Multiple sequence alignment - TraesCS2D01G593600

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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 TraesCS2D01G593600 chr2D 100.000 3601 0 0 1 3601 648101639 648105239 0.000000e+00 6650.0
1 TraesCS2D01G593600 chr2D 96.944 949 8 2 2663 3601 643058659 643057722 0.000000e+00 1572.0
2 TraesCS2D01G593600 chr2D 87.572 1038 116 6 818 1844 648120745 648121780 0.000000e+00 1190.0
3 TraesCS2D01G593600 chr2D 87.384 967 89 14 2662 3601 47304960 47304000 0.000000e+00 1079.0
4 TraesCS2D01G593600 chr2D 91.810 696 32 2 2663 3333 431917085 431916390 0.000000e+00 946.0
5 TraesCS2D01G593600 chr2D 88.604 623 55 7 2662 3273 39816763 39816146 0.000000e+00 743.0
6 TraesCS2D01G593600 chr2D 89.613 491 46 5 2137 2625 648121817 648122304 1.420000e-173 619.0
7 TraesCS2D01G593600 chr2D 98.039 204 3 1 2660 2863 643052217 643052419 1.590000e-93 353.0
8 TraesCS2D01G593600 chr2D 99.471 189 1 0 2661 2849 648110770 648110582 9.570000e-91 344.0
9 TraesCS2D01G593600 chr2D 96.923 65 2 0 1966 2030 648103546 648103610 3.800000e-20 110.0
10 TraesCS2D01G593600 chr2D 96.923 65 2 0 1908 1972 648103604 648103668 3.800000e-20 110.0
11 TraesCS2D01G593600 chrUn 95.665 1684 59 7 297 1972 31327663 31325986 0.000000e+00 2693.0
12 TraesCS2D01G593600 chrUn 97.997 699 12 1 1966 2662 31326050 31325352 0.000000e+00 1212.0
13 TraesCS2D01G593600 chrUn 87.044 1042 122 7 817 1847 31313027 31311988 0.000000e+00 1164.0
14 TraesCS2D01G593600 chrUn 87.391 920 109 6 934 1847 31371289 31370371 0.000000e+00 1050.0
15 TraesCS2D01G593600 chrUn 88.951 534 47 6 2096 2626 31370331 31369807 0.000000e+00 649.0
16 TraesCS2D01G593600 chrUn 88.542 480 49 5 2151 2626 31311939 31311462 8.670000e-161 577.0
17 TraesCS2D01G593600 chrUn 78.638 426 48 18 157 553 31313974 31313563 3.590000e-60 243.0
18 TraesCS2D01G593600 chrUn 82.374 278 23 9 585 856 31371581 31371324 6.050000e-53 219.0
19 TraesCS2D01G593600 chr2B 93.739 1661 71 16 266 1909 781807760 781806116 0.000000e+00 2460.0
20 TraesCS2D01G593600 chr2B 86.143 1465 156 24 413 1847 781829042 781827595 0.000000e+00 1537.0
21 TraesCS2D01G593600 chr2B 90.862 974 54 4 2663 3601 1910441 1909468 0.000000e+00 1273.0
22 TraesCS2D01G593600 chr2B 86.686 1044 123 8 817 1847 781796194 781795154 0.000000e+00 1144.0
23 TraesCS2D01G593600 chr2B 95.912 636 17 6 1996 2626 781806116 781805485 0.000000e+00 1022.0
24 TraesCS2D01G593600 chr2B 89.978 449 42 3 2151 2596 781795102 781794654 8.670000e-161 577.0
25 TraesCS2D01G593600 chr2B 85.582 541 60 10 2097 2626 781827556 781827023 5.250000e-153 551.0
26 TraesCS2D01G593600 chr5D 97.789 950 11 1 2662 3601 367807989 367807040 0.000000e+00 1629.0
27 TraesCS2D01G593600 chr5D 97.015 201 5 1 2663 2863 367799727 367799926 1.600000e-88 337.0
28 TraesCS2D01G593600 chr5D 80.556 180 32 3 2447 2625 6712219 6712042 6.270000e-28 135.0
29 TraesCS2D01G593600 chr5D 93.878 49 3 0 1908 1956 558966863 558966911 1.390000e-09 75.0
30 TraesCS2D01G593600 chr5D 93.878 49 3 0 1966 2014 558966863 558966911 1.390000e-09 75.0
31 TraesCS2D01G593600 chr6D 94.813 964 25 2 2663 3601 113908818 113907855 0.000000e+00 1480.0
32 TraesCS2D01G593600 chr6D 95.588 204 8 1 2660 2863 113904167 113904369 3.470000e-85 326.0
33 TraesCS2D01G593600 chr6D 85.075 67 6 2 1889 1955 26817513 26817451 8.350000e-07 65.8
34 TraesCS2D01G593600 chr6D 85.075 67 6 2 1889 1955 26861261 26861199 8.350000e-07 65.8
