Multiple sequence alignment - TraesCS5A01G426900

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 TraesCS5A01G426900 chr5A 100.000 3095 0 0 1 3095 611655604 611658698 0.000000e+00 5716.0
1 TraesCS5A01G426900 chr5B 93.438 3109 178 22 1 3095 604178418 604181514 0.000000e+00 4588.0
2 TraesCS5A01G426900 chr5D 92.751 2828 167 18 283 3095 490046283 490049087 0.000000e+00 4052.0
3 TraesCS5A01G426900 chr5D 96.319 163 3 1 1 163 490046128 490046287 6.580000e-67 265.0
4 TraesCS5A01G426900 chr2A 82.114 123 21 1 224 345 776208953 776209075 1.520000e-18 104.0
5 TraesCS5A01G426900 chr2A 79.839 124 23 2 224 345 632266841 632266718 4.250000e-14 89.8
6 TraesCS5A01G426900 chr7B 80.315 127 23 2 224 348 123761474 123761348 9.140000e-16 95.3
7 TraesCS5A01G426900 chr7A 80.645 124 22 2 224 345 75074137 75074014 9.140000e-16 95.3
8 TraesCS5A01G426900 chr2B 80.645 124 22 2 224 345 708358912 708359035 9.140000e-16 95.3
9 TraesCS5A01G426900 chr4B 93.023 43 3 0 224 266 500504957 500504915 2.580000e-06 63.9


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 TraesCS5A01G426900 chr5A 611655604 611658698 3094 False 5716.0 5716 100.000 1 3095 1 chr5A.!!$F1 3094
1 TraesCS5A01G426900 chr5B 604178418 604181514 3096 False 4588.0 4588 93.438 1 3095 1 chr5B.!!$F1 3094
2 TraesCS5A01G426900 chr5D 490046128 490049087 2959 False 2158.5 4052 94.535 1 3095 2 chr5D.!!$F1 3094

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
485 489 0.467384 ATCACAATCCGCTCAGGGAG 59.533 55.0 0.0 0.0 40.02 4.30 F
696 701 1.195115 TGAGTGGTGATGTCTAGGGC 58.805 55.0 0.0 0.0 0.00 5.19 F
1626 1631 1.089920 GTGTGGAGCCATGTGTCATC 58.910 55.0 0.0 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1388 0.034380 TCTCGGTGTACTCCTCCCAG 60.034 60.0 11.98 3.31 0.0 4.45 R
1922 1927 0.250081 GCTCCCGATGATCTTCACCC 60.250 60.0 9.10 0.00 0.0 4.61 R
2775 2795 0.108804 TCGCATGGGACTTCTCGTTC 60.109 55.0 8.63 0.00 0.0 3.95 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
55 56 3.447586 CCTACCGAATCTGAAGGAAGACA 59.552 47.826 4.56 0.00 0.00 3.41
232 233 3.906846 TGGTTAATTCCCCAAACTTGCAT 59.093 39.130 0.00 0.00 0.00 3.96
303 305 8.859090 TGTGATTTTTATATTATGGGCCTTGAG 58.141 33.333 4.53 0.00 0.00 3.02
314 316 3.227614 TGGGCCTTGAGTTTTAGTTTCC 58.772 45.455 4.53 0.00 0.00 3.13
315 317 3.117284 TGGGCCTTGAGTTTTAGTTTCCT 60.117 43.478 4.53 0.00 0.00 3.36
345 347 1.497309 AAAATCTCAGGACCGGCCCA 61.497 55.000 10.37 0.00 37.37 5.36
398 401 3.193479 GCCTCAATGGTACCTTCCAAAAG 59.807 47.826 14.36 1.78 41.09 2.27
