Multiple sequence alignment - TraesCS2B01G233700

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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 TraesCS2B01G233700 chr2B 100.000 3068 0 0 1 3068 232292558 232289491 0.000000e+00 5666.0
1 TraesCS2B01G233700 chr2B 94.909 1925 76 10 942 2854 232261212 232263126 0.000000e+00 2992.0
2 TraesCS2B01G233700 chr2B 100.000 666 0 0 3389 4054 232289170 232288505 0.000000e+00 1230.0
3 TraesCS2B01G233700 chr2B 96.483 654 11 4 297 950 232257059 232257700 0.000000e+00 1070.0
4 TraesCS2B01G233700 chr2B 90.683 322 20 8 1 314 232248827 232249146 1.740000e-113 420.0
5 TraesCS2B01G233700 chr2B 86.792 159 18 3 3792 3949 621055338 621055494 1.500000e-39 174.0
6 TraesCS2B01G233700 chr2B 85.625 160 21 2 3790 3949 752669379 752669222 2.510000e-37 167.0
7 TraesCS2B01G233700 chr2B 97.143 35 1 0 110 144 232243837 232243871 4.380000e-05 60.2
8 TraesCS2B01G233700 chr2D 92.919 2076 96 15 1038 3065 165485588 165483516 0.000000e+00 2972.0
9 TraesCS2B01G233700 chr2D 93.715 1591 65 15 749 2316 165333132 165334710 0.000000e+00 2351.0
10 TraesCS2B01G233700 chr2D 94.459 758 40 1 2313 3068 165340077 165340834 0.000000e+00 1166.0
11 TraesCS2B01G233700 chr2D 92.460 557 22 6 1 554 165332587 165333126 0.000000e+00 778.0
12 TraesCS2B01G233700 chr2D 85.997 657 61 18 110 755 165492351 165491715 0.000000e+00 675.0
13 TraesCS2B01G233700 chr2D 90.647 278 12 6 753 1026 165485906 165485639 1.390000e-94 357.0
14 TraesCS2B01G233700 chr2D 86.188 181 19 5 3389 3564 165483498 165483319 1.490000e-44 191.0
15 TraesCS2B01G233700 chr2D 89.744 117 3 3 3947 4054 165341238 165341354 1.520000e-29 141.0
16 TraesCS2B01G233700 chr2A 91.996 2049 134 14 1032 3068 185364923 185362893 0.000000e+00 2848.0
17 TraesCS2B01G233700 chr2A 91.773 1252 78 1 1814 3065 185269378 185270604 0.000000e+00 1718.0
18 TraesCS2B01G233700 chr2A 93.901 787 38 3 1039 1818 185264719 185265502 0.000000e+00 1179.0
19 TraesCS2B01G233700 chr2A 93.333 555 23 7 1 554 185365778 185365237 0.000000e+00 808.0
20 TraesCS2B01G233700 chr2A 87.935 489 29 10 178 651 185262020 185262493 2.130000e-152 549.0
21 TraesCS2B01G233700 chr2A 88.037 326 17 8 709 1026 185264360 185264671 2.300000e-97 366.0
22 TraesCS2B01G233700 chr2A 88.380 284 5 10 749 1026 185365231 185364970 2.350000e-82 316.0
23 TraesCS2B01G233700 chr2A 94.318 176 8 1 3389 3562 185362871 185362696 6.680000e-68 268.0
24 TraesCS2B01G233700 chr2A 98.701 77 1 0 110 186 185261521 185261597 1.970000e-28 137.0