35 TraesCS2D01G593600 chr2A 93.595 968 34 4 2662 3601 766612825 766613792 0.000000e+00 1419.0
36 TraesCS2D01G593600 chr2A 91.057 861 42 9 2667 3500 84227924 84227072 0.000000e+00 1131.0
37 TraesCS2D01G593600 chr2A 83.761 117 18 1 245 361 722131269 722131154 3.800000e-20 110.0
38 TraesCS2D01G593600 chr3D 93.271 966 34 5 2662 3601 460895118 460896078 0.000000e+00 1395.0
39 TraesCS2D01G593600 chr3D 92.284 972 36 5 2654 3601 170566963 170567919 0.000000e+00 1343.0
40 TraesCS2D01G593600 chr3D 93.491 338 11 2 2653 2980 575606448 575606112 3.230000e-135 492.0
41 TraesCS2D01G593600 chr3D 92.308 91 6 1 262 352 434498456 434498367 1.050000e-25 128.0
42 TraesCS2D01G593600 chr4A 92.547 966 45 8 2663 3601 485013654 485012689 0.000000e+00 1360.0
43 TraesCS2D01G593600 chr4A 87.487 951 82 21 2662 3601 465229651 465230575 0.000000e+00 1062.0
44 TraesCS2D01G593600 chr4A 78.712 761 143 16 971 1717 615099581 615100336 1.160000e-134 490.0
45 TraesCS2D01G593600 chr4A 77.792 761 149 17 971 1717 615081652 615082406 5.480000e-123 451.0
46 TraesCS2D01G593600 chr4A 80.782 614 68 27 129 697 59281421 59282029 5.520000e-118 435.0
47 TraesCS2D01G593600 chr4A 95.918 49 1 1 1964 2012 476762474 476762427 1.070000e-10 78.7
48 TraesCS2D01G593600 chr7D 91.701 976 39 9 2653 3601 465829717 465830677 0.000000e+00 1315.0
49 TraesCS2D01G593600 chr7D 90.702 968 26 18 2659 3601 214771377 214770449 0.000000e+00 1230.0
50 TraesCS2D01G593600 chr7D 96.744 215 4 3 2649 2863 219288428 219288639 4.420000e-94 355.0
51 TraesCS2D01G593600 chr7D 92.958 213 12 3 2652 2863 465836237 465836027 1.260000e-79 307.0
52 TraesCS2D01G593600 chr7D 83.117 77 9 2 1880 1956 100311310 100311382 2.320000e-07 67.6
53 TraesCS2D01G593600 chr1B 89.898 980 66 5 2649 3601 688240256 688241229 0.000000e+00 1230.0
54 TraesCS2D01G593600 chr1B 86.528 965 96 16 2663 3601 647253403 647252447 0.000000e+00 1031.0
55 TraesCS2D01G593600 chr7A 87.579 950 95 11 2667 3601 182693361 182692420 0.000000e+00 1079.0
56 TraesCS2D01G593600 chr7A 84.507 71 7 3 1884 1951 555611643 555611712 2.320000e-07 67.6
57 TraesCS2D01G593600 chr1A 87.565 965 73 19 2663 3601 330135468 330134525 0.000000e+00 1074.0
58 TraesCS2D01G593600 chr3A 87.619 420 34 7 3199 3601 487464574 487464992 4.210000e-129 472.0
59 TraesCS2D01G593600 chr3A 90.000 60 5 1 1908 1967 177112437 177112379 3.860000e-10 76.8
60 TraesCS2D01G593600 chr3A 89.831 59 4 2 1966 2023 177112437 177112380 1.390000e-09 75.0
61 TraesCS2D01G593600 chr4D 81.629 577 70 25 150 697 401530311 401530880 2.550000e-121 446.0
62 TraesCS2D01G593600 chr7B 78.084 616 105 18 1225 1819 518395097 518394491 2.640000e-96 363.0
63 TraesCS2D01G593600 chr7B 78.084 616 105 18 1225 1819 518398406 518397800 2.640000e-96 363.0
64 TraesCS2D01G593600 chr7B 83.133 83 8 4 1874 1954 102646751 102646673 1.790000e-08 71.3
65 TraesCS2D01G593600 chr7B 85.294 68 6 4 1977 2043 113570841 113570905 2.320000e-07 67.6
66 TraesCS2D01G593600 chr4B 80.426 470 47 23 245 674 496546571 496547035 2.090000e-82 316.0
67 TraesCS2D01G593600 chr5B 88.525 61 4 3 1962 2020 283199805 283199864 1.790000e-08 71.3
68 TraesCS2D01G593600 chr3B 86.154 65 7 2 1965 2027 717307327 717307263 6.450000e-08 69.4


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 TraesCS2D01G593600 chr2D 648101639 648105239 3600 False 2290.000000 6650 97.948667 1 3601 3 chr2D.!!$F2 3600
