Multiple sequence alignment - TraesCS4D01G188500

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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 TraesCS4D01G188500 chr4D 100.000 3668 0 0 1 3668 327734391 327730724 0.000000e+00 6774.0
1 TraesCS4D01G188500 chr4A 96.288 2775 59 11 197 2946 143239688 143242443 0.000000e+00 4514.0
2 TraesCS4D01G188500 chr4A 97.703 740 16 1 2930 3668 143242643 143243382 0.000000e+00 1271.0
3 TraesCS4D01G188500 chr4A 96.020 201 8 0 1 201 143239461 143239661 9.820000e-86 327.0
4 TraesCS4D01G188500 chr4B 96.059 2766 60 10 197 2946 407072930 407070198 0.000000e+00 4458.0
5 TraesCS4D01G188500 chr4B 97.151 737 18 1 2932 3668 407070016 407069283 0.000000e+00 1242.0
6 TraesCS4D01G188500 chr4B 96.250 80 3 0 1 80 407073381 407073302 8.260000e-27 132.0
7 TraesCS4D01G188500 chr4B 95.082 61 3 0 141 201 407073017 407072957 3.010000e-16 97.1
8 TraesCS4D01G188500 chr7B 100.000 29 0 0 380 408 667770373 667770401 2.000000e-03 54.7
9 TraesCS4D01G188500 chr3D 100.000 29 0 0 378 406 521280700 521280728 2.000000e-03 54.7
10 TraesCS4D01G188500 chr1A 100.000 29 0 0 378 406 4370127 4370099 2.000000e-03 54.7
11 TraesCS4D01G188500 chr2B 100.000 28 0 0 379 406 2031245 2031218 7.000000e-03 52.8


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 TraesCS4D01G188500 chr4D 327730724 327734391 3667 True 6774.000000 6774 100.000000 1 3668 1 chr4D.!!$R1 3667
1 TraesCS4D01G188500 chr4A 143239461 143243382 3921 False 2037.333333 4514 96.670333 1 3668 3 chr4A.!!$F1 3667
2 TraesCS4D01G188500 chr4B 407069283 407073381 4098 True 1482.275000 4458 96.135500 1 3668 4 chr4B.!!$R1 3667

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
68 69 0.590481 GTTTCCGTTGCCGTGTTGAC 60.590 55.000 0.00 0.0 0.00 3.18 F
181 406 0.783206 TGAAGGCCCATGGAAGGAAA 59.217 50.000 15.22 0.0 0.00 3.13 F
471 731 0.954452 GTTCTGTGCTGGTTCTTGGG 59.046 55.000 0.00 0.0 0.00 4.12 F
990 1284 1.353694 AGGAAATCACTTCAGCAGCCT 59.646 47.619 0.00 0.0 35.55 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 2075 4.052518 GACCATGCCCTGCCAGGT 62.053 66.667 10.47 0.0 37.39 4.00 R
2143 2437 2.045926 ACCGCTGCCCTGACATTC 60.046 61.111 0.00 0.0 0.00 2.67 R
2144 2438 2.202236 ATCACCGCTGCCCTGACATT 62.202 55.000 0.00 0.0 0.00 2.71 R
2752 3046 1.853963 AACTCCTGATAGGACGCTGT 58.146 50.000 0.00 0.0 40.06 4.40 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
