Multiple sequence alignment - TraesCS5B01G087400

Loading Multiple Alignment...

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 TraesCS5B01G087400 chr5B 100.000 4046 0 0 1 4046 112022562 112018517 0.000000e+00 7472.0
1 TraesCS5B01G087400 chr5A 95.066 3648 123 23 418 4046 96983024 96986633 0.000000e+00 5686.0
2 TraesCS5B01G087400 chr5A 91.395 430 33 2 1 426 96982269 96982698 1.620000e-163 586.0
3 TraesCS5B01G087400 chr5A 90.909 44 0 4 3642 3685 27546054 27546015 5.650000e-04 56.5
4 TraesCS5B01G087400 chr5D 96.907 3136 74 8 818 3936 102332305 102329176 0.000000e+00 5232.0
5 TraesCS5B01G087400 chr5D 92.281 570 29 11 140 701 102332982 102332420 0.000000e+00 795.0
6 TraesCS5B01G087400 chr5D 95.312 128 5 1 3919 4046 102328663 102328537 6.860000e-48 202.0
7 TraesCS5B01G087400 chr5D 93.382 136 6 1 1 133 102339578 102339443 8.870000e-47 198.0
8 TraesCS5B01G087400 chr5D 96.639 119 3 1 684 801 102332406 102332288 3.190000e-46 196.0
9 TraesCS5B01G087400 chr3A 84.219 1977 279 24 1075 3036 19988359 19990317 0.000000e+00 1892.0
10 TraesCS5B01G087400 chr1D 84.793 1907 254 22 1165 3044 32738145 32740042 0.000000e+00 1882.0
11 TraesCS5B01G087400 chr3B 85.016 1862 255 21 1191 3039 24019166 24017316 0.000000e+00 1871.0
12 TraesCS5B01G087400 chr3B 76.408 1882 382 57 1196 3037 609801992 609803851 0.000000e+00 959.0
13 TraesCS5B01G087400 chr1B 84.298 1917 258 28 1165 3047 50204094 50206001 0.000000e+00 1832.0
14 TraesCS5B01G087400 chr1A 84.099 1893 254 32 1187 3044 31254306 31252426 0.000000e+00 1784.0
15 TraesCS5B01G087400 chr3D 76.592 1884 375 62 1196 3037 460180050 460181909 0.000000e+00 976.0
16 TraesCS5B01G087400 chr3D 86.207 58 5 3 3638 3693 277152213 277152269 4.370000e-05 60.2
17 TraesCS5B01G087400 chr7D 90.820 512 24 11 3554 4044 608862399 608861890 0.000000e+00 664.0
18 TraesCS5B01G087400 chr7D 82.143 168 29 1 331 497 236640589 236640422 4.220000e-30 143.0
19 TraesCS5B01G087400 chr7D 79.412 170 33 2 330 497 13692498 13692329 7.100000e-23 119.0
20 TraesCS5B01G087400 chr7D 79.290 169 33 2 331 497 13688685 13688517 2.560000e-22 117.0
21 TraesCS5B01G087400 chr7D 79.290 169 33 2 331 497 13691227 13691059 2.560000e-22 117.0
22 TraesCS5B01G087400 chr7D 78.107 169 35 2 331 497 13689955 13689787 5.530000e-19 106.0
23 TraesCS5B01G087400 chr4D 79.833 719 135 9 1217 1930 348564324 348565037 2.160000e-142 516.0
24 TraesCS5B01G087400 chr4B 79.580 715 136 9 1203 1912 428845440 428846149 1.680000e-138 503.0
25 TraesCS5B01G087400 chr4A 79.127 733 143 8 1203 1930 116852161 116851434 7.810000e-137 497.0
26 TraesCS5B01G087400 chr4A 100.000 29 0 0 3596 3624 609567967 609567995 2.000000e-03 54.7
