Multiple sequence alignment - TraesCS5D01G060100

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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 TraesCS5D01G060100 chr5D 100.000 2288 0 0 1 2288 56811997 56809710 0 4226
1 TraesCS5D01G060100 chr5D 88.052 2310 240 25 1 2288 529759100 529761395 0 2704
2 TraesCS5D01G060100 chr4D 85.623 2198 290 15 1 2186 12489211 12491394 0 2285
3 TraesCS5D01G060100 chr7B 83.609 2239 338 20 4 2227 121235038 121237262 0 2074
4 TraesCS5D01G060100 chr1B 80.739 2191 367 48 1 2164 19937334 19939496 0 1657
5 TraesCS5D01G060100 chr1B 80.639 2190 369 48 1 2164 19881682 19883842 0 1644
6 TraesCS5D01G060100 chr1B 80.691 2170 367 45 1 2145 19609665 19611807 0 1639
7 TraesCS5D01G060100 chr1B 80.543 2174 367 47 1 2145 19829371 19831517 0 1620
8 TraesCS5D01G060100 chr1B 80.320 2190 383 42 1 2166 651707840 651710005 0 1613
9 TraesCS5D01G060100 chr1B 80.479 2172 367 46 1 2145 19677620 19679761 0 1609


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 TraesCS5D01G060100 chr5D 56809710 56811997 2287 True 4226 4226 100.000 1 2288 1 chr5D.!!$R1 2287
1 TraesCS5D01G060100 chr5D 529759100 529761395 2295 False 2704 2704 88.052 1 2288 1 chr5D.!!$F1 2287
2 TraesCS5D01G060100 chr4D 12489211 12491394 2183 False 2285 2285 85.623 1 2186 1 chr4D.!!$F1 2185
3 TraesCS5D01G060100 chr7B 121235038 121237262 2224 False 2074 2074 83.609 4 2227 1 chr7B.!!$F1 2223
4 TraesCS5D01G060100 chr1B 19937334 19939496 2162 False 1657 1657 80.739 1 2164 1 chr1B.!!$F5 2163
5 TraesCS5D01G060100 chr1B 19881682 19883842 2160 False 1644 1644 80.639 1 2164 1 chr1B.!!$F4 2163
6 TraesCS5D01G060100 chr1B 19609665 19611807 2142 False 1639 1639 80.691 1 2145 1 chr1B.!!$F1 2144
7 TraesCS5D01G060100 chr1B 19829371 19831517 2146 False 1620 1620 80.543 1 2145 1 chr1B.!!$F3 2144
8 TraesCS5D01G060100 chr1B 651707840 651710005 2165 False 1613 1613 80.320 1 2166 1 chr1B.!!$F6 2165
9 TraesCS5D01G060100 chr1B 19677620 19679761 2141 False 1609 1609 80.479 1 2145 1 chr1B.!!$F2 2144

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
891 903 2.25577 AGGACTTTGGAGGTCTAGGG 57.744 55.0 0.0 0.0 34.47 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 1883 0.321671 CCTTGCCACTTCTCGGAGAA 59.678 55.0 18.74 18.74 34.09 2.87 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
33 34 6.051717 GCTTCATTCTATCCACTCTAGCAAA 58.948 40.000 0.00 0.00 0.00 3.68
65 66 6.183360 GGTCTGGTCCTTAAGTTAGACTATGG 60.183 46.154 17.55 3.04 35.93 2.74
72 73 8.041919 GTCCTTAAGTTAGACTATGGAAAAGCT 58.958 37.037 0.97 0.00 0.00 3.74
