Multiple sequence alignment - TraesCS4D01G178400

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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 TraesCS4D01G178400 chr4D 100.000 3023 0 0 1 3023 309705239 309702217 0.000000e+00 5583
1 TraesCS4D01G178400 chr4B 93.312 3080 99 45 1 3023 386751986 386748957 0.000000e+00 4447
2 TraesCS4D01G178400 chr4A 95.979 1318 33 5 1098 2412 165354949 165356249 0.000000e+00 2122
3 TraesCS4D01G178400 chr4A 90.187 1121 24 25 1 1087 165353834 165354902 0.000000e+00 1382
4 TraesCS4D01G178400 chr4A 96.098 615 20 2 2410 3023 165356356 165356967 0.000000e+00 1000
5 TraesCS4D01G178400 chr4A 84.337 166 18 5 2687 2849 662079677 662079517 4.040000e-34 156
6 TraesCS4D01G178400 chr7A 82.524 206 26 2 1988 2193 699910980 699910785 4.010000e-39 172
7 TraesCS4D01G178400 chr7A 86.145 166 15 5 2687 2849 700276534 700276694 4.010000e-39 172
8 TraesCS4D01G178400 chr7A 86.145 166 15 5 2687 2849 700280845 700281005 4.010000e-39 172
9 TraesCS4D01G178400 chr7D 75.806 434 51 21 2246 2660 609746277 609745879 1.440000e-38 171
10 TraesCS4D01G178400 chr7D 85.542 166 16 5 2687 2849 610488139 610487979 1.860000e-37 167
11 TraesCS4D01G178400 chr7D 78.247 308 32 17 2371 2659 609974146 609974437 6.700000e-37 165
12 TraesCS4D01G178400 chr7D 77.922 308 33 17 2371 2659 607916712 607916421 3.120000e-35 159
13 TraesCS4D01G178400 chrUn 84.940 166 17 5 2687 2849 77501400 77501560 8.670000e-36 161
14 TraesCS4D01G178400 chr7B 77.597 308 34 12 2371 2659 694102864 694102573 1.450000e-33 154


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 TraesCS4D01G178400 chr4D 309702217 309705239 3022 True 5583.000000 5583 100.000 1 3023 1 chr4D.!!$R1 3022
1 TraesCS4D01G178400 chr4B 386748957 386751986 3029 True 4447.000000 4447 93.312 1 3023 1 chr4B.!!$R1 3022
2 TraesCS4D01G178400 chr4A 165353834 165356967 3133 False 1501.333333 2122 94.088 1 3023 3 chr4A.!!$F1 3022

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
338 361 0.109723 AGAGCTAGCTAGTCTCCCCG 59.890 60.0 27.38 5.15 31.35 5.73 F
1308 1395 0.539051 CGCCTTTGGTCTCCTCATCT 59.461 55.0 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 1931 0.538287 GGGGCTTGTTCTTGCACTCT 60.538 55.0 0.0 0.0 32.4 3.24 R
2541 2748 0.109132 CCCTGAACTGGATTTTGCGC 60.109 55.0 0.0 0.0 0.0 6.09 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
247 264 0.253327 AGATTCCTTCCCGCCTCAAC 59.747 55.000 0.00 0.00 0.00 3.18