1 TraesCS2D01G593600 chr2D 643057722 643058659 937 True 1572.000000 1572 96.944000 2663 3601 1 chr2D.!!$R4 938
2 TraesCS2D01G593600 chr2D 47304000 47304960 960 True 1079.000000 1079 87.384000 2662 3601 1 chr2D.!!$R2 939
3 TraesCS2D01G593600 chr2D 431916390 431917085 695 True 946.000000 946 91.810000 2663 3333 1 chr2D.!!$R3 670
4 TraesCS2D01G593600 chr2D 648120745 648122304 1559 False 904.500000 1190 88.592500 818 2625 2 chr2D.!!$F3 1807
5 TraesCS2D01G593600 chr2D 39816146 39816763 617 True 743.000000 743 88.604000 2662 3273 1 chr2D.!!$R1 611
6 TraesCS2D01G593600 chrUn 31325352 31327663 2311 True 1952.500000 2693 96.831000 297 2662 2 chrUn.!!$R2 2365
7 TraesCS2D01G593600 chrUn 31311462 31313974 2512 True 661.333333 1164 84.741333 157 2626 3 chrUn.!!$R1 2469
8 TraesCS2D01G593600 chrUn 31369807 31371581 1774 True 639.333333 1050 86.238667 585 2626 3 chrUn.!!$R3 2041
9 TraesCS2D01G593600 chr2B 781805485 781807760 2275 True 1741.000000 2460 94.825500 266 2626 2 chr2B.!!$R3 2360
10 TraesCS2D01G593600 chr2B 1909468 1910441 973 True 1273.000000 1273 90.862000 2663 3601 1 chr2B.!!$R1 938
11 TraesCS2D01G593600 chr2B 781827023 781829042 2019 True 1044.000000 1537 85.862500 413 2626 2 chr2B.!!$R4 2213
12 TraesCS2D01G593600 chr2B 781794654 781796194 1540 True 860.500000 1144 88.332000 817 2596 2 chr2B.!!$R2 1779
13 TraesCS2D01G593600 chr5D 367807040 367807989 949 True 1629.000000 1629 97.789000 2662 3601 1 chr5D.!!$R2 939
14 TraesCS2D01G593600 chr6D 113907855 113908818 963 True 1480.000000 1480 94.813000 2663 3601 1 chr6D.!!$R3 938
15 TraesCS2D01G593600 chr2A 766612825 766613792 967 False 1419.000000 1419 93.595000 2662 3601 1 chr2A.!!$F1 939
16 TraesCS2D01G593600 chr2A 84227072 84227924 852 True 1131.000000 1131 91.057000 2667 3500 1 chr2A.!!$R1 833
17 TraesCS2D01G593600 chr3D 460895118 460896078 960 False 1395.000000 1395 93.271000 2662 3601 1 chr3D.!!$F2 939
18 TraesCS2D01G593600 chr3D 170566963 170567919 956 False 1343.000000 1343 92.284000 2654 3601 1 chr3D.!!$F1 947
19 TraesCS2D01G593600 chr4A 485012689 485013654 965 True 1360.000000 1360 92.547000 2663 3601 1 chr4A.!!$R2 938
20 TraesCS2D01G593600 chr4A 465229651 465230575 924 False 1062.000000 1062 87.487000 2662 3601 1 chr4A.!!$F2 939
21 TraesCS2D01G593600 chr4A 615099581 615100336 755 False 490.000000 490 78.712000 971 1717 1 chr4A.!!$F4 746
22 TraesCS2D01G593600 chr4A 615081652 615082406 754 False 451.000000 451 77.792000 971 1717 1 chr4A.!!$F3 746
23 TraesCS2D01G593600 chr4A 59281421 59282029 608 False 435.000000 435 80.782000 129 697 1 chr4A.!!$F1 568
24 TraesCS2D01G593600 chr7D 465829717 465830677 960 False 1315.000000 1315 91.701000 2653 3601 1 chr7D.!!$F3 948
25 TraesCS2D01G593600 chr7D 214770449 214771377 928 True 1230.000000 1230 90.702000 2659 3601 1 chr7D.!!$R1 942
26 TraesCS2D01G593600 chr1B 688240256 688241229 973 False 1230.000000 1230 89.898000 2649 3601 1 chr1B.!!$F1 952
27 TraesCS2D01G593600 chr1B 647252447 647253403 956 True 1031.000000 1031 86.528000 2663 3601 1 chr1B.!!$R1 938
28 TraesCS2D01G593600 chr7A 182692420 182693361 941 True 1079.000000 1079 87.579000 2667 3601 1 chr7A.!!$R1 934
29 TraesCS2D01G593600 chr1A 330134525 330135468 943 True 1074.000000 1074 87.565000 2663 3601 1 chr1A.!!$R1 938
30 TraesCS2D01G593600 chr4D 401530311 401530880 569 False 446.000000 446 81.629000 150 697 1 chr4D.!!$F1 547
