Multiple sequence alignment - TraesCS3D01G478400

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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 TraesCS3D01G478400 chr3D 100.000 2447 0 0 1 2447 578040096 578042542 0.000000e+00 4519
1 TraesCS3D01G478400 chr3D 86.091 2430 246 47 59 2446 577780535 577778156 0.000000e+00 2531
2 TraesCS3D01G478400 chr3D 93.053 1094 58 8 717 1798 577668970 577667883 0.000000e+00 1583
3 TraesCS3D01G478400 chr3D 84.294 1649 175 37 717 2328 577753004 577751403 0.000000e+00 1533
4 TraesCS3D01G478400 chr3D 90.799 663 46 4 1799 2447 577667850 577667189 0.000000e+00 872
5 TraesCS3D01G478400 chr3D 87.222 180 18 5 553 730 87925999 87926175 1.480000e-47 200
6 TraesCS3D01G478400 chr3D 88.000 125 8 2 430 553 577753125 577753007 9.120000e-30 141
7 TraesCS3D01G478400 chr3D 93.421 76 5 0 430 505 577669216 577669141 1.990000e-21 113
8 TraesCS3D01G478400 chr3B 91.548 2449 156 21 31 2447 770965659 770963230 0.000000e+00 3328
9 TraesCS3D01G478400 chr3B 89.056 1800 139 15 31 1798 771241059 771242832 0.000000e+00 2180
10 TraesCS3D01G478400 chr3B 86.503 1630 130 24 31 1626 771177526 771179099 0.000000e+00 1709
11 TraesCS3D01G478400 chr3B 90.950 663 45 9 1799 2447 771242865 771243526 0.000000e+00 878
12 TraesCS3D01G478400 chr3B 88.989 663 46 14 1799 2447 771179396 771180045 0.000000e+00 795
13 TraesCS3D01G478400 chr3B 91.111 180 10 4 1624 1798 771179185 771179363 3.140000e-59 239
14 TraesCS3D01G478400 chr3A 89.039 1113 83 18 715 1795 713308510 713307405 0.000000e+00 1343
15 TraesCS3D01G478400 chr3A 88.864 907 84 10 907 1798 713342776 713341872 0.000000e+00 1099
16 TraesCS3D01G478400 chr3A 91.114 664 45 4 662 1311 713418434 713417771 0.000000e+00 887
17 TraesCS3D01G478400 chr3A 85.714 665 72 17 1799 2447 713307371 713306714 0.000000e+00 680
18 TraesCS3D01G478400 chr3A 83.409 663 87 14 1799 2447 713341838 713341185 5.830000e-166 593
19 TraesCS3D01G478400 chr3A 86.985 461 51 4 1341 1793 713417774 713417315 6.040000e-141 510
20 TraesCS3D01G478400 chr3A 89.266 354 27 3 317 667 713419200 713418855 1.340000e-117 433
21 TraesCS3D01G478400 chr3A 87.619 105 9 2 714 817 713343477 713343376 4.270000e-23 119
22 TraesCS3D01G478400 chr3A 88.172 93 11 0 343 435 552059852 552059760 7.150000e-21 111
23 TraesCS3D01G478400 chr7D 80.286 350 57 7 1847 2188 120304046 120304391 1.120000e-63 254
24 TraesCS3D01G478400 chr2A 78.947 304 58 4 1847 2145 2741859 2742161 4.130000e-48 202
