Multiple sequence alignment - TraesCS7D01G215400

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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 TraesCS7D01G215400 chr7D 100.000 2535 0 0 1 2535 175442496 175445030 0.000000e+00 4682.0
1 TraesCS7D01G215400 chr7D 87.739 783 82 8 1746 2522 466461627 466462401 0.000000e+00 902.0
2 TraesCS7D01G215400 chr2A 91.358 1377 91 14 366 1717 512441583 512442956 0.000000e+00 1858.0
3 TraesCS7D01G215400 chr2A 86.765 544 64 6 1 537 164870355 164870897 1.300000e-167 599.0
4 TraesCS7D01G215400 chr2D 90.807 1338 83 14 210 1530 378165393 378166707 0.000000e+00 1753.0
5 TraesCS7D01G215400 chr2D 85.900 539 67 7 1 538 529001052 529000522 1.320000e-157 566.0
6 TraesCS7D01G215400 chr2D 92.746 193 12 1 1527 1717 378170908 378171100 6.910000e-71 278.0
7 TraesCS7D01G215400 chr2D 100.000 31 0 0 1720 1750 266502121 266502091 9.800000e-05 58.4
8 TraesCS7D01G215400 chr7B 89.982 1138 90 11 1414 2535 140815811 140816940 0.000000e+00 1448.0
9 TraesCS7D01G215400 chr4D 88.471 798 77 7 1746 2535 399897855 399897065 0.000000e+00 950.0
10 TraesCS7D01G215400 chr4D 100.000 31 0 0 1720 1750 221283382 221283412 9.800000e-05 58.4
11 TraesCS7D01G215400 chr5B 87.833 789 83 10 1748 2533 702563949 702563171 0.000000e+00 913.0
12 TraesCS7D01G215400 chr5B 100.000 31 0 0 1720 1750 159001923 159001893 9.800000e-05 58.4
13 TraesCS7D01G215400 chr3B 87.753 792 82 10 1746 2533 345173360 345174140 0.000000e+00 911.0
14 TraesCS7D01G215400 chr3B 87.384 539 60 5 1 537 794590002 794589470 1.670000e-171 612.0
15 TraesCS7D01G215400 chr3B 85.397 541 70 6 1 539 707042147 707041614 1.020000e-153 553.0
16 TraesCS7D01G215400 chr3B 79.231 650 81 23 1080 1696 738757580 738756952 1.090000e-108 403.0
17 TraesCS7D01G215400 chr3B 81.690 497 79 7 1049 1538 738910767 738910276 1.090000e-108 403.0
18 TraesCS7D01G215400 chr3B 86.723 354 40 5 620 967 738993217 738992865 1.100000e-103 387.0
19 TraesCS7D01G215400 chr3D 87.247 792 89 5 1746 2535 260649484 260648703 0.000000e+00 893.0
20 TraesCS7D01G215400 chr3D 88.228 756 76 9 1746 2498 267482063 267482808 0.000000e+00 891.0
21 TraesCS7D01G215400 chr3D 84.936 551 61 16 1 537 549461102 549461644 2.870000e-149 538.0
22 TraesCS7D01G215400 chr3D 78.470 706 117 23 1049 1723 555912565 555911864 1.800000e-116 429.0
23 TraesCS7D01G215400 chr3D 78.340 711 90 31 1059 1723 555801419 555800727 3.930000e-108 401.0
24 TraesCS7D01G215400 chr4B 85.930 796 103 6 1746 2535 286464169 286463377 0.000000e+00 841.0
25 TraesCS7D01G215400 chr1D 84.217 792 97 14 1746 2521 35323501 35324280 0.000000e+00 745.0
