Multiple sequence alignment - TraesCS1A01G299600

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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 TraesCS1A01G299600 chr1A 100.000 3419 0 0 1 3419 494452611 494449193 0.000000e+00 6314
1 TraesCS1A01G299600 chr1D 95.594 3450 113 14 1 3419 397082469 397079028 0.000000e+00 5493
2 TraesCS1A01G299600 chr1B 94.086 2773 105 15 673 3419 532174312 532171573 0.000000e+00 4157
3 TraesCS1A01G299600 chr1B 91.225 661 46 7 1 655 532175057 532174403 0.000000e+00 889
4 TraesCS1A01G299600 chr3A 80.457 788 147 5 1028 1810 595434956 595435741 2.270000e-166 595
5 TraesCS1A01G299600 chr2D 87.586 435 42 8 1622 2052 520042415 520042841 8.520000e-136 494
6 TraesCS1A01G299600 chr2D 87.739 261 21 7 1327 1579 520042158 520042415 9.280000e-76 294
7 TraesCS1A01G299600 chr2D 85.461 282 39 2 3139 3419 307019551 307019831 3.340000e-75 292
8 TraesCS1A01G299600 chr2B 87.156 436 43 7 1622 2052 612067830 612068257 1.850000e-132 483
9 TraesCS1A01G299600 chr2B 87.028 424 43 6 1634 2052 612074157 612074573 5.170000e-128 468
10 TraesCS1A01G299600 chr2B 90.135 223 21 1 1357 1579 612067609 612067830 4.320000e-74 289
11 TraesCS1A01G299600 chr6A 81.145 297 47 8 3125 3419 452621411 452621700 2.650000e-56 230


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 TraesCS1A01G299600 chr1A 494449193 494452611 3418 True 6314 6314 100.0000 1 3419 1 chr1A.!!$R1 3418
1 TraesCS1A01G299600 chr1D 397079028 397082469 3441 True 5493 5493 95.5940 1 3419 1 chr1D.!!$R1 3418
2 TraesCS1A01G299600 chr1B 532171573 532175057 3484 True 2523 4157 92.6555 1 3419 2 chr1B.!!$R1 3418
3 TraesCS1A01G299600 chr3A 595434956 595435741 785 False 595 595 80.4570 1028 1810 1 chr3A.!!$F1 782
4 TraesCS1A01G299600 chr2D 520042158 520042841 683 False 394 494 87.6625 1327 2052 2 chr2D.!!$F2 725
5 TraesCS1A01G299600 chr2B 612067609 612068257 648 False 386 483 88.6455 1357 2052 2 chr2B.!!$F2 695

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
899 988 0.446616 GTGTTCCGATTTCCGAAGCC 59.553 55.0 0.0 0.0 41.76 4.35 F
911 1000 0.826715 CCGAAGCCTGATGGAGAGAA 59.173 55.0 0.0 0.0 34.57 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2091 0.174162 GCGGCTCATTGGAAGCAAAT 59.826 50.000 0.00 0.0 0.00 2.32 R
2539 2644 1.303317 GGGAAAAGCCGAGCCTTCA 60.303 57.895 9.14 0.0 37.63 3.02 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
275 281 1.153539 TGTGGGACTTGGGAATTCCA 58.846 50.000 25.67 9.48 45.43 3.53
