Multiple sequence alignment - TraesCS6B01G198600

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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 TraesCS6B01G198600 chr6B 100.000 5481 0 0 1 5481 237695479 237700959 0.000000e+00 10122
1 TraesCS6B01G198600 chr6B 88.182 220 25 1 2478 2697 514607429 514607211 1.510000e-65 261
2 TraesCS6B01G198600 chr6D 97.331 5320 110 20 1 5301 138358422 138363728 0.000000e+00 9009
3 TraesCS6B01G198600 chr6D 87.649 251 11 3 5232 5481 138363702 138363933 1.950000e-69 274
4 TraesCS6B01G198600 chr6A 96.146 5501 165 25 3 5481 180919256 180924731 0.000000e+00 8940
5 TraesCS6B01G198600 chr7A 95.548 292 13 0 5190 5481 475840852 475840561 8.310000e-128 468
6 TraesCS6B01G198600 chr2A 86.925 413 46 7 2620 3028 339109702 339110110 1.800000e-124 457
7 TraesCS6B01G198600 chr5A 94.178 292 11 1 5190 5481 509964951 509964666 1.810000e-119 440
8 TraesCS6B01G198600 chr7D 91.603 131 10 1 2478 2607 175877287 175877417 4.360000e-41 180


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 TraesCS6B01G198600 chr6B 237695479 237700959 5480 False 10122.0 10122 100.000 1 5481 1 chr6B.!!$F1 5480
1 TraesCS6B01G198600 chr6D 138358422 138363933 5511 False 4641.5 9009 92.490 1 5481 2 chr6D.!!$F1 5480
2 TraesCS6B01G198600 chr6A 180919256 180924731 5475 False 8940.0 8940 96.146 3 5481 1 chr6A.!!$F1 5478

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
612 620 1.133009 TCCTTCCTCTGAGGGATAGGC 60.133 57.143 23.00 0.0 41.51 3.93 F
1007 1024 0.554865 TGGGGATTGGGAATGGAGGT 60.555 55.000 0.00 0.0 0.00 3.85 F
1422 1442 1.292223 CGTCGACCCATCAACCTGT 59.708 57.895 10.58 0.0 0.00 4.00 F
2033 2054 2.100087 ACGGAACCCACAAATGTTGAAC 59.900 45.455 0.00 0.0 0.00 3.18 F
2860 2881 2.413634 CGGAGGTTGGTATTTGTTTCGC 60.414 50.000 0.00 0.0 0.00 4.70 F
4239 4264 0.107017 ACCCATTCCTCATTCGCCAG 60.107 55.000 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 1459 3.521560 ACGATTTCGATTAGCTTGCTGA 58.478 40.909 7.01 0.0 43.02 4.26 R
1873 1894 5.110814 ACCATCCGAAATTCTATTGTGGA 57.889 39.130 0.00 0.0 0.00 4.02 R
3212 3233 2.778299 TGGTGATTGGTAAGCTCACAC 58.222 47.619 4.52 0.0 40.80 3.82 R
3638 3662 5.124776 TGCTTTTCCGAATACCCATGTTAAG 59.875 40.000 0.00 0.0 0.00 1.85 R
4278 4303 4.314522 TGGAGGACCAAAAATATCAGCA 57.685 40.909 0.00 0.0 43.91 4.41 R
5334 5421 0.037975 GTTGATTTGCCCACTGCTGG 60.038 55.000 0.00 0.0 42.00 4.85 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
35 36 2.158928 ACGGGTGCACTACAAACAGTAA 60.159 45.455 17.98 0.00 30.92 2.24
62 63 4.240881 ATTGGCGCCGACAATGAT 57.759 50.000 18.99 0.00 40.10 2.45
