Multiple sequence alignment - TraesCS6A01G173500

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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 TraesCS6A01G173500 chr6A 100.000 2183 0 0 1 2183 185322855 185320673 0.000000e+00 4032
1 TraesCS6A01G173500 chr6D 92.523 2220 99 23 5 2183 141139168 141136975 0.000000e+00 3118
2 TraesCS6A01G173500 chr6B 90.924 1807 105 22 1 1777 240404583 240402806 0.000000e+00 2374
3 TraesCS6A01G173500 chr6B 94.484 417 11 3 1768 2183 240402771 240402366 1.100000e-177 632


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 TraesCS6A01G173500 chr6A 185320673 185322855 2182 True 4032 4032 100.000 1 2183 1 chr6A.!!$R1 2182
1 TraesCS6A01G173500 chr6D 141136975 141139168 2193 True 3118 3118 92.523 5 2183 1 chr6D.!!$R1 2178
2 TraesCS6A01G173500 chr6B 240402366 240404583 2217 True 1503 2374 92.704 1 2183 2 chr6B.!!$R1 2182

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
861 897 0.043485 GTCCTCCTCCCTTCCTTCCT 59.957 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2251 1.376553 GGGCGAGAAGAAGCTTGCT 60.377 57.895 2.1 0.0 43.42 3.91 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
137 139 3.064545 GCATTCAGCAGTATGAACAGACC 59.935 47.826 0.00 0.00 41.76 3.85
150 152 6.980051 ATGAACAGACCGAATAAAACTACC 57.020 37.500 0.00 0.00 0.00 3.18
151 153 5.240121 TGAACAGACCGAATAAAACTACCC 58.760 41.667 0.00 0.00 0.00 3.69
248 254 1.377229 CTACCCGGCCAAGGAACAA 59.623 57.895 15.70 0.00 0.00 2.83
249 255 0.676782 CTACCCGGCCAAGGAACAAG 60.677 60.000 15.70 3.89 0.00 3.16
250 256 1.128809 TACCCGGCCAAGGAACAAGA 61.129 55.000 15.70 0.00 0.00 3.02
251 257 1.971695 CCCGGCCAAGGAACAAGAC 60.972 63.158 2.24 0.00 0.00 3.01
252 258 1.073199 CCGGCCAAGGAACAAGACT 59.927 57.895 2.24 0.00 0.00 3.24
253 259 0.537371 CCGGCCAAGGAACAAGACTT 60.537 55.000 2.24 0.00 0.00 3.01
254 260 1.318576 CGGCCAAGGAACAAGACTTT 58.681 50.000 2.24 0.00 0.00 2.66
256 262 2.543653 CGGCCAAGGAACAAGACTTTTG 60.544 50.000 2.24 0.00 0.00 2.44
257 263 2.224042 GGCCAAGGAACAAGACTTTTGG 60.224 50.000 10.15 10.15 38.42 3.28
258 264 2.693074 GCCAAGGAACAAGACTTTTGGA 59.307 45.455 16.46 0.00 37.79 3.53
259 265 3.490933 GCCAAGGAACAAGACTTTTGGAC 60.491 47.826 16.46 6.90 37.79 4.02
295 305 6.166982 AGGTTTTACTGCTACACATTCTCTC 58.833 40.000 0.00 0.00 0.00 3.20
303 317 1.805869 ACACATTCTCTCTGCAGTGC 58.194 50.000 14.67 8.58 0.00 4.40
307 321 1.659601 CATTCTCTCTGCAGTGCGAAG 59.340 52.381 21.51 10.31 0.00 3.79
