Multiple sequence alignment - TraesCS3B01G227000

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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 TraesCS3B01G227000 chr3B 100.000 2428 0 0 1 2428 322008393 322005966 0.000000e+00 4484.0
1 TraesCS3B01G227000 chr5A 92.707 2427 173 2 1 2426 472550056 472547633 0.000000e+00 3498.0
2 TraesCS3B01G227000 chr4D 78.344 2415 495 21 24 2426 14568706 14571104 0.000000e+00 1537.0
3 TraesCS3B01G227000 chr4D 90.909 44 4 0 482 525 20471274 20471317 2.610000e-05 60.2
4 TraesCS3B01G227000 chr6A 78.152 2435 508 22 1 2424 617698183 617695762 0.000000e+00 1528.0
5 TraesCS3B01G227000 chr7B 81.538 1365 241 11 1 1359 689727024 689725665 0.000000e+00 1114.0
6 TraesCS3B01G227000 chr2A 75.814 1228 286 9 1202 2426 666649213 666650432 1.600000e-171 612.0
7 TraesCS3B01G227000 chr2A 77.363 804 165 14 1627 2424 329613048 329612256 6.120000e-126 460.0
8 TraesCS3B01G227000 chr2A 76.712 803 177 10 1626 2424 778459606 778458810 2.870000e-119 438.0
9 TraesCS3B01G227000 chr3A 76.461 633 133 13 1674 2298 703167185 703167809 1.800000e-86 329.0
10 TraesCS3B01G227000 chr5B 74.872 585 131 14 1845 2419 565530443 565531021 4.010000e-63 252.0
11 TraesCS3B01G227000 chr4A 100.000 32 0 0 2393 2424 134202657 134202688 2.610000e-05 60.2


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 TraesCS3B01G227000 chr3B 322005966 322008393 2427 True 4484 4484 100.000 1 2428 1 chr3B.!!$R1 2427
1 TraesCS3B01G227000 chr5A 472547633 472550056 2423 True 3498 3498 92.707 1 2426 1 chr5A.!!$R1 2425
2 TraesCS3B01G227000 chr4D 14568706 14571104 2398 False 1537 1537 78.344 24 2426 1 chr4D.!!$F1 2402
3 TraesCS3B01G227000 chr6A 617695762 617698183 2421 True 1528 1528 78.152 1 2424 1 chr6A.!!$R1 2423
4 TraesCS3B01G227000 chr7B 689725665 689727024 1359 True 1114 1114 81.538 1 1359 1 chr7B.!!$R1 1358
5 TraesCS3B01G227000 chr2A 666649213 666650432 1219 False 612 612 75.814 1202 2426 1 chr2A.!!$F1 1224
6 TraesCS3B01G227000 chr2A 329612256 329613048 792 True 460 460 77.363 1627 2424 1 chr2A.!!$R1 797
7 TraesCS3B01G227000 chr2A 778458810 778459606 796 True 438 438 76.712 1626 2424 1 chr2A.!!$R2 798
8 TraesCS3B01G227000 chr3A 703167185 703167809 624 False 329 329 76.461 1674 2298 1 chr3A.!!$F1 624
9 TraesCS3B01G227000 chr5B 565530443 565531021 578 False 252 252 74.872 1845 2419 1 chr5B.!!$F1 574

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
743 745 0.3199 GAAGTGCACAGCTTCCTCGA 60.32 55.0 21.04 0.0 37.08 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 2175 0.92409 TCCTCGATCCCCTAGTGTCA 59.076 55.0 0.0 0.0 0.0 3.58 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
