Multiple sequence alignment - TraesCS7D01G116400

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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 TraesCS7D01G116400 chr7D 100.000 2477 0 0 1 2477 71620227 71617751 0.000000e+00 4575.0
1 TraesCS7D01G116400 chr7D 95.188 2182 84 7 307 2477 135508446 135506275 0.000000e+00 3428.0
2 TraesCS7D01G116400 chr7D 91.417 1538 125 6 941 2475 370972586 370971053 0.000000e+00 2102.0
3 TraesCS7D01G116400 chr5D 97.239 2173 57 2 306 2477 306249544 306247374 0.000000e+00 3677.0
4 TraesCS7D01G116400 chr7A 95.264 2175 94 5 308 2477 80557140 80559310 0.000000e+00 3437.0
5 TraesCS7D01G116400 chr6A 94.470 2188 80 11 308 2477 535298195 535296031 0.000000e+00 3332.0
6 TraesCS7D01G116400 chr3B 91.286 2123 163 13 306 2427 672250068 672252169 0.000000e+00 2876.0
7 TraesCS7D01G116400 chr1B 91.704 1796 139 9 687 2477 52804274 52806064 0.000000e+00 2483.0
8 TraesCS7D01G116400 chr1B 89.433 388 29 5 307 693 52803706 52804082 1.720000e-131 479.0
9 TraesCS7D01G116400 chr1D 91.314 1796 128 11 309 2102 267989790 267991559 0.000000e+00 2427.0
10 TraesCS7D01G116400 chr6B 91.945 1589 123 5 308 1895 431424144 431422560 0.000000e+00 2220.0
11 TraesCS7D01G116400 chr5A 87.339 1477 183 4 999 2474 638078379 638079852 0.000000e+00 1688.0
12 TraesCS7D01G116400 chr3A 86.992 1476 190 2 999 2474 716983108 716984581 0.000000e+00 1661.0
13 TraesCS7D01G116400 chr7B 91.813 1026 78 6 309 1332 54922218 54923239 0.000000e+00 1424.0
14 TraesCS7D01G116400 chr7B 83.673 98 6 6 167 256 14200984 14200889 1.580000e-12 84.2
15 TraesCS7D01G116400 chr3D 84.043 1479 219 12 1000 2474 16636275 16637740 0.000000e+00 1408.0
16 TraesCS7D01G116400 chrUn 83.673 98 6 6 167 256 84378427 84378522 1.580000e-12 84.2


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 TraesCS7D01G116400 chr7D 71617751 71620227 2476 True 4575 4575 100.0000 1 2477 1 chr7D.!!$R1 2476
1 TraesCS7D01G116400 chr7D 135506275 135508446 2171 True 3428 3428 95.1880 307 2477 1 chr7D.!!$R2 2170
2 TraesCS7D01G116400 chr7D 370971053 370972586 1533 True 2102 2102 91.4170 941 2475 1 chr7D.!!$R3 1534
3 TraesCS7D01G116400 chr5D 306247374 306249544 2170 True 3677 3677 97.2390 306 2477 1 chr5D.!!$R1 2171
4 TraesCS7D01G116400 chr7A 80557140 80559310 2170 False 3437 3437 95.2640 308 2477 1 chr7A.!!$F1 2169
5 TraesCS7D01G116400 chr6A 535296031 535298195 2164 True 3332 3332 94.4700 308 2477 1 chr6A.!!$R1 2169
6 TraesCS7D01G116400 chr3B 672250068 672252169 2101 False 2876 2876 91.2860 306 2427 1 chr3B.!!$F1 2121
7 TraesCS7D01G116400 chr1B 52803706 52806064 2358 False 1481 2483 90.5685 307 2477 2 chr1B.!!$F1 2170
8 TraesCS7D01G116400 chr1D 267989790 267991559 1769 False 2427 2427 91.3140 309 2102 1 chr1D.!!$F1 1793
9 TraesCS7D01G116400 chr6B 431422560 431424144 1584 True 2220 2220 91.9450 308 1895 1 chr6B.!!$R1 1587
10 TraesCS7D01G116400 chr5A 638078379 638079852 1473 False 1688 1688 87.3390 999 2474 1 chr5A.!!$F1 1475
11 TraesCS7D01G116400 chr3A 716983108 716984581 1473 False 1661 1661 86.9920 999 2474 1 chr3A.!!$F1 1475
12 TraesCS7D01G116400 chr7B 54922218 54923239 1021 False 1424 1424 91.8130 309 1332 1 chr7B.!!$F1 1023
13 TraesCS7D01G116400 chr3D 16636275 16637740 1465 False 1408 1408 84.0430 1000 2474 1 chr3D.!!$F1 1474

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
272 273 0.040692 TTCTTCGTCGACCGTGACTG 60.041 55.0 10.58 0.0 36.71 3.51 F
293 294 0.686789 CCCACTGGACTGACACATGA 59.313 55.0 0.00 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1118 1335 0.250038 GAGCTCTGGCAGTGACAACA 60.250 55.0 19.98 0.0 41.70 3.33 R
1624 1867 2.762535 TGGAGCTACAGTTTGGCTAC 57.237 50.0 0.00 0.0 37.43 3.58 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
18 19 2.826277 TACGTACTGAGACGCGTGA 58.174 52.632 20.70 0.00 46.87 4.35
19 20 0.717784 TACGTACTGAGACGCGTGAG 59.282 55.000 20.70 12.49 46.87 3.51
20 21 0.947660 ACGTACTGAGACGCGTGAGA 60.948 55.000 20.70 0.00 46.87 3.27
21 22 0.374063 CGTACTGAGACGCGTGAGAT 59.626 55.000 20.70 0.00 35.79 2.75
22 23 1.592590 CGTACTGAGACGCGTGAGATC 60.593 57.143 20.70 10.05 35.79 2.75
23 24 1.015109 TACTGAGACGCGTGAGATCC 58.985 55.000 20.70 0.00 0.00 3.36
24 25 1.064946 CTGAGACGCGTGAGATCCC 59.935 63.158 20.70 0.00 0.00 3.85
25 26 1.657751 CTGAGACGCGTGAGATCCCA 61.658 60.000 20.70 0.00 0.00 4.37
26 27 1.064946 GAGACGCGTGAGATCCCAG 59.935 63.158 20.70 0.00 0.00 4.45
27 28 2.583593 GACGCGTGAGATCCCAGC 60.584 66.667 20.70 0.00 0.00 4.85
28 29 4.148825 ACGCGTGAGATCCCAGCC 62.149 66.667 12.93 0.00 0.00 4.85
30 31 4.148825 GCGTGAGATCCCAGCCGT 62.149 66.667 0.00 0.00 0.00 5.68
31 32 2.202797 CGTGAGATCCCAGCCGTG 60.203 66.667 0.00 0.00 0.00 4.94
32 33 2.187946 GTGAGATCCCAGCCGTGG 59.812 66.667 0.00 0.00 44.56 4.94
33 34 2.284625 TGAGATCCCAGCCGTGGT 60.285 61.111 0.00 0.00 43.23 4.16
34 35 2.359169 TGAGATCCCAGCCGTGGTC 61.359 63.158 0.00 0.00 43.23 4.02
35 36 2.039624 AGATCCCAGCCGTGGTCT 59.960 61.111 0.00 0.00 43.23 3.85
36 37 0.755698 GAGATCCCAGCCGTGGTCTA 60.756 60.000 0.00 0.00 43.23 2.59
37 38 0.757188 AGATCCCAGCCGTGGTCTAG 60.757 60.000 0.00 0.00 43.23 2.43
