Multiple sequence alignment - TraesCS1B01G271600

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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 TraesCS1B01G271600 chr1B 100.000 2387 0 0 1 2387 477131254 477128868 0.000000e+00 4409
1 TraesCS1B01G271600 chr1B 97.133 907 24 2 1 906 112510873 112509968 0.000000e+00 1530
2 TraesCS1B01G271600 chr2B 97.473 910 19 2 1 906 78793399 78794308 0.000000e+00 1550
3 TraesCS1B01G271600 chr2B 97.023 907 25 2 1 906 548694604 548693699 0.000000e+00 1524
4 TraesCS1B01G271600 chr2B 96.619 917 26 3 1 916 371581188 371580276 0.000000e+00 1517
5 TraesCS1B01G271600 chr2B 92.927 509 33 2 906 1412 382563161 382562654 0.000000e+00 737
6 TraesCS1B01G271600 chr2B 90.874 515 42 4 906 1417 593651116 593650604 0.000000e+00 686
7 TraesCS1B01G271600 chr3B 97.244 907 23 2 1 906 704168227 704167322 0.000000e+00 1535
8 TraesCS1B01G271600 chr3B 92.203 513 37 2 906 1416 456318629 456318118 0.000000e+00 723
9 TraesCS1B01G271600 chr4B 97.244 907 22 3 1 906 394156698 394157602 0.000000e+00 1533
10 TraesCS1B01G271600 chr4B 97.023 907 22 3 1 906 422077591 422076689 0.000000e+00 1520
11 TraesCS1B01G271600 chr4B 92.829 516 34 2 906 1419 232154476 232154990 0.000000e+00 745
12 TraesCS1B01G271600 chr4B 91.845 515 34 6 906 1416 613000316 613000826 0.000000e+00 712
13 TraesCS1B01G271600 chr7B 97.039 912 21 2 1 906 421130455 421129544 0.000000e+00 1530
14 TraesCS1B01G271600 chr7B 92.802 514 34 2 906 1417 609891962 609892474 0.000000e+00 741
15 TraesCS1B01G271600 chr5B 96.824 913 23 4 1 912 382158338 382159245 0.000000e+00 1520
16 TraesCS1B01G271600 chr5B 91.051 514 43 2 906 1417 8878677 8878165 0.000000e+00 691
17 TraesCS1B01G271600 chr1A 93.045 532 33 4 1859 2387 454742663 454742133 0.000000e+00 774
18 TraesCS1B01G271600 chr1A 90.293 443 34 7 1420 1857 454743255 454742817 2.660000e-159 571
19 TraesCS1B01G271600 chr5D 91.159 509 43 1 906 1412 547889322 547888814 0.000000e+00 689
20 TraesCS1B01G271600 chr7D 90.963 509 43 2 906 1412 392552084 392551577 0.000000e+00 682
21 TraesCS1B01G271600 chr1D 90.149 538 31 8 1859 2387 355147115 355146591 0.000000e+00 680
22 TraesCS1B01G271600 chr1D 89.953 428 22 8 1434 1856 355147629 355147218 1.260000e-147 532


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 TraesCS1B01G271600 chr1B 477128868 477131254 2386 True 4409.0 4409 100.000 1 2387 1 chr1B.!!$R2 2386
1 TraesCS1B01G271600 chr1B 112509968 112510873 905 True 1530.0 1530 97.133 1 906 1 chr1B.!!$R1 905
2 TraesCS1B01G271600 chr2B 78793399 78794308 909 False 1550.0 1550 97.473 1 906 1 chr2B.!!$F1 905