27 TraesCS5B01G087400 chr7B 82.143 168 29 1 331 497 213248073 213247906 4.220000e-30 143.0
28 TraesCS5B01G087400 chr7B 92.683 41 0 3 3643 3683 191676487 191676450 5.650000e-04 56.5
29 TraesCS5B01G087400 chr7A 80.952 168 31 1 331 497 251743508 251743341 9.120000e-27 132.0
30 TraesCS5B01G087400 chr2A 83.133 83 8 5 3615 3693 210060836 210060916 2.020000e-08 71.3
31 TraesCS5B01G087400 chr2A 92.157 51 3 1 3643 3693 309688835 309688884 2.020000e-08 71.3
32 TraesCS5B01G087400 chr6B 100.000 29 0 0 3644 3672 155228725 155228753 2.000000e-03 54.7


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 TraesCS5B01G087400 chr5B 112018517 112022562 4045 True 7472.00 7472 100.00000 1 4046 1 chr5B.!!$R1 4045
1 TraesCS5B01G087400 chr5A 96982269 96986633 4364 False 3136.00 5686 93.23050 1 4046 2 chr5A.!!$F1 4045
2 TraesCS5B01G087400 chr5D 102328537 102332982 4445 True 1606.25 5232 95.28475 140 4046 4 chr5D.!!$R2 3906
3 TraesCS5B01G087400 chr3A 19988359 19990317 1958 False 1892.00 1892 84.21900 1075 3036 1 chr3A.!!$F1 1961
4 TraesCS5B01G087400 chr1D 32738145 32740042 1897 False 1882.00 1882 84.79300 1165 3044 1 chr1D.!!$F1 1879
5 TraesCS5B01G087400 chr3B 24017316 24019166 1850 True 1871.00 1871 85.01600 1191 3039 1 chr3B.!!$R1 1848
6 TraesCS5B01G087400 chr3B 609801992 609803851 1859 False 959.00 959 76.40800 1196 3037 1 chr3B.!!$F1 1841
7 TraesCS5B01G087400 chr1B 50204094 50206001 1907 False 1832.00 1832 84.29800 1165 3047 1 chr1B.!!$F1 1882
8 TraesCS5B01G087400 chr1A 31252426 31254306 1880 True 1784.00 1784 84.09900 1187 3044 1 chr1A.!!$R1 1857
9 TraesCS5B01G087400 chr3D 460180050 460181909 1859 False 976.00 976 76.59200 1196 3037 1 chr3D.!!$F2 1841
10 TraesCS5B01G087400 chr7D 608861890 608862399 509 True 664.00 664 90.82000 3554 4044 1 chr7D.!!$R2 490
11 TraesCS5B01G087400 chr4D 348564324 348565037 713 False 516.00 516 79.83300 1217 1930 1 chr4D.!!$F1 713
12 TraesCS5B01G087400 chr4B 428845440 428846149 709 False 503.00 503 79.58000 1203 1912 1 chr4B.!!$F1 709
13 TraesCS5B01G087400 chr4A 116851434 116852161 727 True 497.00 497 79.12700 1203 1930 1 chr4A.!!$R1 727

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
778 1156 0.600557 ACTCTGGCACTCGAGTTCAG 59.399 55.000 27.22 27.22 37.19 3.02 F
1698 2090 1.447140 GAGCGCGTTCATGGTGGTA 60.447 57.895 18.62 0.00 0.00 3.25 F
2646 3077 0.395862 TCCTCGCCTACTTCCTCCTG 60.396 60.000 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 2129 0.035152 GCTGGTGGATGGTCATCACA 60.035 55.000 12.33 7.41 39.54 3.58 R
2967 3401 1.813753 GAAGCCGAATGCCGCAGTA 60.814 57.895 0.00 0.00 42.71 2.74 R
