Multiple sequence alignment - TraesCS6D01G249100

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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 TraesCS6D01G249100 chr6D 100.000 2950 0 0 1 2950 352362527 352359578 0.000000e+00 5448.0
1 TraesCS6D01G249100 chr6D 100.000 46 0 0 2905 2950 448792475 448792520 5.240000e-13 86.1
2 TraesCS6D01G249100 chr6A 92.598 2148 76 31 871 2950 490489333 490491465 0.000000e+00 3009.0
3 TraesCS6D01G249100 chr6A 82.483 725 41 37 170 861 490488354 490489025 9.240000e-155 556.0
4 TraesCS6D01G249100 chr6B 97.528 1173 27 2 1779 2950 526715372 526716543 0.000000e+00 2004.0
5 TraesCS6D01G249100 chr6B 92.182 1164 31 12 587 1711 526714228 526715370 0.000000e+00 1591.0


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 TraesCS6D01G249100 chr6D 352359578 352362527 2949 True 5448.0 5448 100.0000 1 2950 1 chr6D.!!$R1 2949
1 TraesCS6D01G249100 chr6A 490488354 490491465 3111 False 1782.5 3009 87.5405 170 2950 2 chr6A.!!$F1 2780
2 TraesCS6D01G249100 chr6B 526714228 526716543 2315 False 1797.5 2004 94.8550 587 2950 2 chr6B.!!$F1 2363

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
161 162 0.035152 AAATGCAGCGATCACCAGGA 60.035 50.0 0.0 0.0 0.0 3.86 F
501 502 0.036010 CCCCATCTCTCTTGCGTTGT 60.036 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 1743 1.281899 GCGAATCGTCAGAAGGGAAG 58.718 55.0 4.07 0.0 0.00 3.46 R
2494 2914 1.155042 CAGGACAAGAGAGCAAGTGC 58.845 55.0 0.00 0.0 42.49 4.40 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
21 22 3.402628 TTTCCAGAGTGACCTAAGTGC 57.597 47.619 0.00 0.00 0.00 4.40
22 23 2.009681 TCCAGAGTGACCTAAGTGCA 57.990 50.000 0.00 0.00 0.00 4.57
23 24 2.325484 TCCAGAGTGACCTAAGTGCAA 58.675 47.619 0.00 0.00 0.00 4.08
24 25 2.037251 TCCAGAGTGACCTAAGTGCAAC 59.963 50.000 0.00 0.00 0.00 4.17
25 26 2.417719 CAGAGTGACCTAAGTGCAACC 58.582 52.381 0.00 0.00 37.80 3.77
26 27 1.000955 AGAGTGACCTAAGTGCAACCG 59.999 52.381 0.00 0.00 37.80 4.44
27 28 1.000506 GAGTGACCTAAGTGCAACCGA 59.999 52.381 0.00 0.00 37.80 4.69
28 29 1.000955 AGTGACCTAAGTGCAACCGAG 59.999 52.381 0.00 0.00 37.80 4.63
29 30 1.045407 TGACCTAAGTGCAACCGAGT 58.955 50.000 0.00 0.00 37.80 4.18
30 31 2.029649 GTGACCTAAGTGCAACCGAGTA 60.030 50.000 0.00 0.00 37.80 2.59
31 32 2.829720 TGACCTAAGTGCAACCGAGTAT 59.170 45.455 0.00 0.00 37.80 2.12
32 33 3.119245 TGACCTAAGTGCAACCGAGTATC 60.119 47.826 0.00 0.00 37.80 2.24
33 34 2.829720 ACCTAAGTGCAACCGAGTATCA 59.170 45.455 0.00 0.00 37.80 2.15
34 35 3.119101 ACCTAAGTGCAACCGAGTATCAG 60.119 47.826 0.00 0.00 37.80 2.90
35 36 1.726853 AAGTGCAACCGAGTATCAGC 58.273 50.000 0.00 0.00 37.80 4.26
36 37 0.608130 AGTGCAACCGAGTATCAGCA 59.392 50.000 0.00 0.00 37.80 4.41
37 38 1.208052 AGTGCAACCGAGTATCAGCAT 59.792 47.619 0.00 0.00 37.80 3.79
38 39 1.594862 GTGCAACCGAGTATCAGCATC 59.405 52.381 0.00 0.00 32.51 3.91
39 40 0.855349 GCAACCGAGTATCAGCATCG 59.145 55.000 0.00 0.00 36.24 3.84
40 41 1.802880 GCAACCGAGTATCAGCATCGT 60.803 52.381 0.00 0.00 34.71 3.73
41 42 2.120232 CAACCGAGTATCAGCATCGTC 58.880 52.381 0.00 0.00 34.71 4.20
42 43 1.389555 ACCGAGTATCAGCATCGTCA 58.610 50.000 0.00 0.00 34.71 4.35
43 44 1.335182 ACCGAGTATCAGCATCGTCAG 59.665 52.381 0.00 0.00 34.71 3.51
44 45 1.604278 CCGAGTATCAGCATCGTCAGA 59.396 52.381 0.00 0.00 34.71 3.27
45 46 2.350293 CCGAGTATCAGCATCGTCAGAG 60.350 54.545 0.00 0.00 34.71 3.35
46 47 2.350293 CGAGTATCAGCATCGTCAGAGG 60.350 54.545 0.00 0.00 33.17 3.69
47 48 2.621055 GAGTATCAGCATCGTCAGAGGT 59.379 50.000 0.00 0.00 33.17 3.85
48 49 2.360483 AGTATCAGCATCGTCAGAGGTG 59.640 50.000 0.00 0.00 0.00 4.00
49 50 0.463204 ATCAGCATCGTCAGAGGTGG 59.537 55.000 0.00 0.00 0.00 4.61
50 51 1.812922 CAGCATCGTCAGAGGTGGC 60.813 63.158 0.00 1.98 0.00 5.01
51 52 2.265739 GCATCGTCAGAGGTGGCA 59.734 61.111 0.00 0.00 0.00 4.92
52 53 1.375908 GCATCGTCAGAGGTGGCAA 60.376 57.895 0.00 0.00 0.00 4.52
53 54 0.955428 GCATCGTCAGAGGTGGCAAA 60.955 55.000 0.00 0.00 0.00 3.68
54 55 0.798776 CATCGTCAGAGGTGGCAAAC 59.201 55.000 0.00 0.00 0.00 2.93
