Multiple sequence alignment - TraesCS7B01G360100

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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 TraesCS7B01G360100 chr7B 100.000 2519 0 0 1 2519 622459957 622462475 0.000000e+00 4652.0
1 TraesCS7B01G360100 chr7B 95.138 617 29 1 1903 2519 461210616 461210001 0.000000e+00 972.0
2 TraesCS7B01G360100 chr7B 86.379 580 68 9 1038 1607 461211304 461210726 7.650000e-175 623.0
3 TraesCS7B01G360100 chr7B 91.250 240 19 2 584 823 655058625 655058388 2.420000e-85 326.0
4 TraesCS7B01G360100 chr7B 77.251 211 29 16 1787 1986 622461664 622461866 3.430000e-19 106.0
5 TraesCS7B01G360100 chr7B 77.251 211 29 16 1708 1910 622461743 622461942 3.430000e-19 106.0
6 TraesCS7B01G360100 chr6A 96.274 832 28 3 1690 2519 480460691 480461521 0.000000e+00 1362.0
7 TraesCS7B01G360100 chr6A 93.886 687 42 0 1021 1707 480459976 480460662 0.000000e+00 1037.0
8 TraesCS7B01G360100 chr6A 90.576 573 53 1 590 1162 480459510 480460081 0.000000e+00 758.0
9 TraesCS7B01G360100 chr6A 77.880 217 27 18 1703 1910 480460784 480460988 5.690000e-22 115.0
10 TraesCS7B01G360100 chr6A 96.429 56 2 0 1855 1910 117401189 117401244 2.670000e-15 93.5
11 TraesCS7B01G360100 chr4A 97.557 655 15 1 1774 2427 500091612 500092266 0.000000e+00 1120.0
12 TraesCS7B01G360100 chr4A 95.197 687 33 0 1021 1707 500090911 500091597 0.000000e+00 1086.0
13 TraesCS7B01G360100 chr4A 91.176 578 49 1 587 1162 500090439 500091016 0.000000e+00 784.0
14 TraesCS7B01G360100 chr4A 77.143 210 31 14 1708 1910 500091625 500091824 3.430000e-19 106.0
15 TraesCS7B01G360100 chr7D 90.618 842 60 7 1021 1854 318858147 318858977 0.000000e+00 1099.0
16 TraesCS7B01G360100 chr7D 95.789 665 27 1 1855 2519 318859021 318859684 0.000000e+00 1072.0
17 TraesCS7B01G360100 chr7D 96.277 591 20 2 1 591 91603128 91603716 0.000000e+00 968.0
18 TraesCS7B01G360100 chr7D 95.770 591 23 2 1 591 184057856 184057268 0.000000e+00 952.0
19 TraesCS7B01G360100 chr7D 88.946 579 39 10 585 1162 318857698 318858252 0.000000e+00 691.0
20 TraesCS7B01G360100 chr7D 94.231 104 2 3 1703 1804 318858905 318859006 3.360000e-34 156.0
21 TraesCS7B01G360100 chr7D 91.667 84 6 1 1903 1986 318858994 318859076 5.690000e-22 115.0
22 TraesCS7B01G360100 chr2D 94.905 687 35 0 1021 1707 177443827 177443141 0.000000e+00 1075.0
23 TraesCS7B01G360100 chr2D 97.453 589 15 0 1931 2519 177443026 177442438 0.000000e+00 1005.0
24 TraesCS7B01G360100 chr2D 95.770 591 23 2 1 591 77502491 77501903 0.000000e+00 952.0
25 TraesCS7B01G360100 chr2D 89.782 597 38 2 589 1162 177444318 177443722 0.000000e+00 743.0
