Multiple sequence alignment - TraesCS4A01G268400

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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 TraesCS4A01G268400 chr4A 100.000 2665 0 0 1 2665 580732116 580729452 0.000000e+00 4922.0
1 TraesCS4A01G268400 chr4A 78.529 503 86 15 646 1137 163351460 163350969 7.160000e-81 311.0
2 TraesCS4A01G268400 chr4D 92.077 2739 98 38 1 2665 21772970 21770277 0.000000e+00 3746.0
3 TraesCS4A01G268400 chr4D 77.891 1176 200 39 7 1137 312917413 312918573 0.000000e+00 676.0
4 TraesCS4A01G268400 chr4D 77.806 1167 199 37 18 1137 312937498 312938651 0.000000e+00 665.0
5 TraesCS4A01G268400 chr4B 90.873 2016 108 25 1 1966 32900812 32902801 0.000000e+00 2634.0
6 TraesCS4A01G268400 chr4B 96.440 955 19 4 1723 2662 32903575 32904529 0.000000e+00 1561.0
7 TraesCS4A01G268400 chr4B 70.933 1211 277 44 1 1166 47616111 47614931 1.610000e-52 217.0
8 TraesCS4A01G268400 chr5D 82.280 1202 160 25 7 1166 400405796 400404606 0.000000e+00 990.0
9 TraesCS4A01G268400 chr5D 76.076 1208 233 33 1 1164 193141432 193142627 1.780000e-161 579.0
10 TraesCS4A01G268400 chr5D 82.383 596 88 13 584 1165 135093048 135093640 1.100000e-138 503.0
11 TraesCS4A01G268400 chr5D 80.142 282 40 13 1178 1449 486244306 486244031 2.090000e-46 196.0
12 TraesCS4A01G268400 chr1A 79.273 1211 193 31 1 1166 334414066 334415263 0.000000e+00 793.0
13 TraesCS4A01G268400 chr7B 75.865 1214 225 41 1 1164 15584235 15583040 8.330000e-155 556.0
14 TraesCS4A01G268400 chr7B 72.063 383 72 26 1191 1553 12956278 12956645 6.110000e-12 82.4
15 TraesCS4A01G268400 chr1D 73.723 1214 254 36 1 1165 142662891 142664088 5.310000e-112 414.0
16 TraesCS4A01G268400 chr1D 90.698 86 6 2 1606 1689 182637220 182637305 2.170000e-21 113.0
17 TraesCS4A01G268400 chr5A 78.149 659 122 14 526 1166 142844694 142845348 1.490000e-107 399.0
18 TraesCS4A01G268400 chr5A 82.886 298 51 0 867 1164 205826626 205826329 4.370000e-68 268.0
19 TraesCS4A01G268400 chr5A 79.277 415 49 26 1166 1553 428967061 428967465 3.400000e-64 255.0
20 TraesCS4A01G268400 chr5A 75.676 296 38 13 1167 1449 26152571 26152845 1.680000e-22 117.0
21 TraesCS4A01G268400 chr5A 76.471 187 26 13 1377 1557 472106204 472106378 4.730000e-13 86.1
22 TraesCS4A01G268400 chr5A 100.000 31 0 0 1524 1554 6461270 6461240 1.030000e-04 58.4
23 TraesCS4A01G268400 chr2A 77.626 657 127 14 526 1164 771491917 771491263 5.380000e-102 381.0
24 TraesCS4A01G268400 chr6D 73.400 1203 221 50 7 1166 18864948 18866094 9.070000e-95 357.0
25 TraesCS4A01G268400 chr1B 79.452 438 77 9 738 1164 137611923 137612358 5.580000e-77 298.0
