Multiple sequence alignment - TraesCS3B01G570200

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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 TraesCS3B01G570200 chr3B 100.000 4535 0 0 1 4535 802099663 802104197 0.000000e+00 8375.0
1 TraesCS3B01G570200 chr3B 80.470 1234 225 10 1659 2883 618080121 618078895 0.000000e+00 929.0
2 TraesCS3B01G570200 chr3B 100.000 305 0 0 1 305 801960024 801960328 8.520000e-157 564.0
3 TraesCS3B01G570200 chr3B 100.000 305 0 0 1 305 802808146 802807842 8.520000e-157 564.0
4 TraesCS3B01G570200 chr1B 98.397 3556 55 2 982 4535 20565173 20561618 0.000000e+00 6250.0
5 TraesCS3B01G570200 chr1B 98.115 3554 52 1 982 4535 321005169 321008707 0.000000e+00 6178.0
6 TraesCS3B01G570200 chr1B 85.678 1564 201 12 2973 4532 395171397 395172941 0.000000e+00 1626.0
7 TraesCS3B01G570200 chr1B 97.950 683 11 3 302 982 20558417 20559098 0.000000e+00 1181.0
8 TraesCS3B01G570200 chr1B 98.077 676 13 0 307 982 321011904 321011229 0.000000e+00 1177.0
9 TraesCS3B01G570200 chr1B 84.545 220 21 6 66 276 35213458 35213673 5.950000e-49 206.0
10 TraesCS3B01G570200 chr1B 92.727 55 4 0 1 55 35182167 35182221 3.760000e-11 80.5
11 TraesCS3B01G570200 chr2B 97.877 2214 46 1 2323 4535 615582480 615584693 0.000000e+00 3827.0
12 TraesCS3B01G570200 chr2B 98.809 1763 21 0 2773 4535 741236650 741238412 0.000000e+00 3140.0
13 TraesCS3B01G570200 chr2B 98.752 1763 22 0 2773 4535 741206917 741208679 0.000000e+00 3134.0
14 TraesCS3B01G570200 chr2B 98.227 677 12 0 306 982 741211876 741211200 0.000000e+00 1184.0
15 TraesCS3B01G570200 chr2B 98.227 677 12 0 306 982 741241609 741240933 0.000000e+00 1184.0
16 TraesCS3B01G570200 chr2B 97.046 677 20 0 306 982 318083054 318083730 0.000000e+00 1140.0
17 TraesCS3B01G570200 chr2B 96.898 677 21 0 306 982 615587889 615587213 0.000000e+00 1134.0
18 TraesCS3B01G570200 chr5B 97.077 1642 46 2 1753 3394 610047405 610045766 0.000000e+00 2765.0
19 TraesCS3B01G570200 chr5B 93.697 1761 91 3 2775 4535 589865291 589863551 0.000000e+00 2619.0
20 TraesCS3B01G570200 chr5B 98.080 1146 22 0 3390 4535 610028444 610027299 0.000000e+00 1995.0
21 TraesCS3B01G570200 chr5B 97.630 675 15 1 308 982 610024105 610024778 0.000000e+00 1157.0
22 TraesCS3B01G570200 chr6A 78.381 2507 479 43 396 2882 593949386 593951849 0.000000e+00 1568.0
23 TraesCS3B01G570200 chr6A 83.433 670 90 10 2970 3636 593952039 593952690 1.800000e-168 603.0
24 TraesCS3B01G570200 chr7B 85.393 1513 200 10 3020 4529 370942772 370944266 0.000000e+00 1550.0
25 TraesCS3B01G570200 chr7B 79.049 1914 358 36 984 2882 370940693 370942578 0.000000e+00 1273.0
26 TraesCS3B01G570200 chr7A 86.746 1260 147 8 3274 4532 452640629 452641869 0.000000e+00 1384.0
27 TraesCS3B01G570200 chr7A 81.377 247 29 8 1 238 700873736 700873498 7.750000e-43 185.0
28 TraesCS3B01G570200 chr6D 93.191 940 64 0 3596 4535 469363121 469362182 0.000000e+00 1382.0
29 TraesCS3B01G570200 chr4A 79.395 1883 344 34 1005 2869 648287434 648289290 0.000000e+00 1288.0
30 TraesCS3B01G570200 chr6B 98.373 676 11 0 307 982 131695262 131695937 0.000000e+00 1188.0
31 TraesCS3B01G570200 chr6B 97.938 679 14 0 304 982 712550671 712549993 0.000000e+00 1177.0
32 TraesCS3B01G570200 chr6B 81.592 201 21 9 1 185 607829728 607829528 7.860000e-33 152.0
33 TraesCS3B01G570200 chr1D 83.539 893 143 4 1684 2574 216316486 216317376 0.000000e+00 832.0
34 TraesCS3B01G570200 chrUn 83.224 763 117 9 1684 2441 403596219 403595463 0.000000e+00 689.0
35 TraesCS3B01G570200 chrUn 100.000 305 0 0 1 305 162825312 162825008 8.520000e-157 564.0
36 TraesCS3B01G570200 chr3D 88.761 436 43 1 2884 3313 67629187 67628752 3.110000e-146 529.0
37 TraesCS3B01G570200 chr3D 78.827 307 38 11 5 289 510360300 510360601 1.000000e-41 182.0
38 TraesCS3B01G570200 chr5D 85.664 286 24 9 1 274 462619403 462619683 7.430000e-73 285.0


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 TraesCS3B01G570200 chr3B 802099663 802104197 4534 False 8375.0 8375 100.000 1 4535 1 chr3B.!!$F2 4534
1 TraesCS3B01G570200 chr3B 618078895 618080121 1226 True 929.0 929 80.470 1659 2883 1 chr3B.!!$R1 1224
2 TraesCS3B01G570200 chr1B 20561618 20565173 3555 True 6250.0 6250 98.397 982 4535 1 chr1B.!!$R1 3553
3 TraesCS3B01G570200 chr1B 321005169 321008707 3538 False 6178.0 6178 98.115 982 4535 1 chr1B.!!$F4 3553
4 TraesCS3B01G570200 chr1B 395171397 395172941 1544 False 1626.0 1626 85.678 2973 4532 1 chr1B.!!$F5 1559
5 TraesCS3B01G570200 chr1B 20558417 20559098 681 False 1181.0 1181 97.950 302 982 1 chr1B.!!$F1 680
6 TraesCS3B01G570200 chr1B 321011229 321011904 675 True 1177.0 1177 98.077 307 982 1 chr1B.!!$R2 675
7 TraesCS3B01G570200 chr2B 615582480 615584693 2213 False 3827.0 3827 97.877 2323 4535 1 chr2B.!!$F2 2212
8 TraesCS3B01G570200 chr2B 741236650 741238412 1762 False 3140.0 3140 98.809 2773 4535 1 chr2B.!!$F4 1762
9 TraesCS3B01G570200 chr2B 741206917 741208679 1762 False 3134.0 3134 98.752 2773 4535 1 chr2B.!!$F3 1762
10 TraesCS3B01G570200 chr2B 741211200 741211876 676 True 1184.0 1184 98.227 306 982 1 chr2B.!!$R2 676
11 TraesCS3B01G570200 chr2B 741240933 741241609 676 True 1184.0 1184 98.227 306 982 1 chr2B.!!$R3 676
12 TraesCS3B01G570200 chr2B 318083054 318083730 676 False 1140.0 1140 97.046 306 982 1 chr2B.!!$F1 676
