Multiple sequence alignment - TraesCS4D01G189000

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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 TraesCS4D01G189000 chr4D 100.000 2090 0 0 934 3023 328806217 328808306 0.000000e+00 3860.0
1 TraesCS4D01G189000 chr4D 100.000 682 0 0 1 682 328805284 328805965 0.000000e+00 1260.0
2 TraesCS4D01G189000 chr4B 93.241 2086 77 20 934 3003 408603903 408605940 0.000000e+00 3013.0
3 TraesCS4D01G189000 chr4B 92.506 387 19 2 306 682 408603477 408603863 2.050000e-151 545.0
4 TraesCS4D01G189000 chr4B 93.137 306 19 2 1 305 408601896 408602200 5.940000e-122 448.0
5 TraesCS4D01G189000 chr4A 92.109 2129 88 19 934 3022 141329695 141327607 0.000000e+00 2928.0
6 TraesCS4D01G189000 chr4A 90.314 382 9 4 306 682 141330095 141329737 2.730000e-130 475.0
7 TraesCS4D01G189000 chr4A 88.024 167 12 2 1 159 141330434 141330268 1.110000e-44 191.0
8 TraesCS4D01G189000 chr4A 86.765 68 9 0 971 1038 141331456 141331389 3.230000e-10 76.8


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 TraesCS4D01G189000 chr4D 328805284 328808306 3022 False 2560.000000 3860 100.000000 1 3023 2 chr4D.!!$F1 3022
1 TraesCS4D01G189000 chr4B 408601896 408605940 4044 False 1335.333333 3013 92.961333 1 3003 3 chr4B.!!$F1 3002
2 TraesCS4D01G189000 chr4A 141327607 141331456 3849 True 917.700000 2928 89.303000 1 3022 4 chr4A.!!$R1 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
55 1086 0.326927 GGAGGGGGTTTGAATGACGA 59.673 55.0 0.0 0.0 0.0 4.20 F
1390 3820 0.109342 CGAGCATCCCATTAGCCCTT 59.891 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 3823 0.179166 TGGATCAAAATCTTGCGCGC 60.179 50.0 27.26 27.26 32.14 6.86 R
2365 4805 0.179040 TCACCACAAGGGGAAACGTC 60.179 55.0 0.00 0.00 46.84 4.34 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 1086 0.326927 GGAGGGGGTTTGAATGACGA 59.673 55.000 0.00 0.00 0.00 4.20
197 1228 7.336931 GGTACTAGATGCCCATAATACAATTGG 59.663 40.741 10.83 0.00 0.00 3.16
246 1277 3.725634 ACTAGGAACCCAGTAATGCTCT 58.274 45.455 0.00 0.00 0.00 4.09
278 1309 2.656560 ACTCGTAAGTGAGGTCATGC 57.343 50.000 0.00 0.00 40.39 4.06
282 1313 3.064207 TCGTAAGTGAGGTCATGCAAAC 58.936 45.455 0.00 0.00 39.48 2.93
306 1337 7.680730 ACGCCTAAGAAATGATTATGTCCTAT 58.319 34.615 0.00 0.00 0.00 2.57
307 1338 8.812972 ACGCCTAAGAAATGATTATGTCCTATA 58.187 33.333 0.00 0.00 0.00 1.31
308 1339 9.307121 CGCCTAAGAAATGATTATGTCCTATAG 57.693 37.037 0.00 0.00 0.00 1.31
309 1340 9.606631 GCCTAAGAAATGATTATGTCCTATAGG 57.393 37.037 13.07 13.07 31.39 2.57
310 1341 9.606631 CCTAAGAAATGATTATGTCCTATAGGC 57.393 37.037 14.50 9.81 34.44 3.93
325 2714 6.092807 GTCCTATAGGCTTTCACTCAGTTTTG 59.907 42.308 14.50 0.00 34.44 2.44
