Multiple sequence alignment - TraesCS4D01G040600

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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 TraesCS4D01G040600 chr4D 100.000 1998 0 0 1 1998 19172147 19170150 0 3690
1 TraesCS4D01G040600 chr4D 96.650 2000 59 7 1 1998 274172101 274174094 0 3315
2 TraesCS4D01G040600 chr4D 100.000 1341 0 0 2431 3771 19169717 19168377 0 2477
3 TraesCS4D01G040600 chr4D 97.545 1344 30 3 2431 3771 65872386 65871043 0 2296
4 TraesCS4D01G040600 chr5D 97.250 2000 48 6 1 1998 424139085 424141079 0 3382
5 TraesCS4D01G040600 chr5D 95.852 2001 76 7 1 1998 65966979 65968975 0 3229
6 TraesCS4D01G040600 chr5D 97.912 1341 25 3 2431 3771 65968961 65970298 0 2318
7 TraesCS4D01G040600 chr5D 97.392 1342 33 2 2431 3771 526637299 526638639 0 2283
8 TraesCS4D01G040600 chr7D 96.950 2000 56 5 1 1998 135381477 135383473 0 3350
9 TraesCS4D01G040600 chr7D 96.304 2002 66 8 1 1998 30314897 30316894 0 3280
10 TraesCS4D01G040600 chr7D 97.915 1343 23 4 2431 3771 54976831 54978170 0 2320
11 TraesCS4D01G040600 chr7D 97.766 1343 21 6 2432 3771 135383460 135384796 0 2305
12 TraesCS4D01G040600 chr2D 96.800 2000 58 6 1 1998 594642783 594640788 0 3334
13 TraesCS4D01G040600 chr2D 96.702 2001 61 5 1 1998 536210614 536212612 0 3325
14 TraesCS4D01G040600 chr2D 97.465 1341 30 4 2431 3771 594640802 594639466 0 2285
15 TraesCS4D01G040600 chr5A 96.495 1997 66 3 4 1998 49889995 49888001 0 3297
16 TraesCS4D01G040600 chr1D 96.252 2001 70 5 1 1998 108796437 108794439 0 3275
17 TraesCS4D01G040600 chr1D 97.915 1343 23 4 2432 3771 58472947 58471607 0 2320
18 TraesCS4D01G040600 chr1D 97.466 1342 30 4 2431 3771 466342123 466340785 0 2287
19 TraesCS4D01G040600 chr3D 98.285 1341 22 1 2432 3771 500621538 500620198 0 2348


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 TraesCS4D01G040600 chr4D 19168377 19172147 3770 True 3083.5 3690 100.0000 1 3771 2 chr4D.!!$R2 3770
1 TraesCS4D01G040600 chr4D 274172101 274174094 1993 False 3315.0 3315 96.6500 1 1998 1 chr4D.!!$F1 1997
2 TraesCS4D01G040600 chr4D 65871043 65872386 1343 True 2296.0 2296 97.5450 2431 3771 1 chr4D.!!$R1 1340
3 TraesCS4D01G040600 chr5D 424139085 424141079 1994 False 3382.0 3382 97.2500 1 1998 1 chr5D.!!$F1 1997
4 TraesCS4D01G040600 chr5D 65966979 65970298 3319 False 2773.5 3229 96.8820 1 3771 2 chr5D.!!$F3 3770
5 TraesCS4D01G040600 chr5D 526637299 526638639 1340 False 2283.0 2283 97.3920 2431 3771 1 chr5D.!!$F2 1340
6 TraesCS4D01G040600 chr7D 30314897 30316894 1997 False 3280.0 3280 96.3040 1 1998 1 chr7D.!!$F1 1997
7 TraesCS4D01G040600 chr7D 135381477 135384796 3319 False 2827.5 3350 97.3580 1 3771 2 chr7D.!!$F3 3770
8 TraesCS4D01G040600 chr7D 54976831 54978170 1339 False 2320.0 2320 97.9150 2431 3771 1 chr7D.!!$F2 1340
9 TraesCS4D01G040600 chr2D 536210614 536212612 1998 False 3325.0 3325 96.7020 1 1998 1 chr2D.!!$F1 1997
