Multiple sequence alignment - TraesCS1B01G087300

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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 TraesCS1B01G087300 chr1B 100.000 6366 0 0 1509 7874 80919823 80926188 0.000000e+00 11756.0
1 TraesCS1B01G087300 chr1B 99.670 5148 16 1 2727 7874 80952843 80957989 0.000000e+00 9411.0
2 TraesCS1B01G087300 chr1B 100.000 1210 0 0 1 1210 80918315 80919524 0.000000e+00 2235.0
3 TraesCS1B01G087300 chr1B 99.256 1210 8 1 1 1210 80950482 80951690 0.000000e+00 2183.0
4 TraesCS1B01G087300 chr1B 100.000 770 0 0 1509 2278 80951951 80952720 0.000000e+00 1423.0
5 TraesCS1B01G087300 chr1B 97.484 636 16 0 1 636 40345395 40344760 0.000000e+00 1086.0
6 TraesCS1B01G087300 chr1B 97.170 636 18 0 1 636 363921312 363920677 0.000000e+00 1075.0
7 TraesCS1B01G087300 chr1B 95.098 102 5 0 1108 1209 80951886 80951987 2.270000e-35 161.0
8 TraesCS1B01G087300 chr5D 91.507 3768 224 32 1644 5340 20959406 20963148 0.000000e+00 5097.0
9 TraesCS1B01G087300 chr5D 91.401 3768 228 32 1644 5340 17243374 17239632 0.000000e+00 5075.0
10 TraesCS1B01G087300 chr5D 90.536 1680 120 25 5478 7127 20963145 20964815 0.000000e+00 2185.0
11 TraesCS1B01G087300 chr5D 89.637 1679 121 30 5478 7127 17239635 17237981 0.000000e+00 2087.0
12 TraesCS1B01G087300 chr5D 83.516 546 66 11 1511 2035 17243837 17243295 9.180000e-134 488.0
13 TraesCS1B01G087300 chr5D 83.708 534 63 9 1511 2023 20958943 20959473 4.270000e-132 483.0
14 TraesCS1B01G087300 chr5D 84.507 142 16 2 1880 2021 17242052 17241917 1.380000e-27 135.0
15 TraesCS1B01G087300 chr5D 84.507 142 16 2 1880 2021 20960728 20960863 1.380000e-27 135.0
16 TraesCS1B01G087300 chr5D 80.102 196 26 9 6893 7079 552439632 552439441 4.960000e-27 134.0
17 TraesCS1B01G087300 chr7B 97.327 636 17 0 1 636 676503073 676503708 0.000000e+00 1081.0
18 TraesCS1B01G087300 chr7B 89.592 759 63 12 7126 7874 148485499 148484747 0.000000e+00 950.0
19 TraesCS1B01G087300 chr7B 98.667 150 1 1 5341 5490 75025555 75025703 1.680000e-66 265.0
20 TraesCS1B01G087300 chr7B 90.476 63 6 0 6583 6645 116376459 116376397 5.060000e-12 84.2
21 TraesCS1B01G087300 chr6B 97.170 636 18 0 1 636 369201135 369200500 0.000000e+00 1075.0
22 TraesCS1B01G087300 chr6B 91.017 757 57 9 7126 7874 680435640 680436393 0.000000e+00 1011.0
23 TraesCS1B01G087300 chr6B 99.324 148 1 0 5341 5488 20920534 20920387 1.300000e-67 268.0
24 TraesCS1B01G087300 chr6B 98.658 149 0 2 5341 5489 159404922 159404776 6.060000e-66 263.0
25 TraesCS1B01G087300 chr6B 87.156 109 11 1 6893 7001 555959888 555959783 3.860000e-23 121.0
26 TraesCS1B01G087300 chr5B 97.170 636 18 0 1 636 612789749 612789114 0.000000e+00 1075.0
