Multiple sequence alignment - TraesCS5B01G051800

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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 TraesCS5B01G051800 chr5B 100.000 2276 0 0 1 2276 56545353 56543078 0.000000e+00 4204.0
1 TraesCS5B01G051800 chr5B 93.783 933 56 1 112 1044 613489568 613490498 0.000000e+00 1400.0
2 TraesCS5B01G051800 chr5B 95.798 119 5 0 1 119 613485185 613485303 2.310000e-45 193.0
3 TraesCS5B01G051800 chr5D 97.631 2279 50 3 1 2276 53868994 53866717 0.000000e+00 3906.0
4 TraesCS5B01G051800 chr5D 88.350 103 11 1 1169 1270 441898185 441898083 3.070000e-24 122.0
5 TraesCS5B01G051800 chr5D 73.399 203 43 5 1448 1640 486995816 486996017 5.250000e-07 65.8
6 TraesCS5B01G051800 chr4A 93.932 1302 77 1 1 1302 122064097 122065396 0.000000e+00 1965.0
7 TraesCS5B01G051800 chr2B 93.012 1288 82 3 3 1290 581473995 581472716 0.000000e+00 1873.0
8 TraesCS5B01G051800 chr3B 94.040 990 56 2 313 1302 528148756 528147770 0.000000e+00 1498.0
9 TraesCS5B01G051800 chr3B 93.891 311 19 0 1 311 528168595 528168285 9.520000e-129 470.0
10 TraesCS5B01G051800 chr3D 94.821 811 39 2 492 1302 566542264 566543071 0.000000e+00 1262.0
11 TraesCS5B01G051800 chr7A 91.479 798 65 2 67 864 81862218 81861424 0.000000e+00 1094.0
12 TraesCS5B01G051800 chr7A 88.800 125 14 0 926 1050 81861416 81861292 1.090000e-33 154.0
13 TraesCS5B01G051800 chr5A 92.958 213 13 1 1093 1303 326432718 326432930 2.200000e-80 309.0
14 TraesCS5B01G051800 chr2A 85.135 74 7 2 1596 1669 507031798 507031867 3.140000e-09 73.1
15 TraesCS5B01G051800 chr3A 100.000 30 0 0 2228 2257 712281299 712281270 3.160000e-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 TraesCS5B01G051800 chr5B 56543078 56545353 2275 True 4204 4204 100.0000 1 2276 1 chr5B.!!$R1 2275
1 TraesCS5B01G051800 chr5B 613489568 613490498 930 False 1400 1400 93.7830 112 1044 1 chr5B.!!$F2 932
2 TraesCS5B01G051800 chr5D 53866717 53868994 2277 True 3906 3906 97.6310 1 2276 1 chr5D.!!$R1 2275
3 TraesCS5B01G051800 chr4A 122064097 122065396 1299 False 1965 1965 93.9320 1 1302 1 chr4A.!!$F1 1301
4 TraesCS5B01G051800 chr2B 581472716 581473995 1279 True 1873 1873 93.0120 3 1290 1 chr2B.!!$R1 1287
5 TraesCS5B01G051800 chr3B 528147770 528148756 986 True 1498 1498 94.0400 313 1302 1 chr3B.!!$R1 989
6 TraesCS5B01G051800 chr3D 566542264 566543071 807 False 1262 1262 94.8210 492 1302 1 chr3D.!!$F1 810
7 TraesCS5B01G051800 chr7A 81861292 81862218 926 True 624 1094 90.1395 67 1050 2 chr7A.!!$R1 983

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
242 243 0.031314 ATCAGCGTACCATGCTCTCG 59.969 55.0 0.0 0.0 38.65 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 1687 0.108186 CAGGCTATGGCTTGTGACGA 60.108 55.0 4.91 0.0 40.11 4.2 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
25 26 7.475015 CAGGTACATTGACAATGAAACCTATG 58.525 38.462 34.21 26.84 46.78 2.23
82 83 9.107177 GTGAGTGACTTAATTGATGATGAGAAT 57.893 33.333 0.00 0.00 0.00 2.40
234 235 2.224185 ACACTGTCAAATCAGCGTACCA 60.224 45.455 0.00 0.00 38.84 3.25
242 243 0.031314 ATCAGCGTACCATGCTCTCG 59.969 55.000 0.00 0.00 38.65 4.04
263 264 7.207383 TCTCGTGATTCAAAAAGAGTGTTCTA 58.793 34.615 0.00 0.00 31.96 2.10
414 415 3.394674 TGAGAAAACACTACATCGGCA 57.605 42.857 0.00 0.00 0.00 5.69
453 454 1.819288 TCGGTGCAAACTTTGTTTGGA 59.181 42.857 20.18 16.39 0.00 3.53
521 522 2.976440 AGGGTTTTTGGGATGAAGCTT 58.024 42.857 0.00 0.00 0.00 3.74
545 546 3.192633 GCGGTGGTTTGATTTCCAGTTAT 59.807 43.478 0.00 0.00 34.16 1.89
551 552 5.642063 TGGTTTGATTTCCAGTTATCTCGAC 59.358 40.000 0.00 0.00 0.00 4.20
