Multiple sequence alignment - TraesCS4B01G256000

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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 TraesCS4B01G256000 chr4B 100.000 3025 0 0 1 3025 520889552 520892576 0 5587
1 TraesCS4B01G256000 chr4A 92.383 1838 100 11 1221 3022 39541767 39539934 0 2582
2 TraesCS4B01G256000 chr4A 93.092 1245 46 16 1 1218 39543042 39541811 0 1786
3 TraesCS4B01G256000 chr4D 92.044 1835 105 19 1221 3022 425227876 425229702 0 2542
4 TraesCS4B01G256000 chr4D 93.709 1224 56 13 1 1218 425226624 425227832 0 1814


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 TraesCS4B01G256000 chr4B 520889552 520892576 3024 False 5587 5587 100.0000 1 3025 1 chr4B.!!$F1 3024
1 TraesCS4B01G256000 chr4A 39539934 39543042 3108 True 2184 2582 92.7375 1 3022 2 chr4A.!!$R1 3021
2 TraesCS4B01G256000 chr4D 425226624 425229702 3078 False 2178 2542 92.8765 1 3022 2 chr4D.!!$F1 3021

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
132 133 0.179161 AGAAGGCTCGAACGACATCG 60.179 55.0 0.0 0.0 44.04 3.84 F
1140 1159 0.598065 ACGCAATGAAAACTGCCTCC 59.402 50.0 0.0 0.0 35.01 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 1248 0.029300 CGAACCAAGCACCAACACAG 59.971 55.0 0.0 0.0 0.0 3.66 R
2377 2484 0.185901 ACCAAGCACCAAGGTCACAT 59.814 50.0 0.0 0.0 0.0 3.21 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
23 24 2.271800 CCTGAGCGTATTCTGGTTGTC 58.728 52.381 0.00 0.00 33.05 3.18
132 133 0.179161 AGAAGGCTCGAACGACATCG 60.179 55.000 0.00 0.00 44.04 3.84
171 172 6.496911 ACACTGCCCAGAAACCTTATAAAATT 59.503 34.615 1.69 0.00 0.00 1.82
188 189 0.802494 ATTTCCGCGCCAGTAACAAG 59.198 50.000 0.00 0.00 0.00 3.16
192 193 1.149987 CCGCGCCAGTAACAAGTTTA 58.850 50.000 0.00 0.00 0.00 2.01
291 292 2.929724 CCTCCTCCATCCTCTATCCCTA 59.070 54.545 0.00 0.00 0.00 3.53
378 379 2.459060 TTCGCCATCTTTACGGTGAA 57.541 45.000 0.44 0.44 46.75 3.18
379 380 2.684001 TCGCCATCTTTACGGTGAAT 57.316 45.000 0.00 0.00 38.83 2.57
380 381 2.546778 TCGCCATCTTTACGGTGAATC 58.453 47.619 0.00 0.00 38.83 2.52
383 384 3.312421 CGCCATCTTTACGGTGAATCAAT 59.688 43.478 0.00 0.00 34.58 2.57
384 385 4.601019 GCCATCTTTACGGTGAATCAATG 58.399 43.478 0.00 0.00 0.00 2.82
385 386 4.335315 GCCATCTTTACGGTGAATCAATGA 59.665 41.667 0.00 0.00 0.00 2.57
386 387 5.009010 GCCATCTTTACGGTGAATCAATGAT 59.991 40.000 0.00 0.00 0.00 2.45
