Multiple sequence alignment - TraesCS3B01G368700

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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 TraesCS3B01G368700 chr3B 100.000 4937 0 0 1 4937 581083189 581078253 0.000000e+00 9118.0
1 TraesCS3B01G368700 chr3A 90.528 3505 190 64 824 4253 584298569 584295132 0.000000e+00 4503.0
2 TraesCS3B01G368700 chr3A 85.475 957 54 33 3779 4668 584292807 584291869 0.000000e+00 918.0
3 TraesCS3B01G368700 chr3A 84.952 525 35 18 4386 4882 584294941 584294433 4.440000e-135 492.0
4 TraesCS3B01G368700 chr3A 79.198 524 53 20 294 788 584299047 584298551 3.710000e-81 313.0
5 TraesCS3B01G368700 chr3A 86.667 225 15 5 4727 4936 584291573 584291349 8.260000e-58 235.0
6 TraesCS3B01G368700 chr3A 92.593 135 10 0 4253 4387 584295103 584294969 1.400000e-45 195.0
7 TraesCS3B01G368700 chr3D 90.765 2144 117 27 2142 4253 443270687 443268593 0.000000e+00 2787.0
8 TraesCS3B01G368700 chr3D 92.608 1177 40 14 975 2113 443271853 443270686 0.000000e+00 1648.0
9 TraesCS3B01G368700 chr3D 88.608 474 22 13 4253 4694 443268565 443268092 9.340000e-152 547.0
10 TraesCS3B01G368700 chr3D 87.433 374 30 6 427 797 443272538 443272179 9.890000e-112 414.0
11 TraesCS3B01G368700 chr3D 79.521 376 35 29 63 429 443272960 443272618 3.840000e-56 230.0
12 TraesCS3B01G368700 chr3D 90.000 160 10 3 4764 4919 443268043 443267886 8.380000e-48 202.0
13 TraesCS3B01G368700 chr3D 87.719 57 6 1 1 56 443273070 443273014 1.150000e-06 65.8
14 TraesCS3B01G368700 chr1D 89.000 100 7 2 4022 4117 465522982 465522883 2.410000e-23 121.0
15 TraesCS3B01G368700 chr1A 88.660 97 10 1 4022 4117 41366842 41366746 3.120000e-22 117.0
16 TraesCS3B01G368700 chr1A 84.762 105 15 1 4014 4117 41366737 41366841 2.430000e-18 104.0
17 TraesCS3B01G368700 chr7B 90.000 90 7 1 4022 4111 64413009 64413096 1.120000e-21 115.0
18 TraesCS3B01G368700 chr6B 87.500 96 10 1 4022 4117 553058987 553059080 5.220000e-20 110.0
19 TraesCS3B01G368700 chr1B 88.889 90 8 1 4022 4111 26096836 26096923 5.220000e-20 110.0
20 TraesCS3B01G368700 chr4D 86.869 99 8 2 4022 4115 14609698 14609600 6.760000e-19 106.0


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 TraesCS3B01G368700 chr3B 581078253 581083189 4936 True 9118.000000 9118 100.000000 1 4937 1 chr3B.!!$R1 4936
1 TraesCS3B01G368700 chr3A 584291349 584299047 7698 True 1109.333333 4503 86.568833 294 4936 6 chr3A.!!$R1 4642
2 TraesCS3B01G368700 chr3D 443267886 443273070 5184 True 841.971429 2787 88.093429 1 4919 7 chr3D.!!$R1 4918

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
131 180 0.116143 AGGACTCTGGAGCTCAGGTT 59.884 55.0 17.19 2.16 43.53 3.50 F
1671 2074 0.034767 TCCTGCTTCCTGCTTGGATG 60.035 55.0 0.09 4.33 45.68 3.51 F
3189 3645 0.104671 TAGCGCTGCATGACATAGCA 59.895 50.0 22.90 10.44 37.29 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 2132 0.740149 TGCCATTGCCATTTAGAGCG 59.260 50.0 0.00 0.0 36.33 5.03 R
3395 3859 0.037790 GAGGGAGATCAGTATGCGGC 60.038 60.0 0.00 0.0 34.76 6.53 R
4383 4897 0.179062 GTGGATCAGCGGATGAGCTT 60.179 55.0 11.52 0.0 46.80 3.74 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
38 39 7.945664 AGTTTGGTACCTATCTTCGAGAGATAT 59.054 37.037 14.36 6.78 44.35 1.63
72 121 1.202533 TCCCTAAAGTAGCGCTCATGC 60.203 52.381 16.34 2.71 0.00 4.06
75 124 2.286294 CCTAAAGTAGCGCTCATGCTTG 59.714 50.000 16.34 4.01 44.46 4.01
83 132 1.594862 GCGCTCATGCTTGTACCTTAG 59.405 52.381 0.00 0.00 36.97 2.18
119 168 2.925170 AACAGGGCGCAGGACTCT 60.925 61.111 10.83 0.00 0.00 3.24
125 174 3.768922 GCGCAGGACTCTGGAGCT 61.769 66.667 0.30 0.00 41.19 4.09
127 176 2.346541 CGCAGGACTCTGGAGCTCA 61.347 63.158 17.19 0.61 41.19 4.26
128 177 1.516892 GCAGGACTCTGGAGCTCAG 59.483 63.158 17.19 11.13 44.68 3.35
130 179 0.614415 CAGGACTCTGGAGCTCAGGT 60.614 60.000 17.19 7.88 43.53 4.00
131 180 0.116143 AGGACTCTGGAGCTCAGGTT 59.884 55.000 17.19 2.16 43.53 3.50
149 209 3.089284 GGTTGGGAATAAGGTTCAGGTG 58.911 50.000 0.00 0.00 0.00 4.00
150 210 2.492088 GTTGGGAATAAGGTTCAGGTGC 59.508 50.000 0.00 0.00 0.00 5.01
151 211 1.992557 TGGGAATAAGGTTCAGGTGCT 59.007 47.619 0.00 0.00 0.00 4.40
154 214 3.536570 GGAATAAGGTTCAGGTGCTCTC 58.463 50.000 0.00 0.00 0.00 3.20
155 215 3.198853 GGAATAAGGTTCAGGTGCTCTCT 59.801 47.826 0.00 0.00 0.00 3.10
156 216 4.438148 GAATAAGGTTCAGGTGCTCTCTC 58.562 47.826 0.00 0.00 0.00 3.20
157 217 2.022718 AAGGTTCAGGTGCTCTCTCT 57.977 50.000 0.00 0.00 0.00 3.10
158 218 2.909504 AGGTTCAGGTGCTCTCTCTA 57.090 50.000 0.00 0.00 0.00 2.43
162 222 4.167113 AGGTTCAGGTGCTCTCTCTATCTA 59.833 45.833 0.00 0.00 0.00 1.98
166 226 6.943899 TCAGGTGCTCTCTCTATCTATCTA 57.056 41.667 0.00 0.00 0.00 1.98
167 227 7.509236 TCAGGTGCTCTCTCTATCTATCTAT 57.491 40.000 0.00 0.00 0.00 1.98
168 228 7.564793 TCAGGTGCTCTCTCTATCTATCTATC 58.435 42.308 0.00 0.00 0.00 2.08
169 229 7.402941 TCAGGTGCTCTCTCTATCTATCTATCT 59.597 40.741 0.00 0.00 0.00 1.98
170 230 8.704668 CAGGTGCTCTCTCTATCTATCTATCTA 58.295 40.741 0.00 0.00 0.00 1.98
