Multiple sequence alignment - TraesCS3D01G493500

Loading Multiple Alignment...

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 TraesCS3D01G493500 chr3D 100.000 2648 0 0 1 2648 586750018 586747371 0.000000e+00 4891
1 TraesCS3D01G493500 chr3D 96.869 1054 31 1 1597 2648 586757589 586758642 0.000000e+00 1762
2 TraesCS3D01G493500 chr3D 96.901 968 29 1 1 967 4056591 4057558 0.000000e+00 1620
3 TraesCS3D01G493500 chr3D 96.804 970 31 0 1 970 586756839 586755870 0.000000e+00 1620
4 TraesCS3D01G493500 chr3D 96.801 969 30 1 3 970 75612056 75611088 0.000000e+00 1616
5 TraesCS3D01G493500 chr3D 96.794 967 31 0 1 967 138804962 138805928 0.000000e+00 1615
6 TraesCS3D01G493500 chr6D 96.562 1687 44 9 969 2648 6964622 6962943 0.000000e+00 2782
7 TraesCS3D01G493500 chr6A 93.688 1109 57 8 969 2070 6597606 6596504 0.000000e+00 1648
8 TraesCS3D01G493500 chr6A 93.247 385 19 4 2265 2648 6596503 6596125 6.400000e-156 560
9 TraesCS3D01G493500 chr6A 89.610 231 23 1 2410 2639 615289509 615289739 2.580000e-75 292
10 TraesCS3D01G493500 chr7D 96.807 971 30 1 1 970 612903373 612902403 0.000000e+00 1620
11 TraesCS3D01G493500 chr7D 96.801 969 29 2 1 967 270985651 270986619 0.000000e+00 1616
12 TraesCS3D01G493500 chr7D 85.258 814 97 11 1857 2648 9173583 9172771 0.000000e+00 817
13 TraesCS3D01G493500 chr4D 96.708 972 30 2 1 970 401250886 401249915 0.000000e+00 1616
14 TraesCS3D01G493500 chr4D 96.601 971 32 1 1 970 335789533 335788563 0.000000e+00 1609
15 TraesCS3D01G493500 chr4D 96.601 971 32 1 1 970 335817037 335816067 0.000000e+00 1609
16 TraesCS3D01G493500 chr6B 92.721 893 60 4 969 1856 12594084 12593192 0.000000e+00 1284
17 TraesCS3D01G493500 chr6B 85.694 692 78 6 1978 2648 378281740 378282431 0.000000e+00 710
18 TraesCS3D01G493500 chr2D 86.047 817 88 11 1857 2648 22936669 22935854 0.000000e+00 854
19 TraesCS3D01G493500 chr1B 85.749 814 94 10 1857 2648 104738535 104737722 0.000000e+00 841
20 TraesCS3D01G493500 chr4B 85.153 815 97 11 1857 2648 604295217 604294404 0.000000e+00 813
21 TraesCS3D01G493500 chr2B 84.521 814 103 11 1857 2648 519127696 519126884 0.000000e+00 784
22 TraesCS3D01G493500 chr2B 84.088 817 102 10 1859 2648 796951425 796952240 0.000000e+00 763
23 TraesCS3D01G493500 chr3B 85.738 603 64 10 1857 2437 730718206 730718808 3.740000e-173 617
24 TraesCS3D01G493500 chr5A 84.385 634 65 13 2049 2648 532567794 532568427 2.270000e-165 592


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 TraesCS3D01G493500 chr3D 586747371 586750018 2647 True 4891 4891 100.0000 1 2648 1 chr3D.!!$R2 2647
