Multiple sequence alignment - TraesCS4A01G064600

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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 TraesCS4A01G064600 chr4A 100.000 4026 0 0 1 4026 61357757 61361782 0.000000e+00 7435.0
1 TraesCS4A01G064600 chr4D 94.531 4059 152 37 1 4025 403908319 403912341 0.000000e+00 6202.0
2 TraesCS4A01G064600 chr4B 93.313 3574 144 48 488 4025 500526634 500530148 0.000000e+00 5188.0
3 TraesCS4A01G064600 chr5D 87.764 237 23 3 91 325 9384193 9384425 5.130000e-69 272.0
4 TraesCS4A01G064600 chr7D 95.745 94 4 0 1 94 221662858 221662951 6.970000e-33 152.0
5 TraesCS4A01G064600 chr7D 94.872 39 2 0 177 215 559022032 559022070 1.210000e-05 62.1
6 TraesCS4A01G064600 chr6D 96.703 91 3 0 1 91 418669120 418669030 6.970000e-33 152.0
7 TraesCS4A01G064600 chr2B 95.745 94 4 0 1 94 489233299 489233392 6.970000e-33 152.0
8 TraesCS4A01G064600 chr2B 95.745 94 4 0 1 94 738288266 738288173 6.970000e-33 152.0
9 TraesCS4A01G064600 chr2B 94.792 96 5 0 1 96 530192594 530192689 2.510000e-32 150.0
10 TraesCS4A01G064600 chr2A 94.845 97 5 0 1 97 587581414 587581318 6.970000e-33 152.0
11 TraesCS4A01G064600 chr1A 95.745 94 4 0 1 94 244769793 244769886 6.970000e-33 152.0
12 TraesCS4A01G064600 chr1A 94.792 96 5 0 1 96 377651678 377651773 2.510000e-32 150.0


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 TraesCS4A01G064600 chr4A 61357757 61361782 4025 False 7435 7435 100.000 1 4026 1 chr4A.!!$F1 4025
1 TraesCS4A01G064600 chr4D 403908319 403912341 4022 False 6202 6202 94.531 1 4025 1 chr4D.!!$F1 4024
2 TraesCS4A01G064600 chr4B 500526634 500530148 3514 False 5188 5188 93.313 488 4025 1 chr4B.!!$F1 3537

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
304 306 0.322546 ATTTGAGGAACCCACCGAGC 60.323 55.0 0.0 0.0 34.73 5.03 F
487 490 1.104577 TCAAAACCCCGTGTCTTGGC 61.105 55.0 0.0 0.0 0.00 4.52 F
1789 1799 1.168714 GGTGCATCAGGGAACTCAAC 58.831 55.0 0.0 0.0 40.21 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2053 0.249741 CAACGGTTTCAGGGACGACT 60.250 55.0 0.00 0.0 0.0 4.18 R
2101 2111 0.319555 TCGCCTTGAACCTCTTGACG 60.320 55.0 0.00 0.0 0.0 4.35 R
3051 3061 0.107459 GAGCTCCCCTGGAATGTCAC 60.107 60.0 0.87 0.0 0.0 3.67 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
67 68 7.402054 TGTCACTTTATGGTGAATGAAGGTAT 58.598 34.615 0.00 0.00 46.00 2.73
97 98 9.617523 CTTGGGGCATAAAATTTCTGAAATATT 57.382 29.630 15.45 9.54 0.00 1.28
108 109 8.450578 AATTTCTGAAATATTCCGCTATGACA 57.549 30.769 15.45 0.00 0.00 3.58
114 115 8.450578 TGAAATATTCCGCTATGACAGAAAAT 57.549 30.769 0.00 0.00 0.00 1.82
