Multiple sequence alignment - TraesCS3D01G185600

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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 TraesCS3D01G185600 chr3D 100.000 2744 0 0 1 2744 170929606 170932349 0.000000e+00 5068.0
1 TraesCS3D01G185600 chr3D 84.270 89 6 1 1199 1287 212868911 212868991 2.270000e-11 80.5
2 TraesCS3D01G185600 chr3A 88.030 2431 170 61 369 2744 208454401 208456765 0.000000e+00 2765.0
3 TraesCS3D01G185600 chr3B 86.562 1280 104 22 1504 2744 246504197 246505447 0.000000e+00 1349.0
4 TraesCS3D01G185600 chr3B 87.244 878 72 26 102 959 246502758 246503615 0.000000e+00 965.0
5 TraesCS3D01G185600 chr3B 86.257 553 37 22 988 1507 246503613 246504159 5.130000e-157 564.0
6 TraesCS3D01G185600 chr3B 97.436 39 1 0 1249 1287 259702050 259702012 1.760000e-07 67.6
7 TraesCS3D01G185600 chr2D 84.712 556 69 9 2191 2744 293714726 293715267 2.400000e-150 542.0
8 TraesCS3D01G185600 chr2D 84.810 79 4 1 1208 1286 291911397 291911467 3.790000e-09 73.1
9 TraesCS3D01G185600 chr5A 83.361 601 74 17 2155 2744 649236229 649235644 1.450000e-147 532.0
10 TraesCS3D01G185600 chr5A 82.833 600 79 14 2155 2744 521195074 521195659 1.460000e-142 516.0
11 TraesCS3D01G185600 chr2A 82.833 600 79 15 2155 2744 88723184 88723769 1.460000e-142 516.0
12 TraesCS3D01G185600 chr5D 83.022 589 76 16 2155 2733 382875510 382874936 1.880000e-141 512.0
13 TraesCS3D01G185600 chr5D 73.052 308 56 19 120 404 477385751 477385448 1.750000e-12 84.2
14 TraesCS3D01G185600 chr4D 81.664 649 89 16 2113 2744 300794981 300795616 1.880000e-141 512.0
15 TraesCS3D01G185600 chr4B 82.667 600 79 16 2155 2744 529353110 529352526 2.440000e-140 508.0
16 TraesCS3D01G185600 chr4A 81.510 649 88 18 2113 2744 477951557 477952190 3.150000e-139 505.0
17 TraesCS3D01G185600 chr4A 82.812 64 10 1 162 224 40868053 40867990 3.820000e-04 56.5
18 TraesCS3D01G185600 chr1B 82.333 600 83 14 2155 2744 405392375 405391789 1.470000e-137 499.0
19 TraesCS3D01G185600 chr7A 82.178 101 14 3 127 226 677660144 677660241 1.750000e-12 84.2
20 TraesCS3D01G185600 chr7A 97.436 39 1 0 1249 1287 238551311 238551273 1.760000e-07 67.6
21 TraesCS3D01G185600 chr7A 97.368 38 1 0 1250 1287 327312285 327312322 6.340000e-07 65.8
22 TraesCS3D01G185600 chr6D 87.879 66 6 2 162 225 36584190 36584255 2.930000e-10 76.8
23 TraesCS3D01G185600 chr6B 87.879 66 6 2 162 226 84859931 84859995 2.930000e-10 76.8
24 TraesCS3D01G185600 chr6B 97.619 42 1 0 1246 1287 471136074 471136115 3.790000e-09 73.1
25 TraesCS3D01G185600 chr6A 97.368 38 1 0 1250 1287 155935681 155935718 6.340000e-07 65.8
26 TraesCS3D01G185600 chr6A 74.194 186 32 12 125 295 150921978 150922162 2.280000e-06 63.9
27 TraesCS3D01G185600 chr1D 78.182 110 18 4 132 239 3184794 3184899 6.340000e-07 65.8
28 TraesCS3D01G185600 chr5B 81.538 65 11 1 163 226 689332282 689332346 5.000000e-03 52.8


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 TraesCS3D01G185600 chr3D 170929606 170932349 2743 False 5068.000000 5068 100.000000 1 2744 1 chr3D.!!$F1 2743
1 TraesCS3D01G185600 chr3A 208454401 208456765 2364 False 2765.000000 2765 88.030000 369 2744 1 chr3A.!!$F1 2375
2 TraesCS3D01G185600 chr3B 246502758 246505447 2689 False 959.333333 1349 86.687667 102 2744 3 chr3B.!!$F1 2642
3 TraesCS3D01G185600 chr2D 293714726 293715267 541 False 542.000000 542 84.712000 2191 2744 1 chr2D.!!$F2 553
4 TraesCS3D01G185600 chr5A 649235644 649236229 585 True 532.000000 532 83.361000 2155 2744 1 chr5A.!!$R1 589
5 TraesCS3D01G185600 chr5A 521195074 521195659 585 False 516.000000 516 82.833000 2155 2744 1 chr5A.!!$F1 589
6 TraesCS3D01G185600 chr2A 88723184 88723769 585 False 516.000000 516 82.833000 2155 2744 1 chr2A.!!$F1 589
7 TraesCS3D01G185600 chr5D 382874936 382875510 574 True 512.000000 512 83.022000 2155 2733 1 chr5D.!!$R1 578
8 TraesCS3D01G185600 chr4D 300794981 300795616 635 False 512.000000 512 81.664000 2113 2744 1 chr4D.!!$F1 631
9 TraesCS3D01G185600 chr4B 529352526 529353110 584 True 508.000000 508 82.667000 2155 2744 1 chr4B.!!$R1 589
