Multiple sequence alignment - TraesCS3B01G605400

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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 TraesCS3B01G605400 chr3B 100.000 2614 0 0 1 2614 823896000 823893387 0.000000e+00 4828
1 TraesCS3B01G605400 chr3B 91.534 189 15 1 1 188 794135625 794135813 2.580000e-65 259
2 TraesCS3B01G605400 chr5D 94.875 2634 83 17 1 2594 437728577 437725956 0.000000e+00 4069
3 TraesCS3B01G605400 chr6A 93.626 2667 100 31 2 2614 577151881 577154531 0.000000e+00 3919
4 TraesCS3B01G605400 chr6A 93.342 2358 81 28 309 2614 553572477 553570144 0.000000e+00 3415
5 TraesCS3B01G605400 chr1A 94.735 2507 94 14 1 2484 16224743 16227234 0.000000e+00 3864
6 TraesCS3B01G605400 chr2B 94.148 2529 84 27 122 2614 563765618 563768118 0.000000e+00 3792
7 TraesCS3B01G605400 chr2B 97.486 1909 47 1 703 2611 32110220 32112127 0.000000e+00 3258
8 TraesCS3B01G605400 chr2B 96.826 1607 47 2 1012 2614 559330219 559328613 0.000000e+00 2682
9 TraesCS3B01G605400 chr2B 96.017 1607 36 8 1012 2614 152882419 152880837 0.000000e+00 2588
10 TraesCS3B01G605400 chr2B 90.476 189 17 1 1 188 34398345 34398533 5.590000e-62 248
11 TraesCS3B01G605400 chr6B 94.029 2529 88 26 122 2614 21617341 21614840 0.000000e+00 3775
12 TraesCS3B01G605400 chr4B 93.911 2529 90 26 122 2614 11627176 11624676 0.000000e+00 3759
13 TraesCS3B01G605400 chr5A 93.983 2360 88 26 305 2611 687969715 687972073 0.000000e+00 3522
14 TraesCS3B01G605400 chr5B 96.281 2124 61 2 491 2614 609507159 609509264 0.000000e+00 3469
15 TraesCS3B01G605400 chr5B 95.105 1859 57 17 123 1956 690081677 690079828 0.000000e+00 2898
16 TraesCS3B01G605400 chr5B 91.996 1112 42 19 1515 2614 188590201 188589125 0.000000e+00 1517
17 TraesCS3B01G605400 chr5B 92.593 189 13 1 1 188 34584600 34584412 1.190000e-68 270
18 TraesCS3B01G605400 chr5B 79.426 418 56 20 2219 2614 421515974 421515565 4.290000e-68 268
19 TraesCS3B01G605400 chr5B 92.063 189 14 1 1 188 547150318 547150130 5.550000e-67 265
20 TraesCS3B01G605400 chr5B 79.048 420 55 23 2219 2614 416463554 416463144 9.280000e-65 257
21 TraesCS3B01G605400 chr5B 91.005 189 15 2 1 188 31737412 31737225 1.200000e-63 254
22 TraesCS3B01G605400 chr5B 94.737 152 8 0 1 152 690081829 690081678 1.210000e-58 237
23 TraesCS3B01G605400 chr5B 94.040 151 9 0 1 151 621788469 621788319 2.020000e-56 230
24 TraesCS3B01G605400 chr5B 93.377 151 10 0 1 151 36453247 36453097 9.410000e-55 224
25 TraesCS3B01G605400 chr2A 93.263 1900 75 24 767 2614 5148332 5150230 0.000000e+00 2750
26 TraesCS3B01G605400 chr2D 93.526 1699 67 21 1 1670 104541989 104540305 0.000000e+00 2488
27 TraesCS3B01G605400 chr7A 91.871 1267 50 24 1400 2614 626871850 626873115 0.000000e+00 1720
28 TraesCS3B01G605400 chr4A 91.817 1112 43 19 1515 2614 741932111 741931036 0.000000e+00 1506
29 TraesCS3B01G605400 chr7B 91.637 1112 46 18 1515 2614 673023370 673024446 0.000000e+00 1495
30 TraesCS3B01G605400 chr7B 92.593 189 13 1 1 188 57241482 57241294 1.190000e-68 270
