Multiple sequence alignment - TraesCS7A01G234000

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 TraesCS7A01G234000 chr7A 100.000 3227 0 0 1 3227 206006118 206002892 0.000000e+00 5960.0
1 TraesCS7A01G234000 chr7D 92.505 2655 114 39 1 2602 196908855 196906233 0.000000e+00 3722.0
2 TraesCS7A01G234000 chr7D 95.462 595 22 3 2635 3227 196906234 196905643 0.000000e+00 944.0
3 TraesCS7A01G234000 chr7B 92.449 2119 81 29 182 2276 161198563 161196500 0.000000e+00 2953.0
4 TraesCS7A01G234000 chr7B 89.602 779 33 16 2282 3033 161196462 161195705 0.000000e+00 946.0
5 TraesCS7A01G234000 chr7B 93.443 183 7 2 1 183 161200405 161200228 1.910000e-67 267.0
6 TraesCS7A01G234000 chr7B 92.121 165 11 2 3065 3227 161195710 161195546 6.960000e-57 231.0
7 TraesCS7A01G234000 chr1B 100.000 28 0 0 540 567 39812410 39812437 6.000000e-03 52.8
8 TraesCS7A01G234000 chr1A 100.000 28 0 0 540 567 13236461 13236488 6.000000e-03 52.8


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 TraesCS7A01G234000 chr7A 206002892 206006118 3226 True 5960.00 5960 100.00000 1 3227 1 chr7A.!!$R1 3226
1 TraesCS7A01G234000 chr7D 196905643 196908855 3212 True 2333.00 3722 93.98350 1 3227 2 chr7D.!!$R1 3226
2 TraesCS7A01G234000 chr7B 161195546 161200405 4859 True 1099.25 2953 91.90375 1 3227 4 chr7B.!!$R1 3226

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
990 2678 0.250467 TCTCCCTTGTGCTGCTTGAC 60.25 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 3985 0.038526 CGCCGGAGTGGGTATATGTC 60.039 60.0 5.05 0.0 38.63 3.06 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
40 41 4.257731 TCAAACAAAGCCCTTTCCAAAAC 58.742 39.130 0.00 0.00 0.00 2.43
41 42 3.990959 AACAAAGCCCTTTCCAAAACA 57.009 38.095 0.00 0.00 0.00 2.83
42 43 3.990959 ACAAAGCCCTTTCCAAAACAA 57.009 38.095 0.00 0.00 0.00 2.83
43 44 4.293662 ACAAAGCCCTTTCCAAAACAAA 57.706 36.364 0.00 0.00 0.00 2.83
98 99 4.752594 TGGCCCCCTACCTCCACC 62.753 72.222 0.00 0.00 0.00 4.61
157 158 2.039879 AGGTTTAAATGCTCGGGAGTGT 59.960 45.455 0.00 0.00 0.00 3.55
192 1859 7.210718 CATGTGTTGCATATCATATTGGAGT 57.789 36.000 0.00 0.00 35.74 3.85
318 1985 5.895534 ACATGCCCTTGAGTAAATCATCATT 59.104 36.000 0.00 0.00 37.89 2.57
337 2004 9.558648 TCATCATTTTGTGATTAAGAAATCGTG 57.441 29.630 0.00 0.00 45.25 4.35
341 2008 2.675844 TGTGATTAAGAAATCGTGGGCG 59.324 45.455 0.00 0.00 43.84 6.13
383 2050 1.517242 GATGCTTCCCGATCATGACC 58.483 55.000 0.00 0.00 0.00 4.02
586 2265 3.926616 TCCGGTGAGAACTGAGAAATTC 58.073 45.455 0.00 0.00 0.00 2.17
643 2322 6.365247 GTGTTTTGACGTAGAGCTCTTGAATA 59.635 38.462 23.84 0.00 0.00 1.75
