Multiple sequence alignment - TraesCS2D01G082300

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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 TraesCS2D01G082300 chr2D 100.000 2747 0 0 1 2747 35530835 35533581 0.000000e+00 5073.0
1 TraesCS2D01G082300 chr2D 91.157 769 39 6 1999 2747 533785265 533786024 0.000000e+00 1016.0
2 TraesCS2D01G082300 chr2D 87.156 763 64 16 1256 1998 42075420 42074672 0.000000e+00 835.0
3 TraesCS2D01G082300 chr2D 81.744 975 109 32 994 1958 35639069 35639984 0.000000e+00 750.0
4 TraesCS2D01G082300 chr2D 83.681 766 77 24 996 1749 35677846 35678575 0.000000e+00 678.0
5 TraesCS2D01G082300 chr2D 85.333 675 48 24 231 894 42092386 42091752 0.000000e+00 651.0
6 TraesCS2D01G082300 chr2D 84.686 542 54 19 1374 1901 35564705 35565231 5.250000e-142 514.0
7 TraesCS2D01G082300 chr2D 93.711 318 17 2 996 1313 35564373 35564687 8.900000e-130 473.0
8 TraesCS2D01G082300 chr2D 95.495 222 9 1 1044 1264 42076260 42076039 1.210000e-93 353.0
9 TraesCS2D01G082300 chr2D 90.370 135 8 3 111 242 42093318 42093186 3.640000e-39 172.0
10 TraesCS2D01G082300 chr2D 95.146 103 5 0 1049 1151 605102527 605102425 2.190000e-36 163.0
11 TraesCS2D01G082300 chr2D 94.444 36 2 0 129 164 35638033 35638068 3.820000e-04 56.5
12 TraesCS2D01G082300 chr2A 88.263 1261 84 34 502 1744 38811644 38812858 0.000000e+00 1450.0
13 TraesCS2D01G082300 chr2A 93.291 790 37 9 498 1286 38754552 38755326 0.000000e+00 1151.0
14 TraesCS2D01G082300 chr2A 83.737 867 65 32 914 1749 38908543 38909364 0.000000e+00 750.0
15 TraesCS2D01G082300 chr2A 86.817 622 50 14 1320 1930 38755325 38755925 0.000000e+00 665.0
16 TraesCS2D01G082300 chr2A 90.524 401 35 3 111 510 38810981 38811379 6.740000e-146 527.0
17 TraesCS2D01G082300 chr2A 89.406 387 26 10 914 1286 38878875 38879260 8.900000e-130 473.0
18 TraesCS2D01G082300 chr2A 87.927 381 41 4 114 491 38651391 38651769 6.980000e-121 444.0
19 TraesCS2D01G082300 chr2A 80.620 387 39 18 1589 1967 38879598 38879956 1.620000e-67 267.0
20 TraesCS2D01G082300 chr2A 82.955 264 35 5 1329 1592 38879262 38879515 2.130000e-56 230.0
21 TraesCS2D01G082300 chr2A 92.568 148 10 1 111 258 38753792 38753938 7.710000e-51 211.0
22 TraesCS2D01G082300 chr2A 92.174 115 4 1 606 715 38908247 38908361 1.020000e-34 158.0
23 TraesCS2D01G082300 chr2B 87.721 1018 72 20 802 1794 58689219 58690208 0.000000e+00 1138.0
24 TraesCS2D01G082300 chr2B 84.067 841 75 28 914 1736 58826118 58826917 0.000000e+00 756.0
25 TraesCS2D01G082300 chr2B 89.262 596 45 6 997 1592 58791520 58792096 0.000000e+00 728.0
26 TraesCS2D01G082300 chr2B 89.157 581 36 13 823 1395 58773222 58773783 0.000000e+00 699.0
27 TraesCS2D01G082300 chr2B 89.336 422 31 6 1380 1794 58773798 58774212 4.060000e-143 518.0
28 TraesCS2D01G082300 chr2B 88.969 417 19 10 317 725 58688798 58689195 8.840000e-135 490.0
29 TraesCS2D01G082300 chr2B 89.071 366 32 6 365 725 58772784 58773146 5.400000e-122 448.0
30 TraesCS2D01G082300 chr2B 96.651 209 6 1 111 319 58683590 58683797 2.020000e-91 346.0
