Multiple sequence alignment - TraesCS5D01G157700

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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 TraesCS5D01G157700 chr5D 100.000 2003 0 0 1 2003 245715385 245717387 0.000000e+00 3699.0
1 TraesCS5D01G157700 chr5D 84.491 1612 191 24 126 1727 275404651 275406213 0.000000e+00 1537.0
2 TraesCS5D01G157700 chr5D 80.000 1165 200 25 265 1406 275147054 275148208 0.000000e+00 830.0
3 TraesCS5D01G157700 chr5D 84.844 673 84 10 534 1189 275167501 275168172 0.000000e+00 662.0
4 TraesCS5D01G157700 chr5D 83.206 524 75 11 272 787 274776102 274776620 3.620000e-128 468.0
5 TraesCS5D01G157700 chr5D 91.489 188 16 0 1211 1398 275168251 275168438 2.370000e-65 259.0
6 TraesCS5D01G157700 chr5D 100.000 123 0 0 2283 2405 245717667 245717789 6.690000e-56 228.0
7 TraesCS5D01G157700 chr5A 95.247 1641 60 8 1 1632 329693162 329694793 0.000000e+00 2582.0
8 TraesCS5D01G157700 chr5A 85.246 1464 179 17 124 1575 364349415 364350853 0.000000e+00 1472.0
9 TraesCS5D01G157700 chr5A 79.897 1164 203 23 265 1406 363919831 363920985 0.000000e+00 824.0
10 TraesCS5D01G157700 chr5A 80.227 440 77 6 752 1181 364147229 364147668 2.980000e-84 322.0
11 TraesCS5D01G157700 chr5A 85.987 314 21 14 1694 2003 329694829 329695123 4.990000e-82 315.0
12 TraesCS5D01G157700 chr5A 82.650 317 40 11 1211 1524 364167450 364167754 1.420000e-67 267.0
13 TraesCS5D01G157700 chr5A 99.187 123 1 0 2283 2405 329695212 329695334 3.110000e-54 222.0
14 TraesCS5D01G157700 chr5B 84.861 1658 194 28 126 1769 312592369 312593983 0.000000e+00 1618.0
15 TraesCS5D01G157700 chr5B 85.145 1104 143 12 104 1189 309882569 309883669 0.000000e+00 1110.0
16 TraesCS5D01G157700 chr5B 96.727 611 20 0 1393 2003 278884425 278883815 0.000000e+00 1018.0
17 TraesCS5D01G157700 chr5B 96.552 551 18 1 728 1277 278863719 278864269 0.000000e+00 911.0
18 TraesCS5D01G157700 chr5B 79.553 1164 207 23 265 1406 309817058 309818212 0.000000e+00 802.0
19 TraesCS5D01G157700 chr5B 91.613 310 24 2 1 309 278863274 278863582 6.140000e-116 427.0
20 TraesCS5D01G157700 chr5B 91.489 188 16 0 1211 1398 309883748 309883935 2.370000e-65 259.0
21 TraesCS5D01G157700 chr5B 97.561 123 3 0 2283 2405 278883595 278883473 6.740000e-51 211.0
22 TraesCS5D01G157700 chr3A 100.000 30 0 0 2285 2314 208254886 208254857 3.340000e-04 56.5


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 TraesCS5D01G157700 chr5D 245715385 245717789 2404 False 1963.500000 3699 100.000000 1 2405 2 chr5D.!!$F4 2404
1 TraesCS5D01G157700 chr5D 275404651 275406213 1562 False 1537.000000 1537 84.491000 126 1727 1 chr5D.!!$F3 1601
2 TraesCS5D01G157700 chr5D 275147054 275148208 1154 False 830.000000 830 80.000000 265 1406 1 chr5D.!!$F2 1141
3 TraesCS5D01G157700 chr5D 274776102 274776620 518 False 468.000000 468 83.206000 272 787 1 chr5D.!!$F1 515
4 TraesCS5D01G157700 chr5D 275167501 275168438 937 False 460.500000 662 88.166500 534 1398 2 chr5D.!!$F5 864
5 TraesCS5D01G157700 chr5A 364349415 364350853 1438 False 1472.000000 1472 85.246000 124 1575 1 chr5A.!!$F4 1451
6 TraesCS5D01G157700 chr5A 329693162 329695334 2172 False 1039.666667 2582 93.473667 1 2405 3 chr5A.!!$F5 2404
7 TraesCS5D01G157700 chr5A 363919831 363920985 1154 False 824.000000 824 79.897000 265 1406 1 chr5A.!!$F1 1141
8 TraesCS5D01G157700 chr5B 312592369 312593983 1614 False 1618.000000 1618 84.861000 126 1769 1 chr5B.!!$F2 1643
9 TraesCS5D01G157700 chr5B 309817058 309818212 1154 False 802.000000 802 79.553000 265 1406 1 chr5B.!!$F1 1141
10 TraesCS5D01G157700 chr5B 309882569 309883935 1366 False 684.500000 1110 88.317000 104 1398 2 chr5B.!!$F4 1294
11 TraesCS5D01G157700 chr5B 278863274 278864269 995 False 669.000000 911 94.082500 1 1277 2 chr5B.!!$F3 1276
12 TraesCS5D01G157700 chr5B 278883473 278884425 952 True 614.500000 1018 97.144000 1393 2405 2 chr5B.!!$R1 1012