63 64 2.267045 GGTGGCAAACCTCATCACC 58.733 57.895 0.00 0.00 46.55 4.02
64 65 0.539438 GGTGGCAAACCTCATCACCA 60.539 55.000 0.00 0.00 46.55 4.17
65 66 1.549203 GTGGCAAACCTCATCACCAT 58.451 50.000 0.00 0.00 36.63 3.55
66 67 1.895131 GTGGCAAACCTCATCACCATT 59.105 47.619 0.00 0.00 36.63 3.16
67 68 1.894466 TGGCAAACCTCATCACCATTG 59.106 47.619 0.00 0.00 36.63 2.82
68 69 1.895131 GGCAAACCTCATCACCATTGT 59.105 47.619 0.00 0.00 0.00 2.71
69 70 3.088532 GGCAAACCTCATCACCATTGTA 58.911 45.455 0.00 0.00 0.00 2.41
70 71 3.701040 GGCAAACCTCATCACCATTGTAT 59.299 43.478 0.00 0.00 0.00 2.29
71 72 4.202050 GGCAAACCTCATCACCATTGTATC 60.202 45.833 0.00 0.00 0.00 2.24
72 73 4.202050 GCAAACCTCATCACCATTGTATCC 60.202 45.833 0.00 0.00 0.00 2.59
73 74 3.475566 ACCTCATCACCATTGTATCCG 57.524 47.619 0.00 0.00 0.00 4.18
74 75 3.038280 ACCTCATCACCATTGTATCCGA 58.962 45.455 0.00 0.00 0.00 4.55
75 76 3.454447 ACCTCATCACCATTGTATCCGAA 59.546 43.478 0.00 0.00 0.00 4.30
76 77 3.809832 CCTCATCACCATTGTATCCGAAC 59.190 47.826 0.00 0.00 0.00 3.95
77 78 4.441792 CTCATCACCATTGTATCCGAACA 58.558 43.478 0.00 0.00 0.00 3.18
78 79 4.441792 TCATCACCATTGTATCCGAACAG 58.558 43.478 0.00 0.00 0.00 3.16
79 80 3.260475 TCACCATTGTATCCGAACAGG 57.740 47.619 0.00 0.00 42.97 4.00
80 81 2.569853 TCACCATTGTATCCGAACAGGT 59.430 45.455 0.00 0.00 41.99 4.00
81 82 3.008594 TCACCATTGTATCCGAACAGGTT 59.991 43.478 0.00 0.00 41.99 3.50
82 83 3.756434 CACCATTGTATCCGAACAGGTTT 59.244 43.478 0.00 0.00 41.99 3.27
83 84 4.217550 CACCATTGTATCCGAACAGGTTTT 59.782 41.667 0.00 0.00 41.99 2.43
84 85 4.217550 ACCATTGTATCCGAACAGGTTTTG 59.782 41.667 0.00 0.00 41.99 2.44
85 86 3.907894 TTGTATCCGAACAGGTTTTGC 57.092 42.857 0.00 0.00 41.99 3.68
86 87 3.134574 TGTATCCGAACAGGTTTTGCT 57.865 42.857 0.00 0.00 41.99 3.91
87 88 2.811431 TGTATCCGAACAGGTTTTGCTG 59.189 45.455 0.00 0.00 41.99 4.41
88 89 2.270352 ATCCGAACAGGTTTTGCTGA 57.730 45.000 0.00 0.00 41.99 4.26
89 90 1.305201 TCCGAACAGGTTTTGCTGAC 58.695 50.000 0.00 0.00 41.99 3.51
90 91 0.041312 CCGAACAGGTTTTGCTGACG 60.041 55.000 0.00 0.00 34.51 4.35
91 92 0.657368 CGAACAGGTTTTGCTGACGC 60.657 55.000 0.00 0.00 0.00 5.19
92 93 0.380378 GAACAGGTTTTGCTGACGCA 59.620 50.000 0.00 0.00 46.24 5.24
100 101 2.202810 TGCTGACGCACGTGTGAA 60.203 55.556 34.03 20.12 42.25 3.18
101 102 1.811679 TGCTGACGCACGTGTGAAA 60.812 52.632 34.03 19.78 42.25 2.69
102 103 1.350319 GCTGACGCACGTGTGAAAA 59.650 52.632 34.03 17.44 35.78 2.29
103 104 0.247894 GCTGACGCACGTGTGAAAAA 60.248 50.000 34.03 15.13 35.78 1.94
104 105 1.452717 CTGACGCACGTGTGAAAAAC 58.547 50.000 34.03 18.37 0.00 2.43
105 106 0.796927 TGACGCACGTGTGAAAAACA 59.203 45.000 34.03 20.36 36.04 2.83
106 107 1.197036 TGACGCACGTGTGAAAAACAA 59.803 42.857 34.03 9.13 41.57 2.83
107 108 2.243407 GACGCACGTGTGAAAAACAAA 58.757 42.857 34.03 0.00 41.57 2.83
108 109 2.849473 GACGCACGTGTGAAAAACAAAT 59.151 40.909 34.03 9.46 41.57 2.32
109 110 2.596419 ACGCACGTGTGAAAAACAAATG 59.404 40.909 34.03 0.00 41.57 2.32
110 111 2.596419 CGCACGTGTGAAAAACAAATGT 59.404 40.909 24.50 0.00 41.57 2.71
111 112 3.060098 CGCACGTGTGAAAAACAAATGTT 59.940 39.130 24.50 0.00 41.57 2.71
112 113 4.564281 GCACGTGTGAAAAACAAATGTTC 58.436 39.130 18.38 0.00 41.57 3.18
113 114 4.090642 GCACGTGTGAAAAACAAATGTTCA 59.909 37.500 18.38 0.00 41.57 3.18
114 115 5.388890 GCACGTGTGAAAAACAAATGTTCAA 60.389 36.000 18.38 0.00 41.57 2.69
115 116 6.006482 CACGTGTGAAAAACAAATGTTCAAC 58.994 36.000 7.58 0.00 41.57 3.18
116 117 5.164138 ACGTGTGAAAAACAAATGTTCAACG 60.164 36.000 0.00 8.71 41.57 4.10
117 118 5.546434 GTGTGAAAAACAAATGTTCAACGG 58.454 37.500 0.00 0.00 41.57 4.44
118 119 5.119434 GTGTGAAAAACAAATGTTCAACGGT 59.881 36.000 0.00 0.00 41.57 4.83
119 120 5.346281 TGTGAAAAACAAATGTTCAACGGTC 59.654 36.000 0.00 0.00 37.25 4.79
120 121 4.865365 TGAAAAACAAATGTTCAACGGTCC 59.135 37.500 0.00 0.00 37.25 4.46
121 122 2.766970 AACAAATGTTCAACGGTCCG 57.233 45.000 10.48 10.48 31.64 4.79
122 123 1.670791 ACAAATGTTCAACGGTCCGT 58.329 45.000 12.23 12.23 43.97 4.69
