Multiple sequence alignment - TraesCS7D01G223400

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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 TraesCS7D01G223400 chr7D 100.000 3170 0 0 1 3170 184499374 184502543 0.000000e+00 5854.0
1 TraesCS7D01G223400 chr7D 88.638 2394 176 45 3 2365 184524855 184522527 0.000000e+00 2826.0
2 TraesCS7D01G223400 chr7D 83.821 581 48 21 2456 3018 503693332 503693884 7.840000e-141 510.0
3 TraesCS7D01G223400 chr7D 85.479 365 31 6 2465 2829 152121866 152122208 8.360000e-96 361.0
4 TraesCS7D01G223400 chr7D 91.775 231 15 4 2823 3052 152122252 152122479 5.100000e-83 318.0
5 TraesCS7D01G223400 chr7D 90.909 77 6 1 3094 3170 152122459 152122534 5.590000e-18 102.0
6 TraesCS7D01G223400 chr7A 94.360 2500 99 23 2 2470 186098219 186095731 0.000000e+00 3797.0
7 TraesCS7D01G223400 chr7A 88.946 1547 124 28 905 2433 185975455 185976972 0.000000e+00 1866.0
8 TraesCS7D01G223400 chr7A 81.990 794 64 37 3 773 185974658 185975395 4.520000e-168 601.0
9 TraesCS7D01G223400 chr7B 88.942 2288 169 39 8 2255 153744632 153742389 0.000000e+00 2747.0
10 TraesCS7D01G223400 chr7B 93.047 1352 54 10 898 2213 153581853 153583200 0.000000e+00 1940.0
11 TraesCS7D01G223400 chr7B 96.255 801 25 4 1 798 153581043 153581841 0.000000e+00 1308.0
12 TraesCS7D01G223400 chr7B 77.465 213 12 14 2270 2467 153583305 153583496 9.360000e-16 95.3
13 TraesCS7D01G223400 chr7B 89.189 74 8 0 825 898 724716625 724716698 3.370000e-15 93.5
14 TraesCS7D01G223400 chr2D 94.543 733 19 5 2458 3170 643672459 643671728 0.000000e+00 1112.0
15 TraesCS7D01G223400 chr2D 91.589 214 17 1 2823 3036 430009011 430009223 8.600000e-76 294.0
16 TraesCS7D01G223400 chr2D 85.135 296 23 5 2534 2829 430008693 430008967 1.860000e-72 283.0
17 TraesCS7D01G223400 chr2D 90.909 77 6 1 823 898 647157973 647158049 5.590000e-18 102.0
18 TraesCS7D01G223400 chr2D 89.610 77 7 1 3094 3170 430009218 430009293 2.600000e-16 97.1
19 TraesCS7D01G223400 chr5D 94.467 723 22 2 2466 3170 480040307 480041029 0.000000e+00 1098.0
20 TraesCS7D01G223400 chr3D 94.348 690 21 4 2499 3170 567242447 567241758 0.000000e+00 1042.0
21 TraesCS7D01G223400 chr1D 92.582 728 23 6 2461 3170 307353865 307353151 0.000000e+00 1016.0
22 TraesCS7D01G223400 chr5A 92.181 729 32 3 2467 3170 693655554 693656282 0.000000e+00 1007.0
23 TraesCS7D01G223400 chr5A 91.892 74 6 0 825 898 536389985 536389912 1.560000e-18 104.0
24 TraesCS7D01G223400 chr3A 91.518 731 36 4 2466 3170 649044155 649043425 0.000000e+00 983.0
25 TraesCS7D01G223400 chr4B 88.762 614 29 8 2580 3170 86761709 86762305 0.000000e+00 715.0
