Multiple sequence alignment - TraesCS6B01G195100

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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 TraesCS6B01G195100 chr6B 100.000 2267 0 0 1 2267 230755777 230758043 0.000000e+00 4187.0
1 TraesCS6B01G195100 chr6B 98.042 766 14 1 1503 2267 661545156 661544391 0.000000e+00 1330.0
2 TraesCS6B01G195100 chr6B 98.011 704 11 3 1 703 438248124 438247423 0.000000e+00 1219.0
3 TraesCS6B01G195100 chr6B 97.727 704 13 3 1 703 441107085 441106384 0.000000e+00 1208.0
4 TraesCS6B01G195100 chr6B 89.231 65 4 3 1327 1390 40795207 40795269 6.710000e-11 78.7
5 TraesCS6B01G195100 chr5B 96.334 1582 36 7 700 2267 69038265 69036692 0.000000e+00 2580.0
6 TraesCS6B01G195100 chr5B 97.650 766 17 1 1503 2267 621300073 621300838 0.000000e+00 1314.0
7 TraesCS6B01G195100 chr5B 97.724 703 14 2 1 703 476213497 476212797 0.000000e+00 1208.0
8 TraesCS6B01G195100 chr5B 89.231 65 4 3 1327 1390 621300019 621300081 6.710000e-11 78.7
9 TraesCS6B01G195100 chr2B 96.215 1585 40 7 700 2267 750447381 750448962 0.000000e+00 2577.0
10 TraesCS6B01G195100 chr2B 97.718 701 14 2 1 700 426949423 426950122 0.000000e+00 1205.0
11 TraesCS6B01G195100 chr2B 97.585 704 13 4 1 703 518491297 518490597 0.000000e+00 1203.0
12 TraesCS6B01G195100 chr2B 93.554 605 32 6 708 1309 69358868 69358268 0.000000e+00 894.0
13 TraesCS6B01G195100 chr5A 90.729 1564 81 31 700 2223 647573851 647572312 0.000000e+00 2026.0
14 TraesCS6B01G195100 chr4A 89.962 1574 89 34 696 2223 604384279 604385829 0.000000e+00 1967.0
15 TraesCS6B01G195100 chr4A 88.194 847 54 19 700 1523 521957230 521956407 0.000000e+00 968.0
16 TraesCS6B01G195100 chr6A 89.930 1569 90 32 700 2223 162661640 162660095 0.000000e+00 1960.0
17 TraesCS6B01G195100 chr3A 89.494 1580 86 38 700 2223 636526823 636528378 0.000000e+00 1925.0
18 TraesCS6B01G195100 chr2A 89.437 1581 87 43 700 2223 769243459 769241902 0.000000e+00 1921.0
19 TraesCS6B01G195100 chr2A 88.104 1387 85 40 700 2029 115136882 115135519 0.000000e+00 1574.0
20 TraesCS6B01G195100 chr2A 87.910 579 61 8 700 1272 165335368 165334793 0.000000e+00 673.0
21 TraesCS6B01G195100 chr7A 87.959 1578 94 45 700 2223 147913181 147914716 0.000000e+00 1773.0
22 TraesCS6B01G195100 chr4B 87.083 1587 94 47 700 2223 657799640 657801178 0.000000e+00 1692.0
23 TraesCS6B01G195100 chr4B 97.650 766 17 1 1503 2267 654067856 654068621 0.000000e+00 1314.0
24 TraesCS6B01G195100 chr4B 97.443 704 16 2 1 703 347655065 347654363 0.000000e+00 1199.0
