Multiple sequence alignment - TraesCS3D01G430500

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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 TraesCS3D01G430500 chr3D 100.000 3780 0 0 1 3780 544780824 544784603 0.000000e+00 6981
1 TraesCS3D01G430500 chr3D 83.810 1328 184 14 687 1998 1663806 1665118 0.000000e+00 1232
2 TraesCS3D01G430500 chr3D 78.774 1338 213 41 688 1998 1650927 1652220 0.000000e+00 832
3 TraesCS3D01G430500 chr3D 80.020 991 176 14 986 1968 1666304 1667280 0.000000e+00 713
4 TraesCS3D01G430500 chr3D 78.999 719 109 20 2085 2788 1665114 1665805 1.600000e-123 453
5 TraesCS3D01G430500 chr3A 93.507 3065 155 18 316 3351 681458644 681461693 0.000000e+00 4518
6 TraesCS3D01G430500 chr3A 82.432 1332 198 19 687 1998 7307369 7306054 0.000000e+00 1131
7 TraesCS3D01G430500 chr3A 78.700 1338 247 23 687 1998 7429090 7430415 0.000000e+00 857
8 TraesCS3D01G430500 chr3A 78.679 1332 229 35 687 1999 7357866 7356571 0.000000e+00 835
9 TraesCS3D01G430500 chr3A 81.345 595 96 12 726 1319 7407186 7407766 1.590000e-128 470
10 TraesCS3D01G430500 chr3B 92.503 1654 77 13 429 2063 720956913 720958538 0.000000e+00 2324
11 TraesCS3D01G430500 chr3B 83.208 1328 192 24 687 1998 3815649 3816961 0.000000e+00 1188
12 TraesCS3D01G430500 chr3B 83.220 1329 190 26 687 1998 4714981 4716293 0.000000e+00 1188
13 TraesCS3D01G430500 chr3B 88.554 996 81 17 2789 3780 720959982 720960948 0.000000e+00 1177
14 TraesCS3D01G430500 chr3B 81.069 1347 208 28 685 1998 3765561 3764229 0.000000e+00 1031
15 TraesCS3D01G430500 chr3B 80.562 1353 212 28 685 1998 4666042 4664702 0.000000e+00 994
16 TraesCS3D01G430500 chr3B 79.537 1339 233 25 687 1998 3739109 3737785 0.000000e+00 917
17 TraesCS3D01G430500 chr3B 94.030 536 29 1 2268 2803 720958719 720959251 0.000000e+00 809
18 TraesCS3D01G430500 chr3B 79.932 887 149 18 685 1550 3785028 3785906 3.210000e-175 625
19 TraesCS3D01G430500 chr3B 81.221 655 85 23 2077 2715 3773285 3773917 9.430000e-136 494
20 TraesCS3D01G430500 chr3B 80.916 655 87 23 2077 2715 4673889 4674521 2.040000e-132 483
21 TraesCS3D01G430500 chr3B 94.982 279 12 2 30 306 684956598 684956320 1.610000e-118 436
22 TraesCS3D01G430500 chr3B 93.785 177 8 1 2040 2213 720958549 720958725 2.900000e-66 263
23 TraesCS3D01G430500 chr3B 88.189 127 15 0 2076 2202 4632101 4632227 6.540000e-33 152
24 TraesCS3D01G430500 chr3B 94.030 67 4 0 304 370 720955845 720955911 6.680000e-18 102
25 TraesCS3D01G430500 chrUn 78.683 2172 339 74 685 2808 296649930 296652025 0.000000e+00 1332
26 TraesCS3D01G430500 chrUn 81.221 655 85 23 2077 2715 344719118 344718486 9.430000e-136 494
27 TraesCS3D01G430500 chrUn 93.333 285 16 3 24 306 153325393 153325110 5.840000e-113 418
28 TraesCS3D01G430500 chr4A 78.683 2172 339 74 685 2808 669458261 669456166 0.000000e+00 1332
29 TraesCS3D01G430500 chr7D 80.346 1328 228 22 685 1998 20614947 20616255 0.000000e+00 976
30 TraesCS3D01G430500 chr7A 83.534 996 133 18 1038 2016 20772680 20771699 0.000000e+00 902
31 TraesCS3D01G430500 chr7B 94.624 279 13 2 30 306 70849204 70849482 7.500000e-117 431
32 TraesCS3D01G430500 chr7B 93.333 285 16 3 24 306 29748927 29749210 5.840000e-113 418
33 TraesCS3D01G430500 chr7B 93.333 285 16 3 24 306 146224067 146223784 5.840000e-113 418
34 TraesCS3D01G430500 chr7B 75.000 344 48 26 3047 3373 327263642 327263964 1.430000e-24 124
35 TraesCS3D01G430500 chr5B 94.624 279 13 2 30 306 97742949 97743227 7.500000e-117 431
36 TraesCS3D01G430500 chr5B 93.333 285 16 3 24 306 264702710 264702993 5.840000e-113 418
37 TraesCS3D01G430500 chr6B 94.306 281 10 4 30 306 628765890 628765612 3.490000e-115 425
38 TraesCS3D01G430500 chr4B 94.306 281 10 4 30 306 285247883 285247605 3.490000e-115 425
39 TraesCS3D01G430500 chr6A 95.050 101 5 0 304 404 1029736 1029836 3.910000e-35 159
40 TraesCS3D01G430500 chr6D 94.000 100 6 0 304 403 1589138 1589039 6.540000e-33 152
41 TraesCS3D01G430500 chr2B 89.815 108 11 0 304 411 253278240 253278133 5.090000e-29 139


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 TraesCS3D01G430500 chr3D 544780824 544784603 3779 False 6981.000000 6981 100.0000 1 3780 1 chr3D.!!$F2 3779
1 TraesCS3D01G430500 chr3D 1650927 1652220 1293 False 832.000000 832 78.7740 688 1998 1 chr3D.!!$F1 1310
2 TraesCS3D01G430500 chr3D 1663806 1667280 3474 False 799.333333 1232 80.9430 687 2788 3 chr3D.!!$F3 2101
3 TraesCS3D01G430500 chr3A 681458644 681461693 3049 False 4518.000000 4518 93.5070 316 3351 1 chr3A.!!$F3 3035
4 TraesCS3D01G430500 chr3A 7306054 7307369 1315 True 1131.000000 1131 82.4320 687 1998 1 chr3A.!!$R1 1311
5 TraesCS3D01G430500 chr3A 7429090 7430415 1325 False 857.000000 857 78.7000 687 1998 1 chr3A.!!$F2 1311
6 TraesCS3D01G430500 chr3A 7356571 7357866 1295 True 835.000000 835 78.6790 687 1999 1 chr3A.!!$R2 1312
7 TraesCS3D01G430500 chr3A 7407186 7407766 580 False 470.000000 470 81.3450 726 1319 1 chr3A.!!$F1 593
8 TraesCS3D01G430500 chr3B 3815649 3816961 1312 False 1188.000000 1188 83.2080 687 1998 1 chr3B.!!$F3 1311
9 TraesCS3D01G430500 chr3B 4714981 4716293 1312 False 1188.000000 1188 83.2200 687 1998 1 chr3B.!!$F6 1311
10 TraesCS3D01G430500 chr3B 3764229 3765561 1332 True 1031.000000 1031 81.0690 685 1998 1 chr3B.!!$R2 1313