1 TraesCS3D01G493500 chr3D 586757589 586758642 1053 False 1762 1762 96.8690 1597 2648 1 chr3D.!!$F3 1051
2 TraesCS3D01G493500 chr3D 4056591 4057558 967 False 1620 1620 96.9010 1 967 1 chr3D.!!$F1 966
3 TraesCS3D01G493500 chr3D 586755870 586756839 969 True 1620 1620 96.8040 1 970 1 chr3D.!!$R3 969
4 TraesCS3D01G493500 chr3D 75611088 75612056 968 True 1616 1616 96.8010 3 970 1 chr3D.!!$R1 967
5 TraesCS3D01G493500 chr3D 138804962 138805928 966 False 1615 1615 96.7940 1 967 1 chr3D.!!$F2 966
6 TraesCS3D01G493500 chr6D 6962943 6964622 1679 True 2782 2782 96.5620 969 2648 1 chr6D.!!$R1 1679
7 TraesCS3D01G493500 chr6A 6596125 6597606 1481 True 1104 1648 93.4675 969 2648 2 chr6A.!!$R1 1679
8 TraesCS3D01G493500 chr7D 612902403 612903373 970 True 1620 1620 96.8070 1 970 1 chr7D.!!$R2 969
9 TraesCS3D01G493500 chr7D 270985651 270986619 968 False 1616 1616 96.8010 1 967 1 chr7D.!!$F1 966
10 TraesCS3D01G493500 chr7D 9172771 9173583 812 True 817 817 85.2580 1857 2648 1 chr7D.!!$R1 791
11 TraesCS3D01G493500 chr4D 401249915 401250886 971 True 1616 1616 96.7080 1 970 1 chr4D.!!$R3 969
12 TraesCS3D01G493500 chr4D 335788563 335789533 970 True 1609 1609 96.6010 1 970 1 chr4D.!!$R1 969
13 TraesCS3D01G493500 chr4D 335816067 335817037 970 True 1609 1609 96.6010 1 970 1 chr4D.!!$R2 969
14 TraesCS3D01G493500 chr6B 12593192 12594084 892 True 1284 1284 92.7210 969 1856 1 chr6B.!!$R1 887
15 TraesCS3D01G493500 chr6B 378281740 378282431 691 False 710 710 85.6940 1978 2648 1 chr6B.!!$F1 670
16 TraesCS3D01G493500 chr2D 22935854 22936669 815 True 854 854 86.0470 1857 2648 1 chr2D.!!$R1 791
17 TraesCS3D01G493500 chr1B 104737722 104738535 813 True 841 841 85.7490 1857 2648 1 chr1B.!!$R1 791
18 TraesCS3D01G493500 chr4B 604294404 604295217 813 True 813 813 85.1530 1857 2648 1 chr4B.!!$R1 791
19 TraesCS3D01G493500 chr2B 519126884 519127696 812 True 784 784 84.5210 1857 2648 1 chr2B.!!$R1 791
20 TraesCS3D01G493500 chr2B 796951425 796952240 815 False 763 763 84.0880 1859 2648 1 chr2B.!!$F1 789
21 TraesCS3D01G493500 chr3B 730718206 730718808 602 False 617 617 85.7380 1857 2437 1 chr3B.!!$F1 580
22 TraesCS3D01G493500 chr5A 532567794 532568427 633 False 592 592 84.3850 2049 2648 1 chr5A.!!$F1 599

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
542 544 0.107116 ACGCCAACCCAACAAGTACA 60.107 50.0 0.0 0.0 0.00 2.90 F
1047 1050 0.609151 TCTACGGCAACCAAATCGGA 59.391 50.0 0.0 0.0 38.63 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1429 0.934496 TCAAGGTCTTCAACGCGTTG 59.066 50.000 39.16 39.16 41.71 4.10 R
