Multiple sequence alignment - TraesCS7D01G135100

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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 TraesCS7D01G135100 chr7D 100.000 2974 0 0 1 2974 86754159 86757132 0.000000e+00 5493.0
1 TraesCS7D01G135100 chr7D 97.704 1916 38 4 812 2725 86918459 86920370 0.000000e+00 3290.0
2 TraesCS7D01G135100 chr7D 91.971 1370 76 7 1382 2725 87206912 87208273 0.000000e+00 1890.0
3 TraesCS7D01G135100 chr7D 84.820 639 50 18 2119 2725 86293459 86294082 1.530000e-167 599.0
4 TraesCS7D01G135100 chr7D 90.789 380 21 8 835 1206 87220317 87220690 2.060000e-136 496.0
5 TraesCS7D01G135100 chr7D 98.425 254 3 1 2722 2974 135348250 135347997 2.100000e-121 446.0
6 TraesCS7D01G135100 chr7D 96.859 191 5 1 1201 1390 87206698 87206888 4.780000e-83 318.0
7 TraesCS7D01G135100 chr7D 95.789 190 8 0 1201 1390 87220731 87220920 1.040000e-79 307.0
8 TraesCS7D01G135100 chr7D 95.767 189 8 0 2387 2575 86784481 86784669 3.720000e-79 305.0
9 TraesCS7D01G135100 chr7D 90.909 220 10 5 990 1206 87206445 87206657 1.350000e-73 287.0
10 TraesCS7D01G135100 chr7D 94.904 157 5 1 2572 2725 86796658 86796814 2.960000e-60 243.0
11 TraesCS7D01G135100 chr7D 90.741 54 4 1 1 53 112895015 112895068 1.480000e-08 71.3
12 TraesCS7D01G135100 chr7D 94.872 39 2 0 2197 2235 85354450 85354412 8.900000e-06 62.1
13 TraesCS7D01G135100 chr7A 88.860 1894 146 36 869 2725 87451162 87453027 0.000000e+00 2268.0
14 TraesCS7D01G135100 chr7A 92.018 1353 80 7 1382 2716 88315962 88317304 0.000000e+00 1875.0
15 TraesCS7D01G135100 chr7A 91.703 1362 75 14 1382 2725 88436371 88437712 0.000000e+00 1855.0
16 TraesCS7D01G135100 chr7A 89.430 1088 66 15 1677 2725 88122403 88123480 0.000000e+00 1327.0
17 TraesCS7D01G135100 chr7A 89.348 1089 66 13 1677 2725 88173170 88174248 0.000000e+00 1323.0
18 TraesCS7D01G135100 chr7A 89.062 1088 69 13 1677 2725 88009123 88010199 0.000000e+00 1304.0
19 TraesCS7D01G135100 chr7A 85.245 1186 101 38 56 1206 88007535 88008681 0.000000e+00 1153.0
20 TraesCS7D01G135100 chr7A 95.970 397 16 0 1201 1597 88172773 88173169 0.000000e+00 645.0
21 TraesCS7D01G135100 chr7A 95.970 397 15 1 1201 1597 88008727 88009122 0.000000e+00 643.0
22 TraesCS7D01G135100 chr7A 91.005 378 21 8 835 1206 88435740 88436110 5.720000e-137 497.0
23 TraesCS7D01G135100 chr7A 90.741 378 23 7 835 1206 88500109 88500480 7.410000e-136 494.0
24 TraesCS7D01G135100 chr7A 95.288 191 8 1 1201 1390 88315748 88315938 4.820000e-78 302.0
25 TraesCS7D01G135100 chr7A 95.213 188 8 1 1201 1388 88436157 88436343 2.240000e-76 296.0