26 TraesCS7B01G360100 chr2D 93.233 266 16 2 590 854 528445945 528446209 8.450000e-105 390.0
27 TraesCS7B01G360100 chr2D 94.488 127 7 0 1787 1913 177443094 177442968 1.980000e-46 196.0
28 TraesCS7B01G360100 chr6D 95.786 617 26 0 1903 2519 87581420 87580804 0.000000e+00 996.0
29 TraesCS7B01G360100 chr6D 95.939 591 22 2 1 591 331601637 331601049 0.000000e+00 957.0
30 TraesCS7B01G360100 chr6D 96.075 586 21 2 6 591 341035170 341035753 0.000000e+00 953.0
31 TraesCS7B01G360100 chr6D 95.601 591 24 2 1 591 111129457 111128869 0.000000e+00 946.0
32 TraesCS7B01G360100 chr6D 85.595 597 74 11 1021 1607 87582124 87581530 1.280000e-172 616.0
33 TraesCS7B01G360100 chr6D 94.915 59 3 0 1855 1913 87581392 87581334 2.670000e-15 93.5
34 TraesCS7B01G360100 chr4D 96.233 584 22 0 1936 2519 498000079 498000662 0.000000e+00 957.0
35 TraesCS7B01G360100 chr4D 93.885 556 30 1 1964 2519 352496892 352497443 0.000000e+00 835.0
36 TraesCS7B01G360100 chr4D 86.519 586 68 9 1032 1607 497999362 497999946 3.540000e-178 634.0
37 TraesCS7B01G360100 chr4D 87.500 512 54 8 1020 1522 352487423 352487933 1.300000e-162 582.0
38 TraesCS7B01G360100 chr4D 87.435 191 23 1 1019 1209 352487386 352487575 4.220000e-53 219.0
39 TraesCS7B01G360100 chr4D 89.831 59 6 0 1632 1690 352487965 352488023 2.690000e-10 76.8
40 TraesCS7B01G360100 chr1D 95.939 591 22 2 1 591 313679285 313678697 0.000000e+00 957.0
41 TraesCS7B01G360100 chr1D 95.770 591 23 2 1 591 104678402 104677814 0.000000e+00 952.0
42 TraesCS7B01G360100 chr1D 95.770 591 23 2 1 591 278862061 278862649 0.000000e+00 952.0
43 TraesCS7B01G360100 chr1D 89.982 549 42 8 1981 2519 194178169 194178714 0.000000e+00 697.0
44 TraesCS7B01G360100 chr1A 90.494 547 42 8 1981 2519 369353036 369352492 0.000000e+00 713.0
45 TraesCS7B01G360100 chr1A 87.123 365 23 3 590 953 216480720 216481061 2.350000e-105 392.0
46 TraesCS7B01G360100 chr1A 95.238 189 9 0 1855 2043 216481266 216481454 1.460000e-77 300.0
47 TraesCS7B01G360100 chr1A 93.000 100 3 3 1707 1804 216481153 216481250 2.610000e-30 143.0
48 TraesCS7B01G360100 chr1A 92.135 89 6 1 1767 1854 216481133 216481221 9.460000e-25 124.0
49 TraesCS7B01G360100 chr5B 90.637 267 22 3 589 854 673670814 673671078 3.990000e-93 351.0
50 TraesCS7B01G360100 chr5A 89.627 241 23 2 590 829 546706909 546706670 3.150000e-79 305.0
51 TraesCS7B01G360100 chr7A 96.429 56 2 0 1855 1910 611912204 611912259 2.670000e-15 93.5
52 TraesCS7B01G360100 chr6B 94.915 59 3 0 1855 1913 6473864 6473806 2.670000e-15 93.5


