Multiple sequence alignment - TraesCS6D01G345100

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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 TraesCS6D01G345100 chr6D 100.000 3027 0 0 1 3027 445262063 445265089 0.000000e+00 5590.0
1 TraesCS6D01G345100 chr6D 98.723 1566 18 2 1463 3027 445191037 445192601 0.000000e+00 2780.0
2 TraesCS6D01G345100 chr6D 96.856 1336 16 2 159 1468 445184474 445185809 0.000000e+00 2211.0
3 TraesCS6D01G345100 chr6D 91.565 1399 85 12 978 2348 445308771 445310164 0.000000e+00 1899.0
4 TraesCS6D01G345100 chr6D 87.143 1050 117 7 1090 2126 444461073 444460029 0.000000e+00 1175.0
5 TraesCS6D01G345100 chr6D 92.051 780 62 0 160 939 445307990 445308769 0.000000e+00 1098.0
6 TraesCS6D01G345100 chr6D 93.474 521 30 3 1636 2155 445311431 445311948 0.000000e+00 771.0
7 TraesCS6D01G345100 chr6D 87.153 576 47 14 2152 2723 445334433 445334985 1.980000e-176 628.0
8 TraesCS6D01G345100 chr6D 88.673 309 20 8 2721 3027 445336135 445336430 2.220000e-96 363.0
9 TraesCS6D01G345100 chr6D 84.561 285 34 4 2113 2395 444459991 444459715 1.070000e-69 274.0
10 TraesCS6D01G345100 chr6D 99.315 146 1 0 1 146 445183512 445183657 6.430000e-67 265.0
11 TraesCS6D01G345100 chr6D 93.617 141 9 0 6 146 445305567 445305707 8.500000e-51 211.0
12 TraesCS6D01G345100 chr6D 90.667 75 7 0 2593 2667 444459593 444459519 1.920000e-17 100.0
13 TraesCS6D01G345100 chr6A 93.367 2367 122 10 357 2696 591984914 591987272 0.000000e+00 3469.0
14 TraesCS6D01G345100 chr6A 86.809 940 115 5 1108 2046 591805045 591804114 0.000000e+00 1040.0
15 TraesCS6D01G345100 chr6A 84.034 357 48 3 2045 2399 591804084 591803735 4.840000e-88 335.0
16 TraesCS6D01G345100 chr6A 87.291 299 15 10 2721 3018 592009786 592010062 1.350000e-83 320.0
17 TraesCS6D01G345100 chr6B 91.573 2219 154 8 191 2382 670211825 670214037 0.000000e+00 3031.0
18 TraesCS6D01G345100 chr6B 89.113 1984 182 14 442 2399 671471965 671469990 0.000000e+00 2436.0
19 TraesCS6D01G345100 chr6B 91.635 789 61 2 191 979 670210990 670211773 0.000000e+00 1086.0
20 TraesCS6D01G345100 chr6B 80.603 763 110 25 849 1577 668911628 668910870 3.410000e-154 555.0
21 TraesCS6D01G345100 chr6B 79.498 239 33 9 2743 2973 670214334 670214564 4.040000e-34 156.0
22 TraesCS6D01G345100 chr6B 89.041 73 7 1 2595 2667 670214134 670214205 4.160000e-14 89.8
23 TraesCS6D01G345100 chrUn 88.537 1893 165 15 1146 3027 79232454 79234305 0.000000e+00 2246.0
24 TraesCS6D01G345100 chr7A 79.144 935 180 10 1239 2167 218245221 218244296 1.530000e-177 632.0
25 TraesCS6D01G345100 chr7A 96.610 59 2 0 200 258 420376061 420376003 6.910000e-17 99.0
26 TraesCS6D01G345100 chr7D 78.367 943 189 12 1239 2176 205748452 205747520 5.590000e-167 597.0
27 TraesCS6D01G345100 chr7B 92.754 69 3 2 200 268 595064708 595064642 6.910000e-17 99.0
28 TraesCS6D01G345100 chr4B 95.161 62 3 0 200 261 63511337 63511276 6.910000e-17 99.0
29 TraesCS6D01G345100 chr3A 91.667 72 2 2 200 267 330696448 330696377 2.480000e-16 97.1
30 TraesCS6D01G345100 chr1D 96.552 58 2 0 200 257 137413932 137413989 2.480000e-16 97.1
31 TraesCS6D01G345100 chr1B 94.286 35 2 0 165 199 638357040 638357074 2.000000e-03 54.7