334 357 2.910199 CACACTCGTGAATCCATCCAT 58.090 47.619 3.74 0.00 46.80 3.41
363 386 6.480981 GCAATAGCAATGCAAATTTCCAGTAT 59.519 34.615 8.35 0.00 43.29 2.12
418 441 9.979270 CTTCAGAAAAGTGCATACATAAACTAG 57.021 33.333 0.00 0.00 0.00 2.57
448 472 2.481449 GCCTTCACCTACGTACCAGATG 60.481 54.545 0.00 0.00 0.00 2.90
517 547 7.769044 AGTGTCAACTGTCAAGTTTTATACTGT 59.231 33.333 0.00 0.00 44.47 3.55
518 548 9.037737 GTGTCAACTGTCAAGTTTTATACTGTA 57.962 33.333 0.00 0.00 44.47 2.74
519 549 9.037737 TGTCAACTGTCAAGTTTTATACTGTAC 57.962 33.333 0.00 0.00 44.47 2.90
557 587 8.872845 CCATCCTTCTTAAACAAATACAAATGC 58.127 33.333 0.00 0.00 0.00 3.56
749 785 0.841289 TTCCTCCGTTTGTCAACCCT 59.159 50.000 0.00 0.00 0.00 4.34
858 894 1.990614 GCGTCCTCCTCCCTTCCTT 60.991 63.158 0.00 0.00 0.00 3.36
859 895 1.962321 GCGTCCTCCTCCCTTCCTTC 61.962 65.000 0.00 0.00 0.00 3.46
860 896 1.331399 CGTCCTCCTCCCTTCCTTCC 61.331 65.000 0.00 0.00 0.00 3.46
861 897 0.043485 GTCCTCCTCCCTTCCTTCCT 59.957 60.000 0.00 0.00 0.00 3.36
921 957 2.566724 CTCTCCTTCTGAAACCAGAGCT 59.433 50.000 0.00 0.00 41.27 4.09
925 961 2.354604 CCTTCTGAAACCAGAGCTCTCC 60.355 54.545 14.96 1.57 41.27 3.71
955 991 3.774702 GACGACCGCCGACAAAGC 61.775 66.667 0.00 0.00 41.76 3.51
966 1002 1.902556 GACAAAGCCCTAGCCCGTA 59.097 57.895 0.00 0.00 41.25 4.02
1021 1059 3.179265 CGAGCTTACGCGTGGTGG 61.179 66.667 24.59 9.31 42.32 4.61
1075 1113 4.329545 TGTTGGCGGAGTGCTCCC 62.330 66.667 12.20 5.60 46.96 4.30
1094 1132 4.596180 GCCGTTGCGCGATCATGG 62.596 66.667 12.10 8.50 44.77 3.66
1146 1184 2.962786 CCGGTGTTTGTCGTCGCA 60.963 61.111 0.00 0.00 0.00 5.10
1187 1225 2.412112 CGCCGGTCACTAGTAGCC 59.588 66.667 1.90 0.00 0.00 3.93
1194 1232 1.134560 GGTCACTAGTAGCCGGTTCTG 59.865 57.143 1.90 0.00 0.00 3.02
1197 1235 3.012518 TCACTAGTAGCCGGTTCTGTAC 58.987 50.000 1.90 0.00 0.00 2.90
1203 1241 2.070262 AGCCGGTTCTGTACGTAAAC 57.930 50.000 1.90 0.00 0.00 2.01
1288 1326 3.554960 GGCTGTTTCATTTGTTCTTCCCC 60.555 47.826 0.00 0.00 0.00 4.81
1319 1357 0.730265 CTTCGGTCGGTCTCTCTCTG 59.270 60.000 0.00 0.00 0.00 3.35
1484 1522 7.602753 AGGTGTTATGTTATCTTTTCCTTTGC 58.397 34.615 0.00 0.00 0.00 3.68
1485 1523 6.526674 GGTGTTATGTTATCTTTTCCTTTGCG 59.473 38.462 0.00 0.00 0.00 4.85
1541 1579 8.451908 AAGATTTATTAAGAATCCCAACGGAG 57.548 34.615 9.53 0.00 43.12 4.63
1557 1595 5.971202 CCAACGGAGATTACATAATGTTTGC 59.029 40.000 0.00 0.00 0.00 3.68
1567 1605 7.726033 TTACATAATGTTTGCCCAGGTTTAT 57.274 32.000 0.00 0.00 0.00 1.40
1589 1634 4.508551 TGCTCATGATCACAGGGTAATT 57.491 40.909 0.00 0.00 0.00 1.40
