Multiple sequence alignment - TraesCS7A01G135700

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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 TraesCS7A01G135700 chr7A 100.000 3866 0 0 1 3866 88499319 88503184 0.000000e+00 7140.0
1 TraesCS7A01G135700 chr7A 98.433 1851 23 4 1 1846 88434947 88436796 0.000000e+00 3253.0
2 TraesCS7A01G135700 chr7A 90.652 920 69 12 933 1846 88315480 88316388 0.000000e+00 1206.0
3 TraesCS7A01G135700 chr7A 89.292 607 37 14 791 1395 88008334 88008914 0.000000e+00 736.0
4 TraesCS7A01G135700 chr7A 87.267 589 69 4 163 751 88144408 88144990 0.000000e+00 667.0
5 TraesCS7A01G135700 chr7A 88.054 519 34 10 878 1395 88172469 88172960 1.200000e-164 590.0
6 TraesCS7A01G135700 chr7A 86.684 383 46 3 369 751 88047215 88047592 1.660000e-113 420.0
7 TraesCS7A01G135700 chr7A 85.443 158 19 4 791 947 88121353 88121507 1.110000e-35 161.0
8 TraesCS7A01G135700 chr7A 100.000 29 0 0 764 792 88435684 88435712 2.000000e-03 54.7
9 TraesCS7A01G135700 chr7A 100.000 29 0 0 735 763 88435713 88435741 2.000000e-03 54.7
10 TraesCS7A01G135700 chr7A 100.000 29 0 0 764 792 88500053 88500081 2.000000e-03 54.7
11 TraesCS7A01G135700 chr7A 100.000 29 0 0 735 763 88500082 88500110 2.000000e-03 54.7
12 TraesCS7A01G135700 chr7B 96.065 1347 43 4 1962 3307 35638466 35639803 0.000000e+00 2185.0
13 TraesCS7A01G135700 chr7B 92.308 1222 65 9 764 1960 35637134 35638351 0.000000e+00 1709.0
14 TraesCS7A01G135700 chr7B 93.042 618 34 7 3173 3789 35639800 35640409 0.000000e+00 894.0
15 TraesCS7A01G135700 chr7B 85.066 904 70 23 947 1846 35307638 35308480 0.000000e+00 861.0
16 TraesCS7A01G135700 chr7B 90.683 644 48 5 764 1401 35507076 35507713 0.000000e+00 846.0
17 TraesCS7A01G135700 chr7B 87.755 539 60 4 164 701 35636538 35637071 3.280000e-175 625.0
18 TraesCS7A01G135700 chr7B 88.290 427 44 5 1423 1846 35507702 35508125 1.240000e-139 507.0
19 TraesCS7A01G135700 chr7B 88.688 221 24 1 164 384 28489533 28489752 6.370000e-68 268.0
20 TraesCS7A01G135700 chr7B 90.850 153 12 1 811 963 35301965 35302115 1.820000e-48 204.0
21 TraesCS7A01G135700 chr7D 96.007 1177 36 7 764 1936 87220290 87221459 0.000000e+00 1903.0
22 TraesCS7A01G135700 chr7D 96.169 1018 30 5 1958 2974 87221728 87222737 0.000000e+00 1655.0
23 TraesCS7A01G135700 chr7D 93.591 905 43 10 947 1846 87206445 87207339 0.000000e+00 1336.0
24 TraesCS7A01G135700 chr7D 89.325 918 56 10 2976 3866 87223191 87224093 0.000000e+00 1114.0
25 TraesCS7A01G135700 chr7D 93.698 603 34 2 164 763 87219717 87220318 0.000000e+00 900.0
26 TraesCS7A01G135700 chr7D 89.979 479 29 9 1377 1846 86292328 86292796 5.530000e-168 601.0
27 TraesCS7A01G135700 chr7D 91.335 427 33 4 1423 1846 86919030 86919455 7.200000e-162 580.0
28 TraesCS7A01G135700 chr7D 90.632 427 35 5 1423 1846 86755540 86755964 2.610000e-156 562.0