123 124 3.119424 AAACAAATGTTCAACGGTCCGTT 60.119 39.130 23.96 23.96 43.42 4.44
124 125 4.966210 AAACAAATGTTCAACGGTCCGTTC 60.966 41.667 26.61 16.07 41.91 3.95
125 126 7.887582 AAACAAATGTTCAACGGTCCGTTCC 62.888 44.000 26.61 16.96 41.91 3.62
132 133 2.922779 ACGGTCCGTTCCATTCAAC 58.077 52.632 12.23 0.00 36.35 3.18
133 134 0.395312 ACGGTCCGTTCCATTCAACT 59.605 50.000 12.23 0.00 36.35 3.16
134 135 0.796312 CGGTCCGTTCCATTCAACTG 59.204 55.000 2.08 0.00 0.00 3.16
135 136 1.876416 CGGTCCGTTCCATTCAACTGT 60.876 52.381 2.08 0.00 0.00 3.55
136 137 2.227194 GGTCCGTTCCATTCAACTGTT 58.773 47.619 0.00 0.00 0.00 3.16
137 138 2.031157 GGTCCGTTCCATTCAACTGTTG 60.031 50.000 14.24 14.24 0.00 3.33
138 139 1.606668 TCCGTTCCATTCAACTGTTGC 59.393 47.619 15.52 0.00 0.00 4.17
139 140 1.336440 CCGTTCCATTCAACTGTTGCA 59.664 47.619 15.52 5.42 0.00 4.08
140 141 2.384382 CGTTCCATTCAACTGTTGCAC 58.616 47.619 15.52 4.68 0.00 4.57
141 142 2.223456 CGTTCCATTCAACTGTTGCACA 60.223 45.455 15.52 2.82 0.00 4.57
142 143 3.733380 CGTTCCATTCAACTGTTGCACAA 60.733 43.478 15.52 5.70 0.00 3.33
143 144 4.180057 GTTCCATTCAACTGTTGCACAAA 58.820 39.130 15.52 5.35 0.00 2.83
144 145 4.462508 TCCATTCAACTGTTGCACAAAA 57.537 36.364 15.52 4.99 0.00 2.44
145 146 5.021033 TCCATTCAACTGTTGCACAAAAT 57.979 34.783 15.52 7.06 0.00 1.82
146 147 4.809958 TCCATTCAACTGTTGCACAAAATG 59.190 37.500 15.52 17.00 0.00 2.32
157 158 1.621107 CACAAAATGCAGCGATCACC 58.379 50.000 0.00 0.00 0.00 4.02
158 159 1.068402 CACAAAATGCAGCGATCACCA 60.068 47.619 0.00 0.00 0.00 4.17
159 160 1.200716 ACAAAATGCAGCGATCACCAG 59.799 47.619 0.00 0.00 0.00 4.00
160 161 0.813184 AAAATGCAGCGATCACCAGG 59.187 50.000 0.00 0.00 0.00 4.45
161 162 0.035152 AAATGCAGCGATCACCAGGA 60.035 50.000 0.00 0.00 0.00 3.86
162 163 0.463295 AATGCAGCGATCACCAGGAG 60.463 55.000 0.00 0.00 0.00 3.69
163 164 1.620739 ATGCAGCGATCACCAGGAGT 61.621 55.000 0.00 0.00 0.00 3.85
164 165 0.970427 TGCAGCGATCACCAGGAGTA 60.970 55.000 0.00 0.00 0.00 2.59
165 166 0.390860 GCAGCGATCACCAGGAGTAT 59.609 55.000 0.00 0.00 0.00 2.12
166 167 1.613925 GCAGCGATCACCAGGAGTATA 59.386 52.381 0.00 0.00 0.00 1.47
167 168 2.232452 GCAGCGATCACCAGGAGTATAT 59.768 50.000 0.00 0.00 0.00 0.86
168 169 3.306364 GCAGCGATCACCAGGAGTATATT 60.306 47.826 0.00 0.00 0.00 1.28
169 170 4.240888 CAGCGATCACCAGGAGTATATTG 58.759 47.826 0.00 0.00 0.00 1.90
170 171 3.898123 AGCGATCACCAGGAGTATATTGT 59.102 43.478 0.00 0.00 0.00 2.71
171 172 5.048013 CAGCGATCACCAGGAGTATATTGTA 60.048 44.000 0.00 0.00 0.00 2.41
176 177 6.465439 TCACCAGGAGTATATTGTAGTGTG 57.535 41.667 0.00 0.00 0.00 3.82
210 211 9.282569 GAGCATATTCTTTCCATTGACTCTATT 57.717 33.333 0.00 0.00 0.00 1.73
237 238 2.620242 CACAAGCCAAGCAAACACTTT 58.380 42.857 0.00 0.00 0.00 2.66
245 246 2.763249 AGCAAACACTTTGAGCTTCG 57.237 45.000 0.00 0.00 43.26 3.79
246 247 1.123655 GCAAACACTTTGAGCTTCGC 58.876 50.000 0.00 0.00 43.26 4.70
247 248 1.268743 GCAAACACTTTGAGCTTCGCT 60.269 47.619 0.00 0.00 43.26 4.93
257 258 1.066929 TGAGCTTCGCTGTGCATCTTA 60.067 47.619 0.00 0.00 39.88 2.10
284 285 0.904394 AATGCATTTTGAGCCGGGGT 60.904 50.000 5.99 0.00 0.00 4.95
286 287 2.710902 GCATTTTGAGCCGGGGTCC 61.711 63.158 22.54 6.28 0.00 4.46
293 294 4.658786 AGCCGGGGTCCTCCTTGT 62.659 66.667 2.18 0.00 35.33 3.16
294 295 4.410400 GCCGGGGTCCTCCTTGTG 62.410 72.222 2.18 0.00 35.33 3.33
295 296 4.410400 CCGGGGTCCTCCTTGTGC 62.410 72.222 0.00 0.00 35.33 4.57
310 311 3.006752 CCTTGTGCCCATGTTAACATTGT 59.993 43.478 18.50 0.00 33.61 2.71
334 335 6.606241 AGGTCAATAAATCTCCCCCATTTA 57.394 37.500 0.00 0.00 31.76 1.40
376 377 1.548719 GCGGGGTGCCTTAAAAGAATT 59.451 47.619 0.00 0.00 37.76 2.17
396 397 3.323751 TTAGCCACGTTTTCCCTCTAC 57.676 47.619 0.00 0.00 0.00 2.59
401 402 3.408634 CCACGTTTTCCCTCTACAACAT 58.591 45.455 0.00 0.00 0.00 2.71
416 417 3.585990 CATCCGGCGCAATGTCCC 61.586 66.667 10.83 0.00 0.00 4.46
426 427 2.358247 AATGTCCCACCGACGTGC 60.358 61.111 0.00 0.00 45.23 5.34
458 459 4.202111 CCAACAACCCCTAACAAGAACAAG 60.202 45.833 0.00 0.00 0.00 3.16
