Multiple sequence alignment - TraesCS2A01G087700

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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 TraesCS2A01G087700 chr2A 100.000 2945 0 0 1 2945 41207003 41209947 0.000000e+00 5439.0
1 TraesCS2A01G087700 chr2A 97.645 1996 32 9 958 2945 41217815 41219803 0.000000e+00 3411.0
2 TraesCS2A01G087700 chr2A 91.244 434 24 8 958 1384 41227490 41227916 1.970000e-161 579.0
3 TraesCS2A01G087700 chr2A 85.242 393 51 4 1464 1852 41227921 41228310 5.910000e-107 398.0
4 TraesCS2A01G087700 chr2A 78.974 390 57 13 1489 1862 41170540 41170920 2.930000e-60 243.0
5 TraesCS2A01G087700 chr2A 81.985 272 45 3 268 539 41227122 41227389 8.210000e-56 228.0
6 TraesCS2A01G087700 chr2A 88.696 115 13 0 752 866 41214529 41214643 1.100000e-29 141.0
7 TraesCS2A01G087700 chr2A 100.000 29 0 0 673 701 165864531 165864559 1.000000e-03 54.7
8 TraesCS2A01G087700 chr2B 91.419 2156 145 15 1 2134 63219891 63222028 0.000000e+00 2920.0
9 TraesCS2A01G087700 chr2B 92.160 1148 58 11 993 2134 63255078 63256199 0.000000e+00 1592.0
10 TraesCS2A01G087700 chr2B 89.863 1164 87 16 993 2134 63249842 63250996 0.000000e+00 1467.0
11 TraesCS2A01G087700 chr2B 86.792 424 49 4 1433 1852 63260976 63261396 1.600000e-127 466.0
12 TraesCS2A01G087700 chr2B 91.379 232 17 3 1176 1407 63260768 63260996 6.130000e-82 315.0
13 TraesCS2A01G087700 chr2B 78.780 377 61 14 1494 1862 63140940 63141305 4.910000e-58 235.0
14 TraesCS2A01G087700 chr2B 85.870 184 23 3 657 840 63247597 63247777 3.000000e-45 193.0
15 TraesCS2A01G087700 chr2B 81.624 234 29 8 610 840 63254516 63254738 6.480000e-42 182.0
16 TraesCS2A01G087700 chr2B 89.091 55 2 4 2133 2184 714493164 714493111 6.810000e-07 65.8
17 TraesCS2A01G087700 chr2B 90.698 43 1 1 1230 1272 456511996 456511957 1.000000e-03 54.7
18 TraesCS2A01G087700 chr2D 93.551 1132 56 7 1018 2134 36783351 36784480 0.000000e+00 1670.0
19 TraesCS2A01G087700 chr2D 84.457 875 107 18 7 877 36782378 36783227 0.000000e+00 835.0
20 TraesCS2A01G087700 chr2D 95.775 497 21 0 2447 2943 20065760 20066256 0.000000e+00 802.0
21 TraesCS2A01G087700 chr2D 95.582 498 22 0 2446 2943 16242050 16241553 0.000000e+00 798.0
22 TraesCS2A01G087700 chr2D 79.553 313 42 15 1489 1793 36751448 36751746 1.380000e-48 204.0
23 TraesCS2A01G087700 chr2D 76.336 131 22 8 666 795 187015529 187015651 8.810000e-06 62.1
24 TraesCS2A01G087700 chrUn 95.984 498 20 0 2446 2943 60979140 60978643 0.000000e+00 809.0
25 TraesCS2A01G087700 chrUn 86.008 243 30 2 1887 2125 326890008 326889766 1.050000e-64 257.0
26 TraesCS2A01G087700 chrUn 86.008 243 30 2 1887 2125 362953267 362953509 1.050000e-64 257.0
27 TraesCS2A01G087700 chrUn 86.905 84 9 2 2372 2454 243508558 243508476 3.130000e-15 93.5
28 TraesCS2A01G087700 chrUn 86.905 84 9 2 2372 2454 276475361 276475279 3.130000e-15 93.5
29 TraesCS2A01G087700 chrUn 86.905 84 9 2 2372 2454 422457276 422457194 3.130000e-15 93.5
