Multiple sequence alignment - TraesCS1A01G275100

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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 TraesCS1A01G275100 chr1A 100.000 2802 0 0 1 2802 469357781 469354980 0.000000e+00 5175
1 TraesCS1A01G275100 chr1A 96.691 2085 49 8 1 2084 469349850 469347785 0.000000e+00 3450
2 TraesCS1A01G275100 chr1A 94.336 1801 76 16 262 2043 168235210 168237003 0.000000e+00 2737
3 TraesCS1A01G275100 chr1A 92.204 744 47 9 2064 2801 470804132 470804870 0.000000e+00 1042
4 TraesCS1A01G275100 chr1A 86.873 259 24 8 1 249 86896819 86896561 5.910000e-72 281
5 TraesCS1A01G275100 chr1A 85.714 259 26 9 1 249 184256756 184256499 2.140000e-66 263
6 TraesCS1A01G275100 chr1A 84.848 264 30 8 1 254 86861416 86861153 9.960000e-65 257
7 TraesCS1A01G275100 chr1A 91.772 158 11 1 1 156 519088668 519088825 4.700000e-53 219
8 TraesCS1A01G275100 chr3A 97.002 2802 79 4 4 2802 279045794 279042995 0.000000e+00 4704
9 TraesCS1A01G275100 chr3A 96.706 2095 64 5 1 2093 279037899 279035808 0.000000e+00 3482
10 TraesCS1A01G275100 chr3A 96.261 2086 63 7 1 2084 271848246 271846174 0.000000e+00 3406
11 TraesCS1A01G275100 chr3A 97.131 1220 30 3 1585 2802 271854542 271853326 0.000000e+00 2054
12 TraesCS1A01G275100 chr3A 93.778 659 25 12 1397 2043 223212001 223212655 0.000000e+00 976
13 TraesCS1A01G275100 chr3A 77.628 666 107 32 1625 2268 259132309 259131664 1.590000e-97 366
14 TraesCS1A01G275100 chr3A 74.620 658 119 41 1478 2102 308225199 308225841 2.160000e-61 246
15 TraesCS1A01G275100 chr6A 91.941 2829 193 28 1 2802 353349383 353346563 0.000000e+00 3928
16 TraesCS1A01G275100 chr6A 95.477 2056 75 14 1 2043 353341475 353339425 0.000000e+00 3265
17 TraesCS1A01G275100 chr6A 84.118 1190 147 30 1634 2802 21493738 21494906 0.000000e+00 1112
18 TraesCS1A01G275100 chr6A 92.693 739 46 7 2064 2800 584496837 584496105 0.000000e+00 1059
19 TraesCS1A01G275100 chr6A 90.763 249 20 3 1 246 414896289 414896537 2.080000e-86 329
20 TraesCS1A01G275100 chr6A 90.361 249 20 4 1 246 414888389 414888636 9.680000e-85 324
21 TraesCS1A01G275100 chr6A 89.474 247 22 4 1 245 398692583 398692827 2.710000e-80 309
22 TraesCS1A01G275100 chr6A 89.474 247 22 4 1 245 408350774 408351018 2.710000e-80 309
23 TraesCS1A01G275100 chr2A 89.641 2423 195 38 3 2385 321742249 321744655 0.000000e+00 3033
24 TraesCS1A01G275100 chr2A 91.390 2021 139 21 3 1999 321750222 321752231 0.000000e+00 2736
25 TraesCS1A01G275100 chr2A 91.228 741 59 6 2064 2802 439038235 439038971 0.000000e+00 1003
26 TraesCS1A01G275100 chr2A 91.168 736 60 5 2069 2800 295626508 295627242 0.000000e+00 994
27 TraesCS1A01G275100 chr2A 77.635 1243 179 72 1614 2802 492736527 492737724 0.000000e+00 664