258 275 2.195567 GCCTCAACTTGGCTGTGCA 61.196 57.895 0.00 0.00 46.38 4.57
319 337 2.483013 GGATGTGCGTTAGGTATCAGCA 60.483 50.000 0.00 0.00 35.27 4.41
320 338 2.293677 TGTGCGTTAGGTATCAGCAG 57.706 50.000 0.00 0.00 38.59 4.24
338 361 0.109723 AGAGCTAGCTAGTCTCCCCG 59.890 60.000 27.38 5.15 31.35 5.73
476 499 3.056322 GGTCCGGCCGAATACAATATACT 60.056 47.826 30.73 0.00 0.00 2.12
479 502 4.766373 TCCGGCCGAATACAATATACTACA 59.234 41.667 30.73 0.00 0.00 2.74
481 504 5.346822 CCGGCCGAATACAATATACTACAAC 59.653 44.000 30.73 0.00 0.00 3.32
482 505 5.921976 CGGCCGAATACAATATACTACAACA 59.078 40.000 24.07 0.00 0.00 3.33
483 506 6.089016 CGGCCGAATACAATATACTACAACAG 59.911 42.308 24.07 0.00 0.00 3.16
623 647 3.652581 GCCACTTGTAGGGCTTTCT 57.347 52.632 0.00 0.00 46.74 2.52
942 988 3.445987 TCCTTTCTTCTTCCTCCTCCTC 58.554 50.000 0.00 0.00 0.00 3.71
944 990 3.449918 CTTTCTTCTTCCTCCTCCTCCT 58.550 50.000 0.00 0.00 0.00 3.69
947 993 1.754226 CTTCTTCCTCCTCCTCCTTCG 59.246 57.143 0.00 0.00 0.00 3.79
950 996 0.705253 TTCCTCCTCCTCCTTCGTCT 59.295 55.000 0.00 0.00 0.00 4.18
1115 1199 0.669318 TGCGGTCAGTTCAATCGGAC 60.669 55.000 0.00 0.00 33.18 4.79
1122 1206 4.562963 GGTCAGTTCAATCGGACTAACCTT 60.563 45.833 0.00 0.00 36.31 3.50
1157 1244 7.875316 TTTCTGAAATGAAACAAACAAACGA 57.125 28.000 0.00 0.00 31.81 3.85
1158 1245 7.875316 TTCTGAAATGAAACAAACAAACGAA 57.125 28.000 0.00 0.00 0.00 3.85
1159 1246 7.271936 TCTGAAATGAAACAAACAAACGAAC 57.728 32.000 0.00 0.00 0.00 3.95
1282 1369 2.955660 CAACTGCAACTTTCCCAGGTTA 59.044 45.455 0.00 0.00 0.00 2.85
1305 1392 2.592993 CCCGCCTTTGGTCTCCTCA 61.593 63.158 0.00 0.00 0.00 3.86
1308 1395 0.539051 CGCCTTTGGTCTCCTCATCT 59.461 55.000 0.00 0.00 0.00 2.90
1311 1398 2.898705 CCTTTGGTCTCCTCATCTTCG 58.101 52.381 0.00 0.00 0.00 3.79
1393 1488 2.498167 GTCTTGGCACATCACAAGTCT 58.502 47.619 0.00 0.00 43.40 3.24
1402 1497 4.024387 GCACATCACAAGTCTTTTTACCGA 60.024 41.667 0.00 0.00 0.00 4.69
1422 1517 3.636300 CGACCTCTCTCTGATGATTCCTT 59.364 47.826 0.00 0.00 0.00 3.36
1509 1604 6.873076 CCAATATATGAAGAGAAGCCTCAGTC 59.127 42.308 0.00 0.00 41.87 3.51
1512 1607 2.175202 TGAAGAGAAGCCTCAGTCCTC 58.825 52.381 0.00 0.00 41.87 3.71
1611 1706 4.531426 AACTGCCCGGCCACCAAA 62.531 61.111 7.03 0.00 0.00 3.28
1626 1721 3.057736 CCACCAAACAGATTCAGCAGAAG 60.058 47.826 0.00 0.00 37.14 2.85
2124 2220 2.026915 AGCACCAGATACTTGCATGTGA 60.027 45.455 15.08 0.69 38.81 3.58