387 388 6.432936 CCATCTTTACGGTGAATCAATGATG 58.567 40.000 0.00 8.42 34.66 3.07
388 389 6.260714 CCATCTTTACGGTGAATCAATGATGA 59.739 38.462 13.67 0.00 40.57 2.92
390 391 8.992073 CATCTTTACGGTGAATCAATGATGATA 58.008 33.333 0.00 0.00 45.60 2.15
391 392 9.730705 ATCTTTACGGTGAATCAATGATGATAT 57.269 29.630 0.00 0.00 45.60 1.63
446 449 8.475331 AAGTTGTATCAGTTACACCGATTTAG 57.525 34.615 0.00 0.00 40.53 1.85
454 457 4.463186 AGTTACACCGATTTAGTGCTCTCT 59.537 41.667 0.00 0.00 38.87 3.10
455 458 3.963428 ACACCGATTTAGTGCTCTCTT 57.037 42.857 0.00 0.00 38.87 2.85
557 564 0.693622 TGGAAATGGGGCACGTTCTA 59.306 50.000 0.00 0.00 0.00 2.10
609 616 2.200170 AAAGAGGCGGCAAATGCGTC 62.200 55.000 13.08 0.00 45.08 5.19
614 621 3.088914 CGGCAAATGCGTCGATCA 58.911 55.556 0.00 0.00 43.26 2.92
621 628 1.560923 AATGCGTCGATCACTACTGC 58.439 50.000 0.00 0.00 0.00 4.40
689 698 1.074775 AATGACAAAGCAGGCCCGA 59.925 52.632 0.00 0.00 0.00 5.14
727 737 2.034221 ACCTTCCTCGCTTTGCCC 59.966 61.111 0.00 0.00 0.00 5.36
977 996 1.008206 AGCTTCTCAGTCTCAGGGGAT 59.992 52.381 0.00 0.00 0.00 3.85
978 997 2.246067 AGCTTCTCAGTCTCAGGGGATA 59.754 50.000 0.00 0.00 0.00 2.59
979 998 2.364002 GCTTCTCAGTCTCAGGGGATAC 59.636 54.545 0.00 0.00 0.00 2.24
1044 1063 3.403057 GCTTTGCTCGTCGTCGCA 61.403 61.111 7.65 7.65 36.96 5.10
1120 1139 0.966370 GTCCTCAGCCTCAGGTACGT 60.966 60.000 0.00 0.00 32.20 3.57
1140 1159 0.598065 ACGCAATGAAAACTGCCTCC 59.402 50.000 0.00 0.00 35.01 4.30
1162 1181 3.137533 GTTTGCTGTTCTCTCTCTTGCT 58.862 45.455 0.00 0.00 0.00 3.91
1166 1185 2.417243 GCTGTTCTCTCTCTTGCTCTCC 60.417 54.545 0.00 0.00 0.00 3.71
1172 1191 2.424601 CTCTCTCTTGCTCTCCTGTCAG 59.575 54.545 0.00 0.00 0.00 3.51
1211 1241 2.484770 CCTGTTCCGTTTCTTCTGTCCA 60.485 50.000 0.00 0.00 0.00 4.02
1214 1244 2.526304 TCCGTTTCTTCTGTCCAGTG 57.474 50.000 0.00 0.00 0.00 3.66
1216 1246 2.169769 TCCGTTTCTTCTGTCCAGTGTT 59.830 45.455 0.00 0.00 0.00 3.32
1218 1248 2.286418 CGTTTCTTCTGTCCAGTGTTGC 60.286 50.000 0.00 0.00 0.00 4.17
1244 1314 1.879380 TGGTGCTTGGTTCGATCTTTG 59.121 47.619 0.00 0.00 0.00 2.77
1341 1431 2.800544 TCTTTCGCTCTCTTTTTGACGG 59.199 45.455 0.00 0.00 0.00 4.79
1437 1527 6.047511 AGTTATCTGCATAGCTCCAATAGG 57.952 41.667 0.00 0.00 0.00 2.57
1548 1638 6.505344 AGGGAATATATGTCCTATGGCTTGAA 59.495 38.462 5.56 0.00 35.33 2.69
