Multiple sequence alignment - TraesCS4D01G250500

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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 TraesCS4D01G250500 chr4D 100.000 3284 0 0 1 3284 419207583 419204300 0.000000e+00 6065.0
1 TraesCS4D01G250500 chr4D 92.219 1812 88 16 558 2340 419245919 419247706 0.000000e+00 2516.0
2 TraesCS4D01G250500 chr4D 91.045 1675 112 17 864 2520 419232843 419231189 0.000000e+00 2228.0
3 TraesCS4D01G250500 chr4D 84.211 209 23 9 2628 2832 323597473 323597271 9.300000e-46 195.0
4 TraesCS4D01G250500 chr4D 86.441 118 7 3 612 720 419233145 419233028 1.600000e-23 121.0
5 TraesCS4D01G250500 chr4B 94.100 2695 82 25 1 2635 517009582 517006905 0.000000e+00 4024.0
6 TraesCS4D01G250500 chr4B 91.618 2052 58 30 495 2497 517082187 517080201 0.000000e+00 2732.0
7 TraesCS4D01G250500 chr4B 95.212 1462 33 3 504 1954 517129712 517128277 0.000000e+00 2278.0
8 TraesCS4D01G250500 chr4B 92.025 1442 89 14 860 2291 517171408 517172833 0.000000e+00 2002.0
9 TraesCS4D01G250500 chr4B 93.529 680 32 4 1 668 517084986 517084307 0.000000e+00 1002.0
10 TraesCS4D01G250500 chr4B 87.652 656 29 23 1947 2568 517127232 517126595 0.000000e+00 715.0
11 TraesCS4D01G250500 chr4B 92.857 378 10 9 2628 3004 517006780 517006419 1.730000e-147 532.0
12 TraesCS4D01G250500 chr4B 96.853 286 6 2 2990 3273 516975957 516975673 2.970000e-130 475.0
13 TraesCS4D01G250500 chr4B 90.435 230 18 4 37 264 517082431 517082204 1.920000e-77 300.0
14 TraesCS4D01G250500 chr4B 86.957 138 10 4 589 720 517171128 517171263 7.340000e-32 148.0
15 TraesCS4D01G250500 chr4A 92.142 1998 112 13 660 2635 45735066 45737040 0.000000e+00 2778.0
16 TraesCS4D01G250500 chr4A 92.325 1785 106 16 866 2635 45469052 45467284 0.000000e+00 2508.0
17 TraesCS4D01G250500 chr4A 88.155 1165 84 25 1415 2554 45366268 45365133 0.000000e+00 1338.0
18 TraesCS4D01G250500 chr4A 90.663 664 42 15 2628 3284 45737165 45737815 0.000000e+00 865.0
19 TraesCS4D01G250500 chr4A 91.638 586 41 6 849 1429 45367014 45366432 0.000000e+00 804.0
20 TraesCS4D01G250500 chr4A 90.468 598 27 17 2628 3217 45467159 45466584 0.000000e+00 761.0
21 TraesCS4D01G250500 chr4A 85.519 366 35 11 2935 3284 45385590 45385227 1.860000e-97 366.0
22 TraesCS4D01G250500 chr4A 85.519 366 31 12 2935 3284 45363799 45363440 2.410000e-96 363.0
23 TraesCS4D01G250500 chr4A 90.476 168 13 2 502 669 45734512 45734676 5.520000e-53 219.0
24 TraesCS4D01G250500 chr4A 91.176 136 9 1 588 720 45376425 45376290 7.240000e-42 182.0
25 TraesCS4D01G250500 chr7A 90.456 241 15 3 261 493 578444490 578444730 8.850000e-81 311.0
26 TraesCS4D01G250500 chr7A 88.797 241 18 3 261 493 48284804 48285043 1.490000e-73 287.0
