Multiple sequence alignment - TraesCS1B01G113900

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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 TraesCS1B01G113900 chr1B 100.000 2216 0 0 1 2216 133111204 133113419 0.000000e+00 4093.0
1 TraesCS1B01G113900 chr1B 90.074 1632 111 21 620 2216 426497404 426499019 0.000000e+00 2069.0
2 TraesCS1B01G113900 chr1B 94.363 479 15 7 1 471 426481795 426482269 0.000000e+00 725.0
3 TraesCS1B01G113900 chr1B 96.648 179 3 2 459 634 426482305 426482483 5.980000e-76 294.0
4 TraesCS1B01G113900 chr1B 85.461 282 27 10 1 275 398962200 398961926 4.660000e-72 281.0
5 TraesCS1B01G113900 chr1B 92.053 151 8 2 1 147 133123860 133124010 2.230000e-50 209.0
6 TraesCS1B01G113900 chr1B 81.633 245 12 9 418 651 426497166 426497388 2.930000e-39 172.0
7 TraesCS1B01G113900 chr1B 100.000 33 0 0 439 471 398961751 398961719 6.610000e-06 62.1
8 TraesCS1B01G113900 chr7A 90.294 1803 110 38 459 2216 627045486 627047268 0.000000e+00 2300.0
9 TraesCS1B01G113900 chr7A 91.073 997 77 9 1004 1998 580505038 580506024 0.000000e+00 1338.0
10 TraesCS1B01G113900 chr7A 86.965 1005 72 32 459 1418 627119674 627120664 0.000000e+00 1075.0
11 TraesCS1B01G113900 chr7A 84.080 804 91 27 1433 2215 627235191 627235978 0.000000e+00 741.0
12 TraesCS1B01G113900 chr7A 86.196 326 22 19 381 700 626992703 626993011 4.560000e-87 331.0
13 TraesCS1B01G113900 chr7A 82.058 379 36 21 1 366 627008416 627008775 5.980000e-76 294.0
14 TraesCS1B01G113900 chr7A 85.816 282 21 10 1 275 626992379 626992648 4.660000e-72 281.0
15 TraesCS1B01G113900 chr7A 82.462 325 33 17 421 737 627008770 627009078 1.690000e-66 263.0
16 TraesCS1B01G113900 chr7A 93.038 158 11 0 2059 2216 627009342 627009499 4.760000e-57 231.0
17 TraesCS1B01G113900 chr7A 78.780 377 56 16 1 363 628385609 628385975 4.760000e-57 231.0
18 TraesCS1B01G113900 chr7A 97.222 36 1 0 436 471 627045413 627045448 6.610000e-06 62.1
19 TraesCS1B01G113900 chr5D 92.297 1389 93 7 830 2216 289421519 289422895 0.000000e+00 1960.0
20 TraesCS1B01G113900 chr5D 92.550 953 66 4 938 1888 289727724 289728673 0.000000e+00 1362.0
21 TraesCS1B01G113900 chr5D 86.357 689 74 13 1051 1730 29905314 29904637 0.000000e+00 734.0
22 TraesCS1B01G113900 chr5D 89.683 252 16 4 496 737 289727311 289727562 1.650000e-81 313.0
23 TraesCS1B01G113900 chr5D 82.385 369 36 19 1 363 289355029 289355374 5.980000e-76 294.0
24 TraesCS1B01G113900 chr5D 81.117 376 39 17 1 366 289726888 289727241 2.800000e-69 272.0
25 TraesCS1B01G113900 chr5D 86.561 253 13 8 496 737 289421261 289421503 2.180000e-65 259.0