131 132 5.663556 CAGAAAATAAGTAGGAGGGGAGAGT 59.336 44.000 0.00 0.00 0.00 3.24
132 133 6.157123 CAGAAAATAAGTAGGAGGGGAGAGTT 59.843 42.308 0.00 0.00 0.00 3.01
133 134 6.736179 AGAAAATAAGTAGGAGGGGAGAGTTT 59.264 38.462 0.00 0.00 0.00 2.66
134 135 6.971932 AAATAAGTAGGAGGGGAGAGTTTT 57.028 37.500 0.00 0.00 0.00 2.43
168 170 3.408634 AGAAAAAGTATGTCGTGGGGTG 58.591 45.455 0.00 0.00 0.00 4.61
186 188 3.070878 GGGTGTGATTTTTGTGTTGGGAT 59.929 43.478 0.00 0.00 0.00 3.85
187 189 4.306600 GGTGTGATTTTTGTGTTGGGATC 58.693 43.478 0.00 0.00 0.00 3.36
194 196 0.816018 TTGTGTTGGGATCGCGTGTT 60.816 50.000 5.77 0.00 0.00 3.32
195 197 1.206578 GTGTTGGGATCGCGTGTTG 59.793 57.895 5.77 0.00 0.00 3.33
210 212 3.507786 CGTGTTGAAGATACATGACGGA 58.492 45.455 0.00 0.00 35.08 4.69
226 228 2.431057 GACGGATAGTCTGGACAACCAT 59.569 50.000 3.51 0.00 45.87 3.55
231 233 6.055588 CGGATAGTCTGGACAACCATATTTT 58.944 40.000 3.51 0.00 45.87 1.82
261 263 9.565090 CTCACATATAGATTGGATTTGAGGAAA 57.435 33.333 0.00 0.00 0.00 3.13
290 292 4.158764 ACTGTCCAAACGGTTGAAATTTGA 59.841 37.500 16.49 0.00 42.51 2.69
300 302 3.244078 GGTTGAAATTTGAGGAACCCACC 60.244 47.826 0.00 0.00 31.57 4.61
302 304 2.158593 TGAAATTTGAGGAACCCACCGA 60.159 45.455 0.00 0.00 34.73 4.69
303 305 2.200373 AATTTGAGGAACCCACCGAG 57.800 50.000 0.00 0.00 34.73 4.63
304 306 0.322546 ATTTGAGGAACCCACCGAGC 60.323 55.000 0.00 0.00 34.73 5.03
306 308 3.692406 GAGGAACCCACCGAGCGT 61.692 66.667 0.00 0.00 34.73 5.07
315 317 2.355481 ACCGAGCGTCCGTTTGAC 60.355 61.111 0.00 0.00 40.81 3.18
381 383 6.575162 AGTTTGAAGACGGCTTTAATCATT 57.425 33.333 16.33 0.00 33.61 2.57
424 426 3.755965 TGTAACCAATAGCAATGCACG 57.244 42.857 8.35 0.00 0.00 5.34
425 427 2.421775 TGTAACCAATAGCAATGCACGG 59.578 45.455 8.35 4.32 0.00 4.94
426 428 1.832883 AACCAATAGCAATGCACGGA 58.167 45.000 8.35 0.00 0.00 4.69
438 440 5.008019 AGCAATGCACGGACATTCTTTATAG 59.992 40.000 8.35 0.00 38.19 1.31
475 478 5.244785 GGAATAGTTCCGGAATCAAAACC 57.755 43.478 22.04 15.39 40.59 3.27
487 490 1.104577 TCAAAACCCCGTGTCTTGGC 61.105 55.000 0.00 0.00 0.00 4.52
531 534 2.185608 GCTCCCTCTGCTCGGTTC 59.814 66.667 0.00 0.00 0.00 3.62
532 535 2.492090 CTCCCTCTGCTCGGTTCG 59.508 66.667 0.00 0.00 0.00 3.95
534 537 4.821589 CCCTCTGCTCGGTTCGGC 62.822 72.222 0.00 0.00 0.00 5.54
540 543 3.330853 GCTCGGTTCGGCGCTATG 61.331 66.667 7.64 0.00 0.00 2.23
612 620 3.374330 CGCGTGTCGTTCATCTCC 58.626 61.111 0.00 0.00 0.00 3.71
645 653 4.436998 CTGCCCTGGACCGTCGTC 62.437 72.222 0.00 0.00 38.38 4.20
715 723 1.228184 GGGAGGAGGCATGCATGAG 60.228 63.158 30.64 5.13 0.00 2.90
