Multiple sequence alignment - TraesCS7D01G013600

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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 TraesCS7D01G013600 chr7D 100.000 5046 0 0 1 5046 5789139 5784094 0.000000e+00 9319
1 TraesCS7D01G013600 chr7D 81.950 3651 594 46 1320 4940 5486537 5482922 0.000000e+00 3031
2 TraesCS7D01G013600 chr7D 79.656 2792 501 51 2245 5014 5665585 5662839 0.000000e+00 1947
3 TraesCS7D01G013600 chr7D 81.299 1909 335 18 3046 4940 5458144 5456244 0.000000e+00 1528
4 TraesCS7D01G013600 chr7D 100.000 517 0 0 5345 5861 5783795 5783279 0.000000e+00 955
5 TraesCS7D01G013600 chr4A 97.392 5062 75 17 1 5035 736434836 736429805 0.000000e+00 8564
6 TraesCS7D01G013600 chr4A 98.040 4796 67 3 277 5045 735733133 735737928 0.000000e+00 8311
7 TraesCS7D01G013600 chr4A 98.761 2664 30 1 2383 5046 736816021 736818681 0.000000e+00 4734
8 TraesCS7D01G013600 chr4A 83.692 3900 598 31 1030 4912 735316355 735320233 0.000000e+00 3644
9 TraesCS7D01G013600 chr4A 83.054 3942 613 43 1030 4940 735562665 735558748 0.000000e+00 3528
10 TraesCS7D01G013600 chr4A 81.610 4062 676 48 937 4980 736119676 736123684 0.000000e+00 3297
11 TraesCS7D01G013600 chr4A 81.632 3958 659 41 993 4937 735020295 735024197 0.000000e+00 3219
12 TraesCS7D01G013600 chr4A 81.976 3795 606 45 1030 4787 736896813 736900566 0.000000e+00 3147
13 TraesCS7D01G013600 chr4A 81.580 3518 619 23 1436 4940 735689506 735693007 0.000000e+00 2880
14 TraesCS7D01G013600 chr4A 83.389 2408 377 11 937 3343 734876163 734878548 0.000000e+00 2209
15 TraesCS7D01G013600 chr4A 84.251 2216 339 10 1001 3212 734480156 734482365 0.000000e+00 2150
16 TraesCS7D01G013600 chr4A 95.022 1386 29 11 254 1609 736810642 736812017 0.000000e+00 2141
17 TraesCS7D01G013600 chr4A 80.637 2448 439 27 2519 4940 735777962 735780400 0.000000e+00 1862
18 TraesCS7D01G013600 chr4A 80.032 2489 445 38 2347 4817 735652463 735650009 0.000000e+00 1796
19 TraesCS7D01G013600 chr4A 82.006 1745 284 22 3207 4938 734482990 734484717 0.000000e+00 1456
20 TraesCS7D01G013600 chr4A 97.099 517 13 2 5345 5861 736818755 736819269 0.000000e+00 870
21 TraesCS7D01G013600 chr4A 92.070 517 19 5 5349 5861 735738225 735738723 0.000000e+00 708
22 TraesCS7D01G013600 chr4A 91.667 492 16 4 5374 5861 736429440 736428970 0.000000e+00 658
23 TraesCS7D01G013600 chr4A 95.406 283 4 4 1 282 735732801 735733075 5.390000e-120 442
24 TraesCS7D01G013600 chr4A 90.837 251 21 2 6 255 736810364 736810613 9.410000e-88 335


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 TraesCS7D01G013600 chr7D 5783279 5789139 5860 True 5137.000000 9319 100.0000 1 5861 2 chr7D.!!$R4 5860
1 TraesCS7D01G013600 chr7D 5482922 5486537 3615 True 3031.000000 3031 81.9500 1320 4940 1 chr7D.!!$R2 3620
2 TraesCS7D01G013600 chr7D 5662839 5665585 2746 True 1947.000000 1947 79.6560 2245 5014 1 chr7D.!!$R3 2769
