Multiple sequence alignment - TraesCS3D01G380100

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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 TraesCS3D01G380100 chr3D 100.000 7690 0 0 1 7690 496731947 496739636 0.000000e+00 14201.0
1 TraesCS3D01G380100 chr3D 96.296 108 4 0 3220 3327 42166761 42166654 2.210000e-40 178.0
2 TraesCS3D01G380100 chr3B 95.129 4393 135 29 3327 7690 655849602 655853944 0.000000e+00 6854.0
3 TraesCS3D01G380100 chr3B 92.698 2876 115 38 244 3071 655846309 655849137 0.000000e+00 4060.0
4 TraesCS3D01G380100 chr3B 96.154 130 2 1 9 138 655846178 655846304 7.820000e-50 209.0
5 TraesCS3D01G380100 chr3B 91.912 136 9 1 3069 3202 655849290 655849425 1.020000e-43 189.0
6 TraesCS3D01G380100 chr3B 87.619 105 12 1 130 234 439865041 439865144 3.770000e-23 121.0
7 TraesCS3D01G380100 chr3A 90.823 2430 119 39 3356 5738 638072332 638069960 0.000000e+00 3157.0
8 TraesCS3D01G380100 chr3A 94.294 1805 72 15 1292 3077 638074306 638072514 0.000000e+00 2734.0
9 TraesCS3D01G380100 chr3A 97.806 1504 29 3 5924 7425 638069685 638068184 0.000000e+00 2591.0
10 TraesCS3D01G380100 chr3A 90.605 1075 48 21 232 1292 638075385 638074350 0.000000e+00 1376.0
11 TraesCS3D01G380100 chr3A 88.077 260 28 2 7434 7690 638068076 638067817 9.690000e-79 305.0
12 TraesCS3D01G380100 chr3A 86.029 136 7 3 9 138 638075512 638075383 1.350000e-27 135.0
13 TraesCS3D01G380100 chr3A 84.158 101 13 3 135 234 569418828 569418730 2.280000e-15 95.3
14 TraesCS3D01G380100 chr2B 87.649 672 41 11 4582 5244 364679134 364679772 0.000000e+00 743.0
15 TraesCS3D01G380100 chr2B 87.240 674 54 9 4582 5244 501731742 501731090 0.000000e+00 739.0
16 TraesCS3D01G380100 chr2B 87.500 672 42 11 4582 5244 364678012 364678650 0.000000e+00 737.0
17 TraesCS3D01G380100 chr2B 92.437 119 8 1 3209 3326 614134774 614134892 1.330000e-37 169.0
18 TraesCS3D01G380100 chr2B 88.321 137 11 5 3214 3346 131290900 131290765 7.990000e-35 159.0
19 TraesCS3D01G380100 chr2B 90.909 99 6 3 136 233 672800349 672800445 6.260000e-26 130.0
20 TraesCS3D01G380100 chr5B 87.926 646 46 10 4608 5244 120215674 120215052 0.000000e+00 732.0
21 TraesCS3D01G380100 chr5B 97.273 110 3 0 3220 3329 381026296 381026187 3.660000e-43 187.0
22 TraesCS3D01G380100 chr5B 96.396 111 4 0 3217 3327 355653056 355653166 4.740000e-42 183.0
23 TraesCS3D01G380100 chr5B 97.222 108 3 0 3220 3327 665971388 665971281 4.740000e-42 183.0
24 TraesCS3D01G380100 chr5B 88.660 97 9 2 5737 5833 708237856 708237950 4.880000e-22 117.0
25 TraesCS3D01G380100 chr5B 100.000 39 0 0 4582 4620 120215735 120215697 1.070000e-08 73.1
26 TraesCS3D01G380100 chr1B 96.429 112 4 0 3220 3331 315353861 315353972 1.320000e-42 185.0
27 TraesCS3D01G380100 chr5D 91.538 130 8 2 3203 3329 554363642 554363513 7.930000e-40 176.0
28 TraesCS3D01G380100 chr6B 90.076 131 7 6 3207 3331 344040969 344040839 1.720000e-36 165.0
29 TraesCS3D01G380100 chr6B 91.011 89 8 0 5736 5824 395857423 395857511 3.770000e-23 121.0
30 TraesCS3D01G380100 chr4D 84.516 155 21 3 1096 1249 344109917 344110069 4.810000e-32 150.0
31 TraesCS3D01G380100 chr4B 83.871 155 22 3 1096 1249 426104769 426104921 2.240000e-30 145.0
32 TraesCS3D01G380100 chr4B 88.462 104 10 2 130 233 658516038 658515937 2.910000e-24 124.0
33 TraesCS3D01G380100 chr4A 82.317 164 26 3 1096 1258 121506119 121505958 1.040000e-28 139.0
34 TraesCS3D01G380100 chr4A 87.368 95 10 2 140 233 570999358 570999265 2.930000e-19 108.0
35 TraesCS3D01G380100 chr4A 88.636 88 9 1 150 237 584057341 584057255 1.060000e-18 106.0
36 TraesCS3D01G380100 chr6D 91.919 99 6 2 5728 5824 122992204 122992106 3.740000e-28 137.0
37 TraesCS3D01G380100 chr6D 93.258 89 6 0 5736 5824 215563306 215563394 1.740000e-26 132.0
38 TraesCS3D01G380100 chr7A 81.595 163 30 0 1100 1262 133058859 133058697 1.350000e-27 135.0
39 TraesCS3D01G380100 chr7A 86.735 98 11 2 132 229 632033294 632033199 2.930000e-19 108.0
40 TraesCS3D01G380100 chr6A 93.258 89 6 0 5736 5824 548408057 548408145 1.740000e-26 132.0
41 TraesCS3D01G380100 chr1D 93.258 89 6 0 5736 5824 258014445 258014357 1.740000e-26 132.0
42 TraesCS3D01G380100 chr1D 86.735 98 12 1 136 233 71277210 71277306 2.930000e-19 108.0
43 TraesCS3D01G380100 chr2A 92.222 90 7 0 5735 5824 385002700 385002789 2.250000e-25 128.0
44 TraesCS3D01G380100 chr7D 80.368 163 32 0 1100 1262 134178575 134178413 2.910000e-24 124.0
45 TraesCS3D01G380100 chr7D 86.869 99 12 1 135 233 53779635 53779732 8.160000e-20 110.0
46 TraesCS3D01G380100 chr7B 80.368 163 32 0 1100 1262 96281871 96281709 2.910000e-24 124.0
47 TraesCS3D01G380100 chr7B 91.209 91 7 1 5730 5820 533304598 533304509 1.050000e-23 122.0