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 TraesCS7B01G360100 chr7B 622459957 622462475 2518 False 1621.333333 4652 84.834000 1 2519 3 chr7B.!!$F1 2518
1 TraesCS7B01G360100 chr7B 461210001 461211304 1303 True 797.500000 972 90.758500 1038 2519 2 chr7B.!!$R2 1481
2 TraesCS7B01G360100 chr6A 480459510 480461521 2011 False 818.000000 1362 89.654000 590 2519 4 chr6A.!!$F2 1929
3 TraesCS7B01G360100 chr4A 500090439 500092266 1827 False 774.000000 1120 90.268250 587 2427 4 chr4A.!!$F1 1840
4 TraesCS7B01G360100 chr7D 91603128 91603716 588 False 968.000000 968 96.277000 1 591 1 chr7D.!!$F1 590
5 TraesCS7B01G360100 chr7D 184057268 184057856 588 True 952.000000 952 95.770000 1 591 1 chr7D.!!$R1 590
6 TraesCS7B01G360100 chr7D 318857698 318859684 1986 False 626.600000 1099 92.250200 585 2519 5 chr7D.!!$F2 1934
7 TraesCS7B01G360100 chr2D 77501903 77502491 588 True 952.000000 952 95.770000 1 591 1 chr2D.!!$R1 590
8 TraesCS7B01G360100 chr2D 177442438 177444318 1880 True 754.750000 1075 94.157000 589 2519 4 chr2D.!!$R2 1930
9 TraesCS7B01G360100 chr6D 331601049 331601637 588 True 957.000000 957 95.939000 1 591 1 chr6D.!!$R2 590
10 TraesCS7B01G360100 chr6D 341035170 341035753 583 False 953.000000 953 96.075000 6 591 1 chr6D.!!$F1 585
11 TraesCS7B01G360100 chr6D 111128869 111129457 588 True 946.000000 946 95.601000 1 591 1 chr6D.!!$R1 590
12 TraesCS7B01G360100 chr6D 87580804 87582124 1320 True 568.500000 996 92.098667 1021 2519 3 chr6D.!!$R3 1498
13 TraesCS7B01G360100 chr4D 352496892 352497443 551 False 835.000000 835 93.885000 1964 2519 1 chr4D.!!$F1 555
14 TraesCS7B01G360100 chr4D 497999362 498000662 1300 False 795.500000 957 91.376000 1032 2519 2 chr4D.!!$F3 1487
15 TraesCS7B01G360100 chr4D 352487386 352488023 637 False 292.600000 582 88.255333 1019 1690 3 chr4D.!!$F2 671
16 TraesCS7B01G360100 chr1D 313678697 313679285 588 True 957.000000 957 95.939000 1 591 1 chr1D.!!$R2 590
17 TraesCS7B01G360100 chr1D 104677814 104678402 588 True 952.000000 952 95.770000 1 591 1 chr1D.!!$R1 590
18 TraesCS7B01G360100 chr1D 278862061 278862649 588 False 952.000000 952 95.770000 1 591 1 chr1D.!!$F2 590
19 TraesCS7B01G360100 chr1D 194178169 194178714 545 False 697.000000 697 89.982000 1981 2519 1 chr1D.!!$F1 538
20 TraesCS7B01G360100 chr1A 369352492 369353036 544 True 713.000000 713 90.494000 1981 2519 1 chr1A.!!$R1 538
21 TraesCS7B01G360100 chr1A 216480720 216481454 734 False 239.750000 392 91.874000 590 2043 4 chr1A.!!$F1 1453

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