28 TraesCS1A01G275100 chr7A 86.133 1024 95 27 1813 2802 157318597 157319607 0.000000e+00 1061
29 TraesCS1A01G275100 chr5A 92.639 720 50 3 2064 2781 197043504 197044222 0.000000e+00 1033
30 TraesCS1A01G275100 chr5A 91.165 249 19 3 1 246 606324909 606325157 4.470000e-88 335
31 TraesCS1A01G275100 chr4A 91.566 249 18 3 1 246 30184622 30184870 9.610000e-90 340
32 TraesCS1A01G275100 chr4A 90.476 252 21 3 1 249 430397986 430397735 2.080000e-86 329
33 TraesCS1A01G275100 chrUn 91.367 139 10 1 1 137 74799451 74799589 3.680000e-44 189
34 TraesCS1A01G275100 chr3D 90.909 110 10 0 253 362 49363590 49363699 6.250000e-32 148
35 TraesCS1A01G275100 chr1D 91.398 93 7 1 424 516 230551624 230551715 2.930000e-25 126


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 TraesCS1A01G275100 chr1A 469354980 469357781 2801 True 5175 5175 100.000 1 2802 1 chr1A.!!$R5 2801
1 TraesCS1A01G275100 chr1A 469347785 469349850 2065 True 3450 3450 96.691 1 2084 1 chr1A.!!$R4 2083
2 TraesCS1A01G275100 chr1A 168235210 168237003 1793 False 2737 2737 94.336 262 2043 1 chr1A.!!$F1 1781
3 TraesCS1A01G275100 chr1A 470804132 470804870 738 False 1042 1042 92.204 2064 2801 1 chr1A.!!$F2 737
4 TraesCS1A01G275100 chr3A 279042995 279045794 2799 True 4704 4704 97.002 4 2802 1 chr3A.!!$R5 2798
5 TraesCS1A01G275100 chr3A 279035808 279037899 2091 True 3482 3482 96.706 1 2093 1 chr3A.!!$R4 2092
6 TraesCS1A01G275100 chr3A 271846174 271848246 2072 True 3406 3406 96.261 1 2084 1 chr3A.!!$R2 2083
7 TraesCS1A01G275100 chr3A 271853326 271854542 1216 True 2054 2054 97.131 1585 2802 1 chr3A.!!$R3 1217
8 TraesCS1A01G275100 chr3A 223212001 223212655 654 False 976 976 93.778 1397 2043 1 chr3A.!!$F1 646
9 TraesCS1A01G275100 chr3A 259131664 259132309 645 True 366 366 77.628 1625 2268 1 chr3A.!!$R1 643
10 TraesCS1A01G275100 chr3A 308225199 308225841 642 False 246 246 74.620 1478 2102 1 chr3A.!!$F2 624
11 TraesCS1A01G275100 chr6A 353346563 353349383 2820 True 3928 3928 91.941 1 2802 1 chr6A.!!$R2 2801
12 TraesCS1A01G275100 chr6A 353339425 353341475 2050 True 3265 3265 95.477 1 2043 1 chr6A.!!$R1 2042
13 TraesCS1A01G275100 chr6A 21493738 21494906 1168 False 1112 1112 84.118 1634 2802 1 chr6A.!!$F1 1168
14 TraesCS1A01G275100 chr6A 584496105 584496837 732 True 1059 1059 92.693 2064 2800 1 chr6A.!!$R3 736
15 TraesCS1A01G275100 chr2A 321742249 321744655 2406 False 3033 3033 89.641 3 2385 1 chr2A.!!$F2 2382
16 TraesCS1A01G275100 chr2A 321750222 321752231 2009 False 2736 2736 91.390 3 1999 1 chr2A.!!$F3 1996
17 TraesCS1A01G275100 chr2A 439038235 439038971 736 False 1003 1003 91.228 2064 2802 1 chr2A.!!$F4 738
18 TraesCS1A01G275100 chr2A 295626508 295627242 734 False 994 994 91.168 2069 2800 1 chr2A.!!$F1 731
19 TraesCS1A01G275100 chr2A 492736527 492737724 1197 False 664 664 77.635 1614 2802 1 chr2A.!!$F5 1188