279 285 2.381618 TGGGACTTGGGAATTCCATTCA 59.618 45.455 25.67 12.00 46.52 2.57
318 324 1.833187 TAATAGCCTGGCCCCTGAAT 58.167 50.000 16.57 0.00 0.00 2.57
321 327 1.936767 TAGCCTGGCCCCTGAATTGG 61.937 60.000 16.57 0.00 0.00 3.16
423 429 1.069668 AGTTTAACGCTCCTGTTCGGT 59.930 47.619 0.00 0.00 33.32 4.69
446 452 2.234143 TCCGATTGCACAATGTTGGAA 58.766 42.857 0.00 0.00 0.00 3.53
447 453 2.824936 TCCGATTGCACAATGTTGGAAT 59.175 40.909 0.00 3.28 39.96 3.01
448 454 3.257873 TCCGATTGCACAATGTTGGAATT 59.742 39.130 0.00 0.00 37.63 2.17
449 455 4.460731 TCCGATTGCACAATGTTGGAATTA 59.539 37.500 0.00 0.00 37.63 1.40
460 466 9.474920 CACAATGTTGGAATTATTACACTTGTT 57.525 29.630 8.39 0.00 0.00 2.83
492 498 1.133792 AGAGGACACCCAGTTTTGTGG 60.134 52.381 0.00 0.00 36.80 4.17
493 499 0.923358 AGGACACCCAGTTTTGTGGA 59.077 50.000 0.00 0.00 40.44 4.02
495 501 2.091333 AGGACACCCAGTTTTGTGGAAT 60.091 45.455 0.00 0.00 40.44 3.01
496 502 3.139397 AGGACACCCAGTTTTGTGGAATA 59.861 43.478 0.00 0.00 40.44 1.75
499 505 5.467035 ACACCCAGTTTTGTGGAATATTG 57.533 39.130 0.00 0.00 40.44 1.90
501 507 4.283212 CACCCAGTTTTGTGGAATATTGGT 59.717 41.667 0.00 0.00 40.44 3.67
544 551 8.742777 CCAATTTTACCATTTCAGATCTCAGAA 58.257 33.333 0.00 0.00 0.00 3.02
593 600 9.823647 ATCCCTAGATAATATATTTCTGCGTTG 57.176 33.333 2.68 0.00 0.00 4.10
645 652 9.882996 TTCGATTCATCACAAATAAATAGATGC 57.117 29.630 0.00 0.00 36.81 3.91
670 740 2.629017 AAATGCCACCTTCATTCCCT 57.371 45.000 0.00 0.00 33.41 4.20
676 756 2.092429 GCCACCTTCATTCCCTGATGTA 60.092 50.000 0.00 0.00 32.72 2.29
879 968 2.982488 ACTGGTTTCATTCCACTCCTCT 59.018 45.455 0.00 0.00 0.00 3.69
899 988 0.446616 GTGTTCCGATTTCCGAAGCC 59.553 55.000 0.00 0.00 41.76 4.35
911 1000 0.826715 CCGAAGCCTGATGGAGAGAA 59.173 55.000 0.00 0.00 34.57 2.87
942 1031 6.249192 TGTCTTCTCTAACATTCCTCTCTGA 58.751 40.000 0.00 0.00 0.00 3.27
960 1049 4.470602 TCTGAAGTCTGAACCAGTCTGTA 58.529 43.478 0.00 0.00 31.06 2.74
977 1066 8.303156 CCAGTCTGTAGATAGACCATCATAAAG 58.697 40.741 3.09 0.00 46.48 1.85
1155 1244 4.392940 ACAAGATCTTGAAGGTTGGTCTG 58.607 43.478 36.15 11.08 42.93 3.51
1710 1812 3.119955 GCCCTCGTTATTTTTCCACTGAC 60.120 47.826 0.00 0.00 0.00 3.51
1867 1969 3.123620 CTGCTGCGTCTGGCCTTC 61.124 66.667 3.32 0.00 42.61 3.46
1878 1980 1.651240 CTGGCCTTCCATGTCGCAAG 61.651 60.000 3.32 0.00 42.51 4.01
2238 2343 3.751175 TGTTGAAAGAAGACATTAGGCCG 59.249 43.478 0.00 0.00 0.00 6.13
2408 2513 1.257055 TTAGCTGCAAATGCCCCACC 61.257 55.000 1.02 0.00 41.18 4.61