13 TraesCS3B01G570200 chr2B 615587213 615587889 676 True 1134.0 1134 96.898 306 982 1 chr2B.!!$R1 676
14 TraesCS3B01G570200 chr5B 610045766 610047405 1639 True 2765.0 2765 97.077 1753 3394 1 chr5B.!!$R3 1641
15 TraesCS3B01G570200 chr5B 589863551 589865291 1740 True 2619.0 2619 93.697 2775 4535 1 chr5B.!!$R1 1760
16 TraesCS3B01G570200 chr5B 610027299 610028444 1145 True 1995.0 1995 98.080 3390 4535 1 chr5B.!!$R2 1145
17 TraesCS3B01G570200 chr5B 610024105 610024778 673 False 1157.0 1157 97.630 308 982 1 chr5B.!!$F1 674
18 TraesCS3B01G570200 chr6A 593949386 593952690 3304 False 1085.5 1568 80.907 396 3636 2 chr6A.!!$F1 3240
19 TraesCS3B01G570200 chr7B 370940693 370944266 3573 False 1411.5 1550 82.221 984 4529 2 chr7B.!!$F1 3545
20 TraesCS3B01G570200 chr7A 452640629 452641869 1240 False 1384.0 1384 86.746 3274 4532 1 chr7A.!!$F1 1258
21 TraesCS3B01G570200 chr6D 469362182 469363121 939 True 1382.0 1382 93.191 3596 4535 1 chr6D.!!$R1 939
22 TraesCS3B01G570200 chr4A 648287434 648289290 1856 False 1288.0 1288 79.395 1005 2869 1 chr4A.!!$F1 1864
23 TraesCS3B01G570200 chr6B 131695262 131695937 675 False 1188.0 1188 98.373 307 982 1 chr6B.!!$F1 675
24 TraesCS3B01G570200 chr6B 712549993 712550671 678 True 1177.0 1177 97.938 304 982 1 chr6B.!!$R2 678
25 TraesCS3B01G570200 chr1D 216316486 216317376 890 False 832.0 832 83.539 1684 2574 1 chr1D.!!$F1 890
26 TraesCS3B01G570200 chrUn 403595463 403596219 756 True 689.0 689 83.224 1684 2441 1 chrUn.!!$R2 757

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
40 41 0.036858 TGCACGTACATAGCAGGCAA 60.037 50.0 0.00 0.00 33.75 4.52 F
289 290 0.101219 GATTCATGGCCGCCTGAAAC 59.899 55.0 20.92 16.69 35.20 2.78 F
290 291 1.656818 ATTCATGGCCGCCTGAAACG 61.657 55.0 20.92 2.43 35.20 3.60 F
2053 2062 1.166531 GCGTGTTCTTCAAGCTGGGT 61.167 55.0 0.00 0.00 45.42 4.51 F
2399 2414 1.490621 AACATCTGTTTTTGCTGCGC 58.509 45.0 0.00 0.00 33.93 6.09 F
2971 3088 0.323302 TAAAGCTCATGGTGGTCGCA 59.677 50.0 0.00 0.00 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1204 0.041684 CCTTCAAATCCCCCTTGCCT 59.958 55.000 0.00 0.00 0.00 4.75 R
2053 2062 1.174078 TCGTTCTGGTAGTGCCACGA 61.174 55.000 7.25 7.25 43.61 4.35 R
2399 2414 1.594293 GTCGTGTGTCCCACCACTG 60.594 63.158 0.00 0.00 41.26 3.66 R
2971 3088 1.677966 CATCAGCAGCAGCACCCTT 60.678 57.895 3.17 0.00 45.49 3.95 R
3489 3609 3.220999 CTCGCCCGTCAGTTGACCA 62.221 63.158 6.68 0.00 41.86 4.02 R
4399 4520 5.772393 ACCAATATGTTCCTTACTCCACA 57.228 39.130 0.00 0.00 0.00 4.17 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
17 18 3.499406 TGGAGCTGGCCTCAACAT 58.501 55.556 3.32 0.00 42.62 2.71
18 19 1.001764 TGGAGCTGGCCTCAACATG 60.002 57.895 3.32 0.00 42.62 3.21
19 20 2.413142 GGAGCTGGCCTCAACATGC 61.413 63.158 3.32 0.00 42.62 4.06
20 21 1.676635 GAGCTGGCCTCAACATGCA 60.677 57.895 3.32 0.00 40.45 3.96
21 22 1.000019 AGCTGGCCTCAACATGCAT 60.000 52.632 3.32 0.00 0.00 3.96
22 23 1.141019 GCTGGCCTCAACATGCATG 59.859 57.895 25.09 25.09 0.00 4.06
23 24 1.141019 CTGGCCTCAACATGCATGC 59.859 57.895 26.53 11.82 0.00 4.06
24 25 1.600511 CTGGCCTCAACATGCATGCA 61.601 55.000 26.53 25.04 0.00 3.96
25 26 1.153706 GGCCTCAACATGCATGCAC 60.154 57.895 25.37 7.38 0.00 4.57
26 27 1.515519 GCCTCAACATGCATGCACG 60.516 57.895 25.37 19.13 0.00 5.34
27 28 1.878070 CCTCAACATGCATGCACGT 59.122 52.632 25.37 19.99 0.00 4.49
28 29 1.085893 CCTCAACATGCATGCACGTA 58.914 50.000 25.37 5.77 0.00 3.57
29 30 1.202065 CCTCAACATGCATGCACGTAC 60.202 52.381 25.37 0.00 0.00 3.67
30 31 1.464219 CTCAACATGCATGCACGTACA 59.536 47.619 25.37 10.05 0.00 2.90
31 32 2.083002 TCAACATGCATGCACGTACAT 58.917 42.857 25.37 2.49 0.00 2.29
32 33 3.265791 TCAACATGCATGCACGTACATA 58.734 40.909 25.37 4.37 0.00 2.29
33 34 3.309410 TCAACATGCATGCACGTACATAG 59.691 43.478 25.37 9.47 0.00 2.23
34 35 1.599071 ACATGCATGCACGTACATAGC 59.401 47.619 25.37 8.33 0.00 2.97
35 36 1.598601 CATGCATGCACGTACATAGCA 59.401 47.619 25.37 20.53 43.14 3.49
36 37 1.289276 TGCATGCACGTACATAGCAG 58.711 50.000 18.46 1.79 42.14 4.24
37 38 0.583438 GCATGCACGTACATAGCAGG 59.417 55.000 14.21 10.53 42.14 4.85
38 39 0.583438 CATGCACGTACATAGCAGGC 59.417 55.000 0.00 0.00 42.14 4.85
39 40 0.177836 ATGCACGTACATAGCAGGCA 59.822 50.000 0.00 0.00 42.14 4.75
40 41 0.036858 TGCACGTACATAGCAGGCAA 60.037 50.000 0.00 0.00 33.75 4.52
41 42 1.299541 GCACGTACATAGCAGGCAAT 58.700 50.000 0.00 0.00 0.00 3.56
42 43 2.159028 TGCACGTACATAGCAGGCAATA 60.159 45.455 0.00 0.00 33.75 1.90
43 44 2.869801 GCACGTACATAGCAGGCAATAA 59.130 45.455 0.00 0.00 0.00 1.40
44 45 3.311322 GCACGTACATAGCAGGCAATAAA 59.689 43.478 0.00 0.00 0.00 1.40
45 46 4.201871 GCACGTACATAGCAGGCAATAAAA 60.202 41.667 0.00 0.00 0.00 1.52
46 47 5.505654 GCACGTACATAGCAGGCAATAAAAT 60.506 40.000 0.00 0.00 0.00 1.82
47 48 6.494842 CACGTACATAGCAGGCAATAAAATT 58.505 36.000 0.00 0.00 0.00 1.82
48 49 7.635423 CACGTACATAGCAGGCAATAAAATTA 58.365 34.615 0.00 0.00 0.00 1.40
49 50 8.126074 CACGTACATAGCAGGCAATAAAATTAA 58.874 33.333 0.00 0.00 0.00 1.40
50 51 8.846211 ACGTACATAGCAGGCAATAAAATTAAT 58.154 29.630 0.00 0.00 0.00 1.40
51 52 9.677567 CGTACATAGCAGGCAATAAAATTAATT 57.322 29.630 0.00 0.00 0.00 1.40
71 72 6.484818 AATTTATTCCACATGTGCAAAAGC 57.515 33.333 20.81 0.00 0.00 3.51
72 73 4.870123 TTATTCCACATGTGCAAAAGCT 57.130 36.364 20.81 0.00 0.00 3.74
73 74 2.512485 TTCCACATGTGCAAAAGCTG 57.488 45.000 20.81 4.26 0.00 4.24
