Multiple sequence alignment - TraesCS2A01G239400

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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 TraesCS2A01G239400 chr2A 100.000 3358 0 0 1 3358 331194513 331197870 0.000000e+00 6202.0
1 TraesCS2A01G239400 chr2A 93.514 185 11 1 1792 1976 12834224 12834407 1.190000e-69 274.0
2 TraesCS2A01G239400 chr2A 95.775 142 4 2 2529 2669 12834409 12834549 9.370000e-56 228.0
3 TraesCS2A01G239400 chr5D 92.911 2370 143 13 323 2669 52664823 52662456 0.000000e+00 3422.0
4 TraesCS2A01G239400 chr5D 94.548 697 29 5 2671 3358 52662369 52661673 0.000000e+00 1068.0
5 TraesCS2A01G239400 chr5D 86.308 409 53 3 2130 2535 327463821 327464229 3.070000e-120 442.0
6 TraesCS2A01G239400 chr5D 86.550 342 40 4 1053 1392 236056527 236056190 4.090000e-99 372.0
7 TraesCS2A01G239400 chr6A 93.318 2140 128 11 538 2669 305127569 305125437 0.000000e+00 3145.0
8 TraesCS2A01G239400 chr6A 94.971 696 24 7 2671 3358 305125350 305124658 0.000000e+00 1081.0
9 TraesCS2A01G239400 chr6A 87.037 54 4 3 197 248 256702265 256702317 1.300000e-04 58.4
10 TraesCS2A01G239400 chr6D 89.236 929 75 7 1053 1977 382129187 382130094 0.000000e+00 1138.0
11 TraesCS2A01G239400 chr6D 91.000 700 48 8 2671 3358 382130321 382131017 0.000000e+00 929.0
12 TraesCS2A01G239400 chr6D 89.490 314 29 3 1973 2283 348871463 348871775 8.730000e-106 394.0
13 TraesCS2A01G239400 chr6D 91.549 142 8 3 2529 2669 382130096 382130234 3.420000e-45 193.0
14 TraesCS2A01G239400 chr4A 87.970 931 85 16 1053 1977 85516499 85517408 0.000000e+00 1074.0
15 TraesCS2A01G239400 chr4A 90.115 698 51 11 2671 3358 85517638 85518327 0.000000e+00 891.0
16 TraesCS2A01G239400 chr4A 93.662 142 8 1 2529 2669 85517411 85517552 9.440000e-51 211.0
17 TraesCS2A01G239400 chr4A 85.057 87 10 3 3076 3160 528596165 528596250 5.970000e-13 86.1
18 TraesCS2A01G239400 chr1D 92.837 698 37 7 2672 3358 444522584 444521889 0.000000e+00 1000.0
19 TraesCS2A01G239400 chr1D 87.346 569 67 4 1973 2538 55029593 55029027 0.000000e+00 647.0
20 TraesCS2A01G239400 chr1D 88.462 390 38 6 657 1041 127920103 127920490 6.560000e-127 464.0
21 TraesCS2A01G239400 chr1D 91.444 187 12 3 1792 1977 444522999 444522816 1.550000e-63 254.0
22 TraesCS2A01G239400 chr1D 93.662 142 7 2 2529 2669 444522812 444522672 9.440000e-51 211.0
23 TraesCS2A01G239400 chr1B 90.756 476 38 5 2887 3358 604573575 604573102 6.110000e-177 630.0
24 TraesCS2A01G239400 chr1B 94.872 117 6 0 716 832 604580085 604579969 2.060000e-42 183.0
25 TraesCS2A01G239400 chr1B 87.209 86 11 0 3273 3358 111903153 111903068 7.670000e-17 99.0
26 TraesCS2A01G239400 chr1B 92.647 68 5 0 199 266 179849435 179849368 7.670000e-17 99.0
27 TraesCS2A01G239400 chr1B 86.111 72 5 4 199 266 632388885 632388955 4.650000e-09 73.1
28 TraesCS2A01G239400 chr2B 86.903 565 67 5 1973 2534 678568810 678569370 7.910000e-176 627.0
29 TraesCS2A01G239400 chr6B 87.305 449 53 3 2095 2539 218672639 218672191 8.310000e-141 510.0
30 TraesCS2A01G239400 chr6B 89.474 76 6 2 192 266 378831176 378831250 9.920000e-16 95.3
31 TraesCS2A01G239400 chr5B 86.174 311 37 4 1084 1392 268981320 268981626 6.940000e-87 331.0
32 TraesCS2A01G239400 chr5B 89.922 129 11 2 4 131 372590296 372590423 7.450000e-37 165.0
33 TraesCS2A01G239400 chr5B 86.822 129 14 3 4 131 524640738 524640864 1.260000e-29 141.0
34 TraesCS2A01G239400 chr1A 90.431 209 13 3 2672 2873 540112641 540112433 5.520000e-68 268.0
35 TraesCS2A01G239400 chr1A 91.176 170 14 1 1809 1977 540113039 540112870 2.610000e-56 230.0
36 TraesCS2A01G239400 chr1A 93.662 142 7 2 2529 2669 540112869 540112729 9.440000e-51 211.0
37 TraesCS2A01G239400 chr3A 89.247 186 20 0 3 188 198256868 198257053 2.010000e-57 233.0
38 TraesCS2A01G239400 chr7A 89.873 158 16 0 65 222 271488799 271488642 1.580000e-48 204.0
39 TraesCS2A01G239400 chr4B 89.209 139 15 0 4 142 36445797 36445659 1.240000e-39 174.0
40 TraesCS2A01G239400 chr4B 87.500 128 14 2 5 131 549460606 549460732 2.700000e-31 147.0
41 TraesCS2A01G239400 chr4B 89.091 55 3 3 199 251 341245818 341245871 7.780000e-07 65.8
42 TraesCS2A01G239400 chr3B 88.800 125 12 2 8 131 167316849 167316726 5.800000e-33 152.0
43 TraesCS2A01G239400 chr3B 93.878 49 3 0 199 247 151850188 151850140 1.290000e-09 75.0
44 TraesCS2A01G239400 chr3B 100.000 28 0 0 272 299 599162006 599161979 6.000000e-03 52.8
45 TraesCS2A01G239400 chr5A 91.209 91 8 0 1887 1977 178559813 178559723 1.270000e-24 124.0
46 TraesCS2A01G239400 chr5A 86.813 91 12 0 1887 1977 217758772 217758862 5.930000e-18 102.0
47 TraesCS2A01G239400 chr7D 90.909 88 5 2 3273 3358 413385347 413385433 7.610000e-22 115.0
