Multiple sequence alignment - TraesCS6D01G372200

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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 TraesCS6D01G372200 chr6D 100.000 2690 0 0 1 2690 457586460 457583771 0.000000e+00 4968.0
1 TraesCS6D01G372200 chr6D 84.830 824 110 10 868 1688 457629923 457630734 0.000000e+00 815.0
2 TraesCS6D01G372200 chr6D 84.220 564 83 3 1119 1676 457593075 457592512 6.550000e-151 544.0
3 TraesCS6D01G372200 chr6D 94.208 259 12 2 418 676 468650855 468651110 2.510000e-105 392.0
4 TraesCS6D01G372200 chr6D 100.000 34 0 0 698 731 468651116 468651149 2.240000e-06 63.9
5 TraesCS6D01G372200 chr6B 94.267 1343 62 10 788 2116 696016068 696014727 0.000000e+00 2039.0
6 TraesCS6D01G372200 chr6B 84.828 758 103 8 941 1697 696079832 696080578 0.000000e+00 752.0
7 TraesCS6D01G372200 chr6B 94.530 457 25 0 2101 2557 696014714 696014258 0.000000e+00 706.0
8 TraesCS6D01G372200 chr6A 95.065 1074 48 2 860 1928 604446484 604445411 0.000000e+00 1685.0
9 TraesCS6D01G372200 chr6A 93.783 563 31 3 1998 2557 604445387 604444826 0.000000e+00 843.0
10 TraesCS6D01G372200 chr6A 84.709 824 108 8 876 1688 604537376 604538192 0.000000e+00 808.0
11 TraesCS6D01G372200 chr6A 84.007 569 80 6 1138 1696 604573547 604572980 1.100000e-148 536.0
12 TraesCS6D01G372200 chr6A 80.116 689 107 17 997 1676 604458239 604457572 1.120000e-133 486.0
13 TraesCS6D01G372200 chr6A 81.547 569 94 6 1138 1696 604455781 604455214 2.440000e-125 459.0
14 TraesCS6D01G372200 chr6A 90.647 139 13 0 2552 2690 604444684 604444546 4.570000e-43 185.0
15 TraesCS6D01G372200 chr6A 94.872 78 4 0 788 865 604451989 604451912 3.640000e-24 122.0
16 TraesCS6D01G372200 chr3D 97.716 788 14 2 1 788 483180607 483181390 0.000000e+00 1352.0
17 TraesCS6D01G372200 chr3D 97.342 790 16 2 3 788 607926128 607925340 0.000000e+00 1338.0
18 TraesCS6D01G372200 chr2A 95.466 794 30 4 1 790 762009268 762008477 0.000000e+00 1262.0
19 TraesCS6D01G372200 chr2A 82.946 387 40 7 114 496 770975639 770975275 2.580000e-85 326.0
20 TraesCS6D01G372200 chr5B 93.813 792 32 8 1 787 221206086 221206865 0.000000e+00 1175.0
21 TraesCS6D01G372200 chr4A 93.451 794 33 9 1 788 652263671 652264451 0.000000e+00 1160.0
22 TraesCS6D01G372200 chr4A 84.787 447 52 5 112 557 193100480 193100911 4.110000e-118 435.0
23 TraesCS6D01G372200 chr4A 82.011 189 16 10 613 789 193100915 193101097 7.760000e-31 145.0
24 TraesCS6D01G372200 chr4A 87.671 73 5 2 90 158 713099575 713099647 6.170000e-12 82.4
25 TraesCS6D01G372200 chr7D 81.433 684 103 15 112 788 178948363 178947697 3.050000e-149 538.0
26 TraesCS6D01G372200 chr2D 82.639 576 91 5 1132 1698 21681441 21682016 4.000000e-138 501.0
27 TraesCS6D01G372200 chr2D 82.308 390 46 5 115 503 645443012 645442645 1.550000e-82 316.0
28 TraesCS6D01G372200 chr2D 86.667 105 11 3 684 787 180339150 180339048 2.190000e-21 113.0