31 TraesCS2D01G593600 chr7B 518394491 518398406 3915 True 363.000000 363 78.084000 1225 1819 2 chr7B.!!$R2 594

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
105 106 0.034337 GTAACGAACCTGGTCTGGCA 59.966 55.0 0.00 0.0 0.0 4.92 F
1912 4027 0.530211 TTGTACGGACGTGGTGGTTG 60.530 55.0 7.73 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 4038 1.018910 GCTTTCGCCCCGCTTTATAA 58.981 50.0 0.0 0.0 0.0 0.98 R
2931 5086 1.566298 CCCTTTCACCTCCTCCCCTG 61.566 65.0 0.0 0.0 0.0 4.45 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
26 27 5.959583 AAAAGAAGGGAGGGAGTACATAG 57.040 43.478 0.00 0.00 0.00 2.23
27 28 4.628661 AAGAAGGGAGGGAGTACATAGT 57.371 45.455 0.00 0.00 0.00 2.12
28 29 4.628661 AGAAGGGAGGGAGTACATAGTT 57.371 45.455 0.00 0.00 0.00 2.24
30 31 5.351405 AGAAGGGAGGGAGTACATAGTTTT 58.649 41.667 0.00 0.00 0.00 2.43
31 32 5.791141 AGAAGGGAGGGAGTACATAGTTTTT 59.209 40.000 0.00 0.00 0.00 1.94
57 58 9.551734 TTGATAATCATCATGTATATAGCTGGC 57.448 33.333 0.00 0.00 40.85 4.85
58 59 8.152898 TGATAATCATCATGTATATAGCTGGCC 58.847 37.037 0.00 0.00 36.22 5.36
60 61 5.760484 TCATCATGTATATAGCTGGCCAA 57.240 39.130 7.01 0.00 0.00 4.52
61 62 6.125589 TCATCATGTATATAGCTGGCCAAA 57.874 37.500 7.01 0.00 0.00 3.28
62 63 6.724351 TCATCATGTATATAGCTGGCCAAAT 58.276 36.000 7.01 3.30 0.00 2.32
64 65 6.125589 TCATGTATATAGCTGGCCAAATGA 57.874 37.500 7.01 0.00 0.00 2.57
66 67 7.860584 TCATGTATATAGCTGGCCAAATGATA 58.139 34.615 7.01 0.00 0.00 2.15
68 69 6.414732 TGTATATAGCTGGCCAAATGATACC 58.585 40.000 7.01 0.00 0.00 2.73
69 70 5.786121 ATATAGCTGGCCAAATGATACCT 57.214 39.130 7.01 0.00 0.00 3.08
70 71 2.834638 AGCTGGCCAAATGATACCTT 57.165 45.000 7.01 0.00 0.00 3.50
73 74 2.760092 GCTGGCCAAATGATACCTTTCA 59.240 45.455 7.01 0.00 0.00 2.69
75 76 4.738541 GCTGGCCAAATGATACCTTTCATG 60.739 45.833 7.01 0.00 36.48 3.07
76 77 3.705579 TGGCCAAATGATACCTTTCATGG 59.294 43.478 0.61 0.00 36.48 3.66
77 78 3.070015 GGCCAAATGATACCTTTCATGGG 59.930 47.826 0.00 0.00 36.48 4.00
79 80 3.070015 CCAAATGATACCTTTCATGGGCC 59.930 47.826 0.00 0.00 36.48 5.80
82 83 0.537371 GATACCTTTCATGGGCCCGG 60.537 60.000 19.37 13.84 0.00 5.73
84 85 4.757355 CCTTTCATGGGCCCGGCA 62.757 66.667 19.37 0.00 0.00 5.69
98 99 3.557824 GGCACGTAACGAACCTGG 58.442 61.111 0.00 0.00 0.00 4.45
99 100 1.301165 GGCACGTAACGAACCTGGT 60.301 57.895 0.00 0.00 0.00 4.00
100 101 1.287041 GGCACGTAACGAACCTGGTC 61.287 60.000 0.00 0.00 0.00 4.02
101 102 0.319297 GCACGTAACGAACCTGGTCT 60.319 55.000 0.00 0.00 0.00 3.85
102 103 1.415374 CACGTAACGAACCTGGTCTG 58.585 55.000 0.00 0.00 0.00 3.51
103 104 0.316204 ACGTAACGAACCTGGTCTGG 59.684 55.000 0.00 0.00 0.00 3.86
105 106 0.034337 GTAACGAACCTGGTCTGGCA 59.966 55.000 0.00 0.00 0.00 4.92
106 107 0.034337 TAACGAACCTGGTCTGGCAC 59.966 55.000 0.00 0.00 0.00 5.01
107 108 1.978455 AACGAACCTGGTCTGGCACA 61.978 55.000 0.00 0.00 0.00 4.57
108 109 1.961277 CGAACCTGGTCTGGCACAC 60.961 63.158 0.00 0.00 0.00 3.82
109 110 1.961277 GAACCTGGTCTGGCACACG 60.961 63.158 0.00 0.00 0.00 4.49
110 111 2.377628 GAACCTGGTCTGGCACACGA 62.378 60.000 0.00 0.00 0.00 4.35
111 112 2.357517 CCTGGTCTGGCACACGAC 60.358 66.667 0.00 0.00 36.34 4.34
113 114 1.956170 CTGGTCTGGCACACGACAC 60.956 63.158 7.54 0.00 37.92 3.67
114 115 2.108157 GGTCTGGCACACGACACA 59.892 61.111 7.54 0.00 37.92 3.72
116 117 2.108157 TCTGGCACACGACACACC 59.892 61.111 0.00 0.00 0.00 4.16