30 TraesCS2A01G087700 chr3D 95.600 500 22 0 2446 2945 596701070 596701569 0.000000e+00 802.0
31 TraesCS2A01G087700 chr3D 91.209 91 7 1 2336 2426 611656328 611656417 3.990000e-24 122.0
32 TraesCS2A01G087700 chr6D 95.582 498 22 0 2446 2943 386160034 386159537 0.000000e+00 798.0
33 TraesCS2A01G087700 chr6D 95.400 500 23 0 2446 2945 30417390 30416891 0.000000e+00 797.0
34 TraesCS2A01G087700 chr6B 95.582 498 22 0 2446 2943 219562530 219563027 0.000000e+00 798.0
35 TraesCS2A01G087700 chr6B 89.130 46 3 2 2135 2179 42198069 42198025 4.100000e-04 56.5
36 TraesCS2A01G087700 chr6A 95.382 498 23 0 2446 2943 106682846 106682349 0.000000e+00 793.0
37 TraesCS2A01G087700 chr6A 91.111 45 3 1 2135 2179 121626563 121626520 3.170000e-05 60.2
38 TraesCS2A01G087700 chr3B 86.420 243 29 2 1887 2125 788978096 788977854 2.250000e-66 263.0
39 TraesCS2A01G087700 chr3B 86.008 243 30 2 1887 2125 788921807 788921565 1.050000e-64 257.0
40 TraesCS2A01G087700 chr3B 93.333 45 2 1 2135 2179 16149141 16149184 6.810000e-07 65.8
41 TraesCS2A01G087700 chr3B 93.333 45 2 1 2135 2179 16172060 16172103 6.810000e-07 65.8
42 TraesCS2A01G087700 chr3B 89.362 47 3 2 2134 2179 28117922 28117877 1.140000e-04 58.4
43 TraesCS2A01G087700 chr3B 90.698 43 1 1 1230 1272 753944550 753944511 1.000000e-03 54.7
44 TraesCS2A01G087700 chr7B 85.714 161 15 6 2255 2410 613232690 613232847 2.350000e-36 163.0
45 TraesCS2A01G087700 chr7B 89.815 108 5 3 2186 2293 613233810 613233911 1.840000e-27 134.0
46 TraesCS2A01G087700 chr7B 89.815 108 5 3 2186 2293 613249751 613249852 1.840000e-27 134.0
47 TraesCS2A01G087700 chr7B 84.028 144 14 7 2273 2410 613244493 613244633 2.380000e-26 130.0
48 TraesCS2A01G087700 chr7B 84.028 144 14 7 2273 2410 613248647 613248787 2.380000e-26 130.0
49 TraesCS2A01G087700 chr1A 95.050 101 4 1 2172 2272 586946181 586946082 1.090000e-34 158.0
50 TraesCS2A01G087700 chr1A 87.069 116 10 4 2278 2391 586945188 586945076 3.080000e-25 126.0
51 TraesCS2A01G087700 chr4B 92.857 70 4 1 2377 2446 656834451 656834383 1.870000e-17 100.0
52 TraesCS2A01G087700 chr4B 92.857 70 4 1 2377 2446 656835147 656835079 1.870000e-17 100.0
53 TraesCS2A01G087700 chr1B 86.905 84 9 2 2372 2454 45467923 45467841 3.130000e-15 93.5
54 TraesCS2A01G087700 chr1B 86.905 84 9 2 2372 2454 45584377 45584295 3.130000e-15 93.5
55 TraesCS2A01G087700 chr7D 97.872 47 1 0 1212 1258 294028689 294028735 6.760000e-12 82.4
56 TraesCS2A01G087700 chr7A 90.385 52 4 1 2128 2179 650590757 650590707 1.890000e-07 67.6
57 TraesCS2A01G087700 chr7A 89.583 48 3 2 2133 2179 14724603 14724649 3.170000e-05 60.2
58 TraesCS2A01G087700 chr5A 89.796 49 5 0 1210 1258 9941706 9941658 2.450000e-06 63.9


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 TraesCS2A01G087700 chr2A 41207003 41209947 2944 False 5439.000000 5439 100.00000 1 2945 1 chr2A.!!$F2 2944
