Multiple sequence alignment - TraesCS1A01G037000

Loading Multiple Alignment...

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 TraesCS1A01G037000 chr1A 100.000 3845 0 0 1 3845 20864534 20868378 0.000000e+00 7101
1 TraesCS1A01G037000 chr3B 95.843 3632 151 0 214 3845 793013416 793009785 0.000000e+00 5871
2 TraesCS1A01G037000 chr4B 95.595 3632 152 1 214 3845 642782231 642785854 0.000000e+00 5814
3 TraesCS1A01G037000 chr2A 96.497 1713 60 0 2133 3845 735302072 735300360 0.000000e+00 2832
4 TraesCS1A01G037000 chr6D 97.302 556 15 0 3290 3845 89075004 89075559 0.000000e+00 944
5 TraesCS1A01G037000 chrUn 96.681 452 15 0 2913 3364 475724708 475724257 0.000000e+00 752
6 TraesCS1A01G037000 chrUn 91.981 212 13 1 3 210 10323253 10323042 1.040000e-75 294
7 TraesCS1A01G037000 chrUn 91.981 212 13 1 3 210 328152367 328152156 1.040000e-75 294
8 TraesCS1A01G037000 chr5D 84.698 745 110 3 3103 3845 526755145 526755887 0.000000e+00 741


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 TraesCS1A01G037000 chr1A 20864534 20868378 3844 False 7101 7101 100.000 1 3845 1 chr1A.!!$F1 3844
1 TraesCS1A01G037000 chr3B 793009785 793013416 3631 True 5871 5871 95.843 214 3845 1 chr3B.!!$R1 3631
2 TraesCS1A01G037000 chr4B 642782231 642785854 3623 False 5814 5814 95.595 214 3845 1 chr4B.!!$F1 3631
3 TraesCS1A01G037000 chr2A 735300360 735302072 1712 True 2832 2832 96.497 2133 3845 1 chr2A.!!$R1 1712
4 TraesCS1A01G037000 chr6D 89075004 89075559 555 False 944 944 97.302 3290 3845 1 chr6D.!!$F1 555
5 TraesCS1A01G037000 chr5D 526755145 526755887 742 False 741 741 84.698 3103 3845 1 chr5D.!!$F1 742

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
141 142 0.534412 GCTCTGCACTAAGAGGAGCA 59.466 55.0 14.85 0.00 45.79 4.26 F
1170 1171 0.173708 CGTGGTCTAGAAGAGTGGGC 59.826 60.0 0.00 0.00 0.00 5.36 F
1911 1912 0.447801 GCCGTCTATGTGCACCAAAG 59.552 55.0 15.69 9.05 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1372 0.179116 CGACAGTGAGAGAGCCCATG 60.179 60.0 0.00 0.0 0.0 3.66 R
1973 1974 0.251297 CAAGTGGCCCTCAACATGGA 60.251 55.0 0.00 0.0 0.0 3.41 R
3484 3493 0.602106 ATGCAGCGATGAGGATTCCG 60.602 55.0 4.02 0.0 0.0 4.30 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
22 23 5.091261 AGTGATGGTCTGACAGAAATACC 57.909 43.478 6.76 5.41 0.00 2.73
23 24 3.865745 GTGATGGTCTGACAGAAATACCG 59.134 47.826 6.76 0.00 32.69 4.02
24 25 3.513912 TGATGGTCTGACAGAAATACCGT 59.486 43.478 6.76 6.10 32.69 4.83
25 26 4.707934 TGATGGTCTGACAGAAATACCGTA 59.292 41.667 6.76 0.00 32.69 4.02
26 27 5.362717 TGATGGTCTGACAGAAATACCGTAT 59.637 40.000 6.76 0.00 32.69 3.06
27 28 5.670792 TGGTCTGACAGAAATACCGTATT 57.329 39.130 6.76 0.00 32.69 1.89
28 29 6.045072 TGGTCTGACAGAAATACCGTATTT 57.955 37.500 15.01 15.01 40.84 1.40
41 42 9.247126 GAAATACCGTATTTCTCTTTAGACTCC 57.753 37.037 26.58 5.99 46.53 3.85
42 43 7.893124 ATACCGTATTTCTCTTTAGACTCCA 57.107 36.000 0.00 0.00 0.00 3.86
43 44 6.210287 ACCGTATTTCTCTTTAGACTCCAG 57.790 41.667 0.00 0.00 0.00 3.86
44 45 5.044558 CCGTATTTCTCTTTAGACTCCAGC 58.955 45.833 0.00 0.00 0.00 4.85
45 46 5.394224 CCGTATTTCTCTTTAGACTCCAGCA 60.394 44.000 0.00 0.00 0.00 4.41
46 47 5.746245 CGTATTTCTCTTTAGACTCCAGCAG 59.254 44.000 0.00 0.00 0.00 4.24
47 48 4.543590 TTTCTCTTTAGACTCCAGCAGG 57.456 45.455 0.00 0.00 0.00 4.85
48 49 3.458044 TCTCTTTAGACTCCAGCAGGA 57.542 47.619 0.00 0.00 43.21 3.86
49 50 3.779444 TCTCTTTAGACTCCAGCAGGAA 58.221 45.455 0.00 0.00 45.19 3.36
50 51 3.766591 TCTCTTTAGACTCCAGCAGGAAG 59.233 47.826 0.00 0.00 45.19 3.46
51 52 3.511477 TCTTTAGACTCCAGCAGGAAGT 58.489 45.455 0.00 0.00 45.19 3.01
52 53 4.673968 TCTTTAGACTCCAGCAGGAAGTA 58.326 43.478 0.00 0.00 45.19 2.24
53 54 5.273208 TCTTTAGACTCCAGCAGGAAGTAT 58.727 41.667 0.00 0.14 45.19 2.12
54 55 5.721960 TCTTTAGACTCCAGCAGGAAGTATT 59.278 40.000 0.00 0.00 45.19 1.89
55 56 6.213600 TCTTTAGACTCCAGCAGGAAGTATTT 59.786 38.462 0.00 0.00 45.19 1.40
56 57 4.479786 AGACTCCAGCAGGAAGTATTTC 57.520 45.455 0.00 0.00 45.19 2.17
57 58 4.100373 AGACTCCAGCAGGAAGTATTTCT 58.900 43.478 0.00 0.00 45.19 2.52
58 59 5.273208 AGACTCCAGCAGGAAGTATTTCTA 58.727 41.667 0.00 0.00 45.19 2.10
59 60 5.902431 AGACTCCAGCAGGAAGTATTTCTAT 59.098 40.000 0.00 0.00 45.19 1.98
60 61 6.385467 AGACTCCAGCAGGAAGTATTTCTATT 59.615 38.462 0.00 0.00 45.19 1.73
61 62 6.963322 ACTCCAGCAGGAAGTATTTCTATTT 58.037 36.000 0.00 0.00 45.19 1.40
62 63 7.051000 ACTCCAGCAGGAAGTATTTCTATTTC 58.949 38.462 0.00 0.00 45.19 2.17
63 64 6.049149 TCCAGCAGGAAGTATTTCTATTTCG 58.951 40.000 0.00 0.00 42.23 3.46
64 65 5.237344 CCAGCAGGAAGTATTTCTATTTCGG 59.763 44.000 0.00 0.00 36.89 4.30
65 66 5.237344 CAGCAGGAAGTATTTCTATTTCGGG 59.763 44.000 0.00 0.00 33.68 5.14
66 67 5.130477 AGCAGGAAGTATTTCTATTTCGGGA 59.870 40.000 0.00 0.00 33.68 5.14
