Multiple sequence alignment - TraesCS4A01G132300

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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 TraesCS4A01G132300 chr4A 100.000 2576 0 0 1 2576 177618958 177616383 0.000000e+00 4758
1 TraesCS4A01G132300 chr4D 89.217 2170 108 68 439 2565 302398533 302400619 0.000000e+00 2595
2 TraesCS4A01G132300 chr4D 86.528 193 12 8 273 452 302397793 302397984 1.560000e-47 200
3 TraesCS4A01G132300 chr4B 93.255 1186 38 12 887 2043 377374572 377375744 0.000000e+00 1709
4 TraesCS4A01G132300 chr4B 91.912 544 22 10 2045 2576 377375946 377376479 0.000000e+00 741
5 TraesCS4A01G132300 chr4B 97.619 84 1 1 287 370 377373305 377373387 2.670000e-30 143
6 TraesCS4A01G132300 chr4B 85.593 118 11 4 701 812 377373536 377373653 4.500000e-23 119
7 TraesCS4A01G132300 chr2A 82.600 523 80 5 1051 1566 57176236 57175718 3.910000e-123 451
8 TraesCS4A01G132300 chr2A 92.754 276 16 4 1 273 740013929 740013655 1.860000e-106 396
9 TraesCS4A01G132300 chr2A 91.575 273 17 6 1 272 543579885 543579618 3.130000e-99 372
10 TraesCS4A01G132300 chr2D 82.218 523 82 5 1051 1566 55764783 55764265 8.460000e-120 440
11 TraesCS4A01G132300 chr2B 82.218 523 82 6 1051 1566 88434970 88434452 8.460000e-120 440
12 TraesCS4A01G132300 chr5A 91.241 274 20 3 1 272 641576660 641576389 1.130000e-98 370
13 TraesCS4A01G132300 chr5A 91.209 273 17 6 1 272 426906166 426906432 5.240000e-97 364
14 TraesCS4A01G132300 chr7A 90.975 277 19 3 1 272 48642746 48643021 4.050000e-98 368
15 TraesCS4A01G132300 chr7A 90.426 282 20 3 1 275 19092921 19093202 5.240000e-97 364
16 TraesCS4A01G132300 chr3A 90.780 282 16 4 1 272 613364702 613364983 4.050000e-98 368
17 TraesCS4A01G132300 chr6A 90.909 275 21 3 1 272 32414375 32414648 1.460000e-97 366
18 TraesCS4A01G132300 chr1A 90.842 273 22 3 1 272 292888610 292888880 1.880000e-96 363


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 TraesCS4A01G132300 chr4A 177616383 177618958 2575 True 4758.0 4758 100.00000 1 2576 1 chr4A.!!$R1 2575
1 TraesCS4A01G132300 chr4D 302397793 302400619 2826 False 1397.5 2595 87.87250 273 2565 2 chr4D.!!$F1 2292
2 TraesCS4A01G132300 chr4B 377373305 377376479 3174 False 678.0 1709 92.09475 287 2576 4 chr4B.!!$F1 2289
3 TraesCS4A01G132300 chr2A 57175718 57176236 518 True 451.0 451 82.60000 1051 1566 1 chr2A.!!$R1 515
4 TraesCS4A01G132300 chr2D 55764265 55764783 518 True 440.0 440 82.21800 1051 1566 1 chr2D.!!$R1 515
5 TraesCS4A01G132300 chr2B 88434452 88434970 518 True 440.0 440 82.21800 1051 1566 1 chr2B.!!$R1 515

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
167 168 0.035725 CTTCCGGGGTGGGACTAAAC 60.036 60.0 0.0 0.0 38.76 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 3061 0.121197 AGGAGATGGGACCAAGGGAA 59.879 55.0 0.0 0.0 0.0 3.97 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
19 20 1.002366 CAACGTGCATAGCTCTGTCC 58.998 55.000 0.00 0.00 0.00 4.02
20 21 0.898320 AACGTGCATAGCTCTGTCCT 59.102 50.000 0.00 0.00 0.00 3.85
21 22 0.457851 ACGTGCATAGCTCTGTCCTC 59.542 55.000 0.00 0.00 0.00 3.71
22 23 0.593518 CGTGCATAGCTCTGTCCTCG 60.594 60.000 0.00 0.00 0.00 4.63
23 24 0.741326 GTGCATAGCTCTGTCCTCGA 59.259 55.000 0.00 0.00 0.00 4.04
24 25 0.741326 TGCATAGCTCTGTCCTCGAC 59.259 55.000 0.00 0.00 0.00 4.20
25 26 1.028905 GCATAGCTCTGTCCTCGACT 58.971 55.000 0.00 0.00 33.15 4.18
26 27 1.001815 GCATAGCTCTGTCCTCGACTC 60.002 57.143 0.00 0.00 33.15 3.36
27 28 1.262950 CATAGCTCTGTCCTCGACTCG 59.737 57.143 0.00 0.00 33.15 4.18
28 29 0.462225 TAGCTCTGTCCTCGACTCGG 60.462 60.000 0.00 0.00 33.15 4.63
29 30 2.795297 CTCTGTCCTCGACTCGGC 59.205 66.667 0.00 0.00 33.15 5.54
30 31 1.747367 CTCTGTCCTCGACTCGGCT 60.747 63.158 0.00 0.00 33.15 5.52
31 32 1.711060 CTCTGTCCTCGACTCGGCTC 61.711 65.000 0.00 0.00 33.15 4.70
32 33 2.033602 TGTCCTCGACTCGGCTCA 59.966 61.111 0.00 0.00 33.15 4.26
33 34 1.587043 CTGTCCTCGACTCGGCTCAA 61.587 60.000 0.00 0.00 33.15 3.02
34 35 0.965866 TGTCCTCGACTCGGCTCAAT 60.966 55.000 0.00 0.00 33.15 2.57
35 36 0.248702 GTCCTCGACTCGGCTCAATC 60.249 60.000 0.00 0.00 0.00 2.67
36 37 1.066587 CCTCGACTCGGCTCAATCC 59.933 63.158 0.00 0.00 0.00 3.01
37 38 1.066587 CTCGACTCGGCTCAATCCC 59.933 63.158 0.00 0.00 0.00 3.85
38 39 2.278857 CGACTCGGCTCAATCCCG 60.279 66.667 0.00 0.00 46.88 5.14
39 40 2.586357 GACTCGGCTCAATCCCGC 60.586 66.667 0.00 0.00 45.19 6.13
40 41 4.162690 ACTCGGCTCAATCCCGCC 62.163 66.667 0.00 0.00 45.19 6.13
68 69 2.516460 GGCGAGCGAGGAGGAGTA 60.516 66.667 0.00 0.00 0.00 2.59
69 70 2.716864 GCGAGCGAGGAGGAGTAC 59.283 66.667 0.00 0.00 0.00 2.73
70 71 3.015677 CGAGCGAGGAGGAGTACG 58.984 66.667 0.00 0.00 0.00 3.67
73 74 3.507009 GCGAGGAGGAGTACGCGT 61.507 66.667 19.17 19.17 41.49 6.01
74 75 2.403987 CGAGGAGGAGTACGCGTG 59.596 66.667 24.59 0.00 0.00 5.34
75 76 2.396955 CGAGGAGGAGTACGCGTGT 61.397 63.158 24.59 9.17 0.00 4.49
76 77 1.086067 CGAGGAGGAGTACGCGTGTA 61.086 60.000 24.59 4.34 0.00 2.90
77 78 0.656785 GAGGAGGAGTACGCGTGTAG 59.343 60.000 24.59 0.00 0.00 2.74
78 79 0.251354 AGGAGGAGTACGCGTGTAGA 59.749 55.000 24.59 0.00 0.00 2.59
79 80 1.134159 AGGAGGAGTACGCGTGTAGAT 60.134 52.381 24.59 4.72 0.00 1.98
80 81 1.263752 GGAGGAGTACGCGTGTAGATC 59.736 57.143 24.59 14.02 0.00 2.75
81 82 2.211806 GAGGAGTACGCGTGTAGATCT 58.788 52.381 24.59 11.47 0.00 2.75