11 TraesCS3D01G430500 chr3B 4664702 4666042 1340 True 994.000000 994 80.5620 685 1998 1 chr3B.!!$R3 1313
12 TraesCS3D01G430500 chr3B 720955845 720960948 5103 False 935.000000 2324 92.5804 304 3780 5 chr3B.!!$F7 3476
13 TraesCS3D01G430500 chr3B 3737785 3739109 1324 True 917.000000 917 79.5370 687 1998 1 chr3B.!!$R1 1311
14 TraesCS3D01G430500 chr3B 3785028 3785906 878 False 625.000000 625 79.9320 685 1550 1 chr3B.!!$F2 865
15 TraesCS3D01G430500 chr3B 3773285 3773917 632 False 494.000000 494 81.2210 2077 2715 1 chr3B.!!$F1 638
16 TraesCS3D01G430500 chr3B 4673889 4674521 632 False 483.000000 483 80.9160 2077 2715 1 chr3B.!!$F5 638
17 TraesCS3D01G430500 chrUn 296649930 296652025 2095 False 1332.000000 1332 78.6830 685 2808 1 chrUn.!!$F1 2123
18 TraesCS3D01G430500 chrUn 344718486 344719118 632 True 494.000000 494 81.2210 2077 2715 1 chrUn.!!$R2 638
19 TraesCS3D01G430500 chr4A 669456166 669458261 2095 True 1332.000000 1332 78.6830 685 2808 1 chr4A.!!$R1 2123
20 TraesCS3D01G430500 chr7D 20614947 20616255 1308 False 976.000000 976 80.3460 685 1998 1 chr7D.!!$F1 1313
21 TraesCS3D01G430500 chr7A 20771699 20772680 981 True 902.000000 902 83.5340 1038 2016 1 chr7A.!!$R1 978

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
39 40 0.035343 GGGTCCACTTTAGGCTGGTC 60.035 60.0 0.00 0.00 0.00 4.02 F
302 303 0.187361 TTACCCCATTATGGCCAGCC 59.813 55.0 13.05 0.38 35.79 4.85 F
1327 2336 0.028902 CGATGACGAGCCGTACATGA 59.971 55.0 0.00 0.00 41.37 3.07 F
1954 3014 0.179034 GGAAGGCAGCCTTGATCGAT 60.179 55.0 32.31 5.11 44.82 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 2336 0.320374 ATGTCCACCGACGTGTTCAT 59.680 50.000 0.00 0.00 42.37 2.57 R
1592 2631 1.264557 CGTCATCGGAATCGTCTAGCT 59.735 52.381 0.00 0.00 37.69 3.32 R
2446 3551 2.667536 CACTTGAGCAGCGGCAGT 60.668 61.111 12.44 2.74 44.61 4.40 R
3590 6415 0.035439 TTTCATCTCCGGCAAGGTCC 60.035 55.000 0.00 0.00 41.99 4.46 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 9.349713 GTTCAATAATAAATGAGTATGGGTCCA 57.650 33.333 0.00 0.00 0.00 4.02
27 28 8.918202 TCAATAATAAATGAGTATGGGTCCAC 57.082 34.615 0.00 0.00 0.00 4.02
28 29 8.723365 TCAATAATAAATGAGTATGGGTCCACT 58.277 33.333 0.00 0.00 0.00 4.00
29 30 9.354673 CAATAATAAATGAGTATGGGTCCACTT 57.645 33.333 0.00 0.00 0.00 3.16
30 31 9.936329 AATAATAAATGAGTATGGGTCCACTTT 57.064 29.630 0.00 0.00 0.00 2.66
32 33 8.980481 AATAAATGAGTATGGGTCCACTTTAG 57.020 34.615 0.00 0.00 0.00 1.85
33 34 5.373812 AATGAGTATGGGTCCACTTTAGG 57.626 43.478 0.00 0.00 0.00 2.69
34 35 2.504175 TGAGTATGGGTCCACTTTAGGC 59.496 50.000 0.00 0.00 0.00 3.93
35 36 2.772515 GAGTATGGGTCCACTTTAGGCT 59.227 50.000 0.00 0.00 0.00 4.58
36 37 2.505819 AGTATGGGTCCACTTTAGGCTG 59.494 50.000 0.00 0.00 0.00 4.85
37 38 0.625849 ATGGGTCCACTTTAGGCTGG 59.374 55.000 0.00 0.00 0.00 4.85
38 39 0.770557 TGGGTCCACTTTAGGCTGGT 60.771 55.000 0.00 0.00 0.00 4.00
39 40 0.035343 GGGTCCACTTTAGGCTGGTC 60.035 60.000 0.00 0.00 0.00 4.02
40 41 0.690762 GGTCCACTTTAGGCTGGTCA 59.309 55.000 0.00 0.00 0.00 4.02
41 42 1.282157 GGTCCACTTTAGGCTGGTCAT 59.718 52.381 0.00 0.00 0.00 3.06
42 43 2.504175 GGTCCACTTTAGGCTGGTCATA 59.496 50.000 0.00 0.00 0.00 2.15
43 44 3.432326 GGTCCACTTTAGGCTGGTCATAG 60.432 52.174 0.00 0.00 0.00 2.23
44 45 3.197983 GTCCACTTTAGGCTGGTCATAGT 59.802 47.826 0.00 0.00 0.00 2.12
45 46 3.197766 TCCACTTTAGGCTGGTCATAGTG 59.802 47.826 0.00 0.00 33.21 2.74
46 47 3.535561 CACTTTAGGCTGGTCATAGTGG 58.464 50.000 0.00 0.00 0.00 4.00
47 48 2.505819 ACTTTAGGCTGGTCATAGTGGG 59.494 50.000 0.00 0.00 0.00 4.61
48 49 1.507140 TTAGGCTGGTCATAGTGGGG 58.493 55.000 0.00 0.00 0.00 4.96
49 50 0.639943 TAGGCTGGTCATAGTGGGGA 59.360 55.000 0.00 0.00 0.00 4.81
50 51 0.692419 AGGCTGGTCATAGTGGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
51 52 0.983378 GGCTGGTCATAGTGGGGAGT 60.983 60.000 0.00 0.00 0.00 3.85
52 53 1.691482 GGCTGGTCATAGTGGGGAGTA 60.691 57.143 0.00 0.00 0.00 2.59
53 54 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
54 55 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
55 56 3.375699 CTGGTCATAGTGGGGAGTAACT 58.624 50.000 0.00 0.00 0.00 2.24
56 57 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
57 58 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
58 59 4.960469 TGGTCATAGTGGGGAGTAACTTAG 59.040 45.833 0.00 0.00 0.00 2.18
59 60 5.206587 GGTCATAGTGGGGAGTAACTTAGA 58.793 45.833 0.00 0.00 0.00 2.10
60 61 5.068855 GGTCATAGTGGGGAGTAACTTAGAC 59.931 48.000 0.00 0.00 32.58 2.59
61 62 5.892686 GTCATAGTGGGGAGTAACTTAGACT 59.107 44.000 0.00 0.00 31.58 3.24
62 63 7.059156 GTCATAGTGGGGAGTAACTTAGACTA 58.941 42.308 0.00 0.00 31.58 2.59
63 64 7.229106 GTCATAGTGGGGAGTAACTTAGACTAG 59.771 44.444 0.00 0.00 31.58 2.57
64 65 5.533333 AGTGGGGAGTAACTTAGACTAGT 57.467 43.478 0.00 0.00 0.00 2.57
65 66 6.649041 AGTGGGGAGTAACTTAGACTAGTA 57.351 41.667 0.00 0.00 0.00 1.82
66 67 7.037342 AGTGGGGAGTAACTTAGACTAGTAA 57.963 40.000 0.00 0.00 0.00 2.24
67 68 6.889177 AGTGGGGAGTAACTTAGACTAGTAAC 59.111 42.308 0.00 0.00 0.00 2.50
68 69 6.660949 GTGGGGAGTAACTTAGACTAGTAACA 59.339 42.308 0.00 0.00 0.00 2.41
69 70 7.341512 GTGGGGAGTAACTTAGACTAGTAACAT 59.658 40.741 0.00 0.00 0.00 2.71
70 71 8.560039 TGGGGAGTAACTTAGACTAGTAACATA 58.440 37.037 0.00 0.00 0.00 2.29