67 68 5.467063 GCAGGAAGTATTTCTATTTCGGGAG 59.533 44.000 0.00 0.00 33.68 4.30
68 69 5.992217 CAGGAAGTATTTCTATTTCGGGAGG 59.008 44.000 0.00 0.00 33.68 4.30
69 70 5.071923 AGGAAGTATTTCTATTTCGGGAGGG 59.928 44.000 0.00 0.00 33.68 4.30
70 71 4.976540 AGTATTTCTATTTCGGGAGGGG 57.023 45.455 0.00 0.00 0.00 4.79
71 72 4.563782 AGTATTTCTATTTCGGGAGGGGA 58.436 43.478 0.00 0.00 0.00 4.81
72 73 4.593634 AGTATTTCTATTTCGGGAGGGGAG 59.406 45.833 0.00 0.00 0.00 4.30
73 74 2.563039 TTCTATTTCGGGAGGGGAGT 57.437 50.000 0.00 0.00 0.00 3.85
74 75 2.563039 TCTATTTCGGGAGGGGAGTT 57.437 50.000 0.00 0.00 0.00 3.01
75 76 2.841795 TCTATTTCGGGAGGGGAGTTT 58.158 47.619 0.00 0.00 0.00 2.66
76 77 2.770232 TCTATTTCGGGAGGGGAGTTTC 59.230 50.000 0.00 0.00 0.00 2.78
77 78 1.670059 ATTTCGGGAGGGGAGTTTCT 58.330 50.000 0.00 0.00 0.00 2.52
78 79 1.441695 TTTCGGGAGGGGAGTTTCTT 58.558 50.000 0.00 0.00 0.00 2.52
79 80 2.330661 TTCGGGAGGGGAGTTTCTTA 57.669 50.000 0.00 0.00 0.00 2.10
80 81 2.330661 TCGGGAGGGGAGTTTCTTAA 57.669 50.000 0.00 0.00 0.00 1.85
81 82 2.623352 TCGGGAGGGGAGTTTCTTAAA 58.377 47.619 0.00 0.00 0.00 1.52
82 83 3.187112 TCGGGAGGGGAGTTTCTTAAAT 58.813 45.455 0.00 0.00 0.00 1.40
83 84 3.199289 TCGGGAGGGGAGTTTCTTAAATC 59.801 47.826 0.00 0.00 0.00 2.17
84 85 3.684697 CGGGAGGGGAGTTTCTTAAATCC 60.685 52.174 0.00 0.00 45.55 3.01
85 86 3.542648 GGAGGGGAGTTTCTTAAATCCG 58.457 50.000 0.00 0.00 46.87 4.18
86 87 3.054582 GGAGGGGAGTTTCTTAAATCCGT 60.055 47.826 0.00 0.00 46.87 4.69
87 88 4.567116 GGAGGGGAGTTTCTTAAATCCGTT 60.567 45.833 0.00 0.00 46.87 4.44
88 89 4.994282 AGGGGAGTTTCTTAAATCCGTTT 58.006 39.130 0.00 0.00 46.87 3.60
89 90 5.008331 AGGGGAGTTTCTTAAATCCGTTTC 58.992 41.667 0.00 0.00 46.87 2.78
90 91 4.157289 GGGGAGTTTCTTAAATCCGTTTCC 59.843 45.833 0.00 0.00 46.87 3.13
91 92 5.008331 GGGAGTTTCTTAAATCCGTTTCCT 58.992 41.667 0.00 0.00 46.87 3.36
92 93 5.106277 GGGAGTTTCTTAAATCCGTTTCCTG 60.106 44.000 0.00 0.00 46.87 3.86
93 94 5.704053 GGAGTTTCTTAAATCCGTTTCCTGA 59.296 40.000 0.00 0.00 38.59 3.86
94 95 6.374613 GGAGTTTCTTAAATCCGTTTCCTGAT 59.625 38.462 0.00 0.00 38.59 2.90
95 96 7.379098 AGTTTCTTAAATCCGTTTCCTGATC 57.621 36.000 0.00 0.00 0.00 2.92
96 97 6.374613 AGTTTCTTAAATCCGTTTCCTGATCC 59.625 38.462 0.00 0.00 0.00 3.36
97 98 5.693769 TCTTAAATCCGTTTCCTGATCCT 57.306 39.130 0.00 0.00 0.00 3.24
98 99 5.671493 TCTTAAATCCGTTTCCTGATCCTC 58.329 41.667 0.00 0.00 0.00 3.71
99 100 2.604046 AATCCGTTTCCTGATCCTCG 57.396 50.000 0.00 0.00 0.00 4.63
100 101 1.486211 ATCCGTTTCCTGATCCTCGT 58.514 50.000 0.00 0.00 0.00 4.18
101 102 1.263356 TCCGTTTCCTGATCCTCGTT 58.737 50.000 0.00 0.00 0.00 3.85
102 103 1.621814 TCCGTTTCCTGATCCTCGTTT 59.378 47.619 0.00 0.00 0.00 3.60
103 104 2.000447 CCGTTTCCTGATCCTCGTTTC 59.000 52.381 0.00 0.00 0.00 2.78
104 105 2.353803 CCGTTTCCTGATCCTCGTTTCT 60.354 50.000 0.00 0.00 0.00 2.52
105 106 2.668457 CGTTTCCTGATCCTCGTTTCTG 59.332 50.000 0.00 0.00 0.00 3.02
106 107 3.614150 CGTTTCCTGATCCTCGTTTCTGA 60.614 47.826 0.00 0.00 0.00 3.27
107 108 4.315803 GTTTCCTGATCCTCGTTTCTGAA 58.684 43.478 0.00 0.00 0.00 3.02
108 109 4.617253 TTCCTGATCCTCGTTTCTGAAA 57.383 40.909 0.00 0.00 0.00 2.69
109 110 4.193826 TCCTGATCCTCGTTTCTGAAAG 57.806 45.455 2.48 0.00 0.00 2.62
110 111 2.675348 CCTGATCCTCGTTTCTGAAAGC 59.325 50.000 2.48 0.00 0.00 3.51
111 112 2.675348 CTGATCCTCGTTTCTGAAAGCC 59.325 50.000 2.48 0.00 0.00 4.35
112 113 2.038426 TGATCCTCGTTTCTGAAAGCCA 59.962 45.455 2.48 0.00 0.00 4.75
113 114 2.631160 TCCTCGTTTCTGAAAGCCAA 57.369 45.000 2.48 0.00 0.00 4.52
114 115 3.140325 TCCTCGTTTCTGAAAGCCAAT 57.860 42.857 2.48 0.00 0.00 3.16
115 116 4.280436 TCCTCGTTTCTGAAAGCCAATA 57.720 40.909 2.48 0.00 0.00 1.90
116 117 4.843728 TCCTCGTTTCTGAAAGCCAATAT 58.156 39.130 2.48 0.00 0.00 1.28
117 118 5.984725 TCCTCGTTTCTGAAAGCCAATATA 58.015 37.500 2.48 0.00 0.00 0.86
118 119 6.049149 TCCTCGTTTCTGAAAGCCAATATAG 58.951 40.000 2.48 0.00 0.00 1.31
119 120 5.277538 CCTCGTTTCTGAAAGCCAATATAGC 60.278 44.000 2.48 0.00 0.00 2.97
120 121 5.182487 TCGTTTCTGAAAGCCAATATAGCA 58.818 37.500 2.48 0.00 0.00 3.49
121 122 5.645929 TCGTTTCTGAAAGCCAATATAGCAA 59.354 36.000 2.48 0.00 0.00 3.91
122 123 5.967674 CGTTTCTGAAAGCCAATATAGCAAG 59.032 40.000 2.48 0.00 0.00 4.01
123 124 5.505173 TTCTGAAAGCCAATATAGCAAGC 57.495 39.130 0.94 0.00 0.00 4.01
124 125 4.785301 TCTGAAAGCCAATATAGCAAGCT 58.215 39.130 0.00 0.00 34.64 3.74
125 126 4.818546 TCTGAAAGCCAATATAGCAAGCTC 59.181 41.667 0.00 0.00 32.19 4.09
126 127 4.785301 TGAAAGCCAATATAGCAAGCTCT 58.215 39.130 0.00 0.00 32.19 4.09
127 128 4.577693 TGAAAGCCAATATAGCAAGCTCTG 59.422 41.667 0.00 0.00 32.19 3.35
139 140 2.891112 CAAGCTCTGCACTAAGAGGAG 58.109 52.381 3.19 0.00 43.37 3.69
140 141 0.823460 AGCTCTGCACTAAGAGGAGC 59.177 55.000 12.54 12.54 46.54 4.70
