Multiple sequence alignment - TraesCS1A01G357600

Loading Multiple Alignment...

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 TraesCS1A01G357600 chr1A 100.000 3608 0 0 1 3608 540065301 540061694 0.000000e+00 6663
1 TraesCS1A01G357600 chr1D 96.725 1893 47 4 95 1975 444384917 444383028 0.000000e+00 3138
2 TraesCS1A01G357600 chr1D 97.449 1333 34 0 1968 3300 444382996 444381664 0.000000e+00 2274
3 TraesCS1A01G357600 chr1D 96.711 304 9 1 3296 3598 444377212 444376909 4.160000e-139 505
4 TraesCS1A01G357600 chr1D 95.062 81 3 1 1 80 444386240 444386160 3.780000e-25 126
5 TraesCS1A01G357600 chr1B 95.732 1640 60 8 1968 3598 604562859 604561221 0.000000e+00 2632
6 TraesCS1A01G357600 chr1B 95.224 1633 63 4 98 1717 604564838 604563208 0.000000e+00 2569
7 TraesCS1A01G357600 chr1B 87.249 698 59 13 2467 3162 604645361 604644692 0.000000e+00 769
8 TraesCS1A01G357600 chr1B 96.109 257 10 0 1719 1975 604563147 604562891 1.550000e-113 420
9 TraesCS1A01G357600 chr1B 97.333 75 1 1 7 80 604566138 604566064 3.780000e-25 126
10 TraesCS1A01G357600 chr7A 76.307 612 129 13 2041 2649 88176280 88175682 2.700000e-81 313


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 TraesCS1A01G357600 chr1A 540061694 540065301 3607 True 6663.00 6663 100.0000 1 3608 1 chr1A.!!$R1 3607
1 TraesCS1A01G357600 chr1D 444381664 444386240 4576 True 1846.00 3138 96.4120 1 3300 3 chr1D.!!$R2 3299
2 TraesCS1A01G357600 chr1B 604561221 604566138 4917 True 1436.75 2632 96.0995 7 3598 4 chr1B.!!$R2 3591
3 TraesCS1A01G357600 chr1B 604644692 604645361 669 True 769.00 769 87.2490 2467 3162 1 chr1B.!!$R1 695
4 TraesCS1A01G357600 chr7A 88175682 88176280 598 True 313.00 313 76.3070 2041 2649 1 chr7A.!!$R1 608

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
86 87 0.036483 TGATAGCAACAGCGCCTTCA 60.036 50.0 2.29 0.0 0.0 3.02 F
1057 2304 0.035915 GGAAGAGGAGGCAAGGTCAC 60.036 60.0 0.00 0.0 0.0 3.67 F
1201 2448 0.669318 TGTCAATCTCGCCGTGGAAC 60.669 55.0 0.00 0.0 0.0 3.62 F
2313 3660 1.803334 TCAACGATGTTGGGCTACAC 58.197 50.0 9.57 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1370 2617 0.107312 TTCCTCCTCCTCTCGTACCG 60.107 60.000 0.00 0.0 0.00 4.02 R
2217 3564 1.202794 TGTGCATGGCTTGAGACTTGA 60.203 47.619 4.32 0.0 30.42 3.02 R
2354 3701 1.539388 CGGTAGAACCAAGCATTTGCA 59.461 47.619 5.20 0.0 40.30 4.08 R
3453 4807 1.071228 ACACTACCCCGTGTTTCCTTC 59.929 52.381 0.00 0.0 45.27 3.46 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
80 81 8.694975 ATTCTATATTAGTGATAGCAACAGCG 57.305 34.615 0.00 0.00 0.00 5.18
81 82 6.093404 TCTATATTAGTGATAGCAACAGCGC 58.907 40.000 0.00 0.00 0.00 5.92
82 83 1.651987 TTAGTGATAGCAACAGCGCC 58.348 50.000 2.29 0.00 0.00 6.53
83 84 0.824109 TAGTGATAGCAACAGCGCCT 59.176 50.000 2.29 0.00 0.00 5.52
