Multiple sequence alignment - TraesCS7D01G189900

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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 TraesCS7D01G189900 chr7D 100.000 3085 0 0 1 3085 143976773 143973689 0.000000e+00 5698.0
1 TraesCS7D01G189900 chr7D 82.989 1887 298 16 423 2300 152947009 152948881 0.000000e+00 1685.0
2 TraesCS7D01G189900 chr7D 94.409 787 41 1 2302 3085 68084507 68085293 0.000000e+00 1206.0
3 TraesCS7D01G189900 chr7D 94.409 787 40 4 2302 3085 225915103 225914318 0.000000e+00 1206.0
4 TraesCS7D01G189900 chr7D 92.486 732 48 5 2302 3028 571297758 571298487 0.000000e+00 1040.0
5 TraesCS7D01G189900 chr7D 88.467 737 79 5 2302 3038 287064208 287064938 0.000000e+00 885.0
6 TraesCS7D01G189900 chr7B 94.194 2308 121 7 1 2301 107821037 107823338 0.000000e+00 3507.0
7 TraesCS7D01G189900 chr7B 82.446 1897 299 20 413 2300 114938575 114940446 0.000000e+00 1628.0
8 TraesCS7D01G189900 chr7B 86.047 86 11 1 275 359 157202878 157202963 1.180000e-14 91.6
9 TraesCS7D01G189900 chr7A 90.702 2323 187 17 1 2300 146024428 146026744 0.000000e+00 3066.0
10 TraesCS7D01G189900 chrUn 82.105 1900 323 13 412 2300 29901514 29899621 0.000000e+00 1609.0
11 TraesCS7D01G189900 chrUn 81.764 1179 210 5 692 1867 29884107 29882931 0.000000e+00 981.0
12 TraesCS7D01G189900 chrUn 81.679 1179 211 5 692 1867 29882697 29881521 0.000000e+00 976.0
13 TraesCS7D01G189900 chr3D 94.951 812 13 2 2302 3085 27867695 27866884 0.000000e+00 1247.0
14 TraesCS7D01G189900 chr3D 80.443 1355 244 15 577 1926 39121084 39119746 0.000000e+00 1014.0
15 TraesCS7D01G189900 chr2A 94.416 788 41 2 2300 3085 365855697 365856483 0.000000e+00 1208.0
16 TraesCS7D01G189900 chr5B 93.766 786 46 2 2302 3085 284751987 284751203 0.000000e+00 1177.0
17 TraesCS7D01G189900 chr5B 86.719 128 13 4 4 128 264290487 264290613 4.150000e-29 139.0
18 TraesCS7D01G189900 chr1A 93.758 785 42 2 2302 3085 193867987 193867209 0.000000e+00 1171.0
19 TraesCS7D01G189900 chr6A 93.280 744 44 3 2302 3040 597135437 597136179 0.000000e+00 1092.0
20 TraesCS7D01G189900 chr6A 87.209 86 8 3 275 358 162806729 162806645 9.110000e-16 95.3
21 TraesCS7D01G189900 chr3B 78.192 1770 322 36 577 2300 61916704 61914953 0.000000e+00 1072.0
22 TraesCS7D01G189900 chr3B 84.545 110 16 1 8 117 550318715 550318823 1.170000e-19 108.0
23 TraesCS7D01G189900 chr1B 92.713 741 51 3 2301 3040 643433606 643432868 0.000000e+00 1066.0
24 TraesCS7D01G189900 chr1B 84.694 98 8 4 269 359 483592032 483592129 1.180000e-14 91.6
25 TraesCS7D01G189900 chr1B 85.870 92 6 4 275 359 684284541 684284450 1.180000e-14 91.6
26 TraesCS7D01G189900 chr5D 86.719 128 13 4 4 128 239273701 239273575 4.150000e-29 139.0