171 231 9.452517 AGGTGCTCTCTCTATCTATCTATCTAT 57.547 37.037 0.00 0.00 0.00 1.98
172 232 9.712305 GGTGCTCTCTCTATCTATCTATCTATC 57.288 40.741 0.00 0.00 0.00 2.08
215 275 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
216 276 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
228 288 7.016296 TCTCTCTCTCTCTGAGTAGATATCCA 58.984 42.308 4.32 0.00 43.13 3.41
229 289 7.679881 TCTCTCTCTCTCTGAGTAGATATCCAT 59.320 40.741 4.32 0.00 43.13 3.41
230 290 8.909423 TCTCTCTCTCTGAGTAGATATCCATA 57.091 38.462 4.32 0.00 43.13 2.74
231 291 8.758829 TCTCTCTCTCTGAGTAGATATCCATAC 58.241 40.741 4.32 0.00 43.13 2.39
232 292 8.679344 TCTCTCTCTGAGTAGATATCCATACT 57.321 38.462 4.32 4.71 43.13 2.12
233 293 8.758829 TCTCTCTCTGAGTAGATATCCATACTC 58.241 40.741 18.64 18.64 45.33 2.59
234 294 8.679344 TCTCTCTGAGTAGATATCCATACTCT 57.321 38.462 22.81 6.29 45.33 3.24
235 295 8.539544 TCTCTCTGAGTAGATATCCATACTCTG 58.460 40.741 22.81 21.95 45.33 3.35
236 296 7.109501 TCTCTGAGTAGATATCCATACTCTGC 58.890 42.308 22.81 7.54 45.33 4.26
249 309 4.268644 CCATACTCTGCAACATTACTCGTG 59.731 45.833 0.00 0.00 0.00 4.35
250 310 3.386768 ACTCTGCAACATTACTCGTGT 57.613 42.857 0.00 0.00 0.00 4.49
272 337 2.034124 GTAATGGGTAGAGGTGCGGTA 58.966 52.381 0.00 0.00 0.00 4.02
273 338 1.120530 AATGGGTAGAGGTGCGGTAG 58.879 55.000 0.00 0.00 0.00 3.18
285 350 4.157120 CGGTAGGGGGAGCGGTTG 62.157 72.222 0.00 0.00 36.70 3.77
286 351 3.007323 GGTAGGGGGAGCGGTTGT 61.007 66.667 0.00 0.00 0.00 3.32
287 352 2.599757 GGTAGGGGGAGCGGTTGTT 61.600 63.158 0.00 0.00 0.00 2.83
288 353 1.376812 GTAGGGGGAGCGGTTGTTG 60.377 63.158 0.00 0.00 0.00 3.33
289 354 1.844289 TAGGGGGAGCGGTTGTTGT 60.844 57.895 0.00 0.00 0.00 3.32
290 355 1.420532 TAGGGGGAGCGGTTGTTGTT 61.421 55.000 0.00 0.00 0.00 2.83
291 356 2.561037 GGGGGAGCGGTTGTTGTTG 61.561 63.158 0.00 0.00 0.00 3.33
292 357 1.527380 GGGGAGCGGTTGTTGTTGA 60.527 57.895 0.00 0.00 0.00 3.18
302 367 4.358851 CGGTTGTTGTTGATGTTGTTGAT 58.641 39.130 0.00 0.00 0.00 2.57
327 392 1.014044 TGCGGATGTTTCGACTGAGC 61.014 55.000 0.00 0.00 0.00 4.26
369 434 2.244000 GTGTCGGACACCACCATTG 58.756 57.895 26.86 0.00 43.05 2.82
462 610 9.774742 GTTTTTCTTGCCATGTTAGTCTTATAG 57.225 33.333 0.00 0.00 0.00 1.31
467 615 7.872993 TCTTGCCATGTTAGTCTTATAGTATGC 59.127 37.037 0.00 0.00 0.00 3.14
492 640 4.037327 TGATTTGTCAAGTTCGATGCCAAA 59.963 37.500 0.00 0.00 0.00 3.28
494 642 3.347958 TGTCAAGTTCGATGCCAAAAC 57.652 42.857 0.00 0.00 0.00 2.43
495 643 2.685388 TGTCAAGTTCGATGCCAAAACA 59.315 40.909 0.00 0.00 0.00 2.83
551 699 0.171007 CTTGAAATGTTCGCGGCCAT 59.829 50.000 6.13 5.88 0.00 4.40
558 706 0.952280 TGTTCGCGGCCATTTGTTAA 59.048 45.000 6.13 0.00 0.00 2.01
560 708 1.982913 GTTCGCGGCCATTTGTTAAAG 59.017 47.619 6.13 0.00 0.00 1.85
566 714 2.065512 GGCCATTTGTTAAAGGTTGCG 58.934 47.619 0.00 0.00 0.00 4.85
616 765 7.511959 ACACTTTCTTCTTGTATTTCCTTCC 57.488 36.000 0.00 0.00 0.00 3.46
657 836 9.860898 GAAATTCTAGTTTTGCCATAAGTCAAT 57.139 29.630 0.00 0.00 0.00 2.57
677 856 9.574516 AGTCAATCTTGTTTAGGTTTGACTAAT 57.425 29.630 12.87 0.00 45.49 1.73
870 1050 9.696917 ATGAGCTTAATCAAACTTAAAAAGGTG 57.303 29.630 0.00 0.00 31.76 4.00
878 1058 7.455641 TCAAACTTAAAAAGGTGTGACTTGA 57.544 32.000 0.00 0.00 0.00 3.02
880 1060 7.810759 TCAAACTTAAAAAGGTGTGACTTGAAC 59.189 33.333 0.00 0.00 0.00 3.18
881 1061 5.875930 ACTTAAAAAGGTGTGACTTGAACG 58.124 37.500 0.00 0.00 0.00 3.95
885 1065 2.802787 AGGTGTGACTTGAACGAGAG 57.197 50.000 0.00 0.00 0.00 3.20
902 1082 6.668541 ACGAGAGTAGTACGTATTGCTTAA 57.331 37.500 9.89 0.00 46.88 1.85
903 1083 6.481984 ACGAGAGTAGTACGTATTGCTTAAC 58.518 40.000 9.89 4.73 46.88 2.01
904 1084 6.092670 ACGAGAGTAGTACGTATTGCTTAACA 59.907 38.462 9.89 0.00 46.88 2.41
905 1085 7.130917 CGAGAGTAGTACGTATTGCTTAACAT 58.869 38.462 9.89 0.00 0.00 2.71
906 1086 7.111732 CGAGAGTAGTACGTATTGCTTAACATG 59.888 40.741 9.89 0.00 0.00 3.21
907 1087 6.696148 AGAGTAGTACGTATTGCTTAACATGC 59.304 38.462 9.89 0.00 0.00 4.06
908 1088 6.570692 AGTAGTACGTATTGCTTAACATGCT 58.429 36.000 2.85 0.00 0.00 3.79
909 1089 5.968387 AGTACGTATTGCTTAACATGCTC 57.032 39.130 0.00 0.00 0.00 4.26
910 1090 5.661458 AGTACGTATTGCTTAACATGCTCT 58.339 37.500 0.00 0.00 0.00 4.09
911 1091 6.106673 AGTACGTATTGCTTAACATGCTCTT 58.893 36.000 0.00 0.00 0.00 2.85
912 1092 5.470845 ACGTATTGCTTAACATGCTCTTC 57.529 39.130 0.00 0.00 0.00 2.87
913 1093 4.332819 ACGTATTGCTTAACATGCTCTTCC 59.667 41.667 0.00 0.00 0.00 3.46
914 1094 4.550831 CGTATTGCTTAACATGCTCTTCCG 60.551 45.833 0.00 0.00 0.00 4.30
940 1120 1.202200 CGAGGCCGAACAAACAACAAA 60.202 47.619 0.00 0.00 38.22 2.83
941 1121 2.542824 CGAGGCCGAACAAACAACAAAT 60.543 45.455 0.00 0.00 38.22 2.32
969 1149 2.431954 TTACACAAAAACACGGGGGA 57.568 45.000 0.00 0.00 0.00 4.81
1180 1580 4.631740 TCACCTCCCACCGGCTCA 62.632 66.667 0.00 0.00 0.00 4.26
1248 1648 2.056223 CATCGTCCACCCGTACCCT 61.056 63.158 0.00 0.00 0.00 4.34
1296 1696 2.485795 CCGCTCCCTCTTCTCCTCG 61.486 68.421 0.00 0.00 0.00 4.63