29 TraesCS7A01G135700 chr7D 90.741 378 23 7 791 1162 86754993 86755364 9.650000e-136 494.0
30 TraesCS7A01G135700 chr7D 89.974 379 25 8 791 1162 86918482 86918854 9.720000e-131 477.0
31 TraesCS7A01G135700 chr7D 95.745 188 7 1 1209 1395 86918849 86919036 6.280000e-78 302.0
32 TraesCS7A01G135700 chr7D 95.213 188 8 1 1209 1395 86755359 86755546 2.920000e-76 296.0
33 TraesCS7A01G135700 chr7D 87.607 234 28 1 1005 1237 86291939 86292172 1.770000e-68 270.0
34 TraesCS7A01G135700 chr7D 90.164 122 12 0 1962 2083 86293021 86293142 4.000000e-35 159.0
35 TraesCS7A01G135700 chr7D 100.000 28 0 0 924 951 87206170 87206197 7.000000e-03 52.8
36 TraesCS7A01G135700 chr4B 97.024 168 5 0 1 168 387795408 387795575 2.270000e-72 283.0
37 TraesCS7A01G135700 chr4B 96.429 168 6 0 1 168 387798671 387798838 1.060000e-70 278.0
38 TraesCS7A01G135700 chr5D 90.476 210 20 0 164 373 35562012 35562221 1.060000e-70 278.0
39 TraesCS7A01G135700 chr5D 96.450 169 5 1 1 168 214552148 214551980 1.060000e-70 278.0
40 TraesCS7A01G135700 chr5D 89.545 220 22 1 164 382 509681500 509681281 1.060000e-70 278.0
41 TraesCS7A01G135700 chr5D 96.429 168 5 1 1 168 214556938 214556772 3.800000e-70 276.0
42 TraesCS7A01G135700 chr3D 89.140 221 23 1 164 384 123618826 123619045 1.370000e-69 274.0
43 TraesCS7A01G135700 chr1B 95.833 168 7 0 1 168 408161150 408161317 4.920000e-69 272.0
44 TraesCS7A01G135700 chr1D 88.288 222 26 0 164 385 439108746 439108967 2.290000e-67 267.0
45 TraesCS7A01G135700 chr1D 100.000 30 0 0 3827 3856 381029793 381029764 5.400000e-04 56.5
46 TraesCS7A01G135700 chr1D 100.000 28 0 0 3401 3428 211683253 211683280 7.000000e-03 52.8
47 TraesCS7A01G135700 chr1A 95.266 169 7 1 1 168 296930204 296930372 2.290000e-67 267.0
48 TraesCS7A01G135700 chr1A 100.000 28 0 0 3402 3429 15320701 15320674 7.000000e-03 52.8
49 TraesCS7A01G135700 chr2A 93.750 176 9 2 1 176 271898669 271898496 2.960000e-66 263.0
50 TraesCS7A01G135700 chr6D 92.697 178 13 0 1 178 173909017 173909194 1.380000e-64 257.0


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 TraesCS7A01G135700 chr7A 88499319 88503184 3865 False 2416.466667 7140 100.000000 1 3866 3 chr7A.!!$F8 3865
1 TraesCS7A01G135700 chr7A 88315480 88316388 908 False 1206.000000 1206 90.652000 933 1846 1 chr7A.!!$F6 913
2 TraesCS7A01G135700 chr7A 88434947 88436796 1849 False 1120.800000 3253 99.477667 1 1846 3 chr7A.!!$F7 1845
3 TraesCS7A01G135700 chr7A 88008334 88008914 580 False 736.000000 736 89.292000 791 1395 1 chr7A.!!$F1 604
4 TraesCS7A01G135700 chr7A 88144408 88144990 582 False 667.000000 667 87.267000 163 751 1 chr7A.!!$F4 588
5 TraesCS7A01G135700 chr7B 35636538 35640409 3871 False 1353.250000 2185 92.292500 164 3789 4 chr7B.!!$F5 3625
6 TraesCS7A01G135700 chr7B 35307638 35308480 842 False 861.000000 861 85.066000 947 1846 1 chr7B.!!$F3 899