74 75 0.675083 TCCACATGTGCAAAAGCTGG 59.325 50.000 20.81 3.52 0.00 4.85
75 76 0.675083 CCACATGTGCAAAAGCTGGA 59.325 50.000 20.81 0.00 0.00 3.86
76 77 1.274167 CCACATGTGCAAAAGCTGGAT 59.726 47.619 20.81 0.00 0.00 3.41
77 78 2.492881 CCACATGTGCAAAAGCTGGATA 59.507 45.455 20.81 0.00 0.00 2.59
78 79 3.504863 CACATGTGCAAAAGCTGGATAC 58.495 45.455 13.94 0.00 0.00 2.24
79 80 2.162208 ACATGTGCAAAAGCTGGATACG 59.838 45.455 0.00 0.00 42.51 3.06
80 81 0.521291 TGTGCAAAAGCTGGATACGC 59.479 50.000 0.00 0.00 42.51 4.42
81 82 0.804989 GTGCAAAAGCTGGATACGCT 59.195 50.000 0.00 0.00 45.89 5.07
82 83 2.006888 GTGCAAAAGCTGGATACGCTA 58.993 47.619 0.00 0.00 43.79 4.26
83 84 2.614057 GTGCAAAAGCTGGATACGCTAT 59.386 45.455 0.00 0.00 43.79 2.97
84 85 2.872245 TGCAAAAGCTGGATACGCTATC 59.128 45.455 0.00 0.00 43.79 2.08
85 86 3.134458 GCAAAAGCTGGATACGCTATCT 58.866 45.455 0.00 0.00 43.79 1.98
86 87 4.202212 TGCAAAAGCTGGATACGCTATCTA 60.202 41.667 0.00 0.13 43.79 1.98
87 88 4.750098 GCAAAAGCTGGATACGCTATCTAA 59.250 41.667 0.00 0.00 43.79 2.10
88 89 5.409826 GCAAAAGCTGGATACGCTATCTAAT 59.590 40.000 0.00 0.00 43.79 1.73
89 90 6.073003 GCAAAAGCTGGATACGCTATCTAATT 60.073 38.462 0.00 0.00 43.79 1.40
90 91 7.293745 CAAAAGCTGGATACGCTATCTAATTG 58.706 38.462 0.00 0.00 43.79 2.32
91 92 5.984695 AGCTGGATACGCTATCTAATTGA 57.015 39.130 0.00 0.00 42.99 2.57
92 93 6.537453 AGCTGGATACGCTATCTAATTGAT 57.463 37.500 0.00 0.00 42.99 2.57
93 94 6.940739 AGCTGGATACGCTATCTAATTGATT 58.059 36.000 0.00 0.00 42.99 2.57
94 95 7.038659 AGCTGGATACGCTATCTAATTGATTC 58.961 38.462 0.00 0.00 42.99 2.52
95 96 6.813649 GCTGGATACGCTATCTAATTGATTCA 59.186 38.462 0.00 0.00 42.51 2.57
96 97 7.201478 GCTGGATACGCTATCTAATTGATTCAC 60.201 40.741 0.00 0.00 42.51 3.18
97 98 6.806739 TGGATACGCTATCTAATTGATTCACG 59.193 38.462 0.00 0.00 42.51 4.35
98 99 6.253727 GGATACGCTATCTAATTGATTCACGG 59.746 42.308 0.00 0.00 36.65 4.94
99 100 3.741344 ACGCTATCTAATTGATTCACGGC 59.259 43.478 0.00 0.00 36.65 5.68
100 101 3.123621 CGCTATCTAATTGATTCACGGCC 59.876 47.826 0.00 0.00 36.65 6.13
101 102 3.123621 GCTATCTAATTGATTCACGGCCG 59.876 47.826 26.86 26.86 36.65 6.13
102 103 1.948104 TCTAATTGATTCACGGCCGG 58.052 50.000 31.76 18.67 0.00 6.13
103 104 0.307760 CTAATTGATTCACGGCCGGC 59.692 55.000 31.76 21.18 0.00 6.13
104 105 1.098712 TAATTGATTCACGGCCGGCC 61.099 55.000 36.69 36.69 0.00 6.13
118 119 4.397832 GGCCGGAAACCTACGCCA 62.398 66.667 5.05 0.00 0.00 5.69
119 120 2.358984 GCCGGAAACCTACGCCAA 60.359 61.111 5.05 0.00 0.00 4.52
120 121 2.683859 GCCGGAAACCTACGCCAAC 61.684 63.158 5.05 0.00 0.00 3.77
121 122 1.004200 CCGGAAACCTACGCCAACT 60.004 57.895 0.00 0.00 0.00 3.16
122 123 0.604511 CCGGAAACCTACGCCAACTT 60.605 55.000 0.00 0.00 0.00 2.66
123 124 0.515564 CGGAAACCTACGCCAACTTG 59.484 55.000 0.00 0.00 0.00 3.16
124 125 0.240145 GGAAACCTACGCCAACTTGC 59.760 55.000 0.00 0.00 0.00 4.01
125 126 0.948678 GAAACCTACGCCAACTTGCA 59.051 50.000 0.00 0.00 0.00 4.08
126 127 0.666374 AAACCTACGCCAACTTGCAC 59.334 50.000 0.00 0.00 0.00 4.57
127 128 0.179029 AACCTACGCCAACTTGCACT 60.179 50.000 0.00 0.00 0.00 4.40
128 129 0.602905 ACCTACGCCAACTTGCACTC 60.603 55.000 0.00 0.00 0.00 3.51
129 130 0.320771 CCTACGCCAACTTGCACTCT 60.321 55.000 0.00 0.00 0.00 3.24
130 131 1.071605 CTACGCCAACTTGCACTCTC 58.928 55.000 0.00 0.00 0.00 3.20
131 132 0.666274 TACGCCAACTTGCACTCTCG 60.666 55.000 0.00 0.00 0.00 4.04
132 133 1.664649 CGCCAACTTGCACTCTCGA 60.665 57.895 0.00 0.00 0.00 4.04
133 134 1.221466 CGCCAACTTGCACTCTCGAA 61.221 55.000 0.00 0.00 0.00 3.71
134 135 0.944386 GCCAACTTGCACTCTCGAAA 59.056 50.000 0.00 0.00 0.00 3.46
135 136 1.537202 GCCAACTTGCACTCTCGAAAT 59.463 47.619 0.00 0.00 0.00 2.17
136 137 2.413371 GCCAACTTGCACTCTCGAAATC 60.413 50.000 0.00 0.00 0.00 2.17
137 138 2.159787 CCAACTTGCACTCTCGAAATCG 60.160 50.000 0.00 0.00 41.45 3.34
138 139 2.440539 ACTTGCACTCTCGAAATCGT 57.559 45.000 2.41 0.00 40.80 3.73
139 140 3.570926 ACTTGCACTCTCGAAATCGTA 57.429 42.857 2.41 0.00 40.80 3.43
140 141 3.909430 ACTTGCACTCTCGAAATCGTAA 58.091 40.909 2.41 0.00 40.80 3.18
141 142 3.673809 ACTTGCACTCTCGAAATCGTAAC 59.326 43.478 2.41 0.00 40.80 2.50
142 143 2.247637 TGCACTCTCGAAATCGTAACG 58.752 47.619 2.41 0.00 40.80 3.18
143 144 1.007319 GCACTCTCGAAATCGTAACGC 60.007 52.381 2.41 0.00 40.80 4.84
144 145 2.516923 CACTCTCGAAATCGTAACGCT 58.483 47.619 2.41 0.00 40.80 5.07
145 146 2.276540 CACTCTCGAAATCGTAACGCTG 59.723 50.000 2.41 0.00 40.80 5.18
146 147 2.161012 ACTCTCGAAATCGTAACGCTGA 59.839 45.455 2.41 0.00 40.80 4.26
147 148 2.778928 CTCTCGAAATCGTAACGCTGAG 59.221 50.000 2.41 0.00 40.80 3.35
148 149 2.417586 TCTCGAAATCGTAACGCTGAGA 59.582 45.455 2.41 0.00 40.80 3.27
149 150 2.512885 TCGAAATCGTAACGCTGAGAC 58.487 47.619 2.41 0.00 40.80 3.36
150 151 2.161012 TCGAAATCGTAACGCTGAGACT 59.839 45.455 2.41 0.00 40.80 3.24
151 152 3.371898 TCGAAATCGTAACGCTGAGACTA 59.628 43.478 2.41 0.00 40.80 2.59
152 153 3.477802 CGAAATCGTAACGCTGAGACTAC 59.522 47.826 0.00 0.00 34.11 2.73
153 154 4.409570 GAAATCGTAACGCTGAGACTACA 58.590 43.478 0.00 0.00 0.00 2.74
154 155 4.634184 AATCGTAACGCTGAGACTACAT 57.366 40.909 0.00 0.00 0.00 2.29
155 156 5.746307 AATCGTAACGCTGAGACTACATA 57.254 39.130 0.00 0.00 0.00 2.29
156 157 4.526970 TCGTAACGCTGAGACTACATAC 57.473 45.455 0.00 0.00 0.00 2.39
