Multiple sequence alignment - TraesCS3A01G171900

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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 TraesCS3A01G171900 chr3A 100.000 2642 0 0 1 2642 186719308 186716667 0 4879
1 TraesCS3A01G171900 chr3D 89.981 2655 244 21 1 2642 314257397 314254752 0 3410
2 TraesCS3A01G171900 chr1D 89.992 2658 233 25 1 2642 80122114 80124754 0 3404
3 TraesCS3A01G171900 chr1D 89.107 2653 271 16 1 2642 198954755 198957400 0 3282
4 TraesCS3A01G171900 chr5D 89.676 2654 255 17 1 2642 204814090 204816736 0 3365
5 TraesCS3A01G171900 chr6D 89.579 2658 245 27 1 2642 79113226 79110585 0 3345
6 TraesCS3A01G171900 chr2D 89.488 2654 256 23 1 2642 416507810 416505168 0 3334
7 TraesCS3A01G171900 chr2D 89.221 2644 266 18 1 2632 351007632 351010268 0 3286
8 TraesCS3A01G171900 chr4D 89.509 2650 253 23 1 2634 304444734 304447374 0 3330
9 TraesCS3A01G171900 chr2A 89.136 2651 271 15 1 2641 641471583 641468940 0 3284


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 TraesCS3A01G171900 chr3A 186716667 186719308 2641 True 4879 4879 100.000 1 2642 1 chr3A.!!$R1 2641
1 TraesCS3A01G171900 chr3D 314254752 314257397 2645 True 3410 3410 89.981 1 2642 1 chr3D.!!$R1 2641
2 TraesCS3A01G171900 chr1D 80122114 80124754 2640 False 3404 3404 89.992 1 2642 1 chr1D.!!$F1 2641
3 TraesCS3A01G171900 chr1D 198954755 198957400 2645 False 3282 3282 89.107 1 2642 1 chr1D.!!$F2 2641
4 TraesCS3A01G171900 chr5D 204814090 204816736 2646 False 3365 3365 89.676 1 2642 1 chr5D.!!$F1 2641
5 TraesCS3A01G171900 chr6D 79110585 79113226 2641 True 3345 3345 89.579 1 2642 1 chr6D.!!$R1 2641
6 TraesCS3A01G171900 chr2D 416505168 416507810 2642 True 3334 3334 89.488 1 2642 1 chr2D.!!$R1 2641
7 TraesCS3A01G171900 chr2D 351007632 351010268 2636 False 3286 3286 89.221 1 2632 1 chr2D.!!$F1 2631
8 TraesCS3A01G171900 chr4D 304444734 304447374 2640 False 3330 3330 89.509 1 2634 1 chr4D.!!$F1 2633
9 TraesCS3A01G171900 chr2A 641468940 641471583 2643 True 3284 3284 89.136 1 2641 1 chr2A.!!$R1 2640

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
875 895 0.46546 TGCTTTGAAAGAGGTGCCGT 60.465 50.0 9.48 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2236 1.217747 TTATGGCCCACCCCATCACA 61.218 55.0 0.0 0.0 44.3 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
36 37 2.764010 AGTAACATGGGCATAGACACGA 59.236 45.455 0.00 0.00 0.00 4.35
48 50 4.202080 GCATAGACACGACTAACCATGGTA 60.202 45.833 20.12 5.85 0.00 3.25
54 56 6.322969 AGACACGACTAACCATGGTATTATCA 59.677 38.462 20.12 0.00 0.00 2.15
63 65 4.253685 CCATGGTATTATCACCCGCTTAG 58.746 47.826 2.57 0.00 37.84 2.18
75 77 1.139058 CCCGCTTAGGCTATTGTCACT 59.861 52.381 0.00 0.00 39.21 3.41
102 104 7.594758 GTGTTGAGTTAAGCATGCATTTCTTTA 59.405 33.333 21.98 5.56 0.00 1.85
