Multiple sequence alignment - TraesCS3A01G508200

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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 TraesCS3A01G508200 chr3A 100.000 3096 0 0 647 3742 729391314 729394409 0.000000e+00 5718.0
1 TraesCS3A01G508200 chr3A 88.940 1293 108 14 1820 3105 729316006 729314742 0.000000e+00 1563.0
2 TraesCS3A01G508200 chr3A 85.514 925 76 28 825 1702 729317207 729316294 0.000000e+00 913.0
3 TraesCS3A01G508200 chr3A 89.171 434 30 11 2971 3398 729314741 729314319 3.310000e-145 525.0
4 TraesCS3A01G508200 chr3A 100.000 115 0 0 1 115 729390668 729390782 2.930000e-51 213.0
5 TraesCS3A01G508200 chr3D 93.736 1804 94 8 1920 3713 599177690 599179484 0.000000e+00 2687.0
6 TraesCS3A01G508200 chr3D 96.750 1077 16 3 647 1704 599175819 599176895 0.000000e+00 1777.0
7 TraesCS3A01G508200 chr3D 89.722 1294 102 17 1820 3105 599268191 599266921 0.000000e+00 1624.0
8 TraesCS3A01G508200 chr3D 86.504 904 73 21 825 1704 599269372 599268494 0.000000e+00 948.0
9 TraesCS3A01G508200 chr3D 89.016 437 31 13 2971 3398 599266920 599266492 3.310000e-145 525.0
10 TraesCS3A01G508200 chr3D 96.429 112 3 1 1 112 599175452 599175562 2.300000e-42 183.0
11 TraesCS3A01G508200 chr2D 91.071 336 25 5 3412 3742 609655885 609656220 2.050000e-122 449.0
12 TraesCS3A01G508200 chr6D 90.476 336 27 5 3412 3742 113909030 113909365 4.440000e-119 438.0
13 TraesCS3A01G508200 chr6D 90.203 296 24 5 3452 3742 283808270 283807975 7.580000e-102 381.0
14 TraesCS3A01G508200 chr5D 89.881 336 29 4 3412 3742 456573381 456573046 9.600000e-116 427.0
15 TraesCS3A01G508200 chr4B 86.186 333 41 4 3414 3742 626777407 626777738 4.600000e-94 355.0
16 TraesCS3A01G508200 chr1B 85.795 176 20 5 3572 3742 629324028 629323853 8.260000e-42 182.0
17 TraesCS3A01G508200 chr7D 95.556 45 1 1 3699 3742 478331393 478331437 1.860000e-08 71.3


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 TraesCS3A01G508200 chr3A 729390668 729394409 3741 False 2965.500000 5718 100.000000 1 3742 2 chr3A.!!$F1 3741
1 TraesCS3A01G508200 chr3A 729314319 729317207 2888 True 1000.333333 1563 87.875000 825 3398 3 chr3A.!!$R1 2573
2 TraesCS3A01G508200 chr3D 599175452 599179484 4032 False 1549.000000 2687 95.638333 1 3713 3 chr3D.!!$F1 3712
3 TraesCS3A01G508200 chr3D 599266492 599269372 2880 True 1032.333333 1624 88.414000 825 3398 3 chr3D.!!$R1 2573

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
837 838 1.033746 CGGCTAGTGGGTCGGTTCTA 61.034 60.000 0.00 0.0 0.00 2.10 F