1417 1820 2.763651 GTGGATGTGTTCTACGGGC 58.236 57.895 0.00 0.00 0.00 6.13
1590 1993 1.979693 GCAGGAGACGTGGGAGAGT 60.980 63.158 0.00 0.00 0.00 3.24
1632 2035 0.250234 CCTTCCAGGATCTCAACGCA 59.750 55.000 0.00 0.00 37.67 5.24
1667 2070 1.811359 CTCTTTCCTGCTTCCTGCTTG 59.189 52.381 0.00 0.00 43.37 4.01
1668 2071 0.886563 CTTTCCTGCTTCCTGCTTGG 59.113 55.000 0.00 0.00 43.37 3.61
1669 2072 0.478072 TTTCCTGCTTCCTGCTTGGA 59.522 50.000 0.00 0.00 44.51 3.53
1670 2073 0.700564 TTCCTGCTTCCTGCTTGGAT 59.299 50.000 0.09 0.00 45.68 3.41
1671 2074 0.034767 TCCTGCTTCCTGCTTGGATG 60.035 55.000 0.09 4.33 45.68 3.51
1675 2078 1.807886 CTTCCTGCTTGGATGCTGC 59.192 57.895 0.00 0.00 45.68 5.25
1677 2080 0.620030 TTCCTGCTTGGATGCTGCTA 59.380 50.000 0.00 0.00 45.68 3.49
1678 2081 0.107508 TCCTGCTTGGATGCTGCTAC 60.108 55.000 0.00 0.00 40.56 3.58
1680 2083 1.139654 CCTGCTTGGATGCTGCTACTA 59.860 52.381 0.00 0.00 38.35 1.82
1681 2084 2.224475 CCTGCTTGGATGCTGCTACTAT 60.224 50.000 0.00 0.00 38.35 2.12
1682 2085 3.065655 CTGCTTGGATGCTGCTACTATC 58.934 50.000 0.00 0.00 0.00 2.08
1683 2086 2.435437 TGCTTGGATGCTGCTACTATCA 59.565 45.455 0.00 0.00 0.00 2.15
1689 2092 7.632462 GCTTGGATGCTGCTACTATCATATAGT 60.632 40.741 0.00 5.04 0.00 2.12
1694 2097 8.768957 ATGCTGCTACTATCATATAGTGTTTG 57.231 34.615 9.35 0.77 0.00 2.93
1718 2132 4.148128 ACATCTGAGATTGGATCACCAC 57.852 45.455 0.00 0.00 46.80 4.16
1735 2149 1.066002 CCACGCTCTAAATGGCAATGG 59.934 52.381 0.00 0.00 0.00 3.16
1736 2150 0.740737 ACGCTCTAAATGGCAATGGC 59.259 50.000 0.00 0.00 40.13 4.40
1737 2151 0.740149 CGCTCTAAATGGCAATGGCA 59.260 50.000 12.96 12.96 43.71 4.92
1738 2152 1.134753 CGCTCTAAATGGCAATGGCAA 59.865 47.619 14.81 0.00 42.43 4.52
1739 2153 2.223876 CGCTCTAAATGGCAATGGCAAT 60.224 45.455 14.81 1.56 42.43 3.56
1740 2154 3.128349 GCTCTAAATGGCAATGGCAATG 58.872 45.455 14.81 0.00 42.43 2.82
1747 2161 1.153588 GCAATGGCAATGAACCGGG 60.154 57.895 6.32 0.00 40.72 5.73
1749 2163 1.608918 AATGGCAATGAACCGGGCA 60.609 52.632 6.32 3.58 41.52 5.36
1762 2176 3.586100 ACCGGGCATAATTTTGTGAAC 57.414 42.857 6.32 0.00 0.00 3.18
1763 2177 2.094957 ACCGGGCATAATTTTGTGAACG 60.095 45.455 6.32 0.00 0.00 3.95
1764 2178 2.094957 CCGGGCATAATTTTGTGAACGT 60.095 45.455 0.00 0.00 0.00 3.99
1765 2179 3.168193 CGGGCATAATTTTGTGAACGTC 58.832 45.455 0.00 0.00 0.00 4.34
1766 2180 3.365465 CGGGCATAATTTTGTGAACGTCA 60.365 43.478 0.00 0.00 0.00 4.35
1767 2181 4.674101 CGGGCATAATTTTGTGAACGTCAT 60.674 41.667 0.00 0.00 0.00 3.06
1769 2183 5.288472 GGGCATAATTTTGTGAACGTCATTC 59.712 40.000 0.00 0.00 37.88 2.67
1771 2185 6.092748 GCATAATTTTGTGAACGTCATTCCT 58.907 36.000 0.00 0.00 36.36 3.36
1772 2186 7.247728 GCATAATTTTGTGAACGTCATTCCTA 58.752 34.615 0.00 0.00 36.36 2.94
1813 2228 5.451520 GGAAATGATGGAATTGGCAGAGAAG 60.452 44.000 0.00 0.00 0.00 2.85
1998 2413 6.348132 CGACAGGTAATTTGTGCTTGTTCATA 60.348 38.462 0.00 0.00 32.18 2.15
2013 2428 5.689383 TGTTCATAGTTTTCCAGCACTTC 57.311 39.130 0.00 0.00 0.00 3.01
2041 2476 5.220529 GCAGCTGAATTGCAATGGAAATAAC 60.221 40.000 20.43 0.00 41.17 1.89
2045 2480 8.259411 AGCTGAATTGCAATGGAAATAACAATA 58.741 29.630 13.82 0.00 34.99 1.90
2093 2528 6.406512 CCAATTACTAAATGTTTACCTGGGGC 60.407 42.308 0.00 0.00 0.00 5.80
2109 2544 3.636764 CTGGGGCCTTTATCACCAAATAC 59.363 47.826 0.84 0.00 0.00 1.89
2112 2547 3.284617 GGCCTTTATCACCAAATACCGT 58.715 45.455 0.00 0.00 0.00 4.83
2118 2553 6.262273 CCTTTATCACCAAATACCGTAAGCAT 59.738 38.462 0.00 0.00 0.00 3.79
2119 2554 7.442969 CCTTTATCACCAAATACCGTAAGCATA 59.557 37.037 0.00 0.00 0.00 3.14
2146 2581 8.446599 AGTAATTTCCGGTATAAAATGTCTGG 57.553 34.615 0.00 0.00 0.00 3.86
2182 2617 4.917415 CAGTCGTTTTCCTTGCCTTTTATG 59.083 41.667 0.00 0.00 0.00 1.90
2252 2688 6.726490 ATGCTTCCATATTTTCATTCTGCT 57.274 33.333 0.00 0.00 0.00 4.24
2289 2725 5.721480 AGATCAAATTTGGACCCCTTTTAGG 59.279 40.000 17.90 0.00 34.30 2.69
2357 2793 4.336889 TGTTCGATCACCTTTCAGTTCT 57.663 40.909 0.00 0.00 0.00 3.01
2404 2841 2.287608 CGAGAAAAACAAACCTGCCCTC 60.288 50.000 0.00 0.00 0.00 4.30
2412 2849 0.261696 AAACCTGCCCTCTGTTTGGT 59.738 50.000 0.00 0.00 31.41 3.67
2420 2857 1.271926 CCCTCTGTTTGGTGGGGTTAG 60.272 57.143 0.00 0.00 36.15 2.34
2492 2930 5.887598 TCTTGCATATTCAGTTGGTAGCAAT 59.112 36.000 11.06 0.00 39.62 3.56
2493 2931 5.503662 TGCATATTCAGTTGGTAGCAATG 57.496 39.130 11.06 10.06 0.00 2.82
2495 2933 4.037208 GCATATTCAGTTGGTAGCAATGCT 59.963 41.667 13.92 13.92 43.41 3.79
2528 2966 7.849804 TCATGCCTTCATAGTTTTCTTCTAC 57.150 36.000 0.00 0.00 0.00 2.59
2533 2971 7.174946 TGCCTTCATAGTTTTCTTCTACTTTGG 59.825 37.037 0.00 0.00 0.00 3.28
2556 2994 5.173854 GGAAGCTGTTTTGTTTTCATCTTCG 59.826 40.000 0.00 0.00 36.10 3.79
2559 2997 4.676924 GCTGTTTTGTTTTCATCTTCGGAG 59.323 41.667 0.00 0.00 0.00 4.63
2573 3011 7.386851 TCATCTTCGGAGTTTTCTTCTGTTAT 58.613 34.615 0.00 0.00 0.00 1.89
2579 3017 4.518970 GGAGTTTTCTTCTGTTATGCCACA 59.481 41.667 0.00 0.00 0.00 4.17
2580 3018 5.183904 GGAGTTTTCTTCTGTTATGCCACAT 59.816 40.000 0.00 0.00 0.00 3.21
