Multiple sequence alignment - TraesCS2A01G165400

Loading Multiple Alignment...

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 TraesCS2A01G165400 chr2A 100.000 2303 0 0 1 2303 117770382 117768080 0.000000e+00 4253.0
1 TraesCS2A01G165400 chr2A 94.972 2307 101 6 1 2303 117793824 117791529 0.000000e+00 3603.0
2 TraesCS2A01G165400 chr5A 92.053 2051 119 19 1 2026 264270332 264268301 0.000000e+00 2844.0
3 TraesCS2A01G165400 chr2D 90.240 707 60 8 1 700 531424156 531423452 0.000000e+00 915.0
4 TraesCS2A01G165400 chr2D 90.849 601 48 7 1 595 531432280 531431681 0.000000e+00 798.0
5 TraesCS2A01G165400 chr2D 88.931 533 46 11 1502 2026 127046913 127047440 0.000000e+00 645.0
6 TraesCS2A01G165400 chr2D 89.251 521 46 7 1514 2026 35827156 35827674 0.000000e+00 643.0
7 TraesCS2A01G165400 chr2D 88.743 533 47 10 1502 2026 127039099 127039626 6.940000e-180 640.0
8 TraesCS2A01G165400 chr2D 90.800 250 21 2 1 249 406876788 406877036 1.320000e-87 333.0
9 TraesCS2A01G165400 chr2D 90.800 250 21 2 1 249 472155449 472155201 1.320000e-87 333.0
10 TraesCS2A01G165400 chr7D 89.869 533 43 8 1502 2026 529576381 529576910 0.000000e+00 675.0
11 TraesCS2A01G165400 chr7D 89.184 527 48 6 1507 2026 529559447 529559971 0.000000e+00 649.0
12 TraesCS2A01G165400 chr7D 96.043 278 11 0 2026 2303 273733726 273734003 9.700000e-124 453.0
13 TraesCS2A01G165400 chr7D 96.043 278 11 0 2026 2303 273741197 273741474 9.700000e-124 453.0
14 TraesCS2A01G165400 chr7D 90.800 250 21 2 1 249 241899553 241899801 1.320000e-87 333.0
15 TraesCS2A01G165400 chr7D 90.000 250 23 2 1 249 241912548 241912796 2.850000e-84 322.0
16 TraesCS2A01G165400 chr7D 90.000 250 22 3 1 249 241920526 241920773 1.030000e-83 320.0
17 TraesCS2A01G165400 chr7D 89.641 251 22 4 1 249 99110882 99110634 1.330000e-82 316.0
18 TraesCS2A01G165400 chr3D 89.054 539 47 9 1502 2032 112734069 112733535 0.000000e+00 658.0
19 TraesCS2A01G165400 chr3D 96.364 275 10 0 2029 2303 605047451 605047177 9.700000e-124 453.0
20 TraesCS2A01G165400 chr3D 79.386 228 32 14 1 220 462408484 462408704 1.840000e-31 147.0
21 TraesCS2A01G165400 chr4D 88.555 533 50 8 1502 2026 338114458 338113929 8.970000e-179 636.0
22 TraesCS2A01G165400 chr4D 77.403 593 95 30 1 575 187265644 187265073 1.330000e-82 316.0
23 TraesCS2A01G165400 chr4D 76.821 604 101 31 1 585 187282010 187281427 1.030000e-78 303.0
24 TraesCS2A01G165400 chr4D 82.105 190 28 6 1 186 169453687 169453874 8.520000e-35 158.0
25 TraesCS2A01G165400 chr4D 82.105 190 28 6 1 186 169462049 169462236 8.520000e-35 158.0
26 TraesCS2A01G165400 chr4D 79.447 253 29 20 1 240 186761955 186761713 8.520000e-35 158.0
27 TraesCS2A01G165400 chr4D 79.111 225 39 8 1 220 423077042 423077263 5.130000e-32 148.0
28 TraesCS2A01G165400 chr1D 96.763 278 9 0 2026 2303 382589672 382589949 4.480000e-127 464.0
29 TraesCS2A01G165400 chr1D 96.043 278 11 0 2026 2303 80212067 80212344 9.700000e-124 453.0
30 TraesCS2A01G165400 chr1D 96.057 279 9 2 2026 2303 250795584 250795861 9.700000e-124 453.0
31 TraesCS2A01G165400 chr1D 79.736 227 31 14 1 219 128497256 128497475 1.430000e-32 150.0
