Multiple sequence alignment - TraesCS6B01G347500

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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 TraesCS6B01G347500 chr6B 100.000 2456 0 0 1 2456 612132426 612134881 0.000000e+00 4536
1 TraesCS6B01G347500 chr6D 91.417 2004 99 38 502 2454 407828491 407830472 0.000000e+00 2680
2 TraesCS6B01G347500 chr6D 86.166 506 52 11 1 500 407827747 407828240 4.650000e-147 531
3 TraesCS6B01G347500 chr6A 91.437 1308 46 23 1142 2401 553188699 553189988 0.000000e+00 1735
4 TraesCS6B01G347500 chr6A 92.849 909 50 10 215 1122 553187751 553188645 0.000000e+00 1304
5 TraesCS6B01G347500 chr6A 93.452 168 11 0 1 168 553187483 553187650 1.460000e-62 250


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 TraesCS6B01G347500 chr6B 612132426 612134881 2455 False 4536.000000 4536 100.000000 1 2456 1 chr6B.!!$F1 2455
1 TraesCS6B01G347500 chr6D 407827747 407830472 2725 False 1605.500000 2680 88.791500 1 2454 2 chr6D.!!$F1 2453
2 TraesCS6B01G347500 chr6A 553187483 553189988 2505 False 1096.333333 1735 92.579333 1 2401 3 chr6A.!!$F1 2400

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
842 1150 0.032267 GTATCCGTAGCTCTGGCCAC 59.968 60.0 0.0 0.0 39.73 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2609 0.750182 GCTACAGAGAGCGAGGGAGT 60.75 60.0 0.0 0.0 31.57 3.85 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
65 68 6.284891 TGAAATCCATTTGAATCCAAGGAC 57.715 37.500 0.00 0.00 31.84 3.85
99 103 1.474330 GGGACCAATTTCTTCGCCAT 58.526 50.000 0.00 0.00 0.00 4.40
121 125 5.524511 TGTTGAAATTCGACTATGAACCG 57.475 39.130 13.89 0.00 32.00 4.44
137 141 3.006003 TGAACCGTGTATGCTCTAACACA 59.994 43.478 6.43 0.00 44.98 3.72
145 149 5.523916 GTGTATGCTCTAACACATTGTAGGG 59.476 44.000 0.94 0.00 44.30 3.53
152 156 2.200373 ACACATTGTAGGGCCACTTC 57.800 50.000 6.18 0.00 0.00 3.01
168 172 5.869888 GGCCACTTCGGATTATAGTATTCTG 59.130 44.000 0.00 0.00 36.56 3.02
203 237 5.006386 AGGAAAATCATAGGATTCGGATGC 58.994 41.667 2.61 0.00 42.87 3.91
221 255 1.663379 GCCGCCTACCACAAAATCCC 61.663 60.000 0.00 0.00 0.00 3.85
222 256 0.034477 CCGCCTACCACAAAATCCCT 60.034 55.000 0.00 0.00 0.00 4.20
315 374 7.986553 AAATTTAGAGGATTGAGGAGAGAGA 57.013 36.000 0.00 0.00 0.00 3.10
328 387 4.227197 AGGAGAGAGAGAGTAGAGAGAGG 58.773 52.174 0.00 0.00 0.00 3.69
397 456 9.342308 GAGTTCATGTTCATATTCCTATGGAAA 57.658 33.333 2.98 0.00 45.41 3.13