2581 3019 6.374333 GGAGTTTTCTTCTGTTATGCCACATA 59.626 38.462 0.00 0.00 0.00 2.29
3056 3512 4.398988 TGATTTGTAATAAGCAGCCCAGTG 59.601 41.667 0.00 0.00 0.00 3.66
3074 3530 2.749621 AGTGATGCTCCGGAAATTTGAC 59.250 45.455 5.23 0.00 0.00 3.18
3149 3605 3.004106 GTGGCAATGATAAGTCCAGATGC 59.996 47.826 0.00 0.00 32.74 3.91
3162 3618 6.808008 AGTCCAGATGCCATTTTATATTCG 57.192 37.500 0.00 0.00 0.00 3.34
3165 3621 7.387948 AGTCCAGATGCCATTTTATATTCGTAC 59.612 37.037 0.00 0.00 0.00 3.67
3166 3622 7.387948 GTCCAGATGCCATTTTATATTCGTACT 59.612 37.037 0.00 0.00 0.00 2.73
3187 3643 3.062042 TGAATAGCGCTGCATGACATAG 58.938 45.455 22.90 0.00 0.00 2.23
3188 3644 1.436600 ATAGCGCTGCATGACATAGC 58.563 50.000 22.90 0.74 0.00 2.97
3189 3645 0.104671 TAGCGCTGCATGACATAGCA 59.895 50.000 22.90 10.44 37.29 3.49
3195 3651 2.320745 TGCATGACATAGCAGGAGTG 57.679 50.000 0.00 0.00 35.51 3.51
3196 3652 1.832998 TGCATGACATAGCAGGAGTGA 59.167 47.619 0.00 0.00 35.51 3.41
3197 3653 2.159000 TGCATGACATAGCAGGAGTGAG 60.159 50.000 0.00 0.00 35.51 3.51
3198 3654 2.481854 CATGACATAGCAGGAGTGAGC 58.518 52.381 0.00 0.00 0.00 4.26
3216 3672 4.999950 GTGAGCTAGCAGCCATACAAATAT 59.000 41.667 18.83 0.00 43.77 1.28
3233 3689 9.723601 ATACAAATATTGTGCCTTGATTTTGTT 57.276 25.926 6.01 0.00 45.03 2.83
3237 3693 9.995003 AAATATTGTGCCTTGATTTTGTTTCTA 57.005 25.926 0.00 0.00 0.00 2.10
3244 3700 6.036470 GCCTTGATTTTGTTTCTATACCTGC 58.964 40.000 0.00 0.00 0.00 4.85
3253 3709 5.815581 TGTTTCTATACCTGCCAAATCTGT 58.184 37.500 0.00 0.00 0.00 3.41
3260 3716 4.322057 ACCTGCCAAATCTGTTTCCTAT 57.678 40.909 0.00 0.00 0.00 2.57
3262 3718 4.018050 ACCTGCCAAATCTGTTTCCTATCT 60.018 41.667 0.00 0.00 0.00 1.98
3263 3719 4.337555 CCTGCCAAATCTGTTTCCTATCTG 59.662 45.833 0.00 0.00 0.00 2.90
3311 3767 2.178912 TGAATGACCGGTTCTGGTTC 57.821 50.000 9.42 9.71 44.01 3.62
3315 3771 2.649531 TGACCGGTTCTGGTTCATTT 57.350 45.000 9.42 0.00 44.01 2.32
3325 3781 5.983118 GGTTCTGGTTCATTTTTGTTAGTGG 59.017 40.000 0.00 0.00 0.00 4.00
3357 3821 4.942852 TGTTTCCATGCACTTTTTACCAG 58.057 39.130 0.00 0.00 0.00 4.00
3360 3824 6.096987 TGTTTCCATGCACTTTTTACCAGTTA 59.903 34.615 0.00 0.00 0.00 2.24
3362 3826 4.521256 TCCATGCACTTTTTACCAGTTACC 59.479 41.667 0.00 0.00 0.00 2.85
3371 3835 2.851263 TACCAGTTACCTTGCACCTG 57.149 50.000 0.00 0.00 0.00 4.00
3386 3850 4.542662 GCACCTGCAATCATTAGTACTG 57.457 45.455 5.39 0.00 41.59 2.74
3395 3859 7.154656 TGCAATCATTAGTACTGGTAGCATAG 58.845 38.462 5.39 0.00 0.00 2.23
3396 3860 6.091441 GCAATCATTAGTACTGGTAGCATAGC 59.909 42.308 5.39 0.00 40.09 2.97
3398 3862 4.217767 TCATTAGTACTGGTAGCATAGCCG 59.782 45.833 5.39 0.00 38.57 5.52
3413 3877 0.470833 AGCCGCATACTGATCTCCCT 60.471 55.000 0.00 0.00 0.00 4.20
3416 3880 1.332195 CGCATACTGATCTCCCTCCA 58.668 55.000 0.00 0.00 0.00 3.86
3422 3886 5.703130 GCATACTGATCTCCCTCCAATAAAC 59.297 44.000 0.00 0.00 0.00 2.01
3453 3917 2.274437 GCAAGAATCTCATCACTCGCA 58.726 47.619 0.00 0.00 0.00 5.10
3507 3971 3.481903 AGCGACGCTGCATTCACG 61.482 61.111 23.84 0.00 37.57 4.35
3577 4041 2.387757 ACAAAGGTGTCCTGCAATTGT 58.612 42.857 7.40 0.00 32.13 2.71
3616 4087 5.885230 CAAGACATGCATTTAGTTCCAGA 57.115 39.130 0.00 0.00 0.00 3.86
3617 4088 5.634896 CAAGACATGCATTTAGTTCCAGAC 58.365 41.667 0.00 0.00 0.00 3.51
3618 4089 5.171339 AGACATGCATTTAGTTCCAGACT 57.829 39.130 0.00 0.00 42.55 3.24
3619 4090 4.940046 AGACATGCATTTAGTTCCAGACTG 59.060 41.667 0.00 0.00 39.48 3.51
3620 4091 4.910195 ACATGCATTTAGTTCCAGACTGA 58.090 39.130 3.32 0.00 39.48 3.41
3621 4092 5.316167 ACATGCATTTAGTTCCAGACTGAA 58.684 37.500 3.32 0.00 39.48 3.02
3633 4104 5.152623 TCCAGACTGAATGAACTAACCAG 57.847 43.478 3.32 0.00 0.00 4.00
3637 4108 7.038302 TCCAGACTGAATGAACTAACCAGTATT 60.038 37.037 3.32 0.00 38.10 1.89
3821 4300 8.499288 TTCCTAGGTTTTCCCATGTTATTTTT 57.501 30.769 9.08 0.00 41.86 1.94
3868 4347 2.616960 TGGTATGCGCTTTACTGACTG 58.383 47.619 9.73 0.00 0.00 3.51
3957 4437 2.775384 ACACAGTTTTGGTAGAGGTGGA 59.225 45.455 0.00 0.00 0.00 4.02
3963 4446 4.010349 GTTTTGGTAGAGGTGGATTCAGG 58.990 47.826 0.00 0.00 0.00 3.86
3994 4477 6.655078 ACTTTGATGTGACTATTTTGCCTT 57.345 33.333 0.00 0.00 0.00 4.35
4054 4539 9.695526 TCTGTAAAGTAACATAAGAGCGTTTAA 57.304 29.630 0.00 0.00 0.00 1.52
4062 4547 9.897349 GTAACATAAGAGCGTTTAAATCACTAC 57.103 33.333 0.00 0.00 0.00 2.73
4063 4548 8.773404 AACATAAGAGCGTTTAAATCACTACT 57.227 30.769 0.00 0.00 0.00 2.57
4064 4549 8.773404 ACATAAGAGCGTTTAAATCACTACTT 57.227 30.769 0.00 0.00 0.00 2.24
4065 4550 9.865321 ACATAAGAGCGTTTAAATCACTACTTA 57.135 29.630 0.00 0.00 0.00 2.24
4070 4555 9.431887 AGAGCGTTTAAATCACTACTTAAATCA 57.568 29.630 0.00 0.00 31.57 2.57
4071 4556 9.474249 GAGCGTTTAAATCACTACTTAAATCAC 57.526 33.333 0.00 0.00 31.57 3.06
4072 4557 9.216117 AGCGTTTAAATCACTACTTAAATCACT 57.784 29.630 0.00 0.00 31.57 3.41
4112 4597 7.502120 ACGCTCTTATATTACTTTACGGAGA 57.498 36.000 0.00 0.00 0.00 3.71
4155 4640 7.381139 ACATAACGTTTTCATCATTTGGTTGAC 59.619 33.333 5.91 0.00 0.00 3.18