31 TraesCS3B01G605400 chr7B 91.534 189 15 1 1 188 18363634 18363446 2.580000e-65 259


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 TraesCS3B01G605400 chr3B 823893387 823896000 2613 True 4828.0 4828 100.000 1 2614 1 chr3B.!!$R1 2613
1 TraesCS3B01G605400 chr5D 437725956 437728577 2621 True 4069.0 4069 94.875 1 2594 1 chr5D.!!$R1 2593
2 TraesCS3B01G605400 chr6A 577151881 577154531 2650 False 3919.0 3919 93.626 2 2614 1 chr6A.!!$F1 2612
3 TraesCS3B01G605400 chr6A 553570144 553572477 2333 True 3415.0 3415 93.342 309 2614 1 chr6A.!!$R1 2305
4 TraesCS3B01G605400 chr1A 16224743 16227234 2491 False 3864.0 3864 94.735 1 2484 1 chr1A.!!$F1 2483
5 TraesCS3B01G605400 chr2B 563765618 563768118 2500 False 3792.0 3792 94.148 122 2614 1 chr2B.!!$F3 2492
6 TraesCS3B01G605400 chr2B 32110220 32112127 1907 False 3258.0 3258 97.486 703 2611 1 chr2B.!!$F1 1908
7 TraesCS3B01G605400 chr2B 559328613 559330219 1606 True 2682.0 2682 96.826 1012 2614 1 chr2B.!!$R2 1602
8 TraesCS3B01G605400 chr2B 152880837 152882419 1582 True 2588.0 2588 96.017 1012 2614 1 chr2B.!!$R1 1602
9 TraesCS3B01G605400 chr6B 21614840 21617341 2501 True 3775.0 3775 94.029 122 2614 1 chr6B.!!$R1 2492
10 TraesCS3B01G605400 chr4B 11624676 11627176 2500 True 3759.0 3759 93.911 122 2614 1 chr4B.!!$R1 2492
11 TraesCS3B01G605400 chr5A 687969715 687972073 2358 False 3522.0 3522 93.983 305 2611 1 chr5A.!!$F1 2306
12 TraesCS3B01G605400 chr5B 609507159 609509264 2105 False 3469.0 3469 96.281 491 2614 1 chr5B.!!$F1 2123
13 TraesCS3B01G605400 chr5B 690079828 690081829 2001 True 1567.5 2898 94.921 1 1956 2 chr5B.!!$R9 1955
14 TraesCS3B01G605400 chr5B 188589125 188590201 1076 True 1517.0 1517 91.996 1515 2614 1 chr5B.!!$R4 1099
15 TraesCS3B01G605400 chr2A 5148332 5150230 1898 False 2750.0 2750 93.263 767 2614 1 chr2A.!!$F1 1847
16 TraesCS3B01G605400 chr2D 104540305 104541989 1684 True 2488.0 2488 93.526 1 1670 1 chr2D.!!$R1 1669
17 TraesCS3B01G605400 chr7A 626871850 626873115 1265 False 1720.0 1720 91.871 1400 2614 1 chr7A.!!$F1 1214
18 TraesCS3B01G605400 chr4A 741931036 741932111 1075 True 1506.0 1506 91.817 1515 2614 1 chr4A.!!$R1 1099
19 TraesCS3B01G605400 chr7B 673023370 673024446 1076 False 1495.0 1495 91.637 1515 2614 1 chr7B.!!$F1 1099

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
82 83 1.073025 CCTTAGTGTGGTGCAGCCA 59.927 57.895 14.36 8.7 46.95 4.75 F
1153 1241 0.102300 TGTATGTCCATCCGTCTGCG 59.898 55.000 0.00 0.0 37.95 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 1254 1.492176 AGTAGGACATCAATGGGGCAG 59.508 52.381 0.0 0.0 0.0 4.85 R
2279 2458 3.002348 GCTCTATCCGTGGCATTACAAAC 59.998 47.826 0.0 0.0 0.0 2.93 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
49 50 1.217511 CTGCACATGGTCGAGCTCT 59.782 57.895 16.64 0.00 0.00 4.09
82 83 1.073025 CCTTAGTGTGGTGCAGCCA 59.927 57.895 14.36 8.70 46.95 4.75
104 105 1.496444 TTGGGCCACTCCAGTGCATA 61.496 55.000 5.23 0.00 44.34 3.14
221 252 6.684686 GCATGTTTGCTAATCATCCATATGT 58.315 36.000 1.24 0.00 45.77 2.29
