Multiple sequence alignment - TraesCS3B01G195400

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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 TraesCS3B01G195400 chr3B 100.000 2956 0 0 1 2956 221978962 221981917 0.000000e+00 5459.0
1 TraesCS3B01G195400 chr3B 97.863 2621 28 8 348 2955 221911829 221914434 0.000000e+00 4505.0
2 TraesCS3B01G195400 chr3B 94.524 2228 83 18 762 2956 215384958 215387179 0.000000e+00 3402.0
3 TraesCS3B01G195400 chr3B 93.060 1974 76 28 334 2269 215571443 215573393 0.000000e+00 2830.0
4 TraesCS3B01G195400 chr3B 94.564 1306 48 14 796 2088 215310364 215311659 0.000000e+00 1997.0
5 TraesCS3B01G195400 chr3B 90.818 1198 76 12 709 1878 215104492 215105683 0.000000e+00 1572.0
6 TraesCS3B01G195400 chr3B 91.979 1122 44 17 813 1924 221457693 221458778 0.000000e+00 1531.0
7 TraesCS3B01G195400 chr3B 89.921 1012 85 7 963 1958 203549124 203550134 0.000000e+00 1288.0
8 TraesCS3B01G195400 chr3B 93.513 817 42 8 1 808 215308542 215309356 0.000000e+00 1205.0
9 TraesCS3B01G195400 chr3B 92.954 809 45 10 1 799 221456717 221457523 0.000000e+00 1168.0
10 TraesCS3B01G195400 chr3B 94.000 750 38 6 1 744 215384016 215384764 0.000000e+00 1129.0
11 TraesCS3B01G195400 chr3B 98.316 475 8 0 1914 2388 221466768 221467242 0.000000e+00 833.0
12 TraesCS3B01G195400 chr3B 94.705 491 22 3 284 771 221748577 221749066 0.000000e+00 760.0
13 TraesCS3B01G195400 chr3B 92.662 477 34 1 2480 2956 221467241 221467716 0.000000e+00 686.0
14 TraesCS3B01G195400 chr3B 92.466 292 18 2 1 288 221747881 221748172 5.890000e-112 414.0
15 TraesCS3B01G195400 chr3B 92.857 168 9 2 1955 2120 221750207 221750373 1.060000e-59 241.0
16 TraesCS3B01G195400 chr3B 95.918 147 6 0 2085 2231 215314370 215314516 3.810000e-59 239.0
17 TraesCS3B01G195400 chr3B 91.463 164 10 3 1959 2120 215114890 215115051 3.830000e-54 222.0
18 TraesCS3B01G195400 chr3B 94.340 106 6 0 2816 2921 221752849 221752954 2.360000e-36 163.0
19 TraesCS3B01G195400 chr3B 84.426 122 11 3 2267 2381 203346827 203346947 2.410000e-21 113.0
20 TraesCS3B01G195400 chr3B 84.426 122 11 3 2267 2381 203553951 203554071 2.410000e-21 113.0
21 TraesCS3B01G195400 chr3B 96.667 60 2 0 2812 2871 203554326 203554385 1.870000e-17 100.0
22 TraesCS3B01G195400 chr3B 92.424 66 3 1 2416 2481 706537472 706537409 3.140000e-15 93.5
23 TraesCS3B01G195400 chr3B 92.424 66 1 2 2418 2481 822221110 822221173 1.130000e-14 91.6
24 TraesCS3B01G195400 chr3B 92.424 66 1 2 2418 2481 822311466 822311529 1.130000e-14 91.6
25 TraesCS3B01G195400 chr3A 89.813 1286 73 21 877 2120 166923328 166924597 0.000000e+00 1596.0
26 TraesCS3B01G195400 chr3A 91.409 1001 70 7 972 1959 159831982 159832979 0.000000e+00 1358.0
27 TraesCS3B01G195400 chr3A 84.872 390 35 11 2566 2955 166924834 166925199 3.600000e-99 372.0