4191 4676 5.006746 GGTGTGCTGTATATGTAAGTTGAGC 59.993 44.000 0.00 0.00 0.00 4.26
4216 4701 5.841237 TGAGGATTTTGGATGGTTTTTACCA 59.159 36.000 0.00 0.00 44.85 3.25
4306 4820 0.955919 AAGCTACTGCAGAAACCGGC 60.956 55.000 23.35 13.80 42.74 6.13
4347 4861 9.423061 TCGTATCAAATGTATCATTGTATCCTG 57.577 33.333 0.00 0.00 0.00 3.86
4359 4873 2.803956 TGTATCCTGTTCAGACCGAGT 58.196 47.619 1.00 0.00 0.00 4.18
4374 4888 4.584743 AGACCGAGTATATGAACAGCATCA 59.415 41.667 0.00 0.00 38.44 3.07
4381 4895 8.223769 CGAGTATATGAACAGCATCAAAATACC 58.776 37.037 13.42 8.52 38.44 2.73
4445 4988 2.825836 CCAATCTCCTGTGCCGCC 60.826 66.667 0.00 0.00 0.00 6.13
4482 5031 7.093377 TGTGCTTGGCCTTCATATTTCTAAAAT 60.093 33.333 3.32 0.00 0.00 1.82
4646 7983 0.175760 GCGCAAGGTCCTCACTGATA 59.824 55.000 0.30 0.00 38.28 2.15
4648 7985 2.477825 CGCAAGGTCCTCACTGATATG 58.522 52.381 0.00 0.00 0.00 1.78
4718 8078 7.509141 TGCGGATGAAACACATTGATTATAT 57.491 32.000 0.00 0.00 39.56 0.86
4719 8079 8.614469 TGCGGATGAAACACATTGATTATATA 57.386 30.769 0.00 0.00 39.56 0.86
4720 8080 9.230122 TGCGGATGAAACACATTGATTATATAT 57.770 29.630 0.00 0.00 39.56 0.86
4761 8343 1.802365 ACCATCACGAAAACGCCTAAC 59.198 47.619 0.00 0.00 0.00 2.34
4787 8369 2.026641 AGCATTACATGGCGAGCAAAT 58.973 42.857 0.00 0.00 34.54 2.32
4868 8461 9.294030 GCACTTCCTAAAATTCTCAATATGTTG 57.706 33.333 0.00 0.00 36.65 3.33
4926 8520 2.358267 CGGAAACTCTACTCGGTAGCAT 59.642 50.000 6.28 0.00 36.22 3.79
4929 8523 4.498345 GGAAACTCTACTCGGTAGCATCAG 60.498 50.000 6.28 2.61 36.22 2.90
4930 8524 3.562343 ACTCTACTCGGTAGCATCAGA 57.438 47.619 6.28 0.00 36.22 3.27
4931 8525 3.207778 ACTCTACTCGGTAGCATCAGAC 58.792 50.000 6.28 0.00 36.22 3.51
4932 8526 3.118186 ACTCTACTCGGTAGCATCAGACT 60.118 47.826 6.28 0.00 36.22 3.24
4933 8527 3.880490 CTCTACTCGGTAGCATCAGACTT 59.120 47.826 6.28 0.00 36.22 3.01
4934 8528 4.270834 TCTACTCGGTAGCATCAGACTTT 58.729 43.478 6.28 0.00 36.22 2.66
4935 8529 3.238108 ACTCGGTAGCATCAGACTTTG 57.762 47.619 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.296056 AGATAGGTACCAAACTACTGGGG 58.704 47.826 15.94 0.00 41.16 4.96
6 7 5.451520 CGAAGATAGGTACCAAACTACTGGG 60.452 48.000 15.94 0.00 41.16 4.45
9 10 6.421485 TCTCGAAGATAGGTACCAAACTACT 58.579 40.000 15.94 1.64 33.89 2.57
46 47 4.587262 TGAGCGCTACTTTAGGGATATTGA 59.413 41.667 11.50 0.00 40.83 2.57
72 121 5.353394 TGTAGGCATTCCTAAGGTACAAG 57.647 43.478 0.00 0.00 46.01 3.16
75 124 4.347000 TCCATGTAGGCATTCCTAAGGTAC 59.653 45.833 0.00 0.00 46.01 3.34
83 132 0.463654 TGCGTCCATGTAGGCATTCC 60.464 55.000 1.11 0.00 35.48 3.01
112 161 0.116143 AACCTGAGCTCCAGAGTCCT 59.884 55.000 12.15 0.00 45.78 3.85
119 168 1.965414 TATTCCCAACCTGAGCTCCA 58.035 50.000 12.15 0.00 0.00 3.86
125 174 3.010138 CCTGAACCTTATTCCCAACCTGA 59.990 47.826 0.00 0.00 0.00 3.86
127 176 2.993863 ACCTGAACCTTATTCCCAACCT 59.006 45.455 0.00 0.00 0.00 3.50
128 177 3.089284 CACCTGAACCTTATTCCCAACC 58.911 50.000 0.00 0.00 0.00 3.77
130 179 2.378547 AGCACCTGAACCTTATTCCCAA 59.621 45.455 0.00 0.00 0.00 4.12
131 180 1.992557 AGCACCTGAACCTTATTCCCA 59.007 47.619 0.00 0.00 0.00 4.37
174 234 9.420118 GAGAGAGAGAGAGAGAGATAGATAGAT 57.580 40.741 0.00 0.00 0.00 1.98
175 235 8.619281 AGAGAGAGAGAGAGAGAGATAGATAGA 58.381 40.741 0.00 0.00 0.00 1.98
176 236 8.821686 AGAGAGAGAGAGAGAGAGATAGATAG 57.178 42.308 0.00 0.00 0.00 2.08
177 237 8.619281 AGAGAGAGAGAGAGAGAGAGATAGATA 58.381 40.741 0.00 0.00 0.00 1.98
178 238 7.477864 AGAGAGAGAGAGAGAGAGAGATAGAT 58.522 42.308 0.00 0.00 0.00 1.98
179 239 6.857848 AGAGAGAGAGAGAGAGAGAGATAGA 58.142 44.000 0.00 0.00 0.00 1.98
180 240 6.947733 AGAGAGAGAGAGAGAGAGAGAGATAG 59.052 46.154 0.00 0.00 0.00 2.08
181 241 6.857848 AGAGAGAGAGAGAGAGAGAGAGATA 58.142 44.000 0.00 0.00 0.00 1.98
182 242 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
183 243 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
184 244 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
185 245 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
186 246 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
187 247 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
188 248 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
189 249 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
190 250 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
191 251 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
215 275 6.777580 TGTTGCAGAGTATGGATATCTACTCA 59.222 38.462 23.74 7.98 44.07 3.41
216 276 7.220741 TGTTGCAGAGTATGGATATCTACTC 57.779 40.000 18.13 18.13 42.67 2.59
228 288 5.073311 ACACGAGTAATGTTGCAGAGTAT 57.927 39.130 0.00 0.00 0.00 2.12
229 289 4.514781 ACACGAGTAATGTTGCAGAGTA 57.485 40.909 0.00 0.00 0.00 2.59
230 290 3.386768 ACACGAGTAATGTTGCAGAGT 57.613 42.857 0.00 0.00 0.00 3.24
249 309 2.277084 CGCACCTCTACCCATTACAAC 58.723 52.381 0.00 0.00 0.00 3.32
250 310 1.208535 CCGCACCTCTACCCATTACAA 59.791 52.381 0.00 0.00 0.00 2.41
252 312 0.828677 ACCGCACCTCTACCCATTAC 59.171 55.000 0.00 0.00 0.00 1.89
