Multiple sequence alignment - TraesCS6B01G086400

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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 TraesCS6B01G086400 chr6B 100.000 2255 0 0 1 2255 62636405 62634151 0.000000e+00 4165.0
1 TraesCS6B01G086400 chr6B 96.454 2284 40 6 2 2255 62693240 62690968 0.000000e+00 3731.0
2 TraesCS6B01G086400 chr6A 93.193 1895 93 17 1 1871 34284551 34282669 0.000000e+00 2752.0
3 TraesCS6B01G086400 chr6A 89.984 1218 75 20 253 1442 34394724 34393526 0.000000e+00 1530.0
4 TraesCS6B01G086400 chr6A 86.188 1448 157 26 254 1673 34282279 34280847 0.000000e+00 1526.0
5 TraesCS6B01G086400 chr6A 81.304 1610 224 46 176 1731 34280377 34278791 0.000000e+00 1234.0
6 TraesCS6B01G086400 chr6A 81.765 1530 201 44 254 1728 34275473 34273967 0.000000e+00 1208.0
7 TraesCS6B01G086400 chr6A 93.103 319 20 1 1552 1870 34276090 34275774 1.220000e-127 466.0
8 TraesCS6B01G086400 chr6A 94.966 298 12 2 1959 2255 34282508 34282213 4.390000e-127 464.0
9 TraesCS6B01G086400 chr6A 94.613 297 14 1 1959 2255 34280529 34280235 2.040000e-125 459.0
10 TraesCS6B01G086400 chr6A 98.095 210 3 1 1 209 34394943 34394734 4.580000e-97 364.0
11 TraesCS6B01G086400 chr6A 90.476 273 17 2 1990 2255 34393072 34392802 3.560000e-93 351.0
12 TraesCS6B01G086400 chr6A 90.244 164 11 4 1708 1870 34280847 34280688 2.270000e-50 209.0
13 TraesCS6B01G086400 chr6A 89.634 164 12 4 1708 1870 34393434 34393275 1.060000e-48 204.0
14 TraesCS6B01G086400 chr6A 85.143 175 8 5 2082 2255 34275564 34275407 1.790000e-36 163.0
15 TraesCS6B01G086400 chr6A 93.258 89 6 0 1585 1673 34393522 34393434 5.050000e-27 132.0
16 TraesCS6B01G086400 chr6A 100.000 29 0 0 1959 1987 34393116 34393088 1.000000e-03 54.7
17 TraesCS6B01G086400 chrUn 91.741 1913 104 19 1 1870 101992250 101990349 0.000000e+00 2608.0
18 TraesCS6B01G086400 chrUn 85.685 1474 149 37 7 1436 41696789 41698244 0.000000e+00 1496.0
19 TraesCS6B01G086400 chrUn 82.303 1537 187 47 254 1731 101989746 101988236 0.000000e+00 1253.0
20 TraesCS6B01G086400 chrUn 79.492 1063 182 28 315 1351 101984245 101983193 0.000000e+00 723.0
21 TraesCS6B01G086400 chrUn 94.231 156 9 0 2100 2255 101989835 101989680 2.890000e-59 239.0
22 TraesCS6B01G086400 chrUn 96.591 88 2 1 1959 2045 101990188 101990101 6.490000e-31 145.0
23 TraesCS6B01G086400 chrUn 82.540 126 17 3 1964 2088 41698786 41698907 3.060000e-19 106.0
24 TraesCS6B01G086400 chr3D 83.307 1917 218 51 7 1872 583029285 583027420 0.000000e+00 1674.0
25 TraesCS6B01G086400 chr3D 83.738 1648 213 36 119 1730 583290124 583288496 0.000000e+00 1507.0
26 TraesCS6B01G086400 chr3D 79.286 280 48 5 1983 2255 583223245 583222969 1.060000e-43 187.0
27 TraesCS6B01G086400 chr3D 85.621 153 20 1 1983 2135 583179554 583179404 2.320000e-35 159.0
28 TraesCS6B01G086400 chr3B 85.209 1244 167 11 330 1566 780301979 780300746 0.000000e+00 1262.0
29 TraesCS6B01G086400 chr3B 81.408 1506 205 46 330 1805 780316073 780314613 0.000000e+00 1160.0
30 TraesCS6B01G086400 chr3B 81.408 1506 205 46 330 1805 780321447 780319987 0.000000e+00 1160.0
31 TraesCS6B01G086400 chr3B 80.645 279 46 3 1983 2255 780339300 780339024 2.270000e-50 209.0
32 TraesCS6B01G086400 chr3B 76.923 234 25 12 1600 1805 780339738 780339506 3.060000e-19 106.0
33 TraesCS6B01G086400 chr7A 83.452 1263 186 13 268 1517 287848598 287849850 0.000000e+00 1153.0


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 TraesCS6B01G086400 chr6B 62634151 62636405 2254 True 4165.000000 4165 100.000000 1 2255 1 chr6B.!!$R1 2254
1 TraesCS6B01G086400 chr6B 62690968 62693240 2272 True 3731.000000 3731 96.454000 2 2255 1 chr6B.!!$R2 2253
2 TraesCS6B01G086400 chr6A 34273967 34284551 10584 True 942.333333 2752 88.946556 1 2255 9 chr6A.!!$R1 2254
3 TraesCS6B01G086400 chr6A 34392802 34394943 2141 True 439.283333 1530 93.574500 1 2255 6 chr6A.!!$R2 2254
4 TraesCS6B01G086400 chrUn 101983193 101992250 9057 True 993.600000 2608 88.871600 1 2255 5 chrUn.!!$R1 2254
5 TraesCS6B01G086400 chrUn 41696789 41698907 2118 False 801.000000 1496 84.112500 7 2088 2 chrUn.!!$F1 2081
6 TraesCS6B01G086400 chr3D 583027420 583029285 1865 True 1674.000000 1674 83.307000 7 1872 1 chr3D.!!$R1 1865
7 TraesCS6B01G086400 chr3D 583288496 583290124 1628 True 1507.000000 1507 83.738000 119 1730 1 chr3D.!!$R4 1611
8 TraesCS6B01G086400 chr3B 780300746 780301979 1233 True 1262.000000 1262 85.209000 330 1566 1 chr3B.!!$R1 1236
9 TraesCS6B01G086400 chr3B 780314613 780321447 6834 True 1160.000000 1160 81.408000 330 1805 2 chr3B.!!$R2 1475
10 TraesCS6B01G086400 chr7A 287848598 287849850 1252 False 1153.000000 1153 83.452000 268 1517 1 chr7A.!!$F1 1249

