Multiple sequence alignment - TraesCS5B01G263400

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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 TraesCS5B01G263400 chr5B 100.000 3990 0 0 1 3990 447870821 447874810 0.000000e+00 7369.0
1 TraesCS5B01G263400 chr3B 97.831 4011 62 8 1 3990 685958648 685954642 0.000000e+00 6902.0
2 TraesCS5B01G263400 chr1B 94.351 3151 124 15 875 3990 24033884 24030753 0.000000e+00 4783.0
3 TraesCS5B01G263400 chr1B 96.133 2353 79 7 1647 3990 328518459 328516110 0.000000e+00 3831.0
4 TraesCS5B01G263400 chr1B 94.504 2511 89 14 875 3356 24062677 24060187 0.000000e+00 3827.0
5 TraesCS5B01G263400 chr1B 95.356 1615 63 8 1 1605 328520071 328518459 0.000000e+00 2556.0
6 TraesCS5B01G263400 chr1B 95.122 41 2 0 875 915 51379750 51379790 9.260000e-07 65.8
7 TraesCS5B01G263400 chr4A 94.131 3152 132 16 875 3990 711810300 711813434 0.000000e+00 4747.0
8 TraesCS5B01G263400 chr4A 94.006 3153 135 18 875 3990 711858368 711861503 0.000000e+00 4726.0
9 TraesCS5B01G263400 chr4A 93.125 960 51 8 1 955 711809391 711810340 0.000000e+00 1393.0
10 TraesCS5B01G263400 chr4A 92.917 960 52 9 1 955 711857460 711858408 0.000000e+00 1382.0
11 TraesCS5B01G263400 chr4B 92.944 2962 173 16 1062 3990 524149578 524146620 0.000000e+00 4279.0
12 TraesCS5B01G263400 chr4B 92.867 2846 156 18 1 2803 668303033 668305874 0.000000e+00 4087.0
13 TraesCS5B01G263400 chr4B 91.304 1587 90 15 1 1542 669215961 669214378 0.000000e+00 2122.0
14 TraesCS5B01G263400 chr4B 91.041 1585 96 13 1 1542 669064826 669066407 0.000000e+00 2098.0
15 TraesCS5B01G263400 chr4B 91.842 380 29 2 2971 3350 669430142 669430519 2.730000e-146 529.0
16 TraesCS5B01G263400 chr4B 91.237 388 32 2 2963 3350 668306436 668306821 9.820000e-146 527.0
17 TraesCS5B01G263400 chr4B 91.623 382 30 2 2969 3350 669203862 669203483 9.820000e-146 527.0
18 TraesCS5B01G263400 chr4B 90.263 380 35 2 2971 3350 669392542 669392165 2.770000e-136 496.0
19 TraesCS5B01G263400 chr2B 92.891 2968 169 15 1062 3988 651659903 651656937 0.000000e+00 4274.0
20 TraesCS5B01G263400 chr2B 92.824 641 40 2 3356 3990 359115456 359114816 0.000000e+00 924.0
21 TraesCS5B01G263400 chr2B 93.023 86 6 0 875 960 622496405 622496320 4.190000e-25 126.0
22 TraesCS5B01G263400 chr6B 94.180 2749 109 15 875 3589 187115644 187112913 0.000000e+00 4143.0
23 TraesCS5B01G263400 chr6B 93.685 2518 113 21 875 3350 55638993 55636480 0.000000e+00 3727.0
24 TraesCS5B01G263400 chr6B 93.958 960 50 5 1 955 187116560 187115604 0.000000e+00 1445.0
25 TraesCS5B01G263400 chr6B 93.125 960 59 5 1 955 55639910 55638953 0.000000e+00 1400.0
26 TraesCS5B01G263400 chr6B 92.200 641 44 2 3356 3990 171979121 171979761 0.000000e+00 902.0
27 TraesCS5B01G263400 chrUn 91.230 1585 93 13 1 1542 291296820 291295239 0.000000e+00 2115.0