647 2326 5.434408 TGACGTAGAGCTCTTGAATACCTA 58.566 41.667 23.84 0.00 0.00 3.08
648 2327 5.884232 TGACGTAGAGCTCTTGAATACCTAA 59.116 40.000 23.84 0.00 0.00 2.69
670 2354 2.309136 ACCACCTTGATTTTCTGGGG 57.691 50.000 0.00 0.00 0.00 4.96
688 2372 1.859302 GGGTGCATACAATTCCCCAA 58.141 50.000 0.00 0.00 30.37 4.12
693 2377 4.323409 GGTGCATACAATTCCCCAACATTT 60.323 41.667 0.00 0.00 0.00 2.32
701 2385 5.186992 ACAATTCCCCAACATTTTAGCCTAC 59.813 40.000 0.00 0.00 0.00 3.18
778 2463 7.891561 AGTAGCTGTCAAATATATCCAGACTC 58.108 38.462 0.00 5.81 0.00 3.36
841 2526 3.163832 AAAAAGCAAGTGGCCGGCC 62.164 57.895 39.40 39.40 46.50 6.13
990 2678 0.250467 TCTCCCTTGTGCTGCTTGAC 60.250 55.000 0.00 0.00 0.00 3.18
1032 2724 4.827087 ATGGCGACGCTGCTCCTG 62.827 66.667 20.77 0.00 34.52 3.86
1043 2735 2.124778 GCTCCTGCTCTCCCTTGC 60.125 66.667 0.00 0.00 36.03 4.01
1100 2792 2.125912 CGTCGTGGAAGGCCTGAG 60.126 66.667 5.69 0.00 34.31 3.35
1131 2823 4.309950 AACAGGACGTGCCCGGAC 62.310 66.667 0.73 0.00 38.78 4.79
1172 2864 0.989890 GTGGTGATGAACGACTACGC 59.010 55.000 0.00 0.00 43.96 4.42
1239 2931 1.594862 GACTGCTTCATCACGGTATGC 59.405 52.381 0.00 0.00 0.00 3.14
1243 2939 1.334419 GCTTCATCACGGTATGCATGC 60.334 52.381 11.82 11.82 0.00 4.06
1279 2981 2.124570 ATCACCACGAGCCATGCC 60.125 61.111 0.00 0.00 0.00 4.40
1280 2982 2.874648 GATCACCACGAGCCATGCCA 62.875 60.000 0.00 0.00 0.00 4.92
1281 2983 2.881539 ATCACCACGAGCCATGCCAG 62.882 60.000 0.00 0.00 0.00 4.85
1282 2984 4.415150 ACCACGAGCCATGCCAGG 62.415 66.667 0.00 0.00 0.00 4.45
1290 2992 3.766691 CCATGCCAGGCAGCCAAC 61.767 66.667 21.51 2.44 43.65 3.77
1305 3007 2.053627 GCCAACGCAGAATGTTTCTTG 58.946 47.619 0.00 0.00 38.11 3.02
1371 3073 1.142748 CATCCTGCTGGACGAGTCC 59.857 63.158 15.36 14.98 46.51 3.85
1558 3260 3.417275 CTGCCGAGCTACGAGGTGG 62.417 68.421 7.07 0.00 45.77 4.61
1562 3264 4.208686 GAGCTACGAGGTGGCCGG 62.209 72.222 0.00 0.00 40.93 6.13
1701 3403 4.135153 CTGGTGACGCTCTCCGGG 62.135 72.222 0.00 0.00 42.52 5.73
1779 3481 1.226974 CAAGACGGCGGACATCGAT 60.227 57.895 13.24 0.00 42.43 3.59
2059 3761 2.806856 GCGATGCAGAAGGTGAGCG 61.807 63.158 0.00 0.00 0.00 5.03
2060 3762 2.806856 CGATGCAGAAGGTGAGCGC 61.807 63.158 0.00 0.00 0.00 5.92
2227 3929 2.716217 GTGGCTTCCAGCAGAACTAAT 58.284 47.619 0.00 0.00 44.75 1.73
2247 3949 1.173043 TAAGTTGCCTTTGCCATCCG 58.827 50.000 0.00 0.00 36.33 4.18
2249 3951 1.212751 GTTGCCTTTGCCATCCGTC 59.787 57.895 0.00 0.00 36.33 4.79
2259 3961 1.402896 GCCATCCGTCTCCATCTCCA 61.403 60.000 0.00 0.00 0.00 3.86
2276 3983 1.570979 TCCATCTGCTCTCCTACTCCA 59.429 52.381 0.00 0.00 0.00 3.86
