Multiple sequence alignment - TraesCS1B01G324600

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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 TraesCS1B01G324600 chr1B 100.000 2264 0 0 1 2264 549918915 549916652 0.000000e+00 4181.0
1 TraesCS1B01G324600 chr1B 94.940 2095 106 0 1 2095 540300147 540298053 0.000000e+00 3282.0
2 TraesCS1B01G324600 chr1B 94.797 2095 108 1 1 2095 540290569 540288476 0.000000e+00 3264.0
3 TraesCS1B01G324600 chr1B 94.115 1937 99 4 1 1937 504247933 504246012 0.000000e+00 2931.0
4 TraesCS1B01G324600 chr1B 90.752 1503 108 14 583 2074 612424167 612425649 0.000000e+00 1977.0
5 TraesCS1B01G324600 chr1B 90.032 311 25 2 1956 2264 504245706 504245400 4.530000e-107 398.0
6 TraesCS1B01G324600 chr1B 81.752 137 17 6 2128 2264 540287949 540287821 8.550000e-20 108.0
7 TraesCS1B01G324600 chr1B 86.957 69 6 3 2028 2094 540288593 540288660 8.670000e-10 75.0
8 TraesCS1B01G324600 chr1B 86.957 69 6 3 2028 2094 540298170 540298237 8.670000e-10 75.0
9 TraesCS1B01G324600 chr2B 91.913 2164 143 15 1 2154 215847181 215849322 0.000000e+00 2998.0
10 TraesCS1B01G324600 chr2B 91.777 2116 135 16 1 2095 430232450 430230353 0.000000e+00 2907.0
11 TraesCS1B01G324600 chr2B 90.724 2156 140 40 1 2139 722906751 722904639 0.000000e+00 2819.0
12 TraesCS1B01G324600 chr2B 95.760 967 39 2 1 967 465664710 465663746 0.000000e+00 1557.0
13 TraesCS1B01G324600 chr2B 89.664 774 44 8 1498 2264 546620617 546621361 0.000000e+00 953.0
14 TraesCS1B01G324600 chr2B 82.251 231 31 10 2029 2254 465662804 465663029 8.250000e-45 191.0
15 TraesCS1B01G324600 chr2B 81.726 197 22 14 2028 2216 430229661 430229851 3.890000e-33 152.0
16 TraesCS1B01G324600 chrUn 89.977 2175 176 25 1 2159 10399185 10401333 0.000000e+00 2771.0
17 TraesCS1B01G324600 chr6B 94.032 1776 92 7 493 2264 605817299 605819064 0.000000e+00 2680.0
18 TraesCS1B01G324600 chr3D 90.235 2089 149 20 1 2070 310406106 310408158 0.000000e+00 2676.0
19 TraesCS1B01G324600 chr3D 81.818 66 12 0 1913 1978 310408059 310407994 3.140000e-04 56.5
20 TraesCS1B01G324600 chr6D 93.119 1831 113 4 1 1830 377212217 377214035 0.000000e+00 2671.0
21 TraesCS1B01G324600 chr5D 93.207 1796 110 3 1 1795 348341255 348343039 0.000000e+00 2630.0
22 TraesCS1B01G324600 chr3B 94.586 1570 73 4 695 2264 809559032 809557475 0.000000e+00 2418.0
23 TraesCS1B01G324600 chr5B 88.309 1668 127 40 575 2226 98046319 98047934 0.000000e+00 1938.0
24 TraesCS1B01G324600 chr7D 84.848 66 8 2 1912 1976 572999135 572999071 5.220000e-07 65.8