81 82 6.974965 AGACTATGGAAAAGCTTTTGACAAG 58.025 36.000 28.42 22.51 0.00 3.16
122 125 4.264373 AGGAGCTCCTCAGATTTAGAGT 57.736 45.455 30.40 2.58 44.77 3.24
165 168 5.831103 ACCCATTGGATCAAACAGATTACT 58.169 37.500 3.62 0.00 37.00 2.24
171 174 6.312141 TGGATCAAACAGATTACTCATGGA 57.688 37.500 0.00 0.00 37.00 3.41
190 193 3.117701 TGGAGGTTCAATTGGTGTCAAGA 60.118 43.478 5.42 0.00 36.19 3.02
232 236 5.155905 ACTTCTTTCTCACTAGGAAAGGGA 58.844 41.667 15.64 7.77 45.49 4.20
273 277 6.406849 CCATATCCCCATTGTTGTTTAACCTG 60.407 42.308 0.00 0.00 35.92 4.00
310 314 8.478775 TCTTACTAGGATGCTGATAAAAGCTA 57.521 34.615 0.00 0.00 43.90 3.32
357 361 2.608988 CCTGAGGTCTGCCCTGGT 60.609 66.667 0.00 0.00 46.51 4.00
510 515 9.503399 AACAAAAGTGAGTTAATCCCTACTAAG 57.497 33.333 0.00 0.00 0.00 2.18
519 524 8.568617 AGTTAATCCCTACTAAGTTGGATGAT 57.431 34.615 0.00 0.00 37.66 2.45
552 557 4.878397 GTCAGTTTCATAGAGATGTTGGGG 59.122 45.833 0.00 0.00 34.41 4.96
741 753 7.084268 AGCTAGTATCCCAATTTATCTGCTT 57.916 36.000 0.00 0.00 0.00 3.91
753 765 7.758528 CCAATTTATCTGCTTTCCTTCTTCAAG 59.241 37.037 0.00 0.00 0.00 3.02
891 903 2.255770 AGGACTTTGGAGGTCTAGGG 57.744 55.000 0.00 0.00 34.47 3.53
975 987 3.960755 AGGAAGGAACAAAACCTTGGAAG 59.039 43.478 0.00 0.00 46.14 3.46
981 993 7.086685 AGGAACAAAACCTTGGAAGTCTATA 57.913 36.000 0.00 0.00 36.82 1.31
1029 1041 6.294731 GGAAACCTAATCTGTTTGCTGTCAAT 60.295 38.462 0.00 0.00 39.87 2.57
1032 1044 4.946157 CCTAATCTGTTTGCTGTCAATCCT 59.054 41.667 0.00 0.00 31.33 3.24
1035 1047 7.284034 CCTAATCTGTTTGCTGTCAATCCTAAT 59.716 37.037 0.00 0.00 31.33 1.73
1040 1052 5.183713 TGTTTGCTGTCAATCCTAATCCAAG 59.816 40.000 0.00 0.00 31.33 3.61
1046 1058 6.560003 TGTCAATCCTAATCCAAGCTCTTA 57.440 37.500 0.00 0.00 0.00 2.10
1128 1145 1.896694 CAGTGGAGAGAGGGTCAGC 59.103 63.158 0.00 0.00 0.00 4.26
1155 1172 2.629051 GAAGATACCTGGTTTGGGACG 58.371 52.381 3.84 0.00 0.00 4.79
1159 1176 1.354101 TACCTGGTTTGGGACGTCAT 58.646 50.000 18.91 0.00 0.00 3.06
1170 1187 2.299521 GGGACGTCATCACTAGCTACT 58.700 52.381 18.91 0.00 0.00 2.57
1174 1191 4.344448 GACGTCATCACTAGCTACTCAAC 58.656 47.826 11.55 0.00 0.00 3.18
1189 1206 2.175202 CTCAACTCTGGCCTGTCTACT 58.825 52.381 3.32 0.00 0.00 2.57
1191 1208 3.764434 CTCAACTCTGGCCTGTCTACTTA 59.236 47.826 3.32 0.00 0.00 2.24
1203 1220 5.181245 GCCTGTCTACTTAGTTTGCAATGAA 59.819 40.000 0.00 0.00 0.00 2.57
1285 1302 5.655532 AGGAATTTTGATAGCAAGCTCATGT 59.344 36.000 0.00 0.00 35.04 3.21
1305 1322 2.698855 AGCAATGGTACCAGCTAGTG 57.301 50.000 23.36 14.88 35.19 2.74
1320 1337 2.114616 CTAGTGGAGATTGCTGGGAGT 58.885 52.381 0.00 0.00 0.00 3.85
