Multiple sequence alignment - TraesCS7D01G552400

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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 TraesCS7D01G552400 chr7D 100.000 3325 0 0 1 3325 635417156 635420480 0.000000e+00 6141
1 TraesCS7D01G552400 chr7D 96.081 2858 110 2 270 3126 634958982 634961838 0.000000e+00 4656
2 TraesCS7D01G552400 chr7D 95.357 2692 104 8 270 2954 634881594 634878917 0.000000e+00 4259
3 TraesCS7D01G552400 chr7D 92.013 2692 183 15 268 2951 634979867 634982534 0.000000e+00 3751
4 TraesCS7D01G552400 chr7D 91.611 2539 181 15 268 2799 634987281 634989794 0.000000e+00 3480
5 TraesCS7D01G552400 chr7D 99.259 270 2 0 1 270 424619014 424618745 3.860000e-134 488
6 TraesCS7D01G552400 chr7D 99.259 270 2 0 1 270 635410326 635410595 3.860000e-134 488
7 TraesCS7D01G552400 chr7D 98.889 270 3 0 1 270 424625836 424625567 1.790000e-132 483
8 TraesCS7D01G552400 chr7D 97.778 270 6 0 1 270 48134485 48134754 1.810000e-127 466
9 TraesCS7D01G552400 chr7B 94.065 2898 138 14 270 3164 741233028 741230162 0.000000e+00 4368
10 TraesCS7D01G552400 chr7B 95.349 2365 102 6 270 2631 741275573 741277932 0.000000e+00 3751
11 TraesCS7D01G552400 chr7B 92.579 539 33 5 2628 3164 741289602 741290135 0.000000e+00 767
12 TraesCS7D01G552400 chr7A 95.731 2483 99 5 270 2751 730702643 730700167 0.000000e+00 3991
13 TraesCS7D01G552400 chr7A 95.717 2265 89 5 489 2751 730680111 730677853 0.000000e+00 3639
14 TraesCS7D01G552400 chr7A 91.118 2702 209 17 268 2954 730591684 730588999 0.000000e+00 3631
15 TraesCS7D01G552400 chr4D 97.818 275 6 0 1 275 269409877 269410151 3.000000e-130 475
16 TraesCS7D01G552400 chr4D 97.417 271 7 0 1 271 468040041 468039771 2.340000e-126 462
17 TraesCS7D01G552400 chr5D 98.148 270 5 0 1 270 402929149 402929418 3.880000e-129 472
18 TraesCS7D01G552400 chr5D 97.753 267 6 0 4 270 375086489 375086223 8.400000e-126 460
19 TraesCS7D01G552400 chr5D 88.127 379 33 10 2950 3325 442046288 442046657 1.090000e-119 440
20 TraesCS7D01G552400 chr1D 98.148 270 5 0 1 270 298038003 298038272 3.880000e-129 472
21 TraesCS7D01G552400 chr1D 89.489 352 33 3 2951 3301 231007434 231007086 3.040000e-120 442
22 TraesCS7D01G552400 chr1D 89.548 354 30 5 2951 3301 341631601 341631252 3.040000e-120 442
23 TraesCS7D01G552400 chr2D 90.571 350 28 4 2953 3301 302535949 302536294 3.020000e-125 459
24 TraesCS7D01G552400 chr2D 89.577 355 28 7 2951 3302 511004686 511005034 3.040000e-120 442
25 TraesCS7D01G552400 chr6D 88.978 372 32 6 2957 3325 24047234 24046869 5.060000e-123 451
26 TraesCS7D01G552400 chr6D 87.798 377 38 5 2951 3325 300015520 300015890 5.090000e-118 435


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 TraesCS7D01G552400 chr7D 635417156 635420480 3324 False 6141 6141 100.000 1 3325 1 chr7D.!!$F6 3324
1 TraesCS7D01G552400 chr7D 634958982 634961838 2856 False 4656 4656 96.081 270 3126 1 chr7D.!!$F2 2856
2 TraesCS7D01G552400 chr7D 634878917 634881594 2677 True 4259 4259 95.357 270 2954 1 chr7D.!!$R3 2684
3 TraesCS7D01G552400 chr7D 634979867 634982534 2667 False 3751 3751 92.013 268 2951 1 chr7D.!!$F3 2683
4 TraesCS7D01G552400 chr7D 634987281 634989794 2513 False 3480 3480 91.611 268 2799 1 chr7D.!!$F4 2531
5 TraesCS7D01G552400 chr7B 741230162 741233028 2866 True 4368 4368 94.065 270 3164 1 chr7B.!!$R1 2894
6 TraesCS7D01G552400 chr7B 741275573 741277932 2359 False 3751 3751 95.349 270 2631 1 chr7B.!!$F1 2361
7 TraesCS7D01G552400 chr7B 741289602 741290135 533 False 767 767 92.579 2628 3164 1 chr7B.!!$F2 536
8 TraesCS7D01G552400 chr7A 730700167 730702643 2476 True 3991 3991 95.731 270 2751 1 chr7A.!!$R3 2481
9 TraesCS7D01G552400 chr7A 730677853 730680111 2258 True 3639 3639 95.717 489 2751 1 chr7A.!!$R2 2262
10 TraesCS7D01G552400 chr7A 730588999 730591684 2685 True 3631 3631 91.118 268 2954 1 chr7A.!!$R1 2686

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
54 55 0.034896 GGGTCTTGCTTCCTCGTCAA 59.965 55.0 0.00 0.0 0.00 3.18 F
142 143 0.038166 GGGCCTTGTTGTCCATCTGA 59.962 55.0 0.84 0.0 0.00 3.27 F
181 182 0.179000 ATGAGTCACCAAGATCGGGC 59.821 55.0 0.00 0.0 0.00 6.13 F
187 188 0.251916 CACCAAGATCGGGCAGGTTA 59.748 55.0 6.40 0.0 0.00 2.85 F
233 234 0.320771 GTCACCAGTGAGTCGCCAAT 60.321 55.0 0.00 0.0 40.75 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1767 0.886490 CAGGTGGCTGGAGTTGTGAC 60.886 60.000 0.0 0.0 0.00 3.67 R
2004 2009 1.447838 CCCGATGTTGAGTCGTGGG 60.448 63.158 0.0 0.0 37.39 4.61 R
2270 2275 2.801342 GCATCTACGAAAGCTCTCCAGG 60.801 54.545 0.0 0.0 0.00 4.45 R
2271 2276 2.100584 AGCATCTACGAAAGCTCTCCAG 59.899 50.000 0.0 0.0 30.05 3.86 R
2508 2519 6.434028 AGGTGCATTGTTGTAATACATGTTCT 59.566 34.615 2.3 0.0 0.00 3.01 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 8.752766 TCTCTTACAAGTTAATTACAAGTCCG 57.247 34.615 0.00 0.00 0.00 4.79
36 37 7.816031 TCTCTTACAAGTTAATTACAAGTCCGG 59.184 37.037 0.00 0.00 0.00 5.14
37 38 6.875195 TCTTACAAGTTAATTACAAGTCCGGG 59.125 38.462 0.00 0.00 0.00 5.73
38 39 4.976864 ACAAGTTAATTACAAGTCCGGGT 58.023 39.130 0.00 0.00 0.00 5.28
39 40 4.999311 ACAAGTTAATTACAAGTCCGGGTC 59.001 41.667 0.00 0.00 0.00 4.46
40 41 5.221783 ACAAGTTAATTACAAGTCCGGGTCT 60.222 40.000 0.00 0.00 0.00 3.85
41 42 5.494390 AGTTAATTACAAGTCCGGGTCTT 57.506 39.130 0.00 4.13 0.00 3.01