141 142 0.534412 GCTCTGCACTAAGAGGAGCA 59.466 55.000 14.85 0.00 45.79 4.26
142 143 1.066573 GCTCTGCACTAAGAGGAGCAA 60.067 52.381 14.85 0.00 45.79 3.91
143 144 2.615869 CTCTGCACTAAGAGGAGCAAC 58.384 52.381 0.00 0.00 40.11 4.17
144 145 2.233431 CTCTGCACTAAGAGGAGCAACT 59.767 50.000 0.00 0.00 40.11 3.16
145 146 2.634940 TCTGCACTAAGAGGAGCAACTT 59.365 45.455 0.00 0.00 36.44 2.66
146 147 3.832490 TCTGCACTAAGAGGAGCAACTTA 59.168 43.478 0.00 0.00 36.44 2.24
147 148 3.926616 TGCACTAAGAGGAGCAACTTAC 58.073 45.455 0.00 0.00 33.48 2.34
148 149 3.578716 TGCACTAAGAGGAGCAACTTACT 59.421 43.478 0.00 0.00 33.48 2.24
149 150 3.929610 GCACTAAGAGGAGCAACTTACTG 59.070 47.826 0.00 0.00 0.00 2.74
150 151 3.929610 CACTAAGAGGAGCAACTTACTGC 59.070 47.826 0.00 0.00 42.97 4.40
162 163 6.737254 GCAACTTACTGCTTTACTATGGAA 57.263 37.500 0.00 0.00 39.34 3.53
163 164 7.321745 GCAACTTACTGCTTTACTATGGAAT 57.678 36.000 0.00 0.00 39.34 3.01
164 165 7.189512 GCAACTTACTGCTTTACTATGGAATG 58.810 38.462 0.00 0.00 39.34 2.67
165 166 7.065803 GCAACTTACTGCTTTACTATGGAATGA 59.934 37.037 0.00 0.00 39.34 2.57
166 167 8.946085 CAACTTACTGCTTTACTATGGAATGAA 58.054 33.333 0.00 0.00 0.00 2.57
167 168 9.515226 AACTTACTGCTTTACTATGGAATGAAA 57.485 29.630 0.00 0.00 0.00 2.69
168 169 9.515226 ACTTACTGCTTTACTATGGAATGAAAA 57.485 29.630 0.00 0.00 0.00 2.29
171 172 7.305474 ACTGCTTTACTATGGAATGAAAAACG 58.695 34.615 0.00 0.00 0.00 3.60
172 173 7.040686 ACTGCTTTACTATGGAATGAAAAACGT 60.041 33.333 0.00 0.00 0.00 3.99
173 174 7.653647 TGCTTTACTATGGAATGAAAAACGTT 58.346 30.769 0.00 0.00 0.00 3.99
174 175 8.138712 TGCTTTACTATGGAATGAAAAACGTTT 58.861 29.630 7.96 7.96 0.00 3.60
175 176 9.615295 GCTTTACTATGGAATGAAAAACGTTTA 57.385 29.630 15.03 0.00 0.00 2.01
178 179 9.615295 TTACTATGGAATGAAAAACGTTTAAGC 57.385 29.630 15.03 7.31 0.00 3.09
179 180 6.799925 ACTATGGAATGAAAAACGTTTAAGCG 59.200 34.615 15.03 10.36 37.94 4.68
180 181 5.171147 TGGAATGAAAAACGTTTAAGCGA 57.829 34.783 18.96 0.00 35.59 4.93
181 182 5.764131 TGGAATGAAAAACGTTTAAGCGAT 58.236 33.333 18.96 3.36 35.59 4.58
182 183 6.210078 TGGAATGAAAAACGTTTAAGCGATT 58.790 32.000 18.96 10.07 35.59 3.34
183 184 6.361214 TGGAATGAAAAACGTTTAAGCGATTC 59.639 34.615 18.96 17.20 35.59 2.52
184 185 6.183359 GGAATGAAAAACGTTTAAGCGATTCC 60.183 38.462 18.96 19.54 35.59 3.01
185 186 4.538917 TGAAAAACGTTTAAGCGATTCCC 58.461 39.130 18.96 8.59 35.59 3.97
186 187 2.886587 AAACGTTTAAGCGATTCCCG 57.113 45.000 18.96 0.00 42.21 5.14
187 188 1.799544 AACGTTTAAGCGATTCCCGT 58.200 45.000 18.96 0.00 41.15 5.28
188 189 1.799544 ACGTTTAAGCGATTCCCGTT 58.200 45.000 18.96 0.00 41.15 4.44
189 190 2.958213 ACGTTTAAGCGATTCCCGTTA 58.042 42.857 18.96 0.00 41.15 3.18
190 191 2.925563 ACGTTTAAGCGATTCCCGTTAG 59.074 45.455 18.96 0.00 41.15 2.34
191 192 2.925563 CGTTTAAGCGATTCCCGTTAGT 59.074 45.455 5.72 0.00 41.15 2.24
192 193 3.241868 CGTTTAAGCGATTCCCGTTAGTG 60.242 47.826 5.72 0.00 41.15 2.74
193 194 3.598019 TTAAGCGATTCCCGTTAGTGT 57.402 42.857 0.00 0.00 41.15 3.55
194 195 2.467566 AAGCGATTCCCGTTAGTGTT 57.532 45.000 0.00 0.00 41.15 3.32
195 196 2.005971 AGCGATTCCCGTTAGTGTTC 57.994 50.000 0.00 0.00 41.15 3.18
196 197 1.274167 AGCGATTCCCGTTAGTGTTCA 59.726 47.619 0.00 0.00 41.15 3.18
197 198 2.070783 GCGATTCCCGTTAGTGTTCAA 58.929 47.619 0.00 0.00 41.15 2.69
198 199 2.481185 GCGATTCCCGTTAGTGTTCAAA 59.519 45.455 0.00 0.00 41.15 2.69
199 200 3.058777 GCGATTCCCGTTAGTGTTCAAAA 60.059 43.478 0.00 0.00 41.15 2.44
200 201 4.460505 CGATTCCCGTTAGTGTTCAAAAC 58.539 43.478 0.00 0.00 0.00 2.43
201 202 4.212636 CGATTCCCGTTAGTGTTCAAAACT 59.787 41.667 0.00 0.00 0.00 2.66
202 203 5.277634 CGATTCCCGTTAGTGTTCAAAACTT 60.278 40.000 0.00 0.00 0.00 2.66
203 204 6.073657 CGATTCCCGTTAGTGTTCAAAACTTA 60.074 38.462 0.00 0.00 0.00 2.24
204 205 6.607735 TTCCCGTTAGTGTTCAAAACTTAG 57.392 37.500 0.00 0.00 0.00 2.18
205 206 4.512571 TCCCGTTAGTGTTCAAAACTTAGC 59.487 41.667 0.00 0.00 0.00 3.09
206 207 4.273969 CCCGTTAGTGTTCAAAACTTAGCA 59.726 41.667 0.00 0.00 0.00 3.49
207 208 5.048991 CCCGTTAGTGTTCAAAACTTAGCAT 60.049 40.000 0.00 0.00 0.00 3.79
208 209 6.435428 CCGTTAGTGTTCAAAACTTAGCATT 58.565 36.000 0.00 0.00 0.00 3.56
209 210 7.308109 CCCGTTAGTGTTCAAAACTTAGCATTA 60.308 37.037 0.00 0.00 0.00 1.90
210 211 8.071368 CCGTTAGTGTTCAAAACTTAGCATTAA 58.929 33.333 0.00 0.00 0.00 1.40
211 212 8.889000 CGTTAGTGTTCAAAACTTAGCATTAAC 58.111 33.333 0.00 0.00 0.00 2.01
212 213 9.724839 GTTAGTGTTCAAAACTTAGCATTAACA 57.275 29.630 0.00 0.00 32.83 2.41
219 220 2.906354 ACTTAGCATTAACAGCCTCCG 58.094 47.619 0.00 0.00 0.00 4.63
277 278 4.161295 CCTTCCGCGATGCCCTCA 62.161 66.667 8.23 0.00 0.00 3.86
311 312 1.302033 CTGCTCCGCCTTCAAGTGT 60.302 57.895 0.00 0.00 0.00 3.55
488 489 1.710996 TTTTGGTGGCGGGAGGAGAA 61.711 55.000 0.00 0.00 0.00 2.87