20 TraesCS1A01G275100 chr7A 157318597 157319607 1010 False 1061 1061 86.133 1813 2802 1 chr7A.!!$F1 989
21 TraesCS1A01G275100 chr5A 197043504 197044222 718 False 1033 1033 92.639 2064 2781 1 chr5A.!!$F1 717

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
337 356 1.172175 GAGGTCGTCGGTAGAGGTTT 58.828 55.000 0.00 0.0 34.19 3.27 F
346 365 1.997606 CGGTAGAGGTTTTCGCGATTT 59.002 47.619 10.88 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1307 1332 0.325296 ATACCCCAACCTCTCGCTCA 60.325 55.0 0.0 0.0 0.00 4.26 R
2074 2187 0.533308 GGTGGAGTGTTGTAACGCCA 60.533 55.0 4.8 0.0 46.25 5.69 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
133 143 3.582120 CACGCTGCAAACACGGGT 61.582 61.111 0.00 0.0 0.00 5.28
164 174 2.063156 TCACAAAACATGCATTCGGC 57.937 45.000 0.00 0.0 45.13 5.54
337 356 1.172175 GAGGTCGTCGGTAGAGGTTT 58.828 55.000 0.00 0.0 34.19 3.27
346 365 1.997606 CGGTAGAGGTTTTCGCGATTT 59.002 47.619 10.88 0.0 0.00 2.17
1044 1069 2.614013 GGGGGAAGGAGAGGGCAA 60.614 66.667 0.00 0.0 0.00 4.52
1307 1332 1.439228 CTGGATCGATCAGGCACGT 59.561 57.895 25.93 0.0 0.00 4.49
2014 2127 1.994916 CACAAATAAAAGGGCAGGCG 58.005 50.000 0.00 0.0 0.00 5.52
2179 2294 8.648693 AGAGAAGAGGTAAAACTAAGTTGCTTA 58.351 33.333 0.00 0.0 0.00 3.09
2241 2360 9.220767 GGTTAAGCCATATCGAGAAAAGAATAT 57.779 33.333 0.00 0.0 37.17 1.28
2520 2671 5.351465 TGTCAACTTCTGTCACAAAGAGTTC 59.649 40.000 6.70 0.0 0.00 3.01
2642 2795 3.087031 AGATGAAAACCTGCCACTCATG 58.913 45.455 0.00 0.0 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 143 6.072783 TGCATGTTTTGTGATACGAGATGAAA 60.073 34.615 0.00 0.00 0.00 2.69
164 174 2.125673 GACACGACCGTCCATGGG 60.126 66.667 13.02 0.00 0.00 4.00
337 356 3.538201 CGTCGCCGAAATCGCGAA 61.538 61.111 15.24 0.00 44.32 4.70
346 365 2.672651 TTCCACTACCGTCGCCGA 60.673 61.111 0.00 0.00 35.63 5.54
1107 1132 1.320507 GTCTCTGGTATCTCCGTCCC 58.679 60.000 0.00 0.00 39.52 4.46
1241 1266 3.785859 GCCATGACCTCGGCCTCA 61.786 66.667 0.00 0.00 42.82 3.86
1307 1332 0.325296 ATACCCCAACCTCTCGCTCA 60.325 55.000 0.00 0.00 0.00 4.26
2014 2127 4.433674 GGTTTCGTTGTGTGTTTCTTTTGC 60.434 41.667 0.00 0.00 0.00 3.68
2074 2187 0.533308 GGTGGAGTGTTGTAACGCCA 60.533 55.000 4.80 0.00 46.25 5.69
2179 2294 3.804036 TGGTCTCACTCGTTTGTCAAAT 58.196 40.909 0.40 0.00 0.00 2.32
2241 2360 7.389330 TGCTTTCAACTTCATTTATCTCCGTTA 59.611 33.333 0.00 0.00 0.00 3.18
2485 2632 8.279103 GTGACAGAAGTTGACATTTTCTTCTAG 58.721 37.037 6.06 4.64 42.80 2.43
2486 2633 7.768582 TGTGACAGAAGTTGACATTTTCTTCTA 59.231 33.333 6.06 0.00 42.80 2.10
2520 2671 4.333926 CCTTCTCCTAAAGATGCCTTTTCG 59.666 45.833 0.00 0.00 42.26 3.46
2642 2795 8.988934 GTTCTTACCAATCAAATTCTTTTTCCC 58.011 33.333 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.