31 TraesCS2D01G082300 chr2B 77.752 427 36 19 1588 1968 58792175 58792588 9.970000e-50 207.0
32 TraesCS2D01G082300 chr2B 84.305 223 16 7 507 726 58791015 58791221 1.670000e-47 200.0
33 TraesCS2D01G082300 chr2B 92.437 119 8 1 1791 1908 58774245 58774363 4.700000e-38 169.0
34 TraesCS2D01G082300 chr5D 90.885 757 45 6 2012 2747 287795085 287794332 0.000000e+00 994.0
35 TraesCS2D01G082300 chr4D 90.013 791 36 7 1996 2747 73323979 73323193 0.000000e+00 983.0
36 TraesCS2D01G082300 chr5A 88.832 779 47 4 2008 2747 34869218 34868441 0.000000e+00 920.0
37 TraesCS2D01G082300 chr5A 87.371 776 60 17 2007 2747 379040085 379039313 0.000000e+00 856.0
38 TraesCS2D01G082300 chr5A 86.916 107 13 1 4 109 69189776 69189882 4.810000e-23 119.0
39 TraesCS2D01G082300 chr5A 86.239 109 14 1 4 111 69191828 69191936 1.730000e-22 117.0
40 TraesCS2D01G082300 chr3D 88.889 765 53 10 2007 2747 300178175 300177419 0.000000e+00 913.0
41 TraesCS2D01G082300 chr1A 88.462 780 50 8 2007 2747 241176745 241175967 0.000000e+00 905.0
42 TraesCS2D01G082300 chr7A 87.814 796 45 17 2001 2747 18945899 18946691 0.000000e+00 885.0
43 TraesCS2D01G082300 chr7A 87.534 730 66 9 2041 2747 547180894 547181621 0.000000e+00 821.0
44 TraesCS2D01G082300 chr7A 87.387 111 12 2 4 112 711801758 711801648 2.870000e-25 126.0
45 TraesCS2D01G082300 chr1D 87.611 791 42 21 1996 2747 20925193 20924420 0.000000e+00 867.0
46 TraesCS2D01G082300 chr1D 88.656 573 43 10 2007 2560 256275557 256274988 0.000000e+00 678.0
47 TraesCS2D01G082300 chr1D 97.368 38 1 0 440 477 434664980 434665017 6.350000e-07 65.8
48 TraesCS2D01G082300 chr1B 87.614 767 65 15 2007 2747 111910592 111909830 0.000000e+00 863.0
49 TraesCS2D01G082300 chr1B 86.207 116 5 5 4 114 636748091 636748200 6.220000e-22 115.0
50 TraesCS2D01G082300 chr5B 87.883 751 62 17 2020 2747 659515865 659516609 0.000000e+00 856.0
51 TraesCS2D01G082300 chr7B 87.035 779 59 11 2007 2747 726013895 726014669 0.000000e+00 841.0
52 TraesCS2D01G082300 chr3A 86.736 769 61 14 2012 2747 700628686 700627926 0.000000e+00 817.0
53 TraesCS2D01G082300 chr3A 87.736 106 12 1 4 108 749151865 749151760 3.710000e-24 122.0
54 TraesCS2D01G082300 chr6D 94.094 254 15 0 2007 2260 463627048 463626795 1.190000e-103 387.0
55 TraesCS2D01G082300 chr3B 86.066 122 12 5 4 121 745175118 745174998 2.870000e-25 126.0
56 TraesCS2D01G082300 chr4A 87.273 110 11 2 4 111 375821470 375821578 3.710000e-24 122.0
57 TraesCS2D01G082300 chr4A 84.956 113 16 1 4 115 605090338 605090226 2.240000e-21 113.0
58 TraesCS2D01G082300 chr7D 86.486 111 12 3 4 112 416422259 416422368 4.810000e-23 119.0
59 TraesCS2D01G082300 chr7D 95.000 40 1 1 445 483 177117127 177117088 8.210000e-06 62.1
60 TraesCS2D01G082300 chr6B 93.103 58 4 0 1405 1462 720673872 720673815 4.870000e-13 86.1
61 TraesCS2D01G082300 chr6B 95.122 41 2 0 440 480 530560402 530560362 6.350000e-07 65.8
62 TraesCS2D01G082300 chr6A 91.111 45 4 0 440 484 41667059 41667103 8.210000e-06 62.1