117 118 3.337889 CTGGCACACGACACACCG 61.338 66.667 0.00 0.00 0.00 4.94
118 119 4.150203 TGGCACACGACACACCGT 62.150 61.111 0.00 0.00 44.43 4.83
127 128 3.144285 ACACACCGTGTACCAGGG 58.856 61.111 3.25 1.61 45.56 4.45
128 129 2.358247 CACACCGTGTACCAGGGC 60.358 66.667 3.25 0.00 42.42 5.19
129 130 2.525877 ACACCGTGTACCAGGGCT 60.526 61.111 1.18 0.00 42.42 5.19
131 132 3.379445 ACCGTGTACCAGGGCTCG 61.379 66.667 8.35 0.00 42.42 5.03
132 133 3.379445 CCGTGTACCAGGGCTCGT 61.379 66.667 0.00 0.00 32.63 4.18
133 134 2.181021 CGTGTACCAGGGCTCGTC 59.819 66.667 0.00 0.00 0.00 4.20
134 135 2.577593 GTGTACCAGGGCTCGTCC 59.422 66.667 0.00 0.00 0.00 4.79
135 136 3.066190 TGTACCAGGGCTCGTCCG 61.066 66.667 0.00 0.00 34.94 4.79
136 137 4.509737 GTACCAGGGCTCGTCCGC 62.510 72.222 0.00 0.00 34.94 5.54
215 224 2.445654 CCCTCTGGCCCTCTCCTC 60.446 72.222 0.00 0.00 0.00 3.71
453 493 3.916989 AGGTACAATTGACCTTCCTTCCT 59.083 43.478 13.59 0.00 45.40 3.36
454 494 4.010349 GGTACAATTGACCTTCCTTCCTG 58.990 47.826 13.59 0.00 33.86 3.86
513 569 2.662866 ACACCGCTCCTGCTTATACTA 58.337 47.619 0.00 0.00 36.97 1.82
553 609 7.281841 TCATGTTCATCTCAGCCATACAATTA 58.718 34.615 0.00 0.00 0.00 1.40
625 701 7.976135 ATTCTGCTTCCTGCTTATATACAAG 57.024 36.000 0.00 0.00 43.37 3.16
626 702 5.858381 TCTGCTTCCTGCTTATATACAAGG 58.142 41.667 0.00 0.00 43.37 3.61
999 1405 1.088340 CAGCCGTCCTGCTTGATGAG 61.088 60.000 0.00 0.00 40.32 2.90
1116 1522 3.843619 TCCACCATGTGATGTCCTTCTTA 59.156 43.478 0.00 0.00 35.23 2.10
1392 3487 5.049129 CCTTCATATTTCTGGATTTCTCCGC 60.049 44.000 0.00 0.00 45.37 5.54
1636 3731 3.726790 TGTGCTAGGAACCTTACCCATA 58.273 45.455 0.00 0.00 0.00 2.74
1822 3932 3.181455 TGCGCCATTACATGAGGTAAGAT 60.181 43.478 4.18 0.00 44.74 2.40
1824 3934 4.275936 GCGCCATTACATGAGGTAAGATTT 59.724 41.667 0.00 0.00 44.74 2.17
1911 4026 0.530431 GTTGTACGGACGTGGTGGTT 60.530 55.000 7.73 0.00 0.00 3.67
1912 4027 0.530211 TTGTACGGACGTGGTGGTTG 60.530 55.000 7.73 0.00 0.00 3.77
1913 4028 2.029369 TACGGACGTGGTGGTTGC 59.971 61.111 7.73 0.00 0.00 4.17
1914 4029 2.500714 TACGGACGTGGTGGTTGCT 61.501 57.895 7.73 0.00 0.00 3.91
1915 4030 2.030490 TACGGACGTGGTGGTTGCTT 62.030 55.000 7.73 0.00 0.00 3.91
1916 4031 2.184167 CGGACGTGGTGGTTGCTTT 61.184 57.895 0.00 0.00 0.00 3.51
1917 4032 1.652563 GGACGTGGTGGTTGCTTTC 59.347 57.895 0.00 0.00 0.00 2.62
1918 4033 0.818040 GGACGTGGTGGTTGCTTTCT 60.818 55.000 0.00 0.00 0.00 2.52
1919 4034 1.021968 GACGTGGTGGTTGCTTTCTT 58.978 50.000 0.00 0.00 0.00 2.52
1920 4035 1.404035 GACGTGGTGGTTGCTTTCTTT 59.596 47.619 0.00 0.00 0.00 2.52
1921 4036 2.614983 GACGTGGTGGTTGCTTTCTTTA 59.385 45.455 0.00 0.00 0.00 1.85
1922 4037 3.219281 ACGTGGTGGTTGCTTTCTTTAT 58.781 40.909 0.00 0.00 0.00 1.40
1923 4038 3.634910 ACGTGGTGGTTGCTTTCTTTATT 59.365 39.130 0.00 0.00 0.00 1.40
1924 4039 4.098807 ACGTGGTGGTTGCTTTCTTTATTT 59.901 37.500 0.00 0.00 0.00 1.40
1925 4040 5.299782 ACGTGGTGGTTGCTTTCTTTATTTA 59.700 36.000 0.00 0.00 0.00 1.40
1926 4041 6.015772 ACGTGGTGGTTGCTTTCTTTATTTAT 60.016 34.615 0.00 0.00 0.00 1.40
1927 4042 7.175293 ACGTGGTGGTTGCTTTCTTTATTTATA 59.825 33.333 0.00 0.00 0.00 0.98
1928 4043 8.024285 CGTGGTGGTTGCTTTCTTTATTTATAA 58.976 33.333 0.00 0.00 0.00 0.98
1929 4044 9.699703 GTGGTGGTTGCTTTCTTTATTTATAAA 57.300 29.630 0.00 0.00 0.00 1.40
1930 4045 9.921637 TGGTGGTTGCTTTCTTTATTTATAAAG 57.078 29.630 13.58 13.58 46.59 1.85