459 460 4.513406 ACAACCCCTAACAAGAACAAGA 57.487 40.909 0.00 0.00 0.00 3.02
460 461 4.862371 ACAACCCCTAACAAGAACAAGAA 58.138 39.130 0.00 0.00 0.00 2.52
461 462 4.643334 ACAACCCCTAACAAGAACAAGAAC 59.357 41.667 0.00 0.00 0.00 3.01
462 463 4.513406 ACCCCTAACAAGAACAAGAACA 57.487 40.909 0.00 0.00 0.00 3.18
463 464 4.862371 ACCCCTAACAAGAACAAGAACAA 58.138 39.130 0.00 0.00 0.00 2.83
464 465 4.887655 ACCCCTAACAAGAACAAGAACAAG 59.112 41.667 0.00 0.00 0.00 3.16
465 466 5.130350 CCCCTAACAAGAACAAGAACAAGA 58.870 41.667 0.00 0.00 0.00 3.02
466 467 5.592688 CCCCTAACAAGAACAAGAACAAGAA 59.407 40.000 0.00 0.00 0.00 2.52
467 468 6.459710 CCCCTAACAAGAACAAGAACAAGAAC 60.460 42.308 0.00 0.00 0.00 3.01
468 469 6.094881 CCCTAACAAGAACAAGAACAAGAACA 59.905 38.462 0.00 0.00 0.00 3.18
469 470 7.362574 CCCTAACAAGAACAAGAACAAGAACAA 60.363 37.037 0.00 0.00 0.00 2.83
470 471 7.698130 CCTAACAAGAACAAGAACAAGAACAAG 59.302 37.037 0.00 0.00 0.00 3.16
471 472 6.817765 ACAAGAACAAGAACAAGAACAAGA 57.182 33.333 0.00 0.00 0.00 3.02
472 473 7.214467 ACAAGAACAAGAACAAGAACAAGAA 57.786 32.000 0.00 0.00 0.00 2.52
473 474 7.084486 ACAAGAACAAGAACAAGAACAAGAAC 58.916 34.615 0.00 0.00 0.00 3.01
474 475 6.817765 AGAACAAGAACAAGAACAAGAACA 57.182 33.333 0.00 0.00 0.00 3.18
475 476 7.214467 AGAACAAGAACAAGAACAAGAACAA 57.786 32.000 0.00 0.00 0.00 2.83
476 477 7.308435 AGAACAAGAACAAGAACAAGAACAAG 58.692 34.615 0.00 0.00 0.00 3.16
495 496 0.393537 GGTGCACCCCATCTCTCTTG 60.394 60.000 26.31 0.00 0.00 3.02
496 497 1.028868 GTGCACCCCATCTCTCTTGC 61.029 60.000 5.22 0.00 0.00 4.01
501 502 0.036010 CCCCATCTCTCTTGCGTTGT 60.036 55.000 0.00 0.00 0.00 3.32
505 506 3.125316 CCCATCTCTCTTGCGTTGTTTAC 59.875 47.826 0.00 0.00 0.00 2.01
506 507 3.745975 CCATCTCTCTTGCGTTGTTTACA 59.254 43.478 0.00 0.00 0.00 2.41
507 508 4.377431 CCATCTCTCTTGCGTTGTTTACAC 60.377 45.833 0.00 0.00 0.00 2.90
508 509 4.054780 TCTCTCTTGCGTTGTTTACACT 57.945 40.909 0.00 0.00 0.00 3.55
509 510 5.190992 TCTCTCTTGCGTTGTTTACACTA 57.809 39.130 0.00 0.00 0.00 2.74
511 512 5.461078 TCTCTCTTGCGTTGTTTACACTAAC 59.539 40.000 0.00 0.00 0.00 2.34
512 513 5.353938 TCTCTTGCGTTGTTTACACTAACT 58.646 37.500 0.00 0.00 0.00 2.24
513 514 6.506147 TCTCTTGCGTTGTTTACACTAACTA 58.494 36.000 0.00 0.00 0.00 2.24
536 537 5.852282 ATACCAACATGCCCAAAGATTAC 57.148 39.130 0.00 0.00 0.00 1.89
549 550 5.242838 CCCAAAGATTACAGCCACACTAAAA 59.757 40.000 0.00 0.00 0.00 1.52
572 573 0.723981 AGCAAAGAAGCGATCGAAGC 59.276 50.000 21.57 10.59 40.15 3.86
576 577 3.751621 CAAAGAAGCGATCGAAGCAAAT 58.248 40.909 21.57 4.46 37.01 2.32
578 579 4.522297 AAGAAGCGATCGAAGCAAATAC 57.478 40.909 21.57 0.00 37.01 1.89
603 624 0.738389 CCACAAACACGGTTTGCTCT 59.262 50.000 21.76 7.13 32.93 4.09
617 638 2.420628 TGCTCTTTTGACAATTGCGG 57.579 45.000 5.05 0.00 0.00 5.69
861 896 4.471726 GCGCCACAGCAGCATCAC 62.472 66.667 0.00 0.00 39.83 3.06
895 1228 7.284034 CACTATTCAACTGCAGATATTTCCCTT 59.716 37.037 23.35 0.00 0.00 3.95
909 1242 1.276622 TCCCTTCCTTCCTTCCTTCG 58.723 55.000 0.00 0.00 0.00 3.79
1009 1382 4.918278 TCCACCCCACACCGTCGA 62.918 66.667 0.00 0.00 0.00 4.20
1062 1445 0.242017 GACAGCAACCCAAGATGCAC 59.758 55.000 0.00 0.00 44.95 4.57
1360 1743 1.074319 TGAAATAGTCGTCGCGTGCC 61.074 55.000 5.77 0.00 0.00 5.01
1558 1951 2.017138 TTCAATCCAACAGCGCGATA 57.983 45.000 12.10 0.00 0.00 2.92
1633 2046 1.303970 GCCTTGCCTCCTTGCTTCT 60.304 57.895 0.00 0.00 0.00 2.85
1635 2048 1.743996 CCTTGCCTCCTTGCTTCTAC 58.256 55.000 0.00 0.00 0.00 2.59
1636 2049 1.003580 CCTTGCCTCCTTGCTTCTACA 59.996 52.381 0.00 0.00 0.00 2.74
1637 2050 2.354259 CTTGCCTCCTTGCTTCTACAG 58.646 52.381 0.00 0.00 0.00 2.74
1638 2051 1.352083 TGCCTCCTTGCTTCTACAGT 58.648 50.000 0.00 0.00 0.00 3.55
1639 2052 2.536066 TGCCTCCTTGCTTCTACAGTA 58.464 47.619 0.00 0.00 0.00 2.74
1640 2053 2.233922 TGCCTCCTTGCTTCTACAGTAC 59.766 50.000 0.00 0.00 0.00 2.73
1737 2150 2.920724 TTTGACGTGATCCAAGGTGA 57.079 45.000 0.00 0.00 0.00 4.02
1962 2381 5.391312 AGAAAATAAACAGACACCATGGC 57.609 39.130 13.04 0.00 0.00 4.40