71 72 9.585369 GGGGAGTAACTTAGACTAGTAACATAT 57.415 37.037 0.00 0.00 0.00 1.78
73 74 9.896263 GGAGTAACTTAGACTAGTAACATATGC 57.104 37.037 1.58 0.00 0.00 3.14
97 98 9.976511 TGCATGTTATTAGTCTATGTTACTACC 57.023 33.333 0.00 0.00 0.00 3.18
107 108 8.851541 AGTCTATGTTACTACCTCTATAGTGC 57.148 38.462 0.00 0.00 36.09 4.40
108 109 8.438373 AGTCTATGTTACTACCTCTATAGTGCA 58.562 37.037 0.00 0.00 36.09 4.57
109 110 9.233649 GTCTATGTTACTACCTCTATAGTGCAT 57.766 37.037 0.00 0.00 36.09 3.96
157 158 5.939447 TGGTCTCATTTATACCATGCATGA 58.061 37.500 28.31 9.57 38.36 3.07
158 159 5.764686 TGGTCTCATTTATACCATGCATGAC 59.235 40.000 28.31 12.59 38.36 3.06
159 160 5.764686 GGTCTCATTTATACCATGCATGACA 59.235 40.000 28.31 14.91 33.28 3.58
160 161 6.293626 GGTCTCATTTATACCATGCATGACAC 60.294 42.308 28.31 3.24 33.28 3.67
161 162 6.260714 GTCTCATTTATACCATGCATGACACA 59.739 38.462 28.31 9.83 0.00 3.72
162 163 6.999871 TCTCATTTATACCATGCATGACACAT 59.000 34.615 28.31 15.80 0.00 3.21
163 164 8.156165 TCTCATTTATACCATGCATGACACATA 58.844 33.333 28.31 14.88 0.00 2.29
164 165 8.326680 TCATTTATACCATGCATGACACATAG 57.673 34.615 28.31 11.52 0.00 2.23
165 166 7.938490 TCATTTATACCATGCATGACACATAGT 59.062 33.333 28.31 16.65 0.00 2.12
166 167 9.218440 CATTTATACCATGCATGACACATAGTA 57.782 33.333 28.31 18.19 0.00 1.82
167 168 8.831715 TTTATACCATGCATGACACATAGTAG 57.168 34.615 28.31 9.32 27.72 2.57
168 169 3.470709 ACCATGCATGACACATAGTAGC 58.529 45.455 28.31 0.00 0.00 3.58
169 170 3.118298 ACCATGCATGACACATAGTAGCA 60.118 43.478 28.31 0.00 37.13 3.49
170 171 4.070009 CCATGCATGACACATAGTAGCAT 58.930 43.478 28.31 0.00 41.24 3.79
171 172 4.153655 CCATGCATGACACATAGTAGCATC 59.846 45.833 28.31 0.00 39.67 3.91
172 173 4.405116 TGCATGACACATAGTAGCATCA 57.595 40.909 0.00 0.00 30.65 3.07
173 174 4.122046 TGCATGACACATAGTAGCATCAC 58.878 43.478 0.00 0.00 30.65 3.06
174 175 4.122046 GCATGACACATAGTAGCATCACA 58.878 43.478 0.00 0.00 0.00 3.58
175 176 4.753610 GCATGACACATAGTAGCATCACAT 59.246 41.667 0.00 0.00 0.00 3.21
176 177 5.237996 GCATGACACATAGTAGCATCACATT 59.762 40.000 0.00 0.00 0.00 2.71
177 178 6.238566 GCATGACACATAGTAGCATCACATTT 60.239 38.462 0.00 0.00 0.00 2.32
178 179 7.041848 GCATGACACATAGTAGCATCACATTTA 60.042 37.037 0.00 0.00 0.00 1.40
179 180 8.996271 CATGACACATAGTAGCATCACATTTAT 58.004 33.333 0.00 0.00 0.00 1.40
180 181 8.962884 TGACACATAGTAGCATCACATTTATT 57.037 30.769 0.00 0.00 0.00 1.40
189 190 8.988934 AGTAGCATCACATTTATTATGTTACGG 58.011 33.333 0.00 0.00 39.53 4.02
190 191 7.801716 AGCATCACATTTATTATGTTACGGT 57.198 32.000 0.00 0.00 0.00 4.83
191 192 8.896320 AGCATCACATTTATTATGTTACGGTA 57.104 30.769 0.00 0.00 0.00 4.02
192 193 9.502091 AGCATCACATTTATTATGTTACGGTAT 57.498 29.630 0.00 0.00 0.00 2.73
193 194 9.755064 GCATCACATTTATTATGTTACGGTATC 57.245 33.333 0.00 0.00 0.00 2.24
206 207 8.930846 ATGTTACGGTATCTACCTATGTTACT 57.069 34.615 4.93 0.00 44.25 2.24
212 213 9.454859 ACGGTATCTACCTATGTTACTATAACC 57.545 37.037 4.93 0.00 44.25 2.85
213 214 9.453572 CGGTATCTACCTATGTTACTATAACCA 57.546 37.037 4.93 0.00 44.25 3.67
221 222 9.080097 ACCTATGTTACTATAACCATGTCTCTC 57.920 37.037 0.00 0.00 0.00 3.20
222 223 9.303116 CCTATGTTACTATAACCATGTCTCTCT 57.697 37.037 0.00 0.00 0.00 3.10
225 226 8.824756 TGTTACTATAACCATGTCTCTCTTCT 57.175 34.615 0.00 0.00 0.00 2.85
226 227 9.256228 TGTTACTATAACCATGTCTCTCTTCTT 57.744 33.333 0.00 0.00 0.00 2.52
236 237 9.442047 ACCATGTCTCTCTTCTTTAATTAACTG 57.558 33.333 0.00 0.00 0.00 3.16
237 238 8.394121 CCATGTCTCTCTTCTTTAATTAACTGC 58.606 37.037 0.00 0.00 0.00 4.40
238 239 7.907214 TGTCTCTCTTCTTTAATTAACTGCC 57.093 36.000 0.00 0.00 0.00 4.85
239 240 7.450074 TGTCTCTCTTCTTTAATTAACTGCCA 58.550 34.615 0.00 0.00 0.00 4.92
240 241 7.387948 TGTCTCTCTTCTTTAATTAACTGCCAC 59.612 37.037 0.00 0.00 0.00 5.01
241 242 7.387948 GTCTCTCTTCTTTAATTAACTGCCACA 59.612 37.037 0.00 0.00 0.00 4.17
242 243 8.103305 TCTCTCTTCTTTAATTAACTGCCACAT 58.897 33.333 0.00 0.00 0.00 3.21
243 244 9.383519 CTCTCTTCTTTAATTAACTGCCACATA 57.616 33.333 0.00 0.00 0.00 2.29
244 245 9.733556 TCTCTTCTTTAATTAACTGCCACATAA 57.266 29.630 0.00 0.00 0.00 1.90
245 246 9.994432 CTCTTCTTTAATTAACTGCCACATAAG 57.006 33.333 0.00 0.00 0.00 1.73
246 247 8.458843 TCTTCTTTAATTAACTGCCACATAAGC 58.541 33.333 0.00 0.00 0.00 3.09
247 248 7.695480 TCTTTAATTAACTGCCACATAAGCA 57.305 32.000 0.00 0.00 38.82 3.91
248 249 8.292444 TCTTTAATTAACTGCCACATAAGCAT 57.708 30.769 0.00 0.00 40.04 3.79
249 250 8.190122 TCTTTAATTAACTGCCACATAAGCATG 58.810 33.333 0.00 0.00 40.04 4.06
250 251 5.920193 AATTAACTGCCACATAAGCATGT 57.080 34.783 0.00 0.00 46.58 3.21
251 252 5.920193 ATTAACTGCCACATAAGCATGTT 57.080 34.783 0.00 0.00 42.98 2.71
252 253 5.720371 TTAACTGCCACATAAGCATGTTT 57.280 34.783 0.00 0.00 42.98 2.83
253 254 3.581024 ACTGCCACATAAGCATGTTTG 57.419 42.857 4.89 0.00 42.98 2.93
254 255 2.231964 ACTGCCACATAAGCATGTTTGG 59.768 45.455 4.89 0.00 42.98 3.28
255 256 1.549620 TGCCACATAAGCATGTTTGGG 59.450 47.619 4.89 2.90 42.98 4.12
256 257 1.824230 GCCACATAAGCATGTTTGGGA 59.176 47.619 4.89 0.00 42.98 4.37
257 258 2.159198 GCCACATAAGCATGTTTGGGAG 60.159 50.000 4.89 0.00 42.98 4.30
258 259 3.091545 CCACATAAGCATGTTTGGGAGT 58.908 45.455 4.89 0.00 42.98 3.85
259 260 3.129287 CCACATAAGCATGTTTGGGAGTC 59.871 47.826 4.89 0.00 42.98 3.36