26 TraesCS4A01G268400 chr1B 91.765 85 4 3 1606 1687 258667936 258668020 6.030000e-22 115.0
27 TraesCS4A01G268400 chr7A 83.566 286 35 8 1168 1443 646553762 646554045 9.470000e-65 257.0
28 TraesCS4A01G268400 chr7A 80.139 287 38 12 1170 1443 648755594 648755874 2.090000e-46 196.0
29 TraesCS4A01G268400 chr7A 84.672 137 15 4 1559 1689 292846863 292846727 5.990000e-27 132.0
30 TraesCS4A01G268400 chr3B 77.751 409 58 19 1165 1551 76456270 76455873 1.240000e-53 220.0
31 TraesCS4A01G268400 chr3D 80.731 301 37 11 1165 1449 48385327 48385032 5.780000e-52 215.0
32 TraesCS4A01G268400 chr3D 84.397 141 19 3 1554 1692 295808591 295808730 4.630000e-28 135.0
33 TraesCS4A01G268400 chrUn 80.822 292 33 10 1175 1449 53926147 53926432 9.670000e-50 207.0
34 TraesCS4A01G268400 chr5B 76.866 402 71 16 1165 1553 597291960 597291568 9.670000e-50 207.0
35 TraesCS4A01G268400 chr5B 76.980 404 55 20 1172 1552 21352649 21353037 2.090000e-46 196.0
36 TraesCS4A01G268400 chr5B 80.233 258 31 9 7 261 228764012 228764252 2.730000e-40 176.0
37 TraesCS4A01G268400 chr2D 80.565 283 39 12 1167 1443 595407406 595407134 1.250000e-48 204.0
38 TraesCS4A01G268400 chr7D 88.333 120 13 1 1558 1676 266893456 266893337 2.770000e-30 143.0
39 TraesCS4A01G268400 chr3A 83.333 144 21 3 1554 1694 595920392 595920535 2.150000e-26 130.0
40 TraesCS4A01G268400 chr6B 87.342 79 6 3 1610 1684 112879927 112879849 1.310000e-13 87.9


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 TraesCS4A01G268400 chr4A 580729452 580732116 2664 True 4922.0 4922 100.0000 1 2665 1 chr4A.!!$R2 2664
1 TraesCS4A01G268400 chr4D 21770277 21772970 2693 True 3746.0 3746 92.0770 1 2665 1 chr4D.!!$R1 2664
2 TraesCS4A01G268400 chr4D 312917413 312918573 1160 False 676.0 676 77.8910 7 1137 1 chr4D.!!$F1 1130
3 TraesCS4A01G268400 chr4D 312937498 312938651 1153 False 665.0 665 77.8060 18 1137 1 chr4D.!!$F2 1119
4 TraesCS4A01G268400 chr4B 32900812 32904529 3717 False 2097.5 2634 93.6565 1 2662 2 chr4B.!!$F1 2661
5 TraesCS4A01G268400 chr4B 47614931 47616111 1180 True 217.0 217 70.9330 1 1166 1 chr4B.!!$R1 1165
6 TraesCS4A01G268400 chr5D 400404606 400405796 1190 True 990.0 990 82.2800 7 1166 1 chr5D.!!$R1 1159
7 TraesCS4A01G268400 chr5D 193141432 193142627 1195 False 579.0 579 76.0760 1 1164 1 chr5D.!!$F2 1163
8 TraesCS4A01G268400 chr5D 135093048 135093640 592 False 503.0 503 82.3830 584 1165 1 chr5D.!!$F1 581
9 TraesCS4A01G268400 chr1A 334414066 334415263 1197 False 793.0 793 79.2730 1 1166 1 chr1A.!!$F1 1165
10 TraesCS4A01G268400 chr7B 15583040 15584235 1195 True 556.0 556 75.8650 1 1164 1 chr7B.!!$R1 1163