1386 1403 6.126420 TGGAAAGTAAAGGGGTTTACTCTTCA 60.126 38.462 20.02 9.78 44.41 3.02
1392 1409 2.028020 AGGGGTTTACTCTTCAAGCTCG 60.028 50.000 0.00 0.00 0.00 5.03
1393 1410 2.289506 GGGGTTTACTCTTCAAGCTCGT 60.290 50.000 0.00 0.00 0.00 4.18
1395 1412 3.813724 GGGTTTACTCTTCAAGCTCGTTT 59.186 43.478 0.00 0.00 0.00 3.60
1452 1470 3.565764 TTCATCCCTGCAGTATGGAAG 57.434 47.619 20.30 13.90 34.45 3.46
1463 1481 4.895889 TGCAGTATGGAAGCTCTATGTACT 59.104 41.667 0.00 0.00 35.86 2.73
1552 1571 7.004086 TGAGGAAAAGACACATCATAAAACCT 58.996 34.615 0.00 0.00 0.00 3.50
1561 1580 5.182001 ACACATCATAAAACCTCTTGAGTGC 59.818 40.000 0.00 0.00 0.00 4.40
1569 1588 2.919228 ACCTCTTGAGTGCGTCTTTTT 58.081 42.857 0.00 0.00 0.00 1.94
1574 1593 5.196341 TCTTGAGTGCGTCTTTTTCTCTA 57.804 39.130 0.00 0.00 0.00 2.43
1578 1597 3.067833 AGTGCGTCTTTTTCTCTAAGGC 58.932 45.455 0.00 0.00 0.00 4.35
1579 1598 2.806244 GTGCGTCTTTTTCTCTAAGGCA 59.194 45.455 0.00 0.00 0.00 4.75
1592 1613 5.010282 TCTCTAAGGCAGAAACCAATTTCC 58.990 41.667 0.00 0.00 44.66 3.13
1593 1614 4.735369 TCTAAGGCAGAAACCAATTTCCA 58.265 39.130 0.00 0.00 44.66 3.53
1596 1617 3.308401 AGGCAGAAACCAATTTCCACTT 58.692 40.909 0.00 0.00 44.66 3.16
1858 1883 2.648059 CTCAAATTCTGGGCGATCCTT 58.352 47.619 0.00 0.00 36.20 3.36
1865 1890 1.676678 CTGGGCGATCCTTTCTCCGA 61.677 60.000 0.00 0.00 36.20 4.55
1866 1892 1.068250 GGGCGATCCTTTCTCCGAG 59.932 63.158 0.00 0.00 29.21 4.63
1883 1909 1.831580 GAGAAGTGGCAAGGCAAGAT 58.168 50.000 0.00 0.00 0.00 2.40
2012 2038 1.118838 AAGCTGAAGATCTCGGAGGG 58.881 55.000 4.96 0.00 31.20 4.30
2092 2118 2.186125 GCCCGGTTTCGACCCTAG 59.814 66.667 0.00 0.00 39.00 3.02
2093 2119 2.186125 CCCGGTTTCGACCCTAGC 59.814 66.667 0.00 0.00 39.00 3.42
2094 2120 2.356780 CCCGGTTTCGACCCTAGCT 61.357 63.158 0.00 0.00 39.00 3.32
2096 2122 1.590147 CGGTTTCGACCCTAGCTGT 59.410 57.895 0.00 0.00 39.00 4.40
2109 2138 2.746359 GCTGTCTGCTGGTCACCT 59.254 61.111 0.00 0.00 38.95 4.00
2166 2195 0.530211 CCAGCGAGATGGAAGCAGAG 60.530 60.000 0.27 0.00 43.57 3.35
2170 2199 0.107993 CGAGATGGAAGCAGAGCCAA 60.108 55.000 0.00 0.00 37.78 4.52
2230 2269 1.067706 CCTGCGTGCCAAAATGAATGA 60.068 47.619 0.00 0.00 0.00 2.57
2232 2271 3.255725 CTGCGTGCCAAAATGAATGAAT 58.744 40.909 0.00 0.00 0.00 2.57
2235 2274 4.624882 TGCGTGCCAAAATGAATGAATAAC 59.375 37.500 0.00 0.00 0.00 1.89
2236 2275 4.624882 GCGTGCCAAAATGAATGAATAACA 59.375 37.500 0.00 0.00 0.00 2.41
2242 2281 9.064706 TGCCAAAATGAATGAATAACATGTTTT 57.935 25.926 17.78 5.99 39.39 2.43
2271 2311 9.355916 AGCTTTTCCTAAGTACTTCATTTTCTT 57.644 29.630 12.39 0.00 0.00 2.52