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 TraesCS2D01G082300 chr2D 35530835 35533581 2746 False 5073.000000 5073 100.00000 1 2747 1 chr2D.!!$F1 2746
1 TraesCS2D01G082300 chr2D 533785265 533786024 759 False 1016.000000 1016 91.15700 1999 2747 1 chr2D.!!$F3 748
2 TraesCS2D01G082300 chr2D 35677846 35678575 729 False 678.000000 678 83.68100 996 1749 1 chr2D.!!$F2 753
3 TraesCS2D01G082300 chr2D 42074672 42076260 1588 True 594.000000 835 91.32550 1044 1998 2 chr2D.!!$R2 954
4 TraesCS2D01G082300 chr2D 35564373 35565231 858 False 493.500000 514 89.19850 996 1901 2 chr2D.!!$F4 905
5 TraesCS2D01G082300 chr2D 42091752 42093318 1566 True 411.500000 651 87.85150 111 894 2 chr2D.!!$R3 783
6 TraesCS2D01G082300 chr2D 35638033 35639984 1951 False 403.250000 750 88.09400 129 1958 2 chr2D.!!$F5 1829
7 TraesCS2D01G082300 chr2A 38810981 38812858 1877 False 988.500000 1450 89.39350 111 1744 2 chr2A.!!$F3 1633
8 TraesCS2D01G082300 chr2A 38753792 38755925 2133 False 675.666667 1151 90.89200 111 1930 3 chr2A.!!$F2 1819
9 TraesCS2D01G082300 chr2A 38908247 38909364 1117 False 454.000000 750 87.95550 606 1749 2 chr2A.!!$F5 1143
10 TraesCS2D01G082300 chr2A 38878875 38879956 1081 False 323.333333 473 84.32700 914 1967 3 chr2A.!!$F4 1053
11 TraesCS2D01G082300 chr2B 58688798 58690208 1410 False 814.000000 1138 88.34500 317 1794 2 chr2B.!!$F3 1477
12 TraesCS2D01G082300 chr2B 58826118 58826917 799 False 756.000000 756 84.06700 914 1736 1 chr2B.!!$F2 822
13 TraesCS2D01G082300 chr2B 58772784 58774363 1579 False 458.500000 699 90.00025 365 1908 4 chr2B.!!$F4 1543
14 TraesCS2D01G082300 chr2B 58791015 58792588 1573 False 378.333333 728 83.77300 507 1968 3 chr2B.!!$F5 1461
15 TraesCS2D01G082300 chr5D 287794332 287795085 753 True 994.000000 994 90.88500 2012 2747 1 chr5D.!!$R1 735
16 TraesCS2D01G082300 chr4D 73323193 73323979 786 True 983.000000 983 90.01300 1996 2747 1 chr4D.!!$R1 751
17 TraesCS2D01G082300 chr5A 34868441 34869218 777 True 920.000000 920 88.83200 2008 2747 1 chr5A.!!$R1 739
18 TraesCS2D01G082300 chr5A 379039313 379040085 772 True 856.000000 856 87.37100 2007 2747 1 chr5A.!!$R2 740
19 TraesCS2D01G082300 chr3D 300177419 300178175 756 True 913.000000 913 88.88900 2007 2747 1 chr3D.!!$R1 740
20 TraesCS2D01G082300 chr1A 241175967 241176745 778 True 905.000000 905 88.46200 2007 2747 1 chr1A.!!$R1 740
21 TraesCS2D01G082300 chr7A 18945899 18946691 792 False 885.000000 885 87.81400 2001 2747 1 chr7A.!!$F1 746
22 TraesCS2D01G082300 chr7A 547180894 547181621 727 False 821.000000 821 87.53400 2041 2747 1 chr7A.!!$F2 706
23 TraesCS2D01G082300 chr1D 20924420 20925193 773 True 867.000000 867 87.61100 1996 2747 1 chr1D.!!$R1 751
24 TraesCS2D01G082300 chr1D 256274988 256275557 569 True 678.000000 678 88.65600 2007 2560 1 chr1D.!!$R2 553
25 TraesCS2D01G082300 chr1B 111909830 111910592 762 True 863.000000 863 87.61400 2007 2747 1 chr1B.!!$R1 740
26 TraesCS2D01G082300 chr5B 659515865 659516609 744 False 856.000000 856 87.88300 2020 2747 1 chr5B.!!$F1 727