259 324 2.132352 CCCCCTACCGCACCTCTAC 61.132 68.421 0.00 0.00 0.00 2.59
272 337 2.763645 AACAACAACCGCTCCCCCT 61.764 57.895 0.00 0.00 0.00 4.79
273 338 2.203437 AACAACAACCGCTCCCCC 60.203 61.111 0.00 0.00 0.00 5.40
280 345 3.763902 TCAACAACATCAACAACAACCG 58.236 40.909 0.00 0.00 0.00 4.44
284 349 6.389830 AGCTTATCAACAACATCAACAACA 57.610 33.333 0.00 0.00 0.00 3.33
285 350 6.346040 GCAAGCTTATCAACAACATCAACAAC 60.346 38.462 0.00 0.00 0.00 3.32
286 351 5.691305 GCAAGCTTATCAACAACATCAACAA 59.309 36.000 0.00 0.00 0.00 2.83
287 352 5.221880 GCAAGCTTATCAACAACATCAACA 58.778 37.500 0.00 0.00 0.00 3.33
288 353 4.321745 CGCAAGCTTATCAACAACATCAAC 59.678 41.667 0.00 0.00 0.00 3.18
289 354 4.475028 CGCAAGCTTATCAACAACATCAA 58.525 39.130 0.00 0.00 0.00 2.57
290 355 3.119884 CCGCAAGCTTATCAACAACATCA 60.120 43.478 0.00 0.00 0.00 3.07
291 356 3.126858 TCCGCAAGCTTATCAACAACATC 59.873 43.478 0.00 0.00 0.00 3.06
292 357 3.081061 TCCGCAAGCTTATCAACAACAT 58.919 40.909 0.00 0.00 0.00 2.71
302 367 1.730064 GTCGAAACATCCGCAAGCTTA 59.270 47.619 0.00 0.00 0.00 3.09
366 431 6.318648 ACCGTGACAACAATAGCAATATCAAT 59.681 34.615 0.00 0.00 0.00 2.57
367 432 5.645929 ACCGTGACAACAATAGCAATATCAA 59.354 36.000 0.00 0.00 0.00 2.57
369 434 5.277345 GGACCGTGACAACAATAGCAATATC 60.277 44.000 0.00 0.00 0.00 1.63
406 472 0.534203 TTCGCTCCTCCACCAACAAC 60.534 55.000 0.00 0.00 0.00 3.32
521 669 9.825972 CCGCGAACATTTCAAGATAAATATATT 57.174 29.630 8.23 0.00 0.00 1.28
522 670 7.962918 GCCGCGAACATTTCAAGATAAATATAT 59.037 33.333 8.23 0.00 0.00 0.86
544 692 2.065512 CAACCTTTAACAAATGGCCGC 58.934 47.619 0.00 0.00 0.00 6.53
545 693 2.065512 GCAACCTTTAACAAATGGCCG 58.934 47.619 0.00 0.00 0.00 6.13
551 699 6.867293 ACAACTTAAACGCAACCTTTAACAAA 59.133 30.769 0.00 0.00 0.00 2.83
558 706 2.480587 GCCACAACTTAAACGCAACCTT 60.481 45.455 0.00 0.00 0.00 3.50
560 708 1.066454 AGCCACAACTTAAACGCAACC 59.934 47.619 0.00 0.00 0.00 3.77
566 714 9.685828 TTGATTATGTAAAGCCACAACTTAAAC 57.314 29.630 0.00 0.00 30.84 2.01
852 1032 8.527810 TCAAGTCACACCTTTTTAAGTTTGATT 58.472 29.630 0.00 0.00 0.00 2.57
870 1050 4.084118 ACGTACTACTCTCGTTCAAGTCAC 60.084 45.833 0.00 0.00 34.07 3.67
878 1058 5.557891 AAGCAATACGTACTACTCTCGTT 57.442 39.130 0.00 0.00 38.69 3.85
880 1060 6.481134 TGTTAAGCAATACGTACTACTCTCG 58.519 40.000 0.00 0.00 0.00 4.04
881 1061 7.096558 GCATGTTAAGCAATACGTACTACTCTC 60.097 40.741 0.00 0.00 0.00 3.20
885 1065 6.696148 AGAGCATGTTAAGCAATACGTACTAC 59.304 38.462 0.00 0.00 0.00 2.73
887 1067 5.661458 AGAGCATGTTAAGCAATACGTACT 58.339 37.500 0.00 0.00 0.00 2.73
889 1069 5.522460 GGAAGAGCATGTTAAGCAATACGTA 59.478 40.000 0.00 0.00 0.00 3.57
891 1071 4.550831 CGGAAGAGCATGTTAAGCAATACG 60.551 45.833 0.00 0.00 0.00 3.06
892 1072 4.570772 TCGGAAGAGCATGTTAAGCAATAC 59.429 41.667 0.00 0.00 34.84 1.89
894 1074 3.609853 TCGGAAGAGCATGTTAAGCAAT 58.390 40.909 0.00 0.00 34.84 3.56
895 1075 3.052455 TCGGAAGAGCATGTTAAGCAA 57.948 42.857 0.00 0.00 34.84 3.91
896 1076 2.760634 TCGGAAGAGCATGTTAAGCA 57.239 45.000 0.00 0.00 34.84 3.91
900 1080 7.898676 CCTCGTCAATCGGAAGAGCATGTTA 62.899 48.000 0.00 0.00 46.77 2.41
902 1082 5.834819 CCTCGTCAATCGGAAGAGCATGT 62.835 52.174 0.00 0.00 46.77 3.21
903 1083 3.368160 CCTCGTCAATCGGAAGAGCATG 61.368 54.545 2.36 0.00 46.77 4.06
904 1084 1.202463 CCTCGTCAATCGGAAGAGCAT 60.202 52.381 2.36 0.00 46.77 3.79
905 1085 0.173481 CCTCGTCAATCGGAAGAGCA 59.827 55.000 2.36 0.00 46.77 4.26
906 1086 1.148759 GCCTCGTCAATCGGAAGAGC 61.149 60.000 2.36 0.00 46.77 4.09
909 1089 1.878522 CGGCCTCGTCAATCGGAAG 60.879 63.158 0.00 0.00 40.32 3.46
910 1090 1.879737 TTCGGCCTCGTCAATCGGAA 61.880 55.000 0.00 0.00 40.32 4.30
911 1091 2.344981 TTCGGCCTCGTCAATCGGA 61.345 57.895 0.00 0.00 40.32 4.55
912 1092 2.165301 GTTCGGCCTCGTCAATCGG 61.165 63.158 0.00 0.00 40.32 4.18
913 1093 1.011968 TTGTTCGGCCTCGTCAATCG 61.012 55.000 0.00 0.00 41.41 3.34
914 1094 1.136057 GTTTGTTCGGCCTCGTCAATC 60.136 52.381 0.00 0.00 37.69 2.67
947 1127 4.467769 TCCCCCGTGTTTTTGTGTAAATA 58.532 39.130 0.00 0.00 0.00 1.40
948 1128 3.297736 TCCCCCGTGTTTTTGTGTAAAT 58.702 40.909 0.00 0.00 0.00 1.40
949 1129 2.731572 TCCCCCGTGTTTTTGTGTAAA 58.268 42.857 0.00 0.00 0.00 2.01
950 1130 2.431954 TCCCCCGTGTTTTTGTGTAA 57.568 45.000 0.00 0.00 0.00 2.41
969 1149 3.118000 AGAGTTTGGACTTCGGAGGTTTT 60.118 43.478 0.00 0.00 35.88 2.43
978 1378 2.879026 GGTTGTGGAGAGTTTGGACTTC 59.121 50.000 0.00 0.00 35.88 3.01
1296 1696 2.462782 CGACGAGGAGGAGGACGAC 61.463 68.421 0.00 0.00 0.00 4.34
1632 2035 3.557264 GGAAAGAGGAACGAACCATGAGT 60.557 47.826 0.00 0.00 0.00 3.41
1667 2070 7.106439 ACACTATATGATAGTAGCAGCATCC 57.894 40.000 0.00 0.00 0.00 3.51
1668 2071 8.867935 CAAACACTATATGATAGTAGCAGCATC 58.132 37.037 0.00 0.00 0.00 3.91
1669 2072 8.370940 ACAAACACTATATGATAGTAGCAGCAT 58.629 33.333 0.00 0.00 0.00 3.79
1670 2073 7.726216 ACAAACACTATATGATAGTAGCAGCA 58.274 34.615 0.00 0.00 0.00 4.41
1671 2074 9.692749 TTACAAACACTATATGATAGTAGCAGC 57.307 33.333 0.00 0.00 0.00 5.25