2027 2049 2.202892 GCTCGCCCGGTTCTTAGG 60.203 66.667 0.00 0.00 0.00 2.69 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
163 165 0.179092 GTTAAGCGTGCGGACCCTAT 60.179 55.000 0.00 0.00 0.00 2.57
214 216 1.203994 ACACCTCTCCGGTCAATAACG 59.796 52.381 0.00 0.00 44.93 3.18
242 244 3.745480 CGGAACCTGGATGCTCATATTGT 60.745 47.826 0.00 0.00 0.00 2.71
335 337 4.196971 GGTATGTTACTTGCCCGAGATTT 58.803 43.478 0.00 0.00 0.00 2.17
387 389 2.858344 CTCGTTACCGGCAAGTCTATTG 59.142 50.000 0.00 0.00 33.95 1.90
542 544 0.107116 ACGCCAACCCAACAAGTACA 60.107 50.000 0.00 0.00 0.00 2.90
577 579 6.156256 ACCTGTAGAGCACCTTTATAATCACA 59.844 38.462 0.00 0.00 0.00 3.58
586 588 6.475207 CACCTTTATAATCACACAGTTACGC 58.525 40.000 0.00 0.00 0.00 4.42
625 627 3.181448 ACACAAAGTGTTCCTCCGGTAAT 60.181 43.478 0.00 0.00 45.08 1.89
698 701 8.335532 AGAAAGCAATAGCAACATACTAAACA 57.664 30.769 0.00 0.00 45.49 2.83
1047 1050 0.609151 TCTACGGCAACCAAATCGGA 59.391 50.000 0.00 0.00 38.63 4.55
1055 1058 3.501950 GCAACCAAATCGGAGAATTGTC 58.498 45.455 0.00 0.00 45.19 3.18
1120 1124 5.538849 TTTTGAATGGTAAGGTCAAACCC 57.461 39.130 0.00 0.00 40.11 4.11
1374 1378 4.662468 TCGCTCTGCAAAGAGAATATCT 57.338 40.909 7.13 0.00 41.27 1.98
1384 1388 5.117584 CAAAGAGAATATCTGCAGCAGACT 58.882 41.667 27.73 19.15 43.63 3.24
1425 1429 2.136196 CTCGCCTCTCCTATGCCGAC 62.136 65.000 0.00 0.00 0.00 4.79
1492 1496 1.836802 ACCATTGCCTCTCTCCTCTTC 59.163 52.381 0.00 0.00 0.00 2.87
1517 1523 6.365247 CGTAGTTAAAGCATACAACTCTGTGT 59.635 38.462 0.00 0.00 36.96 3.72
1539 1545 8.043113 TGTGTTGAGCTTGTTCTGATCTATATT 58.957 33.333 0.00 0.00 0.00 1.28
1562 1568 6.926630 TTACTTTTGCTCCCCAATATTGTT 57.073 33.333 14.25 0.00 32.49 2.83
1563 1569 5.405935 ACTTTTGCTCCCCAATATTGTTC 57.594 39.130 14.25 0.00 32.49 3.18
1631 1642 4.948608 CTCTGAAGCAGACGTTCTACTA 57.051 45.455 0.00 0.00 35.39 1.82
1641 1652 5.393243 GCAGACGTTCTACTATCAGGAAAGT 60.393 44.000 0.00 0.00 35.24 2.66
1738 1749 7.445945 ACAGCAGAGTAGTAGTTTGATTCTTT 58.554 34.615 0.00 0.00 0.00 2.52
1746 1757 8.376270 AGTAGTAGTTTGATTCTTTGCTAGGTT 58.624 33.333 0.00 0.00 0.00 3.50
1760 1771 2.893637 CTAGGTTCCTGTCATTCACGG 58.106 52.381 1.12 0.00 0.00 4.94
1934 1956 3.423539 AGAGCATGAAGTACAAAGCCA 57.576 42.857 0.00 0.00 35.29 4.75
2027 2049 3.005897 TGAAGACAGGTTCAGTAGCACTC 59.994 47.826 0.00 0.00 32.54 3.51
2377 2420 5.132897 GTGAAAGACACCAATGCCATTTA 57.867 39.130 0.00 0.00 43.05 1.40