32 TraesCS2A01G165400 chr1D 78.761 226 39 9 1 220 96275503 96275725 2.390000e-30 143.0
33 TraesCS2A01G165400 chr1D 79.279 222 30 15 1 214 409665293 409665506 8.580000e-30 141.0
34 TraesCS2A01G165400 chr6D 96.043 278 11 0 2026 2303 266156206 266156483 9.700000e-124 453.0
35 TraesCS2A01G165400 chr6D 96.043 278 11 0 2026 2303 266163668 266163945 9.700000e-124 453.0
36 TraesCS2A01G165400 chr6D 91.235 251 18 4 1 249 425114023 425113775 2.830000e-89 339.0
37 TraesCS2A01G165400 chr6D 79.358 218 31 8 1 216 2060242 2060037 8.580000e-30 141.0
38 TraesCS2A01G165400 chr6D 78.855 227 34 14 1 220 156365285 156365504 8.580000e-30 141.0
39 TraesCS2A01G165400 chr6D 78.947 228 33 14 1 220 218960042 218959822 8.580000e-30 141.0
40 TraesCS2A01G165400 chr6D 78.509 228 35 13 1 220 218968709 218968488 1.110000e-28 137.0
41 TraesCS2A01G165400 chr6D 78.414 227 35 13 1 220 156357258 156357477 3.990000e-28 135.0
42 TraesCS2A01G165400 chr6D 78.414 227 35 14 1 220 398074355 398074136 3.990000e-28 135.0
43 TraesCS2A01G165400 chr6D 77.974 227 36 13 1 220 274857296 274857077 1.860000e-26 130.0
44 TraesCS2A01G165400 chr6A 91.600 250 19 2 1 249 36817681 36817929 6.090000e-91 344.0
45 TraesCS2A01G165400 chr6A 91.200 250 20 2 1 249 326051890 326051642 2.830000e-89 339.0
46 TraesCS2A01G165400 chr1B 91.803 244 18 2 7 249 121153192 121152950 2.830000e-89 339.0
47 TraesCS2A01G165400 chr1B 90.438 251 20 4 1 249 384727443 384727691 6.130000e-86 327.0
48 TraesCS2A01G165400 chr1B 90.438 251 20 4 1 249 384735814 384736062 6.130000e-86 327.0
49 TraesCS2A01G165400 chr1B 90.438 251 19 5 1 249 215233955 215233708 2.210000e-85 326.0
50 TraesCS2A01G165400 chr6B 91.393 244 18 3 7 249 577443771 577443530 4.740000e-87 331.0
51 TraesCS2A01G165400 chr1A 90.000 250 23 2 1 249 509077502 509077254 2.850000e-84 322.0
52 TraesCS2A01G165400 chr1A 90.040 251 20 5 1 249 509343693 509343446 1.030000e-83 320.0
53 TraesCS2A01G165400 chr1A 88.845 251 23 5 1 249 509303038 509302791 1.030000e-78 303.0
54 TraesCS2A01G165400 chrUn 79.386 228 32 14 1 220 266805867 266806087 1.840000e-31 147.0
55 TraesCS2A01G165400 chrUn 81.818 154 16 7 1 152 130810249 130810106 4.020000e-23 119.0
56 TraesCS2A01G165400 chrUn 83.929 112 12 6 1 110 426468785 426468678 4.050000e-18 102.0
57 TraesCS2A01G165400 chrUn 85.000 100 11 4 1 99 290040998 290040902 5.240000e-17 99.0
58 TraesCS2A01G165400 chrUn 93.846 65 4 0 1 65 477895184 477895248 5.240000e-17 99.0
59 TraesCS2A01G165400 chrUn 88.235 85 5 5 1 83 80475001 80474920 1.880000e-16 97.1
60 TraesCS2A01G165400 chrUn 92.647 68 3 2 1 67 104577526 104577460 1.880000e-16 97.1
61 TraesCS2A01G165400 chrUn 92.424 66 5 0 1 66 372366830 372366765 6.770000e-16 95.3
62 TraesCS2A01G165400 chrUn 92.424 66 5 0 1 66 407606223 407606158 6.770000e-16 95.3
63 TraesCS2A01G165400 chrUn 81.818 110 16 4 1 109 273685361 273685467 3.150000e-14 89.8
64 TraesCS2A01G165400 chrUn 85.542 83 11 1 1 83 270005147 270005066 4.080000e-13 86.1
65 TraesCS2A01G165400 chr5D 79.386 228 32 14 1 220 100092973 100093193 1.840000e-31 147.0