27 TraesCS7D01G189900 chr4D 84.921 126 15 4 1 124 294346344 294346467 1.160000e-24 124.0
28 TraesCS7D01G189900 chr4D 85.000 120 14 3 11 129 65537836 65537720 5.400000e-23 119.0
29 TraesCS7D01G189900 chr4B 84.921 126 15 4 1 124 362144105 362144228 1.160000e-24 124.0
30 TraesCS7D01G189900 chr4A 82.114 123 18 3 8 129 530174612 530174731 5.440000e-18 102.0
31 TraesCS7D01G189900 chr4A 87.209 86 8 3 275 358 124403071 124403155 9.110000e-16 95.3
32 TraesCS7D01G189900 chr6B 84.694 98 8 4 269 359 184765279 184765376 1.180000e-14 91.6
33 TraesCS7D01G189900 chr3A 82.979 94 9 4 275 361 33428330 33428237 9.170000e-11 78.7


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 TraesCS7D01G189900 chr7D 143973689 143976773 3084 True 5698.0 5698 100.0000 1 3085 1 chr7D.!!$R1 3084
1 TraesCS7D01G189900 chr7D 152947009 152948881 1872 False 1685.0 1685 82.9890 423 2300 1 chr7D.!!$F2 1877
2 TraesCS7D01G189900 chr7D 68084507 68085293 786 False 1206.0 1206 94.4090 2302 3085 1 chr7D.!!$F1 783
3 TraesCS7D01G189900 chr7D 225914318 225915103 785 True 1206.0 1206 94.4090 2302 3085 1 chr7D.!!$R2 783
4 TraesCS7D01G189900 chr7D 571297758 571298487 729 False 1040.0 1040 92.4860 2302 3028 1 chr7D.!!$F4 726
5 TraesCS7D01G189900 chr7D 287064208 287064938 730 False 885.0 885 88.4670 2302 3038 1 chr7D.!!$F3 736
6 TraesCS7D01G189900 chr7B 107821037 107823338 2301 False 3507.0 3507 94.1940 1 2301 1 chr7B.!!$F1 2300
7 TraesCS7D01G189900 chr7B 114938575 114940446 1871 False 1628.0 1628 82.4460 413 2300 1 chr7B.!!$F2 1887
8 TraesCS7D01G189900 chr7A 146024428 146026744 2316 False 3066.0 3066 90.7020 1 2300 1 chr7A.!!$F1 2299
9 TraesCS7D01G189900 chrUn 29899621 29901514 1893 True 1609.0 1609 82.1050 412 2300 1 chrUn.!!$R1 1888
10 TraesCS7D01G189900 chrUn 29881521 29884107 2586 True 978.5 981 81.7215 692 1867 2 chrUn.!!$R2 1175
11 TraesCS7D01G189900 chr3D 27866884 27867695 811 True 1247.0 1247 94.9510 2302 3085 1 chr3D.!!$R1 783
12 TraesCS7D01G189900 chr3D 39119746 39121084 1338 True 1014.0 1014 80.4430 577 1926 1 chr3D.!!$R2 1349
13 TraesCS7D01G189900 chr2A 365855697 365856483 786 False 1208.0 1208 94.4160 2300 3085 1 chr2A.!!$F1 785
14 TraesCS7D01G189900 chr5B 284751203 284751987 784 True 1177.0 1177 93.7660 2302 3085 1 chr5B.!!$R1 783
15 TraesCS7D01G189900 chr1A 193867209 193867987 778 True 1171.0 1171 93.7580 2302 3085 1 chr1A.!!$R1 783
16 TraesCS7D01G189900 chr6A 597135437 597136179 742 False 1092.0 1092 93.2800 2302 3040 1 chr6A.!!$F1 738
17 TraesCS7D01G189900 chr3B 61914953 61916704 1751 True 1072.0 1072 78.1920 577 2300 1 chr3B.!!$R1 1723
18 TraesCS7D01G189900 chr1B 643432868 643433606 738 True 1066.0 1066 92.7130 2301 3040 1 chr1B.!!$R1 739

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