68 69 0.590481 GTTTCCGTTGCCGTGTTGAC 60.590 55.000 0.00 0.00 0.00 3.18
83 84 4.396854 GACGCACTATGGTCCGTC 57.603 61.111 10.04 10.04 46.91 4.79
181 406 0.783206 TGAAGGCCCATGGAAGGAAA 59.217 50.000 15.22 0.00 0.00 3.13
215 471 6.588756 TGGACGAATTTCTAGTACATGTTGTC 59.411 38.462 2.30 0.00 0.00 3.18
234 490 7.600065 TGTTGTCATCCAGTAGTTAGTACTTC 58.400 38.462 0.00 0.00 40.27 3.01
351 607 7.198306 AGGTCGTACAGGAAAACTAAAAATG 57.802 36.000 0.00 0.00 0.00 2.32
356 612 6.141685 CGTACAGGAAAACTAAAAATGCACAC 59.858 38.462 0.00 0.00 0.00 3.82
471 731 0.954452 GTTCTGTGCTGGTTCTTGGG 59.046 55.000 0.00 0.00 0.00 4.12
480 740 2.434336 GCTGGTTCTTGGGTTTCCTTTT 59.566 45.455 0.00 0.00 0.00 2.27
512 772 3.191162 GCAATGTTGTTGTCATAGAGCCA 59.809 43.478 0.00 0.00 0.00 4.75
515 775 3.402110 TGTTGTTGTCATAGAGCCACAG 58.598 45.455 0.00 0.00 0.00 3.66
674 943 8.994500 TGGTAGTATCATGTAGGATTTTTACCA 58.006 33.333 10.01 10.01 35.84 3.25
682 964 9.342308 TCATGTAGGATTTTTACCATGAGATTC 57.658 33.333 0.00 0.00 0.00 2.52
733 1015 1.935799 TTGGCCATACCTGTGCAAAT 58.064 45.000 6.09 0.00 40.22 2.32
810 1092 5.362556 TGCACAAGAAGTAAAGAATCAGC 57.637 39.130 0.00 0.00 0.00 4.26
833 1115 8.466799 CAGCGATGATCTTAATTTTTCATTTCG 58.533 33.333 0.00 0.00 0.00 3.46
869 1151 9.959749 GGCATTCGTTTTGGATAATTATCTTAA 57.040 29.630 21.80 15.29 33.28 1.85
990 1284 1.353694 AGGAAATCACTTCAGCAGCCT 59.646 47.619 0.00 0.00 35.55 4.58
1353 1647 2.616510 GCCAATGCTTGAGTGGAGTACT 60.617 50.000 0.00 0.00 42.94 2.73
1404 1698 2.308866 GGGATTCTTGAAGGGAGGACAA 59.691 50.000 0.00 0.00 0.00 3.18
1500 1794 3.727387 GCAAGGAGCTCCCACCTA 58.273 61.111 29.54 0.00 41.15 3.08
1941 2235 4.143389 CGTCAGTACTTTGAAACGATGTCC 60.143 45.833 0.00 0.00 0.00 4.02
2143 2437 7.495901 AGGTGATGTCACTATTGAACAGATAG 58.504 38.462 12.43 0.00 45.73 2.08
2144 2438 7.343057 AGGTGATGTCACTATTGAACAGATAGA 59.657 37.037 12.43 0.00 45.73 1.98
2169 2463 0.396811 AGGGCAGCGGTGATTATACC 59.603 55.000 20.69 8.52 37.37 2.73
2207 2501 8.742125 ATCTACTCATCAATAAATAGGTGGGA 57.258 34.615 0.00 0.00 0.00 4.37
2367 2661 2.212652 CGAGTGCTGCATGGCTTATTA 58.787 47.619 5.27 0.00 0.00 0.98
2685 2979 1.532437 TGAGCACTTGATGAAGCAACG 59.468 47.619 0.00 0.00 31.68 4.10
2696 2990 3.921119 TGAAGCAACGCAGAAATGATT 57.079 38.095 0.00 0.00 0.00 2.57
2705 2999 3.501828 ACGCAGAAATGATTTGTACAGCA 59.498 39.130 0.00 0.00 0.00 4.41