29 TraesCS6D01G372200 chr5A 96.923 65 2 0 2 66 66195911 66195975 2.830000e-20 110.0
30 TraesCS6D01G372200 chr1A 78.161 174 31 7 631 800 78545217 78545387 1.320000e-18 104.0
31 TraesCS6D01G372200 chr1A 96.970 33 1 0 1928 1960 304038297 304038329 3.740000e-04 56.5
32 TraesCS6D01G372200 chr3B 90.476 63 6 0 724 786 760304385 760304447 1.720000e-12 84.2
33 TraesCS6D01G372200 chr3B 95.349 43 1 1 651 693 414470804 414470763 1.730000e-07 67.6
34 TraesCS6D01G372200 chr1B 96.970 33 1 0 1928 1960 334313476 334313508 3.740000e-04 56.5


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 TraesCS6D01G372200 chr6D 457583771 457586460 2689 True 4968.000000 4968 100.000000 1 2690 1 chr6D.!!$R1 2689
1 TraesCS6D01G372200 chr6D 457629923 457630734 811 False 815.000000 815 84.830000 868 1688 1 chr6D.!!$F1 820
2 TraesCS6D01G372200 chr6D 457592512 457593075 563 True 544.000000 544 84.220000 1119 1676 1 chr6D.!!$R2 557
3 TraesCS6D01G372200 chr6B 696014258 696016068 1810 True 1372.500000 2039 94.398500 788 2557 2 chr6B.!!$R1 1769
4 TraesCS6D01G372200 chr6B 696079832 696080578 746 False 752.000000 752 84.828000 941 1697 1 chr6B.!!$F1 756
5 TraesCS6D01G372200 chr6A 604444546 604446484 1938 True 904.333333 1685 93.165000 860 2690 3 chr6A.!!$R2 1830
6 TraesCS6D01G372200 chr6A 604537376 604538192 816 False 808.000000 808 84.709000 876 1688 1 chr6A.!!$F1 812
7 TraesCS6D01G372200 chr6A 604572980 604573547 567 True 536.000000 536 84.007000 1138 1696 1 chr6A.!!$R1 558
8 TraesCS6D01G372200 chr6A 604451912 604458239 6327 True 355.666667 486 85.511667 788 1696 3 chr6A.!!$R3 908
9 TraesCS6D01G372200 chr3D 483180607 483181390 783 False 1352.000000 1352 97.716000 1 788 1 chr3D.!!$F1 787
10 TraesCS6D01G372200 chr3D 607925340 607926128 788 True 1338.000000 1338 97.342000 3 788 1 chr3D.!!$R1 785
11 TraesCS6D01G372200 chr2A 762008477 762009268 791 True 1262.000000 1262 95.466000 1 790 1 chr2A.!!$R1 789
12 TraesCS6D01G372200 chr5B 221206086 221206865 779 False 1175.000000 1175 93.813000 1 787 1 chr5B.!!$F1 786
13 TraesCS6D01G372200 chr4A 652263671 652264451 780 False 1160.000000 1160 93.451000 1 788 1 chr4A.!!$F1 787
14 TraesCS6D01G372200 chr4A 193100480 193101097 617 False 290.000000 435 83.399000 112 789 2 chr4A.!!$F3 677
15 TraesCS6D01G372200 chr7D 178947697 178948363 666 True 538.000000 538 81.433000 112 788 1 chr7D.!!$R1 676
16 TraesCS6D01G372200 chr2D 21681441 21682016 575 False 501.000000 501 82.639000 1132 1698 1 chr2D.!!$F1 566

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
463 469 0.108186 AACGGATGCAGCTTCATCGA 60.108 50.0 18.26 0.0 42.78 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 4668 0.458669 TCTCGTACCGAAATCAGGGC 59.541 55.0 0.0 0.0 34.74 5.19 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