3 TraesCS1B01G271600 chr2B 548693699 548694604 905 True 1524.0 1524 97.023 1 906 1 chr2B.!!$R3 905
4 TraesCS1B01G271600 chr2B 371580276 371581188 912 True 1517.0 1517 96.619 1 916 1 chr2B.!!$R1 915
5 TraesCS1B01G271600 chr2B 382562654 382563161 507 True 737.0 737 92.927 906 1412 1 chr2B.!!$R2 506
6 TraesCS1B01G271600 chr2B 593650604 593651116 512 True 686.0 686 90.874 906 1417 1 chr2B.!!$R4 511
7 TraesCS1B01G271600 chr3B 704167322 704168227 905 True 1535.0 1535 97.244 1 906 1 chr3B.!!$R2 905
8 TraesCS1B01G271600 chr3B 456318118 456318629 511 True 723.0 723 92.203 906 1416 1 chr3B.!!$R1 510
9 TraesCS1B01G271600 chr4B 394156698 394157602 904 False 1533.0 1533 97.244 1 906 1 chr4B.!!$F2 905
10 TraesCS1B01G271600 chr4B 422076689 422077591 902 True 1520.0 1520 97.023 1 906 1 chr4B.!!$R1 905
11 TraesCS1B01G271600 chr4B 232154476 232154990 514 False 745.0 745 92.829 906 1419 1 chr4B.!!$F1 513
12 TraesCS1B01G271600 chr4B 613000316 613000826 510 False 712.0 712 91.845 906 1416 1 chr4B.!!$F3 510
13 TraesCS1B01G271600 chr7B 421129544 421130455 911 True 1530.0 1530 97.039 1 906 1 chr7B.!!$R1 905
14 TraesCS1B01G271600 chr7B 609891962 609892474 512 False 741.0 741 92.802 906 1417 1 chr7B.!!$F1 511
15 TraesCS1B01G271600 chr5B 382158338 382159245 907 False 1520.0 1520 96.824 1 912 1 chr5B.!!$F1 911
16 TraesCS1B01G271600 chr5B 8878165 8878677 512 True 691.0 691 91.051 906 1417 1 chr5B.!!$R1 511
17 TraesCS1B01G271600 chr1A 454742133 454743255 1122 True 672.5 774 91.669 1420 2387 2 chr1A.!!$R1 967
18 TraesCS1B01G271600 chr5D 547888814 547889322 508 True 689.0 689 91.159 906 1412 1 chr5D.!!$R1 506
19 TraesCS1B01G271600 chr7D 392551577 392552084 507 True 682.0 682 90.963 906 1412 1 chr7D.!!$R1 506
20 TraesCS1B01G271600 chr1D 355146591 355147629 1038 True 606.0 680 90.051 1434 2387 2 chr1D.!!$R1 953

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
977 993 1.229082 TTAGGAGCACGACAGGGGT 60.229 57.895 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2268 0.112995 TGATGGCTGCTTTTCCCACT 59.887 50.0 0.0 0.0 0.0 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
229 230 2.628178 ACGACTTGAGAGGTCATTGTCA 59.372 45.455 0.00 0.00 36.83 3.58
521 522 3.365472 GGAGGTAAAACCCTACGTCCTA 58.635 50.000 12.88 0.00 46.43 2.94
638 651 6.223852 TGTAATGGTTGTTGTTGTTGTTGTT 58.776 32.000 0.00 0.00 0.00 2.83
658 671 1.493446 TCTACGGACTAGAGCCATCCA 59.507 52.381 0.00 0.00 32.35 3.41
833 847 2.557056 GGAGTCCGGTCGATGATGATAA 59.443 50.000 0.00 0.00 0.00 1.75
977 993 1.229082 TTAGGAGCACGACAGGGGT 60.229 57.895 0.00 0.00 0.00 4.95