863 864 1.094785 GCCCATAAAAGAAGCGCAGA 58.905 50.000 11.47 0.0 0.00 4.26 F
1761 2041 1.628846 GTAGGCAAAGTTCCAGAGGGA 59.371 52.381 0.00 0.0 43.03 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 2144 1.134220 TCAAGCACAGGAAAGGACGTT 60.134 47.619 0.00 0.0 0.0 3.99 R
2180 2895 1.445582 GACAACACCGCGACTAGGG 60.446 63.158 8.23 0.0 0.0 3.53 R
3578 4437 0.038599 TACTGTAGCCGAGGTGGACA 59.961 55.000 0.00 0.0 42.0 4.02 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
837 838 1.033746 CGGCTAGTGGGTCGGTTCTA 61.034 60.000 0.00 0.00 0.00 2.10
863 864 1.094785 GCCCATAAAAGAAGCGCAGA 58.905 50.000 11.47 0.00 0.00 4.26
883 899 2.441750 GACCATGGCCCTGGAGTATTTA 59.558 50.000 31.47 0.00 39.73 1.40
887 903 4.536765 CATGGCCCTGGAGTATTTAACTT 58.463 43.478 0.00 0.00 39.07 2.66
1017 1035 3.116590 AGGAGATGGAGGTGATGGATGTA 60.117 47.826 0.00 0.00 0.00 2.29
1417 1478 2.267351 CCCCTGCATGCGTTTCACA 61.267 57.895 14.09 0.00 0.00 3.58
1540 1601 2.728817 CCCCTCGATGTCTACGGC 59.271 66.667 0.00 0.00 0.00 5.68
1711 1776 8.934023 TGGGAACAGAATTCACTAAATAAACT 57.066 30.769 8.44 0.00 35.01 2.66
1761 2041 1.628846 GTAGGCAAAGTTCCAGAGGGA 59.371 52.381 0.00 0.00 43.03 4.20
1863 2144 7.009448 CAGCGCATTTGCAGATCTTTAAATTAA 59.991 33.333 11.47 0.00 42.21 1.40
1891 2172 5.189736 TCCTTTCCTGTGCTTGAGTATACAT 59.810 40.000 5.50 0.00 0.00 2.29
2043 2753 9.685276 AGATGAATTATGTTCCAGTGAATACAA 57.315 29.630 0.00 0.00 31.98 2.41
2049 2759 6.992063 ATGTTCCAGTGAATACAATCTCAC 57.008 37.500 0.00 0.00 41.90 3.51
2087 2797 7.640577 TGGATGGGTTGAATATATTCCACTA 57.359 36.000 22.26 15.07 35.97 2.74
2091 2802 6.769512 TGGGTTGAATATATTCCACTAGAGC 58.230 40.000 22.26 10.30 35.97 4.09
2180 2895 3.887621 TCATACCTAACACTGACAGGC 57.112 47.619 7.51 0.00 32.31 4.85
2228 2943 5.822519 GCATGATAACTCACATTTGGAGGTA 59.177 40.000 0.00 0.00 38.80 3.08
2252 2967 3.251571 GCTCAAAGTGAAGGGTACTACG 58.748 50.000 0.00 0.00 0.00 3.51
2372 3087 6.540189 AGATGCAATACTACACTGCTTTTAGG 59.460 38.462 0.00 0.00 37.00 2.69
2402 3117 2.307049 GCCACGATTTTTGTTCGAGTG 58.693 47.619 0.00 0.00 39.81 3.51
2510 3225 7.696755 TGGAACTTAATGATGATGAATTGTCG 58.303 34.615 0.00 0.00 0.00 4.35
2661 3376 4.121691 CAGCTGAAGATGCCGGAG 57.878 61.111 8.42 0.00 0.00 4.63
2666 3381 0.177604 CTGAAGATGCCGGAGAAGCT 59.822 55.000 5.05 0.00 0.00 3.74
2820 3535 1.884235 ACTGTAGACAAGTGGCTTGC 58.116 50.000 8.59 2.85 44.43 4.01
2997 3714 8.128322 AGTCTTTTAGAAGCTCACAGAGATTA 57.872 34.615 0.00 0.00 38.45 1.75
3127 3976 4.943705 GGTTCAAAGCCATCAGAATCACTA 59.056 41.667 0.00 0.00 0.00 2.74