75 76 4.503123 CCGACAATGATAAGCCACCTATCA 60.503 45.833 0.00 0.00 35.08 2.15
119 120 6.209986 ACTGAAATTTCATGGCTTGAGATCAA 59.790 34.615 20.76 0.00 36.46 2.57
173 176 8.196771 TCTCACAAAAATATAATGCATGAACCC 58.803 33.333 0.00 0.00 0.00 4.11
235 239 4.648651 ACCACGCTAGTTCCAAACTAAAT 58.351 39.130 1.61 0.00 42.99 1.40
521 528 5.156355 GTTTTCAAGTCGAGACGGTATGTA 58.844 41.667 0.00 0.00 36.20 2.29
522 529 5.571784 TTTCAAGTCGAGACGGTATGTAT 57.428 39.130 0.00 0.00 36.20 2.29
523 530 4.547406 TCAAGTCGAGACGGTATGTATG 57.453 45.455 0.00 0.00 36.20 2.39
527 534 3.943381 AGTCGAGACGGTATGTATGTCAA 59.057 43.478 0.00 0.00 35.09 3.18
528 535 4.579340 AGTCGAGACGGTATGTATGTCAAT 59.421 41.667 0.00 0.00 35.09 2.57
529 536 4.910456 GTCGAGACGGTATGTATGTCAATC 59.090 45.833 0.00 0.00 35.09 2.67
530 537 4.577283 TCGAGACGGTATGTATGTCAATCA 59.423 41.667 0.00 0.00 35.09 2.57
531 538 5.240844 TCGAGACGGTATGTATGTCAATCAT 59.759 40.000 0.00 0.00 40.25 2.45
532 539 5.343325 CGAGACGGTATGTATGTCAATCATG 59.657 44.000 0.00 0.00 37.91 3.07
533 540 6.161855 AGACGGTATGTATGTCAATCATGT 57.838 37.500 0.00 0.00 37.91 3.21
534 541 6.582636 AGACGGTATGTATGTCAATCATGTT 58.417 36.000 0.00 0.00 37.91 2.71
535 542 6.479990 AGACGGTATGTATGTCAATCATGTTG 59.520 38.462 0.00 0.00 37.91 3.33
537 544 7.269316 ACGGTATGTATGTCAATCATGTTGTA 58.731 34.615 0.00 0.00 37.91 2.41
555 562 7.223193 CATGTTGTATACATTGGCCAAGAATTG 59.777 37.037 24.94 18.96 45.19 2.32
568 576 5.412286 GGCCAAGAATTGTGCATATGTTTTT 59.588 36.000 0.00 0.00 46.99 1.94
570 578 6.073112 GCCAAGAATTGTGCATATGTTTTTGT 60.073 34.615 4.29 0.00 46.99 2.83
575 583 8.977505 AGAATTGTGCATATGTTTTTGTAACAC 58.022 29.630 4.29 1.37 32.37 3.32
612 620 1.133009 TCCTTCCTCTGAGGGATAGGC 60.133 57.143 23.00 0.00 41.51 3.93
1007 1024 0.554865 TGGGGATTGGGAATGGAGGT 60.555 55.000 0.00 0.00 0.00 3.85
1059 1076 1.990060 GCTGCAGGTGGACCTCCTA 60.990 63.158 17.12 0.00 46.65 2.94
1422 1442 1.292223 CGTCGACCCATCAACCTGT 59.708 57.895 10.58 0.00 0.00 4.00
1686 1706 5.717078 AATCACTGGTGTAAAGACGAGTA 57.283 39.130 0.00 0.00 33.59 2.59
1978 1999 8.258007 TCGATAAGGATAACACTGAATTTGTCT 58.742 33.333 0.00 0.00 0.00 3.41
2033 2054 2.100087 ACGGAACCCACAAATGTTGAAC 59.900 45.455 0.00 0.00 0.00 3.18
2200 2221 5.284079 ACAGAACAAAAGCATGCAGTTAAG 58.716 37.500 21.98 14.93 0.00 1.85
2382 2403 9.429359 CTATATATGTCCTTCTGTGACCATTTC 57.571 37.037 0.00 0.00 31.60 2.17
2603 2624 5.289083 AGGTGGCACATTTAAACACAAAT 57.711 34.783 20.82 0.00 44.52 2.32
2634 2655 4.354587 CGCTTTTTGCTTCTGTCTCTTTT 58.645 39.130 0.00 0.00 40.11 2.27
