Multiple sequence alignment - TraesCS2D01G208200

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 TraesCS2D01G208200 chr2D 100.000 4270 0 0 1 4270 162258756 162254487 0.000000e+00 7886.0
1 TraesCS2D01G208200 chr2B 95.057 2549 87 13 990 3523 221731301 221728777 0.000000e+00 3973.0
2 TraesCS2D01G208200 chr2B 89.775 1819 153 13 992 2788 219297455 219295648 0.000000e+00 2298.0
3 TraesCS2D01G208200 chr2B 96.000 400 9 6 3520 3916 221726353 221725958 1.000000e-180 643.0
4 TraesCS2D01G208200 chr2B 85.799 507 51 8 3156 3643 219295414 219294910 6.330000e-143 518.0
5 TraesCS2D01G208200 chr2B 93.750 336 12 2 3944 4270 221724159 221723824 2.970000e-136 496.0
6 TraesCS2D01G208200 chr2B 87.681 414 41 8 3867 4270 219289628 219289215 1.390000e-129 473.0
7 TraesCS2D01G208200 chr2B 96.319 163 6 0 990 1152 221731737 221731575 7.040000e-68 268.0
8 TraesCS2D01G208200 chr2B 92.405 158 11 1 3001 3158 219295657 219295501 1.550000e-54 224.0
9 TraesCS2D01G208200 chr2B 88.496 113 7 5 3755 3865 219289765 219289657 9.630000e-27 132.0
10 TraesCS2D01G208200 chr2A 95.207 1377 48 5 1371 2738 173358943 173357576 0.000000e+00 2161.0
11 TraesCS2D01G208200 chr2A 95.056 627 22 7 3385 4007 173355544 173354923 0.000000e+00 977.0
12 TraesCS2D01G208200 chr2A 94.479 634 24 8 2711 3343 173356171 173355548 0.000000e+00 966.0
13 TraesCS2D01G208200 chr2A 97.215 395 11 0 990 1384 173359619 173359225 0.000000e+00 669.0
14 TraesCS2D01G208200 chr2A 91.447 152 5 2 4006 4150 173354826 173354676 7.240000e-48 202.0
15 TraesCS2D01G208200 chr2A 80.292 274 39 8 999 1261 513824005 513823736 4.360000e-45 193.0
16 TraesCS2D01G208200 chr2A 100.000 68 0 0 4203 4270 173354686 173354619 4.480000e-25 126.0
17 TraesCS2D01G208200 chr1D 98.384 990 15 1 1 989 246941821 246942810 0.000000e+00 1738.0
18 TraesCS2D01G208200 chr7D 97.994 997 17 3 1 996 184509645 184508651 0.000000e+00 1727.0
19 TraesCS2D01G208200 chr7D 89.397 547 50 7 450 989 135415328 135415873 0.000000e+00 682.0
20 TraesCS2D01G208200 chr7D 89.203 389 38 3 8 393 18832677 18833064 2.310000e-132 483.0
21 TraesCS2D01G208200 chr5D 96.573 992 31 3 1 991 549028232 549027243 0.000000e+00 1640.0
22 TraesCS2D01G208200 chr5D 87.919 596 64 7 401 989 59887305 59886711 0.000000e+00 695.0
23 TraesCS2D01G208200 chr5D 88.279 401 38 6 1 393 357017972 357018371 5.000000e-129 472.0
24 TraesCS2D01G208200 chr5D 88.732 355 37 2 48 399 59887692 59887338 8.480000e-117 431.0
25 TraesCS2D01G208200 chr4A 85.522 967 112 19 48 989 42241385 42242348 0.000000e+00 985.0
26 TraesCS2D01G208200 chr4A 88.750 80 8 1 8 86 713901489 713901410 3.510000e-16 97.1
27 TraesCS2D01G208200 chr1B 84.690 1032 106 26 1 989 647163555 647162533 0.000000e+00 983.0
28 TraesCS2D01G208200 chr3B 85.041 976 106 25 48 989 646249500 646248531 0.000000e+00 957.0
29 TraesCS2D01G208200 chr3D 88.481 599 59 8 398 989 19032059 19031464 0.000000e+00 715.0
