Multiple sequence alignment - TraesCS3D01G154000

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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 TraesCS3D01G154000 chr3D 100.000 4367 0 0 1 4367 121342875 121338509 0.000000e+00 8065.0
1 TraesCS3D01G154000 chr3D 91.910 2571 192 8 840 3408 120142429 120144985 0.000000e+00 3581.0
2 TraesCS3D01G154000 chr3B 95.771 3571 125 12 113 3666 173008624 173005063 0.000000e+00 5734.0
3 TraesCS3D01G154000 chr3B 93.511 2589 150 11 840 3418 172170449 172173029 0.000000e+00 3834.0
4 TraesCS3D01G154000 chr3B 93.589 2558 155 7 869 3418 172052114 172054670 0.000000e+00 3807.0
5 TraesCS3D01G154000 chr3B 92.572 2531 178 7 890 3416 146982472 146979948 0.000000e+00 3624.0
6 TraesCS3D01G154000 chr3B 98.088 680 13 0 3688 4367 173004938 173004259 0.000000e+00 1184.0
7 TraesCS3D01G154000 chr3B 79.932 588 52 32 3332 3863 172054954 172055531 5.330000e-99 372.0
8 TraesCS3D01G154000 chr3B 79.762 588 53 34 3332 3863 172173313 172173890 2.480000e-97 366.0
9 TraesCS3D01G154000 chr3B 81.027 448 38 22 3930 4365 172055525 172055937 3.280000e-81 313.0
10 TraesCS3D01G154000 chr3B 80.580 448 40 22 3930 4365 172173884 172174296 7.100000e-78 302.0
11 TraesCS3D01G154000 chr1D 90.612 4282 286 35 123 4367 465903902 465899700 0.000000e+00 5574.0
12 TraesCS3D01G154000 chr1D 83.511 188 26 5 3383 3567 341027305 341027120 2.090000e-38 171.0
13 TraesCS3D01G154000 chr1D 73.333 195 39 13 3738 3922 386368569 386368760 4.720000e-05 60.2
14 TraesCS3D01G154000 chr3A 90.144 4373 304 57 3 4298 127859832 127855510 0.000000e+00 5570.0
15 TraesCS3D01G154000 chr3A 82.828 198 20 8 3477 3665 735448351 735448543 9.720000e-37 165.0
16 TraesCS3D01G154000 chr3A 82.828 198 20 8 3477 3665 735483146 735482954 9.720000e-37 165.0
17 TraesCS3D01G154000 chr1B 89.781 4286 294 51 123 4367 642702221 642698039 0.000000e+00 5356.0
18 TraesCS3D01G154000 chr6D 91.119 2680 208 18 840 3499 452128075 452125406 0.000000e+00 3603.0
19 TraesCS3D01G154000 chr1A 92.157 51 4 0 3615 3665 440711898 440711848 6.060000e-09 73.1
20 TraesCS3D01G154000 chr5B 88.889 54 6 0 3740 3793 63613504 63613557 2.820000e-07 67.6
21 TraesCS3D01G154000 chr5D 73.298 191 45 6 3740 3925 87848261 87848072 1.010000e-06 65.8


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 TraesCS3D01G154000 chr3D 121338509 121342875 4366 True 8065.000000 8065 100.000000 1 4367 1 chr3D.!!$R1 4366
1 TraesCS3D01G154000 chr3D 120142429 120144985 2556 False 3581.000000 3581 91.910000 840 3408 1 chr3D.!!$F1 2568
2 TraesCS3D01G154000 chr3B 146979948 146982472 2524 True 3624.000000 3624 92.572000 890 3416 1 chr3B.!!$R1 2526
