Multiple sequence alignment - TraesCS5A01G078100

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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 TraesCS5A01G078100 chr5A 100.000 2527 0 0 1 2527 95867642 95870168 0.000000e+00 4667
1 TraesCS5A01G078100 chr5A 100.000 387 0 0 2906 3292 95870547 95870933 0.000000e+00 715
2 TraesCS5A01G078100 chr5D 92.715 2608 89 33 1 2527 103177587 103175000 0.000000e+00 3670
3 TraesCS5A01G078100 chr5D 87.778 360 34 7 2938 3292 103174544 103174190 2.360000e-111 412
4 TraesCS5A01G078100 chr5B 91.496 2540 115 52 34 2527 112196256 112193772 0.000000e+00 3400
5 TraesCS5A01G078100 chr5B 89.779 362 25 5 2938 3292 112193099 112192743 1.390000e-123 453
6 TraesCS5A01G078100 chr5B 86.301 219 27 2 1538 1756 660589477 660589692 5.490000e-58 235
7 TraesCS5A01G078100 chr1B 87.281 228 26 2 1541 1768 24933086 24932862 1.170000e-64 257
8 TraesCS5A01G078100 chr1A 87.281 228 26 2 1541 1768 18461762 18461538 1.170000e-64 257
9 TraesCS5A01G078100 chr1D 85.965 228 29 2 1541 1768 17169108 17168884 1.180000e-59 241
10 TraesCS5A01G078100 chr3B 85.714 224 29 2 1541 1764 828111448 828111668 1.980000e-57 233
11 TraesCS5A01G078100 chr3D 85.268 224 30 2 1541 1764 610544048 610544268 9.190000e-56 228
12 TraesCS5A01G078100 chr3A 84.821 224 31 2 1541 1764 744879518 744879738 4.280000e-54 222


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 TraesCS5A01G078100 chr5A 95867642 95870933 3291 False 2691.0 4667 100.0000 1 3292 2 chr5A.!!$F1 3291
1 TraesCS5A01G078100 chr5D 103174190 103177587 3397 True 2041.0 3670 90.2465 1 3292 2 chr5D.!!$R1 3291
2 TraesCS5A01G078100 chr5B 112192743 112196256 3513 True 1926.5 3400 90.6375 34 3292 2 chr5B.!!$R1 3258

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
916 978 0.031616 TGGTTTGGTTTTGCCCCTCT 60.032 50.0 0.0 0.0 36.04 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 2419 1.338973 GTCCATGCATGCATAACCCAG 59.661 52.381 31.73 18.22 34.91 4.45 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
42 43 4.917906 AAGTCCCTCTTGCAATCTACTT 57.082 40.909 0.00 3.48 34.77 2.24
333 375 2.033372 TCACGTCAAACCAGACCTGTA 58.967 47.619 0.00 0.00 35.07 2.74
388 436 0.871722 TGCACAGTACAAACATCCGC 59.128 50.000 0.00 0.00 0.00 5.54
515 572 6.581919 GCTTTGATCAGCTCTTCTTCTTTTTC 59.418 38.462 0.00 0.00 36.79 2.29
583 641 4.036498 GCCTTCAATTCACTCATCCATCTG 59.964 45.833 0.00 0.00 0.00 2.90
596 654 1.140652 TCCATCTGACACAGCACACAA 59.859 47.619 0.00 0.00 0.00 3.33
607 665 2.286872 CAGCACACAATCATCTCCTCC 58.713 52.381 0.00 0.00 0.00 4.30
655 713 2.192664 TTCCTTAGCATGGCGTTTCA 57.807 45.000 0.00 0.00 0.00 2.69