27 TraesCS2D01G082300 chr7B 726013895 726014669 774 False 841.000000 841 87.03500 2007 2747 1 chr7B.!!$F1 740
28 TraesCS2D01G082300 chr3A 700627926 700628686 760 True 817.000000 817 86.73600 2012 2747 1 chr3A.!!$R1 735

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
44 45 0.033642 TCGCCACATGGTTGTCGTAA 59.966 50.0 0.00 0.0 37.57 3.18 F
94 95 0.100682 CCATCACGACGTTCGATCCT 59.899 55.0 13.06 0.0 43.74 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1186 2924 0.462047 GTTATCCTGGCACCTCCACG 60.462 60.0 0.00 0.00 40.72 4.94 R
1932 4655 1.361793 GGAATAACACGTGCGGCTTA 58.638 50.0 17.22 7.15 0.00 3.09 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
37 38 2.755469 GCCCATCGCCACATGGTT 60.755 61.111 0.00 0.00 41.84 3.67
38 39 3.067480 GCCCATCGCCACATGGTTG 62.067 63.158 0.00 0.00 41.84 3.77
39 40 1.678635 CCCATCGCCACATGGTTGT 60.679 57.895 0.00 0.00 41.84 3.32
40 41 1.656818 CCCATCGCCACATGGTTGTC 61.657 60.000 0.00 0.00 41.84 3.18
41 42 1.425031 CATCGCCACATGGTTGTCG 59.575 57.895 0.00 0.00 37.57 4.35
42 43 1.003839 ATCGCCACATGGTTGTCGT 60.004 52.632 0.00 0.00 37.57 4.34
43 44 0.248012 ATCGCCACATGGTTGTCGTA 59.752 50.000 0.00 0.00 37.57 3.43
44 45 0.033642 TCGCCACATGGTTGTCGTAA 59.966 50.000 0.00 0.00 37.57 3.18
45 46 0.442310 CGCCACATGGTTGTCGTAAG 59.558 55.000 0.00 0.00 37.57 2.34
46 47 1.803334 GCCACATGGTTGTCGTAAGA 58.197 50.000 0.00 0.00 40.55 2.10
47 48 2.147958 GCCACATGGTTGTCGTAAGAA 58.852 47.619 0.00 0.00 43.33 2.52
48 49 2.159627 GCCACATGGTTGTCGTAAGAAG 59.840 50.000 0.00 0.00 43.33 2.85
49 50 4.962384 GCCACATGGTTGTCGTAAGAAGG 61.962 52.174 0.00 0.00 43.33 3.46
58 59 1.905512 CGTAAGAAGGGAGGTGGGG 59.094 63.158 0.00 0.00 43.02 4.96
59 60 0.616679 CGTAAGAAGGGAGGTGGGGA 60.617 60.000 0.00 0.00 43.02 4.81
60 61 1.894699 GTAAGAAGGGAGGTGGGGAT 58.105 55.000 0.00 0.00 0.00 3.85
61 62 1.769465 GTAAGAAGGGAGGTGGGGATC 59.231 57.143 0.00 0.00 0.00 3.36
62 63 0.983378 AAGAAGGGAGGTGGGGATCG 60.983 60.000 0.00 0.00 0.00 3.69
63 64 1.382695 GAAGGGAGGTGGGGATCGA 60.383 63.158 0.00 0.00 0.00 3.59
64 65 0.981277 GAAGGGAGGTGGGGATCGAA 60.981 60.000 0.00 0.00 0.00 3.71
65 66 0.983378 AAGGGAGGTGGGGATCGAAG 60.983 60.000 0.00 0.00 0.00 3.79
66 67 2.444256 GGGAGGTGGGGATCGAAGG 61.444 68.421 0.00 0.00 0.00 3.46
67 68 1.689582 GGAGGTGGGGATCGAAGGT 60.690 63.158 0.00 0.00 0.00 3.50
68 69 1.522569 GAGGTGGGGATCGAAGGTG 59.477 63.158 0.00 0.00 0.00 4.00
69 70 1.972660 GAGGTGGGGATCGAAGGTGG 61.973 65.000 0.00 0.00 0.00 4.61
70 71 2.298661 GGTGGGGATCGAAGGTGGT 61.299 63.158 0.00 0.00 0.00 4.16
71 72 1.221021 GTGGGGATCGAAGGTGGTC 59.779 63.158 0.00 0.00 0.00 4.02
72 73 2.355986 TGGGGATCGAAGGTGGTCG 61.356 63.158 0.00 0.00 42.48 4.79
86 87 4.546637 GTCGAACCATCACGACGT 57.453 55.556 0.00 0.00 46.39 4.34
87 88 2.805277 GTCGAACCATCACGACGTT 58.195 52.632 0.00 0.00 46.39 3.99
88 89 0.706729 GTCGAACCATCACGACGTTC 59.293 55.000 0.00 0.00 46.39 3.95
90 91 3.096541 GAACCATCACGACGTTCGA 57.903 52.632 13.06 0.00 43.74 3.71
91 92 1.625616 GAACCATCACGACGTTCGAT 58.374 50.000 13.06 0.00 43.74 3.59