82 83 2.211806 AGGAGTACGCGTGTAGATCTC 58.788 52.381 24.59 17.34 0.00 2.75
83 84 1.263752 GGAGTACGCGTGTAGATCTCC 59.736 57.143 24.59 21.52 35.47 3.71
84 85 2.211806 GAGTACGCGTGTAGATCTCCT 58.788 52.381 24.59 1.51 0.00 3.69
85 86 2.211806 AGTACGCGTGTAGATCTCCTC 58.788 52.381 24.59 0.00 0.00 3.71
86 87 2.158928 AGTACGCGTGTAGATCTCCTCT 60.159 50.000 24.59 0.00 38.06 3.69
87 88 1.752683 ACGCGTGTAGATCTCCTCTT 58.247 50.000 12.93 0.00 35.28 2.85
88 89 1.671845 ACGCGTGTAGATCTCCTCTTC 59.328 52.381 12.93 0.00 35.28 2.87
89 90 1.944024 CGCGTGTAGATCTCCTCTTCT 59.056 52.381 0.00 0.00 35.28 2.85
90 91 2.032377 CGCGTGTAGATCTCCTCTTCTC 60.032 54.545 0.00 0.00 35.28 2.87
91 92 2.946329 GCGTGTAGATCTCCTCTTCTCA 59.054 50.000 0.00 0.00 35.28 3.27
92 93 3.568007 GCGTGTAGATCTCCTCTTCTCAT 59.432 47.826 0.00 0.00 35.28 2.90
93 94 4.556501 GCGTGTAGATCTCCTCTTCTCATG 60.557 50.000 0.00 0.00 35.28 3.07
94 95 4.556501 CGTGTAGATCTCCTCTTCTCATGC 60.557 50.000 0.00 0.00 35.28 4.06
95 96 4.584325 GTGTAGATCTCCTCTTCTCATGCT 59.416 45.833 0.00 0.00 35.28 3.79
96 97 4.826733 TGTAGATCTCCTCTTCTCATGCTC 59.173 45.833 0.00 0.00 35.28 4.26
97 98 3.913509 AGATCTCCTCTTCTCATGCTCA 58.086 45.455 0.00 0.00 0.00 4.26
98 99 4.485875 AGATCTCCTCTTCTCATGCTCAT 58.514 43.478 0.00 0.00 0.00 2.90
99 100 5.643176 AGATCTCCTCTTCTCATGCTCATA 58.357 41.667 0.00 0.00 0.00 2.15
100 101 5.477984 AGATCTCCTCTTCTCATGCTCATAC 59.522 44.000 0.00 0.00 0.00 2.39
101 102 4.540715 TCTCCTCTTCTCATGCTCATACA 58.459 43.478 0.00 0.00 0.00 2.29
102 103 4.958581 TCTCCTCTTCTCATGCTCATACAA 59.041 41.667 0.00 0.00 0.00 2.41
103 104 5.423290 TCTCCTCTTCTCATGCTCATACAAA 59.577 40.000 0.00 0.00 0.00 2.83
104 105 6.099413 TCTCCTCTTCTCATGCTCATACAAAT 59.901 38.462 0.00 0.00 0.00 2.32
105 106 6.053650 TCCTCTTCTCATGCTCATACAAATG 58.946 40.000 0.00 0.00 0.00 2.32
106 107 5.238868 CCTCTTCTCATGCTCATACAAATGG 59.761 44.000 0.00 0.00 33.61 3.16
107 108 5.748402 TCTTCTCATGCTCATACAAATGGT 58.252 37.500 0.00 0.00 33.61 3.55
108 109 6.888105 TCTTCTCATGCTCATACAAATGGTA 58.112 36.000 0.00 0.00 36.16 3.25
109 110 6.988580 TCTTCTCATGCTCATACAAATGGTAG 59.011 38.462 0.00 0.00 34.92 3.18
110 111 6.484364 TCTCATGCTCATACAAATGGTAGA 57.516 37.500 0.00 0.00 34.92 2.59
111 112 6.888105 TCTCATGCTCATACAAATGGTAGAA 58.112 36.000 0.00 0.00 34.92 2.10
112 113 6.763135 TCTCATGCTCATACAAATGGTAGAAC 59.237 38.462 0.00 0.00 34.92 3.01
113 114 6.413892 TCATGCTCATACAAATGGTAGAACA 58.586 36.000 0.00 0.00 34.92 3.18
114 115 6.539826 TCATGCTCATACAAATGGTAGAACAG 59.460 38.462 0.00 0.00 34.92 3.16
115 116 4.635765 TGCTCATACAAATGGTAGAACAGC 59.364 41.667 0.00 0.00 34.92 4.40
116 117 4.878397 GCTCATACAAATGGTAGAACAGCT 59.122 41.667 0.00 0.00 34.92 4.24
117 118 5.007136 GCTCATACAAATGGTAGAACAGCTC 59.993 44.000 0.00 0.00 34.92 4.09
118 119 6.048732 TCATACAAATGGTAGAACAGCTCA 57.951 37.500 0.00 0.00 34.92 4.26
119 120 5.874810 TCATACAAATGGTAGAACAGCTCAC 59.125 40.000 0.00 0.00 34.92 3.51
120 121 3.412386 ACAAATGGTAGAACAGCTCACC 58.588 45.455 0.00 0.00 0.00 4.02
121 122 3.073062 ACAAATGGTAGAACAGCTCACCT 59.927 43.478 0.00 0.00 32.04 4.00
122 123 4.074970 CAAATGGTAGAACAGCTCACCTT 58.925 43.478 0.00 0.00 32.04 3.50
123 124 5.221843 ACAAATGGTAGAACAGCTCACCTTA 60.222 40.000 0.00 0.00 32.04 2.69
124 125 5.700402 AATGGTAGAACAGCTCACCTTAT 57.300 39.130 0.00 0.00 32.04 1.73
125 126 6.808321 AATGGTAGAACAGCTCACCTTATA 57.192 37.500 0.00 0.00 32.04 0.98
126 127 6.808321 ATGGTAGAACAGCTCACCTTATAA 57.192 37.500 0.00 0.00 32.04 0.98
127 128 6.614694 TGGTAGAACAGCTCACCTTATAAA 57.385 37.500 0.00 0.00 32.04 1.40
128 129 6.640518 TGGTAGAACAGCTCACCTTATAAAG 58.359 40.000 0.00 0.00 32.04 1.85
129 130 6.439375 TGGTAGAACAGCTCACCTTATAAAGA 59.561 38.462 0.00 0.00 32.04 2.52
130 131 6.981559 GGTAGAACAGCTCACCTTATAAAGAG 59.018 42.308 0.00 5.36 0.00 2.85
131 132 5.983540 AGAACAGCTCACCTTATAAAGAGG 58.016 41.667 9.83 0.62 40.24 3.69
141 142 5.735766 ACCTTATAAAGAGGTGCAACTCTC 58.264 41.667 33.62 18.20 46.70 3.20
142 143 5.485708 ACCTTATAAAGAGGTGCAACTCTCT 59.514 40.000 33.62 23.89 46.70 3.10
143 144 6.045955 CCTTATAAAGAGGTGCAACTCTCTC 58.954 44.000 33.62 7.77 46.70 3.20
144 145 6.127196 CCTTATAAAGAGGTGCAACTCTCTCT 60.127 42.308 33.62 22.29 46.70 3.10
145 146 3.676291 AAAGAGGTGCAACTCTCTCTC 57.324 47.619 33.62 6.52 46.70 3.20
146 147 2.300956 AGAGGTGCAACTCTCTCTCA 57.699 50.000 28.85 0.00 44.23 3.27
147 148 2.603021 AGAGGTGCAACTCTCTCTCAA 58.397 47.619 28.85 0.00 44.23 3.02
148 149 2.298729 AGAGGTGCAACTCTCTCTCAAC 59.701 50.000 28.85 0.14 44.23 3.18
149 150 2.298729 GAGGTGCAACTCTCTCTCAACT 59.701 50.000 24.80 0.00 36.74 3.16
150 151 2.703007 AGGTGCAACTCTCTCTCAACTT 59.297 45.455 0.00 0.00 36.74 2.66
151 152 3.063485 GGTGCAACTCTCTCTCAACTTC 58.937 50.000 0.00 0.00 36.74 3.01
152 153 3.063485 GTGCAACTCTCTCTCAACTTCC 58.937 50.000 0.00 0.00 0.00 3.46
153 154 2.288457 TGCAACTCTCTCTCAACTTCCG 60.288 50.000 0.00 0.00 0.00 4.30
154 155 2.928731 GCAACTCTCTCTCAACTTCCGG 60.929 54.545 0.00 0.00 0.00 5.14
155 156 1.551452 ACTCTCTCTCAACTTCCGGG 58.449 55.000 0.00 0.00 0.00 5.73
156 157 0.820871 CTCTCTCTCAACTTCCGGGG 59.179 60.000 0.00 0.00 0.00 5.73
157 158 0.114560 TCTCTCTCAACTTCCGGGGT 59.885 55.000 0.00 0.00 0.00 4.95
158 159 0.247736 CTCTCTCAACTTCCGGGGTG 59.752 60.000 0.00 0.00 0.00 4.61
159 160 1.192146 TCTCTCAACTTCCGGGGTGG 61.192 60.000 0.00 0.00 40.09 4.61