1963 2382 4.220602 AGAAAATAAACAGACACCATGGCC 59.779 41.667 13.04 0.00 0.00 5.36
2353 2773 0.038709 TTTGGGCCTTTGCGATTTCG 60.039 50.000 4.53 0.00 43.27 3.46
2360 2780 1.268234 CCTTTGCGATTTCGGCATCTC 60.268 52.381 1.75 0.00 40.23 2.75
2363 2783 0.249447 TGCGATTTCGGCATCTCGAT 60.249 50.000 1.75 0.00 39.03 3.59
2377 2797 3.217599 TCTCGATCTTTCTGTTCACCG 57.782 47.619 0.00 0.00 0.00 4.94
2412 2832 5.409826 CAGTATCTTCTGGTTTGTTGGTCTC 59.590 44.000 0.00 0.00 0.00 3.36
2420 2840 2.814336 GGTTTGTTGGTCTCTGGACATC 59.186 50.000 0.00 0.00 43.77 3.06
2494 2914 3.539604 CTTAGCTGGATCACTTTCCTGG 58.460 50.000 0.00 0.00 36.68 4.45
2842 3262 3.045601 ACTTTAGCACTTGCAGTCGAT 57.954 42.857 3.62 0.00 45.16 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.135712 TGCACTTAGGTCACTCTGGAAAA 59.864 43.478 0.00 0.00 0.00 2.29
3 4 2.009681 TGCACTTAGGTCACTCTGGA 57.990 50.000 0.00 0.00 0.00 3.86
4 5 2.417719 GTTGCACTTAGGTCACTCTGG 58.582 52.381 0.00 0.00 0.00 3.86
5 6 2.417719 GGTTGCACTTAGGTCACTCTG 58.582 52.381 0.00 0.00 0.00 3.35
6 7 1.000955 CGGTTGCACTTAGGTCACTCT 59.999 52.381 0.00 0.00 0.00 3.24
7 8 1.000506 TCGGTTGCACTTAGGTCACTC 59.999 52.381 0.00 0.00 0.00 3.51
8 9 1.000955 CTCGGTTGCACTTAGGTCACT 59.999 52.381 0.00 0.00 0.00 3.41
9 10 1.270147 ACTCGGTTGCACTTAGGTCAC 60.270 52.381 0.00 0.00 0.00 3.67
10 11 1.045407 ACTCGGTTGCACTTAGGTCA 58.955 50.000 0.00 0.00 0.00 4.02
11 12 3.119245 TGATACTCGGTTGCACTTAGGTC 60.119 47.826 0.00 0.00 0.00 3.85
12 13 2.829720 TGATACTCGGTTGCACTTAGGT 59.170 45.455 0.00 0.00 0.00 3.08
13 14 3.448686 CTGATACTCGGTTGCACTTAGG 58.551 50.000 0.00 0.00 0.00 2.69
14 15 2.860735 GCTGATACTCGGTTGCACTTAG 59.139 50.000 0.00 0.00 0.00 2.18
15 16 2.232696 TGCTGATACTCGGTTGCACTTA 59.767 45.455 0.00 0.00 0.00 2.24
16 17 1.001974 TGCTGATACTCGGTTGCACTT 59.998 47.619 0.00 0.00 0.00 3.16
17 18 0.608130 TGCTGATACTCGGTTGCACT 59.392 50.000 0.00 0.00 0.00 4.40
18 19 1.594862 GATGCTGATACTCGGTTGCAC 59.405 52.381 0.00 0.00 33.16 4.57
19 20 1.802508 CGATGCTGATACTCGGTTGCA 60.803 52.381 0.00 0.00 34.88 4.08
20 21 0.855349 CGATGCTGATACTCGGTTGC 59.145 55.000 0.00 0.00 0.00 4.17
21 22 2.120232 GACGATGCTGATACTCGGTTG 58.880 52.381 0.00 0.00 36.74 3.77
22 23 1.749063 TGACGATGCTGATACTCGGTT 59.251 47.619 0.00 0.00 36.74 4.44
23 24 1.335182 CTGACGATGCTGATACTCGGT 59.665 52.381 0.00 0.00 36.74 4.69
24 25 1.604278 TCTGACGATGCTGATACTCGG 59.396 52.381 0.00 0.00 36.74 4.63
25 26 2.350293 CCTCTGACGATGCTGATACTCG 60.350 54.545 0.00 0.00 38.34 4.18
26 27 2.621055 ACCTCTGACGATGCTGATACTC 59.379 50.000 0.00 0.00 0.00 2.59
27 28 2.360483 CACCTCTGACGATGCTGATACT 59.640 50.000 0.00 0.00 0.00 2.12
28 29 2.544694 CCACCTCTGACGATGCTGATAC 60.545 54.545 0.00 0.00 0.00 2.24
29 30 1.683385 CCACCTCTGACGATGCTGATA 59.317 52.381 0.00 0.00 0.00 2.15
30 31 0.463204 CCACCTCTGACGATGCTGAT 59.537 55.000 0.00 0.00 0.00 2.90
31 32 1.893062 CCACCTCTGACGATGCTGA 59.107 57.895 0.00 0.00 0.00 4.26
32 33 1.812922 GCCACCTCTGACGATGCTG 60.813 63.158 0.00 0.00 0.00 4.41
33 34 1.830587 TTGCCACCTCTGACGATGCT 61.831 55.000 0.00 0.00 0.00 3.79
34 35 0.955428 TTTGCCACCTCTGACGATGC 60.955 55.000 0.00 0.00 0.00 3.91
35 36 0.798776 GTTTGCCACCTCTGACGATG 59.201 55.000 0.00 0.00 0.00 3.84
36 37 0.321653 GGTTTGCCACCTCTGACGAT 60.322 55.000 0.00 0.00 43.29 3.73
37 38 1.070786 GGTTTGCCACCTCTGACGA 59.929 57.895 0.00 0.00 43.29 4.20
38 39 3.655481 GGTTTGCCACCTCTGACG 58.345 61.111 0.00 0.00 43.29 4.35
46 47 1.549203 ATGGTGATGAGGTTTGCCAC 58.451 50.000 0.00 0.00 37.19 5.01
47 48 1.894466 CAATGGTGATGAGGTTTGCCA 59.106 47.619 0.00 0.00 37.19 4.92
48 49 1.895131 ACAATGGTGATGAGGTTTGCC 59.105 47.619 0.00 0.00 0.00 4.52
49 50 4.202050 GGATACAATGGTGATGAGGTTTGC 60.202 45.833 0.00 0.00 0.00 3.68
50 51 4.035558 CGGATACAATGGTGATGAGGTTTG 59.964 45.833 0.00 0.00 0.00 2.93
51 52 4.080582 TCGGATACAATGGTGATGAGGTTT 60.081 41.667 0.00 0.00 0.00 3.27
52 53 3.454447 TCGGATACAATGGTGATGAGGTT 59.546 43.478 0.00 0.00 0.00 3.50
53 54 3.038280 TCGGATACAATGGTGATGAGGT 58.962 45.455 0.00 0.00 0.00 3.85
