Multiple sequence alignment - TraesCS1B01G131700

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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 TraesCS1B01G131700 chr1B 100.000 2513 0 0 1 2513 165063668 165066180 0.000000e+00 4641.0
1 TraesCS1B01G131700 chr1D 95.807 1884 48 10 651 2513 109454581 109456454 0.000000e+00 3013.0
2 TraesCS1B01G131700 chr1D 95.098 306 8 5 296 595 109454281 109454585 2.260000e-130 475.0
3 TraesCS1B01G131700 chr1D 89.286 308 27 2 1 308 109453948 109454249 5.070000e-102 381.0
4 TraesCS1B01G131700 chr1A 97.505 1523 33 4 996 2513 112927806 112929328 0.000000e+00 2597.0
5 TraesCS1B01G131700 chr1A 91.993 612 25 11 1 595 112926897 112927501 0.000000e+00 837.0
6 TraesCS1B01G131700 chr1A 95.380 303 5 3 651 953 112927497 112927790 8.140000e-130 473.0
7 TraesCS1B01G131700 chr5D 95.455 66 3 0 589 654 472275281 472275346 3.420000e-19 106.0
8 TraesCS1B01G131700 chr7B 94.203 69 2 2 590 656 379839701 379839633 1.230000e-18 104.0
9 TraesCS1B01G131700 chr3D 88.889 81 7 2 591 671 602831547 602831625 5.720000e-17 99.0
10 TraesCS1B01G131700 chr2D 92.647 68 1 2 590 653 17142796 17142729 7.400000e-16 95.3
11 TraesCS1B01G131700 chr2D 90.141 71 2 2 588 653 63554918 63554848 1.240000e-13 87.9
12 TraesCS1B01G131700 chrUn 88.462 78 3 4 587 658 134257851 134257774 3.440000e-14 89.8
13 TraesCS1B01G131700 chr3B 94.828 58 1 2 606 663 728615914 728615859 3.440000e-14 89.8
14 TraesCS1B01G131700 chr7D 90.000 70 3 4 588 653 71571906 71571975 1.240000e-13 87.9
15 TraesCS1B01G131700 chr5A 90.000 70 2 3 588 653 590678664 590678596 4.450000e-13 86.1


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 TraesCS1B01G131700 chr1B 165063668 165066180 2512 False 4641.000000 4641 100.000000 1 2513 1 chr1B.!!$F1 2512
1 TraesCS1B01G131700 chr1D 109453948 109456454 2506 False 1289.666667 3013 93.397000 1 2513 3 chr1D.!!$F1 2512
2 TraesCS1B01G131700 chr1A 112926897 112929328 2431 False 1302.333333 2597 94.959333 1 2513 3 chr1A.!!$F1 2512

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
977 1042 0.531532 CAATCGACCAGCTAGGCCAG 60.532 60.0 5.01 0.97 43.14 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2043 2.960384 TGCTTGGCTCCATGGATTATTG 59.04 45.455 16.63 4.0 0.0 1.9 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
40 41 8.376203 CAAACAATCTGTCTAAACACTATCTCG 58.624 37.037 0.00 0.00 0.00 4.04
44 45 8.399425 CAATCTGTCTAAACACTATCTCGTAGT 58.601 37.037 0.00 0.00 44.49 2.73
121 122 5.283457 TGTGTGGGGGTAATTTTGAAAAG 57.717 39.130 0.00 0.00 0.00 2.27
