Multiple sequence alignment - TraesCS7D01G239900

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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 TraesCS7D01G239900 chr7D 100.000 2111 0 0 1 2111 204446100 204443990 0.000000e+00 3899
1 TraesCS7D01G239900 chr7D 90.647 973 51 16 1163 2110 71634646 71633689 0.000000e+00 1256
2 TraesCS7D01G239900 chr7D 90.000 230 19 4 858 1085 549286587 549286360 5.700000e-76 294
3 TraesCS7D01G239900 chr7B 92.511 1175 50 15 1 1150 168352654 168351493 0.000000e+00 1648
4 TraesCS7D01G239900 chr2D 89.837 984 58 21 1158 2111 450874191 450875162 0.000000e+00 1225
5 TraesCS7D01G239900 chr3A 89.938 964 68 14 1163 2111 489756939 489755990 0.000000e+00 1216
6 TraesCS7D01G239900 chr3A 86.687 984 65 31 1164 2111 713945231 713944278 0.000000e+00 1031
7 TraesCS7D01G239900 chr3A 90.996 733 48 10 1392 2110 109144478 109145206 0.000000e+00 972
8 TraesCS7D01G239900 chr3A 81.500 800 56 41 1164 1926 374423912 374424656 6.530000e-160 573
9 TraesCS7D01G239900 chr1A 89.609 972 58 23 1164 2111 139556881 139557833 0.000000e+00 1195
10 TraesCS7D01G239900 chr2A 88.706 974 74 21 1164 2110 699800066 699801030 0.000000e+00 1157
11 TraesCS7D01G239900 chr2A 88.344 978 71 28 1164 2110 38756777 38757742 0.000000e+00 1134
12 TraesCS7D01G239900 chr5A 88.132 969 77 12 1164 2111 12903908 12904859 0.000000e+00 1118
13 TraesCS7D01G239900 chr5A 87.963 972 81 23 1164 2111 566168327 566169286 0.000000e+00 1114
14 TraesCS7D01G239900 chr5A 86.810 978 69 21 1164 2111 423551278 423550331 0.000000e+00 1037
15 TraesCS7D01G239900 chr5A 86.552 989 64 26 1164 2111 423457219 423456259 0.000000e+00 1026
16 TraesCS7D01G239900 chr5A 86.596 664 65 15 1163 1809 323730608 323731264 0.000000e+00 712
17 TraesCS7D01G239900 chr5A 89.749 478 38 8 1164 1634 14133717 14133244 3.000000e-168 601
18 TraesCS7D01G239900 chr5A 91.064 235 18 3 850 1082 619678735 619678968 4.370000e-82 315
19 TraesCS7D01G239900 chr7A 91.047 793 40 12 1 764 216419074 216418284 0.000000e+00 1042
20 TraesCS7D01G239900 chr7A 85.355 437 40 16 1162 1580 607583572 607584002 4.160000e-117 431
21 TraesCS7D01G239900 chr7A 90.625 224 17 4 862 1083 634709464 634709243 5.700000e-76 294
22 TraesCS7D01G239900 chr3B 93.810 210 12 1 875 1083 622767287 622767078 4.370000e-82 315
23 TraesCS7D01G239900 chr3B 92.000 225 13 5 862 1083 708954586 708954808 5.660000e-81 311
24 TraesCS7D01G239900 chr3B 91.593 226 15 4 861 1083 709075246 709075470 2.030000e-80 309
25 TraesCS7D01G239900 chr5D 90.870 230 20 1 855 1083 495614812 495615041 7.320000e-80 307
26 TraesCS7D01G239900 chr5B 90.351 228 19 3 858 1083 612669844 612670070 1.580000e-76 296


