Multiple sequence alignment - TraesCS5B01G433500

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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 TraesCS5B01G433500 chr5B 100.000 3251 0 0 1 3251 608194495 608197745 0.000000e+00 6004
1 TraesCS5B01G433500 chr5B 95.793 2044 45 17 764 2802 608337474 608339481 0.000000e+00 3260
2 TraesCS5B01G433500 chr5B 91.841 1581 87 14 855 2403 608082821 608084391 0.000000e+00 2167
3 TraesCS5B01G433500 chr5B 90.154 843 68 5 1 838 608336685 608337517 0.000000e+00 1083
4 TraesCS5B01G433500 chr5B 81.989 1116 180 16 1169 2266 608654668 608655780 0.000000e+00 928
5 TraesCS5B01G433500 chr5B 82.261 1088 176 12 1179 2262 608644515 608645589 0.000000e+00 924
6 TraesCS5B01G433500 chr5B 93.898 295 15 2 2373 2667 608084320 608084611 2.980000e-120 442
7 TraesCS5B01G433500 chr5B 80.665 331 54 9 1794 2122 608712906 608713228 6.970000e-62 248
8 TraesCS5B01G433500 chr5B 95.105 143 7 0 751 893 608140584 608140726 3.260000e-55 226
9 TraesCS5B01G433500 chr5B 93.836 146 9 0 751 896 608311202 608311347 1.520000e-53 220
10 TraesCS5B01G433500 chr5D 96.354 2496 78 6 760 3244 493115862 493118355 0.000000e+00 4093
11 TraesCS5B01G433500 chr5D 83.288 1113 165 13 1169 2266 493286757 493287863 0.000000e+00 1005
12 TraesCS5B01G433500 chr5D 85.560 554 79 1 6 558 507868251 507868804 2.170000e-161 579
13 TraesCS5B01G433500 chr5D 84.615 559 81 4 1 556 507873805 507874361 4.740000e-153 551
14 TraesCS5B01G433500 chr5D 84.715 543 76 4 16 557 404765501 404764965 1.330000e-148 536
15 TraesCS5B01G433500 chr5A 95.531 2506 96 7 751 3244 616064537 616067038 0.000000e+00 3993
16 TraesCS5B01G433500 chr5A 93.894 1654 84 7 764 2403 616042848 616044498 0.000000e+00 2479
17 TraesCS5B01G433500 chr5A 81.547 1241 194 12 1169 2406 615863352 615864560 0.000000e+00 990
18 TraesCS5B01G433500 chr5A 83.019 1113 162 19 1169 2266 616365787 616366887 0.000000e+00 983
19 TraesCS5B01G433500 chr5A 93.266 297 17 2 2371 2667 615864484 615864777 4.980000e-118 435
20 TraesCS5B01G433500 chr5A 94.366 284 13 2 2384 2667 616044438 616044718 1.790000e-117 433
21 TraesCS5B01G433500 chr5A 87.500 144 9 5 2663 2805 615864915 615865050 1.210000e-34 158
22 TraesCS5B01G433500 chr4D 85.638 564 77 2 1 563 432418481 432417921 1.000000e-164 590
23 TraesCS5B01G433500 chr6D 84.464 560 82 3 1 559 156440989 156441544 6.130000e-152 547
24 TraesCS5B01G433500 chr1D 84.258 559 83 3 2 559 418099411 418099965 1.030000e-149 540
25 TraesCS5B01G433500 chr2D 83.709 577 73 15 1 570 309165741 309166303 2.870000e-145 525
26 TraesCS5B01G433500 chr3A 83.750 560 80 6 1 557 468735595 468736146 1.340000e-143 520


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 TraesCS5B01G433500 chr5B 608194495 608197745 3250 False 6004.000000 6004 100.000000 1 3251 1 chr5B.!!$F2 3250
1 TraesCS5B01G433500 chr5B 608336685 608339481 2796 False 2171.500000 3260 92.973500 1 2802 2 chr5B.!!$F8 2801