719 781 1.472480 CAATCACCTTTAGTTGCCCCG 59.528 52.381 0.00 0.00 0.00 5.73
888 950 2.282745 AGCACTTGCAAGGGGAGC 60.283 61.111 29.24 24.22 45.16 4.70
916 978 0.031616 TGGTTTGGTTTTGCCCCTCT 60.032 50.000 0.00 0.00 36.04 3.69
917 979 0.679505 GGTTTGGTTTTGCCCCTCTC 59.320 55.000 0.00 0.00 36.04 3.20
918 980 1.704641 GTTTGGTTTTGCCCCTCTCT 58.295 50.000 0.00 0.00 36.04 3.10
921 983 0.112412 TGGTTTTGCCCCTCTCTTCC 59.888 55.000 0.00 0.00 36.04 3.46
931 994 2.765699 CCCCTCTCTTCCTCTCTTTCAG 59.234 54.545 0.00 0.00 0.00 3.02
933 996 3.447229 CCCTCTCTTCCTCTCTTTCAGTC 59.553 52.174 0.00 0.00 0.00 3.51
947 1010 2.999507 TCAGTCGTCTTCTCAGCTTC 57.000 50.000 0.00 0.00 0.00 3.86
949 1012 2.822561 TCAGTCGTCTTCTCAGCTTCAT 59.177 45.455 0.00 0.00 0.00 2.57
954 1017 4.095782 GTCGTCTTCTCAGCTTCATACTCT 59.904 45.833 0.00 0.00 0.00 3.24
1061 1124 4.918588 AGTTGGACCCAGGTAATTAACTG 58.081 43.478 21.56 21.56 34.54 3.16
1077 1140 2.548464 ACTGGCTCATCCTCTCTCTT 57.452 50.000 0.00 0.00 35.26 2.85
1078 1141 2.387757 ACTGGCTCATCCTCTCTCTTC 58.612 52.381 0.00 0.00 35.26 2.87
1079 1142 2.292126 ACTGGCTCATCCTCTCTCTTCA 60.292 50.000 0.00 0.00 35.26 3.02
1080 1143 2.765135 CTGGCTCATCCTCTCTCTTCAA 59.235 50.000 0.00 0.00 35.26 2.69
1081 1144 3.176411 TGGCTCATCCTCTCTCTTCAAA 58.824 45.455 0.00 0.00 35.26 2.69
1082 1145 3.197333 TGGCTCATCCTCTCTCTTCAAAG 59.803 47.826 0.00 0.00 35.26 2.77
1087 1168 1.625818 TCCTCTCTCTTCAAAGCACCC 59.374 52.381 0.00 0.00 0.00 4.61
1103 1184 1.752310 CCCACACACACCAGCACAA 60.752 57.895 0.00 0.00 0.00 3.33
1104 1185 1.108727 CCCACACACACCAGCACAAT 61.109 55.000 0.00 0.00 0.00 2.71
1105 1186 0.311790 CCACACACACCAGCACAATC 59.688 55.000 0.00 0.00 0.00 2.67
1106 1187 1.023502 CACACACACCAGCACAATCA 58.976 50.000 0.00 0.00 0.00 2.57
1107 1188 1.610038 CACACACACCAGCACAATCAT 59.390 47.619 0.00 0.00 0.00 2.45
1108 1189 2.034939 CACACACACCAGCACAATCATT 59.965 45.455 0.00 0.00 0.00 2.57
1109 1190 3.252944 CACACACACCAGCACAATCATTA 59.747 43.478 0.00 0.00 0.00 1.90
1110 1191 4.081406 ACACACACCAGCACAATCATTAT 58.919 39.130 0.00 0.00 0.00 1.28
1111 1192 5.123661 CACACACACCAGCACAATCATTATA 59.876 40.000 0.00 0.00 0.00 0.98
1112 1193 5.355071 ACACACACCAGCACAATCATTATAG 59.645 40.000 0.00 0.00 0.00 1.31
1113 1194 5.355071 CACACACCAGCACAATCATTATAGT 59.645 40.000 0.00 0.00 0.00 2.12
1114 1195 5.945784 ACACACCAGCACAATCATTATAGTT 59.054 36.000 0.00 0.00 0.00 2.24
1115 1196 6.127925 ACACACCAGCACAATCATTATAGTTG 60.128 38.462 0.00 0.00 0.00 3.16
1116 1197 5.357878 ACACCAGCACAATCATTATAGTTGG 59.642 40.000 0.00 0.00 0.00 3.77
1472 1556 3.692406 GTGGCCGGGTCGTCTTCT 61.692 66.667 2.18 0.00 0.00 2.85