42 43 5.243207 AGTTAATTACAAGTCCGGGTCTTG 58.757 41.667 25.74 25.74 45.15 3.02
43 44 2.109425 ATTACAAGTCCGGGTCTTGC 57.891 50.000 26.80 5.05 43.97 4.01
44 45 1.053424 TTACAAGTCCGGGTCTTGCT 58.947 50.000 26.80 18.39 43.97 3.91
45 46 1.053424 TACAAGTCCGGGTCTTGCTT 58.947 50.000 26.80 15.17 43.97 3.91
46 47 0.250338 ACAAGTCCGGGTCTTGCTTC 60.250 55.000 26.80 1.91 43.97 3.86
47 48 0.955919 CAAGTCCGGGTCTTGCTTCC 60.956 60.000 18.59 0.00 36.38 3.46
48 49 1.128188 AAGTCCGGGTCTTGCTTCCT 61.128 55.000 0.00 0.00 0.00 3.36
49 50 1.079057 GTCCGGGTCTTGCTTCCTC 60.079 63.158 0.00 0.00 0.00 3.71
50 51 2.125512 CCGGGTCTTGCTTCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
51 52 2.657237 CGGGTCTTGCTTCCTCGT 59.343 61.111 0.00 0.00 0.00 4.18
52 53 1.446272 CGGGTCTTGCTTCCTCGTC 60.446 63.158 0.00 0.00 0.00 4.20
53 54 1.671742 GGGTCTTGCTTCCTCGTCA 59.328 57.895 0.00 0.00 0.00 4.35
54 55 0.034896 GGGTCTTGCTTCCTCGTCAA 59.965 55.000 0.00 0.00 0.00 3.18
55 56 1.433534 GGTCTTGCTTCCTCGTCAAG 58.566 55.000 0.00 0.00 38.73 3.02
70 71 6.204075 CTCGTCAAGGAAATATTCGTCATC 57.796 41.667 0.00 0.00 0.00 2.92
71 72 5.047847 TCGTCAAGGAAATATTCGTCATCC 58.952 41.667 0.00 0.00 0.00 3.51
72 73 4.211374 CGTCAAGGAAATATTCGTCATCCC 59.789 45.833 0.36 0.00 0.00 3.85
73 74 5.368989 GTCAAGGAAATATTCGTCATCCCT 58.631 41.667 0.36 0.00 0.00 4.20
74 75 5.823045 GTCAAGGAAATATTCGTCATCCCTT 59.177 40.000 0.36 0.00 33.46 3.95
75 76 6.318900 GTCAAGGAAATATTCGTCATCCCTTT 59.681 38.462 0.00 0.00 31.07 3.11
76 77 6.542370 TCAAGGAAATATTCGTCATCCCTTTC 59.458 38.462 0.00 0.00 31.07 2.62
77 78 6.253946 AGGAAATATTCGTCATCCCTTTCT 57.746 37.500 0.36 0.00 0.00 2.52
78 79 6.663734 AGGAAATATTCGTCATCCCTTTCTT 58.336 36.000 0.36 0.00 0.00 2.52
79 80 6.768381 AGGAAATATTCGTCATCCCTTTCTTC 59.232 38.462 0.36 0.00 0.00 2.87
80 81 6.768381 GGAAATATTCGTCATCCCTTTCTTCT 59.232 38.462 0.00 0.00 0.00 2.85
81 82 7.283354 GGAAATATTCGTCATCCCTTTCTTCTT 59.717 37.037 0.00 0.00 0.00 2.52
82 83 9.326413 GAAATATTCGTCATCCCTTTCTTCTTA 57.674 33.333 0.00 0.00 0.00 2.10
83 84 9.681062 AAATATTCGTCATCCCTTTCTTCTTAA 57.319 29.630 0.00 0.00 0.00 1.85
84 85 8.894768 ATATTCGTCATCCCTTTCTTCTTAAG 57.105 34.615 0.00 0.00 0.00 1.85
85 86 4.504858 TCGTCATCCCTTTCTTCTTAAGC 58.495 43.478 0.00 0.00 0.00 3.09
86 87 3.623510 CGTCATCCCTTTCTTCTTAAGCC 59.376 47.826 0.00 0.00 0.00 4.35
87 88 3.623510 GTCATCCCTTTCTTCTTAAGCCG 59.376 47.826 0.00 0.00 0.00 5.52
88 89 2.781681 TCCCTTTCTTCTTAAGCCGG 57.218 50.000 0.00 0.00 0.00 6.13
89 90 1.095600 CCCTTTCTTCTTAAGCCGGC 58.904 55.000 21.89 21.89 0.00 6.13
90 91 1.095600 CCTTTCTTCTTAAGCCGGCC 58.904 55.000 26.15 5.07 0.00 6.13
91 92 1.095600 CTTTCTTCTTAAGCCGGCCC 58.904 55.000 26.15 0.00 0.00 5.80
92 93 0.402504 TTTCTTCTTAAGCCGGCCCA 59.597 50.000 26.15 8.47 0.00 5.36
93 94 0.623723 TTCTTCTTAAGCCGGCCCAT 59.376 50.000 26.15 12.97 0.00 4.00
94 95 0.180406 TCTTCTTAAGCCGGCCCATC 59.820 55.000 26.15 0.00 0.00 3.51
95 96 0.107214 CTTCTTAAGCCGGCCCATCA 60.107 55.000 26.15 0.86 0.00 3.07
96 97 0.550914 TTCTTAAGCCGGCCCATCAT 59.449 50.000 26.15 0.00 0.00 2.45
97 98 1.429930 TCTTAAGCCGGCCCATCATA 58.570 50.000 26.15 4.11 0.00 2.15
98 99 1.771854 TCTTAAGCCGGCCCATCATAA 59.228 47.619 26.15 11.91 0.00 1.90
99 100 2.173782 TCTTAAGCCGGCCCATCATAAA 59.826 45.455 26.15 5.05 0.00 1.40
100 101 1.975660 TAAGCCGGCCCATCATAAAC 58.024 50.000 26.15 0.00 0.00 2.01
101 102 1.101049 AAGCCGGCCCATCATAAACG 61.101 55.000 26.15 0.00 0.00 3.60
102 103 1.822186 GCCGGCCCATCATAAACGT 60.822 57.895 18.11 0.00 0.00 3.99
103 104 2.021722 CCGGCCCATCATAAACGTG 58.978 57.895 0.00 0.00 0.00 4.49
104 105 0.462937 CCGGCCCATCATAAACGTGA 60.463 55.000 0.00 0.00 0.00 4.35
105 106 0.937304 CGGCCCATCATAAACGTGAG 59.063 55.000 0.00 0.00 0.00 3.51
106 107 0.663153 GGCCCATCATAAACGTGAGC 59.337 55.000 0.00 0.00 0.00 4.26
107 108 0.663153 GCCCATCATAAACGTGAGCC 59.337 55.000 0.00 0.00 0.00 4.70
108 109 0.937304 CCCATCATAAACGTGAGCCG 59.063 55.000 0.00 0.00 44.03 5.52
109 110 0.937304 CCATCATAAACGTGAGCCGG 59.063 55.000 0.00 0.00 42.24 6.13
110 111 0.304705 CATCATAAACGTGAGCCGGC 59.695 55.000 21.89 21.89 42.24 6.13
111 112 0.814010 ATCATAAACGTGAGCCGGCC 60.814 55.000 26.15 15.80 42.24 6.13
112 113 1.449601 CATAAACGTGAGCCGGCCT 60.450 57.895 26.15 10.99 42.24 5.19
113 114 1.024579 CATAAACGTGAGCCGGCCTT 61.025 55.000 26.15 4.93 42.24 4.35
114 115 0.743345 ATAAACGTGAGCCGGCCTTC 60.743 55.000 26.15 16.53 42.24 3.46
115 116 1.823169 TAAACGTGAGCCGGCCTTCT 61.823 55.000 26.15 3.43 42.24 2.85
116 117 3.883744 AACGTGAGCCGGCCTTCTG 62.884 63.158 26.15 14.15 42.24 3.02
118 119 4.785453 GTGAGCCGGCCTTCTGGG 62.785 72.222 26.15 0.00 39.23 4.45
135 136 3.051210 GCCTTGGGCCTTGTTGTC 58.949 61.111 4.53 0.00 44.06 3.18
136 137 2.574018 GCCTTGGGCCTTGTTGTCC 61.574 63.158 4.53 0.00 44.06 4.02
137 138 1.152567 CCTTGGGCCTTGTTGTCCA 60.153 57.895 4.53 0.00 0.00 4.02
138 139 0.542702 CCTTGGGCCTTGTTGTCCAT 60.543 55.000 4.53 0.00 0.00 3.41
139 140 0.890683 CTTGGGCCTTGTTGTCCATC 59.109 55.000 4.53 0.00 0.00 3.51
140 141 0.482446 TTGGGCCTTGTTGTCCATCT 59.518 50.000 4.53 0.00 0.00 2.90
141 142 0.251297 TGGGCCTTGTTGTCCATCTG 60.251 55.000 4.53 0.00 0.00 2.90
142 143 0.038166 GGGCCTTGTTGTCCATCTGA 59.962 55.000 0.84 0.00 0.00 3.27
143 144 1.168714 GGCCTTGTTGTCCATCTGAC 58.831 55.000 0.00 0.00 44.72 3.51