27 TraesCS1B01G087300 chr5B 85.366 82 9 1 7012 7090 506694906 506694825 1.820000e-11 82.4
28 TraesCS1B01G087300 chr5B 85.366 82 9 1 7012 7090 506727920 506727839 1.820000e-11 82.4
29 TraesCS1B01G087300 chr4B 96.880 641 20 0 1 641 35685751 35685111 0.000000e+00 1074.0
30 TraesCS1B01G087300 chr4B 97.170 636 17 1 1 636 287089971 287089337 0.000000e+00 1074.0
31 TraesCS1B01G087300 chr4B 91.766 753 49 11 7128 7874 170977551 170976806 0.000000e+00 1035.0
32 TraesCS1B01G087300 chr4B 89.235 771 60 14 7116 7874 302701494 302700735 0.000000e+00 942.0
33 TraesCS1B01G087300 chr4B 100.000 144 0 0 5341 5484 673151 673008 4.680000e-67 267.0
34 TraesCS1B01G087300 chr3B 96.330 654 21 3 1 653 656616911 656616260 0.000000e+00 1072.0
35 TraesCS1B01G087300 chr3B 90.591 744 59 9 7126 7862 693781994 693782733 0.000000e+00 976.0
36 TraesCS1B01G087300 chr3B 89.723 759 64 8 7125 7873 362621471 362622225 0.000000e+00 957.0
37 TraesCS1B01G087300 chr2D 90.933 761 56 9 7125 7874 623631761 623632519 0.000000e+00 1011.0
38 TraesCS1B01G087300 chr2D 79.695 197 31 9 6890 7079 190399682 190399876 4.960000e-27 134.0
39 TraesCS1B01G087300 chr4A 90.222 767 68 5 7113 7874 669634974 669634210 0.000000e+00 994.0
40 TraesCS1B01G087300 chr3A 98.675 151 1 1 5341 5490 359345810 359345960 4.680000e-67 267.0
41 TraesCS1B01G087300 chr2A 98.026 152 1 2 5341 5491 660841508 660841358 6.060000e-66 263.0
42 TraesCS1B01G087300 chr2A 95.652 161 3 4 5324 5481 678194947 678195106 1.010000e-63 255.0
43 TraesCS1B01G087300 chr2A 86.364 66 8 1 6580 6645 659705350 659705286 3.940000e-08 71.3
44 TraesCS1B01G087300 chr2B 100.000 141 0 0 5341 5481 67298156 67298296 2.180000e-65 261.0
45 TraesCS1B01G087300 chr7A 85.841 113 14 2 6968 7079 7811191 7811302 1.390000e-22 119.0
46 TraesCS1B01G087300 chr6A 78.462 195 24 13 6894 7079 56376948 56376763 2.320000e-20 111.0
47 TraesCS1B01G087300 chr7D 88.060 67 7 1 6579 6645 154179936 154179871 2.360000e-10 78.7
48 TraesCS1B01G087300 chr6D 89.655 58 5 1 6893 6949 370852999 370852942 1.100000e-08 73.1
49 TraesCS1B01G087300 chr3D 92.857 42 3 0 698 739 16249043 16249002 2.370000e-05 62.1
50 TraesCS1B01G087300 chr3D 94.595 37 1 1 703 739 332508038 332508073 1.000000e-03 56.5
51 TraesCS1B01G087300 chr5A 81.944 72 11 2 708 778 688341246 688341176 8.530000e-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 TraesCS1B01G087300 chr1B 80918315 80926188 7873 False 6995.50 11756 100.00000 1 7874 2 chr1B.!!$F1 7873
1 TraesCS1B01G087300 chr1B 80950482 80957989 7507 False 3294.50 9411 98.50600 1 7874 4 chr1B.!!$F2 7873