526 527 1.755783 GGCAGGAATCCAAGGCCAG 60.756 63.158 20.03 0.00 44.01 4.85
552 553 2.115291 GTGCCCCCTTTCTCGCATC 61.115 63.158 0.00 0.00 33.08 3.91
566 567 2.295629 CTCGCATCCAGCATCTCTTCTA 59.704 50.000 0.00 0.00 46.13 2.10
613 614 1.306141 TGTCTCTCCCCTCGCCATT 60.306 57.895 0.00 0.00 0.00 3.16
615 616 1.306141 TCTCTCCCCTCGCCATTGT 60.306 57.895 0.00 0.00 0.00 2.71
619 620 0.609131 CTCCCCTCGCCATTGTGTTT 60.609 55.000 0.00 0.00 0.00 2.83
632 633 2.787473 TGTGTTTCCTCCTGCCATAG 57.213 50.000 0.00 0.00 0.00 2.23
672 673 0.815213 GCTCGCAATCTGGGCATACA 60.815 55.000 0.00 0.00 0.00 2.29
735 736 3.737172 CCCGCCGAACCTGCTTTG 61.737 66.667 0.00 0.00 0.00 2.77
744 745 2.985282 CCTGCTTTGCCGGCTTCA 60.985 61.111 29.70 17.73 0.00 3.02
748 749 2.398554 GCTTTGCCGGCTTCATCGA 61.399 57.895 29.70 1.01 0.00 3.59
843 844 1.299976 GATGAAGAACCCGGTGCCT 59.700 57.895 0.00 0.00 0.00 4.75
849 850 3.819877 GAACCCGGTGCCTGACGTT 62.820 63.158 0.00 0.00 0.00 3.99
972 973 2.106683 CAATCGCCCGTCCTTCACC 61.107 63.158 0.00 0.00 0.00 4.02
1027 1028 1.447838 GGAATTGCTCGCTCCGACA 60.448 57.895 0.00 0.00 0.00 4.35
1029 1030 0.579156 GAATTGCTCGCTCCGACATC 59.421 55.000 0.00 0.00 0.00 3.06
1032 1033 1.960040 TTGCTCGCTCCGACATCCAT 61.960 55.000 0.00 0.00 0.00 3.41
1158 1159 3.432588 CGTCTCTCGGCGTGGTCT 61.433 66.667 6.85 0.00 35.71 3.85
1170 1171 0.173708 CGTGGTCTAGAAGAGTGGGC 59.826 60.000 0.00 0.00 0.00 5.36
1191 1192 2.765807 ACCCTCATCAGGCTCCCG 60.766 66.667 0.00 0.00 38.72 5.14
1215 1216 1.222936 GATCAGGGTGTGCCTGGAG 59.777 63.158 0.00 0.00 36.11 3.86
1373 1374 2.034066 CACCAAGACCGCCACCAT 59.966 61.111 0.00 0.00 0.00 3.55
1452 1453 1.284111 TGATGGAGGGGAGCAGCAAT 61.284 55.000 0.00 0.00 0.00 3.56
1497 1498 1.071699 GTCAACCTGCTTGTCTACCCA 59.928 52.381 0.00 0.00 0.00 4.51
1518 1519 1.201647 GTTCTGATTCACCTCGACCGA 59.798 52.381 0.00 0.00 0.00 4.69
1548 1549 0.463620 ACACGGTGCAGCCAAAAATT 59.536 45.000 10.90 0.00 36.97 1.82
1682 1683 4.016706 CGGAACCTTCCCCGCACT 62.017 66.667 0.00 0.00 44.67 4.40
1712 1713 4.357947 GCGTCCGGTGCACTCTCA 62.358 66.667 17.98 0.00 0.00 3.27
1734 1735 0.731514 TCAACTTCGGTGATCGCGAC 60.732 55.000 12.93 6.32 39.05 5.19
1736 1737 2.949678 CTTCGGTGATCGCGACGG 60.950 66.667 12.93 4.03 39.05 4.79
1867 1868 1.620819 ACTCCTTCATGCGTGACTCTT 59.379 47.619 8.48 0.00 33.11 2.85
1869 1870 1.895798 TCCTTCATGCGTGACTCTTCT 59.104 47.619 8.48 0.00 33.11 2.85
1911 1912 0.447801 GCCGTCTATGTGCACCAAAG 59.552 55.000 15.69 9.05 0.00 2.77
1918 1919 4.043200 GTGCACCAAAGGGCGCTC 62.043 66.667 7.64 1.48 42.85 5.03
1933 1934 1.851021 CGCTCCGGTCAATGTTGCAA 61.851 55.000 0.00 0.00 0.00 4.08
1934 1935 0.527565 GCTCCGGTCAATGTTGCAAT 59.472 50.000 0.59 0.00 0.00 3.56
1973 1974 4.530857 GCACGCCCACGCCTCTAT 62.531 66.667 0.00 0.00 45.53 1.98
2121 2122 1.442886 TTCCCACCCCTTTGCCTGAT 61.443 55.000 0.00 0.00 0.00 2.90
2164 2165 1.339438 CCATGTCTCCTGTGGGAACAG 60.339 57.143 0.00 0.00 44.46 3.16
2182 2183 4.082523 GTGTGCTGCCGCCCTCTA 62.083 66.667 0.00 0.00 34.43 2.43
2251 2252 1.536907 TTGGCCCCGGTCAACTCTA 60.537 57.895 0.00 0.00 34.53 2.43
2336 2337 1.155859 AGCCCACAAATGAAGCCCA 59.844 52.632 0.00 0.00 0.00 5.36
2340 2341 1.272092 CCCACAAATGAAGCCCAGAGA 60.272 52.381 0.00 0.00 0.00 3.10
2449 2450 2.555448 CCTGAGATCGCTACATCCCCTA 60.555 54.545 0.00 0.00 0.00 3.53
2489 2490 2.470821 CTTCGTCAACTCGTTCACCTT 58.529 47.619 0.00 0.00 0.00 3.50
2493 2494 1.940613 GTCAACTCGTTCACCTTGCTT 59.059 47.619 0.00 0.00 0.00 3.91
2566 2567 2.989824 CCCTCACCGACGACCAGT 60.990 66.667 0.00 0.00 0.00 4.00
2619 2620 3.570550 ACTACAGACTCAACTCACTGACC 59.429 47.826 0.00 0.00 34.88 4.02
2689 2690 4.308458 CACCGACAACCGAGGCCA 62.308 66.667 5.01 0.00 41.76 5.36
2847 2848 2.125512 CCTGCGGTACAGTGAGCC 60.126 66.667 0.00 0.00 45.68 4.70
2895 2896 9.123902 CTCAAAGTTTCCATATGTATCCATTCA 57.876 33.333 1.24 0.00 32.29 2.57
2924 2933 3.576078 TCAGTTGGTCAATTGTGGAGT 57.424 42.857 5.13 0.00 31.10 3.85
2926 2935 3.118075 TCAGTTGGTCAATTGTGGAGTCA 60.118 43.478 5.13 0.00 31.10 3.41
2934 2943 5.232463 GTCAATTGTGGAGTCATTGCATTT 58.768 37.500 5.13 0.00 0.00 2.32
2944 2953 4.841422 AGTCATTGCATTTCTCTAGCTGT 58.159 39.130 0.00 0.00 0.00 4.40
3073 3082 6.045698 CATCTGTATGCTCTGTGTCATTTC 57.954 41.667 0.00 0.00 0.00 2.17
3100 3109 8.615705 TGATATAGATGACCTGTCCTATGTACT 58.384 37.037 0.00 0.00 0.00 2.73
3162 3171 0.676151 CAGCCCCAAGAAGTCTGCTC 60.676 60.000 0.00 0.00 0.00 4.26
3170 3179 1.376553 GAAGTCTGCTCCCCACTGC 60.377 63.158 0.00 0.00 0.00 4.40
3186 3195 1.691976 ACTGCTGTGTGCCTACAACTA 59.308 47.619 0.00 0.00 42.00 2.24
3194 3203 4.517453 TGTGTGCCTACAACTATTTGTTCC 59.483 41.667 3.58 0.00 43.89 3.62
3198 3207 4.202524 TGCCTACAACTATTTGTTCCCTGT 60.203 41.667 3.58 0.00 43.89 4.00