144 145 1.168714 GCCTTGTTGTCCATCTGACC 58.831 55.000 0.00 0.00 43.78 4.02
145 146 1.826385 CCTTGTTGTCCATCTGACCC 58.174 55.000 0.00 0.00 43.78 4.46
146 147 1.442769 CTTGTTGTCCATCTGACCCG 58.557 55.000 0.00 0.00 43.78 5.28
147 148 0.605319 TTGTTGTCCATCTGACCCGC 60.605 55.000 0.00 0.00 43.78 6.13
148 149 1.745489 GTTGTCCATCTGACCCGCC 60.745 63.158 0.00 0.00 43.78 6.13
149 150 2.966732 TTGTCCATCTGACCCGCCC 61.967 63.158 0.00 0.00 43.78 6.13
150 151 4.530857 GTCCATCTGACCCGCCCG 62.531 72.222 0.00 0.00 38.09 6.13
162 163 4.146075 CGCCCGCCGGGTTACTAA 62.146 66.667 25.58 0.00 46.51 2.24
163 164 2.507452 GCCCGCCGGGTTACTAAT 59.493 61.111 25.58 0.00 46.51 1.73
164 165 1.890510 GCCCGCCGGGTTACTAATG 60.891 63.158 25.58 0.00 46.51 1.90
165 166 1.824658 CCCGCCGGGTTACTAATGA 59.175 57.895 15.86 0.00 38.25 2.57
166 167 0.249741 CCCGCCGGGTTACTAATGAG 60.250 60.000 15.86 0.00 38.25 2.90
167 168 0.462789 CCGCCGGGTTACTAATGAGT 59.537 55.000 2.18 0.00 39.92 3.41
168 169 1.537562 CCGCCGGGTTACTAATGAGTC 60.538 57.143 2.18 0.00 37.10 3.36
169 170 1.135527 CGCCGGGTTACTAATGAGTCA 59.864 52.381 2.18 0.00 37.10 3.41
170 171 2.547826 GCCGGGTTACTAATGAGTCAC 58.452 52.381 2.18 0.00 37.10 3.67
171 172 2.740904 GCCGGGTTACTAATGAGTCACC 60.741 54.545 2.18 5.09 45.71 4.02
178 179 5.749109 GGTTACTAATGAGTCACCAAGATCG 59.251 44.000 8.53 0.00 45.73 3.69
179 180 4.392921 ACTAATGAGTCACCAAGATCGG 57.607 45.455 0.00 0.00 0.00 4.18
180 181 2.698855 AATGAGTCACCAAGATCGGG 57.301 50.000 0.00 5.06 0.00 5.14
181 182 0.179000 ATGAGTCACCAAGATCGGGC 59.821 55.000 0.00 0.00 0.00 6.13
182 183 1.191489 TGAGTCACCAAGATCGGGCA 61.191 55.000 6.40 0.00 0.00 5.36
183 184 0.460987 GAGTCACCAAGATCGGGCAG 60.461 60.000 6.40 0.88 0.00 4.85
184 185 1.450312 GTCACCAAGATCGGGCAGG 60.450 63.158 6.40 0.00 0.00 4.85
185 186 1.918293 TCACCAAGATCGGGCAGGT 60.918 57.895 6.40 0.00 0.00 4.00
186 187 1.002134 CACCAAGATCGGGCAGGTT 60.002 57.895 6.40 0.00 0.00 3.50
187 188 0.251916 CACCAAGATCGGGCAGGTTA 59.748 55.000 6.40 0.00 0.00 2.85
188 189 1.134098 CACCAAGATCGGGCAGGTTAT 60.134 52.381 6.40 0.00 0.00 1.89
189 190 1.141053 ACCAAGATCGGGCAGGTTATC 59.859 52.381 6.40 0.00 0.00 1.75
190 191 1.417890 CCAAGATCGGGCAGGTTATCT 59.582 52.381 0.00 0.00 0.00 1.98
191 192 2.487934 CAAGATCGGGCAGGTTATCTG 58.512 52.381 0.00 0.00 46.03 2.90
192 193 1.794714 AGATCGGGCAGGTTATCTGT 58.205 50.000 0.00 0.00 45.08 3.41
193 194 1.414181 AGATCGGGCAGGTTATCTGTG 59.586 52.381 0.00 0.00 45.08 3.66
194 195 1.412710 GATCGGGCAGGTTATCTGTGA 59.587 52.381 0.00 0.00 45.08 3.58
195 196 1.271856 TCGGGCAGGTTATCTGTGAA 58.728 50.000 0.00 0.00 45.08 3.18
196 197 1.837439 TCGGGCAGGTTATCTGTGAAT 59.163 47.619 0.00 0.00 45.08 2.57
197 198 2.158957 TCGGGCAGGTTATCTGTGAATC 60.159 50.000 0.00 0.00 45.08 2.52
198 199 2.213499 GGGCAGGTTATCTGTGAATCG 58.787 52.381 0.00 0.00 45.08 3.34
199 200 1.599542 GGCAGGTTATCTGTGAATCGC 59.400 52.381 0.00 0.00 45.08 4.58
200 201 1.599542 GCAGGTTATCTGTGAATCGCC 59.400 52.381 0.00 0.00 45.08 5.54
201 202 2.905075 CAGGTTATCTGTGAATCGCCA 58.095 47.619 0.00 0.00 38.64 5.69
202 203 3.270027 CAGGTTATCTGTGAATCGCCAA 58.730 45.455 0.00 0.00 38.64 4.52
203 204 3.310774 CAGGTTATCTGTGAATCGCCAAG 59.689 47.826 0.00 0.00 38.64 3.61
204 205 2.032178 GGTTATCTGTGAATCGCCAAGC 59.968 50.000 0.00 0.00 0.00 4.01
205 206 2.939103 GTTATCTGTGAATCGCCAAGCT 59.061 45.455 0.00 0.00 0.00 3.74
206 207 1.661341 ATCTGTGAATCGCCAAGCTC 58.339 50.000 0.00 0.00 0.00 4.09
207 208 0.391661 TCTGTGAATCGCCAAGCTCC 60.392 55.000 0.00 0.00 0.00 4.70
208 209 1.699656 CTGTGAATCGCCAAGCTCCG 61.700 60.000 0.00 0.00 0.00 4.63
209 210 2.125147 TGAATCGCCAAGCTCCGG 60.125 61.111 0.00 0.00 0.00 5.14
210 211 2.897350 GAATCGCCAAGCTCCGGG 60.897 66.667 0.00 0.00 0.00 5.73
225 226 4.394712 GGGCGGGTCACCAGTGAG 62.395 72.222 0.00 0.00 40.75 3.51
226 227 3.626924 GGCGGGTCACCAGTGAGT 61.627 66.667 0.00 0.00 40.75 3.41
227 228 2.048127 GCGGGTCACCAGTGAGTC 60.048 66.667 0.00 0.00 40.75 3.36
228 229 2.258591 CGGGTCACCAGTGAGTCG 59.741 66.667 0.00 4.70 40.75 4.18
229 230 2.048127 GGGTCACCAGTGAGTCGC 60.048 66.667 0.00 0.00 40.75 5.19
230 231 2.048127 GGTCACCAGTGAGTCGCC 60.048 66.667 0.00 0.00 40.75 5.54
231 232 2.734591 GTCACCAGTGAGTCGCCA 59.265 61.111 0.00 0.00 40.75 5.69
232 233 1.069090 GTCACCAGTGAGTCGCCAA 59.931 57.895 0.00 0.00 40.75 4.52
233 234 0.320771 GTCACCAGTGAGTCGCCAAT 60.321 55.000 0.00 0.00 40.75 3.16
234 235 0.396435 TCACCAGTGAGTCGCCAATT 59.604 50.000 0.00 0.00 34.14 2.32
235 236 0.798776 CACCAGTGAGTCGCCAATTC 59.201 55.000 0.00 0.00 0.00 2.17
236 237 0.321653 ACCAGTGAGTCGCCAATTCC 60.322 55.000 0.00 0.00 0.00 3.01
237 238 1.361668 CCAGTGAGTCGCCAATTCCG 61.362 60.000 0.00 0.00 0.00 4.30
238 239 1.079127 AGTGAGTCGCCAATTCCGG 60.079 57.895 0.00 0.00 0.00 5.14
246 247 4.418328 CCAATTCCGGCCGGGTCA 62.418 66.667 42.36 27.21 37.00 4.02
247 248 2.124320 CAATTCCGGCCGGGTCAT 60.124 61.111 42.36 28.15 37.00 3.06
248 249 1.147376 CAATTCCGGCCGGGTCATA 59.853 57.895 42.36 22.14 37.00 2.15
249 250 1.147600 AATTCCGGCCGGGTCATAC 59.852 57.895 42.36 0.00 37.00 2.39
250 251 2.333701 AATTCCGGCCGGGTCATACC 62.334 60.000 42.36 0.00 37.60 2.73
251 252 4.781616 TCCGGCCGGGTCATACCA 62.782 66.667 42.36 19.62 41.02 3.25
252 253 3.556306 CCGGCCGGGTCATACCAT 61.556 66.667 37.42 0.00 41.02 3.55