26 TraesCS1B01G113900 chr5D 80.769 364 38 18 1 354 289420844 289421185 2.820000e-64 255.0
27 TraesCS1B01G113900 chr5D 93.985 133 5 3 1910 2040 289742806 289742937 4.830000e-47 198.0
28 TraesCS1B01G113900 chr7B 85.901 1454 151 43 791 2215 588879002 588880430 0.000000e+00 1500.0
29 TraesCS1B01G113900 chr7B 95.102 245 12 0 794 1038 589734772 589734528 9.600000e-104 387.0
30 TraesCS1B01G113900 chr7B 81.330 391 41 22 1 381 588823195 588823563 2.780000e-74 289.0
31 TraesCS1B01G113900 chr7B 83.090 343 33 11 653 980 588823785 588824117 2.780000e-74 289.0
32 TraesCS1B01G113900 chr7B 80.093 432 43 29 1 417 589735603 589735200 4.660000e-72 281.0
33 TraesCS1B01G113900 chr7B 80.109 367 42 19 1 354 589920219 589919871 6.110000e-61 244.0
34 TraesCS1B01G113900 chr7B 99.206 126 1 0 668 793 589734924 589734799 6.160000e-56 228.0
35 TraesCS1B01G113900 chr7B 97.917 96 2 0 459 554 589696501 589696596 1.360000e-37 167.0
36 TraesCS1B01G113900 chr7B 88.764 89 6 4 791 875 589934764 589934676 3.010000e-19 106.0
37 TraesCS1B01G113900 chr7B 97.143 35 1 0 436 470 589696419 589696453 2.380000e-05 60.2
38 TraesCS1B01G113900 chr6A 90.943 1071 84 9 793 1863 107263802 107262745 0.000000e+00 1428.0
39 TraesCS1B01G113900 chr6A 97.727 44 1 0 309 352 107264372 107264329 2.360000e-10 76.8
40 TraesCS1B01G113900 chr2B 86.957 1081 111 16 649 1723 182134120 182135176 0.000000e+00 1188.0
41 TraesCS1B01G113900 chr2B 86.152 816 92 12 530 1335 127790332 127791136 0.000000e+00 861.0
42 TraesCS1B01G113900 chr2B 91.136 440 26 3 1754 2191 182135174 182135602 3.170000e-163 584.0
43 TraesCS1B01G113900 chr2B 77.156 429 60 25 1 410 182133530 182133939 4.790000e-52 215.0
44 TraesCS1B01G113900 chr2B 100.000 39 0 0 2178 2216 182140525 182140563 3.050000e-09 73.1
45 TraesCS1B01G113900 chr3A 87.236 901 89 12 1098 1998 723440607 723439733 0.000000e+00 1003.0
46 TraesCS1B01G113900 chr3A 79.048 105 14 6 176 274 55501323 55501425 5.110000e-07 65.8
47 TraesCS1B01G113900 chr7D 86.603 418 31 15 1 410 545266731 545267131 2.610000e-119 438.0
48 TraesCS1B01G113900 chr7D 93.976 166 10 0 2051 2216 545268176 545268341 3.650000e-63 252.0
49 TraesCS1B01G113900 chr7D 81.754 285 25 16 1 274 545622351 545622619 1.720000e-51 213.0
50 TraesCS1B01G113900 chr7D 94.792 96 5 0 541 636 545267343 545267438 1.370000e-32 150.0
51 TraesCS1B01G113900 chr7D 88.060 67 5 2 374 440 545267144 545267207 2.360000e-10 76.8
52 TraesCS1B01G113900 chr7D 100.000 33 0 0 439 471 545650306 545650274 6.610000e-06 62.1