26 TraesCS7D01G215400 chr1D 87.896 537 61 2 1 536 67387713 67387180 1.660000e-176 628.0
27 TraesCS7D01G215400 chr2B 82.331 798 126 9 1747 2535 302643039 302643830 0.000000e+00 678.0
28 TraesCS7D01G215400 chr3A 87.638 542 52 7 1 537 724016258 724015727 1.290000e-172 616.0
29 TraesCS7D01G215400 chr3A 77.129 634 117 20 1049 1658 692945284 692944655 2.410000e-90 342.0
30 TraesCS7D01G215400 chr3A 78.719 531 69 21 1101 1605 692723849 692723337 5.260000e-82 315.0
31 TraesCS7D01G215400 chr3A 100.000 31 0 0 1720 1750 241355402 241355432 9.800000e-05 58.4
32 TraesCS7D01G215400 chr6B 87.175 538 64 3 1 537 146670095 146669562 7.760000e-170 606.0
33 TraesCS7D01G215400 chr1A 79.399 466 82 11 1049 1505 510457159 510457619 1.460000e-82 316.0
34 TraesCS7D01G215400 chr1A 100.000 31 0 0 1720 1750 222423135 222423165 9.800000e-05 58.4
35 TraesCS7D01G215400 chr6A 95.349 86 4 0 1086 1171 14073642 14073727 1.220000e-28 137.0
36 TraesCS7D01G215400 chr6A 87.879 66 8 0 1154 1219 14077128 14077193 7.520000e-11 78.7
37 TraesCS7D01G215400 chr5A 100.000 31 0 0 1720 1750 260409160 260409190 9.800000e-05 58.4
38 TraesCS7D01G215400 chr4A 100.000 31 0 0 1720 1750 298003692 298003662 9.800000e-05 58.4


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 TraesCS7D01G215400 chr7D 175442496 175445030 2534 False 4682 4682 100.000 1 2535 1 chr7D.!!$F1 2534
1 TraesCS7D01G215400 chr7D 466461627 466462401 774 False 902 902 87.739 1746 2522 1 chr7D.!!$F2 776
2 TraesCS7D01G215400 chr2A 512441583 512442956 1373 False 1858 1858 91.358 366 1717 1 chr2A.!!$F2 1351
3 TraesCS7D01G215400 chr2A 164870355 164870897 542 False 599 599 86.765 1 537 1 chr2A.!!$F1 536
4 TraesCS7D01G215400 chr2D 378165393 378166707 1314 False 1753 1753 90.807 210 1530 1 chr2D.!!$F1 1320
5 TraesCS7D01G215400 chr2D 529000522 529001052 530 True 566 566 85.900 1 538 1 chr2D.!!$R2 537
6 TraesCS7D01G215400 chr7B 140815811 140816940 1129 False 1448 1448 89.982 1414 2535 1 chr7B.!!$F1 1121
7 TraesCS7D01G215400 chr4D 399897065 399897855 790 True 950 950 88.471 1746 2535 1 chr4D.!!$R1 789
8 TraesCS7D01G215400 chr5B 702563171 702563949 778 True 913 913 87.833 1748 2533 1 chr5B.!!$R2 785
9 TraesCS7D01G215400 chr3B 345173360 345174140 780 False 911 911 87.753 1746 2533 1 chr3B.!!$F1 787
10 TraesCS7D01G215400 chr3B 794589470 794590002 532 True 612 612 87.384 1 537 1 chr3B.!!$R5 536
11 TraesCS7D01G215400 chr3B 707041614 707042147 533 True 553 553 85.397 1 539 1 chr3B.!!$R1 538
12 TraesCS7D01G215400 chr3B 738756952 738757580 628 True 403 403 79.231 1080 1696 1 chr3B.!!$R2 616
13 TraesCS7D01G215400 chr3D 260648703 260649484 781 True 893 893 87.247 1746 2535 1 chr3D.!!$R1 789
