Multiple sequence alignment - TraesCS4D01G162200

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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 TraesCS4D01G162200 chr4D 100.000 2543 0 0 1 2543 245647878 245650420 0 4697
1 TraesCS4D01G162200 chr4D 96.045 986 36 3 1 985 372484964 372485947 0 1602
2 TraesCS4D01G162200 chr4D 95.842 986 40 1 1 985 333191653 333192638 0 1592
3 TraesCS4D01G162200 chr4D 95.833 984 39 2 3 985 292012247 292011265 0 1589
4 TraesCS4D01G162200 chr4D 95.736 985 41 1 2 985 234347596 234346612 0 1585
5 TraesCS4D01G162200 chr2D 96.795 1560 41 3 986 2543 630270473 630272025 0 2595
6 TraesCS4D01G162200 chr2D 96.733 1561 41 4 986 2543 33933996 33935549 0 2591
7 TraesCS4D01G162200 chr3B 96.339 1557 55 2 989 2543 201560591 201559035 0 2558
8 TraesCS4D01G162200 chr3A 96.337 1556 54 3 989 2543 672878249 672876696 0 2555
9 TraesCS4D01G162200 chr1B 95.951 1556 61 2 989 2543 633728681 633727127 0 2523
10 TraesCS4D01G162200 chr5D 95.379 1558 66 6 989 2543 432292535 432290981 0 2473
11 TraesCS4D01G162200 chr5B 95.385 1560 57 4 986 2543 432876904 432878450 0 2468
12 TraesCS4D01G162200 chr5B 96.277 1155 39 3 1393 2543 413608022 413609176 0 1892
13 TraesCS4D01G162200 chr4A 94.808 1560 79 2 986 2543 310762586 310764145 0 2431
14 TraesCS4D01G162200 chr5A 96.528 1008 33 2 1114 2119 442270687 442271694 0 1666
15 TraesCS4D01G162200 chr7D 95.943 986 39 1 1 985 361022842 361023827 0 1598
16 TraesCS4D01G162200 chr1D 95.854 989 38 3 1 987 387561911 387560924 0 1596
17 TraesCS4D01G162200 chr1D 95.838 985 40 1 1 985 392395488 392394505 0 1591
18 TraesCS4D01G162200 chr1D 95.736 985 41 1 2 985 192523214 192522230 0 1585
19 TraesCS4D01G162200 chr6D 95.732 984 41 1 2 985 367820344 367821326 0 1583
20 TraesCS4D01G162200 chr1A 92.814 835 51 5 986 1816 371831594 371832423 0 1201


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 TraesCS4D01G162200 chr4D 245647878 245650420 2542 False 4697 4697 100.000 1 2543 1 chr4D.!!$F1 2542
1 TraesCS4D01G162200 chr4D 372484964 372485947 983 False 1602 1602 96.045 1 985 1 chr4D.!!$F3 984
2 TraesCS4D01G162200 chr4D 333191653 333192638 985 False 1592 1592 95.842 1 985 1 chr4D.!!$F2 984
3 TraesCS4D01G162200 chr4D 292011265 292012247 982 True 1589 1589 95.833 3 985 1 chr4D.!!$R2 982
4 TraesCS4D01G162200 chr4D 234346612 234347596 984 True 1585 1585 95.736 2 985 1 chr4D.!!$R1 983
5 TraesCS4D01G162200 chr2D 630270473 630272025 1552 False 2595 2595 96.795 986 2543 1 chr2D.!!$F2 1557
6 TraesCS4D01G162200 chr2D 33933996 33935549 1553 False 2591 2591 96.733 986 2543 1 chr2D.!!$F1 1557
7 TraesCS4D01G162200 chr3B 201559035 201560591 1556 True 2558 2558 96.339 989 2543 1 chr3B.!!$R1 1554
8 TraesCS4D01G162200 chr3A 672876696 672878249 1553 True 2555 2555 96.337 989 2543 1 chr3A.!!$R1 1554
9 TraesCS4D01G162200 chr1B 633727127 633728681 1554 True 2523 2523 95.951 989 2543 1 chr1B.!!$R1 1554
10 TraesCS4D01G162200 chr5D 432290981 432292535 1554 True 2473 2473 95.379 989 2543 1 chr5D.!!$R1 1554
11 TraesCS4D01G162200 chr5B 432876904 432878450 1546 False 2468 2468 95.385 986 2543 1 chr5B.!!$F2 1557
12 TraesCS4D01G162200 chr5B 413608022 413609176 1154 False 1892 1892 96.277 1393 2543 1 chr5B.!!$F1 1150
13 TraesCS4D01G162200 chr4A 310762586 310764145 1559 False 2431 2431 94.808 986 2543 1 chr4A.!!$F1 1557
14 TraesCS4D01G162200 chr5A 442270687 442271694 1007 False 1666 1666 96.528 1114 2119 1 chr5A.!!$F1 1005
15 TraesCS4D01G162200 chr7D 361022842 361023827 985 False 1598 1598 95.943 1 985 1 chr7D.!!$F1 984
16 TraesCS4D01G162200 chr1D 387560924 387561911 987 True 1596 1596 95.854 1 987 1 chr1D.!!$R2 986
17 TraesCS4D01G162200 chr1D 392394505 392395488 983 True 1591 1591 95.838 1 985 1 chr1D.!!$R3 984
18 TraesCS4D01G162200 chr1D 192522230 192523214 984 True 1585 1585 95.736 2 985 1 chr1D.!!$R1 983
19 TraesCS4D01G162200 chr6D 367820344 367821326 982 False 1583 1583 95.732 2 985 1 chr6D.!!$F1 983
20 TraesCS4D01G162200 chr1A 371831594 371832423 829 False 1201 1201 92.814 986 1816 1 chr1A.!!$F1 830

