Multiple sequence alignment - TraesCS1B01G188600

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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 TraesCS1B01G188600 chr1B 100.000 2288 0 0 1 2288 338431516 338429229 0.000000e+00 4226
1 TraesCS1B01G188600 chr1B 96.548 869 1 3 1442 2288 361800983 361801844 0.000000e+00 1411
2 TraesCS1B01G188600 chr1B 96.360 522 17 2 310 831 340365383 340365902 0.000000e+00 857
3 TraesCS1B01G188600 chr1B 97.217 503 14 0 827 1329 340367044 340367546 0.000000e+00 852
4 TraesCS1B01G188600 chr1B 90.705 312 5 2 1 312 340364837 340365124 5.920000e-106 394
5 TraesCS1B01G188600 chr1B 91.579 95 6 1 1337 1431 340367531 340367623 1.840000e-26 130
6 TraesCS1B01G188600 chr5D 97.636 846 17 3 1443 2288 438042925 438043767 0.000000e+00 1448
7 TraesCS1B01G188600 chr5D 88.953 172 17 2 7 177 377176218 377176048 6.400000e-51 211
8 TraesCS1B01G188600 chr5D 90.299 134 8 3 2033 2166 264487053 264487181 1.090000e-38 171
9 TraesCS1B01G188600 chr3B 97.055 849 11 7 1441 2288 70119242 70120077 0.000000e+00 1417
10 TraesCS1B01G188600 chr3B 85.909 660 49 34 1442 2074 716243452 716242810 0.000000e+00 664
11 TraesCS1B01G188600 chr3B 87.151 179 18 4 1 177 123368117 123368292 4.990000e-47 198
12 TraesCS1B01G188600 chr3B 86.857 175 22 1 1 175 7084290 7084463 6.450000e-46 195
13 TraesCS1B01G188600 chr1D 91.345 751 30 13 691 1431 234656067 234656792 0.000000e+00 994
14 TraesCS1B01G188600 chr1D 84.307 274 21 10 324 588 234655810 234656070 4.880000e-62 248
15 TraesCS1B01G188600 chr1D 96.992 133 3 1 2156 2288 7360398 7360529 2.960000e-54 222
16 TraesCS1B01G188600 chr1A 92.705 658 32 4 691 1332 313007396 313006739 0.000000e+00 935
17 TraesCS1B01G188600 chr1A 93.333 135 4 3 178 312 473908161 473908032 6.450000e-46 195
18 TraesCS1B01G188600 chr1A 94.017 117 7 0 584 700 115437174 115437290 6.500000e-41 178
19 TraesCS1B01G188600 chr1A 92.562 121 6 3 576 695 427816470 427816352 1.090000e-38 171
20 TraesCS1B01G188600 chr1A 89.474 95 4 2 1337 1431 313006757 313006669 5.170000e-22 115
21 TraesCS1B01G188600 chr6D 92.996 514 21 12 1441 1949 334233357 334232854 0.000000e+00 736
22 TraesCS1B01G188600 chr6D 93.333 120 7 1 576 695 68900016 68899898 2.340000e-40 176
23 TraesCS1B01G188600 chr2A 89.813 589 38 19 1443 2022 12159902 12160477 0.000000e+00 736
24 TraesCS1B01G188600 chr2A 96.296 135 3 2 178 312 356707068 356706936 1.060000e-53 220
25 TraesCS1B01G188600 chr2A 93.382 136 8 1 177 312 195977010 195977144 1.390000e-47 200
26 TraesCS1B01G188600 chr2A 86.061 165 11 9 2033 2192 194135675 194135518 1.410000e-37 167
27 TraesCS1B01G188600 chr2A 89.630 135 4 2 178 312 569583421 569583297 1.820000e-36 163
28 TraesCS1B01G188600 chr5B 89.002 591 40 23 1443 2022 572543199 572543775 0.000000e+00 708