26 TraesCS7D01G135100 chr7A 95.213 188 8 1 1201 1388 88500527 88500713 2.240000e-76 296.0
27 TraesCS7D01G135100 chr7A 86.111 288 13 11 919 1206 88172467 88172727 4.850000e-73 285.0
28 TraesCS7D01G135100 chr7B 90.415 1565 94 20 1201 2725 35507525 35509073 0.000000e+00 2008.0
29 TraesCS7D01G135100 chr7B 88.159 1385 84 28 1382 2725 35308069 35309414 0.000000e+00 1576.0
30 TraesCS7D01G135100 chr7B 93.458 428 25 3 1382 1807 35637813 35638239 1.500000e-177 632.0
31 TraesCS7D01G135100 chr7B 81.425 786 107 29 74 831 739346481 739347255 9.120000e-170 606.0
32 TraesCS7D01G135100 chr7B 89.295 383 23 8 835 1206 35507103 35507478 5.810000e-127 464.0
33 TraesCS7D01G135100 chr7B 87.310 394 27 12 835 1206 35637161 35637553 2.120000e-116 429.0
34 TraesCS7D01G135100 chr7B 95.263 190 9 0 1201 1390 35637600 35637789 4.820000e-78 302.0
35 TraesCS7D01G135100 chr7B 89.542 153 13 3 855 1006 35301965 35302115 1.090000e-44 191.0
36 TraesCS7D01G135100 chr6A 82.843 781 104 22 72 831 82088798 82089569 0.000000e+00 673.0
37 TraesCS7D01G135100 chr3A 83.161 772 94 27 82 836 535228838 535228086 0.000000e+00 673.0
38 TraesCS7D01G135100 chr3A 93.182 264 7 2 2722 2974 452612265 452612002 7.780000e-101 377.0
39 TraesCS7D01G135100 chr2D 82.239 777 116 15 73 830 432765484 432764711 0.000000e+00 651.0
40 TraesCS7D01G135100 chr2D 91.667 48 2 1 6 53 131133407 131133362 6.880000e-07 65.8
41 TraesCS7D01G135100 chr1A 82.202 781 106 27 73 833 86012970 86012203 2.500000e-180 641.0
42 TraesCS7D01G135100 chr1A 97.452 157 3 1 2720 2875 464133823 464133667 1.760000e-67 267.0
43 TraesCS7D01G135100 chr1A 83.851 161 17 7 2721 2876 247333464 247333308 8.590000e-31 145.0
44 TraesCS7D01G135100 chr1A 98.734 79 1 0 2896 2974 464128554 464128476 1.110000e-29 141.0
45 TraesCS7D01G135100 chr3B 81.877 778 109 22 72 830 237299151 237298387 7.000000e-176 627.0
46 TraesCS7D01G135100 chr3B 94.340 53 2 1 1 53 730373745 730373694 2.460000e-11 80.5
47 TraesCS7D01G135100 chr6D 82.027 740 106 21 121 839 42922047 42921314 3.280000e-169 604.0
48 TraesCS7D01G135100 chr6D 76.149 457 72 19 3 446 311541899 311542331 3.890000e-49 206.0
49 TraesCS7D01G135100 chr5D 81.576 787 91 22 54 829 540584208 540584951 4.240000e-168 601.0
50 TraesCS7D01G135100 chr5D 94.253 261 5 2 2724 2974 142081679 142081419 9.990000e-105 390.0
51 TraesCS7D01G135100 chr5D 94.253 261 4 2 2725 2974 139512605 139512345 3.590000e-104 388.0
52 TraesCS7D01G135100 chr5D 85.955 178 21 3 2724 2899 480207414 480207239 1.410000e-43 187.0