221 227 0.249868 TGAGCTTTGGTGTCTCGGTG 60.250 55.0 0.0 0.0 0.00 4.94 F
1059 1096 0.482446 TGAATCTGCCACCAGGGTTT 59.518 50.0 0.0 0.0 39.61 3.27 F
1739 3189 0.250338 AACAACAGGGCTTCCTCGAC 60.250 55.0 0.0 0.0 39.29 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1140 1177 0.178973 TCAAGTCCACCTCCTCGACA 60.179 55.000 0.00 0.0 0.00 4.35 R
2044 3530 1.000955 AGGTCACAACGTCCTCATGAC 59.999 52.381 0.00 0.0 40.81 3.06 R
2983 4556 1.604604 TTACAGGCCAGTTTCAGCAC 58.395 50.000 5.94 0.0 0.00 4.40 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
209 215 5.836347 GAGTTTTCTCCACATTTGAGCTTT 58.164 37.500 0.00 0.00 40.79 3.51
220 226 0.468226 TTGAGCTTTGGTGTCTCGGT 59.532 50.000 0.00 0.00 0.00 4.69
221 227 0.249868 TGAGCTTTGGTGTCTCGGTG 60.250 55.000 0.00 0.00 0.00 4.94
273 283 3.311596 GTGGACATTAGGATTACAACCGC 59.688 47.826 0.00 0.00 0.00 5.68
286 296 6.975772 GGATTACAACCGCTGCAATTATAAAA 59.024 34.615 0.00 0.00 0.00 1.52
292 302 7.815068 ACAACCGCTGCAATTATAAAATGTTTA 59.185 29.630 0.00 0.00 0.00 2.01
385 396 2.851263 ACACCGGTACATGACACATT 57.149 45.000 6.87 0.00 0.00 2.71
396 407 3.826157 ACATGACACATTGTAAAGTGGGG 59.174 43.478 0.00 0.00 39.99 4.96
402 413 4.526650 ACACATTGTAAAGTGGGGAAATCC 59.473 41.667 5.18 0.00 39.99 3.01
471 482 1.675552 AAACCAACCGACTTCACCTG 58.324 50.000 0.00 0.00 0.00 4.00
591 612 2.353323 CAACAGAGCAGAGCATAGCAA 58.647 47.619 0.00 0.00 0.00 3.91
724 746 0.676466 TGCCGCCCACAACAAGATAG 60.676 55.000 0.00 0.00 0.00 2.08
752 774 4.943705 CACACAGTTGTAAAGGATAGCCAT 59.056 41.667 0.00 0.00 33.30 4.40
1059 1096 0.482446 TGAATCTGCCACCAGGGTTT 59.518 50.000 0.00 0.00 39.61 3.27
1107 1144 0.613853 TCACCTTCTACCTGGTCCCG 60.614 60.000 0.63 0.00 33.75 5.14
1140 1177 2.413310 AAGTCTTCAACACCACGGTT 57.587 45.000 0.00 0.00 0.00 4.44
1250 1287 3.772025 CAGAAGGACCTCAAGTACTCCAT 59.228 47.826 0.00 0.00 39.50 3.41
1267 1304 3.199551 TCGGGATACGGACCAACG 58.800 61.111 0.00 0.00 44.45 4.10
1556 3004 6.877322 TCATGACTCATGAATATGCCTGTATG 59.123 38.462 17.80 0.00 46.17 2.39
1652 3100 7.824779 GTGGTTTGTAGAATCTTCCATAAGAGT 59.175 37.037 0.00 0.00 44.79 3.24
1739 3189 0.250338 AACAACAGGGCTTCCTCGAC 60.250 55.000 0.00 0.00 39.29 4.20
1768 3218 3.136077 ACATTGGATCCTCTCATGGACTG 59.864 47.826 14.23 0.00 39.17 3.51
1889 3339 2.684881 GGTGCTTCCGATGATGAACAAT 59.315 45.455 0.00 0.00 0.00 2.71
2044 3530 3.873361 AGCGTTTCATCATCCATAGTGTG 59.127 43.478 0.00 0.00 0.00 3.82
2143 3629 4.254039 TGATGAACATGGGAATGGATGT 57.746 40.909 0.00 0.00 34.16 3.06
2570 4087 3.197333 TGGATCCGATAACCCGTTAACAA 59.803 43.478 7.39 0.00 0.00 2.83
2732 4249 1.133199 TGGCCCATTCCTGTGAAAAGT 60.133 47.619 0.00 0.00 33.32 2.66
2855 4372 2.546789 CCGTTACGCCCTATCCAAATTC 59.453 50.000 0.00 0.00 0.00 2.17
