Multiple sequence alignment - TraesCS3D01G377500

Loading Multiple Alignment...

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 TraesCS3D01G377500 chr3D 100.000 2348 0 0 1 2348 495165253 495167600 0.000000e+00 4337.0
1 TraesCS3D01G377500 chr3A 95.678 2059 77 10 1 2055 634573172 634575222 0.000000e+00 3299.0
2 TraesCS3D01G377500 chr3A 95.254 295 14 0 2054 2348 634578396 634578690 3.530000e-128 468.0
3 TraesCS3D01G377500 chr3A 91.781 292 22 2 2056 2346 523610017 523610307 2.810000e-109 405.0
4 TraesCS3D01G377500 chr3A 92.857 42 3 0 2016 2057 724913708 724913667 7.010000e-06 62.1
5 TraesCS3D01G377500 chr3B 91.870 2177 166 10 175 2348 653991293 653993461 0.000000e+00 3029.0
6 TraesCS3D01G377500 chr3B 91.126 293 26 0 2056 2348 548053398 548053690 4.700000e-107 398.0
7 TraesCS3D01G377500 chr5D 84.076 628 77 9 892 1497 556523153 556522527 3.360000e-163 584.0
8 TraesCS3D01G377500 chr5D 91.186 295 23 2 2056 2348 385950373 385950080 4.700000e-107 398.0
9 TraesCS3D01G377500 chr7B 79.073 712 133 14 769 1472 534823751 534824454 2.110000e-130 475.0
10 TraesCS3D01G377500 chr7B 79.284 531 93 15 38 560 643123297 643123818 2.870000e-94 355.0
11 TraesCS3D01G377500 chr7D 78.702 709 134 13 769 1472 506658934 506659630 7.650000e-125 457.0
12 TraesCS3D01G377500 chr7D 92.568 296 21 1 2051 2345 506498639 506498934 7.760000e-115 424.0
13 TraesCS3D01G377500 chr7D 82.625 259 39 5 945 1202 506667431 506667684 8.440000e-55 224.0
14 TraesCS3D01G377500 chr7A 78.200 711 138 14 769 1472 574090433 574091133 2.770000e-119 438.0
15 TraesCS3D01G377500 chr7A 80.565 566 96 12 6 564 662428170 662427612 7.760000e-115 424.0
16 TraesCS3D01G377500 chr5A 91.468 293 25 0 2056 2348 632834135 632833843 1.010000e-108 403.0
17 TraesCS3D01G377500 chr5A 78.750 560 96 20 7 555 695821616 695821069 1.030000e-93 353.0
18 TraesCS3D01G377500 chr6B 91.409 291 24 1 2056 2346 152400460 152400749 4.700000e-107 398.0
19 TraesCS3D01G377500 chr6B 91.111 45 4 0 2013 2057 454079134 454079178 7.010000e-06 62.1
20 TraesCS3D01G377500 chr1D 91.156 294 23 3 2056 2348 37440914 37440623 1.690000e-106 396.0
21 TraesCS3D01G377500 chr2B 79.652 575 93 19 5 563 777687275 777687841 2.190000e-105 392.0
22 TraesCS3D01G377500 chr1A 79.335 571 97 20 2 563 354188866 354188308 4.740000e-102 381.0
23 TraesCS3D01G377500 chr1A 77.313 454 72 22 120 563 271967977 271967545 3.020000e-59 239.0
24 TraesCS3D01G377500 chr1A 82.258 124 22 0 1599 1722 339003045 339002922 8.870000e-20 108.0
25 TraesCS3D01G377500 chr4B 80.000 480 87 9 90 564 55777184 55777659 1.730000e-91 346.0
26 TraesCS3D01G377500 chr4D 77.250 589 91 34 1 573 503446975 503447536 2.930000e-79 305.0
27 TraesCS3D01G377500 chr4D 91.489 47 4 0 2011 2057 493019778 493019732 5.420000e-07 65.8
28 TraesCS3D01G377500 chr2A 93.182 44 3 0 2014 2057 659099345 659099388 5.420000e-07 65.8
29 TraesCS3D01G377500 chr2A 92.857 42 3 0 2020 2061 293968005 293968046 7.010000e-06 62.1
30 TraesCS3D01G377500 chr4A 89.796 49 5 0 2009 2057 661489968 661490016 1.950000e-06 63.9
31 TraesCS3D01G377500 chr1B 92.857 42 3 0 2016 2057 136065563 136065604 7.010000e-06 62.1


