Multiple sequence alignment - TraesCS4B01G244900

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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 TraesCS4B01G244900 chr4B 100.000 3258 0 0 1 3258 506908699 506911956 0.000000e+00 6017.0
1 TraesCS4B01G244900 chr4A 94.997 3278 102 23 1 3258 80858947 80855712 0.000000e+00 5088.0
2 TraesCS4B01G244900 chr4D 93.521 3303 114 41 1 3258 409171047 409167800 0.000000e+00 4822.0
3 TraesCS4B01G244900 chr5D 85.827 127 18 0 1548 1674 344885063 344884937 5.670000e-28 135.0
4 TraesCS4B01G244900 chr5D 84.270 89 10 3 1548 1634 436971839 436971925 2.080000e-12 84.2
5 TraesCS4B01G244900 chr5A 88.991 109 12 0 1548 1656 447305063 447305171 5.670000e-28 135.0
6 TraesCS4B01G244900 chr7D 90.722 97 9 0 1548 1644 117792114 117792210 2.640000e-26 130.0
7 TraesCS4B01G244900 chr7B 89.691 97 10 0 1548 1644 79051426 79051522 1.230000e-24 124.0
8 TraesCS4B01G244900 chr7A 89.691 97 10 0 1548 1644 122207649 122207745 1.230000e-24 124.0
9 TraesCS4B01G244900 chr5B 84.270 89 10 3 1548 1634 531187513 531187599 2.080000e-12 84.2


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 TraesCS4B01G244900 chr4B 506908699 506911956 3257 False 6017 6017 100.000 1 3258 1 chr4B.!!$F1 3257
1 TraesCS4B01G244900 chr4A 80855712 80858947 3235 True 5088 5088 94.997 1 3258 1 chr4A.!!$R1 3257
2 TraesCS4B01G244900 chr4D 409167800 409171047 3247 True 4822 4822 93.521 1 3258 1 chr4D.!!$R1 3257

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
591 613 0.178990 GAGAGGAGAGAGAGGGAGCC 60.179 65.0 0.00 0.00 0.00 4.70 F
1149 1174 0.031994 GCTGCTGCCTCTAGACTAGC 59.968 60.0 3.85 9.93 35.06 3.42 F
2197 2228 0.104120 TGCATTCGGATCGTACCTGG 59.896 55.0 0.00 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2260 0.103390 TTCTCACGTTTCACGAGGCA 59.897 50.000 2.75 0.0 46.05 4.75 R
2239 2270 3.056393 TGGACGGACATATTTCTCACGTT 60.056 43.478 0.00 0.0 32.84 3.99 R
3217 3266 3.388350 CCCCCTTCTCATACCTGTACTTC 59.612 52.174 0.00 0.0 0.00 3.01 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 74 4.634012 ACATAGCTTGGTAGGTGAACAA 57.366 40.909 0.00 0.00 33.36 2.83
85 91 1.615392 ACAAGGCAACAAGATTCCTGC 59.385 47.619 0.00 0.00 41.41 4.85
86 92 1.614903 CAAGGCAACAAGATTCCTGCA 59.385 47.619 0.00 0.00 36.50 4.41
105 111 2.731027 GCATGGTTAGCCGCTTAACAAC 60.731 50.000 0.47 0.00 35.67 3.32
108 114 2.550606 TGGTTAGCCGCTTAACAACAAG 59.449 45.455 0.00 0.00 35.67 3.16
169 176 7.337942 AGTTGGTTAGCTTTTGAGATGAATAGG 59.662 37.037 0.00 0.00 0.00 2.57
