Multiple sequence alignment - TraesCS3B01G609100

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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 TraesCS3B01G609100 chr3B 100.000 3587 0 0 1 3587 828333801 828330215 0.000000e+00 6625.0
1 TraesCS3B01G609100 chr3B 95.273 2581 79 15 1 2557 828294806 828292245 0.000000e+00 4050.0
2 TraesCS3B01G609100 chr3B 93.772 835 42 5 2755 3587 828287223 828286397 0.000000e+00 1245.0
3 TraesCS3B01G609100 chr3B 88.813 876 71 17 258 1133 828256778 828255930 0.000000e+00 1050.0
4 TraesCS3B01G609100 chr3B 81.170 1179 182 20 1349 2503 828254290 828253128 0.000000e+00 911.0
5 TraesCS3B01G609100 chr3B 96.020 201 6 1 2559 2759 828292181 828291983 3.450000e-85 326.0
6 TraesCS3B01G609100 chr3B 86.603 209 23 5 44 249 828257188 828256982 3.600000e-55 226.0
7 TraesCS3B01G609100 chr3D 90.181 1161 92 11 96 1250 610686963 610685819 0.000000e+00 1493.0
8 TraesCS3B01G609100 chr3D 87.041 1034 114 14 2559 3587 610666861 610665843 0.000000e+00 1149.0
9 TraesCS3B01G609100 chr3D 82.332 1098 151 16 1416 2496 610668078 610667007 0.000000e+00 913.0
10 TraesCS3B01G609100 chr3D 85.816 705 91 7 1252 1950 610685753 610685052 0.000000e+00 739.0
11 TraesCS3B01G609100 chr3D 84.245 768 106 13 2823 3587 610627073 610626318 0.000000e+00 734.0
12 TraesCS3B01G609100 chr3D 82.254 834 130 5 1682 2503 610628380 610627553 0.000000e+00 704.0
13 TraesCS3B01G609100 chr3D 89.712 486 39 6 771 1253 610629582 610629105 8.510000e-171 610.0
14 TraesCS3B01G609100 chr3D 85.499 531 73 4 246 772 610561563 610561033 5.230000e-153 551.0
15 TraesCS3B01G609100 chr3D 83.047 466 58 8 2559 3022 610684402 610683956 1.550000e-108 403.0
16 TraesCS3B01G609100 chr3D 85.542 332 46 2 15 344 610602194 610601863 2.650000e-91 346.0
17 TraesCS3B01G609100 chr3D 83.389 301 41 5 893 1192 610597832 610597540 1.640000e-68 270.0
18 TraesCS3B01G609100 chr3D 91.795 195 15 1 3026 3220 610682199 610682006 1.640000e-68 270.0
19 TraesCS3B01G609100 chr3D 85.714 259 30 3 2559 2816 610627414 610627162 2.120000e-67 267.0
20 TraesCS3B01G609100 chr3D 87.097 186 21 3 16 199 610561756 610561572 1.310000e-49 207.0
21 TraesCS3B01G609100 chr3D 79.077 325 42 13 1383 1693 610628765 610628453 2.180000e-47 200.0
22 TraesCS3B01G609100 chr3D 91.000 100 9 0 1252 1351 610629036 610628937 6.250000e-28 135.0
23 TraesCS3B01G609100 chr3A 83.372 1281 175 16 1252 2503 745299041 745297770 0.000000e+00 1151.0
24 TraesCS3B01G609100 chr3A 80.880 1182 183 21 1349 2503 744941051 744939886 0.000000e+00 891.0
25 TraesCS3B01G609100 chr3A 80.678 1180 188 17 1349 2503 745080787 745079623 0.000000e+00 880.0