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 TraesCS3D01G377500 chr3D 495165253 495167600 2347 False 4337.0 4337 100.000 1 2348 1 chr3D.!!$F1 2347
1 TraesCS3D01G377500 chr3A 634573172 634578690 5518 False 1883.5 3299 95.466 1 2348 2 chr3A.!!$F2 2347
2 TraesCS3D01G377500 chr3B 653991293 653993461 2168 False 3029.0 3029 91.870 175 2348 1 chr3B.!!$F2 2173
3 TraesCS3D01G377500 chr5D 556522527 556523153 626 True 584.0 584 84.076 892 1497 1 chr5D.!!$R2 605
4 TraesCS3D01G377500 chr7B 534823751 534824454 703 False 475.0 475 79.073 769 1472 1 chr7B.!!$F1 703
5 TraesCS3D01G377500 chr7B 643123297 643123818 521 False 355.0 355 79.284 38 560 1 chr7B.!!$F2 522
6 TraesCS3D01G377500 chr7D 506658934 506659630 696 False 457.0 457 78.702 769 1472 1 chr7D.!!$F2 703
7 TraesCS3D01G377500 chr7A 574090433 574091133 700 False 438.0 438 78.200 769 1472 1 chr7A.!!$F1 703
8 TraesCS3D01G377500 chr7A 662427612 662428170 558 True 424.0 424 80.565 6 564 1 chr7A.!!$R1 558
9 TraesCS3D01G377500 chr5A 695821069 695821616 547 True 353.0 353 78.750 7 555 1 chr5A.!!$R2 548
10 TraesCS3D01G377500 chr2B 777687275 777687841 566 False 392.0 392 79.652 5 563 1 chr2B.!!$F1 558
11 TraesCS3D01G377500 chr1A 354188308 354188866 558 True 381.0 381 79.335 2 563 1 chr1A.!!$R3 561
12 TraesCS3D01G377500 chr4D 503446975 503447536 561 False 305.0 305 77.250 1 573 1 chr4D.!!$F1 572