170 177 5.590259 TGGTTAGCTTTTGAGATGAATAGGC 59.410 40.000 0.00 0.00 0.00 3.93
570 578 9.090692 CAGAGAAATGAAGAAAGCAAAGAAAAA 57.909 29.630 0.00 0.00 0.00 1.94
591 613 0.178990 GAGAGGAGAGAGAGGGAGCC 60.179 65.000 0.00 0.00 0.00 4.70
814 836 2.104622 TGGACGATGCATGTATCCACAT 59.895 45.455 16.92 0.00 46.58 3.21
815 837 2.738846 GGACGATGCATGTATCCACATC 59.261 50.000 16.92 8.16 43.73 3.06
973 995 5.349817 CCTATCGCTTCTATACATTTGGCAG 59.650 44.000 0.00 0.00 0.00 4.85
1047 1072 1.203237 ACCTTCTCTCTCCTTGGCTCA 60.203 52.381 0.00 0.00 0.00 4.26
1065 1090 4.113815 CTTCTCATGCCCCGGCCA 62.114 66.667 2.24 0.00 41.09 5.36
1066 1091 3.643595 CTTCTCATGCCCCGGCCAA 62.644 63.158 2.24 0.00 41.09 4.52
1121 1146 1.003696 GTTCCTCTTCCTCCCAACAGG 59.996 57.143 0.00 0.00 34.40 4.00
1139 1164 1.294780 GTACTCACTGCTGCTGCCT 59.705 57.895 13.47 0.00 38.71 4.75
1147 1172 1.341482 ACTGCTGCTGCCTCTAGACTA 60.341 52.381 13.47 0.00 38.71 2.59
1148 1173 1.337703 CTGCTGCTGCCTCTAGACTAG 59.662 57.143 13.47 2.81 38.71 2.57
1149 1174 0.031994 GCTGCTGCCTCTAGACTAGC 59.968 60.000 3.85 9.93 35.06 3.42
1150 1175 1.691196 CTGCTGCCTCTAGACTAGCT 58.309 55.000 15.30 0.00 35.50 3.32
1166 1191 1.220206 GCTAGCAGCTGAGCCTGAA 59.780 57.895 20.43 0.00 38.45 3.02
1184 1209 5.173131 GCCTGAAACATTGTTTTGTACTTCG 59.827 40.000 15.54 1.01 0.00 3.79
1188 1213 6.252441 TGAAACATTGTTTTGTACTTCGCAAG 59.748 34.615 15.54 0.00 0.00 4.01
1233 1258 1.833630 TCTGTGCCTTTCTCGATCCAT 59.166 47.619 0.00 0.00 0.00 3.41
1598 1626 1.827399 ATTTCCCGACGTCACAGGCT 61.827 55.000 17.16 0.00 0.00 4.58
1768 1799 1.186917 TTGTACCCGTCGTGGACCAT 61.187 55.000 0.00 0.00 42.00 3.55
1782 1813 2.747460 CCATGGTGAGTGGCGGTG 60.747 66.667 2.57 0.00 0.00 4.94
1847 1878 1.749258 GCCGATCAACAGGAACCCC 60.749 63.158 0.00 0.00 0.00 4.95
1943 1974 1.654220 GGTCACGCTGCACATGTTT 59.346 52.632 0.00 0.00 0.00 2.83
2194 2225 2.787601 TACTGCATTCGGATCGTACC 57.212 50.000 0.00 0.00 0.00 3.34
2195 2226 1.112113 ACTGCATTCGGATCGTACCT 58.888 50.000 0.00 0.00 0.00 3.08
2196 2227 1.202417 ACTGCATTCGGATCGTACCTG 60.202 52.381 0.00 0.00 0.00 4.00
2197 2228 0.104120 TGCATTCGGATCGTACCTGG 59.896 55.000 0.00 0.00 0.00 4.45
2198 2229 1.222115 GCATTCGGATCGTACCTGGC 61.222 60.000 0.00 0.00 0.00 4.85
2199 2230 0.389391 CATTCGGATCGTACCTGGCT 59.611 55.000 0.00 0.00 0.00 4.75
2200 2231 1.611977 CATTCGGATCGTACCTGGCTA 59.388 52.381 0.00 0.00 0.00 3.93
2201 2232 1.027357 TTCGGATCGTACCTGGCTAC 58.973 55.000 0.00 0.00 0.00 3.58