21 22 1.592669 GCGATCACTGGATCCCACG 60.593 63.158 9.90 7.07 45.89 4.94
39 40 4.738998 CATGGAGGGGGCGCAACA 62.739 66.667 10.83 0.00 0.00 3.33
51 52 1.653667 CGCAACATGTCAACCAGCA 59.346 52.632 0.00 0.00 0.00 4.41
72 73 1.843851 TCCCTATAGGCACAAACCAGG 59.156 52.381 13.85 0.00 34.51 4.45
76 77 1.295020 ATAGGCACAAACCAGGGCTA 58.705 50.000 0.00 0.00 42.75 3.93
80 81 1.000843 GGCACAAACCAGGGCTAAAAG 59.999 52.381 0.00 0.00 0.00 2.27
134 135 0.475475 TGCAGGCATTATCAGGGAGG 59.525 55.000 0.00 0.00 0.00 4.30
139 140 0.475906 GCATTATCAGGGAGGGCACT 59.524 55.000 0.00 0.00 0.00 4.40
170 171 2.439507 TCTTCTCCAGCCTTTCTTGTGT 59.560 45.455 0.00 0.00 0.00 3.72
175 176 5.385198 TCTCCAGCCTTTCTTGTGTAAAAT 58.615 37.500 0.00 0.00 0.00 1.82
200 201 1.594833 GGGACATGGCGACTGTGTA 59.405 57.895 0.00 0.00 31.59 2.90
221 222 9.936759 TGTGTATAGATTACAGATGTTTGAACA 57.063 29.630 0.00 0.00 44.06 3.18
266 267 2.361119 CCAGTGCCAATCATTGATGAGG 59.639 50.000 0.00 12.00 40.64 3.86
271 272 4.036027 GTGCCAATCATTGATGAGGTACTG 59.964 45.833 21.73 8.16 41.55 2.74
345 347 3.461085 ACCACCAGATAAGATTGGCAGAT 59.539 43.478 0.00 0.00 38.03 2.90
374 376 7.345914 AGAGGAGTATAAGACAGCCTTTACAAT 59.654 37.037 0.00 0.00 35.80 2.71
389 391 1.636148 ACAATGCACTCAGGCCATTT 58.364 45.000 5.01 0.00 0.00 2.32
446 448 0.460311 CCTCCTACTTTCATCGGCGT 59.540 55.000 6.85 0.00 0.00 5.68
454 456 1.231958 TTTCATCGGCGTTGTGACCC 61.232 55.000 16.65 0.00 0.00 4.46
572 574 5.348986 TCGTCAGGTATTGCAATTACTCTC 58.651 41.667 18.75 9.69 0.00 3.20
619 621 2.626266 TCTAAGTGTGCTTTCGGACAGA 59.374 45.455 0.00 0.00 42.39 3.41
636 638 5.288804 GGACAGAGACAGATTGCTTATCTC 58.711 45.833 0.00 0.00 41.78 2.75
706 708 5.972935 TCGAAACTATCAGAAAGTGGCATA 58.027 37.500 0.00 0.00 0.00 3.14
717 719 5.829924 CAGAAAGTGGCATATCCCTAACAAT 59.170 40.000 0.00 0.00 0.00 2.71
743 745 0.319900 GAAGTGCACAGCTTCCTCGA 60.320 55.000 21.04 0.00 37.08 4.04
751 753 2.217038 AGCTTCCTCGACTTGGCCA 61.217 57.895 0.00 0.00 0.00 5.36
752 754 1.302511 GCTTCCTCGACTTGGCCAA 60.303 57.895 19.25 19.25 0.00 4.52
771 773 6.879993 TGGCCAACTACTATCGAAAATTTGTA 59.120 34.615 0.61 0.00 0.00 2.41
783 785 6.439599 TCGAAAATTTGTAAAGCATTTCGGA 58.560 32.000 21.51 13.16 45.31 4.55
800 802 5.607939 TTCGGAATTATAGCAAGACCTCA 57.392 39.130 0.00 0.00 0.00 3.86
820 822 7.684529 ACCTCATTTCAATCTACTCAAGAAGT 58.315 34.615 0.00 0.00 42.33 3.01
878 880 0.737804 TTCGAGCTGCTGCAACAAAA 59.262 45.000 18.42 6.06 42.74 2.44
940 942 7.467557 ACAAAACAATTCATCATTGACACAC 57.532 32.000 1.59 0.00 44.78 3.82
943 945 5.771153 ACAATTCATCATTGACACACACA 57.229 34.783 1.59 0.00 44.78 3.72
945 947 5.067544 ACAATTCATCATTGACACACACACA 59.932 36.000 1.59 0.00 44.78 3.72
