Multiple sequence alignment - TraesCS4B01G114700

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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 TraesCS4B01G114700 chr4B 100.000 2366 0 0 1 2366 130626202 130623837 0.000000e+00 4370
1 TraesCS4B01G114700 chr4D 94.854 1438 37 17 943 2366 93069960 93068546 0.000000e+00 2211
2 TraesCS4B01G114700 chr4D 90.808 990 29 27 1 943 93070969 93069995 0.000000e+00 1267
3 TraesCS4B01G114700 chr4A 92.931 1457 47 23 943 2366 489434198 489435631 0.000000e+00 2069
4 TraesCS4B01G114700 chr4A 93.803 823 23 11 1 803 489432982 489433796 0.000000e+00 1212
5 TraesCS4B01G114700 chr4A 92.308 52 4 0 802 853 489433957 489434008 9.070000e-10 75
6 TraesCS4B01G114700 chr2D 95.455 110 5 0 1139 1248 81515039 81515148 2.420000e-40 176
7 TraesCS4B01G114700 chr6B 95.327 107 5 0 1142 1248 507373577 507373471 1.120000e-38 171
8 TraesCS4B01G114700 chr6B 93.578 109 7 0 1139 1247 615607424 615607532 1.880000e-36 163
9 TraesCS4B01G114700 chr5B 93.578 109 7 0 1139 1247 625119396 625119504 1.880000e-36 163
10 TraesCS4B01G114700 chr5B 93.578 109 7 0 1139 1247 628698945 628699053 1.880000e-36 163
11 TraesCS4B01G114700 chr7A 93.396 106 7 0 1142 1247 487478638 487478533 8.750000e-35 158
12 TraesCS4B01G114700 chr1D 85.841 113 9 4 248 358 269726379 269726486 1.920000e-21 113
13 TraesCS4B01G114700 chr1A 85.841 113 9 4 248 358 333135563 333135670 1.920000e-21 113
14 TraesCS4B01G114700 chr7D 98.333 60 1 0 299 358 477932212 477932153 3.220000e-19 106
15 TraesCS4B01G114700 chr3B 96.721 61 2 0 298 358 624317534 624317594 4.160000e-18 102
16 TraesCS4B01G114700 chr3A 96.721 61 2 0 298 358 612524213 612524273 4.160000e-18 102
17 TraesCS4B01G114700 chr2A 96.721 61 2 0 298 358 138533284 138533224 4.160000e-18 102
18 TraesCS4B01G114700 chr1B 84.071 113 11 4 248 358 342973154 342973261 4.160000e-18 102


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 TraesCS4B01G114700 chr4B 130623837 130626202 2365 True 4370.000000 4370 100.000 1 2366 1 chr4B.!!$R1 2365
1 TraesCS4B01G114700 chr4D 93068546 93070969 2423 True 1739.000000 2211 92.831 1 2366 2 chr4D.!!$R1 2365
2 TraesCS4B01G114700 chr4A 489432982 489435631 2649 False 1118.666667 2069 93.014 1 2366 3 chr4A.!!$F1 2365

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
290 291 0.103937 GATGCTCCTTGGTCTCCTCG 59.896 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 2006 1.062121 AGATAGGCCCTGCTTGTCCTA 60.062 52.381 0.0 0.0 35.83 2.94 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
28 29 2.743928 CTTCTTGAAGCCGCGCCT 60.744 61.111 0.00 0.00 0.00 5.52
29 30 2.281484 TTCTTGAAGCCGCGCCTT 60.281 55.556 0.14 0.14 0.00 4.35
290 291 0.103937 GATGCTCCTTGGTCTCCTCG 59.896 60.000 0.00 0.00 0.00 4.63
365 366 6.592607 TGAACCAGTTCGACACCTAATAATTC 59.407 38.462 6.08 0.00 42.28 2.17
