Multiple sequence alignment - TraesCS2A01G525700

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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 TraesCS2A01G525700 chr2A 100.000 4881 0 0 1 4881 745815560 745810680 0.000000e+00 9014.0
1 TraesCS2A01G525700 chr2A 95.944 1134 35 4 367 1497 745734851 745733726 0.000000e+00 1829.0
2 TraesCS2A01G525700 chr2A 89.929 705 34 13 1770 2449 745733728 745733036 0.000000e+00 874.0
3 TraesCS2A01G525700 chr2A 85.659 781 70 17 4128 4881 745695789 745695024 0.000000e+00 784.0
4 TraesCS2A01G525700 chr2A 97.548 367 9 0 1 367 745735180 745734814 3.210000e-176 628.0
5 TraesCS2A01G525700 chr2A 81.702 470 54 23 2486 2940 745811486 745811034 3.590000e-96 363.0
6 TraesCS2A01G525700 chr2A 81.702 470 54 23 4075 4527 745813075 745812621 3.590000e-96 363.0
7 TraesCS2A01G525700 chr2A 85.324 293 32 8 3775 4060 88010001 88010289 4.780000e-75 292.0
8 TraesCS2A01G525700 chr2A 94.737 38 2 0 330 367 745815194 745815157 5.280000e-05 60.2
9 TraesCS2A01G525700 chr2B 88.420 829 63 13 367 1190 751003859 751003059 0.000000e+00 968.0
10 TraesCS2A01G525700 chr2B 88.540 829 51 13 372 1195 750442923 750442134 0.000000e+00 965.0
11 TraesCS2A01G525700 chr2B 86.136 779 67 17 4128 4881 750355435 750354673 0.000000e+00 802.0
12 TraesCS2A01G525700 chr2B 86.170 658 53 21 1821 2449 750435322 750434674 0.000000e+00 676.0
13 TraesCS2A01G525700 chr2B 92.643 367 24 1 1 367 750443254 750442891 4.330000e-145 525.0
14 TraesCS2A01G525700 chr2B 86.073 438 41 12 4452 4881 750066650 750066225 2.070000e-123 453.0
15 TraesCS2A01G525700 chr2B 78.348 799 76 37 1956 2698 750334222 750333465 1.260000e-115 427.0
16 TraesCS2A01G525700 chr2B 92.883 281 20 0 1492 1772 748596857 748596577 4.550000e-110 409.0
17 TraesCS2A01G525700 chr2B 81.278 454 52 17 1821 2265 750336460 750336031 2.180000e-88 337.0
18 TraesCS2A01G525700 chr2B 87.903 248 18 6 3382 3619 750333059 750332814 1.030000e-71 281.0
19 TraesCS2A01G525700 chr2B 85.714 259 14 9 4076 4312 750335453 750335196 8.110000e-63 252.0
20 TraesCS2A01G525700 chr2B 91.304 184 13 2 3615 3797 750332779 750332598 1.050000e-61 248.0
21 TraesCS2A01G525700 chr2B 81.818 231 28 8 4127 4344 750124715 750124486 1.080000e-41 182.0
22 TraesCS2A01G525700 chr2B 89.062 128 12 2 2571 2698 750124686 750124561 1.820000e-34 158.0
23 TraesCS2A01G525700 chr2B 90.833 120 8 2 1352 1470 750435528 750435411 1.820000e-34 158.0
24 TraesCS2A01G525700 chr2B 90.164 122 8 2 1934 2054 750081220 750081102 6.540000e-34 156.0
25 TraesCS2A01G525700 chr2B 85.915 142 10 4 4163 4294 750333582 750333441 5.090000e-30 143.0
