Multiple sequence alignment - TraesCS4A01G214600

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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 TraesCS4A01G214600 chr4A 100.000 2967 0 0 1 2967 512837424 512834458 0.000000e+00 5480.0
1 TraesCS4A01G214600 chr4A 92.993 2740 160 12 256 2967 512729906 512727171 0.000000e+00 3967.0
2 TraesCS4A01G214600 chr4A 84.953 1482 180 28 1 1468 331981138 331982590 0.000000e+00 1461.0
3 TraesCS4A01G214600 chr4A 83.300 1497 198 42 1 1472 214280737 214279268 0.000000e+00 1332.0
4 TraesCS4A01G214600 chr4A 91.826 575 43 4 1414 1986 238450332 238449760 0.000000e+00 798.0
5 TraesCS4A01G214600 chr4A 91.213 569 47 3 1414 1981 238417547 238416981 0.000000e+00 771.0
6 TraesCS4A01G214600 chr4A 90.334 569 52 3 1414 1981 238458956 238458390 0.000000e+00 743.0
7 TraesCS4A01G214600 chr4A 91.403 221 19 0 1968 2188 215520747 215520967 1.340000e-78 303.0
8 TraesCS4A01G214600 chr4A 95.105 143 7 0 2456 2598 260379176 260379318 2.980000e-55 226.0
9 TraesCS4A01G214600 chr4A 94.444 144 8 0 2456 2599 260371326 260371469 3.850000e-54 222.0
10 TraesCS4A01G214600 chr4A 82.906 234 37 3 1237 1468 332016705 332016937 1.080000e-49 207.0
11 TraesCS4A01G214600 chr4A 87.500 160 15 3 2224 2383 526176293 526176139 2.350000e-41 180.0
12 TraesCS4A01G214600 chr2A 88.029 2932 274 55 1 2894 445304670 445301778 0.000000e+00 3398.0
13 TraesCS4A01G214600 chr2A 86.272 1435 164 26 1 1422 577948228 577949642 0.000000e+00 1528.0
14 TraesCS4A01G214600 chr2A 92.500 760 52 5 1539 2296 445270227 445269471 0.000000e+00 1083.0
15 TraesCS4A01G214600 chr2A 87.561 611 43 13 2292 2894 445262873 445262288 0.000000e+00 676.0
16 TraesCS4A01G214600 chr2A 90.948 232 20 1 1414 1645 715675997 715675767 7.990000e-81 311.0
17 TraesCS4A01G214600 chr3A 88.133 1323 132 19 1 1315 194909688 194908383 0.000000e+00 1550.0
18 TraesCS4A01G214600 chr3A 86.867 1363 139 33 1 1349 345639724 345638388 0.000000e+00 1489.0
19 TraesCS4A01G214600 chr3A 84.281 1495 170 45 1 1468 283184217 283185673 0.000000e+00 1399.0
20 TraesCS4A01G214600 chr3A 88.525 305 25 10 2662 2960 350532464 350532164 7.820000e-96 361.0
21 TraesCS4A01G214600 chr3A 83.969 393 44 15 2589 2967 480010063 480009676 2.810000e-95 359.0
22 TraesCS4A01G214600 chr3A 92.655 177 13 0 2181 2357 295406695 295406871 3.800000e-64 255.0
23 TraesCS4A01G214600 chr3A 91.111 180 14 2 2021 2200 451852188 451852011 2.950000e-60 243.0
24 TraesCS4A01G214600 chr3A 90.000 180 16 2 2021 2200 451861718 451861541 6.400000e-57 231.0
25 TraesCS4A01G214600 chr3A 94.355 124 6 1 2403 2525 295447839 295447962 3.900000e-44 189.0
26 TraesCS4A01G214600 chr3A 91.791 134 10 1 2391 2523 295406858 295406991 5.050000e-43 185.0
27 TraesCS4A01G214600 chr3A 92.523 107 7 1 2267 2373 675286961 675287066 5.120000e-33 152.0
28 TraesCS4A01G214600 chr3A 81.437 167 22 9 2807 2967 323536210 323536047 8.630000e-26 128.0