2 TraesCS5B01G433500 chr5B 608082821 608084611 1790 False 1304.500000 2167 92.869500 855 2667 2 chr5B.!!$F7 1812
3 TraesCS5B01G433500 chr5B 608654668 608655780 1112 False 928.000000 928 81.989000 1169 2266 1 chr5B.!!$F5 1097
4 TraesCS5B01G433500 chr5B 608644515 608645589 1074 False 924.000000 924 82.261000 1179 2262 1 chr5B.!!$F4 1083
5 TraesCS5B01G433500 chr5D 493115862 493118355 2493 False 4093.000000 4093 96.354000 760 3244 1 chr5D.!!$F1 2484
6 TraesCS5B01G433500 chr5D 493286757 493287863 1106 False 1005.000000 1005 83.288000 1169 2266 1 chr5D.!!$F2 1097
7 TraesCS5B01G433500 chr5D 507868251 507868804 553 False 579.000000 579 85.560000 6 558 1 chr5D.!!$F3 552
8 TraesCS5B01G433500 chr5D 507873805 507874361 556 False 551.000000 551 84.615000 1 556 1 chr5D.!!$F4 555
9 TraesCS5B01G433500 chr5D 404764965 404765501 536 True 536.000000 536 84.715000 16 557 1 chr5D.!!$R1 541
10 TraesCS5B01G433500 chr5A 616064537 616067038 2501 False 3993.000000 3993 95.531000 751 3244 1 chr5A.!!$F1 2493
11 TraesCS5B01G433500 chr5A 616042848 616044718 1870 False 1456.000000 2479 94.130000 764 2667 2 chr5A.!!$F4 1903
12 TraesCS5B01G433500 chr5A 616365787 616366887 1100 False 983.000000 983 83.019000 1169 2266 1 chr5A.!!$F2 1097
13 TraesCS5B01G433500 chr5A 615863352 615865050 1698 False 527.666667 990 87.437667 1169 2805 3 chr5A.!!$F3 1636
14 TraesCS5B01G433500 chr4D 432417921 432418481 560 True 590.000000 590 85.638000 1 563 1 chr4D.!!$R1 562
15 TraesCS5B01G433500 chr6D 156440989 156441544 555 False 547.000000 547 84.464000 1 559 1 chr6D.!!$F1 558
16 TraesCS5B01G433500 chr1D 418099411 418099965 554 False 540.000000 540 84.258000 2 559 1 chr1D.!!$F1 557
17 TraesCS5B01G433500 chr2D 309165741 309166303 562 False 525.000000 525 83.709000 1 570 1 chr2D.!!$F1 569
18 TraesCS5B01G433500 chr3A 468735595 468736146 551 False 520.000000 520 83.750000 1 557 1 chr3A.!!$F1 556

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
663 673 0.093026 CAACGCGGCGCTTATATAGC 59.907 55.0 30.54 0.0 46.83 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 2546 0.544357 ACCAGGACCAGAATCACGGA 60.544 55.0 0.0 0.0 0.0 4.69 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
45 46 4.107051 CGCCCGGCAAGCTTCTTG 62.107 66.667 10.77 2.40 0.00 3.02
52 53 1.518903 GGCAAGCTTCTTGTTCGGCT 61.519 55.000 0.00 0.00 36.53 5.52
69 70 2.018544 CTGCCTAGAGGAGACGTCG 58.981 63.158 10.46 0.00 37.39 5.12
117 118 2.742372 CCCTTCTTCGTGGGCGTG 60.742 66.667 0.00 0.00 36.61 5.34
123 124 3.039202 CTTCGTGGGCGTGGCATTC 62.039 63.158 0.00 0.00 39.49 2.67
309 318 3.379445 GCGACGAAGGAGGGGTCA 61.379 66.667 0.00 0.00 0.00 4.02
476 485 0.732571 AATAAACAGCACGCGATGGG 59.267 50.000 15.93 1.50 30.90 4.00
500 509 1.153628 GGACCGTGCGCTGAACTAT 60.154 57.895 9.73 0.00 0.00 2.12
511 520 1.069906 GCTGAACTATTTATGCCCGCG 60.070 52.381 0.00 0.00 0.00 6.46
513 522 0.110823 GAACTATTTATGCCCGCGCG 60.111 55.000 25.67 25.67 38.08 6.86
578 587 2.210116 CTGAACTATTTATGCCCGCGT 58.790 47.619 4.92 0.00 0.00 6.01
