Multiple sequence alignment - TraesCS4D01G062500

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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 TraesCS4D01G062500 chr4D 100.000 2552 0 0 1 2552 38346192 38343641 0.000000e+00 4713.0
1 TraesCS4D01G062500 chr4A 91.299 1793 81 33 261 2009 562457503 562459264 0.000000e+00 2377.0
2 TraesCS4D01G062500 chr4B 92.208 1078 42 21 796 1839 55727322 55726253 0.000000e+00 1487.0
3 TraesCS4D01G062500 chr4B 89.583 528 27 11 264 777 55728329 55727816 0.000000e+00 645.0
4 TraesCS4D01G062500 chr2B 91.176 544 45 3 2011 2552 712613802 712613260 0.000000e+00 736.0
5 TraesCS4D01G062500 chr7B 91.434 537 43 3 2018 2552 701639048 701638513 0.000000e+00 734.0
6 TraesCS4D01G062500 chr6B 90.993 544 46 3 2011 2552 690314916 690314374 0.000000e+00 730.0
7 TraesCS4D01G062500 chr6B 90.129 466 44 2 2016 2480 137454733 137454269 2.810000e-169 604.0
8 TraesCS4D01G062500 chr6B 97.143 35 1 0 1952 1986 542930749 542930715 2.740000e-05 60.2
9 TraesCS4D01G062500 chr1B 91.095 539 43 4 2018 2552 120471543 120471006 0.000000e+00 725.0
10 TraesCS4D01G062500 chr1B 89.286 56 2 3 1952 2006 437601164 437601112 1.640000e-07 67.6
11 TraesCS4D01G062500 chr5B 89.154 544 57 2 2011 2552 272032177 272031634 0.000000e+00 676.0
12 TraesCS4D01G062500 chr5A 90.097 515 48 3 2041 2552 625916119 625915605 0.000000e+00 665.0
13 TraesCS4D01G062500 chr5A 89.300 514 51 3 2043 2552 689194311 689193798 2.140000e-180 641.0
14 TraesCS4D01G062500 chr5A 86.552 290 33 4 2194 2481 673406546 673406261 5.300000e-82 315.0
15 TraesCS4D01G062500 chr5A 100.000 35 0 0 1952 1986 66842269 66842303 5.890000e-07 65.8
16 TraesCS4D01G062500 chr5A 97.368 38 0 1 1950 1986 184231711 184231674 2.120000e-06 63.9
17 TraesCS4D01G062500 chr1D 90.566 265 24 1 2022 2285 422285347 422285611 1.450000e-92 350.0
18 TraesCS4D01G062500 chr1D 89.474 57 4 1 1952 2008 111003519 111003465 1.270000e-08 71.3
19 TraesCS4D01G062500 chr5D 88.060 67 5 2 1947 2012 138470202 138470266 2.720000e-10 76.8
20 TraesCS4D01G062500 chr2D 92.453 53 2 1 1952 2004 491802927 491802877 9.790000e-10 75.0
21 TraesCS4D01G062500 chr1A 100.000 30 0 0 2011 2040 568762467 568762496 3.550000e-04 56.5


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 TraesCS4D01G062500 chr4D 38343641 38346192 2551 True 4713 4713 100.0000 1 2552 1 chr4D.!!$R1 2551
1 TraesCS4D01G062500 chr4A 562457503 562459264 1761 False 2377 2377 91.2990 261 2009 1 chr4A.!!$F1 1748
2 TraesCS4D01G062500 chr4B 55726253 55728329 2076 True 1066 1487 90.8955 264 1839 2 chr4B.!!$R1 1575
3 TraesCS4D01G062500 chr2B 712613260 712613802 542 True 736 736 91.1760 2011 2552 1 chr2B.!!$R1 541
4 TraesCS4D01G062500 chr7B 701638513 701639048 535 True 734 734 91.4340 2018 2552 1 chr7B.!!$R1 534
5 TraesCS4D01G062500 chr6B 690314374 690314916 542 True 730 730 90.9930 2011 2552 1 chr6B.!!$R3 541
6 TraesCS4D01G062500 chr1B 120471006 120471543 537 True 725 725 91.0950 2018 2552 1 chr1B.!!$R1 534
7 TraesCS4D01G062500 chr5B 272031634 272032177 543 True 676 676 89.1540 2011 2552 1 chr5B.!!$R1 541
8 TraesCS4D01G062500 chr5A 625915605 625916119 514 True 665 665 90.0970 2041 2552 1 chr5A.!!$R2 511
9 TraesCS4D01G062500 chr5A 689193798 689194311 513 True 641 641 89.3000 2043 2552 1 chr5A.!!$R4 509

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
173 174 0.178981 AATCATGCGATCCAAGGGGG 60.179 55.0 0.0 0.0 38.37 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 2620 0.457166 CACGCGTTGGAATACCGAGA 60.457 55.0 10.22 0.0 39.42 4.04 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
28 29 5.089970 TGTATCCACACATGAAGAAGAGG 57.910 43.478 0.00 0.00 0.00 3.69
29 30 4.532126 TGTATCCACACATGAAGAAGAGGT 59.468 41.667 0.00 0.00 0.00 3.85
30 31 3.407424 TCCACACATGAAGAAGAGGTG 57.593 47.619 0.00 0.00 35.66 4.00
31 32 2.705658 TCCACACATGAAGAAGAGGTGT 59.294 45.455 0.00 0.00 42.94 4.16
33 34 3.845781 ACACATGAAGAAGAGGTGTGT 57.154 42.857 0.00 3.82 45.98 3.72
35 36 3.070018 CACATGAAGAAGAGGTGTGTCC 58.930 50.000 0.00 0.00 36.37 4.02
45 46 1.901591 AGGTGTGTCCTGCATTCTTG 58.098 50.000 0.00 0.00 46.19 3.02
46 47 1.143684 AGGTGTGTCCTGCATTCTTGT 59.856 47.619 0.00 0.00 46.19 3.16
47 48 1.956477 GGTGTGTCCTGCATTCTTGTT 59.044 47.619 0.00 0.00 0.00 2.83
48 49 2.362077 GGTGTGTCCTGCATTCTTGTTT 59.638 45.455 0.00 0.00 0.00 2.83
49 50 3.550842 GGTGTGTCCTGCATTCTTGTTTC 60.551 47.826 0.00 0.00 0.00 2.78
50 51 2.622942 TGTGTCCTGCATTCTTGTTTCC 59.377 45.455 0.00 0.00 0.00 3.13
51 52 2.887152 GTGTCCTGCATTCTTGTTTCCT 59.113 45.455 0.00 0.00 0.00 3.36
52 53 3.319122 GTGTCCTGCATTCTTGTTTCCTT 59.681 43.478 0.00 0.00 0.00 3.36
53 54 3.960102 TGTCCTGCATTCTTGTTTCCTTT 59.040 39.130 0.00 0.00 0.00 3.11
54 55 4.405358 TGTCCTGCATTCTTGTTTCCTTTT 59.595 37.500 0.00 0.00 0.00 2.27
55 56 4.746611 GTCCTGCATTCTTGTTTCCTTTTG 59.253 41.667 0.00 0.00 0.00 2.44