10 TraesCS3D01G185600 chr4A 477951557 477952190 633 False 505.000000 505 81.510000 2113 2744 1 chr4A.!!$F1 631
11 TraesCS3D01G185600 chr1B 405391789 405392375 586 True 499.000000 499 82.333000 2155 2744 1 chr1B.!!$R1 589

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
77 78 0.030908 GATGGAGGTCGACATCGTCC 59.969 60.0 22.49 18.34 45.53 4.79 F
1323 1387 0.170561 CTTCTGCAGGTACGTACGCT 59.829 55.0 21.14 15.82 0.00 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1343 1407 0.179059 TCGCACCAAGCAAGAACAGA 60.179 50.000 0.00 0.00 46.13 3.41 R
2514 2677 1.465387 CGTTTACAGGCGCCAACAATA 59.535 47.619 31.54 10.13 0.00 1.90 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
35 36 2.106844 GGCATTGGACCGATGTTCC 58.893 57.895 20.83 11.98 0.00 3.62
36 37 0.394352 GGCATTGGACCGATGTTCCT 60.394 55.000 20.83 0.00 0.00 3.36
37 38 0.734889 GCATTGGACCGATGTTCCTG 59.265 55.000 20.83 0.00 0.00 3.86
38 39 0.734889 CATTGGACCGATGTTCCTGC 59.265 55.000 13.07 0.00 0.00 4.85
39 40 0.394352 ATTGGACCGATGTTCCTGCC 60.394 55.000 0.00 0.00 0.00 4.85
40 41 2.124695 GGACCGATGTTCCTGCCC 60.125 66.667 0.00 0.00 0.00 5.36
41 42 2.668632 GACCGATGTTCCTGCCCA 59.331 61.111 0.00 0.00 0.00 5.36
42 43 1.745489 GACCGATGTTCCTGCCCAC 60.745 63.158 0.00 0.00 0.00 4.61
43 44 2.819595 CCGATGTTCCTGCCCACG 60.820 66.667 0.00 0.00 0.00 4.94
44 45 2.047274 CGATGTTCCTGCCCACGT 60.047 61.111 0.00 0.00 0.00 4.49
45 46 2.390599 CGATGTTCCTGCCCACGTG 61.391 63.158 9.08 9.08 0.00 4.49
46 47 1.003839 GATGTTCCTGCCCACGTGA 60.004 57.895 19.30 0.00 0.00 4.35
47 48 1.003355 ATGTTCCTGCCCACGTGAG 60.003 57.895 19.30 4.39 0.00 3.51
48 49 3.050275 GTTCCTGCCCACGTGAGC 61.050 66.667 19.30 17.55 0.00 4.26
49 50 4.680237 TTCCTGCCCACGTGAGCG 62.680 66.667 19.30 11.83 44.93 5.03
55 56 4.778415 CCCACGTGAGCGGTCGAG 62.778 72.222 19.30 8.77 43.45 4.04
56 57 4.778415 CCACGTGAGCGGTCGAGG 62.778 72.222 19.30 3.95 43.45 4.63
57 58 3.733960 CACGTGAGCGGTCGAGGA 61.734 66.667 10.90 0.00 43.45 3.71
58 59 3.432588 ACGTGAGCGGTCGAGGAG 61.433 66.667 10.46 1.90 43.45 3.69
59 60 3.125573 CGTGAGCGGTCGAGGAGA 61.126 66.667 10.46 0.00 0.00 3.71
60 61 2.473760 CGTGAGCGGTCGAGGAGAT 61.474 63.158 10.46 0.00 0.00 2.75
61 62 1.064946 GTGAGCGGTCGAGGAGATG 59.935 63.158 10.46 0.00 0.00 2.90
62 63 2.121538 TGAGCGGTCGAGGAGATGG 61.122 63.158 10.46 0.00 0.00 3.51
63 64 1.824329 GAGCGGTCGAGGAGATGGA 60.824 63.158 0.00 0.00 0.00 3.41
64 65 1.791103 GAGCGGTCGAGGAGATGGAG 61.791 65.000 0.00 0.00 0.00 3.86
65 66 2.851071 GCGGTCGAGGAGATGGAGG 61.851 68.421 0.00 0.00 0.00 4.30
66 67 1.454111 CGGTCGAGGAGATGGAGGT 60.454 63.158 0.00 0.00 0.00 3.85
67 68 1.448922 CGGTCGAGGAGATGGAGGTC 61.449 65.000 0.00 0.00 0.00 3.85
68 69 1.448922 GGTCGAGGAGATGGAGGTCG 61.449 65.000 0.00 0.00 0.00 4.79
69 70 0.464013 GTCGAGGAGATGGAGGTCGA 60.464 60.000 0.00 0.00 37.32 4.20
70 71 0.464013 TCGAGGAGATGGAGGTCGAC 60.464 60.000 7.13 7.13 34.86 4.20
71 72 0.748367 CGAGGAGATGGAGGTCGACA 60.748 60.000 18.91 0.00 32.32 4.35
72 73 1.698506 GAGGAGATGGAGGTCGACAT 58.301 55.000 18.91 11.04 0.00 3.06
73 74 1.611491 GAGGAGATGGAGGTCGACATC 59.389 57.143 21.44 21.44 42.87 3.06
74 75 0.312416 GGAGATGGAGGTCGACATCG 59.688 60.000 22.49 0.00 46.13 3.84
75 76 1.025812 GAGATGGAGGTCGACATCGT 58.974 55.000 22.49 14.35 46.13 3.73
76 77 1.002251 GAGATGGAGGTCGACATCGTC 60.002 57.143 22.49 21.04 46.13 4.20
77 78 0.030908 GATGGAGGTCGACATCGTCC 59.969 60.000 22.49 18.34 45.53 4.79
81 82 4.420143 GGTCGACATCGTCCATGG 57.580 61.111 18.91 4.97 44.77 3.66
82 83 1.227263 GGTCGACATCGTCCATGGG 60.227 63.158 18.91 0.00 44.77 4.00
83 84 1.883084 GTCGACATCGTCCATGGGC 60.883 63.158 13.02 9.73 40.80 5.36
84 85 2.588877 CGACATCGTCCATGGGCC 60.589 66.667 11.65 0.00 36.72 5.80
85 86 2.911143 GACATCGTCCATGGGCCT 59.089 61.111 11.65 0.00 36.72 5.19
86 87 1.524621 GACATCGTCCATGGGCCTG 60.525 63.158 11.65 11.33 36.72 4.85
87 88 2.257409 GACATCGTCCATGGGCCTGT 62.257 60.000 16.81 16.81 36.72 4.00
88 89 1.820906 CATCGTCCATGGGCCTGTG 60.821 63.158 11.65 3.20 0.00 3.66
89 90 3.047807 ATCGTCCATGGGCCTGTGG 62.048 63.158 11.65 18.81 36.82 4.17
