Multiple sequence alignment - TraesCS5B01G551500

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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 TraesCS5B01G551500 chr5B 100.000 2497 0 0 1 2497 702650388 702647892 0.000000e+00 4612.0
1 TraesCS5B01G551500 chr5B 99.136 2315 17 3 21 2335 702802265 702799954 0.000000e+00 4161.0
2 TraesCS5B01G551500 chr5B 97.751 1423 23 2 21 1443 702628744 702627331 0.000000e+00 2442.0
3 TraesCS5B01G551500 chr5B 97.552 1430 24 4 21 1443 702742801 702741376 0.000000e+00 2436.0
4 TraesCS5B01G551500 chr5B 97.063 1430 30 5 21 1443 702610200 702608776 0.000000e+00 2398.0
5 TraesCS5B01G551500 chr5B 97.048 1423 24 5 21 1443 702760975 702759571 0.000000e+00 2379.0
6 TraesCS5B01G551500 chr5B 86.711 301 23 9 2184 2483 130894203 130894487 4.010000e-83 318.0
7 TraesCS5B01G551500 chr5B 76.220 328 56 6 27 332 407775418 407775091 1.200000e-33 154.0
8 TraesCS5B01G551500 chr2B 96.932 1043 8 4 1444 2486 55621958 55620940 0.000000e+00 1727.0
9 TraesCS5B01G551500 chr2B 88.926 298 21 10 2189 2486 82300702 82300987 8.490000e-95 357.0
10 TraesCS5B01G551500 chr2B 87.291 299 20 13 2191 2486 42960382 42960665 2.400000e-85 326.0
11 TraesCS5B01G551500 chr2B 81.915 94 16 1 1774 1867 324185989 324186081 7.400000e-11 78.7
12 TraesCS5B01G551500 chr4A 94.379 427 21 2 1446 1871 475550118 475549694 0.000000e+00 652.0
13 TraesCS5B01G551500 chr4A 96.273 322 11 1 1871 2192 475549636 475549316 6.120000e-146 527.0
14 TraesCS5B01G551500 chr4A 88.040 301 28 4 933 1230 629110404 629110699 1.420000e-92 350.0
15 TraesCS5B01G551500 chr4A 84.322 236 32 5 1443 1675 5889915 5889682 2.500000e-55 226.0
16 TraesCS5B01G551500 chr4A 79.259 135 23 5 1444 1575 656750347 656750215 3.420000e-14 89.8
17 TraesCS5B01G551500 chr4A 83.333 78 13 0 1790 1867 575058814 575058891 3.450000e-09 73.1
18 TraesCS5B01G551500 chr6A 93.706 429 24 2 1444 1871 124304483 124304909 7.530000e-180 640.0
19 TraesCS5B01G551500 chr6A 96.894 322 9 1 1871 2192 124304967 124305287 2.830000e-149 538.0
20 TraesCS5B01G551500 chr6A 83.691 233 37 1 1444 1675 592565094 592564862 4.180000e-53 219.0
21 TraesCS5B01G551500 chr6A 81.818 88 15 1 1780 1867 149833494 149833408 3.450000e-09 73.1
22 TraesCS5B01G551500 chr7A 97.826 322 6 1 1871 2192 49182521 49182201 2.810000e-154 555.0
23 TraesCS5B01G551500 chr7A 95.167 269 13 0 1603 1871 49182847 49182579 2.300000e-115 425.0
24 TraesCS5B01G551500 chr7A 86.601 306 25 8 2184 2486 630249157 630249449 8.610000e-85 324.0
25 TraesCS5B01G551500 chr7A 85.855 304 25 7 2183 2484 555458413 555458700 8.680000e-80 307.0
26 TraesCS5B01G551500 chr7A 93.605 172 7 2 1444 1613 49183344 49183175 1.150000e-63 254.0
27 TraesCS5B01G551500 chr7A 84.279 229 31 5 1444 1669 61878338 61878564 4.180000e-53 219.0