38 39 2.370647 GATCCCAGCCGTGGTCTAGC 62.371 65.000 0.00 0.00 43.23 3.42
39 40 4.162690 CCCAGCCGTGGTCTAGCC 62.163 72.222 0.00 0.00 43.23 3.93
40 41 3.077556 CCAGCCGTGGTCTAGCCT 61.078 66.667 5.06 0.00 39.30 4.58
41 42 2.496817 CAGCCGTGGTCTAGCCTC 59.503 66.667 5.06 1.21 38.35 4.70
42 43 2.760385 AGCCGTGGTCTAGCCTCC 60.760 66.667 5.06 0.00 38.35 4.30
43 44 3.075005 GCCGTGGTCTAGCCTCCA 61.075 66.667 5.06 1.80 38.35 3.86
46 47 2.184579 GTGGTCTAGCCTCCACGC 59.815 66.667 13.02 0.00 43.34 5.34
47 48 3.075005 TGGTCTAGCCTCCACGCC 61.075 66.667 5.06 0.00 38.35 5.68
48 49 3.851128 GGTCTAGCCTCCACGCCC 61.851 72.222 0.00 0.00 0.00 6.13
49 50 4.208686 GTCTAGCCTCCACGCCCG 62.209 72.222 0.00 0.00 0.00 6.13
50 51 4.435970 TCTAGCCTCCACGCCCGA 62.436 66.667 0.00 0.00 0.00 5.14
51 52 4.208686 CTAGCCTCCACGCCCGAC 62.209 72.222 0.00 0.00 0.00 4.79
62 63 4.891727 GCCCGACGATCGCACCAT 62.892 66.667 16.60 0.00 38.82 3.55
63 64 2.961721 CCCGACGATCGCACCATG 60.962 66.667 16.60 0.00 38.82 3.66
64 65 2.202743 CCGACGATCGCACCATGT 60.203 61.111 16.60 0.00 38.82 3.21
65 66 1.809619 CCGACGATCGCACCATGTT 60.810 57.895 16.60 0.00 38.82 2.71
66 67 1.631072 CGACGATCGCACCATGTTC 59.369 57.895 16.60 1.22 31.14 3.18
67 68 1.752501 CGACGATCGCACCATGTTCC 61.753 60.000 16.60 0.00 31.14 3.62
68 69 0.460284 GACGATCGCACCATGTTCCT 60.460 55.000 16.60 0.00 0.00 3.36
69 70 0.740868 ACGATCGCACCATGTTCCTG 60.741 55.000 16.60 0.00 0.00 3.86
70 71 1.431488 CGATCGCACCATGTTCCTGG 61.431 60.000 0.26 0.00 42.35 4.45
71 72 1.718757 GATCGCACCATGTTCCTGGC 61.719 60.000 0.00 0.00 40.15 4.85
72 73 3.443045 CGCACCATGTTCCTGGCC 61.443 66.667 0.00 0.00 40.15 5.36
73 74 2.036256 GCACCATGTTCCTGGCCT 59.964 61.111 3.32 0.00 40.15 5.19
74 75 1.302949 GCACCATGTTCCTGGCCTA 59.697 57.895 3.32 0.00 40.15 3.93
75 76 0.323360 GCACCATGTTCCTGGCCTAA 60.323 55.000 3.32 0.00 40.15 2.69
76 77 1.463674 CACCATGTTCCTGGCCTAAC 58.536 55.000 3.32 6.78 40.15 2.34
77 78 1.072266 ACCATGTTCCTGGCCTAACA 58.928 50.000 17.38 17.38 40.15 2.41
78 79 1.427368 ACCATGTTCCTGGCCTAACAA 59.573 47.619 18.49 6.80 40.15 2.83
79 80 1.818674 CCATGTTCCTGGCCTAACAAC 59.181 52.381 18.49 10.50 38.95 3.32
80 81 2.555227 CCATGTTCCTGGCCTAACAACT 60.555 50.000 18.49 5.19 38.95 3.16
81 82 3.157087 CATGTTCCTGGCCTAACAACTT 58.843 45.455 18.49 6.52 38.95 2.66
82 83 3.306472 TGTTCCTGGCCTAACAACTTT 57.694 42.857 14.08 0.00 32.86 2.66
83 84 3.219281 TGTTCCTGGCCTAACAACTTTC 58.781 45.455 14.08 0.00 32.86 2.62
84 85 2.178912 TCCTGGCCTAACAACTTTCG 57.821 50.000 3.32 0.00 0.00 3.46
85 86 1.418637 TCCTGGCCTAACAACTTTCGT 59.581 47.619 3.32 0.00 0.00 3.85
86 87 2.158726 TCCTGGCCTAACAACTTTCGTT 60.159 45.455 3.32 0.00 0.00 3.85
87 88 3.071312 TCCTGGCCTAACAACTTTCGTTA 59.929 43.478 3.32 0.00 0.00 3.18
88 89 3.816523 CCTGGCCTAACAACTTTCGTTAA 59.183 43.478 3.32 0.00 0.00 2.01
89 90 4.457949 CCTGGCCTAACAACTTTCGTTAAT 59.542 41.667 3.32 0.00 0.00 1.40
90 91 5.391629 CCTGGCCTAACAACTTTCGTTAATC 60.392 44.000 3.32 0.00 0.00 1.75
91 92 5.310451 TGGCCTAACAACTTTCGTTAATCT 58.690 37.500 3.32 0.00 0.00 2.40
92 93 5.410439 TGGCCTAACAACTTTCGTTAATCTC 59.590 40.000 3.32 0.00 0.00 2.75
93 94 5.410439 GGCCTAACAACTTTCGTTAATCTCA 59.590 40.000 0.00 0.00 0.00 3.27
94 95 6.304882 GCCTAACAACTTTCGTTAATCTCAC 58.695 40.000 0.00 0.00 0.00 3.51
95 96 6.522761 CCTAACAACTTTCGTTAATCTCACG 58.477 40.000 0.00 0.00 39.08 4.35
96 97 4.385244 ACAACTTTCGTTAATCTCACGC 57.615 40.909 0.00 0.00 37.57 5.34
97 98 4.056050 ACAACTTTCGTTAATCTCACGCT 58.944 39.130 0.00 0.00 37.57 5.07
98 99 4.084537 ACAACTTTCGTTAATCTCACGCTG 60.085 41.667 0.00 0.00 37.57 5.18
99 100 3.650139 ACTTTCGTTAATCTCACGCTGT 58.350 40.909 0.00 0.00 37.57 4.40
100 101 3.673809 ACTTTCGTTAATCTCACGCTGTC 59.326 43.478 0.00 0.00 37.57 3.51
101 102 3.291809 TTCGTTAATCTCACGCTGTCA 57.708 42.857 0.00 0.00 37.57 3.58
102 103 2.592194 TCGTTAATCTCACGCTGTCAC 58.408 47.619 0.00 0.00 37.57 3.67
103 104 1.317611 CGTTAATCTCACGCTGTCACG 59.682 52.381 0.00 0.00 39.50 4.35
104 105 1.059264 GTTAATCTCACGCTGTCACGC 59.941 52.381 0.00 0.00 36.19 5.34
129 130 2.967599 TCCGTCAGGATCAAGTCATG 57.032 50.000 0.00 0.00 42.75 3.07
130 131 1.134699 TCCGTCAGGATCAAGTCATGC 60.135 52.381 0.00 0.00 42.75 4.06
131 132 1.293924 CGTCAGGATCAAGTCATGCC 58.706 55.000 0.00 0.00 38.48 4.40
132 133 1.134580 CGTCAGGATCAAGTCATGCCT 60.135 52.381 0.00 0.00 38.48 4.75
133 134 2.559440 GTCAGGATCAAGTCATGCCTC 58.441 52.381 0.00 0.00 38.48 4.70
134 135 1.487976 TCAGGATCAAGTCATGCCTCC 59.512 52.381 0.00 0.00 38.48 4.30
135 136 1.489649 CAGGATCAAGTCATGCCTCCT 59.510 52.381 0.00 0.00 39.89 3.69
136 137 1.767681 AGGATCAAGTCATGCCTCCTC 59.232 52.381 0.00 0.00 36.66 3.71
137 138 1.539929 GGATCAAGTCATGCCTCCTCG 60.540 57.143 0.00 0.00 31.44 4.63
138 139 0.179062 ATCAAGTCATGCCTCCTCGC 60.179 55.000 0.00 0.00 0.00 5.03
139 140 1.817099 CAAGTCATGCCTCCTCGCC 60.817 63.158 0.00 0.00 0.00 5.54
140 141 3.376935 AAGTCATGCCTCCTCGCCG 62.377 63.158 0.00 0.00 0.00 6.46
141 142 4.148825 GTCATGCCTCCTCGCCGT 62.149 66.667 0.00 0.00 0.00 5.68
142 143 4.147449 TCATGCCTCCTCGCCGTG 62.147 66.667 0.00 0.00 0.00 4.94