3 TraesCS7D01G013600 chr7D 5456244 5458144 1900 True 1528.000000 1528 81.2990 3046 4940 1 chr7D.!!$R1 1894
4 TraesCS7D01G013600 chr4A 736428970 736434836 5866 True 4611.000000 8564 94.5295 1 5861 2 chr4A.!!$R3 5860
5 TraesCS7D01G013600 chr4A 735316355 735320233 3878 False 3644.000000 3644 83.6920 1030 4912 1 chr4A.!!$F3 3882
6 TraesCS7D01G013600 chr4A 735558748 735562665 3917 True 3528.000000 3528 83.0540 1030 4940 1 chr4A.!!$R1 3910
7 TraesCS7D01G013600 chr4A 736119676 736123684 4008 False 3297.000000 3297 81.6100 937 4980 1 chr4A.!!$F6 4043
8 TraesCS7D01G013600 chr4A 735020295 735024197 3902 False 3219.000000 3219 81.6320 993 4937 1 chr4A.!!$F2 3944
9 TraesCS7D01G013600 chr4A 735732801 735738723 5922 False 3153.666667 8311 95.1720 1 5861 3 chr4A.!!$F9 5860
10 TraesCS7D01G013600 chr4A 736896813 736900566 3753 False 3147.000000 3147 81.9760 1030 4787 1 chr4A.!!$F7 3757
11 TraesCS7D01G013600 chr4A 735689506 735693007 3501 False 2880.000000 2880 81.5800 1436 4940 1 chr4A.!!$F4 3504
12 TraesCS7D01G013600 chr4A 736816021 736819269 3248 False 2802.000000 4734 97.9300 2383 5861 2 chr4A.!!$F11 3478
13 TraesCS7D01G013600 chr4A 734876163 734878548 2385 False 2209.000000 2209 83.3890 937 3343 1 chr4A.!!$F1 2406
14 TraesCS7D01G013600 chr4A 735777962 735780400 2438 False 1862.000000 1862 80.6370 2519 4940 1 chr4A.!!$F5 2421
15 TraesCS7D01G013600 chr4A 734480156 734484717 4561 False 1803.000000 2150 83.1285 1001 4938 2 chr4A.!!$F8 3937
16 TraesCS7D01G013600 chr4A 735650009 735652463 2454 True 1796.000000 1796 80.0320 2347 4817 1 chr4A.!!$R2 2470
17 TraesCS7D01G013600 chr4A 736810364 736812017 1653 False 1238.000000 2141 92.9295 6 1609 2 chr4A.!!$F10 1603

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
168 172 0.391263 GTTCTTAGGCTGGGTGGTCG 60.391 60.000 0.0 0.0 0.00 4.79 F
260 315 0.741221 GCGCAGGGGTAGAAGAACAG 60.741 60.000 0.3 0.0 0.00 3.16 F
729 850 0.948141 GTATCGCTGCCTGCCTCATC 60.948 60.000 0.0 0.0 38.78 2.92 F
921 1067 5.072741 CACCCCCAATCAATAAGGACTATG 58.927 45.833 0.0 0.0 0.00 2.23 F
3562 4397 5.817816 CCGCTAGGACTTGAAATACTGAAAT 59.182 40.000 0.0 0.0 41.02 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1407 1.165907 TTGCGCTTGAGGAGGTTGTG 61.166 55.000 9.73 0.0 0.0 3.33 R
1299 1449 3.054139 TGGAAGAGTCATTAGGCAGCATT 60.054 43.478 0.00 0.0 0.0 3.56 R
3914 4753 0.318762 AGTCAGTTCACGAAGCCCTC 59.681 55.000 0.00 0.0 0.0 4.30 R
3989 4828 8.178313 GCTCTAAGACCAATGTTTTAAGTGATC 58.822 37.037 0.00 0.0 0.0 2.92 R
5346 6201 0.248661 CGATAGCACCAGAGGACGTG 60.249 60.000 0.00 0.0 0.0 4.49 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
89 93 3.902086 GGCTCCGGCGTACCTCTC 61.902 72.222 6.01 0.00 39.81 3.20
158 162 9.032420 GTAGTACATCTGTTTATGTTCTTAGGC 57.968 37.037 0.00 0.00 40.52 3.93
159 163 7.852263 AGTACATCTGTTTATGTTCTTAGGCT 58.148 34.615 0.00 0.00 40.52 4.58
