Multiple sequence alignment - TraesCS1A01G407900

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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 TraesCS1A01G407900 chr1A 100.000 3192 0 0 1 3192 570158374 570161565 0.000000e+00 5895.0
1 TraesCS1A01G407900 chr1A 78.752 593 89 25 1876 2449 570154759 570154185 2.340000e-96 363.0
2 TraesCS1A01G407900 chr1A 82.784 273 41 6 2533 2802 569193348 569193617 4.120000e-59 239.0
3 TraesCS1A01G407900 chr1A 82.784 273 41 6 2533 2802 570182044 570182313 4.120000e-59 239.0
4 TraesCS1A01G407900 chr1A 91.538 130 11 0 445 574 303946672 303946801 2.530000e-41 180.0
5 TraesCS1A01G407900 chr1A 88.372 86 8 2 1757 1841 443137426 443137342 5.630000e-18 102.0
6 TraesCS1A01G407900 chr4A 97.675 2581 40 6 1 2562 624922658 624920079 0.000000e+00 4416.0
7 TraesCS1A01G407900 chr4A 99.258 539 3 1 2596 3133 624920086 624919548 0.000000e+00 972.0
8 TraesCS1A01G407900 chr4A 97.647 170 4 0 576 745 613568694 613568863 3.110000e-75 292.0
9 TraesCS1A01G407900 chr4A 82.313 294 45 7 2533 2823 624874798 624874509 6.840000e-62 248.0
10 TraesCS1A01G407900 chr4A 83.150 273 40 6 2533 2802 624898721 624898452 8.840000e-61 244.0
11 TraesCS1A01G407900 chr4A 92.000 125 10 0 445 569 730792519 730792395 3.270000e-40 176.0
12 TraesCS1A01G407900 chr4A 91.453 117 9 1 746 861 290687502 290687386 3.300000e-35 159.0
13 TraesCS1A01G407900 chr4A 89.888 89 9 0 1753 1841 24824455 24824543 7.240000e-22 115.0
14 TraesCS1A01G407900 chr4A 98.333 60 1 0 3131 3190 624919300 624919241 4.350000e-19 106.0
15 TraesCS1A01G407900 chr5B 93.222 1313 65 7 1839 3133 687739193 687737887 0.000000e+00 1910.0
16 TraesCS1A01G407900 chr5B 94.337 883 41 4 860 1742 687740075 687739202 0.000000e+00 1345.0
17 TraesCS1A01G407900 chr5B 92.222 180 14 0 1876 2055 687746210 687746389 4.090000e-64 255.0
18 TraesCS1A01G407900 chr5B 89.552 134 12 2 445 577 599701585 599701453 5.480000e-38 169.0
19 TraesCS1A01G407900 chr5B 90.698 86 8 0 1756 1841 612685142 612685227 7.240000e-22 115.0
20 TraesCS1A01G407900 chr5D 93.663 1215 57 11 1840 3042 545123985 545122779 0.000000e+00 1799.0
21 TraesCS1A01G407900 chr5D 87.971 557 42 5 1174 1727 545124539 545124005 4.490000e-178 634.0
22 TraesCS1A01G407900 chr5D 76.551 951 166 44 1876 2796 545146237 545147160 4.820000e-128 468.0
23 TraesCS1A01G407900 chr5D 90.741 324 20 4 860 1179 545124891 545124574 1.060000e-114 424.0
24 TraesCS1A01G407900 chr5D 86.667 135 18 0 2594 2728 545119442 545119308 1.980000e-32 150.0
25 TraesCS1A01G407900 chr5D 91.954 87 7 0 1756 1842 453867951 453867865 4.320000e-24 122.0
26 TraesCS1A01G407900 chr5D 91.765 85 7 0 1757 1841 346693384 346693468 5.590000e-23 119.0
27 TraesCS1A01G407900 chr5D 90.698 86 8 0 1757 1842 180739431 180739346 7.240000e-22 115.0
