Multiple sequence alignment - TraesCS4D01G282900

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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 TraesCS4D01G282900 chr4D 100.000 3429 0 0 1 3429 454661880 454658452 0.000000e+00 6333
1 TraesCS4D01G282900 chr4B 96.243 2289 69 8 1 2274 567383095 567380809 0.000000e+00 3735
2 TraesCS4D01G282900 chr4B 97.049 1186 18 5 2261 3429 567380548 567379363 0.000000e+00 1980
3 TraesCS4D01G282900 chr2D 88.511 235 21 4 2944 3174 332516387 332516155 2.610000e-71 279
4 TraesCS4D01G282900 chr2D 86.640 247 9 9 2615 2837 332516764 332516518 5.680000e-63 252
5 TraesCS4D01G282900 chr2B 89.238 223 17 5 2959 3174 400624549 400624327 4.360000e-69 272
6 TraesCS4D01G282900 chr2B 85.366 246 13 6 2615 2837 400624924 400624679 2.060000e-57 233
7 TraesCS4D01G282900 chr2A 89.100 211 19 3 2968 3174 440927440 440927230 3.390000e-65 259
8 TraesCS4D01G282900 chr2A 84.211 247 13 7 2615 2837 440927812 440927568 2.070000e-52 217


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 TraesCS4D01G282900 chr4D 454658452 454661880 3428 True 6333.0 6333 100.0000 1 3429 1 chr4D.!!$R1 3428
1 TraesCS4D01G282900 chr4B 567379363 567383095 3732 True 2857.5 3735 96.6460 1 3429 2 chr4B.!!$R1 3428
2 TraesCS4D01G282900 chr2D 332516155 332516764 609 True 265.5 279 87.5755 2615 3174 2 chr2D.!!$R1 559
3 TraesCS4D01G282900 chr2B 400624327 400624924 597 True 252.5 272 87.3020 2615 3174 2 chr2B.!!$R1 559
4 TraesCS4D01G282900 chr2A 440927230 440927812 582 True 238.0 259 86.6555 2615 3174 2 chr2A.!!$R1 559

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
727 735 0.600255 CGACAACAACGGCTTCCTCT 60.6 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 2789 0.097674 GTGCAAAGGCTACAGCATCG 59.902 55.0 10.88 0.0 44.36 3.84 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
360 361 4.060038 AACTACCACGTCCCGCCG 62.060 66.667 0.00 0.00 0.00 6.46
450 451 4.379243 CCGCTTCACGCCCAGACT 62.379 66.667 0.00 0.00 41.76 3.24
463 464 1.136984 CAGACTCGACGCACCTACC 59.863 63.158 0.00 0.00 0.00 3.18
502 503 1.941999 CTACCTCGACCCGGACAACC 61.942 65.000 0.73 0.00 0.00 3.77
712 720 4.351938 CCAACGGCTCGGACGACA 62.352 66.667 6.14 0.00 35.20 4.35
727 735 0.600255 CGACAACAACGGCTTCCTCT 60.600 55.000 0.00 0.00 0.00 3.69
772 780 1.130749 CCTCAGACGTCTACAACCTCG 59.869 57.143 19.57 3.12 0.00 4.63
779 787 1.135746 CGTCTACAACCTCGTCCAGAC 60.136 57.143 0.00 0.00 0.00 3.51
883 891 4.484872 GCTCCGGTTACCAGCCCC 62.485 72.222 0.00 0.00 0.00 5.80
955 963 2.270205 CCAGTTCAGGCATCGGCT 59.730 61.111 0.00 0.00 40.87 5.52