475 479 2.428171 CCACATCCAACCATCACAATCC 59.572 50.000 0.00 0.00 0.00 3.01
483 487 0.816825 CCATCACAATCCGCTCAGGG 60.817 60.000 0.00 0.00 41.52 4.45
485 489 0.467384 ATCACAATCCGCTCAGGGAG 59.533 55.000 0.00 0.00 40.02 4.30
524 528 4.579647 TGAACCTAACCCTAAACCATCC 57.420 45.455 0.00 0.00 0.00 3.51
561 566 1.369091 GCCGCATTCCTCACATCGTT 61.369 55.000 0.00 0.00 0.00 3.85
566 571 2.863137 GCATTCCTCACATCGTTCTCTC 59.137 50.000 0.00 0.00 0.00 3.20
628 633 6.358974 TCTTCCAAGTGATCTATGTGTTGA 57.641 37.500 0.00 0.00 0.00 3.18
637 642 6.015095 AGTGATCTATGTGTTGACACTCTTCA 60.015 38.462 14.66 8.24 46.55 3.02
651 656 2.368875 ACTCTTCATCCACTTTCACGGT 59.631 45.455 0.00 0.00 0.00 4.83
693 698 5.107824 CAGACAATGAGTGGTGATGTCTAG 58.892 45.833 6.43 0.00 46.53 2.43
696 701 1.195115 TGAGTGGTGATGTCTAGGGC 58.805 55.000 0.00 0.00 0.00 5.19
768 773 7.602265 CGTAATTTTTCATCAAGGGGAATTTGT 59.398 33.333 0.00 0.00 0.00 2.83
885 890 6.494842 TCATTTGGTTGACGAAGAAGAAAAG 58.505 36.000 0.00 0.00 0.00 2.27
890 895 4.575236 GGTTGACGAAGAAGAAAAGAAGGT 59.425 41.667 0.00 0.00 0.00 3.50
909 914 2.477104 TGGGATCTCCATGCACTAGA 57.523 50.000 0.00 0.00 41.46 2.43
1115 1120 1.594021 CATGGCGCCGCATAGTGTA 60.594 57.895 23.90 0.00 0.00 2.90
1173 1178 1.349688 GTTGTACCAGTGGTCATGGGA 59.650 52.381 20.72 0.00 42.48 4.37
1191 1196 3.075882 TGGGATTCTTCCACAACTCCAAT 59.924 43.478 0.00 0.00 44.60 3.16
1206 1211 1.817941 CAATACACTTCCCCGCCCG 60.818 63.158 0.00 0.00 0.00 6.13
1242 1247 3.514309 ACGACACCACTAGCTTATCCTTT 59.486 43.478 0.00 0.00 0.00 3.11
1278 1283 3.417101 TGGCAATTACTCATGGACGTTT 58.583 40.909 0.00 0.00 0.00 3.60
1347 1352 1.600636 CGTGTGGCACCCAATGACT 60.601 57.895 16.26 0.00 37.17 3.41
1376 1381 1.197721 CCGCCTAATCAATGCCGAATC 59.802 52.381 0.00 0.00 0.00 2.52
1383 1388 1.852942 TCAATGCCGAATCTAGTCGC 58.147 50.000 0.00 0.00 39.74 5.19
1407 1412 3.025262 GGAGGAGTACACCGAGAAGAAT 58.975 50.000 3.50 0.00 34.73 2.40
1491 1496 1.266718 CCCACAAGTCCATTTCGTGTG 59.733 52.381 0.00 0.00 42.00 3.82
1514 1519 3.689347 CCCTTGTCCACAATGATTCTCA 58.311 45.455 0.00 0.00 35.02 3.27
1532 1537 2.047655 GGGTCGTGTTCATGCCGA 60.048 61.111 0.00 0.00 0.00 5.54
1554 1559 2.097791 CGTCTACTCCTCACTTACTGGC 59.902 54.545 0.00 0.00 0.00 4.85
1626 1631 1.089920 GTGTGGAGCCATGTGTCATC 58.910 55.000 0.00 0.00 0.00 2.92
1692 1697 1.927895 CCTACGACATGGACAAGAGC 58.072 55.000 0.00 0.00 0.00 4.09
1887 1892 4.321156 GCATGCTTGTCAAAGGTCACATTA 60.321 41.667 11.37 0.00 33.68 1.90
1912 1917 4.594675 AAGGTAGACTCTAGCTTCCTGA 57.405 45.455 20.32 0.00 33.98 3.86
