Multiple sequence alignment - TraesCS3B01G231000

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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 TraesCS3B01G231000 chr3B 100.000 3281 0 0 1 3281 349222274 349225554 0 6059
1 TraesCS3B01G231000 chr3B 93.017 3308 201 11 1 3281 336851639 336854943 0 4802
2 TraesCS3B01G231000 chr3B 92.122 2983 213 7 2 2969 462786838 462789813 0 4187
3 TraesCS3B01G231000 chr7B 94.224 3307 162 10 1 3281 297393014 297396317 0 5022
4 TraesCS3B01G231000 chr7B 93.349 3308 188 11 1 3281 282738764 282735462 0 4861
5 TraesCS3B01G231000 chr7B 92.498 3306 221 8 1 3280 283625076 283621772 0 4706
6 TraesCS3B01G231000 chr7B 91.979 3304 237 14 1 3281 359415221 359411923 0 4608
7 TraesCS3B01G231000 chr7B 92.640 2962 177 15 349 3281 453714210 453717159 0 4224
8 TraesCS3B01G231000 chr7B 93.893 1441 75 4 1 1428 290768343 290769783 0 2161
9 TraesCS3B01G231000 chr5D 93.799 3306 177 9 1 3281 236470590 236467288 0 4944
10 TraesCS3B01G231000 chr6B 93.602 3298 182 12 1 3281 404403167 404399882 0 4894
11 TraesCS3B01G231000 chr6B 92.563 3308 211 15 1 3279 639906992 639910293 0 4713
12 TraesCS3B01G231000 chr5B 93.386 3296 186 9 1 3281 271656439 271659717 0 4850
13 TraesCS3B01G231000 chr5B 93.283 3305 189 9 1 3279 216254986 216251689 0 4843
14 TraesCS3B01G231000 chr5B 91.960 3296 242 14 1 3281 587150171 587146884 0 4597
15 TraesCS3B01G231000 chr5B 91.486 2220 162 10 1084 3281 153272847 153275061 0 3027
16 TraesCS3B01G231000 chr5B 93.253 1734 91 7 1 1709 177231129 177232861 0 2531
17 TraesCS3B01G231000 chr4B 93.079 3309 197 10 1 3281 235365865 235369169 0 4813
18 TraesCS3B01G231000 chr4B 93.025 3312 197 13 1 3281 310160644 310157336 0 4806
19 TraesCS3B01G231000 chr1B 92.500 3320 198 21 1 3281 250545198 250548505 0 4704
20 TraesCS3B01G231000 chr1B 92.673 1433 100 3 1 1428 279434504 279435936 0 2060


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 TraesCS3B01G231000 chr3B 349222274 349225554 3280 False 6059 6059 100.000 1 3281 1 chr3B.!!$F2 3280
1 TraesCS3B01G231000 chr3B 336851639 336854943 3304 False 4802 4802 93.017 1 3281 1 chr3B.!!$F1 3280
2 TraesCS3B01G231000 chr3B 462786838 462789813 2975 False 4187 4187 92.122 2 2969 1 chr3B.!!$F3 2967
3 TraesCS3B01G231000 chr7B 297393014 297396317 3303 False 5022 5022 94.224 1 3281 1 chr7B.!!$F2 3280
4 TraesCS3B01G231000 chr7B 282735462 282738764 3302 True 4861 4861 93.349 1 3281 1 chr7B.!!$R1 3280
5 TraesCS3B01G231000 chr7B 283621772 283625076 3304 True 4706 4706 92.498 1 3280 1 chr7B.!!$R2 3279
6 TraesCS3B01G231000 chr7B 359411923 359415221 3298 True 4608 4608 91.979 1 3281 1 chr7B.!!$R3 3280
7 TraesCS3B01G231000 chr7B 453714210 453717159 2949 False 4224 4224 92.640 349 3281 1 chr7B.!!$F3 2932