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 TraesCS7D01G239900 chr7D 204443990 204446100 2110 True 3899 3899 100.000 1 2111 1 chr7D.!!$R2 2110
1 TraesCS7D01G239900 chr7D 71633689 71634646 957 True 1256 1256 90.647 1163 2110 1 chr7D.!!$R1 947
2 TraesCS7D01G239900 chr7B 168351493 168352654 1161 True 1648 1648 92.511 1 1150 1 chr7B.!!$R1 1149
3 TraesCS7D01G239900 chr2D 450874191 450875162 971 False 1225 1225 89.837 1158 2111 1 chr2D.!!$F1 953
4 TraesCS7D01G239900 chr3A 489755990 489756939 949 True 1216 1216 89.938 1163 2111 1 chr3A.!!$R1 948
5 TraesCS7D01G239900 chr3A 713944278 713945231 953 True 1031 1031 86.687 1164 2111 1 chr3A.!!$R2 947
6 TraesCS7D01G239900 chr3A 109144478 109145206 728 False 972 972 90.996 1392 2110 1 chr3A.!!$F1 718
7 TraesCS7D01G239900 chr3A 374423912 374424656 744 False 573 573 81.500 1164 1926 1 chr3A.!!$F2 762
8 TraesCS7D01G239900 chr1A 139556881 139557833 952 False 1195 1195 89.609 1164 2111 1 chr1A.!!$F1 947
9 TraesCS7D01G239900 chr2A 699800066 699801030 964 False 1157 1157 88.706 1164 2110 1 chr2A.!!$F2 946
10 TraesCS7D01G239900 chr2A 38756777 38757742 965 False 1134 1134 88.344 1164 2110 1 chr2A.!!$F1 946
11 TraesCS7D01G239900 chr5A 12903908 12904859 951 False 1118 1118 88.132 1164 2111 1 chr5A.!!$F1 947
12 TraesCS7D01G239900 chr5A 566168327 566169286 959 False 1114 1114 87.963 1164 2111 1 chr5A.!!$F3 947
13 TraesCS7D01G239900 chr5A 423550331 423551278 947 True 1037 1037 86.810 1164 2111 1 chr5A.!!$R3 947
14 TraesCS7D01G239900 chr5A 423456259 423457219 960 True 1026 1026 86.552 1164 2111 1 chr5A.!!$R2 947
15 TraesCS7D01G239900 chr5A 323730608 323731264 656 False 712 712 86.596 1163 1809 1 chr5A.!!$F2 646
16 TraesCS7D01G239900 chr7A 216418284 216419074 790 True 1042 1042 91.047 1 764 1 chr7A.!!$R1 763

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
710 752 0.109342 CTAGGCCCAGCATTCCGATT 59.891 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2044 0.320771 CCGTGACTCTTGTGGAAGGG 60.321 60.0 0.0 0.0 35.55 3.95 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
476 486 4.779733 GGGGGAGCTGGGTCTCGA 62.780 72.222 0.00 0.00 33.98 4.04
484 494 1.385756 GCTGGGTCTCGAGGTAGGTC 61.386 65.000 13.56 0.00 0.00 3.85
667 691 0.242825 GAAAAGCCCGCAACTTACCC 59.757 55.000 0.00 0.00 0.00 3.69
691 731 0.971386 CATGGGCTGATTATTGGGCC 59.029 55.000 0.00 0.00 44.50 5.80
710 752 0.109342 CTAGGCCCAGCATTCCGATT 59.891 55.000 0.00 0.00 0.00 3.34
738 780 1.450312 CCGAATGGACAGCTGGGTC 60.450 63.158 19.93 7.26 37.49 4.46
759 801 2.286294 CGTCATATTCTTCAGGCAGTGC 59.714 50.000 6.55 6.55 0.00 4.40