25 TraesCS1B01G324600 chr2D 84.848 66 8 2 1912 1976 632764360 632764296 5.220000e-07 65.8
26 TraesCS1B01G324600 chr7A 100.000 31 0 0 2144 2174 712340808 712340778 8.730000e-05 58.4


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 TraesCS1B01G324600 chr1B 549916652 549918915 2263 True 4181.0 4181 100.0000 1 2264 1 chr1B.!!$R2 2263
1 TraesCS1B01G324600 chr1B 540298053 540300147 2094 True 3282.0 3282 94.9400 1 2095 1 chr1B.!!$R1 2094
2 TraesCS1B01G324600 chr1B 612424167 612425649 1482 False 1977.0 1977 90.7520 583 2074 1 chr1B.!!$F3 1491
3 TraesCS1B01G324600 chr1B 540287821 540290569 2748 True 1686.0 3264 88.2745 1 2264 2 chr1B.!!$R4 2263
4 TraesCS1B01G324600 chr1B 504245400 504247933 2533 True 1664.5 2931 92.0735 1 2264 2 chr1B.!!$R3 2263
5 TraesCS1B01G324600 chr2B 215847181 215849322 2141 False 2998.0 2998 91.9130 1 2154 1 chr2B.!!$F1 2153
6 TraesCS1B01G324600 chr2B 430230353 430232450 2097 True 2907.0 2907 91.7770 1 2095 1 chr2B.!!$R1 2094
7 TraesCS1B01G324600 chr2B 722904639 722906751 2112 True 2819.0 2819 90.7240 1 2139 1 chr2B.!!$R3 2138
8 TraesCS1B01G324600 chr2B 465663746 465664710 964 True 1557.0 1557 95.7600 1 967 1 chr2B.!!$R2 966
9 TraesCS1B01G324600 chr2B 546620617 546621361 744 False 953.0 953 89.6640 1498 2264 1 chr2B.!!$F4 766
10 TraesCS1B01G324600 chrUn 10399185 10401333 2148 False 2771.0 2771 89.9770 1 2159 1 chrUn.!!$F1 2158
11 TraesCS1B01G324600 chr6B 605817299 605819064 1765 False 2680.0 2680 94.0320 493 2264 1 chr6B.!!$F1 1771
12 TraesCS1B01G324600 chr3D 310406106 310408158 2052 False 2676.0 2676 90.2350 1 2070 1 chr3D.!!$F1 2069
13 TraesCS1B01G324600 chr6D 377212217 377214035 1818 False 2671.0 2671 93.1190 1 1830 1 chr6D.!!$F1 1829
14 TraesCS1B01G324600 chr5D 348341255 348343039 1784 False 2630.0 2630 93.2070 1 1795 1 chr5D.!!$F1 1794
15 TraesCS1B01G324600 chr3B 809557475 809559032 1557 True 2418.0 2418 94.5860 695 2264 1 chr3B.!!$R1 1569
16 TraesCS1B01G324600 chr5B 98046319 98047934 1615 False 1938.0 1938 88.3090 575 2226 1 chr5B.!!$F1 1651

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
854 861 0.559205 TAGGGGAAGGCCTATCGACA 59.441 55.0 5.16 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 3075 0.539986 CCTTACCGCCAAGGCTTCTA 59.46 55.0 9.73 0.0 46.52 2.1 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
163 164 2.734755 ATCAAATTGATGAGCCGGGA 57.265 45.000 7.79 0.00 35.43 5.14
198 199 1.687123 CGGTAGGTCTTATGGTGGAGG 59.313 57.143 0.00 0.00 0.00 4.30
225 226 1.336440 CGAGGTGCACATCAAAAACCA 59.664 47.619 28.84 0.00 33.13 3.67
