Multiple sequence alignment - TraesCS4D01G124300

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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 TraesCS4D01G124300 chr4D 100.000 3051 0 0 1 3051 108850623 108853673 0.000000e+00 5635
1 TraesCS4D01G124300 chr4A 90.933 1864 75 50 1 1828 467541103 467539298 0.000000e+00 2420
2 TraesCS4D01G124300 chr4A 93.236 1227 45 12 1831 3051 467539245 467538051 0.000000e+00 1772
3 TraesCS4D01G124300 chr4B 98.018 1009 20 0 2043 3051 167941118 167940110 0.000000e+00 1753
4 TraesCS4D01G124300 chr4B 93.607 1095 47 8 1 1084 167943287 167942205 0.000000e+00 1613
5 TraesCS4D01G124300 chr4B 89.394 726 32 14 1112 1828 167942207 167941518 0.000000e+00 872
6 TraesCS4D01G124300 chr4B 94.009 217 8 2 1829 2040 167941462 167941246 1.060000e-84 324


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 TraesCS4D01G124300 chr4D 108850623 108853673 3050 False 5635.0 5635 100.0000 1 3051 1 chr4D.!!$F1 3050
1 TraesCS4D01G124300 chr4A 467538051 467541103 3052 True 2096.0 2420 92.0845 1 3051 2 chr4A.!!$R1 3050
2 TraesCS4D01G124300 chr4B 167940110 167943287 3177 True 1140.5 1753 93.7570 1 3051 4 chr4B.!!$R1 3050

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
117 118 0.539051 AAATCTGCGGACTGAGGAGG 59.461 55.0 0.0 0.0 0.00 4.30 F
1095 1129 0.374758 CTTGAGCAACGCATACGCAT 59.625 50.0 0.0 0.0 45.53 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 1257 0.319900 AGTATTCATGGCGGCGCTAG 60.32 55.0 32.30 20.66 0.00 3.42 R
2602 2855 0.249955 CAATGCCAAATGGACCACCC 59.75 55.0 2.98 0.00 37.39 4.61 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
70 71 1.203052 CGATGCAAGGAAAATGCTGGT 59.797 47.619 0.00 0.00 44.14 4.00
81 82 5.095490 GGAAAATGCTGGTTGATTAACTCG 58.905 41.667 0.00 0.00 36.99 4.18
115 116 1.066858 GTCAAATCTGCGGACTGAGGA 60.067 52.381 9.00 0.00 0.00 3.71
116 117 1.205655 TCAAATCTGCGGACTGAGGAG 59.794 52.381 0.00 0.00 0.00 3.69
117 118 0.539051 AAATCTGCGGACTGAGGAGG 59.461 55.000 0.00 0.00 0.00 4.30
193 194 6.183360 CCATTTTATAGGCACTGCATTGTGTA 60.183 38.462 5.89 0.00 41.52 2.90
195 204 2.107950 TAGGCACTGCATTGTGTACC 57.892 50.000 5.89 0.88 41.52 3.34
206 215 3.498397 GCATTGTGTACCCATTAGGATCG 59.502 47.826 0.00 0.00 39.89 3.69
212 221 3.964688 TGTACCCATTAGGATCGTCACAT 59.035 43.478 0.00 0.00 39.89 3.21
228 237 5.918011 TCGTCACATTTTTCAATTAACTGGC 59.082 36.000 0.00 0.00 0.00 4.85
304 314 8.086522 AGATGAATCAACTTTCCAAACTTGATG 58.913 33.333 7.34 0.00 34.16 3.07
491 501 4.462280 GTTGGCCGTACCCCTCCG 62.462 72.222 0.00 0.00 37.83 4.63