26 TraesCS2A01G525700 chr2B 87.200 125 13 1 1821 1942 750125083 750124959 6.590000e-29 139.0
27 TraesCS2A01G525700 chr2B 89.583 96 10 0 4330 4425 750123444 750123349 6.630000e-24 122.0
28 TraesCS2A01G525700 chr2B 87.500 96 12 0 4330 4425 750078997 750078902 1.440000e-20 111.0
29 TraesCS2A01G525700 chr2B 77.778 198 25 8 4331 4527 750367498 750367319 2.400000e-18 104.0
30 TraesCS2A01G525700 chr2B 93.182 44 2 1 4075 4118 750333701 750333659 4.080000e-06 63.9
31 TraesCS2A01G525700 chr2D 83.584 865 99 23 452 1305 616429266 616428434 0.000000e+00 771.0
32 TraesCS2A01G525700 chr2D 85.997 657 55 21 1821 2449 616371368 616370721 0.000000e+00 669.0
33 TraesCS2A01G525700 chr2D 89.320 309 29 4 4574 4881 616218904 616218599 7.660000e-103 385.0
34 TraesCS2A01G525700 chr2D 86.184 304 27 12 3775 4070 87754069 87754365 1.020000e-81 315.0
35 TraesCS2A01G525700 chr2D 86.301 292 20 10 4265 4546 616219403 616219122 2.860000e-77 300.0
36 TraesCS2A01G525700 chr2D 86.466 266 18 5 2446 2696 616223819 616223557 4.810000e-70 276.0
37 TraesCS2A01G525700 chr2D 83.696 184 13 6 4075 4241 616223779 616223596 1.820000e-34 158.0
38 TraesCS2A01G525700 chr2D 90.678 118 8 2 1937 2054 616228902 616228788 2.350000e-33 154.0
39 TraesCS2A01G525700 chr2D 89.431 123 11 2 1821 1941 616229062 616228940 2.350000e-33 154.0
40 TraesCS2A01G525700 chr2D 80.374 214 17 8 2446 2637 616370694 616370484 6.590000e-29 139.0
41 TraesCS2A01G525700 chr2D 86.667 120 13 2 1831 1947 616214299 616214180 3.960000e-26 130.0
42 TraesCS2A01G525700 chr2D 88.542 96 11 0 4330 4425 616227046 616226951 3.090000e-22 117.0
43 TraesCS2A01G525700 chr2D 88.421 95 11 0 4128 4222 616370578 616370484 1.110000e-21 115.0
44 TraesCS2A01G525700 chr2D 78.173 197 25 11 4330 4525 616358602 616358423 5.170000e-20 110.0
45 TraesCS2A01G525700 chr7A 94.604 278 15 0 1495 1772 625741272 625740995 9.710000e-117 431.0
46 TraesCS2A01G525700 chr7A 93.525 278 18 0 1495 1772 682179915 682180192 9.770000e-112 414.0
47 TraesCS2A01G525700 chr7A 93.431 274 18 0 1497 1770 681096443 681096716 1.640000e-109 407.0
48 TraesCS2A01G525700 chr7A 87.607 234 15 8 3844 4070 400068996 400068770 4.850000e-65 259.0
49 TraesCS2A01G525700 chr6B 93.885 278 17 0 1495 1772 518679775 518680052 2.100000e-113 420.0
50 TraesCS2A01G525700 chr6B 88.158 76 9 0 366 441 533533040 533533115 1.870000e-14 91.6
51 TraesCS2A01G525700 chr1A 93.548 279 18 0 1494 1772 436890195 436890473 2.720000e-112 416.0
52 TraesCS2A01G525700 chr1A 76.860 363 64 16 10 367 462301415 462301762 2.320000e-43 187.0
53 TraesCS2A01G525700 chr1A 79.651 172 28 7 680 848 434642239 434642406 3.090000e-22 117.0
