Multiple sequence alignment - TraesCS7D01G385200

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 TraesCS7D01G385200 chr7D 100.000 3681 0 0 1 3681 499627697 499624017 0.000000e+00 6798.0
1 TraesCS7D01G385200 chr4B 96.413 3541 67 12 147 3681 642736898 642740384 0.000000e+00 5781.0
2 TraesCS7D01G385200 chr7A 97.763 1609 28 4 403 2006 109230796 109229191 0.000000e+00 2765.0
3 TraesCS7D01G385200 chr7A 97.406 1619 32 6 403 2016 61493737 61492124 0.000000e+00 2748.0
4 TraesCS7D01G385200 chr7A 92.958 71 5 0 1 71 195749048 195749118 1.810000e-18 104.0
5 TraesCS7D01G385200 chr2B 94.743 1636 26 14 1 1625 30335816 30334230 0.000000e+00 2490.0
6 TraesCS7D01G385200 chr2B 95.441 1009 23 6 1870 2877 30332723 30331737 0.000000e+00 1587.0
7 TraesCS7D01G385200 chr2B 96.691 816 18 4 2869 3681 30331547 30330738 0.000000e+00 1349.0
8 TraesCS7D01G385200 chr2B 97.318 261 7 0 1608 1868 30334048 30333788 9.380000e-121 444.0
9 TraesCS7D01G385200 chr2B 76.888 437 38 25 2539 2967 211158611 211158992 4.850000e-44 189.0
10 TraesCS7D01G385200 chr3B 91.058 1644 80 22 286 1868 812459598 812461235 0.000000e+00 2159.0
11 TraesCS7D01G385200 chr3B 79.872 313 36 15 2656 2967 62383708 62383994 1.730000e-48 204.0
12 TraesCS7D01G385200 chr5B 95.969 1017 28 6 1870 2877 649446029 649445017 0.000000e+00 1639.0
13 TraesCS7D01G385200 chr5B 96.929 814 18 3 2869 3681 649444967 649444160 0.000000e+00 1358.0
14 TraesCS7D01G385200 chr5B 96.970 33 1 0 2841 2873 185222848 185222880 5.140000e-04 56.5
15 TraesCS7D01G385200 chr3D 91.742 884 31 8 286 1128 604685813 604686695 0.000000e+00 1190.0
16 TraesCS7D01G385200 chr3D 90.476 756 53 11 1127 1868 604686729 604687479 0.000000e+00 979.0
17 TraesCS7D01G385200 chr3D 95.782 403 14 1 3279 3681 419468685 419469084 0.000000e+00 647.0
18 TraesCS7D01G385200 chr3D 88.698 407 28 8 2873 3278 519173558 519173169 7.150000e-132 481.0
19 TraesCS7D01G385200 chr3D 97.183 71 2 0 1 71 511668115 511668185 1.800000e-23 121.0
20 TraesCS7D01G385200 chr3A 91.053 883 35 8 289 1128 734885639 734886520 0.000000e+00 1153.0
21 TraesCS7D01G385200 chr3A 90.940 883 34 9 289 1128 734840257 734841136 0.000000e+00 1146.0
22 TraesCS7D01G385200 chr3A 94.340 689 29 5 1127 1806 734841170 734841857 0.000000e+00 1048.0
23 TraesCS7D01G385200 chr3A 94.049 689 31 5 1127 1806 734886554 734887241 0.000000e+00 1037.0
24 TraesCS7D01G385200 chr3A 96.040 404 15 1 3279 3681 706834367 706834770 0.000000e+00 656.0
25 TraesCS7D01G385200 chr3A 80.952 315 33 11 2656 2969 33951870 33951582 1.330000e-54 224.0
26 TraesCS7D01G385200 chr3A 97.826 46 1 0 1822 1867 734842093 734842138 3.050000e-11 80.5
27 TraesCS7D01G385200 chr3A 97.826 46 1 0 1822 1867 734887477 734887522 3.050000e-11 80.5
28 TraesCS7D01G385200 chr5A 82.447 1316 119 54 530 1748 623024433 623023133 0.000000e+00 1048.0
29 TraesCS7D01G385200 chr5D 85.017 861 85 17 1952 2775 179360122 179360975 0.000000e+00 835.0
30 TraesCS7D01G385200 chr5D 89.011 455 36 10 1195 1646 498731447 498731004 5.370000e-153 551.0
31 TraesCS7D01G385200 chr6A 95.062 405 19 1 3278 3681 11417748 11417344 1.440000e-178 636.0
32 TraesCS7D01G385200 chr6A 94.554 404 21 1 3279 3681 11432803 11432400 1.120000e-174 623.0
33 TraesCS7D01G385200 chr4A 94.458 415 20 3 3270 3681 727746347 727746761 1.440000e-178 636.0
