Multiple sequence alignment - TraesCS5B01G311100

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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 TraesCS5B01G311100 chr5B 100.000 2222 0 0 1 2222 492816935 492814714 0.000000e+00 4104
1 TraesCS5B01G311100 chr5B 95.137 658 29 3 1559 2215 492816052 492815397 0.000000e+00 1035
2 TraesCS5B01G311100 chr2A 97.343 1656 42 2 560 2215 38298686 38300339 0.000000e+00 2813
3 TraesCS5B01G311100 chr2A 97.522 565 11 2 1 564 38289418 38289980 0.000000e+00 963
4 TraesCS5B01G311100 chr4A 95.850 1542 59 4 1 1540 603339063 603340601 0.000000e+00 2488
5 TraesCS5B01G311100 chr4A 95.649 1540 53 6 1 1540 553534069 553535594 0.000000e+00 2460
6 TraesCS5B01G311100 chr1A 95.519 1540 67 2 1 1539 22341218 22342756 0.000000e+00 2460
7 TraesCS5B01G311100 chr1A 96.448 366 12 1 1 365 446243447 446243812 8.780000e-169 603
8 TraesCS5B01G311100 chr6A 96.228 1405 48 3 1 1401 224099764 224098361 0.000000e+00 2296
9 TraesCS5B01G311100 chr6A 97.534 365 9 0 1 365 472969194 472969558 1.870000e-175 625
10 TraesCS5B01G311100 chr6A 97.260 365 10 0 1 365 595511814 595511450 8.720000e-174 619
11 TraesCS5B01G311100 chr3A 96.531 1182 37 4 361 1539 11605560 11604380 0.000000e+00 1953
12 TraesCS5B01G311100 chr3A 96.447 1182 38 4 361 1539 11598672 11597492 0.000000e+00 1947
13 TraesCS5B01G311100 chr3A 96.444 1181 40 2 361 1540 684744299 684745478 0.000000e+00 1947
14 TraesCS5B01G311100 chr3A 94.985 658 30 3 1559 2215 11598147 11597492 0.000000e+00 1029
15 TraesCS5B01G311100 chr3A 94.977 657 31 2 1559 2215 27583346 27584000 0.000000e+00 1029
16 TraesCS5B01G311100 chr3A 94.681 658 32 3 1559 2215 11605035 11604380 0.000000e+00 1018
17 TraesCS5B01G311100 chr3A 94.260 662 35 3 1559 2220 82243843 82244501 0.000000e+00 1009
18 TraesCS5B01G311100 chr4B 96.359 1181 41 2 361 1540 604143343 604144522 0.000000e+00 1941
19 TraesCS5B01G311100 chr4B 94.825 657 32 2 1559 2215 604143867 604144521 0.000000e+00 1024
20 TraesCS5B01G311100 chr7A 96.274 1181 43 1 361 1540 71221469 71222649 0.000000e+00 1936
21 TraesCS5B01G311100 chr7A 94.825 657 31 3 1564 2219 677975282 677975936 0.000000e+00 1022
22 TraesCS5B01G311100 chr7A 94.681 658 32 3 1559 2215 71221993 71222648 0.000000e+00 1018
23 TraesCS5B01G311100 chr7A 96.721 366 11 1 1 365 609346613 609346978 1.890000e-170 608


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 TraesCS5B01G311100 chr5B 492814714 492816935 2221 True 2569.5 4104 97.5685 1 2222 2 chr5B.!!$R1 2221
1 TraesCS5B01G311100 chr2A 38298686 38300339 1653 False 2813.0 2813 97.3430 560 2215 1 chr2A.!!$F2 1655
2 TraesCS5B01G311100 chr2A 38289418 38289980 562 False 963.0 963 97.5220 1 564 1 chr2A.!!$F1 563
3 TraesCS5B01G311100 chr4A 603339063 603340601 1538 False 2488.0 2488 95.8500 1 1540 1 chr4A.!!$F2 1539
4 TraesCS5B01G311100 chr4A 553534069 553535594 1525 False 2460.0 2460 95.6490 1 1540 1 chr4A.!!$F1 1539