48 TraesCS2A01G239400 chr7B 84.252 127 10 3 10 126 142153335 142153461 7.610000e-22 115.0
49 TraesCS2A01G239400 chr3D 92.727 55 4 0 257 311 231179528 231179474 2.780000e-11 80.5


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 TraesCS2A01G239400 chr2A 331194513 331197870 3357 False 6202.000000 6202 100.000000 1 3358 1 chr2A.!!$F1 3357
1 TraesCS2A01G239400 chr5D 52661673 52664823 3150 True 2245.000000 3422 93.729500 323 3358 2 chr5D.!!$R2 3035
2 TraesCS2A01G239400 chr6A 305124658 305127569 2911 True 2113.000000 3145 94.144500 538 3358 2 chr6A.!!$R1 2820
3 TraesCS2A01G239400 chr6D 382129187 382131017 1830 False 753.333333 1138 90.595000 1053 3358 3 chr6D.!!$F2 2305
4 TraesCS2A01G239400 chr4A 85516499 85518327 1828 False 725.333333 1074 90.582333 1053 3358 3 chr4A.!!$F2 2305
5 TraesCS2A01G239400 chr1D 55029027 55029593 566 True 647.000000 647 87.346000 1973 2538 1 chr1D.!!$R1 565
6 TraesCS2A01G239400 chr1D 444521889 444522999 1110 True 488.333333 1000 92.647667 1792 3358 3 chr1D.!!$R2 1566
7 TraesCS2A01G239400 chr2B 678568810 678569370 560 False 627.000000 627 86.903000 1973 2534 1 chr2B.!!$F1 561
8 TraesCS2A01G239400 chr1A 540112433 540113039 606 True 236.333333 268 91.756333 1809 2873 3 chr1A.!!$R1 1064

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
101 102 0.035458 GGTGAATCGGGAGGCTATGG 59.965 60.0 0.0 0.0 0.00 2.74 F
1076 1093 0.032615 AGATGGAGAAGACCTCGGCT 60.033 55.0 0.0 0.0 42.89 5.52 F
1240 1258 0.178891 AGCCTCCCTTGTCTTCCTCA 60.179 55.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1181 0.250124 ACCCGTGTTGCGATCTTTCA 60.250 50.000 0.00 0.0 44.77 2.69 R
2219 2249 0.896226 AGTCCTTCCGCTGTACCTTC 59.104 55.000 0.00 0.0 0.00 3.46 R
2614 2653 1.065491 TCTGTCGCATTGCACCCTTAT 60.065 47.619 9.69 0.0 0.00 1.73 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
17 18 3.228017 GTCGCTAGGGAGGGAGGC 61.228 72.222 10.19 0.00 44.65 4.70
18 19 4.896829 TCGCTAGGGAGGGAGGCG 62.897 72.222 5.20 0.00 45.93 5.52
37 38 3.474570 CCGGAGCTGGGGAAGGAG 61.475 72.222 0.00 0.00 0.00 3.69
38 39 3.474570 CGGAGCTGGGGAAGGAGG 61.475 72.222 0.00 0.00 0.00 4.30
39 40 2.285743 GGAGCTGGGGAAGGAGGT 60.286 66.667 0.00 0.00 0.00 3.85
40 41 2.371259 GGAGCTGGGGAAGGAGGTC 61.371 68.421 0.00 0.00 36.23 3.85
41 42 2.685380 AGCTGGGGAAGGAGGTCG 60.685 66.667 0.00 0.00 0.00 4.79
42 43 3.003763 GCTGGGGAAGGAGGTCGT 61.004 66.667 0.00 0.00 0.00 4.34
43 44 3.020237 GCTGGGGAAGGAGGTCGTC 62.020 68.421 0.00 0.00 0.00 4.20
44 45 1.609501 CTGGGGAAGGAGGTCGTCA 60.610 63.158 0.00 0.00 0.00 4.35
45 46 1.608717 CTGGGGAAGGAGGTCGTCAG 61.609 65.000 0.00 0.00 0.00 3.51
46 47 1.305046 GGGGAAGGAGGTCGTCAGA 60.305 63.158 0.00 0.00 0.00 3.27
47 48 1.324005 GGGGAAGGAGGTCGTCAGAG 61.324 65.000 0.00 0.00 0.00 3.35
48 49 0.612453 GGGAAGGAGGTCGTCAGAGT 60.612 60.000 0.00 0.00 0.00 3.24
49 50 1.258676 GGAAGGAGGTCGTCAGAGTT 58.741 55.000 0.00 0.00 0.00 3.01
50 51 1.067495 GGAAGGAGGTCGTCAGAGTTG 60.067 57.143 0.00 0.00 0.00 3.16
51 52 0.318762 AAGGAGGTCGTCAGAGTTGC 59.681 55.000 0.00 0.00 0.00 4.17
52 53 1.444553 GGAGGTCGTCAGAGTTGCG 60.445 63.158 0.00 0.00 0.00 4.85
53 54 1.444553 GAGGTCGTCAGAGTTGCGG 60.445 63.158 0.00 0.00 0.00 5.69
54 55 2.432628 GGTCGTCAGAGTTGCGGG 60.433 66.667 0.00 0.00 0.00 6.13
55 56 2.432628 GTCGTCAGAGTTGCGGGG 60.433 66.667 0.00 0.00 0.00 5.73
56 57 3.691342 TCGTCAGAGTTGCGGGGG 61.691 66.667 0.00 0.00 0.00 5.40
57 58 3.691342 CGTCAGAGTTGCGGGGGA 61.691 66.667 0.00 0.00 0.00 4.81
58 59 2.047179 GTCAGAGTTGCGGGGGAC 60.047 66.667 0.00 0.00 0.00 4.46
60 61 4.760047 CAGAGTTGCGGGGGACGG 62.760 72.222 0.00 0.00 44.51 4.79
80 81 4.388499 CCCGACGGTGGAAGGTGG 62.388 72.222 13.94 0.00 0.00 4.61
81 82 3.307906 CCGACGGTGGAAGGTGGA 61.308 66.667 5.48 0.00 0.00 4.02
82 83 2.261671 CGACGGTGGAAGGTGGAG 59.738 66.667 0.00 0.00 0.00 3.86
83 84 2.663196 GACGGTGGAAGGTGGAGG 59.337 66.667 0.00 0.00 0.00 4.30
84 85 2.122547 ACGGTGGAAGGTGGAGGT 60.123 61.111 0.00 0.00 0.00 3.85
85 86 2.347490 CGGTGGAAGGTGGAGGTG 59.653 66.667 0.00 0.00 0.00 4.00
86 87 2.214216 CGGTGGAAGGTGGAGGTGA 61.214 63.158 0.00 0.00 0.00 4.02
87 88 1.764571 CGGTGGAAGGTGGAGGTGAA 61.765 60.000 0.00 0.00 0.00 3.18
88 89 0.698818 GGTGGAAGGTGGAGGTGAAT 59.301 55.000 0.00 0.00 0.00 2.57
89 90 1.340114 GGTGGAAGGTGGAGGTGAATC 60.340 57.143 0.00 0.00 0.00 2.52
90 91 0.613260 TGGAAGGTGGAGGTGAATCG 59.387 55.000 0.00 0.00 0.00 3.34
91 92 0.107654 GGAAGGTGGAGGTGAATCGG 60.108 60.000 0.00 0.00 0.00 4.18
92 93 0.107654 GAAGGTGGAGGTGAATCGGG 60.108 60.000 0.00 0.00 0.00 5.14
93 94 0.546747 AAGGTGGAGGTGAATCGGGA 60.547 55.000 0.00 0.00 0.00 5.14
