Multiple sequence alignment - TraesCS2B01G165000

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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 TraesCS2B01G165000 chr2B 100.000 3494 0 0 1 3494 137015752 137012259 0.000000e+00 6453.0
1 TraesCS2B01G165000 chr2B 96.486 2220 60 12 1 2211 137623443 137621233 0.000000e+00 3651.0
2 TraesCS2B01G165000 chr2B 97.825 1747 33 4 469 2211 136815630 136813885 0.000000e+00 3011.0
3 TraesCS2B01G165000 chr2B 97.518 1410 33 2 803 2211 136639125 136637717 0.000000e+00 2409.0
4 TraesCS2B01G165000 chr2B 94.620 1301 28 19 2206 3494 137621205 137619935 0.000000e+00 1977.0
5 TraesCS2B01G165000 chr2B 97.217 1150 22 5 2206 3345 136813857 136812708 0.000000e+00 1938.0
6 TraesCS2B01G165000 chr2B 90.749 1135 78 14 2206 3330 136637689 136636572 0.000000e+00 1489.0
7 TraesCS2B01G165000 chr2B 91.088 965 60 11 2203 3148 135464710 135465667 0.000000e+00 1282.0
8 TraesCS2B01G165000 chr2B 90.985 954 71 9 2206 3148 182132928 182131979 0.000000e+00 1271.0
9 TraesCS2B01G165000 chr2B 86.486 444 54 4 685 1127 137130903 137130465 1.890000e-132 483.0
10 TraesCS2B01G165000 chr2B 85.523 373 44 9 5 373 136815990 136815624 7.080000e-102 381.0
11 TraesCS2B01G165000 chr2B 84.553 369 48 6 7 373 137131832 137131471 1.190000e-94 357.0
12 TraesCS2B01G165000 chr2B 84.511 368 48 8 7 373 137703120 137702761 4.290000e-94 355.0
13 TraesCS2B01G165000 chr2B 81.622 370 56 7 5 372 136640278 136639919 2.640000e-76 296.0
14 TraesCS2B01G165000 chr2B 87.435 191 11 2 2035 2213 182131328 182131139 1.270000e-49 207.0
15 TraesCS2B01G165000 chr2B 87.912 182 9 2 2035 2204 135466323 135466503 5.910000e-48 202.0
16 TraesCS2B01G165000 chr2B 81.545 233 17 11 469 689 137702767 137702549 6.000000e-38 169.0
17 TraesCS2B01G165000 chr2B 86.928 153 8 7 567 714 136639478 136639333 1.000000e-35 161.0
18 TraesCS2B01G165000 chr2B 82.105 190 13 9 483 657 137463063 137462880 3.640000e-30 143.0
19 TraesCS2B01G165000 chr2B 93.421 76 5 0 3156 3231 182131588 182131513 2.850000e-21 113.0
20 TraesCS2B01G165000 chr2B 89.873 79 8 0 3153 3231 135515463 135515541 6.170000e-18 102.0
21 TraesCS2B01G165000 chr2B 95.082 61 3 0 3434 3494 136636455 136636395 2.870000e-16 97.1
22 TraesCS2B01G165000 chr2B 100.000 43 0 0 3282 3324 136634674 136634632 2.890000e-11 80.5
23 TraesCS2B01G165000 chr2D 94.500 1909 83 5 321 2211 85409432 85407528 0.000000e+00 2924.0
24 TraesCS2B01G165000 chr2D 94.543 1411 59 6 803 2211 84780549 84779155 0.000000e+00 2163.0
25 TraesCS2B01G165000 chr2D 95.323 1347 54 6 872 2211 84938075 84936731 0.000000e+00 2130.0
26 TraesCS2B01G165000 chr2D 92.640 1019 52 3 811 1824 85252000 85251000 0.000000e+00 1445.0
27 TraesCS2B01G165000 chr2D 92.444 900 49 5 925 1824 85703786 85702906 0.000000e+00 1267.0