463 469 0.108186 AACGGATGCAGCTTCATCGA 60.108 50.000 18.26 0.00 42.78 3.59
690 734 2.945984 CCAGCGATGCAAACGTGT 59.054 55.556 15.74 3.95 33.27 4.49
730 793 1.947456 TGGATGACTACACGATCGAGG 59.053 52.381 24.34 15.65 0.00 4.63
795 858 3.768215 ACCCAACGTTTCCCTAAACAAAA 59.232 39.130 0.00 0.00 44.37 2.44
836 899 3.314357 TCTCCGTACACGAATGGATGTAG 59.686 47.826 2.76 0.00 43.02 2.74
1071 1145 1.671054 CGCCACCAAGGACGTTGAT 60.671 57.895 9.42 0.00 41.22 2.57
1095 1169 0.105453 ACGATGAGATACCAGCCCCT 60.105 55.000 0.00 0.00 0.00 4.79
1218 3627 2.436115 GCGCTAAGCCCGTCCTTT 60.436 61.111 0.00 0.00 40.81 3.11
1509 3924 0.392706 TCACAGTGGCGTTCAGTGAT 59.607 50.000 18.06 4.71 46.98 3.06
1961 4575 4.037923 CGATCCATTTTAATTGTCCCTGGG 59.962 45.833 6.33 6.33 0.00 4.45
1969 4583 2.344093 ATTGTCCCTGGGTGAGTAGT 57.656 50.000 13.56 0.00 0.00 2.73
1971 4585 3.263369 TTGTCCCTGGGTGAGTAGTTA 57.737 47.619 13.56 0.00 0.00 2.24
1990 4604 9.120538 AGTAGTTATCTTTTCTCTTGCAAAACA 57.879 29.630 0.00 0.00 0.00 2.83
1991 4605 9.899226 GTAGTTATCTTTTCTCTTGCAAAACAT 57.101 29.630 0.00 0.00 0.00 2.71
1992 4606 8.807667 AGTTATCTTTTCTCTTGCAAAACATG 57.192 30.769 0.00 0.00 0.00 3.21
1993 4607 7.869429 AGTTATCTTTTCTCTTGCAAAACATGG 59.131 33.333 0.00 0.00 0.00 3.66
2048 4668 6.279882 TGTTTTGTTCATTAAAAGGGCTCTG 58.720 36.000 0.00 0.00 0.00 3.35
2142 4790 3.462021 GGAAAGAGACGCATGAGCTATT 58.538 45.455 0.00 0.00 39.10 1.73
2146 4794 3.201290 AGAGACGCATGAGCTATTTTGG 58.799 45.455 0.00 0.00 39.10 3.28
2178 4826 4.501571 GCTGAAACCACTGTGAGTCTTCTA 60.502 45.833 9.86 4.16 0.00 2.10
2366 7337 8.313944 ACCCAATTTATTATAAAGGTTCACCC 57.686 34.615 3.73 0.00 36.42 4.61
2367 7338 7.901861 ACCCAATTTATTATAAAGGTTCACCCA 59.098 33.333 3.73 0.00 36.42 4.51
2405 7376 8.998814 TCCCTAAACATAATAAGAATCAGACCA 58.001 33.333 0.00 0.00 0.00 4.02
2511 7505 0.521735 GCCAAACCTTGTCGATGACC 59.478 55.000 0.00 0.00 0.00 4.02
2567 7708 3.008330 CAGTGCTCAAGGAGGATTGAAG 58.992 50.000 4.62 0.00 39.33 3.02
2597 7738 0.449388 CGGCTCAAAGATGAAGCACC 59.551 55.000 0.00 0.00 34.49 5.01
2600 7741 0.449388 CTCAAAGATGAAGCACCGCC 59.551 55.000 0.00 0.00 34.49 6.13
2603 7744 1.098050 AAAGATGAAGCACCGCCATC 58.902 50.000 0.00 0.00 37.53 3.51
2604 7745 0.254178 AAGATGAAGCACCGCCATCT 59.746 50.000 0.00 0.00 46.23 2.90
2605 7746 1.123077 AGATGAAGCACCGCCATCTA 58.877 50.000 0.00 0.00 43.50 1.98
2609 7750 1.078426 AAGCACCGCCATCTACCAC 60.078 57.895 0.00 0.00 0.00 4.16
2611 7752 2.106683 GCACCGCCATCTACCACAC 61.107 63.158 0.00 0.00 0.00 3.82
2614 7755 0.822164 ACCGCCATCTACCACACTAC 59.178 55.000 0.00 0.00 0.00 2.73
2632 7773 0.531200 ACCGCACCTACAGACTAAGC 59.469 55.000 0.00 0.00 0.00 3.09
2658 7799 9.832445 CAAACCTAATCTAAATTACTAGCAGGA 57.168 33.333 0.00 0.00 0.00 3.86
2666 7807 1.381928 TTACTAGCAGGACCGAGGCG 61.382 60.000 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 69 8.507249 ACATCTCTTGTTATTTTTCTGCTACAC 58.493 33.333 0.00 0.00 33.74 2.90