463 472 5.511386 AACTGAAGAAGGATGGTTGAGAT 57.489 39.130 0.00 0.00 0.00 2.75
576 585 1.838112 GATCAACCAATGGGAGTGCA 58.162 50.000 3.55 0.00 38.05 4.57
690 711 2.574450 TCATGAGCATTGTGTGTGTGT 58.426 42.857 0.00 0.00 0.00 3.72
691 712 2.291190 TCATGAGCATTGTGTGTGTGTG 59.709 45.455 0.00 0.00 0.00 3.82
692 713 1.748950 TGAGCATTGTGTGTGTGTGT 58.251 45.000 0.00 0.00 0.00 3.72
693 714 1.401199 TGAGCATTGTGTGTGTGTGTG 59.599 47.619 0.00 0.00 0.00 3.82
694 715 1.401552 GAGCATTGTGTGTGTGTGTGT 59.598 47.619 0.00 0.00 0.00 3.72
695 716 1.132834 AGCATTGTGTGTGTGTGTGTG 59.867 47.619 0.00 0.00 0.00 3.82
740 766 0.179137 TCTCTCATGCAAGTACCGCG 60.179 55.000 0.00 0.00 0.00 6.46
751 777 1.556564 AGTACCGCGTCATCATTTCG 58.443 50.000 4.92 0.00 0.00 3.46
772 798 2.539142 GCACTCTATCTGTACCACGTCG 60.539 54.545 0.00 0.00 0.00 5.12
867 1115 3.319291 CCTAGCTAGGTTGCATGTGCAG 61.319 54.545 28.90 1.25 42.63 4.41
897 1155 4.751767 ACCTTCCAAACAATTCAAGCAA 57.248 36.364 0.00 0.00 0.00 3.91
902 1160 4.059511 TCCAAACAATTCAAGCAATGCAG 58.940 39.130 8.35 0.00 0.00 4.41
943 1205 6.009115 ACAAGAAAATGGCGGTAAAGTTAG 57.991 37.500 0.00 0.00 0.00 2.34
945 1207 4.076394 AGAAAATGGCGGTAAAGTTAGCA 58.924 39.130 1.61 0.00 0.00 3.49
946 1208 4.705023 AGAAAATGGCGGTAAAGTTAGCAT 59.295 37.500 1.61 0.00 0.00 3.79
947 1209 4.370364 AAATGGCGGTAAAGTTAGCATG 57.630 40.909 1.61 0.00 0.00 4.06
950 1212 1.400494 GGCGGTAAAGTTAGCATGGTG 59.600 52.381 7.89 0.00 0.00 4.17
956 1256 4.082949 GGTAAAGTTAGCATGGTGGTGAAC 60.083 45.833 7.89 3.86 0.00 3.18
957 1257 2.949177 AGTTAGCATGGTGGTGAACA 57.051 45.000 7.89 0.00 0.00 3.18
966 1266 1.485480 TGGTGGTGAACAACTTACGGA 59.515 47.619 0.00 0.00 37.78 4.69
1520 1828 8.099364 ACACGATTAATTGTCTTGTCAGATTT 57.901 30.769 5.29 0.00 0.00 2.17
1584 1892 9.294030 CTGCATTTCTTGTTTATATGGAGAAAC 57.706 33.333 0.00 0.00 38.65 2.78
1947 2264 1.280457 ACTTGGCCACTAGCTAGCTT 58.720 50.000 24.88 1.98 43.05 3.74
1949 2266 0.984230 TTGGCCACTAGCTAGCTTGT 59.016 50.000 24.88 24.17 43.05 3.16
2100 2429 8.515414 ACCAGAGCTGATTTGTAAATTTCTAAC 58.485 33.333 0.00 0.00 0.00 2.34
2178 2511 7.921214 AGACAATACTGGTCAGTGTTTATATCG 59.079 37.037 13.32 3.59 40.13 2.92
2227 2561 1.755959 TGGTGCAAGCTGACAAAACAT 59.244 42.857 0.00 0.00 33.76 2.71
2232 2566 3.189285 GCAAGCTGACAAAACATGTGTT 58.811 40.909 0.00 0.00 44.12 3.32
2236 2570 6.562640 GCAAGCTGACAAAACATGTGTTATTG 60.563 38.462 0.00 6.66 44.12 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.605453 GGTGAGGATGGCGGGTTAA 59.395 57.895 0.00 0.00 0.00 2.01
29 30 2.372074 GGGTGAGGATGGCGGGTTA 61.372 63.158 0.00 0.00 0.00 2.85
80 81 3.947841 CTCGAGCTCGCCGGAGAG 61.948 72.222 30.97 28.81 43.27 3.20
230 231 3.003763 GACAAGGGGAGGCCGTCT 61.004 66.667 0.00 0.00 0.00 4.18
365 366 5.146482 TCCGTGAGAGTTTTTGTAAAACG 57.854 39.130 8.80 0.00 35.42 3.60