92 93 1.582502 GAACCATCACGACGTTCGATC 59.417 52.381 13.06 0.00 43.74 3.69
93 94 0.179145 ACCATCACGACGTTCGATCC 60.179 55.000 13.06 0.00 43.74 3.36
94 95 0.100682 CCATCACGACGTTCGATCCT 59.899 55.000 13.06 0.00 43.74 3.24
95 96 1.467875 CATCACGACGTTCGATCCTC 58.532 55.000 13.06 0.00 43.74 3.71
96 97 0.381089 ATCACGACGTTCGATCCTCC 59.619 55.000 13.06 0.00 43.74 4.30
97 98 0.675837 TCACGACGTTCGATCCTCCT 60.676 55.000 13.06 0.00 43.74 3.69
98 99 0.170561 CACGACGTTCGATCCTCCTT 59.829 55.000 13.06 0.00 43.74 3.36
99 100 0.886563 ACGACGTTCGATCCTCCTTT 59.113 50.000 13.06 0.00 43.74 3.11
100 101 2.086869 ACGACGTTCGATCCTCCTTTA 58.913 47.619 13.06 0.00 43.74 1.85
101 102 2.489329 ACGACGTTCGATCCTCCTTTAA 59.511 45.455 13.06 0.00 43.74 1.52
102 103 3.129988 ACGACGTTCGATCCTCCTTTAAT 59.870 43.478 13.06 0.00 43.74 1.40
103 104 4.336433 ACGACGTTCGATCCTCCTTTAATA 59.664 41.667 13.06 0.00 43.74 0.98
104 105 4.910456 CGACGTTCGATCCTCCTTTAATAG 59.090 45.833 0.00 0.00 43.74 1.73
105 106 5.505324 CGACGTTCGATCCTCCTTTAATAGT 60.505 44.000 0.00 0.00 43.74 2.12
106 107 6.293081 CGACGTTCGATCCTCCTTTAATAGTA 60.293 42.308 0.00 0.00 43.74 1.82
107 108 6.968250 ACGTTCGATCCTCCTTTAATAGTAG 58.032 40.000 0.00 0.00 0.00 2.57
108 109 6.769822 ACGTTCGATCCTCCTTTAATAGTAGA 59.230 38.462 0.00 0.00 0.00 2.59
109 110 7.041235 ACGTTCGATCCTCCTTTAATAGTAGAG 60.041 40.741 0.00 0.00 0.00 2.43
203 207 8.626526 ACATTGTAAACCCTTACTAAGTTTGTG 58.373 33.333 0.00 0.00 38.61 3.33
435 1321 8.862325 ATCCATATTAACTGCCGATGATTTAA 57.138 30.769 0.00 0.00 0.00 1.52
479 1659 2.653234 TGGATCGGAGGGAGTAGTAC 57.347 55.000 0.00 0.00 0.00 2.73
517 1982 2.428890 AGAGCAGTTGAATCCCTCTACG 59.571 50.000 0.00 0.00 35.24 3.51
559 2027 1.912001 TTATGAAACGCGTAGACCCG 58.088 50.000 14.46 0.00 0.00 5.28
580 2054 5.704053 CCCGGTATCTATCATACAAAAACCC 59.296 44.000 0.00 0.00 0.00 4.11
601 2174 4.202461 CCCTACAAGCTGCCCTCAAATATA 60.202 45.833 0.00 0.00 0.00 0.86
675 2256 2.758089 CCTGCAGAGCATTGTCGCC 61.758 63.158 17.39 0.00 38.13 5.54
676 2257 2.032376 TGCAGAGCATTGTCGCCA 59.968 55.556 0.00 0.00 31.71 5.69
677 2258 1.374343 CTGCAGAGCATTGTCGCCAT 61.374 55.000 8.42 0.00 38.13 4.40
678 2259 1.063649 GCAGAGCATTGTCGCCATG 59.936 57.895 0.00 0.00 0.00 3.66
895 2521 7.201548 GCACGTCCGGAAGTAGATTTAAAATTA 60.202 37.037 22.92 0.00 0.00 1.40
912 2562 3.802948 ATTAGTCCTCGCTAACCACAG 57.197 47.619 0.00 0.00 34.25 3.66
935 2602 2.840651 CCTCTCGGCTCCCCATATAATT 59.159 50.000 0.00 0.00 0.00 1.40
1017 2742 3.267233 ATGGGGAACTGCCAGGCA 61.267 61.111 15.23 15.23 38.95 4.75
1156 2882 1.213013 GTCCTGCATCACGTCGACT 59.787 57.895 14.70 0.00 0.00 4.18
1349 3731 4.202050 CGGTTCTTGGATTGGATTCCATTC 60.202 45.833 16.08 16.08 45.08 2.67
1778 4439 5.710567 AGAAAAGTAGAACAAGGTATTGGGC 59.289 40.000 0.00 0.00 40.97 5.36
1833 4542 2.892425 CATCGGCTTCTGTCCCGC 60.892 66.667 0.00 0.00 44.01 6.13
1923 4646 3.018149 GTTCGTGTCTGGAGGATCTACT 58.982 50.000 0.00 0.00 33.73 2.57
1932 4655 6.897966 TGTCTGGAGGATCTACTGTTTTATCT 59.102 38.462 0.00 0.00 33.73 1.98