157 158 3.000623 TCGTAACGCTGAGACTACATACG 59.999 47.826 0.00 0.00 36.99 3.06
158 159 3.242220 CGTAACGCTGAGACTACATACGT 60.242 47.826 0.00 0.00 35.24 3.57
159 160 4.026558 CGTAACGCTGAGACTACATACGTA 60.027 45.833 0.00 0.00 34.07 3.57
160 161 3.940657 ACGCTGAGACTACATACGTAC 57.059 47.619 0.00 0.00 33.22 3.67
161 162 2.611292 ACGCTGAGACTACATACGTACC 59.389 50.000 0.00 0.00 33.22 3.34
162 163 2.032204 CGCTGAGACTACATACGTACCC 60.032 54.545 0.00 0.00 0.00 3.69
163 164 2.947652 GCTGAGACTACATACGTACCCA 59.052 50.000 0.00 0.00 0.00 4.51
164 165 3.003482 GCTGAGACTACATACGTACCCAG 59.997 52.174 0.00 0.00 0.00 4.45
165 166 2.947652 TGAGACTACATACGTACCCAGC 59.052 50.000 0.00 0.00 0.00 4.85
166 167 3.212685 GAGACTACATACGTACCCAGCT 58.787 50.000 0.00 0.00 0.00 4.24
167 168 2.950309 AGACTACATACGTACCCAGCTG 59.050 50.000 6.78 6.78 0.00 4.24
168 169 1.407979 ACTACATACGTACCCAGCTGC 59.592 52.381 8.66 0.00 0.00 5.25
169 170 0.748450 TACATACGTACCCAGCTGCC 59.252 55.000 8.66 0.00 0.00 4.85
170 171 0.976073 ACATACGTACCCAGCTGCCT 60.976 55.000 8.66 0.00 0.00 4.75
171 172 0.178068 CATACGTACCCAGCTGCCTT 59.822 55.000 8.66 0.00 0.00 4.35
172 173 0.464452 ATACGTACCCAGCTGCCTTC 59.536 55.000 8.66 0.00 0.00 3.46
173 174 0.613853 TACGTACCCAGCTGCCTTCT 60.614 55.000 8.66 0.00 0.00 2.85
174 175 1.448540 CGTACCCAGCTGCCTTCTG 60.449 63.158 8.66 0.00 0.00 3.02
175 176 1.746991 GTACCCAGCTGCCTTCTGC 60.747 63.158 8.66 0.00 41.77 4.26
176 177 1.920325 TACCCAGCTGCCTTCTGCT 60.920 57.895 8.66 0.00 46.51 4.24
177 178 1.903877 TACCCAGCTGCCTTCTGCTC 61.904 60.000 8.66 0.00 44.24 4.26
178 179 2.350134 CCAGCTGCCTTCTGCTCA 59.650 61.111 8.66 0.00 44.24 4.26
179 180 1.077644 CCAGCTGCCTTCTGCTCAT 60.078 57.895 8.66 0.00 44.24 2.90
180 181 0.680280 CCAGCTGCCTTCTGCTCATT 60.680 55.000 8.66 0.00 44.24 2.57
181 182 1.407851 CCAGCTGCCTTCTGCTCATTA 60.408 52.381 8.66 0.00 44.24 1.90
182 183 1.669779 CAGCTGCCTTCTGCTCATTAC 59.330 52.381 0.00 0.00 44.24 1.89
183 184 1.558756 AGCTGCCTTCTGCTCATTACT 59.441 47.619 0.00 0.00 42.79 2.24
184 185 2.026449 AGCTGCCTTCTGCTCATTACTT 60.026 45.455 0.00 0.00 42.79 2.24
185 186 2.354199 GCTGCCTTCTGCTCATTACTTC 59.646 50.000 0.00 0.00 42.00 3.01
186 187 3.603532 CTGCCTTCTGCTCATTACTTCA 58.396 45.455 0.00 0.00 42.00 3.02
187 188 3.603532 TGCCTTCTGCTCATTACTTCAG 58.396 45.455 0.00 0.00 42.00 3.02
188 189 2.354199 GCCTTCTGCTCATTACTTCAGC 59.646 50.000 0.00 0.00 36.87 4.26
189 190 3.871485 CCTTCTGCTCATTACTTCAGCT 58.129 45.455 0.00 0.00 34.03 4.24
190 191 3.870419 CCTTCTGCTCATTACTTCAGCTC 59.130 47.826 0.00 0.00 34.03 4.09
191 192 4.502016 CTTCTGCTCATTACTTCAGCTCA 58.498 43.478 0.00 0.00 34.03 4.26
192 193 3.854666 TCTGCTCATTACTTCAGCTCAC 58.145 45.455 0.00 0.00 34.03 3.51
193 194 2.935201 CTGCTCATTACTTCAGCTCACC 59.065 50.000 0.00 0.00 34.03 4.02
194 195 1.929836 GCTCATTACTTCAGCTCACCG 59.070 52.381 0.00 0.00 0.00 4.94
195 196 2.544685 CTCATTACTTCAGCTCACCGG 58.455 52.381 0.00 0.00 0.00 5.28
196 197 2.166459 CTCATTACTTCAGCTCACCGGA 59.834 50.000 9.46 0.00 0.00 5.14
197 198 2.094182 TCATTACTTCAGCTCACCGGAC 60.094 50.000 9.46 0.00 0.00 4.79
198 199 1.334160 TTACTTCAGCTCACCGGACA 58.666 50.000 9.46 0.00 0.00 4.02
199 200 0.888619 TACTTCAGCTCACCGGACAG 59.111 55.000 9.46 3.88 0.00 3.51
200 201 0.827925 ACTTCAGCTCACCGGACAGA 60.828 55.000 9.46 1.55 0.00 3.41
201 202 0.389166 CTTCAGCTCACCGGACAGAC 60.389 60.000 9.46 0.00 0.00 3.51
202 203 2.126307 CAGCTCACCGGACAGACG 60.126 66.667 9.46 0.00 0.00 4.18
203 204 2.597805 AGCTCACCGGACAGACGT 60.598 61.111 9.46 0.00 0.00 4.34
204 205 2.430921 GCTCACCGGACAGACGTG 60.431 66.667 9.46 0.00 0.00 4.49
205 206 2.430921 CTCACCGGACAGACGTGC 60.431 66.667 9.46 0.00 0.00 5.34
212 213 4.702826 GACAGACGTGCGCGCAAC 62.703 66.667 38.24 27.83 42.83 4.17
214 215 4.707840 CAGACGTGCGCGCAACAG 62.708 66.667 38.24 29.96 42.83 3.16
215 216 4.942481 AGACGTGCGCGCAACAGA 62.942 61.111 38.24 10.38 42.83 3.41
216 217 3.777925 GACGTGCGCGCAACAGAT 61.778 61.111 38.24 19.31 42.83 2.90
217 218 3.964729 GACGTGCGCGCAACAGATG 62.965 63.158 38.24 20.71 42.83 2.90
218 219 3.776849 CGTGCGCGCAACAGATGA 61.777 61.111 38.24 7.55 0.00 2.92
219 220 2.555782 GTGCGCGCAACAGATGAA 59.444 55.556 38.24 6.62 0.00 2.57
220 221 1.510623 GTGCGCGCAACAGATGAAG 60.511 57.895 38.24 0.00 0.00 3.02
221 222 2.575262 GCGCGCAACAGATGAAGC 60.575 61.111 29.10 0.00 0.00 3.86
222 223 3.031964 GCGCGCAACAGATGAAGCT 62.032 57.895 29.10 0.00 33.71 3.74
223 224 1.695893 GCGCGCAACAGATGAAGCTA 61.696 55.000 29.10 0.00 33.71 3.32
224 225 0.721154 CGCGCAACAGATGAAGCTAA 59.279 50.000 8.75 0.00 33.71 3.09
225 226 1.527793 CGCGCAACAGATGAAGCTAAC 60.528 52.381 8.75 0.00 33.71 2.34
226 227 1.202076 GCGCAACAGATGAAGCTAACC 60.202 52.381 0.30 0.00 33.29 2.85
227 228 1.061131 CGCAACAGATGAAGCTAACCG 59.939 52.381 0.00 0.00 0.00 4.44
228 229 2.076863 GCAACAGATGAAGCTAACCGT 58.923 47.619 0.00 0.00 0.00 4.83
229 230 2.159653 GCAACAGATGAAGCTAACCGTG 60.160 50.000 0.00 0.00 0.00 4.94
230 231 3.325870 CAACAGATGAAGCTAACCGTGA 58.674 45.455 0.00 0.00 0.00 4.35
231 232 3.678056 ACAGATGAAGCTAACCGTGAA 57.322 42.857 0.00 0.00 0.00 3.18
232 233 4.207891 ACAGATGAAGCTAACCGTGAAT 57.792 40.909 0.00 0.00 0.00 2.57
233 234 5.339008 ACAGATGAAGCTAACCGTGAATA 57.661 39.130 0.00 0.00 0.00 1.75
234 235 5.918608 ACAGATGAAGCTAACCGTGAATAT 58.081 37.500 0.00 0.00 0.00 1.28
