Multiple sequence alignment - TraesCS6A01G275400

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 TraesCS6A01G275400 chr6A 100.000 1747 0 0 632 2378 501887078 501888824 0.000000e+00 3227
1 TraesCS6A01G275400 chr6A 100.000 151 0 0 1 151 501886447 501886597 1.800000e-71 279
2 TraesCS6A01G275400 chr6B 92.607 1542 57 20 632 2152 542368343 542369848 0.000000e+00 2163
3 TraesCS6A01G275400 chr6B 87.135 171 19 3 2209 2378 542369858 542370026 8.680000e-45 191
4 TraesCS6A01G275400 chr6B 95.699 93 4 0 1 93 542368092 542368184 1.470000e-32 150
5 TraesCS6A01G275400 chr6B 98.276 58 1 0 94 151 542368220 542368277 4.180000e-18 102
6 TraesCS6A01G275400 chr6D 93.642 1447 47 12 632 2061 360817257 360818675 0.000000e+00 2121
7 TraesCS6A01G275400 chr6D 90.390 333 28 4 2042 2373 360818825 360819154 3.630000e-118 435
8 TraesCS6A01G275400 chr6D 97.849 93 2 0 1 93 360817006 360817098 6.800000e-36 161
9 TraesCS6A01G275400 chr6D 98.276 58 1 0 94 151 360817134 360817191 4.180000e-18 102


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 TraesCS6A01G275400 chr6A 501886447 501888824 2377 False 1753.00 3227 100.00000 1 2378 2 chr6A.!!$F1 2377
1 TraesCS6A01G275400 chr6B 542368092 542370026 1934 False 651.50 2163 93.42925 1 2378 4 chr6B.!!$F1 2377
2 TraesCS6A01G275400 chr6D 360817006 360819154 2148 False 704.75 2121 95.03925 1 2373 4 chr6D.!!$F1 2372

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
950 993 1.153588 GCTCAGGTCAGCTCAGCTC 60.154 63.158 0.0 0.0 36.4 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2460 0.873054 ATATGTCGTAGTCTCCCGCG 59.127 55.0 0.0 0.0 0.0 6.46 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
54 55 6.377327 AAGTCACTAAACAAACAGATGGTG 57.623 37.500 0.00 0.00 0.00 4.17
136 172 3.827302 CCGAGCAGTATATACCCAGAAGT 59.173 47.826 9.32 0.00 0.00 3.01
784 827 3.840831 GCACCTGCATGAGACTACA 57.159 52.632 0.00 0.00 41.59 2.74
785 828 2.322355 GCACCTGCATGAGACTACAT 57.678 50.000 0.00 0.00 41.59 2.29
786 829 2.208431 GCACCTGCATGAGACTACATC 58.792 52.381 0.00 0.00 41.59 3.06
787 830 2.467838 CACCTGCATGAGACTACATCG 58.532 52.381 0.00 0.00 0.00 3.84
788 831 2.099756 CACCTGCATGAGACTACATCGA 59.900 50.000 0.00 0.00 0.00 3.59
789 832 2.961741 ACCTGCATGAGACTACATCGAT 59.038 45.455 0.00 0.00 0.00 3.59
790 833 3.005261 ACCTGCATGAGACTACATCGATC 59.995 47.826 0.00 0.00 0.00 3.69