29 TraesCS1B01G188600 chr5B 86.592 179 19 4 1 177 43891145 43891320 2.320000e-45 193
30 TraesCS1B01G188600 chr5B 91.057 123 9 1 572 692 655407401 655407523 5.060000e-37 165
31 TraesCS1B01G188600 chr3D 87.714 643 26 11 1443 2085 566965755 566966344 0.000000e+00 701
32 TraesCS1B01G188600 chr3D 97.674 129 3 0 2160 2288 120125667 120125795 2.960000e-54 222
33 TraesCS1B01G188600 chr4B 91.262 515 32 12 1443 1949 384296623 384296114 0.000000e+00 689
34 TraesCS1B01G188600 chr4B 86.916 214 22 4 1873 2083 634415829 634416039 3.800000e-58 235
35 TraesCS1B01G188600 chr4B 86.452 155 12 6 2031 2183 569761146 569760999 6.540000e-36 161
36 TraesCS1B01G188600 chr4B 84.921 126 15 3 571 692 417537581 417537456 8.580000e-25 124
37 TraesCS1B01G188600 chr4B 89.773 88 9 0 571 658 653000656 653000743 1.860000e-21 113
38 TraesCS1B01G188600 chr7B 89.734 526 30 17 1442 1946 504816692 504816170 0.000000e+00 651
39 TraesCS1B01G188600 chr7B 86.111 180 20 4 1 178 162625812 162625988 3.000000e-44 189
40 TraesCS1B01G188600 chr2D 97.606 376 9 0 1913 2288 591189591 591189216 0.000000e+00 645
41 TraesCS1B01G188600 chr2D 90.588 170 13 2 7 174 394653185 394653353 2.960000e-54 222
42 TraesCS1B01G188600 chr2D 95.536 112 5 0 584 695 639487599 639487488 1.810000e-41 180
43 TraesCS1B01G188600 chr2D 85.897 156 11 8 2031 2183 425476344 425476491 3.040000e-34 156
44 TraesCS1B01G188600 chr2B 90.698 172 14 2 7 177 230976268 230976438 6.360000e-56 228
45 TraesCS1B01G188600 chr2B 94.545 110 6 0 585 694 546978484 546978375 1.090000e-38 171
46 TraesCS1B01G188600 chr2B 86.452 155 12 6 2031 2183 451119943 451120090 6.540000e-36 161
47 TraesCS1B01G188600 chrUn 96.992 133 4 0 2156 2288 19850990 19851122 8.230000e-55 224
48 TraesCS1B01G188600 chr6A 96.241 133 5 0 2156 2288 357408018 357408150 3.830000e-53 219
49 TraesCS1B01G188600 chr3A 96.241 133 5 0 2156 2288 721250850 721250982 3.830000e-53 219
50 TraesCS1B01G188600 chr3A 92.593 135 7 2 178 312 673487850 673487981 8.340000e-45 191
51 TraesCS1B01G188600 chr6B 87.006 177 22 1 1 177 508191835 508191660 4.990000e-47 198
52 TraesCS1B01G188600 chr7D 92.754 138 7 1 178 312 59736466 59736329 1.790000e-46 196
53 TraesCS1B01G188600 chr7D 96.296 108 4 0 585 692 144501269 144501162 6.500000e-41 178
54 TraesCS1B01G188600 chr5A 85.556 180 24 2 1 180 475782203 475782026 1.080000e-43 187
55 TraesCS1B01G188600 chr4A 91.667 132 10 1 178 309 556535168 556535298 5.020000e-42 182
56 TraesCS1B01G188600 chr4D 93.443 122 7 1 192 312 501151964 501152085 1.810000e-41 180
57 TraesCS1B01G188600 chr7A 95.413 109 5 0 585 693 638699075 638698967 8.400000e-40 174
58 TraesCS1B01G188600 chr7A 93.162 117 8 0 585 701 538102528 538102644 3.020000e-39 172


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 TraesCS1B01G188600 chr1B 338429229 338431516 2287 True 4226.00 4226 100.00000 1 2288 1 chr1B.!!$R1 2287