2938 4456 4.481368 TGTATAGCCCATGACGTCTTTT 57.519 40.909 17.92 0.00 0.00 2.27
2987 4560 4.856801 CCATTAGCGGCCCGTGCT 62.857 66.667 4.45 8.74 46.29 4.40
2998 4571 2.281761 CCGTGCTGAAACTGGCCT 60.282 61.111 3.32 0.00 0.00 5.19
3062 4635 2.161609 GTGAAACTGGCCCGTAATGAAG 59.838 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 119 9.444600 TCACCAACAAAGATAAATACTACCTTC 57.555 33.333 0.00 0.00 0.00 3.46
118 120 9.975218 ATCACCAACAAAGATAAATACTACCTT 57.025 29.630 0.00 0.00 0.00 3.50
170 175 4.769345 AAACTCTCATCTCCTTCCATCC 57.231 45.455 0.00 0.00 0.00 3.51
220 226 1.872237 GCTATATTTCGGGCACTCGCA 60.872 52.381 0.00 0.00 41.24 5.10
221 227 0.790814 GCTATATTTCGGGCACTCGC 59.209 55.000 0.00 0.00 37.44 5.03
385 396 3.161866 GCTTGGATTTCCCCACTTTACA 58.838 45.455 0.00 0.00 35.62 2.41
396 407 2.165998 AGCCTCAGTTGCTTGGATTTC 58.834 47.619 0.00 0.00 34.87 2.17
430 441 7.393234 GGTTTACATATTCCAGCCTATGCATTA 59.607 37.037 3.54 0.00 41.13 1.90
591 612 4.750021 ATGTATCCATATGCGCTGATCT 57.250 40.909 9.73 0.00 0.00 2.75
627 648 6.734104 CCAAATTGAACACTTTTGGTTTGA 57.266 33.333 14.85 0.00 42.78 2.69
724 746 3.211045 TCCTTTACAACTGTGTGCTTCC 58.789 45.455 0.00 0.00 38.82 3.46
752 774 9.654919 TGAGCTAGCTAGATAGATAGAGATAGA 57.345 37.037 25.15 0.00 43.14 1.98
839 872 0.106769 TGGCAAGACACTTGCAGGAA 60.107 50.000 28.81 14.21 46.58 3.36
843 876 1.134250 TGTACTGGCAAGACACTTGCA 60.134 47.619 28.81 17.85 46.58 4.08
1140 1177 0.178973 TCAAGTCCACCTCCTCGACA 60.179 55.000 0.00 0.00 0.00 4.35
1250 1287 2.417257 CCGTTGGTCCGTATCCCGA 61.417 63.158 0.00 0.00 39.56 5.14
1514 2962 8.630917 TGAGTCATGAGTACTAATAGTTAAGGC 58.369 37.037 2.17 0.00 0.00 4.35
1652 3100 4.416516 TCATCACCTTCTTCAGTCCAGTA 58.583 43.478 0.00 0.00 0.00 2.74
1889 3339 3.325716 GGTAGTGGTTCCCAAAGTAGTGA 59.674 47.826 0.00 0.00 34.18 3.41
2044 3530 1.000955 AGGTCACAACGTCCTCATGAC 59.999 52.381 0.00 0.00 40.81 3.06
2122 3608 4.209538 GACATCCATTCCCATGTTCATCA 58.790 43.478 0.00 0.00 33.22 3.07
2143 3629 5.937975 TGATCATCAGTAGTTCCACATGA 57.062 39.130 0.00 0.00 0.00 3.07
2207 3695 5.662657 TCAACTGATCTTCTGGTGGATGATA 59.337 40.000 0.00 0.00 38.44 2.15
2468 3982 2.221981 CCTTGACGAAAGCACTTCTGTC 59.778 50.000 0.00 12.32 37.73 3.51
2732 4249 2.281208 CAAGTCAAACGGGCCGGA 60.281 61.111 31.78 15.46 0.00 5.14
2855 4372 2.279517 GATGACGCTACTGGGCCG 60.280 66.667 0.00 0.00 0.00 6.13
2983 4556 1.604604 TTACAGGCCAGTTTCAGCAC 58.395 50.000 5.94 0.00 0.00 4.40
2987 4560 3.826524 TGTTCATTACAGGCCAGTTTCA 58.173 40.909 5.94 0.00 31.68 2.69
3024 4597 2.826738 CCACGGGCCGTTAATGGG 60.827 66.667 32.12 23.39 38.32 4.00


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

AutoCloner maintained by Alex Coulton.