25 TraesCS2B01G233700 chr2A 98.214 56 1 0 3999 4054 185361036 185360981 9.270000e-17 99.0
26 TraesCS2B01G233700 chr2A 97.619 42 0 1 32 72 757556926 757556885 2.020000e-08 71.3
27 TraesCS2B01G233700 chr7D 83.544 2054 280 42 1021 3050 149181061 149183080 0.000000e+00 1868.0
28 TraesCS2B01G233700 chr7D 84.470 1848 262 19 1232 3063 149085779 149083941 0.000000e+00 1799.0
29 TraesCS2B01G233700 chr7A 84.248 1841 265 18 1232 3065 149862722 149860900 0.000000e+00 1770.0
30 TraesCS2B01G233700 chr7A 85.458 1616 225 10 1232 2840 150021870 150023482 0.000000e+00 1674.0
31 TraesCS2B01G233700 chr7A 86.310 168 21 2 3781 3948 232336869 232337034 8.950000e-42 182.0
32 TraesCS2B01G233700 chr7B 85.847 1611 209 16 1232 2840 111942447 111944040 0.000000e+00 1694.0
33 TraesCS2B01G233700 chr7B 89.024 164 18 0 2887 3050 111944120 111944283 1.910000e-48 204.0
34 TraesCS2B01G233700 chr3A 81.592 1206 196 22 1858 3048 608195756 608194562 0.000000e+00 974.0
35 TraesCS2B01G233700 chr5B 89.739 536 53 2 1232 1766 679311136 679311670 0.000000e+00 684.0
36 TraesCS2B01G233700 chr3B 86.792 159 19 2 3790 3948 655667836 655667680 4.160000e-40 176.0
37 TraesCS2B01G233700 chr3B 87.013 154 18 2 3784 3937 68913477 68913628 5.390000e-39 172.0
38 TraesCS2B01G233700 chr1B 88.435 147 15 1 3790 3936 443742209 443742065 4.160000e-40 176.0
39 TraesCS2B01G233700 chr1B 85.625 160 21 2 3778 3936 53067343 53067501 2.510000e-37 167.0
40 TraesCS2B01G233700 chr4B 86.420 162 18 3 3790 3949 93724614 93724773 1.500000e-39 174.0
41 TraesCS2B01G233700 chr6B 85.890 163 20 3 3792 3953 73077907 73077747 1.940000e-38 171.0
42 TraesCS2B01G233700 chr1A 82.635 167 22 7 2888 3050 481675571 481675734 1.520000e-29 141.0
43 TraesCS2B01G233700 chrUn 82.022 89 12 3 1 86 67135397 67135310 5.620000e-09 73.1


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 TraesCS2B01G233700 chr2B 232288505 232292558 4053 True 3448.000000 5666 100.0000 1 4054 2 chr2B.!!$R2 4053
1 TraesCS2B01G233700 chr2B 232257059 232263126 6067 False 2031.000000 2992 95.6960 297 2854 2 chr2B.!!$F4 2557
2 TraesCS2B01G233700 chr2D 165332587 165334710 2123 False 1564.500000 2351 93.0875 1 2316 2 chr2D.!!$F1 2315
3 TraesCS2B01G233700 chr2D 165483319 165485906 2587 True 1173.333333 2972 89.9180 753 3564 3 chr2D.!!$R2 2811
4 TraesCS2B01G233700 chr2D 165491715 165492351 636 True 675.000000 675 85.9970 110 755 1 chr2D.!!$R1 645