222 225 4.631813 CAGGAAGTTTAAGATGGACCTTCG 59.368 45.833 1.90 0.00 0.00 3.79
245 249 5.588648 CGGGAAGCTGTATTTGATAAGGAAA 59.411 40.000 0.00 0.00 0.00 3.13
379 384 3.838565 TGCTAAGGATGTTGAAACCCAA 58.161 40.909 0.00 0.00 0.00 4.12
453 461 4.236147 CGTCAATAGAGATGATCTGGCAG 58.764 47.826 8.58 8.58 39.20 4.85
455 463 5.336610 CGTCAATAGAGATGATCTGGCAGAT 60.337 44.000 29.19 29.19 39.20 2.90
485 497 0.603569 AGACAAGCACGATCGGAAGT 59.396 50.000 20.98 10.14 0.00 3.01
507 519 2.040813 AGCCACTGGAGACATGAACAAT 59.959 45.455 0.00 0.00 41.51 2.71
510 522 3.941483 CCACTGGAGACATGAACAATACC 59.059 47.826 0.00 0.00 41.51 2.73
549 562 8.225107 CGACGTTGAAGATTTATTGACCTTTAA 58.775 33.333 0.00 0.00 0.00 1.52
566 579 4.038763 CCTTTAAAAGACCAAACCCCTGTC 59.961 45.833 0.00 0.00 0.00 3.51
589 602 3.564235 ACACTTACGTTAGATGCGACA 57.436 42.857 8.83 0.00 0.00 4.35
626 642 6.423905 TCATTTGTTTGTTGTTTTTCCGACAA 59.576 30.769 0.00 0.00 34.83 3.18
655 673 7.979537 ACAATAAAAACCTGTCTCTTCAAAACC 59.020 33.333 0.00 0.00 0.00 3.27
758 778 4.263550 TGAACCCATATTTTCTGGACCGAA 60.264 41.667 0.00 0.00 35.70 4.30
820 840 8.152898 TGGAAGATCATATGGAGAATAACACTG 58.847 37.037 2.13 0.00 0.00 3.66
847 867 2.041620 GGAAAGGATATGGCCCAGCATA 59.958 50.000 0.00 0.00 0.00 3.14
873 893 1.000938 CAGTGCTTTGAAAGAGGTGCC 60.001 52.381 9.48 0.00 0.00 5.01
875 895 0.465460 TGCTTTGAAAGAGGTGCCGT 60.465 50.000 9.48 0.00 0.00 5.68
957 977 6.349300 AGAACTTAAGTTGACTCTGCAAAGA 58.651 36.000 25.17 0.00 38.56 2.52
973 993 3.862642 GCAAAGATCTCGTCTTGTGTCCT 60.863 47.826 0.00 0.00 46.39 3.85
983 1003 4.023107 TCGTCTTGTGTCCTAGAAGTTGAG 60.023 45.833 0.00 0.00 31.87 3.02
992 1012 4.406003 GTCCTAGAAGTTGAGGCCTTATGA 59.594 45.833 6.77 0.00 32.40 2.15
997 1017 7.993183 CCTAGAAGTTGAGGCCTTATGAAAATA 59.007 37.037 6.77 0.00 0.00 1.40
1024 1044 4.202131 TGAAGAAACATTGTGCATGCAAGA 60.202 37.500 24.58 14.50 36.14 3.02
1038 1058 4.328983 GCATGCAAGATTTGTGGAGAAATG 59.671 41.667 14.21 0.00 0.00 2.32
1086 1106 3.128242 GTGAATGCCCTCATTGTGAAGAG 59.872 47.826 0.00 0.00 42.60 2.85
1144 1165 2.427095 ACTTGTTTCTTGTGTGAAGGGC 59.573 45.455 0.00 0.00 0.00 5.19
1223 1244 5.533903 AGCAGAAGAAAGAAGCAATGAAAGA 59.466 36.000 0.00 0.00 0.00 2.52
1251 1272 6.437162 CCCTCATGGAAATTTTAGAAGAACCA 59.563 38.462 0.00 0.00 35.39 3.67
1252 1273 7.039082 CCCTCATGGAAATTTTAGAAGAACCAA 60.039 37.037 0.00 0.00 35.39 3.67
1300 1321 5.663556 ACACCCAAAGAAGACCCAATTAAAA 59.336 36.000 0.00 0.00 0.00 1.52
1381 1402 7.234577 GTCTGAATGGGGATCTAGTAGAATTCT 59.765 40.741 13.56 13.56 0.00 2.40
1406 1427 6.270463 TCGATAGAGGAAGTAGAGTATGACCT 59.730 42.308 0.00 0.00 42.67 3.85
1424 1445 2.434702 ACCTACAGGAAATAGAAGCCCG 59.565 50.000 1.29 0.00 38.94 6.13