7 TraesCS7A01G135700 chr7B 35507076 35508125 1049 False 676.500000 846 89.486500 764 1846 2 chr7B.!!$F4 1082
8 TraesCS7A01G135700 chr7D 87219717 87224093 4376 False 1393.000000 1903 93.799750 164 3866 4 chr7D.!!$F5 3702
9 TraesCS7A01G135700 chr7D 87206170 87207339 1169 False 694.400000 1336 96.795500 924 1846 2 chr7D.!!$F4 922
10 TraesCS7A01G135700 chr7D 86918482 86919455 973 False 453.000000 580 92.351333 791 1846 3 chr7D.!!$F3 1055
11 TraesCS7A01G135700 chr7D 86754993 86755964 971 False 450.666667 562 92.195333 791 1846 3 chr7D.!!$F2 1055
12 TraesCS7A01G135700 chr7D 86291939 86293142 1203 False 343.333333 601 89.250000 1005 2083 3 chr7D.!!$F1 1078
13 TraesCS7A01G135700 chr4B 387795408 387798838 3430 False 280.500000 283 96.726500 1 168 2 chr4B.!!$F1 167

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
668 679 0.108898 CTCTCGGAACTGCCACTGAG 60.109 60.000 0.0 0.0 39.88 3.35 F
1183 2185 1.203001 CCTTTACCTGTTGCCCCTTCA 60.203 52.381 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 3577 0.239347 CTGTTGTTACTGCTGCAGGC 59.761 55.0 31.00 20.69 42.22 4.85 R
2893 4447 0.607489 GTGGCTGAAGCAGTCCATGT 60.607 55.0 4.43 0.00 44.36 3.21 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
184 185 7.550551 CCACATGACAACATCATTACTCTAGTT 59.449 37.037 0.00 0.00 46.54 2.24
210 211 8.581578 TCAATTGAAACCTATTTACCAAAGTCC 58.418 33.333 5.45 0.00 0.00 3.85
470 475 6.681816 AATGAGCCACATGGGGTTATTCATG 61.682 44.000 17.28 0.00 46.83 3.07
668 679 0.108898 CTCTCGGAACTGCCACTGAG 60.109 60.000 0.00 0.00 39.88 3.35
1037 1697 2.099756 GCTTGGATTTGGGAAAGATCGG 59.900 50.000 0.00 0.00 0.00 4.18
1038 1698 3.356290 CTTGGATTTGGGAAAGATCGGT 58.644 45.455 0.00 0.00 0.00 4.69
1183 2185 1.203001 CCTTTACCTGTTGCCCCTTCA 60.203 52.381 0.00 0.00 0.00 3.02
1983 3536 6.404184 CGAGATCTGGCACTATTATGTCTAGG 60.404 46.154 0.00 0.00 0.00 3.02
2024 3577 4.794248 TTTGACATGTGAAGTCTGTTCG 57.206 40.909 1.15 0.00 36.94 3.95
2085 3638 3.055094 GTGCCCCTCTGAATCAGTCTTAA 60.055 47.826 10.36 0.00 32.61 1.85
2086 3639 3.782523 TGCCCCTCTGAATCAGTCTTAAT 59.217 43.478 10.36 0.00 32.61 1.40
2087 3640 4.228210 TGCCCCTCTGAATCAGTCTTAATT 59.772 41.667 10.36 0.00 32.61 1.40
2088 3641 4.819088 GCCCCTCTGAATCAGTCTTAATTC 59.181 45.833 10.36 0.00 32.61 2.17
2089 3642 5.630069 GCCCCTCTGAATCAGTCTTAATTCA 60.630 44.000 10.36 7.05 39.06 2.57
2090 3643 6.418101 CCCCTCTGAATCAGTCTTAATTCAA 58.582 40.000 10.36 0.00 40.38 2.69
2091 3644 6.886459 CCCCTCTGAATCAGTCTTAATTCAAA 59.114 38.462 10.36 0.00 40.38 2.69
2092 3645 7.148171 CCCCTCTGAATCAGTCTTAATTCAAAC 60.148 40.741 10.36 0.00 40.38 2.93
2105 3658 9.063615 GTCTTAATTCAAACTTCAAAGGGAGTA 57.936 33.333 0.00 0.00 0.00 2.59
2245 3798 3.254060 ACTCTTGGTCGATGTGAAATCG 58.746 45.455 0.00 0.00 42.38 3.34