56 57 3.495753 CCTGCATTCTTGTTTCCTTTTGC 59.504 43.478 0.00 0.00 0.00 3.68
57 58 4.121317 CTGCATTCTTGTTTCCTTTTGCA 58.879 39.130 0.00 0.00 37.32 4.08
58 59 4.511527 TGCATTCTTGTTTCCTTTTGCAA 58.488 34.783 0.00 0.00 36.06 4.08
59 60 4.940046 TGCATTCTTGTTTCCTTTTGCAAA 59.060 33.333 8.05 8.05 36.06 3.68
60 61 5.163774 TGCATTCTTGTTTCCTTTTGCAAAC 60.164 36.000 12.39 0.00 36.06 2.93
61 62 5.065090 GCATTCTTGTTTCCTTTTGCAAACT 59.935 36.000 12.39 0.00 34.22 2.66
62 63 6.403527 GCATTCTTGTTTCCTTTTGCAAACTT 60.404 34.615 12.39 0.00 34.22 2.66
63 64 7.201600 GCATTCTTGTTTCCTTTTGCAAACTTA 60.202 33.333 12.39 0.00 34.22 2.24
64 65 7.589574 TTCTTGTTTCCTTTTGCAAACTTAC 57.410 32.000 12.39 6.74 34.22 2.34
65 66 6.930731 TCTTGTTTCCTTTTGCAAACTTACT 58.069 32.000 12.39 0.00 34.22 2.24
66 67 7.033185 TCTTGTTTCCTTTTGCAAACTTACTC 58.967 34.615 12.39 2.78 34.22 2.59
67 68 6.274157 TGTTTCCTTTTGCAAACTTACTCA 57.726 33.333 12.39 5.37 34.22 3.41
68 69 6.872920 TGTTTCCTTTTGCAAACTTACTCAT 58.127 32.000 12.39 0.00 34.22 2.90
69 70 6.978080 TGTTTCCTTTTGCAAACTTACTCATC 59.022 34.615 12.39 0.00 34.22 2.92
70 71 5.705609 TCCTTTTGCAAACTTACTCATCC 57.294 39.130 12.39 0.00 0.00 3.51
71 72 5.136828 TCCTTTTGCAAACTTACTCATCCA 58.863 37.500 12.39 0.00 0.00 3.41
72 73 5.009610 TCCTTTTGCAAACTTACTCATCCAC 59.990 40.000 12.39 0.00 0.00 4.02
73 74 5.221224 CCTTTTGCAAACTTACTCATCCACA 60.221 40.000 12.39 0.00 0.00 4.17
74 75 4.829064 TTGCAAACTTACTCATCCACAC 57.171 40.909 0.00 0.00 0.00 3.82
75 76 4.085357 TGCAAACTTACTCATCCACACT 57.915 40.909 0.00 0.00 0.00 3.55
76 77 4.460263 TGCAAACTTACTCATCCACACTT 58.540 39.130 0.00 0.00 0.00 3.16
77 78 4.275689 TGCAAACTTACTCATCCACACTTG 59.724 41.667 0.00 0.00 0.00 3.16
78 79 4.320494 GCAAACTTACTCATCCACACTTGG 60.320 45.833 0.00 0.00 45.56 3.61
79 80 3.059352 ACTTACTCATCCACACTTGGC 57.941 47.619 0.00 0.00 43.56 4.52
80 81 2.371841 ACTTACTCATCCACACTTGGCA 59.628 45.455 0.00 0.00 43.56 4.92
81 82 3.181445 ACTTACTCATCCACACTTGGCAA 60.181 43.478 0.00 0.00 43.56 4.52
82 83 2.363306 ACTCATCCACACTTGGCAAA 57.637 45.000 0.00 0.00 43.56 3.68
83 84 2.880443 ACTCATCCACACTTGGCAAAT 58.120 42.857 0.00 0.00 43.56 2.32
84 85 2.821969 ACTCATCCACACTTGGCAAATC 59.178 45.455 0.00 0.00 43.56 2.17
85 86 3.087031 CTCATCCACACTTGGCAAATCT 58.913 45.455 0.00 0.00 43.56 2.40
86 87 4.263462 ACTCATCCACACTTGGCAAATCTA 60.263 41.667 0.00 0.00 43.56 1.98
87 88 4.858850 TCATCCACACTTGGCAAATCTAT 58.141 39.130 0.00 0.00 43.56 1.98
88 89 4.883585 TCATCCACACTTGGCAAATCTATC 59.116 41.667 0.00 0.00 43.56 2.08
89 90 4.299586 TCCACACTTGGCAAATCTATCA 57.700 40.909 0.00 0.00 43.56 2.15
90 91 4.661222 TCCACACTTGGCAAATCTATCAA 58.339 39.130 0.00 0.00 43.56 2.57
91 92 4.458989 TCCACACTTGGCAAATCTATCAAC 59.541 41.667 0.00 0.00 43.56 3.18
92 93 4.406069 CACACTTGGCAAATCTATCAACG 58.594 43.478 0.00 0.00 0.00 4.10
93 94 3.440173 ACACTTGGCAAATCTATCAACGG 59.560 43.478 0.00 0.00 0.00 4.44
94 95 3.440173 CACTTGGCAAATCTATCAACGGT 59.560 43.478 0.00 0.00 0.00 4.83
95 96 4.079253 ACTTGGCAAATCTATCAACGGTT 58.921 39.130 0.00 0.00 0.00 4.44
96 97 4.156008 ACTTGGCAAATCTATCAACGGTTC 59.844 41.667 0.00 0.00 0.00 3.62
97 98 3.680490 TGGCAAATCTATCAACGGTTCA 58.320 40.909 0.00 0.00 0.00 3.18
98 99 4.075682 TGGCAAATCTATCAACGGTTCAA 58.924 39.130 0.00 0.00 0.00 2.69
99 100 4.520874 TGGCAAATCTATCAACGGTTCAAA 59.479 37.500 0.00 0.00 0.00 2.69
100 101 5.184864 TGGCAAATCTATCAACGGTTCAAAT 59.815 36.000 0.00 0.00 0.00 2.32
101 102 5.743872 GGCAAATCTATCAACGGTTCAAATC 59.256 40.000 0.00 0.00 0.00 2.17
102 103 6.321717 GCAAATCTATCAACGGTTCAAATCA 58.678 36.000 0.00 0.00 0.00 2.57
103 104 6.974622 GCAAATCTATCAACGGTTCAAATCAT 59.025 34.615 0.00 0.00 0.00 2.45
104 105 8.128582 GCAAATCTATCAACGGTTCAAATCATA 58.871 33.333 0.00 0.00 0.00 2.15
107 108 9.559732 AATCTATCAACGGTTCAAATCATATGA 57.440 29.630 8.10 8.10 0.00 2.15
108 109 8.365399 TCTATCAACGGTTCAAATCATATGAC 57.635 34.615 7.78 0.00 0.00 3.06
109 110 5.811399 TCAACGGTTCAAATCATATGACC 57.189 39.130 7.78 3.21 0.00 4.02
110 111 5.249420 TCAACGGTTCAAATCATATGACCA 58.751 37.500 7.78 0.00 0.00 4.02
111 112 5.707764 TCAACGGTTCAAATCATATGACCAA 59.292 36.000 7.78 0.00 0.00 3.67
112 113 5.560966 ACGGTTCAAATCATATGACCAAC 57.439 39.130 7.78 8.20 0.00 3.77
113 114 5.253330 ACGGTTCAAATCATATGACCAACT 58.747 37.500 7.78 0.00 0.00 3.16
114 115 6.411376 ACGGTTCAAATCATATGACCAACTA 58.589 36.000 7.78 0.00 0.00 2.24
115 116 6.882140 ACGGTTCAAATCATATGACCAACTAA 59.118 34.615 7.78 0.00 0.00 2.24
116 117 7.065803 ACGGTTCAAATCATATGACCAACTAAG 59.934 37.037 7.78 0.37 0.00 2.18
117 118 7.196331 GGTTCAAATCATATGACCAACTAAGC 58.804 38.462 7.78 4.50 0.00 3.09
118 119 7.148086 GGTTCAAATCATATGACCAACTAAGCA 60.148 37.037 7.78 0.00 0.00 3.91
119 120 7.936496 TCAAATCATATGACCAACTAAGCAA 57.064 32.000 7.78 0.00 0.00 3.91