253 254 2.280797 CGGCCGGGTCATACCATG 60.281 66.667 20.10 0.00 41.02 3.66
254 255 2.113139 GGCCGGGTCATACCATGG 59.887 66.667 11.19 11.19 41.02 3.66
255 256 2.113139 GCCGGGTCATACCATGGG 59.887 66.667 18.09 0.00 41.02 4.00
256 257 2.836154 CCGGGTCATACCATGGGG 59.164 66.667 18.09 5.28 41.02 4.96
290 291 7.309744 CCGACACATATTATTTTATGGGCCATT 60.310 37.037 26.58 9.21 36.61 3.16
413 414 9.208022 CATATGTGTTATACCATGACTTACCAG 57.792 37.037 0.00 0.00 0.00 4.00
482 483 9.640963 GTTGCTATCTCAGTTTCTAAGTTAAGA 57.359 33.333 0.00 0.00 0.00 2.10
535 536 6.702723 CGTATTATGGATTAAAGGACGACCAA 59.297 38.462 6.71 0.00 38.94 3.67
870 872 4.913335 AGGATGTCAATGCATTCACATC 57.087 40.909 35.29 35.29 42.97 3.06
878 880 8.091385 TGTCAATGCATTCACATCTGTATATC 57.909 34.615 12.54 0.00 0.00 1.63
884 886 5.641209 GCATTCACATCTGTATATCTGGACC 59.359 44.000 0.00 0.00 0.00 4.46
1033 1037 7.035468 AGGGGAGTACATCTTCTCATATCCTAT 60.035 40.741 0.00 0.00 32.93 2.57
1048 1052 9.896645 CTCATATCCTATACCAATATGCTGTTT 57.103 33.333 0.00 0.00 34.70 2.83
1144 1149 4.523083 TCTTTGTCCACATTAGTATGCCC 58.477 43.478 0.00 0.00 35.03 5.36
1579 1584 9.187455 GATCTCGGTCTTGAAGATCTAAATAAC 57.813 37.037 3.71 0.00 34.31 1.89
1762 1767 1.012086 CATCGTGGCCTCACAATCTG 58.988 55.000 3.32 0.00 43.79 2.90
2004 2009 3.715628 ACCAGAACAAAGTGATGCAAC 57.284 42.857 0.00 0.00 0.00 4.17
2250 2255 0.322008 CCCTCTTCCACTGGACAAGC 60.322 60.000 0.00 0.00 0.00 4.01
2283 2288 4.896482 TCTTATAGACCCTGGAGAGCTTTC 59.104 45.833 0.00 0.00 0.00 2.62
2460 2471 6.123651 TCACCAATACCTACAGTTTTGTTGT 58.876 36.000 0.00 0.00 38.76 3.32
2508 2519 7.165460 TGTCATCTTACGAATGAAGGAAGTA 57.835 36.000 0.00 0.00 0.00 2.24
2711 2730 7.701539 ACAACTGCACCTCATATGAATTAAA 57.298 32.000 6.90 0.00 0.00 1.52
2784 2804 7.606456 TCAAGAAATTAGAACCATAGTGGACAC 59.394 37.037 2.45 0.00 40.96 3.67
2790 2810 2.450609 ACCATAGTGGACACGTGAAC 57.549 50.000 25.01 16.64 40.96 3.18
2817 2839 0.962356 GGCCGCCTATGATCCATTGG 60.962 60.000 0.71 0.00 39.18 3.16
2955 2982 6.285990 ACAAACTTACAAGGACATAACGAGT 58.714 36.000 0.00 0.00 0.00 4.18
2993 3020 3.521560 GATGCTTGATACGTCTCCAACA 58.478 45.455 0.00 0.00 0.00 3.33
3111 3140 0.326927 TTAACCTAGTGCCCAGTGCC 59.673 55.000 0.00 0.00 40.16 5.01
3112 3141 0.546747 TAACCTAGTGCCCAGTGCCT 60.547 55.000 0.00 0.00 40.16 4.75
3170 3199 9.781834 TTTATAGAAAATCAATACCAAACGCAG 57.218 29.630 0.00 0.00 0.00 5.18
3172 3201 5.699839 AGAAAATCAATACCAAACGCAGTC 58.300 37.500 0.00 0.00 45.00 3.51
3173 3202 4.434713 AAATCAATACCAAACGCAGTCC 57.565 40.909 0.00 0.00 45.00 3.85
3174 3203 2.552599 TCAATACCAAACGCAGTCCA 57.447 45.000 0.00 0.00 45.00 4.02
3175 3204 2.852449 TCAATACCAAACGCAGTCCAA 58.148 42.857 0.00 0.00 45.00 3.53
3176 3205 3.215151 TCAATACCAAACGCAGTCCAAA 58.785 40.909 0.00 0.00 45.00 3.28
3177 3206 3.823873 TCAATACCAAACGCAGTCCAAAT 59.176 39.130 0.00 0.00 45.00 2.32
3178 3207 5.004448 TCAATACCAAACGCAGTCCAAATA 58.996 37.500 0.00 0.00 45.00 1.40
3179 3208 5.123186 TCAATACCAAACGCAGTCCAAATAG 59.877 40.000 0.00 0.00 45.00 1.73
3180 3209 3.134574 ACCAAACGCAGTCCAAATAGA 57.865 42.857 0.00 0.00 45.00 1.98
3181 3210 3.482436 ACCAAACGCAGTCCAAATAGAA 58.518 40.909 0.00 0.00 45.00 2.10
3182 3211 4.079253 ACCAAACGCAGTCCAAATAGAAT 58.921 39.130 0.00 0.00 45.00 2.40
3183 3212 5.250200 ACCAAACGCAGTCCAAATAGAATA 58.750 37.500 0.00 0.00 45.00 1.75
3184 3213 5.708230 ACCAAACGCAGTCCAAATAGAATAA 59.292 36.000 0.00 0.00 45.00 1.40
3185 3214 6.207810 ACCAAACGCAGTCCAAATAGAATAAA 59.792 34.615 0.00 0.00 45.00 1.40
3186 3215 7.087639 CCAAACGCAGTCCAAATAGAATAAAA 58.912 34.615 0.00 0.00 45.00 1.52
3187 3216 7.061789 CCAAACGCAGTCCAAATAGAATAAAAC 59.938 37.037 0.00 0.00 45.00 2.43
3188 3217 7.448748 AACGCAGTCCAAATAGAATAAAACT 57.551 32.000 0.00 0.00 45.00 2.66
3189 3218 7.448748 ACGCAGTCCAAATAGAATAAAACTT 57.551 32.000 0.00 0.00 29.74 2.66
3190 3219 7.882179 ACGCAGTCCAAATAGAATAAAACTTT 58.118 30.769 0.00 0.00 29.74 2.66
3191 3220 9.005777 ACGCAGTCCAAATAGAATAAAACTTTA 57.994 29.630 0.00 0.00 29.74 1.85
3192 3221 9.274065 CGCAGTCCAAATAGAATAAAACTTTAC 57.726 33.333 0.00 0.00 0.00 2.01
3193 3222 9.274065 GCAGTCCAAATAGAATAAAACTTTACG 57.726 33.333 0.00 0.00 0.00 3.18
3209 3238 8.782533 AAACTTTACGATGATTTTTGTGAGAC 57.217 30.769 0.00 0.00 0.00 3.36
3210 3239 6.899114 ACTTTACGATGATTTTTGTGAGACC 58.101 36.000 0.00 0.00 0.00 3.85
3211 3240 6.485313 ACTTTACGATGATTTTTGTGAGACCA 59.515 34.615 0.00 0.00 0.00 4.02
3212 3241 6.480524 TTACGATGATTTTTGTGAGACCAG 57.519 37.500 0.00 0.00 0.00 4.00
3213 3242 4.641396 ACGATGATTTTTGTGAGACCAGA 58.359 39.130 0.00 0.00 0.00 3.86
3214 3243 5.063204 ACGATGATTTTTGTGAGACCAGAA 58.937 37.500 0.00 0.00 0.00 3.02
3215 3244 5.180117 ACGATGATTTTTGTGAGACCAGAAG 59.820 40.000 0.00 0.00 0.00 2.85
3216 3245 5.409520 CGATGATTTTTGTGAGACCAGAAGA 59.590 40.000 0.00 0.00 0.00 2.87
3217 3246 6.566197 ATGATTTTTGTGAGACCAGAAGAC 57.434 37.500 0.00 0.00 0.00 3.01
3218 3247 5.436175 TGATTTTTGTGAGACCAGAAGACA 58.564 37.500 0.00 0.00 0.00 3.41
3219 3248 5.885352 TGATTTTTGTGAGACCAGAAGACAA 59.115 36.000 0.00 0.00 0.00 3.18
3220 3249 5.560966 TTTTTGTGAGACCAGAAGACAAC 57.439 39.130 0.00 0.00 0.00 3.32
3221 3250 2.910688 TGTGAGACCAGAAGACAACC 57.089 50.000 0.00 0.00 0.00 3.77
3222 3251 2.115427 TGTGAGACCAGAAGACAACCA 58.885 47.619 0.00 0.00 0.00 3.67
3223 3252 2.158957 TGTGAGACCAGAAGACAACCAC 60.159 50.000 0.00 0.00 0.00 4.16