10 TraesCS4D01G040600 chr2D 594639466 594642783 3317 True 2809.5 3334 97.1325 1 3771 2 chr2D.!!$R1 3770
11 TraesCS4D01G040600 chr5A 49888001 49889995 1994 True 3297.0 3297 96.4950 4 1998 1 chr5A.!!$R1 1994
12 TraesCS4D01G040600 chr1D 108794439 108796437 1998 True 3275.0 3275 96.2520 1 1998 1 chr1D.!!$R2 1997
13 TraesCS4D01G040600 chr1D 58471607 58472947 1340 True 2320.0 2320 97.9150 2432 3771 1 chr1D.!!$R1 1339
14 TraesCS4D01G040600 chr1D 466340785 466342123 1338 True 2287.0 2287 97.4660 2431 3771 1 chr1D.!!$R3 1340
15 TraesCS4D01G040600 chr3D 500620198 500621538 1340 True 2348.0 2348 98.2850 2432 3771 1 chr3D.!!$R1 1339

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
375 380 0.704076 TTGGGTGGATGGCTTAGCTT 59.296 50.000 3.59 0.0 0.00 3.74 F
1595 1605 1.428219 CAGCACGTACCGAGATCGT 59.572 57.895 1.09 0.0 38.34 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 1707 1.058428 TGGATGATGAGCCCCCTGAG 61.058 60.0 0.0 0.0 0.00 3.35 R
2983 3312 0.396974 ACCACACAGCCCATGTTGTT 60.397 50.0 0.0 0.0 41.41 2.83 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
209 212 3.367910 GCCATTCGGACCAAAGCAATAAA 60.368 43.478 0.00 0.00 0.00 1.40
279 282 3.004629 TGATTGAGACAATTGCGCACTTT 59.995 39.130 11.12 3.81 0.00 2.66
375 380 0.704076 TTGGGTGGATGGCTTAGCTT 59.296 50.000 3.59 0.00 0.00 3.74
607 612 3.551890 CCTAACAACTTCATCACCGATCG 59.448 47.826 8.51 8.51 0.00 3.69
835 840 3.024547 AGTACGAGGCTATGACACACAT 58.975 45.455 0.00 0.00 42.39 3.21
921 926 4.016479 TCTTCCCCTTCCTACAGTCTACAT 60.016 45.833 0.00 0.00 0.00 2.29
1003 1008 4.093408 GCTGAACTTCGTCAAGCAATATGA 59.907 41.667 0.00 0.00 32.09 2.15
1199 1207 3.193267 GCATTCCAAGTTGGTGCTGATAA 59.807 43.478 23.61 10.43 36.80 1.75
1500 1510 5.247110 GCAGATAAGGGAGAGGAACATGATA 59.753 44.000 0.00 0.00 0.00 2.15
1501 1511 6.070309 GCAGATAAGGGAGAGGAACATGATAT 60.070 42.308 0.00 0.00 0.00 1.63
1595 1605 1.428219 CAGCACGTACCGAGATCGT 59.572 57.895 1.09 0.00 38.34 3.73
1622 1632 5.714806 ACCTGAACAAGTCCAAGAAAAAGAA 59.285 36.000 0.00 0.00 0.00 2.52
1623 1633 6.127619 ACCTGAACAAGTCCAAGAAAAAGAAG 60.128 38.462 0.00 0.00 0.00 2.85
1696 1707 3.618780 CTCCACCTCCAGGCAGCAC 62.619 68.421 0.00 0.00 39.32 4.40
1847 1858 1.010574 GTTGCGCACGCTGTGTTAA 60.011 52.632 11.12 0.00 42.51 2.01
1851 1862 1.120147 GCGCACGCTGTGTTAATTCG 61.120 55.000 7.96 5.55 35.75 3.34
1983 1995 3.636231 CCCGTGTGCTCCTCCCAA 61.636 66.667 0.00 0.00 0.00 4.12
1984 1996 2.671070 CCGTGTGCTCCTCCCAAT 59.329 61.111 0.00 0.00 0.00 3.16
1985 1997 1.746615 CCGTGTGCTCCTCCCAATG 60.747 63.158 0.00 0.00 0.00 2.82
1986 1998 1.003355 CGTGTGCTCCTCCCAATGT 60.003 57.895 0.00 0.00 0.00 2.71
1987 1999 1.021390 CGTGTGCTCCTCCCAATGTC 61.021 60.000 0.00 0.00 0.00 3.06
1988 2000 0.678048 GTGTGCTCCTCCCAATGTCC 60.678 60.000 0.00 0.00 0.00 4.02
1989 2001 1.077429 GTGCTCCTCCCAATGTCCC 60.077 63.158 0.00 0.00 0.00 4.46
1990 2002 1.229951 TGCTCCTCCCAATGTCCCT 60.230 57.895 0.00 0.00 0.00 4.20