94 95 0.978146 AGGTGGAGGTGAATCGGGAG 60.978 60.000 0.00 0.00 0.00 4.30
95 96 1.522569 GTGGAGGTGAATCGGGAGG 59.477 63.158 0.00 0.00 0.00 4.30
96 97 2.367202 TGGAGGTGAATCGGGAGGC 61.367 63.158 0.00 0.00 0.00 4.70
97 98 2.066999 GGAGGTGAATCGGGAGGCT 61.067 63.158 0.00 0.00 0.00 4.58
98 99 0.759436 GGAGGTGAATCGGGAGGCTA 60.759 60.000 0.00 0.00 0.00 3.93
99 100 1.343069 GAGGTGAATCGGGAGGCTAT 58.657 55.000 0.00 0.00 0.00 2.97
100 101 1.001406 GAGGTGAATCGGGAGGCTATG 59.999 57.143 0.00 0.00 0.00 2.23
101 102 0.035458 GGTGAATCGGGAGGCTATGG 59.965 60.000 0.00 0.00 0.00 2.74
102 103 0.035458 GTGAATCGGGAGGCTATGGG 59.965 60.000 0.00 0.00 0.00 4.00
103 104 1.127567 TGAATCGGGAGGCTATGGGG 61.128 60.000 0.00 0.00 0.00 4.96
104 105 1.073706 AATCGGGAGGCTATGGGGT 60.074 57.895 0.00 0.00 0.00 4.95
105 106 1.418908 AATCGGGAGGCTATGGGGTG 61.419 60.000 0.00 0.00 0.00 4.61
106 107 3.560251 CGGGAGGCTATGGGGTGG 61.560 72.222 0.00 0.00 0.00 4.61
107 108 3.890926 GGGAGGCTATGGGGTGGC 61.891 72.222 0.00 0.00 0.00 5.01
108 109 4.256180 GGAGGCTATGGGGTGGCG 62.256 72.222 0.00 0.00 34.68 5.69
109 110 3.161450 GAGGCTATGGGGTGGCGA 61.161 66.667 0.00 0.00 34.68 5.54
110 111 3.164269 AGGCTATGGGGTGGCGAG 61.164 66.667 0.00 0.00 34.68 5.03
111 112 3.480133 GGCTATGGGGTGGCGAGT 61.480 66.667 0.00 0.00 34.68 4.18
112 113 2.203070 GCTATGGGGTGGCGAGTG 60.203 66.667 0.00 0.00 0.00 3.51
113 114 2.505982 CTATGGGGTGGCGAGTGG 59.494 66.667 0.00 0.00 0.00 4.00
114 115 2.039787 TATGGGGTGGCGAGTGGA 59.960 61.111 0.00 0.00 0.00 4.02
115 116 1.383943 TATGGGGTGGCGAGTGGAT 60.384 57.895 0.00 0.00 0.00 3.41
116 117 0.105401 TATGGGGTGGCGAGTGGATA 60.105 55.000 0.00 0.00 0.00 2.59
117 118 0.986019 ATGGGGTGGCGAGTGGATAA 60.986 55.000 0.00 0.00 0.00 1.75
118 119 1.146263 GGGGTGGCGAGTGGATAAG 59.854 63.158 0.00 0.00 0.00 1.73
119 120 1.335132 GGGGTGGCGAGTGGATAAGA 61.335 60.000 0.00 0.00 0.00 2.10
120 121 0.105039 GGGTGGCGAGTGGATAAGAG 59.895 60.000 0.00 0.00 0.00 2.85
121 122 0.824759 GGTGGCGAGTGGATAAGAGT 59.175 55.000 0.00 0.00 0.00 3.24
122 123 1.207329 GGTGGCGAGTGGATAAGAGTT 59.793 52.381 0.00 0.00 0.00 3.01
123 124 2.354805 GGTGGCGAGTGGATAAGAGTTT 60.355 50.000 0.00 0.00 0.00 2.66
124 125 3.335579 GTGGCGAGTGGATAAGAGTTTT 58.664 45.455 0.00 0.00 0.00 2.43
125 126 3.751698 GTGGCGAGTGGATAAGAGTTTTT 59.248 43.478 0.00 0.00 0.00 1.94
152 153 2.368591 CTTGGGTAGGACGGGAACA 58.631 57.895 0.00 0.00 0.00 3.18
153 154 0.909623 CTTGGGTAGGACGGGAACAT 59.090 55.000 0.00 0.00 0.00 2.71
154 155 2.112998 CTTGGGTAGGACGGGAACATA 58.887 52.381 0.00 0.00 0.00 2.29
155 156 1.488390 TGGGTAGGACGGGAACATAC 58.512 55.000 0.00 0.00 0.00 2.39
156 157 0.755079 GGGTAGGACGGGAACATACC 59.245 60.000 0.00 0.00 41.87 2.73
162 163 4.097828 CGGGAACATACCGGTTCG 57.902 61.111 15.04 6.95 46.34 3.95
172 173 2.203238 CCGGTTCGGGTTGGTGTT 60.203 61.111 0.00 0.00 44.15 3.32
173 174 1.824760 CCGGTTCGGGTTGGTGTTT 60.825 57.895 0.00 0.00 44.15 2.83
174 175 1.385756 CCGGTTCGGGTTGGTGTTTT 61.386 55.000 0.00 0.00 44.15 2.43
175 176 0.456628 CGGTTCGGGTTGGTGTTTTT 59.543 50.000 0.00 0.00 0.00 1.94
176 177 1.799548 CGGTTCGGGTTGGTGTTTTTG 60.800 52.381 0.00 0.00 0.00 2.44
177 178 1.205179 GGTTCGGGTTGGTGTTTTTGT 59.795 47.619 0.00 0.00 0.00 2.83
178 179 2.353903 GGTTCGGGTTGGTGTTTTTGTT 60.354 45.455 0.00 0.00 0.00 2.83
179 180 3.327626 GTTCGGGTTGGTGTTTTTGTTT 58.672 40.909 0.00 0.00 0.00 2.83
180 181 3.233684 TCGGGTTGGTGTTTTTGTTTC 57.766 42.857 0.00 0.00 0.00 2.78
181 182 2.826725 TCGGGTTGGTGTTTTTGTTTCT 59.173 40.909 0.00 0.00 0.00 2.52
182 183 2.926838 CGGGTTGGTGTTTTTGTTTCTG 59.073 45.455 0.00 0.00 0.00 3.02
183 184 3.367498 CGGGTTGGTGTTTTTGTTTCTGA 60.367 43.478 0.00 0.00 0.00 3.27
184 185 4.679372 CGGGTTGGTGTTTTTGTTTCTGAT 60.679 41.667 0.00 0.00 0.00 2.90
185 186 4.570369 GGGTTGGTGTTTTTGTTTCTGATG 59.430 41.667 0.00 0.00 0.00 3.07
186 187 4.570369 GGTTGGTGTTTTTGTTTCTGATGG 59.430 41.667 0.00 0.00 0.00 3.51
187 188 5.415221 GTTGGTGTTTTTGTTTCTGATGGA 58.585 37.500 0.00 0.00 0.00 3.41
188 189 5.667539 TGGTGTTTTTGTTTCTGATGGAA 57.332 34.783 0.00 0.00 0.00 3.53
189 190 5.659463 TGGTGTTTTTGTTTCTGATGGAAG 58.341 37.500 0.00 0.00 35.16 3.46
190 191 5.049828 GGTGTTTTTGTTTCTGATGGAAGG 58.950 41.667 0.00 0.00 35.16 3.46
191 192 4.507756 GTGTTTTTGTTTCTGATGGAAGGC 59.492 41.667 0.00 0.00 35.16 4.35
192 193 3.641437 TTTTGTTTCTGATGGAAGGCG 57.359 42.857 0.00 0.00 35.16 5.52
193 194 0.881118 TTGTTTCTGATGGAAGGCGC 59.119 50.000 0.00 0.00 35.16 6.53
194 195 0.960364 TGTTTCTGATGGAAGGCGCC 60.960 55.000 21.89 21.89 35.16 6.53
195 196 1.745115 TTTCTGATGGAAGGCGCCG 60.745 57.895 23.20 3.70 35.16 6.46