3224 3253 1.068588 TGAGACCAGAAGACAACCACG 59.931 52.381 0.00 0.00 0.00 4.94
3225 3254 1.340248 GAGACCAGAAGACAACCACGA 59.660 52.381 0.00 0.00 0.00 4.35
3226 3255 1.760613 AGACCAGAAGACAACCACGAA 59.239 47.619 0.00 0.00 0.00 3.85
3227 3256 2.135933 GACCAGAAGACAACCACGAAG 58.864 52.381 0.00 0.00 0.00 3.79
3228 3257 0.868406 CCAGAAGACAACCACGAAGC 59.132 55.000 0.00 0.00 0.00 3.86
3229 3258 1.541233 CCAGAAGACAACCACGAAGCT 60.541 52.381 0.00 0.00 0.00 3.74
3230 3259 2.213499 CAGAAGACAACCACGAAGCTT 58.787 47.619 0.00 0.00 0.00 3.74
3231 3260 2.221981 CAGAAGACAACCACGAAGCTTC 59.778 50.000 16.84 16.84 33.72 3.86
3240 3269 4.504132 CGAAGCTTCGGGAAGAGG 57.496 61.111 35.58 9.90 46.30 3.69
3244 3273 2.124942 GCTTCGGGAAGAGGCCAG 60.125 66.667 5.01 0.00 45.10 4.85
3245 3274 2.660064 GCTTCGGGAAGAGGCCAGA 61.660 63.158 5.01 0.00 45.10 3.86
3246 3275 1.983224 CTTCGGGAAGAGGCCAGAA 59.017 57.895 5.01 0.00 40.79 3.02
3247 3276 1.983224 TTCGGGAAGAGGCCAGAAG 59.017 57.895 5.01 0.00 37.24 2.85
3248 3277 0.544357 TTCGGGAAGAGGCCAGAAGA 60.544 55.000 5.01 0.00 37.24 2.87
3249 3278 1.219393 CGGGAAGAGGCCAGAAGAC 59.781 63.158 5.01 0.00 0.00 3.01
3250 3279 1.604915 GGGAAGAGGCCAGAAGACC 59.395 63.158 5.01 0.00 0.00 3.85
3251 3280 1.604915 GGAAGAGGCCAGAAGACCC 59.395 63.158 5.01 0.00 0.00 4.46
3252 3281 1.201429 GGAAGAGGCCAGAAGACCCA 61.201 60.000 5.01 0.00 0.00 4.51
3253 3282 0.915364 GAAGAGGCCAGAAGACCCAT 59.085 55.000 5.01 0.00 0.00 4.00
3254 3283 0.622665 AAGAGGCCAGAAGACCCATG 59.377 55.000 5.01 0.00 0.00 3.66
3255 3284 0.252881 AGAGGCCAGAAGACCCATGA 60.253 55.000 5.01 0.00 0.00 3.07
3256 3285 0.179936 GAGGCCAGAAGACCCATGAG 59.820 60.000 5.01 0.00 0.00 2.90
3257 3286 1.225704 GGCCAGAAGACCCATGAGG 59.774 63.158 0.00 0.00 43.78 3.86
3267 3296 2.043652 CCATGAGGGGGCCACAAG 60.044 66.667 9.35 0.47 0.00 3.16
3268 3297 2.757099 CATGAGGGGGCCACAAGC 60.757 66.667 9.35 0.00 42.60 4.01
3277 3306 3.339093 GCCACAAGCCCTAGGGGT 61.339 66.667 27.44 27.44 46.51 4.95
3278 3307 2.998949 CCACAAGCCCTAGGGGTC 59.001 66.667 32.37 15.17 46.51 4.46
3279 3308 2.680370 CCACAAGCCCTAGGGGTCC 61.680 68.421 32.37 14.39 46.51 4.46
3280 3309 2.687566 ACAAGCCCTAGGGGTCCG 60.688 66.667 32.37 26.43 46.51 4.79
3281 3310 4.176752 CAAGCCCTAGGGGTCCGC 62.177 72.222 32.37 15.71 46.51 5.54
3320 3349 1.132500 CCCCCATGACTCCTCTAACC 58.868 60.000 0.00 0.00 0.00 2.85
3321 3350 1.132500 CCCCATGACTCCTCTAACCC 58.868 60.000 0.00 0.00 0.00 4.11
3322 3351 1.344496 CCCCATGACTCCTCTAACCCT 60.344 57.143 0.00 0.00 0.00 4.34
3323 3352 2.090719 CCCCATGACTCCTCTAACCCTA 60.091 54.545 0.00 0.00 0.00 3.53
3324 3353 3.632645 CCCCATGACTCCTCTAACCCTAA 60.633 52.174 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.199982 CGGACTTGTAATTAACTTGTAAGAGAA 57.800 33.333 0.00 0.00 0.00 2.87
10 11 7.816031 CCGGACTTGTAATTAACTTGTAAGAGA 59.184 37.037 0.00 0.00 0.00 3.10
11 12 7.064253 CCCGGACTTGTAATTAACTTGTAAGAG 59.936 40.741 0.73 0.00 0.00 2.85
12 13 6.875195 CCCGGACTTGTAATTAACTTGTAAGA 59.125 38.462 0.73 0.00 0.00 2.10
13 14 6.652062 ACCCGGACTTGTAATTAACTTGTAAG 59.348 38.462 0.73 0.00 0.00 2.34
14 15 6.532826 ACCCGGACTTGTAATTAACTTGTAA 58.467 36.000 0.73 0.00 0.00 2.41
15 16 6.014327 AGACCCGGACTTGTAATTAACTTGTA 60.014 38.462 0.73 0.00 0.00 2.41
16 17 4.976864 ACCCGGACTTGTAATTAACTTGT 58.023 39.130 0.73 0.00 0.00 3.16
17 18 5.243207 AGACCCGGACTTGTAATTAACTTG 58.757 41.667 0.73 0.00 0.00 3.16
18 19 5.494390 AGACCCGGACTTGTAATTAACTT 57.506 39.130 0.73 0.00 0.00 2.66
19 20 5.243207 CAAGACCCGGACTTGTAATTAACT 58.757 41.667 23.60 0.00 39.57 2.24
20 21 4.142752 GCAAGACCCGGACTTGTAATTAAC 60.143 45.833 28.36 14.97 44.25 2.01
21 22 4.004982 GCAAGACCCGGACTTGTAATTAA 58.995 43.478 28.36 0.00 44.25 1.40
22 23 3.262405 AGCAAGACCCGGACTTGTAATTA 59.738 43.478 28.36 0.00 44.25 1.40
23 24 2.039879 AGCAAGACCCGGACTTGTAATT 59.960 45.455 28.36 16.52 44.25 1.40
24 25 1.628846 AGCAAGACCCGGACTTGTAAT 59.371 47.619 28.36 18.44 44.25 1.89
25 26 1.053424 AGCAAGACCCGGACTTGTAA 58.947 50.000 28.36 0.00 44.25 2.41
26 27 1.001633 GAAGCAAGACCCGGACTTGTA 59.998 52.381 28.36 0.00 44.25 2.41
27 28 0.250338 GAAGCAAGACCCGGACTTGT 60.250 55.000 28.36 17.57 44.25 3.16
28 29 0.955919 GGAAGCAAGACCCGGACTTG 60.956 60.000 25.93 25.93 44.92 3.16
29 30 1.128188 AGGAAGCAAGACCCGGACTT 61.128 55.000 0.73 5.42 0.00 3.01
30 31 1.536662 AGGAAGCAAGACCCGGACT 60.537 57.895 0.73 0.00 0.00 3.85
31 32 1.079057 GAGGAAGCAAGACCCGGAC 60.079 63.158 0.73 0.00 0.00 4.79
32 33 2.646175 CGAGGAAGCAAGACCCGGA 61.646 63.158 0.73 0.00 0.00 5.14
33 34 2.125512 CGAGGAAGCAAGACCCGG 60.126 66.667 0.00 0.00 0.00 5.73
34 35 1.446272 GACGAGGAAGCAAGACCCG 60.446 63.158 0.00 0.00 0.00 5.28
35 36 0.034896 TTGACGAGGAAGCAAGACCC 59.965 55.000 0.00 0.00 0.00 4.46
36 37 1.433534 CTTGACGAGGAAGCAAGACC 58.566 55.000 0.00 0.00 41.03 3.85
47 48 5.175856 GGATGACGAATATTTCCTTGACGAG 59.824 44.000 0.00 0.00 0.00 4.18
48 49 5.047847 GGATGACGAATATTTCCTTGACGA 58.952 41.667 0.00 0.00 0.00 4.20
49 50 4.211374 GGGATGACGAATATTTCCTTGACG 59.789 45.833 3.69 0.00 0.00 4.35
50 51 5.368989 AGGGATGACGAATATTTCCTTGAC 58.631 41.667 3.69 0.00 0.00 3.18
51 52 5.630415 AGGGATGACGAATATTTCCTTGA 57.370 39.130 3.69 0.00 0.00 3.02
52 53 6.543831 AGAAAGGGATGACGAATATTTCCTTG 59.456 38.462 3.69 0.00 34.10 3.61