1936 4051 5.690409 GCTTTCTTTATTTATAAAGCGGGGC 59.310 40.000 14.54 12.10 45.46 5.80
1937 4052 5.427036 TTCTTTATTTATAAAGCGGGGCG 57.573 39.130 14.54 0.00 45.46 6.13
1938 4053 4.706035 TCTTTATTTATAAAGCGGGGCGA 58.294 39.130 14.54 0.00 45.46 5.54
1939 4054 5.124645 TCTTTATTTATAAAGCGGGGCGAA 58.875 37.500 14.54 0.00 45.46 4.70
1940 4055 5.589452 TCTTTATTTATAAAGCGGGGCGAAA 59.411 36.000 14.54 0.00 45.46 3.46
1941 4056 3.982576 ATTTATAAAGCGGGGCGAAAG 57.017 42.857 3.94 0.00 0.00 2.62
1960 4075 6.523676 GAAAGCCTATTTCGAGAGAGAATG 57.476 41.667 0.00 0.00 43.69 2.67
1961 4076 5.606348 AAGCCTATTTCGAGAGAGAATGT 57.394 39.130 0.00 0.00 43.69 2.71
1962 4077 4.942852 AGCCTATTTCGAGAGAGAATGTG 58.057 43.478 0.00 0.00 43.69 3.21
1963 4078 4.404073 AGCCTATTTCGAGAGAGAATGTGT 59.596 41.667 0.00 0.00 43.69 3.72
1964 4079 5.105146 AGCCTATTTCGAGAGAGAATGTGTT 60.105 40.000 0.00 0.00 43.69 3.32
1965 4080 5.582665 GCCTATTTCGAGAGAGAATGTGTTT 59.417 40.000 0.00 0.00 43.69 2.83
1966 4081 6.456181 GCCTATTTCGAGAGAGAATGTGTTTG 60.456 42.308 0.00 0.00 43.69 2.93
1967 4082 5.869753 ATTTCGAGAGAGAATGTGTTTGG 57.130 39.130 0.00 0.00 43.69 3.28
1968 4083 4.336889 TTCGAGAGAGAATGTGTTTGGT 57.663 40.909 0.00 0.00 43.69 3.67
1994 4109 5.690409 GCTTTCTTTATTTATAAAGCGGGGC 59.310 40.000 14.54 12.10 45.46 5.80
2072 4187 3.735591 TCAAAGTTAAGGGACGGTCTTG 58.264 45.455 8.23 2.45 0.00 3.02
2143 4261 4.037446 TCTTTGCAACACTAACATGTTCCC 59.963 41.667 15.85 0.00 40.89 3.97
2149 4267 4.081322 ACACTAACATGTTCCCTTCGTT 57.919 40.909 15.85 0.00 0.00 3.85
2534 4660 1.204941 CGAGAAGAACATCCGAGGGTT 59.795 52.381 0.00 0.00 0.00 4.11
2931 5086 2.115348 TCGGCTTCGATCATAACGAC 57.885 50.000 0.00 0.00 39.46 4.34
3078 5256 0.179250 CTGTTTCGTCGCGATGTTGG 60.179 55.000 26.40 10.71 35.23 3.77
3324 5523 0.537143 TTTGGTGCTGTAGGGTGCTG 60.537 55.000 0.00 0.00 0.00 4.41
3592 5801 2.839486 TGCAGTTACTTGGTCTCCAG 57.161 50.000 0.00 0.00 33.81 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.628661 AACTATGTACTCCCTCCCTTCT 57.371 45.455 0.00 0.00 0.00 2.85
8 9 5.695424 AAAACTATGTACTCCCTCCCTTC 57.305 43.478 0.00 0.00 0.00 3.46
31 32 9.551734 GCCAGCTATATACATGATGATTATCAA 57.448 33.333 4.05 0.00 45.82 2.57
33 34 8.152898 TGGCCAGCTATATACATGATGATTATC 58.847 37.037 0.00 0.00 0.00 1.75
34 35 8.037723 TGGCCAGCTATATACATGATGATTAT 57.962 34.615 0.00 0.00 0.00 1.28
36 37 6.317663 TGGCCAGCTATATACATGATGATT 57.682 37.500 0.00 0.00 0.00 2.57
37 38 5.963214 TGGCCAGCTATATACATGATGAT 57.037 39.130 0.00 0.00 0.00 2.45
38 39 5.760484 TTGGCCAGCTATATACATGATGA 57.240 39.130 5.11 0.00 0.00 2.92
39 40 6.600427 TCATTTGGCCAGCTATATACATGATG 59.400 38.462 5.11 0.00 0.00 3.07
40 41 6.724351 TCATTTGGCCAGCTATATACATGAT 58.276 36.000 5.11 0.00 0.00 2.45
41 42 6.125589 TCATTTGGCCAGCTATATACATGA 57.874 37.500 5.11 1.48 0.00 3.07
43 44 7.056635 GGTATCATTTGGCCAGCTATATACAT 58.943 38.462 19.99 5.10 0.00 2.29
44 45 6.215431 AGGTATCATTTGGCCAGCTATATACA 59.785 38.462 19.99 0.00 0.00 2.29
45 46 6.653989 AGGTATCATTTGGCCAGCTATATAC 58.346 40.000 5.11 11.45 0.00 1.47
46 47 6.891306 AGGTATCATTTGGCCAGCTATATA 57.109 37.500 5.11 0.00 0.00 0.86
47 48 5.786121 AGGTATCATTTGGCCAGCTATAT 57.214 39.130 5.11 0.00 0.00 0.86
49 50 4.459852 AAGGTATCATTTGGCCAGCTAT 57.540 40.909 5.11 1.16 0.00 2.97
51 52 2.834638 AAGGTATCATTTGGCCAGCT 57.165 45.000 5.11 0.00 0.00 4.24
52 53 2.760092 TGAAAGGTATCATTTGGCCAGC 59.240 45.455 5.11 0.00 0.00 4.85
