Multiple sequence alignment - TraesCS1A01G063200

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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 TraesCS1A01G063200 chr1A 100.000 2767 0 0 1 2767 43393155 43390389 0.000000e+00 5110.0
1 TraesCS1A01G063200 chr1A 93.888 2798 126 20 1 2767 43272534 43269751 0.000000e+00 4178.0
2 TraesCS1A01G063200 chr1A 81.013 474 55 21 2312 2767 43952522 43952978 7.340000e-91 344.0
3 TraesCS1A01G063200 chr1A 79.741 232 29 16 245 462 590863742 590863515 4.770000e-33 152.0
4 TraesCS1A01G063200 chr1B 89.672 2740 201 39 52 2740 63807952 63810660 0.000000e+00 3417.0
5 TraesCS1A01G063200 chr1B 90.400 2625 184 38 184 2761 63479076 63481679 0.000000e+00 3389.0
6 TraesCS1A01G063200 chr1B 89.859 2623 193 39 184 2761 63467844 63470438 0.000000e+00 3302.0
7 TraesCS1A01G063200 chr1B 89.585 2602 186 28 58 2608 63758353 63760920 0.000000e+00 3225.0
8 TraesCS1A01G063200 chr1B 92.334 2074 141 11 58 2120 63613357 63615423 0.000000e+00 2933.0
9 TraesCS1A01G063200 chr1B 92.595 1850 118 11 58 1895 63888247 63890089 0.000000e+00 2639.0
10 TraesCS1A01G063200 chr1B 82.000 150 15 11 310 455 679384611 679384470 1.740000e-22 117.0
11 TraesCS1A01G063200 chr1D 89.489 2055 159 35 755 2767 43823105 43825144 0.000000e+00 2545.0
12 TraesCS1A01G063200 chr1D 88.954 2055 151 31 755 2767 44275023 44277043 0.000000e+00 2468.0
13 TraesCS1A01G063200 chr1D 90.013 1582 119 28 623 2193 44628791 44630344 0.000000e+00 2010.0
14 TraesCS1A01G063200 chr1D 87.036 1265 111 22 1546 2767 44370322 44371576 0.000000e+00 1378.0
15 TraesCS1A01G063200 chr1D 85.956 769 64 22 2035 2767 44160032 44160792 0.000000e+00 782.0
16 TraesCS1A01G063200 chr1D 91.912 272 19 3 466 735 43822424 43822694 7.230000e-101 377.0
17 TraesCS1A01G063200 chr1D 91.209 273 20 3 466 735 44274341 44274612 4.350000e-98 368.0
18 TraesCS1A01G063200 chr1D 85.099 302 41 4 2468 2767 43825153 43825452 3.460000e-79 305.0
19 TraesCS1A01G063200 chr1D 83.056 301 43 7 2471 2767 44160804 44161100 1.630000e-67 267.0
20 TraesCS1A01G063200 chr2D 80.789 963 131 35 1828 2756 630306416 630307358 0.000000e+00 704.0
21 TraesCS1A01G063200 chr7B 76.498 634 108 29 1830 2441 591059865 591060479 9.630000e-80 307.0
22 TraesCS1A01G063200 chr7D 74.755 713 123 42 1928 2600 264738215 264737520 1.630000e-67 267.0
23 TraesCS1A01G063200 chr4B 77.157 197 31 12 2251 2441 189010946 189010758 4.880000e-18 102.0
24 TraesCS1A01G063200 chr6D 77.483 151 24 8 2297 2441 387762919 387762773 6.350000e-12 82.4


