Multiple sequence alignment - TraesCS1B01G138100

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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 TraesCS1B01G138100 chr1B 100.000 4326 0 0 1 4326 177839345 177835020 0.000000e+00 7989.0
1 TraesCS1B01G138100 chr1B 88.034 117 9 2 3660 3776 1823677 1823566 2.710000e-27 134.0
2 TraesCS1B01G138100 chr1B 86.325 117 11 3 3660 3776 666933558 666933669 5.870000e-24 122.0
3 TraesCS1B01G138100 chr1B 95.312 64 3 0 4263 4326 177811140 177811077 7.650000e-18 102.0
4 TraesCS1B01G138100 chr1B 83.178 107 16 2 4010 4115 158531307 158531202 3.560000e-16 97.1
5 TraesCS1B01G138100 chr1D 94.293 2243 77 28 56 2277 116006329 116004117 0.000000e+00 3386.0
6 TraesCS1B01G138100 chr1D 96.438 1151 37 4 2309 3456 116004120 116002971 0.000000e+00 1895.0
7 TraesCS1B01G138100 chr1D 94.286 175 7 1 3467 3641 128530466 128530637 9.220000e-67 265.0
8 TraesCS1B01G138100 chr1D 91.489 47 4 0 3843 3889 437855315 437855361 1.000000e-06 65.8
9 TraesCS1B01G138100 chr1A 93.858 2133 76 22 58 2152 127078579 127076464 0.000000e+00 3162.0
10 TraesCS1B01G138100 chr1A 95.311 1301 45 7 2184 3475 127076467 127075174 0.000000e+00 2050.0
11 TraesCS1B01G138100 chr1A 82.108 408 48 14 3942 4326 432625910 432625505 4.170000e-85 326.0
12 TraesCS1B01G138100 chr1A 92.818 181 10 1 3462 3642 90767726 90767549 4.290000e-65 259.0
13 TraesCS1B01G138100 chr1A 88.485 165 19 0 4162 4326 127074594 127074430 2.640000e-47 200.0
14 TraesCS1B01G138100 chr1A 91.892 37 3 0 3787 3823 475311171 475311135 8.000000e-03 52.8
15 TraesCS1B01G138100 chr1A 100.000 28 0 0 3788 3815 564450555 564450582 8.000000e-03 52.8
16 TraesCS1B01G138100 chr5A 84.424 321 19 10 3459 3778 436260748 436260458 1.970000e-73 287.0
17 TraesCS1B01G138100 chr5A 95.322 171 5 1 3474 3644 367790241 367790074 7.130000e-68 268.0
18 TraesCS1B01G138100 chr5A 79.143 350 54 15 3942 4285 146935700 146935364 1.570000e-54 224.0
19 TraesCS1B01G138100 chr5A 92.424 66 5 0 1730 1795 57375666 57375601 1.280000e-15 95.3
20 TraesCS1B01G138100 chr5A 82.292 96 17 0 1694 1789 575658615 575658710 2.770000e-12 84.2
21 TraesCS1B01G138100 chr5A 95.455 44 2 0 3846 3889 549400456 549400499 2.160000e-08 71.3
22 TraesCS1B01G138100 chr7D 85.714 259 31 5 3948 4201 270711981 270711724 7.130000e-68 268.0
23 TraesCS1B01G138100 chr7D 89.109 202 19 2 3455 3656 519969083 519968885 9.290000e-62 248.0
24 TraesCS1B01G138100 chr7D 100.000 45 0 0 3890 3934 141135481 141135525 2.770000e-12 84.2
25 TraesCS1B01G138100 chr7D 96.000 50 1 1 3887 3935 84326818 84326769 3.590000e-11 80.5
26 TraesCS1B01G138100 chr7D 97.368 38 1 0 3852 3889 600490439 600490402 1.000000e-06 65.8
27 TraesCS1B01G138100 chr5D 94.767 172 5 2 3474 3644 445106652 445106484 9.220000e-67 265.0
28 TraesCS1B01G138100 chr5D 88.095 210 18 5 3440 3647 64274867 64275071 4.320000e-60 243.0
