Multiple sequence alignment - TraesCS1D01G304400

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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 TraesCS1D01G304400 chr1D 100.000 2978 0 0 1 2978 402052543 402049566 0.000000e+00 5500.0
1 TraesCS1D01G304400 chr1D 99.067 2358 18 3 45 2402 402109015 402106662 0.000000e+00 4229.0
2 TraesCS1D01G304400 chr1D 98.770 2358 24 4 45 2402 402007452 402005100 0.000000e+00 4189.0
3 TraesCS1D01G304400 chr1D 99.180 2194 17 1 45 2238 401922236 401920044 0.000000e+00 3951.0
4 TraesCS1D01G304400 chr1D 93.984 1413 71 5 830 2241 401775169 401773770 0.000000e+00 2126.0
5 TraesCS1D01G304400 chr1D 99.132 576 5 0 2403 2978 402004124 402003549 0.000000e+00 1037.0
6 TraesCS1D01G304400 chr1D 99.132 576 5 0 2403 2978 402105686 402105111 0.000000e+00 1037.0
7 TraesCS1D01G304400 chr1D 88.571 280 12 9 899 1158 401700044 401699765 3.700000e-84 322.0
8 TraesCS1D01G304400 chr1D 88.571 210 17 2 352 557 401775569 401775363 6.370000e-62 248.0
9 TraesCS1D01G304400 chr1D 78.233 317 50 11 45 356 443174852 443174550 5.070000e-43 185.0
10 TraesCS1D01G304400 chr1D 96.939 98 3 0 2192 2289 401920052 401919955 6.600000e-37 165.0
11 TraesCS1D01G304400 chr1D 100.000 48 0 0 1 48 402109101 402109054 4.090000e-14 89.8
12 TraesCS1D01G304400 chr1D 97.917 48 1 0 1 48 401922322 401922275 1.900000e-12 84.2
13 TraesCS1D01G304400 chr1D 97.917 48 1 0 1 48 402007538 402007491 1.900000e-12 84.2
14 TraesCS1D01G304400 chr1B 90.603 2139 128 38 50 2154 539590496 539588397 0.000000e+00 2769.0
15 TraesCS1D01G304400 chr1B 95.349 43 2 0 553 595 642509309 642509351 5.330000e-08 69.4
16 TraesCS1D01G304400 chr1A 92.246 1870 94 16 552 2402 497585909 497584072 0.000000e+00 2603.0
17 TraesCS1D01G304400 chr1A 92.892 1421 66 12 830 2241 497580598 497579204 0.000000e+00 2032.0
18 TraesCS1D01G304400 chr1A 89.455 275 13 6 899 1158 497537649 497537376 1.710000e-87 333.0
19 TraesCS1D01G304400 chr1A 89.744 156 8 4 353 501 497580965 497580811 3.030000e-45 193.0
20 TraesCS1D01G304400 chr1A 88.073 109 9 2 452 556 497587962 497587854 3.120000e-25 126.0
21 TraesCS1D01G304400 chr1A 97.727 44 1 0 552 595 402259129 402259172 3.180000e-10 76.8
22 TraesCS1D01G304400 chr7B 87.433 1122 126 11 997 2115 535506115 535507224 0.000000e+00 1277.0
23 TraesCS1D01G304400 chr7B 96.707 577 18 1 2403 2978 539933146 539933722 0.000000e+00 959.0
24 TraesCS1D01G304400 chr7B 95.841 577 20 2 2403 2977 680693239 680693813 0.000000e+00 929.0
25 TraesCS1D01G304400 chr7B 95.337 579 24 2 2403 2978 73654991 73654413 0.000000e+00 917.0
26 TraesCS1D01G304400 chr7B 83.117 231 38 1 45 275 517606999 517607228 3.010000e-50 209.0
27 TraesCS1D01G304400 chr7B 93.750 48 3 0 1 48 324062306 324062353 4.120000e-09 73.1
28 TraesCS1D01G304400 chr7B 91.667 48 4 0 1 48 450244398 450244445 1.920000e-07 67.6
29 TraesCS1D01G304400 chr7D 86.881 1151 126 19 983 2127 506882674 506883805 0.000000e+00 1266.0
30 TraesCS1D01G304400 chr7D 97.920 577 11 1 2403 2978 185381400 185381976 0.000000e+00 998.0
31 TraesCS1D01G304400 chr7D 95.675 578 22 3 2403 2978 55870295 55869719 0.000000e+00 926.0
32 TraesCS1D01G304400 chr7D 95.652 46 2 0 3 48 239520940 239520895 1.140000e-09 75.0
33 TraesCS1D01G304400 chr7D 95.652 46 2 0 3 48 259623358 259623403 1.140000e-09 75.0
34 TraesCS1D01G304400 chr7D 79.412 102 16 3 261 357 467515784 467515885 1.920000e-07 67.6
35 TraesCS1D01G304400 chr6D 95.675 578 20 3 2403 2978 367503711 367503137 0.000000e+00 924.0
36 TraesCS1D01G304400 chr4D 95.329 578 22 4 2403 2978 85890214 85890788 0.000000e+00 913.0
37 TraesCS1D01G304400 chr4D 81.915 94 14 1 266 356 28834860 28834767 3.180000e-10 76.8
38 TraesCS1D01G304400 chr7A 83.916 286 33 7 45 330 680339032 680338760 8.190000e-66 261.0
39 TraesCS1D01G304400 chr7A 83.043 230 33 5 45 273 169018016 169018240 1.400000e-48 204.0
40 TraesCS1D01G304400 chr7A 77.778 99 18 4 236 332 127350468 127350564 1.150000e-04 58.4
41 TraesCS1D01G304400 chr2A 80.851 235 39 5 45 276 566206078 566205847 2.360000e-41 180.0
42 TraesCS1D01G304400 chr5D 80.617 227 40 3 50 276 487448338 487448116 3.950000e-39 172.0
43 TraesCS1D01G304400 chr5D 97.727 44 1 0 552 595 135648487 135648530 3.180000e-10 76.8
44 TraesCS1D01G304400 chr3D 85.526 76 8 3 287 359 509686273 509686348 3.180000e-10 76.8
45 TraesCS1D01G304400 chr3D 80.000 95 16 2 266 357 303791382 303791288 1.920000e-07 67.6
46 TraesCS1D01G304400 chr5A 95.652 46 2 0 550 595 47964341 47964386 1.140000e-09 75.0
47 TraesCS1D01G304400 chr2B 81.250 96 15 2 266 358 508409675 508409580 1.140000e-09 75.0
48 TraesCS1D01G304400 chr6B 95.556 45 2 0 1 45 321711484 321711528 4.120000e-09 73.1
49 TraesCS1D01G304400 chr4B 93.750 48 3 0 1 48 49149526 49149479 4.120000e-09 73.1
50 TraesCS1D01G304400 chr2D 88.710 62 2 5 552 609 492655317 492655377 1.480000e-08 71.3