235 236 5.755375 ACAGATGAAGCTAACCGTGAATATG 59.245 40.000 0.00 0.00 0.00 1.78
236 237 5.755375 CAGATGAAGCTAACCGTGAATATGT 59.245 40.000 0.00 0.00 0.00 2.29
237 238 6.923508 CAGATGAAGCTAACCGTGAATATGTA 59.076 38.462 0.00 0.00 0.00 2.29
238 239 7.438160 CAGATGAAGCTAACCGTGAATATGTAA 59.562 37.037 0.00 0.00 0.00 2.41
239 240 8.150945 AGATGAAGCTAACCGTGAATATGTAAT 58.849 33.333 0.00 0.00 0.00 1.89
240 241 9.419297 GATGAAGCTAACCGTGAATATGTAATA 57.581 33.333 0.00 0.00 0.00 0.98
241 242 8.812147 TGAAGCTAACCGTGAATATGTAATAG 57.188 34.615 0.00 0.00 28.50 1.73
242 243 8.418662 TGAAGCTAACCGTGAATATGTAATAGT 58.581 33.333 0.00 0.00 28.50 2.12
243 244 9.903682 GAAGCTAACCGTGAATATGTAATAGTA 57.096 33.333 0.00 0.00 28.50 1.82
245 246 9.856488 AGCTAACCGTGAATATGTAATAGTATG 57.144 33.333 0.00 0.00 28.50 2.39
246 247 9.635520 GCTAACCGTGAATATGTAATAGTATGT 57.364 33.333 0.00 0.00 28.50 2.29
248 249 8.827177 AACCGTGAATATGTAATAGTATGTGG 57.173 34.615 0.00 0.00 28.50 4.17
249 250 6.872020 ACCGTGAATATGTAATAGTATGTGGC 59.128 38.462 0.00 0.00 28.50 5.01
250 251 6.312918 CCGTGAATATGTAATAGTATGTGGCC 59.687 42.308 0.00 0.00 28.50 5.36
251 252 6.871492 CGTGAATATGTAATAGTATGTGGCCA 59.129 38.462 0.00 0.00 28.50 5.36
252 253 7.063426 CGTGAATATGTAATAGTATGTGGCCAG 59.937 40.741 5.11 0.00 28.50 4.85
253 254 6.878923 TGAATATGTAATAGTATGTGGCCAGC 59.121 38.462 5.11 1.20 28.50 4.85
254 255 4.982241 ATGTAATAGTATGTGGCCAGCT 57.018 40.909 5.11 4.86 0.00 4.24
255 256 7.733773 ATATGTAATAGTATGTGGCCAGCTA 57.266 36.000 5.11 7.22 28.50 3.32
256 257 5.468540 TGTAATAGTATGTGGCCAGCTAG 57.531 43.478 5.11 0.00 0.00 3.42
257 258 3.409026 AATAGTATGTGGCCAGCTAGC 57.591 47.619 5.11 6.62 0.00 3.42
268 269 3.971245 GCCAGCTAGCCTCTATGTAAT 57.029 47.619 12.13 0.00 0.00 1.89
269 270 4.278975 GCCAGCTAGCCTCTATGTAATT 57.721 45.455 12.13 0.00 0.00 1.40
270 271 3.999663 GCCAGCTAGCCTCTATGTAATTG 59.000 47.826 12.13 0.00 0.00 2.32
271 272 4.262635 GCCAGCTAGCCTCTATGTAATTGA 60.263 45.833 12.13 0.00 0.00 2.57
272 273 5.570439 GCCAGCTAGCCTCTATGTAATTGAT 60.570 44.000 12.13 0.00 0.00 2.57
273 274 6.471146 CCAGCTAGCCTCTATGTAATTGATT 58.529 40.000 12.13 0.00 0.00 2.57
274 275 6.593382 CCAGCTAGCCTCTATGTAATTGATTC 59.407 42.308 12.13 0.00 0.00 2.52
275 276 7.157347 CAGCTAGCCTCTATGTAATTGATTCA 58.843 38.462 12.13 0.00 0.00 2.57
276 277 7.823310 CAGCTAGCCTCTATGTAATTGATTCAT 59.177 37.037 12.13 0.00 0.00 2.57
277 278 7.823310 AGCTAGCCTCTATGTAATTGATTCATG 59.177 37.037 12.13 0.00 0.00 3.07
278 279 7.065563 GCTAGCCTCTATGTAATTGATTCATGG 59.934 40.741 2.29 0.00 0.00 3.66
279 280 5.709164 AGCCTCTATGTAATTGATTCATGGC 59.291 40.000 0.00 0.00 32.21 4.40
280 281 5.105997 GCCTCTATGTAATTGATTCATGGCC 60.106 44.000 0.00 0.00 0.00 5.36
281 282 5.122869 CCTCTATGTAATTGATTCATGGCCG 59.877 44.000 0.00 0.00 0.00 6.13
282 283 3.648339 ATGTAATTGATTCATGGCCGC 57.352 42.857 0.00 0.00 0.00 6.53
283 284 1.680735 TGTAATTGATTCATGGCCGCC 59.319 47.619 1.04 1.04 0.00 6.13
284 285 1.956477 GTAATTGATTCATGGCCGCCT 59.044 47.619 11.61 0.00 0.00 5.52
285 286 0.748450 AATTGATTCATGGCCGCCTG 59.252 50.000 11.61 6.74 0.00 4.85
286 287 0.106569 ATTGATTCATGGCCGCCTGA 60.107 50.000 11.61 9.06 0.00 3.86
287 288 0.323269 TTGATTCATGGCCGCCTGAA 60.323 50.000 19.93 19.93 35.95 3.02
288 289 0.323269 TGATTCATGGCCGCCTGAAA 60.323 50.000 20.92 9.80 35.20 2.69
289 290 0.101219 GATTCATGGCCGCCTGAAAC 59.899 55.000 20.92 16.69 35.20 2.78
290 291 1.656818 ATTCATGGCCGCCTGAAACG 61.657 55.000 20.92 2.43 35.20 3.60
291 292 4.481112 CATGGCCGCCTGAAACGC 62.481 66.667 11.61 0.00 0.00 4.84
295 296 4.683334 GCCGCCTGAAACGCACAC 62.683 66.667 0.00 0.00 0.00 3.82
678 679 1.667830 CAGTTCCGCTTCTTCCGCA 60.668 57.895 0.00 0.00 0.00 5.69
912 913 7.308649 CCTTTGATGCTAATCTCCATCTTGATG 60.309 40.741 3.77 3.77 38.84 3.07
926 927 1.747355 CTTGATGTTGGGATGACAGGC 59.253 52.381 0.00 0.00 0.00 4.85
1203 1204 8.774586 GTGAGTAAGTTTTTCAATTCAGAGCTA 58.225 33.333 0.00 0.00 0.00 3.32
1271 1276 2.654877 GGAGGCGAAGTTCACGGA 59.345 61.111 3.32 0.00 0.00 4.69
1473 1478 1.810151 GGCGAGTTTCAGGTTATGCAA 59.190 47.619 0.00 0.00 0.00 4.08
2053 2062 1.166531 GCGTGTTCTTCAAGCTGGGT 61.167 55.000 0.00 0.00 45.42 4.51
2383 2398 3.423539 AGTATGAGAAGCTGCCAAACA 57.576 42.857 0.00 0.00 0.00 2.83
2399 2414 1.490621 AACATCTGTTTTTGCTGCGC 58.509 45.000 0.00 0.00 33.93 6.09
2971 3088 0.323302 TAAAGCTCATGGTGGTCGCA 59.677 50.000 0.00 0.00 0.00 5.10
3027 3144 0.835971 TGGCTACTGCTGGAGTCCAA 60.836 55.000 14.17 0.00 39.59 3.53
4399 4520 7.238486 ACAGTCTTATGAAGTCTCTTCATGT 57.762 36.000 25.59 16.68 39.30 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.413142 GCATGTTGAGGCCAGCTCC 61.413 63.158 5.01 0.00 0.00 4.70
2 3 1.035932 ATGCATGTTGAGGCCAGCTC 61.036 55.000 5.01 0.00 0.00 4.09
3 4 1.000019 ATGCATGTTGAGGCCAGCT 60.000 52.632 5.01 0.00 0.00 4.24
7 8 1.153706 GTGCATGCATGTTGAGGCC 60.154 57.895 25.64 9.65 0.00 5.19
8 9 1.515519 CGTGCATGCATGTTGAGGC 60.516 57.895 28.25 12.66 0.00 4.70
9 10 1.085893 TACGTGCATGCATGTTGAGG 58.914 50.000 41.50 19.06 42.86 3.86
10 11 1.464219 TGTACGTGCATGCATGTTGAG 59.536 47.619 41.50 22.46 42.86 3.02
11 12 1.517242 TGTACGTGCATGCATGTTGA 58.483 45.000 41.50 28.14 42.86 3.18
12 13 2.547913 ATGTACGTGCATGCATGTTG 57.452 45.000 41.50 25.30 42.86 3.33
13 14 2.032054 GCTATGTACGTGCATGCATGTT 59.968 45.455 41.50 29.16 42.86 2.71