28 TraesCS1A01G407900 chr7A 98.824 170 2 0 576 745 23351052 23350883 1.440000e-78 303.0
29 TraesCS1A01G407900 chr7A 86.667 105 13 1 1738 1842 473897474 473897577 7.240000e-22 115.0
30 TraesCS1A01G407900 chr7A 91.228 57 5 0 1217 1273 692762431 692762487 9.490000e-11 78.7
31 TraesCS1A01G407900 chr6A 98.182 165 3 0 581 745 18464790 18464626 4.030000e-74 289.0
32 TraesCS1A01G407900 chr6A 94.706 170 9 0 576 745 51753236 51753067 6.790000e-67 265.0
33 TraesCS1A01G407900 chr3A 95.882 170 6 1 576 745 652496498 652496330 1.130000e-69 274.0
34 TraesCS1A01G407900 chr3A 94.675 169 9 0 576 744 652291525 652291357 2.440000e-66 263.0
35 TraesCS1A01G407900 chr3A 88.356 146 14 3 441 585 603877563 603877420 4.230000e-39 172.0
36 TraesCS1A01G407900 chr2A 95.858 169 6 1 577 745 715425247 715425080 4.060000e-69 272.0
37 TraesCS1A01G407900 chr2A 94.767 172 9 0 576 747 765962678 765962507 5.250000e-68 268.0
38 TraesCS1A01G407900 chr2A 86.559 186 25 0 1202 1387 107316623 107316808 4.170000e-49 206.0
39 TraesCS1A01G407900 chr4B 91.538 130 11 0 445 574 139756236 139756107 2.530000e-41 180.0
40 TraesCS1A01G407900 chr4B 93.043 115 7 1 750 863 448046252 448046366 1.970000e-37 167.0
41 TraesCS1A01G407900 chr4B 90.698 86 8 0 1757 1842 592354518 592354433 7.240000e-22 115.0
42 TraesCS1A01G407900 chr3B 91.538 130 11 0 445 574 254760819 254760690 2.530000e-41 180.0
43 TraesCS1A01G407900 chr3B 91.453 117 9 1 746 861 654567626 654567510 3.300000e-35 159.0
44 TraesCS1A01G407900 chr3B 88.550 131 13 2 746 874 188638590 188638460 1.190000e-34 158.0
45 TraesCS1A01G407900 chr2D 91.538 130 11 0 445 574 385285516 385285387 2.530000e-41 180.0
46 TraesCS1A01G407900 chr2D 92.308 117 8 1 746 861 72845316 72845432 7.080000e-37 165.0
47 TraesCS1A01G407900 chr1B 90.840 131 10 2 445 574 271833750 271833621 1.180000e-39 174.0
48 TraesCS1A01G407900 chr7D 92.373 118 6 3 746 861 528029723 528029607 7.080000e-37 165.0
49 TraesCS1A01G407900 chr7D 90.805 87 8 0 1756 1842 310968301 310968215 2.010000e-22 117.0
50 TraesCS1A01G407900 chr3D 91.453 117 9 1 746 861 209677610 209677726 3.300000e-35 159.0
51 TraesCS1A01G407900 chr3D 91.525 118 7 3 746 861 593241530 593241646 3.300000e-35 159.0
52 TraesCS1A01G407900 chr3D 89.773 88 9 0 1757 1844 23941558 23941471 2.600000e-21 113.0
53 TraesCS1A01G407900 chr3D 89.888 89 8 1 1754 1841 561754055 561753967 2.600000e-21 113.0
54 TraesCS1A01G407900 chr7B 90.909 88 8 0 1755 1842 100745925 100745838 5.590000e-23 119.0
55 TraesCS1A01G407900 chr7B 79.412 136 28 0 1201 1336 679930677 679930542 2.620000e-16 97.1
56 TraesCS1A01G407900 chr6D 91.765 85 7 0 1757 1841 413065931 413065847 5.590000e-23 119.0