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 TraesCS1A01G063200 chr1A 43390389 43393155 2766 True 5110.000000 5110 100.000000 1 2767 1 chr1A.!!$R2 2766
1 TraesCS1A01G063200 chr1A 43269751 43272534 2783 True 4178.000000 4178 93.888000 1 2767 1 chr1A.!!$R1 2766
2 TraesCS1A01G063200 chr1B 63807952 63810660 2708 False 3417.000000 3417 89.672000 52 2740 1 chr1B.!!$F5 2688
3 TraesCS1A01G063200 chr1B 63479076 63481679 2603 False 3389.000000 3389 90.400000 184 2761 1 chr1B.!!$F2 2577
4 TraesCS1A01G063200 chr1B 63467844 63470438 2594 False 3302.000000 3302 89.859000 184 2761 1 chr1B.!!$F1 2577
5 TraesCS1A01G063200 chr1B 63758353 63760920 2567 False 3225.000000 3225 89.585000 58 2608 1 chr1B.!!$F4 2550
6 TraesCS1A01G063200 chr1B 63613357 63615423 2066 False 2933.000000 2933 92.334000 58 2120 1 chr1B.!!$F3 2062
7 TraesCS1A01G063200 chr1B 63888247 63890089 1842 False 2639.000000 2639 92.595000 58 1895 1 chr1B.!!$F6 1837
8 TraesCS1A01G063200 chr1D 44628791 44630344 1553 False 2010.000000 2010 90.013000 623 2193 1 chr1D.!!$F2 1570
9 TraesCS1A01G063200 chr1D 44274341 44277043 2702 False 1418.000000 2468 90.081500 466 2767 2 chr1D.!!$F5 2301
10 TraesCS1A01G063200 chr1D 44370322 44371576 1254 False 1378.000000 1378 87.036000 1546 2767 1 chr1D.!!$F1 1221
11 TraesCS1A01G063200 chr1D 43822424 43825452 3028 False 1075.666667 2545 88.833333 466 2767 3 chr1D.!!$F3 2301
12 TraesCS1A01G063200 chr1D 44160032 44161100 1068 False 524.500000 782 84.506000 2035 2767 2 chr1D.!!$F4 732
13 TraesCS1A01G063200 chr2D 630306416 630307358 942 False 704.000000 704 80.789000 1828 2756 1 chr2D.!!$F1 928
14 TraesCS1A01G063200 chr7B 591059865 591060479 614 False 307.000000 307 76.498000 1830 2441 1 chr7B.!!$F1 611
15 TraesCS1A01G063200 chr7D 264737520 264738215 695 True 267.000000 267 74.755000 1928 2600 1 chr7D.!!$R1 672

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
299 310 0.105039 GCCCGCTACTAGCATCAACT 59.895 55.0 8.78 0.0 42.58 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2592 0.040646 ACCGTGACCCTAGGTGATGA 59.959 55.0 8.29 0.0 35.25 2.92 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
30 31 9.479549 AAACCCTAGATTGATGAATACACAAAT 57.520 29.630 0.00 0.00 0.00 2.32
54 55 0.329596 AAGAGGGGATGGTGCTCAAC 59.670 55.000 0.00 0.00 0.00 3.18
90 91 8.527810 AGAAACAATAACTGGACAGAAACAAAA 58.472 29.630 6.29 0.00 0.00 2.44
97 98 5.261216 ACTGGACAGAAACAAAAAGGAAGA 58.739 37.500 6.29 0.00 0.00 2.87
159 164 2.630158 CGTCTCTCTCCCTTCTCGTTA 58.370 52.381 0.00 0.00 0.00 3.18
200 210 2.945890 GCCGAAGAGGAATGGGAAATGT 60.946 50.000 0.00 0.00 45.00 2.71