8 TraesCS3B01G231000 chr7B 290768343 290769783 1440 False 2161 2161 93.893 1 1428 1 chr7B.!!$F1 1427
9 TraesCS3B01G231000 chr5D 236467288 236470590 3302 True 4944 4944 93.799 1 3281 1 chr5D.!!$R1 3280
10 TraesCS3B01G231000 chr6B 404399882 404403167 3285 True 4894 4894 93.602 1 3281 1 chr6B.!!$R1 3280
11 TraesCS3B01G231000 chr6B 639906992 639910293 3301 False 4713 4713 92.563 1 3279 1 chr6B.!!$F1 3278
12 TraesCS3B01G231000 chr5B 271656439 271659717 3278 False 4850 4850 93.386 1 3281 1 chr5B.!!$F3 3280
13 TraesCS3B01G231000 chr5B 216251689 216254986 3297 True 4843 4843 93.283 1 3279 1 chr5B.!!$R1 3278
14 TraesCS3B01G231000 chr5B 587146884 587150171 3287 True 4597 4597 91.960 1 3281 1 chr5B.!!$R2 3280
15 TraesCS3B01G231000 chr5B 153272847 153275061 2214 False 3027 3027 91.486 1084 3281 1 chr5B.!!$F1 2197
16 TraesCS3B01G231000 chr5B 177231129 177232861 1732 False 2531 2531 93.253 1 1709 1 chr5B.!!$F2 1708
17 TraesCS3B01G231000 chr4B 235365865 235369169 3304 False 4813 4813 93.079 1 3281 1 chr4B.!!$F1 3280
18 TraesCS3B01G231000 chr4B 310157336 310160644 3308 True 4806 4806 93.025 1 3281 1 chr4B.!!$R1 3280
19 TraesCS3B01G231000 chr1B 250545198 250548505 3307 False 4704 4704 92.500 1 3281 1 chr1B.!!$F1 3280
20 TraesCS3B01G231000 chr1B 279434504 279435936 1432 False 2060 2060 92.673 1 1428 1 chr1B.!!$F2 1427

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
858 874 0.103026 TGCAAGGATGGACGAGATCG 59.897 55.0 0.0 0.0 46.33 3.69 F
964 980 2.359848 CCGGATCAAGTACACCGACATA 59.640 50.0 0.0 0.0 46.94 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1743 0.185901 AGGCCAAGTGGTGATGTGTT 59.814 50.0 5.01 0.0 37.57 3.32 R
2280 2326 0.743688 TCATGGTGCGCTTGTTTGTT 59.256 45.0 9.73 0.0 0.00 2.83 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
238 244 1.877576 AATCGTGCCAGCGTCTCTCA 61.878 55.000 0.00 0.00 0.00 3.27
312 318 3.900601 TGGTTTGCACAATCCCACTTATT 59.099 39.130 7.78 0.00 30.87 1.40
525 533 2.420022 AGTGCTATTTCATTGTCCGCAC 59.580 45.455 0.00 0.00 44.64 5.34
605 621 4.154918 CCTTCTACCACTCACATTTTGCTC 59.845 45.833 0.00 0.00 0.00 4.26
803 819 5.242795 AGCAACATACCAAGGACTACTTT 57.757 39.130 0.00 0.00 37.29 2.66
858 874 0.103026 TGCAAGGATGGACGAGATCG 59.897 55.000 0.00 0.00 46.33 3.69
964 980 2.359848 CCGGATCAAGTACACCGACATA 59.640 50.000 0.00 0.00 46.94 2.29
1245 1271 2.416893 GCCCTTCAAGAATCAAGTCGAC 59.583 50.000 7.70 7.70 0.00 4.20
1251 1277 4.253685 TCAAGAATCAAGTCGACCCATTC 58.746 43.478 13.01 16.10 0.00 2.67
1309 1335 3.748568 GCACTTCGAGAAGAAATCCAAGT 59.251 43.478 18.54 0.00 40.79 3.16
1319 1345 4.015872 AGAAATCCAAGTGCGGAACTAA 57.984 40.909 0.00 0.00 38.56 2.24
1513 1559 3.119531 CGGCAAGCTAAAATTCACCATGA 60.120 43.478 0.00 0.00 0.00 3.07
1697 1743 1.270305 CCGAGAAGCAAGAGGTGAACA 60.270 52.381 0.00 0.00 0.00 3.18
1700 1746 3.206150 GAGAAGCAAGAGGTGAACAACA 58.794 45.455 0.00 0.00 0.00 3.33