28 TraesCS3B01G195400 chr3A 79.331 508 61 22 405 879 166922769 166923265 1.710000e-82 316.0
29 TraesCS3B01G195400 chr3A 88.372 129 14 1 2011 2139 177889141 177889268 1.420000e-33 154.0
30 TraesCS3B01G195400 chr3A 90.598 117 8 3 2267 2381 159833074 159833189 5.100000e-33 152.0
31 TraesCS3B01G195400 chr3A 92.683 82 4 1 798 879 177859730 177859809 1.860000e-22 117.0
32 TraesCS3B01G195400 chr3A 98.039 51 1 0 1955 2005 159833004 159833054 4.060000e-14 89.8
33 TraesCS3B01G195400 chr3A 95.556 45 2 0 2719 2763 159433569 159433613 4.090000e-09 73.1
34 TraesCS3B01G195400 chr3D 91.697 1084 62 13 877 1935 149204949 149206029 0.000000e+00 1478.0
35 TraesCS3B01G195400 chr3D 91.536 1087 62 13 877 1935 149544110 149545194 0.000000e+00 1471.0
36 TraesCS3B01G195400 chr3D 92.864 1023 50 8 877 1876 147336153 147335131 0.000000e+00 1463.0
37 TraesCS3B01G195400 chr3D 85.280 1216 99 29 813 1959 149770155 149768951 0.000000e+00 1181.0
38 TraesCS3B01G195400 chr3D 85.009 587 58 18 1 579 149204179 149204743 1.190000e-158 569.0
39 TraesCS3B01G195400 chr3D 84.864 588 58 9 1 579 149543335 149543900 5.530000e-157 564.0
40 TraesCS3B01G195400 chr3D 83.816 414 55 10 1 407 149518160 149518568 1.660000e-102 383.0
41 TraesCS3B01G195400 chr3D 86.624 314 29 9 1959 2263 149206090 149206399 4.720000e-88 335.0
42 TraesCS3B01G195400 chr3D 85.981 321 31 11 1959 2269 147334720 147334404 6.110000e-87 331.0
43 TraesCS3B01G195400 chr3D 82.398 392 32 17 2566 2956 149545624 149545979 1.030000e-79 307.0
44 TraesCS3B01G195400 chr3D 92.683 164 10 1 1959 2120 149545261 149545424 4.930000e-58 235.0
45 TraesCS3B01G195400 chr3D 88.415 164 9 8 423 579 147336523 147336363 3.890000e-44 189.0
46 TraesCS3B01G195400 chr3D 97.826 92 2 0 696 787 149204737 149204828 3.050000e-35 159.0
47 TraesCS3B01G195400 chr3D 96.774 93 3 0 696 788 149543894 149543986 3.940000e-34 156.0
48 TraesCS3B01G195400 chr3D 85.535 159 5 7 696 850 147336369 147336225 1.840000e-32 150.0
49 TraesCS3B01G195400 chr3D 96.053 76 3 0 2812 2887 141412094 141412169 1.110000e-24 124.0
50 TraesCS3B01G195400 chr3D 90.123 81 8 0 2302 2382 147334643 147334563 4.030000e-19 106.0
51 TraesCS3B01G195400 chr3D 90.123 81 8 0 2302 2382 149206167 149206247 4.030000e-19 106.0
52 TraesCS3B01G195400 chr3D 92.537 67 2 2 2416 2481 534687115 534687051 3.140000e-15 93.5
53 TraesCS3B01G195400 chr3D 98.039 51 1 0 1955 2005 141411677 141411727 4.060000e-14 89.8
54 TraesCS3B01G195400 chr3D 92.063 63 3 1 2424 2486 550253858 550253918 1.460000e-13 87.9
55 TraesCS3B01G195400 chr5D 79.464 224 41 5 157 378 456599906 456599686 1.420000e-33 154.0
56 TraesCS3B01G195400 chr6A 88.618 123 11 3 2270 2390 146440536 146440415 2.370000e-31 147.0