973 975 6.554982 TGATTATGGAGTAGGAGCAGTGTTAT 59.445 38.462 0.00 0.00 0.00 1.89
975 977 7.907841 TTATGGAGTAGGAGCAGTGTTATAA 57.092 36.000 0.00 0.00 0.00 0.98
1075 1078 6.656693 GGAATGTTTAGCTATACTCATGGCAT 59.343 38.462 14.32 0.00 40.92 4.40
1087 1090 3.220110 CTCATGGCATTAGAGCAATGGT 58.780 45.455 2.42 0.00 44.39 3.55
1092 1095 2.648059 GCATTAGAGCAATGGTGTCCT 58.352 47.619 0.00 0.00 43.70 3.85
1125 1128 7.662604 TCATGATGAATTTCTGATATGGACG 57.337 36.000 0.00 0.00 0.00 4.79
1131 1134 6.591001 TGAATTTCTGATATGGACGGATCAA 58.409 36.000 0.00 0.00 31.83 2.57
1223 1226 4.769859 TGGGGTTACGCTACAAAATTTC 57.230 40.909 0.00 0.00 0.00 2.17
1253 1256 0.250901 GGATCCACCAACAGTGCTGT 60.251 55.000 6.95 0.00 45.83 4.40
1254 1257 0.877071 GATCCACCAACAGTGCTGTG 59.123 55.000 5.53 0.00 45.83 3.66
1380 1383 2.546373 GCATGCTCAAAAGTTGCTGGAA 60.546 45.455 11.37 0.00 33.55 3.53
1434 1437 4.579869 GTTTTTCTGTCTCTGATGGCCTA 58.420 43.478 3.32 0.00 0.00 3.93
1450 1453 7.977818 TGATGGCCTATTATACTTCAGACAAT 58.022 34.615 3.32 0.00 0.00 2.71
1462 1465 3.815133 AGACAATGGCTATGGCTGG 57.185 52.632 0.00 0.00 33.98 4.85
1463 1466 0.184451 AGACAATGGCTATGGCTGGG 59.816 55.000 0.00 0.00 33.98 4.45
1495 1498 2.636647 TGCAGTCCAACAATCTGTGA 57.363 45.000 0.00 0.00 0.00 3.58
1556 1559 3.844211 AGTTTCCCAGTGACTTATAGGCA 59.156 43.478 0.00 0.00 0.00 4.75
1561 1564 3.900601 CCCAGTGACTTATAGGCATCTCT 59.099 47.826 0.00 0.00 34.53 3.10
1589 1592 4.057406 TGTTTGCCTGACCAAAAATGAG 57.943 40.909 0.00 0.00 36.55 2.90
1594 1597 2.242043 CCTGACCAAAAATGAGGCAGT 58.758 47.619 0.00 0.00 31.46 4.40
1615 1618 4.711846 AGTAGGTTCATCAGTATGTGCAGA 59.288 41.667 0.00 0.00 37.40 4.26
1701 1704 0.909610 CACTACTGGAAGGGGCCTGA 60.910 60.000 0.84 0.00 39.30 3.86
1729 1732 3.941483 GGTGACGATGGATTTCATTGACT 59.059 43.478 0.00 0.00 39.16 3.41
1745 1748 2.167662 TGACTGTCTACCGCAATCAGA 58.832 47.619 9.51 0.00 0.00 3.27
1757 1760 2.287788 CGCAATCAGACAAGGCAAACTT 60.288 45.455 0.00 0.00 41.00 2.66
1823 1826 2.178580 GCCCCTTCAACATCCATTCAA 58.821 47.619 0.00 0.00 0.00 2.69
1873 1876 4.219944 TGGATAACGTCTACAAGCTTCACT 59.780 41.667 0.00 0.00 0.00 3.41
1936 1940 1.270785 TGAGCAAATTCTGGCGTGAGA 60.271 47.619 0.00 0.00 34.54 3.27
2013 2017 2.762327 GGATGGGCAATCAGAACATGTT 59.238 45.455 11.78 11.78 36.98 2.71
2055 2059 2.089201 CTGAGGTGCTTCATTCATGCA 58.911 47.619 0.00 0.00 32.83 3.96
2091 2095 1.270550 AGCCAATTCCTTTCACTTGCG 59.729 47.619 0.00 0.00 0.00 4.85
2186 2195 0.924090 TGACACTAGGGGATCGAGGA 59.076 55.000 0.00 0.00 0.00 3.71
2245 2254 3.812167 GCTGGAGGAAAGGAAGACAATGT 60.812 47.826 0.00 0.00 0.00 2.71
2261 2270 3.679980 ACAATGTAGCAAGTACTCAAGCG 59.320 43.478 0.00 0.00 32.19 4.68