564 578 4.863689 CGATCTGAATCTGTAGGATGCATC 59.136 45.833 18.81 18.81 39.13 3.91
570 584 1.065551 TCTGTAGGATGCATCGTCACG 59.934 52.381 24.21 13.59 0.00 4.35
573 587 1.001706 GTAGGATGCATCGTCACGCTA 60.002 52.381 24.21 13.49 0.00 4.26
610 625 2.423185 CTGCGTGCCATAGAAAATGGAA 59.577 45.455 8.20 0.00 41.64 3.53
655 670 6.979817 CACATGAAACCAGTCAAAAAGATCAA 59.020 34.615 0.00 0.00 0.00 2.57
659 674 5.424121 AACCAGTCAAAAAGATCAACTCG 57.576 39.130 0.00 0.00 0.00 4.18
674 689 3.508012 TCAACTCGGAAGAAGAGGAAGAG 59.492 47.826 0.00 0.00 41.32 2.85
859 882 6.237569 CGCTGCACATATATTCTATGTAACGG 60.238 42.308 0.00 1.39 36.49 4.44
909 938 0.822532 GGATGAATCAGCTGGCTGGG 60.823 60.000 20.41 0.00 43.75 4.45
910 939 1.453762 GATGAATCAGCTGGCTGGGC 61.454 60.000 20.41 11.51 43.75 5.36
943 972 0.970937 TCCAGATCTCGGGGTGACAC 60.971 60.000 10.23 0.00 0.00 3.67
1041 1075 0.605319 TTCACTCCATGTTCCCACGC 60.605 55.000 0.00 0.00 0.00 5.34
1090 1124 2.925594 TGCACTTGAGCAACGCATA 58.074 47.368 0.00 0.00 42.46 3.14
1091 1125 0.516877 TGCACTTGAGCAACGCATAC 59.483 50.000 0.00 0.00 42.46 2.39
1092 1126 3.109472 TGCACTTGAGCAACGCATACG 62.109 52.381 0.00 0.00 42.46 3.06
1093 1127 0.519175 CACTTGAGCAACGCATACGC 60.519 55.000 0.00 0.00 45.53 4.42
1094 1128 0.948623 ACTTGAGCAACGCATACGCA 60.949 50.000 0.00 0.00 45.53 5.24
1095 1129 0.374758 CTTGAGCAACGCATACGCAT 59.625 50.000 0.00 0.00 45.53 4.73
1104 1138 2.330393 CATACGCATGCTGCTGGC 59.670 61.111 17.13 3.52 42.25 4.85
1166 1210 2.038295 CAGCTCCAACTCTTCAACTCCT 59.962 50.000 0.00 0.00 0.00 3.69
1169 1214 1.978580 TCCAACTCTTCAACTCCTCCC 59.021 52.381 0.00 0.00 0.00 4.30
1179 1224 1.492993 AACTCCTCCCCACTCCAAGC 61.493 60.000 0.00 0.00 0.00 4.01
1180 1225 2.610859 TCCTCCCCACTCCAAGCC 60.611 66.667 0.00 0.00 0.00 4.35
1205 1250 2.005971 ACCTTACGGTTTGATCGAGC 57.994 50.000 0.00 0.00 42.13 5.03
1210 1255 1.908089 CGGTTTGATCGAGCGTACG 59.092 57.895 11.84 11.84 33.70 3.67
1212 1257 1.629504 GTTTGATCGAGCGTACGGC 59.370 57.895 18.39 9.46 44.05 5.68
1228 1273 2.974698 GCTAGCGCCGCCATGAAT 60.975 61.111 4.98 0.00 0.00 2.57
1229 1274 1.667830 GCTAGCGCCGCCATGAATA 60.668 57.895 4.98 0.00 0.00 1.75
1230 1275 1.901650 GCTAGCGCCGCCATGAATAC 61.902 60.000 4.98 0.00 0.00 1.89
1231 1276 0.319900 CTAGCGCCGCCATGAATACT 60.320 55.000 4.98 0.00 0.00 2.12
1303 1348 2.108566 CTCCTCGCCTCCATGCTG 59.891 66.667 0.00 0.00 0.00 4.41
1356 1401 4.681978 AACAGCCGCCGTGTCTCC 62.682 66.667 0.00 0.00 0.00 3.71
1440 1485 2.671619 GCTGGCCGCACAACCTAA 60.672 61.111 13.61 0.00 38.92 2.69