160 161 2.185310 CTCTCAACTTCCGGGGTGGG 62.185 65.000 0.00 0.00 38.76 4.61
161 162 2.122324 TCAACTTCCGGGGTGGGA 60.122 61.111 0.00 0.56 38.76 4.37
162 163 2.033602 CAACTTCCGGGGTGGGAC 59.966 66.667 0.00 0.00 38.76 4.46
163 164 2.122099 AACTTCCGGGGTGGGACT 60.122 61.111 0.00 0.00 38.76 3.85
164 165 1.159184 AACTTCCGGGGTGGGACTA 59.841 57.895 0.00 0.00 38.76 2.59
165 166 0.474273 AACTTCCGGGGTGGGACTAA 60.474 55.000 0.00 0.00 38.76 2.24
166 167 0.474273 ACTTCCGGGGTGGGACTAAA 60.474 55.000 0.00 0.00 38.76 1.85
167 168 0.035725 CTTCCGGGGTGGGACTAAAC 60.036 60.000 0.00 0.00 38.76 2.01
168 169 0.474273 TTCCGGGGTGGGACTAAACT 60.474 55.000 0.00 0.00 38.76 2.66
169 170 0.474273 TCCGGGGTGGGACTAAACTT 60.474 55.000 0.00 0.00 38.76 2.66
170 171 0.402887 CCGGGGTGGGACTAAACTTT 59.597 55.000 0.00 0.00 0.00 2.66
171 172 1.629861 CCGGGGTGGGACTAAACTTTA 59.370 52.381 0.00 0.00 0.00 1.85
172 173 2.355412 CCGGGGTGGGACTAAACTTTAG 60.355 54.545 6.96 6.96 0.00 1.85
173 174 2.303890 CGGGGTGGGACTAAACTTTAGT 59.696 50.000 13.09 13.09 0.00 2.24
174 175 3.618263 CGGGGTGGGACTAAACTTTAGTC 60.618 52.174 24.83 24.83 42.28 2.59
175 176 3.586174 GGGGTGGGACTAAACTTTAGTCT 59.414 47.826 28.74 6.53 42.54 3.24
176 177 4.323333 GGGGTGGGACTAAACTTTAGTCTC 60.323 50.000 28.74 27.28 43.52 3.36
180 181 6.342338 TGGGACTAAACTTTAGTCTCACTC 57.658 41.667 29.15 17.55 46.65 3.51
181 182 5.836898 TGGGACTAAACTTTAGTCTCACTCA 59.163 40.000 29.15 19.69 46.65 3.41
182 183 6.157904 GGGACTAAACTTTAGTCTCACTCAC 58.842 44.000 28.74 16.70 42.92 3.51
183 184 6.015265 GGGACTAAACTTTAGTCTCACTCACT 60.015 42.308 28.74 2.38 42.92 3.41
184 185 7.435305 GGACTAAACTTTAGTCTCACTCACTT 58.565 38.462 28.74 1.97 42.54 3.16
185 186 7.595875 GGACTAAACTTTAGTCTCACTCACTTC 59.404 40.741 28.74 13.10 42.54 3.01
186 187 8.008513 ACTAAACTTTAGTCTCACTCACTTCA 57.991 34.615 8.19 0.00 0.00 3.02
187 188 7.921745 ACTAAACTTTAGTCTCACTCACTTCAC 59.078 37.037 8.19 0.00 0.00 3.18
188 189 6.472686 AACTTTAGTCTCACTCACTTCACT 57.527 37.500 0.00 0.00 0.00 3.41
189 190 6.079424 ACTTTAGTCTCACTCACTTCACTC 57.921 41.667 0.00 0.00 0.00 3.51
190 191 5.594725 ACTTTAGTCTCACTCACTTCACTCA 59.405 40.000 0.00 0.00 0.00 3.41
191 192 5.440234 TTAGTCTCACTCACTTCACTCAC 57.560 43.478 0.00 0.00 0.00 3.51
192 193 3.291584 AGTCTCACTCACTTCACTCACA 58.708 45.455 0.00 0.00 0.00 3.58
193 194 3.894427 AGTCTCACTCACTTCACTCACAT 59.106 43.478 0.00 0.00 0.00 3.21
194 195 3.986572 GTCTCACTCACTTCACTCACATG 59.013 47.826 0.00 0.00 0.00 3.21
195 196 3.638627 TCTCACTCACTTCACTCACATGT 59.361 43.478 0.00 0.00 0.00 3.21
196 197 3.721035 TCACTCACTTCACTCACATGTG 58.279 45.455 20.18 20.18 39.15 3.21
197 198 3.132824 TCACTCACTTCACTCACATGTGT 59.867 43.478 24.63 4.31 38.90 3.72
198 199 4.340950 TCACTCACTTCACTCACATGTGTA 59.659 41.667 24.63 11.15 38.90 2.90
199 200 4.445718 CACTCACTTCACTCACATGTGTAC 59.554 45.833 24.63 0.00 38.90 2.90
200 201 4.099419 ACTCACTTCACTCACATGTGTACA 59.901 41.667 24.63 5.64 38.90 2.90
201 202 5.213891 TCACTTCACTCACATGTGTACAT 57.786 39.130 24.63 6.88 38.90 2.29
211 212 2.824689 ATGTGTACATGAATGGGCCA 57.175 45.000 9.61 9.61 34.83 5.36
212 213 2.593925 TGTGTACATGAATGGGCCAA 57.406 45.000 11.89 0.00 0.00 4.52
213 214 2.881734 TGTGTACATGAATGGGCCAAA 58.118 42.857 11.89 0.00 0.00 3.28
214 215 3.234353 TGTGTACATGAATGGGCCAAAA 58.766 40.909 11.89 0.00 0.00 2.44
215 216 3.643320 TGTGTACATGAATGGGCCAAAAA 59.357 39.130 11.89 0.00 0.00 1.94
243 244 6.959671 TTAGAATTTTAATTGGGCTTTGCG 57.040 33.333 0.00 0.00 0.00 4.85
244 245 4.893608 AGAATTTTAATTGGGCTTTGCGT 58.106 34.783 0.00 0.00 0.00 5.24
245 246 4.929211 AGAATTTTAATTGGGCTTTGCGTC 59.071 37.500 0.00 0.00 0.00 5.19
246 247 3.735237 TTTTAATTGGGCTTTGCGTCA 57.265 38.095 0.00 0.00 0.00 4.35
247 248 3.735237 TTTAATTGGGCTTTGCGTCAA 57.265 38.095 0.00 0.00 0.00 3.18
248 249 3.735237 TTAATTGGGCTTTGCGTCAAA 57.265 38.095 5.20 5.20 0.00 2.69
258 259 4.278678 CTTTGCGTCAAAGGCCTATTAG 57.721 45.455 5.16 0.00 44.75 1.73
259 260 1.663695 TGCGTCAAAGGCCTATTAGC 58.336 50.000 5.16 9.53 0.00 3.09
260 261 1.065782 TGCGTCAAAGGCCTATTAGCA 60.066 47.619 5.16 12.32 0.00 3.49
261 262 2.014128 GCGTCAAAGGCCTATTAGCAA 58.986 47.619 5.16 0.00 0.00 3.91
262 263 2.422127 GCGTCAAAGGCCTATTAGCAAA 59.578 45.455 5.16 0.00 0.00 3.68
263 264 3.119637 GCGTCAAAGGCCTATTAGCAAAA 60.120 43.478 5.16 0.00 0.00 2.44
264 265 4.440112 GCGTCAAAGGCCTATTAGCAAAAT 60.440 41.667 5.16 0.00 0.00 1.82
265 266 5.650543 CGTCAAAGGCCTATTAGCAAAATT 58.349 37.500 5.16 0.00 0.00 1.82
266 267 5.743872 CGTCAAAGGCCTATTAGCAAAATTC 59.256 40.000 5.16 0.00 0.00 2.17
267 268 6.042777 GTCAAAGGCCTATTAGCAAAATTCC 58.957 40.000 5.16 0.00 0.00 3.01
268 269 5.719085 TCAAAGGCCTATTAGCAAAATTCCA 59.281 36.000 5.16 0.00 0.00 3.53
269 270 6.212388 TCAAAGGCCTATTAGCAAAATTCCAA 59.788 34.615 5.16 0.00 0.00 3.53
270 271 5.598416 AGGCCTATTAGCAAAATTCCAAC 57.402 39.130 1.29 0.00 0.00 3.77
271 272 5.022787 AGGCCTATTAGCAAAATTCCAACA 58.977 37.500 1.29 0.00 0.00 3.33
296 297 4.131088 GGAGGGCGGACAGTCGTC 62.131 72.222 0.00 0.00 41.80 4.20
383 393 7.475137 AGATAGACACTGACTAAAAGCTCTT 57.525 36.000 0.00 0.00 0.00 2.85
452 1044 9.804758 CTTCTTTCTACGAGGAGTACAAATTAT 57.195 33.333 0.00 0.00 0.00 1.28
463 1055 6.672657 AGGAGTACAAATTATGGACCTGTAGT 59.327 38.462 0.00 0.00 44.72 2.73
464 1056 6.985059 GGAGTACAAATTATGGACCTGTAGTC 59.015 42.308 12.56 12.56 44.72 2.59
