Multiple sequence alignment - TraesCS3B01G235700

Loading Multiple Alignment...

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 TraesCS3B01G235700 chr3B 100.000 2321 0 0 1 2321 368725297 368727617 0 4287
1 TraesCS3B01G235700 chr3B 97.313 856 22 1 1 856 368705030 368705884 0 1452
2 TraesCS3B01G235700 chr5B 95.856 1472 56 3 851 2321 679659746 679661213 0 2375
3 TraesCS3B01G235700 chr5B 89.884 860 78 9 1 856 190834613 190835467 0 1098
4 TraesCS3B01G235700 chr5B 89.779 861 77 11 1 856 190842162 190843016 0 1092
5 TraesCS3B01G235700 chrUn 95.720 1472 57 3 851 2321 189393389 189394855 0 2364
6 TraesCS3B01G235700 chrUn 85.867 842 108 11 21 856 170361883 170361047 0 885
7 TraesCS3B01G235700 chrUn 85.629 842 110 11 21 856 174107883 174108719 0 874
8 TraesCS3B01G235700 chr5A 95.720 1472 57 3 851 2321 300073829 300075295 0 2364
9 TraesCS3B01G235700 chr5A 95.380 1472 60 3 851 2321 16602071 16600607 0 2335
10 TraesCS3B01G235700 chr2A 95.652 1472 58 3 851 2321 618279106 618277640 0 2359
11 TraesCS3B01G235700 chr7D 95.448 1472 61 3 851 2321 626697640 626696174 0 2342
12 TraesCS3B01G235700 chr7D 95.380 1472 62 3 851 2321 203555496 203554030 0 2337
13 TraesCS3B01G235700 chr7B 95.451 1473 60 5 851 2321 743087048 743088515 0 2342
14 TraesCS3B01G235700 chr7B 86.429 840 106 8 21 856 301043531 301042696 0 913
15 TraesCS3B01G235700 chr6A 95.448 1472 60 3 851 2321 289129481 289130946 0 2340
16 TraesCS3B01G235700 chr6B 88.515 862 85 14 1 856 335506618 335505765 0 1031
17 TraesCS3B01G235700 chr4B 87.857 840 94 7 21 856 320836202 320837037 0 979
18 TraesCS3B01G235700 chr4B 87.247 839 101 6 21 856 320828137 320828972 0 952


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 TraesCS3B01G235700 chr3B 368725297 368727617 2320 False 4287 4287 100.000 1 2321 1 chr3B.!!$F2 2320
1 TraesCS3B01G235700 chr3B 368705030 368705884 854 False 1452 1452 97.313 1 856 1 chr3B.!!$F1 855
2 TraesCS3B01G235700 chr5B 679659746 679661213 1467 False 2375 2375 95.856 851 2321 1 chr5B.!!$F3 1470
3 TraesCS3B01G235700 chr5B 190834613 190835467 854 False 1098 1098 89.884 1 856 1 chr5B.!!$F1 855
4 TraesCS3B01G235700 chr5B 190842162 190843016 854 False 1092 1092 89.779 1 856 1 chr5B.!!$F2 855
5 TraesCS3B01G235700 chrUn 189393389 189394855 1466 False 2364 2364 95.720 851 2321 1 chrUn.!!$F2 1470
6 TraesCS3B01G235700 chrUn 170361047 170361883 836 True 885 885 85.867 21 856 1 chrUn.!!$R1 835
7 TraesCS3B01G235700 chrUn 174107883 174108719 836 False 874 874 85.629 21 856 1 chrUn.!!$F1 835
8 TraesCS3B01G235700 chr5A 300073829 300075295 1466 False 2364 2364 95.720 851 2321 1 chr5A.!!$F1 1470
9 TraesCS3B01G235700 chr5A 16600607 16602071 1464 True 2335 2335 95.380 851 2321 1 chr5A.!!$R1 1470
10 TraesCS3B01G235700 chr2A 618277640 618279106 1466 True 2359 2359 95.652 851 2321 1 chr2A.!!$R1 1470
11 TraesCS3B01G235700 chr7D 626696174 626697640 1466 True 2342 2342 95.448 851 2321 1 chr7D.!!$R2 1470