143 144 4.147449 CATGCCTCCTCGCCGTGA 62.147 66.667 0.00 0.00 0.00 4.35
144 145 4.148825 ATGCCTCCTCGCCGTGAC 62.149 66.667 0.00 0.00 0.00 3.67
147 148 3.518998 CCTCCTCGCCGTGACGAT 61.519 66.667 6.54 0.00 42.02 3.73
148 149 2.024871 CTCCTCGCCGTGACGATC 59.975 66.667 6.54 0.00 42.02 3.69
149 150 2.748647 TCCTCGCCGTGACGATCA 60.749 61.111 6.54 0.00 42.02 2.92
150 151 2.579787 CCTCGCCGTGACGATCAC 60.580 66.667 6.54 7.74 43.65 3.06
159 160 1.629013 GTGACGATCACGCTTCATCA 58.371 50.000 0.00 0.00 43.96 3.07
160 161 2.196749 GTGACGATCACGCTTCATCAT 58.803 47.619 0.00 0.00 43.96 2.45
161 162 2.604914 GTGACGATCACGCTTCATCATT 59.395 45.455 0.00 0.00 43.96 2.57
162 163 3.062639 GTGACGATCACGCTTCATCATTT 59.937 43.478 0.00 0.00 43.96 2.32
163 164 3.306973 TGACGATCACGCTTCATCATTTC 59.693 43.478 0.00 0.00 43.96 2.17
164 165 3.261580 ACGATCACGCTTCATCATTTCA 58.738 40.909 0.00 0.00 43.96 2.69
165 166 3.062639 ACGATCACGCTTCATCATTTCAC 59.937 43.478 0.00 0.00 43.96 3.18
166 167 3.601356 GATCACGCTTCATCATTTCACG 58.399 45.455 0.00 0.00 0.00 4.35
167 168 2.682836 TCACGCTTCATCATTTCACGA 58.317 42.857 0.00 0.00 0.00 4.35
168 169 3.063485 TCACGCTTCATCATTTCACGAA 58.937 40.909 0.00 0.00 0.00 3.85
169 170 3.496507 TCACGCTTCATCATTTCACGAAA 59.503 39.130 0.00 0.00 34.46 3.46
170 171 4.154015 TCACGCTTCATCATTTCACGAAAT 59.846 37.500 0.00 0.00 41.33 2.17
171 172 5.350091 TCACGCTTCATCATTTCACGAAATA 59.650 36.000 4.75 0.00 38.84 1.40
172 173 6.020984 CACGCTTCATCATTTCACGAAATAA 58.979 36.000 4.75 0.00 38.84 1.40
173 174 6.193410 CACGCTTCATCATTTCACGAAATAAG 59.807 38.462 4.75 6.55 38.84 1.73
174 175 6.092122 ACGCTTCATCATTTCACGAAATAAGA 59.908 34.615 13.30 6.15 38.84 2.10
175 176 6.626488 CGCTTCATCATTTCACGAAATAAGAG 59.374 38.462 13.30 8.51 38.84 2.85
176 177 6.909357 GCTTCATCATTTCACGAAATAAGAGG 59.091 38.462 13.30 7.25 38.84 3.69
177 178 7.201644 GCTTCATCATTTCACGAAATAAGAGGA 60.202 37.037 13.30 8.89 38.84 3.71
178 179 7.539712 TCATCATTTCACGAAATAAGAGGAC 57.460 36.000 4.75 0.00 38.84 3.85
179 180 7.102993 TCATCATTTCACGAAATAAGAGGACA 58.897 34.615 4.75 0.00 38.84 4.02
180 181 7.770433 TCATCATTTCACGAAATAAGAGGACAT 59.230 33.333 4.75 0.00 38.84 3.06
181 182 7.307493 TCATTTCACGAAATAAGAGGACATG 57.693 36.000 4.75 0.00 38.84 3.21
182 183 6.878923 TCATTTCACGAAATAAGAGGACATGT 59.121 34.615 0.00 0.00 38.84 3.21
183 184 6.480524 TTTCACGAAATAAGAGGACATGTG 57.519 37.500 1.15 0.00 0.00 3.21
184 185 4.503910 TCACGAAATAAGAGGACATGTGG 58.496 43.478 1.15 0.00 0.00 4.17
185 186 3.063997 CACGAAATAAGAGGACATGTGGC 59.936 47.826 1.15 0.00 0.00 5.01
186 187 3.270027 CGAAATAAGAGGACATGTGGCA 58.730 45.455 1.15 0.00 0.00 4.92
187 188 3.689161 CGAAATAAGAGGACATGTGGCAA 59.311 43.478 1.15 0.00 0.00 4.52
188 189 4.155826 CGAAATAAGAGGACATGTGGCAAA 59.844 41.667 1.15 0.00 0.00 3.68
189 190 5.335583 CGAAATAAGAGGACATGTGGCAAAA 60.336 40.000 1.15 0.00 0.00 2.44
190 191 6.610075 AAATAAGAGGACATGTGGCAAAAT 57.390 33.333 1.15 0.00 0.00 1.82
191 192 5.841957 ATAAGAGGACATGTGGCAAAATC 57.158 39.130 1.15 0.00 0.00 2.17
192 193 3.159213 AGAGGACATGTGGCAAAATCA 57.841 42.857 1.15 0.00 0.00 2.57
193 194 3.499338 AGAGGACATGTGGCAAAATCAA 58.501 40.909 1.15 0.00 0.00 2.57
194 195 3.896888 AGAGGACATGTGGCAAAATCAAA 59.103 39.130 1.15 0.00 0.00 2.69
195 196 3.989817 GAGGACATGTGGCAAAATCAAAC 59.010 43.478 1.15 0.00 0.00 2.93
196 197 2.730928 GGACATGTGGCAAAATCAAACG 59.269 45.455 1.15 0.00 0.00 3.60
197 198 3.551863 GGACATGTGGCAAAATCAAACGA 60.552 43.478 1.15 0.00 0.00 3.85
198 199 4.236935 GACATGTGGCAAAATCAAACGAT 58.763 39.130 1.15 0.00 0.00 3.73
199 200 3.989167 ACATGTGGCAAAATCAAACGATG 59.011 39.130 0.00 0.00 0.00 3.84
200 201 3.998099 TGTGGCAAAATCAAACGATGA 57.002 38.095 0.00 0.00 43.67 2.92
201 202 3.899734 TGTGGCAAAATCAAACGATGAG 58.100 40.909 0.00 0.00 42.53 2.90
202 203 3.567585 TGTGGCAAAATCAAACGATGAGA 59.432 39.130 0.00 0.00 42.53 3.27
203 204 4.218200 TGTGGCAAAATCAAACGATGAGAT 59.782 37.500 0.00 0.00 42.53 2.75
204 205 4.560035 GTGGCAAAATCAAACGATGAGATG 59.440 41.667 0.00 0.00 42.53 2.90
205 206 4.458642 TGGCAAAATCAAACGATGAGATGA 59.541 37.500 0.00 0.00 42.53 2.92
206 207 5.125900 TGGCAAAATCAAACGATGAGATGAT 59.874 36.000 0.00 0.00 42.53 2.45
207 208 5.684626 GGCAAAATCAAACGATGAGATGATC 59.315 40.000 0.00 0.00 42.53 2.92
208 209 6.260377 GCAAAATCAAACGATGAGATGATCA 58.740 36.000 0.00 0.00 42.53 2.92
209 210 6.414109 GCAAAATCAAACGATGAGATGATCAG 59.586 38.462 0.09 0.00 42.53 2.90
210 211 7.470079 CAAAATCAAACGATGAGATGATCAGT 58.530 34.615 0.09 0.00 42.53 3.41
211 212 8.606602 CAAAATCAAACGATGAGATGATCAGTA 58.393 33.333 0.09 0.00 42.53 2.74
212 213 7.706281 AATCAAACGATGAGATGATCAGTAC 57.294 36.000 0.09 0.00 42.53 2.73
213 214 6.207691 TCAAACGATGAGATGATCAGTACA 57.792 37.500 0.09 1.27 42.53 2.90
214 215 6.036470 TCAAACGATGAGATGATCAGTACAC 58.964 40.000 0.09 0.00 42.53 2.90
215 216 5.843673 AACGATGAGATGATCAGTACACT 57.156 39.130 0.09 0.00 42.53 3.55
216 217 6.944234 AACGATGAGATGATCAGTACACTA 57.056 37.500 0.09 0.00 42.53 2.74
217 218 6.307031 ACGATGAGATGATCAGTACACTAC 57.693 41.667 0.09 0.00 42.53 2.73