1922 1927 2.890109 GCTTCCTGATGATGCCGCG 61.890 63.158 0.00 0.00 38.00 6.46
1942 1947 0.465705 GGTGAAGATCATCGGGAGCA 59.534 55.000 0.00 0.00 33.23 4.26
2042 2047 0.392461 GTGCATGAGGCCGTTAAGGA 60.392 55.000 0.00 0.00 45.00 3.36
2080 2085 2.224621 CCATATACTGCCTTCCCCACTG 60.225 54.545 0.00 0.00 0.00 3.66
2152 2159 0.909610 TTCCCTCTGTTGCCCGAGAT 60.910 55.000 0.00 0.00 0.00 2.75
2154 2161 1.227089 CCTCTGTTGCCCGAGATCG 60.227 63.158 0.00 0.00 39.44 3.69
2188 2195 0.600782 AGTTGCAAGCATTTTGGCCG 60.601 50.000 0.00 0.00 0.00 6.13
2418 2426 6.260714 TGTGAGCAACATTACATCATGGATAC 59.739 38.462 0.00 0.00 32.36 2.24
2469 2478 9.462174 TTTATGAACTAAACAGAGCAACATTTG 57.538 29.630 0.00 0.00 0.00 2.32
2471 2480 6.494842 TGAACTAAACAGAGCAACATTTGTC 58.505 36.000 0.00 0.00 0.00 3.18
2499 2508 5.457473 GGTGAAACTGGAAACAACATTTACG 59.543 40.000 0.00 0.00 42.06 3.18
2605 2614 5.872070 GCTAGAACATCAATATCCTAGCACC 59.128 44.000 12.61 0.00 44.87 5.01
2630 2639 6.317140 CAGCTTCTCATTGTAGCCTTATTTGA 59.683 38.462 0.00 0.00 39.50 2.69
2679 2696 2.851824 GCCGAAAACTGTGTGAAAGTTG 59.148 45.455 0.00 0.00 37.90 3.16
2775 2795 0.166597 CAACCACACATGCAGTAGCG 59.833 55.000 0.00 0.00 46.23 4.26
2778 2800 0.443869 CCACACATGCAGTAGCGAAC 59.556 55.000 0.00 0.00 46.23 3.95
2788 2810 0.810016 AGTAGCGAACGAGAAGTCCC 59.190 55.000 0.00 0.00 0.00 4.46
2792 2814 1.696832 GCGAACGAGAAGTCCCATGC 61.697 60.000 0.00 0.00 0.00 4.06
2802 2824 3.838271 TCCCATGCGACGCTCTCC 61.838 66.667 22.08 0.00 0.00 3.71
2834 2856 2.742372 CCCCGAAGCACAACGAGG 60.742 66.667 0.00 0.00 0.00 4.63
2837 2859 2.034879 CCGAAGCACAACGAGGCAT 61.035 57.895 0.00 0.00 0.00 4.40
2860 2882 7.815068 GCATGAATAGGTCGACTCATTTACTAT 59.185 37.037 16.46 8.77 0.00 2.12
2869 2891 4.681942 CGACTCATTTACTATGCCTGTAGC 59.318 45.833 0.00 0.00 44.14 3.58
3051 3075 7.043458 TGAGACTGCGATTTGTTTTTGAAATTC 60.043 33.333 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 8.677300 CAAGGAATGCAACTATGTACAGTATTT 58.323 33.333 0.33 0.00 0.00 1.40
210 211 3.309296 TGCAAGTTTGGGGAATTAACCA 58.691 40.909 1.52 0.00 34.29 3.67
215 216 2.833943 GGAGATGCAAGTTTGGGGAATT 59.166 45.455 0.00 0.00 0.00 2.17
303 305 3.266254 AGGGGCTAGGAGGAAACTAAAAC 59.734 47.826 0.00 0.00 44.43 2.43
314 316 3.326297 CCTGAGATTTTAGGGGCTAGGAG 59.674 52.174 0.00 0.00 0.00 3.69
315 317 3.051341 TCCTGAGATTTTAGGGGCTAGGA 60.051 47.826 0.00 0.00 34.76 2.94
368 370 2.350522 GTACCATTGAGGCAGACTGTG 58.649 52.381 3.99 0.00 43.14 3.66