26 TraesCS3B01G609100 chr3A 80.525 1181 189 18 1349 2503 745013978 745012813 0.000000e+00 869.0
27 TraesCS3B01G609100 chr3A 80.508 1180 190 17 1349 2503 745193990 745192826 0.000000e+00 869.0
28 TraesCS3B01G609100 chr3A 84.994 773 101 11 2819 3586 745297298 745296536 0.000000e+00 771.0
29 TraesCS3B01G609100 chr3A 84.000 775 98 18 2819 3587 745012338 745011584 0.000000e+00 721.0
30 TraesCS3B01G609100 chr3A 83.871 775 99 18 2819 3587 745192351 745191597 0.000000e+00 715.0
31 TraesCS3B01G609100 chr3A 83.763 776 99 19 2819 3587 745079148 745078393 0.000000e+00 710.0
32 TraesCS3B01G609100 chr3A 86.567 603 64 8 7 606 745300876 745300288 0.000000e+00 649.0
33 TraesCS3B01G609100 chr3A 86.242 596 70 9 264 855 745015112 745014525 1.400000e-178 636.0
34 TraesCS3B01G609100 chr3A 86.242 596 69 9 264 855 744942184 744941598 5.050000e-178 634.0
35 TraesCS3B01G609100 chr3A 86.074 596 71 9 264 855 745195123 745194536 6.540000e-177 630.0
36 TraesCS3B01G609100 chr3A 86.074 596 70 10 264 855 745081920 745081334 2.350000e-176 628.0
37 TraesCS3B01G609100 chr3A 91.843 331 27 0 923 1253 745299435 745299105 2.520000e-126 462.0
38 TraesCS3B01G609100 chr3A 92.095 253 13 3 897 1149 744941595 744941350 2.050000e-92 350.0
39 TraesCS3B01G609100 chr3A 92.095 253 13 3 897 1149 745014522 745014277 2.050000e-92 350.0
40 TraesCS3B01G609100 chr3A 92.095 253 13 3 897 1149 745081331 745081086 2.050000e-92 350.0
41 TraesCS3B01G609100 chr3A 92.095 253 12 4 897 1149 745194533 745194289 2.050000e-92 350.0
42 TraesCS3B01G609100 chr3A 88.031 259 20 5 2559 2816 745297631 745297383 2.710000e-76 296.0
43 TraesCS3B01G609100 chr3A 84.825 257 31 6 2561 2816 745079481 745079232 5.940000e-63 252.0
44 TraesCS3B01G609100 chr3A 84.825 257 31 6 2561 2816 745192684 745192435 5.940000e-63 252.0
45 TraesCS3B01G609100 chr3A 84.436 257 32 6 2561 2816 744939744 744939495 2.770000e-61 246.0
46 TraesCS3B01G609100 chr3A 84.047 257 33 6 2561 2816 745012671 745012422 1.290000e-59 241.0
47 TraesCS3B01G609100 chr5B 87.037 54 7 0 3139 3192 64295054 64295001 1.080000e-05 62.1


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 TraesCS3B01G609100 chr3B 828330215 828333801 3586 True 6625.000000 6625 100.000000 1 3587 1 chr3B.!!$R2 3586
1 TraesCS3B01G609100 chr3B 828291983 828294806 2823 True 2188.000000 4050 95.646500 1 2759 2 chr3B.!!$R4 2758
2 TraesCS3B01G609100 chr3B 828286397 828287223 826 True 1245.000000 1245 93.772000 2755 3587 1 chr3B.!!$R1 832
3 TraesCS3B01G609100 chr3B 828253128 828257188 4060 True 729.000000 1050 85.528667 44 2503 3 chr3B.!!$R3 2459
4 TraesCS3B01G609100 chr3D 610665843 610668078 2235 True 1031.000000 1149 84.686500 1416 3587 2 chr3D.!!$R5 2171