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 TraesCS3D01G380100 chr3D 496731947 496739636 7689 False 14201.000000 14201 100.000000 1 7690 1 chr3D.!!$F1 7689
1 TraesCS3D01G380100 chr3B 655846178 655853944 7766 False 2828.000000 6854 93.973250 9 7690 4 chr3B.!!$F2 7681
2 TraesCS3D01G380100 chr3A 638067817 638075512 7695 True 1716.333333 3157 91.272333 9 7690 6 chr3A.!!$R2 7681
3 TraesCS3D01G380100 chr2B 364678012 364679772 1760 False 740.000000 743 87.574500 4582 5244 2 chr2B.!!$F3 662
4 TraesCS3D01G380100 chr2B 501731090 501731742 652 True 739.000000 739 87.240000 4582 5244 1 chr2B.!!$R2 662
5 TraesCS3D01G380100 chr5B 120215052 120215735 683 True 402.550000 732 93.963000 4582 5244 2 chr5B.!!$R3 662

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
944 975 0.039764 TTCCTCGCTCCTTCTCTCCA 59.960 55.000 0.00 0.00 0.00 3.86 F
1431 1509 0.254462 TGGGCTGCAATATGAACGGA 59.746 50.000 0.50 0.00 0.00 4.69 F
1432 1510 0.663153 GGGCTGCAATATGAACGGAC 59.337 55.000 0.50 0.00 0.00 4.79 F
3234 3555 1.000163 CATCATACTCCCTCCGTTCGG 60.000 57.143 4.74 4.74 0.00 4.30 F
4135 4564 1.438469 ATGCCTAGCTGCCCTTCATA 58.562 50.000 0.00 0.00 0.00 2.15 F
4968 6579 1.209504 GGTCACAGCACTATTGGCCTA 59.790 52.381 3.32 0.00 0.00 3.93 F
6454 8183 0.377203 GATGGCTACGGGAAAAAGCG 59.623 55.000 0.00 0.00 37.11 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2723 2848 0.396435 ACACTCCAGTCGCCATTGAA 59.604 50.000 0.00 0.00 0.00 2.69 R
3310 3689 0.822164 AATGTACTCCCTCCGTTCGG 59.178 55.000 4.74 4.74 0.00 4.30 R
3311 3690 2.667473 AAATGTACTCCCTCCGTTCG 57.333 50.000 0.00 0.00 0.00 3.95 R
4950 6561 1.209504 GGTAGGCCAATAGTGCTGTGA 59.790 52.381 5.01 0.00 34.09 3.58 R
5643 7258 0.178903 TAGCTAGCCATGGTAGGGGG 60.179 60.000 14.67 0.00 34.62 5.40 R
6478 8207 0.325296 ATCAGCACGAACCCTCCCTA 60.325 55.000 0.00 0.00 0.00 3.53 R
7509 9340 4.655963 ACTACTACTGGACAGGTACGAAA 58.344 43.478 4.14 0.00 0.00 3.46 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
75 76 3.314357 AGGGCGACAACAAAAAGAACTAC 59.686 43.478 0.00 0.00 0.00 2.73
76 77 3.314357 GGGCGACAACAAAAAGAACTACT 59.686 43.478 0.00 0.00 0.00 2.57
77 78 4.512571 GGGCGACAACAAAAAGAACTACTA 59.487 41.667 0.00 0.00 0.00 1.82
142 149 9.440761 AAGGAGTACTCATAAATGATACTTCCT 57.559 33.333 23.91 4.40 34.42 3.36
143 150 9.084533 AGGAGTACTCATAAATGATACTTCCTC 57.915 37.037 23.91 0.54 34.42 3.71
144 151 9.084533 GGAGTACTCATAAATGATACTTCCTCT 57.915 37.037 23.91 0.00 34.42 3.69
145 152 9.906660 GAGTACTCATAAATGATACTTCCTCTG 57.093 37.037 18.20 0.00 34.42 3.35
146 153 9.427821 AGTACTCATAAATGATACTTCCTCTGT 57.572 33.333 0.00 0.00 36.02 3.41
147 154 9.685828 GTACTCATAAATGATACTTCCTCTGTC 57.314 37.037 0.00 0.00 36.02 3.51
148 155 8.546083 ACTCATAAATGATACTTCCTCTGTCT 57.454 34.615 0.00 0.00 36.02 3.41
149 156 8.637986 ACTCATAAATGATACTTCCTCTGTCTC 58.362 37.037 0.00 0.00 36.02 3.36
150 157 8.539117 TCATAAATGATACTTCCTCTGTCTCA 57.461 34.615 0.00 0.00 0.00 3.27
151 158 8.981659 TCATAAATGATACTTCCTCTGTCTCAA 58.018 33.333 0.00 0.00 0.00 3.02
152 159 9.605275 CATAAATGATACTTCCTCTGTCTCAAA 57.395 33.333 0.00 0.00 0.00 2.69
157 164 9.829507 ATGATACTTCCTCTGTCTCAAAATAAG 57.170 33.333 0.00 0.00 0.00 1.73
158 165 8.816894 TGATACTTCCTCTGTCTCAAAATAAGT 58.183 33.333 0.00 0.00 0.00 2.24
159 166 9.092876 GATACTTCCTCTGTCTCAAAATAAGTG 57.907 37.037 0.00 0.00 0.00 3.16
160 167 6.831976 ACTTCCTCTGTCTCAAAATAAGTGT 58.168 36.000 0.00 0.00 0.00 3.55
161 168 6.931840 ACTTCCTCTGTCTCAAAATAAGTGTC 59.068 38.462 0.00 0.00 0.00 3.67
162 169 6.672266 TCCTCTGTCTCAAAATAAGTGTCT 57.328 37.500 0.00 0.00 0.00 3.41
163 170 7.067496 TCCTCTGTCTCAAAATAAGTGTCTT 57.933 36.000 0.00 0.00 0.00 3.01
164 171 8.190326 TCCTCTGTCTCAAAATAAGTGTCTTA 57.810 34.615 0.00 0.00 0.00 2.10
165 172 8.647796 TCCTCTGTCTCAAAATAAGTGTCTTAA 58.352 33.333 0.00 0.00 0.00 1.85
166 173 9.273016 CCTCTGTCTCAAAATAAGTGTCTTAAA 57.727 33.333 0.00 0.00 0.00 1.52
168 175 9.832445 TCTGTCTCAAAATAAGTGTCTTAAACT 57.168 29.630 0.00 0.00 0.00 2.66
175 182 9.944663 CAAAATAAGTGTCTTAAACTTAGTGCA 57.055 29.630 4.92 0.00 41.95 4.57
181 188 9.869757 AAGTGTCTTAAACTTAGTGCAATTTTT 57.130 25.926 0.00 0.00 36.11 1.94
182 189 9.301153 AGTGTCTTAAACTTAGTGCAATTTTTG 57.699 29.630 0.00 0.00 0.00 2.44
183 190 9.083080 GTGTCTTAAACTTAGTGCAATTTTTGT 57.917 29.630 0.00 0.00 0.00 2.83
222 229 9.899226 ATAAAGTTGAGACACTTATTTTGAAGC 57.101 29.630 0.00 0.00 35.87 3.86
223 230 5.990408 AGTTGAGACACTTATTTTGAAGCG 58.010 37.500 0.00 0.00 0.00 4.68
224 231 5.049405 AGTTGAGACACTTATTTTGAAGCGG 60.049 40.000 0.00 0.00 0.00 5.52
225 232 4.637276 TGAGACACTTATTTTGAAGCGGA 58.363 39.130 0.00 0.00 0.00 5.54
226 233 4.690748 TGAGACACTTATTTTGAAGCGGAG 59.309 41.667 0.00 0.00 0.00 4.63
