Multiple sequence alignment - TraesCS7D01G025100

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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 TraesCS7D01G025100 chr7D 100.000 2681 0 0 1 2681 11707298 11704618 0.000000e+00 4951.0
1 TraesCS7D01G025100 chr7D 81.967 366 33 16 2054 2390 11693584 11693223 2.030000e-71 279.0
2 TraesCS7D01G025100 chr7D 81.250 384 39 16 2036 2390 23654124 23654503 2.030000e-71 279.0
3 TraesCS7D01G025100 chr7D 79.767 257 26 12 2045 2276 49175592 49175337 2.140000e-36 163.0
4 TraesCS7D01G025100 chr7D 80.455 220 36 6 2184 2396 11927434 11927215 7.680000e-36 161.0
5 TraesCS7D01G025100 chr7A 93.459 1544 73 12 1 1528 11313198 11311667 0.000000e+00 2266.0
6 TraesCS7D01G025100 chr7A 96.731 1132 28 7 1557 2681 11311147 11310018 0.000000e+00 1877.0
7 TraesCS7D01G025100 chr7A 82.078 385 35 16 2036 2390 11228646 11228266 5.610000e-77 298.0
8 TraesCS7D01G025100 chr7A 83.172 309 27 14 1568 1870 11229231 11228942 2.650000e-65 259.0
9 TraesCS7D01G025100 chr7A 82.410 307 30 10 1557 1858 11345226 11344939 2.060000e-61 246.0
10 TraesCS7D01G025100 chr4A 96.633 594 17 1 966 1559 726072940 726073530 0.000000e+00 983.0
11 TraesCS7D01G025100 chr4A 94.194 620 24 4 1 609 726072220 726072838 0.000000e+00 935.0
12 TraesCS7D01G025100 chr4A 93.451 565 18 6 1557 2113 726074029 726074582 0.000000e+00 821.0
13 TraesCS7D01G025100 chr4A 82.372 312 31 11 1557 1863 726064786 726065078 1.590000e-62 250.0
14 TraesCS7D01G025100 chr4A 95.238 105 5 0 830 934 726072837 726072941 1.650000e-37 167.0
15 TraesCS7D01G025100 chr4A 86.897 145 16 3 1559 1700 725865242 725865386 2.760000e-35 159.0
16 TraesCS7D01G025100 chr4A 78.095 210 29 7 1555 1754 726108651 726108853 1.690000e-22 117.0
17 TraesCS7D01G025100 chr4A 88.608 79 9 0 711 789 143447458 143447536 2.200000e-16 97.1
18 TraesCS7D01G025100 chr4A 84.810 79 12 0 711 789 588511811 588511889 2.210000e-11 80.5
19 TraesCS7D01G025100 chr7B 80.882 340 51 12 1008 1344 750116613 750116285 3.430000e-64 255.0
20 TraesCS7D01G025100 chr7B 84.706 170 20 3 1559 1725 750115536 750115370 5.940000e-37 165.0
21 TraesCS7D01G025100 chrUn 80.632 253 28 7 2045 2277 333781044 333780793 2.740000e-40 176.0
22 TraesCS7D01G025100 chr3A 89.362 141 11 3 1568 1704 731843211 731843071 9.870000e-40 174.0
23 TraesCS7D01G025100 chr3A 85.816 141 16 3 1568 1704 731893271 731893131 2.150000e-31 147.0
24 TraesCS7D01G025100 chr3D 87.234 141 14 3 1568 1704 602260454 602260314 9.940000e-35 158.0
25 TraesCS7D01G025100 chr4B 74.839 310 59 16 418 719 78034250 78033952 3.620000e-24 122.0
26 TraesCS7D01G025100 chr4D 74.367 316 66 11 411 719 222935044 222934737 1.300000e-23 121.0
27 TraesCS7D01G025100 chr3B 77.957 186 28 9 615 789 757867810 757867627 1.310000e-18 104.0
28 TraesCS7D01G025100 chr1D 91.026 78 6 1 719 795 459832847 459832770 1.310000e-18 104.0
29 TraesCS7D01G025100 chr1D 91.549 71 6 0 719 789 103741277 103741207 6.110000e-17 99.0
30 TraesCS7D01G025100 chr5B 88.608 79 9 0 711 789 61558896 61558974 2.200000e-16 97.1