1001 1017 3.107601 TCCTCGGAGATGACAAAGGAAT 58.892 45.455 6.58 0.00 33.89 3.01
1026 1042 1.988293 TTGTTGGCGGAAATTGGAGA 58.012 45.000 0.00 0.00 0.00 3.71
1094 1110 2.595386 GTTTGGCTTAATCCTTGCACG 58.405 47.619 0.00 0.00 0.00 5.34
1102 1118 2.463589 AATCCTTGCACGGAAGGCGA 62.464 55.000 16.83 0.00 42.18 5.54
1129 1145 4.570772 GCAATCGCCTTATTGTCAACTCTA 59.429 41.667 0.00 0.00 38.78 2.43
1216 1232 6.533723 AGTGTTCGACGATTGCTATTTTATGA 59.466 34.615 0.00 0.00 0.00 2.15
1335 1352 2.972713 GGATTGGTGTGAGGAGCCTATA 59.027 50.000 0.00 0.00 0.00 1.31
1339 1356 4.741928 TGGTGTGAGGAGCCTATAGATA 57.258 45.455 0.00 0.00 0.00 1.98
1341 1358 4.833380 TGGTGTGAGGAGCCTATAGATAAC 59.167 45.833 0.00 0.00 0.00 1.89
1345 1362 7.093992 GTGTGAGGAGCCTATAGATAACATTC 58.906 42.308 0.00 0.00 0.00 2.67
1449 1466 3.741476 GCGCACAAGGGAGCAAGG 61.741 66.667 0.30 0.00 0.00 3.61
1469 1486 5.552870 AGGAAGCCATCTACATAATTCGT 57.447 39.130 0.00 0.00 0.00 3.85
1552 1570 4.380531 ACCATAGAGATATGCAAACACGG 58.619 43.478 0.00 0.00 0.00 4.94
1569 1589 3.479269 GCGCGCGCCTATGTATCC 61.479 66.667 42.83 12.59 34.56 2.59
1600 1620 1.675801 CTGCTCTCTGAACCCAGCA 59.324 57.895 0.00 0.00 40.20 4.41
1601 1621 0.252479 CTGCTCTCTGAACCCAGCAT 59.748 55.000 0.00 0.00 41.00 3.79
1657 1678 0.247537 CGGTCGCCTTGTTTAATCGC 60.248 55.000 0.00 0.00 0.00 4.58
1658 1679 0.247537 GGTCGCCTTGTTTAATCGCG 60.248 55.000 0.00 0.00 44.00 5.87
1695 1718 1.226379 GCACGATGCATGGTTTCCG 60.226 57.895 12.10 6.64 44.26 4.30
1696 1719 1.429021 CACGATGCATGGTTTCCGG 59.571 57.895 12.10 0.00 0.00 5.14
1697 1720 2.406616 ACGATGCATGGTTTCCGGC 61.407 57.895 8.73 0.00 0.00 6.13
1698 1721 2.807622 GATGCATGGTTTCCGGCC 59.192 61.111 2.46 0.00 0.00 6.13
1703 1726 4.419921 ATGGTTTCCGGCCGGTCC 62.420 66.667 41.57 36.02 36.47 4.46
1728 1752 6.458232 ACTATCGTTAGCTTGATCTTGTCT 57.542 37.500 0.00 0.00 0.00 3.41
1731 1755 3.679980 TCGTTAGCTTGATCTTGTCTTGC 59.320 43.478 0.00 0.00 0.00 4.01
1857 1884 6.426025 GGCCATTACCGGAAACTAATTACTAG 59.574 42.308 9.46 0.00 0.00 2.57
1922 2101 7.633789 ACAGGGCATAATTATACTCCATTAGG 58.366 38.462 0.00 0.00 0.00 2.69
1925 2104 9.346515 AGGGCATAATTATACTCCATTAGGTAA 57.653 33.333 0.00 0.00 35.89 2.85
1959 2138 0.031917 TAGCACCCCACCCGATAAGA 60.032 55.000 0.00 0.00 0.00 2.10
1991 2173 0.246635 AGACGAGATTGTTGGACGGG 59.753 55.000 0.00 0.00 0.00 5.28
2004 2186 3.153270 GACGGGCGGGATTCTCTCC 62.153 68.421 0.00 0.00 44.11 3.71
2048 2232 4.884668 ACCTTAACAAGACTGAATCGGA 57.115 40.909 0.00 0.00 0.00 4.55
2084 2268 0.671472 CTCGTCTGCTTGCATCACCA 60.671 55.000 0.00 0.00 0.00 4.17
2086 2270 0.952497 CGTCTGCTTGCATCACCAGT 60.952 55.000 0.00 0.00 0.00 4.00