11 TraesCS4A01G268400 chr1D 142662891 142664088 1197 False 414.0 414 73.7230 1 1165 1 chr1D.!!$F1 1164
12 TraesCS4A01G268400 chr5A 142844694 142845348 654 False 399.0 399 78.1490 526 1166 1 chr5A.!!$F2 640
13 TraesCS4A01G268400 chr2A 771491263 771491917 654 True 381.0 381 77.6260 526 1164 1 chr2A.!!$R1 638
14 TraesCS4A01G268400 chr6D 18864948 18866094 1146 False 357.0 357 73.4000 7 1166 1 chr6D.!!$F1 1159

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
562 601 0.108585 TTGATTATGCGGGAGAGGCC 59.891 55.0 0.0 0.00 0.0 5.19 F
840 897 0.734889 AATGTGGATGCTGCTTACGC 59.265 50.0 0.0 2.42 0.0 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 1693 0.618968 AGGCTCCTCGAACCAATCCT 60.619 55.000 0.0 0.0 0.0 3.24 R
1781 1913 1.751924 GGGCTTTCTCTCGCTCTCTTA 59.248 52.381 0.0 0.0 0.0 2.10 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
32 33 6.155827 TCCCGAATTGTGCAAATAGAAAAAG 58.844 36.000 0.00 0.00 0.00 2.27
333 340 6.253946 AGGTCAATCCTATTTGAGGTAAGG 57.746 41.667 0.00 0.00 46.10 2.69
334 341 5.731678 AGGTCAATCCTATTTGAGGTAAGGT 59.268 40.000 0.00 0.00 46.10 3.50
335 342 6.056236 GGTCAATCCTATTTGAGGTAAGGTC 58.944 44.000 0.00 0.00 46.76 3.85
336 343 6.126739 GGTCAATCCTATTTGAGGTAAGGTCT 60.127 42.308 0.00 0.00 46.76 3.85
337 344 6.763610 GTCAATCCTATTTGAGGTAAGGTCTG 59.236 42.308 0.00 0.00 46.76 3.51
338 345 5.896073 ATCCTATTTGAGGTAAGGTCTGG 57.104 43.478 0.00 0.00 46.76 3.86
339 346 4.955335 TCCTATTTGAGGTAAGGTCTGGA 58.045 43.478 0.00 0.00 46.76 3.86
340 347 5.347124 TCCTATTTGAGGTAAGGTCTGGAA 58.653 41.667 0.00 0.00 46.76 3.53
341 348 5.788533 TCCTATTTGAGGTAAGGTCTGGAAA 59.211 40.000 0.00 0.00 46.76 3.13
342 349 6.447084 TCCTATTTGAGGTAAGGTCTGGAAAT 59.553 38.462 0.00 0.00 46.76 2.17
418 443 4.738740 GTCGTGTTACGCTTGCTAATAGAT 59.261 41.667 0.00 0.00 42.21 1.98
451 484 1.210234 TGTCCATCATGCTCGAATGGT 59.790 47.619 11.81 0.00 34.23 3.55
460 493 0.537188 GCTCGAATGGTCCAGAGGAA 59.463 55.000 8.33 0.00 31.38 3.36
548 587 9.559958 CGATTAAGAAAGCTTGTGTTATTGATT 57.440 29.630 0.00 0.00 35.56 2.57
562 601 0.108585 TTGATTATGCGGGAGAGGCC 59.891 55.000 0.00 0.00 0.00 5.19
775 829 4.107636 CCCACTCCCCTAATACTACTAGGT 59.892 50.000 0.00 0.00 35.10 3.08
837 894 2.019249 GCTGAATGTGGATGCTGCTTA 58.981 47.619 0.00 0.00 30.86 3.09
840 897 0.734889 AATGTGGATGCTGCTTACGC 59.265 50.000 0.00 2.42 0.00 4.42
845 912 0.938008 GGATGCTGCTTACGCCTTAC 59.062 55.000 0.00 0.00 34.43 2.34
892 959 9.934784 TCAGGGATGATAAAGGAAAATTCATTA 57.065 29.630 0.00 0.00 30.13 1.90
1170 1241 7.471721 CAAATAAAATAGCTCATGAACGGACA 58.528 34.615 0.00 0.00 0.00 4.02