359 360 0.179032 TCCGAAAGCAAAGTCAGCCA 60.179 50.000 0.00 0.0 0.0 4.75 F
840 842 1.440850 CCGCATGCAAGTGTGAACG 60.441 57.895 19.57 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1353 0.608856 AAGCCGGATGAATGCACACA 60.609 50.0 5.05 0.0 0.0 3.72 R
1807 2004 2.031157 GGTGCATTTGAGTGGTGTGTAC 60.031 50.0 0.00 0.0 0.0 2.90 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
33 34 7.061673 CAGTTTCGACAACAAAATTCAGTTTCA 59.938 33.333 11.33 0.00 0.00 2.69
80 81 9.710979 CAGTTAAGTTCAATTTCGACAGTTAAA 57.289 29.630 0.00 0.00 0.00 1.52
93 94 6.800216 TCGACAGTTAAATTTAGTTTCGACG 58.200 36.000 12.99 8.66 0.00 5.12
128 129 5.368145 AGATGAGCGGCTGATGTATTTTAA 58.632 37.500 7.50 0.00 0.00 1.52
204 205 1.873698 TCCACTCAGGTTAACGTTGC 58.126 50.000 11.99 3.49 39.02 4.17
249 250 1.800315 CCTCGGCGTCGTACAACTG 60.800 63.158 10.18 0.00 37.69 3.16
288 289 3.420893 GATGAAACCCTCCATCACAACA 58.579 45.455 0.00 0.00 39.08 3.33
345 346 0.412244 TCTTCTTCCCCTCCTCCGAA 59.588 55.000 0.00 0.00 0.00 4.30
359 360 0.179032 TCCGAAAGCAAAGTCAGCCA 60.179 50.000 0.00 0.00 0.00 4.75
677 678 3.507411 AGGGCGCATCTCCTTAACTATA 58.493 45.455 10.83 0.00 0.00 1.31
720 722 3.737850 ACTGCTTCTGTTTCTCTTCCTG 58.262 45.455 0.00 0.00 0.00 3.86
722 724 3.733337 TGCTTCTGTTTCTCTTCCTGAC 58.267 45.455 0.00 0.00 0.00 3.51
745 747 2.592194 GCATGCAAGTGTGAACATGAG 58.408 47.619 14.21 0.00 41.93 2.90
803 805 3.243737 GCAAGTGGGAATCGGTTTCTTTT 60.244 43.478 0.00 0.00 34.56 2.27
840 842 1.440850 CCGCATGCAAGTGTGAACG 60.441 57.895 19.57 0.00 0.00 3.95
948 976 5.423015 CATTCACAAGTGTAGATAGCAGGT 58.577 41.667 0.00 0.00 0.00 4.00
1101 1165 3.157949 GAGGGGCTAGGCGCTCTT 61.158 66.667 39.59 21.18 39.79 2.85
1245 1353 1.056660 ACCCGACCTCAACTTGTGAT 58.943 50.000 0.00 0.00 35.07 3.06
1345 1453 3.418047 CTCCCGGTACCAAAAGATTTGT 58.582 45.455 13.54 0.00 0.00 2.83
1429 1537 3.602483 ACTACGGTGGCGATAAACAAAT 58.398 40.909 0.00 0.00 0.00 2.32
1480 1588 4.289934 ACCCATCTATCTATCTCGAGGACA 59.710 45.833 13.56 0.00 0.00 4.02
1628 1736 2.644299 TGGAGGGAGTATTGCCATATGG 59.356 50.000 18.07 18.07 37.25 2.74
1640 1748 8.103305 AGTATTGCCATATGGTCTTATGTAAGG 58.897 37.037 22.79 0.00 37.57 2.69
1782 1978 4.280677 CCAAACACAAGGGAGAAAAGCATA 59.719 41.667 0.00 0.00 0.00 3.14
1808 2005 9.705290 AAAATTTTCAGTTCAAAACAGTACAGT 57.295 25.926 0.00 0.00 0.00 3.55
1901 2098 2.191400 AGTAGCACCATCACATGAGGT 58.809 47.619 0.00 0.00 35.65 3.85
2240 2437 6.857964 ACATAACAGCAAGAAAACTCAAATCG 59.142 34.615 0.00 0.00 0.00 3.34
2506 2716 8.721133 TTTATATGAGTCCTAGCATTGTCCTA 57.279 34.615 0.00 0.00 0.00 2.94