3 TraesCS3D01G154000 chr3B 173004259 173008624 4365 True 3459.000000 5734 96.929500 113 4367 2 chr3B.!!$R2 4254
4 TraesCS3D01G154000 chr3B 172170449 172174296 3847 False 1500.666667 3834 84.617667 840 4365 3 chr3B.!!$F2 3525
5 TraesCS3D01G154000 chr3B 172052114 172055937 3823 False 1497.333333 3807 84.849333 869 4365 3 chr3B.!!$F1 3496
6 TraesCS3D01G154000 chr1D 465899700 465903902 4202 True 5574.000000 5574 90.612000 123 4367 1 chr1D.!!$R2 4244
7 TraesCS3D01G154000 chr3A 127855510 127859832 4322 True 5570.000000 5570 90.144000 3 4298 1 chr3A.!!$R1 4295
8 TraesCS3D01G154000 chr1B 642698039 642702221 4182 True 5356.000000 5356 89.781000 123 4367 1 chr1B.!!$R1 4244
9 TraesCS3D01G154000 chr6D 452125406 452128075 2669 True 3603.000000 3603 91.119000 840 3499 1 chr6D.!!$R1 2659

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
937 968 1.059994 GCAAATCAGCGCTCGACAG 59.940 57.895 7.13 0.0 0.00 3.51 F
1977 2020 0.035152 TGATGGACGGCATGAAAGCT 60.035 50.000 0.00 0.0 34.17 3.74 F
2514 2557 1.601419 CGTCCAAGGGCGTCCTCTTA 61.601 60.000 10.20 0.0 44.07 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 2471 0.106708 TGAACGGTCTCTTGCAGCTT 59.893 50.0 0.33 0.0 0.0 3.74 R
3081 3125 0.337773 TCCTCTGCCTCTCCATGTCT 59.662 55.0 0.00 0.0 0.0 3.41 R
4070 5041 0.613777 CTCTTCTTAGGGGTTGGCGT 59.386 55.0 0.00 0.0 0.0 5.68 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
25 26 6.209192 TGGCTCTAAAATTTGAATGAAGCTCA 59.791 34.615 0.00 0.00 0.00 4.26
32 33 8.758633 AAAATTTGAATGAAGCTCAATCTCTG 57.241 30.769 0.00 0.00 32.98 3.35
35 36 5.156608 TGAATGAAGCTCAATCTCTGTCA 57.843 39.130 0.00 0.00 28.07 3.58
56 58 3.473113 AATGCAAAATAGACACCCCCT 57.527 42.857 0.00 0.00 0.00 4.79
148 156 4.517952 AAATTGAAACATGTCGATGCCA 57.482 36.364 0.00 0.00 32.14 4.92
153 161 4.006319 TGAAACATGTCGATGCCACAATA 58.994 39.130 0.00 0.00 32.14 1.90
210 221 1.336702 GCTCATCAGGTAGCATCTCCG 60.337 57.143 0.00 0.00 38.63 4.63
228 239 2.995872 GCCTCGAGCTTCCTGACGT 61.996 63.158 6.99 0.00 38.99 4.34
314 325 2.109126 GTCTCCAGCGCCCATTGTC 61.109 63.158 2.29 0.00 0.00 3.18
404 415 1.671742 GTCTTCTCCCGCACTTCCA 59.328 57.895 0.00 0.00 0.00 3.53
692 709 1.082169 CACGGACACGCCATTGTTG 60.082 57.895 0.00 0.00 46.04 3.33
937 968 1.059994 GCAAATCAGCGCTCGACAG 59.940 57.895 7.13 0.00 0.00 3.51
1095 1138 2.515901 GTGTGCAACCTCCACCCT 59.484 61.111 0.00 0.00 34.36 4.34
1297 1340 2.665185 GCCACGACGCCAAGTTCT 60.665 61.111 0.00 0.00 0.00 3.01
1332 1375 1.304547 CCTCCCTCTGGACGACACT 60.305 63.158 0.00 0.00 35.03 3.55
1733 1776 2.125552 CAAGACGCTGATCGCCCA 60.126 61.111 4.37 0.00 43.23 5.36
1734 1777 2.169789 CAAGACGCTGATCGCCCAG 61.170 63.158 4.37 0.00 43.23 4.45