99 100 3.903783 GCCTGTGGCGATGCTAAA 58.096 55.556 0.00 0.00 39.62 1.85
100 101 2.408333 GCCTGTGGCGATGCTAAAT 58.592 52.632 0.00 0.00 39.62 1.40
101 102 0.308993 GCCTGTGGCGATGCTAAATC 59.691 55.000 0.00 0.00 39.62 2.17
102 103 0.947244 CCTGTGGCGATGCTAAATCC 59.053 55.000 0.00 0.00 0.00 3.01
103 104 1.667236 CTGTGGCGATGCTAAATCCA 58.333 50.000 0.00 0.00 0.00 3.41
104 105 2.016318 CTGTGGCGATGCTAAATCCAA 58.984 47.619 0.00 0.00 0.00 3.53
105 106 2.423185 CTGTGGCGATGCTAAATCCAAA 59.577 45.455 0.00 0.00 0.00 3.28
106 107 2.822561 TGTGGCGATGCTAAATCCAAAA 59.177 40.909 0.00 0.00 0.00 2.44
107 108 3.256879 TGTGGCGATGCTAAATCCAAAAA 59.743 39.130 0.00 0.00 0.00 1.94
108 109 3.612423 GTGGCGATGCTAAATCCAAAAAC 59.388 43.478 0.00 0.00 0.00 2.43
109 110 3.509575 TGGCGATGCTAAATCCAAAAACT 59.490 39.130 0.00 0.00 0.00 2.66
170 171 7.805071 TGTTTACAAAGTTTGGCAAATGTTTTG 59.195 29.630 27.31 27.31 34.12 2.44
172 173 6.566197 ACAAAGTTTGGCAAATGTTTTGAA 57.434 29.167 31.37 6.50 34.12 2.69
182 184 5.035443 GCAAATGTTTTGAATGCTTGCAAA 58.965 33.333 0.00 1.61 38.03 3.68
196 198 4.178545 CTTGCAAAGTTTCATCCGGAAT 57.821 40.909 9.01 0.00 39.70 3.01
197 199 3.574284 TGCAAAGTTTCATCCGGAATG 57.426 42.857 9.01 7.95 34.91 2.67
199 201 2.879826 CAAAGTTTCATCCGGAATGGC 58.120 47.619 9.01 0.00 37.80 4.40
200 202 2.214376 AAGTTTCATCCGGAATGGCA 57.786 45.000 9.01 0.00 37.80 4.92
201 203 2.442236 AGTTTCATCCGGAATGGCAT 57.558 45.000 9.01 0.00 37.80 4.40
203 205 2.689983 AGTTTCATCCGGAATGGCATTC 59.310 45.455 28.02 28.02 37.80 2.67
204 206 1.308047 TTCATCCGGAATGGCATTCG 58.692 50.000 28.48 23.10 40.17 3.34
205 207 0.180171 TCATCCGGAATGGCATTCGT 59.820 50.000 28.48 14.81 40.17 3.85
206 208 0.308684 CATCCGGAATGGCATTCGTG 59.691 55.000 28.48 23.28 40.17 4.35
212 215 2.095263 CGGAATGGCATTCGTGAAAGTT 60.095 45.455 28.48 0.00 40.17 2.66
219 222 2.797792 GCATTCGTGAAAGTTGTGGCAA 60.798 45.455 0.00 0.00 0.00 4.52
265 268 7.378181 AGTTAATTTGGATCGCTGATTTTGTT 58.622 30.769 0.00 0.00 0.00 2.83
266 269 8.519526 AGTTAATTTGGATCGCTGATTTTGTTA 58.480 29.630 0.00 0.00 0.00 2.41
271 274 7.579589 TTGGATCGCTGATTTTGTTATTTTG 57.420 32.000 0.00 0.00 0.00 2.44
276 279 4.447054 CGCTGATTTTGTTATTTTGCCACA 59.553 37.500 0.00 0.00 0.00 4.17
281 284 8.273780 TGATTTTGTTATTTTGCCACAACTTT 57.726 26.923 0.00 0.00 30.12 2.66
300 303 8.084073 ACAACTTTCACAAATGTCATTCTATGG 58.916 33.333 0.00 0.00 0.00 2.74
301 304 7.765695 ACTTTCACAAATGTCATTCTATGGT 57.234 32.000 0.00 0.00 0.00 3.55
306 309 7.592938 TCACAAATGTCATTCTATGGTGAAAC 58.407 34.615 0.00 0.00 30.63 2.78
319 322 7.669427 TCTATGGTGAAACTTTGCAATCATTT 58.331 30.769 0.00 1.10 36.74 2.32
326 329 8.124199 GTGAAACTTTGCAATCATTTGAAACAT 58.876 29.630 0.00 0.00 34.60 2.71
433 436 1.202533 AGGTAATCCGCGTCCTGATTG 60.203 52.381 15.68 0.00 39.05 2.67
471 474 2.498885 TGAGAGATCGATGGGCATATGG 59.501 50.000 0.54 0.00 0.00 2.74
553 557 6.553100 TGAGACCTGACAAATAATTGGGTTTT 59.447 34.615 0.00 0.00 41.01 2.43
554 558 6.758254 AGACCTGACAAATAATTGGGTTTTG 58.242 36.000 0.00 0.00 41.01 2.44
702 711 1.850345 GGTGATCCCATCCCAGGTTTA 59.150 52.381 0.00 0.00 0.00 2.01
772 788 1.353804 GCCAACAAAAGTCGTGCGA 59.646 52.632 0.00 0.00 0.00 5.10
812 828 6.425504 CAGAGCAAAAGAGGCGATAAATAAG 58.574 40.000 0.00 0.00 36.08 1.73
868 884 3.386402 TGTGAACAGTGTATCCACAGTCA 59.614 43.478 17.00 4.44 44.39 3.41
869 885 4.141824 TGTGAACAGTGTATCCACAGTCAA 60.142 41.667 17.00 1.24 44.39 3.18
870 886 4.814234 GTGAACAGTGTATCCACAGTCAAA 59.186 41.667 14.65 0.00 44.39 2.69
871 887 4.814234 TGAACAGTGTATCCACAGTCAAAC 59.186 41.667 0.00 0.00 44.39 2.93
872 888 3.740115 ACAGTGTATCCACAGTCAAACC 58.260 45.455 0.00 0.00 44.39 3.27
873 889 2.736721 CAGTGTATCCACAGTCAAACCG 59.263 50.000 0.00 0.00 44.39 4.44
874 890 2.073816 GTGTATCCACAGTCAAACCGG 58.926 52.381 0.00 0.00 41.44 5.28
895 911 5.815964 GGAAACATTTGCGTTTTCGTATT 57.184 34.783 0.00 0.00 46.03 1.89
897 913 4.623122 AACATTTGCGTTTTCGTATTGC 57.377 36.364 0.00 0.00 46.03 3.56
898 914 2.983803 ACATTTGCGTTTTCGTATTGCC 59.016 40.909 0.00 0.00 46.03 4.52
903 934 0.875728 CGTTTTCGTATTGCCCACCA 59.124 50.000 0.00 0.00 38.65 4.17