184 188 9.880157 ATCATGTTAAATAGCTTTGAGCAAATT 57.120 25.926 0.00 0.00 45.56 1.82
185 189 9.142515 TCATGTTAAATAGCTTTGAGCAAATTG 57.857 29.630 0.00 0.00 45.56 2.32
186 190 8.928733 CATGTTAAATAGCTTTGAGCAAATTGT 58.071 29.630 0.00 0.00 45.56 2.71
187 191 8.885494 TGTTAAATAGCTTTGAGCAAATTGTT 57.115 26.923 0.00 0.00 45.56 2.83
188 192 9.323985 TGTTAAATAGCTTTGAGCAAATTGTTT 57.676 25.926 0.00 2.98 45.56 2.83
280 284 8.665685 TGCCTTTTCTATTTCTTCGTAATTCTC 58.334 33.333 0.00 0.00 0.00 2.87
285 289 9.706691 TTTCTATTTCTTCGTAATTCTCTGTGT 57.293 29.630 0.00 0.00 0.00 3.72
346 394 1.148027 TGCAAAACCCATACCCCAAGA 59.852 47.619 0.00 0.00 0.00 3.02
471 528 3.195396 GCTGTGGGAATAATTGAGGCAAA 59.805 43.478 0.00 0.00 0.00 3.68
589 651 4.021229 TCTACTGCCTCGTCCTTTGATTA 58.979 43.478 0.00 0.00 0.00 1.75
595 657 4.142227 TGCCTCGTCCTTTGATTAGTACTC 60.142 45.833 0.00 0.00 0.00 2.59
596 658 4.737055 GCCTCGTCCTTTGATTAGTACTCC 60.737 50.000 0.00 0.00 0.00 3.85
597 659 4.202131 CCTCGTCCTTTGATTAGTACTCCC 60.202 50.000 0.00 0.00 0.00 4.30
598 660 4.607239 TCGTCCTTTGATTAGTACTCCCT 58.393 43.478 0.00 0.00 0.00 4.20
599 661 4.643784 TCGTCCTTTGATTAGTACTCCCTC 59.356 45.833 0.00 0.00 0.00 4.30
600 662 4.645588 CGTCCTTTGATTAGTACTCCCTCT 59.354 45.833 0.00 0.00 0.00 3.69
601 663 5.450688 CGTCCTTTGATTAGTACTCCCTCTG 60.451 48.000 0.00 0.00 0.00 3.35
602 664 5.422650 GTCCTTTGATTAGTACTCCCTCTGT 59.577 44.000 0.00 0.00 0.00 3.41
603 665 6.606395 GTCCTTTGATTAGTACTCCCTCTGTA 59.394 42.308 0.00 0.00 0.00 2.74
604 666 7.123847 GTCCTTTGATTAGTACTCCCTCTGTAA 59.876 40.741 0.00 0.00 0.00 2.41
605 667 7.676893 TCCTTTGATTAGTACTCCCTCTGTAAA 59.323 37.037 0.00 0.00 0.00 2.01
606 668 7.764901 CCTTTGATTAGTACTCCCTCTGTAAAC 59.235 40.741 0.00 0.00 0.00 2.01
607 669 8.431910 TTTGATTAGTACTCCCTCTGTAAACT 57.568 34.615 0.00 0.00 0.00 2.66
608 670 9.537852 TTTGATTAGTACTCCCTCTGTAAACTA 57.462 33.333 0.00 0.00 0.00 2.24
609 671 9.537852 TTGATTAGTACTCCCTCTGTAAACTAA 57.462 33.333 0.00 0.00 0.00 2.24
610 672 9.537852 TGATTAGTACTCCCTCTGTAAACTAAA 57.462 33.333 0.00 0.00 0.00 1.85
615 677 9.544579 AGTACTCCCTCTGTAAACTAAAATAGT 57.455 33.333 0.00 0.00 41.73 2.12
616 678 9.583765 GTACTCCCTCTGTAAACTAAAATAGTG 57.416 37.037 0.00 0.00 39.39 2.74
617 679 8.431910 ACTCCCTCTGTAAACTAAAATAGTGA 57.568 34.615 0.00 0.00 39.39 3.41
618 680 9.047947 ACTCCCTCTGTAAACTAAAATAGTGAT 57.952 33.333 0.00 0.00 39.39 3.06
619 681 9.535878 CTCCCTCTGTAAACTAAAATAGTGATC 57.464 37.037 0.00 0.00 39.39 2.92
620 682 9.268282 TCCCTCTGTAAACTAAAATAGTGATCT 57.732 33.333 0.00 0.00 39.39 2.75