160 164 6.992063 ACATCTGTTTATGTTCTTAGGCTG 57.008 37.500 0.00 0.00 36.71 4.85
161 165 5.882557 ACATCTGTTTATGTTCTTAGGCTGG 59.117 40.000 0.00 0.00 36.71 4.85
162 166 4.843728 TCTGTTTATGTTCTTAGGCTGGG 58.156 43.478 0.00 0.00 0.00 4.45
163 167 4.288626 TCTGTTTATGTTCTTAGGCTGGGT 59.711 41.667 0.00 0.00 0.00 4.51
164 168 4.331968 TGTTTATGTTCTTAGGCTGGGTG 58.668 43.478 0.00 0.00 0.00 4.61
165 169 3.644966 TTATGTTCTTAGGCTGGGTGG 57.355 47.619 0.00 0.00 0.00 4.61
166 170 1.372501 ATGTTCTTAGGCTGGGTGGT 58.627 50.000 0.00 0.00 0.00 4.16
167 171 0.690762 TGTTCTTAGGCTGGGTGGTC 59.309 55.000 0.00 0.00 0.00 4.02
168 172 0.391263 GTTCTTAGGCTGGGTGGTCG 60.391 60.000 0.00 0.00 0.00 4.79
169 173 1.550130 TTCTTAGGCTGGGTGGTCGG 61.550 60.000 0.00 0.00 0.00 4.79
170 174 3.682292 CTTAGGCTGGGTGGTCGGC 62.682 68.421 0.00 0.00 38.26 5.54
171 175 4.715130 TAGGCTGGGTGGTCGGCT 62.715 66.667 0.00 0.00 38.94 5.52
175 179 4.135153 CTGGGTGGTCGGCTCGAG 62.135 72.222 8.45 8.45 36.23 4.04
255 280 2.125106 GTGGCGCAGGGGTAGAAG 60.125 66.667 10.83 0.00 0.00 2.85
260 315 0.741221 GCGCAGGGGTAGAAGAACAG 60.741 60.000 0.30 0.00 0.00 3.16
296 414 6.238925 GGCAAGTAGTATGTGTTTTGGACTTT 60.239 38.462 0.00 0.00 0.00 2.66
324 442 7.701078 TGTACGACTCAGAACATAATAAGAAGC 59.299 37.037 0.00 0.00 0.00 3.86
461 581 7.174772 TGACATCAAAATTTGCTACTCTTGCTA 59.825 33.333 0.00 0.00 0.00 3.49
575 696 5.181811 TGCCTTGTACAATCATCAAGACAAG 59.818 40.000 9.13 5.75 42.09 3.16
729 850 0.948141 GTATCGCTGCCTGCCTCATC 60.948 60.000 0.00 0.00 38.78 2.92
794 915 6.379988 TCTGGTGTAAGCTCATCACTATGTTA 59.620 38.462 13.01 0.00 34.50 2.41
921 1067 5.072741 CACCCCCAATCAATAAGGACTATG 58.927 45.833 0.00 0.00 0.00 2.23
3562 4397 5.817816 CCGCTAGGACTTGAAATACTGAAAT 59.182 40.000 0.00 0.00 41.02 2.17
4501 5343 1.546029 ACTCATTCGTAGTGAGCAGCA 59.454 47.619 12.16 0.00 45.42 4.41
4761 5606 1.575788 TCCTCCCTCCAGCTCATAAGA 59.424 52.381 0.00 0.00 0.00 2.10
5366 6221 0.680280 ACGTCCTCTGGTGCTATCGT 60.680 55.000 0.00 0.00 0.00 3.73
5400 6281 3.181473 ACTGTACTCGTGTTGCCAGTTAA 60.181 43.478 0.00 0.00 29.99 2.01
5593 6478 9.280174 TCTCTTTTACCATTCACTTTCGTAATT 57.720 29.630 0.00 0.00 0.00 1.40
5676 6561 3.417101 TGTTGGAGGCACGTATGATTTT 58.583 40.909 0.00 0.00 0.00 1.82
5727 6612 6.645827 TCTGTTTCGAACCGTGTCATAATTTA 59.354 34.615 0.00 0.00 0.00 1.40
5750 6635 4.838986 ACTGAAGGTAGACTGTTGTACCAT 59.161 41.667 17.64 9.38 41.19 3.55
5753 6638 7.180408 ACTGAAGGTAGACTGTTGTACCATTAT 59.820 37.037 17.64 5.77 41.19 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 92 2.768527 GGAGATGGATGTTCTCACCTGA 59.231 50.000 3.39 0.00 41.16 3.86
89 93 2.158842 GGGAGATGGATGTTCTCACCTG 60.159 54.545 3.39 0.00 41.16 4.00
158 162 4.135153 CTCGAGCCGACCACCCAG 62.135 72.222 0.00 0.00 0.00 4.45
162 166 4.131088 GTCCCTCGAGCCGACCAC 62.131 72.222 16.18 0.32 0.00 4.16