930 961 1.217882 CAGACGGCTCTTTGAACGTT 58.782 50.000 0.00 0.00 39.95 3.99
935 966 0.660300 GGCTCTTTGAACGTTTGCGG 60.660 55.000 0.46 0.00 43.45 5.69
1002 1033 2.747460 CACCGCCACCCACAGATG 60.747 66.667 0.00 0.00 0.00 2.90
1086 1117 1.603802 ACTGTGCACAAGTCAAATCGG 59.396 47.619 21.98 7.42 0.00 4.18
1125 1160 3.004106 AGCAAAGAAGCACAACACATCTC 59.996 43.478 0.00 0.00 36.85 2.75
1127 1162 4.534168 CAAAGAAGCACAACACATCTCTG 58.466 43.478 0.00 0.00 0.00 3.35
1161 1202 3.540014 CGTGCGCGCAAGAGAGAG 61.540 66.667 38.03 18.22 40.82 3.20
1162 1203 2.126307 GTGCGCGCAAGAGAGAGA 60.126 61.111 38.24 6.62 40.82 3.10
1163 1204 2.157701 GTGCGCGCAAGAGAGAGAG 61.158 63.158 38.24 0.00 40.82 3.20
1164 1205 2.335712 TGCGCGCAAGAGAGAGAGA 61.336 57.895 34.66 2.51 40.82 3.10
1165 1206 1.586042 GCGCGCAAGAGAGAGAGAG 60.586 63.158 29.10 0.00 40.82 3.20
1166 1207 1.987704 GCGCGCAAGAGAGAGAGAGA 61.988 60.000 29.10 0.00 40.82 3.10
1174 1215 4.141846 GCAAGAGAGAGAGAGAGAGAGAGA 60.142 50.000 0.00 0.00 0.00 3.10
1246 1310 4.595538 AACGACAACGGCGCCTCA 62.596 61.111 26.68 0.00 44.46 3.86
1318 1382 2.261671 CGGCTTCTGCAGGTACGT 59.738 61.111 15.13 0.00 41.91 3.57
1321 1385 0.801067 GGCTTCTGCAGGTACGTACG 60.801 60.000 18.98 15.01 41.91 3.67
1322 1386 1.411493 GCTTCTGCAGGTACGTACGC 61.411 60.000 16.72 17.32 39.41 4.42
1323 1387 0.170561 CTTCTGCAGGTACGTACGCT 59.829 55.000 21.14 15.82 0.00 5.07
1324 1388 1.399440 CTTCTGCAGGTACGTACGCTA 59.601 52.381 21.14 4.31 0.00 4.26
1325 1389 1.452110 TCTGCAGGTACGTACGCTAA 58.548 50.000 21.14 10.26 0.00 3.09
1326 1390 1.131126 TCTGCAGGTACGTACGCTAAC 59.869 52.381 21.14 11.15 0.00 2.34
1327 1391 1.131883 CTGCAGGTACGTACGCTAACT 59.868 52.381 21.14 11.96 0.00 2.24
1329 1393 2.095853 TGCAGGTACGTACGCTAACTAC 59.904 50.000 21.14 9.71 0.00 2.73
1330 1394 2.847254 GCAGGTACGTACGCTAACTACG 60.847 54.545 16.72 5.70 42.22 3.51
1338 1402 3.689411 GCTAACTACGCGAGCACC 58.311 61.111 15.93 0.00 36.20 5.01
1339 1403 2.222217 GCTAACTACGCGAGCACCG 61.222 63.158 15.93 0.00 42.21 4.94
1340 1404 1.585521 CTAACTACGCGAGCACCGG 60.586 63.158 15.93 0.00 39.04 5.28
1366 1433 3.058160 CTTGCTTGGTGCGAGGGG 61.058 66.667 0.00 0.00 46.81 4.79
1371 1438 1.528309 CTTGGTGCGAGGGGTTGTT 60.528 57.895 0.00 0.00 0.00 2.83
1382 1449 3.684788 CGAGGGGTTGTTTTACAGATCAG 59.315 47.826 0.00 0.00 0.00 2.90
1390 1457 4.627058 TGTTTTACAGATCAGTCGCTTCA 58.373 39.130 0.00 0.00 0.00 3.02
1393 1460 4.718940 TTACAGATCAGTCGCTTCATCA 57.281 40.909 0.00 0.00 0.00 3.07
1398 1465 3.387374 AGATCAGTCGCTTCATCAATCCT 59.613 43.478 0.00 0.00 0.00 3.24
1408 1475 0.661552 CATCAATCCTTGCAGCGAGG 59.338 55.000 21.92 21.92 36.39 4.63
1409 1476 0.543277 ATCAATCCTTGCAGCGAGGA 59.457 50.000 30.60 30.60 46.80 3.71
1418 1485 2.575993 CAGCGAGGACTGACCCTG 59.424 66.667 0.00 0.00 40.25 4.45
1419 1486 2.681778 AGCGAGGACTGACCCTGG 60.682 66.667 0.00 0.00 40.05 4.45
1438 1505 4.161295 CGGAAGGATGGAGCGGCA 62.161 66.667 1.45 0.00 0.00 5.69
1460 1527 4.379243 CGCTGGACAAGGCCGAGT 62.379 66.667 0.00 0.00 0.00 4.18
1477 1544 1.008538 GTCACAGGTTTGCCTTGCG 60.009 57.895 0.00 0.00 44.18 4.85
1493 1560 3.610669 CGCCTCTCTCCATCCCCG 61.611 72.222 0.00 0.00 0.00 5.73
1500 1567 1.152419 TCTCCATCCCCGCCGATTA 60.152 57.895 0.00 0.00 0.00 1.75
1556 1664 2.787994 AGCAAAACTGGAGTGGAGATG 58.212 47.619 0.00 0.00 0.00 2.90
1581 1689 3.058224 CCTTTTCTGTTTCATCCGTGGTC 60.058 47.826 0.00 0.00 0.00 4.02
1713 1821 2.515991 CGGTATGGCGCCAATGGT 60.516 61.111 36.33 20.30 0.00 3.55
1891 1999 3.632080 CACCACCACCCGTGCCTA 61.632 66.667 0.00 0.00 41.53 3.93
1947 2055 2.420568 CCGTAGGCCCGTAGCTTCA 61.421 63.158 0.00 0.00 46.14 3.02
1952 2060 1.272807 AGGCCCGTAGCTTCACTTTA 58.727 50.000 0.00 0.00 43.05 1.85
1960 2068 3.673809 CGTAGCTTCACTTTACGCTTTCT 59.326 43.478 0.00 0.00 34.55 2.52
1991 2107 0.109226 GTCTTCCGCTACTGCTTCGT 60.109 55.000 0.00 0.00 36.97 3.85
1993 2109 0.992802 CTTCCGCTACTGCTTCGTTC 59.007 55.000 0.00 0.00 36.97 3.95
1994 2110 0.731514 TTCCGCTACTGCTTCGTTCG 60.732 55.000 0.00 0.00 36.97 3.95