29 TraesCS4A01G214600 chr5D 86.617 1345 137 31 1 1328 118226286 118224968 0.000000e+00 1447.0
30 TraesCS4A01G214600 chr5D 76.000 275 50 16 2699 2964 506355109 506355376 8.630000e-26 128.0
31 TraesCS4A01G214600 chr3D 86.503 1341 141 30 1 1328 479639357 479638044 0.000000e+00 1437.0
32 TraesCS4A01G214600 chr3D 86.438 1342 141 31 1 1328 479761988 479763302 0.000000e+00 1432.0
33 TraesCS4A01G214600 chr6A 86.103 1360 154 28 1 1349 257446480 257445145 0.000000e+00 1432.0
34 TraesCS4A01G214600 chr6A 86.218 312 34 9 2662 2967 113835420 113835112 2.200000e-86 329.0
35 TraesCS4A01G214600 chr6A 89.641 251 20 6 2648 2894 345201657 345201409 6.170000e-82 315.0
36 TraesCS4A01G214600 chr6A 90.909 231 19 2 1416 1645 396908935 396908706 2.870000e-80 309.0
37 TraesCS4A01G214600 chr6A 91.960 199 13 3 2003 2200 223635231 223635427 2.910000e-70 276.0
38 TraesCS4A01G214600 chr6A 96.528 144 5 0 2456 2599 396450326 396450469 3.820000e-59 239.0
39 TraesCS4A01G214600 chr6A 95.890 146 6 0 2456 2601 396401124 396401269 1.370000e-58 237.0
40 TraesCS4A01G214600 chr7D 86.486 1332 142 26 1 1314 321151319 321152630 0.000000e+00 1428.0
41 TraesCS4A01G214600 chr7D 95.455 88 4 0 2569 2656 198277564 198277651 1.110000e-29 141.0
42 TraesCS4A01G214600 chr5A 90.614 586 49 6 1618 2200 193666779 193667361 0.000000e+00 773.0
43 TraesCS4A01G214600 chr5A 87.469 407 46 4 1572 1974 362569805 362570210 5.790000e-127 464.0
44 TraesCS4A01G214600 chr5A 89.003 291 20 12 2646 2928 399894549 399894835 1.690000e-92 350.0
45 TraesCS4A01G214600 chr5A 93.878 49 3 0 1968 2016 183811841 183811793 1.140000e-09 75.0
46 TraesCS4A01G214600 chr2D 88.136 413 43 5 1566 1974 233149516 233149106 1.240000e-133 486.0
47 TraesCS4A01G214600 chr7A 89.172 314 26 8 2638 2945 575069327 575069638 4.640000e-103 385.0
48 TraesCS4A01G214600 chr7A 93.966 232 13 1 1414 1645 428310999 428310769 1.690000e-92 350.0
49 TraesCS4A01G214600 chr7A 92.672 232 16 1 1414 1645 428319233 428319003 1.700000e-87 333.0
50 TraesCS4A01G214600 chr7A 92.760 221 15 1 1970 2190 444471939 444472158 4.770000e-83 318.0
51 TraesCS4A01G214600 chr7A 78.592 341 49 20 2568 2902 370761879 370762201 1.390000e-48 204.0
52 TraesCS4A01G214600 chr7A 94.382 89 5 0 2224 2312 89026446 89026534 1.430000e-28 137.0
53 TraesCS4A01G214600 chr7A 95.918 49 2 0 1968 2016 133707554 133707506 2.450000e-11 80.5
54 TraesCS4A01G214600 chr1A 86.174 311 37 6 2662 2967 188557546 188557237 6.130000e-87 331.0


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 TraesCS4A01G214600 chr4A 512834458 512837424 2966 True 5480 5480 100.000 1 2967 1 chr4A.!!$R6 2966
1 TraesCS4A01G214600 chr4A 512727171 512729906 2735 True 3967 3967 92.993 256 2967 1 chr4A.!!$R5 2711
2 TraesCS4A01G214600 chr4A 331981138 331982590 1452 False 1461 1461 84.953 1 1468 1 chr4A.!!$F4 1467
3 TraesCS4A01G214600 chr4A 214279268 214280737 1469 True 1332 1332 83.300 1 1472 1 chr4A.!!$R1 1471