373 374 0.818040 GAACAAGGTTGACGTGGGCT 60.818 55.000 0.00 0.00 32.45 5.19
455 456 1.099879 GCCAGATCCCACACTCATGC 61.100 60.000 0.00 0.00 0.00 4.06
515 518 5.825151 CGGAGTGATATGGATGATCTAGCTA 59.175 44.000 0.00 0.00 0.00 3.32
525 528 4.944930 GGATGATCTAGCTAGATACACCGT 59.055 45.833 31.49 21.27 42.79 4.83
562 565 0.734889 GTGGTCATTTCATGGAGCCG 59.265 55.000 0.00 0.00 0.00 5.52
593 596 4.141981 ACAACAATTGTGGAGAATGCAACA 60.142 37.500 20.05 0.00 39.09 3.33
689 695 2.757099 GCCTTGGAGGTGGCCATG 60.757 66.667 9.72 0.00 43.11 3.66
691 697 2.757099 CTTGGAGGTGGCCATGGC 60.757 66.667 29.47 29.47 37.86 4.40
741 748 2.370445 ATGGCCGTGGAGGAAGGAG 61.370 63.158 0.00 0.00 45.00 3.69
800 807 3.850098 CTTTGAGTGGGCCGTGGCT 62.850 63.158 11.25 0.00 41.60 4.75
826 833 1.246056 CCGGTGGTTCTAGGACACGA 61.246 60.000 12.14 0.00 36.02 4.35
854 861 0.559205 TAGGGGAAGGCCTATCGACA 59.441 55.000 5.16 0.00 0.00 4.35
1021 1046 1.728490 GGCTTCATCCGGTTCCATGC 61.728 60.000 0.00 0.20 0.00 4.06
1129 1155 1.678635 CCGCCATGTTGGTGTGGAT 60.679 57.895 6.37 0.00 46.25 3.41
1151 1177 1.476085 TGTTTGCAAGGTGAAGGTGTG 59.524 47.619 0.00 0.00 0.00 3.82
1211 1237 7.526041 AGATATTTTGTATGCCCCAACTATGA 58.474 34.615 0.00 0.00 0.00 2.15
1331 1357 1.257750 TGTATGCAGTCACCGCCTCT 61.258 55.000 0.00 0.00 0.00 3.69
1332 1358 0.807667 GTATGCAGTCACCGCCTCTG 60.808 60.000 0.00 0.00 0.00 3.35
1412 1438 6.904626 ACCAATATCAAGATTGTCTTAGGCT 58.095 36.000 0.00 0.00 33.78 4.58
1419 1445 3.177228 AGATTGTCTTAGGCTCCAGTGT 58.823 45.455 0.00 0.00 0.00 3.55
1604 1630 0.033504 GAGGCACGTGACAAGAAGGA 59.966 55.000 26.11 0.00 0.00 3.36
1923 1989 4.778143 GCCACACCCTACCGCCAG 62.778 72.222 0.00 0.00 0.00 4.85
2118 3075 5.235516 CAAACCTACTATGACGGTGAAACT 58.764 41.667 0.00 0.00 36.74 2.66
2140 3097 4.043100 GCCTTGGCGGTAAGGGGT 62.043 66.667 13.00 0.00 45.91 4.95
2222 3212 2.032426 CCGTCACAACAAGTTTACACCC 59.968 50.000 0.00 0.00 0.00 4.61
2223 3213 2.032426 CGTCACAACAAGTTTACACCCC 59.968 50.000 0.00 0.00 0.00 4.95
2224 3214 2.359848 GTCACAACAAGTTTACACCCCC 59.640 50.000 0.00 0.00 0.00 5.40
2225 3215 2.242708 TCACAACAAGTTTACACCCCCT 59.757 45.455 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.039856 ACTTGGCCGTGCTTTCAAAT 58.960 45.000 0.00 0.00 0.00 2.32
133 134 8.985805 GGCTCATCAATTTGATAAATCATTTCC 58.014 33.333 11.44 1.11 34.28 3.13
151 152 2.764128 GTCCCTCCCGGCTCATCA 60.764 66.667 0.00 0.00 0.00 3.07
163 164 0.472352 TACCGTCCCTTGTTGTCCCT 60.472 55.000 0.00 0.00 0.00 4.20