2 TraesCS1B01G087300 chr1B 40344760 40345395 635 True 1086.00 1086 97.48400 1 636 1 chr1B.!!$R1 635
3 TraesCS1B01G087300 chr1B 363920677 363921312 635 True 1075.00 1075 97.17000 1 636 1 chr1B.!!$R2 635
4 TraesCS1B01G087300 chr5D 20958943 20964815 5872 False 1975.00 5097 87.56450 1511 7127 4 chr5D.!!$F1 5616
5 TraesCS1B01G087300 chr5D 17237981 17243837 5856 True 1946.25 5075 87.26525 1511 7127 4 chr5D.!!$R2 5616
6 TraesCS1B01G087300 chr7B 676503073 676503708 635 False 1081.00 1081 97.32700 1 636 1 chr7B.!!$F2 635
7 TraesCS1B01G087300 chr7B 148484747 148485499 752 True 950.00 950 89.59200 7126 7874 1 chr7B.!!$R2 748
8 TraesCS1B01G087300 chr6B 369200500 369201135 635 True 1075.00 1075 97.17000 1 636 1 chr6B.!!$R3 635
9 TraesCS1B01G087300 chr6B 680435640 680436393 753 False 1011.00 1011 91.01700 7126 7874 1 chr6B.!!$F1 748
10 TraesCS1B01G087300 chr5B 612789114 612789749 635 True 1075.00 1075 97.17000 1 636 1 chr5B.!!$R3 635
11 TraesCS1B01G087300 chr4B 35685111 35685751 640 True 1074.00 1074 96.88000 1 641 1 chr4B.!!$R2 640
12 TraesCS1B01G087300 chr4B 287089337 287089971 634 True 1074.00 1074 97.17000 1 636 1 chr4B.!!$R4 635
13 TraesCS1B01G087300 chr4B 170976806 170977551 745 True 1035.00 1035 91.76600 7128 7874 1 chr4B.!!$R3 746
14 TraesCS1B01G087300 chr4B 302700735 302701494 759 True 942.00 942 89.23500 7116 7874 1 chr4B.!!$R5 758
15 TraesCS1B01G087300 chr3B 656616260 656616911 651 True 1072.00 1072 96.33000 1 653 1 chr3B.!!$R1 652
16 TraesCS1B01G087300 chr3B 693781994 693782733 739 False 976.00 976 90.59100 7126 7862 1 chr3B.!!$F2 736
17 TraesCS1B01G087300 chr3B 362621471 362622225 754 False 957.00 957 89.72300 7125 7873 1 chr3B.!!$F1 748
18 TraesCS1B01G087300 chr2D 623631761 623632519 758 False 1011.00 1011 90.93300 7125 7874 1 chr2D.!!$F2 749
19 TraesCS1B01G087300 chr4A 669634210 669634974 764 True 994.00 994 90.22200 7113 7874 1 chr4A.!!$R1 761

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
335 336 1.297364 GCTACAGCCCGGTTTACCA 59.703 57.895 0.00 0.0 32.91 3.25 F
730 731 3.833442 CCGACCCAAATAGACAAAAAGC 58.167 45.455 0.00 0.0 0.00 3.51 F
2348 2670 1.406614 GCAGGAGATGAAGGTGACCAG 60.407 57.143 3.63 0.0 0.00 4.00 F
2426 2748 0.244721 CACAGTCATGTCTCCGAGCA 59.755 55.000 0.00 0.0 37.65 4.26 F
2576 2901 0.671251 CCTACCTTAGAGGAGCAGCG 59.329 60.000 0.07 0.0 37.67 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 2624 5.335191 CCTGAATTGGAGTTTCAGTAGCAAC 60.335 44.000 11.29 0.0 45.56 4.17 R
2407 2729 0.244721 TGCTCGGAGACATGACTGTG 59.755 55.000 9.69 0.0 35.14 3.66 R
3603 3961 2.982488 TCTCCTTTGCTTCTTCTCCCTT 59.018 45.455 0.00 0.0 0.00 3.95 R
4417 4802 7.122204 TCAGAACTCTCATCGGTCAAATTAGTA 59.878 37.037 0.00 0.0 0.00 1.82 R