500 559 2.822707 TCTAGGGAGGGTGACACTAC 57.177 55.000 5.39 0.00 0.00 2.73
503 811 2.112279 AGGGAGGGTGACACTACAAA 57.888 50.000 0.00 0.00 0.00 2.83
548 856 3.980775 GTGGTACGTACGTGTACAATGTT 59.019 43.478 30.25 1.85 45.16 2.71
592 900 1.203523 ACCATCTCTGTCTCTTGCGAC 59.796 52.381 0.00 0.00 34.52 5.19
593 901 1.470632 CCATCTCTGTCTCTTGCGACC 60.471 57.143 0.00 0.00 32.97 4.79
594 902 1.476085 CATCTCTGTCTCTTGCGACCT 59.524 52.381 0.00 0.00 32.97 3.85
635 943 1.965754 GCGGCATCTCAGTCTCCCTT 61.966 60.000 0.00 0.00 0.00 3.95
737 1045 4.846940 ACCTTCTTTTACCCTCTGATGTCT 59.153 41.667 0.00 0.00 0.00 3.41
779 1087 2.914289 GGCCATCTGCACTAGCCT 59.086 61.111 0.00 0.00 43.89 4.58
780 1088 1.225704 GGCCATCTGCACTAGCCTT 59.774 57.895 0.00 0.00 43.89 4.35
781 1089 0.469917 GGCCATCTGCACTAGCCTTA 59.530 55.000 0.00 0.00 43.89 2.69
782 1090 1.542108 GGCCATCTGCACTAGCCTTAG 60.542 57.143 0.00 0.00 43.89 2.18
783 1091 1.876322 CCATCTGCACTAGCCTTAGC 58.124 55.000 0.00 0.00 41.13 3.09
784 1092 1.139654 CCATCTGCACTAGCCTTAGCA 59.860 52.381 0.00 0.00 43.56 3.49
788 1096 2.704572 CTGCACTAGCCTTAGCAGTTT 58.295 47.619 9.80 0.00 46.92 2.66
797 1105 2.680339 GCCTTAGCAGTTTAGCTCCAAG 59.320 50.000 0.00 0.00 45.26 3.61
799 1107 4.579869 CCTTAGCAGTTTAGCTCCAAGAA 58.420 43.478 0.00 0.00 45.26 2.52
814 1122 5.161943 TCCAAGAAAGTAGCTAGGTTTCC 57.838 43.478 18.65 7.10 31.68 3.13
829 1137 1.070289 GTTTCCCCTAGGCTGTATCCG 59.930 57.143 2.05 0.00 0.00 4.18
842 1150 0.032267 GTATCCGTAGCTCTGGCCAC 59.968 60.000 0.00 0.00 39.73 5.01
959 1268 1.025113 TAGCCTCACTCTCACCGTCG 61.025 60.000 0.00 0.00 0.00 5.12
1124 1455 0.947180 TCCGCTTTTCAGGTACGCAC 60.947 55.000 0.00 0.00 0.00 5.34
1139 1470 2.430921 CACAGCGTCACCGTCTCC 60.431 66.667 0.00 0.00 36.15 3.71
1140 1471 4.039357 ACAGCGTCACCGTCTCCG 62.039 66.667 0.00 0.00 36.15 4.63
1170 1513 3.877508 GCTCCATTAATTTACGTGGCTCT 59.122 43.478 0.00 0.00 0.00 4.09
1205 1554 1.442769 ACTGACGGTGATGTTCATGC 58.557 50.000 0.00 0.00 0.00 4.06
1273 1622 4.622456 GCCACAACCGGTGCAACG 62.622 66.667 19.45 19.45 46.50 4.10
1571 1928 2.036890 AGCTACGGTCCCGGTCTT 59.963 61.111 10.91 0.00 44.69 3.01
1723 2080 7.041916 ACGCATGTACTACTACTAAGAGTGATC 60.042 40.741 0.00 0.00 0.00 2.92
1725 2082 7.041916 GCATGTACTACTACTAAGAGTGATCGT 60.042 40.741 0.00 0.00 0.00 3.73
1750 2107 1.261619 GATGGAGCGAGCGGTAAATTG 59.738 52.381 0.00 0.00 0.00 2.32