28 TraesCS2B01G165000 chr2D 87.335 1137 86 27 2203 3330 85250905 85249818 0.000000e+00 1249.0
29 TraesCS2B01G165000 chr2D 89.783 920 75 12 2203 3111 127820367 127819456 0.000000e+00 1160.0
30 TraesCS2B01G165000 chr2D 85.769 1054 66 32 2203 3196 83530934 83531963 0.000000e+00 1038.0
31 TraesCS2B01G165000 chr2D 93.238 488 26 6 321 805 84938585 84938102 0.000000e+00 712.0
32 TraesCS2B01G165000 chr2D 92.705 329 22 1 5 331 84938978 84938650 1.140000e-129 473.0
33 TraesCS2B01G165000 chr2D 89.728 331 23 3 5 335 85409812 85409493 2.510000e-111 412.0
34 TraesCS2B01G165000 chr2D 84.677 372 48 4 5 375 85252818 85252455 2.560000e-96 363.0
35 TraesCS2B01G165000 chr2D 86.420 243 16 7 3081 3323 84935524 84935299 2.080000e-62 250.0
36 TraesCS2B01G165000 chr2D 86.008 243 17 7 3081 3323 85406320 85406095 9.690000e-61 244.0
37 TraesCS2B01G165000 chr2D 92.771 166 6 4 3335 3494 84935260 84935095 5.830000e-58 235.0
38 TraesCS2B01G165000 chr2D 93.548 155 5 2 3343 3494 85406045 85405893 3.510000e-55 226.0
39 TraesCS2B01G165000 chr2D 87.500 152 6 4 3343 3494 84777662 84777524 2.790000e-36 163.0
40 TraesCS2B01G165000 chr2D 95.082 61 3 0 3434 3494 85249701 85249641 2.870000e-16 97.1
41 TraesCS2B01G165000 chr7A 93.821 1230 58 8 605 1824 618195694 618194473 0.000000e+00 1834.0
42 TraesCS2B01G165000 chr7A 83.815 346 47 8 30 373 618196529 618196191 1.560000e-83 320.0
43 TraesCS2B01G165000 chr7A 93.023 86 3 3 2132 2216 627006928 627006845 4.740000e-24 122.0
44 TraesCS2B01G165000 chr2A 93.226 1240 53 3 910 2142 85613727 85612512 0.000000e+00 1796.0
45 TraesCS2B01G165000 chr2A 93.226 1240 53 3 910 2142 85927152 85925937 0.000000e+00 1796.0
46 TraesCS2B01G165000 chr2A 92.903 1240 57 3 910 2142 85811245 85810030 0.000000e+00 1773.0
47 TraesCS2B01G165000 chr2A 95.079 1138 32 11 2203 3330 85612509 85611386 0.000000e+00 1770.0
48 TraesCS2B01G165000 chr2A 90.729 960 69 12 2203 3148 84144627 84145580 0.000000e+00 1262.0
49 TraesCS2B01G165000 chr2A 89.846 975 78 14 2203 3162 83991123 83992091 0.000000e+00 1232.0
50 TraesCS2B01G165000 chr2A 94.268 157 6 1 3341 3494 85611330 85611174 1.620000e-58 237.0
51 TraesCS2B01G165000 chr2A 90.164 122 12 0 3153 3274 84146006 84146127 3.610000e-35 159.0
52 TraesCS2B01G165000 chr2A 90.741 54 5 0 3178 3231 83992282 83992335 4.840000e-09 73.1
53 TraesCS2B01G165000 chr4A 93.065 1240 55 3 910 2142 349806780 349805565 0.000000e+00 1784.0
54 TraesCS2B01G165000 chr7D 85.285 333 34 8 1896 2215 518766779 518767109 2.600000e-86 329.0


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 TraesCS2B01G165000 chr2B 137012259 137015752 3493 True 6453.000000 6453 100.000000 1 3494 1 chr2B.!!$R1 3493
1 TraesCS2B01G165000 chr2B 137619935 137623443 3508 True 2814.000000 3651 95.553000 1 3494 2 chr2B.!!$R6 3493