54 55 3.751479 TCGGATACAATGGTGATGAGG 57.249 47.619 0.00 0.00 0.00 3.86
55 56 4.441792 TGTTCGGATACAATGGTGATGAG 58.558 43.478 0.00 0.00 0.00 2.90
56 57 4.441792 CTGTTCGGATACAATGGTGATGA 58.558 43.478 0.00 0.00 0.00 2.92
57 58 3.561310 CCTGTTCGGATACAATGGTGATG 59.439 47.826 0.00 0.00 33.16 3.07
58 59 3.199946 ACCTGTTCGGATACAATGGTGAT 59.800 43.478 0.00 0.00 36.31 3.06
59 60 2.569853 ACCTGTTCGGATACAATGGTGA 59.430 45.455 0.00 0.00 36.31 4.02
60 61 2.985896 ACCTGTTCGGATACAATGGTG 58.014 47.619 0.00 0.00 36.31 4.17
61 62 3.713826 AACCTGTTCGGATACAATGGT 57.286 42.857 0.00 0.00 36.31 3.55
62 63 4.732784 CAAAACCTGTTCGGATACAATGG 58.267 43.478 0.00 0.00 36.31 3.16
63 64 4.082787 AGCAAAACCTGTTCGGATACAATG 60.083 41.667 0.00 0.00 36.31 2.82
64 65 4.079253 AGCAAAACCTGTTCGGATACAAT 58.921 39.130 0.00 0.00 36.31 2.71
65 66 3.252215 CAGCAAAACCTGTTCGGATACAA 59.748 43.478 0.00 0.00 36.31 2.41
66 67 2.811431 CAGCAAAACCTGTTCGGATACA 59.189 45.455 0.00 0.00 36.31 2.29
67 68 3.071479 TCAGCAAAACCTGTTCGGATAC 58.929 45.455 0.00 0.00 36.31 2.24
68 69 3.071479 GTCAGCAAAACCTGTTCGGATA 58.929 45.455 0.00 0.00 36.31 2.59
69 70 1.880027 GTCAGCAAAACCTGTTCGGAT 59.120 47.619 0.00 0.00 36.31 4.18
70 71 1.305201 GTCAGCAAAACCTGTTCGGA 58.695 50.000 0.00 0.00 36.31 4.55
71 72 0.041312 CGTCAGCAAAACCTGTTCGG 60.041 55.000 0.00 0.00 39.35 4.30
72 73 0.657368 GCGTCAGCAAAACCTGTTCG 60.657 55.000 0.00 0.00 44.35 3.95
73 74 3.164028 GCGTCAGCAAAACCTGTTC 57.836 52.632 0.00 0.00 44.35 3.18
84 85 0.247894 TTTTTCACACGTGCGTCAGC 60.248 50.000 17.22 0.00 45.41 4.26
85 86 1.201976 TGTTTTTCACACGTGCGTCAG 60.202 47.619 17.22 0.61 0.00 3.51
86 87 0.796927 TGTTTTTCACACGTGCGTCA 59.203 45.000 17.22 2.90 0.00 4.35
87 88 1.884756 TTGTTTTTCACACGTGCGTC 58.115 45.000 17.22 0.16 33.98 5.19
88 89 2.333389 TTTGTTTTTCACACGTGCGT 57.667 40.000 17.22 0.00 33.98 5.24
89 90 2.596419 ACATTTGTTTTTCACACGTGCG 59.404 40.909 17.22 6.29 33.98 5.34
90 91 4.090642 TGAACATTTGTTTTTCACACGTGC 59.909 37.500 17.22 0.00 38.56 5.34
91 92 5.753713 TGAACATTTGTTTTTCACACGTG 57.246 34.783 15.48 15.48 38.56 4.49
92 93 5.164138 CGTTGAACATTTGTTTTTCACACGT 60.164 36.000 0.00 0.00 38.56 4.49
93 94 5.236969 CGTTGAACATTTGTTTTTCACACG 58.763 37.500 0.00 0.00 38.56 4.49
94 95 5.119434 ACCGTTGAACATTTGTTTTTCACAC 59.881 36.000 0.00 0.00 38.56 3.82
95 96 5.230942 ACCGTTGAACATTTGTTTTTCACA 58.769 33.333 0.00 0.00 38.56 3.58
96 97 5.220322 GGACCGTTGAACATTTGTTTTTCAC 60.220 40.000 0.00 0.00 38.56 3.18
97 98 4.865365 GGACCGTTGAACATTTGTTTTTCA 59.135 37.500 0.00 0.00 38.56 2.69
98 99 4.027214 CGGACCGTTGAACATTTGTTTTTC 60.027 41.667 5.48 0.00 38.56 2.29
99 100 3.860536 CGGACCGTTGAACATTTGTTTTT 59.139 39.130 5.48 0.00 38.56 1.94
100 101 3.119424 ACGGACCGTTGAACATTTGTTTT 60.119 39.130 15.37 0.00 36.35 2.43
101 102 2.424246 ACGGACCGTTGAACATTTGTTT 59.576 40.909 15.37 0.00 36.35 2.83
102 103 2.018515 ACGGACCGTTGAACATTTGTT 58.981 42.857 15.37 0.00 36.35 2.83
103 104 1.670791 ACGGACCGTTGAACATTTGT 58.329 45.000 15.37 0.00 36.35 2.83
114 115 0.395312 AGTTGAATGGAACGGACCGT 59.605 50.000 15.37 15.37 43.97 4.83
115 116 0.796312 CAGTTGAATGGAACGGACCG 59.204 55.000 13.61 13.61 0.00 4.79
116 117 1.892209 ACAGTTGAATGGAACGGACC 58.108 50.000 0.00 0.00 0.00 4.46
117 118 2.604614 GCAACAGTTGAATGGAACGGAC 60.605 50.000 17.99 0.00 0.00 4.79
118 119 1.606668 GCAACAGTTGAATGGAACGGA 59.393 47.619 17.99 0.00 0.00 4.69
119 120 1.336440 TGCAACAGTTGAATGGAACGG 59.664 47.619 17.99 0.00 0.00 4.44
120 121 2.223456 TGTGCAACAGTTGAATGGAACG 60.223 45.455 17.99 0.00 45.67 3.95
121 122 3.435105 TGTGCAACAGTTGAATGGAAC 57.565 42.857 17.99 5.34 45.67 3.62
138 139 1.068402 TGGTGATCGCTGCATTTTGTG 60.068 47.619 6.18 0.00 0.00 3.33
139 140 1.200716 CTGGTGATCGCTGCATTTTGT 59.799 47.619 6.18 0.00 0.00 2.83
140 141 1.468565 CCTGGTGATCGCTGCATTTTG 60.469 52.381 6.18 0.00 0.00 2.44
141 142 0.813184 CCTGGTGATCGCTGCATTTT 59.187 50.000 6.18 0.00 0.00 1.82
142 143 0.035152 TCCTGGTGATCGCTGCATTT 60.035 50.000 6.18 0.00 0.00 2.32