1304 1376 2.606725 TGCTTGCAAAATTTCAACACGG 59.393 40.909 0.00 0.00 0.00 4.94
1363 1435 6.424812 GCTCCAAACATGCTAGTTTTGAAAAT 59.575 34.615 7.17 0.00 39.55 1.82
1402 1474 1.464734 TTGCCACAACTTCCACGAAA 58.535 45.000 0.00 0.00 0.00 3.46
1422 1494 3.581024 ATGTCATTTCGTGCTGCAATT 57.419 38.095 2.77 0.00 0.00 2.32
1423 1495 3.367992 TGTCATTTCGTGCTGCAATTT 57.632 38.095 2.77 0.00 0.00 1.82
1424 1496 3.051327 TGTCATTTCGTGCTGCAATTTG 58.949 40.909 2.77 0.00 0.00 2.32
1425 1497 3.052036 GTCATTTCGTGCTGCAATTTGT 58.948 40.909 2.77 0.00 0.00 2.83
1426 1498 3.490526 GTCATTTCGTGCTGCAATTTGTT 59.509 39.130 2.77 0.00 0.00 2.83
1427 1499 4.679197 GTCATTTCGTGCTGCAATTTGTTA 59.321 37.500 2.77 0.00 0.00 2.41
1428 1500 5.174761 GTCATTTCGTGCTGCAATTTGTTAA 59.825 36.000 2.77 0.00 0.00 2.01
1429 1501 5.750547 TCATTTCGTGCTGCAATTTGTTAAA 59.249 32.000 2.77 0.00 0.00 1.52
1430 1502 5.382573 TTTCGTGCTGCAATTTGTTAAAC 57.617 34.783 2.77 0.00 0.00 2.01
1431 1503 4.033990 TCGTGCTGCAATTTGTTAAACA 57.966 36.364 2.77 0.00 0.00 2.83
1432 1504 4.615949 TCGTGCTGCAATTTGTTAAACAT 58.384 34.783 2.77 0.00 0.00 2.71
1433 1505 5.763088 TCGTGCTGCAATTTGTTAAACATA 58.237 33.333 2.77 0.00 0.00 2.29
1434 1506 5.627367 TCGTGCTGCAATTTGTTAAACATAC 59.373 36.000 2.77 0.00 0.00 2.39
1435 1507 5.400782 CGTGCTGCAATTTGTTAAACATACA 59.599 36.000 2.77 0.00 0.00 2.29
1436 1508 6.074623 CGTGCTGCAATTTGTTAAACATACAA 60.075 34.615 2.77 0.00 33.92 2.41
1437 1509 7.515841 CGTGCTGCAATTTGTTAAACATACAAA 60.516 33.333 2.77 0.00 46.12 2.83
1438 1510 8.119226 GTGCTGCAATTTGTTAAACATACAAAA 58.881 29.630 2.77 0.00 45.46 2.44
1439 1511 8.119226 TGCTGCAATTTGTTAAACATACAAAAC 58.881 29.630 0.00 0.68 45.46 2.43
1440 1512 8.119226 GCTGCAATTTGTTAAACATACAAAACA 58.881 29.630 5.40 4.43 45.46 2.83
1592 1693 5.277825 GTTCGTGAAATGTTCCATGACAAA 58.722 37.500 0.00 0.00 32.47 2.83
1711 1816 8.761575 AAAATCATGTTACCACACATTCATTC 57.238 30.769 0.00 0.00 35.03 2.67
1713 1818 5.320277 TCATGTTACCACACATTCATTCCA 58.680 37.500 0.00 0.00 35.03 3.53
1714 1819 5.951148 TCATGTTACCACACATTCATTCCAT 59.049 36.000 0.00 0.00 35.03 3.41
1715 1820 5.641783 TGTTACCACACATTCATTCCATG 57.358 39.130 0.00 0.00 0.00 3.66
1716 1821 5.320277 TGTTACCACACATTCATTCCATGA 58.680 37.500 0.00 0.00 37.55 3.07
1717 1822 5.415389 TGTTACCACACATTCATTCCATGAG 59.585 40.000 0.00 0.00 40.94 2.90
1781 1913 6.248569 ACGACCATCATATTCCCTTTAACT 57.751 37.500 0.00 0.00 0.00 2.24
1939 3088 5.991328 ATAAGACACAGGTGCGATATTTG 57.009 39.130 0.00 0.00 0.00 2.32
2090 3244 5.127031 TCATCCAGAGAATATGTCAACGACA 59.873 40.000 0.00 0.00 46.90 4.35
2434 3598 3.088532 GGTCCATTTGTTGTAGGCATCA 58.911 45.455 0.00 0.00 0.00 3.07
