Multiple sequence alignment - TraesCS1A01G047800

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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 TraesCS1A01G047800 chr1A 100.000 2567 0 0 1 2567 29789720 29792286 0.000000e+00 4741
1 TraesCS1A01G047800 chr5A 97.738 2210 47 2 361 2567 671174980 671172771 0.000000e+00 3801
2 TraesCS1A01G047800 chr5A 97.833 1569 32 2 1000 2567 132296901 132295334 0.000000e+00 2708
3 TraesCS1A01G047800 chr5A 97.385 1568 36 3 1001 2567 6674433 6672870 0.000000e+00 2663
4 TraesCS1A01G047800 chr2A 97.283 2208 47 6 361 2567 98134603 98132408 0.000000e+00 3733
5 TraesCS1A01G047800 chr4A 96.213 2218 63 7 357 2567 257019845 257022048 0.000000e+00 3611
6 TraesCS1A01G047800 chr4A 97.829 1566 31 3 1003 2567 625823807 625825370 0.000000e+00 2700
7 TraesCS1A01G047800 chr4A 97.511 1567 34 3 1002 2567 521546967 521545405 0.000000e+00 2673
8 TraesCS1A01G047800 chr4A 88.749 1271 138 5 359 1626 321128210 321126942 0.000000e+00 1550
9 TraesCS1A01G047800 chr4A 96.022 729 17 5 357 1075 278349853 278350579 0.000000e+00 1175
10 TraesCS1A01G047800 chr6A 97.959 1568 30 2 1001 2567 463536537 463534971 0.000000e+00 2717
11 TraesCS1A01G047800 chr7A 97.640 1568 35 2 1001 2567 5440228 5438662 0.000000e+00 2689
12 TraesCS1A01G047800 chr7A 97.321 1568 40 2 1001 2567 696841535 696843101 0.000000e+00 2662
13 TraesCS1A01G047800 chr1D 89.694 359 26 6 2 350 28567064 28567421 5.040000e-122 448
14 TraesCS1A01G047800 chr6D 85.174 317 34 9 40 348 470858583 470858272 1.920000e-81 313
15 TraesCS1A01G047800 chr2D 87.654 243 20 7 361 595 159860985 159860745 9.050000e-70 274
16 TraesCS1A01G047800 chr2D 87.190 242 20 7 360 595 196351127 196351363 5.450000e-67 265
17 TraesCS1A01G047800 chr3D 87.654 243 18 8 361 595 545055456 545055694 3.250000e-69 272
18 TraesCS1A01G047800 chr1B 91.837 196 10 5 1 192 47175268 47175461 4.210000e-68 268
19 TraesCS1A01G047800 chr1B 91.150 113 9 1 237 348 47175461 47175573 4.420000e-33 152
20 TraesCS1A01G047800 chr7D 87.137 241 19 7 361 595 554145806 554146040 1.960000e-66 263
21 TraesCS1A01G047800 chr4B 81.567 217 27 5 40 248 24551254 24551465 1.580000e-37 167


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 TraesCS1A01G047800 chr1A 29789720 29792286 2566 False 4741 4741 100.000 1 2567 1 chr1A.!!$F1 2566
1 TraesCS1A01G047800 chr5A 671172771 671174980 2209 True 3801 3801 97.738 361 2567 1 chr5A.!!$R3 2206
2 TraesCS1A01G047800 chr5A 132295334 132296901 1567 True 2708 2708 97.833 1000 2567 1 chr5A.!!$R2 1567
3 TraesCS1A01G047800 chr5A 6672870 6674433 1563 True 2663 2663 97.385 1001 2567 1 chr5A.!!$R1 1566
4 TraesCS1A01G047800 chr2A 98132408 98134603 2195 True 3733 3733 97.283 361 2567 1 chr2A.!!$R1 2206
5 TraesCS1A01G047800 chr4A 257019845 257022048 2203 False 3611 3611 96.213 357 2567 1 chr4A.!!$F1 2210
6 TraesCS1A01G047800 chr4A 625823807 625825370 1563 False 2700 2700 97.829 1003 2567 1 chr4A.!!$F3 1564
7 TraesCS1A01G047800 chr4A 521545405 521546967 1562 True 2673 2673 97.511 1002 2567 1 chr4A.!!$R2 1565
8 TraesCS1A01G047800 chr4A 321126942 321128210 1268 True 1550 1550 88.749 359 1626 1 chr4A.!!$R1 1267
9 TraesCS1A01G047800 chr4A 278349853 278350579 726 False 1175 1175 96.022 357 1075 1 chr4A.!!$F2 718
10 TraesCS1A01G047800 chr6A 463534971 463536537 1566 True 2717 2717 97.959 1001 2567 1 chr6A.!!$R1 1566
11 TraesCS1A01G047800 chr7A 5438662 5440228 1566 True 2689 2689 97.640 1001 2567 1 chr7A.!!$R1 1566
12 TraesCS1A01G047800 chr7A 696841535 696843101 1566 False 2662 2662 97.321 1001 2567 1 chr7A.!!$F1 1566

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
345 346 0.03467 GATGGAGCCCATGATAGCCC 60.035 60.0 10.99 0.0 45.26 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2005 0.465705 GTCCCGGAAGATGATGAGCA 59.534 55.0 0.73 0.0 0.0 4.26 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
23 24 6.733721 CTTTTTAAGTCCGCAACTCTTTTC 57.266 37.500 0.00 0.00 37.17 2.29
24 25 4.823790 TTTAAGTCCGCAACTCTTTTCC 57.176 40.909 0.00 0.00 37.17 3.13
25 26 2.341846 AAGTCCGCAACTCTTTTCCA 57.658 45.000 0.00 0.00 37.17 3.53
26 27 2.341846 AGTCCGCAACTCTTTTCCAA 57.658 45.000 0.00 0.00 30.02 3.53
27 28 2.650322 AGTCCGCAACTCTTTTCCAAA 58.350 42.857 0.00 0.00 30.02 3.28
28 29 3.222603 AGTCCGCAACTCTTTTCCAAAT 58.777 40.909 0.00 0.00 30.02 2.32
29 30 3.253432 AGTCCGCAACTCTTTTCCAAATC 59.747 43.478 0.00 0.00 30.02 2.17
30 31 2.556622 TCCGCAACTCTTTTCCAAATCC 59.443 45.455 0.00 0.00 0.00 3.01
31 32 2.584791 CGCAACTCTTTTCCAAATCCG 58.415 47.619 0.00 0.00 0.00 4.18
32 33 2.031157 CGCAACTCTTTTCCAAATCCGT 60.031 45.455 0.00 0.00 0.00 4.69
33 34 3.308530 GCAACTCTTTTCCAAATCCGTG 58.691 45.455 0.00 0.00 0.00 4.94
34 35 3.857010 GCAACTCTTTTCCAAATCCGTGG 60.857 47.826 0.00 0.00 40.33 4.94
35 36 3.223674 ACTCTTTTCCAAATCCGTGGT 57.776 42.857 0.00 0.00 39.88 4.16
36 37 3.562182 ACTCTTTTCCAAATCCGTGGTT 58.438 40.909 0.00 0.00 39.88 3.67
37 38 3.958147 ACTCTTTTCCAAATCCGTGGTTT 59.042 39.130 0.00 0.00 39.88 3.27
38 39 4.404394 ACTCTTTTCCAAATCCGTGGTTTT 59.596 37.500 0.00 0.00 39.88 2.43
39 40 5.105106 ACTCTTTTCCAAATCCGTGGTTTTT 60.105 36.000 0.00 0.00 39.88 1.94
80 81 9.538508 ACTAAAACAGTAAAGATACGACAAACT 57.461 29.630 0.00 0.00 34.98 2.66
83 84 7.880059 AACAGTAAAGATACGACAAACTACC 57.120 36.000 0.00 0.00 37.11 3.18
84 85 6.393171 ACAGTAAAGATACGACAAACTACCC 58.607 40.000 0.00 0.00 37.11 3.69