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 TraesCS1B01G113900 chr1B 133111204 133113419 2215 False 4093.000000 4093 100.000000 1 2216 1 chr1B.!!$F1 2215
1 TraesCS1B01G113900 chr1B 426497166 426499019 1853 False 1120.500000 2069 85.853500 418 2216 2 chr1B.!!$F4 1798
2 TraesCS1B01G113900 chr1B 426481795 426482483 688 False 509.500000 725 95.505500 1 634 2 chr1B.!!$F3 633
3 TraesCS1B01G113900 chr7A 580505038 580506024 986 False 1338.000000 1338 91.073000 1004 1998 1 chr7A.!!$F1 994
4 TraesCS1B01G113900 chr7A 627045413 627047268 1855 False 1181.050000 2300 93.758000 436 2216 2 chr7A.!!$F7 1780
5 TraesCS1B01G113900 chr7A 627119674 627120664 990 False 1075.000000 1075 86.965000 459 1418 1 chr7A.!!$F2 959
6 TraesCS1B01G113900 chr7A 627235191 627235978 787 False 741.000000 741 84.080000 1433 2215 1 chr7A.!!$F3 782
7 TraesCS1B01G113900 chr7A 626992379 626993011 632 False 306.000000 331 86.006000 1 700 2 chr7A.!!$F5 699
8 TraesCS1B01G113900 chr7A 627008416 627009499 1083 False 262.666667 294 85.852667 1 2216 3 chr7A.!!$F6 2215
9 TraesCS1B01G113900 chr5D 289420844 289422895 2051 False 824.666667 1960 86.542333 1 2216 3 chr5D.!!$F3 2215
10 TraesCS1B01G113900 chr5D 29904637 29905314 677 True 734.000000 734 86.357000 1051 1730 1 chr5D.!!$R1 679
11 TraesCS1B01G113900 chr5D 289726888 289728673 1785 False 649.000000 1362 87.783333 1 1888 3 chr5D.!!$F4 1887
12 TraesCS1B01G113900 chr7B 588879002 588880430 1428 False 1500.000000 1500 85.901000 791 2215 1 chr7B.!!$F1 1424
13 TraesCS1B01G113900 chr7B 589734528 589735603 1075 True 298.666667 387 91.467000 1 1038 3 chr7B.!!$R3 1037
14 TraesCS1B01G113900 chr7B 588823195 588824117 922 False 289.000000 289 82.210000 1 980 2 chr7B.!!$F2 979
15 TraesCS1B01G113900 chr6A 107262745 107264372 1627 True 752.400000 1428 94.335000 309 1863 2 chr6A.!!$R1 1554
16 TraesCS1B01G113900 chr2B 127790332 127791136 804 False 861.000000 861 86.152000 530 1335 1 chr2B.!!$F1 805
17 TraesCS1B01G113900 chr2B 182133530 182135602 2072 False 662.333333 1188 85.083000 1 2191 3 chr2B.!!$F3 2190
18 TraesCS1B01G113900 chr3A 723439733 723440607 874 True 1003.000000 1003 87.236000 1098 1998 1 chr3A.!!$R1 900
19 TraesCS1B01G113900 chr7D 545266731 545268341 1610 False 229.200000 438 90.857750 1 2216 4 chr7D.!!$F2 2215

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
696 1154 0.391661 ACATGCCGGCTAAGTGTCAG 60.392 55.0 29.7 8.82 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 2449 0.610174 TGGTTCAGCTAGAGCACTGG 59.39 55.0 4.01 0.0 45.16 4.0 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