1558 1606 1.064654 GACGCCAGCATGAGGAAATTC 59.935 52.381 8.66 0.00 39.69 2.17
1594 1642 8.798153 GGCTCAAACAAAAATCATAATTAGTCG 58.202 33.333 0.00 0.00 0.00 4.18
1621 1669 4.835284 ACTGAATCTCCTTCCTTCCTTC 57.165 45.455 0.00 0.00 32.49 3.46
1622 1670 3.521531 ACTGAATCTCCTTCCTTCCTTCC 59.478 47.826 0.00 0.00 32.49 3.46
1623 1671 3.779738 CTGAATCTCCTTCCTTCCTTCCT 59.220 47.826 0.00 0.00 32.49 3.36
1624 1672 4.179133 TGAATCTCCTTCCTTCCTTCCTT 58.821 43.478 0.00 0.00 32.49 3.36
1625 1673 4.226168 TGAATCTCCTTCCTTCCTTCCTTC 59.774 45.833 0.00 0.00 32.49 3.46
1626 1674 2.552367 TCTCCTTCCTTCCTTCCTTCC 58.448 52.381 0.00 0.00 0.00 3.46
1627 1675 2.114506 TCTCCTTCCTTCCTTCCTTCCT 59.885 50.000 0.00 0.00 0.00 3.36
1628 1676 2.503765 CTCCTTCCTTCCTTCCTTCCTC 59.496 54.545 0.00 0.00 0.00 3.71
1629 1677 1.562008 CCTTCCTTCCTTCCTTCCTCC 59.438 57.143 0.00 0.00 0.00 4.30
1781 1837 6.590292 GTGTGTATCAATTTTCGAGAGGAGAA 59.410 38.462 0.00 0.00 0.00 2.87
1869 1984 5.376854 ACCTCAAATCCGAATTTCTTGTG 57.623 39.130 0.00 0.00 32.69 3.33
1959 2075 7.487189 CAGTTAAATCAAACATCCTTCATGCTC 59.513 37.037 0.00 0.00 35.65 4.26
2041 2163 5.296780 CAGCAGGACGGACATTACAAAATAT 59.703 40.000 0.00 0.00 0.00 1.28
2130 2380 3.005554 TCGGTAAGTTCTACGACTGAGG 58.994 50.000 0.00 0.00 0.00 3.86
2131 2381 3.005554 CGGTAAGTTCTACGACTGAGGA 58.994 50.000 0.00 0.00 0.00 3.71
2132 2382 3.063725 CGGTAAGTTCTACGACTGAGGAG 59.936 52.174 0.00 0.00 0.00 3.69
2215 2465 5.386958 TGTCTCTGAGCTAATTAACGTGT 57.613 39.130 0.00 0.00 0.00 4.49
2252 2502 8.824756 AAGTCTAACTACTTCATATGGTCAGA 57.175 34.615 2.13 0.00 34.60 3.27
2325 2575 1.783140 CCGTACGCCTATTTTCGTAGC 59.217 52.381 10.49 0.00 41.13 3.58
2498 2748 1.699634 CCTGAACTGGAGGGAAGAACA 59.300 52.381 0.00 0.00 0.00 3.18
2566 2819 2.745492 GCCTGTGGAGACTGCTGC 60.745 66.667 0.00 0.00 0.00 5.25
2567 2820 3.067091 CCTGTGGAGACTGCTGCT 58.933 61.111 0.00 0.00 33.04 4.24
2568 2821 1.375652 CCTGTGGAGACTGCTGCTG 60.376 63.158 4.89 4.89 33.04 4.41
2602 2855 3.086600 GGCAGAGGAGGTGGAGGG 61.087 72.222 0.00 0.00 0.00 4.30
2865 3118 3.348119 TCTGTTGTTGCACTTGTGGTAA 58.652 40.909 2.81 0.00 0.00 2.85
2870 3123 2.223923 TGTTGCACTTGTGGTAATTGGC 60.224 45.455 2.81 0.00 0.00 4.52
2898 3151 3.480133 GGCAGCCCCCGTATCACT 61.480 66.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 1.351080 CCATGGACCATCTGCCTCCT 61.351 60.000 5.56 0.00 0.00 3.69
116 117 1.150081 CCATGGACCATCTGCCTCC 59.850 63.158 5.56 0.00 0.00 4.30
117 118 1.527844 GCCATGGACCATCTGCCTC 60.528 63.158 18.40 0.00 0.00 4.70