260 261 3.129287 CACATAAGCATGTTTGGGAGTCC 59.871 47.826 4.89 0.00 42.98 3.85
261 262 2.507407 TAAGCATGTTTGGGAGTCCC 57.493 50.000 22.54 22.54 45.71 4.46
262 263 6.350870 ACATAAGCATGTTTGGGAGTCCCA 62.351 45.833 28.04 28.04 46.84 4.37
263 264 7.754719 ACATAAGCATGTTTGGGAGTCCCAA 62.755 44.000 35.59 35.59 46.37 4.12
270 271 4.326255 GGGAGTCCCAAGTGCATG 57.674 61.111 24.35 0.00 44.65 4.06
271 272 1.685224 GGGAGTCCCAAGTGCATGA 59.315 57.895 24.35 0.00 44.65 3.07
272 273 0.257039 GGGAGTCCCAAGTGCATGAT 59.743 55.000 24.35 0.00 44.65 2.45
273 274 1.490490 GGGAGTCCCAAGTGCATGATA 59.510 52.381 24.35 0.00 44.65 2.15
274 275 2.565841 GGAGTCCCAAGTGCATGATAC 58.434 52.381 0.00 0.00 0.00 2.24
275 276 2.171448 GGAGTCCCAAGTGCATGATACT 59.829 50.000 0.00 0.00 0.00 2.12
276 277 3.388024 GGAGTCCCAAGTGCATGATACTA 59.612 47.826 0.00 0.00 0.00 1.82
277 278 4.372656 GAGTCCCAAGTGCATGATACTAC 58.627 47.826 0.00 0.00 0.00 2.73
278 279 4.033709 AGTCCCAAGTGCATGATACTACT 58.966 43.478 0.00 0.00 0.00 2.57
279 280 4.471386 AGTCCCAAGTGCATGATACTACTT 59.529 41.667 0.00 0.00 33.94 2.24
280 281 5.661312 AGTCCCAAGTGCATGATACTACTTA 59.339 40.000 0.00 0.00 32.53 2.24
281 282 6.327626 AGTCCCAAGTGCATGATACTACTTAT 59.672 38.462 0.00 0.00 32.53 1.73
282 283 6.425114 GTCCCAAGTGCATGATACTACTTATG 59.575 42.308 0.00 0.00 32.53 1.90
283 284 6.099701 TCCCAAGTGCATGATACTACTTATGT 59.900 38.462 0.00 0.00 32.53 2.29
284 285 6.767902 CCCAAGTGCATGATACTACTTATGTT 59.232 38.462 0.00 0.00 32.53 2.71
285 286 7.931407 CCCAAGTGCATGATACTACTTATGTTA 59.069 37.037 0.00 0.00 32.53 2.41
286 287 8.765219 CCAAGTGCATGATACTACTTATGTTAC 58.235 37.037 0.00 0.00 32.53 2.50
287 288 8.765219 CAAGTGCATGATACTACTTATGTTACC 58.235 37.037 0.00 0.00 32.53 2.85
288 289 7.442656 AGTGCATGATACTACTTATGTTACCC 58.557 38.462 0.00 0.00 0.00 3.69
289 290 6.649557 GTGCATGATACTACTTATGTTACCCC 59.350 42.308 0.00 0.00 0.00 4.95
290 291 6.327887 TGCATGATACTACTTATGTTACCCCA 59.672 38.462 0.00 0.00 0.00 4.96
291 292 7.017155 TGCATGATACTACTTATGTTACCCCAT 59.983 37.037 0.00 0.00 0.00 4.00
292 293 7.883311 GCATGATACTACTTATGTTACCCCATT 59.117 37.037 0.00 0.00 0.00 3.16
296 297 9.886132 GATACTACTTATGTTACCCCATTATGG 57.114 37.037 3.85 3.85 37.25 2.74
297 298 6.540083 ACTACTTATGTTACCCCATTATGGC 58.460 40.000 5.57 0.00 35.79 4.40
298 299 4.736473 ACTTATGTTACCCCATTATGGCC 58.264 43.478 5.57 0.00 35.79 5.36
299 300 4.169068 ACTTATGTTACCCCATTATGGCCA 59.831 41.667 8.56 8.56 35.79 5.36
300 301 2.746279 TGTTACCCCATTATGGCCAG 57.254 50.000 13.05 0.00 35.79 4.85
301 302 1.328279 GTTACCCCATTATGGCCAGC 58.672 55.000 13.05 0.00 35.79 4.85
302 303 0.187361 TTACCCCATTATGGCCAGCC 59.813 55.000 13.05 0.38 35.79 4.85
361 362 1.787012 TCCCAAAACTAACGACGAGC 58.213 50.000 0.00 0.00 0.00 5.03
364 1286 1.134226 CAAAACTAACGACGAGCGGT 58.866 50.000 0.00 0.00 46.49 5.68
384 1306 3.081804 GTTTAGATTCTGGTGGGTGTGG 58.918 50.000 0.00 0.00 0.00 4.17
385 1307 2.335681 TAGATTCTGGTGGGTGTGGA 57.664 50.000 0.00 0.00 0.00 4.02
404 1331 2.506438 GCCGTGTGCTACTCGTCC 60.506 66.667 8.95 0.00 33.75 4.79
406 1333 2.559840 CGTGTGCTACTCGTCCGT 59.440 61.111 0.00 0.00 31.32 4.69
423 1353 1.183549 CGTGTCCTTGTAGTAGGCCT 58.816 55.000 11.78 11.78 35.15 5.19
625 1571 3.668141 ACATCAACCATAATGAGGCCA 57.332 42.857 5.01 0.00 32.09 5.36
658 1604 0.719465 CCGTCTCCGTGTACATTTGC 59.281 55.000 0.00 0.00 0.00 3.68
659 1605 1.671850 CCGTCTCCGTGTACATTTGCT 60.672 52.381 0.00 0.00 0.00 3.91
717 1663 4.640364 CTCTCCTTCAGCTTCAACTTCTT 58.360 43.478 0.00 0.00 0.00 2.52
784 1742 2.434884 CACATGGGCTTCGACGCT 60.435 61.111 14.02 0.00 0.00 5.07
785 1743 1.153647 CACATGGGCTTCGACGCTA 60.154 57.895 14.02 3.97 0.00 4.26
854 1815 1.300156 GAGCGTCATATGCTCGGCA 60.300 57.895 17.10 1.01 45.95 5.69
879 1840 1.598130 GCTCTGGAACAACGCCACT 60.598 57.895 0.00 0.00 38.70 4.00
915 1876 3.181490 GCTTTTCCTCCAACTTCACGTTT 60.181 43.478 0.00 0.00 32.27 3.60
1327 2336 0.028902 CGATGACGAGCCGTACATGA 59.971 55.000 0.00 0.00 41.37 3.07
1506 2526 2.481919 CGGCGACTAGTGCGTGTA 59.518 61.111 0.00 0.00 0.00 2.90
1563 2602 2.663520 TGCGCCATCGTTGTCGTT 60.664 55.556 4.18 0.00 38.14 3.85
1592 2631 1.069090 GGCGACGCATATGGGAGAA 59.931 57.895 25.04 0.00 0.00 2.87
1954 3014 0.179034 GGAAGGCAGCCTTGATCGAT 60.179 55.000 32.31 5.11 44.82 3.59
2026 3086 3.865302 GCAACAAAACCATCATGGCATGA 60.865 43.478 30.53 30.53 42.67 3.07
2071 3163 7.718314 CCATTCCCATTACTAGTTAACCTAACC 59.282 40.741 0.00 0.00 39.47 2.85
2080 3175 3.050835 AGTTAACCTAACCCACCACACT 58.949 45.455 0.88 0.00 39.47 3.55
2204 3306 2.202479 TCGACTCATCACGCAGCG 60.202 61.111 14.82 14.82 0.00 5.18
2446 3551 3.940852 CAGCTGACAAAGTATACATGGCA 59.059 43.478 8.42 14.40 0.00 4.92
2966 4856 5.106515 GGGCTCAAAAGACTAAAGCACTAAG 60.107 44.000 0.00 0.00 33.58 2.18
3008 4898 2.044123 AATTTCTGGAGCGGACCATC 57.956 50.000 0.00 0.00 39.34 3.51
3009 4899 0.911769 ATTTCTGGAGCGGACCATCA 59.088 50.000 0.00 0.00 39.34 3.07
3033 4923 0.390603 TAGTGTCGTGGGAAATGCCG 60.391 55.000 0.00 0.00 37.63 5.69
3036 4926 2.033448 TCGTGGGAAATGCCGCTT 59.967 55.556 3.00 0.00 37.63 4.68
3040 4930 0.388520 GTGGGAAATGCCGCTTGTTC 60.389 55.000 0.00 0.00 37.63 3.18
3043 4933 0.171231 GGAAATGCCGCTTGTTCCTC 59.829 55.000 11.06 0.00 37.21 3.71
3056 4946 4.444720 GCTTGTTCCTCGCTGTATATACAC 59.555 45.833 11.62 8.12 31.93 2.90