394 2783 1.079405 CTACCGACGTGCATTGGGT 60.079 57.895 9.46 9.46 34.81 4.51
395 2784 0.672401 CTACCGACGTGCATTGGGTT 60.672 55.000 9.74 0.00 32.29 4.11
396 2785 0.951525 TACCGACGTGCATTGGGTTG 60.952 55.000 9.74 1.41 32.29 3.77
397 2786 2.560861 CGACGTGCATTGGGTTGG 59.439 61.111 0.00 0.00 0.00 3.77
398 2787 2.961768 GACGTGCATTGGGTTGGG 59.038 61.111 0.00 0.00 0.00 4.12
399 2788 1.901464 GACGTGCATTGGGTTGGGT 60.901 57.895 0.00 0.00 0.00 4.51
400 2789 1.862602 GACGTGCATTGGGTTGGGTC 61.863 60.000 0.00 0.00 0.00 4.46
401 2790 2.961768 GTGCATTGGGTTGGGTCG 59.038 61.111 0.00 0.00 0.00 4.79
402 2791 2.988684 TGCATTGGGTTGGGTCGC 60.989 61.111 0.00 0.00 0.00 5.19
403 2792 2.988684 GCATTGGGTTGGGTCGCA 60.989 61.111 0.00 0.00 0.00 5.10
404 2793 2.993471 GCATTGGGTTGGGTCGCAG 61.993 63.158 0.00 0.00 0.00 5.18
405 2794 2.035626 ATTGGGTTGGGTCGCAGG 59.964 61.111 0.00 0.00 0.00 4.85
406 2795 3.583882 ATTGGGTTGGGTCGCAGGG 62.584 63.158 0.00 0.00 0.00 4.45
456 2875 1.443802 CCCAAAAGCTCGAGAGTTCC 58.556 55.000 18.75 0.00 0.00 3.62
457 2876 1.270839 CCCAAAAGCTCGAGAGTTCCA 60.271 52.381 18.75 0.00 0.00 3.53
553 2972 4.278170 CCTTAAAAATATCTGGCATCGGCA 59.722 41.667 0.00 0.00 43.71 5.69
954 3378 3.080647 GCAATAGCAGCTTACCCGT 57.919 52.632 0.00 0.00 41.58 5.28
960 3384 1.235724 AGCAGCTTACCCGTGTTTTC 58.764 50.000 0.00 0.00 0.00 2.29
976 3400 2.702751 TTTCTTTCCTCGCCGTCGCA 62.703 55.000 0.00 0.00 35.26 5.10
977 3401 2.501223 TTCTTTCCTCGCCGTCGCAT 62.501 55.000 0.00 0.00 35.26 4.73
1119 3549 1.035932 CCTCCTCCACCGACATACGT 61.036 60.000 0.00 0.00 40.78 3.57
1147 3577 2.185867 GACGGCTCGCCATGGTAA 59.814 61.111 14.67 0.38 35.37 2.85
1376 3806 2.202878 GGTAAGGCATCGCGAGCA 60.203 61.111 24.72 8.36 0.00 4.26
1390 3820 0.109342 CGAGCATCCCATTAGCCCTT 59.891 55.000 0.00 0.00 0.00 3.95
1392 3822 0.186873 AGCATCCCATTAGCCCTTGG 59.813 55.000 0.00 0.00 0.00 3.61
1411 3841 0.867329 GGCGCGCAAGATTTTGATCC 60.867 55.000 34.42 6.39 43.02 3.36
1426 3856 2.091541 TGATCCAATTCTTTGTCGGCC 58.908 47.619 0.00 0.00 0.00 6.13
1427 3857 1.405463 GATCCAATTCTTTGTCGGCCC 59.595 52.381 0.00 0.00 0.00 5.80
1428 3858 0.404040 TCCAATTCTTTGTCGGCCCT 59.596 50.000 0.00 0.00 0.00 5.19
1429 3859 0.811281 CCAATTCTTTGTCGGCCCTC 59.189 55.000 0.00 0.00 0.00 4.30
1430 3860 0.811281 CAATTCTTTGTCGGCCCTCC 59.189 55.000 0.00 0.00 0.00 4.30
1431 3861 0.323451 AATTCTTTGTCGGCCCTCCC 60.323 55.000 0.00 0.00 0.00 4.30
1432 3862 1.208165 ATTCTTTGTCGGCCCTCCCT 61.208 55.000 0.00 0.00 0.00 4.20
1433 3863 1.423794 TTCTTTGTCGGCCCTCCCTT 61.424 55.000 0.00 0.00 0.00 3.95
1434 3864 1.074951 CTTTGTCGGCCCTCCCTTT 59.925 57.895 0.00 0.00 0.00 3.11
1435 3865 1.228429 TTTGTCGGCCCTCCCTTTG 60.228 57.895 0.00 0.00 0.00 2.77