2277 3984 2.178764 TCCATCTGCTCTCCTACTCCAT 59.821 50.000 0.00 0.00 0.00 3.41
2278 3985 2.299582 CCATCTGCTCTCCTACTCCATG 59.700 54.545 0.00 0.00 0.00 3.66
2279 3986 3.229293 CATCTGCTCTCCTACTCCATGA 58.771 50.000 0.00 0.00 0.00 3.07
2323 4062 4.735338 GCTGTCAAGTTTAAGTTTCACTGC 59.265 41.667 7.18 7.18 0.00 4.40
2439 4195 5.464722 TGCCGTTTGTACGTTTACTTATCAA 59.535 36.000 0.00 0.00 46.20 2.57
2442 4198 7.005380 CCGTTTGTACGTTTACTTATCAACTG 58.995 38.462 0.00 0.00 46.20 3.16
2480 4236 3.474600 TCACCGAAACCGAATAAACCAA 58.525 40.909 0.00 0.00 0.00 3.67
2522 4279 3.885484 ATTGCGTCACTTGTTCTTCAG 57.115 42.857 0.00 0.00 0.00 3.02
2543 4300 6.846350 TCAGCTAGTACTTCTACCGTTTTAC 58.154 40.000 0.00 0.00 0.00 2.01
2560 4317 6.202188 CCGTTTTACCCATACTACAATGCTAG 59.798 42.308 0.00 0.00 0.00 3.42
2561 4318 6.759827 CGTTTTACCCATACTACAATGCTAGT 59.240 38.462 0.00 2.24 0.00 2.57
2562 4319 7.922278 CGTTTTACCCATACTACAATGCTAGTA 59.078 37.037 0.00 5.61 34.43 1.82
2563 4320 9.257651 GTTTTACCCATACTACAATGCTAGTAG 57.742 37.037 8.56 8.56 43.51 2.57
2589 4349 2.698855 ATCAACGACCCTTGATCCTG 57.301 50.000 0.00 0.00 36.32 3.86
2663 4423 6.705782 ACGACATGATTTGCTATTTTCGTAG 58.294 36.000 0.00 0.00 35.55 3.51
2688 4448 1.078709 GTTCTCACGCAGCAGCATAA 58.921 50.000 0.82 0.00 42.27 1.90
2689 4449 1.061711 GTTCTCACGCAGCAGCATAAG 59.938 52.381 0.82 0.00 42.27 1.73
2690 4450 0.460811 TCTCACGCAGCAGCATAAGG 60.461 55.000 0.82 0.00 42.27 2.69
2691 4451 0.460811 CTCACGCAGCAGCATAAGGA 60.461 55.000 0.82 0.00 42.27 3.36
2708 4468 3.207265 AGGAGCATAACACAACACACA 57.793 42.857 0.00 0.00 0.00 3.72
2733 4498 5.215239 TGTACATAACACAATGATGCACG 57.785 39.130 0.00 0.00 31.43 5.34
2747 4512 5.491323 TGATGCACGATATATAAACCCCA 57.509 39.130 0.00 0.00 0.00 4.96
2778 4543 1.166989 TCCATGCGTACGTGACTACA 58.833 50.000 17.90 5.26 34.49 2.74
2984 4761 5.512232 GGACAGCATATCTAGGAAAGGGAAG 60.512 48.000 0.00 0.00 0.00 3.46
3044 4821 7.573710 AGGATTCTATGCAGTGGTAATACAAA 58.426 34.615 0.00 0.00 0.00 2.83
3173 4951 2.290323 GCAAGAAGAGGGGTAGAAAGCA 60.290 50.000 0.00 0.00 0.00 3.91
3211 4989 3.431233 CGTCAGCCATATATGTCTGCAAG 59.569 47.826 17.10 8.24 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 1.238439 ACCGTCATTGACAAAGCTGG 58.762 50.000 16.61 10.39 32.09 4.85
318 1985 4.378978 CGCCCACGATTTCTTAATCACAAA 60.379 41.667 0.00 0.00 43.93 2.83
337 2004 2.028385 TGAGTTTCTAACCTCTTCGCCC 60.028 50.000 0.00 0.00 0.00 6.13
341 2008 3.586892 CCCGTGAGTTTCTAACCTCTTC 58.413 50.000 0.00 0.00 0.00 2.87
383 2050 3.742369 GGTTCATTGTTGTTGCATTGGAG 59.258 43.478 0.00 0.00 0.00 3.86
496 2163 6.432783 ACCACGAATAGGTTGATTTTGATCAA 59.567 34.615 3.38 3.38 35.33 2.57