53 TraesCS7D01G135100 chr5D 90.141 142 13 1 2722 2862 100860640 100860499 1.820000e-42 183.0
54 TraesCS7D01G135100 chr2B 80.876 753 101 29 98 830 214129614 214128885 1.200000e-153 553.0
55 TraesCS7D01G135100 chr2B 87.702 309 31 7 55 357 734937340 734937647 1.310000e-93 353.0
56 TraesCS7D01G135100 chr2B 96.154 52 2 0 2 53 401279526 401279475 5.280000e-13 86.1
57 TraesCS7D01G135100 chr4D 98.828 256 2 1 2720 2974 55301800 55301545 3.490000e-124 455.0
58 TraesCS7D01G135100 chr1D 98.031 254 2 2 2723 2974 258344586 258344334 3.520000e-119 438.0
59 TraesCS7D01G135100 chr1D 94.677 263 2 3 2724 2974 474060931 474060669 5.970000e-107 398.0
60 TraesCS7D01G135100 chr6B 94.636 261 4 1 2724 2974 368760384 368760644 2.150000e-106 396.0
61 TraesCS7D01G135100 chr6B 86.885 244 28 4 2722 2963 692453576 692453817 1.360000e-68 270.0
62 TraesCS7D01G135100 chr4B 94.318 264 3 3 2722 2974 454673840 454673578 7.730000e-106 394.0
63 TraesCS7D01G135100 chr4B 98.246 171 3 0 2804 2974 454673238 454673068 1.730000e-77 300.0
64 TraesCS7D01G135100 chr4B 92.308 52 3 1 3 53 630342047 630342098 4.110000e-09 73.1
65 TraesCS7D01G135100 chr1B 97.297 185 1 2 2724 2907 95228544 95228725 8.000000e-81 311.0
66 TraesCS7D01G135100 chrUn 96.226 53 2 0 1 53 98200327 98200275 1.470000e-13 87.9
67 TraesCS7D01G135100 chr5A 92.308 52 4 0 2 53 530785484 530785535 1.140000e-09 75.0
68 TraesCS7D01G135100 chr5B 88.889 54 4 1 2 53 696481753 696481700 6.880000e-07 65.8


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 TraesCS7D01G135100 chr7D 86754159 86757132 2973 False 5493.000000 5493 100.000000 1 2974 1 chr7D.!!$F2 2973
1 TraesCS7D01G135100 chr7D 86918459 86920370 1911 False 3290.000000 3290 97.704000 812 2725 1 chr7D.!!$F5 1913
2 TraesCS7D01G135100 chr7D 87206445 87208273 1828 False 831.666667 1890 93.246333 990 2725 3 chr7D.!!$F7 1735
3 TraesCS7D01G135100 chr7D 86293459 86294082 623 False 599.000000 599 84.820000 2119 2725 1 chr7D.!!$F1 606
4 TraesCS7D01G135100 chr7D 87220317 87220920 603 False 401.500000 496 93.289000 835 1390 2 chr7D.!!$F8 555
5 TraesCS7D01G135100 chr7A 87451162 87453027 1865 False 2268.000000 2268 88.860000 869 2725 1 chr7A.!!$F1 1856
6 TraesCS7D01G135100 chr7A 88122403 88123480 1077 False 1327.000000 1327 89.430000 1677 2725 1 chr7A.!!$F2 1048
7 TraesCS7D01G135100 chr7A 88315748 88317304 1556 False 1088.500000 1875 93.653000 1201 2716 2 chr7A.!!$F5 1515
8 TraesCS7D01G135100 chr7A 88007535 88010199 2664 False 1033.333333 1304 90.092333 56 2725 3 chr7A.!!$F3 2669