764 806 2.472695 TTCTTCAGGCAGTGCGTTAT 57.527 45.000 7.77 0.00 0.00 1.89
765 807 1.725641 TCTTCAGGCAGTGCGTTATG 58.274 50.000 7.77 4.81 0.00 1.90
766 808 1.001974 TCTTCAGGCAGTGCGTTATGT 59.998 47.619 7.77 0.00 0.00 2.29
798 840 7.970061 GTGATTATTGAAGCAATTCTAAGCACA 59.030 33.333 13.35 0.00 36.79 4.57
859 903 9.434420 AAACAGAAAACAATCATCAGTTTGAAA 57.566 25.926 0.00 0.00 37.94 2.69
913 957 2.674380 CCCAGGCAGCAGTGGAAC 60.674 66.667 13.62 0.00 35.67 3.62
939 983 3.717294 GACACACGAGGGCCCCAT 61.717 66.667 21.43 0.00 0.00 4.00
942 986 4.047125 ACACGAGGGCCCCATTGG 62.047 66.667 21.43 7.40 37.09 3.16
959 1003 2.658422 GCAAGCCAATGTGGTGGG 59.342 61.111 0.00 0.00 40.46 4.61
1085 1130 2.673368 CCGAGAAAGGTATGAGTTGTGC 59.327 50.000 0.00 0.00 0.00 4.57
1087 1132 3.369147 CGAGAAAGGTATGAGTTGTGCTG 59.631 47.826 0.00 0.00 0.00 4.41
1090 1135 1.813513 AGGTATGAGTTGTGCTGTGC 58.186 50.000 0.00 0.00 0.00 4.57
1152 1197 2.045242 TCGCTAGTCGAGGTGCCT 60.045 61.111 5.35 0.00 43.16 4.75
1153 1198 1.677966 TCGCTAGTCGAGGTGCCTT 60.678 57.895 5.35 0.00 43.16 4.35
1154 1199 1.226717 CGCTAGTCGAGGTGCCTTC 60.227 63.158 0.98 0.00 41.67 3.46
1155 1200 1.658686 CGCTAGTCGAGGTGCCTTCT 61.659 60.000 0.98 0.00 41.67 2.85
1156 1201 0.101579 GCTAGTCGAGGTGCCTTCTC 59.898 60.000 0.00 0.00 0.00 2.87
1157 1202 1.757682 CTAGTCGAGGTGCCTTCTCT 58.242 55.000 0.00 0.00 0.00 3.10
1158 1203 2.096248 CTAGTCGAGGTGCCTTCTCTT 58.904 52.381 0.00 0.00 0.00 2.85
1159 1204 0.892063 AGTCGAGGTGCCTTCTCTTC 59.108 55.000 0.00 0.00 0.00 2.87
1160 1205 0.892063 GTCGAGGTGCCTTCTCTTCT 59.108 55.000 0.00 0.00 0.00 2.85
1161 1206 0.891373 TCGAGGTGCCTTCTCTTCTG 59.109 55.000 0.00 0.00 0.00 3.02
1239 1284 2.510012 CGCGCTCTCAGCCATTCA 60.510 61.111 5.56 0.00 38.18 2.57
1309 1394 4.278058 CGTTTTCGGCTTTTTAAACGGTA 58.722 39.130 10.17 0.00 45.26 4.02
1433 1559 0.031043 TCCTTTCGCGAAAGTCACGA 59.969 50.000 42.71 33.74 44.66 4.35
1441 1567 3.121126 TCGCGAAAGTCACGATTTTTCTC 60.121 43.478 6.20 0.00 0.00 2.87
1478 1604 1.339929 TGTGCTTTAGCGAGAGTCACA 59.660 47.619 9.26 9.26 45.83 3.58
1847 2065 0.393077 CCTTCCACAAGAGTCACGGT 59.607 55.000 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
464 474 1.076632 CCTACCTCGAGACCCAGCT 60.077 63.158 15.71 0.00 0.00 4.24
476 486 2.754658 CACTCGCCCGACCTACCT 60.755 66.667 0.00 0.00 0.00 3.08
484 494 1.024579 AATTAACAGCCACTCGCCCG 61.025 55.000 0.00 0.00 38.78 6.13
667 691 1.881973 CAATAATCAGCCCATGGTCCG 59.118 52.381 11.73 0.00 0.00 4.79
691 731 0.109342 AATCGGAATGCTGGGCCTAG 59.891 55.000 12.68 12.68 0.00 3.02
710 752 2.359354 CCATTCGGCCCGTTGTCA 60.359 61.111 1.63 0.00 0.00 3.58