28 TraesCS5B01G551500 chr7A 92.929 99 7 0 234 332 92811156 92811254 7.200000e-31 145.0
29 TraesCS5B01G551500 chr7A 85.039 127 16 3 1747 1871 449699613 449699738 2.610000e-25 126.0
30 TraesCS5B01G551500 chr1B 91.864 295 14 7 2191 2484 563527368 563527083 1.080000e-108 403.0
31 TraesCS5B01G551500 chr1B 81.915 94 16 1 1774 1867 669213677 669213769 7.400000e-11 78.7
32 TraesCS5B01G551500 chr1B 88.525 61 7 0 1444 1504 624835137 624835197 9.580000e-10 75.0
33 TraesCS5B01G551500 chr3D 88.498 313 21 7 2172 2483 19310730 19310432 5.080000e-97 364.0
34 TraesCS5B01G551500 chr3D 89.139 267 15 5 2191 2457 480389111 480389363 1.110000e-83 320.0
35 TraesCS5B01G551500 chr2D 89.333 300 16 8 2189 2486 528992925 528992640 1.830000e-96 363.0
36 TraesCS5B01G551500 chr2D 85.897 234 32 1 1443 1675 21065722 21065489 5.330000e-62 248.0
37 TraesCS5B01G551500 chr6B 89.298 299 17 7 2188 2484 140766386 140766671 6.570000e-96 361.0
38 TraesCS5B01G551500 chr6B 86.275 306 19 8 2191 2486 526045461 526045169 6.710000e-81 311.0
39 TraesCS5B01G551500 chr6B 91.860 86 7 0 244 329 614411533 614411448 1.210000e-23 121.0
40 TraesCS5B01G551500 chr5D 89.037 301 18 7 2188 2486 406328034 406328321 2.360000e-95 359.0
41 TraesCS5B01G551500 chr5D 87.000 300 24 7 2189 2486 379614019 379613733 8.610000e-85 324.0
42 TraesCS5B01G551500 chr5D 82.958 311 49 4 21 329 6647803 6648111 6.800000e-71 278.0
43 TraesCS5B01G551500 chr5D 78.485 330 47 8 21 328 5351048 5351375 7.050000e-46 195.0
44 TraesCS5B01G551500 chr5D 81.818 88 15 1 1780 1867 354481606 354481520 3.450000e-09 73.1
45 TraesCS5B01G551500 chr5D 80.851 94 17 1 1774 1867 531479633 531479725 3.450000e-09 73.1
46 TraesCS5B01G551500 chr1D 89.000 300 18 7 2189 2486 438222029 438222315 8.490000e-95 357.0
47 TraesCS5B01G551500 chr1D 86.774 310 23 9 2182 2486 442418975 442419271 1.850000e-86 329.0
48 TraesCS5B01G551500 chr1D 85.852 311 26 10 2180 2486 5321516 5321812 5.180000e-82 315.0
49 TraesCS5B01G551500 chr7B 87.138 311 26 7 2178 2486 143246122 143246420 8.550000e-90 340.0
50 TraesCS5B01G551500 chrUn 93.392 227 14 1 1006 1232 110462727 110462952 3.980000e-88 335.0
51 TraesCS5B01G551500 chr3B 87.748 302 18 6 2189 2486 732059597 732059883 3.980000e-88 335.0
52 TraesCS5B01G551500 chr3B 79.042 334 48 9 21 332 501789294 501789627 2.520000e-50 209.0
53 TraesCS5B01G551500 chr2A 87.500 296 21 12 2191 2482 757676790 757677073 6.660000e-86 327.0
54 TraesCS5B01G551500 chr5A 90.244 246 22 2 998 1241 700178882 700178637 1.110000e-83 320.0
55 TraesCS5B01G551500 chr5A 84.277 318 31 9 932 1230 640399892 640400209 2.430000e-75 292.0
56 TraesCS5B01G551500 chr5A 85.714 84 12 0 1784 1867 650304806 650304889 3.420000e-14 89.8
57 TraesCS5B01G551500 chr7D 82.484 314 45 8 21 332 45069948 45070253 1.470000e-67 267.0
58 TraesCS5B01G551500 chr7D 85.837 233 32 1 1444 1675 265254601 265254833 1.920000e-61 246.0