3180 5077 8.635765 AATAAAAACCTAGCATTGACTTCAGA 57.364 30.769 0.00 0.00 0.00 3.27
3182 5079 3.258971 ACCTAGCATTGACTTCAGAGC 57.741 47.619 0.00 0.00 0.00 4.09
3183 5080 2.568956 ACCTAGCATTGACTTCAGAGCA 59.431 45.455 7.46 0.00 32.32 4.26
3184 5081 3.008375 ACCTAGCATTGACTTCAGAGCAA 59.992 43.478 7.46 0.00 32.32 3.91
3185 5082 4.005650 CCTAGCATTGACTTCAGAGCAAA 58.994 43.478 7.46 0.00 32.32 3.68
3186 5083 4.456911 CCTAGCATTGACTTCAGAGCAAAA 59.543 41.667 7.46 0.00 32.32 2.44
3187 5084 4.924305 AGCATTGACTTCAGAGCAAAAA 57.076 36.364 7.46 0.00 32.32 1.94
3242 5145 8.783093 CACTCTTCACACTATTTTGACCAAATA 58.217 33.333 0.00 0.00 36.43 1.40
3314 5218 9.860898 AATTCTTTTTATGAGTACAATGGAAGC 57.139 29.630 0.00 0.00 0.00 3.86
3407 5326 7.900782 GTGTATATACGCCCATAGAACAAAT 57.099 36.000 14.37 0.00 0.00 2.32
3409 5328 7.601130 GTGTATATACGCCCATAGAACAAATGA 59.399 37.037 14.37 0.00 0.00 2.57
3412 5331 1.330521 CGCCCATAGAACAAATGACCG 59.669 52.381 0.00 0.00 0.00 4.79
3416 5335 1.014352 ATAGAACAAATGACCGCGCC 58.986 50.000 0.00 0.00 0.00 6.53
3434 5353 2.285083 GCCCATAGTGTCGTGCAATAA 58.715 47.619 0.00 0.00 31.05 1.40
3435 5354 2.031683 GCCCATAGTGTCGTGCAATAAC 59.968 50.000 0.00 0.00 31.05 1.89
3471 5390 7.547227 AGGCAATAATAAGAACACAATTGGTC 58.453 34.615 10.83 4.27 40.12 4.02
3491 6316 8.731275 TTGGTCTTACACATATACTGGAATTG 57.269 34.615 0.00 0.00 0.00 2.32
3509 6334 7.831753 TGGAATTGTTTTACAGTTCAGTTGAA 58.168 30.769 14.33 0.00 43.81 2.69
3540 6365 5.220854 CCAGAGAAGAACAACGTCAAATGTT 60.221 40.000 3.08 3.08 42.18 2.71
3545 6370 2.383298 ACAACGTCAAATGTTGAGCG 57.617 45.000 16.63 9.58 45.45 5.03
3557 6382 2.367202 TTGAGCGGGAGATGGGGAC 61.367 63.158 0.00 0.00 0.00 4.46
3583 6408 2.126031 GACGTCCGTGAGAAGGGC 60.126 66.667 3.51 0.00 0.00 5.19
3594 6419 1.950973 GAGAAGGGCTCGTCAGGACC 61.951 65.000 1.37 0.00 33.17 4.46
3606 6431 1.153289 CAGGACCTTGCCGGAGATG 60.153 63.158 5.05 0.00 36.31 2.90
3617 6442 0.108992 CCGGAGATGAAAACGACGGA 60.109 55.000 0.00 0.00 42.19 4.69
3618 6443 1.269166 CGGAGATGAAAACGACGGAG 58.731 55.000 0.00 0.00 0.00 4.63
3619 6444 1.135489 CGGAGATGAAAACGACGGAGA 60.135 52.381 0.00 0.00 0.00 3.71
3620 6445 2.479730 CGGAGATGAAAACGACGGAGAT 60.480 50.000 0.00 0.00 0.00 2.75
3630 6455 0.525668 CGACGGAGATTCGACCAAGG 60.526 60.000 0.00 0.00 38.85 3.61
3664 6489 0.179073 CAGCTGATCGTACTTGGGGG 60.179 60.000 8.42 0.00 0.00 5.40
3669 6494 0.690077 GATCGTACTTGGGGGAGGGT 60.690 60.000 0.00 0.00 0.00 4.34
3670 6495 0.981277 ATCGTACTTGGGGGAGGGTG 60.981 60.000 0.00 0.00 0.00 4.61
3671 6496 2.675371 GTACTTGGGGGAGGGTGC 59.325 66.667 0.00 0.00 0.00 5.01
3672 6497 3.006728 TACTTGGGGGAGGGTGCG 61.007 66.667 0.00 0.00 0.00 5.34
3675 6500 4.660611 TTGGGGGAGGGTGCGGTA 62.661 66.667 0.00 0.00 0.00 4.02
3677 6502 4.105553 GGGGGAGGGTGCGGTAAC 62.106 72.222 0.00 0.00 0.00 2.50
3704 6529 1.482593 GAGGAAGAAGATGAAGGCCGA 59.517 52.381 0.00 0.00 0.00 5.54
3765 6590 9.500785 AATTGTCTGAAACTCAAAAAGGAAAAA 57.499 25.926 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.349713 TGGACCCATACTCATTTATTATTGAAC 57.650 33.333 0.00 0.00 0.00 3.18
1 2 9.349713 GTGGACCCATACTCATTTATTATTGAA 57.650 33.333 0.00 0.00 0.00 2.69
2 3 8.723365 AGTGGACCCATACTCATTTATTATTGA 58.277 33.333 0.00 0.00 0.00 2.57
3 4 8.924511 AGTGGACCCATACTCATTTATTATTG 57.075 34.615 0.00 0.00 0.00 1.90
4 5 9.936329 AAAGTGGACCCATACTCATTTATTATT 57.064 29.630 0.00 0.00 0.00 1.40
7 8 7.998964 CCTAAAGTGGACCCATACTCATTTATT 59.001 37.037 0.00 0.00 0.00 1.40
8 9 7.518188 CCTAAAGTGGACCCATACTCATTTAT 58.482 38.462 0.00 0.00 0.00 1.40
9 10 6.634039 GCCTAAAGTGGACCCATACTCATTTA 60.634 42.308 0.00 0.00 0.00 1.40
10 11 5.755849 CCTAAAGTGGACCCATACTCATTT 58.244 41.667 0.00 0.00 0.00 2.32
11 12 4.385310 GCCTAAAGTGGACCCATACTCATT 60.385 45.833 0.00 0.00 0.00 2.57
12 13 3.136626 GCCTAAAGTGGACCCATACTCAT 59.863 47.826 0.00 0.00 0.00 2.90
13 14 2.504175 GCCTAAAGTGGACCCATACTCA 59.496 50.000 0.00 0.00 0.00 3.41
14 15 2.772515 AGCCTAAAGTGGACCCATACTC 59.227 50.000 0.00 0.00 0.00 2.59
15 16 2.505819 CAGCCTAAAGTGGACCCATACT 59.494 50.000 0.00 0.00 0.00 2.12
16 17 2.421529 CCAGCCTAAAGTGGACCCATAC 60.422 54.545 0.00 0.00 35.67 2.39
17 18 1.843851 CCAGCCTAAAGTGGACCCATA 59.156 52.381 0.00 0.00 35.67 2.74
18 19 0.625849 CCAGCCTAAAGTGGACCCAT 59.374 55.000 0.00 0.00 35.67 4.00
19 20 0.770557 ACCAGCCTAAAGTGGACCCA 60.771 55.000 0.00 0.00 37.27 4.51
20 21 0.035343 GACCAGCCTAAAGTGGACCC 60.035 60.000 0.00 0.00 37.27 4.46
21 22 0.690762 TGACCAGCCTAAAGTGGACC 59.309 55.000 0.00 0.00 37.27 4.46
22 23 2.789409 ATGACCAGCCTAAAGTGGAC 57.211 50.000 0.00 0.00 37.27 4.02
23 24 3.197766 CACTATGACCAGCCTAAAGTGGA 59.802 47.826 0.00 0.00 37.27 4.02
24 25 3.535561 CACTATGACCAGCCTAAAGTGG 58.464 50.000 0.00 0.00 39.98 4.00
25 26 3.535561 CCACTATGACCAGCCTAAAGTG 58.464 50.000 0.00 0.00 34.15 3.16
26 27 2.505819 CCCACTATGACCAGCCTAAAGT 59.494 50.000 0.00 0.00 0.00 2.66
27 28 2.158755 CCCCACTATGACCAGCCTAAAG 60.159 54.545 0.00 0.00 0.00 1.85
28 29 1.843851 CCCCACTATGACCAGCCTAAA 59.156 52.381 0.00 0.00 0.00 1.85
29 30 1.009060 TCCCCACTATGACCAGCCTAA 59.991 52.381 0.00 0.00 0.00 2.69
30 31 0.639943 TCCCCACTATGACCAGCCTA 59.360 55.000 0.00 0.00 0.00 3.93
31 32 0.692419 CTCCCCACTATGACCAGCCT 60.692 60.000 0.00 0.00 0.00 4.58
32 33 0.983378 ACTCCCCACTATGACCAGCC 60.983 60.000 0.00 0.00 0.00 4.85