25 TraesCS3D01G478400 chr2A 93.694 111 5 2 192 301 34657965 34658074 5.410000e-37 165
26 TraesCS3D01G478400 chr4D 88.485 165 17 2 554 717 334164391 334164554 5.340000e-47 198
27 TraesCS3D01G478400 chr4D 84.293 191 26 4 527 715 355565100 355565288 1.490000e-42 183
28 TraesCS3D01G478400 chr7A 88.415 164 17 2 553 715 691723809 691723647 1.920000e-46 196
29 TraesCS3D01G478400 chr7A 91.589 107 9 0 191 297 565767107 565767001 5.450000e-32 148
30 TraesCS3D01G478400 chr6B 88.095 168 16 4 553 718 314546986 314547151 1.920000e-46 196
31 TraesCS3D01G478400 chr1B 75.931 403 84 8 1847 2239 18435069 18435468 6.900000e-46 195
32 TraesCS3D01G478400 chr6D 93.694 111 5 2 191 301 377566396 377566288 5.410000e-37 165
33 TraesCS3D01G478400 chr4B 94.175 103 6 0 192 294 36809746 36809848 9.060000e-35 158
34 TraesCS3D01G478400 chr4B 87.368 95 12 0 340 434 581528364 581528458 2.570000e-20 110
35 TraesCS3D01G478400 chr2D 93.204 103 7 0 192 294 284574912 284574810 4.210000e-33 152
36 TraesCS3D01G478400 chr5B 82.394 142 20 4 296 435 100663161 100663299 4.270000e-23 119


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 TraesCS3D01G478400 chr3D 578040096 578042542 2446 False 4519.000000 4519 100.000000 1 2447 1 chr3D.!!$F2 2446
1 TraesCS3D01G478400 chr3D 577778156 577780535 2379 True 2531.000000 2531 86.091000 59 2446 1 chr3D.!!$R1 2387
2 TraesCS3D01G478400 chr3D 577667189 577669216 2027 True 856.000000 1583 92.424333 430 2447 3 chr3D.!!$R2 2017
3 TraesCS3D01G478400 chr3D 577751403 577753125 1722 True 837.000000 1533 86.147000 430 2328 2 chr3D.!!$R3 1898
4 TraesCS3D01G478400 chr3B 770963230 770965659 2429 True 3328.000000 3328 91.548000 31 2447 1 chr3B.!!$R1 2416
5 TraesCS3D01G478400 chr3B 771241059 771243526 2467 False 1529.000000 2180 90.003000 31 2447 2 chr3B.!!$F2 2416
6 TraesCS3D01G478400 chr3B 771177526 771180045 2519 False 914.333333 1709 88.867667 31 2447 3 chr3B.!!$F1 2416
7 TraesCS3D01G478400 chr3A 713306714 713308510 1796 True 1011.500000 1343 87.376500 715 2447 2 chr3A.!!$R2 1732
8 TraesCS3D01G478400 chr3A 713417315 713419200 1885 True 610.000000 887 89.121667 317 1793 3 chr3A.!!$R4 1476
9 TraesCS3D01G478400 chr3A 713341185 713343477 2292 True 603.666667 1099 86.630667 714 2447 3 chr3A.!!$R3 1733

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
27 28 0.034089 GGAAGGGGATGTTCTGGTGG 60.034 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 3244 0.937304 CTGTTCTGGTGTGTTGGTCG 59.063 55.0 0.0 0.0 0.0 4.79 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