4 TraesCS4A01G214600 chr4A 238449760 238450332 572 True 798 798 91.826 1414 1986 1 chr4A.!!$R3 572
5 TraesCS4A01G214600 chr4A 238416981 238417547 566 True 771 771 91.213 1414 1981 1 chr4A.!!$R2 567
6 TraesCS4A01G214600 chr4A 238458390 238458956 566 True 743 743 90.334 1414 1981 1 chr4A.!!$R4 567
7 TraesCS4A01G214600 chr2A 445301778 445304670 2892 True 3398 3398 88.029 1 2894 1 chr2A.!!$R3 2893
8 TraesCS4A01G214600 chr2A 577948228 577949642 1414 False 1528 1528 86.272 1 1422 1 chr2A.!!$F1 1421
9 TraesCS4A01G214600 chr2A 445269471 445270227 756 True 1083 1083 92.500 1539 2296 1 chr2A.!!$R2 757
10 TraesCS4A01G214600 chr2A 445262288 445262873 585 True 676 676 87.561 2292 2894 1 chr2A.!!$R1 602
11 TraesCS4A01G214600 chr3A 194908383 194909688 1305 True 1550 1550 88.133 1 1315 1 chr3A.!!$R1 1314
12 TraesCS4A01G214600 chr3A 345638388 345639724 1336 True 1489 1489 86.867 1 1349 1 chr3A.!!$R3 1348
13 TraesCS4A01G214600 chr3A 283184217 283185673 1456 False 1399 1399 84.281 1 1468 1 chr3A.!!$F1 1467
14 TraesCS4A01G214600 chr5D 118224968 118226286 1318 True 1447 1447 86.617 1 1328 1 chr5D.!!$R1 1327
15 TraesCS4A01G214600 chr3D 479638044 479639357 1313 True 1437 1437 86.503 1 1328 1 chr3D.!!$R1 1327
16 TraesCS4A01G214600 chr3D 479761988 479763302 1314 False 1432 1432 86.438 1 1328 1 chr3D.!!$F1 1327
17 TraesCS4A01G214600 chr6A 257445145 257446480 1335 True 1432 1432 86.103 1 1349 1 chr6A.!!$R2 1348
18 TraesCS4A01G214600 chr7D 321151319 321152630 1311 False 1428 1428 86.486 1 1314 1 chr7D.!!$F2 1313
19 TraesCS4A01G214600 chr5A 193666779 193667361 582 False 773 773 90.614 1618 2200 1 chr5A.!!$F1 582

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
329 340 1.282157 GGGTTAGAGGCTTGACATGGT 59.718 52.381 0.00 0.0 0.0 3.55 F
1034 1066 0.394352 GGGGCCATGTCAACGAATCT 60.394 55.000 4.39 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1798 0.101759 GTGCCGATGCCTAGTACGAA 59.898 55.0 0.0 0.0 36.33 3.85 R
2238 2314 0.108615 GCTTCTTCTCCGTGCTGCTA 60.109 55.0 0.0 0.0 0.00 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
78 81 3.516300 AGGAACATAACACCGGTATGACA 59.484 43.478 20.21 0.00 0.00 3.58
276 285 2.049156 GGGTTGAGCAAAAGCGGC 60.049 61.111 0.00 0.00 0.00 6.53
329 340 1.282157 GGGTTAGAGGCTTGACATGGT 59.718 52.381 0.00 0.00 0.00 3.55
393 404 6.736123 ACATAGCGATAGAACGAACAACTAT 58.264 36.000 0.00 0.00 39.76 2.12
697 711 4.039124 TGGAGCTCAATATGCAACGAGATA 59.961 41.667 17.19 0.00 0.00 1.98
759 775 6.342906 TCTCGTTTAGGTACCCAACAATATG 58.657 40.000 19.72 7.40 0.00 1.78
860 879 7.233389 TCAAACAATAATTCCGGAAAATCCA 57.767 32.000 23.08 5.00 35.91 3.41
935 959 1.792949 GTTATCACGATGCGGATGACC 59.207 52.381 0.00 0.00 0.00 4.02
943 967 2.124151 GCGGATGACCCCTGCAAT 60.124 61.111 0.00 0.00 0.00 3.56
1034 1066 0.394352 GGGGCCATGTCAACGAATCT 60.394 55.000 4.39 0.00 0.00 2.40
1100 1134 1.067250 TGCCGGTGCAAAAGAAAGC 59.933 52.632 1.90 0.00 46.66 3.51