218 219 5.050023 ACGATGAGATGATCAGTACACTACG 60.050 44.000 0.09 9.79 42.53 3.51
219 220 4.553756 TGAGATGATCAGTACACTACGC 57.446 45.455 0.09 0.00 32.77 4.42
220 221 3.945285 TGAGATGATCAGTACACTACGCA 59.055 43.478 0.09 0.00 32.77 5.24
221 222 4.201920 TGAGATGATCAGTACACTACGCAC 60.202 45.833 0.09 0.00 32.77 5.34
222 223 2.537639 TGATCAGTACACTACGCACG 57.462 50.000 0.00 0.00 0.00 5.34
223 224 1.189403 GATCAGTACACTACGCACGC 58.811 55.000 0.00 0.00 0.00 5.34
224 225 0.524414 ATCAGTACACTACGCACGCA 59.476 50.000 0.00 0.00 0.00 5.24
225 226 0.386352 TCAGTACACTACGCACGCAC 60.386 55.000 0.00 0.00 0.00 5.34
226 227 1.441515 AGTACACTACGCACGCACG 60.442 57.895 0.00 0.00 39.50 5.34
227 228 2.801996 TACACTACGCACGCACGC 60.802 61.111 0.00 0.00 36.19 5.34
228 229 3.539560 TACACTACGCACGCACGCA 62.540 57.895 0.00 0.00 36.19 5.24
229 230 4.409588 CACTACGCACGCACGCAC 62.410 66.667 0.00 0.00 36.19 5.34
241 242 4.595538 ACGCACGCGGTGGAGAAA 62.596 61.111 16.70 0.00 44.69 2.52
242 243 3.118454 CGCACGCGGTGGAGAAAT 61.118 61.111 12.47 0.00 33.64 2.17
243 244 2.677003 CGCACGCGGTGGAGAAATT 61.677 57.895 12.47 0.00 33.64 1.82
244 245 1.134694 GCACGCGGTGGAGAAATTC 59.865 57.895 12.47 0.00 33.64 2.17
245 246 1.298859 GCACGCGGTGGAGAAATTCT 61.299 55.000 12.47 0.00 33.64 2.40
246 247 2.004583 CACGCGGTGGAGAAATTCTA 57.995 50.000 12.47 0.00 0.00 2.10
247 248 1.659098 CACGCGGTGGAGAAATTCTAC 59.341 52.381 12.47 0.00 36.62 2.59
248 249 1.274167 ACGCGGTGGAGAAATTCTACA 59.726 47.619 12.47 3.32 38.92 2.74
249 250 2.093658 ACGCGGTGGAGAAATTCTACAT 60.094 45.455 11.54 0.00 39.95 2.29
250 251 2.285220 CGCGGTGGAGAAATTCTACATG 59.715 50.000 11.54 8.43 39.95 3.21
251 252 2.614057 GCGGTGGAGAAATTCTACATGG 59.386 50.000 11.54 7.55 39.95 3.66
252 253 2.614057 CGGTGGAGAAATTCTACATGGC 59.386 50.000 11.54 0.00 39.95 4.40
253 254 3.682718 CGGTGGAGAAATTCTACATGGCT 60.683 47.826 11.54 0.00 39.95 4.75
254 255 4.273318 GGTGGAGAAATTCTACATGGCTT 58.727 43.478 11.54 0.00 39.95 4.35
255 256 4.336713 GGTGGAGAAATTCTACATGGCTTC 59.663 45.833 11.54 0.00 39.95 3.86
256 257 5.189180 GTGGAGAAATTCTACATGGCTTCT 58.811 41.667 11.54 0.00 39.95 2.85
257 258 5.649831 GTGGAGAAATTCTACATGGCTTCTT 59.350 40.000 11.54 0.00 39.95 2.52
258 259 5.882557 TGGAGAAATTCTACATGGCTTCTTC 59.117 40.000 3.32 0.00 30.99 2.87
259 260 5.007136 GGAGAAATTCTACATGGCTTCTTCG 59.993 44.000 0.00 0.00 0.00 3.79
260 261 5.491982 AGAAATTCTACATGGCTTCTTCGT 58.508 37.500 0.00 0.00 0.00 3.85
261 262 5.582665 AGAAATTCTACATGGCTTCTTCGTC 59.417 40.000 0.00 0.00 0.00 4.20
262 263 2.561733 TCTACATGGCTTCTTCGTCG 57.438 50.000 0.00 0.00 0.00 5.12
263 264 2.089201 TCTACATGGCTTCTTCGTCGA 58.911 47.619 0.00 0.00 0.00 4.20
264 265 2.159421 TCTACATGGCTTCTTCGTCGAC 60.159 50.000 5.18 5.18 0.00 4.20
265 266 0.389948 ACATGGCTTCTTCGTCGACC 60.390 55.000 10.58 0.00 0.00 4.79
266 267 1.153823 ATGGCTTCTTCGTCGACCG 60.154 57.895 10.58 5.50 38.13 4.79
267 268 1.874345 ATGGCTTCTTCGTCGACCGT 61.874 55.000 10.58 0.00 37.94 4.83
268 269 2.087009 GGCTTCTTCGTCGACCGTG 61.087 63.158 10.58 0.00 37.94 4.94
269 270 1.081641 GCTTCTTCGTCGACCGTGA 60.082 57.895 10.58 2.41 37.94 4.35
270 271 1.335697 GCTTCTTCGTCGACCGTGAC 61.336 60.000 10.58 0.00 37.94 3.67
271 272 0.237761 CTTCTTCGTCGACCGTGACT 59.762 55.000 10.58 0.00 36.71 3.41
272 273 0.040692 TTCTTCGTCGACCGTGACTG 60.041 55.000 10.58 0.00 36.71 3.51
273 274 1.442184 CTTCGTCGACCGTGACTGG 60.442 63.158 10.58 0.00 36.71 4.00
274 275 3.547249 TTCGTCGACCGTGACTGGC 62.547 63.158 10.58 0.00 36.71 4.85
276 277 4.736896 GTCGACCGTGACTGGCCC 62.737 72.222 3.51 0.00 35.95 5.80
279 280 3.626924 GACCGTGACTGGCCCACT 61.627 66.667 0.00 0.00 32.64 4.00
280 281 3.883744 GACCGTGACTGGCCCACTG 62.884 68.421 0.00 0.00 32.64 3.66
281 282 4.704833 CCGTGACTGGCCCACTGG 62.705 72.222 0.00 3.83 32.64 4.00
282 283 3.625897 CGTGACTGGCCCACTGGA 61.626 66.667 0.00 0.00 32.64 3.86
283 284 2.032681 GTGACTGGCCCACTGGAC 59.967 66.667 0.00 0.00 41.75 4.02
284 285 2.122413 TGACTGGCCCACTGGACT 60.122 61.111 0.00 0.00 42.00 3.85
285 286 2.348998 GACTGGCCCACTGGACTG 59.651 66.667 0.00 0.00 42.00 3.51
286 287 2.122413 ACTGGCCCACTGGACTGA 60.122 61.111 0.00 0.00 42.00 3.41
287 288 2.348998 CTGGCCCACTGGACTGAC 59.651 66.667 0.00 0.00 42.00 3.51
288 289 2.447572 TGGCCCACTGGACTGACA 60.448 61.111 0.00 0.00 42.00 3.58
289 290 2.032681 GGCCCACTGGACTGACAC 59.967 66.667 0.00 0.00 36.35 3.67
290 291 2.818169 GGCCCACTGGACTGACACA 61.818 63.158 0.00 0.00 36.35 3.72
291 292 1.376466 GCCCACTGGACTGACACAT 59.624 57.895 0.00 0.00 0.00 3.21
292 293 0.957395 GCCCACTGGACTGACACATG 60.957 60.000 0.00 0.00 0.00 3.21
293 294 0.686789 CCCACTGGACTGACACATGA 59.313 55.000 0.00 0.00 0.00 3.07
294 295 1.338484 CCCACTGGACTGACACATGAG 60.338 57.143 0.00 0.00 0.00 2.90
295 296 1.620323 CCACTGGACTGACACATGAGA 59.380 52.381 0.00 0.00 0.00 3.27
296 297 2.235650 CCACTGGACTGACACATGAGAT 59.764 50.000 0.00 0.00 0.00 2.75
297 298 3.259902 CACTGGACTGACACATGAGATG 58.740 50.000 0.00 0.00 0.00 2.90
298 299 3.056322 CACTGGACTGACACATGAGATGA 60.056 47.826 0.00 0.00 0.00 2.92