30 TraesCS2D01G208200 chr5B 88.889 396 41 2 1 393 421718947 421719342 6.420000e-133 484.0
31 TraesCS2D01G208200 chr1A 89.244 344 34 2 48 388 6200746 6200403 1.100000e-115 427.0


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 TraesCS2D01G208200 chr2D 162254487 162258756 4269 True 7886.000000 7886 100.000000 1 4270 1 chr2D.!!$R1 4269
1 TraesCS2D01G208200 chr2B 221723824 221731737 7913 True 1345.000000 3973 95.281500 990 4270 4 chr2B.!!$R3 3280
2 TraesCS2D01G208200 chr2B 219294910 219297455 2545 True 1013.333333 2298 89.326333 992 3643 3 chr2B.!!$R2 2651
3 TraesCS2D01G208200 chr2B 219289215 219289765 550 True 302.500000 473 88.088500 3755 4270 2 chr2B.!!$R1 515
4 TraesCS2D01G208200 chr2A 173354619 173359619 5000 True 850.166667 2161 95.567333 990 4270 6 chr2A.!!$R2 3280
5 TraesCS2D01G208200 chr1D 246941821 246942810 989 False 1738.000000 1738 98.384000 1 989 1 chr1D.!!$F1 988
6 TraesCS2D01G208200 chr7D 184508651 184509645 994 True 1727.000000 1727 97.994000 1 996 1 chr7D.!!$R1 995
7 TraesCS2D01G208200 chr7D 135415328 135415873 545 False 682.000000 682 89.397000 450 989 1 chr7D.!!$F2 539
8 TraesCS2D01G208200 chr5D 549027243 549028232 989 True 1640.000000 1640 96.573000 1 991 1 chr5D.!!$R1 990
9 TraesCS2D01G208200 chr5D 59886711 59887692 981 True 563.000000 695 88.325500 48 989 2 chr5D.!!$R2 941
10 TraesCS2D01G208200 chr4A 42241385 42242348 963 False 985.000000 985 85.522000 48 989 1 chr4A.!!$F1 941
11 TraesCS2D01G208200 chr1B 647162533 647163555 1022 True 983.000000 983 84.690000 1 989 1 chr1B.!!$R1 988
12 TraesCS2D01G208200 chr3B 646248531 646249500 969 True 957.000000 957 85.041000 48 989 1 chr3B.!!$R1 941
13 TraesCS2D01G208200 chr3D 19031464 19032059 595 True 715.000000 715 88.481000 398 989 1 chr3D.!!$R1 591

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
957 1010 2.875933 CTGGTGTTTTCGCAAACCTAGA 59.124 45.455 8.19 0.00 41.60 2.43 F
1582 2366 1.132640 GCAAGCAATCGTCGTCACC 59.867 57.895 0.00 0.00 0.00 4.02 F
2228 3015 0.955919 GACCTCTTGGGCAAAGACGG 60.956 60.000 14.81 14.81 42.34 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 3015 0.110373 GTTTCGCCGAACCATGTCAC 60.110 55.000 0.0 0.0 0.00 3.67 R
2939 5178 1.997791 GGGGAGGGAAAGGGACTAAAA 59.002 52.381 0.0 0.0 38.49 1.52 R
3796 8584 0.106469 TTGCTGCCCAAACCAGTGTA 60.106 50.000 0.0 0.0 32.93 2.90 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
957 1010 2.875933 CTGGTGTTTTCGCAAACCTAGA 59.124 45.455 8.19 0.00 41.60 2.43
996 1049 7.432252 GGTTTTATGCAATTTACTCAATCTCCG 59.568 37.037 0.00 0.00 0.00 4.63
1049 1102 3.065015 CGAGCGCTTCGTGTTCTC 58.935 61.111 13.26 0.00 44.27 2.87
1129 1182 4.947147 ACGGCGGCAGCTTTTCCA 62.947 61.111 13.24 0.00 44.37 3.53
1516 2300 4.039973 AGTTGAACTTCCGTAGATCCAACA 59.960 41.667 0.00 0.00 0.00 3.33