5 TraesCS2B01G233700 chr2D 165340077 165341354 1277 False 653.500000 1166 92.1015 2313 4054 2 chr2D.!!$F2 1741
6 TraesCS2B01G233700 chr2A 185360981 185365778 4797 True 867.800000 2848 93.2482 1 4054 5 chr2A.!!$R2 4053
7 TraesCS2B01G233700 chr2A 185261521 185270604 9083 False 789.800000 1718 92.0694 110 3065 5 chr2A.!!$F1 2955
8 TraesCS2B01G233700 chr7D 149181061 149183080 2019 False 1868.000000 1868 83.5440 1021 3050 1 chr7D.!!$F1 2029
9 TraesCS2B01G233700 chr7D 149083941 149085779 1838 True 1799.000000 1799 84.4700 1232 3063 1 chr7D.!!$R1 1831
10 TraesCS2B01G233700 chr7A 149860900 149862722 1822 True 1770.000000 1770 84.2480 1232 3065 1 chr7A.!!$R1 1833
11 TraesCS2B01G233700 chr7A 150021870 150023482 1612 False 1674.000000 1674 85.4580 1232 2840 1 chr7A.!!$F1 1608
12 TraesCS2B01G233700 chr7B 111942447 111944283 1836 False 949.000000 1694 87.4355 1232 3050 2 chr7B.!!$F1 1818
13 TraesCS2B01G233700 chr3A 608194562 608195756 1194 True 974.000000 974 81.5920 1858 3048 1 chr3A.!!$R1 1190
14 TraesCS2B01G233700 chr5B 679311136 679311670 534 False 684.000000 684 89.7390 1232 1766 1 chr5B.!!$F1 534

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
733 3012 0.243907 GAAGCAGTGCGTGACTAGGA 59.756 55.000 8.72 0.0 31.73 2.94 F
1577 7516 0.546122 CCATCGTCATCCTCCCCAAA 59.454 55.000 0.00 0.0 0.00 3.28 F
2199 12041 1.293498 GCCTCCGAGTCAAGCTTCA 59.707 57.895 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 11691 0.229753 GAACGTGTCTGCGAAGTGTG 59.770 55.000 0.0 0.0 35.59 3.82 R
2615 12457 1.003355 CATCACCAGCTCCACCGTT 60.003 57.895 0.0 0.0 0.00 4.44 R
3840 13958 3.933155 ATATTCACGCTTCTTGCTTCG 57.067 42.857 0.0 0.0 40.11 3.79 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
68 72 6.070995 AGGATGAATGCTGATTGTTTTCACAT 60.071 34.615 0.00 0.00 31.06 3.21
248 683 5.717078 ATTGTCAAGTGATCATGCAAACT 57.283 34.783 0.00 0.00 0.00 2.66
373 813 1.550976 ACCTGTTTCGGAGGAAGCTAG 59.449 52.381 0.00 0.00 34.78 3.42
514 954 3.997021 CGCAGAACCTAACTTTGACTGAT 59.003 43.478 0.00 0.00 0.00 2.90
515 955 4.143030 CGCAGAACCTAACTTTGACTGATG 60.143 45.833 0.00 0.00 0.00 3.07
516 956 4.757149 GCAGAACCTAACTTTGACTGATGT 59.243 41.667 0.00 0.00 0.00 3.06
517 957 5.239525 GCAGAACCTAACTTTGACTGATGTT 59.760 40.000 0.00 0.00 0.00 2.71
518 958 6.566753 GCAGAACCTAACTTTGACTGATGTTC 60.567 42.308 0.00 0.00 0.00 3.18
719 2998 0.814457 AGTGTTTTGCAACGGAAGCA 59.186 45.000 0.00 0.00 40.85 3.91
733 3012 0.243907 GAAGCAGTGCGTGACTAGGA 59.756 55.000 8.72 0.00 31.73 2.94