1 TraesCS1B01G188600 chr1B 361800983 361801844 861 False 1411.00 1411 96.54800 1442 2288 1 chr1B.!!$F1 846
2 TraesCS1B01G188600 chr1B 340364837 340367623 2786 False 558.25 857 93.96525 1 1431 4 chr1B.!!$F2 1430
3 TraesCS1B01G188600 chr5D 438042925 438043767 842 False 1448.00 1448 97.63600 1443 2288 1 chr5D.!!$F2 845
4 TraesCS1B01G188600 chr3B 70119242 70120077 835 False 1417.00 1417 97.05500 1441 2288 1 chr3B.!!$F2 847
5 TraesCS1B01G188600 chr3B 716242810 716243452 642 True 664.00 664 85.90900 1442 2074 1 chr3B.!!$R1 632
6 TraesCS1B01G188600 chr1D 234655810 234656792 982 False 621.00 994 87.82600 324 1431 2 chr1D.!!$F2 1107
7 TraesCS1B01G188600 chr1A 313006669 313007396 727 True 525.00 935 91.08950 691 1431 2 chr1A.!!$R3 740
8 TraesCS1B01G188600 chr6D 334232854 334233357 503 True 736.00 736 92.99600 1441 1949 1 chr6D.!!$R2 508
9 TraesCS1B01G188600 chr2A 12159902 12160477 575 False 736.00 736 89.81300 1443 2022 1 chr2A.!!$F1 579
10 TraesCS1B01G188600 chr5B 572543199 572543775 576 False 708.00 708 89.00200 1443 2022 1 chr5B.!!$F2 579
11 TraesCS1B01G188600 chr3D 566965755 566966344 589 False 701.00 701 87.71400 1443 2085 1 chr3D.!!$F2 642
12 TraesCS1B01G188600 chr4B 384296114 384296623 509 True 689.00 689 91.26200 1443 1949 1 chr4B.!!$R1 506
13 TraesCS1B01G188600 chr7B 504816170 504816692 522 True 651.00 651 89.73400 1442 1946 1 chr7B.!!$R1 504

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
540 805 0.036105 TGATGCATTGCCGACTGTCT 60.036 50.0 6.12 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 2876 0.326264 GCAGATCACTGACCCAACCT 59.674 55.0 0.0 0.0 46.03 3.5 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
134 135 3.558411 GAGACGCGCCTGTGCATC 61.558 66.667 5.73 0.00 37.32 3.91
150 151 2.230940 ATCCGCTCGACAATTCGCG 61.231 57.895 0.00 0.00 45.46 5.87
155 156 1.715585 CTCGACAATTCGCGGCAAT 59.284 52.632 6.13 0.00 45.46 3.56
219 220 0.812549 GGGTCGCTAGCTAGCTATCC 59.187 60.000 36.02 32.10 46.85 2.59
312 313 2.276732 AAATACTCCATCATGGGCCG 57.723 50.000 3.05 0.00 38.32 6.13
322 583 2.588464 TCATGGGCCGAAAACCTTTA 57.412 45.000 0.00 0.00 0.00 1.85
335 596 6.458342 CCGAAAACCTTTATAGATGAGTTGGC 60.458 42.308 0.00 0.00 0.00 4.52
339 600 6.006275 ACCTTTATAGATGAGTTGGCACAT 57.994 37.500 0.00 0.00 39.30 3.21
362 623 9.347240 ACATATAGAGAGTTCAATTTTGATGGG 57.653 33.333 0.00 0.00 37.00 4.00
540 805 0.036105 TGATGCATTGCCGACTGTCT 60.036 50.000 6.12 0.00 0.00 3.41
593 863 7.946776 CCATTTCCAATTATCATTACTCCCTCT 59.053 37.037 0.00 0.00 0.00 3.69
604 874 7.452880 TCATTACTCCCTCTGTTCAATTTTG 57.547 36.000 0.00 0.00 0.00 2.44
607 877 8.792633 CATTACTCCCTCTGTTCAATTTTGTAA 58.207 33.333 0.00 0.00 0.00 2.41
611 881 5.768164 TCCCTCTGTTCAATTTTGTAAGACC 59.232 40.000 0.00 0.00 0.00 3.85