5 TraesCS5B01G311100 chr1A 22341218 22342756 1538 False 2460.0 2460 95.5190 1 1539 1 chr1A.!!$F1 1538
6 TraesCS5B01G311100 chr6A 224098361 224099764 1403 True 2296.0 2296 96.2280 1 1401 1 chr6A.!!$R1 1400
7 TraesCS5B01G311100 chr3A 684744299 684745478 1179 False 1947.0 1947 96.4440 361 1540 1 chr3A.!!$F3 1179
8 TraesCS5B01G311100 chr3A 11597492 11598672 1180 True 1488.0 1947 95.7160 361 2215 2 chr3A.!!$R1 1854
9 TraesCS5B01G311100 chr3A 11604380 11605560 1180 True 1485.5 1953 95.6060 361 2215 2 chr3A.!!$R2 1854
10 TraesCS5B01G311100 chr3A 27583346 27584000 654 False 1029.0 1029 94.9770 1559 2215 1 chr3A.!!$F1 656
11 TraesCS5B01G311100 chr3A 82243843 82244501 658 False 1009.0 1009 94.2600 1559 2220 1 chr3A.!!$F2 661
12 TraesCS5B01G311100 chr4B 604143343 604144522 1179 False 1482.5 1941 95.5920 361 2215 2 chr4B.!!$F1 1854
13 TraesCS5B01G311100 chr7A 71221469 71222649 1180 False 1477.0 1936 95.4775 361 2215 2 chr7A.!!$F3 1854
14 TraesCS5B01G311100 chr7A 677975282 677975936 654 False 1022.0 1022 94.8250 1564 2219 1 chr7A.!!$F2 655

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
918 925 2.413371 GCTTGAAGCCACACGATTCTTC 60.413 50.0 5.74 0.0 34.48 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1801 0.52847 CGAGGAGCTTCGTCTTCCTT 59.472 55.0 0.0 0.0 35.91 3.36 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
497 503 2.538449 AGTGACGCGTGTAAGTTTTCTG 59.462 45.455 20.70 0.00 0.00 3.02
918 925 2.413371 GCTTGAAGCCACACGATTCTTC 60.413 50.000 5.74 0.00 34.48 2.87
1068 1075 2.182030 GTAGCGGCAGAAGAGCGT 59.818 61.111 1.45 0.00 35.78 5.07
1213 1220 5.370880 AGCTTCCTAATAGGATGGATGTGTT 59.629 40.000 19.76 0.00 45.34 3.32
1472 1480 1.373590 AATCGTGCGGTGGTATTGGC 61.374 55.000 0.00 0.00 0.00 4.52
1487 1495 1.225855 TTGGCTCTGTGTACGCTTTG 58.774 50.000 8.10 0.00 0.00 2.77
1488 1496 0.105964 TGGCTCTGTGTACGCTTTGT 59.894 50.000 8.10 0.00 0.00 2.83
1489 1497 0.512952 GGCTCTGTGTACGCTTTGTG 59.487 55.000 8.10 1.08 0.00 3.33
1490 1498 0.512952 GCTCTGTGTACGCTTTGTGG 59.487 55.000 8.10 0.00 0.00 4.17
1491 1499 1.148310 CTCTGTGTACGCTTTGTGGG 58.852 55.000 8.10 0.00 0.00 4.61
1492 1500 0.250124 TCTGTGTACGCTTTGTGGGG 60.250 55.000 8.10 0.00 0.00 4.96
1493 1501 0.534203 CTGTGTACGCTTTGTGGGGT 60.534 55.000 8.10 0.00 36.39 4.95
1494 1502 0.816018 TGTGTACGCTTTGTGGGGTG 60.816 55.000 8.10 0.00 34.32 4.61
1495 1503 0.816421 GTGTACGCTTTGTGGGGTGT 60.816 55.000 0.00 0.00 34.32 4.16
1496 1504 0.816018 TGTACGCTTTGTGGGGTGTG 60.816 55.000 0.00 0.00 34.32 3.82
1497 1505 1.894756 TACGCTTTGTGGGGTGTGC 60.895 57.895 0.00 0.00 34.32 4.57
1498 1506 2.332312 TACGCTTTGTGGGGTGTGCT 62.332 55.000 0.00 0.00 34.32 4.40
1499 1507 2.489275 CGCTTTGTGGGGTGTGCTT 61.489 57.895 0.00 0.00 0.00 3.91
1500 1508 1.169661 CGCTTTGTGGGGTGTGCTTA 61.170 55.000 0.00 0.00 0.00 3.09
1501 1509 1.036707 GCTTTGTGGGGTGTGCTTAA 58.963 50.000 0.00 0.00 0.00 1.85