465 1057 7.147707 GGAGTACAAATTATGGACCTGTAGTCT 60.148 40.741 17.28 3.13 44.72 3.24
466 1058 8.834004 AGTACAAATTATGGACCTGTAGTCTA 57.166 34.615 0.00 0.00 44.72 2.59
467 1059 8.915036 AGTACAAATTATGGACCTGTAGTCTAG 58.085 37.037 0.00 0.00 44.72 2.43
468 1060 7.973048 ACAAATTATGGACCTGTAGTCTAGA 57.027 36.000 0.00 0.00 45.54 2.43
469 1061 7.783042 ACAAATTATGGACCTGTAGTCTAGAC 58.217 38.462 15.41 15.41 45.54 2.59
487 1079 8.846211 AGTCTAGACTCTAGATTTATGCAACTC 58.154 37.037 20.00 2.46 36.92 3.01
509 1101 8.094798 ACTCAAAATGACAAACGCTAATCTAA 57.905 30.769 0.00 0.00 0.00 2.10
510 1102 8.230486 ACTCAAAATGACAAACGCTAATCTAAG 58.770 33.333 0.00 0.00 0.00 2.18
533 1125 4.753516 AAAAACGCAAACACGATTGAAG 57.246 36.364 0.00 0.00 36.70 3.02
535 1127 2.663279 ACGCAAACACGATTGAAGAC 57.337 45.000 0.00 0.00 36.70 3.01
536 1128 2.210116 ACGCAAACACGATTGAAGACT 58.790 42.857 0.00 0.00 36.70 3.24
537 1129 2.221055 ACGCAAACACGATTGAAGACTC 59.779 45.455 0.00 0.00 36.70 3.36
538 1130 2.718789 CGCAAACACGATTGAAGACTCG 60.719 50.000 0.00 0.00 40.62 4.18
539 1131 2.475111 GCAAACACGATTGAAGACTCGA 59.525 45.455 0.00 0.00 38.24 4.04
541 1133 4.326278 GCAAACACGATTGAAGACTCGATA 59.674 41.667 0.00 0.00 38.24 2.92
544 1136 6.473778 CAAACACGATTGAAGACTCGATAGAT 59.526 38.462 0.00 0.00 37.14 1.98
545 1137 7.514280 CAAACACGATTGAAGACTCGATAGATG 60.514 40.741 0.00 0.00 37.14 2.90
549 1141 5.850653 CGATTGAAGACTCGATAGATGTCTG 59.149 44.000 5.16 0.00 45.93 3.51
550 1142 6.512578 CGATTGAAGACTCGATAGATGTCTGT 60.513 42.308 5.16 0.00 45.93 3.41
551 1143 5.491635 TGAAGACTCGATAGATGTCTGTG 57.508 43.478 5.16 0.00 45.93 3.66
567 1159 8.803235 AGATGTCTGTGTTGTAAATACTACTCA 58.197 33.333 6.69 7.79 38.88 3.41
570 1162 8.418662 TGTCTGTGTTGTAAATACTACTCACTT 58.581 33.333 6.69 0.00 38.88 3.16
665 1264 0.319641 AAGAACGCCACCTTCTCGTC 60.320 55.000 0.00 0.00 35.18 4.20
676 1275 5.067544 GCCACCTTCTCGTCTAATACTACTT 59.932 44.000 0.00 0.00 0.00 2.24
678 1277 6.318144 CCACCTTCTCGTCTAATACTACTTCA 59.682 42.308 0.00 0.00 0.00 3.02
679 1278 7.013464 CCACCTTCTCGTCTAATACTACTTCAT 59.987 40.741 0.00 0.00 0.00 2.57
680 1279 8.071368 CACCTTCTCGTCTAATACTACTTCATC 58.929 40.741 0.00 0.00 0.00 2.92
681 1280 7.041916 ACCTTCTCGTCTAATACTACTTCATCG 60.042 40.741 0.00 0.00 0.00 3.84
694 1296 7.596749 ACTACTTCATCGTCCAAAATACAAG 57.403 36.000 0.00 0.00 0.00 3.16
744 1350 7.602753 TCTCATTTACGATATGTAGTCCATGG 58.397 38.462 4.97 4.97 34.86 3.66
763 1369 9.283768 GTCCATGGTTACAACATCATCATTATA 57.716 33.333 12.58 0.00 0.00 0.98
862 1486 4.471904 TCACGCTACTTTCCAAGATCAT 57.528 40.909 0.00 0.00 0.00 2.45
976 2445 5.465056 CAGAAAGAACAGAGAGAAAGACACC 59.535 44.000 0.00 0.00 0.00 4.16
1046 2515 0.741221 GCTAAGCCGTCCTTGTCCAG 60.741 60.000 0.00 0.00 34.95 3.86
1583 3061 4.070552 GGGAGCTTGACGGCGTCT 62.071 66.667 36.17 19.67 37.29 4.18
1584 3062 2.048127 GGAGCTTGACGGCGTCTT 60.048 61.111 36.17 20.99 37.29 3.01
1585 3063 2.095252 GGAGCTTGACGGCGTCTTC 61.095 63.158 36.17 26.23 37.29 2.87
1588 3066 2.657237 CTTGACGGCGTCTTCCCT 59.343 61.111 36.17 2.00 33.15 4.20
1589 3067 1.004918 CTTGACGGCGTCTTCCCTT 60.005 57.895 36.17 1.13 33.15 3.95
1591 3069 2.434359 GACGGCGTCTTCCCTTGG 60.434 66.667 31.15 0.00 0.00 3.61
1592 3070 3.236003 GACGGCGTCTTCCCTTGGT 62.236 63.158 31.15 0.00 0.00 3.67
1593 3071 2.434359 CGGCGTCTTCCCTTGGTC 60.434 66.667 0.00 0.00 0.00 4.02
1596 3085 2.890766 GCGTCTTCCCTTGGTCCCA 61.891 63.158 0.00 0.00 0.00 4.37
1733 3229 2.226437 GACAACCATGGTCACATCACAC 59.774 50.000 20.07 0.00 34.35 3.82
1742 3238 1.441515 CACATCACACGCAAGCAGC 60.442 57.895 0.00 0.00 45.62 5.25
1817 3316 3.732849 CCTTGACCAGCCTCCCCC 61.733 72.222 0.00 0.00 0.00 5.40
1864 3363 1.303970 GCTTTCCTGCTCCTGCCTT 60.304 57.895 0.00 0.00 38.71 4.35
1878 3377 0.036765 TGCCTTACCTGTTACTGCCG 60.037 55.000 0.00 0.00 0.00 5.69
1900 3399 2.732094 GCGTTGACGTGCGGTACT 60.732 61.111 0.00 0.00 42.22 2.73
1913 3412 4.260051 CGTGCGGTACTGTATTACATTTGG 60.260 45.833 3.10 0.00 0.00 3.28
1995 3497 3.686016 TCTATGGTTCTCCTTTGGCAAC 58.314 45.455 0.00 0.00 34.23 4.17
2015 3517 4.918810 ACAAATTTGACACCTGTTCCTC 57.081 40.909 24.64 0.00 0.00 3.71
2066 3770 5.893824 ACTAGGATTCACATGGGGAATTTTC 59.106 40.000 13.89 5.15 35.23 2.29
2143 3858 6.226052 TCAGTAGACAGTACTGTTTCTCGTA 58.774 40.000 28.49 5.94 45.05 3.43
2220 3935 7.010160 ACCAACCAGATGAATTTTCCTTTCTA 58.990 34.615 0.00 0.00 0.00 2.10
2282 4000 4.569943 TGGTCTGCACTTCAATAGAGTTC 58.430 43.478 0.00 0.00 0.00 3.01
2321 4040 1.415374 TACGCGTCTTGCTTTGAGTC 58.585 50.000 18.63 0.00 43.27 3.36
2428 4147 3.196007 GATCCGTAGATCGCTTCAGAG 57.804 52.381 0.00 0.00 39.66 3.35
2429 4148 2.039818 TCCGTAGATCGCTTCAGAGT 57.960 50.000 0.00 0.00 38.35 3.24
2430 4149 2.366533 TCCGTAGATCGCTTCAGAGTT 58.633 47.619 0.00 0.00 38.35 3.01
2431 4150 2.355132 TCCGTAGATCGCTTCAGAGTTC 59.645 50.000 0.00 0.00 38.35 3.01
2432 4151 2.097629 CCGTAGATCGCTTCAGAGTTCA 59.902 50.000 0.00 0.00 38.35 3.18
2433 4152 3.358775 CGTAGATCGCTTCAGAGTTCAG 58.641 50.000 0.00 0.00 0.00 3.02
2434 4153 3.064134 CGTAGATCGCTTCAGAGTTCAGA 59.936 47.826 0.00 0.00 0.00 3.27
2443 4162 5.236478 CGCTTCAGAGTTCAGACCTTAAAAA 59.764 40.000 0.00 0.00 0.00 1.94
2495 4214 3.630312 GTGTTGGTTTTTCAGTGCTAGGA 59.370 43.478 0.00 0.00 0.00 2.94
2508 4227 2.548480 GTGCTAGGAAGTTGGTGTGTTC 59.452 50.000 0.00 0.00 0.00 3.18