3771 4225 2.108168 AGGTAGCTATGGTCGCAGAAA 58.892 47.619 0.00 0.00 39.69 2.52 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
20 21 1.006102 GGGCGATGGTCGGATACAG 60.006 63.158 1.29 0.00 40.84 2.74
27 28 0.681887 TGGTCGGATACAGCGGAAGA 60.682 55.000 0.00 0.00 0.00 2.87
52 53 3.416955 GCAAAAGGTAATGCGGGTG 57.583 52.632 0.00 0.00 32.17 4.61
82 86 5.066764 AGCTCCTAGAAGAGTAAAGTAAGCG 59.933 44.000 0.00 0.00 36.20 4.68
91 95 1.392510 GTAAAGTAAGCGGTCCTTGCG 59.607 52.381 0.00 0.00 40.60 4.85
133 137 3.442625 CGTTCACTGGACTAGGTGTATCA 59.557 47.826 0.00 0.00 35.26 2.15
171 175 1.972872 ATCACGCAATCCCTCATTCC 58.027 50.000 0.00 0.00 0.00 3.01
223 227 3.736126 CGACGGTTGAGGTTAGGGTTATC 60.736 52.174 0.00 0.00 0.00 1.75
235 239 1.209747 AGGGTTATCCTTGTCTTCCGC 59.790 52.381 0.00 0.00 45.47 5.54
237 241 1.065709 GGTTATCCTTGTCTTCCGCCA 60.066 52.381 0.00 0.00 0.00 5.69
268 273 2.019807 TTGAAGTCTCCCCCGTAAGT 57.980 50.000 0.00 0.00 0.00 2.24
275 280 1.358787 TCTCCCCCGTAAGTCAAGGTA 59.641 52.381 0.00 0.00 0.00 3.08
302 308 1.205417 GGGAAGCACAAACATCATGGG 59.795 52.381 0.00 0.00 0.00 4.00
305 311 1.549203 AGCACAAACATCATGGGGAC 58.451 50.000 0.00 0.00 0.00 4.46
350 356 5.587043 TCATTGTCCCCAAATTATGTCGTAC 59.413 40.000 0.00 0.00 33.44 3.67
352 358 4.509616 TGTCCCCAAATTATGTCGTACAG 58.490 43.478 0.00 0.00 0.00 2.74
355 361 5.465724 GTCCCCAAATTATGTCGTACAGATC 59.534 44.000 0.00 0.00 0.00 2.75
388 394 8.674263 AATGTCAATGCTTTCCAAATTAAACA 57.326 26.923 0.00 0.00 0.00 2.83
778 1156 0.600557 ACTCTGGCACTCGAGTTCAG 59.399 55.000 27.22 27.22 37.19 3.02
783 1161 1.684450 TGGCACTCGAGTTCAGTTGTA 59.316 47.619 17.26 0.00 0.00 2.41
785 1163 1.714460 GCACTCGAGTTCAGTTGTACG 59.286 52.381 17.26 1.25 0.00 3.67
787 1165 3.607775 GCACTCGAGTTCAGTTGTACGTA 60.608 47.826 17.26 0.00 0.00 3.57
789 1167 5.672073 GCACTCGAGTTCAGTTGTACGTATA 60.672 44.000 17.26 0.00 0.00 1.47
791 1169 4.885838 TCGAGTTCAGTTGTACGTATACG 58.114 43.478 23.24 23.24 46.33 3.06
805 1183 4.386716 CGTATACGTAGCGATCTTGTCT 57.613 45.455 17.16 0.00 34.11 3.41
806 1184 4.384529 CGTATACGTAGCGATCTTGTCTC 58.615 47.826 17.16 0.00 34.11 3.36
807 1185 4.084693 CGTATACGTAGCGATCTTGTCTCA 60.085 45.833 17.16 0.00 34.11 3.27
808 1186 4.895224 ATACGTAGCGATCTTGTCTCAA 57.105 40.909 0.08 0.00 0.00 3.02
810 1188 3.502920 ACGTAGCGATCTTGTCTCAAAG 58.497 45.455 0.00 0.00 0.00 2.77
813 1191 4.621460 CGTAGCGATCTTGTCTCAAAGAAA 59.379 41.667 0.00 0.00 39.54 2.52
814 1192 5.118664 CGTAGCGATCTTGTCTCAAAGAAAA 59.881 40.000 0.00 0.00 39.54 2.29
815 1193 6.346598 CGTAGCGATCTTGTCTCAAAGAAAAA 60.347 38.462 0.00 0.00 39.54 1.94
875 1255 5.339990 CAAAGTTCAAACCAAACACGAGAT 58.660 37.500 0.00 0.00 0.00 2.75
947 1329 1.951130 CCCACCAATCGATCGAGCG 60.951 63.158 23.84 18.51 0.00 5.03