25 TraesCS6B01G195100 chr1B 97.911 766 15 1 1503 2267 569433565 569432800 0.000000e+00 1325.0
26 TraesCS6B01G195100 chr1B 97.778 765 17 0 1503 2267 364282018 364282782 0.000000e+00 1319.0
27 TraesCS6B01G195100 chr1B 97.650 766 17 1 1503 2267 94930034 94930799 0.000000e+00 1314.0
28 TraesCS6B01G195100 chr1B 97.523 767 17 2 1503 2267 448521516 448520750 0.000000e+00 1310.0
29 TraesCS6B01G195100 chr1B 97.730 705 13 3 1 703 350343239 350342536 0.000000e+00 1210.0
30 TraesCS6B01G195100 chr1B 97.854 699 12 3 3 700 153705696 153706392 0.000000e+00 1205.0
31 TraesCS6B01G195100 chr1B 94.617 613 26 6 700 1309 460148696 460149304 0.000000e+00 942.0
32 TraesCS6B01G195100 chr1B 94.127 613 28 7 700 1309 544793229 544793836 0.000000e+00 926.0
33 TraesCS6B01G195100 chr1B 88.406 69 5 3 1323 1390 94929976 94930042 1.870000e-11 80.5
34 TraesCS6B01G195100 chr1B 89.231 65 4 3 1327 1390 448521570 448521508 6.710000e-11 78.7
35 TraesCS6B01G195100 chr1B 89.231 65 4 3 1327 1390 460149277 460149339 6.710000e-11 78.7
36 TraesCS6B01G195100 chr1B 89.231 65 4 3 1327 1390 544793809 544793871 6.710000e-11 78.7
37 TraesCS6B01G195100 chr1B 89.231 65 4 3 1327 1390 668663760 668663698 6.710000e-11 78.7
38 TraesCS6B01G195100 chr3B 97.727 704 14 2 1 703 368161032 368160330 0.000000e+00 1210.0
39 TraesCS6B01G195100 chr6D 81.860 1505 171 53 700 2125 24260306 24258825 0.000000e+00 1173.0
40 TraesCS6B01G195100 chr2D 88.621 580 55 9 700 1272 601082289 601082864 0.000000e+00 695.0


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 TraesCS6B01G195100 chr6B 230755777 230758043 2266 False 4187.00 4187 100.0000 1 2267 1 chr6B.!!$F2 2266
1 TraesCS6B01G195100 chr6B 661544391 661545156 765 True 1330.00 1330 98.0420 1503 2267 1 chr6B.!!$R3 764
2 TraesCS6B01G195100 chr6B 438247423 438248124 701 True 1219.00 1219 98.0110 1 703 1 chr6B.!!$R1 702
3 TraesCS6B01G195100 chr6B 441106384 441107085 701 True 1208.00 1208 97.7270 1 703 1 chr6B.!!$R2 702
4 TraesCS6B01G195100 chr5B 69036692 69038265 1573 True 2580.00 2580 96.3340 700 2267 1 chr5B.!!$R1 1567
5 TraesCS6B01G195100 chr5B 476212797 476213497 700 True 1208.00 1208 97.7240 1 703 1 chr5B.!!$R2 702
6 TraesCS6B01G195100 chr5B 621300019 621300838 819 False 696.35 1314 93.4405 1327 2267 2 chr5B.!!$F1 940
7 TraesCS6B01G195100 chr2B 750447381 750448962 1581 False 2577.00 2577 96.2150 700 2267 1 chr2B.!!$F2 1567
8 TraesCS6B01G195100 chr2B 426949423 426950122 699 False 1205.00 1205 97.7180 1 700 1 chr2B.!!$F1 699
9 TraesCS6B01G195100 chr2B 518490597 518491297 700 True 1203.00 1203 97.5850 1 703 1 chr2B.!!$R2 702