2467 2524 7.680730 AGATCAGTTTTAAGAGTGCTTTCCTA 58.319 34.615 0.00 0.00 35.56 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 165 6.212589 TCATGTCTACATAGTTCTTGAACCCA 59.787 38.462 9.58 0.00 34.26 4.51
170 172 5.886474 TCTCGGTCATGTCTACATAGTTCTT 59.114 40.000 0.00 0.00 34.26 2.52
214 216 1.202698 AGCATCCAGGTTCCGCTATTC 60.203 52.381 0.00 0.00 0.00 1.75
242 244 7.361457 AGATCTTCGTAGAATATGTGGGAAA 57.639 36.000 0.00 0.00 45.90 3.13
433 435 3.684908 TCACTATAAGCCTTGCAAGCAA 58.315 40.909 21.43 7.33 0.00 3.91
542 544 2.906389 TGCTCTACAGGTGTCTCCAAAT 59.094 45.455 0.00 0.00 39.02 2.32
586 588 2.877786 TGTGTGCTACCAAATGTCACAG 59.122 45.455 0.00 0.00 38.19 3.66
593 595 4.202111 GGAACACTTTGTGTGCTACCAAAT 60.202 41.667 8.51 0.00 46.79 2.32
625 627 4.588951 ACTATGAGATTATGCAACTCCCGA 59.411 41.667 0.00 0.00 0.00 5.14
698 701 2.426024 TCCGTTAGCTTAGCACTCGATT 59.574 45.455 7.07 0.00 0.00 3.34
1047 1050 7.682787 ATATGGAAGACTGTAGGACAATTCT 57.317 36.000 0.00 0.00 0.00 2.40
1055 1058 6.978674 TCAAGGTATATGGAAGACTGTAGG 57.021 41.667 0.00 0.00 0.00 3.18
1120 1124 4.928661 ACTACAGCAAAATCTAACAGCG 57.071 40.909 0.00 0.00 0.00 5.18
1425 1429 0.934496 TCAAGGTCTTCAACGCGTTG 59.066 50.000 39.16 39.16 41.71 4.10
1492 1496 6.365247 ACACAGAGTTGTATGCTTTAACTACG 59.635 38.462 0.00 0.00 35.25 3.51
1539 1545 6.723977 AGAACAATATTGGGGAGCAAAAGTAA 59.276 34.615 19.37 0.00 0.00 2.24
1557 1563 7.677276 GCGTATGCTGAAACATAGAAGAACAAT 60.677 37.037 0.00 0.00 38.39 2.71
1560 1566 5.493735 GCGTATGCTGAAACATAGAAGAAC 58.506 41.667 0.00 0.00 38.39 3.01
1562 1568 3.796717 CGCGTATGCTGAAACATAGAAGA 59.203 43.478 5.20 0.00 39.65 2.87
1563 1569 3.060272 CCGCGTATGCTGAAACATAGAAG 60.060 47.826 4.92 0.00 39.65 2.85
1622 1633 6.030849 CAGTCACTTTCCTGATAGTAGAACG 58.969 44.000 0.00 0.00 0.00 3.95
1631 1642 2.300152 TCGCTTCAGTCACTTTCCTGAT 59.700 45.455 0.00 0.00 37.54 2.90
1641 1652 2.310233 GCACGCTTCGCTTCAGTCA 61.310 57.895 0.00 0.00 0.00 3.41
1738 1749 2.353704 CGTGAATGACAGGAACCTAGCA 60.354 50.000 0.00 0.00 36.62 3.49
1746 1757 1.003839 GGCACCGTGAATGACAGGA 60.004 57.895 1.65 0.00 36.62 3.86
1760 1771 1.221414 GGCAGACGATCATTAGGCAC 58.779 55.000 0.00 0.00 0.00 5.01
1934 1956 5.340891 TCCTCTATACCTTGCCTCTACAT 57.659 43.478 0.00 0.00 0.00 2.29
1950 1972 5.138758 TGCCCTGTAACTTCTATCCTCTA 57.861 43.478 0.00 0.00 0.00 2.43
2027 2049 2.202892 GCTCGCCCGGTTCTTAGG 60.203 66.667 0.00 0.00 0.00 2.69
2377 2420 4.338400 GTGCTCAAAAGTTCCAGGTTTACT 59.662 41.667 0.00 0.00 0.00 2.24
2467 2524 3.902218 AGTGCTATTATGTTGCCACCAT 58.098 40.909 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.