33 34 1.789523 TACTCCCCACTATGACCAGC 58.210 55.000 0.00 0.00 0.00 4.85
34 35 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
35 36 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
36 37 5.068855 GTCTAAGTTACTCCCCACTATGACC 59.931 48.000 0.00 0.00 0.00 4.02
37 38 5.892686 AGTCTAAGTTACTCCCCACTATGAC 59.107 44.000 0.00 0.00 0.00 3.06
38 39 6.088541 AGTCTAAGTTACTCCCCACTATGA 57.911 41.667 0.00 0.00 0.00 2.15
39 40 7.061688 ACTAGTCTAAGTTACTCCCCACTATG 58.938 42.308 0.00 0.00 0.00 2.23
40 41 7.223472 ACTAGTCTAAGTTACTCCCCACTAT 57.777 40.000 0.00 0.00 0.00 2.12
41 42 6.649041 ACTAGTCTAAGTTACTCCCCACTA 57.351 41.667 0.00 0.00 0.00 2.74
42 43 5.533333 ACTAGTCTAAGTTACTCCCCACT 57.467 43.478 0.00 0.00 0.00 4.00
43 44 6.660949 TGTTACTAGTCTAAGTTACTCCCCAC 59.339 42.308 0.00 0.00 31.82 4.61
44 45 6.793478 TGTTACTAGTCTAAGTTACTCCCCA 58.207 40.000 0.00 0.00 31.82 4.96
45 46 7.894753 ATGTTACTAGTCTAAGTTACTCCCC 57.105 40.000 0.00 0.00 31.82 4.81
47 48 9.896263 GCATATGTTACTAGTCTAAGTTACTCC 57.104 37.037 0.00 0.00 31.82 3.85
71 72 9.976511 GGTAGTAACATAGACTAATAACATGCA 57.023 33.333 0.00 0.00 31.33 3.96
81 82 9.941325 GCACTATAGAGGTAGTAACATAGACTA 57.059 37.037 6.78 0.00 33.29 2.59
82 83 8.438373 TGCACTATAGAGGTAGTAACATAGACT 58.562 37.037 6.78 0.00 33.29 3.24
83 84 8.618702 TGCACTATAGAGGTAGTAACATAGAC 57.381 38.462 6.78 0.00 33.29 2.59
135 136 5.764686 TGTCATGCATGGTATAAATGAGACC 59.235 40.000 25.97 0.00 40.14 3.85
136 137 6.260714 TGTGTCATGCATGGTATAAATGAGAC 59.739 38.462 25.97 13.22 40.23 3.36
137 138 6.355747 TGTGTCATGCATGGTATAAATGAGA 58.644 36.000 25.97 0.10 0.00 3.27
138 139 6.622833 TGTGTCATGCATGGTATAAATGAG 57.377 37.500 25.97 0.00 0.00 2.90
139 140 7.938490 ACTATGTGTCATGCATGGTATAAATGA 59.062 33.333 25.97 1.44 36.51 2.57
140 141 8.102800 ACTATGTGTCATGCATGGTATAAATG 57.897 34.615 25.97 12.67 36.51 2.32
141 142 9.440773 CTACTATGTGTCATGCATGGTATAAAT 57.559 33.333 25.97 14.26 38.80 1.40
142 143 7.387673 GCTACTATGTGTCATGCATGGTATAAA 59.612 37.037 25.97 2.92 38.80 1.40
143 144 6.873605 GCTACTATGTGTCATGCATGGTATAA 59.126 38.462 25.97 9.33 38.80 0.98
144 145 6.014669 TGCTACTATGTGTCATGCATGGTATA 60.015 38.462 25.97 16.50 38.80 1.47
145 146 5.221702 TGCTACTATGTGTCATGCATGGTAT 60.222 40.000 25.97 16.29 38.80 2.73
146 147 4.100808 TGCTACTATGTGTCATGCATGGTA 59.899 41.667 25.97 16.09 38.62 3.25
147 148 3.118298 TGCTACTATGTGTCATGCATGGT 60.118 43.478 25.97 15.83 40.35 3.55
148 149 3.469739 TGCTACTATGTGTCATGCATGG 58.530 45.455 25.97 10.76 0.00 3.66
149 150 4.753107 TGATGCTACTATGTGTCATGCATG 59.247 41.667 21.07 21.07 38.93 4.06
150 151 4.753610 GTGATGCTACTATGTGTCATGCAT 59.246 41.667 0.00 0.00 40.30 3.96
151 152 4.122046 GTGATGCTACTATGTGTCATGCA 58.878 43.478 0.00 0.00 35.34 3.96
152 153 4.122046 TGTGATGCTACTATGTGTCATGC 58.878 43.478 0.00 0.00 0.00 4.06
153 154 6.856135 AATGTGATGCTACTATGTGTCATG 57.144 37.500 0.00 0.00 0.00 3.07
154 155 9.565090 AATAAATGTGATGCTACTATGTGTCAT 57.435 29.630 0.00 0.00 0.00 3.06
155 156 8.962884 AATAAATGTGATGCTACTATGTGTCA 57.037 30.769 0.00 0.00 0.00 3.58
163 164 8.988934 CCGTAACATAATAAATGTGATGCTACT 58.011 33.333 0.00 0.00 31.80 2.57
164 165 8.770828 ACCGTAACATAATAAATGTGATGCTAC 58.229 33.333 0.00 0.00 31.80 3.58
165 166 8.896320 ACCGTAACATAATAAATGTGATGCTA 57.104 30.769 0.00 0.00 31.80 3.49
166 167 7.801716 ACCGTAACATAATAAATGTGATGCT 57.198 32.000 0.00 0.00 31.80 3.79
167 168 9.755064 GATACCGTAACATAATAAATGTGATGC 57.245 33.333 0.00 0.00 31.80 3.91
195 196 9.080097 GAGAGACATGGTTATAGTAACATAGGT 57.920 37.037 0.00 0.00 0.00 3.08
196 197 9.303116 AGAGAGACATGGTTATAGTAACATAGG 57.697 37.037 0.00 0.00 0.00 2.57
199 200 9.427821 AGAAGAGAGACATGGTTATAGTAACAT 57.572 33.333 0.00 0.00 0.00 2.71
200 201 8.824756 AGAAGAGAGACATGGTTATAGTAACA 57.175 34.615 0.00 0.00 0.00 2.41
210 211 9.442047 CAGTTAATTAAAGAAGAGAGACATGGT 57.558 33.333 0.00 0.00 0.00 3.55
211 212 8.394121 GCAGTTAATTAAAGAAGAGAGACATGG 58.606 37.037 0.00 0.00 0.00 3.66
212 213 8.394121 GGCAGTTAATTAAAGAAGAGAGACATG 58.606 37.037 0.00 0.00 0.00 3.21
213 214 8.103305 TGGCAGTTAATTAAAGAAGAGAGACAT 58.897 33.333 0.00 0.00 0.00 3.06
214 215 7.387948 GTGGCAGTTAATTAAAGAAGAGAGACA 59.612 37.037 0.00 0.00 0.00 3.41
215 216 7.387948 TGTGGCAGTTAATTAAAGAAGAGAGAC 59.612 37.037 0.00 0.00 0.00 3.36
216 217 7.450074 TGTGGCAGTTAATTAAAGAAGAGAGA 58.550 34.615 0.00 0.00 0.00 3.10
217 218 7.672983 TGTGGCAGTTAATTAAAGAAGAGAG 57.327 36.000 0.00 0.00 0.00 3.20
218 219 9.733556 TTATGTGGCAGTTAATTAAAGAAGAGA 57.266 29.630 0.00 0.00 0.00 3.10
219 220 9.994432 CTTATGTGGCAGTTAATTAAAGAAGAG 57.006 33.333 0.00 0.00 0.00 2.85
220 221 8.458843 GCTTATGTGGCAGTTAATTAAAGAAGA 58.541 33.333 0.00 0.00 0.00 2.87
221 222 8.243426 TGCTTATGTGGCAGTTAATTAAAGAAG 58.757 33.333 0.00 0.00 34.56 2.85
222 223 8.116651 TGCTTATGTGGCAGTTAATTAAAGAA 57.883 30.769 0.00 0.00 34.56 2.52
223 224 7.695480 TGCTTATGTGGCAGTTAATTAAAGA 57.305 32.000 0.00 0.00 34.56 2.52
224 225 7.975616 ACATGCTTATGTGGCAGTTAATTAAAG 59.024 33.333 0.00 0.00 43.15 1.85
225 226 7.835822 ACATGCTTATGTGGCAGTTAATTAAA 58.164 30.769 0.00 0.00 43.15 1.52
226 227 7.403312 ACATGCTTATGTGGCAGTTAATTAA 57.597 32.000 0.00 0.00 43.15 1.40
227 228 7.403312 AACATGCTTATGTGGCAGTTAATTA 57.597 32.000 0.00 0.00 43.15 1.40