1714 1760 1.032014 ACAACACATCACCACTTGGC 58.968 50.000 0.00 0.00 39.32 4.52
1863 1909 1.406539 GCCATGATTCGAGCCAATGTT 59.593 47.619 0.00 0.00 0.00 2.71
1891 1937 4.726583 AGATGATGAGCAAACTATGGCAT 58.273 39.130 4.88 4.88 0.00 4.40
1926 1972 5.103813 TGGACTCAATCATCCCATCAAGAAT 60.104 40.000 0.00 0.00 33.69 2.40
2007 2053 1.470098 GAACGCCAAGTGCAAGATGAT 59.530 47.619 0.00 0.00 41.33 2.45
2082 2128 1.000607 TCAACGACTCCTCCAACTTCG 60.001 52.381 0.00 0.00 35.80 3.79
2084 2130 1.546961 ACGACTCCTCCAACTTCGAT 58.453 50.000 0.00 0.00 33.87 3.59
2112 2158 3.009723 CAAGCCATCTACAACCAACGAT 58.990 45.455 0.00 0.00 0.00 3.73
2122 2168 2.872245 ACAACCAACGATGACAAGTCAG 59.128 45.455 8.99 0.00 43.61 3.51
2137 2183 6.093495 TGACAAGTCAGGTTACAAGAAAACTG 59.907 38.462 0.00 0.00 44.09 3.16
2247 2293 2.213499 AGCTCCTTCAAGTGTTTCACG 58.787 47.619 0.00 0.00 39.64 4.35
2280 2326 1.066430 GGCCACAAGTCCTACGAATGA 60.066 52.381 0.00 0.00 0.00 2.57
2499 2545 3.771216 AGACCAAAGATGCCACATCTTT 58.229 40.909 23.33 23.33 45.99 2.52
2585 2631 5.536161 ACAACTTGGCAAGTGATGAACTATT 59.464 36.000 31.75 10.64 41.91 1.73
2719 2765 2.279741 GCGCATATGAGGACACTTTGA 58.720 47.619 6.97 0.00 0.00 2.69
2906 2952 0.754217 CAAGCCACCCATCATGGAGG 60.754 60.000 4.75 8.06 40.96 4.30
2924 2970 3.306433 GGAGGGAAGAGTGAGAAAGTGAC 60.306 52.174 0.00 0.00 0.00 3.67
2956 3002 3.660621 GTGAGAGCCACAAGCCAC 58.339 61.111 0.00 0.00 45.47 5.01
3042 3091 2.039084 AGAAGTGTGTGAGAACCCATCC 59.961 50.000 0.00 0.00 0.00 3.51
3044 3093 1.774254 AGTGTGTGAGAACCCATCCAA 59.226 47.619 0.00 0.00 0.00 3.53
3054 3103 4.352009 AGAACCCATCCAATGTTATGCAA 58.648 39.130 0.00 0.00 0.00 4.08
3162 3211 3.088532 CCAAGATGTTTTCCCCGATGAA 58.911 45.455 0.00 0.00 0.00 2.57
3220 3270 3.808265 GCATCAAATCGATCTCATCCCCA 60.808 47.826 0.00 0.00 29.21 4.96
3262 3312 2.266372 CATACCGCGTCAACCCCA 59.734 61.111 4.92 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 233 2.283617 GCACAATACATGAGAGACGCTG 59.716 50.000 0.00 0.00 0.00 5.18
238 244 5.395682 AATGCTCTTGTTGCACAATACAT 57.604 34.783 0.00 0.00 43.59 2.29
312 318 2.355132 ACGGAAACACACACGCAAATAA 59.645 40.909 0.00 0.00 0.00 1.40
624 640 3.853207 AGAGTGGGTTGGTAGAAGTACA 58.147 45.455 0.00 0.00 0.00 2.90
729 745 0.178068 ATGCGGTCGGTCATAGCTTT 59.822 50.000 0.00 0.00 0.00 3.51
803 819 3.625232 GCGTCGAGCTTGTTGTCA 58.375 55.556 0.00 0.00 44.04 3.58
858 874 2.335011 GTTCACCAACAAGGCGCC 59.665 61.111 21.89 21.89 43.14 6.53
964 980 0.241481 GGCTCGTCGAAGAGTGTTCT 59.759 55.000 25.76 0.00 40.26 3.01
1093 1109 1.190323 GTCGTTGTCGTTCTTGAGCTG 59.810 52.381 0.00 0.00 38.33 4.24
1143 1159 4.184629 GCGTCTTGTTCCTCTTGATGTAT 58.815 43.478 0.00 0.00 0.00 2.29
1245 1271 2.645192 GGTTGCGGTTGGGAATGGG 61.645 63.158 0.00 0.00 0.00 4.00
1251 1277 2.046314 ATCTCGGTTGCGGTTGGG 60.046 61.111 0.00 0.00 0.00 4.12