5 TraesCS3B01G609100 chr3D 610682006 610686963 4957 True 726.250000 1493 87.709750 96 3220 4 chr3D.!!$R6 3124
6 TraesCS3B01G609100 chr3D 610626318 610629582 3264 True 441.666667 734 85.333667 771 3587 6 chr3D.!!$R4 2816
7 TraesCS3B01G609100 chr3D 610561033 610561756 723 True 379.000000 551 86.298000 16 772 2 chr3D.!!$R3 756
8 TraesCS3B01G609100 chr3A 745296536 745300876 4340 True 665.800000 1151 86.961400 7 3586 5 chr3A.!!$R5 3579
9 TraesCS3B01G609100 chr3A 745078393 745081920 3527 True 564.000000 880 85.487000 264 3587 5 chr3A.!!$R3 3323
10 TraesCS3B01G609100 chr3A 745011584 745015112 3528 True 563.400000 869 85.381800 264 3587 5 chr3A.!!$R2 3323
11 TraesCS3B01G609100 chr3A 745191597 745195123 3526 True 563.200000 869 85.474600 264 3587 5 chr3A.!!$R4 3323
12 TraesCS3B01G609100 chr3A 744939495 744942184 2689 True 530.250000 891 85.913250 264 2816 4 chr3A.!!$R1 2552

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
256 455 3.646162 TCCAACACCAACACTAGAGTCAT 59.354 43.478 0.00 0.00 0.00 3.06 F
1525 3803 1.001974 TCGTGTTGTCATCCTGGGAAG 59.998 52.381 0.00 0.00 0.00 3.46 F
2320 4691 0.680618 CCACAACCATGCACATTGGT 59.319 50.000 4.57 4.57 37.57 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 4157 0.102481 TCGACTTGCTATTCCCGCTC 59.898 55.0 0.0 0.0 0.0 5.03 R
2442 4828 0.172578 CACCGACGCTCTGTAATCCA 59.827 55.0 0.0 0.0 0.0 3.41 R
3221 7536 0.463620 GGATGTCTGTGAGGAGGAGC 59.536 60.0 0.0 0.0 0.0 4.70 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
100 102 4.457496 CCGCCACATCGCTGGTCT 62.457 66.667 0.00 0.00 33.30 3.85
149 151 9.822185 ATCAAATCATCCAGCCTTTAATTTTAC 57.178 29.630 0.00 0.00 0.00 2.01
256 455 3.646162 TCCAACACCAACACTAGAGTCAT 59.354 43.478 0.00 0.00 0.00 3.06
351 551 4.157656 CACGTTTTATGACATCATTGGGGT 59.842 41.667 0.00 0.00 37.76 4.95
818 1331 6.305272 TCTCTCTCATCTATTTTGGTGCTT 57.695 37.500 0.00 0.00 0.00 3.91
855 1374 6.681368 GCTCTCTCCATTTTCTCTCTCTTCTC 60.681 46.154 0.00 0.00 0.00 2.87
856 1375 5.656416 TCTCTCCATTTTCTCTCTCTTCTCC 59.344 44.000 0.00 0.00 0.00 3.71
1509 3787 4.630069 AGATTTATCAGAAACCGGTTCGTG 59.370 41.667 22.53 20.13 41.52 4.35
1525 3803 1.001974 TCGTGTTGTCATCCTGGGAAG 59.998 52.381 0.00 0.00 0.00 3.46
1575 3855 3.627577 GCTCCATATACATATTTGGCCGG 59.372 47.826 0.00 0.00 35.55 6.13
1635 3921 3.067106 ACAAATCGGCACTAACACTCAG 58.933 45.455 0.00 0.00 0.00 3.35
1692 4059 4.782019 TGGAGGATGCAACAACAATAAC 57.218 40.909 0.00 0.00 28.48 1.89
1837 4207 4.749310 AGCGAGCTCAGTTGGCGG 62.749 66.667 15.40 0.00 34.52 6.13
1925 4295 8.548880 TGCTACTTCAATAACTACTCCCTTAT 57.451 34.615 0.00 0.00 0.00 1.73