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 TraesCS5B01G263400 chr5B 447870821 447874810 3989 False 7369.0 7369 100.0000 1 3990 1 chr5B.!!$F1 3989
1 TraesCS5B01G263400 chr3B 685954642 685958648 4006 True 6902.0 6902 97.8310 1 3990 1 chr3B.!!$R1 3989
2 TraesCS5B01G263400 chr1B 24030753 24033884 3131 True 4783.0 4783 94.3510 875 3990 1 chr1B.!!$R1 3115
3 TraesCS5B01G263400 chr1B 24060187 24062677 2490 True 3827.0 3827 94.5040 875 3356 1 chr1B.!!$R2 2481
4 TraesCS5B01G263400 chr1B 328516110 328520071 3961 True 3193.5 3831 95.7445 1 3990 2 chr1B.!!$R3 3989
5 TraesCS5B01G263400 chr4A 711809391 711813434 4043 False 3070.0 4747 93.6280 1 3990 2 chr4A.!!$F1 3989
6 TraesCS5B01G263400 chr4A 711857460 711861503 4043 False 3054.0 4726 93.4615 1 3990 2 chr4A.!!$F2 3989
7 TraesCS5B01G263400 chr4B 524146620 524149578 2958 True 4279.0 4279 92.9440 1062 3990 1 chr4B.!!$R1 2928
8 TraesCS5B01G263400 chr4B 668303033 668306821 3788 False 2307.0 4087 92.0520 1 3350 2 chr4B.!!$F3 3349
9 TraesCS5B01G263400 chr4B 669214378 669215961 1583 True 2122.0 2122 91.3040 1 1542 1 chr4B.!!$R3 1541
10 TraesCS5B01G263400 chr4B 669064826 669066407 1581 False 2098.0 2098 91.0410 1 1542 1 chr4B.!!$F1 1541
11 TraesCS5B01G263400 chr2B 651656937 651659903 2966 True 4274.0 4274 92.8910 1062 3988 1 chr2B.!!$R3 2926
12 TraesCS5B01G263400 chr2B 359114816 359115456 640 True 924.0 924 92.8240 3356 3990 1 chr2B.!!$R1 634
13 TraesCS5B01G263400 chr6B 187112913 187116560 3647 True 2794.0 4143 94.0690 1 3589 2 chr6B.!!$R2 3588
14 TraesCS5B01G263400 chr6B 55636480 55639910 3430 True 2563.5 3727 93.4050 1 3350 2 chr6B.!!$R1 3349
15 TraesCS5B01G263400 chr6B 171979121 171979761 640 False 902.0 902 92.2000 3356 3990 1 chr6B.!!$F1 634
16 TraesCS5B01G263400 chrUn 291295239 291296820 1581 True 2115.0 2115 91.2300 1 1542 1 chrUn.!!$R1 1541