1274 1300 4.462834 TCTCGAAGTGCTTCCTCTTGATTA 59.537 41.667 6.38 0.00 36.27 1.75
1309 1335 0.104487 TCGTGGTTGTTAGTTCCGCA 59.896 50.000 0.00 0.00 0.00 5.69
1319 1345 0.944386 GATGTTGCACTCGTGGTTGT 59.056 50.000 0.00 0.00 0.00 3.32
1513 1559 3.896888 TCATTGCTTCCATTGAACTTGGT 59.103 39.130 0.00 0.00 35.64 3.67
1641 1687 4.080072 TGTTCCCACCATATGAGCACATAA 60.080 41.667 7.96 0.00 41.46 1.90
1697 1743 0.185901 AGGCCAAGTGGTGATGTGTT 59.814 50.000 5.01 0.00 37.57 3.32
1700 1746 0.478072 TTGAGGCCAAGTGGTGATGT 59.522 50.000 5.01 0.00 37.57 3.06
1701 1747 1.619654 TTTGAGGCCAAGTGGTGATG 58.380 50.000 5.01 0.00 37.57 3.07
1714 1760 3.242969 CGCATGACATCCTTCATTTGAGG 60.243 47.826 0.00 0.00 33.74 3.86
1863 1909 4.471904 AGTTTGCTCATCATCTTCCGTA 57.528 40.909 0.00 0.00 0.00 4.02
1891 1937 6.151648 GGATGATTGAGTCCATTCAAGAAACA 59.848 38.462 0.00 0.00 40.16 2.83
1926 1972 0.988832 AGGGTTGGAAGTCGGCAATA 59.011 50.000 0.00 0.00 0.00 1.90
2082 2128 4.142609 TGTAGATGGCTTGGTTGAGATC 57.857 45.455 0.00 0.00 0.00 2.75
2084 2130 3.559171 GGTTGTAGATGGCTTGGTTGAGA 60.559 47.826 0.00 0.00 0.00 3.27
2112 2158 6.093495 CAGTTTTCTTGTAACCTGACTTGTCA 59.907 38.462 3.32 3.32 0.00 3.58
2122 2168 4.267690 GCTTGTTGCAGTTTTCTTGTAACC 59.732 41.667 4.26 0.00 42.31 2.85
2137 2183 1.221414 AGACGACTTGAGCTTGTTGC 58.779 50.000 0.00 0.00 43.29 4.17
2280 2326 0.743688 TCATGGTGCGCTTGTTTGTT 59.256 45.000 9.73 0.00 0.00 2.83
2387 2433 6.429385 ACAAAAGACTTGATCATCTTCACCTC 59.571 38.462 11.13 0.00 34.01 3.85
2390 2436 7.194607 TCACAAAAGACTTGATCATCTTCAC 57.805 36.000 11.13 0.00 34.01 3.18
2499 2545 1.971167 GATGCCGGCCTTTGTGTGA 60.971 57.895 26.77 0.73 0.00 3.58
2577 2623 6.151648 CCAATTGAAGCTTGGAGAATAGTTCA 59.848 38.462 2.10 0.00 44.95 3.18
2585 2631 3.507162 TGACCAATTGAAGCTTGGAGA 57.493 42.857 2.10 0.00 44.95 3.71
2719 2765 2.237143 ACATCGGGATGACATCACACTT 59.763 45.455 17.70 0.00 41.20 3.16
2906 2952 2.368875 TGGGTCACTTTCTCACTCTTCC 59.631 50.000 0.00 0.00 0.00 3.46
2924 2970 2.880890 CTCTCACTCACTTTTTGGTGGG 59.119 50.000 0.00 0.00 42.85 4.61
2956 3002 3.468007 CGAAGAGGCGCTCAAGTG 58.532 61.111 7.64 0.00 32.06 3.16
2975 3021 8.905660 AAAAAGGACTAGGTTTTTCTCTCTAC 57.094 34.615 0.00 0.00 31.68 2.59
3001 3050 2.035961 CTCTCGTCTCACTTTTGGTGGA 59.964 50.000 0.00 0.00 45.38 4.02
3017 3066 2.608261 GGGTTCTCACACACTTCTCTCG 60.608 54.545 0.00 0.00 0.00 4.04
3042 3091 6.424509 ACACAAGGACAAATTGCATAACATTG 59.575 34.615 0.00 0.00 0.00 2.82
3044 3093 5.927689 CACACAAGGACAAATTGCATAACAT 59.072 36.000 0.00 0.00 0.00 2.71
3210 3260 3.157252 GGCGCTCTGGGGATGAGA 61.157 66.667 7.64 0.00 33.68 3.27
3220 3270 1.774894 TTGTTTGGTAGGGGCGCTCT 61.775 55.000 7.48 8.21 0.00 4.09


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

AutoCloner maintained by Alex Coulton.