2432 2537 6.038161 CCGCCACAATAATCTAACTGAAATCA 59.962 38.462 0.00 0.00 0.00 2.57
2483 2588 3.785887 AGACCCAGAACCATATTTGCCTA 59.214 43.478 0.00 0.00 0.00 3.93
2515 2620 0.870393 ATGTGCTTGCAGTTCTCACG 59.130 50.000 0.00 0.00 0.00 4.35
2539 2644 6.538742 CGTAGATGTCTACCATTGTTGGAAAT 59.461 38.462 13.10 0.00 46.92 2.17
2847 2952 2.092212 CCTTTGACTCATGCCCTACCAT 60.092 50.000 0.00 0.00 0.00 3.55
2855 2960 4.403432 ACTCATGCCCTACCATTTTTCATG 59.597 41.667 0.00 0.00 33.24 3.07
2902 3007 4.865905 TGGCTAGAGGAAATAAAATGGCA 58.134 39.130 0.00 0.00 0.00 4.92
2903 3008 5.268387 TGGCTAGAGGAAATAAAATGGCAA 58.732 37.500 0.00 0.00 0.00 4.52
2904 3009 5.360714 TGGCTAGAGGAAATAAAATGGCAAG 59.639 40.000 0.00 0.00 0.00 4.01
2970 3078 1.726192 AAAACGCTTCCCCCTCCCTT 61.726 55.000 0.00 0.00 0.00 3.95
3015 3123 0.613777 CAGGAGGAAACCCTAGCGTT 59.386 55.000 0.00 0.00 33.25 4.84
3021 3129 0.036294 GAAACCCTAGCGTTGCCTCT 60.036 55.000 0.00 0.00 0.00 3.69
3181 3305 2.279073 CTCTCCCTCCTACCGGCA 59.721 66.667 0.00 0.00 0.00 5.69
3184 3308 1.457643 CTCCCTCCTACCGGCATCA 60.458 63.158 0.00 0.00 0.00 3.07
3243 3368 2.042843 CTCGGGGCTCCAGTACCT 60.043 66.667 1.96 0.00 0.00 3.08
3401 3526 0.322816 GATGTGGTGGTGGTGATGCT 60.323 55.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
275 281 4.720773 ACCTCACCTGATCTGAAGATGAAT 59.279 41.667 0.38 0.00 34.37 2.57
279 285 6.821616 ATTAACCTCACCTGATCTGAAGAT 57.178 37.500 0.38 0.00 37.51 2.40
318 324 2.203422 CCAAGAACCGCACCCCAA 60.203 61.111 0.00 0.00 0.00 4.12
321 327 1.658114 GAAACCAAGAACCGCACCC 59.342 57.895 0.00 0.00 0.00 4.61
323 329 1.370051 GCGAAACCAAGAACCGCAC 60.370 57.895 0.00 0.00 44.55 5.34
325 331 1.206831 GAGCGAAACCAAGAACCGC 59.793 57.895 0.00 0.00 45.39 5.68
382 388 3.596214 TCCTAGAATTGAGGCGACAAAC 58.404 45.455 0.00 3.28 33.73 2.93
423 429 4.013050 TCCAACATTGTGCAATCGGATTA 58.987 39.130 2.35 0.00 0.00 1.75
447 453 9.891828 CTGCAAGATTTACAACAAGTGTAATAA 57.108 29.630 0.11 0.00 44.03 1.40
448 454 9.278978 TCTGCAAGATTTACAACAAGTGTAATA 57.721 29.630 0.11 0.00 44.52 0.98
449 455 8.165239 TCTGCAAGATTTACAACAAGTGTAAT 57.835 30.769 0.11 0.00 44.52 1.89
460 466 3.559171 GGGTGTCCTCTGCAAGATTTACA 60.559 47.826 0.00 0.00 45.62 2.41
492 498 7.649306 GGACATTAAACAGCATGACCAATATTC 59.351 37.037 0.00 0.00 39.69 1.75
493 499 7.417797 GGGACATTAAACAGCATGACCAATATT 60.418 37.037 0.00 0.00 39.69 1.28
495 501 5.359576 GGGACATTAAACAGCATGACCAATA 59.640 40.000 0.00 0.00 39.69 1.90
496 502 4.160252 GGGACATTAAACAGCATGACCAAT 59.840 41.667 0.00 0.00 39.69 3.16