552 553 5.875359 GGTTTGATTTCCAGTTATCTCGACT 59.125 40.000 0.00 0.00 0.00 4.18
623 626 3.942130 TGATCAAGTCAGAGCGAAGAA 57.058 42.857 0.00 0.00 31.80 2.52
838 841 4.615901 CTGGCATTGACAGCGGTA 57.384 55.556 6.57 0.00 29.34 4.02
999 1002 1.531149 CGAGGTTTGCAAGATGTCGTT 59.469 47.619 0.00 0.00 0.00 3.85
1028 1031 1.613630 ACTGCCTGGAGGTGGTAGG 60.614 63.158 0.00 0.00 40.82 3.18
1143 1147 9.606631 AGTATTCAACATGTTTCTAGATCTTCC 57.393 33.333 8.77 0.00 0.00 3.46
1399 1403 3.012934 TCTTATACTGGCCCCAAAAGC 57.987 47.619 0.00 0.00 0.00 3.51
1536 1542 2.359531 GTCTCCTCCGATTTCGATGAGT 59.640 50.000 0.67 0.00 43.02 3.41
1618 1624 1.474332 TTAAGCCGGACGACAACCCT 61.474 55.000 5.05 0.00 0.00 4.34
1640 1646 0.394565 ACCCTAGGCGCATCTCATTC 59.605 55.000 10.83 0.00 0.00 2.67
1681 1687 1.153369 CACCCATCCGCTCGTCATT 60.153 57.895 0.00 0.00 0.00 2.57
1688 1694 1.443702 CCGCTCGTCATTCGTCACA 60.444 57.895 0.00 0.00 40.80 3.58
1777 1783 1.065418 AGGAGATTTGGGTTAGGCACG 60.065 52.381 0.00 0.00 0.00 5.34
1923 1929 1.079888 GTTTGAGGCGGCCCAAATG 60.080 57.895 26.99 0.00 35.14 2.32
1925 1931 1.531739 TTTGAGGCGGCCCAAATGAC 61.532 55.000 23.17 7.16 0.00 3.06
1934 1940 1.153168 CCCAAATGACGGAGGCGAT 60.153 57.895 0.00 0.00 0.00 4.58
1953 1959 0.322816 TGGAGCAGCAAACCATCCTC 60.323 55.000 0.00 0.00 0.00 3.71
2119 2126 2.303163 ACGTTGCAATGGCGAGTATA 57.697 45.000 22.20 0.00 45.35 1.47
2172 2179 1.502190 GCTAGCACTTTTGACGCCC 59.498 57.895 10.63 0.00 0.00 6.13
2257 2264 7.288605 AATCACGTGATTGCAACATTTTGCG 62.289 40.000 36.26 4.60 46.61 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.002792 GAAGTGTTCGCAGGTTTGACC 60.003 52.381 0.00 0.00 38.99 4.02
82 83 3.315140 TCCATCCGCCACGACCAA 61.315 61.111 0.00 0.00 0.00 3.67
234 235 4.999950 ACTCTTTTTGAATCACGAGAGCAT 59.000 37.500 13.35 0.00 35.26 3.79
263 264 1.331399 GCCGGCCCTTCTTCTAGAGT 61.331 60.000 18.11 0.00 0.00 3.24
414 415 6.365247 GCACCGACTAATATCACGAATATGTT 59.635 38.462 0.00 0.00 30.68 2.71
453 454 1.134371 GCATTAGGTCCTCTTCCGCTT 60.134 52.381 0.00 0.00 0.00 4.68
521 522 2.224670 ACTGGAAATCAAACCACCGCTA 60.225 45.455 0.00 0.00 32.44 4.26
545 546 2.242047 CTCGGGATGTAGAGTCGAGA 57.758 55.000 5.26 0.00 46.89 4.04
623 626 7.549839 CCAAATGATCCACATAAATGACACTT 58.450 34.615 0.00 0.00 38.38 3.16
838 841 2.378634 CCGCCCCTCCTTTCTCCAT 61.379 63.158 0.00 0.00 0.00 3.41
999 1002 1.062198 TCCAGGCAGTCCATCTCCATA 60.062 52.381 0.00 0.00 33.74 2.74
1028 1031 1.228245 TGGCAAGTGTTCCAGAGGC 60.228 57.895 0.00 0.00 0.00 4.70
1249 1253 3.964875 AAAAGCGCACCTGGCACG 61.965 61.111 11.47 4.71 45.17 5.34
1324 1328 3.470888 CCGAACCATCCTCCCGCT 61.471 66.667 0.00 0.00 0.00 5.52
1611 1617 0.616891 CGCCTAGGGTTTAGGGTTGT 59.383 55.000 11.72 0.00 35.29 3.32
1618 1624 1.491668 TGAGATGCGCCTAGGGTTTA 58.508 50.000 11.72 0.00 0.00 2.01
1681 1687 0.108186 CAGGCTATGGCTTGTGACGA 60.108 55.000 4.91 0.00 40.11 4.20
1688 1694 1.211457 CCTTCTGTCAGGCTATGGCTT 59.789 52.381 0.00 0.00 35.88 4.35
1716 1722 0.602638 CCGGCGTGTGTATGGCATAT 60.603 55.000 10.92 0.00 38.22 1.78
1747 1753 3.330701 ACCCAAATCTCCTCAAGCAGTTA 59.669 43.478 0.00 0.00 0.00 2.24
1890 1896 2.034879 AAACTCTGCCATGGCGTCG 61.035 57.895 30.87 22.15 45.51 5.12
1923 1929 3.781770 CTGCTCCATCGCCTCCGTC 62.782 68.421 0.00 0.00 35.54 4.79
1934 1940 0.322816 GAGGATGGTTTGCTGCTCCA 60.323 55.000 12.27 12.27 35.64 3.86
1953 1959 1.749638 AGTAGTGCGGAGGGAGTCG 60.750 63.158 0.00 0.00 0.00 4.18
2046 2052 2.751166 CTGGGACTGTTCTACCAGTG 57.249 55.000 0.00 0.00 45.46 3.66
2172 2179 2.527100 GGATTTCTACCTGTGACGACG 58.473 52.381 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.