2227 2323 6.587990 ACTCTCATGTTATTTCTGTTGAGACG 59.412 38.462 0.00 0.00 35.82 4.18
2323 2420 8.594881 ACACAATAAGAATGGATTAGACGATC 57.405 34.615 0.00 0.00 0.00 3.69
2454 2661 4.718961 AGCACAACATAGAAAAGACCACT 58.281 39.130 0.00 0.00 0.00 4.00
2516 2723 4.647424 ACCATATTTTGTACATTGGCCG 57.353 40.909 0.00 0.00 0.00 6.13
2622 2850 4.471386 ACATACCAGCTTTACCATCTCAGT 59.529 41.667 0.00 0.00 0.00 3.41
2727 2963 6.152831 GGAGAGGTTATTGGTGCAAATTTACT 59.847 38.462 0.00 0.00 0.00 2.24
2767 3003 2.620585 AGACTTCTTTGCCTTCAAGCAC 59.379 45.455 0.00 0.00 43.97 4.40
2960 3199 8.716674 AATATATCCACAGAATTTGCCATCTT 57.283 30.769 0.00 0.00 0.00 2.40
2997 3236 4.019321 ACCAAGCAGAGACAAATAGGCTTA 60.019 41.667 0.00 0.00 39.36 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 78 2.587194 ATCACGATGCCGCTCTGC 60.587 61.111 0.00 0.00 39.95 4.26
179 191 2.091720 CCCCCAAACATGAGATCATCCA 60.092 50.000 0.00 0.00 33.61 3.41
247 264 2.273179 ACATGCCTGCACAGCCAAG 61.273 57.895 0.00 0.00 0.00 3.61
258 275 3.931907 TTATAAGACCTGCACATGCCT 57.068 42.857 0.49 0.00 41.18 4.75
319 337 0.109723 CGGGGAGACTAGCTAGCTCT 59.890 60.000 28.57 24.41 31.57 4.09
320 338 1.520600 GCGGGGAGACTAGCTAGCTC 61.521 65.000 23.26 25.06 0.00 4.09
338 361 1.298859 AATCGTCTCGTTGCTTGGGC 61.299 55.000 0.00 0.00 39.26 5.36
398 421 0.935196 CCCGGCGATTAAACTAGTGC 59.065 55.000 9.30 0.00 0.00 4.40
399 422 0.935196 GCCCGGCGATTAAACTAGTG 59.065 55.000 9.30 0.00 0.00 2.74
476 499 0.386476 CGCCCGGCTATACTGTTGTA 59.614 55.000 8.05 0.00 0.00 2.41
479 502 1.041447 ACTCGCCCGGCTATACTGTT 61.041 55.000 8.05 0.00 0.00 3.16
481 504 1.286260 GACTCGCCCGGCTATACTG 59.714 63.158 8.05 0.00 0.00 2.74
482 505 1.902432 GGACTCGCCCGGCTATACT 60.902 63.158 8.05 0.00 0.00 2.12
483 506 2.649614 GGACTCGCCCGGCTATAC 59.350 66.667 8.05 0.00 0.00 1.47
592 616 0.907704 AAGTGGCCTCGGGTGATGTA 60.908 55.000 3.32 0.00 0.00 2.29
623 647 1.338107 TTCTCCGCACCTTCTTCAGA 58.662 50.000 0.00 0.00 0.00 3.27
731 765 2.041405 GTCCTCCCTCCCTCCCTG 60.041 72.222 0.00 0.00 0.00 4.45
876 922 5.536916 AGCCTTAATCAGAAGCGTACTAGAT 59.463 40.000 0.00 0.00 0.00 1.98
942 988 2.021457 GAGAGGAGAGGAAGACGAAGG 58.979 57.143 0.00 0.00 0.00 3.46
944 990 1.636519 AGGAGAGGAGAGGAAGACGAA 59.363 52.381 0.00 0.00 0.00 3.85
947 993 2.654863 CAGAGGAGAGGAGAGGAAGAC 58.345 57.143 0.00 0.00 0.00 3.01
950 996 0.395036 CGCAGAGGAGAGGAGAGGAA 60.395 60.000 0.00 0.00 0.00 3.36
1115 1199 9.801873 TTTCAGAAACAAATCAAGAAAGGTTAG 57.198 29.630 0.00 0.00 0.00 2.34