1600 1645 2.081462 CAGGGTAATTGTTGTCGGTCC 58.919 52.381 0.00 0.00 0.00 4.46
1604 1649 2.609350 GTAATTGTTGTCGGTCCGCTA 58.391 47.619 6.34 0.00 0.00 4.26
1854 1957 2.680913 CGTCTGCCGCTTTTCAGGG 61.681 63.158 0.00 0.00 0.00 4.45
1873 1976 7.537596 TCAGGGCTTCATTCAGAAAATAAAA 57.462 32.000 0.00 0.00 35.40 1.52
1877 1980 7.233348 AGGGCTTCATTCAGAAAATAAAACAGA 59.767 33.333 0.00 0.00 35.40 3.41
1998 2101 3.137360 AGGAGGGTTGCTCAATATTCTCC 59.863 47.826 7.25 7.25 39.67 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.815233 TTCTTGGGATGAGGAGATATGAC 57.185 43.478 0.00 0.00 0.00 3.06
54 55 6.709846 GGATTTAGCTATCTGCATATCCATCC 59.290 42.308 0.00 0.00 45.94 3.51
105 107 6.376299 TCATACTGCTGAATGCTGAATCTTTT 59.624 34.615 0.00 0.00 42.27 2.27
122 124 6.092259 AGTTTTATTCGGTCTGTTCATACTGC 59.908 38.462 0.00 0.00 0.00 4.40
137 139 5.447279 GCTGTGTCATGGGTAGTTTTATTCG 60.447 44.000 0.00 0.00 0.00 3.34
150 152 4.391869 AGCAGTGCTGTGTCATGG 57.608 55.556 18.98 0.00 37.57 3.66
180 186 1.003839 TGGTTGGCCAGAGCGTTAG 60.004 57.895 5.11 0.00 40.46 2.34
222 228 3.440415 GGCCGGGTAGCAAAGCAC 61.440 66.667 2.18 0.00 0.00 4.40
271 281 6.014156 AGAGAGAATGTGTAGCAGTAAAACCT 60.014 38.462 0.00 0.00 0.00 3.50
281 291 2.928757 CACTGCAGAGAGAATGTGTAGC 59.071 50.000 23.35 0.00 38.30 3.58
295 305 1.334054 GAATTTGCTTCGCACTGCAG 58.666 50.000 13.48 13.48 38.71 4.41
303 317 2.949714 ACGAGTGTGAATTTGCTTCG 57.050 45.000 0.00 0.00 36.60 3.79
314 328 5.049886 CATAATGGATGGATTCACGAGTGTG 60.050 44.000 2.97 0.00 38.46 3.82
363 386 7.618019 AACTGATTACTGGCAGGAGATATAA 57.382 36.000 20.34 7.43 36.47 0.98
418 441 3.631227 ACGTAGGTGAAGGCTCATACTAC 59.369 47.826 14.38 14.38 39.30 2.73
420 443 2.736347 ACGTAGGTGAAGGCTCATACT 58.264 47.619 0.00 0.00 33.05 2.12
421 444 3.243334 GGTACGTAGGTGAAGGCTCATAC 60.243 52.174 0.00 0.00 33.05 2.39
422 445 2.954318 GGTACGTAGGTGAAGGCTCATA 59.046 50.000 0.00 0.00 33.05 2.15
448 472 5.372373 CCTATCTGGAAATTCAGGTTCTCC 58.628 45.833 0.00 0.00 38.35 3.71
517 547 1.027357 GGATGGACTCCGCGTTAGTA 58.973 55.000 10.91 0.00 33.29 1.82
518 548 1.814527 GGATGGACTCCGCGTTAGT 59.185 57.895 10.75 10.75 33.29 2.24
519 549 4.732106 GGATGGACTCCGCGTTAG 57.268 61.111 4.92 4.57 33.29 2.34
557 587 4.397481 TCAGAGCTGTAGTGAATGGATG 57.603 45.455 0.00 0.00 0.00 3.51
627 658 3.423154 CGCTCAGTTTGACCGGCC 61.423 66.667 0.00 0.00 0.00 6.13
749 785 4.916293 GCGCGCATGGAGGGATGA 62.916 66.667 29.10 0.00 0.00 2.92