791 834 3.232771 CTGCATGAGACTACATCGATCG 58.767 50.000 9.36 9.36 0.00 3.69
921 964 4.868116 ACGGGCACACACCACACC 62.868 66.667 0.00 0.00 0.00 4.16
949 992 2.980475 GCTCAGGTCAGCTCAGCT 59.020 61.111 0.00 0.00 40.77 4.24
950 993 1.153588 GCTCAGGTCAGCTCAGCTC 60.154 63.158 0.00 0.00 36.40 4.09
951 994 1.516892 CTCAGGTCAGCTCAGCTCC 59.483 63.158 0.00 0.00 36.40 4.70
956 999 3.819920 TCAGCTCAGCTCCGCTCG 61.820 66.667 0.00 0.00 36.40 5.03
974 1017 2.415010 CCACTGCTCTATCGCGCT 59.585 61.111 5.56 0.00 0.00 5.92
1104 1147 2.831742 TACTACCAGGGCTCCGCG 60.832 66.667 0.00 0.00 0.00 6.46
1209 1252 2.665185 GCGGTGTCCTGCGTCTTT 60.665 61.111 0.00 0.00 0.00 2.52
1427 1470 1.571460 CTGCTGGCGTGTTCTTGTC 59.429 57.895 0.00 0.00 0.00 3.18
1468 1511 5.262009 AGCACAGTAAGTAGTAGTGATCCA 58.738 41.667 0.00 0.00 36.72 3.41
1469 1512 5.894393 AGCACAGTAAGTAGTAGTGATCCAT 59.106 40.000 0.00 0.00 36.72 3.41
1470 1513 6.039941 AGCACAGTAAGTAGTAGTGATCCATC 59.960 42.308 0.00 0.00 36.72 3.51
1471 1514 6.039941 GCACAGTAAGTAGTAGTGATCCATCT 59.960 42.308 0.00 0.00 36.72 2.90
1472 1515 7.416890 GCACAGTAAGTAGTAGTGATCCATCTT 60.417 40.741 0.00 0.00 36.72 2.40
1473 1516 9.121658 CACAGTAAGTAGTAGTGATCCATCTTA 57.878 37.037 0.00 0.00 36.72 2.10
1474 1517 9.344772 ACAGTAAGTAGTAGTGATCCATCTTAG 57.655 37.037 0.00 0.00 36.72 2.18
1475 1518 9.562408 CAGTAAGTAGTAGTGATCCATCTTAGA 57.438 37.037 0.00 0.00 35.41 2.10
1476 1519 9.563748 AGTAAGTAGTAGTGATCCATCTTAGAC 57.436 37.037 0.00 0.00 0.00 2.59
1500 1543 4.509230 TCTTAGTGTATCTACGCCAGTACG 59.491 45.833 0.00 0.00 37.41 3.67
1501 1544 1.945394 AGTGTATCTACGCCAGTACGG 59.055 52.381 0.00 0.06 37.41 4.02
1502 1545 1.942657 GTGTATCTACGCCAGTACGGA 59.057 52.381 7.77 0.00 36.56 4.69
1503 1546 2.032204 GTGTATCTACGCCAGTACGGAG 60.032 54.545 7.77 6.88 45.72 4.63
1576 1622 1.403780 CCTCGTTCCTTTGTACTCGGG 60.404 57.143 0.00 0.00 0.00 5.14
1683 1729 0.506932 ACGTTTGCGATTCACGAGTG 59.493 50.000 3.71 0.00 45.77 3.51
1746 1792 6.811253 TGGTGGTGACAATAAAGAATGTAC 57.189 37.500 0.00 0.00 46.06 2.90
1825 1871 4.841246 ACCAACCAAGCCAAATATTACCAA 59.159 37.500 0.00 0.00 0.00 3.67
2049 2105 2.166459 CCAGGCGAGAGTGACATTTCTA 59.834 50.000 0.00 0.00 0.00 2.10
2050 2106 3.181471 CCAGGCGAGAGTGACATTTCTAT 60.181 47.826 0.00 0.00 0.00 1.98
2057 2113 7.176741 GCGAGAGTGACATTTCTATTTCTTTC 58.823 38.462 0.00 0.00 0.00 2.62
2061 2117 7.878127 AGAGTGACATTTCTATTTCTTTCGGAA 59.122 33.333 0.00 0.00 0.00 4.30