1763 2120 4.033129 GCGGTAAATTGTGTATTGTAGCGA 59.967 41.667 4.48 0.00 35.36 4.93
1764 2121 5.277154 GCGGTAAATTGTGTATTGTAGCGAT 60.277 40.000 4.48 0.00 35.36 4.58
1852 2215 1.529226 CACGTGACTCTCCTCTGACT 58.471 55.000 10.90 0.00 0.00 3.41
2019 2388 1.712350 CGTACGTGAAAACTCTCGGTG 59.288 52.381 7.22 0.00 0.00 4.94
2020 2389 2.735823 GTACGTGAAAACTCTCGGTGT 58.264 47.619 0.00 0.00 0.00 4.16
2021 2390 3.606846 CGTACGTGAAAACTCTCGGTGTA 60.607 47.826 7.22 0.00 0.00 2.90
2162 2537 1.731433 GCTCGGCTCGTATGGGTGTA 61.731 60.000 0.00 0.00 0.00 2.90
2167 2542 0.822164 GCTCGTATGGGTGTAGTGGT 59.178 55.000 0.00 0.00 0.00 4.16
2194 2569 4.736631 GTTCGCCGCGCTTGGAAC 62.737 66.667 8.21 11.88 32.92 3.62
2197 2572 3.554692 CGCCGCGCTTGGAACTAG 61.555 66.667 5.56 0.00 0.00 2.57
2234 2609 4.373116 GTCGCTTGTCGGGCCTCA 62.373 66.667 0.84 0.00 39.05 3.86
2335 2721 1.728069 GACTAGCGACGATGCAGGA 59.272 57.895 0.00 0.00 37.31 3.86
2338 2724 0.945099 CTAGCGACGATGCAGGAGTA 59.055 55.000 0.00 0.00 37.31 2.59
2340 2726 0.748367 AGCGACGATGCAGGAGTAGA 60.748 55.000 0.00 0.00 37.31 2.59
2384 2790 2.031420 GGGGTAGTTTTCGTCTGCAAAC 60.031 50.000 0.00 0.00 33.75 2.93
2401 2807 3.119849 GCAAACAAGTGTGTGTCAAGACT 60.120 43.478 3.63 0.00 38.27 3.24
2403 2809 3.610040 ACAAGTGTGTGTCAAGACTCA 57.390 42.857 1.53 1.35 36.31 3.41
2406 2812 3.185246 AGTGTGTGTCAAGACTCAAGG 57.815 47.619 6.55 0.00 36.70 3.61
2428 2835 3.605664 GTTTGCGGGGTGCTGCTT 61.606 61.111 0.00 0.00 46.63 3.91
2429 2836 3.604667 TTTGCGGGGTGCTGCTTG 61.605 61.111 0.00 0.00 46.63 4.01
2454 2861 2.727777 TCTGAGTTTCTGAACACGACG 58.272 47.619 0.00 0.00 38.26 5.12
2455 2862 2.098607 TCTGAGTTTCTGAACACGACGT 59.901 45.455 0.00 0.00 38.26 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 68 1.691976 GGTCCCCAAACTTTTCAAGGG 59.308 52.381 0.00 0.00 39.29 3.95
99 103 4.992319 ACGGTTCATAGTCGAATTTCAACA 59.008 37.500 0.00 0.00 0.00 3.33
121 125 5.523916 CCCTACAATGTGTTAGAGCATACAC 59.476 44.000 0.00 0.00 43.76 2.90
137 141 1.213296 ATCCGAAGTGGCCCTACAAT 58.787 50.000 0.00 0.00 37.80 2.71
145 149 6.688578 TCAGAATACTATAATCCGAAGTGGC 58.311 40.000 0.00 0.00 37.80 5.01
178 212 6.015940 GCATCCGAATCCTATGATTTTCCTTT 60.016 38.462 0.00 0.00 41.30 3.11
203 237 0.034477 AGGGATTTTGTGGTAGGCGG 60.034 55.000 0.00 0.00 0.00 6.13
221 255 9.482627 GAATTCCTGTGTTCTGTAATCCTATAG 57.517 37.037 0.00 0.00 0.00 1.31
