412 3.282157 AGCAACAGCAGCACCGTG 61.282 61.111 0.00 0.00 0.00 4.94
1674 1772 1.448013 GAAGCCCGTCCCTTTCGAG 60.448 63.158 0.00 0.00 0.00 4.04
1790 1891 3.732048 TTTTTGCCCCTAGTAGGAAGG 57.268 47.619 18.43 12.11 37.67 3.46
1797 1899 4.079958 TGCCCCTAGTAGGAAGGAAATTTC 60.080 45.833 18.43 9.83 37.67 2.17
1900 2005 3.136750 CCGGAGAGGCAGAGATGG 58.863 66.667 0.00 0.00 0.00 3.51
2048 2154 4.202223 TGCGAATCCTCTACTCCATTTACC 60.202 45.833 0.00 0.00 0.00 2.85
2161 2289 1.297967 CGCCGTCTCGTCTCATCTG 60.298 63.158 0.00 0.00 0.00 2.90
2163 2291 0.248296 GCCGTCTCGTCTCATCTGAC 60.248 60.000 0.00 0.00 0.00 3.51
2164 2292 0.378962 CCGTCTCGTCTCATCTGACC 59.621 60.000 0.00 0.00 33.70 4.02
2165 2293 0.026933 CGTCTCGTCTCATCTGACCG 59.973 60.000 0.00 0.00 33.70 4.79
2166 2294 1.370609 GTCTCGTCTCATCTGACCGA 58.629 55.000 0.00 0.00 33.70 4.69
2167 2295 1.329292 GTCTCGTCTCATCTGACCGAG 59.671 57.143 14.07 14.07 38.10 4.63
2201 2340 2.033372 TGCAGCATGGTCATTATTGGG 58.967 47.619 0.00 0.00 35.86 4.12
2204 2343 1.133823 AGCATGGTCATTATTGGGCGA 60.134 47.619 0.00 0.00 0.00 5.54
2205 2344 1.680735 GCATGGTCATTATTGGGCGAA 59.319 47.619 0.00 0.00 0.00 4.70
2216 2356 1.523758 TTGGGCGAAGAAGAAAGCTC 58.476 50.000 0.00 0.00 0.00 4.09
2217 2357 0.670546 TGGGCGAAGAAGAAAGCTCG 60.671 55.000 0.00 0.00 31.66 5.03
2218 2358 1.362406 GGGCGAAGAAGAAAGCTCGG 61.362 60.000 0.00 0.00 0.00 4.63
2219 2359 1.421877 GCGAAGAAGAAAGCTCGGC 59.578 57.895 0.00 0.00 0.00 5.54
2220 2360 1.016653 GCGAAGAAGAAAGCTCGGCT 61.017 55.000 0.00 0.00 42.56 5.52
2221 2361 0.995728 CGAAGAAGAAAGCTCGGCTC 59.004 55.000 0.00 0.00 38.25 4.70
2222 2362 0.995728 GAAGAAGAAAGCTCGGCTCG 59.004 55.000 0.00 0.00 38.25 5.03
2223 2363 0.390472 AAGAAGAAAGCTCGGCTCGG 60.390 55.000 0.00 0.00 38.25 4.63
2224 2364 1.811679 GAAGAAAGCTCGGCTCGGG 60.812 63.158 0.00 0.00 38.25 5.14
2225 2365 2.508586 GAAGAAAGCTCGGCTCGGGT 62.509 60.000 0.00 0.00 38.25 5.28
2346 2500 5.133264 CGATCTGTCGCAATAATAAACAGC 58.867 41.667 0.00 0.00 41.49 4.40
2419 2573 3.066481 CGTCCGTCCTTTTGGGTTTTAAA 59.934 43.478 0.00 0.00 40.87 1.52
2421 2575 5.048852 CGTCCGTCCTTTTGGGTTTTAAATA 60.049 40.000 0.00 0.00 40.87 1.40
2470 2628 4.222114 GCAGCACAAGTGTCAAATTACTC 58.778 43.478 1.79 0.00 0.00 2.59
2473 2631 5.911280 CAGCACAAGTGTCAAATTACTCAAG 59.089 40.000 1.79 0.00 0.00 3.02
2477 2635 7.746475 GCACAAGTGTCAAATTACTCAAGATAC 59.254 37.037 1.79 0.00 0.00 2.24
2480 2638 8.873830 CAAGTGTCAAATTACTCAAGATACGAT 58.126 33.333 0.00 0.00 0.00 3.73