3160 4011 4.640201 TGTGAAAATATGAGGCCAGTTAGC 59.360 41.667 5.01 0.00 0.00 3.09
3199 4051 2.093181 TGTACCGCCATATTCAGCACTT 60.093 45.455 0.00 0.00 0.00 3.16
3242 4094 7.290857 TGATGTAGTTGACTTAGCGAATTTC 57.709 36.000 0.00 0.00 0.00 2.17
3244 4096 7.386573 TGATGTAGTTGACTTAGCGAATTTCAA 59.613 33.333 0.00 1.19 0.00 2.69
3403 4257 0.760945 AGCTTCATCCTAGTCCCCCG 60.761 60.000 0.00 0.00 0.00 5.73
3404 4258 1.749033 CTTCATCCTAGTCCCCCGC 59.251 63.158 0.00 0.00 0.00 6.13
3405 4259 2.088674 CTTCATCCTAGTCCCCCGCG 62.089 65.000 0.00 0.00 0.00 6.46
3406 4260 2.838225 CATCCTAGTCCCCCGCGT 60.838 66.667 4.92 0.00 0.00 6.01
3407 4261 1.529948 CATCCTAGTCCCCCGCGTA 60.530 63.158 4.92 0.00 0.00 4.42
3408 4262 1.228490 ATCCTAGTCCCCCGCGTAG 60.228 63.158 4.92 0.00 0.00 3.51
3409 4263 2.004408 ATCCTAGTCCCCCGCGTAGT 62.004 60.000 4.92 0.00 0.00 2.73
3410 4264 2.487532 CCTAGTCCCCCGCGTAGTG 61.488 68.421 4.92 0.00 38.04 2.74
3476 4335 2.364448 GTCGCTCTCCCTCCCCTT 60.364 66.667 0.00 0.00 0.00 3.95
3482 4341 3.787001 CTCCCTCCCCTTGCCGTC 61.787 72.222 0.00 0.00 0.00 4.79
3578 4437 4.787280 CTCGGTGGGGGAGGCTCT 62.787 72.222 15.23 0.00 0.00 4.09
3595 4454 0.965866 TCTGTCCACCTCGGCTACAG 60.966 60.000 0.00 0.00 39.10 2.74
3596 4455 1.228769 TGTCCACCTCGGCTACAGT 60.229 57.895 0.00 0.00 33.14 3.55
3597 4456 0.038599 TGTCCACCTCGGCTACAGTA 59.961 55.000 0.00 0.00 33.14 2.74
3598 4457 0.455005 GTCCACCTCGGCTACAGTAC 59.545 60.000 0.00 0.00 33.14 2.73
3599 4458 1.028330 TCCACCTCGGCTACAGTACG 61.028 60.000 0.00 0.00 33.14 3.67
3601 4460 1.676635 ACCTCGGCTACAGTACGCA 60.677 57.895 4.92 0.00 0.00 5.24
3605 4464 0.109458 TCGGCTACAGTACGCAGTTG 60.109 55.000 4.92 0.00 37.78 3.16
3610 4469 2.334838 CTACAGTACGCAGTTGTTCCC 58.665 52.381 0.00 0.00 37.78 3.97
3611 4470 0.466543 ACAGTACGCAGTTGTTCCCA 59.533 50.000 0.00 0.00 37.78 4.37
3613 4472 0.599204 AGTACGCAGTTGTTCCCACG 60.599 55.000 0.00 0.00 37.78 4.94
3615 4474 0.598158 TACGCAGTTGTTCCCACGAC 60.598 55.000 0.00 0.00 37.78 4.34
3639 4498 3.108289 CAGCGGCGCTCATATCCG 61.108 66.667 34.22 15.56 45.46 4.18
3647 4506 3.514777 GCTCATATCCGGCGATTCA 57.485 52.632 9.30 0.00 0.00 2.57
3696 4555 2.202851 CAGCTGGCTCGCGAATCT 60.203 61.111 11.33 0.00 34.40 2.40
3708 4567 0.179171 GCGAATCTGACCTTCGACGA 60.179 55.000 15.39 0.00 46.36 4.20
3713 4572 2.979197 CTGACCTTCGACGACGGCT 61.979 63.158 19.41 7.61 40.21 5.52
3714 4573 2.202453 GACCTTCGACGACGGCTC 60.202 66.667 19.41 12.35 40.21 4.70
3715 4574 3.680338 GACCTTCGACGACGGCTCC 62.680 68.421 19.41 6.32 40.21 4.70