85 86 0.375106 GTGATAGCAACAGCGCCTTC 59.625 55.000 2.29 0.00 0.00 3.46
86 87 0.036483 TGATAGCAACAGCGCCTTCA 60.036 50.000 2.29 0.00 0.00 3.02
87 88 1.086696 GATAGCAACAGCGCCTTCAA 58.913 50.000 2.29 0.00 0.00 2.69
88 89 1.468520 GATAGCAACAGCGCCTTCAAA 59.531 47.619 2.29 0.00 0.00 2.69
89 90 0.874390 TAGCAACAGCGCCTTCAAAG 59.126 50.000 2.29 0.00 0.00 2.77
90 91 2.018324 GCAACAGCGCCTTCAAAGC 61.018 57.895 2.29 0.00 0.00 3.51
91 92 1.372128 CAACAGCGCCTTCAAAGCC 60.372 57.895 2.29 0.00 0.00 4.35
92 93 2.564721 AACAGCGCCTTCAAAGCCC 61.565 57.895 2.29 0.00 0.00 5.19
185 1419 6.619329 ATTATTTGGAGAGAGATAGAGGGC 57.381 41.667 0.00 0.00 0.00 5.19
335 1582 6.801575 TCATGTGTTGTATGCGAGATAAGTA 58.198 36.000 0.00 0.00 0.00 2.24
386 1633 5.447818 GCTTACATTCACTGGTAATGAGTGC 60.448 44.000 10.12 7.36 40.64 4.40
507 1754 4.842531 TCGACATTGATATATGGGCCAT 57.157 40.909 24.69 24.69 0.00 4.40
577 1824 1.676006 GGCGAATACCATGGTTTCAGG 59.324 52.381 25.38 14.27 0.00 3.86
632 1879 1.677576 CATGCACAACACAGGTGTCTT 59.322 47.619 5.41 0.00 44.13 3.01
676 1923 1.893808 AACACTCAACAGGCCTGCG 60.894 57.895 33.06 23.47 0.00 5.18
937 2184 0.688087 GTCCTCTCTCCGTCCCCATT 60.688 60.000 0.00 0.00 0.00 3.16
1011 2258 6.440010 ACCTATCTAGTCTCATGGATCCATTG 59.560 42.308 25.20 19.30 33.90 2.82
1057 2304 0.035915 GGAAGAGGAGGCAAGGTCAC 60.036 60.000 0.00 0.00 0.00 3.67
1201 2448 0.669318 TGTCAATCTCGCCGTGGAAC 60.669 55.000 0.00 0.00 0.00 3.62
1301 2548 1.816224 CAATAACTTTGGGGTGTCGGG 59.184 52.381 0.00 0.00 0.00 5.14
1364 2611 2.093306 GGTGACCATGTGATTGACGA 57.907 50.000 0.00 0.00 0.00 4.20
1370 2617 3.198068 ACCATGTGATTGACGACTATGC 58.802 45.455 0.00 0.00 0.00 3.14
1598 2845 7.815068 ACACAAGTAATCAATGTCTACTCTGAC 59.185 37.037 0.00 0.00 37.47 3.51
2211 3558 5.652744 AGCACTTTGTCACTACTAAAACG 57.347 39.130 0.00 0.00 0.00 3.60
2217 3564 5.994887 TTGTCACTACTAAAACGCATGTT 57.005 34.783 0.00 0.00 40.98 2.71
2313 3660 1.803334 TCAACGATGTTGGGCTACAC 58.197 50.000 9.57 0.00 0.00 2.90
2354 3701 6.326583 TCGATGAATAATAGTTCTGGTCCCTT 59.673 38.462 0.00 0.00 0.00 3.95
2479 3826 6.770785 GCCACCTTTCATATATAGTCACCAAA 59.229 38.462 0.00 0.00 0.00 3.28
2511 3858 1.065636 CCAGTGTGGAGTGAGCATCAT 60.066 52.381 0.00 0.00 44.81 2.45
2669 4016 6.706270 GTGAAGCTATAGCATTAAGGTAAGCA 59.294 38.462 26.07 3.06 45.16 3.91
2685 4032 8.747538 AAGGTAAGCATATAAACGAATTTCCT 57.252 30.769 0.00 0.00 0.00 3.36
2898 4247 8.364894 TGGCGTATATGTTGTCTCTATATGTTT 58.635 33.333 0.00 0.00 0.00 2.83
2948 4297 9.723601 ATTGTTGCCTTCATTACAAAATTGTAT 57.276 25.926 6.82 0.00 42.66 2.29
3268 4621 4.713824 TCCCAGTTGTCTCGTAGTATTG 57.286 45.455 0.00 0.00 0.00 1.90
3327 4681 0.520404 GCAATGACCAGCACTCACTG 59.480 55.000 0.00 0.00 37.42 3.66
3349 4703 6.379133 ACTGGTATTCATTTTGTCATGCTCAT 59.621 34.615 0.00 0.00 0.00 2.90