53 54 6.663734 AGAAAGGGATGACGAATATTTCCTT 58.336 36.000 3.69 0.00 35.17 3.36
54 55 6.253946 AGAAAGGGATGACGAATATTTCCT 57.746 37.500 3.69 0.00 0.00 3.36
55 56 6.768381 AGAAGAAAGGGATGACGAATATTTCC 59.232 38.462 0.00 0.00 0.00 3.13
56 57 7.793927 AGAAGAAAGGGATGACGAATATTTC 57.206 36.000 0.00 0.00 0.00 2.17
57 58 9.681062 TTAAGAAGAAAGGGATGACGAATATTT 57.319 29.630 0.00 0.00 0.00 1.40
58 59 9.331282 CTTAAGAAGAAAGGGATGACGAATATT 57.669 33.333 0.00 0.00 0.00 1.28
59 60 7.442666 GCTTAAGAAGAAAGGGATGACGAATAT 59.557 37.037 6.67 0.00 0.00 1.28
60 61 6.761714 GCTTAAGAAGAAAGGGATGACGAATA 59.238 38.462 6.67 0.00 0.00 1.75
61 62 5.586643 GCTTAAGAAGAAAGGGATGACGAAT 59.413 40.000 6.67 0.00 0.00 3.34
62 63 4.935808 GCTTAAGAAGAAAGGGATGACGAA 59.064 41.667 6.67 0.00 0.00 3.85
63 64 4.504858 GCTTAAGAAGAAAGGGATGACGA 58.495 43.478 6.67 0.00 0.00 4.20
64 65 3.623510 GGCTTAAGAAGAAAGGGATGACG 59.376 47.826 6.67 0.00 0.00 4.35
65 66 3.623510 CGGCTTAAGAAGAAAGGGATGAC 59.376 47.826 6.67 0.00 0.00 3.06
66 67 3.370527 CCGGCTTAAGAAGAAAGGGATGA 60.371 47.826 6.67 0.00 0.00 2.92
67 68 2.945668 CCGGCTTAAGAAGAAAGGGATG 59.054 50.000 6.67 0.00 0.00 3.51
68 69 2.684038 GCCGGCTTAAGAAGAAAGGGAT 60.684 50.000 22.15 0.00 0.00 3.85
69 70 1.339727 GCCGGCTTAAGAAGAAAGGGA 60.340 52.381 22.15 0.00 0.00 4.20
70 71 1.095600 GCCGGCTTAAGAAGAAAGGG 58.904 55.000 22.15 0.00 0.00 3.95
71 72 1.095600 GGCCGGCTTAAGAAGAAAGG 58.904 55.000 28.56 0.70 0.00 3.11
72 73 1.095600 GGGCCGGCTTAAGAAGAAAG 58.904 55.000 28.56 0.00 0.00 2.62
73 74 0.402504 TGGGCCGGCTTAAGAAGAAA 59.597 50.000 28.56 0.00 0.00 2.52
74 75 0.623723 ATGGGCCGGCTTAAGAAGAA 59.376 50.000 28.56 1.67 0.00 2.52
75 76 0.180406 GATGGGCCGGCTTAAGAAGA 59.820 55.000 28.56 1.44 0.00 2.87
76 77 0.107214 TGATGGGCCGGCTTAAGAAG 60.107 55.000 28.56 0.00 0.00 2.85
77 78 0.550914 ATGATGGGCCGGCTTAAGAA 59.449 50.000 28.56 8.61 0.00 2.52
78 79 1.429930 TATGATGGGCCGGCTTAAGA 58.570 50.000 28.56 8.51 0.00 2.10
79 80 2.270352 TTATGATGGGCCGGCTTAAG 57.730 50.000 28.56 0.00 0.00 1.85
80 81 2.303175 GTTTATGATGGGCCGGCTTAA 58.697 47.619 28.56 12.80 0.00 1.85
81 82 1.812324 CGTTTATGATGGGCCGGCTTA 60.812 52.381 28.56 16.30 0.00 3.09
82 83 1.101049 CGTTTATGATGGGCCGGCTT 61.101 55.000 28.56 11.93 0.00 4.35
83 84 1.525995 CGTTTATGATGGGCCGGCT 60.526 57.895 28.56 6.33 0.00 5.52
84 85 1.822186 ACGTTTATGATGGGCCGGC 60.822 57.895 21.18 21.18 0.00 6.13
85 86 0.462937 TCACGTTTATGATGGGCCGG 60.463 55.000 0.00 0.00 0.00 6.13
86 87 0.937304 CTCACGTTTATGATGGGCCG 59.063 55.000 0.00 0.00 0.00 6.13
87 88 0.663153 GCTCACGTTTATGATGGGCC 59.337 55.000 0.00 0.00 0.00 5.80
88 89 0.663153 GGCTCACGTTTATGATGGGC 59.337 55.000 0.00 0.00 0.00 5.36
89 90 0.937304 CGGCTCACGTTTATGATGGG 59.063 55.000 0.00 0.00 37.93 4.00
90 91 0.937304 CCGGCTCACGTTTATGATGG 59.063 55.000 0.00 0.00 42.24 3.51
91 92 0.304705 GCCGGCTCACGTTTATGATG 59.695 55.000 22.15 0.00 42.24 3.07
92 93 0.814010 GGCCGGCTCACGTTTATGAT 60.814 55.000 28.56 0.00 42.24 2.45
93 94 1.448893 GGCCGGCTCACGTTTATGA 60.449 57.895 28.56 0.00 42.24 2.15
94 95 1.024579 AAGGCCGGCTCACGTTTATG 61.025 55.000 28.56 0.00 42.24 1.90
95 96 0.743345 GAAGGCCGGCTCACGTTTAT 60.743 55.000 28.56 1.67 42.24 1.40
96 97 1.375013 GAAGGCCGGCTCACGTTTA 60.375 57.895 28.56 0.00 42.24 2.01
97 98 2.668550 GAAGGCCGGCTCACGTTT 60.669 61.111 28.56 11.16 42.24 3.60
98 99 3.626924 AGAAGGCCGGCTCACGTT 61.627 61.111 28.56 12.13 42.24 3.99
99 100 4.379243 CAGAAGGCCGGCTCACGT 62.379 66.667 28.56 8.02 42.24 4.49
101 102 4.785453 CCCAGAAGGCCGGCTCAC 62.785 72.222 28.56 17.04 0.00 3.51
119 120 3.777556 GGACAACAAGGCCCAAGG 58.222 61.111 0.00 0.00 40.85 3.61
133 134 4.530857 CGGGCGGGTCAGATGGAC 62.531 72.222 0.00 0.00 46.20 4.02
147 148 2.910440 ACTCATTAGTAACCCGGCGGG 61.910 57.143 41.89 41.89 41.03 6.13
148 149 0.462789 ACTCATTAGTAACCCGGCGG 59.537 55.000 21.46 21.46 32.84 6.13
149 150 1.135527 TGACTCATTAGTAACCCGGCG 59.864 52.381 0.00 0.00 35.56 6.46
150 151 2.547826 GTGACTCATTAGTAACCCGGC 58.452 52.381 0.00 0.00 35.56 6.13
155 156 5.749109 CCGATCTTGGTGACTCATTAGTAAC 59.251 44.000 0.00 0.00 36.45 2.50
156 157 5.163447 CCCGATCTTGGTGACTCATTAGTAA 60.163 44.000 0.00 0.00 35.56 2.24
157 158 4.341235 CCCGATCTTGGTGACTCATTAGTA 59.659 45.833 0.00 0.00 35.56 1.82
158 159 3.133003 CCCGATCTTGGTGACTCATTAGT 59.867 47.826 0.00 0.00 39.21 2.24
159 160 3.722147 CCCGATCTTGGTGACTCATTAG 58.278 50.000 0.00 0.00 0.00 1.73
160 161 2.158957 GCCCGATCTTGGTGACTCATTA 60.159 50.000 0.00 0.00 0.00 1.90
161 162 1.407437 GCCCGATCTTGGTGACTCATT 60.407 52.381 0.00 0.00 0.00 2.57
162 163 0.179000 GCCCGATCTTGGTGACTCAT 59.821 55.000 0.00 0.00 0.00 2.90
163 164 1.191489 TGCCCGATCTTGGTGACTCA 61.191 55.000 0.00 0.00 0.00 3.41
164 165 0.460987 CTGCCCGATCTTGGTGACTC 60.461 60.000 0.00 0.00 0.00 3.36
165 166 1.599047 CTGCCCGATCTTGGTGACT 59.401 57.895 0.00 0.00 0.00 3.41
166 167 1.450312 CCTGCCCGATCTTGGTGAC 60.450 63.158 0.00 0.00 0.00 3.67
167 168 1.488705 AACCTGCCCGATCTTGGTGA 61.489 55.000 0.00 0.00 0.00 4.02
168 169 0.251916 TAACCTGCCCGATCTTGGTG 59.748 55.000 0.00 0.00 0.00 4.17
169 170 1.141053 GATAACCTGCCCGATCTTGGT 59.859 52.381 0.00 0.00 0.00 3.67
170 171 1.417890 AGATAACCTGCCCGATCTTGG 59.582 52.381 0.00 0.00 0.00 3.61
171 172 2.158900 ACAGATAACCTGCCCGATCTTG 60.159 50.000 0.00 0.00 46.81 3.02
172 173 2.119495 ACAGATAACCTGCCCGATCTT 58.881 47.619 0.00 0.00 46.81 2.40