1623 1645 2.027192 CGGAGATTGTCCCAAGGAGAAA 60.027 50.000 0.00 0.00 43.47 2.52
1732 1760 4.713321 AGGCATGTAATGGAAAAGCAAGAT 59.287 37.500 0.00 0.00 46.86 2.40
1735 1763 6.643770 GGCATGTAATGGAAAAGCAAGATATG 59.356 38.462 0.00 0.00 46.86 1.78
1796 1826 8.106462 TGGTACTGATTGGATTTTATGAGTTGA 58.894 33.333 0.00 0.00 0.00 3.18
1913 1945 1.978580 GACCCTTGACCTCTGGAAAGA 59.021 52.381 0.00 0.00 0.00 2.52
1923 1955 8.964476 TTGACCTCTGGAAAGAATAATGATAC 57.036 34.615 0.00 0.00 0.00 2.24
1929 1961 8.089625 TCTGGAAAGAATAATGATACTCCACA 57.910 34.615 0.00 0.00 0.00 4.17
1951 1985 6.878923 CACAGAGTGGACCACAGATAAAATAA 59.121 38.462 26.30 0.00 36.74 1.40
1952 1986 7.065085 CACAGAGTGGACCACAGATAAAATAAG 59.935 40.741 26.30 5.31 36.74 1.73
1953 1987 7.106239 CAGAGTGGACCACAGATAAAATAAGT 58.894 38.462 26.30 0.36 36.74 2.24
1954 1988 8.258007 CAGAGTGGACCACAGATAAAATAAGTA 58.742 37.037 26.30 0.00 36.74 2.24
1955 1989 8.993424 AGAGTGGACCACAGATAAAATAAGTAT 58.007 33.333 26.30 0.00 36.74 2.12
1956 1990 8.964476 AGTGGACCACAGATAAAATAAGTATG 57.036 34.615 26.30 0.00 36.74 2.39
1957 1991 8.768397 AGTGGACCACAGATAAAATAAGTATGA 58.232 33.333 26.30 0.00 36.74 2.15
1958 1992 9.046296 GTGGACCACAGATAAAATAAGTATGAG 57.954 37.037 20.14 0.00 34.08 2.90
2049 2084 9.890629 GATAGAATGTTGGTATATGGAGCAATA 57.109 33.333 0.00 0.00 38.92 1.90
2120 2155 3.579151 AGAAGGAAGGGAGACAGTACAAC 59.421 47.826 0.00 0.00 0.00 3.32
2177 2213 2.893489 GGAATAATGATCAGTTGCCCCC 59.107 50.000 0.00 0.00 0.00 5.40
2178 2214 3.437052 GGAATAATGATCAGTTGCCCCCT 60.437 47.826 0.00 0.00 0.00 4.79
2198 2234 6.183361 CCCCCTATGATGAGTTCAAGGATTAA 60.183 42.308 0.23 0.00 38.03 1.40
2200 2236 7.946776 CCCCTATGATGAGTTCAAGGATTAAAT 59.053 37.037 0.23 0.00 38.03 1.40
2274 2310 4.978580 GCACACTCTTGCTAAAGGAAAAAG 59.021 41.667 0.00 0.00 39.59 2.27
2339 2377 3.873529 GTTTACGCAAAACCTGAGAGTG 58.126 45.455 3.24 0.00 41.44 3.51
2354 2393 5.071519 CCTGAGAGTGGTGAAGGAATGATAT 59.928 44.000 0.00 0.00 0.00 1.63
2572 2611 4.623932 TGGTAAATCTGAGTGACTTGCT 57.376 40.909 0.00 0.00 0.00 3.91
2577 2616 8.318412 TGGTAAATCTGAGTGACTTGCTTATAA 58.682 33.333 0.00 0.00 0.00 0.98
2590 2629 7.282450 TGACTTGCTTATAATAGAGAGACGACA 59.718 37.037 0.00 0.00 0.00 4.35
2615 2656 8.547894 CAATCAAAACCTTGTTTAAACCTTAGC 58.452 33.333 15.59 0.00 33.94 3.09
2634 2677 6.491403 CCTTAGCATGGTATAGCAATTTTCCT 59.509 38.462 8.98 2.44 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.374184 TGCCCATGTTACTGCCATAAC 58.626 47.619 0.00 1.22 35.89 1.89
9 10 3.650461 TCTATGCCCATGTTACTGCCATA 59.350 43.478 0.00 0.00 0.00 2.74
36 37 4.504340 GCGGGTGATAATACCATGGTTAGT 60.504 45.833 25.38 11.20 42.69 2.24
48 50 4.041691 ACAATAGCCTAAGCGGGTGATAAT 59.958 41.667 0.00 0.00 44.90 1.28
54 56 1.134491 GTGACAATAGCCTAAGCGGGT 60.134 52.381 0.00 0.00 46.67 5.28