2757 3051 7.303634 AGTGGACTAAATAATTTGTACAGCG 57.696 36.000 0.00 0.00 36.08 5.18
2758 3052 6.877322 AGTGGACTAAATAATTTGTACAGCGT 59.123 34.615 0.00 0.00 36.08 5.07
2759 3053 7.064253 AGTGGACTAAATAATTTGTACAGCGTC 59.936 37.037 0.00 0.00 36.08 5.19
2760 3054 6.314400 TGGACTAAATAATTTGTACAGCGTCC 59.686 38.462 0.00 0.00 31.40 4.79
2761 3055 6.537660 GGACTAAATAATTTGTACAGCGTCCT 59.462 38.462 0.00 0.00 34.68 3.85
2762 3056 7.707893 GGACTAAATAATTTGTACAGCGTCCTA 59.292 37.037 0.00 0.00 34.68 2.94
2763 3057 9.257651 GACTAAATAATTTGTACAGCGTCCTAT 57.742 33.333 0.00 0.00 0.00 2.57
2764 3058 9.257651 ACTAAATAATTTGTACAGCGTCCTATC 57.742 33.333 0.00 0.00 0.00 2.08
2765 3059 9.256477 CTAAATAATTTGTACAGCGTCCTATCA 57.744 33.333 0.00 0.00 0.00 2.15
2766 3060 7.715265 AATAATTTGTACAGCGTCCTATCAG 57.285 36.000 0.00 0.00 0.00 2.90
2767 3061 3.520290 TTTGTACAGCGTCCTATCAGG 57.480 47.619 0.00 0.00 36.46 3.86
2768 3062 2.430248 TGTACAGCGTCCTATCAGGA 57.570 50.000 0.00 0.00 43.43 3.86
2876 3170 9.944376 TGTTATCAGTTTAGCTTTGAGATAAGT 57.056 29.630 0.00 0.00 26.94 2.24
3134 3647 6.513806 TGCTTATTTGTGCTGACATTACAT 57.486 33.333 0.00 0.00 30.13 2.29
3136 3649 5.230726 GCTTATTTGTGCTGACATTACATGC 59.769 40.000 0.00 0.00 30.13 4.06
3269 3782 5.708736 TTTCAGGATTAATAGAGGTGGCA 57.291 39.130 0.00 0.00 0.00 4.92
3387 3900 4.338118 TCTTTTTGCTGTGGTAACTTCCAG 59.662 41.667 0.00 0.00 38.23 3.86
3515 4028 4.995487 ACCTTTTAGTGCAACAGTACTAGC 59.005 41.667 0.00 0.78 41.43 3.42
3526 4039 3.775202 ACAGTACTAGCGAGAAATGCAG 58.225 45.455 0.00 0.00 33.85 4.41
3545 4058 4.588528 TGCAGGAAAAGGAAGTAAGCAATT 59.411 37.500 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 5.127031 CACCAAATCCCCCAAACAGTATAAG 59.873 44.000 0.00 0.00 0.00 1.73
215 471 6.777213 ACCAGAAGTACTAACTACTGGATG 57.223 41.667 25.30 10.63 45.02 3.51
365 621 2.340328 CGGGGGCCCTTTTCGAAAG 61.340 63.158 24.38 5.63 0.00 2.62
367 623 4.354162 CCGGGGGCCCTTTTCGAA 62.354 66.667 24.38 0.00 0.00 3.71
471 731 5.363979 TTGCCAAACAAACAAAAGGAAAC 57.636 34.783 0.00 0.00 34.56 2.78
480 740 4.067896 ACAACAACATTGCCAAACAAACA 58.932 34.783 0.00 0.00 42.86 2.83
512 772 0.034756 TACATTCACGTGCAGCCTGT 59.965 50.000 11.67 11.34 0.00 4.00
515 775 0.391130 TCCTACATTCACGTGCAGCC 60.391 55.000 11.67 0.00 0.00 4.85
663 932 5.757850 AGCGAATCTCATGGTAAAAATCC 57.242 39.130 0.00 0.00 0.00 3.01