835 3132 3.132801 GCTCAAGCTCCTGCCTGC 61.133 66.667 0.00 0.00 40.80 4.85
1084 6950 3.042871 GCTCCTTGCTATCTCCTCATG 57.957 52.381 0.00 0.00 38.95 3.07
1085 6951 2.289569 GCTCCTTGCTATCTCCTCATGG 60.290 54.545 0.00 0.00 38.95 3.66
1086 6952 1.696336 TCCTTGCTATCTCCTCATGGC 59.304 52.381 0.00 0.00 0.00 4.40
1488 7427 2.889045 AGCTACGTCTACAACTTCACCA 59.111 45.455 0.00 0.00 0.00 4.17
1577 7516 0.546122 CCATCGTCATCCTCCCCAAA 59.454 55.000 0.00 0.00 0.00 3.28
1669 7608 2.377628 GACACGGAGGCACTGGTCAA 62.378 60.000 0.00 0.00 41.55 3.18
1760 7699 1.933853 CTATACAACTGCTCCGCCAAC 59.066 52.381 0.00 0.00 0.00 3.77
1845 11682 1.405526 CCAGTATGCTTACCGTGCACT 60.406 52.381 16.19 0.00 43.59 4.40
1849 11691 1.656652 ATGCTTACCGTGCACTCATC 58.343 50.000 16.19 0.00 43.59 2.92
2069 11911 1.898574 CCTCACAGCCAAGCCGTTT 60.899 57.895 0.00 0.00 0.00 3.60
2087 11929 4.461431 CCGTTTTATCCCAAGGCTAACTTT 59.539 41.667 0.00 0.00 37.29 2.66
2199 12041 1.293498 GCCTCCGAGTCAAGCTTCA 59.707 57.895 0.00 0.00 0.00 3.02
2206 12048 1.532868 CGAGTCAAGCTTCAACAAGGG 59.467 52.381 0.00 0.00 0.00 3.95
2300 12142 4.892965 AGCCTTGCCACACCGCAA 62.893 61.111 0.00 0.00 46.23 4.85
3456 13340 5.363979 TTTGTGTATTTAATCAGTGCGCA 57.636 34.783 5.66 5.66 0.00 6.09
3480 13364 8.178313 GCAGGTCTTGTAATTTTCTTGTATCTC 58.822 37.037 0.00 0.00 0.00 2.75
3482 13366 9.660180 AGGTCTTGTAATTTTCTTGTATCTCTC 57.340 33.333 0.00 0.00 0.00 3.20
3564 13681 6.947733 TGTCAACTGAATGTCCAAATCCTTAT 59.052 34.615 0.00 0.00 0.00 1.73
3570 13687 7.280205 ACTGAATGTCCAAATCCTTATAACGTC 59.720 37.037 0.00 0.00 0.00 4.34
3594 13711 8.971321 GTCTTTGTTAGTAGTTTCACGTTGATA 58.029 33.333 0.00 0.00 0.00 2.15
3595 13712 9.701098 TCTTTGTTAGTAGTTTCACGTTGATAT 57.299 29.630 0.00 0.00 0.00 1.63
3606 13723 8.287503 AGTTTCACGTTGATATTTAAACTCCAC 58.712 33.333 0.00 0.00 31.89 4.02
3702 13819 7.277760 GGCAAAAGACTTGTCAAATAAGTGTTT 59.722 33.333 7.05 7.05 46.84 2.83
3735 13852 7.676947 TCAGTAAAACTATAGCTTCAGTGGTT 58.323 34.615 0.00 0.00 0.00 3.67
3739 13856 7.817418 AAAACTATAGCTTCAGTGGTTCAAA 57.183 32.000 0.00 0.00 0.00 2.69
3807 13925 9.382275 GTTTACAACCTCCGTTCCTAAATATAA 57.618 33.333 0.00 0.00 0.00 0.98
3809 13927 6.053650 ACAACCTCCGTTCCTAAATATAAGC 58.946 40.000 0.00 0.00 0.00 3.09
3814 13932 6.427242 CCTCCGTTCCTAAATATAAGCCTTTC 59.573 42.308 0.00 0.00 0.00 2.62
3848 13966 9.678941 TTCAATATAGACTACATACGAAGCAAG 57.321 33.333 0.00 0.00 0.00 4.01
3849 13967 9.063615 TCAATATAGACTACATACGAAGCAAGA 57.936 33.333 0.00 0.00 0.00 3.02