2512 2722 5.459505 AGTCCTAGCATTGTCCTACTGTAT 58.540 41.667 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.873164 ACTGTCGAAACTGAACTTAACTGTT 59.127 36.000 0.00 0.00 0.00 3.16
80 81 5.540911 TGAACCTAACCGTCGAAACTAAAT 58.459 37.500 0.00 0.00 0.00 1.40
83 84 3.820467 TCTGAACCTAACCGTCGAAACTA 59.180 43.478 0.00 0.00 0.00 2.24
93 94 2.482142 CCGCTCATCTCTGAACCTAACC 60.482 54.545 0.00 0.00 0.00 2.85
128 129 8.807948 AATACATAACCACAAAGTGCTAGATT 57.192 30.769 0.00 0.00 31.34 2.40
168 169 6.450545 TGAGTGGAATTCTAATAGCATCTCG 58.549 40.000 5.23 0.00 0.00 4.04
204 205 2.924454 GCAGGACAAGAGAGACAACGAG 60.924 54.545 0.00 0.00 0.00 4.18
288 289 1.755008 GAGCCCGAGGTACTGCTCT 60.755 63.158 9.77 0.00 45.21 4.09
345 346 0.179009 TGCTCTGGCTGACTTTGCTT 60.179 50.000 5.26 0.00 39.59 3.91
359 360 0.687757 TTAGCCGGTGAGGATGCTCT 60.688 55.000 15.82 0.00 45.00 4.09
530 531 6.597832 TTGAAAAGGAGGACAAGTGAAAAA 57.402 33.333 0.00 0.00 0.00 1.94
569 570 6.544564 GGAGTACTATCTCTTAGTCTTGTGCT 59.455 42.308 0.00 0.00 40.41 4.40
649 650 0.108585 GGAGATGCGCCCTATTTCCA 59.891 55.000 4.18 0.00 31.11 3.53
677 678 6.772716 CAGTCTAATGCACCCCAATTAATAGT 59.227 38.462 0.00 0.00 0.00 2.12
699 700 3.389329 TCAGGAAGAGAAACAGAAGCAGT 59.611 43.478 0.00 0.00 0.00 4.40
720 722 1.514678 TTCACACTTGCATGCGGGTC 61.515 55.000 14.09 0.00 0.00 4.46
722 724 1.081242 GTTCACACTTGCATGCGGG 60.081 57.895 14.09 10.60 0.00 6.13
745 747 2.017783 CATGCGCTGCACAAACCAC 61.018 57.895 9.73 0.00 43.04 4.16
771 773 3.500448 TTCCCACTTGCACTCATGTTA 57.500 42.857 0.00 0.00 0.00 2.41
840 842 0.945743 TCACACTCGCATGCACTCAC 60.946 55.000 19.57 0.00 0.00 3.51
852 854 3.466712 CATGCACTCATGTTCACACTC 57.533 47.619 0.00 0.00 43.85 3.51
994 1022 3.434309 CATCCTTGGAGTCCATTGGTTT 58.566 45.455 23.24 13.91 31.53 3.27
1101 1165 2.038813 TCCACGGCAGGATCCTCA 59.961 61.111 12.69 0.00 31.23 3.86
1245 1353 0.608856 AAGCCGGATGAATGCACACA 60.609 50.000 5.05 0.00 0.00 3.72
1391 1499 1.308047 AGTCGCACAATCTTTGCACA 58.692 45.000 0.00 0.00 40.20 4.57
1719 1913 2.504175 AGTGGTGTGTAGTGGACTGTTT 59.496 45.455 0.00 0.00 0.00 2.83
1782 1978 9.705290 ACTGTACTGTTTTGAACTGAAAATTTT 57.295 25.926 2.28 2.28 34.78 1.82
1804 2001 2.878406 GCATTTGAGTGGTGTGTACTGT 59.122 45.455 0.00 0.00 0.00 3.55
1807 2004 2.031157 GGTGCATTTGAGTGGTGTGTAC 60.031 50.000 0.00 0.00 0.00 2.90
1808 2005 2.226330 GGTGCATTTGAGTGGTGTGTA 58.774 47.619 0.00 0.00 0.00 2.90
1901 2098 7.768807 ATATTTTGTGGCCTGTTTTGTACTA 57.231 32.000 3.32 0.00 0.00 1.82
2014 2211 5.835911 ATTGATCGAGAATATGTTGAGCG 57.164 39.130 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.