1781 1865 0.037790 GCTCCAGCAAGAAGTCGTCT 60.038 55.000 0.00 0.00 41.59 4.18
1850 1940 2.203938 TCCACCACCTCCACCTCC 60.204 66.667 0.00 0.00 0.00 4.30
2153 2243 2.036992 GTCGATCAAGATGGAGGAGCAT 59.963 50.000 0.00 0.00 0.00 3.79
2194 2284 4.394712 AGGCGGCTTTGTCGGAGG 62.395 66.667 5.25 0.00 0.00 4.30
2347 2437 1.067974 CACTGGGTTATGCATGCATGG 59.932 52.381 37.43 22.35 37.82 3.66
2390 2488 1.197812 GGTCTCCCCGCCTTAGTTTA 58.802 55.000 0.00 0.00 0.00 2.01
2513 2611 5.545658 ATTAGCTAAATGGTGTGTGTTCG 57.454 39.130 10.85 0.00 0.00 3.95
2523 2621 1.525619 GTGTGTGTTCGTGCCTACTTC 59.474 52.381 0.00 0.00 0.00 3.01
2938 3128 4.684242 TGTCGTTAGAGTGTTGCTAATGTG 59.316 41.667 0.00 0.00 36.62 3.21
2945 3135 5.804639 AGAGTGTTGCTAATGTGTATGGAA 58.195 37.500 0.00 0.00 0.00 3.53
2946 3136 5.877012 AGAGTGTTGCTAATGTGTATGGAAG 59.123 40.000 0.00 0.00 0.00 3.46
2963 3380 2.502295 GAAGGAGCTCCAATGGCATAG 58.498 52.381 33.90 0.00 38.89 2.23
2980 3397 6.361433 TGGCATAGCTAAATTACAAGGCTAA 58.639 36.000 0.00 0.00 38.67 3.09
3001 3421 6.490040 GCTAAGCCATATTTGATGGACCTAAA 59.510 38.462 7.78 0.00 41.64 1.85
3002 3422 6.715347 AAGCCATATTTGATGGACCTAAAC 57.285 37.500 7.78 0.00 41.64 2.01
3075 3502 3.342719 TCAAAGCAAGTATGATTCGCCA 58.657 40.909 0.00 0.00 33.12 5.69
3076 3503 3.126858 TCAAAGCAAGTATGATTCGCCAC 59.873 43.478 0.00 0.00 33.12 5.01
3083 3510 4.882671 AGTATGATTCGCCACAATCAAC 57.117 40.909 1.86 2.98 44.18 3.18
3086 3513 3.829886 TGATTCGCCACAATCAACTTC 57.170 42.857 0.00 0.00 39.37 3.01
3135 3562 2.358898 GGTATGCGCTTGTGAAATGGAT 59.641 45.455 9.73 0.00 0.00 3.41
3140 3567 2.223340 GCGCTTGTGAAATGGATGTAGG 60.223 50.000 0.00 0.00 0.00 3.18
3146 3573 4.780815 TGTGAAATGGATGTAGGATGGAC 58.219 43.478 0.00 0.00 0.00 4.02
3177 3604 4.631234 TGTAAGGAATACCATGGGACTCT 58.369 43.478 18.09 3.04 38.94 3.24
3179 3606 4.779993 AAGGAATACCATGGGACTCTTC 57.220 45.455 18.09 8.52 38.94 2.87
3198 3627 4.637534 TCTTCCACATGCTTATTTCAGCTC 59.362 41.667 0.00 0.00 40.79 4.09
3227 3656 5.538849 TTCCCTGTAAAAACAATTGACCC 57.461 39.130 13.59 0.00 0.00 4.46
3228 3657 4.547671 TCCCTGTAAAAACAATTGACCCA 58.452 39.130 13.59 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.486993 GCAAGAGGGACTTAGAAGAAGAAAAA 59.513 38.462 0.00 0.00 41.55 1.94
13 14 4.543590 TGCAAGAGGGACTTAGAAGAAG 57.456 45.455 0.00 0.00 41.55 2.85
17 18 5.721960 AGTAGATTGCAAGAGGGACTTAGAA 59.278 40.000 4.94 0.00 41.55 2.10
209 217 6.825721 AGAATCAAGAGGGTGTATCACAAATC 59.174 38.462 2.41 0.00 35.86 2.17
326 368 0.243095 GTGGTGAGACGGTACAGGTC 59.757 60.000 7.93 7.93 34.62 3.85
333 375 1.145377 GTGTTGGTGGTGAGACGGT 59.855 57.895 0.00 0.00 0.00 4.83