225 226 0.037303 CCTCTCACACTGGCACCAAT 59.963 55.000 0.00 0.00 0.00 3.16
373 374 2.266279 AGGAAAGGATTGAACCGAGGA 58.734 47.619 0.00 0.00 34.73 3.71
455 456 2.402564 TCTTCTTCCCCTCATAGGCAG 58.597 52.381 0.00 0.00 32.73 4.85
515 518 6.183360 CCAAATTGCTTCATTACGGTGTATCT 60.183 38.462 0.00 0.00 0.00 1.98
525 528 6.007076 TGACCACTACCAAATTGCTTCATTA 58.993 36.000 0.00 0.00 0.00 1.90
562 565 1.335872 CCACAATTGTTGTTCTCCGGC 60.336 52.381 8.77 0.00 43.23 6.13
593 596 4.134563 GTCCTAATGTTGTGTCCTGTGTT 58.865 43.478 0.00 0.00 0.00 3.32
687 693 0.625683 AGTCCTTCCTCCATGGCCAT 60.626 55.000 14.09 14.09 35.26 4.40
688 694 0.044092 TAGTCCTTCCTCCATGGCCA 59.956 55.000 8.56 8.56 35.26 5.36
689 695 0.761802 CTAGTCCTTCCTCCATGGCC 59.238 60.000 6.96 0.00 35.26 5.36
691 697 0.761802 GGCTAGTCCTTCCTCCATGG 59.238 60.000 4.97 4.97 37.10 3.66
800 807 1.191535 CTAGAACCACCGGATCCACA 58.808 55.000 9.46 0.00 0.00 4.17
826 833 1.632965 GCCTTCCCCTATCAACCCGT 61.633 60.000 0.00 0.00 0.00 5.28
854 861 1.064463 ACCATCCGGATTGAGCAACAT 60.064 47.619 21.66 0.00 35.59 2.71
1021 1046 2.535485 TTAGCACATGGTGGCCTCGG 62.535 60.000 3.32 0.00 33.64 4.63
1129 1155 3.317711 CACACCTTCACCTTGCAAACATA 59.682 43.478 0.00 0.00 0.00 2.29
1151 1177 1.305201 TGACTTCTTTTGGTCGGTGC 58.695 50.000 0.00 0.00 35.45 5.01
1211 1237 2.238942 TGGAAGCGCACGATCATAAT 57.761 45.000 11.47 0.00 0.00 1.28
1331 1357 2.993220 CACGTGAAGTACTTGCATAGCA 59.007 45.455 14.14 0.12 36.47 3.49
1332 1358 2.348666 CCACGTGAAGTACTTGCATAGC 59.651 50.000 19.30 0.00 0.00 2.97
1412 1438 3.492656 CCTTTCTTCGAACAGACACTGGA 60.493 47.826 0.00 0.00 35.51 3.86
1419 1445 5.878116 TCTTTGAAACCTTTCTTCGAACAGA 59.122 36.000 0.00 0.00 38.02 3.41
1576 1602 0.033503 TCACGTGCCTCATCCTCCTA 60.034 55.000 11.67 0.00 0.00 2.94
1604 1630 1.141053 GAGTCATACGGGGCCATTTCT 59.859 52.381 4.39 0.00 0.00 2.52
1642 1669 2.168521 CCGGTTACATGATGAGTCCACT 59.831 50.000 0.00 0.00 0.00 4.00
1764 1806 1.872952 CCTTGCAAACATCTCGACACA 59.127 47.619 0.00 0.00 0.00 3.72
2092 2588 1.903860 ACCGTCATAGTAGGTTTGCCA 59.096 47.619 0.00 0.00 33.96 4.92
2105 2603 2.567615 AGGCTTCTAGTTTCACCGTCAT 59.432 45.455 0.00 0.00 0.00 3.06
2118 3075 0.539986 CCTTACCGCCAAGGCTTCTA 59.460 55.000 9.73 0.00 46.52 2.10
2222 3212 3.470888 CTGTGGCGGTAGGGAGGG 61.471 72.222 0.00 0.00 0.00 4.30
2223 3213 3.470888 CCTGTGGCGGTAGGGAGG 61.471 72.222 0.00 0.00 0.00 4.30
2224 3214 4.162690 GCCTGTGGCGGTAGGGAG 62.163 72.222 4.07 0.00 39.62 4.30


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

AutoCloner maintained by Alex Coulton.