3351 4705 7.933396 TGGTATTCATTTTGTCATGCTCATAG 58.067 34.615 0.00 0.00 0.00 2.23
3363 4717 2.398588 TGCTCATAGGACCTAGGGTTG 58.601 52.381 14.81 3.59 35.25 3.77
3451 4805 6.006275 ACATATACTGGCATGGAAGTCTTT 57.994 37.500 0.00 0.00 0.00 2.52
3453 4807 6.319658 ACATATACTGGCATGGAAGTCTTTTG 59.680 38.462 0.00 0.00 0.00 2.44
3488 4842 7.064966 ACGGGGTAGTGTTTTATTATTCTTTCG 59.935 37.037 0.00 0.00 0.00 3.46
3490 4844 7.337689 GGGGTAGTGTTTTATTATTCTTTCGGT 59.662 37.037 0.00 0.00 0.00 4.69
3524 4878 8.734386 GTTGATTCAATCCTACTGAAGTTCATT 58.266 33.333 5.91 3.25 36.30 2.57
3559 4913 9.109393 TGTAACTTGGTTGATAGCTCATATTTC 57.891 33.333 0.00 0.00 0.00 2.17
3598 4955 3.087031 ACATGAGCATTTCTTGGGAGTG 58.913 45.455 0.00 0.00 35.76 3.51
3599 4956 2.957402 TGAGCATTTCTTGGGAGTGT 57.043 45.000 0.00 0.00 0.00 3.55
3600 4957 2.783135 TGAGCATTTCTTGGGAGTGTC 58.217 47.619 0.00 0.00 0.00 3.67
3601 4958 1.734465 GAGCATTTCTTGGGAGTGTCG 59.266 52.381 0.00 0.00 0.00 4.35
3602 4959 1.072331 AGCATTTCTTGGGAGTGTCGT 59.928 47.619 0.00 0.00 0.00 4.34
3603 4960 1.880027 GCATTTCTTGGGAGTGTCGTT 59.120 47.619 0.00 0.00 0.00 3.85
3604 4961 2.095718 GCATTTCTTGGGAGTGTCGTTC 60.096 50.000 0.00 0.00 0.00 3.95
3605 4962 2.992124 TTTCTTGGGAGTGTCGTTCA 57.008 45.000 0.00 0.00 0.00 3.18
3606 4963 3.485463 TTTCTTGGGAGTGTCGTTCAT 57.515 42.857 0.00 0.00 0.00 2.57
3607 4964 4.610605 TTTCTTGGGAGTGTCGTTCATA 57.389 40.909 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.163195 ACAGTCCTGTGATGGTTTTACTTCT 60.163 40.000 0.00 0.00 43.11 2.85
81 82 3.944015 CACTATTCAGAGGGCTTTGAAGG 59.056 47.826 0.00 0.00 36.81 3.46
82 83 4.633565 GTCACTATTCAGAGGGCTTTGAAG 59.366 45.833 0.00 0.00 36.81 3.02
83 84 4.565652 GGTCACTATTCAGAGGGCTTTGAA 60.566 45.833 0.00 0.00 37.68 2.69
85 86 3.274288 GGTCACTATTCAGAGGGCTTTG 58.726 50.000 0.00 0.00 0.00 2.77
86 87 2.912956 TGGTCACTATTCAGAGGGCTTT 59.087 45.455 0.00 0.00 0.00 3.51
87 88 2.551270 TGGTCACTATTCAGAGGGCTT 58.449 47.619 0.00 0.00 0.00 4.35
88 89 2.254152 TGGTCACTATTCAGAGGGCT 57.746 50.000 0.00 0.00 0.00 5.19
89 90 4.530161 AGATATGGTCACTATTCAGAGGGC 59.470 45.833 0.00 0.00 0.00 5.19
90 91 7.178573 TCTAGATATGGTCACTATTCAGAGGG 58.821 42.308 0.00 0.00 0.00 4.30
91 92 8.642935 TTCTAGATATGGTCACTATTCAGAGG 57.357 38.462 0.00 0.00 0.00 3.69
185 1419 0.179181 GACACCATGATGTTGCAGCG 60.179 55.000 0.00 0.00 31.24 5.18
386 1633 6.930722 TGAGTAACTATGCCACACATATGATG 59.069 38.462 10.38 7.21 40.48 3.07
444 1691 6.125327 TGTCAACGACATTTTGTTGTGTAT 57.875 33.333 10.97 0.00 43.82 2.29
507 1754 0.899019 TCATCCGGTTTGGTCATCGA 59.101 50.000 0.00 0.00 39.52 3.59
577 1824 1.135139 TCCTCTCATCGCAGTGTAAGC 59.865 52.381 0.00 0.00 0.00 3.09
632 1879 5.432680 AAATCTCAATCTTGCCAGAGAGA 57.567 39.130 8.62 8.62 40.14 3.10