14 15 1.599071 GCTATGTACGTGCATGCATGT 59.401 47.619 39.17 39.17 46.53 3.21
15 16 1.598601 TGCTATGTACGTGCATGCATG 59.401 47.619 33.18 33.18 38.78 4.06
16 17 1.869132 CTGCTATGTACGTGCATGCAT 59.131 47.619 28.67 11.73 34.77 3.96
17 18 1.289276 CTGCTATGTACGTGCATGCA 58.711 50.000 27.60 27.60 36.07 3.96
18 19 0.583438 CCTGCTATGTACGTGCATGC 59.417 55.000 26.72 24.82 36.07 4.06
19 20 0.583438 GCCTGCTATGTACGTGCATG 59.417 55.000 26.72 17.54 36.07 4.06
20 21 0.177836 TGCCTGCTATGTACGTGCAT 59.822 50.000 22.72 22.72 36.07 3.96
21 22 0.036858 TTGCCTGCTATGTACGTGCA 60.037 50.000 9.28 9.28 35.30 4.57
22 23 1.299541 ATTGCCTGCTATGTACGTGC 58.700 50.000 0.00 0.00 0.00 5.34
23 24 5.478233 TTTTATTGCCTGCTATGTACGTG 57.522 39.130 0.00 0.00 0.00 4.49
24 25 6.693315 AATTTTATTGCCTGCTATGTACGT 57.307 33.333 0.00 0.00 0.00 3.57
25 26 9.677567 AATTAATTTTATTGCCTGCTATGTACG 57.322 29.630 0.00 0.00 0.00 3.67
45 46 8.667463 GCTTTTGCACATGTGGAATAAATTAAT 58.333 29.630 29.94 0.00 46.58 1.40
46 47 8.027440 GCTTTTGCACATGTGGAATAAATTAA 57.973 30.769 29.94 19.50 46.58 1.40
47 48 7.593875 GCTTTTGCACATGTGGAATAAATTA 57.406 32.000 29.94 13.83 46.58 1.40
48 49 6.484818 GCTTTTGCACATGTGGAATAAATT 57.515 33.333 29.94 0.00 46.58 1.82
60 61 9.777173 TAGATAGCGTATCCAGCTTTTGCACAT 62.777 40.741 0.00 0.00 43.24 3.21
61 62 7.872962 AGATAGCGTATCCAGCTTTTGCACA 62.873 44.000 0.00 0.00 43.24 4.57
62 63 5.507345 AGATAGCGTATCCAGCTTTTGCAC 61.507 45.833 0.00 0.00 43.24 4.57
63 64 3.432186 AGATAGCGTATCCAGCTTTTGCA 60.432 43.478 0.00 0.00 43.24 4.08
64 65 3.134458 AGATAGCGTATCCAGCTTTTGC 58.866 45.455 0.00 0.00 43.24 3.68
65 66 7.171508 TCAATTAGATAGCGTATCCAGCTTTTG 59.828 37.037 0.00 0.00 43.24 2.44
66 67 7.217200 TCAATTAGATAGCGTATCCAGCTTTT 58.783 34.615 0.00 0.00 43.24 2.27
67 68 6.759272 TCAATTAGATAGCGTATCCAGCTTT 58.241 36.000 0.00 0.00 43.24 3.51
68 69 6.346477 TCAATTAGATAGCGTATCCAGCTT 57.654 37.500 0.00 0.00 43.24 3.74
70 71 6.813649 TGAATCAATTAGATAGCGTATCCAGC 59.186 38.462 2.62 0.00 35.39 4.85
71 72 7.008719 CGTGAATCAATTAGATAGCGTATCCAG 59.991 40.741 0.00 0.00 35.39 3.86
72 73 6.806739 CGTGAATCAATTAGATAGCGTATCCA 59.193 38.462 0.00 0.00 35.39 3.41
73 74 6.253727 CCGTGAATCAATTAGATAGCGTATCC 59.746 42.308 0.00 0.00 35.39 2.59
74 75 6.237595 GCCGTGAATCAATTAGATAGCGTATC 60.238 42.308 0.00 0.00 35.39 2.24
75 76 5.577164 GCCGTGAATCAATTAGATAGCGTAT 59.423 40.000 0.00 0.00 35.39 3.06
76 77 4.921515 GCCGTGAATCAATTAGATAGCGTA 59.078 41.667 0.00 0.00 35.39 4.42
77 78 3.741344 GCCGTGAATCAATTAGATAGCGT 59.259 43.478 0.00 0.00 35.39 5.07
78 79 3.123621 GGCCGTGAATCAATTAGATAGCG 59.876 47.826 0.00 0.00 35.39 4.26
79 80 3.123621 CGGCCGTGAATCAATTAGATAGC 59.876 47.826 19.50 0.00 35.39 2.97
80 81 3.679980 CCGGCCGTGAATCAATTAGATAG 59.320 47.826 26.12 0.00 35.39 2.08
81 82 3.659786 CCGGCCGTGAATCAATTAGATA 58.340 45.455 26.12 0.00 35.39 1.98
82 83 2.494059 CCGGCCGTGAATCAATTAGAT 58.506 47.619 26.12 0.00 39.09 1.98
83 84 1.948104 CCGGCCGTGAATCAATTAGA 58.052 50.000 26.12 0.00 0.00 2.10
84 85 0.307760 GCCGGCCGTGAATCAATTAG 59.692 55.000 26.12 4.68 0.00 1.73
85 86 1.098712 GGCCGGCCGTGAATCAATTA 61.099 55.000 33.60 0.00 0.00 1.40
86 87 2.414785 GGCCGGCCGTGAATCAATT 61.415 57.895 33.60 0.00 0.00 2.32
87 88 2.828549 GGCCGGCCGTGAATCAAT 60.829 61.111 33.60 0.00 0.00 2.57
103 104 0.604511 AAGTTGGCGTAGGTTTCCGG 60.605 55.000 0.00 0.00 0.00 5.14
104 105 0.515564 CAAGTTGGCGTAGGTTTCCG 59.484 55.000 0.00 0.00 0.00 4.30
105 106 0.240145 GCAAGTTGGCGTAGGTTTCC 59.760 55.000 4.75 0.00 0.00 3.13
106 107 0.948678 TGCAAGTTGGCGTAGGTTTC 59.051 50.000 4.75 0.00 36.28 2.78
107 108 0.666374 GTGCAAGTTGGCGTAGGTTT 59.334 50.000 4.75 0.00 36.28 3.27
108 109 0.179029 AGTGCAAGTTGGCGTAGGTT 60.179 50.000 4.75 0.00 36.28 3.50
109 110 0.602905 GAGTGCAAGTTGGCGTAGGT 60.603 55.000 4.75 0.00 36.28 3.08
110 111 0.320771 AGAGTGCAAGTTGGCGTAGG 60.321 55.000 4.75 0.00 36.28 3.18
111 112 1.071605 GAGAGTGCAAGTTGGCGTAG 58.928 55.000 4.75 0.00 36.28 3.51
112 113 0.666274 CGAGAGTGCAAGTTGGCGTA 60.666 55.000 4.75 0.00 36.28 4.42
113 114 1.956170 CGAGAGTGCAAGTTGGCGT 60.956 57.895 4.75 0.00 36.28 5.68
114 115 1.221466 TTCGAGAGTGCAAGTTGGCG 61.221 55.000 4.75 0.00 36.28 5.69
115 116 0.944386 TTTCGAGAGTGCAAGTTGGC 59.056 50.000 4.75 0.00 0.00 4.52
116 117 2.159787 CGATTTCGAGAGTGCAAGTTGG 60.160 50.000 4.75 0.00 43.02 3.77
117 118 2.476619 ACGATTTCGAGAGTGCAAGTTG 59.523 45.455 7.01 0.00 43.02 3.16
118 119 2.755650 ACGATTTCGAGAGTGCAAGTT 58.244 42.857 7.01 0.00 43.02 2.66
119 120 2.440539 ACGATTTCGAGAGTGCAAGT 57.559 45.000 7.01 0.00 43.02 3.16
120 121 3.241364 CGTTACGATTTCGAGAGTGCAAG 60.241 47.826 7.01 0.00 43.02 4.01
121 122 2.659757 CGTTACGATTTCGAGAGTGCAA 59.340 45.455 7.01 0.00 43.02 4.08
122 123 2.247637 CGTTACGATTTCGAGAGTGCA 58.752 47.619 7.01 0.00 43.02 4.57
123 124 1.007319 GCGTTACGATTTCGAGAGTGC 60.007 52.381 9.62 0.77 43.02 4.40
124 125 2.276540 CAGCGTTACGATTTCGAGAGTG 59.723 50.000 9.62 0.00 43.02 3.51
125 126 2.161012 TCAGCGTTACGATTTCGAGAGT 59.839 45.455 9.62 0.00 43.02 3.24
126 127 2.778928 CTCAGCGTTACGATTTCGAGAG 59.221 50.000 9.62 0.46 43.02 3.20
127 128 2.417586 TCTCAGCGTTACGATTTCGAGA 59.582 45.455 9.62 8.21 43.02 4.04
128 129 2.526688 GTCTCAGCGTTACGATTTCGAG 59.473 50.000 9.62 5.69 43.02 4.04
129 130 2.161012 AGTCTCAGCGTTACGATTTCGA 59.839 45.455 9.62 0.00 43.02 3.71