1517 2301 4.188247 TGAACTTCCGTAGATCCAACAG 57.812 45.455 0.00 0.00 0.00 3.16
1565 2349 2.035442 GTGTCCTCCGCTCCAAAGC 61.035 63.158 0.00 0.00 45.56 3.51
1582 2366 1.132640 GCAAGCAATCGTCGTCACC 59.867 57.895 0.00 0.00 0.00 4.02
1609 2393 2.743928 GTGAGAAGTGGCTGCCGG 60.744 66.667 14.98 0.00 0.00 6.13
1687 2471 4.036971 TGGTTCCGTTCAACAAGTATTTGG 59.963 41.667 2.81 0.00 38.66 3.28
1888 2672 5.297547 TGAGGTTTGTTGATGTAGTCTGTC 58.702 41.667 0.00 0.00 0.00 3.51
2082 2866 4.770795 AGCATCCTGTTGTAAGTATGGAC 58.229 43.478 0.00 0.00 0.00 4.02
2182 2969 4.036734 TGAGTACCAAAAAGCTGCTTTCAG 59.963 41.667 26.17 20.17 43.16 3.02
2228 3015 0.955919 GACCTCTTGGGCAAAGACGG 60.956 60.000 14.81 14.81 42.34 4.79
2319 3106 1.064017 TCCCACCAGGTATTTGCATCC 60.064 52.381 0.00 0.00 36.75 3.51
2557 3361 1.273048 TGTCCACCTTGCATGCAAATC 59.727 47.619 31.37 17.94 35.33 2.17
2632 3440 3.762288 AGATCACCGCTGTTCAGTAACTA 59.238 43.478 0.00 0.00 36.51 2.24
2694 3502 9.095065 GAAATACGTACTCATTTTATCACCTGT 57.905 33.333 0.00 0.00 0.00 4.00
2695 3503 8.420374 AATACGTACTCATTTTATCACCTGTG 57.580 34.615 0.00 0.00 0.00 3.66
2696 3504 5.790593 ACGTACTCATTTTATCACCTGTGT 58.209 37.500 0.00 0.00 0.00 3.72
2697 3505 6.228258 ACGTACTCATTTTATCACCTGTGTT 58.772 36.000 0.00 0.00 0.00 3.32
2698 3506 6.367969 ACGTACTCATTTTATCACCTGTGTTC 59.632 38.462 0.00 0.00 0.00 3.18
2699 3507 6.183360 CGTACTCATTTTATCACCTGTGTTCC 60.183 42.308 0.00 0.00 0.00 3.62
2700 3508 5.880901 ACTCATTTTATCACCTGTGTTCCT 58.119 37.500 0.00 0.00 0.00 3.36
2701 3509 5.707298 ACTCATTTTATCACCTGTGTTCCTG 59.293 40.000 0.00 0.00 0.00 3.86
2800 5039 2.976882 AGTACAGTTTTGGGAGGCTGTA 59.023 45.455 0.00 0.00 41.67 2.74
2812 5051 3.097614 GGAGGCTGTAACTTGAGGTCTA 58.902 50.000 0.00 0.00 0.00 2.59
2862 5101 5.710513 TCATGGACCATTTTCTCTGTTTG 57.289 39.130 3.52 0.00 0.00 2.93
2915 5154 1.966451 CTTCAGGGTTCACCGGCAC 60.966 63.158 0.00 0.00 46.96 5.01
2917 5156 1.122632 TTCAGGGTTCACCGGCACTA 61.123 55.000 0.00 0.00 46.96 2.74
2939 5178 8.634444 CACTATTCTATACTGTACTTTGGAGCT 58.366 37.037 0.00 0.00 0.00 4.09
2952 5191 4.827835 ACTTTGGAGCTTTTAGTCCCTTTC 59.172 41.667 0.00 0.00 31.04 2.62
2972 5216 6.183361 CCTTTCCCTCCCCTTATATGAATTGA 60.183 42.308 0.00 0.00 0.00 2.57
3076 5320 3.241091 CGCGCGATGTATAACAAGTACAA 59.759 43.478 28.94 0.00 35.84 2.41
3247 5592 8.887036 TCGTTACATGTCATTATTTATGAGCT 57.113 30.769 0.00 0.00 43.78 4.09
3355 5702 6.636705 ACTGAAGCAAACCAGTTATACGATA 58.363 36.000 0.00 0.00 40.40 2.92
3729 8513 6.128499 CGTCGAGGTTTTCATGTTTGGTATTA 60.128 38.462 0.00 0.00 0.00 0.98
3730 8514 7.571613 CGTCGAGGTTTTCATGTTTGGTATTAA 60.572 37.037 0.00 0.00 0.00 1.40
3796 8584 4.820173 GTCTTGTTGGGCTTGTAAGTTACT 59.180 41.667 14.00 0.00 0.00 2.24
3797 8585 5.993441 GTCTTGTTGGGCTTGTAAGTTACTA 59.007 40.000 14.00 5.84 0.00 1.82
3798 8586 5.993441 TCTTGTTGGGCTTGTAAGTTACTAC 59.007 40.000 14.00 3.76 0.00 2.73