14 TraesCS7D01G215400 chr3D 267482063 267482808 745 False 891 891 88.228 1746 2498 1 chr3D.!!$F1 752
15 TraesCS7D01G215400 chr3D 549461102 549461644 542 False 538 538 84.936 1 537 1 chr3D.!!$F2 536
16 TraesCS7D01G215400 chr3D 555911864 555912565 701 True 429 429 78.470 1049 1723 1 chr3D.!!$R3 674
17 TraesCS7D01G215400 chr3D 555800727 555801419 692 True 401 401 78.340 1059 1723 1 chr3D.!!$R2 664
18 TraesCS7D01G215400 chr4B 286463377 286464169 792 True 841 841 85.930 1746 2535 1 chr4B.!!$R1 789
19 TraesCS7D01G215400 chr1D 35323501 35324280 779 False 745 745 84.217 1746 2521 1 chr1D.!!$F1 775
20 TraesCS7D01G215400 chr1D 67387180 67387713 533 True 628 628 87.896 1 536 1 chr1D.!!$R1 535
21 TraesCS7D01G215400 chr2B 302643039 302643830 791 False 678 678 82.331 1747 2535 1 chr2B.!!$F1 788
22 TraesCS7D01G215400 chr3A 724015727 724016258 531 True 616 616 87.638 1 537 1 chr3A.!!$R3 536
23 TraesCS7D01G215400 chr3A 692944655 692945284 629 True 342 342 77.129 1049 1658 1 chr3A.!!$R2 609
24 TraesCS7D01G215400 chr3A 692723337 692723849 512 True 315 315 78.719 1101 1605 1 chr3A.!!$R1 504
25 TraesCS7D01G215400 chr6B 146669562 146670095 533 True 606 606 87.175 1 537 1 chr6B.!!$R1 536

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
221 222 0.108774 GCAGGTTATCTACAGGGCCC 59.891 60.0 16.46 16.46 0.00 5.80 F
1198 1264 0.104855 CGCCATGGCTAACTGCTCTA 59.895 55.0 33.07 0.00 42.39 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 1278 1.070134 CGAGGGTGGTCAGAAACAGAA 59.930 52.381 0.00 0.0 0.0 3.02 R
2401 2583 0.179045 GGCGCATGTACTCCCATCTT 60.179 55.000 10.83 0.0 0.0 2.40 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
95 96 3.097614 ACGTGGCTAAATGGAGTAGAGT 58.902 45.455 0.00 0.00 0.00 3.24
107 108 4.693283 TGGAGTAGAGTCAAATATTGCGG 58.307 43.478 0.00 0.00 0.00 5.69
115 116 5.934625 AGAGTCAAATATTGCGGGACATATC 59.065 40.000 10.53 3.05 0.00 1.63
117 118 5.003804 GTCAAATATTGCGGGACATATCCT 58.996 41.667 0.00 0.00 45.46 3.24
221 222 0.108774 GCAGGTTATCTACAGGGCCC 59.891 60.000 16.46 16.46 0.00 5.80
360 361 3.056749 CGGTCCAGTAATAGGATAGGTGC 60.057 52.174 0.00 0.00 37.52 5.01
371 372 7.863901 AATAGGATAGGTGCTTAGTCATCTT 57.136 36.000 0.00 0.00 0.00 2.40
376 377 3.944087 AGGTGCTTAGTCATCTTGTTCC 58.056 45.455 0.00 0.00 0.00 3.62
528 546 2.158579 GGCCGGGGTAATCCTCATTTTA 60.159 50.000 2.18 0.00 32.73 1.52
654 682 8.556589 AGATAGTAGATGCTATCCACACTATCT 58.443 37.037 21.41 21.41 45.08 1.98
712 740 7.272978 TGCTAGGGATACATTGTAGAAAGTTC 58.727 38.462 2.53 0.00 39.74 3.01
865 893 5.235186 ACGTGTGATATGAGAAAGCTAATGC 59.765 40.000 0.00 0.00 40.05 3.56
911 939 0.250945 ATCGAGGAGAGCTATGGCGA 60.251 55.000 0.00 0.00 44.37 5.54