222 256 9.213777 AGAATTCCTGTGTTCTGTAATCCTATA 57.786 33.333 0.65 0.00 33.64 1.31
234 293 3.367703 CCCATTGCAGAATTCCTGTGTTC 60.368 47.826 0.65 0.00 44.71 3.18
289 348 8.830741 TCTCTCTCCTCAATCCTCTAAATTTTT 58.169 33.333 0.00 0.00 0.00 1.94
293 352 6.921412 TCTCTCTCTCCTCAATCCTCTAAAT 58.079 40.000 0.00 0.00 0.00 1.40
314 373 5.609533 ACACTCTACCTCTCTCTACTCTC 57.390 47.826 0.00 0.00 0.00 3.20
315 374 7.419750 CCAATACACTCTACCTCTCTCTACTCT 60.420 44.444 0.00 0.00 0.00 3.24
328 387 7.603651 TCTTTGAGAAGTCCAATACACTCTAC 58.396 38.462 0.00 0.00 35.90 2.59
374 433 9.919416 TCTTTTCCATAGGAATATGAACATGAA 57.081 29.630 0.00 0.00 41.71 2.57
397 456 6.677920 GCGTCACCAAATTTATATGCTGTCTT 60.678 38.462 0.00 0.00 0.00 3.01
503 811 4.178169 TCGGTGCAAACCCACGGT 62.178 61.111 0.00 0.00 37.34 4.83
548 856 2.584064 CCCTCGCTGCCACATGTA 59.416 61.111 0.00 0.00 0.00 2.29
592 900 0.110104 GAATGGAGCCATGGAGGAGG 59.890 60.000 18.40 0.00 41.22 4.30
593 901 1.138568 AGAATGGAGCCATGGAGGAG 58.861 55.000 18.40 0.00 41.22 3.69
594 902 0.841961 CAGAATGGAGCCATGGAGGA 59.158 55.000 18.40 0.00 41.22 3.71
635 943 1.820519 GACGGGCGTATATGTATGGGA 59.179 52.381 0.00 0.00 0.00 4.37
737 1045 2.190313 GATGGTGCCGCTGGATCA 59.810 61.111 0.00 0.00 0.00 2.92
763 1071 1.876322 CTAAGGCTAGTGCAGATGGC 58.124 55.000 0.00 0.00 41.91 4.40
779 1087 5.621193 ACTTTCTTGGAGCTAAACTGCTAA 58.379 37.500 0.00 0.00 44.17 3.09
780 1088 5.228945 ACTTTCTTGGAGCTAAACTGCTA 57.771 39.130 0.00 0.00 44.17 3.49
781 1089 8.428407 AGCTACTTTCTTGGAGCTAAACTGCT 62.428 42.308 0.00 0.00 43.37 4.24
782 1090 4.142795 GCTACTTTCTTGGAGCTAAACTGC 60.143 45.833 0.00 0.00 37.22 4.40
783 1091 5.241662 AGCTACTTTCTTGGAGCTAAACTG 58.758 41.667 0.00 0.00 43.37 3.16
784 1092 5.491323 AGCTACTTTCTTGGAGCTAAACT 57.509 39.130 0.00 0.00 43.37 2.66
785 1093 5.813157 CCTAGCTACTTTCTTGGAGCTAAAC 59.187 44.000 9.38 0.00 44.63 2.01
788 1096 4.611367 ACCTAGCTACTTTCTTGGAGCTA 58.389 43.478 8.02 8.02 43.37 3.32
814 1122 0.889306 GCTACGGATACAGCCTAGGG 59.111 60.000 11.72 0.00 29.63 3.53
819 1127 0.315568 CCAGAGCTACGGATACAGCC 59.684 60.000 0.00 0.00 36.30 4.85
842 1150 4.082733 TGTGTGTAGGTTCTTCGATCAGAG 60.083 45.833 0.00 0.00 0.00 3.35
1139 1470 6.255020 ACGTAAATTAATGGAGCTACAAGTCG 59.745 38.462 0.66 2.60 0.00 4.18
1140 1471 7.399523 CACGTAAATTAATGGAGCTACAAGTC 58.600 38.462 0.66 0.00 0.00 3.01