66 TraesCS2A01G165400 chr4A 75.521 192 40 6 1206 1394 583769402 583769215 1.130000e-13 87.9


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 TraesCS2A01G165400 chr2A 117768080 117770382 2302 True 4253 4253 100.000 1 2303 1 chr2A.!!$R1 2302
1 TraesCS2A01G165400 chr2A 117791529 117793824 2295 True 3603 3603 94.972 1 2303 1 chr2A.!!$R2 2302
2 TraesCS2A01G165400 chr5A 264268301 264270332 2031 True 2844 2844 92.053 1 2026 1 chr5A.!!$R1 2025
3 TraesCS2A01G165400 chr2D 531423452 531424156 704 True 915 915 90.240 1 700 1 chr2D.!!$R2 699
4 TraesCS2A01G165400 chr2D 531431681 531432280 599 True 798 798 90.849 1 595 1 chr2D.!!$R3 594
5 TraesCS2A01G165400 chr2D 127046913 127047440 527 False 645 645 88.931 1502 2026 1 chr2D.!!$F3 524
6 TraesCS2A01G165400 chr2D 35827156 35827674 518 False 643 643 89.251 1514 2026 1 chr2D.!!$F1 512
7 TraesCS2A01G165400 chr2D 127039099 127039626 527 False 640 640 88.743 1502 2026 1 chr2D.!!$F2 524
8 TraesCS2A01G165400 chr7D 529576381 529576910 529 False 675 675 89.869 1502 2026 1 chr7D.!!$F7 524
9 TraesCS2A01G165400 chr7D 529559447 529559971 524 False 649 649 89.184 1507 2026 1 chr7D.!!$F6 519
10 TraesCS2A01G165400 chr3D 112733535 112734069 534 True 658 658 89.054 1502 2032 1 chr3D.!!$R1 530
11 TraesCS2A01G165400 chr4D 338113929 338114458 529 True 636 636 88.555 1502 2026 1 chr4D.!!$R4 524
12 TraesCS2A01G165400 chr4D 187265073 187265644 571 True 316 316 77.403 1 575 1 chr4D.!!$R2 574
13 TraesCS2A01G165400 chr4D 187281427 187282010 583 True 303 303 76.821 1 585 1 chr4D.!!$R3 584

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
576 602 3.390521 AGGCGACGAAGATGGGCA 61.391 61.111 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2212 0.107945 CTACTCCCTCCTGTTGCTGC 60.108 60.0 0.0 0.0 0.0 5.25 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
328 332 4.547886 ACTACTAAGTGGGGCCATACTA 57.452 45.455 4.39 0.00 33.57 1.82
329 333 4.481072 ACTACTAAGTGGGGCCATACTAG 58.519 47.826 4.39 6.05 33.57 2.57
576 602 3.390521 AGGCGACGAAGATGGGCA 61.391 61.111 0.00 0.00 0.00 5.36
1066 1111 2.653726 GATCTGAGAGAGGAGCTCACA 58.346 52.381 17.19 4.66 46.45 3.58
1083 1128 0.830444 ACAGTGAGTCCGTTGGCCTA 60.830 55.000 3.32 0.00 0.00 3.93
1182 1227 0.608130 TGACATGTACGCAGCTCCTT 59.392 50.000 0.00 0.00 0.00 3.36
1201 1246 3.706373 GCTCAAGCTGGTCCCCGA 61.706 66.667 0.00 0.00 38.21 5.14
1204 1249 0.035056 CTCAAGCTGGTCCCCGAAAT 60.035 55.000 0.00 0.00 0.00 2.17
1224 1269 4.034258 ACGAAGTCGAGCGCGGAA 62.034 61.111 10.69 0.00 29.74 4.30
1272 1317 2.564975 GACGACGGTGTCCACGAT 59.435 61.111 0.00 0.00 32.61 3.73
1275 1320 0.813184 ACGACGGTGTCCACGATAAT 59.187 50.000 0.00 0.00 34.93 1.28
1297 1342 2.828868 GTGAGGCAGTGGTCACCA 59.171 61.111 0.00 0.00 37.67 4.17
1334 1379 2.110578 TGATTCCGAGCAGATGAGGAA 58.889 47.619 0.00 0.00 45.49 3.36
1340 1385 2.203126 GCAGATGAGGAAGGGGCG 60.203 66.667 0.00 0.00 0.00 6.13
1362 1408 3.421386 GGGGAAGGAGGGGGAAGC 61.421 72.222 0.00 0.00 0.00 3.86
1376 1422 1.289380 GAAGCGGACAAGGACGAGT 59.711 57.895 0.00 0.00 0.00 4.18
1385 1431 3.259123 GGACAAGGACGAGTTAGGGTTTA 59.741 47.826 0.00 0.00 0.00 2.01