971 979 1.435515 GCTGAGACGGATTCGAGCT 59.564 57.895 0.00 0.00 40.11 4.09
987 995 4.457496 CTGGACGCAGCATCCCGT 62.457 66.667 4.72 0.00 40.85 5.28
1006 1017 1.732259 GTCACTTCTACAACATGGCGG 59.268 52.381 0.00 0.00 0.00 6.13
1095 1106 4.521062 GGGTCGATGCTCAGCGCT 62.521 66.667 2.64 2.64 40.42 5.92
1226 1237 0.332972 ACCAAGGAGGGAATGAAGGC 59.667 55.000 0.00 0.00 43.89 4.35
1274 1285 1.083806 CAGAATTACGCAGCGCTGGA 61.084 55.000 36.47 7.70 0.00 3.86
1342 1353 5.357257 CGTATAGGTACAGTTTCATTGCCT 58.643 41.667 0.00 0.00 0.00 4.75
1431 1442 5.693104 TCTGATTTGCTTTGACTCAATTTGC 59.307 36.000 0.00 0.00 0.00 3.68
1575 1586 5.697826 ACTACTTCACTACTGCTTTACGTC 58.302 41.667 0.00 0.00 0.00 4.34
1587 1598 3.187700 GCTTTACGTCCATGGACTACAG 58.812 50.000 35.84 27.26 42.54 2.74
1588 1599 3.119245 GCTTTACGTCCATGGACTACAGA 60.119 47.826 35.84 19.70 42.54 3.41
1593 1604 3.190079 CGTCCATGGACTACAGACATTG 58.810 50.000 35.84 16.91 42.54 2.82
1610 1621 6.316140 CAGACATTGCAAGGTAGTAATGCTAA 59.684 38.462 17.89 0.00 42.87 3.09
1645 1656 7.607607 TGCAATAAGAAAGTAGTGACATGACAT 59.392 33.333 0.00 0.00 0.00 3.06
1651 1662 9.778741 AAGAAAGTAGTGACATGACATTAGAAA 57.221 29.630 0.00 0.00 0.00 2.52
1672 1683 1.939974 TGTGCATTGACCTATCTCGC 58.060 50.000 0.00 0.00 0.00 5.03
1683 1694 4.099419 TGACCTATCTCGCTGCAGATTTTA 59.901 41.667 20.43 0.00 34.75 1.52
1695 1706 2.796032 GCAGATTTTAATCCAGCACGGC 60.796 50.000 10.72 0.00 37.10 5.68
1696 1707 2.423185 CAGATTTTAATCCAGCACGGCA 59.577 45.455 0.00 0.00 36.04 5.69
1715 1726 3.124297 GGCATCGACTCTTTGAGAACAAG 59.876 47.826 1.25 0.00 37.32 3.16
1716 1727 3.990469 GCATCGACTCTTTGAGAACAAGA 59.010 43.478 1.25 0.00 37.32 3.02
1762 1773 6.813649 GTCTGATTACTACATTGAGTGCTTCA 59.186 38.462 0.00 0.00 0.00 3.02
1857 1868 7.400599 TGGACAGTATAGGTACACTAACTTG 57.599 40.000 0.00 0.00 34.79 3.16
1873 1884 0.792640 CTTGCAATCTCGTTCGCTGT 59.207 50.000 0.00 0.00 0.00 4.40
2040 2054 5.105023 ACTCATGCTGTGTCTAGATGAACAT 60.105 40.000 0.00 0.00 0.00 2.71
2091 2105 0.698238 AGGCTGACAATGCACCCTTA 59.302 50.000 0.00 0.00 0.00 2.69
2096 2110 2.357009 CTGACAATGCACCCTTAGATGC 59.643 50.000 0.00 2.17 42.40 3.91
2125 2139 4.699735 TGTTGGTAATTGTGCTGGATACTG 59.300 41.667 0.00 0.00 38.80 2.74
2139 2153 0.698238 ATACTGTGCTTGGCCTTGGA 59.302 50.000 3.32 0.00 0.00 3.53
2142 2156 1.075374 ACTGTGCTTGGCCTTGGAATA 59.925 47.619 3.32 0.00 0.00 1.75
2240 2254 1.526917 GCCTTCATCCCCCATCACG 60.527 63.158 0.00 0.00 0.00 4.35
2288 2578 4.966965 AACTAGTTCGATCTCACACGAT 57.033 40.909 1.12 0.00 38.30 3.73