57 TraesCS1A01G407900 chr6D 90.588 85 8 0 1757 1841 85039235 85039151 2.600000e-21 113.0
58 TraesCS1A01G407900 chr6D 89.412 85 9 0 1757 1841 97902320 97902404 1.210000e-19 108.0
59 TraesCS1A01G407900 chr2B 90.110 91 9 0 1752 1842 254692212 254692302 5.590000e-23 119.0
60 TraesCS1A01G407900 chr2B 90.698 86 8 0 1757 1842 785893264 785893179 7.240000e-22 115.0
61 TraesCS1A01G407900 chr1D 90.588 85 8 0 1757 1841 9228657 9228741 2.600000e-21 113.0
62 TraesCS1A01G407900 chr1D 90.588 85 8 0 1757 1841 212378746 212378662 2.600000e-21 113.0
63 TraesCS1A01G407900 chr1D 89.011 91 9 1 1757 1847 492948129 492948040 9.360000e-21 111.0
64 TraesCS1A01G407900 chr1D 89.412 85 9 0 1757 1841 50021603 50021687 1.210000e-19 108.0
65 TraesCS1A01G407900 chr1D 88.636 88 10 0 1757 1844 104577302 104577215 1.210000e-19 108.0
66 TraesCS1A01G407900 chr1D 89.873 79 8 0 1763 1841 63428364 63428286 5.630000e-18 102.0
67 TraesCS1A01G407900 chr1D 89.744 78 7 1 1755 1831 80036893 80036970 7.290000e-17 99.0
68 TraesCS1A01G407900 chrUn 83.495 103 15 2 1740 1842 144811828 144811928 9.430000e-16 95.3
69 TraesCS1A01G407900 chrUn 85.556 90 12 1 1753 1842 12068805 12068893 3.390000e-15 93.5
70 TraesCS1A01G407900 chrUn 85.556 90 12 1 1753 1842 144742261 144742349 3.390000e-15 93.5
71 TraesCS1A01G407900 chrUn 85.556 90 12 1 1753 1842 144779372 144779460 3.390000e-15 93.5
72 TraesCS1A01G407900 chrUn 85.556 90 12 1 1753 1842 144892375 144892463 3.390000e-15 93.5
73 TraesCS1A01G407900 chrUn 85.556 90 12 1 1753 1842 144930913 144931001 3.390000e-15 93.5
74 TraesCS1A01G407900 chrUn 85.556 90 12 1 1753 1842 179856086 179856174 3.390000e-15 93.5
75 TraesCS1A01G407900 chrUn 85.556 90 12 1 1753 1842 343170947 343171035 3.390000e-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 TraesCS1A01G407900 chr1A 570158374 570161565 3191 False 5895.000000 5895 100.0000 1 3192 1 chr1A.!!$F3 3191
1 TraesCS1A01G407900 chr1A 570154185 570154759 574 True 363.000000 363 78.7520 1876 2449 1 chr1A.!!$R2 573
2 TraesCS1A01G407900 chr4A 624919241 624922658 3417 True 1831.333333 4416 98.4220 1 3190 3 chr4A.!!$R5 3189
3 TraesCS1A01G407900 chr5B 687737887 687740075 2188 True 1627.500000 1910 93.7795 860 3133 2 chr5B.!!$R2 2273
4 TraesCS1A01G407900 chr5D 545119308 545124891 5583 True 751.750000 1799 89.7605 860 3042 4 chr5D.!!$R3 2182
5 TraesCS1A01G407900 chr5D 545146237 545147160 923 False 468.000000 468 76.5510 1876 2796 1 chr5D.!!$F2 920

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
623 626 0.535553 AGCGGCGACCCTTAAAAACA 60.536 50.0 12.98 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 2502 2.034124 GGTAGGTACCTGGATACGCAA 58.966 52.381 25.33 0.0 43.1 4.85 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