1436 3866 2.706952 TTTGTCGGCCCTCCCTTTGG 62.707 60.000 0.00 0.00 0.00 3.28
1438 3868 4.995058 TCGGCCCTCCCTTTGGGT 62.995 66.667 0.00 0.00 46.22 4.51
1552 3984 5.278315 GGTTTCTTTCCGTGCTTATTGTCTT 60.278 40.000 0.00 0.00 0.00 3.01
1567 3999 7.064016 GCTTATTGTCTTGTCGAAATTCTCTCT 59.936 37.037 0.00 0.00 0.00 3.10
1643 4075 2.466846 GGACATACCGACGTACAATGG 58.533 52.381 0.00 0.00 0.00 3.16
1770 4202 2.572104 GACCCAACTACCCTTGAGACAT 59.428 50.000 0.00 0.00 0.00 3.06
1783 4217 8.738645 ACCCTTGAGACATCATTAGTTTAATC 57.261 34.615 0.00 0.00 34.73 1.75
2138 4578 3.829948 AGCAAATCAGAATTGTTGCTCG 58.170 40.909 3.99 0.00 35.12 5.03
2149 4589 0.400213 TGTTGCTCGATCCCCTTGTT 59.600 50.000 0.00 0.00 0.00 2.83
2221 4661 5.313623 CCGTCGATCTGTTTAATTGTGTTC 58.686 41.667 0.00 0.00 0.00 3.18
2242 4682 0.685785 TTTGGCTGGTTGGTGCTTCA 60.686 50.000 0.00 0.00 0.00 3.02
2248 4688 1.891919 GGTTGGTGCTTCAGTCGCA 60.892 57.895 0.00 0.00 34.52 5.10
2356 4796 5.333339 CCAATTGTTGCTCGAATATACCTCG 60.333 44.000 4.43 0.58 37.66 4.63
2364 4804 4.673061 GCTCGAATATACCTCGTCTCCATG 60.673 50.000 6.09 0.00 37.56 3.66
2365 4805 3.756963 TCGAATATACCTCGTCTCCATGG 59.243 47.826 4.97 4.97 37.56 3.66
2396 4836 0.105709 TGTGGTGAGTCCTGTCCTGA 60.106 55.000 0.00 0.00 37.07 3.86
2404 4863 2.891580 GAGTCCTGTCCTGAGTTGTGTA 59.108 50.000 0.00 0.00 0.00 2.90
2418 4877 4.215109 AGTTGTGTATGGTCTTTTTGGCT 58.785 39.130 0.00 0.00 0.00 4.75
2419 4878 4.037923 AGTTGTGTATGGTCTTTTTGGCTG 59.962 41.667 0.00 0.00 0.00 4.85
2420 4879 2.295909 TGTGTATGGTCTTTTTGGCTGC 59.704 45.455 0.00 0.00 0.00 5.25
2422 4881 1.892474 GTATGGTCTTTTTGGCTGCCA 59.108 47.619 19.30 19.30 0.00 4.92
2423 4882 1.648116 ATGGTCTTTTTGGCTGCCAT 58.352 45.000 24.03 0.16 31.53 4.40
2425 4884 2.603021 TGGTCTTTTTGGCTGCCATTA 58.397 42.857 24.03 11.13 31.53 1.90
2426 4885 2.298729 TGGTCTTTTTGGCTGCCATTAC 59.701 45.455 24.03 15.06 31.53 1.89
2620 5086 4.492604 TGGTAACACAAGCCCAGC 57.507 55.556 0.00 0.00 46.17 4.85
2621 5087 1.228429 TGGTAACACAAGCCCAGCC 60.228 57.895 0.00 0.00 46.17 4.85
2875 5341 3.070018 CTGCGTGGAGAAATATCATCCC 58.930 50.000 0.00 0.00 31.73 3.85
3008 5480 1.296056 CGTGGTCCACCGATTGAACC 61.296 60.000 16.60 0.00 39.43 3.62
3009 5481 0.250553 GTGGTCCACCGATTGAACCA 60.251 55.000 11.30 0.00 39.43 3.67
3013 5485 1.950909 GTCCACCGATTGAACCAAACA 59.049 47.619 0.00 0.00 0.00 2.83
3022 5494 4.858692 CGATTGAACCAAACATCAATGGAC 59.141 41.667 5.79 0.00 44.15 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.554692 GAAGCGTCGTGGATGGCG 61.555 66.667 0.00 0.00 0.00 5.69
44 1075 3.824151 CACATGCATGTCGTCATTCAAA 58.176 40.909 29.23 0.00 39.39 2.69
55 1086 2.205022 AGTACTTGGCACATGCATGT 57.795 45.000 26.61 26.61 44.36 3.21