59 TraesCS5B01G551500 chr6D 79.344 305 44 16 2189 2486 467119212 467118920 1.960000e-46 196.0
60 TraesCS5B01G551500 chr1A 77.564 156 26 8 1444 1594 364624522 364624371 4.430000e-13 86.1
61 TraesCS5B01G551500 chr1A 81.818 88 15 1 1780 1867 590753830 590753744 3.450000e-09 73.1


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 TraesCS5B01G551500 chr5B 702647892 702650388 2496 True 4612.000000 4612 100.000000 1 2497 1 chr5B.!!$R4 2496
1 TraesCS5B01G551500 chr5B 702799954 702802265 2311 True 4161.000000 4161 99.136000 21 2335 1 chr5B.!!$R7 2314
2 TraesCS5B01G551500 chr5B 702627331 702628744 1413 True 2442.000000 2442 97.751000 21 1443 1 chr5B.!!$R3 1422
3 TraesCS5B01G551500 chr5B 702741376 702742801 1425 True 2436.000000 2436 97.552000 21 1443 1 chr5B.!!$R5 1422
4 TraesCS5B01G551500 chr5B 702608776 702610200 1424 True 2398.000000 2398 97.063000 21 1443 1 chr5B.!!$R2 1422
5 TraesCS5B01G551500 chr5B 702759571 702760975 1404 True 2379.000000 2379 97.048000 21 1443 1 chr5B.!!$R6 1422
6 TraesCS5B01G551500 chr2B 55620940 55621958 1018 True 1727.000000 1727 96.932000 1444 2486 1 chr2B.!!$R1 1042
7 TraesCS5B01G551500 chr4A 475549316 475550118 802 True 589.500000 652 95.326000 1446 2192 2 chr4A.!!$R3 746
8 TraesCS5B01G551500 chr6A 124304483 124305287 804 False 589.000000 640 95.300000 1444 2192 2 chr6A.!!$F1 748
9 TraesCS5B01G551500 chr7A 49182201 49183344 1143 True 411.333333 555 95.532667 1444 2192 3 chr7A.!!$R1 748

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
169 171 3.947132 CTGTGTCCAGCTGCTCCCG 62.947 68.421 8.66 0.0 0.0 5.14 F
1322 1344 2.164422 CGAGATCTGGTTCTAGCACACA 59.836 50.000 0.00 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1349 0.039165 TCACACGCTGAGCACTACTG 60.039 55.000 4.88 0.0 0.0 2.74 R
2435 2855 1.228124 TTGGTGGGAGAAAGCGTGG 60.228 57.895 0.00 0.0 0.0 4.94 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
112 113 6.151648 GGTACGACACTACCCAATGCTATATA 59.848 42.308 0.00 0.00 31.29 0.86
169 171 3.947132 CTGTGTCCAGCTGCTCCCG 62.947 68.421 8.66 0.00 0.00 5.14
703 712 4.631131 TGCCGATACTAATTGATCACCTG 58.369 43.478 0.00 0.00 0.00 4.00
1262 1278 2.975410 TGGAGACGTTGTACAGTACG 57.025 50.000 16.49 16.49 43.08 3.67
1270 1286 6.672147 AGACGTTGTACAGTACGAGTATTTT 58.328 36.000 23.11 2.58 40.03 1.82
1322 1344 2.164422 CGAGATCTGGTTCTAGCACACA 59.836 50.000 0.00 0.00 0.00 3.72
1323 1345 3.733380 CGAGATCTGGTTCTAGCACACAG 60.733 52.174 0.00 0.37 0.00 3.66
1324 1346 3.169099 AGATCTGGTTCTAGCACACAGT 58.831 45.455 0.00 1.10 0.00 3.55
1325 1347 4.344978 AGATCTGGTTCTAGCACACAGTA 58.655 43.478 0.00 1.13 0.00 2.74
1326 1348 4.772624 AGATCTGGTTCTAGCACACAGTAA 59.227 41.667 0.00 0.00 0.00 2.24
1327 1349 4.252971 TCTGGTTCTAGCACACAGTAAC 57.747 45.455 9.52 0.00 0.00 2.50