2363 3916 7.717436 TCCGAGCAATATAACCATTTTATGTGA 59.283 33.333 0.00 0.00 0.00 3.58
2400 3953 8.191446 TGATCCATTTGTCAACTTTTTCGTTTA 58.809 29.630 0.00 0.00 0.00 2.01
2498 4051 8.869109 TGGATTTCATTCTGGTTTCTTAATTGT 58.131 29.630 0.00 0.00 0.00 2.71
2593 4146 6.294176 GGAGTCTACTACGGTAGTTTTGTTCA 60.294 42.308 24.46 5.44 44.13 3.18
2594 4147 7.042797 AGTCTACTACGGTAGTTTTGTTCAA 57.957 36.000 24.46 4.75 44.13 2.69
2893 4447 5.237815 GTGGTTAGCGATGAATGGATGATA 58.762 41.667 0.00 0.00 0.00 2.15
3173 5180 1.824230 CAAATTCAGGGCCATTCGGAA 59.176 47.619 6.18 0.00 0.00 4.30
3213 5220 4.573607 TCATATGCTCTGTGAATTGACTGC 59.426 41.667 0.00 0.00 0.00 4.40
3345 5935 7.065204 GTCCAATGAAGGAAGAAGTTCTATGTC 59.935 40.741 5.65 0.00 39.92 3.06
3347 5937 6.627087 ATGAAGGAAGAAGTTCTATGTCCA 57.373 37.500 19.67 10.73 32.72 4.02
3571 6187 3.130164 ACGGCTGCATTTTTGCATATACA 59.870 39.130 0.50 0.00 44.47 2.29
3602 6218 3.690139 TGGAGTAGCGTTTTTGACACAAA 59.310 39.130 0.00 0.00 0.00 2.83
3724 6340 2.416547 CGATTTTCAGGCGTGATGAACT 59.583 45.455 10.35 0.00 36.44 3.01
3725 6341 3.120199 CGATTTTCAGGCGTGATGAACTT 60.120 43.478 10.35 0.00 36.44 2.66
3764 6380 2.219458 GCAGACACATGATCTGATGGG 58.781 52.381 25.95 8.15 45.46 4.00
3821 6672 0.840617 TTTTTCTTTTGGGTGGGGCC 59.159 50.000 0.00 0.00 0.00 5.80
3837 6688 1.135228 GGGCCGCGTTTTTACATCATT 60.135 47.619 4.92 0.00 0.00 2.57
3843 6694 4.143431 CCGCGTTTTTACATCATTTGTTGG 60.143 41.667 4.92 0.00 39.87 3.77
3857 6708 4.908601 TTTGTTGGAGATGCTCTTAGGA 57.091 40.909 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.400439 GGTATTAGTTGGAAAGGTTTAGTCCT 58.600 38.462 0.00 0.00 39.84 3.85
184 185 8.581578 GGACTTTGGTAAATAGGTTTCAATTGA 58.418 33.333 3.38 3.38 0.00 2.57
210 211 4.748892 TCTGCTCGAAGAAATACTCCAAG 58.251 43.478 0.00 0.00 34.09 3.61
470 475 4.773510 CAAACTAGGTTTGTTCTTCGAGC 58.226 43.478 13.10 0.00 45.19 5.03
668 679 0.322546 AGGAAGTTCCGGGTCAATGC 60.323 55.000 16.31 0.00 42.75 3.56
1846 3102 2.048597 TAGCAGTGTTCGGCCACG 60.049 61.111 2.24 0.00 40.33 4.94
1983 3536 6.364435 GTCAAATGAGCTTGGAAAAACTCATC 59.636 38.462 4.94 0.00 44.42 2.92
2024 3577 0.239347 CTGTTGTTACTGCTGCAGGC 59.761 55.000 31.00 20.69 42.22 4.85
2058 3611 1.355381 TGATTCAGAGGGGCACAACAT 59.645 47.619 0.00 0.00 0.00 2.71
2067 3620 7.609532 AGTTTGAATTAAGACTGATTCAGAGGG 59.390 37.037 20.33 0.00 41.67 4.30
2085 3638 5.185828 GGCATACTCCCTTTGAAGTTTGAAT 59.814 40.000 0.00 0.00 0.00 2.57
2086 3639 4.522789 GGCATACTCCCTTTGAAGTTTGAA 59.477 41.667 0.00 0.00 0.00 2.69
2087 3640 4.079253 GGCATACTCCCTTTGAAGTTTGA 58.921 43.478 0.00 0.00 0.00 2.69
2088 3641 3.826157 TGGCATACTCCCTTTGAAGTTTG 59.174 43.478 0.00 0.00 0.00 2.93
2089 3642 4.112634 TGGCATACTCCCTTTGAAGTTT 57.887 40.909 0.00 0.00 0.00 2.66
2090 3643 3.806949 TGGCATACTCCCTTTGAAGTT 57.193 42.857 0.00 0.00 0.00 2.66