647 709 7.704789 ACGCTTTTATATTAGTTTACGGAGG 57.295 36.000 0.00 0.00 0.00 4.30
648 710 6.703165 ACGCTTTTATATTAGTTTACGGAGGG 59.297 38.462 0.00 0.00 0.00 4.30
649 711 6.925165 CGCTTTTATATTAGTTTACGGAGGGA 59.075 38.462 0.00 0.00 0.00 4.20
650 712 7.115947 CGCTTTTATATTAGTTTACGGAGGGAG 59.884 40.741 0.00 0.00 0.00 4.30
651 713 7.930325 GCTTTTATATTAGTTTACGGAGGGAGT 59.070 37.037 0.00 0.00 0.00 3.85
654 716 8.995027 TTATATTAGTTTACGGAGGGAGTACA 57.005 34.615 0.00 0.00 0.00 2.90
753 815 4.771577 ACCAAACCATGCACATCATCTTTA 59.228 37.500 0.00 0.00 31.79 1.85
816 878 4.320608 ACGCAAAGACCATGACAAAAAT 57.679 36.364 0.00 0.00 0.00 1.82
818 880 5.837437 ACGCAAAGACCATGACAAAAATAA 58.163 33.333 0.00 0.00 0.00 1.40
820 882 6.928492 ACGCAAAGACCATGACAAAAATAAAT 59.072 30.769 0.00 0.00 0.00 1.40
821 883 8.085296 ACGCAAAGACCATGACAAAAATAAATA 58.915 29.630 0.00 0.00 0.00 1.40
822 884 8.920665 CGCAAAGACCATGACAAAAATAAATAA 58.079 29.630 0.00 0.00 0.00 1.40
919 981 1.332195 AGGAAAAGGACTTGCAAGCC 58.668 50.000 26.27 25.00 0.00 4.35
952 1017 1.815613 CTCGACCTCAAAGCAGAGAGA 59.184 52.381 2.80 0.13 37.87 3.10
953 1018 1.815613 TCGACCTCAAAGCAGAGAGAG 59.184 52.381 2.80 0.00 37.87 3.20
963 1028 0.809241 GCAGAGAGAGGTGGCAATCG 60.809 60.000 0.00 0.00 0.00 3.34
975 1040 1.889573 GCAATCGACCAGCTAGGCC 60.890 63.158 0.00 0.00 43.14 5.19
977 1042 0.531532 CAATCGACCAGCTAGGCCAG 60.532 60.000 5.01 0.97 43.14 4.85
1102 1182 3.807538 GCGTCGAGGAGTACGGCA 61.808 66.667 9.75 0.00 39.46 5.69
1236 1316 0.393077 AGCGCGGCCAGATATACTTT 59.607 50.000 8.83 0.00 0.00 2.66
1289 1369 0.610687 AAGAAGAAGACCGGCTCCAG 59.389 55.000 0.00 0.00 0.00 3.86
1612 1692 4.035558 CGCATGGTTAATGTGTATGCTTCT 59.964 41.667 0.00 0.00 41.13 2.85
1618 1698 6.488344 TGGTTAATGTGTATGCTTCTTTGTGA 59.512 34.615 0.00 0.00 0.00 3.58
1627 1707 4.385358 TGCTTCTTTGTGACCCTTTTTC 57.615 40.909 0.00 0.00 0.00 2.29
1662 1742 5.480073 TCCATGTAATGTTTTTCCCTTCCTG 59.520 40.000 0.00 0.00 44.81 3.86
1663 1743 5.337491 CCATGTAATGTTTTTCCCTTCCTGG 60.337 44.000 0.00 0.00 44.81 4.45
1720 1800 6.769512 TGAATTCTTGTTCTAACTACTGCCT 58.230 36.000 7.05 0.00 0.00 4.75
1752 1832 9.042450 TCTCCTCTAACTATTATTGTTGTTCCA 57.958 33.333 2.51 0.00 0.00 3.53
1801 1882 3.157087 GTTTGATTGGCTCAAGGAGGAA 58.843 45.455 0.00 0.00 44.48 3.36
1816 1897 9.790344 CTCAAGGAGGAAGATAACATATGAAAT 57.210 33.333 10.38 1.88 0.00 2.17
1831 1912 2.250031 TGAAATTGGGCATGTGCTTCT 58.750 42.857 4.84 0.00 41.70 2.85
1832 1913 2.633967 TGAAATTGGGCATGTGCTTCTT 59.366 40.909 4.84 0.00 41.70 2.52
1833 1914 3.071312 TGAAATTGGGCATGTGCTTCTTT 59.929 39.130 4.84 1.00 41.70 2.52
