Multiple sequence alignment - TraesCS7A01G433700

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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 TraesCS7A01G433700 chr7A 100.000 3125 0 0 1 3125 627050306 627047182 0.000000e+00 5771.0
1 TraesCS7A01G433700 chr7A 99.423 2598 14 1 529 3125 627012010 627009413 0.000000e+00 4713.0
2 TraesCS7A01G433700 chr7A 96.346 520 18 1 1 519 627012628 627012109 0.000000e+00 854.0
3 TraesCS7A01G433700 chr7D 87.148 1455 71 33 1007 2371 545270527 545269099 0.000000e+00 1544.0
4 TraesCS7A01G433700 chr7D 94.024 753 41 3 2373 3125 545269003 545268255 0.000000e+00 1138.0
5 TraesCS7A01G433700 chr7D 100.000 30 0 0 984 1013 545270562 545270533 4.350000e-04 56.5
6 TraesCS7A01G433700 chr1B 90.069 1158 58 16 1994 3125 426500059 426498933 0.000000e+00 1448.0
7 TraesCS7A01G433700 chr1B 92.011 701 46 8 2426 3125 133114024 133113333 0.000000e+00 976.0
8 TraesCS7A01G433700 chr1B 89.789 617 39 4 908 1504 426502678 426502066 0.000000e+00 769.0
9 TraesCS7A01G433700 chr1B 88.782 312 27 6 211 517 542689725 542689417 2.940000e-100 375.0
10 TraesCS7A01G433700 chr1B 94.714 227 12 0 1696 1922 426501874 426501648 1.380000e-93 353.0
11 TraesCS7A01G433700 chr1B 79.580 524 43 28 1924 2392 133114679 133114165 1.810000e-82 316.0
12 TraesCS7A01G433700 chr1B 84.337 83 3 5 1544 1626 426501990 426501918 4.320000e-09 73.1
13 TraesCS7A01G433700 chr1B 93.182 44 3 0 1793 1836 133114831 133114788 7.230000e-07 65.8
14 TraesCS7A01G433700 chr5D 88.557 1206 57 27 780 1922 289425417 289424230 0.000000e+00 1387.0
15 TraesCS7A01G433700 chr5D 94.583 720 31 5 2410 3125 289423524 289422809 0.000000e+00 1107.0
16 TraesCS7A01G433700 chr5D 90.313 702 60 8 2426 3125 289743645 289742950 0.000000e+00 913.0
17 TraesCS7A01G433700 chr5D 88.576 604 41 10 925 1504 289798956 289798357 0.000000e+00 708.0
18 TraesCS7A01G433700 chr5D 91.014 434 36 2 1007 1440 289501125 289500695 1.620000e-162 582.0
19 TraesCS7A01G433700 chr5D 89.238 223 20 3 2081 2303 289744118 289743900 3.070000e-70 276.0
20 TraesCS7A01G433700 chr5D 85.909 220 29 2 2878 3096 289498795 289498577 1.870000e-57 233.0
21 TraesCS7A01G433700 chr5D 92.958 142 9 1 1696 1836 289744550 289744409 4.090000e-49 206.0
22 TraesCS7A01G433700 chr5D 88.272 162 7 4 1924 2082 289744300 289744148 1.910000e-42 183.0
23 TraesCS7A01G433700 chr5D 93.617 47 2 1 718 764 541992592 541992637 5.590000e-08 69.4
24 TraesCS7A01G433700 chr5D 100.000 30 0 0 984 1013 289501160 289501131 4.350000e-04 56.5
25 TraesCS7A01G433700 chr2B 91.225 661 48 9 2417 3075 182141179 182140527 0.000000e+00 891.0
26 TraesCS7A01G433700 chr2B 89.954 438 44 0 1007 1444 182147777 182147340 1.630000e-157 566.0
27 TraesCS7A01G433700 chr2B 82.637 311 34 10 2081 2373 182141564 182141256 1.110000e-64 257.0
28 TraesCS7A01G433700 chr2B 79.832 357 46 17 1734 2082 182141932 182141594 1.450000e-58 237.0
29 TraesCS7A01G433700 chr2B 77.901 181 29 7 1 175 707249432 707249607 5.510000e-18 102.0
30 TraesCS7A01G433700 chr2B 85.484 62 2 1 1544 1605 182142036 182141982 1.210000e-04 58.4
31 TraesCS7A01G433700 chrUn 87.500 664 57 9 908 1547 383291300 383291961 0.000000e+00 743.0
32 TraesCS7A01G433700 chrUn 97.143 70 2 0 1716 1785 383292142 383292211 5.470000e-23 119.0
33 TraesCS7A01G433700 chrUn 87.097 62 0 4 1544 1605 383291976 383292029 2.600000e-06 63.9
34 TraesCS7A01G433700 chrUn 100.000 32 0 0 1665 1696 383292045 383292076 3.370000e-05 60.2
35 TraesCS7A01G433700 chr7B 88.925 614 36 8 908 1504 588502441 588501843 0.000000e+00 728.0
36 TraesCS7A01G433700 chr7B 90.421 428 38 2 1013 1440 588882869 588882445 7.570000e-156 560.0
37 TraesCS7A01G433700 chr7B 77.273 660 131 15 2479 3125 588880995 588880342 1.370000e-98 370.0
38 TraesCS7A01G433700 chr7B 95.217 230 9 2 1696 1924 588501651 588501423 2.290000e-96 363.0
39 TraesCS7A01G433700 chr7B 89.051 274 19 5 1952 2225 588501272 588501010 2.320000e-86 329.0
40 TraesCS7A01G433700 chr7B 78.453 181 28 7 1 175 41322581 41322406 1.190000e-19 108.0
41 TraesCS7A01G433700 chr7B 92.308 52 2 2 713 764 731107226 731107275 4.320000e-09 73.1
42 TraesCS7A01G433700 chr7B 82.278 79 4 5 1548 1626 588501763 588501695 3.370000e-05 60.2
43 TraesCS7A01G433700 chr6B 90.751 519 44 4 2 517 476120569 476121086 0.000000e+00 689.0
44 TraesCS7A01G433700 chr1D 90.578 329 25 6 203 527 76085836 76086162 6.190000e-117 431.0
45 TraesCS7A01G433700 chr1D 88.644 317 30 5 206 517 448612568 448612253 6.320000e-102 381.0
46 TraesCS7A01G433700 chr1D 92.437 119 8 1 400 517 447505410 447505528 5.360000e-38 169.0
47 TraesCS7A01G433700 chr3B 90.000 320 28 4 203 519 548041486 548041804 8.070000e-111 411.0
48 TraesCS7A01G433700 chr5B 89.937 318 25 6 203 517 476915731 476916044 1.350000e-108 403.0
49 TraesCS7A01G433700 chr5B 79.670 182 25 8 1 175 512933431 512933255 1.520000e-23 121.0
50 TraesCS7A01G433700 chr5B 81.250 128 14 4 1 118 671904585 671904712 9.230000e-16 95.3
51 TraesCS7A01G433700 chr3D 78.453 181 30 8 1 175 425976529 425976352 3.300000e-20 110.0
52 TraesCS7A01G433700 chr2D 79.412 136 19 5 1 127 365582483 365582348 1.540000e-13 87.9
53 TraesCS7A01G433700 chr2A 97.368 38 0 1 725 762 19902063 19902099 2.600000e-06 63.9