2220 2251 4.998033 GCTACCTGGCTGATATTACCTTTC 59.002 45.833 0.00 0.00 0.00 2.62
2229 2260 5.452077 GCTGATATTACCTTTCTCCACTCGT 60.452 44.000 0.00 0.00 0.00 4.18
2231 2262 2.450609 TTACCTTTCTCCACTCGTGC 57.549 50.000 0.00 0.00 0.00 5.34
2239 2270 2.142357 CTCCACTCGTGCCTCGTGAA 62.142 60.000 7.29 0.00 40.80 3.18
2257 2288 4.882447 GTGAAACGTGAGAAATATGTCCG 58.118 43.478 0.00 0.00 0.00 4.79
2268 2299 5.745227 AGAAATATGTCCGTCCATCAAAGT 58.255 37.500 0.00 0.00 0.00 2.66
2393 2424 9.768662 ATACTCAATTGCAAATTCTTTGAAACT 57.231 25.926 1.71 0.00 40.82 2.66
2509 2554 9.461312 TCTTGCCATTTAGATAACAAACAGTAT 57.539 29.630 0.00 0.00 0.00 2.12
2631 2676 9.965902 CTAGCATCCATTTATAGGAAGGTTATT 57.034 33.333 0.00 0.00 38.93 1.40
2633 2678 9.301897 AGCATCCATTTATAGGAAGGTTATTTC 57.698 33.333 0.00 0.00 38.93 2.17
2712 2757 3.630769 CAGTCATCAATTAGCTGCCACAT 59.369 43.478 0.00 0.00 0.00 3.21
2731 2776 3.244875 ACATGGTCTGTATGAACCTGCAA 60.245 43.478 0.00 0.00 35.91 4.08
2732 2777 3.500448 TGGTCTGTATGAACCTGCAAA 57.500 42.857 0.00 0.00 0.00 3.68
2809 2854 6.085198 CACACGCAAATGCAAATGTTAAAATG 59.915 34.615 6.18 0.00 42.21 2.32
2837 2882 3.045518 CCACCAGGGGTTTAACCAC 57.954 57.895 16.58 12.91 43.77 4.16
2838 2883 0.186386 CCACCAGGGGTTTAACCACA 59.814 55.000 19.42 0.00 46.63 4.17
2843 2888 2.419667 CAGGGGTTTAACCACAGTACG 58.580 52.381 19.42 0.00 46.63 3.67
2932 2977 7.924940 GCTTTATAGCAGTAGATTCAGCTTTT 58.075 34.615 0.00 0.00 46.95 2.27
2937 2982 4.829492 AGCAGTAGATTCAGCTTTTTGGTT 59.171 37.500 0.00 0.00 32.52 3.67
2969 3014 8.277713 TCAAGATAGTTTGCACGTACTAAAAAC 58.722 33.333 0.31 2.31 31.20 2.43
3117 3166 1.751437 AGGATCGATGTCTCGTGTGA 58.249 50.000 0.54 0.00 45.25 3.58
3217 3266 1.710816 AGAGAAAGATAGGCGAGGGG 58.289 55.000 0.00 0.00 0.00 4.79
3249 3303 0.618968 GAGAAGGGGGAGCAGGAAGA 60.619 60.000 0.00 0.00 0.00 2.87
3250 3304 0.045469 AGAAGGGGGAGCAGGAAGAT 59.955 55.000 0.00 0.00 0.00 2.40
3251 3305 1.295292 AGAAGGGGGAGCAGGAAGATA 59.705 52.381 0.00 0.00 0.00 1.98
3253 3307 1.813102 AGGGGGAGCAGGAAGATAAG 58.187 55.000 0.00 0.00 0.00 1.73
3255 3309 1.695989 GGGGGAGCAGGAAGATAAGGA 60.696 57.143 0.00 0.00 0.00 3.36
3256 3310 1.696884 GGGGAGCAGGAAGATAAGGAG 59.303 57.143 0.00 0.00 0.00 3.69
3257 3311 2.403561 GGGAGCAGGAAGATAAGGAGT 58.596 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 74 1.822990 CATGCAGGAATCTTGTTGCCT 59.177 47.619 0.00 0.00 35.75 4.75
85 91 2.486203 TGTTGTTAAGCGGCTAACCATG 59.514 45.455 1.35 0.00 34.57 3.66
86 92 2.785562 TGTTGTTAAGCGGCTAACCAT 58.214 42.857 1.35 0.00 34.57 3.55