120 121 8.347004 TCAAATCATATGACCAACTAAGCAAA 57.653 30.769 7.78 0.00 0.00 3.68
121 122 8.801299 TCAAATCATATGACCAACTAAGCAAAA 58.199 29.630 7.78 0.00 0.00 2.44
122 123 9.421806 CAAATCATATGACCAACTAAGCAAAAA 57.578 29.630 7.78 0.00 0.00 1.94
139 140 3.720949 AAAAACTTAACCTTGGACGGC 57.279 42.857 0.00 0.00 0.00 5.68
140 141 2.351706 AAACTTAACCTTGGACGGCA 57.648 45.000 0.00 0.00 0.00 5.69
141 142 2.579410 AACTTAACCTTGGACGGCAT 57.421 45.000 0.00 0.00 0.00 4.40
142 143 2.109425 ACTTAACCTTGGACGGCATC 57.891 50.000 0.00 0.00 0.00 3.91
152 153 3.364277 GACGGCATCCAGTTCTACC 57.636 57.895 0.00 0.00 0.00 3.18
153 154 0.535335 GACGGCATCCAGTTCTACCA 59.465 55.000 0.00 0.00 0.00 3.25
154 155 0.981183 ACGGCATCCAGTTCTACCAA 59.019 50.000 0.00 0.00 0.00 3.67
155 156 1.349688 ACGGCATCCAGTTCTACCAAA 59.650 47.619 0.00 0.00 0.00 3.28
156 157 2.026262 ACGGCATCCAGTTCTACCAAAT 60.026 45.455 0.00 0.00 0.00 2.32
157 158 2.614057 CGGCATCCAGTTCTACCAAATC 59.386 50.000 0.00 0.00 0.00 2.17
158 159 3.620488 GGCATCCAGTTCTACCAAATCA 58.380 45.455 0.00 0.00 0.00 2.57
159 160 4.210331 GGCATCCAGTTCTACCAAATCAT 58.790 43.478 0.00 0.00 0.00 2.45
160 161 4.037208 GGCATCCAGTTCTACCAAATCATG 59.963 45.833 0.00 0.00 0.00 3.07
161 162 4.498682 GCATCCAGTTCTACCAAATCATGC 60.499 45.833 0.00 0.00 0.00 4.06
162 163 3.270027 TCCAGTTCTACCAAATCATGCG 58.730 45.455 0.00 0.00 0.00 4.73
163 164 3.055458 TCCAGTTCTACCAAATCATGCGA 60.055 43.478 0.00 0.00 0.00 5.10
164 165 3.879295 CCAGTTCTACCAAATCATGCGAT 59.121 43.478 0.00 0.00 0.00 4.58
165 166 4.024556 CCAGTTCTACCAAATCATGCGATC 60.025 45.833 0.00 0.00 0.00 3.69
166 167 4.024556 CAGTTCTACCAAATCATGCGATCC 60.025 45.833 0.00 0.00 0.00 3.36
167 168 3.836365 TCTACCAAATCATGCGATCCA 57.164 42.857 0.00 0.00 0.00 3.41
168 169 4.149511 TCTACCAAATCATGCGATCCAA 57.850 40.909 0.00 0.00 0.00 3.53
169 170 4.129380 TCTACCAAATCATGCGATCCAAG 58.871 43.478 0.00 0.00 0.00 3.61
170 171 2.026641 ACCAAATCATGCGATCCAAGG 58.973 47.619 0.00 0.00 0.00 3.61
171 172 1.338973 CCAAATCATGCGATCCAAGGG 59.661 52.381 0.00 0.00 0.00 3.95
172 173 1.338973 CAAATCATGCGATCCAAGGGG 59.661 52.381 0.00 0.00 0.00 4.79
173 174 0.178981 AATCATGCGATCCAAGGGGG 60.179 55.000 0.00 0.00 38.37 5.40
182 183 2.189266 TCCAAGGGGGAGAGTACCA 58.811 57.895 0.00 0.00 42.15 3.25
183 184 0.494551 TCCAAGGGGGAGAGTACCAA 59.505 55.000 0.00 0.00 42.15 3.67
184 185 1.132332 TCCAAGGGGGAGAGTACCAAA 60.132 52.381 0.00 0.00 42.15 3.28
185 186 1.004394 CCAAGGGGGAGAGTACCAAAC 59.996 57.143 0.00 0.00 40.01 2.93
186 187 1.004394 CAAGGGGGAGAGTACCAAACC 59.996 57.143 0.00 0.00 0.00 3.27
187 188 0.549413 AGGGGGAGAGTACCAAACCC 60.549 60.000 0.00 0.00 39.79 4.11
188 189 0.843343 GGGGGAGAGTACCAAACCCA 60.843 60.000 13.39 0.00 42.03 4.51
189 190 1.069775 GGGGAGAGTACCAAACCCAA 58.930 55.000 14.14 0.00 42.03 4.12
190 191 1.639108 GGGGAGAGTACCAAACCCAAT 59.361 52.381 14.14 0.00 42.03 3.16
191 192 2.848071 GGGGAGAGTACCAAACCCAATA 59.152 50.000 14.14 0.00 42.03 1.90
192 193 3.267551 GGGGAGAGTACCAAACCCAATAA 59.732 47.826 14.14 0.00 42.03 1.40
193 194 4.079385 GGGGAGAGTACCAAACCCAATAAT 60.079 45.833 14.14 0.00 42.03 1.28
194 195 5.516044 GGGAGAGTACCAAACCCAATAATT 58.484 41.667 0.00 0.00 40.20 1.40
195 196 5.359860 GGGAGAGTACCAAACCCAATAATTG 59.640 44.000 0.00 0.00 40.20 2.32
208 209 4.644103 CAATAATTGGGCTCTGGTTCTG 57.356 45.455 0.00 0.00 0.00 3.02
209 210 4.272489 CAATAATTGGGCTCTGGTTCTGA 58.728 43.478 0.00 0.00 0.00 3.27
210 211 2.978156 AATTGGGCTCTGGTTCTGAA 57.022 45.000 0.00 0.00 0.00 3.02
211 212 2.206576 ATTGGGCTCTGGTTCTGAAC 57.793 50.000 12.05 12.05 0.00 3.18
212 213 1.140312 TTGGGCTCTGGTTCTGAACT 58.860 50.000 19.05 0.00 0.00 3.01
213 214 0.687354 TGGGCTCTGGTTCTGAACTC 59.313 55.000 19.05 10.48 0.00 3.01
214 215 0.980423 GGGCTCTGGTTCTGAACTCT 59.020 55.000 19.05 0.00 0.00 3.24
215 216 1.338579 GGGCTCTGGTTCTGAACTCTG 60.339 57.143 19.05 12.93 0.00 3.35
216 217 1.620819 GGCTCTGGTTCTGAACTCTGA 59.379 52.381 19.05 15.74 0.00 3.27
217 218 2.037772 GGCTCTGGTTCTGAACTCTGAA 59.962 50.000 19.05 1.99 0.00 3.02
218 219 3.324993 GCTCTGGTTCTGAACTCTGAAG 58.675 50.000 19.05 11.03 35.07 3.02
219 220 3.006323 GCTCTGGTTCTGAACTCTGAAGA 59.994 47.826 19.05 12.85 35.07 2.87
220 221 4.502259 GCTCTGGTTCTGAACTCTGAAGAA 60.502 45.833 19.05 0.00 35.07 2.52
221 222 5.605534 CTCTGGTTCTGAACTCTGAAGAAA 58.394 41.667 19.05 0.00 35.07 2.52
222 223 5.605534 TCTGGTTCTGAACTCTGAAGAAAG 58.394 41.667 19.05 5.01 35.07 2.62
223 224 4.708177 TGGTTCTGAACTCTGAAGAAAGG 58.292 43.478 19.05 0.00 35.07 3.11
224 225 4.164221 TGGTTCTGAACTCTGAAGAAAGGT 59.836 41.667 19.05 0.00 35.07 3.50
225 226 5.365605 TGGTTCTGAACTCTGAAGAAAGGTA 59.634 40.000 19.05 0.00 35.07 3.08
226 227 6.126883 TGGTTCTGAACTCTGAAGAAAGGTAA 60.127 38.462 19.05 0.00 35.07 2.85
227 228 6.203145 GGTTCTGAACTCTGAAGAAAGGTAAC 59.797 42.308 19.05 0.00 35.07 2.50