299 300 3.195182 ACTGGACTGACACATGAGATGAG 59.805 47.826 0.00 0.00 0.00 2.90
300 301 3.434309 TGGACTGACACATGAGATGAGA 58.566 45.455 0.00 0.00 0.00 3.27
301 302 4.028825 TGGACTGACACATGAGATGAGAT 58.971 43.478 0.00 0.00 0.00 2.75
302 303 4.142004 TGGACTGACACATGAGATGAGATG 60.142 45.833 0.00 0.00 0.00 2.90
303 304 4.099113 GGACTGACACATGAGATGAGATGA 59.901 45.833 0.00 0.00 0.00 2.92
304 305 5.265350 ACTGACACATGAGATGAGATGAG 57.735 43.478 0.00 0.00 0.00 2.90
359 360 1.587946 ACGCGTCGTCGTTTTTAAACT 59.412 42.857 5.58 0.00 40.07 2.66
365 366 4.492247 CGTCGTCGTTTTTAAACTCCAACA 60.492 41.667 4.08 0.00 36.77 3.33
545 547 2.262915 CCGCTCCTCGCTCACTTT 59.737 61.111 0.00 0.00 36.73 2.66
852 1061 8.719596 TGCCTTAGATGGATTGTAGGTTTAATA 58.280 33.333 0.00 0.00 0.00 0.98
983 1196 8.109705 TGATTGCATATTTGTGTTTCTGTAGT 57.890 30.769 0.00 0.00 0.00 2.73
1011 1226 2.106566 AGTCAGTTCATGGATCGAGCT 58.893 47.619 0.00 0.00 0.00 4.09
1037 1252 4.214332 GGTTCTCAATGTCAGGTTTCACTC 59.786 45.833 0.00 0.00 0.00 3.51
1073 1290 1.837439 TCGTATTGGGCCATCTCTTGT 59.163 47.619 7.26 0.00 0.00 3.16
1118 1335 6.070881 GCATTGTCAGAGATACAGAGGGATAT 60.071 42.308 0.00 0.00 0.00 1.63
1177 1394 4.452455 ACCATTTGACAGTTAAAGAGAGCG 59.548 41.667 0.00 0.00 0.00 5.03
1421 1639 5.104193 AGGAAGAACCAGATGCAGTTATCAT 60.104 40.000 0.00 0.00 42.04 2.45
1705 1948 6.752285 TTCAGATGATCCTGATTATGTGGA 57.248 37.500 8.53 0.00 42.18 4.02
1747 1990 4.167113 AGAGGAATCTGAGGTAGTAGAGCA 59.833 45.833 0.00 0.00 0.00 4.26
1837 2083 0.470341 GGTCCAGTTCCCATAGAGCC 59.530 60.000 0.00 0.00 0.00 4.70
1858 2104 4.326826 CCAGTTGCTAATGTGGAAGAAGA 58.673 43.478 0.00 0.00 31.04 2.87
1867 2113 6.017605 GCTAATGTGGAAGAAGATGTACATGG 60.018 42.308 14.43 0.00 0.00 3.66
1942 2188 3.970640 GGTCAGATGGTTAGGAGGAAGAT 59.029 47.826 0.00 0.00 0.00 2.40
1978 2224 5.942826 GGTTCAATCCAGAGACAGAAATTCT 59.057 40.000 0.00 0.00 0.00 2.40
2314 2561 0.523072 AGCATTAAAGCCACAGTGCG 59.477 50.000 0.00 0.00 37.63 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.717784 CTCACGCGTCTCAGTACGTA 59.282 55.000 9.86 0.00 44.64 3.57
1 2 0.947660 TCTCACGCGTCTCAGTACGT 60.948 55.000 9.86 0.00 44.64 3.57
2 3 0.374063 ATCTCACGCGTCTCAGTACG 59.626 55.000 9.86 0.00 45.58 3.67
3 4 1.268133 GGATCTCACGCGTCTCAGTAC 60.268 57.143 9.86 4.67 0.00 2.73
4 5 1.015109 GGATCTCACGCGTCTCAGTA 58.985 55.000 9.86 0.00 0.00 2.74
5 6 1.658686 GGGATCTCACGCGTCTCAGT 61.659 60.000 9.86 0.00 0.00 3.41
6 7 1.064946 GGGATCTCACGCGTCTCAG 59.935 63.158 9.86 5.83 0.00 3.35
7 8 1.657751 CTGGGATCTCACGCGTCTCA 61.658 60.000 9.86 2.28 0.00 3.27
8 9 1.064946 CTGGGATCTCACGCGTCTC 59.935 63.158 9.86 3.76 0.00 3.36
9 10 3.069980 GCTGGGATCTCACGCGTCT 62.070 63.158 9.86 0.00 0.00 4.18
10 11 2.583593 GCTGGGATCTCACGCGTC 60.584 66.667 9.86 0.00 0.00 5.19
11 12 4.148825 GGCTGGGATCTCACGCGT 62.149 66.667 5.58 5.58 0.00 6.01
13 14 4.148825 ACGGCTGGGATCTCACGC 62.149 66.667 5.56 6.94 0.00 5.34
14 15 2.202797 CACGGCTGGGATCTCACG 60.203 66.667 4.17 4.17 0.00 4.35
15 16 2.187946 CCACGGCTGGGATCTCAC 59.812 66.667 0.00 0.00 33.23 3.51
16 17 2.284625 ACCACGGCTGGGATCTCA 60.285 61.111 0.00 0.00 42.74 3.27
17 18 0.755698 TAGACCACGGCTGGGATCTC 60.756 60.000 0.00 0.00 42.74 2.75
18 19 0.757188 CTAGACCACGGCTGGGATCT 60.757 60.000 0.00 0.00 42.74 2.75
19 20 1.742768 CTAGACCACGGCTGGGATC 59.257 63.158 0.00 0.00 42.74 3.36
20 21 2.435693 GCTAGACCACGGCTGGGAT 61.436 63.158 0.00 0.00 42.74 3.85
21 22 3.075005 GCTAGACCACGGCTGGGA 61.075 66.667 0.00 0.00 42.74 4.37
22 23 4.162690 GGCTAGACCACGGCTGGG 62.163 72.222 0.00 0.00 42.74 4.45
23 24 3.077556 AGGCTAGACCACGGCTGG 61.078 66.667 0.00 0.00 43.14 4.85
24 25 2.496817 GAGGCTAGACCACGGCTG 59.503 66.667 0.00 0.00 43.14 4.85
25 26 2.760385 GGAGGCTAGACCACGGCT 60.760 66.667 0.00 0.00 43.14 5.52
26 27 3.075005 TGGAGGCTAGACCACGGC 61.075 66.667 0.00 0.00 43.14 5.68
27 28 2.893398 GTGGAGGCTAGACCACGG 59.107 66.667 14.89 0.00 45.16 4.94
30 31 3.075005 GGCGTGGAGGCTAGACCA 61.075 66.667 0.00 0.00 43.14 4.02
31 32 3.851128 GGGCGTGGAGGCTAGACC 61.851 72.222 0.00 0.00 45.89 3.85
32 33 4.208686 CGGGCGTGGAGGCTAGAC 62.209 72.222 0.00 0.00 45.89 2.59
33 34 4.435970 TCGGGCGTGGAGGCTAGA 62.436 66.667 0.00 0.00 45.89 2.43
34 35 4.208686 GTCGGGCGTGGAGGCTAG 62.209 72.222 0.00 0.00 45.89 3.42
38 39 4.570663 GATCGTCGGGCGTGGAGG 62.571 72.222 0.49 0.00 42.13 4.30
39 40 4.907034 CGATCGTCGGGCGTGGAG 62.907 72.222 7.03 0.00 42.13 3.86
45 46 4.891727 ATGGTGCGATCGTCGGGC 62.892 66.667 17.81 0.00 40.84 6.13
46 47 2.961721 CATGGTGCGATCGTCGGG 60.962 66.667 17.81 0.00 40.84 5.14
47 48 1.752501 GAACATGGTGCGATCGTCGG 61.753 60.000 17.81 3.61 40.84 4.79
48 49 1.631072 GAACATGGTGCGATCGTCG 59.369 57.895 17.81 1.80 43.89 5.12
49 50 0.460284 AGGAACATGGTGCGATCGTC 60.460 55.000 17.81 9.69 0.00 4.20
50 51 0.740868 CAGGAACATGGTGCGATCGT 60.741 55.000 17.81 0.00 0.00 3.73
51 52 1.431488 CCAGGAACATGGTGCGATCG 61.431 60.000 11.69 11.69 35.47 3.69
52 53 1.718757 GCCAGGAACATGGTGCGATC 61.719 60.000 7.32 0.00 42.75 3.69
53 54 1.750399 GCCAGGAACATGGTGCGAT 60.750 57.895 7.32 0.00 42.75 4.58
54 55 2.359850 GCCAGGAACATGGTGCGA 60.360 61.111 7.32 0.00 42.75 5.10