1938 4661 6.750148 AGGATCTACTGTTTTATCTAAGCCG 58.250 40.000 0.00 0.00 0.00 5.52
1958 4681 1.664151 GCACGTGTTATTCCCAGTAGC 59.336 52.381 18.38 0.00 0.00 3.58
1961 4684 1.296727 GTGTTATTCCCAGTAGCGCC 58.703 55.000 2.29 0.00 0.00 6.53
1970 4693 0.889638 CCAGTAGCGCCGAGGATAGA 60.890 60.000 2.29 0.00 0.00 1.98
1973 4696 2.096174 CAGTAGCGCCGAGGATAGATAC 59.904 54.545 2.29 0.00 0.00 2.24
1974 4697 2.082231 GTAGCGCCGAGGATAGATACA 58.918 52.381 2.29 0.00 0.00 2.29
1977 4700 1.914634 CGCCGAGGATAGATACATGC 58.085 55.000 0.00 0.00 0.00 4.06
1979 4702 2.683362 CGCCGAGGATAGATACATGCTA 59.317 50.000 0.00 0.00 0.00 3.49
1981 4704 3.490078 GCCGAGGATAGATACATGCTAGC 60.490 52.174 8.10 8.10 0.00 3.42
1993 4716 6.703607 AGATACATGCTAGCTGTGTTTGTATC 59.296 38.462 24.41 24.37 42.07 2.24
1998 4721 4.709886 TGCTAGCTGTGTTTGTATCCTCTA 59.290 41.667 17.23 0.00 0.00 2.43
1999 4722 5.363868 TGCTAGCTGTGTTTGTATCCTCTAT 59.636 40.000 17.23 0.00 0.00 1.98
2000 4723 5.923684 GCTAGCTGTGTTTGTATCCTCTATC 59.076 44.000 7.70 0.00 0.00 2.08
2001 4724 4.938080 AGCTGTGTTTGTATCCTCTATCG 58.062 43.478 0.00 0.00 0.00 2.92
2002 4725 3.491267 GCTGTGTTTGTATCCTCTATCGC 59.509 47.826 0.00 0.00 0.00 4.58
2003 4726 4.051922 CTGTGTTTGTATCCTCTATCGCC 58.948 47.826 0.00 0.00 0.00 5.54
2004 4727 3.181469 TGTGTTTGTATCCTCTATCGCCC 60.181 47.826 0.00 0.00 0.00 6.13
2005 4728 3.069729 GTGTTTGTATCCTCTATCGCCCT 59.930 47.826 0.00 0.00 0.00 5.19
2078 4802 3.083997 AGGCACGTCCATCCTCCC 61.084 66.667 6.78 0.00 37.29 4.30
2279 5065 4.537433 GGTGCTGCTAGGCTCCGG 62.537 72.222 0.00 0.00 36.39 5.14
2398 5225 4.269523 TGGCGGCAGGTGAAGCTT 62.270 61.111 7.97 0.00 0.00 3.74
2486 5313 0.598942 GTTTTGCCGCGGATTGGTTT 60.599 50.000 33.48 0.00 0.00 3.27
2501 5328 2.176045 TGGTTTAGATCAGAGACGGCA 58.824 47.619 0.00 0.00 0.00 5.69
2625 5455 4.162690 CAGGCTCCTACGGTGGCC 62.163 72.222 0.00 0.00 41.66 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.755469 AACCATGTGGCGATGGGC 60.755 61.111 17.10 0.00 46.46 5.36
21 22 1.656818 GACAACCATGTGGCGATGGG 61.657 60.000 17.10 5.51 46.46 4.00
27 28 1.803334 TCTTACGACAACCATGTGGC 58.197 50.000 0.00 0.00 40.74 5.01
28 29 2.742053 CCTTCTTACGACAACCATGTGG 59.258 50.000 0.00 0.00 40.74 4.17
29 30 2.742053 CCCTTCTTACGACAACCATGTG 59.258 50.000 0.00 0.00 40.74 3.21
30 31 2.635915 TCCCTTCTTACGACAACCATGT 59.364 45.455 0.00 0.00 44.25 3.21
31 32 3.262420 CTCCCTTCTTACGACAACCATG 58.738 50.000 0.00 0.00 0.00 3.66
32 33 2.236395 CCTCCCTTCTTACGACAACCAT 59.764 50.000 0.00 0.00 0.00 3.55
33 34 1.621814 CCTCCCTTCTTACGACAACCA 59.378 52.381 0.00 0.00 0.00 3.67
34 35 1.622312 ACCTCCCTTCTTACGACAACC 59.378 52.381 0.00 0.00 0.00 3.77
35 36 2.612221 CCACCTCCCTTCTTACGACAAC 60.612 54.545 0.00 0.00 0.00 3.32
36 37 1.621814 CCACCTCCCTTCTTACGACAA 59.378 52.381 0.00 0.00 0.00 3.18
37 38 1.263356 CCACCTCCCTTCTTACGACA 58.737 55.000 0.00 0.00 0.00 4.35
38 39 0.535797 CCCACCTCCCTTCTTACGAC 59.464 60.000 0.00 0.00 0.00 4.34
39 40 0.616679 CCCCACCTCCCTTCTTACGA 60.617 60.000 0.00 0.00 0.00 3.43