34 TraesCS7D01G385200 chr4A 94.581 406 19 3 3279 3681 727754345 727754750 3.120000e-175 625.0
35 TraesCS7D01G385200 chrUn 88.698 407 28 8 2873 3278 368435668 368436057 7.150000e-132 481.0
36 TraesCS7D01G385200 chrUn 88.206 407 30 8 2873 3278 31637323 31636934 1.550000e-128 470.0
37 TraesCS7D01G385200 chr1A 88.698 407 28 8 2873 3278 514937359 514936970 7.150000e-132 481.0
38 TraesCS7D01G385200 chr1A 88.698 407 28 8 2873 3278 515194058 515193669 7.150000e-132 481.0
39 TraesCS7D01G385200 chr1A 78.492 451 52 17 2539 2972 48876499 48876077 1.700000e-63 254.0
40 TraesCS7D01G385200 chr4D 88.452 407 29 8 2873 3278 31538681 31539070 3.330000e-130 475.0
41 TraesCS7D01G385200 chr4D 100.000 28 0 0 2846 2873 425163402 425163375 7.000000e-03 52.8
42 TraesCS7D01G385200 chr6D 88.559 236 23 1 286 521 7262162 7262393 2.160000e-72 283.0
43 TraesCS7D01G385200 chr6D 92.188 128 9 1 1870 1996 130277666 130277539 2.920000e-41 180.0
44 TraesCS7D01G385200 chr6D 92.188 128 9 1 1870 1996 367003398 367003271 2.920000e-41 180.0
45 TraesCS7D01G385200 chr2A 89.130 230 21 1 292 521 17648024 17647799 2.160000e-72 283.0
46 TraesCS7D01G385200 chr2A 79.205 327 42 14 2656 2982 429128121 429127821 1.730000e-48 204.0
47 TraesCS7D01G385200 chr2D 80.685 321 47 12 293 603 547166308 547165993 6.150000e-58 235.0
48 TraesCS7D01G385200 chr2D 92.188 128 9 1 1870 1996 476921951 476921824 2.920000e-41 180.0
49 TraesCS7D01G385200 chr1B 86.628 172 22 1 2656 2827 348055708 348055878 4.850000e-44 189.0
50 TraesCS7D01G385200 chr7B 85.484 124 17 1 3 126 329695812 329695934 1.070000e-25 128.0
51 TraesCS7D01G385200 chr1D 96.970 33 1 0 2841 2873 111818625 111818657 5.140000e-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 TraesCS7D01G385200 chr7D 499624017 499627697 3680 True 6798.000000 6798 100.000000 1 3681 1 chr7D.!!$R1 3680
1 TraesCS7D01G385200 chr4B 642736898 642740384 3486 False 5781.000000 5781 96.413000 147 3681 1 chr4B.!!$F1 3534
2 TraesCS7D01G385200 chr7A 109229191 109230796 1605 True 2765.000000 2765 97.763000 403 2006 1 chr7A.!!$R2 1603
3 TraesCS7D01G385200 chr7A 61492124 61493737 1613 True 2748.000000 2748 97.406000 403 2016 1 chr7A.!!$R1 1613
4 TraesCS7D01G385200 chr2B 30330738 30335816 5078 True 1467.500000 2490 96.048250 1 3681 4 chr2B.!!$R1 3680
5 TraesCS7D01G385200 chr3B 812459598 812461235 1637 False 2159.000000 2159 91.058000 286 1868 1 chr3B.!!$F2 1582
6 TraesCS7D01G385200 chr5B 649444160 649446029 1869 True 1498.500000 1639 96.449000 1870 3681 2 chr5B.!!$R1 1811
7 TraesCS7D01G385200 chr3D 604685813 604687479 1666 False 1084.500000 1190 91.109000 286 1868 2 chr3D.!!$F3 1582
8 TraesCS7D01G385200 chr3A 734840257 734842138 1881 False 758.166667 1146 94.368667 289 1867 3 chr3A.!!$F2 1578
9 TraesCS7D01G385200 chr3A 734885639 734887522 1883 False 756.833333 1153 94.309333 289 1867 3 chr3A.!!$F3 1578
10 TraesCS7D01G385200 chr5A 623023133 623024433 1300 True 1048.000000 1048 82.447000 530 1748 1 chr5A.!!$R1 1218
11 TraesCS7D01G385200 chr5D 179360122 179360975 853 False 835.000000 835 85.017000 1952 2775 1 chr5D.!!$F1 823

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
143 151 2.517919 GCATCCCCACCATCTCCC 59.482 66.667 0.0 0.0 0.0 4.30 F