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 TraesCS1D01G304400 chr1D 402049566 402052543 2977 True 5500.000000 5500 100.000000 1 2978 1 chr1D.!!$R2 2977
1 TraesCS1D01G304400 chr1D 402105111 402109101 3990 True 1785.266667 4229 99.399667 1 2978 3 chr1D.!!$R7 2977
2 TraesCS1D01G304400 chr1D 402003549 402007538 3989 True 1770.066667 4189 98.606333 1 2978 3 chr1D.!!$R6 2977
3 TraesCS1D01G304400 chr1D 401919955 401922322 2367 True 1400.066667 3951 98.012000 1 2289 3 chr1D.!!$R5 2288
4 TraesCS1D01G304400 chr1D 401773770 401775569 1799 True 1187.000000 2126 91.277500 352 2241 2 chr1D.!!$R4 1889
5 TraesCS1D01G304400 chr1B 539588397 539590496 2099 True 2769.000000 2769 90.603000 50 2154 1 chr1B.!!$R1 2104
6 TraesCS1D01G304400 chr1A 497579204 497587962 8758 True 1238.500000 2603 90.738750 353 2402 4 chr1A.!!$R2 2049
7 TraesCS1D01G304400 chr7B 535506115 535507224 1109 False 1277.000000 1277 87.433000 997 2115 1 chr7B.!!$F4 1118
8 TraesCS1D01G304400 chr7B 539933146 539933722 576 False 959.000000 959 96.707000 2403 2978 1 chr7B.!!$F5 575
9 TraesCS1D01G304400 chr7B 680693239 680693813 574 False 929.000000 929 95.841000 2403 2977 1 chr7B.!!$F6 574
10 TraesCS1D01G304400 chr7B 73654413 73654991 578 True 917.000000 917 95.337000 2403 2978 1 chr7B.!!$R1 575
11 TraesCS1D01G304400 chr7D 506882674 506883805 1131 False 1266.000000 1266 86.881000 983 2127 1 chr7D.!!$F4 1144
12 TraesCS1D01G304400 chr7D 185381400 185381976 576 False 998.000000 998 97.920000 2403 2978 1 chr7D.!!$F1 575
13 TraesCS1D01G304400 chr7D 55869719 55870295 576 True 926.000000 926 95.675000 2403 2978 1 chr7D.!!$R1 575
14 TraesCS1D01G304400 chr6D 367503137 367503711 574 True 924.000000 924 95.675000 2403 2978 1 chr6D.!!$R1 575
15 TraesCS1D01G304400 chr4D 85890214 85890788 574 False 913.000000 913 95.329000 2403 2978 1 chr4D.!!$F1 575

