Multiple sequence alignment - TraesCS1A01G327500

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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 TraesCS1A01G327500 chr1A 100.000 2357 0 0 1 2357 517092428 517090072 0.000000e+00 4353.0
1 TraesCS1A01G327500 chr1A 74.739 479 72 22 1801 2249 313266535 313266076 4.030000e-38 169.0
2 TraesCS1A01G327500 chr1A 91.429 70 3 2 1406 1475 517081496 517081430 2.490000e-15 93.5
3 TraesCS1A01G327500 chr1D 90.744 659 41 12 830 1475 420641477 420640826 0.000000e+00 861.0
4 TraesCS1A01G327500 chr1D 89.721 574 42 12 4 566 420642281 420641714 0.000000e+00 717.0
5 TraesCS1A01G327500 chr1D 87.291 598 51 15 1778 2357 420637342 420636752 0.000000e+00 660.0
6 TraesCS1A01G327500 chr1D 86.517 534 51 17 4 526 420644419 420643896 3.400000e-158 568.0
7 TraesCS1A01G327500 chr1D 83.362 583 67 20 1194 1767 420638048 420637487 1.620000e-141 512.0
8 TraesCS1A01G327500 chr1D 91.617 167 10 4 586 750 420641726 420641562 6.550000e-56 228.0
9 TraesCS1A01G327500 chr1D 74.104 502 79 25 1778 2249 234066661 234067141 2.420000e-35 159.0
10 TraesCS1A01G327500 chr1B 87.241 580 59 8 1788 2357 568875806 568875232 0.000000e+00 647.0
11 TraesCS1A01G327500 chr1B 83.577 548 44 21 585 1095 568877728 568877190 2.740000e-129 472.0
12 TraesCS1A01G327500 chr7B 93.023 43 2 1 2316 2357 682289386 682289428 7.030000e-06 62.1
13 TraesCS1A01G327500 chr6B 100.000 30 0 0 2043 2072 704801874 704801903 3.270000e-04 56.5
14 TraesCS1A01G327500 chr2B 96.970 33 1 0 2043 2075 31438897 31438865 3.270000e-04 56.5
15 TraesCS1A01G327500 chr2B 100.000 29 0 0 1629 1657 754470361 754470389 1.000000e-03 54.7


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 TraesCS1A01G327500 chr1A 517090072 517092428 2356 True 4353.0 4353 100.000000 1 2357 1 chr1A.!!$R3 2356
1 TraesCS1A01G327500 chr1D 420636752 420644419 7667 True 591.0 861 88.208667 4 2357 6 chr1D.!!$R1 2353
2 TraesCS1A01G327500 chr1B 568875232 568877728 2496 True 559.5 647 85.409000 585 2357 2 chr1B.!!$R1 1772

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
622 2772 1.271379 GCCCAACAGTGTGTCCTGTAT 60.271 52.381 0.0 0.0 44.74 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 8223 0.179127 ATCATCGCACTCACAGGACG 60.179 55.0 0.0 0.0 0.0 4.79 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 1.512926 AGATGCACGGTGAACAGTTC 58.487 50.000 13.29 6.32 0.00 3.01
49 50 1.400142 TGCACGGTGAACAGTTCTTTG 59.600 47.619 13.29 6.32 0.00 2.77
57 58 5.465390 CGGTGAACAGTTCTTTGAATACTCA 59.535 40.000 14.51 0.00 0.00 3.41
84 85 6.866770 TGAACACTTTCTTAATACTCCGTGAG 59.133 38.462 0.00 0.03 32.53 3.51
100 101 3.254657 CCGTGAGCATTTTCTTAAACCCA 59.745 43.478 0.00 0.00 0.00 4.51