9 TraesCS7D01G135100 chr7A 88435740 88437712 1972 False 882.666667 1855 92.640333 835 2725 3 chr7A.!!$F6 1890
10 TraesCS7D01G135100 chr7A 88172467 88174248 1781 False 751.000000 1323 90.476333 919 2725 3 chr7A.!!$F4 1806
11 TraesCS7D01G135100 chr7A 88500109 88500713 604 False 395.000000 494 92.977000 835 1388 2 chr7A.!!$F7 553
12 TraesCS7D01G135100 chr7B 35308069 35309414 1345 False 1576.000000 1576 88.159000 1382 2725 1 chr7B.!!$F2 1343
13 TraesCS7D01G135100 chr7B 35507103 35509073 1970 False 1236.000000 2008 89.855000 835 2725 2 chr7B.!!$F4 1890
14 TraesCS7D01G135100 chr7B 739346481 739347255 774 False 606.000000 606 81.425000 74 831 1 chr7B.!!$F3 757
15 TraesCS7D01G135100 chr7B 35637161 35638239 1078 False 454.333333 632 92.010333 835 1807 3 chr7B.!!$F5 972
16 TraesCS7D01G135100 chr6A 82088798 82089569 771 False 673.000000 673 82.843000 72 831 1 chr6A.!!$F1 759
17 TraesCS7D01G135100 chr3A 535228086 535228838 752 True 673.000000 673 83.161000 82 836 1 chr3A.!!$R2 754
18 TraesCS7D01G135100 chr2D 432764711 432765484 773 True 651.000000 651 82.239000 73 830 1 chr2D.!!$R2 757
19 TraesCS7D01G135100 chr1A 86012203 86012970 767 True 641.000000 641 82.202000 73 833 1 chr1A.!!$R1 760
20 TraesCS7D01G135100 chr3B 237298387 237299151 764 True 627.000000 627 81.877000 72 830 1 chr3B.!!$R1 758
21 TraesCS7D01G135100 chr6D 42921314 42922047 733 True 604.000000 604 82.027000 121 839 1 chr6D.!!$R1 718
22 TraesCS7D01G135100 chr5D 540584208 540584951 743 False 601.000000 601 81.576000 54 829 1 chr5D.!!$F1 775
23 TraesCS7D01G135100 chr2B 214128885 214129614 729 True 553.000000 553 80.876000 98 830 1 chr2B.!!$R1 732
24 TraesCS7D01G135100 chr4B 454673068 454673840 772 True 347.000000 394 96.282000 2722 2974 2 chr4B.!!$R1 252

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
49 50 0.036306 TCCCTTTCCGAAAGAGGCAC 59.964 55.0 20.43 0.0 41.02 5.01 F
151 155 0.661020 CGGAAGCAAAACCGTGACTT 59.339 50.0 0.00 0.0 43.53 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 2495 0.318762 ACAAACGTCCTCAGAGGCTC 59.681 55.000 12.26 6.34 34.61 4.70 R
2235 2845 4.331717 CGACGGCCAAGATAACAAAAGTAT 59.668 41.667 2.24 0.00 0.00 2.12 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
31 32 3.053896 CGGGAGCACGGGGTTTTC 61.054 66.667 0.00 0.00 0.00 2.29
32 33 2.675423 GGGAGCACGGGGTTTTCC 60.675 66.667 0.00 0.00 39.75 3.13
45 46 3.917329 GGTTTTCCCTTTCCGAAAGAG 57.083 47.619 20.43 9.08 41.02 2.85
46 47 2.557056 GGTTTTCCCTTTCCGAAAGAGG 59.443 50.000 20.43 18.19 41.02 3.69
47 48 1.905637 TTTCCCTTTCCGAAAGAGGC 58.094 50.000 20.43 0.00 41.02 4.70