1895 1982 7.202526 CACAACTTGTGTATGGAGTTTCAATT 58.797 34.615 13.02 0.00 43.08 2.32
1956 2043 0.919710 ATCCCCACTGCTTACCTTCC 59.080 55.000 0.00 0.00 0.00 3.46
2022 2109 8.429641 ACAACCAAGATACATATCGAAGGTTAT 58.570 33.333 17.52 9.82 40.49 1.89
2039 2126 7.096147 CGAAGGTTATATTAGAAACGAAGCCTC 60.096 40.741 0.00 0.00 0.00 4.70
2488 2576 8.591072 AGGATGCTACTACACTTTAAAGTAACA 58.409 33.333 20.15 7.03 37.08 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.713713 AAAATTAGGAGAAGAGAGAACAACTAC 57.286 33.333 0.00 0.00 0.00 2.73
44 45 9.277783 CTTCAAAATTAGGAGAAGAGAGAACAA 57.722 33.333 0.00 0.00 39.78 2.83
98 99 5.189934 ACTTTTCAAAATTACCCCCACACAA 59.810 36.000 0.00 0.00 0.00 3.33
99 100 4.717280 ACTTTTCAAAATTACCCCCACACA 59.283 37.500 0.00 0.00 0.00 3.72
121 122 4.065321 ACAGCTAGCACTGGAATGATAC 57.935 45.455 18.83 0.00 42.21 2.24
191 195 6.073657 GCAATTGCTCAAAGATACTGCAAAAA 60.074 34.615 23.21 0.00 44.90 1.94
280 284 4.183865 TGAGATCCGCAGAAAATACACAG 58.816 43.478 0.00 0.00 0.00 3.66
285 289 6.115446 AGACAAATGAGATCCGCAGAAAATA 58.885 36.000 0.00 0.00 0.00 1.40
346 394 3.873801 GCCAGTGTAGATGGGTGTTGATT 60.874 47.826 0.00 0.00 38.33 2.57
471 528 1.540115 TCTCTCCCTCCCATCTAGCT 58.460 55.000 0.00 0.00 0.00 3.32
520 579 4.006989 CACGTTCAGTGGAATTTATGGGA 58.993 43.478 0.00 0.00 46.77 4.37
589 651 9.544579 ACTATTTTAGTTTACAGAGGGAGTACT 57.455 33.333 0.00 0.00 34.86 2.73
621 683 8.606602 CCTCCGTAAACTAATATAAAAGCGTTT 58.393 33.333 2.53 2.53 0.00 3.60
622 684 7.225341 CCCTCCGTAAACTAATATAAAAGCGTT 59.775 37.037 0.00 0.00 0.00 4.84
623 685 6.703165 CCCTCCGTAAACTAATATAAAAGCGT 59.297 38.462 0.00 0.00 0.00 5.07
624 686 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
625 687 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
628 690 9.420118 TGTACTCCCTCCGTAAACTAATATAAA 57.580 33.333 0.00 0.00 0.00 1.40
629 691 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
630 692 9.592196 AATGTACTCCCTCCGTAAACTAATATA 57.408 33.333 0.00 0.00 0.00 0.86
631 693 8.488308 AATGTACTCCCTCCGTAAACTAATAT 57.512 34.615 0.00 0.00 0.00 1.28
632 694 7.902920 AATGTACTCCCTCCGTAAACTAATA 57.097 36.000 0.00 0.00 0.00 0.98
633 695 6.803366 AATGTACTCCCTCCGTAAACTAAT 57.197 37.500 0.00 0.00 0.00 1.73
634 696 7.118723 TCTAATGTACTCCCTCCGTAAACTAA 58.881 38.462 0.00 0.00 0.00 2.24
635 697 6.662755 TCTAATGTACTCCCTCCGTAAACTA 58.337 40.000 0.00 0.00 0.00 2.24
636 698 5.513233 TCTAATGTACTCCCTCCGTAAACT 58.487 41.667 0.00 0.00 0.00 2.66
637 699 5.841957 TCTAATGTACTCCCTCCGTAAAC 57.158 43.478 0.00 0.00 0.00 2.01