3226 3235 2.967929 ATCGGCTCGCTGCACATCTC 62.968 60.000 0.00 0.00 45.15 2.75
3365 3374 6.880822 ATTTTGTTCAGAATCATCAATGCG 57.119 33.333 0.00 0.00 0.00 4.73
3424 3433 9.132521 GTCATCAACAACCAAATTATTTCTGAG 57.867 33.333 0.00 0.00 0.00 3.35
3446 3455 2.018515 GTTTGGGGAGTCGTTTTGTCA 58.981 47.619 0.00 0.00 0.00 3.58
3484 3493 2.513897 GCTGATGGTACCCGTGGC 60.514 66.667 10.07 5.38 0.00 5.01
3506 3515 2.028658 GGAATCCTCATCGCTGCATCTA 60.029 50.000 0.00 0.00 0.00 1.98
3515 3524 4.460382 TCATCGCTGCATCTACAGATCATA 59.540 41.667 0.00 0.00 40.25 2.15
3675 3684 4.219288 GCTGGAAATGAGACACCTGAAAAT 59.781 41.667 0.00 0.00 0.00 1.82
3721 3730 5.283876 TCCTTGGGGATTTTAACCTGATT 57.716 39.130 0.00 0.00 36.57 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.382040 CGGTATTTCTGTCAGACCATCACT 60.382 45.833 0.78 0.00 0.00 3.41
1 2 3.865745 CGGTATTTCTGTCAGACCATCAC 59.134 47.826 0.78 0.00 0.00 3.06
2 3 3.513912 ACGGTATTTCTGTCAGACCATCA 59.486 43.478 0.78 0.00 0.00 3.07
3 4 4.124851 ACGGTATTTCTGTCAGACCATC 57.875 45.455 0.78 0.00 0.00 3.51
4 5 5.871396 ATACGGTATTTCTGTCAGACCAT 57.129 39.130 0.78 0.57 36.91 3.55
5 6 5.670792 AATACGGTATTTCTGTCAGACCA 57.329 39.130 7.56 0.00 36.91 4.02
6 7 6.585389 GAAATACGGTATTTCTGTCAGACC 57.415 41.667 31.80 13.71 46.53 3.85
16 17 8.755977 TGGAGTCTAAAGAGAAATACGGTATTT 58.244 33.333 22.46 22.46 40.84 1.40
17 18 8.302515 TGGAGTCTAAAGAGAAATACGGTATT 57.697 34.615 7.56 7.56 31.96 1.89
18 19 7.470286 GCTGGAGTCTAAAGAGAAATACGGTAT 60.470 40.741 0.00 0.00 31.96 2.73
19 20 6.183360 GCTGGAGTCTAAAGAGAAATACGGTA 60.183 42.308 0.00 0.00 31.96 4.02
20 21 5.394333 GCTGGAGTCTAAAGAGAAATACGGT 60.394 44.000 0.00 0.00 31.96 4.83
21 22 5.044558 GCTGGAGTCTAAAGAGAAATACGG 58.955 45.833 0.00 0.00 31.96 4.02
22 23 5.651530 TGCTGGAGTCTAAAGAGAAATACG 58.348 41.667 0.00 0.00 31.96 3.06
23 24 6.045955 CCTGCTGGAGTCTAAAGAGAAATAC 58.954 44.000 2.92 0.00 31.37 1.89
24 25 5.958380 TCCTGCTGGAGTCTAAAGAGAAATA 59.042 40.000 8.48 0.00 37.46 1.40
25 26 4.780021 TCCTGCTGGAGTCTAAAGAGAAAT 59.220 41.667 8.48 0.00 37.46 2.17
26 27 4.160329 TCCTGCTGGAGTCTAAAGAGAAA 58.840 43.478 8.48 0.00 37.46 2.52
27 28 3.779444 TCCTGCTGGAGTCTAAAGAGAA 58.221 45.455 8.48 0.00 37.46 2.87
28 29 3.458044 TCCTGCTGGAGTCTAAAGAGA 57.542 47.619 8.48 0.00 37.46 3.10
29 30 3.513515 ACTTCCTGCTGGAGTCTAAAGAG 59.486 47.826 12.54 7.22 44.24 2.85
30 31 3.511477 ACTTCCTGCTGGAGTCTAAAGA 58.489 45.455 12.54 0.00 44.24 2.52
31 32 3.971245 ACTTCCTGCTGGAGTCTAAAG 57.029 47.619 12.54 8.60 44.24 1.85
32 33 6.213600 AGAAATACTTCCTGCTGGAGTCTAAA 59.786 38.462 12.54 0.00 44.24 1.85
33 34 5.721960 AGAAATACTTCCTGCTGGAGTCTAA 59.278 40.000 12.54 0.00 44.24 2.10
34 35 5.273208 AGAAATACTTCCTGCTGGAGTCTA 58.727 41.667 12.54 4.29 44.24 2.59
35 36 4.100373 AGAAATACTTCCTGCTGGAGTCT 58.900 43.478 12.54 7.17 44.24 3.24
36 37 4.479786 AGAAATACTTCCTGCTGGAGTC 57.520 45.455 12.54 5.24 44.24 3.36
37 38 6.567602 AATAGAAATACTTCCTGCTGGAGT 57.432 37.500 12.54 14.26 44.24 3.85
38 39 6.201806 CGAAATAGAAATACTTCCTGCTGGAG 59.798 42.308 12.54 9.49 44.24 3.86
39 40 6.049149 CGAAATAGAAATACTTCCTGCTGGA 58.951 40.000 8.48 8.48 41.36 3.86
40 41 5.237344 CCGAAATAGAAATACTTCCTGCTGG 59.763 44.000 2.58 2.58 31.28 4.85
41 42 5.237344 CCCGAAATAGAAATACTTCCTGCTG 59.763 44.000 0.00 0.00 31.28 4.41
42 43 5.130477 TCCCGAAATAGAAATACTTCCTGCT 59.870 40.000 0.00 0.00 31.28 4.24
43 44 5.365619 TCCCGAAATAGAAATACTTCCTGC 58.634 41.667 0.00 0.00 31.28 4.85
44 45 5.992217 CCTCCCGAAATAGAAATACTTCCTG 59.008 44.000 0.00 0.00 31.28 3.86
45 46 5.071923 CCCTCCCGAAATAGAAATACTTCCT 59.928 44.000 0.00 0.00 31.28 3.36
46 47 5.306394 CCCTCCCGAAATAGAAATACTTCC 58.694 45.833 0.00 0.00 31.28 3.46
47 48 5.071384 TCCCCTCCCGAAATAGAAATACTTC 59.929 44.000 0.00 0.00 0.00 3.01
48 49 4.973211 TCCCCTCCCGAAATAGAAATACTT 59.027 41.667 0.00 0.00 0.00 2.24
49 50 4.563782 TCCCCTCCCGAAATAGAAATACT 58.436 43.478 0.00 0.00 0.00 2.12
50 51 4.347292 ACTCCCCTCCCGAAATAGAAATAC 59.653 45.833 0.00 0.00 0.00 1.89
51 52 4.563782 ACTCCCCTCCCGAAATAGAAATA 58.436 43.478 0.00 0.00 0.00 1.40
52 53 3.394645 ACTCCCCTCCCGAAATAGAAAT 58.605 45.455 0.00 0.00 0.00 2.17
53 54 2.841795 ACTCCCCTCCCGAAATAGAAA 58.158 47.619 0.00 0.00 0.00 2.52
54 55 2.563039 ACTCCCCTCCCGAAATAGAA 57.437 50.000 0.00 0.00 0.00 2.10
55 56 2.563039 AACTCCCCTCCCGAAATAGA 57.437 50.000 0.00 0.00 0.00 1.98
56 57 2.772515 AGAAACTCCCCTCCCGAAATAG 59.227 50.000 0.00 0.00 0.00 1.73
57 58 2.841795 AGAAACTCCCCTCCCGAAATA 58.158 47.619 0.00 0.00 0.00 1.40
58 59 1.670059 AGAAACTCCCCTCCCGAAAT 58.330 50.000 0.00 0.00 0.00 2.17
59 60 1.441695 AAGAAACTCCCCTCCCGAAA 58.558 50.000 0.00 0.00 0.00 3.46
60 61 2.330661 TAAGAAACTCCCCTCCCGAA 57.669 50.000 0.00 0.00 0.00 4.30
61 62 2.330661 TTAAGAAACTCCCCTCCCGA 57.669 50.000 0.00 0.00 0.00 5.14