12 TraesCS3B01G235700 chr7D 203554030 203555496 1466 True 2337 2337 95.380 851 2321 1 chr7D.!!$R1 1470
13 TraesCS3B01G235700 chr7B 743087048 743088515 1467 False 2342 2342 95.451 851 2321 1 chr7B.!!$F1 1470
14 TraesCS3B01G235700 chr7B 301042696 301043531 835 True 913 913 86.429 21 856 1 chr7B.!!$R1 835
15 TraesCS3B01G235700 chr6A 289129481 289130946 1465 False 2340 2340 95.448 851 2321 1 chr6A.!!$F1 1470
16 TraesCS3B01G235700 chr6B 335505765 335506618 853 True 1031 1031 88.515 1 856 1 chr6B.!!$R1 855
17 TraesCS3B01G235700 chr4B 320836202 320837037 835 False 979 979 87.857 21 856 1 chr4B.!!$F2 835
18 TraesCS3B01G235700 chr4B 320828137 320828972 835 False 952 952 87.247 21 856 1 chr4B.!!$F1 835

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
790 799 1.082756 GTGCTTCCGCGTGTTCTTG 60.083 57.895 4.92 0.0 39.65 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 1940 0.976641 TACCACAAGCTCTGACCTGG 59.023 55.0 0.0 0.0 0.0 4.45 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
109 110 1.940883 TACTACCGCTGAAGCCACCG 61.941 60.000 0.00 0.00 37.91 4.94
279 281 1.134280 CATACACCTCCAGAAGCCAGG 60.134 57.143 0.00 0.00 0.00 4.45
488 491 5.042827 TCCACCTCCTCCTAGTTAGGTTTAT 60.043 44.000 5.16 0.00 44.02 1.40
790 799 1.082756 GTGCTTCCGCGTGTTCTTG 60.083 57.895 4.92 0.00 39.65 3.02
838 847 3.615614 ACGTGAAAGATCGACGCTATAC 58.384 45.455 8.80 0.00 35.15 1.47
872 881 3.160269 CATCAGAACCCTTTCCTGCTTT 58.840 45.455 0.00 0.00 31.28 3.51
888 897 3.831911 CTGCTTTCCCTTTTTACCCATCA 59.168 43.478 0.00 0.00 0.00 3.07
915 925 6.097554 ACTCGACTCACATTTTGATCTCCTAT 59.902 38.462 0.00 0.00 32.17 2.57
933 943 2.283145 ATGCTTGCTTTCACAGTCCT 57.717 45.000 0.00 0.00 0.00 3.85
966 976 3.684413 GCCCGGAATCAATGAAGGAGTTA 60.684 47.826 0.73 0.00 0.00 2.24
999 1010 1.007319 GTCGAGCGAGCGTAATTCAAC 60.007 52.381 0.00 0.00 0.00 3.18
1049 1060 3.119495 GCCTTATCACGAAAGCCACATTT 60.119 43.478 0.00 0.00 0.00 2.32
1070 1081 2.605818 TGTTTCGTTTGAGGAAGTCACG 59.394 45.455 0.00 0.00 33.71 4.35
1075 1086 0.387929 TTTGAGGAAGTCACGCGTCT 59.612 50.000 9.86 0.95 33.71 4.18
1082 1093 0.179094 AAGTCACGCGTCTTGTTCCA 60.179 50.000 9.86 0.00 0.00 3.53
1162 1173 1.281867 CCCCTATCACAAGACCAAGCA 59.718 52.381 0.00 0.00 0.00 3.91
1302 1313 6.273825 ACTACCGCTTCTACACATAAATCAG 58.726 40.000 0.00 0.00 0.00 2.90
1351 1362 8.514136 TTTCGTTAATGGCTAAAATGTTCTTG 57.486 30.769 0.00 0.00 0.00 3.02
1366 1377 0.260230 TCTTGGTGAAAGGGTTGCCA 59.740 50.000 0.00 0.00 36.46 4.92
1393 1404 0.603975 GGCAAACTCAGAGCGGTCTT 60.604 55.000 15.83 0.00 0.00 3.01
1395 1406 2.413837 GCAAACTCAGAGCGGTCTTTA 58.586 47.619 15.83 5.30 0.00 1.85
1436 1447 2.973694 GCATCATCCAAGCCAAACAT 57.026 45.000 0.00 0.00 0.00 2.71
1447 1458 1.701847 AGCCAAACATGTCTCCTCAGT 59.298 47.619 0.00 0.00 0.00 3.41
1448 1459 2.079925 GCCAAACATGTCTCCTCAGTC 58.920 52.381 0.00 0.00 0.00 3.51
1449 1460 2.341257 CCAAACATGTCTCCTCAGTCG 58.659 52.381 0.00 0.00 0.00 4.18