54 TraesCS2A01G525700 chr4B 93.165 278 18 1 1497 1774 479214696 479214972 1.640000e-109 407.0
55 TraesCS2A01G525700 chr3A 93.165 278 18 1 1497 1774 724060394 724060670 1.640000e-109 407.0
56 TraesCS2A01G525700 chr3A 80.447 179 27 6 680 854 585012908 585013082 3.960000e-26 130.0
57 TraesCS2A01G525700 chr3A 92.105 76 6 0 366 441 120354501 120354426 1.860000e-19 108.0
58 TraesCS2A01G525700 chr3A 91.892 74 5 1 372 444 1004199 1004272 8.640000e-18 102.0
59 TraesCS2A01G525700 chr4A 92.014 288 22 1 1497 1784 36082008 36081722 2.120000e-108 403.0
60 TraesCS2A01G525700 chr4A 84.768 302 32 7 3775 4070 572843237 572842944 1.720000e-74 291.0
61 TraesCS2A01G525700 chr5D 85.197 304 32 8 3775 4070 393057980 393058278 2.860000e-77 300.0
62 TraesCS2A01G525700 chr5D 84.868 304 33 8 3775 4070 390694444 390694146 1.330000e-75 294.0
63 TraesCS2A01G525700 chr5A 85.149 303 33 8 3775 4070 494231292 494230995 2.860000e-77 300.0
64 TraesCS2A01G525700 chr5B 85.050 301 32 11 3775 4070 473116640 473116932 1.330000e-75 294.0
65 TraesCS2A01G525700 chr5B 77.860 271 51 7 587 852 605319100 605318834 5.060000e-35 159.0
66 TraesCS2A01G525700 chr1D 79.282 362 64 9 9 367 363058306 363058659 4.880000e-60 243.0
67 TraesCS2A01G525700 chr1D 82.534 292 32 12 3775 4060 324747206 324746928 6.310000e-59 239.0
68 TraesCS2A01G525700 chr3D 77.077 349 74 5 11 356 3545350 3545695 3.850000e-46 196.0
69 TraesCS2A01G525700 chr3D 78.810 269 44 8 10 278 141235023 141234768 8.400000e-38 169.0
70 TraesCS2A01G525700 chr3D 89.333 75 8 0 367 441 594061660 594061586 1.450000e-15 95.3
71 TraesCS2A01G525700 chr7D 80.347 173 23 8 689 857 33775661 33775826 2.390000e-23 121.0
72 TraesCS2A01G525700 chr3B 78.974 195 24 7 3248 3442 485409608 485409785 3.090000e-22 117.0
73 TraesCS2A01G525700 chr3B 90.909 66 6 0 302 367 388108316 388108381 6.730000e-14 89.8
74 TraesCS2A01G525700 chr7B 82.203 118 18 2 729 846 707817969 707818083 1.120000e-16 99.0
75 TraesCS2A01G525700 chr6D 84.783 92 11 1 350 441 327722341 327722429 6.730000e-14 89.8
76 TraesCS2A01G525700 chr6D 88.889 72 8 0 370 441 347136599 347136528 6.730000e-14 89.8
77 TraesCS2A01G525700 chrUn 87.500 80 3 4 2370 2449 302653404 302653332 8.700000e-13 86.1
78 TraesCS2A01G525700 chrUn 87.500 80 3 4 2370 2449 304066605 304066533 8.700000e-13 86.1
79 TraesCS2A01G525700 chrUn 87.500 80 3 4 2370 2449 304071009 304070937 8.700000e-13 86.1


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 TraesCS2A01G525700 chr2A 745810680 745815560 4880 True 9014.000000 9014 100.000000 1 4881 1 chr2A.!!$R2 4880
1 TraesCS2A01G525700 chr2A 745733036 745735180 2144 True 1110.333333 1829 94.473667 1 2449 3 chr2A.!!$R3 2448