2146 2331 3.098555 CCAAAGCGCCCGATACAC 58.901 61.111 2.29 0.00 0.00 2.90
2212 2397 1.078708 AATTGGCCGACGGGTACAG 60.079 57.895 17.22 0.00 34.97 2.74
2235 2420 1.613317 CGCATCCGGGGCATCCTATA 61.613 60.000 17.27 0.00 0.00 1.31
2291 2482 1.678101 GTATCTGTCCTTGGCCATTGC 59.322 52.381 6.09 0.00 0.00 3.56
2310 2501 2.187946 CCGCCCGAATTCAGAGCT 59.812 61.111 6.22 0.00 0.00 4.09
2316 2507 3.471680 GCCCGAATTCAGAGCTATCTTT 58.528 45.455 6.22 0.00 31.64 2.52
2317 2508 3.496507 GCCCGAATTCAGAGCTATCTTTC 59.503 47.826 6.22 0.00 31.64 2.62
2324 2515 7.171167 CGAATTCAGAGCTATCTTTCATCACAT 59.829 37.037 6.22 0.00 31.64 3.21
2328 2519 5.177142 CAGAGCTATCTTTCATCACATTCCG 59.823 44.000 0.00 0.00 31.64 4.30
2334 2525 3.189080 TCTTTCATCACATTCCGTTGCAG 59.811 43.478 0.00 0.00 0.00 4.41
2362 2553 1.630878 CAAGCCCTTCTGGTTAGTCCT 59.369 52.381 0.00 0.00 37.07 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
183 184 1.001293 AGCAATCTTCACGTCAGCTCA 59.999 47.619 0.00 0.00 0.00 4.26
229 230 2.281761 CTGTCCAGCCACCGCTTT 60.282 61.111 0.00 0.00 45.55 3.51
240 241 0.616395 TTCCTATGACCGCCTGTCCA 60.616 55.000 0.00 0.00 43.78 4.02
256 257 0.255033 ATCCGGCTAGGTGGTTTTCC 59.745 55.000 0.00 0.00 41.99 3.13
328 329 2.090550 TGATAGGAAGGATGCCTCCTCA 60.091 50.000 11.33 0.00 46.61 3.86
362 363 3.149196 GGTGCTTTCATTGAGAGTTCCA 58.851 45.455 6.13 0.00 0.00 3.53
543 544 6.440647 TGGTAGATCCACTCTTGTAAACATCT 59.559 38.462 0.00 0.00 41.93 2.90
638 651 1.493446 TGGATGGCTCTAGTCCGTAGA 59.507 52.381 0.00 0.00 36.28 2.59
658 671 5.078256 CCCTCTCCGGTGTCTATATAAACT 58.922 45.833 0.00 0.00 0.00 2.66
727 741 3.903783 GGCAAGCTTGGCGATACA 58.096 55.556 33.68 0.00 43.97 2.29
774 788 1.000145 GATTGAAGACTTCGTCCCGC 59.000 55.000 10.56 0.00 32.18 6.13
797 811 4.500545 CCGGACTCCAAGACTATGAAGATG 60.501 50.000 0.00 0.00 0.00 2.90
833 847 0.243907 CGAACTATCATCGGCCGGAT 59.756 55.000 27.83 22.58 36.68 4.18
985 1001 6.071728 ACAATGAACATTCCTTTGTCATCTCC 60.072 38.462 0.00 0.00 31.16 3.71
1001 1017 3.388308 CAATTTCCGCCAACAATGAACA 58.612 40.909 0.00 0.00 0.00 3.18
1026 1042 6.534475 AATACATCAGCACACCAATCAATT 57.466 33.333 0.00 0.00 0.00 2.32
1060 1076 2.907042 AGCCAAACCTTAGAGCTAGTGT 59.093 45.455 0.00 0.00 30.46 3.55
1094 1110 1.425428 CGATTGCAACTCGCCTTCC 59.575 57.895 0.00 0.00 41.33 3.46
1102 1118 3.081061 TGACAATAAGGCGATTGCAACT 58.919 40.909 0.00 0.00 45.35 3.16
1216 1232 8.691661 AACCTAGTAACAGAAAAATCACATGT 57.308 30.769 0.00 0.00 0.00 3.21
1256 1272 6.148948 TCATGAGCAACCTTATTTGTTTTCG 58.851 36.000 0.00 0.00 0.00 3.46
1339 1356 9.838339 ATCGTCAATAAGGAAAGATAGAATGTT 57.162 29.630 0.00 0.00 0.00 2.71