105 111 3.870419 CCTAGCTAGCTTGCTTCTTCTTG 59.130 47.826 27.19 9.32 43.74 3.02
108 114 3.810310 TCCTAGCTAGCTTGCTTCTTC 57.190 47.619 27.19 0.00 43.74 2.87
169 176 1.419107 GCTACTCCTGTTTACCGCGC 61.419 60.000 0.00 0.00 0.00 6.86
170 177 0.108992 TGCTACTCCTGTTTACCGCG 60.109 55.000 0.00 0.00 0.00 6.46
498 506 1.269723 TGAGTACGTGACAAGCTCTGG 59.730 52.381 0.00 0.00 0.00 3.86
570 578 1.215423 GCTCCCTCTCTCTCCTCTCTT 59.785 57.143 0.00 0.00 0.00 2.85
586 606 2.716017 CCTCACTCTCACGGGCTCC 61.716 68.421 0.00 0.00 0.00 4.70
591 613 0.609406 TCACTCCCTCACTCTCACGG 60.609 60.000 0.00 0.00 0.00 4.94
735 757 1.977009 GCTGGGGCCTTGTGGTTAC 60.977 63.158 0.84 0.00 35.27 2.50
736 758 2.438795 GCTGGGGCCTTGTGGTTA 59.561 61.111 0.84 0.00 35.27 2.85
814 836 2.069775 CTAGATGGGAGGGAGGAGAGA 58.930 57.143 0.00 0.00 0.00 3.10
815 837 1.549950 GCTAGATGGGAGGGAGGAGAG 60.550 61.905 0.00 0.00 0.00 3.20
973 995 1.066858 TCATGTCGCTCAAAGGAGGAC 60.067 52.381 0.00 0.00 41.67 3.85
1047 1072 4.115199 GGCCGGGGCATGAGAAGT 62.115 66.667 16.76 0.00 44.11 3.01
1065 1090 1.923148 CATGGAGTTAAGGAGGGGGTT 59.077 52.381 0.00 0.00 0.00 4.11
1066 1091 1.082194 TCATGGAGTTAAGGAGGGGGT 59.918 52.381 0.00 0.00 0.00 4.95
1121 1146 0.739112 GAGGCAGCAGCAGTGAGTAC 60.739 60.000 2.65 0.00 44.61 2.73
1148 1173 0.392193 TTTCAGGCTCAGCTGCTAGC 60.392 55.000 16.99 16.99 42.84 3.42
1149 1174 1.338484 TGTTTCAGGCTCAGCTGCTAG 60.338 52.381 9.47 3.05 0.00 3.42
1150 1175 0.686789 TGTTTCAGGCTCAGCTGCTA 59.313 50.000 9.47 0.00 0.00 3.49
1166 1191 5.040635 CCTTGCGAAGTACAAAACAATGTT 58.959 37.500 0.00 0.00 34.75 2.71
1233 1258 0.251297 CCCATGCAACCAGAACCAGA 60.251 55.000 0.00 0.00 0.00 3.86
1334 1362 1.207791 ATGGCAACTCGGAGAAGGAT 58.792 50.000 12.86 0.00 34.09 3.24
1376 1404 0.035458 CAGAGTTGGGGCTTTCTCGT 59.965 55.000 0.00 0.00 32.90 4.18
1697 1725 1.218047 GAGATGGTAGTGGTGCGCA 59.782 57.895 5.66 5.66 0.00 6.09
1707 1735 1.802553 GGGTAGCCAAGGAGATGGTA 58.197 55.000 5.96 0.00 42.75 3.25
1768 1799 2.842462 AGACACCGCCACTCACCA 60.842 61.111 0.00 0.00 0.00 4.17
1782 1813 0.543749 AACTGCTGGCCATAGGAGAC 59.456 55.000 18.67 0.00 38.28 3.36
1888 1919 2.648143 AACGGCATGCCCATGTTGG 61.648 57.895 30.79 16.96 40.80 3.77
1986 2017 2.835156 GCAGTAAAGAGGAAGAGGAGGT 59.165 50.000 0.00 0.00 0.00 3.85
2128 2159 6.983906 AAAGATTGGGAAATCAGTTCTTGT 57.016 33.333 1.64 0.00 36.40 3.16
2130 2161 8.255111 AGAAAAAGATTGGGAAATCAGTTCTT 57.745 30.769 1.64 0.00 36.40 2.52