62 63 3.542648 GATTTAAGAAACTCCCCTCCCG 58.457 50.000 0.00 0.00 0.00 5.14
63 64 3.684697 CGGATTTAAGAAACTCCCCTCCC 60.685 52.174 0.00 0.00 0.00 4.30
64 65 3.054582 ACGGATTTAAGAAACTCCCCTCC 60.055 47.826 0.00 0.00 0.00 4.30
65 66 4.217836 ACGGATTTAAGAAACTCCCCTC 57.782 45.455 0.00 0.00 0.00 4.30
66 67 4.652679 AACGGATTTAAGAAACTCCCCT 57.347 40.909 0.00 0.00 0.00 4.79
67 68 4.157289 GGAAACGGATTTAAGAAACTCCCC 59.843 45.833 0.00 0.00 0.00 4.81
68 69 5.008331 AGGAAACGGATTTAAGAAACTCCC 58.992 41.667 0.00 0.00 0.00 4.30
69 70 5.704053 TCAGGAAACGGATTTAAGAAACTCC 59.296 40.000 0.00 0.00 0.00 3.85
70 71 6.796705 TCAGGAAACGGATTTAAGAAACTC 57.203 37.500 0.00 0.00 0.00 3.01
71 72 6.374613 GGATCAGGAAACGGATTTAAGAAACT 59.625 38.462 0.00 0.00 45.65 2.66
72 73 6.374613 AGGATCAGGAAACGGATTTAAGAAAC 59.625 38.462 0.00 0.00 45.65 2.78
73 74 6.481643 AGGATCAGGAAACGGATTTAAGAAA 58.518 36.000 0.00 0.00 45.65 2.52
74 75 6.062258 AGGATCAGGAAACGGATTTAAGAA 57.938 37.500 0.00 0.00 45.65 2.52
75 76 5.671493 GAGGATCAGGAAACGGATTTAAGA 58.329 41.667 0.00 0.00 45.65 2.10
76 77 4.508124 CGAGGATCAGGAAACGGATTTAAG 59.492 45.833 0.00 0.00 45.65 1.85
77 78 4.081309 ACGAGGATCAGGAAACGGATTTAA 60.081 41.667 0.00 0.00 45.65 1.52
78 79 3.449737 ACGAGGATCAGGAAACGGATTTA 59.550 43.478 0.00 0.00 45.65 1.40
79 80 2.236395 ACGAGGATCAGGAAACGGATTT 59.764 45.455 0.00 0.00 45.65 2.17
80 81 1.831736 ACGAGGATCAGGAAACGGATT 59.168 47.619 0.00 0.00 45.65 3.01
82 83 1.263356 AACGAGGATCAGGAAACGGA 58.737 50.000 0.00 0.00 39.42 4.69
83 84 2.000447 GAAACGAGGATCAGGAAACGG 59.000 52.381 0.00 0.00 33.17 4.44
84 85 2.668457 CAGAAACGAGGATCAGGAAACG 59.332 50.000 0.00 0.00 33.17 3.60
85 86 3.926616 TCAGAAACGAGGATCAGGAAAC 58.073 45.455 0.00 0.00 33.17 2.78
86 87 4.617253 TTCAGAAACGAGGATCAGGAAA 57.383 40.909 0.00 0.00 33.17 3.13
87 88 4.569943 CTTTCAGAAACGAGGATCAGGAA 58.430 43.478 0.00 0.00 33.17 3.36
88 89 3.617531 GCTTTCAGAAACGAGGATCAGGA 60.618 47.826 0.00 0.00 33.17 3.86
89 90 2.675348 GCTTTCAGAAACGAGGATCAGG 59.325 50.000 0.00 0.00 33.17 3.86
90 91 2.675348 GGCTTTCAGAAACGAGGATCAG 59.325 50.000 0.00 0.00 33.17 2.90
91 92 2.038426 TGGCTTTCAGAAACGAGGATCA 59.962 45.455 0.00 0.00 33.17 2.92
92 93 2.699954 TGGCTTTCAGAAACGAGGATC 58.300 47.619 0.00 0.00 0.00 3.36
93 94 2.859165 TGGCTTTCAGAAACGAGGAT 57.141 45.000 0.00 0.00 0.00 3.24
94 95 2.631160 TTGGCTTTCAGAAACGAGGA 57.369 45.000 0.00 0.00 0.00 3.71
95 96 5.277538 GCTATATTGGCTTTCAGAAACGAGG 60.278 44.000 0.00 0.00 0.00 4.63
96 97 5.294306 TGCTATATTGGCTTTCAGAAACGAG 59.706 40.000 0.00 0.00 0.00 4.18
97 98 5.182487 TGCTATATTGGCTTTCAGAAACGA 58.818 37.500 0.00 0.00 0.00 3.85
98 99 5.484173 TGCTATATTGGCTTTCAGAAACG 57.516 39.130 0.00 0.00 0.00 3.60
99 100 5.745769 GCTTGCTATATTGGCTTTCAGAAAC 59.254 40.000 0.00 0.00 0.00 2.78
100 101 5.653769 AGCTTGCTATATTGGCTTTCAGAAA 59.346 36.000 0.00 0.00 0.00 2.52
101 102 5.195940 AGCTTGCTATATTGGCTTTCAGAA 58.804 37.500 0.00 0.00 0.00 3.02
102 103 4.785301 AGCTTGCTATATTGGCTTTCAGA 58.215 39.130 0.00 0.00 0.00 3.27
103 104 4.820716 AGAGCTTGCTATATTGGCTTTCAG 59.179 41.667 0.00 0.00 33.13 3.02
104 105 4.577693 CAGAGCTTGCTATATTGGCTTTCA 59.422 41.667 0.00 0.00 33.13 2.69
105 106 5.105834 CAGAGCTTGCTATATTGGCTTTC 57.894 43.478 0.00 0.00 33.13 2.62
119 120 2.891112 CTCCTCTTAGTGCAGAGCTTG 58.109 52.381 0.00 0.00 39.33 4.01
120 121 1.206849 GCTCCTCTTAGTGCAGAGCTT 59.793 52.381 13.03 0.00 45.11 3.74
121 122 0.823460 GCTCCTCTTAGTGCAGAGCT 59.177 55.000 13.03 0.00 45.11 4.09
122 123 3.360886 GCTCCTCTTAGTGCAGAGC 57.639 57.895 6.16 6.16 42.74 4.09
123 124 2.233431 AGTTGCTCCTCTTAGTGCAGAG 59.767 50.000 0.00 0.00 40.23 3.35
124 125 2.251818 AGTTGCTCCTCTTAGTGCAGA 58.748 47.619 0.00 0.00 36.75 4.26
125 126 2.758736 AGTTGCTCCTCTTAGTGCAG 57.241 50.000 0.00 0.00 36.75 4.41
126 127 3.578716 AGTAAGTTGCTCCTCTTAGTGCA 59.421 43.478 0.00 0.00 31.29 4.57
127 128 3.929610 CAGTAAGTTGCTCCTCTTAGTGC 59.070 47.826 0.00 0.00 39.25 4.40
128 129 3.929610 GCAGTAAGTTGCTCCTCTTAGTG 59.070 47.826 12.54 12.54 44.09 2.74
129 130 4.195225 GCAGTAAGTTGCTCCTCTTAGT 57.805 45.455 0.00 0.00 40.89 2.24
139 140 6.737254 TTCCATAGTAAAGCAGTAAGTTGC 57.263 37.500 0.00 0.00 44.41 4.17
140 141 8.492673 TCATTCCATAGTAAAGCAGTAAGTTG 57.507 34.615 0.00 0.00 0.00 3.16
141 142 9.515226 TTTCATTCCATAGTAAAGCAGTAAGTT 57.485 29.630 0.00 0.00 0.00 2.66
142 143 9.515226 TTTTCATTCCATAGTAAAGCAGTAAGT 57.485 29.630 0.00 0.00 0.00 2.24
145 146 8.447833 CGTTTTTCATTCCATAGTAAAGCAGTA 58.552 33.333 0.00 0.00 0.00 2.74
146 147 7.040686 ACGTTTTTCATTCCATAGTAAAGCAGT 60.041 33.333 0.00 0.00 0.00 4.40
147 148 7.305474 ACGTTTTTCATTCCATAGTAAAGCAG 58.695 34.615 0.00 0.00 0.00 4.24
148 149 7.209471 ACGTTTTTCATTCCATAGTAAAGCA 57.791 32.000 0.00 0.00 0.00 3.91
