Multiple sequence alignment - TraesCS7D01G202200

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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 TraesCS7D01G202200 chr7D 100.000 2195 0 0 1 2195 160980513 160978319 0.000000e+00 4054.0
1 TraesCS7D01G202200 chr7D 87.013 231 24 3 967 1197 161040103 161039879 2.800000e-64 255.0
2 TraesCS7D01G202200 chr7D 85.714 203 23 4 993 1195 161057402 161057206 2.210000e-50 209.0
3 TraesCS7D01G202200 chr7B 93.427 1567 71 18 6 1543 123279336 123277773 0.000000e+00 2294.0
4 TraesCS7D01G202200 chr7B 91.244 651 49 6 1550 2195 434999943 434999296 0.000000e+00 880.0
5 TraesCS7D01G202200 chr7B 84.649 228 29 4 970 1197 123288285 123288064 2.840000e-54 222.0
6 TraesCS7D01G202200 chr7B 84.685 222 28 4 974 1195 123285064 123284849 1.320000e-52 217.0
7 TraesCS7D01G202200 chr7A 89.666 1229 82 20 4 1216 162409201 162408002 0.000000e+00 1524.0
8 TraesCS7D01G202200 chr7A 91.906 1112 55 19 450 1530 162400996 162399889 0.000000e+00 1522.0
9 TraesCS7D01G202200 chr7A 91.020 657 47 9 1549 2195 157418717 157418063 0.000000e+00 876.0
10 TraesCS7D01G202200 chr7A 89.677 310 20 7 4 309 162405419 162405118 3.420000e-103 385.0
11 TraesCS7D01G202200 chr7A 84.513 226 29 4 970 1195 162414357 162414138 3.670000e-53 219.0
12 TraesCS7D01G202200 chr7A 93.878 49 3 0 267 315 162407263 162407311 8.400000e-10 75.0
13 TraesCS7D01G202200 chr7A 100.000 34 0 0 1230 1263 162408003 162407970 1.820000e-06 63.9
14 TraesCS7D01G202200 chr7A 97.059 34 1 0 1230 1263 162405094 162405061 8.460000e-05 58.4
15 TraesCS7D01G202200 chr5D 92.226 656 37 6 1551 2195 93738607 93737955 0.000000e+00 917.0
16 TraesCS7D01G202200 chr3D 91.958 659 39 9 1549 2195 558703586 558704242 0.000000e+00 911.0
17 TraesCS7D01G202200 chr4A 91.463 656 44 6 1551 2195 731250711 731250057 0.000000e+00 891.0
18 TraesCS7D01G202200 chrUn 91.337 658 46 5 1549 2195 29278728 29279385 0.000000e+00 889.0
19 TraesCS7D01G202200 chr6D 91.159 656 48 6 1550 2195 472911154 472911809 0.000000e+00 881.0
20 TraesCS7D01G202200 chr1D 91.159 656 46 8 1551 2195 414348432 414349086 0.000000e+00 880.0
21 TraesCS7D01G202200 chr5B 90.909 660 48 7 1548 2195 595134543 595135202 0.000000e+00 876.0


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 TraesCS7D01G202200 chr7D 160978319 160980513 2194 True 4054.000 4054 100.0000 1 2195 1 chr7D.!!$R1 2194
1 TraesCS7D01G202200 chr7B 123277773 123279336 1563 True 2294.000 2294 93.4270 6 1543 1 chr7B.!!$R1 1537
2 TraesCS7D01G202200 chr7B 434999296 434999943 647 True 880.000 880 91.2440 1550 2195 1 chr7B.!!$R2 645
3 TraesCS7D01G202200 chr7B 123284849 123288285 3436 True 219.500 222 84.6670 970 1197 2 chr7B.!!$R3 227
4 TraesCS7D01G202200 chr7A 162399889 162400996 1107 True 1522.000 1522 91.9060 450 1530 1 chr7A.!!$R2 1080
5 TraesCS7D01G202200 chr7A 157418063 157418717 654 True 876.000 876 91.0200 1549 2195 1 chr7A.!!$R1 646
6 TraesCS7D01G202200 chr7A 162405061 162409201 4140 True 507.825 1524 94.1005 4 1263 4 chr7A.!!$R4 1259
7 TraesCS7D01G202200 chr5D 93737955 93738607 652 True 917.000 917 92.2260 1551 2195 1 chr5D.!!$R1 644
8 TraesCS7D01G202200 chr3D 558703586 558704242 656 False 911.000 911 91.9580 1549 2195 1 chr3D.!!$F1 646
9 TraesCS7D01G202200 chr4A 731250057 731250711 654 True 891.000 891 91.4630 1551 2195 1 chr4A.!!$R1 644
10 TraesCS7D01G202200 chrUn 29278728 29279385 657 False 889.000 889 91.3370 1549 2195 1 chrUn.!!$F1 646
11 TraesCS7D01G202200 chr6D 472911154 472911809 655 False 881.000 881 91.1590 1550 2195 1 chr6D.!!$F1 645
12 TraesCS7D01G202200 chr1D 414348432 414349086 654 False 880.000 880 91.1590 1551 2195 1 chr1D.!!$F1 644
13 TraesCS7D01G202200 chr5B 595134543 595135202 659 False 876.000 876 90.9090 1548 2195 1 chr5B.!!$F1 647