228 229 5.920193 ACATGCTTATGTGGCAGTTAATT 57.080 34.783 0.00 0.00 43.15 1.40
229 230 5.920193 AACATGCTTATGTGGCAGTTAAT 57.080 34.783 0.00 0.00 43.15 1.40
230 231 5.468592 CAAACATGCTTATGTGGCAGTTAA 58.531 37.500 0.00 0.00 43.15 2.01
231 232 4.082300 CCAAACATGCTTATGTGGCAGTTA 60.082 41.667 0.00 0.00 43.15 2.24
232 233 3.306225 CCAAACATGCTTATGTGGCAGTT 60.306 43.478 0.00 0.00 43.15 3.16
233 234 2.231964 CCAAACATGCTTATGTGGCAGT 59.768 45.455 0.00 0.00 43.15 4.40
234 235 2.417651 CCCAAACATGCTTATGTGGCAG 60.418 50.000 0.00 0.00 43.15 4.85
235 236 1.549620 CCCAAACATGCTTATGTGGCA 59.450 47.619 0.00 0.00 44.05 4.92
236 237 1.824230 TCCCAAACATGCTTATGTGGC 59.176 47.619 0.00 0.00 34.56 5.01
237 238 3.091545 ACTCCCAAACATGCTTATGTGG 58.908 45.455 0.00 0.00 34.56 4.17
238 239 3.129287 GGACTCCCAAACATGCTTATGTG 59.871 47.826 0.00 0.00 34.56 3.21
239 240 3.356290 GGACTCCCAAACATGCTTATGT 58.644 45.455 0.00 0.00 36.10 2.29
240 241 2.689983 GGGACTCCCAAACATGCTTATG 59.310 50.000 9.53 0.00 44.65 1.90
241 242 3.018423 GGGACTCCCAAACATGCTTAT 57.982 47.619 9.53 0.00 44.65 1.73
242 243 2.507407 GGGACTCCCAAACATGCTTA 57.493 50.000 9.53 0.00 44.65 3.09
243 244 3.363787 GGGACTCCCAAACATGCTT 57.636 52.632 9.53 0.00 44.65 3.91
253 254 0.257039 ATCATGCACTTGGGACTCCC 59.743 55.000 7.25 7.25 45.71 4.30
254 255 2.171448 AGTATCATGCACTTGGGACTCC 59.829 50.000 0.00 0.00 0.00 3.85
255 256 3.550437 AGTATCATGCACTTGGGACTC 57.450 47.619 0.00 0.00 0.00 3.36
256 257 4.033709 AGTAGTATCATGCACTTGGGACT 58.966 43.478 5.29 0.00 0.00 3.85
257 258 4.408182 AGTAGTATCATGCACTTGGGAC 57.592 45.455 5.29 0.00 0.00 4.46
258 259 6.099701 ACATAAGTAGTATCATGCACTTGGGA 59.900 38.462 5.29 0.00 33.47 4.37
259 260 6.291377 ACATAAGTAGTATCATGCACTTGGG 58.709 40.000 5.29 2.16 33.47 4.12
260 261 7.792374 AACATAAGTAGTATCATGCACTTGG 57.208 36.000 5.29 2.42 33.47 3.61
261 262 8.765219 GGTAACATAAGTAGTATCATGCACTTG 58.235 37.037 5.29 0.00 33.47 3.16
262 263 7.931948 GGGTAACATAAGTAGTATCATGCACTT 59.068 37.037 5.29 4.15 39.74 3.16
263 264 7.442656 GGGTAACATAAGTAGTATCATGCACT 58.557 38.462 0.00 5.31 39.74 4.40
264 265 6.649557 GGGGTAACATAAGTAGTATCATGCAC 59.350 42.308 0.00 0.00 39.74 4.57
265 266 6.327887 TGGGGTAACATAAGTAGTATCATGCA 59.672 38.462 0.00 0.00 39.74 3.96
266 267 6.765403 TGGGGTAACATAAGTAGTATCATGC 58.235 40.000 0.00 0.00 39.74 4.06
270 271 9.886132 CCATAATGGGGTAACATAAGTAGTATC 57.114 37.037 0.00 0.00 39.74 2.24
271 272 8.326529 GCCATAATGGGGTAACATAAGTAGTAT 58.673 37.037 0.00 0.00 38.19 2.12
272 273 7.256763 GGCCATAATGGGGTAACATAAGTAGTA 60.257 40.741 0.00 0.00 38.19 1.82
273 274 6.466759 GGCCATAATGGGGTAACATAAGTAGT 60.467 42.308 0.00 0.00 38.19 2.73
274 275 5.944007 GGCCATAATGGGGTAACATAAGTAG 59.056 44.000 0.00 0.00 38.19 2.57
275 276 5.372959 TGGCCATAATGGGGTAACATAAGTA 59.627 40.000 0.00 0.00 38.19 2.24
276 277 4.169068 TGGCCATAATGGGGTAACATAAGT 59.831 41.667 0.00 0.00 38.19 2.24
277 278 4.735369 TGGCCATAATGGGGTAACATAAG 58.265 43.478 0.00 0.00 38.19 1.73
278 279 4.735369 CTGGCCATAATGGGGTAACATAA 58.265 43.478 5.51 0.00 38.19 1.90
279 280 3.499563 GCTGGCCATAATGGGGTAACATA 60.500 47.826 5.51 0.00 38.19 2.29
280 281 2.756233 GCTGGCCATAATGGGGTAACAT 60.756 50.000 5.51 0.00 38.19 2.71
281 282 1.410932 GCTGGCCATAATGGGGTAACA 60.411 52.381 5.51 0.00 38.19 2.41
282 283 1.328279 GCTGGCCATAATGGGGTAAC 58.672 55.000 5.51 0.00 38.19 2.50
283 284 0.187361 GGCTGGCCATAATGGGGTAA 59.813 55.000 5.51 0.00 38.19 2.85
284 285 0.700963 AGGCTGGCCATAATGGGGTA 60.701 55.000 5.51 0.00 38.19 3.69
285 286 1.593166 AAGGCTGGCCATAATGGGGT 61.593 55.000 5.51 0.00 38.19 4.95
286 287 0.482446 TAAGGCTGGCCATAATGGGG 59.518 55.000 5.51 0.00 38.19 4.96
287 288 2.173519 CATAAGGCTGGCCATAATGGG 58.826 52.381 5.51 0.00 38.19 4.00
288 289 3.159213 TCATAAGGCTGGCCATAATGG 57.841 47.619 5.51 0.00 41.55 3.16
289 290 4.147321 ACTTCATAAGGCTGGCCATAATG 58.853 43.478 5.51 12.86 38.92 1.90
290 291 4.141181 TGACTTCATAAGGCTGGCCATAAT 60.141 41.667 5.51 0.00 37.45 1.28
291 292 3.201930 TGACTTCATAAGGCTGGCCATAA 59.798 43.478 5.51 0.00 37.45 1.90
292 293 2.777114 TGACTTCATAAGGCTGGCCATA 59.223 45.455 5.51 6.71 37.45 2.74
293 294 1.565759 TGACTTCATAAGGCTGGCCAT 59.434 47.619 5.51 4.39 37.45 4.40
294 295 0.991146 TGACTTCATAAGGCTGGCCA 59.009 50.000 14.39 4.71 37.45 5.36
295 296 1.065126 AGTGACTTCATAAGGCTGGCC 60.065 52.381 3.00 3.00 37.45 5.36
296 297 2.012673 CAGTGACTTCATAAGGCTGGC 58.987 52.381 0.00 0.00 37.45 4.85
297 298 2.012673 GCAGTGACTTCATAAGGCTGG 58.987 52.381 0.00 0.00 37.45 4.85
298 299 2.012673 GGCAGTGACTTCATAAGGCTG 58.987 52.381 0.00 0.00 37.45 4.85
299 300 1.630369 TGGCAGTGACTTCATAAGGCT 59.370 47.619 0.00 0.00 37.45 4.58
300 301 2.113860 TGGCAGTGACTTCATAAGGC 57.886 50.000 0.00 0.00 36.92 4.35
301 302 4.701651 TGAATTGGCAGTGACTTCATAAGG 59.298 41.667 0.00 0.00 0.00 2.69
302 303 5.885230 TGAATTGGCAGTGACTTCATAAG 57.115 39.130 0.00 0.00 0.00 1.73
361 362 2.290071 ACACCCACCAGAATCTAAACCG 60.290 50.000 0.00 0.00 0.00 4.44
364 1286 2.983192 TCCACACCCACCAGAATCTAAA 59.017 45.455 0.00 0.00 0.00 1.85
404 1331 3.735181 GGCCTACTACAAGGACACG 57.265 57.895 0.00 0.00 44.97 4.49
423 1353 1.673626 GGCATTCCGTCGGTTTCTACA 60.674 52.381 11.88 0.00 0.00 2.74
515 1459 0.250234 CCGGACAGCTTCAGGATCAA 59.750 55.000 0.00 0.00 42.00 2.57