2272 2312 9.967346 GCTTTTCCTAAGTACTTCATTTTCTTT 57.033 29.630 12.39 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 6.183360 GCTCCTCAAGGAATTCTAAATTGACC 60.183 42.308 5.23 0.00 44.91 4.02
133 136 1.289244 ATCCAATGGGTCCACTCCCC 61.289 60.000 0.00 0.00 46.48 4.81
135 138 0.918983 TGATCCAATGGGTCCACTCC 59.081 55.000 10.47 0.00 34.93 3.85
136 139 2.755103 GTTTGATCCAATGGGTCCACTC 59.245 50.000 10.47 0.00 34.93 3.51
137 140 2.109834 TGTTTGATCCAATGGGTCCACT 59.890 45.455 10.47 0.00 34.93 4.00
138 141 2.493278 CTGTTTGATCCAATGGGTCCAC 59.507 50.000 10.47 7.50 34.93 4.02
165 168 3.181435 TGACACCAATTGAACCTCCATGA 60.181 43.478 7.12 0.00 0.00 3.07
171 174 6.549364 TGTTTATCTTGACACCAATTGAACCT 59.451 34.615 7.12 0.00 0.00 3.50
273 277 4.471548 TCCTAGTAAGAGCATCCACTACC 58.528 47.826 0.00 0.00 33.50 3.18
310 314 3.087031 CTGCAATCATCTCCTGGTTTGT 58.913 45.455 0.00 0.00 0.00 2.83
357 361 4.659115 CATATTGAAGGCAGATGATCCCA 58.341 43.478 0.00 0.00 0.00 4.37
421 426 3.456277 AGGACCATCTTAAGGTTAGCAGG 59.544 47.826 1.85 0.00 40.09 4.85
498 503 5.672194 ACCATCATCCAACTTAGTAGGGATT 59.328 40.000 13.61 1.51 38.05 3.01
506 511 5.707298 ACAGTTTCACCATCATCCAACTTAG 59.293 40.000 0.00 0.00 0.00 2.18
510 515 3.820467 TGACAGTTTCACCATCATCCAAC 59.180 43.478 0.00 0.00 0.00 3.77
540 545 0.037303 CAGTGCACCCCAACATCTCT 59.963 55.000 14.63 0.00 0.00 3.10
662 668 3.532102 AGTAGTTTCCCTCTCCAACCAT 58.468 45.455 0.00 0.00 0.00 3.55
741 753 6.010219 CCATTTAGGGAACTTGAAGAAGGAA 58.990 40.000 0.00 0.00 43.67 3.36
857 869 6.043243 TCCAAAGTCCTTCTTCATACAGACTT 59.957 38.462 0.00 0.00 44.23 3.01
858 870 5.544176 TCCAAAGTCCTTCTTCATACAGACT 59.456 40.000 0.00 0.00 36.17 3.24
859 871 5.794894 TCCAAAGTCCTTCTTCATACAGAC 58.205 41.667 0.00 0.00 35.02 3.51
987 999 9.944079 TTAGGTTTCCCCATCATATATTTTTGA 57.056 29.630 0.00 0.00 34.66 2.69
1029 1041 4.362677 ACCTGTAAGAGCTTGGATTAGGA 58.637 43.478 9.82 0.00 34.07 2.94
1032 1044 7.610305 CCTTTAAACCTGTAAGAGCTTGGATTA 59.390 37.037 0.00 0.00 34.07 1.75
1035 1047 5.072600 TCCTTTAAACCTGTAAGAGCTTGGA 59.927 40.000 0.00 0.00 34.07 3.53
1040 1052 7.448748 TGAAATCCTTTAAACCTGTAAGAGC 57.551 36.000 0.00 0.00 34.07 4.09
1128 1145 4.265073 CAAACCAGGTATCTTCCCAGAAG 58.735 47.826 0.00 0.00 30.76 2.85
1155 1172 5.449862 CCAGAGTTGAGTAGCTAGTGATGAC 60.450 48.000 5.62 0.00 0.00 3.06
1159 1176 2.755655 GCCAGAGTTGAGTAGCTAGTGA 59.244 50.000 5.62 0.00 0.00 3.41
1170 1187 2.310779 AGTAGACAGGCCAGAGTTGA 57.689 50.000 5.01 0.00 0.00 3.18
1174 1191 4.499183 CAAACTAAGTAGACAGGCCAGAG 58.501 47.826 5.01 0.00 0.00 3.35
1203 1220 9.074576 CAAACCTCCCTAATAGTTTTAGTTTGT 57.925 33.333 0.00 0.00 36.96 2.83