1996 2112 1.801913 CGCTACTGCTTCGTTCGCT 60.802 57.895 0.00 0.00 36.97 4.93
1997 2113 1.344942 CGCTACTGCTTCGTTCGCTT 61.345 55.000 0.00 0.00 36.97 4.68
1998 2114 0.790814 GCTACTGCTTCGTTCGCTTT 59.209 50.000 0.00 0.00 36.03 3.51
1999 2115 1.194772 GCTACTGCTTCGTTCGCTTTT 59.805 47.619 0.00 0.00 36.03 2.27
2000 2116 2.349532 GCTACTGCTTCGTTCGCTTTTT 60.350 45.455 0.00 0.00 36.03 1.94
2055 2171 0.610232 GCTGCTGGACCTGGACATTT 60.610 55.000 0.00 0.00 0.00 2.32
2092 2213 2.782615 GTATGGCGCGTGTGTTCC 59.217 61.111 8.43 0.00 0.00 3.62
2153 2281 2.096013 GCGGGATTCTGCAGAACTAAAC 59.904 50.000 30.66 16.54 44.43 2.01
2166 2294 6.205464 TGCAGAACTAAACAAATTCTCTCAGG 59.795 38.462 0.00 0.00 30.17 3.86
2186 2314 5.104402 TCAGGATCTGCTTTCCACATAATCA 60.104 40.000 0.00 0.00 35.59 2.57
2187 2315 5.591472 CAGGATCTGCTTTCCACATAATCAA 59.409 40.000 0.00 0.00 35.59 2.57
2189 2317 4.944962 TCTGCTTTCCACATAATCAACG 57.055 40.909 0.00 0.00 0.00 4.10
2211 2339 4.686554 CGGTCGAGTTCTTTTCTGAGATTT 59.313 41.667 0.00 0.00 0.00 2.17
2243 2371 2.020720 TGTGGATTGAGTTGTGCGTTT 58.979 42.857 0.00 0.00 0.00 3.60
2253 2381 4.142578 TGAGTTGTGCGTTTAAATGTGTGT 60.143 37.500 9.12 0.00 0.00 3.72
2416 2551 3.280295 TGTTCGTTACAAATGTGTGGGT 58.720 40.909 0.00 0.00 38.82 4.51
2417 2552 3.065510 TGTTCGTTACAAATGTGTGGGTG 59.934 43.478 0.00 0.00 38.82 4.61
2418 2553 2.920524 TCGTTACAAATGTGTGGGTGT 58.079 42.857 0.00 0.00 38.82 4.16
2438 2600 7.073883 GGGTGTGAACTAAAAATAGAACGAAC 58.926 38.462 0.00 0.00 0.00 3.95
2467 2630 5.104776 TCAAGGTATGAGAGTAGCAGCAATT 60.105 40.000 0.00 0.00 33.04 2.32
2514 2677 4.506271 GCCATCATCATCTTCTGGTGGTAT 60.506 45.833 3.96 0.00 36.56 2.73
2516 2679 6.577838 GCCATCATCATCTTCTGGTGGTATAT 60.578 42.308 3.96 0.00 36.56 0.86
2524 2687 2.912771 TCTGGTGGTATATTGTTGGCG 58.087 47.619 0.00 0.00 0.00 5.69
2548 2711 1.201414 GTAAACGGCAATGGAGGTTGG 59.799 52.381 0.00 0.00 0.00 3.77
2557 2720 2.260844 ATGGAGGTTGGACATATGCG 57.739 50.000 1.58 0.00 0.00 4.73
2560 2723 1.209128 GAGGTTGGACATATGCGTCG 58.791 55.000 1.58 0.00 36.73 5.12
2574 2737 0.027586 GCGTCGTTGTCAAACTTGCT 59.972 50.000 0.00 0.00 33.87 3.91
2617 2780 6.992123 ACTTGCTATCACGAATCCAATTATGA 59.008 34.615 0.00 0.00 0.00 2.15
2621 2784 7.879677 TGCTATCACGAATCCAATTATGAAGAT 59.120 33.333 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.394352 AGGAACATCGGTCCAATGCC 60.394 55.000 0.06 0.00 0.00 4.40
18 19 0.734889 CAGGAACATCGGTCCAATGC 59.265 55.000 0.06 0.00 0.00 3.56
19 20 0.734889 GCAGGAACATCGGTCCAATG 59.265 55.000 0.06 0.00 0.00 2.82
20 21 0.394352 GGCAGGAACATCGGTCCAAT 60.394 55.000 0.06 0.00 0.00 3.16
21 22 1.002624 GGCAGGAACATCGGTCCAA 60.003 57.895 0.06 0.00 0.00 3.53
22 23 2.668632 GGCAGGAACATCGGTCCA 59.331 61.111 0.06 0.00 0.00 4.02
23 24 2.124695 GGGCAGGAACATCGGTCC 60.125 66.667 0.00 0.00 0.00 4.46
24 25 1.745489 GTGGGCAGGAACATCGGTC 60.745 63.158 0.00 0.00 0.00 4.79
25 26 2.351276 GTGGGCAGGAACATCGGT 59.649 61.111 0.00 0.00 0.00 4.69
26 27 2.819595 CGTGGGCAGGAACATCGG 60.820 66.667 0.00 0.00 0.00 4.18
27 28 2.047274 ACGTGGGCAGGAACATCG 60.047 61.111 0.00 0.00 0.00 3.84
28 29 1.003839 TCACGTGGGCAGGAACATC 60.004 57.895 17.00 0.00 0.00 3.06
29 30 1.003355 CTCACGTGGGCAGGAACAT 60.003 57.895 17.00 0.00 0.00 2.71
30 31 2.425592 CTCACGTGGGCAGGAACA 59.574 61.111 17.00 0.00 0.00 3.18
31 32 3.050275 GCTCACGTGGGCAGGAAC 61.050 66.667 34.79 3.85 0.00 3.62
32 33 4.680237 CGCTCACGTGGGCAGGAA 62.680 66.667 37.31 5.92 33.53 3.36
38 39 4.778415 CTCGACCGCTCACGTGGG 62.778 72.222 17.00 14.73 45.28 4.61
39 40 4.778415 CCTCGACCGCTCACGTGG 62.778 72.222 17.00 7.71 46.44 4.94
40 41 3.669036 CTCCTCGACCGCTCACGTG 62.669 68.421 9.94 9.94 37.70 4.49
41 42 3.432588 CTCCTCGACCGCTCACGT 61.433 66.667 0.00 0.00 37.70 4.49
42 43 2.473760 ATCTCCTCGACCGCTCACG 61.474 63.158 0.00 0.00 39.67 4.35
43 44 1.064946 CATCTCCTCGACCGCTCAC 59.935 63.158 0.00 0.00 0.00 3.51
44 45 2.121538 CCATCTCCTCGACCGCTCA 61.122 63.158 0.00 0.00 0.00 4.26
45 46 1.791103 CTCCATCTCCTCGACCGCTC 61.791 65.000 0.00 0.00 0.00 5.03
46 47 1.826054 CTCCATCTCCTCGACCGCT 60.826 63.158 0.00 0.00 0.00 5.52