27 TraesCS4D01G250500 chr7A 79.573 328 39 15 2628 2932 156321332 156321010 3.320000e-50 209.0
28 TraesCS4D01G250500 chr5A 89.540 239 16 3 264 493 3711300 3711062 8.910000e-76 294.0
29 TraesCS4D01G250500 chr3D 89.167 240 18 2 262 493 91831890 91831651 3.210000e-75 292.0
30 TraesCS4D01G250500 chr3D 81.517 211 25 13 2628 2832 564173112 564172910 9.430000e-36 161.0
31 TraesCS4D01G250500 chr2A 89.451 237 17 2 265 493 101848169 101848405 3.210000e-75 292.0
32 TraesCS4D01G250500 chr6B 88.889 243 16 3 259 493 240396526 240396765 4.150000e-74 289.0
33 TraesCS4D01G250500 chr5D 88.571 245 19 3 257 493 470232504 470232747 4.150000e-74 289.0
34 TraesCS4D01G250500 chr5D 87.866 239 20 4 263 493 333119771 333120008 4.180000e-69 272.0
35 TraesCS4D01G250500 chr1A 88.430 242 20 2 260 493 147365960 147365719 5.360000e-73 285.0
36 TraesCS4D01G250500 chr1A 82.381 210 26 10 2628 2832 437724302 437724099 4.360000e-39 172.0
37 TraesCS4D01G250500 chr1A 76.129 310 53 17 2634 2932 576096687 576096388 3.420000e-30 143.0
38 TraesCS4D01G250500 chr1B 83.209 268 29 7 257 509 660102260 660102526 7.090000e-57 231.0
39 TraesCS4D01G250500 chr1B 82.126 207 28 9 2628 2829 648790525 648790323 5.640000e-38 169.0
40 TraesCS4D01G250500 chrUn 84.034 238 29 4 265 493 87229312 87229549 1.530000e-53 220.0
41 TraesCS4D01G250500 chr6D 88.360 189 12 4 313 493 31811981 31812167 5.520000e-53 219.0
42 TraesCS4D01G250500 chr6D 100.000 35 0 0 459 493 409845396 409845430 7.610000e-07 65.8
43 TraesCS4D01G250500 chr6A 82.700 237 33 2 265 493 465349118 465348882 1.540000e-48 204.0
44 TraesCS4D01G250500 chr1D 82.938 211 27 8 2628 2832 379456976 379457183 7.240000e-42 182.0
45 TraesCS4D01G250500 chr5B 89.437 142 11 2 264 404 706422926 706423064 3.370000e-40 176.0
46 TraesCS4D01G250500 chr3B 82.673 202 28 7 2633 2832 680220157 680220353 4.360000e-39 172.0
47 TraesCS4D01G250500 chr2D 97.143 35 1 0 2890 2924 542196396 542196362 3.540000e-05 60.2


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 TraesCS4D01G250500 chr4D 419204300 419207583 3283 True 6065.000000 6065 100.000000 1 3284 1 chr4D.!!$R2 3283
1 TraesCS4D01G250500 chr4D 419245919 419247706 1787 False 2516.000000 2516 92.219000 558 2340 1 chr4D.!!$F1 1782
2 TraesCS4D01G250500 chr4D 419231189 419233145 1956 True 1174.500000 2228 88.743000 612 2520 2 chr4D.!!$R3 1908
3 TraesCS4D01G250500 chr4B 517006419 517009582 3163 True 2278.000000 4024 93.478500 1 3004 2 chr4B.!!$R2 3003
4 TraesCS4D01G250500 chr4B 517126595 517129712 3117 True 1496.500000 2278 91.432000 504 2568 2 chr4B.!!$R4 2064
5 TraesCS4D01G250500 chr4B 517080201 517084986 4785 True 1344.666667 2732 91.860667 1 2497 3 chr4B.!!$R3 2496