200 211 2.363361 GGACGGGAGGGAGGAAGA 59.637 66.667 0.00 0.00 0.00 2.87
202 213 1.758906 GACGGGAGGGAGGAAGAGG 60.759 68.421 0.00 0.00 0.00 3.69
203 214 2.226149 GACGGGAGGGAGGAAGAGGA 62.226 65.000 0.00 0.00 0.00 3.71
204 215 1.234529 CGGGAGGGAGGAAGAGGAT 59.765 63.158 0.00 0.00 0.00 3.24
277 327 0.680061 AAAGAAGAGACGCGGGAAGT 59.320 50.000 12.47 0.00 0.00 3.01
293 350 4.034048 CGGGAAGTAATTTGAATCCGAGTG 59.966 45.833 0.00 0.00 38.64 3.51
692 1150 1.135689 GTTGAACATGCCGGCTAAGTG 60.136 52.381 29.70 21.71 0.00 3.16
696 1154 0.391661 ACATGCCGGCTAAGTGTCAG 60.392 55.000 29.70 8.82 0.00 3.51
729 1187 4.754114 GCCATGTATGATCTCAGAAACCTC 59.246 45.833 0.00 0.00 0.00 3.85
944 1473 6.258507 GCCCATAATCCTTGCTTACATTTTTG 59.741 38.462 0.00 0.00 0.00 2.44
1020 1593 4.098654 AGAATGATTCGAACTCTGGTCGAT 59.901 41.667 8.54 0.00 35.75 3.59
1028 1601 3.315470 CGAACTCTGGTCGATATTGGAGA 59.685 47.826 0.00 0.00 0.00 3.71
1035 1608 5.363868 TCTGGTCGATATTGGAGATGAACTT 59.636 40.000 0.00 0.00 0.00 2.66
1038 1611 6.097696 TGGTCGATATTGGAGATGAACTTGTA 59.902 38.462 0.00 0.00 0.00 2.41
1091 1664 1.577578 CACGTATGTCGATGTCGTGTG 59.422 52.381 19.27 8.83 44.07 3.82
1093 1666 1.577578 CGTATGTCGATGTCGTGTGTG 59.422 52.381 2.04 0.00 42.86 3.82
1096 1669 1.212455 TGTCGATGTCGTGTGTGTGC 61.212 55.000 2.04 0.00 40.80 4.57
1143 1719 1.596477 CTGCTTAGGCTCCATCGGC 60.596 63.158 0.00 0.00 39.59 5.54
1191 1767 1.170442 CAGCAACATCTGTCATGGCA 58.830 50.000 0.00 0.00 0.00 4.92
1358 1934 6.268566 AGAGTTTTTCAACAAGCTTGACATC 58.731 36.000 32.50 15.38 35.05 3.06
1492 2068 4.327357 CACATCTCGTACAAGATCACCAAC 59.673 45.833 0.00 0.00 33.68 3.77
1493 2069 4.021456 ACATCTCGTACAAGATCACCAACA 60.021 41.667 0.00 0.00 33.68 3.33
1494 2070 4.174411 TCTCGTACAAGATCACCAACAG 57.826 45.455 0.00 0.00 0.00 3.16
1495 2071 3.572682 TCTCGTACAAGATCACCAACAGT 59.427 43.478 0.00 0.00 0.00 3.55
1496 2072 4.763279 TCTCGTACAAGATCACCAACAGTA 59.237 41.667 0.00 0.00 0.00 2.74
1497 2073 5.417894 TCTCGTACAAGATCACCAACAGTAT 59.582 40.000 0.00 0.00 0.00 2.12
1552 2134 4.576463 GCCACTAATAATCACCAGAACCAG 59.424 45.833 0.00 0.00 0.00 4.00
1634 2227 3.634910 GGGCTTTGTAACCACTGAAAAGA 59.365 43.478 0.00 0.00 31.01 2.52
1730 2405 9.975218 TGATATATCAAGTGTAGCTGATACCTA 57.025 33.333 13.12 0.00 33.08 3.08
1774 2449 2.869897 CTCTTCTGCTACGTCTGAACC 58.130 52.381 0.00 0.00 0.00 3.62
1971 2646 1.000938 GCCCTTTTGTTCTGTCTGCAG 60.001 52.381 7.63 7.63 43.87 4.41
1991 2666 8.963725 TCTGCAGAATGTTCAAAGAATGATTAT 58.036 29.630 15.67 0.00 39.31 1.28