54 55 3.705579 CCATGAAAGGTATCATTTGGCCA 59.294 43.478 0.00 0.00 37.96 5.36
55 56 3.070015 CCCATGAAAGGTATCATTTGGCC 59.930 47.826 0.00 0.00 37.96 5.36
56 57 3.493176 GCCCATGAAAGGTATCATTTGGC 60.493 47.826 10.21 10.21 42.89 4.52
57 58 3.070015 GGCCCATGAAAGGTATCATTTGG 59.930 47.826 0.00 0.00 37.96 3.28
58 59 3.070015 GGGCCCATGAAAGGTATCATTTG 59.930 47.826 19.95 0.00 37.96 2.32
60 61 2.752829 CGGGCCCATGAAAGGTATCATT 60.753 50.000 24.92 0.00 37.96 2.57
61 62 1.202927 CGGGCCCATGAAAGGTATCAT 60.203 52.381 24.92 0.00 40.64 2.45
62 63 0.182537 CGGGCCCATGAAAGGTATCA 59.817 55.000 24.92 0.00 0.00 2.15
64 65 1.536676 CCGGGCCCATGAAAGGTAT 59.463 57.895 24.92 0.00 0.00 2.73
66 67 4.759205 GCCGGGCCCATGAAAGGT 62.759 66.667 24.92 0.00 0.00 3.50
68 69 3.451894 GTGCCGGGCCCATGAAAG 61.452 66.667 24.92 3.40 0.00 2.62
73 74 4.789123 GTTACGTGCCGGGCCCAT 62.789 66.667 24.92 3.77 0.00 4.00
77 78 3.781162 GTTCGTTACGTGCCGGGC 61.781 66.667 13.32 13.32 0.00 6.13
79 80 2.048877 AGGTTCGTTACGTGCCGG 60.049 61.111 4.24 0.00 0.00 6.13
82 83 0.319297 AGACCAGGTTCGTTACGTGC 60.319 55.000 4.24 0.00 40.46 5.34
84 85 0.316204 CCAGACCAGGTTCGTTACGT 59.684 55.000 4.24 0.00 0.00 3.57
87 88 0.034337 GTGCCAGACCAGGTTCGTTA 59.966 55.000 0.00 0.00 0.00 3.18
89 90 2.426023 GTGCCAGACCAGGTTCGT 59.574 61.111 0.00 0.00 0.00 3.85
90 91 1.961277 GTGTGCCAGACCAGGTTCG 60.961 63.158 0.00 0.00 0.00 3.95
91 92 1.961277 CGTGTGCCAGACCAGGTTC 60.961 63.158 0.00 0.00 0.00 3.62
92 93 2.111043 CGTGTGCCAGACCAGGTT 59.889 61.111 0.00 0.00 0.00 3.50
93 94 2.842462 TCGTGTGCCAGACCAGGT 60.842 61.111 0.00 0.00 0.00 4.00
94 95 2.357517 GTCGTGTGCCAGACCAGG 60.358 66.667 0.00 0.00 0.00 4.45
95 96 1.956170 GTGTCGTGTGCCAGACCAG 60.956 63.158 0.00 0.00 36.61 4.00
96 97 2.108157 GTGTCGTGTGCCAGACCA 59.892 61.111 0.00 0.00 36.61 4.02
97 98 2.108157 TGTGTCGTGTGCCAGACC 59.892 61.111 0.00 0.00 36.61 3.85
98 99 2.244651 GGTGTGTCGTGTGCCAGAC 61.245 63.158 0.00 0.00 37.85 3.51
99 100 2.108157 GGTGTGTCGTGTGCCAGA 59.892 61.111 0.00 0.00 0.00 3.86
100 101 3.337889 CGGTGTGTCGTGTGCCAG 61.338 66.667 0.00 0.00 0.00 4.85
101 102 4.150203 ACGGTGTGTCGTGTGCCA 62.150 61.111 0.00 0.00 42.21 4.92
107 108 1.361271 CTGGTACACGGTGTGTCGT 59.639 57.895 23.36 0.00 43.92 4.34
108 109 1.372499 CCTGGTACACGGTGTGTCG 60.372 63.158 23.36 8.94 43.92 4.35
109 110 1.005394 CCCTGGTACACGGTGTGTC 60.005 63.158 23.36 15.17 43.92 3.67
111 112 2.358247 GCCCTGGTACACGGTGTG 60.358 66.667 23.36 6.69 36.86 3.82
113 114 2.264794 GAGCCCTGGTACACGGTG 59.735 66.667 6.58 6.58 36.86 4.94
114 115 3.379445 CGAGCCCTGGTACACGGT 61.379 66.667 0.00 0.00 36.86 4.83
116 117 2.181021 GACGAGCCCTGGTACACG 59.819 66.667 0.00 0.00 0.00 4.49
117 118 2.577593 GGACGAGCCCTGGTACAC 59.422 66.667 0.00 0.00 0.00 2.90
118 119 3.066190 CGGACGAGCCCTGGTACA 61.066 66.667 0.00 0.00 0.00 2.90
119 120 4.509737 GCGGACGAGCCCTGGTAC 62.510 72.222 0.00 0.00 0.00 3.34
127 128 4.373116 TCACTTGGGCGGACGAGC 62.373 66.667 0.00 0.00 0.00 5.03
128 129 2.432628 GTCACTTGGGCGGACGAG 60.433 66.667 0.00 0.00 0.00 4.18
241 250 3.978571 GAAAGCCGACAGGGGAGCC 62.979 68.421 0.00 0.00 38.20 4.70
242 251 2.436824 GAAAGCCGACAGGGGAGC 60.437 66.667 0.00 0.00 38.20 4.70
243 252 2.125512 CGAAAGCCGACAGGGGAG 60.126 66.667 0.00 0.00 41.76 4.30
453 493 3.109928 TCTTCATCTTCCCAGATCTGCA 58.890 45.455 17.76 2.72 37.71 4.41
454 494 3.834489 TCTTCATCTTCCCAGATCTGC 57.166 47.619 17.76 0.00 37.71 4.26