738 780 2.286294 GCACTGCCTGAAGAATATGACG 59.714 50.000 0.00 0.00 0.00 4.35
759 801 9.092322 GCTTCAATAATCACGATAAACATAACG 57.908 33.333 0.00 0.00 0.00 3.18
764 806 9.502145 GAATTGCTTCAATAATCACGATAAACA 57.498 29.630 0.00 0.00 32.43 2.83
765 807 9.722056 AGAATTGCTTCAATAATCACGATAAAC 57.278 29.630 0.00 0.00 32.43 2.01
793 835 2.991250 AGTTATTTCGATGGCTGTGCT 58.009 42.857 0.00 0.00 0.00 4.40
798 840 6.238374 CCGATAACAAAGTTATTTCGATGGCT 60.238 38.462 12.06 0.00 0.00 4.75
830 874 8.749499 CAAACTGATGATTGTTTTCTGTTTCTC 58.251 33.333 0.00 0.00 38.59 2.87
832 876 8.633075 TCAAACTGATGATTGTTTTCTGTTTC 57.367 30.769 0.00 0.00 38.59 2.78
859 903 7.255070 CCCAACCAAATCGAATTTCAAATTTGT 60.255 33.333 17.47 0.00 37.39 2.83
866 910 3.006323 CACCCCAACCAAATCGAATTTCA 59.994 43.478 0.00 0.00 0.00 2.69
934 978 3.730158 ATTGGCTTGCCAATGGGG 58.270 55.556 31.55 0.00 38.74 4.96
939 983 1.747145 CACCACATTGGCTTGCCAA 59.253 52.632 26.43 26.43 42.67 4.52
942 986 2.658422 CCCACCACATTGGCTTGC 59.342 61.111 0.00 0.00 42.67 4.01
1090 1135 1.976728 CTATATAACGACGCGTGGCTG 59.023 52.381 20.70 6.11 39.99 4.85
1099 1144 4.333690 TGGGAGGAGCTCTATATAACGAC 58.666 47.826 14.64 0.00 0.00 4.34
1102 1147 3.449377 GGCTGGGAGGAGCTCTATATAAC 59.551 52.174 14.64 0.00 39.11 1.89
1150 1195 0.979665 TGCTCCCACAGAAGAGAAGG 59.020 55.000 0.00 0.00 31.43 3.46
1151 1196 2.038295 AGTTGCTCCCACAGAAGAGAAG 59.962 50.000 0.00 0.00 31.43 2.85
1152 1197 2.050144 AGTTGCTCCCACAGAAGAGAA 58.950 47.619 0.00 0.00 31.43 2.87
1153 1198 1.722034 AGTTGCTCCCACAGAAGAGA 58.278 50.000 0.00 0.00 31.43 3.10
1154 1199 2.564947 ACTAGTTGCTCCCACAGAAGAG 59.435 50.000 0.00 0.00 0.00 2.85
1155 1200 2.609747 ACTAGTTGCTCCCACAGAAGA 58.390 47.619 0.00 0.00 0.00 2.87
1156 1201 3.409026 AACTAGTTGCTCCCACAGAAG 57.591 47.619 7.48 0.00 0.00 2.85
1157 1202 4.638304 GTTAACTAGTTGCTCCCACAGAA 58.362 43.478 18.56 0.00 0.00 3.02
1158 1203 3.305813 CGTTAACTAGTTGCTCCCACAGA 60.306 47.826 18.56 0.00 0.00 3.41
1159 1204 2.993899 CGTTAACTAGTTGCTCCCACAG 59.006 50.000 18.56 0.00 0.00 3.66
1160 1205 2.629137 TCGTTAACTAGTTGCTCCCACA 59.371 45.455 18.56 0.00 0.00 4.17
1161 1206 3.251571 CTCGTTAACTAGTTGCTCCCAC 58.748 50.000 18.56 4.51 0.00 4.61
1239 1284 2.433145 CAGAGCGCGACACATGGT 60.433 61.111 12.10 0.00 0.00 3.55
1528 1662 1.947456 GGAAGCAAAACCGTGACTCTT 59.053 47.619 0.00 0.00 0.00 2.85
1750 1965 1.329292 CGAAAGCAAAACCGTGACTCA 59.671 47.619 0.00 0.00 0.00 3.41
1827 2044 0.320771 CCGTGACTCTTGTGGAAGGG 60.321 60.000 0.00 0.00 35.55 3.95
1847 2065 1.478510 TGCCTTTCGTGGAAGCAAAAA 59.521 42.857 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.