2062 2118 8.567285 AGTGACATTTCTATTTCTTTCGGAAT 57.433 30.769 0.00 0.00 33.53 3.01
2107 2333 0.879090 TAAGCACTCTCGAGCGAACA 59.121 50.000 9.87 0.00 35.48 3.18
2207 2433 6.238731 CGATGTATATGTTGTTCCTTGCCAAT 60.239 38.462 0.00 0.00 0.00 3.16
2223 2449 3.099141 GCCAATGATTTTTCCCTCCTCA 58.901 45.455 0.00 0.00 0.00 3.86
2228 2454 5.927281 ATGATTTTTCCCTCCTCATGTTG 57.073 39.130 0.00 0.00 0.00 3.33
2234 2460 0.543749 CCCTCCTCATGTTGTCCTCC 59.456 60.000 0.00 0.00 0.00 4.30
2263 2489 4.105057 AGACTACGACATATCCTCTTCCCT 59.895 45.833 0.00 0.00 0.00 4.20
2279 2505 0.325671 CCCTGCTCCCACTTCCTCTA 60.326 60.000 0.00 0.00 0.00 2.43
2299 2525 3.390521 CCTAGGTGGTGCTGCGGA 61.391 66.667 0.00 0.00 0.00 5.54
2305 2531 1.218047 GTGGTGCTGCGGAGACATA 59.782 57.895 8.65 0.00 0.00 2.29
2308 2534 1.218047 GTGCTGCGGAGACATACCA 59.782 57.895 8.65 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.098050 GTGGAGGTTGTGATGCATCC 58.902 55.000 23.67 15.02 37.25 3.51
54 55 3.679980 CACTGTGACTGTACCTTGTATGC 59.320 47.826 0.32 0.00 0.00 3.14
747 790 2.437895 GTAAGGCTGGGGGCGAAC 60.438 66.667 0.00 0.00 42.94 3.95
751 794 4.047125 TGCAGTAAGGCTGGGGGC 62.047 66.667 0.00 0.00 45.14 5.80
752 795 2.044946 GTGCAGTAAGGCTGGGGG 60.045 66.667 0.00 0.00 45.14 5.40
784 827 1.074727 AGGACCAGAGGATCGATCGAT 59.925 52.381 29.76 29.76 42.67 3.59
785 828 0.474614 AGGACCAGAGGATCGATCGA 59.525 55.000 21.86 21.86 42.67 3.59
786 829 1.268352 GAAGGACCAGAGGATCGATCG 59.732 57.143 18.81 9.36 42.67 3.69
787 830 1.268352 CGAAGGACCAGAGGATCGATC 59.732 57.143 17.36 17.36 42.67 3.69
788 831 1.133761 TCGAAGGACCAGAGGATCGAT 60.134 52.381 0.00 0.00 42.67 3.59
789 832 0.255033 TCGAAGGACCAGAGGATCGA 59.745 55.000 0.00 0.00 42.67 3.59
790 833 0.382515 GTCGAAGGACCAGAGGATCG 59.617 60.000 0.00 0.00 37.43 3.69
791 834 1.135333 GTGTCGAAGGACCAGAGGATC 59.865 57.143 0.00 0.00 42.73 3.36
867 910 2.125552 CGAGCCGAGGCATGTGAA 60.126 61.111 17.18 0.00 44.88 3.18
963 1006 0.237235 GAGTCCAGAGCGCGATAGAG 59.763 60.000 12.10 0.00 39.76 2.43
974 1017 1.607801 CGCATCCAGGTGAGTCCAGA 61.608 60.000 0.00 0.00 39.02 3.86
1053 1096 2.379634 CGGCGTGAAGAACATCGCA 61.380 57.895 0.00 0.00 44.28 5.10
1239 1282 2.032528 TCGTACACCTCGTCGGGT 59.967 61.111 0.00 0.00 40.73 5.28
1297 1340 2.123854 CCTGACGATCCGGGGAGA 60.124 66.667 0.00 0.00 0.00 3.71
1427 1470 2.859273 CTAACCGGAGCCTGCACTGG 62.859 65.000 9.46 12.18 38.71 4.00