57 TraesCS3B01G195400 chr6A 96.774 62 2 0 2812 2873 146438854 146438793 1.450000e-18 104.0
58 TraesCS3B01G195400 chr5A 80.503 159 24 6 186 340 416184515 416184670 6.700000e-22 115.0
59 TraesCS3B01G195400 chr4B 90.000 70 3 2 2418 2485 413089365 413089298 1.460000e-13 87.9
60 TraesCS3B01G195400 chr1B 76.879 173 29 10 541 707 416831648 416831481 1.460000e-13 87.9
61 TraesCS3B01G195400 chr5B 85.227 88 5 4 2406 2487 436465263 436465178 1.890000e-12 84.2


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 TraesCS3B01G195400 chr3B 221978962 221981917 2955 False 5459.000000 5459 100.000000 1 2956 1 chr3B.!!$F6 2955
1 TraesCS3B01G195400 chr3B 221911829 221914434 2605 False 4505.000000 4505 97.863000 348 2955 1 chr3B.!!$F5 2607
2 TraesCS3B01G195400 chr3B 215571443 215573393 1950 False 2830.000000 2830 93.060000 334 2269 1 chr3B.!!$F4 1935
3 TraesCS3B01G195400 chr3B 215384016 215387179 3163 False 2265.500000 3402 94.262000 1 2956 2 chr3B.!!$F11 2955
4 TraesCS3B01G195400 chr3B 215104492 215105683 1191 False 1572.000000 1572 90.818000 709 1878 1 chr3B.!!$F2 1169
5 TraesCS3B01G195400 chr3B 221456717 221458778 2061 False 1349.500000 1531 92.466500 1 1924 2 chr3B.!!$F12 1923
6 TraesCS3B01G195400 chr3B 215308542 215314516 5974 False 1147.000000 1997 94.665000 1 2231 3 chr3B.!!$F10 2230
7 TraesCS3B01G195400 chr3B 221466768 221467716 948 False 759.500000 833 95.489000 1914 2956 2 chr3B.!!$F13 1042
8 TraesCS3B01G195400 chr3B 203549124 203554385 5261 False 500.333333 1288 90.338000 963 2871 3 chr3B.!!$F9 1908
9 TraesCS3B01G195400 chr3B 221747881 221752954 5073 False 394.500000 760 93.592000 1 2921 4 chr3B.!!$F14 2920
10 TraesCS3B01G195400 chr3A 166922769 166925199 2430 False 761.333333 1596 84.672000 405 2955 3 chr3A.!!$F5 2550
11 TraesCS3B01G195400 chr3A 159831982 159833189 1207 False 533.266667 1358 93.348667 972 2381 3 chr3A.!!$F4 1409
12 TraesCS3B01G195400 chr3D 149768951 149770155 1204 True 1181.000000 1181 85.280000 813 1959 1 chr3D.!!$R1 1146
13 TraesCS3B01G195400 chr3D 149543335 149545979 2644 False 546.600000 1471 89.651000 1 2956 5 chr3D.!!$F5 2955
14 TraesCS3B01G195400 chr3D 149204179 149206399 2220 False 529.400000 1478 90.255800 1 2382 5 chr3D.!!$F4 2381
15 TraesCS3B01G195400 chr3D 147334404 147336523 2119 True 447.800000 1463 88.583600 423 2382 5 chr3D.!!$R3 1959

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
163 171 0.469917 TTGGCCTAGCATAGACCTGC 59.530 55.0 3.32 0.00 42.39 4.85 F
171 179 0.604780 GCATAGACCTGCGCATGGAT 60.605 55.0 26.07 17.79 31.49 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 3380 4.441356 GGACTCTCAGATTGATCCACTGAC 60.441 50.000 8.73 2.12 36.04 3.51 R
2413 11018 6.537301 ACACGAGTGTCAAAAAGTCTTAATGA 59.463 34.615 2.62 0.00 40.24 2.57 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