3801 8589 5.163280 TGTTGGGCTTGTAAGTTACTACACT 60.163 40.000 14.00 0.00 31.52 3.55
3925 8781 5.415077 AGCCTGCATATCAAAATAGATGAGC 59.585 40.000 0.00 0.00 32.91 4.26
3991 10582 9.708222 GTTGAAGTGTCAATGTTATGCTATTAG 57.292 33.333 0.00 0.00 45.38 1.73
4040 10729 4.100963 ACCACTGTCCCAAATTTTTCCTTC 59.899 41.667 0.00 0.00 0.00 3.46
4065 10761 9.166173 TCCTGATATTTGTTTACACTCTTCATG 57.834 33.333 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
938 990 2.031420 GGTCTAGGTTTGCGAAAACACC 60.031 50.000 20.48 14.72 34.46 4.16
957 1010 4.896482 TGCATAAAACCACCACTTTAAGGT 59.104 37.500 0.00 0.00 40.85 3.50
1129 1182 2.128507 GGAGGACGAGGAAGGCGAT 61.129 63.158 0.00 0.00 0.00 4.58
1516 2300 1.377725 CAATCTTGCCCCACTCGCT 60.378 57.895 0.00 0.00 0.00 4.93
1517 2301 1.372087 CTCAATCTTGCCCCACTCGC 61.372 60.000 0.00 0.00 0.00 5.03
1565 2349 0.865111 TTGGTGACGACGATTGCTTG 59.135 50.000 0.00 0.00 0.00 4.01
1582 2366 2.746362 GCCACTTCTCACTCTTCCATTG 59.254 50.000 0.00 0.00 0.00 2.82
1687 2471 0.734309 CCGCCGTAATTAACCCAACC 59.266 55.000 0.00 0.00 0.00 3.77
2228 3015 0.110373 GTTTCGCCGAACCATGTCAC 60.110 55.000 0.00 0.00 0.00 3.67
2557 3361 2.634982 TTTAAATGCAGAGCTTGGCG 57.365 45.000 6.14 0.00 0.00 5.69
2675 3483 6.879458 AGGAACACAGGTGATAAAATGAGTAC 59.121 38.462 6.40 0.00 0.00 2.73
2714 3522 3.187637 TCGTTGTGCCATAAGTAAGCAAC 59.812 43.478 0.00 0.00 38.45 4.17
2745 4984 6.976349 GGTTTTGGTCGTAGTTTTCAATTTCT 59.024 34.615 0.00 0.00 0.00 2.52
2800 5039 2.909217 AGAAGGGCTAGACCTCAAGTT 58.091 47.619 20.36 0.00 40.87 2.66
2812 5051 4.797743 AGAAGAAAAGACAAAGAAGGGCT 58.202 39.130 0.00 0.00 0.00 5.19
2842 5081 4.482990 ACCAAACAGAGAAAATGGTCCAT 58.517 39.130 0.00 0.00 40.23 3.41
2862 5101 3.057734 CACCACGAACTCTAACTGAACC 58.942 50.000 0.00 0.00 0.00 3.62
2939 5178 1.997791 GGGGAGGGAAAGGGACTAAAA 59.002 52.381 0.00 0.00 38.49 1.52
2952 5191 5.073691 ACTGTCAATTCATATAAGGGGAGGG 59.926 44.000 0.00 0.00 0.00 4.30
3076 5320 7.759433 CAGTTGTGACCACTTTCAACTAAAAAT 59.241 33.333 8.67 0.00 45.36 1.82
3729 8513 3.290710 AGCTTTGTCAACCATGAGTGTT 58.709 40.909 0.00 0.00 35.88 3.32
3730 8514 2.880890 GAGCTTTGTCAACCATGAGTGT 59.119 45.455 0.00 0.00 35.88 3.55
3796 8584 0.106469 TTGCTGCCCAAACCAGTGTA 60.106 50.000 0.00 0.00 32.93 2.90
3797 8585 0.975040 TTTGCTGCCCAAACCAGTGT 60.975 50.000 0.00 0.00 38.46 3.55
3798 8586 0.177604 TTTTGCTGCCCAAACCAGTG 59.822 50.000 0.00 0.00 42.81 3.66
3801 8589 1.524482 GGTTTTGCTGCCCAAACCA 59.476 52.632 26.64 0.00 42.81 3.67
3925 8781 4.579869 AGTGGTTAGGCAAGTTGATACTG 58.420 43.478 7.16 0.00 34.01 2.74
4017 10706 3.653164 AGGAAAAATTTGGGACAGTGGT 58.347 40.909 0.00 0.00 42.39 4.16
4040 10729 7.912250 GCATGAAGAGTGTAAACAAATATCAGG 59.088 37.037 0.00 0.00 0.00 3.86
4065 10761 0.462759 GGAGCACATAGTGACCTGGC 60.463 60.000 0.58 0.00 35.23 4.85


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

AutoCloner maintained by Alex Coulton.