227 234 4.003648 AGACACTTATTTTGAAGCGGAGG 58.996 43.478 0.00 0.00 0.00 4.30
228 235 3.081804 ACACTTATTTTGAAGCGGAGGG 58.918 45.455 0.00 0.00 0.00 4.30
229 236 3.244770 ACACTTATTTTGAAGCGGAGGGA 60.245 43.478 0.00 0.00 0.00 4.20
230 237 3.375299 CACTTATTTTGAAGCGGAGGGAG 59.625 47.826 0.00 0.00 0.00 4.30
231 238 3.009143 ACTTATTTTGAAGCGGAGGGAGT 59.991 43.478 0.00 0.00 0.00 3.85
232 239 4.224370 ACTTATTTTGAAGCGGAGGGAGTA 59.776 41.667 0.00 0.00 0.00 2.59
233 240 2.467566 TTTTGAAGCGGAGGGAGTAC 57.532 50.000 0.00 0.00 0.00 2.73
256 263 4.142752 CGTGCATAGCATAGCATAGCAAAT 60.143 41.667 0.00 0.00 43.44 2.32
260 267 6.430616 TGCATAGCATAGCATAGCAAATAACA 59.569 34.615 0.00 0.00 35.51 2.41
283 290 2.887568 GGAGCCGCAGACATGTCG 60.888 66.667 19.85 15.27 34.09 4.35
305 312 1.337728 TGTCGCAGTGGTGAACCTATG 60.338 52.381 0.37 1.02 34.84 2.23
314 322 2.375174 TGGTGAACCTATGCAAACCTCT 59.625 45.455 0.37 0.00 36.82 3.69
346 354 4.272504 GTCACAGAACAGAACGGAATTTCA 59.727 41.667 0.00 0.00 0.00 2.69
427 435 0.535102 AGTTTGCTCCCCTCACGTTG 60.535 55.000 0.00 0.00 0.00 4.10
467 475 5.723405 CACCCATGATTATCCTCCATCTAGA 59.277 44.000 0.00 0.00 0.00 2.43
565 589 3.444737 CCTCCAGGTACCGATCGG 58.555 66.667 32.20 32.20 42.03 4.18
813 837 2.225017 GGACCAAAAGGACAAGGATGGA 60.225 50.000 0.00 0.00 0.00 3.41
814 838 3.564352 GGACCAAAAGGACAAGGATGGAT 60.564 47.826 0.00 0.00 0.00 3.41
815 839 3.434309 ACCAAAAGGACAAGGATGGATG 58.566 45.455 0.00 0.00 0.00 3.51
816 840 2.762327 CCAAAAGGACAAGGATGGATGG 59.238 50.000 0.00 0.00 0.00 3.51
907 938 2.763902 CCACCCCACCCCTTTCTC 59.236 66.667 0.00 0.00 0.00 2.87
931 962 4.870991 CCTCTAACCTTTAGCTTTTCCTCG 59.129 45.833 0.00 0.00 0.00 4.63
936 967 2.355209 CCTTTAGCTTTTCCTCGCTCCT 60.355 50.000 0.00 0.00 37.68 3.69
939 970 0.980423 AGCTTTTCCTCGCTCCTTCT 59.020 50.000 0.00 0.00 0.00 2.85
944 975 0.039764 TTCCTCGCTCCTTCTCTCCA 59.960 55.000 0.00 0.00 0.00 3.86
945 976 0.681564 TCCTCGCTCCTTCTCTCCAC 60.682 60.000 0.00 0.00 0.00 4.02
946 977 1.671901 CCTCGCTCCTTCTCTCCACC 61.672 65.000 0.00 0.00 0.00 4.61
947 978 0.682855 CTCGCTCCTTCTCTCCACCT 60.683 60.000 0.00 0.00 0.00 4.00
948 979 0.681564 TCGCTCCTTCTCTCCACCTC 60.682 60.000 0.00 0.00 0.00 3.85
949 980 0.682855 CGCTCCTTCTCTCCACCTCT 60.683 60.000 0.00 0.00 0.00 3.69
1231 1263 1.455786 GTCATCACCGACAAGAACACG 59.544 52.381 0.00 0.00 35.88 4.49
1249 1281 1.772819 CGGGCAGATCCAAGGGCTAT 61.773 60.000 0.00 0.00 36.21 2.97
1269 1301 6.017523 GGCTATGGATTTGTAAGCTTCTTCTC 60.018 42.308 0.00 0.00 33.67 2.87
1273 1305 7.246171 TGGATTTGTAAGCTTCTTCTCTACT 57.754 36.000 0.00 0.00 0.00 2.57
1275 1307 8.157476 TGGATTTGTAAGCTTCTTCTCTACTTT 58.843 33.333 0.00 0.00 0.00 2.66
1292 1325 6.755206 TCTACTTTTACTATGCACACACACT 58.245 36.000 0.00 0.00 0.00 3.55
1311 1389 2.979678 ACTCTCTTGCTGGTTTTCCCTA 59.020 45.455 0.00 0.00 39.73 3.53
1376 1454 4.495422 GCTTCTAGCTAGTGCAAGTGTTA 58.505 43.478 25.22 2.85 42.74 2.41
1378 1456 5.582665 GCTTCTAGCTAGTGCAAGTGTTATT 59.417 40.000 25.22 0.00 42.74 1.40
1384 1462 4.385748 GCTAGTGCAAGTGTTATTTTTGCC 59.614 41.667 6.04 0.00 44.91 4.52
1414 1492 4.984161 CACATACTTTTTCTGTTTGCCTGG 59.016 41.667 0.00 0.00 0.00 4.45
1431 1509 0.254462 TGGGCTGCAATATGAACGGA 59.746 50.000 0.50 0.00 0.00 4.69
1432 1510 0.663153 GGGCTGCAATATGAACGGAC 59.337 55.000 0.50 0.00 0.00 4.79
1493 1574 2.663188 GATGCGGCGATGAGGTCC 60.663 66.667 12.98 0.00 0.00 4.46
1620 1704 1.794714 TCCCATTCTCTCTACCAGCC 58.205 55.000 0.00 0.00 0.00 4.85
1630 1717 4.085733 CTCTCTACCAGCCAGCTACATAT 58.914 47.826 0.00 0.00 0.00 1.78
1638 1725 4.752101 CCAGCCAGCTACATATACAAAGTC 59.248 45.833 0.00 0.00 0.00 3.01
1797 1886 8.494347 CATTATAGATGCACTGCTAACTCTTTC 58.506 37.037 1.98 0.00 0.00 2.62
2006 2095 3.196469 TGATTTTCCCAAGCACAACAACA 59.804 39.130 0.00 0.00 0.00 3.33
2165 2254 2.423538 AGTGCCTTGTTTCGGATAATGC 59.576 45.455 0.00 0.00 0.00 3.56
2166 2255 2.163412 GTGCCTTGTTTCGGATAATGCA 59.837 45.455 0.00 0.00 30.04 3.96
2167 2256 3.023119 TGCCTTGTTTCGGATAATGCAT 58.977 40.909 0.00 0.00 28.16 3.96
2168 2257 3.181488 TGCCTTGTTTCGGATAATGCATG 60.181 43.478 0.00 0.00 28.16 4.06
2446 2555 7.628769 AACCTTTGTTTTGCTGATGATTTTT 57.371 28.000 0.00 0.00 0.00 1.94
2449 2558 7.226523 ACCTTTGTTTTGCTGATGATTTTTACC 59.773 33.333 0.00 0.00 0.00 2.85
2455 2564 3.763360 TGCTGATGATTTTTACCACAGGG 59.237 43.478 0.00 0.00 41.29 4.45
2635 2751 2.957680 TCTCATCTCTCTCTCATGTGGC 59.042 50.000 0.00 0.00 0.00 5.01
2723 2848 3.194116 GCATTGTGACATCCCATCTTTGT 59.806 43.478 0.00 0.00 0.00 2.83
2738 2863 1.879380 CTTTGTTCAATGGCGACTGGA 59.121 47.619 0.00 0.00 0.00 3.86
2867 2994 1.615883 GTCTCACACTCTTGCTCCTCA 59.384 52.381 0.00 0.00 0.00 3.86
2926 3058 6.986904 AAGCTAGCTGGTTTTATCAAGTAC 57.013 37.500 20.16 0.00 31.57 2.73