388 436 1.577328 GATTCGCCTGTGGGTGTGTG 61.577 60.000 0.00 0.00 43.20 3.82
515 572 6.609081 GTATTTATACACCCCCGGAGGCAG 62.609 54.167 0.00 0.00 38.76 4.85
583 641 2.417933 GGAGATGATTGTGTGCTGTGTC 59.582 50.000 0.00 0.00 0.00 3.67
596 654 0.491371 GAGGGAGGGGAGGAGATGAT 59.509 60.000 0.00 0.00 0.00 2.45
607 665 1.277580 ACAGCAATGGAGAGGGAGGG 61.278 60.000 0.00 0.00 0.00 4.30
655 713 0.741915 GCTAGCTTAGTGCGAGAGGT 59.258 55.000 7.70 0.00 45.45 3.85
719 781 2.224821 TCATGGGTCATGAGAGGGC 58.775 57.895 6.50 0.00 44.60 5.19
815 877 3.244044 GCTAAGGGAGAATGAGCCAGTAG 60.244 52.174 0.00 0.00 0.00 2.57
888 950 2.017138 AAACCAAACCACGCCTTTTG 57.983 45.000 0.00 0.00 33.30 2.44
916 978 3.757270 AGACGACTGAAAGAGAGGAAGA 58.243 45.455 0.00 0.00 37.43 2.87
917 979 4.217550 AGAAGACGACTGAAAGAGAGGAAG 59.782 45.833 0.00 0.00 37.43 3.46
918 980 4.145807 AGAAGACGACTGAAAGAGAGGAA 58.854 43.478 0.00 0.00 37.43 3.36
921 983 4.722194 CTGAGAAGACGACTGAAAGAGAG 58.278 47.826 0.00 0.00 37.43 3.20
931 994 4.095782 AGAGTATGAAGCTGAGAAGACGAC 59.904 45.833 0.00 0.00 0.00 4.34
933 996 4.095632 TGAGAGTATGAAGCTGAGAAGACG 59.904 45.833 0.00 0.00 0.00 4.18
954 1017 3.578716 CCTTGGTCCTCTCTACTTTGTGA 59.421 47.826 0.00 0.00 0.00 3.58
971 1034 1.065126 GTGATGAGGAGTTCCCCTTGG 60.065 57.143 0.00 0.00 36.49 3.61
1061 1124 3.795877 CTTTGAAGAGAGAGGATGAGCC 58.204 50.000 0.00 0.00 0.00 4.70
1065 1128 3.269178 GGTGCTTTGAAGAGAGAGGATG 58.731 50.000 0.00 0.00 0.00 3.51
1067 1130 1.625818 GGGTGCTTTGAAGAGAGAGGA 59.374 52.381 0.00 0.00 0.00 3.71
1077 1140 1.034838 GGTGTGTGTGGGTGCTTTGA 61.035 55.000 0.00 0.00 0.00 2.69
1078 1141 1.318886 TGGTGTGTGTGGGTGCTTTG 61.319 55.000 0.00 0.00 0.00 2.77
1079 1142 1.000270 TGGTGTGTGTGGGTGCTTT 60.000 52.632 0.00 0.00 0.00 3.51
1080 1143 1.453745 CTGGTGTGTGTGGGTGCTT 60.454 57.895 0.00 0.00 0.00 3.91
1081 1144 2.192979 CTGGTGTGTGTGGGTGCT 59.807 61.111 0.00 0.00 0.00 4.40
1082 1145 3.595758 GCTGGTGTGTGTGGGTGC 61.596 66.667 0.00 0.00 0.00 5.01
1087 1168 1.023502 TGATTGTGCTGGTGTGTGTG 58.976 50.000 0.00 0.00 0.00 3.82
1103 1184 9.388506 GAAATGATCCGATCCAACTATAATGAT 57.611 33.333 5.91 0.00 0.00 2.45
1104 1185 8.374743 TGAAATGATCCGATCCAACTATAATGA 58.625 33.333 5.91 0.00 0.00 2.57
1105 1186 8.446273 GTGAAATGATCCGATCCAACTATAATG 58.554 37.037 5.91 0.00 0.00 1.90
1106 1187 8.378565 AGTGAAATGATCCGATCCAACTATAAT 58.621 33.333 5.91 0.00 0.00 1.28
1107 1188 7.657354 CAGTGAAATGATCCGATCCAACTATAA 59.343 37.037 5.91 0.00 0.00 0.98
1108 1189 7.154656 CAGTGAAATGATCCGATCCAACTATA 58.845 38.462 5.91 0.00 0.00 1.31
1109 1190 5.994054 CAGTGAAATGATCCGATCCAACTAT 59.006 40.000 5.91 0.00 0.00 2.12