40 41 0.616679 TCCCCACCTCCCTTCTTACG 60.617 60.000 0.00 0.00 0.00 3.18
41 42 1.769465 GATCCCCACCTCCCTTCTTAC 59.231 57.143 0.00 0.00 0.00 2.34
42 43 1.691482 CGATCCCCACCTCCCTTCTTA 60.691 57.143 0.00 0.00 0.00 2.10
43 44 0.983378 CGATCCCCACCTCCCTTCTT 60.983 60.000 0.00 0.00 0.00 2.52
44 45 1.383248 CGATCCCCACCTCCCTTCT 60.383 63.158 0.00 0.00 0.00 2.85
45 46 0.981277 TTCGATCCCCACCTCCCTTC 60.981 60.000 0.00 0.00 0.00 3.46
46 47 0.983378 CTTCGATCCCCACCTCCCTT 60.983 60.000 0.00 0.00 0.00 3.95
47 48 1.383248 CTTCGATCCCCACCTCCCT 60.383 63.158 0.00 0.00 0.00 4.20
48 49 2.444256 CCTTCGATCCCCACCTCCC 61.444 68.421 0.00 0.00 0.00 4.30
49 50 1.689582 ACCTTCGATCCCCACCTCC 60.690 63.158 0.00 0.00 0.00 4.30
50 51 1.522569 CACCTTCGATCCCCACCTC 59.477 63.158 0.00 0.00 0.00 3.85
51 52 1.995626 CCACCTTCGATCCCCACCT 60.996 63.158 0.00 0.00 0.00 4.00
52 53 2.253403 GACCACCTTCGATCCCCACC 62.253 65.000 0.00 0.00 0.00 4.61
53 54 1.221021 GACCACCTTCGATCCCCAC 59.779 63.158 0.00 0.00 0.00 4.61
54 55 2.355986 CGACCACCTTCGATCCCCA 61.356 63.158 0.00 0.00 41.78 4.96
55 56 1.610554 TTCGACCACCTTCGATCCCC 61.611 60.000 0.00 0.00 46.94 4.81
56 57 0.459759 GTTCGACCACCTTCGATCCC 60.460 60.000 0.00 0.00 46.94 3.85
57 58 0.459759 GGTTCGACCACCTTCGATCC 60.460 60.000 6.82 6.82 46.94 3.36
58 59 0.245539 TGGTTCGACCACCTTCGATC 59.754 55.000 7.76 0.00 44.79 3.69
59 60 2.358039 TGGTTCGACCACCTTCGAT 58.642 52.632 7.76 0.00 44.79 3.59
60 61 3.859221 TGGTTCGACCACCTTCGA 58.141 55.556 7.76 0.00 44.79 3.71
70 71 3.096541 GAACGTCGTGATGGTTCGA 57.903 52.632 0.00 0.00 31.82 3.71
72 73 1.582502 GATCGAACGTCGTGATGGTTC 59.417 52.381 0.00 6.67 41.35 3.62
73 74 1.625616 GATCGAACGTCGTGATGGTT 58.374 50.000 0.00 0.00 41.35 3.67
74 75 0.179145 GGATCGAACGTCGTGATGGT 60.179 55.000 0.00 0.00 41.35 3.55
75 76 0.100682 AGGATCGAACGTCGTGATGG 59.899 55.000 0.00 0.00 41.35 3.51
76 77 1.467875 GAGGATCGAACGTCGTGATG 58.532 55.000 0.00 0.00 41.35 3.07
77 78 0.381089 GGAGGATCGAACGTCGTGAT 59.619 55.000 0.00 0.00 41.35 3.06
78 79 0.675837 AGGAGGATCGAACGTCGTGA 60.676 55.000 9.35 0.00 41.35 4.35
79 80 0.170561 AAGGAGGATCGAACGTCGTG 59.829 55.000 10.63 0.00 41.35 4.35
80 81 0.886563 AAAGGAGGATCGAACGTCGT 59.113 50.000 8.94 6.98 41.35 4.34
81 82 2.838386 TAAAGGAGGATCGAACGTCG 57.162 50.000 8.94 0.00 42.10 5.12
82 83 5.829829 ACTATTAAAGGAGGATCGAACGTC 58.170 41.667 6.82 6.82 34.37 4.34
83 84 5.848833 ACTATTAAAGGAGGATCGAACGT 57.151 39.130 0.00 0.00 34.37 3.99
84 85 7.172875 TCTCTACTATTAAAGGAGGATCGAACG 59.827 40.741 0.00 0.00 36.71 3.95
85 86 8.393671 TCTCTACTATTAAAGGAGGATCGAAC 57.606 38.462 0.00 0.00 36.71 3.95
91 92 9.810870 GACCTTATCTCTACTATTAAAGGAGGA 57.189 37.037 5.28 0.00 36.71 3.71
92 93 9.589461 TGACCTTATCTCTACTATTAAAGGAGG 57.411 37.037 5.28 0.00 36.71 4.30
108 109 9.793259 TGAGAGTTTTTACAAATGACCTTATCT 57.207 29.630 0.00 0.00 0.00 1.98
109 110 9.827411 GTGAGAGTTTTTACAAATGACCTTATC 57.173 33.333 0.00 0.00 0.00 1.75
203 207 8.352942 GGTATTGTGGATGTCAATATTCTTTCC 58.647 37.037 0.00 0.00 39.10 3.13