85 86 6.015180 ACAGTAAAGATACGACAAACTACCCA 60.015 38.462 0.00 0.00 37.11 4.51
86 87 7.039882 CAGTAAAGATACGACAAACTACCCAT 58.960 38.462 0.00 0.00 37.11 4.00
87 88 7.010183 CAGTAAAGATACGACAAACTACCCATG 59.990 40.741 0.00 0.00 37.11 3.66
88 89 5.416271 AAGATACGACAAACTACCCATGT 57.584 39.130 0.00 0.00 0.00 3.21
89 90 5.416271 AGATACGACAAACTACCCATGTT 57.584 39.130 0.00 0.00 0.00 2.71
90 91 5.175859 AGATACGACAAACTACCCATGTTG 58.824 41.667 0.00 0.00 35.12 3.33
91 92 3.478857 ACGACAAACTACCCATGTTGA 57.521 42.857 0.00 0.00 33.56 3.18
92 93 3.811083 ACGACAAACTACCCATGTTGAA 58.189 40.909 0.00 0.00 33.56 2.69
93 94 4.200874 ACGACAAACTACCCATGTTGAAA 58.799 39.130 0.00 0.00 33.56 2.69
94 95 4.825085 ACGACAAACTACCCATGTTGAAAT 59.175 37.500 0.00 0.00 33.56 2.17
95 96 5.048991 ACGACAAACTACCCATGTTGAAATC 60.049 40.000 0.00 0.00 33.56 2.17
96 97 5.049060 CGACAAACTACCCATGTTGAAATCA 60.049 40.000 0.00 0.00 31.40 2.57
97 98 6.514212 CGACAAACTACCCATGTTGAAATCAA 60.514 38.462 0.00 0.00 31.40 2.57
98 99 7.301868 ACAAACTACCCATGTTGAAATCAAT 57.698 32.000 0.00 0.00 38.24 2.57
99 100 7.153985 ACAAACTACCCATGTTGAAATCAATG 58.846 34.615 0.00 0.00 38.24 2.82
100 101 6.916360 AACTACCCATGTTGAAATCAATGT 57.084 33.333 0.00 0.00 38.24 2.71
101 102 6.271488 ACTACCCATGTTGAAATCAATGTG 57.729 37.500 0.00 2.21 38.24 3.21
102 103 6.009589 ACTACCCATGTTGAAATCAATGTGA 58.990 36.000 0.00 0.00 38.24 3.58
103 104 5.804944 ACCCATGTTGAAATCAATGTGAA 57.195 34.783 0.00 0.00 38.24 3.18
104 105 5.786311 ACCCATGTTGAAATCAATGTGAAG 58.214 37.500 0.00 1.00 38.24 3.02
105 106 5.305128 ACCCATGTTGAAATCAATGTGAAGT 59.695 36.000 0.00 1.50 38.24 3.01
106 107 5.636121 CCCATGTTGAAATCAATGTGAAGTG 59.364 40.000 0.00 0.00 38.24 3.16
107 108 5.636121 CCATGTTGAAATCAATGTGAAGTGG 59.364 40.000 0.00 0.00 38.24 4.00
108 109 5.850557 TGTTGAAATCAATGTGAAGTGGT 57.149 34.783 0.00 0.00 38.24 4.16
109 110 6.951062 TGTTGAAATCAATGTGAAGTGGTA 57.049 33.333 0.00 0.00 38.24 3.25
110 111 6.969366 TGTTGAAATCAATGTGAAGTGGTAG 58.031 36.000 0.00 0.00 38.24 3.18
111 112 6.545666 TGTTGAAATCAATGTGAAGTGGTAGT 59.454 34.615 0.00 0.00 38.24 2.73
112 113 6.801539 TGAAATCAATGTGAAGTGGTAGTC 57.198 37.500 0.00 0.00 0.00 2.59
113 114 6.295249 TGAAATCAATGTGAAGTGGTAGTCA 58.705 36.000 0.00 0.00 0.00 3.41
114 115 6.942005 TGAAATCAATGTGAAGTGGTAGTCAT 59.058 34.615 0.00 0.00 0.00 3.06
115 116 7.448161 TGAAATCAATGTGAAGTGGTAGTCATT 59.552 33.333 0.00 0.00 0.00 2.57
116 117 8.862325 AAATCAATGTGAAGTGGTAGTCATTA 57.138 30.769 0.00 0.00 0.00 1.90
117 118 8.862325 AATCAATGTGAAGTGGTAGTCATTAA 57.138 30.769 0.00 0.00 0.00 1.40
118 119 8.862325 ATCAATGTGAAGTGGTAGTCATTAAA 57.138 30.769 0.00 0.00 0.00 1.52
119 120 8.862325 TCAATGTGAAGTGGTAGTCATTAAAT 57.138 30.769 0.00 0.00 0.00 1.40
120 121 9.952030 TCAATGTGAAGTGGTAGTCATTAAATA 57.048 29.630 0.00 0.00 0.00 1.40
123 124 8.263940 TGTGAAGTGGTAGTCATTAAATAAGC 57.736 34.615 0.00 0.00 0.00 3.09
124 125 7.880713 TGTGAAGTGGTAGTCATTAAATAAGCA 59.119 33.333 0.00 0.00 0.00 3.91
125 126 8.391106 GTGAAGTGGTAGTCATTAAATAAGCAG 58.609 37.037 0.00 0.00 0.00 4.24
126 127 8.318412 TGAAGTGGTAGTCATTAAATAAGCAGA 58.682 33.333 0.00 0.00 0.00 4.26
127 128 9.331282 GAAGTGGTAGTCATTAAATAAGCAGAT 57.669 33.333 0.00 0.00 0.00 2.90
128 129 9.686683 AAGTGGTAGTCATTAAATAAGCAGATT 57.313 29.630 0.00 0.00 0.00 2.40
129 130 9.686683 AGTGGTAGTCATTAAATAAGCAGATTT 57.313 29.630 1.98 1.98 33.60 2.17
143 144 9.770097 AATAAGCAGATTTATTCTCGATCAAGA 57.230 29.630 0.00 0.00 29.49 3.02
144 145 9.941325 ATAAGCAGATTTATTCTCGATCAAGAT 57.059 29.630 0.00 0.00 29.93 2.40
145 146 8.674263 AAGCAGATTTATTCTCGATCAAGATT 57.326 30.769 0.00 0.00 29.93 2.40
146 147 8.085720 AGCAGATTTATTCTCGATCAAGATTG 57.914 34.615 0.00 0.00 29.93 2.67
147 148 6.796072 GCAGATTTATTCTCGATCAAGATTGC 59.204 38.462 0.00 0.00 29.93 3.56
148 149 7.307870 GCAGATTTATTCTCGATCAAGATTGCT 60.308 37.037 0.00 0.00 29.93 3.91
149 150 8.557864 CAGATTTATTCTCGATCAAGATTGCTT 58.442 33.333 0.00 0.00 29.93 3.91
150 151 9.118300 AGATTTATTCTCGATCAAGATTGCTTT 57.882 29.630 0.00 0.00 30.14 3.51
151 152 9.727627 GATTTATTCTCGATCAAGATTGCTTTT 57.272 29.630 0.00 0.00 30.14 2.27
152 153 9.727627 ATTTATTCTCGATCAAGATTGCTTTTC 57.272 29.630 0.00 0.00 30.14 2.29
153 154 6.748333 ATTCTCGATCAAGATTGCTTTTCA 57.252 33.333 0.00 0.00 30.14 2.69
154 155 5.536554 TCTCGATCAAGATTGCTTTTCAC 57.463 39.130 0.00 0.00 30.14 3.18
155 156 4.996758 TCTCGATCAAGATTGCTTTTCACA 59.003 37.500 0.00 0.00 30.14 3.58
156 157 5.469760 TCTCGATCAAGATTGCTTTTCACAA 59.530 36.000 0.00 0.00 30.14 3.33
157 158 5.692814 TCGATCAAGATTGCTTTTCACAAG 58.307 37.500 0.00 0.00 30.14 3.16
158 159 5.469760 TCGATCAAGATTGCTTTTCACAAGA 59.530 36.000 0.00 0.00 30.14 3.02
159 160 6.017192 TCGATCAAGATTGCTTTTCACAAGAA 60.017 34.615 0.00 0.00 30.14 2.52
160 161 6.087291 CGATCAAGATTGCTTTTCACAAGAAC 59.913 38.462 0.00 0.00 32.39 3.01
161 162 6.455360 TCAAGATTGCTTTTCACAAGAACT 57.545 33.333 0.00 0.00 32.39 3.01
162 163 6.866480 TCAAGATTGCTTTTCACAAGAACTT 58.134 32.000 0.00 0.00 32.39 2.66
163 164 6.753279 TCAAGATTGCTTTTCACAAGAACTTG 59.247 34.615 12.22 12.22 38.20 3.16
164 165 6.455360 AGATTGCTTTTCACAAGAACTTGA 57.545 33.333 19.35 0.00 42.93 3.02
165 166 6.268566 AGATTGCTTTTCACAAGAACTTGAC 58.731 36.000 19.35 2.95 42.93 3.18
166 167 5.384063 TTGCTTTTCACAAGAACTTGACA 57.616 34.783 19.35 4.31 42.93 3.58