193 194 4.503714 AAATGTGACGATCCTAATGGGT 57.496 40.909 0.00 0.00 36.25 4.51
195 204 6.435430 TGAAAAATGTGACGATCCTAATGG 57.565 37.500 0.00 0.00 0.00 3.16
206 215 6.701400 ACTGCCAGTTAATTGAAAAATGTGAC 59.299 34.615 0.00 0.00 0.00 3.67
212 221 8.729805 AATTGAACTGCCAGTTAATTGAAAAA 57.270 26.923 10.65 0.00 38.80 1.94
322 332 6.796785 AAATATCTCAAGAAACAATGGGGG 57.203 37.500 0.00 0.00 0.00 5.40
323 333 7.839907 TCAAAATATCTCAAGAAACAATGGGG 58.160 34.615 0.00 0.00 0.00 4.96
324 334 9.709495 TTTCAAAATATCTCAAGAAACAATGGG 57.291 29.630 0.00 0.00 0.00 4.00
491 501 4.850347 AAGTATAGGTGTGGTAGATCGC 57.150 45.455 0.00 0.00 0.00 4.58
564 578 5.402568 AGCATAATATCAAACTAGCGTGACG 59.597 40.000 0.00 0.00 0.00 4.35
570 584 5.406780 ACGCAGAGCATAATATCAAACTAGC 59.593 40.000 0.00 0.00 0.00 3.42
573 587 4.024556 GCACGCAGAGCATAATATCAAACT 60.025 41.667 0.00 0.00 45.32 2.66
655 670 1.822371 GCTCTTCCTCTTCTTCCGAGT 59.178 52.381 0.00 0.00 0.00 4.18
659 674 2.100087 CCTACGCTCTTCCTCTTCTTCC 59.900 54.545 0.00 0.00 0.00 3.46
674 689 1.952635 CCGGCCGAAATACCTACGC 60.953 63.158 30.73 0.00 0.00 4.42
859 882 8.739649 ACGAATTCTGTAGAAACTAACACTAC 57.260 34.615 3.52 0.00 37.61 2.73
909 938 1.978454 CTGGATCCATTTCCTCCAGC 58.022 55.000 16.63 0.00 46.89 4.85
1041 1075 1.680522 CTGGTGGATCGGAGGGAGTG 61.681 65.000 0.00 0.00 0.00 3.51
1093 1127 3.138798 GTGGAGGCCAGCAGCATG 61.139 66.667 5.01 0.00 46.50 4.06
1094 1128 4.790962 CGTGGAGGCCAGCAGCAT 62.791 66.667 5.01 0.00 46.50 3.79
1166 1210 2.610859 GAGGGCTTGGAGTGGGGA 60.611 66.667 0.00 0.00 0.00 4.81
1169 1214 1.303643 GTTGGAGGGCTTGGAGTGG 60.304 63.158 0.00 0.00 0.00 4.00
1212 1257 0.319900 AGTATTCATGGCGGCGCTAG 60.320 55.000 32.30 20.66 0.00 3.42
1213 1258 0.963225 TAGTATTCATGGCGGCGCTA 59.037 50.000 32.30 27.83 0.00 4.26
1214 1259 0.600255 GTAGTATTCATGGCGGCGCT 60.600 55.000 32.30 13.41 0.00 5.92
1215 1260 0.600255 AGTAGTATTCATGGCGGCGC 60.600 55.000 26.17 26.17 0.00 6.53
1216 1261 2.717580 TAGTAGTATTCATGGCGGCG 57.282 50.000 0.51 0.51 0.00 6.46
1217 1262 2.737252 GCTTAGTAGTATTCATGGCGGC 59.263 50.000 0.00 0.00 0.00 6.53
1218 1263 3.990469 CAGCTTAGTAGTATTCATGGCGG 59.010 47.826 0.00 0.00 0.00 6.13
1219 1264 3.430218 GCAGCTTAGTAGTATTCATGGCG 59.570 47.826 0.00 0.00 0.00 5.69
1220 1265 4.380531 TGCAGCTTAGTAGTATTCATGGC 58.619 43.478 0.00 0.00 0.00 4.40
1221 1266 4.993584 CCTGCAGCTTAGTAGTATTCATGG 59.006 45.833 8.66 0.00 0.00 3.66
1222 1267 4.450419 GCCTGCAGCTTAGTAGTATTCATG 59.550 45.833 8.66 0.00 38.99 3.07
1223 1268 4.636249 GCCTGCAGCTTAGTAGTATTCAT 58.364 43.478 8.66 0.00 38.99 2.57