454 2599 9.743057 TTTTAATATGCGATGACCATTTTAAGG 57.257 29.630 0.00 0.00 32.08 2.69
461 2606 9.733556 ATGCGATGACCATTTTAAGGTAATATA 57.266 29.630 0.00 0.00 40.09 0.86
566 2714 7.328737 GCATTTCGAAGTAGTTTCTTCAGTAGA 59.671 37.037 0.00 0.00 42.53 2.59
567 2715 9.193133 CATTTCGAAGTAGTTTCTTCAGTAGAA 57.807 33.333 0.00 0.00 42.53 2.10
577 2725 3.742433 CTTCAGTAGAAGCGATCCCAT 57.258 47.619 0.00 0.00 44.25 4.00
578 2726 4.855715 CTTCAGTAGAAGCGATCCCATA 57.144 45.455 0.00 0.00 44.25 2.74
579 2727 4.551388 CTTCAGTAGAAGCGATCCCATAC 58.449 47.826 0.00 0.00 44.25 2.39
580 2728 2.552743 TCAGTAGAAGCGATCCCATACG 59.447 50.000 0.00 0.00 0.00 3.06
581 2729 1.887198 AGTAGAAGCGATCCCATACGG 59.113 52.381 0.00 0.00 0.00 4.02
583 2731 1.410004 AGAAGCGATCCCATACGGAA 58.590 50.000 0.00 0.00 46.47 4.30
622 2772 1.271379 GCCCAACAGTGTGTCCTGTAT 60.271 52.381 0.00 0.00 44.74 2.29
818 2978 3.490759 GTACGAGCCGACCGACGA 61.491 66.667 0.00 0.00 45.77 4.20
819 2979 3.190849 TACGAGCCGACCGACGAG 61.191 66.667 0.00 0.00 45.77 4.18
820 2980 3.647649 TACGAGCCGACCGACGAGA 62.648 63.158 0.00 0.00 45.77 4.04
821 2981 4.225340 CGAGCCGACCGACGAGAG 62.225 72.222 0.00 0.00 45.77 3.20
822 2982 3.878519 GAGCCGACCGACGAGAGG 61.879 72.222 0.00 0.00 45.77 3.69
928 3113 2.786495 CCGACGGGTCCTCATCCTG 61.786 68.421 5.81 0.00 37.36 3.86
951 3136 1.762222 CTTGCTACCCACATACGCGC 61.762 60.000 5.73 0.00 0.00 6.86
958 3143 3.783327 CACATACGCGCGCCAACA 61.783 61.111 32.58 10.59 0.00 3.33
959 3144 2.817834 ACATACGCGCGCCAACAT 60.818 55.556 32.58 12.24 0.00 2.71
987 3172 4.876125 CCGATCCATCTATTATCCATCGG 58.124 47.826 3.26 3.26 43.75 4.18
990 3175 2.771943 TCCATCTATTATCCATCGGGGC 59.228 50.000 0.00 0.00 36.21 5.80
1007 3192 1.520342 GCCAGGTCACGATGAGAGC 60.520 63.158 0.00 0.00 0.00 4.09
1192 3377 1.591863 GAGTACGGCCGGATGAAGC 60.592 63.158 31.76 8.75 0.00 3.86
1218 3403 4.144727 GAGGAGGAGGAGGGCCGA 62.145 72.222 0.00 0.00 39.96 5.54
1361 6610 2.687805 CGGACGACGCCTGAAGAGA 61.688 63.158 0.00 0.00 34.82 3.10
1366 6615 0.457851 CGACGCCTGAAGAGAAGGAT 59.542 55.000 0.00 0.00 36.91 3.24
1367 6616 1.800655 CGACGCCTGAAGAGAAGGATG 60.801 57.143 0.00 0.00 36.91 3.51
1368 6617 1.478510 GACGCCTGAAGAGAAGGATGA 59.521 52.381 0.00 0.00 36.91 2.92
1369 6618 1.205893 ACGCCTGAAGAGAAGGATGAC 59.794 52.381 0.00 0.00 36.91 3.06
1372 6621 2.886081 CCTGAAGAGAAGGATGACGTG 58.114 52.381 0.00 0.00 36.91 4.49
1390 6639 1.400494 GTGGACGTTGTTGTTGCTTCT 59.600 47.619 0.00 0.00 0.00 2.85
1393 6642 1.846175 GACGTTGTTGTTGCTTCTTGC 59.154 47.619 0.00 0.00 43.25 4.01
1435 6685 2.158726 AGTTGAAGCTTGTTTCGGGGTA 60.159 45.455 2.10 0.00 0.00 3.69
1507 6757 4.385748 GTCGACTGAATTTCAAATTTGGGC 59.614 41.667 17.90 1.45 0.00 5.36