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 TraesCS6D01G345100 chr6D 445262063 445265089 3026 False 5590.000000 5590 100.00000 1 3027 1 chr6D.!!$F2 3026
1 TraesCS6D01G345100 chr6D 445191037 445192601 1564 False 2780.000000 2780 98.72300 1463 3027 1 chr6D.!!$F1 1564
2 TraesCS6D01G345100 chr6D 445183512 445185809 2297 False 1238.000000 2211 98.08550 1 1468 2 chr6D.!!$F3 1467
3 TraesCS6D01G345100 chr6D 445305567 445311948 6381 False 994.750000 1899 92.67675 6 2348 4 chr6D.!!$F4 2342
4 TraesCS6D01G345100 chr6D 444459519 444461073 1554 True 516.333333 1175 87.45700 1090 2667 3 chr6D.!!$R1 1577
5 TraesCS6D01G345100 chr6D 445334433 445336430 1997 False 495.500000 628 87.91300 2152 3027 2 chr6D.!!$F5 875
6 TraesCS6D01G345100 chr6A 591984914 591987272 2358 False 3469.000000 3469 93.36700 357 2696 1 chr6A.!!$F1 2339
7 TraesCS6D01G345100 chr6A 591803735 591805045 1310 True 687.500000 1040 85.42150 1108 2399 2 chr6A.!!$R1 1291
8 TraesCS6D01G345100 chr6B 671469990 671471965 1975 True 2436.000000 2436 89.11300 442 2399 1 chr6B.!!$R2 1957
9 TraesCS6D01G345100 chr6B 670210990 670214564 3574 False 1090.700000 3031 87.93675 191 2973 4 chr6B.!!$F1 2782
10 TraesCS6D01G345100 chr6B 668910870 668911628 758 True 555.000000 555 80.60300 849 1577 1 chr6B.!!$R1 728
11 TraesCS6D01G345100 chrUn 79232454 79234305 1851 False 2246.000000 2246 88.53700 1146 3027 1 chrUn.!!$F1 1881
12 TraesCS6D01G345100 chr7A 218244296 218245221 925 True 632.000000 632 79.14400 1239 2167 1 chr7A.!!$R1 928
13 TraesCS6D01G345100 chr7D 205747520 205748452 932 True 597.000000 597 78.36700 1239 2176 1 chr7D.!!$R1 937