167 168 4.985413 TGCTTTTCACAAGAACTTGACAG 58.015 39.130 19.35 9.77 42.93 3.51
168 169 4.142403 TGCTTTTCACAAGAACTTGACAGG 60.142 41.667 19.35 7.46 42.93 4.00
169 170 4.096382 GCTTTTCACAAGAACTTGACAGGA 59.904 41.667 19.35 9.27 42.93 3.86
170 171 5.393027 GCTTTTCACAAGAACTTGACAGGAA 60.393 40.000 19.35 13.47 42.93 3.36
171 172 5.818136 TTTCACAAGAACTTGACAGGAAG 57.182 39.130 19.35 0.00 42.93 3.46
172 173 3.808728 TCACAAGAACTTGACAGGAAGG 58.191 45.455 19.35 1.57 42.93 3.46
173 174 2.880890 CACAAGAACTTGACAGGAAGGG 59.119 50.000 19.35 0.00 42.93 3.95
174 175 2.158608 ACAAGAACTTGACAGGAAGGGG 60.159 50.000 19.35 0.00 42.93 4.79
175 176 2.106511 CAAGAACTTGACAGGAAGGGGA 59.893 50.000 8.65 0.00 42.93 4.81
176 177 2.418669 AGAACTTGACAGGAAGGGGAA 58.581 47.619 0.00 0.00 0.00 3.97
177 178 2.373502 AGAACTTGACAGGAAGGGGAAG 59.626 50.000 0.00 0.00 0.00 3.46
178 179 1.068121 ACTTGACAGGAAGGGGAAGG 58.932 55.000 0.00 0.00 0.00 3.46
179 180 1.362224 CTTGACAGGAAGGGGAAGGA 58.638 55.000 0.00 0.00 0.00 3.36
180 181 1.705186 CTTGACAGGAAGGGGAAGGAA 59.295 52.381 0.00 0.00 0.00 3.36
181 182 1.362224 TGACAGGAAGGGGAAGGAAG 58.638 55.000 0.00 0.00 0.00 3.46
182 183 0.621082 GACAGGAAGGGGAAGGAAGG 59.379 60.000 0.00 0.00 0.00 3.46
183 184 0.196118 ACAGGAAGGGGAAGGAAGGA 59.804 55.000 0.00 0.00 0.00 3.36
184 185 0.915364 CAGGAAGGGGAAGGAAGGAG 59.085 60.000 0.00 0.00 0.00 3.69
185 186 0.253394 AGGAAGGGGAAGGAAGGAGG 60.253 60.000 0.00 0.00 0.00 4.30
186 187 1.282653 GGAAGGGGAAGGAAGGAGGG 61.283 65.000 0.00 0.00 0.00 4.30
187 188 1.230314 AAGGGGAAGGAAGGAGGGG 60.230 63.158 0.00 0.00 0.00 4.79
188 189 1.772561 AAGGGGAAGGAAGGAGGGGA 61.773 60.000 0.00 0.00 0.00 4.81
189 190 1.694525 GGGGAAGGAAGGAGGGGAG 60.695 68.421 0.00 0.00 0.00 4.30
190 191 1.694525 GGGAAGGAAGGAGGGGAGG 60.695 68.421 0.00 0.00 0.00 4.30
191 192 1.694525 GGAAGGAAGGAGGGGAGGG 60.695 68.421 0.00 0.00 0.00 4.30
192 193 2.286502 AAGGAAGGAGGGGAGGGC 60.287 66.667 0.00 0.00 0.00 5.19
193 194 3.208342 AAGGAAGGAGGGGAGGGCA 62.208 63.158 0.00 0.00 0.00 5.36
194 195 2.368878 GGAAGGAGGGGAGGGCAT 60.369 66.667 0.00 0.00 0.00 4.40
195 196 1.073706 GGAAGGAGGGGAGGGCATA 60.074 63.158 0.00 0.00 0.00 3.14
196 197 1.419720 GGAAGGAGGGGAGGGCATAC 61.420 65.000 0.00 0.00 0.00 2.39
197 198 1.386057 AAGGAGGGGAGGGCATACC 60.386 63.158 0.00 0.00 40.67 2.73
207 208 3.191182 GGGCATACCTTGGACCTTG 57.809 57.895 0.00 0.00 35.85 3.61
208 209 0.331616 GGGCATACCTTGGACCTTGT 59.668 55.000 0.00 0.00 35.85 3.16
209 210 1.682087 GGGCATACCTTGGACCTTGTC 60.682 57.143 0.00 0.00 35.85 3.18
210 211 1.282157 GGCATACCTTGGACCTTGTCT 59.718 52.381 0.00 0.00 32.47 3.41
211 212 2.504175 GGCATACCTTGGACCTTGTCTA 59.496 50.000 0.00 0.00 32.47 2.59
212 213 3.054655 GGCATACCTTGGACCTTGTCTAA 60.055 47.826 0.00 0.00 32.45 2.10
213 214 4.192317 GCATACCTTGGACCTTGTCTAAG 58.808 47.826 11.93 11.93 46.10 2.18
219 220 1.623811 TGGACCTTGTCTAAGACCTGC 59.376 52.381 0.00 0.00 35.92 4.85
220 221 1.623811 GGACCTTGTCTAAGACCTGCA 59.376 52.381 0.00 0.00 35.92 4.41
221 222 2.354203 GGACCTTGTCTAAGACCTGCAG 60.354 54.545 6.78 6.78 35.92 4.41
222 223 1.002544 ACCTTGTCTAAGACCTGCAGC 59.997 52.381 8.66 0.00 35.92 5.25
223 224 1.277557 CCTTGTCTAAGACCTGCAGCT 59.722 52.381 8.66 0.00 35.92 4.24
224 225 2.615869 CTTGTCTAAGACCTGCAGCTC 58.384 52.381 8.66 4.17 35.92 4.09
225 226 0.528017 TGTCTAAGACCTGCAGCTCG 59.472 55.000 8.66 0.00 0.00 5.03
226 227 0.528470 GTCTAAGACCTGCAGCTCGT 59.472 55.000 8.66 5.35 0.00 4.18
227 228 0.811915 TCTAAGACCTGCAGCTCGTC 59.188 55.000 8.66 10.84 0.00 4.20
228 229 0.528017 CTAAGACCTGCAGCTCGTCA 59.472 55.000 19.58 3.76 0.00 4.35
229 230 0.528017 TAAGACCTGCAGCTCGTCAG 59.472 55.000 19.58 3.76 0.00 3.51
233 234 4.928398 CTGCAGCTCGTCAGGAAT 57.072 55.556 0.00 0.00 0.00 3.01
234 235 2.381109 CTGCAGCTCGTCAGGAATG 58.619 57.895 0.00 0.00 0.00 2.67
235 236 0.108472 CTGCAGCTCGTCAGGAATGA 60.108 55.000 0.00 0.00 0.00 2.57
236 237 0.108472 TGCAGCTCGTCAGGAATGAG 60.108 55.000 0.00 0.00 42.95 2.90
237 238 0.108424 GCAGCTCGTCAGGAATGAGT 60.108 55.000 0.00 0.00 42.20 3.41
238 239 1.919918 CAGCTCGTCAGGAATGAGTC 58.080 55.000 0.00 0.00 42.20 3.36
239 240 0.453793 AGCTCGTCAGGAATGAGTCG 59.546 55.000 0.00 0.00 42.20 4.18
240 241 0.526524 GCTCGTCAGGAATGAGTCGG 60.527 60.000 0.00 0.00 42.20 4.79
241 242 1.095600 CTCGTCAGGAATGAGTCGGA 58.904 55.000 0.00 0.00 36.43 4.55
242 243 1.064803 CTCGTCAGGAATGAGTCGGAG 59.935 57.143 0.00 0.00 36.43 4.63
243 244 1.095600 CGTCAGGAATGAGTCGGAGA 58.904 55.000 0.00 0.00 0.00 3.71
244 245 1.678627 CGTCAGGAATGAGTCGGAGAT 59.321 52.381 0.00 0.00 40.67 2.75
245 246 2.542618 CGTCAGGAATGAGTCGGAGATG 60.543 54.545 0.00 0.00 40.67 2.90
246 247 1.410517 TCAGGAATGAGTCGGAGATGC 59.589 52.381 0.00 0.00 40.67 3.91
247 248 1.411977 CAGGAATGAGTCGGAGATGCT 59.588 52.381 0.00 0.00 40.67 3.79
248 249 1.411977 AGGAATGAGTCGGAGATGCTG 59.588 52.381 0.00 0.00 40.67 4.41
249 250 1.216122 GAATGAGTCGGAGATGCTGC 58.784 55.000 0.00 0.00 40.67 5.25
250 251 0.829333 AATGAGTCGGAGATGCTGCT 59.171 50.000 0.00 0.00 40.67 4.24
251 252 0.104487 ATGAGTCGGAGATGCTGCTG 59.896 55.000 0.00 0.00 40.67 4.41
252 253 1.882167 GAGTCGGAGATGCTGCTGC 60.882 63.158 8.89 8.89 40.67 5.25
253 254 2.186384 GTCGGAGATGCTGCTGCT 59.814 61.111 17.00 2.26 40.67 4.24
254 255 1.882167 GTCGGAGATGCTGCTGCTC 60.882 63.158 17.00 11.22 40.67 4.26