1521 6771 3.591196 TTTGGGCCAATCGATTTTGAG 57.409 42.857 21.65 0.00 0.00 3.02
1539 6789 6.465439 TTTGAGTAGTTTGTCAGAGTGAGA 57.535 37.500 0.00 0.00 0.00 3.27
1540 6790 5.697473 TGAGTAGTTTGTCAGAGTGAGAG 57.303 43.478 0.00 0.00 0.00 3.20
1543 6793 4.764823 AGTAGTTTGTCAGAGTGAGAGGAG 59.235 45.833 0.00 0.00 0.00 3.69
1544 6794 3.838565 AGTTTGTCAGAGTGAGAGGAGA 58.161 45.455 0.00 0.00 0.00 3.71
1547 6813 4.862902 TTGTCAGAGTGAGAGGAGAAAG 57.137 45.455 0.00 0.00 0.00 2.62
1555 6821 1.305718 AGAGGAGAAAGGGCTCGCT 60.306 57.895 0.00 0.00 35.74 4.93
1556 6822 1.153469 GAGGAGAAAGGGCTCGCTG 60.153 63.158 0.00 0.00 35.74 5.18
1557 6823 1.608717 GAGGAGAAAGGGCTCGCTGA 61.609 60.000 0.00 0.00 35.74 4.26
1560 6826 0.813210 GAGAAAGGGCTCGCTGATGG 60.813 60.000 0.00 0.00 0.00 3.51
1565 6831 3.512516 GGCTCGCTGATGGGCAAC 61.513 66.667 0.00 0.00 0.00 4.17
1583 6849 6.374417 GGCAACCCCATTATCTATCTTAGA 57.626 41.667 0.00 0.00 39.50 2.10
1584 6850 6.779860 GGCAACCCCATTATCTATCTTAGAA 58.220 40.000 0.00 0.00 38.50 2.10
1592 6870 9.620259 CCCATTATCTATCTTAGAATTTAGGGC 57.380 37.037 0.00 0.00 38.50 5.19
1613 6895 2.604614 CGGGGCTTCGTCAAAGAAAAAG 60.605 50.000 0.00 0.00 37.12 2.27
1647 6929 1.460305 GGGCTAGAGGGATGGCTGA 60.460 63.158 0.00 0.00 0.00 4.26
1691 6974 4.021925 GTGGGAGGCGGTTCAGCT 62.022 66.667 0.00 0.00 37.29 4.24
1743 7046 9.905713 AGGCAGAAAATTACAAACATCTAGATA 57.094 29.630 4.54 0.00 0.00 1.98
1776 8167 0.327924 ATTTCACATCGACTGGGCCA 59.672 50.000 5.85 5.85 0.00 5.36
1821 8237 0.597637 AAGAACGTCCTGTGAGTGCG 60.598 55.000 0.00 0.00 0.00 5.34
1862 8278 1.684450 TCTGTTGGTGCACTCGTCTTA 59.316 47.619 17.98 0.00 0.00 2.10
1870 8286 1.001974 TGCACTCGTCTTACAAGCCAT 59.998 47.619 0.00 0.00 0.00 4.40
1922 8340 7.649370 AAAGTAGAGCGTAGTTTAAAGAACC 57.351 36.000 0.00 0.00 0.00 3.62
1926 8344 5.608449 AGAGCGTAGTTTAAAGAACCAACT 58.392 37.500 0.00 0.00 35.00 3.16
2021 8440 2.248280 TGCGAGCAGGTTTCTAAACA 57.752 45.000 7.80 0.00 40.63 2.83
2129 8561 5.649557 TCGGAGCAATATTTGAAAACATGG 58.350 37.500 0.00 0.00 0.00 3.66
2132 8564 5.516339 GGAGCAATATTTGAAAACATGGACG 59.484 40.000 0.00 0.00 0.00 4.79
2342 8776 8.958119 TTGGTGAACAAACTAGCCTTATATAG 57.042 34.615 0.00 0.00 35.79 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.559536 TCAATGAGTATTCAAAGAACTGTTCAC 58.440 33.333 21.50 9.55 36.78 3.18
45 46 9.956720 AAGAAAGTGTTCAATGAGTATTCAAAG 57.043 29.630 0.00 0.00 34.95 2.77
57 58 7.876068 TCACGGAGTATTAAGAAAGTGTTCAAT 59.124 33.333 0.00 0.00 41.61 2.57
84 85 6.223120 AGTGTTCATGGGTTTAAGAAAATGC 58.777 36.000 0.00 0.00 0.00 3.56
269 2413 9.529325 TCGTCGAGTATTCAGAAAATATTCAAT 57.471 29.630 0.00 0.00 38.06 2.57
275 2419 8.752766 AACTTTCGTCGAGTATTCAGAAAATA 57.247 30.769 0.00 0.00 0.00 1.40