664 933 7.484035 ACTAGCGAATCTCATGGTAAAAATC 57.516 36.000 0.00 0.00 0.00 2.17
665 934 8.421784 TCTACTAGCGAATCTCATGGTAAAAAT 58.578 33.333 0.00 0.00 0.00 1.82
666 935 7.778083 TCTACTAGCGAATCTCATGGTAAAAA 58.222 34.615 0.00 0.00 0.00 1.94
667 936 7.342769 TCTACTAGCGAATCTCATGGTAAAA 57.657 36.000 0.00 0.00 0.00 1.52
668 937 6.954487 TCTACTAGCGAATCTCATGGTAAA 57.046 37.500 0.00 0.00 0.00 2.01
669 938 6.490381 ACATCTACTAGCGAATCTCATGGTAA 59.510 38.462 0.00 0.00 0.00 2.85
670 939 6.004574 ACATCTACTAGCGAATCTCATGGTA 58.995 40.000 0.00 0.00 0.00 3.25
671 940 4.830046 ACATCTACTAGCGAATCTCATGGT 59.170 41.667 0.00 0.00 0.00 3.55
672 941 5.384063 ACATCTACTAGCGAATCTCATGG 57.616 43.478 0.00 0.00 0.00 3.66
673 942 8.978564 AAATACATCTACTAGCGAATCTCATG 57.021 34.615 0.00 0.00 0.00 3.07
674 943 9.416794 CAAAATACATCTACTAGCGAATCTCAT 57.583 33.333 0.00 0.00 0.00 2.90
675 944 8.414003 ACAAAATACATCTACTAGCGAATCTCA 58.586 33.333 0.00 0.00 0.00 3.27
748 1030 2.582687 GCTAGCGCATAGTAAGTACGG 58.417 52.381 11.47 0.00 33.65 4.02
810 1092 8.841444 ACCGAAATGAAAAATTAAGATCATCG 57.159 30.769 0.00 0.00 31.58 3.84
833 1115 5.818857 TCCAAAACGAATGCCTATAGTTACC 59.181 40.000 0.00 0.00 0.00 2.85
837 1119 8.691661 AATTATCCAAAACGAATGCCTATAGT 57.308 30.769 0.00 0.00 0.00 2.12
843 1125 9.959749 TTAAGATAATTATCCAAAACGAATGCC 57.040 29.630 19.67 0.00 33.17 4.40
869 1151 5.595542 AGCCTGATGCACACATAATGTTAAT 59.404 36.000 0.00 0.00 40.64 1.40
963 1257 5.809001 TGCTGAAGTGATTTCCTAGAATGT 58.191 37.500 0.00 0.00 34.77 2.71
990 1284 5.584649 GCTTGTGTAGGACATAGTGCAAATA 59.415 40.000 0.00 0.00 33.40 1.40
1353 1647 6.183360 GCATCAAATTACCATGGAAAGGATCA 60.183 38.462 21.47 0.00 0.00 2.92
1404 1698 7.568349 TGAAAATCTGATATGCCTTGTCTAGT 58.432 34.615 0.00 0.00 0.00 2.57
1557 1851 6.147492 CAGACAGGACTGAAGAGAATGAAAAG 59.853 42.308 6.29 0.00 39.94 2.27
1738 2032 5.690865 TGTGGACAGGTGTTTTCTCTTAAT 58.309 37.500 0.00 0.00 0.00 1.40
1781 2075 4.052518 GACCATGCCCTGCCAGGT 62.053 66.667 10.47 0.00 37.39 4.00
1941 2235 7.086376 CCTTTGGAGTGATTGAATACTTTGTG 58.914 38.462 0.00 0.00 0.00 3.33
2143 2437 2.045926 ACCGCTGCCCTGACATTC 60.046 61.111 0.00 0.00 0.00 2.67
2144 2438 2.202236 ATCACCGCTGCCCTGACATT 62.202 55.000 0.00 0.00 0.00 2.71
2199 2493 3.706389 TCCTCTGAATCATCCCACCTA 57.294 47.619 0.00 0.00 0.00 3.08
2207 2501 7.346698 TCTCTTTCCATACTTCCTCTGAATCAT 59.653 37.037 0.00 0.00 0.00 2.45