1101 1136 1.067250 GCCGGTGCAAAAGAAAGCA 59.933 52.632 1.90 0.00 38.65 3.91
1173 1220 1.250154 CCCATGTGTCGGTGGCAAAT 61.250 55.000 0.00 0.00 34.08 2.32
1328 1397 5.159925 GGTTCGAGTTTGTAGAGGAAGTAC 58.840 45.833 0.00 0.00 0.00 2.73
1342 1412 3.946558 AGGAAGTACTTATTCTCGCGACT 59.053 43.478 3.71 0.00 0.00 4.18
1401 1472 2.875080 AGTTGTATTCGCGAACTTGC 57.125 45.000 26.00 13.65 0.00 4.01
1475 1546 0.394352 ATGTTCGGGTCAATGAGGGC 60.394 55.000 0.00 0.00 0.00 5.19
1520 1591 1.007387 GGTCGTCGGGTACACGTTT 60.007 57.895 18.57 0.00 38.45 3.60
1537 1608 7.076842 ACACGTTTACATAGTAGTCGTACAT 57.923 36.000 0.00 0.00 0.00 2.29
1564 1635 8.082852 GTCGATGGTAGTTGTACTCATATCATT 58.917 37.037 0.00 0.00 0.00 2.57
1702 1773 1.250328 AGATGTACACGTTGTCGGGA 58.750 50.000 0.00 0.00 43.98 5.14
1722 1793 3.450578 GATACTTGTCGCATTCCGGTTA 58.549 45.455 0.00 0.00 37.59 2.85
1727 1798 3.462483 TGTCGCATTCCGGTTATGTAT 57.538 42.857 16.78 0.00 37.59 2.29
1881 1956 0.957395 CTGCGGCAGAGGACAAACAT 60.957 55.000 25.33 0.00 32.44 2.71
1931 2007 1.050204 GATGAGGCAGAGATGGAGCT 58.950 55.000 0.00 0.00 0.00 4.09
1964 2040 3.775654 GGCGCAGGGTGCTAGAGT 61.776 66.667 10.83 0.00 42.25 3.24
2016 2092 2.925170 AGCGGGACTTGCAGAGGT 60.925 61.111 0.00 0.00 33.85 3.85
2103 2179 2.049627 GAGATGAAGAGGGCGGCCAT 62.050 60.000 31.59 15.24 0.00 4.40
2238 2314 4.335647 CAAGGCGGTGCTGGAGGT 62.336 66.667 0.00 0.00 0.00 3.85
2324 2400 3.733960 CGGCGTGACTGGAGACGA 61.734 66.667 0.00 0.00 37.81 4.20
2342 2418 4.115199 GCCATGAGGGTCGGGCTT 62.115 66.667 0.00 0.00 43.09 4.35
2530 2607 4.501714 GTGTGGCGGCGGTCGATA 62.502 66.667 6.02 0.00 42.43 2.92
2563 2640 4.925861 GAGAGATGGGGCGCTGGC 62.926 72.222 7.64 0.00 38.90 4.85
2747 2852 3.905591 CTGGGCATGGGGATAATTTTCAT 59.094 43.478 0.00 0.00 0.00 2.57
2903 3010 4.829872 TTACGGAGGAGCCTCAATAAAA 57.170 40.909 17.68 2.69 44.40 1.52
2913 3020 5.501156 GAGCCTCAATAAAAGGAGAAGGAA 58.499 41.667 0.00 0.00 35.83 3.36
2941 3048 1.812571 CAAGGTTTGGGGATCAACTCG 59.187 52.381 0.00 0.00 34.67 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 81 0.250513 CTCTTGCCGCCCTAGTTTCT 59.749 55.000 0.00 0.00 0.00 2.52
124 128 2.177016 ACTTGGTAAAGGTGGAAGGCTT 59.823 45.455 0.00 0.00 37.76 4.35
242 251 1.257743 CCCCTCTTATAGCGCTGCTA 58.742 55.000 22.90 8.93 45.55 3.49
243 252 0.760945 ACCCCTCTTATAGCGCTGCT 60.761 55.000 22.90 10.07 43.41 4.24
244 253 0.106894 AACCCCTCTTATAGCGCTGC 59.893 55.000 22.90 0.00 0.00 5.25
245 254 1.412710 TCAACCCCTCTTATAGCGCTG 59.587 52.381 22.90 2.42 0.00 5.18
246 255 1.689273 CTCAACCCCTCTTATAGCGCT 59.311 52.381 17.26 17.26 0.00 5.92
247 256 1.874320 GCTCAACCCCTCTTATAGCGC 60.874 57.143 0.00 0.00 0.00 5.92
248 257 1.412710 TGCTCAACCCCTCTTATAGCG 59.587 52.381 0.00 0.00 0.00 4.26
276 285 3.430333 AACCGTTGTTTGGCTAAGTTG 57.570 42.857 0.00 0.00 0.00 3.16
393 404 6.873605 TCGAAATCACTTCTATCTTTGCTTGA 59.126 34.615 0.00 0.00 31.20 3.02