228 229 6.479972 TCTGAACTCTGAAGAAAGGTAACA 57.520 37.500 0.00 0.00 41.41 2.41
229 230 6.281405 TCTGAACTCTGAAGAAAGGTAACAC 58.719 40.000 0.00 0.00 41.41 3.32
230 231 5.365619 TGAACTCTGAAGAAAGGTAACACC 58.634 41.667 0.00 0.00 38.99 4.16
231 232 5.104693 TGAACTCTGAAGAAAGGTAACACCA 60.105 40.000 0.00 0.00 41.95 4.17
232 233 5.568620 ACTCTGAAGAAAGGTAACACCAT 57.431 39.130 0.00 0.00 41.95 3.55
233 234 5.941788 ACTCTGAAGAAAGGTAACACCATT 58.058 37.500 0.00 0.00 41.95 3.16
234 235 5.765182 ACTCTGAAGAAAGGTAACACCATTG 59.235 40.000 0.00 0.00 41.95 2.82
235 236 4.518970 TCTGAAGAAAGGTAACACCATTGC 59.481 41.667 0.00 0.00 41.95 3.56
236 237 4.469657 TGAAGAAAGGTAACACCATTGCT 58.530 39.130 0.00 0.00 41.95 3.91
237 238 4.278170 TGAAGAAAGGTAACACCATTGCTG 59.722 41.667 0.00 0.00 41.95 4.41
238 239 4.098914 AGAAAGGTAACACCATTGCTGA 57.901 40.909 0.00 0.00 41.95 4.26
239 240 4.074970 AGAAAGGTAACACCATTGCTGAG 58.925 43.478 0.00 0.00 41.95 3.35
240 241 3.508845 AAGGTAACACCATTGCTGAGT 57.491 42.857 0.00 0.00 41.95 3.41
241 242 4.634012 AAGGTAACACCATTGCTGAGTA 57.366 40.909 0.00 0.00 41.95 2.59
242 243 3.939066 AGGTAACACCATTGCTGAGTAC 58.061 45.455 0.00 0.00 41.95 2.73
243 244 3.326588 AGGTAACACCATTGCTGAGTACA 59.673 43.478 0.00 0.00 41.95 2.90
244 245 3.435671 GGTAACACCATTGCTGAGTACAC 59.564 47.826 0.00 0.00 38.42 2.90
245 246 2.185004 ACACCATTGCTGAGTACACC 57.815 50.000 0.00 0.00 0.00 4.16
246 247 1.078709 CACCATTGCTGAGTACACCG 58.921 55.000 0.00 0.00 0.00 4.94
247 248 0.685097 ACCATTGCTGAGTACACCGT 59.315 50.000 0.00 0.00 0.00 4.83
248 249 1.071699 ACCATTGCTGAGTACACCGTT 59.928 47.619 0.00 0.00 0.00 4.44
249 250 2.151202 CCATTGCTGAGTACACCGTTT 58.849 47.619 0.00 0.00 0.00 3.60
250 251 2.552315 CCATTGCTGAGTACACCGTTTT 59.448 45.455 0.00 0.00 0.00 2.43
251 252 3.749088 CCATTGCTGAGTACACCGTTTTA 59.251 43.478 0.00 0.00 0.00 1.52
252 253 4.142902 CCATTGCTGAGTACACCGTTTTAG 60.143 45.833 0.00 0.00 0.00 1.85
253 254 3.034721 TGCTGAGTACACCGTTTTAGG 57.965 47.619 0.00 0.00 37.30 2.69
254 255 1.730612 GCTGAGTACACCGTTTTAGGC 59.269 52.381 0.00 0.00 33.69 3.93
255 256 2.344025 CTGAGTACACCGTTTTAGGCC 58.656 52.381 0.00 0.00 33.69 5.19
256 257 1.337074 TGAGTACACCGTTTTAGGCCG 60.337 52.381 0.00 0.00 33.69 6.13
257 258 0.681175 AGTACACCGTTTTAGGCCGT 59.319 50.000 0.00 0.00 33.69 5.68
258 259 1.892474 AGTACACCGTTTTAGGCCGTA 59.108 47.619 0.00 0.00 33.69 4.02
259 260 2.094545 AGTACACCGTTTTAGGCCGTAG 60.095 50.000 0.00 0.00 33.69 3.51
266 267 1.736126 GTTTTAGGCCGTAGAAGCACC 59.264 52.381 0.00 0.00 0.00 5.01
276 277 2.541556 GTAGAAGCACCGATCTGAACC 58.458 52.381 0.00 0.00 0.00 3.62
283 284 1.065701 CACCGATCTGAACCTCGTAGG 59.934 57.143 0.00 0.03 42.49 3.18
286 287 1.134367 CGATCTGAACCTCGTAGGCAA 59.866 52.381 1.36 0.00 39.63 4.52
323 325 6.584954 CAAGTTGCCTAATCGAATAATCTCG 58.415 40.000 0.00 0.00 40.25 4.04
348 350 0.867746 TTCTGCACGCATCTTCACAC 59.132 50.000 0.00 0.00 0.00 3.82
381 383 4.655762 TCGTCCTCGATCAGAATCATTT 57.344 40.909 0.00 0.00 41.35 2.32
405 407 2.132089 TTTTCGCCCCGAAGTCCCAT 62.132 55.000 0.22 0.00 46.43 4.00
441 443 3.896317 GGATCTATCCACGCCTCAC 57.104 57.895 4.04 0.00 46.38 3.51
442 444 1.040646 GGATCTATCCACGCCTCACA 58.959 55.000 4.04 0.00 46.38 3.58
451 466 1.069022 CCACGCCTCACAATCTGTTTG 60.069 52.381 0.00 0.00 41.36 2.93
473 488 1.802636 GACGTGCACAATCCCCATG 59.197 57.895 18.64 0.00 0.00 3.66
480 495 2.281091 CAATCCCCATGGCTGGCT 59.719 61.111 6.09 0.00 41.64 4.75
511 526 4.357947 TCAGGTCACGCAGCCGAC 62.358 66.667 1.59 1.59 38.29 4.79
561 582 2.280592 GGTTGCGTCCGTCCAAGT 60.281 61.111 0.00 0.00 0.00 3.16
563 584 2.029964 TTGCGTCCGTCCAAGTCC 59.970 61.111 0.00 0.00 0.00 3.85
596 617 1.943340 CTGATCTGGATCTCGACACGA 59.057 52.381 11.23 0.00 38.60 4.35
816 1327 0.391130 GTACAAGTGAGCCATCGCCA 60.391 55.000 0.00 0.00 36.56 5.69
908 1419 0.249657 CGCTAGCTGACAATCCCTCC 60.250 60.000 13.93 0.00 0.00 4.30
925 1436 4.662961 CCGCGCACACTCCACTCA 62.663 66.667 8.75 0.00 0.00 3.41
928 1439 2.357517 CGCACACTCCACTCACCC 60.358 66.667 0.00 0.00 0.00 4.61
929 1440 2.828868 GCACACTCCACTCACCCA 59.171 61.111 0.00 0.00 0.00 4.51
931 1442 0.250901 GCACACTCCACTCACCCATT 60.251 55.000 0.00 0.00 0.00 3.16
932 1443 1.813513 CACACTCCACTCACCCATTC 58.186 55.000 0.00 0.00 0.00 2.67
933 1444 1.072173 CACACTCCACTCACCCATTCA 59.928 52.381 0.00 0.00 0.00 2.57
934 1445 1.072331 ACACTCCACTCACCCATTCAC 59.928 52.381 0.00 0.00 0.00 3.18
935 1446 0.321671 ACTCCACTCACCCATTCACG 59.678 55.000 0.00 0.00 0.00 4.35
937 1448 0.834261 TCCACTCACCCATTCACGGA 60.834 55.000 0.00 0.00 0.00 4.69
938 1449 0.673644 CCACTCACCCATTCACGGAC 60.674 60.000 0.00 0.00 0.00 4.79
939 1450 0.321671 CACTCACCCATTCACGGACT 59.678 55.000 0.00 0.00 0.00 3.85
940 1451 0.608640 ACTCACCCATTCACGGACTC 59.391 55.000 0.00 0.00 0.00 3.36
941 1452 0.898320 CTCACCCATTCACGGACTCT 59.102 55.000 0.00 0.00 0.00 3.24