197 1228 8.148351 TCACTTCATATTAATAGTGTACAGCCC 58.852 37.037 13.31 0.00 39.16 5.19
246 1277 1.324383 TACGAGTGCTCTGACCAACA 58.676 50.000 0.00 0.00 0.00 3.33
272 1303 3.552604 TTTCTTAGGCGTTTGCATGAC 57.447 42.857 0.00 0.00 45.35 3.06
277 1308 6.265577 ACATAATCATTTCTTAGGCGTTTGC 58.734 36.000 0.00 0.00 41.71 3.68
278 1309 6.912591 GGACATAATCATTTCTTAGGCGTTTG 59.087 38.462 0.00 0.00 0.00 2.93
282 1313 9.307121 CTATAGGACATAATCATTTCTTAGGCG 57.693 37.037 0.00 0.00 0.00 5.52
306 1337 4.755123 GCTACAAAACTGAGTGAAAGCCTA 59.245 41.667 0.00 0.00 0.00 3.93
307 1338 3.565902 GCTACAAAACTGAGTGAAAGCCT 59.434 43.478 0.00 0.00 0.00 4.58
308 1339 3.607078 CGCTACAAAACTGAGTGAAAGCC 60.607 47.826 0.00 0.00 0.00 4.35
309 1340 3.247648 TCGCTACAAAACTGAGTGAAAGC 59.752 43.478 0.00 0.00 0.00 3.51
310 1341 5.198274 GTTCGCTACAAAACTGAGTGAAAG 58.802 41.667 0.00 0.00 40.38 2.62
325 2714 2.156891 TCGCTTCATTGTTGTTCGCTAC 59.843 45.455 0.00 0.00 0.00 3.58
406 2795 0.243365 TGGTTTGTGAATGGCATCGC 59.757 50.000 0.00 2.02 0.00 4.58
407 2796 2.792196 CGATGGTTTGTGAATGGCATCG 60.792 50.000 0.00 0.00 35.52 3.84
408 2797 2.423185 TCGATGGTTTGTGAATGGCATC 59.577 45.455 0.00 0.00 0.00 3.91
409 2798 2.424601 CTCGATGGTTTGTGAATGGCAT 59.575 45.455 0.00 0.00 0.00 4.40
410 2799 1.811965 CTCGATGGTTTGTGAATGGCA 59.188 47.619 0.00 0.00 0.00 4.92
411 2800 1.133025 CCTCGATGGTTTGTGAATGGC 59.867 52.381 0.00 0.00 0.00 4.40
412 2801 1.133025 GCCTCGATGGTTTGTGAATGG 59.867 52.381 0.00 0.00 38.35 3.16
413 2802 1.133025 GGCCTCGATGGTTTGTGAATG 59.867 52.381 0.00 0.00 38.35 2.67
414 2803 1.463674 GGCCTCGATGGTTTGTGAAT 58.536 50.000 0.00 0.00 38.35 2.57
456 2875 3.059868 ACTGTCTGCGTTTTATGTTCGTG 60.060 43.478 0.00 0.00 0.00 4.35
457 2876 3.059868 CACTGTCTGCGTTTTATGTTCGT 60.060 43.478 0.00 0.00 0.00 3.85
553 2972 2.040178 ACTGAAGGTTCCAGAGTTCGT 58.960 47.619 0.00 0.00 35.69 3.85
950 3374 0.237498 GCGAGGAAAGAAAACACGGG 59.763 55.000 0.00 0.00 0.00 5.28
954 3378 1.223187 GACGGCGAGGAAAGAAAACA 58.777 50.000 16.62 0.00 0.00 2.83
960 3384 2.509336 ATGCGACGGCGAGGAAAG 60.509 61.111 18.90 0.00 44.10 2.62
1147 3577 3.386237 GGAGGACAGGAGCGCACT 61.386 66.667 11.47 4.05 0.00 4.40
1178 3608 1.810151 GAAACCAATCAAGCGCCTACA 59.190 47.619 2.29 0.00 0.00 2.74
1181 3611 0.251341 AGGAAACCAATCAAGCGCCT 60.251 50.000 2.29 0.00 0.00 5.52
1184 3614 4.243007 AGAAAAGGAAACCAATCAAGCG 57.757 40.909 0.00 0.00 0.00 4.68
1390 3820 1.594194 ATCAAAATCTTGCGCGCCCA 61.594 50.000 30.77 14.78 32.14 5.36
1392 3822 0.867329 GGATCAAAATCTTGCGCGCC 60.867 55.000 30.77 11.42 32.14 6.53
1393 3823 0.179166 TGGATCAAAATCTTGCGCGC 60.179 50.000 27.26 27.26 32.14 6.86