1968 4338 4.111016 TGTCGCCGCTACTGGACG 62.111 66.667 0.00 0.00 32.17 4.79
2111 4481 1.680735 GACAACAACCATGTCCAGCAA 59.319 47.619 0.00 0.00 41.02 3.91
2209 4580 4.329545 GCCAGTTCGCCCACAGGA 62.330 66.667 0.00 0.00 33.47 3.86
2259 4630 2.866028 GACAGGCTGCTCTTTGCG 59.134 61.111 15.89 0.00 46.63 4.85
2313 4684 0.685785 AACACCACCACAACCATGCA 60.686 50.000 0.00 0.00 0.00 3.96
2320 4691 0.680618 CCACAACCATGCACATTGGT 59.319 50.000 4.57 4.57 37.57 3.67
2322 4693 2.496871 CCACAACCATGCACATTGGTAT 59.503 45.455 10.82 0.39 34.39 2.73
2352 4723 2.983030 TGGTCGGCAGCGCAAATT 60.983 55.556 11.47 0.00 0.00 1.82
2385 4756 1.357690 CATGCACGCCATGGATCAC 59.642 57.895 18.40 1.72 46.09 3.06
2442 4828 1.607467 GCAGGGCATGTTCCACCTT 60.607 57.895 0.00 0.00 0.00 3.50
2492 4878 1.462238 ACAACAGAGGAGGCCACCT 60.462 57.895 23.18 23.18 43.64 4.00
2557 4964 2.120909 GGGGACATGGTCAATGGCG 61.121 63.158 0.00 0.00 46.45 5.69
2620 5094 2.239150 TGGGCCGGCTATTGTACTAAAA 59.761 45.455 28.56 0.00 0.00 1.52
2632 5106 9.556030 GCTATTGTACTAAAATGAACTTTGGTC 57.444 33.333 0.00 0.00 32.84 4.02
2796 5270 0.178068 CAGCTTGGTAGGCGGTACAT 59.822 55.000 0.00 0.00 32.62 2.29
2871 5430 6.830324 ACCACTATATTGCTGACATTGACAAT 59.170 34.615 0.00 0.00 36.70 2.71
2872 5431 7.340232 ACCACTATATTGCTGACATTGACAATT 59.660 33.333 0.00 0.00 34.69 2.32
2927 5487 4.112331 AGATAAGGTTTTCAGGGGTAGCT 58.888 43.478 0.00 0.00 0.00 3.32
3098 7412 7.061905 CACATGCTTCTCAAATGAAAGTTCATC 59.938 37.037 6.99 0.00 46.60 2.92
3114 7428 9.601217 GAAAGTTCATCACATTAGGTAGTACAT 57.399 33.333 2.06 0.00 0.00 2.29
3202 7517 0.040067 GTCTTGTGCAAAGGAAGCCG 60.040 55.000 0.00 0.00 0.00 5.52
3221 7536 1.328680 CGTTTCATGCTTCCTCATCCG 59.671 52.381 0.00 0.00 0.00 4.18
3288 7603 0.385390 CCCACTTTCGTGCTTGCTTT 59.615 50.000 0.00 0.00 39.86 3.51
3378 7694 5.595885 CACCTATCACTCTACAGGTCATTG 58.404 45.833 0.00 0.00 39.40 2.82
3418 7734 5.039984 CCTCATGATCTACGCATGTATAGC 58.960 45.833 0.00 0.00 42.77 2.97
3488 7807 4.799564 TGTACTGCAAAATGGGATTTCC 57.200 40.909 0.00 0.00 0.00 3.13
3567 7886 1.267334 CGTGTTCATATTTGGGACGCG 60.267 52.381 3.53 3.53 37.15 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 1.668237 GGTTTTGCGCACAAACCAATT 59.332 42.857 35.86 0.00 45.29 2.32
100 102 5.904941 TCGCCGACCTAGTGAAATTTATAA 58.095 37.500 0.00 0.00 0.00 0.98
149 151 9.148104 GCTAAGTTTATTTGTATCCCTATACCG 57.852 37.037 0.00 0.00 37.72 4.02
279 479 5.945191 TCAATCTTGAAATGTGCATGTCCTA 59.055 36.000 0.00 0.00 33.55 2.94
281 481 5.063180 TCAATCTTGAAATGTGCATGTCC 57.937 39.130 0.00 0.00 33.55 4.02
351 551 9.327628 CAAATTCCACATTTCCATAATATTGCA 57.672 29.630 0.00 0.00 0.00 4.08
818 1331 2.242452 TGGAGAGAGCAAGGTAGCTAGA 59.758 50.000 0.00 0.00 46.75 2.43