942 1453 0.895530 TCACCCATTCACGGACTCTC 59.104 55.000 0.00 0.00 0.00 3.20
943 1454 0.608130 CACCCATTCACGGACTCTCA 59.392 55.000 0.00 0.00 0.00 3.27
944 1455 0.898320 ACCCATTCACGGACTCTCAG 59.102 55.000 0.00 0.00 0.00 3.35
945 1456 0.898320 CCCATTCACGGACTCTCAGT 59.102 55.000 0.00 0.00 0.00 3.41
946 1457 1.134965 CCCATTCACGGACTCTCAGTC 60.135 57.143 0.00 0.00 44.32 3.51
960 1476 1.617850 CTCAGTCCTCACTTCACTGCT 59.382 52.381 0.00 0.00 37.95 4.24
1638 2186 4.042398 GCATCGATCGCTGTTAGAGTTAA 58.958 43.478 19.11 0.00 0.00 2.01
1690 2241 7.425606 GTTCAGTTAAGGATGATTTGTGTTGT 58.574 34.615 0.00 0.00 0.00 3.32
1692 2243 5.630680 CAGTTAAGGATGATTTGTGTTGTGC 59.369 40.000 0.00 0.00 0.00 4.57
1781 2332 5.913137 TTGTGTGGAAAATGAACTTGTCT 57.087 34.783 0.00 0.00 0.00 3.41
1785 2336 5.516339 GTGTGGAAAATGAACTTGTCTTGTG 59.484 40.000 0.00 0.00 0.00 3.33
1799 2350 2.771763 CTTGTGCTCGGCGAGTTCCT 62.772 60.000 34.41 0.00 31.39 3.36
2162 2723 2.623705 GCGTTTGCCAAATCGTTTTTG 58.376 42.857 11.68 6.61 33.98 2.44
2164 2725 3.484393 GCGTTTGCCAAATCGTTTTTGTT 60.484 39.130 11.68 0.00 33.98 2.83
2165 2726 4.642953 CGTTTGCCAAATCGTTTTTGTTT 58.357 34.783 0.00 0.00 0.00 2.83
2205 2766 2.228822 CCTGTTGTTAGGTTGCATGGAC 59.771 50.000 0.00 0.00 32.99 4.02
2231 2792 3.068732 CCTGAAGATATCGAGCTGAACCA 59.931 47.826 0.00 0.00 0.00 3.67
2366 2927 1.611673 CCTTCCCATGTGTCGAGCTTT 60.612 52.381 0.00 0.00 0.00 3.51
2430 2992 0.320374 AGTTGACGGCCGAAAGATGA 59.680 50.000 35.90 0.00 0.00 2.92
2437 2999 1.804151 CGGCCGAAAGATGAAGTTGAA 59.196 47.619 24.07 0.00 0.00 2.69
2456 3020 1.025113 AAGACCGACGAGAGCGATCA 61.025 55.000 2.38 0.00 41.64 2.92
2463 3027 2.286713 CGACGAGAGCGATCATTTCTCT 60.287 50.000 2.38 9.06 41.64 3.10
2469 3033 5.516696 CGAGAGCGATCATTTCTCTGTTTTA 59.483 40.000 2.38 0.00 40.82 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.872691 CACCTCTTCTTCATGTGTGGATAC 59.127 45.833 0.00 0.00 0.00 2.24
8 9 4.532126 ACACCTCTTCTTCATGTGTGGATA 59.468 41.667 0.00 0.00 38.63 2.59
9 10 3.328931 ACACCTCTTCTTCATGTGTGGAT 59.671 43.478 0.00 0.00 38.63 3.41
10 11 2.705658 ACACCTCTTCTTCATGTGTGGA 59.294 45.455 0.00 0.00 38.63 4.02
11 12 3.131709 ACACCTCTTCTTCATGTGTGG 57.868 47.619 0.00 0.00 38.63 4.17
13 14 3.845781 ACACACCTCTTCTTCATGTGT 57.154 42.857 2.59 2.59 46.81 3.72
14 15 3.070018 GGACACACCTCTTCTTCATGTG 58.930 50.000 1.29 1.29 44.92 3.21
15 16 3.409026 GGACACACCTCTTCTTCATGT 57.591 47.619 0.00 0.00 35.41 3.21
27 28 1.609208 ACAAGAATGCAGGACACACC 58.391 50.000 0.00 0.00 39.35 4.16
28 29 3.550842 GGAAACAAGAATGCAGGACACAC 60.551 47.826 0.00 0.00 0.00 3.82
29 30 2.622942 GGAAACAAGAATGCAGGACACA 59.377 45.455 0.00 0.00 0.00 3.72
30 31 2.887152 AGGAAACAAGAATGCAGGACAC 59.113 45.455 0.00 0.00 0.00 3.67
31 32 3.228188 AGGAAACAAGAATGCAGGACA 57.772 42.857 0.00 0.00 0.00 4.02
32 33 4.590850 AAAGGAAACAAGAATGCAGGAC 57.409 40.909 0.00 0.00 0.00 3.85
33 34 4.740334 GCAAAAGGAAACAAGAATGCAGGA 60.740 41.667 0.00 0.00 33.00 3.86
34 35 3.495753 GCAAAAGGAAACAAGAATGCAGG 59.504 43.478 0.00 0.00 33.00 4.85
35 36 4.121317 TGCAAAAGGAAACAAGAATGCAG 58.879 39.130 0.00 0.00 37.61 4.41
36 37 4.134379 TGCAAAAGGAAACAAGAATGCA 57.866 36.364 0.00 0.00 39.95 3.96
37 38 5.065090 AGTTTGCAAAAGGAAACAAGAATGC 59.935 36.000 14.67 0.00 35.00 3.56
38 39 6.667007 AGTTTGCAAAAGGAAACAAGAATG 57.333 33.333 14.67 0.00 35.00 2.67
39 40 8.040727 AGTAAGTTTGCAAAAGGAAACAAGAAT 58.959 29.630 14.67 0.00 35.00 2.40
40 41 7.382898 AGTAAGTTTGCAAAAGGAAACAAGAA 58.617 30.769 14.67 0.00 35.00 2.52
41 42 6.930731 AGTAAGTTTGCAAAAGGAAACAAGA 58.069 32.000 14.67 0.00 35.00 3.02
42 43 6.811170 TGAGTAAGTTTGCAAAAGGAAACAAG 59.189 34.615 14.67 0.00 35.00 3.16
43 44 6.692486 TGAGTAAGTTTGCAAAAGGAAACAA 58.308 32.000 14.67 0.00 35.00 2.83
44 45 6.274157 TGAGTAAGTTTGCAAAAGGAAACA 57.726 33.333 14.67 8.16 35.00 2.83
45 46 6.420903 GGATGAGTAAGTTTGCAAAAGGAAAC 59.579 38.462 14.67 8.18 33.11 2.78
46 47 6.097554 TGGATGAGTAAGTTTGCAAAAGGAAA 59.902 34.615 14.67 0.00 0.00 3.13
47 48 5.596361 TGGATGAGTAAGTTTGCAAAAGGAA 59.404 36.000 14.67 0.00 0.00 3.36
48 49 5.009610 GTGGATGAGTAAGTTTGCAAAAGGA 59.990 40.000 14.67 0.00 0.00 3.36
49 50 5.221224 TGTGGATGAGTAAGTTTGCAAAAGG 60.221 40.000 14.67 0.00 0.00 3.11
50 51 5.687285 GTGTGGATGAGTAAGTTTGCAAAAG 59.313 40.000 14.67 0.00 0.00 2.27
51 52 5.359576 AGTGTGGATGAGTAAGTTTGCAAAA 59.640 36.000 14.67 0.00 0.00 2.44
52 53 4.887071 AGTGTGGATGAGTAAGTTTGCAAA 59.113 37.500 8.05 8.05 0.00 3.68
53 54 4.460263 AGTGTGGATGAGTAAGTTTGCAA 58.540 39.130 0.00 0.00 0.00 4.08
54 55 4.085357 AGTGTGGATGAGTAAGTTTGCA 57.915 40.909 0.00 0.00 0.00 4.08
55 56 4.787598 CAAGTGTGGATGAGTAAGTTTGC 58.212 43.478 0.00 0.00 0.00 3.68
70 71 4.406069 CGTTGATAGATTTGCCAAGTGTG 58.594 43.478 0.00 0.00 0.00 3.82
71 72 3.440173 CCGTTGATAGATTTGCCAAGTGT 59.560 43.478 0.00 0.00 0.00 3.55