328 331 4.521146 TGTGATTGTTTTTGGGCACAATT 58.479 34.783 0.06 0.00 42.46 2.32
403 406 4.725556 TGACGTCTGACTTTGCAATTAC 57.274 40.909 17.92 0.00 0.00 1.89
454 457 5.573669 CGTTTCTTGCTTCTTACTACCTCTC 59.426 44.000 0.00 0.00 0.00 3.20
470 473 5.584551 ACCTCTCTTCTGGTTTATTGGTT 57.415 39.130 0.00 0.00 31.62 3.67
471 474 5.561679 ACCTCTCTTCTGGTTTATTGGTTC 58.438 41.667 0.00 0.00 31.62 3.62
473 476 6.183361 ACCTCTCTTCTGGTTTATTGGTTCTT 60.183 38.462 0.00 0.00 31.62 2.52
474 477 7.017254 ACCTCTCTTCTGGTTTATTGGTTCTTA 59.983 37.037 0.00 0.00 31.62 2.10
623 626 0.535553 AGCGGCGACCCTTAAAAACA 60.536 50.000 12.98 0.00 0.00 2.83
790 804 8.932945 TTTTGTTGACATGCACTAACATTTTA 57.067 26.923 0.00 0.00 33.56 1.52
1200 1260 1.271934 TGCATGTGTAATGTGTTGCCC 59.728 47.619 0.00 0.00 0.00 5.36
1376 1436 1.002087 ACGAGTCGCCCAAAATCTTCT 59.998 47.619 13.59 0.00 0.00 2.85
1766 1835 4.101645 TGCTACCTATGTACTCCCTCTC 57.898 50.000 0.00 0.00 0.00 3.20
2133 2216 0.528466 ATCTCACGTGCATGGCTACG 60.528 55.000 11.67 0.09 45.19 3.51
2415 2502 1.051812 CGGCTCCTCCCATCAATACT 58.948 55.000 0.00 0.00 0.00 2.12
2572 2695 6.824196 TGCTACGGTAATTAATGAATGGTTGA 59.176 34.615 0.00 0.00 0.00 3.18
3028 3155 9.669353 CATGGAATTATTATTGCTACTGTGTTC 57.331 33.333 0.00 0.00 33.63 3.18
3162 4950 5.698741 TGAGAAAAGCCTTGATCATCCTA 57.301 39.130 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
353 356 6.372659 AGGACAGAACACAACTAATGCTAATG 59.627 38.462 0.00 0.00 0.00 1.90
474 477 8.970020 TGATCAAAATTTGGCACAGATTACTAT 58.030 29.630 5.83 0.00 42.53 2.12
477 480 9.585099 TTATGATCAAAATTTGGCACAGATTAC 57.415 29.630 5.83 0.00 42.53 1.89
578 581 6.812879 ATACCATAGCCCGCTATTTAAAAC 57.187 37.500 6.48 0.00 37.16 2.43
1200 1260 1.447314 GGCCCGTCCAGTTTCTACG 60.447 63.158 0.00 0.00 36.42 3.51
1376 1436 1.798223 GTTGCATGCGTACTTCTGTGA 59.202 47.619 14.09 0.00 0.00 3.58
1622 1684 4.722700 CCCCGTCCAGCTTGGTGG 62.723 72.222 12.20 12.20 39.03 4.61
1744 1809 4.355588 AGAGAGGGAGTACATAGGTAGCAT 59.644 45.833 0.00 0.00 0.00 3.79
1812 1881 9.250246 CTCCCTTGGTCCTAAAATATAAAAACA 57.750 33.333 0.00 0.00 0.00 2.83
2133 2216 2.608261 GGCTCATCGCATAGTGTCTACC 60.608 54.545 0.00 0.00 41.67 3.18
2249 2336 5.524281 GTCCTTAGCACTATACTTGCCTTTC 59.476 44.000 0.00 0.00 41.18 2.62
2393 2480 2.049627 ATTGATGGGAGGAGCCGAGC 62.050 60.000 0.00 0.00 37.63 5.03
2415 2502 2.034124 GGTAGGTACCTGGATACGCAA 58.966 52.381 25.33 0.00 43.10 4.85
2972 3099 3.482436 TGAACCAGATTACAACGCCTTT 58.518 40.909 0.00 0.00 0.00 3.11
3028 3155 9.981114 AAATTACAATTACTGACTTTGAAAGGG 57.019 29.630 10.02 2.04 0.00 3.95
3162 4950 7.669427 TGATCTAAGGCAATGAAACATTTGTT 58.331 30.769 0.00 0.00 40.50 2.83


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

AutoCloner maintained by Alex Coulton.