55 56 2.535485 TAGGCCAGGAACATGGTGCG 62.535 60.000 5.01 0.00 42.75 5.34
56 57 0.323360 TTAGGCCAGGAACATGGTGC 60.323 55.000 5.01 0.00 42.75 5.01
57 58 1.271871 TGTTAGGCCAGGAACATGGTG 60.272 52.381 5.01 0.00 42.75 4.17
58 59 1.072266 TGTTAGGCCAGGAACATGGT 58.928 50.000 5.01 0.00 42.75 3.55
59 60 1.818674 GTTGTTAGGCCAGGAACATGG 59.181 52.381 15.98 0.88 43.72 3.66
60 61 2.795329 AGTTGTTAGGCCAGGAACATG 58.205 47.619 15.98 0.00 35.57 3.21
61 62 3.525800 AAGTTGTTAGGCCAGGAACAT 57.474 42.857 15.98 3.00 35.57 2.71
62 63 3.219281 GAAAGTTGTTAGGCCAGGAACA 58.781 45.455 5.01 9.78 33.81 3.18
63 64 2.225727 CGAAAGTTGTTAGGCCAGGAAC 59.774 50.000 5.01 6.90 0.00 3.62
64 65 2.158726 ACGAAAGTTGTTAGGCCAGGAA 60.159 45.455 5.01 0.00 46.40 3.36
65 66 1.418637 ACGAAAGTTGTTAGGCCAGGA 59.581 47.619 5.01 0.00 46.40 3.86
66 67 1.892209 ACGAAAGTTGTTAGGCCAGG 58.108 50.000 5.01 0.00 46.40 4.45
79 80 3.673338 TGACAGCGTGAGATTAACGAAAG 59.327 43.478 0.00 0.00 43.68 2.62
80 81 3.427528 GTGACAGCGTGAGATTAACGAAA 59.572 43.478 0.00 0.00 43.68 3.46
81 82 2.984471 GTGACAGCGTGAGATTAACGAA 59.016 45.455 0.00 0.00 43.68 3.85
82 83 2.592194 GTGACAGCGTGAGATTAACGA 58.408 47.619 0.00 0.00 43.68 3.85
83 84 1.317611 CGTGACAGCGTGAGATTAACG 59.682 52.381 0.00 0.00 43.81 3.18
84 85 1.059264 GCGTGACAGCGTGAGATTAAC 59.941 52.381 0.00 0.00 0.00 2.01
85 86 1.346365 GCGTGACAGCGTGAGATTAA 58.654 50.000 0.00 0.00 0.00 1.40
86 87 3.030209 GCGTGACAGCGTGAGATTA 57.970 52.632 0.00 0.00 0.00 1.75
87 88 3.862124 GCGTGACAGCGTGAGATT 58.138 55.556 0.00 0.00 0.00 2.40
108 109 0.532573 TGACTTGATCCTGACGGAGC 59.467 55.000 0.00 0.00 45.98 4.70
109 110 2.819115 CATGACTTGATCCTGACGGAG 58.181 52.381 0.00 0.00 44.06 4.63
110 111 1.134699 GCATGACTTGATCCTGACGGA 60.135 52.381 0.00 0.00 45.16 4.69
111 112 1.293924 GCATGACTTGATCCTGACGG 58.706 55.000 0.00 0.00 0.00 4.79
112 113 1.134580 AGGCATGACTTGATCCTGACG 60.135 52.381 0.00 0.00 36.14 4.35
113 114 2.559440 GAGGCATGACTTGATCCTGAC 58.441 52.381 0.41 0.00 31.22 3.51
114 115 1.487976 GGAGGCATGACTTGATCCTGA 59.512 52.381 0.41 0.00 32.61 3.86
115 116 1.489649 AGGAGGCATGACTTGATCCTG 59.510 52.381 0.41 0.00 40.00 3.86
116 117 1.767681 GAGGAGGCATGACTTGATCCT 59.232 52.381 0.41 4.25 42.61 3.24
117 118 1.539929 CGAGGAGGCATGACTTGATCC 60.540 57.143 0.41 0.00 34.51 3.36
118 119 1.863267 CGAGGAGGCATGACTTGATC 58.137 55.000 0.41 0.02 0.00 2.92
119 120 0.179062 GCGAGGAGGCATGACTTGAT 60.179 55.000 0.41 0.00 0.00 2.57
120 121 1.219124 GCGAGGAGGCATGACTTGA 59.781 57.895 0.41 0.00 0.00 3.02
121 122 1.817099 GGCGAGGAGGCATGACTTG 60.817 63.158 0.41 0.00 45.92 3.16
122 123 2.586792 GGCGAGGAGGCATGACTT 59.413 61.111 0.41 0.00 45.92 3.01
125 126 4.147449 CACGGCGAGGAGGCATGA 62.147 66.667 16.62 0.00 41.38 3.07
130 131 3.471244 GATCGTCACGGCGAGGAGG 62.471 68.421 16.62 16.07 44.43 4.30
131 132 2.024871 GATCGTCACGGCGAGGAG 59.975 66.667 16.62 3.55 44.43 3.69
132 133 2.748647 TGATCGTCACGGCGAGGA 60.749 61.111 16.62 8.07 44.43 3.71
133 134 2.579787 GTGATCGTCACGGCGAGG 60.580 66.667 16.62 5.27 44.43 4.63
140 141 1.629013 TGATGAAGCGTGATCGTCAC 58.371 50.000 7.74 7.74 43.65 3.67
141 142 2.584492 ATGATGAAGCGTGATCGTCA 57.416 45.000 10.21 10.21 44.48 4.35
142 143 3.306973 TGAAATGATGAAGCGTGATCGTC 59.693 43.478 0.00 0.00 39.49 4.20
143 144 3.062639 GTGAAATGATGAAGCGTGATCGT 59.937 43.478 0.00 0.00 39.49 3.73
144 145 3.601356 GTGAAATGATGAAGCGTGATCG 58.399 45.455 0.00 0.00 40.37 3.69
145 146 3.306973 TCGTGAAATGATGAAGCGTGATC 59.693 43.478 0.00 0.00 0.00 2.92
146 147 3.261580 TCGTGAAATGATGAAGCGTGAT 58.738 40.909 0.00 0.00 0.00 3.06
147 148 2.682836 TCGTGAAATGATGAAGCGTGA 58.317 42.857 0.00 0.00 0.00 4.35
148 149 3.454042 TTCGTGAAATGATGAAGCGTG 57.546 42.857 0.00 0.00 0.00 5.34
149 150 4.685169 ATTTCGTGAAATGATGAAGCGT 57.315 36.364 7.02 0.00 39.36 5.07
150 151 6.477742 TCTTATTTCGTGAAATGATGAAGCG 58.522 36.000 16.12 0.00 40.83 4.68
151 152 6.909357 CCTCTTATTTCGTGAAATGATGAAGC 59.091 38.462 16.12 0.00 40.83 3.86
152 153 8.119226 GTCCTCTTATTTCGTGAAATGATGAAG 58.881 37.037 16.12 11.80 40.83 3.02
153 154 7.606073 TGTCCTCTTATTTCGTGAAATGATGAA 59.394 33.333 16.12 3.78 40.83 2.57
154 155 7.102993 TGTCCTCTTATTTCGTGAAATGATGA 58.897 34.615 16.12 10.59 40.83 2.92
155 156 7.307493 TGTCCTCTTATTTCGTGAAATGATG 57.693 36.000 16.12 7.56 40.83 3.07
156 157 7.554118 ACATGTCCTCTTATTTCGTGAAATGAT 59.446 33.333 16.12 0.00 40.83 2.45
157 158 6.878923 ACATGTCCTCTTATTTCGTGAAATGA 59.121 34.615 16.12 8.49 40.83 2.57
158 159 6.963242 CACATGTCCTCTTATTTCGTGAAATG 59.037 38.462 16.12 2.93 40.83 2.32
159 160 6.094048 CCACATGTCCTCTTATTTCGTGAAAT 59.906 38.462 12.10 12.10 42.95 2.17
160 161 5.411361 CCACATGTCCTCTTATTTCGTGAAA 59.589 40.000 0.00 0.00 34.46 2.69
161 162 4.935205 CCACATGTCCTCTTATTTCGTGAA 59.065 41.667 0.00 0.00 0.00 3.18
162 163 4.503910 CCACATGTCCTCTTATTTCGTGA 58.496 43.478 0.00 0.00 0.00 4.35
163 164 3.063997 GCCACATGTCCTCTTATTTCGTG 59.936 47.826 0.00 0.00 0.00 4.35
164 165 3.270877 GCCACATGTCCTCTTATTTCGT 58.729 45.455 0.00 0.00 0.00 3.85
165 166 3.270027 TGCCACATGTCCTCTTATTTCG 58.730 45.455 0.00 0.00 0.00 3.46