31 TraesCS7D01G025100 chr6B 88.732 71 8 0 719 789 378205017 378205087 1.320000e-13 87.9
32 TraesCS7D01G025100 chr1A 84.810 79 12 0 711 789 384069351 384069273 2.210000e-11 80.5


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 TraesCS7D01G025100 chr7D 11704618 11707298 2680 True 4951.0 4951 100.000 1 2681 1 chr7D.!!$R2 2680
1 TraesCS7D01G025100 chr7A 11310018 11313198 3180 True 2071.5 2266 95.095 1 2681 2 chr7A.!!$R3 2680
2 TraesCS7D01G025100 chr7A 11228266 11229231 965 True 278.5 298 82.625 1568 2390 2 chr7A.!!$R2 822
3 TraesCS7D01G025100 chr4A 726072220 726074582 2362 False 726.5 983 94.879 1 2113 4 chr4A.!!$F6 2112
4 TraesCS7D01G025100 chr7B 750115370 750116613 1243 True 210.0 255 82.794 1008 1725 2 chr7B.!!$R1 717

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
148 150 1.343142 CACCAAAGGCCAAACTAACCC 59.657 52.381 5.01 0.0 0.0 4.11 F
1279 1303 0.820226 CGACTTCTCCTGCTCATCCA 59.180 55.000 0.00 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1536 1.000993 GAGGAGGTCCAGCTGAGGA 59.999 63.158 17.39 0.86 38.89 3.71 R
2451 3209 4.891992 TCATAATACCCTTGCTAGCCTC 57.108 45.455 13.29 0.00 0.00 4.70 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
23 24 1.922545 GATTTCCCGGTAGTCGTTTCG 59.077 52.381 0.00 0.00 37.11 3.46
148 150 1.343142 CACCAAAGGCCAAACTAACCC 59.657 52.381 5.01 0.00 0.00 4.11
180 182 2.431057 ACTTCGACAACACTCTCACCTT 59.569 45.455 0.00 0.00 0.00 3.50
200 202 5.359860 ACCTTGACGATGACATGTACTGATA 59.640 40.000 0.00 0.00 0.00 2.15
424 428 2.939261 CGGGCCGGCCTATCGTAAT 61.939 63.158 42.70 0.00 36.10 1.89
488 492 2.986979 TCGTGTCGTGCTGGCCTA 60.987 61.111 3.32 0.00 0.00 3.93
521 525 3.494254 AACCCAGGCACGACCCAA 61.494 61.111 0.00 0.00 40.58 4.12
539 543 4.545706 CTGCTAATCGGGCCGGCA 62.546 66.667 30.85 25.00 0.00 5.69
541 545 4.849310 GCTAATCGGGCCGGCACA 62.849 66.667 31.47 16.83 0.00 4.57
701 713 2.352422 CCTAGCAGCCCAAGCACA 59.648 61.111 0.00 0.00 43.56 4.57
778 790 4.047125 CTGGTTGGCCCGGTCCAT 62.047 66.667 4.33 0.00 35.77 3.41
796 808 3.633525 TCCATTTAGCCAGCTTTGCATAG 59.366 43.478 7.67 0.00 0.00 2.23
818 830 1.351017 CTTGAACCCTAGGCAGTTCCA 59.649 52.381 21.41 13.51 41.36 3.53
913 925 4.742201 ACGCAGCAGTCGCCGATT 62.742 61.111 0.00 0.00 39.83 3.34
914 926 4.214383 CGCAGCAGTCGCCGATTG 62.214 66.667 5.12 5.12 39.83 2.67
934 952 4.220693 TGTGAGAGAGAGAGAAGAGAGG 57.779 50.000 0.00 0.00 0.00 3.69
970 988 2.874457 GCCACGCCTTTCCTTTAGAAGA 60.874 50.000 0.00 0.00 35.40 2.87
1071 1089 0.984230 AAATCTTCCTCCGCCTCACA 59.016 50.000 0.00 0.00 0.00 3.58
1279 1303 0.820226 CGACTTCTCCTGCTCATCCA 59.180 55.000 0.00 0.00 0.00 3.41
1484 1556 1.612395 CCTCAGCTGGACCTCCTCAC 61.612 65.000 15.13 0.00 36.82 3.51
1506 1578 2.273776 GAGGCCTTCCTTGCTCCC 59.726 66.667 6.77 0.00 44.46 4.30
1522 1597 2.507944 CCGGCCAGAATGAGGAGG 59.492 66.667 2.24 0.00 39.69 4.30
1523 1598 2.507944 CGGCCAGAATGAGGAGGG 59.492 66.667 2.24 0.00 39.69 4.30
1572 2151 3.066380 GGCGCAATTTGGATGTTTTTCT 58.934 40.909 10.83 0.00 0.00 2.52