47 48 2.725008 CTCCATCTCCTCGACCGC 59.275 66.667 0.00 0.00 0.00 5.68
48 49 1.448922 GACCTCCATCTCCTCGACCG 61.449 65.000 0.00 0.00 0.00 4.79
49 50 1.448922 CGACCTCCATCTCCTCGACC 61.449 65.000 0.00 0.00 0.00 4.79
50 51 0.464013 TCGACCTCCATCTCCTCGAC 60.464 60.000 0.00 0.00 0.00 4.20
51 52 0.464013 GTCGACCTCCATCTCCTCGA 60.464 60.000 3.51 0.00 0.00 4.04
52 53 0.748367 TGTCGACCTCCATCTCCTCG 60.748 60.000 14.12 0.00 0.00 4.63
53 54 1.611491 GATGTCGACCTCCATCTCCTC 59.389 57.143 14.12 0.00 35.63 3.71
54 55 1.698506 GATGTCGACCTCCATCTCCT 58.301 55.000 14.12 0.00 35.63 3.69
55 56 0.312416 CGATGTCGACCTCCATCTCC 59.688 60.000 14.12 0.00 43.02 3.71
56 57 1.002251 GACGATGTCGACCTCCATCTC 60.002 57.143 14.12 5.51 43.02 2.75
57 58 1.025812 GACGATGTCGACCTCCATCT 58.974 55.000 14.12 0.00 43.02 2.90
58 59 3.553597 GACGATGTCGACCTCCATC 57.446 57.895 14.12 8.33 43.02 3.51
65 66 1.883084 GCCCATGGACGATGTCGAC 60.883 63.158 15.22 9.11 43.02 4.20
66 67 2.499205 GCCCATGGACGATGTCGA 59.501 61.111 15.22 0.00 43.02 4.20
67 68 2.588877 GGCCCATGGACGATGTCG 60.589 66.667 15.22 0.11 46.33 4.35
68 69 1.524621 CAGGCCCATGGACGATGTC 60.525 63.158 15.22 0.00 34.63 3.06
69 70 2.300967 ACAGGCCCATGGACGATGT 61.301 57.895 15.22 7.56 34.63 3.06
70 71 1.820906 CACAGGCCCATGGACGATG 60.821 63.158 15.22 6.84 34.63 3.84
71 72 2.591753 CACAGGCCCATGGACGAT 59.408 61.111 15.22 0.00 34.63 3.73
72 73 3.716195 CCACAGGCCCATGGACGA 61.716 66.667 15.22 0.00 38.34 4.20
82 83 0.308993 GATTTAGCATCGCCACAGGC 59.691 55.000 0.00 0.00 46.75 4.85
83 84 0.947244 GGATTTAGCATCGCCACAGG 59.053 55.000 0.00 0.00 0.00 4.00
84 85 1.667236 TGGATTTAGCATCGCCACAG 58.333 50.000 0.00 0.00 0.00 3.66
85 86 2.121291 TTGGATTTAGCATCGCCACA 57.879 45.000 0.00 0.00 0.00 4.17
86 87 3.502191 TTTTGGATTTAGCATCGCCAC 57.498 42.857 0.00 0.00 0.00 5.01
87 88 3.509575 AGTTTTTGGATTTAGCATCGCCA 59.490 39.130 0.00 0.00 0.00 5.69
88 89 4.110036 AGTTTTTGGATTTAGCATCGCC 57.890 40.909 0.00 0.00 0.00 5.54
89 90 7.755582 AATTAGTTTTTGGATTTAGCATCGC 57.244 32.000 0.00 0.00 0.00 4.58
142 143 6.836953 ACATTTGCCAAACTTTGTAAACAAC 58.163 32.000 0.00 0.00 35.28 3.32
143 144 7.440523 AACATTTGCCAAACTTTGTAAACAA 57.559 28.000 0.00 0.00 0.00 2.83
145 146 8.017946 TCAAAACATTTGCCAAACTTTGTAAAC 58.982 29.630 15.31 0.00 0.00 2.01
146 147 8.099364 TCAAAACATTTGCCAAACTTTGTAAA 57.901 26.923 15.31 3.04 0.00 2.01
148 149 7.672983 TTCAAAACATTTGCCAAACTTTGTA 57.327 28.000 15.31 7.98 0.00 2.41
160 161 6.259638 ACTTTGCAAGCATTCAAAACATTTG 58.740 32.000 0.00 0.00 32.55 2.32
170 171 3.365820 CGGATGAAACTTTGCAAGCATTC 59.634 43.478 0.00 6.26 0.00 2.67
172 173 2.353011 CCGGATGAAACTTTGCAAGCAT 60.353 45.455 0.00 0.10 0.00 3.79
182 184 2.442236 ATGCCATTCCGGATGAAACT 57.558 45.000 4.15 0.00 38.03 2.66
192 194 3.244976 CAACTTTCACGAATGCCATTCC 58.755 45.455 11.68 0.00 35.89 3.01
196 198 1.336440 CCACAACTTTCACGAATGCCA 59.664 47.619 0.00 0.00 0.00 4.92
197 199 1.930371 GCCACAACTTTCACGAATGCC 60.930 52.381 0.00 0.00 0.00 4.40
199 201 2.772568 TGCCACAACTTTCACGAATG 57.227 45.000 0.00 0.00 0.00 2.67
200 202 3.791973 TTTGCCACAACTTTCACGAAT 57.208 38.095 0.00 0.00 0.00 3.34
201 203 3.577649 TTTTGCCACAACTTTCACGAA 57.422 38.095 0.00 0.00 0.00 3.85
240 243 6.924111 ACAAAATCAGCGATCCAAATTAACT 58.076 32.000 0.00 0.00 0.00 2.24
241 244 7.581011 AACAAAATCAGCGATCCAAATTAAC 57.419 32.000 0.00 0.00 0.00 2.01
243 246 9.868277 AAATAACAAAATCAGCGATCCAAATTA 57.132 25.926 0.00 0.00 0.00 1.40
244 247 8.776376 AAATAACAAAATCAGCGATCCAAATT 57.224 26.923 0.00 0.00 0.00 1.82
252 255 4.683781 GTGGCAAAATAACAAAATCAGCGA 59.316 37.500 0.00 0.00 0.00 4.93
253 256 4.447054 TGTGGCAAAATAACAAAATCAGCG 59.553 37.500 0.00 0.00 0.00 5.18
255 258 7.481275 AGTTGTGGCAAAATAACAAAATCAG 57.519 32.000 0.00 0.00 35.70 2.90
265 268 6.820656 ACATTTGTGAAAGTTGTGGCAAAATA 59.179 30.769 0.00 0.00 31.10 1.40
266 269 5.647225 ACATTTGTGAAAGTTGTGGCAAAAT 59.353 32.000 0.00 0.00 31.10 1.82
271 274 3.779759 TGACATTTGTGAAAGTTGTGGC 58.220 40.909 0.00 0.00 0.00 5.01
276 279 8.084073 CACCATAGAATGACATTTGTGAAAGTT 58.916 33.333 1.39 0.00 0.00 2.66