579 588 2.206750 TGAACTATTTATGCCCGCGTC 58.793 47.619 4.92 0.00 0.00 5.19
580 589 1.529865 GAACTATTTATGCCCGCGTCC 59.470 52.381 4.92 0.00 0.00 4.79
599 608 1.068333 CCGGTTTTTGCATCTCCACTG 60.068 52.381 0.00 0.00 0.00 3.66
602 611 3.610114 CGGTTTTTGCATCTCCACTGAAG 60.610 47.826 0.00 0.00 0.00 3.02
605 614 2.574006 TTGCATCTCCACTGAAGCTT 57.426 45.000 0.00 0.00 32.62 3.74
607 616 1.005340 GCATCTCCACTGAAGCTTCG 58.995 55.000 21.11 17.22 0.00 3.79
611 620 0.321671 CTCCACTGAAGCTTCGGGAA 59.678 55.000 33.15 19.32 37.89 3.97
655 665 2.414840 AAAATTTCCAACGCGGCGCT 62.415 50.000 30.54 14.21 33.14 5.92
656 666 2.414840 AAATTTCCAACGCGGCGCTT 62.415 50.000 30.54 19.26 33.14 4.68
657 667 1.579084 AATTTCCAACGCGGCGCTTA 61.579 50.000 30.54 5.12 33.14 3.09
658 668 1.373590 ATTTCCAACGCGGCGCTTAT 61.374 50.000 30.54 12.51 33.14 1.73
659 669 0.740164 TTTCCAACGCGGCGCTTATA 60.740 50.000 30.54 8.52 33.14 0.98
660 670 0.531090 TTCCAACGCGGCGCTTATAT 60.531 50.000 30.54 8.11 33.14 0.86
661 671 0.314618 TCCAACGCGGCGCTTATATA 59.685 50.000 30.54 7.96 33.14 0.86
662 672 0.713883 CCAACGCGGCGCTTATATAG 59.286 55.000 30.54 14.71 0.00 1.31
663 673 0.093026 CAACGCGGCGCTTATATAGC 59.907 55.000 30.54 0.00 46.83 2.97
676 686 4.208460 GCTTATATAGCGCGTCTGTTTGAA 59.792 41.667 8.43 0.00 40.71 2.69
686 696 4.151798 GCGTCTGTTTGAAATGCTCTAAC 58.848 43.478 0.00 0.00 39.41 2.34
704 714 2.260154 CGCATCACAACACCTGCCA 61.260 57.895 0.00 0.00 0.00 4.92
744 754 1.663379 TATATCGCCATCCCGCTCCG 61.663 60.000 0.00 0.00 0.00 4.63
1542 1616 1.372683 GCAGCTCACAGACCTTCCA 59.627 57.895 0.00 0.00 0.00 3.53
1621 1695 7.167535 TCAGATAGGACAAACAATCAATGTGA 58.832 34.615 0.00 0.00 42.99 3.58
1722 1796 2.450476 GGCAATGAGAGTTGGACCATT 58.550 47.619 0.00 0.00 0.00 3.16
1884 1971 0.918983 TTGATTTCTCCCGGATGGCT 59.081 50.000 0.73 0.00 0.00 4.75
2166 2260 1.674817 GGGTACAATATCGCGGATGGG 60.675 57.143 6.13 0.00 0.00 4.00
2425 2546 3.832237 CTGCTGGGTGCGGTGTCTT 62.832 63.158 0.00 0.00 46.63 3.01
2606 2727 9.512435 CAAAATTATCTGCATCTTCCTACTTTG 57.488 33.333 0.00 0.00 0.00 2.77
2849 3113 1.003580 TCTGTCCATTGGCCAAGACTC 59.996 52.381 28.35 18.14 0.00 3.36
2919 3187 3.257393 CTTGAATCTCCAGGAGTTCACG 58.743 50.000 23.57 20.03 33.28 4.35
3067 3335 7.363007 GCCATGAGCAATATAGTACTAGCAGTA 60.363 40.741 8.85 0.00 42.97 2.74
3073 3341 9.415008 AGCAATATAGTACTAGCAGTATAGCAT 57.585 33.333 8.85 0.00 32.65 3.79
3247 3515 9.830975 ATTATTGTTCCAAAAATAGTAATGGCC 57.169 29.630 0.00 0.00 32.87 5.36
3248 3516 5.317733 TGTTCCAAAAATAGTAATGGCCG 57.682 39.130 0.00 0.00 32.87 6.13
3249 3517 4.767928 TGTTCCAAAAATAGTAATGGCCGT 59.232 37.500 0.00 0.00 32.87 5.68
3250 3518 5.944599 TGTTCCAAAAATAGTAATGGCCGTA 59.055 36.000 0.00 0.00 32.87 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.081175 GCCGAACAAGAAGCTTGCC 60.081 57.895 2.10 0.00 0.00 4.52
45 46 1.038130 TCTCCTCTAGGCAGCCGAAC 61.038 60.000 5.55 0.00 34.44 3.95
52 53 1.451567 CCGACGTCTCCTCTAGGCA 60.452 63.158 14.70 0.00 34.44 4.75