2705 2726 7.223260 TCTCGTTTTCTGTAGGTATTTCTCA 57.777 36.000 0.00 0.00 0.00 3.27
2708 2729 9.751542 CTCGTTTTCTGTAGGTATTTCTCATAT 57.248 33.333 0.00 0.00 0.00 1.78
2860 2881 2.413634 CGGAGGTTGGTATTTGTTTCGC 60.414 50.000 0.00 0.00 0.00 4.70
2896 2917 6.072838 TCAGATCATTCAAGTTTCTGCACTTC 60.073 38.462 0.00 0.00 34.60 3.01
2935 2956 5.871465 TGCAGCGATTCTTTACAATTACA 57.129 34.783 0.00 0.00 0.00 2.41
2937 2958 6.486248 TGCAGCGATTCTTTACAATTACATC 58.514 36.000 0.00 0.00 0.00 3.06
3141 3162 4.216257 TCTTCAGTTAAGCAATGCTCCAAC 59.784 41.667 19.04 19.04 38.25 3.77
3212 3233 6.318648 TGTGCATTACCTAAAATCTAAGCCAG 59.681 38.462 0.00 0.00 0.00 4.85
3215 3236 6.318900 GCATTACCTAAAATCTAAGCCAGTGT 59.681 38.462 0.00 0.00 0.00 3.55
3248 3269 9.425248 ACCAATCACCAATAATGTTATGATTCT 57.575 29.630 0.00 0.00 33.18 2.40
3265 3289 6.244552 TGATTCTCATGTCTATGCCTCTTT 57.755 37.500 0.00 0.00 34.21 2.52
3348 3372 2.548067 GCCGATAAACCGTGGATCAGAT 60.548 50.000 0.00 0.00 0.00 2.90
3361 3385 7.442364 ACCGTGGATCAGATGATGTTTTATTAG 59.558 37.037 0.00 0.00 34.37 1.73
3618 3642 9.605275 TTGAAAAATGATTATGTGGTTTGTGAA 57.395 25.926 0.00 0.00 0.00 3.18
3638 3662 6.695278 TGTGAAGACGTTCATTGAAATTTTCC 59.305 34.615 6.68 0.73 44.58 3.13
3746 3770 3.677156 AGGGGATTTCTTGCAATAGCT 57.323 42.857 0.00 0.00 42.74 3.32
3932 3957 6.401474 GCATACTCACACACATTGAACTACAG 60.401 42.308 0.00 0.00 0.00 2.74
4239 4264 0.107017 ACCCATTCCTCATTCGCCAG 60.107 55.000 0.00 0.00 0.00 4.85
4278 4303 6.071560 TCACAAGTATTCTACATCCAACGAGT 60.072 38.462 0.00 0.00 0.00 4.18
4295 4320 3.689649 ACGAGTGCTGATATTTTTGGTCC 59.310 43.478 0.00 0.00 0.00 4.46
4317 4342 4.889409 CCTCCATGGTGCTAACATTATGTT 59.111 41.667 15.22 15.22 43.88 2.71
4980 5009 5.104776 TCAATAAGGTCACCCTCATCAAGAG 60.105 44.000 0.00 0.00 41.56 2.85
5161 5191 6.094186 CAGTACTGTACAACTATCAGCTCTGA 59.906 42.308 19.27 1.67 44.59 3.27
5211 5241 7.373617 AGGGATAATTTGAACCAGTTTTGTT 57.626 32.000 0.00 0.00 0.00 2.83
5288 5362 7.011763 GCTGAATTGATGTGCAGTAAAGATAGA 59.988 37.037 0.00 0.00 0.00 1.98
5329 5416 0.746063 TGGTCTTGGCAAAAGCAGTG 59.254 50.000 0.49 0.00 0.00 3.66
5330 5417 0.746659 GGTCTTGGCAAAAGCAGTGT 59.253 50.000 0.00 0.00 0.00 3.55
5331 5418 1.269257 GGTCTTGGCAAAAGCAGTGTC 60.269 52.381 0.00 0.00 0.00 3.67
5332 5419 1.405105 GTCTTGGCAAAAGCAGTGTCA 59.595 47.619 0.00 0.00 0.00 3.58
5333 5420 1.405105 TCTTGGCAAAAGCAGTGTCAC 59.595 47.619 0.00 0.00 28.28 3.67
5334 5421 0.459489 TTGGCAAAAGCAGTGTCACC 59.541 50.000 0.00 0.00 28.28 4.02
5335 5422 1.363807 GGCAAAAGCAGTGTCACCC 59.636 57.895 0.00 0.00 0.00 4.61