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 TraesCS7A01G433700 chr7A 627047182 627050306 3124 True 5771.000000 5771 100.000000 1 3125 1 chr7A.!!$R1 3124
1 TraesCS7A01G433700 chr7A 627009413 627012628 3215 True 2783.500000 4713 97.884500 1 3125 2 chr7A.!!$R2 3124
2 TraesCS7A01G433700 chr7D 545268255 545270562 2307 True 912.833333 1544 93.724000 984 3125 3 chr7D.!!$R1 2141
3 TraesCS7A01G433700 chr1B 426498933 426502678 3745 True 660.775000 1448 89.727250 908 3125 4 chr1B.!!$R3 2217
4 TraesCS7A01G433700 chr1B 133113333 133114831 1498 True 452.600000 976 88.257667 1793 3125 3 chr1B.!!$R2 1332
5 TraesCS7A01G433700 chr5D 289422809 289425417 2608 True 1247.000000 1387 91.570000 780 3125 2 chr5D.!!$R2 2345
6 TraesCS7A01G433700 chr5D 289798357 289798956 599 True 708.000000 708 88.576000 925 1504 1 chr5D.!!$R1 579
7 TraesCS7A01G433700 chr5D 289742950 289744550 1600 True 394.500000 913 90.195250 1696 3125 4 chr5D.!!$R4 1429
8 TraesCS7A01G433700 chr5D 289498577 289501160 2583 True 290.500000 582 92.307667 984 3096 3 chr5D.!!$R3 2112
9 TraesCS7A01G433700 chr2B 182140527 182142036 1509 True 360.850000 891 84.794500 1544 3075 4 chr2B.!!$R2 1531
10 TraesCS7A01G433700 chrUn 383291300 383292211 911 False 246.525000 743 92.935000 908 1785 4 chrUn.!!$F1 877
11 TraesCS7A01G433700 chr7B 588880342 588882869 2527 True 465.000000 560 83.847000 1013 3125 2 chr7B.!!$R3 2112
12 TraesCS7A01G433700 chr7B 588501010 588502441 1431 True 370.050000 728 88.867750 908 2225 4 chr7B.!!$R2 1317
13 TraesCS7A01G433700 chr6B 476120569 476121086 517 False 689.000000 689 90.751000 2 517 1 chr6B.!!$F1 515