1502 1510 1.410882 GCTTTGTGGGGTGTGCTTAAA 59.589 47.619 0.00 0.00 0.00 1.52
1503 1511 2.545742 GCTTTGTGGGGTGTGCTTAAAG 60.546 50.000 0.00 0.00 0.00 1.85
1504 1512 2.738587 TTGTGGGGTGTGCTTAAAGA 57.261 45.000 0.00 0.00 0.00 2.52
1505 1513 2.738587 TGTGGGGTGTGCTTAAAGAA 57.261 45.000 0.00 0.00 0.00 2.52
1506 1514 2.582052 TGTGGGGTGTGCTTAAAGAAG 58.418 47.619 0.00 0.00 35.60 2.85
1507 1515 2.092103 TGTGGGGTGTGCTTAAAGAAGT 60.092 45.455 0.00 0.00 34.90 3.01
1508 1516 2.956333 GTGGGGTGTGCTTAAAGAAGTT 59.044 45.455 0.00 0.00 34.90 2.66
1509 1517 3.004419 GTGGGGTGTGCTTAAAGAAGTTC 59.996 47.826 0.00 0.00 34.90 3.01
1510 1518 3.117663 TGGGGTGTGCTTAAAGAAGTTCT 60.118 43.478 0.00 0.00 34.90 3.01
1511 1519 3.889538 GGGGTGTGCTTAAAGAAGTTCTT 59.110 43.478 12.50 12.50 38.59 2.52
1512 1520 4.261614 GGGGTGTGCTTAAAGAAGTTCTTG 60.262 45.833 18.70 7.86 36.71 3.02
1513 1521 4.338400 GGGTGTGCTTAAAGAAGTTCTTGT 59.662 41.667 18.70 11.18 36.71 3.16
1514 1522 5.163550 GGGTGTGCTTAAAGAAGTTCTTGTT 60.164 40.000 18.70 6.95 36.71 2.83
1515 1523 6.330278 GGTGTGCTTAAAGAAGTTCTTGTTT 58.670 36.000 18.70 6.23 36.71 2.83
1516 1524 6.253512 GGTGTGCTTAAAGAAGTTCTTGTTTG 59.746 38.462 18.70 10.41 36.71 2.93
1517 1525 7.027161 GTGTGCTTAAAGAAGTTCTTGTTTGA 58.973 34.615 18.70 8.15 36.71 2.69
1518 1526 7.702348 GTGTGCTTAAAGAAGTTCTTGTTTGAT 59.298 33.333 18.70 4.81 36.71 2.57
1519 1527 8.250332 TGTGCTTAAAGAAGTTCTTGTTTGATT 58.750 29.630 18.70 4.10 36.71 2.57
1520 1528 8.534778 GTGCTTAAAGAAGTTCTTGTTTGATTG 58.465 33.333 18.70 5.39 36.71 2.67
1521 1529 8.250332 TGCTTAAAGAAGTTCTTGTTTGATTGT 58.750 29.630 18.70 2.69 36.71 2.71
1522 1530 9.087424 GCTTAAAGAAGTTCTTGTTTGATTGTT 57.913 29.630 18.70 1.99 36.71 2.83
1720 1728 3.724478 AGTCCTGGACATGGATGAAGTA 58.276 45.455 27.48 0.00 35.87 2.24
1764 1772 1.202927 CCTGGCCTCCAAACAGAAGAA 60.203 52.381 3.32 0.00 34.21 2.52
1793 1801 0.454600 GATAGCACGTCTGTTCCCGA 59.545 55.000 0.00 0.00 0.00 5.14
1846 1854 1.524621 GGCTAGCGTGCATGATGGT 60.525 57.895 10.93 0.00 34.04 3.55
1851 1859 2.777972 GCGTGCATGATGGTGGCAT 61.778 57.895 10.93 0.00 40.05 4.40
1935 2618 7.772757 GGATGGATTTGTCTGAGATTAGTTTCT 59.227 37.037 0.00 0.00 0.00 2.52
2034 2718 4.879545 GGCGTGGAGTTTCATATTTTCCTA 59.120 41.667 0.00 0.00 0.00 2.94
2124 2808 7.279313 GGCTAACCGTTAGATTGATTTTAGTGA 59.721 37.037 20.39 0.00 35.20 3.41
2167 2851 1.732259 GATCTGTGTACGCTTTGTGGG 59.268 52.381 8.10 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.045223 TCAGTTTCTATACGTATAAAGCGTCTA 57.955 33.333 15.80 0.00 42.85 2.59
621 627 7.287696 TCCCCTTGATTAGAATTGCCTTATTTC 59.712 37.037 0.00 0.00 0.00 2.17
890 897 2.159653 CGTGTGGCTTCAAGCAATCTAC 60.160 50.000 12.53 0.35 44.75 2.59
918 925 5.737290 GGTGCACGTGCTTTACATATTAAAG 59.263 40.000 37.59 0.00 42.66 1.85
931 938 3.399105 TTCAGTGGGTGCACGTGCT 62.399 57.895 37.59 16.84 42.66 4.40