1220 1237 0.999712 TTCTCCATCCCAAACCTCCC 59.000 55.000 0.00 0.00 0.00 4.30
1285 1302 2.434336 CCACTAGCTGGTACCATTGCTA 59.566 50.000 26.02 26.02 37.02 3.49
1305 1322 2.225467 GCAATACTCCCAGCAATCTCC 58.775 52.381 0.00 0.00 0.00 3.71
1320 1337 6.611642 AGTCTATGTCTTCACTAAGGGCAATA 59.388 38.462 0.00 0.00 33.22 1.90
1386 1403 6.430000 AGTTAATCACATGGTAAAACGAGCTT 59.570 34.615 0.00 0.00 0.00 3.74
1392 1409 8.237267 CCTCTGAAGTTAATCACATGGTAAAAC 58.763 37.037 0.00 0.00 0.00 2.43
1393 1410 7.393234 CCCTCTGAAGTTAATCACATGGTAAAA 59.607 37.037 0.00 0.00 0.00 1.52
1395 1412 6.414732 CCCTCTGAAGTTAATCACATGGTAA 58.585 40.000 0.00 0.00 0.00 2.85
1452 1470 7.934120 ACATGAATTTTAGGGAGTACATAGAGC 59.066 37.037 0.00 0.00 0.00 4.09
1463 1481 6.014669 CCACAGGAAAACATGAATTTTAGGGA 60.015 38.462 0.00 0.00 31.90 4.20
1496 1515 8.634335 TCTTTGGTCATCAATTTGTCATAAGA 57.366 30.769 0.00 0.00 34.98 2.10
1518 1537 7.939039 TGATGTGTCTTTTCCTCAAGTTATCTT 59.061 33.333 0.00 0.00 0.00 2.40
1552 1571 4.060038 AGAGAAAAAGACGCACTCAAGA 57.940 40.909 0.00 0.00 0.00 3.02
1561 1580 5.334182 GGTTTCTGCCTTAGAGAAAAAGACG 60.334 44.000 0.00 0.00 40.30 4.18
1569 1588 5.010282 GGAAATTGGTTTCTGCCTTAGAGA 58.990 41.667 1.50 0.00 42.66 3.10
1574 1593 3.308401 AGTGGAAATTGGTTTCTGCCTT 58.692 40.909 1.50 0.00 42.66 4.35
1628 1649 9.388506 CTTAAAGTGATCAGATACAAATGACCT 57.611 33.333 0.00 0.00 0.00 3.85
1738 1759 1.095228 ACAAACACCACAGGACTGCG 61.095 55.000 0.00 0.00 0.00 5.18
1858 1883 0.321671 CCTTGCCACTTCTCGGAGAA 59.678 55.000 18.74 18.74 34.09 2.87
1865 1890 1.891150 CAATCTTGCCTTGCCACTTCT 59.109 47.619 0.00 0.00 0.00 2.85
1866 1892 1.067354 CCAATCTTGCCTTGCCACTTC 60.067 52.381 0.00 0.00 0.00 3.01
1985 2011 3.663025 GAGATCTTCAGCTTATCCCAGC 58.337 50.000 0.00 0.00 40.44 4.85
2012 2038 2.158885 GGGGATTGGAAGCTCTAGTCAC 60.159 54.545 0.00 0.00 0.00 3.67
2092 2118 1.375268 GAGGTGACCAGCAGACAGC 60.375 63.158 3.63 0.00 46.19 4.40
2093 2119 0.394192 TTGAGGTGACCAGCAGACAG 59.606 55.000 3.63 0.00 0.00 3.51
2094 2120 0.394192 CTTGAGGTGACCAGCAGACA 59.606 55.000 3.63 0.00 0.00 3.41
2096 2122 1.123861 AGCTTGAGGTGACCAGCAGA 61.124 55.000 13.94 0.00 0.00 4.26
2166 2195 5.105554 TCAGACTGAAATCTCTAGAGTTGGC 60.106 44.000 19.21 8.66 32.01 4.52
2170 2199 7.096551 GCTTTTCAGACTGAAATCTCTAGAGT 58.903 38.462 26.94 4.45 44.75 3.24
2174 2203 6.212388 AGAGGCTTTTCAGACTGAAATCTCTA 59.788 38.462 31.34 19.65 44.75 2.43
2194 2223 0.813210 CAGGCCAGAAATCGAGAGGC 60.813 60.000 5.01 7.57 44.48 4.70


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

AutoCloner maintained by Alex Coulton.