1682 1776 9.264719 TCTTCACACATCAGCATAATATACAAG 57.735 33.333 0.00 0.00 0.00 3.16
1691 1785 6.205270 TCAGCATAATATACAAGCACCACATG 59.795 38.462 0.00 0.00 0.00 3.21
1821 1920 5.295292 CAGGAAAGTAGGCATGATGTTACTG 59.705 44.000 10.85 1.97 0.00 2.74
1854 1953 9.310449 AGACTAGGAACTTACAAGATGTAAAGA 57.690 33.333 4.68 0.00 41.70 2.52
1874 1973 6.472686 AAGACTGATGACTACCAACCTATC 57.527 41.667 0.00 0.00 0.00 2.08
1892 1991 1.376037 CGACCCAAGTCCAAGCTCC 60.376 63.158 0.00 0.00 40.12 4.70
2006 2105 2.811317 CGTTCTGCTCAGTCCGCC 60.811 66.667 0.00 0.00 0.00 6.13
2234 2333 4.319177 GTGGTCAATTAGTCAACTGCTCT 58.681 43.478 0.00 0.00 0.00 4.09
2263 2362 5.918608 TGAGGGCATGTTTCTAGATTAGAC 58.081 41.667 0.00 0.00 33.84 2.59
2363 2470 9.765795 AATAACTATGGTATTAGTCAGAACTGC 57.234 33.333 0.00 0.00 36.92 4.40
2377 2484 7.671302 AGTCAGAACTGCTTACTGAATTCTTA 58.329 34.615 7.05 0.00 41.31 2.10
2483 2591 4.584638 TGGGCAGGTGTATTCACTAATT 57.415 40.909 2.29 0.00 43.41 1.40
2551 2659 6.380846 TGGGTTCCAGATTGAATTATTTCCTG 59.619 38.462 0.00 0.00 0.00 3.86
2552 2660 6.276091 GGTTCCAGATTGAATTATTTCCTGC 58.724 40.000 0.00 0.00 0.00 4.85
2561 2669 9.305925 GATTGAATTATTTCCTGCGAAATTCTT 57.694 29.630 5.11 1.04 44.62 2.52
2562 2670 8.687824 TTGAATTATTTCCTGCGAAATTCTTC 57.312 30.769 5.11 8.61 44.62 2.87
2576 2684 5.630680 CGAAATTCTTCTTGTCCCAAACATG 59.369 40.000 0.00 0.00 37.82 3.21
2580 2688 0.482446 TCTTGTCCCAAACATGCCCT 59.518 50.000 0.00 0.00 37.82 5.19
2648 2757 4.825085 GGTGGATTTGACAACCTACTGAAA 59.175 41.667 0.00 0.00 0.00 2.69
2665 2774 4.783242 CTGAAAGTGGTATTGTCAAACCG 58.217 43.478 10.44 0.00 38.70 4.44
2670 2779 2.624364 GTGGTATTGTCAAACCGGGTTT 59.376 45.455 19.22 19.22 38.70 3.27
2677 2786 4.775058 TGTCAAACCGGGTTTCATAATG 57.225 40.909 21.88 11.06 33.10 1.90
2680 2789 5.302059 TGTCAAACCGGGTTTCATAATGAAA 59.698 36.000 21.88 8.80 43.37 2.69
2681 2790 5.861787 GTCAAACCGGGTTTCATAATGAAAG 59.138 40.000 21.88 7.46 45.83 2.62
2689 2798 7.145323 CGGGTTTCATAATGAAAGAAAGTTGT 58.855 34.615 0.00 0.00 45.83 3.32
2777 2887 9.995594 TTTTCTAAGTATGGTACCCTCTAGTTA 57.004 33.333 10.07 10.47 0.00 2.24
2824 2934 4.508124 GCTAGTTAGTCCATGTCATTTCCG 59.492 45.833 0.00 0.00 0.00 4.30
2885 2995 2.414058 TGTGCTGGTTACATTTTGCG 57.586 45.000 0.00 0.00 0.00 4.85
3022 3133 3.091633 ACAAAGCATGCCACCTATCTT 57.908 42.857 15.66 0.00 0.00 2.40