2647 3811 6.942005 TGGACAGACAACATTGTAATCAGAAT 59.058 34.615 0.00 0.00 42.43 2.40
2662 3826 3.954200 TCAGAATAATGCAGTGCAAGGA 58.046 40.909 23.90 10.68 43.62 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
418 443 6.209192 AGCATGATGGACAAAACTTTCATGTA 59.791 34.615 0.00 0.00 36.89 2.29
494 533 2.858768 ACATCCCCAACTTATCCCACAT 59.141 45.455 0.00 0.00 0.00 3.21
562 601 4.260375 GGCATGAGTAGTAATTCAAGTGCG 60.260 45.833 0.00 0.00 31.55 5.34
621 669 6.238456 CCAAGCAGTTATAGCGATCAATTCAA 60.238 38.462 0.00 0.00 37.01 2.69
775 829 2.092753 GTCTGCTCCATCCTCCATTTCA 60.093 50.000 0.00 0.00 0.00 2.69
811 867 3.441222 CAGCATCCACATTCAGCTTAACA 59.559 43.478 0.00 0.00 32.35 2.41
892 959 9.391006 CCAATCAATCATCCAATTTTCTTCAAT 57.609 29.630 0.00 0.00 0.00 2.57
908 975 3.423749 ACATCAGCACACCAATCAATCA 58.576 40.909 0.00 0.00 0.00 2.57
985 1054 2.320745 ATCATGAGACGATTGCAGCA 57.679 45.000 0.09 0.00 0.00 4.41
1304 1376 3.594603 TGACTTCCTCGAATGTCCTTC 57.405 47.619 0.00 0.00 0.00 3.46
1333 1405 2.283298 CTAGCATGTTTGGAGCATCGT 58.717 47.619 0.00 0.00 34.37 3.73
1363 1435 7.492994 GTGGCAAACAAAAAGTACTCCAAAATA 59.507 33.333 0.00 0.00 0.00 1.40
1402 1474 3.581024 AATTGCAGCACGAAATGACAT 57.419 38.095 0.00 0.00 0.00 3.06
1505 1581 4.551388 TCAAATGCACCACGGTAAAATTC 58.449 39.130 0.00 0.00 0.00 2.17
1514 1590 1.133253 CGAGCTCAAATGCACCACG 59.867 57.895 15.40 0.00 34.99 4.94
1592 1693 0.618968 AGGCTCCTCGAACCAATCCT 60.619 55.000 0.00 0.00 0.00 3.24
1709 1814 6.777580 TGAGTGCTATACTGATACTCATGGAA 59.222 38.462 0.00 0.00 41.82 3.53
1711 1816 6.208402 ACTGAGTGCTATACTGATACTCATGG 59.792 42.308 0.00 0.00 44.54 3.66
1713 1818 8.160765 AGTACTGAGTGCTATACTGATACTCAT 58.839 37.037 0.00 0.00 44.54 2.90
1714 1819 7.442666 CAGTACTGAGTGCTATACTGATACTCA 59.557 40.741 18.45 0.00 44.81 3.41
1715 1820 7.658167 TCAGTACTGAGTGCTATACTGATACTC 59.342 40.741 21.74 0.00 45.32 2.59
1716 1821 7.510407 TCAGTACTGAGTGCTATACTGATACT 58.490 38.462 21.74 0.00 45.32 2.12
1717 1822 7.731882 TCAGTACTGAGTGCTATACTGATAC 57.268 40.000 21.74 0.00 45.32 2.24
1732 1864 7.126061 TCTTTTCTCCTCCATATCAGTACTGA 58.874 38.462 27.07 27.07 44.59 3.41
1735 1867 6.697892 CGTTCTTTTCTCCTCCATATCAGTAC 59.302 42.308 0.00 0.00 0.00 2.73
1781 1913 1.751924 GGGCTTTCTCTCGCTCTCTTA 59.248 52.381 0.00 0.00 0.00 2.10
1939 3088 4.025813 ACAATTTCATTTGCGCTTTGACAC 60.026 37.500 9.73 0.00 0.00 3.67
1978 3129 4.430908 CCCGTCCAGTAGTGTAAGATTTC 58.569 47.826 0.00 0.00 0.00 2.17
2434 3598 3.410631 TTCATGGTACGGACATGTGTT 57.589 42.857 1.15 0.00 44.57 3.32


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

AutoCloner maintained by Alex Coulton.