676 1923 3.651803 AGACTGCTAGAGACAACACAC 57.348 47.619 0.00 0.00 0.00 3.82
759 2006 2.611751 CACCGACACATGTGAAGTTGAA 59.388 45.455 31.94 0.00 34.37 2.69
891 2138 8.350852 AGGATAGTGTATTTATAGTCCTTCCG 57.649 38.462 0.00 0.00 31.05 4.30
937 2184 9.973450 GTATGAACTATGAAGAATGCTTAGAGA 57.027 33.333 0.00 0.00 33.61 3.10
1011 2258 4.494515 GTCCACCCTTGGTTGACC 57.505 61.111 6.28 0.00 40.94 4.02
1092 2339 3.141398 GTGCCTCTTGTTCTTGTCATCA 58.859 45.455 0.00 0.00 0.00 3.07
1201 2448 3.119137 TCCCTCGAATGCATCATATACGG 60.119 47.826 0.00 0.00 0.00 4.02
1301 2548 1.208052 TGCTAGCACCAATCTCCTGAC 59.792 52.381 14.93 0.00 0.00 3.51
1364 2611 1.595466 CTCCTCTCGTACCGCATAGT 58.405 55.000 0.00 0.00 0.00 2.12
1370 2617 0.107312 TTCCTCCTCCTCTCGTACCG 60.107 60.000 0.00 0.00 0.00 4.02
1529 2776 1.706995 TTGGCGTGGGGGAACAACTA 61.707 55.000 0.00 0.00 0.00 2.24
1920 3226 9.425248 AACATTTTGGAACATAGATGACCATAT 57.575 29.630 11.56 7.69 39.30 1.78
1926 3232 9.022884 TGAATGAACATTTTGGAACATAGATGA 57.977 29.630 1.56 0.00 39.30 2.92
2211 3558 1.881973 TGGCTTGAGACTTGAACATGC 59.118 47.619 0.00 0.00 35.15 4.06
2217 3564 1.202794 TGTGCATGGCTTGAGACTTGA 60.203 47.619 4.32 0.00 30.42 3.02
2354 3701 1.539388 CGGTAGAACCAAGCATTTGCA 59.461 47.619 5.20 0.00 40.30 4.08
2479 3826 2.025981 TCCACACTGGCTGCTGATTTAT 60.026 45.455 0.00 0.00 37.47 1.40
2855 4204 4.139038 ACGCCAACTTAAGTGTGGTAATT 58.861 39.130 24.96 12.68 0.00 1.40
2867 4216 6.216801 AGAGACAACATATACGCCAACTTA 57.783 37.500 0.00 0.00 0.00 2.24
2948 4297 4.464244 TCTTGTGTTTTGTCATTGGGTGAA 59.536 37.500 0.00 0.00 38.90 3.18
3206 4559 4.766891 GCAAGGCATTATAGCTATTTGGGA 59.233 41.667 12.39 0.00 34.17 4.37
3223 4576 1.379576 AATGAGGAGCAGGCAAGGC 60.380 57.895 0.00 0.00 0.00 4.35
3268 4621 2.159517 CCGCTATCAGACAAACAAAGGC 60.160 50.000 0.00 0.00 0.00 4.35
3318 4672 5.048782 TGACAAAATGAATACCAGTGAGTGC 60.049 40.000 0.00 0.00 0.00 4.40
3327 4681 7.229306 TCCTATGAGCATGACAAAATGAATACC 59.771 37.037 0.00 0.00 0.00 2.73
3349 4703 3.381335 GTCATTCCAACCCTAGGTCCTA 58.619 50.000 8.29 0.00 33.12 2.94
3351 4705 1.134491 CGTCATTCCAACCCTAGGTCC 60.134 57.143 8.29 0.00 33.12 4.46
3363 4717 4.521130 TCTCCTATGCATACGTCATTCC 57.479 45.455 1.16 0.00 0.00 3.01
3451 4805 1.770061 ACTACCCCGTGTTTCCTTCAA 59.230 47.619 0.00 0.00 0.00 2.69
3453 4807 1.071228 ACACTACCCCGTGTTTCCTTC 59.929 52.381 0.00 0.00 45.27 3.46
3488 4842 4.946157 AGGATTGAATCAACTCATGTCACC 59.054 41.667 7.56 0.00 0.00 4.02
3490 4844 6.820152 CAGTAGGATTGAATCAACTCATGTCA 59.180 38.462 7.56 0.00 0.00 3.58
3524 4878 2.366916 CAACCAAGTTACAATGGCCCAA 59.633 45.455 0.00 0.00 40.51 4.12
3568 4925 6.294675 CCAAGAAATGCTCATGTTAACCAGAA 60.295 38.462 2.48 0.00 0.00 3.02
3578 4935 3.087031 ACACTCCCAAGAAATGCTCATG 58.913 45.455 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.