2509 4228 2.152016 GCTAGGAAGTTGGTGTGTTCC 58.848 52.381 0.00 0.00 40.19 3.62
2572 4291 5.972382 GCGTGTCCTAATCTGTTCTACTAAG 59.028 44.000 0.00 0.00 0.00 2.18
2573 4292 6.404513 GCGTGTCCTAATCTGTTCTACTAAGT 60.405 42.308 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.002366 GGACAGAGCTATGCACGTTG 58.998 55.000 8.60 0.00 0.00 4.10
1 2 0.898320 AGGACAGAGCTATGCACGTT 59.102 50.000 8.60 0.00 0.00 3.99
2 3 0.457851 GAGGACAGAGCTATGCACGT 59.542 55.000 8.60 4.69 0.00 4.49
3 4 0.593518 CGAGGACAGAGCTATGCACG 60.594 60.000 8.60 5.54 0.00 5.34
4 5 0.741326 TCGAGGACAGAGCTATGCAC 59.259 55.000 8.60 1.13 0.00 4.57
5 6 0.741326 GTCGAGGACAGAGCTATGCA 59.259 55.000 8.60 0.00 32.09 3.96
6 7 1.001815 GAGTCGAGGACAGAGCTATGC 60.002 57.143 8.60 1.04 34.60 3.14
7 8 1.262950 CGAGTCGAGGACAGAGCTATG 59.737 57.143 6.73 6.84 34.60 2.23
8 9 1.588674 CGAGTCGAGGACAGAGCTAT 58.411 55.000 6.73 0.00 34.60 2.97
9 10 0.462225 CCGAGTCGAGGACAGAGCTA 60.462 60.000 15.64 0.00 34.60 3.32
10 11 1.747367 CCGAGTCGAGGACAGAGCT 60.747 63.158 15.64 0.00 34.60 4.09
11 12 2.795297 CCGAGTCGAGGACAGAGC 59.205 66.667 15.64 0.00 34.60 4.09
12 13 1.711060 GAGCCGAGTCGAGGACAGAG 61.711 65.000 15.64 0.00 34.60 3.35
13 14 1.745864 GAGCCGAGTCGAGGACAGA 60.746 63.158 15.64 0.00 34.60 3.41
14 15 1.587043 TTGAGCCGAGTCGAGGACAG 61.587 60.000 15.64 0.00 34.60 3.51
15 16 0.965866 ATTGAGCCGAGTCGAGGACA 60.966 55.000 15.64 5.88 34.60 4.02
16 17 0.248702 GATTGAGCCGAGTCGAGGAC 60.249 60.000 15.64 3.21 0.00 3.85
17 18 1.384989 GGATTGAGCCGAGTCGAGGA 61.385 60.000 15.64 0.00 0.00 3.71
18 19 1.066587 GGATTGAGCCGAGTCGAGG 59.933 63.158 15.64 0.00 0.00 4.63
19 20 1.066587 GGGATTGAGCCGAGTCGAG 59.933 63.158 15.64 5.33 0.00 4.04
20 21 2.771639 CGGGATTGAGCCGAGTCGA 61.772 63.158 15.64 0.00 0.00 4.20
21 22 2.278857 CGGGATTGAGCCGAGTCG 60.279 66.667 5.29 5.29 0.00 4.18
22 23 2.586357 GCGGGATTGAGCCGAGTC 60.586 66.667 0.00 0.00 0.00 3.36
23 24 4.162690 GGCGGGATTGAGCCGAGT 62.163 66.667 0.00 0.00 44.22 4.18
51 52 2.516460 TACTCCTCCTCGCTCGCC 60.516 66.667 0.00 0.00 0.00 5.54
52 53 2.716864 GTACTCCTCCTCGCTCGC 59.283 66.667 0.00 0.00 0.00 5.03
53 54 3.015677 CGTACTCCTCCTCGCTCG 58.984 66.667 0.00 0.00 0.00 5.03
54 55 2.716864 GCGTACTCCTCCTCGCTC 59.283 66.667 0.00 0.00 44.28 5.03
55 56 3.203412 CGCGTACTCCTCCTCGCT 61.203 66.667 0.00 0.00 45.25 4.93
56 57 3.507009 ACGCGTACTCCTCCTCGC 61.507 66.667 11.67 0.00 44.23 5.03
57 58 1.086067 TACACGCGTACTCCTCCTCG 61.086 60.000 13.44 0.00 0.00 4.63
58 59 0.656785 CTACACGCGTACTCCTCCTC 59.343 60.000 13.44 0.00 0.00 3.71
59 60 0.251354 TCTACACGCGTACTCCTCCT 59.749 55.000 13.44 0.00 0.00 3.69
60 61 1.263752 GATCTACACGCGTACTCCTCC 59.736 57.143 13.44 0.00 0.00 4.30
61 62 2.211806 AGATCTACACGCGTACTCCTC 58.788 52.381 13.44 6.82 0.00 3.71
62 63 2.211806 GAGATCTACACGCGTACTCCT 58.788 52.381 13.44 4.47 0.00 3.69
63 64 1.263752 GGAGATCTACACGCGTACTCC 59.736 57.143 13.44 18.02 33.60 3.85
64 65 2.211806 AGGAGATCTACACGCGTACTC 58.788 52.381 13.44 13.30 0.00 2.59
65 66 2.158928 AGAGGAGATCTACACGCGTACT 60.159 50.000 13.44 1.90 36.10 2.73
66 67 2.211806 AGAGGAGATCTACACGCGTAC 58.788 52.381 13.44 0.00 36.10 3.67
67 68 2.616634 AGAGGAGATCTACACGCGTA 57.383 50.000 13.44 0.00 36.10 4.42
68 69 1.671845 GAAGAGGAGATCTACACGCGT 59.328 52.381 5.58 5.58 37.23 6.01
69 70 1.944024 AGAAGAGGAGATCTACACGCG 59.056 52.381 7.93 3.53 37.23 6.01
70 71 2.946329 TGAGAAGAGGAGATCTACACGC 59.054 50.000 7.93 0.00 37.23 5.34
71 72 4.556501 GCATGAGAAGAGGAGATCTACACG 60.557 50.000 7.93 0.00 37.23 4.49
72 73 4.584325 AGCATGAGAAGAGGAGATCTACAC 59.416 45.833 7.93 0.00 37.23 2.90
73 74 4.802307 AGCATGAGAAGAGGAGATCTACA 58.198 43.478 7.93 0.00 37.23 2.74
74 75 4.826733 TGAGCATGAGAAGAGGAGATCTAC 59.173 45.833 0.00 0.00 37.23 2.59
75 76 5.059134 TGAGCATGAGAAGAGGAGATCTA 57.941 43.478 0.00 0.00 37.23 1.98
76 77 3.913509 TGAGCATGAGAAGAGGAGATCT 58.086 45.455 0.00 0.00 41.27 2.75
77 78 4.877378 ATGAGCATGAGAAGAGGAGATC 57.123 45.455 0.00 0.00 0.00 2.75
78 79 5.146298 TGTATGAGCATGAGAAGAGGAGAT 58.854 41.667 0.00 0.00 0.00 2.75
79 80 4.540715 TGTATGAGCATGAGAAGAGGAGA 58.459 43.478 0.00 0.00 0.00 3.71
80 81 4.933505 TGTATGAGCATGAGAAGAGGAG 57.066 45.455 0.00 0.00 0.00 3.69
81 82 5.682234 TTTGTATGAGCATGAGAAGAGGA 57.318 39.130 0.00 0.00 0.00 3.71
82 83 5.238868 CCATTTGTATGAGCATGAGAAGAGG 59.761 44.000 0.00 0.00 33.37 3.69
83 84 5.821470 ACCATTTGTATGAGCATGAGAAGAG 59.179 40.000 0.00 0.00 33.37 2.85
84 85 5.748402 ACCATTTGTATGAGCATGAGAAGA 58.252 37.500 0.00 0.00 33.37 2.87
85 86 6.988580 TCTACCATTTGTATGAGCATGAGAAG 59.011 38.462 0.00 0.00 33.37 2.85
86 87 6.888105 TCTACCATTTGTATGAGCATGAGAA 58.112 36.000 0.00 0.00 33.37 2.87
87 88 6.484364 TCTACCATTTGTATGAGCATGAGA 57.516 37.500 0.00 0.00 33.37 3.27
88 89 6.539826 TGTTCTACCATTTGTATGAGCATGAG 59.460 38.462 0.00 0.00 33.37 2.90
89 90 6.413892 TGTTCTACCATTTGTATGAGCATGA 58.586 36.000 0.00 0.00 33.37 3.07
90 91 6.682423 TGTTCTACCATTTGTATGAGCATG 57.318 37.500 0.00 0.00 33.37 4.06
91 92 5.297776 GCTGTTCTACCATTTGTATGAGCAT 59.702 40.000 0.00 0.00 33.37 3.79
92 93 4.635765 GCTGTTCTACCATTTGTATGAGCA 59.364 41.667 0.00 0.00 33.37 4.26
93 94 4.878397 AGCTGTTCTACCATTTGTATGAGC 59.122 41.667 0.00 0.00 33.37 4.26
94 95 6.036517 GTGAGCTGTTCTACCATTTGTATGAG 59.963 42.308 0.00 0.00 33.37 2.90
95 96 5.874810 GTGAGCTGTTCTACCATTTGTATGA 59.125 40.000 0.00 0.00 33.37 2.15