1689 2092 7.119699 GTGATCCAATCTCAGATGTTACAAACA 59.880 37.037 0.00 0.00 46.94 2.83
1694 2097 5.525378 GTGGTGATCCAATCTCAGATGTTAC 59.475 44.000 0.00 0.00 46.15 2.50
1718 2132 0.740149 TGCCATTGCCATTTAGAGCG 59.260 50.000 0.00 0.00 36.33 5.03
1735 2149 2.888834 AATTATGCCCGGTTCATTGC 57.111 45.000 11.08 1.59 0.00 3.56
1736 2150 4.329528 CACAAAATTATGCCCGGTTCATTG 59.670 41.667 11.08 7.08 0.00 2.82
1737 2151 4.221703 TCACAAAATTATGCCCGGTTCATT 59.778 37.500 11.08 0.00 0.00 2.57
1738 2152 3.766591 TCACAAAATTATGCCCGGTTCAT 59.233 39.130 0.00 6.18 0.00 2.57
1739 2153 3.157881 TCACAAAATTATGCCCGGTTCA 58.842 40.909 0.00 0.00 0.00 3.18
1740 2154 3.859411 TCACAAAATTATGCCCGGTTC 57.141 42.857 0.00 0.00 0.00 3.62
1747 2161 6.092748 AGGAATGACGTTCACAAAATTATGC 58.907 36.000 9.56 0.00 38.64 3.14
1762 2176 4.210120 GCTTTGCTCTGTATAGGAATGACG 59.790 45.833 0.00 0.00 0.00 4.35
1763 2177 4.513318 GGCTTTGCTCTGTATAGGAATGAC 59.487 45.833 0.00 0.00 0.00 3.06
1764 2178 4.164030 TGGCTTTGCTCTGTATAGGAATGA 59.836 41.667 0.00 0.00 0.00 2.57
1765 2179 4.454678 TGGCTTTGCTCTGTATAGGAATG 58.545 43.478 0.00 0.00 0.00 2.67
1766 2180 4.778213 TGGCTTTGCTCTGTATAGGAAT 57.222 40.909 0.00 0.00 0.00 3.01
1767 2181 4.517285 CTTGGCTTTGCTCTGTATAGGAA 58.483 43.478 0.00 0.00 0.00 3.36
1769 2183 3.118261 TCCTTGGCTTTGCTCTGTATAGG 60.118 47.826 0.00 0.00 0.00 2.57
1771 2185 4.568072 TTCCTTGGCTTTGCTCTGTATA 57.432 40.909 0.00 0.00 0.00 1.47
1772 2186 3.439857 TTCCTTGGCTTTGCTCTGTAT 57.560 42.857 0.00 0.00 0.00 2.29
2041 2476 6.958255 TGCGATTCTCCAAATACATGTATTG 58.042 36.000 27.50 20.58 36.04 1.90
2045 2480 4.261322 GCATGCGATTCTCCAAATACATGT 60.261 41.667 0.00 2.69 36.80 3.21
2058 2493 6.208644 ACATTTAGTAATTGGCATGCGATTC 58.791 36.000 17.84 11.52 0.00 2.52
2093 2528 5.587043 TGCTTACGGTATTTGGTGATAAAGG 59.413 40.000 0.00 0.00 0.00 3.11
2109 2544 4.684703 CCGGAAATTACTCTATGCTTACGG 59.315 45.833 0.00 0.00 0.00 4.02
2119 2554 9.326413 CAGACATTTTATACCGGAAATTACTCT 57.674 33.333 9.46 0.79 0.00 3.24
2146 2581 0.321653 ACGACTGTTTCCATCCAGCC 60.322 55.000 0.00 0.00 31.76 4.85
2182 2617 2.808906 ATGGTAGAGGTTCCCTTTGC 57.191 50.000 0.00 0.00 31.76 3.68
2186 2621 5.036916 TGTTCAATATGGTAGAGGTTCCCT 58.963 41.667 0.00 0.00 36.03 4.20
2208 2644 5.745294 GCATACAAATGACCAGCAAGTATTG 59.255 40.000 0.00 0.00 41.74 1.90
2252 2688 9.187996 TCCAAATTTGATCTAGTTCATGCATAA 57.812 29.630 19.86 0.00 0.00 1.90
2265 2701 5.721480 CCTAAAAGGGGTCCAAATTTGATCT 59.279 40.000 19.86 6.37 0.00 2.75
2289 2725 2.791655 ACCCAACTAGCTAAACAAGGC 58.208 47.619 0.00 0.00 0.00 4.35
2357 2793 5.003804 GGGATTGTTTCACTAGCTTGAAGA 58.996 41.667 1.04 0.00 36.84 2.87
2404 2841 0.251608 CCCCTAACCCCACCAAACAG 60.252 60.000 0.00 0.00 0.00 3.16
2412 2849 3.422809 GGAAGTACCCCTAACCCCA 57.577 57.895 0.00 0.00 0.00 4.96
2462 2900 9.330063 CTACCAACTGAATATGCAAGAAAGATA 57.670 33.333 0.00 0.00 0.00 1.98
2492 2930 1.985473 AGGCATGAACAGTTTCAGCA 58.015 45.000 0.00 0.00 45.07 4.41
2493 2931 2.294233 TGAAGGCATGAACAGTTTCAGC 59.706 45.455 0.00 0.00 45.07 4.26
2495 2933 5.316167 ACTATGAAGGCATGAACAGTTTCA 58.684 37.500 0.00 0.00 45.93 2.69
2528 2966 6.536224 AGATGAAAACAAAACAGCTTCCAAAG 59.464 34.615 0.00 0.00 0.00 2.77
2533 2971 5.173854 CCGAAGATGAAAACAAAACAGCTTC 59.826 40.000 12.31 12.31 46.51 3.86
2556 2994 4.518970 TGTGGCATAACAGAAGAAAACTCC 59.481 41.667 0.00 0.00 0.00 3.85
2559 2997 9.503427 GTATTATGTGGCATAACAGAAGAAAAC 57.497 33.333 4.00 0.00 34.96 2.43
2754 3192 2.293399 ACAAGTGACAAGGGAATTTCGC 59.707 45.455 5.37 5.37 0.00 4.70
2967 3420 6.272318 CAACAAACCAGCTGAAAAGACATTA 58.728 36.000 17.39 0.00 0.00 1.90
2968 3421 5.111293 CAACAAACCAGCTGAAAAGACATT 58.889 37.500 17.39 0.00 0.00 2.71
3056 3512 2.749621 ACTGTCAAATTTCCGGAGCATC 59.250 45.455 3.34 0.00 0.00 3.91
3074 3530 1.625315 TGGATCACCTTCACTCCACTG 59.375 52.381 0.00 0.00 32.92 3.66
3149 3605 7.898309 GCGCTATTCAGTACGAATATAAAATGG 59.102 37.037 15.60 7.72 43.94 3.16
3162 3618 2.219674 GTCATGCAGCGCTATTCAGTAC 59.780 50.000 10.99 7.33 0.00 2.73
3165 3621 1.292992 TGTCATGCAGCGCTATTCAG 58.707 50.000 10.99 0.00 0.00 3.02
3166 3622 1.957668 ATGTCATGCAGCGCTATTCA 58.042 45.000 10.99 9.31 0.00 2.57
3172 3628 3.413166 TGCTATGTCATGCAGCGC 58.587 55.556 0.00 0.00 38.15 5.92
3187 3643 1.521234 GCTGCTAGCTCACTCCTGC 60.521 63.158 17.23 3.90 38.45 4.85
3188 3644 1.143620 GGCTGCTAGCTCACTCCTG 59.856 63.158 17.23 0.00 41.99 3.86
3189 3645 0.690411 ATGGCTGCTAGCTCACTCCT 60.690 55.000 17.23 0.00 41.99 3.69
3190 3646 1.043816 TATGGCTGCTAGCTCACTCC 58.956 55.000 17.23 9.85 41.99 3.85
3191 3647 1.410517 TGTATGGCTGCTAGCTCACTC 59.589 52.381 17.23 8.78 41.99 3.51
3192 3648 1.489481 TGTATGGCTGCTAGCTCACT 58.511 50.000 17.23 0.00 41.99 3.41
3193 3649 2.315925 TTGTATGGCTGCTAGCTCAC 57.684 50.000 17.23 6.23 41.99 3.51
3194 3650 3.565764 ATTTGTATGGCTGCTAGCTCA 57.434 42.857 17.23 11.89 41.99 4.26
3195 3651 5.471456 ACAATATTTGTATGGCTGCTAGCTC 59.529 40.000 17.23 7.63 43.27 4.09