3015 3147 3.133003 GCTGCAGGTACTCTCCTTATTCA 59.867 47.826 17.12 0.00 34.60 2.57
3033 3165 2.381911 TCACCAGACTACGGTTATCCC 58.618 52.381 0.00 0.00 33.25 3.85
3046 3178 3.195661 GGTTATCCCGCAGTAAGTTCAG 58.804 50.000 0.00 0.00 0.00 3.02
3057 3189 5.622378 GCAGTAAGTTCAGTCTTTGCATAC 58.378 41.667 0.00 0.00 33.79 2.39
3170 3491 9.935241 TGGCTTTATTATTTAGTTTGCATTTCA 57.065 25.926 0.00 0.00 0.00 2.69
3200 3521 8.605325 ACCAGTATATGTAACTGTTTCCTACT 57.395 34.615 0.00 0.00 42.30 2.57
3201 3522 8.693625 ACCAGTATATGTAACTGTTTCCTACTC 58.306 37.037 0.00 0.00 42.30 2.59
3202 3523 7.861372 CCAGTATATGTAACTGTTTCCTACTCG 59.139 40.741 0.00 0.00 42.30 4.18
3204 3525 9.618890 AGTATATGTAACTGTTTCCTACTCGTA 57.381 33.333 0.00 0.00 0.00 3.43
3205 3526 9.875675 GTATATGTAACTGTTTCCTACTCGTAG 57.124 37.037 0.00 0.00 0.00 3.51
3207 3528 6.882610 TGTAACTGTTTCCTACTCGTAGAA 57.117 37.500 0.00 0.00 35.21 2.10
3208 3529 7.458409 TGTAACTGTTTCCTACTCGTAGAAT 57.542 36.000 0.00 0.00 35.21 2.40
3209 3530 7.310664 TGTAACTGTTTCCTACTCGTAGAATG 58.689 38.462 0.00 0.00 35.21 2.67
3210 3531 4.745649 ACTGTTTCCTACTCGTAGAATGC 58.254 43.478 5.68 0.00 35.21 3.56
3211 3532 4.219944 ACTGTTTCCTACTCGTAGAATGCA 59.780 41.667 5.68 0.00 35.21 3.96
3212 3533 5.105310 ACTGTTTCCTACTCGTAGAATGCAT 60.105 40.000 5.68 0.00 35.21 3.96
3213 3534 5.730550 TGTTTCCTACTCGTAGAATGCATT 58.269 37.500 12.83 12.83 35.21 3.56
3214 3535 5.810587 TGTTTCCTACTCGTAGAATGCATTC 59.189 40.000 28.44 28.44 35.21 2.67
3215 3536 5.592104 TTCCTACTCGTAGAATGCATTCA 57.408 39.130 34.59 20.80 39.23 2.57
3218 3539 5.301805 TCCTACTCGTAGAATGCATTCATCA 59.698 40.000 34.59 19.81 39.23 3.07
3233 3554 1.954382 TCATCATACTCCCTCCGTTCG 59.046 52.381 0.00 0.00 0.00 3.95
3234 3555 1.000163 CATCATACTCCCTCCGTTCGG 60.000 57.143 4.74 4.74 0.00 4.30
3240 3561 1.479730 ACTCCCTCCGTTCGGAAATAC 59.520 52.381 14.79 0.00 33.41 1.89
3243 3564 3.364549 TCCCTCCGTTCGGAAATACTTA 58.635 45.455 14.79 0.00 33.41 2.24
3246 3567 4.202182 CCCTCCGTTCGGAAATACTTATCA 60.202 45.833 14.79 0.00 33.41 2.15
3249 3570 6.073765 CCTCCGTTCGGAAATACTTATCATTG 60.074 42.308 14.79 0.00 33.41 2.82
3250 3571 6.575267 TCCGTTCGGAAATACTTATCATTGA 58.425 36.000 11.66 0.00 0.00 2.57
3252 3573 7.549842 TCCGTTCGGAAATACTTATCATTGAAA 59.450 33.333 11.66 0.00 0.00 2.69
3253 3574 8.342634 CCGTTCGGAAATACTTATCATTGAAAT 58.657 33.333 5.19 0.00 0.00 2.17
3255 3576 9.450807 GTTCGGAAATACTTATCATTGAAATGG 57.549 33.333 3.31 0.00 37.03 3.16
3256 3577 8.972458 TCGGAAATACTTATCATTGAAATGGA 57.028 30.769 3.31 0.00 37.03 3.41
3304 3683 9.112725 TCTACATACATCCATTTTGATGACAAG 57.887 33.333 7.93 0.00 43.94 3.16
3307 3686 9.241919 ACATACATCCATTTTGATGACAAGTAA 57.758 29.630 7.93 0.00 43.94 2.24
3311 3690 8.253113 ACATCCATTTTGATGACAAGTAATTCC 58.747 33.333 7.93 0.00 43.94 3.01
3312 3691 6.851609 TCCATTTTGATGACAAGTAATTCCG 58.148 36.000 0.00 0.00 37.32 4.30
3782 4180 5.163478 TGTCATATCCACAGTCATGTCTCAG 60.163 44.000 0.00 0.00 37.65 3.35
3899 4304 4.209452 TCGTTTTGTTCTGTTGCTGATC 57.791 40.909 0.00 0.00 0.00 2.92
3932 4350 7.013655 TCTCTTTCTTCCTTTGGTGAAAATGAG 59.986 37.037 0.00 0.00 31.08 2.90
4082 4511 7.968405 AGTACTTCTTAGCACAAACAAACAAAG 59.032 33.333 0.00 0.00 0.00 2.77
4131 4560 1.511613 TCTTATGCCTAGCTGCCCTT 58.488 50.000 0.00 0.00 0.00 3.95
4135 4564 1.438469 ATGCCTAGCTGCCCTTCATA 58.562 50.000 0.00 0.00 0.00 2.15
4152 4581 8.129211 GCCCTTCATATTGTTTGACAGTAATAC 58.871 37.037 0.00 0.00 0.00 1.89
4206 4635 3.573967 GCCATTCCCTTTCTTCAAACAGA 59.426 43.478 0.00 0.00 0.00 3.41
4323 4752 6.516718 CAGTGCTAAAGGTACATATAGTGCT 58.483 40.000 0.00 0.00 32.88 4.40
4722 5193 1.620819 CTCTGTTCTACAGGCCAGTGT 59.379 52.381 11.70 6.98 45.94 3.55
4911 6522 7.699391 CAGAGCATGGTTTATGAACAACTATTG 59.301 37.037 0.00 0.00 39.21 1.90
4949 6560 9.799106 ATAAGATTCCTTGGTAATTATCACAGG 57.201 33.333 15.44 15.44 33.94 4.00
4950 6561 7.213178 AGATTCCTTGGTAATTATCACAGGT 57.787 36.000 18.54 7.68 0.00 4.00
4951 6562 7.283329 AGATTCCTTGGTAATTATCACAGGTC 58.717 38.462 18.54 13.22 0.00 3.85
4952 6563 6.381498 TTCCTTGGTAATTATCACAGGTCA 57.619 37.500 18.54 9.86 0.00 4.02
4953 6564 5.741011 TCCTTGGTAATTATCACAGGTCAC 58.259 41.667 18.54 0.00 0.00 3.67
4954 6565 5.249622 TCCTTGGTAATTATCACAGGTCACA 59.750 40.000 18.54 5.22 0.00 3.58
4955 6566 5.586243 CCTTGGTAATTATCACAGGTCACAG 59.414 44.000 14.20 2.34 0.00 3.66
4968 6579 1.209504 GGTCACAGCACTATTGGCCTA 59.790 52.381 3.32 0.00 0.00 3.93
4969 6580 2.280628 GTCACAGCACTATTGGCCTAC 58.719 52.381 3.32 0.00 0.00 3.18
5007 6619 6.323739 ACTGAGAATGCTTAAAGTTGGGAAAA 59.676 34.615 0.00 0.00 0.00 2.29
5021 6633 6.314917 AGTTGGGAAAATAGACCACAAATCT 58.685 36.000 0.00 0.00 33.20 2.40