6 TraesCS4D01G250500 chr4B 517171128 517172833 1705 False 1075.000000 2002 89.491000 589 2291 2 chr4B.!!$F1 1702
7 TraesCS4D01G250500 chr4A 45466584 45469052 2468 True 1634.500000 2508 91.396500 866 3217 2 chr4A.!!$R4 2351
8 TraesCS4D01G250500 chr4A 45734512 45737815 3303 False 1287.333333 2778 91.093667 502 3284 3 chr4A.!!$F1 2782
9 TraesCS4D01G250500 chr4A 45363440 45367014 3574 True 835.000000 1338 88.437333 849 3284 3 chr4A.!!$R3 2435

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
276 279 2.973694 TGTTATGTACTCCTTCCGGC 57.026 50.000 0.00 0.0 0.0 6.13 F
1833 4816 1.080434 GCCGCGAGTGTTCTTCTCT 60.080 57.895 8.23 0.0 0.0 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 6085 0.320073 CCGCACAACGTTCCTCCTTA 60.320 55.000 0.0 0.0 41.42 2.69 R
3051 8188 1.133823 TGTGTGTGAACATGGGCTTCT 60.134 47.619 0.0 0.0 0.00 2.85 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
55 56 4.116747 GTGTGATGAAAACACCAAACCA 57.883 40.909 0.00 0.00 39.09 3.67
149 152 7.754851 AAAATTGTTCACCTCTAACCGTAAT 57.245 32.000 0.00 0.00 0.00 1.89
164 167 6.709018 AACCGTAATAGCCTGCAAATAATT 57.291 33.333 0.00 0.00 0.00 1.40
192 195 6.472016 TGTAACTTATGACTGAGAAATGGCA 58.528 36.000 0.00 0.00 0.00 4.92
270 273 4.399303 GCCAAATGCTTGTTATGTACTCCT 59.601 41.667 0.00 0.00 36.87 3.69
276 279 2.973694 TGTTATGTACTCCTTCCGGC 57.026 50.000 0.00 0.00 0.00 6.13
411 414 6.090898 GCGTCATGACTTTAGTTTCATACTGT 59.909 38.462 22.95 0.00 37.73 3.55
542 555 3.330405 AGGCCCACATATATGTACATGCA 59.670 43.478 17.86 6.16 39.39 3.96
600 616 4.338400 AGCCAACTCCAACTTTGACTAAAC 59.662 41.667 0.00 0.00 0.00 2.01
703 3392 6.039605 TCCGAGTACAATCACAATACGGATAA 59.960 38.462 0.00 0.00 41.32 1.75
1210 4012 2.066999 ATCAAGGTCCTCCGCTCCC 61.067 63.158 0.00 0.00 39.05 4.30
1833 4816 1.080434 GCCGCGAGTGTTCTTCTCT 60.080 57.895 8.23 0.00 0.00 3.10
1926 4917 2.568623 TCCAAGTCTTGAAAGGGCTC 57.431 50.000 14.42 0.00 0.00 4.70
1941 4932 2.125912 CTCCTCGAGTGCAACCCG 60.126 66.667 12.31 0.00 37.80 5.28
2014 6063 2.900167 CTCCACACCGACGACGTGA 61.900 63.158 4.58 0.00 37.88 4.35
2016 6065 1.800315 CCACACCGACGACGTGATC 60.800 63.158 4.58 0.00 37.88 2.92
2136 6191 1.291877 CGGCGACACCCAAGAAGAAG 61.292 60.000 0.00 0.00 33.26 2.85
2137 6192 0.034896 GGCGACACCCAAGAAGAAGA 59.965 55.000 0.00 0.00 0.00 2.87
2138 6193 1.542547 GGCGACACCCAAGAAGAAGAA 60.543 52.381 0.00 0.00 0.00 2.52
2139 6194 1.531578 GCGACACCCAAGAAGAAGAAC 59.468 52.381 0.00 0.00 0.00 3.01
2141 6196 2.224305 CGACACCCAAGAAGAAGAACCT 60.224 50.000 0.00 0.00 0.00 3.50
2157 6212 2.436646 CTGCGGCGGATCAAGGTT 60.437 61.111 9.78 0.00 0.00 3.50
2232 6287 4.920112 CCACCGGCGACACCACAA 62.920 66.667 9.30 0.00 39.03 3.33
2349 6447 0.878416 TCGTAGCATGGTGGTTTTGC 59.122 50.000 7.89 0.00 36.63 3.68