96 97 5.065218 GGTGAGCTGTTCTACCATTTGTATG 59.935 44.000 0.00 0.00 33.42 2.39
97 98 5.045578 AGGTGAGCTGTTCTACCATTTGTAT 60.046 40.000 0.00 0.00 35.66 2.29
98 99 4.286032 AGGTGAGCTGTTCTACCATTTGTA 59.714 41.667 0.00 0.00 35.66 2.41
99 100 3.073062 AGGTGAGCTGTTCTACCATTTGT 59.927 43.478 0.00 0.00 35.66 2.83
100 101 3.679389 AGGTGAGCTGTTCTACCATTTG 58.321 45.455 0.00 0.00 35.66 2.32
101 102 4.373156 AAGGTGAGCTGTTCTACCATTT 57.627 40.909 0.00 1.36 35.66 2.32
102 103 5.700402 ATAAGGTGAGCTGTTCTACCATT 57.300 39.130 0.00 8.30 35.66 3.16
103 104 6.808321 TTATAAGGTGAGCTGTTCTACCAT 57.192 37.500 0.00 6.19 35.66 3.55
104 105 6.439375 TCTTTATAAGGTGAGCTGTTCTACCA 59.561 38.462 0.00 0.00 35.66 3.25
105 106 6.875076 TCTTTATAAGGTGAGCTGTTCTACC 58.125 40.000 0.00 5.45 0.00 3.18
106 107 6.981559 CCTCTTTATAAGGTGAGCTGTTCTAC 59.018 42.308 0.00 0.00 0.00 2.59
107 108 6.668283 ACCTCTTTATAAGGTGAGCTGTTCTA 59.332 38.462 0.00 0.00 45.50 2.10
108 109 5.485708 ACCTCTTTATAAGGTGAGCTGTTCT 59.514 40.000 0.00 0.00 45.50 3.01
109 110 5.735766 ACCTCTTTATAAGGTGAGCTGTTC 58.264 41.667 0.00 0.00 45.50 3.18
110 111 5.763876 ACCTCTTTATAAGGTGAGCTGTT 57.236 39.130 0.00 0.00 45.50 3.16
119 120 5.983540 AGAGAGTTGCACCTCTTTATAAGG 58.016 41.667 15.62 0.00 41.85 2.69
120 121 6.872920 AGAGAGAGTTGCACCTCTTTATAAG 58.127 40.000 15.62 0.00 41.85 1.73
121 122 6.437477 TGAGAGAGAGTTGCACCTCTTTATAA 59.563 38.462 15.62 0.00 41.85 0.98
122 123 5.952347 TGAGAGAGAGTTGCACCTCTTTATA 59.048 40.000 15.62 0.00 41.85 0.98
123 124 4.774726 TGAGAGAGAGTTGCACCTCTTTAT 59.225 41.667 15.62 6.95 41.85 1.40
124 125 4.152647 TGAGAGAGAGTTGCACCTCTTTA 58.847 43.478 15.62 0.00 41.85 1.85
125 126 2.968574 TGAGAGAGAGTTGCACCTCTTT 59.031 45.455 15.62 9.81 41.85 2.52
126 127 2.603021 TGAGAGAGAGTTGCACCTCTT 58.397 47.619 15.62 5.53 41.85 2.85
127 128 2.298729 GTTGAGAGAGAGTTGCACCTCT 59.701 50.000 14.36 14.36 44.44 3.69
128 129 2.298729 AGTTGAGAGAGAGTTGCACCTC 59.701 50.000 2.46 2.46 0.00 3.85
129 130 2.324541 AGTTGAGAGAGAGTTGCACCT 58.675 47.619 0.00 0.00 0.00 4.00
130 131 2.829741 AGTTGAGAGAGAGTTGCACC 57.170 50.000 0.00 0.00 0.00 5.01
131 132 3.063485 GGAAGTTGAGAGAGAGTTGCAC 58.937 50.000 0.00 0.00 0.00 4.57
132 133 2.288457 CGGAAGTTGAGAGAGAGTTGCA 60.288 50.000 0.00 0.00 0.00 4.08
133 134 2.333014 CGGAAGTTGAGAGAGAGTTGC 58.667 52.381 0.00 0.00 0.00 4.17
134 135 2.353208 CCCGGAAGTTGAGAGAGAGTTG 60.353 54.545 0.73 0.00 0.00 3.16
135 136 1.896465 CCCGGAAGTTGAGAGAGAGTT 59.104 52.381 0.73 0.00 0.00 3.01
136 137 1.551452 CCCGGAAGTTGAGAGAGAGT 58.449 55.000 0.73 0.00 0.00 3.24
137 138 0.820871 CCCCGGAAGTTGAGAGAGAG 59.179 60.000 0.73 0.00 0.00 3.20
138 139 0.114560 ACCCCGGAAGTTGAGAGAGA 59.885 55.000 0.73 0.00 0.00 3.10
139 140 0.247736 CACCCCGGAAGTTGAGAGAG 59.752 60.000 0.73 0.00 0.00 3.20
140 141 1.192146 CCACCCCGGAAGTTGAGAGA 61.192 60.000 0.73 0.00 36.56 3.10
141 142 1.296715 CCACCCCGGAAGTTGAGAG 59.703 63.158 0.73 0.00 36.56 3.20
142 143 2.221299 CCCACCCCGGAAGTTGAGA 61.221 63.158 0.73 0.00 36.56 3.27
143 144 2.221299 TCCCACCCCGGAAGTTGAG 61.221 63.158 0.73 0.00 36.56 3.02
144 145 2.122324 TCCCACCCCGGAAGTTGA 60.122 61.111 0.73 0.00 36.56 3.18
145 146 1.196104 TAGTCCCACCCCGGAAGTTG 61.196 60.000 0.73 0.00 36.56 3.16
146 147 0.474273 TTAGTCCCACCCCGGAAGTT 60.474 55.000 0.73 0.00 36.56 2.66
147 148 0.474273 TTTAGTCCCACCCCGGAAGT 60.474 55.000 0.73 0.00 36.56 3.01
148 149 0.035725 GTTTAGTCCCACCCCGGAAG 60.036 60.000 0.73 0.00 36.56 3.46
149 150 0.474273 AGTTTAGTCCCACCCCGGAA 60.474 55.000 0.73 0.00 36.56 4.30
150 151 0.474273 AAGTTTAGTCCCACCCCGGA 60.474 55.000 0.73 0.00 36.56 5.14
151 152 0.402887 AAAGTTTAGTCCCACCCCGG 59.597 55.000 0.00 0.00 0.00 5.73
152 153 2.303890 ACTAAAGTTTAGTCCCACCCCG 59.696 50.000 20.34 0.00 0.00 5.73
153 154 3.586174 AGACTAAAGTTTAGTCCCACCCC 59.414 47.826 35.91 20.13 43.61 4.95
154 155 4.285260 TGAGACTAAAGTTTAGTCCCACCC 59.715 45.833 35.91 24.74 43.61 4.61
155 156 5.236282 GTGAGACTAAAGTTTAGTCCCACC 58.764 45.833 36.58 26.33 43.22 4.61
156 157 6.099159 AGTGAGACTAAAGTTTAGTCCCAC 57.901 41.667 37.99 37.99 46.75 4.61
157 158 5.836898 TGAGTGAGACTAAAGTTTAGTCCCA 59.163 40.000 35.91 31.63 43.61 4.37
158 159 6.015265 AGTGAGTGAGACTAAAGTTTAGTCCC 60.015 42.308 35.91 29.95 43.61 4.46
159 160 6.983984 AGTGAGTGAGACTAAAGTTTAGTCC 58.016 40.000 35.91 29.29 43.61 3.85
160 161 8.136165 TGAAGTGAGTGAGACTAAAGTTTAGTC 58.864 37.037 34.14 34.14 43.08 2.59
161 162 7.921745 GTGAAGTGAGTGAGACTAAAGTTTAGT 59.078 37.037 24.91 24.91 0.00 2.24
162 163 8.138712 AGTGAAGTGAGTGAGACTAAAGTTTAG 58.861 37.037 19.07 19.07 0.00 1.85
163 164 8.008513 AGTGAAGTGAGTGAGACTAAAGTTTA 57.991 34.615 0.00 0.00 0.00 2.01
164 165 6.879400 AGTGAAGTGAGTGAGACTAAAGTTT 58.121 36.000 0.00 0.00 0.00 2.66
165 166 6.096987 TGAGTGAAGTGAGTGAGACTAAAGTT 59.903 38.462 0.00 0.00 0.00 2.66
166 167 5.594725 TGAGTGAAGTGAGTGAGACTAAAGT 59.405 40.000 0.00 0.00 0.00 2.66
167 168 5.918011 GTGAGTGAAGTGAGTGAGACTAAAG 59.082 44.000 0.00 0.00 0.00 1.85
168 169 5.359860 TGTGAGTGAAGTGAGTGAGACTAAA 59.640 40.000 0.00 0.00 0.00 1.85
169 170 4.887655 TGTGAGTGAAGTGAGTGAGACTAA 59.112 41.667 0.00 0.00 0.00 2.24
170 171 4.461198 TGTGAGTGAAGTGAGTGAGACTA 58.539 43.478 0.00 0.00 0.00 2.59
171 172 3.291584 TGTGAGTGAAGTGAGTGAGACT 58.708 45.455 0.00 0.00 0.00 3.24