5072 6684 4.403015 TGTTATGTGTCAAATGCGACAG 57.597 40.909 0.00 0.00 46.23 3.51
5118 6730 2.380064 ATCTGGTGAAACTTTGGGCA 57.620 45.000 0.00 0.00 36.74 5.36
5146 6758 6.154445 AGCAAGCAAATTGACAGAAATGTAG 58.846 36.000 0.00 0.00 41.83 2.74
5219 6833 7.744087 AACTGCATACAAACATAACTCAAGA 57.256 32.000 0.00 0.00 0.00 3.02
5393 7008 4.846940 GGAACCAGTCCCTTCTATCCATAT 59.153 45.833 0.00 0.00 41.10 1.78
5405 7020 6.015940 CCTTCTATCCATATTTCCAGTTTGGC 60.016 42.308 0.00 0.00 37.47 4.52
5423 7038 1.972198 CCAGTCCGGAAGCACTACA 59.028 57.895 5.23 0.00 36.56 2.74
5759 7393 4.589374 ACTACTCCCTCCGATCCAAAATAG 59.411 45.833 0.00 0.00 0.00 1.73
5760 7394 2.706190 ACTCCCTCCGATCCAAAATAGG 59.294 50.000 0.00 0.00 0.00 2.57
5797 7432 2.936498 CTGGGGTTAGTTCAATACTGCG 59.064 50.000 0.00 0.00 37.73 5.18
5879 7514 7.094631 TGCTCTAGCGAATTACTAAGAACAAA 58.905 34.615 0.00 0.00 45.83 2.83
5900 7535 9.435688 AACAAATTAGCTTTTGGTATGGATTTC 57.564 29.630 13.92 0.00 40.20 2.17
5901 7536 8.592809 ACAAATTAGCTTTTGGTATGGATTTCA 58.407 29.630 13.92 0.00 40.20 2.69
6231 7958 1.613437 CCAAAGGGTGTCACCAATGTC 59.387 52.381 23.48 5.74 41.02 3.06
6371 8100 0.533308 ACTAACAGTCGGGCGCAAAA 60.533 50.000 10.83 0.00 0.00 2.44
6446 8175 1.000283 CTAGCAAGAGATGGCTACGGG 60.000 57.143 0.00 0.00 41.41 5.28
6451 8180 3.343617 CAAGAGATGGCTACGGGAAAAA 58.656 45.455 0.00 0.00 0.00 1.94
6454 8183 0.377203 GATGGCTACGGGAAAAAGCG 59.623 55.000 0.00 0.00 37.11 4.68
6478 8207 3.624777 CCTAACAATCAAGCATGACCCT 58.375 45.455 0.00 0.00 38.69 4.34
6611 8340 1.003580 CTTAGGCCAAGTGCTTCTGGA 59.996 52.381 5.01 0.00 40.92 3.86
7375 9105 7.884257 TCTGTTGCACATTTCTTATTCAATGA 58.116 30.769 0.00 0.00 34.89 2.57
7436 9265 9.467258 AATGAAAGAAGTAATGTGAAATGTGTG 57.533 29.630 0.00 0.00 0.00 3.82
7437 9266 7.995289 TGAAAGAAGTAATGTGAAATGTGTGT 58.005 30.769 0.00 0.00 0.00 3.72
7509 9340 4.097892 ACGGTTGAGAGTTTCAAAGCAAAT 59.902 37.500 0.00 0.00 46.85 2.32
7579 9411 4.453751 GGTGGGCTAATCGTTTGGTAATA 58.546 43.478 0.00 0.00 0.00 0.98
7621 9453 1.222936 CAATCCAGGCGCCTTCTCT 59.777 57.895 30.60 9.40 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.203530 CCTAATCCACTACACACATAGCATTG 59.796 42.308 0.00 0.00 0.00 2.82
1 2 6.099701 TCCTAATCCACTACACACATAGCATT 59.900 38.462 0.00 0.00 0.00 3.56
2 3 5.602561 TCCTAATCCACTACACACATAGCAT 59.397 40.000 0.00 0.00 0.00 3.79
3 4 4.959839 TCCTAATCCACTACACACATAGCA 59.040 41.667 0.00 0.00 0.00 3.49
4 5 5.531122 TCCTAATCCACTACACACATAGC 57.469 43.478 0.00 0.00 0.00 2.97
5 6 9.645059 CAATATCCTAATCCACTACACACATAG 57.355 37.037 0.00 0.00 0.00 2.23
6 7 8.593679 CCAATATCCTAATCCACTACACACATA 58.406 37.037 0.00 0.00 0.00 2.29
7 8 7.453393 CCAATATCCTAATCCACTACACACAT 58.547 38.462 0.00 0.00 0.00 3.21
75 76 3.064207 TGCTTTGCTTCCGTGTTACTAG 58.936 45.455 0.00 0.00 0.00 2.57
76 77 3.114668 TGCTTTGCTTCCGTGTTACTA 57.885 42.857 0.00 0.00 0.00 1.82
77 78 1.961793 TGCTTTGCTTCCGTGTTACT 58.038 45.000 0.00 0.00 0.00 2.24
138 145 7.067496 AGACACTTATTTTGAGACAGAGGAA 57.933 36.000 0.00 0.00 0.00 3.36
139 146 6.672266 AGACACTTATTTTGAGACAGAGGA 57.328 37.500 0.00 0.00 0.00 3.71
140 147 8.833231 TTAAGACACTTATTTTGAGACAGAGG 57.167 34.615 0.00 0.00 0.00 3.69
142 149 9.832445 AGTTTAAGACACTTATTTTGAGACAGA 57.168 29.630 0.00 0.00 0.00 3.41
149 156 9.944663 TGCACTAAGTTTAAGACACTTATTTTG 57.055 29.630 0.00 0.75 36.39 2.44
155 162 9.869757 AAAAATTGCACTAAGTTTAAGACACTT 57.130 25.926 0.00 0.00 35.70 3.16
156 163 9.301153 CAAAAATTGCACTAAGTTTAAGACACT 57.699 29.630 0.00 0.00 35.70 3.55
157 164 9.083080 ACAAAAATTGCACTAAGTTTAAGACAC 57.917 29.630 0.00 0.00 35.70 3.67
196 203 9.899226 GCTTCAAAATAAGTGTCTCAACTTTAT 57.101 29.630 0.00 0.00 40.77 1.40
197 204 8.067784 CGCTTCAAAATAAGTGTCTCAACTTTA 58.932 33.333 0.00 0.00 40.77 1.85
198 205 6.912591 CGCTTCAAAATAAGTGTCTCAACTTT 59.087 34.615 0.00 0.00 40.77 2.66
199 206 6.430451 CGCTTCAAAATAAGTGTCTCAACTT 58.570 36.000 0.00 0.00 42.89 2.66
200 207 5.049405 CCGCTTCAAAATAAGTGTCTCAACT 60.049 40.000 0.00 0.00 35.62 3.16
201 208 5.049680 TCCGCTTCAAAATAAGTGTCTCAAC 60.050 40.000 0.00 0.00 35.62 3.18
202 209 5.060506 TCCGCTTCAAAATAAGTGTCTCAA 58.939 37.500 0.00 0.00 35.62 3.02
203 210 4.637276 TCCGCTTCAAAATAAGTGTCTCA 58.363 39.130 0.00 0.00 35.62 3.27
204 211 4.093556 CCTCCGCTTCAAAATAAGTGTCTC 59.906 45.833 0.00 0.00 35.62 3.36
205 212 4.003648 CCTCCGCTTCAAAATAAGTGTCT 58.996 43.478 0.00 0.00 35.62 3.41
206 213 3.127030 CCCTCCGCTTCAAAATAAGTGTC 59.873 47.826 0.00 0.00 35.62 3.67
207 214 3.081804 CCCTCCGCTTCAAAATAAGTGT 58.918 45.455 0.00 0.00 35.62 3.55
208 215 3.343617 TCCCTCCGCTTCAAAATAAGTG 58.656 45.455 0.00 0.00 36.85 3.16
209 216 3.009143 ACTCCCTCCGCTTCAAAATAAGT 59.991 43.478 0.00 0.00 0.00 2.24