196 197 2.463589 TTTCTGATGGAAGGCGCCGT 62.464 55.000 23.20 20.21 35.16 5.68
197 198 1.609635 TTCTGATGGAAGGCGCCGTA 61.610 55.000 23.20 9.23 0.00 4.02
198 199 1.069765 CTGATGGAAGGCGCCGTAT 59.930 57.895 23.20 14.01 0.00 3.06
199 200 0.317160 CTGATGGAAGGCGCCGTATA 59.683 55.000 23.20 10.83 0.00 1.47
200 201 0.973632 TGATGGAAGGCGCCGTATAT 59.026 50.000 23.20 15.49 0.00 0.86
201 202 2.165641 CTGATGGAAGGCGCCGTATATA 59.834 50.000 23.20 7.23 0.00 0.86
202 203 2.165641 TGATGGAAGGCGCCGTATATAG 59.834 50.000 23.20 0.00 0.00 1.31
203 204 0.892755 TGGAAGGCGCCGTATATAGG 59.107 55.000 23.20 0.00 0.00 2.57
204 205 0.175073 GGAAGGCGCCGTATATAGGG 59.825 60.000 23.20 15.79 0.00 3.53
205 206 1.180029 GAAGGCGCCGTATATAGGGA 58.820 55.000 23.20 0.00 33.17 4.20
206 207 0.893447 AAGGCGCCGTATATAGGGAC 59.107 55.000 23.20 13.99 33.17 4.46
207 208 1.138247 GGCGCCGTATATAGGGACG 59.862 63.158 22.80 22.72 38.79 4.79
208 209 1.308069 GGCGCCGTATATAGGGACGA 61.308 60.000 27.29 0.00 41.60 4.20
209 210 0.098376 GCGCCGTATATAGGGACGAG 59.902 60.000 27.29 16.35 41.60 4.18
210 211 1.730501 CGCCGTATATAGGGACGAGA 58.269 55.000 22.80 0.00 41.60 4.04
211 212 1.664659 CGCCGTATATAGGGACGAGAG 59.335 57.143 22.80 4.89 41.60 3.20
255 256 9.857957 GTTACTAGTAACAAAATAGCTCTGTCT 57.142 33.333 31.74 0.00 43.55 3.41
272 273 9.391006 AGCTCTGTCTTATATAGATAGTAGCAC 57.609 37.037 19.18 0.00 41.74 4.40
273 274 9.391006 GCTCTGTCTTATATAGATAGTAGCACT 57.609 37.037 16.25 0.00 41.47 4.40
287 288 8.052748 AGATAGTAGCACTATTCTGATCCTAGG 58.947 40.741 0.82 0.82 41.21 3.02
288 289 6.207509 AGTAGCACTATTCTGATCCTAGGA 57.792 41.667 15.46 15.46 0.00 2.94
289 290 6.799827 AGTAGCACTATTCTGATCCTAGGAT 58.200 40.000 24.78 24.78 37.59 3.24
314 315 8.196802 TCAAAATAGTTATTCTGATCACACCG 57.803 34.615 0.00 0.00 0.00 4.94
315 316 7.822334 TCAAAATAGTTATTCTGATCACACCGT 59.178 33.333 0.00 0.00 0.00 4.83
316 317 7.539712 AAATAGTTATTCTGATCACACCGTG 57.460 36.000 0.00 0.00 34.45 4.94
317 318 3.861840 AGTTATTCTGATCACACCGTGG 58.138 45.455 3.03 0.00 33.87 4.94
318 319 2.936498 GTTATTCTGATCACACCGTGGG 59.064 50.000 3.03 0.00 33.87 4.61
319 320 0.984230 ATTCTGATCACACCGTGGGT 59.016 50.000 0.00 0.00 35.62 4.51
320 321 0.320374 TTCTGATCACACCGTGGGTC 59.680 55.000 0.00 0.00 31.02 4.46
321 322 0.541998 TCTGATCACACCGTGGGTCT 60.542 55.000 0.00 0.00 31.02 3.85
360 361 4.877378 TCTGGAAACGTTAAGAAGGCTA 57.123 40.909 0.00 0.00 0.00 3.93
375 376 0.108281 GGCTACCCACTCGAACTTCC 60.108 60.000 0.00 0.00 0.00 3.46
379 380 0.763223 ACCCACTCGAACTTCCCACT 60.763 55.000 0.00 0.00 0.00 4.00
380 381 0.037232 CCCACTCGAACTTCCCACTC 60.037 60.000 0.00 0.00 0.00 3.51
384 385 1.269998 ACTCGAACTTCCCACTCGAAG 59.730 52.381 0.00 0.00 44.07 3.79
482 498 4.910585 GGCCTCCACCGCCATACG 62.911 72.222 0.00 0.00 46.27 3.06
501 517 2.050351 CGTCGTGGACTCTGCGTT 60.050 61.111 0.00 0.00 0.00 4.84
536 552 1.003051 GGTCTCCCTCCCCTGCTTA 59.997 63.158 0.00 0.00 0.00 3.09
659 675 4.200283 GCCGACTCGCCTCCTCTG 62.200 72.222 0.00 0.00 0.00 3.35
722 738 2.282462 AACCAAGCTCCGCCCTTG 60.282 61.111 0.00 0.00 39.44 3.61
759 775 1.617018 CGCTCCTCCACATCTTGGGA 61.617 60.000 0.00 0.00 46.92 4.37
783 799 4.263572 CGCACCACCACCCTCCAA 62.264 66.667 0.00 0.00 0.00 3.53
790 806 0.537371 CACCACCCTCCAAAGGTCAC 60.537 60.000 0.00 0.00 41.59 3.67
869 885 2.260639 ACATCTGTGATCCACCTCCT 57.739 50.000 0.00 0.00 32.73 3.69
946 962 2.666190 CCGCACACTCCACACTGG 60.666 66.667 0.00 0.00 39.43 4.00
955 971 2.360350 CCACACTGGCGCCATCTT 60.360 61.111 32.87 15.04 0.00 2.40
1015 1032 2.888447 GCTATGCTCCCCATCGCCT 61.888 63.158 0.00 0.00 36.82 5.52
1023 1040 1.077501 CCCCATCGCCTCACATGTT 60.078 57.895 0.00 0.00 0.00 2.71
1032 1049 1.945819 GCCTCACATGTTGTCGTCCAT 60.946 52.381 0.00 0.00 0.00 3.41
1043 1060 1.679641 TCGTCCATCGTGCCTACCA 60.680 57.895 0.00 0.00 40.80 3.25
1045 1062 1.594833 GTCCATCGTGCCTACCACA 59.405 57.895 0.00 0.00 44.91 4.17
1076 1093 0.032615 AGATGGAGAAGACCTCGGCT 60.033 55.000 0.00 0.00 42.89 5.52
1117 1134 3.378742 CGACCTGCAGTTCTACAGTAGAT 59.621 47.826 13.81 0.00 34.22 1.98
1124 1141 4.082190 GCAGTTCTACAGTAGATGTGTCCA 60.082 45.833 11.25 0.00 43.80 4.02
1128 1145 5.446260 TCTACAGTAGATGTGTCCAGGTA 57.554 43.478 6.15 0.00 43.80 3.08
1164 1181 0.605589 GTGCCGGCTTCCTACTGTTT 60.606 55.000 29.70 0.00 0.00 2.83
1176 1194 4.637276 TCCTACTGTTTGAAAGATCGCAA 58.363 39.130 0.00 0.00 0.00 4.85
1192 1210 1.963855 CAACACGGGTCGGCATCAA 60.964 57.895 0.00 0.00 0.00 2.57
1195 1213 1.745115 CACGGGTCGGCATCAACAT 60.745 57.895 0.00 0.00 0.00 2.71
1240 1258 0.178891 AGCCTCCCTTGTCTTCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