2406 2415 1.898574 CCGAGCCAACCACAAGCTT 60.899 57.895 0.00 0.00 36.87 3.74
2427 2436 6.939551 CTTGCATTCAAGTATTTTGGTCAG 57.060 37.500 0.00 0.00 43.55 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.745308 CCTCCATGCGTGGGATCCA 61.745 63.158 24.78 4.04 46.06 3.41
39 40 3.328931 CCTATAGGGATGCTGGTTGACAT 59.671 47.826 11.33 0.00 37.23 3.06
51 52 2.443255 CCTGGTTTGTGCCTATAGGGAT 59.557 50.000 20.58 0.00 38.01 3.85
72 73 4.986622 ACGCTCAATTTCATCTTTTAGCC 58.013 39.130 0.00 0.00 0.00 3.93
76 77 5.916883 CACTTGACGCTCAATTTCATCTTTT 59.083 36.000 1.76 0.00 35.59 2.27
80 81 4.668576 TCACTTGACGCTCAATTTCATC 57.331 40.909 1.76 0.00 35.59 2.92
134 135 3.942115 GGAGAAGAAAATGGACTAGTGCC 59.058 47.826 12.28 8.04 0.00 5.01
139 140 3.846588 AGGCTGGAGAAGAAAATGGACTA 59.153 43.478 0.00 0.00 0.00 2.59
170 171 3.547746 GCCATGTCCCGTCCTTATTTTA 58.452 45.455 0.00 0.00 0.00 1.52
175 176 1.683025 TCGCCATGTCCCGTCCTTA 60.683 57.895 0.00 0.00 0.00 2.69
266 267 2.101582 CACCTACCAGCTCATCCAGTAC 59.898 54.545 0.00 0.00 0.00 2.73
271 272 1.342819 CTAGCACCTACCAGCTCATCC 59.657 57.143 0.00 0.00 42.05 3.51
345 347 3.205507 AGGCTGTCTTATACTCCTCTCCA 59.794 47.826 0.00 0.00 29.44 3.86
374 376 0.609957 CTCCAAATGGCCTGAGTGCA 60.610 55.000 3.32 0.00 34.44 4.57
389 391 3.973206 ACGACATGACCAAATACTCCA 57.027 42.857 0.00 0.00 0.00 3.86
495 497 7.294017 ACTGAAAACCAAGATGTCATCAAAT 57.706 32.000 15.20 0.00 0.00 2.32
572 574 0.460987 GACTTGCCAGTGATCCCTCG 60.461 60.000 0.00 0.00 31.22 4.63
619 621 2.224161 GCCCGAGATAAGCAATCTGTCT 60.224 50.000 6.33 0.00 45.35 3.41
636 638 1.948834 TGCTCATTGATAACATGCCCG 59.051 47.619 0.00 0.00 0.00 6.13
706 708 5.358160 GCACTTCTTTGCTATTGTTAGGGAT 59.642 40.000 0.00 0.00 39.59 3.85
717 719 2.260844 AGCTGTGCACTTCTTTGCTA 57.739 45.000 19.41 0.00 43.41 3.49
731 733 1.004440 GCCAAGTCGAGGAAGCTGT 60.004 57.895 0.00 0.00 0.00 4.40
743 745 4.546829 TTTCGATAGTAGTTGGCCAAGT 57.453 40.909 28.29 28.29 37.40 3.16
771 773 7.196331 GTCTTGCTATAATTCCGAAATGCTTT 58.804 34.615 0.00 0.00 0.00 3.51
783 785 9.638176 AGATTGAAATGAGGTCTTGCTATAATT 57.362 29.630 0.00 0.00 0.00 1.40
789 791 6.059787 AGTAGATTGAAATGAGGTCTTGCT 57.940 37.500 0.00 0.00 0.00 3.91
800 802 7.612677 ACGGTACTTCTTGAGTAGATTGAAAT 58.387 34.615 0.00 0.00 41.41 2.17
844 846 1.270550 CTCGAATGCCTTGGCAGTTTT 59.729 47.619 19.53 9.37 0.00 2.43
878 880 4.262549 GCAGAATAGGTGCAGAGATCAGAT 60.263 45.833 0.00 0.00 40.86 2.90
940 942 5.917462 TCCTACTCCATAATCACATGTGTG 58.083 41.667 24.63 15.34 46.91 3.82
943 945 4.655649 TGCTCCTACTCCATAATCACATGT 59.344 41.667 0.00 0.00 0.00 3.21
945 947 4.904251 ACTGCTCCTACTCCATAATCACAT 59.096 41.667 0.00 0.00 0.00 3.21