728 736 4.534168 CATGCATGAGGAGATAAAAAGCG 58.466 43.478 22.59 0.00 0.00 4.68
984 993 4.989168 GGTATAATAACGGACTTGCAGAGG 59.011 45.833 0.00 0.00 0.00 3.69
1054 1063 3.952675 CGCCGATCAAATGCCCCG 61.953 66.667 0.00 0.00 0.00 5.73
1056 1065 3.595758 CCGATCAAATGCCCCGCC 61.596 66.667 0.00 0.00 0.00 6.13
1057 1066 3.952675 CGATCAAATGCCCCGCCG 61.953 66.667 0.00 0.00 0.00 6.46
1058 1067 2.828549 GATCAAATGCCCCGCCGT 60.829 61.111 0.00 0.00 0.00 5.68
1168 1178 1.676014 GGAATGGTTCAGGACGTGGAG 60.676 57.143 0.00 0.00 0.00 3.86
1457 1467 3.939837 TTCTGCAAGCTCGCCGAGG 62.940 63.158 16.95 0.00 0.00 4.63
1699 1709 2.455674 TCAAGAACATCACCGTGGAG 57.544 50.000 0.00 0.00 0.00 3.86
1783 1793 1.299648 CTTCCGGTGCATCAGGGAA 59.700 57.895 0.00 6.22 37.07 3.97
1787 1797 1.296392 CGGTGCATCAGGGAACTCA 59.704 57.895 0.00 0.00 40.21 3.41
1789 1799 1.168714 GGTGCATCAGGGAACTCAAC 58.831 55.000 0.00 0.00 40.21 3.18
1954 1964 3.489398 GCTTCAACCGTATGATCGACTCT 60.489 47.826 0.00 0.00 0.00 3.24
2017 2027 6.709846 GTCTCCTGAAATCCATAATCCTGAAG 59.290 42.308 0.00 0.00 0.00 3.02
2351 2361 3.081554 CAGGGTTCCACCTCCTGG 58.918 66.667 0.00 0.00 43.09 4.45
2465 2475 4.796231 CGTCGGACTTGGAGGCGG 62.796 72.222 6.57 0.00 0.00 6.13
2772 2782 1.654774 CGATCATCGAGAAGCGGGA 59.345 57.895 0.00 0.00 43.74 5.14
3051 3061 3.120338 CCGGTTACATGCAAACACACTAG 60.120 47.826 12.18 0.00 0.00 2.57
3159 3174 7.846644 AGACGGTCGATTAGGAGTATATAAG 57.153 40.000 1.89 0.00 0.00 1.73
3461 3487 1.274167 TCTGCCTGGTTTAGTGTACGG 59.726 52.381 0.00 0.00 0.00 4.02
3467 3493 4.555313 GCCTGGTTTAGTGTACGGTTTTTC 60.555 45.833 0.00 0.00 0.00 2.29
3468 3494 4.818005 CCTGGTTTAGTGTACGGTTTTTCT 59.182 41.667 0.00 0.00 0.00 2.52
3747 3777 9.432077 GAACAAAATTTTACATTGCACGAAAAT 57.568 25.926 2.44 0.00 33.92 1.82
3920 3965 7.617225 TGATGTAAAGAGAATAGGACGGAAAA 58.383 34.615 0.00 0.00 0.00 2.29
3921 3966 7.548075 TGATGTAAAGAGAATAGGACGGAAAAC 59.452 37.037 0.00 0.00 0.00 2.43
3922 3967 7.001099 TGTAAAGAGAATAGGACGGAAAACT 57.999 36.000 0.00 0.00 0.00 2.66
3932 3977 2.865551 GGACGGAAAACTAAACACACGA 59.134 45.455 0.00 0.00 0.00 4.35
4020 4069 3.040147 AGGACGTAACATGTGGTTCAG 57.960 47.619 0.00 0.00 40.96 3.02
4021 4070 1.463444 GGACGTAACATGTGGTTCAGC 59.537 52.381 0.00 0.00 40.96 4.26
4022 4071 2.139917 GACGTAACATGTGGTTCAGCA 58.860 47.619 0.00 0.00 40.96 4.41
4023 4072 2.742053 GACGTAACATGTGGTTCAGCAT 59.258 45.455 0.00 0.00 40.96 3.79
4024 4073 2.483877 ACGTAACATGTGGTTCAGCATG 59.516 45.455 0.00 0.00 45.61 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 7.174946 GTGACAGTTCTCCCAATTCAAGATAAA 59.825 37.037 0.00 0.00 0.00 1.40