497 2164 5.943416 ACCACGAATAGGTTGATTTTGATCA 59.057 36.000 0.00 0.00 35.33 2.92
516 2183 3.304659 GCCCAATCAGCATAATAACCACG 60.305 47.826 0.00 0.00 0.00 4.94
518 2185 3.230134 GGCCCAATCAGCATAATAACCA 58.770 45.455 0.00 0.00 0.00 3.67
519 2186 2.228822 CGGCCCAATCAGCATAATAACC 59.771 50.000 0.00 0.00 0.00 2.85
586 2265 6.554334 TCTTCTCATTAAGTGGTTTTTCGG 57.446 37.500 0.00 0.00 0.00 4.30
643 2322 6.183360 CCAGAAAATCAAGGTGGTTTTTAGGT 60.183 38.462 1.06 0.00 40.44 3.08
647 2326 4.141505 CCCCAGAAAATCAAGGTGGTTTTT 60.142 41.667 1.06 0.00 40.44 1.94
648 2327 3.390967 CCCCAGAAAATCAAGGTGGTTTT 59.609 43.478 0.00 0.00 42.78 2.43
670 2354 2.175202 TGTTGGGGAATTGTATGCACC 58.825 47.619 0.00 0.00 0.00 5.01
688 2372 6.520272 TGCAAAAATGTGTAGGCTAAAATGT 58.480 32.000 0.00 0.00 0.00 2.71
693 2377 5.720371 ACATGCAAAAATGTGTAGGCTAA 57.280 34.783 0.00 0.00 39.32 3.09
753 2438 7.308891 CGAGTCTGGATATATTTGACAGCTACT 60.309 40.741 12.79 8.12 0.00 2.57
775 2460 1.008079 GACGGACGGTCAAACGAGT 60.008 57.895 10.76 0.00 45.36 4.18
778 2463 2.051076 TCGACGGACGGTCAAACG 60.051 61.111 10.76 11.28 46.42 3.60
841 2526 5.591877 AGCAACTTAGGCCTCATATTCTTTG 59.408 40.000 9.68 4.00 0.00 2.77
917 2605 2.789092 CGGAATGAGCTGCATTTTCGTC 60.789 50.000 1.02 0.00 46.90 4.20
920 2608 2.789092 CGACGGAATGAGCTGCATTTTC 60.789 50.000 1.02 1.24 46.90 2.29
1100 2792 0.037734 CCTGTTGTAGAACCCCACCC 59.962 60.000 0.00 0.00 0.00 4.61
1172 2864 2.114670 GCGATGGTGTGGTCCATGG 61.115 63.158 4.97 4.97 46.72 3.66
1279 2981 2.338015 ATTCTGCGTTGGCTGCCTG 61.338 57.895 21.03 10.79 40.82 4.85
1280 2982 2.034687 ATTCTGCGTTGGCTGCCT 59.965 55.556 21.03 0.00 40.82 4.75
1281 2983 2.146073 AACATTCTGCGTTGGCTGCC 62.146 55.000 12.87 12.87 40.82 4.85
1282 2984 0.318955 AAACATTCTGCGTTGGCTGC 60.319 50.000 0.00 0.00 40.82 5.25
1290 2992 5.674148 CGTGATAATCAAGAAACATTCTGCG 59.326 40.000 0.00 0.00 40.59 5.18
1305 3007 1.772063 GCACACCGGCCGTGATAATC 61.772 60.000 26.12 2.76 46.20 1.75
1323 3025 0.539669 ACCCCTACACCAAAGCAAGC 60.540 55.000 0.00 0.00 0.00 4.01
1324 3026 1.247567 CACCCCTACACCAAAGCAAG 58.752 55.000 0.00 0.00 0.00 4.01
1325 3027 0.825840 GCACCCCTACACCAAAGCAA 60.826 55.000 0.00 0.00 0.00 3.91
1326 3028 1.228429 GCACCCCTACACCAAAGCA 60.228 57.895 0.00 0.00 0.00 3.91
1384 3086 0.752376 GACGACTCCTTCTCCGGGAT 60.752 60.000 0.00 0.00 31.89 3.85
2059 3761 1.083806 TTGATGATCACGTCCAGCGC 61.084 55.000 0.00 0.00 46.11 5.92
2247 3949 2.297033 GAGAGCAGATGGAGATGGAGAC 59.703 54.545 0.00 0.00 0.00 3.36
2249 3951 1.619827 GGAGAGCAGATGGAGATGGAG 59.380 57.143 0.00 0.00 0.00 3.86
2259 3961 3.230134 GTCATGGAGTAGGAGAGCAGAT 58.770 50.000 0.00 0.00 0.00 2.90