72 73 3.440173 ACCGTTGATAGATTTGCCAAGTG 59.560 43.478 0.00 0.00 0.00 3.16
73 74 3.686016 ACCGTTGATAGATTTGCCAAGT 58.314 40.909 0.00 0.00 0.00 3.16
74 75 4.155826 TGAACCGTTGATAGATTTGCCAAG 59.844 41.667 0.00 0.00 0.00 3.61
75 76 4.075682 TGAACCGTTGATAGATTTGCCAA 58.924 39.130 0.00 0.00 0.00 4.52
76 77 3.680490 TGAACCGTTGATAGATTTGCCA 58.320 40.909 0.00 0.00 0.00 4.92
77 78 4.695217 TTGAACCGTTGATAGATTTGCC 57.305 40.909 0.00 0.00 0.00 4.52
78 79 6.321717 TGATTTGAACCGTTGATAGATTTGC 58.678 36.000 0.00 0.00 0.00 3.68
81 82 9.559732 TCATATGATTTGAACCGTTGATAGATT 57.440 29.630 0.00 0.00 0.00 2.40
82 83 8.993121 GTCATATGATTTGAACCGTTGATAGAT 58.007 33.333 9.02 0.00 0.00 1.98
83 84 7.441157 GGTCATATGATTTGAACCGTTGATAGA 59.559 37.037 9.02 0.00 0.00 1.98
84 85 7.226523 TGGTCATATGATTTGAACCGTTGATAG 59.773 37.037 9.02 0.00 29.40 2.08
85 86 7.051000 TGGTCATATGATTTGAACCGTTGATA 58.949 34.615 9.02 0.00 29.40 2.15
86 87 5.885352 TGGTCATATGATTTGAACCGTTGAT 59.115 36.000 9.02 0.00 29.40 2.57
87 88 5.249420 TGGTCATATGATTTGAACCGTTGA 58.751 37.500 9.02 0.00 29.40 3.18
88 89 5.559427 TGGTCATATGATTTGAACCGTTG 57.441 39.130 9.02 0.00 29.40 4.10
89 90 5.710099 AGTTGGTCATATGATTTGAACCGTT 59.290 36.000 9.02 0.00 29.40 4.44
90 91 5.253330 AGTTGGTCATATGATTTGAACCGT 58.747 37.500 9.02 0.00 29.40 4.83
91 92 5.818136 AGTTGGTCATATGATTTGAACCG 57.182 39.130 9.02 0.00 29.40 4.44
92 93 7.148086 TGCTTAGTTGGTCATATGATTTGAACC 60.148 37.037 9.02 5.40 29.40 3.62
93 94 7.761409 TGCTTAGTTGGTCATATGATTTGAAC 58.239 34.615 9.02 9.28 0.00 3.18
94 95 7.936496 TGCTTAGTTGGTCATATGATTTGAA 57.064 32.000 9.02 0.00 0.00 2.69
95 96 7.936496 TTGCTTAGTTGGTCATATGATTTGA 57.064 32.000 9.02 0.00 0.00 2.69
96 97 8.984891 TTTTGCTTAGTTGGTCATATGATTTG 57.015 30.769 9.02 0.00 0.00 2.32
119 120 3.025262 TGCCGTCCAAGGTTAAGTTTTT 58.975 40.909 0.00 0.00 0.00 1.94
120 121 2.657143 TGCCGTCCAAGGTTAAGTTTT 58.343 42.857 0.00 0.00 0.00 2.43
121 122 2.351706 TGCCGTCCAAGGTTAAGTTT 57.648 45.000 0.00 0.00 0.00 2.66
122 123 2.433436 GATGCCGTCCAAGGTTAAGTT 58.567 47.619 0.00 0.00 0.00 2.66
123 124 1.339727 GGATGCCGTCCAAGGTTAAGT 60.340 52.381 0.00 0.00 46.96 2.24
124 125 1.379527 GGATGCCGTCCAAGGTTAAG 58.620 55.000 0.00 0.00 46.96 1.85
125 126 3.562397 GGATGCCGTCCAAGGTTAA 57.438 52.632 0.00 0.00 46.96 2.01
134 135 0.535335 TGGTAGAACTGGATGCCGTC 59.465 55.000 0.00 0.00 0.00 4.79
135 136 0.981183 TTGGTAGAACTGGATGCCGT 59.019 50.000 0.00 0.00 0.00 5.68
136 137 2.107950 TTTGGTAGAACTGGATGCCG 57.892 50.000 0.00 0.00 0.00 5.69
137 138 3.620488 TGATTTGGTAGAACTGGATGCC 58.380 45.455 0.00 0.00 0.00 4.40
138 139 4.498682 GCATGATTTGGTAGAACTGGATGC 60.499 45.833 0.00 0.00 0.00 3.91
139 140 4.260907 CGCATGATTTGGTAGAACTGGATG 60.261 45.833 0.00 0.00 0.00 3.51
140 141 3.879295 CGCATGATTTGGTAGAACTGGAT 59.121 43.478 0.00 0.00 0.00 3.41
141 142 3.055458 TCGCATGATTTGGTAGAACTGGA 60.055 43.478 0.00 0.00 0.00 3.86
142 143 3.270027 TCGCATGATTTGGTAGAACTGG 58.730 45.455 0.00 0.00 0.00 4.00
143 144 4.024556 GGATCGCATGATTTGGTAGAACTG 60.025 45.833 0.00 0.00 34.09 3.16
144 145 4.130118 GGATCGCATGATTTGGTAGAACT 58.870 43.478 0.00 0.00 34.09 3.01
145 146 3.876914 TGGATCGCATGATTTGGTAGAAC 59.123 43.478 0.00 0.00 34.09 3.01
146 147 4.149511 TGGATCGCATGATTTGGTAGAA 57.850 40.909 0.00 0.00 34.09 2.10
147 148 3.836365 TGGATCGCATGATTTGGTAGA 57.164 42.857 0.00 0.00 34.09 2.59
148 149 3.251729 CCTTGGATCGCATGATTTGGTAG 59.748 47.826 0.00 0.00 34.09 3.18
149 150 3.213506 CCTTGGATCGCATGATTTGGTA 58.786 45.455 0.00 0.00 34.09 3.25
150 151 2.026641 CCTTGGATCGCATGATTTGGT 58.973 47.619 0.00 0.00 34.09 3.67
151 152 1.338973 CCCTTGGATCGCATGATTTGG 59.661 52.381 0.00 0.00 34.09 3.28
152 153 1.338973 CCCCTTGGATCGCATGATTTG 59.661 52.381 0.00 0.00 34.09 2.32
153 154 1.696063 CCCCTTGGATCGCATGATTT 58.304 50.000 0.00 0.00 34.09 2.17
154 155 0.178981 CCCCCTTGGATCGCATGATT 60.179 55.000 0.00 0.00 34.09 2.57
155 156 1.061905 TCCCCCTTGGATCGCATGAT 61.062 55.000 0.00 0.00 38.61 2.45
156 157 1.692395 TCCCCCTTGGATCGCATGA 60.692 57.895 0.00 0.00 38.61 3.07
157 158 1.228063 CTCCCCCTTGGATCGCATG 60.228 63.158 0.00 0.00 44.07 4.06
158 159 1.384502 TCTCCCCCTTGGATCGCAT 60.385 57.895 0.00 0.00 44.07 4.73
159 160 2.040442 TCTCCCCCTTGGATCGCA 59.960 61.111 0.00 0.00 44.07 5.10
160 161 0.759436 TACTCTCCCCCTTGGATCGC 60.759 60.000 0.00 0.00 44.07 4.58
161 162 1.041437 GTACTCTCCCCCTTGGATCG 58.959 60.000 0.00 0.00 44.07 3.69
162 163 1.344087 TGGTACTCTCCCCCTTGGATC 60.344 57.143 0.00 0.00 44.07 3.36
163 164 0.722676 TGGTACTCTCCCCCTTGGAT 59.277 55.000 0.00 0.00 44.07 3.41
164 165 0.494551 TTGGTACTCTCCCCCTTGGA 59.505 55.000 0.00 0.00 42.41 3.53
165 166 1.004394 GTTTGGTACTCTCCCCCTTGG 59.996 57.143 0.00 0.00 0.00 3.61
166 167 1.004394 GGTTTGGTACTCTCCCCCTTG 59.996 57.143 0.00 0.00 0.00 3.61
167 168 1.369403 GGTTTGGTACTCTCCCCCTT 58.631 55.000 0.00 0.00 0.00 3.95