3196 3652 5.240183 CACAATATTTGTATGGCTGCTAGCT 59.760 40.000 17.23 0.00 43.23 3.32
3197 3653 5.455392 CACAATATTTGTATGGCTGCTAGC 58.545 41.667 8.10 8.10 43.23 3.42
3198 3654 5.455392 GCACAATATTTGTATGGCTGCTAG 58.545 41.667 0.00 0.00 43.23 3.42
3216 3672 7.232534 AGGTATAGAAACAAAATCAAGGCACAA 59.767 33.333 0.00 0.00 0.00 3.33
3233 3689 5.885912 GGAAACAGATTTGGCAGGTATAGAA 59.114 40.000 0.00 0.00 0.00 2.10
3237 3693 4.322057 AGGAAACAGATTTGGCAGGTAT 57.678 40.909 0.00 0.00 0.00 2.73
3238 3694 3.806949 AGGAAACAGATTTGGCAGGTA 57.193 42.857 0.00 0.00 0.00 3.08
3244 3700 7.870509 TGATTCAGATAGGAAACAGATTTGG 57.129 36.000 0.00 0.00 0.00 3.28
3278 3734 6.432783 ACCGGTCATTCATTTCATACTTTTGA 59.567 34.615 0.00 0.00 0.00 2.69
3300 3756 5.685511 CACTAACAAAAATGAACCAGAACCG 59.314 40.000 0.00 0.00 0.00 4.44
3371 3835 6.091441 GCTATGCTACCAGTACTAATGATTGC 59.909 42.308 0.00 0.00 0.00 3.56
3373 3837 6.572509 CGGCTATGCTACCAGTACTAATGATT 60.573 42.308 0.00 0.00 0.00 2.57
3377 3841 3.056749 GCGGCTATGCTACCAGTACTAAT 60.057 47.826 0.00 0.00 0.00 1.73
3384 3848 1.273606 AGTATGCGGCTATGCTACCAG 59.726 52.381 0.00 0.00 35.36 4.00
3385 3849 1.000843 CAGTATGCGGCTATGCTACCA 59.999 52.381 0.00 0.00 35.36 3.25
3386 3850 1.272490 TCAGTATGCGGCTATGCTACC 59.728 52.381 0.00 0.00 34.76 3.18
3395 3859 0.037790 GAGGGAGATCAGTATGCGGC 60.038 60.000 0.00 0.00 34.76 6.53
3396 3860 0.605589 GGAGGGAGATCAGTATGCGG 59.394 60.000 0.00 0.00 34.76 5.69
3398 3862 5.489792 TTATTGGAGGGAGATCAGTATGC 57.510 43.478 0.00 0.00 34.76 3.14
3413 3877 8.815565 TCTTGCAAATACCTATGTTTATTGGA 57.184 30.769 0.00 0.00 33.94 3.53
3422 3886 8.288208 GTGATGAGATTCTTGCAAATACCTATG 58.712 37.037 0.00 0.00 0.00 2.23
3441 3905 1.135859 GGCTTTTGTGCGAGTGATGAG 60.136 52.381 0.00 0.00 0.00 2.90
3474 3938 0.740737 CGCTGGGGCTTATTCCTTTG 59.259 55.000 0.00 0.00 36.09 2.77
3504 3968 3.443045 GGTGCAATCCCCAGCGTG 61.443 66.667 0.00 0.00 0.00 5.34
3577 4041 5.136828 TGTCTTGCCAATACTTGAAAGGAA 58.863 37.500 0.00 0.00 0.00 3.36
3603 4067 7.678947 AGTTCATTCAGTCTGGAACTAAATG 57.321 36.000 16.75 10.69 45.81 2.32
3647 4119 0.324738 TCCCTGCAGAGTAGACCTGG 60.325 60.000 17.39 4.23 32.51 4.45
3655 4127 0.901124 GACTGACATCCCTGCAGAGT 59.099 55.000 17.39 8.63 33.48 3.24
3821 4300 8.462589 TTTCTTACAATATAATGCATGCTCCA 57.537 30.769 20.33 3.58 0.00 3.86
3868 4347 3.194861 GAGTTTTTGGCCTGGAAAACAC 58.805 45.455 28.13 22.73 44.25 3.32
3912 4392 3.058160 GCTGCCGTTGCCACAGAT 61.058 61.111 0.00 0.00 36.33 2.90
3957 4437 6.491062 TCACATCAAAGTTCAATCACCTGAAT 59.509 34.615 0.00 0.00 37.63 2.57
3963 4446 9.683069 AAAATAGTCACATCAAAGTTCAATCAC 57.317 29.630 0.00 0.00 0.00 3.06
3994 4477 6.199376 TGAGATACAACACAGGGGAGTATTA 58.801 40.000 0.00 0.00 0.00 0.98
4070 4555 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
4071 4556 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
4112 4597 6.426937 ACGTTATGTCTTGTAATTTGCACTCT 59.573 34.615 0.00 0.00 0.00 3.24
4117 4602 8.276060 TGAAAACGTTATGTCTTGTAATTTGC 57.724 30.769 0.00 0.00 0.00 3.68
4155 4640 3.784338 ACAGCACACCAAAAGTCATTTG 58.216 40.909 0.00 0.00 46.54 2.32
4191 4676 6.014669 TGGTAAAAACCATCCAAAATCCTCAG 60.015 38.462 0.00 0.00 34.33 3.35
4216 4701 4.799564 TTGTTGAAACTCTTTGTGGCTT 57.200 36.364 0.00 0.00 0.00 4.35
4306 4820 4.183865 TGATACGATGCCAAAACAGAGAG 58.816 43.478 0.00 0.00 0.00 3.20
4347 4861 4.740695 GCTGTTCATATACTCGGTCTGAAC 59.259 45.833 6.75 6.75 43.67 3.18
4350 4864 4.307443 TGCTGTTCATATACTCGGTCTG 57.693 45.455 0.00 0.00 0.00 3.51
4374 4888 4.130118 CAGCGGATGAGCTTAGGTATTTT 58.870 43.478 0.00 0.00 46.80 1.82
4381 4895 1.342496 TGGATCAGCGGATGAGCTTAG 59.658 52.381 11.52 0.00 46.80 2.18
4383 4897 0.179062 GTGGATCAGCGGATGAGCTT 60.179 55.000 11.52 0.00 46.80 3.74
4445 4988 0.607489 CCAAGCACAGGACCTTGAGG 60.607 60.000 0.00 0.00 40.59 3.86
4449 4992 2.011617 AAGGCCAAGCACAGGACCTT 62.012 55.000 5.01 10.02 37.63 3.50
4482 5031 3.556004 GGGAAAATGGTCGGCAAAAATCA 60.556 43.478 0.00 0.00 0.00 2.57
4561 7898 1.873591 GCCAATACTCATTACCCGCAG 59.126 52.381 0.00 0.00 0.00 5.18
4646 7983 2.436173 GTCCTTTCTACCCTAGCTGCAT 59.564 50.000 1.02 0.00 0.00 3.96
4648 7985 1.831736 TGTCCTTTCTACCCTAGCTGC 59.168 52.381 0.00 0.00 0.00 5.25
4725 8085 9.607988 TTCGTGATGGTAAACAAGTGATTATAT 57.392 29.630 0.00 0.00 0.00 0.86
4761 8343 0.578683 CGCCATGTAATGCTCAGACG 59.421 55.000 0.00 0.00 44.97 4.18
4887 8480 9.353999 GAGTTTCCGAGCAAAATATTACAAATT 57.646 29.630 0.00 0.00 0.00 1.82
4888 8481 8.739972 AGAGTTTCCGAGCAAAATATTACAAAT 58.260 29.630 0.00 0.00 0.00 2.32
4889 8482 8.106247 AGAGTTTCCGAGCAAAATATTACAAA 57.894 30.769 0.00 0.00 0.00 2.83
4890 8483 7.681939 AGAGTTTCCGAGCAAAATATTACAA 57.318 32.000 0.00 0.00 0.00 2.41
4895 8489 5.749109 CGAGTAGAGTTTCCGAGCAAAATAT 59.251 40.000 0.00 0.00 0.00 1.28
4905 8499 1.741706 TGCTACCGAGTAGAGTTTCCG 59.258 52.381 13.28 0.00 38.29 4.30
4910 8504 3.118186 AGTCTGATGCTACCGAGTAGAGT 60.118 47.826 13.28 3.01 38.29 3.24


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

AutoCloner maintained by Alex Coulton.