1419 1465 1.557099 ATAGTGTTCAGGAGGCGACA 58.443 50.000 0.00 0.00 0.00 4.35
1424 1470 0.179000 GTTCAGGAGGCGACATGGAT 59.821 55.000 0.00 0.00 0.00 3.41
1440 1486 3.100545 GATGACATCCACGGCCATT 57.899 52.632 2.24 0.00 0.00 3.16
1474 1520 2.320587 GCCACGCACCTTCTCTGTG 61.321 63.158 0.00 0.00 36.79 3.66
1480 1526 0.391793 GCACCTTCTCTGTGTAGGGC 60.392 60.000 7.22 4.46 37.52 5.19
1845 1896 3.023119 TGATTTCACCGCCATAATTGCT 58.977 40.909 0.00 0.00 0.00 3.91
1975 2028 1.830279 TCGACAGTAACCGAGGTGAT 58.170 50.000 0.00 0.00 0.00 3.06
2026 2079 2.519377 TAATTATCCGGGCGTCACAG 57.481 50.000 0.00 0.00 0.00 3.66
2050 2103 8.526978 CAGTAAGGATCTACACTACATATGCAT 58.473 37.037 3.79 3.79 0.00 3.96
2089 2142 5.072600 AGGGTTGTATTTGTGAACTGGACTA 59.927 40.000 0.00 0.00 0.00 2.59
2159 2212 3.754965 TCTTCTGGAAACCACCATCTTG 58.245 45.455 0.00 0.00 39.34 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
513 539 3.077556 CCTGCCTACCCTGCTCGT 61.078 66.667 0.00 0.00 0.00 4.18
564 590 2.185350 CGCTCTGCCCATCTTCGT 59.815 61.111 0.00 0.00 0.00 3.85
567 593 4.496336 GCCCGCTCTGCCCATCTT 62.496 66.667 0.00 0.00 0.00 2.40
860 905 0.879765 CTGCTGCTTGCTTTAGCTGT 59.120 50.000 0.00 0.00 41.76 4.40
867 912 3.141522 TTTGCGCTGCTGCTTGCTT 62.142 52.632 9.73 0.00 43.37 3.91
888 933 3.077556 CTACCGGTGCTCCTGGCT 61.078 66.667 19.93 0.00 42.39 4.75
1066 1111 0.542232 AGTAGGCCAACGGACTCACT 60.542 55.000 5.01 0.00 35.03 3.41
1168 1213 2.047274 GCCAAGGAGCTGCGTACA 60.047 61.111 0.00 0.00 0.00 2.90
1169 1214 1.811679 GAGCCAAGGAGCTGCGTAC 60.812 63.158 0.00 0.00 45.15 3.67
1201 1246 1.352156 GCGCTCGACTTCGTCCATTT 61.352 55.000 0.00 0.00 40.80 2.32
1204 1249 4.753877 CGCGCTCGACTTCGTCCA 62.754 66.667 5.56 0.00 40.80 4.02
1272 1317 1.915489 ACCACTGCCTCACCATCATTA 59.085 47.619 0.00 0.00 0.00 1.90
1275 1320 1.126948 TGACCACTGCCTCACCATCA 61.127 55.000 0.00 0.00 0.00 3.07
1297 1342 1.254026 TCAATCTCGGGAACTCACGT 58.746 50.000 0.63 0.00 44.39 4.49
1340 1385 3.878667 CCCCTCCTTCCCCATCGC 61.879 72.222 0.00 0.00 0.00 4.58
1362 1408 0.172803 CCCTAACTCGTCCTTGTCCG 59.827 60.000 0.00 0.00 0.00 4.79
1376 1422 2.210644 CCAGTCCCCCATAAACCCTAA 58.789 52.381 0.00 0.00 0.00 2.69
1385 1431 3.954662 ACACTATAATCCAGTCCCCCAT 58.045 45.455 0.00 0.00 0.00 4.00
1424 1470 2.045708 GCAATGGCCGTGGATGTCA 61.046 57.895 2.48 0.00 0.00 3.58
1474 1520 1.224870 GCCTTTCTCCCTGCCCTAC 59.775 63.158 0.00 0.00 0.00 3.18
1480 1526 0.113190 ACCAAAGGCCTTTCTCCCTG 59.887 55.000 28.16 16.19 0.00 4.45
1975 2028 0.609151 CCTTTGCCAATGATGCCACA 59.391 50.000 0.00 0.00 0.00 4.17
2026 2079 7.698550 CGATGCATATGTAGTGTAGATCCTTAC 59.301 40.741 0.00 0.00 0.00 2.34
2050 2103 4.658063 ACAACCCTTTTCATTGATACCGA 58.342 39.130 0.00 0.00 0.00 4.69
2089 2142 4.230502 TCCCCTTCTCTTTTGGCATTCTAT 59.769 41.667 0.00 0.00 0.00 1.98
2159 2212 0.107945 CTACTCCCTCCTGTTGCTGC 60.108 60.000 0.00 0.00 0.00 5.25
2203 2256 0.390603 TGGCCGAGGTTGATAACACG 60.391 55.000 0.00 0.00 34.37 4.49
2226 2279 1.134965 CGCAAGGAGTCGAGAAAGGAT 60.135 52.381 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.