960 1347 4.738345 GAGCGCTCGTCGTGTCGT 62.738 66.667 23.61 0.00 41.07 4.34
963 1350 3.157523 CGCTCGTCGTGTCGTGTC 61.158 66.667 0.00 0.00 0.00 3.67
964 1351 3.157523 GCTCGTCGTGTCGTGTCG 61.158 66.667 0.00 0.00 0.00 4.35
965 1352 3.157523 CTCGTCGTGTCGTGTCGC 61.158 66.667 0.00 0.00 0.00 5.19
966 1353 4.999532 TCGTCGTGTCGTGTCGCG 63.000 66.667 0.00 0.00 41.75 5.87
1698 2090 1.447140 GAGCGCGTTCATGGTGGTA 60.447 57.895 18.62 0.00 0.00 3.25
1803 2195 2.441901 CGCCTCCTGCTCCTCTCT 60.442 66.667 0.00 0.00 38.05 3.10
2209 2640 1.153309 CGCCTGAGCACCATCATGA 60.153 57.895 0.00 0.00 39.83 3.07
2646 3077 0.395862 TCCTCGCCTACTTCCTCCTG 60.396 60.000 0.00 0.00 0.00 3.86
2886 3320 3.354678 GGCACAAACATGACGGCT 58.645 55.556 0.00 0.00 0.00 5.52
2967 3401 1.136329 AGTGGATGTGCCTCCTGGTT 61.136 55.000 0.00 0.00 36.20 3.67
2970 3404 0.912486 GGATGTGCCTCCTGGTTACT 59.088 55.000 0.00 0.00 35.27 2.24
3332 3768 5.964887 TTTTTCAGAATTCGCTGTTTTGG 57.035 34.783 0.00 0.00 37.20 3.28
3392 3829 5.664457 CTGCTACAATGTCTCAACTATCCA 58.336 41.667 0.00 0.00 0.00 3.41
3393 3830 5.419542 TGCTACAATGTCTCAACTATCCAC 58.580 41.667 0.00 0.00 0.00 4.02
3418 3855 7.231925 ACGTAATAATTTCCAAACAACCTCCTT 59.768 33.333 0.00 0.00 0.00 3.36
3434 3871 3.181439 CCTCCTTTCCTTTGTTCTGGAGT 60.181 47.826 0.00 0.00 38.24 3.85
3640 4077 8.000780 ACTTGTCTTTCTTTTTAAGCACTGAT 57.999 30.769 0.00 0.00 0.00 2.90
3750 4204 6.318900 AGAGTATTCGTCACATGACATAGACA 59.681 38.462 12.32 3.23 44.99 3.41
3889 4344 9.992442 TTCTAGAAGAAGATTAAACTCCTCCTA 57.008 33.333 0.00 0.00 29.50 2.94
3915 4370 2.427232 GCAAATCTGAAGCACTTGCA 57.573 45.000 3.62 0.00 45.16 4.08
3927 4382 7.121020 TCTGAAGCACTTGCATTGTATTATGAA 59.879 33.333 3.62 0.00 45.16 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.371758 CCGCTGTATCCGACCATCG 60.372 63.158 0.00 0.00 40.07 3.84
27 28 1.539827 GCATTACCTTTTGCGGTGTCT 59.460 47.619 0.00 0.00 37.93 3.41
42 43 2.499205 CTCCGAGCACCCGCATTA 59.501 61.111 0.00 0.00 42.27 1.90
52 53 0.951558 CTCTTCTAGGAGCTCCGAGC 59.048 60.000 31.84 12.80 42.84 5.03
133 137 5.059161 GTGATATGTACATGCATGAGTGGT 58.941 41.667 32.75 12.71 0.00 4.16
171 175 0.370273 CGCTTTCGTCGATTCCTTGG 59.630 55.000 0.00 0.00 0.00 3.61
204 208 2.770232 AGGATAACCCTAACCTCAACCG 59.230 50.000 0.00 0.00 45.48 4.44
235 239 6.229733 GGAGACTTCAATATGATCCTCTTGG 58.770 44.000 0.00 0.00 0.00 3.61
237 241 5.309282 GGGGAGACTTCAATATGATCCTCTT 59.691 44.000 0.00 0.00 0.00 2.85
268 273 1.263356 CTTCCCCGACTGTACCTTGA 58.737 55.000 0.00 0.00 0.00 3.02
275 280 0.818040 GTTTGTGCTTCCCCGACTGT 60.818 55.000 0.00 0.00 0.00 3.55
302 308 2.798148 ATTGTGTTCCTCGCGGGTCC 62.798 60.000 4.71 2.16 36.25 4.46