1399 3829 7.092716 CCGACAAAGAATTGGATCAAAATCTT 58.907 34.615 7.26 7.26 41.01 2.40
1411 3841 0.811281 GGAGGGCCGACAAAGAATTG 59.189 55.000 0.00 0.00 42.46 2.32
1430 3860 2.278854 CAAAACTGCAACACCCAAAGG 58.721 47.619 0.00 0.00 40.04 3.11
1431 3861 2.929398 GACAAAACTGCAACACCCAAAG 59.071 45.455 0.00 0.00 0.00 2.77
1432 3862 2.354203 GGACAAAACTGCAACACCCAAA 60.354 45.455 0.00 0.00 0.00 3.28
1433 3863 1.205893 GGACAAAACTGCAACACCCAA 59.794 47.619 0.00 0.00 0.00 4.12
1434 3864 0.820871 GGACAAAACTGCAACACCCA 59.179 50.000 0.00 0.00 0.00 4.51
1435 3865 0.248866 CGGACAAAACTGCAACACCC 60.249 55.000 0.00 0.00 0.00 4.61
1436 3866 0.736053 TCGGACAAAACTGCAACACC 59.264 50.000 0.00 0.00 0.00 4.16
1437 3867 1.131504 TGTCGGACAAAACTGCAACAC 59.868 47.619 8.68 0.00 0.00 3.32
1438 3868 1.454201 TGTCGGACAAAACTGCAACA 58.546 45.000 8.68 0.00 0.00 3.33
1486 3916 0.528684 CGTCGAGGGGATCAAAGAGC 60.529 60.000 0.00 0.00 0.00 4.09
1608 4040 2.606519 TCCCCGGTGGACAGAAGG 60.607 66.667 7.51 0.00 38.61 3.46
1628 4060 0.971959 AGGGCCATTGTACGTCGGTA 60.972 55.000 6.18 0.00 0.00 4.02
1643 4075 2.071540 GCAAGAGCAAAATTTCAGGGC 58.928 47.619 0.00 0.00 41.58 5.19
2112 4552 6.694447 AGCAACAATTCTGATTTGCTAATGT 58.306 32.000 5.89 0.00 37.49 2.71
2149 4589 2.778850 ACACTAAGTTGTAACCACCCCA 59.221 45.455 0.00 0.00 0.00 4.96
2221 4661 1.402107 AAGCACCAACCAGCCAAAGG 61.402 55.000 0.00 0.00 0.00 3.11
2242 4682 2.559785 CCAATTCTTGGCTGCGACT 58.440 52.632 0.00 0.00 45.17 4.18
2364 4804 1.149854 ACCACAAGGGGAAACGTCC 59.850 57.895 0.00 0.00 44.10 4.79
2365 4805 0.179040 TCACCACAAGGGGAAACGTC 60.179 55.000 0.00 0.00 46.84 4.34
2396 4836 4.037923 CAGCCAAAAAGACCATACACAACT 59.962 41.667 0.00 0.00 0.00 3.16
2404 4863 1.648116 ATGGCAGCCAAAAAGACCAT 58.352 45.000 20.84 0.00 36.95 3.55
2418 4877 1.206132 CCTGTGGTACTCGTAATGGCA 59.794 52.381 0.00 0.00 0.00 4.92
2419 4878 1.935933 CCTGTGGTACTCGTAATGGC 58.064 55.000 0.00 0.00 0.00 4.40
2420 4879 1.206132 TGCCTGTGGTACTCGTAATGG 59.794 52.381 0.00 0.00 0.00 3.16
2422 4881 1.897133 TGTGCCTGTGGTACTCGTAAT 59.103 47.619 6.41 0.00 39.07 1.89
2423 4882 1.330234 TGTGCCTGTGGTACTCGTAA 58.670 50.000 6.41 0.00 39.07 3.18
2425 4884 0.466543 TTTGTGCCTGTGGTACTCGT 59.533 50.000 6.41 0.00 39.07 4.18
2426 4885 0.865769 GTTTGTGCCTGTGGTACTCG 59.134 55.000 6.41 0.00 39.07 4.18
2556 5019 2.799126 ACAATACAAGGGCATCCGAA 57.201 45.000 0.00 0.00 38.33 4.30
2687 5153 2.548875 CGAGCCATCCAGAAGAGAAAG 58.451 52.381 0.00 0.00 0.00 2.62
2875 5341 1.676006 GATAGGTGACCGGCCATTTTG 59.324 52.381 0.00 0.00 0.00 2.44
2985 5457 1.202663 TCAATCGGTGGACCACGAAAA 60.203 47.619 18.40 4.10 42.88 2.29


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

AutoCloner maintained by Alex Coulton.