48 49 0.768622 TTCCCTTTCCGAAAGAGGCA 59.231 50.000 20.43 8.95 41.02 4.75
49 50 0.036306 TCCCTTTCCGAAAGAGGCAC 59.964 55.000 20.43 0.00 41.02 5.01
50 51 1.298859 CCCTTTCCGAAAGAGGCACG 61.299 60.000 20.43 4.41 41.02 5.34
51 52 1.497722 CTTTCCGAAAGAGGCACGC 59.502 57.895 14.72 0.00 41.02 5.34
52 53 1.912371 CTTTCCGAAAGAGGCACGCC 61.912 60.000 14.72 0.00 41.02 5.68
151 155 0.661020 CGGAAGCAAAACCGTGACTT 59.339 50.000 0.00 0.00 43.53 3.01
155 159 1.658994 AGCAAAACCGTGACTTTCGA 58.341 45.000 0.00 0.00 0.00 3.71
165 171 3.746492 CCGTGACTTTCGAGGAAGAAAAT 59.254 43.478 3.89 0.00 39.33 1.82
251 376 1.227999 TGCCTCTCGCGGAAACAAAG 61.228 55.000 6.13 0.00 42.08 2.77
265 390 1.373497 CAAAGTCGTGCCTCTCGCT 60.373 57.895 0.00 0.00 38.78 4.93
440 725 1.006102 CCGTGCCTCTCGTGAAAGT 60.006 57.895 0.00 0.00 0.00 2.66
464 749 1.900351 CATGCCTCTCGTGGAAGGA 59.100 57.895 0.00 0.00 0.00 3.36
466 751 0.984230 ATGCCTCTCGTGGAAGGAAA 59.016 50.000 0.00 0.00 0.00 3.13
467 752 0.984230 TGCCTCTCGTGGAAGGAAAT 59.016 50.000 0.00 0.00 0.00 2.17
482 767 8.600625 GTGGAAGGAAATAAAAACAGAAAACAC 58.399 33.333 0.00 0.00 0.00 3.32
521 806 2.468015 AGGCACACCCATGACTCTT 58.532 52.632 0.00 0.00 29.04 2.85
699 1004 4.329801 ACCGTTTAGAAAGACGAAAACGTT 59.670 37.500 15.37 0.00 43.75 3.99
1510 2011 1.136336 GTTTAAGTTCAGACTGCGCGG 60.136 52.381 16.39 16.39 35.91 6.46
1551 2052 7.051623 AGTAACAATGGCTCATATTTAACGGA 58.948 34.615 0.00 0.00 0.00 4.69
1903 2495 3.062763 GTGATCTCCACACAGTTGTCTG 58.937 50.000 0.00 0.00 45.03 3.51
2235 2845 8.285350 TCTAATCTAGGTCTAAACTAGGGCTA 57.715 38.462 0.00 0.00 38.71 3.93
2323 2935 1.663739 CCGGTCTTGAGTCGGTTGA 59.336 57.895 0.00 0.00 39.04 3.18
2466 3100 8.689972 AGGCCTTGATTATAAATGTTCTCTTTG 58.310 33.333 0.00 0.00 0.00 2.77
2856 3522 0.762418 TGAGAAAAAGCTGGGGTCGA 59.238 50.000 0.00 0.00 0.00 4.20
2917 4102 1.980844 GGACGTGCCCCTCTAGTTT 59.019 57.895 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.529119 CTCCCGGGTCGGTTTATTCG 60.529 60.000 22.86 0.00 46.80 3.34
1 2 0.812811 GCTCCCGGGTCGGTTTATTC 60.813 60.000 22.86 0.00 46.80 1.75
2 3 1.222661 GCTCCCGGGTCGGTTTATT 59.777 57.895 22.86 0.00 46.80 1.40
4 5 2.604079 TGCTCCCGGGTCGGTTTA 60.604 61.111 22.86 0.00 46.80 2.01
14 15 3.053896 GAAAACCCCGTGCTCCCG 61.054 66.667 0.00 0.00 0.00 5.14
15 16 2.675423 GGAAAACCCCGTGCTCCC 60.675 66.667 0.00 0.00 0.00 4.30
24 25 2.557056 CTCTTTCGGAAAGGGAAAACCC 59.443 50.000 22.99 0.00 41.66 4.11
25 26 2.557056 CCTCTTTCGGAAAGGGAAAACC 59.443 50.000 27.71 0.00 41.66 3.27