26 TraesCS7D01G223400 chr4B 93.137 102 7 0 2485 2586 86761354 86761455 1.970000e-32 150.0
27 TraesCS7D01G223400 chr6D 74.270 1267 249 56 945 2168 114224858 114226090 2.230000e-126 462.0
28 TraesCS7D01G223400 chr6A 74.016 1270 242 65 952 2168 142773005 142774239 1.350000e-118 436.0
29 TraesCS7D01G223400 chr6B 73.059 1262 268 54 952 2168 203894330 203895564 6.420000e-102 381.0
30 TraesCS7D01G223400 chr4D 93.421 76 5 0 823 898 488485364 488485439 2.580000e-21 113.0


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 TraesCS7D01G223400 chr7D 184499374 184502543 3169 False 5854.000000 5854 100.000000 1 3170 1 chr7D.!!$F1 3169
1 TraesCS7D01G223400 chr7D 184522527 184524855 2328 True 2826.000000 2826 88.638000 3 2365 1 chr7D.!!$R1 2362
2 TraesCS7D01G223400 chr7D 503693332 503693884 552 False 510.000000 510 83.821000 2456 3018 1 chr7D.!!$F2 562
3 TraesCS7D01G223400 chr7D 152121866 152122534 668 False 260.333333 361 89.387667 2465 3170 3 chr7D.!!$F3 705
4 TraesCS7D01G223400 chr7A 186095731 186098219 2488 True 3797.000000 3797 94.360000 2 2470 1 chr7A.!!$R1 2468
5 TraesCS7D01G223400 chr7A 185974658 185976972 2314 False 1233.500000 1866 85.468000 3 2433 2 chr7A.!!$F1 2430
6 TraesCS7D01G223400 chr7B 153742389 153744632 2243 True 2747.000000 2747 88.942000 8 2255 1 chr7B.!!$R1 2247
7 TraesCS7D01G223400 chr7B 153581043 153583496 2453 False 1114.433333 1940 88.922333 1 2467 3 chr7B.!!$F2 2466
8 TraesCS7D01G223400 chr2D 643671728 643672459 731 True 1112.000000 1112 94.543000 2458 3170 1 chr2D.!!$R1 712
9 TraesCS7D01G223400 chr2D 430008693 430009293 600 False 224.700000 294 88.778000 2534 3170 3 chr2D.!!$F2 636
10 TraesCS7D01G223400 chr5D 480040307 480041029 722 False 1098.000000 1098 94.467000 2466 3170 1 chr5D.!!$F1 704
11 TraesCS7D01G223400 chr3D 567241758 567242447 689 True 1042.000000 1042 94.348000 2499 3170 1 chr3D.!!$R1 671
12 TraesCS7D01G223400 chr1D 307353151 307353865 714 True 1016.000000 1016 92.582000 2461 3170 1 chr1D.!!$R1 709
13 TraesCS7D01G223400 chr5A 693655554 693656282 728 False 1007.000000 1007 92.181000 2467 3170 1 chr5A.!!$F1 703
14 TraesCS7D01G223400 chr3A 649043425 649044155 730 True 983.000000 983 91.518000 2466 3170 1 chr3A.!!$R1 704
15 TraesCS7D01G223400 chr4B 86761354 86762305 951 False 432.500000 715 90.949500 2485 3170 2 chr4B.!!$F1 685
16 TraesCS7D01G223400 chr6D 114224858 114226090 1232 False 462.000000 462 74.270000 945 2168 1 chr6D.!!$F1 1223
17 TraesCS7D01G223400 chr6A 142773005 142774239 1234 False 436.000000 436 74.016000 952 2168 1 chr6A.!!$F1 1216