928 956 3.118592 TGGCGACATACATCCAACACATA 60.119 43.478 0.00 0.00 33.40 2.29
944 972 3.436704 ACACATAATTGCACCTCTGAACG 59.563 43.478 0.00 0.00 0.00 3.95
969 997 6.692486 CCTAGACTATACATGGATCACAACC 58.308 44.000 0.00 0.00 0.00 3.77
1013 1041 3.270877 ACAAGGCTATGTTGACGATTCC 58.729 45.455 0.00 0.00 0.00 3.01
1014 1042 2.614057 CAAGGCTATGTTGACGATTCCC 59.386 50.000 0.00 0.00 0.00 3.97
1133 1199 1.135083 CATAGGAGTGTGGTGGACGAC 60.135 57.143 0.00 0.00 0.00 4.34
1198 1264 0.104855 CGCCATGGCTAACTGCTCTA 59.895 55.000 33.07 0.00 42.39 2.43
1200 1266 1.414181 GCCATGGCTAACTGCTCTAGA 59.586 52.381 29.98 0.00 42.39 2.43
1212 1278 3.117169 ACTGCTCTAGAGACATCCCTGAT 60.117 47.826 24.24 0.00 0.00 2.90
1341 1433 5.986135 GGTACATCATCTGTGGTGAGATTAC 59.014 44.000 0.00 0.00 38.83 1.89
1354 1446 0.968901 AGATTACTGCGACGTGGGGA 60.969 55.000 0.00 0.00 0.00 4.81
1643 1772 7.996385 AGGGAAAAATAACCGTTCTCATAATG 58.004 34.615 0.00 0.00 0.00 1.90
1662 1795 2.790433 TGTGTGGGAACTGCTATTTCC 58.210 47.619 3.65 3.65 41.76 3.13
1663 1796 2.107378 TGTGTGGGAACTGCTATTTCCA 59.893 45.455 11.97 5.40 43.96 3.53
1669 1802 5.127682 GTGGGAACTGCTATTTCCAATTGAT 59.872 40.000 7.12 0.00 43.96 2.57
1727 1875 9.364989 GTTCATCATAACCTAGAAGATAGCATC 57.635 37.037 0.00 0.00 0.00 3.91
1728 1876 8.655935 TCATCATAACCTAGAAGATAGCATCA 57.344 34.615 0.00 0.00 0.00 3.07
1729 1877 9.093458 TCATCATAACCTAGAAGATAGCATCAA 57.907 33.333 0.00 0.00 0.00 2.57
1732 1880 8.580720 TCATAACCTAGAAGATAGCATCAAGAC 58.419 37.037 0.00 0.00 0.00 3.01
1734 1882 6.798427 ACCTAGAAGATAGCATCAAGACAA 57.202 37.500 0.00 0.00 0.00 3.18
1903 2052 3.051392 GCAAAGGCAATACCGCGCT 62.051 57.895 5.56 0.00 46.52 5.92
1978 2127 1.599518 TTTCCTGCATTGACGCCGT 60.600 52.632 0.00 0.00 0.00 5.68
1985 2134 2.024868 CATTGACGCCGTTGACCGA 61.025 57.895 0.00 0.00 39.56 4.69
2049 2198 4.227134 CGGATCAGGGACCAGCGG 62.227 72.222 0.00 0.00 0.00 5.52
2100 2255 0.615331 ACCGCCATCTTGTGTGAGAT 59.385 50.000 0.00 0.00 36.84 2.75
2282 2461 5.231991 GTCAAGTCGCAATTTGTTTGTTCAT 59.768 36.000 0.00 0.00 37.65 2.57
2344 2523 2.932855 TGTCAAATTACCACGTGGGA 57.067 45.000 36.47 28.80 41.15 4.37
2347 2526 2.422127 GTCAAATTACCACGTGGGATGG 59.578 50.000 36.47 23.02 43.43 3.51
2370 2552 5.414144 GGCTTTCATATAGAAATGAGCTCCC 59.586 44.000 12.15 0.00 44.75 4.30
2401 2583 2.128507 GCGGGTGTGGTTGGGAAAA 61.129 57.895 0.00 0.00 0.00 2.29
2414 2596 4.403734 GTTGGGAAAAAGATGGGAGTACA 58.596 43.478 0.00 0.00 0.00 2.90
2448 2630 1.345741 CACCTCTTCTCTTCCTGCACA 59.654 52.381 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 5.003160 CAGGATATGTCCCGCAATATTTGA 58.997 41.667 4.63 0.0 46.34 2.69
