Multiple sequence alignment - TraesCS1A01G231600

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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 TraesCS1A01G231600 chr1A 100.000 3088 0 0 1 3088 405009873 405006786 0.000000e+00 5703
1 TraesCS1A01G231600 chr1D 93.923 2962 114 24 154 3088 318737632 318740554 0.000000e+00 4412
2 TraesCS1A01G231600 chr1B 91.110 3071 176 37 1 3019 431196697 431199722 0.000000e+00 4069
3 TraesCS1A01G231600 chr7A 81.081 148 25 3 2090 2236 701239952 701239807 7.000000e-22 115


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 TraesCS1A01G231600 chr1A 405006786 405009873 3087 True 5703 5703 100.000 1 3088 1 chr1A.!!$R1 3087
1 TraesCS1A01G231600 chr1D 318737632 318740554 2922 False 4412 4412 93.923 154 3088 1 chr1D.!!$F1 2934
2 TraesCS1A01G231600 chr1B 431196697 431199722 3025 False 4069 4069 91.110 1 3019 1 chr1B.!!$F1 3018

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
58 59 0.183971 TGTGACCCATCCACCGTTTT 59.816 50.0 0.0 0.0 33.8 2.43 F
769 777 1.254975 AATAAAAGGCGTGGGTGGGC 61.255 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1655 0.396435 ATTGGTGCAGAGTTGGTCGA 59.604 50.0 0.0 0.0 0.0 4.20 R
2551 2598 0.099791 GCCTCTCGTGTAGTCTGCTC 59.900 60.0 0.0 0.0 0.0 4.26 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
32 33 8.797438 AGTCCATTTTCCTTATTTTCTCTGTTC 58.203 33.333 0.00 0.00 0.00 3.18
38 39 8.871686 TTTCCTTATTTTCTCTGTTCTTTTGC 57.128 30.769 0.00 0.00 0.00 3.68
45 46 3.206150 TCTCTGTTCTTTTGCTGTGACC 58.794 45.455 0.00 0.00 0.00 4.02
54 55 2.436646 GCTGTGACCCATCCACCG 60.437 66.667 0.00 0.00 33.80 4.94
58 59 0.183971 TGTGACCCATCCACCGTTTT 59.816 50.000 0.00 0.00 33.80 2.43
65 66 1.606313 ATCCACCGTTTTGGGGCAG 60.606 57.895 0.00 0.00 41.26 4.85
67 68 2.561037 CCACCGTTTTGGGGCAGAC 61.561 63.158 0.00 0.00 41.26 3.51
68 69 1.826054 CACCGTTTTGGGGCAGACA 60.826 57.895 0.00 0.00 44.64 3.41
140 141 7.029563 CACATGCCTTTAGGTTGATTCTAAAC 58.970 38.462 0.00 0.00 34.29 2.01
478 485 2.745100 GGAACCGAGGCGAAACCC 60.745 66.667 0.00 0.00 40.58 4.11
482 489 2.125512 CCGAGGCGAAACCCTGAG 60.126 66.667 0.00 0.00 40.58 3.35
769 777 1.254975 AATAAAAGGCGTGGGTGGGC 61.255 55.000 0.00 0.00 0.00 5.36
864 873 6.405397 GGCCCACACGTCATTCTTTATATTTT 60.405 38.462 0.00 0.00 0.00 1.82
1062 1071 3.372822 ACAACATTTTCCATACCTACGCG 59.627 43.478 3.53 3.53 0.00 6.01