149 150 8.515473 AAACGTTTTTCATTCCATAGTAAAGC 57.485 30.769 7.96 0.00 0.00 3.51
152 153 9.615295 GCTTAAACGTTTTTCATTCCATAGTAA 57.385 29.630 20.19 1.00 0.00 2.24
153 154 7.958567 CGCTTAAACGTTTTTCATTCCATAGTA 59.041 33.333 20.19 0.00 0.00 1.82
154 155 6.799925 CGCTTAAACGTTTTTCATTCCATAGT 59.200 34.615 20.19 0.00 0.00 2.12
155 156 7.018826 TCGCTTAAACGTTTTTCATTCCATAG 58.981 34.615 20.19 0.00 0.00 2.23
156 157 6.900189 TCGCTTAAACGTTTTTCATTCCATA 58.100 32.000 20.19 0.00 0.00 2.74
157 158 5.764131 TCGCTTAAACGTTTTTCATTCCAT 58.236 33.333 20.19 0.00 0.00 3.41
158 159 5.171147 TCGCTTAAACGTTTTTCATTCCA 57.829 34.783 20.19 0.00 0.00 3.53
159 160 6.183359 GGAATCGCTTAAACGTTTTTCATTCC 60.183 38.462 20.19 21.03 31.39 3.01
160 161 6.183359 GGGAATCGCTTAAACGTTTTTCATTC 60.183 38.462 20.19 17.05 0.00 2.67
161 162 5.631929 GGGAATCGCTTAAACGTTTTTCATT 59.368 36.000 20.19 10.32 0.00 2.57
162 163 5.158494 GGGAATCGCTTAAACGTTTTTCAT 58.842 37.500 20.19 0.00 0.00 2.57
163 164 4.538917 GGGAATCGCTTAAACGTTTTTCA 58.461 39.130 20.19 0.00 0.00 2.69
164 165 3.600786 CGGGAATCGCTTAAACGTTTTTC 59.399 43.478 20.19 14.62 0.00 2.29
165 166 3.003585 ACGGGAATCGCTTAAACGTTTTT 59.996 39.130 20.19 5.94 43.89 1.94
166 167 2.549329 ACGGGAATCGCTTAAACGTTTT 59.451 40.909 20.19 0.00 43.89 2.43
167 168 2.145536 ACGGGAATCGCTTAAACGTTT 58.854 42.857 18.90 18.90 43.89 3.60
168 169 1.799544 ACGGGAATCGCTTAAACGTT 58.200 45.000 0.00 0.00 43.89 3.99
169 170 1.799544 AACGGGAATCGCTTAAACGT 58.200 45.000 0.00 0.00 43.89 3.99
170 171 2.925563 ACTAACGGGAATCGCTTAAACG 59.074 45.455 0.00 0.00 43.89 3.60
171 172 3.681417 ACACTAACGGGAATCGCTTAAAC 59.319 43.478 0.00 0.00 43.89 2.01
172 173 3.929094 ACACTAACGGGAATCGCTTAAA 58.071 40.909 0.00 0.00 43.89 1.52
173 174 3.598019 ACACTAACGGGAATCGCTTAA 57.402 42.857 0.00 0.00 43.89 1.85
174 175 3.056678 TGAACACTAACGGGAATCGCTTA 60.057 43.478 0.00 0.00 43.89 3.09
175 176 2.289195 TGAACACTAACGGGAATCGCTT 60.289 45.455 0.00 0.00 43.89 4.68
176 177 1.274167 TGAACACTAACGGGAATCGCT 59.726 47.619 0.00 0.00 43.89 4.93
177 178 1.717194 TGAACACTAACGGGAATCGC 58.283 50.000 0.00 0.00 43.89 4.58
178 179 4.212636 AGTTTTGAACACTAACGGGAATCG 59.787 41.667 0.00 0.00 45.88 3.34
179 180 5.684550 AGTTTTGAACACTAACGGGAATC 57.315 39.130 0.00 0.00 0.00 2.52
180 181 6.293790 GCTAAGTTTTGAACACTAACGGGAAT 60.294 38.462 0.00 0.00 0.00 3.01
181 182 5.007921 GCTAAGTTTTGAACACTAACGGGAA 59.992 40.000 0.00 0.00 0.00 3.97
182 183 4.512571 GCTAAGTTTTGAACACTAACGGGA 59.487 41.667 0.00 0.00 0.00 5.14
183 184 4.273969 TGCTAAGTTTTGAACACTAACGGG 59.726 41.667 0.00 0.00 0.00 5.28
184 185 5.412526 TGCTAAGTTTTGAACACTAACGG 57.587 39.130 0.00 0.00 0.00 4.44
185 186 8.889000 GTTAATGCTAAGTTTTGAACACTAACG 58.111 33.333 0.00 0.00 0.00 3.18
186 187 9.724839 TGTTAATGCTAAGTTTTGAACACTAAC 57.275 29.630 0.00 0.00 0.00 2.34
187 188 9.944663 CTGTTAATGCTAAGTTTTGAACACTAA 57.055 29.630 0.00 0.00 0.00 2.24
188 189 8.073768 GCTGTTAATGCTAAGTTTTGAACACTA 58.926 33.333 0.00 0.00 0.00 2.74
189 190 6.918022 GCTGTTAATGCTAAGTTTTGAACACT 59.082 34.615 0.00 0.00 0.00 3.55
190 191 6.143919 GGCTGTTAATGCTAAGTTTTGAACAC 59.856 38.462 3.96 0.00 0.00 3.32
191 192 6.040391 AGGCTGTTAATGCTAAGTTTTGAACA 59.960 34.615 0.00 0.00 0.00 3.18
192 193 6.447162 AGGCTGTTAATGCTAAGTTTTGAAC 58.553 36.000 0.00 0.00 0.00 3.18
193 194 6.294508 GGAGGCTGTTAATGCTAAGTTTTGAA 60.295 38.462 0.00 0.00 0.00 2.69
194 195 5.183140 GGAGGCTGTTAATGCTAAGTTTTGA 59.817 40.000 0.00 0.00 0.00 2.69
195 196 5.402398 GGAGGCTGTTAATGCTAAGTTTTG 58.598 41.667 0.00 0.00 0.00 2.44
196 197 4.156008 CGGAGGCTGTTAATGCTAAGTTTT 59.844 41.667 0.00 0.00 0.00 2.43
197 198 3.689649 CGGAGGCTGTTAATGCTAAGTTT 59.310 43.478 0.00 0.00 0.00 2.66
198 199 3.270877 CGGAGGCTGTTAATGCTAAGTT 58.729 45.455 0.00 0.00 0.00 2.66
199 200 2.906354 CGGAGGCTGTTAATGCTAAGT 58.094 47.619 0.00 0.00 0.00 2.24
200 201 1.599542 GCGGAGGCTGTTAATGCTAAG 59.400 52.381 0.00 0.00 35.83 2.18
201 202 1.663695 GCGGAGGCTGTTAATGCTAA 58.336 50.000 0.00 0.00 35.83 3.09
202 203 3.379650 GCGGAGGCTGTTAATGCTA 57.620 52.632 0.00 0.00 35.83 3.49
203 204 4.225497 GCGGAGGCTGTTAATGCT 57.775 55.556 0.00 0.00 35.83 3.79
277 278 0.251341 GCAGGTGGGTTGTTGGAGAT 60.251 55.000 0.00 0.00 0.00 2.75
470 471 2.124507 CTTCTCCTCCCGCCACCAAA 62.125 60.000 0.00 0.00 0.00 3.28
535 536 2.272146 GATGCGAGAAAGGGGGCA 59.728 61.111 0.00 0.00 40.06 5.36
552 553 4.440880 CTCTGGTTTAGAAGAGATGCTGG 58.559 47.826 0.00 0.00 42.15 4.85
588 589 0.174617 GAGGGGAGAGACAGCGAAAG 59.825 60.000 0.00 0.00 0.00 2.62
613 614 1.340017 GCTATGGCAGGAGGAAACACA 60.340 52.381 0.00 0.00 38.54 3.72
615 616 0.255890 GGCTATGGCAGGAGGAAACA 59.744 55.000 2.58 0.00 40.87 2.83
619 620 2.072487 GTGGGCTATGGCAGGAGGA 61.072 63.158 2.58 0.00 40.87 3.71