7258 7674 1.682005 CGGGCCAAACATGACCCAT 60.682 57.895 4.39 0.0 42.97 4.00 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
72 73 4.405116 AATGTTGTGATGCCTTGTTGTT 57.595 36.364 0.00 0.00 0.00 2.83
335 336 1.297364 GCTACAGCCCGGTTTACCA 59.703 57.895 0.00 0.00 32.91 3.25
730 731 3.833442 CCGACCCAAATAGACAAAAAGC 58.167 45.455 0.00 0.00 0.00 3.51
2302 2624 8.369424 AGATATTCTCATCTCCTTCAACATCTG 58.631 37.037 0.00 0.00 28.83 2.90
2335 2657 1.956869 TCCAATTCAGGAGCAGGAGA 58.043 50.000 0.00 0.00 32.77 3.71
2336 2658 2.485659 TCCAATTCAGGAGCAGGAGAT 58.514 47.619 0.00 0.00 32.77 2.75
2348 2670 1.406614 GCAGGAGATGAAGGTGACCAG 60.407 57.143 3.63 0.00 0.00 4.00
2355 2677 2.638480 TGAAGGTGACCAGGAAACAG 57.362 50.000 3.63 0.00 0.00 3.16
2407 2729 2.268076 ATGCCGTTGCCACTTCACC 61.268 57.895 0.00 0.00 36.33 4.02
2408 2730 2.904866 GCCGTTGCCACTTCACCA 60.905 61.111 0.00 0.00 0.00 4.17
2410 2732 1.821759 CCGTTGCCACTTCACCACA 60.822 57.895 0.00 0.00 0.00 4.17
2412 2734 1.095228 CGTTGCCACTTCACCACAGT 61.095 55.000 0.00 0.00 0.00 3.55
2413 2735 0.663153 GTTGCCACTTCACCACAGTC 59.337 55.000 0.00 0.00 0.00 3.51
2426 2748 0.244721 CACAGTCATGTCTCCGAGCA 59.755 55.000 0.00 0.00 37.65 4.26
2429 2751 1.153549 GTCATGTCTCCGAGCACCC 60.154 63.158 0.00 0.00 0.00 4.61
2476 2798 0.931005 CGCTCCTGAAATCCTAACGC 59.069 55.000 0.00 0.00 0.00 4.84
2478 2800 2.205911 GCTCCTGAAATCCTAACGCTC 58.794 52.381 0.00 0.00 0.00 5.03
2482 2804 4.000988 TCCTGAAATCCTAACGCTCAAAC 58.999 43.478 0.00 0.00 0.00 2.93
2492 2814 4.410743 GCTCAAACAGGCGGCAGC 62.411 66.667 13.08 6.33 44.18 5.25
2511 2833 4.201990 GCAGCGATGATGAGAAAAAGGAAT 60.202 41.667 4.02 0.00 0.00 3.01
2538 2860 1.878656 AAGAGGAGAAGGTGGACGCG 61.879 60.000 3.53 3.53 0.00 6.01
2553 2875 4.729856 GCGCTGCCTTTTGCCCAG 62.730 66.667 0.00 0.00 40.16 4.45
2576 2901 0.671251 CCTACCTTAGAGGAGCAGCG 59.329 60.000 0.07 0.00 37.67 5.18
2646 2971 3.776969 AGCAGATATTGTCACCTCCTTCA 59.223 43.478 0.00 0.00 0.00 3.02
2647 2972 4.225942 AGCAGATATTGTCACCTCCTTCAA 59.774 41.667 0.00 0.00 0.00 2.69
2670 2995 5.853936 ACATCTGTTGCTGTAGAAACTACA 58.146 37.500 10.49 10.49 34.63 2.74
2702 3027 2.708325 AGGAGGTGAAGAAACAGAAGCT 59.292 45.455 0.00 0.00 0.00 3.74
2718 3043 0.977108 AGCTGAGGAGAAGGCAGGAG 60.977 60.000 0.00 0.00 0.00 3.69
3603 3961 4.349365 AGGAAAACCCTGAAAACAAGACA 58.651 39.130 0.00 0.00 45.61 3.41
4417 4802 3.094572 CCATTGAACTGAATTCCTGCCT 58.905 45.455 2.27 0.00 36.36 4.75
7111 7526 1.878953 CAGGTGCCGTCTGTTAGTTT 58.121 50.000 0.00 0.00 0.00 2.66
7258 7674 2.483714 GCAGAGAGTTGTGGTGTTCTCA 60.484 50.000 3.52 0.00 38.78 3.27