1991 2003 0.044092 TGCTCCTCCCAATGTCCCTA 59.956 55.000 0.00 0.00 0.00 3.53
1992 2004 0.470341 GCTCCTCCCAATGTCCCTAC 59.530 60.000 0.00 0.00 0.00 3.18
1993 2005 1.879575 CTCCTCCCAATGTCCCTACA 58.120 55.000 0.00 0.00 40.69 2.74
1994 2006 1.765314 CTCCTCCCAATGTCCCTACAG 59.235 57.143 0.00 0.00 39.49 2.74
1995 2007 0.839946 CCTCCCAATGTCCCTACAGG 59.160 60.000 0.00 0.00 39.49 4.00
1996 2008 0.181350 CTCCCAATGTCCCTACAGGC 59.819 60.000 0.00 0.00 39.49 4.85
1997 2009 0.548926 TCCCAATGTCCCTACAGGCA 60.549 55.000 0.00 0.00 39.49 4.75
2661 2985 0.252927 CTCAAAGACCTCCTCCCCCT 60.253 60.000 0.00 0.00 0.00 4.79
2697 3021 3.775654 GCCCTGCGTGCTACTCCT 61.776 66.667 0.00 0.00 0.00 3.69
2841 3166 2.508439 GCCTAGTTGCGTGCGCTA 60.508 61.111 17.49 7.39 42.51 4.26
3281 3611 0.465705 CTGGTGTGTGTCCACTCAGT 59.534 55.000 2.65 0.00 42.34 3.41
3586 3918 3.976942 GTGTGCAACTACAAAATCTGCTG 59.023 43.478 0.00 0.00 38.04 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 212 6.987992 TCTACGGAAACTTGTACACAGATTTT 59.012 34.615 0.00 0.00 0.00 1.82
279 282 7.929785 GTCTGGATCGGTTTTTGTATATCCTTA 59.070 37.037 0.00 0.00 35.08 2.69
375 380 1.094785 GCCTCCGCATAAGCTTTTCA 58.905 50.000 3.20 0.00 39.10 2.69
607 612 1.380246 TGCCTCATTGCACCATCCC 60.380 57.895 0.00 0.00 36.04 3.85
761 766 6.458232 AACTCGTCTATAGTGAAGCTGAAT 57.542 37.500 0.00 0.00 0.00 2.57
835 840 3.787785 TCGTACAACTTCTCAAAGTGCA 58.212 40.909 0.00 0.00 45.07 4.57
921 926 1.547372 GTTGAACCCCTCACTACGCTA 59.453 52.381 0.00 0.00 32.21 4.26
1199 1207 3.126001 TGTTCGGTCTGAGCTCAAATT 57.874 42.857 18.85 0.00 0.00 1.82
1362 1370 2.943033 CCTTTCCGGTATGACATCAACC 59.057 50.000 0.00 0.00 0.00 3.77
1443 1451 1.681780 GGAGGCATTTCATCCGGTTGA 60.682 52.381 11.25 11.25 35.76 3.18
1500 1510 6.370718 ACTTTGCTAGTTTCCGAAAATCGTAT 59.629 34.615 0.00 0.00 33.50 3.06
1501 1511 5.697633 ACTTTGCTAGTTTCCGAAAATCGTA 59.302 36.000 0.00 0.00 33.50 3.43
1595 1605 2.123589 TCTTGGACTTGTTCAGGTGGA 58.876 47.619 0.00 0.00 0.00 4.02
1696 1707 1.058428 TGGATGATGAGCCCCCTGAG 61.058 60.000 0.00 0.00 0.00 3.35
1782 1793 1.881324 CACCATGATGTGTGCAACTGA 59.119 47.619 0.00 0.00 38.04 3.41
1847 1858 5.877012 AGTTGTGTTATCTTGATGCTCGAAT 59.123 36.000 0.00 0.00 0.00 3.34
1851 1862 7.602517 AGTTAGTTGTGTTATCTTGATGCTC 57.397 36.000 0.00 0.00 0.00 4.26
2661 2985 1.195115 CACTGCTAGTTGGGCTAGGA 58.805 55.000 3.82 0.15 45.61 2.94
2697 3021 2.116238 GTCCTGCCTGTAGGTCCATTA 58.884 52.381 1.08 0.00 38.99 1.90
2841 3166 8.635765 TTTTAGCTTGATCCTCAAACTAACAT 57.364 30.769 10.64 0.00 41.76 2.71
2983 3312 0.396974 ACCACACAGCCCATGTTGTT 60.397 50.000 0.00 0.00 41.41 2.83
3281 3611 6.025749 ACGATGAAACAGAATCACAGTAGA 57.974 37.500 0.00 0.00 0.00 2.59
3586 3918 4.094739 AGTTGCTGGTTTGCACAATTTTTC 59.905 37.500 0.00 0.00 43.20 2.29
3708 4041 3.752222 CAGGAAGAAGCTGGCATATGATC 59.248 47.826 6.97 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.