173 174 1.414181 CACAGATAACCTGCCCGATCT 59.586 52.381 0.00 0.00 46.81 2.75
174 175 1.412710 TCACAGATAACCTGCCCGATC 59.587 52.381 0.00 0.00 46.81 3.69
175 176 1.496060 TCACAGATAACCTGCCCGAT 58.504 50.000 0.00 0.00 46.81 4.18
176 177 1.271856 TTCACAGATAACCTGCCCGA 58.728 50.000 0.00 0.00 46.81 5.14
177 178 2.213499 GATTCACAGATAACCTGCCCG 58.787 52.381 0.00 0.00 46.81 6.13
178 179 2.213499 CGATTCACAGATAACCTGCCC 58.787 52.381 0.00 0.00 46.81 5.36
179 180 1.599542 GCGATTCACAGATAACCTGCC 59.400 52.381 0.00 0.00 46.81 4.85
180 181 1.599542 GGCGATTCACAGATAACCTGC 59.400 52.381 0.00 0.00 46.81 4.85
182 183 3.535561 CTTGGCGATTCACAGATAACCT 58.464 45.455 0.00 0.00 0.00 3.50
183 184 2.032178 GCTTGGCGATTCACAGATAACC 59.968 50.000 0.00 0.00 0.00 2.85
184 185 2.939103 AGCTTGGCGATTCACAGATAAC 59.061 45.455 0.00 0.00 0.00 1.89
185 186 3.198068 GAGCTTGGCGATTCACAGATAA 58.802 45.455 0.00 0.00 0.00 1.75
186 187 2.483714 GGAGCTTGGCGATTCACAGATA 60.484 50.000 0.00 0.00 0.00 1.98
187 188 1.661341 GAGCTTGGCGATTCACAGAT 58.339 50.000 0.00 0.00 0.00 2.90
188 189 0.391661 GGAGCTTGGCGATTCACAGA 60.392 55.000 0.00 0.00 0.00 3.41
189 190 1.699656 CGGAGCTTGGCGATTCACAG 61.700 60.000 0.00 0.00 0.00 3.66
190 191 1.741401 CGGAGCTTGGCGATTCACA 60.741 57.895 0.00 0.00 0.00 3.58
191 192 2.464459 CCGGAGCTTGGCGATTCAC 61.464 63.158 0.00 0.00 0.00 3.18
192 193 2.125147 CCGGAGCTTGGCGATTCA 60.125 61.111 0.00 0.00 0.00 2.57
193 194 2.897350 CCCGGAGCTTGGCGATTC 60.897 66.667 0.73 0.00 0.00 2.52
208 209 4.394712 CTCACTGGTGACCCGCCC 62.395 72.222 0.00 0.00 35.46 6.13
209 210 3.591254 GACTCACTGGTGACCCGCC 62.591 68.421 0.00 0.00 35.46 6.13
210 211 2.048127 GACTCACTGGTGACCCGC 60.048 66.667 0.00 0.00 35.46 6.13
211 212 2.258591 CGACTCACTGGTGACCCG 59.741 66.667 0.00 0.00 35.46 5.28
212 213 2.048127 GCGACTCACTGGTGACCC 60.048 66.667 0.00 0.00 35.46 4.46
213 214 2.048127 GGCGACTCACTGGTGACC 60.048 66.667 0.00 0.00 35.46 4.02
214 215 0.320771 ATTGGCGACTCACTGGTGAC 60.321 55.000 0.00 0.00 35.46 3.67
215 216 0.396435 AATTGGCGACTCACTGGTGA 59.604 50.000 3.34 3.34 38.06 4.02
216 217 0.798776 GAATTGGCGACTCACTGGTG 59.201 55.000 0.00 0.00 0.00 4.17
217 218 0.321653 GGAATTGGCGACTCACTGGT 60.322 55.000 0.00 0.00 0.00 4.00
218 219 1.361668 CGGAATTGGCGACTCACTGG 61.362 60.000 0.00 0.00 0.00 4.00
219 220 1.361668 CCGGAATTGGCGACTCACTG 61.362 60.000 0.00 0.00 0.00 3.66
220 221 1.079127 CCGGAATTGGCGACTCACT 60.079 57.895 0.00 0.00 0.00 3.41
221 222 2.750888 GCCGGAATTGGCGACTCAC 61.751 63.158 5.05 0.00 46.75 3.51
222 223 2.435938 GCCGGAATTGGCGACTCA 60.436 61.111 5.05 0.00 46.75 3.41
229 230 2.332312 TATGACCCGGCCGGAATTGG 62.332 60.000 45.44 29.46 37.50 3.16
230 231 1.147376 TATGACCCGGCCGGAATTG 59.853 57.895 45.44 29.86 37.50 2.32
231 232 1.147600 GTATGACCCGGCCGGAATT 59.852 57.895 45.44 28.29 37.50 2.17
232 233 2.814835 GGTATGACCCGGCCGGAAT 61.815 63.158 45.44 33.01 37.50 3.01
233 234 3.472726 GGTATGACCCGGCCGGAA 61.473 66.667 45.44 29.29 37.50 4.30
234 235 4.781616 TGGTATGACCCGGCCGGA 62.782 66.667 45.44 27.01 37.50 5.14
235 236 3.556306 ATGGTATGACCCGGCCGG 61.556 66.667 37.99 37.99 37.50 6.13
236 237 2.280797 CATGGTATGACCCGGCCG 60.281 66.667 21.04 21.04 37.50 6.13
237 238 2.113139 CCATGGTATGACCCGGCC 59.887 66.667 2.57 0.00 37.50 6.13
238 239 2.113139 CCCATGGTATGACCCGGC 59.887 66.667 11.73 0.00 37.50 6.13
239 240 0.765135 TACCCCATGGTATGACCCGG 60.765 60.000 11.73 4.34 45.45 5.73
240 241 2.842994 TACCCCATGGTATGACCCG 58.157 57.895 11.73 0.00 45.45 5.28
258 259 9.627123 CCATAAAATAATATGTGTCGGGGATAT 57.373 33.333 0.00 0.00 32.48 1.63
259 260 8.050325 CCCATAAAATAATATGTGTCGGGGATA 58.950 37.037 0.00 0.00 32.48 2.59
260 261 6.889722 CCCATAAAATAATATGTGTCGGGGAT 59.110 38.462 0.00 0.00 32.48 3.85
261 262 6.242396 CCCATAAAATAATATGTGTCGGGGA 58.758 40.000 0.00 0.00 32.48 4.81
262 263 5.105917 GCCCATAAAATAATATGTGTCGGGG 60.106 44.000 0.00 0.00 32.48 5.73
263 264 5.105917 GGCCCATAAAATAATATGTGTCGGG 60.106 44.000 0.00 0.00 32.48 5.14
264 265 5.475220 TGGCCCATAAAATAATATGTGTCGG 59.525 40.000 0.00 0.00 32.48 4.79
265 266 6.567687 TGGCCCATAAAATAATATGTGTCG 57.432 37.500 0.00 0.00 32.48 4.35
290 291 2.891191 ATCTTGGGCCCTCGTTTTTA 57.109 45.000 25.70 0.00 0.00 1.52
297 298 3.073062 ACACATGTATATCTTGGGCCCTC 59.927 47.826 25.70 0.00 0.00 4.30
482 483 0.188342 ACATGGACCTTGCTTTGGGT 59.812 50.000 7.28 0.00 38.70 4.51
821 823 4.696877 TGCAACCACTGATATGTCTTTCTG 59.303 41.667 0.00 0.00 0.00 3.02
1119 1124 5.186198 GCATACTAATGTGGACAAAGAGGT 58.814 41.667 0.00 0.00 35.38 3.85
1144 1149 2.815647 GACCGCCGCTCTTTCCTG 60.816 66.667 0.00 0.00 0.00 3.86
1400 1405 5.254115 GTTTTGTAGGCTTCCAATCCTAGT 58.746 41.667 0.00 0.00 35.76 2.57
1579 1584 2.357637 CCGAGAGAGCTCACTTAAGAGG 59.642 54.545 17.77 10.55 41.36 3.69
1585 1590 0.968393 GGACCCGAGAGAGCTCACTT 60.968 60.000 17.77 0.00 41.36 3.16
1762 1767 0.886490 CAGGTGGCTGGAGTTGTGAC 60.886 60.000 0.00 0.00 0.00 3.67
1946 1951 7.625185 GCAAGGACTTTCATAGTTCTGAACATC 60.625 40.741 21.50 6.46 42.19 3.06
1988 1993 2.742774 GTGGGTTGCATCACTTTGTTC 58.257 47.619 0.00 0.00 0.00 3.18
2004 2009 1.447838 CCCGATGTTGAGTCGTGGG 60.448 63.158 0.00 0.00 37.39 4.61
2270 2275 2.801342 GCATCTACGAAAGCTCTCCAGG 60.801 54.545 0.00 0.00 0.00 4.45
2271 2276 2.100584 AGCATCTACGAAAGCTCTCCAG 59.899 50.000 0.00 0.00 30.05 3.86