2 TraesCS2A01G525700 chr2A 745695024 745695789 765 True 784.000000 784 85.659000 4128 4881 1 chr2A.!!$R1 753
3 TraesCS2A01G525700 chr2A 745811034 745815194 4160 True 262.066667 363 86.047000 330 4527 3 chr2A.!!$R4 4197
4 TraesCS2A01G525700 chr2B 751003059 751003859 800 True 968.000000 968 88.420000 367 1190 1 chr2B.!!$R5 823
5 TraesCS2A01G525700 chr2B 750354673 750355435 762 True 802.000000 802 86.136000 4128 4881 1 chr2B.!!$R3 753
6 TraesCS2A01G525700 chr2B 750442134 750443254 1120 True 745.000000 965 90.591500 1 1195 2 chr2B.!!$R10 1194
7 TraesCS2A01G525700 chr2B 750434674 750435528 854 True 417.000000 676 88.501500 1352 2449 2 chr2B.!!$R9 1097
8 TraesCS2A01G525700 chr2B 750332598 750336460 3862 True 250.271429 427 86.234857 1821 4312 7 chr2B.!!$R8 2491
9 TraesCS2A01G525700 chr2D 616428434 616429266 832 True 771.000000 771 83.584000 452 1305 1 chr2D.!!$R3 853
10 TraesCS2A01G525700 chr2D 616218599 616219403 804 True 342.500000 385 87.810500 4265 4881 2 chr2D.!!$R4 616
11 TraesCS2A01G525700 chr2D 616370484 616371368 884 True 307.666667 669 84.930667 1821 4222 3 chr2D.!!$R6 2401

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
388 389 2.093711 TGTAGCATTGTACACTGCCGAT 60.094 45.455 28.49 16.42 37.67 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4557 7300 1.067283 CACGGATCAGCTGACTTGTCT 60.067 52.381 20.97 0.66 0.0 3.41 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 2.206223 GAGGAATTGGGGTTACCTCCT 58.794 52.381 8.63 8.63 42.51 3.69
57 58 4.919754 CGTTTCGGTTGCCCTATATACTAC 59.080 45.833 0.00 0.00 0.00 2.73
287 288 6.137559 CCCCCTTCTTAGTACTCATTCTAGT 58.862 44.000 0.00 0.00 0.00 2.57
363 364 4.517285 ACACTGCCGATATGTGAGAATTT 58.483 39.130 0.00 0.00 35.83 1.82
364 365 4.333649 ACACTGCCGATATGTGAGAATTTG 59.666 41.667 0.00 0.00 35.83 2.32
365 366 4.571984 CACTGCCGATATGTGAGAATTTGA 59.428 41.667 0.00 0.00 33.95 2.69
374 375 8.501580 CGATATGTGAGAATTTGATTGTAGCAT 58.498 33.333 0.00 0.00 0.00 3.79
388 389 2.093711 TGTAGCATTGTACACTGCCGAT 60.094 45.455 28.49 16.42 37.67 4.18
393 394 3.303329 GCATTGTACACTGCCGATATGTG 60.303 47.826 23.64 0.00 37.67 3.21
395 396 3.878160 TGTACACTGCCGATATGTGAA 57.122 42.857 0.00 0.00 35.83 3.18
4568 7311 6.582672 GCCTAATTAAAACAAGACAAGTCAGC 59.417 38.462 2.72 0.00 0.00 4.26
4577 7320 1.067283 AGACAAGTCAGCTGATCCGTG 60.067 52.381 21.47 17.83 0.00 4.94
4584 7327 1.895798 TCAGCTGATCCGTGAAGTTCT 59.104 47.619 13.74 0.00 0.00 3.01
4596 7339 4.334481 CCGTGAAGTTCTGTTGGTTTAGTT 59.666 41.667 4.17 0.00 0.00 2.24
4598 7341 5.499047 GTGAAGTTCTGTTGGTTTAGTTCG 58.501 41.667 4.17 0.00 0.00 3.95
4638 7385 4.691860 TTTTTCGTTTGGTTGGTCGTAA 57.308 36.364 0.00 0.00 0.00 3.18