281 284 7.448161 AGTTTCACCATAGAATGACATTTGTGA 59.552 33.333 1.39 7.89 0.00 3.58
300 303 7.462731 TGTTTCAAATGATTGCAAAGTTTCAC 58.537 30.769 1.71 3.02 36.45 3.18
301 304 7.606858 TGTTTCAAATGATTGCAAAGTTTCA 57.393 28.000 1.71 2.55 36.45 2.69
384 387 4.250464 CAGCGGGTGAACAGTAAAATCTA 58.750 43.478 0.00 0.00 0.00 1.98
433 436 4.864806 TCTCTCATCGAGTAAAATGCACAC 59.135 41.667 0.00 0.00 40.75 3.82
456 459 0.679002 GCTGCCATATGCCCATCGAT 60.679 55.000 0.00 0.00 40.16 3.59
471 474 2.029518 GGTGTTTGGCTTGGCTGC 59.970 61.111 0.00 0.00 0.00 5.25
553 557 0.683412 ACTGCAGATCACACAGAGCA 59.317 50.000 23.35 0.00 34.30 4.26
554 558 2.266554 GTACTGCAGATCACACAGAGC 58.733 52.381 23.35 5.16 35.38 4.09
702 711 1.625818 CGGCCCTCCTATTCTAAGCAT 59.374 52.381 0.00 0.00 0.00 3.79
794 810 3.564225 CCGCCTTATTTATCGCCTCTTTT 59.436 43.478 0.00 0.00 0.00 2.27
868 884 2.588027 AACGCAAATGTTTCCGGTTT 57.412 40.000 0.00 0.00 0.00 3.27
869 885 2.588027 AAACGCAAATGTTTCCGGTT 57.412 40.000 0.00 0.00 37.50 4.44
870 886 2.465855 GAAAACGCAAATGTTTCCGGT 58.534 42.857 0.00 0.00 41.01 5.28
871 887 1.450161 CGAAAACGCAAATGTTTCCGG 59.550 47.619 0.00 0.00 41.01 5.14
872 888 2.113289 ACGAAAACGCAAATGTTTCCG 58.887 42.857 0.00 0.00 43.88 4.30
873 889 5.595065 CAATACGAAAACGCAAATGTTTCC 58.405 37.500 0.00 0.00 41.01 3.13
874 890 5.063722 GCAATACGAAAACGCAAATGTTTC 58.936 37.500 0.00 0.00 41.01 2.78
889 905 3.244422 GGATAGATTGGTGGGCAATACGA 60.244 47.826 0.00 0.00 0.00 3.43
890 906 3.074412 GGATAGATTGGTGGGCAATACG 58.926 50.000 0.00 0.00 0.00 3.06
891 907 4.074970 CTGGATAGATTGGTGGGCAATAC 58.925 47.826 0.00 0.00 0.00 1.89
892 908 3.980022 TCTGGATAGATTGGTGGGCAATA 59.020 43.478 0.00 0.00 0.00 1.90
893 909 2.785269 TCTGGATAGATTGGTGGGCAAT 59.215 45.455 0.00 0.00 0.00 3.56
895 911 1.490490 GTCTGGATAGATTGGTGGGCA 59.510 52.381 0.00 0.00 34.94 5.36
897 913 1.070758 CCGTCTGGATAGATTGGTGGG 59.929 57.143 0.00 0.00 37.49 4.61
898 914 1.541233 GCCGTCTGGATAGATTGGTGG 60.541 57.143 0.00 0.00 37.49 4.61
903 934 3.706594 TCAAAGAGCCGTCTGGATAGATT 59.293 43.478 0.00 0.00 37.49 2.40
930 961 2.224428 GTTACCGACGAAACCGCAA 58.776 52.632 0.00 0.00 0.00 4.85
998 1029 2.041922 TAGCGAGTGGGGGCATCT 60.042 61.111 0.00 0.00 0.00 2.90
1002 1033 4.208686 CGAGTAGCGAGTGGGGGC 62.209 72.222 0.00 0.00 44.57 5.80
1086 1117 1.311651 GCTTGGCTTCTCCTCTTGGC 61.312 60.000 0.00 0.00 35.26 4.52
1125 1160 0.179240 GCGCGTGTGAATGAAGACAG 60.179 55.000 8.43 0.00 0.00 3.51
1127 1162 1.225475 CGCGCGTGTGAATGAAGAC 60.225 57.895 24.19 0.00 0.00 3.01
1160 1201 4.103785 CAGGAATCCTCTCTCTCTCTCTCT 59.896 50.000 0.00 0.00 0.00 3.10
1161 1202 4.392940 CAGGAATCCTCTCTCTCTCTCTC 58.607 52.174 0.00 0.00 0.00 3.20
1162 1203 3.139025 CCAGGAATCCTCTCTCTCTCTCT 59.861 52.174 0.00 0.00 0.00 3.10
1163 1204 3.117512 ACCAGGAATCCTCTCTCTCTCTC 60.118 52.174 0.00 0.00 0.00 3.20
1164 1205 2.858768 ACCAGGAATCCTCTCTCTCTCT 59.141 50.000 0.00 0.00 0.00 3.10
1165 1206 3.312736 ACCAGGAATCCTCTCTCTCTC 57.687 52.381 0.00 0.00 0.00 3.20
1166 1207 3.642141 GAACCAGGAATCCTCTCTCTCT 58.358 50.000 0.00 0.00 0.00 3.10
1174 1215 1.991230 CCACCGAACCAGGAATCCT 59.009 57.895 0.00 0.00 34.73 3.24
1321 1385 2.222217 CGGTGCTCGCGTAGTTAGC 61.222 63.158 5.77 8.05 37.78 3.09
1322 1386 1.585521 CCGGTGCTCGCGTAGTTAG 60.586 63.158 5.77 0.00 37.59 2.34
1323 1387 2.486504 CCGGTGCTCGCGTAGTTA 59.513 61.111 5.77 0.00 37.59 2.24
1332 1396 2.435059 GAACAGAGGCCGGTGCTC 60.435 66.667 1.90 1.56 37.74 4.26
1334 1398 2.032681 AAGAACAGAGGCCGGTGC 59.967 61.111 1.90 1.41 0.00 5.01
1336 1400 2.032681 GCAAGAACAGAGGCCGGT 59.967 61.111 1.90 0.00 0.00 5.28
1337 1401 1.302832 AAGCAAGAACAGAGGCCGG 60.303 57.895 0.00 0.00 0.00 6.13
1338 1402 1.580845 CCAAGCAAGAACAGAGGCCG 61.581 60.000 0.00 0.00 0.00 6.13
1339 1403 0.538287 ACCAAGCAAGAACAGAGGCC 60.538 55.000 0.00 0.00 0.00 5.19
1340 1404 0.595095 CACCAAGCAAGAACAGAGGC 59.405 55.000 0.00 0.00 0.00 4.70
1342 1406 0.236711 CGCACCAAGCAAGAACAGAG 59.763 55.000 0.00 0.00 46.13 3.35
1343 1407 0.179059 TCGCACCAAGCAAGAACAGA 60.179 50.000 0.00 0.00 46.13 3.41