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
898 4002 0.961019 GCTTTGCCCAGACATTGACA 59.039 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2879 8364 0.321564 AGCTGTCGCCACAATTGCTA 60.322 50.0 5.05 0.0 31.5 3.49 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
90 91 5.642491 GGTTTCGGTTATTATAGATCCTGGC 59.358 44.000 0.00 0.00 0.00 4.85
146 150 5.801947 GCTTAACGTGACGGACTATTCTTAA 59.198 40.000 10.66 1.66 0.00 1.85
147 151 6.474751 GCTTAACGTGACGGACTATTCTTAAT 59.525 38.462 10.66 0.00 0.00 1.40
148 152 7.514747 GCTTAACGTGACGGACTATTCTTAATG 60.515 40.741 10.66 0.00 0.00 1.90
149 153 5.320549 ACGTGACGGACTATTCTTAATGT 57.679 39.130 10.66 0.00 0.00 2.71
151 155 5.100259 CGTGACGGACTATTCTTAATGTGT 58.900 41.667 0.00 0.00 0.00 3.72
152 156 5.575606 CGTGACGGACTATTCTTAATGTGTT 59.424 40.000 0.00 0.00 0.00 3.32
153 157 6.748658 CGTGACGGACTATTCTTAATGTGTTA 59.251 38.462 0.00 0.00 0.00 2.41
155 159 9.095065 GTGACGGACTATTCTTAATGTGTTAAT 57.905 33.333 0.00 0.00 0.00 1.40
156 160 9.661563 TGACGGACTATTCTTAATGTGTTAATT 57.338 29.630 0.00 0.00 0.00 1.40
301 2572 6.655078 GGACTTATCCATGCCACAATTATT 57.345 37.500 0.00 0.00 45.47 1.40
699 2970 1.452651 CTGGCTTCATGGGCGATGT 60.453 57.895 9.39 0.00 33.29 3.06
898 4002 0.961019 GCTTTGCCCAGACATTGACA 59.039 50.000 0.00 0.00 0.00 3.58
1136 4296 7.777910 TGATACCATATTTTACAGGTTTGGGAG 59.222 37.037 0.00 0.00 35.62 4.30
1469 4631 5.897050 AGATCGTTGTACAGAGAGAAATCC 58.103 41.667 0.00 0.00 0.00 3.01
2131 5408 5.126061 GCATTAAATTGAAGGGAGAAGAGCA 59.874 40.000 0.00 0.00 0.00 4.26
2444 5725 0.734889 AGCATGACAATACAAGCCGC 59.265 50.000 0.00 0.00 35.50 6.53
2837 8175 2.237143 CCTAGTTGCATCAAGGGTCTGA 59.763 50.000 0.00 0.00 0.00 3.27
2838 8176 2.191128 AGTTGCATCAAGGGTCTGAC 57.809 50.000 0.00 0.00 0.00 3.51
2839 8177 1.168714 GTTGCATCAAGGGTCTGACC 58.831 55.000 18.65 18.65 37.60 4.02
2879 8364 6.552008 TGGAGAGAAATAAACCTGGAAACAT 58.448 36.000 0.00 0.00 41.51 2.71
2913 8398 1.217001 CAGCTTGTTGACGCTACACA 58.783 50.000 0.00 0.00 34.58 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 8.070171 GTCCGATTCCATAATTAACACATTGAG 58.930 37.037 0.00 0.00 0.00 3.02
146 150 9.664332 TTTAATTGCAGCCAATAATTAACACAT 57.336 25.926 7.54 0.00 40.69 3.21
147 151 9.664332 ATTTAATTGCAGCCAATAATTAACACA 57.336 25.926 7.54 0.00 40.69 3.72
699 2970 6.098982 ACCTTCACATCCATTTGGTGTAAAAA 59.901 34.615 0.00 0.00 36.34 1.94
815 3086 5.855740 GGTAACTAGCTGGACTATTCTGT 57.144 43.478 3.17 0.00 0.00 3.41
898 4002 8.865090 TGGATATGTTTCCTTGTGTTTACATTT 58.135 29.630 0.00 0.00 36.68 2.32
939 4043 3.198417 GGAATGTCCCAGGCAAATTGATT 59.802 43.478 0.00 0.00 0.00 2.57
1065 4225 2.779755 TTCGGGCAGCTGAATTCTTA 57.220 45.000 20.43 0.00 0.00 2.10
1136 4296 1.405661 GCCACTAGCCACAAGACCTAC 60.406 57.143 0.00 0.00 34.35 3.18
1469 4631 4.154015 TGCAACCTCGTTTATGAAGTCATG 59.846 41.667 4.00 0.00 37.15 3.07
1856 5018 7.458409 ACCAGTATAATACGTACATAGGGTG 57.542 40.000 15.04 7.85 0.00 4.61
2444 5725 5.264060 TCGAATACAAAGAAAGAAGCACG 57.736 39.130 0.00 0.00 0.00 5.34
2633 5919 9.177608 CATTGAAGGTTATGATTTACTTCCTGA 57.822 33.333 0.00 0.00 37.37 3.86
2833 8171 0.400594 TCCTGTCGTCAGAGGTCAGA 59.599 55.000 16.13 0.00 43.76 3.27
2837 8175 1.276421 CCAATTCCTGTCGTCAGAGGT 59.724 52.381 11.41 0.00 43.76 3.85
2838 8176 1.550524 TCCAATTCCTGTCGTCAGAGG 59.449 52.381 11.41 5.27 43.76 3.69
2839 8177 2.493675 TCTCCAATTCCTGTCGTCAGAG 59.506 50.000 11.41 1.91 43.76 3.35
2879 8364 0.321564 AGCTGTCGCCACAATTGCTA 60.322 50.000 5.05 0.00 31.50 3.49
2913 8398 4.393155 TTCCGTCTGCATGCCGCT 62.393 61.111 16.68 0.00 43.06 5.52
2919 8406 3.121030 GCAGCGTTCCGTCTGCAT 61.121 61.111 20.11 0.00 46.95 3.96


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

AutoCloner maintained by Alex Coulton.