10 TraesCS6B01G195100 chr2B 69358268 69358868 600 True 894.00 894 93.5540 708 1309 1 chr2B.!!$R1 601
11 TraesCS6B01G195100 chr5A 647572312 647573851 1539 True 2026.00 2026 90.7290 700 2223 1 chr5A.!!$R1 1523
12 TraesCS6B01G195100 chr4A 604384279 604385829 1550 False 1967.00 1967 89.9620 696 2223 1 chr4A.!!$F1 1527
13 TraesCS6B01G195100 chr4A 521956407 521957230 823 True 968.00 968 88.1940 700 1523 1 chr4A.!!$R1 823
14 TraesCS6B01G195100 chr6A 162660095 162661640 1545 True 1960.00 1960 89.9300 700 2223 1 chr6A.!!$R1 1523
15 TraesCS6B01G195100 chr3A 636526823 636528378 1555 False 1925.00 1925 89.4940 700 2223 1 chr3A.!!$F1 1523
16 TraesCS6B01G195100 chr2A 769241902 769243459 1557 True 1921.00 1921 89.4370 700 2223 1 chr2A.!!$R3 1523
17 TraesCS6B01G195100 chr2A 115135519 115136882 1363 True 1574.00 1574 88.1040 700 2029 1 chr2A.!!$R1 1329
18 TraesCS6B01G195100 chr2A 165334793 165335368 575 True 673.00 673 87.9100 700 1272 1 chr2A.!!$R2 572
19 TraesCS6B01G195100 chr7A 147913181 147914716 1535 False 1773.00 1773 87.9590 700 2223 1 chr7A.!!$F1 1523
20 TraesCS6B01G195100 chr4B 657799640 657801178 1538 False 1692.00 1692 87.0830 700 2223 1 chr4B.!!$F2 1523
21 TraesCS6B01G195100 chr4B 654067856 654068621 765 False 1314.00 1314 97.6500 1503 2267 1 chr4B.!!$F1 764
22 TraesCS6B01G195100 chr4B 347654363 347655065 702 True 1199.00 1199 97.4430 1 703 1 chr4B.!!$R1 702
23 TraesCS6B01G195100 chr1B 569432800 569433565 765 True 1325.00 1325 97.9110 1503 2267 1 chr1B.!!$R2 764
24 TraesCS6B01G195100 chr1B 364282018 364282782 764 False 1319.00 1319 97.7780 1503 2267 1 chr1B.!!$F2 764
25 TraesCS6B01G195100 chr1B 350342536 350343239 703 True 1210.00 1210 97.7300 1 703 1 chr1B.!!$R1 702
26 TraesCS6B01G195100 chr1B 153705696 153706392 696 False 1205.00 1205 97.8540 3 700 1 chr1B.!!$F1 697
27 TraesCS6B01G195100 chr1B 94929976 94930799 823 False 697.25 1314 93.0280 1323 2267 2 chr1B.!!$F3 944
28 TraesCS6B01G195100 chr1B 448520750 448521570 820 True 694.35 1310 93.3770 1327 2267 2 chr1B.!!$R4 940
29 TraesCS6B01G195100 chr1B 460148696 460149339 643 False 510.35 942 91.9240 700 1390 2 chr1B.!!$F4 690
30 TraesCS6B01G195100 chr1B 544793229 544793871 642 False 502.35 926 91.6790 700 1390 2 chr1B.!!$F5 690
31 TraesCS6B01G195100 chr3B 368160330 368161032 702 True 1210.00 1210 97.7270 1 703 1 chr3B.!!$R1 702
32 TraesCS6B01G195100 chr6D 24258825 24260306 1481 True 1173.00 1173 81.8600 700 2125 1 chr6D.!!$R1 1425
33 TraesCS6B01G195100 chr2D 601082289 601082864 575 False 695.00 695 88.6210 700 1272 1 chr2D.!!$F1 572