255 256 2.588314 CGGAGATGCTGCTGCTCC 60.588 66.667 22.85 22.85 43.73 4.70
256 257 2.909577 GGAGATGCTGCTGCTCCT 59.090 61.111 24.40 12.70 43.79 3.69
257 258 1.524165 GGAGATGCTGCTGCTCCTG 60.524 63.158 24.40 0.00 43.79 3.86
258 259 2.124653 AGATGCTGCTGCTCCTGC 60.125 61.111 17.00 1.02 40.48 4.85
259 260 2.124653 GATGCTGCTGCTCCTGCT 60.125 61.111 17.00 0.00 40.48 4.24
260 261 1.145598 GATGCTGCTGCTCCTGCTA 59.854 57.895 17.00 0.00 40.48 3.49
261 262 1.153208 ATGCTGCTGCTCCTGCTAC 60.153 57.895 17.00 0.00 40.48 3.58
262 263 1.624479 ATGCTGCTGCTCCTGCTACT 61.624 55.000 17.00 0.00 40.48 2.57
263 264 1.814586 GCTGCTGCTCCTGCTACTG 60.815 63.158 8.53 0.00 40.48 2.74
264 265 1.814586 CTGCTGCTCCTGCTACTGC 60.815 63.158 0.00 0.00 40.48 4.40
274 275 3.490890 GCTACTGCAAGCTTCCGG 58.509 61.111 0.00 0.00 39.50 5.14
275 276 1.376037 GCTACTGCAAGCTTCCGGT 60.376 57.895 7.12 7.12 39.50 5.28
276 277 1.362406 GCTACTGCAAGCTTCCGGTC 61.362 60.000 4.77 0.00 39.50 4.79
277 278 1.078759 CTACTGCAAGCTTCCGGTCG 61.079 60.000 4.77 0.00 37.60 4.79
278 279 1.812686 TACTGCAAGCTTCCGGTCGT 61.813 55.000 4.77 0.00 37.60 4.34
279 280 2.357034 TGCAAGCTTCCGGTCGTC 60.357 61.111 0.00 0.00 0.00 4.20
280 281 2.048127 GCAAGCTTCCGGTCGTCT 60.048 61.111 0.00 0.00 0.00 4.18
281 282 1.214589 GCAAGCTTCCGGTCGTCTA 59.785 57.895 0.00 0.00 0.00 2.59
282 283 0.179108 GCAAGCTTCCGGTCGTCTAT 60.179 55.000 0.00 0.00 0.00 1.98
283 284 1.066605 GCAAGCTTCCGGTCGTCTATA 59.933 52.381 0.00 0.00 0.00 1.31
284 285 2.859032 GCAAGCTTCCGGTCGTCTATAG 60.859 54.545 0.00 0.00 0.00 1.31
285 286 1.606903 AGCTTCCGGTCGTCTATAGG 58.393 55.000 0.00 0.00 0.00 2.57
286 287 0.597072 GCTTCCGGTCGTCTATAGGG 59.403 60.000 0.00 0.00 0.00 3.53
287 288 1.816961 GCTTCCGGTCGTCTATAGGGA 60.817 57.143 0.00 0.00 0.00 4.20
288 289 2.152830 CTTCCGGTCGTCTATAGGGAG 58.847 57.143 0.00 0.00 0.00 4.30
289 290 0.399454 TCCGGTCGTCTATAGGGAGG 59.601 60.000 0.00 0.00 0.00 4.30
290 291 1.242665 CCGGTCGTCTATAGGGAGGC 61.243 65.000 0.00 0.00 0.00 4.70
291 292 0.250814 CGGTCGTCTATAGGGAGGCT 60.251 60.000 0.00 0.00 0.00 4.58
292 293 1.249407 GGTCGTCTATAGGGAGGCTG 58.751 60.000 0.00 0.00 0.00 4.85
293 294 1.249407 GTCGTCTATAGGGAGGCTGG 58.751 60.000 0.00 0.00 0.00 4.85
294 295 0.112606 TCGTCTATAGGGAGGCTGGG 59.887 60.000 0.00 0.00 0.00 4.45
295 296 0.900647 CGTCTATAGGGAGGCTGGGG 60.901 65.000 0.00 0.00 0.00 4.96
296 297 0.191314 GTCTATAGGGAGGCTGGGGT 59.809 60.000 0.00 0.00 0.00 4.95
297 298 0.191064 TCTATAGGGAGGCTGGGGTG 59.809 60.000 0.00 0.00 0.00 4.61
298 299 1.461461 TATAGGGAGGCTGGGGTGC 60.461 63.158 0.00 0.00 0.00 5.01
318 319 2.425592 CATCGAGGGCCGGCAATA 59.574 61.111 30.85 8.84 39.14 1.90
319 320 1.669115 CATCGAGGGCCGGCAATAG 60.669 63.158 30.85 16.17 39.14 1.73
320 321 2.883828 ATCGAGGGCCGGCAATAGG 61.884 63.158 30.85 13.09 39.14 2.57
321 322 4.626081 CGAGGGCCGGCAATAGGG 62.626 72.222 30.85 7.97 33.91 3.53
329 330 3.348236 GGCAATAGGGCGCAGATG 58.652 61.111 10.83 1.28 33.57 2.90
330 331 2.263741 GGCAATAGGGCGCAGATGG 61.264 63.158 10.83 0.00 33.57 3.51
331 332 1.227943 GCAATAGGGCGCAGATGGA 60.228 57.895 10.83 0.00 0.00 3.41
332 333 1.233285 GCAATAGGGCGCAGATGGAG 61.233 60.000 10.83 0.00 0.00 3.86
333 334 1.072159 AATAGGGCGCAGATGGAGC 59.928 57.895 10.83 0.00 42.17 4.70
338 339 3.285215 GCGCAGATGGAGCCCATG 61.285 66.667 10.99 1.75 45.26 3.66
339 340 2.507452 CGCAGATGGAGCCCATGA 59.493 61.111 10.99 0.00 45.26 3.07
340 341 1.072678 CGCAGATGGAGCCCATGAT 59.927 57.895 10.99 0.00 45.26 2.45
341 342 0.322648 CGCAGATGGAGCCCATGATA 59.677 55.000 10.99 0.00 45.26 2.15
342 343 1.675116 CGCAGATGGAGCCCATGATAG 60.675 57.143 10.99 1.08 45.26 2.08
343 344 1.949547 GCAGATGGAGCCCATGATAGC 60.950 57.143 10.99 6.33 45.26 2.97
344 345 0.990374 AGATGGAGCCCATGATAGCC 59.010 55.000 10.99 0.00 45.26 3.93
345 346 0.034670 GATGGAGCCCATGATAGCCC 60.035 60.000 10.99 0.00 45.26 5.19
346 347 0.477202 ATGGAGCCCATGATAGCCCT 60.477 55.000 5.97 0.00 43.39 5.19
347 348 1.130054 TGGAGCCCATGATAGCCCTC 61.130 60.000 0.00 0.00 0.00 4.30
348 349 1.130054 GGAGCCCATGATAGCCCTCA 61.130 60.000 0.00 0.00 0.00 3.86
349 350 0.036022 GAGCCCATGATAGCCCTCAC 59.964 60.000 0.00 0.00 0.00 3.51
350 351 0.695462 AGCCCATGATAGCCCTCACA 60.695 55.000 0.00 0.00 0.00 3.58
351 352 0.250640 GCCCATGATAGCCCTCACAG 60.251 60.000 0.00 0.00 0.00 3.66
352 353 1.427809 CCCATGATAGCCCTCACAGA 58.572 55.000 0.00 0.00 0.00 3.41
353 354 1.983691 CCCATGATAGCCCTCACAGAT 59.016 52.381 0.00 0.00 0.00 2.90
354 355 3.176411 CCCATGATAGCCCTCACAGATA 58.824 50.000 0.00 0.00 0.00 1.98
355 356 3.197333 CCCATGATAGCCCTCACAGATAG 59.803 52.174 0.00 0.00 0.00 2.08
367 368 6.680872 GCCCTCACAGATAGTTACTGTTAGAC 60.681 46.154 0.00 0.00 44.69 2.59
402 405 7.133133 AGTCATGTACCCCTTCGTATTTATT 57.867 36.000 0.00 0.00 0.00 1.40
415 418 9.467258 CCTTCGTATTTATTCCGTTGTATAAGA 57.533 33.333 0.00 0.00 0.00 2.10
651 657 3.730761 CGCTGCCGCTGCTTCTTT 61.731 61.111 18.66 0.00 38.71 2.52
686 692 2.427245 CCCTCCCACGCTCGATCTT 61.427 63.158 0.00 0.00 0.00 2.40
776 782 3.822192 CGTGATCCAGTCGCCCGA 61.822 66.667 0.00 0.00 33.71 5.14
1253 1270 2.664402 AAGGTTGCTGATGAGGTTGT 57.336 45.000 0.00 0.00 0.00 3.32
1450 1467 0.813184 GATGTGGACCCGTCTTCGTA 59.187 55.000 0.00 0.00 35.01 3.43
1495 1512 4.809193 TGCCTTATACCTCTCTGTGATCT 58.191 43.478 0.00 0.00 0.00 2.75
1714 1731 0.248621 GCGTGCTCAGTTGTTTGCTT 60.249 50.000 0.00 0.00 0.00 3.91