1992 2667 9.234384 CTGCAGAATGTTCAAAGAATGATTATC 57.766 33.333 8.42 0.00 39.31 1.75
2080 2782 4.842380 AGAACTAGGGTTGTTGTAGCCTTA 59.158 41.667 0.00 0.00 43.28 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.681778 CACTCCTGCTCCTCCCGT 60.682 66.667 0.00 0.0 0.00 5.28
196 207 1.107114 TCTCACCTCGCATCCTCTTC 58.893 55.000 0.00 0.0 0.00 2.87
197 208 1.786937 ATCTCACCTCGCATCCTCTT 58.213 50.000 0.00 0.0 0.00 2.85
200 211 2.666272 TCTATCTCACCTCGCATCCT 57.334 50.000 0.00 0.0 0.00 3.24
202 213 2.159448 CCGATCTATCTCACCTCGCATC 60.159 54.545 0.00 0.0 0.00 3.91
203 214 1.815613 CCGATCTATCTCACCTCGCAT 59.184 52.381 0.00 0.0 0.00 4.73
204 215 1.239347 CCGATCTATCTCACCTCGCA 58.761 55.000 0.00 0.0 0.00 5.10
277 327 4.868171 CGACTTCCACTCGGATTCAAATTA 59.132 41.667 0.00 0.0 42.41 1.40
293 350 2.266055 CTGCCTGGGACGACTTCC 59.734 66.667 0.00 0.0 45.00 3.46
653 1095 8.777413 TGTTCAACTTCAGAATAATCAGACTTG 58.223 33.333 0.00 0.0 0.00 3.16
692 1150 3.715628 ACATGGCAAACTGAAACTGAC 57.284 42.857 0.00 0.0 0.00 3.51
696 1154 6.127925 TGAGATCATACATGGCAAACTGAAAC 60.128 38.462 0.00 0.0 0.00 2.78
729 1187 5.404096 TGCAAGCTTGATGTAATGATGTTG 58.596 37.500 30.39 0.0 0.00 3.33
912 1440 6.813293 AAGCAAGGATTATGGGCTTTTTAT 57.187 33.333 0.00 0.0 41.67 1.40
1035 1608 6.765989 GCAGGACAATAGACATAACCATTACA 59.234 38.462 0.00 0.0 0.00 2.41
1038 1611 6.006275 AGCAGGACAATAGACATAACCATT 57.994 37.500 0.00 0.0 0.00 3.16
1096 1669 2.516930 GATCCATGGGTGTGCCGG 60.517 66.667 13.02 0.0 34.97 6.13
1143 1719 5.669848 GCTGAACTCTGAAAACATAAGCTCG 60.670 44.000 0.00 0.0 0.00 5.03
1191 1767 3.146182 GATCCAGCAGATCGGCCT 58.854 61.111 14.56 0.0 42.06 5.19
1358 1934 0.308684 TTTTGCGCTGCAGTTCTCTG 59.691 50.000 16.64 0.0 40.61 3.35
1492 2068 0.249073 CGACAAGCGAGGGGATACTG 60.249 60.000 0.00 0.0 44.57 2.74
1493 2069 0.395311 TCGACAAGCGAGGGGATACT 60.395 55.000 0.00 0.0 45.59 2.12
1494 2070 2.112898 TCGACAAGCGAGGGGATAC 58.887 57.895 0.00 0.0 45.59 2.24
1495 2071 4.670199 TCGACAAGCGAGGGGATA 57.330 55.556 0.00 0.0 45.59 2.59
1552 2134 0.961019 TGTGTTCAGCTTTGGCATCC 59.039 50.000 0.00 0.0 41.70 3.51
1634 2227 6.877236 ACAGTTTTGACATCCTTTGTTTCAT 58.123 32.000 0.00 0.0 39.18 2.57
1665 2258 6.402550 CCCACTATTTTGTCTTCAGATGTTCG 60.403 42.308 0.00 0.0 0.00 3.95
1730 2405 0.964358 CGAGTAGGGTCGTGGGAACT 60.964 60.000 0.00 0.0 35.14 3.01
1774 2449 0.610174 TGGTTCAGCTAGAGCACTGG 59.390 55.000 4.01 0.0 45.16 4.00
2122 2826 0.739813 AGCGCGCCTCGTTTAATTCT 60.740 50.000 30.33 0.0 41.07 2.40


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

AutoCloner maintained by Alex Coulton.