1429 1450 5.236478 CACAAGGACGAACAAAGTGATTAGT 59.764 40.000 0.00 0.00 0.00 2.24
1562 1584 1.405105 GCGCATTTCTCCATGGCTTTA 59.595 47.619 6.96 0.00 0.00 1.85
1599 1621 6.766467 TCATAGATTAACTAGAGCGACACAGA 59.234 38.462 0.00 0.00 34.35 3.41
1626 1648 3.515630 CTGACATCAGCGAATAGTGTGT 58.484 45.455 0.00 0.00 37.15 3.72
1710 1735 9.030301 GCTGTCATACAAAATTAGTTGTTGTTT 57.970 29.630 1.04 0.00 41.84 2.83
1782 1810 0.466189 AGATGGGTAGCATTTGGCCG 60.466 55.000 0.00 0.00 46.50 6.13
1810 1838 7.124147 CCATGTGGGTGTTTATTCTTATTCCTT 59.876 37.037 0.00 0.00 0.00 3.36
1984 2014 2.818274 GGTTTGCTAGGCCGTCCG 60.818 66.667 0.00 0.00 37.47 4.79
2011 2041 1.819288 GATCTGGACTTCGGACAGACA 59.181 52.381 0.00 0.00 43.29 3.41
2123 2153 0.250901 ATGCCAGTCAGGTGTGGTTC 60.251 55.000 0.00 0.00 40.61 3.62
2219 2249 0.739561 CTTCGAGGAAGAGGGTACCG 59.260 60.000 5.65 0.00 41.80 4.02
2239 2269 2.097825 GAAGGTACAGCGGAAGGACTA 58.902 52.381 0.00 0.00 0.00 2.59
2240 2270 2.456073 AGGTACAGCGGAAGGACTAT 57.544 50.000 0.00 0.00 0.00 2.12
2254 2286 4.392921 AGGACTATGATTCTTGTCACGG 57.607 45.455 0.00 0.00 0.00 4.94
2355 2388 0.250513 GGACATTCTCAGGGAACGCT 59.749 55.000 0.00 0.00 36.70 5.07
2431 2464 1.194781 TGGAGCTGGTTGAGGAGGAC 61.195 60.000 0.00 0.00 0.00 3.85
2456 2489 1.078848 ACGCCTTCTGGTGATGCTC 60.079 57.895 2.42 0.00 46.34 4.26
2478 2511 4.743151 TCGCGGCTTGTAATATCTTGTAAG 59.257 41.667 6.13 0.00 0.00 2.34
2512 2545 5.116882 CCTTTCTATAAAGCTAAGGCACGT 58.883 41.667 0.00 0.00 40.73 4.49
2669 2708 2.091885 TGGGATATTGAAACAGAGGGCC 60.092 50.000 0.00 0.00 0.00 5.80
2695 2819 3.127030 CCTTAATTCCCAGAAACGAGTGC 59.873 47.826 0.00 0.00 0.00 4.40
2800 2927 6.647481 TCGAAACAAGAATGACGGAAAGATTA 59.353 34.615 0.00 0.00 0.00 1.75
2885 3020 5.986135 ACAACACACTTGCAGTTTGTAAAAA 59.014 32.000 8.02 0.00 38.09 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.474570 CTCCTTCCCCAGCTCCGG 61.475 72.222 0.00 0.00 0.00 5.14
21 22 3.474570 CCTCCTTCCCCAGCTCCG 61.475 72.222 0.00 0.00 0.00 4.63
22 23 2.285743 ACCTCCTTCCCCAGCTCC 60.286 66.667 0.00 0.00 0.00 4.70
23 24 2.726351 CGACCTCCTTCCCCAGCTC 61.726 68.421 0.00 0.00 0.00 4.09
24 25 2.685380 CGACCTCCTTCCCCAGCT 60.685 66.667 0.00 0.00 0.00 4.24
25 26 3.003763 ACGACCTCCTTCCCCAGC 61.004 66.667 0.00 0.00 0.00 4.85
26 27 1.608717 CTGACGACCTCCTTCCCCAG 61.609 65.000 0.00 0.00 0.00 4.45
27 28 1.609501 CTGACGACCTCCTTCCCCA 60.610 63.158 0.00 0.00 0.00 4.96
28 29 1.305046 TCTGACGACCTCCTTCCCC 60.305 63.158 0.00 0.00 0.00 4.81
29 30 0.612453 ACTCTGACGACCTCCTTCCC 60.612 60.000 0.00 0.00 0.00 3.97
30 31 1.067495 CAACTCTGACGACCTCCTTCC 60.067 57.143 0.00 0.00 0.00 3.46
31 32 1.670380 GCAACTCTGACGACCTCCTTC 60.670 57.143 0.00 0.00 0.00 3.46
32 33 0.318762 GCAACTCTGACGACCTCCTT 59.681 55.000 0.00 0.00 0.00 3.36
33 34 1.867919 CGCAACTCTGACGACCTCCT 61.868 60.000 0.00 0.00 0.00 3.69
34 35 1.444553 CGCAACTCTGACGACCTCC 60.445 63.158 0.00 0.00 0.00 4.30
35 36 1.444553 CCGCAACTCTGACGACCTC 60.445 63.158 0.00 0.00 0.00 3.85
36 37 2.651361 CCGCAACTCTGACGACCT 59.349 61.111 0.00 0.00 0.00 3.85
37 38 2.432628 CCCGCAACTCTGACGACC 60.433 66.667 0.00 0.00 0.00 4.79
38 39 2.432628 CCCCGCAACTCTGACGAC 60.433 66.667 0.00 0.00 0.00 4.34
39 40 3.691342 CCCCCGCAACTCTGACGA 61.691 66.667 0.00 0.00 0.00 4.20
40 41 3.691342 TCCCCCGCAACTCTGACG 61.691 66.667 0.00 0.00 0.00 4.35
41 42 2.047179 GTCCCCCGCAACTCTGAC 60.047 66.667 0.00 0.00 0.00 3.51
42 43 3.691342 CGTCCCCCGCAACTCTGA 61.691 66.667 0.00 0.00 0.00 3.27
43 44 4.760047 CCGTCCCCCGCAACTCTG 62.760 72.222 0.00 0.00 34.38 3.35
63 64 4.388499 CCACCTTCCACCGTCGGG 62.388 72.222 17.28 4.45 40.11 5.14
64 65 3.296709 CTCCACCTTCCACCGTCGG 62.297 68.421 10.48 10.48 0.00 4.79
65 66 2.261671 CTCCACCTTCCACCGTCG 59.738 66.667 0.00 0.00 0.00 5.12
66 67 2.214920 ACCTCCACCTTCCACCGTC 61.215 63.158 0.00 0.00 0.00 4.79
67 68 2.122547 ACCTCCACCTTCCACCGT 60.123 61.111 0.00 0.00 0.00 4.83
68 69 1.764571 TTCACCTCCACCTTCCACCG 61.765 60.000 0.00 0.00 0.00 4.94
69 70 0.698818 ATTCACCTCCACCTTCCACC 59.301 55.000 0.00 0.00 0.00 4.61
70 71 1.676014 CGATTCACCTCCACCTTCCAC 60.676 57.143 0.00 0.00 0.00 4.02
71 72 0.613260 CGATTCACCTCCACCTTCCA 59.387 55.000 0.00 0.00 0.00 3.53
72 73 0.107654 CCGATTCACCTCCACCTTCC 60.108 60.000 0.00 0.00 0.00 3.46
73 74 0.107654 CCCGATTCACCTCCACCTTC 60.108 60.000 0.00 0.00 0.00 3.46
74 75 0.546747 TCCCGATTCACCTCCACCTT 60.547 55.000 0.00 0.00 0.00 3.50
75 76 0.978146 CTCCCGATTCACCTCCACCT 60.978 60.000 0.00 0.00 0.00 4.00
76 77 1.522569 CTCCCGATTCACCTCCACC 59.477 63.158 0.00 0.00 0.00 4.61
77 78 1.522569 CCTCCCGATTCACCTCCAC 59.477 63.158 0.00 0.00 0.00 4.02