1919 1937 4.715523 CCCCCGTCCACATTGCGT 62.716 66.667 0.00 0.00 0.00 5.24
2036 2054 1.447489 CCTCGACAGCTTCAGCCAG 60.447 63.158 0.00 0.00 43.38 4.85
2077 2095 3.577649 TTCTGAGACTTAAGCGTCTGG 57.422 47.619 1.29 0.00 43.91 3.86
2150 2168 1.376424 CCCGCACTGAGCAATCACT 60.376 57.895 0.00 0.00 46.13 3.41
2437 2458 4.340097 TCCTTGACGTTGACTCTTGTTCTA 59.660 41.667 0.00 0.00 0.00 2.10
2496 2517 2.586079 CGCCGCCGTGATTCTCAT 60.586 61.111 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.685954 GGAAAAGAGTTGCGGACTTAAAAAG 59.314 40.000 0.00 0.00 39.19 2.27
2 3 4.641094 TGGAAAAGAGTTGCGGACTTAAAA 59.359 37.500 0.00 0.00 39.19 1.52
3 4 4.200874 TGGAAAAGAGTTGCGGACTTAAA 58.799 39.130 0.00 0.00 39.19 1.52
4 5 3.811083 TGGAAAAGAGTTGCGGACTTAA 58.189 40.909 0.00 0.00 39.19 1.85
5 6 3.478857 TGGAAAAGAGTTGCGGACTTA 57.521 42.857 0.00 0.00 39.19 2.24
6 7 2.341846 TGGAAAAGAGTTGCGGACTT 57.658 45.000 0.00 0.00 39.19 3.01
7 8 2.341846 TTGGAAAAGAGTTGCGGACT 57.658 45.000 0.00 0.00 42.70 3.85
8 9 3.565516 GATTTGGAAAAGAGTTGCGGAC 58.434 45.455 0.00 0.00 0.00 4.79
9 10 2.556622 GGATTTGGAAAAGAGTTGCGGA 59.443 45.455 0.00 0.00 0.00 5.54
10 11 2.668279 CGGATTTGGAAAAGAGTTGCGG 60.668 50.000 0.00 0.00 0.00 5.69
11 12 2.031157 ACGGATTTGGAAAAGAGTTGCG 60.031 45.455 0.00 0.00 0.00 4.85
12 13 3.308530 CACGGATTTGGAAAAGAGTTGC 58.691 45.455 0.00 0.00 0.00 4.17
13 14 3.317993 ACCACGGATTTGGAAAAGAGTTG 59.682 43.478 0.00 0.00 39.24 3.16
14 15 3.562182 ACCACGGATTTGGAAAAGAGTT 58.438 40.909 0.00 0.00 39.24 3.01
15 16 3.223674 ACCACGGATTTGGAAAAGAGT 57.776 42.857 0.00 0.00 39.24 3.24
16 17 4.584327 AAACCACGGATTTGGAAAAGAG 57.416 40.909 0.00 0.00 39.24 2.85
17 18 5.346181 AAAAACCACGGATTTGGAAAAGA 57.654 34.783 0.00 0.00 39.24 2.52
54 55 9.538508 AGTTTGTCGTATCTTTACTGTTTTAGT 57.461 29.630 0.00 0.00 43.56 2.24
57 58 8.768019 GGTAGTTTGTCGTATCTTTACTGTTTT 58.232 33.333 0.00 0.00 0.00 2.43
58 59 7.386025 GGGTAGTTTGTCGTATCTTTACTGTTT 59.614 37.037 0.00 0.00 0.00 2.83
59 60 6.870439 GGGTAGTTTGTCGTATCTTTACTGTT 59.130 38.462 0.00 0.00 0.00 3.16
60 61 6.015180 TGGGTAGTTTGTCGTATCTTTACTGT 60.015 38.462 0.00 0.00 0.00 3.55
61 62 6.392354 TGGGTAGTTTGTCGTATCTTTACTG 58.608 40.000 0.00 0.00 0.00 2.74
62 63 6.594788 TGGGTAGTTTGTCGTATCTTTACT 57.405 37.500 0.00 0.00 0.00 2.24
63 64 6.815142 ACATGGGTAGTTTGTCGTATCTTTAC 59.185 38.462 0.00 0.00 0.00 2.01
64 65 6.938507 ACATGGGTAGTTTGTCGTATCTTTA 58.061 36.000 0.00 0.00 0.00 1.85
65 66 5.801380 ACATGGGTAGTTTGTCGTATCTTT 58.199 37.500 0.00 0.00 0.00 2.52
66 67 5.416271 ACATGGGTAGTTTGTCGTATCTT 57.584 39.130 0.00 0.00 0.00 2.40
67 68 5.046878 TCAACATGGGTAGTTTGTCGTATCT 60.047 40.000 0.00 0.00 0.00 1.98
68 69 5.172934 TCAACATGGGTAGTTTGTCGTATC 58.827 41.667 0.00 0.00 0.00 2.24
69 70 5.155278 TCAACATGGGTAGTTTGTCGTAT 57.845 39.130 0.00 0.00 0.00 3.06
70 71 4.603989 TCAACATGGGTAGTTTGTCGTA 57.396 40.909 0.00 0.00 0.00 3.43
71 72 3.478857 TCAACATGGGTAGTTTGTCGT 57.521 42.857 0.00 0.00 0.00 4.34
72 73 4.822036 TTTCAACATGGGTAGTTTGTCG 57.178 40.909 0.00 0.00 0.00 4.35
73 74 6.325919 TGATTTCAACATGGGTAGTTTGTC 57.674 37.500 0.00 0.00 0.00 3.18
74 75 6.723298 TTGATTTCAACATGGGTAGTTTGT 57.277 33.333 0.00 0.00 0.00 2.83
75 76 7.116662 CACATTGATTTCAACATGGGTAGTTTG 59.883 37.037 0.00 0.00 38.86 2.93
76 77 7.015098 TCACATTGATTTCAACATGGGTAGTTT 59.985 33.333 0.00 0.00 38.86 2.66
77 78 6.493115 TCACATTGATTTCAACATGGGTAGTT 59.507 34.615 0.00 0.00 38.86 2.24
78 79 6.009589 TCACATTGATTTCAACATGGGTAGT 58.990 36.000 0.00 0.00 38.86 2.73
79 80 6.513806 TCACATTGATTTCAACATGGGTAG 57.486 37.500 0.00 0.00 38.86 3.18
80 81 6.493115 ACTTCACATTGATTTCAACATGGGTA 59.507 34.615 0.00 0.00 38.86 3.69
81 82 5.305128 ACTTCACATTGATTTCAACATGGGT 59.695 36.000 0.00 0.00 38.86 4.51
82 83 5.636121 CACTTCACATTGATTTCAACATGGG 59.364 40.000 0.00 0.00 38.86 4.00
83 84 5.636121 CCACTTCACATTGATTTCAACATGG 59.364 40.000 0.00 0.00 38.86 3.66
84 85 6.218019 ACCACTTCACATTGATTTCAACATG 58.782 36.000 0.00 0.00 38.86 3.21
85 86 6.409524 ACCACTTCACATTGATTTCAACAT 57.590 33.333 0.00 0.00 38.86 2.71
86 87 5.850557 ACCACTTCACATTGATTTCAACA 57.149 34.783 0.00 0.00 38.86 3.33
87 88 6.970484 ACTACCACTTCACATTGATTTCAAC 58.030 36.000 0.00 0.00 38.86 3.18
88 89 6.770303 TGACTACCACTTCACATTGATTTCAA 59.230 34.615 0.00 0.00 40.51 2.69
89 90 6.295249 TGACTACCACTTCACATTGATTTCA 58.705 36.000 0.00 0.00 0.00 2.69
90 91 6.801539 TGACTACCACTTCACATTGATTTC 57.198 37.500 0.00 0.00 0.00 2.17
91 92 7.765695 AATGACTACCACTTCACATTGATTT 57.234 32.000 0.00 0.00 0.00 2.17
92 93 8.862325 TTAATGACTACCACTTCACATTGATT 57.138 30.769 0.00 0.00 31.85 2.57
93 94 8.862325 TTTAATGACTACCACTTCACATTGAT 57.138 30.769 0.00 0.00 31.85 2.57
94 95 8.862325 ATTTAATGACTACCACTTCACATTGA 57.138 30.769 0.00 0.00 31.85 2.57
97 98 8.893727 GCTTATTTAATGACTACCACTTCACAT 58.106 33.333 0.00 0.00 0.00 3.21
98 99 7.880713 TGCTTATTTAATGACTACCACTTCACA 59.119 33.333 0.00 0.00 0.00 3.58
99 100 8.263940 TGCTTATTTAATGACTACCACTTCAC 57.736 34.615 0.00 0.00 0.00 3.18
100 101 8.318412 TCTGCTTATTTAATGACTACCACTTCA 58.682 33.333 0.00 0.00 0.00 3.02
101 102 8.718102 TCTGCTTATTTAATGACTACCACTTC 57.282 34.615 0.00 0.00 0.00 3.01
102 103 9.686683 AATCTGCTTATTTAATGACTACCACTT 57.313 29.630 0.00 0.00 0.00 3.16
103 104 9.686683 AAATCTGCTTATTTAATGACTACCACT 57.313 29.630 0.00 0.00 0.00 4.00
117 118 9.770097 TCTTGATCGAGAATAAATCTGCTTATT 57.230 29.630 10.43 0.00 38.96 1.40