1533 1544 1.153449 CCGCCCGCTCTCAATACAA 60.153 57.895 0.00 0.00 0.00 2.41
1590 1601 5.937975 ACCGATTCATCCAATCCAATTTT 57.062 34.783 0.00 0.00 38.17 1.82
1591 1602 5.906073 ACCGATTCATCCAATCCAATTTTC 58.094 37.500 0.00 0.00 38.17 2.29
1601 1612 5.047802 TCCAATCCAATTTTCTCAGAAGTGC 60.048 40.000 0.00 0.00 0.00 4.40
1602 1613 5.279106 CCAATCCAATTTTCTCAGAAGTGCA 60.279 40.000 0.00 0.00 0.00 4.57
1753 1764 5.127194 TGCGATTAGAAACCAGTGACTCTAT 59.873 40.000 0.00 0.00 0.00 1.98
1762 1773 2.424957 CCAGTGACTCTATAGCCAGGGA 60.425 54.545 0.00 0.00 0.00 4.20
1802 1813 7.321530 AGATATAAAGAATGGGGAGTTAGGGA 58.678 38.462 0.00 0.00 0.00 4.20
1814 1825 3.054582 GGAGTTAGGGATTCGGTTTCCTT 60.055 47.826 0.00 0.00 33.53 3.36
1929 1940 3.568007 TGGGTGAATCAAGTACAACAAGC 59.432 43.478 0.00 0.00 0.00 4.01
1962 1973 1.559682 TGTGGTAGAAGATTGGGCTCC 59.440 52.381 0.00 0.00 0.00 4.70
2009 2020 3.868757 AGAAGTACGCATTGCTGACTA 57.131 42.857 7.12 0.00 0.00 2.59
2021 2032 5.733091 GCATTGCTGACTAACTGTTTGAACA 60.733 40.000 8.91 7.46 37.37 3.18
2027 2038 6.566753 GCTGACTAACTGTTTGAACAATCCTC 60.567 42.308 8.91 0.00 38.66 3.71
2101 2112 1.300853 CCCCCAAAAGCAAAGCACG 60.301 57.895 0.00 0.00 0.00 5.34
2120 2131 1.676916 CGGACTCTACTCACCCACGTA 60.677 57.143 0.00 0.00 0.00 3.57
2134 2145 2.094078 CCCACGTATTTTCCACCTACGA 60.094 50.000 8.17 0.00 40.38 3.43
2211 2222 3.546417 CGAGAGTGGATAGCGTGACTAAC 60.546 52.174 0.00 0.00 33.57 2.34
2212 2223 3.353557 AGAGTGGATAGCGTGACTAACA 58.646 45.455 0.00 0.00 33.57 2.41
2217 2228 2.159085 GGATAGCGTGACTAACAAGGCT 60.159 50.000 0.00 0.00 41.31 4.58
2221 2232 1.993370 GCGTGACTAACAAGGCTGTAG 59.007 52.381 0.00 0.00 33.45 2.74
2224 2235 3.921021 CGTGACTAACAAGGCTGTAGAAG 59.079 47.826 7.03 0.00 33.45 2.85
2285 2296 5.075670 CGAGAGCAGCATAATTGTTAGTG 57.924 43.478 0.00 0.00 0.00 2.74
2289 2300 4.848357 AGCAGCATAATTGTTAGTGAGGT 58.152 39.130 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 262 1.207791 CCTGGCTTCTGGAGGTGTAT 58.792 55.000 0.00 0.00 0.00 2.29
282 284 1.537814 TAGTTCCGCTCGAAGCCCAA 61.538 55.000 0.00 0.00 38.18 4.12
488 491 7.774625 TCACACAAATATGAGCTAATCCAATGA 59.225 33.333 0.00 0.00 0.00 2.57
809 818 2.069273 CGATCTTTCACGTTTGGAGCT 58.931 47.619 0.00 0.00 0.00 4.09
838 847 3.458189 GTTCTGATGTAGGATGGAACCG 58.542 50.000 0.00 0.00 34.73 4.44
846 855 3.519510 CAGGAAAGGGTTCTGATGTAGGA 59.480 47.826 0.00 0.00 33.92 2.94
872 881 3.055385 CGAGTCTGATGGGTAAAAAGGGA 60.055 47.826 0.00 0.00 0.00 4.20
888 897 5.398603 AGATCAAAATGTGAGTCGAGTCT 57.601 39.130 20.51 0.00 40.43 3.24
915 925 1.597742 GAGGACTGTGAAAGCAAGCA 58.402 50.000 0.00 0.00 0.00 3.91
933 943 3.949885 TTCCGGGCTGCTCGTAGGA 62.950 63.158 21.69 8.27 0.00 2.94
966 976 0.737715 GCTCGACTCGGTGCTGAATT 60.738 55.000 0.00 0.00 0.00 2.17
999 1010 5.408299 TCCTTCGTTCAGTACAATCAACATG 59.592 40.000 0.00 0.00 0.00 3.21
1049 1060 2.605818 CGTGACTTCCTCAAACGAAACA 59.394 45.455 0.00 0.00 0.00 2.83