1341 1358 9.265901 ACATCGTCAATAAGGAAAGATAGAATG 57.734 33.333 0.00 0.00 0.00 2.67
1345 1362 9.751542 AGTTACATCGTCAATAAGGAAAGATAG 57.248 33.333 0.00 0.00 0.00 2.08
1412 1429 3.118157 CGCGCGCTTGTGTTTTTATTTTA 59.882 39.130 30.48 0.00 0.00 1.52
1416 1433 1.334288 GCGCGCGCTTGTGTTTTTAT 61.334 50.000 44.38 0.00 38.26 1.40
1417 1434 2.006587 GCGCGCGCTTGTGTTTTTA 61.007 52.632 44.38 0.00 38.26 1.52
1418 1435 3.319316 GCGCGCGCTTGTGTTTTT 61.319 55.556 44.38 0.00 38.26 1.94
1439 1456 0.918310 AGATGGCTTCCTTGCTCCCT 60.918 55.000 0.00 0.00 0.00 4.20
1442 1459 2.698855 TGTAGATGGCTTCCTTGCTC 57.301 50.000 0.00 0.00 0.00 4.26
1449 1466 6.368791 TGCATACGAATTATGTAGATGGCTTC 59.631 38.462 0.00 0.00 40.02 3.86
1469 1486 3.081061 GCATATTGGACGGGATTGCATA 58.919 45.455 0.00 0.00 0.00 3.14
1552 1570 2.537792 TAGGATACATAGGCGCGCGC 62.538 60.000 44.40 44.40 41.41 6.86
1564 1584 2.288186 GCAGCGGCTTTTCTTAGGATAC 59.712 50.000 0.00 0.00 36.96 2.24
1600 1620 4.965119 TCGTATCAGCGTATCAGCATAT 57.035 40.909 0.00 0.00 40.15 1.78
1601 1621 4.965119 ATCGTATCAGCGTATCAGCATA 57.035 40.909 0.00 0.00 40.15 3.14
1657 1678 1.069703 CATGCACCGGATATTTCTGCG 60.070 52.381 9.46 0.00 0.00 5.18
1658 1679 1.335324 GCATGCACCGGATATTTCTGC 60.335 52.381 14.21 6.16 0.00 4.26
1681 1702 2.807622 GGCCGGAAACCATGCATC 59.192 61.111 5.05 0.00 0.00 3.91
1706 1729 6.292061 GCAAGACAAGATCAAGCTAACGATAG 60.292 42.308 0.00 0.00 46.19 2.08
1911 2090 7.700846 AGATAGCTAGCTTACCTAATGGAGTA 58.299 38.462 24.88 0.00 37.04 2.59
1959 2138 2.228059 TCTCGTCTCGTGGTCTCTTTT 58.772 47.619 0.00 0.00 0.00 2.27
2084 2268 0.112995 TGATGGCTGCTTTTCCCACT 59.887 50.000 0.00 0.00 0.00 4.00
2086 2270 1.619827 CTTTGATGGCTGCTTTTCCCA 59.380 47.619 0.00 0.00 0.00 4.37
2159 2344 1.272147 GGCAGACCCTGAAGATTTGGT 60.272 52.381 0.00 0.00 32.44 3.67
2229 2414 0.536687 CGAGTGCGGGGTCTATAGGA 60.537 60.000 0.00 0.00 0.00 2.94
2232 2417 3.440151 GCGAGTGCGGGGTCTATA 58.560 61.111 0.00 0.00 38.16 1.31
2291 2482 3.264897 CTCTGAATTCGGGCGGCG 61.265 66.667 14.33 0.51 0.00 6.46
2310 2501 4.940654 TGCAACGGAATGTGATGAAAGATA 59.059 37.500 0.00 0.00 0.00 1.98
2316 2507 0.804364 GCTGCAACGGAATGTGATGA 59.196 50.000 0.00 0.00 0.00 2.92
2317 2508 0.522626 TGCTGCAACGGAATGTGATG 59.477 50.000 0.00 0.00 0.00 3.07
2324 2515 0.533978 TGCTACTTGCTGCAACGGAA 60.534 50.000 11.69 0.00 43.37 4.30
2328 2519 0.387750 GGCTTGCTACTTGCTGCAAC 60.388 55.000 11.69 2.22 43.17 4.17
2334 2525 0.807496 CAGAAGGGCTTGCTACTTGC 59.193 55.000 7.54 0.00 43.25 4.01


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

AutoCloner maintained by Alex Coulton.