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
715 728 4.037684 GTCTCTACGTGTAGCCATTATGGT 59.962 45.833 13.28 2.6 40.46 3.55 F
1645 1865 1.068954 GCTAGAAGGTGCTGCAACAAC 60.069 52.381 21.23 12.8 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 2366 2.095415 GGTCAACACGGGTTAATTGCTC 60.095 50.0 0.85 0.0 34.87 4.26 R
3182 3837 0.252927 AGAAGCTAGACCCCTTGCCT 60.253 55.0 0.00 0.0 41.12 4.75 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
33 34 8.710239 TCTTGGTATTATTGTCTATGCTGGTAA 58.290 33.333 0.00 0.00 0.00 2.85
715 728 4.037684 GTCTCTACGTGTAGCCATTATGGT 59.962 45.833 13.28 2.60 40.46 3.55
1645 1865 1.068954 GCTAGAAGGTGCTGCAACAAC 60.069 52.381 21.23 12.80 0.00 3.32
1807 2028 4.388469 GCTCAATCTGGATAAGAAGCGATC 59.612 45.833 0.00 0.00 38.79 3.69
1998 2219 2.730090 GCAGTTTCATGCTCAATCACGG 60.730 50.000 0.00 0.00 43.07 4.94
2156 2378 4.589908 TCTTTCCTGAGAGCAATTAACCC 58.410 43.478 0.00 0.00 0.00 4.11
2894 3155 9.562408 TTTTTGGGTTTGGAATATTTAAGAACC 57.438 29.630 12.10 12.10 35.49 3.62
3060 3699 6.949352 AATAAGCTAACATCCATGTCCTTG 57.051 37.500 0.00 0.00 40.80 3.61
3172 3827 2.079020 AACCGCTCCGACGACAAAGA 62.079 55.000 0.00 0.00 34.06 2.52
3182 3837 5.291178 TCCGACGACAAAGAAACTTATTCA 58.709 37.500 0.00 0.00 0.00 2.57
3233 3888 0.721718 CGAGCTTGACATTCCGGTTC 59.278 55.000 0.00 0.00 0.00 3.62
3314 3980 2.040464 GGATGAGGGGGAGAGGCA 60.040 66.667 0.00 0.00 0.00 4.75
3485 4155 2.024176 AGCTACTTATGTGGTTGGCG 57.976 50.000 0.00 0.00 0.00 5.69
3605 4275 4.460948 GGATCACATCCTTGCAAAATGT 57.539 40.909 17.23 17.23 46.19 2.71
3677 4347 0.918258 TGCAGCTGATACCCAATGGA 59.082 50.000 20.43 0.00 34.81 3.41
3689 4359 4.396357 ACCCAATGGACATGAAAAGGTA 57.604 40.909 0.00 0.00 34.81 3.08
3722 4392 1.205893 GTGGCTTCGAGTGAGAGGATT 59.794 52.381 0.00 0.00 0.00 3.01
3726 4396 1.066303 CTTCGAGTGAGAGGATTCCCG 59.934 57.143 0.00 0.00 37.58 5.14
3842 4514 2.418368 AATGAGCAATAACTGGCCGA 57.582 45.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.770286 ATGAATCCCACCTATGTTGTATCT 57.230 37.500 0.00 0.00 0.00 1.98
715 728 5.456497 GCTCGCGTACAAAATATACACACTA 59.544 40.000 5.77 0.00 0.00 2.74
794 807 8.947055 AAGGATTGCCATATTTACAATTCAAC 57.053 30.769 0.00 0.00 34.28 3.18
847 860 4.021016 GGTGGCGTATCAGATATTTCTCCT 60.021 45.833 0.00 0.00 0.00 3.69
1001 1149 1.011333 TCGATACGCGTGAGTGATCA 58.989 50.000 24.59 0.00 46.66 2.92
1998 2219 3.558109 GCATCCAGGAATACCTTAGAGCC 60.558 52.174 0.00 0.00 45.36 4.70
2041 2262 3.293311 AACAGCATTGTTGATCAGCAC 57.707 42.857 12.23 0.74 45.54 4.40
2144 2366 2.095415 GGTCAACACGGGTTAATTGCTC 60.095 50.000 0.85 0.00 34.87 4.26
2156 2378 5.312120 AGATACTACAGAAGGTCAACACG 57.688 43.478 0.00 0.00 0.00 4.49
2270 2492 2.301870 TGCTATTTCCCACTTGTCGTCT 59.698 45.455 0.00 0.00 0.00 4.18
3060 3699 4.065789 CCGGTTAAGCTGATTTATCTCCC 58.934 47.826 2.76 0.00 0.00 4.30
3172 3827 3.076032 AGACCCCTTGCCTGAATAAGTTT 59.924 43.478 0.00 0.00 0.00 2.66
3182 3837 0.252927 AGAAGCTAGACCCCTTGCCT 60.253 55.000 0.00 0.00 41.12 4.75
3233 3888 1.769098 CGATTGCAGCACTGATCGGG 61.769 60.000 16.94 0.00 35.20 5.14
3314 3980 4.952071 ATGTGCATAGTCTACTCATGCT 57.048 40.909 17.50 4.15 44.27 3.79
3677 4347 5.308825 CACCACTCTTCTACCTTTTCATGT 58.691 41.667 0.00 0.00 0.00 3.21
3689 4359 1.062488 AAGCCACCCACCACTCTTCT 61.062 55.000 0.00 0.00 0.00 2.85
3722 4392 0.679505 CCTTTCAGTGTGTCTCGGGA 59.320 55.000 0.00 0.00 0.00 5.14
3726 4396 3.053455 CGAAGTCCTTTCAGTGTGTCTC 58.947 50.000 0.00 0.00 35.43 3.36
3842 4514 1.474077 GGCGCTCCATGAAAATGTTCT 59.526 47.619 7.64 0.00 34.60 3.01


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

AutoCloner maintained by Alex Coulton.