2500 2985 9.810870 ATACGATAGAAGAGTAAGGTAAATCCT 57.189 33.333 0.00 0.00 44.85 3.24
2538 3034 6.293244 CCGACGGAGGAAATGGTATTTTATTC 60.293 42.308 8.64 0.00 0.00 1.75
2542 3038 6.238925 CGGAGGAAATGGTATTTTATTCCCAC 60.239 42.308 0.00 0.00 40.31 4.61
2543 3039 6.041637 GGAGGAAATGGTATTTTATTCCCACC 59.958 42.308 0.00 0.00 40.31 4.61
2544 3040 5.903010 AGGAAATGGTATTTTATTCCCACCC 59.097 40.000 0.00 0.00 40.31 4.61
2545 3041 5.221362 GGAAATGGTATTTTATTCCCACCCG 60.221 44.000 0.00 0.00 34.74 5.28
2549 3045 1.388837 ATTTTATTCCCACCCGCGCC 61.389 55.000 0.00 0.00 0.00 6.53
2612 3455 0.891904 TGTCCGGTGTCAGATCGTGA 60.892 55.000 0.00 0.00 0.00 4.35
2630 3473 4.876107 TCGTGAGAGGGAAAAATAATCAGC 59.124 41.667 0.00 0.00 34.84 4.26
2651 3494 4.118995 CCTGCCGCCGTACGTACA 62.119 66.667 24.50 3.94 41.42 2.90
2682 3525 1.303643 CCACTCCAGGCTGTTTCCC 60.304 63.158 14.43 0.00 0.00 3.97
2698 3541 4.253257 CCGCGGAGAGACGTAGGC 62.253 72.222 24.07 0.00 35.98 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.690460 AGGTTCCAAGCAATAAGAGTGG 58.310 45.455 0.00 0.00 0.00 4.00
87 89 3.682718 GCTAGTGCTTGGCCAGATTTCTA 60.683 47.826 5.11 6.11 36.03 2.10
145 148 0.973632 TCAACATACACCGCTCCAGT 59.026 50.000 0.00 0.00 0.00 4.00
194 197 6.653320 ACATGTATGTACACCCACACTAAAAG 59.347 38.462 0.00 0.00 39.68 2.27
205 208 3.190327 TGCAAGCAACATGTATGTACACC 59.810 43.478 0.00 0.00 40.80 4.16
284 288 5.811399 TTATTCTTTGAGTACGCCAATGG 57.189 39.130 0.00 0.00 0.00 3.16
290 294 4.259356 AGGGGTTTATTCTTTGAGTACGC 58.741 43.478 0.00 0.00 0.00 4.42
345 353 2.028203 GCCTAGAGAAGAGGATGATGCC 60.028 54.545 0.00 0.00 35.99 4.40
390 398 1.353103 CTGCCATGAAACGCCGATC 59.647 57.895 0.00 0.00 0.00 3.69
492 500 5.175127 ACTTGCACATACGAATGACACATA 58.825 37.500 0.00 0.00 36.54 2.29
494 502 3.398406 ACTTGCACATACGAATGACACA 58.602 40.909 0.00 0.00 36.54 3.72
498 506 2.094442 TCCGACTTGCACATACGAATGA 60.094 45.455 0.00 0.00 36.54 2.57
503 511 1.920574 CTTCTCCGACTTGCACATACG 59.079 52.381 0.00 0.00 0.00 3.06
535 543 5.638657 TCATATTGCACAACTGAATTTTGGC 59.361 36.000 0.00 0.00 0.00 4.52
546 554 6.073657 ACACAAAAAGCATCATATTGCACAAC 60.074 34.615 2.38 0.00 45.23 3.32
553 561 9.217278 TGCATAAAACACAAAAAGCATCATATT 57.783 25.926 0.00 0.00 0.00 1.28
597 610 0.317799 GCATGATGTTTGTGTGCCCA 59.682 50.000 0.00 0.00 0.00 5.36
598 611 3.126729 GCATGATGTTTGTGTGCCC 57.873 52.632 0.00 0.00 0.00 5.36
643 666 0.939419 GCGGTTACGAACTTTGTGGT 59.061 50.000 0.00 0.00 44.60 4.16