633 903 8.784043 AGACCATTTAGACATTTAAGACAACAC 58.216 33.333 0.00 0.00 0.00 3.32
969 2402 0.317479 CGAGTCCGGAGAAGGTTGTT 59.683 55.000 3.06 0.00 0.00 2.83
1041 2480 4.827087 ATGTGCGCGCTGCTAGCT 62.827 61.111 33.29 6.85 46.63 3.32
1170 2609 1.667830 CTCGAACCTGAAGGCGCAA 60.668 57.895 10.83 0.00 39.32 4.85
1194 2633 2.047274 TGCCTCTGCAAGTACGCC 60.047 61.111 0.00 0.00 46.66 5.68
1275 2714 3.171388 GGCATCCCCATCCCGACT 61.171 66.667 0.00 0.00 0.00 4.18
1314 2753 0.109827 GTGTATGCATGCACGCACAA 60.110 50.000 33.37 17.64 46.56 3.33
1315 2754 0.595095 TGTATGCATGCACGCACAAA 59.405 45.000 25.37 0.00 46.56 2.83
1316 2755 1.000938 TGTATGCATGCACGCACAAAA 60.001 42.857 25.37 3.10 46.56 2.44
1317 2756 2.057316 GTATGCATGCACGCACAAAAA 58.943 42.857 25.37 0.00 46.56 1.94
1318 2757 1.141645 ATGCATGCACGCACAAAAAG 58.858 45.000 25.37 0.00 46.56 2.27
1319 2758 0.179116 TGCATGCACGCACAAAAAGT 60.179 45.000 18.46 0.00 36.86 2.66
1375 2814 5.245075 TGTGGTGTGTGTTGATCTAGTGATA 59.755 40.000 0.00 0.00 32.19 2.15
1376 2815 6.070824 TGTGGTGTGTGTTGATCTAGTGATAT 60.071 38.462 0.00 0.00 32.19 1.63
1391 2830 7.883217 TCTAGTGATATTAACTGTCCGGATTC 58.117 38.462 7.81 0.00 0.00 2.52
1424 2863 0.109226 AACAGAGAAGTACGAGCGCC 60.109 55.000 2.29 0.00 0.00 6.53
1434 2873 3.900892 CGAGCGCCGTGGATAGGT 61.901 66.667 2.29 0.00 0.00 3.08
1435 2874 2.499685 GAGCGCCGTGGATAGGTT 59.500 61.111 2.29 0.00 0.00 3.50
1436 2875 1.153429 GAGCGCCGTGGATAGGTTT 60.153 57.895 2.29 0.00 0.00 3.27
1437 2876 0.103572 GAGCGCCGTGGATAGGTTTA 59.896 55.000 2.29 0.00 0.00 2.01
1438 2877 0.104304 AGCGCCGTGGATAGGTTTAG 59.896 55.000 2.29 0.00 0.00 1.85
1439 2878 0.878961 GCGCCGTGGATAGGTTTAGG 60.879 60.000 0.00 0.00 0.00 2.69
1440 2879 0.462789 CGCCGTGGATAGGTTTAGGT 59.537 55.000 0.00 0.00 0.00 3.08
1441 2880 1.134610 CGCCGTGGATAGGTTTAGGTT 60.135 52.381 0.00 0.00 0.00 3.50
1442 2881 2.285977 GCCGTGGATAGGTTTAGGTTG 58.714 52.381 0.00 0.00 0.00 3.77
1443 2882 2.914059 CCGTGGATAGGTTTAGGTTGG 58.086 52.381 0.00 0.00 0.00 3.77
1444 2883 2.420967 CCGTGGATAGGTTTAGGTTGGG 60.421 54.545 0.00 0.00 0.00 4.12
1445 2884 2.237893 CGTGGATAGGTTTAGGTTGGGT 59.762 50.000 0.00 0.00 0.00 4.51
2042 3527 4.475051 TGTATAAAGCGGGTTGAAGCTA 57.525 40.909 0.00 0.00 43.78 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 3.558411 GATGCACAGGCGCGTCTC 61.558 66.667 11.99 0.0 43.30 3.36
124 125 4.819761 TCGAGCGGATGCACAGGC 62.820 66.667 0.00 0.0 46.23 4.85
125 126 2.887568 GTCGAGCGGATGCACAGG 60.888 66.667 0.00 0.0 46.23 4.00
126 127 1.086067 ATTGTCGAGCGGATGCACAG 61.086 55.000 0.00 0.0 46.23 3.66
127 128 0.673333 AATTGTCGAGCGGATGCACA 60.673 50.000 0.00 0.0 46.23 4.57
128 129 0.026803 GAATTGTCGAGCGGATGCAC 59.973 55.000 0.00 0.0 46.23 4.57
129 130 2.383170 GAATTGTCGAGCGGATGCA 58.617 52.632 0.00 0.0 46.23 3.96
150 151 3.245948 CTATGCGCCGCTCATTGCC 62.246 63.158 11.67 0.0 38.78 4.52