4647 7394 1.165270 GTTGGTCGTAATTGCTGCCT 58.835 50.000 0.00 0.00 0.00 4.75
4698 7445 1.809547 GCAGTGAAAGGGCTCTTCTTC 59.190 52.381 0.00 0.00 31.82 2.87
4714 7461 6.293462 GCTCTTCTTCGTTTTGTACATTTCCT 60.293 38.462 0.00 0.00 0.00 3.36
4728 7475 3.181443 ACATTTCCTGTTTTCTCCTCGGT 60.181 43.478 0.00 0.00 32.90 4.69
4749 7496 4.281264 GTTCTATCGCTACTCTTCGTTCC 58.719 47.826 0.00 0.00 0.00 3.62
4752 7499 3.870633 ATCGCTACTCTTCGTTCCTTT 57.129 42.857 0.00 0.00 0.00 3.11
4761 7508 5.539979 ACTCTTCGTTCCTTTAGTTCTTCC 58.460 41.667 0.00 0.00 0.00 3.46
4858 7607 0.599991 CCCTTTGCTTTTTCACCGGC 60.600 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.109106 AGGTGAAGGGTAGTATATAGGGCA 59.891 45.833 0.00 0.00 0.00 5.36
57 58 2.067932 TTGGGCAGTGAGGTGAAGGG 62.068 60.000 0.00 0.00 0.00 3.95
136 137 2.442188 GCGTCGTTTACCTGCTCGG 61.442 63.158 0.00 0.00 39.35 4.63
287 288 6.442564 ACCCTACCACATACTCACAAATCTAA 59.557 38.462 0.00 0.00 0.00 2.10
374 375 3.878160 TCACATATCGGCAGTGTACAA 57.122 42.857 0.00 0.00 34.94 2.41
388 389 6.065976 ACCAGGACATCAGATTTTCACATA 57.934 37.500 0.00 0.00 0.00 2.29
393 394 4.775236 AGCTACCAGGACATCAGATTTTC 58.225 43.478 0.00 0.00 0.00 2.29
395 396 4.965532 ACTAGCTACCAGGACATCAGATTT 59.034 41.667 0.00 0.00 0.00 2.17
4557 7300 1.067283 CACGGATCAGCTGACTTGTCT 60.067 52.381 20.97 0.66 0.00 3.41
4565 7308 1.998315 CAGAACTTCACGGATCAGCTG 59.002 52.381 7.63 7.63 0.00 4.24
4568 7311 2.738846 CCAACAGAACTTCACGGATCAG 59.261 50.000 0.00 0.00 0.00 2.90
4577 7320 5.064325 ACACGAACTAAACCAACAGAACTTC 59.936 40.000 0.00 0.00 0.00 3.01
4584 7327 3.864243 AGACACACGAACTAAACCAACA 58.136 40.909 0.00 0.00 0.00 3.33
4596 7339 5.493133 AAACAAAAATGCTAGACACACGA 57.507 34.783 0.00 0.00 0.00 4.35
4638 7385 2.318908 TGAGGTGAAAAAGGCAGCAAT 58.681 42.857 0.00 0.00 36.28 3.56
4647 7394 5.798125 TTGTGGCATATTGAGGTGAAAAA 57.202 34.783 0.00 0.00 0.00 1.94
4684 7431 3.288092 ACAAAACGAAGAAGAGCCCTTT 58.712 40.909 0.00 0.00 31.62 3.11
4685 7432 2.932261 ACAAAACGAAGAAGAGCCCTT 58.068 42.857 0.00 0.00 34.81 3.95
4698 7445 6.416750 GGAGAAAACAGGAAATGTACAAAACG 59.583 38.462 0.00 0.00 43.00 3.60
4714 7461 3.675228 GCGATAGAACCGAGGAGAAAACA 60.675 47.826 0.00 0.00 39.76 2.83
4728 7475 4.197750 AGGAACGAAGAGTAGCGATAGAA 58.802 43.478 0.00 0.00 39.76 2.10
4781 7528 8.895932 TCAGAGAAAACGAAAAAGAGAAAAAG 57.104 30.769 0.00 0.00 0.00 2.27
4782 7529 9.855021 AATCAGAGAAAACGAAAAAGAGAAAAA 57.145 25.926 0.00 0.00 0.00 1.94
4790 7537 7.862372 CCATGAAGAATCAGAGAAAACGAAAAA 59.138 33.333 0.00 0.00 39.39 1.94


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

AutoCloner maintained by Alex Coulton.