1468 1511 7.388500 GGCGTAGATACACTAAGAGTCTAAGAT 59.612 40.741 0.00 0.00 33.55 2.40
1469 1512 6.705381 GGCGTAGATACACTAAGAGTCTAAGA 59.295 42.308 0.00 0.00 33.55 2.10
1470 1513 6.482641 TGGCGTAGATACACTAAGAGTCTAAG 59.517 42.308 0.00 0.00 33.55 2.18
1471 1514 6.351711 TGGCGTAGATACACTAAGAGTCTAA 58.648 40.000 0.00 0.00 33.55 2.10
1472 1515 5.922053 TGGCGTAGATACACTAAGAGTCTA 58.078 41.667 0.00 0.00 33.55 2.59
1473 1516 4.778579 TGGCGTAGATACACTAAGAGTCT 58.221 43.478 0.00 0.00 33.55 3.24
1474 1517 4.575645 ACTGGCGTAGATACACTAAGAGTC 59.424 45.833 0.00 0.00 33.55 3.36
1475 1518 4.525024 ACTGGCGTAGATACACTAAGAGT 58.475 43.478 0.00 0.00 33.55 3.24
1476 1519 5.333187 CGTACTGGCGTAGATACACTAAGAG 60.333 48.000 0.00 0.00 33.55 2.85
1500 1543 2.531206 GAGAGCACAACGATGTACTCC 58.469 52.381 19.19 9.62 46.83 3.85
1501 1544 2.531206 GGAGAGCACAACGATGTACTC 58.469 52.381 16.09 16.09 46.25 2.59
1502 1545 1.135373 CGGAGAGCACAACGATGTACT 60.135 52.381 0.00 0.00 37.82 2.73
1503 1546 1.269166 CGGAGAGCACAACGATGTAC 58.731 55.000 0.00 0.00 37.82 2.90
1675 1721 1.532604 ATTGGCTCGGACACTCGTGA 61.533 55.000 3.74 0.00 0.00 4.35
1676 1722 1.078759 GATTGGCTCGGACACTCGTG 61.079 60.000 0.00 0.00 0.00 4.35
1825 1871 4.532126 TGGAAGATCGGCAAGATATGGTAT 59.468 41.667 0.00 0.00 40.26 2.73
2081 2307 4.265949 GCTCGAGAGTGCTTAAAAATCC 57.734 45.455 18.75 0.00 46.33 3.01
2125 2351 3.002042 CGCTTCAAGATCAGTGCAATAGG 59.998 47.826 0.00 0.00 0.00 2.57
2162 2388 6.035005 ACATCGAACAACTATCTTTGATGACG 59.965 38.462 12.53 0.00 39.33 4.35
2174 2400 8.255206 AGGAACAACATATACATCGAACAACTA 58.745 33.333 0.00 0.00 0.00 2.24
2176 2402 7.303634 AGGAACAACATATACATCGAACAAC 57.696 36.000 0.00 0.00 0.00 3.32
2207 2433 4.739793 ACAACATGAGGAGGGAAAAATCA 58.260 39.130 0.00 0.00 0.00 2.57
2223 2449 3.000819 TCCCGCGGAGGACAACAT 61.001 61.111 30.73 0.00 45.00 2.71
2234 2460 0.873054 ATATGTCGTAGTCTCCCGCG 59.127 55.000 0.00 0.00 0.00 6.46
2245 2471 1.689273 GCAGGGAAGAGGATATGTCGT 59.311 52.381 0.00 0.00 0.00 4.34
2263 2489 2.119495 GGAATAGAGGAAGTGGGAGCA 58.881 52.381 0.00 0.00 0.00 4.26
2279 2505 1.221840 CGCAGCACCACCTAGGAAT 59.778 57.895 17.98 0.00 41.22 3.01
2299 2525 1.384989 CGCCGGAGTCTGGTATGTCT 61.385 60.000 19.47 0.00 0.00 3.41
2326 2552 1.070445 GATGCCTCCTCATCCCACG 59.930 63.158 0.00 0.00 37.47 4.94


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

AutoCloner maintained by Alex Coulton.