107 108 6.406400 GCACATACTCCTATCAGGATATGTCC 60.406 46.154 17.87 0.0 44.81 4.02
115 116 6.352016 AGTAATGCACATACTCCTATCAGG 57.648 41.667 7.94 0.0 36.46 3.86
117 118 7.093333 CCCATAGTAATGCACATACTCCTATCA 60.093 40.741 15.28 0.9 0.00 2.15
221 222 1.942657 CCACATACGAATCCAAGCAGG 59.057 52.381 0.00 0.0 39.47 4.85
712 740 1.062002 GTACGATGTTTGGCATGGTCG 59.938 52.381 9.50 9.5 43.82 4.79
911 939 6.405731 GGTGCAATTATGTGTTGGATGTATGT 60.406 38.462 0.00 0.0 29.68 2.29
928 956 0.250901 AGGCGTTCAGAGGTGCAATT 60.251 50.000 0.00 0.0 0.00 2.32
944 972 5.984695 TGTGATCCATGTATAGTCTAGGC 57.015 43.478 0.00 0.0 0.00 3.93
969 997 3.255642 CGGTTGGGGGCTATTATCATTTG 59.744 47.826 0.00 0.0 0.00 2.32
1078 1128 1.360393 TGTTTGGTTGCTCCTCCCCT 61.360 55.000 0.80 0.0 37.07 4.79
1133 1199 7.542477 TCAGTTTCAGTAATAAGCTCTTCTTCG 59.458 37.037 0.00 0.0 36.25 3.79
1198 1264 4.782156 AGAAACAGAATCAGGGATGTCTCT 59.218 41.667 0.00 0.0 0.00 3.10
1200 1266 4.533707 TCAGAAACAGAATCAGGGATGTCT 59.466 41.667 0.00 0.0 0.00 3.41
1212 1278 1.070134 CGAGGGTGGTCAGAAACAGAA 59.930 52.381 0.00 0.0 0.00 3.02
1341 1433 3.423154 GCTTTCCCCACGTCGCAG 61.423 66.667 0.00 0.0 0.00 5.18
1567 1686 9.753674 TGGAAATGAGATTTATTTCACTAACCT 57.246 29.630 11.24 0.0 43.14 3.50
1621 1748 9.061610 CACACATTATGAGAACGGTTATTTTTC 57.938 33.333 0.00 0.0 0.00 2.29
1637 1766 6.455360 AAATAGCAGTTCCCACACATTATG 57.545 37.500 0.00 0.0 0.00 1.90
1643 1772 2.790433 TGGAAATAGCAGTTCCCACAC 58.210 47.619 11.19 0.0 43.43 3.82
1662 1795 4.701651 TGGTAGGCAGTTCTTCATCAATTG 59.298 41.667 0.00 0.0 0.00 2.32
1663 1796 4.922206 TGGTAGGCAGTTCTTCATCAATT 58.078 39.130 0.00 0.0 0.00 2.32
1669 1802 3.857157 AACTTGGTAGGCAGTTCTTCA 57.143 42.857 0.00 0.0 0.00 3.02
1727 1875 4.818534 TCTTTGCTTGCTAGTTGTCTTG 57.181 40.909 0.00 0.0 0.00 3.02
1728 1876 4.457257 GGATCTTTGCTTGCTAGTTGTCTT 59.543 41.667 0.00 0.0 0.00 3.01
1729 1877 4.006319 GGATCTTTGCTTGCTAGTTGTCT 58.994 43.478 0.00 0.0 0.00 3.41
1732 1880 3.503363 TGTGGATCTTTGCTTGCTAGTTG 59.497 43.478 0.00 0.0 0.00 3.16
1734 1882 3.423539 TGTGGATCTTTGCTTGCTAGT 57.576 42.857 0.00 0.0 0.00 2.57
1903 2052 4.019860 ACCATTCTCTCTAAGCAAGCTTCA 60.020 41.667 11.05 0.0 37.47 3.02
2049 2198 4.160439 TCTCACTCTCTCTCTCTCTCTCAC 59.840 50.000 0.00 0.0 0.00 3.51
2100 2255 1.918262 TGGGGTCGGTCTCTTCTACTA 59.082 52.381 0.00 0.0 0.00 1.82
2344 2523 6.658391 GGAGCTCATTTCTATATGAAAGCCAT 59.342 38.462 17.19 0.0 46.39 4.40
2347 2526 5.414144 GGGGAGCTCATTTCTATATGAAAGC 59.586 44.000 17.19 0.0 46.39 3.51
2401 2583 0.179045 GGCGCATGTACTCCCATCTT 60.179 55.000 10.83 0.0 0.00 2.40


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

AutoCloner maintained by Alex Coulton.