118 119 9.941325 ATCTTGATCGAGAATAAATCTGCTTAT 57.059 29.630 16.73 0.00 38.96 1.73
119 120 9.770097 AATCTTGATCGAGAATAAATCTGCTTA 57.230 29.630 16.73 0.00 38.96 3.09
120 121 8.557864 CAATCTTGATCGAGAATAAATCTGCTT 58.442 33.333 16.73 0.00 38.96 3.91
121 122 7.307870 GCAATCTTGATCGAGAATAAATCTGCT 60.308 37.037 16.73 0.00 38.96 4.24
122 123 6.796072 GCAATCTTGATCGAGAATAAATCTGC 59.204 38.462 16.73 12.00 38.96 4.26
123 124 8.085720 AGCAATCTTGATCGAGAATAAATCTG 57.914 34.615 16.73 6.95 38.96 2.90
124 125 8.674263 AAGCAATCTTGATCGAGAATAAATCT 57.326 30.769 16.73 5.89 42.61 2.40
125 126 9.727627 AAAAGCAATCTTGATCGAGAATAAATC 57.272 29.630 16.73 3.90 31.78 2.17
126 127 9.727627 GAAAAGCAATCTTGATCGAGAATAAAT 57.272 29.630 16.73 0.00 31.78 1.40
127 128 8.729756 TGAAAAGCAATCTTGATCGAGAATAAA 58.270 29.630 16.73 0.00 31.78 1.40
128 129 8.177663 GTGAAAAGCAATCTTGATCGAGAATAA 58.822 33.333 16.73 0.00 31.78 1.40
129 130 7.334171 TGTGAAAAGCAATCTTGATCGAGAATA 59.666 33.333 16.73 0.00 31.78 1.75
130 131 6.149973 TGTGAAAAGCAATCTTGATCGAGAAT 59.850 34.615 16.73 5.69 31.78 2.40
131 132 5.469760 TGTGAAAAGCAATCTTGATCGAGAA 59.530 36.000 16.73 0.96 31.78 2.87
132 133 4.996758 TGTGAAAAGCAATCTTGATCGAGA 59.003 37.500 15.18 15.18 31.78 4.04
133 134 5.287170 TGTGAAAAGCAATCTTGATCGAG 57.713 39.130 3.24 3.24 31.78 4.04
134 135 5.469760 TCTTGTGAAAAGCAATCTTGATCGA 59.530 36.000 0.00 0.00 31.78 3.59
135 136 5.692814 TCTTGTGAAAAGCAATCTTGATCG 58.307 37.500 0.00 0.00 31.78 3.69
136 137 7.144000 AGTTCTTGTGAAAAGCAATCTTGATC 58.856 34.615 0.00 0.00 33.52 2.92
137 138 7.047460 AGTTCTTGTGAAAAGCAATCTTGAT 57.953 32.000 0.00 0.00 33.52 2.57
138 139 6.455360 AGTTCTTGTGAAAAGCAATCTTGA 57.545 33.333 0.00 0.00 33.52 3.02
139 140 6.753279 TCAAGTTCTTGTGAAAAGCAATCTTG 59.247 34.615 11.52 0.00 34.46 3.02
140 141 6.753744 GTCAAGTTCTTGTGAAAAGCAATCTT 59.246 34.615 11.52 0.00 33.52 2.40
141 142 6.127647 TGTCAAGTTCTTGTGAAAAGCAATCT 60.128 34.615 11.52 0.00 33.52 2.40
142 143 6.035843 TGTCAAGTTCTTGTGAAAAGCAATC 58.964 36.000 11.52 0.00 33.52 2.67
143 144 5.964758 TGTCAAGTTCTTGTGAAAAGCAAT 58.035 33.333 11.52 0.00 33.52 3.56
144 145 5.384063 TGTCAAGTTCTTGTGAAAAGCAA 57.616 34.783 11.52 0.00 33.52 3.91
145 146 4.142403 CCTGTCAAGTTCTTGTGAAAAGCA 60.142 41.667 11.52 2.48 33.52 3.91
146 147 4.096382 TCCTGTCAAGTTCTTGTGAAAAGC 59.904 41.667 11.52 0.00 33.52 3.51
147 148 5.818136 TCCTGTCAAGTTCTTGTGAAAAG 57.182 39.130 11.52 0.00 33.52 2.27
148 149 5.125417 CCTTCCTGTCAAGTTCTTGTGAAAA 59.875 40.000 11.52 2.76 33.52 2.29
149 150 4.640201 CCTTCCTGTCAAGTTCTTGTGAAA 59.360 41.667 11.52 2.22 33.52 2.69
150 151 4.199310 CCTTCCTGTCAAGTTCTTGTGAA 58.801 43.478 11.52 9.49 0.00 3.18
151 152 3.433598 CCCTTCCTGTCAAGTTCTTGTGA 60.434 47.826 11.52 3.63 0.00 3.58
152 153 2.880890 CCCTTCCTGTCAAGTTCTTGTG 59.119 50.000 11.52 4.85 0.00 3.33
153 154 2.158608 CCCCTTCCTGTCAAGTTCTTGT 60.159 50.000 11.52 0.00 0.00 3.16
154 155 2.106511 TCCCCTTCCTGTCAAGTTCTTG 59.893 50.000 6.24 6.24 0.00 3.02
155 156 2.418669 TCCCCTTCCTGTCAAGTTCTT 58.581 47.619 0.00 0.00 0.00 2.52
156 157 2.118403 TCCCCTTCCTGTCAAGTTCT 57.882 50.000 0.00 0.00 0.00 3.01
157 158 2.553247 CCTTCCCCTTCCTGTCAAGTTC 60.553 54.545 0.00 0.00 0.00 3.01
158 159 1.425448 CCTTCCCCTTCCTGTCAAGTT 59.575 52.381 0.00 0.00 0.00 2.66
159 160 1.068121 CCTTCCCCTTCCTGTCAAGT 58.932 55.000 0.00 0.00 0.00 3.16
160 161 1.362224 TCCTTCCCCTTCCTGTCAAG 58.638 55.000 0.00 0.00 0.00 3.02
161 162 1.705186 CTTCCTTCCCCTTCCTGTCAA 59.295 52.381 0.00 0.00 0.00 3.18
162 163 1.362224 CTTCCTTCCCCTTCCTGTCA 58.638 55.000 0.00 0.00 0.00 3.58
163 164 0.621082 CCTTCCTTCCCCTTCCTGTC 59.379 60.000 0.00 0.00 0.00 3.51
164 165 0.196118 TCCTTCCTTCCCCTTCCTGT 59.804 55.000 0.00 0.00 0.00 4.00
165 166 0.915364 CTCCTTCCTTCCCCTTCCTG 59.085 60.000 0.00 0.00 0.00 3.86
166 167 0.253394 CCTCCTTCCTTCCCCTTCCT 60.253 60.000 0.00 0.00 0.00 3.36
167 168 1.282653 CCCTCCTTCCTTCCCCTTCC 61.283 65.000 0.00 0.00 0.00 3.46
168 169 1.282653 CCCCTCCTTCCTTCCCCTTC 61.283 65.000 0.00 0.00 0.00 3.46
169 170 1.230314 CCCCTCCTTCCTTCCCCTT 60.230 63.158 0.00 0.00 0.00 3.95
170 171 2.191846 TCCCCTCCTTCCTTCCCCT 61.192 63.158 0.00 0.00 0.00 4.79
171 172 1.694525 CTCCCCTCCTTCCTTCCCC 60.695 68.421 0.00 0.00 0.00 4.81
172 173 1.694525 CCTCCCCTCCTTCCTTCCC 60.695 68.421 0.00 0.00 0.00 3.97
173 174 1.694525 CCCTCCCCTCCTTCCTTCC 60.695 68.421 0.00 0.00 0.00 3.46
174 175 2.379459 GCCCTCCCCTCCTTCCTTC 61.379 68.421 0.00 0.00 0.00 3.46
175 176 2.286502 GCCCTCCCCTCCTTCCTT 60.287 66.667 0.00 0.00 0.00 3.36
176 177 1.613284 TATGCCCTCCCCTCCTTCCT 61.613 60.000 0.00 0.00 0.00 3.36
177 178 1.073706 TATGCCCTCCCCTCCTTCC 60.074 63.158 0.00 0.00 0.00 3.46
178 179 1.419720 GGTATGCCCTCCCCTCCTTC 61.420 65.000 0.00 0.00 0.00 3.46
179 180 1.386057 GGTATGCCCTCCCCTCCTT 60.386 63.158 0.00 0.00 0.00 3.36
180 181 1.914496 AAGGTATGCCCTCCCCTCCT 61.914 60.000 0.00 0.00 45.47 3.69
181 182 1.386057 AAGGTATGCCCTCCCCTCC 60.386 63.158 0.00 0.00 45.47 4.30
182 183 1.709994 CCAAGGTATGCCCTCCCCTC 61.710 65.000 0.00 0.00 45.47 4.30
183 184 1.697754 CCAAGGTATGCCCTCCCCT 60.698 63.158 0.00 0.00 45.47 4.79
184 185 1.696314 TCCAAGGTATGCCCTCCCC 60.696 63.158 0.00 0.00 45.47 4.81
185 186 1.532238 GTCCAAGGTATGCCCTCCC 59.468 63.158 0.00 0.00 45.47 4.30
186 187 0.988678 AGGTCCAAGGTATGCCCTCC 60.989 60.000 0.00 0.00 45.47 4.30