858 894 2.206900 TGTTGGCCTGGAGGAGGA 59.793 61.111 3.32 0.00 46.33 3.71
859 895 2.352805 GTGTTGGCCTGGAGGAGG 59.647 66.667 3.32 0.00 46.13 4.30
860 896 2.046892 CGTGTTGGCCTGGAGGAG 60.047 66.667 3.32 0.00 37.39 3.69
861 897 2.525629 TCGTGTTGGCCTGGAGGA 60.526 61.111 3.32 0.00 37.39 3.71
921 957 1.076995 TCGATCGGCAAGAGGGAGA 60.077 57.895 16.41 0.00 0.00 3.71
925 961 1.586564 GTCGTCGATCGGCAAGAGG 60.587 63.158 21.12 2.60 44.22 3.69
955 991 0.031721 GTGTCGATTACGGGCTAGGG 59.968 60.000 0.00 0.00 40.21 3.53
966 1002 1.445582 GTCGAAGGCGGTGTCGATT 60.446 57.895 8.42 0.00 46.91 3.34
1187 1225 4.043750 TCACAAGTTTACGTACAGAACCG 58.956 43.478 0.00 0.00 0.00 4.44
1203 1241 6.483307 ACCGGTGATATGATACATTTCACAAG 59.517 38.462 24.49 19.51 38.71 3.16
1288 1326 2.163815 CCGACCGAAGCCTATACCTATG 59.836 54.545 0.00 0.00 0.00 2.23
1319 1357 7.988028 ACAATTAGCAGTACCTATCTTTTCTCC 59.012 37.037 0.00 0.00 0.00 3.71
1484 1522 2.203252 CCATCTGCACATCCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
1485 1523 1.150081 CTCCATCTGCACATCCCCC 59.850 63.158 0.00 0.00 0.00 5.40
1524 1562 6.302535 TGTAATCTCCGTTGGGATTCTTAA 57.697 37.500 0.00 0.00 42.83 1.85
1525 1563 5.943349 TGTAATCTCCGTTGGGATTCTTA 57.057 39.130 0.00 0.00 42.83 2.10
1526 1564 4.837093 TGTAATCTCCGTTGGGATTCTT 57.163 40.909 0.00 0.00 42.83 2.52
1538 1576 5.010012 CCTGGGCAAACATTATGTAATCTCC 59.990 44.000 0.00 0.00 0.00 3.71
1541 1579 5.852282 ACCTGGGCAAACATTATGTAATC 57.148 39.130 0.00 0.00 0.00 1.75
1557 1595 4.037208 GTGATCATGAGCAATAAACCTGGG 59.963 45.833 16.53 0.00 0.00 4.45
1567 1605 3.998913 TTACCCTGTGATCATGAGCAA 57.001 42.857 16.53 5.51 0.00 3.91
1589 1634 2.260434 GCTAGCGGACCGACAACA 59.740 61.111 20.50 0.00 0.00 3.33
1604 1649 3.070159 TCTTCTGAGTAACTTGTGCAGCT 59.930 43.478 0.00 0.00 0.00 4.24
1664 1709 4.088634 TCCTTCCAAATTTGATGGTCCTG 58.911 43.478 19.86 0.26 39.09 3.86
1666 1711 4.082026 CACTCCTTCCAAATTTGATGGTCC 60.082 45.833 19.86 0.00 39.09 4.46
1854 1957 9.683069 TCTTCTGTTTTATTTTCTGAATGAAGC 57.317 29.630 0.00 0.00 35.89 3.86
1873 1976 5.073428 TGCTATCTATCGGACATCTTCTGT 58.927 41.667 0.00 0.00 42.15 3.41
1877 1980 5.279206 CCAACTGCTATCTATCGGACATCTT 60.279 44.000 0.00 0.00 0.00 2.40
1977 2080 3.481453 GGAGAATATTGAGCAACCCTCC 58.519 50.000 0.00 0.00 39.98 4.30
1998 2101 2.609737 GGGTAACAGGAGAACACACTCG 60.610 54.545 0.00 0.00 36.57 4.18
2148 2251 1.376553 GGGCGAGAAGAAGCTTGCT 60.377 57.895 2.10 0.00 43.42 3.91


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

AutoCloner maintained by Alex Coulton.