69 70 1.876664 GAAGAAGAACAAGGCGGCC 59.123 57.895 12.11 12.11 0.00 6.13
117 118 1.884926 CTCGAAGCTCCCGAATGCC 60.885 63.158 11.48 0.00 35.48 4.40
123 124 3.532155 CCCCTCTCGAAGCTCCCG 61.532 72.222 2.44 2.44 0.00 5.14
222 225 1.971505 CTCCTCCAAGCACCGGCATA 61.972 60.000 0.00 0.00 44.61 3.14
298 304 2.390777 TACACCCGTGACCCCTCCTT 62.391 60.000 0.96 0.00 0.00 3.36
309 318 1.916777 CACCCCTTCCTACACCCGT 60.917 63.158 0.00 0.00 0.00 5.28
438 447 4.742201 GTTGCTCCCGCTCTCGCA 62.742 66.667 0.00 0.00 36.97 5.10
454 463 2.414029 CCATCGCGTGCTGTTTATTTGT 60.414 45.455 5.77 0.00 0.00 2.83
488 497 1.946768 GGGCATAAATAGTTCAGCGCA 59.053 47.619 11.47 0.00 35.38 6.09
492 501 1.069906 GCGCGGGCATAAATAGTTCAG 60.070 52.381 20.76 0.00 39.62 3.02
561 570 1.589803 GGACGCGGGCATAAATAGTT 58.410 50.000 12.47 0.00 0.00 2.24
578 587 1.202879 AGTGGAGATGCAAAAACCGGA 60.203 47.619 9.46 0.00 0.00 5.14
579 588 1.068333 CAGTGGAGATGCAAAAACCGG 60.068 52.381 0.00 0.00 0.00 5.28
580 589 1.879380 TCAGTGGAGATGCAAAAACCG 59.121 47.619 0.00 0.00 0.00 4.44
582 591 3.005155 AGCTTCAGTGGAGATGCAAAAAC 59.995 43.478 1.33 0.00 40.13 2.43
599 608 1.866925 CAACCGTTCCCGAAGCTTC 59.133 57.895 16.84 16.84 35.63 3.86
602 611 4.084888 CGCAACCGTTCCCGAAGC 62.085 66.667 0.00 0.00 35.63 3.86
655 665 6.645705 CATTTCAAACAGACGCGCTATATAA 58.354 36.000 5.73 0.00 0.00 0.98
656 666 5.333035 GCATTTCAAACAGACGCGCTATATA 60.333 40.000 5.73 0.00 0.00 0.86
657 667 4.552767 GCATTTCAAACAGACGCGCTATAT 60.553 41.667 5.73 0.00 0.00 0.86
658 668 3.242284 GCATTTCAAACAGACGCGCTATA 60.242 43.478 5.73 0.00 0.00 1.31
659 669 2.476185 GCATTTCAAACAGACGCGCTAT 60.476 45.455 5.73 0.00 0.00 2.97
660 670 1.136085 GCATTTCAAACAGACGCGCTA 60.136 47.619 5.73 0.00 0.00 4.26
661 671 0.385974 GCATTTCAAACAGACGCGCT 60.386 50.000 5.73 0.50 0.00 5.92
662 672 0.385974 AGCATTTCAAACAGACGCGC 60.386 50.000 5.73 0.00 0.00 6.86
663 673 1.195448 AGAGCATTTCAAACAGACGCG 59.805 47.619 3.53 3.53 0.00 6.01
686 696 1.794151 TTGGCAGGTGTTGTGATGCG 61.794 55.000 0.00 0.00 39.58 4.73
715 725 2.882927 TGGCGATATAAACTGCGTCT 57.117 45.000 0.00 0.00 0.00 4.18
716 726 2.412089 GGATGGCGATATAAACTGCGTC 59.588 50.000 0.00 0.00 0.00 5.19
744 754 1.509923 CTCGAACGGGAGGTGTACC 59.490 63.158 0.00 0.00 0.00 3.34
1533 1607 2.214920 GGTCACCGGTGGAAGGTCT 61.215 63.158 33.40 0.00 40.59 3.85
1621 1695 1.525995 CAACAAGACCCACGCCAGT 60.526 57.895 0.00 0.00 0.00 4.00
1705 1779 3.007940 TCGACAATGGTCCAACTCTCATT 59.992 43.478 0.00 0.00 41.13 2.57
1722 1796 5.290885 CGAATTCATGTATTCCTTGTCGACA 59.709 40.000 15.76 15.76 32.12 4.35
1884 1971 1.451504 CACCAGGTGAAGGCTGTCA 59.548 57.895 15.35 0.00 35.23 3.58
2084 2177 1.448013 GCAGCGACAGAGGGGTAAC 60.448 63.158 0.00 0.00 0.00 2.50
2425 2546 0.544357 ACCAGGACCAGAATCACGGA 60.544 55.000 0.00 0.00 0.00 4.69
2840 3104 6.681777 ACAAAGTCAAAATATGAGTCTTGGC 58.318 36.000 0.00 0.00 40.94 4.52
2849 3113 8.733458 TCAGGATCAGAACAAAGTCAAAATATG 58.267 33.333 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.