1452 1461 3.053455 GGTAGTAATCTCTGCATGCGAC 58.947 50.000 14.09 2.28 0.00 5.19
1460 1469 2.051435 TGCATGCGACGTGTTTGC 60.051 55.556 14.09 0.00 0.00 3.68
1645 1654 4.368808 CGTGCACCAAAGGCGTCG 62.369 66.667 12.15 0.00 0.00 5.12
1646 1655 3.276846 GTGCACCAAAGGCGTCGT 61.277 61.111 5.22 0.00 0.00 4.34
1647 1656 2.970324 TGCACCAAAGGCGTCGTC 60.970 61.111 0.00 0.00 0.00 4.20
1664 1673 0.531974 GTCGACCAACTCTGCACCAA 60.532 55.000 3.51 0.00 0.00 3.67
1815 1832 1.676968 CAACAGGGATCGGTGACCA 59.323 57.895 1.11 0.00 0.00 4.02
1847 1864 8.846943 TGTTTGCGATCCTTTCATGTATATAT 57.153 30.769 0.00 0.00 0.00 0.86
1848 1865 9.936759 TGTTTGCGATCCTTTCATGTATATATA 57.063 29.630 0.00 0.00 0.00 0.86
1928 1948 3.753070 GAGCCGGGCTAAGACGACG 62.753 68.421 23.92 0.00 39.88 5.12
2253 2294 1.828660 ATCTCTAGCCCACCCGTCG 60.829 63.158 0.00 0.00 0.00 5.12
2270 2311 2.277591 CGGGTCCACGTGGGTTCTA 61.278 63.158 33.40 12.08 38.11 2.10
2279 2320 1.448013 GTGGGTTCTAGCAGACGGC 60.448 63.158 0.00 0.00 45.30 5.68
2298 2339 3.089784 CGTGTGCTAACGGCCATC 58.910 61.111 2.24 0.00 39.89 3.51
2373 2414 3.181329 TCACTCTGTCTCCTCTCTCTCT 58.819 50.000 0.00 0.00 0.00 3.10
2374 2415 3.197766 TCACTCTGTCTCCTCTCTCTCTC 59.802 52.174 0.00 0.00 0.00 3.20
2397 2438 3.215151 CTCGATCTGGTAGACCTAAGCA 58.785 50.000 0.00 0.00 36.82 3.91
2422 2463 3.044114 GCGACGACGAAAGCACTCG 62.044 63.158 12.29 5.97 44.50 4.18
2426 2467 4.528002 GACGAAAGCACTCGACGA 57.472 55.556 13.62 0.00 41.44 4.20
2430 2471 2.717809 GAAAGCACTCGACGACGGC 61.718 63.158 7.55 7.69 40.21 5.68
2540 2587 4.394712 GCCGCCACAGCCTACACT 62.395 66.667 0.00 0.00 34.57 3.55
2545 2592 1.153628 CCACAGCCTACACTACCGC 60.154 63.158 0.00 0.00 0.00 5.68
2551 2598 2.104331 CTACACTACCGCGGCAGG 59.896 66.667 28.42 19.06 37.30 4.85
2564 2627 1.153745 GGCAGGAGCAGACTACACG 60.154 63.158 0.00 0.00 44.61 4.49
2640 2712 0.326264 AAGCGATCAGGGCTCTTGTT 59.674 50.000 0.00 0.00 40.53 2.83
2650 2722 2.257353 GCTCTTGTTGCCACGGATT 58.743 52.632 0.00 0.00 0.00 3.01
2683 2755 1.402896 CCGCTGGGCCTCTAGATTGA 61.403 60.000 4.53 0.00 0.00 2.57
2733 2805 7.679783 TCATCTACTCCTTGACTTGAATTGAA 58.320 34.615 0.00 0.00 0.00 2.69
2871 2943 9.111519 TGGTTTAGATAGGGAATATAGATGCAA 57.888 33.333 0.00 0.00 0.00 4.08
2903 2975 3.837213 TTAAGCAAGCATCAGCACTTC 57.163 42.857 0.00 0.00 45.49 3.01
2927 2999 7.268586 TCTACTCATTAGCTCTGGAATTTGAC 58.731 38.462 0.00 0.00 0.00 3.18