688 689 2.352805 CCTGGGCTTGAGGTGGAC 59.647 66.667 0.00 0.00 0.00 4.02
720 721 4.404654 GGCAAAGCAGGTTCGGCG 62.405 66.667 0.00 0.00 36.08 6.46
822 823 2.106683 CACCGGGTTCTTCATCGGC 61.107 63.158 6.32 0.00 45.65 5.54
843 844 1.962306 GGGGCGCAAGTTAACGTCA 60.962 57.895 10.83 0.00 35.09 4.35
849 850 3.404438 ATCCGGGGGCGCAAGTTA 61.404 61.111 10.83 0.00 41.68 2.24
876 877 2.693762 CGGAGACCAAGCGACCGTA 61.694 63.158 0.00 0.00 38.97 4.02
940 941 4.702274 ATTGCCCAGGGTGGTGGC 62.702 66.667 7.55 0.00 45.56 5.01
1027 1028 3.370315 GGCTCAAAGACAGAGACATGGAT 60.370 47.826 0.00 0.00 40.93 3.41
1029 1030 2.354259 GGCTCAAAGACAGAGACATGG 58.646 52.381 0.00 0.00 40.93 3.66
1032 1033 0.318441 CGGGCTCAAAGACAGAGACA 59.682 55.000 0.00 0.00 43.10 3.41
1158 1159 2.707849 GGTCGCGCCCACTCTTCTA 61.708 63.158 0.00 0.00 0.00 2.10
1191 1192 1.279271 AGGCACACCCTGATCTTGTAC 59.721 52.381 0.00 0.00 44.28 2.90
1371 1372 0.179116 CGACAGTGAGAGAGCCCATG 60.179 60.000 0.00 0.00 0.00 3.66
1373 1374 0.962855 CTCGACAGTGAGAGAGCCCA 60.963 60.000 12.74 0.00 38.28 5.36
1377 1378 0.732571 GCTCCTCGACAGTGAGAGAG 59.267 60.000 17.58 12.36 38.28 3.20
1471 1472 3.570212 AAGCAGGTTGACGGGGCT 61.570 61.111 0.00 0.00 36.13 5.19
1497 1498 1.202582 CGGTCGAGGTGAATCAGAACT 59.797 52.381 0.00 0.00 0.00 3.01
1548 1549 2.047844 GAGCTTCTGCCGCTGTCA 60.048 61.111 0.00 0.00 37.96 3.58
1610 1611 1.008194 GCACAGTCGTCGTACACCA 60.008 57.895 0.00 0.00 0.00 4.17
1682 1683 4.373116 GACGCCTGCCAGTTCGGA 62.373 66.667 8.18 0.00 36.56 4.55
1712 1713 1.799181 CGCGATCACCGAAGTTGAGAT 60.799 52.381 0.00 0.00 41.76 2.75
1756 1757 2.345244 CCTGCCTCTGTCGTTGCT 59.655 61.111 0.00 0.00 0.00 3.91
1809 1810 4.514577 CCGCCGTCGCTGGATCTT 62.515 66.667 0.00 0.00 32.47 2.40
1844 1845 0.388649 GTCACGCATGAAGGAGTCGT 60.389 55.000 0.00 0.00 36.31 4.34
1894 1895 1.086696 CCCTTTGGTGCACATAGACG 58.913 55.000 20.43 0.54 30.65 4.18
1911 1912 4.778143 ACATTGACCGGAGCGCCC 62.778 66.667 9.46 3.94 0.00 6.13
1918 1919 2.721274 TCAATTGCAACATTGACCGG 57.279 45.000 10.69 0.00 32.46 5.28
1933 1934 2.072874 CTCCCGGCCCCATCATCAAT 62.073 60.000 0.00 0.00 0.00 2.57
1934 1935 2.694240 TCCCGGCCCCATCATCAA 60.694 61.111 0.00 0.00 0.00 2.57
1965 1966 1.270518 CCCTCAACATGGATAGAGGCG 60.271 57.143 15.47 8.35 44.95 5.52
1973 1974 0.251297 CAAGTGGCCCTCAACATGGA 60.251 55.000 0.00 0.00 0.00 3.41
2109 2110 0.329261 TCTGTCCATCAGGCAAAGGG 59.671 55.000 0.00 0.00 43.76 3.95
2121 2122 1.227943 GGCAACTGCACTCTGTCCA 60.228 57.895 3.76 0.00 44.36 4.02
2169 2170 4.858680 GGGTTAGAGGGCGGCAGC 62.859 72.222 12.47 0.00 44.18 5.25
2182 2183 2.351276 GTCGTCCATGCCAGGGTT 59.649 61.111 0.00 0.00 0.00 4.11
2232 2233 1.833787 TAGAGTTGACCGGGGCCAAC 61.834 60.000 21.46 21.46 42.02 3.77
2251 2252 0.608640 GACACCTCTGGGTCAATCGT 59.391 55.000 0.00 0.00 45.41 3.73
2301 2302 1.404047 GGCTGCAGAGAAGACTGTCTC 60.404 57.143 20.43 5.09 43.80 3.36
2336 2337 1.210204 TGGCCAGCCCAAAGATCTCT 61.210 55.000 0.00 0.00 41.82 3.10
2350 2351 2.203480 GGGTTGCAGAAGTGGCCA 60.203 61.111 0.00 0.00 0.00 5.36
2391 2392 2.692368 TCCTCCATCACTGGGGCC 60.692 66.667 0.00 0.00 42.29 5.80
2399 2400 2.850833 AGGAAATGAGGTCCTCCATCA 58.149 47.619 16.60 0.00 42.02 3.07
2449 2450 1.949547 GCACTGCAGCTGGATCTCTTT 60.950 52.381 17.12 0.00 0.00 2.52
2489 2490 4.619320 CAGGGGTGGGGCAAAGCA 62.619 66.667 0.00 0.00 0.00 3.91
2689 2690 4.946157 CAGGTCCTTGTATTTCTGCAGATT 59.054 41.667 19.04 11.00 0.00 2.40
2847 2848 1.069765 CCTGATCCACGGAATCGGG 59.930 63.158 7.23 7.23 41.39 5.14
2924 2933 5.247862 TCAACAGCTAGAGAAATGCAATGA 58.752 37.500 0.00 0.00 0.00 2.57
2926 2935 5.251764 ACTCAACAGCTAGAGAAATGCAAT 58.748 37.500 14.71 0.00 35.83 3.56
2934 2943 2.451490 CCAGGACTCAACAGCTAGAGA 58.549 52.381 14.71 0.00 35.83 3.10
2944 2953 1.118965 TCGAGGTTGCCAGGACTCAA 61.119 55.000 0.00 0.00 0.00 3.02
3073 3082 7.953005 ACATAGGACAGGTCATCTATATCAG 57.047 40.000 1.41 0.00 0.00 2.90
3100 3109 6.112734 CCCATGCAACAGATACTAACTTGTA 58.887 40.000 0.00 0.00 0.00 2.41
3186 3195 6.294508 CCGATCAAACTAAACAGGGAACAAAT 60.295 38.462 0.00 0.00 0.00 2.32
3194 3203 2.348666 CGAGCCGATCAAACTAAACAGG 59.651 50.000 0.00 0.00 0.00 4.00
3198 3207 1.999735 CAGCGAGCCGATCAAACTAAA 59.000 47.619 0.00 0.00 0.00 1.85
3226 3235 3.077359 CCCTCAACAGCAGGAAGTAAAG 58.923 50.000 0.00 0.00 31.91 1.85
3365 3374 4.950479 CTGGATGCAGACCAGTCC 57.050 61.111 25.37 13.23 46.71 3.85
3424 3433 1.746787 ACAAAACGACTCCCCAAACAC 59.253 47.619 0.00 0.00 0.00 3.32
3446 3455 3.157087 CTGGGAGGTATGCAAAGTTGTT 58.843 45.455 0.00 0.00 0.00 2.83
3484 3493 0.602106 ATGCAGCGATGAGGATTCCG 60.602 55.000 4.02 0.00 0.00 4.30
3675 3684 1.406887 GCCATTCCGGAGAGCAAACTA 60.407 52.381 15.28 0.00 36.56 2.24
3721 3730 3.012518 GCTCTTTTCATCTGCCTTGCTA 58.987 45.455 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.