2194 2225 3.307059 GGTAATATCAGCCAGGTAGCCAG 60.307 52.174 0.00 0.00 0.00 4.85
2195 2226 2.637872 GGTAATATCAGCCAGGTAGCCA 59.362 50.000 0.00 0.00 0.00 4.75
2196 2227 2.907042 AGGTAATATCAGCCAGGTAGCC 59.093 50.000 0.00 0.00 0.00 3.93
2197 2228 4.625607 AAGGTAATATCAGCCAGGTAGC 57.374 45.455 0.00 0.00 0.00 3.58
2198 2229 6.426646 AGAAAGGTAATATCAGCCAGGTAG 57.573 41.667 0.00 0.00 0.00 3.18
2199 2230 5.307196 GGAGAAAGGTAATATCAGCCAGGTA 59.693 44.000 0.00 0.00 0.00 3.08
2200 2231 4.103311 GGAGAAAGGTAATATCAGCCAGGT 59.897 45.833 0.00 0.00 0.00 4.00
2201 2232 4.103153 TGGAGAAAGGTAATATCAGCCAGG 59.897 45.833 0.00 0.00 0.00 4.45
2220 2251 2.126307 CACGAGGCACGAGTGGAG 60.126 66.667 12.15 0.00 45.77 3.86
2229 2260 0.103390 TTCTCACGTTTCACGAGGCA 59.897 50.000 2.75 0.00 46.05 4.75
2231 2262 4.625742 ACATATTTCTCACGTTTCACGAGG 59.374 41.667 2.75 0.00 46.05 4.63
2239 2270 3.056393 TGGACGGACATATTTCTCACGTT 60.056 43.478 0.00 0.00 32.84 3.99
2257 2288 3.181506 GCAGGATCGAAACTTTGATGGAC 60.182 47.826 0.00 0.00 31.50 4.02
2296 2327 8.786898 CCTAATCATACAACCCATAATGTTCTG 58.213 37.037 0.00 0.00 0.00 3.02
2560 2605 9.994432 CACCAGTCTCTTCAAATTTATATTGTC 57.006 33.333 0.00 0.00 0.00 3.18
2631 2676 8.541899 AAAAGTAAACTCCTACCAAAATGGAA 57.458 30.769 2.85 0.00 40.96 3.53
2633 2678 8.417884 TGAAAAAGTAAACTCCTACCAAAATGG 58.582 33.333 0.00 0.00 45.02 3.16
2670 2715 7.977818 TGACTGGCCATTATCTCAATATTAGT 58.022 34.615 5.51 0.00 0.00 2.24
2671 2716 9.107177 GATGACTGGCCATTATCTCAATATTAG 57.893 37.037 5.51 0.00 0.00 1.73
2672 2717 8.605065 TGATGACTGGCCATTATCTCAATATTA 58.395 33.333 5.51 0.00 0.00 0.98
2673 2718 7.464273 TGATGACTGGCCATTATCTCAATATT 58.536 34.615 5.51 0.00 0.00 1.28
2712 2757 3.411446 CTTTGCAGGTTCATACAGACCA 58.589 45.455 0.00 0.00 0.00 4.02
2755 2800 8.492673 TCTTTCAGAACTTTATATGCGTTCAT 57.507 30.769 12.88 0.00 39.48 2.57
2809 2854 3.777556 CCTGGTGGGGCTCAAAAC 58.222 61.111 0.00 0.00 0.00 2.43
2837 2882 9.474249 CTCACATATATATGAACGTACGTACTG 57.526 37.037 26.05 17.55 37.15 2.74
2838 2883 9.428097 TCTCACATATATATGAACGTACGTACT 57.572 33.333 26.05 6.86 37.15 2.73
2917 2962 7.346751 TCAAAACCAAAAAGCTGAATCTACT 57.653 32.000 0.00 0.00 0.00 2.57
2932 2977 7.437862 GTGCAAACTATCTTGAATCAAAACCAA 59.562 33.333 0.00 0.00 0.00 3.67
2937 2982 6.312399 ACGTGCAAACTATCTTGAATCAAA 57.688 33.333 0.00 0.00 0.00 2.69
3001 3048 7.172532 CACTGCACATACCTAGTCAACTTTAAA 59.827 37.037 0.00 0.00 0.00 1.52
3217 3266 3.388350 CCCCCTTCTCATACCTGTACTTC 59.612 52.174 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.