5336 5423 1.391157 GGCAAAAGCAGTGTCACCCA 61.391 55.000 0.00 0.00 0.00 4.51
5337 5424 0.031178 GCAAAAGCAGTGTCACCCAG 59.969 55.000 0.00 0.00 0.00 4.45
5338 5425 0.031178 CAAAAGCAGTGTCACCCAGC 59.969 55.000 0.00 1.94 0.00 4.85
5339 5426 0.395586 AAAAGCAGTGTCACCCAGCA 60.396 50.000 13.17 0.00 0.00 4.41
5340 5427 0.820891 AAAGCAGTGTCACCCAGCAG 60.821 55.000 13.17 0.00 0.00 4.24
5341 5428 1.987807 AAGCAGTGTCACCCAGCAGT 61.988 55.000 13.17 1.01 0.00 4.40
5378 5465 8.992073 ACAGATGCTTTGACCATTTTTATTTTC 58.008 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.179468 ACTGTTTGTAGTGCACCCGT 59.821 50.000 14.63 0.00 0.00 5.28
35 36 1.529244 GGCGCCAATGATAAGCCCT 60.529 57.895 24.80 0.00 41.81 5.19
62 63 5.303259 TGTGCATTATGATAGGTGGCTTA 57.697 39.130 0.00 0.00 0.00 3.09
95 96 6.203808 TGATCTCAAGCCATGAAATTTCAG 57.796 37.500 24.17 13.78 41.08 3.02
150 153 9.985730 ATAGGGTTCATGCATTATATTTTTGTG 57.014 29.630 0.00 0.00 0.00 3.33
158 161 7.078249 ACTCACATAGGGTTCATGCATTATA 57.922 36.000 0.00 0.00 0.00 0.98
235 239 5.584649 GCTACTTTGGTACATGCATGTTCTA 59.415 40.000 35.45 25.66 41.97 2.10
268 272 0.999406 CACCGATAAACTCGCACCAG 59.001 55.000 0.00 0.00 46.25 4.00
270 274 0.390735 ACCACCGATAAACTCGCACC 60.391 55.000 0.00 0.00 46.25 5.01
425 430 2.158158 ACCGGATGGGATCTCCTAATGA 60.158 50.000 9.46 0.00 40.75 2.57
486 493 2.884639 ACTTGAAAACCAGGTCGAATGG 59.115 45.455 14.79 14.79 43.87 3.16
530 537 7.093377 ACAATTCTTGGCCAATGTATACAACAT 60.093 33.333 20.85 0.00 42.19 2.71
531 538 6.210385 ACAATTCTTGGCCAATGTATACAACA 59.790 34.615 20.85 1.96 37.48 3.33
532 539 6.531240 CACAATTCTTGGCCAATGTATACAAC 59.469 38.462 20.85 0.05 34.12 3.32
533 540 6.629128 CACAATTCTTGGCCAATGTATACAA 58.371 36.000 20.85 3.90 34.12 2.41
534 541 5.394005 GCACAATTCTTGGCCAATGTATACA 60.394 40.000 20.85 8.27 34.12 2.29
535 542 5.043248 GCACAATTCTTGGCCAATGTATAC 58.957 41.667 20.85 9.42 34.12 1.47
537 544 3.514706 TGCACAATTCTTGGCCAATGTAT 59.485 39.130 20.85 9.86 34.12 2.29
555 562 7.359595 TCTCAGTGTTACAAAAACATATGCAC 58.640 34.615 1.58 0.00 32.23 4.57
568 576 7.062749 AGTAAATCCTGTTCTCAGTGTTACA 57.937 36.000 0.00 0.00 39.82 2.41
570 578 6.698380 GGAGTAAATCCTGTTCTCAGTGTTA 58.302 40.000 0.00 0.00 45.64 2.41
584 592 3.389656 CCCTCAGAGGAAGGAGTAAATCC 59.610 52.174 19.21 0.00 43.08 3.01
603 611 2.659428 GCAAATGAACAGCCTATCCCT 58.341 47.619 0.00 0.00 0.00 4.20
612 620 9.079833 CAAATAGATACTTTGGCAAATGAACAG 57.920 33.333 13.89 2.80 31.43 3.16
641 649 6.541641 GCAAATTCCTAGAGAAGTGATGTGAT 59.458 38.462 0.00 0.00 38.07 3.06
650 658 6.917533 ACATTTGTGCAAATTCCTAGAGAAG 58.082 36.000 7.36 0.00 38.84 2.85