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
300 303 0.455815 GCACAAATTTAGGGGGAGCG 59.544 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1874 2.60775 GCCTCCACACCCTCCAGA 60.608 66.667 0.0 0.0 0.0 3.86 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
300 303 0.455815 GCACAAATTTAGGGGGAGCG 59.544 55.000 0.00 0.00 0.00 5.03
517 520 1.410004 AGCTCAATGAATGGCATGGG 58.590 50.000 0.00 0.00 37.28 4.00
544 547 4.226427 TGATGAAAGTGGATCCCTCAAG 57.774 45.455 9.90 0.00 0.00 3.02
592 595 4.827304 GCTCAAAAGCTCAAGACTCTTT 57.173 40.909 0.00 0.00 45.55 2.52
698 701 1.271656 GCCTCTTGCTTCATGTTGCTT 59.728 47.619 12.28 0.00 36.87 3.91
702 705 5.100259 CCTCTTGCTTCATGTTGCTTAATG 58.900 41.667 12.28 0.00 0.00 1.90
729 732 9.374838 GCATAAAGCTACTAGTTTACAGGTTAA 57.625 33.333 0.00 0.00 41.15 2.01
874 878 4.662961 TGTCAGCTCACGTGGCCG 62.663 66.667 17.00 10.55 40.83 6.13
948 952 1.632948 GAACCAAAGTAGCCGACGCC 61.633 60.000 0.00 0.00 34.57 5.68
1285 1350 3.877559 TGAGGTAATCACTGCTCAATGG 58.122 45.455 0.00 0.00 31.12 3.16
1286 1351 3.264193 TGAGGTAATCACTGCTCAATGGT 59.736 43.478 0.00 0.00 31.12 3.55
1287 1352 4.263462 TGAGGTAATCACTGCTCAATGGTT 60.263 41.667 0.00 0.00 31.12 3.67
1289 1354 4.018960 AGGTAATCACTGCTCAATGGTTCT 60.019 41.667 0.00 0.00 0.00 3.01
1290 1355 4.095483 GGTAATCACTGCTCAATGGTTCTG 59.905 45.833 0.00 0.00 0.00 3.02
1291 1356 2.936919 TCACTGCTCAATGGTTCTGT 57.063 45.000 0.00 0.00 0.00 3.41
1292 1357 2.497138 TCACTGCTCAATGGTTCTGTG 58.503 47.619 0.00 0.00 0.00 3.66
1293 1358 2.158769 TCACTGCTCAATGGTTCTGTGT 60.159 45.455 0.00 0.00 32.56 3.72
1294 1359 2.225019 CACTGCTCAATGGTTCTGTGTC 59.775 50.000 0.00 0.00 0.00 3.67
1295 1360 2.158769 ACTGCTCAATGGTTCTGTGTCA 60.159 45.455 0.00 0.00 0.00 3.58
1296 1361 3.079578 CTGCTCAATGGTTCTGTGTCAT 58.920 45.455 0.00 0.00 0.00 3.06
1297 1362 3.489355 TGCTCAATGGTTCTGTGTCATT 58.511 40.909 0.00 0.00 0.00 2.57
1298 1363 3.890756 TGCTCAATGGTTCTGTGTCATTT 59.109 39.130 0.00 0.00 0.00 2.32
1299 1364 4.341806 TGCTCAATGGTTCTGTGTCATTTT 59.658 37.500 0.00 0.00 0.00 1.82
1300 1365 4.682860 GCTCAATGGTTCTGTGTCATTTTG 59.317 41.667 0.00 0.00 0.00 2.44
1301 1366 5.737063 GCTCAATGGTTCTGTGTCATTTTGT 60.737 40.000 0.00 0.00 0.00 2.83
1302 1367 6.219417 TCAATGGTTCTGTGTCATTTTGTT 57.781 33.333 0.00 0.00 0.00 2.83
1303 1368 7.340122 TCAATGGTTCTGTGTCATTTTGTTA 57.660 32.000 0.00 0.00 0.00 2.41
1315 1380 9.838339 TGTGTCATTTTGTTAAAATTTATGGGT 57.162 25.926 0.00 0.00 38.97 4.51
1337 1460 6.495872 GGGTCCTTTAGTTAAATTTTCTGGGT 59.504 38.462 0.00 0.00 0.00 4.51