1110 1191 5.359756 CAGTGAAATGATCCGATCCAACTA 58.640 41.667 5.91 0.00 0.00 2.24
1111 1192 4.194640 CAGTGAAATGATCCGATCCAACT 58.805 43.478 5.91 0.50 0.00 3.16
1112 1193 3.313526 CCAGTGAAATGATCCGATCCAAC 59.686 47.826 5.91 0.00 0.00 3.77
1113 1194 3.544684 CCAGTGAAATGATCCGATCCAA 58.455 45.455 5.91 0.00 0.00 3.53
1114 1195 2.746142 GCCAGTGAAATGATCCGATCCA 60.746 50.000 5.91 0.00 0.00 3.41
1115 1196 1.876156 GCCAGTGAAATGATCCGATCC 59.124 52.381 5.91 0.00 0.00 3.36
1116 1197 2.547211 CAGCCAGTGAAATGATCCGATC 59.453 50.000 1.01 1.01 0.00 3.69
1328 1412 2.711009 TCCTCCCATGAAACACTGAAGT 59.289 45.455 0.00 0.00 0.00 3.01
1463 1547 1.803519 CAGCGAGGCAGAAGACGAC 60.804 63.158 0.00 0.00 0.00 4.34
1826 1916 1.687493 GGAGGTGGTGGAGGAGGAG 60.687 68.421 0.00 0.00 0.00 3.69
2171 2261 4.269523 ACAAAGCCGCCTCCAGCA 62.270 61.111 0.00 0.00 44.04 4.41
2194 2284 2.815647 GCCAGTACTGCTCGTGCC 60.816 66.667 17.86 0.00 38.71 5.01
2329 2419 1.338973 GTCCATGCATGCATAACCCAG 59.661 52.381 31.73 18.22 34.91 4.45
2390 2488 7.648770 AGACCATACCACATAACCCTAAATTT 58.351 34.615 0.00 0.00 0.00 1.82
2938 3128 2.856222 CCATTGGAGCTCCTTCCATAC 58.144 52.381 32.28 4.83 46.22 2.39
2945 3135 0.110104 GCTATGCCATTGGAGCTCCT 59.890 55.000 32.28 11.81 36.82 3.69
2946 3136 0.110104 AGCTATGCCATTGGAGCTCC 59.890 55.000 26.78 26.78 41.40 4.70
2957 3374 6.568653 GCTTAGCCTTGTAATTTAGCTATGCC 60.569 42.308 13.98 1.56 44.78 4.40
2980 3397 5.594317 GTGTTTAGGTCCATCAAATATGGCT 59.406 40.000 0.00 0.00 39.01 4.75
3001 3421 8.713971 TCCAACAGGATCAAACATATATAGTGT 58.286 33.333 0.00 0.00 0.00 3.55
3002 3422 9.730705 ATCCAACAGGATCAAACATATATAGTG 57.269 33.333 0.00 0.00 37.63 2.74
3075 3502 7.147976 GCAAAATTGAGGTAGAAGTTGATTGT 58.852 34.615 0.00 0.00 0.00 2.71
3076 3503 6.306356 CGCAAAATTGAGGTAGAAGTTGATTG 59.694 38.462 0.00 0.00 0.00 2.67
3083 3510 2.749621 AGGCGCAAAATTGAGGTAGAAG 59.250 45.455 10.83 0.00 0.00 2.85
3086 3513 1.401905 GGAGGCGCAAAATTGAGGTAG 59.598 52.381 10.83 0.00 0.00 3.18
3135 3562 7.713507 CCTTACAATTATTTCGTCCATCCTACA 59.286 37.037 0.00 0.00 0.00 2.74
3146 3573 8.296713 CCCATGGTATTCCTTACAATTATTTCG 58.703 37.037 11.73 0.00 31.99 3.46
3177 3604 4.334552 TGAGCTGAAATAAGCATGTGGAA 58.665 39.130 0.00 0.00 46.08 3.53
3179 3606 4.913335 ATGAGCTGAAATAAGCATGTGG 57.087 40.909 0.00 0.00 46.08 4.17
3227 3656 3.033909 TCACTGGATATCTCCACTGGTG 58.966 50.000 10.21 10.21 46.95 4.17
3228 3657 3.303938 CTCACTGGATATCTCCACTGGT 58.696 50.000 2.05 0.00 46.95 4.00
3239 3668 6.064060 CCAAATATTGCTTCCTCACTGGATA 58.936 40.000 0.00 0.00 45.68 2.59


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

AutoCloner maintained by Alex Coulton.