130 131 2.516923 AGTCTCAGCGTTACGATTTCG 58.483 47.619 9.62 0.00 46.33 3.46
131 132 4.409570 TGTAGTCTCAGCGTTACGATTTC 58.590 43.478 9.62 0.00 0.00 2.17
132 133 4.430137 TGTAGTCTCAGCGTTACGATTT 57.570 40.909 9.62 0.00 0.00 2.17
133 134 4.634184 ATGTAGTCTCAGCGTTACGATT 57.366 40.909 9.62 0.00 0.00 3.34
134 135 4.318618 CGTATGTAGTCTCAGCGTTACGAT 60.319 45.833 9.62 0.00 0.00 3.73
135 136 3.000623 CGTATGTAGTCTCAGCGTTACGA 59.999 47.826 9.62 0.00 0.00 3.43
136 137 3.242220 ACGTATGTAGTCTCAGCGTTACG 60.242 47.826 0.00 0.00 32.38 3.18
137 138 4.270178 ACGTATGTAGTCTCAGCGTTAC 57.730 45.455 0.00 0.00 32.38 2.50
138 139 4.271049 GGTACGTATGTAGTCTCAGCGTTA 59.729 45.833 0.00 0.00 35.67 3.18
139 140 3.064545 GGTACGTATGTAGTCTCAGCGTT 59.935 47.826 0.00 0.00 35.67 4.84
140 141 2.611292 GGTACGTATGTAGTCTCAGCGT 59.389 50.000 0.00 0.00 37.00 5.07
141 142 2.032204 GGGTACGTATGTAGTCTCAGCG 60.032 54.545 0.00 0.00 0.00 5.18
142 143 2.947652 TGGGTACGTATGTAGTCTCAGC 59.052 50.000 0.00 0.00 0.00 4.26
143 144 3.003482 GCTGGGTACGTATGTAGTCTCAG 59.997 52.174 0.00 7.82 0.00 3.35
144 145 2.947652 GCTGGGTACGTATGTAGTCTCA 59.052 50.000 0.00 0.00 0.00 3.27
145 146 3.003482 CAGCTGGGTACGTATGTAGTCTC 59.997 52.174 5.57 0.00 0.00 3.36
146 147 2.950309 CAGCTGGGTACGTATGTAGTCT 59.050 50.000 5.57 0.00 0.00 3.24
147 148 2.543238 GCAGCTGGGTACGTATGTAGTC 60.543 54.545 17.12 0.00 0.00 2.59
148 149 1.407979 GCAGCTGGGTACGTATGTAGT 59.592 52.381 17.12 0.00 0.00 2.73
149 150 1.269621 GGCAGCTGGGTACGTATGTAG 60.270 57.143 17.12 0.00 0.00 2.74
150 151 0.748450 GGCAGCTGGGTACGTATGTA 59.252 55.000 17.12 0.00 0.00 2.29
151 152 0.976073 AGGCAGCTGGGTACGTATGT 60.976 55.000 17.12 0.00 0.00 2.29
152 153 0.178068 AAGGCAGCTGGGTACGTATG 59.822 55.000 17.12 0.00 0.00 2.39
153 154 0.464452 GAAGGCAGCTGGGTACGTAT 59.536 55.000 17.12 0.00 0.00 3.06
154 155 0.613853 AGAAGGCAGCTGGGTACGTA 60.614 55.000 17.12 0.00 0.00 3.57
155 156 1.913762 AGAAGGCAGCTGGGTACGT 60.914 57.895 17.12 0.00 0.00 3.57
156 157 1.448540 CAGAAGGCAGCTGGGTACG 60.449 63.158 17.12 0.00 0.00 3.67
157 158 1.746991 GCAGAAGGCAGCTGGGTAC 60.747 63.158 17.12 0.00 43.97 3.34
158 159 2.671070 GCAGAAGGCAGCTGGGTA 59.329 61.111 17.12 0.00 43.97 3.69
167 168 2.354199 GCTGAAGTAATGAGCAGAAGGC 59.646 50.000 0.00 0.00 45.30 4.35
168 169 3.870419 GAGCTGAAGTAATGAGCAGAAGG 59.130 47.826 0.00 0.00 35.03 3.46
169 170 4.329528 GTGAGCTGAAGTAATGAGCAGAAG 59.670 45.833 0.00 0.00 35.03 2.85
170 171 4.248859 GTGAGCTGAAGTAATGAGCAGAA 58.751 43.478 0.00 0.00 35.03 3.02
171 172 3.368843 GGTGAGCTGAAGTAATGAGCAGA 60.369 47.826 0.00 0.00 35.03 4.26
172 173 2.935201 GGTGAGCTGAAGTAATGAGCAG 59.065 50.000 0.00 0.00 35.03 4.24
173 174 2.675032 CGGTGAGCTGAAGTAATGAGCA 60.675 50.000 0.00 0.00 35.03 4.26
174 175 1.929836 CGGTGAGCTGAAGTAATGAGC 59.070 52.381 0.00 0.00 0.00 4.26
175 176 2.166459 TCCGGTGAGCTGAAGTAATGAG 59.834 50.000 0.00 0.00 0.00 2.90
176 177 2.094182 GTCCGGTGAGCTGAAGTAATGA 60.094 50.000 0.00 0.00 0.00 2.57
177 178 2.271800 GTCCGGTGAGCTGAAGTAATG 58.728 52.381 0.00 0.00 0.00 1.90
178 179 1.899814 TGTCCGGTGAGCTGAAGTAAT 59.100 47.619 0.00 0.00 0.00 1.89
179 180 1.272490 CTGTCCGGTGAGCTGAAGTAA 59.728 52.381 0.00 0.00 0.00 2.24
180 181 0.888619 CTGTCCGGTGAGCTGAAGTA 59.111 55.000 0.00 0.00 0.00 2.24
181 182 0.827925 TCTGTCCGGTGAGCTGAAGT 60.828 55.000 0.00 0.00 0.00 3.01
182 183 0.389166 GTCTGTCCGGTGAGCTGAAG 60.389 60.000 0.00 0.00 0.00 3.02
183 184 1.666011 GTCTGTCCGGTGAGCTGAA 59.334 57.895 0.00 0.00 0.00 3.02
184 185 2.626780 CGTCTGTCCGGTGAGCTGA 61.627 63.158 0.00 0.00 0.00 4.26
185 186 2.126307 CGTCTGTCCGGTGAGCTG 60.126 66.667 0.00 0.00 0.00 4.24
186 187 2.597805 ACGTCTGTCCGGTGAGCT 60.598 61.111 0.00 0.00 0.00 4.09
187 188 2.430921 CACGTCTGTCCGGTGAGC 60.431 66.667 0.00 0.00 0.00 4.26
188 189 2.430921 GCACGTCTGTCCGGTGAG 60.431 66.667 0.00 0.00 0.00 3.51
189 190 4.337060 CGCACGTCTGTCCGGTGA 62.337 66.667 0.00 0.00 0.00 4.02
195 196 4.702826 GTTGCGCGCACGTCTGTC 62.703 66.667 36.72 13.93 42.83 3.51
197 198 4.707840 CTGTTGCGCGCACGTCTG 62.708 66.667 36.72 24.36 42.83 3.51
198 199 4.942481 TCTGTTGCGCGCACGTCT 62.942 61.111 36.72 0.00 42.83 4.18
199 200 3.777925 ATCTGTTGCGCGCACGTC 61.778 61.111 36.72 25.84 42.83 4.34
200 201 4.075910 CATCTGTTGCGCGCACGT 62.076 61.111 36.72 15.13 42.83 4.49
201 202 3.293872 TTCATCTGTTGCGCGCACG 62.294 57.895 36.72 24.40 44.07 5.34
202 203 1.510623 CTTCATCTGTTGCGCGCAC 60.511 57.895 36.72 27.52 0.00 5.34
203 204 2.862436 CTTCATCTGTTGCGCGCA 59.138 55.556 33.09 33.09 0.00 6.09
204 205 1.695893 TAGCTTCATCTGTTGCGCGC 61.696 55.000 27.26 27.26 0.00 6.86
205 206 0.721154 TTAGCTTCATCTGTTGCGCG 59.279 50.000 0.00 0.00 0.00 6.86
206 207 1.202076 GGTTAGCTTCATCTGTTGCGC 60.202 52.381 0.00 0.00 0.00 6.09
207 208 1.061131 CGGTTAGCTTCATCTGTTGCG 59.939 52.381 0.00 0.00 0.00 4.85
208 209 2.076863 ACGGTTAGCTTCATCTGTTGC 58.923 47.619 0.00 0.00 0.00 4.17
209 210 3.325870 TCACGGTTAGCTTCATCTGTTG 58.674 45.455 0.00 0.00 0.00 3.33
210 211 3.678056 TCACGGTTAGCTTCATCTGTT 57.322 42.857 0.00 0.00 0.00 3.16
211 212 3.678056 TTCACGGTTAGCTTCATCTGT 57.322 42.857 0.00 0.00 0.00 3.41
212 213 5.755375 ACATATTCACGGTTAGCTTCATCTG 59.245 40.000 0.00 0.00 0.00 2.90
213 214 5.918608 ACATATTCACGGTTAGCTTCATCT 58.081 37.500 0.00 0.00 0.00 2.90