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
266 276 0.527600 CCTCGCCGATTTCGACATCA 60.528 55.000 11.85 0.0 43.02 3.07 F
479 492 4.824515 CCCTCGACGCCTCCTCCT 62.825 72.222 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1388 0.756294 TGCCGGTGTCCATATCGAAT 59.244 50.000 1.9 0.0 0.0 3.34 R
1472 1576 1.667724 GATCCGAGTGTGCAAATGAGG 59.332 52.381 0.0 0.0 0.0 3.86 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
31 32 3.055891 CCAGGCGGGAATCTCAAAATTTT 60.056 43.478 0.00 0.00 40.01 1.82
76 78 1.070175 CGAAGCCGACGTCACAAAAAT 60.070 47.619 17.16 0.00 38.22 1.82
113 123 1.609794 GGTCTCCAGAACCCTCCGT 60.610 63.158 0.00 0.00 0.00 4.69
121 131 4.675029 AACCCTCCGTCAACCGCG 62.675 66.667 0.00 0.00 34.38 6.46
266 276 0.527600 CCTCGCCGATTTCGACATCA 60.528 55.000 11.85 0.00 43.02 3.07
479 492 4.824515 CCCTCGACGCCTCCTCCT 62.825 72.222 0.00 0.00 0.00 3.69
1284 1388 1.852309 TGGGGATACGGGTACTACTCA 59.148 52.381 0.00 0.00 37.60 3.41
1449 1553 4.576463 GCCCACTCCTGTTAATGATGTTAG 59.424 45.833 0.00 0.00 0.00 2.34
1472 1576 2.686558 TTGTTCAGCGATGTTGCTTC 57.313 45.000 0.00 0.00 44.46 3.86
1655 1796 4.780021 AGGGAGTTCTTCTTGCAAGATAGA 59.220 41.667 28.89 26.44 34.49 1.98
1745 1888 9.997482 GTCTGTTTTACAAGTTAAGATCACAAA 57.003 29.630 0.00 0.00 0.00 2.83
1979 2129 3.005684 ACGCTCTGAATGAATTTTTGGCA 59.994 39.130 0.00 0.00 0.00 4.92
2352 2502 5.250982 GTGGTAGGTAATTTTGGCACTAGT 58.749 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 3.399330 TCCCTCTGATTTTTGTGACGTC 58.601 45.455 9.11 9.11 0.00 4.34
76 78 4.361971 ACGCGGGTCTCCCTCTGA 62.362 66.667 12.47 0.00 42.67 3.27
90 92 2.126031 GGTTCTGGAGACCGACGC 60.126 66.667 0.00 0.00 0.00 5.19
121 131 3.439540 TTCTTCGGCGCCATTGGC 61.440 61.111 28.98 18.10 46.75 4.52
132 142 2.734079 GTCTTCTTGCCTCTGTTCTTCG 59.266 50.000 0.00 0.00 0.00 3.79
256 266 2.674852 GAGAATGCTGCTGATGTCGAAA 59.325 45.455 0.00 0.00 0.00 3.46
266 276 4.087892 ACGGCGGAGAATGCTGCT 62.088 61.111 13.24 0.00 42.55 4.24
479 492 0.395862 AAATCGAGGGAGAGGCGAGA 60.396 55.000 0.00 0.00 37.48 4.04
578 597 1.971357 GAAGCGGGGGATCATCTTCTA 59.029 52.381 0.00 0.00 32.64 2.10
725 753 4.722700 GCAGAGCTTTCCCGGGCA 62.723 66.667 18.49 0.00 0.00 5.36
1117 1164 1.274712 CTCCTCTCCAGAAGCCAACT 58.725 55.000 0.00 0.00 0.00 3.16
1284 1388 0.756294 TGCCGGTGTCCATATCGAAT 59.244 50.000 1.90 0.00 0.00 3.34
1449 1553 3.115554 AGCAACATCGCTGAACAAAAAC 58.884 40.909 0.00 0.00 41.85 2.43
1472 1576 1.667724 GATCCGAGTGTGCAAATGAGG 59.332 52.381 0.00 0.00 0.00 3.86
1627 1732 7.200434 TCTTGCAAGAAGAACTCCCTATAAT 57.800 36.000 26.61 0.00 30.73 1.28
1745 1888 6.791867 TGTATAGTCTACAGCCAACAGAAT 57.208 37.500 0.00 0.00 0.00 2.40
1884 2034 8.373048 AGTTTCAGAATGTACAATACAACGAA 57.627 30.769 0.00 0.00 42.76 3.85
1948 2098 5.654603 TTCATTCAGAGCGTACTAGGAAA 57.345 39.130 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.