988 1005 0.554865 ACCTCCATTCCCAATCCCCA 60.555 55.000 0.00 0.00 0.00 4.96
1439 1459 3.521560 ACGATTTCGATTAGCTTGCTGA 58.478 40.909 7.01 0.00 43.02 4.26
1873 1894 5.110814 ACCATCCGAAATTCTATTGTGGA 57.889 39.130 0.00 0.00 0.00 4.02
2033 2054 7.448469 CCCTGGAAGAAATACCATAATGTAAGG 59.552 40.741 0.00 0.00 34.07 2.69
2708 2729 7.444299 TGCAGTATATCACATAGAAATGCTCA 58.556 34.615 0.00 0.00 36.50 4.26
2860 2881 8.503458 ACTTGAATGATCTGAAAATGGTAGAG 57.497 34.615 0.00 0.00 0.00 2.43
3141 3162 6.187125 ACATTACAGTGCTGCTCAAAATAG 57.813 37.500 0.00 0.00 0.00 1.73
3212 3233 2.778299 TGGTGATTGGTAAGCTCACAC 58.222 47.619 4.52 0.00 40.80 3.82
3215 3236 6.186957 ACATTATTGGTGATTGGTAAGCTCA 58.813 36.000 0.00 0.00 0.00 4.26
3248 3269 9.679661 TTGTTTATAAAAGAGGCATAGACATGA 57.320 29.630 0.00 0.00 33.67 3.07
3284 3308 9.248291 CTCTGAAAGAAAGATCTAATAGTGCTC 57.752 37.037 0.00 0.00 46.34 4.26
3361 3385 6.224584 AGAACAAAGCTACAAAGACCTACTC 58.775 40.000 0.00 0.00 0.00 2.59
3465 3489 5.280830 GGGTTTAGATACAAGGGAGAAACCA 60.281 44.000 13.82 0.00 43.92 3.67
3618 3642 8.410141 TGTTAAGGAAAATTTCAATGAACGTCT 58.590 29.630 8.09 0.00 0.00 4.18
3638 3662 5.124776 TGCTTTTCCGAATACCCATGTTAAG 59.875 40.000 0.00 0.00 0.00 1.85
3857 3882 9.581289 TTAAACCTGACAAGAGAATAATGGAAA 57.419 29.630 0.00 0.00 0.00 3.13
4239 4264 4.965119 ACTTGTGAAAACTTGACTCACC 57.035 40.909 0.00 0.00 38.97 4.02
4278 4303 4.314522 TGGAGGACCAAAAATATCAGCA 57.685 40.909 0.00 0.00 43.91 4.41
4295 4320 5.824624 AGAACATAATGTTAGCACCATGGAG 59.175 40.000 21.47 12.70 41.28 3.86
4317 4342 6.605471 TCTGCAGTTACATTAGGAGAAAGA 57.395 37.500 14.67 0.00 0.00 2.52
4553 4578 6.370593 CACAATACTTCACACCATAACACAC 58.629 40.000 0.00 0.00 0.00 3.82
4980 5009 2.067453 GAATACACGAGCGCGACTGC 62.067 60.000 19.05 0.00 41.64 4.40
5288 5362 5.835280 CCATAGAAAATATTTGCCTCCTGGT 59.165 40.000 0.39 0.00 35.27 4.00
5334 5421 0.037975 GTTGATTTGCCCACTGCTGG 60.038 55.000 0.00 0.00 42.00 4.85
5335 5422 0.675083 TGTTGATTTGCCCACTGCTG 59.325 50.000 0.00 0.00 42.00 4.41
5336 5423 0.963962 CTGTTGATTTGCCCACTGCT 59.036 50.000 0.00 0.00 42.00 4.24
5337 5424 0.961019 TCTGTTGATTTGCCCACTGC 59.039 50.000 0.00 0.00 41.77 4.40
5338 5425 2.673043 GCATCTGTTGATTTGCCCACTG 60.673 50.000 0.00 0.00 0.00 3.66
5339 5426 1.547372 GCATCTGTTGATTTGCCCACT 59.453 47.619 0.00 0.00 0.00 4.00
5340 5427 1.547372 AGCATCTGTTGATTTGCCCAC 59.453 47.619 0.00 0.00 0.00 4.61
5341 5428 1.927487 AGCATCTGTTGATTTGCCCA 58.073 45.000 0.00 0.00 0.00 5.36
5378 5465 2.883386 GCTAATCCCCTCATCTGCAAAG 59.117 50.000 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.