434 437 5.248020 TGTGGATCCAATGGCTACAAAATTT 59.752 36.000 18.20 0.00 0.00 1.82
483 487 7.502561 AGGTTCAAGTGGTATATTTATTGGCTC 59.497 37.037 0.00 0.00 0.00 4.70
485 489 7.582667 AGGTTCAAGTGGTATATTTATTGGC 57.417 36.000 0.00 0.00 0.00 4.52
561 566 1.577729 AGATGAGGGTGGATGGAGAGA 59.422 52.381 0.00 0.00 0.00 3.10
566 571 4.989875 AAAGATAGATGAGGGTGGATGG 57.010 45.455 0.00 0.00 0.00 3.51
628 633 3.393800 CGTGAAAGTGGATGAAGAGTGT 58.606 45.455 0.00 0.00 0.00 3.55
696 701 5.215160 GCTATTATCTTTTTGTGGGATGCG 58.785 41.667 0.00 0.00 0.00 4.73
744 749 7.816995 CGACAAATTCCCCTTGATGAAAAATTA 59.183 33.333 0.00 0.00 0.00 1.40
768 773 0.671163 AAGTGATTTTACGGCGGCGA 60.671 50.000 38.93 18.70 0.00 5.54
977 982 8.981647 CCATAACTGCAAAATTATTGGATTAGC 58.018 33.333 0.00 0.00 0.00 3.09
1115 1120 0.329596 GTGGAGGAAACCAGGAGCAT 59.670 55.000 0.00 0.00 40.85 3.79
1157 1162 2.845659 AGAATCCCATGACCACTGGTA 58.154 47.619 0.00 0.00 35.25 3.25
1173 1178 5.880901 AGTGTATTGGAGTTGTGGAAGAAT 58.119 37.500 0.00 0.00 0.00 2.40
1191 1196 2.924101 AACGGGCGGGGAAGTGTA 60.924 61.111 0.00 0.00 0.00 2.90
1206 1211 2.660236 GGTGTCGTTGATCTGTACGAAC 59.340 50.000 16.05 15.10 46.87 3.95
1242 1247 5.913137 AATTGCCATCATTAGGAAAACGA 57.087 34.783 0.00 0.00 0.00 3.85
1278 1283 4.846551 CCGTGACGGCAATCCATA 57.153 55.556 12.53 0.00 41.17 2.74
1321 1326 2.110213 GTGCCACACGAGGAACCA 59.890 61.111 0.00 0.00 30.25 3.67
1376 1381 1.310904 GTACTCCTCCCAGCGACTAG 58.689 60.000 0.00 0.00 0.00 2.57
1383 1388 0.034380 TCTCGGTGTACTCCTCCCAG 60.034 60.000 11.98 3.31 0.00 4.45
1491 1496 1.478105 GAATCATTGTGGACAAGGGCC 59.522 52.381 0.00 0.00 39.47 5.80
1514 1519 2.047274 CGGCATGAACACGACCCT 60.047 61.111 0.00 0.00 0.00 4.34
1532 1537 3.345414 CCAGTAAGTGAGGAGTAGACGT 58.655 50.000 0.00 0.00 0.00 4.34
1591 1596 1.668237 CACACGGATGTCACACAACAA 59.332 47.619 0.00 0.00 36.72 2.83
1626 1631 8.041323 AGAGGTTGGTACATAGTGTTAAAGATG 58.959 37.037 0.00 0.00 39.30 2.90
1677 1682 1.067283 AGAGTGCTCTTGTCCATGTCG 60.067 52.381 0.00 0.00 36.31 4.35
1692 1697 1.413382 GCTCGAACACAGTGAGAGTG 58.587 55.000 7.81 0.00 42.56 3.51
1774 1779 0.544357 AATGTGAGGTCCTCCACGGA 60.544 55.000 16.60 0.00 40.30 4.69
1820 1825 3.846955 GTGCGTAGTACCCAACCAT 57.153 52.632 0.00 0.00 37.07 3.55
1854 1859 1.143183 CAAGCATGCAATGGCCTCC 59.857 57.895 21.98 0.00 46.86 4.30
1887 1892 4.479425 AGGAAGCTAGAGTCTACCTTAGGT 59.521 45.833 9.57 9.57 40.16 3.08
1912 1917 2.329539 ATCTTCACCCGCGGCATCAT 62.330 55.000 22.85 2.94 0.00 2.45
1922 1927 0.250081 GCTCCCGATGATCTTCACCC 60.250 60.000 9.10 0.00 0.00 4.61