143 144 0.463295 CTCCTGGTGATCGCTGCATT 60.463 55.000 6.18 0.00 0.00 3.56
144 145 1.145598 CTCCTGGTGATCGCTGCAT 59.854 57.895 6.18 0.00 0.00 3.96
145 146 0.970427 TACTCCTGGTGATCGCTGCA 60.970 55.000 6.18 0.00 0.00 4.41
146 147 0.390860 ATACTCCTGGTGATCGCTGC 59.609 55.000 6.18 0.00 0.00 5.25
147 148 4.240888 CAATATACTCCTGGTGATCGCTG 58.759 47.826 6.18 0.00 0.00 5.18
148 149 3.898123 ACAATATACTCCTGGTGATCGCT 59.102 43.478 6.18 0.00 0.00 4.93
149 150 4.258702 ACAATATACTCCTGGTGATCGC 57.741 45.455 2.23 0.00 0.00 4.58
150 151 6.016192 ACACTACAATATACTCCTGGTGATCG 60.016 42.308 2.23 0.00 0.00 3.69
151 152 7.148641 CACACTACAATATACTCCTGGTGATC 58.851 42.308 2.23 0.00 0.00 2.92
152 153 6.611642 ACACACTACAATATACTCCTGGTGAT 59.388 38.462 2.23 0.00 0.00 3.06
153 154 5.955959 ACACACTACAATATACTCCTGGTGA 59.044 40.000 2.23 0.00 0.00 4.02
154 155 6.222038 ACACACTACAATATACTCCTGGTG 57.778 41.667 0.00 0.00 0.00 4.17
155 156 6.405508 CGAACACACTACAATATACTCCTGGT 60.406 42.308 0.00 0.00 0.00 4.00
156 157 5.977725 CGAACACACTACAATATACTCCTGG 59.022 44.000 0.00 0.00 0.00 4.45
157 158 5.977725 CCGAACACACTACAATATACTCCTG 59.022 44.000 0.00 0.00 0.00 3.86
158 159 5.451520 GCCGAACACACTACAATATACTCCT 60.452 44.000 0.00 0.00 0.00 3.69
159 160 4.743644 GCCGAACACACTACAATATACTCC 59.256 45.833 0.00 0.00 0.00 3.85
160 161 4.440103 CGCCGAACACACTACAATATACTC 59.560 45.833 0.00 0.00 0.00 2.59
161 162 4.357142 CGCCGAACACACTACAATATACT 58.643 43.478 0.00 0.00 0.00 2.12
162 163 3.488310 CCGCCGAACACACTACAATATAC 59.512 47.826 0.00 0.00 0.00 1.47
163 164 3.380954 TCCGCCGAACACACTACAATATA 59.619 43.478 0.00 0.00 0.00 0.86
164 165 2.166870 TCCGCCGAACACACTACAATAT 59.833 45.455 0.00 0.00 0.00 1.28
165 166 1.545136 TCCGCCGAACACACTACAATA 59.455 47.619 0.00 0.00 0.00 1.90
166 167 0.319083 TCCGCCGAACACACTACAAT 59.681 50.000 0.00 0.00 0.00 2.71
167 168 0.319211 CTCCGCCGAACACACTACAA 60.319 55.000 0.00 0.00 0.00 2.41
168 169 1.287815 CTCCGCCGAACACACTACA 59.712 57.895 0.00 0.00 0.00 2.74
169 170 2.092882 GCTCCGCCGAACACACTAC 61.093 63.158 0.00 0.00 0.00 2.73
170 171 1.884075 ATGCTCCGCCGAACACACTA 61.884 55.000 0.00 0.00 0.00 2.74
171 172 1.884075 TATGCTCCGCCGAACACACT 61.884 55.000 0.00 0.00 0.00 3.55
176 177 1.583054 AAGAATATGCTCCGCCGAAC 58.417 50.000 0.00 0.00 0.00 3.95
199 200 2.025981 TGTGCTGGCCAATAGAGTCAAT 60.026 45.455 7.01 0.00 0.00 2.57
245 246 5.335127 CATTTGGTAGTTAAGATGCACAGC 58.665 41.667 0.00 0.00 0.00 4.40
246 247 5.106197 TGCATTTGGTAGTTAAGATGCACAG 60.106 40.000 4.85 0.00 43.25 3.66
247 248 4.764308 TGCATTTGGTAGTTAAGATGCACA 59.236 37.500 4.85 0.00 43.25 4.57
257 258 4.568956 GGCTCAAAATGCATTTGGTAGTT 58.431 39.130 24.74 5.71 46.85 2.24
284 285 1.367346 TAACATGGGCACAAGGAGGA 58.633 50.000 0.00 0.00 0.00 3.71
286 287 2.513753 TGTTAACATGGGCACAAGGAG 58.486 47.619 3.59 0.00 0.00 3.69
293 294 4.013728 GACCTACAATGTTAACATGGGCA 58.986 43.478 23.82 12.16 36.56 5.36
294 295 4.013728 TGACCTACAATGTTAACATGGGC 58.986 43.478 23.82 20.63 36.56 5.36
295 296 6.773976 ATTGACCTACAATGTTAACATGGG 57.226 37.500 23.82 21.34 45.99 4.00
310 311 6.606241 AAATGGGGGAGATTTATTGACCTA 57.394 37.500 0.00 0.00 0.00 3.08
334 335 8.132995 CCCGCGAAATTTATATTCTTTTAAGGT 58.867 33.333 8.23 0.00 0.00 3.50
350 351 0.609681 TTAAGGCACCCCGCGAAATT 60.610 50.000 8.23 0.00 43.84 1.82
351 352 0.609681 TTTAAGGCACCCCGCGAAAT 60.610 50.000 8.23 0.00 43.84 2.17
355 356 1.238625 TTCTTTTAAGGCACCCCGCG 61.239 55.000 0.00 0.00 43.84 6.46
376 377 2.633967 TGTAGAGGGAAAACGTGGCTAA 59.366 45.455 0.00 0.00 0.00 3.09
396 397 1.226379 GACATTGCGCCGGATGTTG 60.226 57.895 18.24 0.00 36.67 3.33
426 427 0.313987 GGGGTTGTTGGCTTCGAAAG 59.686 55.000 0.00 0.00 0.00 2.62
458 459 4.105486 GCACCTTGTTCTTGTTCTTGTTC 58.895 43.478 0.00 0.00 0.00 3.18
459 460 3.509575 TGCACCTTGTTCTTGTTCTTGTT 59.490 39.130 0.00 0.00 0.00 2.83
460 461 3.088532 TGCACCTTGTTCTTGTTCTTGT 58.911 40.909 0.00 0.00 0.00 3.16
461 462 3.438360 GTGCACCTTGTTCTTGTTCTTG 58.562 45.455 5.22 0.00 0.00 3.02