18 TraesCS7D01G223400 chr6B 203894330 203895564 1234 False 381.000000 381 73.059000 952 2168 1 chr6B.!!$F1 1216

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
642 677 0.107268 TCTGCTCTTGTGCTTGCTCA 59.893 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2421 2620 0.030369 ACGTTGGCTATCGGTCGATC 59.97 55.0 9.25 0.0 36.17 3.69 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
61 65 0.330604 TAGTACCGAGACACCTGGCT 59.669 55.000 0.00 0.00 34.94 4.75
642 677 0.107268 TCTGCTCTTGTGCTTGCTCA 59.893 50.000 0.00 0.00 0.00 4.26
714 749 1.131126 GAAAGCATGTCATCACCCGTG 59.869 52.381 0.00 0.00 0.00 4.94
725 760 3.632080 ACCCGTGCGTCCCATGAA 61.632 61.111 0.00 0.00 31.89 2.57
850 901 5.940617 TGAAATATATTGTCCACCTCCCTG 58.059 41.667 0.00 0.00 0.00 4.45
885 936 6.187727 ACTTTTGGATGAGTTAACTGGAGA 57.812 37.500 14.14 0.00 0.00 3.71
899 950 8.897752 AGTTAACTGGAGAATGAATTCAATAGC 58.102 33.333 13.09 2.91 39.23 2.97
1125 1192 2.058595 CCTGGTCGACCTTCCGGAT 61.059 63.158 33.39 0.00 36.82 4.18
1420 1503 1.079750 GAGAAGGACACCCTCACGC 60.080 63.158 0.00 0.00 43.48 5.34
1863 1984 4.033709 ACCTGTTCAGGTATGCTATGAGT 58.966 43.478 21.13 0.00 41.04 3.41
2198 2322 1.280746 CCAGTCAAAGCAGCACGTG 59.719 57.895 12.28 12.28 0.00 4.49
2209 2333 3.104766 GCACGTGCTAGCATGCAT 58.895 55.556 32.12 14.75 45.23 3.96
2252 2418 5.407407 TCTTCGAAAATAAGGCTCTCACT 57.593 39.130 0.00 0.00 0.00 3.41
2255 2421 5.263968 TCGAAAATAAGGCTCTCACTAGG 57.736 43.478 0.00 0.00 0.00 3.02
2410 2609 2.478539 GCCTCGGCATCTTGATTGTTTC 60.479 50.000 2.41 0.00 41.49 2.78
2411 2610 2.749076 CCTCGGCATCTTGATTGTTTCA 59.251 45.455 0.00 0.00 0.00 2.69
2412 2611 3.181503 CCTCGGCATCTTGATTGTTTCAG 60.182 47.826 0.00 0.00 35.27 3.02
2414 2613 2.733227 CGGCATCTTGATTGTTTCAGGC 60.733 50.000 0.00 0.00 35.27 4.85
2417 2616 3.057033 GCATCTTGATTGTTTCAGGCTGT 60.057 43.478 15.27 0.00 35.27 4.40
2418 2617 4.156556 GCATCTTGATTGTTTCAGGCTGTA 59.843 41.667 15.27 1.01 35.27 2.74
2419 2618 5.163581 GCATCTTGATTGTTTCAGGCTGTAT 60.164 40.000 15.27 1.80 35.27 2.29
2420 2619 6.493116 CATCTTGATTGTTTCAGGCTGTATC 58.507 40.000 15.27 4.79 35.27 2.24
2421 2620 4.631377 TCTTGATTGTTTCAGGCTGTATCG 59.369 41.667 15.27 0.00 35.27 2.92
2439 2641 0.997226 CGATCGACCGATAGCCAACG 60.997 60.000 10.26 0.25 34.60 4.10
2456 2661 5.054390 CCAACGTGCTTGGTATTTACATT 57.946 39.130 0.00 0.00 44.30 2.71
2487 2692 5.803237 AACGGATTCTATAACTCCCGAAT 57.197 39.130 0.00 0.00 40.10 3.34
2510 2715 3.751698 GTCAGGATTTTAGCGTTTGGTCT 59.248 43.478 0.00 0.00 0.00 3.85
2578 3043 0.107263 TGACACTGCCAAGTCAGCAA 60.107 50.000 0.00 0.00 39.65 3.91
2598 3063 5.535030 AGCAAAGAAGTAGTTCGGGATTTTT 59.465 36.000 4.65 0.00 37.79 1.94