305 311 0.673644 AAGATTGTGTTCCTCGCGGG 60.674 55.000 6.13 0.59 0.00 6.13
317 323 3.524095 TGGGGACAATGACAAGATTGT 57.476 42.857 0.00 0.00 46.89 2.71
352 358 9.508567 GGAAAGCATTGACATTTTAACTAGATC 57.491 33.333 0.00 0.00 0.00 2.75
355 361 9.474920 TTTGGAAAGCATTGACATTTTAACTAG 57.525 29.630 0.00 0.00 0.00 2.57
682 1028 1.343465 CCACCAGTACAACTCCGTCTT 59.657 52.381 0.00 0.00 0.00 3.01
785 1163 5.340010 TGAGACAAGATCGCTACGTATAC 57.660 43.478 0.00 0.00 0.00 1.47
787 1165 4.895224 TTGAGACAAGATCGCTACGTAT 57.105 40.909 0.00 0.00 0.00 3.06
789 1167 3.190744 TCTTTGAGACAAGATCGCTACGT 59.809 43.478 0.00 0.00 0.00 3.57
791 1169 6.467723 TTTTCTTTGAGACAAGATCGCTAC 57.532 37.500 0.00 0.00 0.00 3.58
875 1255 1.367659 GTGGTTTGCTTTGCTTTGCA 58.632 45.000 0.00 0.00 36.47 4.08
947 1329 3.157523 CGACACGACACGACGAGC 61.158 66.667 0.00 0.00 37.03 5.03
960 1347 0.588980 CGATGATCTTCGACGCGACA 60.589 55.000 22.68 0.00 41.62 4.35
963 1350 4.589967 TCGATGATCTTCGACGCG 57.410 55.556 24.91 3.53 42.81 6.01
967 1354 1.359117 GGCGGTCGATGATCTTCGA 59.641 57.895 24.91 24.91 45.27 3.71
1519 1911 3.075005 GGTGAGGCCGAGCTGGTA 61.075 66.667 0.00 0.00 41.21 3.25
1737 2129 0.035152 GCTGGTGGATGGTCATCACA 60.035 55.000 12.33 7.41 39.54 3.58
2197 2628 3.391736 CCGTCATCATGATGGTGCT 57.608 52.632 30.54 0.00 46.07 4.40
2209 2640 2.446848 CCAGGATGAGCCCCGTCAT 61.447 63.158 0.00 0.00 39.69 3.06
2337 2768 1.602605 TCGCTCCTGGACGAAGACA 60.603 57.895 15.61 0.00 34.93 3.41
2340 2771 1.444553 GTGTCGCTCCTGGACGAAG 60.445 63.158 18.32 0.35 40.47 3.79
2646 3077 2.386661 TGATGAAGAAGCCGGAGAAC 57.613 50.000 5.05 0.00 0.00 3.01
2967 3401 1.813753 GAAGCCGAATGCCGCAGTA 60.814 57.895 0.00 0.00 42.71 2.74
2970 3404 2.359850 AAGAAGCCGAATGCCGCA 60.360 55.556 0.00 0.00 42.71 5.69
3315 3751 5.717038 AAAAACCAAAACAGCGAATTCTG 57.283 34.783 3.52 0.00 39.86 3.02
3353 3790 7.776933 TTGTAGCAGCTGAGTAATATCAAAG 57.223 36.000 20.43 0.00 0.00 2.77
3392 3829 6.717997 AGGAGGTTGTTTGGAAATTATTACGT 59.282 34.615 0.00 0.00 0.00 3.57
3393 3830 7.153217 AGGAGGTTGTTTGGAAATTATTACG 57.847 36.000 0.00 0.00 0.00 3.18
3418 3855 4.165372 ACCAACTACTCCAGAACAAAGGAA 59.835 41.667 0.00 0.00 32.57 3.36
3434 3871 2.976882 AGGTAGAAGGTTGCACCAACTA 59.023 45.455 7.88 7.41 43.14 2.24
3453 3890 4.520492 AGATTGTGTTCCACTAGCAAAAGG 59.480 41.667 0.00 0.00 35.11 3.11
3695 4148 7.429340 GTCAGCGACAAGTAATATGGATTTTTG 59.571 37.037 4.20 0.00 32.09 2.44
3771 4225 2.108168 AGGTAGCTATGGTCGCAGAAA 58.892 47.619 0.00 0.00 39.69 2.52
3889 4344 5.909621 AGTGCTTCAGATTTGCAATACAT 57.090 34.783 0.00 0.00 38.50 2.29


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

AutoCloner maintained by Alex Coulton.