1 TraesCS2A01G087700 chr2A 41214529 41219803 5274 False 1776.000000 3411 93.17050 752 2945 2 chr2A.!!$F4 2193
2 TraesCS2A01G087700 chr2A 41227122 41228310 1188 False 401.666667 579 86.15700 268 1852 3 chr2A.!!$F5 1584
3 TraesCS2A01G087700 chr2B 63219891 63222028 2137 False 2920.000000 2920 91.41900 1 2134 1 chr2B.!!$F2 2133
4 TraesCS2A01G087700 chr2B 63247597 63256199 8602 False 858.500000 1592 87.37925 610 2134 4 chr2B.!!$F3 1524
5 TraesCS2A01G087700 chr2B 63260768 63261396 628 False 390.500000 466 89.08550 1176 1852 2 chr2B.!!$F4 676
6 TraesCS2A01G087700 chr2D 36782378 36784480 2102 False 1252.500000 1670 89.00400 7 2134 2 chr2D.!!$F4 2127

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
980 5274 0.179119 AAGCCGGTTCCGATTCTACG 60.179 55.0 13.08 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2744 12314 0.729116 TATCCTCGTCGTCAACCGTC 59.271 55.0 0.0 0.0 37.94 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
42 43 2.975799 GTTCCCTTCGCGCAACCA 60.976 61.111 8.75 0.0 0.00 3.67
151 152 1.136774 CTCGGCGATCGTGAAGTCA 59.863 57.895 17.81 0.0 40.32 3.41
159 160 3.499737 CGTGAAGTCATGCGGGCC 61.500 66.667 0.00 0.0 0.00 5.80
233 234 0.468226 TCGGTGTTGAAGAAGGCAGT 59.532 50.000 0.00 0.0 0.00 4.40
399 400 1.202879 TGCCACCTCAACGGAAATCTT 60.203 47.619 0.00 0.0 36.31 2.40
435 436 1.549170 AGTGGTCACTCAACGATACCC 59.451 52.381 0.00 0.0 36.92 3.69
529 530 1.572447 GGCGCAAGACGTAGCAAAA 59.428 52.632 10.83 0.0 46.11 2.44
542 543 2.260869 GCAAAACGGCTCCTCTGCA 61.261 57.895 0.00 0.0 34.04 4.41
618 1112 2.404995 GGACCACTCCGACGACGAT 61.405 63.158 9.28 0.0 42.66 3.73
655 1149 1.826921 GGAGGTGCCATCAGCCATG 60.827 63.158 0.00 0.0 42.71 3.66
873 2139 6.398095 CCGGATGTGTCAGCAGATAAATATA 58.602 40.000 0.00 0.0 0.00 0.86
950 5244 2.577700 AGGTAGAGGCAGAGTCATACG 58.422 52.381 0.00 0.0 0.00 3.06
980 5274 0.179119 AAGCCGGTTCCGATTCTACG 60.179 55.000 13.08 0.0 0.00 3.51
1012 5310 3.009143 GGTCATACCCCAGAAGTTTCAGT 59.991 47.826 0.00 0.0 30.04 3.41
1060 5358 0.308376 GGTAGAGTCTCGTCGCATCC 59.692 60.000 0.00 0.0 0.00 3.51
1064 5362 0.382158 GAGTCTCGTCGCATCCATCA 59.618 55.000 0.00 0.0 0.00 3.07
1076 5378 4.923281 TCGCATCCATCATAAGATACGTTG 59.077 41.667 0.00 0.0 32.37 4.10
1340 5642 2.625790 GAGGATCTGTTGCTACCTCGAT 59.374 50.000 0.00 0.0 37.87 3.59
1975 11545 4.774726 ACACAACCCATGCATAAATAACCA 59.225 37.500 0.00 0.0 0.00 3.67
2051 11621 3.857052 TGTGTCATCATCCCTAAACGTC 58.143 45.455 0.00 0.0 0.00 4.34
2418 11988 5.015178 TCCCCCTAATCTTGACTTTGTCATT 59.985 40.000 1.05 0.0 42.40 2.57
2488 12058 2.918712 AAGATGGAGGCGGATAACTG 57.081 50.000 0.00 0.0 0.00 3.16
2625 12195 3.006430 TCAGTTTATGTCCAAGACTGCGA 59.994 43.478 0.00 0.0 38.04 5.10
2672 12242 3.144506 GTTGTATGGGATGAGGATGCAG 58.855 50.000 0.00 0.0 0.00 4.41
2798 12368 5.716094 CTTCTTTGTTCATTGCCATCATCA 58.284 37.500 0.00 0.0 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.369091 GCATCTGATTTGGACGCCGT 61.369 55.000 0.00 0.00 0.00 5.68