187 188 0.919710 AAGGTCCAAGGTATGCCCTC 59.080 55.000 0.00 0.00 45.47 4.30
188 189 6.927542 TAGACAAGGTCCAAGGTATGCCCT 62.928 50.000 0.00 0.00 38.14 5.19
189 190 0.331616 ACAAGGTCCAAGGTATGCCC 59.668 55.000 0.00 0.00 34.57 5.36
190 191 1.282157 AGACAAGGTCCAAGGTATGCC 59.718 52.381 0.00 0.00 32.18 4.40
191 192 2.789409 AGACAAGGTCCAAGGTATGC 57.211 50.000 0.00 0.00 32.18 3.14
192 193 5.420409 GTCTTAGACAAGGTCCAAGGTATG 58.580 45.833 7.59 0.00 33.41 2.39
193 194 4.470304 GGTCTTAGACAAGGTCCAAGGTAT 59.530 45.833 14.72 0.00 33.41 2.73
194 195 3.836562 GGTCTTAGACAAGGTCCAAGGTA 59.163 47.826 14.72 0.00 33.41 3.08
195 196 2.638363 GGTCTTAGACAAGGTCCAAGGT 59.362 50.000 14.72 0.00 33.41 3.50
196 197 2.907042 AGGTCTTAGACAAGGTCCAAGG 59.093 50.000 14.72 0.00 33.41 3.61
197 198 3.866449 GCAGGTCTTAGACAAGGTCCAAG 60.866 52.174 14.72 0.00 33.76 3.61
198 199 2.038557 GCAGGTCTTAGACAAGGTCCAA 59.961 50.000 14.72 0.00 33.68 3.53
199 200 1.623811 GCAGGTCTTAGACAAGGTCCA 59.376 52.381 14.72 0.00 33.68 4.02
200 201 1.623811 TGCAGGTCTTAGACAAGGTCC 59.376 52.381 14.72 0.00 33.68 4.46
201 202 2.933056 GCTGCAGGTCTTAGACAAGGTC 60.933 54.545 17.12 0.00 33.68 3.85
202 203 1.002544 GCTGCAGGTCTTAGACAAGGT 59.997 52.381 17.12 0.00 33.68 3.50
203 204 1.277557 AGCTGCAGGTCTTAGACAAGG 59.722 52.381 13.85 3.97 33.68 3.61
204 205 2.615869 GAGCTGCAGGTCTTAGACAAG 58.384 52.381 33.19 6.80 39.31 3.16
205 206 1.067565 CGAGCTGCAGGTCTTAGACAA 60.068 52.381 35.49 0.00 40.17 3.18
206 207 0.528017 CGAGCTGCAGGTCTTAGACA 59.472 55.000 35.49 0.00 40.17 3.41
207 208 0.528470 ACGAGCTGCAGGTCTTAGAC 59.472 55.000 35.49 15.64 40.17 2.59
208 209 0.811915 GACGAGCTGCAGGTCTTAGA 59.188 55.000 35.49 0.00 40.17 2.10
209 210 0.528017 TGACGAGCTGCAGGTCTTAG 59.472 55.000 35.49 25.26 40.17 2.18
210 211 0.528017 CTGACGAGCTGCAGGTCTTA 59.472 55.000 35.49 22.88 40.17 2.10
211 212 1.291588 CTGACGAGCTGCAGGTCTT 59.708 57.895 35.49 29.87 40.17 3.01
212 213 2.644212 CCTGACGAGCTGCAGGTCT 61.644 63.158 35.49 25.10 45.21 3.85
213 214 2.125753 CCTGACGAGCTGCAGGTC 60.126 66.667 31.39 31.39 45.21 3.85
216 217 0.108472 TCATTCCTGACGAGCTGCAG 60.108 55.000 10.11 10.11 0.00 4.41
217 218 0.108472 CTCATTCCTGACGAGCTGCA 60.108 55.000 1.02 0.00 0.00 4.41
218 219 0.108424 ACTCATTCCTGACGAGCTGC 60.108 55.000 0.00 0.00 0.00 5.25
219 220 1.796982 CGACTCATTCCTGACGAGCTG 60.797 57.143 0.00 0.00 0.00 4.24
220 221 0.453793 CGACTCATTCCTGACGAGCT 59.546 55.000 0.00 0.00 0.00 4.09
221 222 0.526524 CCGACTCATTCCTGACGAGC 60.527 60.000 0.00 0.00 0.00 5.03
222 223 1.064803 CTCCGACTCATTCCTGACGAG 59.935 57.143 0.00 0.00 0.00 4.18
223 224 1.095600 CTCCGACTCATTCCTGACGA 58.904 55.000 0.00 0.00 0.00 4.20
224 225 1.095600 TCTCCGACTCATTCCTGACG 58.904 55.000 0.00 0.00 0.00 4.35
225 226 2.801342 GCATCTCCGACTCATTCCTGAC 60.801 54.545 0.00 0.00 0.00 3.51
226 227 1.410517 GCATCTCCGACTCATTCCTGA 59.589 52.381 0.00 0.00 0.00 3.86
227 228 1.411977 AGCATCTCCGACTCATTCCTG 59.588 52.381 0.00 0.00 0.00 3.86
228 229 1.411977 CAGCATCTCCGACTCATTCCT 59.588 52.381 0.00 0.00 0.00 3.36
229 230 1.863267 CAGCATCTCCGACTCATTCC 58.137 55.000 0.00 0.00 0.00 3.01
230 231 1.202510 AGCAGCATCTCCGACTCATTC 60.203 52.381 0.00 0.00 0.00 2.67
231 232 0.829333 AGCAGCATCTCCGACTCATT 59.171 50.000 0.00 0.00 0.00 2.57
232 233 0.104487 CAGCAGCATCTCCGACTCAT 59.896 55.000 0.00 0.00 0.00 2.90
233 234 1.514553 CAGCAGCATCTCCGACTCA 59.485 57.895 0.00 0.00 0.00 3.41
234 235 1.882167 GCAGCAGCATCTCCGACTC 60.882 63.158 0.00 0.00 41.58 3.36
235 236 2.186384 GCAGCAGCATCTCCGACT 59.814 61.111 0.00 0.00 41.58 4.18
236 237 1.882167 GAGCAGCAGCATCTCCGAC 60.882 63.158 3.17 0.00 45.49 4.79
237 238 2.498248 GAGCAGCAGCATCTCCGA 59.502 61.111 3.17 0.00 45.49 4.55
238 239 2.588314 GGAGCAGCAGCATCTCCG 60.588 66.667 14.83 0.00 45.49 4.63
239 240 1.524165 CAGGAGCAGCAGCATCTCC 60.524 63.158 19.89 19.89 45.11 3.71
240 241 2.181521 GCAGGAGCAGCAGCATCTC 61.182 63.158 3.17 0.00 45.49 2.75
241 242 1.335882 TAGCAGGAGCAGCAGCATCT 61.336 55.000 3.17 0.00 45.49 2.90
242 243 1.145598 TAGCAGGAGCAGCAGCATC 59.854 57.895 3.17 0.00 45.49 3.91
243 244 1.153208 GTAGCAGGAGCAGCAGCAT 60.153 57.895 3.17 0.00 45.49 3.79
244 245 2.267006 GTAGCAGGAGCAGCAGCA 59.733 61.111 3.17 0.00 45.49 4.41
245 246 1.814586 CAGTAGCAGGAGCAGCAGC 60.815 63.158 0.00 0.00 45.49 5.25
246 247 1.814586 GCAGTAGCAGGAGCAGCAG 60.815 63.158 0.00 0.00 45.49 4.24
247 248 2.267006 GCAGTAGCAGGAGCAGCA 59.733 61.111 0.00 0.00 45.49 4.41
257 258 1.362406 GACCGGAAGCTTGCAGTAGC 61.362 60.000 18.65 1.95 41.53 3.58
258 259 1.078759 CGACCGGAAGCTTGCAGTAG 61.079 60.000 18.65 9.32 0.00 2.57
259 260 1.080093 CGACCGGAAGCTTGCAGTA 60.080 57.895 18.65 0.00 0.00 2.74
260 261 2.357517 CGACCGGAAGCTTGCAGT 60.358 61.111 18.65 12.94 0.00 4.40
261 262 2.357517 ACGACCGGAAGCTTGCAG 60.358 61.111 18.65 9.34 0.00 4.41
262 263 1.529152 TAGACGACCGGAAGCTTGCA 61.529 55.000 18.65 0.00 0.00 4.08
263 264 0.179108 ATAGACGACCGGAAGCTTGC 60.179 55.000 9.46 5.53 0.00 4.01
264 265 2.287668 CCTATAGACGACCGGAAGCTTG 60.288 54.545 9.46 0.00 0.00 4.01
265 266 1.955080 CCTATAGACGACCGGAAGCTT 59.045 52.381 9.46 0.00 0.00 3.74
266 267 1.606903 CCTATAGACGACCGGAAGCT 58.393 55.000 9.46 1.90 0.00 3.74
267 268 0.597072 CCCTATAGACGACCGGAAGC 59.403 60.000 9.46 0.00 0.00 3.86
268 269 2.152830 CTCCCTATAGACGACCGGAAG 58.847 57.143 9.46 3.42 0.00 3.46