63 65 3.403038 ACTCAACACAGTGACAATAGCC 58.597 45.455 7.81 0.00 0.00 3.93
75 77 4.852134 AATGCATGCTTAACTCAACACA 57.148 36.364 20.33 0.00 0.00 3.72
102 104 3.137360 GCCTTCTACCATCCAATCCTTCT 59.863 47.826 0.00 0.00 0.00 2.85
142 145 5.869649 AAGGTTAAAAGTGCATCCTTTGT 57.130 34.783 3.30 0.00 34.94 2.83
222 225 6.377146 TGTTTCCTTATCAAATACAGCTTCCC 59.623 38.462 0.00 0.00 0.00 3.97
245 249 4.058817 GTCCTGAGTTCTTCACGAAATGT 58.941 43.478 0.00 0.00 32.41 2.71
340 345 1.064758 GCATGAACCATGGTCCCACTA 60.065 52.381 20.07 1.48 41.64 2.74
379 384 2.096248 TGGAGTTGCGTTCCAAACTTT 58.904 42.857 1.55 0.00 41.61 2.66
453 461 5.084722 CGTGCTTGTCTTTCTCAATTCATC 58.915 41.667 0.00 0.00 0.00 2.92
455 463 4.126437 TCGTGCTTGTCTTTCTCAATTCA 58.874 39.130 0.00 0.00 0.00 2.57
485 497 2.256306 TGTTCATGTCTCCAGTGGCTA 58.744 47.619 3.51 0.00 0.00 3.93
507 519 1.336517 CGTCGCCAAACTCTTCAGGTA 60.337 52.381 0.00 0.00 0.00 3.08
510 522 1.070577 CAACGTCGCCAAACTCTTCAG 60.071 52.381 0.00 0.00 0.00 3.02
549 562 3.139397 TGTATGACAGGGGTTTGGTCTTT 59.861 43.478 0.00 0.00 32.84 2.52
589 602 5.663456 ACAAACAAATGACAGCTCACAAAT 58.337 33.333 0.00 0.00 0.00 2.32
626 642 6.126409 TGAAGAGACAGGTTTTTATTGTGGT 58.874 36.000 0.00 0.00 0.00 4.16
655 673 4.626604 GGGATACACACAATGCAAACAATG 59.373 41.667 0.00 0.00 39.74 2.82
713 733 5.848369 TCATCTCCATTCATCCTCTATTGGT 59.152 40.000 0.00 0.00 0.00 3.67
772 792 5.299949 CATGTTATGAATCCATCGGTCTGA 58.700 41.667 0.00 0.00 34.31 3.27
820 840 2.289506 GGGCCATATCCTTTCCGACTAC 60.290 54.545 4.39 0.00 0.00 2.73
847 867 4.133078 CCTCTTTCAAAGCACTGAAGAGT 58.867 43.478 16.63 0.00 36.69 3.24
873 893 2.762535 ACATCCTCCACCAAGTAACG 57.237 50.000 0.00 0.00 0.00 3.18
875 895 3.522759 TGGTACATCCTCCACCAAGTAA 58.477 45.455 0.00 0.00 39.36 2.24
957 977 4.337145 ACTTCTAGGACACAAGACGAGAT 58.663 43.478 0.00 0.00 0.00 2.75
973 993 9.920946 ATTATTTTCATAAGGCCTCAACTTCTA 57.079 29.630 5.23 0.00 0.00 2.10
997 1017 6.399743 TGCATGCACAATGTTTCTTCATATT 58.600 32.000 18.46 0.00 38.65 1.28
1010 1030 3.007074 TCCACAAATCTTGCATGCACAAT 59.993 39.130 22.58 14.01 0.00 2.71
1024 1044 3.573967 GTGTGTCCCATTTCTCCACAAAT 59.426 43.478 0.00 0.00 37.74 2.32
1051 1071 2.029918 GGCATTCACCCTTGTGTTCTTC 60.030 50.000 0.00 0.00 43.26 2.87
1086 1106 2.354259 CATTCTTCAGCTGGGTGACTC 58.646 52.381 15.13 0.00 0.00 3.36
1144 1165 1.482593 CTGAGCAAGGTAGTGGGTAGG 59.517 57.143 0.00 0.00 0.00 3.18
1157 1178 3.146066 GGGTAAATGTGACACTGAGCAA 58.854 45.455 7.20 0.00 0.00 3.91
1223 1244 6.256053 TCTTCTAAAATTTCCATGAGGGCTT 58.744 36.000 0.00 0.00 36.21 4.35
1251 1272 3.201708 CCTCCACCTCTTCCTTCATCATT 59.798 47.826 0.00 0.00 0.00 2.57
1252 1273 2.776536 CCTCCACCTCTTCCTTCATCAT 59.223 50.000 0.00 0.00 0.00 2.45