52 53 1.278985 TCCTTCACGTGGCATCTGATT 59.721 47.619 17.00 0.00 0.00 2.57
151 152 4.172232 TAGAGGAGGGGCCCGCAT 62.172 66.667 28.19 22.42 37.37 4.73
159 160 0.549950 TACCACCGAGTAGAGGAGGG 59.450 60.000 3.93 0.91 42.74 4.30
233 234 2.992689 TACGCGCCACCTTCCTGA 60.993 61.111 5.73 0.00 0.00 3.86
346 347 2.501223 GATGTCTCCGCGGTGGTCAA 62.501 60.000 27.15 9.57 39.52 3.18
388 389 3.126343 CCGATTCCGAAAAGATTTCCGTT 59.874 43.478 0.00 0.00 38.22 4.44
399 400 0.535335 CACTCCTCCCGATTCCGAAA 59.465 55.000 0.00 0.00 38.22 3.46
529 530 2.475371 AATGCTTGCAGAGGAGCCGT 62.475 55.000 5.68 0.00 38.11 5.68
583 584 2.436646 CTTCCAGCGGCGGAATGT 60.437 61.111 20.75 0.00 44.06 2.71
618 1112 0.102300 CATCGTAGGCCGTGTCATCA 59.898 55.000 0.00 0.00 37.94 3.07
655 1149 1.524621 CGTCTGACCATGATGGCCC 60.525 63.158 12.25 4.38 42.67 5.80
656 1150 0.464036 TACGTCTGACCATGATGGCC 59.536 55.000 12.25 0.00 42.67 5.36
657 1151 1.134818 TGTACGTCTGACCATGATGGC 60.135 52.381 12.25 5.15 42.67 4.40
658 1152 2.959507 TGTACGTCTGACCATGATGG 57.040 50.000 10.53 10.53 45.02 3.51
659 1153 3.190079 CCTTGTACGTCTGACCATGATG 58.810 50.000 1.55 0.00 0.00 3.07
660 1154 2.832129 ACCTTGTACGTCTGACCATGAT 59.168 45.455 1.55 0.00 0.00 2.45
661 1155 2.230508 GACCTTGTACGTCTGACCATGA 59.769 50.000 1.55 0.00 0.00 3.07
662 1156 2.029380 TGACCTTGTACGTCTGACCATG 60.029 50.000 1.55 0.00 0.00 3.66
663 1157 2.029290 GTGACCTTGTACGTCTGACCAT 60.029 50.000 1.55 0.00 0.00 3.55
664 1158 1.338973 GTGACCTTGTACGTCTGACCA 59.661 52.381 1.55 0.00 0.00 4.02
665 1159 1.336609 GGTGACCTTGTACGTCTGACC 60.337 57.143 1.55 0.00 0.00 4.02
666 1160 1.665161 CGGTGACCTTGTACGTCTGAC 60.665 57.143 0.00 0.00 0.00 3.51
667 1161 0.594602 CGGTGACCTTGTACGTCTGA 59.405 55.000 0.00 0.00 0.00 3.27
736 1230 7.416817 TCACATAAATCAGCCGATATTTTGTG 58.583 34.615 14.65 14.65 35.69 3.33
873 2139 4.244862 CAAAGCCGGCAAAAGTTTGATAT 58.755 39.130 31.54 0.00 40.55 1.63
950 5244 5.713025 TCGGAACCGGCTTGTATAATATAC 58.287 41.667 13.29 3.56 40.25 1.47
1012 5310 8.306038 GGTTTGGAAGATTTATATATGCATGCA 58.694 33.333 25.04 25.04 0.00 3.96
1060 5358 2.157668 GCGGCCAACGTATCTTATGATG 59.842 50.000 2.24 0.00 46.52 3.07
1064 5362 0.599204 CGGCGGCCAACGTATCTTAT 60.599 55.000 20.71 0.00 46.52 1.73
1975 11545 7.354751 TGTTTTAGGGTGCTCTTTGTTATTT 57.645 32.000 0.00 0.00 0.00 1.40
2051 11621 1.664649 TTGCAGGAGTCTTGTCGCG 60.665 57.895 0.00 0.00 0.00 5.87
2418 11988 4.389374 AGATGAGAAAAAGCACGAGGAAA 58.611 39.130 0.00 0.00 0.00 3.13
2488 12058 4.353383 ACTTTCAACTGTAACTCCTCCC 57.647 45.455 0.00 0.00 0.00 4.30
2625 12195 2.353803 GCTTCAGATACACCTTGGTCGT 60.354 50.000 0.00 0.00 0.00 4.34
2672 12242 2.436173 CTCCACAAGATCTAACCCCTCC 59.564 54.545 0.00 0.00 0.00 4.30
2744 12314 0.729116 TATCCTCGTCGTCAACCGTC 59.271 55.000 0.00 0.00 37.94 4.79
2798 12368 9.113838 GTCAAAGTAGTGATCAAATGGTCATAT 57.886 33.333 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.