1752 1795 4.980805 GCGGTGGCCAACGAGACA 62.981 66.667 45.74 0.00 45.97 3.41
1782 1825 1.452108 CTTCCTCATCAACGGCCCC 60.452 63.158 0.00 0.00 0.00 5.80
1794 1837 1.046472 ACGGCCCCGAGATAATGTCA 61.046 55.000 14.44 0.00 42.83 3.58
1818 1861 3.591835 GCCGGAGAGAGCGAGAGG 61.592 72.222 5.05 0.00 0.00 3.69
1905 1948 0.904865 ACTCCATCGCTCCCAACAGA 60.905 55.000 0.00 0.00 0.00 3.41
1948 1991 4.148825 GGCGCATCGTCTCCCAGT 62.149 66.667 10.83 0.00 0.00 4.00
1977 2020 0.035152 TGATGGACGGCATGAAAGCT 60.035 50.000 0.00 0.00 34.17 3.74
2246 2289 2.011046 GCAGTGCATCAGGGAGAAGAC 61.011 57.143 11.09 0.00 0.00 3.01
2305 2348 1.918262 AGATCTTGAACTCCATGGCCA 59.082 47.619 8.56 8.56 0.00 5.36
2391 2434 2.110213 GAGGTGCCCAACGTCACA 59.890 61.111 7.33 0.00 42.17 3.58
2428 2471 2.670592 TCGACGGCGTCAAGAGGA 60.671 61.111 35.62 22.82 38.98 3.71
2514 2557 1.601419 CGTCCAAGGGCGTCCTCTTA 61.601 60.000 10.20 0.00 44.07 2.10
3081 3125 5.335113 CGCCATCAGAGAAGACATTGAAAAA 60.335 40.000 0.00 0.00 0.00 1.94
3388 3818 8.109634 AGTGATCCAGTAACCATTGTTAGAAAT 58.890 33.333 0.00 0.00 37.62 2.17
3472 4291 9.132521 CACTTTGTATTGTTGATTCCTTTCATC 57.867 33.333 0.00 0.00 0.00 2.92
3553 4384 9.816354 TCGTGAATTAGAATCTCATTATTGTCA 57.184 29.630 0.00 0.00 0.00 3.58
3762 4727 5.343715 TGGGGGTGTCTAGTTATCAGTTAA 58.656 41.667 0.00 0.00 0.00 2.01
3967 4934 3.513912 GGCCCTTGCAAAAACCTATTACT 59.486 43.478 0.00 0.00 40.13 2.24
4106 5077 6.284891 AGAAGAGAGGAATGAAAGACTGAG 57.715 41.667 0.00 0.00 0.00 3.35
4195 5179 3.075134 AGAAAGGAAAGCTGACTCCCATT 59.925 43.478 6.21 3.15 31.50 3.16
4205 5189 3.879892 GCTGACTCCCATTTGAACTATCC 59.120 47.826 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.209192 TGAGCTTCATTCAAATTTTAGAGCCA 59.791 34.615 0.00 0.00 0.00 4.75
2 3 8.699283 ATTGAGCTTCATTCAAATTTTAGAGC 57.301 30.769 0.00 0.00 38.01 4.09
18 19 4.155462 TGCATTTGACAGAGATTGAGCTTC 59.845 41.667 0.00 0.00 0.00 3.86
19 20 4.077108 TGCATTTGACAGAGATTGAGCTT 58.923 39.130 0.00 0.00 0.00 3.74
25 26 8.025445 GTGTCTATTTTGCATTTGACAGAGATT 58.975 33.333 8.54 0.00 35.51 2.40
32 33 4.494484 GGGGTGTCTATTTTGCATTTGAC 58.506 43.478 0.00 0.00 0.00 3.18
35 36 3.790126 AGGGGGTGTCTATTTTGCATTT 58.210 40.909 0.00 0.00 0.00 2.32
85 87 4.211374 GCGCACTAACATTCTTCCGAATAT 59.789 41.667 0.30 0.00 37.77 1.28
91 93 1.448985 TGGCGCACTAACATTCTTCC 58.551 50.000 10.83 0.00 0.00 3.46
99 101 0.526096 CATTGCCATGGCGCACTAAC 60.526 55.000 30.87 3.39 45.51 2.34
148 156 2.401583 TTCGTCCAGCATGCTATTGT 57.598 45.000 22.19 0.00 31.97 2.71
153 161 0.105593 ATCGATTCGTCCAGCATGCT 59.894 50.000 16.30 16.30 31.97 3.79
157 165 0.525455 CGTGATCGATTCGTCCAGCA 60.525 55.000 5.89 0.00 39.71 4.41