3716 4575 3.441290 CCTTCGACGACGGCTCCT 61.441 66.667 7.52 0.00 40.21 3.69
3717 4576 2.100603 CTTCGACGACGGCTCCTC 59.899 66.667 7.55 0.00 40.21 3.71
3718 4577 2.359602 TTCGACGACGGCTCCTCT 60.360 61.111 7.55 0.00 40.21 3.69
3719 4578 1.924320 CTTCGACGACGGCTCCTCTT 61.924 60.000 7.55 0.00 40.21 2.85
3720 4579 1.919956 TTCGACGACGGCTCCTCTTC 61.920 60.000 7.55 0.00 40.21 2.87
3721 4580 2.100603 GACGACGGCTCCTCTTCG 59.899 66.667 0.00 0.00 37.50 3.79
3722 4581 3.398353 GACGACGGCTCCTCTTCGG 62.398 68.421 0.00 0.00 35.77 4.30
3723 4582 4.856607 CGACGGCTCCTCTTCGGC 62.857 72.222 0.00 0.00 0.00 5.54
3729 4588 4.521062 CTCCTCTTCGGCGGCCAG 62.521 72.222 20.71 10.04 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
863 864 1.308877 AAATACTCCAGGGCCATGGT 58.691 50.000 34.18 19.96 41.43 3.55
883 899 2.288729 GGGTCGCGTTGTCTAAAAAGTT 59.711 45.455 5.77 0.00 0.00 2.66
887 903 0.106335 TGGGGTCGCGTTGTCTAAAA 59.894 50.000 5.77 0.00 0.00 1.52
1017 1035 2.194056 CGCTCCATCCCAATGCCT 59.806 61.111 0.00 0.00 0.00 4.75
1424 1485 2.087646 GAAATCAGGGTGCCTCAAGTC 58.912 52.381 0.00 0.00 0.00 3.01
1644 1705 5.832539 ATCCATGTCCTATAGTGGGAAAG 57.167 43.478 7.15 0.00 34.35 2.62
1707 1772 9.461312 TGTATGGCTTTGAGATTATACAAGTTT 57.539 29.630 0.00 0.00 30.61 2.66
1708 1773 9.632638 ATGTATGGCTTTGAGATTATACAAGTT 57.367 29.630 0.00 0.00 35.44 2.66
1709 1774 9.060347 CATGTATGGCTTTGAGATTATACAAGT 57.940 33.333 0.00 0.00 35.44 3.16
1710 1775 8.509690 CCATGTATGGCTTTGAGATTATACAAG 58.490 37.037 0.00 0.00 41.75 3.16
1711 1776 8.394971 CCATGTATGGCTTTGAGATTATACAA 57.605 34.615 0.00 0.00 41.75 2.41
1739 2019 2.040412 CCCTCTGGAACTTTGCCTACTT 59.960 50.000 0.00 0.00 0.00 2.24
1769 2049 5.509716 AAACTGGACATATGCATCATGTG 57.490 39.130 19.77 11.29 38.59 3.21
1818 2099 3.853831 TGCAAACAGAGCCATTACATG 57.146 42.857 0.00 0.00 0.00 3.21
1863 2144 1.134220 TCAAGCACAGGAAAGGACGTT 60.134 47.619 0.00 0.00 0.00 3.99
1868 2149 4.832248 TGTATACTCAAGCACAGGAAAGG 58.168 43.478 4.17 0.00 0.00 3.11
1941 2651 9.778741 AAGACCGCAGAGAAATATATTCAATTA 57.221 29.630 0.00 0.00 0.00 1.40
2070 2780 9.998106 TTAAGGCTCTAGTGGAATATATTCAAC 57.002 33.333 21.09 21.09 40.31 3.18
2087 2797 9.959721 TTGTCTTTCAGTAATAATTAAGGCTCT 57.040 29.630 0.00 0.00 0.00 4.09
2102 2813 8.547967 ACGATGTAATGTATTTGTCTTTCAGT 57.452 30.769 0.00 0.00 0.00 3.41
2103 2814 9.825972 AAACGATGTAATGTATTTGTCTTTCAG 57.174 29.630 0.00 0.00 0.00 3.02
2180 2895 1.445582 GACAACACCGCGACTAGGG 60.446 63.158 8.23 0.00 0.00 3.53
2228 2943 4.373156 AGTACCCTTCACTTTGAGCATT 57.627 40.909 0.00 0.00 0.00 3.56