1380 1402 1.868498 GTTACTGTTTGCGCAGGTACA 59.132 47.619 11.31 15.26 40.59 2.90
1784 2146 2.205074 CATCACACTATTGTCCTCGGC 58.795 52.381 0.00 0.00 31.66 5.54
1955 2375 4.811908 TCGGTAAACTCATCGATCAACAA 58.188 39.130 0.00 0.00 0.00 2.83
2248 2668 3.304826 CCGTAAAATAACCGCCAAAATGC 59.695 43.478 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.988580 TGCTACTGAAGAACATATCCATGAAG 59.011 38.462 0.00 0.0 35.96 3.02
1 2 6.888105 TGCTACTGAAGAACATATCCATGAA 58.112 36.000 0.00 0.0 35.96 2.57
2 3 6.484364 TGCTACTGAAGAACATATCCATGA 57.516 37.500 0.00 0.0 35.96 3.07
3 4 6.293298 GCTTGCTACTGAAGAACATATCCATG 60.293 42.308 0.00 0.0 38.21 3.66
4 5 5.762218 GCTTGCTACTGAAGAACATATCCAT 59.238 40.000 0.00 0.0 0.00 3.41
5 6 5.118990 GCTTGCTACTGAAGAACATATCCA 58.881 41.667 0.00 0.0 0.00 3.41
6 7 4.513318 GGCTTGCTACTGAAGAACATATCC 59.487 45.833 0.00 0.0 0.00 2.59
7 8 5.118990 TGGCTTGCTACTGAAGAACATATC 58.881 41.667 0.00 0.0 0.00 1.63
8 9 5.102953 TGGCTTGCTACTGAAGAACATAT 57.897 39.130 0.00 0.0 0.00 1.78
9 10 4.507710 CTGGCTTGCTACTGAAGAACATA 58.492 43.478 0.00 0.0 0.00 2.29
10 11 3.341823 CTGGCTTGCTACTGAAGAACAT 58.658 45.455 0.00 0.0 0.00 2.71
11 12 2.771089 CTGGCTTGCTACTGAAGAACA 58.229 47.619 0.00 0.0 0.00 3.18
12 13 1.466558 GCTGGCTTGCTACTGAAGAAC 59.533 52.381 0.00 0.0 0.00 3.01
13 14 1.072173 TGCTGGCTTGCTACTGAAGAA 59.928 47.619 4.89 0.0 0.00 2.52
14 15 0.686789 TGCTGGCTTGCTACTGAAGA 59.313 50.000 4.89 0.0 0.00 2.87
15 16 1.085091 CTGCTGGCTTGCTACTGAAG 58.915 55.000 4.89 0.0 0.00 3.02
16 17 0.397941 ACTGCTGGCTTGCTACTGAA 59.602 50.000 0.00 0.0 0.00 3.02
17 18 0.321034 CACTGCTGGCTTGCTACTGA 60.321 55.000 0.00 0.0 0.00 3.41
18 19 1.919956 GCACTGCTGGCTTGCTACTG 61.920 60.000 10.82 0.0 33.26 2.74
19 20 1.673665 GCACTGCTGGCTTGCTACT 60.674 57.895 10.82 0.0 33.26 2.57
112 113 2.034687 AACGGCAGGAGCAAGCAT 59.965 55.556 0.00 0.0 44.61 3.79
169 171 3.849708 GGAACGTGTTTTATTGCGGAATC 59.150 43.478 5.06 0.0 0.00 2.52
1322 1344 1.887198 ACGCTGAGCACTACTGTTACT 59.113 47.619 4.88 0.0 0.00 2.24
1323 1345 1.986378 CACGCTGAGCACTACTGTTAC 59.014 52.381 4.88 0.0 0.00 2.50
1324 1346 1.611977 ACACGCTGAGCACTACTGTTA 59.388 47.619 4.88 0.0 0.00 2.41
1325 1347 0.389391 ACACGCTGAGCACTACTGTT 59.611 50.000 4.88 0.0 0.00 3.16
1326 1348 0.319040 CACACGCTGAGCACTACTGT 60.319 55.000 4.88 0.0 0.00 3.55
1327 1349 0.039165 TCACACGCTGAGCACTACTG 60.039 55.000 4.88 0.0 0.00 2.74
1380 1402 1.679032 GCTTGTCTTGAATACCGGGCT 60.679 52.381 6.32 0.0 0.00 5.19
1630 1992 3.589988 CAACTGGTATGTCTCACACTCC 58.410 50.000 0.00 0.0 0.00 3.85
1784 2146 1.005867 GGGCAAGCAACATGTGTGG 60.006 57.895 0.00 0.0 0.00 4.17
2435 2855 1.228124 TTGGTGGGAGAAAGCGTGG 60.228 57.895 0.00 0.0 0.00 4.94
2437 2857 1.228154 GGTTGGTGGGAGAAAGCGT 60.228 57.895 0.00 0.0 0.00 5.07


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

AutoCloner maintained by Alex Coulton.