163 167 4.671590 TGTCCCTCGAGCCGACCA 62.672 66.667 21.39 11.29 0.00 4.02
164 168 3.827898 CTGTCCCTCGAGCCGACC 61.828 72.222 21.39 9.47 0.00 4.79
165 169 3.063084 ACTGTCCCTCGAGCCGAC 61.063 66.667 18.87 18.87 0.00 4.79
166 170 3.062466 CACTGTCCCTCGAGCCGA 61.062 66.667 6.99 1.14 0.00 5.54
167 171 4.135153 CCACTGTCCCTCGAGCCG 62.135 72.222 6.99 0.00 0.00 5.52
168 172 1.617947 AATCCACTGTCCCTCGAGCC 61.618 60.000 6.99 0.00 0.00 4.70
169 173 0.179097 GAATCCACTGTCCCTCGAGC 60.179 60.000 6.99 0.00 0.00 5.03
170 174 0.461961 GGAATCCACTGTCCCTCGAG 59.538 60.000 5.13 5.13 0.00 4.04
171 175 0.252057 TGGAATCCACTGTCCCTCGA 60.252 55.000 0.00 0.00 32.48 4.04
172 176 2.286826 TGGAATCCACTGTCCCTCG 58.713 57.895 0.00 0.00 32.48 4.63
241 266 0.741221 CTGTTCTTCTACCCCTGCGC 60.741 60.000 0.00 0.00 0.00 6.09
255 280 1.446966 GCCAGCGACTCCTCTGTTC 60.447 63.158 0.00 0.00 0.00 3.18
260 315 0.179124 CTACTTGCCAGCGACTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
296 414 8.047413 TCTTATTATGTTCTGAGTCGTACACA 57.953 34.615 0.00 0.00 0.00 3.72
324 442 4.210120 GCAGCGAATACAATCTCAGGTAAG 59.790 45.833 0.00 0.00 0.00 2.34
461 581 7.992754 AGCAGAGAGAACATGAATAAAACTT 57.007 32.000 0.00 0.00 0.00 2.66
794 915 6.702329 AGATTTGTAGAGGAAAACAGACGAT 58.298 36.000 0.00 0.00 0.00 3.73
921 1067 2.056094 GTGCTGAATGAACACCAAGC 57.944 50.000 0.00 0.00 0.00 4.01
1261 1407 1.165907 TTGCGCTTGAGGAGGTTGTG 61.166 55.000 9.73 0.00 0.00 3.33
1299 1449 3.054139 TGGAAGAGTCATTAGGCAGCATT 60.054 43.478 0.00 0.00 0.00 3.56
1304 1454 4.164030 TGCTAATGGAAGAGTCATTAGGCA 59.836 41.667 19.16 15.50 46.86 4.75
3914 4753 0.318762 AGTCAGTTCACGAAGCCCTC 59.681 55.000 0.00 0.00 0.00 4.30
3989 4828 8.178313 GCTCTAAGACCAATGTTTTAAGTGATC 58.822 37.037 0.00 0.00 0.00 2.92
4501 5343 5.165961 AGCATGGTGTTGAGTATTGTAGT 57.834 39.130 0.00 0.00 0.00 2.73
4761 5606 2.742053 GTGCTCACCACATGAACGTATT 59.258 45.455 0.00 0.00 44.06 1.89
5346 6201 0.248661 CGATAGCACCAGAGGACGTG 60.249 60.000 0.00 0.00 0.00 4.49
5347 6202 0.680280 ACGATAGCACCAGAGGACGT 60.680 55.000 0.00 0.00 42.67 4.34
5366 6221 1.338973 GAGTACAGTGTCCACCGTCAA 59.661 52.381 0.00 0.00 0.00 3.18
5593 6478 7.495606 CCAAGTACTGAAATACATGCATGACTA 59.504 37.037 32.75 16.06 0.00 2.59
5597 6482 5.357878 ACCCAAGTACTGAAATACATGCATG 59.642 40.000 25.09 25.09 0.00 4.06
5676 6561 9.558396 AAGCATTATTGTCAAATGGAAAGAAAA 57.442 25.926 0.00 0.00 35.34 2.29
5679 6564 8.030692 CAGAAGCATTATTGTCAAATGGAAAGA 58.969 33.333 0.00 0.00 35.34 2.52
5680 6565 7.816031 ACAGAAGCATTATTGTCAAATGGAAAG 59.184 33.333 0.00 0.00 35.34 2.62
5727 6612 4.220724 TGGTACAACAGTCTACCTTCAGT 58.779 43.478 8.31 0.00 34.52 3.41
5750 6635 7.334844 ACATCTAGACAAGTGACGATGATAA 57.665 36.000 0.00 0.00 34.10 1.75
5753 6638 5.416013 AGAACATCTAGACAAGTGACGATGA 59.584 40.000 0.00 0.00 34.10 2.92


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

AutoCloner maintained by Alex Coulton.