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
41 42 0.250295 TCAAACCAAGAGGCCTCACG 60.25 55.0 33.9 22.98 39.06 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 5069 0.533491 AAATGGCTGCATGCATCGTT 59.467 45.0 22.97 19.59 45.15 3.85 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
41 42 0.250295 TCAAACCAAGAGGCCTCACG 60.250 55.000 33.90 22.98 39.06 4.35
438 442 2.092646 CCGACCCTACAATCAAATCCCA 60.093 50.000 0.00 0.00 0.00 4.37
447 452 4.082125 ACAATCAAATCCCAGTTGGTCTC 58.918 43.478 0.00 0.00 34.77 3.36
686 711 1.061570 GCATGTGAAGCTAGTGCGC 59.938 57.895 0.00 0.00 45.42 6.09
823 848 7.722285 GGACTCTTCCGAGAAGCCTATATATAT 59.278 40.741 0.00 0.00 39.74 0.86
868 893 1.639722 GCCCCAAGTTAACCCACAAT 58.360 50.000 0.88 0.00 0.00 2.71
870 895 2.883026 CCCCAAGTTAACCCACAATCA 58.117 47.619 0.88 0.00 0.00 2.57
893 925 1.741706 GACTACCTGTGATCCGTCGAA 59.258 52.381 0.00 0.00 0.00 3.71
1027 4284 2.970639 CCTTCTTCGCCGTCTCCA 59.029 61.111 0.00 0.00 0.00 3.86
1214 4488 4.832248 TGACCTGTGTAATCTAGCCAAAG 58.168 43.478 0.00 0.00 0.00 2.77
1215 4489 4.530553 TGACCTGTGTAATCTAGCCAAAGA 59.469 41.667 0.00 0.00 0.00 2.52
1216 4490 5.012664 TGACCTGTGTAATCTAGCCAAAGAA 59.987 40.000 0.00 0.00 0.00 2.52
1279 4553 4.027050 GTCGTGCGCTTATAGAAACCTTAC 60.027 45.833 9.73 0.00 0.00 2.34
1479 4760 6.846350 ACAATTATTCTTTCTACTGTGCAGC 58.154 36.000 0.00 0.00 0.00 5.25
1544 5020 5.803020 ATAAAGTAGCTTTGTAGTGCAGC 57.197 39.130 0.00 0.00 35.21 5.25
1545 5021 1.714794 AGTAGCTTTGTAGTGCAGCG 58.285 50.000 0.00 0.00 0.00 5.18
1546 5022 0.721718 GTAGCTTTGTAGTGCAGCGG 59.278 55.000 0.00 0.00 0.00 5.52
1587 5069 3.473647 CCCGGCCTCTGCATCTGA 61.474 66.667 0.00 0.00 40.13 3.27
1720 6765 3.326006 TGATGAAGGGATGCTGATAGTCC 59.674 47.826 0.00 0.00 0.00 3.85
1754 7000 1.302033 CAGACCTCGCAGCCAAACT 60.302 57.895 0.00 0.00 0.00 2.66
1774 7020 5.283457 ACTTACCATCTAAGACATGAGGC 57.717 43.478 0.00 0.00 0.00 4.70
1966 7212 2.753043 GACCGCGTCACCCTCCTA 60.753 66.667 4.92 0.00 32.09 2.94
2035 7281 3.680786 CCGAGATCCGCCGCCATA 61.681 66.667 0.00 0.00 36.84 2.74
2148 7598 0.249699 AACAACACTCGCCGTCATCA 60.250 50.000 0.00 0.00 0.00 3.07
2169 7619 6.581388 TCAGATCATCCAATCTAGGGTTTT 57.419 37.500 0.00 0.00 34.21 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.393866 AGGCCTCTTGGTTTGATTTCTTTA 58.606 37.500 0.00 0.00 35.27 1.85