2336 2627 1.270785 TGATGAAGGAAAGAGTGCGCA 60.271 47.619 5.66 5.66 0.00 6.09
2356 2647 3.304525 GCATACTGGCTTTGATGATCAGC 60.305 47.826 3.40 3.40 0.00 4.26
2416 2707 1.519455 CGTCATGGCTCGACTTCCC 60.519 63.158 0.00 0.00 0.00 3.97
2447 2738 2.092968 TGAAGCAATAGGAACTGGCGAT 60.093 45.455 0.00 0.00 41.52 4.58
2498 2789 1.136057 GCGTTCTCACCGGAATTTCAC 60.136 52.381 9.46 0.00 0.00 3.18
2752 3067 7.551262 GGATCAACCATATTTGTGTACAGTACA 59.449 37.037 9.51 9.51 38.79 2.90
2854 3185 6.647067 GCTCTACAGTTGTGTCTACAGAAATT 59.353 38.462 0.00 0.00 38.23 1.82
2956 3381 4.094684 CTGTACAGCTAGTGCGCC 57.905 61.111 10.54 0.00 45.42 6.53
2988 3413 4.729227 ACATCGTTTTGTTTGTCCCTTT 57.271 36.364 0.00 0.00 0.00 3.11
3196 3628 2.000447 GCACTCGTACCTTTGGATGAC 59.000 52.381 0.00 0.00 0.00 3.06
3276 3708 4.513692 TCAGTTGAATAACCAGTTTGTCCG 59.486 41.667 0.00 0.00 37.52 4.79
3325 3757 7.546250 TTCCTCTTCTTCATTTGAGTACTCT 57.454 36.000 23.01 0.58 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
321 322 3.066190 CGGGTCTGGCCGTACAGA 61.066 66.667 9.30 2.52 44.74 3.41
360 361 3.138798 TCGAGGTAGGCAGACGGC 61.139 66.667 0.00 0.00 43.74 5.68
449 450 2.202440 CGTGGTAGGTGCGTCGAG 60.202 66.667 0.00 0.00 0.00 4.04
450 451 2.969806 GACGTGGTAGGTGCGTCGA 61.970 63.158 0.00 0.00 43.91 4.20
700 708 2.654912 CGTTGTTGTCGTCCGAGCC 61.655 63.158 0.00 0.00 0.00 4.70
712 720 1.668151 GCGAGAGGAAGCCGTTGTT 60.668 57.895 0.00 0.00 0.00 2.83
727 735 4.415332 GTCAACGGAGAGCGGCGA 62.415 66.667 12.98 0.00 0.00 5.54
745 753 0.549950 TAGACGTCTGAGGGGTAGGG 59.450 60.000 28.12 0.00 0.00 3.53
955 963 0.679960 TCCAGCTCGAATCCGTCTCA 60.680 55.000 0.00 0.00 37.05 3.27
971 979 4.451150 GACGGGATGCTGCGTCCA 62.451 66.667 34.74 1.19 41.05 4.02
982 990 2.028476 CCATGTTGTAGAAGTGACGGGA 60.028 50.000 0.00 0.00 0.00 5.14
983 991 2.346803 CCATGTTGTAGAAGTGACGGG 58.653 52.381 0.00 0.00 0.00 5.28
984 992 1.732259 GCCATGTTGTAGAAGTGACGG 59.268 52.381 0.00 0.00 0.00 4.79
986 994 1.732259 CCGCCATGTTGTAGAAGTGAC 59.268 52.381 0.00 0.00 0.00 3.67
987 995 1.338674 CCCGCCATGTTGTAGAAGTGA 60.339 52.381 0.00 0.00 0.00 3.41
1070 1081 3.245315 GCATCGACCCGAACGACG 61.245 66.667 0.00 0.00 42.37 5.12
1074 1085 2.167861 GCTGAGCATCGACCCGAAC 61.168 63.158 0.00 0.00 39.99 3.95
1194 1205 1.081892 CCTTGGTTGACAGAGCATCG 58.918 55.000 0.00 0.00 42.67 3.84
1226 1237 1.328069 CACGCAGTAGTAGACGGAGAG 59.672 57.143 0.00 0.00 41.61 3.20
1342 1353 0.955428 GCAGATTGGAGTGGTCGCAA 60.955 55.000 0.00 0.00 0.00 4.85
1431 1442 1.396648 TCATAATGTTTCGGCTGCACG 59.603 47.619 0.50 2.89 0.00 5.34