78 79 2.367202 GCCTCCCGATTCACCTCCA 61.367 63.158 0.00 0.00 0.00 3.86
79 80 0.759436 TAGCCTCCCGATTCACCTCC 60.759 60.000 0.00 0.00 0.00 4.30
80 81 1.001406 CATAGCCTCCCGATTCACCTC 59.999 57.143 0.00 0.00 0.00 3.85
81 82 1.051812 CATAGCCTCCCGATTCACCT 58.948 55.000 0.00 0.00 0.00 4.00
82 83 0.035458 CCATAGCCTCCCGATTCACC 59.965 60.000 0.00 0.00 0.00 4.02
83 84 0.035458 CCCATAGCCTCCCGATTCAC 59.965 60.000 0.00 0.00 0.00 3.18
84 85 1.127567 CCCCATAGCCTCCCGATTCA 61.128 60.000 0.00 0.00 0.00 2.57
85 86 1.128188 ACCCCATAGCCTCCCGATTC 61.128 60.000 0.00 0.00 0.00 2.52
86 87 1.073706 ACCCCATAGCCTCCCGATT 60.074 57.895 0.00 0.00 0.00 3.34
87 88 1.843376 CACCCCATAGCCTCCCGAT 60.843 63.158 0.00 0.00 0.00 4.18
88 89 2.445845 CACCCCATAGCCTCCCGA 60.446 66.667 0.00 0.00 0.00 5.14
89 90 3.560251 CCACCCCATAGCCTCCCG 61.560 72.222 0.00 0.00 0.00 5.14
90 91 3.890926 GCCACCCCATAGCCTCCC 61.891 72.222 0.00 0.00 0.00 4.30
91 92 4.256180 CGCCACCCCATAGCCTCC 62.256 72.222 0.00 0.00 0.00 4.30
92 93 3.161450 TCGCCACCCCATAGCCTC 61.161 66.667 0.00 0.00 0.00 4.70
93 94 3.164269 CTCGCCACCCCATAGCCT 61.164 66.667 0.00 0.00 0.00 4.58
94 95 3.480133 ACTCGCCACCCCATAGCC 61.480 66.667 0.00 0.00 0.00 3.93
95 96 2.203070 CACTCGCCACCCCATAGC 60.203 66.667 0.00 0.00 0.00 2.97
96 97 1.410850 ATCCACTCGCCACCCCATAG 61.411 60.000 0.00 0.00 0.00 2.23
97 98 0.105401 TATCCACTCGCCACCCCATA 60.105 55.000 0.00 0.00 0.00 2.74
98 99 0.986019 TTATCCACTCGCCACCCCAT 60.986 55.000 0.00 0.00 0.00 4.00
99 100 1.613928 TTATCCACTCGCCACCCCA 60.614 57.895 0.00 0.00 0.00 4.96
100 101 1.146263 CTTATCCACTCGCCACCCC 59.854 63.158 0.00 0.00 0.00 4.95
101 102 0.105039 CTCTTATCCACTCGCCACCC 59.895 60.000 0.00 0.00 0.00 4.61
102 103 0.824759 ACTCTTATCCACTCGCCACC 59.175 55.000 0.00 0.00 0.00 4.61
103 104 2.674796 AACTCTTATCCACTCGCCAC 57.325 50.000 0.00 0.00 0.00 5.01
104 105 3.695830 AAAACTCTTATCCACTCGCCA 57.304 42.857 0.00 0.00 0.00 5.69
134 135 0.909623 ATGTTCCCGTCCTACCCAAG 59.090 55.000 0.00 0.00 0.00 3.61
135 136 1.832998 GTATGTTCCCGTCCTACCCAA 59.167 52.381 0.00 0.00 0.00 4.12
136 137 1.488390 GTATGTTCCCGTCCTACCCA 58.512 55.000 0.00 0.00 0.00 4.51
137 138 0.755079 GGTATGTTCCCGTCCTACCC 59.245 60.000 0.00 0.00 0.00 3.69
138 139 0.386838 CGGTATGTTCCCGTCCTACC 59.613 60.000 0.00 0.00 40.59 3.18
139 140 0.386838 CCGGTATGTTCCCGTCCTAC 59.613 60.000 0.00 0.00 43.98 3.18
140 141 0.033208 ACCGGTATGTTCCCGTCCTA 60.033 55.000 4.49 0.00 43.98 2.94
141 142 0.906282 AACCGGTATGTTCCCGTCCT 60.906 55.000 8.00 0.00 43.98 3.85
142 143 0.460811 GAACCGGTATGTTCCCGTCC 60.461 60.000 8.00 0.00 43.98 4.79
143 144 0.803380 CGAACCGGTATGTTCCCGTC 60.803 60.000 8.00 0.00 43.98 4.79
144 145 1.216178 CGAACCGGTATGTTCCCGT 59.784 57.895 8.00 0.00 43.98 5.28
145 146 1.519898 CCGAACCGGTATGTTCCCG 60.520 63.158 8.00 3.12 42.73 5.14
146 147 1.153309 CCCGAACCGGTATGTTCCC 60.153 63.158 8.00 0.00 46.80 3.97
147 148 0.036105 AACCCGAACCGGTATGTTCC 60.036 55.000 8.00 0.00 46.80 3.62
148 149 1.081094 CAACCCGAACCGGTATGTTC 58.919 55.000 8.00 0.00 46.80 3.18
149 150 0.321830 CCAACCCGAACCGGTATGTT 60.322 55.000 8.00 6.32 46.80 2.71
150 151 1.297364 CCAACCCGAACCGGTATGT 59.703 57.895 8.00 0.00 46.80 2.29
151 152 1.022451 CACCAACCCGAACCGGTATG 61.022 60.000 8.00 2.60 46.80 2.39
152 153 1.297364 CACCAACCCGAACCGGTAT 59.703 57.895 8.00 0.00 46.80 2.73
153 154 1.694133 AACACCAACCCGAACCGGTA 61.694 55.000 8.00 0.00 46.80 4.02
154 155 2.555302 AAACACCAACCCGAACCGGT 62.555 55.000 0.00 0.00 46.80 5.28
156 157 0.456628 AAAAACACCAACCCGAACCG 59.543 50.000 0.00 0.00 0.00 4.44
157 158 1.205179 ACAAAAACACCAACCCGAACC 59.795 47.619 0.00 0.00 0.00 3.62
158 159 2.658373 ACAAAAACACCAACCCGAAC 57.342 45.000 0.00 0.00 0.00 3.95
159 160 3.258622 AGAAACAAAAACACCAACCCGAA 59.741 39.130 0.00 0.00 0.00 4.30
160 161 2.826725 AGAAACAAAAACACCAACCCGA 59.173 40.909 0.00 0.00 0.00 5.14
161 162 2.926838 CAGAAACAAAAACACCAACCCG 59.073 45.455 0.00 0.00 0.00 5.28
162 163 4.195225 TCAGAAACAAAAACACCAACCC 57.805 40.909 0.00 0.00 0.00 4.11
163 164 4.570369 CCATCAGAAACAAAAACACCAACC 59.430 41.667 0.00 0.00 0.00 3.77
164 165 5.415221 TCCATCAGAAACAAAAACACCAAC 58.585 37.500 0.00 0.00 0.00 3.77
165 166 5.667539 TCCATCAGAAACAAAAACACCAA 57.332 34.783 0.00 0.00 0.00 3.67
166 167 5.395103 CCTTCCATCAGAAACAAAAACACCA 60.395 40.000 0.00 0.00 32.88 4.17
167 168 5.049828 CCTTCCATCAGAAACAAAAACACC 58.950 41.667 0.00 0.00 32.88 4.16
168 169 4.507756 GCCTTCCATCAGAAACAAAAACAC 59.492 41.667 0.00 0.00 32.88 3.32
169 170 4.692228 GCCTTCCATCAGAAACAAAAACA 58.308 39.130 0.00 0.00 32.88 2.83
170 171 3.735746 CGCCTTCCATCAGAAACAAAAAC 59.264 43.478 0.00 0.00 32.88 2.43