573 1519 1.595993 CGAGAGACGGGGTGTGACAT 61.596 60.000 0.00 0.00 38.46 3.06
625 1571 2.043248 ACGGGTAGGAGGCGATGT 60.043 61.111 0.00 0.00 0.00 3.06
658 1604 3.119316 ACAAGGACGATGAGTAGCTGAAG 60.119 47.826 0.00 0.00 0.00 3.02
659 1605 2.826128 ACAAGGACGATGAGTAGCTGAA 59.174 45.455 0.00 0.00 0.00 3.02
784 1742 5.913514 GCTCGTTCTTTGTTAGCTCGATATA 59.086 40.000 0.00 0.00 31.98 0.86
785 1743 4.740695 GCTCGTTCTTTGTTAGCTCGATAT 59.259 41.667 0.00 0.00 31.98 1.63
854 1815 2.818169 TTGTTCCAGAGCGGCACCT 61.818 57.895 1.45 0.00 28.11 4.00
915 1876 1.602237 GTTCTTGGGCCTGATCCGA 59.398 57.895 4.53 0.00 0.00 4.55
1327 2336 0.320374 ATGTCCACCGACGTGTTCAT 59.680 50.000 0.00 0.00 42.37 2.57
1506 2526 3.362870 ACTACTACGGAAGGCACTAGT 57.637 47.619 0.00 0.00 38.49 2.57
1592 2631 1.264557 CGTCATCGGAATCGTCTAGCT 59.735 52.381 0.00 0.00 37.69 3.32
1954 3014 8.672823 AGTAGACGATCAGTGTTGTATATGTA 57.327 34.615 0.00 0.00 0.00 2.29
2045 3137 7.718314 GGTTAGGTTAACTAGTAATGGGAATGG 59.282 40.741 5.42 0.00 38.68 3.16
2071 3163 4.271696 TCTGTATCTGAAAGTGTGGTGG 57.728 45.455 0.00 0.00 33.76 4.61
2080 3175 7.577303 AGCCAAGGATAATTCTGTATCTGAAA 58.423 34.615 0.00 0.00 32.09 2.69
2446 3551 2.667536 CACTTGAGCAGCGGCAGT 60.668 61.111 12.44 2.74 44.61 4.40
2874 4764 6.760298 TGTAATGGTCGTAGTAAACAACAACA 59.240 34.615 0.00 0.00 0.00 3.33
2875 4765 7.176285 TGTAATGGTCGTAGTAAACAACAAC 57.824 36.000 0.00 0.00 0.00 3.32
2876 4766 7.783090 TTGTAATGGTCGTAGTAAACAACAA 57.217 32.000 0.00 0.00 0.00 2.83
2966 4856 8.922058 ATTTCATGTGATCAACTCAAATAAGC 57.078 30.769 0.00 0.00 35.07 3.09
3008 4898 4.449068 GCATTTCCCACGACACTATAGATG 59.551 45.833 6.78 3.90 0.00 2.90
3009 4899 4.503296 GGCATTTCCCACGACACTATAGAT 60.503 45.833 6.78 0.00 0.00 1.98
3033 4923 4.444720 GTGTATATACAGCGAGGAACAAGC 59.555 45.833 15.93 0.00 36.78 4.01
3036 4926 4.579454 GGTGTATATACAGCGAGGAACA 57.421 45.455 24.80 0.00 43.57 3.18
3148 5045 7.702348 GTCAATGCTAGGTTTTTATTCATGACC 59.298 37.037 0.00 0.00 0.00 4.02
3149 5046 8.462016 AGTCAATGCTAGGTTTTTATTCATGAC 58.538 33.333 0.00 0.00 0.00 3.06
3259 5163 2.764010 AGAAAAACGCCCCTTTGACTTT 59.236 40.909 0.00 0.00 0.00 2.66
3375 5294 6.665992 ATGGGCGTATATACACCCTATATG 57.334 41.667 30.33 7.24 46.39 1.78
3393 5312 1.065551 GCGGTCATTTGTTCTATGGGC 59.934 52.381 0.00 0.00 0.00 5.36
3396 5315 1.268032 GGCGCGGTCATTTGTTCTATG 60.268 52.381 8.83 0.00 0.00 2.23
3407 5326 3.365291 GACACTATGGGCGCGGTCA 62.365 63.158 8.83 0.00 0.00 4.02
3409 5328 4.508128 CGACACTATGGGCGCGGT 62.508 66.667 8.83 0.00 0.00 5.68
3412 5331 3.564027 GCACGACACTATGGGCGC 61.564 66.667 0.00 0.00 0.00 6.53
3416 5335 6.785488 ATATGTTATTGCACGACACTATGG 57.215 37.500 0.00 0.00 0.00 2.74
3444 5363 9.030452 ACCAATTGTGTTCTTATTATTGCCTAA 57.970 29.630 4.43 0.00 0.00 2.69
3445 5364 8.588290 ACCAATTGTGTTCTTATTATTGCCTA 57.412 30.769 4.43 0.00 0.00 3.93
3446 5365 7.397192 AGACCAATTGTGTTCTTATTATTGCCT 59.603 33.333 4.43 0.00 0.00 4.75
3447 5366 7.547227 AGACCAATTGTGTTCTTATTATTGCC 58.453 34.615 4.43 0.00 0.00 4.52
3491 6316 9.020813 GGAAGAAATTCAACTGAACTGTAAAAC 57.979 33.333 0.00 0.00 36.80 2.43
3496 6321 6.122277 TCTGGAAGAAATTCAACTGAACTGT 58.878 36.000 0.00 0.00 42.31 3.55
3531 6356 1.808411 TCTCCCGCTCAACATTTGAC 58.192 50.000 0.00 0.00 35.46 3.18
3540 6365 2.764128 GTCCCCATCTCCCGCTCA 60.764 66.667 0.00 0.00 0.00 4.26
3567 6392 2.600769 AGCCCTTCTCACGGACGT 60.601 61.111 0.00 0.00 0.00 4.34
3586 6411 1.617947 ATCTCCGGCAAGGTCCTGAC 61.618 60.000 0.00 0.00 41.99 3.51
3587 6412 1.306141 ATCTCCGGCAAGGTCCTGA 60.306 57.895 0.00 0.00 41.99 3.86
3590 6415 0.035439 TTTCATCTCCGGCAAGGTCC 60.035 55.000 0.00 0.00 41.99 4.46
3594 6419 1.128692 GTCGTTTTCATCTCCGGCAAG 59.871 52.381 0.00 0.00 0.00 4.01
3606 6431 1.652619 GGTCGAATCTCCGTCGTTTTC 59.347 52.381 0.00 0.00 39.52 2.29
3617 6442 1.987855 TCCCGCCTTGGTCGAATCT 60.988 57.895 0.00 0.00 35.15 2.40
3618 6443 1.814169 GTCCCGCCTTGGTCGAATC 60.814 63.158 0.00 0.00 35.15 2.52
3619 6444 2.267961 GTCCCGCCTTGGTCGAAT 59.732 61.111 0.00 0.00 35.15 3.34
3620 6445 4.011517 GGTCCCGCCTTGGTCGAA 62.012 66.667 0.00 0.00 35.15 3.71
3640 6465 0.101399 AAGTACGATCAGCTGAGGCG 59.899 55.000 29.24 29.24 44.37 5.52
3642 6467 1.202463 CCCAAGTACGATCAGCTGAGG 60.202 57.143 22.96 18.08 0.00 3.86
3648 6473 0.753262 CCTCCCCCAAGTACGATCAG 59.247 60.000 0.00 0.00 0.00 2.90
3653 6478 2.987125 CACCCTCCCCCAAGTACG 59.013 66.667 0.00 0.00 0.00 3.67
3664 6489 0.179108 CAGCTAGTTACCGCACCCTC 60.179 60.000 0.00 0.00 0.00 4.30
3669 6494 0.323999 TCCTCCAGCTAGTTACCGCA 60.324 55.000 0.00 0.00 0.00 5.69
3670 6495 0.822164 TTCCTCCAGCTAGTTACCGC 59.178 55.000 0.00 0.00 0.00 5.68
3671 6496 2.376109 TCTTCCTCCAGCTAGTTACCG 58.624 52.381 0.00 0.00 0.00 4.02
3672 6497 4.024670 TCTTCTTCCTCCAGCTAGTTACC 58.975 47.826 0.00 0.00 0.00 2.85
3674 6499 5.519808 TCATCTTCTTCCTCCAGCTAGTTA 58.480 41.667 0.00 0.00 0.00 2.24
3675 6500 4.357325 TCATCTTCTTCCTCCAGCTAGTT 58.643 43.478 0.00 0.00 0.00 2.24
3677 6502 4.202243 CCTTCATCTTCTTCCTCCAGCTAG 60.202 50.000 0.00 0.00 0.00 3.42
3704 6529 4.570772 CGTTAGATTGAATCCAATGACGGT 59.429 41.667 0.75 0.00 42.66 4.83
3711 6536 4.561500 TGGACCGTTAGATTGAATCCAA 57.438 40.909 0.75 0.00 31.90 3.53


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

AutoCloner maintained by Alex Coulton.