430 439 5.065914 TCCTTCTTCAGTTTGATCCAGTTG 58.934 41.667 0.00 0.00 0.00 3.16
576 585 2.273179 TACTCAGCGCCCTCGTGTT 61.273 57.895 2.29 0.00 38.14 3.32
690 711 0.879090 AGCACGAGATACGACACACA 59.121 50.000 0.00 0.00 45.77 3.72
691 712 2.819422 TAGCACGAGATACGACACAC 57.181 50.000 0.00 0.00 45.77 3.82
692 713 2.681344 ACATAGCACGAGATACGACACA 59.319 45.455 0.00 0.00 45.77 3.72
693 714 3.002451 AGACATAGCACGAGATACGACAC 59.998 47.826 0.00 0.00 45.77 3.67
694 715 3.203716 AGACATAGCACGAGATACGACA 58.796 45.455 0.00 0.00 45.77 4.35
695 716 3.881780 AGACATAGCACGAGATACGAC 57.118 47.619 0.00 0.00 45.77 4.34
740 766 5.046529 ACAGATAGAGTGCGAAATGATGAC 58.953 41.667 0.00 0.00 0.00 3.06
751 777 2.539142 CGACGTGGTACAGATAGAGTGC 60.539 54.545 0.00 0.00 41.80 4.40
772 798 3.325293 TGCATTTCTCTCTCTGTCACC 57.675 47.619 0.00 0.00 0.00 4.02
820 1014 0.109412 GTACAGGTGAACTCCGTCGG 60.109 60.000 4.39 4.39 0.00 4.79
824 1022 3.924686 GTGTATTGTACAGGTGAACTCCG 59.075 47.826 0.00 0.00 39.77 4.63
867 1115 3.467374 TGTTTGGAAGGTTTTGCATCC 57.533 42.857 0.00 0.00 34.44 3.51
879 1127 4.449131 TGCATTGCTTGAATTGTTTGGAA 58.551 34.783 10.49 0.00 0.00 3.53
880 1128 4.059511 CTGCATTGCTTGAATTGTTTGGA 58.940 39.130 10.49 0.00 0.00 3.53
924 1185 4.428615 TGCTAACTTTACCGCCATTTTC 57.571 40.909 0.00 0.00 0.00 2.29
943 1205 2.350388 CGTAAGTTGTTCACCACCATGC 60.350 50.000 0.00 0.00 0.00 4.06
945 1207 2.105134 TCCGTAAGTTGTTCACCACCAT 59.895 45.455 0.00 0.00 0.00 3.55
946 1208 1.485480 TCCGTAAGTTGTTCACCACCA 59.515 47.619 0.00 0.00 0.00 4.17
947 1209 2.243602 TCCGTAAGTTGTTCACCACC 57.756 50.000 0.00 0.00 0.00 4.61
950 1212 3.000727 CTCCATCCGTAAGTTGTTCACC 58.999 50.000 0.00 0.00 0.00 4.02
956 1256 3.262420 CACTTCCTCCATCCGTAAGTTG 58.738 50.000 0.00 0.00 0.00 3.16
957 1257 2.354805 GCACTTCCTCCATCCGTAAGTT 60.355 50.000 0.00 0.00 0.00 2.66
966 1266 1.480137 CTCTTCGAGCACTTCCTCCAT 59.520 52.381 0.00 0.00 0.00 3.41
1383 1683 3.780294 TGTACTGGGATCTAATGTGGCTT 59.220 43.478 0.00 0.00 0.00 4.35
1520 1828 6.475504 TGCTAAAATCCACTTGATTCTCTCA 58.524 36.000 0.00 0.00 42.97 3.27
1584 1892 6.264518 TCTTTTTAGGGAGCTTTAGTTTGTGG 59.735 38.462 0.00 0.00 0.00 4.17
1630 1943 2.354729 CCGGGTTTCCCTCATGCA 59.645 61.111 0.00 0.00 42.67 3.96
1693 2006 1.062121 AGATAGGCCCTGCTTGTCCTA 60.062 52.381 0.00 0.00 35.83 2.94
1775 2088 9.338291 CTGATCAAATATGTGTCTCTTTTTGTG 57.662 33.333 0.00 0.00 0.00 3.33
2036 2365 8.864069 AACGAAAATTATTTGTGAATGTGTGA 57.136 26.923 0.00 0.00 0.00 3.58
2057 2386 9.309516 CAGCTCTGGTAGTAATTAAATAAACGA 57.690 33.333 0.00 0.00 0.00 3.85
2227 2561 7.343316 TCCCTTTTTCCTTTTCTCAATAACACA 59.657 33.333 0.00 0.00 0.00 3.72
2232 2566 6.858941 TCCTCCCTTTTTCCTTTTCTCAATA 58.141 36.000 0.00 0.00 0.00 1.90
2236 2570 4.082845 CCTCCTCCCTTTTTCCTTTTCTC 58.917 47.826 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.