21 22 4.225497 CGCTGGAAGGGGATGTTC 57.775 61.111 0.00 0.00 44.19 3.18
22 23 1.604378 CGCTGGAAGGGGATGTTCT 59.396 57.895 0.00 0.00 44.19 3.01
23 24 0.745845 CGCTGGAAGGGGATGTTCTG 60.746 60.000 0.00 0.00 44.19 3.02
24 25 0.394899 GCTGGAAGGGGATGTTCTGG 60.395 60.000 0.00 0.00 0.00 3.86
25 26 0.995024 CTGGAAGGGGATGTTCTGGT 59.005 55.000 0.00 0.00 0.00 4.00
26 27 0.698238 TGGAAGGGGATGTTCTGGTG 59.302 55.000 0.00 0.00 0.00 4.17
27 28 0.034089 GGAAGGGGATGTTCTGGTGG 60.034 60.000 0.00 0.00 0.00 4.61
28 29 0.681243 GAAGGGGATGTTCTGGTGGC 60.681 60.000 0.00 0.00 0.00 5.01
29 30 2.438434 GGGGATGTTCTGGTGGCG 60.438 66.667 0.00 0.00 0.00 5.69
36 37 2.281484 TTCTGGTGGCGGCTTGAC 60.281 61.111 11.43 0.00 0.00 3.18
42 43 3.621805 TGGCGGCTTGACGGAAGA 61.622 61.111 11.43 0.00 32.82 2.87
51 52 2.667137 CTTGACGGAAGAGTGTGAGTC 58.333 52.381 0.00 0.00 32.82 3.36
77 78 6.939132 AGCATCTTGAATGATAGTTTCCTG 57.061 37.500 0.00 0.00 0.00 3.86
99 100 1.625315 GGGCTTTGAATGGGCTTCTTT 59.375 47.619 0.00 0.00 34.75 2.52
120 121 2.656055 GCCAAATCTTGCGCCCAA 59.344 55.556 4.18 0.00 0.00 4.12
213 216 1.458445 CGATCTATGCTGCATCAACGG 59.542 52.381 19.90 3.56 0.00 4.44
259 262 4.995124 CTTCATGAGAAGGCAGGAAAATG 58.005 43.478 0.00 0.00 46.01 2.32
261 264 4.863548 TCATGAGAAGGCAGGAAAATGAT 58.136 39.130 0.00 0.00 0.00 2.45
315 318 3.244561 ACTTGACCAACACTTGATCGGAT 60.245 43.478 0.00 0.00 0.00 4.18
333 338 2.029828 GGATGGCTGTAGACTACCGATG 60.030 54.545 10.14 0.00 0.00 3.84
352 357 1.737236 TGTATGTTGCATCAACGGCTC 59.263 47.619 0.75 0.00 46.13 4.70
362 367 1.872388 TCAACGGCTCGAACAATTCA 58.128 45.000 1.50 0.00 0.00 2.57
364 369 1.798223 CAACGGCTCGAACAATTCAGA 59.202 47.619 1.50 0.00 0.00 3.27
376 381 3.937814 ACAATTCAGATGACGTGGCTTA 58.062 40.909 0.00 0.00 0.00 3.09
405 410 9.429359 GAGAAGACAGAAAAATCATCTAGTGAA 57.571 33.333 0.00 0.00 40.97 3.18
464 469 5.185442 TGCATGATTCAAAAGGTATTGCAGA 59.815 36.000 0.00 0.00 0.00 4.26
484 498 8.408043 TGCAGACCAAGATAAATAATAATGGG 57.592 34.615 0.00 0.00 30.82 4.00
506 520 2.617532 CCTCAGGGCCTTTGAGAAGAAG 60.618 54.545 28.36 14.28 43.75 2.85
516 530 5.563671 GCCTTTGAGAAGAAGTTGGTGAATC 60.564 44.000 0.00 0.00 34.71 2.52
711 1280 3.306613 ACTTATCTTTAGGACGGAGGGG 58.693 50.000 0.00 0.00 0.00 4.79
719 1288 0.638292 AGGACGGAGGGGGTACATAA 59.362 55.000 0.00 0.00 0.00 1.90
967 2105 7.916977 GCATTCACACAAATATATCTGCAAAGA 59.083 33.333 0.00 0.00 0.00 2.52
1531 2674 6.515272 TGGCATTTCCTTCTTTCTTCATAC 57.485 37.500 0.00 0.00 35.26 2.39
1683 2931 7.156000 TGTGAGATTTCAATTAACGAGGTGTA 58.844 34.615 0.00 0.00 34.49 2.90