499 505 3.088532 TGGGACATTAAACAGCATGACC 58.911 45.455 0.00 0.00 39.69 4.02
501 507 5.999205 AATTGGGACATTAAACAGCATGA 57.001 34.783 0.00 0.00 36.36 3.07
544 551 3.181429 CCCATATGTCTACCAGGGCAAAT 60.181 47.826 1.24 0.00 0.00 2.32
584 591 5.240623 ACATTTCCATAAGAACAACGCAGAA 59.759 36.000 0.00 0.00 32.95 3.02
593 600 4.770010 TCCAACCCACATTTCCATAAGAAC 59.230 41.667 0.00 0.00 32.95 3.01
642 649 3.577848 TGAAGGTGGCATTTTTACAGCAT 59.422 39.130 0.00 0.00 35.24 3.79
643 650 2.961741 TGAAGGTGGCATTTTTACAGCA 59.038 40.909 0.00 0.00 35.24 4.41
645 652 5.170748 GGAATGAAGGTGGCATTTTTACAG 58.829 41.667 0.00 0.00 36.19 2.74
717 797 6.325919 TGACAAATTCTACCTGCGAAAAAT 57.674 33.333 0.00 0.00 0.00 1.82
719 799 4.215399 CCTGACAAATTCTACCTGCGAAAA 59.785 41.667 0.00 0.00 0.00 2.29
879 968 1.153353 GCTTCGGAAATCGGAACACA 58.847 50.000 0.00 0.00 39.77 3.72
911 1000 5.420739 GGAATGTTAGAGAAGACAGAGTCCT 59.579 44.000 0.00 0.00 32.18 3.85
942 1031 6.376018 GTCTATCTACAGACTGGTTCAGACTT 59.624 42.308 7.51 0.00 41.49 3.01
960 1049 7.237263 AGCCTGAATCTTTATGATGGTCTATCT 59.763 37.037 0.00 0.00 36.71 1.98
1155 1244 4.227197 TCTCCCTCTTTATCTGATCCACC 58.773 47.826 0.00 0.00 0.00 4.61
1983 2088 1.474077 GGCTCATTGGAAGCAAATCGT 59.526 47.619 0.45 0.00 0.00 3.73
1986 2091 0.174162 GCGGCTCATTGGAAGCAAAT 59.826 50.000 0.00 0.00 0.00 2.32
2238 2343 3.632145 ACCAAACAATGTCCTTGAGTGAC 59.368 43.478 0.00 0.00 38.29 3.67
2408 2513 6.907212 GTGATTTCAGTTAGATTATTGTGGCG 59.093 38.462 0.00 0.00 0.00 5.69
2432 2537 7.011389 CCATGAAATATGTGTGTGTTCGATAGT 59.989 37.037 0.00 0.00 37.40 2.12
2483 2588 8.511604 ACTGCAAGCACATTTACTAATCTAAT 57.488 30.769 0.00 0.00 37.60 1.73
2539 2644 1.303317 GGGAAAAGCCGAGCCTTCA 60.303 57.895 9.14 0.00 37.63 3.02
2655 2760 4.693566 TCCTACAGAACTTAAATGCAACCG 59.306 41.667 0.00 0.00 0.00 4.44
2847 2952 5.070981 TGGCTGGTTAATGGTTCATGAAAAA 59.929 36.000 10.35 1.44 0.00 1.94
2855 2960 4.329462 TTGTTTGGCTGGTTAATGGTTC 57.671 40.909 0.00 0.00 0.00 3.62
2902 3007 3.312736 TCCCTTTCAACAAGCCTTCTT 57.687 42.857 0.00 0.00 0.00 2.52
2903 3008 3.117512 TCTTCCCTTTCAACAAGCCTTCT 60.118 43.478 0.00 0.00 0.00 2.85
2904 3009 3.222603 TCTTCCCTTTCAACAAGCCTTC 58.777 45.455 0.00 0.00 0.00 3.46
2992 3100 0.044244 CTAGGGTTTCCTCCTGGGGA 59.956 60.000 0.00 0.00 43.66 4.81
3329 3454 0.034574 TCACCATCCACCGGATTTGG 60.035 55.000 9.46 12.14 39.79 3.28
3401 3526 2.666190 GCAGCGAGAACACCAGCA 60.666 61.111 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.