973 975 2.317040 GATCGGATGTCCTCCCTGTTA 58.683 52.381 0.00 0.00 41.49 2.41
975 977 1.109920 CGATCGGATGTCCTCCCTGT 61.110 60.000 7.38 0.00 41.49 4.00
1024 1027 1.580059 TAGGTGGACAATCCCCTGTC 58.420 55.000 12.61 0.00 44.21 3.51
1032 1035 5.192522 ACATTCCTTCTCATAGGTGGACAAT 59.807 40.000 0.00 0.00 36.63 2.71
1075 1078 3.844211 AGGTAAGGACACCATTGCTCTAA 59.156 43.478 0.00 0.00 41.40 2.10
1087 1090 6.806668 TTCATCATGATGTAGGTAAGGACA 57.193 37.500 30.01 8.18 39.72 4.02
1125 1128 1.639298 GCACCAGACTGCGTTGATCC 61.639 60.000 0.00 0.00 0.00 3.36
1131 1134 1.518056 CCAAATGCACCAGACTGCGT 61.518 55.000 0.00 0.00 40.31 5.24
1223 1226 0.181350 GGTGGATCCCTGCCTGTAAG 59.819 60.000 9.90 0.00 0.00 2.34
1253 1256 2.265739 GGCGAGACAGTGCATCCA 59.734 61.111 0.00 0.00 0.00 3.41
1254 1257 2.887568 CGGCGAGACAGTGCATCC 60.888 66.667 0.00 0.00 0.00 3.51
1380 1383 2.358003 GGCTGCTGCGAGAACTGT 60.358 61.111 9.65 0.00 40.82 3.55
1434 1437 6.656693 GCCATAGCCATTGTCTGAAGTATAAT 59.343 38.462 0.00 0.00 0.00 1.28
1475 1478 2.929641 TCACAGATTGTTGGACTGCAA 58.070 42.857 0.00 0.00 35.38 4.08
1495 1498 2.684374 TGCTATCATGAAAAGCACGCAT 59.316 40.909 24.57 0.00 41.15 4.73
1533 1536 4.192317 GCCTATAAGTCACTGGGAAACTG 58.808 47.826 0.00 0.00 0.00 3.16
1534 1537 3.844211 TGCCTATAAGTCACTGGGAAACT 59.156 43.478 0.00 0.00 0.00 2.66
1578 1581 3.525800 ACCTACTGCCTCATTTTTGGT 57.474 42.857 0.00 0.00 0.00 3.67
1589 1592 4.122776 CACATACTGATGAACCTACTGCC 58.877 47.826 0.00 0.00 36.48 4.85
1594 1597 4.956075 TCTCTGCACATACTGATGAACCTA 59.044 41.667 0.00 0.00 36.48 3.08
1615 1618 2.916702 TGTTGACAGACTGCACATCT 57.083 45.000 1.25 0.00 0.00 2.90
1701 1704 2.859165 AATCCATCGTCACCACTTGT 57.141 45.000 0.00 0.00 0.00 3.16
1729 1732 2.353704 CCTTGTCTGATTGCGGTAGACA 60.354 50.000 8.30 8.30 46.42 3.41
1745 1748 4.190772 CACCAAAATGAAGTTTGCCTTGT 58.809 39.130 0.00 0.00 37.20 3.16
1757 1760 2.692709 ATCCACCACCACCAAAATGA 57.307 45.000 0.00 0.00 0.00 2.57
1873 1876 2.025037 AGATGATGCCTTTTGGTAGCCA 60.025 45.455 0.00 0.00 39.94 4.75
1936 1940 1.337074 CGTTCCAATGCAGGCAAACAT 60.337 47.619 0.00 0.00 0.00 2.71
2091 2095 6.811665 GGTAGCTGGAATTGTACCAAAATTTC 59.188 38.462 0.00 0.00 36.95 2.17
2167 2175 0.924090 TCCTCGATCCCCTAGTGTCA 59.076 55.000 0.00 0.00 0.00 3.58
2186 2195 3.573538 TGGTATTTTGCACACTGATGCTT 59.426 39.130 9.40 0.00 46.28 3.91
2245 2254 3.444034 AGATGTCGCTTGAGTACTTGCTA 59.556 43.478 0.00 0.00 0.00 3.49
2348 2357 6.285829 GCACATATGCCTGCAACTTAGCAT 62.286 45.833 12.18 11.13 46.97 3.79
2351 2360 3.344904 GCACATATGCCTGCAACTTAG 57.655 47.619 12.18 0.00 46.97 2.18


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

AutoCloner maintained by Alex Coulton.