3023 3134 3.434309 ACAAAGCATGCCACCTATCTTT 58.566 40.909 15.66 2.53 0.00 2.52
3024 3135 3.834231 ACAAAGCATGCCACCTATCTTTT 59.166 39.130 15.66 1.74 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.035139 AGGCTGCAAAAGACAACCAG 58.965 50.000 0.50 0.00 35.71 4.00
23 24 3.269178 TGTTTTTCCAAGGCTGCAAAAG 58.731 40.909 0.50 0.00 0.00 2.27
132 133 1.374252 AGTGTCATCGGTTCGGCAC 60.374 57.895 0.00 0.00 0.00 5.01
171 172 0.533308 AACTTGTTACTGGCGCGGAA 60.533 50.000 8.83 0.00 0.00 4.30
391 392 9.627123 CCAAAACCTTTACAGATCATAGGATAA 57.373 33.333 0.00 0.00 32.67 1.75
446 449 4.376146 AGTTCAGACTTCAAAGAGAGCAC 58.624 43.478 0.00 0.00 29.87 4.40
454 457 4.965814 AGCATCAGAGTTCAGACTTCAAA 58.034 39.130 0.00 0.00 35.88 2.69
455 458 4.613925 AGCATCAGAGTTCAGACTTCAA 57.386 40.909 0.00 0.00 35.88 2.69
548 554 4.034394 TGCAATCTCATGAATAGAACGTGC 59.966 41.667 0.00 3.98 33.41 5.34
621 628 7.608376 TGCTGCCTCTGAATATACTACTACTAG 59.392 40.741 0.00 0.00 0.00 2.57
689 698 1.528824 CCTCCATGCATTCCTCCGT 59.471 57.895 0.00 0.00 0.00 4.69
727 737 1.079888 GGTGCAGGAAAAATGGCCG 60.080 57.895 0.00 0.00 0.00 6.13
958 975 1.494960 ATCCCCTGAGACTGAGAAGC 58.505 55.000 0.00 0.00 0.00 3.86
977 996 0.898326 TCTCTCCACCGCTTGCAGTA 60.898 55.000 0.00 0.00 0.00 2.74
978 997 1.758440 TTCTCTCCACCGCTTGCAGT 61.758 55.000 0.00 0.00 0.00 4.40
979 998 1.004560 TTCTCTCCACCGCTTGCAG 60.005 57.895 0.00 0.00 0.00 4.41
1044 1063 1.898154 CAGGTTCCCTCCGACGAAT 59.102 57.895 0.00 0.00 0.00 3.34
1120 1139 1.810151 GGAGGCAGTTTTCATTGCGTA 59.190 47.619 0.00 0.00 41.17 4.42
1140 1159 2.096516 GCAAGAGAGAGAACAGCAAACG 60.097 50.000 0.00 0.00 0.00 3.60
1162 1181 3.574396 CCTGAACTACAACTGACAGGAGA 59.426 47.826 7.51 0.00 45.02 3.71
1166 1185 4.322080 TCACCTGAACTACAACTGACAG 57.678 45.455 0.00 0.00 0.00 3.51
1211 1241 0.680921 AGCACCAACACAGCAACACT 60.681 50.000 0.00 0.00 0.00 3.55
1214 1244 0.528249 CCAAGCACCAACACAGCAAC 60.528 55.000 0.00 0.00 0.00 4.17
1216 1246 0.969917 AACCAAGCACCAACACAGCA 60.970 50.000 0.00 0.00 0.00 4.41
1218 1248 0.029300 CGAACCAAGCACCAACACAG 59.971 55.000 0.00 0.00 0.00 3.66
1244 1314 1.594862 CCTCGCATCCACGATCTTTTC 59.405 52.381 0.00 0.00 42.02 2.29
1341 1431 0.687354 TGCAGAGAAGAGGACCCAAC 59.313 55.000 0.00 0.00 0.00 3.77
1368 1458 4.441792 ACCAAACATTTCCTTCAAGTTGC 58.558 39.130 0.00 0.00 0.00 4.17