29 TraesCS1B01G138100 chr5D 88.182 110 9 1 3682 3787 279302838 279302729 1.260000e-25 128.0
30 TraesCS1B01G138100 chr5D 86.842 114 9 4 3660 3773 241946305 241946412 5.870000e-24 122.0
31 TraesCS1B01G138100 chr5D 78.453 181 34 5 3942 4119 443309853 443310031 3.540000e-21 113.0
32 TraesCS1B01G138100 chr5D 95.238 63 3 0 1727 1789 66756451 66756513 2.750000e-17 100.0
33 TraesCS1B01G138100 chr5D 83.333 96 16 0 1694 1789 457777221 457777316 5.960000e-14 89.8
34 TraesCS1B01G138100 chr5D 95.556 45 2 0 3788 3832 150835347 150835303 6.000000e-09 73.1
35 TraesCS1B01G138100 chr5D 100.000 31 0 0 3271 3301 21021100 21021070 1.680000e-04 58.4
36 TraesCS1B01G138100 chr3B 93.820 178 8 1 3466 3643 499167810 499167636 9.220000e-67 265.0
37 TraesCS1B01G138100 chr3B 86.667 135 18 0 1673 1807 126921207 126921341 2.690000e-32 150.0
38 TraesCS1B01G138100 chr3B 85.124 121 13 3 3656 3776 755450075 755449960 7.600000e-23 119.0
39 TraesCS1B01G138100 chr3B 86.364 88 9 3 4002 4088 415648489 415648404 4.610000e-15 93.5
40 TraesCS1B01G138100 chr3D 87.500 216 22 3 3442 3657 496740156 496739946 1.200000e-60 244.0
41 TraesCS1B01G138100 chr3D 81.553 206 23 8 1094 1287 81206732 81206934 5.790000e-34 156.0
42 TraesCS1B01G138100 chr3D 75.477 367 54 21 1441 1795 81207160 81207502 3.490000e-31 147.0
43 TraesCS1B01G138100 chr3D 87.500 112 9 1 3660 3771 583473251 583473357 1.630000e-24 124.0
44 TraesCS1B01G138100 chr3D 86.325 117 11 2 3660 3776 130497918 130498029 5.870000e-24 122.0
45 TraesCS1B01G138100 chr3D 96.078 51 1 1 3887 3936 545176667 545176717 9.970000e-12 82.4
46 TraesCS1B01G138100 chr2D 79.167 264 50 5 3942 4201 50440580 50440318 1.240000e-40 178.0
47 TraesCS1B01G138100 chr2D 84.733 131 12 2 3660 3787 373883454 373883579 1.630000e-24 124.0
48 TraesCS1B01G138100 chr2D 91.489 47 3 1 3788 3833 616608452 616608406 3.610000e-06 63.9
49 TraesCS1B01G138100 chr2D 100.000 31 0 0 3271 3301 209185675 209185645 1.680000e-04 58.4
50 TraesCS1B01G138100 chr2D 90.476 42 4 0 3789 3830 206242376 206242335 6.040000e-04 56.5
51 TraesCS1B01G138100 chr3A 86.667 135 18 0 1673 1807 95477817 95477951 2.690000e-32 150.0
52 TraesCS1B01G138100 chr3A 86.747 83 10 1 1441 1522 95477584 95477666 1.660000e-14 91.6
53 TraesCS1B01G138100 chr3A 100.000 45 0 0 3890 3934 647021286 647021330 2.770000e-12 84.2
54 TraesCS1B01G138100 chr4D 86.777 121 11 1 3656 3776 40952276 40952161 3.510000e-26 130.0
55 TraesCS1B01G138100 chr4D 100.000 38 0 0 3852 3889 326379924 326379887 2.160000e-08 71.3
56 TraesCS1B01G138100 chr4D 95.556 45 1 1 3845 3889 427269615 427269658 2.160000e-08 71.3
57 TraesCS1B01G138100 chr6B 86.325 117 12 2 3660 3776 256326159 256326271 1.630000e-24 124.0
58 TraesCS1B01G138100 chr6B 79.348 184 30 8 3942 4119 694447605 694447786 5.870000e-24 122.0
59 TraesCS1B01G138100 chr6B 84.071 113 13 4 3942 4049 310390884 310390996 2.130000e-18 104.0
60 TraesCS1B01G138100 chr6B 97.727 44 1 0 3846 3889 437150784 437150741 4.640000e-10 76.8