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
995 1053 1.376609 ATTTCGGCAGATTGCGGGAC 61.377 55.0 8.45 0.0 46.21 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 9524 3.059306 CGAGTTTTTGTTGTGTGCTTGTG 59.941 43.478 0.0 0.0 0.0 3.33 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
566 617 3.266772 TCAGACATGGCTTTCCACCTAAT 59.733 43.478 0.00 0.0 46.92 1.73
973 1031 8.171373 AGAATCATTTCAAGAAGACCACGAAGT 61.171 37.037 0.00 0.0 35.93 3.01
995 1053 1.376609 ATTTCGGCAGATTGCGGGAC 61.377 55.000 8.45 0.0 46.21 4.46
1075 1133 5.487433 TCCATCTCTTGTCGAAGCAAATTA 58.513 37.500 0.00 0.0 0.00 1.40
1532 9010 2.494870 GTCACACGGTCCCTACTTGTAT 59.505 50.000 0.00 0.0 0.00 2.29
1696 9187 8.186821 TGTCGACATCTATATCATCTAAGCATG 58.813 37.037 15.76 0.0 0.00 4.06
1910 9522 1.541379 AAAAATAGGGTGGACACGGC 58.459 50.000 0.00 0.0 0.00 5.68
1911 9523 0.402504 AAAATAGGGTGGACACGGCA 59.597 50.000 0.00 0.0 0.00 5.69
1912 9524 0.322187 AAATAGGGTGGACACGGCAC 60.322 55.000 0.00 0.0 0.00 5.01
1913 9525 1.485294 AATAGGGTGGACACGGCACA 61.485 55.000 0.00 0.0 0.00 4.57
1914 9526 2.180159 ATAGGGTGGACACGGCACAC 62.180 60.000 0.00 0.0 0.00 3.82
1915 9527 4.555709 GGGTGGACACGGCACACA 62.556 66.667 0.00 0.0 36.87 3.72
1916 9528 2.515057 GGTGGACACGGCACACAA 60.515 61.111 0.00 0.0 36.87 3.33
2040 9699 5.163854 CCGATCATCGAAGCTTTAACTTGTT 60.164 40.000 9.16 0.0 43.74 2.83
2092 9964 3.809832 CCTGATTAAATACAGGCACTCCG 59.190 47.826 11.74 0.0 45.30 4.63
2097 9969 2.184020 AATACAGGCACTCCGCAGCA 62.184 55.000 0.00 0.0 45.17 4.41
2098 9970 2.184020 ATACAGGCACTCCGCAGCAA 62.184 55.000 0.00 0.0 45.17 3.91
2225 10104 5.704354 TGGAACATAATAATGTGATGGCCT 58.296 37.500 3.32 0.0 45.79 5.19
2240 10119 2.398588 TGGCCTATCTTAGGGACAGTG 58.601 52.381 3.32 0.0 46.32 3.66
2251 10130 5.487488 TCTTAGGGACAGTGGACACATAAAT 59.513 40.000 5.14 0.0 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
973 1031 1.581934 CCGCAATCTGCCGAAATCTA 58.418 50.000 0.00 0.00 41.12 1.98
995 1053 1.651240 CTTGGCCAAGAGCATGACCG 61.651 60.000 37.60 9.68 46.50 4.79
1075 1133 6.715347 AACAAGAGACTGTTTAGGCATTTT 57.285 33.333 0.00 0.00 36.05 1.82
1355 8818 9.948964 TTGCTATAGTATCATGTGCATTTCTAT 57.051 29.630 0.84 0.00 0.00 1.98
1364 8834 8.877808 TGTTTCTCTTGCTATAGTATCATGTG 57.122 34.615 0.84 0.00 0.00 3.21
1910 9522 3.740321 AGTTTTTGTTGTGTGCTTGTGTG 59.260 39.130 0.00 0.00 0.00 3.82
1911 9523 3.987220 GAGTTTTTGTTGTGTGCTTGTGT 59.013 39.130 0.00 0.00 0.00 3.72
1912 9524 3.059306 CGAGTTTTTGTTGTGTGCTTGTG 59.941 43.478 0.00 0.00 0.00 3.33
1913 9525 3.241701 CGAGTTTTTGTTGTGTGCTTGT 58.758 40.909 0.00 0.00 0.00 3.16
1914 9526 3.241701 ACGAGTTTTTGTTGTGTGCTTG 58.758 40.909 0.00 0.00 0.00 4.01
1915 9527 3.569250 ACGAGTTTTTGTTGTGTGCTT 57.431 38.095 0.00 0.00 0.00 3.91
1916 9528 3.569250 AACGAGTTTTTGTTGTGTGCT 57.431 38.095 0.00 0.00 29.55 4.40
2225 10104 4.055710 TGTGTCCACTGTCCCTAAGATA 57.944 45.455 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.