855 940 2.675348 GCTCTGCTCATGTTGTTAGACC 59.325 50.000 0.00 0.00 0.00 3.85
900 985 5.068636 CCAGCCTTCTATCATGCTTACAAT 58.931 41.667 0.00 0.00 30.08 2.71
1113 1198 1.081376 CGACTTCAAGGACGCTCGT 60.081 57.895 0.00 0.00 0.00 4.18
1153 1241 0.102300 TGTATGTCCATCCGTCTGCG 59.898 55.000 0.00 0.00 37.95 5.18
1166 1254 3.967080 CGTCTGCGGTTAACTAAGTTC 57.033 47.619 5.42 0.09 0.00 3.01
1328 1416 6.874134 ACTTGGTACTGCATGAGTTTTACTAG 59.126 38.462 0.00 0.00 35.96 2.57
1525 1658 9.120538 GTCACTTGATATATGGGTTAATGTTGT 57.879 33.333 0.00 0.00 0.00 3.32
1628 1764 3.614092 CATCTAAAGCACACCATGGACT 58.386 45.455 21.47 7.14 0.00 3.85
1886 2024 7.335171 GCCATGCATATTCATATTGTGTCTCTA 59.665 37.037 0.00 0.00 0.00 2.43
1959 2100 5.584649 GCATGGTACTAGCTGAATTTGTGTA 59.415 40.000 0.00 0.00 0.00 2.90
2101 2263 1.489481 TGGTCTCAGCCCTGACTATG 58.511 55.000 0.00 0.00 35.46 2.23
2279 2458 9.210329 TGTAAAGTATTGTATTATACATGGCCG 57.790 33.333 5.85 0.00 38.68 6.13
2289 2468 3.708563 ATACATGGCCGTTTGTAATGC 57.291 42.857 14.65 0.00 32.46 3.56
2373 2584 5.804639 TGTGTCTGCCAATCTAAATACTGT 58.195 37.500 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.202419 ACACTAAGGCACTGTTGTTCCATA 60.202 41.667 0.00 0.00 40.86 2.74
82 83 1.151450 CACTGGAGTGGCCCAACTT 59.849 57.895 0.00 0.00 42.10 2.66
104 105 0.250901 AACGGCATGCAGAGTTCCTT 60.251 50.000 24.99 4.04 0.00 3.36
218 249 7.903481 AGGTAGGGATCATATAACATGAGACAT 59.097 37.037 0.00 0.00 0.00 3.06
221 252 8.624670 ACTAGGTAGGGATCATATAACATGAGA 58.375 37.037 0.00 0.00 0.00 3.27
411 476 2.217750 TCAACTCCATTGGTTGTCACG 58.782 47.619 1.86 0.00 42.97 4.35
721 806 7.143340 TGATGCTAGCAATCTCAATTTTATGC 58.857 34.615 23.54 0.00 0.00 3.14
722 807 9.692749 AATGATGCTAGCAATCTCAATTTTATG 57.307 29.630 23.54 0.00 0.00 1.90
729 814 6.598850 TGTGTAAATGATGCTAGCAATCTCAA 59.401 34.615 23.54 3.58 0.00 3.02
855 940 1.533625 TGGCAGGAAGTGAAAATCCG 58.466 50.000 0.00 0.00 40.78 4.18
900 985 4.614993 GCTACTGCCGTGCAAAGAAAAATA 60.615 41.667 0.00 0.00 38.41 1.40
1153 1241 3.428413 TGGGGCAGAACTTAGTTAACC 57.572 47.619 0.88 0.00 0.00 2.85
1166 1254 1.492176 AGTAGGACATCAATGGGGCAG 59.508 52.381 0.00 0.00 0.00 4.85
1328 1416 8.460428 AGTAGTAAATACTCTCTGTGTTAGCAC 58.540 37.037 2.25 2.25 40.99 4.40
1525 1658 6.214191 TGCATCCAAGTAGAACAAAACAAA 57.786 33.333 0.00 0.00 0.00 2.83
1527 1660 6.215121 CAATGCATCCAAGTAGAACAAAACA 58.785 36.000 0.00 0.00 0.00 2.83
1628 1764 3.686405 GCATTGATGAGGAAGTGGATGGA 60.686 47.826 0.00 0.00 0.00 3.41
1904 2042 7.602644 TGTTGTCGAGCTAGTTAAAATCAGATT 59.397 33.333 0.00 0.00 0.00 2.40
1909 2047 8.776680 TTTTTGTTGTCGAGCTAGTTAAAATC 57.223 30.769 0.00 0.00 0.00 2.17
1959 2100 9.205513 AGAAAAGGGCATGTATTTAGAATGATT 57.794 29.630 0.00 0.00 0.00 2.57
1977 2118 4.584325 TGAACAGACCATTCAAGAAAAGGG 59.416 41.667 8.78 4.13 33.16 3.95
2279 2458 3.002348 GCTCTATCCGTGGCATTACAAAC 59.998 47.826 0.00 0.00 0.00 2.93
2289 2468 6.455647 TCACATAATAAAGCTCTATCCGTGG 58.544 40.000 0.00 0.00 0.00 4.94
2353 2564 7.377766 TCAAACAGTATTTAGATTGGCAGAC 57.622 36.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.