2508 2519 6.434028 AGGTGCATTGTTGTAATACATGTTCT 59.566 34.615 2.30 0.00 0.00 3.01
2620 2632 7.012799 AGTCTCTTGAGTTGAAGTTTGGAATTC 59.987 37.037 0.00 0.00 0.00 2.17
2623 2635 5.745227 AGTCTCTTGAGTTGAAGTTTGGAA 58.255 37.500 0.00 0.00 0.00 3.53
2784 2804 2.310233 CGGCCACTGTCTGTTCACG 61.310 63.158 2.24 0.00 0.00 4.35
2790 2810 1.522355 CATAGGCGGCCACTGTCTG 60.522 63.158 23.09 5.05 0.00 3.51
2817 2839 6.127869 TGTTGTTAATGGTGCATATGTGGTAC 60.128 38.462 4.29 0.00 0.00 3.34
2910 2937 9.264782 GTTTGTTGTAATTGCAATGATTAATGC 57.735 29.630 13.82 0.00 42.86 3.56
2955 2982 3.463329 AGCATCCCCAAGCTTAATTCCTA 59.537 43.478 0.00 0.00 38.01 2.94
3074 3103 9.916360 CTAGGTTAATAGGTTAGTCCCAAAAAT 57.084 33.333 0.00 0.00 36.75 1.82
3164 3193 7.448748 AGTTTTATTCTATTTGGACTGCGTT 57.551 32.000 0.00 0.00 0.00 4.84
3165 3194 7.448748 AAGTTTTATTCTATTTGGACTGCGT 57.551 32.000 0.00 0.00 0.00 5.24
3166 3195 9.274065 GTAAAGTTTTATTCTATTTGGACTGCG 57.726 33.333 0.00 0.00 0.00 5.18
3167 3196 9.274065 CGTAAAGTTTTATTCTATTTGGACTGC 57.726 33.333 0.00 0.00 0.00 4.40
3183 3212 9.233232 GTCTCACAAAAATCATCGTAAAGTTTT 57.767 29.630 0.00 0.00 0.00 2.43
3184 3213 7.860872 GGTCTCACAAAAATCATCGTAAAGTTT 59.139 33.333 0.00 0.00 0.00 2.66
3185 3214 7.012894 TGGTCTCACAAAAATCATCGTAAAGTT 59.987 33.333 0.00 0.00 0.00 2.66
3186 3215 6.485313 TGGTCTCACAAAAATCATCGTAAAGT 59.515 34.615 0.00 0.00 0.00 2.66
3187 3216 6.898041 TGGTCTCACAAAAATCATCGTAAAG 58.102 36.000 0.00 0.00 0.00 1.85
3188 3217 6.708502 TCTGGTCTCACAAAAATCATCGTAAA 59.291 34.615 0.00 0.00 0.00 2.01
3189 3218 6.227522 TCTGGTCTCACAAAAATCATCGTAA 58.772 36.000 0.00 0.00 0.00 3.18
3190 3219 5.789521 TCTGGTCTCACAAAAATCATCGTA 58.210 37.500 0.00 0.00 0.00 3.43
3191 3220 4.641396 TCTGGTCTCACAAAAATCATCGT 58.359 39.130 0.00 0.00 0.00 3.73
3192 3221 5.409520 TCTTCTGGTCTCACAAAAATCATCG 59.590 40.000 0.00 0.00 0.00 3.84
3193 3222 6.205464 TGTCTTCTGGTCTCACAAAAATCATC 59.795 38.462 0.00 0.00 0.00 2.92
3194 3223 6.064060 TGTCTTCTGGTCTCACAAAAATCAT 58.936 36.000 0.00 0.00 0.00 2.45
3195 3224 5.436175 TGTCTTCTGGTCTCACAAAAATCA 58.564 37.500 0.00 0.00 0.00 2.57
3196 3225 6.202226 GTTGTCTTCTGGTCTCACAAAAATC 58.798 40.000 0.00 0.00 0.00 2.17
3197 3226 5.067805 GGTTGTCTTCTGGTCTCACAAAAAT 59.932 40.000 0.00 0.00 0.00 1.82
3198 3227 4.398044 GGTTGTCTTCTGGTCTCACAAAAA 59.602 41.667 0.00 0.00 0.00 1.94
3199 3228 3.945285 GGTTGTCTTCTGGTCTCACAAAA 59.055 43.478 0.00 0.00 0.00 2.44
3200 3229 3.054728 TGGTTGTCTTCTGGTCTCACAAA 60.055 43.478 0.00 0.00 0.00 2.83
3201 3230 2.503765 TGGTTGTCTTCTGGTCTCACAA 59.496 45.455 0.00 0.00 0.00 3.33
3202 3231 2.115427 TGGTTGTCTTCTGGTCTCACA 58.885 47.619 0.00 0.00 0.00 3.58
3203 3232 2.484889 GTGGTTGTCTTCTGGTCTCAC 58.515 52.381 0.00 0.00 0.00 3.51
3204 3233 1.068588 CGTGGTTGTCTTCTGGTCTCA 59.931 52.381 0.00 0.00 0.00 3.27
3205 3234 1.340248 TCGTGGTTGTCTTCTGGTCTC 59.660 52.381 0.00 0.00 0.00 3.36
3206 3235 1.410004 TCGTGGTTGTCTTCTGGTCT 58.590 50.000 0.00 0.00 0.00 3.85
3207 3236 2.135933 CTTCGTGGTTGTCTTCTGGTC 58.864 52.381 0.00 0.00 0.00 4.02
3208 3237 1.810412 GCTTCGTGGTTGTCTTCTGGT 60.810 52.381 0.00 0.00 0.00 4.00
3209 3238 0.868406 GCTTCGTGGTTGTCTTCTGG 59.132 55.000 0.00 0.00 0.00 3.86
3210 3239 1.871080 AGCTTCGTGGTTGTCTTCTG 58.129 50.000 0.00 0.00 0.00 3.02
3211 3240 2.484889 GAAGCTTCGTGGTTGTCTTCT 58.515 47.619 11.40 0.00 36.40 2.85
3212 3241 1.192534 CGAAGCTTCGTGGTTGTCTTC 59.807 52.381 34.97 1.85 45.09 2.87
3213 3242 1.217882 CGAAGCTTCGTGGTTGTCTT 58.782 50.000 34.97 0.00 45.09 3.01
3214 3243 2.900528 CGAAGCTTCGTGGTTGTCT 58.099 52.632 34.97 0.00 45.09 3.41
3224 3253 1.450491 GGCCTCTTCCCGAAGCTTC 60.450 63.158 16.84 16.84 38.28 3.86
3225 3254 2.190488 CTGGCCTCTTCCCGAAGCTT 62.190 60.000 3.32 0.00 38.28 3.74
3226 3255 2.607750 TGGCCTCTTCCCGAAGCT 60.608 61.111 3.32 0.00 38.28 3.74
3227 3256 2.124942 CTGGCCTCTTCCCGAAGC 60.125 66.667 3.32 0.00 38.28 3.86
3228 3257 0.107945 CTTCTGGCCTCTTCCCGAAG 60.108 60.000 3.32 0.00 39.71 3.79
3229 3258 0.544357 TCTTCTGGCCTCTTCCCGAA 60.544 55.000 3.32 0.00 0.00 4.30
3230 3259 1.078528 TCTTCTGGCCTCTTCCCGA 59.921 57.895 3.32 0.00 0.00 5.14
3231 3260 1.219393 GTCTTCTGGCCTCTTCCCG 59.781 63.158 3.32 0.00 0.00 5.14
3232 3261 1.604915 GGTCTTCTGGCCTCTTCCC 59.395 63.158 3.32 0.00 0.00 3.97
3233 3262 1.201429 TGGGTCTTCTGGCCTCTTCC 61.201 60.000 3.32 0.00 0.00 3.46
3234 3263 0.915364 ATGGGTCTTCTGGCCTCTTC 59.085 55.000 3.32 0.00 0.00 2.87
3235 3264 0.622665 CATGGGTCTTCTGGCCTCTT 59.377 55.000 3.32 0.00 0.00 2.85
3236 3265 0.252881 TCATGGGTCTTCTGGCCTCT 60.253 55.000 3.32 0.00 0.00 3.69
3237 3266 0.179936 CTCATGGGTCTTCTGGCCTC 59.820 60.000 3.32 0.00 0.00 4.70
3238 3267 1.277580 CCTCATGGGTCTTCTGGCCT 61.278 60.000 3.32 0.00 0.00 5.19
3239 3268 1.225704 CCTCATGGGTCTTCTGGCC 59.774 63.158 0.00 0.00 0.00 5.36
3240 3269 4.972875 CCTCATGGGTCTTCTGGC 57.027 61.111 0.00 0.00 0.00 4.85
3250 3279 2.043652 CTTGTGGCCCCCTCATGG 60.044 66.667 0.00 0.00 0.00 3.66
3251 3280 2.757099 GCTTGTGGCCCCCTCATG 60.757 66.667 0.00 0.00 34.27 3.07
3301 3330 1.132500 GGTTAGAGGAGTCATGGGGG 58.868 60.000 0.00 0.00 0.00 5.40
3302 3331 1.132500 GGGTTAGAGGAGTCATGGGG 58.868 60.000 0.00 0.00 0.00 4.96
3303 3332 2.182516 AGGGTTAGAGGAGTCATGGG 57.817 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.