172 173 3.717400 TGTGAGTGAAGTGAGTGAGAC 57.283 47.619 0.00 0.00 0.00 3.36
173 174 3.638627 ACATGTGAGTGAAGTGAGTGAGA 59.361 43.478 0.00 0.00 0.00 3.27
174 175 3.739810 CACATGTGAGTGAAGTGAGTGAG 59.260 47.826 21.64 0.00 42.05 3.51
175 176 3.132824 ACACATGTGAGTGAAGTGAGTGA 59.867 43.478 31.94 0.00 42.05 3.41
176 177 3.461061 ACACATGTGAGTGAAGTGAGTG 58.539 45.455 31.94 0.49 42.05 3.51
177 178 3.827008 ACACATGTGAGTGAAGTGAGT 57.173 42.857 31.94 1.87 42.05 3.41
178 179 4.620982 TGTACACATGTGAGTGAAGTGAG 58.379 43.478 31.94 1.10 42.05 3.51
179 180 4.664150 TGTACACATGTGAGTGAAGTGA 57.336 40.909 31.94 2.65 42.05 3.41
180 181 5.273523 CATGTACACATGTGAGTGAAGTG 57.726 43.478 31.94 15.52 46.40 3.16
192 193 2.824689 TGGCCCATTCATGTACACAT 57.175 45.000 0.00 0.00 36.96 3.21
193 194 2.593925 TTGGCCCATTCATGTACACA 57.406 45.000 0.00 0.00 0.00 3.72
194 195 3.951775 TTTTGGCCCATTCATGTACAC 57.048 42.857 0.00 0.00 0.00 2.90
217 218 8.450180 CGCAAAGCCCAATTAAAATTCTAAAAT 58.550 29.630 0.00 0.00 0.00 1.82
218 219 7.442666 ACGCAAAGCCCAATTAAAATTCTAAAA 59.557 29.630 0.00 0.00 0.00 1.52
219 220 6.931840 ACGCAAAGCCCAATTAAAATTCTAAA 59.068 30.769 0.00 0.00 0.00 1.85
220 221 6.459923 ACGCAAAGCCCAATTAAAATTCTAA 58.540 32.000 0.00 0.00 0.00 2.10
221 222 6.031751 ACGCAAAGCCCAATTAAAATTCTA 57.968 33.333 0.00 0.00 0.00 2.10
222 223 4.893608 ACGCAAAGCCCAATTAAAATTCT 58.106 34.783 0.00 0.00 0.00 2.40
223 224 4.688413 TGACGCAAAGCCCAATTAAAATTC 59.312 37.500 0.00 0.00 0.00 2.17
224 225 4.636249 TGACGCAAAGCCCAATTAAAATT 58.364 34.783 0.00 0.00 0.00 1.82
225 226 4.264460 TGACGCAAAGCCCAATTAAAAT 57.736 36.364 0.00 0.00 0.00 1.82
226 227 3.735237 TGACGCAAAGCCCAATTAAAA 57.265 38.095 0.00 0.00 0.00 1.52
227 228 3.735237 TTGACGCAAAGCCCAATTAAA 57.265 38.095 0.00 0.00 0.00 1.52
228 229 3.553922 CCTTTGACGCAAAGCCCAATTAA 60.554 43.478 20.13 0.00 46.44 1.40
229 230 2.029470 CCTTTGACGCAAAGCCCAATTA 60.029 45.455 20.13 0.00 46.44 1.40
230 231 1.270252 CCTTTGACGCAAAGCCCAATT 60.270 47.619 20.13 0.00 46.44 2.32
231 232 0.318120 CCTTTGACGCAAAGCCCAAT 59.682 50.000 20.13 0.00 46.44 3.16
232 233 1.739049 CCTTTGACGCAAAGCCCAA 59.261 52.632 20.13 0.00 46.44 4.12
233 234 2.855514 GCCTTTGACGCAAAGCCCA 61.856 57.895 20.13 0.00 46.44 5.36
234 235 2.049156 GCCTTTGACGCAAAGCCC 60.049 61.111 20.13 12.64 46.44 5.19
235 236 1.241315 TAGGCCTTTGACGCAAAGCC 61.241 55.000 12.58 21.42 46.44 4.35
236 237 0.811281 ATAGGCCTTTGACGCAAAGC 59.189 50.000 12.58 16.26 46.44 3.51
238 239 2.422127 GCTAATAGGCCTTTGACGCAAA 59.578 45.455 12.58 0.00 0.00 3.68
239 240 2.014128 GCTAATAGGCCTTTGACGCAA 58.986 47.619 12.58 0.00 0.00 4.85
240 241 1.065782 TGCTAATAGGCCTTTGACGCA 60.066 47.619 12.58 11.53 0.00 5.24
241 242 1.663695 TGCTAATAGGCCTTTGACGC 58.336 50.000 12.58 8.74 0.00 5.19
242 243 4.695217 TTTTGCTAATAGGCCTTTGACG 57.305 40.909 12.58 0.00 0.00 4.35
243 244 6.042777 GGAATTTTGCTAATAGGCCTTTGAC 58.957 40.000 12.58 0.00 0.00 3.18
244 245 5.719085 TGGAATTTTGCTAATAGGCCTTTGA 59.281 36.000 12.58 0.00 0.00 2.69
245 246 5.976458 TGGAATTTTGCTAATAGGCCTTTG 58.024 37.500 12.58 0.00 0.00 2.77
246 247 6.013812 TGTTGGAATTTTGCTAATAGGCCTTT 60.014 34.615 12.58 8.06 0.00 3.11
247 248 5.483583 TGTTGGAATTTTGCTAATAGGCCTT 59.516 36.000 12.58 0.00 0.00 4.35
248 249 5.022787 TGTTGGAATTTTGCTAATAGGCCT 58.977 37.500 11.78 11.78 0.00 5.19
249 250 5.105351 ACTGTTGGAATTTTGCTAATAGGCC 60.105 40.000 0.00 0.00 0.00 5.19
250 251 5.965922 ACTGTTGGAATTTTGCTAATAGGC 58.034 37.500 0.00 0.00 0.00 3.93
251 252 7.273381 CGAAACTGTTGGAATTTTGCTAATAGG 59.727 37.037 0.00 0.00 0.00 2.57
252 253 8.020819 TCGAAACTGTTGGAATTTTGCTAATAG 58.979 33.333 0.00 0.00 0.00 1.73
253 254 7.877003 TCGAAACTGTTGGAATTTTGCTAATA 58.123 30.769 0.00 0.00 0.00 0.98
254 255 6.744112 TCGAAACTGTTGGAATTTTGCTAAT 58.256 32.000 0.00 0.00 0.00 1.73
255 256 6.137794 TCGAAACTGTTGGAATTTTGCTAA 57.862 33.333 0.00 0.00 0.00 3.09
256 257 5.278266 CCTCGAAACTGTTGGAATTTTGCTA 60.278 40.000 0.00 0.00 0.00 3.49
257 258 4.499696 CCTCGAAACTGTTGGAATTTTGCT 60.500 41.667 0.00 0.00 0.00 3.91
258 259 3.735746 CCTCGAAACTGTTGGAATTTTGC 59.264 43.478 0.00 0.00 0.00 3.68
259 260 5.181690 TCCTCGAAACTGTTGGAATTTTG 57.818 39.130 0.00 0.00 0.00 2.44
260 261 4.278419 CCTCCTCGAAACTGTTGGAATTTT 59.722 41.667 0.00 0.00 0.00 1.82
261 262 3.821033 CCTCCTCGAAACTGTTGGAATTT 59.179 43.478 0.00 0.00 0.00 1.82
262 263 3.412386 CCTCCTCGAAACTGTTGGAATT 58.588 45.455 0.00 0.00 0.00 2.17
263 264 2.290323 CCCTCCTCGAAACTGTTGGAAT 60.290 50.000 0.00 0.00 0.00 3.01
264 265 1.071699 CCCTCCTCGAAACTGTTGGAA 59.928 52.381 0.00 0.00 0.00 3.53
265 266 0.685097 CCCTCCTCGAAACTGTTGGA 59.315 55.000 0.00 0.00 0.00 3.53
266 267 0.955919 GCCCTCCTCGAAACTGTTGG 60.956 60.000 0.00 0.00 0.00 3.77
267 268 1.291877 CGCCCTCCTCGAAACTGTTG 61.292 60.000 0.00 0.00 0.00 3.33
268 269 1.004918 CGCCCTCCTCGAAACTGTT 60.005 57.895 0.00 0.00 0.00 3.16
269 270 2.657237 CGCCCTCCTCGAAACTGT 59.343 61.111 0.00 0.00 0.00 3.55
270 271 2.125512 CCGCCCTCCTCGAAACTG 60.126 66.667 0.00 0.00 0.00 3.16
271 272 2.283676 TCCGCCCTCCTCGAAACT 60.284 61.111 0.00 0.00 0.00 2.66
296 297 1.068083 CCGATCTCCCATGTGTCGG 59.932 63.158 0.00 0.00 44.72 4.79
408 421 2.789491 AGCCCGTATTCGTTAGTAGC 57.211 50.000 0.00 0.00 35.01 3.58
409 422 4.564940 AGAAGCCCGTATTCGTTAGTAG 57.435 45.455 0.00 0.00 35.01 2.57
452 1044 5.278873 TCTAGAGTCTAGACTACAGGTCCA 58.721 45.833 25.23 6.78 45.54 4.02