238 249 5.837829 AGGGAGAAAACTACTCTGAGAGAT 58.162 41.667 17.71 3.16 35.10 2.75
299 310 0.105039 GCCCGCTACTAGCATCAACT 59.895 55.000 8.78 0.00 42.58 3.16
385 396 3.780902 TGCGCGAATCTTGAAGATAGAA 58.219 40.909 12.10 0.00 32.89 2.10
398 409 7.566509 TCTTGAAGATAGAAGAGATCCAATGGA 59.433 37.037 3.67 3.67 35.55 3.41
780 1189 4.926832 CGATGTGGAGTTAATGTACACACA 59.073 41.667 13.53 13.53 43.81 3.72
1061 1477 1.462283 CACATTCACAGAGAAGCCACG 59.538 52.381 0.00 0.00 40.15 4.94
1217 1633 0.605319 GGTGACCGACAGGCAATGAA 60.605 55.000 0.00 0.00 42.76 2.57
1226 1642 2.887152 GACAGGCAATGAACAAGGAGTT 59.113 45.455 0.00 0.00 44.93 3.01
1245 1661 7.168219 AGGAGTTTGCTAAGTATCAACAATGA 58.832 34.615 0.00 0.00 40.57 2.57
1508 1924 6.147821 ACTTGTTATTCTTCAGATTCACACGG 59.852 38.462 0.00 0.00 0.00 4.94
1610 2049 2.838202 GTTACACATTCCCTCCTCTGGA 59.162 50.000 0.00 0.00 0.00 3.86
1645 2084 3.468071 TTAGCTGTGGGAGGAGAAGTA 57.532 47.619 0.00 0.00 0.00 2.24
1684 2125 1.209504 GTACCTGGCCTCACAATAGCA 59.790 52.381 3.32 0.00 0.00 3.49
1689 2130 1.284491 TGGCCTCACAATAGCATTCCA 59.716 47.619 3.32 0.00 0.00 3.53
1710 2151 6.639563 TCCATTCAGATCTGTAATTCGTGAA 58.360 36.000 21.92 6.65 0.00 3.18
1720 2161 1.160137 AATTCGTGAAGCTGTGCTCC 58.840 50.000 0.00 0.00 38.25 4.70
1779 2220 7.860872 CGTTTGTGAAACTAATAAAGCCTTCTT 59.139 33.333 0.00 0.00 39.23 2.52
1888 2333 7.210718 ACAATCAGATTATGCATATGTGGTG 57.789 36.000 7.36 10.25 0.00 4.17
1899 2348 7.844493 ATGCATATGTGGTGGAGATAAAAAT 57.156 32.000 0.00 0.00 0.00 1.82
1940 2390 7.779798 CAGGATGAGATTGGGACCTTTAAATTA 59.220 37.037 0.00 0.00 39.69 1.40
1961 2411 6.715344 TTACGATTTCATAAACTGCGTCTT 57.285 33.333 0.00 0.00 31.55 3.01
2075 2531 5.757320 CACCACAACAAAATATTTTCTGGCA 59.243 36.000 10.53 0.00 0.00 4.92
2120 2577 6.668283 ACTCCACCTAAGCTAGACTAATGAAA 59.332 38.462 0.00 0.00 0.00 2.69
2121 2578 7.180408 ACTCCACCTAAGCTAGACTAATGAAAA 59.820 37.037 0.00 0.00 0.00 2.29
2133 2590 7.856145 AGACTAATGAAAATGATGTGTCTCC 57.144 36.000 0.00 0.00 0.00 3.71
2135 2592 6.173339 ACTAATGAAAATGATGTGTCTCCGT 58.827 36.000 0.00 0.00 0.00 4.69
2137 2594 4.001618 TGAAAATGATGTGTCTCCGTCA 57.998 40.909 0.00 0.00 34.99 4.35
2165 2622 1.232621 GGTCACGGTGTTTACCCTGC 61.233 60.000 8.17 0.00 44.53 4.85
2180 2637 8.995577 TGTTTACCCTGCCTAGTAAAACTATAT 58.004 33.333 4.46 0.00 39.46 0.86
2459 2975 8.916628 TCAAATTCCCGAAATACATGATCATA 57.083 30.769 8.15 0.00 0.00 2.15
2651 3175 3.576078 ACTGGACATTTTGTGACTCCA 57.424 42.857 0.00 0.00 33.37 3.86
2664 3188 9.612066 ATTTTGTGACTCCAAAACATTTTATGT 57.388 25.926 1.58 0.00 44.51 2.29