24 25 5.006386 GTGACAGTTCTCCCAATTCAAGAT 58.994 41.667 0.00 0.00 0.00 2.40
67 68 5.541868 TCAGAAATTTTATGCCCCAAGACAA 59.458 36.000 0.00 0.00 0.00 3.18
97 98 6.322969 TCCTACTTATTTTCTGTCATAGCGGA 59.677 38.462 0.00 0.00 0.00 5.54
104 105 5.347124 TCCCCTCCTACTTATTTTCTGTCA 58.653 41.667 0.00 0.00 0.00 3.58
108 109 5.855988 ACTCTCCCCTCCTACTTATTTTCT 58.144 41.667 0.00 0.00 0.00 2.52
134 135 9.581099 GACATACTTTTTCTTTTCCTGTTGAAA 57.419 29.630 0.00 0.00 41.18 2.69
156 158 2.286365 AAAATCACACCCCACGACAT 57.714 45.000 0.00 0.00 0.00 3.06
168 170 2.986479 GCGATCCCAACACAAAAATCAC 59.014 45.455 0.00 0.00 0.00 3.06
186 188 2.921121 GTCATGTATCTTCAACACGCGA 59.079 45.455 15.93 0.00 0.00 5.87
187 189 2.284457 CGTCATGTATCTTCAACACGCG 60.284 50.000 3.53 3.53 0.00 6.01
194 196 5.241728 CCAGACTATCCGTCATGTATCTTCA 59.758 44.000 0.00 0.00 45.32 3.02
195 197 5.473846 TCCAGACTATCCGTCATGTATCTTC 59.526 44.000 0.00 0.00 45.32 2.87
231 233 9.565090 CTCAAATCCAATCTATATGTGAGGAAA 57.435 33.333 0.00 0.00 0.00 3.13
234 236 7.918536 CCTCAAATCCAATCTATATGTGAGG 57.081 40.000 6.41 6.41 42.54 3.86
244 246 5.165961 TCGAGTTTCCTCAAATCCAATCT 57.834 39.130 0.00 0.00 37.59 2.40
261 263 0.462789 ACCGTTTGGACAGTTCGAGT 59.537 50.000 0.00 0.00 39.21 4.18
290 292 3.692406 GACGCTCGGTGGGTTCCT 61.692 66.667 1.27 0.00 42.14 3.36
315 317 9.086336 GTCATACATTTTGGTTATGTTTGGATG 57.914 33.333 0.00 0.00 36.34 3.51
408 410 1.094785 GTCCGTGCATTGCTATTGGT 58.905 50.000 10.49 0.00 0.00 3.67
411 413 3.282021 AGAATGTCCGTGCATTGCTATT 58.718 40.909 10.49 1.70 38.98 1.73
412 414 2.923121 AGAATGTCCGTGCATTGCTAT 58.077 42.857 10.49 0.00 38.98 2.97
419 421 7.624360 AATTTCTATAAAGAATGTCCGTGCA 57.376 32.000 0.00 0.00 41.36 4.57
467 470 1.616159 CCAAGACACGGGGTTTTGAT 58.384 50.000 14.60 0.00 42.58 2.57
469 472 1.106944 AGCCAAGACACGGGGTTTTG 61.107 55.000 6.67 6.67 40.36 2.44
474 477 2.919494 GCAAAGCCAAGACACGGGG 61.919 63.158 0.00 0.00 0.00 5.73
475 478 1.733402 TTGCAAAGCCAAGACACGGG 61.733 55.000 0.00 0.00 0.00 5.28
487 490 2.871633 GGGTCACCACAAATTTGCAAAG 59.128 45.455 18.19 6.69 36.50 2.77
534 537 1.340465 GACGTGCGTTGACATAGCG 59.660 57.895 0.00 0.00 35.97 4.26
540 543 2.586635 TGGTGGACGTGCGTTGAC 60.587 61.111 1.60 0.00 0.00 3.18
643 651 2.109126 GGCCGCATCACTGGAAGAC 61.109 63.158 0.00 0.00 37.43 3.01
644 652 1.913951 ATGGCCGCATCACTGGAAGA 61.914 55.000 0.00 0.00 37.43 2.87
645 653 1.452651 ATGGCCGCATCACTGGAAG 60.453 57.895 0.00 0.00 42.29 3.46
715 723 1.609072 GATGGGGCGCTTTTTATCTCC 59.391 52.381 7.64 0.00 0.00 3.71