638 700 7.232127 CCTTATCTAATGTACTCCCTCCGTAAA 59.768 40.741 0.00 0.00 0.00 2.01
639 701 6.718454 CCTTATCTAATGTACTCCCTCCGTAA 59.282 42.308 0.00 0.00 0.00 3.18
640 702 6.183361 ACCTTATCTAATGTACTCCCTCCGTA 60.183 42.308 0.00 0.00 0.00 4.02
641 703 5.078256 CCTTATCTAATGTACTCCCTCCGT 58.922 45.833 0.00 0.00 0.00 4.69
642 704 5.078256 ACCTTATCTAATGTACTCCCTCCG 58.922 45.833 0.00 0.00 0.00 4.63
643 705 6.997942 AACCTTATCTAATGTACTCCCTCC 57.002 41.667 0.00 0.00 0.00 4.30
753 815 6.957853 AAGAGGAAATGAAAATTGGGGAAT 57.042 33.333 0.00 0.00 0.00 3.01
818 880 8.588290 TGTCCAAGGTAGCATACAAATTTATT 57.412 30.769 0.00 0.00 45.43 1.40
820 882 9.860650 ATATGTCCAAGGTAGCATACAAATTTA 57.139 29.630 0.00 0.00 45.43 1.40
821 883 8.632679 CATATGTCCAAGGTAGCATACAAATTT 58.367 33.333 0.00 0.00 45.43 1.82
822 884 7.998383 TCATATGTCCAAGGTAGCATACAAATT 59.002 33.333 1.90 0.00 45.43 1.82
823 885 7.517320 TCATATGTCCAAGGTAGCATACAAAT 58.483 34.615 1.90 0.00 45.43 2.32
824 886 6.894682 TCATATGTCCAAGGTAGCATACAAA 58.105 36.000 1.90 0.00 45.43 2.83
919 981 1.028905 GGTCGAGGAGGATGTCTCTG 58.971 60.000 0.00 0.00 42.10 3.35
952 1017 1.264749 TAGCTGGTCGATTGCCACCT 61.265 55.000 0.00 0.00 33.36 4.00
953 1018 0.811616 CTAGCTGGTCGATTGCCACC 60.812 60.000 0.00 0.00 31.85 4.61
963 1028 0.107945 CAGAACTGGCCTAGCTGGTC 60.108 60.000 3.32 0.00 41.87 4.02
975 1040 7.397892 TGTATTCTCTCTAGGTTCAGAACTG 57.602 40.000 13.13 4.55 0.00 3.16
977 1042 7.708752 CCATTGTATTCTCTCTAGGTTCAGAAC 59.291 40.741 4.52 4.52 0.00 3.01
1236 1316 2.833582 GAGGACGCCGGGATGAGA 60.834 66.667 2.18 0.00 0.00 3.27
1357 1437 4.794241 CTTAACGTGGCTGCGCGC 62.794 66.667 27.26 27.26 38.13 6.86
1612 1692 6.885376 TGTACACTTAGAAAAAGGGTCACAAA 59.115 34.615 0.00 0.00 35.23 2.83
1618 1698 6.195600 TGGATGTACACTTAGAAAAAGGGT 57.804 37.500 0.00 0.00 37.67 4.34
1662 1742 7.038445 CCCTCTCCATGTCCATCATATATATCC 60.038 44.444 0.00 0.00 34.67 2.59
1663 1743 7.732140 TCCCTCTCCATGTCCATCATATATATC 59.268 40.741 0.00 0.00 34.67 1.63
1752 1832 5.174037 TCCACAAAAACGGAGGATAGAAT 57.826 39.130 0.00 0.00 0.00 2.40
1801 1882 7.663827 CACATGCCCAATTTCATATGTTATCT 58.336 34.615 1.90 0.00 0.00 1.98
1956 2043 2.960384 TGCTTGGCTCCATGGATTATTG 59.040 45.455 16.63 4.00 0.00 1.90
2022 2109 6.882140 TGGAAATTGAGGCTTCGTTTCTAATA 59.118 34.615 19.01 7.35 34.04 0.98
2039 2126 7.325694 AGAAACTAAGGCATGATTGGAAATTG 58.674 34.615 0.00 0.00 0.00 2.32
2488 2576 5.302357 GCTTTAGCACACATTCTTAAGCT 57.698 39.130 0.00 0.00 40.06 3.74


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

AutoCloner maintained by Alex Coulton.