3850 13968 9.678941 CAATATAGACTACATACGAAGCAAGAA 57.321 33.333 0.00 0.00 0.00 2.52
3851 13969 9.900710 AATATAGACTACATACGAAGCAAGAAG 57.099 33.333 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 57 5.509272 GTGCGTATCATGTGAAAACAATCAG 59.491 40.000 0.00 0.00 0.00 2.90
68 72 3.474904 GCGTGCACGTGCGTATCA 61.475 61.111 36.80 14.79 45.83 2.15
113 117 2.553172 CCCAACCCGATCAACGTTTTTA 59.447 45.455 0.00 0.00 40.78 1.52
248 683 7.787028 TCAGTATACTATGTGCATGTACCAAA 58.213 34.615 11.66 0.00 0.00 3.28
373 813 1.002468 CGCCATAACAACCAGCATAGC 60.002 52.381 0.00 0.00 0.00 2.97
514 954 3.214328 GGAGAAAAGGCAGAACAGAACA 58.786 45.455 0.00 0.00 0.00 3.18
515 955 3.214328 TGGAGAAAAGGCAGAACAGAAC 58.786 45.455 0.00 0.00 0.00 3.01
516 956 3.480470 CTGGAGAAAAGGCAGAACAGAA 58.520 45.455 0.00 0.00 0.00 3.02
517 957 2.224621 CCTGGAGAAAAGGCAGAACAGA 60.225 50.000 0.00 0.00 0.00 3.41
518 958 2.157738 CCTGGAGAAAAGGCAGAACAG 58.842 52.381 0.00 0.00 0.00 3.16
719 2998 1.281287 TCCTACTCCTAGTCACGCACT 59.719 52.381 0.00 0.00 39.41 4.40
733 3012 4.402474 GGTTTAATTTGCATGCCTCCTACT 59.598 41.667 16.68 0.00 0.00 2.57
835 3132 1.134818 TCGGTGGATGAACGATCAAGG 60.135 52.381 0.00 0.00 39.49 3.61
915 3220 1.804326 GCGTGTACCACCAGCTACG 60.804 63.158 0.00 0.00 34.93 3.51
916 3221 0.037605 AAGCGTGTACCACCAGCTAC 60.038 55.000 0.00 0.00 31.81 3.58
917 3222 0.037697 CAAGCGTGTACCACCAGCTA 60.038 55.000 0.00 0.00 31.81 3.32
918 3223 1.301716 CAAGCGTGTACCACCAGCT 60.302 57.895 0.00 0.00 33.75 4.24
1084 6950 4.521062 AGCATCAGAGTCGCCGCC 62.521 66.667 0.00 0.00 0.00 6.13
1085 6951 3.260483 CAGCATCAGAGTCGCCGC 61.260 66.667 0.00 0.00 0.00 6.53
1086 6952 3.260483 GCAGCATCAGAGTCGCCG 61.260 66.667 0.00 0.00 0.00 6.46
1556 7495 2.427753 GGGAGGATGACGATGGCC 59.572 66.667 0.00 0.00 0.00 5.36
1577 7516 4.078516 GGGTAAGGCACGCCGAGT 62.079 66.667 1.61 0.00 41.95 4.18
1760 7699 1.522676 CATAGTGAGCGCAATGTACCG 59.477 52.381 11.47 0.00 0.00 4.02
1845 11682 1.783284 GTGTCTGCGAAGTGTGATGA 58.217 50.000 0.00 0.00 0.00 2.92
1849 11691 0.229753 GAACGTGTCTGCGAAGTGTG 59.770 55.000 0.00 0.00 35.59 3.82
2069 11911 7.179269 ACATGTAAAAGTTAGCCTTGGGATAA 58.821 34.615 0.00 0.00 30.64 1.75
2199 12041 2.011617 AAGAGTGGCAGGCCCTTGTT 62.012 55.000 8.02 0.00 34.56 2.83
2561 12403 1.298041 GGCCACGTTCGTGTTGTTG 60.298 57.895 20.93 8.82 34.59 3.33
2588 12430 1.070615 TGGCAACACGAGCAGCTTA 59.929 52.632 0.00 0.00 46.17 3.09