1068 1075 1.072331 GTCTTCTGTTTGGAGGCCAGA 59.928 52.381 5.01 0.00 33.81 3.86
1472 1480 1.148310 CCCACAAAGCGTACACAGAG 58.852 55.000 0.00 0.00 0.00 3.35
1487 1495 2.583143 ACTTCTTTAAGCACACCCCAC 58.417 47.619 0.00 0.00 36.05 4.61
1488 1496 3.117663 AGAACTTCTTTAAGCACACCCCA 60.118 43.478 0.00 0.00 36.05 4.96
1489 1497 3.487372 AGAACTTCTTTAAGCACACCCC 58.513 45.455 0.00 0.00 36.05 4.95
1490 1498 4.338400 ACAAGAACTTCTTTAAGCACACCC 59.662 41.667 0.92 0.00 33.78 4.61
1491 1499 5.500645 ACAAGAACTTCTTTAAGCACACC 57.499 39.130 0.92 0.00 33.78 4.16
1492 1500 7.027161 TCAAACAAGAACTTCTTTAAGCACAC 58.973 34.615 0.92 0.00 33.78 3.82
1493 1501 7.151999 TCAAACAAGAACTTCTTTAAGCACA 57.848 32.000 0.92 0.00 33.78 4.57
1494 1502 8.534778 CAATCAAACAAGAACTTCTTTAAGCAC 58.465 33.333 0.92 0.00 33.78 4.40
1495 1503 8.250332 ACAATCAAACAAGAACTTCTTTAAGCA 58.750 29.630 0.92 0.00 33.78 3.91
1496 1504 8.634475 ACAATCAAACAAGAACTTCTTTAAGC 57.366 30.769 0.92 0.00 33.78 3.09
1551 1559 9.941325 CAAGCAATCTAGAATCTATACTTCCAT 57.059 33.333 0.00 0.00 0.00 3.41
1552 1560 9.147732 TCAAGCAATCTAGAATCTATACTTCCA 57.852 33.333 0.00 0.00 0.00 3.53
1553 1561 9.988815 TTCAAGCAATCTAGAATCTATACTTCC 57.011 33.333 0.00 0.00 0.00 3.46
1555 1563 9.487790 GCTTCAAGCAATCTAGAATCTATACTT 57.512 33.333 3.89 0.00 41.89 2.24
1556 1564 8.093927 GGCTTCAAGCAATCTAGAATCTATACT 58.906 37.037 12.53 0.00 44.75 2.12
1557 1565 7.333174 GGGCTTCAAGCAATCTAGAATCTATAC 59.667 40.741 12.53 0.00 44.75 1.47
1558 1566 7.390027 GGGCTTCAAGCAATCTAGAATCTATA 58.610 38.462 12.53 0.00 44.75 1.31
1559 1567 6.237154 GGGCTTCAAGCAATCTAGAATCTAT 58.763 40.000 12.53 0.00 44.75 1.98
1560 1568 5.455326 GGGGCTTCAAGCAATCTAGAATCTA 60.455 44.000 12.53 0.00 44.75 1.98
1561 1569 4.459330 GGGCTTCAAGCAATCTAGAATCT 58.541 43.478 12.53 0.00 44.75 2.40
1562 1570 3.567585 GGGGCTTCAAGCAATCTAGAATC 59.432 47.826 12.53 0.00 44.75 2.52
1623 1631 0.655733 CGCCGACAAAGTGTCTGTTT 59.344 50.000 6.80 0.00 44.85 2.83
1655 1663 1.862806 GTGTTGACTTCAGCTCCGC 59.137 57.895 0.00 0.00 0.00 5.54
1699 1707 2.555664 ACTTCATCCATGTCCAGGACT 58.444 47.619 20.82 3.50 38.13 3.85
1701 1709 3.706594 GACTACTTCATCCATGTCCAGGA 59.293 47.826 0.00 0.00 39.97 3.86
1764 1772 2.029666 GTGCTATCGCCGCCATCT 59.970 61.111 0.00 0.00 34.43 2.90
1793 1801 0.528470 CGAGGAGCTTCGTCTTCCTT 59.472 55.000 0.00 0.00 35.91 3.36
1908 2591 5.934781 ACTAATCTCAGACAAATCCATCCC 58.065 41.667 0.00 0.00 0.00 3.85
1935 2618 8.985315 AAATCAGAGTGCATTCATCCTATTAA 57.015 30.769 12.16 0.00 0.00 1.40
1946 2629 7.624549 TCTAGGAAACTAAATCAGAGTGCATT 58.375 34.615 0.00 0.00 43.83 3.56
2034 2718 1.521450 CTGACCGTACTCCACCGTGT 61.521 60.000 0.00 0.00 0.00 4.49
2124 2808 1.324740 TACCACCGCACGATTAGGCT 61.325 55.000 0.00 0.00 0.00 4.58
2167 2851 4.338400 ACAAGAACTTCTTTAAGCACACCC 59.662 41.667 0.92 0.00 33.78 4.61


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

AutoCloner maintained by Alex Coulton.