513 569 3.726557 ACATGAACTGACATCCATGGT 57.273 42.857 12.58 0.00 40.32 3.55
553 609 9.961265 GATATGACATGAACATGAATTGACATT 57.039 29.630 19.56 0.00 41.20 2.71
625 701 4.612264 AGCAATGGCATCAATTATTCCC 57.388 40.909 0.00 0.00 44.61 3.97
626 702 4.682860 CGAAGCAATGGCATCAATTATTCC 59.317 41.667 0.00 0.00 44.61 3.01
734 1087 3.624861 CACCATCCTTGACATAAGCTCAC 59.375 47.826 0.00 0.00 0.00 3.51
1392 3487 4.418392 GAAACATTGCTGTGCTATCCAAG 58.582 43.478 0.00 0.00 35.22 3.61
1636 3731 5.348833 AGCATATGGGTGAAGGATAGAGAT 58.651 41.667 4.56 0.00 0.00 2.75
1918 4033 5.733937 GCTTTCGCCCCGCTTTATAAATAAA 60.734 40.000 0.00 0.00 0.00 1.40
1919 4034 4.261280 GCTTTCGCCCCGCTTTATAAATAA 60.261 41.667 0.00 0.00 0.00 1.40
1920 4035 3.251487 GCTTTCGCCCCGCTTTATAAATA 59.749 43.478 0.00 0.00 0.00 1.40
1921 4036 2.034179 GCTTTCGCCCCGCTTTATAAAT 59.966 45.455 0.00 0.00 0.00 1.40
1922 4037 1.402613 GCTTTCGCCCCGCTTTATAAA 59.597 47.619 0.00 0.00 0.00 1.40
1923 4038 1.018910 GCTTTCGCCCCGCTTTATAA 58.981 50.000 0.00 0.00 0.00 0.98
1924 4039 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
1925 4040 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
1937 4052 6.019156 CACATTCTCTCTCGAAATAGGCTTTC 60.019 42.308 0.00 0.00 0.00 2.62
1938 4053 5.814705 CACATTCTCTCTCGAAATAGGCTTT 59.185 40.000 0.00 0.00 0.00 3.51
1939 4054 5.105146 ACACATTCTCTCTCGAAATAGGCTT 60.105 40.000 0.00 0.00 0.00 4.35
1940 4055 4.404073 ACACATTCTCTCTCGAAATAGGCT 59.596 41.667 0.00 0.00 0.00 4.58
1941 4056 4.688021 ACACATTCTCTCTCGAAATAGGC 58.312 43.478 0.00 0.00 0.00 3.93
1942 4057 6.036517 CCAAACACATTCTCTCTCGAAATAGG 59.963 42.308 0.00 0.00 0.00 2.57
1943 4058 6.591834 ACCAAACACATTCTCTCTCGAAATAG 59.408 38.462 0.00 0.00 0.00 1.73
1944 4059 6.464222 ACCAAACACATTCTCTCTCGAAATA 58.536 36.000 0.00 0.00 0.00 1.40
1945 4060 5.308825 ACCAAACACATTCTCTCTCGAAAT 58.691 37.500 0.00 0.00 0.00 2.17
1946 4061 4.703897 ACCAAACACATTCTCTCTCGAAA 58.296 39.130 0.00 0.00 0.00 3.46
1947 4062 4.336889 ACCAAACACATTCTCTCTCGAA 57.663 40.909 0.00 0.00 0.00 3.71
1948 4063 4.058124 CAACCAAACACATTCTCTCTCGA 58.942 43.478 0.00 0.00 0.00 4.04
1949 4064 3.364366 GCAACCAAACACATTCTCTCTCG 60.364 47.826 0.00 0.00 0.00 4.04
1950 4065 3.817647 AGCAACCAAACACATTCTCTCTC 59.182 43.478 0.00 0.00 0.00 3.20
1951 4066 3.825328 AGCAACCAAACACATTCTCTCT 58.175 40.909 0.00 0.00 0.00 3.10
1952 4067 4.574599 AAGCAACCAAACACATTCTCTC 57.425 40.909 0.00 0.00 0.00 3.20
1953 4068 4.646492 AGAAAGCAACCAAACACATTCTCT 59.354 37.500 0.00 0.00 0.00 3.10
1954 4069 4.936891 AGAAAGCAACCAAACACATTCTC 58.063 39.130 0.00 0.00 0.00 2.87
1955 4070 5.343307 AAGAAAGCAACCAAACACATTCT 57.657 34.783 0.00 0.00 0.00 2.40
1956 4071 7.713764 ATAAAGAAAGCAACCAAACACATTC 57.286 32.000 0.00 0.00 0.00 2.67
1957 4072 8.504812 AAATAAAGAAAGCAACCAAACACATT 57.495 26.923 0.00 0.00 0.00 2.71
1958 4073 9.777297 ATAAATAAAGAAAGCAACCAAACACAT 57.223 25.926 0.00 0.00 0.00 3.21
2143 4261 6.845302 TCAAATTCATCCATCAGAAACGAAG 58.155 36.000 0.00 0.00 0.00 3.79
2149 4267 4.439153 GCGCTTCAAATTCATCCATCAGAA 60.439 41.667 0.00 0.00 0.00 3.02
2534 4660 1.672030 CGCCTGCACCAACTCATCA 60.672 57.895 0.00 0.00 0.00 3.07
2931 5086 1.566298 CCCTTTCACCTCCTCCCCTG 61.566 65.000 0.00 0.00 0.00 4.45
3078 5256 4.814294 ATCGGGGCGACGAACAGC 62.814 66.667 0.00 0.00 46.92 4.40
3324 5523 6.158598 ACATCTTCAACATGCACCAAAATAC 58.841 36.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.