2276 3983 1.623811 GCCGGAGTGGGTATATGTCAT 59.376 52.381 5.05 0.00 38.63 3.06
2277 3984 1.045407 GCCGGAGTGGGTATATGTCA 58.955 55.000 5.05 0.00 38.63 3.58
2278 3985 0.038526 CGCCGGAGTGGGTATATGTC 60.039 60.000 5.05 0.00 38.63 3.06
2279 3986 2.046938 CGCCGGAGTGGGTATATGT 58.953 57.895 5.05 0.00 38.63 2.29
2323 4062 2.937469 TAAAATGGCGACCAATGCAG 57.063 45.000 2.68 0.00 36.95 4.41
2439 4195 5.413523 GGTGAACGTACAAATTATTCCCAGT 59.586 40.000 0.00 0.00 0.00 4.00
2442 4198 4.630940 TCGGTGAACGTACAAATTATTCCC 59.369 41.667 0.00 0.00 44.69 3.97
2450 4206 1.592081 CGGTTTCGGTGAACGTACAAA 59.408 47.619 0.00 0.00 44.69 2.83
2480 4236 3.050835 ACTTGTTACCAGTACCAAGGGT 58.949 45.455 16.45 6.75 39.11 4.34
2509 4266 6.451393 AGAAGTACTAGCTGAAGAACAAGTG 58.549 40.000 0.00 0.00 0.00 3.16
2522 4279 5.105756 TGGGTAAAACGGTAGAAGTACTAGC 60.106 44.000 0.00 0.00 43.60 3.42
2560 4317 8.658499 ATCAAGGGTCGTTGATAAAATACTAC 57.342 34.615 14.73 0.00 43.85 2.73
2561 4318 7.929785 GGATCAAGGGTCGTTGATAAAATACTA 59.070 37.037 15.87 0.00 45.32 1.82
2562 4319 6.766467 GGATCAAGGGTCGTTGATAAAATACT 59.234 38.462 15.87 0.00 45.32 2.12
2563 4320 6.766467 AGGATCAAGGGTCGTTGATAAAATAC 59.234 38.462 15.87 5.76 45.32 1.89
2564 4321 6.765989 CAGGATCAAGGGTCGTTGATAAAATA 59.234 38.462 15.87 0.00 45.32 1.40
2565 4322 5.590259 CAGGATCAAGGGTCGTTGATAAAAT 59.410 40.000 15.87 0.00 45.32 1.82
2567 4324 4.019681 ACAGGATCAAGGGTCGTTGATAAA 60.020 41.667 15.87 0.00 45.32 1.40
2589 4349 8.094548 TGTATAAGTGGTCCTGCATAATGATAC 58.905 37.037 0.00 0.00 0.00 2.24
2641 4401 6.959701 GCTACGAAAATAGCAAATCATGTC 57.040 37.500 0.00 0.00 45.83 3.06
2663 4423 1.293963 TGCTGCGTGAGAACAGATGC 61.294 55.000 0.00 0.00 35.90 3.91
2688 4448 3.207265 TGTGTGTTGTGTTATGCTCCT 57.793 42.857 0.00 0.00 0.00 3.69
2689 4449 3.980646 TTGTGTGTTGTGTTATGCTCC 57.019 42.857 0.00 0.00 0.00 4.70
2690 4450 5.280945 ACATTTGTGTGTTGTGTTATGCTC 58.719 37.500 0.00 0.00 0.00 4.26
2691 4451 5.261209 ACATTTGTGTGTTGTGTTATGCT 57.739 34.783 0.00 0.00 0.00 3.79
2708 4468 6.746822 CGTGCATCATTGTGTTATGTACATTT 59.253 34.615 14.77 0.00 39.39 2.32
2747 4512 4.261489 CGTACGCATGGATAGGAACTTAGT 60.261 45.833 0.52 0.00 41.75 2.24
2904 4677 5.806366 GACTTGTCAGTCTACTCCTAGAC 57.194 47.826 0.00 0.36 46.70 2.59
2984 4761 4.685628 CCTGTGTTGTATTGATTTTGTGCC 59.314 41.667 0.00 0.00 0.00 5.01
3044 4821 2.142356 TTGGAAACCCATGCGATGAT 57.858 45.000 0.00 0.00 32.92 2.45
3173 4951 3.493350 GCTGACGAGTCATTCCATGGTAT 60.493 47.826 12.58 4.51 39.13 2.73


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

AutoCloner maintained by Alex Coulton.