3003 3075 8.006027 AGTTAAGTTTTTATTTGACTACGCGTC 58.994 33.333 18.63 1.04 43.14 5.19
3025 3097 7.406553 CGTCAGAAAGATTTGTGAGTTAACAA 58.593 34.615 8.61 0.00 40.52 2.83
3064 3136 5.572271 GCTAGATGATGCCATTTGGGAGATA 60.572 44.000 0.00 0.00 39.50 1.98
3077 3149 5.441718 TTGGGAGATAAGACTGCATTTCT 57.558 39.130 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.797438 AGAACAGAGAAAATAAGGAAAATGGAC 58.203 33.333 0.00 0.00 0.00 4.02
32 33 1.270550 GTGGATGGGTCACAGCAAAAG 59.729 52.381 0.00 0.00 37.17 2.27
38 39 0.250727 AAACGGTGGATGGGTCACAG 60.251 55.000 0.00 0.00 36.90 3.66
45 46 2.645192 GCCCCAAAACGGTGGATGG 61.645 63.158 3.80 0.00 41.65 3.51
54 55 2.231235 CCATAACTGTCTGCCCCAAAAC 59.769 50.000 0.00 0.00 0.00 2.43
58 59 1.557832 GTACCATAACTGTCTGCCCCA 59.442 52.381 0.00 0.00 0.00 4.96
346 353 5.794687 TGTGAGCATTTTTGATAGTACCG 57.205 39.130 0.00 0.00 0.00 4.02
439 446 9.780413 GTTCCAAAAATGCATTCTTTTAAAACA 57.220 25.926 13.38 0.00 0.00 2.83
442 449 7.495934 TCGGTTCCAAAAATGCATTCTTTTAAA 59.504 29.630 13.38 6.06 0.00 1.52
449 456 3.253230 CCTCGGTTCCAAAAATGCATTC 58.747 45.455 13.38 0.00 0.00 2.67
452 459 0.316841 GCCTCGGTTCCAAAAATGCA 59.683 50.000 0.00 0.00 0.00 3.96
706 714 8.785946 CCATTTTTATCTTTTGAACCAAATGCT 58.214 29.630 0.00 0.00 34.27 3.79
769 777 3.920412 GCCAAAAGGAAATTTAGCTCACG 59.080 43.478 0.00 0.00 31.01 4.35
776 784 9.267084 GTATGTTTTGAGCCAAAAGGAAATTTA 57.733 29.630 11.76 0.00 42.77 1.40
864 873 7.921786 AATGGATTGAATCACGTTCTTCTTA 57.078 32.000 7.56 0.00 37.72 2.10
933 942 3.143211 ACGGCAATTACAGGGTGTAAA 57.857 42.857 3.74 0.00 44.84 2.01
934 943 2.814919 CAACGGCAATTACAGGGTGTAA 59.185 45.455 2.14 2.14 45.63 2.41
935 944 2.428491 CAACGGCAATTACAGGGTGTA 58.572 47.619 0.00 0.00 0.00 2.90
1062 1071 3.195698 GACGAGGACGCCATTGGC 61.196 66.667 18.10 18.10 46.75 4.52
1378 1387 1.952990 GTAAGGGTACTACCTCTCGGC 59.047 57.143 5.19 0.00 40.87 5.54
1452 1461 2.542907 AACGGCCAGAGCAAACACG 61.543 57.895 2.24 0.00 42.56 4.49
1645 1654 0.531974 TTGGTGCAGAGTTGGTCGAC 60.532 55.000 7.13 7.13 0.00 4.20
1646 1655 0.396435 ATTGGTGCAGAGTTGGTCGA 59.604 50.000 0.00 0.00 0.00 4.20
1647 1656 0.518636 CATTGGTGCAGAGTTGGTCG 59.481 55.000 0.00 0.00 0.00 4.79
1664 1673 1.520120 CGAGTGACTGATGCGGCAT 60.520 57.895 16.65 16.65 0.00 4.40
1815 1832 1.981256 AGGATCGCAAACAAAGGTGT 58.019 45.000 0.00 0.00 40.75 4.16