566 2714 3.680842 GTTCCGTATGGGATCGCTT 57.319 52.632 11.46 7.35 46.62 4.68
570 2718 3.722728 AGTAACGTTCCGTATGGGATC 57.277 47.619 2.82 0.00 46.62 3.36
571 2719 3.489738 CGAAGTAACGTTCCGTATGGGAT 60.490 47.826 2.82 0.00 46.62 3.85
572 2720 2.159393 CGAAGTAACGTTCCGTATGGGA 60.159 50.000 2.82 0.00 45.40 4.37
573 2721 2.187707 CGAAGTAACGTTCCGTATGGG 58.812 52.381 2.82 0.00 39.99 4.00
574 2722 2.867429 ACGAAGTAACGTTCCGTATGG 58.133 47.619 2.82 0.00 44.14 2.74
575 2723 4.031028 CCTACGAAGTAACGTTCCGTATG 58.969 47.826 18.44 14.38 45.13 2.39
576 2724 3.487544 GCCTACGAAGTAACGTTCCGTAT 60.488 47.826 18.44 2.26 45.13 3.06
577 2725 2.159572 GCCTACGAAGTAACGTTCCGTA 60.160 50.000 2.82 13.40 45.13 4.02
578 2726 1.401539 GCCTACGAAGTAACGTTCCGT 60.402 52.381 2.82 12.97 45.13 4.69
579 2727 1.262882 GCCTACGAAGTAACGTTCCG 58.737 55.000 2.82 7.40 45.13 4.30
580 2728 1.067635 TGGCCTACGAAGTAACGTTCC 60.068 52.381 2.82 0.00 45.13 3.62
581 2729 2.257034 CTGGCCTACGAAGTAACGTTC 58.743 52.381 2.82 0.00 45.13 3.95
582 2730 1.067354 CCTGGCCTACGAAGTAACGTT 60.067 52.381 5.88 5.88 45.13 3.99
583 2731 0.529378 CCTGGCCTACGAAGTAACGT 59.471 55.000 3.32 0.00 45.13 3.99
597 2745 3.297620 CACACTGTTGGGCCTGGC 61.298 66.667 11.05 11.05 0.00 4.85
622 2772 3.826754 CTAGACGCCTGCCTCGCA 61.827 66.667 0.00 0.00 36.92 5.10
770 2925 1.485514 CGTACACGTGTTCTTGGCG 59.514 57.895 28.55 16.71 34.11 5.69
818 2978 2.030717 GTGATATGATGTCGTCGCCTCT 60.031 50.000 0.00 0.00 0.00 3.69
819 2979 2.030717 AGTGATATGATGTCGTCGCCTC 60.031 50.000 0.00 0.00 0.00 4.70
820 2980 1.957177 AGTGATATGATGTCGTCGCCT 59.043 47.619 0.00 0.00 0.00 5.52
821 2981 2.320367 GAGTGATATGATGTCGTCGCC 58.680 52.381 0.00 0.00 0.00 5.54
822 2982 1.972640 CGAGTGATATGATGTCGTCGC 59.027 52.381 1.94 0.00 0.00 5.19
823 2983 1.972640 GCGAGTGATATGATGTCGTCG 59.027 52.381 8.66 8.66 33.19 5.12
824 2984 1.972640 CGCGAGTGATATGATGTCGTC 59.027 52.381 0.00 0.00 33.19 4.20
825 2985 1.333931 ACGCGAGTGATATGATGTCGT 59.666 47.619 15.93 0.00 46.97 4.34
928 3113 2.755650 CGTATGTGGGTAGCAAGGATC 58.244 52.381 0.00 0.00 0.00 3.36
958 3143 5.221263 GGATAATAGATGGATCGGCGTGTAT 60.221 44.000 6.85 0.00 0.00 2.29
959 3144 4.097437 GGATAATAGATGGATCGGCGTGTA 59.903 45.833 6.85 0.00 0.00 2.90
987 3172 2.187946 CTCATCGTGACCTGGCCC 59.812 66.667 0.00 0.00 0.00 5.80
990 3175 1.226802 CGCTCTCATCGTGACCTGG 60.227 63.158 0.00 0.00 0.00 4.45
1007 3192 4.580551 CCGCTAAGGGTACGGCCG 62.581 72.222 26.86 26.86 40.55 6.13
1072 3257 4.824515 CGGGTCCTCCTCCTCGCT 62.825 72.222 0.00 0.00 0.00 4.93
1074 3259 4.124943 TCCGGGTCCTCCTCCTCG 62.125 72.222 0.00 0.00 0.00 4.63
1140 3325 4.554363 CAGTACCGCCGCTCCTCG 62.554 72.222 0.00 0.00 38.08 4.63