462 463 2.427095 GGTGCACCTTGTTCTTGTTCTT 59.573 45.455 29.12 0.00 0.00 2.52
463 464 2.024414 GGTGCACCTTGTTCTTGTTCT 58.976 47.619 29.12 0.00 0.00 3.01
464 465 1.067060 GGGTGCACCTTGTTCTTGTTC 59.933 52.381 33.91 10.13 35.85 3.18
465 466 1.111277 GGGTGCACCTTGTTCTTGTT 58.889 50.000 33.91 0.00 35.85 2.83
466 467 0.755327 GGGGTGCACCTTGTTCTTGT 60.755 55.000 33.91 0.00 40.03 3.16
467 468 0.754957 TGGGGTGCACCTTGTTCTTG 60.755 55.000 33.91 0.00 40.03 3.02
468 469 0.188342 ATGGGGTGCACCTTGTTCTT 59.812 50.000 33.91 14.04 40.03 2.52
469 470 0.251341 GATGGGGTGCACCTTGTTCT 60.251 55.000 33.91 13.82 40.03 3.01
470 471 0.251341 AGATGGGGTGCACCTTGTTC 60.251 55.000 33.91 23.51 40.03 3.18
471 472 0.251341 GAGATGGGGTGCACCTTGTT 60.251 55.000 33.91 17.14 40.03 2.83
472 473 1.136329 AGAGATGGGGTGCACCTTGT 61.136 55.000 33.91 19.89 40.03 3.16
473 474 0.393537 GAGAGATGGGGTGCACCTTG 60.394 60.000 33.91 0.00 40.03 3.61
474 475 0.548682 AGAGAGATGGGGTGCACCTT 60.549 55.000 33.91 19.66 40.03 3.50
475 476 0.548682 AAGAGAGATGGGGTGCACCT 60.549 55.000 33.91 16.27 40.03 4.00
476 477 0.393537 CAAGAGAGATGGGGTGCACC 60.394 60.000 28.57 28.57 39.11 5.01
495 496 7.350110 TGGTATTAGTTAGTGTAAACAACGC 57.650 36.000 0.00 0.00 38.99 4.84
496 497 8.763356 TGTTGGTATTAGTTAGTGTAAACAACG 58.237 33.333 0.00 0.00 36.91 4.10
501 502 7.337436 GGGCATGTTGGTATTAGTTAGTGTAAA 59.663 37.037 0.00 0.00 0.00 2.01
505 506 5.189928 TGGGCATGTTGGTATTAGTTAGTG 58.810 41.667 0.00 0.00 0.00 2.74
506 507 5.444744 TGGGCATGTTGGTATTAGTTAGT 57.555 39.130 0.00 0.00 0.00 2.24
507 508 6.601613 TCTTTGGGCATGTTGGTATTAGTTAG 59.398 38.462 0.00 0.00 0.00 2.34
508 509 6.486056 TCTTTGGGCATGTTGGTATTAGTTA 58.514 36.000 0.00 0.00 0.00 2.24
509 510 5.329399 TCTTTGGGCATGTTGGTATTAGTT 58.671 37.500 0.00 0.00 0.00 2.24
511 512 6.469782 AATCTTTGGGCATGTTGGTATTAG 57.530 37.500 0.00 0.00 0.00 1.73
512 513 6.892456 TGTAATCTTTGGGCATGTTGGTATTA 59.108 34.615 0.00 0.00 0.00 0.98
513 514 5.719085 TGTAATCTTTGGGCATGTTGGTATT 59.281 36.000 0.00 0.00 0.00 1.89
536 537 3.435105 TGCTTTGTTTTAGTGTGGCTG 57.565 42.857 0.00 0.00 0.00 4.85
549 550 2.143122 TCGATCGCTTCTTTGCTTTGT 58.857 42.857 11.09 0.00 0.00 2.83
572 573 3.721798 CGTGTTTGTGGTCAACGTATTTG 59.278 43.478 0.00 0.00 36.42 2.32
576 577 1.288350 CCGTGTTTGTGGTCAACGTA 58.712 50.000 0.00 0.00 32.93 3.57
578 579 0.448593 AACCGTGTTTGTGGTCAACG 59.551 50.000 0.00 0.00 37.54 4.10
603 624 2.034053 GTGGAGACCGCAATTGTCAAAA 59.966 45.455 7.40 0.00 35.15 2.44
692 713 2.956964 CTGTCTCCGGAATCGCGC 60.957 66.667 5.23 0.00 34.56 6.86
697 720 1.067821 GATTCTCGCTGTCTCCGGAAT 59.932 52.381 5.23 0.00 32.40 3.01
895 1228 0.321653 GCAAGCGAAGGAAGGAAGGA 60.322 55.000 0.00 0.00 0.00 3.36
909 1242 1.400142 GGTTTGGTTTGGTTTGCAAGC 59.600 47.619 4.46 4.46 0.00 4.01
1009 1382 1.460689 TTTGGTCTGGGGTCGGAGT 60.461 57.895 0.00 0.00 0.00 3.85
1062 1445 2.125350 GAGAGGTTGAGCTGCCGG 60.125 66.667 0.00 0.00 0.00 6.13
1200 1583 2.764128 TGGATGGACCTCTCCGGC 60.764 66.667 0.00 0.00 39.88 6.13
1360 1743 1.281899 GCGAATCGTCAGAAGGGAAG 58.718 55.000 4.07 0.00 0.00 3.46
1640 2053 3.799035 CAACTCAAACGACCAAGAATCG 58.201 45.455 0.00 0.00 45.17 3.34
1712 2125 5.586243 CACCTTGGATCACGTCAAATTATCT 59.414 40.000 0.00 0.00 0.00 1.98
1727 2140 8.582437 CATAATTGCATCTATTTCACCTTGGAT 58.418 33.333 0.00 0.00 0.00 3.41
1728 2141 7.944061 CATAATTGCATCTATTTCACCTTGGA 58.056 34.615 0.00 0.00 0.00 3.53
2353 2773 3.308323 GTGAACAGAAAGATCGAGATGCC 59.692 47.826 0.00 0.00 0.00 4.40
2360 2780 3.367025 GGTAACGGTGAACAGAAAGATCG 59.633 47.826 0.00 0.00 0.00 3.69
2363 2783 2.435069 TGGGTAACGGTGAACAGAAAGA 59.565 45.455 0.00 0.00 37.60 2.52
2377 2797 6.415573 ACCAGAAGATACTGAAATGGGTAAC 58.584 40.000 0.00 0.00 39.94 2.50
2412 2832 2.765807 AGGAGGGCGGATGTCCAG 60.766 66.667 0.00 0.00 44.71 3.86
2420 2840 4.247380 GGCTGATCAGGAGGGCGG 62.247 72.222 23.89 0.00 0.00 6.13
2494 2914 1.155042 CAGGACAAGAGAGCAAGTGC 58.845 55.000 0.00 0.00 42.49 4.40
2842 3262 2.524569 TGAAACACATCAGCTCACGA 57.475 45.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.