2649 3115 1.384525 CGACATCGTCTCCTTCTCCT 58.615 55.000 0.00 0.00 34.11 3.69
2658 3124 1.933765 TCTCCTTCTCCTCCCTTAGCT 59.066 52.381 0.00 0.00 0.00 3.32
3158 3740 1.311059 GGTGAATTGGGGGAGGCAT 59.689 57.895 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 65 2.147958 GGACGTTGTTACCTTGCATCA 58.852 47.619 0.00 0.00 0.00 3.07
252 267 2.474526 CGACACTGAGGCTAAAATTGCG 60.475 50.000 0.00 0.00 0.00 4.85
615 650 1.612726 GCACAAGAGCAGACAGGGAAT 60.613 52.381 0.00 0.00 0.00 3.01
642 677 1.202627 GCCGAGATGAGGAGCAAGAAT 60.203 52.381 0.00 0.00 0.00 2.40
714 749 1.750193 TTCTTGGATTCATGGGACGC 58.250 50.000 0.00 0.00 0.00 5.19
725 760 2.941415 GCAGGTCGATGGTTTCTTGGAT 60.941 50.000 0.00 0.00 0.00 3.41
839 882 0.842030 AACTGATGCAGGGAGGTGGA 60.842 55.000 0.00 0.00 35.51 4.02
850 901 2.151202 TCCAAAAGTCCGAACTGATGC 58.849 47.619 0.00 0.00 35.36 3.91
899 950 5.292101 GCACAAGGTGTAGATAAGTTAGCAG 59.708 44.000 0.28 0.00 35.75 4.24
1076 1134 1.817209 GAGGGGATCGTCAGACCAC 59.183 63.158 0.00 0.00 0.00 4.16
1125 1192 1.079681 GACGTGGTATTCCGGTGCA 60.080 57.895 0.00 0.00 36.30 4.57
1863 1984 0.745128 CCGGCGCCACCTTGTAATTA 60.745 55.000 28.98 0.00 35.61 1.40
2209 2333 4.227300 AGAACCAACCCTCAATATACTGCA 59.773 41.667 0.00 0.00 0.00 4.41
2222 2388 4.617530 GCCTTATTTTCGAAGAACCAACCC 60.618 45.833 0.00 0.00 45.90 4.11
2403 2602 3.804325 CGATCGATACAGCCTGAAACAAT 59.196 43.478 10.26 0.00 0.00 2.71
2410 2609 0.386100 CGGTCGATCGATACAGCCTG 60.386 60.000 22.50 8.32 0.00 4.85
2411 2610 0.534427 TCGGTCGATCGATACAGCCT 60.534 55.000 22.50 0.00 33.92 4.58
2412 2611 0.522180 ATCGGTCGATCGATACAGCC 59.478 55.000 30.97 15.84 46.47 4.85
2414 2613 2.223066 GGCTATCGGTCGATCGATACAG 60.223 54.545 31.41 26.06 46.47 2.74
2417 2616 2.103537 TGGCTATCGGTCGATCGATA 57.896 50.000 32.31 32.31 46.47 2.92
2419 2618 0.309922 GTTGGCTATCGGTCGATCGA 59.690 55.000 24.83 24.83 43.61 3.59
2420 2619 0.997226 CGTTGGCTATCGGTCGATCG 60.997 60.000 12.98 12.98 36.17 3.69
2421 2620 0.030369 ACGTTGGCTATCGGTCGATC 59.970 55.000 9.25 0.00 36.17 3.69
2487 2692 3.482436 ACCAAACGCTAAAATCCTGACA 58.518 40.909 0.00 0.00 0.00 3.58
2578 3043 6.770542 AGAGAAAAATCCCGAACTACTTCTT 58.229 36.000 0.00 0.00 0.00 2.52
2598 3063 0.879765 GTCGTTCGGGAGTTGAGAGA 59.120 55.000 0.00 0.00 0.00 3.10
2649 3115 6.402981 AAAGAAAGGGATAAAGCTAAGGGA 57.597 37.500 0.00 0.00 0.00 4.20
2658 3124 5.255207 TGGATGAGGGAAAGAAAGGGATAAA 59.745 40.000 0.00 0.00 0.00 1.40
2970 3552 0.258194 GGAGGGGAGACGACCTAGAA 59.742 60.000 0.00 0.00 37.18 2.10


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

AutoCloner maintained by Alex Coulton.