697 711 7.857734 TTGATGTGGTGTTTCGTCAATATAT 57.142 32.000 0.00 0.00 35.53 0.86
759 775 4.038642 TCTTGCCATGTTAACCAACCTTTC 59.961 41.667 2.48 0.00 33.41 2.62
860 879 9.146984 GCATCAATTTGCTAAATATGCATATGT 57.853 29.630 19.77 16.72 40.26 2.29
901 922 9.885743 GCATCGTGATAACAACATTTAAAATTC 57.114 29.630 0.00 0.00 0.00 2.17
1034 1066 4.397481 TGTTGTTGTGGCATCATTTTCA 57.603 36.364 0.00 0.00 0.00 2.69
1100 1134 2.261361 TGACACGCTCCCGTCATG 59.739 61.111 0.00 0.00 46.39 3.07
1101 1136 3.298958 ATGACACGCTCCCGTCAT 58.701 55.556 0.00 0.00 46.39 3.06
1173 1220 2.650116 GCTTGCTCGGTCCTCCTCA 61.650 63.158 0.00 0.00 0.00 3.86
1292 1352 0.888619 TCGAACCGCTCTGAGAATGT 59.111 50.000 9.28 0.00 0.00 2.71
1328 1397 7.133513 ACTTTCACTATAGTCGCGAGAATAAG 58.866 38.462 10.24 8.56 44.42 1.73
1342 1412 5.165911 CGAGAACCGCTACTTTCACTATA 57.834 43.478 0.00 0.00 0.00 1.31
1475 1546 2.671396 GACCTATGTTGTGCCAAGTACG 59.329 50.000 0.00 0.00 0.00 3.67
1520 1591 6.146673 CCATCGACATGTACGACTACTATGTA 59.853 42.308 18.26 0.00 42.37 2.29
1537 1608 6.544564 TGATATGAGTACAACTACCATCGACA 59.455 38.462 0.00 0.00 0.00 4.35
1564 1635 2.034939 CGTGTGTACCACTACTTCCACA 59.965 50.000 11.21 0.00 42.20 4.17
1702 1773 2.396590 AACCGGAATGCGACAAGTAT 57.603 45.000 9.46 0.00 0.00 2.12
1722 1793 3.367087 GCCGATGCCTAGTACGAATACAT 60.367 47.826 0.00 0.00 33.30 2.29
1727 1798 0.101759 GTGCCGATGCCTAGTACGAA 59.898 55.000 0.00 0.00 36.33 3.85
1770 1841 1.202818 ACCAGGACCTTTGTTCTGCTC 60.203 52.381 0.00 0.00 45.42 4.26
1914 1989 2.209475 CAGCTCCATCTCTGCCTCA 58.791 57.895 0.00 0.00 0.00 3.86
1959 2035 1.041447 GCGCCAAGTCCCCTACTCTA 61.041 60.000 0.00 0.00 37.50 2.43
1960 2036 2.359967 GCGCCAAGTCCCCTACTCT 61.360 63.158 0.00 0.00 37.50 3.24
2016 2092 1.617018 CGAACAGGGAGGAGGATGCA 61.617 60.000 0.00 0.00 0.00 3.96
2019 2095 1.196012 GTTCGAACAGGGAGGAGGAT 58.804 55.000 23.12 0.00 0.00 3.24
2103 2179 3.781307 CCGGATCCGCAAGTCCCA 61.781 66.667 29.12 0.00 38.24 4.37
2238 2314 0.108615 GCTTCTTCTCCGTGCTGCTA 60.109 55.000 0.00 0.00 0.00 3.49
2450 2527 1.152247 CGATCCCCATCTCCCTCCA 60.152 63.158 0.00 0.00 0.00 3.86
2530 2607 0.705253 TCTCTTCCTCCCCTCGTTCT 59.295 55.000 0.00 0.00 0.00 3.01
2563 2640 1.139853 CCTTCTAACCCTAGCCTGCAG 59.860 57.143 6.78 6.78 0.00 4.41
2599 2676 2.246483 TTGGGCCTAACCAACCAGT 58.754 52.632 4.53 0.00 45.19 4.00
2687 2784 8.898761 ACCTTCTCTTTCTTTTCTTTCTCTTTC 58.101 33.333 0.00 0.00 0.00 2.62
2747 2852 2.222213 CGTGCACATTTTTACGAGTCCA 59.778 45.455 18.64 0.00 38.72 4.02
2831 2936 6.442541 TCCTAGTCCTTGTTCAAACCATTA 57.557 37.500 0.00 0.00 0.00 1.90
2885 2992 2.170607 TCCTTTTATTGAGGCTCCTCCG 59.829 50.000 12.86 0.00 42.09 4.63
2903 3010 0.984230 TGCCGACAATTCCTTCTCCT 59.016 50.000 0.00 0.00 0.00 3.69
2913 3020 1.184970 CCCCAAACCTTGCCGACAAT 61.185 55.000 0.00 0.00 34.61 2.71
2941 3048 0.533951 CCCCATGCCTTTTCTGCTTC 59.466 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.