463 1055 8.753497 TGAGTTGCATAAATCTAGAGTCTAGA 57.247 34.615 27.92 27.92 32.39 2.43
464 1056 9.809096 TTTGAGTTGCATAAATCTAGAGTCTAG 57.191 33.333 19.55 19.55 32.39 2.43
466 1058 9.678260 ATTTTGAGTTGCATAAATCTAGAGTCT 57.322 29.630 0.00 0.00 32.39 3.24
467 1059 9.713740 CATTTTGAGTTGCATAAATCTAGAGTC 57.286 33.333 0.00 0.00 32.39 3.36
468 1060 9.453572 TCATTTTGAGTTGCATAAATCTAGAGT 57.546 29.630 0.00 0.00 32.39 3.24
469 1061 9.713740 GTCATTTTGAGTTGCATAAATCTAGAG 57.286 33.333 0.00 0.00 32.39 2.43
487 1079 8.948853 TTCTTAGATTAGCGTTTGTCATTTTG 57.051 30.769 0.00 0.00 0.00 2.44
524 1116 5.529430 AGACATCTATCGAGTCTTCAATCGT 59.471 40.000 0.00 0.00 39.45 3.73
527 1119 6.096141 ACACAGACATCTATCGAGTCTTCAAT 59.904 38.462 1.78 0.00 40.42 2.57
528 1120 5.416013 ACACAGACATCTATCGAGTCTTCAA 59.584 40.000 1.78 0.00 40.42 2.69
529 1121 4.944317 ACACAGACATCTATCGAGTCTTCA 59.056 41.667 1.78 0.00 40.42 3.02
530 1122 5.493133 ACACAGACATCTATCGAGTCTTC 57.507 43.478 1.78 0.00 40.42 2.87
531 1123 5.184096 ACAACACAGACATCTATCGAGTCTT 59.816 40.000 1.78 0.00 40.42 3.01
533 1125 4.987832 ACAACACAGACATCTATCGAGTC 58.012 43.478 0.00 0.00 0.00 3.36
535 1127 7.993821 ATTTACAACACAGACATCTATCGAG 57.006 36.000 0.00 0.00 0.00 4.04
536 1128 8.683615 AGTATTTACAACACAGACATCTATCGA 58.316 33.333 0.00 0.00 0.00 3.59
537 1129 8.858003 AGTATTTACAACACAGACATCTATCG 57.142 34.615 0.00 0.00 0.00 2.92
541 1133 8.803235 TGAGTAGTATTTACAACACAGACATCT 58.197 33.333 0.00 0.00 0.00 2.90
544 1136 7.948357 AGTGAGTAGTATTTACAACACAGACA 58.052 34.615 0.00 0.00 33.23 3.41
545 1137 8.813643 AAGTGAGTAGTATTTACAACACAGAC 57.186 34.615 0.00 0.00 33.23 3.51
605 1202 8.823220 TCTATGCTAAGGCTATCATACATGTA 57.177 34.615 8.27 8.27 39.59 2.29
606 1203 7.724490 TCTATGCTAAGGCTATCATACATGT 57.276 36.000 2.69 2.69 39.59 3.21
607 1204 9.043079 CAATCTATGCTAAGGCTATCATACATG 57.957 37.037 0.00 0.00 39.59 3.21
648 1247 0.524862 TAGACGAGAAGGTGGCGTTC 59.475 55.000 0.00 0.00 38.51 3.95
676 1275 2.675844 CGGCTTGTATTTTGGACGATGA 59.324 45.455 0.00 0.00 31.11 2.92
678 1277 2.706890 ACGGCTTGTATTTTGGACGAT 58.293 42.857 0.00 0.00 34.03 3.73
679 1278 2.172851 ACGGCTTGTATTTTGGACGA 57.827 45.000 0.00 0.00 34.03 4.20
1022 2491 2.722201 AAGGACGGCTTAGCGGGAG 61.722 63.158 15.86 1.83 33.14 4.30
1581 3059 1.584724 GAGATGGGACCAAGGGAAGA 58.415 55.000 0.00 0.00 0.00 2.87
1583 3061 0.121197 AGGAGATGGGACCAAGGGAA 59.879 55.000 0.00 0.00 0.00 3.97
1584 3062 0.621571 CAGGAGATGGGACCAAGGGA 60.622 60.000 0.00 0.00 0.00 4.20
1585 3063 0.916358 ACAGGAGATGGGACCAAGGG 60.916 60.000 0.00 0.00 0.00 3.95
1588 3066 2.305927 GAGAAACAGGAGATGGGACCAA 59.694 50.000 0.00 0.00 0.00 3.67
1589 3067 1.909302 GAGAAACAGGAGATGGGACCA 59.091 52.381 0.00 0.00 0.00 4.02
1591 3069 3.054802 ACATGAGAAACAGGAGATGGGAC 60.055 47.826 0.00 0.00 34.19 4.46
1592 3070 3.184628 ACATGAGAAACAGGAGATGGGA 58.815 45.455 0.00 0.00 34.19 4.37
1593 3071 3.641434 ACATGAGAAACAGGAGATGGG 57.359 47.619 0.00 0.00 34.19 4.00
1596 3085 8.255111 TGATACATACATGAGAAACAGGAGAT 57.745 34.615 0.00 0.00 34.19 2.75
1733 3229 3.207474 AGAAACTAATTGCTGCTTGCG 57.793 42.857 0.00 0.00 46.63 4.85
1823 3322 2.069273 CACGAAACTGCGGAGAGAATT 58.931 47.619 12.26 0.00 35.12 2.17
1864 3363 0.668096 CGCAACGGCAGTAACAGGTA 60.668 55.000 0.00 0.00 41.24 3.08
1891 3390 4.632688 ACCAAATGTAATACAGTACCGCAC 59.367 41.667 0.00 0.00 0.00 5.34
1892 3391 4.834534 ACCAAATGTAATACAGTACCGCA 58.165 39.130 0.00 0.00 0.00 5.69
1893 3392 4.871557 TGACCAAATGTAATACAGTACCGC 59.128 41.667 0.00 0.00 0.00 5.68
1894 3393 7.548196 AATGACCAAATGTAATACAGTACCG 57.452 36.000 0.00 0.00 0.00 4.02
1895 3394 8.952278 TCAAATGACCAAATGTAATACAGTACC 58.048 33.333 0.00 0.00 0.00 3.34
1995 3497 3.891366 AGGAGGAACAGGTGTCAAATTTG 59.109 43.478 12.15 12.15 0.00 2.32
2007 3509 4.757149 CCTAGTGTTTTTCAGGAGGAACAG 59.243 45.833 0.00 0.00 34.56 3.16
2043 3545 5.302823 GGAAAATTCCCCATGTGAATCCTAG 59.697 44.000 7.84 0.00 41.62 3.02
2066 3770 2.555325 TGTACCATACTAATCGCGGAGG 59.445 50.000 6.13 0.00 0.00 4.30
2149 3864 5.823045 GCACTAGCACCATACTATTCCTTTT 59.177 40.000 0.00 0.00 41.58 2.27
2152 3867 4.227197 AGCACTAGCACCATACTATTCCT 58.773 43.478 0.00 0.00 45.49 3.36
2153 3868 4.608948 AGCACTAGCACCATACTATTCC 57.391 45.455 0.00 0.00 45.49 3.01
2220 3935 3.314693 TCAACAACTGGTAGGTCCTCTT 58.685 45.455 0.00 0.00 37.07 2.85
2282 4000 5.274718 CGTAATGAAGTGCTGTAGGTCTAG 58.725 45.833 0.00 0.00 0.00 2.43
2321 4040 1.001487 TGATGGCTTGCGACAAACTTG 60.001 47.619 0.00 0.00 0.00 3.16
2428 4147 8.406297 ACTGACTTTCATTTTTAAGGTCTGAAC 58.594 33.333 10.42 0.00 36.25 3.18
2429 4148 8.519799 ACTGACTTTCATTTTTAAGGTCTGAA 57.480 30.769 10.42 0.00 36.25 3.02
2430 4149 7.993183 AGACTGACTTTCATTTTTAAGGTCTGA 59.007 33.333 10.42 0.00 36.25 3.27
2431 4150 8.159344 AGACTGACTTTCATTTTTAAGGTCTG 57.841 34.615 0.00 0.00 37.66 3.51
2432 4151 8.753497 AAGACTGACTTTCATTTTTAAGGTCT 57.247 30.769 0.00 0.00 34.87 3.85
2443 4162 5.765182 CACAACCCTAAAGACTGACTTTCAT 59.235 40.000 8.32 0.00 44.36 2.57
2495 4214 3.883489 GCTTCTAAGGAACACACCAACTT 59.117 43.478 0.00 0.00 0.00 2.66
2508 4227 2.613133 GCTGCATTCTGAGCTTCTAAGG 59.387 50.000 0.00 0.00 32.12 2.69
2509 4228 3.533547 AGCTGCATTCTGAGCTTCTAAG 58.466 45.455 1.02 0.00 43.15 2.18


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

AutoCloner maintained by Alex Coulton.