214 218 8.490311 TGTATCTATTTGGTATTGTGGATGTCA 58.510 33.333 0.00 0.00 0.00 3.58
215 219 8.902540 TGTATCTATTTGGTATTGTGGATGTC 57.097 34.615 0.00 0.00 0.00 3.06
300 1114 8.193438 AGTTCACCAAAGAAGAAGAAAAATCAG 58.807 33.333 0.00 0.00 0.00 2.90
454 1340 5.511363 ACTACTCCCTCCGATCCATATTAG 58.489 45.833 0.00 0.00 0.00 1.73
559 2027 9.841295 TTGTAGGGTTTTTGTATGATAGATACC 57.159 33.333 0.00 0.00 0.00 2.73
580 2054 6.318648 TGTTTATATTTGAGGGCAGCTTGTAG 59.681 38.462 0.00 0.00 0.00 2.74
601 2174 5.815740 AGAGTCGTCACATGTAAACTTGTTT 59.184 36.000 0.00 4.14 32.76 2.83
675 2256 4.409218 GGGCGCGCCATATGCATG 62.409 66.667 46.88 0.00 41.33 4.06
676 2257 4.953010 TGGGCGCGCCATATGCAT 62.953 61.111 46.88 3.79 41.33 3.96
770 2355 7.561021 ACAAGGAGAAGAGAAGAAAAAGTTC 57.439 36.000 0.00 0.00 0.00 3.01
895 2521 0.889306 GACTGTGGTTAGCGAGGACT 59.111 55.000 0.00 0.00 0.00 3.85
1186 2924 0.462047 GTTATCCTGGCACCTCCACG 60.462 60.000 0.00 0.00 40.72 4.94
1349 3731 3.011760 GAACCGGACAAGAAGCGCG 62.012 63.158 9.46 0.00 0.00 6.86
1411 3847 2.046892 GGTCACCTCTGCACGCAT 60.047 61.111 0.00 0.00 0.00 4.73
1778 4439 4.383052 CGCCTAATGTACATTTCTAGCTCG 59.617 45.833 25.31 16.83 32.50 5.03
1833 4542 5.181245 ACTGTATCACCAAAACGGATTCAAG 59.819 40.000 0.00 0.00 38.63 3.02
1886 4607 3.612860 CACGAACGGGTAATCTTCAGAAG 59.387 47.826 3.45 3.45 0.00 2.85
1923 4646 2.413796 CACGTGCGGCTTAGATAAAACA 59.586 45.455 0.82 0.00 0.00 2.83
1932 4655 1.361793 GGAATAACACGTGCGGCTTA 58.638 50.000 17.22 7.15 0.00 3.09
1938 4661 1.664151 GCTACTGGGAATAACACGTGC 59.336 52.381 17.22 0.00 0.00 5.34
1958 4681 1.474478 AGCATGTATCTATCCTCGGCG 59.526 52.381 0.00 0.00 0.00 6.46
1961 4684 4.397730 ACAGCTAGCATGTATCTATCCTCG 59.602 45.833 18.83 0.00 0.00 4.63
1970 4693 5.760253 GGATACAAACACAGCTAGCATGTAT 59.240 40.000 21.05 19.28 35.76 2.29
1973 4696 4.194640 AGGATACAAACACAGCTAGCATG 58.805 43.478 18.83 16.84 41.41 4.06
1974 4697 4.163078 AGAGGATACAAACACAGCTAGCAT 59.837 41.667 18.83 0.78 41.41 3.79
1977 4700 6.146216 CGATAGAGGATACAAACACAGCTAG 58.854 44.000 0.00 0.00 41.41 3.42
1979 4702 4.737946 GCGATAGAGGATACAAACACAGCT 60.738 45.833 0.00 0.00 41.41 4.24
1981 4704 4.051922 GGCGATAGAGGATACAAACACAG 58.948 47.826 0.00 0.00 41.41 3.66
1993 4716 3.686045 GCGGGAGGGCGATAGAGG 61.686 72.222 0.00 0.00 39.76 3.69
2119 4843 3.731728 GCCATCAGCCACCTGGGA 61.732 66.667 0.00 0.00 40.01 4.37
2279 5065 2.514824 GCGCCACCAGATCTTCCC 60.515 66.667 0.00 0.00 0.00 3.97
2321 5107 2.484062 GCGACCAAGGCCATCATGG 61.484 63.158 5.01 10.52 41.55 3.66
2424 5251 0.475906 GCCTTGGATAGGGACAGCAT 59.524 55.000 0.00 0.00 44.91 3.79
2486 5313 3.067320 CACTCATTGCCGTCTCTGATCTA 59.933 47.826 0.00 0.00 0.00 1.98
2501 5328 3.928005 AGATGATCCTGCACACTCATT 57.072 42.857 0.00 0.00 0.00 2.57
2566 5395 2.954684 CGCCACCACTGGAGCCTAA 61.955 63.158 0.71 0.00 40.55 2.69
2567 5396 3.390521 CGCCACCACTGGAGCCTA 61.391 66.667 0.71 0.00 40.55 3.93
2625 5455 0.248458 GACCAACCGCAACAACAGTG 60.248 55.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.