210 221 2.202676 CGTCAGGAAGCTCGAGGC 60.203 66.667 15.58 6.66 42.19 4.70
314 325 1.860399 GCTAGTGCTACGTGATGACGG 60.860 57.143 10.07 0.00 42.23 4.79
317 328 2.952310 AGATGCTAGTGCTACGTGATGA 59.048 45.455 0.00 0.00 40.48 2.92
548 559 2.591429 CTGGGCAGTCAACGTGCA 60.591 61.111 0.00 0.00 43.12 4.57
592 603 1.750399 GCTGTGGGATGCCAACGAT 60.750 57.895 7.86 0.00 0.00 3.73
871 893 3.713936 GGTTCGCACCCTTTATTGC 57.286 52.632 0.00 0.00 37.03 3.56
937 968 4.743151 TCGTGTATTACTTTCGATGGATGC 59.257 41.667 0.00 0.00 0.00 3.91
1095 1138 1.203441 AGAGCTTCTCCATGGTGGCA 61.203 55.000 12.58 0.00 37.47 4.92
1167 1210 2.805546 GCCAGTGCCATGCAGATG 59.194 61.111 0.00 0.00 40.08 2.90
1332 1375 2.897207 CCCGTTATGCCCTCGACA 59.103 61.111 0.00 0.00 0.00 4.35
1344 1387 1.301479 GTCGAAGAGGTTGCCCGTT 60.301 57.895 0.00 0.00 36.95 4.44
1609 1652 0.679960 TCGACGAGCTCCCTGATCAA 60.680 55.000 8.47 0.00 0.00 2.57
1752 1795 1.194781 TGAGGAAGAAGAAGGCGCCT 61.195 55.000 27.08 27.08 0.00 5.52
1755 1798 2.675348 GTTGATGAGGAAGAAGAAGGCG 59.325 50.000 0.00 0.00 0.00 5.52
1782 1825 3.185188 CGGCCATCTTTGACATTATCTCG 59.815 47.826 2.24 0.00 0.00 4.04
1794 1837 1.524482 GCTCTCTCCGGCCATCTTT 59.476 57.895 2.24 0.00 0.00 2.52
1818 1861 0.391793 CGAAGGCCTTCCTCAGGTTC 60.392 60.000 34.54 12.21 46.07 3.62
1905 1948 1.309499 CCTCGCCGTGAGTCTTCTCT 61.309 60.000 8.14 0.00 43.64 3.10
1948 1991 0.247460 CCGTCCATCAGAGTCAGCAA 59.753 55.000 0.00 0.00 0.00 3.91
2246 2289 1.003759 CCTCTAAGTCGATCACGTCCG 60.004 57.143 0.00 0.00 40.69 4.79
2305 2348 4.589908 GTCTTAAGGTGGTCATTGGTGAT 58.410 43.478 1.85 0.00 36.60 3.06
2391 2434 0.392998 GGCCGCCGATATCATTCCAT 60.393 55.000 3.12 0.00 0.00 3.41
2428 2471 0.106708 TGAACGGTCTCTTGCAGCTT 59.893 50.000 0.33 0.00 0.00 3.74
3039 3083 1.292223 GTACTTGCACGCCCTCTGA 59.708 57.895 0.00 0.00 0.00 3.27
3081 3125 0.337773 TCCTCTGCCTCTCCATGTCT 59.662 55.000 0.00 0.00 0.00 3.41
3553 4384 0.730265 TCACGCACGCTTTCTTTTGT 59.270 45.000 0.00 0.00 0.00 2.83
3762 4727 6.553953 ACCTAAACCAAATGGAAAAACACT 57.446 33.333 6.42 0.00 38.94 3.55
3799 4766 6.654582 ACAATACATGCATCACAAACTGACTA 59.345 34.615 0.00 0.00 0.00 2.59
3813 4780 7.880105 TGACTGAAATTACAACAATACATGCA 58.120 30.769 0.00 0.00 0.00 3.96
3814 4781 8.741101 TTGACTGAAATTACAACAATACATGC 57.259 30.769 0.00 0.00 0.00 4.06
3967 4934 1.003696 TGTTGTTGTCTGTGTGGGACA 59.996 47.619 0.00 0.00 41.23 4.02
4070 5041 0.613777 CTCTTCTTAGGGGTTGGCGT 59.386 55.000 0.00 0.00 0.00 5.68
4195 5179 6.096987 CCTAGTGTAGCTCTTGGATAGTTCAA 59.903 42.308 0.00 0.00 31.39 2.69
4205 5189 4.281941 TCCATATGCCTAGTGTAGCTCTTG 59.718 45.833 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.