166 167 5.643379 TTTGCCACATGTCCTCTTATTTC 57.357 39.130 0.00 0.00 0.00 2.17
167 168 6.211184 TGATTTTGCCACATGTCCTCTTATTT 59.789 34.615 0.00 0.00 0.00 1.40
168 169 5.716228 TGATTTTGCCACATGTCCTCTTATT 59.284 36.000 0.00 0.00 0.00 1.40
169 170 5.263599 TGATTTTGCCACATGTCCTCTTAT 58.736 37.500 0.00 0.00 0.00 1.73
170 171 4.661222 TGATTTTGCCACATGTCCTCTTA 58.339 39.130 0.00 0.00 0.00 2.10
171 172 3.499338 TGATTTTGCCACATGTCCTCTT 58.501 40.909 0.00 0.00 0.00 2.85
172 173 3.159213 TGATTTTGCCACATGTCCTCT 57.841 42.857 0.00 0.00 0.00 3.69
173 174 3.940209 TTGATTTTGCCACATGTCCTC 57.060 42.857 0.00 0.00 0.00 3.71
174 175 3.552684 CGTTTGATTTTGCCACATGTCCT 60.553 43.478 0.00 0.00 0.00 3.85
175 176 2.730928 CGTTTGATTTTGCCACATGTCC 59.269 45.455 0.00 0.00 0.00 4.02
176 177 3.637432 TCGTTTGATTTTGCCACATGTC 58.363 40.909 0.00 0.00 0.00 3.06
177 178 3.724508 TCGTTTGATTTTGCCACATGT 57.275 38.095 0.00 0.00 0.00 3.21
178 179 4.236147 TCATCGTTTGATTTTGCCACATG 58.764 39.130 0.00 0.00 30.49 3.21
179 180 4.218200 TCTCATCGTTTGATTTTGCCACAT 59.782 37.500 0.00 0.00 32.72 3.21
180 181 3.567585 TCTCATCGTTTGATTTTGCCACA 59.432 39.130 0.00 0.00 32.72 4.17
181 182 4.159377 TCTCATCGTTTGATTTTGCCAC 57.841 40.909 0.00 0.00 32.72 5.01
182 183 4.458642 TCATCTCATCGTTTGATTTTGCCA 59.541 37.500 0.00 0.00 32.72 4.92
183 184 4.985413 TCATCTCATCGTTTGATTTTGCC 58.015 39.130 0.00 0.00 32.72 4.52
184 185 6.260377 TGATCATCTCATCGTTTGATTTTGC 58.740 36.000 0.00 0.00 32.72 3.68
185 186 7.470079 ACTGATCATCTCATCGTTTGATTTTG 58.530 34.615 0.00 0.00 32.72 2.44
186 187 7.621428 ACTGATCATCTCATCGTTTGATTTT 57.379 32.000 0.00 0.00 32.72 1.82
187 188 7.765819 TGTACTGATCATCTCATCGTTTGATTT 59.234 33.333 0.00 0.00 32.72 2.17
188 189 7.223582 GTGTACTGATCATCTCATCGTTTGATT 59.776 37.037 0.00 0.00 32.72 2.57
189 190 6.699204 GTGTACTGATCATCTCATCGTTTGAT 59.301 38.462 0.00 0.00 32.72 2.57
190 191 6.036470 GTGTACTGATCATCTCATCGTTTGA 58.964 40.000 0.00 0.00 32.10 2.69
191 192 6.038985 AGTGTACTGATCATCTCATCGTTTG 58.961 40.000 0.00 0.00 32.10 2.93
192 193 6.214191 AGTGTACTGATCATCTCATCGTTT 57.786 37.500 0.00 0.00 32.10 3.60
193 194 5.843673 AGTGTACTGATCATCTCATCGTT 57.156 39.130 0.00 0.00 32.10 3.85
194 195 5.050023 CGTAGTGTACTGATCATCTCATCGT 60.050 44.000 0.00 0.00 32.10 3.73
195 196 5.378180 CGTAGTGTACTGATCATCTCATCG 58.622 45.833 0.00 0.41 32.10 3.84
196 197 5.150683 GCGTAGTGTACTGATCATCTCATC 58.849 45.833 0.00 0.00 32.10 2.92
197 198 4.580580 TGCGTAGTGTACTGATCATCTCAT 59.419 41.667 0.00 0.00 32.10 2.90
198 199 3.945285 TGCGTAGTGTACTGATCATCTCA 59.055 43.478 0.00 0.00 0.00 3.27
199 200 4.283678 GTGCGTAGTGTACTGATCATCTC 58.716 47.826 0.00 0.00 0.00 2.75
200 201 3.242772 CGTGCGTAGTGTACTGATCATCT 60.243 47.826 0.00 0.00 0.00 2.90
201 202 3.036633 CGTGCGTAGTGTACTGATCATC 58.963 50.000 0.00 0.00 0.00 2.92
202 203 2.794981 GCGTGCGTAGTGTACTGATCAT 60.795 50.000 0.00 0.00 0.00 2.45
203 204 1.466866 GCGTGCGTAGTGTACTGATCA 60.467 52.381 0.00 0.00 0.00 2.92
204 205 1.189403 GCGTGCGTAGTGTACTGATC 58.811 55.000 0.00 0.00 0.00 2.92
205 206 0.524414 TGCGTGCGTAGTGTACTGAT 59.476 50.000 0.00 0.00 0.00 2.90
206 207 0.386352 GTGCGTGCGTAGTGTACTGA 60.386 55.000 0.00 0.00 0.00 3.41
207 208 1.661948 CGTGCGTGCGTAGTGTACTG 61.662 60.000 0.00 0.00 0.00 2.74
208 209 1.441515 CGTGCGTGCGTAGTGTACT 60.442 57.895 0.00 0.00 0.00 2.73
209 210 3.051171 GCGTGCGTGCGTAGTGTAC 62.051 63.158 3.11 0.00 0.00 2.90
210 211 2.801996 GCGTGCGTGCGTAGTGTA 60.802 61.111 3.11 0.00 0.00 2.90
211 212 4.934942 TGCGTGCGTGCGTAGTGT 62.935 61.111 3.11 0.00 37.81 3.55
212 213 4.409588 GTGCGTGCGTGCGTAGTG 62.410 66.667 3.11 0.00 37.81 2.74
224 225 3.876589 ATTTCTCCACCGCGTGCGT 62.877 57.895 13.70 0.00 37.81 5.24
225 226 2.563086 GAATTTCTCCACCGCGTGCG 62.563 60.000 4.92 7.38 39.44 5.34
226 227 1.134694 GAATTTCTCCACCGCGTGC 59.865 57.895 4.92 0.00 31.34 5.34
227 228 1.659098 GTAGAATTTCTCCACCGCGTG 59.341 52.381 4.92 3.32 0.00 5.34
228 229 1.274167 TGTAGAATTTCTCCACCGCGT 59.726 47.619 4.92 0.00 0.00 6.01
229 230 2.004583 TGTAGAATTTCTCCACCGCG 57.995 50.000 1.27 0.00 0.00 6.46
230 231 2.614057 CCATGTAGAATTTCTCCACCGC 59.386 50.000 1.27 0.00 0.00 5.68
231 232 2.614057 GCCATGTAGAATTTCTCCACCG 59.386 50.000 1.27 0.00 0.00 4.94
232 233 3.891049 AGCCATGTAGAATTTCTCCACC 58.109 45.455 1.27 0.00 0.00 4.61
233 234 5.189180 AGAAGCCATGTAGAATTTCTCCAC 58.811 41.667 1.27 0.00 0.00 4.02
234 235 5.441718 AGAAGCCATGTAGAATTTCTCCA 57.558 39.130 1.27 0.00 0.00 3.86
235 236 5.007136 CGAAGAAGCCATGTAGAATTTCTCC 59.993 44.000 1.27 0.00 0.00 3.71
236 237 5.582665 ACGAAGAAGCCATGTAGAATTTCTC 59.417 40.000 1.27 0.00 0.00 2.87
237 238 5.491982 ACGAAGAAGCCATGTAGAATTTCT 58.508 37.500 4.03 4.03 0.00 2.52
238 239 5.500931 CGACGAAGAAGCCATGTAGAATTTC 60.501 44.000 0.00 0.00 0.00 2.17
239 240 4.330074 CGACGAAGAAGCCATGTAGAATTT 59.670 41.667 0.00 0.00 0.00 1.82
240 241 3.865745 CGACGAAGAAGCCATGTAGAATT 59.134 43.478 0.00 0.00 0.00 2.17
241 242 3.130516 TCGACGAAGAAGCCATGTAGAAT 59.869 43.478 0.00 0.00 0.00 2.40
242 243 2.490509 TCGACGAAGAAGCCATGTAGAA 59.509 45.455 0.00 0.00 0.00 2.10