1338 1461 7.375834 GGTCCTTTAGTTAAATTTTCTGGGTG 58.624 38.462 0.00 0.00 0.00 4.61
1340 1464 6.780522 TCCTTTAGTTAAATTTTCTGGGTGCT 59.219 34.615 0.00 0.00 0.00 4.40
1420 1568 6.076981 AGAAAGTGCATTTGGTTAGTTCAG 57.923 37.500 0.00 0.00 0.00 3.02
1691 1874 3.332968 TGTAAAGGAAGAGGGAAAGGGT 58.667 45.455 0.00 0.00 0.00 4.34
2243 2532 4.552674 TGGCATAAGTGATCCTGGTACTA 58.447 43.478 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 18 7.332926 TCAAGCAATCAAAAGCAAACAAGTTTA 59.667 29.630 0.00 0.00 0.00 2.01
300 303 6.668541 TTGAGAAGTATGTGATAAGCAAGC 57.331 37.500 0.00 0.00 0.00 4.01
359 362 9.399797 TGATGACAACATATAGATCAAAGCTTT 57.600 29.630 5.69 5.69 36.82 3.51
517 520 4.077822 GGGATCCACTTTCATCATCCATC 58.922 47.826 15.23 0.00 35.60 3.51
544 547 5.685728 AGCCAATCCTTTGTCCTTAGTATC 58.314 41.667 0.00 0.00 0.00 2.24
698 701 9.542462 CTGTAAACTAGTAGCTTTATGCCATTA 57.458 33.333 0.00 0.00 44.23 1.90
702 705 6.346896 ACCTGTAAACTAGTAGCTTTATGCC 58.653 40.000 0.00 0.00 44.23 4.40
948 952 1.507174 GGAGTGAGAGAACCGGACG 59.493 63.158 9.46 0.00 0.00 4.79
1289 1354 9.838339 ACCCATAAATTTTAACAAAATGACACA 57.162 25.926 0.00 0.00 40.05 3.72
1291 1356 9.495572 GGACCCATAAATTTTAACAAAATGACA 57.504 29.630 0.00 0.00 40.05 3.58
1292 1357 9.719355 AGGACCCATAAATTTTAACAAAATGAC 57.281 29.630 0.00 0.00 40.05 3.06
1310 1375 7.180229 CCCAGAAAATTTAACTAAAGGACCCAT 59.820 37.037 0.00 0.00 0.00 4.00
1315 1380 6.780522 AGCACCCAGAAAATTTAACTAAAGGA 59.219 34.615 0.00 0.00 0.00 3.36
1320 1385 8.261522 ACAAAAAGCACCCAGAAAATTTAACTA 58.738 29.630 0.00 0.00 0.00 2.24
1322 1401 7.315247 ACAAAAAGCACCCAGAAAATTTAAC 57.685 32.000 0.00 0.00 0.00 2.01
1326 1405 5.495640 TGAACAAAAAGCACCCAGAAAATT 58.504 33.333 0.00 0.00 0.00 1.82
1328 1407 4.543590 TGAACAAAAAGCACCCAGAAAA 57.456 36.364 0.00 0.00 0.00 2.29
1329 1408 4.543590 TTGAACAAAAAGCACCCAGAAA 57.456 36.364 0.00 0.00 0.00 2.52
1332 1416 6.279882 TCTAATTTGAACAAAAAGCACCCAG 58.720 36.000 4.12 0.00 33.56 4.45
1334 1457 6.983890 TCTTCTAATTTGAACAAAAAGCACCC 59.016 34.615 4.12 0.00 33.56 4.61
1337 1460 9.651913 ACTTTCTTCTAATTTGAACAAAAAGCA 57.348 25.926 17.50 0.00 33.56 3.91
1338 1461 9.906111 CACTTTCTTCTAATTTGAACAAAAAGC 57.094 29.630 17.50 0.00 33.56 3.51
1340 1464 9.651913 AGCACTTTCTTCTAATTTGAACAAAAA 57.348 25.926 4.12 0.73 33.56 1.94
1691 1874 2.607750 GCCTCCACACCCTCCAGA 60.608 66.667 0.00 0.00 0.00 3.86
1783 1966 3.092301 GGGCTTGGATCAGTAGCTTTTT 58.908 45.455 11.25 0.00 35.30 1.94


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

AutoCloner maintained by Alex Coulton.