41 42 8.908786 TGGAGTGAATCAAGGTTATATTGATC 57.091 34.615 1.96 0.00 44.57 2.92
382 385 3.646611 TCGATCGTGTGTTTTGGTCTA 57.353 42.857 15.94 0.00 0.00 2.59
385 388 3.806316 GATTCGATCGTGTGTTTTGGT 57.194 42.857 15.94 0.00 0.00 3.67
686 711 7.228308 GGATTTCAGTCAGGAATGATTCTAAGG 59.772 40.741 5.03 0.00 35.22 2.69
823 848 4.097286 TGTGTATATGAACGCAGCTGTAGA 59.903 41.667 16.64 0.00 35.05 2.59
868 893 2.100197 CGGATCACAGGTAGTCCTTGA 58.900 52.381 0.00 0.00 43.07 3.02
870 895 2.100989 GACGGATCACAGGTAGTCCTT 58.899 52.381 0.00 0.00 43.07 3.36
893 925 1.669265 TCGACGTACTGCTCGATCAAT 59.331 47.619 0.00 0.00 34.04 2.57
1096 4353 1.302752 GGAGCTGCACCATCACACA 60.303 57.895 11.41 0.00 0.00 3.72
1188 4445 2.483889 GCTAGATTACACAGGTCAGGGC 60.484 54.545 0.00 0.00 0.00 5.19
1214 4488 2.325393 ATCTCCCCGCACCCGAATTC 62.325 60.000 0.00 0.00 36.29 2.17
1215 4489 2.325393 GATCTCCCCGCACCCGAATT 62.325 60.000 0.00 0.00 36.29 2.17
1216 4490 2.768344 ATCTCCCCGCACCCGAAT 60.768 61.111 0.00 0.00 36.29 3.34
1279 4553 2.559840 CTGAAAGGCAGCACGCAG 59.440 61.111 0.00 0.00 45.17 5.18
1338 4612 3.841643 ACTTCGACCATTAACTACGTGG 58.158 45.455 0.00 0.00 38.96 4.94
1501 4876 8.612486 TTTATAATATAATGAGCCGTCCCCTA 57.388 34.615 0.00 0.00 0.00 3.53
1587 5069 0.533491 AAATGGCTGCATGCATCGTT 59.467 45.000 22.97 19.59 45.15 3.85
1655 6386 5.409826 CAGATGTTTCCTAGACTGTGGTTTC 59.590 44.000 0.00 0.00 0.00 2.78
1663 6394 3.093057 AGCGACAGATGTTTCCTAGACT 58.907 45.455 0.00 0.00 0.00 3.24
1720 6765 2.285977 GTCTGTTTGGTATTAGGCCCG 58.714 52.381 0.00 0.00 0.00 6.13
1754 7000 3.391296 GGGCCTCATGTCTTAGATGGTAA 59.609 47.826 0.84 0.00 0.00 2.85
1928 7174 4.771356 CGTCGTGGTGGCGTCGAT 62.771 66.667 0.00 0.00 43.57 3.59
1966 7212 2.419198 GCGGAGATGGACTCGCAT 59.581 61.111 0.00 0.00 45.76 4.73
2035 7281 3.005554 CGGTGCTTCATCTCACTCATTT 58.994 45.455 0.00 0.00 33.91 2.32
2128 7563 0.865769 GATGACGGCGAGTGTTGTTT 59.134 50.000 16.62 0.00 0.00 2.83
2148 7598 5.163045 GGGAAAACCCTAGATTGGATGATCT 60.163 44.000 0.00 0.00 39.59 2.75
2169 7619 2.279073 CTCTGCTACCTCCGGGGA 59.721 66.667 0.37 0.00 38.76 4.81


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

AutoCloner maintained by Alex Coulton.