1344 1408 0.236711 CTCGCACCAAGCAAGAACAG 59.763 55.000 0.00 0.00 46.13 3.16
1363 1430 3.435671 CGACTGATCTGTAAAACAACCCC 59.564 47.826 5.09 0.00 0.00 4.95
1364 1431 3.120304 GCGACTGATCTGTAAAACAACCC 60.120 47.826 5.09 0.00 0.00 4.11
1366 1433 4.992381 AGCGACTGATCTGTAAAACAAC 57.008 40.909 5.09 0.00 0.00 3.32
1371 1438 5.072040 TGATGAAGCGACTGATCTGTAAA 57.928 39.130 5.09 0.00 0.00 2.01
1393 1460 0.392193 CAGTCCTCGCTGCAAGGATT 60.392 55.000 13.26 5.61 44.54 3.01
1398 1465 2.343758 GGTCAGTCCTCGCTGCAA 59.656 61.111 0.00 0.00 36.49 4.08
1408 1475 3.316573 CTTCCGGCCAGGGTCAGTC 62.317 68.421 2.24 0.00 41.52 3.51
1409 1476 3.322466 CTTCCGGCCAGGGTCAGT 61.322 66.667 2.24 0.00 41.52 3.41
1418 1485 4.918201 CGCTCCATCCTTCCGGCC 62.918 72.222 0.00 0.00 0.00 6.13
1419 1486 4.918201 CCGCTCCATCCTTCCGGC 62.918 72.222 0.00 0.00 31.87 6.13
1438 1505 2.980233 GCCTTGTCCAGCGCAGTT 60.980 61.111 11.47 0.00 0.00 3.16
1477 1544 3.934962 GCGGGGATGGAGAGAGGC 61.935 72.222 0.00 0.00 0.00 4.70
1493 1560 3.685836 AACGGCAACTAATTAATCGGC 57.314 42.857 0.00 0.00 0.00 5.54
1500 1567 7.120726 AGCAACTATCTAAAACGGCAACTAATT 59.879 33.333 0.00 0.00 0.00 1.40
1556 1664 4.537015 CACGGATGAAACAGAAAAGGTTC 58.463 43.478 0.00 0.00 0.00 3.62
1581 1689 1.830477 GCCTCCTCCTCCTGCATATAG 59.170 57.143 0.00 0.00 0.00 1.31
1630 1738 4.479993 CCCTCGCCCTTGCTCCTG 62.480 72.222 0.00 0.00 34.43 3.86
1836 1944 4.421948 CGAACCAACCTAGCTGTAACTAG 58.578 47.826 0.00 0.00 39.54 2.57
1837 1945 3.367703 GCGAACCAACCTAGCTGTAACTA 60.368 47.826 0.00 0.00 0.00 2.24
1838 1946 2.612221 GCGAACCAACCTAGCTGTAACT 60.612 50.000 0.00 0.00 0.00 2.24
1947 2055 3.450578 TCAACGTCAGAAAGCGTAAAGT 58.549 40.909 0.00 0.00 40.70 2.66
1952 2060 2.612212 ACAAATCAACGTCAGAAAGCGT 59.388 40.909 0.00 0.00 43.64 5.07
1960 2068 1.529438 GCGGAAGACAAATCAACGTCA 59.471 47.619 0.00 0.00 34.48 4.35
2049 2165 2.032799 TGCCGTCACAACTCAAAATGTC 59.967 45.455 0.00 0.00 0.00 3.06
2055 2171 1.444119 GGCTTGCCGTCACAACTCAA 61.444 55.000 0.00 0.00 0.00 3.02
2081 2202 1.157870 AACAAGGAGGAACACACGCG 61.158 55.000 3.53 3.53 0.00 6.01
2082 2203 0.586802 GAACAAGGAGGAACACACGC 59.413 55.000 0.00 0.00 0.00 5.34
2092 2213 3.904136 AAACATGCGAAGAACAAGGAG 57.096 42.857 0.00 0.00 0.00 3.69
2153 2281 5.066246 GGAAAGCAGATCCTGAGAGAATTTG 59.934 44.000 0.00 0.00 32.44 2.32
2166 2294 5.504665 CCGTTGATTATGTGGAAAGCAGATC 60.505 44.000 0.00 0.00 0.00 2.75
2186 2314 3.067742 TCTCAGAAAAGAACTCGACCGTT 59.932 43.478 0.00 0.00 0.00 4.44
2187 2315 2.621998 TCTCAGAAAAGAACTCGACCGT 59.378 45.455 0.00 0.00 0.00 4.83
2189 2317 5.696724 TCAAATCTCAGAAAAGAACTCGACC 59.303 40.000 0.00 0.00 0.00 4.79
2211 2339 7.502226 ACAACTCAATCCACAATCTTAAACTCA 59.498 33.333 0.00 0.00 0.00 3.41
2316 2445 6.149308 TCACTTTCGTGCTCATATTCAACAAT 59.851 34.615 0.00 0.00 40.99 2.71
2360 2491 8.641499 AACCATTGTATTTGTAATATTTGGCG 57.359 30.769 0.00 0.00 0.00 5.69
2375 2510 9.589111 ACGAACAAAACTTTAAAACCATTGTAT 57.411 25.926 0.00 2.18 0.00 2.29
2408 2543 6.358178 TCTATTTTTAGTTCACACCCACACA 58.642 36.000 0.00 0.00 0.00 3.72
2412 2547 6.289834 TCGTTCTATTTTTAGTTCACACCCA 58.710 36.000 0.00 0.00 0.00 4.51
2414 2549 7.632721 TGTTCGTTCTATTTTTAGTTCACACC 58.367 34.615 0.00 0.00 0.00 4.16
2416 2551 9.872757 GATTGTTCGTTCTATTTTTAGTTCACA 57.127 29.630 0.00 0.00 0.00 3.58
2467 2630 2.512745 AACACAACACGCGAGGCA 60.513 55.556 15.93 0.00 0.00 4.75
2514 2677 1.465387 CGTTTACAGGCGCCAACAATA 59.535 47.619 31.54 10.13 0.00 1.90
2516 2679 1.649815 CGTTTACAGGCGCCAACAA 59.350 52.632 31.54 15.91 0.00 2.83
2548 2711 3.122948 AGTTTGACAACGACGCATATGTC 59.877 43.478 4.29 13.50 41.90 3.06
2557 2720 5.331532 GCATTTTAGCAAGTTTGACAACGAC 60.332 40.000 0.00 0.00 38.03 4.34
2560 2723 5.748152 TGAGCATTTTAGCAAGTTTGACAAC 59.252 36.000 0.00 0.00 36.85 3.32
2574 2737 5.411361 AGCAAGTTACGTGATGAGCATTTTA 59.589 36.000 1.88 0.00 0.00 1.52
2617 2780 5.585820 TTGTCATTGCATGCATGTATCTT 57.414 34.783 26.79 8.80 0.00 2.40
2621 2784 4.985538 TGATTGTCATTGCATGCATGTA 57.014 36.364 26.79 20.88 0.00 2.29


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

AutoCloner maintained by Alex Coulton.