1895 3567 1.626686 CCACTGCCTCCTCGATCTAT 58.373 55.000 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 3775 0.946221 CAAGTGGTCTGAGGTCACGC 60.946 60.0 0.0 0.0 36.6 5.34 R
3317 5315 1.719600 CGTGAGCTTTGAGAGGAAGG 58.280 55.0 0.0 0.0 0.0 3.46 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 62 2.821366 CCGCTGCTTCCGCATCTT 60.821 61.111 0.00 0.00 46.74 2.40
95 96 2.591429 CACAGCCAACGCACAGGA 60.591 61.111 0.00 0.00 37.52 3.86
143 151 2.517919 GCATCCCCACCATCTCCC 59.482 66.667 0.00 0.00 0.00 4.30
387 395 6.555315 GGAAAGCTAATGAACGTGAATGAAT 58.445 36.000 0.00 0.00 0.00 2.57
522 530 9.289782 AGCAACAATTTTACTTCATCTTACTCT 57.710 29.630 0.00 0.00 0.00 3.24
523 531 9.334693 GCAACAATTTTACTTCATCTTACTCTG 57.665 33.333 0.00 0.00 0.00 3.35
1895 3567 1.626686 CCACTGCCTCCTCGATCTAT 58.373 55.000 0.00 0.00 0.00 1.98
2101 3775 5.177881 GCAGAGAGATCATAGCACTGATTTG 59.822 44.000 0.00 0.60 36.01 2.32
2152 3826 4.561105 CAGTCTCTCCCTACAGAACAAAC 58.439 47.826 0.00 0.00 0.00 2.93
2264 3938 8.828644 CAGAAGAAGAATAGGACATCTCATTTG 58.171 37.037 0.00 0.00 0.00 2.32
2494 4191 6.710295 TCACACAAACTAAGCAATGTAGACAT 59.290 34.615 0.00 0.00 38.41 3.06
2826 4566 2.543777 TTTAACGCTGAGCTCTGGTT 57.456 45.000 20.66 21.34 0.00 3.67
3215 5213 7.841956 ACACATTCAACTTCTAGCATACTACT 58.158 34.615 0.00 0.00 0.00 2.57
3222 5220 8.712103 TCAACTTCTAGCATACTACTAGTCCTA 58.288 37.037 0.00 0.00 38.60 2.94
3231 5229 7.392113 AGCATACTACTAGTCCTAATGTAGCTG 59.608 40.741 0.00 0.00 36.72 4.24
3317 5315 3.692593 AGCTCCTCTTCTTCTTCGTCTAC 59.307 47.826 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 0.322816 GTGGAGCTCAAGGATGGCAA 60.323 55.000 17.19 0.0 0.00 4.52
85 86 0.832135 TCCTCCTCTTCCTGTGCGTT 60.832 55.000 0.00 0.0 0.00 4.84
123 131 3.482232 GAGATGGTGGGGATGCGGG 62.482 68.421 0.00 0.0 0.00 6.13
143 151 4.570663 GGATCGGACGTGAGGGCG 62.571 72.222 0.00 0.0 37.94 6.13
514 522 9.781633 GAGAGGACATAAGTATACAGAGTAAGA 57.218 37.037 5.50 0.0 0.00 2.10
515 523 9.787435 AGAGAGGACATAAGTATACAGAGTAAG 57.213 37.037 5.50 0.0 0.00 2.34
536 544 7.520937 GCCCGAGAGAAGTATAACTAAAGAGAG 60.521 44.444 0.00 0.0 0.00 3.20
941 1017 4.037446 TGACCTAATTCCACAAAGCAACAC 59.963 41.667 0.00 0.0 0.00 3.32
1125 1273 1.065854 GTCCACACAAGAGGAGGGATG 60.066 57.143 0.00 0.0 35.05 3.51
1646 2029 6.140303 ACTGGCATATCATAACAAAGCTTG 57.860 37.500 0.00 0.0 0.00 4.01
2101 3775 0.946221 CAAGTGGTCTGAGGTCACGC 60.946 60.000 0.00 0.0 36.60 5.34
2152 3826 6.587608 GCTGAAGTTATTTTCCATTTCACCTG 59.412 38.462 0.00 0.0 0.00 4.00
2494 4191 6.941857 TGCTCTGTTGGTGTTAACATAGATA 58.058 36.000 12.26 0.0 39.60 1.98
2826 4566 7.749377 TGGAGGAAGTAGAAAATAGGATGAA 57.251 36.000 0.00 0.0 0.00 2.57
3026 5024 9.595823 GTATATGACTGCTTTCCTTTGTAGTTA 57.404 33.333 0.00 0.0 29.71 2.24
3027 5025 8.322091 AGTATATGACTGCTTTCCTTTGTAGTT 58.678 33.333 0.00 0.0 36.87 2.24
3028 5026 7.852263 AGTATATGACTGCTTTCCTTTGTAGT 58.148 34.615 0.00 0.0 36.87 2.73
3215 5213 6.407074 GGAAAAGCTCAGCTACATTAGGACTA 60.407 42.308 0.00 0.0 38.25 2.59
3222 5220 3.754965 TGTGGAAAAGCTCAGCTACATT 58.245 40.909 0.00 0.0 38.25 2.71
3231 5229 2.229784 CAGGGTCAATGTGGAAAAGCTC 59.770 50.000 0.00 0.0 0.00 4.09
3317 5315 1.719600 CGTGAGCTTTGAGAGGAAGG 58.280 55.000 0.00 0.0 0.00 3.46


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

AutoCloner maintained by Alex Coulton.