243 244 2.089201 TCGACGAAGAAGCCATGTAGA 58.911 47.619 0.00 0.00 0.00 2.59
244 245 2.186076 GTCGACGAAGAAGCCATGTAG 58.814 52.381 0.00 0.00 0.00 2.74
245 246 1.135199 GGTCGACGAAGAAGCCATGTA 60.135 52.381 9.92 0.00 0.00 2.29
246 247 0.389948 GGTCGACGAAGAAGCCATGT 60.390 55.000 9.92 0.00 0.00 3.21
247 248 2.373938 GGTCGACGAAGAAGCCATG 58.626 57.895 9.92 0.00 0.00 3.66
248 249 4.913126 GGTCGACGAAGAAGCCAT 57.087 55.556 9.92 0.00 0.00 4.40
259 260 4.736896 GGGCCAGTCACGGTCGAC 62.737 72.222 7.13 7.13 36.08 4.20
262 263 3.626924 AGTGGGCCAGTCACGGTC 61.627 66.667 6.40 0.00 39.86 4.79
263 264 3.941188 CAGTGGGCCAGTCACGGT 61.941 66.667 11.93 0.00 39.86 4.83
264 265 4.704833 CCAGTGGGCCAGTCACGG 62.705 72.222 11.93 6.34 39.86 4.94
265 266 3.625897 TCCAGTGGGCCAGTCACG 61.626 66.667 11.93 0.00 39.86 4.35
266 267 2.032681 GTCCAGTGGGCCAGTCAC 59.967 66.667 11.93 7.57 35.51 3.67
267 268 2.122413 AGTCCAGTGGGCCAGTCA 60.122 61.111 11.93 0.00 0.00 3.41
268 269 2.217038 TCAGTCCAGTGGGCCAGTC 61.217 63.158 11.93 0.00 0.00 3.51
269 270 2.122413 TCAGTCCAGTGGGCCAGT 60.122 61.111 11.02 7.51 0.00 4.00
270 271 2.348998 GTCAGTCCAGTGGGCCAG 59.651 66.667 11.02 3.49 0.00 4.85
271 272 2.447572 TGTCAGTCCAGTGGGCCA 60.448 61.111 11.02 0.00 0.00 5.36
272 273 2.032681 GTGTCAGTCCAGTGGGCC 59.967 66.667 11.02 0.00 0.00 5.80
273 274 0.957395 CATGTGTCAGTCCAGTGGGC 60.957 60.000 5.33 5.33 0.00 5.36
274 275 0.686789 TCATGTGTCAGTCCAGTGGG 59.313 55.000 9.92 0.00 0.00 4.61
275 276 1.620323 TCTCATGTGTCAGTCCAGTGG 59.380 52.381 1.40 1.40 0.00 4.00
276 277 3.056322 TCATCTCATGTGTCAGTCCAGTG 60.056 47.826 0.00 0.00 0.00 3.66
277 278 3.168292 TCATCTCATGTGTCAGTCCAGT 58.832 45.455 0.00 0.00 0.00 4.00
278 279 3.446516 TCTCATCTCATGTGTCAGTCCAG 59.553 47.826 0.00 0.00 0.00 3.86
279 280 3.434309 TCTCATCTCATGTGTCAGTCCA 58.566 45.455 0.00 0.00 0.00 4.02
280 281 4.099113 TCATCTCATCTCATGTGTCAGTCC 59.901 45.833 0.00 0.00 0.00 3.85
281 282 5.067544 TCTCATCTCATCTCATGTGTCAGTC 59.932 44.000 0.00 0.00 0.00 3.51
282 283 4.954826 TCTCATCTCATCTCATGTGTCAGT 59.045 41.667 0.00 0.00 0.00 3.41
283 284 5.517322 TCTCATCTCATCTCATGTGTCAG 57.483 43.478 0.00 0.00 0.00 3.51
284 285 5.221461 CCATCTCATCTCATCTCATGTGTCA 60.221 44.000 0.00 0.00 0.00 3.58
285 286 5.231702 CCATCTCATCTCATCTCATGTGTC 58.768 45.833 0.00 0.00 0.00 3.67
286 287 4.040584 CCCATCTCATCTCATCTCATGTGT 59.959 45.833 0.00 0.00 0.00 3.72
287 288 4.563786 CCCCATCTCATCTCATCTCATGTG 60.564 50.000 0.00 0.00 0.00 3.21
288 289 3.583526 CCCCATCTCATCTCATCTCATGT 59.416 47.826 0.00 0.00 0.00 3.21
289 290 3.583526 ACCCCATCTCATCTCATCTCATG 59.416 47.826 0.00 0.00 0.00 3.07
290 291 3.871810 ACCCCATCTCATCTCATCTCAT 58.128 45.455 0.00 0.00 0.00 2.90
291 292 3.341318 ACCCCATCTCATCTCATCTCA 57.659 47.619 0.00 0.00 0.00 3.27
292 293 5.306678 ACTTTACCCCATCTCATCTCATCTC 59.693 44.000 0.00 0.00 0.00 2.75
293 294 5.222870 ACTTTACCCCATCTCATCTCATCT 58.777 41.667 0.00 0.00 0.00 2.90
294 295 5.306678 AGACTTTACCCCATCTCATCTCATC 59.693 44.000 0.00 0.00 0.00 2.92
295 296 5.071519 CAGACTTTACCCCATCTCATCTCAT 59.928 44.000 0.00 0.00 0.00 2.90
296 297 4.406972 CAGACTTTACCCCATCTCATCTCA 59.593 45.833 0.00 0.00 0.00 3.27
297 298 4.407296 ACAGACTTTACCCCATCTCATCTC 59.593 45.833 0.00 0.00 0.00 2.75
298 299 4.366267 ACAGACTTTACCCCATCTCATCT 58.634 43.478 0.00 0.00 0.00 2.90
299 300 4.762289 ACAGACTTTACCCCATCTCATC 57.238 45.455 0.00 0.00 0.00 2.92
300 301 5.520748 AAACAGACTTTACCCCATCTCAT 57.479 39.130 0.00 0.00 0.00 2.90
301 302 4.993705 AAACAGACTTTACCCCATCTCA 57.006 40.909 0.00 0.00 0.00 3.27
302 303 7.309012 GGTTTAAAACAGACTTTACCCCATCTC 60.309 40.741 0.00 0.00 0.00 2.75
303 304 6.492429 GGTTTAAAACAGACTTTACCCCATCT 59.508 38.462 0.00 0.00 0.00 2.90
304 305 6.294899 GGGTTTAAAACAGACTTTACCCCATC 60.295 42.308 5.45 0.00 34.80 3.51
359 360 0.995803 TCCGGGATTTGGATGTTGGA 59.004 50.000 0.00 0.00 0.00 3.53
628 632 4.104417 GACGTCGGAGCTCGCTGT 62.104 66.667 7.83 3.35 39.05 4.40
1007 1222 3.260740 CTGACATTGAGAACCTCAGCTC 58.739 50.000 0.00 0.00 41.75 4.09
1011 1226 4.141505 TGAAACCTGACATTGAGAACCTCA 60.142 41.667 0.00 0.00 38.87 3.86
1037 1252 0.905357 ACGAATGAACTCCCCTCCAG 59.095 55.000 0.00 0.00 0.00 3.86
1073 1290 3.525609 TGCAGTATCTCCCCCAACATAAA 59.474 43.478 0.00 0.00 0.00 1.40
1118 1335 0.250038 GAGCTCTGGCAGTGACAACA 60.250 55.000 19.98 0.00 41.70 3.33
1177 1394 6.194796 TGGCATAAGAAAATACAGCTTCAC 57.805 37.500 0.00 0.00 0.00 3.18
1421 1639 5.999600 TGAACATGATCTTCTTCTTCTGCAA 59.000 36.000 0.00 0.00 0.00 4.08
1624 1867 2.762535 TGGAGCTACAGTTTGGCTAC 57.237 50.000 0.00 0.00 37.43 3.58
1747 1990 7.769970 TCTTGAATTTCCTTGCATGTTTTCTTT 59.230 29.630 0.00 0.00 0.00 2.52
1837 2083 5.413833 ACATCTTCTTCCACATTAGCAACTG 59.586 40.000 0.00 0.00 0.00 3.16
1858 2104 5.994250 ACTCAAACTCTATGCCATGTACAT 58.006 37.500 1.41 1.41 0.00 2.29
1867 2113 4.727507 TCAGAGGACTCAAACTCTATGC 57.272 45.455 1.75 0.00 41.90 3.14
1942 2188 5.724370 TCTGGATTGAACCTAACATACTGGA 59.276 40.000 0.00 0.00 0.00 3.86
1978 2224 7.604657 AACACCATTCCCAAACTAAAATGTA 57.395 32.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.