2 TraesCS2B01G165000 chr2B 136812708 136815990 3282 True 1776.666667 3011 93.521667 5 3345 3 chr2B.!!$R4 3340
3 TraesCS2B01G165000 chr2B 136634632 136640278 5646 True 755.433333 2409 91.983167 5 3494 6 chr2B.!!$R3 3489
4 TraesCS2B01G165000 chr2B 135464710 135466503 1793 False 742.000000 1282 89.500000 2035 3148 2 chr2B.!!$F2 1113
5 TraesCS2B01G165000 chr2B 182131139 182132928 1789 True 530.333333 1271 90.613667 2035 3231 3 chr2B.!!$R8 1196
6 TraesCS2B01G165000 chr2B 137130465 137131832 1367 True 420.000000 483 85.519500 7 1127 2 chr2B.!!$R5 1120
7 TraesCS2B01G165000 chr2B 137702549 137703120 571 True 262.000000 355 83.028000 7 689 2 chr2B.!!$R7 682
8 TraesCS2B01G165000 chr2D 85702906 85703786 880 True 1267.000000 1267 92.444000 925 1824 1 chr2D.!!$R1 899
9 TraesCS2B01G165000 chr2D 84777524 84780549 3025 True 1163.000000 2163 91.021500 803 3494 2 chr2D.!!$R3 2691
10 TraesCS2B01G165000 chr2D 127819456 127820367 911 True 1160.000000 1160 89.783000 2203 3111 1 chr2D.!!$R2 908
11 TraesCS2B01G165000 chr2D 83530934 83531963 1029 False 1038.000000 1038 85.769000 2203 3196 1 chr2D.!!$F1 993
12 TraesCS2B01G165000 chr2D 85405893 85409812 3919 True 951.500000 2924 90.946000 5 3494 4 chr2D.!!$R6 3489
13 TraesCS2B01G165000 chr2D 85249641 85252818 3177 True 788.525000 1445 89.933500 5 3494 4 chr2D.!!$R5 3489
14 TraesCS2B01G165000 chr2D 84935095 84938978 3883 True 760.000000 2130 92.091400 5 3494 5 chr2D.!!$R4 3489
15 TraesCS2B01G165000 chr7A 618194473 618196529 2056 True 1077.000000 1834 88.818000 30 1824 2 chr7A.!!$R2 1794
16 TraesCS2B01G165000 chr2A 85925937 85927152 1215 True 1796.000000 1796 93.226000 910 2142 1 chr2A.!!$R2 1232
17 TraesCS2B01G165000 chr2A 85810030 85811245 1215 True 1773.000000 1773 92.903000 910 2142 1 chr2A.!!$R1 1232
18 TraesCS2B01G165000 chr2A 85611174 85613727 2553 True 1267.666667 1796 94.191000 910 3494 3 chr2A.!!$R3 2584
19 TraesCS2B01G165000 chr2A 84144627 84146127 1500 False 710.500000 1262 90.446500 2203 3274 2 chr2A.!!$F2 1071
20 TraesCS2B01G165000 chr2A 83991123 83992335 1212 False 652.550000 1232 90.293500 2203 3231 2 chr2A.!!$F1 1028
21 TraesCS2B01G165000 chr4A 349805565 349806780 1215 True 1784.000000 1784 93.065000 910 2142 1 chr4A.!!$R1 1232

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
1044 2431 0.610174 AGCTGCTCCAACTCGATTCA 59.39 50.0 0.0 0.0 0.00 2.57 F
1490 2878 0.250467 GTGTCTGGTGTGTCAGCCAT 60.25 55.0 0.0 0.0 34.91 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 3469 0.967887 TCTCGAGGAGGTGAGCTTGG 60.968 60.0 13.56 0.0 32.2 3.61 R
2827 4566 1.679139 CTCAAAGCTTCACCCACACA 58.321 50.0 0.00 0.0 0.0 3.72 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
1044 2431 0.610174 AGCTGCTCCAACTCGATTCA 59.390 50.000 0.00 0.00 0.00 2.57