2685 2979 5.039333 GGATGCTGTACAAATCATTTCTGC 58.961 41.667 16.20 5.33 0.00 4.26
2696 2990 4.290093 ACTCCTGATAGGATGCTGTACAA 58.710 43.478 0.00 0.00 44.81 2.41
2705 2999 4.102367 GCTTCTCCAAACTCCTGATAGGAT 59.898 45.833 0.00 0.00 44.81 3.24
2748 3042 2.688446 CTCCTGATAGGACGCTGTACAA 59.312 50.000 0.00 0.00 40.06 2.41
2750 3044 2.299521 ACTCCTGATAGGACGCTGTAC 58.700 52.381 0.00 0.00 40.06 2.90
2751 3045 2.730934 ACTCCTGATAGGACGCTGTA 57.269 50.000 0.00 0.00 40.06 2.74
2752 3046 1.853963 AACTCCTGATAGGACGCTGT 58.146 50.000 0.00 0.00 40.06 4.40
2753 3047 3.319405 ACATAACTCCTGATAGGACGCTG 59.681 47.826 0.00 0.00 40.06 5.18
2754 3048 3.567397 ACATAACTCCTGATAGGACGCT 58.433 45.455 0.00 0.00 40.06 5.07
2755 3049 4.299978 GAACATAACTCCTGATAGGACGC 58.700 47.826 0.00 0.00 40.06 5.19
2756 3050 4.556898 CGGAACATAACTCCTGATAGGACG 60.557 50.000 0.00 0.00 40.06 4.79
2757 3051 4.796618 GCGGAACATAACTCCTGATAGGAC 60.797 50.000 0.00 0.00 40.06 3.85
2758 3052 3.321111 GCGGAACATAACTCCTGATAGGA 59.679 47.826 0.00 0.00 43.43 2.94
2759 3053 3.322254 AGCGGAACATAACTCCTGATAGG 59.678 47.826 0.00 0.00 36.46 2.57
2760 3054 4.592485 AGCGGAACATAACTCCTGATAG 57.408 45.455 0.00 0.00 0.00 2.08
2761 3055 4.442893 CCAAGCGGAACATAACTCCTGATA 60.443 45.833 0.00 0.00 0.00 2.15
2762 3056 3.535561 CAAGCGGAACATAACTCCTGAT 58.464 45.455 0.00 0.00 0.00 2.90
2763 3057 2.354704 CCAAGCGGAACATAACTCCTGA 60.355 50.000 0.00 0.00 0.00 3.86
2764 3058 2.009774 CCAAGCGGAACATAACTCCTG 58.990 52.381 0.00 0.00 0.00 3.86
2765 3059 1.906574 TCCAAGCGGAACATAACTCCT 59.093 47.619 0.00 0.00 38.83 3.69
2766 3060 2.396590 TCCAAGCGGAACATAACTCC 57.603 50.000 0.00 0.00 38.83 3.85
2876 3170 6.654582 ACAATACATTTCTGTGTCTGCATACA 59.345 34.615 0.00 0.00 36.79 2.29
2913 3207 4.982241 AGAGAAAATCTTGTGGACCAGA 57.018 40.909 0.00 0.00 32.99 3.86
3134 3647 4.524328 AGTCATCACATATATCTCACCGCA 59.476 41.667 0.00 0.00 0.00 5.69
3136 3649 6.681777 TGAAGTCATCACATATATCTCACCG 58.318 40.000 0.00 0.00 31.50 4.94
3387 3900 5.351740 GTGTCCTATTGAGTTCCTTAGTTGC 59.648 44.000 0.00 0.00 0.00 4.17
3515 4028 3.503748 ACTTCCTTTTCCTGCATTTCTCG 59.496 43.478 0.00 0.00 0.00 4.04
3526 4039 6.981722 TGAAGAATTGCTTACTTCCTTTTCC 58.018 36.000 0.00 0.00 39.14 3.13
3545 4058 0.035152 ATGGCGGTCATTGCTGAAGA 60.035 50.000 0.00 0.00 31.85 2.87


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

AutoCloner maintained by Alex Coulton.