210 217 3.610911 ACTCCCTCCGCTTCAAAATAAG 58.389 45.455 0.00 0.00 0.00 1.73
211 218 3.713826 ACTCCCTCCGCTTCAAAATAA 57.286 42.857 0.00 0.00 0.00 1.40
212 219 3.429822 CGTACTCCCTCCGCTTCAAAATA 60.430 47.826 0.00 0.00 0.00 1.40
213 220 2.677037 CGTACTCCCTCCGCTTCAAAAT 60.677 50.000 0.00 0.00 0.00 1.82
214 221 1.337447 CGTACTCCCTCCGCTTCAAAA 60.337 52.381 0.00 0.00 0.00 2.44
215 222 0.245539 CGTACTCCCTCCGCTTCAAA 59.754 55.000 0.00 0.00 0.00 2.69
216 223 0.896940 ACGTACTCCCTCCGCTTCAA 60.897 55.000 0.00 0.00 0.00 2.69
217 224 1.303888 ACGTACTCCCTCCGCTTCA 60.304 57.895 0.00 0.00 0.00 3.02
218 225 1.139095 CACGTACTCCCTCCGCTTC 59.861 63.158 0.00 0.00 0.00 3.86
219 226 3.003113 GCACGTACTCCCTCCGCTT 62.003 63.158 0.00 0.00 0.00 4.68
220 227 3.450115 GCACGTACTCCCTCCGCT 61.450 66.667 0.00 0.00 0.00 5.52
221 228 1.731433 TATGCACGTACTCCCTCCGC 61.731 60.000 0.00 0.00 0.00 5.54
222 229 0.311165 CTATGCACGTACTCCCTCCG 59.689 60.000 0.00 0.00 0.00 4.63
223 230 0.032267 GCTATGCACGTACTCCCTCC 59.968 60.000 0.00 0.00 0.00 4.30
224 231 0.744874 TGCTATGCACGTACTCCCTC 59.255 55.000 0.00 0.00 31.71 4.30
225 232 1.414158 ATGCTATGCACGTACTCCCT 58.586 50.000 0.00 0.00 43.04 4.20
226 233 2.927014 GCTATGCTATGCACGTACTCCC 60.927 54.545 0.00 0.00 43.04 4.30
227 234 2.288213 TGCTATGCTATGCACGTACTCC 60.288 50.000 0.00 0.00 43.04 3.85
228 235 3.013276 TGCTATGCTATGCACGTACTC 57.987 47.619 0.00 0.00 43.04 2.59
229 236 3.667497 ATGCTATGCTATGCACGTACT 57.333 42.857 0.00 0.00 43.04 2.73
230 237 3.304559 GCTATGCTATGCTATGCACGTAC 59.695 47.826 0.00 0.00 43.04 3.67
231 238 3.056891 TGCTATGCTATGCTATGCACGTA 60.057 43.478 0.00 0.00 43.04 3.57
232 239 2.289010 TGCTATGCTATGCTATGCACGT 60.289 45.455 0.00 0.00 43.04 4.49
233 240 2.340337 TGCTATGCTATGCTATGCACG 58.660 47.619 0.00 0.00 43.04 5.34
256 263 0.605319 CTGCGGCTCCAGGTTTGTTA 60.605 55.000 0.00 0.00 0.00 2.41
260 267 2.032681 GTCTGCGGCTCCAGGTTT 59.967 61.111 0.00 0.00 33.64 3.27
283 290 0.814010 AGGTTCACCACTGCGACAAC 60.814 55.000 0.00 0.00 38.89 3.32
305 312 2.163412 TGACACAACACAAGAGGTTTGC 59.837 45.455 0.00 0.00 0.00 3.68
346 354 4.360405 GGTGGGGTTGGCCGATGT 62.360 66.667 0.00 0.00 34.97 3.06
370 378 2.035442 GTCCAACAGAAGAGGGCGC 61.035 63.158 0.00 0.00 0.00 6.53
427 435 4.077184 TGATCGGCCGGTGACACC 62.077 66.667 27.83 15.13 34.05 4.16
467 475 1.588932 CGTGCGTCGTCATGGCTAT 60.589 57.895 0.00 0.00 34.52 2.97
813 837 3.693807 CTGGCTATAATGCACCATCCAT 58.306 45.455 0.00 0.00 34.04 3.41
814 838 2.815215 GCTGGCTATAATGCACCATCCA 60.815 50.000 0.00 0.00 34.04 3.41
815 839 1.815003 GCTGGCTATAATGCACCATCC 59.185 52.381 0.00 0.00 34.04 3.51
816 840 1.466167 CGCTGGCTATAATGCACCATC 59.534 52.381 0.00 0.00 34.04 3.51
907 938 5.180810 AGGAAAAGCTAAAGGTTAGAGGG 57.819 43.478 0.00 0.00 35.00 4.30
931 962 1.111277 GAGAGGTGGAGAGAAGGAGC 58.889 60.000 0.00 0.00 0.00 4.70
936 967 0.699399 ACGGAGAGAGGTGGAGAGAA 59.301 55.000 0.00 0.00 0.00 2.87
939 970 0.323542 GGAACGGAGAGAGGTGGAGA 60.324 60.000 0.00 0.00 0.00 3.71
944 975 2.041350 TGTTAGAGGAACGGAGAGAGGT 59.959 50.000 0.00 0.00 41.35 3.85
945 976 2.724454 TGTTAGAGGAACGGAGAGAGG 58.276 52.381 0.00 0.00 41.35 3.69
946 977 4.011023 TCTTGTTAGAGGAACGGAGAGAG 58.989 47.826 0.00 0.00 41.35 3.20
947 978 4.011023 CTCTTGTTAGAGGAACGGAGAGA 58.989 47.826 11.96 1.17 45.15 3.10
948 979 3.428316 GCTCTTGTTAGAGGAACGGAGAG 60.428 52.174 12.59 12.59 46.64 3.20
949 980 2.492484 GCTCTTGTTAGAGGAACGGAGA 59.508 50.000 11.68 4.67 46.64 3.71
1022 1054 3.307445 CTCAGCACCAGAGGGGAG 58.693 66.667 0.00 0.00 41.15 4.30
1231 1263 0.251077 CATAGCCCTTGGATCTGCCC 60.251 60.000 0.00 0.00 34.97 5.36
1249 1281 7.246171 AGTAGAGAAGAAGCTTACAAATCCA 57.754 36.000 0.00 0.00 0.00 3.41
1269 1301 6.868864 AGAGTGTGTGTGCATAGTAAAAGTAG 59.131 38.462 0.00 0.00 0.00 2.57
1273 1305 5.853936 AGAGAGTGTGTGTGCATAGTAAAA 58.146 37.500 0.00 0.00 0.00 1.52
1275 1307 5.230182 CAAGAGAGTGTGTGTGCATAGTAA 58.770 41.667 0.00 0.00 0.00 2.24
1292 1325 2.039879 GGTAGGGAAAACCAGCAAGAGA 59.960 50.000 0.00 0.00 43.89 3.10
1311 1389 2.301346 CTGCACTGAAACTGAAAGGGT 58.699 47.619 0.00 0.00 39.30 4.34
1376 1454 2.914695 ATGTGCAGTGTGGCAAAAAT 57.085 40.000 0.00 0.00 46.93 1.82
1378 1456 2.305928 AGTATGTGCAGTGTGGCAAAA 58.694 42.857 0.00 0.00 46.93 2.44
1384 1462 5.173774 ACAGAAAAAGTATGTGCAGTGTG 57.826 39.130 0.00 0.00 0.00 3.82
1414 1492 0.304705 CGTCCGTTCATATTGCAGCC 59.695 55.000 0.00 0.00 0.00 4.85
1431 1509 0.465460 ACCACCAATTCACAGTGCGT 60.465 50.000 0.00 0.00 0.00 5.24
1432 1510 0.667993 AACCACCAATTCACAGTGCG 59.332 50.000 0.00 0.00 0.00 5.34
1478 1559 4.147449 CAGGACCTCATCGCCGCA 62.147 66.667 0.00 0.00 0.00 5.69
1620 1704 9.750125 TCTAATGTGACTTTGTATATGTAGCTG 57.250 33.333 0.00 0.00 0.00 4.24