214 215 7.709269 TTACATATTCACGGTTAGCTTCATC 57.291 36.000 0.00 0.00 0.00 2.92
215 216 9.424319 CTATTACATATTCACGGTTAGCTTCAT 57.576 33.333 0.00 0.00 0.00 2.57
216 217 8.418662 ACTATTACATATTCACGGTTAGCTTCA 58.581 33.333 0.00 0.00 0.00 3.02
217 218 8.813643 ACTATTACATATTCACGGTTAGCTTC 57.186 34.615 0.00 0.00 0.00 3.86
219 220 9.856488 CATACTATTACATATTCACGGTTAGCT 57.144 33.333 0.00 0.00 0.00 3.32
220 221 9.635520 ACATACTATTACATATTCACGGTTAGC 57.364 33.333 0.00 0.00 0.00 3.09
222 223 9.917129 CCACATACTATTACATATTCACGGTTA 57.083 33.333 0.00 0.00 0.00 2.85
223 224 7.386848 GCCACATACTATTACATATTCACGGTT 59.613 37.037 0.00 0.00 0.00 4.44
224 225 6.872020 GCCACATACTATTACATATTCACGGT 59.128 38.462 0.00 0.00 0.00 4.83
225 226 6.312918 GGCCACATACTATTACATATTCACGG 59.687 42.308 0.00 0.00 0.00 4.94
226 227 6.871492 TGGCCACATACTATTACATATTCACG 59.129 38.462 0.00 0.00 0.00 4.35
227 228 7.148407 GCTGGCCACATACTATTACATATTCAC 60.148 40.741 0.00 0.00 0.00 3.18
228 229 6.878923 GCTGGCCACATACTATTACATATTCA 59.121 38.462 0.00 0.00 0.00 2.57
229 230 7.106239 AGCTGGCCACATACTATTACATATTC 58.894 38.462 0.00 0.00 0.00 1.75
230 231 7.020827 AGCTGGCCACATACTATTACATATT 57.979 36.000 0.00 0.00 0.00 1.28
231 232 6.627087 AGCTGGCCACATACTATTACATAT 57.373 37.500 0.00 0.00 0.00 1.78
232 233 6.351033 GCTAGCTGGCCACATACTATTACATA 60.351 42.308 11.66 0.00 0.00 2.29
233 234 4.982241 AGCTGGCCACATACTATTACAT 57.018 40.909 0.00 0.00 0.00 2.29
234 235 4.262463 GCTAGCTGGCCACATACTATTACA 60.262 45.833 11.66 0.00 0.00 2.41
235 236 4.246458 GCTAGCTGGCCACATACTATTAC 58.754 47.826 11.66 0.00 0.00 1.89
236 237 4.537135 GCTAGCTGGCCACATACTATTA 57.463 45.455 11.66 0.00 0.00 0.98
237 238 3.409026 GCTAGCTGGCCACATACTATT 57.591 47.619 11.66 0.00 0.00 1.73
248 249 3.971245 ATTACATAGAGGCTAGCTGGC 57.029 47.619 14.65 14.65 42.15 4.85
249 250 5.474578 TCAATTACATAGAGGCTAGCTGG 57.525 43.478 15.72 0.00 0.00 4.85
250 251 7.157347 TGAATCAATTACATAGAGGCTAGCTG 58.843 38.462 15.72 7.04 0.00 4.24
251 252 7.308450 TGAATCAATTACATAGAGGCTAGCT 57.692 36.000 15.72 0.00 0.00 3.32
252 253 7.065563 CCATGAATCAATTACATAGAGGCTAGC 59.934 40.741 6.04 6.04 0.00 3.42
253 254 7.065563 GCCATGAATCAATTACATAGAGGCTAG 59.934 40.741 0.00 0.00 32.02 3.42
254 255 6.881065 GCCATGAATCAATTACATAGAGGCTA 59.119 38.462 0.00 0.00 32.02 3.93
255 256 5.709164 GCCATGAATCAATTACATAGAGGCT 59.291 40.000 0.00 0.00 32.02 4.58
256 257 5.105997 GGCCATGAATCAATTACATAGAGGC 60.106 44.000 0.00 0.00 33.12 4.70
257 258 5.122869 CGGCCATGAATCAATTACATAGAGG 59.877 44.000 2.24 0.00 0.00 3.69
258 259 5.391310 GCGGCCATGAATCAATTACATAGAG 60.391 44.000 2.24 0.00 0.00 2.43
259 260 4.455533 GCGGCCATGAATCAATTACATAGA 59.544 41.667 2.24 0.00 0.00 1.98
260 261 4.379813 GGCGGCCATGAATCAATTACATAG 60.380 45.833 15.62 0.00 0.00 2.23
261 262 3.505680 GGCGGCCATGAATCAATTACATA 59.494 43.478 15.62 0.00 0.00 2.29
262 263 2.297033 GGCGGCCATGAATCAATTACAT 59.703 45.455 15.62 0.00 0.00 2.29
263 264 1.680735 GGCGGCCATGAATCAATTACA 59.319 47.619 15.62 0.00 0.00 2.41
264 265 1.956477 AGGCGGCCATGAATCAATTAC 59.044 47.619 23.09 0.00 0.00 1.89
265 266 1.955778 CAGGCGGCCATGAATCAATTA 59.044 47.619 23.09 0.00 0.00 1.40
266 267 0.748450 CAGGCGGCCATGAATCAATT 59.252 50.000 23.09 0.00 0.00 2.32
267 268 0.106569 TCAGGCGGCCATGAATCAAT 60.107 50.000 23.09 0.00 0.00 2.57
268 269 0.323269 TTCAGGCGGCCATGAATCAA 60.323 50.000 23.09 4.38 30.67 2.57
269 270 0.323269 TTTCAGGCGGCCATGAATCA 60.323 50.000 24.51 14.14 35.47 2.57
270 271 0.101219 GTTTCAGGCGGCCATGAATC 59.899 55.000 24.51 21.10 35.47 2.52
271 272 1.656818 CGTTTCAGGCGGCCATGAAT 61.657 55.000 24.51 3.68 35.47 2.57
272 273 2.331893 CGTTTCAGGCGGCCATGAA 61.332 57.895 23.09 22.36 33.73 2.57
273 274 2.745884 CGTTTCAGGCGGCCATGA 60.746 61.111 23.09 18.04 0.00 3.07
274 275 4.481112 GCGTTTCAGGCGGCCATG 62.481 66.667 23.09 16.02 0.00 3.66
278 279 4.683334 GTGTGCGTTTCAGGCGGC 62.683 66.667 0.00 0.00 0.00 6.53
279 280 4.368808 CGTGTGCGTTTCAGGCGG 62.369 66.667 0.00 0.00 0.00 6.13
678 679 6.010219 GGATTATATTGGGGTGTGCAATAGT 58.990 40.000 0.00 0.00 0.00 2.12
912 913 1.450312 CTCGGCCTGTCATCCCAAC 60.450 63.158 0.00 0.00 0.00 3.77
926 927 1.171308 TTACTGGACGTCCTTCTCGG 58.829 55.000 33.39 15.23 36.82 4.63
1203 1204 0.041684 CCTTCAAATCCCCCTTGCCT 59.958 55.000 0.00 0.00 0.00 4.75
1261 1266 3.251004 GCAAAATCAGAGTCCGTGAACTT 59.749 43.478 0.00 0.00 0.00 2.66
1271 1276 5.623824 GCATCTTTCATGGCAAAATCAGAGT 60.624 40.000 0.00 0.00 0.00 3.24
1338 1343 5.167845 GTGGTCAAATTGGATTTAACGCAT 58.832 37.500 0.00 0.00 0.00 4.73
1381 1386 9.067986 AGAATTAATCCCCAAATTAATCTCGTC 57.932 33.333 3.16 0.00 39.67 4.20
1473 1478 3.493176 GCTGAAACTGAAAAATGGCCTGT 60.493 43.478 3.32 0.00 0.00 4.00
1861 1870 1.448540 CGACGAGCTTGCCCTTCAT 60.449 57.895 0.00 0.00 0.00 2.57
2053 2062 1.174078 TCGTTCTGGTAGTGCCACGA 61.174 55.000 7.25 7.25 43.61 4.35
2399 2414 1.594293 GTCGTGTGTCCCACCACTG 60.594 63.158 0.00 0.00 41.26 3.66
2971 3088 1.677966 CATCAGCAGCAGCACCCTT 60.678 57.895 3.17 0.00 45.49 3.95
3027 3144 2.611225 GATGAAGCCTCTTCCATCGT 57.389 50.000 4.35 0.00 0.00 3.73
3489 3609 3.220999 CTCGCCCGTCAGTTGACCA 62.221 63.158 6.68 0.00 41.86 4.02
3746 3866 3.738282 GCTGCAGAGTATAAAGGTCATCG 59.262 47.826 20.43 0.00 0.00 3.84
4399 4520 5.772393 ACCAATATGTTCCTTACTCCACA 57.228 39.130 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.