1697 2945 3.442625 CGAGGTGTAGGACAGTGAATGTA 59.557 47.826 0.00 0.00 44.17 2.29
1710 2958 8.768955 GGACAGTGAATGTATTTATCTGATCAC 58.231 37.037 0.00 0.00 44.17 3.06
1952 3244 2.361230 GGTGCTAAGGCCCCACAC 60.361 66.667 0.00 2.81 36.00 3.82
2039 3331 3.996363 TGAAGACACACGAATGAAGATGG 59.004 43.478 0.00 0.00 0.00 3.51
2131 3423 3.041940 CACCACGTGCCCTTCGAC 61.042 66.667 10.91 0.00 0.00 4.20
2202 3496 4.283337 TCCATCTTTAGGTGATACCGTCA 58.717 43.478 0.00 0.00 44.90 4.35
2249 3555 7.982354 CACAAACTCACAAAACCCCTAAAAATA 59.018 33.333 0.00 0.00 0.00 1.40
2270 3577 1.153086 GCAAGATCCCTCATGCCGT 60.153 57.895 0.00 0.00 39.59 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153289 CATCCCCTTCCAGCGACTG 60.153 63.158 0.00 0.00 0.00 3.51
1 2 1.201429 AACATCCCCTTCCAGCGACT 61.201 55.000 0.00 0.00 0.00 4.18
2 3 0.744771 GAACATCCCCTTCCAGCGAC 60.745 60.000 0.00 0.00 0.00 5.19
4 5 0.745845 CAGAACATCCCCTTCCAGCG 60.746 60.000 0.00 0.00 0.00 5.18
5 6 0.394899 CCAGAACATCCCCTTCCAGC 60.395 60.000 0.00 0.00 0.00 4.85
7 8 0.698238 CACCAGAACATCCCCTTCCA 59.302 55.000 0.00 0.00 0.00 3.53
8 9 0.034089 CCACCAGAACATCCCCTTCC 60.034 60.000 0.00 0.00 0.00 3.46
9 10 0.681243 GCCACCAGAACATCCCCTTC 60.681 60.000 0.00 0.00 0.00 3.46
10 11 1.384191 GCCACCAGAACATCCCCTT 59.616 57.895 0.00 0.00 0.00 3.95
11 12 2.971598 CGCCACCAGAACATCCCCT 61.972 63.158 0.00 0.00 0.00 4.79
12 13 2.438434 CGCCACCAGAACATCCCC 60.438 66.667 0.00 0.00 0.00 4.81
13 14 2.438434 CCGCCACCAGAACATCCC 60.438 66.667 0.00 0.00 0.00 3.85
14 15 3.134127 GCCGCCACCAGAACATCC 61.134 66.667 0.00 0.00 0.00 3.51
15 16 1.675641 AAGCCGCCACCAGAACATC 60.676 57.895 0.00 0.00 0.00 3.06
16 17 1.973281 CAAGCCGCCACCAGAACAT 60.973 57.895 0.00 0.00 0.00 2.71
17 18 2.594303 CAAGCCGCCACCAGAACA 60.594 61.111 0.00 0.00 0.00 3.18
18 19 2.281484 TCAAGCCGCCACCAGAAC 60.281 61.111 0.00 0.00 0.00 3.01
19 20 2.281484 GTCAAGCCGCCACCAGAA 60.281 61.111 0.00 0.00 0.00 3.02
20 21 4.680237 CGTCAAGCCGCCACCAGA 62.680 66.667 0.00 0.00 0.00 3.86
24 25 3.423154 CTTCCGTCAAGCCGCCAC 61.423 66.667 0.00 0.00 0.00 5.01
25 26 3.589654 CTCTTCCGTCAAGCCGCCA 62.590 63.158 0.00 0.00 31.26 5.69
26 27 2.815647 CTCTTCCGTCAAGCCGCC 60.816 66.667 0.00 0.00 31.26 6.13
27 28 2.048127 ACTCTTCCGTCAAGCCGC 60.048 61.111 0.00 0.00 31.26 6.53
28 29 1.006102 ACACTCTTCCGTCAAGCCG 60.006 57.895 0.00 0.00 31.26 5.52
29 30 0.033504 TCACACTCTTCCGTCAAGCC 59.966 55.000 0.00 0.00 31.26 4.35
36 37 1.466024 GCTACGACTCACACTCTTCCG 60.466 57.143 0.00 0.00 0.00 4.30