168 169 0.549413 GGGTTTGGTACTCTCCCCCT 60.549 60.000 0.00 0.00 32.66 4.79
169 170 0.843343 TGGGTTTGGTACTCTCCCCC 60.843 60.000 11.29 7.15 37.52 5.40
170 171 1.069775 TTGGGTTTGGTACTCTCCCC 58.930 55.000 11.29 8.25 37.52 4.81
171 172 4.579647 TTATTGGGTTTGGTACTCTCCC 57.420 45.455 0.00 1.17 38.68 4.30
172 173 6.451064 CAATTATTGGGTTTGGTACTCTCC 57.549 41.667 0.00 0.00 0.00 3.71
187 188 4.272489 TCAGAACCAGAGCCCAATTATTG 58.728 43.478 0.00 0.00 0.00 1.90
188 189 4.591321 TCAGAACCAGAGCCCAATTATT 57.409 40.909 0.00 0.00 0.00 1.40
189 190 4.018050 AGTTCAGAACCAGAGCCCAATTAT 60.018 41.667 9.85 0.00 0.00 1.28
190 191 3.330701 AGTTCAGAACCAGAGCCCAATTA 59.669 43.478 9.85 0.00 0.00 1.40
191 192 2.108952 AGTTCAGAACCAGAGCCCAATT 59.891 45.455 9.85 0.00 0.00 2.32
192 193 1.707427 AGTTCAGAACCAGAGCCCAAT 59.293 47.619 9.85 0.00 0.00 3.16
193 194 1.072331 GAGTTCAGAACCAGAGCCCAA 59.928 52.381 9.85 0.00 0.00 4.12
194 195 0.687354 GAGTTCAGAACCAGAGCCCA 59.313 55.000 9.85 0.00 0.00 5.36
195 196 0.980423 AGAGTTCAGAACCAGAGCCC 59.020 55.000 9.85 0.00 0.00 5.19
196 197 1.620819 TCAGAGTTCAGAACCAGAGCC 59.379 52.381 9.85 0.00 0.00 4.70
197 198 3.006323 TCTTCAGAGTTCAGAACCAGAGC 59.994 47.826 9.85 0.00 0.00 4.09
198 199 4.862902 TCTTCAGAGTTCAGAACCAGAG 57.137 45.455 9.85 2.22 0.00 3.35
199 200 5.453903 CCTTTCTTCAGAGTTCAGAACCAGA 60.454 44.000 9.85 3.01 0.00 3.86
200 201 4.754114 CCTTTCTTCAGAGTTCAGAACCAG 59.246 45.833 9.85 0.59 0.00 4.00
201 202 4.164221 ACCTTTCTTCAGAGTTCAGAACCA 59.836 41.667 9.85 0.00 0.00 3.67
202 203 4.709250 ACCTTTCTTCAGAGTTCAGAACC 58.291 43.478 9.85 1.94 0.00 3.62
203 204 6.761714 TGTTACCTTTCTTCAGAGTTCAGAAC 59.238 38.462 5.00 5.00 0.00 3.01
204 205 6.761714 GTGTTACCTTTCTTCAGAGTTCAGAA 59.238 38.462 0.00 0.00 0.00 3.02
205 206 6.281405 GTGTTACCTTTCTTCAGAGTTCAGA 58.719 40.000 0.00 0.00 0.00 3.27
206 207 5.467063 GGTGTTACCTTTCTTCAGAGTTCAG 59.533 44.000 0.00 0.00 34.73 3.02
207 208 5.104693 TGGTGTTACCTTTCTTCAGAGTTCA 60.105 40.000 0.00 0.00 39.58 3.18
208 209 5.365619 TGGTGTTACCTTTCTTCAGAGTTC 58.634 41.667 0.00 0.00 39.58 3.01
209 210 5.367945 TGGTGTTACCTTTCTTCAGAGTT 57.632 39.130 0.00 0.00 39.58 3.01
210 211 5.568620 ATGGTGTTACCTTTCTTCAGAGT 57.431 39.130 0.00 0.00 39.58 3.24
211 212 5.335191 GCAATGGTGTTACCTTTCTTCAGAG 60.335 44.000 0.00 0.00 39.58 3.35
212 213 4.518970 GCAATGGTGTTACCTTTCTTCAGA 59.481 41.667 0.00 0.00 39.58 3.27
213 214 4.520492 AGCAATGGTGTTACCTTTCTTCAG 59.480 41.667 0.00 0.00 39.58 3.02
214 215 4.278170 CAGCAATGGTGTTACCTTTCTTCA 59.722 41.667 3.99 0.00 39.58 3.02
215 216 4.518970 TCAGCAATGGTGTTACCTTTCTTC 59.481 41.667 12.41 0.00 39.58 2.87
216 217 4.469657 TCAGCAATGGTGTTACCTTTCTT 58.530 39.130 12.41 0.00 39.58 2.52
217 218 4.074970 CTCAGCAATGGTGTTACCTTTCT 58.925 43.478 12.41 0.00 39.58 2.52
218 219 3.821033 ACTCAGCAATGGTGTTACCTTTC 59.179 43.478 12.41 0.00 39.58 2.62
219 220 3.832527 ACTCAGCAATGGTGTTACCTTT 58.167 40.909 12.41 0.00 39.58 3.11
220 221 3.508845 ACTCAGCAATGGTGTTACCTT 57.491 42.857 12.41 0.00 39.58 3.50
221 222 3.326588 TGTACTCAGCAATGGTGTTACCT 59.673 43.478 12.41 0.00 39.58 3.08
222 223 3.435671 GTGTACTCAGCAATGGTGTTACC 59.564 47.826 12.41 6.17 39.22 2.85
223 224 3.435671 GGTGTACTCAGCAATGGTGTTAC 59.564 47.826 12.41 14.08 41.16 2.50
224 225 3.670625 GGTGTACTCAGCAATGGTGTTA 58.329 45.455 12.41 2.75 41.16 2.41
225 226 2.504367 GGTGTACTCAGCAATGGTGTT 58.496 47.619 12.41 3.69 41.16 3.32
226 227 1.608025 CGGTGTACTCAGCAATGGTGT 60.608 52.381 12.41 0.00 41.52 4.16
227 228 1.078709 CGGTGTACTCAGCAATGGTG 58.921 55.000 6.03 6.03 41.52 4.17
228 229 0.685097 ACGGTGTACTCAGCAATGGT 59.315 50.000 0.00 0.00 41.52 3.55
229 230 1.808411 AACGGTGTACTCAGCAATGG 58.192 50.000 0.00 0.00 41.52 3.16
230 231 3.896648 AAAACGGTGTACTCAGCAATG 57.103 42.857 0.00 0.00 41.52 2.82
231 232 4.000988 CCTAAAACGGTGTACTCAGCAAT 58.999 43.478 0.00 0.00 41.52 3.56
232 233 3.395639 CCTAAAACGGTGTACTCAGCAA 58.604 45.455 0.00 0.00 41.52 3.91
233 234 2.868839 GCCTAAAACGGTGTACTCAGCA 60.869 50.000 0.00 0.00 41.52 4.41
234 235 1.730612 GCCTAAAACGGTGTACTCAGC 59.269 52.381 0.00 0.00 38.52 4.26
235 236 2.344025 GGCCTAAAACGGTGTACTCAG 58.656 52.381 0.00 0.00 0.00 3.35
236 237 1.337074 CGGCCTAAAACGGTGTACTCA 60.337 52.381 0.00 0.00 0.00 3.41
237 238 1.337167 ACGGCCTAAAACGGTGTACTC 60.337 52.381 0.00 0.00 0.00 2.59
238 239 0.681175 ACGGCCTAAAACGGTGTACT 59.319 50.000 0.00 0.00 0.00 2.73
239 240 2.094752 TCTACGGCCTAAAACGGTGTAC 60.095 50.000 0.00 0.00 0.00 2.90
240 241 2.166829 TCTACGGCCTAAAACGGTGTA 58.833 47.619 0.00 0.00 0.00 2.90
241 242 0.968405 TCTACGGCCTAAAACGGTGT 59.032 50.000 0.00 0.00 0.00 4.16
242 243 1.997606 CTTCTACGGCCTAAAACGGTG 59.002 52.381 0.00 0.00 0.00 4.94
243 244 1.673923 GCTTCTACGGCCTAAAACGGT 60.674 52.381 0.00 0.00 0.00 4.83
244 245 1.004595 GCTTCTACGGCCTAAAACGG 58.995 55.000 0.00 0.00 0.00 4.44