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
335 380 0.917333 TTGAGGGGCCGGATTTACCT 60.917 55.0 5.05 3.73 36.31 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 9555 5.975693 TTCAAAAATATTTGCCGAGACCT 57.024 34.783 0.39 0.0 44.52 3.85 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
335 380 0.917333 TTGAGGGGCCGGATTTACCT 60.917 55.000 5.05 3.73 36.31 3.08
398 447 1.468520 CGACCAACGAAGCAATCCAAT 59.531 47.619 0.00 0.00 45.77 3.16
614 2618 7.067615 GGAGGGATAAATGAAGAGAGGAAAAAC 59.932 40.741 0.00 0.00 0.00 2.43
627 2645 8.703378 AGAGAGGAAAAACAATGAATTCTCTT 57.297 30.769 7.05 0.00 36.42 2.85
774 2798 6.992123 CACATCCATCTAACTAACTATTGGCA 59.008 38.462 0.00 0.00 0.00 4.92
775 2799 7.498900 CACATCCATCTAACTAACTATTGGCAA 59.501 37.037 0.68 0.68 0.00 4.52
1340 8459 2.202492 CAAGGACGCCGTCGAGAG 60.202 66.667 11.60 0.00 39.41 3.20
2392 9555 3.058983 CGCATAAAATATCAAGGCGAGCA 60.059 43.478 0.00 0.00 45.19 4.26
2395 9558 2.717639 AAATATCAAGGCGAGCAGGT 57.282 45.000 0.00 0.00 0.00 4.00
2397 9560 1.418334 ATATCAAGGCGAGCAGGTCT 58.582 50.000 0.00 0.00 0.00 3.85
2398 9561 0.747255 TATCAAGGCGAGCAGGTCTC 59.253 55.000 0.00 0.00 38.47 3.36
2497 10635 1.604308 CCCACATGGCAGCTGACAA 60.604 57.895 29.42 10.59 36.16 3.18
2539 10677 2.510238 GTCTCGGCAATGCTCGCT 60.510 61.111 4.82 0.00 0.00 4.93
2547 10685 2.407090 GGCAATGCTCGCTTTCTTTTT 58.593 42.857 4.82 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 231 5.749620 ACACATGCACGTACGAAAATAAAA 58.250 33.333 24.41 0.0 0.00 1.52
2392 9555 5.975693 TTCAAAAATATTTGCCGAGACCT 57.024 34.783 0.39 0.0 44.52 3.85
2497 10635 5.468072 CAGCTCTCGGCAAAGATATGTAAAT 59.532 40.000 0.00 0.0 44.79 1.40
2539 10677 3.733337 AGAGCAGCTCTCGAAAAAGAAA 58.267 40.909 20.04 0.0 46.44 2.52


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

AutoCloner maintained by Alex Coulton.