1437 1527 4.634991 CAAACGTAACGGAATCTAACAGC 58.365 43.478 0.00 0.00 0.00 4.40
1535 1625 5.188434 CAGTTCAGATTTCAAGCCATAGGA 58.812 41.667 0.00 0.00 0.00 2.94
1576 1666 0.978146 AGCTCAGCGGTTCCATAGGT 60.978 55.000 0.00 0.00 0.00 3.08
1577 1667 1.040646 TAGCTCAGCGGTTCCATAGG 58.959 55.000 0.00 0.00 0.00 2.57
1682 1776 1.831736 AGTAGAGGGTACATGTGGTGC 59.168 52.381 9.11 0.00 0.00 5.01
1691 1785 8.265764 AGGAAAATTATGTGAAGTAGAGGGTAC 58.734 37.037 0.00 0.00 0.00 3.34
1806 1905 2.840038 TCCTGTCAGTAACATCATGCCT 59.160 45.455 0.00 0.00 37.23 4.75
1808 1907 4.331168 GTCTTCCTGTCAGTAACATCATGC 59.669 45.833 0.00 0.00 37.23 4.06
1811 1910 5.419155 CCTAGTCTTCCTGTCAGTAACATCA 59.581 44.000 0.00 0.00 37.23 3.07
1821 1920 5.979288 TGTAAGTTCCTAGTCTTCCTGTC 57.021 43.478 0.00 0.00 0.00 3.51
1854 1953 4.338682 GTCGATAGGTTGGTAGTCATCAGT 59.661 45.833 0.00 0.00 0.00 3.41
1874 1973 1.376037 GGAGCTTGGACTTGGGTCG 60.376 63.158 0.00 0.00 42.97 4.79
1892 1991 1.386533 CTGGCCTGATACTTGCCTTG 58.613 55.000 3.32 0.00 45.56 3.61
1972 2071 2.802667 CGCGCATCCTTCGGTTGAG 61.803 63.158 8.75 0.00 0.00 3.02
2006 2105 4.492160 TAAGCGACAGGAGCGGCG 62.492 66.667 0.51 0.51 40.04 6.46
2234 2333 6.560003 TCTAGAAACATGCCCTCAAGATTA 57.440 37.500 0.00 0.00 0.00 1.75
2337 2444 9.765795 GCAGTTCTGACTAATACCATAGTTATT 57.234 33.333 3.84 0.00 36.28 1.40
2363 2470 7.607991 ACCAAGGTCACATAAGAATTCAGTAAG 59.392 37.037 8.44 0.00 0.00 2.34
2377 2484 0.185901 ACCAAGCACCAAGGTCACAT 59.814 50.000 0.00 0.00 0.00 3.21
2436 2543 7.864108 TGATTCACACTGGAAATAGGTATTG 57.136 36.000 0.00 0.00 0.00 1.90
2483 2591 2.764572 CCGGACCTTCTAAGAGGCTTAA 59.235 50.000 0.00 0.00 40.65 1.85
2576 2684 6.775594 AGTGGATGAATAAACTTTTAGGGC 57.224 37.500 0.00 0.00 0.00 5.19
2648 2757 1.422402 ACCCGGTTTGACAATACCACT 59.578 47.619 0.00 0.61 33.94 4.00
2665 2774 8.141268 TGACAACTTTCTTTCATTATGAAACCC 58.859 33.333 15.46 0.48 41.02 4.11
2697 2806 8.840200 ATACCCATAAGAGAAACACTTAGAGA 57.160 34.615 0.00 0.00 34.13 3.10
2777 2887 3.576861 TCCTTCTCATCATACCGACCAT 58.423 45.455 0.00 0.00 0.00 3.55
2869 2979 1.777101 TTGCGCAAAATGTAACCAGC 58.223 45.000 22.78 0.00 0.00 4.85
2885 2995 2.389962 TGGTAACGGTAGGTGATTGC 57.610 50.000 0.00 0.00 42.51 3.56


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

AutoCloner maintained by Alex Coulton.