847 855 7.359598 CGATCGGTTAGAAGGAATCAATCAATC 60.360 40.741 7.38 0.00 0.00 2.67
848 856 6.425114 CGATCGGTTAGAAGGAATCAATCAAT 59.575 38.462 7.38 0.00 0.00 2.57
849 857 5.753438 CGATCGGTTAGAAGGAATCAATCAA 59.247 40.000 7.38 0.00 0.00 2.57
984 993 0.679505 TCATCGATCGGGGATCAACC 59.320 55.000 16.41 0.00 38.84 3.77
999 1008 3.555967 AGGCCGTCCTCCATCATC 58.444 61.111 0.00 0.00 38.72 2.92
1082 1091 0.458543 GCGCCGATCAAGAGAACTCA 60.459 55.000 0.00 0.00 0.00 3.41
1457 1467 4.500116 GGAGAGGTCGTCGCAGGC 62.500 72.222 0.00 0.00 0.00 4.85
1699 1709 3.424105 ATCCTGGCCTTGGCCTCC 61.424 66.667 28.37 5.89 0.00 4.30
1783 1793 2.040412 GTGGAAGAAGGGGATGTTGAGT 59.960 50.000 0.00 0.00 0.00 3.41
1787 1797 1.075536 GTGGTGGAAGAAGGGGATGTT 59.924 52.381 0.00 0.00 0.00 2.71
1789 1799 0.392998 CGTGGTGGAAGAAGGGGATG 60.393 60.000 0.00 0.00 0.00 3.51
1876 1886 2.182030 GACGCCGACTTGAGGAGG 59.818 66.667 0.00 0.00 32.63 4.30
1954 1964 0.933047 CGAGCGTCAAGTCGTCAACA 60.933 55.000 0.00 0.00 0.00 3.33
2017 2027 4.821589 CAGCCCTCCGACGAAGCC 62.822 72.222 0.00 0.00 0.00 4.35
2043 2053 0.249741 CAACGGTTTCAGGGACGACT 60.250 55.000 0.00 0.00 0.00 4.18
2101 2111 0.319555 TCGCCTTGAACCTCTTGACG 60.320 55.000 0.00 0.00 0.00 4.35
2608 2618 3.386237 ACCTCGCTCAGCTCCCAC 61.386 66.667 0.00 0.00 0.00 4.61
2772 2782 2.992114 AGAGGCGCTCGTCCTTGT 60.992 61.111 7.64 0.00 35.36 3.16
2994 3004 2.542907 GCAATGCCATCCGGTACCG 61.543 63.158 27.68 27.68 39.44 4.02
2995 3005 3.432186 GCAATGCCATCCGGTACC 58.568 61.111 0.16 0.16 33.28 3.34
3051 3061 0.107459 GAGCTCCCCTGGAATGTCAC 60.107 60.000 0.87 0.00 0.00 3.67
3159 3174 3.987404 ACATTTCCTGTGCGAGCC 58.013 55.556 0.00 0.00 36.48 4.70
3390 3405 9.559732 AGGAAAGGAAAACTGAAAATAAAATGG 57.440 29.630 0.00 0.00 0.00 3.16
3422 3445 6.490040 AGGCAGATTAAAAAGCAACAACTCTA 59.510 34.615 0.00 0.00 0.00 2.43
3433 3459 6.981722 ACACTAAACCAGGCAGATTAAAAAG 58.018 36.000 0.00 0.00 0.00 2.27
3559 3587 9.905171 TTCACATGTTTTCGAAAATATTCATGA 57.095 25.926 34.79 28.37 34.72 3.07
3718 3748 6.531594 TCGTGCAATGTAAAATTTTGTTCACA 59.468 30.769 13.76 9.85 0.00 3.58
3728 3758 9.994432 TTTTGAAATTTTCGTGCAATGTAAAAT 57.006 22.222 4.76 0.00 34.00 1.82
3904 3949 6.647895 TGTGTTTAGTTTTCCGTCCTATTCTC 59.352 38.462 0.00 0.00 0.00 2.87
3988 4036 9.142515 CACATGTTACGTCCTATTTTACAAGTA 57.857 33.333 0.00 0.00 0.00 2.24
3990 4039 7.118680 ACCACATGTTACGTCCTATTTTACAAG 59.881 37.037 0.00 0.00 0.00 3.16
3996 4045 5.553123 TGAACCACATGTTACGTCCTATTT 58.447 37.500 0.00 0.00 37.29 1.40


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

AutoCloner maintained by Alex Coulton.