84 87 6.857964 CGTTGACAAAATTTGCTACATCTCTT 59.142 34.615 5.52 0.00 0.00 2.85
283 288 3.391965 GGTGACAATTTTTGCTGCATCA 58.608 40.909 1.84 0.00 0.00 3.07
463 469 1.678101 GAAAGAGCTGCAACCACAACT 59.322 47.619 1.02 0.00 0.00 3.16
649 693 1.362237 TCCCTTTCTTTGGCCCATCAT 59.638 47.619 0.00 0.00 0.00 2.45
660 704 0.110486 TCGCTGGCTTTCCCTTTCTT 59.890 50.000 0.00 0.00 0.00 2.52
690 734 1.208535 ACGGCTCAACATTTCCCGATA 59.791 47.619 4.24 0.00 41.34 2.92
795 858 5.190677 GGAGACTTCAACTCTCTAGCTAGT 58.809 45.833 20.10 0.22 35.43 2.57
836 899 3.635268 CTGGGTGCTGGAAGGGCTC 62.635 68.421 0.00 0.00 0.00 4.70
977 1051 7.309255 CCATTGTAGGTACTAAGCTCGATATGT 60.309 40.741 0.00 0.00 45.48 2.29
1071 1145 1.333931 GCTGGTATCTCATCGTCGTCA 59.666 52.381 0.00 0.00 0.00 4.35
1218 3627 1.894756 GCACTTGCCGTGGTTGGTA 60.895 57.895 5.53 0.00 43.97 3.25
1509 3924 2.113774 CAGTTCTGCAGCCCCACA 59.886 61.111 9.47 0.00 0.00 4.17
1961 4575 7.891183 TGCAAGAGAAAAGATAACTACTCAC 57.109 36.000 0.00 0.00 0.00 3.51
1969 4583 7.950512 TCCATGTTTTGCAAGAGAAAAGATAA 58.049 30.769 0.00 0.00 28.28 1.75
1971 4585 6.409524 TCCATGTTTTGCAAGAGAAAAGAT 57.590 33.333 0.00 0.00 29.01 2.40
2048 4668 0.458669 TCTCGTACCGAAATCAGGGC 59.541 55.000 0.00 0.00 34.74 5.19
2066 4686 5.001232 TGTTTTCTACAAGCCACTATGGTC 58.999 41.667 0.00 0.00 35.04 4.02
2142 4790 1.754226 GTTTCAGCCCAAGTGTCCAAA 59.246 47.619 0.00 0.00 0.00 3.28
2146 4794 0.668535 GTGGTTTCAGCCCAAGTGTC 59.331 55.000 0.00 0.00 32.72 3.67
2178 4826 3.674682 CGAAGGTTCTTTCTCAGCGATCT 60.675 47.826 0.00 0.00 0.00 2.75
2366 7337 6.575162 ATGTTTAGGGAGCTTTGTAGTTTG 57.425 37.500 0.00 0.00 0.00 2.93
2367 7338 8.879427 ATTATGTTTAGGGAGCTTTGTAGTTT 57.121 30.769 0.00 0.00 0.00 2.66
2370 7341 9.832445 TCTTATTATGTTTAGGGAGCTTTGTAG 57.168 33.333 0.00 0.00 0.00 2.74
2405 7376 4.080863 GTGGTTCACTGGTCCATAGATCTT 60.081 45.833 0.00 0.00 33.68 2.40
2511 7505 2.034842 CGCGTATTAAGACTTTCTGGCG 60.035 50.000 0.00 4.11 0.00 5.69
2567 7708 1.194772 CTTTGAGCCGGTCTTTCGAAC 59.805 52.381 1.90 0.00 0.00 3.95
2597 7738 0.248907 CGGTAGTGTGGTAGATGGCG 60.249 60.000 0.00 0.00 0.00 5.69
2600 7741 1.470979 GGTGCGGTAGTGTGGTAGATG 60.471 57.143 0.00 0.00 0.00 2.90
2603 7744 1.133790 GTAGGTGCGGTAGTGTGGTAG 59.866 57.143 0.00 0.00 0.00 3.18
2604 7745 1.176527 GTAGGTGCGGTAGTGTGGTA 58.823 55.000 0.00 0.00 0.00 3.25
2605 7746 0.828762 TGTAGGTGCGGTAGTGTGGT 60.829 55.000 0.00 0.00 0.00 4.16
2609 7750 1.174783 AGTCTGTAGGTGCGGTAGTG 58.825 55.000 0.00 0.00 0.00 2.74
2611 7752 2.223525 GCTTAGTCTGTAGGTGCGGTAG 60.224 54.545 0.00 0.00 0.00 3.18
2614 7755 0.530744 TGCTTAGTCTGTAGGTGCGG 59.469 55.000 0.00 0.00 0.00 5.69
2632 7773 9.832445 TCCTGCTAGTAATTTAGATTAGGTTTG 57.168 33.333 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.