855 1374 0.612453 GGGGAGGATCTAGCTACCGG 60.612 65.000 0.00 0.00 33.73 5.28
856 1375 0.612453 GGGGGAGGATCTAGCTACCG 60.612 65.000 0.00 0.00 33.73 4.02
876 1395 4.460382 GGAATGGATGCTAGAGAGAGAGAG 59.540 50.000 0.00 0.00 0.00 3.20
877 1396 4.141065 TGGAATGGATGCTAGAGAGAGAGA 60.141 45.833 0.00 0.00 0.00 3.10
1381 3642 6.215636 ACCTACATCAGACATAAACTTCCCTT 59.784 38.462 0.00 0.00 0.00 3.95
1509 3787 3.486383 TGTTTCTTCCCAGGATGACAAC 58.514 45.455 1.91 9.79 39.69 3.32
1567 3847 3.623960 CGAGTAATCAAATACCGGCCAAA 59.376 43.478 0.00 0.00 0.00 3.28
1575 3855 7.544566 TCAACAAGGAGACGAGTAATCAAATAC 59.455 37.037 0.00 0.00 0.00 1.89
1635 3921 3.428532 TGGTGAAGGAGTGGTAGTACTC 58.571 50.000 0.00 0.00 44.96 2.59
1692 4059 0.322456 TGGCCATGAACCCTTCTTCG 60.322 55.000 0.00 0.00 0.00 3.79
1787 4156 0.103208 CGACTTGCTATTCCCGCTCT 59.897 55.000 0.00 0.00 0.00 4.09
1788 4157 0.102481 TCGACTTGCTATTCCCGCTC 59.898 55.000 0.00 0.00 0.00 5.03
1925 4295 1.830408 CAAAAGTGGCGGGGTTGGA 60.830 57.895 0.00 0.00 0.00 3.53
2209 4580 3.717294 AAGGCTTGCCGGGTCGAT 61.717 61.111 2.18 0.00 0.00 3.59
2259 4630 3.723348 GCGCAAGAACCACCGTCC 61.723 66.667 0.30 0.00 43.02 4.79
2313 4684 1.852309 TGCTCCATCCCATACCAATGT 59.148 47.619 0.00 0.00 0.00 2.71
2320 4691 1.131638 GACCACTGCTCCATCCCATA 58.868 55.000 0.00 0.00 0.00 2.74
2322 4693 2.659063 CGACCACTGCTCCATCCCA 61.659 63.158 0.00 0.00 0.00 4.37
2352 4723 1.324740 GCATGAATGGGAAGCTGCCA 61.325 55.000 14.44 5.93 43.78 4.92
2442 4828 0.172578 CACCGACGCTCTGTAATCCA 59.827 55.000 0.00 0.00 0.00 3.41
2492 4878 2.007113 CTGCTGCTTGTGGTGCAACA 62.007 55.000 0.00 0.00 40.13 3.33
2586 5059 2.877691 GCCCATTTCACGAGGCAC 59.122 61.111 0.00 0.00 45.07 5.01
2796 5270 2.261361 CGATGGTCGCACTCCACA 59.739 61.111 0.00 0.00 37.81 4.17
2871 5430 0.533491 CACAACCGGACCCTATCGAA 59.467 55.000 9.46 0.00 0.00 3.71
2872 5431 0.612732 ACACAACCGGACCCTATCGA 60.613 55.000 9.46 0.00 0.00 3.59
2927 5487 6.491745 CAGCCTTATCTGACAGTAGAATCCTA 59.508 42.308 1.59 0.00 36.19 2.94
3202 7517 1.064654 GCGGATGAGGAAGCATGAAAC 59.935 52.381 0.00 0.00 0.00 2.78
3221 7536 0.463620 GGATGTCTGTGAGGAGGAGC 59.536 60.000 0.00 0.00 0.00 4.70
3288 7603 3.131396 GGAGTTTCGTGAGCTTTTGAGA 58.869 45.455 0.00 0.00 0.00 3.27
3378 7694 5.822519 TCATGAGGTACCAAAACATATCTGC 59.177 40.000 15.94 0.00 0.00 4.26
3418 7734 2.003548 CCCCCTCCTCCTTGGAAGG 61.004 68.421 0.00 0.00 45.63 3.46
3434 7750 3.489785 CAGACATATTTTCGTAGTCGCCC 59.510 47.826 0.00 0.00 36.96 6.13
3472 7791 3.839490 ACATCAGGAAATCCCATTTTGCA 59.161 39.130 0.00 0.00 37.41 4.08


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

AutoCloner maintained by Alex Coulton.