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
576 668 1.136828 AGCCTGTCCCACAGTTTACA 58.863 50.0 3.07 0.0 44.5 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3044 6143 3.998341 CCAAGGAACCATTTTGCATGAAG 59.002 43.478 0.0 0.0 0.0 3.02 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
148 149 2.100991 GCCATCGGAAAAGCTGCG 59.899 61.111 0.00 0.0 40.85 5.18
200 201 3.117452 GCCAGAGCCTAGCCAGCAT 62.117 63.158 0.00 0.0 0.00 3.79
282 283 4.641645 TGCCCAAGACGCCACCAG 62.642 66.667 0.00 0.0 0.00 4.00
361 363 1.589727 GCAACAGGCACACAACAGC 60.590 57.895 0.00 0.0 43.97 4.40
395 397 4.767255 GGAGCGAGGCCACACCAG 62.767 72.222 5.01 0.0 43.14 4.00
433 435 4.779733 GGGGAGGTCGGAGCCAGA 62.780 72.222 3.13 0.0 0.00 3.86
570 662 4.729918 GGGCAGCCTGTCCCACAG 62.730 72.222 12.43 0.0 45.53 3.66
576 668 1.136828 AGCCTGTCCCACAGTTTACA 58.863 50.000 3.07 0.0 44.50 2.41
3044 6143 7.496263 GGGAAAGAAAGGATTCTAGTGTATGAC 59.504 40.741 0.00 0.0 45.19 3.06
3079 6178 6.734502 TGGTTCCTTGGATCGTTACATATA 57.265 37.500 0.00 0.0 0.00 0.86
3117 6216 7.496591 CCCTAATGTAAGTTATTTCCAAGCGTA 59.503 37.037 0.00 0.0 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 2.202932 AGCTAAGGTGGATGCGCG 60.203 61.111 0.0 0.0 0.00 6.86
261 262 2.594303 TGGCGTCTTGGGCAACTG 60.594 61.111 0.0 0.0 39.78 3.16
262 263 2.594592 GTGGCGTCTTGGGCAACT 60.595 61.111 0.0 0.0 44.64 3.16
347 349 2.941333 CTCGCTGTTGTGTGCCTG 59.059 61.111 0.0 0.0 0.00 4.85
348 350 2.974698 GCTCGCTGTTGTGTGCCT 60.975 61.111 0.0 0.0 37.26 4.75
433 435 2.031163 GTGGTGCGGCTCTTGTCT 59.969 61.111 0.0 0.0 0.00 3.41
694 786 6.269307 ACTGCTTTAGTACTCCCTCTGTAAAA 59.731 38.462 0.0 0.0 38.04 1.52
3044 6143 3.998341 CCAAGGAACCATTTTGCATGAAG 59.002 43.478 0.0 0.0 0.00 3.02
3096 6195 6.412214 AGGTACGCTTGGAAATAACTTACAT 58.588 36.000 0.0 0.0 0.00 2.29


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

AutoCloner maintained by Alex Coulton.