1622 2201 1.877637 TTCGCTGAGCTTAGCAAACA 58.122 45.000 27.73 7.69 43.87 2.83
1632 2214 3.072476 AGCTTAGCAAACACTTACCTGGA 59.928 43.478 7.07 0.00 0.00 3.86
1903 2486 7.900782 TTAATACTAACCTTGTCTGCAGTTC 57.099 36.000 14.67 9.03 0.00 3.01
1928 2511 7.335924 TCAATACTAACCTCTGTACCAAAATGC 59.664 37.037 0.00 0.00 0.00 3.56
2093 2823 2.687935 ACAACCACTGGCTGTTTACAAG 59.312 45.455 0.00 0.00 25.98 3.16
2097 2827 2.487265 CCACTGGCTGTTTACAAGACCT 60.487 50.000 0.00 0.00 0.00 3.85
2127 2857 6.615726 ATCTCTAAAAGAATAGGTGTGCCCTA 59.384 38.462 0.00 0.00 42.15 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 150 4.905866 GTGTTGTCGAAGTCATCACATTTG 59.094 41.667 9.59 0.00 42.62 2.32
180 182 5.828299 TGTATCAGTACATGTCATCGTCA 57.172 39.130 0.00 0.00 35.94 4.35
283 287 6.389869 TCATGTAGAAAGGGGGAATACTTGAT 59.610 38.462 0.00 0.00 30.27 2.57
290 294 7.898636 TGTTTAAATCATGTAGAAAGGGGGAAT 59.101 33.333 0.00 0.00 0.00 3.01
293 297 7.660030 ATGTTTAAATCATGTAGAAAGGGGG 57.340 36.000 0.00 0.00 0.00 5.40
446 450 3.681594 CGTATAATAATCATGCCCCGGCT 60.682 47.826 7.35 0.00 42.51 5.52
488 492 1.961277 GTTGCAGGCTGTAGCACGT 60.961 57.895 17.16 0.00 44.36 4.49
521 525 4.547367 GCCGGCCCGATTAGCAGT 62.547 66.667 18.11 0.00 0.00 4.40
642 654 6.225318 CACAACACATCCCAATCATCTTTTT 58.775 36.000 0.00 0.00 0.00 1.94
643 655 5.786311 CACAACACATCCCAATCATCTTTT 58.214 37.500 0.00 0.00 0.00 2.27
650 662 0.171007 CGGCACAACACATCCCAATC 59.829 55.000 0.00 0.00 0.00 2.67
652 664 1.900981 CCGGCACAACACATCCCAA 60.901 57.895 0.00 0.00 0.00 4.12
682 694 4.783621 TGCTTGGGCTGCTAGGCG 62.784 66.667 0.00 0.00 42.43 5.52
778 790 1.750778 GCCTATGCAAAGCTGGCTAAA 59.249 47.619 11.44 0.00 37.24 1.85
796 808 0.038310 AACTGCCTAGGGTTCAAGCC 59.962 55.000 11.72 0.00 35.59 4.35
913 925 3.054434 CCCTCTCTTCTCTCTCTCTCACA 60.054 52.174 0.00 0.00 0.00 3.58
914 926 3.054361 ACCCTCTCTTCTCTCTCTCTCAC 60.054 52.174 0.00 0.00 0.00 3.51
934 952 1.016653 GTGGCGCTTCTCTTCTCACC 61.017 60.000 7.64 0.00 0.00 4.02
970 988 1.076014 GGTGGGGATTCGGTTTGGT 59.924 57.895 0.00 0.00 0.00 3.67
1279 1303 4.124126 GGGGGTGGAGGGGAGGAT 62.124 72.222 0.00 0.00 0.00 3.24
1356 1380 4.400529 AAATTGGCGGTCTTCTTTGTTT 57.599 36.364 0.00 0.00 0.00 2.83
1357 1381 4.119136 CAAAATTGGCGGTCTTCTTTGTT 58.881 39.130 0.00 0.00 0.00 2.83
1438 1510 1.673033 CGCTTTCAGGTCGTCTGGAAT 60.673 52.381 8.24 0.00 40.04 3.01
1464 1536 1.000993 GAGGAGGTCCAGCTGAGGA 59.999 63.158 17.39 0.86 38.89 3.71
1506 1578 2.507944 CCCTCCTCATTCTGGCCG 59.492 66.667 0.00 0.00 0.00 6.13
1572 2151 1.225855 GCAATGTCTTGACGTCCACA 58.774 50.000 14.12 13.33 34.04 4.17
1622 2201 4.278669 CAGCATATAGTCGTCCAGGTAAGT 59.721 45.833 0.00 0.00 0.00 2.24
1903 2486 7.120579 TGCATTTTGGTACAGAGGTTAGTATTG 59.879 37.037 0.00 0.00 42.39 1.90
2093 2823 9.674068 ACCTATTCTTTTAGAGATTCAAAGGTC 57.326 33.333 0.00 0.00 33.49 3.85
2097 2827 8.730680 GCACACCTATTCTTTTAGAGATTCAAA 58.269 33.333 0.00 0.00 33.49 2.69
2451 3209 4.891992 TCATAATACCCTTGCTAGCCTC 57.108 45.455 13.29 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.