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
125 128 0.240945 AAAGGAAAATGTGCCGAGCG 59.759 50.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 1912 1.138859 GGCAGAATAAATGGGGTTGGC 59.861 52.381 0.0 0.0 0.0 4.52 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
125 128 0.240945 AAAGGAAAATGTGCCGAGCG 59.759 50.000 0.00 0.00 0.00 5.03
182 186 1.074775 ATGACCCGTGTGCAACCAT 59.925 52.632 0.00 0.00 34.36 3.55
231 235 7.123997 TGCATATCTGTCATTTTGGGTATGTTT 59.876 33.333 0.00 0.00 0.00 2.83
390 394 3.081061 GCACTGTTCATATGGACACCAA 58.919 45.455 13.10 0.00 36.95 3.67
398 402 3.716353 TCATATGGACACCAATAGCAGGT 59.284 43.478 2.13 0.00 40.85 4.00
453 457 9.023962 ACCATTGATTACATACAACAAGTCATT 57.976 29.630 0.00 0.00 0.00 2.57
538 542 9.490663 CTAGTAAAGTTTTTCTCACACAACAAG 57.509 33.333 0.00 0.00 0.00 3.16
644 648 1.661341 GGCCAGCTACTGTCAATCTG 58.339 55.000 0.00 0.00 0.00 2.90
747 751 7.434492 CAATGTCCGAGGTATAGATACAGTTT 58.566 38.462 2.28 0.00 34.98 2.66
754 758 7.292292 CGAGGTATAGATACAGTTTCTTCTCG 58.708 42.308 14.54 14.54 34.98 4.04
776 780 8.522003 TCTCGTAAATGGTAGTAACATTGTGTA 58.478 33.333 14.15 0.81 38.47 2.90
819 823 4.955450 TCCACCATCATTGGATAGTTTTGG 59.045 41.667 0.00 0.00 46.92 3.28
840 844 2.894902 CTAAGGAAGAGCGAGTTTCCC 58.105 52.381 8.17 0.00 43.12 3.97
914 918 0.399949 TCCATCCCGAATACCCTGCT 60.400 55.000 0.00 0.00 0.00 4.24
927 931 0.469917 CCCTGCTACGGATGTTGGAT 59.530 55.000 0.00 0.00 0.00 3.41
987 991 5.945784 TGCTTCCTTAGTAACATCAGCAATT 59.054 36.000 0.00 0.00 33.18 2.32
1040 1046 3.374058 GGGTTCATGAGTTATGGTCAACG 59.626 47.826 0.00 0.00 37.39 4.10
1072 1078 3.765511 TGCTACAAGGTACGTAGGTCAAT 59.234 43.478 0.00 0.00 37.42 2.57
1075 1081 4.184079 ACAAGGTACGTAGGTCAATGTC 57.816 45.455 0.00 0.00 0.00 3.06
1109 1115 5.413213 CCTTATCCCACACAAATCGTTTACA 59.587 40.000 0.00 0.00 0.00 2.41
1188 1194 6.253512 GGCGAATCCACTTTGAATTTGATAAC 59.746 38.462 0.00 0.00 34.01 1.89
1237 1243 6.548251 TCACGTATGTCTGATAGATTTACCCA 59.452 38.462 0.00 0.00 0.00 4.51
1369 1375 7.275888 ACAAGCTGTTTATCAATGACTGAAA 57.724 32.000 0.00 0.00 37.67 2.69
1429 1435 9.979578 TGAATTACAATCAAATTGCTGTAAGTT 57.020 25.926 18.41 14.31 43.98 2.66
1474 1480 8.519526 TGGGAGATTACACAATACAAACAATTC 58.480 33.333 0.00 0.00 0.00 2.17
1822 1840 5.375354 TCCATAATGGATTTACCTGGACCAT 59.625 40.000 0.00 4.68 42.67 3.55
1891 1912 5.774184 GGGGGTCTAGGAGTAGTATTACTTG 59.226 48.000 0.85 0.00 40.21 3.16
2114 2138 2.557317 TGGGTTCACTTCACTCGTTTC 58.443 47.619 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 59 4.456566 GCATCCGGGTGTTCTAACTAAAAA 59.543 41.667 17.87 0.00 0.00 1.94