40 41 2.717390 AGATGCTACGACTCACACTCT 58.283 47.619 0.00 0.00 0.00 3.24
42 43 2.820197 TCAAGATGCTACGACTCACACT 59.180 45.455 0.00 0.00 0.00 3.55
51 52 6.703607 AGGAAACTATCATTCAAGATGCTACG 59.296 38.462 0.00 0.00 40.61 3.51
77 78 0.247460 GAAGCCCATTCAAAGCCCAC 59.753 55.000 0.00 0.00 37.88 4.61
99 100 2.650196 GCGCAAGATTTGGCCACA 59.350 55.556 3.88 0.00 43.02 4.17
213 216 0.521735 GTCACCCGAATTGTTCCAGC 59.478 55.000 0.00 0.00 0.00 4.85
259 262 2.383442 TAGAGGCACCCCACTAGATC 57.617 55.000 0.00 0.00 33.78 2.75
261 264 2.868964 AATAGAGGCACCCCACTAGA 57.131 50.000 0.00 0.00 37.65 2.43
315 318 2.139323 ACATCGGTAGTCTACAGCCA 57.861 50.000 12.08 0.00 0.00 4.75
333 338 1.267532 CGAGCCGTTGATGCAACATAC 60.268 52.381 10.48 0.00 43.70 2.39
352 357 2.474526 GCCACGTCATCTGAATTGTTCG 60.475 50.000 0.00 0.00 0.00 3.95
362 367 4.160439 TCTTCTCATTAAGCCACGTCATCT 59.840 41.667 0.00 0.00 0.00 2.90
364 369 4.184629 GTCTTCTCATTAAGCCACGTCAT 58.815 43.478 0.00 0.00 0.00 3.06
376 381 9.956640 ACTAGATGATTTTTCTGTCTTCTCATT 57.043 29.630 0.00 0.00 32.90 2.57
464 469 7.534852 TGAGGCCCATTATTATTTATCTTGGT 58.465 34.615 0.00 0.00 0.00 3.67
610 752 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
657 799 7.886970 AGAGATGGCAATATAAACTACATGCAT 59.113 33.333 0.00 0.00 35.57 3.96
689 1257 3.710165 CCCCTCCGTCCTAAAGATAAGTT 59.290 47.826 0.00 0.00 0.00 2.66
696 1264 1.117994 GTACCCCCTCCGTCCTAAAG 58.882 60.000 0.00 0.00 0.00 1.85
719 1288 9.590451 CTTTACATTCATTGAGGTGCAATTAAT 57.410 29.630 0.00 0.00 44.68 1.40
856 1981 7.870954 TGTGTATTCAGTACTCACCAAAGTTAG 59.129 37.037 8.66 0.00 33.23 2.34
1479 2621 1.965754 ATCGAAGAGGCAGACTGGGC 61.966 60.000 4.26 0.00 43.63 5.36
1510 2653 6.422776 TCGTATGAAGAAAGAAGGAAATGC 57.577 37.500 0.00 0.00 0.00 3.56
1531 2674 1.459756 GCAACGTGCATCATCAATCG 58.540 50.000 0.00 0.00 44.26 3.34
1611 2763 7.930865 GGCACTTCTTTATATCATTCAGTCTCT 59.069 37.037 0.00 0.00 0.00 3.10
1683 2931 8.708378 TGATCAGATAAATACATTCACTGTCCT 58.292 33.333 0.00 0.00 39.39 3.85
1710 2958 3.317149 CCACAATACCATCATGCCTTCTG 59.683 47.826 0.00 0.00 0.00 3.02
1824 3109 7.503549 TGCTGACATGACATGATTACTAGATT 58.496 34.615 22.19 0.00 0.00 2.40
1952 3244 0.937304 CTGTTCTGGTGTGTTGGTCG 59.063 55.000 0.00 0.00 0.00 4.79
2039 3331 1.065926 TGCATGGATCCAGTCTGTGTC 60.066 52.381 21.33 9.59 0.00 3.67
2202 3496 1.895798 TCTTGCTCAGGAAGACGATGT 59.104 47.619 4.15 0.00 0.00 3.06
2270 3577 3.948719 GTGGACCGTGGCCCTTGA 61.949 66.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.