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
920 948 2.408271 TCATCTTTAGCCAGCACCAG 57.592 50.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1802 2.609459 CGTTTGCTCTTGTCTGAGTGTT 59.391 45.455 0.0 0.0 36.51 3.32 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
58 59 6.497259 TCTCACTACTCAGTTTTCCCACTAAT 59.503 38.462 0.00 0.00 30.46 1.73
61 62 8.475639 TCACTACTCAGTTTTCCCACTAATATC 58.524 37.037 0.00 0.00 30.46 1.63
186 190 5.394443 CCAAAATACTCATGGACCAACATGG 60.394 44.000 0.00 0.00 46.33 3.66
249 253 3.081061 CTCAAATCCCCAACATCGTTCA 58.919 45.455 0.00 0.00 0.00 3.18
260 264 5.965334 CCCAACATCGTTCATATTTTTCTCG 59.035 40.000 0.00 0.00 0.00 4.04
437 455 7.334421 AGCGAATATTTAATGGAACGATAGCAT 59.666 33.333 0.00 0.00 42.67 3.79
534 558 6.506500 AATGGCAAAACTGAATAGTGAGAG 57.493 37.500 0.00 0.00 37.19 3.20
920 948 2.408271 TCATCTTTAGCCAGCACCAG 57.592 50.000 0.00 0.00 0.00 4.00
1056 1084 0.881159 TTGTTGTCGTGGCTTACCCG 60.881 55.000 0.00 0.00 35.87 5.28
1065 1093 0.466555 TGGCTTACCCGTTTGCAACT 60.467 50.000 0.00 0.00 35.87 3.16
1115 1143 1.296056 GACCCCGACAATGAACCACG 61.296 60.000 0.00 0.00 0.00 4.94
1130 1158 3.362797 ACGCGTCCAAGAGCTCGA 61.363 61.111 5.58 0.00 0.00 4.04
1270 1298 1.310904 GAACAACAACGGCCAACCTA 58.689 50.000 2.24 0.00 0.00 3.08
1560 1611 9.991906 TCCACTTTTCTCCGGTATTATTATAAG 57.008 33.333 0.00 0.00 0.00 1.73
1751 1802 9.984190 ATATGTAATTTCATATGCAATGCAACA 57.016 25.926 13.45 9.08 43.62 3.33
1855 1906 6.733509 AGGACTATCAAGAACTACAGTACCT 58.266 40.000 0.00 0.00 0.00 3.08
2005 2057 6.371825 ACTTATAGGCCTTCTTTTCAAAGACG 59.628 38.462 12.58 0.53 44.18 4.18
2337 5564 5.188359 ACCGTACTCCCTAATTTTGAAGCTA 59.812 40.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 9.337091 GCGAGCATTTTTAAACAGTTAAAGATA 57.663 29.630 0.00 0.00 39.69 1.98
61 62 7.591426 AGAGCGAGCATTTTTAAACAGTTAAAG 59.409 33.333 0.00 0.00 39.69 1.85
70 71 5.619086 GCCTAACAGAGCGAGCATTTTTAAA 60.619 40.000 0.00 0.00 0.00 1.52
186 190 1.613437 GTGAGATAGAGGGAGAGCTGC 59.387 57.143 0.00 0.00 0.00 5.25
233 237 6.607198 AGAAAAATATGAACGATGTTGGGGAT 59.393 34.615 0.00 0.00 0.00 3.85
534 558 8.647226 GTTTTGTCATTTATGCCATTAGTTGTC 58.353 33.333 0.00 0.00 0.00 3.18
576 601 2.412089 GCGCTAAACACTGGAGTAACAG 59.588 50.000 0.00 0.00 44.03 3.16
859 886 0.031994 GGCACGACAATTGCAAGGTT 59.968 50.000 4.94 0.00 42.12 3.50
870 897 2.434336 AGGCATCTAAATAGGCACGACA 59.566 45.455 0.00 0.00 0.00 4.35
920 948 3.265791 AGACCAATCTCGATGCTTGTTC 58.734 45.455 0.00 0.00 0.00 3.18
1056 1084 2.458006 CCTCGGCGGAAGTTGCAAAC 62.458 60.000 7.21 0.00 40.95 2.93
1115 1143 2.876645 CGTCGAGCTCTTGGACGC 60.877 66.667 23.38 3.11 45.55 5.19
1270 1298 4.759782 AGTAAAATCGCTCTGTATGCACT 58.240 39.130 0.00 0.00 0.00 4.40
1560 1611 1.562017 GGCGAGCTTGCTACTTAGAC 58.438 55.000 25.01 2.34 34.52 2.59
1751 1802 2.609459 CGTTTGCTCTTGTCTGAGTGTT 59.391 45.455 0.00 0.00 36.51 3.32
2005 2057 9.974980 TTTTCCTAAAATTACAACACTCCATTC 57.025 29.630 0.00 0.00 0.00 2.67
2139 5366 5.232838 GCTTTGAGAAATTGTTGACTTGGTG 59.767 40.000 0.00 0.00 0.00 4.17
2192 5419 7.970614 GTGAGGACTTAAAAATTAGGAAGCATG 59.029 37.037 0.00 0.00 0.00 4.06
2236 5463 7.981102 AAATCAGGTGACTAAGTTCTAAACC 57.019 36.000 0.00 0.00 40.21 3.27


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

AutoCloner maintained by Alex Coulton.