61 TraesCS1B01G138100 chr6B 95.349 43 2 0 3788 3830 225541849 225541891 7.760000e-08 69.4
62 TraesCS1B01G138100 chr6B 76.364 110 24 2 3942 4049 632431504 632431613 1.680000e-04 58.4
63 TraesCS1B01G138100 chr6D 79.348 184 30 7 3942 4119 456647892 456648073 5.870000e-24 122.0
64 TraesCS1B01G138100 chr5B 93.939 66 4 0 1730 1795 64265119 64265054 2.750000e-17 100.0
65 TraesCS1B01G138100 chr5B 83.333 96 16 0 1694 1789 559992274 559992369 5.960000e-14 89.8
66 TraesCS1B01G138100 chr5B 97.872 47 1 0 3888 3934 56695161 56695207 9.970000e-12 82.4
67 TraesCS1B01G138100 chr5B 97.368 38 1 0 3852 3889 563123151 563123188 1.000000e-06 65.8
68 TraesCS1B01G138100 chr7B 76.923 182 37 5 3942 4119 411357431 411357611 9.900000e-17 99.0
69 TraesCS1B01G138100 chr7B 82.143 112 17 3 3942 4050 193801060 193800949 4.610000e-15 93.5
70 TraesCS1B01G138100 chr7B 97.778 45 1 0 3890 3934 611239570 611239614 1.290000e-10 78.7
71 TraesCS1B01G138100 chr6A 96.000 50 1 1 3886 3934 64321628 64321677 3.590000e-11 80.5
72 TraesCS1B01G138100 chr2B 94.231 52 3 0 3883 3934 799555105 799555054 3.590000e-11 80.5
73 TraesCS1B01G138100 chr4B 87.302 63 6 1 3889 3951 556997974 556998034 2.160000e-08 71.3
74 TraesCS1B01G138100 chr7A 91.489 47 4 0 3843 3889 24673625 24673671 1.000000e-06 65.8
75 TraesCS1B01G138100 chr2A 93.182 44 3 0 3787 3830 656371991 656372034 1.000000e-06 65.8
76 TraesCS1B01G138100 chr2A 91.489 47 4 0 3843 3889 731536423 731536469 1.000000e-06 65.8


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 TraesCS1B01G138100 chr1B 177835020 177839345 4325 True 7989.0 7989 100.000000 1 4326 1 chr1B.!!$R4 4325
1 TraesCS1B01G138100 chr1D 116002971 116006329 3358 True 2640.5 3386 95.365500 56 3456 2 chr1D.!!$R1 3400
2 TraesCS1B01G138100 chr1A 127074430 127078579 4149 True 1804.0 3162 92.551333 58 4326 3 chr1A.!!$R4 4268


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
732 757 0.178992 GGGAATGGGGATTGCGATGA 60.179 55.000 0.00 0.00 0.00 2.92 F
834 859 0.240945 GAATGCAAATATCGGCGGGG 59.759 55.000 7.21 0.00 0.00 5.73 F
858 883 0.909843 GCATCGCGACAAGAAATTGC 59.090 50.000 12.93 11.62 0.00 3.56 F
1507 1554 1.215647 CGACCTCAAGGCTTACGCT 59.784 57.895 0.00 0.00 39.32 5.07 F
2365 2416 1.151668 CAGCTGTTCAGTTTCTCGGG 58.848 55.000 5.25 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 2348 0.594602 CATCATTCGCCGCCAATCAT 59.405 50.000 0.00 0.0 0.00 2.45 R
2299 2350 1.370900 GCATCATTCGCCGCCAATC 60.371 57.895 0.00 0.0 0.00 2.67 R
2300 2351 1.789078 GAGCATCATTCGCCGCCAAT 61.789 55.000 0.00 0.0 33.17 3.16 R
3316 3376 1.609501 CTCGGGAGAACAGGGACCA 60.610 63.158 0.00 0.0 39.18 4.02 R
4022 4136 0.101759 TACGGCTAGCGTTGGATGTC 59.898 55.000 15.48 0.0 0.00 3.06 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)



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AutoCloner maintained by Alex Coulton.