691 714 0.690762 CTTTTCCTTCCGGACCCTCA 59.309 55.000 1.83 0.00 39.60 3.86
703 726 0.535553 TTGTAACGCCCGCTTTTCCT 60.536 50.000 0.00 0.00 0.00 3.36
739 762 2.032071 CCGCCCCTCGTCTTTTGT 59.968 61.111 0.00 0.00 36.19 2.83
873 901 4.937116 AGGAGGGACTTATTATAGGGGGTA 59.063 45.833 0.00 0.00 41.55 3.69
1617 1715 1.153823 CAGATCCACCACCGACGAC 60.154 63.158 0.00 0.00 0.00 4.34
1674 1772 2.435059 GGGCAGTTCAGGTCGAGC 60.435 66.667 6.48 6.48 0.00 5.03
1897 2002 4.582869 CGACAATACATCCATCCATCCAT 58.417 43.478 0.00 0.00 0.00 3.41
1898 2003 3.806858 GCGACAATACATCCATCCATCCA 60.807 47.826 0.00 0.00 0.00 3.41
1899 2004 2.744202 GCGACAATACATCCATCCATCC 59.256 50.000 0.00 0.00 0.00 3.51
1900 2005 2.744202 GGCGACAATACATCCATCCATC 59.256 50.000 0.00 0.00 0.00 3.51
2072 2178 7.499232 ACCAAAGATATGCTGGTTAATGTCTAC 59.501 37.037 0.00 0.00 40.65 2.59
2145 2273 0.378962 GGTCAGATGAGACGAGACGG 59.621 60.000 0.00 0.00 39.42 4.79
2161 2289 3.112709 GGTCGCAAGCACTCGGTC 61.113 66.667 0.00 0.00 37.18 4.79
2163 2291 3.958147 ATGGGTCGCAAGCACTCGG 62.958 63.158 0.00 0.00 37.18 4.63
2164 2292 2.434884 ATGGGTCGCAAGCACTCG 60.435 61.111 0.00 0.00 37.18 4.18
2165 2293 3.044059 GCATGGGTCGCAAGCACTC 62.044 63.158 11.73 0.00 37.18 3.51
2166 2294 3.058160 GCATGGGTCGCAAGCACT 61.058 61.111 11.73 0.00 37.18 4.40
2167 2295 3.332493 CTGCATGGGTCGCAAGCAC 62.332 63.158 14.90 0.00 39.30 4.40
2201 2340 1.016653 AGCCGAGCTTTCTTCTTCGC 61.017 55.000 0.00 0.00 33.89 4.70
2204 2343 0.390472 CCGAGCCGAGCTTTCTTCTT 60.390 55.000 0.00 0.00 39.88 2.52
2205 2344 1.216710 CCGAGCCGAGCTTTCTTCT 59.783 57.895 0.00 0.00 39.88 2.85
2363 2517 0.601841 TTTTCCAAGGAGCCGTCGTC 60.602 55.000 0.00 0.00 0.00 4.20
2364 2518 0.179040 TTTTTCCAAGGAGCCGTCGT 60.179 50.000 0.00 0.00 0.00 4.34
2365 2519 2.624169 TTTTTCCAAGGAGCCGTCG 58.376 52.632 0.00 0.00 0.00 5.12
2419 2573 4.729227 CCAGCGGTTGGGTTAAATTTAT 57.271 40.909 2.48 0.00 43.75 1.40
2549 3045 3.672295 GAGGACTCGGCCAAGGCAG 62.672 68.421 13.87 9.33 44.11 4.85
2553 3049 1.219393 GGAAGAGGACTCGGCCAAG 59.781 63.158 2.24 0.00 34.09 3.61
2560 3058 2.202676 CGCTGCGGAAGAGGACTC 60.203 66.667 15.40 0.00 0.00 3.36
2612 3455 2.614057 CGCGCTGATTATTTTTCCCTCT 59.386 45.455 5.56 0.00 0.00 3.69
2661 3504 0.108585 GAAACAGCCTGGAGTGGACA 59.891 55.000 0.00 0.00 0.00 4.02
2682 3525 4.592936 CGCCTACGTCTCTCCGCG 62.593 72.222 0.00 0.00 33.53 6.46


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

AutoCloner maintained by Alex Coulton.