171 172 3.798548 GCGCCTTCCATCAGAAACAAAAA 60.799 43.478 0.00 0.00 32.88 1.94
172 173 2.288152 GCGCCTTCCATCAGAAACAAAA 60.288 45.455 0.00 0.00 32.88 2.44
173 174 1.269448 GCGCCTTCCATCAGAAACAAA 59.731 47.619 0.00 0.00 32.88 2.83
174 175 0.881118 GCGCCTTCCATCAGAAACAA 59.119 50.000 0.00 0.00 32.88 2.83
175 176 0.960364 GGCGCCTTCCATCAGAAACA 60.960 55.000 22.15 0.00 32.88 2.83
176 177 1.803289 GGCGCCTTCCATCAGAAAC 59.197 57.895 22.15 0.00 32.88 2.78
177 178 1.745115 CGGCGCCTTCCATCAGAAA 60.745 57.895 26.68 0.00 32.88 2.52
178 179 1.609635 TACGGCGCCTTCCATCAGAA 61.610 55.000 26.68 0.00 0.00 3.02
179 180 1.399744 ATACGGCGCCTTCCATCAGA 61.400 55.000 26.68 0.00 0.00 3.27
180 181 0.317160 TATACGGCGCCTTCCATCAG 59.683 55.000 26.68 8.67 0.00 2.90
181 182 0.973632 ATATACGGCGCCTTCCATCA 59.026 50.000 26.68 0.00 0.00 3.07
182 183 2.481449 CCTATATACGGCGCCTTCCATC 60.481 54.545 26.68 0.00 0.00 3.51
183 184 1.480954 CCTATATACGGCGCCTTCCAT 59.519 52.381 26.68 14.10 0.00 3.41
184 185 0.892755 CCTATATACGGCGCCTTCCA 59.107 55.000 26.68 6.88 0.00 3.53
185 186 0.175073 CCCTATATACGGCGCCTTCC 59.825 60.000 26.68 0.00 0.00 3.46
186 187 1.135170 GTCCCTATATACGGCGCCTTC 60.135 57.143 26.68 0.00 0.00 3.46
187 188 0.893447 GTCCCTATATACGGCGCCTT 59.107 55.000 26.68 19.30 0.00 4.35
188 189 1.310933 CGTCCCTATATACGGCGCCT 61.311 60.000 26.68 14.27 35.51 5.52
189 190 1.138247 CGTCCCTATATACGGCGCC 59.862 63.158 19.07 19.07 35.51 6.53
190 191 0.098376 CTCGTCCCTATATACGGCGC 59.902 60.000 6.90 0.00 39.52 6.53
191 192 1.664659 CTCTCGTCCCTATATACGGCG 59.335 57.143 4.80 4.80 39.52 6.46
192 193 2.709213 ACTCTCGTCCCTATATACGGC 58.291 52.381 0.00 0.00 39.52 5.68
193 194 5.240891 TGTTACTCTCGTCCCTATATACGG 58.759 45.833 0.00 0.00 39.52 4.02
194 195 6.791887 TTGTTACTCTCGTCCCTATATACG 57.208 41.667 0.00 0.00 40.40 3.06
229 230 9.857957 AGACAGAGCTATTTTGTTACTAGTAAC 57.142 33.333 30.62 30.62 44.16 2.50
246 247 9.391006 GTGCTACTATCTATATAAGACAGAGCT 57.609 37.037 0.00 0.00 35.09 4.09
247 248 9.391006 AGTGCTACTATCTATATAAGACAGAGC 57.609 37.037 0.00 0.00 36.93 4.09
261 262 8.052748 CCTAGGATCAGAATAGTGCTACTATCT 58.947 40.741 1.05 6.13 40.32 1.98
262 263 8.050325 TCCTAGGATCAGAATAGTGCTACTATC 58.950 40.741 7.62 4.55 40.32 2.08
263 264 7.934313 TCCTAGGATCAGAATAGTGCTACTAT 58.066 38.462 7.62 3.78 42.86 2.12
264 265 7.331089 TCCTAGGATCAGAATAGTGCTACTA 57.669 40.000 7.62 0.00 34.82 1.82
265 266 6.207509 TCCTAGGATCAGAATAGTGCTACT 57.792 41.667 7.62 0.00 0.00 2.57
288 289 8.830580 CGGTGTGATCAGAATAACTATTTTGAT 58.169 33.333 12.78 12.78 44.95 2.57
289 290 7.822334 ACGGTGTGATCAGAATAACTATTTTGA 59.178 33.333 0.00 5.45 39.91 2.69
290 291 7.904977 CACGGTGTGATCAGAATAACTATTTTG 59.095 37.037 0.00 0.00 35.23 2.44
291 292 7.065803 CCACGGTGTGATCAGAATAACTATTTT 59.934 37.037 7.45 0.00 35.23 1.82
292 293 6.538742 CCACGGTGTGATCAGAATAACTATTT 59.461 38.462 7.45 0.00 35.23 1.40
293 294 6.049149 CCACGGTGTGATCAGAATAACTATT 58.951 40.000 7.45 0.00 35.23 1.73
294 295 5.453339 CCCACGGTGTGATCAGAATAACTAT 60.453 44.000 7.45 0.00 35.23 2.12
295 296 4.142026 CCCACGGTGTGATCAGAATAACTA 60.142 45.833 7.45 0.00 35.23 2.24
296 297 3.369471 CCCACGGTGTGATCAGAATAACT 60.369 47.826 7.45 0.00 35.23 2.24
297 298 2.936498 CCCACGGTGTGATCAGAATAAC 59.064 50.000 7.45 0.00 35.23 1.89
298 299 2.569853 ACCCACGGTGTGATCAGAATAA 59.430 45.455 7.45 0.00 35.23 1.40
299 300 2.167693 GACCCACGGTGTGATCAGAATA 59.832 50.000 7.45 0.00 35.25 1.75
300 301 0.984230 ACCCACGGTGTGATCAGAAT 59.016 50.000 7.45 0.00 35.23 2.40
301 302 0.320374 GACCCACGGTGTGATCAGAA 59.680 55.000 7.45 0.00 35.25 3.02
302 303 0.541998 AGACCCACGGTGTGATCAGA 60.542 55.000 7.45 0.00 35.25 3.27
303 304 1.975327 AGACCCACGGTGTGATCAG 59.025 57.895 7.45 0.00 35.25 2.90
304 305 4.208426 AGACCCACGGTGTGATCA 57.792 55.556 7.45 0.00 35.25 2.92
308 309 1.446099 CGATCAGACCCACGGTGTG 60.446 63.158 7.45 1.62 46.59 3.82
309 310 2.970639 CGATCAGACCCACGGTGT 59.029 61.111 7.45 0.00 35.25 4.16
310 311 2.509336 GCGATCAGACCCACGGTG 60.509 66.667 0.00 0.00 35.25 4.94
311 312 2.359169 ATGCGATCAGACCCACGGT 61.359 57.895 0.00 0.00 39.44 4.83
312 313 1.884464 CATGCGATCAGACCCACGG 60.884 63.158 0.00 0.00 0.00 4.94
313 314 0.740868 AACATGCGATCAGACCCACG 60.741 55.000 0.00 0.00 0.00 4.94
314 315 1.398390 GAAACATGCGATCAGACCCAC 59.602 52.381 0.00 0.00 0.00 4.61
315 316 1.278985 AGAAACATGCGATCAGACCCA 59.721 47.619 0.00 0.00 0.00 4.51
316 317 1.667724 CAGAAACATGCGATCAGACCC 59.332 52.381 0.00 0.00 0.00 4.46
317 318 2.621338 TCAGAAACATGCGATCAGACC 58.379 47.619 0.00 0.00 0.00 3.85
318 319 4.569966 AGATTCAGAAACATGCGATCAGAC 59.430 41.667 0.00 0.00 0.00 3.51