2354 6452 1.490069 AGCATGGTGGTTTTGCCTTTT 59.510 42.857 0.00 0.00 37.07 2.27
2586 6696 5.979517 GCAAATTTGAGGGCATCATACTAAC 59.020 40.000 22.31 0.00 37.89 2.34
3032 8169 7.039504 CCACTAGAAGTGTACTTTACCAAGGTA 60.040 40.741 0.00 0.00 44.50 3.08
3047 8184 6.087276 ACCAAGGTAAAGGGCAAATATAGT 57.913 37.500 0.00 0.00 0.00 2.12
3050 8187 6.039382 CCAAGGTAAAGGGCAAATATAGTGTC 59.961 42.308 0.00 0.00 0.00 3.67
3051 8188 6.321821 AGGTAAAGGGCAAATATAGTGTCA 57.678 37.500 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.929049 TCATCACACTACTAGGAAAAACACTG 59.071 38.462 0.00 0.00 0.00 3.66
54 55 9.703892 TTCTGGTTTATTGATTTATGGTGTTTG 57.296 29.630 0.00 0.00 0.00 2.93
270 273 1.202794 ACGAACTAAAAAGGGCCGGAA 60.203 47.619 5.05 0.00 0.00 4.30
476 489 5.299279 CCGGTCCTTGCATATAAGAATTGTT 59.701 40.000 0.00 0.00 0.00 2.83
493 506 1.858246 ACTATTACTCCCTCCGGTCCT 59.142 52.381 0.00 0.00 0.00 3.85
520 533 3.330405 TGCATGTACATATATGTGGGCCT 59.670 43.478 25.48 8.27 41.89 5.19
542 555 1.880675 CGAGTAGGTCTCTGTGTGTGT 59.119 52.381 0.00 0.00 40.75 3.72
600 616 2.918230 GATGTTGCCCTACGGACGGG 62.918 65.000 1.91 1.91 44.89 5.28
703 3392 4.262808 GGATGCTGATGGAGTTAGCTATGT 60.263 45.833 0.00 0.00 39.98 2.29
1210 4012 3.578456 GGTGGCAAGATCACCGTG 58.422 61.111 0.00 0.00 44.16 4.94
1215 4017 2.433888 TTGGCGGTGGCAAGATCA 59.566 55.556 1.29 0.00 42.98 2.92
1749 4732 1.003839 AAGAACGCGGAAGATGGCA 60.004 52.632 12.47 0.00 0.00 4.92
1968 6011 1.003718 GAACCACGGGAGTTGGAGG 60.004 63.158 0.00 0.00 44.67 4.30
2033 6085 0.320073 CCGCACAACGTTCCTCCTTA 60.320 55.000 0.00 0.00 41.42 2.69
2141 6196 0.531974 GATAACCTTGATCCGCCGCA 60.532 55.000 0.00 0.00 0.00 5.69
2181 6236 0.957362 GCTGCAGCAGGTTCTTCTTT 59.043 50.000 33.36 0.00 41.59 2.52
2232 6287 4.631813 GGTATTCTGAGCACGTTCTTCATT 59.368 41.667 0.00 0.00 0.00 2.57
2349 6447 4.332543 GGTTTCAAAAGGTCAGCAAAAAGG 59.667 41.667 0.00 0.00 0.00 3.11
2354 6452 3.513515 ACAAGGTTTCAAAAGGTCAGCAA 59.486 39.130 0.00 0.00 0.00 3.91
2684 6958 9.927668 TCTGAAAAGAAGTCAATGTTTTTCTTT 57.072 25.926 12.52 12.52 46.27 2.52
2685 6959 9.927668 TTCTGAAAAGAAGTCAATGTTTTTCTT 57.072 25.926 8.78 4.51 40.53 2.52
2975 8107 7.879962 TGTTCGTTGTTACACTTTTTATTCG 57.120 32.000 0.00 0.00 0.00 3.34
3032 8169 5.358160 GCTTCTGACACTATATTTGCCCTTT 59.642 40.000 0.00 0.00 0.00 3.11
3047 8184 1.142667 TGTGAACATGGGCTTCTGACA 59.857 47.619 0.00 0.00 0.00 3.58
3050 8187 1.267806 GTGTGTGAACATGGGCTTCTG 59.732 52.381 0.00 0.00 0.00 3.02
3051 8188 1.133823 TGTGTGTGAACATGGGCTTCT 60.134 47.619 0.00 0.00 0.00 2.85
3139 8290 9.947433 AATGTTTGTTTGTTCATGAATATCCAT 57.053 25.926 12.12 3.98 0.00 3.41
3235 8388 1.201181 CGGTCAATTTTCGCCCAATGA 59.799 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.