108 111 1.003839 TCGCTCGGCACATTTTCCT 60.004 52.632 0.00 0.00 0.00 3.36
125 128 3.064545 CGTTGAAGGGATGCAGAAATCTC 59.935 47.826 0.00 0.00 0.00 2.75
182 186 6.926272 GCAAATCTTACCCAATTGTTTGTACA 59.074 34.615 4.43 0.00 0.00 2.90
231 235 8.690203 TCAATCTTTCTAGTTTGACAAATGGA 57.310 30.769 3.49 0.75 35.95 3.41
390 394 2.840038 TCCATCAACTCACACCTGCTAT 59.160 45.455 0.00 0.00 0.00 2.97
398 402 3.197265 CATATGCGTCCATCAACTCACA 58.803 45.455 0.00 0.00 32.85 3.58
453 457 0.319211 CTCGTTGTCGTTGTGGGCTA 60.319 55.000 0.00 0.00 38.33 3.93
538 542 6.855914 TGAAGTTCATTTCATCGCTTTGTTAC 59.144 34.615 0.08 0.00 32.39 2.50
644 648 1.374758 CAGTCCTGCGTTGGTCTCC 60.375 63.158 0.00 0.00 0.00 3.71
747 751 8.308931 ACAATGTTACTACCATTTACGAGAAGA 58.691 33.333 0.00 0.00 30.28 2.87
776 780 2.042831 GGCGATCCAGCTGCTGTTT 61.043 57.895 26.41 14.27 37.29 2.83
819 823 2.272678 GGAAACTCGCTCTTCCTTAGC 58.727 52.381 2.93 0.00 38.48 3.09
927 931 1.001764 TCGCACTCTCCGGACCTAA 60.002 57.895 0.00 0.00 0.00 2.69
987 991 7.893302 ACCACAGGGAACATATTCATTCTAAAA 59.107 33.333 0.00 0.00 36.46 1.52
1040 1046 4.030977 CGTACCTTGTAGCACGTATTGTTC 59.969 45.833 0.00 0.00 0.00 3.18
1063 1069 7.349412 AGGTAGTTATGAGACATTGACCTAC 57.651 40.000 0.00 0.00 33.05 3.18
1072 1078 6.097839 GTGTGGGATAAGGTAGTTATGAGACA 59.902 42.308 0.00 0.00 30.93 3.41
1075 1081 6.479972 TGTGTGGGATAAGGTAGTTATGAG 57.520 41.667 0.00 0.00 30.93 2.90
1188 1194 6.486253 ACACATACTTCACAAGCAATACAG 57.514 37.500 0.00 0.00 0.00 2.74
1237 1243 6.497954 TCCTTTTCAAATCTCCAATCCACAAT 59.502 34.615 0.00 0.00 0.00 2.71
1323 1329 5.650266 TGTTGGACAGTACTCAACACAATTT 59.350 36.000 19.33 0.00 43.65 1.82
1423 1429 4.612264 TGGAGAGTGGTAACCAACTTAC 57.388 45.455 0.00 0.00 34.18 2.34
1429 1435 3.458118 CCCATTATGGAGAGTGGTAACCA 59.542 47.826 13.63 0.00 40.96 3.67
1464 1470 4.513692 TCAGACGAATTCCGAATTGTTTGT 59.486 37.500 11.15 4.59 41.76 2.83
1474 1480 9.047871 GTTTATTTTACTTTCAGACGAATTCCG 57.952 33.333 0.00 0.00 45.44 4.30
1822 1840 9.288576 CCCAAATAGCATAAGAATCTCATGTAA 57.711 33.333 0.00 0.00 0.00 2.41
1891 1912 1.138859 GGCAGAATAAATGGGGTTGGC 59.861 52.381 0.00 0.00 0.00 4.52
1958 1981 8.665685 CGACAGCTACAAAGTAGGAATTTAATT 58.334 33.333 6.34 0.00 0.00 1.40
2088 2112 2.569404 GAGTGAAGTGAACCCATCTCCT 59.431 50.000 0.00 0.00 0.00 3.69
2146 2170 1.382522 TACCACGACGTATCTGGGAC 58.617 55.000 0.00 0.00 31.15 4.46
2321 2345 1.737793 AGTTTTCTTATTGCCGAGCCG 59.262 47.619 0.00 0.00 0.00 5.52
2409 2433 5.647658 TGTTGGCAGTAGATGGATTTTACTG 59.352 40.000 6.53 6.53 44.39 2.74


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

AutoCloner maintained by Alex Coulton.