2091 3644 5.456763 GGATATGGCATACTCCCTTTGAAGT 60.457 44.000 9.83 0.00 0.00 3.01
2092 3645 5.006386 GGATATGGCATACTCCCTTTGAAG 58.994 45.833 9.83 0.00 0.00 3.02
2105 3658 3.400322 AGGTTGATTCTGGGATATGGCAT 59.600 43.478 4.88 4.88 0.00 4.40
2245 3798 3.904136 ACTAGTGCAAAATCACACAGC 57.096 42.857 0.00 0.00 39.30 4.40
2259 3812 6.595716 AGGTAAGCTCTTTTGCATAACTAGTG 59.404 38.462 0.00 0.00 33.19 2.74
2363 3916 9.206870 GTTGACAAATGGATCACATGTTAAATT 57.793 29.630 0.00 0.00 40.44 1.82
2400 3953 3.118112 CAGGATAGCTCCAGACAAATGGT 60.118 47.826 0.00 0.00 44.79 3.55
2498 4051 4.309099 AGTACCGTTTCAAAATGACGCTA 58.691 39.130 0.00 0.00 35.60 4.26
2552 4105 3.680786 CCGTCGACCTCCAGCACA 61.681 66.667 10.58 0.00 0.00 4.57
2593 4146 4.467438 GTGGGGAATGACCAATTGAGATTT 59.533 41.667 7.12 0.00 40.24 2.17
2594 4147 4.026052 GTGGGGAATGACCAATTGAGATT 58.974 43.478 7.12 1.75 40.24 2.40
2868 4422 1.557371 TCCATTCATCGCTAACCACCA 59.443 47.619 0.00 0.00 0.00 4.17
2893 4447 0.607489 GTGGCTGAAGCAGTCCATGT 60.607 55.000 4.43 0.00 44.36 3.21
3033 5040 1.825090 TACTGCATGCAACAGAAGGG 58.175 50.000 22.88 9.78 38.55 3.95
3213 5220 8.032952 TCAGATATTGCAACTTTCACAGTTAG 57.967 34.615 0.00 0.00 44.60 2.34
3345 5935 0.180406 GCACCCTACCACTACCATGG 59.820 60.000 11.19 11.19 46.10 3.66
3347 5937 1.204146 CTGCACCCTACCACTACCAT 58.796 55.000 0.00 0.00 0.00 3.55
3382 5972 1.465188 TCTGAACATGGGGTGGGGT 60.465 57.895 0.00 0.00 0.00 4.95
3417 6033 3.947196 GGCATCAACTTGTACATCATCCA 59.053 43.478 0.00 0.00 0.00 3.41
3457 6073 9.145865 GTGATGTAAAAACCTTCTCTCTTCTAG 57.854 37.037 0.00 0.00 0.00 2.43
3571 6187 3.402628 AACGCTACTCCAACAAGTGAT 57.597 42.857 0.00 0.00 0.00 3.06
3602 6218 3.823873 TGAAAATGGCCGTTTACATCACT 59.176 39.130 23.11 5.79 0.00 3.41
3749 6365 1.133884 AGTGCCCCATCAGATCATGTG 60.134 52.381 0.00 0.00 0.00 3.21
3754 6370 2.167075 CCAAAAAGTGCCCCATCAGATC 59.833 50.000 0.00 0.00 0.00 2.75
3764 6380 2.447714 TTGGCCCCCAAAAAGTGCC 61.448 57.895 0.00 0.00 40.92 5.01
3804 6655 1.834822 CGGCCCCACCCAAAAGAAA 60.835 57.895 0.00 0.00 33.26 2.52
3813 6664 2.984718 TAAAAACGCGGCCCCACC 60.985 61.111 12.47 0.00 0.00 4.61
3814 6665 1.868987 ATGTAAAAACGCGGCCCCAC 61.869 55.000 12.47 3.05 0.00 4.61
3815 6666 1.587933 GATGTAAAAACGCGGCCCCA 61.588 55.000 12.47 0.00 0.00 4.96
3816 6667 1.138036 GATGTAAAAACGCGGCCCC 59.862 57.895 12.47 0.00 0.00 5.80
3817 6668 0.454196 ATGATGTAAAAACGCGGCCC 59.546 50.000 12.47 0.00 0.00 5.80
3818 6669 2.271821 AATGATGTAAAAACGCGGCC 57.728 45.000 12.47 0.00 0.00 6.13
3819 6670 2.983803 ACAAATGATGTAAAAACGCGGC 59.016 40.909 12.47 0.00 41.63 6.53
3820 6671 4.143431 CCAACAAATGATGTAAAAACGCGG 60.143 41.667 12.47 0.00 42.99 6.46
3821 6672 4.677378 TCCAACAAATGATGTAAAAACGCG 59.323 37.500 3.53 3.53 42.99 6.01


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

AutoCloner maintained by Alex Coulton.