1959 1964 3.427503 CGACCATGGTCCACAAAAATAGC 60.428 47.826 34.05 9.97 41.76 2.97
2007 2012 2.507484 TGCACCTTCTTGAACTCCATG 58.493 47.619 0.00 0.00 0.00 3.66
2042 2047 5.912149 ATATGGGTACACAATCTCCATGT 57.088 39.130 0.00 0.00 38.51 3.21
2080 2085 3.119708 GCATATAATTACCAGCTGGCAGC 60.120 47.826 33.06 31.56 42.84 5.25
2152 2159 5.119694 TGCAACTAACACATTATATGCCGA 58.880 37.500 0.00 0.00 33.77 5.54
2154 2161 5.687285 GCTTGCAACTAACACATTATATGCC 59.313 40.000 0.00 0.00 33.77 4.40
2159 2166 7.118101 CCAAAATGCTTGCAACTAACACATTAT 59.882 33.333 0.00 0.00 0.00 1.28
2234 2241 5.230306 GCACTGATAGTAAACTTGCTACTCG 59.770 44.000 0.00 0.00 31.98 4.18
2285 2292 8.574196 AAATAAACAAGGAAAAACATCTCACG 57.426 30.769 0.00 0.00 0.00 4.35
2316 2323 6.391227 TCTCAATCAAGTTTTGTCCCTTTC 57.609 37.500 0.00 0.00 0.00 2.62
2394 2402 5.762825 ATCCATGATGTAATGTTGCTCAC 57.237 39.130 0.00 0.00 0.00 3.51
2418 2426 5.972107 ATGGATGACCTGTCTTTGAAAAG 57.028 39.130 0.00 0.00 35.85 2.27
2456 2464 4.696877 TCACCATAGACAAATGTTGCTCTG 59.303 41.667 0.00 0.00 0.00 3.35
2469 2478 5.298276 TGTTGTTTCCAGTTTCACCATAGAC 59.702 40.000 0.00 0.00 0.00 2.59
2471 2480 5.766150 TGTTGTTTCCAGTTTCACCATAG 57.234 39.130 0.00 0.00 0.00 2.23
2499 2508 2.546368 TCTTATGCACAACAACACGGTC 59.454 45.455 0.00 0.00 0.00 4.79
2605 2614 6.317140 TCAAATAAGGCTACAATGAGAAGCTG 59.683 38.462 0.00 0.00 36.48 4.24
2617 2626 4.207165 TGGCTCCATTCAAATAAGGCTAC 58.793 43.478 0.00 0.00 33.98 3.58
2630 2639 0.906066 TTGCATTGCATGGCTCCATT 59.094 45.000 12.95 0.00 38.76 3.16
2661 2678 7.581011 AATTGTCAACTTTCACACAGTTTTC 57.419 32.000 0.00 0.00 31.83 2.29
2712 2730 5.701290 AGGCAGTAAAGGAATATTACGATGC 59.299 40.000 0.00 6.93 38.11 3.91
2775 2795 0.108804 TCGCATGGGACTTCTCGTTC 60.109 55.000 8.63 0.00 0.00 3.95
2778 2800 1.874019 CGTCGCATGGGACTTCTCG 60.874 63.158 32.32 19.72 34.75 4.04
2802 2824 0.319900 CGGGGTCTCTATTGGATGCG 60.320 60.000 0.00 0.00 0.00 4.73
2834 2856 5.986135 AGTAAATGAGTCGACCTATTCATGC 59.014 40.000 16.12 10.82 31.11 4.06
2837 2859 7.145985 GCATAGTAAATGAGTCGACCTATTCA 58.854 38.462 13.01 9.90 0.00 2.57
2860 2882 1.153449 GTACCATGCGCTACAGGCA 60.153 57.895 9.73 0.00 45.71 4.75
2869 2891 0.673333 TTGCTCCAGTGTACCATGCG 60.673 55.000 0.00 0.00 0.00 4.73
2888 2910 1.356527 GCCGCTACAACGAATCGGTT 61.357 55.000 7.80 0.00 41.89 4.44
2890 2912 2.522638 GGCCGCTACAACGAATCGG 61.523 63.158 7.80 0.00 42.68 4.18
3026 3050 6.753897 ATTTCAAAAACAAATCGCAGTCTC 57.246 33.333 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.