245 246 1.392510 GTGCTTCTACGGCCTAAAACG 59.607 52.381 0.00 0.00 0.00 3.60
246 247 1.736126 GGTGCTTCTACGGCCTAAAAC 59.264 52.381 0.00 0.00 0.00 2.43
247 248 1.673626 CGGTGCTTCTACGGCCTAAAA 60.674 52.381 0.00 0.00 0.00 1.52
248 249 0.108520 CGGTGCTTCTACGGCCTAAA 60.109 55.000 0.00 0.00 0.00 1.85
249 250 0.966875 TCGGTGCTTCTACGGCCTAA 60.967 55.000 0.00 0.00 0.00 2.69
250 251 0.754217 ATCGGTGCTTCTACGGCCTA 60.754 55.000 0.00 0.00 0.00 3.93
251 252 2.017559 GATCGGTGCTTCTACGGCCT 62.018 60.000 0.00 0.00 0.00 5.19
252 253 1.591863 GATCGGTGCTTCTACGGCC 60.592 63.158 0.00 0.00 0.00 6.13
253 254 0.872021 CAGATCGGTGCTTCTACGGC 60.872 60.000 0.00 0.00 0.00 5.68
254 255 0.738975 TCAGATCGGTGCTTCTACGG 59.261 55.000 0.00 0.00 0.00 4.02
255 256 2.186076 GTTCAGATCGGTGCTTCTACG 58.814 52.381 0.00 0.00 0.00 3.51
256 257 2.166664 AGGTTCAGATCGGTGCTTCTAC 59.833 50.000 0.00 0.00 0.00 2.59
257 258 2.427453 GAGGTTCAGATCGGTGCTTCTA 59.573 50.000 0.00 0.00 0.00 2.10
258 259 1.205893 GAGGTTCAGATCGGTGCTTCT 59.794 52.381 0.00 0.00 0.00 2.85
259 260 1.646189 GAGGTTCAGATCGGTGCTTC 58.354 55.000 0.00 0.00 0.00 3.86
266 267 0.738975 TGCCTACGAGGTTCAGATCG 59.261 55.000 0.00 0.00 44.36 3.69
276 277 1.344942 GACGTGCTGTTGCCTACGAG 61.345 60.000 0.00 0.00 39.82 4.18
283 284 0.164647 CTTGCTAGACGTGCTGTTGC 59.835 55.000 0.00 0.00 40.20 4.17
286 287 1.502231 CAACTTGCTAGACGTGCTGT 58.498 50.000 1.04 0.00 0.00 4.40
323 325 3.181507 TGAAGATGCGTGCAGAAAATAGC 60.182 43.478 0.00 0.00 0.00 2.97
381 383 0.247185 ACTTCGGGGCGAAAATACGA 59.753 50.000 0.00 0.00 45.23 3.43
405 407 2.061848 TCCAAGACCAAGTTGATGGGA 58.938 47.619 3.87 0.00 45.18 4.37
440 442 0.534203 ACGTCGGGCAAACAGATTGT 60.534 50.000 0.00 0.00 41.32 2.71
441 443 0.110238 CACGTCGGGCAAACAGATTG 60.110 55.000 0.00 0.00 42.21 2.67
442 444 1.852067 GCACGTCGGGCAAACAGATT 61.852 55.000 16.15 0.00 0.00 2.40
451 466 3.799755 GGATTGTGCACGTCGGGC 61.800 66.667 13.87 13.87 0.00 6.13
748 777 1.900016 ACAGCTCGTGTACGGGTGA 60.900 57.895 22.25 0.00 42.89 4.02
777 806 1.303236 CGTTGATGTTGGGGCCTCA 60.303 57.895 0.00 0.00 0.00 3.86
781 810 1.084289 GTACTCGTTGATGTTGGGGC 58.916 55.000 0.00 0.00 0.00 5.80
908 1419 4.662961 TGAGTGGAGTGTGCGCGG 62.663 66.667 8.83 0.00 0.00 6.46
924 1435 0.608130 TGAGAGTCCGTGAATGGGTG 59.392 55.000 0.00 0.00 0.00 4.61
925 1436 0.898320 CTGAGAGTCCGTGAATGGGT 59.102 55.000 0.00 0.00 0.00 4.51
937 1448 2.890311 CAGTGAAGTGAGGACTGAGAGT 59.110 50.000 0.00 0.00 39.64 3.24
938 1449 2.352617 GCAGTGAAGTGAGGACTGAGAG 60.353 54.545 0.00 0.00 39.64 3.20
939 1450 1.615883 GCAGTGAAGTGAGGACTGAGA 59.384 52.381 0.00 0.00 39.64 3.27
940 1451 1.617850 AGCAGTGAAGTGAGGACTGAG 59.382 52.381 0.00 0.00 39.64 3.35
941 1452 1.615883 GAGCAGTGAAGTGAGGACTGA 59.384 52.381 0.00 0.00 39.64 3.41
942 1453 1.342496 TGAGCAGTGAAGTGAGGACTG 59.658 52.381 0.00 0.00 40.14 3.51
943 1454 1.342819 GTGAGCAGTGAAGTGAGGACT 59.657 52.381 0.00 0.00 0.00 3.85
944 1455 1.342819 AGTGAGCAGTGAAGTGAGGAC 59.657 52.381 0.00 0.00 0.00 3.85
945 1456 1.342496 CAGTGAGCAGTGAAGTGAGGA 59.658 52.381 0.00 0.00 33.67 3.71
946 1457 1.793258 CAGTGAGCAGTGAAGTGAGG 58.207 55.000 0.00 0.00 33.67 3.86
960 1476 0.108186 CCAGTAATGGCGAGCAGTGA 60.108 55.000 0.00 0.00 0.00 3.41
1626 2174 9.224058 GCTAGATCGTACTTTTAACTCTAACAG 57.776 37.037 0.00 0.00 0.00 3.16
1663 2214 6.306987 ACACAAATCATCCTTAACTGAACCT 58.693 36.000 0.00 0.00 0.00 3.50
1728 2279 2.221749 CACGTCACCACATGAGTTTCTG 59.778 50.000 0.00 0.00 38.28 3.02
1781 2332 1.529152 TAGGAACTCGCCGAGCACAA 61.529 55.000 15.20 0.00 41.75 3.33
1785 2336 0.525882 GAAGTAGGAACTCGCCGAGC 60.526 60.000 15.20 0.00 41.75 5.03
1799 2350 2.322658 ACAAGTTCACCCTCGGAAGTA 58.677 47.619 0.00 0.00 0.00 2.24
1927 2487 8.110860 AGTACCATTTTCAACTTAGTTCATGG 57.889 34.615 15.23 15.23 0.00 3.66
2060 2620 0.457166 CACGCGTTGGAATACCGAGA 60.457 55.000 10.22 0.00 39.42 4.04
2155 2716 7.800847 ACAATTGGAGAAAACAAAACAAAAACG 59.199 29.630 10.83 0.00 0.00 3.60
2156 2717 9.112789 GACAATTGGAGAAAACAAAACAAAAAC 57.887 29.630 10.83 0.00 0.00 2.43
2162 2723 6.035975 CAGGTGACAATTGGAGAAAACAAAAC 59.964 38.462 10.83 0.00 0.00 2.43
2164 2725 5.186797 ACAGGTGACAATTGGAGAAAACAAA 59.813 36.000 10.83 0.00 0.00 2.83
2165 2726 4.709397 ACAGGTGACAATTGGAGAAAACAA 59.291 37.500 10.83 0.00 0.00 2.83
2205 2766 3.068732 TCAGCTCGATATCTTCAGGGTTG 59.931 47.826 0.34 0.00 0.00 3.77
2315 2876 2.774687 CCCTTGTACGCCTACTTTGTT 58.225 47.619 0.00 0.00 0.00 2.83
2411 2972 0.320374 TCATCTTTCGGCCGTCAACT 59.680 50.000 27.15 5.71 0.00 3.16
2430 2992 2.862921 GCTCTCGTCGGTCTTTCAACTT 60.863 50.000 0.00 0.00 0.00 2.66
2437 2999 1.025113 TGATCGCTCTCGTCGGTCTT 61.025 55.000 0.00 0.00 37.89 3.01
2521 3088 6.352222 CCAGTTTACAGAACCATGGTATCTCT 60.352 42.308 20.12 14.97 0.00 3.10


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

AutoCloner maintained by Alex Coulton.