35 36 2.750166 TCCAAAGAAAACACGCTCACAA 59.250 40.909 0.00 0.00 0.00 3.33
134 142 2.497770 GCCGCTACGCCTAAAGGA 59.502 61.111 0.00 0.00 37.39 3.36
163 171 0.469917 TTGGCCTAGCATAGACCTGC 59.530 55.000 3.32 0.00 42.39 4.85
171 179 0.604780 GCATAGACCTGCGCATGGAT 60.605 55.000 26.07 17.79 31.49 3.41
243 251 1.270465 GCCTGAAAGCCAGCACAAAAT 60.270 47.619 0.00 0.00 41.57 1.82
365 786 5.835113 AGTGCACTATTCTTGTGTTTTGT 57.165 34.783 20.16 0.00 37.70 2.83
475 899 5.814188 TCAGTCATCATGCTAATGTCACTTC 59.186 40.000 0.00 0.00 35.15 3.01
1439 3380 0.100861 GAGAAGCCCTCGTACTTCGG 59.899 60.000 0.00 0.00 45.56 4.30
2403 11008 0.338814 ACTACTCCCTCCGTCCCATT 59.661 55.000 0.00 0.00 0.00 3.16
2406 11011 1.201424 ACTCCCTCCGTCCCATTAAC 58.799 55.000 0.00 0.00 0.00 2.01
2409 11014 0.468648 CCCTCCGTCCCATTAACTCC 59.531 60.000 0.00 0.00 0.00 3.85
2410 11015 0.104304 CCTCCGTCCCATTAACTCCG 59.896 60.000 0.00 0.00 0.00 4.63
2412 11017 0.819582 TCCGTCCCATTAACTCCGTC 59.180 55.000 0.00 0.00 0.00 4.79
2413 11018 0.822164 CCGTCCCATTAACTCCGTCT 59.178 55.000 0.00 0.00 0.00 4.18
2452 11057 2.538449 ACTCGTGTAGTGTCAAAAAGCG 59.462 45.455 0.00 0.00 36.93 4.68
2612 11306 1.577328 CCCAATCGACAGCGCAAACT 61.577 55.000 11.47 0.00 37.46 2.66
2620 11315 1.264288 GACAGCGCAAACTTGTAAGCT 59.736 47.619 11.47 4.28 36.53 3.74
2905 13670 0.249238 TCCAACACAAATGCCAACGC 60.249 50.000 0.00 0.00 0.00 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 59 2.351350 CCCGTTGCATACTTTTGGACAC 60.351 50.000 0.00 0.00 0.00 3.67
53 60 1.883275 CCCGTTGCATACTTTTGGACA 59.117 47.619 0.00 0.00 0.00 4.02
55 62 1.074084 TCCCCGTTGCATACTTTTGGA 59.926 47.619 0.00 0.00 0.00 3.53
134 142 1.097547 GCTAGGCCAATCACATGCGT 61.098 55.000 5.01 0.00 0.00 5.24
171 179 4.751820 GGCTTTTGGGCCGGGCTA 62.752 66.667 28.80 20.86 42.82 3.93
243 251 4.157656 CCATGTTCGGGCTTATTTTTGAGA 59.842 41.667 0.00 0.00 0.00 3.27
341 761 7.192913 CACAAAACACAAGAATAGTGCACTTA 58.807 34.615 27.06 11.47 40.59 2.24
379 800 0.251341 AAAATCACAAGCCCGAGCCT 60.251 50.000 0.00 0.00 41.25 4.58
1439 3380 4.441356 GGACTCTCAGATTGATCCACTGAC 60.441 50.000 8.73 2.12 36.04 3.51
2412 11017 7.065894 CACGAGTGTCAAAAAGTCTTAATGAG 58.934 38.462 0.00 0.00 0.00 2.90
2413 11018 6.537301 ACACGAGTGTCAAAAAGTCTTAATGA 59.463 34.615 2.62 0.00 40.24 2.57
2434 11039 2.538449 AGACGCTTTTTGACACTACACG 59.462 45.455 0.00 0.00 0.00 4.49
2452 11057 6.837568 TCCCTCCGTCCCATATAATATAAGAC 59.162 42.308 0.00 0.00 0.00 3.01
2612 11306 4.825422 CTTCATCTGAGGACAGCTTACAA 58.175 43.478 0.00 0.00 43.17 2.41
2620 11315 1.274703 GGGGGCTTCATCTGAGGACA 61.275 60.000 0.00 0.00 29.53 4.02
2905 13670 5.316770 GCGTTTATGTAAGAGCTTGACAAG 58.683 41.667 11.02 11.02 0.00 3.16


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

AutoCloner maintained by Alex Coulton.