1490 2878 0.250467 GTGTCTGGTGTGTCAGCCAT 60.250 55.000 0.00 0.00 34.91 4.40
1750 3138 1.620819 GCCTGTGAAGAAGGTCTCTCA 59.379 52.381 0.00 0.00 37.13 3.27
1848 3236 3.687321 AAGCCGCCGATCAGCATGT 62.687 57.895 1.15 0.00 37.40 3.21
1854 3242 1.731433 GCCGATCAGCATGTGCCAAT 61.731 55.000 0.57 0.00 43.38 3.16
2081 3469 0.179189 GACAGCAAGCATGGCGTTAC 60.179 55.000 0.00 0.00 42.81 2.50
2149 3537 1.750778 GATGCAAATCCACGGGTGATT 59.249 47.619 0.00 0.00 0.00 2.57
2331 4062 3.514309 TCCCTCTAGGTTCTGCACTTAAC 59.486 47.826 0.00 0.00 36.75 2.01
2334 4065 4.080863 CCTCTAGGTTCTGCACTTAACCAT 60.081 45.833 18.37 9.37 46.29 3.55
2749 4486 5.757850 AATTAATCTTGGCTGAATCGGAC 57.242 39.130 0.00 0.00 0.00 4.79
2820 4559 8.211629 AGAGTAACATTGGTTAGTGAACTCTTT 58.788 33.333 0.03 0.00 41.95 2.52
2826 4565 7.554835 ACATTGGTTAGTGAACTCTTTTGTGTA 59.445 33.333 0.00 0.00 35.74 2.90
2827 4566 8.567948 CATTGGTTAGTGAACTCTTTTGTGTAT 58.432 33.333 0.00 0.00 35.74 2.29
3043 5145 0.744414 GCTGAAGCACGGAGGCAATA 60.744 55.000 0.00 0.00 41.59 1.90
3044 5146 1.009829 CTGAAGCACGGAGGCAATAC 58.990 55.000 0.00 0.00 35.83 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 122 8.017418 TGACTTGTTCATTTTTAATCCACCTT 57.983 30.769 0.00 0.0 0.00 3.50
121 125 6.922957 TGCTGACTTGTTCATTTTTAATCCAC 59.077 34.615 0.00 0.0 32.17 4.02
292 298 3.406595 GATGGCGGCCCTAGTGCTT 62.407 63.158 17.97 0.0 0.00 3.91
541 648 6.989155 TCCAACTTTCAGAAGGTCTAGTAA 57.011 37.500 0.00 0.0 37.19 2.24
1044 2431 3.776016 ATCGGGGAGGGAGGCGAAT 62.776 63.158 0.00 0.0 0.00 3.34
1490 2878 2.747460 GCATGGCTGCGTTCTCCA 60.747 61.111 0.00 0.0 38.92 3.86
1750 3138 1.078143 GCCTTGGAAGCGACCTGAT 60.078 57.895 0.00 0.0 0.00 2.90
1814 3202 1.525995 CTTCGGTTGCACACTGGGT 60.526 57.895 0.00 0.0 31.75 4.51
1848 3236 1.065199 AGCCTTCTCGATCAATTGGCA 60.065 47.619 5.42 0.0 41.12 4.92
2081 3469 0.967887 TCTCGAGGAGGTGAGCTTGG 60.968 60.000 13.56 0.0 32.20 3.61
2149 3537 1.710244 TGATTTCCTTCCCCTGCTTCA 59.290 47.619 0.00 0.0 0.00 3.02
2331 4062 8.327941 TCAAAGAACACTAGAAATCTTGATGG 57.672 34.615 0.00 0.0 32.72 3.51
2334 4065 9.003658 GGATTCAAAGAACACTAGAAATCTTGA 57.996 33.333 0.00 0.0 32.72 3.02
2645 4382 5.462530 TCGACAAGTTCAATTCTACTCCA 57.537 39.130 0.00 0.0 0.00 3.86
2749 4486 4.514441 CACTAAGATGCCAATGCCTAAGAG 59.486 45.833 0.00 0.0 36.33 2.85
2820 4559 2.158682 AGCTTCACCCACACATACACAA 60.159 45.455 0.00 0.0 0.00 3.33
2826 4565 2.233271 CTCAAAGCTTCACCCACACAT 58.767 47.619 0.00 0.0 0.00 3.21
2827 4566 1.679139 CTCAAAGCTTCACCCACACA 58.321 50.000 0.00 0.0 0.00 3.72
3037 5139 7.137426 GTGAAATCAGAGATGAATGTATTGCC 58.863 38.462 0.00 0.0 0.00 4.52
3043 5145 9.458727 AAGTATTGTGAAATCAGAGATGAATGT 57.541 29.630 0.00 0.0 0.00 2.71


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

AutoCloner maintained by Alex Coulton.