1170 1513 4.229096 CGTCAGTGCGGTTTAGTTAGTTA 58.771 43.478 0.00 0.00 0.00 2.24
1193 1542 1.466167 AGTTCTGCGCATGAACATCAC 59.534 47.619 33.68 19.75 44.30 3.06
1571 1928 5.163395 GGGACCAAATGAACTAACCAAAACA 60.163 40.000 0.00 0.00 0.00 2.83
1704 2061 7.594386 CGATCACGATCACTCTTAGTAGTAGTA 59.406 40.741 7.75 0.00 42.66 1.82
1705 2062 6.421501 CGATCACGATCACTCTTAGTAGTAGT 59.578 42.308 7.75 0.00 42.66 2.73
1706 2063 6.641723 TCGATCACGATCACTCTTAGTAGTAG 59.358 42.308 7.75 0.00 43.81 2.57
1707 2064 6.510536 TCGATCACGATCACTCTTAGTAGTA 58.489 40.000 7.75 0.00 43.81 1.82
1708 2065 5.358090 TCGATCACGATCACTCTTAGTAGT 58.642 41.667 7.75 0.00 43.81 2.73
1709 2066 5.908916 TCGATCACGATCACTCTTAGTAG 57.091 43.478 7.75 0.00 43.81 2.57
1723 2080 2.013483 GCTCGCTCCATCGATCACG 61.013 63.158 0.00 0.00 37.87 4.35
1725 2082 2.332869 CGCTCGCTCCATCGATCA 59.667 61.111 0.00 0.00 37.87 2.92
1763 2120 9.760077 GCACCAGTACTGTTATTACTATTACAT 57.240 33.333 21.18 0.00 0.00 2.29
1764 2121 8.974238 AGCACCAGTACTGTTATTACTATTACA 58.026 33.333 21.18 0.00 0.00 2.41
1852 2215 3.263170 TCCACTCGGGATTTCAGATTCAA 59.737 43.478 0.00 0.00 42.15 2.69
2019 2388 1.509923 CCTCGGACCCACGTCTTAC 59.490 63.158 0.00 0.00 39.15 2.34
2020 2389 2.345760 GCCTCGGACCCACGTCTTA 61.346 63.158 0.00 0.00 39.15 2.10
2021 2390 3.692406 GCCTCGGACCCACGTCTT 61.692 66.667 0.00 0.00 39.15 3.01
2162 2537 1.226262 GAACCCCACACACACCACT 59.774 57.895 0.00 0.00 0.00 4.00
2167 2542 4.920112 CGGCGAACCCCACACACA 62.920 66.667 0.00 0.00 0.00 3.72
2194 2569 4.554363 CCACGTCCGAGCGGCTAG 62.554 72.222 0.60 1.89 35.98 3.42
2234 2609 0.750182 GCTACAGAGAGCGAGGGAGT 60.750 60.000 0.00 0.00 31.57 3.85
2242 2625 2.278271 GACGCCGCTACAGAGAGC 60.278 66.667 0.00 0.00 39.20 4.09
2244 2627 3.506096 CGGACGCCGCTACAGAGA 61.506 66.667 5.38 0.00 41.17 3.10
2335 2721 8.084684 GCCTCACTTCAATTTGAAAAATCTACT 58.915 33.333 12.62 0.00 35.73 2.57
2338 2724 6.819284 TGCCTCACTTCAATTTGAAAAATCT 58.181 32.000 12.62 0.00 35.73 2.40
2340 2726 5.993441 CCTGCCTCACTTCAATTTGAAAAAT 59.007 36.000 12.62 0.00 35.73 1.82
2384 2790 3.310774 CCTTGAGTCTTGACACACACTTG 59.689 47.826 3.49 0.00 0.00 3.16
2428 2835 3.863424 GTGTTCAGAAACTCAGAACGTCA 59.137 43.478 7.24 0.00 43.22 4.35
2429 2836 3.061139 CGTGTTCAGAAACTCAGAACGTC 60.061 47.826 7.24 3.56 43.22 4.34


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

AutoCloner maintained by Alex Coulton.