1638 1725 9.906660 CCTAGCTATTAACTCTTCTCTAATGTG 57.093 37.037 0.00 0.00 0.00 3.21
1797 1886 3.456280 GCTAGAGCTCACAGAGAAATGG 58.544 50.000 17.77 0.00 38.21 3.16
1975 2064 1.337118 TGGGAAAATCAGGTTGCACC 58.663 50.000 0.00 0.00 38.99 5.01
2031 2120 6.325919 TGTCAAGGCCACTATTTAGTTTTG 57.674 37.500 5.01 0.00 33.46 2.44
2165 2254 5.571357 GGTTTTCTAATTACCGTTGCACATG 59.429 40.000 0.00 0.00 0.00 3.21
2166 2255 5.336134 GGGTTTTCTAATTACCGTTGCACAT 60.336 40.000 0.00 0.00 32.61 3.21
2167 2256 4.023021 GGGTTTTCTAATTACCGTTGCACA 60.023 41.667 0.00 0.00 32.61 4.57
2168 2257 4.216902 AGGGTTTTCTAATTACCGTTGCAC 59.783 41.667 0.00 0.00 32.61 4.57
2212 2301 2.540265 ATCTGGCATTCATCTCGGTC 57.460 50.000 0.00 0.00 0.00 4.79
2425 2534 8.063630 GTGGTAAAAATCATCAGCAAAACAAAG 58.936 33.333 0.00 0.00 0.00 2.77
2446 2555 2.762459 CTAGCGCCCCCTGTGGTA 60.762 66.667 2.29 0.00 36.42 3.25
2449 2558 3.854669 CTCCTAGCGCCCCCTGTG 61.855 72.222 2.29 0.00 0.00 3.66
2635 2751 3.195825 AGACACTTTCCATAGGTTCCTCG 59.804 47.826 0.00 0.00 0.00 4.63
2723 2848 0.396435 ACACTCCAGTCGCCATTGAA 59.604 50.000 0.00 0.00 0.00 2.69
2738 2863 5.221224 TGCATGCAAGCTAAAAAGTTACACT 60.221 36.000 20.30 0.00 34.99 3.55
2840 2965 2.556189 GCAAGAGTGTGAGACTGAGAGA 59.444 50.000 0.00 0.00 33.83 3.10
2867 2994 4.081420 GTGTGAGAGAGAGAGAGAGAGAGT 60.081 50.000 0.00 0.00 0.00 3.24
3033 3165 2.543848 TGCAAAGACTGAACTTACTGCG 59.456 45.455 0.00 0.00 36.80 5.18
3099 3413 4.641396 TCGTCTTCACAAATCAACCTCAT 58.359 39.130 0.00 0.00 0.00 2.90
3185 3506 6.253083 GCATTCTACGAGTAGGAAACAGTTAC 59.747 42.308 10.04 0.00 34.06 2.50
3195 3516 5.532557 TGATGAATGCATTCTACGAGTAGG 58.467 41.667 33.23 0.00 37.67 3.18
3197 3518 7.886338 AGTATGATGAATGCATTCTACGAGTA 58.114 34.615 33.23 16.47 37.67 2.59
3198 3519 6.753180 AGTATGATGAATGCATTCTACGAGT 58.247 36.000 33.23 19.64 37.67 4.18
3199 3520 6.309980 GGAGTATGATGAATGCATTCTACGAG 59.690 42.308 33.23 0.00 37.67 4.18
3200 3521 6.159293 GGAGTATGATGAATGCATTCTACGA 58.841 40.000 33.23 18.13 37.67 3.43
3201 3522 5.349817 GGGAGTATGATGAATGCATTCTACG 59.650 44.000 33.23 0.00 37.67 3.51
3202 3523 6.471146 AGGGAGTATGATGAATGCATTCTAC 58.529 40.000 33.23 26.41 37.67 2.59
3204 3525 5.514484 GGAGGGAGTATGATGAATGCATTCT 60.514 44.000 33.23 21.63 37.67 2.40
3205 3526 4.699257 GGAGGGAGTATGATGAATGCATTC 59.301 45.833 28.83 28.83 34.11 2.67
3207 3528 3.307269 CGGAGGGAGTATGATGAATGCAT 60.307 47.826 0.00 0.00 37.47 3.96
3208 3529 2.037641 CGGAGGGAGTATGATGAATGCA 59.962 50.000 0.00 0.00 0.00 3.96
3209 3530 2.037772 ACGGAGGGAGTATGATGAATGC 59.962 50.000 0.00 0.00 0.00 3.56
3210 3531 4.310769 GAACGGAGGGAGTATGATGAATG 58.689 47.826 0.00 0.00 0.00 2.67
3211 3532 3.005897 CGAACGGAGGGAGTATGATGAAT 59.994 47.826 0.00 0.00 0.00 2.57
3212 3533 2.361119 CGAACGGAGGGAGTATGATGAA 59.639 50.000 0.00 0.00 0.00 2.57
3213 3534 1.954382 CGAACGGAGGGAGTATGATGA 59.046 52.381 0.00 0.00 0.00 2.92
3214 3535 1.000163 CCGAACGGAGGGAGTATGATG 60.000 57.143 7.53 0.00 37.50 3.07
3215 3536 1.133575 TCCGAACGGAGGGAGTATGAT 60.134 52.381 12.04 0.00 39.76 2.45
3218 3539 1.856629 TTTCCGAACGGAGGGAGTAT 58.143 50.000 15.34 0.00 46.06 2.12
3276 3597 8.892723 TGTCATCAAAATGGATGTATGTAGAAC 58.107 33.333 0.00 0.00 44.00 3.01
3277 3598 9.460019 TTGTCATCAAAATGGATGTATGTAGAA 57.540 29.630 0.00 0.00 44.00 2.10
3278 3599 9.112725 CTTGTCATCAAAATGGATGTATGTAGA 57.887 33.333 0.00 0.00 44.00 2.59
3279 3600 8.896744 ACTTGTCATCAAAATGGATGTATGTAG 58.103 33.333 0.00 0.00 44.00 2.74
3280 3601 8.806429 ACTTGTCATCAAAATGGATGTATGTA 57.194 30.769 0.00 0.00 44.00 2.29
3281 3602 7.707624 ACTTGTCATCAAAATGGATGTATGT 57.292 32.000 0.00 0.00 44.00 2.29
3286 3607 7.433131 CGGAATTACTTGTCATCAAAATGGATG 59.567 37.037 0.00 0.00 44.78 3.51
3287 3608 7.339212 TCGGAATTACTTGTCATCAAAATGGAT 59.661 33.333 0.00 0.00 33.42 3.41
3288 3609 6.657117 TCGGAATTACTTGTCATCAAAATGGA 59.343 34.615 0.00 0.00 33.42 3.41
3289 3610 6.851609 TCGGAATTACTTGTCATCAAAATGG 58.148 36.000 0.00 0.00 33.42 3.16
3290 3611 7.007367 CGTTCGGAATTACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
3291 3612 7.021196 CGTTCGGAATTACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
3292 3613 6.367421 CGTTCGGAATTACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
3293 3614 5.106869 CCGTTCGGAATTACTTGTCATCAAA 60.107 40.000 5.19 0.00 32.87 2.69
3295 3616 3.930229 CCGTTCGGAATTACTTGTCATCA 59.070 43.478 5.19 0.00 0.00 3.07
3296 3617 4.178540 TCCGTTCGGAATTACTTGTCATC 58.821 43.478 11.66 0.00 0.00 2.92
3298 3619 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
3304 3683 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3307 3686 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