1575 1586 2.989909 TGCAATGTCTGTAGTCCATGG 58.010 47.619 4.97 4.97 0.00 3.66
1587 1598 6.677781 TTAGCATTACTACCTTGCAATGTC 57.322 37.500 10.84 0.00 38.84 3.06
1588 1599 7.993183 AGTATTAGCATTACTACCTTGCAATGT 59.007 33.333 12.17 12.17 38.84 2.71
1593 1604 9.490379 ACATTAGTATTAGCATTACTACCTTGC 57.510 33.333 0.00 0.00 33.12 4.01
1645 1656 7.011389 CGAGATAGGTCAATGCACATTTTCTAA 59.989 37.037 0.00 0.00 0.00 2.10
1651 1662 2.874701 GCGAGATAGGTCAATGCACATT 59.125 45.455 0.00 0.00 0.00 2.71
1672 1683 3.488047 CCGTGCTGGATTAAAATCTGCAG 60.488 47.826 7.63 7.63 41.45 4.41
1683 1694 1.815421 GTCGATGCCGTGCTGGATT 60.815 57.895 0.00 0.00 42.00 3.01
1695 1706 5.463392 TGTTCTTGTTCTCAAAGAGTCGATG 59.537 40.000 0.00 0.00 32.87 3.84
1696 1707 5.463724 GTGTTCTTGTTCTCAAAGAGTCGAT 59.536 40.000 0.00 0.00 32.87 3.59
1715 1726 1.079875 ACGACGTGTGTGGTGTGTTC 61.080 55.000 0.00 0.00 35.55 3.18
1716 1727 0.173029 TACGACGTGTGTGGTGTGTT 59.827 50.000 11.56 0.00 37.62 3.32
1857 1868 1.194547 TGAAACAGCGAACGAGATTGC 59.805 47.619 0.00 0.00 0.00 3.56
1873 1884 8.924511 ATCAAGGAAAGTAGAACAAGATGAAA 57.075 30.769 0.00 0.00 0.00 2.69
2040 2054 0.840288 ACTGCACCACATACCCTCCA 60.840 55.000 0.00 0.00 0.00 3.86
2091 2105 6.238842 GCACAATTACCAACATATCAGCATCT 60.239 38.462 0.00 0.00 0.00 2.90
2096 2110 5.589855 TCCAGCACAATTACCAACATATCAG 59.410 40.000 0.00 0.00 0.00 2.90
2125 2139 2.019984 CTCTATTCCAAGGCCAAGCAC 58.980 52.381 5.01 0.00 0.00 4.40
2139 2153 5.053978 CCATTTGGGTTAGCTCCTCTATT 57.946 43.478 0.00 0.00 0.00 1.73
2288 2578 4.085357 ACACAGCCAAGAGTAACATCAA 57.915 40.909 0.00 0.00 0.00 2.57
2356 2647 0.109226 GGACGGTCTCTGAAAGTCGG 60.109 60.000 8.23 0.00 33.76 4.79
2416 2707 0.800683 TATTGCTTCAGGACGTCGCG 60.801 55.000 9.92 0.00 0.00 5.87
2447 2738 3.308053 CACGAACGAACGGAGACTAGATA 59.692 47.826 0.00 0.00 37.61 1.98
2498 2789 0.097674 GTGCAAAGGCTACAGCATCG 59.902 55.000 10.88 0.00 44.36 3.84
2752 3067 7.315066 AGTTTGAATTTTTGTACCATCCCAT 57.685 32.000 0.00 0.00 0.00 4.00
2949 3374 3.755526 TTGAGCACACAGGCGCACT 62.756 57.895 10.83 0.02 43.28 4.40
2956 3381 3.038017 CAAAACGATGTTGAGCACACAG 58.962 45.455 0.00 0.00 38.61 3.66
2988 3413 3.743911 CGTAGTTGCACTGTTGGACAATA 59.256 43.478 0.00 0.00 0.00 1.90
3008 3433 1.450848 CCATGGACTGCTGCATCGT 60.451 57.895 5.56 0.00 0.00 3.73
3276 3708 3.820557 TCTTGGGCAGCTATTGGTATTC 58.179 45.455 0.00 0.00 0.00 1.75
3325 3757 5.248477 ACAGCTAACTTTCAGGGAGTTATGA 59.752 40.000 0.00 0.00 38.51 2.15
3334 3766 3.744660 ACTTGGACAGCTAACTTTCAGG 58.255 45.455 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.