2457 3172 5.119434 GTGAGATTTGGACGTCTCTTTTCTC 59.881 44.000 16.46 18.52 41.10 2.87
2544 3259 6.423604 CCATCCTTTTCAACACAAATAACACC 59.576 38.462 0.00 0.00 0.00 4.16
2820 3535 2.095768 CGCACCAGTTCACACTAATTGG 60.096 50.000 0.00 0.00 40.91 3.16
3098 3947 4.671831 TCTGATGGCTTTGAACCCAAATA 58.328 39.130 0.00 0.00 41.03 1.40
3127 3976 7.603784 GGCCTCATATTTTCACAAAAACAGATT 59.396 33.333 0.00 0.00 37.20 2.40
3160 4011 5.570589 CGGTACAAGGTACTAAACGAAAGAG 59.429 44.000 6.50 0.00 38.49 2.85
3199 4051 0.251297 AGCTTGCCATGGTTAGCACA 60.251 50.000 29.71 11.97 39.10 4.57
3403 4257 0.870307 CCTATGTCGCCACACTACGC 60.870 60.000 0.00 0.00 34.48 4.42
3404 4258 0.870307 GCCTATGTCGCCACACTACG 60.870 60.000 0.00 0.00 34.48 3.51
3405 4259 0.870307 CGCCTATGTCGCCACACTAC 60.870 60.000 0.00 0.00 34.48 2.73
3406 4260 1.435925 CGCCTATGTCGCCACACTA 59.564 57.895 0.00 0.00 34.48 2.74
3407 4261 2.184322 CGCCTATGTCGCCACACT 59.816 61.111 0.00 0.00 34.48 3.55
3408 4262 2.845752 TTCCGCCTATGTCGCCACAC 62.846 60.000 0.00 0.00 34.48 3.82
3409 4263 2.572095 CTTCCGCCTATGTCGCCACA 62.572 60.000 0.00 0.00 36.78 4.17
3410 4264 1.883084 CTTCCGCCTATGTCGCCAC 60.883 63.158 0.00 0.00 0.00 5.01
3419 4278 1.681076 GGTTTGGGTCTTCCGCCTA 59.319 57.895 0.00 0.00 38.76 3.93
3447 4306 2.829458 AGCGACGAGGAGGGTAGC 60.829 66.667 0.00 0.00 36.44 3.58
3553 4412 3.083349 CCCCACCGAGATCTGCCA 61.083 66.667 0.00 0.00 0.00 4.92
3578 4437 0.038599 TACTGTAGCCGAGGTGGACA 59.961 55.000 0.00 0.00 42.00 4.02
3595 4454 0.598158 TCGTGGGAACAACTGCGTAC 60.598 55.000 0.00 0.00 46.06 3.67
3596 4455 0.598158 GTCGTGGGAACAACTGCGTA 60.598 55.000 0.00 0.00 46.06 4.42
3597 4456 1.885850 GTCGTGGGAACAACTGCGT 60.886 57.895 0.00 0.00 46.06 5.24
3598 4457 1.157870 AAGTCGTGGGAACAACTGCG 61.158 55.000 0.00 0.00 46.06 5.18
3599 4458 0.586802 GAAGTCGTGGGAACAACTGC 59.413 55.000 0.00 0.00 46.06 4.40
3601 4460 0.878961 GCGAAGTCGTGGGAACAACT 60.879 55.000 2.25 0.00 46.06 3.16
3635 4494 1.152963 CCCCTTTGAATCGCCGGAT 60.153 57.895 5.05 0.00 0.00 4.18
3639 4498 1.890174 CCAACCCCTTTGAATCGCC 59.110 57.895 0.00 0.00 37.39 5.54
3642 4501 1.644509 AAGGCCAACCCCTTTGAATC 58.355 50.000 5.01 0.00 42.48 2.52
3678 4537 2.510238 GATTCGCGAGCCAGCTGT 60.510 61.111 13.81 0.00 34.40 4.40
3692 4551 0.170561 CCGTCGTCGAAGGTCAGATT 59.829 55.000 17.88 0.00 39.71 2.40
3696 4555 2.974489 GAGCCGTCGTCGAAGGTCA 61.974 63.158 24.99 0.00 39.71 4.02


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

AutoCloner maintained by Alex Coulton.