269 270 1.202855 CCTCCCTATAGACGACCGGAA 60.203 57.143 9.46 0.00 0.00 4.30
270 271 0.399454 CCTCCCTATAGACGACCGGA 59.601 60.000 9.46 0.00 0.00 5.14
271 272 1.242665 GCCTCCCTATAGACGACCGG 61.243 65.000 0.00 0.00 0.00 5.28
272 273 0.250814 AGCCTCCCTATAGACGACCG 60.251 60.000 0.00 0.00 0.00 4.79
273 274 1.249407 CAGCCTCCCTATAGACGACC 58.751 60.000 0.00 0.00 0.00 4.79
274 275 1.249407 CCAGCCTCCCTATAGACGAC 58.751 60.000 0.00 0.00 0.00 4.34
275 276 0.112606 CCCAGCCTCCCTATAGACGA 59.887 60.000 0.00 0.00 0.00 4.20
276 277 0.900647 CCCCAGCCTCCCTATAGACG 60.901 65.000 0.00 0.00 0.00 4.18
277 278 0.191314 ACCCCAGCCTCCCTATAGAC 59.809 60.000 0.00 0.00 0.00 2.59
278 279 0.191064 CACCCCAGCCTCCCTATAGA 59.809 60.000 0.00 0.00 0.00 1.98
279 280 1.484444 GCACCCCAGCCTCCCTATAG 61.484 65.000 0.00 0.00 0.00 1.31
280 281 1.461461 GCACCCCAGCCTCCCTATA 60.461 63.158 0.00 0.00 0.00 1.31
281 282 2.774351 GCACCCCAGCCTCCCTAT 60.774 66.667 0.00 0.00 0.00 2.57
300 301 3.825160 TATTGCCGGCCCTCGATGC 62.825 63.158 26.77 0.00 42.43 3.91
301 302 1.669115 CTATTGCCGGCCCTCGATG 60.669 63.158 26.77 3.60 42.43 3.84
302 303 2.743718 CTATTGCCGGCCCTCGAT 59.256 61.111 26.77 12.37 42.43 3.59
303 304 3.546543 CCTATTGCCGGCCCTCGA 61.547 66.667 26.77 0.09 42.43 4.04
304 305 4.626081 CCCTATTGCCGGCCCTCG 62.626 72.222 26.77 10.04 38.88 4.63
305 306 4.956932 GCCCTATTGCCGGCCCTC 62.957 72.222 26.77 1.83 39.39 4.30
310 311 3.832237 ATCTGCGCCCTATTGCCGG 62.832 63.158 4.18 0.00 0.00 6.13
311 312 2.281070 ATCTGCGCCCTATTGCCG 60.281 61.111 4.18 0.00 0.00 5.69
312 313 2.263741 CCATCTGCGCCCTATTGCC 61.264 63.158 4.18 0.00 0.00 4.52
313 314 1.227943 TCCATCTGCGCCCTATTGC 60.228 57.895 4.18 0.00 0.00 3.56
314 315 1.233285 GCTCCATCTGCGCCCTATTG 61.233 60.000 4.18 0.00 0.00 1.90
315 316 1.072159 GCTCCATCTGCGCCCTATT 59.928 57.895 4.18 0.00 0.00 1.73
316 317 2.746359 GCTCCATCTGCGCCCTAT 59.254 61.111 4.18 0.00 0.00 2.57
317 318 3.550431 GGCTCCATCTGCGCCCTA 61.550 66.667 4.18 0.00 37.86 3.53
320 321 4.575973 ATGGGCTCCATCTGCGCC 62.576 66.667 4.18 0.00 40.74 6.53
321 322 3.285215 CATGGGCTCCATCTGCGC 61.285 66.667 0.00 0.00 43.15 6.09
322 323 0.322648 TATCATGGGCTCCATCTGCG 59.677 55.000 3.93 0.00 43.15 5.18
323 324 1.949547 GCTATCATGGGCTCCATCTGC 60.950 57.143 3.93 3.65 43.15 4.26
324 325 1.339824 GGCTATCATGGGCTCCATCTG 60.340 57.143 3.93 0.00 43.15 2.90
325 326 0.990374 GGCTATCATGGGCTCCATCT 59.010 55.000 3.93 0.00 43.15 2.90
326 327 0.034670 GGGCTATCATGGGCTCCATC 60.035 60.000 3.93 0.00 43.15 3.51
327 328 0.477202 AGGGCTATCATGGGCTCCAT 60.477 55.000 1.21 1.21 46.37 3.41
328 329 1.073474 AGGGCTATCATGGGCTCCA 60.073 57.895 0.00 0.00 38.19 3.86
329 330 1.130054 TGAGGGCTATCATGGGCTCC 61.130 60.000 0.00 0.17 0.00 4.70
330 331 0.036022 GTGAGGGCTATCATGGGCTC 59.964 60.000 0.00 0.00 0.00 4.70
331 332 0.695462 TGTGAGGGCTATCATGGGCT 60.695 55.000 0.00 0.00 0.00 5.19
332 333 0.250640 CTGTGAGGGCTATCATGGGC 60.251 60.000 0.00 0.00 0.00 5.36
333 334 1.427809 TCTGTGAGGGCTATCATGGG 58.572 55.000 0.00 0.00 0.00 4.00
334 335 3.837146 ACTATCTGTGAGGGCTATCATGG 59.163 47.826 0.00 0.00 0.00 3.66
335 336 5.480642 AACTATCTGTGAGGGCTATCATG 57.519 43.478 0.00 0.00 0.00 3.07
336 337 6.210385 CAGTAACTATCTGTGAGGGCTATCAT 59.790 42.308 0.00 0.00 0.00 2.45
337 338 5.536538 CAGTAACTATCTGTGAGGGCTATCA 59.463 44.000 0.00 0.00 0.00 2.15
338 339 5.536916 ACAGTAACTATCTGTGAGGGCTATC 59.463 44.000 0.00 0.00 43.32 2.08
339 340 5.459505 ACAGTAACTATCTGTGAGGGCTAT 58.540 41.667 0.00 0.00 43.32 2.97
340 341 4.868268 ACAGTAACTATCTGTGAGGGCTA 58.132 43.478 0.00 0.00 43.32 3.93
341 342 3.714144 ACAGTAACTATCTGTGAGGGCT 58.286 45.455 0.00 0.00 43.32 5.19
342 343 4.473477 AACAGTAACTATCTGTGAGGGC 57.527 45.455 0.00 0.00 44.03 5.19
343 344 6.603997 AGTCTAACAGTAACTATCTGTGAGGG 59.396 42.308 9.63 0.00 44.03 4.30
344 345 7.633193 AGTCTAACAGTAACTATCTGTGAGG 57.367 40.000 9.63 0.88 44.03 3.86
393 396 8.807667 ACCTCTTATACAACGGAATAAATACG 57.192 34.615 0.00 0.00 0.00 3.06
402 405 4.622220 GCAGGAAACCTCTTATACAACGGA 60.622 45.833 0.00 0.00 0.00 4.69
415 418 3.245229 TGTGGAACATATGCAGGAAACCT 60.245 43.478 1.58 0.00 45.67 3.50
651 657 1.002624 GGAGGGCGTTGACCAATGA 60.003 57.895 6.17 0.00 29.21 2.57
686 692 2.047655 GACCACGGGCGTTGATGA 60.048 61.111 0.00 0.00 0.00 2.92
776 782 3.550431 CTGGATCGTGGGCGGGAT 61.550 66.667 0.00 0.00 38.89 3.85
882 888 1.612146 TCTCAATCGGGACCTGGCA 60.612 57.895 0.00 0.00 0.00 4.92
1253 1270 4.502087 CCCTCTCATCATAAGCACGATCAA 60.502 45.833 0.00 0.00 0.00 2.57
1495 1512 0.978907 TGAAGAGCATGCTCCTGACA 59.021 50.000 37.79 28.38 43.70 3.58
1714 1731 2.419990 CCATGAGAGAAATACGGCCACA 60.420 50.000 2.24 0.00 0.00 4.17
1919 1937 6.124340 AGATGACCATCATTGTTGCAATAGA 58.876 36.000 0.59 0.00 37.20 1.98
1987 2005 0.465705 GTCCCGGAAGATGATGAGCA 59.534 55.000 0.73 0.00 0.00 4.26
1989 2007 2.544694 CGAAGTCCCGGAAGATGATGAG 60.545 54.545 0.73 0.00 0.00 2.90
2036 2054 1.818642 ATCCTGCTCAGTCAAAGCAC 58.181 50.000 0.00 0.00 44.51 4.40
2077 2095 1.627550 GAAGAACCTGAAGCCGCGAC 61.628 60.000 8.23 0.00 0.00 5.19
2150 2168 4.270834 GGATGTACCTGACTGTGTAGAGA 58.729 47.826 0.00 0.00 35.41 3.10
2437 2458 2.970639 CGTGTGACGGTCCTGGAT 59.029 61.111 5.55 0.00 38.08 3.41
2496 2517 1.073763 CAGTCCAACTCCCAATGACCA 59.926 52.381 0.00 0.00 0.00 4.02
2501 2522 0.779997 AAGCCAGTCCAACTCCCAAT 59.220 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.