2615 12457 1.003355 CATCACCAGCTCCACCGTT 60.003 57.895 0.00 0.00 0.00 4.44
3456 13340 9.660180 GAGAGATACAAGAAAATTACAAGACCT 57.340 33.333 0.00 0.00 0.00 3.85
3564 13681 6.972328 ACGTGAAACTACTAACAAAGACGTTA 59.028 34.615 0.00 0.00 31.75 3.18
3581 13698 8.287503 AGTGGAGTTTAAATATCAACGTGAAAC 58.712 33.333 0.00 0.00 0.00 2.78
3594 13711 7.418337 AAAGACAACCAAGTGGAGTTTAAAT 57.582 32.000 3.83 0.00 38.94 1.40
3595 13712 6.844097 AAAGACAACCAAGTGGAGTTTAAA 57.156 33.333 3.83 0.00 38.94 1.52
3673 13790 6.321181 ACTTATTTGACAAGTCTTTTGCCTCA 59.679 34.615 1.53 0.00 30.36 3.86
3735 13852 6.882610 AGTTTAGTGAATCATGCTGTTTGA 57.117 33.333 0.00 0.00 0.00 2.69
3739 13856 7.661437 TCAAGTAAGTTTAGTGAATCATGCTGT 59.339 33.333 0.00 0.00 0.00 4.40
3784 13902 7.212274 GCTTATATTTAGGAACGGAGGTTGTA 58.788 38.462 0.00 0.00 36.24 2.41
3785 13903 6.053650 GCTTATATTTAGGAACGGAGGTTGT 58.946 40.000 0.00 0.00 36.24 3.32
3786 13904 5.469084 GGCTTATATTTAGGAACGGAGGTTG 59.531 44.000 0.00 0.00 36.24 3.77
3787 13905 5.368816 AGGCTTATATTTAGGAACGGAGGTT 59.631 40.000 0.00 0.00 39.63 3.50
3788 13906 4.906060 AGGCTTATATTTAGGAACGGAGGT 59.094 41.667 0.00 0.00 0.00 3.85
3789 13907 5.485209 AGGCTTATATTTAGGAACGGAGG 57.515 43.478 0.00 0.00 0.00 4.30
3790 13908 7.217906 AGAAAGGCTTATATTTAGGAACGGAG 58.782 38.462 0.00 0.00 0.00 4.63
3791 13909 7.133133 AGAAAGGCTTATATTTAGGAACGGA 57.867 36.000 0.00 0.00 0.00 4.69
3792 13910 8.365647 TCTAGAAAGGCTTATATTTAGGAACGG 58.634 37.037 0.00 0.00 0.00 4.44
3793 13911 9.413048 CTCTAGAAAGGCTTATATTTAGGAACG 57.587 37.037 0.00 0.00 0.00 3.95
3830 13948 4.425520 GCTTCTTGCTTCGTATGTAGTCT 58.574 43.478 0.00 0.00 38.95 3.24
3840 13958 3.933155 ATATTCACGCTTCTTGCTTCG 57.067 42.857 0.00 0.00 40.11 3.79
3841 13959 5.292101 AGTGTATATTCACGCTTCTTGCTTC 59.708 40.000 6.81 0.00 42.40 3.86
3842 13960 5.178797 AGTGTATATTCACGCTTCTTGCTT 58.821 37.500 6.81 0.00 42.40 3.91
3843 13961 4.759782 AGTGTATATTCACGCTTCTTGCT 58.240 39.130 6.81 0.00 42.40 3.91
3844 13962 6.771188 ATAGTGTATATTCACGCTTCTTGC 57.229 37.500 6.81 0.00 42.40 4.01
3938 14056 8.841757 TCTAGATGAGCCTTAGATACTTCCTAT 58.158 37.037 0.00 0.00 0.00 2.57
3939 14057 8.104566 GTCTAGATGAGCCTTAGATACTTCCTA 58.895 40.741 0.00 0.00 0.00 2.94
3941 14059 6.128117 CGTCTAGATGAGCCTTAGATACTTCC 60.128 46.154 6.03 0.00 0.00 3.46
3942 14060 6.651643 TCGTCTAGATGAGCCTTAGATACTTC 59.348 42.308 10.73 0.00 0.00 3.01
3943 14061 6.535540 TCGTCTAGATGAGCCTTAGATACTT 58.464 40.000 10.73 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.