1114 1125 4.719273 AGGAGGAAGAAGAGGGTATTTCTG 59.281 45.833 0.00 0.00 34.09 3.02
1121 1132 2.545810 CTTGAGGAGGAAGAAGAGGGT 58.454 52.381 0.00 0.00 0.00 4.34
1162 1173 3.638160 GAGTCTTCTGCAGGATGAGATCT 59.362 47.826 15.13 0.00 39.69 2.75
1216 1227 2.887783 ACGAGAATAGATCACATCCGCT 59.112 45.455 0.00 0.00 0.00 5.52
1302 1313 3.065925 GCCACTATTCCACAATGCTTCTC 59.934 47.826 0.00 0.00 0.00 2.87
1351 1362 0.827368 TTTGTGGCAACCCTTTCACC 59.173 50.000 0.00 0.00 0.00 4.02
1366 1377 1.676006 CTCTGAGTTTGCCGGTTTTGT 59.324 47.619 1.90 0.00 0.00 2.83
1393 1404 5.758296 CCGCTATGCTCCTATTCACTTTTAA 59.242 40.000 0.00 0.00 0.00 1.52
1395 1406 4.130118 CCGCTATGCTCCTATTCACTTTT 58.870 43.478 0.00 0.00 0.00 2.27
1436 1447 1.248486 CCTTGACGACTGAGGAGACA 58.752 55.000 0.00 0.00 32.11 3.41
1447 1458 1.585006 GCGAGAAGACCCTTGACGA 59.415 57.895 0.00 0.00 0.00 4.20
1448 1459 1.801913 CGCGAGAAGACCCTTGACG 60.802 63.158 0.00 0.00 0.00 4.35
1449 1460 2.095252 GCGCGAGAAGACCCTTGAC 61.095 63.158 12.10 0.00 0.00 3.18
1533 1544 4.037446 GTCTTGTGAGAGAGAGTCACTTGT 59.963 45.833 4.96 0.00 44.02 3.16
1590 1601 4.823442 ACAACAATGAATGCACTTCTGAGA 59.177 37.500 0.00 0.00 34.75 3.27
1591 1602 5.117355 ACAACAATGAATGCACTTCTGAG 57.883 39.130 0.00 0.00 34.75 3.35
1601 1612 7.008266 GGTTTCGCTATACAACAACAATGAATG 59.992 37.037 0.00 0.00 0.00 2.67
1602 1613 7.027161 GGTTTCGCTATACAACAACAATGAAT 58.973 34.615 0.00 0.00 0.00 2.57
1663 1674 4.045207 ACCCTGATCTGGATAGATAGCTCA 59.955 45.833 19.59 0.00 43.63 4.26
1782 1793 5.163237 CGAATCCCTAACTCCCCATTCTTTA 60.163 44.000 0.00 0.00 0.00 1.85
1802 1813 3.081804 CTGGCTACAAAGGAAACCGAAT 58.918 45.455 0.00 0.00 0.00 3.34
1814 1825 5.860941 TTTGGAATTGAAACTGGCTACAA 57.139 34.783 0.00 0.00 0.00 2.41
1929 1940 0.976641 TACCACAAGCTCTGACCTGG 59.023 55.000 0.00 0.00 0.00 4.45
2009 2020 5.820947 AGTAACGAGGATTGTTCAAACAGTT 59.179 36.000 0.00 0.00 38.69 3.16
2021 2032 8.461249 TTGATTAGCTACTAGTAACGAGGATT 57.539 34.615 3.76 0.00 0.00 3.01
2027 2038 7.917597 TCTGACTTGATTAGCTACTAGTAACG 58.082 38.462 3.76 0.00 0.00 3.18
2101 2112 2.119801 TACGTGGGTGAGTAGAGTCC 57.880 55.000 0.00 0.00 0.00 3.85
2120 2131 3.178865 TCTCCCTTCGTAGGTGGAAAAT 58.821 45.455 7.37 0.00 40.19 1.82
2134 2145 7.084268 AGGATATTTCGATGATTTCTCCCTT 57.916 36.000 0.00 0.00 0.00 3.95
2184 2195 1.140452 ACGCTATCCACTCTCGTCCTA 59.860 52.381 0.00 0.00 0.00 2.94
2202 2213 3.570926 TCTACAGCCTTGTTAGTCACG 57.429 47.619 0.00 0.00 38.76 4.35
2211 2222 4.865365 GCACTACTAACTTCTACAGCCTTG 59.135 45.833 0.00 0.00 0.00 3.61
2212 2223 4.527038 TGCACTACTAACTTCTACAGCCTT 59.473 41.667 0.00 0.00 0.00 4.35
2217 2228 8.896320 TCAAAAATGCACTACTAACTTCTACA 57.104 30.769 0.00 0.00 0.00 2.74
2221 2232 9.899226 ATCTTTCAAAAATGCACTACTAACTTC 57.101 29.630 0.00 0.00 0.00 3.01
2285 2296 1.328430 CCCGTCCCCTCTTACACCTC 61.328 65.000 0.00 0.00 0.00 3.85
2289 2300 2.686106 GGCCCGTCCCCTCTTACA 60.686 66.667 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.