1357 6606 0.811915 CGTCCACGTCATCCTTCTCT 59.188 55.000 0.00 0.00 34.11 3.10
1369 6618 0.098025 AAGCAACAACAACGTCCACG 59.902 50.000 0.00 0.00 46.33 4.94
1372 6621 2.450160 CAAGAAGCAACAACAACGTCC 58.550 47.619 0.00 0.00 0.00 4.79
1390 6639 3.003068 GCTCGACTAGTAATACTCCGCAA 59.997 47.826 0.00 0.00 0.00 4.85
1393 6642 3.055591 TCGCTCGACTAGTAATACTCCG 58.944 50.000 0.00 0.04 0.00 4.63
1482 6732 6.569610 GCCCAAATTTGAAATTCAGTCGACTA 60.570 38.462 19.57 3.69 0.00 2.59
1507 6757 6.898041 TGACAAACTACTCAAAATCGATTGG 58.102 36.000 12.25 7.56 0.00 3.16
1521 6771 4.762765 TCTCCTCTCACTCTGACAAACTAC 59.237 45.833 0.00 0.00 0.00 2.73
1539 6789 0.980231 ATCAGCGAGCCCTTTCTCCT 60.980 55.000 0.00 0.00 0.00 3.69
1540 6790 0.813210 CATCAGCGAGCCCTTTCTCC 60.813 60.000 0.00 0.00 0.00 3.71
1543 6793 1.821332 CCCATCAGCGAGCCCTTTC 60.821 63.158 0.00 0.00 0.00 2.62
1544 6794 2.273449 CCCATCAGCGAGCCCTTT 59.727 61.111 0.00 0.00 0.00 3.11
1547 6813 4.802051 TTGCCCATCAGCGAGCCC 62.802 66.667 0.00 0.00 34.65 5.19
1560 6826 6.374417 TCTAAGATAGATAATGGGGTTGCC 57.626 41.667 0.00 0.00 0.00 4.52
1574 6840 4.833390 CCCCGCCCTAAATTCTAAGATAG 58.167 47.826 0.00 0.00 0.00 2.08
1583 6849 1.453197 CGAAGCCCCGCCCTAAATT 60.453 57.895 0.00 0.00 0.00 1.82
1584 6850 2.192175 CGAAGCCCCGCCCTAAAT 59.808 61.111 0.00 0.00 0.00 1.40
1592 6870 0.948678 TTTTCTTTGACGAAGCCCCG 59.051 50.000 0.00 0.00 35.24 5.73
1613 6895 2.096442 CCCCGTCCGCGTTTAGTTC 61.096 63.158 4.92 0.00 36.15 3.01
1664 6947 4.760047 CCTCCCACCGCTGAACCG 62.760 72.222 0.00 0.00 0.00 4.44
1679 6962 3.553095 GAACCCAGCTGAACCGCCT 62.553 63.158 17.39 0.00 0.00 5.52
1691 6974 2.434331 CGCCCTTTCCTGAACCCA 59.566 61.111 0.00 0.00 0.00 4.51
1743 7046 7.653713 GTCGATGTGAAATAATGTCATACTCCT 59.346 37.037 0.00 0.00 0.00 3.69
1759 7062 1.003839 GTGGCCCAGTCGATGTGAA 60.004 57.895 0.00 0.00 0.00 3.18
1760 7063 2.171209 CTGTGGCCCAGTCGATGTGA 62.171 60.000 0.00 0.00 36.37 3.58
1776 8167 4.742201 ATTCTCGCACGCGGCTGT 62.742 61.111 12.47 0.00 41.67 4.40
1807 8223 0.179127 ATCATCGCACTCACAGGACG 60.179 55.000 0.00 0.00 0.00 4.79
1821 8237 1.488261 GGTCCGCGGTTCGAATCATC 61.488 60.000 27.15 0.00 41.67 2.92
1862 8278 4.215109 ACTACTTTGTTTCCATGGCTTGT 58.785 39.130 6.96 1.55 0.00 3.16
1898 8316 7.212274 TGGTTCTTTAAACTACGCTCTACTTT 58.788 34.615 0.00 0.00 0.00 2.66
2002 8421 2.248280 TGTTTAGAAACCTGCTCGCA 57.752 45.000 2.80 0.00 38.11 5.10
2075 8501 9.527566 CTGTTCACATTTTAAAGTTTTGTTGTG 57.472 29.630 0.00 4.20 35.67 3.33
2108 8540 5.516339 CGTCCATGTTTTCAAATATTGCTCC 59.484 40.000 0.00 0.00 0.00 4.70
2250 8682 4.116747 TGTGTCCACCAATTCACAAAAC 57.883 40.909 0.00 0.00 37.77 2.43
2255 8687 5.355596 TCAAAATTGTGTCCACCAATTCAC 58.644 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.