1300 1321 5.430886 TGAATAGCATGACTTAGTGCATGT 58.569 37.500 18.55 11.85 43.63 3.21
1381 1402 6.270463 AGGTCATACTCTACTTCCTCTATCGA 59.730 42.308 0.00 0.00 0.00 3.59
1406 1427 2.754465 TCCGGGCTTCTATTTCCTGTA 58.246 47.619 0.00 0.00 0.00 2.74
1424 1445 2.229784 CTGGACTTTTCTGTGCCAATCC 59.770 50.000 0.00 0.00 0.00 3.01
1597 1618 1.299648 TGGGACAATCTCCGGCAAG 59.700 57.895 0.00 0.00 40.56 4.01
1623 1645 8.589338 AGACACAACTAATTATCACAAGTCTCT 58.411 33.333 0.00 0.00 0.00 3.10
1680 1707 5.997746 TCATCGCCTCAATATAAAGGGAAAG 59.002 40.000 5.66 1.26 32.98 2.62
1767 1795 7.888021 ACTCATAAAATCCAATCAGTACCAACA 59.112 33.333 0.00 0.00 0.00 3.33
1929 1961 7.259088 ACTTATTTTATCTGTGGTCCACTCT 57.741 36.000 22.56 9.69 35.11 3.24
1951 1985 7.670140 TCCCACATATCGAGATAAACTCATACT 59.330 37.037 0.00 0.00 45.14 2.12
1952 1986 7.827701 TCCCACATATCGAGATAAACTCATAC 58.172 38.462 0.00 0.00 45.14 2.39
1953 1987 8.595362 ATCCCACATATCGAGATAAACTCATA 57.405 34.615 0.00 0.00 45.14 2.15
1954 1988 6.918067 TCCCACATATCGAGATAAACTCAT 57.082 37.500 0.00 0.00 45.14 2.90
1955 1989 6.918067 ATCCCACATATCGAGATAAACTCA 57.082 37.500 0.00 0.00 45.14 3.41
1956 1990 7.259161 GGTATCCCACATATCGAGATAAACTC 58.741 42.308 0.00 0.00 41.79 3.01
1957 1991 6.154706 GGGTATCCCACATATCGAGATAAACT 59.845 42.308 0.00 0.00 44.65 2.66
1958 1992 6.338937 GGGTATCCCACATATCGAGATAAAC 58.661 44.000 0.00 0.00 44.65 2.01
1983 2017 6.875469 AGTACTCCATCCCCTCATAATCTTA 58.125 40.000 0.00 0.00 0.00 2.10
1988 2022 5.785423 CCAATAGTACTCCATCCCCTCATAA 59.215 44.000 0.00 0.00 0.00 1.90
1994 2028 7.989947 TTATATCCAATAGTACTCCATCCCC 57.010 40.000 0.00 0.00 0.00 4.81
2067 2102 4.988540 CCAAACTCAGACGTGATTACTCAA 59.011 41.667 0.00 0.00 31.85 3.02
2120 2155 6.537355 TCCTAGCATTCTTAAATCCATCCAG 58.463 40.000 0.00 0.00 0.00 3.86
2178 2214 9.904198 TCACATTTAATCCTTGAACTCATCATA 57.096 29.630 0.00 0.00 38.03 2.15
2198 2234 1.889010 ATGGCCCACCCCATCACATT 61.889 55.000 0.00 0.00 41.75 2.71
2200 2236 1.217747 TTATGGCCCACCCCATCACA 61.218 55.000 0.00 0.00 44.30 3.58
2264 2300 4.290093 ACTTCTTCCAGGCTTTTTCCTTT 58.710 39.130 0.00 0.00 33.25 3.11
2274 2310 6.679327 ATAAAATCGTAACTTCTTCCAGGC 57.321 37.500 0.00 0.00 0.00 4.85
2302 2339 5.297527 TGCGTAAACTCCTATAAGATCGTCA 59.702 40.000 0.00 0.00 0.00 4.35
2339 2377 9.520204 CAAACAAACATATATCATTCCTTCACC 57.480 33.333 0.00 0.00 0.00 4.02
2354 2393 4.662468 TTCTGCAAGCCAAACAAACATA 57.338 36.364 0.00 0.00 0.00 2.29
2410 2449 3.575256 TCACAGGCATTGCAGAATTTCTT 59.425 39.130 11.39 0.00 0.00 2.52
2577 2616 6.287589 AGGTTTTGATTGTCGTCTCTCTAT 57.712 37.500 0.00 0.00 0.00 1.98
2590 2629 8.261522 TGCTAAGGTTTAAACAAGGTTTTGATT 58.738 29.630 19.57 2.09 37.73 2.57
2615 2656 8.465999 TGTACAAAGGAAAATTGCTATACCATG 58.534 33.333 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.