1155 1242 3.143807 TCCTGCAAGTTTGTTTGTTCG 57.856 42.857 0.00 0.00 0.00 3.95
1156 1243 5.167845 TCTTTCCTGCAAGTTTGTTTGTTC 58.832 37.500 0.00 0.00 0.00 3.18
1157 1244 5.047377 TCTCTTTCCTGCAAGTTTGTTTGTT 60.047 36.000 0.00 0.00 0.00 2.83
1158 1245 4.462483 TCTCTTTCCTGCAAGTTTGTTTGT 59.538 37.500 0.00 0.00 0.00 2.83
1159 1246 4.997565 TCTCTTTCCTGCAAGTTTGTTTG 58.002 39.130 0.00 0.00 0.00 2.93
1305 1392 3.981071 TCACCAAATGAGGACGAAGAT 57.019 42.857 0.00 0.00 31.91 2.40
1308 1395 3.599343 CAGATCACCAAATGAGGACGAA 58.401 45.455 0.00 0.00 41.91 3.85
1311 1398 2.715046 TGCAGATCACCAAATGAGGAC 58.285 47.619 0.00 0.00 41.91 3.85
1393 1488 4.770531 TCATCAGAGAGAGGTCGGTAAAAA 59.229 41.667 0.00 0.00 0.00 1.94
1402 1497 3.710677 CCAAGGAATCATCAGAGAGAGGT 59.289 47.826 0.00 0.00 0.00 3.85
1422 1517 5.047566 TGAGAAGAATGAAAAGACCACCA 57.952 39.130 0.00 0.00 0.00 4.17
1509 1604 4.720649 TCTTCTGTGAGTAAATCGGAGG 57.279 45.455 0.00 0.00 0.00 4.30
1512 1607 5.103000 ACGAATCTTCTGTGAGTAAATCGG 58.897 41.667 0.00 0.00 0.00 4.18
1611 1706 3.262660 TGTGATCCTTCTGCTGAATCTGT 59.737 43.478 6.48 0.00 0.00 3.41
1836 1931 0.538287 GGGGCTTGTTCTTGCACTCT 60.538 55.000 0.00 0.00 32.40 3.24
1840 1935 2.428834 CAAGGGGCTTGTTCTTGCA 58.571 52.632 0.00 0.00 36.79 4.08
2124 2220 5.574188 ACTAAGAAAATCTTGGCCACATCT 58.426 37.500 3.88 0.00 38.36 2.90
2227 2323 1.399791 GAAGGTACAAGATGCTGCAGC 59.600 52.381 31.89 31.89 42.50 5.25
2290 2386 8.732746 AATCCATTCTTATTGTGTACAGTACC 57.267 34.615 8.30 0.74 0.00 3.34
2323 2420 1.872237 CGTGTGTGTGTTCCTACCCTG 60.872 57.143 0.00 0.00 0.00 4.45
2454 2661 5.822519 GCCCATCTTTCATGTTCATGTACTA 59.177 40.000 11.73 0.00 0.00 1.82
2516 2723 2.288030 GCATTGGCATCCTGCTATTGAC 60.288 50.000 10.32 1.09 44.28 3.18
2541 2748 0.109132 CCCTGAACTGGATTTTGCGC 60.109 55.000 0.00 0.00 0.00 6.09
2542 2749 0.527565 CCCCTGAACTGGATTTTGCG 59.472 55.000 0.00 0.00 0.00 4.85
2656 2892 1.489481 TCCTCCGACTTCATCAGCAT 58.511 50.000 0.00 0.00 0.00 3.79
2657 2893 1.066858 GTTCCTCCGACTTCATCAGCA 60.067 52.381 0.00 0.00 0.00 4.41
2658 2894 1.646189 GTTCCTCCGACTTCATCAGC 58.354 55.000 0.00 0.00 0.00 4.26
2750 2986 1.039856 GGGTGCTTGAAGGCAAAGAA 58.960 50.000 0.00 0.00 44.18 2.52
2960 3199 3.745799 TGCTTGGTATTCTTTTGACCGA 58.254 40.909 0.00 0.00 35.91 4.69
2997 3236 2.365293 GGCCAACAGTGAAAACCTGAAT 59.635 45.455 0.00 0.00 34.04 2.57


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

AutoCloner maintained by Alex Coulton.