155 156 4.592192 GCTCCTATGCGCCGCTCA 62.592 66.667 11.67 0.0 0.00 4.26
219 220 4.884164 AGAAAAGAAATAAGAGGCCCATCG 59.116 41.667 0.00 0.0 0.00 3.84
312 313 7.094377 TGTGCCAACTCATCTATAAAGGTTTTC 60.094 37.037 0.00 0.0 0.00 2.29
322 583 7.673504 ACTCTCTATATGTGCCAACTCATCTAT 59.326 37.037 0.00 0.0 32.48 1.98
339 600 7.710907 CGACCCATCAAAATTGAACTCTCTATA 59.289 37.037 0.00 0.0 41.13 1.31
481 746 5.003804 GCCTCACATACGGGATGATTTATT 58.996 41.667 7.33 0.0 39.06 1.40
540 805 3.543884 GGCGGAACCTGTGATTACA 57.456 52.632 0.00 0.0 34.51 2.41
593 863 9.959749 GTCTAAATGGTCTTACAAAATTGAACA 57.040 29.630 0.00 0.0 0.00 3.18
607 877 8.784043 GTGTTGTCTTAAATGTCTAAATGGTCT 58.216 33.333 0.00 0.0 0.00 3.85
633 903 5.471456 ACAGCTGAGATTGAACTGTTTTAGG 59.529 40.000 23.35 0.0 38.38 2.69
792 1071 2.688446 TGGAGTATACGCTTCACCTCAG 59.312 50.000 6.57 0.0 0.00 3.35
969 2402 1.819288 CTAGCTCCGACTTCTCCAACA 59.181 52.381 0.00 0.0 0.00 3.33
1036 2475 1.513158 CGACCACCACCAGAGCTAG 59.487 63.158 0.00 0.0 0.00 3.42
1194 2633 2.469516 GGAATACGCCGGGTTGCTG 61.470 63.158 2.18 0.0 0.00 4.41
1275 2714 1.164411 CATGTTTCTACTGCGGGCAA 58.836 50.000 0.00 0.0 0.00 4.52
1336 2775 4.036734 CACACCACATCTAGCACACTTTTT 59.963 41.667 0.00 0.0 0.00 1.94
1375 2814 9.367444 GAAATATATCGAATCCGGACAGTTAAT 57.633 33.333 6.12 0.0 36.24 1.40
1376 2815 8.361889 TGAAATATATCGAATCCGGACAGTTAA 58.638 33.333 6.12 0.0 36.24 2.01
1424 2863 2.237893 ACCCAACCTAAACCTATCCACG 59.762 50.000 0.00 0.0 0.00 4.94
1431 2870 2.414612 TCACTGACCCAACCTAAACCT 58.585 47.619 0.00 0.0 0.00 3.50
1432 2871 2.943036 TCACTGACCCAACCTAAACC 57.057 50.000 0.00 0.0 0.00 3.27
1433 2872 4.003648 CAGATCACTGACCCAACCTAAAC 58.996 47.826 0.00 0.0 46.03 2.01
1434 2873 3.559171 GCAGATCACTGACCCAACCTAAA 60.559 47.826 0.00 0.0 46.03 1.85
1435 2874 2.027192 GCAGATCACTGACCCAACCTAA 60.027 50.000 0.00 0.0 46.03 2.69
1436 2875 1.555075 GCAGATCACTGACCCAACCTA 59.445 52.381 0.00 0.0 46.03 3.08
1437 2876 0.326264 GCAGATCACTGACCCAACCT 59.674 55.000 0.00 0.0 46.03 3.50
1438 2877 1.021390 CGCAGATCACTGACCCAACC 61.021 60.000 0.00 0.0 46.03 3.77
1439 2878 1.639298 GCGCAGATCACTGACCCAAC 61.639 60.000 0.30 0.0 46.03 3.77
1440 2879 1.375908 GCGCAGATCACTGACCCAA 60.376 57.895 0.30 0.0 46.03 4.12
1441 2880 2.265739 GCGCAGATCACTGACCCA 59.734 61.111 0.30 0.0 46.03 4.51
1442 2881 2.512515 GGCGCAGATCACTGACCC 60.513 66.667 10.83 0.0 46.03 4.46
1443 2882 2.887568 CGGCGCAGATCACTGACC 60.888 66.667 10.83 0.0 46.03 4.02
1444 2883 2.887568 CCGGCGCAGATCACTGAC 60.888 66.667 10.83 0.0 46.03 3.51
1445 2884 3.381983 ACCGGCGCAGATCACTGA 61.382 61.111 10.83 0.0 46.03 3.41
2042 3527 6.610075 AATGCTACAACCCTTGATGAAAAT 57.390 33.333 0.00 0.0 0.00 1.82


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

AutoCloner maintained by Alex Coulton.