26 27 2.030185 GCCTCTTTCGGAAAGGGAAAAC 60.030 50.000 27.71 12.67 41.66 2.43
27 28 2.235891 GCCTCTTTCGGAAAGGGAAAA 58.764 47.619 27.71 9.72 41.66 2.29
28 29 1.144093 TGCCTCTTTCGGAAAGGGAAA 59.856 47.619 27.71 14.52 41.66 3.13
29 30 0.768622 TGCCTCTTTCGGAAAGGGAA 59.231 50.000 27.71 19.29 41.66 3.97
30 31 0.036306 GTGCCTCTTTCGGAAAGGGA 59.964 55.000 27.71 14.21 41.66 4.20
31 32 1.298859 CGTGCCTCTTTCGGAAAGGG 61.299 60.000 25.66 23.41 38.75 3.95
32 33 1.912371 GCGTGCCTCTTTCGGAAAGG 61.912 60.000 25.66 15.57 39.01 3.11
33 34 1.497722 GCGTGCCTCTTTCGGAAAG 59.502 57.895 21.64 21.64 39.88 2.62
34 35 1.964373 GGCGTGCCTCTTTCGGAAA 60.964 57.895 2.98 2.78 0.00 3.13
35 36 2.358247 GGCGTGCCTCTTTCGGAA 60.358 61.111 2.98 0.00 0.00 4.30
36 37 4.735132 CGGCGTGCCTCTTTCGGA 62.735 66.667 9.55 0.00 0.00 4.55
37 38 4.735132 TCGGCGTGCCTCTTTCGG 62.735 66.667 6.85 0.00 0.00 4.30
38 39 1.837538 TTTTCGGCGTGCCTCTTTCG 61.838 55.000 6.85 0.00 0.00 3.46
39 40 0.309612 TTTTTCGGCGTGCCTCTTTC 59.690 50.000 6.85 0.00 0.00 2.62
40 41 2.410466 TTTTTCGGCGTGCCTCTTT 58.590 47.368 6.85 0.00 0.00 2.52
41 42 4.150994 TTTTTCGGCGTGCCTCTT 57.849 50.000 6.85 0.00 0.00 2.85
90 94 2.653702 GAGAGTCACGGCTGTGCT 59.346 61.111 21.33 19.76 46.01 4.40
246 371 1.664965 GCGAGAGGCACGACTTTGT 60.665 57.895 0.00 0.00 42.87 2.83
440 725 1.626321 TCCACGAGAGGCATGGTTTTA 59.374 47.619 0.00 0.00 34.89 1.52
535 820 1.790090 TTGCTTCCGCGAAATGCACA 61.790 50.000 8.23 4.29 46.97 4.57
536 821 0.662970 TTTGCTTCCGCGAAATGCAC 60.663 50.000 8.23 0.00 46.97 4.57
620 923 4.527816 TCCACCGGTCTTACTTAGCTTTTA 59.472 41.667 2.59 0.00 0.00 1.52
773 1091 1.005037 AACGATCAGCGCCACTTGA 60.005 52.632 2.29 0.40 46.04 3.02
1184 1544 2.959707 AGATCTACCATTGGAGGACGAC 59.040 50.000 10.37 3.35 0.00 4.34
1510 2011 6.854496 TTGTTACTTCAGTGTATGTCCAAC 57.146 37.500 0.00 0.00 0.00 3.77
1551 2052 2.608988 AGCCCAGCTGCACCTACT 60.609 61.111 8.66 0.00 37.57 2.57
1858 2450 1.468506 TTCAGTAGCAGTGGTCGGCA 61.469 55.000 0.00 0.00 37.23 5.69
1903 2495 0.318762 ACAAACGTCCTCAGAGGCTC 59.681 55.000 12.26 6.34 34.61 4.70
2235 2845 4.331717 CGACGGCCAAGATAACAAAAGTAT 59.668 41.667 2.24 0.00 0.00 2.12
2323 2935 0.250770 GACCAGGAAAGGAAGGCGTT 60.251 55.000 0.00 0.00 0.00 4.84
2466 3100 2.231716 AAGGGGGAAACTTGTATGCC 57.768 50.000 0.00 0.00 0.00 4.40
2493 3127 5.241728 AGAGTTGCTCAAACCCTTAATGTTC 59.758 40.000 0.00 0.00 39.85 3.18
2917 4102 9.013229 GGTGGCAATATTGATGTAATAAGATCA 57.987 33.333 19.73 0.00 35.03 2.92


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

AutoCloner maintained by Alex Coulton.