3310 3689 0.822164 AATGTACTCCCTCCGTTCGG 59.178 55.000 4.74 4.74 0.00 4.30
3311 3690 2.667473 AAATGTACTCCCTCCGTTCG 57.333 50.000 0.00 0.00 0.00 3.95
3312 3691 5.667466 TGATAAAATGTACTCCCTCCGTTC 58.333 41.667 0.00 0.00 0.00 3.95
3367 3762 5.887598 TGTAGTGCTATTTTTCATGCATCCT 59.112 36.000 0.00 0.00 37.76 3.24
3450 3845 5.986741 GCACATCATTGCATTTTATGATCCA 59.013 36.000 8.35 0.00 42.49 3.41
3604 3999 5.723492 AACAAAGCAAGCATTCTGTTTTC 57.277 34.783 0.00 0.00 0.00 2.29
3648 4044 6.884295 TGCTGGTGATAGCTTACTGTTAATTT 59.116 34.615 0.00 0.00 44.01 1.82
3806 4204 5.124457 CAGTAACATCCAAATCACAAGGAGG 59.876 44.000 0.00 0.00 39.03 4.30
3899 4304 5.772169 ACCAAAGGAAGAAAGAGAAATCAGG 59.228 40.000 0.00 0.00 0.00 3.86
3932 4350 6.768381 CCTGGGTCAAAGGAAATCTATACTTC 59.232 42.308 0.00 0.00 36.91 3.01
4082 4511 4.697352 TCTTTTAAGAGCAGTTGCCTCATC 59.303 41.667 0.00 0.00 43.38 2.92
4107 4536 2.614987 GGCAGCTAGGCATAAGATGGAG 60.615 54.545 0.00 0.00 43.51 3.86
4131 4560 8.103935 TGGGTGTATTACTGTCAAACAATATGA 58.896 33.333 0.00 0.00 0.00 2.15
4135 4564 6.539173 TCTGGGTGTATTACTGTCAAACAAT 58.461 36.000 0.00 0.00 0.00 2.71
4152 4581 2.771943 TGGTTAAGAGGCTATCTGGGTG 59.228 50.000 0.00 0.00 38.67 4.61
4230 4659 7.016153 ACAACCATCTATCCTTGTGTAGAAA 57.984 36.000 0.00 0.00 31.29 2.52
4323 4752 4.715534 TGGAAGTTGATAGGACCACAAA 57.284 40.909 0.00 0.00 0.00 2.83
4770 6363 6.440647 TCTTTGTCTACCTCACACCTATTGAT 59.559 38.462 0.00 0.00 0.00 2.57
4949 6560 2.280628 GTAGGCCAATAGTGCTGTGAC 58.719 52.381 5.01 0.00 0.00 3.67
4950 6561 1.209504 GGTAGGCCAATAGTGCTGTGA 59.790 52.381 5.01 0.00 34.09 3.58
4951 6562 1.210478 AGGTAGGCCAATAGTGCTGTG 59.790 52.381 5.01 0.00 37.19 3.66
4952 6563 1.584724 AGGTAGGCCAATAGTGCTGT 58.415 50.000 5.01 0.00 37.19 4.40
4953 6564 2.965831 TCTAGGTAGGCCAATAGTGCTG 59.034 50.000 5.01 0.00 37.19 4.41
4954 6565 2.966516 GTCTAGGTAGGCCAATAGTGCT 59.033 50.000 5.01 0.00 37.19 4.40
4955 6566 2.698797 TGTCTAGGTAGGCCAATAGTGC 59.301 50.000 5.01 0.69 37.19 4.40
4968 6579 7.237982 AGCATTCTCAGTATATCTGTCTAGGT 58.762 38.462 0.00 0.00 43.97 3.08
4969 6580 7.701539 AGCATTCTCAGTATATCTGTCTAGG 57.298 40.000 0.00 0.00 43.97 3.02
5050 6662 4.455533 ACTGTCGCATTTGACACATAACAT 59.544 37.500 0.00 0.00 43.62 2.71
5072 6684 4.976116 GCTTTGTGTTGGTGTTTCTGATAC 59.024 41.667 0.00 0.00 0.00 2.24
5118 6730 5.772825 TTCTGTCAATTTGCTTGCTTACT 57.227 34.783 0.00 0.00 34.66 2.24
5146 6758 9.956720 AGATGTTAATTTAAGTATTCATGCTGC 57.043 29.630 0.00 0.00 0.00 5.25
5393 7008 0.821711 CGGACTGGCCAAACTGGAAA 60.822 55.000 7.01 0.00 40.96 3.13
5405 7020 0.389948 GTGTAGTGCTTCCGGACTGG 60.390 60.000 1.83 0.00 42.22 4.00
5423 7038 1.423541 TGTCCAGTTGCATAGTTGGGT 59.576 47.619 0.00 0.00 0.00 4.51
5531 7146 1.002134 AAGTGACAATGGCCCTCCG 60.002 57.895 0.00 0.00 34.14 4.63
5609 7224 8.232913 TGAAAGCCAAACATTTAGAAAGTAGT 57.767 30.769 0.00 0.00 0.00 2.73
5610 7225 9.696917 AATGAAAGCCAAACATTTAGAAAGTAG 57.303 29.630 0.00 0.00 31.46 2.57
5643 7258 0.178903 TAGCTAGCCATGGTAGGGGG 60.179 60.000 14.67 0.00 34.62 5.40
5791 7426 7.149307 TCCGATTCATAATAAATGTCGCAGTA 58.851 34.615 0.00 0.00 0.00 2.74
5812 7447 5.074804 TGCAATATAAGCTACTACCTCCGA 58.925 41.667 0.00 0.00 0.00 4.55
5851 7486 6.307031 TCTTAGTAATTCGCTAGAGCAGAG 57.693 41.667 1.89 0.00 42.21 3.35
5879 7514 6.380846 TGCTGAAATCCATACCAAAAGCTAAT 59.619 34.615 0.00 0.00 0.00 1.73
5900 7535 8.827177 ATCTTTGCAAATGGATTATATTGCTG 57.173 30.769 13.23 0.00 46.27 4.41
6291 8020 1.606531 GGCTCAAGCTGGTCTCCAT 59.393 57.895 1.46 0.00 41.70 3.41
6371 8100 0.470766 TGGACTGGTTAAACGGCTGT 59.529 50.000 0.00 0.00 0.00 4.40
6446 8175 4.759516 TGATTGTTAGGGTCGCTTTTTC 57.240 40.909 0.00 0.00 0.00 2.29
6451 8180 1.003118 TGCTTGATTGTTAGGGTCGCT 59.997 47.619 0.00 0.00 0.00 4.93
6454 8183 3.378427 GGTCATGCTTGATTGTTAGGGTC 59.622 47.826 5.49 0.00 33.56 4.46
6478 8207 0.325296 ATCAGCACGAACCCTCCCTA 60.325 55.000 0.00 0.00 0.00 3.53
6490 8219 5.581126 TCCAATTTGGATTGTATCAGCAC 57.419 39.130 14.24 0.00 42.67 4.40
6611 8340 3.293337 TGCTAAATGCCTCATGCTTCAT 58.707 40.909 0.00 0.00 42.00 2.57
6652 8381 7.548196 TTTTATTTGCTCTAGATAACACCCG 57.452 36.000 0.00 0.00 0.00 5.28
7436 9265 6.635030 AAGTGAAGGGAGAATGTTGTTAAC 57.365 37.500 0.00 0.00 0.00 2.01
7437 9266 8.934023 ATAAAGTGAAGGGAGAATGTTGTTAA 57.066 30.769 0.00 0.00 0.00 2.01
7509 9340 4.655963 ACTACTACTGGACAGGTACGAAA 58.344 43.478 4.14 0.00 0.00 3.46
7558 9389 6.439675 TTTATTACCAAACGATTAGCCCAC 57.560 37.500 0.00 0.00 0.00 4.61
7561 9392 6.017687 ACCGATTTATTACCAAACGATTAGCC 60.018 38.462 0.00 0.00 0.00 3.93
7579 9411 5.761165 TTTTCTTCGAAAGGAACCGATTT 57.239 34.783 0.00 0.00 34.58 2.17


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

AutoCloner maintained by Alex Coulton.