2725 3249 6.544928 AAACTGACAACTTTTGGAAATCCT 57.455 33.333 0.44 0.00 36.82 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.222337 ACCATCCCCTCTTCTTTATTTGTGT 60.222 40.000 0.00 0.00 0.00 3.72
30 31 2.505819 GAGCACCATCCCCTCTTCTTTA 59.494 50.000 0.00 0.00 0.00 1.85
54 55 6.599244 TCCAGTTATTGTTTCTTGCTCATAGG 59.401 38.462 0.00 0.00 0.00 2.57
200 210 1.473677 CTCCCTCGCATTCATTTTGCA 59.526 47.619 0.00 0.00 40.14 4.08
463 474 7.904977 CACATCTACATGCTACAACATTACAAC 59.095 37.037 0.00 0.00 32.57 3.32
780 1189 6.701841 AGATACGAAATAGCATCGAACAATGT 59.298 34.615 2.65 0.00 42.76 2.71
1061 1477 8.947055 ATCCCTTTGATGTTATAATTGTTTGC 57.053 30.769 0.00 0.00 30.54 3.68
1217 1633 6.296026 TGTTGATACTTAGCAAACTCCTTGT 58.704 36.000 0.00 0.00 37.36 3.16
1226 1642 5.123820 GCTGGTCATTGTTGATACTTAGCAA 59.876 40.000 0.00 0.00 33.56 3.91
1245 1661 1.555075 TCTAGCTTCGGATTTGCTGGT 59.445 47.619 0.00 0.00 37.62 4.00
1287 1703 0.610174 TGTTTGCCTTTTGCCACACA 59.390 45.000 0.00 0.00 40.16 3.72
1484 1900 6.147821 ACCGTGTGAATCTGAAGAATAACAAG 59.852 38.462 0.00 0.00 0.00 3.16
1497 1913 7.272037 ACTAAAATCAAAACCGTGTGAATCT 57.728 32.000 0.00 0.00 0.00 2.40
1610 2049 5.416326 CCACAGCTAAACTAGAGTCACTACT 59.584 44.000 0.00 0.00 39.21 2.57
1684 2125 7.275183 TCACGAATTACAGATCTGAATGGAAT 58.725 34.615 29.27 15.29 0.00 3.01
1689 2130 6.257411 CAGCTTCACGAATTACAGATCTGAAT 59.743 38.462 29.27 19.15 0.00 2.57
1710 2151 1.680338 AAACTTTTCGGAGCACAGCT 58.320 45.000 0.00 0.00 43.88 4.24
1720 2161 8.335256 ACAAAGTGCTTAACATAAACTTTTCG 57.665 30.769 0.00 0.00 38.63 3.46
1819 2260 6.267928 ACGAGCATATTTTCTAGTAGGACCAT 59.732 38.462 0.00 0.00 0.00 3.55
1888 2333 9.468532 GGCATATGTTTCAGAATTTTTATCTCC 57.531 33.333 4.29 0.00 0.00 3.71
1899 2348 5.104402 TCTCATCCTGGCATATGTTTCAGAA 60.104 40.000 18.03 4.92 0.00 3.02
2075 2531 6.013379 TGGAGTCCATCAATACAGTTTTCTCT 60.013 38.462 8.12 0.00 0.00 3.10
2120 2577 3.525537 GTGATGACGGAGACACATCATT 58.474 45.455 0.00 0.00 46.98 2.57
2121 2578 2.159043 GGTGATGACGGAGACACATCAT 60.159 50.000 0.00 0.00 46.98 2.45
2133 2590 0.100682 CGTGACCCTAGGTGATGACG 59.899 60.000 8.29 5.32 35.25 4.35
2135 2592 0.040646 ACCGTGACCCTAGGTGATGA 59.959 55.000 8.29 0.00 35.25 2.92
2180 2637 5.960704 TGCCTCCATACTATTCTGGTACTA 58.039 41.667 0.00 0.00 34.03 1.82
2181 2638 4.816126 TGCCTCCATACTATTCTGGTACT 58.184 43.478 0.00 0.00 34.03 2.73
2522 3044 9.601971 TCTAGTATTTTGAATAAACGTTTGCAC 57.398 29.630 23.46 13.55 0.00 4.57


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

AutoCloner maintained by Alex Coulton.