1847 1864 7.273320 AGCACGTACTAATTTCTCTGCTATA 57.727 36.000 0.00 0.00 32.03 1.31
1848 1865 6.150396 AGCACGTACTAATTTCTCTGCTAT 57.850 37.500 0.00 0.00 32.03 2.97
1996 2016 9.320352 AGAAACCAAATGTAACATTTTTGTACC 57.680 29.630 0.00 0.00 0.00 3.34
2208 2249 7.808856 GTCATAACCGCACTTAAATTTTAACCA 59.191 33.333 0.00 0.00 0.00 3.67
2253 2294 1.595357 CTAGAACCCACGTGGACCC 59.405 63.158 36.07 21.71 37.39 4.46
2263 2304 2.202756 CGCCGTCTGCTAGAACCC 60.203 66.667 0.00 0.00 38.05 4.11
2373 2414 1.223501 AGGTCTACCAGATCGAGGGA 58.776 55.000 11.27 2.47 38.89 4.20
2374 2415 2.953284 TAGGTCTACCAGATCGAGGG 57.047 55.000 11.27 5.98 38.89 4.30
2397 2438 4.728102 TTCGTCGTCGCCGCCATT 62.728 61.111 0.00 0.00 36.96 3.16
2407 2448 1.724929 CGTCGAGTGCTTTCGTCGT 60.725 57.895 16.61 0.00 43.48 4.34
2422 2463 2.025727 CATAGGGTCGCCGTCGTC 59.974 66.667 0.00 0.00 36.96 4.20
2462 2509 0.395312 TTCCGAATAATCTCCGCCCC 59.605 55.000 0.00 0.00 0.00 5.80
2505 2552 1.515519 CGGCTACGTTGCGAAGCTA 60.516 57.895 15.58 0.00 45.84 3.32
2545 2592 1.153745 GTGTAGTCTGCTCCTGCCG 60.154 63.158 0.00 0.00 38.71 5.69
2551 2598 0.099791 GCCTCTCGTGTAGTCTGCTC 59.900 60.000 0.00 0.00 0.00 4.26
2564 2627 1.448013 GGCGTAGGTTGTGCCTCTC 60.448 63.158 0.00 0.00 46.96 3.20
2619 2682 1.012841 CAAGAGCCCTGATCGCTTTC 58.987 55.000 0.00 0.00 36.48 2.62
2677 2749 4.273148 ACTTACTCAACGCCTTCAATCT 57.727 40.909 0.00 0.00 0.00 2.40
2683 2755 7.916914 ATATAACAAACTTACTCAACGCCTT 57.083 32.000 0.00 0.00 0.00 4.35
2733 2805 5.552870 AAGTTCAGTCATCCACAACTACT 57.447 39.130 0.00 0.00 0.00 2.57
2894 2966 4.952957 AGAGCTAATGAGTAGAAGTGCTGA 59.047 41.667 0.00 0.00 30.50 4.26
2897 2969 4.098654 TCCAGAGCTAATGAGTAGAAGTGC 59.901 45.833 0.00 0.00 30.50 4.40
2903 2975 7.271511 AGTCAAATTCCAGAGCTAATGAGTAG 58.728 38.462 0.00 0.00 0.00 2.57
2927 2999 6.311445 CAGTAATGTCAACCAGCAGTACTAAG 59.689 42.308 0.00 0.00 42.26 2.18
2976 3048 8.977505 ACGCGTAGTCAAATAAAAACTTAACTA 58.022 29.630 11.67 0.00 0.00 2.24
2998 3070 2.476619 ACTCACAAATCTTTCTGACGCG 59.523 45.455 3.53 3.53 0.00 6.01
3000 3072 6.943981 TGTTAACTCACAAATCTTTCTGACG 58.056 36.000 7.22 0.00 0.00 4.35
3051 3123 3.889815 TGCAGTCTTATCTCCCAAATGG 58.110 45.455 0.00 0.00 0.00 3.16
3064 3136 3.439857 TTGCCCTAGAAATGCAGTCTT 57.560 42.857 7.92 0.00 36.21 3.01


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

AutoCloner maintained by Alex Coulton.