7304 7721 8.808240 AGATCTTTATAGTAATGGGGTTGGTA 57.192 34.615 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.405116 AACAACAAGGCATCACAACATT 57.595 36.364 0.00 0.00 0.00 2.71
335 336 0.975040 CACTGGGCTAGCAGGACTCT 60.975 60.000 18.24 0.00 0.00 3.24
730 731 0.179029 ACCAACCCTTGTTCTGTCCG 60.179 55.000 0.00 0.00 30.42 4.79
2302 2624 5.335191 CCTGAATTGGAGTTTCAGTAGCAAC 60.335 44.000 11.29 0.00 45.56 4.17
2335 2657 2.711009 TCTGTTTCCTGGTCACCTTCAT 59.289 45.455 0.00 0.00 0.00 2.57
2336 2658 2.123589 TCTGTTTCCTGGTCACCTTCA 58.876 47.619 0.00 0.00 0.00 3.02
2348 2670 2.363683 CCATCCTCTGCTTCTGTTTCC 58.636 52.381 0.00 0.00 0.00 3.13
2355 2677 1.153005 CAGCCCCATCCTCTGCTTC 60.153 63.158 0.00 0.00 30.08 3.86
2407 2729 0.244721 TGCTCGGAGACATGACTGTG 59.755 55.000 9.69 0.00 35.14 3.66
2408 2730 0.244994 GTGCTCGGAGACATGACTGT 59.755 55.000 9.69 0.00 38.67 3.55
2410 2732 1.608717 GGGTGCTCGGAGACATGACT 61.609 60.000 9.69 0.00 0.00 3.41
2412 2734 1.609210 TGGGTGCTCGGAGACATGA 60.609 57.895 9.69 0.00 0.00 3.07
2413 2735 1.448540 GTGGGTGCTCGGAGACATG 60.449 63.158 9.69 0.00 0.00 3.21
2438 2760 1.378514 GCGGCTTGAAGGAATGGGA 60.379 57.895 0.00 0.00 0.00 4.37
2463 2785 3.751175 CCTGTTTGAGCGTTAGGATTTCA 59.249 43.478 0.00 0.00 0.00 2.69
2476 2798 4.093952 CGCTGCCGCCTGTTTGAG 62.094 66.667 0.00 0.00 0.00 3.02
2478 2800 3.434319 ATCGCTGCCGCCTGTTTG 61.434 61.111 0.00 0.00 0.00 2.93
2482 2804 3.646976 CATCATCGCTGCCGCCTG 61.647 66.667 0.00 0.00 0.00 4.85
2492 2814 6.962686 TGCATATTCCTTTTTCTCATCATCG 58.037 36.000 0.00 0.00 0.00 3.84
2511 2833 4.968719 TCCACCTTCTCCTCTTTATGCATA 59.031 41.667 1.16 1.16 0.00 3.14
2553 2875 3.006430 GCTGCTCCTCTAAGGTAGGATTC 59.994 52.174 0.00 0.00 42.25 2.52
2576 2901 2.081161 ACCATCATGGCCTCCTCCC 61.081 63.158 2.52 0.00 42.67 4.30
2646 2971 6.288294 TGTAGTTTCTACAGCAACAGATGTT 58.712 36.000 5.64 0.00 39.12 2.71
2647 2972 5.853936 TGTAGTTTCTACAGCAACAGATGT 58.146 37.500 5.64 0.00 35.77 3.06
2656 2981 5.064071 GCTCCTGAATTGTAGTTTCTACAGC 59.936 44.000 9.11 4.48 0.00 4.40
2660 2985 5.483937 TCCTGCTCCTGAATTGTAGTTTCTA 59.516 40.000 0.00 0.00 0.00 2.10
2668 2993 1.004044 CACCTCCTGCTCCTGAATTGT 59.996 52.381 0.00 0.00 0.00 2.71
2670 2995 1.661463 TCACCTCCTGCTCCTGAATT 58.339 50.000 0.00 0.00 0.00 2.17
2702 3027 3.719121 GCTCCTGCCTTCTCCTCA 58.281 61.111 0.00 0.00 0.00 3.86
3603 3961 2.982488 TCTCCTTTGCTTCTTCTCCCTT 59.018 45.455 0.00 0.00 0.00 3.95
4417 4802 7.122204 TCAGAACTCTCATCGGTCAAATTAGTA 59.878 37.037 0.00 0.00 0.00 1.82
7258 7674 1.682005 CGGGCCAAACATGACCCAT 60.682 57.895 4.39 0.00 42.97 4.00
7277 7694 7.349859 ACCAACCCCATTACTATAAAGATCTCA 59.650 37.037 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.