1224 1269 4.060038 GCCTGCAGCTTAGTAGTATTCA 57.940 45.455 8.66 0.00 38.99 2.57
1263 1308 2.750637 AGACGACGGCGAGGACAT 60.751 61.111 22.49 0.00 41.64 3.06
1268 1313 4.838486 GCAGGAGACGACGGCGAG 62.838 72.222 22.49 10.00 41.64 5.03
1303 1348 0.814812 GCAAGAGGAGATGGAGCAGC 60.815 60.000 0.00 0.00 0.00 5.25
1594 1642 1.213182 GGAAGGAGATTCAGTTCCCCC 59.787 57.143 0.00 0.00 39.91 5.40
1621 1669 3.177228 TCAAAGAGAGAAGGGAGGAAGG 58.823 50.000 0.00 0.00 0.00 3.46
1622 1670 4.469227 TGATCAAAGAGAGAAGGGAGGAAG 59.531 45.833 0.00 0.00 0.00 3.46
1623 1671 4.429505 TGATCAAAGAGAGAAGGGAGGAA 58.570 43.478 0.00 0.00 0.00 3.36
1624 1672 4.029520 CTGATCAAAGAGAGAAGGGAGGA 58.970 47.826 0.00 0.00 0.00 3.71
1625 1673 3.432046 GCTGATCAAAGAGAGAAGGGAGG 60.432 52.174 0.00 0.00 0.00 4.30
1626 1674 3.451902 AGCTGATCAAAGAGAGAAGGGAG 59.548 47.826 0.00 0.00 0.00 4.30
1627 1675 3.197333 CAGCTGATCAAAGAGAGAAGGGA 59.803 47.826 8.42 0.00 0.00 4.20
1628 1676 3.055240 ACAGCTGATCAAAGAGAGAAGGG 60.055 47.826 23.35 0.00 0.00 3.95
1629 1677 4.205065 ACAGCTGATCAAAGAGAGAAGG 57.795 45.455 23.35 0.00 0.00 3.46
1719 1775 5.123227 GCACTAGATTACACATGCCCTAAA 58.877 41.667 0.00 0.00 0.00 1.85
1771 1827 2.289072 TGGAGCAAACTTTCTCCTCTCG 60.289 50.000 9.17 0.00 46.90 4.04
1781 1837 4.067896 CACATCAGTACTGGAGCAAACTT 58.932 43.478 22.48 0.00 0.00 2.66
1869 1984 1.202604 TCGCCGGAAATCTAATGGGAC 60.203 52.381 5.05 0.00 0.00 4.46
1959 2075 4.455533 TCATTGGTGTTGCTGCTAGTTTAG 59.544 41.667 0.00 0.00 0.00 1.85
2093 2340 5.478679 ACTTACCGATAGATGGGATCTGAAG 59.521 44.000 0.00 0.00 40.51 3.02
2130 2380 8.306761 CCCAATGATATTAACATTTTAGGGCTC 58.693 37.037 7.29 0.00 36.07 4.70
2131 2381 8.193953 CCCAATGATATTAACATTTTAGGGCT 57.806 34.615 7.29 0.00 36.07 5.19
2132 2382 6.873605 GCCCAATGATATTAACATTTTAGGGC 59.126 38.462 20.28 20.28 46.62 5.19
2252 2502 5.635700 GTCTGAGAAGTTTGCTCGATACTTT 59.364 40.000 0.00 0.00 35.15 2.66
2498 2748 2.092429 TCTTCCCAACTTCAAGCACTGT 60.092 45.455 0.00 0.00 0.00 3.55
2566 2819 1.677966 ACCCATTCAGCAGCAGCAG 60.678 57.895 3.17 0.00 45.49 4.24
2567 2820 1.974875 CACCCATTCAGCAGCAGCA 60.975 57.895 3.17 0.00 45.49 4.41
2568 2821 2.707849 CCACCCATTCAGCAGCAGC 61.708 63.158 0.00 0.00 42.56 5.25
2602 2855 0.249955 CAATGCCAAATGGACCACCC 59.750 55.000 2.98 0.00 37.39 4.61
2865 3118 0.473501 TGCCCCTTTCTTTGGCCAAT 60.474 50.000 21.26 0.00 44.72 3.16
2870 3123 3.380995 GGCTGCCCCTTTCTTTGG 58.619 61.111 7.66 0.00 0.00 3.28
2883 3136 1.367840 GCTAGTGATACGGGGGCTG 59.632 63.158 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.