319 320 4.569564 CAGATTCAGAAACATGCGATCAGA 59.430 41.667 0.00 0.00 0.00 3.27
320 321 4.260661 CCAGATTCAGAAACATGCGATCAG 60.261 45.833 0.00 0.00 0.00 2.90
321 322 3.624410 CCAGATTCAGAAACATGCGATCA 59.376 43.478 0.00 0.00 0.00 2.92
353 354 0.896226 AGTTCGAGTGGGTAGCCTTC 59.104 55.000 13.11 9.02 0.00 3.46
360 361 0.763223 AGTGGGAAGTTCGAGTGGGT 60.763 55.000 0.00 0.00 0.00 4.51
397 398 1.146263 GGGGATCGGCGATGACTTT 59.854 57.895 29.20 1.61 0.00 2.66
398 399 2.063979 TGGGGATCGGCGATGACTT 61.064 57.895 29.20 2.55 0.00 3.01
399 400 2.443952 TGGGGATCGGCGATGACT 60.444 61.111 29.20 3.03 0.00 3.41
406 407 3.124921 CGTTGTGTGGGGATCGGC 61.125 66.667 0.00 0.00 0.00 5.54
436 437 1.878775 GTGGTTGCCAGATGCTGTC 59.121 57.895 0.00 0.00 42.00 3.51
440 441 4.465512 CGCGTGGTTGCCAGATGC 62.466 66.667 0.00 0.00 41.77 3.91
485 501 2.081212 CGAACGCAGAGTCCACGAC 61.081 63.158 9.19 2.90 0.00 4.34
524 540 1.893801 CGTAGGTATAAGCAGGGGAGG 59.106 57.143 0.00 0.00 0.00 4.30
562 578 1.973281 CGCCATGGGTTGAAGCAGT 60.973 57.895 15.13 0.00 0.00 4.40
783 799 2.722201 GCGAGATCCCGGTGACCTT 61.722 63.158 0.00 0.00 0.00 3.50
850 866 2.260639 AGGAGGTGGATCACAGATGT 57.739 50.000 0.00 0.00 35.86 3.06
869 885 3.117625 TCGGAGGATCTAGGACTTTGCTA 60.118 47.826 0.00 0.00 33.73 3.49
996 1013 2.427320 GCGATGGGGAGCATAGCA 59.573 61.111 0.00 0.00 32.25 3.49
1015 1032 1.000394 ACGATGGACGACAACATGTGA 60.000 47.619 0.00 0.00 45.77 3.58
1023 1040 1.509463 GTAGGCACGATGGACGACA 59.491 57.895 0.00 0.00 45.77 4.35
1032 1049 2.738480 GTGGTGTGGTAGGCACGA 59.262 61.111 0.00 0.00 37.70 4.35
1043 1060 1.073722 CATCTGCAGGTGGTGGTGT 59.926 57.895 19.79 0.00 0.00 4.16
1045 1062 1.845627 CTCCATCTGCAGGTGGTGGT 61.846 60.000 38.59 0.00 36.84 4.16
1076 1093 0.978146 GAGGCCTCCTCTACCTGCAA 60.978 60.000 23.19 0.00 46.41 4.08
1117 1134 0.685097 GGCAGAGTTACCTGGACACA 59.315 55.000 0.00 0.00 34.82 3.72
1124 1141 2.567615 CAACTACCTGGCAGAGTTACCT 59.432 50.000 17.94 0.00 32.22 3.08
1128 1145 1.543429 GCACAACTACCTGGCAGAGTT 60.543 52.381 17.94 15.60 33.71 3.01
1164 1181 0.250124 ACCCGTGTTGCGATCTTTCA 60.250 50.000 0.00 0.00 44.77 2.69
1176 1194 2.358247 GTTGATGCCGACCCGTGT 60.358 61.111 0.00 0.00 0.00 4.49
1192 1210 2.800544 GACTGCACTACGACAAACATGT 59.199 45.455 0.00 0.00 0.00 3.21
1195 1213 1.411246 AGGACTGCACTACGACAAACA 59.589 47.619 0.00 0.00 0.00 2.83
1240 1258 1.106351 TGGACACCAACGCAAGCAAT 61.106 50.000 0.00 0.00 45.62 3.56
1429 1450 3.492102 AGAAGAGTAGCAGCAAACCAA 57.508 42.857 0.00 0.00 0.00 3.67
1599 1621 0.976641 TTCGCTGATGTCAGGAGGTT 59.023 50.000 11.66 0.00 43.94 3.50
1646 1668 2.327592 CGCACGCACACAACATGT 59.672 55.556 0.00 0.00 44.81 3.21
1810 1838 9.273016 GCTAGCACATACAATTTCCTCTTTATA 57.727 33.333 10.63 0.00 0.00 0.98
1817 1845 5.102953 TGAGCTAGCACATACAATTTCCT 57.897 39.130 18.83 0.00 0.00 3.36
1819 1847 5.333645 CCGATGAGCTAGCACATACAATTTC 60.334 44.000 24.91 12.39 0.00 2.17
1897 1927 8.579850 TCAATACATTTCAGATGCTAAAACCT 57.420 30.769 0.00 0.00 0.00 3.50
1984 2014 3.004944 GTCCGAAGTCCAGATCCTGTATC 59.995 52.174 0.00 0.00 34.52 2.24
2123 2153 1.962807 TCAACCTTGGTGAAGCATTGG 59.037 47.619 0.00 1.97 30.28 3.16
2219 2249 0.896226 AGTCCTTCCGCTGTACCTTC 59.104 55.000 0.00 0.00 0.00 3.46
2239 2269 2.859165 ACCACCGTGACAAGAATCAT 57.141 45.000 0.00 0.00 0.00 2.45
2240 2270 2.616376 CAAACCACCGTGACAAGAATCA 59.384 45.455 0.00 0.00 0.00 2.57
2254 2286 4.929211 GCTCCATAAATTCCAACAAACCAC 59.071 41.667 0.00 0.00 0.00 4.16
2355 2388 3.411446 CTCTCGCCAATGCCCATAATTA 58.589 45.455 0.00 0.00 0.00 1.40
2456 2489 4.506654 ACTTACAAGATATTACAAGCCGCG 59.493 41.667 0.00 0.00 0.00 6.46
2614 2653 1.065491 TCTGTCGCATTGCACCCTTAT 60.065 47.619 9.69 0.00 0.00 1.73
2669 2708 4.497300 TCGTTTCTGGGAATTAAGGTACG 58.503 43.478 0.00 0.00 0.00 3.67
2695 2819 6.288294 TGGAATGTGATCCGTATAGAAAAGG 58.712 40.000 0.00 0.00 42.76 3.11
2769 2896 5.008217 TCCGTCATTCTTGTTTCGACATTTT 59.992 36.000 0.00 0.00 0.00 1.82
2800 2927 5.009610 AGCGTCACAGGAACAAATTAACAAT 59.990 36.000 0.00 0.00 0.00 2.71
2851 2979 4.683781 TGCAAGTGTGTTGTTTTTCTGAAC 59.316 37.500 0.00 0.00 0.00 3.18
2852 2980 4.876125 TGCAAGTGTGTTGTTTTTCTGAA 58.124 34.783 0.00 0.00 0.00 3.02
2853 2981 4.484236 CTGCAAGTGTGTTGTTTTTCTGA 58.516 39.130 0.00 0.00 0.00 3.27
2854 2982 4.828291 CTGCAAGTGTGTTGTTTTTCTG 57.172 40.909 0.00 0.00 0.00 3.02
3233 3371 6.381420 TCTTCAGTAACAGGGAAGATCTAAGG 59.619 42.308 0.00 0.00 41.38 2.69
3325 3467 6.051179 AGCCTCTAGGTTTTTCGTAGAAAT 57.949 37.500 0.00 0.00 41.15 2.17


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

AutoCloner maintained by Alex Coulton.